Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold211
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: 1275876
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 151255 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1080145 original size:29 final size:29
Alignment explanation
Indices: 1080103--1080446 Score: 395
Period size: 29 Copynumber: 11.9 Consensus size: 29
1080093 CCGCTCAGAC
*
1080103 AGCTATAAAATGGGTAAGTTAGTACAGGG
1 AGCTATAAAATGGGTAAGTTATTACAGGG
* *
1080132 AGCTATAGAATGGGTAAATTATTAC-GTAGG
1 AGCTATAAAATGGGTAAGTTATTACAG--GG
**
1080162 -GCTATAAAATGGGTAAGTTATTACAAAG
1 AGCTATAAAATGGGTAAGTTATTACAGGG
* ** **
1080190 AGCTATAAAATGGATAAGTTATTTTATAG
1 AGCTATAAAATGGGTAAGTTATTACAGGG
* **
1080219 AGCTATAAAATAGGTAAGTTATTACATAG
1 AGCTATAAAATGGGTAAGTTATTACAGGG
*
1080248 AGCTATAAAATGGGTAAGTTAGTACAGGG
1 AGCTATAAAATGGGTAAGTTATTACAGGG
* * *
1080277 AGTTACAGAATGGGTAAGTTATTACAGGG
1 AGCTATAAAATGGGTAAGTTATTACAGGG
* * *
1080306 AACTATAAAATGGATAAGTTAGTACAGGG
1 AGCTATAAAATGGGTAAGTTATTACAGGG
*
1080335 AGTTATAAAATGGGTAAGTTATTACAGGG
1 AGCTATAAAATGGGTAAGTTATTACAGGG
* * *
1080364 AGCTGTAGAATGGGTAAGTTATTGCAGGG
1 AGCTATAAAATGGGTAAGTTATTACAGGG
* * *
1080393 AGTTATAAAATAGGTATGTTATTACAGGG
1 AGCTATAAAATGGGTAAGTTATTACAGGG
* *
1080422 AGCTGTAGAATGGGTAAGTTATTAC
1 AGCTATAAAATGGGTAAGTTATTAC
1080447 TGGGTGGGGG
Statistics
Matches: 263, Mismatches: 48, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
28 2 0.01
29 259 0.98
30 2 0.01
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.29
Consensus pattern (29 bp):
AGCTATAAAATGGGTAAGTTATTACAGGG
Found at i:1082274 original size:62 final size:62
Alignment explanation
Indices: 1082177--1082322 Score: 265
Period size: 62 Copynumber: 2.4 Consensus size: 62
1082167 TAATGCGTTT
* *
1082177 AGTATTGTATGTAGTGAGTTCACTGTGTCTGTGTGTTCCAGGGTTGACTCTGTAATACATTA
1 AGTATTGTATGCAGTGAGTTCACTGAGTCTGTGTGTTCCAGGGTTGACTCTGTAATACATTA
*
1082239 AGTATTGTATGCAGTAAGTTCACTGAGTCTGTGTGTTCCAGGGTTGACTCTGTAATACATTA
1 AGTATTGTATGCAGTGAGTTCACTGAGTCTGTGTGTTCCAGGGTTGACTCTGTAATACATTA
1082301 AGTATTGTATGCAGTGAGTTCA
1 AGTATTGTATGCAGTGAGTTCA
1082323 TTGTATATGT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 80 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (62 bp):
AGTATTGTATGCAGTGAGTTCACTGAGTCTGTGTGTTCCAGGGTTGACTCTGTAATACATTA
Found at i:1084923 original size:26 final size:26
Alignment explanation
Indices: 1084894--1084981 Score: 113
Period size: 26 Copynumber: 3.4 Consensus size: 26
1084884 GCAGGGTCAT
* *
1084894 GAAGGATGTAATAGTGAATATCAAGG
1 GAAGGATGTAATAGTGTACATCAAGG
** *
1084920 GAAGGATGTTTTGGTGTACATCAAGG
1 GAAGGATGTAATAGTGTACATCAAGG
*
1084946 GAAGGATGTTATAGTGTACATCAAGG
1 GAAGGATGTAATAGTGTACATCAAGG
*
1084972 AAAGGATGTA
1 GAAGGATGTA
1084982 GAAATGTTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.36, C:0.06, G:0.32, T:0.26
Consensus pattern (26 bp):
GAAGGATGTAATAGTGTACATCAAGG
Found at i:1088613 original size:16 final size:17
Alignment explanation
Indices: 1088582--1088615 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1088572 AAGCTGTCCA
1088582 AAAATAAAACAGTTCAC
1 AAAATAAAACAGTTCAC
*
1088599 AAAAT-AAATAGTTCAC
1 AAAATAAAACAGTTCAC
1088615 A
1 A
1088616 GCTGAAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.15, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAATAAAACAGTTCAC
Found at i:1088677 original size:21 final size:22
Alignment explanation
Indices: 1088624--1088677 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
1088614 CAGCTGAAGG
* *
1088624 AAATCAATTCAGAATGAAAATT
1 AAATCAGTTCACAATGAAAATT
*
1088646 AATAT-AGTTCACAATTAAAA-T
1 AA-ATCAGTTCACAATGAAAATT
1088667 AAATCAGTTCA
1 AAATCAGTTCA
1088678 TAGTTGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.07
21 9 0.33
22 14 0.52
23 2 0.07
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (22 bp):
AAATCAGTTCACAATGAAAATT
Found at i:1090471 original size:168 final size:168
Alignment explanation
Indices: 1089704--1090786 Score: 1465
Period size: 168 Copynumber: 6.4 Consensus size: 168
1089694 AAAAACTGGT
* * *
1089704 TGCATGGTTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTTATGGCCCCTGGGTCAGG
1 TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGG
* * * *
1089769 GGTTCTGGCTCTAGGGTGGGGCCAATATGACCATATAGTAAAAATGTTTTAAATCTTGGAAAATC
66 GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTTTTAAATCTTAGAAAATC
* * *
1089834 TTCTTCTCTACTACCATATATATTTTTTGAAAACTAGA
131 TTCTTCTCTACTCCCATATATATTTTTTAAAAACTAAA
* * * *
1089872 TGCATGATTATGATGTCCATGAAGCCCTCTACCTTAATTGTGAAATTCATGACCCCT-AGTCAAG
1 TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGG
*
1089936 GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATC
66 GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTTTTAAATCTTAGAAAATC
* ** *
1090001 TTCTTCTCTGCTATCATATATATTTGTT-AAAACTAAA
131 TTCTTCTCTACTCCCATATATATTTTTTAAAAACTAAA
* * * * *
1090038 T-CTATGGTTATAATGTCCATGAATCCCTCAACCTAAATTGTGAAATTCATGACTCCTTGGTCAG
1 TGC-ATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAG
* * * *
1090102 GGGTTCAGGCTCTAGGGTGGGGCCAATATTGTCATATAGTAAAAATGTATTAAATCTTAGAAAAT
65 GGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTTTTAAATCTTAGAAAAT
1090167 CTTCTTCTCTACTCCCATATATACCGGTATTTGTTAAAAACTAAA
130 CTTCTTCTCTACTCCCATATATA----T-TTT-TTAAAAACTAAA
* * * * *
1090212 TGCATGATTATGATGTGCATGAGGCCCTCTATCAAAATTGTGAAATTCATGACCCCTGGGTCAGG
1 TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGG
* *
1090277 GGTTCAGGCTCTAAGGTGGTGCCAATA-GGACCAAATAGTAAAAATGTTTTAAATCTTAGAAAAT
66 GGTTCAGGCTCTAGGGTGGGGCCAATATGG-CCAAATAGTAAAAATGTTTTAAATCTTAGAAAAT
* *
1090341 CATCTTCTCTACTCCCATATATATTTTTTGAAAACTAAA
130 CTTCTTCTCTACTCCCATATATATTTTTTAAAAACTAAA
* *
1090380 TGCATGGTTATGATGTCCATGAAGCCCTCTACTTAAATTGTGAAATTCATGACCCCTCGGTCAGG
1 TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGG
* * *
1090445 GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAAAAATGAAAATGTTTTAAATCTTAGAAAATC
66 GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTTTTAAATCTTAGAAAATC
*
1090510 TTCTTCTCTACTCCCATATATATTTGTTAAAAACTAAA
131 TTCTTCTCTACTCCCATATATATTTTTTAAAAACTAAA
*
1090548 TGCATGGTTATGATGTCCATGAGGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGG
1 TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGG
* * * *
1090613 TGTTCAGGCCCTAGGGTGGGGCCAATATGGCCAAATAGTGAAAATGTTTTAAATCTTAAAAAATC
66 GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTTTTAAATCTTAGAAAATC
* * * ***** *
1090678 TTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAA
131 TTCTTCTCTACTCCCATATATATTTTTTAAAAACTAAA
* * ** * * * *
1090716 TACATGGTTATGATATCC-CCAATCTCCTTTACCTAAATTGTGAAATTTATGGCCCCTGGGTCAG
1 TGCATGGTTATGATGTCCATGAAGC-CCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAG
1090780 GGGTTCA
65 GGGTTCA
1090787 TGACATGAGG
Statistics
Matches: 812, Mismatches: 90, Indels: 26
0.88 0.10 0.03
Matches are distributed among these distances:
165 1 0.00
166 57 0.07
167 178 0.22
168 423 0.52
169 5 0.01
170 1 0.00
171 1 0.00
172 2 0.00
173 3 0.00
174 140 0.17
175 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (168 bp):
TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGG
GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTTTTAAATCTTAGAAAATC
TTCTTCTCTACTCCCATATATATTTTTTAAAAACTAAA
Found at i:1092115 original size:20 final size:20
Alignment explanation
Indices: 1092087--1093146 Score: 1661
Period size: 20 Copynumber: 52.7 Consensus size: 20
1092077 TGAGATCTGC
* *
1092087 TGTAAAGAGCAGCACTCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092107 TGTATAGAGCAGCAACCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092127 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092147 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
1092167 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
1092187 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092207 TGTATAGAGCAGCAACCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092227 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092247 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
1092267 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092287 TGTATAGATCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092307 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092327 TGTATAGATCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092347 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092367 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
