Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 130 of 171
Found at i:40759912 original size:30 final size:30
Alignment explanation
Indices: 40759876--40759961 Score: 147
Period size: 30 Copynumber: 2.9 Consensus size: 30
40759866 AAATTTCAAA
*
40759876 AATTGAAACGAACTAG-GACTGTAATGACAG
1 AATTGAAAAGAA-TAGAGACTGTAATGACAG
40759906 AATTGAAAAGAATAGAGACTGTAATGACAG
1 AATTGAAAAGAATAGAGACTGTAATGACAG
40759936 AATTGAAAAGAATAGAGACTGTAATG
1 AATTGAAAAGAATAGAGACTGTAATG
40759962 GCAAAAATTC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 3 0.06
30 51 0.94
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.21
Consensus pattern (30 bp):
AATTGAAAAGAATAGAGACTGTAATGACAG
Found at i:40760475 original size:25 final size:23
Alignment explanation
Indices: 40760426--40760477 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
40760416 CTAATCTCTC
* *
40760426 CTTTTTTTTTTTTTGTTTATATT
1 CTTTTTTTTTTTTTGCTCATATT
*
40760449 CTTTTTTCTTTTCTTTGCTCATCTT
1 CTTTTTT-TTTT-TTTGCTCATATT
40760474 CTTT
1 CTTT
40760478 AGTGTCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.29
24 4 0.17
25 13 0.54
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (23 bp):
CTTTTTTTTTTTTTGCTCATATT
Found at i:40768244 original size:52 final size:52
Alignment explanation
Indices: 40768166--40768343 Score: 284
Period size: 52 Copynumber: 3.4 Consensus size: 52
40768156 AAACAGATCT
* * *
40768166 GATGACTATGTGTCATCGTTAGTATATGAATCCTCTACGGATTATGAGGTTC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTTC
*
40768218 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTTC
* * *
40768270 GATGAGTATGTGTCATCGTGAGCATATGAATCCTTTACAGATTAAGAGGTTC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTTC
*
40768322 GATGACTATATGTCATCGTGAG
1 GATGACTATGTGTCATCGTGAG
40768344 GTCCGATGGC
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 116 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTTC
Found at i:40768344 original size:26 final size:26
Alignment explanation
Indices: 40768315--40768364 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
40768305 TACAGATTAA
*
40768315 GAGGTTCGATGACTATATGTCATCGT
1 GAGGTCCGATGACTATATGTCATCGT
* *
40768341 GAGGTCCGATGGCTATGTGTCATC
1 GAGGTCCGATGACTATATGTCATC
40768365 ATGGGTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (26 bp):
GAGGTCCGATGACTATATGTCATCGT
Found at i:40769037 original size:21 final size:21
Alignment explanation
Indices: 40769011--40769051 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40769001 GGTATTTCTG
* *
40769011 TATGTGGAAGTATCGGTAGAT
1 TATGTGCAAGTATCGATAGAT
*
40769032 TATGTGCATGTATCGATAGA
1 TATGTGCAAGTATCGATAGA
40769052 AGTTACATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.34
Consensus pattern (21 bp):
TATGTGCAAGTATCGATAGAT
Found at i:40777443 original size:52 final size:52
Alignment explanation
Indices: 40777365--40777557 Score: 278
Period size: 52 Copynumber: 3.7 Consensus size: 52
40777355 TAAATGAAAC
* *
40777365 AGGTCCGACGACTATGTGTCATCGTGAGTATATGAATTCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTATG
* *
40777417 AGGTCCGATGACTATGTGTCGTCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTATG
**
40777469 AGGTCCGATGACTATACGTCATCGTGAGTATATGAATTCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTATG
** * * * *
40777521 AGGTGTGGTGGCTATGTGTCATCATGAATATATGAAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
40777558 GAAATGAAAT
Statistics
Matches: 125, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTATG
Found at i:40780658 original size:30 final size:30
Alignment explanation
Indices: 40780624--40780685 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
40780614 CAACTTAACA
* * * *
40780624 AACAAATGTCTCTAAAATAGTAATAAAATT
1 AACAAATATCTCTAAAACAATAACAAAATT
40780654 AACAAATATCTCTAAAACAATAACAAAATT
1 AACAAATATCTCTAAAACAATAACAAAATT
40780684 AA
1 AA
40780686 TAATAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (30 bp):
AACAAATATCTCTAAAACAATAACAAAATT
Found at i:40783409 original size:17 final size:17
Alignment explanation
Indices: 40783387--40783447 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
40783377 CTCAAACCAT
40783387 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
40783404 TTTAAATTTATTTT-TA
1 TTTAAATTTATTTTAAA
* *
40783420 TTCAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
40783438 TTTAAATTTA
1 TTTAAATTTA
40783448 AAATTATTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 13 0.36
17 14 0.39
18 9 0.25
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:40783428 original size:16 final size:17
Alignment explanation
Indices: 40783390--40783447 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
40783380 AAACCATTTT
*
40783390 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTC
*
40783407 AAATTTATTTT-TATTC
1 AAATTTATTTTAAATTC
* *
40783423 AAATTTGTTTTAAAATTT
1 AAATTTATTTT-AAATTC
40783441 AAATTTA
1 AAATTTA
40783448 AAATTATTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.39
17 11 0.33
18 9 0.27
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
AAATTTATTTTAAATTC
Found at i:40783455 original size:34 final size:34
Alignment explanation
Indices: 40783389--40783464 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
40783379 CAAACCATTT
***
40783389 TAAATTTATTTTAAATTTAAATTTATTTTTATTC
1 TAAATTTATTTTAAATTTAAATTTAAAATTATTC
*
40783423 -AAATTTGTTTTAAAATTTAAATTTAAAATTATTC
1 TAAATTTATTTT-AAATTTAAATTTAAAATTATTC
40783457 TAAATTTA
1 TAAATTTA
40783465 AATGATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 10 0.29
34 19 0.54
35 6 0.17
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (34 bp):
TAAATTTATTTTAAATTTAAATTTAAAATTATTC
Found at i:40784171 original size:3 final size:3
Alignment explanation
Indices: 40784163--40784199 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
40784153 CATTAAATGA
40784163 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40784200 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40785371 original size:30 final size:29
Alignment explanation
Indices: 40785319--40785634 Score: 192
Period size: 29 Copynumber: 10.7 Consensus size: 29
40785309 CCCTACACTG
* * *
40785319 TCCAAAAATCATATTTCTACCCCTGAAGTCT
1 TCCAAAAATTACATTT-TACCCCTGAA-ACT
40785350 T-CAAAAATTACATTTTGACCCC-GAAACT
1 TCCAAAAATTACATTTT-ACCCCTGAAACT
* *
40785378 TCTAAAAATTACCATTTTA-CCCTTAAACT
1 TCCAAAAATTA-CATTTTACCCCTGAAACT
*
40785407 TCCAAAAACTT-CATTTTTA-ACCTCGAAACT
1 TCCAAAAA-TTACA-TTTTACCCCT-GAAACT
*
40785437 TCCAAAAATTACATTTTAACCCTCG-AACT
1 TCCAAAAATTACATTTTACCCCT-GAAACT
* *
40785466 TCCAAAAATTCCATTTTTGAGCCC-GAAACT
1 TCCAAAAATTACA-TTTT-ACCCCTGAAACT
*
40785496 TCAAAAAATTACATTTTTACCCCCT--AACT
1 TCCAAAAATTACA-TTTTA-CCCCTGAAACT
* * * *
40785525 TCCAAACATTCCATTTTAAACCC-AAAACT
1 TCCAAAAATTACATTTT-ACCCCTGAAACT
*
40785554 TCTAAAAATTACCATTTTA-CCCTCG-AA-T
1 TCCAAAAATTA-CATTTTACCCCT-GAAACT
* * * *
40785582 GTCCAAAAATTCCAATTTAAACCTTG-AACTT
1 -TCCAAAAATTAC-ATTTTACCCCTGAAAC-T
40785613 TCCAAAAATTACCATTTTACCC
1 TCCAAAAATTA-CATTTTACCC
40785635 TCAAATATCC
Statistics
Matches: 230, Mismatches: 29, Indels: 53
0.74 0.09 0.17
Matches are distributed among these distances:
28 20 0.09
29 105 0.46
30 98 0.43
31 7 0.03
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTACATTTTACCCCTGAAACT
Found at i:40785388 original size:29 final size:29
Alignment explanation
Indices: 40785351--40785631 Score: 225
Period size: 29 Copynumber: 9.6 Consensus size: 29
40785341 CTGAAGTCTT
*
40785351 CAAAAATTACATTTTGACCCCGAAACTTC
1 CAAAAATTACATTTTAACCCCGAAACTTC
* **
40785380 TAAAAATTACCATTTT-ACCCTTAAACTTC
1 CAAAAATTA-CATTTTAACCCCGAAACTTC
*
40785409 CAAAAACTT-CATTTTTAACCTCGAAACTTC
1 CAAAAA-TTACA-TTTTAACCCCGAAACTTC
40785439 CAAAAATTACATTTTAACCCTCG-AACTTC
1 CAAAAATTACATTTTAACCC-CGAAACTTC
* * *
40785468 CAAAAATTCCATTTTTGAGCCCGAAACTTC
1 CAAAAATTACA-TTTTAACCCCGAAACTTC
* * **
40785498 AAAAAATTACATTTTTACCCCCTAACTTC
1 CAAAAATTACATTTTAACCCCGAAACTTC
* * * *
40785527 CAAACATTCCATTTTAAACCCAAAACTTC
1 CAAAAATTACATTTTAACCCCGAAACTTC
*
40785556 TAAAAATTACCATTTT-ACCCTCG-AA-TGTC
1 CAAAAATTA-CATTTTAACCC-CGAAACT-TC
* * **
40785585 CAAAAATTCCAATTTAAACCTTG-AACTTTC
1 CAAAAATTAC-ATTTTAACCCCGAAAC-TTC
40785615 CAAAAATTACCATTTTA
1 CAAAAATTA-CATTTTA
40785632 CCCTCAAATA
Statistics
Matches: 200, Mismatches: 36, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
28 4 0.02
29 119 0.60
30 75 0.38
31 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (29 bp):
CAAAAATTACATTTTAACCCCGAAACTTC
Found at i:40785434 original size:59 final size:59
Alignment explanation
Indices: 40785351--40785811 Score: 410
Period size: 59 Copynumber: 7.9 Consensus size: 59
40785341 CTGAAGTCTT
* * * *
40785351 CAAAAATTACA-TTTTGACCCCGAAACTTCTAAAAATTACCATTTTACCCTTAAACT-TC
1 CAAAAATTCCATTTTTAACCTCGAAACTTCTAAAAATTACCATTTTACCCTCAAA-TATC
* *
40785409 CAAAAACTT-CATTTTTAACCTCGAAACTTCCAAAAATTA-CATTTTAACCCTCGAACT-TC
1 CAAAAA-TTCCATTTTTAACCTCGAAACTTCTAAAAATTACCATTTT-ACCCTC-AAATATC
* * * *
40785468 CAAAAATTCCATTTTTGAGCC-CGAAACTTCAAAAAATTA-CATTTTTACCCCCTAACT-TC
1 CAAAAATTCCATTTTT-AACCTCGAAACTTCTAAAAATTACCA-TTTTACCCTC-AAATATC
* * * * *
40785527 CAAACATTCCATTTTAAACC-CAAAACTTCTAAAAATTACCATTTTACCCTCGAATGTC
1 CAAAAATTCCATTTTTAACCTCGAAACTTCTAAAAATTACCATTTTACCCTCAAATATC
* * * *
40785585 CAAAAATTCCAATTTAAACCTTG-AACTTTCCAAAAATTACCATTTTACCCTCAAATATC
1 CAAAAATTCCATTTTTAACCTCGAAAC-TTCTAAAAATTACCATTTTACCCTCAAATATC
* * * * * *
40785644 CAAAAACT-CATTTTTGACATCG-AACTTTTCAAAAAGTACCATTTTACCCTCGAATATC
1 CAAAAATTCCATTTTTAACCTCGAAACTTCT-AAAAATTACCATTTTACCCTCAAATATC
* * * * * * *
40785702 CAAAAATACCATTTTTGACC-CCAAACTTTTCAAAAATCACCATTTTACCCCCAAATGTC
1 CAAAAATTCCATTTTTAACCTCGAAACTTCT-AAAAATTACCATTTTACCCTCAAATATC
* * * *
40785761 CAAAGATTCCCTTTTTGACCTCGAACCTT-TAAAAATTACCATTTTACCCTC
1 CAAAAATTCCATTTTTAACCTCGAAACTTCTAAAAATTACCATTTTACCCTC
40785812 GAAGTGTCTA
Statistics
Matches: 338, Mismatches: 50, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
57 4 0.01
58 131 0.39
59 188 0.56
60 15 0.04
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (59 bp):
CAAAAATTCCATTTTTAACCTCGAAACTTCTAAAAATTACCATTTTACCCTCAAATATC
Found at i:40785473 original size:88 final size:86
Alignment explanation
Indices: 40785351--40785838 Score: 288
Period size: 88 Copynumber: 5.6 Consensus size: 86
40785341 CTGAAGTCTT
* * *
40785351 CAAAAATTACATTTTGACCCCGAAACTTCTAAAAATTACCATTTTACCCTTAAACTTCCAAAAAC
1 CAAAAATTACATTTTAACCCCG-AACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAA-
40785416 TT-CATTTTTAACCTCGAAACTTC
64 TTACATTTTTAACCTCG-AACTTC
* *
40785439 CAAAAATTACATTTTAACCCTCGAACTTCCAAAAATT-CCATTTTTGAGCCC-GAAACTTCAAAA
1 CAAAAATTACATTTTAACCC-CGAACTTCCAAAAATTACCA-TTTT-A-CCCTCAAACTTCCAAA
* * *
40785502 AATTACATTTTTACCCCCTAACTTC
62 AATTACATTTTTAACCTCGAACTTC
* * ** * *
40785527 CAAACATTCCATTTTAAACCCAAAACTTCTAAAAATTACCATTTTACCCTCGAA-TGTCCAAAAA
1 CAAAAATTACATTTT-AACCCCGAACTTCCAAAAATTACCATTTTACCCTCAAACT-TCCAAAAA
* * * *
40785591 TTCCAATTTAAACCTTGAACTTTC
64 TTACATTTTTAACCTCGAAC-TTC
* * * * *
40785615 CAAAAATTACCATTTT-ACCCTC-AAATATCCAAAAACT--CATTTTTGA-CATCGAACTTTTCA
1 CAAAAATTA-CATTTTAACCC-CGAACT-TCCAAAAATTACCA-TTTT-ACCCTCAAAC-TTCCA
* *
40785675 AAAAGTACCA-TTTTACCCTCGAA-TATC
60 AAAATTA-CATTTTTAACCTCGAACT-TC
* * * * *
40785702 CAAAAA-TACCATTTTTGACCCCAAACTTTTCAAAAATCACCATTTTACCCCCAAA-TGTCCAAA
1 CAAAAATTA-CA-TTTTAACCCCGAAC-TTCCAAAAATTACCATTTTACCCTCAAACT-TCCAAA
* * * *
40785765 GATTCCCTTTTTGACCTCGAACCTT-
62 AATTACATTTTTAACCTCGAA-CTTC
* * * *
40785790 TAAAAATTACCATTTT-ACCCTCGAAGTGT-CTAAAATTACCGTTTTACCC
1 CAAAAATTA-CATTTTAACCC-CGAACT-TCCAAAAATTACCATTTTACCC
40785839 CTGGGCATCC
Statistics
Matches: 312, Mismatches: 55, Indels: 67
0.72 0.13 0.15
Matches are distributed among these distances:
86 12 0.04
87 80 0.26
88 156 0.50
89 58 0.19
90 6 0.02
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (86 bp):
CAAAAATTACATTTTAACCCCGAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATT
ACATTTTTAACCTCGAACTTC
Found at i:40785646 original size:29 final size:28
Alignment explanation
Indices: 40785351--40785838 Score: 195
Period size: 29 Copynumber: 16.7 Consensus size: 28
40785341 CTGAAGTCTT
40785351 CAAAAATTA-CATTTTGACCC-CGAAACTTC
