Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 11 of 187
Found at i:3961689 original size:31 final size:31
Alignment explanation
Indices: 3961645--3961768 Score: 182
Period size: 31 Copynumber: 4.1 Consensus size: 31
3961635 TAGAGGATGC
**
3961645 AAAATTTTCAGGGTCAAAATGTAATTTTAGG
1 AAAATTTAGAGGGTCAAAATGTAATTTTAGG
*
3961676 AAAATTTAGAGGGTTAAAATGTAATTTTAGG
1 AAAATTTAGAGGGTCAAAATGTAATTTTAGG
*
3961707 AAAAGTTAGAGGGTC-AAATGTAATTTTAGG
1 AAAATTTAGAGGGTCAAAATGTAATTTTAGG
*
3961737 AAAATTT--AGGGTTAAAATGTAATTTTAGG
1 AAAATTTAGAGGGTCAAAATGTAATTTTAGG
3961766 AAA
1 AAA
3961769 GTTGGAGACC
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.06
29 18 0.21
30 21 0.25
31 41 0.48
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.34
Consensus pattern (31 bp):
AAAATTTAGAGGGTCAAAATGTAATTTTAGG
Found at i:3961782 original size:29 final size:31
Alignment explanation
Indices: 3961654--3961789 Score: 174
Period size: 31 Copynumber: 4.5 Consensus size: 31
3961644 CAAAATTTTC
*
3961654 AGGGTCAAAATGTAATTTTAGGAAAATTTAG
1 AGGGTCAAAATGTAATTTTAGGAAAAGTTAG
*
3961685 AGGGTTAAAATGTAATTTTAGGAAAAGTTAG
1 AGGGTCAAAATGTAATTTTAGGAAAAGTTAG
*
3961716 AGGGTC-AAATGTAATTTTAGGAAAA-TT-T
1 AGGGTCAAAATGTAATTTTAGGAAAAGTTAG
* *
3961744 AGGGTTAAAATGTAATTTTAGG-AAAGTTGG
1 AGGGTCAAAATGTAATTTTAGGAAAAGTTAG
**
3961774 A-GACCAAAATGTAATT
1 AGGGTCAAAATGTAATT
3961790 AGTTAATTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
28 8 0.09
29 31 0.33
30 20 0.22
31 34 0.37
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (31 bp):
AGGGTCAAAATGTAATTTTAGGAAAAGTTAG
Found at i:3976626 original size:2 final size:2
Alignment explanation
Indices: 3976619--3976644 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3976609 TATAAAACTA
3976619 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
3976645 TTAAAAAAAA
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:3983571 original size:45 final size:46
Alignment explanation
Indices: 3983518--3983659 Score: 187
Period size: 47 Copynumber: 3.0 Consensus size: 46
3983508 TAAAAGGTGG
* *
3983518 GACCAAGGTGAAAGCCTATAAAGGGCGCTTTGAGTAAAAAAAAAG-
1 GACCAAGGTGAAACCCTACAAAGGGCGCTTTGAGTAAAAAAAAAGA
* *
3983563 GGCCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTCAAAAAAAAAGA
1 GACCAAGGTGAAACCCTACAAA-GGGCGCTTTGAGT-AAAAAAAAAGA
* * *
3983611 GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAATAGA
1 GACCAAGGTGAAACCCTACAAAGGGCGCTTTGAGTAAAAAAAA-AGA
3983658 GA
1 GA
3983660 GGCTAAGGTG
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
45 19 0.23
46 20 0.24
47 25 0.30
48 20 0.24
ACGTcount: A:0.44, C:0.16, G:0.26, T:0.14
Consensus pattern (46 bp):
GACCAAGGTGAAACCCTACAAAGGGCGCTTTGAGTAAAAAAAAAGA
Found at i:3983624 original size:48 final size:46
Alignment explanation
Indices: 3983518--3983659 Score: 182
Period size: 48 Copynumber: 3.0 Consensus size: 46
3983508 TAAAAGGTGG
* *
3983518 GACCAAGGTGAAAGCCTATAAA-GGGCGCTTTGAGTAAAAAAAAAG-
1 GACCAAGGTGAAACCCTACAAAGGGGC-CTTTGAGTAAAAAAAAAGA
*
3983563 GGCCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTCAAAAAAAAAGA
1 GACCAAGGTGAAACCCTACAAAGGGGC-CTTTGAGT-AAAAAAAAAGA
*
3983611 GACCAGGGTGAAACCCTACAAAGGGAGCC-TTGAGTAAAAAAAATAGA
1 GACCAAGGTGAAACCCTACAAAGGG-GCCTTTGAGTAAAAAAAA-AGA
3983658 GA
1 GA
3983660 GGCTAAGGTG
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
45 19 0.22
46 20 0.23
47 21 0.24
48 24 0.28
49 2 0.02
ACGTcount: A:0.44, C:0.16, G:0.26, T:0.14
Consensus pattern (46 bp):
GACCAAGGTGAAACCCTACAAAGGGGCCTTTGAGTAAAAAAAAAGA
Found at i:3985068 original size:100 final size:100
Alignment explanation
Indices: 3984895--3985462 Score: 924
Period size: 100 Copynumber: 5.7 Consensus size: 100
3984885 ACCATAGATT
* *
3984895 TTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACGACGGCGGATCTGGTTTTCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
3984960 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
*
3984995 TTACTTCCTTAGCAGTGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
3985060 TGCAATTAAAAAGATTGAAGCCACAACAGCGGA-C
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* *
3985094 TTAATTCCTTAGCAGCGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
3985159 TGCAATTAAAAAGATTGAAGCCACAACGGCGTATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * * *
3985194 TTAATTCTTTAGTAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
3985259 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * * *
3985294 TTACTTCCTTAGTAGTGTAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
* *
3985359 TACAATTAAAAAGATTGAAGCCACAACGGTGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * * *
3985394 TTACTTCCCT-GACAGTGCAGTGGAACAGATTGAAGCTACGACGGAGGATCTGGTTTCCCCGACA
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA
3985458 TTGCA
65 TTGCA
3985463 GTTGAACAAA
Statistics
Matches: 437, Mismatches: 29, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
99 95 0.22
100 342 0.78
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (100 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
Found at i:3985246 original size:199 final size:200
Alignment explanation
Indices: 3984899--3985462 Score: 909
Period size: 199 Copynumber: 2.8 Consensus size: 200
3984889 TAGATTTTAC
* *
3984899 TTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACGACGGCGGATCTGGTTTTCCTGATATTGCA
1 TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCA
*
3984964 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCGGTGGAACAGATTGAA
66 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAA
*
3985029 GCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAACAGCGGA-
131 GCTACGACGGCAGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAACAGCGGAT
3985093 CTTAA
196 CTTAA
*
3985098 TTCCTTAGCAGCGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCA
1 TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCA
* * * *
3985163 ATTAAAAAGATTGAAGCCACAACGGCGTATCTTAATTCTTTAGTAGTGCAGTGGAACAGATTGAA
66 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAA
*
3985228 GCTACGACGGCAGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAACGGCGGAT
131 GCTACGACGGCAGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAACAGCGGAT
*
3985293 CTTAC
196 CTTAA
* * * * *
3985298 TTCCTTAGTAGTGTAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATATTACA
1 TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCA
* *
3985363 ATTAAAAAGATTGAAGCCACAACGGTGGATCTTACTTCCCT-GACAGTGCAGTGGAACAGATTGA
66 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGCAGTGGAACAGATTGA
* *
3985427 AGCTACGACGG-AGGATCTGGTTTCCCCGACATTGCA
130 AGCTACGACGGCA-GATCTGGTTTCCCTGATATTGCA
3985463 GTTGAACAAA
Statistics
Matches: 337, Mismatches: 25, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
199 186 0.55
200 151 0.45
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (200 bp):
TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCA
ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAA
GCTACGACGGCAGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAACAGCGGAT
CTTAA
Found at i:3985424 original size:50 final size:50
Alignment explanation
Indices: 3984908--3985478 Score: 380
Period size: 50 Copynumber: 11.4 Consensus size: 50
3984898 CTTCCTTAGC
* ** *
3984908 AGTGCAGTGGAACAGATTAAAGCTACGACGGCGGATCTGGTTTTCCTGAT
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGAT
* * ** * * * * * *
3984958 ATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGC
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGA-T
* **
3985008 AGTGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGAT
* * ** * * * * * * *
3985058 ATTGCAATTAAAAAGATTGAAGCCACAACAGCGGA-CTTAATT-CCTTAGC
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGA-T
* **
3985107 AGCGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGAT
* * ** * * * * * * *
3985157 ATTGCAATTAAAAAGATTGAAGCCACAACGGCGTATCTTAATT-CTTTAGT
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGA-T
* **
3985207 AGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGAT
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGAT
* * ** * * * * *
3985257 ATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGT
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGA-T
* *
3985307 AGTGTAGTGGAACAGATTGAAGCTACGACGGCAGATC-TAGTTTCCCTGAT
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTA-TTTCCCTGAT
* * * ** * * * * * *
3985357 ATTACAATTAAAAAGATTGAAGCCACAACGGTGGATCTTACTTCCCTGAC
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGAT
* ** * *
3985407 AGTGCAGTGGAACAGATTGAAGCTACGACGGAGGATCTGGTTTCCCCGAC
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGAT
* * *
3985457 ATTGCAGTTGAACAAATTGAAG
1 AGTGCAGTGGAACAGATTGAAG
3985479 TTTACAGATC
Statistics
Matches: 376, Mismatches: 134, Indels: 22
0.71 0.25 0.04
Matches are distributed among these distances:
48 4 0.01
49 43 0.11
50 312 0.83
51 17 0.05
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (50 bp):
AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCTGAT
Found at i:3985690 original size:45 final size:42
Alignment explanation
Indices: 3985651--3985731 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
3985641 GGAGCAGATC
* *
3985651 GAAGATGGTAGATTTTACCTCCCTGAAGTTGCAGTGGAGCAG
1 GAAGATGGCAGATTTTACCTCCCTGAAGTTACAGTGGAGCAG
* * *
3985693 GTAGATGGCGGATTTTACCTCCCTGATGTTACAGTGGAG
1 GAAGATGGCAGATTTTACCTCCCTGAAGTTACAGTGGAG
3985732 TACATTGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (42 bp):
GAAGATGGCAGATTTTACCTCCCTGAAGTTACAGTGGAGCAG
Found at i:3985738 original size:174 final size:175
Alignment explanation
Indices: 3985521--3985864 Score: 489
Period size: 174 Copynumber: 2.0 Consensus size: 175
3985511 AGCAGATCGA
3985521 AGATGGCGGATTTTACCTCCCTGAGGTTACAATGGACTACATTGAAGCCAGTAATTCTATCTCCC
1 AGATGGCGGATTTTACCTCCCTGAGGTTACAATGGACTACATTGAAGCCAGTAATTCTATCTCCC
