Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 100 of 206
Found at i:29291966 original size:51 final size:50
Alignment explanation
Indices: 29291836--29291966 Score: 147
Period size: 51 Copynumber: 2.6 Consensus size: 50
29291826 ATACACGCAG
* * * * *
29291836 TAGCCTTCACATAGTACTACACACGTGATCACGCTTTTCGGTTCACGTAG
1 TAGCCTACACATAGTACTACACACGTGACCACGCTTCTCGGTTCACATAA
* *
29291886 TAGCCTACACATAGTACTACACACATGACCAAGGCCTTCT-GGTTCACATAA
1 TAGCCTACACATAGTACTACACACGTGACC-ACG-CTTCTCGGTTCACATAA
* * *
29291937 TAGCCTGCACTTAGTACTACACATGTGACC
1 TAGCCTACACATAGTACTACACACGTGACC
29291967 GTTATTTATC
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 27 0.40
51 37 0.54
52 4 0.06
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (50 bp):
TAGCCTACACATAGTACTACACACGTGACCACGCTTCTCGGTTCACATAA
Found at i:29295240 original size:21 final size:21
Alignment explanation
Indices: 29295214--29295257 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
29295204 TGTAATGCAC
29295214 TTGGAACATACCTTTTCGACA
1 TTGGAACATACCTTTTCGACA
29295235 TTGGAACATACCTTTTCGACA
1 TTGGAACATACCTTTTCGACA
29295256 TT
1 TT
29295258 CTTCTTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (21 bp):
TTGGAACATACCTTTTCGACA
Found at i:29303577 original size:113 final size:112
Alignment explanation
Indices: 29303457--29303665 Score: 253
Period size: 113 Copynumber: 1.9 Consensus size: 112
29303447 TCACATTCTA
* * **
29303457 ACTTCGAAAGAATTTGA-TCAAATACATTTTTATTGAT-ACTTTGCAAAAACTATCGATGTCT-C
1 ACTTCGAAAGAATTTGAGT-AAACACATTTTTATCGATGA-TTTGCAAAAACTATCGATACCTAC
* *
29303519 AAGAAAAATTATTGATACCTTTTTCAGTATTGATACCAAAATAGCTTAGTG
64 -A-AAAAATTATTGATACATTTTTCAGCATTGATACCAAAATAGCTTAGTG
* * **
29303570 ACTTCGAAGGAATTTGAGTAAACATATTTTTATCGATGATTTGCAAAAGGTATCGATACCTACAA
1 ACTTCGAAAGAATTTGAGTAAACACATTTTTATCGATGATTTGCAAAAACTATCGATACCTACAA
* *
29303635 AATATTATTGATACATTTTTCGGCATTGATA
66 AAAATTATTGATACATTTTTCAGCATTGATA
29303666 TGAAAAATGA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
112 28 0.35
113 50 0.62
114 3 0.04
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (112 bp):
ACTTCGAAAGAATTTGAGTAAACACATTTTTATCGATGATTTGCAAAAACTATCGATACCTACAA
AAAATTATTGATACATTTTTCAGCATTGATACCAAAATAGCTTAGTG
Found at i:29312620 original size:21 final size:22
Alignment explanation
Indices: 29312576--29312616 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
29312566 TAATATTTTA
*
29312576 AAATATATATATAAAATACAAT
1 AAATATATATATAAAATAAAAT
29312598 AAATA-ATATA-AAAATAAAA
1 AAATATATATATAAAATAAAA
29312617 ATAATTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATATATATATAAAATAAAAT
Found at i:29312768 original size:9 final size:9
Alignment explanation
Indices: 29312754--29312800 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
29312744 ATGTAAATTT
29312754 TTTTATATA
1 TTTTATATA
29312763 TTTTAT-TA
1 TTTTATATA
* *
29312771 ATTTATACA
1 TTTTATATA
*
29312780 TTTTA-AAA
1 TTTTATATA
29312788 TTTTATATA
1 TTTTATATA
29312797 TTTT
1 TTTT
29312801 TAATTTCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
8 14 0.45
9 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTATATA
Found at i:29312777 original size:17 final size:17
Alignment explanation
Indices: 29312754--29312800 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
29312744 ATGTAAATTT
*
29312754 TTTTATATATTTTATTAA
1 TTTTATATATTTTA-AAA
*
29312772 -TTTATACATTTTAAAA
1 TTTTATATATTTTAAAA
29312788 TTTTATATATTTT
1 TTTTATATATTTT
29312801 TAATTTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 23 0.92
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATATATTTTAAAA
Found at i:29312799 original size:25 final size:24
Alignment explanation
Indices: 29312762--29312812 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
29312752 TTTTTTATAT
*
29312762 ATTTTATTAATTTATACATTTTAAA
1 ATTTTATTAATTTATA-ATTTCAAA
*
