Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold22
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: 1964558
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 137786 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:1427542 original size:2 final size:2
Alignment explanation
Indices: 1427535--1427603 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1427525 NNNNNNNNNN
1427535 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
1427577 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 C
1427604 CTGTTCTGCC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1428430 original size:2 final size:2
Alignment explanation
Indices: 1428423--1428480 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1428413 TAATTTGCAG
1428423 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
1428465 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
1428481 CATACACGCC
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:1439563 original size:30 final size:29
Alignment explanation
Indices: 1439527--1439587 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
1439517 GTATATGTGC
1439527 TCTGAAAATCTGTGA-ATGAATCTTTTTCCT
1 TCTGAAAATCTG-GATATGAATC-TTTTCCT
*
1439557 TCTGAAAATCTGGATATTAATCTTTTCCT
1 TCTGAAAATCTGGATATGAATCTTTTCCT
1439586 TC
1 TC
1439588 CAGAATTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.44
Consensus pattern (29 bp):
TCTGAAAATCTGGATATGAATCTTTTCCT
Found at i:1447066 original size:84 final size:77
Alignment explanation
Indices: 1446896--1447136 Score: 229
Period size: 84 Copynumber: 3.1 Consensus size: 77
1446886 TCATCTGTTC
* ** * * * *
1446896 TACACCCAACCCTTGCACC-TCAATCA-CCCCCTACTCATCCAAATTCAACAAA-TTTTGCACTA
1 TACACCCAACCCTTGC-CCATCAATGACCCCCCCCCTTATCCCAATT-AAAAAACATTTGCACTA
**
1446958 ACAAA-TAAACCAAT
64 ACAAACT-AAGGAAT
* * *
1446972 TACACTCAACCCTTGCCCCTCAATGACCCCCCCCCCCCCCCTTCATTCCAATTAAAAAACATTTG
1 TACACCCAACCCTTGCCCATCAATGA------CCCCCCCCCTT-ATCCCAATTAAAAAACATTTG
1447037 CACTAACAAACTAAGGAAT
59 CACTAACAAACTAAGGAAT
* * *
1447056 TACACCCAACCCTTGCCCATCAATGACCCCCCTCCTTATCCCAATTCAAAAACATTTGCATTAAC
1 TACACCCAACCCTTGCCCATCAATGACCCCCCCCCTTATCCCAATTAAAAAACATTTGCACTAAC
1447121 AAACTAAGGAAT
66 AAACTAAGGAAT
1447133 TACA
1 TACA
1447137 TTTTTTCCAG
Statistics
Matches: 137, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
75 2 0.01
76 21 0.15
77 41 0.30
78 10 0.07
83 12 0.09
84 50 0.36
85 1 0.01
ACGTcount: A:0.35, C:0.37, G:0.05, T:0.22
Consensus pattern (77 bp):
TACACCCAACCCTTGCCCATCAATGACCCCCCCCCTTATCCCAATTAAAAAACATTTGCACTAAC
AAACTAAGGAAT
Found at i:1447677 original size:180 final size:180
Alignment explanation
Indices: 1447369--1448452 Score: 1875
Period size: 180 Copynumber: 6.0 Consensus size: 180
1447359 GGCTGCCAAA
* *
1447369 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTCCAAGATAGGAAGTTGTTGTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
* *
1447434 GATCAATTGTACATATATCAGAGGTGTGCATTTTGCTAGGATTTTGATTTCTAATAGTTTATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTAATAATTTATGAA
*
1447499 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
* * * *
1447549 AGGGTACCCTCATTGTACAGATAACTCCTCCTACAGTTTTCAAGATATGATGTTGTTGTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
* *
1447614 GATCAATTGTACATATATCAGAAGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTAATAATTTATGAA
*
1447679 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
* *
1447729 AGGGTACCCTCATTGTACAGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
*
1447794 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCAATAATTTATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTAATAATTTATGAA
*
1447859 AAAAATACTAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
* *
1447909 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGGA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
* * *
1447974 GATCAATTGTACATATATCAGAGGTGTGCATATTGTTAGGATTTTGATTTCTGATAATTAATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTAATAATTTATGAA
* *
1448039 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTTGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
*
1448089 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGATTTT-AAGATAAGAAGTTGTTCTTTTGC
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAG-TTTTCAAGATAGGAAGTTGTTCTTTTGC
* *
1448153 AGATCAATTGTACATATATCAGAGGTGTGCATATTGTTAGGATTTTGATTTCCAATAATTTATGA
65 AGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTAATAATTTATGA
*
1448218 AAAAAATACTAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
130 AAAAAATACCAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
*
1448269 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGATTTT-AAGATAAGAAGTTGTTCTTTTGC
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAG-TTTTCAAGATAGGAAGTTGTTCTTTTGC
*
1448333 AGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGA
65 AGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTAATAATTTATGA
1448398 AAAAAATACCAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
130 AAAAAATACCAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
1448449 AGGG
1 AGGG
1448453 GTACACCATT
Statistics
Matches: 864, Mismatches: 39, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
180 860 1.00
181 4 0.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (180 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTAATAATTTATGAA
AAAAATACCAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
Found at i:1449243 original size:35 final size:35
Alignment explanation
Indices: 1449199--1449692 Score: 855
Period size: 35 Copynumber: 14.1 Consensus size: 35
1449189 CCTACCCGCG
*
1449199 CTCATCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
*** *
1449234 CTCACCAGTAATCAGGTATGTCAGGTATACAGGCT
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
*
1449269 CTTACCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
*
1449304 CTCATCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
*
1449339 CTCACCAGTAATCAGGTATGTCAGGTAAACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
*
1449374 CTCCCCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
*
1449409 CTTACCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
*
1449444 CTCACCAGTAAAT-AGGTATGTCAGGTAAACCCACC
1 CTCACCAGT-AATCAGGTATGTCAGGTATACCCACC
1449479 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
1449514 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
*
1449549 CTCATCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
1449584 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
1449619 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
*
1449654 CTCATCAGTAATCAGGTATGTCAGGTATACCCACC
1 CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
1449689 CTCA
1 CTCA
1449693 NNNNNNNNNN
Statistics
Matches: 433, Mismatches: 24, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
34 3 0.01
35 427 0.99
36 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (35 bp):
CTCACCAGTAATCAGGTATGTCAGGTATACCCACC
Found at i:1454366 original size:68 final size:69
Alignment explanation
Indices: 1454291--1454426 Score: 175
Period size: 70 Copynumber: 2.0 Consensus size: 69
1454281 CTGACATGTT
* * * *
1454291 CATGTACATGTA-TGTCTATGAAAAGATAAGGAATGTTTCTTTTGTTTTGATAGATATGCTAGGT
1 CATGTACATGTAGTGTCTATGAAAAGATAAGGAATGTTTCTTTTATGTTGACAGACATGCTAGGT
1454355 TGTA
66 TGTA
* * * * *
1454359 CATGTACATGTATGTGTCTGTGGAAAGATTAGGACTGTTTCTTTTATGTTGGCAGACATGCTAGG
1 CATGTACATGTA-GTGTCTATGAAAAGATAAGGAATGTTTCTTTTATGTTGACAGACATGCTAGG
1454424 TTG
65 TTG
1454427 GTGTCCCTGC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 12 0.21
70 45 0.79
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.40
Consensus pattern (69 bp):
CATGTACATGTAGTGTCTATGAAAAGATAAGGAATGTTTCTTTTATGTTGACAGACATGCTAGGT
TGTA
Found at i:1458219 original size:32 final size:32
Alignment explanation
Indices: 1458170--1458491 Score: 500
Period size: 32 Copynumber: 10.1 Consensus size: 32
1458160 TTTGTAGACT
*
1458170 GCCATCTCACTATCATCATCATATGTAAGTCA
1 GCCATCTCACTACCATCATCATATGTAAGTCA
** *
1458202 GTTATCTCAGTACCATCATCATATGTAAGTCA
1 GCCATCTCACTACCATCATCATATGTAAGTCA
* * *
1458234 GCTATCTCAGTACCATCATCATATGAAAGTCA
1 GCCATCTCACTACCATCATCATATGTAAGTCA
*
1458266 GTCATCTCACTACCATCATCATATGTAAGTCA
1 GCCATCTCACTACCATCATCATATGTAAGTCA
*
1458298 GCCATCTCACTACCATCATCTTATGTAAGTCA
1 GCCATCTCACTACCATCATCATATGTAAGTCA
1458330 GCCATCTCACTACCATCATCATATGTAAGTCA
1 GCCATCTCACTACCATCATCATATGTAAGTCA
1458362 GCCATCTCACTACCATCATCATATGTAAGTCA
1 GCCATCTCACTACCATCATCATATGTAAGTCA
**
1458394 GCCATCTCACTACCATCATCATACATAAGTCA
1 GCCATCTCACTACCATCATCATATGTAAGTCA
**
1458426 GCCATCTCACTACCATCATCATACATAAGTCA
1 GCCATCTCACTACCATCATCATATGTAAGTCA
* * *
1458458 GCCAGCTCACGACCATCGTCATATGTAAGTCA
1 GCCATCTCACTACCATCATCATATGTAAGTCA
1458490 GC
1 GC
1458492 TACAATAAAC
Statistics
Matches: 270, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 270 1.00
ACGTcount: A:0.31, C:0.30, G:0.11, T:0.28
Consensus pattern (32 bp):
GCCATCTCACTACCATCATCATATGTAAGTCA
Found at i:1458803 original size:2 final size:2
Alignment explanation
Indices: 1458796--1458864 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
1458786 TTAGTTTGAA
1458796 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
*
1458838 CT CT CT CT CT CT CT CT GT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1458865 AAAAAGCTGC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.49, G:0.01, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1463108 original size:26 final size:26
Alignment explanation
Indices: 1463072--1463121 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1463062 AGACGCCATC
1463072 GTCAAACTAGGTGTGGACAGGTAAGA
1 GTCAAACTAGGTGTGGACAGGTAAGA
*
1463098 GTCAAACTAGGTGTGGATAGGTAA
1 GTCAAACTAGGTGTGGACAGGTAA
1463122 CAAACTCCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.10, G:0.34, T:0.22
Consensus pattern (26 bp):
GTCAAACTAGGTGTGGACAGGTAAGA
Found at i:1464277 original size:25 final size:25
Alignment explanation
Indices: 1464238--1464607 Score: 473
Period size: 25 Copynumber: 14.8 Consensus size: 25
1464228 TGGTCGTGTT
1464238 CCAGGTACTGTAGTGTAATATGTAC
1 CCAGGTACTGTAGTGTAATATGTAC
* * *
1464263 CTTA-ATACTATAGTGTAATATGTAC
1 C-CAGGTACTGTAGTGTAATATGTAC
* ** *
1464288 ACTA-GTACTCCAGTGTAATATGTTC
1 -CCAGGTACTGTAGTGTAATATGTAC
* *
1464313 ACTA-GTACTATAGTGTAATATGTAC
1 -CCAGGTACTGTAGTGTAATATGTAC
*
1464338 CCTA-GTACTGTGGTGTAATATGTAC
1 CC-AGGTACTGTAGTGTAATATGTAC
1464363 CCAGGTACTGTAGTGTAATATGTAC
1 CCAGGTACTGTAGTGTAATATGTAC
1464388 CCAGGTACTGTAGTGTAATATGTAC
1 CCAGGTACTGTAGTGTAATATGTAC
*
1464413 CCATGTACTGTAGTGTAATATGTAC
1 CCAGGTACTGTAGTGTAATATGTAC
*
1464438 CCAGGTTCTGTAGTGTAATATGTAC
1 CCAGGTACTGTAGTGTAATATGTAC
*
1464463 CCAGGTTCTGTAGTGTAATATGTAC
1 CCAGGTACTGTAGTGTAATATGTAC
*
1464488 CCTA-GTACTCTAGTGTAATATGTAC
1 CC-AGGTACTGTAGTGTAATATGTAC
1464513 CCAGGTACTGTAGTGTAATATGTAC
1 CCAGGTACTGTAGTGTAATATGTAC
1464538 CCAGGTACTGTAGTGTAATATGTAC
1 CCAGGTACTGTAGTGTAATATGTAC
* **
1464563 TCTTGTACTGTAGTGTAATATGTAC
1 CCAGGTACTGTAGTGTAATATGTAC
* *
1464588 CCTA-GTGCAGTAGTGTAATA
1 CC-AGGTACTGTAGTGTAATA
1464608 ATCTTGGATT
Statistics
Matches: 311, Mismatches: 27, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
24 3 0.01
25 305 0.98
26 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (25 bp):
CCAGGTACTGTAGTGTAATATGTAC
Found at i:1464371 original size:75 final size:75
Alignment explanation
Indices: 1464238--1464607 Score: 523
Period size: 75 Copynumber: 4.9 Consensus size: 75
1464228 TGGTCGTGTT
* * * * **
1464238 CCAGGTACTGTAGTGTAATATGTACCTTAATACTATAGTGTAATATGTACACTA-GTACTCCAGT
1 CCAGGTACTGTAGTGTAATATGTACCCTAGTACTGTAGTGTAATATGTAC-CCAGGTACTGTAGT
*
1464302 GTAATATGTTC
65 GTAATATGTAC
* * *
1464313 ACTA-GTACTATAGTGTAATATGTACCCTAGTACTGTGGTGTAATATGTACCCAGGTACTGTAGT
1 -CCAGGTACTGTAGTGTAATATGTACCCTAGTACTGTAGTGTAATATGTACCCAGGTACTGTAGT
1464377 GTAATATGTAC
65 GTAATATGTAC
*
1464388 CCAGGTACTGTAGTGTAATATGTACCC-ATGTACTGTAGTGTAATATGTACCCAGGTTCTGTAGT
1 CCAGGTACTGTAGTGTAATATGTACCCTA-GTACTGTAGTGTAATATGTACCCAGGTACTGTAGT
1464452 GTAATATGTAC
65 GTAATATGTAC
* *
1464463 CCAGGTTCTGTAGTGTAATATGTACCCTAGTACTCTAGTGTAATATGTACCCAGGTACTGTAGTG
1 CCAGGTACTGTAGTGTAATATGTACCCTAGTACTGTAGTGTAATATGTACCCAGGTACTGTAGTG
1464528 TAATATGTAC
66 TAATATGTAC
* * * *
1464538 CCAGGTACTGTAGTGTAATATGTACTCTTGTACTGTAGTGTAATATGTACCCTA-GTGCAGTAGT
1 CCAGGTACTGTAGTGTAATATGTACCCTAGTACTGTAGTGTAATATGTACCC-AGGTACTGTAGT
1464602 GTAATA
65 GTAATA
1464608 ATCTTGGATT
Statistics
Matches: 266, Mismatches: 23, Indels: 11
0.89 0.08 0.04
Matches are distributed among these distances:
74 5 0.02
75 257 0.97
76 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (75 bp):
