Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 190 of 204
Found at i:56051149 original size:29 final size:27
Alignment explanation
Indices: 56051092--56051152 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
56051082 TATAATATTG
*
56051092 AATTTAGTTTTCAATTTTTTTTTTGTC
1 AATTTAGTTTTCAATTTTTTTTTAGTC
*
56051119 AATTTAGTTTT-TATTCTTTTTTTGAGCTC
1 AATTTAGTTTTCAATT-TTTTTTT-AG-TC
56051148 AATTT
1 AATTT
56051153 GACCCATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 18 0.62
28 1 0.03
29 7 0.24
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (27 bp):
AATTTAGTTTTCAATTTTTTTTTAGTC
Found at i:56051933 original size:121 final size:121
Alignment explanation
Indices: 56051781--56052000 Score: 289
Period size: 121 Copynumber: 1.8 Consensus size: 121
56051771 TCAAATAATT
* * *
56051781 AAAAAATAATTTTTAATCTCCACTCATGAAAATGAAATACAATTTATTGTCAATCATTTATCTTT
1 AAAAAATAATTTTTAATCTCCACTCACGAAAATGAAACACAATTTATTGTCAATCATTTAACTTT
* *
56051846 TCGGAATACATCCACAATTAGAAGATTAATCACTATTACTGATTATGGATATTCAA
66 TCGGAAAACATCCACAATTAGAAAATTAATCACTATTACTGATTATGGATATTCAA
* * * * * *
56051902 AAAATAATATTTTTTAATC-CCGCTCACGAAAATGGAACATATTTTATTGTCACTCATTTAACTT
1 AAAA-AATAATTTTTAATCTCCACTCACGAAAATGAAACACAATTTATTGTCAATCATTTAACTT
* ** *
56051966 TTCGGAAAATATCTTCAGTTAGAAAATTAATCACT
65 TTCGGAAAACATCCACAATTAGAAAATTAATCACT
56052001 GCTATCAATG
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
121 70 0.84
122 13 0.16
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (121 bp):
AAAAAATAATTTTTAATCTCCACTCACGAAAATGAAACACAATTTATTGTCAATCATTTAACTTT
TCGGAAAACATCCACAATTAGAAAATTAATCACTATTACTGATTATGGATATTCAA
Found at i:56052111 original size:19 final size:20
Alignment explanation
Indices: 56052071--56052112 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
56052061 CAGATTTAAG
*
56052071 TTGAATTTTTAAAAGTAATAT
1 TTGAAGTTTTAAAAG-AATAT
56052092 TTGAAGTTTTAAAA-AATAT
1 TTGAAGTTTTAAAAGAATAT
56052111 TT
1 TT
56052113 TATTCACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (20 bp):
TTGAAGTTTTAAAAGAATAT
Found at i:56055770 original size:7 final size:7
Alignment explanation
Indices: 56055758--56055783 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
56055748 ATTTTCCCTT
56055758 TCTCTTC
1 TCTCTTC
56055765 TCTCTTC
1 TCTCTTC
56055772 TCTCTTC
1 TCTCTTC
56055779 TCTCT
1 TCTCT
56055784 AACTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TCTCTTC
Found at i:56058376 original size:72 final size:72
Alignment explanation
Indices: 56058258--56058414 Score: 197
Period size: 72 Copynumber: 2.2 Consensus size: 72
56058248 ACCAATCTCG
* * * * * * *
56058258 AAAATCAATTAAATGGTCAAGTTCCATTGTCTATAGGGGAGCTATCATCTTTGAAGTTGTTTAAT
1 AAAATCAATTAAACGGCCAAATTCCATCGTCTATAGGGCAGCTATCATCTTTGAAGGTATTTAAT
56058323 GTTTCAA
66 GTTTCAA
* * * * *
56058330 AAAATCAGTTAAACGGCCAAATTCCCTCGTCTATAGGGCAGTTATCATCTTTGGAGGTATTTGAT
1 AAAATCAATTAAACGGCCAAATTCCATCGTCTATAGGGCAGCTATCATCTTTGAAGGTATTTAAT
*
56058395 GTTTCAG
66 GTTTCAA
56058402 AAAATCAATTAAA
1 AAAATCAATTAAA
56058415 TGGTACTTTT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (72 bp):
AAAATCAATTAAACGGCCAAATTCCATCGTCTATAGGGCAGCTATCATCTTTGAAGGTATTTAAT
GTTTCAA
Found at i:56069037 original size:2 final size:2
Alignment explanation
Indices: 56069030--56069083 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
56069020 GTGTATAAGG
* * *
56069030 AT AT AT AT AT AT AT AT AT A- AT A- AG AT AG A- AG 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
56069069 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
56069084 CGAGAATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (2 bp):
AT
Found at i:56069103 original size:35 final size:32
Alignment explanation
Indices: 56069030--56069116 Score: 84
Period size: 35 Copynumber: 2.6 Consensus size: 32
56069020 GTGTATAAGG
* * *
56069030 ATATATATATATATATATAATAAGATAGAAGAT
1 ATATATATATATATATAT-ATAAGATAAAAAAC
56069063 ATATATATATATATATATATACGAGAATAAAAAAC
1 ATATATATATATATATATATA--AG-ATAAAAAAC
* * *
56069098 GTATATAAAGATATATATA
1 ATATATATATATATATATA
56069117 ATATAAGGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 3 0.07
33 18 0.40
34 2 0.04
35 22 0.49
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.34
Consensus pattern (32 bp):
ATATATATATATATATATATAAGATAAAAAAC
Found at i:56069395 original size:28 final size:28
Alignment explanation
Indices: 56069342--56069396 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
56069332 TAAATAATTA
* *
56069342 TAATAATATTAATGATGTAATGTGATAG
1 TAATAATATTAATGATGAAATATGATAG
56069370 TAATAATATTAATGAT-AAATAATGATA
1 TAATAATATTAATGATGAAAT-ATGATA
56069397 ATAAGTGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (28 bp):
TAATAATATTAATGATGAAATATGATAG
Found at i:56069427 original size:3 final size:3
Alignment explanation
Indices: 56069419--56069566 Score: 68
Period size: 3 Copynumber: 48.7 Consensus size: 3
56069409 GAGATATGAA
* * * *
56069419 AAT AAT AAT AAT AAT AGT AAT -AT CAGT GAA- AAT ATT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT
* * * * * **
56069464 AAAT AAAT AAT AAT AAC AAT ATT AAC AAT AATT TAT AAT TAT GTT AAT
1 -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
** * * * **
56069512 AGG AAC AA- AAT AAC AAT AAT ACT AAT AAT AAT AAT AAT AAT GCT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56069559 AAT AAT AA
1 AAT AAT AA
56069567 GTGTCGAAAC
Statistics
Matches: 105, Mismatches: 34, Indels: 12
0.70 0.23 0.08
Matches are distributed among these distances:
2 6 0.06
3 89 0.85
4 10 0.10
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:56071363 original size:15 final size:16
Alignment explanation
Indices: 56071331--56071366 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
56071321 TAAAAACGCA
56071331 AAAAAAAAAGAAAGAT
1 AAAAAAAAAGAAAGAT
*
56071347 AAAAAAAAATAAA-AT
1 AAAAAAAAAGAAAGAT
56071362 AAAAA
1 AAAAA
56071367 CTACAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.86, C:0.00, G:0.06, T:0.08
Consensus pattern (16 bp):
AAAAAAAAAGAAAGAT
Found at i:56072263 original size:44 final size:44
Alignment explanation
Indices: 56072209--56072322 Score: 147
Period size: 44 Copynumber: 2.6 Consensus size: 44
56072199 ACCGGTATGG
** * *
56072209 GAAGACAAGATCTACTTTCTTTGATCTACTTCATGCCAGTACAT
1 GAAGACAAGATCTACTTTCTCCGATCTACTTCACGCCAATACAT
** *
56072253 GAAGACAAGATCTGTTTTCTCCGATCTACTTCACGTCAATACAT
1 GAAGACAAGATCTACTTTCTCCGATCTACTTCACGCCAATACAT
* *
56072297 GAAGACAAGATCTTCTTTTTCCGATC
1 GAAGACAAGATCTACTTTCTCCGATC
56072323 GATTCCACTG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (44 bp):
GAAGACAAGATCTACTTTCTCCGATCTACTTCACGCCAATACAT
Found at i:56072581 original size:44 final size:44
Alignment explanation
Indices: 56072514--56072802 Score: 202
Period size: 45 Copynumber: 6.5 Consensus size: 44
56072504 ACCGATATAG
* * * * *
56072514 GAAGACAAGACCTACTATCTTTGATCTGTTTCACGCCGGTACAT
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTCACGCCAGTACAT
* * * ***
56072558 GAAAACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTC-ACGCCAGTACAT
* * * * * *
56072603 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTCACGCCAGTACAT
* * * ***
56072647 GAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTC-ACGCCAGTACAT
* * * * * * **
56072692 GAAGGCAAGATCTGCTTTCTTCGATCTACTCCACCACCTGTACGG
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTCA-CGCCAGTACAT
* * * * *
56072737 GGAGACAAGATCTGGTATCTATGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTCACGCCAGTACAT
*
56072781 GAAGACATGATCTG-TTATCTTT
1 GAAGACAAGATCTGCTT-TCTTT
56072803 CAACCTGCTC
Statistics
Matches: 183, Mismatches: 58, Indels: 8
0.73 0.23 0.03
Matches are distributed among these distances:
43 1 0.01
44 82 0.45
45 100 0.55
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTTTCTTTGATCTGCTTCACGCCAGTACAT
Found at i:56072718 original size:89 final size:89
Alignment explanation
Indices: 56072513--56072721 Score: 294
Period size: 89 Copynumber: 2.3 Consensus size: 89
56072503 TACCGATATA
* * * * ** ** *
56072513 GGAAGACAAGACCTACTATCTTTGATCTGTTTCACGCCGGTACATGAAAACAAGATCTGCTTTCT
1 GGAAGGCAAGATCTGCTATCTCTGATCTACTTCACGCCAATACATGAAAACAAGATCTACTTTCT
56072578 TTGATCTGCTTCGCCACCAGTATG
66 TTGATCTGCTTCGCCACCAGTATG
* *
56072602 GGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCT
1 GGAAGGCAAGATCTGCTATCTCTGATCTACTTCACGCCAATACATGAAAACAAGATCTACTTTCT
56072667 TTGATCTGCTTCGCCACCAGTATG
66 TTGATCTGCTTCGCCACCAGTATG
*
56072691 GGAAGGCAAGATCTGCTTTCT-TCGATCTACT
1 GGAAGGCAAGATCTGCTATCTCT-GATCTACT
56072722 CCACCACCTG
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
88 1 0.01
89 105 0.99
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (89 bp):
GGAAGGCAAGATCTGCTATCTCTGATCTACTTCACGCCAATACATGAAAACAAGATCTACTTTCT
TTGATCTGCTTCGCCACCAGTATG
Found at i:56072777 original size:89 final size:89
Alignment explanation
Indices: 56072553--56072768 Score: 263
Period size: 89 Copynumber: 2.4 Consensus size: 89
56072543 TTCACGCCGG
* * *
56072553 TACATGAAAACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGG
1 TACAGGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGC
* *
56072618 TATCTCTGATCTACTTCACGCCAA
66 TATCTCTGATCTACTCCACACCAA
* *
56072642 TACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGC
1 TACAGGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGC
* **
56072707 TTTCT-TCGATCTACTCCACCACCTG
66 TATCTCT-GATCTACTCCA-CACCAA
* * * * * *
56072732 TACGGGGAGACAAGATCTGGTATCTATGATCTACTTC
1 TACAGGAAGACAAGATCTGCTTTCTTTGATCTGCTTC
56072769 ACGCCAGTAC
Statistics