* * * * *
3985586 TGGGTAGCAGTGGAATAGATTGAAAATTACAGATCTTATCTCCCTAAGCAGTA-A-TG-G-AGCA
66 TGGGCAACAGTGGAATAGACTGAAAATTACAGATCTTACCTCCCT--GCA-TAGACAGCGAAGCA
* *
3985647 GATCGAAGATGGTAGATTTTACCTCCCTGAAGTTGCAGTGGAGCAGGT
128 GATCGAAGACGGCAGATTTTACCTCCCTGAAGTTGCAGTGGAGCAGGT
* * *
3985695 AGATGGCGGATTTTACCTCCCTGATGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCC
1 AGATGGCGGATTTTACCTCCCTGAGGTTACAATGGACTACATTGAAGCCAGTAATTCTATCTCCC
* ** *
3985760 TGGGCAACAGTGGAATAGACTGAAGATTTTAGATCTTACCTTCCTGCATAGACAGCGAAGCAGAT
66 TGGGCAACAGTGGAATAGACTGAAAATTACAGATCTTACCTCCCTGCATAGACAGCGAAGCAGAT
* *
3985825 CGTAGACGGCAGATTTTACCTCCTTGAAGTTGCAGTGGAG
131 CGAAGACGGCAGATTTTACCTCCCTGAAGTTGCAGTGGAG
3985865 TATATTGAAG
Statistics
Matches: 150, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
171 2 0.01
172 4 0.03
173 1 0.01
174 100 0.67
175 43 0.29
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (175 bp):
AGATGGCGGATTTTACCTCCCTGAGGTTACAATGGACTACATTGAAGCCAGTAATTCTATCTCCC
TGGGCAACAGTGGAATAGACTGAAAATTACAGATCTTACCTCCCTGCATAGACAGCGAAGCAGAT
CGAAGACGGCAGATTTTACCTCCCTGAAGTTGCAGTGGAGCAGGT
Found at i:3987434 original size:21 final size:20
Alignment explanation
Indices: 3987405--3987446 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3987395 CTTAATTCGT
* *
3987405 TGTTTTATTTTTTATTAATTA
1 TGTTATATTTATTATT-ATTA
3987426 TGTTATATTTATTATTATTA
1 TGTTATATTTATTATTATTA
3987446 T
1 T
3987447 TATTTCTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
TGTTATATTTATTATTATTA
Found at i:3993855 original size:27 final size:28
Alignment explanation
Indices: 3993797--3993855 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
3993787 ATTATCATAG
*
3993797 ATAT-AATAAATGTTTTATTATATTATA
1 ATATAAATAAATATTTTATTATATTATA
*
3993824 A-ATAAATAAATATTTTATTGTATTA-A
1 ATATAAATAAATATTTTATTATATTATA
3993850 ATATAA
1 ATATAA
3993856 TTTTTAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (28 bp):
ATATAAATAAATATTTTATTATATTATA
Found at i:3995494 original size:22 final size:23
Alignment explanation
Indices: 3995467--3995509 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3995457 TTATAATCAA
3995467 ATATAAACACATAATT-TTATTT
1 ATATAAACACATAATTATTATTT
* *
3995489 ATATAAATATATAATTATTAT
1 ATATAAACACATAATTATTAT
3995510 ATTTTATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAAACACATAATTATTATTT
Found at i:4002504 original size:10 final size:10
Alignment explanation
Indices: 4002437--4002504 Score: 54
Period size: 10 Copynumber: 6.8 Consensus size: 10
4002427 TTTATTTTTT
4002437 TAAAAAT-TA
1 TAAAAATATA
4002446 TAAAAACTTATA
1 TAAAAA--TATA
4002458 TAAAAACTA-A
1 TAAAAA-TATA
*
4002468 T-AAATTATA
1 TAAAAATATA
4002477 -AACAAATATA
1 TAA-AAATATA
4002487 TAAAAATATA
1 TAAAAATATA
*
4002497 TATAAATA
1 TAAAAATA
4002505 AAAAAAATCA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
8 2 0.04
9 11 0.23
10 22 0.46
11 5 0.10
12 8 0.17
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (10 bp):
TAAAAATATA
Found at i:4002512 original size:29 final size:29
Alignment explanation
Indices: 4002439--4002512 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
4002429 TATTTTTTTA
**
4002439 AAAATTATAAAAACTTATATAAAAACTAAT
1 AAAA-TATAAAAAAATATATAAAAACTAAT
* *
4002469 AAATTATAAACAAATATATAAAAA-TATAT
1 AAAATATAAAAAAATATATAAAAACTA-AT
4002498 ATAAATA-AAAAAAAT
1 A-AAATATAAAAAAAT
4002513 CATTTATCGG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
28 2 0.06
29 27 0.75
30 7 0.19
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAATATAAAAAAATATATAAAAACTAAT
Found at i:4006577 original size:4 final size:4
Alignment explanation
Indices: 4006568--4006691 Score: 60
Period size: 4 Copynumber: 30.8 Consensus size: 4
4006558 ACGGTTTCCT
* * *
4006568 TTTA TTTA TTTA TTTA TTTA -TTA TTCCT- TTTA TTTTA TTCA TATA CTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA -TTTA TTTA TTTA TTTA
* * * * *
4006617 CTTA CTTA CTTA TTTA TTTA TATA -TTA TTCA TTTA TTTA CTTT- TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
** *
4006663 TTTA CTTTAA TTCC TTTA TTCA TTTA TTT
1 TTTA -TTT-A TTTA TTTA TTTA TTTA TTT
4006692 GTTATTCCTT
Statistics
Matches: 94, Mismatches: 16, Indels: 20
0.72 0.12 0.15
Matches are distributed among these distances:
3 12 0.13
4 66 0.70
5 14 0.15
6 2 0.02
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:4012923 original size:50 final size:50
Alignment explanation
Indices: 4012806--4012999 Score: 280
Period size: 50 Copynumber: 3.9 Consensus size: 50
4012796 TGATAATAAC
* ** *
4012806 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCG
* * **
4012857 GTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
4012907 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* *
4012957 GTGCCAATGCCATGTCTCAGACATGGTCTTACATGGGACCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4013000 TTACCCAAAT
Statistics
Matches: 127, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 94 0.74
51 33 0.26
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:4012986 original size:100 final size:101
Alignment explanation
Indices: 4012806--4012999 Score: 309
Period size: 100 Copynumber: 1.9 Consensus size: 101
4012796 TGATAATAAC
** *
4012806 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATG
*
4012871 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
66 TCCCAGACATGGTCTTACAGGGGACCTCTCATCTCG
* *
4012907 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATG
* *
4012971 TCTCAGACATGGTCTTACATGGGACCTCT
66 TCCCAGACATGGTCTTACAGGGGACCTCT
4013000 TTACCCAAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
100 48 0.56
101 37 0.44
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (101 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATG
TCCCAGACATGGTCTTACAGGGGACCTCTCATCTCG
Found at i:4013115 original size:13 final size:13
Alignment explanation
Indices: 4013094--4013124 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4013084 GCTTAGATCA
*
4013094 TCATCAAATAAAT
1 TCATAAAATAAAT
4013107 TCATAAAATAAAT
1 TCATAAAATAAAT
4013120 TCATA
1 TCATA
4013125 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:4020010 original size:50 final size:50
Alignment explanation
Indices: 4019893--4020086 Score: 289
Period size: 50 Copynumber: 3.9 Consensus size: 50
4019883 TGATAATAAC
* ** *
4019893 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCG
* * **
4019944 GTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
4019994 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
4020044 GTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4020087 TTACCCAAAT
Statistics
Matches: 128, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 95 0.74
51 33 0.26
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:4020072 original size:100 final size:101
Alignment explanation
Indices: 4019893--4020086 Score: 318
Period size: 100 Copynumber: 1.9 Consensus size: 101
4019883 TGATAATAAC
** *
4019893 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATG
*
4019958 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
66 TCCCAGACATGGTCTTACAGGGGACCTCTCATCTCG
* *
4019994 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATG
*
4020058 TCCCAGACATGGTCTTACATGGGACCTCT
66 TCCCAGACATGGTCTTACAGGGGACCTCT
4020087 TTACCCAAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
100 49 0.57
101 37 0.43
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (101 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATG
TCCCAGACATGGTCTTACAGGGGACCTCTCATCTCG
Found at i:4020202 original size:13 final size:13
Alignment explanation
Indices: 4020181--4020211 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4020171 GCTTAGATCA
*
4020181 TCATCAAATAAAT
1 TCATAAAATAAAT
4020194 TCATAAAATAAAT
1 TCATAAAATAAAT
4020207 TCATA
1 TCATA
4020212 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:4020455 original size:29 final size:30
Alignment explanation
Indices: 4020423--4020479 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
4020413 CCTCGACTCT
4020423 AACTTTT-CAAAATTACAATTT-TGCCCCTA
1 AACTTTTACAAAATTAC-ATTTGTGCCCCTA
*
4020452 AACTTTTACATAATTACATTTGTGCCCC
1 AACTTTTACAAAATTACATTTGTGCCCC
4020480 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.39
Consensus pattern (30 bp):
AACTTTTACAAAATTACATTTGTGCCCCTA
Found at i:4033430 original size:2 final size:2
Alignment explanation
Indices: 4033423--4033448 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4033413 ATTTTATTCT
4033423 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
4033449 AAAGGGAAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4037169 original size:30 final size:31
Alignment explanation
Indices: 4037102--4037169 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
4037092 ACATTCTGGT
* *
4037102 ATACAAA-ATCAGATGTATTTTCATAATCAG
1 ATACAAATATCAGATGCATATTCATAATCAG
4037132 ATACAAATA-CAGATGCATATTCA-AATTCAG
1 ATACAAATATCAGATGCATATTCATAA-TCAG
4037162 ATACAAAT
1 ATACAAAT
4037170 GTAGACACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 31 0.91
31 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (31 bp):
ATACAAATATCAGATGCATATTCATAATCAG
Found at i:4037894 original size:2 final size:2
Alignment explanation
Indices: 4037887--4037925 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4037877 ACACATTTGA
4037887 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4037926 ACATGCTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4038363 original size:46 final size:47
Alignment explanation
Indices: 4038238--4038636 Score: 626
Period size: 46 Copynumber: 8.6 Consensus size: 47
4038228 ATTCATGAAT
* ** ** *
4038238 TTGGTCAGCATATATAAAACAGTTTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
*
4038285 TTGGACAGCATATATGTAACAAATTGGGCAGCTTTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
