Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold885
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1053811
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 99868 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:517678 original size:16 final size:16
Alignment explanation
Indices: 517657--517689 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
517647 AACTGAAGTG
517657 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
517673 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
517689 G
1 G
517690 CAGAGGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.39, T:0.00
Consensus pattern (16 bp):
GGACAGACAGACGGAC
Found at i:518680 original size:7 final size:7
Alignment explanation
Indices: 518670--518715 Score: 83
Period size: 7 Copynumber: 6.4 Consensus size: 7
518660 CTTCGTCCGT
518670 CGTCGTG
1 CGTCGTG
518677 CGTCGTG
1 CGTCGTG
518684 CGTCGTG
1 CGTCGTG
518691 CGTCTGTG
1 CGTC-GTG
518699 CGTCGTG
1 CGTCGTG
518706 CGTCGTG
1 CGTCGTG
518713 CGT
1 CGT
518716 TAACAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 31 0.82
8 7 0.18
ACGTcount: A:0.00, C:0.28, G:0.41, T:0.30
Consensus pattern (7 bp):
CGTCGTG
Found at i:518702 original size:22 final size:21
Alignment explanation
Indices: 518670--518715 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 21
518660 CTTCGTCCGT
518670 CGTCGTGCGTCGTGCGTCGTG
1 CGTCGTGCGTCGTGCGTCGTG
518691 CGTCTGTGCGTCGTGCGTCGTG
1 CGTC-GTGCGTCGTGCGTCGTG
518713 CGT
1 CGT
518716 TAACAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.00, C:0.28, G:0.41, T:0.30
Consensus pattern (21 bp):
CGTCGTGCGTCGTGCGTCGTG
Found at i:519138 original size:168 final size:168
Alignment explanation
Indices: 518920--519841 Score: 1347
Period size: 168 Copynumber: 5.5 Consensus size: 168
518910 CATGTGAGGA
* * * * * * *
518920 AAAAACTGAATGCATGGTTATAATTTCCATGATGCCCTCTACCAAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTTCCTAAATTGTGAAATTCATGACCC
518985 CTGGGTCAGGGATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
519050 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
131 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
519088 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTTCCTAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTTCCTAAATTGTGAAATTCATGACCC
*
519153 CTGGGTCAGGGATTCAGGCTCTAGGGAGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
519218 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
131 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
519256 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTTCCTAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTTCCTAAATTGTGAAATTCATGACCC
*
519321 CTGGGTCAGGGATTCAGGCTCTAGGGAGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
**
519386 TTAGAAAATCTTCTTCTCTACTATCATATATATTTGTT
131 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* * *
519424 AAAACCTAAATGCATGATAATGATGTCCATGAAGCCCTCATCCTAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTTCCTAAATTGTGAAATTCATGACCC
* * *
519489 CTCGGTCAGGGGTTCAGGCTCT-GGGATGGGGCC-GTCA-GGCCAAATAGTAAAAATGTATTAAA
66 CTGGGTCAGGGATTCAGGCTCTAGGG-TGGGGCCAAT-ATGGCCAAATAGTAAAAATGTATTAAA
519551 TCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
129 TCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* * * *
519591 AAAAACGAAATGCATGATTATGATGTCCATGAGGCTCTC-TACTAAAATTGTGAAATTCATGACC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTTCCT-AAATTGTGAAATTCATGACC
* * * *
519655 CCTGGGTAAGGTG-TTCATGCTCTGGGGTGGGGCCAATATGGCCATATAGTAAAAATG-ATTTAA
65 CCTGGGTCAGG-GATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTA-TTAA
* * * * * ** **
519718 ATCTTAAAAAATCTTCTTCTCTACTCCAACACATGTGGGCA
128 ATCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* * * * * * *
519759 AAAAACTGAATACATGGTTATGATATCCA-CAATCTCCT-TTACCTAAATTGTGAAATTCATGGC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGC-CCTCTT-CCTAAATTGTGAAATTCATGAC
*
519822 CCCTGGGTCAGGGGTTCAGG
64 CCCTGGGTCAGGGATTCAGG
519842 ACATGGGGGG
Statistics
Matches: 690, Mismatches: 52, Indels: 24
0.90 0.07 0.03
Matches are distributed among these distances:
166 3 0.00
167 151 0.22
168 534 0.77
169 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (168 bp):
AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTTCCTAAATTGTGAAATTCATGACCC
CTGGGTCAGGGATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
Found at i:519806 original size:335 final size:334
Alignment explanation
Indices: 518928--519841 Score: 1333
Period size: 335 Copynumber: 2.7 Consensus size: 334
518918 GAAAAAACTG
* * * * *
518928 AATGCATGGTTATAATTTCCATGATGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCA
1 AATGCATGATTATGATGTCCATGAAGCCCTCTACTAAAATTGTGAAATTCATGACCCCTGGGTCA
518993 GGGATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAA
66 GGGATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAA
519058 TCTTCTTCTCTACTCCCATATATATTTGTTAAAAACTAAATGCATGATTATGATGTCCATGAAGC
131 TCTTCTTCTCTACT-CCA-ATATATTTGTTAAAAACTAAATGCATGATTATGATGTCCATGAAGC
*
519123 CCTCTT-CCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGATTCAGGCTCTAGGGAGGGGCCA
194 CCT-TTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGAGGGGCCA
519187 ATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATATATT
258 ATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATATATT
*
519252 TGTTAAAAACTA
323 TGTTAAAAACGA
*
519264 AATGCATGATTATGATGTCCATGAAGCCCTCTTCCT-AAATTGTGAAATTCATGACCCCTGGGTC
1 AATGCATGATTATGATGTCCATGAAGCCCTC-TACTAAAATTGTGAAATTCATGACCCCTGGGTC
*
519328 AGGGATTCAGGCTCTAGGGAGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAA
65 AGGGATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAA
* * *
519393 ATCTTCTTCTCTACTATCATATATATTTGTTAAAACCTAAATGCATGATAATGATGTCCATGAAG
130 ATCTTCTTCTCTACT-CCA-ATATATTTGTTAAAAACTAAATGCATGATTATGATGTCCATGAAG
* *
519458 CCC-TCATCCTAAATTGTGAAATTCATGACCCCTCGGTCAGGGGTTCAGGCTCT-GGGATGGGGC
193 CCCTTTA-CCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGA-GGGGC
*
519521 C-GTCA-GGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATAT
256 CAAT-ATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATAT
519584 ATTTGTTAAAAACGA
320 ATTTGTTAAAAACGA
* * *
519599 AATGCATGATTATGATGTCCATGAGGCTCTCTACTAAAATTGTGAAATTCATGACCCCTGGGTAA
1 AATGCATGATTATGATGTCCATGAAGCCCTCTACTAAAATTGTGAAATTCATGACCCCTGGGTCA
* * * *
519664 GGTG-TTCATGCTCTGGGGTGGGGCCAATATGGCCATATAGTAAAAATG-ATTTAAATCTTAAAA
66 GG-GATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTA-TTAAATCTTAGAA
* * * ** * * * * *
519727 AATCTTCTTCTCTACTCCAACACATGTGGGCAAAAAACTGAATACATGGTTATGATATCCA-CAA
129 AATCTTCTTCTCTACTCCAATATAT-T-TGTTAAAAACTAAATGCATGATTATGATGTCCATGAA
* *
519791 TCTCCTTTACCTAAATTGTGAAATTCATGGCCCCTGGGTCAGGGGTTCAGG
192 GC-CCTTTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGG
519842 ACATGGGGGG
Statistics
Matches: 524, Mismatches: 42, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
333 4 0.01
334 11 0.02
335 270 0.52
336 237 0.45
337 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (334 bp):
AATGCATGATTATGATGTCCATGAAGCCCTCTACTAAAATTGTGAAATTCATGACCCCTGGGTCA
GGGATTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAA
TCTTCTTCTCTACTCCAATATATTTGTTAAAAACTAAATGCATGATTATGATGTCCATGAAGCCC
TTTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGAGGGGCCAATA
TGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGT
TAAAAACGA
Found at i:524619 original size:14 final size:14
Alignment explanation
Indices: 524600--524629 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
524590 TTATTCCTTA
524600 AATGAAAACAATGG
1 AATGAAAACAATGG
*
524614 AATGAACACAATGG
1 AATGAAAACAATGG
524628 AA
1 AA
524630 ACCACACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.10, G:0.20, T:0.13
Consensus pattern (14 bp):
AATGAAAACAATGG
Found at i:527556 original size:2 final size:2
Alignment explanation
Indices: 527549--527601 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
527539 CCAAATACCA
527549 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
527591 TC TC TC TC TC T
1 TC TC TC TC TC T
527602 GCTAAAGGTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:529118 original size:2 final size:2
Alignment explanation
Indices: 529111--529148 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
529101 CACCCACAAA
529111 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
529149 GAATAAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:532268 original size:22 final size:22
Alignment explanation
Indices: 532209--532268 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
532199 ATGATTAGGC
* *
532209 GATATAACCTTTTCGAATAAAT
1 GATATCACCTTTTCAAATAAAT
* *
532231 GATATCA-CTTAATCAAATAAGT
1 GATATCACCTT-TTCAAATAAAT
532253 GATATCACCTTTTCAA
1 GATATCACCTTTTCAA
532269 TGTTGTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 3 0.10
22 25 0.81
23 3 0.10
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (22 bp):
GATATCACCTTTTCAAATAAAT
Found at i:532946 original size:9 final size:10
Alignment explanation
Indices: 532920--532948 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
532910 TGTAACAGTG
532920 TCAGAAAATA
1 TCAGAAAATA
532930 TCAGAAAATA
1 TCAGAAAATA
532940 T-AGAAAATA
1 TCAGAAAATA
532949 GCACAAAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (10 bp):
TCAGAAAATA
Found at i:540920 original size:4 final size:4
Alignment explanation
Indices: 540911--540986 Score: 71
Period size: 4 Copynumber: 19.0 Consensus size: 4
540901 TTAAAAGCAT
* * * * * *
540911 GAGA GAGA GAAA GAAA GAAA GAAA GAGA GAGA GACA AAGA GAGA GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * *
540959 CAAA GAGA GAAA GAGA GAGA GAGA GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA
540987 TATTTTCAGT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.59, C:0.03, G:0.38, T:0.00
Consensus pattern (4 bp):
GAGA
Found at i:540951 original size:14 final size:14
Alignment explanation
Indices: 540911--540986 Score: 93
Period size: 14 Copynumber: 5.6 Consensus size: 14
540901 TTAAAAGCAT
540911 GAGAGAGAGAAAGA
1 GAGAGAGAGAAAGA
*
540925 -A-AGAAAGAAAGA
1 GAGAGAGAGAAAGA
*
540937 GAGAGAGACAAAGA
1 GAGAGAGAGAAAGA
*
540951 GAGAGAGACAAAGA
1 GAGAGAGAGAAAGA
* *
540965 GAGAAAGAGAGAGA
1 GAGAGAGAGAAAGA
540979 GAGAGAGA
1 GAGAGAGA
540987 TATTTTCAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
12 10 0.19
13 2 0.04
14 41 0.77
ACGTcount: A:0.59, C:0.03, G:0.38, T:0.00
Consensus pattern (14 bp):
GAGAGAGAGAAAGA
Found at i:540953 original size:10 final size:10
Alignment explanation
Indices: 540912--540986 Score: 68
Period size: 10 Copynumber: 7.7 Consensus size: 10
540902 TAAAAGCATG
540912 AGAGAGAGAA
1 AGAGAGAGAA
540922 AGA-A-AGAA
1 AGAGAGAGAA
*
540930 AGA-A-AGAG
1 AGAGAGAGAA
*
540938 AGAGAGACAA
1 AGAGAGAGAA
540948 AGAGAGAGAGA
1 AGAGAGAGA-A
*
540959 CAAAGAGAGAA
1 -AGAGAGAGAA
*
540970 AGAGAGAGAG
1 AGAGAGAGAA
540980 AGAGAGA
1 AGAGAGA
540987 TATTTTCAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
8 14 0.26
9 2 0.04
10 28 0.52
11 2 0.04
12 8 0.15
ACGTcount: A:0.60, C:0.03, G:0.37, T:0.00
Consensus pattern (10 bp):
AGAGAGAGAA
Found at i:546509 original size:30 final size:30
Alignment explanation
Indices: 546473--546563 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
546463 TATTTGAACT
*
546473 GCCGGTCAATAGACTGCGATCTATTAGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
546503 GCCGGTCAATAGACTGCGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
*
546533 GCCGGTCAATAGACTGCAATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
546563 G
1 G
546564 GCAACGTATT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.23
Consensus pattern (30 bp):
GCCGGTCAATAGACTGCGATCTATTGGACC
Found at i:546840 original size:90 final size:90
Alignment explanation
Indices: 546687--546868 Score: 364
Period size: 90 Copynumber: 2.0 Consensus size: 90
546677 ATGTTATCAA
546687 AATGGAGTATCAAATAATCAACAGCTTTAAAGCCTGACTATTTAAAATCTAACGGGTTTAAGCCC
1 AATGGAGTATCAAATAATCAACAGCTTTAAAGCCTGACTATTTAAAATCTAACGGGTTTAAGCCC
546752 CCCTTCTTTTGTTTAAACTACTATT
66 CCCTTCTTTTGTTTAAACTACTATT
546777 AATGGAGTATCAAATAATCAACAGCTTTAAAGCCTGACTATTTAAAATCTAACGGGTTTAAGCCC
1 AATGGAGTATCAAATAATCAACAGCTTTAAAGCCTGACTATTTAAAATCTAACGGGTTTAAGCCC
546842 CCCTTCTTTTGTTTAAACTACTATT
66 CCCTTCTTTTGTTTAAACTACTATT
546867 AA
1 AA
546869 ATTGAGATGT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 92 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (90 bp):
AATGGAGTATCAAATAATCAACAGCTTTAAAGCCTGACTATTTAAAATCTAACGGGTTTAAGCCC
CCCTTCTTTTGTTTAAACTACTATT
Found at i:553226 original size:76 final size:76
Alignment explanation
Indices: 553096--553246 Score: 266
Period size: 76 Copynumber: 2.0 Consensus size: 76
553086 CGTTCGNGAT
*
553096 CGTTATACTTCAAATACCCCCGTTCGTATTTGATTTTATAAATTAAACTATATTACTATCAGTTA
1 CGTTATACTTCAAATACCCCCGTTCGTATTTGATTTTATAAATTAAACTATATTACTATCAGATA
553161 TTATGTACAAC
66 TTATGTACAAC
* * *
553172 CGTTATACTTCAAATACCCCCGTTTGTATTTGATTTTATGAATTAAACTCTATTACTATCAGATA
1 CGTTATACTTCAAATACCCCCGTTCGTATTTGATTTTATAAATTAAACTATATTACTATCAGATA
553237 TTATGTACAA
66 TTATGTACAA
553247 TTGACAAAGA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (76 bp):
CGTTATACTTCAAATACCCCCGTTCGTATTTGATTTTATAAATTAAACTATATTACTATCAGATA
TTATGTACAAC
Found at i:571777 original size:3 final size:3
Alignment explanation