29312787 ATTTTA-TATATTTTTAATTTCAAA
1 ATTTTATTA-ATTTATAATTTCAAA
29312811 AT
1 AT
29312813 AATAATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTATTAATTTATAATTTCAAA
Found at i:29313495 original size:22 final size:24
Alignment explanation
Indices: 29313462--29313508 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
29313452 CGTCATACTG
29313462 ATATGTTACCA-T-GTGTCACCATC
1 ATATGTTACCATTAGTGTCA-CATC
29313485 ATAT-TTACCATTAGTGTCACATC
1 ATATGTTACCATTAGTGTCACATC
29313508 A
1 A
29313509 ACACAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 10 0.45
24 6 0.27
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (24 bp):
ATATGTTACCATTAGTGTCACATC
Found at i:29318149 original size:59 final size:59
Alignment explanation
Indices: 29318057--29318181 Score: 223
Period size: 59 Copynumber: 2.1 Consensus size: 59
29318047 CATTGTAAAC
29318057 AAATTATATTTTTTTGTACCAATCAAAACATTTTGTAAAAACGCAAGAGTTTGTTAGTA
1 AAATTATATTTTTTTGTACCAATCAAAACATTTTGTAAAAACGCAAGAGTTTGTTAGTA
* * *
29318116 AAATTATATTTTTTTGTACCAATCGAAACATTTTGTAAAAACGCTATAGTTTGTTAGTA
1 AAATTATATTTTTTTGTACCAATCAAAACATTTTGTAAAAACGCAAGAGTTTGTTAGTA
29318175 AAATTAT
1 AAATTAT
29318182 TAATTGTTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (59 bp):
AAATTATATTTTTTTGTACCAATCAAAACATTTTGTAAAAACGCAAGAGTTTGTTAGTA
Found at i:29318281 original size:21 final size:21
Alignment explanation
Indices: 29318245--29318471 Score: 321
Period size: 21 Copynumber: 10.7 Consensus size: 21
29318235 GGTTGGGTTT
29318245 AGGGTTAGGG-TTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
29318265 AGGGTTAGGGTTTTTAAATTA
1 AGGGTTAGGGTTTTTAAGTTA
*
29318286 AGGGTTAAGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
29318307 AGGGTTAGGGTTTTTAAATTA
1 AGGGTTAGGGTTTTTAAGTTA
*
29318328 AGGGTTAAGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
29318349 AGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
* *
29318370 AGGGTTTATGGTTTTTAAGTTG
1 AGGG-TTAGGGTTTTTAAGTTA
***
29318392 TTTGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
29318413 AGGGTTAAGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
29318434 AGGGTTTAGGGTTTTTAAGTTAA
1 AGGG-TTAGGGTTTTTAAGTT-A
*
29318457 AGTGTTAGGGTTTTT
1 AGGGTTAGGGTTTTT
29318472 GTTAGGGTTT
Statistics
Matches: 182, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.05
21 126 0.69
22 42 0.23
23 4 0.02
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (21 bp):
AGGGTTAGGGTTTTTAAGTTA
Found at i:29318416 original size:64 final size:64
Alignment explanation
Indices: 29318245--29318471 Score: 334
Period size: 64 Copynumber: 3.6 Consensus size: 64
29318235 GGTTGGGTTT
*
29318245 AGGG-TTAGGG-TTTTAAGTTAAGGGTTAGGGTTTTTAAATTAAGGGTTAAGGTTTTTAAGTTA
1 AGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTTAAGTTA
* * *
29318307 AGGG-TTAGGGTTTTTAAATTAAGGGTTAAGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTA
1 AGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTTAAGTTA
* ****
29318370 AGGGTTTATGGTTTTTAAGTTGTTTGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTTAAGTTA
1 AGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTTAAGTTA
*
29318434 AGGGTTTAGGGTTTTTAAGTTAAAGTGTTAGGGTTTTT
1 AGGGTTTAGGGTTTTTAAGTT-AAGGGTTAGGGTTTTT
29318472 GTTAGGGTTT
Statistics
Matches: 146, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
62 10 0.07
63 52 0.36
64 71 0.49
65 13 0.09
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (64 bp):
AGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTTAAGTTA
Found at i:29318565 original size:21 final size:21
Alignment explanation
Indices: 29318541--29318590 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
29318531 ATAAATTAGT
29318541 TTAGGGTTTTTAAATTAAGGG
1 TTAGGGTTTTTAAATTAAGGG
* *
29318562 TTAGAGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAATTAAGGG
29318583 TTAGGGTT
1 TTAGGGTT