Matches: 109, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
88 1 0.01
89 76 0.70
90 32 0.29
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (89 bp):
TACAGGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGC
TATCTCTGATCTACTCCACACCAA
Found at i:56084724 original size:23 final size:22
Alignment explanation
Indices: 56084655--56084724 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
56084645 AAAAATACAT
* *
56084655 ATAAAAAAATGTATATAT-TTC
1 ATAAAAAAATGCATATATATAC
* *
56084676 ATATAAAAATATGCGTATGTACTAC
1 ATA-AAAAA-ATGCATATATA-TAC
56084701 ATGAAAAAAATGCATATATATAC
1 AT-AAAAAAATGCATATATATAC
56084724 A
1 A
56084725 AATTATGTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
21 3 0.08
22 5 0.13
23 11 0.29
24 9 0.24
25 9 0.24
26 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (22 bp):
ATAAAAAAATGCATATATATAC
Found at i:56086029 original size:17 final size:15
Alignment explanation
Indices: 56086003--56086046 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
56085993 AAAAAAATAG
*
56086003 ATAAATATAATAAAAA
1 ATAAAAATAA-AAAAA
56086019 AGTAAAAATAAAAAAA
1 A-TAAAAATAAAAAAA
56086035 AT-AAAATAAAAA
1 ATAAAAATAAAAA
56086047 GAATGCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.38
15 1 0.04
16 7 0.27
17 8 0.31
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (15 bp):
ATAAAAATAAAAAAA
Found at i:56086991 original size:6 final size:7
Alignment explanation
Indices: 56086974--56087000 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
56086964 TTTTGCTAGG
56086974 TTTTTTC
1 TTTTTTC
56086981 TTTTTTC
1 TTTTTTC
56086988 TTTTTTC
1 TTTTTTC
56086995 TTTTTT
1 TTTTTT
56087001 TAGATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:56088451 original size:23 final size:23
Alignment explanation
Indices: 56088421--56088541 Score: 136
Period size: 23 Copynumber: 5.2 Consensus size: 23
56088411 TTATCATCAA
* *
56088421 TATTATTTTAATTTATAATATAT
1 TATTATTTTAATTTATCATGTAT
*
56088444 TATTATTTTAAATTTATCAT-TAA
1 TATTATTTT-AATTTATCATGTAT
*
56088467 CATTATTTTAAGTTTATCATGTAT
1 TATTATTTTAA-TTTATCATGTAT
* * *
56088491 TTTTATTTAAAGTTATCATGTAT
1 TATTATTTTAATTTATCATGTAT
*
56088514 TATTATTTTGAACTTATCATGTAT
1 TATTATTTT-AATTTATCATGTAT
56088538 TATT
1 TATT
56088542 TTATGCATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.02
23 45 0.54
24 36 0.43
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (23 bp):
TATTATTTTAATTTATCATGTAT
Found at i:56088503 original size:24 final size:23
Alignment explanation
Indices: 56088421--56088541 Score: 109
Period size: 24 Copynumber: 5.2 Consensus size: 23
56088411 TTATCATCAA
* * * *
56088421 TATTATTTTAATTTATAATATAT
1 TATTATTTAAAGTTATCATGTAT
* *
56088444 TATTATTTTAAATTTATCAT-TAA
1 TATTA-TTTAAAGTTATCATGTAT
* *
56088467 CATTATTTTAAGTTTATCATGTAT
1 TATTATTTAAAG-TTATCATGTAT
*
56088491 TTTTATTTAAAGTTATCATGTAT
1 TATTATTTAAAGTTATCATGTAT
* *
56088514 TATTATTTTGAACTTATCATGTAT
1 TATTA-TTTAAAGTTATCATGTAT
56088538 TATT
1 TATT
56088542 TTATGCATTC
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
22 5 0.06
23 33 0.41
24 43 0.53
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (23 bp):
TATTATTTAAAGTTATCATGTAT
Found at i:56088519 original size:47 final size:46
Alignment explanation
Indices: 56088411--56088541 Score: 156
Period size: 47 Copynumber: 2.8 Consensus size: 46
56088401 CATATATTTT
* * * *
56088411 TTATCATCAATATTATTTTAATTTATAATATATTATTATTTTAAAT
1 TTATCATTAATATTATTTTAATTTATCATGTATTATTATTTTAAAG
* *
56088457 TTATCATTAACATTATTTTAAGTTTATCATGTATTTTTA-TTTAAAG
1 TTATCATTAATATTATTTTAA-TTTATCATGTATTATTATTTTAAAG
* *
56088503 TTATCATGTATTATTATTTTGAACTTATCATGTATTATT
1 TTATCAT-TAATATTATTTT-AATTTATCATGTATTATT
56088542 TTATGCATTC
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
46 32 0.44
47 38 0.53
48 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.56
Consensus pattern (46 bp):
TTATCATTAATATTATTTTAATTTATCATGTATTATTATTTTAAAG
Found at i:56088730 original size:23 final size:22
Alignment explanation
Indices: 56088704--56088779 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
56088694 ATATTAAATT
56088704 TTTCATTTTATATATATTATTGA
1 TTTCATTTTATATATATTATT-A
*
56088727 TTTCATATTAT-TATTATT-TTA
1 TTTCATTTTATATA-TATTATTA
*
56088748 TTT-ATTTCTATATATATAATTTA
1 TTTCATTT-TATATATATTA-TTA
56088771 TTTC-TTTTA
1 TTTCATTTTA
56088780 AAAACTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
20 3 0.07
21 10 0.23
22 8 0.18
23 23 0.52
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.64
Consensus pattern (22 bp):
TTTCATTTTATATATATTATTA
Found at i:56088740 original size:17 final size:17
Alignment explanation
Indices: 56088708--56088745 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
56088698 TAAATTTTTC
*
56088708 ATTTTATATATATTATT
1 ATTTCATATATATTATT
56088725 GATTTCATAT-TATTATT
1 -ATTTCATATATATTATT
56088742 ATTT
1 ATTT
56088746 TATTTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 7 0.37
18 8 0.42
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTCATATATATTATT
Found at i:56088748 original size:25 final size:27
Alignment explanation
Indices: 56088711--56088760 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
56088701 ATTTTTCATT
56088711 TTATATATATTATTGATTTC-ATATTA
1 TTATATATATTATTGATTTCTATATTA
* *
56088737 TTAT-TATTTTATTTATTTCTATAT
1 TTATATATATTATTGATTTCTATAT
56088761 ATATAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATATATATTATTGATTTCTATATTA
Found at i:56089040 original size:27 final size:28
Alignment explanation
Indices: 56088995--56089053 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
56088985 ATTTTTAATC
* **
56088995 TATTTCAAACTTTCTTATATATATTATT
1 TATTTCAAAATTTCTTATATATACAATT
*
56089023 TATTTTAAAATTT-TTATATATACAATT
1 TATTTCAAAATTTCTTATATATACAATT
56089050 TATT
1 TATT
56089054 GATTATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTTCAAAATTTCTTATATATACAATT
Found at i:56089249 original size:17 final size:18
Alignment explanation
Indices: 56089216--56089253 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
56089206 ATTGCTCTTG
56089216 TGTATTGTATTACTTATT
1 TGTATTGTATTACTTATT
56089234 TGTATT-TATTGA-TTATT
1 TGTATTGTATT-ACTTATT
56089251 TGT
1 TGT
56089254 GGTTCATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.21, C:0.03, G:0.13, T:0.63
Consensus pattern (18 bp):
TGTATTGTATTACTTATT
Found at i:56090719 original size:104 final size:103
Alignment explanation
Indices: 56090570--56090759 Score: 326
Period size: 104 Copynumber: 1.8 Consensus size: 103
56090560 TACCTTTTCT
* *
56090570 TTCTTTTTTTCTCCTTTAGCTTTTAAGACCTAAAAAGTCTTAAAGAATTTGGGAGTGAGGCTTTC
1 TTCTTTTTTTCTCCTTTAGCTTTTAAGACCTAAAAAGTCTTAAAGAATGTGGGAGTG-GACTTTC
* *
56090635 TTCGTAGACTTCTGTTTGGCTCGGGTTTTCAAGTCTATA
65 TTCATACACTTCTGTTTGGCTCGGGTTTTCAAGTCTATA
56090674 TTCTTTTTTTCTCCTTTAGCTTTTAAGACCTAAAAAGTCTTAAAGAATGTGGGAGTGGACTTTCT
1 TTCTTTTTTTCTCCTTTAGCTTTTAAGACCTAAAAAGTCTTAAAGAATGTGGGAGTGGACTTTCT
*
56090739 TCATACACTTTTGTTTGGCTC
66 TCATACACTTCTGTTTGGCTC
56090760 TACTTTTTAA
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 25 0.31
104 56 0.69
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.44
Consensus pattern (103 bp):
TTCTTTTTTTCTCCTTTAGCTTTTAAGACCTAAAAAGTCTTAAAGAATGTGGGAGTGGACTTTCT
TCATACACTTCTGTTTGGCTCGGGTTTTCAAGTCTATA
Found at i:56092035 original size:72 final size:72
Alignment explanation
Indices: 56091930--56092245 Score: 427
Period size: 72 Copynumber: 4.4 Consensus size: 72
56091920 CTTACTCAGC
* * * *
56091930 TTGATCTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTCTG
1 TTGATGTTTCAGAAAATCAATTAAATGGCCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
*
56091995 AAGTTGT
66 AAGGTGT
* *
56092002 TTGATGTTTCA-AGAAATCAATTAAATGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTT
1 TTGATGTTTCAGA-AAATCAATTAAATGGCCAAATTCCATTGTCTATAGGGCAGTTATCATCTTT
* *
56092066 GGAGGAGT
65 GAAGGTGT
* * * *
56092074 TTCATGTTTCAGAAAATCAATTAAATGGTCAAGTTCCATTGTCTATAGGGGAGTTATCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAATGGCCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
*
56092139 AAGTTGT
66 AAGGTGT
* * * * *
56092146 TTGCTGTTTCAAAAAATCAGTTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTATCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAATGGCCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
* *
56092211 GAGGTAT
66 AAGGTGT
56092218 TTGATGTTTCAGAAAATCAATTAAATGG
1 TTGATGTTTCAGAAAATCAATTAAATGG
56092246 TACTTTTCCT
Statistics
Matches: 208, Mismatches: 34, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
71 1 0.00
72 206 0.99
73 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (72 bp):
TTGATGTTTCAGAAAATCAATTAAATGGCCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
AAGGTGT
Found at i:56092196 original size:144 final size:144
Alignment explanation
Indices: 56091936--56092246 Score: 534
Period size: 144 Copynumber: 2.2 Consensus size: 144
56091926 CAGCTTGATC
56091936 TTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTCTGAAGTTG
1 TTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTCTGAAGTTG
* * *
56092001 TTTGATGTTTCAAGAAATCAATTAAATGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTT
66 TTTGATGTTTCAAAAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTATCATCTTT
56092066 GGAGG-AGTTTCATG
131 GGAGGTA-TTTCATG
* *
56092080 TTTCAGAAAATCAATTAAATGGTCAAGTTCCATTGTCTATAGGGGAGTTATCATCTTTGAAGTTG
1 TTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTCTGAAGTTG
* *
56092145 TTTGCTGTTTCAAAAAATCAGTTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTATCATCTTT
66 TTTGATGTTTCAAAAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTATCATCTTT
*
56092210 GGAGGTATTTGATG
131 GGAGGTATTTCATG
56092224 TTTCAGAAAATCAATTAAATGGT
1 TTTCAGAAAATCAATTAAATGGT
56092247 ACTTTTCCTC
Statistics
Matches: 158, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
144 157 0.99
145 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (144 bp):
TTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTCTGAAGTTG
TTTGATGTTTCAAAAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTATCATCTTT
GGAGGTATTTCATG
Found at i:56095520 original size:42 final size:41
Alignment explanation
Indices: 56095468--56095552 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 41
56095458 CGTTTTTTAA
**
56095468 TTACTTAACTATTTTTATTATTA-TTGTTATTATTATTA-ATG
1 TTACTTAACTATTAGTATTATTATTTG-TATTATT-TTATATG
56095509 TTACTATAACTATTAGTATTATTATTTGTATTATTTTATATG
1 TTACT-TAACTATTAGTATTATTATTTGTATTATTTTATATG
56095551 TT
1 TT
56095553 TATTTACCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
41 8 0.21
42 28 0.72
43 3 0.08
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (41 bp):
TTACTTAACTATTAGTATTATTATTTGTATTATTTTATATG
Found at i:56102889 original size:2 final size:2
Alignment explanation
Indices: 56102882--56102924 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
56102872 NNNNNNNTAT
56102882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56102924 T
1 T
56102925 TGTTCATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56105003 original size:17 final size:16
Alignment explanation
Indices: 56104964--56105003 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
56104954 TTTTTATTTT
56104964 TATTTTTAATAAAATA
1 TATTTTTAATAAAATA
* *
56104980 TACTTTTATTAAATATA
1 TATTTTTAATAAA-ATA
56104997 TATTTTT
1 TATTTTT
56105004 TGGACTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTTTAATAAAATA
Found at i:56113225 original size:17 final size:17
Alignment explanation
Indices: 56113205--56113247 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
56113195 TTTTCAAAAA
56113205 TATAAAATTTTGAAATT
1 TATAAAATTTTGAAATT
*
56113222 TATAAATATTTTGAATTT
1 TATAAA-ATTTTGAAATT
*
56113240 TAAAAAAT
1 TATAAAAT
56113248 ATTTTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
TATAAAATTTTGAAATT
Found at i:56113232 original size:18 final size:18
Alignment explanation
Indices: 56113205--56113255 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
56113195 TTTTCAAAAA
56113205 TATAAA-ATTTTGAAATT
1 TATAAATATTTTGAAATT
*
56113222 TATAAATATTTTGAATTT
1 TATAAATATTTTGAAATT
*
56113240 TAAAAAATATTTTGAA
1 T-ATAAATATTTTGAA
56113256 TTTTTTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.20
18 11 0.37
19 13 0.43
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TATAAATATTTTGAAATT
Found at i:56113249 original size:19 final size:18
Alignment explanation
Indices: 56113211--56113259 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
56113201 AAAATATAAA
* *
56113211 ATTTTGAAATTTATAAAT
1 ATTTTGAATTTTAAAAAT
56113229 ATTTTGAATTTTAAAAAAT
1 ATTTTGAATTTT-AAAAAT
56113248 ATTTTGAATTTT
1 ATTTTGAATTTT
56113260 TTGATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTTGAATTTTAAAAAT
Found at i:56114129 original size:15 final size:14
Alignment explanation
Indices: 56114102--56114137 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
56114092 TTTAGTCCAT
56114102 TGATAAATAATAAA
1 TGATAAATAATAAA
*
56114116 TTATAAATTAATAAA
1 TGATAAA-TAATAAA
56114131 TGATAAA
1 TGATAAA
56114138 ATTATACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (14 bp):
TGATAAATAATAAA
Found at i:56114246 original size:22 final size:23
Alignment explanation
Indices: 56114203--56114246 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
56114193 TTAATAAATA
* *
56114203 ATAAAATTATATTTTAACTTCTT
1 ATAAAATTATAATTCAACTTCTT
*
56114226 ATAAATTTATAATTCAA-TTCT
1 ATAAAATTATAATTCAACTTCT
56114247 AATCACTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAAAATTATAATTCAACTTCTT
Found at i:56117044 original size:16 final size:16
Alignment explanation
Indices: 56117005--56117043 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
56116995 TTTATTTTTT
*
56117005 ATAAAAAAGTTAAATA
1 ATAAAAAAGTGAAATA
56117021 ATAAAAAAGTGAAA-A
1 ATAAAAAAGTGAAATA
56117036 ATAAAAAA
1 ATAAAAAA
56117044 ATAAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (16 bp):
ATAAAAAAGTGAAATA
Found at i:56117807 original size:7 final size:7
Alignment explanation
Indices: 56117795--56117835 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
56117785 TAGTCCATTC
56117795 ATAAATT
1 ATAAATT
56117802 ATAAATT
1 ATAAATT
*
56117809 ATAAAAT
1 ATAAATT
56117816 ATAAATT
1 ATAAATT
*
56117823 AATAAATG
1 -ATAAATT
56117831 ATAAA
1 ATAAA
56117836 ATTGTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (7 bp):
ATAAATT
Found at i:56117834 original size:22 final size:21
Alignment explanation
Indices: 56117795--56117837 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
56117785 TAGTCCATTC
*
56117795 ATAAATTATAAATTATAAAAT
1 ATAAATTATAAATGATAAAAT
56117816 ATAAATTAATAAATGATAAAAT
1 ATAAATT-ATAAATGATAAAAT
56117838 TGTATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAATTATAAATGATAAAAT
Found at i:56118262 original size:21 final size:20
Alignment explanation
Indices: 56118238--56118276 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
56118228 ATTGCGAGGT
*
56118238 TTTAAAATAAATAATAATTTA
1 TTTAAAAGAAAT-ATAATTTA
*
56118259 TTTAATAGAAATATAATT
1 TTTAAAAGAAATATAATT
56118277 AAAAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
TTTAAAAGAAATATAATTTA
Found at i:56135252 original size:3 final size:3
Alignment explanation
Indices: 56135246--56135285 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
56135236 GGAGATCAAT
*
56135246 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
56135286 ATAGTTAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:56136195 original size:19 final size:18
Alignment explanation
Indices: 56136161--56136197 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
56136151 TATTGAACGT
*
56136161 TAACAAAAATGAATAAAA
1 TAACAAAAATAAATAAAA
56136179 TAACAAAAATAATATAAAA
1 TAACAAAAATAA-ATAAAA
56136198 AGGGCAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (18 bp):
TAACAAAAATAAATAAAA
Found at i:56136626 original size:28 final size:28
Alignment explanation
Indices: 56136575--56136628 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
56136565 TATAAATAAT
**
56136575 AAAAAAATGATTTATTTCCTTAATTTTG
1 AAAAAAATGATTTATTTCAATAATTTTG
56136603 AAAAAAATGGATTTATTT-AATAATTT
1 AAAAAAAT-GATTTATTTCAATAATTT
56136629 GGTTGTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (28 bp):
AAAAAAATGATTTATTTCAATAATTTTG
Found at i:56136979 original size:15 final size:16
Alignment explanation
Indices: 56136959--56136991 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
56136949 CACTTCATGC
*
56136959 TATTTTTTGA-ATTTT
1 TATTTTTTAATATTTT
56136974 TATTTTTTAATATTTT
1 TATTTTTTAATATTTT
56136990 TA
1 TA
56136992 AATTATTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TATTTTTTAATATTTT
Found at i:56144313 original size:11 final size:11
Alignment explanation
Indices: 56144297--56144322 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56144287 GTCTTGAAGG
56144297 TTTGTTTGAAA
1 TTTGTTTGAAA
56144308 TTTGTTTGAAA
1 TTTGTTTGAAA
56144319 TTTG
1 TTTG
56144323 CGTATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (11 bp):
TTTGTTTGAAA
Found at i:56144690 original size:15 final size:15
Alignment explanation
Indices: 56144670--56144701 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
56144660 TTTAAGTTCA
56144670 TATTTCGAGTTAGGC
1 TATTTCGAGTTAGGC
56144685 TATTTCGAGTTAGGC
1 TATTTCGAGTTAGGC
56144700 TA
1 TA
56144702 AATTTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (15 bp):
TATTTCGAGTTAGGC
Found at i:56147456 original size:119 final size:120
Alignment explanation
Indices: 56147307--56147524 Score: 312
Period size: 119 Copynumber: 1.8 Consensus size: 120
56147297 CATTGATAGC
* * * ** *
56147307 AGTGATTAATTTTCTAACCGTGTATACTTTCTGAAAATTTAAATGAGTGACAATAAAATATGTTC
1 AGTGATTAATCTTCTAACCGTGGATACTTTCCGAAAAGATAAATGAGTGACAATAAAATATATTC
56147372 CATTTCCGTGAGCAG-GATTAAAAATTATTTTTTTCGGTATCCATCATCGGTATT
66 CATTTCCGTGAGCAGAGATTAAAAATTATTTTTTTCGGTATCCATCATCGGTATT
* * * *
56147426 AGTGATTAATCTTCTAACTGTGGATGCTTTCCGAAAAGATAAATGATTGACAATAAAATGTATTC
1 AGTGATTAATCTTCTAACCGTGGATACTTTCCGAAAAGATAAATGAGTGACAATAAAATATATTC
* **
56147491 CATTTTCGTGAGTGGAGATTAAAAATTATTTTTT
66 CATTTCCGTGAGCAGAGATTAAAAATTATTTTTT
56147525 AATTATTTAA
Statistics
Matches: 85, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
119 67 0.79
120 18 0.21
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (120 bp):
AGTGATTAATCTTCTAACCGTGGATACTTTCCGAAAAGATAAATGAGTGACAATAAAATATATTC
CATTTCCGTGAGCAGAGATTAAAAATTATTTTTTTCGGTATCCATCATCGGTATT
Found at i:56152969 original size:72 final size:72
Alignment explanation
Indices: 56152852--56153164 Score: 430
Period size: 72 Copynumber: 4.3 Consensus size: 72
56152842 AAAAGTACCA
* *
56152852 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTGCCCTATAGACCAGGGAAT
1 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAAGGGAAT
56152917 TTGGCCG
66 TTGGCCG
* * * *
56152924 TTTAACTAATTTTTTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
1 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAAGGGAAT
* *
56152989 TTGACCA
66 TTGGCCG
** * *
56152996 TTTAATTGATTTTCTGAAACATCAAACTTCTCCAAAGATG-TCAACTGCCCTATAGACAAGGGAA
