Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 7 of 120
Found at i:2017439 original size:15 final size:16
Alignment explanation
Indices: 2017419--2017449 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2017409 ACATGTCTTT
2017419 TTTTTAATATT-TACA
1 TTTTTAATATTATACA
2017434 TTTTTAATATTATACA
1 TTTTTAATATTATACA
2017450 CCCCTATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTAATATTATACA
Found at i:2018210 original size:20 final size:20
Alignment explanation
Indices: 2018187--2018224 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2018177 TTTGTAAAAA
*
2018187 TAAAAAAATTATAAAATTAT
1 TAAAAAAATTAAAAAATTAT
*
2018207 TAAAAAATTTAAAAAATT
1 TAAAAAAATTAAAAAATT
2018225 TAAAAGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAAAATTAAAAAATTAT
Found at i:2018222 original size:9 final size:9
Alignment explanation
Indices: 2018187--2018229 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
2018177 TTTGTAAAAA
*
2018187 TAAAAAAAT
1 TAAAAAATT
*
2018196 TATAAAATTAT
1 TA-AAAAAT-T
2018207 TAAAAAATT
1 TAAAAAATT
2018216 TAAAAAATT
1 TAAAAAATT
2018225 TAAAA
1 TAAAA
2018230 GTAATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 17 0.59
10 9 0.31
11 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAAAATT
Found at i:2019390 original size:294 final size:282
Alignment explanation
Indices: 2018763--2019400 Score: 681
Period size: 282 Copynumber: 2.2 Consensus size: 282
2018753 TTTCATTGTG
* * * * * * * * * * * *
2018763 TTTTATATATTTTTATTTCAATATGCACAATTTATTATCTCTACTAGTTATAAATTTATACTTAC
1 TTTTATACATTTTAATTTTATTATGCACACTTTATTACCTCCACCAATTGTATATCTATACTTAC
* * * * * *
2018828 TATTATTTAAGCCCCTGATTGAGTTGGTTTTACAAGTCAACTAGACACCAACTCAATTAGAAAAA
66 TATTATTTAAACCCCTGATTGAGCTGGTATCACAAGTCAACCAGACAACAACTCAATTAGAAAAA
* * * * *
2018893 TTACAAAAAAATCTTTTCATATTTAAAATAAGTTATATTATTCGAGGGTGCCTTAGTCTTTTTAT
131 TTACAAAAAAATCATTTCAAATTTAAAATAAGTTATATTATTCGAGGATACCTTAATCTTTTTAT
* * * *
2018958 TAAAAAAAATACTTATGGTGAGATTTGAACTCACACCAATGCATAAAGCTTTAAATTTACCATTC
196 TAAAAAAAATACTTATGGTGAGATTTGAACCCACACCAACGCATAAAGCTTTAAATTTACCACTA
2019023 AATCAAAGCTTTATTTTAAACT
261 AATCAAAGCTTTATTTTAAACT
* *
2019045 TTTTATACGTTTTAATTTTATTATGTACACTTTATTACCTCCACCAATTGTATATCTATACTTAC
1 TTTTATACATTTTAATTTTATTATGCACACTTTATTACCTCCACCAATTGTATATCTATACTTAC
* * * * *
2019110 TATTATTTAAACCCTTGATTGAGCTGGTATCACGAGTCAACCGGACAACAACTTAGA-TAGGAAA
66 TATTATTTAAACCCCTGATTGAGCTGGTATCACAAGTCAACCAGACAACAACTCA-ATTAGAAAA
* *
2019174 ATTACAAAAATATCATTTCAAATTTAAAATAAGTTATATTATTCGAGGATACTTTAAT-TTTTCT
130 ATTACAAAAAAATCATTTCAAATTTAAAATAAGTTATATTATTCGAGGATACCTTAATCTTTT-T
* * * * *
2019238 ATTAAAAAAAACAAAAACAAAAATGCTTATGGTGGGATTTGAACCCACGCCAACGCGTAAA-ATC
194 ATT-----------AAA-AAAAATACTTATGGTGAGATTTGAACCCACACCAACGCATAAAGCT-
* * *
2019302 TTAAATTTACTACTAAA-CTAAAGCTTTATTTTCAATT
246 TTAAATTTACCACTAAATC-AAAGCTTTATTTTAAACT
* * *
2019339 TTTTATACATTTTAATTTTATTATGCACACTTTATTACTTCCATCAATTGTATATTTATACT
1 TTTTATACATTTTAATTTTATTATGCACACTTTATTACCTCCACCAATTGTATATCTATACT
2019401 ATTTAGAAAA
Statistics
Matches: 291, Mismatches: 49, Indels: 20
0.81 0.14 0.06
Matches are distributed among these distances:
281 4 0.01
282 157 0.54
283 1 0.00
293 5 0.02
294 124 0.43
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (282 bp):
TTTTATACATTTTAATTTTATTATGCACACTTTATTACCTCCACCAATTGTATATCTATACTTAC
TATTATTTAAACCCCTGATTGAGCTGGTATCACAAGTCAACCAGACAACAACTCAATTAGAAAAA
TTACAAAAAAATCATTTCAAATTTAAAATAAGTTATATTATTCGAGGATACCTTAATCTTTTTAT
TAAAAAAAATACTTATGGTGAGATTTGAACCCACACCAACGCATAAAGCTTTAAATTTACCACTA
AATCAAAGCTTTATTTTAAACT
Found at i:2024789 original size:44 final size:44
Alignment explanation
Indices: 2024687--2024790 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
2024677 ATATGTTTCG
* * * *
2024687 ATATGAAATCTGATATGCTATCATATGTTGTAAGTTATGCTCCA
1 ATATGAAATCTGATATGCTATAATATGTTGTAAGATAAGCACCA
* *
2024731 TTACGAAATCTGATATGCTATAATATGTTGTAAGATAAGCACCA
1 ATATGAAATCTGATATGCTATAATATGTTGTAAGATAAGCACCA
* *
2024775 ATATGTAATATGATAT
1 ATATGAAATCTGATAT
2024791 ATTTTGACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (44 bp):
ATATGAAATCTGATATGCTATAATATGTTGTAAGATAAGCACCA
Found at i:2044923 original size:43 final size:43
Alignment explanation
Indices: 2044840--2044964 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
2044830 GCGTTTTCTC
* * * **
2044840 ACAAACGCCGCTAAAGAA-CATGATCTTTAGCAGCGCTTTTACT-
1 ACAAACGCCGCTAAA-AATTATGTTCTTTAGCGGCATTTTTA-TG
2044883 ACAAACGCCGCTAAAAATTATGTTCTTTAGCGGCATTTTTATG
1 ACAAACGCCGCTAAAAATTATGTTCTTTAGCGGCATTTTTATG
* * * * *
2044926 AGAAGCACCGCTAAAGATTATGTTCTATAGCGGCATTTT
1 ACAAACGCCGCTAAAAATTATGTTCTTTAGCGGCATTTT
2044965 CCCACATAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 3 0.04
43 67 0.96
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (43 bp):
ACAAACGCCGCTAAAAATTATGTTCTTTAGCGGCATTTTTATG
Found at i:2062118 original size:2 final size:2
Alignment explanation
Indices: 2062111--2062135 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2062101 AATCCTCTAC
2062111 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2062136 CTTTTTCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2066136 original size:14 final size:15
Alignment explanation
Indices: 2066108--2066140 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2066098 TAATATAAAA
2066108 TATT-ATAATTATTT
1 TATTAATAATTATTT
2066122 TATTAATAATT-TTT
1 TATTAATAATTATTT
2066136 TATTA
1 TATTA
2066141 CGATCATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTAATAATTATTT
Found at i:2066581 original size:2 final size:2
Alignment explanation
Indices: 2066574--2066613 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2066564 GTGAAACTTA
2066574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2066614 TTAACACCTA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2067569 original size:31 final size:31
Alignment explanation
Indices: 2067533--2067600 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
2067523 TACAAAATAG
*
2067533 TCACTGAACTATTTGAAAGTTTTCATTTAAA
1 TCACTGAACTATTCGAAAGTTTTCATTTAAA
* *
2067564 TCACTGAACTATTCGAAAGTTTTTATTTAAG
1 TCACTGAACTATTCGAAAGTTTTCATTTAAA
2067595 TCACTG
1 TCACTG
2067601 GGATGTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (31 bp):
TCACTGAACTATTCGAAAGTTTTCATTTAAA
Found at i:2081304 original size:45 final size:45
Alignment explanation
Indices: 2081240--2081337 Score: 196
Period size: 45 Copynumber: 2.2 Consensus size: 45
2081230 GAGCAGTCTG
2081240 ATTTACCTATTAGTGTCATGTGTTTGGGGGAATAGACACTTCCTC
1 ATTTACCTATTAGTGTCATGTGTTTGGGGGAATAGACACTTCCTC
2081285 ATTTACCTATTAGTGTCATGTGTTTGGGGGAATAGACACTTCCTC
1 ATTTACCTATTAGTGTCATGTGTTTGGGGGAATAGACACTTCCTC
2081330 ATTTACCT
1 ATTTACCT
2081338 TATCAGTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (45 bp):
ATTTACCTATTAGTGTCATGTGTTTGGGGGAATAGACACTTCCTC
Found at i:2087429 original size:20 final size:20
Alignment explanation
Indices: 2087380--2087429 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 20
2087370 TTTAAAAATC
* *
2087380 TTAAAAATTATAAAGATTAT
1 TTAAAAATTATAAAAATGAT
*
2087400 TT-TAAA--ATAAAAATGAT
1 TTAAAAATTATAAAAATGAT
2087417 TTAAAAATTATAA
1 TTAAAAATTATAA
2087430 TTATAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 6
0.70 0.12 0.18
Matches are distributed among these distances:
17 11 0.48
18 3 0.13
19 3 0.13
20 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (20 bp):
TTAAAAATTATAAAAATGAT
Found at i:2087892 original size:21 final size:21
Alignment explanation
Indices: 2087861--2087921 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
2087851 CGAAATTAGG
2087861 ATTATAAATAATTAATTAATGT
1 ATTA-AAATAATTAATTAATGT
*
2087883 ATTAAAATAATATAA-TCATGT
1 ATTAAAATAAT-TAATTAATGT
**
2087904 ATTATTAT-ATTAATTAAT
1 ATTAAAATAATTAATTAAT
2087922 TTAAAAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 18 0.55
22 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (21 bp):
ATTAAAATAATTAATTAATGT
Found at i:2089448 original size:34 final size:35
Alignment explanation
Indices: 2089410--2089476 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
2089400 CTAAATTGAA
* * *
2089410 CTGTTATAATCAT-ATTGAATGCTACCGTATTGTT
1 CTGTTAAAAGCATAATTAAATGCTACCGTATTGTT
* *
2089444 CTGTTAAAAGCATAATTAAATGTTACCTTATTG
1 CTGTTAAAAGCATAATTAAATGCTACCGTATTG
2089477 ATCCATTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 11 0.41
35 16 0.59
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (35 bp):
CTGTTAAAAGCATAATTAAATGCTACCGTATTGTT
Found at i:2089611 original size:40 final size:41
Alignment explanation