1 CAAAAATTACCATTTT-ACCCTC-AAA-TTC
* *
40785380 TAAAAATTACCATTTTACCCTTAAACTTC
1 CAAAAATTACCATTTTACCCTCAAA-TTC
*
40785409 CAAAAACTT--CATTTTTAACCTCGAAACTTC
1 CAAAAA-TTACCA-TTTTACCCTC-AAA-TTC
*
40785439 CAAAAATTA-CATTTTAACCCTCGAACTTC
1 CAAAAATTACCATTTT-ACCCTC-AAATTC
*
40785468 CAAAAATT-CCATTTTTGAGCCC-GAAACTTC
1 CAAAAATTACCA-TTTT-A-CCCTCAAA-TTC
* * *
40785498 AAAAAATTA-CATTTTTACCCCCTAACTTC
1 CAAAAATTACCA-TTTTACCCTC-AAATTC
* *
40785527 CAAACATT-CCATTTTAAACCC-AAAACTTC
1 CAAAAATTACCATTTT--ACCCTCAAA-TTC
* *
40785556 TAAAAATTACCATTTTACCCTCGAATGTC
1 CAAAAATTACCATTTTACCCTCAAAT-TC
* * * *
40785585 CAAAAATT-CCAATTTAAACCTTGAACTTTC
1 CAAAAATTACC-ATTT-TACCCTCAA-ATTC
40785615 CAAAAATTACCATTTTACCCTCAAATATC
1 CAAAAATTACCATTTTACCCTCAAAT-TC
* * * *
40785644 CAAAAACT--CATTTTTGA-CATCGAACTTTT
1 CAAAAATTACCA-TTTT-ACCCTC-AA-ATTC
* *
40785673 CAAAAAGTACCATTTTACCCTCGAATATC
1 CAAAAATTACCATTTTACCCTCAAAT-TC
*
40785702 CAAAAA-TACCATTTTTGACCC-CAAACTTTT
1 CAAAAATTACCA-TTTT-ACCCTCAAA--TTC
* *
40785732 CAAAAATCACCATTTTACCCCCAAATGTC
1 CAAAAATTACCATTTTACCCTCAAAT-TC
* * * *
40785761 CAAAGATTCCCTTTTTGA-CCTCGAACCTT-
1 CAAAAATTACCATTTT-ACCCTC-AA-ATTC
* *
40785790 TAAAAATTACCATTTTACCCTCGAAGTGT-
1 CAAAAATTACCATTTTACCCTC-AAAT-TC
* *
40785819 CTAAAATTACCGTTTTACCC
1 CAAAAATTACCATTTTACCC
40785839 CTGGGCATCC
Statistics
Matches: 355, Mismatches: 58, Indels: 92
0.70 0.11 0.18
Matches are distributed among these distances:
27 2 0.01
28 35 0.10
29 188 0.53
30 116 0.33
31 14 0.04
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (28 bp):
CAAAAATTACCATTTTACCCTCAAATTC
Found at i:40785825 original size:117 final size:116
Alignment explanation
Indices: 40785362--40785834 Score: 451
Period size: 117 Copynumber: 4.0 Consensus size: 116
40785352 AAAAATTACA
* **
40785362 TTTTGACCCCGAAACTTCT-AAAAATTACCATTTTACCCTTAAACTTCCAAAAACTTCATTTTTA
1 TTTTGACCCC-AAACTTTTCAAAAATTACCATTTTACCCCCAAA-TTCCAAAAA-TTCATTTTTA
* *
40785426 ACCTCGAAACTTCCAAAAATTA-CATTTTAACCCTCGAACT-TCCAAAAATTCCAT
63 ACCTCGAAACTTCTAAAAATTACCATTTT-ACCCTCGAA-TGTCCAAAAATACCAT
* * *
40785480 TTTTGAGCCCGAAAC--TTCAAAAAATTA-CATTTTTACCCCCTAACTTCCAAACATTCCATTTT
1 TTTTGA-CCCCAAACTTTTC-AAAAATTACCA-TTTTACCCCC-AAATTCCAAAAATT-CATTTT
* * * *
40785542 AAACC-CAAAACTTCTAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCAA
61 TAACCTCGAAACTTCTAAAAATTACCATTTTACCCTCGAATGTCCAAAAATACCAT
** *** * * * *
40785597 TTTAAACCTTGAACTTTCCAAAAATTACCATTTTACCCTCAAATATCCAAAAACTCATTTTTGAC
1 TTTTGACCCCAAACTTTTCAAAAATTACCATTTTACCCCCAAAT-TCCAAAAATTCATTTTTAAC
* * * *
40785662 ATCG-AACTTTTCAAAAAGTACCATTTTACCCTCGAATATCCAAAAATACCAT
65 CTCGAAACTTCT-AAAAATTACCATTTTACCCTCGAATGTCCAAAAATACCAT
* * * *
40785714 TTTTGACCCCAAACTTTTCAAAAATCACCATTTTACCCCCAAATGTCCAAAGATTCCCTTTTTGA
1 TTTTGACCCCAAACTTTTCAAAAATTACCATTTTACCCCCAAAT-TCCAAAAATT-CATTTTTAA
* * * *
40785779 CCTCGAACCTT-TAAAAATTACCATTTTACCCTCGAAGTGTCTAAAATTACCGT
64 CCTCGAAACTTCTAAAAATTACCATTTTACCCTCGAA-TGTCCAAAAATACCAT
40785832 TTT
1 TTT
40785835 ACCCCTGGGC
Statistics
Matches: 290, Mismatches: 48, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
116 24 0.08
117 175 0.60
118 82 0.28
119 9 0.03
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.33
Consensus pattern (116 bp):
TTTTGACCCCAAACTTTTCAAAAATTACCATTTTACCCCCAAATTCCAAAAATTCATTTTTAACC
TCGAAACTTCTAAAAATTACCATTTTACCCTCGAATGTCCAAAAATACCAT
Found at i:40791355 original size:2 final size:2
Alignment explanation
Indices: 40791339--40791397 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
40791329 AATAGTTTGG
*
40791339 AT AT -T AT AC 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 AT
40791380 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
40791398 TGATATTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40795470 original size:59 final size:59
Alignment explanation
Indices: 40795369--40795648 Score: 333
Period size: 58 Copynumber: 4.8 Consensus size: 59
40795359 CATTCGGGGT
* * * *
40795369 TTAAAAAGG-ATTTTGGAAGGTTTGAGGGGTAAAATAGT-ATTTTTTGGTGAAATCGAGA
1 TTAAAATGGAATTTTGGAAAGTTTGA-GGGTAAAATGGTAATTTTTTGGTGAAATCGAGG
* * * * *
40795427 TTAAAATGGGATTTCGAAAAGTTCGAGGGTAAAATGGTAATTTTTT-GTGAAAT-TAGGG
1 TTAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTTGGTGAAATCGA-GG
* *
40795485 TTAAAATGGAATTTTGGAAAGTTTG-GTGGTAAAATGATAA-TTTTTGGTGAAATCGGGG
1 TTAAAATGGAATTTTGGAAAGTTTGAG-GGTAAAATGGTAATTTTTTGGTGAAATCGAGG
* * *
40795543 TTAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTGA-TTTTTGGTGAAATCGGGG
1 TTAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTTGGTGAAATCGAGG
40795601 TTAAAAATGGAATTTTGGAAAGTTT-AGGGGTAAAATGGTAATTTTTTG
1 TT-AAAATGGAATTTTGGAAAGTTTGA-GGGTAAAATGGTAATTTTTTG
40795649 AAGTTTTTGG
Statistics
Matches: 193, Mismatches: 19, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
57 7 0.04
58 125 0.65
59 55 0.28
60 6 0.03
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (59 bp):
TTAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTTGGTGAAATCGAGG
Found at i:40795484 original size:29 final size:29
Alignment explanation
Indices: 40795444--40795648 Score: 128
Period size: 28 Copynumber: 7.0 Consensus size: 29
40795434 GGGATTTCGA
40795444 AAAGTTCGAGGGTAAAATGGTAATTTTTTGTG
1 AAAGTT-G-GGGTAAAATGGTAATTTTTTG-G
*
40795476 AAA-TTAGGGTTAAAATGG-AA--TTTTGG
1 AAAGTT-GGGGTAAAATGGTAATTTTTTGG
* *
40795502 AAAGTTTGGTGGTAAAATGATAATTTTTGGTG
1 AAAG-TTGG-GGTAAAATGGTAATTTTTTG-G
*
40795534 AAA-TCGGGGTTAAAATGG-AA--TTTTGG
1 AAAGTTGGGG-TAAAATGGTAATTTTTTGG
* *
40795560 AAAGTTTGGGGGTAAAATGGTGATTTTTGGTG
1 AAAG-TT-GGGGTAAAATGGTAATTTTTTG-G
*
40795592 AAA-TCGGGGTTAAAAATGG-AA--TTTTGG
1 AAAGTTGGGG-T-AAAATGGTAATTTTTTGG
40795619 AAAGTTTAGGGGTAAAATGGTAATTTTTTG
1 AAAG-TT-GGGGTAAAATGGTAATTTTTTG
40795649 AAGTTTTTGG
Statistics
Matches: 135, Mismatches: 15, Indels: 47
0.69 0.08 0.24
Matches are distributed among these distances:
26 8 0.06
27 15 0.11
28 30 0.22
29 21 0.16
30 27 0.20
31 23 0.17
32 11 0.08
ACGTcount: A:0.33, C:0.01, G:0.30, T:0.36
Consensus pattern (29 bp):
AAAGTTGGGGTAAAATGGTAATTTTTTGG
Found at i:40795652 original size:29 final size:29
Alignment explanation
Indices: 40795453--40795705 Score: 113
Period size: 29 Copynumber: 8.7 Consensus size: 29
40795443 AAAAGTTCGA
*
40795453 GGGTAAAATGGTAATTTTTTGTGAA-ATTAG
1 GGGTAAAATGGTAA-TTTTT-TGAAGTTTAG
* *
40795483 GGTTAAAATGG-AA-TTTTGGAAAGTTT-G
1 GGGTAAAATGGTAATTTTTTG-AAGTTTAG
* * *
40795510 GTGGTAAAATGATAATTTTTGGTGAA--ATCG
1 G-GGTAAAATGGTAATTTTT--TGAAGTTTAG
* *
40795540 GGGTTAAAATGG-AA-TTTTGGAAAGTTTGG
1 GGG-TAAAATGGTAATTTTTTG-AAGTTTAG
* * *
40795569 GGGTAAAATGGTGATTTTTGGTGAA--ATCG
1 GGGTAAAATGGTAATTTTT--TGAAGTTTAG
*
40795598 GGGTTAAAAATGG-AA-TTTTGGAAAGTTTAG
1 GGG-T-AAAATGGTAATTTTTTG-AAGTTTAG
**
40795628 GGGTAAAATGGTAATTTTTTGAAGTTTTT
1 GGGTAAAATGGTAATTTTTTGAAGTTTAG
*
40795657 GGGTTAAA-GTGTAATTTTTTGAAGTTTTA-
1 GGGTAAAATG-GTAATTTTTTGAAG-TTTAG
40795686 GGGTCAAAAAT-GTAATTTTT
1 GGGT--AAAATGGTAATTTTT
40795706 GGATAGTTCA
Statistics
Matches: 170, Mismatches: 25, Indels: 56
0.68 0.10 0.22
Matches are distributed among these distances:
26 2 0.01
27 11 0.06
28 32 0.19
29 58 0.34
30 51 0.30
31 14 0.08
32 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.28, T:0.39
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTTGAAGTTTAG
Found at i:40797677 original size:17 final size:17
Alignment explanation
Indices: 40797637--40797696 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
40797627 GGTTAATATC
* **
40797637 AATTTAAATTTCAATTA
1 AATTTAAATTTAAAACA
* * *
40797654 AACTTAAATTTAGAGCA
1 AATTTAAATTTAAAACA
*
40797671 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAACA
40797688 AATTTAAAT
1 AATTTAAAT
40797697 CCATTTTAAC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (17 bp):
AATTTAAATTTAAAACA
Found at i:40809762 original size:24 final size:24
Alignment explanation
Indices: 40809705--40809767 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
40809695 TCGGAGGACC
* *
40809705 CGGTGGCATCCCACCCATGTTATT
1 CGGTGGCATTCCTCCCATGTTATT
* * *
40809729 CGGCGGCATTCCTCTCATGTTGTT
1 CGGTGGCATTCCTCCCATGTTATT
40809753 CGGTGGCATTCCTCC
1 CGGTGGCATTCCTCC
40809768 TCCCATATTG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.11, C:0.33, G:0.24, T:0.32
Consensus pattern (24 bp):
CGGTGGCATTCCTCCCATGTTATT
Found at i:40809790 original size:30 final size:30
Alignment explanation
Indices: 40809757--40809974 Score: 334
Period size: 30 Copynumber: 7.4 Consensus size: 30
40809747 GTTGTTCGGT
*
40809757 GGCATTCCTCCTCCCATATTGTTAGGAGGT
1 GGCATTCCTCCTCCCATATTGTTAGGAGGC
40809787 GGCATTCCTCCTCCCATATTGTTAGGAGGC
1 GGCATTCCTCCTCCCATATTGTTAGGAGGC
40809817 GGCATTCCTCCTCCCATATTGTTAGGAGGC
1 GGCATTCCTCCTCCCATATTGTTAGGAGGC
40809847 GGCATTCCTCCTCCCATATTGTTAGGAGGC
1 GGCATTCCTCCTCCCATATTGTTAGGAGGC
* * * *
40809877 GGCATTCTTCCTCCCATGTTGTTCGGTGGC
1 GGCATTCCTCCTCCCATATTGTTAGGAGGC
40809907 GGCA-T--TCCTCCCATATTGTTAGGAGGC
1 GGCATTCCTCCTCCCATATTGTTAGGAGGC
* * * *
40809934 GGTATTCCTCCTCCCATGTTGTTCGGCGGC
1 GGCATTCCTCCTCCCATATTGTTAGGAGGC
40809964 GGCATTCCTCC
1 GGCATTCCTCC
40809975 CATGTTATTG
Statistics
Matches: 172, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.13
28 1 0.01
29 1 0.01
30 148 0.86
ACGTcount: A:0.14, C:0.30, G:0.24, T:0.32
Consensus pattern (30 bp):
GGCATTCCTCCTCCCATATTGTTAGGAGGC
Found at i:40809975 original size:57 final size:57
Alignment explanation
Indices: 40809757--40810037 Score: 310
Period size: 60 Copynumber: 5.0 Consensus size: 57
40809747 GTTGTTCGGT
*
40809757 GGCATTCCTCCTCCCATATTGTTAGGAGGTGGCATTCCTCCTCCCATATTGTTAGGAGGC
1 GGCATTCCTCCTCCCATATTGTTAGGAGGCGGCA-T--TCCTCCCATATTGTTAGGAGGC
40809817 GGCATTCCTCCTCCCATATTGTTAGGAGGCGGCATTCCTCCTCCCATATTGTTAGGAGGC
1 GGCATTCCTCCTCCCATATTGTTAGGAGGCGGCA-T--TCCTCCCATATTGTTAGGAGGC
* * * *
40809877 GGCATTCTTCCTCCCATGTTGTTCGGTGGCGGCATTCCTCCCATATTGTTAGGAGGC
1 GGCATTCCTCCTCCCATATTGTTAGGAGGCGGCATTCCTCCCATATTGTTAGGAGGC
* * * * * * *
40809934 GGTATTCCTCCTCCCATGTTGTTCGGCGGCGGCATTCCTCCCATGTTATT--G-GCC
1 GGCATTCCTCCTCCCATATTGTTAGGAGGCGGCATTCCTCCCATATTGTTAGGAGGC
* * *
40809988 GGCATACCT-C-CCC-TATTGTT-GTA-G-GGCATTCCTCCCATGTTGTTAGGAGG
1 GGCATTCCTCCTCCCATATTGTTAGGAGGCGGCATTCCTCCCATATTGTTAGGAGG
40810038 TGGAGCTCCA
Statistics
Matches: 200, Mismatches: 18, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
48 19 0.09
49 1 0.00
50 2 0.01
51 7 0.04
52 3 0.01
53 1 0.00
54 9 0.05
55 1 0.00
57 67 0.34
59 1 0.00
60 89 0.44
ACGTcount: A:0.14, C:0.29, G:0.25, T:0.32
Consensus pattern (57 bp):
GGCATTCCTCCTCCCATATTGTTAGGAGGCGGCATTCCTCCCATATTGTTAGGAGGC
Found at i:40809990 original size:24 final size:24
Alignment explanation
Indices: 40809942--40810031 Score: 90
Period size: 24 Copynumber: 3.6 Consensus size: 24
40809932 GCGGTATTCC
40809942 TCCTCCCATGTTGTTCGGCGGCGGCAT
1 TCCTCCCATGTTGTT-GGC--CGGCAT
*
40809969 TCCTCCCATGTTATTGGCCGGCAT
1 TCCTCCCATGTTGTTGGCCGGCAT
* * * ***
40809993 ACCTCCCCTATTGTTGTAGGGCAT
1 TCCTCCCATGTTGTTGGCCGGCAT
40810017 TCCTCCCATGTTGTT
1 TCCTCCCATGTTGTT
40810032 AGGAGGTGGA
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
24 35 0.67
26 3 0.06
27 14 0.27
ACGTcount: A:0.11, C:0.32, G:0.22, T:0.34
Consensus pattern (24 bp):
TCCTCCCATGTTGTTGGCCGGCAT
Found at i:40819111 original size:4 final size:4
Alignment explanation
Indices: 40819102--40819137 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
40819092 TAAGTATGAA
*
40819102 AAAT AAAT AAAT AAAT AAAT AAAT ATAT ATAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAA
40819138 AATCCTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.90
5 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:40819211 original size:26 final size:27
Alignment explanation
Indices: 40819182--40819248 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 27
40819172 TTATTTTTGA
40819182 ATTATTTTAATTATTA-TTCTT-AATAT
1 ATTATTTTAATTATTACTT-TTAAATAT
*
40819208 ATTATTTTACTTA-TACTTTTAAATAT
1 ATTATTTTAATTATTACTTTTAAATAT
*
40819234 ATTGTTTTCAATTAT
1 ATTATTTT-AATTAT
40819249 CATTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 4 0.12
26 26 0.76
27 4 0.12
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (27 bp):
ATTATTTTAATTATTACTTTTAAATAT