Indices: 571762--571817 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
571752 GCTTTAAGCT
*
571762 TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
571810 TTA TTA TT
1 TTA TTA TT
571818 CTGCATCAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:572103 original size:7 final size:7
Alignment explanation
Indices: 572091--572159 Score: 84
Period size: 7 Copynumber: 9.9 Consensus size: 7
572081 GAGAAGGATC
572091 ATTCGAG
1 ATTCGAG
572098 ATTCGAG
1 ATTCGAG
* *
572105 ATTCAAA
1 ATTCGAG
*
572112 ATACGAG
1 ATTCGAG
*
572119 ATTCGAA
1 ATTCGAG
*
572126 ATACGAG
1 ATTCGAG
572133 ATTCGAG
1 ATTCGAG
*
572140 ATTCGAA
1 ATTCGAG
572147 ATTCGAG
1 ATTCGAG
572154 ATTCGA
1 ATTCGA
572160 TATCTAAATT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (7 bp):
ATTCGAG
Found at i:573387 original size:21 final size:21
Alignment explanation
Indices: 573349--573487 Score: 192
Period size: 21 Copynumber: 6.7 Consensus size: 21
573339 GACAACCCTG
*
573349 AATACAAAT-GAAATTTATAC
1 AATACAAATGGAAAATTATAC
*
573369 AATACGAATGGAAAATTATAC
1 AATACAAATGGAAAATTATAC
* *
573390 AATACAAATAGAAAATTATAG
1 AATACAAATGGAAAATTATAC
*
573411 AATACAAAT-GAAATTTATAC
1 AATACAAATGGAAAATTATAC
*
573431 AATACAAATAGAAAATTATAC
1 AATACAAATGGAAAATTATAC
* *
573452 AATACAAATGAAAAATTATAT
1 AATACAAATGGAAAATTATAC
573473 AATACAAATGGAAAA
1 AATACAAATGGAAAA
573488 GATCGAATAT
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
20 26 0.25
21 79 0.75
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.25
Consensus pattern (21 bp):
AATACAAATGGAAAATTATAC
Found at i:573429 original size:41 final size:41
Alignment explanation
Indices: 573349--573487 Score: 199
Period size: 41 Copynumber: 3.4 Consensus size: 41
573339 GACAACCCTG
* *
573349 AATACAAAT-GAAATTTATACAATACGAATGGAAAATTATAC
1 AATACAAATAGAAAATTATACAATACAAAT-GAAAATTATAC
* *
573390 AATACAAATAGAAAATTATAGAATACAAATGAAATTTATAC
1 AATACAAATAGAAAATTATACAATACAAATGAAAATTATAC
*
573431 AATACAAATAGAAAATTATACAATACAAATGAAAAATTATAT
1 AATACAAATAGAAAATTATACAATACAAATG-AAAATTATAC
*
573473 AATACAAATGGAAAA
1 AATACAAATAGAAAA
573488 GATCGAATAT
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
41 49 0.56
42 39 0.44
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.25
Consensus pattern (41 bp):
AATACAAATAGAAAATTATACAATACAAATGAAAATTATAC
Found at i:573445 original size:62 final size:62
Alignment explanation
Indices: 573348--573482 Score: 227
Period size: 62 Copynumber: 2.2 Consensus size: 62
573338 AGACAACCCT
* *
573348 GAATACAAATGAAATTTATACAATACGAATGGAAAATTATACAATACAAAT-AGAAAATTATA
1 GAATACAAATGAAATTTATACAATACAAATAGAAAATTATACAATACAAATGA-AAAATTATA
573410 GAATACAAATGAAATTTATACAATACAAATAGAAAATTATACAATACAAATGAAAAATTATA
1 GAATACAAATGAAATTTATACAATACAAATAGAAAATTATACAATACAAATGAAAAATTATA
*
573472 TAATACAAATG
1 GAATACAAATG
573483 GAAAAGATCG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
62 68 0.99
63 1 0.01
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (62 bp):
GAATACAAATGAAATTTATACAATACAAATAGAAAATTATACAATACAAATGAAAAATTATA
Found at i:576801 original size:13 final size:13
Alignment explanation
Indices: 576783--576810 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
576773 TTGTTCATTC
576783 GTTGTTAGTTTAT
1 GTTGTTAGTTTAT
576796 GTTGTTAGTTTAT
1 GTTGTTAGTTTAT
576809 GT
1 GT
576811 AATATTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.25, T:0.61
Consensus pattern (13 bp):
GTTGTTAGTTTAT
Found at i:582076 original size:333 final size:329
Alignment explanation
Indices: 581121--582657 Score: 2019
Period size: 333 Copynumber: 4.6 Consensus size: 329
581111 AAGAATCATT
* *
581121 TGGCTGATTAGTTTCTGAGAAGAAAATTTTTAAAGATTTACTCTCTATATTCCTATGTAAAACTT
1 TGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-T
* * *
581186 TAAC-ACCTTCCCAATGTGGCCCCACCCTA-CCTCCAGGGATCATGCTTTTCACAACTTGGAATC
65 T--CGACC--CCCATTGTGGCCCCACCCTACCCT-C-GGGGTCATGATTTTCACAACTTGGAATC
* * *
581249 TACACTACCTGAGAATACTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAA
124 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTTTGAGAAGAA
* * ** *
581314 GATTTTTAAATATTTACTCTATATATTCCTAAGTAAAACTTCGCCCCCCCCCCCCCCATTGT-GC
189 GATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT--------CAACCCCCATGGTGGC
* * * *
581378 CCCATCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTATACTACCTC-AGGATGCTTC
246 CCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAATCTACACTACC-CGAGGATGCTTC
581442 CACACAAGTTTCAGCTTTCC
310 CACACAAGTTTCAGCTTTCC
*
581462 TGGCTGATTAGTTTCTTG-GAAGAAGATTTTTAAAGATTTACTCTTTATATTCCTATGTAAAACT
1 TGGCTGATTAGTTTC-TGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* *
581526 TCGACCCCCATTGTGGCCCCACCTTACCCCCAGGGGTCATGATTTTCACAACTTGGAATCTACAC
65 TCGACCCCCATTGTGGCCCCACCCTACCCTC-GGGGTCATGATTTTCACAACTTGGAATCTACAC
*
581591 TACCTGAGGATGCTT---C-CAAGTTTCAGCTTTCCTGGTTGATTAGTTTTTGAGAAGAAGATTT
129 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTTTGAGAAGAAGATTT
* * *
581652 TTACAGATTTACTCTATATATTCCTATGTAAAACTTCGAGCCCCCATGGTGGCCCCACCCT-GCC
194 TTAAAGATTTACTCTATATATTCCTATGTAAAACTTC-AACCCCCATGGTGGCCCCACCCTACCC
*
581716 CCCGGAGGTCATGACTTTCACAACTTTGAATCTACACTACCCGAGGATGCTTCCACACAAGTTTC
258 CCCGG-GGTCATGATTTTCACAACTTTGAATCTACACTACCCGAGGATGCTTCCACACAAGTTTC
*
581781 CGCTTTCC
322 AGCTTTCC
* * * *
581789 TGGCTGATTAGTTTCTGAGAACATGATTTTTAAAGATTTACTCTATAGATATATTCCTACGTAAG
1 TGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTC--T--ATATATTCCTATGTAAA
* * * *
581854 ACTTCGACCCCCATTGTGGCCCCACCCTATCCTCGGGGTCATAATTTTCACAACTTTGAATCAAC
62 ACTTCGACCCCCATTGTGGCCCCACCCTACCCTCGGGGTCATGATTTTCACAACTTGGAATCTAC
* *
581919 ACTACCTCAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTAATTAGTTTTTG-GAAGAAGAT
127 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTTTGAGAAGAAGAT
* * *
581983 TTTAAAAGATTGACTCTATATATTCCTATGTAAAACTTCAAACCCCTATGGTGGCCCCACCCTAC
192 TTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC-AACCCCCATGGTGGCCCCACCCTAC
* *
582048 CCCCCGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCATACAAGTTT
256 CCCCCGGGGTCATGATTTTCACAACTTTGAATCTACACTACCCGAGGATGCTTCCACACAAGTTT
582113 CAGCTTTCC
321 CAGCTTTCC
*
582122 TGGCTGATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACTCTATATATTCCTGTGTAAAACTT
1 TGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
* * * *
582184 CGACCCCAATTTGTGGCCCCACCCTACCCCTGGGGGTCATGAATTTCACAACTTGGAATCTACAT
66 CGACCCCCA-TTGTGGCCCCACCCTA-CCCTCGGGGTCATGATTTTCACAACTTGGAATCTACAC
* * * * *
582249 TACCTGGGGATGCTTCCAGATAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGGGAAGAAGATTT
129 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTTTGAGAAGAAGATTT
* * * * *
582314 TTAAAGATTTACTCTTTATATTCCTATGTAAAACTTCGACCCCCATTGTGGCCTCACCCTACCCA
194 TTAAAGATTTACTCTATATATTCCTATGTAAAACTTCAACCCCCATGGTGGCCCCACCCTACCCC
* * * *
582379 CCGGGGTCATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACTCAAGTGTCAG
259 CCGGGGTCATGATTTTCACAACTTTGAATCTACACTACCCGAGGATGCTTCCACACAAGTTTCAG
582444 CTTTCC
324 CTTTCC
*
582450 TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
1 TGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
* * * * *
582515 CGACCCCCTCCCATTGTGGCCCCACCCTACCCCCGGGGTTTATGACTTTCACAACTTTGAATCAA
66 CGA---CC-CCCATTGTGGCCCCACCCTACCCTCGGGG-TCATGATTTTCACAACTTGGAATCTA
* * *
582580 CACTACCTGAGGATGCCTCCACACAAGTTTCAGCTTTCATGGCT--TTATGGTTCTTGAGAAGAA
126 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTA--GTTTTTGAGAAGAA
582643 GATTTTTGAAA-ATTT
189 GATTTTT-AAAGATTT
582658 CTCGAAATTT
Statistics
Matches: 1067, Mismatches: 98, Indels: 69
0.86 0.08 0.06
Matches are distributed among these distances:
325 1 0.00
326 44 0.04
327 124 0.12
328 184 0.17
329 46 0.04
330 66 0.06
331 93 0.09
332 3 0.00
333 229 0.21
334 139 0.13
335 6 0.01
337 64 0.06
338 3 0.00
339 3 0.00
340 2 0.00
341 58 0.05
342 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (329 bp):
TGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
CGACCCCCATTGTGGCCCCACCCTACCCTCGGGGTCATGATTTTCACAACTTGGAATCTACACTA
CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTTTGAGAAGAAGATTTTT
AAAGATTTACTCTATATATTCCTATGTAAAACTTCAACCCCCATGGTGGCCCCACCCTACCCCCC
GGGGTCATGATTTTCACAACTTTGAATCTACACTACCCGAGGATGCTTCCACACAAGTTTCAGCT
TTCC
Found at i:582098 original size:165 final size:165
Alignment explanation
Indices: 581121--582657 Score: 1981
Period size: 165 Copynumber: 9.2 Consensus size: 165
581111 AAGAATCATT
* * *
581121 TGGCTGATTAGTTTCTGAGAAGAAAATTTTTAAAGATTTACTCTCTATATTCCTATGTAAAACTT
1 TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-T
* * * * * * *
581186 TAACACCTTCCCAATGTGGCCCCACCCTACCTCCAGGGATCATGCTTTTCACAACTTGGAATCTA
65 TCA-ACC--CCCATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAATCTA
* *
581251 CACTACCTGAGAATACTTCCACACAAGTTTCAGCTTTCC
127 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
* * *
581290 TGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAATATTTACTCTATATATTCCTAAGTAAAACTT
1 TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
** * * *
581355 CGCCCCCCCCCCCCCCATTGT-GCCCCATCCTACCCCCAGGGATCATGATTTTCACAACTTTGAA
66 --------CAACCCCCATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAA
* *
581419 TCTATACTACCTCAGGATGCTTCCACACAAGTTTCAGCTTTCC
123 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
*
581462 TGGCTGATTAGTTTCTTG-GAAGAAGATTTTTAAAGATTTACTCTTTATATTCCTATGTAAAACT
1 TGGCTGATTAGTTT-TTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * * *
581526 TCGACCCCCATTGTGGCCCCACCTTACCCCCAGGGGTCATGATTTTCACAACTTGGAATCTACAC
65 TCAACCCCCATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAATCTACAC
581591 TACCTGAGGATGCTT---C-CAAGTTTCAGCTTTCC
130 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
* *
581623 TGGTTGATTAGTTTTTGAGAAGAAGATTTTTACAGATTTACTCTATATATTCCTATGTAAAACTT
1 TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
* * * *
581688 CGAGCCCCCATGGTGGCCCCACCCT-GCCCCCGGAGGTCATGACTTTCACAACTTTGAATCTACA
66 C-AACCCCCATTGTGGCCCCACCCTACCCCCCGG-GGTCATGATTTTCACAACTTTGAATCTACA
* *
581752 CTACCCGAGGATGCTTCCACACAAGTTTCCGCTTTCC
129 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
* * * * *
581789 TGGCTGATTAGTTTCTGAGAACATGATTTTTAAAGATTTACTCTATAGATATATTCCTACGTAAG
1 TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTC--T--ATATATTCCTATGTAAA
* * * * *
581854 ACTTCGACCCCCATTGTGGCCCCACCCTA-TCCTCGGGGTCATAATTTTCACAACTTTGAATCAA
62 ACTTCAACCCCCATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAATCTA
*
581918 CACTACCTCAGGATGCTTCCACACAAGTTTCAGCTTTCC
127 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
* * *
581957 TGGCTAATTAGTTTTTG-GAAGAAGATTTTAAAAGATTGACTCTATATATTCCTATGTAAAACTT
1 TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
* *
582021 CAAACCCCTATGGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAATCTACAC
66 C-AACCCCCATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAATCTACAC
*
582086 TACCTGAGGATGCTTCCATACAAGTTTCAGCTTTCC
130 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
* *
582122 TGGCTGATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACTCTATATATTCCTGTGTAAAACTT
1 TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
* * ** * * *
582184 CGACCCCAATTTGTGGCCCCACCCTACCCCTGGGGGTCATGAATTTCACAACTTGGAATCTACAT
66 CAACCCCCA-TTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAATCTACAC
* * *
582249 TACCTGGGGATGCTTCCAGATAAGTTTCAGCTTTCC
130 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
* * *
582285 TGGCTGATTAGTTTCTGGGAAGAAGATTTTTAAAGATTTACTCTTTATATTCCTATGTAAAACTT
1 TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
* * * *
582350 CGACCCCCATTGTGGCCTCACCCTACCCACCGGGGTCATGATTTTCACAACTTGGAATCTACACT
66 CAACCCCCATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAATCTACACT
* *
582415 ACCTGAGGATGCTTCCACTCAAGTGTCAGCTTTCC
131 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
582450 TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
1 TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
* * * *
582515 CGACCCCCTCCCATTGTGGCCCCACCCTA-CCCCCGGGGTTTATGACTTTCACAACTTTGAATCA
66 C-A--ACC-CCCATTGTGGCCCCACCCTACCCCCCGGGG-TCATGATTTTCACAACTTTGAATCT
* *
582579 ACACTACCTGAGGATGCCTCCACACAAGTTTCAGCTTTCA
126 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
*
582619 TGGCT--TTATGGTTCTTGAGAAGAAGATTTTTGAAA-ATTT
1 TGGCTGATTA--GTTTTTGAGAAGAAGATTTTT-AAAGATTT
582658 CTCGAAATTT
Statistics
Matches: 1210, Mismatches: 122, Indels: 72
0.86 0.09 0.05
Matches are distributed among these distances:
160 3 0.00
161 81 0.07
162 69 0.06
163 161 0.13
164 33 0.03
165 287 0.24
166 104 0.09
167 24 0.02
168 89 0.07
169 189 0.16
170 23 0.02
172 136 0.11
173 9 0.01
175 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (165 bp):
TGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
CAACCCCCATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAATCTACACT
ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
Found at i:582328 original size:496 final size:490
Alignment explanation
Indices: 581121--582623 Score: 2056
Period size: 496 Copynumber: 3.0 Consensus size: 490
581111 AAGAATCATT
*
581121 TGGCTGATTAGTTTCTGAGAAGAAAATTTTTAAAGATTTACTCTCTATATTCCTATGTAAAACTT
1 TGGCTGATTAGTTTCTGAGAAG---ATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-T
* * **
581186 TAAC-ACCTTCCCAA-TGTGGCCCCACCCTACCTCCAGGGATCATGCTTTTCACAACTTGGAATC
62 T--CGACC--CCCAATTGTGGCCCCACCCTACC-CCGGGGGTCATGAATTTCACAACTTGGAATC