CCAGGTACTGTAGTGTAATATGTACCCTAGTACTGTAGTGTAATATGTACCCAGGTACTGTAGTG
TAATATGTAC
Found at i:1469414 original size:2 final size:2
Alignment explanation
Indices: 1469407--1469446 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1469397 AAAGAGCACC
1469407 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
1469447 GGGCTTACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1473797 original size:13 final size:13
Alignment explanation
Indices: 1473779--1473805 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1473769 TTAATTTCTT
1473779 TTTCCCATTGTTG
1 TTTCCCATTGTTG
1473792 TTTCCCATTGTTG
1 TTTCCCATTGTTG
1473805 T
1 T
1473806 ATTATGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.22, G:0.15, T:0.56
Consensus pattern (13 bp):
TTTCCCATTGTTG
Found at i:1476428 original size:20 final size:21
Alignment explanation
Indices: 1476403--1476447 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1476393 CACAGGATCA
1476403 AAAACAAAT-TTTTTATCAAT
1 AAAACAAATGTTTTTATCAAT
* * *
1476423 AAAACATATGTTTTTGTCATT
1 AAAACAAATGTTTTTATCAAT
1476444 AAAA
1 AAAA
1476448 TTCAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (21 bp):
AAAACAAATGTTTTTATCAAT
Found at i:1477294 original size:22 final size:22
Alignment explanation
Indices: 1477240--1477287 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1477230 AGTTTTTCTC
1477240 TGCA-AATATTTAATAGCTTCA
1 TGCAGAATATTTAATAGCTTCA
*
1477261 TTCAGAATATTTAATAGCTTCA
1 TGCAGAATATTTAATAGCTTCA
1477283 TGCAG
1 TGCAG
1477288 CTCATTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (22 bp):
TGCAGAATATTTAATAGCTTCA
Found at i:1490351 original size:21 final size:22
Alignment explanation
Indices: 1490327--1490384 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
1490317 TTTCTATCAA
1490327 ATATGTCGACATGCAAGATA-T
1 ATATGTCGACATGCAAGATAGT
*
1490348 ATATGTTGACATGCAAGATAGT
1 ATATGTCGACATGCAAGATAGT
*
1490370 -TATGTCAACATGCAA
1 ATATGTCGACATGCAA
1490385 CATAACTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (22 bp):
ATATGTCGACATGCAAGATAGT
Found at i:1490576 original size:21 final size:21
Alignment explanation
Indices: 1490552--1490614 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1490542 TTGACATGCA
1490552 ATTTATAAGTTGCATGTCAAC
1 ATTTATAAGTTGCATGTCAAC
* *
1490573 ATTTAT--CTCGCATGTCAAC
1 ATTTATAAGTTGCATGTCAAC
* *
1490592 A-TAACTAAGTTGCGTGTCAAC
1 ATTTA-TAAGTTGCATGTCAAC
1490613 AT
1 AT
1490615 ATTTATCTCG
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.06
19 13 0.41
21 17 0.53
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATTTATAAGTTGCATGTCAAC
Found at i:1490615 original size:21 final size:21
Alignment explanation
Indices: 1490582--1490860 Score: 184
Period size: 21 Copynumber: 13.0 Consensus size: 21
1490572 CATTTATCTC
1490582 GCATGTCAACATAACTAAGTT
1 GCATGTCAACATAACTAAGTT
* ** ** *
1490603 GCGTGTCAACATATTTATCTC
1 GCATGTCAACATAACTAAGTT
* *
1490624 GCATGTGAACGTAACTAAGTT
1 GCATGTCAACATAACTAAGTT
* * *
1490645 GCATGTCGACATAAATAAGTA
1 GCATGTCAACATAACTAAGTT
* *
1490666 GCATGTGAACATAACTAAGCT
1 GCATGTCAACATAACTAAGTT
**
1490687 GCATGTGGACATAACTAAGTT
1 GCATGTCAACATAACTAAGTT
* ** ** *
1490708 GCATGTCAGCATATTTATCTC
1 GCATGTCAACATAACTAAGTT
* * *
1490729 GCATATGAACGTAACTAAGTT
1 GCATGTCAACATAACTAAGTT
* * *
1490750 GCATGTCGACATAAATAAGTA
1 GCATGTCAACATAACTAAGTT
1490771 GCATGTGAACATACATGTAACTAAGTT
1 GCATGT---CA-ACA--TAACTAAGTT
**
1490798 GCATGTGGACATAACTAAGTT
1 GCATGTCAACATAACTAAGTT
* *
1490819 GCATTTC-ACAT-ATTGAAGTT
1 GCATGTCAACATAACT-AAGTT
* *
1490839 GCATGTTAACATAAATAAGTT
1 GCATGTCAACATAACTAAGTT
1490860 G
1 G
1490861 TATTTCGACA
Statistics
Matches: 189, Mismatches: 60, Indels: 18
0.71 0.22 0.07
Matches are distributed among these distances:
19 2 0.01
20 14 0.07
21 150 0.79
22 2 0.01
23 3 0.02
24 1 0.01
25 3 0.02
27 14 0.07
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (21 bp):
GCATGTCAACATAACTAAGTT
Found at i:1490639 original size:42 final size:42
Alignment explanation
Indices: 1490557--1490692 Score: 168
Period size: 42 Copynumber: 3.3 Consensus size: 42
1490547 ATGCAATTTA
*
1490557 TAAGTTGCATGTCAAC--ATTTATCTCGCATGTCAACATAAC
1 TAAGTTGCATGTCAACATATTTATCTCGCATGTGAACATAAC
* *
1490597 TAAGTTGCGTGTCAACATATTTATCTCGCATGTGAACGTAAC
1 TAAGTTGCATGTCAACATATTTATCTCGCATGTGAACATAAC
* ** ** *
1490639 TAAGTTGCATGTCGACATAAATAAGTAGCATGTGAACATAAC
1 TAAGTTGCATGTCAACATATTTATCTCGCATGTGAACATAAC
*
1490681 TAAGCTGCATGT
1 TAAGTTGCATGT
1490693 GGACATAACT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
40 15 0.18
42 67 0.82
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (42 bp):
TAAGTTGCATGTCAACATATTTATCTCGCATGTGAACATAAC
Found at i:1490705 original size:105 final size:108
Alignment explanation
Indices: 1490590--1490884 Score: 391
Period size: 105 Copynumber: 2.7 Consensus size: 108
1490580 TCGCATGTCA
*
1490590 ACATAACTAAGTTGCGTGTCAACATATTTATCTCGCATGTGAACGTAACTAAGTTGCATGTCGAC
1 ACATAACTAAGTTGCATGTCAACATATTTATCTCGCATGTGAACGTAACTAAGTTGCATGTCGAC
1490655 ATAAATAAGTAGCATGTG-A-ACA-TAACTAAGCTGCATGTGG
66 ATAAATAAGTAGCATGTGAATACAGTAACTAAGCTGCATGTGG
* *
1490695 ACATAACTAAGTTGCATGTCAGCATATTTATCTCGCATATGAACGTAACTAAGTTGCATGTCGAC
1 ACATAACTAAGTTGCATGTCAACATATTTATCTCGCATGTGAACGTAACTAAGTTGCATGTCGAC
*
1490760 ATAAATAAGTAGCATGTGAACATACATGTAACTAAGTTGCATGTGG
66 ATAAATAAGTAGCATGTG-A-ATACA-GTAACTAAGCTGCATGTGG
* * ** * * * * * *
1490806 ACATAACTAAGTTGCATTTC-ACATATTGAAGTTGCATGTTAACATAAATAAGTTGTATTTCGAC
1 ACATAACTAAGTTGCATGTCAACATATTTATCTCGCATGTGAACGTAACTAAGTTGCATGTCGAC
* *
1490870 ATAGATAAATAGCAT
66 ATAAATAAGTAGCAT
1490885 TTAGCATCCT
Statistics
Matches: 166, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
105 80 0.48
108 1 0.01
109 3 0.02
110 46 0.28
111 36 0.22
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (108 bp):
ACATAACTAAGTTGCATGTCAACATATTTATCTCGCATGTGAACGTAACTAAGTTGCATGTCGAC
ATAAATAAGTAGCATGTGAATACAGTAACTAAGCTGCATGTGG
Found at i:1490851 original size:41 final size:42
Alignment explanation
Indices: 1490793--1490872 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 42
1490783 ACATGTAACT
* *
1490793 AAGTTGCATGTGGACATAACTAAGTTGCATTTC-ACATATTG
1 AAGTTGCATGTGAACATAAATAAGTTGCATTTCGACATATTG
* *
1490834 AAGTTGCATGTTAACATAAATAAGTTGTATTTCGACATA
1 AAGTTGCATGTGAACATAAATAAGTTGCATTTCGACATA
1490873 GATAAATAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 29 0.85
42 5 0.15
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (42 bp):
AAGTTGCATGTGAACATAAATAAGTTGCATTTCGACATATTG
Found at i:1491014 original size:42 final size:42
Alignment explanation
Indices: 1490945--1491024 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
1490935 ATTGCAATTT
*
1490945 TCTTGCATGTCAACATAGTTACGTTGCATGTTGACATAACTA
1 TCTTGCATGTCAACATAGTTACGTTGCATGTCGACATAACTA
* *
1490987 TCTTGCATGTCAACTTATTTATC-TTGCATGTCGACATA
1 TCTTGCATGTCAACATAGTTA-CGTTGCATGTCGACATA
1491025 TTAATATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (42 bp):
TCTTGCATGTCAACATAGTTACGTTGCATGTCGACATAACTA
Found at i:1491026 original size:21 final size:21
Alignment explanation
Indices: 1490941--1491026 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 21
1490931 TTTGATTGCA
1490941 ATTT-TCTTGCATGTCAACAT
1 ATTTATCTTGCATGTCAACAT
* **
1490961 AGTTA-CGTTGCATGTTGACAT
1 ATTTATC-TTGCATGTCAACAT
** *
1490982 AACTATCTTGCATGTCAACTT
1 ATTTATCTTGCATGTCAACAT
*
1491003 ATTTATCTTGCATGTCGACAT
1 ATTTATCTTGCATGTCAACAT
1491024 ATT
1 ATT
1491027 AATATTTGAT
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
20 4 0.08
21 46 0.90
22 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (21 bp):
ATTTATCTTGCATGTCAACAT
Found at i:1494097 original size:2 final size:2
Alignment explanation
Indices: 1494090--1494142 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1494080 GGTCTTCGAG
1494090 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
1494132 GA GA GA GA GA G
1 GA GA GA GA GA G
1494143 TTTGTTTATA
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1507110 original size:2 final size:2
Alignment explanation
Indices: 1507103--1507183 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
1507093 TACATATCTC
1507103 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
1507145 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1507184 TNNNNNNNNN
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1507247 original size:2 final size:2
Alignment explanation
Indices: 1507240--1507267 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1507230 GAAAGAAAAG
1507240 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
1507268 TTTTGTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1510812 original size:2 final size:2
Alignment explanation
Indices: 1510805--1510852 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1510795 TAGTCAAAAT
1510805 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
1510847 GA GA GA
1 GA GA GA
1510853 TTTTGCATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1513679 original size:4 final size:4
Alignment explanation
Indices: 1513670--1513877 Score: 375
Period size: 4 Copynumber: 52.5 Consensus size: 4
1513660 CCAGCACTTG
1513670 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
* *
1513718 GATA GATA GATA GATA GATA GATA GAAA GATA TATA GATA GAT- GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
*
1513765 GATC GATA GATA GATA GATA GATA GATA GATA GATA GAT- GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1513812 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1513860 GATA GATA GATA GATA GA
1 GATA GATA GATA GATA GA
1513878 ATGATAACAT
Statistics
Matches: 196, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
3 6 0.03
4 190 0.97
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:1514802 original size:8 final size:8
Alignment explanation
Indices: 1514788--1514862 Score: 78
Period size: 8 Copynumber: 9.4 Consensus size: 8
1514778 GGAATCACCT
1514788 TGTCCGTC
1 TGTCCGTC
*
1514796 CGTCCGTC
1 TGTCCGTC
*
1514804 TGTCTGTC
1 TGTCCGTC
1514812 TGTCCGTC
1 TGTCCGTC
*
1514820 TGTCTGTC
1 TGTCCGTC
*
1514828 TGTCTGTC
1 TGTCCGTC
*
1514836 TGTCTGTC
1 TGTCCGTC
*
1514844 TGTCTGTC
1 TGTCCGTC
* *
1514852 CGTCTGTC
1 TGTCCGTC
1514860 TGT
1 TGT
1514863 GCAATCGTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 60 1.00
ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44
Consensus pattern (8 bp):
TGTCCGTC
Found at i:1514824 original size:4 final size:4
Alignment explanation
Indices: 1514801--1514862 Score: 106
Period size: 4 Copynumber: 15.5 Consensus size: 4
1514791 CCGTCCGTCC
*
1514801 GTCT GTCT GTCT GTCC GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
*
1514849 GTCC GTCT GTCT GT
1 GTCT GTCT GTCT GT
1514863 GCAATCGTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.00, C:0.27, G:0.26, T:0.47
Consensus pattern (4 bp):
GTCT
Found at i:1515131 original size:146 final size:146
Alignment explanation
Indices: 1514867--1515283 Score: 728
Period size: 146 Copynumber: 2.9 Consensus size: 146
1514857 GTCTGTGCAA
1514867 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
1514932 TTATGACCTAAGGGTGTGTCATAACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
*
1514997 AGAAAAAGTGCAAAAT
131 AGAAAAAATGCAAAAT
1515013 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1515078 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
1515143 AGAAAAAATGCAAAAT
131 AGAAAAAATGCAAAAT
* *
1515159 TCGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTTCTTACTTTACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * * * *
1515224 TTATGA-TTAAAGGGTGTGTCATGACCTTGACCCAAGGTCAATTGAGAAAGTTCAAGGTCA
66 TTATGACCT-AAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCA
1515284 TTGTTTCAAA
Statistics
Matches: 260, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
145 1 0.00
146 259 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (146 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
AGAAAAAATGCAAAAT
Found at i:1518781 original size:54 final size:54
Alignment explanation
Indices: 1518660--1520035 Score: 1844
Period size: 54 Copynumber: 25.6 Consensus size: 54
1518650 ATCATACCTT
* *
1518660 GCTTGTCATACAGCCCTATCATACTTCGCTTGACATACAG-----CCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * * *
1518709 GCTTGTCATACAGTCCTACCATACTTCGCTTGTCATACAGCCCTATCAGACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * *
1518763 GCTTGACATACAGCCCTACCATACTTCCCTTGTCATACAGCCCTATCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * *
1518817 GCTTGTCATACAGTCCTACCATACTTCGCTTGTCATACAGCCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1518871 GCTTGACATACAGCCCTATCATACTTCGCTTGTCATACAGTCTTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1518925 CCTTGACATACAACCCTATCATACTTCGCTTGACATACAGCCCTATCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1518979 GCTTGTCATACAGTCTTACCATACTTCGCTTGACATACAGCCCTACCATGCTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519033 CCTTGACATACAGCCCTACCATACTTCGCTTGTCATTCAGTCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519087 CCTTGACATACAACCCTATCATACTTCGCTTGACATACAGCCCTATCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519141 GCTTGTCATACAGTCTTACCATACTTCGCTTGACATACAGCCCTACCATGCTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519195 CCTTGACATACAGCCCTACCATACTTCGCTTGTCATTCAGTCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519249 CCTTGACATACAACCCTATCATACTTCGCTTGACATACAGCCCTATCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519303 GCTTGTCATACAGTCTTACCATACTTCGCTTGACATACAGCCCTACCATGCTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519357 CCTTGACATACAGCCCTACCATACTTCGCTTGTCATTCAGTCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519411 CCTTGACATACAACCCTATCATACTTCGCTTGACATACAGCCCTATCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519465 GCTTGTCATACAGTCTTACCATACTTCGCTTGACATACAGCCCTACCATGCTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * *
1519519 CCTTGACATACAGCCCTACCATACTTCCCTTGACATACAGCCCTATCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
*
1519573 GCTTGACATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * * * *
1519627 CCTTGACATACAGCCCTATCATACTTCGCTTGAAATACAGTCCAACCATACTCC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519681 GCTTGACATACAACCCTATCATATTTCGCTTGACATACAGTCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519735 GCTTGTCATACAGCCCTACCATACTTCGCTCGCCATACAGTCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519789 GCTTGTCATACAGCCCTACCATACTTCGCTCGCCATACAGTCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519843 GCTTGTCATACAGCCCTACCATACTTCGCTCGCCATACAGTCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * * *
1519897 GCTTGTCATACAGCCCTACCATACTTCGCTCGCCATACAGTCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * *
1519951 GCTTGTCATACAGTCCTACCATACTTCGCTTGTCATACAGCCCTACCATACTTC
1 GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
* * *
1520005 CCTTGACATACAACCCTACCATGCTTCGCTT
1 GCTTGACATACAGCCCTACCATACTTCGCTT
1520036 CGAACATTTA
Statistics
Matches: 1185, Mismatches: 137, Indels: 5
0.89 0.10 0.00
Matches are distributed among these distances:
49 37 0.03
54 1148 0.97
ACGTcount: A:0.24, C:0.36, G:0.10, T:0.30
Consensus pattern (54 bp):
GCTTGACATACAGCCCTACCATACTTCGCTTGACATACAGCCCTACCATACTTC
Found at i:1518932 original size:162 final size:162
Alignment explanation
Indices: 1518644--1520035 Score: 2033
Period size: 162 Copynumber: 8.6 Consensus size: 162
1518634 CACCGTTGTA
* * *
1518644 AGCCCCATCATACCTT-GCTTGTCATACAGCCCTATCATACTTCGCTTGACATACAG-----CCA
1 AGCCCTATCATA-CTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCA
* * * * * * *
1518703 TACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGTCATACAGCCCTATCAGACTTCGCTTG
65 TACTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATACAGTCCTACCATACTTCCCTTG
* * *
1518768 ACATACAGCCCTACCATACTTCCCTTGTCATAC
130 ACATACAACCCTACCATACTTCGCTTGACATAC
*
1518801 AGCCCTATCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGTCATACAGCCCTACCAT
1 AGCCCTATCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCAT
* * *
1518866 ACTTCGCTTGACATACAGCCCTATCATACTTCGCTTGTCATACAGTCTTACCATACTTCCCTTGA
66 ACTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATACAGTCCTACCATACTTCCCTTGA
*
1518931 CATACAACCCTATCATACTTCGCTTGACATAC
131 CATACAACCCTACCATACTTCGCTTGACATAC
*
1518963 AGCCCTATCATACTTCGCTTGTCATACAGTCTTACCATACTTCGCTTGACATACAGCCCTACCAT
1 AGCCCTATCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCAT
* *
1519028 GCTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATTCAGTCCTACCATACTTCCCTTGA
66 ACTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATACAGTCCTACCATACTTCCCTTGA
*
1519093 CATACAACCCTATCATACTTCGCTTGACATAC
131 CATACAACCCTACCATACTTCGCTTGACATAC
*
1519125 AGCCCTATCATACTTCGCTTGTCATACAGTCTTACCATACTTCGCTTGACATACAGCCCTACCAT
1 AGCCCTATCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCAT
* *
1519190 GCTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATTCAGTCCTACCATACTTCCCTTGA
66 ACTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATACAGTCCTACCATACTTCCCTTGA
*
1519255 CATACAACCCTATCATACTTCGCTTGACATAC
131 CATACAACCCTACCATACTTCGCTTGACATAC
*
1519287 AGCCCTATCATACTTCGCTTGTCATACAGTCTTACCATACTTCGCTTGACATACAGCCCTACCAT
1 AGCCCTATCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCAT
* *
1519352 GCTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATTCAGTCCTACCATACTTCCCTTGA
66 ACTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATACAGTCCTACCATACTTCCCTTGA
*
1519417 CATACAACCCTATCATACTTCGCTTGACATAC
131 CATACAACCCTACCATACTTCGCTTGACATAC
*
1519449 AGCCCTATCATACTTCGCTTGTCATACAGTCTTACCATACTTCGCTTGACATACAGCCCTACCAT
1 AGCCCTATCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCAT
* * * * * *
1519514 GCTTCCCTTGACATACAGCCCTACCATACTTCCCTTGACATACAGCCCTATCATACTTCGCTTGA
66 ACTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATACAGTCCTACCATACTTCCCTTGA
**
1519579 CATACAGTCCTACCATACTTCGCTTGACATAC
131 CATACAACCCTACCATACTTCGCTTGACATAC
* * * * * * * *
1519611 AGCCCTACCATACTTCCCTTGACATACAGCCCTATCATACTTCGCTTGAAATACAGTCCAACCAT
1 AGCCCTATCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCAT
* * * * *
1519676 AC-TCCGCTTGACATACAACCCTATCATATTTCGCTTGACATACAGTCCTACCATACTTCGCTTG
66 ACTTCC-CTTGACATACAGCCCTACCATACTTCGCTTGTCATACAGTCCTACCATACTTCCCTTG
* * * *
1519740 TCATACAGCCCTACCATACTTCGCTCGCCATAC
130 ACATACAACCCTACCATACTTCGCTTGACATAC
* * * * * *
1519773 AGTCCTACCATACTTCGCTTGTCATACAGCCCTACCATACTTCGCTCGCCATACAGTCCTACCAT
1 AGCCCTATCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCAT
* * * * * *
1519838 ACTTCGCTTGTCATACAGCCCTACCATACTTCGCTCGCCATACAGTCCTACCATACTTCGCTTGT
66 ACTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATACAGTCCTACCATACTTCCCTTGA
* * *
1519903 CATACAGCCCTACCATACTTCGCTCGCCATAC
131 CATACAACCCTACCATACTTCGCTTGACATAC
* * *
1519935 AGTCCTACCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGTCATACAGCCCTACCAT
1 AGCCCTATCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCAT
* *
1520000 ACTTCCCTTGACATACAACCCTACCATGCTTCGCTT
66 ACTTCCCTTGACATACAGCCCTACCATACTTCGCTT
1520036 CGAACATTTA
Statistics
Matches: 1151, Mismatches: 76, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
156 3 0.00
157 48 0.04
161 3 0.00
162 1095 0.95
163 2 0.00
ACGTcount: A:0.24, C:0.36, G:0.10, T:0.30
Consensus pattern (162 bp):
AGCCCTATCATACTTCGCTTGTCATACAGTCCTACCATACTTCGCTTGACATACAGCCCTACCAT
ACTTCCCTTGACATACAGCCCTACCATACTTCGCTTGTCATACAGTCCTACCATACTTCCCTTGA
CATACAACCCTACCATACTTCGCTTGACATAC
Found at i:1527934 original size:2 final size:2
Alignment explanation
Indices: 1527927--1527960 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1527917 AAATAAAAAT
1527927 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
1527961 CAGAAATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1548921 original size:22 final size:22
Alignment explanation
Indices: 1548896--1548967 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
1548886 GCTAGTACCT
*
1548896 TTTCCCTGCTTTA-TCAGTAGCC
1 TTTCCCTGCTTCAGT-AGTAGCC
* *
1548918 TTTCCCAGCTTCAGTAGTAGCT
1 TTTCCCTGCTTCAGTAGTAGCC
*
1548940 TTTCCCTGCTTCAGTAGTAACC
1 TTTCCCTGCTTCAGTAGTAGCC
1548962 TTTCCC
1 TTTCCC
1548968 ACCGGGGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 42 0.98
23 1 0.02
ACGTcount: A:0.15, C:0.32, G:0.14, T:0.39
Consensus pattern (22 bp):
TTTCCCTGCTTCAGTAGTAGCC
Found at i:1551468 original size:22 final size:22
Alignment explanation
Indices: 1551443--1551513 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
1551433 GCTAGTATCT
1551443 TTTCCCTGCTTTA-TCAGTAGCC
1 TTTCCCTGCTTTAGT-AGTAGCC
* *
1551465 TTTCCCGGCTTTAGTAGTAGCT
1 TTTCCCTGCTTTAGTAGTAGCC
* *
1551487 TTTCCCTGCTTCAGTAGTAACC
1 TTTCCCTGCTTTAGTAGTAGCC
1551509 TTTCC
1 TTTCC
1551514 AACCGGGGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 41 0.98
23 1 0.02
ACGTcount: A:0.14, C:0.30, G:0.15, T:0.41
Consensus pattern (22 bp):
TTTCCCTGCTTTAGTAGTAGCC
Found at i:1555013 original size:9 final size:9
Alignment explanation
Indices: 1554999--1555023 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1554989 CGAAGCTTTA
1554999 TGAGTACAT
1 TGAGTACAT
1555008 TGAGTACAT
1 TGAGTACAT
1555017 TGAGTAC
1 TGAGTAC
1555024 CTCAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (9 bp):
TGAGTACAT
Found at i:1563567 original size:13 final size:13
Alignment explanation
Indices: 1563549--1563574 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1563539 CTTGAAAATT
1563549 TGTGATGTATGTA
1 TGTGATGTATGTA
1563562 TGTGATGTATGTA
1 TGTGATGTATGTA
1563575 GAAGCAGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
TGTGATGTATGTA
Found at i:1571083 original size:180 final size:180
Alignment explanation
Indices: 1570584--1571123 Score: 1003
Period size: 180 Copynumber: 3.0 Consensus size: 180
1570574 ACCCTACATG
* *
1570584 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTC-ATAAATAATC
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTA-TTTTTTCGATAAATTATC
1570648 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
65 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
1570713 CTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
130 CTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
**
1570764 TATATGCAATATTTTGCC-AAAAATGACTAAGTTCAAAAGCTAATATTTTTTCGATAAATTATCG
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1570828 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
*
1570893 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
1570943 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
*
1571008 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGACCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
1571073 TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
1571123 T
1 T
1571124 TTTGGCAANN
Statistics
Matches: 349, Mismatches: 9, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
178 7 0.02
179 167 0.48
180 175 0.50
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (180 bp):
TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
Found at i:1593518 original size:2 final size:2
Alignment explanation
Indices: 1593511--1593555 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1593501 GCTAGGTGAT
1593511 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
1593553 GA G
1 GA G
1593556 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1593817 original size:4 final size:4
Alignment explanation
Indices: 1593799--1593871 Score: 74
Period size: 4 Copynumber: 18.2 Consensus size: 4
1593789 CACTACAAAA
* * * * * *
1593799 CTCT CTCT GTTT CTGT CTGT CTCT GTCT CTCT CTCT CTCT CTCT CTGT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
* *
1593847 CTGT CTCT GTCT CTCT CTCT CTCT C
1 CTCT CTCT CTCT CTCT CTCT CTCT C
1593872 ATATCGACAA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.00, C:0.40, G:0.10, T:0.51
Consensus pattern (4 bp):
CTCT
Found at i:1593823 original size:6 final size:6
Alignment explanation
Indices: 1593802--1593871 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
1593792 TACAAAACTC
* * * *
1593802 TCTCTG TTTCTG --TCTG TCTCTG TCTCTC TCTCTC TCTCTC TCTGTCTG
1 TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TC--TCTG
* *
1593850 TCTCTG TCTCTC TCTCTC TCTC
1 TCTCTG TCTCTG TCTCTG TCTC
1593872 ATATCGACAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
4 4 0.07
6 47 0.84
8 5 0.09
ACGTcount: A:0.00, C:0.39, G:0.10, T:0.51
Consensus pattern (6 bp):
TCTCTG
Found at i:1593823 original size:10 final size:10
Alignment explanation
Indices: 1593799--1593871 Score: 78
Period size: 10 Copynumber: 7.5 Consensus size: 10
1593789 CACTACAAAA
1593799 CTCTCTCTGT
1 CTCTCTCTGT
* *
1593809 TTCTGTCTGT
1 CTCTCTCTGT
*
1593819 CTCTGTC--T
1 CTCTCTCTGT
*
1593827 CTCTCTCTCT
1 CTCTCTCTGT
1593837 CTCTCTCTGT
1 CTCTCTCTGT
*
1593847 CTGTCTCTGT
1 CTCTCTCTGT
*
1593857 CTCTCTCTCT
1 CTCTCTCTGT
1593867 CTCTC
1 CTCTC
1593872 ATATCGACAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
8 7 0.13
10 46 0.87
ACGTcount: A:0.00, C:0.40, G:0.10, T:0.51
Consensus pattern (10 bp):
CTCTCTCTGT
Found at i:1594382 original size:7 final size:7
Alignment explanation
Indices: 1594367--1594433 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
1594357 TTTAGATATT
1594367 GAATCTC
1 GAATCTC
*
1594374 GAATTTC
1 GAATCTC
1594381 GAATCTC
1 GAATCTC
1594388 GAATCTC
1 GAATCTC