1 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGAT-AACTCCCCTATAGACAAGGGAA
56153060 TTTGGCCG
65 TTTGGCCG
* * *
56153068 TTTAATTGATTTTTTGAAACATCAAACAACTTCAAAGACGATAACTCCCCTATAGACAATGGAAT
1 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAAGGGAAT
** *
56153133 TTGATCA
66 TTGGCCG
* *
56153140 TTTAATTGATTTACTGAAAGATCAA
1 TTTAATTGATTTTCTGAAACATCAA
56153165 GCTGAGTAAC
Statistics
Matches: 208, Mismatches: 31, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
71 1 0.00
72 206 0.99
73 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (72 bp):
TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAAGGGAAT
TTGGCCG
Found at i:56153111 original size:144 final size:144
Alignment explanation
Indices: 56152848--56153164 Score: 528
Period size: 144 Copynumber: 2.2 Consensus size: 144
56152838 GAGGAAAAGT
* *
56152848 ACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTGCCCTATAGACCAGG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGATAACTGCCCTATAGACAAGG
*
56152913 GAATTTGGCCGTTTAACTAATTTTTTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATA
66 GAATTTGGCCGTTTAACTAATTTTTTGAAACATCAAACAACTTCAAAGACGATAACTCCCCTATA
56152978 GACAATGGAATTTG
131 GACAATGGAATTTG
**
56152992 ACCATTTAATTGATTTTCTGAAACATCAAACTTCTCCAAAGATG-TCAACTGCCCTATAGACAAG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGAT-AACTGCCCTATAGACAAG
* *
56153056 GGAATTTGGCCGTTTAATTGATTTTTTGAAACATCAAACAACTTCAAAGACGATAACTCCCCTAT
65 GGAATTTGGCCGTTTAACTAATTTTTTGAAACATCAAACAACTTCAAAGACGATAACTCCCCTAT
56153121 AGACAATGGAATTTG
130 AGACAATGGAATTTG
* * *
56153136 ATCATTTAATTGATTTACTGAAAGATCAA
1 ACCATTTAATTGATTTTCTGAAACATCAA
56153165 GCTGAGTAAC
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
143 1 0.01
144 161 0.99
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (144 bp):
ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGATAACTGCCCTATAGACAAGG
GAATTTGGCCGTTTAACTAATTTTTTGAAACATCAAACAACTTCAAAGACGATAACTCCCCTATA
GACAATGGAATTTG
Found at i:56160437 original size:21 final size:21
Alignment explanation
Indices: 56160408--56160489 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
56160398 TAATATGCAT
56160408 AAACAATAATAATAATGATGA
1 AAACAATAATAATAATGATGA
* **
56160429 AAACGATAAT-ATAAAT-AACA
1 AAACAATAATAAT-AATGATGA
* *
56160449 ATAACGATAATAACAATGATGA
1 A-AACAATAATAATAATGATGA
** *
56160471 TGATAATAATAATAATGAT
1 AAACAATAATAATAATGAT
56160490 AATAATAATC
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
20 5 0.11
21 38 0.83
22 3 0.07
ACGTcount: A:0.59, C:0.06, G:0.10, T:0.26
Consensus pattern (21 bp):
AAACAATAATAATAATGATGA
Found at i:56160476 original size:15 final size:15
Alignment explanation
Indices: 56160413--56160498 Score: 66
Period size: 15 Copynumber: 5.7 Consensus size: 15
56160403 TGCATAAACA
*
56160413 ATAATAATAATGATG
1 ATAACAATAATGATG
* * *
56160428 AAAACGATAAT-ATAA
1 ATAACAATAATGAT-G
* *
56160443 ATAACAATAACGATA
1 ATAACAATAATGATG
*
56160458 ATAACAATGATGATG
1 ATAACAATAATGATG
* *
56160473 ATAATAATAATAATG
1 ATAACAATAATGATG
*
56160488 ATAATAATAAT
1 ATAACAATAAT
56160499 CTAAGTTTTG
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
14 2 0.04
15 52 0.93
16 2 0.04
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (15 bp):
ATAACAATAATGATG
Found at i:56160477 original size:18 final size:18
Alignment explanation
Indices: 56160454--56160497 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
56160444 TAACAATAAC
*
56160454 GATAATAACAATGATGAT
1 GATAATAACAATAATGAT
*
56160472 GATAATAATAATAATGAT
1 GATAATAACAATAATGAT
*
56160490 AATAATAA
1 GATAATAA
56160498 TCTAAGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (18 bp):
GATAATAACAATAATGAT
Found at i:56161062 original size:73 final size:73
Alignment explanation
Indices: 56160971--56161117 Score: 276
Period size: 73 Copynumber: 2.0 Consensus size: 73
56160961 CGCACGCGAA
*
56160971 AATAACCCATGCTCTAGAAAACACGCGGATCCTCTAGGCAAATGGGTCGGGTCACAGGTCAGAGG
1 AATAACCCATGCTCTAGAAAACACGCGGATCCTCTAGGCAAAAGGGTCGGGTCACAGGTCAGAGG
56161036 CCAAAACG
66 CCAAAACG
*
56161044 AATAACCCATGCTCTAGAAGACACGCGGATCCTCTAGGCAAAAGGGTCGGGTCACAGGTCAGAGG
1 AATAACCCATGCTCTAGAAAACACGCGGATCCTCTAGGCAAAAGGGTCGGGTCACAGGTCAGAGG
56161109 CCAAAACG
66 CCAAAACG
56161117 A
1 A
56161118 CGTCGTTTTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.33, C:0.26, G:0.27, T:0.14
Consensus pattern (73 bp):
AATAACCCATGCTCTAGAAAACACGCGGATCCTCTAGGCAAAAGGGTCGGGTCACAGGTCAGAGG
CCAAAACG
Found at i:56164799 original size:118 final size:119
Alignment explanation
Indices: 56164607--56164821 Score: 333
Period size: 118 Copynumber: 1.8 Consensus size: 119
56164597 TTGATAGCAC
* * * *
56164607 TGATTAATTTTCTAACCCTGGATACTTTCTGAAAAGTTAAATGAGTGACAATAAAATGTGTTCCA
1 TGATTAATCTTCTAACCCTGGATACTTTCCGAAAAGATAAATGAGTGACAATAAAATGTATTCCA
56164672 TTTTCGTGAGCGG-GATTAAAAATTATTTTTTTGGTATCCATCATCAGTAATAG
66 TTTTCGTGAGCGGAGATTAAAAATTATTTTTTTGGTATCCATCATCAGTAATAG
** * *
56164725 TGATTAATCTTCTAACTGTGGATGCTTTCCGAAAAGATAAATGATTGACAATAAAATGTATTCCA
1 TGATTAATCTTCTAACCCTGGATACTTTCCGAAAAGATAAATGAGTGACAATAAAATGTATTCCA
* *
56164790 TTTTTGTGAGTGGAGATTAAAAATTATTTTTT
66 TTTTCGTGAGCGGAGATTAAAAATTATTTTTT
56164822 AATTATTTGA
Statistics
Matches: 86, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
118 68 0.79
119 18 0.21
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (119 bp):
TGATTAATCTTCTAACCCTGGATACTTTCCGAAAAGATAAATGAGTGACAATAAAATGTATTCCA
TTTTCGTGAGCGGAGATTAAAAATTATTTTTTTGGTATCCATCATCAGTAATAG
Found at i:56165261 original size:22 final size:22
Alignment explanation
Indices: 56165220--56165262 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56165210 GACCATTAAT
*
56165220 TTTTAAAAAAAAATCAAATTGC
1 TTTTAAAAAAAAATAAAATTGC
56165242 TTTTAAAAAAAAA-AAGAATTG
1 TTTTAAAAAAAAATAA-AATTG
56165263 TTGACTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (22 bp):
TTTTAAAAAAAAATAAAATTGC
Found at i:56172427 original size:72 final size:72
Alignment explanation
Indices: 56172341--56172657 Score: 411
Period size: 72 Copynumber: 4.4 Consensus size: 72
56172331 GAGGAAAAGT
* * * * *
56172341 ACCATTTAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGATAACTGCCCAAAAGACAAGG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGATAACTCCCCTATAGACAAGG
56172406 GAATTTG
66 GAATTTG
* * * * *
56172413 GCCGTTTAATTGATTTTTTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGATAACTCCCCTATAGACAAGG
56172478 GAATTTG
66 GAATTTG
** * *
56172485 ACCATTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGATAACTCCCCTATAGACAAGG
56172550 GAATTTG
66 GAATTTG
* * * * *
56172557 GCCGTTTAATTGATTATT-TGAAACATCAAACAACTTCAGAGATGATAACTCCCCTATAGACAAT
1 ACCATTTAATTGATT-TTCTGAAACATCAAACAACTCCAAAGATGATAACTCCCCTATAGACAAG
56172621 GGAATTTG
65 GGAATTTG
* * * *
56172629 ACCACTTAATTGACTATCTGAAAGATCAA
1 ACCATTTAATTGATTTTCTGAAACATCAA
56172658 GGTGAGTAAC
Statistics
Matches: 209, Mismatches: 34, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
71 1 0.00
72 206 0.99
73 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (72 bp):
ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGATAACTCCCCTATAGACAAGG
GAATTTG
Found at i:56172601 original size:144 final size:144
Alignment explanation
Indices: 56172341--56172657 Score: 537
Period size: 144 Copynumber: 2.2 Consensus size: 144
56172331 GAGGAAAAGT
*
56172341 ACCATTTAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGATAACTGCCCAAAAGACAAGG
1 ACCATTTAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGACAACTGCCCAAAAGACAAGG
*
56172406 GAATTTGGCCGTTTAATTGATTTTTTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATA
66 GAATTTGGCCGTTTAATTGATTATTTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATA
56172471 GACAATGGAATTTG
131 GACAATGGAATTTG
* *
56172485 ACCATTTAATTGATTTTCTGAAACATCAAACT-CCTCCAAAGATGACAACTGCCCTATAGACAAG
1 ACCATTTAATTGATTTTCTGAAACATCAAA-TACCTCCAAAGATGACAACTGCCCAAAAGACAAG
*
56172549 GGAATTTGGCCGTTTAATTGATTATTTGAAACATCAAACAACTTCAGAGATGATAACTCCCCTAT
65 GGAATTTGGCCGTTTAATTGATTATTTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTAT
56172614 AGACAATGGAATTTG
130 AGACAATGGAATTTG
* * * *
56172629 ACCACTTAATTGACTATCTGAAAGATCAA
1 ACCATTTAATTGATTTTCTGAAACATCAA
56172658 GGTGAGTAAC
Statistics
Matches: 163, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
144 162 0.99
145 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (144 bp):
ACCATTTAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGACAACTGCCCAAAAGACAAGG
GAATTTGGCCGTTTAATTGATTATTTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATA
GACAATGGAATTTG
Found at i:56174650 original size:27 final size:29
Alignment explanation
Indices: 56174597--56174650 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
56174587 TATTTAATTA
* *
56174597 ATTTTATAAAATTTAAAATTTTATAAATC
1 ATTTTATAAAATTAAAAATTATATAAATC
56174626 ATTTT-TAAAATTAAAAATTAT-TAAA
1 ATTTTATAAAATTAAAAATTATATAAA
56174651 AAAATATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 14 0.61
29 5 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTTTATAAAATTAAAAATTATATAAATC
Found at i:56178742 original size:119 final size:119
Alignment explanation
Indices: 56178526--56178743 Score: 330
Period size: 119 Copynumber: 1.8 Consensus size: 119
56178516 CATTGATAGC
* * * *
56178526 AGTGATTAATTTTCTAACCGTGGATACGTTCTGAAACGTTAAATGAGTGACAATAAAATGTGTTC
1 AGTGATTAATTTTCTAAACGTGGATACGTTCTGAAAAGATAAATGAGTGACAATAAAATGTATTC
*
56178591 CATTTTTGTGAGCGGGATTAAAAATTATTTTTTTCGATACCCATCATCGGTAAT
66 CATTTTCGTGAGCGGGATTAAAAATTATTTTTTTCGATACCCATCATCGGTAAT
* * *
56178645 AGTGATTAATTTTCTAAATGTGGATGC-TTGCTGAAAAGATAAATGATTGACAATAAAATGTATT