* *
581249 TACACTACCTGAGAATACTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAA
122 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAA
* *
581314 GATTTTTAAATATTTACTC-TATATATTCCTAAGTAAAACTTCGCCCCCCCCCCCCCCATTGT-G
187 GATTTTTAAAGATTTACTCTTATATATTCCTAAGTAAAACTTCG--------ACCCCCATTGTGG
* * *
581377 CCCCATCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTATACTACCTCAGGATGCTTC
244 CCCCACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATCTACACTACCTCAGGATGCTTC
*
581442 CACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTTGGAAGAAGATTTTTAAAGATTTACTCTT
308 CACACAAGTTTCAGCTTTCCTGGCTGATTAGTTT-TTGGAAGAAGATTTTTAAAGATTTACTCTA
* * * *
581507 TATATTCCTATGTAAAACTTCGACCCCCATTGTGGCCCCACCTTACCCCCAGGGGTCATGATTTT
372 TATATTCCTATGTAAAACTTCAACCCCTATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTT
*
581572 CACAACTTGGAATCTACACTACCTGAGGATGCTT-C--CAAGTTTCAGCTTTCC
437 CACAACTTTGAATCTACACTACCTGAGGATGCTTCCAACAAGTTTCAGCTTTCC
* * *
581623 TGGTTGATTAGTTTTTGAGAAGAAGATTTTTACAGATTTACTCTATATATTCCTATGTAAAACTT
1 TGGCTGATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTT
* * * * *
581688 CGAGCCCCC-ATGGTGGCCCCACCCTGCCCCCGGAGGTCATGACTTTCACAACTTTGAATCTACA
63 CGA-CCCCCAATTGTGGCCCCACCCT-ACCCCGGGGGTCATGAATTTCACAACTTGGAATCTACA
* * * *
581752 CTACCCGAGGATGCTTCCACACAAGTTTCCGCTTTCCTGGCTGATTAGTTTCTGAGAACATGATT
126 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATT
* *
581817 TTTAAAGATTTACTCTATAGATATATTCCTACGTAAGACTTCGACCCCCATTGTGGCCCCACCCT
191 TTTAAAGATTTACTCT-T--ATATATTCCTAAGTAAAACTTCGACCCCCATTGTGGCCCCACCCT
* * * *
581882 ATCCTCGGGGTCATAATTTTCACAACTTTGAATCAACACTACCTCAGGATGCTTCCACACAAGTT
253 ACCCCCGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTCAGGATGCTTCCACACAAGTT
* * *
581947 TCAGCTTTCCTGGCTAATTAGTTTTTGGAAGAAGATTTTAAAAGATTGACTCTATATATTCCTAT
318 TCAGCTTTCCTGGCTGATTAGTTTTTGGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTAT
*
582012 GTAAAACTTCAAACCCCTATGGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTG
383 GTAAAACTTC-AACCCCTATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTG
582077 AATCTACACTACCTGAGGATGCTTCCATACAAGTTTCAGCTTTCC
447 AATCTACACTACCTGAGGATGCTTCCA-ACAAGTTTCAGCTTTCC
*
582122 TGGCTGATTAGTTTCTGAGAAGATTTTTAAAGATTTACTCTATATATTCCTGTGTAAAACTTCGA
1 TGGCTGATTAGTTTCTGAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGA
*
582187 -CCCCAATTTGTGGCCCCACCCTACCCCTGGGGGTCATGAATTTCACAACTTGGAATCTACATTA
66 CCCCCAA-TTGTGGCCCCACCCTACCCC-GGGGGTCATGAATTTCACAACTTGGAATCTACACTA
* * * *
582251 CCTGGGGATGCTTCCAGATAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGGGAAGAAGATTTTT
129 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTT
* *
582316 AAAGATTTACTCTT-TATATTCCTATGTAAAACTTCGACCCCCATTGTGGCCTCACCCTACCCAC
194 AAAGATTTACTCTTATATATTCCTAAGTAAAACTTCGACCCCCATTGTGGCCCCACCCTACCC-C
* * * *
582380 CGGGGTCATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACTCAAGTGTCAGC
258 CGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTCAGGATGCTTCCACACAAGTTTCAGC
582445 TTTCCTGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAA
323 TTTCCTGGCTGATTAGTTTTTG-GAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAA
* * *
582510 AACTTCGACCCCCTCCCATTGTGGCCCCACCCTA-CCCCCGGGGTTTATGACTTTCACAACTTTG
387 AACTTC-AACCCCT---ATTGTGGCCCCACCCTACCCCCCGGGG-TCATGATTTTCACAACTTTG
* * *
582574 AATCAACACTACCTGAGGATGCCTCCACACAAGTTTCAGCTTTCA
447 AATCTACACTACCTGAGGATGCTTCCA-ACAAGTTTCAGCTTTCC
582619 TGGCT
1 TGGCT
582624 TTATGGTTCT
Statistics
Matches: 895, Mismatches: 80, Indels: 57
0.87 0.08 0.06
Matches are distributed among these distances:
492 44 0.05
493 80 0.09
494 104 0.12
495 166 0.19
496 185 0.21
497 81 0.09
498 1 0.00
499 149 0.17
500 3 0.00
501 5 0.01
502 50 0.06
503 21 0.02
504 1 0.00
505 5 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (490 bp):
TGGCTGATTAGTTTCTGAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGA
CCCCCAATTGTGGCCCCACCCTACCCCGGGGGTCATGAATTTCACAACTTGGAATCTACACTACC
TGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAA
AGATTTACTCTTATATATTCCTAAGTAAAACTTCGACCCCCATTGTGGCCCCACCCTACCCCCGG
GGTCATGATTTTCACAACTTTGAATCTACACTACCTCAGGATGCTTCCACACAAGTTTCAGCTTT
CCTGGCTGATTAGTTTTTGGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
TCAACCCCTATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTCACAACTTTGAATCTACAC
TACCTGAGGATGCTTCCAACAAGTTTCAGCTTTCC
Found at i:582830 original size:8 final size:8
Alignment explanation
Indices: 582819--582848 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
582809 TGAAAAGTTT
582819 ACGGACAG
1 ACGGACAG
*
582827 ACGGACGG
1 ACGGACAG
582835 ACGGACAG
1 ACGGACAG
582843 ACGGAC
1 ACGGAC
582849 GACAGACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.40, T:0.00
Consensus pattern (8 bp):
ACGGACAG
Found at i:582840 original size:16 final size:16
Alignment explanation
Indices: 582819--582849 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
582809 TGAAAAGTTT
582819 ACGGACAGACGGACGG
1 ACGGACAGACGGACGG
582835 ACGGACAGACGGACG
1 ACGGACAGACGGACG
582850 ACAGACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.42, T:0.00
Consensus pattern (16 bp):
ACGGACAGACGGACGG
Found at i:585531 original size:177 final size:174
Alignment explanation
Indices: 585311--585845 Score: 631
Period size: 169 Copynumber: 3.1 Consensus size: 174
585301 TGGTCCTAAA
* * * * * * *
585311 TTTCAGATGCTGGAGGAGATTAAGGTTGTTGGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
1 TTTCAGATGCTGAAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * * * *
585376 GATAGCA-ATATCTAAGTTACT-GTTGGTTCGT-ACTTCACCAAACTTGCATGGATGGTGTGTCT
66 GAT-G-ATATATCTTAGTTACTACTT-G-TCCTAACTTCACCAAACTTACATGGATGGTGCGTCT
* * *
585438 TATGATACTGATGCACCAGGCAGGCTTGGGTGCTGAATCTGAGCTATAGG
127 TATGATACTGATGCACCTGACAGGCTT--GTGCTGAATCTGAGCCATAGG
*
585488 TTACAGATGCTGAAGGAGG-TAACGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTC
1 TTTCAGATGCTGAAGGAGGTTAA-GGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTC
* * *
585552 TGATGATTATATCTTAGTTACTACTTGTCCTAACTTCACCAGACTTATATGG-TTGTGCGTCTTA
65 TGATGA-TATATCTTAGTTACTACTTGTCCTAACTTCACCAAACTTACATGGATGGTGCGTCTTA
*
585616 TGATACCGATGCACCTGACAGGC---T--TGAATCTGAGCCATAGG
129 TGATACTGATGCACCTGACAGGCTTGTGCTGAATCTGAGCCATAGG
* * ***
585657 TTTCGGATGCTGAAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTATTTGAAACAGGTGCCCTCT
1 TTTCAGATGCTGAAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * *
585722 GATGATTATATCTTAGTTATTACTTGTCCTAACTTCACTAAACTTCCATGGATGGTGCGTCTTAT
66 GATGA-TATATCTTAGTTACTACTTGTCCTAACTTCACCAAACTTACATGGATGGTGCGTCTTAT
* *
585787 GATACTGATGCACCTGACAAGCTTGAATGCTGAGTCTGAGCCATAGG
130 GATACTGATGCACCTGACAGGCTTG--TGCTGAATCTGAGCCATAGG
585834 TTTCAGATGCTG
1 TTTCAGATGCTG
585846 GATATGGTTA
Statistics
Matches: 308, Mismatches: 36, Indels: 28
0.83 0.10 0.08
Matches are distributed among these distances:
169 117 0.38
170 35 0.11
171 1 0.00
175 2 0.01
176 37 0.12
177 114 0.37
178 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (174 bp):
TTTCAGATGCTGAAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
GATGATATATCTTAGTTACTACTTGTCCTAACTTCACCAAACTTACATGGATGGTGCGTCTTATG
ATACTGATGCACCTGACAGGCTTGTGCTGAATCTGAGCCATAGG
Found at i:587674 original size:15 final size:15
Alignment explanation
Indices: 587654--587684 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
587644 ATGATACAAA
*
587654 TGTATAATATAATAT
1 TGTATAACATAATAT
587669 TGTATAACATAATAT
1 TGTATAACATAATAT
587684 T
1 T
587685 TTACTTTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (15 bp):
TGTATAACATAATAT
Found at i:587803 original size:10 final size:10
Alignment explanation
Indices: 587784--587822 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
587774 ATCAAAAATG
*
587784 ATACAGTATC
1 ATACAATATC
587794 ATACAATATC
1 ATACAATATC
* *
587804 ATACTATATT
1 ATACAATATC
587814 ATACAATAT
1 ATACAATAT
587823 AATATCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (10 bp):
ATACAATATC
Found at i:588567 original size:16 final size:16
Alignment explanation
Indices: 588546--588577 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
588536 TATGCGGGAC
588546 ATACTAAAGACCTGAA
1 ATACTAAAGACCTGAA
588562 ATACTAAAGACCTGAA
1 ATACTAAAGACCTGAA
588578 TGTCATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (16 bp):
ATACTAAAGACCTGAA
Found at i:588863 original size:15 final size:15
Alignment explanation
Indices: 588843--588877 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
588833 CAATTCAATG
588843 CAAAAAA-AACAAAAA
1 CAAAAAACAA-AAAAA
588858 CAAAAAACAAAAAAA
1 CAAAAAACAAAAAAA
588873 CAAAA
1 CAAAA
588878 TGGTTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (15 bp):
CAAAAAACAAAAAAA
Found at i:588864 original size:13 final size:13
Alignment explanation
Indices: 588846--588870 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
588836 TTCAATGCAA
588846 AAAAAACAAAAAC
1 AAAAAACAAAAAC
588859 AAAAAACAAAAA
1 AAAAAACAAAAA
588871 AACAAAATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:591392 original size:6 final size:6
Alignment explanation
Indices: 591369--591417 Score: 66
Period size: 6 Copynumber: 8.3 Consensus size: 6
591359 TGATCACAAT
*
591369 TTGTCCG TTGTC- -TGTCG TTGTCG TTGTCG TAGTCG TTGTCG TTGTCG
1 TTGT-CG TTGTCG TTGTCG TTGTCG TTGTCG TTGTCG TTGTCG TTGTCG
591416 TT
1 TT
591418 AACTTTTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
4 4 0.11
6 30 0.79
7 4 0.11
ACGTcount: A:0.02, C:0.18, G:0.31, T:0.49
Consensus pattern (6 bp):
TTGTCG
Found at i:592016 original size:166 final size:165
Alignment explanation
Indices: 591742--593405 Score: 1829
Period size: 166 Copynumber: 10.2 Consensus size: 165
591732 ATATATAGAG
* * * *
591742 AAAATCTTCTCCTCAAAAACTATTGGGCCAGAAAAGCTCAAATTATAATGGAATCATCTTCAGGT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAATGGAAGCATC-TCAGGT
*
591807 AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTCGGGGAT
65 AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAGGGGAT
591872 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
130 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
* * * *
591908 AAAATCTTCTTCTCAAAAATTATTGGGCCAGAAAAGCTCAAATTAAAATGGGAGCATCTACAGGT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAATGGAAGCATCT-CAGGT
* * *
591973 AGTGTAGTTTCAAATTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTCGGGGAT
65 AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAGGGGAT
592038 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
130 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
* * *
592074 AAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCTTCAGAT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAATGGAAGCATC-TCAGGT
* *
592139 ATTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCAGGGGTAGGGTGGGGCCACAA-TAGGAGGA
65 AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAGG-GGA
* * * *
592203 TGAATTTTTACATAGGAATATATAGATAAAATCTTAA
129 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
* * **
592240 AAAATCGTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTATAATGGAATTATCTTCAGGT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAATGGAAGCATC-TCAGGT
* * * * * * **
592305 AGTGTAGATTCAAGCTCGTTCAAATCATTGTCCCCAGGTGTAGGGTGGGGCCAAAATGGGGGGAT
65 AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAGGGGAT
592370 CAAGTTTTACATAGGAATATATAGAG----------
130 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
* * *
592396 AAAA---TCTTCTCAAAATCTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCCTCAGGT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAATGGAAGCAT-CTCAGGT
*
592458 AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGAT
65 AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAGGGGAT
*
592523 CAATTTTTACATAGGAATATATAGAGAAAATCTTTA
130 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
* * * * *
592559 AAAA---TCTTCTCAAAAACTATTTGACCA-AGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGA
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGA-AAAGCTCAAATTAGAATGGAAGCAT-CTCAGG
*
592620 TAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-TAGGAGG
64 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAGG-GG
* *
592684 ATGAA-TATTTACATAGGAATATATAGAGGAAATCTTTA
128 ATCAAGT-TTTACATAGGAATATATAGAGAAAATCTTTA
* * * *
592722 AAAATCTTCTTCTCAAAAACTATTGGGGCAGAAAAGCTCAAATTATAATGGAATCATCTTCAGGT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAATGGAAGCATC-TCAGGT
* * * * **
592787 AGTGTAGATTCAAGCTCGTTCAAATCATGGTCCCCAGGGGTAGGGAGGGGCCACAAGAAGGGGAT
65 AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAGGGGAT
*
592852 CAAGTTTTACATA-AAATATATAGAG----------
130 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
* *
592877 AAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATTCTCAGGT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAATGGAAGCA-TCTCAGGT
* * * *
592942 ATTGTAGATTTAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCCACAATT-GGGTAT
65 AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAGGGGAT
593006 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
130 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
* * * * *** *
593042 AAAATCTTCTTCTCGAAAACTATTTGACTA-AGAAAGCTCAAATT-GGCGGGTAACCATCCTCAG
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGA-AAAGCTCAAATTAGAATGG-AAGCAT-CTCAG
* * * * *