* *
1594395 GTATTTC
1 GAATCTC
1594402 GAATCTC
1 GAATCTC
* *
1594409 GTATTTC
1 GAATCTC
1594416 GAATCTC
1 GAATCTC
1594423 GAATCTC
1 GAATCTC
1594430 GAAT
1 GAAT
1594434 GATCCTTCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:1594392 original size:21 final size:21
Alignment explanation
Indices: 1594367--1594433 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
1594357 TTTAGATATT
1594367 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
1594388 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * *
1594409 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
1594430 GAAT
1 GAAT
1594434 GATCCTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:1606777 original size:4 final size:4
Alignment explanation
Indices: 1606768--1606829 Score: 63
Period size: 4 Copynumber: 15.8 Consensus size: 4
1606758 ACTGAAGTGG
* * * * * *
1606768 GACA GACA GACG GACG GACG GACA GAAA GACA GACA GACA GTCA GGCA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
1606816 G-CA GACA GACA GAC
1 GACA GACA GACA GAC
1606830 TGACGGACGC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 3 0.06
4 48 0.94
ACGTcount: A:0.42, C:0.24, G:0.32, T:0.02
Consensus pattern (4 bp):
GACA
Found at i:1615926 original size:2 final size:2
Alignment explanation
Indices: 1615919--1615958 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
1615909 TATTTCAATC
*
1615919 GT GT GT GT GT GT GT GT GT GG GT GT G- GAT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G-T GT GT GT GT GT GT
1615959 TTTATCATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.03, C:0.00, G:0.53, T:0.45
Consensus pattern (2 bp):
GT
Found at i:1620547 original size:12 final size:12
Alignment explanation
Indices: 1620527--1620579 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
1620517 AACTGAAGTG
*
1620527 GGACAGACAGAC
1 GGACGGACAGAC
1620539 GGACGGACAGAC
1 GGACGGACAGAC
*
1620551 GGACGGACGGAC
1 GGACGGACAGAC
* *
1620563 GGACGGGCTGAC
1 GGACGGACAGAC
1620575 GGACG
1 GGACG
1620580 CAGAGGTAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.45, T:0.02
Consensus pattern (12 bp):
GGACGGACAGAC
Found at i:1620548 original size:16 final size:16
Alignment explanation
Indices: 1620527--1620562 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1620517 AACTGAAGTG
1620527 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
*
1620543 GGACAGACGGACGGAC
1 GGACAGACAGACGGAC
1620559 GGAC
1 GGAC
1620563 GGACGGGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.42, T:0.00
Consensus pattern (16 bp):
GGACAGACAGACGGAC
Found at i:1620555 original size:4 final size:4
Alignment explanation
Indices: 1620536--1620579 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
1620526 GGGACAGACA
* * *
1620536 GACG GACG GACA GACG GACG GACG GACG GACG GGCT GACG GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
1620580 CAGAGGTAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.48, T:0.02
Consensus pattern (4 bp):
GACG
Found at i:1637217 original size:2 final size:2
Alignment explanation
Indices: 1637210--1637271 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1637200 GAGATTATTT
1637210 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
1637252 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
1637272 ATTAATGATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1645415 original size:2 final size:2
Alignment explanation
Indices: 1645408--1645456 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1645398 TGTAAGCTAA
1645408 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
1645450 TC TC TC T
1 TC TC TC T
1645457 TTGAGATGTA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1646775 original size:437 final size:434
Alignment explanation
Indices: 1645839--1647128 Score: 1628
Period size: 437 Copynumber: 2.9 Consensus size: 434
1645829 AAGAGCTTTC
* * * * * *
1645839 TTCAACAAGTGTTAAGAAATTCGTCACCGTTCTTGAGATATCTGAGAAAAAAAAAACGTTTTAGG
1 TTCAACAACTGTTTAGAAATTCGTTACCGTTCTTGAGATATAT--G--ATAAAAAACATTTTAGG
* * * * * **
1645904 GGCC-AGTCCCTTATCTCCTTATTGGAG-CTGCTGAACCAAATTTTGAAGGTTGCATTT-TGTAA
62 GGCCGA-TCCCTTAACTCCTTATAGGGGCCT-TTAAACCAAATTTTGAAAATTGCATTTAT-T-A
* * *
1645966 AGTACATCATTTTAAGCACCTTATT-TTCTATACTGCATTTCAAAA-ATATTTTCCTTTTTGAGA
123 AGTACATCATTCTGAGCATCTT-TTCTTCTATACTGCATTTCAAAATAT-TTTTCCTTTTTGAGA
* * ** * * * *
1646029 TATAGGTGGTCATAGTTTATGGACTCTTGACCCCAAAAAAATCCTTATTACATAACACATGA-AT
186 TATTGGTGATCA-AAATTCTGGACTTTTGGCCCCTAAAAAATCCTTATTACATAACACATGATA-
* * * *
1646093 AAATCATTATATTACTTGGATACATAACTGAAAGATAAACATATTTGCTTCTATAGCCTTTCAAA
249 AAATCATTACATTGCTTGGATACATAACTGTAAGATAAACATATTTGCTTCTATAACCTTTCAAA
* * * * ** * * * *
1646158 AATTTCCCTCGGCAAA-GATCTACAGATGAACA-TTTTTAGAGCCATTTAGTTCCCTAATTTGCA
314 AATATCCCTCAGTAAAGGA-CTACAGAT-AAAAGACTTTAGAGCCCTTTGGTCCCCTAATTT-TA
*
1646221 GGGCTAG-CCCTTTTTCTTGATATCAAATAAAAGGTCATTTAAATCTCAACACATTTTG
376 GGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTAAATCTCAACACATTTTG
* *
1646279 TTCAACAACTGTTTAGAAATTCGTTACCGTTCTTGAGATATATAATAAAGAACATTTTAGGGGCC
1 TTCAACAACTGTTTAGAAATTCGTTACCGTTCTTGAGATATATGATAAAAAACATTTTAGGGGCC
* * *
1646344 GATCCTTTAACTCCTTATAGGGGCCTTTTAACGAAATTTTGAAAATTGCATATTATTAAGTACAT
66 GATCCCTTAACTCCTTATAGGGGCCTTTAAACCAAATTTTGAAAATTGCAT-TTATTAAGTACAT
* * *
1646409 CATTCTGAGTATCTTTTCTTCTATAATGCATTTCAAAATATTTTTCCTTTCTGAGATATTGGTGA
130 CATTCTGAGCATCTTTTCTTCTATACTGCATTTCAAAATATTTTTCCTTTTTGAGATATTGGTGA
* * * ***
1646474 TCAAAATTCTGGAATTTTGGCTCCTAAAAAATCGTTATTTTGTAACACATGATAAAATCATTACA
195 TCAAAATTCTGGACTTTTGGCCCCTAAAAAATCCTTATTACATAACACATGATAAAATCATTACA
* * *
1646539 TTGCTTGGATACATAACTGTAAGATAAACATATTTGCCTCTATAACCGTTCATAAAATATCCCCC
260 TTGCTTGGATACATAACTGTAAGATAAACATATTTGCTTCTATAACCTTTCA-AAAATATCCCTC
1646604 AGTAAAGGACTACAGATAAAAGACTTTAGAGCCCTTTGGTCCCCTAATTTTAGAGGCCAGCCCCT
324 AGTAAAGGACTACAGATAAAAGACTTTAGAGCCCTTTGGTCCCCTAATTTTAG-GGCCAGCCCCT
*
1646669 TTTTCTTGATATCAAATAAAAGGTCATTTAAATCTCAACCCATTTTG
388 TTTTCTTGATATCAAATAAAAGGTCATTTAAATCTCAACACATTTTG
1646716 TTCAACAACTGTTTAGAAATTCGTTACCGTTCTTGAGATATATGATAAAAAACATTTTAGGGGCC
1 TTCAACAACTGTTTAGAAATTCGTTACCGTTCTTGAGATATATGATAAAAAACATTTTAGGGGCC
* * * * * * *
1646781 GATCCCTTAAATCCTTGTAGGGGCCGTTAAACTAAATTTTGAGAATTGGATTTGATTTAAAT-CA
66 GATCCCTTAACTCCTTATAGGGGCCTTTAAACCAAATTTTGAAAATTGCATTT-A-TTAAGTACA
1646845 TCATTCTGAGCATCTTTTCTTCTATACTGCATTTCAAAATATTTTTCCTTTTTGAGATATTGGTG
129 TCATTCTGAGCATCTTTTCTTCTATACTGCATTTCAAAATATTTTTCCTTTTTGAGATATTGGTG
** * * **
1646910 ATCAAAATTCTGGACTTTTGGCCCCTAAAAACCCCTAATTACATAATACATGATATTATCATTAC
194 ATCAAAATTCTGGACTTTTGGCCCCTAAAAAATCCTTATTACATAACACATGATAAAATCATTAC
*
1646975 ATTGCTTGGATACATAACTGTAAGATAAACATATTTGCTTCTATAACTTTTCACAAAATATCCCT
259 ATTGCTTGGATACATAACTGTAAGATAAACATATTTGCTTCTATAACCTTTCA-AAAATATCCCT
* *
1647040 CAGTAAAGGGCTACAGATGAAAGACTTTAGAGCCCTTTGGTCCCCTAATTTTAGGGGCCAGCCCC
323 CAGTAAAGGACTACAGATAAAAGACTTTAGAGCCCTTTGGTCCCCTAATTTTA-GGGCCAGCCCC
* * *
1647105 TTTTTTTTGAAATCAAATGAAAGG
387 TTTTTCTTGATATCAAATAAAAGG
1647129 ACTTGTAGAT
Statistics
Matches: 743, Mismatches: 92, Indels: 33
0.86 0.11 0.04
Matches are distributed among these distances:
435 101 0.14
436 170 0.23
437 426 0.57
438 7 0.01
440 39 0.05
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (434 bp):
TTCAACAACTGTTTAGAAATTCGTTACCGTTCTTGAGATATATGATAAAAAACATTTTAGGGGCC
GATCCCTTAACTCCTTATAGGGGCCTTTAAACCAAATTTTGAAAATTGCATTTATTAAGTACATC
ATTCTGAGCATCTTTTCTTCTATACTGCATTTCAAAATATTTTTCCTTTTTGAGATATTGGTGAT
CAAAATTCTGGACTTTTGGCCCCTAAAAAATCCTTATTACATAACACATGATAAAATCATTACAT
TGCTTGGATACATAACTGTAAGATAAACATATTTGCTTCTATAACCTTTCAAAAATATCCCTCAG
TAAAGGACTACAGATAAAAGACTTTAGAGCCCTTTGGTCCCCTAATTTTAGGGCCAGCCCCTTTT
TCTTGATATCAAATAAAAGGTCATTTAAATCTCAACACATTTTG
Found at i:1650330 original size:1 final size:1
Alignment explanation
Indices: 1650324--1650362 Score: 69
Period size: 1 Copynumber: 39.0 Consensus size: 1
1650314 CTCCAGAAGA
*
1650324 CCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1650363 GTTGCTTCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1658596 original size:41 final size:41
Alignment explanation
Indices: 1658539--1658669 Score: 248
Period size: 41 Copynumber: 3.2 Consensus size: 41
1658529 TCTGATTAAA
1658539 ATCAGATCCTTTGATCCGCTCACTCAGATCGCTACACTAGG
1 ATCAGATCCTTTGATCCGCTCACTCAGATCGCTACACTAGG
1658580 ATCAGATCCTTTGATCCGCTCACTCAGATCGCTACACTAGG
1 ATCAGATCCTTTGATCCGCTCACTCAGATCGCTACACTAGG
1658621 ATCAGATCCTTTGATCCGCTCACTCAGATCGCTACACTAGG
1 ATCAGATCCTTTGATCCGCTCACTCAGATCGCTACACTAGG
1658662 --CAGATCCT
1 ATCAGATCCT
1658670 AGTGTAGATC
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
39 8 0.09
41 82 0.91
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (41 bp):
ATCAGATCCTTTGATCCGCTCACTCAGATCGCTACACTAGG
Found at i:1660331 original size:4 final size:4
Alignment explanation
Indices: 1660322--1660407 Score: 95
Period size: 4 Copynumber: 21.8 Consensus size: 4
1660312 TCAGAGATAC
* *
1660322 AGAA AGAA AGAA AGAA ACAA AGAA ACAA AGAA AGAA AGAA A-AA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
* * * *
1660369 ACAA AGAA AGAA ACAA ATAA AGAA ACAA A-AA GAGAA AGA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA -AGAA AGA
1660408 GAGGAAAATA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
3 5 0.07
4 62 0.90
5 2 0.03
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.01
Consensus pattern (4 bp):
AGAA
Found at i:1660405 original size:12 final size:12
Alignment explanation
Indices: 1660324--1660397 Score: 105
Period size: 12 Copynumber: 6.2 Consensus size: 12
1660314 AGAGATACAG
*
1660324 AAAGAAAGAAAG
1 AAAGAAAGAAAC
*
1660336 AAACAAAGAAAC
1 AAAGAAAGAAAC
*
1660348 AAAGAAAGAAAG
1 AAAGAAAGAAAC
1660360 AAA-AAAGAAAC
1 AAAGAAAGAAAC
1660371 AAAGAAAGAAAC
1 AAAGAAAGAAAC
*
1660383 AAATAAAGAAAC
1 AAAGAAAGAAAC
1660395 AAA
1 AAA
1660398 AAGAGAAAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
11 10 0.18
12 45 0.82
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (12 bp):
AAAGAAAGAAAC
Found at i:1660914 original size:2 final size:2
Alignment explanation
Indices: 1660909--1660958 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1660899 AAAAAAGTCA
1660909 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
1660951 TC TC TC TC
1 TC TC TC TC
1660959 CACGACCTAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1671338 original size:165 final size:166
Alignment explanation
Indices: 1671116--1671740 Score: 877
Period size: 165 Copynumber: 3.8 Consensus size: 166
1671106 GTGAATATGC
* * * * * * *
1671116 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACG
* * *
1671181 ATATGGCATACCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATACCTAAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
*
1671246 AATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCT-
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* *
1671281 AAAATAAACAAAGTAC-TCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAG
1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCAC
* * * *
1671345 GATATGGCATACCTTAACAAACAC--TGTAAAAATTTCAAGCATCTGCGACAAACAGTTGCTGAG
65 GATATGGCATACCTAAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
*
1671408 AAATCTTTGACAAAAATTTGTTTGAAAATGTTT-GCTA
130 AAATCTTTGACGAAAATTTGTTTGAAAAT-TTTGGCTA
*
1671445 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCTGATTGGTACAAAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACG
* * * * *
1671510 ATATGGCATGCC-AATAC-AATACTGTGTAAAAATTTCAAGGATCTGCAATAAATAGTTGCTGAG
66 ATATGGCATACCTAA-ACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
*
1671573 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCT-A
* * * * *
1671611 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATACATCCCATG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACG
* *
1671676 ATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATACCTAAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
1671741 TAAATGCGAC
Statistics
Matches: 410, Mismatches: 39, Indels: 20
0.87 0.08 0.04
Matches are distributed among these distances:
163 71 0.17
164 79 0.19
165 139 0.34
166 77 0.19
167 44 0.11
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (166 bp):
AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACG
ATATGGCATACCTAAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
Found at i:1678464 original size:83 final size:83
Alignment explanation
Indices: 1678320--1678475 Score: 231
Period size: 83 Copynumber: 1.9 Consensus size: 83
1678310 CTCTTATGCT
** * * **
1678320 ACTGGCGTGCGGTCAGTTCTCGCCAAGTACCATTTTTTGCCAGCGCATTGTTATGTCATTTTATC
1 ACTGGCGTGCGACCAGTTCTCGCCAAGTACCATTTCTCGCCAGCGCATTGTTACATCATTTTATC
1678385 AACACATATTAAAATTAA