Indices: 2089535--2089715 Score: 143
Period size: 40 Copynumber: 4.3 Consensus size: 41
2089525 GTACGGAGGA
*
2089535 CAAGTGGCAGTTTAATCTGCAAACAGTGTGGTTCAATCACGAAC
1 CAAGTGGCAG--TAATCTGCAAATA-TGTGGTTCAATCACGAAC
2089579 CAAGTGGCAGTAA-CTGCAAATATGTGGTTCAATCACGAAC
1 CAAGTGGCAGTAATCTGCAAATATGTGGTTCAATCACGAAC
* * * * * * *
2089619 CGAGTGGTAGTTTGTTTAATCTGTAAATATGTTGTGCACTCAC-AAA
1 CAAGTGGCA----G--TAATCTGCAAATATGTGGTTCAATCACGAAC
* * * *
2089665 AAAATGGCAGTAA-CTGCAAATACGTGGTTCAATCATGAAC
1 CAAGTGGCAGTAATCTGCAAATATGTGGTTCAATCACGAAC
*
2089705 CAAGTCGCAGT
1 CAAGTGGCAGT
2089716 TTGTTTAATC
Statistics
Matches: 107, Mismatches: 22, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
39 17 0.16
40 38 0.36
41 8 0.07
42 4 0.04
44 11 0.10
46 10 0.09
47 19 0.18
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (41 bp):
CAAGTGGCAGTAATCTGCAAATATGTGGTTCAATCACGAAC
Found at i:2089680 original size:86 final size:81
Alignment explanation
Indices: 2089583--2089825 Score: 300
Period size: 86 Copynumber: 3.0 Consensus size: 81
2089573 ACGAACCAAG
* * * *
2089583 TGGCAGTAACTGCAAATATGTGGTTCAATCACGAACCGAGTGGTAGTTTGTTTAATCTGTAAATA
1 TGGCAGTAACTGCAAATATGTGGTTCAATCATGAACCAAGTGGCAGTTTGTTTAATCTGAAAATA
2089648 TGTTGTGCACTCACAAAAAAA
66 TGTTGTGCACTCAC-----AA
* * *
2089669 TGGCAGTAACTGCAAATACGTGGTTCAATCATGAACCAAGTCGCAGTTTGTTTAATCTGCAAATA
1 TGGCAGTAACTGCAAATATGTGGTTCAATCATGAACCAAGTGGCAGTTTGTTTAATCTGAAAATA
2089734 TGTTGTGCACT-----
66 TGTTGTGCACTCACAA
* *
2089745 T-GCAGTAACTGCAAACAATATGGTTCAATCATGAACCAAGTGGCAGTTTGTTTAATCTGAAAAT
1 TGGCAGTAACTGCAAA-TATGTGGTTCAATCATGAACCAAGTGGCAGTTTGTTTAATCTGAAAAT
*
2089809 ATGTTGTGCACCCACAA
65 ATGTTGTGCACTCACAA
2089826 CAAGTGGCTG
Statistics
Matches: 139, Mismatches: 12, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
75 14 0.10
76 55 0.40
86 70 0.50
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (81 bp):
TGGCAGTAACTGCAAATATGTGGTTCAATCATGAACCAAGTGGCAGTTTGTTTAATCTGAAAATA
TGTTGTGCACTCACAA
Found at i:2089796 original size:76 final size:75
Alignment explanation
Indices: 2089671--2089819 Score: 244
Period size: 76 Copynumber: 2.0 Consensus size: 75
2089661 CAAAAAAATG
* * *
2089671 GCAGTAACTGCAAATACGTGGTTCAATCATGAACCAAGTCGCAGTTTGTTTAATCTGCAAATATG
1 GCAGTAACTGCAAAAACATGGTTCAATCATGAACCAAGTCGCAGTTTGTTTAATCTGAAAATATG
2089736 TTGTGCACTT
66 TTGTGCACTT
* *
2089746 GCAGTAACTGCAAACAATATGGTTCAATCATGAACCAAGTGGCAGTTTGTTTAATCTGAAAATAT
1 GCAGTAACTGCAAA-AACATGGTTCAATCATGAACCAAGTCGCAGTTTGTTTAATCTGAAAATAT
2089811 GTTGTGCAC
65 GTTGTGCAC
2089820 CCACAACAAG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 14 0.21
76 54 0.79
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (75 bp):
GCAGTAACTGCAAAAACATGGTTCAATCATGAACCAAGTCGCAGTTTGTTTAATCTGAAAATATG
TTGTGCACTT
Found at i:2091083 original size:9 final size:10
Alignment explanation
Indices: 2091057--2091090 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2091047 AGTTTTCATA
2091057 ATTTTTATTG
1 ATTTTTATTG
*
2091067 AATTTTATT-
1 ATTTTTATTG
2091076 ATTTTTATTG
1 ATTTTTATTG
2091086 ATTTT
1 ATTTT
2091091 ACGTACACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (10 bp):
ATTTTTATTG
Found at i:2091270 original size:18 final size:18
Alignment explanation
Indices: 2091228--2091270 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2091218 AATATGAAAT
*
2091228 ATTTTTAAAATAAATTTC
1 ATTTTTAAAATAAATTTA
*
2091246 ATATTTAAAATAAATTTA
1 ATTTTTAAAATAAATTTA
2091264 ATTTTTA
1 ATTTTTA
2091271 TTATTTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTTAAAATAAATTTA
Found at i:2094593 original size:19 final size:20
Alignment explanation
Indices: 2094571--2094622 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2094561 ATTTTATTTT
*
2094571 AAAACACGAGAA-TTTTTGA
1 AAAACACGAAAATTTTTTGA
2094590 AAAACACGAAAATTTTTTG-
1 AAAACACGAAAATTTTTTGA
2094609 -AAACAC-AAAATTTT
1 AAAACACGAAAATTTT
2094623 GATAAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 8 0.26
18 6 0.19
19 11 0.35
20 6 0.19
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (20 bp):
AAAACACGAAAATTTTTTGA
Found at i:2094605 original size:18 final size:18
Alignment explanation
Indices: 2094571--2094624 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
2094561 ATTTTATTTT
*
2094571 AAAACACGAGAATTTTTGA
1 AAAACACGA-AAATTTTGA
**
2094590 AAAACACGAAAATTTTTT
1 AAAACACGAAAATTTTGA
*
2094608 GAAACAC-AAAATTTTGA
1 AAAACACGAAAATTTTGA
2094625 TAAATTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 8 0.28
18 12 0.41
19 9 0.31
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
AAAACACGAAAATTTTGA
Found at i:2094658 original size:125 final size:125
Alignment explanation
Indices: 2094480--2094840 Score: 618
Period size: 123 Copynumber: 2.9 Consensus size: 125
2094470 TATGATCCGA
* *
2094480 TTGAAACACAAAAATTTTGATAAACTACATATTATTATATATCCATTTAAATATAATTTGATAAT
1 TTGAAACAC-AAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAAT
* * **
2094545 TTACAAAAAAATAAACATTTTATTTTAAAACACGAGAATTTTTGAAAAACACGAAAATTTT
65 TTACAAAAAAATAAACATTTTATTTTAAAACACAAGAATTTTTGAAAAACACAAAAAAATT
2094606 TTGAAACACAAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAATT
1 TTGAAACACAAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAATT
* *
2094671 TAC--AAAAATAAAAATTTTATTTTAAAACACAAGAATTTTTAAAAAACACAAAAAAATT
66 TACAAAAAAATAAACATTTTATTTTAAAACACAAGAATTTTTGAAAAACACAAAAAAATT
2094729 TTGAAACACAAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAATT
1 TTGAAACACAAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAATT
2094794 TACAAAAAAAATAAACATTTTATTTTAAAACACAAGAATTTTTGAAA
66 TAC-AAAAAAATAAACATTTTATTTTAAAACACAAGAATTTTTGAAA
2094841 TACGAGAATT
Statistics
Matches: 222, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
123 117 0.53
125 57 0.26
126 48 0.22
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (125 bp):
TTGAAACACAAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAATT
TACAAAAAAATAAACATTTTATTTTAAAACACAAGAATTTTTGAAAAACACAAAAAAATT
Found at i:2094729 original size:144 final size:139
Alignment explanation
Indices: 2094567--2095119 Score: 565
Period size: 141 Copynumber: 4.0 Consensus size: 139
2094557 AAACATTTTA
*
2094567 TTTTAAAACACGAGAATTTTTGAAAAACACGAAAATTTTTTGAAACAC-AAAATTTTGATAAATT
1 TTTTGAAACACGAGAATTTTTG--AAACACGAAAATTTTTTGAAACACGAAAATTTTGATAAATT
* * *
2094631 ATATATTATTATATATCCATTTAAATATAATTTGATAATTTACAAAAATAAAAATTTTATTTTAA
64 ACATATTATTATATATCCATTTAAATATAATTTGATAATTTAAAAAAATAAACATTTTATTTTAA
2094696 AACACAAGAAT
129 AACACAAGAAT
* * * * ** *
2094707 TTTTAAAAAACACAAAAAAATTTTGAAACAC-AAAA--TTTTGATAA-ATTATATATTATT-ATA
1 TTTT--GAAACAC-GAGAATTTTTGAAACACGAAAATTTTTTGA-AACACGA-AAATT-TTGATA
* * * * *
2094767 TA-TCCAT-TTA--A-ATAT-AATTT---GATAATTT-A-CA---AAAAAAATAAACATTTTATT
60 AATTACATATTATTATATATCCATTTAAATATAATTTGATAATTTAAAAAAATAAACATTTTATT
2094818 TTAAAACACAAGAAT
125 TTAAAACACAAGAAT
* ***
2094833 TTTTGAAATACGAGAATTTTTGAAAACACGATTTTTTTTTTGAAACACGAAAATTTTGATAAATT
1 TTTTGAAACACGAGAATTTTTG-AAACACGA-AAATTTTTTGAAACACGAAAATTTTGATAAATT
*
2094898 ACATAATATTATATATCCATTTAAATATAATTTGATAATTTAGAAAAAAATTAAACATTTTATTT
64 ACATATTATTATATATCCATTTAAATATAATTTGATAATTT--AAAAAAA-TAAACATTTTATTT
*
2094963 TAAAACACGAGAAT
126 TAAAACACAAGAAT
* * *
2094977 TTTTGAAACACGAGAATTTTTGAAACATG-AAATTTTTTAAAACACGAAAAATTTGATAAATTAC
1 TTTTGAAACACGAGAATTTTTGAAACACGAAAATTTTTTGAAACACGAAAATTTTGATAAATTAC
* *
2095041 ATATTATTATATCTCCGTTTAAATATAATTTGATAATTTTAAAAAAATAAACATTTTATTTTAAA
66 ATATTATTATATATCCATTTAAATATAATTTGATAA-TTTAAAAAAATAAACATTTTATTTTAAA
*
2095106 GCACTAA-AAT
130 ACAC-AAGAAT
2095116 TTTT
1 TTTT
2095120 TAATTTTTTA
Statistics
Matches: 337, Mismatches: 43, Indels: 67
0.75 0.10 0.15
Matches are distributed among these distances:
123 8 0.02
124 11 0.03
125 1 0.00
126 39 0.12
127 10 0.03
128 12 0.04
129 3 0.01
130 1 0.00
131 8 0.02
132 4 0.01
133 4 0.01
134 4 0.01
135 4 0.01
136 8 0.02
137 1 0.00
138 11 0.03
139 34 0.10
140 24 0.07
141 71 0.21
142 10 0.03
143 21 0.06
144 48 0.14
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (139 bp):
TTTTGAAACACGAGAATTTTTGAAACACGAAAATTTTTTGAAACACGAAAATTTTGATAAATTAC
ATATTATTATATATCCATTTAAATATAATTTGATAATTTAAAAAAATAAACATTTTATTTTAAAA
CACAAGAAT
Found at i:2094863 original size:18 final size:18
Alignment explanation
Indices: 2094816--2094863 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
2094806 AAACATTTTA
*
2094816 TTTT-AAAACACAAGAAT
1 TTTTGAAAACACGAGAAT
*
2094833 TTTTG-AAATACGAGAAT
1 TTTTGAAAACACGAGAAT
2094850 TTTTGAAAACACGA
1 TTTTGAAAACACGA
2094864 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.31