1 AGTGATTAATTTTCTAAACGTGGATACGTT-CTGAAAAGATAAATGAGTGACAATAAAATGTATT
*
56178709 CCATTTTCGTGAGTGGAGATTAAAAATTATTTTTT
65 CCATTTTCGTGAGCGG-GATTAAAAATTATTTTTT
56178744 AATTATTTGA
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
118 2 0.02
119 68 0.77
120 18 0.20
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (119 bp):
AGTGATTAATTTTCTAAACGTGGATACGTTCTGAAAAGATAAATGAGTGACAATAAAATGTATTC
CATTTTCGTGAGCGGGATTAAAAATTATTTTTTTCGATACCCATCATCGGTAAT
Found at i:56192334 original size:72 final size:72
Alignment explanation
Indices: 56192224--56192466 Score: 328
Period size: 72 Copynumber: 3.4 Consensus size: 72
56192214 GGAAAAGTAT
*
56192224 CATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGGCAACTCCCCTATAGACAAAGGA
1 CATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGACAACTCCCCTATAGACAAAGGA
56192289 ATTTGAC
66 ATTTGAC
* * * ** *
56192296 CATTTAATTGATTTTCTGAAACATCAAA-ATCCTCCAAAGATGACAATTGTCCTATAGACAAGGG
1 CATTTAATTGATTTTCTGAAACATCAAACA-ACTTCAAAGATGACAACTCCCCTATAGACAAAGG
*
56192360 AATTTGGC
65 AATTTGAC
* * * *
56192368 CGTTTAATTGATTGTT-TGAAACATCAAACAACTTCAGAGATGATAACTCCCCTATAGACAATGG
1 CATTTAATTGATT-TTCTGAAACATCAAACAACTTCAAAGATGACAACTCCCCTATAGACAAAGG
56192432 AATTTGAC
65 AATTTGAC
* *
56192440 CATTTAATTGACTTTCTGAAAGATCAA
1 CATTTAATTGATTTTCTGAAACATCAA
56192467 GGTGAGTAAC
Statistics
Matches: 146, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
71 3 0.02
72 140 0.96
73 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (72 bp):
CATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGACAACTCCCCTATAGACAAAGGA
ATTTGAC
Found at i:56193788 original size:104 final size:103
Alignment explanation
Indices: 56193637--56193826 Score: 326
Period size: 104 Copynumber: 1.8 Consensus size: 103
56193627 TTAAAAAGTA
* * * *
56193637 GAGCCAAACAAAAGTGTATGAAGAAAGTCCACTCCCACATTCTTTAAGACTTTTTAGGTCTTAAA
1 GAGCCAAACAAAAGTCTACGAAGAAAGCCCACTCCCAAATTCTTTAAGACTTTTTAGGTCTTAAA
56193702 AGCTAAAGGAGAAAAAAAGAATATAGACTTGAAAACCC
66 AGCTAAAGGAGAAAAAAAGAATATAGACTTGAAAACCC
*
56193740 GAGCCAAACAGAAGTCTACGAAGAAAGCCTCACTCCCAAATTCTTTAAGACTTTTTAGGTCTTAA
1 GAGCCAAACAAAAGTCTACGAAGAAAGCC-CACTCCCAAATTCTTTAAGACTTTTTAGGTCTTAA
56193805 AAGCTAAAGGAGAAAAAAAGAA
65 AAGCTAAAGGAGAAAAAAAGAA
56193827 AGAAAAGGTA
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 25 0.31
104 56 0.69
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.22
Consensus pattern (103 bp):
GAGCCAAACAAAAGTCTACGAAGAAAGCCCACTCCCAAATTCTTTAAGACTTTTTAGGTCTTAAA
AGCTAAAGGAGAAAAAAAGAATATAGACTTGAAAACCC
Found at i:56195279 original size:17 final size:18
Alignment explanation
Indices: 56195257--56195294 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
56195247 CAATAATCTC
*
56195257 ACAAATAATCAATA-AAT
1 ACAAATAAGCAATACAAT
56195274 ACAAATAAGCAATACAAT
1 ACAAATAAGCAATACAAT
56195292 ACA
1 ACA
56195295 CAAGAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.63, C:0.16, G:0.03, T:0.18
Consensus pattern (18 bp):
ACAAATAAGCAATACAAT
Found at i:56195502 original size:27 final size:28
Alignment explanation
Indices: 56195470--56195528 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
56195460 AATTATAATC
** *
56195470 AATAAATTGTATATATAA-AAATTTTAA
1 AATAAATAATATATATAACAAAGTTTAA
*
56195497 AATAAATAATATATATAACAAAGTTTGA
1 AATAAATAATATATATAACAAAGTTTAA
56195525 AATA
1 AATA
56195529 GATTAAAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (28 bp):
AATAAATAATATATATAACAAAGTTTAA
Found at i:56195818 original size:25 final size:23
Alignment explanation
Indices: 56195766--56195835 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
56195756 TTTTTAAAAG
*
56195766 AAATAAATTATAT-ATATAGAAAT
1 AAATAAAATATATAATAT-GAAAT
56195789 AAATAAAATAATAATAATATGAAAT
1 AAATAAAAT-AT-ATAATATGAAAT
* * *
56195814 CAATAATATATATAAAATGAAA
1 AAATAAAATATATAATATGAAA
56195836 AATTTAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 18 0.45
24 4 0.10
25 14 0.35
26 4 0.10
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (23 bp):
AAATAAAATATATAATATGAAAT
Found at i:56195820 original size:17 final size:17
Alignment explanation
Indices: 56195791--56195831 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
56195781 ATAGAAATAA
56195791 ATAAAATAATAATA-AT
1 ATAAAATAATAATATAT
*
56195807 ATGAAATCAATAATATAT
1 ATAAAAT-AATAATATAT
56195825 ATAAAAT
1 ATAAAAT
56195832 GAAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 6 0.29
17 7 0.33
18 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
ATAAAATAATAATATAT
Found at i:56195878 original size:17 final size:19
Alignment explanation
Indices: 56195842--56195879 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
56195832 GAAAAATTTA
*
56195842 ATATAAACTATGTATGTAT
1 ATATAAAATATGTATGTAT
56195861 ATATAAAATA-GTAT-TAT
1 ATATAAAATATGTATGTAT
56195878 AT
1 AT
56195880 GAGAGTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 4 0.22
19 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (19 bp):
ATATAAAATATGTATGTAT
Found at i:56196049 original size:24 final size:23
Alignment explanation
Indices: 56196000--56196131 Score: 124
Period size: 23 Copynumber: 5.7 Consensus size: 23
56195990 GAATGCATAA
* *
56196000 AATAATACATGATAAATTTAAAT
1 AATAATAGATGATAAATTAAAAT
* *
56196023 AATCATAGATGATAAGTTCAAAAT
1 AATAATAGATGATAAATT-AAAAT
* *
56196047 AATAATACATGATAAAATTAAAAA
1 AATAATAGATGAT-AAATTAAAAT
**
56196071 AATGTTA-ATGATAAATTTAAAAT
1 AATAATAGATGATAAA-TTAAAAT
* *
56196094 AATAATATATTATAAATTAAAAT
1 AATAATAGATGATAAATTAAAAT
*
56196117 AAT-ATTGATGATAAA
1 AATAATAGATGATAAA
56196132 AAATATATTA
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
22 12 0.14
23 41 0.47
24 31 0.35
25 4 0.05
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (23 bp):
AATAATAGATGATAAATTAAAAT
Found at i:56196055 original size:47 final size:46
Alignment explanation
Indices: 56196000--56196131 Score: 158
Period size: 47 Copynumber: 2.8 Consensus size: 46
56195990 GAATGCATAA
* *
56196000 AATAATACATGATAAATTTAAATAATCATAGATGATAAGTTCAAAAT
1 AATAATACATGATAAATTAAAATAAT-ATAGATGATAAATTCAAAAT
* * *
56196047 AATAATACATGATAAAATTAAAAAAATGTTA-ATGATAAATTTAAAAT
1 AATAATACATGAT-AAATTAAAATAAT-ATAGATGATAAATTCAAAAT
* * *
56196094 AATAATATATTATAAATTAAAATAATATTGATGATAAA
1 AATAATACATGATAAATTAAAATAATATAGATGATAAA
56196132 AAATATATTA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
45 1 0.01
46 20 0.28
47 38 0.53
48 13 0.18
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (46 bp):
AATAATACATGATAAATTAAAATAATATAGATGATAAATTCAAAAT
Found at i:56200280 original size:72 final size:72
Alignment explanation
Indices: 56200189--56200429 Score: 351
Period size: 72 Copynumber: 3.3 Consensus size: 72
56200179 AAAAGTACCA
56200189 TTTAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGATAACTGCCCTATAGACAAGGGAAT
1 TTTAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGATAACTGCCCTATAGACAAGGGAAT
56200254 TTGGCCG
66 TTGGCCG
* * * * * * *
56200261 CTTAACTGATTTT-TCGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAA
1 TTTAATTGATTTTCT-GAAACATCAAATACCTCCAAAGATGATAACTGCCCTATAGACAAGGGAA
* *
56200325 TTTGACCA
65 TTTGGCCG
*
56200333 TTTAATTGATTTTCTGAAACATCAAACT-CCTCCAAAGATGACAACTGCCCTATAGACAAGGGAA
1 TTTAATTGATTTTCTGAAACATCAAA-TACCTCCAAAGATGATAACTGCCCTATAGACAAGGGAA
56200397 TTTGGCCG
65 TTTGGCCG
*
56200405 TTTAATTGATTTACTGAAACATCAA
1 TTTAATTGATTTTCTGAAACATCAA
56200430 GCTGAGTAAC
Statistics
Matches: 146, Mismatches: 20, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
71 1 0.01
72 144 0.99
73 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (72 bp):
TTTAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGATAACTGCCCTATAGACAAGGGAAT
TTGGCCG
Found at i:56211366 original size:2 final size:2
Alignment explanation
Indices: 56211359--56211384 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56211349 GTATACTTAC
56211359 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
56211385 CTTCTTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56213482 original size:14 final size:14
Alignment explanation
Indices: 56213463--56213498 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
56213453 AACGTCTCTT
56213463 TTTGCATTCATGCA
1 TTTGCATTCATGCA
56213477 TTTGCATTCATGCA
1 TTTGCATTCATGCA
*
56213491 TCTGCATT
1 TTTGCATT
56213499 ACATTGCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.44
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:56214868 original size:12 final size:11
Alignment explanation
Indices: 56214851--56214907 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
56214841 AGTGGAGGCA
56214851 AAAAAAAAAAGC
1 AAAAAAAAAA-C
*
56214863 -AAAAAAAAAG
1 AAAAAAAAAAC
* *
56214873 AACAAAAAAAT
1 AAAAAAAAAAC
56214884 AAAATAAAAAAC
1 AAAA-AAAAAAC
56214896 AAGAAAAAAAAC
1 AA-AAAAAAAAC
56214908 CTCTACCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
11 20 0.54
12 15 0.41
13 2 0.05
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.04
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:56214878 original size:26 final size:26
Alignment explanation
Indices: 56214849--56214906 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
56214839 TCAGTGGAGG
56214849 CAAAAAAA-AAAAGCAAAAAAAAAGAA
1 CAAAAAAATAAAA-CAAAAAAAAAGAA
* *
56214875 CAAAAAAATAAAATAAAAAACAAGAA
1 CAAAAAAATAAAACAAAAAAAAAGAA
56214901 -AAAAAA
1 CAAAAAA
56214907 CCTCTACCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 6 0.21
26 19 0.66
27 4 0.14
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.03
Consensus pattern (26 bp):
CAAAAAAATAAAACAAAAAAAAAGAA