66 AACACATATTAAAATTAA
* * *
1678403 ACTGGCGTGCGACCAGTTCTCGCCGAGTACCATTTCTCGCCAGTGCATTGTTACATTATTTTATC
1 ACTGGCGTGCGACCAGTTCTCGCCAAGTACCATTTCTCGCCAGCGCATTGTTACATCATTTTATC
1678468 AACACATA
66 AACACATA
1678476 AAATTATATA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 64 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (83 bp):
ACTGGCGTGCGACCAGTTCTCGCCAAGTACCATTTCTCGCCAGCGCATTGTTACATCATTTTATC
AACACATATTAAAATTAA
Found at i:1684835 original size:24 final size:26
Alignment explanation
Indices: 1684803--1684866 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
1684793 GTGCACAAGT
*
1684803 ATTTTAGTGTTTGCAAAG-T-CAAAC
1 ATTTTAGTGTTTACAAAGTTCCAAAC
* *
1684827 ATTTTAGTGTTTACACAGTTCCAATC
1 ATTTTAGTGTTTACAAAGTTCCAAAC
1684853 ATGTTTAGTGTTTA
1 AT-TTTAGTGTTTA
1684867 ACAACATCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.47
25 1 0.03
26 6 0.18
27 11 0.32
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (26 bp):
ATTTTAGTGTTTACAAAGTTCCAAAC
Found at i:1685986 original size:2 final size:2
Alignment explanation
Indices: 1685979--1686015 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1685969 CGTTAGCTAG
1685979 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 C
1686016 ATTTACCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1686111 original size:2 final size:2
Alignment explanation
Indices: 1686106--1686143 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1686096 TTATTTTTTA
1686106 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
1686144 ATTTACCAGT
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):
TC
Found at i:1686201 original size:122 final size:125
Alignment explanation
Indices: 1685979--1686219 Score: 416
Period size: 128 Copynumber: 1.9 Consensus size: 125
1685969 CGTTAGCTAG
*
1685979 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATTTACCAGTTTAAGTTGCAATTCAGGA
1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATTTACCAGTTAAAGTTGCAATTCAGG-
1686044 TATATATATATATATATCACGATAAAGAGTGTTAACTGTAAAATGTTTTATTTTATTTTTTAT
65 -A-ATATATATATATATCACGATAAAGAGTGTTAACTGTAAAATGTTTTATTTTATTTTTTAT
1686107 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATTTACCAGTTAAAGTTGCAATTCAGG-
1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATTTACCAGTTAAAGTTGCAATTCAGGA
*
1686171 ATATAT-T-TATATCACGATAAAGAGTGTTAACTGTAAAATGTTTTGTTTT
66 ATATATATATATATCACGATAAAGAGTGTTAACTGTAAAATGTTTTATTTT
1686220 TTTCTGTAGG
Statistics
Matches: 111, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
122 41 0.37
123 1 0.01
124 6 0.05
128 63 0.57
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.45
Consensus pattern (125 bp):
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATTTACCAGTTAAAGTTGCAATTCAGGA
ATATATATATATATCACGATAAAGAGTGTTAACTGTAAAATGTTTTATTTTATTTTTTAT
Found at i:1689099 original size:2 final size:2
Alignment explanation
Indices: 1689092--1689126 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1689082 ATCGACCTTT
*
1689092 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1689127 TTGGTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1691367 original size:20 final size:20
Alignment explanation
Indices: 1691342--1691381 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1691332 TGAGAACTCA
1691342 AACCCTGAGTAAACAACACC
1 AACCCTGAGTAAACAACACC
1691362 AACCCTGAGTAAACAACACC
1 AACCCTGAGTAAACAACACC
1691382 CTTAACACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.35, G:0.10, T:0.10
Consensus pattern (20 bp):
AACCCTGAGTAAACAACACC
Found at i:1695045 original size:17 final size:18
Alignment explanation
Indices: 1695025--1695064 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1695015 AAAGAGAAAA
*
1695025 CAATTGTAAAATCA-CAT
1 CAATTATAAAATCATCAT
*
1695042 CAATTATAAATTCATCAT
1 CAATTATAAAATCATCAT
1695060 CAATT
1 CAATT
1695065 TTCAACGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (18 bp):
CAATTATAAAATCATCAT
Found at i:1696777 original size:16 final size:16
Alignment explanation
Indices: 1696756--1696786 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1696746 TAATTAACAA
1696756 ATCAATAAATCAAATT
1 ATCAATAAATCAAATT
*
1696772 ATCAATCAATCAAAT
1 ATCAATAAATCAAAT
1696787 ACACAGATCT
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:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (16 bp):
ATCAATAAATCAAATT
Found at i:1700158 original size:11 final size:11
Alignment explanation
Indices: 1700142--1700166 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1700132 TTTTTATTTA
1700142 TTTATTTTTTT
1 TTTATTTTTTT
1700153 TTTATTTTTTT
1 TTTATTTTTTT
1700164 TTT
1 TTT
1700167 GAAAATGTAA
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:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:1700166 original size:15 final size:15
Alignment explanation
Indices: 1700131--1700165 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1700121 GAAAAAATTG
1700131 TTTTTTATTTATTTA
1 TTTTTTATTTATTTA
*
1700146 TTTTTTTTTTATTT-
1 TTTTTTATTTATTTA
1700160 TTTTTT
1 TTTTTT
1700166 TGAAAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTATTTATTTA
Found at i:1700588 original size:4 final size:4
Alignment explanation
Indices: 1700579--1700609 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1700569 ATTACGACTT
1700579 GATA GATA GATA GATA GATA GATA GATA GAT
1 GATA GATA GATA GATA GATA GATA GATA GAT
1700610 GGATGATGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
GATA
Found at i:1700635 original size:4 final size:4
Alignment explanation
Indices: 1700628--1700655 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1700618 GATGATGGAT
1700628 GGAC GGAC GGAC GGAC GGAC GGAC GGAC
1 GGAC GGAC GGAC GGAC GGAC GGAC GGAC
1700656 AGACAGACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.50, T:0.00
Consensus pattern (4 bp):
GGAC
Found at i:1706312 original size:14 final size:15
Alignment explanation
Indices: 1706288--1706316 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1706278 ACAAAAAGCA
1706288 AAAATGAATGCACTT
1 AAAATGAATGCACTT
1706303 AAAA-GAATGCACTT
1 AAAATGAATGCACTT
1706317 TCCAACCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (15 bp):
AAAATGAATGCACTT
Found at i:1709458 original size:12 final size:13
Alignment explanation
Indices: 1709425--1709459 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1709415 AATACTAATT
1709425 ATTAATAATATTTA
1 ATTAA-AATATTTA
1709439 ATTAAAATATTTA
1 ATTAAAATATTTA
1709452 A-TAAAATA
1 ATTAAAATA
1709460 ATTACTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.33
13 9 0.43
14 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATTAAAATATTTA
Found at i:1710925 original size:4 final size:4
Alignment explanation
Indices: 1710916--1710942 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1710906 TAAGCAACAA
1710916 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1710943 TAATTTGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:1711894 original size:2 final size:2
Alignment explanation
Indices: 1711887--1711941 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1711877 AATGAAAAAT
1711887 TC TC TC TC TC TC TC T- 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
1711928 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
1711942 ATTGCTAGCG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1712615 original size:4 final size:4
Alignment explanation
Indices: 1712600--1712649 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
1712590 ATCACCCGTT
* * * *
1712600 GTCC GT-C GTCC GTCC GTCC GTCT GTCT GTCC GTCC GTCT GTCT GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
1712647 GTC
1 GTC
1712650 TGTAAACTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (4 bp):
GTCC
Found at i:1712630 original size:12 final size:12
Alignment explanation
Indices: 1712606--1712652 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
1712596 CGTTGTCCGT
*
1712606 CGTCCGTCCGTC
1 CGTCCGTCTGTC
*
1712618 CGTCTGTCTGTC
1 CGTCCGTCTGTC
1712630 CGTCCGTCTGTC
1 CGTCCGTCTGTC
*
1712642 TGTCCGTCTGT
1 CGTCCGTCTGT
1712653 AAACTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36
Consensus pattern (12 bp):
CGTCCGTCTGTC
Found at i:1712632 original size:16 final size:16
Alignment explanation
Indices: 1712600--1712649 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
1712590 ATCACCCGTT
*
1712600 GTCCGTC-GTCCGTCC
1 GTCCGTCTGTCTGTCC
1712615 GTCCGTCTGTCTGTCC
1 GTCCGTCTGTCTGTCC
1712631 GTCCGTCTGTCTGTCC
1 GTCCGTCTGTCTGTCC
1712647 GTC
1 GTC
1712650 TGTAAACTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 7 0.21
16 26 0.79
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (16 bp):
GTCCGTCTGTCTGTCC
Found at i:1717838 original size:2 final size:2
Alignment explanation
Indices: 1717831--1717883 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1717821 TAAAAGAAAC
1717831 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
1717873 AG AG AG AG AG A
1 AG AG AG AG AG A
1717884 AGGAGATCAT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1722998 original size:138 final size:135
Alignment explanation
Indices: 1722750--1723027 Score: 459
Period size: 138 Copynumber: 2.0 Consensus size: 135
1722740 ACCATGCATA
* *
1722750 ACTATATGAAAGCATTGAGTCAAAGCTTGTTTCCTGTTGTCGAATCTGTCATCACAAATTACCAT
1 ACTATATGAAAGCATTGAGTCAAAGCTTGATCCCTGTTGTCGAATCTGTCATCACAAATTACCAT
1722815 AATGTTGACGTTTAAAAGCACACAATTGAAAGTGTCTTGCATAAAATAACTTAGTAATATTACAT
66 AATGTTGACGTTTAAAAGCACACAATTGAAAGTGTCTTGCATAAAATAACTTAGT-A-A-TACAT
1722880 TAATATAT
128 TAATATAT
* **
1722888 ACTATATGAAAGCATTGAGTCAAAGCTTGATCCCTGTTGTTGCCTCTGTCATCACAAATTACCAT
1 ACTATATGAAAGCATTGAGTCAAAGCTTGATCCCTGTTGTCGAATCTGTCATCACAAATTACCAT
* *
1722953 AATGTTGACTTTTACAAGCACACAATTGAAAGTGTCTTGCATAAAATAACTTAGTAATACATTAA
66 AATGTTGACGTTTAAAAGCACACAATTGAAAGTGTCTTGCATAAAATAACTTAGTAATACATTAA
1723018 TATAT
131 TATAT
1723023 A-TATA
1 ACTATA
1723028 CCGGTACACC
Statistics
Matches: 133, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
134 4 0.03
135 14 0.11
136 1 0.01
137 1 0.01
138 113 0.85
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (135 bp):
ACTATATGAAAGCATTGAGTCAAAGCTTGATCCCTGTTGTCGAATCTGTCATCACAAATTACCAT
AATGTTGACGTTTAAAAGCACACAATTGAAAGTGTCTTGCATAAAATAACTTAGTAATACATTAA
TATAT
Found at i:1736944 original size:33 final size:31
Alignment explanation
Indices: 1736866--1736932 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1736856 ACAATGGTAA
1736866 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1736897 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1736928 C-TTCT
1 CATTCT
1736933 TATGCATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.15, C:0.33, G:0.09, T:0.43
Consensus pattern (31 bp):
CATTCTCAGCAGTTATCTCTCTTTGCCCATT
Found at i:1737134 original size:16 final size:16
Alignment explanation
Indices: 1737113--1737150 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1737103 ACGGAAGAGT
*
1737113 GACAGACGGACGGACG
1 GACAGAAGGACGGACG
1737129 GACAGAAGGACGGACG
1 GACAGAAGGACGGACG
1737145 GACAGA
1 GACAGA
1737151 GTGATTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.42, T:0.00
Consensus pattern (16 bp):
GACAGAAGGACGGACG
Found at i:1739208 original size:21 final size:21
Alignment explanation
Indices: 1739177--1739395 Score: 170
Period size: 21 Copynumber: 10.2 Consensus size: 21
1739167 AAAACTAAGT
1739177 AAAGTATCTCGTTATTACGAGA
1 AAAG-ATCTCGTTATTACGAGA
* *
1739199 AAAGAGCTCGTAATTACGAGA
1 AAAGATCTCGTTATTACGAGA
* *
1739220 AAAGATATCGTTATTATGAGA
1 AAAGATCTCGTTATTACGAGA
* * *
1739241 AAATATCTCGTAATTACGTGA
1 AAAGATCTCGTTATTACGAGA
1739262 AAAGATCTCGTTATTACGA-A
1 AAAGATCTCGTTATTACGAGA
* ** * * *
1739282 TTGATTATCTCATTATTGCGAGTT
1 --AAAGATCTCGTTATTACGAG-A
** * *
1739306 AATTATCTCGTTATTATGAGTT
1 AAAGATCTCGTTATTACGAG-A
*
1739328 AAATATCTCGTTATTACGAGA
1 AAAGATCTCGTTATTACGAGA
*
1739349 AAAGATCTCGTTTTTACGAGTA
1 AAAGATCTCGTTATTACGAG-A
* * * *
1739371 AAACATATTGTCATTACGAGA
1 AAAGATCTCGTTATTACGAGA
1739392 AAAG
1 AAAG
1739396 GTCTGTTTAA
Statistics
Matches: 157, Mismatches: 35, Indels: 11
0.77 0.17 0.05
Matches are distributed among these distances:
20 1 0.01
21 86 0.55
22 70 0.45
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (21 bp):
AAAGATCTCGTTATTACGAGA
Found at i:1739251 original size:42 final size:42
Alignment explanation
Indices: 1739177--1739395 Score: 188
Period size: 43 Copynumber: 5.1 Consensus size: 42
1739167 AAAACTAAGT
* *
1739177 AAAGTATCTCGTTATTACGAGAAAAGAGCTCGTAATTACGAGA
1 AAAG-ATCTCGTTATTACGAGAAAATATCTCGTAATTACGAGA
* * *
1739220 AAAGATATCGTTATTATGAGAAAATATCTCGTAATTACGTGA
1 AAAGATCTCGTTATTACGAGAAAATATCTCGTAATTACGAGA
* * * * * *
1739262 AAAGATCTCGTTATTACGA-ATTGATTATCTCATTATTGCGAGTT