Consensus pattern (18 bp):
TTTTGAAAACACGAGAAT
Found at i:2094889 original size:17 final size:17
Alignment explanation
Indices: 2094816--2094889 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 17
2094806 AAACATTTTA
*
2094816 TTTTAAAACAC-AAGAAT
1 TTTTGAAACACGAA-AAT
* *
2094833 TTTTGAAATACGAGAAT
1 TTTTGAAACACGAAAAT
***
2094850 TTTTGAAAACACGATTTTTT
1 TTTTG-AAACACGA--AAAT
2094870 TTTTGAAACACGAAAAT
1 TTTTGAAACACGAAAAT
2094887 TTT
1 TTT
2094890 GATAAATTAC
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
17 21 0.49
18 8 0.19
19 8 0.19
20 6 0.14
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (17 bp):
TTTTGAAACACGAAAAT
Found at i:2095023 original size:141 final size:142
Alignment explanation
Indices: 2094690--2095119 Score: 591
Period size: 144 Copynumber: 3.0 Consensus size: 142
2094680 AAAAATTTTA
* * * * * **
2094690 TTTTAAAACACAAGAATTTTTAAAAAACACAAAAAAATTTTGAAACAC-AAAATTTTGATAAATT
1 TTTTGAAACACGAGAATTTTT-GAAAACACGATAATTTTTTGAAACACGAAAATTTTGATAAATT
*
2094754 ATATATTATTATATATCCATTTAAATATAATTTGATAATTTACAAAAAAAATAAACATTTTATTT
65 ACATATTATTATATATCCATTTAAATATAATTTGATAATTTAC-AAAAAAATAAACATTTTATTT
2094819 TAAAACACAAGAAT
129 TAAAACACAAGAAT
* **
2094833 TTTTGAAATACGAGAATTTTTGAAAACACGATTTTTTTTTTGAAACACGAAAATTTTGATAAATT
1 TTTTGAAACACGAGAATTTTTGAAAACACGA-TAATTTTTTGAAACACGAAAATTTTGATAAATT
* *
2094898 ACATAATATTATATATCCATTTAAATATAATTTGATAATTTAGAAAAAAATTAAACATTTTATTT
65 ACATATTATTATATATCCATTTAAATATAATTTGATAATTTACAAAAAAA-TAAACATTTTATTT
*
2094963 TAAAACACGAGAAT
129 TAAAACACAAGAAT
* * *
2094977 TTTTGAAACACGAGAATTTTTG-AAACATGA-AATTTTTTAAAACACGAAAAATTTGATAAATTA
1 TTTTGAAACACGAGAATTTTTGAAAACACGATAATTTTTTGAAACACGAAAATTTTGATAAATTA
* * *
2095040 CATATTATTATATCTCCGTTTAAATATAATTTGATAATTT-TAAAAAAATAAACATTTTATTTTA
66 CATATTATTATATATCCATTTAAATATAATTTGATAATTTACAAAAAAATAAACATTTTATTTTA
*
2095104 AAGCACTAA-AAT
131 AAACAC-AAGAAT
2095116 TTTT
1 TTTT
2095120 TAATTTTTTA
Statistics
Matches: 257, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
139 28 0.11
140 8 0.03
141 66 0.26
142 8 0.03
143 43 0.17
144 104 0.40
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (142 bp):
TTTTGAAACACGAGAATTTTTGAAAACACGATAATTTTTTGAAACACGAAAATTTTGATAAATTA
CATATTATTATATATCCATTTAAATATAATTTGATAATTTACAAAAAAATAAACATTTTATTTTA
AAACACAAGAAT
Found at i:2095025 original size:17 final size:17
Alignment explanation
Indices: 2094960--2095023 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
2094950 AAACATTTTA
2094960 TTTTAAAACACGAGAAT
1 TTTTAAAACACGAGAAT
*
2094977 TTTTGAAACACGAGAAT
1 TTTTAAAACACGAGAAT
* *
2094994 TTTTGAAACATGA-AATT
1 TTTTAAAACACGAGAA-T
2095011 TTTTAAAACACGA
1 TTTTAAAACACGA
2095024 AAAATTTGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
16 2 0.05
17 40 0.95
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTAAAACACGAGAAT
Found at i:2095291 original size:12 final size:13
Alignment explanation
Indices: 2095258--2095298 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
2095248 TTAAAAAATT
*
2095258 AAAT-TAAATTAA
1 AAATATAAATAAA
*
2095270 AAATATAAATACA
1 AAATATAAATAAA
2095283 AAATA-AAATAAA
1 AAATATAAATAAA
2095295 AAAT
1 AAAT
2095299 GCGTAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATATAAATAAA
Found at i:2099400 original size:27 final size:27
Alignment explanation
Indices: 2099370--2099452 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
2099360 CTTTGTGTAT
*
2099370 TCCACCGAGACACTAAACACATAGTAG
1 TCCATCGAGACACTAAACACATAGTAG
* *
2099397 TCCATC-AGGATACTAAACACATGGTAG
1 TCCATCGA-GACACTAAACACATAGTAG
2099424 TCCATCGAGACA-TCAAACACA-AGGTAG
1 TCCATCGAGACACT-AAACACATA-GTAG
2099451 TC
1 TC
2099453 AACTGGGACT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
26 2 0.04
27 44 0.94
28 1 0.02
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.18
Consensus pattern (27 bp):
TCCATCGAGACACTAAACACATAGTAG
Found at i:2101779 original size:21 final size:21
Alignment explanation
Indices: 2101729--2101779 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2101719 GCTCTCACGG
*
2101729 GCTTCTGTTCAACTCTAATGA
1 GCTTCTATTCAACTCTAATGA
* * * *
2101750 GTTTTTATTCAGCTCTACTGA
1 GCTTCTATTCAACTCTAATGA
2101771 GCTTCTATT
1 GCTTCTATT
2101780 TAACCCTTAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.45
Consensus pattern (21 bp):
GCTTCTATTCAACTCTAATGA
Found at i:2104778 original size:8 final size:8
Alignment explanation
Indices: 2104767--2104796 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2104757 TAAGTTATTA
2104767 TATTATAT
1 TATTATAT
*
2104775 TATTATAA
1 TATTATAT
2104783 TATTATAT
1 TATTATAT
2104791 TATTAT
1 TATTAT
2104797 TATATACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:2104785 original size:16 final size:16
Alignment explanation
Indices: 2104761--2104801 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
2104751 AATAAGTAAG
2104761 TTATTATATTATATTA
1 TTATTATATTATATTA
*
2104777 TTATAATATTATATTA
1 TTATTATATTATATTA
2104793 TTATTATAT
1 TTATTATAT
2104802 ACATAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTATATTATATTA
Found at i:2105883 original size:25 final size:24
Alignment explanation
Indices: 2105855--2105989 Score: 118
Period size: 25 Copynumber: 5.6 Consensus size: 24
2105845 ACTTTAGTGC
*
2105855 GCTCTCTGATTATTAGCACATTGGT
1 GCTCTCTG-TTATTAGCACATTAGT
* * * *
2105880 GCTCTCTGACTACTAGCACGTTGGT
1 GCTCTCTG-TTATTAGCACATTAGT
* *
2105905 GCTCTCTGATTATTAGCACGTCAGT
1 GCTCTCTG-TTATTAGCACATTAGT
2105930 GCTCTCTG-T-TTAGCACATCT-GT
1 GCTCTCTGTTATTAGCACAT-TAGT
*
2105952 GCTCTCTG-TA-TAGCACTTTAGT
1 GCTCTCTGTTATTAGCACATTAGT
2105974 GCTCTCTGTTCATTAG
1 GCTCTCTGTT-ATTAG
2105990 TGCATATCAA
Statistics
Matches: 94, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
21 1 0.01
22 36 0.38
23 2 0.02
24 1 0.01
25 54 0.57
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (24 bp):
GCTCTCTGTTATTAGCACATTAGT
Found at i:2105945 original size:22 final size:22
Alignment explanation
Indices: 2105893--2105983 Score: 92
Period size: 22 Copynumber: 4.0 Consensus size: 22
2105883 CTCTGACTAC
**
2105893 TAGCACGTTGGTGCTCTCTGATTAT
1 TAGCACGTCAGTGCTCTCTG--T-T
2105918 TAGCACGTCAGTGCTCTCTGTT
1 TAGCACGTCAGTGCTCTCTGTT
* * *
2105940 TAGCACATCTGTGCTCTCTGTA
1 TAGCACGTCAGTGCTCTCTGTT
* *
2105962 TAGCACTTTAGTGCTCTCTGTT
1 TAGCACGTCAGTGCTCTCTGTT
2105984 CATTAGTGCA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
22 38 0.67
23 1 0.02
25 18 0.32
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (22 bp):
TAGCACGTCAGTGCTCTCTGTT
Found at i:2106446 original size:2 final size:2
Alignment explanation
Indices: 2106439--2106463 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2106429 ACGTATTTTG
2106439 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2106464 AAATGAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2106731 original size:14 final size:13
Alignment explanation
Indices: 2106700--2106737 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
2106690 TTTTTAAACA
2106700 TTTTTTG-AGAATT
1 TTTTTTGCA-AATT
2106713 TTTTTTGCAAATT
1 TTTTTTGCAAATT
2106726 TCTTTTTGCAAA
1 T-TTTTTGCAAA
2106738 ATCCTTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.58
Consensus pattern (13 bp):
TTTTTTGCAAATT
Found at i:2115450 original size:14 final size:13
Alignment explanation
Indices: 2115431--2115469 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2115421 ATTTGTTAAT
2115431 ATTTTAATATATAA
1 ATTTTAA-ATATAA
*
2115445 ATTTTAAATTTTAA
1 ATTTTAAA-TATAA
2115459 ATTTTAAATAT
1 ATTTTAAATAT
2115470 TTTTAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTAAATATAA
Found at i:2115454 original size:7 final size:7
Alignment explanation
Indices: 2115442--2115467 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2115432 TTTTAATATA
2115442 TAAATTT
1 TAAATTT
2115449 TAAATTT
1 TAAATTT
2115456 TAAATTT
1 TAAATTT
2115463 TAAAT
1 TAAAT
2115468 ATTTTTAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TAAATTT
Found at i:2115455 original size:21 final size:23
Alignment explanation
Indices: 2115417--2115458 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2115407 AATAATTTAT
*
2115417 TATAATTTGTTAATATTTTAATA
1 TATAAATTGTTAATATTTTAATA
2115440 TATAAATT-TTAA-ATTTTAA
1 TATAAATTGTTAATATTTTAA
2115459 ATTTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATAAATTGTTAATATTTTAATA
Found at i:2118043 original size:89 final size:89
Alignment explanation
Indices: 2117892--2118072 Score: 362
Period size: 89 Copynumber: 2.0 Consensus size: 89
2117882 AAGAACACCA
2117892 TTTCAAAAGAAACTCTGAAAATGACAGCAAATTGCAATCCATCACAATAACAATGGAAGAGTTGA