29318591 AGGGTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (21 bp):
TTAGGGTTTTTAAATTAAGGG
Found at i:29319157 original size:17 final size:19
Alignment explanation
Indices: 29319125--29319167 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
29319115 GACTCGAAAA
* *
29319125 AGGAAACATATAA-GGGTT
1 AGGATACATATAAGGGGCT
29319143 AGGATACAT-TAAGGGGCT
1 AGGATACATATAAGGGGCT
29319161 AGGATAC
1 AGGATAC
29319168 GCACCTGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (19 bp):
AGGATACATATAAGGGGCT
Found at i:29321143 original size:11 final size:11
Alignment explanation
Indices: 29321127--29321168 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
29321117 ATTTGGAAGG
29321127 AAATTGAGAGC
1 AAATTGAGAGC
*
29321138 AAATTGAGAAC
1 AAATTGAGAGC
* *
29321149 AATTTGAGAGA
1 AAATTGAGAGC
29321160 AAATTGAGA
1 AAATTGAGA
29321169 AAATAATTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.21
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:29340498 original size:27 final size:27
Alignment explanation
Indices: 29340479--29340702 Score: 250
Period size: 27 Copynumber: 8.3 Consensus size: 27
29340469 GGTATAACAG
* *
29340479 TCATTGTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCAA
** *
29340506 TCATCCTACCCTATGTGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCAA
*
29340533 TCATTTTACCCTATGAGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCAA
***
29340560 TCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCAA
* ***
29340587 TGATTTTACCCTATAATGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCAA
* *
29340614 TCATTTTACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCAA
* * ***
29340641 TCATTTTACCCTATAGTGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCAA
**
29340668 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCAA
29340695 TCATTTTA
1 TCATTTTA
29340703 TTGACCTCTC
Statistics
Matches: 167, Mismatches: 30, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 167 1.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCAA
Found at i:29340597 original size:81 final size:81
Alignment explanation
Indices: 29340479--29340702 Score: 315
Period size: 81 Copynumber: 2.8 Consensus size: 81
29340469 GGTATAACAG
* * * **
29340479 TCATTGTACCCTATGGGGGTATTTCGATCATCCTACCCTATGTGGGTATTTCAATCATTTTACCC
1 TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGTGGGTATTTCAATCATTTTACCC
29340544 TATGAGGGTATTTCAA
66 TATGAGGGTATTTCAA
* *
29340560 TCATTTTACCCTATGGGGGTATTTTGGTGATTTTACCCTATAAT-GGTATTTCAATCATTTTACC
1 TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTAT-GTGGGTATTTCAATCATTTTACC
*
29340624 CTATGAGGGTATTTCGA
65 CTATGAGGGTATTTCAA
* * * **
29340641 TCATTTTACCCTATAGTGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTA
1 TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGTGGGTATTTCAATCATTTTA
29340703 TTGACCTCTC
Statistics
Matches: 126, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
81 125 0.99
82 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGTGGGTATTTCAATCATTTTACCC
TATGAGGGTATTTCAA
Found at i:29345459 original size:8 final size:8
Alignment explanation
Indices: 29345446--29345483 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
29345436 AATGTTAATT
29345446 TTATTTAA
1 TTATTTAA
29345454 TTATTTAA
1 TTATTTAA
29345462 TTATTTAA
1 TTATTTAA
*
29345470 TTTATTGAA
1 -TTATTTAA
29345479 TTATT
1 TTATT
29345484 AATATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (8 bp):
TTATTTAA
Found at i:29345486 original size:16 final size:17
Alignment explanation
Indices: 29345446--29345483 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
29345436 AATGTTAATT
*
29345446 TTATTTAA-TTATTTAA
1 TTATTTAATTTATTGAA
29345462 TTATTTAATTTATTGAA
1 TTATTTAATTTATTGAA
29345479 TTATT
1 TTATT
29345484 AATATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTATTTAATTTATTGAA
Found at i:29350900 original size:100 final size:99
Alignment explanation
Indices: 29350719--29350909 Score: 231
Period size: 100 Copynumber: 1.9 Consensus size: 99
29350709 TTGTAGGCTA
* *
29350719 AATGCATTAGCTGCTCATCAACAGATTCATTGGATGGCATTAAAGGAAGACATGCACCTGGACCA
1 AATGCATTAGCTGCTCACCAACAGATTCATTGGACGGCATTAAAGGAAGACATGCACCTGGACCA
29350784 CATGCACCAAGAAGCTGCTGTTTGCTTATAGCTG
66 CATGCACCAAGAAGCTGCTGTTTGCTTATAGCTG
* * * * * * * * *
29350818 AATGTATTGGCTGCTCACCAATAGGTTCATTGGACGTCAGTTAAGGGAGGACATGCGCTTGGACA
1 AATGCATTAGCTGCTCACCAACAGATTCATTGGACGGCA-TTAAAGGAAGACATGCACCTGGAC-
* * *
29350883 TATATGCACCAAG-AGCTGTTGTTTGCT
64 CACATGCACCAAGAAGCTGCTGTTTGCT
29350910 CCCTCCCAAG
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
99 32 0.42
100 33 0.43
101 11 0.14
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (99 bp):
AATGCATTAGCTGCTCACCAACAGATTCATTGGACGGCATTAAAGGAAGACATGCACCTGGACCA
CATGCACCAAGAAGCTGCTGTTTGCTTATAGCTG
Found at i:29358104 original size:51 final size:51
Alignment explanation
Indices: 29358024--29358125 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
29358014 GAGATTTAGT
* * *
29358024 GTGATGCCTCAGGTATAGGTATTGGGGCTGTGTTGACTCAAGATGGGCATC
1 GTGATGCCTCAGGTATAGGTATTGAGGCTGTGCTGACTCAAGATAGGCATC
29358075 GTGATGCCTCAGGTATAGGTATTGAGGCTGTGCTGACTCAAGATAGGCATC
1 GTGATGCCTCAGGTATAGGTATTGAGGCTGTGCTGACTCAAGATAGGCATC
29358126 CTATAGCCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (51 bp):
GTGATGCCTCAGGTATAGGTATTGAGGCTGTGCTGACTCAAGATAGGCATC
Found at i:29365929 original size:13 final size:13
Alignment explanation
Indices: 29365911--29365935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29365901 TTGTCGTGTT
29365911 ATTTAGTTAATTA
1 ATTTAGTTAATTA
29365924 ATTTAGTTAATT
1 ATTTAGTTAATT
29365936 TTAGTTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTTAGTTAATTA
Found at i:29374570 original size:23 final size:22
Alignment explanation
Indices: 29374505--29374570 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 22
29374495 CGGCTTTACA
*
29374505 TTTATTTGTTTTATTTATG-TTAT
1 TTTA-TTGTTTTATTT-TGATTTT
*
29374528 TTT-TTGTTGTACTTTT-ATTTT
1 TTTATTGTTTTA-TTTTGATTTT
29374549 TTTAGTTGTTTTATTTTGATTT
1 TTTA-TTGTTTTATTTTGATTT
29374571 GTGATACTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
21 14 0.40
22 7 0.20
23 14 0.40
ACGTcount: A:0.14, C:0.02, G:0.11, T:0.74
Consensus pattern (22 bp):
TTTATTGTTTTATTTTGATTTT
Found at i:29377279 original size:13 final size:13
Alignment explanation
Indices: 29377261--29377285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29377251 TGTCGTTTTC
29377261 TTTAGTTAATTAA
1 TTTAGTTAATTAA
29377274 TTTAGTTAATTA
1 TTTAGTTAATTA
29377286 TAGTTTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TTTAGTTAATTAA
Found at i:29386974 original size:40 final size:40
Alignment explanation
Indices: 29386929--29387125 Score: 234
Period size: 40 Copynumber: 4.9 Consensus size: 40
29386919 GAATTTAGGA
* * * *
29386929 GTATCGTAGTACAAATAGGGGCACGTATGTGCATTCAGGG
1 GTATCGAAGTACAAACAAGGGCACTTATGTGCATTCAGGG
* ** * *
29386969 GTATCGAAGTACAAATAAAAGCATTTAGGTGCATTCAGGG
1 GTATCGAAGTACAAACAAGGGCACTTATGTGCATTCAGGG
* * * *
29387009 GTACCAAAGTACAAACATGGGCACTTATGTGCATTTAGGG
1 GTATCGAAGTACAAACAAGGGCACTTATGTGCATTCAGGG
* *
29387049 GTATCAAAGTACAAACAGGGGCACTTATGTGCATTCAGGG
1 GTATCGAAGTACAAACAAGGGCACTTATGTGCATTCAGGG
*
29387089 GTA-CAGAAGTACAAACAATGGCACTTATGTGCATTCA
1 GTATC-GAAGTACAAACAAGGGCACTTATGTGCATTCA
29387126 TATATATACT
Statistics
Matches: 134, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 1 0.01
40 133 0.99
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (40 bp):
GTATCGAAGTACAAACAAGGGCACTTATGTGCATTCAGGG
Found at i:29392494 original size:21 final size:21
Alignment explanation
Indices: 29392468--29392509 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29392458 TAAAAAATCA
*