1092387 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092407 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092427 TGTATAGATCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
* *
1092447 TGTATAGAGCAACAGTCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092467 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092487 CGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
* *
1092507 TGTATAGAGAAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
1092527 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
1092547 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
1092567 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092587 TGTATAGTGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092607 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
1092627 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
1092647 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
1092667 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092687 TGTATAGAGCAGCAATCTTT
1 TGTATAGAGCAGCAATCTAT
1092707 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092727 TGTATAGATCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092747 TGTATAGATCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
* *
1092767 TGTATAGAGCAACAGTCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092787 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092807 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
* *
1092827 CGTATAGAGCAGCAATCAAT
1 TGTATAGAGCAGCAATCTAT
*
1092847 TGTATAGAGCAGCAATCAAT
1 TGTATAGAGCAGCAATCTAT
* *
1092867 TGTATAGAGCAACAGTCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092887 TGTATAGAGCAGCAATCTAC
1 TGTATAGAGCAGCAATCTAT
* *
1092907 TGTATAGAACATCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092927 TGTATATATATAGAGCAGCCATCTAT
1 TG------TATAGAGCAGCAATCTAT
*
1092953 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092973 TGTATAGAGCAGCAACCTAT
1 TGTATAGAGCAGCAATCTAT
*
1092993 TGTATAGAGCAGCCATCTAT
1 TGTATAGAGCAGCAATCTAT
1093013 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
*
1093033 TGTATAGATCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
* *
1093053 TGTATAGAGCAACAGTCTAT
1 TGTATAGAGCAGCAATCTAT
1093073 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
1093093 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
1093113 TGTATAGAGCAGCAATCTAT
1 TGTATAGAGCAGCAATCTAT
1093133 TGTATAGAGCAGCA
1 TGTATAGAGCAGCA
1093147 GGGGCTGTAA
Statistics
Matches: 960, Mismatches: 74, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
20 943 0.98
26 17 0.02
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
TGTATAGAGCAGCAATCTAT
Found at i:1093440 original size:25 final size:25
Alignment explanation
Indices: 1093412--1093722 Score: 297
Period size: 25 Copynumber: 12.3 Consensus size: 25
1093402 TATTTTATAA
*
1093412 GCATACATTTGCCAGTACATCCTAG
1 GCATACATTTGTCAGTACATCCTAG
*
1093437 GCATACATTTGTCATTACATCCTAG
1 GCATACATTTGTCAGTACATCCTAG
1093462 GCATACATTTGTC-GTTACATCCTAG
1 GCATACATTTGTCAG-TACATCCTAG
* * *
1093487 GCATACATCTGTCATTACATCCTAA
1 GCATACATTTGTCAGTACATCCTAG
*
1093512 GCATATATACATTTGTC-GTTACATCCTAA
1 GC----ATACATTTGTCAG-TACATCCTAG
* * * *
1093541 ACATACATTCGCCAGAACATCCTAG
1 GCATACATTTGTCAGTACATCCTAG
*** * *
1093566 GCATACATCCATCATTACATCCTAA
1 GCATACATTTGTCAGTACATCCTAG
1093591 GCATACATTTGTC-GTTACATCCTAG
1 GCATACATTTGTCAG-TACATCCTAG
*
1093616 GCATACATTTGTCATTACATCCTAG
1 GCATACATTTGTCAGTACATCCTAG
* * * * *
1093641 GCATACATCTGTTATTGCATCCTAA
1 GCATACATTTGTCAGTACATCCTAG
*
1093666 GCATGCATTTGTC-GTTACATCCTAG
1 GCATACATTTGTCAG-TACATCCTAG
* * *
1093691 GCATACATCTGTCATTACATCCTAA
1 GCATACATTTGTCAGTACATCCTAG
1093716 GCATACA
1 GCATACA
1093723 GTGCCTTGTA
Statistics
Matches: 234, Mismatches: 40, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
25 212 0.91
26 1 0.00
29 21 0.09
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (25 bp):
GCATACATTTGTCAGTACATCCTAG
Found at i:1093470 original size:50 final size:50
Alignment explanation
Indices: 1093409--1093722 Score: 371
Period size: 50 Copynumber: 6.2 Consensus size: 50
1093399 CGATATTTTA
* *
1093409 TAAGCATACATTTGCCAG-TACATCCTAGGCATACATTTGTCATTACATCC
1 TAAGCATACATTTGTC-GTTACATCCTAGGCATACATCTGTCATTACATCC
*
1093459 TAGGCATACATTTGTCGTTACATCCTAGGCATACATCTGTCATTACATCC
1 TAAGCATACATTTGTCGTTACATCCTAGGCATACATCTGTCATTACATCC
** * **
1093509 TAAGCATATATACATTTGTCGTTACATCCTAAACATACAT-TCGCCAGAACATCC
1 TAAGC----ATACATTTGTCGTTACATCCTAGGCATACATCT-GTCATTACATCC
* *** * * * *
1093563 TAGGCATACATCCATCATTACATCCTAAGCATACATTTGTCGTTACATCC
1 TAAGCATACATTTGTCGTTACATCCTAGGCATACATCTGTCATTACATCC
* * * *
1093613 TAGGCATACATTTGTCATTACATCCTAGGCATACATCTGTTATTGCATCC
1 TAAGCATACATTTGTCGTTACATCCTAGGCATACATCTGTCATTACATCC
*
1093663 TAAGCATGCATTTGTCGTTACATCCTAGGCATACATCTGTCATTACATCC
1 TAAGCATACATTTGTCGTTACATCCTAGGCATACATCTGTCATTACATCC
1093713 TAAGCATACA
1 TAAGCATACA
1093723 GTGCCTTGTA
Statistics
Matches: 224, Mismatches: 33, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.00
50 179 0.80
51 1 0.00
53 1 0.00
54 42 0.19
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (50 bp):
TAAGCATACATTTGTCGTTACATCCTAGGCATACATCTGTCATTACATCC
Found at i:1093638 original size:75 final size:75
Alignment explanation
Indices: 1093412--1093722 Score: 415
Period size: 75 Copynumber: 4.1 Consensus size: 75
1093402 TATTTTATAA
* * * * * *
1093412 GCATACATTTGCCAGTACATCCTAGGCATACATTTGTCATTACATCCTAGGCATACATTTGTCGT
1 GCATACATCTGTCATTACATCCTAAGCATACATTTGTCGTTACATCCTAGGCATACATTTGTCAT
1093477 TACATCCTAG
66 TACATCCTAG
** *
1093487 GCATACATCTGTCATTACATCCTAAGCATATATACATTTGTCGTTACATCCTAAACATACATTCG
1 GCATACATCTGTCATTACATCCTAAGC----ATACATTTGTCGTTACATCCTAGGCATACATTTG
* **
1093552 CCAGAACATCCTAG
62 TCATTACATCCTAG
**
1093566 GCATACATCCATCATTACATCCTAAGCATACATTTGTCGTTACATCCTAGGCATACATTTGTCAT
1 GCATACATCTGTCATTACATCCTAAGCATACATTTGTCGTTACATCCTAGGCATACATTTGTCAT
1093631 TACATCCTAG
66 TACATCCTAG
* * * *
1093641 GCATACATCTGTTATTGCATCCTAAGCATGCATTTGTCGTTACATCCTAGGCATACATCTGTCAT
1 GCATACATCTGTCATTACATCCTAAGCATACATTTGTCGTTACATCCTAGGCATACATTTGTCAT
*
1093706 TACATCCTAA
66 TACATCCTAG
1093716 GCATACA
1 GCATACA
1093723 GTGCCTTGTA
Statistics
Matches: 205, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
75 140 0.68
79 65 0.32
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (75 bp):
GCATACATCTGTCATTACATCCTAAGCATACATTTGTCGTTACATCCTAGGCATACATTTGTCAT
TACATCCTAG
Found at i:1094052 original size:25 final size:25
Alignment explanation
Indices: 1094024--1094091 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
1094014 TGCCAGGATC
* *
1094024 TTGTAAGTATACATTT-TTCAGTACA
1 TTGTAAGCATACATTTGTT-AATACA
*
1094049 TTGTAAGCATATATTTGTTAATACA
1 TTGTAAGCATACATTTGTTAATACA
1094074 TTGTAAGCATACATTTGT
1 TTGTAAGCATACATTTGT
1094092 AAGCATACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.44
Consensus pattern (25 bp):
TTGTAAGCATACATTTGTTAATACA
Found at i:1094093 original size:14 final size:14
Alignment explanation
Indices: 1094024--1094101 Score: 69
Period size: 14 Copynumber: 6.0 Consensus size: 14
1094014 TGCCAGGATC
*
1094024 TTGTAAGTATACAT
1 TTGTAAGCATACAT
* *
1094038 TTTTCAG--TACA-
1 TTGTAAGCATACAT
*
1094049 TTGTAAGCATATAT
1 TTGTAAGCATACAT
*
1094063 TTGTTA--ATACA-
1 TTGTAAGCATACAT
1094074 TTGTAAGCATACAT
1 TTGTAAGCATACAT
1094088 TTGTAAGCATACAT
1 TTGTAAGCATACAT
1094102 GTGTCATGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
11 10 0.20
12 8 0.16
13 8 0.16
14 24 0.48
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (14 bp):
TTGTAAGCATACAT
Found at i:1095934 original size:2 final size:2
Alignment explanation
Indices: 1095927--1095981 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1095917 ATTTGGAATC
1095927 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
1095969 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
1095982 ATAAATTTGG
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:1101331 original size:2 final size:2
Alignment explanation
Indices: 1101324--1101388 Score: 103
Period size: 2 Copynumber: 32.0 Consensus size: 2
1101314 TATCACCATT
* *
1101324 AG AG AG AG AG AT CG CAG 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
1101367 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
1101389 TCTTACCTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 57 0.98
3 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:1103518 original size:2 final size:2
Alignment explanation
Indices: 1103511--1103548 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1103501 TTAAAAGCAT