Found at i:56214887 original size:20 final size:21
Alignment explanation
Indices: 56214863--56214903 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56214853 AAAAAAAAGC
*
56214863 AAAAAAAAAGAACAA-AAAAAT
1 AAAATAAAA-AACAAGAAAAAT
56214884 AAAATAAAAAACAAGAAAAA
1 AAAATAAAAAACAAGAAAAA
56214904 AAACCTCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.85, C:0.05, G:0.05, T:0.05
Consensus pattern (21 bp):
AAAATAAAAAACAAGAAAAAT
Found at i:56214892 original size:13 final size:12
Alignment explanation
Indices: 56214849--56214894 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
56214839 TCAGTGGAGG
56214849 CAAAAAAAAAAA
1 CAAAAAAAAAAA
56214861 GCAAAAAAAAAGAA
1 -CAAAAAAAAA-AA
56214875 CAAAAAAATAAAA
1 CAAAAAAA-AAAA
*
56214888 TAAAAAA
1 CAAAAAA
56214895 CAAGAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.85, C:0.07, G:0.04, T:0.04
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:56214905 original size:13 final size:12
Alignment explanation
Indices: 56214850--56214906 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
56214840 CAGTGGAGGC
56214850 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
56214862 -CAAAAAAAAAG
1 AAAAAAAAAAAG
56214873 AACAAAAAAATAA-
1 AA-AAAAAAA-AAG
*
56214886 AATAAAAAACAAG
1 AA-AAAAAAAAAG
56214899 AAAAAAAA
1 AAAAAAAA
56214907 CCTCTACCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 10 0.27
12 8 0.22
13 17 0.46
14 2 0.05
ACGTcount: A:0.86, C:0.05, G:0.05, T:0.04
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:56215361 original size:19 final size:19
Alignment explanation
Indices: 56215338--56215385 Score: 80
Period size: 18 Copynumber: 2.6 Consensus size: 19
56215328 TTCATTTGAA
56215338 AAAAAAGAAAAGAA-AAAG
1 AAAAAAGAAAAGAAGAAAG
*
56215356 AAAAAAGAAAAGAAGAACG
1 AAAAAAGAAAAGAAGAAAG
56215375 AAAAAAGAAAA
1 AAAAAAGAAAA
56215386 AGGAGAGGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAGAAGAAAG
Found at i:56215372 original size:26 final size:26
Alignment explanation
Indices: 56215337--56215386 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
56215327 CTTCATTTGA
56215337 AAAAAAAGAAA-AGAAAAAGAAAAAAG
1 AAAAAAAGAAAGA-AAAAAGAAAAAAG
* *
56215363 AAAAGAAGAACGAAAAAAGAAAAA
1 AAAAAAAGAAAGAAAAAAGAAAAA
56215387 GGAGAGGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (26 bp):
AAAAAAAGAAAGAAAAAAGAAAAAAG
Found at i:56215913 original size:108 final size:108
Alignment explanation
Indices: 56215724--56215919 Score: 304
Period size: 108 Copynumber: 1.8 Consensus size: 108
56215714 TTTGTATTCT
56215724 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAACAAATTTCCATCTT
1 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAACAAATTTCCATCTT
56215789 ATCCATTGTGATAATCTTTTTCATCTTATACATATCGTATCTC
66 ATCCATTGTGATAATCTTTTTCATCTTATACATATCGTATCTC
* * * ** *
56215832 AGCAAAATTTTCTGTCTTGATTGATTTGTTTGTTTAGAGCTTTGCTCTCAACAAAATTT-CATTT
1 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAAC-AAATTTCCATCT
* *
56215896 TGTCCATTTTGATAATCTTTTTCA
65 TATCCATTGTGATAATCTTTTTCA
56215920 AGCATTTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 73 0.92
109 6 0.08
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (108 bp):
AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAACAAATTTCCATCTT
ATCCATTGTGATAATCTTTTTCATCTTATACATATCGTATCTC
Found at i:56216592 original size:86 final size:86
Alignment explanation
Indices: 56216357--56216795 Score: 610
Period size: 86 Copynumber: 5.1 Consensus size: 86
56216347 ATCAGTAAAA
* ** * * *
56216357 ATCGAAGACAAACATTGTTTCTCTTGGTTGTAGCAGAGCTGGTTGAAGACAACAGATCTTTCCTT
1 ATCGAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTT
*
56216422 CCTGCATTGACGGCGAAGCAG
66 CCTGCATTGACAGCGAAGCAG
* *
56216443 ATCGAAGACACAAACCTTGCCTCTCTTGGTTGTAGCAGAGCTGGTTGAAGACAACAGATCTTGCC
1 ATCGAAG--ACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGACAACAGATCTTGCC
*
56216508 CTCCTGCATTGACAGCGAAGCAG
64 TTCCTGCATTGACAGCGAAGCAG
* * *
56216531 ATCGAAGACAAACCTTGCCTCTCTCGTTTGTTGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTT
1 ATCGAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTT
56216596 CCTGCATTGACAGCGAAGCAG
66 CCTGCATTGACAGCGAAGCAG
* *
56216617 ATCGAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTT
1 ATCGAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTT
56216682 CCTGCATTGACAGCGAAGCAG
66 CCTGCATTGACAGCGAAGCAG
* * * * * **
56216703 ATCGAAGACAAACCTTGCATCTCTCGTTTGTAGCAGAGTTGATTAAAAATTACAGATCTTGCCTT
1 ATCGAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTT
* * *
56216768 CC-GATATTTGGCAGCGAAGTAG
66 CCTG-CA-TTGACAGCGAAGCAG
56216790 ATCGAA
1 ATCGAA
56216796 AATGGCAGAT
Statistics
Matches: 326, Mismatches: 23, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
85 1 0.00
86 226 0.69
87 19 0.06
88 80 0.25
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (86 bp):
ATCGAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTT
CCTGCATTGACAGCGAAGCAG
Found at i:56216594 original size:44 final size:44
Alignment explanation
Indices: 56216544--56216680 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 44
56216534 GAAGACAAAC
56216544 CTTGCCTCTCTCGTTTGTTGCAGAGCTGGTTGAAGATAGCAGAT
1 CTTGCCTCTCTCGTTTGTTGCAGAGCTGGTTGAAGATAGCAGAT
*** * * * * *
56216588 CTTGCCT-TC-C-TGCATTGACAGCGAAGCAGATCGAAG--A-CAAAC
1 CTTGCCTCTCTCGTTTGTTG-CA--G-AGCTGGTTGAAGATAGCAGAT
*
56216630 CTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGAT
1 CTTGCCTCTCTCGTTTGTTGCAGAGCTGGTTGAAGATAGCAGAT
56216674 CTTGCCT
1 CTTGCCT
56216681 TCCTGCATTG
Statistics
Matches: 66, Mismatches: 17, Indels: 20
0.64 0.17 0.19
Matches are distributed among these distances:
41 13 0.20
42 14 0.21
43 6 0.09
44 21 0.32
45 12 0.18
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (44 bp):
CTTGCCTCTCTCGTTTGTTGCAGAGCTGGTTGAAGATAGCAGAT
Found at i:56216873 original size:45 final size:46
Alignment explanation
Indices: 56216822--56217154 Score: 170
Period size: 46 Copynumber: 7.4 Consensus size: 46
56216812 TCCCTGACTA
* **
56216822 CAGTGGAGTACATTGAAGCCGATA-ACTCTATCTCCCTGTATTTGG
1 CAGTGGAGTAGATTGAAGATGATAGACTCTATCTCCCTGTATTTGG
* * * *
56216867 CAGTGGAATAGATTGAAGATTACAGA-TCT-TGCCTTCCTGTATTTGG
1 CAGTGGAGTAGATTGAAGATGATAGACTCTAT--CTCCCTGTATTTGG
* * * * * * * * *
56216913 CAGCGAAGTAGATCGAAGATGGTAGATTTTACCTCCCTG-A-CT-A
1 CAGTGGAGTAGATTGAAGATGATAGACTCTATCTCCCTGTATTTGG
* *
56216956 CAGTGGAGTACATTGAAGCTGATA-ACTCTATCTCCCTGTATTTGG
1 CAGTGGAGTAGATTGAAGATGATAGACTCTATCTCCCTGTATTTGG
* * * * *
56217001 TAGTGGAATAGATTGAAGATTACAGA-TCT-TGCCTTCCTGTATTTGG
1 CAGTGGAGTAGATTGAAGATGATAGACTCTAT--CTCCCTGTATTTGG
* * * * ** * * * * *
56217047 CAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTG-A-CT-A
1 CAGTGGAGTAGATTGAAGATGATAGACTCTATCTCCCTGTATTTGG
* ** * *
56217090 CAGTGGAGTACATTGAAGCCGATA-ACTTTATCTCCCTGTATTTAG
1 CAGTGGAGTAGATTGAAGATGATAGACTCTATCTCCCTGTATTTGG
* *
56217135 CAGTGGAATAGGTTGAAGAT
1 CAGTGGAGTAGATTGAAGAT
56217155 CAAATATGGC
Statistics
Matches: 204, Mismatches: 68, Indels: 32
0.67 0.22 0.11
Matches are distributed among these distances:
42 23 0.11
43 35 0.17
44 6 0.03
45 59 0.29
46 77 0.38
47 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (46 bp):
CAGTGGAGTAGATTGAAGATGATAGACTCTATCTCCCTGTATTTGG
Found at i:56216991 original size:134 final size:134
Alignment explanation
Indices: 56216751--56217154 Score: 720
Period size: 134 Copynumber: 3.0 Consensus size: 134
56216741 TTGATTAAAA
*
56216751 ATTACAGATCTTGCCTTCC-GATATTTGGCAGCGAAGTAGATCGAAAATGGCAGATTTTACCTCC
1 ATTACAGATCTTGCCTTCCTG-TATTTGGCAGCGAAGTAGATCGAAGATGGCAGATTTTACCTCC
56216815 CTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGAT
65 CTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGAT
56216880 TGAAG
130 TGAAG
*
56216885 ATTACAGATCTTGCCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGATGGTAGATTTTACCTCCC
1 ATTACAGATCTTGCCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGATGGCAGATTTTACCTCCC
* *
56216950 TGACTACAGTGGAGTACATTGAAGCTGATAACTCTATCTCCCTGTATTTGGTAGTGGAATAGATT
66 TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
56217015 GAAG
131 GAAG
*
56217019 ATTACAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCC
1 ATTACAGATCTTGCCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGATGGCAGATTTTACCTCCC
* * *
56217084 TGACTACAGTGGAGTACATTGAAGCCGATAACTTTATCTCCCTGTATTTAGCAGTGGAATAGGTT
66 TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
56217149 GAAG
131 GAAG
56217153 AT
1 AT
56217155 CAAATATGGC
Statistics
Matches: 258, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
134 257 1.00
135 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (134 bp):
ATTACAGATCTTGCCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGATGGCAGATTTTACCTCCC
TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
GAAG
Found at i:56220447 original size:70 final size:70
Alignment explanation
Indices: 56220361--56220501 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
56220351 ACTGACTTTC
56220361 TTACTTAAACCATTTAATCATTTTAAGTTATCGAGTAAATATTATGATATTAGATTAAAACAATA
1 TTACTTAAACCATTTAATCATTTTAAGTTATCGAGTAAATATTATGATATTAGATTAAAACAATA
56220426 ACAAG
66 ACAAG
56220431 TTACTTAAACCATTTAATCATTTTAAGTTATCGAGTAAATATTATGATATTAGATTAAAACAATA
1 TTACTTAAACCATTTAATCATTTTAAGTTATCGAGTAAATATTATGATATTAGATTAAAACAATA
56220496 ACAAG
66 ACAAG
56220501 T
1 T
56220502 CAACTTACAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.38
Consensus pattern (70 bp):
TTACTTAAACCATTTAATCATTTTAAGTTATCGAGTAAATATTATGATATTAGATTAAAACAATA
ACAAG
Found at i:56225820 original size:22 final size:22