29392468 AAATTTACATTAA-ATAATTTT
1 AAATTTAAATTAATAT-ATTTT
29392489 AAATTTAAATTAATATATTTT
1 AAATTTAAATTAATATATTTT
29392510 CATTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATTTAAATTAATATATTTT
Found at i:29394497 original size:30 final size:30
Alignment explanation
Indices: 29394461--29394540 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
29394451 TAACTTTGAA
* *
29394461 ATAATGTCAGCTTATGTGAGCAATAC-AATT
1 ATAATGTCAGCTTGTGTGAGCAACACTAA-T
* *
29394491 ATAATGTTAGCTTGTGTGAGCAACCCTAAT
1 ATAATGTCAGCTTGTGTGAGCAACACTAAT
*
29394521 ATATTGTCAGCTTGTGTGAG
1 ATAATGTCAGCTTGTGTGAG
29394541 TAATTTATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 41 0.95
31 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (30 bp):
ATAATGTCAGCTTGTGTGAGCAACACTAAT
Found at i:29401939 original size:30 final size:30
Alignment explanation
Indices: 29401882--29401939 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29401872 CTAGGCATTT
** **
29401882 CCACACAGGCTAGCCACAGGCTTATGTGAG
1 CCACACAGGCTAGCCACACACCCATGTGAG
29401912 CCACACAGGCTAGCCACACACCCATGTG
1 CCACACAGGCTAGCCACACACCCATGTG
29401940 TCAGCCCGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.36, G:0.22, T:0.14
Consensus pattern (30 bp):
CCACACAGGCTAGCCACACACCCATGTGAG
Found at i:29403547 original size:3 final size:3
Alignment explanation
Indices: 29403539--29403573 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29403529 GTAGATCTAC
29403539 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29403574 GTTGTTGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29403578 original size:3 final size:3
Alignment explanation
Indices: 29403572--29403623 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
29403562 ATTATTATTA
*
29403572 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
29403620 TTG T
1 TTG T
29403624 AATATTCAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:29408623 original size:25 final size:26
Alignment explanation
Indices: 29408588--29408648 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
29408578 TACATCTTTG
*
29408588 CATTCATTTTTGAACTAA-TATTTTTC
1 CATTC-TTTTTGAAATAATTATTTTTC
* *
29408614 CATTCTTTTTTAAATAATTATTTTTT
1 CATTCTTTTTGAAATAATTATTTTTC
29408640 CATTCTTTT
1 CATTCTTTT
29408649 AGATTTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 10 0.32
26 21 0.68
ACGTcount: A:0.25, C:0.13, G:0.02, T:0.61
Consensus pattern (26 bp):
CATTCTTTTTGAAATAATTATTTTTC
Found at i:29409418 original size:5 final size:5
Alignment explanation
Indices: 29409417--29409449 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
29409407 AAAAAAACAA
*
29409417 AAAAC AAAAA AAAAC AAAAC AAAAC AAAA- AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
29409450 GGGAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:29409420 original size:10 final size:10
Alignment explanation
Indices: 29409404--29409449 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
29409394 GAAATATTTC
29409404 AAAAAAAA-A
1 AAAAAAAACA
*
29409413 ACAAAAAACA
1 AAAAAAAACA
29409423 AAAAAAAACA
1 AAAAAAAACA
*
29409433 AAACAAAACA
1 AAAAAAAACA
29409443 AAAAAAA
1 AAAAAAA
29409450 GGGAAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 7 0.22
10 25 0.78
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:29409427 original size:15 final size:14
Alignment explanation
Indices: 29409407--29409449 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
29409397 ATATTTCAAA
29409407 AAAAAAACAAAAAAC
1 AAAAAAA-AAAAAAC
29409422 AAAAAAAAACAAAAC
1 AAAAAAAAA-AAAAC
29409437 AAAACAAAAAAAA
1 AAAA-AAAAAAAA
29409450 GGGAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.08
15 19 0.73
16 5 0.19
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:29409427 original size:17 final size:17
Alignment explanation
Indices: 29409404--29409448 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