Found at i:40819841 original size:2 final size:2
Alignment explanation
Indices: 40819829--40819859 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
40819819 CATGCATGAA
40819829 AT AT GAT 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
40819860 TTGCAAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40822535 original size:123 final size:118
Alignment explanation
Indices: 40822386--40822631 Score: 348
Period size: 122 Copynumber: 2.0 Consensus size: 118
40822376 AAAAAAAGAA
* *
40822386 AAGATTGGTCTGGTAGTGTATGTTTTTTTTTTTATATTGTAATAATAATTTGTATATTTAAAGAT
1 AAGATTGGTCTGGTAGTATATG-TTTTTTTTTTATATTGTAATAATAAATTGTATATTTAAAGAT
* ** *
40822451 ATAACATTGAACACTATATTTCTATTTGAATGATTAGATTTGTGTTGAAAGTAATACT
65 ATAACATTGAACA-T-TA-TACT-TTTGAATGATTAGATTTGTACTAAAAGTAATACT
* * *
40822509 AAGATTGGTTTGGTAGTATATGTTTTTTTTTTATATTGTAATAATAAATTGTATGTTTTAAGATA
1 AAGATTGGTCTGGTAGTATATGTTTTTTTTTTATATTGTAATAATAAATTGTATATTTAAAGATA
* *
40822574 TAACATTGAATATTATACTTTTGAATGATTAGATTTGTACTAAAAGTAATATT
66 TAACATTGAACATTATACTTTTGAATGATTAGATTTGTACTAAAAGTAATACT
40822627 AAGAT
1 AAGAT
40822632 ATAATTTAAA
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
118 35 0.31
119 3 0.03
120 2 0.02
121 1 0.01
122 51 0.46
123 20 0.18
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (118 bp):
AAGATTGGTCTGGTAGTATATGTTTTTTTTTTATATTGTAATAATAAATTGTATATTTAAAGATA
TAACATTGAACATTATACTTTTGAATGATTAGATTTGTACTAAAAGTAATACT
Found at i:40824449 original size:20 final size:21
Alignment explanation
Indices: 40824412--40824450 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40824402 AAATTAGAGT
*
40824412 GAAATTGTTTGAGTTTTGATA
1 GAAATTGTTAGAGTTTTGATA
40824433 GAAATTGTTAG-GTTTTGA
1 GAAATTGTTAGAGTTTTGA
40824451 AGCTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (21 bp):
GAAATTGTTAGAGTTTTGATA
Found at i:40825498 original size:24 final size:24
Alignment explanation
Indices: 40825460--40825576 Score: 144
Period size: 24 Copynumber: 4.9 Consensus size: 24
40825450 AATGTTTCTT
40825460 ATATTAGCTGGCGAGCGTAAACGC
1 ATATTAGCTGGCGAGCGTAAACGC
* * ***
40825484 ATATTAACTGACGAGCGTAAATAT
1 ATATTAGCTGGCGAGCGTAAACGC
* *
40825508 ATATTAGATGGCGAGAGTAAACGC
1 ATATTAGCTGGCGAGCGTAAACGC
*
40825532 ATATTAGCTGGCGAGCGTAAACGT
1 ATATTAGCTGGCGAGCGTAAACGC
* *
40825556 ATCTTAGCTGACGAGCGTAAA
1 ATATTAGCTGGCGAGCGTAAA
40825577 TGTACTGAAC
Statistics
Matches: 76, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (24 bp):
ATATTAGCTGGCGAGCGTAAACGC
Found at i:40825576 original size:48 final size:48
Alignment explanation
Indices: 40825459--40825576 Score: 164
Period size: 48 Copynumber: 2.5 Consensus size: 48
40825449 CAATGTTTCT
*
40825459 TATATTAGCTGGCGAGCGTAAACGCATATTAACTGACGAGCGTAAATA
1 TATATTAGCTGGCGAGCGTAAACGCATATTAACTGACGAGCGTAAACA
* * * * *
40825507 TATATTAGATGGCGAGAGTAAACGCATATTAGCTGGCGAGCGTAAACG
1 TATATTAGCTGGCGAGCGTAAACGCATATTAACTGACGAGCGTAAACA
* *
40825555 TATCTTAGCTGACGAGCGTAAA
1 TATATTAGCTGGCGAGCGTAAA
40825577 TGTACTGAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (48 bp):
TATATTAGCTGGCGAGCGTAAACGCATATTAACTGACGAGCGTAAACA
Found at i:40828491 original size:19 final size:19
Alignment explanation
Indices: 40828467--40828504 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40828457 GTTTTCGATG
40828467 GTATCGTGAACAAGTTTTT
1 GTATCGTGAACAAGTTTTT
40828486 GTATCGTGAACAAGTTTTT
1 GTATCGTGAACAAGTTTTT
40828505 TTTAGATGGT
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:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (19 bp):
GTATCGTGAACAAGTTTTT
Found at i:40829826 original size:93 final size:92
Alignment explanation
Indices: 40829706--40829891 Score: 282
Period size: 93 Copynumber: 2.0 Consensus size: 92
40829696 AATTCATGGG
* *
40829706 TTTCATATACAATAATATAAATTCAAGTTCAAGGAATATATAATCAAGTTCATGTAAATATGGTA
1 TTTCATATACAAGAATATAAATTCAAGTTCAACGAATATATAATCAAGTTCATGTAAATATGGTA
* *
40829771 GTAGTTAATAAAAATATCATTTCGTTCA
66 GTAATTAATAAAAA-ATCATTTCATTCA
* * *
40829799 TTTCTTATACAAGAATATAAATTCAAGTTCGACGAATATATAATCAAGTTCATGTAAATATGTTA
1 TTTCATATACAAGAATATAAATTCAAGTTCAACGAATATATAATCAAGTTCATGTAAATATGGTA
* *
40829864 GTAATTAATGAGAAATCATTTCATTCA
66 GTAATTAATAAAAAATCATTTCATTCA
40829891 T
1 T
40829892 ATTGATAAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
92 13 0.15
93 71 0.85
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (92 bp):
TTTCATATACAAGAATATAAATTCAAGTTCAACGAATATATAATCAAGTTCATGTAAATATGGTA
GTAATTAATAAAAAATCATTTCATTCA
Found at i:40832173 original size:21 final size:21
Alignment explanation
Indices: 40832147--40832203 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
40832137 TACTGCAAAC
**
40832147 TTCTACCGATGCAAGTGACAG
1 TTCTACCGAAACAAGTGACAG
* **
40832168 TTCTACCAAAACAAGTGACTT
1 TTCTACCGAAACAAGTGACAG
40832189 TTCTACCGAAACAAG
1 TTCTACCGAAACAAG
40832204 CCTTACTTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (21 bp):
TTCTACCGAAACAAGTGACAG
Found at i:40832943 original size:52 final size:51
Alignment explanation
Indices: 40832875--40833116 Score: 315
Period size: 52 Copynumber: 4.7 Consensus size: 51
40832865 GTATTTCTTT
* ** *
40832875 TATACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTATTGGGAATCA
1 TATACTCACGATGACACATAGTCATCGGACCTTTAATCCGTA-AAGGATTCA
* *
40832927 TATACTCACGAGGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCA
1 TATACTCACGATGACACATAGTCATCGGACCT-TTAATCCGTAAAGGATTCA
* * *
40832979 TTTACTCACGATGATACATAGTCATCGGA-CTTCATGATCCGTAAAGGATTCA
1 TATACTCACGATGACACATAGTCATCGGACCTT--TAATCCGTAAAGGATTCA
* * * *
40833031 TGTACTCACGATAACACATAGTCATCGGACCTTATGATCTGTAAAGGATTCA
1 TATACTCACGATGACACATAGTCATCGGACCTT-TAATCCGTAAAGGATTCA
40833083 TATACTCACGATGACACATAGTCATCGGACCTTT
1 TATACTCACGATGACACATAGTCATCGGACCTTT
40833117 TTTATTTACG
Statistics
Matches: 169, Mismatches: 17, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
51 3 0.02
52 154 0.91
53 12 0.07
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (51 bp):
TATACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAAAGGATTCA
Found at i:40836248 original size:23 final size:23
Alignment explanation
Indices: 40836220--40836340 Score: 147
Period size: 23 Copynumber: 5.2 Consensus size: 23
40836210 ACACTAGCGC
*
40836220 GCTCTCTGATTAACACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
40836243 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
40836266 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
40836291 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
40836314 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
40836337 GCTC
1 GCTC
40836341 AGTACTTTGT
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
22 4 0.05
23 61 0.72
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:40836272 original size:25 final size:24
Alignment explanation
Indices: 40836244--40836329 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 24
40836234 ACTGTGTGTG
*
40836244 CTCTCTGTTTAGCACGTCTCGTGCT
1 CTCTCTGATTAGCACGT-TCGTGCT
* *
40836269 CTCTGTTATTAGCACTGTGT-GTGCT
1 CTCTCTGATTAGCAC-GT-TCGTGCT
40836294 CTC-C-GATTAGCAC-TTCGTG-T
1 CTCTCTGATTAGCACGTTCGTGCT
40836314 GCTCTCTGATTAGCAC
1 -CTCTCTGATTAGCAC
40836330 TTTGTGTGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
20 2 0.04
21 7 0.14
22 1 0.02
23 17 0.34
25 20 0.40
26 3 0.06
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (24 bp):
CTCTCTGATTAGCACGTTCGTGCT
Found at i:40836294 original size:48 final size:46
Alignment explanation
Indices: 40836220--40836340 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
40836210 ACACTAGCGC
* * *
40836220 GCTCTCTGATTAACACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
40836266 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
*
40836314 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
40836341 AGTACTTTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
46 26 0.39
48 40 0.60
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:40837608 original size:17 final size:17
Alignment explanation
Indices: 40837568--40837608 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
40837558 TATTGTTGAC
*
40837568 TTAACGAAGTTACATCT
1 TTAACGGAGTTACATCT
40837585 TTAACGGAGTTACATCT
1 TTAACGGAGTTACATCT
40837602 TTAACGG
1 TTAACGG
40837609 GCTCCACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (17 bp):
TTAACGGAGTTACATCT
Found at i:40840775 original size:4 final size:4
Alignment explanation
Indices: 40840766--40840823 Score: 64
Period size: 4 Copynumber: 13.8 Consensus size: 4
40840756 ATAACTCATG
*
40840766 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTTA ATTTG A-TA ATTTA TATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A-TTA A-TTA ATTA A-TTA -ATTA
40840817 ATTA ATT
1 ATTA ATT
40840824 GAACTTGTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
3 2 0.04
4 32 0.67
5 13 0.27
6 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (4 bp):
ATTA
Found at i:40846535 original size:8 final size:8
Alignment explanation
Indices: 40846522--40846554 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
40846512 GAAAAGATAA
40846522 GAAAAGTG
1 GAAAAGTG
40846530 GAAAAGTG
1 GAAAAGTG
40846538 GAAAAGTG
1 GAAAAGTG
*
40846546 AAAAAGTG
1 GAAAAGTG
40846554 G
1 G
40846555 TGTTCACAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.36, T:0.12
Consensus pattern (8 bp):
GAAAAGTG
Found at i:40846849 original size:24 final size:26
Alignment explanation
Indices: 40846821--40846868 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
40846811 ATTATTTTAT
*
40846821 TATAT-AAATA-ATTTTAAAATATGA
1 TATATCAAATACATTTAAAAATATGA
40846845 TATATCAAATACATTTAAAAATAT
1 TATATCAAATACATTTAAAAATAT
40846869 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (26 bp):
TATATCAAATACATTTAAAAATATGA
Found at i:40848769 original size:17 final size:18
Alignment explanation
Indices: 40848744--40848780 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40848734 TCTTTTAAAA
40848744 ATTAT-AAAAATATAAATT
1 ATTATAAAAAATA-AAATT
40848762 ATTA-AAAAAATAAAATT
1 ATTATAAAAAATAAAATT
40848779 AT
1 AT
40848781 ATTTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTATAAAAAATAAAATT
Found at i:40848770 original size:18 final size:17
Alignment explanation
Indices: 40848741--40848780 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
40848731 TAATCTTTTA
*
40848741 AAAATTA-TAAAAATAT
1 AAAATTATTAAAAAAAT
40848757 -AAATTATTAAAAAAAT
1 AAAATTATTAAAAAAAT
40848773 AAAATTAT
1 AAAATTAT
40848781 ATTTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 8 0.38
17 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTATTAAAAAAAT
Found at i:40849853 original size:30 final size:32
Alignment explanation
Indices: 40849810--40849876 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
40849800 AATTCTCTAT
*
40849810 ATTTTTATATTTTTAA-AAA-ATTAAATTA-A
1 ATTTTTATATTTTTAAGAAAGATTAAAGTATA
40849839 ATTTTTATTATTTTTAAGAAAGATTAAAGTATA
1 ATTTTTA-TATTTTTAAGAAAGATTAAAGTATA
40849872 ATTTT
1 ATTTT
40849877 AATTTTACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 7 0.21
30 9 0.27
31 3 0.09
32 8 0.24
33 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (32 bp):
ATTTTTATATTTTTAAGAAAGATTAAAGTATA
Found at i:40849882 original size:30 final size:29
Alignment explanation
Indices: 40849807--40849882 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
40849797 TTAAATTCTC
* *
40849807 TATATTTTTATATTTTTAAAAAATTAAAT
1 TATAATTTTATATTTTTAAAAAATTAAAG
40849836 TA-AATTTTTATTATTTTTAAGAAAGATTAAAG
1 TATAA-TTTTA-TATTTTTAA-AAA-ATTAAAG
40849868 TATAATTTTA-ATTTT
1 TATAATTTTATATTTT
40849883 ACTAATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 1 0.03
29 7 0.17
30 14 0.35
31 3 0.08
32 13 0.32
33 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
TATAATTTTATATTTTTAAAAAATTAAAG
Found at i:40855013 original size:11 final size:12
Alignment explanation
Indices: 40854984--40855011 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40854974 TTTTAACTTG
40854984 TTTTTAAGTATT
1 TTTTTAAGTATT
40854996 TTTTTAAGTATT
1 TTTTTAAGTATT
40855008 TTTT
1 TTTT
40855012 AATTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (12 bp):
TTTTTAAGTATT
Found at i:40855989 original size:20 final size:19
Alignment explanation