1103511 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1103549 TATTTTCAGT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1108731 original size:15 final size:14
Alignment explanation
Indices: 1108702--1108739 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
1108692 TCGATGTCGC
1108702 TACACAAAT-TGTG
1 TACACAAATCTGTG
1108715 TAGCACAAATCTGTG
1 TA-CACAAATCTGTG
1108730 TACACAAATC
1 TACACAAATC
1108740 GCAACGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 15 0.65
15 6 0.26
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (14 bp):
TACACAAATCTGTG
Found at i:1119407 original size:17 final size:16
Alignment explanation
Indices: 1119387--1119438 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1119377 TATAACGAGT
1119387 TATCGAGTAAACGTAAG
1 TATCGA-TAAACGTAAG
* * *
1119404 TATCGAAAAAAGAAAG
1 TATCGATAAACGTAAG
*
1119420 TATCGAATAATCGTAAG
1 TATCG-ATAAACGTAAG
1119437 TA
1 TA
1119439 AACGTAAGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (16 bp):
TATCGATAAACGTAAG
Found at i:1119657 original size:17 final size:17
Alignment explanation
Indices: 1119628--1119684 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
1119618 ATCAAATAAT
*
1119628 AGTAAATGTAAGTATTG
1 AGTAAACGTAAGTATTG
* *
1119645 AGTTAACGTAAGTATCG
1 AGTAAACGTAAGTATTG
**
1119662 AGTAAACAAAAGTATTG
1 AGTAAACGTAAGTATTG
*
1119679 TGTAAA
1 AGTAAA
1119685 AGTATGTAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (17 bp):
AGTAAACGTAAGTATTG
Found at i:1120114 original size:17 final size:16
Alignment explanation
Indices: 1120094--1120140 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
1120084 AGCAAAATTT
1120094 AGTATCGAGTAAACGGA
1 AGTATCGAGTAAA-GGA
*
1120111 AGTATCGAGTTAAAGTA
1 AGTATCGAG-TAAAGGA
*
1120128 ATTATCGAGTAAA
1 AGTATCGAGTAAA
1120141 TAAAGTACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 4 0.15
17 19 0.70
18 4 0.15
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.26
Consensus pattern (16 bp):
AGTATCGAGTAAAGGA
Found at i:1120200 original size:26 final size:26
Alignment explanation
Indices: 1120170--1120334 Score: 321
Period size: 26 Copynumber: 6.3 Consensus size: 26
1120160 AAGTATCGAA
*
1120170 TAATTGTTAGTATCAGTAAACATTAG
1 TAATTGTAAGTATCAGTAAACATTAG
1120196 TAATTGTAAGTATCAGTAAACATTAG
1 TAATTGTAAGTATCAGTAAACATTAG
1120222 TAATTGTAAGTATCAGTAAACATTAG
1 TAATTGTAAGTATCAGTAAACATTAG
1120248 TAATTGTAAGTATCAGTAAACATTAG
1 TAATTGTAAGTATCAGTAAACATTAG
1120274 TAATTGTAAGTATCAGTAAACATTAG
1 TAATTGTAAGTATCAGTAAACATTAG
1120300 TAATTGTAAGTATCAGTAAACATTAG
1 TAATTGTAAGTATCAGTAAACATTAG
1120326 TAATTGTAA
1 TAATTGTAA
1120335 ACGCAAGAAT
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 138 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (26 bp):
TAATTGTAAGTATCAGTAAACATTAG
Found at i:1135163 original size:2 final size:2
Alignment explanation
Indices: 1135156--1135194 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1135146 CTGAGTTTAT
1135156 TC TC 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 TC TC T
1135195 GCCATCACCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1136292 original size:9 final size:9
Alignment explanation
Indices: 1136271--1136313 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1136261 ACAATTTGTC
1136271 CGTTGTCTGT
1 CGTTGTC-GT
* *
1136281 CGTCGTTGT
1 CGTTGTCGT
1136290 CGTTGTCGT
1 CGTTGTCGT
*
1136299 CGTCGTCGT
1 CGTTGTCGT
1136308 CGTTGT
1 CGTTGT
1136314 AAACTTTTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 22 0.81
10 5 0.19
ACGTcount: A:0.00, C:0.23, G:0.33, T:0.44
Consensus pattern (9 bp):
CGTTGTCGT
Found at i:1136293 original size:6 final size:6
Alignment explanation
Indices: 1136266--1136313 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
1136256 TGATCACAAT
* * *
1136266 TTGTCCG TTGTCTG TCGTCG TTGTCG TTGTCG TCGTCG TCGTCG TTGT
1 TTGT-CG TTGTC-G TTGTCG TTGTCG TTGTCG TTGTCG TTGTCG TTGT
1136314 AAACTTTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 27 0.75
7 9 0.25
ACGTcount: A:0.00, C:0.23, G:0.31, T:0.46
Consensus pattern (6 bp):
TTGTCG
Found at i:1136792 original size:2 final size:2
Alignment explanation
Indices: 1136785--1136823 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1136775 NNNNNNNNNN
1136785 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1136824 ATATGCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1140237 original size:22 final size:21
Alignment explanation
Indices: 1140205--1140263 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1140195 AAACGGATTT
*
1140205 TTTCCTAGACTTTCCGAAGTTG
1 TTTCCTGGACTTTCCGAA-TTG
* *
1140227 TTTCCTGGACTTTCTGGATTG
1 TTTCCTGGACTTTCCGAATTG
*
1140248 TGTCCTGGACTTTCCG
1 TTTCCTGGACTTTCCG
1140264 TTGGGTATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (21 bp):
TTTCCTGGACTTTCCGAATTG
Found at i:1151993 original size:28 final size:28
Alignment explanation
Indices: 1151953--1152009 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1151943 CTAAGATTAG
1151953 TTCAAAATAGTGTCTATGTGTTATGAAC
1 TTCAAAATAGTGTCTATGTGTTATGAAC
*
1151981 TTCAAAATAGTGTCTATGTGTTCTGAAC
1 TTCAAAATAGTGTCTATGTGTTATGAAC
1152009 T
1 T
1152010 AGAGTACTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (28 bp):
TTCAAAATAGTGTCTATGTGTTATGAAC
Found at i:1163910 original size:2 final size:2
Alignment explanation
Indices: 1163903--1163934 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1163893 ATGCTAATAA
1163903 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
1163935 CTCGCAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1164458 original size:30 final size:29
Alignment explanation
Indices: 1164419--1164508 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 29
1164409 CTGAGAAACA
*
1164419 CTAAACCCTAACCTGCCCCACTGATTATT
1 CTAAACCCTAACCTGCCCCACTGATAATT
1164448 CTAAATCCCTAACCTGCCCCACTGATAATT
1 CTAAA-CCCTAACCTGCCCCACTGATAATT
*
1164478 CCT-AACCCTTACCGTGCCCCACTGATAATT
1 -CTAAACCCTAACC-TGCCCCACTGATAATT
1164508 C
1 C
1164509 AGGTTCCTAC
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
29 13 0.23
30 41 0.73
31 2 0.04
ACGTcount: A:0.27, C:0.39, G:0.08, T:0.27
Consensus pattern (29 bp):
CTAAACCCTAACCTGCCCCACTGATAATT
Found at i:1165164 original size:28 final size:29
Alignment explanation
Indices: 1165097--1165152 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
1165087 AGAAATAAGT
1165097 ATCTAGAAGTCCTAAAAACAGATATCAGG
1 ATCTAGAAGTCCTAAAAACAGATATCAGG
*
1165126 ATCTAAAAGTCCT-AAAACAGATATCAG
1 ATCTAGAAGTCCTAAAAACAGATATCAG
1165153 TATTTGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (29 bp):
ATCTAGAAGTCCTAAAAACAGATATCAGG
Found at i:1167341 original size:2 final size:2
Alignment explanation
Indices: 1167334--1167375 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1167324 CAACGTCAAC
1167334 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
1167376 CTTTATAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1168023 original size:2 final size:2
Alignment explanation
Indices: 1168016--1168081 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1168006 CGTCCACTCT
1168016 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1168058 GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
1168082 CACACACACA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1169820 original size:24 final size:24
Alignment explanation
Indices: 1169785--1169840 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1169775 GAAAAATGTC
1169785 TGCTGTCCACCCATTACTTTCCGA
1 TGCTGTCCACCCATTACTTTCCGA
*
1169809 TGTTGTCCACCCATTACTTTCCGA
1 TGCTGTCCACCCATTACTTTCCGA
1169833 TGCTGTCC
1 TGCTGTCC
1169841 TTTTGTCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (24 bp):
TGCTGTCCACCCATTACTTTCCGA
Found at i:1170687 original size:47 final size:47
Alignment explanation
Indices: 1170618--1170763 Score: 283
Period size: 47 Copynumber: 3.1 Consensus size: 47
1170608 TATGTTTTAT
1170618 AATGTTTAGTTATTTTCAATATTAACATGCCAACTATATACATGTAA
1 AATGTTTAGTTATTTTCAATATTAACATGCCAACTATATACATGTAA
1170665 AATGTTTAGTTATTTTCAATATTAACATGCCAACTATATACATGTAA
1 AATGTTTAGTTATTTTCAATATTAACATGCCAACTATATACATGTAA
*
1170712 AATGTTTAGTTATTTTCAATATTAACATGCCAACTATATACATGTAC
1 AATGTTTAGTTATTTTCAATATTAACATGCCAACTATATACATGTAA
1170759 AATGT
1 AATGT
1170764 CCTACATTAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 98 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (47 bp):
AATGTTTAGTTATTTTCAATATTAACATGCCAACTATATACATGTAA
Found at i:1172716 original size:2 final size:2
Alignment explanation