1 TTTCAAAAGAAACTCTGAAAATGACAGCAAATTGCAATCCATCACAATAACAATGGAAGAGTTGA
2117957 GAAAAGACTGAAACACTTGATTGG
66 GAAAAGACTGAAACACTTGATTGG
2117981 TTTCAAAAGAAACTCTGAAAATGACAGCAAATTGCAATCCATCACAATAACAATGGAAGAGTTGA
1 TTTCAAAAGAAACTCTGAAAATGACAGCAAATTGCAATCCATCACAATAACAATGGAAGAGTTGA
2118046 GAAAAGACTGAAACACTTGATTGG
66 GAAAAGACTGAAACACTTGATTGG
2118070 TTT
1 TTT
2118073 ACTCAGTTTT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 92 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (89 bp):
TTTCAAAAGAAACTCTGAAAATGACAGCAAATTGCAATCCATCACAATAACAATGGAAGAGTTGA
GAAAAGACTGAAACACTTGATTGG
Found at i:2119869 original size:43 final size:43
Alignment explanation
Indices: 2119803--2119890 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
2119793 CTCAAAAAGA
*
2119803 TTTTAAATTTTCTTTAAGTTGTTCAACTTGCAATTGGATTGAG
1 TTTTAAATTTTCTTTAAGCTGTTCAACTTGCAATTGGATTGAG
2119846 TTTTAAATTTTCTTTAAGCTGTTCAACTTGCAATTGGATTGAG
1 TTTTAAATTTTCTTTAAGCTGTTCAACTTGCAATTGGATTGAG
2119889 TT
1 TT
2119891 AACGAAGCGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (43 bp):
TTTTAAATTTTCTTTAAGCTGTTCAACTTGCAATTGGATTGAG
Found at i:2121653 original size:2 final size:2
Alignment explanation
Indices: 2121648--2121681 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2121638 TCAAAATTAC
2121648 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2121682 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2123860 original size:13 final size:13
Alignment explanation
Indices: 2123844--2123873 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2123834 AGTGACGTGG
*
2123844 AAAAGTGTTTTTA
1 AAAAGTATTTTTA
2123857 AAAAGTATTTTTA
1 AAAAGTATTTTTA
2123870 AAAA
1 AAAA
2123874 TTTTGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (13 bp):
AAAAGTATTTTTA
Found at i:2124078 original size:21 final size:23
Alignment explanation
Indices: 2124040--2124081 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2124030 AATAATTTAT
*
2124040 TATAATTTGTTAATATTTTAATA
1 TATAAATTGTTAATATTTTAATA
2124063 TATAAATT-TTAA-ATTTTAA
1 TATAAATTGTTAATATTTTAA
2124082 ATAGTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATAAATTGTTAATATTTTAATA
Found at i:2125153 original size:21 final size:20
Alignment explanation
Indices: 2125124--2125175 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
2125114 TTTCAATTTT
* *
2125124 TTAATAAAATCATTAAAAATG
1 TTAAAAAAATC-TTAAAAATC
* *
2125145 TTAAAAAAAACTTATAAATC
1 TTAAAAAAATCTTAAAAATC
2125165 TATAAAAAAAT
1 T-TAAAAAAAT
2125176 TGTAAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (20 bp):
TTAAAAAAATCTTAAAAATC
Found at i:2129013 original size:3 final size:3
Alignment explanation
Indices: 2129005--2129060 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
2128995 TTTATGTATC
2129005 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2129053 TTA TTA TT
1 TTA TTA TT
2129061 TACTTAATTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2129201 original size:32 final size:31
Alignment explanation
Indices: 2129148--2129243 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
2129138 TTTAGATAAT
2129148 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
*
2129179 TTTAAAGAGTTTTTATTGGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
2129211 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
2129242 TT
1 TT
2129244 GTAATTTGCC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 32 0.52
32 29 0.48
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:2131548 original size:11 final size:11
Alignment explanation
Indices: 2131528--2131624 Score: 59
Period size: 11 Copynumber: 9.3 Consensus size: 11
2131518 TAAAAATTAA
2131528 AAAAAGTATTTT
1 AAAAA-TATTTT
2131540 AAAAATATTTT
1 AAAAATATTTT
*
2131551 --AAA-A-TTA
1 AAAAATATTTT
2131558 AAAAAGTATTTT
1 AAAAA-TATTTT
*
2131570 AAAAAAATTTT
1 AAAAATATTTT
2131581 --AAA-A-TTT
1 AAAAATATTTT
2131588 AAAAA-ATTTAAT
1 AAAAATATTT--T
*
2131600 AAAAGTATTTT
1 AAAAATATTTT
*
2131611 AAAAGTATTTT
1 AAAAATATTTT
2131622 AAA
1 AAA
2131625 TTAAAAAAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
7 5 0.07
8 2 0.03
9 13 0.19
10 2 0.03
11 27 0.39
12 17 0.24
13 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:2131563 original size:30 final size:30
Alignment explanation
Indices: 2131513--2131614 Score: 127
Period size: 30 Copynumber: 3.3 Consensus size: 30
2131503 ACCAAAAATT
2131513 TATTTTAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAAAAAGTATTTTAAAAA
2131545 TATTTTAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAGTATTTTAAAAA
* * *
2131575 AATTTTAAAATTTAAAAAA-T-TTAATAAAAG
1 TATTTTAAAA-TTAAAAAAGTATT-TTAAAAA
2131605 TATTTTAAAA
1 TATTTTAAAA
2131615 GTATTTTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
29 2 0.03
30 42 0.66
31 14 0.22
32 6 0.09
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (30 bp):
TATTTTAAAATTAAAAAAGTATTTTAAAAA
Found at i:2131604 original size:41 final size:39
Alignment explanation
Indices: 2131551--2131634 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 39
2131541 AAAATATTTT
*
2131551 AAAA-TTAAAAAAGTATTTTAAAAAAATTTTAAAATTTAA
1 AAAATTTAAAAAAGTATTTTAAAAAAATTTT-AAATTAAA
**
2131590 AAAATTTAATAAAAGTATTTTAAAAGTATTTTAAATTAAA
1 AAAATTTAA-AAAAGTATTTTAAAAAAATTTTAAATTAAA
2131630 AAAAT
1 AAAAT
2131635 AAAAAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 4 0.10
40 16 0.40
41 20 0.50
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (39 bp):
AAAATTTAAAAAAGTATTTTAAAAAAATTTTAAATTAAA
Found at i:2132354 original size:22 final size:22
Alignment explanation
Indices: 2132312--2132352 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2132302 AAGTTGAAAA
2132312 TAATTTTTAAAAATATTTTTAT
1 TAATTTTTAAAAATATTTTTAT
*
2132334 TAATTTTT-AATATATTTTT
1 TAATTTTTAAAAATATTTTT
2132353 TAGATTACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TAATTTTTAAAAATATTTTTAT
Found at i:2135984 original size:9 final size:9
Alignment explanation
Indices: 2135972--2136031 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 9
2135962 TTTTTTTATT
2135972 TTTTTATAA
1 TTTTTATAA
2135981 TTTTTA-AA
1 TTTTTATAA
*
2135989 TATTTA-AA
1 TTTTTATAA
2135997 TTTTTATAACA
1 TTTTTAT-A-A
*
2136008 TTTTTAATAG
1 TTTTT-ATAA
2136018 TTTTTATAA
1 TTTTTATAA
2136027 TTTTT
1 TTTTT
2136032 TTAAAAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 14 0.33
9 14 0.33
10 6 0.14
11 7 0.16
12 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:2136010 original size:17 final size:17
Alignment explanation
Indices: 2135974--2136015 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2135964 TTTTTATTTT
*
2135974 TTTATAATTTTTAAATA
1 TTTATAATTTTTAAACA
2135991 TTTA-AATTTTTATAACA
1 TTTATAATTTTTA-AACA
*
2136008 TTTTTAAT
1 TTTATAAT
2136016 AGTTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 8 0.38
17 10 0.48
18 3 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATAATTTTTAAACA
Found at i:2139715 original size:92 final size:95
Alignment explanation
Indices: 2139611--2139801 Score: 237
Period size: 95 Copynumber: 2.0 Consensus size: 95
2139601 TTTAAAAAAT
* * *
2139611 AAAATATATTTAACATAATGATAAATATAA-AAAAATATATT-T-TTATTATATAATTATTAATT
1 AAAATATATTTAACATAATCATAAATATAATAAAAATATATTGTATAATTACATAATTATTAATT
*
2139673 TATTTATATAAATAAAGGAGTTATT-AATTA
66 TATTTATATAAATAAAAGAGTT-TTAAATTA
* * * ** * * *
2139703 AAAATATTTTTAACATAATCATATATATAATATATTTTTATTGTATAATTACATATTTATTATTT
1 AAAATATATTTAACATAATCATAAATATAATAAAAATATATTGTATAATTACATAATTATTAATT
2139768 TATTTATATAAATAAAAGAGTTTTAAATTA
66 TATTTATATAAATAAAAGAGTTTTAAATTA
2139798 AAAA
1 AAAA
2139802 GATGAATTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
92 27 0.33
93 7 0.08
94 3 0.04
95 46 0.55
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (95 bp):
AAAATATATTTAACATAATCATAAATATAATAAAAATATATTGTATAATTACATAATTATTAATT
TATTTATATAAATAAAAGAGTTTTAAATTA
Found at i:2139749 original size:22 final size:23
Alignment explanation
Indices: 2139724--2139775 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
2139714 AACATAATCA
*
2139724 TATATATAATATATTT-TTATTG
1 TATATATAACATATTTATTATTG
* *
2139746 TATA-ATTACATATTTATTATTT
1 TATATATAACATATTTATTATTG
*
2139768 TATTTATA
1 TATATATA
2139776 TAAATAAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 9 0.39
22 12 0.52
23 2 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATAACATATTTATTATTG
Found at i:2140308 original size:10 final size:11
Alignment explanation
Indices: 2140288--2140329 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
2140278 TCTTCTTAAA
2140288 AATTAATATTT
1 AATTAATATTT
2140299 AATT-ATATTT