1 AAAGATCTCGTTATTACGAGA--AAATATCTCGTAATTACGAG-A
** * * *
1739306 AATTATCTCGTTATTATGAGTTAAATATCTCGTTATTACGAGA
1 AAAGATCTCGTTATTACGAG-AAAATATCTCGTAATTACGAGA
* * * * *
1739349 AAAGATCTCGTTTTTACGAGTAAAACATATTGTCATTACGAGA
1 AAAGATCTCGTTATTACGAG-AAAATATCTCGTAATTACGAGA
1739392 AAAG
1 AAAG
1739396 GTCTGTTTAA
Statistics
Matches: 139, Mismatches: 32, Indels: 10
0.77 0.18 0.06
Matches are distributed among these distances:
41 1 0.01
42 50 0.36
43 56 0.40
44 32 0.23
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (42 bp):
AAAGATCTCGTTATTACGAGAAAATATCTCGTAATTACGAGA
Found at i:1739297 original size:22 final size:22
Alignment explanation
Indices: 1739266--1739369 Score: 111
Period size: 22 Copynumber: 4.8 Consensus size: 22
1739256 ACGTGAAAAG
* *
1739266 ATCTCGTTATTACGAATTGATT
1 ATCTCGTTATTACGAGTTAATT
* *
1739288 ATCTCATTATTGCGAGTTAATT
1 ATCTCGTTATTACGAGTTAATT
* *
1739310 ATCTCGTTATTATGAGTTAAAT
1 ATCTCGTTATTACGAGTTAATT
* **
1739332 ATCTCGTTATTACGAG-AAAAG
1 ATCTCGTTATTACGAGTTAATT
*
1739353 ATCTCGTTTTTACGAGT
1 ATCTCGTTATTACGAGT
1739370 AAAACATATT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
21 18 0.26
22 51 0.74
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (22 bp):
ATCTCGTTATTACGAGTTAATT
Found at i:1740092 original size:21 final size:21
Alignment explanation
Indices: 1740068--1740168 Score: 121
Period size: 21 Copynumber: 4.8 Consensus size: 21
1740058 CATTATATAT
*
1740068 AGATCTTTTCTCGTATTAACG
1 AGATCTTTTCTCGTAATAACG
1740089 AGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACG
** * * *
1740110 AGAAAATTATCTAGCAATAACG
1 AG-ATCTTTTCTCGTAATAACG
* *
1740132 AGATCTTTTCTCGTATTTACG
1 AGATCTTTTCTCGTAATAACG
1740153 AGATCTTTTCTCGTAA
1 AGATCTTTTCTCGTAA
1740169 ACACGATATA
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
21 49 0.75
22 16 0.25
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (21 bp):
AGATCTTTTCTCGTAATAACG
Found at i:1740193 original size:64 final size:64
Alignment explanation
Indices: 1740068--1740198 Score: 185
Period size: 64 Copynumber: 2.0 Consensus size: 64
1740058 CATTATATAT
* *
1740068 AGATCTTTTCTCGTATTAACGAGATCTTTTCTCGTAATAACGAGAAAATTATCTAGCAATAACG
1 AGATCTTTTCTCGTATTAACGAGATCTTTTCTCGTAATAACGAGAAAATTAACTACCAATAACG
* * *
1740132 AGATCTTTTCTCGTATTTACGAGATCTTTTCTCGTAA-ACACGATATAATTAACT-CCTAATAAC
1 AGATCTTTTCTCGTATTAACGAGATCTTTTCTCGTAATA-ACGAGAAAATTAACTACC-AATAAC
1740195 G
64 G
1740196 AGA
1 AGA
1740199 AAATTATCTC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
63 2 0.03
64 58 0.97
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (64 bp):
AGATCTTTTCTCGTATTAACGAGATCTTTTCTCGTAATAACGAGAAAATTAACTACCAATAACG
Found at i:1742666 original size:23 final size:23
Alignment explanation
Indices: 1742640--1742687 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1742630 AAAATACGCC
* * *
1742640 AAGATGAGAAAATGTTTGAATAA
1 AAGAGGAGAAAATATTTGAACAA
*
1742663 AAGAGGAGAAAGTATTTGAACAA
1 AAGAGGAGAAAATATTTGAACAA
1742686 AA
1 AA
1742688 TTGCACCTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.21
Consensus pattern (23 bp):
AAGAGGAGAAAATATTTGAACAA
Found at i:1748217 original size:2 final size:2
Alignment explanation
Indices: 1748210--1748264 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1748200 AATGTTAGCT
1748210 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
1748252 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
1748265 CACACACATT
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1754569 original size:12 final size:12
Alignment explanation
Indices: 1754552--1754577 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1754542 TATATAGGAG
1754552 AAGTCTATACAT
1 AAGTCTATACAT
1754564 AAGTCTATACAT
1 AAGTCTATACAT
1754576 AA
1 AA
1754578 ATTAAGTTGG
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
AAGTCTATACAT
Found at i:1757751 original size:16 final size:17
Alignment explanation
Indices: 1757725--1757758 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1757715 TGTTGATTAT
1757725 AAAAGTGCTTTATAATC
1 AAAAGTGCTTTATAATC
*
1757742 AAAA-TGCTTTCTAATC
1 AAAAGTGCTTTATAATC
1757758 A
1 A
1757759 CCAGTTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (17 bp):
AAAAGTGCTTTATAATC
Found at i:1765856 original size:2 final size:2
Alignment explanation
Indices: 1765849--1765901 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
1765839 TGTTAAATAT
*
1765849 TC TC TC TC TC TT TC TC TC -C 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
1765890 TC TC TC TC TC TC
1 TC TC TC TC TC TC
1765902 CAGCCTGAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1766406 original size:260 final size:259
Alignment explanation
Indices: 1765944--1766463 Score: 1031
Period size: 260 Copynumber: 2.0 Consensus size: 259
1765934 GCAAGCTTAT
1765944 TAATTGGGCTTATATGACACAACAAGCTGGATGCCAGGAGACCTAATCTGTGTTCATTGTGAAGT
1 TAATTGGGCTTATATGACACAACAAGCTGGATGCCAGGAGACCTAATCTGTGTTCATTGTGAAGT
1766009 TATCTAAAGCCAGTTTTGCTGATAAAACTAGTGAATTATTAATGTTGACCAACAGGTGCATGCCA
66 TATCTAAAGCCAGTTTTGCTGATAAAACTAGTGAATTATTAATGTTGACCAACAGGTGCATGCCA
1766074 ACCCTTCAGACAAAGGTATAGGTAACATGTGGTCCACATTTTATCCAAAAATTATAAACATACAC
131 ACCCTTCAGACAAAGGTATAGGTAACATGTGGTCCACATTTTATCCAAAAATTATAAACATACAC
1766139 CAAATGATCAAGACCACATTTTACATTTTCTTGGCAATGATAAGGGATACATATTGAAAAAAAA
196 CAAATGATCAAGACCACATTTTACATTTTCTTGGCAATGATAAGGGATACATATTGAAAAAAAA
1766203 TNAATTGGGCTTATATGACACAACAAGCTGGATGCCAGGAGACCTAATCTGTGTTCATTGTGAAG
1 T-AATTGGGCTTATATGACACAACAAGCTGGATGCCAGGAGACCTAATCTGTGTTCATTGTGAAG
1766268 TTATCTAAAGCCAGTTTTGCTGATAAAACTAGTGAATTATTAATGTTGACCAACAGGTGCATGCC
65 TTATCTAAAGCCAGTTTTGCTGATAAAACTAGTGAATTATTAATGTTGACCAACAGGTGCATGCC
1766333 AACCCTTCAGACAAAGGTATAGGTAACATGTGGTCCACATTTTATCCAAAAATTATAAACATACA
130 AACCCTTCAGACAAAGGTATAGGTAACATGTGGTCCACATTTTATCCAAAAATTATAAACATACA
1766398 CCAAATGATCAAGACCACATTTTACATTTTCTTGGCAATGATAAGGGATACATATTGAAAAAAAA
195 CCAAATGATCAAGACCACATTTTACATTTTCTTGGCAATGATAAGGGATACATATTGAAAAAAAA
1766463 T
1 T
1766464 TCAGTTACAT
Statistics
Matches: 260, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
259 1 0.00
260 259 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (259 bp):
TAATTGGGCTTATATGACACAACAAGCTGGATGCCAGGAGACCTAATCTGTGTTCATTGTGAAGT
TATCTAAAGCCAGTTTTGCTGATAAAACTAGTGAATTATTAATGTTGACCAACAGGTGCATGCCA
ACCCTTCAGACAAAGGTATAGGTAACATGTGGTCCACATTTTATCCAAAAATTATAAACATACAC
CAAATGATCAAGACCACATTTTACATTTTCTTGGCAATGATAAGGGATACATATTGAAAAAAAA
Found at i:1770754 original size:19 final size:19
Alignment explanation
Indices: 1770730--1770770 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1770720 TATCCTTGTC
* *
1770730 ATGCATTTATGTGATTATT
1 ATGCATTTATATGATCATT
1770749 ATGCATTTATATGATCATT
1 ATGCATTTATATGATCATT
1770768 ATG
1 ATG
1770771 TTGAAAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (19 bp):
ATGCATTTATATGATCATT
Found at i:1777020 original size:360 final size:357
Alignment explanation
Indices: 1776280--1777456 Score: 1487
Period size: 360 Copynumber: 3.2 Consensus size: 357
1776270 AATTTTTTTT
*
1776280 GATAATTTATGGAAAACAAAATACCAGCTTTTGAACTTGGTCATTTTTTGGCAAAATATTGCATA
1 GATAATTTAT-G-AAA-AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATA
* *
1776345 TAGGGTACCATCATTGTATGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTTGC
63 TAGGGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTTGC
1776410 AGATCAATTAAACATATATCAGAGGTATGCATATTGCTAGGATTTTGATTTTCGATAATTTATGA
128 AGATCAATTAAACATATATCAGAGGTATGCATATTGCTAGGATTTTGATTTTCGATAATTTATGA
* *
1776475 AAATAATACCAGCTTTTGAACTTGGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
193 AAAAAATACCAGCTTTTGAACTTAGTCA-TTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
* * *
1776540 GTACGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTTGCAGATCAGTTATACAT
257 GTACGGATAACTCCTCCTACAG-TTTCAAGATAGGAAATTGTTCTTTTGCAGATCAGTTATACAT
*
1776605 ATATCAGAGGTATGCATATTGCTAGGATTTTGATTTTC
321 ATATCAGAGGTGTGCATATTGCTAGGATTTTGA-TTTC
*
1776643 GATAATTTATGAAAAAAATACCAGCTTTTGAACTTTGTCATTTTTTGGCAAAATATTGCATATAG
1 GATAATTTATGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
*
1776708 GGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAACAGGAAGTTGTTCTTTTGCAGA
66 GGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTTGCAGA
* *
1776773 TCAATTACACATATATCAGAGGTATGCATATTGTTAGGATTTTGATTTTCGATAATTTATGAAAA
131 TCAATTAAACATATATCAGAGGTATGCATATTGCTAGGATTTTGATTTTCGATAATTTATGAAAA
1776838 AAATACCAGCTTTTGAACTTAGTCATTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGTAC
196 AAATACCAGCTTTTGAACTTAGTCATTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGTAC
*
1776903 GGATAACTCCTCCTACAGTTCTCAAGATAGGAAATTTTTCTTTTGCAGATCAGTTATACATATAT
261 GGATAACTCCTCCTACAGTT-TCAAGATAGGAAATTGTTCTTTTGCAGATCAGTTATACATATAT
* * * *
1776968 CAGAGGTGTGCTTATTGCTAGGAGTTTGGTTAC
325 CAGAGGTGTGCATATTGCTAGGATTTTGATTTC
* * *
1777001 GGATAATTTATGAAAAAAAATTGCTTGTATTTTGGTTACTGATAATTTATGAAAAAAAAATTAAG
1 -GATAATTTATG-AAAAAAA-TAC---CA-----G---C------TTT-TG------AACTT-AG
** * *
1777066 TCATTTTTTGGCAAAATATTGCATATGATATAGCATACCCTCATTGTACGGATAACTCCTCTTAC
38 TCATTTTTTGGCAAAATATTGC-----ATATAGGGTACCCTCATTGTACGGATAAGTCCTCCTAC
* * * *
1777131 AGTTTTCAAGATAAGAAGTTGTTCTTTTGCAGATCAATTATACATATATCAGAGGTGTGCATATT
98 AGTTTTCAAAATAGGAAGTTGTTCTTTTGCAGATCAATTAAACATATATCAGAGGTATGCATATT
* * *
1777196 GCTAGGATTTTGA-TTACTGATAATTTGTGAAAAAAATACCAGCTTTTGAAGTTAGTCAATTTTT
163 GCTAGGATTTTGATTTTC-GATAATTTATGAAAAAAATACCAGCTTTTGAACTTAGTC-ATTTTT
* ** *
1777260 AGCAAAATATTGCATATAGGGTTA-CCTCATTGTACGGATAACTATTCCTACAGTTTTATAGATA
226 GGCAAAATATTGCATATAGGG-TACCCTCATTGTACGGATAACTCCTCCTACAGTTTCA-AGATA
* * * * * * ** *
1777324 -AAAAGTTGTTCTTTTGCAGATTAATTGTACATGTATCAGAGGTGTGAATATTTTTAGGATTTTT
289 GGAAA-TTGTTCTTTTGCAGATCAGTTATACATATATCAGAGGTGTGCATATTGCTAGGATTTTG
1777388 ATTTC
353 ATTTC
* * *
1777393 TGATTATTTATGAAAAAAATACCAGCTTTTGAACTTAGTCTTTTTTTAGCAAAATATTGCATAT
1 -GATAATTTATGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
1777457 GAGGTACTTT
Statistics
Matches: 716, Mismatches: 59, Indels: 81
0.84 0.07 0.09
Matches are distributed among these distances:
358 5 0.01
359 134 0.19
360 209 0.29
361 5 0.01
362 1 0.00
363 10 0.01
364 1 0.00
365 22 0.03
366 4 0.01
369 1 0.00
372 3 0.00
373 3 0.00
378 3 0.00
379 3 0.00
382 1 0.00
385 4 0.01
386 23 0.03
387 1 0.00
390 5 0.01
391 155 0.22
392 121 0.17
393 2 0.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (357 bp):
GATAATTTATGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
GGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTTGCAGA
TCAATTAAACATATATCAGAGGTATGCATATTGCTAGGATTTTGATTTTCGATAATTTATGAAAA
AAATACCAGCTTTTGAACTTAGTCATTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGTAC
GGATAACTCCTCCTACAGTTTCAAGATAGGAAATTGTTCTTTTGCAGATCAGTTATACATATATC
AGAGGTGTGCATATTGCTAGGATTTTGATTTC
Found at i:1777021 original size:180 final size:180
Alignment explanation
Indices: 1776275--1777019 Score: 1242
Period size: 180 Copynumber: 4.1 Consensus size: 180
1776265 AAAAAAATTT
*
1776275 TTTTTGATAATTTATGGAAAACAAAATACCAGCTTTTGAACTTGGTCATTTTTTGGCAAAATATT
1 TTTTCGATAATTTAT-G-AAA-AAAATACCAGCTTTTGAACTTGGTCATTTTTTGGCAAAATATT
* *
1776340 GCATATAGGGTACCATCATTGTATGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCT
63 GCATATAGGGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCT
*
1776405 TTTGCAGATCAATTAAACATATATCAGAGGTATGCATATTGCTAGGATTTTGA
128 TTTGCAGATCAATTATACATATATCAGAGGTATGCATATTGCTAGGATTTTGA
*
1776458 TTTTCGATAATTTATGAAAATAATACCAGCTTTTGAACTTGGTCATTTTTTGGCAAAATATTGCA
1 TTTTCGATAATTTATGAAAAAAATACCAGCTTTTGAACTTGGTCATTTTTTGGCAAAATATTGCA
1776523 TATAGGGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTT
66 TATAGGGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTT
*
1776588 GCAGATCAGTTATACATATATCAGAGGTATGCATATTGCTAGGATTTTGA
131 GCAGATCAATTATACATATATCAGAGGTATGCATATTGCTAGGATTTTGA
*
1776638 TTTTCGATAATTTATGAAAAAAATACCAGCTTTTGAACTTTGTCATTTTTTGGCAAAATATTGCA
1 TTTTCGATAATTTATGAAAAAAATACCAGCTTTTGAACTTGGTCATTTTTTGGCAAAATATTGCA
*
1776703 TATAGGGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAACAGGAAGTTGTTCTTTT
66 TATAGGGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTT
* *
1776768 GCAGATCAATTACACATATATCAGAGGTATGCATATTGTTAGGATTTTGA
131 GCAGATCAATTATACATATATCAGAGGTATGCATATTGCTAGGATTTTGA
*
1776818 TTTTCGATAATTTATGAAAAAAATACCAGCTTTTGAACTTAGTCA-TTTTTGGCAAAATATTGCA
1 TTTTCGATAATTTATGAAAAAAATACCAGCTTTTGAACTTGGTCATTTTTTGGCAAAATATTGCA
* * * * *
1776882 TATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAATTTTTCTTTT
66 TATAGGGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTT
* * * *
1776947 GCAGATCAGTTATACATATATCAGAGGTGTGCTTATTGCTAGGAGTTTG-