Indices: 40855965--40856013 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
40855955 TTAAGGAAAT
40855965 TTTTAGAAACATCGATAAA
1 TTTTAGAAACATCGATAAA
* * *
40855984 TATTTATAAGCATTGATAAA
1 T-TTTAGAAACATCGATAAA
40856004 TTCTTAGAAA
1 TT-TTAGAAA
40856014 ATCTAATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (19 bp):
TTTTAGAAACATCGATAAA
Found at i:40858547 original size:25 final size:24
Alignment explanation
Indices: 40858501--40858548 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40858491 ATTTATTCAA
*
40858501 AAAATATTTTTATTCATGTTAAAT
1 AAAATATTTTTATTCATATTAAAT
*
40858525 AAAATATTTTTATTATATATTAAA
1 AAAATATTTTTATT-CATATTAAA
40858549 AGATTTACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
AAAATATTTTTATTCATATTAAAT
Found at i:40869175 original size:10 final size:10
Alignment explanation
Indices: 40869162--40869365 Score: 66
Period size: 10 Copynumber: 20.3 Consensus size: 10
40869152 TTATGGTTTT
40869162 TTTTTTATAA
1 TTTTTTATAA
40869172 -TTTTTATAA
1 TTTTTTATAA
* *
40869181 GTTTATATAA
1 TTTTTTATAA
*
40869191 TTTTAGTTTTTAA
1 -TTT--TTTATAA
* * *
40869204 TATGTAATAA
1 TTTTTTATAA
* *
40869214 -ATTTTATGA
1 TTTTTTATAA
*
40869223 GTTTTTATAA
1 TTTTTTATAA
* *
40869233 CTTTTTAATGA
1 -TTTTTTATAA
40869244 -TTTTTATAA
1 TTTTTTATAA
*
40869253 GTTTTTA-AGA
1 TTTTTTATA-A
*
40869263 ATTTTTATAA
1 TTTTTTATAA
**
40869273 AATTTTA-AA
1 TTTTTTATAA
*
40869282 TATGTTTTATTA
1 T-T-TTTTATAA
40869294 TTTTTT-T-A
1 TTTTTTATAA
40869302 TATTTTTATAA
1 T-TTTTTATAA
*
40869313 -TATTTATAA
1 TTTTTTATAA
* *
40869322 TATTTTATTA
1 TTTTTTATAA
40869332 TTTTATTATAA
1 TTTT-TTATAA
40869343 -TTTTTATAA
1 TTTTTTATAA
* *
40869352 GTTTATATCAA
1 TTTTTTAT-AA
40869363 TTT
1 TTT
40869366 AGTATTTTTA
Statistics
Matches: 144, Mismatches: 31, Indels: 37
0.68 0.15 0.17
Matches are distributed among these distances:
8 2 0.01
9 45 0.31
10 62 0.43
11 26 0.18
12 4 0.03
13 5 0.03
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:40869341 original size:30 final size:30
Alignment explanation
Indices: 40869275--40869351 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
40869265 TTTTATAAAA
* * *
40869275 TTTTA-AATATGTTTTATTATTTTTTTATAT
1 TTTTATAATAT-TTATAATATTTTATTATAT
40869305 TTTTATAATATTTATAATATTTTATTAT-T
1 TTTTATAATATTTATAATATTTTATTATAT
*
40869334 TTATTATAATTTTTATAA
1 TT-TTATAATATTTATAA
40869352 GTTTATATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 3 0.07
30 33 0.80
31 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (30 bp):
TTTTATAATATTTATAATATTTTATTATAT
Found at i:40869341 original size:38 final size:40
Alignment explanation
Indices: 40869262--40869351 Score: 123
Period size: 38 Copynumber: 2.3 Consensus size: 40
40869252 AGTTTTTAAG
*
40869262 AATTTTTATAAAATTTTAAATATGTTTTATTATTTTTTTAT
1 AATTTTTATAAAATTTTAAATA-GTTTTATTATTTTATTAT
*
40869303 -ATTTTTATAATA-TTTATAATA-TTTTATTATTTTATTAT
1 AATTTTTATAAAATTTTA-AATAGTTTTATTATTTTATTAT
40869341 AATTTTTATAA
1 AATTTTTATAA
40869352 GTTTATATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
38 16 0.36
39 14 0.31
40 15 0.33
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (40 bp):
AATTTTTATAAAATTTTAAATAGTTTTATTATTTTATTAT
Found at i:40869356 original size:20 final size:19
Alignment explanation
Indices: 40869163--40869365 Score: 100
Period size: 20 Copynumber: 10.6 Consensus size: 19
40869153 TATGGTTTTT
40869163 TTTTTATAATTTTTATAAG
1 TTTTTATAATTTTTATAAG
*
40869182 TTTATATAA--TTT-T-AG
1 TTTTTATAATTTTTATAAG
* *
40869197 -TTTT-TAATATGTAATAA-
1 TTTTTATAAT-TTTTATAAG
* * *
40869214 ATTTTATGAGTTTTTATAAC
1 TTTTTAT-AATTTTTATAAG
*
40869234 TTTTTAATGATTTTTATAAG
1 TTTTT-ATAATTTTTATAAG
* *
40869254 TTTTTAAGAATTTTTATAAA
1 TTTTT-ATAATTTTTATAAG
* * *
40869274 ATTTTAAATATGTTTTATTA-
1 TTTTTATA-AT-TTTTATAAG
*
40869294 TTTTTTTATATTTTTATAA-
1 TTTTTATA-ATTTTTATAAG
* * *
40869313 TATTTATAATATTTTATTAT
1 TTTTTATAAT-TTTTATAAG
40869333 TTTATTATAATTTTTATAAG
1 TTT-TTATAATTTTTATAAG
*
40869353 TTTATATCAATTT
1 TTTTTAT-AATTT
40869366 AGTATTTTTA
Statistics
Matches: 140, Mismatches: 28, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
13 3 0.02
14 3 0.02
15 2 0.01
16 2 0.01
17 4 0.03
18 7 0.05
19 40 0.29
20 63 0.45
21 16 0.11
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAG
Found at i:40869358 original size:38 final size:38
Alignment explanation
Indices: 40869263--40869351 Score: 117
Period size: 40 Copynumber: 2.3 Consensus size: 38
40869253 GTTTTTAAGA
* *
40869263 ATTTTTATAAAATTT-TAAATATGTTTTATTATTTTTTTAT
1 ATTTTTATAATATTTAT-AATA--TTTTATTATTTTATTAT
40869303 ATTTTTATAATATTTATAATATTTTATTATTTTATTAT
1 ATTTTTATAATATTTATAATATTTTATTATTTTATTAT
40869341 AATTTTTATAA
1 -ATTTTTATAA
40869352 GTTTATATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
38 16 0.36
39 10 0.22
40 18 0.40
41 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (38 bp):
ATTTTTATAATATTTATAATATTTTATTATTTTATTAT
Found at i:40869372 original size:38 final size:38
Alignment explanation
Indices: 40869287--40869373 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
40869277 TTAAATATGT
* *
40869287 TTTATTATTTTTTTATATTTTTATAATATTTATAATAT
1 TTTATTATTTTATTATATTTTTATAATATTTATAATAA
*
40869325 TTTATTATTTTATTATAATTTTTATAA-GTTTAT-ATCAA
1 TTTATTATTTTATTAT-ATTTTTATAATATTTATAAT-AA
*
40869363 TTTAGTATTTT
1 TTTATTATTTT
40869374 TAAATTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 2 0.05
38 31 0.72
39 10 0.23
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (38 bp):
TTTATTATTTTATTATATTTTTATAATATTTATAATAA
Found at i:40870115 original size:26 final size:26
Alignment explanation
Indices: 40870064--40870115 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
40870054 AAAAAAATAA
*
40870064 GTAAATTAATTTTTATACTTAGAAAT
1 GTAAATTAATTTTTATACTTAAAAAT
* *
40870090 GTAAATTGATTATTTCTA-TTAAAAAT
1 GTAAATTAATT-TTTATACTTAAAAAT
40870116 TTCATCCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (26 bp):
GTAAATTAATTTTTATACTTAAAAAT
Found at i:40875610 original size:24 final size:23
Alignment explanation
Indices: 40875568--40875612 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
40875558 ATACCTCCAA
40875568 ACAGAAGCAAAGAACAACAAAAG
1 ACAGAAGCAAAGAACAACAAAAG
40875591 ACAGCAAGACAAAG-ACAACAAA
1 ACAG-AAG-CAAAGAACAACAAA
40875613 GAATAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.64, C:0.20, G:0.16, T:0.00
Consensus pattern (23 bp):
ACAGAAGCAAAGAACAACAAAAG
Found at i:40876555 original size:30 final size:30
Alignment explanation
Indices: 40876515--40876681 Score: 239
Period size: 30 Copynumber: 5.6 Consensus size: 30
40876505 ATTTTATTCG
* *
40876515 AAAATGATATTTTAA-CCCTCAAACTTTTTA
1 AAAATTATATTTTAACCCCT-AAACTTTTCA
*
40876545 AAAATCATATTTTAACCCCTAAACTTTTCA
1 AAAATTATATTTTAACCCCTAAACTTTTCA
*
40876575 AAAATTATATTTTAACCCTTAAA-TTTTCCA
1 AAAATTATATTTTAACCCCTAAACTTTT-CA
* *
40876605 AAAATTATATTTTGACCCCAAAACTTTTCA
1 AAAATTATATTTTAACCCCTAAACTTTTCA
40876635 AAAATTATATTTTAACCCCTAAACTTTTCA
1 AAAATTATATTTTAACCCCTAAACTTTTCA
*
40876665 AAAATTATATCTTAACC
1 AAAATTATATTTTAACC
40876682 TCGAACTTTT
Statistics
Matches: 124, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.03
30 112 0.90
31 8 0.06
ACGTcount: A:0.41, C:0.19, G:0.01, T:0.39
Consensus pattern (30 bp):
AAAATTATATTTTAACCCCTAAACTTTTCA
Found at i:40876668 original size:90 final size:90
Alignment explanation
Indices: 40876515--40876681 Score: 273
Period size: 90 Copynumber: 1.9 Consensus size: 90
40876505 ATTTTATTCG
*
40876515 AAAATGATATTTTAACCCTCAAACTTTTTAAAAATCATATTTTAACCCCTAAACTTTTCAAAAAT
1 AAAATGATATTTTAACCCTCAAACTTTTCAAAAATCATATTTTAACCCCTAAACTTTTCAAAAAT
*
40876580 TATATTTTAACCCTTAAATTTTCCA
66 TATATCTTAACCCTTAAATTTTCCA
* * *
40876605 AAAATTATATTTTGACCC-CAAAACTTTTCAAAAATTATATTTTAACCCCTAAACTTTTCAAAAA
1 AAAATGATATTTTAACCCTC-AAACTTTTCAAAAATCATATTTTAACCCCTAAACTTTTCAAAAA
40876669 TTATATCTTAACC
65 TTATATCTTAACC
40876682 TCGAACTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
89 1 0.01
90 70 0.99
ACGTcount: A:0.41, C:0.19, G:0.01, T:0.39
Consensus pattern (90 bp):
AAAATGATATTTTAACCCTCAAACTTTTCAAAAATCATATTTTAACCCCTAAACTTTTCAAAAAT
TATATCTTAACCCTTAAATTTTCCA
Found at i:40884530 original size:18 final size:18
Alignment explanation
Indices: 40884507--40884543 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40884497 TTTGTGATCA
40884507 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
40884525 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
40884543 A
1 A
40884544 TATGAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:40884532 original size:12 final size:12
Alignment explanation
Indices: 40884507--40884543 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
40884497 TTTGTGATCA
40884507 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
40884519 AAAGTGAAATTG
1 AAATTGAAAGTG
40884531 AAATTGAAAGTG
1 AAATTGAAAGTG
40884543 A
1 A
40884544 TATGAATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:40884693 original size:41 final size:40
Alignment explanation
Indices: 40884645--40884745 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
40884635 TCGACCTTGA
** *
40884645 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
40884685 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
40884723 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
40884746 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:40885985 original size:29 final size:29
Alignment explanation
Indices: 40885953--40886029 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
40885943 ATACAAATAC
* * *
40885953 AGTTACATATATAGTCATGTCATAGATAT
1 AGTTACAGATACAGTCATGTCACAGATAT
40885982 AGTTACAGATACAGTCATGTCACAGATAT
1 AGTTACAGATACAGTCATGTCACAGATAT
* *
40886011 AGTTACAGATGCAGACATG
1 AGTTACAGATACAGTCATG
40886030 ATACATATAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (29 bp):
AGTTACAGATACAGTCATGTCACAGATAT
Found at i:40886043 original size:29 final size:29
Alignment explanation
Indices: 40885982--40886075 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
40885972 TCATAGATAT
* * * *
40885982 AGTTACAGATACAGTCATG-TCACAGATAT
1 AGTTACAGATGCAGACATGAT-ACATATAC
40886011 AGTTACAGATGCAGACATGATACATATAC
1 AGTTACAGATGCAGACATGATACATATAC
* * *
40886040 AGTTATAGATGTAGGCATGATACATATAC
1 AGTTACAGATGCAGACATGATACATATAC
*
40886069 AATTACA
1 AGTTACA
40886076 AATACAGATA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 54 0.98
30 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (29 bp):
AGTTACAGATGCAGACATGATACATATAC
Found at i:40886086 original size:18 final size:18
Alignment explanation
Indices: 40886059--40886103 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
40886049 TGTAGGCATG
*
40886059 ATACATATACAATTACAA
1 ATACAGATACAATTACAA
40886077 ATACAGATACAATTACAA
1 ATACAGATACAATTACAA
40886095 ATACAGATA
1 ATACAGATA
40886104 TGATACCCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (18 bp):
ATACAGATACAATTACAA
Found at i:40886968 original size:31 final size:31
Alignment explanation
Indices: 40886919--40887048 Score: 156
Period size: 31 Copynumber: 4.3 Consensus size: 31
40886909 ACACACCTTG
*
40886919 ACACACAC-CC-GTGCGCCTCCAAACAGTAT
1 ACACACACGCCTGTGTGCCTCCAAACAGTAT
* * *
40886948 ACACACATGCCTGTGTGCCTCTAAATAGTAT
1 ACACACACGCCTGTGTGCCTCCAAACAGTAT
* * *
40886979 ACACATACACCTGTGTGCCTCCAAATAGTAT
1 ACACACACGCCTGTGTGCCTCCAAACAGTAT
* * *
40887010 ACACACACGCTTGTGTGCCTCTAAACATTAT
1 ACACACACGCCTGTGTGCCTCCAAACAGTAT
40887041 ACACACAC
1 ACACACAC
40887049 ACCTTGACAC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 7 0.08
30 2 0.02
31 76 0.89
ACGTcount: A:0.32, C:0.32, G:0.13, T:0.23
Consensus pattern (31 bp):
ACACACACGCCTGTGTGCCTCCAAACAGTAT
Found at i:40886999 original size:62 final size:62
Alignment explanation
Indices: 40886919--40887052 Score: 196
Period size: 62 Copynumber: 2.2 Consensus size: 62
40886909 ACACACCTTG
* * *
40886919 ACACACACCCGTGCGCCTCCAAACAGTATACACACATGCCTGTGTGCCTCTAAATAGTATAC
1 ACACACACCTGTGCGCCTCCAAACAGTATACACACACGCCTGTGTGCCTCTAAACAGTATAC
* * * * *
40886981 ACATACACCTGTGTGCCTCCAAATAGTATACACACACGCTTGTGTGCCTCTAAACATTATAC
1 ACACACACCTGTGCGCCTCCAAACAGTATACACACACGCCTGTGTGCCTCTAAACAGTATAC
40887043 ACACACACCT
1 ACACACACCT