Alignment explanation
Indices: 56225779--56225820 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
56225769 GTGAGCGTTT
* * *
56225779 AAAAATGCCGCTATAGGCCTAA
1 AAAAATACCGCTAAAAGCCTAA
56225801 AAAAATACCGCTAAAAGCCT
1 AAAAATACCGCTAAAAGCCT
56225821 GTTTTGTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.17
Consensus pattern (22 bp):
AAAAATACCGCTAAAAGCCTAA
Found at i:56227990 original size:18 final size:18
Alignment explanation
Indices: 56227952--56227987 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
56227942 TTATTATTTT
*
56227952 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
56227970 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
56227988 TAATTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:56233115 original size:34 final size:34
Alignment explanation
Indices: 56233074--56233160 Score: 129
Period size: 34 Copynumber: 2.6 Consensus size: 34
56233064 TTACTTTTAA
* * **
56233074 AAAATCAAATTGAAGTCAAGGAGAATTCATTATT
1 AAAATCAAATTAAAGTCAAGGACAACACATTATT
56233108 AAAATCAAATTAAAGTCAAGGACAACACATTATT
1 AAAATCAAATTAAAGTCAAGGACAACACATTATT
*
56233142 AAAATCAAACTAAAGTCAA
1 AAAATCAAATTAAAGTCAA
56233161 CGTGTGTGGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (34 bp):
AAAATCAAATTAAAGTCAAGGACAACACATTATT
Found at i:56233500 original size:30 final size:30
Alignment explanation
Indices: 56233464--56233523 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
56233454 ACTTAAGAAG
*
56233464 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAAAAATAACAAAATTAA
*
56233494 CAAATGTCTTTAAAAAAATAACAAAATTAA
1 CAAATGTCTCTAAAAAAATAACAAAATTAA
56233524 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAAAAATAACAAAATTAA
Found at i:56241893 original size:3 final size:3
Alignment explanation
Indices: 56241885--56241997 Score: 142
Period size: 3 Copynumber: 37.0 Consensus size: 3
56241875 TTGTATTTTC
*
56241885 ATT ATT ATTT ATTT ATT CATT ATT A-T ATT ATT A-T ATT A-T ACT ATT
1 ATT ATT A-TT A-TT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
56241930 AGTT CTAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 A-TT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56241977 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
56241998 TACTCATTTA
Statistics
Matches: 100, Mismatches: 3, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
2 6 0.06
3 80 0.80
4 14 0.14
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:56242743 original size:72 final size:72
Alignment explanation
Indices: 56242604--56242743 Score: 208
Period size: 72 Copynumber: 1.9 Consensus size: 72
56242594 TTTCAAACTT
* * * * **
56242604 AAGTTTTAAACGATCTCGGGAATTAAGAGAAGATCGTGTCCTAGCTTACTGGGAATGATCCTTTT
1 AAGTTTTAAACAATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGAATAATCCCCTT
56242669 TTTCCTC
66 TTTCCTC
* *
56242676 AAGTTTTAAACAATCTCGGGAATTAAGAAAAGATTGTGTCCTAACTTACTGGGCATAATCCCCTT
1 AAGTTTTAAACAATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGAATAATCCCCTT
56242741 TTT
66 TTT
56242744 TAATCTGAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (72 bp):
AAGTTTTAAACAATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGAATAATCCCCTT
TTTCCTC
Found at i:56243369 original size:39 final size:39
Alignment explanation
Indices: 56243315--56243394 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
56243305 TAGATAAAAG
56243315 ATAGATTTGAGAATAAGGAAATTTCTACGGCATTCTATT
1 ATAGATTTGAGAATAAGGAAATTTCTACGGCATTCTATT
56243354 ATAGATTTGAGAATAAGGAAATTTCTACGGCATTCTATT
1 ATAGATTTGAGAATAAGGAAATTTCTACGGCATTCTATT
56243393 AT
1 AT
56243395 TTTTCATCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (39 bp):
ATAGATTTGAGAATAAGGAAATTTCTACGGCATTCTATT
Found at i:56243522 original size:7 final size:7
Alignment explanation
Indices: 56243512--56243536 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56243502 GAAGAATTAA
56243512 GAAAGAT
1 GAAAGAT
56243519 GAAAGAT
1 GAAAGAT
56243526 GAAAGAT
1 GAAAGAT
56243533 GAAA
1 GAAA
56243537 AATTAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (7 bp):
GAAAGAT
Found at i:56244050 original size:16 final size:15
Alignment explanation
Indices: 56244010--56244054 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 15
56244000 AAACTAAAAA
*
56244010 TTTAAGTGTTGAATT
1 TTTAAGTGTTAAATT
56244025 TTT-A-TGTTAAATT
1 TTTAAGTGTTAAATT
56244038 TTATAAGTGTTAAATT
1 TT-TAAGTGTTAAATT
56244054 T
1 T
56244055 ATATTAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 10 0.38
14 2 0.08
15 4 0.15
16 10 0.38
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (15 bp):
TTTAAGTGTTAAATT
Found at i:56244057 original size:15 final size:15
Alignment explanation
Indices: 56244012--56244057 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
56244002 ACTAAAAATT
*
56244012 TAAGTGTTGAATTT-
1 TAAGTGTTAAATTTA
*
56244026 TTA-TGTTAAATTTTA
1 TAAGTGTTAAA-TTTA
56244041 TAAGTGTTAAATTTA
1 TAAGTGTTAAATTTA
56244056 TA
1 TA
56244058 TTAGAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 6 0.23
14 5 0.19
15 8 0.31
16 7 0.27
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (15 bp):
TAAGTGTTAAATTTA
Found at i:56250638 original size:24 final size:23
Alignment explanation
Indices: 56250589--56250639 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
56250579 AAGAGAATGA
56250589 AAAATAAAATAAAAAAGGAAAGTT
1 AAAATAAAATAAAAAA-GAAAGTT
*
56250613 AAAATAACATAAAAGAA-AAAGATT
1 AAAATAAAATAAAA-AAGAAAG-TT
56250637 AAA
1 AAA
56250640 TTGCTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 18 0.75
25 2 0.08
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.16
Consensus pattern (23 bp):
AAAATAAAATAAAAAAGAAAGTT
Found at i:56252880 original size:31 final size:31
Alignment explanation
Indices: 56252843--56252903 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
56252833 ATGTGTTCTA
*
56252843 TTAAATTATTTAAATATCATATATTATTATG
1 TTAAATTATTTAAATATCATATATCATTATG
* *
56252874 TTAAATTATTTAAATGTCATTTATCATTAT
1 TTAAATTATTTAAATATCATATATCATTAT
56252904 ATTTAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.52
Consensus pattern (31 bp):
TTAAATTATTTAAATATCATATATCATTATG
Found at i:56254981 original size:3 final size:3
Alignment explanation
Indices: 56254973--56255023 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
56254963 TTGACCCACT
56254973 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56255021 ATA
1 ATA
56255024 GATGAAAGAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:56268153 original size:29 final size:28
Alignment explanation
Indices: 56268111--56268165 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
56268101 CAATATTCAT
* *
56268111 TAATTTTACAATTTAATTTTTTATACAC
1 TAATTTGACAATTTAAGTTTTTATACAC
*
56268139 TAATTTGATCAATTTTAGTTTTTATAC
1 TAATTTGA-CAATTTAAGTTTTTATAC
56268166 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.55
Consensus pattern (28 bp):
TAATTTGACAATTTAAGTTTTTATACAC
Found at i:56273852 original size:72 final size:72
Alignment explanation
Indices: 56273536--56273839 Score: 446
Period size: 72 Copynumber: 4.2 Consensus size: 72
56273526 GAGGAAATGT
* * * * *
56273536 ACCATTAAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGACAACTGCCCTATAGACAAGG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGACAACTCCCCTATAGACAATG
56273601 GAATTTG
66 GAATTTG
* * * * * * *
56273608 GCCGTTTAATTGATTTTTTGAAACATCAAACCACTTCAGAGATGATAACTCCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGACAACTCCCCTATAGACAATG
56273673 GAATTTG
66 GAATTTG
** *
56273680 ACCATTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGACAACTCCCCTATAGACAATG
56273745 GAATTTG
66 GAATTTG
* * *
56273752 ACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAGAGATGATAACTCCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGACAACTCCCCTATAGACAATG
56273817 GAATTTG
66 GAATTTG
56273824 ACCATTTAATTGATTT
1 ACCATTTAATTGATTT
56273840 ACCGAAAGAT
Statistics
Matches: 205, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 205 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (72 bp):
ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGACAACTCCCCTATAGACAATG
GAATTTG
Found at i:56273852 original size:144 final size:144
Alignment explanation
Indices: 56273536--56273839 Score: 538
Period size: 144 Copynumber: 2.1 Consensus size: 144
56273526 GAGGAAATGT
*
56273536 ACCATTAAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGACAACTGCCCTATAGACAAGG
1 ACCATTTAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGACAACTGCCCTATAGACAAGG
* * * *
56273601 GAATTTGGCCGTTTAATTGATTTTTTGAAACATCAAACCACTTCAGAGATGATAACTCCCCTATA
66 GAATTTGACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAGAGATGATAACTCCCCTATA
56273666 GACAATGGAATTTG
131 GACAATGGAATTTG
*
56273680 ACCATTTAATTGATTTTCTGAAACATCAAACT-CCTCCAAAGATGACAACTGCCCTATAGACAAT
1 ACCATTTAATTGATTTTCTGAAACATCAAA-TACCTCCAAAGATGACAACTGCCCTATAGACAAG
56273744 GGAATTTGACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAGAGATGATAACTCCCCTAT
65 GGAATTTGACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAGAGATGATAACTCCCCTAT
56273809 AGACAATGGAATTTG
130 AGACAATGGAATTTG
56273824 ACCATTTAATTGATTT
1 ACCATTTAATTGATTT
56273840 ACCGAAAGAT
Statistics
Matches: 153, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
144 152 0.99
145 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (144 bp):
ACCATTTAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGACAACTGCCCTATAGACAAGG
GAATTTGACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAGAGATGATAACTCCCCTATA
GACAATGGAATTTG