131 GCAGATCAATTATACATATATCAGAGGTATGCATATTGCTAGGATTTTGA
* *
1776996 GTTACGGATAATTTATGAAAAAAA
1 TTTTC-GATAATTTATGAAAAAAA
1777020 ATTGCTTGTA
Statistics
Matches: 534, Mismatches: 27, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
178 3 0.01
179 139 0.26
180 374 0.70
181 3 0.01
182 1 0.00
183 14 0.03
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (180 bp):
TTTTCGATAATTTATGAAAAAAATACCAGCTTTTGAACTTGGTCATTTTTTGGCAAAATATTGCA
TATAGGGTACCCTCATTGTACGGATAAGTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTT
GCAGATCAATTATACATATATCAGAGGTATGCATATTGCTAGGATTTTGA
Found at i:1777072 original size:39 final size:38
Alignment explanation
Indices: 1776992--1777072 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 38
1776982 TTGCTAGGAG
**
1776992 TTTGGTTACGGATAATTTATGAAAAAAAATTGCTTGTAT
1 TTTGGTTACGGATAATTTATGAAAAAAAATT-CAAGTAT
*
1777031 TTTGGTTACTGATAATTTATGAAAAAAAAATT-AAGTCAT
1 TTTGGTTACGGATAATTTATG-AAAAAAAATTCAAGT-AT
1777070 TTT
1 TTT
1777073 TTGGCAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 2 0.05
39 25 0.68
40 10 0.27
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (38 bp):
TTTGGTTACGGATAATTTATGAAAAAAAATTCAAGTAT
Found at i:1777332 original size:180 final size:180
Alignment explanation
Indices: 1777104--1777456 Score: 537
Period size: 180 Copynumber: 2.0 Consensus size: 180
1777094 TATAGCATAC
* * *
1777104 CCTCATTGTACGGATAACTCCTCTTACAGTTTTCAAGATAAGAAGTTGTTCTTTTGCAGATCAAT
1 CCTCATTGTACGGATAACTACTCCTACAGTTTTCAAGATAAAAAGTTGTTCTTTTGCAGATCAAT
* *
1777169 TATACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTACTGATAATTTGTGAAAAAAATA
66 TATACATATATCAGAGGTGTGAATATTGCTAGGATTTTGATTACTGATAATTTATGAAAAAAATA
*
1777234 CCAGCTTTTGAAGTTAGTCAATTTTTAGCAAAATATTGCATATAGGGTTA
131 CCAGCTTTTGAACTTAGTCAATTTTTAGCAAAATATTGCATATAGGGTTA
* *
1777284 CCTCATTGTACGGATAACTATTCCTACAGTTTT-ATAGATAAAAAGTTGTTCTTTTGCAGATTAA
1 CCTCATTGTACGGATAACTACTCCTACAGTTTTCA-AGATAAAAAGTTGTTCTTTTGCAGATCAA
* * ** * * *
1777348 TTGTACATGTATCAGAGGTGTGAATATTTTTAGGATTTTTATTTCTGATTATTTATGAAAAAAAT
65 TTATACATATATCAGAGGTGTGAATATTGCTAGGATTTTGATTACTGATAATTTATGAAAAAAAT
**
1777413 ACCAGCTTTTGAACTTAGTCTTTTTTTAGCAAAATATTGCATAT
130 ACCAGCTTTTGAACTTAGTCAATTTTTAGCAAAATATTGCATAT
1777457 GAGGTACTTT
Statistics
Matches: 155, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
179 1 0.01
180 154 0.99
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (180 bp):
CCTCATTGTACGGATAACTACTCCTACAGTTTTCAAGATAAAAAGTTGTTCTTTTGCAGATCAAT
TATACATATATCAGAGGTGTGAATATTGCTAGGATTTTGATTACTGATAATTTATGAAAAAAATA
CCAGCTTTTGAACTTAGTCAATTTTTAGCAAAATATTGCATATAGGGTTA
Found at i:1787522 original size:21 final size:21
Alignment explanation
Indices: 1787498--1787541 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1787488 TATAAATATA
*
1787498 GATATAGAAAGG-GAGAAGATC
1 GATAAAGAAAGGAG-GAAGATC
*
1787519 GATAAAGAAATGAGGAAGATC
1 GATAAAGAAAGGAGGAAGATC
1787540 GA
1 GA
1787542 CGAGATATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.50, C:0.05, G:0.32, T:0.14
Consensus pattern (21 bp):
GATAAAGAAAGGAGGAAGATC
Found at i:1789965 original size:44 final size:44
Alignment explanation
Indices: 1789874--1789958 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
1789864 GTACAGAAGC
* *
1789874 TACAGAGTAACTACTATCTTACTACCCACTGTGGATAAACAGAG
1 TACAAAGTAACTACTATCTCACTACCCACTGTGGATAAACAGAG
1789918 TACAAAGTAACTA-TAATCTCACTACCCACTGTGGATAAACA
1 TACAAAGTAACTACT-ATCTCACTACCCACTGTGGATAAACA
1789959 CGGTACAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 1 0.03
44 37 0.97
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (44 bp):
TACAAAGTAACTACTATCTCACTACCCACTGTGGATAAACAGAG
Found at i:1796581 original size:2 final size:2
Alignment explanation
Indices: 1796574--1796607 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1796564 ATAAAACCAA
1796574 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
1796608 GTTTCGTCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1800260 original size:11 final size:11
Alignment explanation
Indices: 1800244--1800269 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1800234 TGTGTTATAT
1800244 ATCTACTAAAA
1 ATCTACTAAAA
1800255 ATCTACTAAAA
1 ATCTACTAAAA
1800266 ATCT
1 ATCT
1800270 GTTTGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (11 bp):
ATCTACTAAAA
Found at i:1808010 original size:4 final size:4
Alignment explanation
Indices: 1808001--1808114 Score: 210
Period size: 4 Copynumber: 28.5 Consensus size: 4
1807991 TTTCGTTTTC
*
1808001 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAA ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
*
1808049 ATAG ATGG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1808097 ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG AT
1808115 TCAAGTAATC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 106 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:1811477 original size:15 final size:15
Alignment explanation
Indices: 1811457--1811485 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1811447 GAACTTGCAC
1811457 AAAAAAAAACCAAAA
1 AAAAAAAAACCAAAA
1811472 AAAAAAAAACCAAA
1 AAAAAAAAACCAAA
1811486 GCTCAAGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAACCAAAA
Found at i:1815272 original size:4 final size:4
Alignment explanation
Indices: 1815263--1815288 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1815253 TAAAAAACAA
1815263 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
1815289 TTCACCTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:1816448 original size:12 final size:12
Alignment explanation
Indices: 1816431--1816466 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1816421 TTTGTCGACT
1816431 TTCTTATTCTTC
1 TTCTTATTCTTC
1816443 TTCTTATTCTTC
1 TTCTTATTCTTC
* *
1816455 TTATTCTTCTTC
1 TTCTTATTCTTC
1816467 ATCCAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.67
Consensus pattern (12 bp):
TTCTTATTCTTC
Found at i:1816452 original size:9 final size:9
Alignment explanation
Indices: 1816440--1816465 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1816430 TTTCTTATTC
1816440 TTCTTCTTA
1 TTCTTCTTA
1816449 TTCTTCTTA
1 TTCTTCTTA
1816458 TTCTTCTT
1 TTCTTCTT
1816466 CATCCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (9 bp):
TTCTTCTTA
Found at i:1817103 original size:147 final size:144
Alignment explanation
Indices: 1816952--1817572 Score: 312
Period size: 147 Copynumber: 4.2 Consensus size: 144
1816942 TTTGACATTT
1816952 AGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGGAGTGCACTCCACCAAAAGTTTTGA
1 AGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGGAGTGCACTCCACCAAAAGTTTTGA
*
1817017 CCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAAAAATATTGTCCAGACCATAACACA
66 CCTTGACCTATTTT-TTCTTCAAGGTCAA-CTTATCATAAAAAATATTGTCCAGACCATAACACA
*
1817082 AGACTCCTTTAACATA
129 AGACTCCTTTAACAGA
** * * * ** * * *
1817098 CAGACTTTTAACTTGTATCATAGATAGATGGTATATAACCTA-G-CTGAAC-CCAACCAAAATTT
1 -AGACTTCAAACTTGGAACATAGGTAGATGGTAT-TAA-GAAGGAGTGCACTCC-ACCAAAAGTT
* * *
1817160 TTGACCTTGACCTAGAATTTTTAT-TTCAAGGTC-A--TATGAGAAAAAACTTCATTGTTCA-A-
62 TTGACCTTGACCT---ATTTTT-TCTTCAAGGTCAACTTATCATAAAAAA--T-ATTGTCCAGAC
* ** * * *
1817219 C-T-TCTGAATA-TACTTTGACAGA
120 CATAACACAAGACTCCTTTAACAGA
** * *** * * ** * **
1817241 AGGACTTCAAACTTTAAACA-AAG-A-ACAATAATAATACACTTAAGTGTACT--ATTGAATAA-
1 A-GACTTCAAACTTGGAACATAGGTAGATGGTATTAAGA-A--GGAGTGCACTCCA-CCAA-AAG
* * * ** * **
1817300 TATTTGACCTTGACCT-TGTTTTGTTCAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTG
60 T-TTTGACCTTGACCTATTTTTTCTTCAAGGTCAACTT------ATCATAA-AAAATATTGTCCA
** * * *
1817364 GGTCATAAC-CTTAATAC-CCTTTGACATTA
117 GACCATAACAC--AAGACTCCTTTAACA-GA
*
1817393 AGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGGAGTGCACTCCACCAAAAGTTTTGA
1 AGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGGAGTGCACTCCACCAAAAGTTTTGA
*
1817458 CCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAAAAATATTGTCCAGACCATAACACA
66 CCTTGACCTATTTT-TTCTTCAAGGTCAA-CTTATCATAAAAAATATTGTCCAGACCATAACACA
1817523 AGACTCCTTTAACAGA
129 AGACTCCTTTAACAGA
** * * *
1817539 CAGACTTTTAACTTGTATCATAGATAGATGGTAT
1 -AGACTTCAAACTTGGAACATAGGTAGATGGTAT
1817573 ATAACCTAGC
Statistics
Matches: 338, Mismatches: 85, Indels: 102
0.64 0.16 0.19
Matches are distributed among these distances:
138 1 0.00
139 17 0.05
140 4 0.01
141 2 0.01
142 6 0.02
143 42 0.12
144 4 0.01
145 10 0.03
146 12 0.04
147 110 0.33
148 22 0.07
149 16 0.05
150 7 0.02
151 51 0.15
152 10 0.03
153 16 0.05
154 8 0.02
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (144 bp):
AGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGGAGTGCACTCCACCAAAAGTTTTGA
CCTTGACCTATTTTTTCTTCAAGGTCAACTTATCATAAAAAATATTGTCCAGACCATAACACAAG
ACTCCTTTAACAGA
Found at i:1817316 original size:441 final size:441
Alignment explanation
Indices: 1816494--1817619 Score: 2153
Period size: 441 Copynumber: 2.6 Consensus size: 441
1816484 CCGTAACTTA
*
1816494 AATACCCTTTGACATTAAGACTTCAAACTTGGAATATAGGTAGATGGTATTGAGAAGGAGTGCAC
1 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGGAGTGCAC
*
1816559 GCCACCAAAAGTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAAAAATATT
66 TCCACCAAAAGTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAAAAATATT
1816624 GTCCAGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATGGT
131 GTCCAGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATGGT
*
1816689 ATATAACCTAGTTGAACCCAACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAAGGTCAT
196 ATATAACCTAGCTGAACCCAACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAAGGTCAT
*
1816754 ATGAGAAAAAACTTCATTGTTTAACTTCTGAACATACTTTGACAGAAGGACTTCAAACTTTAAAC
261 ATGAGAAAAAACTTCATTGTTCAACTTCTGAACATACTTTGACAGAAGGACTTCAAACTTTAAAC
1816819 AAAGAACAATAATAATACACTTAAGTGTACTATTGAATAATATTTGACCTTGACCTTGTTTTACT
326 AAAGAACAATAATAATACACTTAAGTGTACTATTGAATAATATTTGACCTTGACCTTGTTTTACT
1816884 CAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTGGGTCATAACCTT
391 CAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTGGGTCATAACCTT
* *
1816935 AATACCCTTTGACATTTAGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGGAGTGCAC
1 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGGAGTGCAC
1817000 TCCACCAAAAGTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAAAAATATT
66 TCCACCAAAAGTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAAAAATATT
1817065 GTCCAGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATGGT
131 GTCCAGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATGGT
1817130 ATATAACCTAGCTGAACCCAACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAAGGTCAT
196 ATATAACCTAGCTGAACCCAACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAAGGTCAT
*
1817195 ATGAGAAAAAACTTCATTGTTCAACTTCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAAC
261 ATGAGAAAAAACTTCATTGTTCAACTTCTGAACATACTTTGACAGAAGGACTTCAAACTTTAAAC
**
1817260 AAAGAACAATAATAATACACTTAAGTGTACTATTGAATAATATTTGACCTTGACCTTGTTTTGTT
326 AAAGAACAATAATAATACACTTAAGTGTACTATTGAATAATATTTGACCTTGACCTTGTTTTACT
1817325 CAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTGGGTCATAACCTT
391 CAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTGGGTCATAACCTT
1817376 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGGAGTGCAC
1 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGGAGTGCAC
1817441 TCCACCAAAAGTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAAAAATATT
66 TCCACCAAAAGTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAAAAATATT
*
1817506 GTCCAGACCATAACACAAGACTCCTTTAACAGACAGACTTTTAACTTGTATCATAGATAGATGGT
131 GTCCAGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATGGT
*
1817571 ATATAACCTAGCTGAACCCAACCAAAATTTTTGACCTTGACCTAAAATT
196 ATATAACCTAGCTGAACCCAACCAAAATTTTTGACCTTGACCTAGAATT
1817620 AATGTCTCCT
Statistics
Matches: 672, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
441 672 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (441 bp):
AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGGAGTGCAC
TCCACCAAAAGTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAAAAATATT
GTCCAGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATGGT
ATATAACCTAGCTGAACCCAACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAAGGTCAT
ATGAGAAAAAACTTCATTGTTCAACTTCTGAACATACTTTGACAGAAGGACTTCAAACTTTAAAC
AAAGAACAATAATAATACACTTAAGTGTACTATTGAATAATATTTGACCTTGACCTTGTTTTACT
CAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTGGGTCATAACCTT
Found at i:1820445 original size:17 final size:17
Alignment explanation
Indices: 1820418--1820459 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1820408 TACATTATGT
1820418 TTTAG-TTCCATAGAAA
1 TTTAGTTTCCATAGAAA
1820434 TTTAGTTTCCATAGAAA
1 TTTAGTTTCCATAGAAA