40887053 TGACACACGC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.31, C:0.33, G:0.13, T:0.23
Consensus pattern (62 bp):
ACACACACCTGTGCGCCTCCAAACAGTATACACACACGCCTGTGTGCCTCTAAACAGTATAC
Found at i:40887513 original size:11 final size:11
Alignment explanation
Indices: 40887495--40887529 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40887485 TTCATTGTTA
40887495 AATTTAAATTT
1 AATTTAAATTT
*
40887506 ATTTTAAATTT
1 AATTTAAATTT
*
40887517 AATTAAAATTT
1 AATTTAAATTT
40887528 AA
1 AA
40887530 ATCAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:40887514 original size:17 final size:18
Alignment explanation
Indices: 40887475--40887518 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
40887465 TGGGTTTAAA
40887475 TAAATTTAAATTCATTGT
1 TAAATTTAAATTCATTGT
*
40887493 TAAATTTAAATTTATT-T
1 TAAATTTAAATTCATTGT
40887510 TAAATTTAA
1 TAAATTTAA
40887519 TTAAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TAAATTTAAATTCATTGT
Found at i:40887574 original size:13 final size:13
Alignment explanation
Indices: 40887556--40887580 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40887546 CAAATAGAAA
40887556 GTCCAATTACAAT
1 GTCCAATTACAAT
40887569 GTCCAATTACAA
1 GTCCAATTACAA
40887581 AAGCCCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (13 bp):
GTCCAATTACAAT
Found at i:40889518 original size:29 final size:30
Alignment explanation
Indices: 40889457--40889807 Score: 344
Period size: 29 Copynumber: 11.9 Consensus size: 30
40889447 GAAGGTCCCT
* *
40889457 AAACTATCCAAAAATTATATTTTTGACCCCG
1 AAACT-TCCAAAAATTACATTTTTAACCCCG
*
40889488 AAACTTCCAAAAATTACATTTTT-ACCTCG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * *
40889517 -AACTTTCTAAAATTACATTTTTAA-CCCT
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* **
40889545 AAAGCTTCTAAAAATTACATTTTTGCCCCCG
1 AAA-CTTCCAAAAATTACATTTTTAACCCCG
* *
40889576 -AACTTCCAAAAATTCCATTTTT-TCCCTC-
1 AAACTTCCAAAAATTACATTTTTAACCC-CG
* * **
40889604 AAACTTCCGAAAATTCCATTTTTAACTTCG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
*
40889634 AAACTTCCAAAAATTACATTTTTACCCCCG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * *
40889664 -AACTTCCAAAAGTTCCATTTTTAACCCCT
1 AAACTTCCAAAAATTACATTTTTAACCCCG
*
40889693 AAACTTCCAAAAATTACATTTTT-ACCCCT
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * * **
40889722 AAACTTTCAAAAATTCCATTTTTGACCTTG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* *
40889752 AAACTTCCAAAAATTACA-TTTT-CCCCCA
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* *
40889780 AAACTTCCAAAAATTCCATTTTTGACCC
1 AAACTTCCAAAAATTACATTTTTAACCC
40889808 TAAAACTTTC
Statistics
Matches: 265, Mismatches: 43, Indels: 25
0.80 0.13 0.08
Matches are distributed among these distances:
28 44 0.17
29 109 0.41
30 104 0.39
31 8 0.03
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTAACCCCG
Found at i:40889596 original size:59 final size:58
Alignment explanation
Indices: 40889458--40889862 Score: 399
Period size: 59 Copynumber: 6.9 Consensus size: 58
40889448 AAGGTCCCTA
* * *
40889458 AACTATCCAAAAATTATATTTTTGACCCCGAAACTTCCAAAAATTACATTTTT-ACCTCG
1 AACT-TCCAAAAATTACATTTTT-ACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCG
* * * * * * *
40889517 AACTTTCTAAAATTACATTTTTAACCCTAAAGCTTCTAAAAATTACATTTTTGCCCCCG
1 AACTTCCAAAAATTACATTTTTACCCCTAAA-CTTCCAAAAATTCCATTTTTGACCTCG
* * * * *
40889576 AACTTCCAAAAATTCCATTTTT-TCCCTCAAACTTCCGAAAATTCCATTTTTAACTTCG
1 AACTTCCAAAAATTACATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGACCTCG
** * * * *
40889634 AAACTTCCAAAAATTACATTTTTACCCCCGAACTTCCAAAAGTTCCATTTTTAACCCCTA
1 -AACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTC-G
* *
40889694 AACTTCCAAAAATTACATTTTTACCCCTAAACTTTCAAAAATTCCATTTTTGACCTTG
1 AACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCG
* * **
40889752 AAACTTCCAAAAATTACA-TTTTCCCCCAAAACTTCCAAAAATTCCATTTTTGACCCTAA
1 -AACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGA-CCTCG
* * * *
40889811 AACTTTC-AAGATTACCA-TTTTACCCC-AAAATATCCAAAAACTCCATTTTTGA
1 AACTTCCAAAAATTA-CATTTTTACCCCTAAACT-TCCAAAAATTCCATTTTTGA
40889863 TCCCGATTTT
Statistics
Matches: 290, Mismatches: 46, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
57 17 0.06
58 125 0.43
59 145 0.50
60 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (58 bp):
AACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:40889609 original size:88 final size:88
Alignment explanation
Indices: 40889453--40889811 Score: 399
Period size: 88 Copynumber: 4.1 Consensus size: 88
40889443 CCTTGAAGGT
* * *
40889453 CCCTAAACTATCCAAAAATTATATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCTC-G
1 CCCTAAACT-TCCAAAAATTACATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTCCCTCAA
* *
40889517 AACTTTCTAAAATTACATTTTTAA
65 AACTTCCAAAAATTACATTTTTAA
* * *
40889541 CCCTAAAGCTTCTAAAAATTACATTTTTGCCCCCG-AACTTCCAAAAATTCCATTTTTTCCCTC-
1 CCCTAAA-CTTCCAAAAATTACATTTTTGACCCCGAAACTTCCAAAAATTACA-TTTTTCCCTCA
* *
40889604 AAACTTCCGAAAATTCCATTTTTAA
64 AAACTTCCAAAAATTACATTTTTAA
* * * *
40889629 CTTCGAAACTTCCAAAAATTACATTTTT-ACCCCCG-AACTTCCAAAAGTTCCATTTTTAACCC-
1 C-CCTAAACTTCCAAAAATTACATTTTTGA-CCCCGAAACTTCCAAAAATTACATTTTT--CCCT
* *
40889691 CTAAACTTCCAAAAATTACATTTTTAC
62 CAAAACTTCCAAAAATTACATTTTTAA
* * ** *
40889718 CCCTAAACTTTCAAAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTACA-TTTTCCCCCAAA
1 CCCTAAACTTCCAAAAATTACATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTCCCTCAAA
* *
40889782 ACTTCCAAAAATTCCATTTTTGA
66 ACTTCCAAAAATTACATTTTTAA
40889805 CCCTAAA
1 CCCTAAA
40889812 ACTTTCAAGA
Statistics
Matches: 232, Mismatches: 29, Indels: 21
0.82 0.10 0.07
Matches are distributed among these distances:
86 3 0.01
87 51 0.22
88 130 0.56
89 48 0.21
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (88 bp):
CCCTAAACTTCCAAAAATTACATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTCCCTCAAA
ACTTCCAAAAATTACATTTTTAA
Found at i:40889803 original size:58 final size:59
Alignment explanation
Indices: 40889453--40889862 Score: 403
Period size: 58 Copynumber: 7.0 Consensus size: 59
40889443 CCTTGAAGGT
* * *
40889453 CCCT-AAACTATCCAAAAATTATATTTTTGACCCCGAAACTTCCAAAAATTACATTTTT-A
1 CCCTGAAACT-TCCAAAAATTACATTTTT-ACCCCAAAACTTCCAAAAATTCCATTTTTGA
* * * * * * *
40889512 -CCTCG-AACTTTCTAAAATTACATTTTTAACCCTAAAGCTTCTAAAAATTACATTTTTGC
1 CCCT-GAAACTTCCAAAAATTACATTTTT-ACCCCAAAACTTCCAAAAATTCCATTTTTGA
* * * *
40889571 CCCCG-AACTTCCAAAAATTCCATTTTTTCCCTC-AAACTTCCGAAAATTCCATTTTT-A
1 CCCTGAAACTTCCAAAAATTACATTTTTACCC-CAAAACTTCCAAAAATTCCATTTTTGA
* * ** * *
40889628 ACTTCGAAACTTCCAAAAATTACATTTTTACCCCCGAACTTCCAAAAGTTCCATTTTTAA
1 CCCT-GAAACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTGA
* *
40889688 CCCCT-AAACTTCCAAAAATTACATTTTTACCCCTAAACTTTCAAAAATTCCATTTTTGA
1 -CCCTGAAACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTGA
* *
40889747 CCTTGAAACTTCCAAAAATTACA-TTTTCCCCCAAAACTTCCAAAAATTCCATTTTTGA
1 CCCTGAAACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTGA
* * * *
40889805 CCCTAAAACTTTC-AAGATTACCA-TTTTACCCCAAAA-TATCCAAAAACTCCATTTTTGA
1 CCCTGAAACTTCCAAAAATTA-CATTTTTACCCCAAAACT-TCCAAAAATTCCATTTTTGA
40889863 TCCCGATTTT
Statistics
Matches: 293, Mismatches: 45, Indels: 27
0.80 0.12 0.07
Matches are distributed among these distances:
57 8 0.03
58 145 0.49
59 135 0.46
60 3 0.01
61 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (59 bp):
CCCTGAAACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTGA
Found at i:40893403 original size:16 final size:16
Alignment explanation
Indices: 40893378--40893408 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40893368 AAATATAATA
40893378 ATGTACATATAAAACC
1 ATGTACATATAAAACC
*
40893394 ATGTATATATAAAAC
1 ATGTACATATAAAAC
40893409 TTATTTTTGA
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:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (16 bp):
ATGTACATATAAAACC
Found at i:40899065 original size:12 final size:12
Alignment explanation
Indices: 40899050--40899089 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
40899040 TAAGTAGGGA
40899050 TTTTTAATATAC
1 TTTTTAATATAC
**
40899062 TTTTTGTTATA-
1 TTTTTAATATAC
40899073 TTTTTAATATAC
1 TTTTTAATATAC
40899085 TTTTT
1 TTTTT
40899090 GTTATATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTTAATATAC
Found at i:40899075 original size:23 final size:23
Alignment explanation
Indices: 40899049--40899096 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
40899039 TTAAGTAGGG
40899049 ATTTTTAATATACTTTTTGTTAT
1 ATTTTTAATATACTTTTTGTTAT
40899072 ATTTTTAATATACTTTTTGTTAT
1 ATTTTTAATATACTTTTTGTTAT
40899095 AT
1 AT
40899097 CAAAATACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (23 bp):
ATTTTTAATATACTTTTTGTTAT
Found at i:40899095 original size:12 final size:12
Alignment explanation
Indices: 40899057--40899095 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
40899047 GGATTTTTAA
40899057 TATACTTTTTGT
1 TATACTTTTTGT
**
40899069 TATA-TTTTTAA
1 TATACTTTTTGT
40899080 TATACTTTTTGT
1 TATACTTTTTGT
40899092 TATA
1 TATA
40899096 TCAAAATACT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (12 bp):
TATACTTTTTGT
Found at i:40899500 original size:36 final size:36
Alignment explanation
Indices: 40899453--40899536 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
40899443 TGTTGAACCA
40899453 AAAGCAATCAAACATAATCAAAGTAAAAAAAATCCC
1 AAAGCAATCAAACATAATCAAAGTAAAAAAAATCCC
* *
40899489 AAAGCATTCAAACATAATCAAAGTAAAAAACATCCC
1 AAAGCAATCAAACATAATCAAAGTAAAAAAAATCCC
*
40899525 AAAGCAACCAAA
1 AAAGCAATCAAA
40899537 TAAGAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.60, C:0.21, G:0.06, T:0.13
Consensus pattern (36 bp):
AAAGCAATCAAACATAATCAAAGTAAAAAAAATCCC
Found at i:40908324 original size:2 final size:2
Alignment explanation
Indices: 40908319--40908351 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40908309 TTTTTTCCAT
40908319 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40908352 GATGTTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40911735 original size:16 final size:16
Alignment explanation
Indices: 40911714--40911747 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
40911704 CTATTCAAAA
40911714 ATGCGGGAAAATAACT
1 ATGCGGGAAAATAACT
40911730 ATGCGGGAAAATAACT
1 ATGCGGGAAAATAACT
40911746 AT
1 AT
40911748 TTTTCTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.21
Consensus pattern (16 bp):
ATGCGGGAAAATAACT
Found at i:40915234 original size:17 final size:18
Alignment explanation
Indices: 40915193--40915234 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
40915183 TATTTTAATA
*
40915193 TTTAATA-TTTAATAATT
1 TTTAATATTTTAATAAAT
*
40915210 TTTTATATTTTAA-AAAT
1 TTTAATATTTTAATAAAT
40915227 TTTAATAT
1 TTTAATAT
40915235 AGTCATCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAATATTTTAATAAAT
Found at i:40920443 original size:11 final size:10
Alignment explanation
Indices: 40920271--40920462 Score: 56
Period size: 11 Copynumber: 18.3 Consensus size: 10
40920261 ATTTGATCCC
40920271 ATTT-TTTTT
1 ATTTATTTTT
40920280 ATTTTATTTGTT
1 A-TTTATTT-TT
*
40920292 ATTTAATTTT
1 ATTTATTTTT
* *
40920302 ATTTGTTGTT
1 ATTTATTTTT
40920312 -TTTATTTATT
1 ATTTATTT-TT
* *
40920322 GTTCT-TTCACTT
1 ATT-TATT--TTT
40920334 ATTTATTTGTT
1 ATTTATTT-TT
* *
40920345 ATTCAATTTT
1 ATTTATTTTT
*
40920355 ATGTTATTTAT
1 AT-TTATTTTT
*
40920366 ATTTCCACTTTT
1 ATTT--ATTTTT
*
40920378 ATTTAATTTT
1 ATTTATTTTT
*
40920388 A-TT-TCTTT
1 ATTTATTTTT
*
40920396 A-CTATTTTT
1 ATTTATTTTT
*
40920405 ATGTGTTTTATTT
1 AT-T-TATT-TTT
*
40920418 ATTTGATATTT
1 ATTT-ATTTTT
40920429 -TTTATTTTCT
1 ATTTATTTT-T
40920439 ATTTAATTTTT
1 ATTT-ATTTTT
*
40920450 ATTTATTGTT
1 ATTTATTTTT
40920460 ATT
1 ATT
40920463 ATCTAGTTTT
Statistics
Matches: 134, Mismatches: 27, Indels: 43
0.66 0.13 0.21
Matches are distributed among these distances:
8 5 0.04
9 17 0.13
10 38 0.28
11 41 0.31
12 28 0.21
13 5 0.04
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:40920688 original size:19 final size:21
Alignment explanation
Indices: 40920645--40920689 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
40920635 ATAATTATAT
40920645 TGTTA-TTTTATTTGCTATTA
1 TGTTATTTTTATTTGCTATTA
*
40920665 T-TTATTTTTATTT-C-ATTG