593105 ATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCAC-ATTGGGGG
63 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAGGGG
* *
593169 AT-ACA-TTTT---T----ATACATAGAGAAAATCTCTAA
128 ATCA-AGTTTTACATAGGAATATATAGAGAAAATCT-TTA
* * * ** * * *
593200 AAAATCTTCTTCTCAAAACTACCGGTATTATGCCAGGAAAGCCCAAATCGGAGTTGAAGCATTTC
1 AAAATCTTCTTCTCAAAA--A-C--TATTAGGCCAGAAAAGCTCAAATTAGAATGGAAGCATCT-
** * * * * * * * * * * * *
593265 CAAATTGTATAGATTCAAGTTTTTTAAAATAATAGT--CCAGTGGTATGGTGAGGCCAC-AGTGG
60 CAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAG
* *
593327 GGGATGAATTTTTACATAGGAATATATAGAGAAAATCTTTA
125 GGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
* * * * *
593368 AAAATCTTCTTTTTAAAGACCATTTGGCCAGAAAAGCT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCT
593406 TTAACTTGTG
Statistics
Matches: 1284, Mismatches: 154, Indels: 123
0.82 0.10 0.08
Matches are distributed among these distances:
153 133 0.10
154 19 0.01
155 116 0.09
156 6 0.00
157 16 0.01
158 19 0.01
160 1 0.00
161 27 0.02
162 10 0.01
163 212 0.17
164 14 0.01
165 122 0.10
166 548 0.43
167 8 0.01
168 17 0.01
169 16 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (165 bp):
AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAATGGAAGCATCTCAGGTA
GTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTAGGGGATC
AAGTTTTACATAGGAATATATAGAGAAAATCTTTA
Found at i:592525 original size:153 final size:153
Alignment explanation
Indices: 592247--593039 Score: 930
Period size: 163 Copynumber: 5.0 Consensus size: 153
592237 TAAAAAATCG
* ** *
592247 TCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAT-AATGGAATTATCTTCAGGTAGTGTA
1 TCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATT-TGAATGGAAGCATCCTCAGGTAGTGTA
* * * * * * *
592311 GATTCAAGCTCGTTCAAATCATTGTCCCCAGGTGTAGGGTGGGGCCAAAATGGGGGGATCAAGTT
65 GATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTT
592376 TTACATAGGAATATATAGAGAAAA
130 TTACATAGGAATATATAGAGAAAA
*
592400 TCTTCTCAAAATCTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCCTCAGGTAGTGTAG
1 TCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCCTCAGGTAGTGTAG
* *
592465 ATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAATTTT
66 ATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTT
592530 TACATAGGAATATATAGAGAAAATCTTTAAAAA
131 TACATAGGAATATATAGAG----------AAAA
* * * * * *
592563 TCTTCTCAAAAACTATTTGACCAAGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTGTTG
1 TCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCCTCAGGTAGTGTAG
* *
592628 ATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGAGGATGAA-TAT
66 ATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGT-T
592692 TTACATAGGAATATATAGAGGAAATCTTTAAAAA
130 TTACATAGGAATATATAGA-G---------AAAA
* * * * *
592726 TCTTCTTCTCAAAAACTATTGGGGCAGAAAAGCTCAAATTAT-AATGGAATCATCTTCAGGTAGT
1 ---TCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATT-TGAATGGAAGCATCCTCAGGTAGT
* * * * * *
592790 GTAGATTCAAGCTCGTTCAAATCATGGTCCCCAGGGGTAGGGAGGGGCCACAAGAAGGGGATCAA
62 GTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAA
*
592855 GTTTTACATA-AAATATATAGAGAAAA
127 GTTTTACATAGGAATATATAGAGAAAA
* *
592881 TCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATTCTCAGGTATTG
1 ---TCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCCTCAGGTAGTG
* * * *
592946 TAGATTTAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCCACAAT-TGGGTATCAAG
63 TAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAG
593010 TTTTACATAGGAATATATAGAGAAAA
128 TTTTACATAGGAATATATAGAGAAAA
593036 TCTT
1 TCTT
593040 TAAAAATCTT
Statistics
Matches: 561, Mismatches: 59, Indels: 41
0.85 0.09 0.06
Matches are distributed among these distances:
152 5 0.01
153 134 0.24
154 19 0.03
155 121 0.22
162 1 0.00
163 153 0.27
164 2 0.00
165 10 0.02
166 114 0.20
167 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (153 bp):
TCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCCTCAGGTAGTGTAG
ATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTT
TACATAGGAATATATAGAGAAAA
Found at i:592666 original size:163 final size:163
Alignment explanation
Indices: 592396--593377 Score: 983
Period size: 163 Copynumber: 6.1 Consensus size: 163
592386 ATATATAGAG
* * * *
592396 AAAATCTTCTCAAAATCTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCCTCAGGTAGT
1 AAAATCTTCTCAAAAACTATTTGGCCAAGAAAGCTCAAATTTGAATGGAAGCATCCTCAGATAGT
592461 GTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAA
66 GTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAA
592526 TTTTTACATAGGAATATATAGAGAAAATCTTTA
131 TTTTTACATAGGAATATATAGAGAAAATCTTTA
* *
592559 AAAATCTTCTCAAAAACTATTTGACCAAGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGT
1 AAAATCTTCTCAAAAACTATTTGGCCAAGAAAGCTCAAATTTGAATGGAAGCATCCTCAGATAGT
* * * *
592624 GTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGAGGATGAA
66 GTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAA
* *
592689 TATTTACATAGGAATATATAGAGGAAATCTTTA
131 TTTTTACATAGGAATATATAGAGAAAATCTTTA
* * * *
592722 AAAATCTTCTTCTCAAAAACTATTGGGGC-AGAAAAGCTCAAATTAT-AATGGAATCATCTTCAG
1 AAAA---TCTTCTCAAAAACTATTTGGCCAAG-AAAGCTCAAATT-TGAATGGAAGCATCCTCAG
* * * * * ***
592785 GTAGTGTAGATTCAAGCTCGTTCAAATCATGGTCCCCAGGGGTAGGGAGGGGCCACAAGAAGGGG
61 ATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGG
* *
592850 ATCAAGTTTTACATA-AAATATATAGAGAAAATC--T-
126 ATCAATTTTTACATAGGAATATATAGAGAAAATCTTTA
* * * * *
592884 ----TCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATTCTCAGGTATT
1 AAAATCTTCTCAAAAACTATTTGGCCAAGAAAGCTCAAATTTGAATGGAAGCATCCTCAGATAGT
* * *
592945 GTAGATTTAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCCACAATT-GGGTATCAA
66 GTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAA
*
593009 GTTTTACATAGGAATATATAGAGAAAATCTTTA
131 TTTTTACATAGGAATATATAGAGAAAATCTTTA
* * * *** *
593042 AAAATCTTCTTCTCGAAAACTATTTGACTAAGAAAGCTCAAA-TTGGCGGGTAACCATCCTCAGA
1 AAAA---TCTTCTCAAAAACTATTTGGCCAAGAAAGCTCAAATTTGAATGG-AAGCATCCTCAGA
* * *
593106 TAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCAC-ATTGGGGGA
62 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA
* *
593170 T-ACA-TTTT---T----ATACATAGAGAAAATCTCTAA
127 TCA-ATTTTTACATAGGAATATATAGAGAAAATCT-TTA
* * ** * * *
593200 AAAATCTTCTTCTCAAAACTACCGGTATTAT-GCCAGGAAAGCCCAAATCGGAGTTGAAGCAT-T
1 AAAA---TCTTCTCAAAA--A-C--TATT-TGGCCAAGAAAGCTCAAATTTGAATGGAAGCATCC
* * * * * * * * * * * *
593263 TCCAAATTGTATAGATTCAAGTTTTTTAAAATAATAGT--CCAGTGGTATGGTGAGGCCAC-AGT
57 T-CAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATT
*
593325 GGGGGATGAATTTTTACATAGGAATATATAGAGAAAATCTTTA
121 GGGGGATCAATTTTTACATAGGAATATATAGAGAAAATCTTTA
593368 AAAATCTTCT
1 AAAATCTTCT
593378 TTTTAAAGAC
Statistics
Matches: 683, Mismatches: 97, Indels: 76
0.80 0.11 0.09
Matches are distributed among these distances:
154 19 0.03
155 114 0.17
156 1 0.00
157 17 0.02
158 19 0.03
160 1 0.00
161 27 0.04
162 6 0.01
163 205 0.30
164 16 0.02
165 122 0.18
166 113 0.17
167 1 0.00
168 6 0.01
169 16 0.02
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (163 bp):
AAAATCTTCTCAAAAACTATTTGGCCAAGAAAGCTCAAATTTGAATGGAAGCATCCTCAGATAGT
GTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAA
TTTTTACATAGGAATATATAGAGAAAATCTTTA
Found at i:592823 original size:482 final size:479
Alignment explanation
Indices: 591593--593161 Score: 2173
Period size: 482 Copynumber: 3.2 Consensus size: 479
591583 TTCAAAAATC
* * * * * * * *
591593 TTCTTCTCAAAAACTATTCGGCC-TGAGAAGCTAAAACTTGTGTGGAGGCATCCTCAGGTAGTGT
1 TTCTTCTCAAAAACTATTTGACCAAGA-AAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTGT
* * * *
591657 AGATTTAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAAGAAGG-GGATCAAG
65 AGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-TAGGAGGATGAA-
* *
591721 TTTTACATA-AAATATATAGAG--------AAAATCTTCTCCTCAAAAACTATTGGGCCAGAAAA
128 TTTTACATAGGAATATATAGAGAAATCTTAAAAATCTTCTTCTCAAAAACTATTGGGCCAGAAAA
* *
591777 GCTCAAATTATAATGGAATCATCTTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCC
193 GCTCAAATTATAATGGAATCATCTTCAGGTAGTGTAGATTCAAGCTCGTTCAAATCATGGTCCCC
* **
591842 GGGGGTAGGGTGGGGCCACAATTCGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
258 AGGGGTAGGGTGGGGCCACAATGAGGGGATCAAGTTTTACATAGGAATATATAGAG---------
* * ** *
591907 AAAAATCTTCTTCTCAAAAAT-TATTGGGCCAGAAAAGCTCAAATTAAAATGGGAGCATCTACAG
314 -AAAA--TTCTTCTC-AAAATCTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCT-CAG
* *
591971 GTAGTGTAGTTTCAAATTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTCGGGG
374 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATT-GGGG
592036 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAA
438 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAA
* * * * * *
592078 TCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCTTCAGATATTG
1 --TTCTTCTCAAAAACTATTTGACCAAGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTG
*
592143 TAGATTCAAGTTTGTTCAAATCATGGTCCCCAGGGGTAGGGTGGGGCCACAATAGGAGGATGAAT
64 TAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGAGGATGAA-
* * *
592208 TTTTACATAGGAATATATAGATAAAATCTTAAAAAATCGTCTTCTCAAAAACTATTAGGCCAGAA
128 TTTTACATAGGAATATATAGA-GAAATCTT-AAAAATCTTCTTCTCAAAAACTATTGGGCCAGAA
* *
592273 AAGCTCAAATTATAATGGAATTATCTTCAGGTAGTGTAGATTCAAGCTCGTTCAAATCATTGTCC
191 AAGCTCAAATTATAATGGAATCATCTTCAGGTAGTGTAGATTCAAGCTCGTTCAAATCATGGTCC
* * *
592338 CCAGGTGTAGGGTGGGGCCAAAATGGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAA-TC
256 CCAGGGGTAGGGTGGGGCCACAATGAGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATTC
592402 TTCTCAAAATCTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCCTCAGGTAGTGTAGAT
321 TTCTCAAAATCTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCAT-CTCAGGTAGTGTAGAT
*
592467 TCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAATTTTTA
385 TCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATT-GGGGATCAAGTTTTA
592532 CATAGGAATATATAGAGAAAATCTTTAAAAA
449 CATAGGAATATATAGAGAAAATCTTTAAAAA
*
592563 -TCTTCTCAAAAACTATTTGACCAAGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTGTT
1 TTCTTCTCAAAAACTATTTGACCAAGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTGTA
592627 GATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGAGGATGAATAT
66 GATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGAGGATGAAT-T
*
592692 TTACATAGGAATATATAGAGGAAATCTTTAAAAATCTTCTTCTCAAAAACTATTGGGGCAGAAAA
130 TTACATAGGAATATATAGA-GAAATC-TTAAAAATCTTCTTCTCAAAAACTATTGGGCCAGAAAA
592757 GCTCAAATTATAATGGAATCATCTTCAGGTAGTGTAGATTCAAGCTCGTTCAAATCATGGTCCCC
193 GCTCAAATTATAATGGAATCATCTTCAGGTAGTGTAGATTCAAGCTCGTTCAAATCATGGTCCCC
* *
592822 AGGGGTAGGGAGGGGCCACAA-GAAGGGGATCAAGTTTTACATA-AAATATATAGAGAAAATCTT
258 AGGGGTAGGGTGGGGCCACAATG-AGGGGATCAAGTTTTACATAGGAATATATAGAGAAAA--TT
* *
592885 CTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATTCTCAGGTATTGTAGA
320 CTTCTCAAAATCTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCA-TCTCAGGTAGTGTAGA
* * *
592950 TTTAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCCACAATTGGGTATCAAGTTTTA
384 TTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGATCAAGTTTTA
593015 CATAGGAATATATAGAGAAAATCTTTAAAAA
449 CATAGGAATATATAGAGAAAATCTTTAAAAA
* * * * * *
593046 TCTTCTTCTCGAAAACTATTTGACTAAGAAAGCTCAAATTGGCG-GGTAACCATCCTCAGATAAT
1 --TTCTTCTCAAAAACTATTTGACCAAGAAAGCTCAAATTTGAGTGG-AAGCATCCTCAGATAGT
* *
593110 GTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACA
63 GTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACA
593162 TTGGGGGATA
Statistics
Matches: 982, Mismatches: 74, Indels: 53
0.89 0.07 0.05
Matches are distributed among these distances:
481 17 0.02
482 276 0.28
483 46 0.05
484 115 0.12
485 148 0.15
486 106 0.11
487 114 0.12
488 16 0.02
498 144 0.15
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (479 bp):
TTCTTCTCAAAAACTATTTGACCAAGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTGTA
GATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGAGGATGAATTT
TACATAGGAATATATAGAGAAATCTTAAAAATCTTCTTCTCAAAAACTATTGGGCCAGAAAAGCT
CAAATTATAATGGAATCATCTTCAGGTAGTGTAGATTCAAGCTCGTTCAAATCATGGTCCCCAGG
GGTAGGGTGGGGCCACAATGAGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATTCTTCTC
AAAATCTATTAGGCCAGGAAAGCTCAAATTTGAATGGAAGCATCTCAGGTAGTGTAGATTCAAGT
TTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGATCAAGTTTTACATAGGA
ATATATAGAGAAAATCTTTAAAAA
Found at i:594692 original size:260 final size:252
Alignment explanation
Indices: 594237--594751 Score: 730
Period size: 260 Copynumber: 2.0 Consensus size: 252
594227 AACACAACGA
*
594237 ATTGTTACATGCGCGTAAATAATGCGCGTACGTCGCCGTAAAATTCACGTCATTTCTATACAAAA
1 ATTGTTACATGCACGTAAATAATGCGCGTACGTCGCCGTAAAATTCACGTCATTTCTATACAAAA
* * **
594302 GCAGTAAAACTTTCTCTAAATTAAGACATTCAGTATAATAAAATAAATAGTGCGTGTTTGGGAGG
66 GCAGTAAAACTTTCTCTAAATTAAGACATTCAGTATAATAAAAAAAATAGTGCCTGTTTGAAAGG
*
594367 ATAACAGTTGAAATTGACACCCCTCTAAAACCATTGTCAACCTCCACTTTGCGTCGGTTGACAAT
131 ATAACAGTTGAAATTGACACCCCTCTAAAACCATTGTCAACCTCCACTTGGCGTCGGTTGACAAT
*
594432 GGTTTTCTCGGGGTGTCAATTTCAACTGTTACCCTCCCAAACAGGCACTATTTATAT
196 GGTTTTCTCGGGGTGTCAATTTCAACAGTTACCCTCCCAAACAGGCACTATTTATAT
* * * *
594489 ATTGTTACATGCACGTAAATTATGCGCGTACGGTTCGCCGTAGAATTCACTTCATTTCTATATAA
1 ATTGTTACATGCACGTAAATAATGCGCGTAC-G-TCGCCGTAAAATTCACGTCATTTCTATACAA
* * * *
594554 ATA-TA-TATAAATTTTTTTTAAATTAAGACATTCAGTATAATAAAACAAATACCGGTAGTGCCT