1 AATTAATATTT
*
2140309 AAATAATA-TT
1 AATTAATATTT
2140319 -ATTAATATTT
1 AATTAATATTT
2140329 A
1 A
2140330 TTTATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.23
10 13 0.50
11 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTAATATTT
Found at i:2143125 original size:23 final size:23
Alignment explanation
Indices: 2143076--2143126 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2143066 ACAAATGTCC
***
2143076 GTAACCCCTAAATTCATTATCTT
1 GTAACCCCTAAATTCATTATAAA
2143099 GTAACCCCTAAATT-ATTTATAAA
1 GTAACCCCTAAATTCA-TTATAAA
2143122 GTAAC
1 GTAAC
2143127 TTAATGCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (23 bp):
GTAACCCCTAAATTCATTATAAA
Found at i:2155693 original size:9 final size:9
Alignment explanation
Indices: 2155681--2155757 Score: 102
Period size: 9 Copynumber: 8.4 Consensus size: 9
2155671 AAAATAAAAA
2155681 AATTCGGGT
1 AATTCGGGT
2155690 AATTCGGGT
1 AATTCGGGT
*
2155699 ATTTTTC-GGT
1 A--ATTCGGGT
*
2155709 AATTCGGTT
1 AATTCGGGT
*
2155718 AATTCGGTT
1 AATTCGGGT
2155727 AATTCGGGT
1 AATTCGGGT
2155736 AATTCGGGT
1 AATTCGGGT
2155745 AATTCGGGT
1 AATTCGGGT
2155754 AATT
1 AATT
2155758 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
8 3 0.05
9 51 0.84
10 4 0.07
11 3 0.05
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:2159838 original size:14 final size:13
Alignment explanation
Indices: 2159804--2159845 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
2159794 ACTATCAAGC
2159804 TTAAATTA-TAAA
1 TTAAATTATTAAA
*
2159816 TTTAATTATTAAA
1 TTAAATTATTAAA
2159829 TCTAAATTATTAAA
1 T-TAAATTATTAAA
2159843 TTA
1 TTA
2159846 TAAATTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.27
13 7 0.27
14 12 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTATTAAA
Found at i:2162544 original size:17 final size:17
Alignment explanation
Indices: 2162518--2162552 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2162508 ATACTACAAA
*
2162518 AATTATTTCGATTAATT
1 AATTAATTCGATTAATT
2162535 AATTAATTCGATTAATT
1 AATTAATTCGATTAATT
2162552 A
1 A
2162553 CTTGATTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (17 bp):
AATTAATTCGATTAATT
Found at i:2164134 original size:18 final size:18
Alignment explanation
Indices: 2164111--2164164 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
2164101 AAATCGTGTC
2164111 ATTCATTTTCAAAACATT
1 ATTCATTTTCAAAACATT
* * *
2164129 ATTCATTTACAAATCTTT
1 ATTCATTTTCAAAACATT
*
2164147 ATTCAATTTCAAAACATT
1 ATTCATTTTCAAAACATT
2164165 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTCATTTTCAAAACATT
Found at i:2178262 original size:22 final size:22
Alignment explanation
Indices: 2178230--2178285 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
2178220 GTGACGATTC
*
2178230 TCAGTGACACAACATCCACTAG
1 TCAGTGTCACAACATCCACTAG
2178252 TCAGTGTCACAACATCCACTAG
1 TCAGTGTCACAACATCCACTAG
*
2178274 TCGGTGTCACAA
1 TCAGTGTCACAA
2178286 TTTCTTCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.21
Consensus pattern (22 bp):
TCAGTGTCACAACATCCACTAG
Found at i:2185089 original size:3 final size:3
Alignment explanation
Indices: 2185081--2185124 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2185071 ATTTTAGAGC
2185081 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2185125 GTTTTAAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2187224 original size:20 final size:21
Alignment explanation
Indices: 2187185--2187226 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2187175 ATCATAAAAG
*
2187185 AAGAAAAAAAGTCTATTTTTAT
1 AAGAAAAAAAG-CTAGTTTTAT
2187207 AAGAAAAAAA-CTAGTTTTAT
1 AAGAAAAAAAGCTAGTTTTAT
2187227 TTAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
AAGAAAAAAAGCTAGTTTTAT
Found at i:2188141 original size:26 final size:27
Alignment explanation
Indices: 2188106--2188172 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
2188096 TTTGGAATAA
2188106 ATTTTAATTAT-ATT-TTTATAATGTGG
1 ATTTTAATTATAATTATTTA-AATGTGG
*
2188132 ATTTTGATTATAATTATTTAAATGT--
1 ATTTTAATTATAATTATTTAAATGTGG
*
2188157 ATATTAATTAT-ATTAT
1 ATTTTAATTATAATTAT
2188173 AATTGTGCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 5 0.14
25 9 0.25
26 10 0.28
27 8 0.22
28 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (27 bp):
ATTTTAATTATAATTATTTAAATGTGG
Found at i:2196696 original size:17 final size:18
Alignment explanation
Indices: 2196674--2196707 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2196664 GTGAAATTTT
2196674 TTAATATA-TATTTTTAA
1 TTAATATATTATTTTTAA
2196691 TTAATATATTATTTTTA
1 TTAATATATTATTTTTA
2196708 TTATTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATATATTATTTTTAA
Found at i:2196710 original size:17 final size:16
Alignment explanation
Indices: 2196670--2196710 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
2196660 TTTTGTGAAA
2196670 TTTT-TTAATATATAT
1 TTTTATTAATATATAT
2196685 TTTTAATTAATATATTAT
1 TTTT-ATTAATATA-TAT
2196703 TTTTATTA
1 TTTTATTA
2196711 TTTTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
17 12 0.52
18 7 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATTAATATATAT
Found at i:2197360 original size:67 final size:68
Alignment explanation
Indices: 2197238--2197368 Score: 183
Period size: 67 Copynumber: 1.9 Consensus size: 68
2197228 TATTTAATTA
* * * *
2197238 AAAGATGTATTTAATTAACATTTTTATATATAAAATATTTACATATATTATAATTT-AGTGCATA
1 AAAGATGTAATTAATTAACATTTTTATATATAAAATATTTACACATACTACAATTTAAGTGCATA
2197302 TAT
66 TAT
* * * *
2197305 AAAGATTTAATTAATTCACATTTTTATATATAAAATATTTACGCATGCTACAATTTAAGTGCAT
1 AAAGATGTAATTAATTAACATTTTTATATATAAAATATTTACACATACTACAATTTAAGTGCAT
2197369 TTACTAATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
67 48 0.87
68 7 0.13
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (68 bp):
AAAGATGTAATTAATTAACATTTTTATATATAAAATATTTACACATACTACAATTTAAGTGCATA
TAT
Found at i:2197650 original size:43 final size:44
Alignment explanation
Indices: 2197573--2197656 Score: 152
Period size: 43 Copynumber: 1.9 Consensus size: 44
2197563 CTAGTCAATA
*
2197573 TGGGATTGAAATTAACTTTTTTTAATAAAAATAGTGAAGAATTG
1 TGGGATTAAAATTAACTTTTTTTAATAAAAATAGTGAAGAATTG
2197617 TGGGATTAAAATTAA-TTTTTTTAATAAAAATAGTGAAGAA
1 TGGGATTAAAATTAACTTTTTTTAATAAAAATAGTGAAGAA
2197657 GTGAGCTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 25 0.64
44 14 0.36
ACGTcount: A:0.44, C:0.01, G:0.17, T:0.38
Consensus pattern (44 bp):
TGGGATTAAAATTAACTTTTTTTAATAAAAATAGTGAAGAATTG
Found at i:2197710 original size:114 final size:111
Alignment explanation
Indices: 2197506--2197724 Score: 307
Period size: 114 Copynumber: 1.9 Consensus size: 111
2197496 AACACATCAA
* *
2197506 GGGATTAAAATTAATTTTTAATGAAAATAATGAAGAAGTGAGCTATGGAAGTCTTCTCTAGTCAA
1 GGGATTAAAATTAATTTTTAATAAAAATAATGAAGAAGTGAGCTATGGAAGTATTCTCTAGTCAA
*
2197571 TATGGGATTGAAATTAACTTTTTTTAATAAAAATAGTGAAGAATTGT
66 TATGGGATTAAAATTAAC-TTTTTTAATAAAAATAGTGAAGAATTGT
*
2197618 GGGATTAAAATTAATTTTTTTAATAAAAATAGTGAAGAAGTGAGCTAT-GAGAGTATTCTCTAGT
1 GGGATTAAAATTAA--TTTTTAATAAAAATAATGAAGAAGTGAGCTATGGA-AGTATTCTCTAGT
* **
2197682 CAATGTGGGATTAAAAATTTAAC-TTTTTAATGGAAATAGTGAA
63 CAATATGGGATT-AAAA-TTAACTTTTTTAATAAAAATAGTGAA
2197725 TAAATTGTCA
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
112 14 0.15
113 2 0.02
114 71 0.75
115 3 0.03
116 5 0.05
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (111 bp):
GGGATTAAAATTAATTTTTAATAAAAATAATGAAGAAGTGAGCTATGGAAGTATTCTCTAGTCAA
TATGGGATTAAAATTAACTTTTTTAATAAAAATAGTGAAGAATTGT
Found at i:2197849 original size:93 final size:93
Alignment explanation
Indices: 2197664--2197897 Score: 267
Period size: 93 Copynumber: 2.5 Consensus size: 93
2197654 GAAGTGAGCT
* * * * * *
2197664 ATGAGAGTATTCTCTAGTCAATGTGGGATTAAAAATTTAACTTTTTAATGGAAATAGTGAATAAA
1 ATGAGAGTGTTCTATAGTAAATGTGGGATT-AAAA-TTAACTTTTTAATGAAAAGAGTGAAGAAA
*
2197729 TTGTCACTTATTTATAAGGAAAATGTGAA-
64 TTGACACTTATTTATAAGGAAAATGTGAAC
* * *
2197758 ATATAGGAGTGTT-TATAGTTAATGTGAGATTAAAATTAACTTTTTAATGAAAAGAGTGAAGAAA
1 AT-GA-GAGTGTTCTATAGTAAATGTGGGATTAAAATTAACTTTTTAATGAAAAGAGTGAAGAAA
* * *
2197822 -TGAACACTTATTTATAGGGTAAGTGTGAAC
64 TTG-ACACTTATTTATAAGGAAAATGTGAAC
* *
2197852 ATGAGAGTGTTCTCTAGCAAATGTGGGATTAAAATTAACTTTTTAA
1 ATGAGAGTGTTCTATAGTAAATGTGGGATTAAAATTAACTTTTTAA
2197898 GGAATCAAAA
Statistics
Matches: 118, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
92 9 0.08
93 79 0.67
94 8 0.07
95 16 0.14
96 6 0.05
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (93 bp):
ATGAGAGTGTTCTATAGTAAATGTGGGATTAAAATTAACTTTTTAATGAAAAGAGTGAAGAAATT
GACACTTATTTATAAGGAAAATGTGAAC
Found at i:2198447 original size:40 final size:40