Found at i:56275611 original size:3 final size:3
Alignment explanation
Indices: 56275603--56275700 Score: 85
Period size: 3 Copynumber: 33.0 Consensus size: 3
56275593 CAAAACTTAG
* **
56275603 ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT AGC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * ** *
56275651 AGTT -TT ATT GTT ATT -TT ATT ACT ATT AAC ATT ATT A-T ATAA ATT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
56275695 ATT ATT
1 ATT ATT
56275701 GAATGTTATT
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
2 6 0.08
3 64 0.86
4 4 0.05
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:56278798 original size:22 final size:21
Alignment explanation
Indices: 56278750--56278806 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
56278740 TCATTTTTTA
*
56278750 ATTT-TTATATATTTTAAAAT
1 ATTTATTATATTTTTTAAAAT
*
56278770 TTATTATTATATTTTTTGAAAAT
1 AT-TTATTATATTTTTT-AAAAT
*
56278793 ATTTA-TGTATTTTT
1 ATTTATTATATTTTT
56278807 ATATATTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.03
21 10 0.33
22 13 0.43
23 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
ATTTATTATATTTTTTAAAAT
Found at i:56291943 original size:23 final size:23
Alignment explanation
Indices: 56291910--56291965 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
56291900 ATAAAGGAAT
*
56291910 ATAATAATAATGA-CATAATTATA
1 ATAATAATAATAATCAT-ATTATA
*
56291933 ATAATATTAATAATCATATTATA
1 ATAATAATAATAATCATATTATA
*
56291956 GTAATAATAA
1 ATAATAATAA
56291966 ATAAATGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (23 bp):
ATAATAATAATAATCATATTATA
Found at i:56292214 original size:23 final size:23
Alignment explanation
Indices: 56292164--56292232 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
56292154 TTAAGGATGT
* *
56292164 ATAAAA-A-ATAAAGAGGTAATA
1 ATAAAATAGATAAATAGATAATA
56292185 A-ATAAATAGATAAATAGATAATA
1 ATA-AAATAGATAAATAGATAATA
56292208 ATAAAATAG-T-AATA-ATAATA
1 ATAAAATAGATAAATAGATAATA
56292228 ATAAA
1 ATAAA
56292233 GACACAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 12 0.29
21 8 0.19
22 2 0.05
23 19 0.45
24 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.25
Consensus pattern (23 bp):
ATAAAATAGATAAATAGATAATA
Found at i:56292220 original size:14 final size:15
Alignment explanation
Indices: 56292196--56292230 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
56292186 ATAAATAGAT
56292196 AAATAGATAATAATA
1 AAATAGATAATAATA
56292211 AAATAG-TAATAATA
1 AAATAGATAATAATA
56292225 ATAATA
1 A-AATA
56292231 AAGACACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
AAATAGATAATAATA
Found at i:56292322 original size:28 final size:26
Alignment explanation
Indices: 56292270--56292322 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
56292260 AAATTATCGA
*
56292270 TAAAAGAAAATAAAAAAAATTAATAT
1 TAAAAGAAAATAAAAAAAATGAATAT
56292296 TAAAA-AAATATAATAAATAAATGAATA
1 TAAAAGAAA-ATAA-AAA-AAATGAATA
56292323 AAAGGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 3 0.13
26 9 0.39
27 3 0.13
28 8 0.35
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (26 bp):
TAAAAGAAAATAAAAAAAATGAATAT
Found at i:56292896 original size:5 final size:5
Alignment explanation
Indices: 56292880--56292937 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
56292870 TCTAAGGACC
*
56292880 AAAAT GAAAAT AAAAT AAAAT AAAGT GAAAAAT AAAA- AAAAT AAAA-
1 AAAAT -AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAAT
56292926 AATAA- AAAAT AA
1 AA-AAT AAAAT AA
56292938 GATATGACTA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
4 8 0.18
5 28 0.62
6 5 0.11
7 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:56292926 original size:16 final size:16
Alignment explanation
Indices: 56292891--56292934 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
56292881 AAATGAAAAT
* *
56292891 AAAATAAAATAAAGTGA
1 AAAATAAAA-AAAATAA
56292908 AAAATAAAAAAAATAA
1 AAAATAAAAAAAATAA
56292924 AAAATAAAAAA
1 AAAATAAAAAA
56292935 TAAGATATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (16 bp):
AAAATAAAAAAAATAA
Found at i:56292932 original size:21 final size:22
Alignment explanation
Indices: 56292886--56292937 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
56292876 GACCAAAATG
* *
56292886 AAAATAAAATAAAATAAAGTGA
1 AAAATAAAATAAAATAAAATAA
56292908 AAAATAAAA-AAAATAAAAAATAA
1 AAAATAAAATAAAAT--AAAATAA
56292931 AAAATAA
1 AAAATAA
56292938 GATATGACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 5 0.19
22 9 0.35
23 12 0.46
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (22 bp):
AAAATAAAATAAAATAAAATAA
Found at i:56293551 original size:16 final size:15
Alignment explanation
Indices: 56293525--56293554 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
56293515 ATTTATTACG
56293525 AAAAAATAAAAAATA
1 AAAAAATAAAAAATA
56293540 AAAAAATCAAAAAAT
1 AAAAAAT-AAAAAAT
56293555 TACCTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATA
Found at i:56297563 original size:36 final size:36
Alignment explanation
Indices: 56297516--56297589 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
56297506 TCAAAGCAAA
* *
56297516 AAAAAAATGTTTTGGATTAATCATAGAGAGGTCCCT
1 AAAAAAATGTTTAGGATTAATCATAGAAAGGTCCCT
56297552 AAAAAAATGTTTAGGATTAATCATAGAAAGGTCCCT
1 AAAAAAATGTTTAGGATTAATCATAGAAAGGTCCCT
56297588 AA
1 AA
56297590 GTTTTTGTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (36 bp):
AAAAAAATGTTTAGGATTAATCATAGAAAGGTCCCT
Found at i:56308748 original size:10 final size:10
Alignment explanation
Indices: 56308733--56308757 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56308723 ACCAAAATAG
56308733 AAACGATCTA
1 AAACGATCTA
56308743 AAACGATCTA
1 AAACGATCTA
56308753 AAACG
1 AAACG
56308758 TTATGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.12, T:0.16
Consensus pattern (10 bp):
AAACGATCTA
Found at i:56319121 original size:4 final size:4
Alignment explanation
Indices: 56319112--56319142 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
56319102 AAAAGAAAAG
56319112 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
56319143 AAGATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:56329044 original size:72 final size:72
Alignment explanation
Indices: 56328897--56329044 Score: 199
Period size: 72 Copynumber: 2.1 Consensus size: 72
56328887 GAGGAAATGT
* *
56328897 ACCATTTAATTGATTTTCTGAAACATCAAATAACTTCAAAGATGACAGCTCCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAAGAACTTCAAAGATGAAAGCTCCCCTATAGACAATG
*
56328962 GAATTCG
66 GAATGCG
* * * **
56328969 ACCATTTAATTGATTTTCTGAAATATCAAAGAATTTCAAAGATGATAAG-TCCCCTATCGATGAT
1 ACCATTTAATTGATTTTCTGAAACATCAAAGAACTTCAAAGATGA-AAGCTCCCCTATAGACAAT
*
56329033 GGAATGGG
65 GGAATGCG
56329041 ACCA
1 ACCA
56329045 GAAATTTTGT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
72 64 0.97
73 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (72 bp):
ACCATTTAATTGATTTTCTGAAACATCAAAGAACTTCAAAGATGAAAGCTCCCCTATAGACAATG
GAATGCG
Found at i:56334485 original size:16 final size:15
Alignment explanation
Indices: 56334459--56334488 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
56334449 TTATAATATT
56334459 AAAATTTCTAAATTA
1 AAAATTTCTAAATTA
56334474 AAAATATTCTAAATT
1 AAAAT-TTCTAAATT
56334489 TATATACTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTTCTAAATTA
Found at i:56343112 original size:24 final size:24
Alignment explanation
Indices: 56343085--56343137 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
56343075 ATATGGAAAG
* *
56343085 AAATAAAAAATATTTTATGCTAAT
1 AAATAAAAAATATATTATACTAAT
**
56343109 AAATGTAAAATATATTATACTAAT
1 AAATAAAAAATATATTATACTAAT
56343133 AAATA
1 AAATA
56343138 CTAAACATCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (24 bp):
AAATAAAAAATATATTATACTAAT
Found at i:56343117 original size:26 final size:24
Alignment explanation
Indices: 56343091--56343136 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
56343081 AAAGAAATAA
* *
56343091 AAAATATTTTATGCTAATAAATGT
1 AAAATATATTATACTAATAAATGT
56343115 AAAATATATTATACTAATAAAT
1 AAAATATATTATACTAATAAAT
56343137 ACTAAACATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (24 bp):
AAAATATATTATACTAATAAATGT
Found at i:56350554 original size:23 final size:23
Alignment explanation
Indices: 56350504--56350572 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
56350494 TTAAGGATGT
* *
56350504 ATAAAA-A-ATAAAGAGGTAATA
1 ATAAAATAGATAAATAGATAATA
56350525 A-ATAAATAGATAAATAGATAATA
1 ATA-AAATAGATAAATAGATAATA
56350548 ATAAAATAG-T-AATA-ATAATA
1 ATAAAATAGATAAATAGATAATA
56350568 ATAAA
1 ATAAA
56350573 GACACAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 12 0.29
21 8 0.19
22 2 0.05
23 19 0.45
24 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.25
Consensus pattern (23 bp):
ATAAAATAGATAAATAGATAATA
Found at i:56350560 original size:14 final size:15
Alignment explanation
Indices: 56350536--56350570 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
56350526 ATAAATAGAT
56350536 AAATAGATAATAATA
1 AAATAGATAATAATA
56350551 AAATAG-TAATAATA
1 AAATAGATAATAATA
56350565 ATAATA
1 A-AATA
56350571 AAGACACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
AAATAGATAATAATA
Found at i:56355458 original size:24 final size:25
Alignment explanation
Indices: 56355431--56355478 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
56355421 TGTCAGCAAT
*
56355431 AATTTTTTA-TTTTATATATTTTTA
1 AATTTATTATTTTTATATATTTTTA
56355455 AATTTATTATTTTTATATATTTTT
1 AATTTATTATTTTTATATATTTTT
56355479 GTTGTTTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
AATTTATTATTTTTATATATTTTTA
Done.