Indices: 1172709--1172738 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1172699 GATGCTGGAA
1172709 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1172739 ATATATATAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:1176731 original size:92 final size:91
Alignment explanation
Indices: 1176627--1176809 Score: 357
Period size: 92 Copynumber: 2.0 Consensus size: 91
1176617 AATGGTAATA
1176627 TTACTGTTACATGTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCGGTAC
1 TTACTGTTACATGTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCGGTAC
1176692 ACGCAGTAAGTAGCGACAGAGTTCCC
66 ACGCAGTAAGTAGCGACAGAGTTCCC
1176718 NTTACTGTTACATGTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCGGTA
1 -TTACTGTTACATGTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCGGTA
1176783 CACGCAGTAAGTAGCGACAGAGTTCCC
65 CACGCAGTAAGTAGCGACAGAGTTCCC
1176810 CTATGTACTG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (91 bp):
TTACTGTTACATGTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCGGTAC
ACGCAGTAAGTAGCGACAGAGTTCCC
Found at i:1176784 original size:49 final size:49
Alignment explanation
Indices: 1176639--1176785 Score: 126
Period size: 49 Copynumber: 3.1 Consensus size: 49
1176629 ACTGTTACAT
1176639 GTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCG
1 GTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCG
* * * *** * ***** * *
1176688 GTACACGCAGTAAGTA-GCGACAGAGT-TCCCNTTACT-GTTA-CAT--
1 GTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCG
1176731 GTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCG
1 GTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCG
1176780 GTACAC
1 GTACAC
1176786 GCAGTAAGTA
Statistics
Matches: 64, Mismatches: 28, Indels: 12
0.62 0.27 0.12
Matches are distributed among these distances:
43 13 0.20
44 6 0.09
45 6 0.09
46 8 0.12
47 6 0.09
48 6 0.09
49 19 0.30
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (49 bp):
GTACACACTGTAACTATTATACAGAATATTGTAATAATAGTTACCTTCG
Found at i:1181961 original size:20 final size:20
Alignment explanation
Indices: 1181936--1181977 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1181926 TATTTAATTA
1181936 ATTAAAATTAGAATAAGTCC
1 ATTAAAATTAGAATAAGTCC
1181956 ATTAAAATTAGAATAAGTCC
1 ATTAAAATTAGAATAAGTCC
1181976 AT
1 AT
1181978 GGGTGTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTAAAATTAGAATAAGTCC
Found at i:1190218 original size:19 final size:19
Alignment explanation
Indices: 1190194--1190236 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1190184 TATCAGAAAT
*
1190194 CAGTGTGTTTACAGTATTA
1 CAGTGTGTTTACAGTATCA
1190213 CAGTGTGTTTACAGTATCA
1 CAGTGTGTTTACAGTATCA
1190232 CAGTG
1 CAGTG
1190237 AGGGTGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (19 bp):
CAGTGTGTTTACAGTATCA
Found at i:1196278 original size:47 final size:47
Alignment explanation
Indices: 1196185--1196818 Score: 920
Period size: 47 Copynumber: 13.7 Consensus size: 47
1196175 AGCTAGGCGC
* * *
1196185 CTCCTCGGCGGTAAACATCGCAACTTGATTAGGTGGTAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAAC----TTAGGGGGTAATTTCATCAGTAG
* *
1196236 CTCCTCCACGGTGAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
* *
1196283 CTCCTCCGCGGTAAACATCTCAACTTGGGGGGAAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
*
1196330 CTTCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
* *
1196377 CTCCTCCGCAGTAAACA--TC-ACTTAGGGGGTAATTTCATCAATAG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
*
1196421 CTCCTCCGCGGTAAACATCTCAACTTGGGGGGTAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
1196468 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
*
1196515 CTCCTCCGCAGTAAACA--TC-ACTTAGGGGGTAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
* *
1196559 CTCCTCCGCGGTAAACATCTTAACTTGGGGGGGTAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAACTT-AGGGGGTAATTTCATCAGTAG
*
1196607 CTCCCCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
*
1196654 CTCCTCCGCAGTAAACA--TC-ACTTAGGGGGTAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
*
1196698 CTCCTCCGCAGTAAACA--TC-ACTTAGGGGGTAATTTCATCAGTAG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
* *
1196742 CTCCTCCGCAGTAAACA--TC-ACTTAGGGGGGTAATTTCATCAATAG
1 CTCCTCCGCGGTAAACATCTCAACTTA-GGGGGTAATTTCATCAGTAG
* *
1196787 CTCTTCCGCGGTAAACATCTCAACCTAGGGGG
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGG
1196819 GATTTTCACC
Statistics
Matches: 540, Mismatches: 32, Indels: 26
0.90 0.05 0.04
Matches are distributed among these distances:
44 174 0.32
45 40 0.07
46 3 0.01
47 255 0.47
48 48 0.09
51 20 0.04
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (47 bp):
CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAG
Found at i:1196447 original size:138 final size:138
Alignment explanation
Indices: 1196185--1196805 Score: 966
Period size: 138 Copynumber: 4.5 Consensus size: 138
1196175 AGCTAGGCGC
* * * * * *
1196185 CTCCTCGGCGGTAAACATCGCAACTTGATTAGGTGGTAATTTCATCAGTAGCTCCTCCACGGTGA
1 CTCCTCCGCGGTAAACATCTCAAC----TTAGGGGGTAATTTCATCAGTAGCTCCTCCGCAGTAA
1196250 ACATCTCAACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCGGTAAACATCTCAACTTGGGGGG
62 ACA--TC-ACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCGGTAAACATCTCAACTTGGGGGG
*
1196315 AAATTTCATCAGTAG
124 TAATTTCATCAGTAG
*
1196330 CTTCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCAGTAAACAT
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCAGTAAACAT
*
1196395 CACTTAGGGGGTAATTTCATCAATAGCTCCTCCGCGGTAAACATCTCAACTTGGGGGGTAATTTC
66 CACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCGGTAAACATCTCAACTTGGGGGGTAATTTC
1196460 ATCAGTAG
131 ATCAGTAG
1196468 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCAGTAAACAT
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCAGTAAACAT
*
1196533 CACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCGGTAAACATCTTAACTTGGGGGGGTAATTT
66 CACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCGGTAAACATCTCAACTT-GGGGGGTAATTT
1196598 CATCAGTAG
130 CATCAGTAG
*
1196607 CTCCCCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCAGTAAACAT
1 CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCAGTAAACAT
* *
1196672 CACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCAGTAAACA--TC-ACTTAGGGGGTAATTTC
66 CACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCGGTAAACATCTCAACTTGGGGGGTAATTTC
1196734 ATCAGTAG
131 ATCAGTAG
* * * *
1196742 CTCCTCCGCAGTAAACA--TC-ACTTAGGGGGGTAATTTCATCAATAGCTCTTCCGCGGTAAACA
1 CTCCTCCGCGGTAAACATCTCAACTTA-GGGGGTAATTTCATCAGTAGCTCCTCCGCAGTAAACA
1196804 TC
65 TC
1196806 TCAACCTAGG
Statistics
Matches: 453, Mismatches: 21, Indels: 16
0.92 0.04 0.03
Matches are distributed among these distances:
132 5 0.01
133 38 0.08
135 35 0.08
136 4 0.01
137 1 0.00
138 184 0.41
139 129 0.28
141 36 0.08
145 21 0.05
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (138 bp):
CTCCTCCGCGGTAAACATCTCAACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCAGTAAACAT
CACTTAGGGGGTAATTTCATCAGTAGCTCCTCCGCGGTAAACATCTCAACTTGGGGGGTAATTTC
ATCAGTAG
Found at i:1200504 original size:28 final size:28
Alignment explanation
Indices: 1200459--1200657 Score: 292
Period size: 28 Copynumber: 7.1 Consensus size: 28
1200449 ACTGAATAAC
1200459 TAACTGAAAAACATG-TGGGATAACTAAG
1 TAACTGAAAAAC-TGATGGGATAACTAAG
* *
1200487 TAACTGAATAACTGGTGGGATAACTAAG
1 TAACTGAAAAACTGATGGGATAACTAAG
* *
1200515 TAATTGAAAAACTGGTGGGATAACTAAG
1 TAACTGAAAAACTGATGGGATAACTAAG
* **
1200543 TAGCTGAGTAACTGATGGGATAACTAAG
1 TAACTGAAAAACTGATGGGATAACTAAG
*
1200571 TAGCTGAAAAACTGATGGGATAACTAAG
1 TAACTGAAAAACTGATGGGATAACTAAG
1200599 TAACTGAAAAACTGATGGGATAACTAAG
1 TAACTGAAAAACTGATGGGATAACTAAG
**
1200627 TAACTGAAAAACTGATATGATAACTAAG
1 TAACTGAAAAACTGATGGGATAACTAAG
1200655 TAA
1 TAA
1200658 TTAAATATCT
Statistics
Matches: 157, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
27 2 0.01
28 155 0.99
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.24
Consensus pattern (28 bp):
TAACTGAAAAACTGATGGGATAACTAAG
Found at i:1200536 original size:56 final size:56
Alignment explanation
Indices: 1200459--1200689 Score: 306
Period size: 56 Copynumber: 4.1 Consensus size: 56
1200449 ACTGAATAAC
*
1200459 TAACTGAAAAACATG-TGGGATAACTAAGTAACTGAATAACTGGTGGGATAACTAAG
1 TAACTGAAAAAC-TGATGGGATAACTAAGTAACTGAATAACTGATGGGATAACTAAG
* * * *
1200515 TAATTGAAAAACTGGTGGGATAACTAAGTAGCTGAGTAACTGATGGGATAACTAAG
1 TAACTGAAAAACTGATGGGATAACTAAGTAACTGAATAACTGATGGGATAACTAAG
* *
1200571 TAGCTGAAAAACTGATGGGATAACTAAGTAACTGAAAAACTGATGGGATAACTAAG
1 TAACTGAAAAACTGATGGGATAACTAAGTAACTGAATAACTGATGGGATAACTAAG