1 TGTTATTTTTATTTGCTATTA
40920683 TGTTATT
1 TGTTATT
40920690 AATTATATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 4 0.18
19 9 0.41
20 9 0.41
ACGTcount: A:0.18, C:0.04, G:0.09, T:0.69
Consensus pattern (21 bp):
TGTTATTTTTATTTGCTATTA
Found at i:40920695 original size:26 final size:27
Alignment explanation
Indices: 40920636--40920698 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 27
40920626 ATTATTACTA
*
40920636 TAATTATATTGTTATTTTATTTGCTAT
1 TAATTATATTGTTATTTCATTTGCTAT
* *
40920663 T-ATT-TATTTTTATTTCATTGTGTTAT
1 TAATTATATTGTTATTTCATT-TGCTAT
40920689 TAATTATATT
1 TAATTATATT
40920699 CATTTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 13 0.43
26 9 0.30
27 4 0.13
28 4 0.13
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.65
Consensus pattern (27 bp):
TAATTATATTGTTATTTCATTTGCTAT
Found at i:40921830 original size:29 final size:27
Alignment explanation
Indices: 40921791--40921871 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 27
40921781 ATATATGTCT
40921791 ATTTTGTAAAATAATTAGGGTTTTGCATC
1 ATTTT-TAAAATAATTAGGGTTTTG-ATC
* * ** *
40921820 GTTTTTAAAAATATTTAGGAGAATAGATC
1 ATTTTT-AAAATAATTAGG-GTTTTGATC
40921849 ATTTTTAAAATAATTAGGGTTTT
1 ATTTTTAAAATAATTAGGGTTTT
40921872 ACACCATGGC
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
27 2 0.05
28 12 0.30
29 23 0.57
30 3 0.08
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (27 bp):
ATTTTTAAAATAATTAGGGTTTTGATC
Found at i:40924176 original size:3 final size:3
Alignment explanation
Indices: 40924170--40924195 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40924160 TGATGACTGT
40924170 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
40924196 AGTCTACAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:40925723 original size:43 final size:43
Alignment explanation
Indices: 40925669--40925776 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 43
40925659 GTCGCTACAA
40925669 AACATGATCTTTAGCGGCGCTTCTCCCACAAACACCGCTATAG
1 AACATGATCTTTAGCGGCGCTTCTCCCACAAACACCGCTATAG
* * * * * **
40925712 AACATGGTCTTTAGCGGTGTTTTTCTCACAAATGCCGCTATAG
1 AACATGATCTTTAGCGGCGCTTCTCCCACAAACACCGCTATAG
* *
40925755 AACATGATTTTTAGTGGCGCTT
1 AACATGATCTTTAGCGGCGCTT
40925777 TTACTACAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
AACATGATCTTTAGCGGCGCTTCTCCCACAAACACCGCTATAG
Found at i:40925786 original size:43 final size:43
Alignment explanation
Indices: 40925655--40925786 Score: 131
Period size: 43 Copynumber: 3.1 Consensus size: 43
40925645 TTTTGCGGGA
* * * * * *
40925655 AAATGTCGCTACAAAACATGATCTTTAGCGGCGCTTCTCCCAC
1 AAATGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTACTAC
** * * *
40925698 AAACACCGCTATAGAACATGGTCTTTAGCGGTG-TTTTTCTCAC
1 AAATGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTACT-AC
* *
40925741 AAATGCCGCTATAGAACATGATTTTTAGTGGCGCTTTTACTAC
1 AAATGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTACTAC
40925784 AAA
1 AAA
40925787 CGCCACTAAC
Statistics
Matches: 70, Mismatches: 17, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
42 4 0.06
43 60 0.86
44 6 0.09
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (43 bp):
AAATGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTACTAC
Found at i:40931678 original size:24 final size:24
Alignment explanation
Indices: 40931651--40931697 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
40931641 TGTTGTGGTG
* *
40931651 GTAGTTAATTTAGTTAGACTGTTA
1 GTAGTTAAGTCAGTTAGACTGTTA
*
40931675 GTAGTTAAGTCAGTTAGTCTGTT
1 GTAGTTAAGTCAGTTAGACTGTT
40931698 TAGTTCAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (24 bp):
GTAGTTAAGTCAGTTAGACTGTTA
Found at i:40939647 original size:25 final size:25
Alignment explanation
Indices: 40939605--40939652 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
40939595 CCTATTATTT
* *
40939605 CCCAGCACTTAAGTGCTTTTGTTTC
1 CCCAGCACTTAAGCGCTTCTGTTTC
* *
40939630 CCCAGCATTTATGCGCTTCTGTT
1 CCCAGCACTTAAGCGCTTCTGTT
40939653 AAGTACTTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.15, C:0.29, G:0.17, T:0.40
Consensus pattern (25 bp):
CCCAGCACTTAAGCGCTTCTGTTTC
Found at i:40944810 original size:41 final size:41
Alignment explanation
Indices: 40944746--40945123 Score: 379
Period size: 41 Copynumber: 9.1 Consensus size: 41
40944736 AAAGGTAAAG
* ** * * *
40944746 CATTAGTGGCGCTTTCCCTCAAGCGCCGTTACAGGTCGGGT
1 CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGGGT
**
40944787 CATTAGCGGATCTTTATCACAAGCGCCGCTAAAGGTCGGGT
1 CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGGGT
** * *
40944828 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGAT
1 CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGGGT
* *
40944869 CATTAGCGGCGCTTCATCACAAGCGCCGCTAAAGATCGGGT
1 CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGGGT
* *
40944910 TATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCTGGT
1 CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGGGT
** *
40944951 CATTAGCGGCGCTTTCCCTA-AAACGCCGCTAAAGGTCGGGT
1 CATTAGCGGCGCTTTATC-ACAAGCGCCGCTAAAGGTCGGGT
* *
40944992 CATTAGCGACGC-TTA-CCCTAAAGCGCCGCTAAAGGTCGGGT
1 CATTAGCGGCGCTTTATCAC--AAGCGCCGCTAAAGGTCGGGT
* * **
40945033 CATTAGCGGGGCTTGAAGGGTCATTAGCGCCGCTAAAGGTCGGGT
1 CATTAGCGGCGCTT-TA---TCACAAGCGCCGCTAAAGGTCGGGT
* * * * *
40945078 CATAAGCGGCGCTTTCTAATC-AGCACCGCTAAA-GTCAGGT
1 CATTAGCGGCGCTTTATCA-CAAGCGCCGCTAAAGGTCGGGT
40945118 CATTAG
1 CATTAG
40945124 TGGCACTTAT
Statistics
Matches: 278, Mismatches: 48, Indels: 23
0.80 0.14 0.07
Matches are distributed among these distances:
39 1 0.00
40 13 0.05
41 228 0.82
42 2 0.01
43 1 0.00
45 32 0.12
47 1 0.00
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.23
Consensus pattern (41 bp):
CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGGGT
Found at i:40944844 original size:82 final size:82
Alignment explanation
Indices: 40944746--40945189 Score: 436
Period size: 82 Copynumber: 5.4 Consensus size: 82
40944736 AAAGGTAAAG
* * * **
40944746 CATTAGTGGCGCTTTCCCTCAAGCGCCGTTACAGGTCGGGTCATTAGCGGATCTTTATCACAAGC
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTATCACAAGC
40944811 GCCGCTAAAGGTCGGGT
66 GCCGCTAAAGGTCGGGT
* *
40944828 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGATCATTAGCGGCGCTTCATCACAAGC
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTATCACAAGC
*
40944893 GCCGCTAAAGATCGGGT
66 GCCGCTAAAGGTCGGGT
* ** * * ** *
40944910 TATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCTGGTCATTAGCGGCGCTTTCCCTA-AAA
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTATC-ACAAG
40944974 CGCCGCTAAAGGTCGGGT
65 CGCCGCTAAAGGTCGGGT
* * * * * *
40944992 CATTAGCGACGCTTACCCTAAAGCGCCGCTAAAGGTCGGGTCATTAGCGGGGCTTGAAGGGTCAT
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTT-TA---TCAC
*
40945057 TAGCGCCGCTAAAGGTCGGGT
62 AAGCGCCGCTAAAGGTCGGGT
* ** * * * * * *
40945078 CATAAGCGGCGCTTTCTAATC-AGCACCGCTAAA-GTCAGGTCATTAGTGGCAC-TTATTAGAAA
1 CATTAGCGGCGCTTTC-CCTCAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTA-T-CACA
*
40945140 AGCGCCGCTAAA--T-GTGT
63 AGCGCCGCTAAAGGTCGGGT
*
40945157 GAGTTAGCGGCGCTTTCCCAT-AAGCGCCGCTAA
1 CA-TTAGCGGCGCTTTCCC-TCAAGCGCCGCTAA
40945190 TTTATTTAAA
Statistics
Matches: 296, Mismatches: 55, Indels: 24
0.79 0.15 0.06
Matches are distributed among these distances:
79 4 0.01
80 25 0.08
81 1 0.00
82 202 0.68
83 2 0.01
84 1 0.00
85 16 0.05
86 44 0.15
87 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (82 bp):
CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTATCACAAGC
GCCGCTAAAGGTCGGGT
Found at i:40944926 original size:123 final size:121
Alignment explanation
Indices: 40944765--40945093 Score: 433
Period size: 123 Copynumber: 2.7 Consensus size: 121
40944755 CGCTTTCCCT
* * *
40944765 CAAGCGCCGTTACAGGTCGGGTCATTAGCGGATCTTTATCACAAGCGCCGCTAAAGGTCGGGTCA
1 CAAGCGCCGCTAAAGGTCGGGTCATTAGCGGAGCTTTATCACAAGCGCCGCTAAAGGTCGGGTCA
* * *
40944830 TTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGATCATTAGCGGCGCTTCATCA
66 TTAGCGGCGCTTTCCCTAAAACGCCGCTAAAGGTCGGATCATTAGCGACGCTT-A-CA
* * * *
40944888 CAAGCGCCGCTAAAGATCGGGTTATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCTGGTCA
1 CAAGCGCCGCTAAAGGTCGGGTCATTAGCGGAGCTTTATCACAAGCGCCGCTAAAGGTCGGGTCA
* *
40944953 TTAGCGGCGCTTTCCCTAAAACGCCGCTAAAGGTCGGGTCATTAGCGACGCTTACC
66 TTAGCGGCGCTTTCCCTAAAACGCCGCTAAAGGTCGGATCATTAGCGACGCTTACA
* * **
40945009 CTAAAGCGCCGCTAAAGGTCGGGTCATTAGCGGGGCTTGAAGGGTCATTAGCGCCGCTAAAGGTC
1 C--AAGCGCCGCTAAAGGTCGGGTCATTAGCGGAGCTT-TA---TCACAAGCGCCGCTAAAGGTC
*
40945074 GGGTCATAAGCGGCGCTTTC
60 GGGTCATTAGCGGCGCTTTC
40945094 TAATCAGCAC
Statistics
Matches: 180, Mismatches: 20, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
121 2 0.01
122 1 0.01
123 139 0.77
124 1 0.01
127 37 0.21
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Consensus pattern (121 bp):
CAAGCGCCGCTAAAGGTCGGGTCATTAGCGGAGCTTTATCACAAGCGCCGCTAAAGGTCGGGTCA
TTAGCGGCGCTTTCCCTAAAACGCCGCTAAAGGTCGGATCATTAGCGACGCTTACA
Found at i:40945085 original size:24 final size:24
Alignment explanation
Indices: 40945012--40945090 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 24
40945002 GCTTACCCTA
40945012 AAGCGCCGCTAAAGGTCGGGTCAT
1 AAGCGCCGCTAAAGGTCGGGTCAT
* ** *
40945036 TAGCGGGGCTTGAA----GGGTCAT
1 AAGCGCCGC-TAAAGGTCGGGTCAT
*
40945057 TAGCGCCGCTAAAGGTCGGGTCAT
1 AAGCGCCGCTAAAGGTCGGGTCAT
*
40945081 AAGCGGCGCT
1 AAGCGCCGCT
40945091 TTCTAATCAG
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
20 3 0.07
21 14 0.34
24 21 0.51
25 3 0.07
ACGTcount: A:0.22, C:0.23, G:0.37, T:0.19
Consensus pattern (24 bp):
AAGCGCCGCTAAAGGTCGGGTCAT
Found at i:40947746 original size:112 final size:112
Alignment explanation
Indices: 40947574--40948499 Score: 1462
Period size: 112 Copynumber: 8.3 Consensus size: 112
40947564 AATAATTAAA
* * * *
40947574 TAATTATATATTTAATTATAAATAGTATCAATTAATTAAAAATTTAATTT-GAATGATTTAATTA
1 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAAAATTTAATTTAAAAT-ATTTAATTA
40947638 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
65 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
* * *
40947686 TAATTATGTATTTAATTATAAATAGTATCAATTAATTAAAAATTTAATTTAAAAGATTTAATTAT
1 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAAAATTTAATTTAAAATATTTAATTAT
*
40947751 TTAATTATATTAAAGTAAATAACTATATTAAATTATTTAATTATGTT
66 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
* * *
40947798 TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAATAA-TTAAGTCAAAATATTTAATTA
1 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAA-AATTTAATTTAAAATATTTAATTA
*
40947862 TTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATTATGTT
65 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
40947910 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAATAA-TTAATTTAAAATATTT-A--A
1 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAA-AATTTAATTTAAAATATTTAATTA
* *
40947971 -TT-A--AT-TGAAACTAAATAATTATATTAAATTATTTAATTATGTT
65 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
* * * * * *
40948014 TAATTATGTATTTAATTATAAACAGTACCAATTACTTAAATATTTAATTTAATAGATTTAATTAT
1 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAAAATTTAATTTAAAATATTTAATTAT
* *
40948079 TTAATTATATTAAAGTAAATAATTATATTAAATCAATTAATTATGTT
66 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
*
40948126 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAATATTTAATTTAAAATATTTAATTAT
1 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAAAATTTAATTTAAAATATTTAATTAT
* *
40948191 TTAATTATATTAAAGTAAATAATTATATTAAATCAATTAATTATGTT
66 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
*
40948238 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAATATTTAATTTAAAATATTTAATTAT
1 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAAAATTTAATTTAAAATATTTAATTAT
*
40948303 TTAATTATATTAAAGTAAATAACTATATTAAATTATTTAATTATGTT
66 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
*
40948350 TAATTATGTATTTAATTGTAAACAGTA-CAAATTAATTAAATATTTAATTTAAAATATTTAATTA
1 TAATTATGTATTTAATTGTAAACAGTATC-AATTAATTAAAAATTTAATTTAAAATATTTAATTA
* *
40948414 TTTAATTATATTAAAGTAAATAACTATATTAAATTATTTAATTATGCT
65 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