*
4038332 TTGGACAGCAT-TATGTAACAAATTGGGCAGCTTTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
*
4038378 TTGGACAGCATATATGTAACAAATTGGGCAGCTTTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
*
4038425 TTGGACAGCAT-TATGTAACAAATTGGGCAGCTTTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
* *
4038471 TTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
*
4038518 TTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
*
4038564 TTGGACAGCAT-TATGTAACAAATTTGGCAGCATTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
* *
4038610 TTTGACAGCATATATGTAATAAATTGG
1 TTGGACAGCATATATGTAACAAATTGG
4038637 TTCAACTCAT
Statistics
Matches: 333, Mismatches: 16, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
46 180 0.54
47 153 0.46
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (47 bp):
TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
Found at i:4038379 original size:93 final size:93
Alignment explanation
Indices: 4038261--4038636 Score: 637
Period size: 93 Copynumber: 4.0 Consensus size: 93
4038251 ATAAAACAGT
*
4038261 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCTTTTATGCA
1 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCA
4038326 TCAAAATTGGACAGCATTATGTAACAAA
66 TCAAAATTGGACAGCATTATGTAACAAA
* * *
4038354 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCTTTTATGCA
1 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCA
4038419 TCAAAATTGGACAGCATTATGTAACAAA
66 TCAAAATTGGACAGCATTATGTAACAAA
* * * *
4038447 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
1 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCA
4038512 TCAAAATTGGACAGCATTATGTAACAAA
66 TCAAAATTGGACAGCATTATGTAACAAA
*
4038540 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCAT-TATGTAACAAATTTGGCAGCATTTATGCA
1 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCA
* *
4038604 TCAAAATTTGACAGCATATATGTAATAAA
66 TCAAAATTGGACAGCAT-TATGTAACAAA
4038633 TTGG
1 TTGG
4038637 TTCAACTCAT
Statistics
Matches: 270, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
92 42 0.16
93 228 0.84
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (93 bp):
TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCA
TCAAAATTGGACAGCATTATGTAACAAA
Found at i:4038470 original size:139 final size:140
Alignment explanation
Indices: 4038215--4038636 Score: 661
Period size: 139 Copynumber: 3.0 Consensus size: 140
4038205 TCTACCCTAT
* * * * * ** **
4038215 TTGGACAGCTTTTATTCAT-GAATTTGGTCAGCATATATAAAACAGTTTGGGCAGCATTTAAGCA
1 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
4038279 TCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCTTTTATGCATCAAAATTGGACAGCAT-
66 TCAAAATTGGACAGCAT-TATGTAACAAATTGGGCAGCTTTTATGCATCAAAATTGGACAGCATA
*
4038343 TATGTAACAAA
130 TATGTAATAAA
* *
4038354 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCTTTTATGCA
1 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
4038419 TCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTATGCATCAAAATTGGACAGCATAT
66 TCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTATGCATCAAAATTGGACAGCATAT
4038484 ATGTAATAAA
131 ATGTAATAAA
* *
4038494 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTAAGCA
1 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
* * *
4038558 TCAAAATTGGACAGCATTATGTAACAAATTTGGCAGCATTTATGCATCAAAATTTGACAGCATAT
66 TCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTATGCATCAAAATTGGACAGCATAT
4038623 ATGTAATAAA
131 ATGTAATAAA
4038633 TTGG
1 TTGG
4038637 TTCAACTCAT
Statistics
Matches: 262, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
139 166 0.63
140 96 0.37
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (140 bp):
TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
TCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTATGCATCAAAATTGGACAGCATAT
ATGTAATAAA
Found at i:4039544 original size:43 final size:42
Alignment explanation
Indices: 4039478--4039607 Score: 158
Period size: 43 Copynumber: 3.0 Consensus size: 42
4039468 AACTCGTACA
* *
4039478 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGAAGTGGTCTTACACGTAA-CACATATCG
4039521 ATGCC-ACTGTCCCAGATAG-GGTCTTACACGTAAACACA-AGTCG
1 ATGCCAAC-GTCCCAGA-AGTGGTCTTACACGT-AACACATA-TCG
*
4039564 ATGCCAACGTCCCAGACGTGGTCTTACACGATAACACATATCG
1 ATGCCAACGTCCCAGAAGTGGTCTTACACG-TAACACATATCG
4039607 A
1 A
4039608 AAATCCTATG
Statistics
Matches: 76, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
42 4 0.05
43 65 0.86
44 7 0.09
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAGAAGTGGTCTTACACGTAACACATATCG
Found at i:4041458 original size:23 final size:23
Alignment explanation
Indices: 4041421--4041494 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
4041411 CCATCAACAG
*
4041421 TGTAATATCCC-GAAAATTACTAT
1 TGTAATA-CCCTGAAAATTACTAC
4041444 TGTAATACCCTGAAAATTACTAC
1 TGTAATACCCTGAAAATTACTAC
* *
4041467 AGTAATACCCTAAAAATTACTAC
1 TGTAATACCCTGAAAATTACTAC
*
4041490 AGTAA
1 TGTAA
4041495 GGAAGTAGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 3 0.06
23 44 0.94
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (23 bp):
TGTAATACCCTGAAAATTACTAC
Found at i:4052822 original size:28 final size:28
Alignment explanation
Indices: 4052738--4052832 Score: 124
Period size: 28 Copynumber: 3.5 Consensus size: 28
4052728 TAATGAGATT
4052738 AGCACTAAGTGT--GAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGTTTAATTGTAA
*
4052764 AGCACTTAA-TGTGCGAGTTTAATGGTAA
1 AGCAC-TAAGTGTGCGAGTTTAATTGTAA
* * *
4052792 AGCACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTTTAATTGTAA
4052820 AGCACTAAGTGTG
1 AGCACTAAGTGTG
4052833 TGAACTTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
26 8 0.13
27 6 0.10
28 46 0.77
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTAATTGTAA
Found at i:4054090 original size:46 final size:46
Alignment explanation
Indices: 4054017--4054242 Score: 384
Period size: 46 Copynumber: 4.9 Consensus size: 46
4054007 GCTATACCTT
4054017 AGTATGGTTTTCTTCAC-GAAAATACCATACCTACTTTTCACAACTC
1 AGTATGGTTTTCTTCACTG-AAATACCATACCTACTTTTCACAACTC
*
4054063 AGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACTC
1 AGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAACTC
*
4054109 AGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACTC
1 AGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAACTC
*
4054155 AGTATGGTTTTCTTTA-TCGAAATACCATACCTACTTTTCACAACTC
1 AGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCACAACTC
*
4054201 AGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCACA
1 AGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACA
4054243 CTTTGCCATG
Statistics
Matches: 172, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
45 1 0.01
46 169 0.98
47 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (46 bp):
AGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAACTC
Found at i:4070602 original size:37 final size:37
Alignment explanation
Indices: 4070558--4070666 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
4070548 GATAGCTTTA
4070558 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
4070595 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
4070632 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
4070667 ATCATACGTA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 12 0.17
36 4 0.06
37 53 0.77
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:4075788 original size:20 final size:19
Alignment explanation
Indices: 4075735--4075815 Score: 74
Period size: 20 Copynumber: 4.2 Consensus size: 19
4075725 AATTAAAAGT
*
4075735 AAAAAATCTTAAATTTTTA
1 AAAAAATCTTAAAATTTTA
**
4075754 AAAAATATCAGAAAATTTTA
1 AAAAA-ATCTTAAAATTTTA
*
4075774 AAAAAATCTTTAAAA-TCTA
1 AAAAAATC-TTAAAATTTTA
**
4075793 AAAAAAAATTAAAATATTTA
1 AAAAAATCTTAAAAT-TTTA
4075813 AAA
1 AAA
4075816 CTTGGAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
18 6 0.12
19 17 0.35
20 26 0.53
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (19 bp):
AAAAAATCTTAAAATTTTA
Found at i:4076660 original size:10 final size:10
Alignment explanation
Indices: 4076645--4076680 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
4076635 GGGTCCATAT
4076645 TTTTTTATGA
1 TTTTTTATGA
4076655 TTTTTTAT-A
1 TTTTTTATGA
*
4076664 TTTTTAATGA
1 TTTTTTATGA
4076674 TTTTTTA
1 TTTTTTA
4076681 AATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (10 bp):
TTTTTTATGA
Found at i:4076673 original size:19 final size:20
Alignment explanation
Indices: 4076645--4076693 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
4076635 GGGTCCATAT
*
4076645 TTTTTTATGATTTTTT-ATA
1 TTTTTAATGATTTTTTAATA
4076664 TTTTTAATGATTTTTTAAATA
1 TTTTTAATGATTTTTT-AATA
4076685 TTTTTAATG
1 TTTTTAATG
4076694 TCCAACAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 15 0.56
21 12 0.44
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTTTAATGATTTTTTAATA
Found at i:4082225 original size:22 final size:23
Alignment explanation
Indices: 4082197--4082239 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
4082187 AAAAATATAT
4082197 TAAATATATAAATTT-ATTATCA
1 TAAATATATAAATTTAATTATCA
*
4082219 TAAATATATAAGTTTAATTAT
1 TAAATATATAAATTTAATTAT
4082240 TATTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAATATATAAATTTAATTATCA
Found at i:4087012 original size:21 final size:20
Alignment explanation
Indices: 4086979--4087017 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4086969 GCTAGAATAA
*
4086979 TTTTCTTAAATAATATATATT
1 TTTTATTAAATAAT-TATATT
*
4087000 TTTTATTATATAATTATA
1 TTTTATTAAATAATTATA
4087018 ATAATAATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATTAAATAATTATATT
Found at i:4094908 original size:4 final size:4
Alignment explanation
Indices: 4094899--4094972 Score: 148
Period size: 4 Copynumber: 18.5 Consensus size: 4
4094889 ATCTACTTCA