** * * *
1200627 TAACTGAAAAACTGATATGATAACTAAGTAATTAAATATCTGACT-GGATAACCTAA-
1 TAACTGAAAAACTGATGGGATAACTAAGTAACTGAATAACTGA-TGGGATAA-CTAAG
1200683 TAACTGA
1 TAACTGA
1200690 CCAGATAACT
Statistics
Matches: 155, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
55 2 0.01
56 148 0.95
57 5 0.03
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (56 bp):
TAACTGAAAAACTGATGGGATAACTAAGTAACTGAATAACTGATGGGATAACTAAG
Found at i:1200676 original size:84 final size:84
Alignment explanation
Indices: 1200459--1200689 Score: 281
Period size: 84 Copynumber: 2.8 Consensus size: 84
1200449 ACTGAATAAC
* * * *
1200459 TAACTGAAAAACATG-TGGGATAACTAAGTAACTGAATAACTGGTGGGATAACTAAGTAATTGAA
1 TAACTGAAAAAC-TGATGGGATAACTAAGTAATTAAATAACTGATGGGATAACTAAGTAACTGAA
*
1200523 AAACTGGTGGGATAACTAAG
65 AAACTGATGGGATAACTAAG
* ** * *
1200543 TAGCTGAGTAACTGATGGGATAACTAAGTAGCTGAAA-AACTGATGGGATAACTAAGTAACTGAA
1 TAACTGAAAAACTGATGGGATAACTAAGTA-ATTAAATAACTGATGGGATAACTAAGTAACTGAA
1200607 AAACTGATGGGATAACTAAG
65 AAACTGATGGGATAACTAAG
** *
1200627 TAACTGAAAAACTGATATGATAACTAAGTAATTAAATATCTGACT-GGATAACCTAA-TAACTGA
1 TAACTGAAAAACTGATGGGATAACTAAGTAATTAAATAACTGA-TGGGATAA-CTAAGTAACTGA
1200690 CCAGATAACT
Statistics
Matches: 124, Mismatches: 18, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
83 6 0.05
84 111 0.90
85 7 0.06
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (84 bp):
TAACTGAAAAACTGATGGGATAACTAAGTAATTAAATAACTGATGGGATAACTAAGTAACTGAAA
AACTGATGGGATAACTAAG
Found at i:1202198 original size:2 final size:2
Alignment explanation
Indices: 1202191--1202234 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1202181 CGTTTATGAT
*
1202191 TC TC TC TC TC TC TC T- TT TC TC TC TC TC T- 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
1202231 TC TC
1 TC TC
1202235 CAGTTTCCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:1202213 original size:11 final size:11
Alignment explanation
Indices: 1202191--1202234 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
1202181 CGTTTATGAT
1202191 TCTCTC-TCTC
1 TCTCTCTTCTC
*
1202201 TCTCTTTTCTC
1 TCTCTCTTCTC
1202212 TCTCTCTTCTC
1 TCTCTCTTCTC
1202223 TCTCTC-TCTC
1 TCTCTCTTCTC
1202233 TC
1 TC
1202235 CAGTTTCCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 11 0.35
11 20 0.65
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (11 bp):
TCTCTCTTCTC
Found at i:1202213 original size:13 final size:13
Alignment explanation
Indices: 1202193--1202231 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1202183 TTTATGATTC
1202193 TCTCTCTCTCTCT
1 TCTCTCTCTCTCT
*
1202206 TTTCTCTCTCTCT
1 TCTCTCTCTCTCT
1202219 TCTCTCTCTCTCT
1 TCTCTCTCTCTCT
1202232 CTCCAGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (13 bp):
TCTCTCTCTCTCT
Found at i:1202213 original size:15 final size:16
Alignment explanation
Indices: 1202190--1202234 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
1202180 ACGTTTATGA
1202190 TTCTCTCTCTCTCTCT
1 TTCTCTCTCTCTCTCT
1202206 TT-TCTCTCTCTCT-T
1 TTCTCTCTCTCTCTCT
*
1202220 CTCTCTCTCTCTCTC
1 TTCTCTCTCTCTCTC
1202235 CAGTTTCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (16 bp):
TTCTCTCTCTCTCTCT
Found at i:1202483 original size:2 final size:2
Alignment explanation
Indices: 1202476--1202533 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1202466 ACCCTGAAAT
1202476 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
1202518 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
1202534 CCCTTAGGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1208995 original size:31 final size:30
Alignment explanation
Indices: 1208939--1209037 Score: 155
Period size: 31 Copynumber: 3.3 Consensus size: 30
1208929 CCACATCCCG
* *
1208939 ACACCTTCCTCTGTATAT-ATAAGTTACAC
1 ACACCTCCCTCTATATATCATAAGTTACAC
1208968 ACACCTCCCTCTATATATACATAAGTTACAC
1 ACACCTCCCTCTATATAT-CATAAGTTACAC
1208999 ACACCTCCCTCTATATATTCATAAGTTACAC
1 ACACCTCCCTCTATATA-TCATAAGTTACAC
1209030 ACACCTCC
1 ACACCTCC
1209038 TCGGATAGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
29 16 0.25
31 48 0.74
32 1 0.02
ACGTcount: A:0.32, C:0.33, G:0.04, T:0.30
Consensus pattern (30 bp):
ACACCTCCCTCTATATATCATAAGTTACAC
Found at i:1216926 original size:25 final size:25
Alignment explanation
Indices: 1216892--1217492 Score: 698
Period size: 25 Copynumber: 23.8 Consensus size: 25
1216882 TCAAATATAC
1216892 ATGTAGGTAACTATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
1216917 ATGTAGGTAACTATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
* *
1216942 ATGTAGATAATTATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
1216967 ATGTAGGTAACTATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
*
1216992 ATGTAGGAAACTATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
* * *
1217017 ATGTAGATAATTATGTTACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
1217042 ATGTAGGTAACTATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
*
1217067 GTGTAGGTAACTATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
1217092 ATGTAGGTAACTATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
1217117 ATGTAGGTAACTATGATACACTCAAATATATA
1 ATGTAGGTAACTATGATACACTC------A-A
*
1217149 CATGTAGGTAATTATGATACACTCAA
1 -ATGTAGGTAACTATGATACACTCAA
*
1217175 ATGTAGGTAACTATGATACACTCAG
1 ATGTAGGTAACTATGATACACTCAA
*
1217200 ATATAGGTAACTATGAT--A--C--
1 ATGTAGGTAACTATGATACACTCAA
1217219 ATGTAGGTAACTATGATACACTCAAATATATA
1 ATGTAGGTAACTATGATACACTC------A-A
*
1217251 CATGTAGGTAATTATGATACACTCAA
1 -ATGTAGGTAACTATGATACACTCAA
1217277 ATGTAGGTAACTATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
*
1217302 ATATAGGTAACTATGAT--A--C--
1 ATGTAGGTAACTATGATACACTCAA
*
1217321 ATGTAGGTAACTCTGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
*
1217346 ATATAGGTAACTATGAT--A--C--
1 ATGTAGGTAACTATGATACACTCAA
1217365 ATGTAGGTAACTATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
1217390 ATGTAGGTAACTATGATACACTCAAATATATA
1 ATGTAGGTAACTATGATACACTC------A-A
* * *
1217422 CATGAAGGTAACTATGAAACACTCAG
1 -ATGTAGGTAACTATGATACACTCAA
*
1217448 ATGTAGGTAACCATGATACACTCAA
1 ATGTAGGTAACTATGATACACTCAA
1217473 ATGTAGGTAACTATGATACA
1 ATGTAGGTAACTATGATACA
1217493 TCACCAGGAT
Statistics
Matches: 499, Mismatches: 35, Indels: 84
0.81 0.06 0.14
Matches are distributed among these distances:
19 47 0.09
21 6 0.01
23 6 0.01
25 366 0.73
26 2 0.00
27 3 0.01
31 2 0.00
32 2 0.00
33 65 0.13
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.29
Consensus pattern (25 bp):
ATGTAGGTAACTATGATACACTCAA
Found at i:1217182 original size:58 final size:58
Alignment explanation
Indices: 1217092--1217204 Score: 208
Period size: 58 Copynumber: 1.9 Consensus size: 58
1217082 ATACACTCAA
1217092 ATGTAGGTAACTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATATAC
1 ATGTAGGTAACTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATATAC
* *
1217150 ATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAGATATA
1 ATGTAGGTAACTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATA
1217205 GGTAACTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (58 bp):
ATGTAGGTAACTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATATAC
Found at i:1217225 original size:44 final size:42
Alignment explanation
Indices: 1217175--1217296 Score: 136
Period size: 44 Copynumber: 3.0 Consensus size: 42
1217165 ATACACTCAA
1217175 ATGTAGGTAACTATGATACACTCAGATATAGGTAACTATGATAC
1 ATGTAGGTAACTATGATACACTCA-AT-TAGGTAACTATGATAC
1217219 ATGTAGGTAACTATGATACACTC----A---AA-TAT-ATAC
1 ATGTAGGTAACTATGATACACTCAATTAGGTAACTATGATAC
*
1217252 ATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATAC
1 ATGTAGGTAACTATGATACACTC-AAT-TAGGTAACTATGATAC
1217296 A
1 A
1217297 CTCAAATATA
Statistics
Matches: 66, Mismatches: 1, Indels: 22
0.74 0.01 0.25
Matches are distributed among these distances:
33 26 0.39
34 3 0.05
35 2 0.03
38 1 0.02
39 1 0.02
42 2 0.03
43 3 0.05
44 28 0.42
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGTAGGTAACTATGATACACTCAATTAGGTAACTATGATAC
Found at i:1217252 original size:58 final size:55
Alignment explanation
Indices: 1217203--1217391 Score: 158
Period size: 44 Copynumber: 3.8 Consensus size: 55
1217193 CACTCAGATA
1217203 TAGGTAACTATGAT-A-C-ATGTAGGTAACTATGATACACTCAAATATATACATG
1 TAGGTAACTATGATAACCAATGTAGGTAACTATGATACACTCAAATATATACATG
*
1217255 TAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTC--A-A-AT--A--
1 TAGGTAACTATGATA-AC-C-AATGTAGGTAACTATGATACACTCAAATATATACATG
*
1217305 TAGGTAACTATGAT-A-C-ATGTAGGTAACTCTGATACACTC--A-A-AT--A--