64 A-AGCAGTA-AAACTTTCTCTAAATTAAGACATTCAGTATAATAAAA-AAA-A----TAGTGCCT
* * **
594617 GTTTGAAA-GAGTAACTGTTGAAATTGACACCCCTCTGAAACCATTGTCAACCTCTGCTTGGCGT
121 GTTTGAAAGGA-TAACAGTTGAAATTGACACCCCTCTAAAACCATTGTCAACCTCCACTTGGCGT
*
594681 CGGTTGACAATGGTTTTCTCGGGTTGTCAATTTCAACAGTTACCCTCCCAAACAGGCACTATTTA
185 CGGTTGACAATGGTTTTCTCGGGGTGTCAATTTCAACAGTTACCCTCCCAAACAGGCACTATTTA
594746 TAT
250 TAT
594749 ATT
1 ATT
594752 ATAGCATAAA
Statistics
Matches: 232, Mismatches: 20, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
252 29 0.12
253 3 0.01
254 64 0.28
255 3 0.01
256 1 0.00
259 2 0.01
260 130 0.56
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (252 bp):
ATTGTTACATGCACGTAAATAATGCGCGTACGTCGCCGTAAAATTCACGTCATTTCTATACAAAA
GCAGTAAAACTTTCTCTAAATTAAGACATTCAGTATAATAAAAAAAATAGTGCCTGTTTGAAAGG
ATAACAGTTGAAATTGACACCCCTCTAAAACCATTGTCAACCTCCACTTGGCGTCGGTTGACAAT
GGTTTTCTCGGGGTGTCAATTTCAACAGTTACCCTCCCAAACAGGCACTATTTATAT
Found at i:607259 original size:16 final size:17
Alignment explanation
Indices: 607238--607275 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
607228 CCAAACTTTC
607238 TGAAAAAATA-TTAAAA
1 TGAAAAAATATTTAAAA
*
607254 TG-AAAATTATTTAAAA
1 TGAAAAAATATTTAAAA
607270 TGAAAA
1 TGAAAA
607276 TCAAGTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 10 0.53
17 3 0.16
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (17 bp):
TGAAAAAATATTTAAAA
Found at i:610518 original size:336 final size:335
Alignment explanation
Indices: 609809--611048 Score: 1585
Period size: 335 Copynumber: 3.7 Consensus size: 335
609799 CTCTTCATGT
* * * * * ** *
609809 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACTATTTAGGTAAAGGAG-ATTGTGGATATCAT
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGG-GCCTCATGGACATCAT
** * ** ** * * * * *
609873 AACCATATATTCAGTTTTTTGCCCACATGTGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTAAA
65 AA-CATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT
* * * * * * *
609938 ACGTTTTTACTATTTGGCCATATTGGCCCAACCCTAGAGCCTGAACACCTAACTAAGGGGTCATG
129 ACATTTGTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCAAGGGGTCATG
* * * * * * * * * * ** *
610003 AATTTCAAAATTTTAGTAGAGGCCCTCATGAACATCATTACCATGTATTAAGTTTTT-GCTCACA
194 AATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTAACAAATA
* * * * ** *
610067 TGTGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTAAAATTTTTTTACTATATGGCCATATTGGC
259 TATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGC
*
610132 CCCACCCTAAAG
324 CCCACCCTAGAG
* * *
610144 CCTGAACACCTAACACAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
*
610209 ACAATGCATTTAGTTTTTGACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
66 AC-ATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
* * * * * *
610274 CATTT-TATTTATTTGTCCATATTGGCCCCACCCTAGAGTCTGAACCCCTGACCCAGGAGTCATG
130 CATTTGTA-CTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCAAGGGGTCATG
* *
610338 AATTTCATAATTTTGGTAGAGGGCTTCATGGGCATCATAATCATGCATTTAGTTTTTAACAAATA
194 AATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTAACAAATA
*
610403 TATATGGGAGTAGAGGAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGC
259 TATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGC
610468 CCCACCCTAGAG
324 CCCACCCTAGAG
* * * *
610480 CCTGAACCCCTGACCCAGGGGTCATGAATTGCACAATTTTGATAGAAGGTCTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
610545 ATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
66 A-CATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
610610 CATTTGTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCAAGGGGTCATGA
130 CATTTGTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCAAGGGGTCATGA
** * *
610675 ATTTCACAATTAAGGTTGAGGGCTTCATGGACATCATTATCATGCATTTAG-TTTTAGACAAATA
195 ATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTA-ACAAATA
** *
610739 TATATGATAGTAGAGAAGAAGATTTTCTAAGATTTAATACA-TTTTACTATTTGGCCACATTGGC
259 TATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGC
*
610803 CCCACCCTAGAT
324 CCCACCCTAGAG
* * *
610815 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGGCATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
* * * *
610880 ATTATGCATTTAGTTTTTTAA-AAATATATATGGTAGTAGAGAAGATGATTTTCTAAGGTTTAAT
66 A-CATGCATTTAG-TTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT
* * *
610944 ACATTTGTACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAACCCCTGACCCA-GGGTACCT
129 ACATTTGTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCAAGGGGT-CAT
* *
611008 AAATTTCACAATTTTGGTAGAGGGCTTCATGGGCATCATAA
193 GAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAA
611049 CCATAGAACC
Statistics
Matches: 795, Mismatches: 101, Indels: 18
0.87 0.11 0.02
Matches are distributed among these distances:
334 8 0.01
335 440 0.55
336 344 0.43
337 3 0.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (335 bp):
CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
ACATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATAC
ATTTGTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCAAGGGGTCATGAA
TTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTAACAAATATA
TATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCC
CACCCTAGAG
Found at i:611092 original size:168 final size:168
Alignment explanation
Indices: 609809--611052 Score: 1582
Period size: 168 Copynumber: 7.4 Consensus size: 168
609799 CTCTTCATGT
* * * * * * *
609809 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACTATTTAGGTAAAGGAGATT-GTGGATATCAT
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGG-GCTTCATGGACATCAT
** * * ** * * * * *
609873 AACCATATATTCAGTTTTTTGCCCACATGTGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTAAA
65 AACCATGCATTTAGTTTTTTACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT
* *
609938 ACGTTTTTACTATTTGGCCATATTGGCCCAACCCTAGAG
130 ACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
* * ** * * * * * *
609977 CCTGAACACCTAACTAAGGGGTCATGAATTTCAAAATTTTAGTAGAGGCCCTCATGAACATCATT
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
* * * ** * * * * *
610042 ACCATGTATTAAG-TTTTTGCTCACATGTGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTAAAA
66 ACCATGCATTTAGTTTTTTACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
** * *
610106 TTTTTTTACTATATGGCCATATTGGCCCCACCCTAAAG
131 CATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
* * * *
610144 CCTGAACACCTAACACAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
* *
610209 ACAATGCATTTAGTTTTTGACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
66 ACCATGCATTTAGTTTTTTACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
* *
610274 CA-TTTTATTTATTTGTCCATATTGGCCCCACCCTAGAG
131 CATTTTTA-CTATTTGGCCATATTGGCCCCACCCTAGAG
* * * *
610312 TCTGAACCCCTGACCCAGGAGTCATGAATTTCATAATTTTGGTAGAGGGCTTCATGGGCATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
* * *
610377 ATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGGAGAAGATTTTCTAAGATTTAATA
66 ACCATGCATTTAGTTTTTTACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
610442 CATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
131 CATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
* * *
610480 CCTGAACCCCTGACCCAGGGGTCATGAATTGCACAATTTTGATAGAAGG-TCTCATGGACATCAT
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCT-TCATGGACATCAT
* *
610544 AATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT
65 AACCATGCATTTAGTTTTTTACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT
* *
610609 ACATTTGTACTATATGGCCATATTGGCCCCACCCTAGAG
130 ACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
* ** * *
610648 CCTGAACCCCTGACCAAGGGGTCATGAATTTCACAATTAAGGTTGAGGGCTTCATGGACATCATT
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
* ** **
610713 ATCATGCATTTAGTTTTAGACAAATATATATGATAGTAGAGAAGAAGATTTTCTAAGATTTAATA
66 ACCATGCATTTAGTTTTTTACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
* *
610778 CA-TTTTACTATTTGGCCACATTGGCCCCACCCTAGAT
131 CATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
* *
610815 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGGCATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
** * * * *
610880 ATTATGCATTTAGTTTTTTAAAAATATATATGGTAGTAGAGAAGATGATTTTCTAAGGTTTAATA
66 ACCATGCATTTAGTTTTTTACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
* *
610945 CATTTGTACTATATGGCCATATTGGCCCCACCCTAGAG
131 CATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
* * * *
610983 CCAGAACCCCTGACCCA-GGGTACCTAAATTTCACAATTTTGGTAGAGGGCTTCATGGGCATCAT
1 CCTGAACCCCTGACCCAGGGGT-CATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCAT
611047 AACCAT
65 AACCAT
611053 AGAACCAGTT
Statistics
Matches: 956, Mismatches: 112, Indels: 16
0.88 0.10 0.01
Matches are distributed among these distances:
167 313 0.33
168 637 0.67
169 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (168 bp):
CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
ACCATGCATTTAGTTTTTTACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
CATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
Found at i:613471 original size:41 final size:41
Alignment explanation
Indices: 613412--613492 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
613402 AGGCAAATCA
* *
613412 CTAATATTACTATGAATAGCACAACTTTGAAGATAAACAAG
1 CTAATATTACTATAAATAGCAAAACTTTGAAGATAAACAAG
*
613453 CTAATCTTACTATAAATAGCAAAACTTTGAAGATAAACAA
1 CTAATATTACTATAAATAGCAAAACTTTGAAGATAAACAA
613493 AAAACCAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (41 bp):
CTAATATTACTATAAATAGCAAAACTTTGAAGATAAACAAG
Found at i:613763 original size:2 final size:2
Alignment explanation
Indices: 613756--613801 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
613746 TGACATATAA
613756 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
613798 AG AG
1 AG AG
613802 TCAGAGAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:616247 original size:31 final size:31
Alignment explanation
Indices: 616212--616276 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
616202 AAATACACAC
616212 TTGTGTATTTATATATAGTAGGGGTAAAATT
1 TTGTGTATTTATATATAGTAGGGGTAAAATT
*
616243 TTGTGTATTTATATATAGTAGGGGTAGAATT
1 TTGTGTATTTATATATAGTAGGGGTAAAATT
616274 TTG
1 TTG
616277 AGATATGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (31 bp):
TTGTGTATTTATATATAGTAGGGGTAAAATT
Found at i:621676 original size:2 final size:2
Alignment explanation
Indices: 621669--621723 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
621659 NNNNNNNNNN
621669 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
621711 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
621724 AGAGCGTAGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:626439 original size:17 final size:17
Alignment explanation
Indices: 626417--626465 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
626407 AACCTGTTAG
626417 TATGATAATCTACATAA
1 TATGATAATCTACATAA
*
626434 TATGATAATCTACATAG
1 TATGATAATCTACATAA
626451 TATGATAATCTACAT
1 TATGATAATCTACAT
626466 GCAGACGGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (17 bp):
TATGATAATCTACATAA
Found at i:633600 original size:17 final size:17
Alignment explanation
Indices: 633578--633610 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
633568 ATCTCATCAC
633578 GGGCCTTGACAGTTAAA
1 GGGCCTTGACAGTTAAA
633595 GGGCCTTGACAGTTAA
1 GGGCCTTGACAGTTAA
633611 CTTAGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (17 bp):
GGGCCTTGACAGTTAAA
Found at i:634582 original size:2 final size:2
Alignment explanation
Indices: 634575--634639 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
634565 AAGGACTAGG
*
634575 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
634617 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
634640 GGTCGGAAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:644859 original size:14 final size:14
Alignment explanation
Indices: 644840--644868 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
644830 TATGTTGTAA
644840 CAATCTCTCTCTCT
1 CAATCTCTCTCTCT
644854 CAATCTCTCTCTCT
1 CAATCTCTCTCTCT
644868 C
1 C
644869 TCTCTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.45, G:0.00, T:0.41
Consensus pattern (14 bp):
CAATCTCTCTCTCT
Found at i:645737 original size:118 final size:116
Alignment explanation
Indices: 645613--645858 Score: 282
Period size: 117 Copynumber: 2.1 Consensus size: 116
645603 TATTATAGTT
* * * * *
645613 CAAGAAAAGGTCCGCACCGCTCAAATACTGAATGAATAAAATTAATATTTATATTCAAT-CTTGT
1 CAAGAAAAGGTCCGC-CCGCTCAAATACGGAATGAAGAAAATTAAAATTAATATT-AATACTTGC
* *
645677 TTTGAATT-ACC-CTGATGATCTTTTAATATAGGGGTAAGACTTAATATTATGGCC
64 TTTG-ATTGACCTC-GATGATCTTTT-ATATAGGGGTAAGACCTAATATAATGGCC
* * * * *
645731 CAAGAAAAGGTCCGCCTGTTGAAATACGGAATGCAGAAAATTAAAATTAATATTGATACTTGCTT
1 CAAGAAAAGGTCCGCCCGCTCAAATACGGAATGAAGAAAATTAAAATTAATATTAATACTTGCTT
* * * *
645796 TGATTGACCTCGATGTTCTTTTATTTAGGGGTAGGACCTAATATAATGGCT
66 TGATTGACCTCGATGATCTTTTATATAGGGGTAAGACCTAATATAATGGCC
645847 CAAGAAAAGGTC
1 CAAGAAAAGGTC
645859 TGCCTGTTGA
Statistics
Matches: 109, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
116 41 0.38
117 52 0.48
118 16 0.15
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (116 bp):
CAAGAAAAGGTCCGCCCGCTCAAATACGGAATGAAGAAAATTAAAATTAATATTAATACTTGCTT
TGATTGACCTCGATGATCTTTTATATAGGGGTAAGACCTAATATAATGGCC