4094899 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4094947 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
4094973 ATCTAGCTTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 70 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:4126552 original size:27 final size:27
Alignment explanation
Indices: 4126511--4126594 Score: 132
Period size: 27 Copynumber: 3.1 Consensus size: 27
4126501 TAGTATTGGC
*
4126511 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
4126538 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
* *
4126565 GCCTATCTAGGAGGCGCCAATAGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
4126592 GCC
1 GCC
4126595 ATATTAGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.18, C:0.23, G:0.37, T:0.23
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:4126608 original size:27 final size:26
Alignment explanation
Indices: 4126522--4126613 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 26
4126512 CCTATCTGGA
*
4126522 AGGCGCCAATGGTGGTGCCTATTTGGG
1 AGGCGCCAATGGTGGTGCCTA-TTAGG
4126549 AGGCGCCAATGGTGGTGCCTATCTAGG
1 AGGCGCCAATGGTGGTGCCTAT-TAGG
* *
4126576 AGGCGCCAATAGTGGTGCCATATTAGA
1 AGGCGCCAATGGTGGTGCC-TATTAGG
*
4126603 AAGCGCCAATG
1 AGGCGCCAATG
4126614 CTGTGATTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
26 1 0.02
27 54 0.93
28 3 0.05
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.22
Consensus pattern (26 bp):
AGGCGCCAATGGTGGTGCCTATTAGG
Found at i:4126609 original size:54 final size:54
Alignment explanation
Indices: 4126511--4126613 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
4126501 TAGTATTGGC
* * * *
4126511 GCCTATCTGGAAGGCGCCAATGGTGGTGCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATAGTGGTGCCTATTTAGAAAGCGCCAATGGTGGT
4126565 GCCTATCTAGG-AGGCGCCAATAGTGGTGCC-ATATTAGAAAGCGCCAATG
1 GCCTATCT-GGAAGGCGCCAATAGTGGTGCCTAT-TTAGAAAGCGCCAATG
4126614 CTGTGATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
53 2 0.05
54 39 0.91
55 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (54 bp):
GCCTATCTGGAAGGCGCCAATAGTGGTGCCTATTTAGAAAGCGCCAATGGTGGT
Found at i:4129249 original size:38 final size:38
Alignment explanation
Indices: 4129206--4129287 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
4129196 AAAAAGTCAG
4129206 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
4129244 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
4129282 TTATAA
1 TTATAA
4129288 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:4129568 original size:27 final size:24
Alignment explanation
Indices: 4129510--4129718 Score: 189
Period size: 21 Copynumber: 9.0 Consensus size: 24
4129500 CAGACATAAG
4129510 ATATTACAATATTCATAC--AAAA
1 ATATTACAATATTCATACAAAAAA
*
4129532 A-ATTGCAATATTCATACAAAATTATA
1 ATATTACAATATTCATACAAAA--A-A
4129558 ATATTACAATATTCATACAAAAAA
1 ATATTACAATATTCATACAAAAAA
4129582 ATA-T--AATATTCATACAAAATTACA
1 ATATTACAATATTCATACAAAA--A-A
*
4129606 AAATTACAATATTCATAC--AAAA
1 ATATTACAATATTCATACAAAAAA
*
4129628 A-ATTGCAATATTCATACAAAACTATA
1 ATATTACAATATTCATACAAAA--A-A
4129654 ATATTACAATATTCATAC-AAAAA
1 ATATTACAATATTCATACAAAAAA
*
4129677 AT-TTATAATATTCATAC----AA
1 ATATTACAATATTCATACAAAAAA
4129696 A-ATTACAATATTCATACAAAAAA
1 ATATTACAATATTCATACAAAAAA
4129719 TTACTAATCC
Statistics
Matches: 157, Mismatches: 7, Indels: 45
0.75 0.03 0.22
Matches are distributed among these distances:
19 17 0.11
21 45 0.29
22 17 0.11
23 12 0.08
24 8 0.05
25 6 0.04
26 7 0.04
27 45 0.29
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.32
Consensus pattern (24 bp):
ATATTACAATATTCATACAAAAAA
Found at i:4129568 original size:48 final size:48
Alignment explanation
Indices: 4129510--4129707 Score: 306
Period size: 48 Copynumber: 4.1 Consensus size: 48
4129500 CAGACATAAG
* *
4129510 ATATTACAATATTCATACAAAAAATTGCAATATTCATACAAAATTATA
1 ATATTACAATATTCATACAAAAAATTACAATATTCATACAAAATTACA
* *
4129558 ATATTACAATATTCATACAAAAAAATATAATATTCATACAAAATTACA
1 ATATTACAATATTCATACAAAAAATTACAATATTCATACAAAATTACA
* * * *
4129606 AAATTACAATATTCATACAAAAAATTGCAATATTCATACAAAACTATA
1 ATATTACAATATTCATACAAAAAATTACAATATTCATACAAAATTACA
*
4129654 ATATTACAATATTCATACAAAAAATTTATAATATTCATACAAAATTACA
1 ATATTACAATATTCATACAAAAAA-TTACAATATTCATACAAAATTACA
4129703 ATATT
1 ATATT
4129708 CATACAAAAA
Statistics
Matches: 134, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
48 109 0.81
49 25 0.19
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.33
Consensus pattern (48 bp):
ATATTACAATATTCATACAAAAAATTACAATATTCATACAAAATTACA
Found at i:4129627 original size:96 final size:97
Alignment explanation
Indices: 4129512--4129703 Score: 359
Period size: 96 Copynumber: 2.0 Consensus size: 97
4129502 GACATAAGAT
*
4129512 ATTACAATATTCATACAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATACA
1 ATTACAATATTCATACAAAAAATTGCAATATTCATACAAAACTATAATATTACAATATTCATACA
4129577 AAAAA-ATATAATATTCATACAAAATTACAAA
66 AAAAATATATAATATTCATACAAAATTACAAA
4129608 ATTACAATATTCATACAAAAAATTGCAATATTCATACAAAACTATAATATTACAATATTCATACA
1 ATTACAATATTCATACAAAAAATTGCAATATTCATACAAAACTATAATATTACAATATTCATACA
*
4129673 AAAAATTTATAATATTCATACAAAATTACAA
66 AAAAATATATAATATTCATACAAAATTACAA
4129704 TATTCATACA
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 69 0.74
97 24 0.26
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (97 bp):
ATTACAATATTCATACAAAAAATTGCAATATTCATACAAAACTATAATATTACAATATTCATACA
AAAAATATATAATATTCATACAAAATTACAAA
Found at i:4129686 original size:30 final size:27
Alignment explanation
Indices: 4129510--4129707 Score: 154
Period size: 27 Copynumber: 8.2 Consensus size: 27
4129500 CAGACATAAG
4129510 ATATTACAATATTCATAC--AA--A-A
1 ATATTACAATATTCATACAAAACTATA
* *
4129532 A-ATTGCAATATTCATACAAAATTATA
1 ATATTACAATATTCATACAAAACTATA
4129558 ATATTACAATATTCATACAAAA--A-A
1 ATATTACAATATTCATACAAAACTATA
* *
4129582 ATA-T--AATATTCATACAAAATTACA
1 ATATTACAATATTCATACAAAACTATA
*
4129606 AAATTACAATATTCATAC--AA--A-A
1 ATATTACAATATTCATACAAAACTATA
*
4129628 A-ATTGCAATATTCATACAAAACTATA
1 ATATTACAATATTCATACAAAACTATA
4129654 ATATTACAATATTCATAC-AAA--A-A
1 ATATTACAATATTCATACAAAACTATA
* * *
4129677 AT-TTATAATATTCATACAAAATTACA
1 ATATTACAATATTCATACAAAACTATA
4129703 ATATT
1 ATATT
4129708 CATACAAAAA
Statistics
Matches: 147, Mismatches: 6, Indels: 41
0.76 0.03 0.21
Matches are distributed among these distances:
21 45 0.31
22 17 0.12
23 13 0.09
24 8 0.05
25 7 0.05
26 10 0.07
27 47 0.32
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.33
Consensus pattern (27 bp):
ATATTACAATATTCATACAAAACTATA
Found at i:4129713 original size:41 final size:41
Alignment explanation
Indices: 4129656--4129841 Score: 170
Period size: 41 Copynumber: 4.5 Consensus size: 41
4129646 AAACTATAAT
4129656 ATTACAATATTCATACAAAAAATTTATAATATTCATAC-AAA
1 ATTACAATATTCATACAAAAAA-TTATAATATTCATACAAAA
* * *
4129697 ATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAA
1 ATTACAATATTCATACAAAAAATTA-TAATATTC-ATAC-AAAA
* * * *
4129739 A-TACAA-ATTTAATTATAAAATAATTACAATATTCATAC-AAC
1 ATTACAATA-TTCA-TACAAAA-AATTATAATATTCATACAAAA
4129780 ATTACAATATTCATA-AAAAAATTATAATATTCATACAAAAA
1 ATTACAATATTCATACAAAAAATTATAATATTCATAC-AAAA
*
4129821 ATTTAAAATATTCATACAAAA
1 A-TTACAATATTCATACAAAA
4129842 TTCTAATCTA
Statistics
Matches: 116, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
39 19 0.16
40 12 0.10
41 38 0.33
42 30 0.26
43 14 0.12
44 3 0.03
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (41 bp):
ATTACAATATTCATACAAAAAATTATAATATTCATACAAAA
Found at i:4129785 original size:19 final size:19
Alignment explanation
Indices: 4129760--4129843 Score: 96
Period size: 20 Copynumber: 4.2 Consensus size: 19
4129750 ATTATAAAAT
4129760 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* *
4129779 CATTACAATATTCATAAAAA
1 AATTACAATATTCAT-ACAA
*
4129799 AATTATAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
*
4129820 AATTTAAAATATTCATACAA
1 AA-TTACAATATTCATACAA
4129840 AATT
1 AATT
4129844 CTAATCTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
19 17 0.31
20 20 0.36
21 4 0.07
22 14 0.25
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:4129830 original size:22 final size:21
Alignment explanation
Indices: 4129605--4129841 Score: 107
Period size: 21 Copynumber: 11.1 Consensus size: 21
4129595 ACAAAATTAC
*
4129605 AAAATTACAATATTCATACAA
1 AAAATTAAAATATTCATACAA
**
4129626 AAAATTGCAATATTCATAC--
1 AAAATTAAAATATTCATACAA
* *
4129645 AAAACTATAATATTACAATATTCATACA
1 AAAATTAAAATATT-C-ATA--C--A-A
*
4129673 AAAAATTTATAATATTCATAC--
1 AAA-A-TTAAAATATTCATACAA
*
4129694 AAAATTACAATATTCATACAA
1 AAAATTAAAATATTCATACAA
** * * *
4129715 AAAATTACTA-ATCCAAAACTA
1 AAAATTAAAATATTC-ATACAA
* * *
4129736 TAAA-TACAAAT-TTAATTATAA
1 AAAATTA-AAATATTCA-TACAA
*
4129757 AATAATTACAATATTCATAC--
1 AA-AATTAAAATATTCATACAA
* *
4129777 AACATTACAATATTCATA-AA
1 AAAATTAAAATATTCATACAA
*
4129797 AAAATTATAATATTCATACAA
1 AAAATTAAAATATTCATACAA
4129818 AAAATTTAAAATATTCATACAA
1 AAAA-TTAAAATATTCATACAA
4129840 AA
1 AA
4129842 TTCTAATCTA
Statistics
Matches: 166, Mismatches: 26, Indels: 47
0.69 0.11 0.20
Matches are distributed among these distances:
19 40 0.24
20 26 0.16
21 51 0.31
22 25 0.15
23 6 0.04
26 1 0.01
28 6 0.04
29 2 0.01
30 9 0.05
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTAAAATATTCATACAA
Found at i:4129842 original size:83 final size:85
Alignment explanation
Indices: 4129602--4129842 Score: 246
Period size: 83 Copynumber: 2.8 Consensus size: 85
4129592 CATACAAAAT
** *
4129602 TACAAAATTACAATATTCATACAAAAAATTGCAATATTCATACAAAACTATAATATTACAATATT
1 TACAAAATTACAATATTCATACAAAAAATTATAATATTCATAC-AAA--A-AAT-TTAAAATATT
*
4129667 CATACAAAA-AATTTATAATATTCA
61 CATACAAAATAATTTACAATATTCA
* * * * *
4129691 TACAAAATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAAA--TACAAAT-TTAA