1 TAGGTAACTATGATAACCAATGTAGGTAACTATGATACACTCAAATATATACATG
1217349 TAGGTAACTATGAT-A-C-ATGTAGGTAACTATGATACACTCAAAT
1 TAGGTAACTATGATAACCAATGTAGGTAACTATGATACACTCAAAT
1217392 GTAGGTAACT
Statistics
Matches: 124, Mismatches: 4, Indels: 23
0.82 0.03 0.15
Matches are distributed among these distances:
44 65 0.52
46 2 0.02
48 1 0.01
50 13 0.10
52 14 0.11
54 3 0.02
55 1 0.01
56 2 0.02
58 23 0.19
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (55 bp):
TAGGTAACTATGATAACCAATGTAGGTAACTATGATACACTCAAATATATACATG
Found at i:1217272 original size:102 final size:105
Alignment explanation
Indices: 1216942--1217350 Score: 567
Period size: 102 Copynumber: 4.0 Consensus size: 105
1216932 ATACACTCAA
* * *
1216942 ATGTAGATAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATGTAGGAAACTATG
1 ATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATAGGTAACTATG
* * *
1217007 ATACACTCAAATGTAGATAATTATGTTACACTC------A-A-
66 ATA-AC-C-AATGTAGGTAACTATGATACACTCAAATATATAC
* * *
1217042 ATGTAGGTAACTATGATACACTCAAGTGTAGGTAACTATGATACACTCAAATGTAGGTAACTATG
1 ATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATAGGTAACTATG
1217107 ATACACTCAAATGTAGGTAACTATGATACACTCAAATATATAC
66 ATA-AC-C-AATGTAGGTAACTATGATACACTCAAATATATAC
*
1217150 ATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAGATATAGGTAACTATG
1 ATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATAGGTAACTATG
1217215 AT-A-C-ATGTAGGTAACTATGATACACTCAAATATATAC
66 ATAACCAATGTAGGTAACTATGATACACTCAAATATATAC
1217252 ATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATAGGTAACTATG
1 ATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATAGGTAACTATG
*
1217317 AT-A-C-ATGTAGGTAACTCTGATACACTCAAATATA
66 ATAACCAATGTAGGTAACTATGATACACTCAAATATA
1217351 GGTAACTATG
Statistics
Matches: 288, Mismatches: 13, Indels: 14
0.91 0.04 0.04
Matches are distributed among these distances:
100 91 0.32
102 130 0.45
104 1 0.00
106 2 0.01
107 1 0.00
108 63 0.22
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (105 bp):
ATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATAGGTAACTATG
ATAACCAATGTAGGTAACTATGATACACTCAAATATATAC
Found at i:1217327 original size:44 final size:44
Alignment explanation
Indices: 1217277--1217409 Score: 248
Period size: 44 Copynumber: 3.0 Consensus size: 44
1217267 ATACACTCAA
1217277 ATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATAC
1 ATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATAC
*
1217321 ATGTAGGTAACTCTGATACACTCAAATATAGGTAACTATGATAC
1 ATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATAC
*
1217365 ATGTAGGTAACTATGATACACTCAAATGTAGGTAACTATGATAC
1 ATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATAC
1217409 A
1 A
1217410 CTCAAATATA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 86 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (44 bp):
ATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATAC
Found at i:1217344 original size:171 final size:168
Alignment explanation
Indices: 1217146--1217493 Score: 513
Period size: 171 Copynumber: 2.0 Consensus size: 168
1217136 ACTCAAATAT
* *
1217146 ATACATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAGATATAGGTAAC
1 ATACATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATACA-T--G---TAGGTAAC
* * *
1217211 TATGAT-A-C-ATGTAGGTAACTATGATACACTCAAATATATACATGTAGGTAATTATGATACAC
60 TATGATAACCAATGTAGGTAACTATGATACACTCAAATATATACATGAAGGTAACTATGAAACAC
*
1217273 TCAAATGTAGGTAACTATGATACACTCAAATATAGGTAACTATG
125 TCAAATGTAGGTAACCATGATACACTCAAATATAGGTAACTATG
*
1217317 ATACATGTAGGTAACTCTGATACACTCAAATATAGGTAACTATGATACATGTAGGTAACTATGAT
1 ATACATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATACATGTAGGTAACTATGAT
1217382 ACACTCAAATGTAGGTAACTATGATACACTCAAATATATACATGAAGGTAACTATGAAACACTCA
66 A-AC-C-AATGTAGGTAACTATGATACACTCAAATATATACATGAAGGTAACTATGAAACACTCA
* *
1217447 GATGTAGGTAACCATGATACACTCAAATGTAGGTAACTATG
128 AATGTAGGTAACCATGATACACTCAAATATAGGTAACTATG
1217488 ATACAT
1 ATACAT
1217494 CACCAGGATA
Statistics
Matches: 162, Mismatches: 9, Indels: 12
0.89 0.05 0.07
Matches are distributed among these distances:
165 14 0.09
167 1 0.01
168 1 0.01
169 1 0.01
170 1 0.01
171 144 0.89
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.29
Consensus pattern (168 bp):
ATACATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATACATGTAGGTAACTATGAT
AACCAATGTAGGTAACTATGATACACTCAAATATATACATGAAGGTAACTATGAAACACTCAAAT
GTAGGTAACCATGATACACTCAAATATAGGTAACTATG
Found at i:1217394 original size:69 final size:66
Alignment explanation
Indices: 1217248--1217419 Score: 206
Period size: 69 Copynumber: 2.5 Consensus size: 66
1217238 ACTCAAATAT
* *
1217248 ATACATGTAGGTAATTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATATAGGTAAC
1 ATACATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATA-AC-C-AATATAGGTAAC
1217313 TATG
63 TATG
* *
1217317 ATACATGTAGGTAACTCTGATACACTCAAATATAGGTAACTATGAT-A-C-ATGTAGGTAACTAT
1 ATACATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATAACCAATATAGGTAACTAT
1217379 G
66 G
1217380 ATACACTCAAATGTAGGTAACTATGATACACTCAAATATA
1 AT--A--C--ATGTAGGTAACTATGATACACTCAAATATA
1217420 TACATGAAGG
Statistics
Matches: 92, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
63 16 0.17
65 2 0.02
67 2 0.02
69 72 0.78
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (66 bp):
ATACATGTAGGTAACTATGATACACTCAAATATAGGTAACTATGATAACCAATATAGGTAACTAT
G
Found at i:1217436 original size:58 final size:58
Alignment explanation
Indices: 1217361--1217474 Score: 192
Period size: 58 Copynumber: 2.0 Consensus size: 58
1217351 GGTAACTATG
* * *
1217361 ATACATGTAGGTAACTATGATACACTCAAATGTAGGTAACTATGATACACTCAAATAT
1 ATACATGAAGGTAACTATGAAACACTCAAATGTAGGTAACCATGATACACTCAAATAT
*
1217419 ATACATGAAGGTAACTATGAAACACTCAGATGTAGGTAACCATGATACACTCAAAT
1 ATACATGAAGGTAACTATGAAACACTCAAATGTAGGTAACCATGATACACTCAAAT
1217475 GTAGGTAACT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (58 bp):
ATACATGAAGGTAACTATGAAACACTCAAATGTAGGTAACCATGATACACTCAAATAT
Found at i:1218233 original size:45 final size:45
Alignment explanation
Indices: 1218131--1219170 Score: 1413
Period size: 45 Copynumber: 23.1 Consensus size: 45
1218121 ACAACTCATT
** *
1218131 AGACTGTTGTAGACAACTTTTAGACCATAAGATAACGTATACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACG--TACACAAC
* * *
1218178 AGACTGTTGTAGACAACTACTTGACCATAACGTAACATACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
*
1218223 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACAAAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* * *
1218268 AGACTATTGTAGACAACTACTAGACTAAAAGGTAACGTACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* * * *
1218313 AGACCGTTATAGACAACTACTAGATCATAAAGTAACGTACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* * *
1218358 AGACAGTTCTAGACAACTACTAGACCATAAGGTAACGTACAAAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* * * * *
1218403 AGACTGTTGTAGACAACGACTAGACTATAAGATAAGGTACAGAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* * * *
1218448 AGACTGTTGTCGACAACTACTAGATCATAAGGTATCGTACATAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* *
1218493 AGACTGTTGTAGACAACTACTAGACCATAAGGTCACGTAAACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* *
1218538 AGACTGTTGTGGACAACTA-TATGACCATAAGGTAGCGTACACAAC
1 AGACTGTTGTAGACAACTACTA-GACCATAAGGTAACGTACACAAC
* *
1218583 AGACTGTTGTGGACAACTA-TATGACCATAAGGTAGCGTACACAAC
1 AGACTGTTGTAGACAACTACTA-GACCATAAGGTAACGTACACAAC
* *
1218628 AGACTGTTGTGGACAACTA-TATGACCATAAGGTAGCGTACACAAC
1 AGACTGTTGTAGACAACTACTA-GACCATAAGGTAACGTACACAAC
* *
1218673 AGACTGTTGTGGACAACTA-TATGACCATAAGGTAGCGTACACAAC
1 AGACTGTTGTAGACAACTACTA-GACCATAAGGTAACGTACACAAC
*
1218718 AGACTGTTGTAGACAACTACTAGACCATCAGGTAACGTACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* * * * * *
1218763 ATACTGTTGTATACAACTACTTGACTAAAAGGTAACATACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* * * * *
1218808 AGACTGTTGTAGACAACTACCAGACTAAAAGGTAACATACACAAT
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
*
1218853 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACATACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
*
1218898 ATACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* * * *
1218943 AGACTGTTGTAGACAACTACTAGACTAAAAGGTAACATACATAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* *
1218988 ATACTGTTGTAGACAACTACTAGACCAAAAGGTAACGTACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* *
1219033 AGACTGTTGTAGACAACTACTAGACCATACGGTAACATACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* * * *