1820451 TTTAGTTTC
1 TTTAGTTTC
1820460 ATTATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTAGTTTCCATAGAAA
Found at i:1821254 original size:51 final size:50
Alignment explanation
Indices: 1821199--1821589 Score: 423
Period size: 51 Copynumber: 7.7 Consensus size: 50
1821189 ACAATATTGC
*
1821199 ATTCCAGAGAATGCAGATAAAAAGAAACAGAGGATCAGGAAAAATTACAGT
1 ATTCCAGAGAATGCAGA-AAAAAGAAACAGAGGATAAGGAAAAATTACAGT
* * * *
1821250 ATTCCAAAGATTGCAGAAAAAATGAAACAGAGTAGGAAGG-AAAATTACAGT
1 ATTCCAGAGAATGCAGAAAAAA-GAAACAGAGGA-TAAGGAAAAATTACAGT
* *
1821301 ATTCCAGAGAATGCAGAAAAAAAGAAACAGAGCATGAAAGAAAAA-TACAGT
1 ATTCCAGAGAATGCAG-AAAAAAGAAACAGAGGAT-AAGGAAAAATTACAGT
* * *
1821352 ATTCCAGAGAATGCTGAGAAAAAGAAACAGAGGATCAGGAAAAGTTACAGT
1 ATTCCAGAGAATGCAGA-AAAAAGAAACAGAGGATAAGGAAAAATTACAGT
* *
1821403 ATTCCTA-AGATTGCAGAAAAAATGAAACAGAGTATGAAGG-AAAATTACAGT
1 ATTCC-AGAGAATGCAGAAAAAA-GAAACAGAGGAT-AAGGAAAAATTACAGT
** * * *
1821454 ATTCCAGAGAATGCAGAAAAAAAGAAACAGAGCCTCAGGAAAAAATATAGT
1 ATTCCAGAGAATGCAG-AAAAAAGAAACAGAGGATAAGGAAAAATTACAGT
* * * * **
1821505 ATTCC-GCGGATTGCAGAAAAAATGAAACAGAGTATAAAGAAAAGGTACAGT
1 ATTCCAG-AGAATGCAGAAAAAA-GAAACAGAGGATAAGGAAAAATTACAGT
1821556 ATTCCAGAGAATGCAGAAAAAAAGAAACAGAGGA
1 ATTCCAGAGAATGCAG-AAAAAAGAAACAGAGGA
1821590 CCAGGGAAAA
Statistics
Matches: 285, Mismatches: 38, Indels: 34
0.80 0.11 0.10
Matches are distributed among these distances:
50 28 0.10
51 227 0.80
52 30 0.11
ACGTcount: A:0.51, C:0.12, G:0.22, T:0.16
Consensus pattern (50 bp):
ATTCCAGAGAATGCAGAAAAAAGAAACAGAGGATAAGGAAAAATTACAGT
Found at i:1821337 original size:153 final size:152
Alignment explanation
Indices: 1821180--1821587 Score: 577
Period size: 153 Copynumber: 2.7 Consensus size: 152
1821170 AAAAGCAGTA
* * * *
1821180 CATGAGAGAACAATATTGCATTCCAGAGAATGCAGATAAAAAGAAACAGAGGATCAGGAAAAATT
1 CATGAGAGAAAAATATAGTATTCCAGAGAATGCAGA-AAAAAGAAACAGAGGATCAGGAAAAGTT
1821245 ACAGTATTCCAAAGATTGCAGAAAAAATGAAACAGAGTAGGAAGGAAAATTACAGTATTCCAGAG
65 ACAGTATTCCAAAGATTGCAGAAAAAATGAAACAGAGTAGGAAGGAAAATTACAGTATTCCAGAG
1821310 AATGCAGAAAAAAAGAAACAGAG
130 AATGCAGAAAAAAAGAAACAGAG
* * *
1821333 CATGAAAGAAAAATACAGTATTCCAGAGAATGCTGAGAAAAAGAAACAGAGGATCAGGAAAAGTT
1 CATGAGAGAAAAATATAGTATTCCAGAGAATGCAGA-AAAAAGAAACAGAGGATCAGGAAAAGTT
* *
1821398 ACAGTATTCCTAAGATTGCAGAAAAAATGAAACAGAGTATGAAGGAAAATTACAGTATTCCAGAG
65 ACAGTATTCCAAAGATTGCAGAAAAAATGAAACAGAGTAGGAAGGAAAATTACAGTATTCCAGAG
1821463 AATGCAGAAAAAAAGAAACAGAG
130 AATGCAGAAAAAAAGAAACAGAG
* * * * * * *
1821486 CCTCAG-GAAAAAATATAGTATTCC-GCGGATTGCAGAAAAAATGAAACAGAGTATAAAGAAAAG
1 CATGAGAG-AAAAATATAGTATTCCAG-AGAATGCAGAAAAAA-GAAACAGAGGATCAGGAAAAG
* * * *
1821549 GTACAGTATTCCAGAGAATGCAGAAAAAAAGAAACAGAG
63 TTACAGTATTCCAAAGATTGCAGAAAAAATGAAACAGAG
1821588 GACCAGGGAA
Statistics
Matches: 227, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
152 7 0.03
153 220 0.97
ACGTcount: A:0.51, C:0.12, G:0.22, T:0.16
Consensus pattern (152 bp):
CATGAGAGAAAAATATAGTATTCCAGAGAATGCAGAAAAAAGAAACAGAGGATCAGGAAAAGTTA
CAGTATTCCAAAGATTGCAGAAAAAATGAAACAGAGTAGGAAGGAAAATTACAGTATTCCAGAGA
ATGCAGAAAAAAAGAAACAGAG
Found at i:1823047 original size:268 final size:268
Alignment explanation
Indices: 1822570--1823106 Score: 1047
Period size: 268 Copynumber: 2.0 Consensus size: 268
1822560 TTAAGTAAAT
*
1822570 TATTTACAAAACAGGTGCTGATAAGGAGAGGGAATCTGAACCTGGAAATAATGCCCACAATGAAA
1 TATTTACAAAACAGGTGCTGATAAGGAGAGGGAATCTGAACCTGGAAATAATGACCACAATGAAA
1822635 GCAACATCAATGCTGAATGTGATGGTAAAAACTATTGAACTGTTGTTTGGAAATCCATGTTTTAA
66 GCAACATCAATGCTGAATGTGATGGTAAAAACTATTGAACTGTTGTTTGGAAATCCATGTTTTAA
1822700 CAGAAGTCTTGGGGCACTTTGTTGGTGCATCAGAAGTAAACAGTTAAATAATGCCTTTTTGTTTT
131 CAGAAGTCTTGGGGCACTTTGTTGGTGCATCAGAAGTAAACAGTTAAATAATGCCTTTTTGTTTT
1822765 CAACAGATCCTGACACAGAGGAAGAAGAGTCAACAGAAGAATCTCATGACTTTGCACCACCACTT
196 CAACAGATCCTGACACAGAGGAAGAAGAGTCAACAGAAGAATCTCATGACTTTGCACCACCACTT
1822830 GATACATC
261 GATACATC
*
1822838 TATTTACAAAACAGGTGCTGATAAGGAGAGTGAATCTGAACCTGGAAATAATGACCACAATGAAA
1 TATTTACAAAACAGGTGCTGATAAGGAGAGGGAATCTGAACCTGGAAATAATGACCACAATGAAA
*
1822903 GCAACATCAATGCTGAATGTGATGGTAAAATCTATTGAACTGTTGTTTGGAAATCCATGTTTTAA
66 GCAACATCAATGCTGAATGTGATGGTAAAAACTATTGAACTGTTGTTTGGAAATCCATGTTTTAA
1822968 CAGAAGTCTTGGGGCACTTTGTTGGTGCATCAGAAGTAAACAGTTAAATAATGCCTTTTTGTTTT
131 CAGAAGTCTTGGGGCACTTTGTTGGTGCATCAGAAGTAAACAGTTAAATAATGCCTTTTTGTTTT
1823033 CAACAGATCCTGACACAGAGGAAGAAGAGTCAACAGAAGAATCTCATGACTTTGCACCACCACTT
196 CAACAGATCCTGACACAGAGGAAGAAGAGTCAACAGAAGAATCTCATGACTTTGCACCACCACTT
1823098 GATACATC
261 GATACATC
1823106 T
1 T
1823107 CTTCAACCAT
Statistics
Matches: 266, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
268 266 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (268 bp):
TATTTACAAAACAGGTGCTGATAAGGAGAGGGAATCTGAACCTGGAAATAATGACCACAATGAAA
GCAACATCAATGCTGAATGTGATGGTAAAAACTATTGAACTGTTGTTTGGAAATCCATGTTTTAA
CAGAAGTCTTGGGGCACTTTGTTGGTGCATCAGAAGTAAACAGTTAAATAATGCCTTTTTGTTTT
CAACAGATCCTGACACAGAGGAAGAAGAGTCAACAGAAGAATCTCATGACTTTGCACCACCACTT
GATACATC
Found at i:1827734 original size:26 final size:27
Alignment explanation
Indices: 1827698--1827760 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
1827688 AAGTTCAGCA
1827698 TGTAAAAGCAGAAAAG-AAAAAACAAG
1 TGTAAAAGCAGAAAAGAAAAAAACAAG
1827724 TGTAAAAGCAGAAAAGAAAAAAACAAG
1 TGTAAAAGCAGAAAAGAAAAAAACAAG
1827751 TGTAAAAGCA
1 TGTAAAAGCA
1827761 AACACCAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 16 0.44
27 20 0.56
ACGTcount: A:0.63, C:0.08, G:0.19, T:0.10
Consensus pattern (27 bp):
TGTAAAAGCAGAAAAGAAAAAAACAAG
Found at i:1828601 original size:16 final size:17
Alignment explanation
Indices: 1828564--1828604 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
1828554 TTTATTTTAC
1828564 ATCACATATGACACAAAT
1 ATCACATATGA-ACAAAT
*
1828582 ATCACATATG-ACATAT
1 ATCACATATGAACAAAT
1828598 ATCACAT
1 ATCACAT
1828605 TATCTCAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.55
18 10 0.45
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (17 bp):
ATCACATATGAACAAAT
Found at i:1833094 original size:165 final size:166
Alignment explanation
Indices: 1832820--1833580 Score: 1014
Period size: 165 Copynumber: 4.6 Consensus size: 166
1832810 GCAAAGTCGA
* * * * * *
1832820 CATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACAATATGGCATGCCTAAAC
1 CATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTAAAC
* * * * *
1832885 AAATAGTGTGTTAAAATTTCAAACCTCTGCGATAAATAGCTGCTGAGAAATCTTTGAGGAAAATT
66 AAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATT
*
1832950 TGTTTTAAAATTTTGGCT-AAAATAAACAAAGTACT
131 TGTTTGAAAATTTTGGCTAAAAATAAACAAAGTACT
* *
1832985 CATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCATGATATGGCATGCCTTAAC
1 CATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTAAAC
* *
1833050 AAAAACTGTGTAAAAATTTCAAGCATCTGCGATAAATTGCTGCTGAGAAATCTTTGACGAAAATT
66 AAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATT
1833115 TGTTTGAAAATTTTGGCTAAAAATAAAC--AGT-CAT
131 TGTTTGAAAATTTTGGCTAAAAATAAACAAAGTAC-T
* * * * *
1833149 TATTTAACAGGAAGTTGATGTCCGATTGATACAAAAATATATCCCACAATATGGCATGCCAAAAC
1 CATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTAAAC
* * * * * *
1833214 AAATAGTTTGTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGAAATCTTTGACGGAAATT
66 AAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATT
* *
1833279 TGTTTTAAAATTTTGGCTAAAAATAAATAAAGTACT
131 TGTTTGAAAATTTTGGCTAAAAATAAACAAAGTACT
* * * * *
1833315 CATTAAACAGGAAGTTGACATCCGATTGGTACAAAAATACATCCCACGATATAGCATGCC-AATT
1 CATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTAA-A
* * * * *
1833379 CAAATACTGTGTAAAAA-TTCAAGCATCTGCAATAAATGGTTGCTGAGAATTCTTTGACAAAAAT
65 CAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAAT
** **
1833443 TTGTTTGAAAATTTTTACTAAAAATAAACAAAGTTGT
130 TTGTTTGAAAATTTTGGCTAAAAATAAACAAAGTACT
* * *
1833480 GATTTAA-ACGGAAGTTGACGTTCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAA
1 CATTTAACA-GGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTAAA
* *
1833544 CAAATTCTGTGTAAAAATTTCAAGCATCTGTGATAAA
65 CAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAA
1833581 AAGTAGCTGA
Statistics
Matches: 521, Mismatches: 66, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
163 1 0.00
164 146 0.28
165 276 0.53
166 97 0.19
167 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (166 bp):
CATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTAAAC
AAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATT
TGTTTGAAAATTTTGGCTAAAAATAAACAAAGTACT
Found at i:1833425 original size:329 final size:329
Alignment explanation
Indices: 1832840--1833592 Score: 1093
Period size: 329 Copynumber: 2.3 Consensus size: 329
1832830 AAAGCTGGCA
*
1832840 TCCGATTGGTACAGAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTC
1 TCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTC
* * *
1832905 AAACCTCTGCGATAAATAGCTGCTGAGAAATCTTTGAGGAAAATTTGTTTTAAAATTTTGGCTAA
66 AAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGAGGAAAATTTGTTTTAAAATTTTGGCTAA
* * * *
1832970 AATAAACAAAGTACTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCATGAT
131 AATAAACAAAGTACTCATTAAACAGGAAGTTGACATCCGATTGGTACAAAAATACATCCCACGAT
* * *
1833035 ATGGCATGCCTTAACAAAAACTGTGTAAAAATTTCAAGCATCTGCGATAAATTGCTGCTGAGAAA
196 ATAGCATGCCTT-ACAAAAACTGTGTAAAAATTTCAAGCATCTGCAATAAATGGCTGCTGAGAAA
* * *
1833100 TCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAATAAAC-AGTCATTATTT-AACAGGAAG
260 TCTTTGACAAAAATTTGTTTGAAAATTTTGACTAAAAATAAACAAGTCATGATTTAAAC-GGAAG
*
1833163 TTGATG
324 TTGACG
* * *
1833169 TCCGATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATAGTTTGTTAAAATTTC
1 TCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTC
*
1833234 AAGCATCTGCAATAAATAGTTGCTGAGAAATCTTTGACGG-AAATTTGTTTTAAAATTTTGGCTA
66 AAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGA-GGAAAATTTGTTTTAAAATTTTGGCT-
*
1833298 AAAATAAATAAAGTACTCATTAAACAGGAAGTTGACATCCGATTGGTACAAAAATACATCCCACG
129 AAAATAAACAAAGTACTCATTAAACAGGAAGTTGACATCCGATTGGTACAAAAATACATCCCACG
* *
1833363 ATATAGCATGCCAATT-CAAATACTGTGTAAAAA-TTCAAGCATCTGCAATAAATGGTTGCTGAG
194 ATATAGCATGCC--TTACAAAAACTGTGTAAAAATTTCAAGCATCTGCAATAAATGGCTGCTGAG
* * **
1833426 AATTCTTTGACAAAAATTTGTTTGAAAATTTTTACTAAAAATAAACAAAGTTGTGATTTAAACGG
257 AAATCTTTGACAAAAATTTGTTTGAAAATTTTGACTAAAAATAAAC-AAGTCATGATTTAAACGG
1833491 AAGTTGACG
321 AAGTTGACG
* * * ** *
1833500 TTCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAACAAATTCTGTGTAAAAATTTC
1 TCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTC
* * *
1833565 AAGCATCTGTGATAAAAAGTAGCTGAGA
66 AAGCATCTGCGATAAATAGTTGCTGAGA
1833593 TAAATGCAAC
Statistics
Matches: 378, Mismatches: 39, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
329 186 0.49
330 89 0.24
331 98 0.26
332 5 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (329 bp):
TCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTC
AAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGAGGAAAATTTGTTTTAAAATTTTGGCTAA
AATAAACAAAGTACTCATTAAACAGGAAGTTGACATCCGATTGGTACAAAAATACATCCCACGAT
ATAGCATGCCTTACAAAAACTGTGTAAAAATTTCAAGCATCTGCAATAAATGGCTGCTGAGAAAT
CTTTGACAAAAATTTGTTTGAAAATTTTGACTAAAAATAAACAAGTCATGATTTAAACGGAAGTT
GACG
Found at i:1839429 original size:79 final size:79
Alignment explanation
Indices: 1839208--1839579 Score: 311
Period size: 79 Copynumber: 4.7 Consensus size: 79
1839198 GACAAGACAA
* * * *
1839208 GCCTCGGGGAGGCTAAAAAAATATGAAAAATATCTGGAAAACACTAGTAAATTGTGTTTG-TTCC
1 GCCTCAGGGAGGCTAAAAAAATATGAAAAATCTCAGGAAAACACAAGTAAATTGTG-TTGATTCC
1839272 AGTGCAATGAGATCC
65 AGTGCAATGAGATCC
* * * *
1839287 ACAC-CAGGGAGGCAAAAATTAAATATGAAAAATCTCAGGTAAACACAAGTAAATTGCGTTGATT
1 GC-CTCAGGGAGGCTAAAA--AAATATGAAAAATCTCAGGAAAACACAAGTAAATTGTGTTGATT
* *
1839351 CCAGTGCAATAAGATCT
63 CCAGTGCAATGAGATCC
* * * * *
1839368 GCCTCAGGGAGGCTAAACAAATCTGAAAAATCTCGGGAAAACACCAGTAAATTGTGATGATTCCA
1 GCCTCAGGGAGGCTAAAAAAATATGAAAAATCTCAGGAAAACACAAGTAAATTGTGTTGATTCCA
1839433 GTGCAATGAGATCC
66 GTGCAATGAGATCC
** * * * * * * * * **
1839447 GCCTGTGAGAGAC-AAAACATAAAATGAAAATTATAATGAAAACACAAGTAAATTATACTGATTC
1 GCCTCAGGGAGGCTAAAA-A-AATATGAAAAATCTCAGGAAAACACAAGTAAATTGTGTTGATTC
* *
1839511 CAGTGCAACGAGATCT
64 CAGTGCAATGAGATCC
* * * * * ** * *
1839527 GCTTCAGTGAGGC-AGTACAAATTTGAAATTTTTTAGGAAAACACAAGTAAATT
1 GCCTCAGGGAGGCTA-AAAAAATATGAAAAATCTCAGGAAAACACAAGTAAATT
1839580 ATGATAAAAC
Statistics
Matches: 233, Mismatches: 52, Indels: 16
0.77 0.17 0.05
Matches are distributed among these distances:
78 3 0.01
79 104 0.45
80 62 0.27
81 64 0.27
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (79 bp):
GCCTCAGGGAGGCTAAAAAAATATGAAAAATCTCAGGAAAACACAAGTAAATTGTGTTGATTCCA
GTGCAATGAGATCC
Done.