1 TACAAAATTACAATATTCATACAAAAAATTA-TAATATTC-ATACAAAAAATTTA-AAATATTCA
*
4129751 TTATAAAATAA-TTACAATATTCA
63 -TACAAAATAATTTACAATATTCA
*
4129774 TACAACATTACAATATTCATA-AAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
1 TACAAAATTACAATATTCATACAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
4129838 AAAAT
66 AAAAT
4129843 TCTAATCTAA
Statistics
Matches: 125, Mismatches: 17, Indels: 26
0.74 0.10 0.15
Matches are distributed among these distances:
81 1 0.01
82 22 0.18
83 54 0.43
84 7 0.06
85 2 0.02
86 1 0.01
88 4 0.03
89 34 0.27
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (85 bp):
TACAAAATTACAATATTCATACAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
AAAATAATTTACAATATTCA
Found at i:4130001 original size:3 final size:3
Alignment explanation
Indices: 4129995--4130034 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
4129985 TTTTTTTTCT
*
4129995 TTC TTC TTC -TC TTC -TC TTC TTC TTC TCC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4130035 CCTTTCTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.19
3 26 0.81
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:4130009 original size:8 final size:8
Alignment explanation
Indices: 4129991--4130035 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
4129981 ACCTTTTTTT
4129991 TTCTT-TC
1 TTCTTCTC
4129998 TTCTTCTC
1 TTCTTCTC
4130006 TTC-TCTTC
1 TTCTTC-TC
4130014 TTCTTCTC
1 TTCTTCTC
4130022 --CTTCTC
1 TTCTTCTC
4130028 TTCTTCTC
1 TTCTTCTC
4130036 CTTTCTCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.18
7 7 0.21
8 18 0.55
9 2 0.06
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (8 bp):
TTCTTCTC
Found at i:4130025 original size:17 final size:16
Alignment explanation
Indices: 4129991--4130043 Score: 74
Period size: 17 Copynumber: 3.4 Consensus size: 16
4129981 ACCTTTTTTT
4129991 TTCT-TTCTTCTTCTC
1 TTCTCTTCTTCTTCTC
4130006 TTCTCTTCTTCTTCTCC
1 TTCTCTTCTTCTTCT-C
*
4130023 TTCTCTTCTTCTCCT-
1 TTCTCTTCTTCTTCTC
4130038 TTCTCT
1 TTCTCT
4130044 CTTTTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
15 10 0.29
16 10 0.29
17 15 0.43
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCTCTTCTTCTTCTC
Found at i:4130044 original size:17 final size:16
Alignment explanation
Indices: 4129991--4130046 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 16
4129981 ACCTTTTTTT
*
4129991 TTCTTTCTTCTTCT-C
1 TTCTCTCTTCTTCTCC
4130006 TTCTCTTCTTCTTCTCC
1 TTCTC-TCTTCTTCTCC
4130023 -T-TCTCTTCTTCTCC
1 TTCTCTCTTCTTCTCC
4130037 TTTCTCTCTT
1 -TTCTCTCTT
4130047 TTTTTTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 11 0.31
15 6 0.17
16 11 0.31
17 7 0.20
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCTCTCTTCTTCTCC
Found at i:4139411 original size:21 final size:22
Alignment explanation
Indices: 4139387--4139436 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
4139377 TTTTCCCCTA
4139387 CTGTTTTACTG-CTTTATGTTG
1 CTGTTTTACTGTCTTTATGTTG
* *
4139408 CTGTTTTATTGTTTTTATGTTG
1 CTGTTTTACTGTCTTTATGTTG
*
4139430 TTGTTTT
1 CTGTTTT
4139437 GTTACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.66
Consensus pattern (22 bp):
CTGTTTTACTGTCTTTATGTTG
Found at i:4140953 original size:30 final size:30
Alignment explanation
Indices: 4140913--4140974 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
4140903 GTTAATAATT
* * *
4140913 TACAAGAATTGGATCAAATCAAAATTTCATG
1 TACAAGAATTGCATAAAATC-AAAGTTCATG
4140944 TACAA-AATTGCATAAAATCAAAGTTCATG
1 TACAAGAATTGCATAAAATCAAAGTTCATG
4140973 TA
1 TA
4140975 TACAATTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (30 bp):
TACAAGAATTGCATAAAATCAAAGTTCATG
Found at i:4140981 original size:29 final size:30
Alignment explanation
Indices: 4140913--4140984 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
4140903 GTTAATAATT
* * *
4140913 TACAAGAATTGGATCAAATCAAAATTTCATG
1 TACAA-AATTGCATAAAATCAAAAGTTCATG
4140944 TACAAAATTGCATAAAATC-AAAGTTCATG
1 TACAAAATTGCATAAAATCAAAAGTTCATG
* *
4140973 TATACAATTGCA
1 TACAAAATTGCA
4140985 CATTAAACCA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 19 0.53
30 12 0.33
31 5 0.14
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (30 bp):
TACAAAATTGCATAAAATCAAAAGTTCATG
Found at i:4152166 original size:22 final size:22
Alignment explanation
Indices: 4152104--4152175 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
4152094 ATTGTTCAAA
* **
4152104 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
4152126 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
4152148 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
4152170 CATGAG
1 CATGAG
4152176 TTGGGCTGGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:4156685 original size:19 final size:19
Alignment explanation
Indices: 4156647--4156695 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
4156637 ATTACTAAAC
*
4156647 CAGCCCAAACATTAAACCCT
1 CAGCCCAAA-TTTAAACCCT
*
4156667 CAGCCCAAATTTTAACCCT
1 CAGCCCAAATTTAAACCCT
*
4156686 AAGCCCAAAT
1 CAGCCCAAAT
4156696 GGCCCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.39, C:0.37, G:0.06, T:0.18
Consensus pattern (19 bp):
CAGCCCAAATTTAAACCCT
Found at i:4156887 original size:15 final size:16
Alignment explanation
Indices: 4156863--4156894 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4156853 ACGCAAACAC
4156863 AAAACAACAAAAAGAA
1 AAAACAACAAAAAGAA
4156879 AAAAC-ACAAAAAGAA
1 AAAACAACAAAAAGAA
4156894 A
1 A
4156895 GTCGAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.81, C:0.12, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAACAACAAAAAGAA
Found at i:4157922 original size:11 final size:12
Alignment explanation
Indices: 4157893--4157924 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
4157883 AAAAAGAAGG
4157893 TTTTATTTAATA
1 TTTTATTTAATA
4157905 TTTTATTTAATA
1 TTTTATTTAATA
4157917 -TTTATTTA
1 TTTTATTTA
4157925 TTTACTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATTTAATA
Found at i:4157987 original size:20 final size:20
Alignment explanation
Indices: 4157958--4158007 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
4157948 CAAACTTACA
4157958 TTATTA-TTTATTTCATTT-C
1 TTATTATTTTATTT-ATTTGC
4157977 ATT-TTATTTTATTTATTTGC
1 -TTATTATTTTATTTATTTGC
4157997 TTATTATTTTA
1 TTATTATTTTA
4158008 GTATCGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (20 bp):
TTATTATTTTATTTATTTGC
Found at i:4158151 original size:15 final size:15
Alignment explanation
Indices: 4158131--4158164 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4158121 TTATCGTTGA
4158131 TTATTATTATTGTT-T
1 TTATTA-TATTGTTAT
4158146 TTATTATATTGTTAT
1 TTATTATATTGTTAT
4158161 TTAT
1 TTAT
4158165 ATCATTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (15 bp):
TTATTATATTGTTAT
Found at i:4158507 original size:107 final size:108
Alignment explanation
Indices: 4158385--4158828 Score: 624
Period size: 110 Copynumber: 4.1 Consensus size: 108
4158375 TATCCAAATA
** * *
4158385 AAAATTTCAAAATAAGGCAATATTTTGTGTTTGGAAATTCGAGAAAATGTGCCCTAACTTGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
*
4158450 GTCTCGA-TTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
66 GTTTCGATTTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
*
4158492 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
4158557 GTTTCGATTTTTTTCGTTCGACCAAATAGCTAAAAATATCCTTTT
66 GTTTCGA-TTTTTTCGTTCGACCAAATAGCT-AAAATATCCTTTT
* * * *
4158602 AAAATTTCAAAATAAGGCAATATTTCACGTTTAGAAGTTCGAGAAAACGTGCTCTAACGTGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* * * *
4158667 GTTTAGATTTTTTTTGTTCGACCAAATAGCTAAAATATCATTCT
66 GTTTCGA-TTTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
* * * *
4158711 AAAATTTCATAATAAAGGTAATATTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
1 AAAATTTCAAAAT-AAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
* * * *
4158776 GGTTTCGA-TTTCTCGTTTGACCAAATAGC-CAAATATCCTCTT
65 GGTTTCGATTTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
*
4158818 AAAACTTCAAA
1 AAAATTTCAAA
4158829 GTATGTTTTT
Statistics
Matches: 302, Mismatches: 31, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
107 84 0.28
108 18 0.06
109 45 0.15
110 155 0.51
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (108 bp):
AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
GTTTCGATTTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
Found at i:4159104 original size:13 final size:14
Alignment explanation
Indices: 4159088--4159120 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
4159078 AACGAAAATT
4159088 GAGAAAGAA-AAAA
1 GAGAAAGAAGAAAA
4159101 GAGAAAGAAGAAAA
1 GAGAAAGAAGAAAA
4159115 -AGAAAG
1 GAGAAAG
4159121 TGAACCATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
GAGAAAGAAGAAAA
Found at i:4159759 original size:21 final size:22
Alignment explanation
Indices: 4159734--4159777 Score: 56
Period size: 20 Copynumber: 2.0 Consensus size: 22
4159724 GGATTTATAT
4159734 TATTCCGGGTGTG-TT-GTTGGA
1 TATT-CGGGTGTGTTTGGTTGGA
*
4159755 TATTCTGGTGTGTTTGGTTGGA
1 TATTCGGGTGTGTTTGGTTGGA
4159777 T
1 T
4159778 CCATATATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 6 0.30
22 7 0.35
ACGTcount: A:0.09, C:0.07, G:0.36, T:0.48
Consensus pattern (22 bp):
TATTCGGGTGTGTTTGGTTGGA
Found at i:4161072 original size:11 final size:11
Alignment explanation
Indices: 4161058--4161123 Score: 51
Period size: 11 Copynumber: 6.0 Consensus size: 11
4161048 ATATCAAAAC
4161058 AATAACAACAA
1 AATAACAACAA
**
4161069 AATAGTAACAA
1 AATAACAACAA
* * *
4161080 TATAATAGCAA
1 AATAACAACAA
** *
4161091 AATGTCATCAA
1 AATAACAACAA
*
4161102 AACAACAACAA
1 AATAACAACAA
4161113 AATAACAACAA
1 AATAACAACAA
4161124 GAAAAAGAAT
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.64, C:0.17, G:0.05, T:0.15
Consensus pattern (11 bp):
AATAACAACAA
Found at i:4161084 original size:22 final size:23