40948462 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTA
1 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTA
40948500 TTTAATTATA
Statistics
Matches: 768, Mismatches: 33, Indels: 26
0.93 0.04 0.03
Matches are distributed among these distances:
103 1 0.00
104 88 0.11
105 3 0.00
107 2 0.00
108 4 0.01
109 2 0.00
111 4 0.01
112 659 0.86
113 5 0.01
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (112 bp):
TAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAAAATTTAATTTAAAATATTTAATTAT
TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
Found at i:40948399 original size:440 final size:446
Alignment explanation
Indices: 40947574--40948499 Score: 1526
Period size: 440 Copynumber: 2.1 Consensus size: 446
40947564 AATAATTAAA
* *
40947574 TAATTATATATTTAATTATAAATAGTATCAATTAATTAAAAATTTAATTTGAATGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAAAATTTAATTTGAATGATTTAATTAT
* *
40947639 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAATTA
66 TTAATTATATTAAAGTAAATAATTATATTAAATCAATTAATTATGTTTAATTATGTATTTAATTA
*
40947704 TAAATAGTATCAATTAATTAAAAATTTAATTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
131 TAAACAGTATCAATTAATTAAAAATTTAATTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
* *
40947769 ATAACTATATTAAATTATTTAATTATGTTTAATTATGTATTTAATTATAAACAGTATCAATTAAT
196 ATAACTATATTAAATCAATTAATTATGTTTAATTATGTATTTAATTATAAACAGTATCAATTAAT
*
40947834 TAAATAATTAAGTCAAAATATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTAT
261 TAAATAATTAAGTCAAAATATTTAATTATTTAATTATATTAAACTAAATAACTATATTAAATTAT
40947899 TTAATTATGTTTAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAATAATTAATTTAAAA
326 TTAATTATGTTTAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAATAATTAATTTAAAA
* *
40947964 TATTT-A-A-TT-A-AT-TGAAACTAAATAATTATATTAAATTATTTAATTATGTT
391 TATTTAATATTTAATATATGAAACTAAATAACTATATTAAATTATTTAATTATGCT
* * *
40948014 TAATTATGTATTTAATTATAAACAGTACCAATTACTTAAATATTTAATTT-AATAGATTTAATTA
1 TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAAAATTTAATTTGAAT-GATTTAATTA
40948078 TTTAATTATATTAAAGTAAATAATTATATTAAATCAATTAATTATGTTTAATTATGTATTTAATT
65 TTTAATTATATTAAAGTAAATAATTATATTAAATCAATTAATTATGTTTAATTATGTATTTAATT
* * *
40948143 GTAAACAGTATCAATTAATTAAATATTTAATTTAAAATATTTAATTATTTAATTATATTAAAGTA
130 ATAAACAGTATCAATTAATTAAAAATTTAATTTAAAAGATTTAATTATTTAATTATATTAAAGTA
* *
40948208 AATAATTATATTAAATCAATTAATTATGTTTAATTATGTATTTAATTGTAAACAGTATCAATTAA
195 AATAACTATATTAAATCAATTAATTATGTTTAATTATGTATTTAATTATAAACAGTATCAATTAA
* * * *
40948273 TTAAATATTTAATTTAAAATATTTAATTATTTAATTATATTAAAGTAAATAACTATATTAAATTA
260 TTAAATAATTAAGTCAAAATATTTAATTATTTAATTATATTAAACTAAATAACTATATTAAATTA
*
40948338 TTTAATTATGTTTAATTATGTATTTAATTGTAAACAGTA-CAAATTAATTAAATATTTAATTTAA
325 TTTAATTATGTTTAATTATGTATTTAATTGTAAACAGTATC-AATTAATTAAATAATTAATTTAA
* *
40948402 AATATTTAATTATTTAATTATATTAAAGTAAATAACTATATTAAATTATTTAATTATGCT
389 AATATTTAA-TATTTAA-TATATGAAACTAAATAACTATATTAAATTATTTAATTATGCT
*
40948462 TAATTATGTATTTAATTGTAAACAGTATCAATTAATTA
1 TAATTATGTATTTAATTATAAACAGTATCAATTAATTA
40948500 TTTAATTATA
Statistics
Matches: 448, Mismatches: 28, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
439 4 0.01
440 368 0.82
441 1 0.00
443 1 0.00
444 2 0.00
445 1 0.00
447 2 0.00
448 69 0.15
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (446 bp):
TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAAAATTTAATTTGAATGATTTAATTAT
TTAATTATATTAAAGTAAATAATTATATTAAATCAATTAATTATGTTTAATTATGTATTTAATTA
TAAACAGTATCAATTAATTAAAAATTTAATTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
ATAACTATATTAAATCAATTAATTATGTTTAATTATGTATTTAATTATAAACAGTATCAATTAAT
TAAATAATTAAGTCAAAATATTTAATTATTTAATTATATTAAACTAAATAACTATATTAAATTAT
TTAATTATGTTTAATTATGTATTTAATTGTAAACAGTATCAATTAATTAAATAATTAATTTAAAA
TATTTAATATTTAATATATGAAACTAAATAACTATATTAAATTATTTAATTATGCT
Found at i:40948523 original size:22 final size:22
Alignment explanation
Indices: 40948491--40948626 Score: 79
Period size: 22 Copynumber: 6.3 Consensus size: 22
40948481 AAACAGTATC
*
40948491 AATTAATTATTTAATTATATTT
1 AATTAAATATTTAATTATATTT
40948513 AATTAAATATTTAATTTAAAATATTT
1 AATTAAATATTTAA-TT---ATATTT
*** * *
40948539 TCGTAAATAATT-ATATATAATT
1 AATTAAATATTTAAT-TATATTT
*
40948561 -ATTTAAT-TTTAATTA-A-TT
1 AATTAAATATTTAATTATATTT
* * * *
40948579 ATTTAATTATTTAATTATACTA
1 AATTAAATATTTAATTATATTT
40948601 AATTAAATATTTAA-T-TATTT
1 AATTAAATATTTAATTATATTT
40948621 AATTAA
1 AATTAA
40948627 TAAAAACAAT
Statistics
Matches: 86, Mismatches: 18, Indels: 22
0.68 0.14 0.17
Matches are distributed among these distances:
18 2 0.02
19 5 0.06
20 21 0.24
21 8 0.09
22 31 0.36
23 2 0.02
24 1 0.01
25 2 0.02
26 14 0.16
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (22 bp):
AATTAAATATTTAATTATATTT
Found at i:40948534 original size:14 final size:12
Alignment explanation
Indices: 40948381--40948617 Score: 66
Period size: 12 Copynumber: 19.6 Consensus size: 12
40948371 ACAGTACAAA
40948381 TTAATTAAATAT
1 TTAATTAAATAT
40948393 TTAATTTAAAATAT
1 TTAA-TT-AAATAT
40948407 TTAA-T---TAT
1 TTAATTAAATAT
40948415 TTAATT--ATAT
1 TTAATTAAATAT
* * *
40948425 TAAAGTAAATAA
1 TTAATTAAATAT
*
40948437 CTATATTAAATTAT
1 TTA-ATTAAA-TAT
**
40948451 TTAATT--ATGC
1 TTAATTAAATAT
**
40948461 TTAATTATGTAT
1 TTAATTAAATAT
*
40948473 TTAATTGTAAACAGT
1 TTAA-T-TAAATA-T
* *
40948488 ATCAATTAATTAT
1 -TTAATTAAATAT
40948501 TTAATT--ATAT
1 TTAATTAAATAT
40948511 TTAATTAAATAT
1 TTAATTAAATAT
40948523 TTAATTTAAAATAT
1 TTAA-TT-AAATAT
*** *
40948537 TTTCGTAAATAA
1 TTAATTAAATAT
*
40948549 TTATATATAATTAT
1 TTA-AT-TAAATAT
* *
40948563 TTAATTTTAATTAA
1 TTAA--TTAAATAT
* *
40948577 TTATTTAATTAT
1 TTAATTAAATAT
*
40948589 TTAATT--ATAC
1 TTAATTAAATAT
*
40948599 TAAATTAAATAT
1 TTAATTAAATAT
40948611 TTAATTA
1 TTAATTA
40948618 TTTAATTAAT
Statistics
Matches: 162, Mismatches: 39, Indels: 48
0.65 0.16 0.19
Matches are distributed among these distances:
8 7 0.04
9 1 0.01
10 30 0.19
11 1 0.01
12 55 0.34
13 16 0.10
14 46 0.28
15 3 0.02
16 3 0.02
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (12 bp):
TTAATTAAATAT
Found at i:40948576 original size:4 final size:4
Alignment explanation
Indices: 40948546--40948627 Score: 51
Period size: 4 Copynumber: 20.0 Consensus size: 4
40948536 TTTTCGTAAA
* * *
40948546 TAAT TATAT ATAAT TATT TAAT T--T TAAT TAAT TATT TAAT TATT TAAT
1 TAAT TA-AT -TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
* * * *
40948594 TATACT AAAT TAAA TATT TAAT TATT TAAT TAAT
1 TA-A-T TAAT TAAT TAAT TAAT TAAT TAAT TAAT
40948628 AAAAACAATC
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
2 2 0.03
4 46 0.79
5 6 0.10
6 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (4 bp):
TAAT
Found at i:40948580 original size:224 final size:223
Alignment explanation
Indices: 40947964--40948568 Score: 891
Period size: 224 Copynumber: 2.7 Consensus size: 223
40947954 TAATTTAAAA
*
40947964 TATTTAATTA-ATTGAAACTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTA
1 TATTTAATTATATT-AAAGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTA
* * * * *
40948028 ATTATAAACAGTACCAATTACTTAAATATTTAATTTAATAGAT-TTAATTATTTAATTATATTAA
65 ATTGTAAACAGTATCAATTAATTAAATATTTAATTTAATAAATATT--TAATTTAATTATATTAA
* *
40948092 AGTAAATAATTATATTAAATCAATTAATTATGTTTAATTATGTATTTAATTGTAAACAGTATCAA
128 AGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAATTGTAAACAGTATCAA
40948157 TTAATTAAATATTTAATTTAAAATATTTAAT
193 TTAATTAAATATTTAATTTAAAATATTTAAT
* *
40948188 TATTTAATTATATTAAAGTAAATAATTATATTAAATCAATTAATTATGTTTAATTATGTATTTAA
1 TATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAA
40948253 TTGTAAACAGTATCAATTAATTAAATATTTAATTT-A-AAATATTTAATTATTTAATTATATTAA
66 TTGTAAACAGTATCAATTAATTAAATATTTAATTTAATAAATATTT-A--ATTTAATTATATTAA
*
40948316 AGTAAATAACTATATTAAATTATTTAATTATGTTTAATTATGTATTTAATTGTAAACAGTA-CAA
128 AGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAATTGTAAACAGTATC-A
40948380 ATTAATTAAATATTTAATTTAAAATATTTAAT
192 ATTAATTAAATATTTAATTTAAAATATTTAAT
* *
40948412 TATTTAATTATATTAAAGTAAATAACTATATTAAATTATTTAATTATGCTTAATTATGTATTTAA
1 TATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAA
** * * ***
40948477 TTGTAAACAGTATCAATTAATTATTTAATTATATTTAATTAAATATTTAATTTAA-AATATTTTC
66 TTGTAAACAGTATCAATTAATTAAATATTTA-ATTTAA-TAAATATTTAATTTAATTATATTAAA
40948541 GTAAATAATTATA-TATAATTATTTAATT
129 GTAAATAATTATATTA-AATTATTTAATT
40948569 TTAATTAATT
Statistics
Matches: 347, Mismatches: 23, Indels: 22
0.89 0.06 0.06
Matches are distributed among these distances:
221 1 0.00
222 3 0.01
223 6 0.02
224 314 0.90
225 13 0.04
226 1 0.00
227 1 0.00
228 8 0.02
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (223 bp):
TATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAA
TTGTAAACAGTATCAATTAATTAAATATTTAATTTAATAAATATTTAATTTAATTATATTAAAGT
AAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAATTGTAAACAGTATCAATTA
ATTAAATATTTAATTTAAAATATTTAAT
Found at i:40948584 original size:8 final size:8
Alignment explanation
Indices: 40948546--40948625 Score: 67
Period size: 8 Copynumber: 9.8 Consensus size: 8
40948536 TTTTCGTAAA
40948546 TAATTATAT
1 TAATTAT-T
40948555 ATAATTATT
1 -TAATTATT
*
40948564 TAATTTTAAT
1 TAA--TTATT
40948574 TAATTATT
1 TAATTATT
40948582 TAATTATT
1 TAATTATT
*
40948590 TAATTATAC
1 TAATTAT-T
40948599 TAA--A-T
1 TAATTATT
*
40948604 TAAATATT
1 TAATTATT
40948612 TAATTATT
1 TAATTATT
40948620 TAATTA
1 TAATTA
40948626 ATAAAAACAA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
5 3 0.05
7 2 0.03
8 36 0.61
9 4 0.07
10 14 0.24
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (8 bp):
TAATTATT
Found at i:40948585 original size:26 final size:27
Alignment explanation
Indices: 40948491--40948624 Score: 100
Period size: 30 Copynumber: 4.9 Consensus size: 27
40948481 AAACAGTATC
40948491 AATTAATTATTTAATTA--T-A-TT-T
1 AATTAATTATTTAATTATTTAATTTCT
* ** *
40948513 AATTAAATATTTAATTTAAAATATTTTCGT
1 AATTAATTATTTAA-TT-ATTTAATTTC-T
*
40948543 AAATAATTATATATAATTATTTAATTT-T
1 AATTAATTAT-T-TAATTATTTAATTTCT
40948571 AATTAATTATTTAATTATTTAATTATACT
1 AATTAATTATTTAATTATTTAATT-T-CT
*
40948600 AAATTAAATATTTAATTATTTAATT
1 -AATTAATTATTTAATTATTTAATT
40948625 AATAAAAACA
Statistics
Matches: 89, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
22 13 0.15
23 2 0.02
24 1 0.01
26 14 0.16
27 2 0.02
28 12 0.13
29 1 0.01
30 38 0.43
31 3 0.03
32 3 0.03
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (27 bp):
AATTAATTATTTAATTATTTAATTTCT
Found at i:40948702 original size:31 final size:32
Alignment explanation
Indices: 40948647--40948712 Score: 116
Period size: 33 Copynumber: 2.1 Consensus size: 32
40948637 CAAAATATTT
40948647 AAGTAAATGTTGTCACTAATATATATATTTTA
1 AAGTAAATGTTGTCACTAATATATATATTTTA
40948679 AAGTAAAATGTTGTCACTAATATATAT-TTTTA
1 AAGT-AAATGTTGTCACTAATATATATATTTTA
40948711 AA
1 AA
40948713 TTTAAATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 11 0.33
33 22 0.67
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (32 bp):
AAGTAAATGTTGTCACTAATATATATATTTTA
Found at i:40954291 original size:65 final size:66
Alignment explanation
Indices: 40954145--40954301 Score: 217
Period size: 66 Copynumber: 2.4 Consensus size: 66
40954135 GCAAATTGCT
* * *
40954145 CAACTTAAGGAGGAGGCTGCAGCGAGAGAAGCAAAGGCTCAAAAAAAATATGATGAACTCCATCT
1 CAACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAAAGGCTCAAAAAAAATATGAAGAACTCCACCT
40954210 A
66 A
* * * * *
40954211 AAACTTAAAGAGGAGGCTGCAGTGAGAGAAGCAGAGTCTCGAAAAAAA-ATGAAGAACTCCACCT
1 CAACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAAAGGCTCAAAAAAAATATGAAGAACTCCACCT
40954275 A
66 A
* *
40954276 CAACTTAAAGTGGAGGCAGCAGCGAG
1 CAACTTAAAGAGGAGGCTGCAGCGAG
40954302 GCAAGCGAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
65 37 0.47
66 42 0.53
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.14
Consensus pattern (66 bp):
CAACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAAAGGCTCAAAAAAAATATGAAGAACTCCACCT
A
Found at i:40954539 original size:15 final size:15
Alignment explanation
Indices: 40954519--40954547 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40954509 ATTTGAAGTT
40954519 ATTGGTTGGATTTGC
1 ATTGGTTGGATTTGC
40954534 ATTGGTTGGATTTG