Alignment explanation
Indices: 2198403--2198495 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
2198393 TTGAGGGAAT
2198403 CATATTTTGTAAAGATTACATTAGATTAGATTTGATATGA
1 CATATTTTGTAAAGATTACATTAGATTAGATTTGATATGA
* * *
2198443 CATATTTTGTAAAGATTAGATTAGATTATATTTGATATGG
1 CATATTTTGTAAAGATTACATTAGATTAGATTTGATATGA
*
2198483 CATATCTTGTAAA
1 CATATTTTGTAAA
2198496 TCCCTAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (40 bp):
CATATTTTGTAAAGATTACATTAGATTAGATTTGATATGA
Found at i:2201440 original size:10 final size:10
Alignment explanation
Indices: 2201425--2201456 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2201415 GTGCACTCTT
2201425 TTTGTTGTTC
1 TTTGTTGTTC
2201435 TTTGTTGTTC
1 TTTGTTGTTC
*
2201445 TTTGTTGGTC
1 TTTGTTGTTC
2201455 TT
1 TT
2201457 CTTTTGGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.09, G:0.22, T:0.69
Consensus pattern (10 bp):
TTTGTTGTTC
Found at i:2201681 original size:21 final size:22
Alignment explanation
Indices: 2201642--2201682 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2201632 GTCAATGTAG
2201642 GATTAAAATTAACTTTTTAAGA
1 GATTAAAATTAACTTTTTAAGA
2201664 GATTAAAATTAA-TTTTTAA
1 GATTAAAATTAACTTTTTAA
2201683 TGAAAATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
GATTAAAATTAACTTTTTAAGA
Found at i:2201987 original size:22 final size:23
Alignment explanation
Indices: 2201943--2201990 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
2201933 TTAGCCAATG
*
2201943 AGGGATTAAAATTTACTTTTTTA
1 AGGGATTAAAATTTAATTTTTTA
*
2201966 AGGGGTTAAAA-TTAATTTTTTA
1 AGGGATTAAAATTTAATTTTTTA
2201988 AGG
1 AGG
2201991 AAATAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (23 bp):
AGGGATTAAAATTTAATTTTTTA
Found at i:2202268 original size:152 final size:152
Alignment explanation
Indices: 2202066--2202353 Score: 445
Period size: 152 Copynumber: 1.9 Consensus size: 152
2202056 ATGAAAATAG
* * * *
2202066 TAAAAGTATTATCTAGTTAATGTGGGAGTAAAAATAACTTTTTAATGAAAACAGTGAAGAAATTG
1 TAAAAGTATTATCTAGTCAATATGAGAGTAAAAATAACTTTTTAATGAAAACAGTAAAGAAATTG
* * *
2202131 TCACTTATTTATAAGGTAAATATGAGATATGGGAGTATTCTCCGGTCAAT-ATGGAATTAAAATT
66 TCACTTATTTATAACGTAAATATGAGATACGAGAGTATTCTCCGGTCAATGATGG-ATTAAAATT
2202195 AACTTTTTTATGAAAGCGAGCTA
130 AACTTTTTTATGAAAGCGAGCTA
*
2202218 TAAAAGTATTATCTAGTCAATATGAGA-TAAAAATTAACTTTTTAATGAAAACAGTAAAGAAGTT
1 TAAAAGTATTATCTAGTCAATATGAGAGTAAAAA-TAACTTTTTAATGAAAACAGTAAAGAAATT
* * *
2202282 GTCACTTATTTATAACGTAAATGTGAGATACGAGAGTATTCTCCTGTCAATGTTGGATTAAAATT
65 GTCACTTATTTATAACGTAAATATGAGATACGAGAGTATTCTCCGGTCAATGATGGATTAAAATT
2202347 AACTTTT
130 AACTTTT
2202354 AACCTTTTAA
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
151 6 0.05
152 114 0.93
153 3 0.02
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.35
Consensus pattern (152 bp):
TAAAAGTATTATCTAGTCAATATGAGAGTAAAAATAACTTTTTAATGAAAACAGTAAAGAAATTG
TCACTTATTTATAACGTAAATATGAGATACGAGAGTATTCTCCGGTCAATGATGGATTAAAATTA
ACTTTTTTATGAAAGCGAGCTA
Found at i:2208039 original size:13 final size:13
Alignment explanation
Indices: 2208014--2208054 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2208004 GTGTATGGTG
2208014 TTTAAATATTATTT
1 TTTAAA-ATTATTT
*
2208028 TTTAAAATTATTC
1 TTTAAAATTATTT
2208041 TTT-AAA-TATTT
1 TTTAAAATTATTT
2208052 TTT
1 TTT
2208055 CACTAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.28
12 3 0.12
13 9 0.36
14 6 0.24
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAAAATTATTT
Found at i:2212654 original size:6 final size:6
Alignment explanation
Indices: 2212643--2212671 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2212633 TGAATGTTTT
2212643 TATTTA TATTTA TATTTA TATTTA TATTT
1 TATTTA TATTTA TATTTA TATTTA TATTT
2212672 TCTTCTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATTTA
Found at i:2216766 original size:12 final size:12
Alignment explanation
Indices: 2216749--2216774 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2216739 TGTCACGAAA
2216749 ATTTAGTAGCAT
1 ATTTAGTAGCAT
2216761 ATTTAGTAGCAT
1 ATTTAGTAGCAT
2216773 AT
1 AT
2216775 GCTCTTAGTG
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:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATTTAGTAGCAT
Found at i:2223087 original size:12 final size:12
Alignment explanation
Indices: 2223057--2223081 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2223047 CCCCCCCCCC
2223057 AAAAAAAAAACA
1 AAAAAAAAAACA
2223069 AAAAAAAAAACA
1 AAAAAAAAAACA
2223081 A
1 A
2223082 CGAAAAGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:2226263 original size:19 final size:19
Alignment explanation
Indices: 2226239--2226276 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2226229 AAACATGCAG
2226239 AAGCATTCCATGGCAAAGA
1 AAGCATTCCATGGCAAAGA
2226258 AAGCATTCCATGGCAAAGA
1 AAGCATTCCATGGCAAAGA
2226277 TTTTTTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (19 bp):
AAGCATTCCATGGCAAAGA
Found at i:2232850 original size:21 final size:18
Alignment explanation
Indices: 2232826--2232873 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 18
2232816 AATCCCCATT
*
2232826 TTCATCATCATCCTCCCTCCC
1 TTCATCATCATCAT--CT-CC
2232847 TTCATCATCATCATCTCC
1 TTCATCATCATCATCTCC
2232865 TTCATCATC
1 TTCATCATC
2232874 CGTGTAATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.42
19 2 0.08
21 13 0.50
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.38
Consensus pattern (18 bp):
TTCATCATCATCATCTCC
Found at i:2232851 original size:18 final size:18
Alignment explanation
Indices: 2232830--2232874 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2232820 CCCATTTTCA
*
2232830 TCATCATCCTC-CCTCCCT
1 TCATCATCCTCATCT-CCT
*
2232848 TCATCATCATCATCTCCT
1 TCATCATCCTCATCTCCT
2232866 TCATCATCC
1 TCATCATCC
2232875 GTGTAATCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.36
Consensus pattern (18 bp):
TCATCATCCTCATCTCCT
Found at i:2243631 original size:24 final size:24
Alignment explanation
Indices: 2243590--2243675 Score: 75
Period size: 25 Copynumber: 3.5 Consensus size: 24
2243580 GTCACAACCA
* * *
2243590 ATCGGGATGCTTCGAAGAGCTAT-T
1 ATCGGGAAGC-TCGAAGAACCATAT
2243614 ATCGGGAAGCTCGCAAGAACCATAT
1 ATCGGGAAGCTCG-AAGAACCATAT
* **
2243639 AACGGGAAGCTCGAGAGGGCCATAT
1 ATCGGGAAGCTCGA-AGAACCATAT
*
2243664 ATCGGGATGCTC
1 ATCGGGAAGCTC
2243676 ATGAGAGCTA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
23 3 0.06
24 17 0.33
25 31 0.61
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (24 bp):
ATCGGGAAGCTCGAAGAACCATAT
Found at i:2246096 original size:22 final size:20
Alignment explanation
Indices: 2246066--2246113 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
2246056 AGAAATTAAC
* *
2246066 AATAATATATTTTATAATAAAA
1 AATATTATATATT-TAAT-AAA
*
2246088 AATATTATATATTTCATAAA
1 AATATTATATATTTAATAAA
2246108 AATATT
1 AATATT
2246114 TTTGTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 9 0.39
21 3 0.13
22 11 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTATATATTTAATAAA
Found at i:2248478 original size:15 final size:13
Alignment explanation
Indices: 2248429--2248481 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
2248419 TATTAACTTA
* *
2248429 TATTCTTAAAATA
1 TATTTTTAAAATT
2248442 TATTTTTAAAATT
1 TATTTTTAAAATT
2248455 TATACTTTTACTAAATT
1 TAT--TTTTA--AAATT
2248472 TATTTTTAAA
1 TATTTTTAAA
2248482 CTAAATAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 16 0.47
15 10 0.29
17 8 0.24
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTTTAAAATT
Found at i:2251697 original size:42 final size:42
Alignment explanation
Indices: 2251586--2251683 Score: 153
Period size: 42 Copynumber: 2.3 Consensus size: 42
2251576 TTATTTTGTC
* *
2251586 CACACGGGCATGTGTCTCAGTCC-TGTGTAACACATGGCCATG
1 CACACTGGCATGTGTCTCAG-CCGTGTGTAACACACGGCCATG
2251628 CACACTGGCATGTGTCTCAGCCGTGTGTAACACACGGCCATG
1 CACACTGGCATGTGTCTCAGCCGTGTGTAACACACGGCCATG
*
2251670 CACACTGGCGTGTG
1 CACACTGGCATGTG
2251684 GTTTGGCCGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 2 0.04
42 50 0.96
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.22
Consensus pattern (42 bp):
CACACTGGCATGTGTCTCAGCCGTGTGTAACACACGGCCATG
Found at i:2252682 original size:40 final size:40
Alignment explanation
Indices: 2252636--2252722 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
2252626 AATTCATTAC
* * * *
2252636 TTCAGTAATTTCATAGTTCAATGCAGTACACATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
** *
2252676 TTCAGTAACTTCACAATTCAATTTAGTACTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
*
2252716 TTTAGTA
1 TTCAGTA