Found at i:645864 original size:116 final size:117
Alignment explanation
Indices: 645570--645871 Score: 333
Period size: 116 Copynumber: 2.6 Consensus size: 117
645560 TTTCATTTAG
** * * * * * *
645570 TGATGATCTTTTGTTTTAGTGGGTAGGACCCAATATTATAGTTCAAGAAAAGGTCCGCACCGCTC
1 TGATGATCTTTTAATTTAG-GGGTAGGACCTAATATTATGGCTCAAGAAAAGGTCCGC-CTGTTG
* * * * *
645635 AAATACTGAATGAATAAAATTAATATTTATATTCAATCTTGTTTTGAATTACCC
64 AAATACGGAATGAAGAAAATTAAAATTAATATTCAATCTTGCTTTGAATTACCC
* * * *
645689 TGATGATCTTTTAATATAGGGGTAAGACTTAATATTATGGCCCAAGAAAAGGTCCGCCTGTTGAA
1 TGATGATCTTTTAATTTAGGGGTAGGACCTAATATTATGGCTCAAGAAAAGGTCCGCCTGTTGAA
* *
645754 ATACGGAATGCAGAAAATTAAAATTAATATT-GATACTTGCTTTG-ATTGA-CC
66 ATACGGAATGAAGAAAATTAAAATTAATATTCAAT-CTTGCTTTGAATT-ACCC
* * *
645805 TCGATGTTCTTTT-ATTTAGGGGTAGGACCTAATATAATGGCTCAAGAAAAGGTCTGCCTGTTGA
1 T-GATGATCTTTTAATTTAGGGGTAGGACCTAATATTATGGCTCAAGAAAAGGTCCGCCTGTTGA
645869 AAT
65 AAT
645872 GCTGGATGTA
Statistics
Matches: 154, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
116 56 0.36
117 50 0.32
118 32 0.21
119 16 0.10
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (117 bp):
TGATGATCTTTTAATTTAGGGGTAGGACCTAATATTATGGCTCAAGAAAAGGTCCGCCTGTTGAA
ATACGGAATGAAGAAAATTAAAATTAATATTCAATCTTGCTTTGAATTACCC
Found at i:647925 original size:12 final size:12
Alignment explanation
Indices: 647908--647933 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
647898 GACACTTTAT
647908 ATAGATTGTAAC
1 ATAGATTGTAAC
647920 ATAGATTGTAAC
1 ATAGATTGTAAC
647932 AT
1 AT
647934 CCCTCTGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
ATAGATTGTAAC
Found at i:655572 original size:2 final size:2
Alignment explanation
Indices: 655565--655613 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
655555 AAATATGATC
655565 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
655607 AG AG AG A
1 AG AG AG A
655614 TGAGTATCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:681655 original size:21 final size:21
Alignment explanation
Indices: 681631--681674 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
681621 TTTAAGTATG
*
681631 TTATCATTAATTTATGTTTAA
1 TTATCATCAATTTATGTTTAA
*
681652 TTATCATCAGTTTATGTTTAA
1 TTATCATCAATTTATGTTTAA
681673 TT
1 TT
681675 TACGGACTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATCATCAATTTATGTTTAA
Found at i:685716 original size:26 final size:26
Alignment explanation
Indices: 685680--685734 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
685670 GATATAATTA
685680 TAATCGTATCATTATGGTTTACATTT
1 TAATCGTATCATTATGGTTTACATTT
*
685706 TAATTGTATCATTATGGTTTACATTT
1 TAATCGTATCATTATGGTTTACATTT
685732 TAA
1 TAA
685735 ATCACTGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (26 bp):
TAATCGTATCATTATGGTTTACATTT
Found at i:689587 original size:17 final size:17
Alignment explanation
Indices: 689562--689599 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
689552 TAAATTTCAA
*
689562 TTTTCATTTCTTTTT-TC
1 TTTTAATTT-TTTTTATC
689579 TTTTAATTTTTTTTATC
1 TTTTAATTTTTTTTATC
689596 TTTT
1 TTTT
689600 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTAATTTTTTTTATC
Found at i:693441 original size:18 final size:17
Alignment explanation
Indices: 693414--693457 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
693404 GGTTAACTAG
*
693414 GTTTTTTTTTAAATTTT
1 GTTTTTTTTTAAATTTA
*
693431 GTTTTTGTTTTATATTTA
1 GTTTTT-TTTTAAATTTA
693449 GTTTGTTTT
1 GTTT-TTTT
693458 GTTTTGGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 15 0.65
19 2 0.09
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (17 bp):
GTTTTTTTTTAAATTTA
Found at i:706189 original size:26 final size:26
Alignment explanation
Indices: 706167--706218 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
706157 TGAATTAGAT
*
706167 CGAAGATTTAAATTTTGATATTAAAC
1 CGAAGATTTAAATTTAGATATTAAAC
*
706193 CGAAGATTTAAATTTAGATATAAAAC
1 CGAAGATTTAAATTTAGATATTAAAC
706219 TAAGCTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (26 bp):
CGAAGATTTAAATTTAGATATTAAAC
Found at i:709391 original size:180 final size:180
Alignment explanation
Indices: 709089--709509 Score: 806
Period size: 180 Copynumber: 2.3 Consensus size: 180
709079 NNNNNNNNNN
709089 TGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTC
1 TGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTC
*
709154 ATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTT
66 ATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTA
*
709219 CATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTA
131 CATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTA
709269 TGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTC
1 TGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTC
709334 ATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTA
66 ATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTA
709399 CATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTA
131 CATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTA
* *
709449 TGAAAAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATATAGGGTAC
1 TGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTAC
709510 TCCATTTCAC
Statistics
Matches: 237, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 237 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (180 bp):
TGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTC
ATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTA
CATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTA
Found at i:714838 original size:18 final size:19
Alignment explanation
Indices: 714803--714844 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
714793 TCAATAACCA
714803 TATTCTAGGTTAAATTTTT
1 TATTCTAGGTTAAATTTTT
714822 TATTCTAGGTT-AATTTTT
1 TATTCTAGGTTAAATTTTT
714840 T-TTCT
1 TATTCT
714845 CCCTTTATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (19 bp):
TATTCTAGGTTAAATTTTT
Found at i:716885 original size:12 final size:12
Alignment explanation
Indices: 716868--716893 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
716858 TATTTAATTG
716868 TATTTCAAATAT
1 TATTTCAAATAT
716880 TATTTCAAATAT
1 TATTTCAAATAT
716892 TA
1 TA
716894 CCCCCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTTCAAATAT
Found at i:722720 original size:28 final size:28
Alignment explanation
Indices: 722679--722735 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
722669 AGTTGTTCCT
* * *
722679 AAAAGTTACAATTTTATCATCTTGGATA
1 AAAAGTTACAATTTGATCAACTTGAATA
722707 AAAAGTTATC-ATTTGATCAACTTGAATA
1 AAAAGTTA-CAATTTGATCAACTTGAATA
722735 A
1 A
722736 CAGGAGTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (28 bp):
AAAAGTTACAATTTGATCAACTTGAATA
Found at i:723749 original size:12 final size:12
Alignment explanation
Indices: 723717--723763 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
723707 GAAGTGTATT
*
723717 GTATAGTATGTA
1 GTATAGTATATA
*
723729 GTATA--CTATA
1 GTATAGTATATA
*
723739 GTATAGTCTATA
1 GTATAGTATATA
723751 GTATAGTATATA
1 GTATAGTATATA
723763 G
1 G
723764 ATCAATTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 8 0.27
12 22 0.73
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.40
Consensus pattern (12 bp):
GTATAGTATATA
Found at i:732277 original size:2 final size:2
Alignment explanation
Indices: 732270--732320 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
732260 CATGGAAGTC
732270 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
732312 AG AG AG AG A
1 AG AG AG AG A
732321 CTTTAATAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:732767 original size:2 final size:2
Alignment explanation
Indices: 732762--732816 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
732752 GAAAAAAAAC
732762 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
732804 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
732817 TTATTACCAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:734453 original size:9 final size:9
Alignment explanation
Indices: 734425--734467 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
734415 AAATCAGCTA
734425 AATCAACTTG
1 AATCAAC-TG
*
734435 -ATCGACTG
1 AATCAACTG
734443 AATCAACTG
1 AATCAACTG
734452 AATCAACTG
1 AATCAACTG
*
734461 AAACAAC
1 AATCAAC
734468 GTATTTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
8 2 0.07
9 27 0.93
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (9 bp):
AATCAACTG
Found at i:742027 original size:12 final size:12
Alignment explanation
Indices: 742010--742034 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
742000 AGAAATCTGC
742010 ATAAAACTGACA
1 ATAAAACTGACA
742022 ATAAAACTGACA
1 ATAAAACTGACA
742034 A
1 A
742035 ATACAATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
ATAAAACTGACA
Found at i:742400 original size:15 final size:15
Alignment explanation
Indices: 742380--742409 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
742370 CATATCCATT
742380 GTAATCGAGATATCG
1 GTAATCGAGATATCG
742395 GTAATCGAGATATCG
1 GTAATCGAGATATCG
742410 AAGTTCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (15 bp):
GTAATCGAGATATCG
Found at i:763537 original size:39 final size:39
Alignment explanation
Indices: 763486--763764 Score: 404
Period size: 39 Copynumber: 7.1 Consensus size: 39
763476 CTACCCACAG
* *
763486 CACACACATGGTAAGTCATTATGTGTTAACGGTCCTCCA
1 CACATACATGGTAGGTCATTATGTGTTAACGGTCCTCCA
*
763525 CACATACATGGTAGGTCATTATGTGTTAACTGTCCTCCA
1 CACATACATGGTAGGTCATTATGTGTTAACGGTCCTCCA
* * *
763564 CACATACATGGTAAGTCATTGTGTGTTAACTGTCCTCCA
1 CACATACATGGTAGGTCATTATGTGTTAACGGTCCTCCA
763603 CACATACATGGTAGGTCATTATGTGTTAACGGTCCT---
1 CACATACATGGTAGGTCATTATGTGTTAACGGTCCTCCA
763639 C-CATACATGGTAGGTCATTATGTGTTAACGGTCCTCCA
1 CACATACATGGTAGGTCATTATGTGTTAACGGTCCTCCA
*
763677 TACATACATGGTACATGTAGGTCATTATGTGTTAACGGTCCTCCA
1 CACATACAT-G-----GTAGGTCATTATGTGTTAACGGTCCTCCA
*
763722 CACATACATGGTAGGTCATTATGTGTTAACAGTCCTCCA
1 CACATACATGGTAGGTCATTATGTGTTAACGGTCCTCCA
763761 CACA
1 CACA
763765 CTATGTGTTA
Statistics
Matches: 219, Mismatches: 11, Indels: 20
0.88 0.04 0.08
Matches are distributed among these distances:
35 34 0.16
36 1 0.00
39 145 0.66
40 1 0.00
44 1 0.00
45 37 0.17
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (39 bp):
CACATACATGGTAGGTCATTATGTGTTAACGGTCCTCCA
Found at i:763707 original size:45 final size:44
Alignment explanation
Indices: 763642--763764 Score: 175
Period size: 45 Copynumber: 2.9 Consensus size: 44
763632 CGGTCCTCCA
*
763642 TACATGGTAGGTCATTATGTGTTAACGGTCCTCCATACATACATGG
1 TACAT-GTAGGTCATTATGTGTTAACGGTCCTCCACACATACAT-G
763688 TACATGTAGGTCATTATGTGTTAACGGTCCTCCACACATACATG
1 TACATGTAGGTCATTATGTGTTAACGGTCCTCCACACATACATG
*
763732 -----GTAGGTCATTATGTGTTAACAGTCCTCCACACA
1 TACATGTAGGTCATTATGTGTTAACGGTCCTCCACACA
763765 CTATGTGTTA
Statistics
Matches: 75, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
39 32 0.43
44 1 0.01
45 37 0.49
46 5 0.07
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (44 bp):
TACATGTAGGTCATTATGTGTTAACGGTCCTCCACACATACATG
Found at i:768202 original size:1 final size:1
Alignment explanation
Indices: 768198--768225 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
768188 TTTTGTGGCC
768198 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
768226 ATAAATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:769931 original size:13 final size:13
Alignment explanation
Indices: 769915--769949 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
769905 TGTTTTCAAA
*
769915 TTTTGTAATGAAT
1 TTTTGTAATGAAC
*
769928 TTTTGTAATGTAC
1 TTTTGTAATGAAC
769941 TTTTGTAAT
1 TTTTGTAAT
769950 TGTGTATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (13 bp):
TTTTGTAATGAAC
Found at i:770223 original size:2 final size:2
Alignment explanation
Indices: 770216--770245 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
770206 TAATATTTTA
770216 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
770246 GTATTTCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:771276 original size:30 final size:30
Alignment explanation
Indices: 771219--771276 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
771209 TGTCAAATTA
*
771219 ATAATTTTCATAATATAATATATATTATAT
1 ATAATTTTAATAATATAATATATATTATAT
771249 ATAATTTTTAATAATAATAAT-TA-ATTAT
1 ATAA-TTTTAATAAT-ATAATATATATTAT
771277 TTTGAAGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 9 0.36
31 11 0.44
32 5 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
ATAATTTTAATAATATAATATATATTATAT
Found at i:771483 original size:21 final size:20
Alignment explanation
Indices: 771454--771610 Score: 190
Period size: 21 Copynumber: 7.7 Consensus size: 20
771444 ATAATAATCT
*
771454 TATTCGTTCGGACGAATTAG
1 TATTTGTTCGGACGAATTAG
*
771474 CTATTTGTTCGGACGAATAAG
1 -TATTTGTTCGGACGAATTAG
771495 TTATTTGTTCGGACGAATTAG
1 -TATTTGTTCGGACGAATTAG
*
771516 GATTTGTTCGGACGAATTAG
1 TATTTGTTCGGACGAATTAG
* * * * *
771536 GATTCGTTCGGACAAATAAAT
1 TATTTGTTCGGACGAAT-TAG
771557 TATTTGTTCGGACGAATTAAG
1 TATTTGTTCGGACGAATT-AG
771578 -ATTTGTTCGGACGAATTAG
1 TATTTGTTCGGACGAATTAG
771597 CTATTTGTTCGGAC
1 -TATTTGTTCGGAC
771611 AAATANNNNN
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 51 0.43
21 65 0.55
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (20 bp):
TATTTGTTCGGACGAATTAG
Found at i:771560 original size:61 final size:62
Alignment explanation
Indices: 771459--771615 Score: 262
Period size: 61 Copynumber: 2.5 Consensus size: 62