1219078 ATACTGTTGTAGACAACTACTAGACCATACGGTAATGTAAACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
* * *
1219123 AGACTGTTGTAGATAACTACTAGACTATAAGGTAATGTACACAAC
1 AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
1219168 AGA
1 AGA
1219171 TGTCGACAAC
Statistics
Matches: 897, Mismatches: 94, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
44 2 0.00
45 862 0.96
46 2 0.00
47 31 0.03
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (45 bp):
AGACTGTTGTAGACAACTACTAGACCATAAGGTAACGTACACAAC
Found at i:1226915 original size:2 final size:2
Alignment explanation
Indices: 1226908--1226951 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
1226898 AGACTTATGT
* *
1226908 TC TC TC TC TC TC TC TC TC TC TGC -C TC TC TC TT TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC
1226950 TC
1 TC
1226952 CATAATATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.95
3 1 0.03
ACGTcount: A:0.00, C:0.45, G:0.02, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1227092 original size:10 final size:10
Alignment explanation
Indices: 1227077--1227181 Score: 104
Period size: 10 Copynumber: 10.1 Consensus size: 10
1227067 GCGTCGATTT
1227077 ACCCAAATGG
1 ACCCAAATGG
1227087 ACCCAAATGG
1 ACCCAAATGG
***
1227097 AATGTAAAAT-G
1 -A-CCCAAATGG
1227108 ACCCAAATGG
1 ACCCAAATGG
1227118 ACCCAAATGG
1 ACCCAAATGG
*
1227128 AGCACAAATGG
1 A-CCCAAATGG
1227139 ACCCAAATGG
1 ACCCAAATGG
1227149 AAACCCAAATGG
1 --ACCCAAATGG
**
1227161 AAACAAATGG
1 ACCCAAATGG
1227171 ACCCAAATGG
1 ACCCAAATGG
1227181 A
1 A
1227182 ATCACAAATG
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
9 4 0.05
10 48 0.62
11 11 0.14
12 14 0.18
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (10 bp):
ACCCAAATGG
Found at i:1227115 original size:31 final size:32
Alignment explanation
Indices: 1227077--1227181 Score: 139
Period size: 31 Copynumber: 3.3 Consensus size: 32
1227067 GCGTCGATTT
*
1227077 ACCCAAATGGACCCAAATGGAATGTA-AAAT-G
1 ACCCAAATGGACCCAAATGGAA-GCACAAATGG
1227108 ACCCAAATGGACCCAAATGG-AGCACAAATGG
1 ACCCAAATGGACCCAAATGGAAGCACAAATGG
1227139 ACCCAAATGGAAACCCAAATGGAA--ACAAATGG
1 ACCCAAATGG--ACCCAAATGGAAGCACAAATGG
1227171 ACCCAAATGGA
1 ACCCAAATGGA
1227182 ATCACAAATG
Statistics
Matches: 68, Mismatches: 1, Indels: 11
0.85 0.01 0.14
Matches are distributed among these distances:
29 2 0.03
30 6 0.09
31 31 0.46
32 18 0.26
33 10 0.15
34 1 0.01
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (32 bp):
ACCCAAATGGACCCAAATGGAAGCACAAATGG
Found at i:1227135 original size:21 final size:20
Alignment explanation
Indices: 1227077--1227181 Score: 104
Period size: 21 Copynumber: 5.0 Consensus size: 20
1227067 GCGTCGATTT
1227077 ACCCAAATGGACCCAAATGG
1 ACCCAAATGGACCCAAATGG
***
1227097 AATGTAAAAT-GACCCAAATGG
1 -A-CCCAAATGGACCCAAATGG
*
1227118 ACCCAAATGGAGCACAAATGG
1 ACCCAAATGGA-CCCAAATGG
1227139 ACCCAAATGGAAACCCAAATGG
1 ACCCAAATGG--ACCCAAATGG
**
1227161 AAACAAATGGACCCAAATGG
1 ACCCAAATGGACCCAAATGG
1227181 A
1 A
1227182 ATCACAAATG
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 30 0.43
22 20 0.29
23 1 0.01
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (20 bp):
ACCCAAATGGACCCAAATGG
Found at i:1227160 original size:22 final size:21
Alignment explanation
Indices: 1227108--1227194 Score: 95
Period size: 22 Copynumber: 4.0 Consensus size: 21
1227098 ATGTAAAATG
*
1227108 ACCCAAATGGACCCAAATGGA
1 ACCCAAATGGACACAAATGGA
* * *
1227129 GCACAAATGGACCCAAATGGAA
1 ACCCAAATGGACACAAATGG-A
*
1227151 ACCCAAATGGAAACAAATGG-
1 ACCCAAATGGACACAAATGGA
1227171 ACCCAAATGGAATCACAAATGGA
1 ACCCAAATGG-A-CACAAATGGA
1227194 A
1 A
1227195 ATAGAATGGC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 10 0.18
21 19 0.35
22 25 0.45
23 1 0.02
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (21 bp):
ACCCAAATGGACACAAATGGA
Found at i:1227646 original size:183 final size:182
Alignment explanation
Indices: 1227339--1227697 Score: 625
Period size: 183 Copynumber: 2.0 Consensus size: 182
1227329 TACAGCACTT
*
1227339 GGTACCACTTAACTATTAATAAAATCATATATTAACATTGTAACTACATCGTTGTAGAAACAGAA
1 GGTACCACTTAACTATTAATAAAATCATATATTAACATTGTAACTACATCGTTGTACAAACAGAA
1227404 ATAAGACTGTATTTAGAAACTGTTCCTATCGTGTTAAACACGACGCCCTACCAGGGCCCGGACTC
66 ATAAGACTGTATTTAGAAACTGTTCCTATCGTGTTAAACACGACGCCCTACCAGGGCCCGGACTC
* *
1227469 AGTTACCTCAAACAATCTTATTCTAA-AACCATT-TCATTAATAAGTTTTTATA
131 AGTTACCTCAAACAATCTTACTC-AAGAACAATTCT-ATTAATAAGTTTTTATA
1227521 GGTACCACTTAACTATTAAT-AAATCATATATTAACATTGTAACTACATCGTTGTACAAACAGAA
1 GGTACCACTTAACTATTAATAAAATCATATATTAACATTGTAACTACATCGTTGTACAAACAGAA
*
1227585 ATATCAGACTGTATTTAGAAACTGTTCCTATCGTGTTAAACACGACGCTCTACCAGGGCCCGGAC
66 ATA--AGACTGTATTTAGAAACTGTTCCTATCGTGTTAAACACGACGCCCTACCAGGGCCCGGAC
1227650 TCAGTTACCTCAAACAATCTTACTCAAGAACAATTCTATTAATAAGTT
129 TCAGTTACCTCAAACAATCTTACTCAAGAACAATTCTATTAATAAGTT
1227698 CTTTTATGAA
Statistics
Matches: 169, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
181 46 0.27
182 22 0.13
183 100 0.59
184 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (182 bp):
GGTACCACTTAACTATTAATAAAATCATATATTAACATTGTAACTACATCGTTGTACAAACAGAA
ATAAGACTGTATTTAGAAACTGTTCCTATCGTGTTAAACACGACGCCCTACCAGGGCCCGGACTC
AGTTACCTCAAACAATCTTACTCAAGAACAATTCTATTAATAAGTTTTTATA
Found at i:1228014 original size:10 final size:10
Alignment explanation
Indices: 1227999--1228072 Score: 76
Period size: 10 Copynumber: 7.0 Consensus size: 10
1227989 TGCCATTCAA
1227999 TTTCCATTTG
1 TTTCCATTTG
1228009 TTTCCATTTG
1 TTTCCATTTG
1228019 TGATTCCATTTG
1 T--TTCCATTTG
**
1228031 GGTCCATTTG
1 TTTCCATTTG
1228041 TTTCCATTTGGG
1 TTTCCATTT--G
1228053 TTTCCATTTG
1 TTTCCATTTG
**
1228063 GGTCCATTTG
1 TTTCCATTTG
1228073 GGTCATTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
10 35 0.65
12 19 0.35
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.51
Consensus pattern (10 bp):
TTTCCATTTG
Found at i:1228040 original size:32 final size:32
Alignment explanation
Indices: 1228001--1228103 Score: 138
Period size: 32 Copynumber: 3.2 Consensus size: 32
1227991 CCATTCAATT
1228001 TCCATTTGTTTCCATTTGTGATTCCATTTGGG
1 TCCATTTGTTTCCATTTGTGATTCCATTTGGG
* *
1228033 TCCATTTGTTTCCATTTGGGTTTCCATTTGGG
1 TCCATTTGTTTCCATTTGTGATTCCATTTGGG
** *
1228065 TCCATTTGGGT-CATTT-TACATTCCATTTGGG
1 TCCATTTGTTTCCATTTGT-GATTCCATTTGGG
1228096 TCCATTTG
1 TCCATTTG
1228104 GGTAAATCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
31 24 0.38
32 39 0.62
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.49
Consensus pattern (32 bp):
TCCATTTGTTTCCATTTGTGATTCCATTTGGG
Found at i:1228073 original size:10 final size:10
Alignment explanation
Indices: 1228023--1228106 Score: 80
Period size: 10 Copynumber: 8.1 Consensus size: 10
1228013 CATTTGTGAT
1228023 TCCATTTGGG
1 TCCATTTGGG
**
1228033 TCCATTTGTT
1 TCCATTTGGG
1228043 TCCATTTGGG
1 TCCATTTGGG
1228053 TTTCCATTTGGG
1 --TCCATTTGGG
1228065 TCCATTTGGG
1 TCCATTTGGG
***
1228075 T-CATTTTACAT
1 TCCA-TTT-GGG
1228086 TCCATTTGGG
1 TCCATTTGGG
1228096 TCCATTTGGG
1 TCCATTTGGG
1228106 T
1 T
1228107 AAATCGACGC
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
9 2 0.03
10 41 0.69
11 4 0.07
12 12 0.20
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (10 bp):
TCCATTTGGG
Found at i:1228073 original size:22 final size:22
Alignment explanation
Indices: 1228000--1228075 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
1227990 GCCATTCAAT
1228000 TTCCATTT--GTTTCCATTTGTG
1 TTCCATTTGGGTTTCCATTTG-G
*
1228021 ATTCCATTTGGG--TCCATTTGT
1 -TTCCATTTGGGTTTCCATTTGG
1228042 TTCCATTTGGGTTTCCATTTGG
1 TTCCATTTGGGTTTCCATTTGG
*
1228064 GTCCATTTGGGT
1 TTCCATTTGGGT
1228076 CATTTTACAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 11 0.23
22 35 0.74
24 1 0.02
ACGTcount: A:0.11, C:0.18, G:0.21, T:0.50
Consensus pattern (22 bp):
TTCCATTTGGGTTTCCATTTGG
Found at i:1240895 original size:24 final size:24
Alignment explanation
Indices: 1240845--1240931 Score: 108
Period size: 24 Copynumber: 3.8 Consensus size: 24
1240835 AAACGCAATG
*
1240845 TATTGCGTTTAATCGC--AA-AAA
1 TATTGCGTTTAAACGCAAAACAAA
*
1240866 TATTGCATTTAAACGCAAAACAAA
1 TATTGCGTTTAAACGCAAAACAAA
* * *
1240890 TATTGCGTTTAAACGCAAAGCTAT
1 TATTGCGTTTAAACGCAAAACAAA
1240914 TATTGCGTTTAAACGCAA
1 TATTGCGTTTAAACGCAA
1240932 TATATTTTGC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.25
23 2 0.04
24 41 0.72
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (24 bp):
TATTGCGTTTAAACGCAAAACAAA
Found at i:1241006 original size:21 final size:21
Alignment explanation
Indices: 1240740--1241062 Score: 196
Period size: 22 Copynumber: 15.0 Consensus size: 21