Alignment explanation
Indices: 4161058--4161116 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 23
4161048 ATATCAAAAC
4161058 AATAACAACAAAATAGT-AACAA
1 AATAACAACAAAATAGTCAACAA
* * * *
4161080 TATAATAGCAAAAT-GTCATCAA
1 AATAACAACAAAATAGTCAACAA
*
4161102 AACAACAACAAAATA
1 AATAACAACAAAATA
4161117 ACAACAAGAA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.63, C:0.15, G:0.05, T:0.17
Consensus pattern (23 bp):
AATAACAACAAAATAGTCAACAA
Found at i:4176594 original size:9 final size:9
Alignment explanation
Indices: 4176580--4176685 Score: 140
Period size: 9 Copynumber: 11.6 Consensus size: 9
4176570 TTTGGTTAAA
*
4176580 AATTACCTG
1 AATTACCCG
4176589 AATTACCCG
1 AATTACCCG
*
4176598 ATTTACCCG
1 AATTACCCG
4176607 AATTACCCG
1 AATTACCCG
*
4176616 ATTTACCCG
1 AATTACCCG
*
4176625 ATTTACCCG
1 AATTACCCG
*
4176634 ATTTACCCG
1 AATTACCCG
4176643 AATTACCCG
1 AATTACCCG
*
4176652 AAAATTACCCA
1 --AATTACCCG
4176663 AATTACCCG
1 AATTACCCG
4176672 AATTACCCG
1 AATTACCCG
4176681 AATTA
1 AATTA
4176686 AATCACTACA
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
9 80 0.91
11 8 0.09
ACGTcount: A:0.33, C:0.30, G:0.09, T:0.27
Consensus pattern (9 bp):
AATTACCCG
Found at i:4176714 original size:17 final size:17
Alignment explanation
Indices: 4176692--4176826 Score: 67
Period size: 17 Copynumber: 7.4 Consensus size: 17
4176682 ATTAAATCAC
*
4176692 TACATAATTAAAAGCAT
1 TACATAATTAAAAACAT
* * *
4176709 TACATAAATCTTTAAATCAC
1 TACAT-AA--TTAAAAACAT
*
4176729 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
** * *
4176746 TACATAAGTCCTTGAATCAC
1 TACATAA-T--TAAAAACAT
4176766 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
*
4176783 TACATAAGTCTTGAATTAAC--
1 TACATAA---TT-AA-AAACAT
4176803 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
4176820 TACATAA
1 TACATAA
4176827 GTCTCCATTT
Statistics
Matches: 87, Mismatches: 18, Indels: 26
0.66 0.14 0.20
Matches are distributed among these distances:
15 3 0.03
16 2 0.02
17 39 0.45
18 3 0.03
19 3 0.03
20 32 0.37
21 2 0.02
22 3 0.03
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.32
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:4176729 original size:37 final size:37
Alignment explanation
Indices: 4176683--4176830 Score: 224
Period size: 37 Copynumber: 4.0 Consensus size: 37
4176673 ATTACCCGAA
* *
4176683 TTAAATCACTACATAATTAAAAGCATTACATAAATCT
1 TTAAATCACTACATAATTAAAAACATTACATAAGTCT
* *
4176720 TTAAATCACTACATAATTAAAAATATTACATAAGTCC
1 TTAAATCACTACATAATTAAAAACATTACATAAGTCT
*
4176757 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTAAATCACTACATAATTAAAAACATTACATAAGTCT
* * *
4176794 TGAATTAACTACATAATTAAAAACATTACATAAGTCT
1 TTAAATCACTACATAATTAAAAACATTACATAAGTCT
4176831 CCATTTATAT
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 100 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (37 bp):
TTAAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:4176734 original size:20 final size:18
Alignment explanation
Indices: 4176683--4176735 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 18
4176673 ATTACCCGAA
4176683 TTAAATCACTACAT-AAT
1 TTAAATCACTACATAAAT
* * *
4176700 TAAAAGCATTACATAAATCT
1 TTAAATCACTACATAAA--T
4176720 TTAAATCACTACATAA
1 TTAAATCACTACATAA
4176736 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 11 0.41
18 2 0.07
20 14 0.52
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (18 bp):
TTAAATCACTACATAAAT
Found at i:4176863 original size:24 final size:24
Alignment explanation
Indices: 4176836--4176891 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
4176826 AGTCTCCATT
*
4176836 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
4176860 TATATCCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
4176884 TATCTCCA
1 TATATCCA
4176892 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:4179257 original size:20 final size:20
Alignment explanation
Indices: 4179232--4179273 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4179222 TCTGCAAGAA
4179232 AAAAAAGTATATAATAAATT
1 AAAAAAGTATATAATAAATT
4179252 AAAAAAGTATATAATAAATT
1 AAAAAAGTATATAATAAATT
4179272 AA
1 AA
4179274 TCAGCATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAAAGTATATAATAAATT
Found at i:4179528 original size:22 final size:22
Alignment explanation
Indices: 4179502--4179547 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
4179492 ATCAGTAATT
*
4179502 ATTTGTATGACTTTAGAACCTA
1 ATTTGCATGACTTTAGAACCTA
4179524 ATTTGCATGACTTTAGAACCTA
1 ATTTGCATGACTTTAGAACCTA
4179546 AT
1 AT
4179548 AATAATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (22 bp):
ATTTGCATGACTTTAGAACCTA
Found at i:4179550 original size:25 final size:25
Alignment explanation
Indices: 4179497--4179550 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 25
4179487 AATTCATCAG
* *
4179497 TAATTATTTGTATGACTTTAGAACC
1 TAATAATTTGCATGACTTTAGAACC
4179522 ---TAATTTGCATGACTTTAGAACC
1 TAATAATTTGCATGACTTTAGAACC
4179544 TAATAAT
1 TAATAAT
4179551 AATGATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
22 20 0.83
25 4 0.17
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (25 bp):
TAATAATTTGCATGACTTTAGAACC
Found at i:4180520 original size:17 final size:17
Alignment explanation
Indices: 4180479--4180522 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
4180469 CAGCCAGCAA
* *
4180479 GTTTAAAATTGGGTTGG
1 GTTTAAATTTGGGCTGG
4180496 GTTTAAATTTGGGCTGG
1 GTTTAAATTTGGGCTGG
4180513 GTTTAAATTT
1 GTTTAAATTT
4180523 AACTGGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.45
Consensus pattern (17 bp):
GTTTAAATTTGGGCTGG
Found at i:4187055 original size:30 final size:30
Alignment explanation
Indices: 4187013--4187167 Score: 124
Period size: 30 Copynumber: 5.2 Consensus size: 30
4187003 CAAAAAATAA
* *
4187013 AAAATTAT-ATTTTGGCCTCTAAACTTTTTT
1 AAAATT-TCATTTTGACCCCTAAACTTTTTT
* *
4187043 CAAATTTCATTTTGACCCCTAAA-TTTTCCT
1 AAAATTTCATTTTGACCCCTAAACTTTT-TT
4187073 AAAATTAT-ATTTTGACCCCTAAACTTTTTTT
1 AAAATT-TCATTTTGACCCCTAAAC-TTTTTT
* * * *
4187104 GAAATTACATTTTAACCCATAAAC-TTTTT
1 AAAATTTCATTTTGACCCCTAAACTTTTTT
* * *
4187133 -AAATTACATTATGACCCCTAAA-TTTTCTC
1 AAAATTTCATTTTGACCCCTAAACTTTT-TT
4187162 AAAATT
1 AAAATT
4187168 ATGTTTTGGA
Statistics
Matches: 102, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
28 22 0.22
29 11 0.11
30 44 0.43
31 21 0.21
32 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.44
Consensus pattern (30 bp):
AAAATTTCATTTTGACCCCTAAACTTTTTT
Found at i:4187078 original size:60 final size:62
Alignment explanation
Indices: 4187013--4187158 Score: 178
Period size: 61 Copynumber: 2.5 Consensus size: 62
4187003 CAAAAAATAA
* * * * *
4187013 AAAATTATATTTTGGCCTCTAAAC-TTTTTTCAAATTTCATTTTGACCCCTAAA-TTTTCCT
1 AAAATTATATTTTGACCCCTAAACTTTTTTTCAAATTACATTTTAACCCATAAACTTTTCCT
*
4187073 AAAATTATATTTTGACCCCTAAACTTTTTTTGAAATTACATTTTAACCCATAAACTTTT--T
1 AAAATTATATTTTGACCCCTAAACTTTTTTTCAAATTACATTTTAACCCATAAACTTTTCCT
* *
4187133 -AAATTACATTATGACCCCTAAA-TTTT
1 AAAATTATATTTTGACCCCTAAACTTTT
4187159 CTCAAAATTA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 4 0.05
59 20 0.26
60 23 0.30
61 25 0.33
62 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (62 bp):
AAAATTATATTTTGACCCCTAAACTTTTTTTCAAATTACATTTTAACCCATAAACTTTTCCT
Found at i:4187525 original size:17 final size:16
Alignment explanation
Indices: 4187487--4187527 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
4187477 CTTGAAGAAG
4187487 AAAAAAGGAAAAAAAA
1 AAAAAAGGAAAAAAAA
4187503 AGAAAAAGGAAAAAATATA
1 A-AAAAAGGAAAAAA-A-A
4187522 AAAAAA
1 AAAAAA
4187528 TTAAATAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.05
17 13 0.59
18 6 0.27
19 2 0.09
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (16 bp):
AAAAAAGGAAAAAAAA
Found at i:4187635 original size:16 final size:15
Alignment explanation
Indices: 4187614--4187651 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
4187604 ACCCAACAGC
4187614 CAAAAAAAAAAGTAAG
1 CAAAAAAAAAAG-AAG
4187630 CAAAAAAAAAAGAAG
1 CAAAAAAAAAAGAAG
4187645 -AAAAAAA
1 CAAAAAAA
4187652 GCAACACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 7 0.32
15 3 0.14
16 12 0.55
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.03
Consensus pattern (15 bp):
CAAAAAAAAAAGAAG
Found at i:4187700 original size:22 final size:25
Alignment explanation
Indices: 4187665--4187709 Score: 69
Period size: 22 Copynumber: 1.9 Consensus size: 25
4187655 ACACACAAAA
4187665 AAAACAAATCAGCCCAA-AAGAAAG
1 AAAACAAATCAGCCCAAGAAGAAAG
4187689 AAAA-AAA-CAGCCCAAGAAGAA
1 AAAACAAATCAGCCCAAGAAGAA
4187710 GCAAGAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 8 0.40
24 4 0.20
ACGTcount: A:0.64, C:0.20, G:0.13, T:0.02
Consensus pattern (25 bp):
AAAACAAATCAGCCCAAGAAGAAAG
Found at i:4187860 original size:14 final size:13
Alignment explanation
Indices: 4187836--4187881 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 13
4187826 AAAAAAAGGG
4187836 AAAAAGAAGAGAA
1 AAAAAGAAGAGAA
4187849 AAAAAGAGAGAGAA
1 AAAAAGA-AGAGAA
*
4187863 AAGAA-AA-AG-A
1 AAAAAGAAGAGAA
4187873 AAAAAGAAG
1 AAAAAGAAG
4187882 TCCAAGTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
10 5 0.18
11 4 0.14
12 1 0.04
13 8 0.29
14 10 0.36
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAGAA
Found at i:4188229 original size:17 final size:17
Alignment explanation
Indices: 4188207--4188266 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
4188197 TTTTTTGTGT
4188207 TTTCAAAAATCCTCGTG
1 TTTCAAAAATCCTCGTG
*
4188224 TTTCAAAAATCCTCATG
1 TTTCAAAAATCCTCGTG
* *
4188241 TTTTCAAAAATTCTGGTG
1 -TTTCAAAAATCCTCGTG
4188259 TTTCAAAA
1 TTTCAAAA
4188267 TTTTTGTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
17 24 0.63
18 14 0.37
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (17 bp):
TTTCAAAAATCCTCGTG