771449 AATCTTATTC
* * *
771459 GTTCGGACGAATTAGCTATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGGATTT
1 GTTCGGACGAATTAGCTATTTGTTCGGACAAATAAATTATTTGTTCGGACGAATTAAGATTT
* *
771521 GTTCGGACGAATTAG-GATTCGTTCGGACAAATAAATTATTTGTTCGGACGAATTAAGATTT
1 GTTCGGACGAATTAGCTATTTGTTCGGACAAATAAATTATTTGTTCGGACGAATTAAGATTT
771582 GTTCGGACGAATTAGCTATTTGTTCGGACAAATA
1 GTTCGGACGAATTAGCTATTTGTTCGGACAAATA
771616 NNNNNNNNNN
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
61 56 0.64
62 31 0.36
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (62 bp):
GTTCGGACGAATTAGCTATTTGTTCGGACAAATAAATTATTTGTTCGGACGAATTAAGATTT
Found at i:771562 original size:41 final size:41
Alignment explanation
Indices: 771455--771610 Score: 188
Period size: 41 Copynumber: 3.8 Consensus size: 41
771445 TAATAATCTT
* * *
771455 ATTCGTTCGGACGAATTAGCTATTTGTTCGGACGAATAAGTT
1 ATTCGTTCGGACGAATTAACTATTTGTTCGGACGAATTAG-G
* **
771497 ATTTGTTCGGACGAATT-AGGATTTGTTCGGACGAATTAGG
1 ATTCGTTCGGACGAATTAACTATTTGTTCGGACGAATTAGG
* * * *
771537 ATTCGTTCGGACAAATAAATTATTTGTTCGGACGAATTAAG
1 ATTCGTTCGGACGAATTAACTATTTGTTCGGACGAATTAGG
* *
771578 ATTTGTTCGGACGAATTAGCTATTTGTTCGGAC
1 ATTCGTTCGGACGAATTAACTATTTGTTCGGAC
771611 AAATANNNNN
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
40 14 0.15
41 66 0.69
42 16 0.17
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (41 bp):
ATTCGTTCGGACGAATTAACTATTTGTTCGGACGAATTAGG
Found at i:776503 original size:13 final size:13
Alignment explanation
Indices: 776487--776521 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
776477 TGTTTTCAAA
*
776487 TTTTGTAATGAAT
1 TTTTGTAATGAAC
*
776500 TTTTGTAATGTAC
1 TTTTGTAATGAAC
776513 TTTTGTAAT
1 TTTTGTAAT
776522 TGTGTATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (13 bp):
TTTTGTAATGAAC
Found at i:776795 original size:2 final size:2
Alignment explanation
Indices: 776788--776817 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
776778 TAATATTTTA
776788 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
776818 GTATTTCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:779110 original size:1 final size:1
Alignment explanation
Indices: 779104--779140 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
779094 GAGCGGGGAA
779104 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
779141 TGGTCCGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:782122 original size:2 final size:2
Alignment explanation
Indices: 782115--782149 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
782105 TTCAGTTAAG
782115 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
782150 GTACAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:784003 original size:1 final size:1
Alignment explanation
Indices: 783997--784031 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
783987 ACCAAGAACC
783997 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
784032 GAGAAGAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:796986 original size:19 final size:19
Alignment explanation
Indices: 796942--796987 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
796932 TTTTTGGTAT
* *
796942 GACCATCAGACTTTTGCGT
1 GACCATCAGACTTTTGAGC
* *
796961 GATCATCGGACTTTTGAGC
1 GACCATCAGACTTTTGAGC
796980 GACCATCA
1 GACCATCA
796988 AATTTCATTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (19 bp):
GACCATCAGACTTTTGAGC
Found at i:801155 original size:92 final size:92
Alignment explanation
Indices: 800986--801253 Score: 421
Period size: 92 Copynumber: 2.8 Consensus size: 92
800976 AAATTCTATA
800986 TCTGTTGTGTGTTGTCAAAATCAAAAAAATGAAGATCTGACAAAACAAACAAATACACAATGTTT
1 TCTGTTGTGTGTTGTCAAAATCAAAAAAA--AAGA--TGACAAAACAAACAAATACACAATGTTT
*
801051 GATATATATTTTATTTCTATACAAATCTTATG
62 GATATAT-TTTTATTTCTATACAAATCGTATG
801083 TCTGTTGTGTGTTGTCAAAATCAAAAAAAAA-ATGACAAAACAAACAAATACACAATGTTTGATA
1 TCTGTTGTGTGTTGTCAAAATCAAAAAAAAAGATGACAAAACAAACAAATACACAATGTTTGATA
*
801147 TATGTTTTATTTCTATGCAAATCGTATG
66 TAT-TTTTATTTCTATACAAATCGTATG
801175 TCTGTTGTGTGTTGTCAAAATCAAAAAAAGAAGATATGACAAAACAAACAAATACACAATGTTTG
1 TCTGTTGTGTGTTGTCAAAATCAAAAAAA-AAG--ATGACAAAACAAACAAATACACAATGTTTG
*
801240 ATAGATTTTTATTT
63 ATATATTTTTATTT
801254 TTTTCCCCCT
Statistics
Matches: 163, Mismatches: 4, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
92 86 0.53
93 2 0.01
94 1 0.01
95 10 0.06
96 35 0.21
97 29 0.18
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (92 bp):
TCTGTTGTGTGTTGTCAAAATCAAAAAAAAAGATGACAAAACAAACAAATACACAATGTTTGATA
TATTTTTATTTCTATACAAATCGTATG
Found at i:803361 original size:14 final size:14
Alignment explanation
Indices: 803340--803400 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
803330 TCAAAATAAT
*
803340 ACAGAGAGAGAGAG
1 ACAGAGAGACAGAG
* * *
803354 AGAGAGAGAGACAG
1 ACAGAGAGACAGAG
*
803368 ACAGACAGACAGAG
1 ACAGAGAGACAGAG
*
803382 ACAGACAGACAGAG
1 ACAGAGAGACAGAG
803396 A-AGAG
1 ACAGAG
803401 GGCAGTATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
13 3 0.08
14 37 0.93
ACGTcount: A:0.51, C:0.13, G:0.36, T:0.00
Consensus pattern (14 bp):
ACAGAGAGACAGAG
Found at i:805454 original size:15 final size:12
Alignment explanation
Indices: 805413--805441 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
805403 ACCAGATCCA
805413 CCCCCTATACCG
1 CCCCCTATACCG
805425 CCCCCTATACCG
1 CCCCCTATACCG
805437 CCCCC
1 CCCCC
805442 ATATCCACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.66, G:0.07, T:0.14
Consensus pattern (12 bp):
CCCCCTATACCG
Found at i:805569 original size:15 final size:15
Alignment explanation
Indices: 805549--805579 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
805539 TACTGGGGCC
*
805549 GAGGTTGAATGTACT
1 GAGGTTGAACGTACT
805564 GAGGTTGAACGTACT
1 GAGGTTGAACGTACT
805579 G
1 G
805580 GGCGTAATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.35, T:0.29
Consensus pattern (15 bp):
GAGGTTGAACGTACT
Found at i:807125 original size:2 final size:2
Alignment explanation
Indices: 807118--807181 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
807108 AAATAAATTG
807118 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
807160 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
807182 TATGGAACGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:821735 original size:2 final size:2
Alignment explanation
Indices: 821728--821788 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
821718 CCACAAGCTT
821728 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
821770 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
821789 CAATTGGATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:822920 original size:27 final size:27
Alignment explanation
Indices: 822882--823114 Score: 177
Period size: 27 Copynumber: 8.4 Consensus size: 27
822872 TAAACCAACT
*
822882 ACAACCATCTAATCCCTTGAAATGACC
1 ACAACCATCTAATCCCTTGAACTGACC
* *
822909 ACCACCATCTAATCCCTT-CACTGGCCACAACC
1 ACAACCATCTAATCCCTTGAACT-G-----ACC
* * *
822941 ACCTAACCATCTAATCTCTTGAAATGGCC
1 A-C-AACCATCTAATCCCTTGAACTGACC
* * *
822970 ACAACCATCTAATCCATTTAACTTG-TC
1 ACAACCATCTAATCCCTTGAAC-TGACC
* *
822997 ATAACCATCTAATCCCTTG-ACTGGCC
1 ACAACCATCTAATCCCTTGAACTGACC
* *
823023 ACAACCATCTAATCTCTTGAACCGACC
1 ACAACCATCTAATCCCTTGAACTGACC
* ***
823050 ACAACCATCGAATTTTTTGAACTGACC
1 ACAACCATCTAATCCCTTGAACTGACC
** *
823077 ACAACTTTCTAATCCCTTG-ACTGGCC
1 ACAACCATCTAATCCCTTGAACTGACC
823103 ACAACCATCTAA
1 ACAACCATCTAA
823115 CCACCTAATA
Statistics
Matches: 160, Mismatches: 34, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
25 2 0.01
26 38 0.24
27 92 0.57
28 3 0.02
29 3 0.02
32 4 0.03
33 1 0.01
34 15 0.09
35 2 0.01
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (27 bp):
ACAACCATCTAATCCCTTGAACTGACC
Found at i:822975 original size:35 final size:34
Alignment explanation
Indices: 822912--822986 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 34
822902 AATGACCACC
* *
822912 ACCATCTAATCCCTTCACTGGCCACAACCACCTA
1 ACCATCTAATCCCTTAAATGGCCACAACCACCTA
* *
822946 ACCATCTAATCTCTTGAAATGGCCACAACCATCTA
1 ACCATCTAATCCCTT-AAATGGCCACAACCACCTA
822981 ATCCAT
1 A-CCAT
822987 TTAACTTGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 14 0.40
35 17 0.49
36 4 0.11
ACGTcount: A:0.32, C:0.37, G:0.07, T:0.24
Consensus pattern (34 bp):
ACCATCTAATCCCTTAAATGGCCACAACCACCTA
Found at i:823056 original size:53 final size:52
Alignment explanation
Indices: 822945--823114 Score: 164
Period size: 53 Copynumber: 3.2 Consensus size: 52
822935 ACAACCACCT
* * * *
822945 AACCATCTAATCTCTTGAAATGGCCACAACCATCTAATCCATTTAACTTGTCAT
1 AACCATCTAATCTCTTGAACTGGCCACAACCATCTAATCC-TTGAAC-TGCCAC
* *
822999 AACCATCTAATCCCTTG-ACTGGCCACAACCATCTAATCTCTTGAACCGACCAC
1 AACCATCTAATCTCTTGAACTGGCCACAACCATCTAATC-CTTGAACTG-CCAC
* * * * **
823052 AACCATCGAATTTTTTGAACTGACCACAACTTTCTAATCCCTTG-ACTGGCCAC
1 AACCATCTAATCTCTTGAACTGGCCACAACCATCTAAT-CCTTGAACT-GCCAC
823105 AACCATCTAA
1 AACCATCTAA
823115 CCACCTAATA
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
52 1 0.01
53 55 0.57
54 39 0.41
55 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.28
Consensus pattern (52 bp):
AACCATCTAATCTCTTGAACTGGCCACAACCATCTAATCCTTGAACTGCCAC
Found at i:826800 original size:3 final size:3
Alignment explanation
Indices: 826792--826835 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
826782 GTAAGTACAT
826792 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
826836 GAGAGAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:826840 original size:2 final size:2
Alignment explanation
Indices: 826833--826882 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
826823 AAGAAGAAGA
826833 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
826875 AG AG AG AG
1 AG AG AG AG
826883 CATTAATTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:834919 original size:2 final size:2
Alignment explanation
Indices: 834914--834991 Score: 108
Period size: 2 Copynumber: 39.5 Consensus size: 2
834904 AAAATACTAC
834914 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
834956 AG AG A- AG AG AG A- ATG AC AG AG A- ATG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A-G AG AG AG AG A-G AG AG AG AG AG A
834992 AACCCCGATT
Statistics
Matches: 69, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
1 3 0.04
2 64 0.93
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.45, T:0.03
Consensus pattern (2 bp):
AG
Found at i:838244 original size:26 final size:26
Alignment explanation
Indices: 838215--838268 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
838205 TTACAACAAT
* *
838215 ATATAAACCTCACTCCATACAGCAAC
1 ATATAAACCACACTCCACACAGCAAC
838241 ATATAAACCACACTCCACACAGCAAC
1 ATATAAACCACACTCCACACAGCAAC
838267 AT
1 AT
838269 TTACAACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.35, G:0.04, T:0.17
Consensus pattern (26 bp):
ATATAAACCACACTCCACACAGCAAC
Found at i:838260 original size:64 final size:64
Alignment explanation
Indices: 838191--838382 Score: 240
Period size: 76 Copynumber: 2.8 Consensus size: 64
838181 ACATACAAAA
838191 CCACACAGCAACATTTACAACAATATATAAACCTCACTCCATACAGCAACATATAAACCACACT
1 CCACACAGCAACATTTACAACAATATATAAACCTCACTCCATACAGCAACATATAAACCACACT
* *
838255 CCACACAGCAACATTTACAACAATATATAAACCTCACTGCACACAGCAACATTTACAACAATATA
1 CCACACAGCAACATTTACAACAATATATAAACCTCACT--------C--CA--TACAGCAACATA
*
838320 TAAACCTCACT
54 TAAACCACACT
*
838331 CCACACAGCAACATTTACAACAATATATAAACCTCACTCCACACAGCAACAT
1 CCACACAGCAACATTTACAACAATATATAAACCTCACTCCATACAGCAACAT
838383 TTACAACAAC
Statistics
Matches: 110, Mismatches: 6, Indels: 24
0.79 0.04 0.17
Matches are distributed among these distances:
64 46 0.42
66 2 0.02
68 1 0.01
72 1 0.01
74 2 0.02
76 58 0.53
ACGTcount: A:0.45, C:0.32, G:0.04, T:0.19
Consensus pattern (64 bp):
CCACACAGCAACATTTACAACAATATATAAACCTCACTCCATACAGCAACATATAAACCACACT
Found at i:838285 original size:38 final size:38
Alignment explanation
Indices: 838241--838391 Score: 284
Period size: 38 Copynumber: 4.0 Consensus size: 38
838231 ATACAGCAAC
*
838241 ATATAAACCACACTCCACACAGCAACATTTACAACAAT
1 ATATAAACCTCACTCCACACAGCAACATTTACAACAAT
*
838279 ATATAAACCTCACTGCACACAGCAACATTTACAACAAT
1 ATATAAACCTCACTCCACACAGCAACATTTACAACAAT
838317 ATATAAACCTCACTCCACACAGCAACATTTACAACAAT
1 ATATAAACCTCACTCCACACAGCAACATTTACAACAAT
838355 ATATAAACCTCACTCCACACAGCAACATTTACAACAA
1 ATATAAACCTCACTCCACACAGCAACATTTACAACAA
838392 CACAAAAAAC
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 110 1.00
ACGTcount: A:0.46, C:0.31, G:0.03, T:0.20
Consensus pattern (38 bp):
ATATAAACCTCACTCCACACAGCAACATTTACAACAAT
Found at i:838722 original size:29 final size:29
Alignment explanation
Indices: 838684--838756 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
838674 AACACCTACG
* *
838684 ACAATAAATAACACCACAACATGTATATA
1 ACAATAAATAACACCACAAAATATATATA
* *
838713 ACAATGAATAACACCACAAAATATCTATA
1 ACAATAAATAACACCACAAAATATATATA
*
838742 ACAACAAATAACACC
1 ACAATAAATAACACC
838757 CCAAGGACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.56, C:0.23, G:0.03, T:0.18
Consensus pattern (29 bp):
ACAATAAATAACACCACAAAATATATATA
Found at i:841836 original size:92 final size:91
Alignment explanation
Indices: 841678--841861 Score: 316
Period size: 92 Copynumber: 2.0 Consensus size: 91
841668 ACGAAATCGA
*
841678 TGATATGTGAAATAATACGTCATCTATCATTGTGGCAGCATTCCTTTCAGTAGCTTACATAAATC