1 ATTGGTTGGATTTG
40954548 AATTTACAGG
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:0.14, C:0.03, G:0.34, T:0.48
Consensus pattern (15 bp):
ATTGGTTGGATTTGC
Found at i:40960193 original size:24 final size:24
Alignment explanation
Indices: 40960164--40960220 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
40960154 TAGAGAAATA
*
40960164 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
40960188 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
40960212 AGAGTTTAA
1 AGAGTTTAA
40960221 TTGAAAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:40960221 original size:24 final size:24
Alignment explanation
Indices: 40960176--40960226 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
40960166 AGTTTGACTC
40960176 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
40960200 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
40960224 AAA
1 AAA
40960227 GATTATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:40964737 original size:20 final size:21
Alignment explanation
Indices: 40964700--40964739 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
40964690 TGTTTAATAG
40964700 AAGTAGTGAAAGTGAGAAAAA
1 AAGTAGTGAAAGTGAGAAAAA
40964721 AAGT-GTGAAAGAT-AGAAAA
1 AAGTAGTGAAAG-TGAGAAAA
40964740 CTAGCAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.28, T:0.15
Consensus pattern (21 bp):
AAGTAGTGAAAGTGAGAAAAA
Found at i:40972868 original size:14 final size:14
Alignment explanation
Indices: 40972851--40972888 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
40972841 AACAGACTAT
40972851 AACTGACACATTAC
1 AACTGACACATTAC
40972865 AACTGACACATTAC
1 AACTGACACATTAC
*
40972879 AACTAACACA
1 AACTGACACA
40972889 CTATCACTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.29, G:0.05, T:0.18
Consensus pattern (14 bp):
AACTGACACATTAC
Found at i:40975355 original size:58 final size:57
Alignment explanation
Indices: 40975284--40975539 Score: 218
Period size: 58 Copynumber: 4.4 Consensus size: 57
40975274 TTTTGGATAC
* * *
40975284 TCGAGTGGCAAAATGGTAATTTTGGTTGAAAT-TGGGTCAAAAACGAG-ATTTTGGAAAGT
1 TCGAG-GGTAAAATGGTAATTTTGG-TAAAATCAGGGT-AAAAA-GAGAATTTTGGAAAGT
* *
40975343 TCGAGGGTAAAATGGTAATTTTTTGTAAAAATCGAGGGTAAAAATG-GAATTTTGGAAAGC
1 TCGAGGGTAAAATGGTAA-TTTTGGT-AAAATC-AGGGTAAAAA-GAGAATTTTGGAAAGT
* * * *
40975403 TGGAGGGTAAAATGGTAATTTTGGTAAAATCGGGGTTAAAAATAGAATTTTAGAAAGT
1 TCGAGGGTAAAATGGTAATTTTGGTAAAATCAGGG-TAAAAAGAGAATTTTGGAAAGT
* * * * *
40975461 AT-GGGGGTAAAATGGTAATTTTGGTGAAATCGGTGGTAAAATG-GAATTTTGGAAAAT
1 -TCGAGGGTAAAATGGTAATTTTGGTAAAATCAG-GGTAAAAAGAGAATTTTGGAAAGT
**
40975518 TTAAGGGTAAAAAT-GTAATTTT
1 TCGAGGGT-AAAATGGTAATTTT
40975540 TAGAAAGTTT
Statistics
Matches: 166, Mismatches: 20, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
56 1 0.01
57 27 0.16
58 76 0.46
59 24 0.14
60 34 0.20
61 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (57 bp):
TCGAGGGTAAAATGGTAATTTTGGTAAAATCAGGGTAAAAAGAGAATTTTGGAAAGT
Found at i:40975363 original size:29 final size:29
Alignment explanation
Indices: 40975331--40975548 Score: 141
Period size: 29 Copynumber: 7.4 Consensus size: 29
40975321 CAAAAACGAG
40975331 ATTTTGGAAAGTTCGAGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGAGGGTAAAATGGTA
* **
40975360 ATTTTTTGTAAAAATCGAGGGTAAAAATGG-A
1 A--TTTTGGAAAGTTCGAGGGT-AAAATGGTA
* *
40975391 ATTTTGGAAAGCTGGAGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGAGGGTAAAATGGTA
* *
40975420 ATTTTGGTAAA-ATCG-GGGTTAAAAATAG-A
1 ATTTTGG-AAAGTTCGAGGG-T-AAAATGGTA
* *
40975449 ATTTTAGAAAGTAT-GGGGGTAAAATGGTA
1 ATTTTGGAAAGT-TCGAGGGTAAAATGGTA
40975478 ATTTTGGTGAAA--TCG-GTGGTAAAATGG-A
1 ATTTT-G-GAAAGTTCGAG-GGTAAAATGGTA
* **
40975506 ATTTTGGAAAATTTAAGGGTAAAAAT-GTA
1 ATTTTGGAAAGTTCGAGGGT-AAAATGGTA
*
40975535 ATTTTTAGAAAGTT
1 A-TTTTGGAAAGTT
40975549 TTAGGGTTAA
Statistics
Matches: 150, Mismatches: 18, Indels: 41
0.72 0.09 0.20
Matches are distributed among these distances:
26 4 0.03
27 1 0.01
28 32 0.21
29 61 0.41
30 23 0.15
31 22 0.15
32 7 0.05
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (29 bp):
ATTTTGGAAAGTTCGAGGGTAAAATGGTA
Found at i:40975482 original size:118 final size:115
Alignment explanation
Indices: 40975293--40975515 Score: 283
Period size: 118 Copynumber: 1.9 Consensus size: 115
40975283 CTCGAGTGGC
* * * *
40975293 AAAATGGTAATTTTGGTTGAAATTGGGTCAAAAACGAGATTTTGGAAAGTTCGAGGGTAAAATGG
1 AAAATGGTAATTTTGGTTAAAATGGGGTCAAAAAAGAGATTTTAGAAAGTTCGAGGGTAAAATGG
*
40975358 TAATTTTTTGTAAAAATCGAG-GGTAAAAATGGAATTTTGGAAAGCTGGAGGGT
66 TAA-TTTTGGT-AAAATCG-GTGGT-AAAATGGAATTTTGGAAAGCTGGAGGGT
* *
40975411 AAAATGGTAATTTTGG-TAAAATCGGGGTTAAAAATAGA-ATTTTAGAAAGTAT-GGGGGTAAAA
1 AAAATGGTAATTTTGGTTAAAAT-GGGGTCAAAAA-AGAGATTTTAGAAAGT-TCGAGGGTAAAA
*
40975473 TGGTAATTTTGGTGAAATCGGTGGTAAAATGGAATTTTGGAAA
63 TGGTAATTTTGGTAAAATCGGTGGTAAAATGGAATTTTGGAAA
40975516 ATTTAAGGGT
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
115 19 0.20
116 9 0.10
117 11 0.12
118 51 0.55
119 3 0.03
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (115 bp):
AAAATGGTAATTTTGGTTAAAATGGGGTCAAAAAAGAGATTTTAGAAAGTTCGAGGGTAAAATGG
TAATTTTGGTAAAATCGGTGGTAAAATGGAATTTTGGAAAGCTGGAGGGT
Found at i:40975594 original size:30 final size:30
Alignment explanation
Indices: 40975521--40975743 Score: 161
Period size: 30 Copynumber: 7.4 Consensus size: 30
40975511 GGAAAATTTA
* * *
40975521 AGGGTAAAAATGTAATTTTTAGAAAGTTTT
1 AGGGTTAAAATATAATTTTTAGAAAGGTTT
* *
40975551 AGGGTTAAAAATATAATTTTCAAAAAGGTTT
1 AGGGTT-AAAATATAATTTTTAGAAAGGTTT
*
40975582 AGGGTTAAAATATAA-TTTTGGAGAA-GTTT
1 AGGGTTAAAATATAATTTTTAGA-AAGGTTT
* * * *
40975611 GGGGGGTTAAAATGTATTTTTTTGAAA-GTTT
1 --AGGGTTAAAATATAATTTTTAGAAAGGTTT
* * *
40975642 AGGGGTTAAAATGTAA-CTTTAGAAAGTTTT
1 A-GGGTTAAAATATAATTTTTAGAAAGGTTT
* *
40975672 AGGGTCAAAATATAA-TTTTGGTAAA-GTTT
1 AGGGTTAAAATATAATTTTTAG-AAAGGTTT
* * * *
40975701 GGGGGTTAAAATGTGATTTTTAGAAAGTTTT
1 -AGGGTTAAAATATAATTTTTAGAAAGGTTT
*
40975732 AGGGTCAAAATA
1 AGGGTTAAAATA
40975744 CTATTTCTGG
Statistics
Matches: 151, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
29 34 0.23
30 59 0.39
31 52 0.34
32 6 0.04
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (30 bp):
AGGGTTAAAATATAATTTTTAGAAAGGTTT
Found at i:40975732 original size:60 final size:59
Alignment explanation
Indices: 40975505--40975743 Score: 223
Period size: 60 Copynumber: 4.0 Consensus size: 59
40975495 GGTAAAATGG
* * *
40975505 AATTTTGG-AAAATTTAAGGGTAAAAATGTAATTTTTAGAAAGTTTTAGGGTTAAAAATAT
1 AATTTTGGTAAAGTTTAAGGGTTAAAATGTAA-TTTTAGAAAGTTTTAGGG-TCAAAATAT
*** * * ** * *
40975565 AATTTTCAAAAAGGTTT-AGGGTTAAAATATAATTTTGGAGAAGTTTGGGGGGTTAAAATGT
1 AATTTTGGTAAA-GTTTAAGGGTTAAAATGTAATTTTAGA-AAGTTT-TAGGGTCAAAATAT
** * *
40975626 -ATTTTTTTGAAAGTTTAGGGGTTAAAATGTAACTTTAGAAAGTTTTAGGGTCAAAATAT
1 AATTTTGGT-AAAGTTTAAGGGTTAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATAT
** *
40975685 AATTTTGGTAAAGTTTGGGGGTTAAAATGTGATTTTTAGAAAGTTTTAGGGTCAAAATA
1 AATTTTGGTAAAGTTTAAGGGTTAAAATGT-AATTTTAGAAAGTTTTAGGGTCAAAATA
40975744 CTATTTCTGG
Statistics
Matches: 145, Mismatches: 26, Indels: 16
0.78 0.14 0.09
Matches are distributed among these distances:
59 30 0.21
60 59 0.41
61 50 0.34
62 6 0.04
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (59 bp):
AATTTTGGTAAAGTTTAAGGGTTAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATAT
Found at i:40975760 original size:30 final size:29
Alignment explanation
Indices: 40975505--40975760 Score: 156
Period size: 30 Copynumber: 8.5 Consensus size: 29
40975495 GGTAAAATGG
* * * *
40975505 AATTTTGGAAAATTTAAGGGTAAAAATGT
1 AATTTTGGAAAGTTTTAGGGTCAAAATAT
* *
40975534 AATTTTTAGAAAGTTTTAGGGTTAAAAATAT
1 AA-TTTTGGAAAGTTTTAGGG-TCAAAATAT
** * *
40975565 AATTTTCAAAAAGGTTTAGGGTTAAAATAT
1 AATTTT-GGAAAGTTTTAGGGTCAAAATAT
** * *
40975595 AATTTTGGAGAAGTTTGGGGGGTTAAAATGT
1 AATTTTGGA-AAGTTT-TAGGGTCAAAATAT
* * * *
40975626 ATTTTTTTGAAAG-TTTAGGGGTTAAAATGT
1 A-ATTTTGGAAAGTTTTA-GGGTCAAAATAT
* *
40975656 AACTTTAGAAAGTTTTAGGGTCAAAATAT
1 AATTTTGGAAAGTTTTAGGGTCAAAATAT
** * *
40975685 AATTTTGGTAAAGTTTGGGGGTTAAAATGT
1 AATTTTGG-AAAGTTTTAGGGTCAAAATAT
* *
40975715 GATTTTTAGAAAGTTTTAGGGTCAAAATACT
1 -AATTTTGGAAAGTTTTAGGGTCAAAATA-T
*
40975746 -ATTTCTGGATAGTTT
1 AATTT-TGGAAAGTTT
40975761 CAGGACTTCT
Statistics
Matches: 178, Mismatches: 37, Indels: 23
0.75 0.16 0.10
Matches are distributed among these distances:
29 30 0.17
30 98 0.55
31 44 0.25
32 6 0.03
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.39
Consensus pattern (29 bp):
AATTTTGGAAAGTTTTAGGGTCAAAATAT
Found at i:40975760 original size:90 final size:87
Alignment explanation
Indices: 40975505--40975743 Score: 282
Period size: 90 Copynumber: 2.7 Consensus size: 87
40975495 GGTAAAATGG
* ** *
40975505 AATTTTGGAAAATTTAAGGGTAAAAATGTAATTTTTAGAAAGTTTTAGGGTTAAAAATATAATTT
1 AATTTTGGAAAGTTTGGGGGTTAAAATGT-ATTTTTAGAAAGTTTTAGGG-TAAAAATATAATTT
* * *
40975570 TCAAAAAGGTTTAGGGTTAAAATAT
64 T-AGAAAGTTTTAGGGTCAAAATAT
* * * *
40975595 AATTTTGGAGAAGTTTGGGGGGTTAAAATGTATTTTTTTGAAAG-TTTAGGGGTTAAAATGTAAC
1 AATTTTGGA-AAGTTT-GGGGGTTAAAATGTA-TTTTTAGAAAGTTTTA-GGGTAAAAATATAAT
40975659 TTTAGAAAGTTTTAGGGTCAAAATAT
62 TTTAGAAAGTTTTAGGGTCAAAATAT
*
40975685 AATTTTGGTAAAGTTTGGGGGTTAAAATGTGATTTTTAGAAAGTTTTAGGGTCAAAATA
1 AATTTTGG-AAAGTTTGGGGGTTAAAATGT-ATTTTTAGAAAGTTTTAGGGTAAAAATA
40975744 CTATTTCTGG
Statistics
Matches: 128, Mismatches: 14, Indels: 15
0.82 0.09 0.10
Matches are distributed among these distances:
89 33 0.26
90 48 0.38
91 23 0.18
92 24 0.19
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (87 bp):
AATTTTGGAAAGTTTGGGGGTTAAAATGTATTTTTAGAAAGTTTTAGGGTAAAAATATAATTTTA
GAAAGTTTTAGGGTCAAAATAT
Found at i:40978136 original size:92 final size:92
Alignment explanation
Indices: 40977973--40978930 Score: 1605
Period size: 92 Copynumber: 10.4 Consensus size: 92
40977963 TGATTTCGAG
* * *
40977973 GCTT-ATCTTACTCCTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
40978037 TCAAGAGGATAAGAATTGACGTTTGAA
66 TCAAGAGGATAAGAATTGACGTTTGAA
* *
40978064 GCTTCATCTTGCTCTTACTATAACTTCGGAGAGATAAAGGTTTGTTATCCAACTTTACTATAACT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
* *
40978129 TCGAGAGGATAAGAATTGAAGTTTGAA
66 TCAAGAGGATAAGAATTGACGTTTGAA
* *
40978156 GCTTCATCTTGCTCTTATTATAACTTCAAAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
*
40978221 TCAAGAGGATAAGAATTGATGTTTGAA
66 TCAAGAGGATAAGAATTGACGTTTGAA
* * *
40978248 GCTTTATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTTGTTATCCAACTTTACTATAACT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
* * *
40978313 TCGAGAGGAT-AGTAATTAACGCTTGAA
66 TCAAGAGGATAAG-AATTGACGTTTGAA
40978340 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
* *
40978405 TCAAGAGGATAAGAATTGACATTTAAA
66 TCAAGAGGATAAGAATTGACGTTTGAA
* *
40978432 GCTTCATCTTGCTCTTACTACAACTTTAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
40978497 TCAAGAGGATAAGAATTGACGTTTGAA
66 TCAAGAGGATAAGAATTGACGTTTGAA
* *
40978524 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAAAT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
40978589 TCAAGAGGATAAGAATTGACGTTTGAA
66 TCAAGAGGATAAGAATTGACGTTTGAA
* *
40978616 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAAAT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
*
40978681 TCAAGAGGATAAGAATTGATGTTTGAA
66 TCAAGAGGATAAGAATTGACGTTTGAA
* *
40978708 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGGTTCGTCATCCAACTTTACTATAACT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
*
40978773 TCGAGAGGATAAGAATTGACGTTTGAA
66 TCAAGAGGATAAGAATTGACGTTTGAA
* * * *
40978800 GCTTCATCTTGCTCTTACTACAACTTTAGAGAGATAAAGGCTCGTTATCCAACTTTACTTTAACT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
40978865 TCAAGAGGATAAGAATTGACGTTTGAA
66 TCAAGAGGATAAGAATTGACGTTTGAA
40978892 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAG
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAG
40978931 ACTTGCTATT
Statistics
Matches: 816, Mismatches: 48, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
91 6 0.01
92 808 0.99
93 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (92 bp):
GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACT
TCAAGAGGATAAGAATTGACGTTTGAA
Done.