Found at i:4188299 original size:53 final size:53
Alignment explanation
Indices: 4188239--4188409 Score: 199
Period size: 52 Copynumber: 3.2 Consensus size: 53
4188229 AAAATCCTCA
* *
4188239 TGTTTTCAAAAATTCTGGTG-TTTCAAAATTTTTGTATTAAAAAAAATTTCCCG
1 TGTTTTCAAAAATTTTCGTGTTTTCAAAATTTTTGTATTAAAAAAAA-TTCCCG
* *
4188292 TGTTTTC-AAAATTTTCGTGTTTTCAAAATTTTTGTATTTAAAAAACTTCCCG
1 TGTTTTCAAAAATTTTCGTGTTTTCAAAATTTTTGTATTAAAAAAAATTCCCG
**
4188344 TGTTTT-TTAAATTTTCGTGTTTTCAAAAATTATTGTGT-TTCAAAAAAAATT-CCG
1 TGTTTTCAAAAATTTTCGTGTTTTC-AAAATT-TT-TGTATT-AAAAAAAATTCCCG
*
4188398 TGTTTTAAAAAA
1 TGTTTTCAAAAA
4188410 ATATTATGTC
Statistics
Matches: 102, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
52 38 0.37
53 37 0.36
54 13 0.13
55 14 0.14
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (53 bp):
TGTTTTCAAAAATTTTCGTGTTTTCAAAATTTTTGTATTAAAAAAAATTCCCG
Found at i:4188312 original size:17 final size:17
Alignment explanation
Indices: 4188290--4188388 Score: 85
Period size: 17 Copynumber: 5.8 Consensus size: 17
4188280 AAAAATTTCC
4188290 CGTGTTTTCAAAATTTT
1 CGTGTTTTCAAAATTTT
4188307 CGTGTTTTCAAAATTTT
1 CGTGTTTTCAAAATTTT
* * ** **
4188324 TGTATTTAAAAAACTTCC
1 CGTGTTTTCAAAA-TTTT
**
4188342 CGTGTTTTTTAAATTTT
1 CGTGTTTTCAAAATTTT
4188359 CGTGTTTTCAAAAATTATT
1 CGTGTTTTC-AAAATT-TT
4188378 -GTG-TTTCAAAA
1 CGTGTTTTCAAAA
4188389 AAAATTCCGT
Statistics
Matches: 64, Mismatches: 15, Indels: 7
0.74 0.17 0.08
Matches are distributed among these distances:
16 4 0.06
17 40 0.62
18 18 0.28
19 2 0.03
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
CGTGTTTTCAAAATTTT
Found at i:4188320 original size:35 final size:34
Alignment explanation
Indices: 4188198--4188322 Score: 90
Period size: 35 Copynumber: 3.6 Consensus size: 34
4188188 AAAATTGTGT
* *
4188198 TTTTTGTGTTTTCAAAA-ATCCTCGTGTTTCAAAAA
1 TTTTCGTGTTTTCAAAATTTCC-CGTGTTTC-AAAA
** * * **
4188233 TCCTCATGTTTTCAAAAATTCTGGTGTTTCAAAA
1 TTTTCGTGTTTTCAAAATTTCCCGTGTTTCAAAA
* * ***
4188267 TTTTTGTATTAAAAAAAATTTCCCGTGTTTTCAAAA
1 TTTTCGTGTT-TTCAAAATTTCCCGTG-TTTCAAAA
4188303 TTTTCGTGTTTTCAAAATTT
1 TTTTCGTGTTTTCAAAATTT
4188323 TTGTATTTAA
Statistics
Matches: 64, Mismatches: 23, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
34 9 0.14
35 37 0.58
36 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (34 bp):
TTTTCGTGTTTTCAAAATTTCCCGTGTTTCAAAA
Found at i:4188342 original size:52 final size:52
Alignment explanation
Indices: 4188239--4188408 Score: 200
Period size: 53 Copynumber: 3.2 Consensus size: 52
4188229 AAAATCCTCA
* * *
4188239 TGTTTTCAAAAATTCTGGTG-TTTCAAAATTTTTGTATTAAAAAAAATTTCCCG
1 TGTTTTC-AAAATTTTCGTGTTTTCAAAATTTTTGTATTTAAAAAAA-TTCCCG
*
4188292 TGTTTTCAAAATTTTCGTGTTTTCAAAATTTTTGTATTTAAAAAACTTCCCG
1 TGTTTTCAAAATTTTCGTGTTTTCAAAATTTTTGTATTTAAAAAAATTCCCG
** * *
4188344 TGTTTTTTAAATTTTCGTGTTTTCAAAAATTATTGTGTTTCAAAAAAAATT-CCG
1 TGTTTTCAAAATTTTCGTGTTTTC-AAAATTTTTGTATTT--AAAAAAATTCCCG
*
4188398 TGTTTTAAAAA
1 TGTTTTCAAAA
4188409 AATATTATGT
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
52 38 0.37
53 44 0.43
54 12 0.12
55 8 0.08
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (52 bp):
TGTTTTCAAAATTTTCGTGTTTTCAAAATTTTTGTATTTAAAAAAATTCCCG
Found at i:4188381 original size:18 final size:18
Alignment explanation
Indices: 4188360--4188414 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
4188350 TTAAATTTTC
*
4188360 GTGTTTTCAAAAATTATT
1 GTGTTTTCAAAAAATATT
*
4188378 GTG-TTTCAAAAAAAATT
1 GTGTTTTCAAAAAATATT
*
4188395 CCGTGTTTTAAAAAAATATT
1 --GTGTTTTCAAAAAATATT
4188415 ATGTCTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 12 0.40
18 3 0.10
19 3 0.10
20 12 0.40
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (18 bp):
GTGTTTTCAAAAAATATT
Found at i:4188393 original size:20 final size:20
Alignment explanation
Indices: 4188368--4188416 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
4188358 TCGTGTTTTC
*
4188368 AAAAATTATTGTGTTTCAAA
1 AAAAATTATCGTGTTTCAAA
* *
4188388 AAAAATT-CCGTGTTTTAAA
1 AAAAATTATCGTGTTTCAAA
4188407 AAAATATTAT
1 AAAA-ATTAT
4188417 GTCTTAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (20 bp):
AAAAATTATCGTGTTTCAAA
Found at i:4188407 original size:17 final size:17
Alignment explanation
Indices: 4188279--4188409 Score: 50
Period size: 17 Copynumber: 7.4 Consensus size: 17
4188269 TTTGTATTAA
4188279 AAAAAATTTCCCGTGTTTT
1 AAAAAA-TT-CCGTGTTTT
* * *
4188298 CAAAATTTTCGTGTTTT
1 AAAAAATTCCGTGTTTT
* **
4188315 -CAAAATT-TTTGTATTT
1 AAAAAATTCCGTGT-TTT
4188331 AAAAAACTTCCCGTGTTTT
1 AAAAAA-TT-CCGTGTTTT
** * *
4188350 TTAAATTTTCGTGTTTT
1 AAAAAATTCCGTGTTTT
* ** *
4188367 CAAAAATTATTGTGTTTCAA
1 AAAAAATT-CCGTGTTT--T
4188387 AAAAAATTCCGTGTTTT
1 AAAAAATTCCGTGTTTT
4188404 AAAAAA
1 AAAAAA
4188410 ATATTATGTC
Statistics
Matches: 81, Mismatches: 23, Indels: 18
0.66 0.19 0.15
Matches are distributed among these distances:
15 3 0.04
16 8 0.10
17 31 0.38
18 13 0.16
19 16 0.20
20 10 0.12
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (17 bp):
AAAAAATTCCGTGTTTT
Found at i:4192602 original size:16 final size:18
Alignment explanation
Indices: 4192563--4192596 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4192553 TAAGTTTATA
4192563 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
4192580 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
4192597 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:4198126 original size:17 final size:16
Alignment explanation
Indices: 4198099--4198131 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
4198089 TTTTAATTTG
4198099 TAACTTTTAATTTATT
1 TAACTTTTAATTTATT
4198115 TAACTATTTAATTTATT
1 TAACT-TTTAATTTATT
4198132 ACTTATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TAACTTTTAATTTATT
Found at i:4199456 original size:24 final size:24
Alignment explanation
Indices: 4199394--4199457 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
4199384 TTTCTAGAAG
* * *
4199394 ATTTAGCATTTATGAGTATAATAT
1 ATTTAACATTTATTAGCATAATAT
4199418 ATTTAACATTTATTAGCATAATAT
1 ATTTAACATTTATTAGCATAATAT
4199442 ATTTAAC-TTTGATTAG
1 ATTTAACATTT-ATTAG
4199458 AATTAGGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 3 0.08
24 33 0.92
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTTAACATTTATTAGCATAATAT
Found at i:4203844 original size:24 final size:24
Alignment explanation
Indices: 4203781--4203832 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4203771 TTTCTAGAAG
* * *
4203781 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
4203805 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
4203829 ATTT
1 ATTT
4203833 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:4211739 original size:2 final size:2
Alignment explanation
Indices: 4211732--4211756 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4211722 ATTCAGCCAA
4211732 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4211757 AATTCATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4212295 original size:18 final size:17
Alignment explanation
Indices: 4212268--4212302 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
4212258 ATTCATAATG
4212268 TTTAATATTATGTTATT
1 TTTAATATTATGTTATT
4212285 TTTACATATTATGTTATT
1 TTTA-ATATTATGTTATT
4212303 CATAACACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (17 bp):
TTTAATATTATGTTATT
Found at i:4213439 original size:16 final size:17
Alignment explanation
Indices: 4213420--4213477 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
4213410 TAAGGGGTTT
4213420 AAAATTTAATTTATACA
1 AAAATTTAATTTATACA
* * *
4213437 AAAATTCACATATATGACT
1 AAAATTTA-ATTTAT-ACA
*
4213456 TAAATATTAATTTATACA
1 AAAAT-TTAATTTATACA
4213474 AAAA
1 AAAA
4213478 AAAAAACATT
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
17 7 0.23
18 10 0.33
19 11 0.37
20 2 0.07
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (17 bp):
AAAATTTAATTTATACA
Found at i:4214617 original size:4 final size:4
Alignment explanation
Indices: 4214606--4214641 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
4214596 AAATATATAT
4214606 TTAA -TAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
4214642 ATATTCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:4223281 original size:18 final size:18
Alignment explanation
Indices: 4223235--4223282 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
4223225 TTTAGTAAAT
**
4223235 TTTTATTTTGATAATTTA
1 TTTTATTTTTTTAATTTA
*
4223253 TTTTATCTTTTTAATTT-
1 TTTTATTTTTTTAATTTA
4223270 TCTTTATTTTTTT
1 T-TTTATTTTTTT
4223283 CTGTTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTTTAATTTA
Found at i:4223383 original size:18 final size:18
Alignment explanation
Indices: 4223356--4223390 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4223346 GAAAAAATAT
4223356 TTTATCTTTTTAATTTTC
1 TTTATCTTTTTAATTTTC
* *
4223374 TTTATTTTTTTCATTTT
1 TTTATCTTTTTAATTTT
4223391 GTAATTAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATCTTTTTAATTTTC
Found at i:4223706 original size:21 final size:22
Alignment explanation
Indices: 4223674--4223717 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
4223664 GTAAAGGGGG
4223674 AAAATTAGAG-TTTTACATGGA
1 AAAATTAGAGTTTTTACATGGA
4223695 AAAATATA-AGTTTTTACATGGA
1 AAAAT-TAGAGTTTTTACATGGA
4223717 A
1 A
4223718 TTGAGTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (22 bp):
AAAATTAGAGTTTTTACATGGA
Found at i:4235408 original size:20 final size:20
Alignment explanation
Indices: 4235367--4235421 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
4235357 AAAGAATAAT
4235367 AAATA-ATAAATTTT-AGAA
1 AAATATATAAATTTTAAGAA
*
4235385 AAAT-TATTAAATTTTAATAA
1 AAATATA-TAAATTTTAAGAA
*
4235405 AAATATAAAAATTTTAA
1 AAATATATAAATTTTAA
4235422 ATTTATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 5 0.16
19 8 0.26
20 16 0.52