1 TGATATGTGAAATAATACATCATCTATCATTGTGGCAGCATTCCTTTCAGTAGCTTACATAAATC
841743 AT-CTATACGAATTATTTATGATTTCT
66 ATGC-ATACGAATTATTTATGATTTCT
* *
841769 TNGATATGTGAAATAATACATCATCTTTCATTGTGGCAGCATTCTTTTCAGTAGCTTACATAAAT
1 T-GATATGTGAAATAATACATCATCTATCATTGTGGCAGCATTCCTTTCAGTAGCTTACATAAAT
841834 CATGCATACGAATTATTTATGATTTCT
65 CATGCATACGAATTATTTATGATTTCT
841861 T
1 T
841862 TTTATATTTA
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
91 1 0.01
92 86 0.98
93 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (91 bp):
TGATATGTGAAATAATACATCATCTATCATTGTGGCAGCATTCCTTTCAGTAGCTTACATAAATC
ATGCATACGAATTATTTATGATTTCT
Found at i:844674 original size:17 final size:19
Alignment explanation
Indices: 844639--844674 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
844629 TTGTAAAACA
844639 TCTTTTGTATACTAGTAAT
1 TCTTTTGTATACTAGTAAT
844658 TCTTTTG-ATAC-AGTAAT
1 TCTTTTGTATACTAGTAAT
844675 GATCATGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 4 0.24
19 7 0.41
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (19 bp):
TCTTTTGTATACTAGTAAT
Found at i:845599 original size:33 final size:33
Alignment explanation
Indices: 845551--845683 Score: 221
Period size: 33 Copynumber: 4.0 Consensus size: 33
845541 AATTCAGTTT
* *
845551 ATATATTGACAATAAGAGACACAAATATCTTCC
1 ATATATTGGCGATAAGAGACACAAATATCTTCC
845584 ATATATTGGCGATAAGAGACACAAATATCTTCC
1 ATATATTGGCGATAAGAGACACAAATATCTTCC
* *
845617 ATATATTGGTGATAAAAGACACAAATATCTTCC
1 ATATATTGGCGATAAGAGACACAAATATCTTCC
*
845650 ATATATTGGTGATAAGAGACACAAATATCTTCC
1 ATATATTGGCGATAAGAGACACAAATATCTTCC
845683 A
1 A
845684 CTTACAGATG
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 95 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.29
Consensus pattern (33 bp):
ATATATTGGCGATAAGAGACACAAATATCTTCC
Found at i:845788 original size:12 final size:12
Alignment explanation
Indices: 845770--845803 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
845760 TTCAGTCCAT
845770 AACCGGCACCAG
1 AACCGGCACCAG
* *
845782 CACCGGCACCAT
1 AACCGGCACCAG
845794 AACCGGCACC
1 AACCGGCACC
845804 GTATCCAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.47, G:0.21, T:0.03
Consensus pattern (12 bp):
AACCGGCACCAG
Found at i:848895 original size:22 final size:21
Alignment explanation
Indices: 848869--848909 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
848859 GCACAACATT
*
848869 GATTTTATTTGTGAAATCAACA
1 GATTTT-TTTGTAAAATCAACA
*
848891 GATTTTTTTTTAAAATCAA
1 GATTTTTTTGTAAAATCAA
848910 ATTCAACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (21 bp):
GATTTTTTTGTAAAATCAACA
Found at i:855376 original size:2 final size:2
Alignment explanation
Indices: 855369--855470 Score: 163
Period size: 2 Copynumber: 52.0 Consensus size: 2
855359 GAACTAGGAA
855369 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
855411 -C TC TT TC TC TC TC TC TC TC TC TC TC TC -C TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
855451 TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
855471 AGAAGTGAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
1 2 0.02
2 90 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:864051 original size:16 final size:16
Alignment explanation
Indices: 864030--864060 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
864020 AAGAAATTAC
*
864030 TTCGTTATATCCGTAA
1 TTCGTTATAACCGTAA
864046 TTCGTTATAACCGTA
1 TTCGTTATAACCGTA
864061 TAAGAAATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (16 bp):
TTCGTTATAACCGTAA
Found at i:870082 original size:4 final size:4
Alignment explanation
Indices: 870075--870128 Score: 90
Period size: 4 Copynumber: 13.5 Consensus size: 4
870065 ATTTCTTTCT
* *
870075 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTCA TATA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
870123 TTTA TT
1 TTTA TT
870129 GAGTCTTAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:877429 original size:29 final size:29
Alignment explanation
Indices: 877395--877456 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
877385 GATTTGAAAT
*
877395 AAATTTCATTGCTTGTAAATACCCAAAAA
1 AAATTTCATTGCTTGGAAATACCCAAAAA
**
877424 AAATTTCATTGCTTGGAAATACTGAAAAA
1 AAATTTCATTGCTTGGAAATACCCAAAAA
877453 AAAT
1 AAAT
877457 CATAATGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.31
Consensus pattern (29 bp):
AAATTTCATTGCTTGGAAATACCCAAAAA
Found at i:877762 original size:13 final size:13
Alignment explanation
Indices: 877744--877768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
877734 ATATTGTTCA
877744 TTAAAAAGACTTT
1 TTAAAAAGACTTT
877757 TTAAAAAGACTT
1 TTAAAAAGACTT
877769 CAAAAATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
TTAAAAAGACTTT
Found at i:879131 original size:31 final size:31
Alignment explanation
Indices: 879090--879153 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
879080 ATATTGTAAT
879090 AGACCAGGGTTACGGAATCAATAATATTATG
1 AGACCAGGGTTACGGAATCAATAATATTATG
*
879121 AGACTAGGGTTACGGAATCAATAATATTATG
1 AGACCAGGGTTACGGAATCAATAATATTATG
879152 AG
1 AG
879154 TCAGGATCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (31 bp):
AGACCAGGGTTACGGAATCAATAATATTATG
Found at i:885010 original size:90 final size:90
Alignment explanation
Indices: 884857--885057 Score: 242
Period size: 90 Copynumber: 2.2 Consensus size: 90
884847 CCCTCAAGAC
* ** * * *
884857 TTCAGTGTCACCCAGGGAACGACCTTTATCCCCCAGGGATCCAGAATCCCTCAAGAGACACAAGA
1 TTCAGTGTCACCCAGGGAATGACCAATATCCCACAGGGACCCAGAATCCCTCAACAGACACAAGA
884922 CCATGC-CATCTATATGCATCAGGGA
66 CCAT-CTCATCTATATGCATCAGGGA
* * * * *
884947 TTCAGCGTCACCCAGGGAATGGCCAATATCCCACAGGGACCCAGAATCCTTCCACAGGCACAAGA
1 TTCAGTGTCACCCAGGGAATGACCAATATCCCACAGGGACCCAGAATCCCTCAACAGACACAAGA
* * * *
885012 CGATCTTATCTGTATGCCTCAGGGA
66 CCATCTCATCTATATGCATCAGGGA
*
885037 TTCAGTATCACCCAGGGAATG
1 TTCAGTGTCACCCAGGGAATG
885058 CAAGAAGAGA
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 1 0.01
90 92 0.99
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.19
Consensus pattern (90 bp):
TTCAGTGTCACCCAGGGAATGACCAATATCCCACAGGGACCCAGAATCCCTCAACAGACACAAGA
CCATCTCATCTATATGCATCAGGGA
Found at i:891834 original size:438 final size:435
Alignment explanation
Indices: 890833--891901 Score: 1518
Period size: 438 Copynumber: 2.4 Consensus size: 435
890823 CAAATCCATT
* ** * * *
890833 ATTACGTAATAAATGGGTGTGGCAATGAGTTTTCC-AGATAGATATTGCTACAATTAACAACTTT
1 ATTACGTAATAAATGGGCGTGGCAATGTTTTTTCCTA-ATAGATATTGGTACGATCAACAACTTT
* * * * * * *
890897 GCTTTTATAATGCATTACGACATCTTAATCGTTTTTATGTAATTTGTAATAGACTTTACGAGTTT
65 GCTTCTATAATGCATTACAAAATCTTTATCGTTTTTATGTTATTTGTAATAGAGTTTACGAGTGT
* * * *
890962 CTTGCCCCCCCCCCCCCCAAGAAAAAAAAGGGGACAGCCCCTTTTTCTTGAATTCTTTGAAAAGG
130 CTTG---------GCCCC---TAAAAAAAGGGGCCAGCCCCTTTTTCTTG-ATTTTTTGAAAAGG
* *
891027 TCTTAAGAATACTAACAATGTTTGTTCTTACACCCATCTAAAATTGTTGATCATTTTTGAGATCA
182 TCTTAAGAATACAAACAATGTTTGTTCTTACACCCATCTAAAATTGTTGATCATTTCTGAGATCA
891092 AATGTATGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAATTCGTGTTTTGA
247 AATGTATGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAATTCGTGTTTTGA
* *
891157 TAAGTGGAATCGATTTAAATCATAAATTCAAACATTTTCTTTTCTATGATGTCTAACAAAATATG
312 TAAGTGGAATCAATTTAAATCATAAATTCAAACATTTTCTCTTCTATGATGTCTAACAAAATATG
*
891222 TCTACTTCTCTAGTTATATTGCGTCAAAGTTTAAGTACTTTAGCCCCTAAAAATTCCCA
377 TATACTTCTCTAGTTATATTGCGTCAAAGTTTAAGTACTTTAGCCCCTAAAAATTCCCA
891281 ATTAC-TAATTATAAATGGGCGTGGCAATGATTTTTT-CTAATAGATATTGGTACGATCAACAAC
1 ATTACGT-A--ATAAATGGGCGTGGCAATG-TTTTTTCCTAATAGATATTGGTACGATCAACAAC
* *
891344 TTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTTACTTGTAATAGAGTTTACGAG
62 TTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTATGTTATTTGTAATAGAGTTTACGAG
* *
891409 TGCCTTGGCCCCTAAAAAAAGGGGCCAGCCCCTTTTTCTTGATTTGTTTGAAAAGGTCTTGAGAA
127 TGTCTTGGCCCCTAAAAAAAGGGGCCAGCCCCTTTTTCTTGATTT-TTTGAAAAGGTCTTAAGAA
* * * *
891474 TACAAATATTTTTTGTTCTTACACCCATGTAAAATTGTTGATCATTTCTGAGATACAAATG-ATT
191 TACAAACAATGTTTGTTCTTACACCCATCTAAAATTGTTGATCATTTCTGAGAT-CAAATGTA-T
891538 GAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAATTCGTGTTTTGATAAGTGG
254 GAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAATTCGTGTTTTGATAAGTGG
**
891603 AATCAATTTAAATCATTTATTCAAACATTTTCTCTTCTATGATGTCTAACAAAATATGTATACTT
319 AATCAATTTAAATCATAAATTCAAACATTTTCTCTTCTATGATGTCTAACAAAATATGTATACTT
* * * * *
891668 CTCTGGTTATTTTTCGTCAAAGTTTAAGTTCTTTGGCCCCTAAAAA-TCCCTA
384 CTCTAGTTATATTGCGTCAAAGTTTAAGTACTTTAGCCCCTAAAAATTCCC-A
*
891720 ATTACGTAATAAATGGGCGTGGCAATGTTTTTTTCCTAATAGATATTGGAACGATCAACAACTTT
1 ATTACGTAATAAATGGGCGTGGCAATG-TTTTTTCCTAATAGATATTGGTACGATCAACAACTTT
*
891785 GCTTCTATAATGCATTACAAAATCTTTATCGTTTTTATGTTATTTGTAATAGAGTTTATGAGTGT
65 GCTTCTATAATGCATTACAAAATCTTTATCGTTTTTATGTTATTTGTAATAGAGTTTACGAGTGT
* *
891850 CTTGGCCCCTAAAAAAGGGGGCCAGCCCCTATTTCTTGATTTTGTTGAAAAG
130 CTTGGCCCCTAAAAAAAGGGGCCAGCCCCTTTTTCTTGATTTT-TTGAAAAG
891902 AACTTTCGAT
Statistics
Matches: 564, Mismatches: 45, Indels: 34
0.88 0.07 0.05
Matches are distributed among these distances:
437 29 0.05
438 236 0.42
439 180 0.32
440 1 0.00
441 4 0.01
447 1 0.00
448 6 0.01
450 102 0.18
451 5 0.01
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (435 bp):
ATTACGTAATAAATGGGCGTGGCAATGTTTTTTCCTAATAGATATTGGTACGATCAACAACTTTG
CTTCTATAATGCATTACAAAATCTTTATCGTTTTTATGTTATTTGTAATAGAGTTTACGAGTGTC
TTGGCCCCTAAAAAAAGGGGCCAGCCCCTTTTTCTTGATTTTTTGAAAAGGTCTTAAGAATACAA
ACAATGTTTGTTCTTACACCCATCTAAAATTGTTGATCATTTCTGAGATCAAATGTATGAATATT
TTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAATTCGTGTTTTGATAAGTGGAATCAAT
TTAAATCATAAATTCAAACATTTTCTCTTCTATGATGTCTAACAAAATATGTATACTTCTCTAGT
TATATTGCGTCAAAGTTTAAGTACTTTAGCCCCTAAAAATTCCCA
Found at i:920798 original size:19 final size:19
Alignment explanation
Indices: 920774--920811 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
920764 TATAAATTCT
920774 TACAGGAAAAAAAAAATCC
1 TACAGGAAAAAAAAAATCC
*
920793 TACAGGAAAAACAAAATCC
1 TACAGGAAAAAAAAAATCC
920812 CTGTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.18, G:0.11, T:0.11
Consensus pattern (19 bp):
TACAGGAAAAAAAAAATCC
Found at i:922221 original size:14 final size:14
Alignment explanation
Indices: 922202--922235 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
922192 AAATAATCAT
*
922202 TTTATTATTATTTA
1 TTTATTATCATTTA
922216 TTTATTATCATTTA
1 TTTATTATCATTTA
922230 TTTATT
1 TTTATT
922236 TATATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTATCATTTA
Found at i:924352 original size:29 final size:28
Alignment explanation
Indices: 924320--924397 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 28
924310 AGTCGATGAC
*
924320 GATGCGATGTTCATGTTGATGACGACGAT
1 GATG-GATGGTCATGTTGATGACGACGAT
* * * *
924349 GATGTTATGGTGATGATGACGACGACGAT
1 GATG-GATGGTCATGTTGATGACGACGAT
*
924378 GAT-GATGGTCATGTCGATGA
1 GATGGATGGTCATGTTGATGA
924398 AGATGATGTA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
27 12 0.32
29 26 0.68
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.29
Consensus pattern (28 bp):
GATGGATGGTCATGTTGATGACGACGAT
Found at i:924362 original size:23 final size:24
Alignment explanation
Indices: 924325--924370 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
924315 ATGACGATGC
*
924325 GATGTTCATGTTGATGACGACGAT
1 GATGTTCATGGTGATGACGACGAT
*
924349 GATGTT-ATGGTGATGATGACGA
1 GATGTTCATGGTGATGACGACGA
924371 CGACGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.33
Consensus pattern (24 bp):
GATGTTCATGGTGATGACGACGAT
Found at i:924427 original size:118 final size:119
Alignment explanation
Indices: 924207--924432 Score: 348
Period size: 118 Copynumber: 1.9 Consensus size: 119
924197 AGTGTCATAT
* * * *
924207 TGTTGATGTTGAGAAGATGATGATGTTATGGTGATGTCGATGACTACGATGATGATGATGGTCAT
1 TGTTCATGTTGAGAAGACGATGATGTTATGGTGA-GTCGATGACGACGACGATGATGATGGTCAT
*
924272 GTCGATGATGATGATGTAGATGAAGTCGTTCATGGTGAAGTCGATGACGATGCGA
65 GTCGATGAAGATGATGTAGATGAAGTCGTTCATGGTGAAGTCGATGACGATGCGA
*
924327 TGTTCATGTTGATGACGACGATGATGTTATGGTGA-T-GATGACGACGACGATGATGATGGTCAT
1 TGTTCATGTTGA-GAAGACGATGATGTTATGGTGAGTCGATGACGACGACGATGATGATGGTCAT
* *
924390 GTCGATGAAGATGATGTAGATGATGTCGTTCATGGTGACGTCG
65 GTCGATGAAGATGATGTAGATGAAGTCGTTCATGGTGAAGTCG
924433 GTGATGATTA
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
118 65 0.67
119 1 0.01
120 11 0.11
121 20 0.21
ACGTcount: A:0.26, C:0.10, G:0.33, T:0.31
Consensus pattern (119 bp):
TGTTCATGTTGAGAAGACGATGATGTTATGGTGAGTCGATGACGACGACGATGATGATGGTCATG
TCGATGAAGATGATGTAGATGAAGTCGTTCATGGTGAAGTCGATGACGATGCGA
Found at i:924538 original size:18 final size:18
Alignment explanation
Indices: 924503--924541 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
924493 TTGTAGTTGA
*
924503 TGATGTTGACGATAGTGG
1 TGATGATGACGATAGTGG
* *
924521 TGATGATGATGATTGTGG
1 TGATGATGACGATAGTGG
924539 TGA
1 TGA
924542 CGAAACTACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.36
Consensus pattern (18 bp):
TGATGATGACGATAGTGG
Found at i:961548 original size:15 final size:17
Alignment explanation
Indices: 961528--961560 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
961518 CACTCTGTAT
961528 ATAGCCAC-AGA-CATC
1 ATAGCCACGAGATCATC
961543 ATAGCCACGAGATCATC
1 ATAGCCACGAGATCATC
961560 A
1 A
961561 CTGACCCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.39, C:0.30, G:0.15, T:0.15
Consensus pattern (17 bp):
ATAGCCACGAGATCATC
Done.