2252723 TTCTATAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.34
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:2259877 original size:9 final size:9
Alignment explanation
Indices: 2259863--2259900 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2259853 AATATTATTT
2259863 ATTAAATTA
1 ATTAAATTA
2259872 ATTAAATT-
1 ATTAAATTA
*
2259880 ATTAAGTTA
1 ATTAAATTA
*
2259889 ACTAAATTA
1 ATTAAATTA
2259898 ATT
1 ATT
2259901 TCTCAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (9 bp):
ATTAAATTA
Found at i:2259883 original size:17 final size:17
Alignment explanation
Indices: 2259861--2259897 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2259851 TAAATATTAT
*
2259861 TTATTAAATTAATTAAA
1 TTATTAAATTAACTAAA
*
2259878 TTATTAAGTTAACTAAA
1 TTATTAAATTAACTAAA
2259895 TTA
1 TTA
2259898 ATTTCTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTATTAAATTAACTAAA
Found at i:2259917 original size:16 final size:18
Alignment explanation
Indices: 2259891--2259923 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2259881 TTAAGTTAAC
2259891 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
2259908 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
2259924 CCAATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:2267098 original size:35 final size:35
Alignment explanation
Indices: 2267047--2267116 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
2267037 GAAAACTTAG
*
2267047 GCTAGAAACCAAGTAATTCACTTATTTTCACACTC
1 GCTAAAAACCAAGTAATTCACTTATTTTCACACTC
2267082 GCTAAAAACCAAGTAATTCACTTATTTTCACACTC
1 GCTAAAAACCAAGTAATTCACTTATTTTCACACTC
2267117 AGTGCACTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (35 bp):
GCTAAAAACCAAGTAATTCACTTATTTTCACACTC
Found at i:2271760 original size:3 final size:3
Alignment explanation
Indices: 2271752--2271779 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2271742 AAAGAAAAAC
2271752 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
2271780 TTCGATCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:2274052 original size:32 final size:32
Alignment explanation
Indices: 2274011--2274075 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2274001 GTTTAAGTTT
* *
2274011 TTTATGTTTAAAAAATATATATATTTTTTATG
1 TTTAAGTTTAAAAAAAATATATATTTTTTATG
2274043 TTTAAGTTTAAAAAAAATATATATTTTTTATG
1 TTTAAGTTTAAAAAAAATATATATTTTTTATG
2274075 T
1 T
2274076 AACAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (32 bp):
TTTAAGTTTAAAAAAAATATATATTTTTTATG
Found at i:2274239 original size:16 final size:16
Alignment explanation
Indices: 2274218--2274259 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2274208 AATAATTTGA
*
2274218 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
2274234 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
2274250 TAGTTTTAAT
1 TAATTTTAAT
2274260 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:2279566 original size:29 final size:26
Alignment explanation
Indices: 2279505--2279567 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 26
2279495 TTAATTAATT
*
2279505 TTTTAAAATTTAAAAATTTAAAAATA
1 TTTTAAAATTTAAAAATTAAAAAATA
*
2279531 TTATAAAATCATTAAAACATTAAAAAATA
1 TTTTAAAAT--TTAAAA-ATTAAAAAATA
2279560 TTTTAAAA
1 TTTTAAAA
2279568 GGTATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.26
28 6 0.19
29 17 0.55
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
TTTTAAAATTTAAAAATTAAAAAATA
Found at i:2279727 original size:2 final size:2
Alignment explanation
Indices: 2279720--2279756 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2279710 AATAGAAGTA
2279720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2279757 CATCCAATAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2281469 original size:21 final size:20
Alignment explanation
Indices: 2281443--2281482 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2281433 ACAAGAAAAG
2281443 AAAAAAAGATTTAAGTACCT
1 AAAAAAAGATTTAAGTACCT
2281463 AAAAAAAGATTTAAGTACCT
1 AAAAAAAGATTTAAGTACCT
2281483 TGGATGTCCG
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:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (20 bp):
AAAAAAAGATTTAAGTACCT
Found at i:2286527 original size:11 final size:11
Alignment explanation
Indices: 2286513--2286537 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2286503 AAAAGGAAGT
2286513 TAAAATAATAA
1 TAAAATAATAA
2286524 TAAAATAATAA
1 TAAAATAATAA
2286535 TAA
1 TAA
2286538 TCTACCGTTC
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:2288274 original size:210 final size:210
Alignment explanation
Indices: 2287909--2288333 Score: 841
Period size: 210 Copynumber: 2.0 Consensus size: 210
2287899 ACATTTGGAG
2287909 TAATTGAAAAGAAAATTATGAAATGTAGTTTGGTGGTTGATTTCTTTTAATCATGATATTAAATA
1 TAATTGAAAAGAAAATTATGAAATGTAGTTTGGTGGTTGATTTCTTTTAATCATGATATTAAATA
2287974 TTTAGTCTCTGTTTAAAAGAATAAAACACATTTCATAATTATTTATTTATTTATTAAGAGAGTAT
66 TTTAGTCTCTGTTTAAAAGAATAAAACACATTTCATAATTATTTATTTATTTATTAAGAGAGTAT
*
2288039 CTGCACCTTAACTCGATTTGTATGAGCAATGTTGCTAATGCAGAAGGATGTGAGTTCGAATGCGT
131 CTGCACCTTAACTCGATTGGTATGAGCAATGTTGCTAATGCAGAAGGATGTGAGTTCGAATGCGT
2288104 TGAAACCAGTACAAC
196 TGAAACCAGTACAAC
2288119 TAATTGAAAAGAAAATTATGAAATGTAGTTTGGTGGTTGATTTCTTTTAATCATGATATTAAATA
1 TAATTGAAAAGAAAATTATGAAATGTAGTTTGGTGGTTGATTTCTTTTAATCATGATATTAAATA
2288184 TTTAGTCTCTGTTTAAAAGAATAAAACACATTTCATAATTATTTATTTATTTATTAAGAGAGTAT
66 TTTAGTCTCTGTTTAAAAGAATAAAACACATTTCATAATTATTTATTTATTTATTAAGAGAGTAT
2288249 CTGCACCTTAACTCGATTGGTATGAGCAATGTTGCTAATGCAGAAGGATGTGAGTTCGAATGCGT
131 CTGCACCTTAACTCGATTGGTATGAGCAATGTTGCTAATGCAGAAGGATGTGAGTTCGAATGCGT
2288314 TGAAACCAGTACAAC
196 TGAAACCAGTACAAC
2288329 TAATT
1 TAATT
2288334 TCAAGAACAA
Statistics
Matches: 214, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
210 214 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (210 bp):
TAATTGAAAAGAAAATTATGAAATGTAGTTTGGTGGTTGATTTCTTTTAATCATGATATTAAATA
TTTAGTCTCTGTTTAAAAGAATAAAACACATTTCATAATTATTTATTTATTTATTAAGAGAGTAT
CTGCACCTTAACTCGATTGGTATGAGCAATGTTGCTAATGCAGAAGGATGTGAGTTCGAATGCGT
TGAAACCAGTACAAC
Found at i:2291078 original size:23 final size:23
Alignment explanation
Indices: 2291017--2291078 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
2291007 CAACAGGCAA
*
2291017 CGACATCACAACGAGAAGGCTTC
1 CGACATCACAACGAGGAGGCTTC
** * * * *
2291040 TAACGTCACGATGAGGAGGTTTC
1 CGACATCACAACGAGGAGGCTTC
2291063 CGACATCACAACGAGG
1 CGACATCACAACGAGG
2291079 GCGAATATGA
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (23 bp):
CGACATCACAACGAGGAGGCTTC
Found at i:2292650 original size:20 final size:20
Alignment explanation
Indices: 2292625--2292683 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
2292615 CTAAAATTAA
2292625 AAAAATTATAAAATTATTTT
1 AAAAATTATAAAATTATTTT
2292645 AAAAATTA-AAAATTATTTT
1 AAAAATTATAAAATTATTTT
*
2292664 AAAACA-TATAAAAATATTTT
1 AAAA-ATTATAAAATTATTTT
2292684 TATATATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTATAAAATTATTTT
Found at i:2315418 original size:30 final size:30
Alignment explanation
Indices: 2315376--2315440 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
2315366 TGGCAAAAAA
2315376 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
* * *
2315406 TTCTCAACTTTCTCCTTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
2315436 CTCTC
1 CTCTC
2315441 TTTAATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.31, G:0.03, T:0.40
Consensus pattern (30 bp):
CTCTCAAATTTCTCCCTAAATTTCTCAAAG
Found at i:2317591 original size:24 final size:23
Alignment explanation
Indices: 2317564--2317611 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
2317554 CATTTAATAA
2317564 AATA-AAATTTATTTTTAATATTTT
1 AATAGAAA-TTATTTTT-ATATTTT
2317588 AATAGTAAATTATTTTTATATTTT
1 AATAG-AAATTATTTTTATATTTT
2317612 TATTTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.50
25 8 0.36
26 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
AATAGAAATTATTTTTATATTTT
Found at i:2317631 original size:29 final size:28
Alignment explanation
Indices: 2317540--2317633 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 28
2317530 TACAAACTTT
2317540 TTTTTATATTATTTCATTTAATAAAATAAA
1 TTTTTATATT-TTT-ATTTAATAAAATAAA
* *
2317570 -ATTTAT-TTTTAATATTTTAATAGTAAAT-TA
1 TTTTTATATTTT--TA-TTTAATA--AAATAAA
2317600 TTTTTATATTTTTATTTAATAAAATAGAA
1 TTTTTATATTTTTATTTAATAAAATA-AA
2317629 TTTTT
1 TTTTT
2317634 TTGAATAAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
27 6 0.12
28 3 0.06
29 26 0.51
30 3 0.06
31 9 0.18
32 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTTATATTTTTATTTAATAAAATAAA