1240730 TTCGCATTGT
* *
1240740 ATTTTGCGTTTAAATGCAA-A
1 ATTTTGCGATTAAACGCAATA
** * *
1240760 AGATTGCGATAAAACGCAAAA
1 ATTTTGCGATTAAACGCAATA
* *
1240781 AGTATTGCGATTAAACGCGAAGTGG
1 A-TTTTGCGATTAAACGC-AA-T-A
*
1240806 A--TTGCGTTTAAACGCAA-A
1 ATTTTGCGATTAAACGCAATA
* *
1240824 GTTTTGCGTTTAAACGCAAT-
1 ATTTTGCGATTAAACGCAATA
* * * * *
1240844 GTATTGCGTTTAATCGCAAAA
1 ATTTTGCGATTAAACGCAATA
* *
1240865 ATATTGC-ATTTAAACGCAAAACAA
1 ATTTTGCGA-TTAAACGC--AA-TA
* *
1240889 ATATTGCGTTTAAACGCAA-A
1 ATTTTGCGATTAAACGCAATA
*
1240909 GCTATTATTGCGTTTAAACGCAATA
1 ---ATT-TTGCGATTAAACGCAATA
*
1240934 TATTTTGCGAATAAACGCAA-A
1 -ATTTTGCGATTAAACGCAATA
1240955 AGTTTTTGCGATTAAACGCAATA
1 A--TTTTGCGATTAAACGCAATA
1240978 AGTTTTGCGATTAAACGCAATA
1 A-TTTTGCGATTAAACGCAATA
* *
1241000 ATTTTGCGATTAAATGCAATG
1 ATTTTGCGATTAAACGCAATA
1241021 ATTTTGCGATTAAACGCAATGA
1 ATTTTGCGATTAAACGCAAT-A
*
1241043 TTTTTGCG-TTAAATCGCAAT
1 ATTTTGCGATTAAA-CGCAAT
1241063 TTATTCATTT
Statistics
Matches: 250, Mismatches: 29, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
20 49 0.20
21 60 0.24
22 94 0.38
23 12 0.05
24 33 0.13
25 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (21 bp):
ATTTTGCGATTAAACGCAATA
Found at i:1241038 original size:64 final size:65
Alignment explanation
Indices: 1240916--1241067 Score: 200
Period size: 64 Copynumber: 2.3 Consensus size: 65
1240906 AAAGCTATTA
*
1240916 TTGCGTTTAAACGCAATATATTTTGCGAATAAACGCAAAAGTTTTTGCGATTAAACGCAATAAGT
1 TTGCG-TTAAACGCAATATATTTTGCGAATAAACGCAAAAGATTTTGCGATTAAACGCAATAAGT
1240981 T
65 T
* * * * *
1240982 TTGCGATTAAACGCAATA-ATTTTGCGATTAAATGC-AATGATTTTGCGATTAAACGCAATGATT
1 TTGCG-TTAAACGCAATATATTTTGCGAATAAACGCAAAAGATTTTGCGATTAAACGCAATAAGT
1241045 T
65 T
*
1241046 TTGCGTTAAATCGCAATTTATT
1 TTGCGTTAAA-CGCAATATATT
1241068 CATTTGCTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
63 5 0.07
64 36 0.47
65 18 0.24
66 17 0.22
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (65 bp):
TTGCGTTAAACGCAATATATTTTGCGAATAAACGCAAAAGATTTTGCGATTAAACGCAATAAGTT
Found at i:1251620 original size:16 final size:16
Alignment explanation
Indices: 1251587--1251620 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1251577 TATCGAATTA
*
1251587 TATATATATGTATATG
1 TATATATATATATATG
*
1251603 TATATATATATATGTG
1 TATATATATATATATG
1251619 TA
1 TA
1251621 GACAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
TATATATATATATATG
Found at i:1257197 original size:150 final size:158
Alignment explanation
Indices: 1256970--1257407 Score: 561
Period size: 167 Copynumber: 2.8 Consensus size: 158
1256960 CCCAGAATAT
* * * *
1256970 TTTTTAAAGATTTTCTCTATATATTCCTCTGTAAAAATGCATCTCCCCCATTGTGACCCCACCCT
1 TTTTTAAAGATTTTCTCAATATATTTCTCTGTAAAAATTCATC-CCCCCATTGTGACCCCACCAT
* * * *
1257035 ACTCCTGAGGACCATGATTTAAACAAACTTAAATCTACACTATCTGAGGA-G-TT-T-G-AGC-T
65 ACCCCTG-GGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCTAGTAGCTT
* *
1257094 TCTGGCCT-AA-TGGTTATTAAGAAGAAGA
129 TCTGGCCTAAAGTAGTTATCAAGAAGAAGA
1257122 TTTTTAAAGA-TTTCTCAATATATTTCTCTGTAAAAATTCATCCCCCCATTGTGACCCCACCATA
1 TTTTTAAAGATTTTCTCAATATATTTCTCTGTAAAAATTCATCCCCCCATTGTGACCCCACCATA
*
1257186 CGCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCTACAAGTTA
66 C-CCCTGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTT-CT---AG-T-
1257251 CAGCTTTTCTGGCCTAAAGTAGTTATCAAGAAGAAGA
124 -AGC-TTTCTGGCCTAAAGTAGTTATCAAGAAGAAGA
*
1257288 TTTTTAAAGATTTTCTCAATATATTTCTCTGTAAAAATTCATCCCCCCATTGTGGCCCCACCATA
1 TTTTTAAAGATTTTCTCAATATATTTCTCTGTAAAAATTCATCCCCCCATTGTGACCCCACCATA
* ** *
1257353 CCCACTGGAATGATGATTTGAACAAATTTGAATCTACACTACCTGAGGATGCTTC
66 CCC-CTGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTC
1257408 CATACAAGTT
Statistics
Matches: 250, Mismatches: 17, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
150 61 0.24
151 33 0.13
152 12 0.05
154 1 0.00
158 1 0.00
162 3 0.01
164 9 0.04
165 2 0.01
166 29 0.12
167 99 0.40
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (158 bp):
TTTTTAAAGATTTTCTCAATATATTTCTCTGTAAAAATTCATCCCCCCATTGTGACCCCACCATA
CCCCTGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCTAGTAGCTTTC
TGGCCTAAAGTAGTTATCAAGAAGAAGA
Found at i:1257291 original size:166 final size:167
Alignment explanation
Indices: 1257093--1257440 Score: 571
Period size: 167 Copynumber: 2.1 Consensus size: 167
1257083 GAGTTTGAGC
* *
1257093 TTCTGGCCT-AATGGTTATTAAGAAGAAGATTTTTAAAGA-TTTCTCAATATATTTCTCTGTAAA
1 TTCTGGCCTAAATAGTTATCAAGAAGAAGATTTTTAAAGATTTTCTCAATATATTTCTCTGTAAA
*
1257156 AATTCATCCCCCCATTGTGACCCCACCATACGCC-CAGGGACCATGATTTGAACAAACTTGAATC
66 AATTCATCCCCCCATTGTGACCCCACCATAC-CCACAGGAACCATGATTTGAACAAACTTGAATC
1257220 TACACTACCTGAGGATGCTTCC-TACAAGTTACAGCTT
130 TACACTACCTGAGGATGCTTCCATACAAGTTACAGCTT
1257257 TTCTGGCCTAAAGTAGTTATCAAGAAGAAGATTTTTAAAGATTTTCTCAATATATTTCTCTGTAA
1 TTCTGGCCTAAA-TAGTTATCAAGAAGAAGATTTTTAAAGATTTTCTCAATATATTTCTCTGTAA
* * ** *
1257322 AAATTCATCCCCCCATTGTGGCCCCACCATACCCACTGGAATGATGATTTGAACAAATTTGAATC
65 AAATTCATCCCCCCATTGTGACCCCACCATACCCACAGGAACCATGATTTGAACAAACTTGAATC
1257387 TACACTACCTGAGGATGCTTCCATACAAGTTACAGCTT
130 TACACTACCTGAGGATGCTTCCATACAAGTTACAGCTT
1257425 TTCTGGCCT-AATAGTT
1 TTCTGGCCTAAATAGTT
1257441 TTGAGAAAAG
Statistics
Matches: 171, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
164 9 0.05
165 2 0.01
166 33 0.19
167 103 0.60
168 24 0.14
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (167 bp):
TTCTGGCCTAAATAGTTATCAAGAAGAAGATTTTTAAAGATTTTCTCAATATATTTCTCTGTAAA
AATTCATCCCCCCATTGTGACCCCACCATACCCACAGGAACCATGATTTGAACAAACTTGAATCT
ACACTACCTGAGGATGCTTCCATACAAGTTACAGCTT
Found at i:1259895 original size:16 final size:16
Alignment explanation
Indices: 1259870--1259961 Score: 103
Period size: 16 Copynumber: 5.5 Consensus size: 16
1259860 AATTGCAGAC
* *
1259870 GTTTAAGCCCCAACAT
1 GTTTAGGCCCCAAGAT
*
1259886 GTTTAGGCCCCAAGAC
1 GTTTAGGCCCCAAGAT
*
1259902 GGTTAGGCCCCAGGTAAGAT
1 GTTTAGGCCCC----AAGAT
*
1259922 GTTTAGTCCCCAAGAT
1 GTTTAGGCCCCAAGAT
1259938 GTTTAGGCCCCAAGAT
1 GTTTAGGCCCCAAGAT
1259954 GTTTAGGC
1 GTTTAGGC
1259962 ACCTGTTGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
16 51 0.80
20 13 0.20
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (16 bp):
GTTTAGGCCCCAAGAT
Found at i:1260133 original size:93 final size:93
Alignment explanation
Indices: 1259974--1260161 Score: 358
Period size: 93 Copynumber: 2.0 Consensus size: 93
1259964 CTGTTGTTTA
*
1259974 TAATAATAACTGATAGTTGAAAGAACATGGCTTTTAAGCACTTTTGAGCCAATAAATGCAATTTA
1 TAATAATAACTGATAGTTGAAAGAACATGGCTTTTAAGCACTTTGGAGCCAATAAATGCAATTTA
1260039 CTTTAATTTGTAGTAAACTAACAATCGT
66 CTTTAATTTGTAGTAAACTAACAATCGT
*
1260067 TAATAATAACTGATAGTTGAAAGAACATGGCTTTTAAGCACTTTGGAGCCAATAGATGCAATTTA
1 TAATAATAACTGATAGTTGAAAGAACATGGCTTTTAAGCACTTTGGAGCCAATAAATGCAATTTA
1260132 CTTTAATTTGTAGTAAACTAACAATCGT
66 CTTTAATTTGTAGTAAACTAACAATCGT
1260160 TA
1 TA
1260162 CGCAAACATA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (93 bp):
TAATAATAACTGATAGTTGAAAGAACATGGCTTTTAAGCACTTTGGAGCCAATAAATGCAATTTA
CTTTAATTTGTAGTAAACTAACAATCGT
Found at i:1262575 original size:1 final size:1
Alignment explanation
Indices: 1262569--1262593 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1262559 CCAAATAATT
1262569 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
1262594 TCTAAGCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1263573 original size:11 final size:11
Alignment explanation
Indices: 1263557--1263581 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1263547 ATTTTCAAAA
1263557 ACAATTTTATT
1 ACAATTTTATT
1263568 ACAATTTTATT
1 ACAATTTTATT
1263579 ACA
1 ACA
1263582 GTAACAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (11 bp):
ACAATTTTATT
Found at i:1268029 original size:15 final size:15
Alignment explanation
Indices: 1268009--1268038 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1267999 TGGCAGCCGC
1268009 CCGCCCGCCCGCCAT
1 CCGCCCGCCCGCCAT
1268024 CCGCCCGCCCGCCAT
1 CCGCCCGCCCGCCAT
1268039 TTTCACCATT
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:0.07, C:0.67, G:0.20, T:0.07
Consensus pattern (15 bp):
CCGCCCGCCCGCCAT
Found at i:1269701 original size:16 final size:16
Alignment explanation
Indices: 1269680--1269711 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1269670 GACAGACTAT
1269680 AGGAGAAAACGTACCC
1 AGGAGAAAACGTACCC
1269696 AGGAGAAAACGTACCC
1 AGGAGAAAACGTACCC
1269712 TATGAAAATC
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:0.44, C:0.25, G:0.25, T:0.06
Consensus pattern (16 bp):
AGGAGAAAACGTACCC
Done.