21 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATATATAAATTTTAAGAA
Found at i:4235431 original size:18 final size:16
Alignment explanation
Indices: 4235410--4235448 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
4235400 AATAAAAATA
*
4235410 TAAAAATTTTAAATTTAT
1 TAAAAATTAT-AATTT-T
4235428 TAAAAATTATAATTTT
1 TAAAAATTATAATTTT
4235444 TAAAA
1 TAAAA
4235449 GAAAATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
18 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAAAATTATAATTTT
Found at i:4235444 original size:25 final size:27
Alignment explanation
Indices: 4235384--4235447 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
4235374 AAATTTTAGA
*
4235384 AAAATTATTAAATTTTAATAAAAATAT
1 AAAATTTTTAAATTTTAATAAAAATAT
* *
4235411 AAAAATTTTAAA-TTTATTAAAAAT-T
1 AAAATTTTTAAATTTTAATAAAAATAT
*
4235436 ATAATTTTTAAA
1 AAAATTTTTAAA
4235448 AGAAAATCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 11 0.34
26 11 0.34
27 10 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AAAATTTTTAAATTTTAATAAAAATAT
Found at i:4240460 original size:14 final size:14
Alignment explanation
Indices: 4240441--4240479 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4240431 TTGTTTCACT
4240441 GAAAATGACTTCCG
1 GAAAATGACTTCCG
* *
4240455 GAAAATGATTTCTG
1 GAAAATGACTTCCG
*
4240469 AAAAATGACTT
1 GAAAATGACTT
4240480 ATTTTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:4241185 original size:10 final size:9
Alignment explanation
Indices: 4241156--4241181 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4241146 ATTTTATGCT
4241156 AATATTTTA
1 AATATTTTA
4241165 AATATTTTA
1 AATATTTTA
4241174 AATATTTT
1 AATATTTT
4241182 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Found at i:4248558 original size:22 final size:22
Alignment explanation
Indices: 4248506--4248558 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
4248496 AGTTAGTTGA
** *
4248506 AATTTAAATCTAAATTTTAATT
1 AATTTAAAAATAAATTTAAATT
*
4248528 -ATCTAAAAAATAAATTTAAATT
1 AAT-TTAAAAATAAATTTAAATT
4248550 AATTTAAAA
1 AATTTAAAA
4248559 TAATTTCAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 2 0.08
22 20 0.83
23 2 0.08
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTTAAAAATAAATTTAAATT
Found at i:4254445 original size:158 final size:154
Alignment explanation
Indices: 4254269--4254554 Score: 400
Period size: 158 Copynumber: 1.8 Consensus size: 154
4254259 TTTTAATAAA
* * *
4254269 AATTTTATAGCTTTTTTTTAATAAATTTTGTTTATAATTTTTATG-TTTTTAAATATTTTTAAAA
1 AATTTTATAACTTTTTTTTAATAAATTTTGTTTATAATTTTTATGATTTTT-AATAATCTT-AAA
* * *
4254333 TT-TTAAA-GGACTTAATTATTCTTTTTTTAATTTGTTACTAAGGCCTTTTTGA-TCCTTTAGTC
64 TTATAAAAGGGA-TT-A--ATT-TTTTTTTAATTTGTTACTAAGGCATTTTTGAGT-CTTTAGCC
4254395 TTATTAGTTTCAAGATTTTCTATTTTACTTCC
123 TTATTAGTTTCAAGATTTTCTATTTTACTTCC
*
4254427 AATTTTATAACTTTTTTTTTATAAATTTTGTTTATAATTTTTATGATTTTTAATAATCTTAAATT
1 AATTTTATAACTTTTTTTTAATAAATTTTGTTTATAATTTTTATGATTTTTAATAATCTTAAATT
*
4254492 ATAAAAGGGATTAATTTTTTTTTAGTTTGTTACTAAGGCATTTTTGAGTCTTTAGCCTTATTA
66 ATAAAAGGGATTAATTTTTTTTTAATTTGTTACTAAGGCATTTTTGAGTCTTTAGCCTTATTA
4254555 ATTTTTAAAG
Statistics
Matches: 116, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
154 42 0.36
155 4 0.03
157 6 0.05
158 56 0.48
159 8 0.07
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.56
Consensus pattern (154 bp):
AATTTTATAACTTTTTTTTAATAAATTTTGTTTATAATTTTTATGATTTTTAATAATCTTAAATT
ATAAAAGGGATTAATTTTTTTTTAATTTGTTACTAAGGCATTTTTGAGTCTTTAGCCTTATTAGT
TTCAAGATTTTCTATTTTACTTCC
Found at i:4254448 original size:14 final size:13
Alignment explanation
Indices: 4254429--4254468 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
4254419 TTACTTCCAA
4254429 TTTTATAACTTTTT
1 TTTTATAA-TTTTT
*
4254443 TTTTATAAATTTT
1 TTTTATAATTTTT
*
4254456 GTTTATAATTTTT
1 TTTTATAATTTTT
4254469 ATGATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTATAATTTTT
Found at i:4255123 original size:21 final size:22
Alignment explanation
Indices: 4255099--4255139 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
4255089 AATCAAGCCC
4255099 AATATTAGT-ATA-TTAATATCA
1 AATATTA-TAATATTTAATATCA
4255120 AATATTATAATATTTAATAT
1 AATATTATAATATTTAATAT
4255140 TATTAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 10 0.56
22 7 0.39
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AATATTATAATATTTAATATCA
Found at i:4255263 original size:14 final size:15
Alignment explanation
Indices: 4255237--4255266 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4255227 ATTTAATTTT
4255237 AATAATAAATTTTAA
1 AATAATAAATTTTAA
4255252 AATAAT-AATTTTAA
1 AATAATAAATTTTAA
4255266 A
1 A
4255267 TCTTAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAATAAATTTTAA
Found at i:4255267 original size:13 final size:13
Alignment explanation
Indices: 4255230--4255267 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
4255220 TCTTACAATT
4255230 TAATTTT-AATAA
1 TAATTTTAAATAA
4255242 TAAATTTTAAAATAA
1 T-AATTTT-AAATAA
4255257 TAATTTTAAAT
1 TAATTTTAAAT
4255268 CTTAAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 6 0.26
15 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATTTTAAATAA
Found at i:4255387 original size:23 final size:23
Alignment explanation
Indices: 4255360--4255412 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
4255350 ATTAATAATA
4255360 AATATTTTATAGTATA-AAATATG
1 AATATTTTA-AGTATATAAATATG
*
4255383 AATATTTTAATTATATAAATATG
1 AATATTTTAAGTATATAAATATG
*
4255406 AGTATTT
1 AATATTT
4255413 GTCAATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (23 bp):
AATATTTTAAGTATATAAATATG
Found at i:4261526 original size:15 final size:13
Alignment explanation
Indices: 4261498--4261539 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
4261488 TATTATTAAC
4261498 AAATATTTTAATA
1 AAATATTTTAATA
4261511 AAATA-TTTAATA
1 AAATATTTTAATA
4261523 ATAATACTTTTCAATA
1 A-AATA-TTTT-AATA
4261539 A
1 A
4261540 TCTTTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.32
13 9 0.36
15 3 0.12
16 5 0.20
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATATTTTAATA
Found at i:4282149 original size:3 final size:3
Alignment explanation
Indices: 4282137--4282199 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
4282127 CATGTATGTT
4282137 ATA A-A 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
4282184 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
4282200 ACAGTTTAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4285239 original size:33 final size:33
Alignment explanation
Indices: 4285170--4285267 Score: 115
Period size: 33 Copynumber: 2.9 Consensus size: 33
4285160 GCTCCTACTT
4285170 ATGCTTCTCCTAGAAGATCTTACAGGACTTCCGCTA
1 ATGCTTCTCCT---AGATCTTACAGGACTTCCGCTA
** * *
4285206 ATGCTTCTCCTAGATCTTATGGGGCTTCTGCTA
1 ATGCTTCTCCTAGATCTTACAGGACTTCCGCTA
* *
4285239 ATGCTTCTCCGAGATCTTGCAGGACTTCC
1 ATGCTTCTCCTAGATCTTACAGGACTTCC
4285268 ACTTCTGCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
33 41 0.79
36 11 0.21
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (33 bp):
ATGCTTCTCCTAGATCTTACAGGACTTCCGCTA
Found at i:4289178 original size:373 final size:376
Alignment explanation
Indices: 4288448--4289193 Score: 1000
Period size: 373 Copynumber: 2.0 Consensus size: 376
4288438 ATCTAAGAGT
* * * * *
4288448 CAAGGAAAGAACCTATTACAATGTTATCCAGGTATAATAACCCTAACATCTAACCTGAAATTAGG
1 CAAGGAAAGAACCTAATACAATGTGATCCAGGTATAATAACCCTAACACCAAACCTGAAATCAGG
* * * * * *
4288513 TCCAAAATAATTTGATAAATTCCATATTATATAGCAAAAATTAAAAATTGAAGATAAAGATTTGA
66 TCCAAAACAAATTGACAAATTCCATATTATATAGAAAAAATTAAAAATTAAAAATAAAGATTTGA
*
4288578 GATTTTACGCACAAAGTGAATATAAATACATTAAACACATATGCATTAGCAACACAATTATAACT
131 GATTTTA-GCACAAAGTCAATATAAATA-ATTAAACACA-ATGCATTAGCAACACAATTATAACT
*
4288643 TGATAACAACAATAGAAATTTTGATCACTTATGGAGAGTACAATACTATGTATATTAGCATGTAT
193 TGATAACAACAATAGAAATTTTGATCACTTATGGAGAGTACAATACTATGTATATTAGCATGCAT
*
4288708 GACCACTTCCATCACGTACAGGATTATAATCTAGTTAGAATATTATTAAATTTTCATGCACAAGT
258 GACCACTTCCATCACG-ACAGGATTATAATCTAGTTAGAATATTATTAAATTTTCATGAACAAGT
* *
4288773 AGTAATTACAAACAAAAGCATGTGCGTAACACAAATAGTAAAAAGTTTCTACAGC
322 AGTAATTACAAACAAAAGCATGTGCATAACACAAATACTAAAAAGTTTCTACAGC
* * *
4288828 CAAGGAAAGAACTTAATACAATGTGATCCTGGTATAAATAACCCTAATACCAAACCTGAAATCAG
1 CAAGGAAAGAACCTAATACAATGTGATCCAGGTAT-AATAACCCTAACACCAAACCTGAAATCAG
* *
4288893 GTCCAAAACAAATTGACAAATTCCATATTATATAGAAACAAATTATAAATTAAAAATAAAGTTTT
65 GTCCAAAACAAATTGACAAATTCCATATTATATAGAAA-AAATTAAAAATTAAAAATAAAGATTT
* * * *
4288958 GATATTTT-G-ACCAATTCACA-A-GAAT-A-TAAACAC-ATGCATTAGCAACACAATTATAACT
129 GAGATTTTAGCACAAAGTCA-ATATAAATAATTAAACACAATGCATTAGCAACACAATTATAACT
*
4289016 TGATAACAA-AATTAGAGATTTTGATCACTTGA-GGAG-GATACAATACTACT-TATATTAGCAT
193 TGATAACAACAA-TAGAAATTTTGATCACTT-ATGGAGAG-TACAATACTA-TGTATATTAGCAT
4289077 GCATGACCACTTCCATCAC-ACA-GATTATAATCTAGTTAGAATATTATT-AATTTTCCATGAAC
254 GCATGACCACTTCCATCACGACAGGATTATAATCTAGTTAGAATATTATTAAATTTT-CATGAAC
*
4289139 AGAG-AGTAATTACAAACAACAAAAGCATGTGCATAACACAAATACTAAAACGTTT
318 A-AGTAGTAATTAC--A-AACAAAAGCATGTGCATAACACAAATACTAAAAAGTTT
4289194 AAAACATTTA
Statistics
Matches: 327, Mismatches: 27, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
369 6 0.02
370 42 0.13
371 5 0.02
372 4 0.01
373 129 0.39
374 2 0.01
375 7 0.02
376 1 0.00
378 3 0.01
379 7 0.02
380 33 0.10
381 59 0.18
382 29 0.09
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.29
Consensus pattern (376 bp):
CAAGGAAAGAACCTAATACAATGTGATCCAGGTATAATAACCCTAACACCAAACCTGAAATCAGG
TCCAAAACAAATTGACAAATTCCATATTATATAGAAAAAATTAAAAATTAAAAATAAAGATTTGA
GATTTTAGCACAAAGTCAATATAAATAATTAAACACAATGCATTAGCAACACAATTATAACTTGA
TAACAACAATAGAAATTTTGATCACTTATGGAGAGTACAATACTATGTATATTAGCATGCATGAC
CACTTCCATCACGACAGGATTATAATCTAGTTAGAATATTATTAAATTTTCATGAACAAGTAGTA
ATTACAAACAAAAGCATGTGCATAACACAAATACTAAAAAGTTTCTACAGC
Done.