Found at i:2320847 original size:126 final size:126
Alignment explanation
Indices: 2320622--2321142 Score: 832
Period size: 126 Copynumber: 4.1 Consensus size: 126
2320612 GGCCAAACAT
* * *
2320622 GAACTACTGTAGAAAAATAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGAAAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
*
2320687 CTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAG
*
2320748 GAACTACTGTAGAAAAAGAACGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
*** * *
2320813 CTGCTTGAATTGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAG
* *
2320874 GAACTACTGTAGAAAAAGAGCATCCATGT-AGGAGCTTTTTTCATCAATTTTGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGA-GAGCTTTTTTCATCAATTTTGCTGACAGTGCAT
* *
2320938 CCTGCTTGAA-CTATTTTTGACACTATTTGTTTAAAACTGTCTTCTCAAAATTATTTTTTCAG
65 CCTGCTTGAAGC-ATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAG
* * *
2321000 GAACTACTATAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
*
2321065 C-GTCTTGAAGCATTTTTGACACTATTTGTTCAGAACTATCTTCTCAAAATTATTTTTTCAG
66 CTG-CTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAG
2321126 GAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
2321143 AATCCTTATT
Statistics
Matches: 362, Mismatches: 28, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
125 2 0.01
126 359 0.99
127 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
CTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAG
Found at i:2321434 original size:14 final size:15
Alignment explanation
Indices: 2321403--2321439 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2321393 TTAGTTTAAC
2321403 AAAACCCTAAACCTA
1 AAAACCCTAAACCTA
* *
2321418 AAAACCCTAAATCAA
1 AAAACCCTAAACCTA
2321433 AAAACCC
1 AAAACCC
2321440 CAGGGACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.57, C:0.32, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAACCCTAAACCTA
Found at i:2329910 original size:22 final size:22
Alignment explanation
Indices: 2329875--2329926 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2329865 CTTTTTTAAC
*
2329875 TAATAATTAT-AAAT-TAAATT
1 TAATAATTTTCAAATATAAATT
*
2329895 ATAATTATTTTCAAATATAAATT
1 -TAATAATTTTCAAATATAAATT
2329918 TAATAATTT
1 TAATAATTT
2329927 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 8 0.31
22 12 0.46
23 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATTTTCAAATATAAATT
Found at i:2331407 original size:21 final size:21
Alignment explanation
Indices: 2331347--2331407 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
2331337 AATCACTTTA
2331347 ATTAATTTATCA-TTAA-AA-
1 ATTAATTTATCATTTAATAAT
* ** *
2331365 A-TAATTTACCATCGAATCAT
1 ATTAATTTATCATTTAATAAT
2331385 ATTAATTTATCATTTAATAAT
1 ATTAATTTATCATTTAATAAT
2331406 AT
1 AT
2331408 AATAAATAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
17 9 0.29
18 3 0.10
19 1 0.03
20 1 0.03
21 17 0.55
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTAATTTATCATTTAATAAT
Found at i:2334158 original size:104 final size:104
Alignment explanation
Indices: 2333978--2334176 Score: 319
Period size: 104 Copynumber: 1.9 Consensus size: 104
2333968 ATCGAGCTCC
* * * *
2333978 TAAGAATAAAATAGGAAGATTAATAGCGTTAGTGTAAAAATATCTTAAAGATTGATTAAGTAATT
1 TAAGAATAAAATAGGAAGATGAATAGAGTTAGTGTAAAAATATATTAAAGATAGATTAAGTAATT
* *
2334043 TAACCGGGAAAATTGTTAATTAAAGCTCAGGGACTCTCA
66 TAACCGAGAAAATCGTTAATTAAAGCTCAGGGACTCTCA
*
2334082 TAAGAATAAAATAGGAAGATGAATAGAGTTAGTGTAATAATATATTAAAGATCAG-TTAAGTAAT
1 TAAGAATAAAATAGGAAGATGAATAGAGTTAGTGTAAAAATATATTAAAGAT-AGATTAAGTAAT
2334146 TTAACCGAGAAAATCGTTAATTAAAGCTCAG
65 TTAACCGAGAAAATCGTTAATTAAAGCTCAG
2334177 TGGCTAAATT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
104 86 0.99
105 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (104 bp):
TAAGAATAAAATAGGAAGATGAATAGAGTTAGTGTAAAAATATATTAAAGATAGATTAAGTAATT
TAACCGAGAAAATCGTTAATTAAAGCTCAGGGACTCTCA
Found at i:2335414 original size:28 final size:29
Alignment explanation
Indices: 2335384--2335440 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2335374 ACCGACAGAA
**
2335384 TTTACTGAAAAAATTTCGGTTCGGTTAAT
1 TTTACTGAAAAAATTTCAATTCGGTTAAT
**
2335413 TTTTTTGAAAAAATTTCAATTCGGTTAA
1 TTTACTGAAAAAATTTCAATTCGGTTAA
2335441 CAGTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (29 bp):
TTTACTGAAAAAATTTCAATTCGGTTAAT
Found at i:2336911 original size:12 final size:12
Alignment explanation
Indices: 2336870--2336914 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
2336860 GGATTGCAAG
*
2336870 TTTCCATTTTCA
1 TTTCCATTTCCA
* * *
2336882 TTTTCATCTCCT
1 TTTCCATTTCCA
2336894 TTTCCATTTCCA
1 TTTCCATTTCCA
2336906 TTTCCATTT
1 TTTCCATTT
2336915 TTGGAAACCT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTCCATTTCCA
Found at i:2343080 original size:16 final size:16
Alignment explanation
Indices: 2343059--2343110 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
2343049 CCGCCTATAT
2343059 TTAATTTTTTTTTAAA
1 TTAATTTTTTTTTAAA
*
2343075 TTAATTTTTATTTAAA
1 TTAATTTTTTTTTAAA
*
2343091 --AATATTTTTTTAAA
1 TTAATTTTTTTTTAAA
2343105 TATAAT
1 T-TAAT
2343111 ACAATAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 12 0.40
16 15 0.50
17 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAATTTTTTTTTAAA
Found at i:2343102 original size:14 final size:14
Alignment explanation
Indices: 2343064--2343106 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
2343054 TATATTTAAT
2343064 TTTTTTTTAAATTAA
1 TTTTTTTTAAA-TAA
2343079 TTTTTATTTAAA-AA
1 TTTTT-TTTAAATAA
2343093 TATTTTTTTAAATA
1 T-TTTTTTTAAATA
2343107 TAATACAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 9 0.36
15 10 0.40
16 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTTTAAATAA
Found at i:2348610 original size:33 final size:34
Alignment explanation
Indices: 2348552--2348620 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
2348542 AAGAAAGGAA
* *
2348552 ATGTGAGAATATATATTTGTTTTATT-TTATTTT
1 ATGTGAGAATATATATTTGTATTATTATAATTTT
2348585 ATGTG-GAATATTATATATT-TATTATTATAATTTT
1 ATGTGAGAATA-TATAT-TTGTATTATTATAATTTT
2348619 AT
1 AT
2348621 ACGAAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 5 0.16
33 16 0.52
34 10 0.32
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (34 bp):
ATGTGAGAATATATATTTGTATTATTATAATTTT
Found at i:2349103 original size:2 final size:2
Alignment explanation
Indices: 2349096--2349129 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2349086 AATTGTTCCA
*
2349096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2349130 TGACTAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2349851 original size:2 final size:2
Alignment explanation
Indices: 2349844--2349872 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2349834 NNNNNNNNNA
2349844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2349873 GCATTTGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2350568 original size:20 final size:18
Alignment explanation
Indices: 2350565--2350619 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
2350555 AAAGTATTTT
2350565 AAAAAAATTTTAAAATTA
1 AAAAAAATTTTAAAATTA
* *
2350583 AAAAAAGTATT----TT-
1 AAAAAAATTTTAAAATTA
2350596 AAAAAAATTTTAAAATTA
1 AAAAAAATTTTAAAATTA
2350614 AAAAAA
1 AAAAAA
2350620 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
13 9 0.32
14 2 0.07
17 2 0.07
18 15 0.54
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAAAAATTTTAAAATTA
Found at i:2350574 original size:11 final size:11
Alignment explanation
Indices: 2350544--2350610 Score: 54
Period size: 13 Copynumber: 6.2 Consensus size: 11
2350534 AAATTAAAAT
2350544 AAAAA-TTTAA
1 AAAAATTTTAA
2350554 AAAAGTATTTTAA
1 AAAA--ATTTTAA
2350567 AAAAATTTT--
1 AAAAATTTTAA
*
2350576 -AAAA-TTAAA
1 AAAAATTTTAA
2350585 AAAAGTATTTTAA
1 AAAA--ATTTTAA
2350598 AAAAATTTTAA
1 AAAAATTTTAA
2350609 AA
1 AA
2350611 TTAAAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
7 2 0.04
8 4 0.09
10 7 0.15
11 14 0.30
12 2 0.04
13 17 0.37
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:2350586 original size:30 final size:30
Alignment explanation
Indices: 2350545--2350629 Score: 131
Period size: 31 Copynumber: 2.9 Consensus size: 30
2350535 AATTAAAATA
2350545 AAAATTTAAAAAAGTATTTTAAAAAAATTTT
1 AAAA-TTAAAAAAGTATTTTAAAAAAATTTT
2350576 AAAATTAAAAAAAGTATTTTAAAAAAATTTT
1 AAAATT-AAAAAAGTATTTTAAAAAAATTTT
2350607 AAAATTAAAAAA--A-TTTAAAAAAA
1 AAAATTAAAAAAGTATTTTAAAAAAA
2350630 GTATTTTAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
27 10 0.19
28 1 0.02
30 8 0.15
31 34 0.64
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAATTAAAAAAGTATTTTAAAAAAATTTT
Done.