29409394 GAAATATTTC
29409404 AAAAAAAAAACAAAA-A
1 AAAAAAAAAACAAAACA
29409420 ACAAAAAAAAACAAAACA
1 A-AAAAAAAAACAAAACA
29409438 AAACAAAAAAA
1 AAA-AAAAAAA
29409449 AGGGAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.04
17 16 0.62
18 9 0.35
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAACA
Found at i:29410719 original size:44 final size:44
Alignment explanation
Indices: 29410671--29410902 Score: 189
Period size: 44 Copynumber: 5.3 Consensus size: 44
29410661 AGACACCAGC
29410671 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* * ** * * * * * * *
29410715 CTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACATCAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
*
29410759 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* * ** * ** ** * * * *
29410803 CTTGCCTTCCTGCGCCGACAGCGAAGCAAATCGAAGACACCAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
*
29410847 CTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
*
29410891 CTTGCCTTCCTG
1 CTTGCCTCCCTG
29410903 CACCGACAGC
Statistics
Matches: 132, Mismatches: 52, Indels: 8
0.69 0.27 0.04
Matches are distributed among these distances:
43 35 0.27
44 61 0.46
45 36 0.27
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.21
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:29410769 original size:88 final size:88
Alignment explanation
Indices: 29410614--29410943 Score: 554
Period size: 88 Copynumber: 3.8 Consensus size: 88
29410604 AGCAGATCAG
*
29410614 TAAAAA-AGCAGATCTTGCCTTCCTGCACCGACAGAGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
29410678 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * *
29410701 TAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACATCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
29410766 CCCTAGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* *
29410789 TAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAAATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
29410854 CCCTGGGTTGCAGCAGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * *
29410877 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGTCCCCAGCCTTGTCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
29410942 CC
66 CC
29410944 TTGAGCAGCA
Statistics
Matches: 227, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
87 6 0.03
88 221 0.97
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGCGGAGCAGGT
Found at i:29411028 original size:87 final size:87
Alignment explanation
Indices: 29410915--29411792 Score: 1492
Period size: 87 Copynumber: 10.1 Consensus size: 87
29410905 CCGACAGCGA
* *
29410915 AGCAGATCGAAGTCCCCAGCCTTGTCTCCTTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATA
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
29410980 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* *
29411002 AGCAGATCGAAGTCCCTAGCCATGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
29411067 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* *
29411089 AGCAGATCAAAGTCCCCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
*
29411154 TTATCTCCCTAAGTAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* *
29411176 AGCAGATTGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGTAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
* *
29411241 TTATCTCCTTAAGCGGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* *
29411263 AGCAGATCGAAATCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATA
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
29411328 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* * **
29411350 AGCAGATCGAAGTCCCTAGCCATGTCTCCCTGAGCAGCAGTGGAGTAGGTAAAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
29411415 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
29411437 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
29411502 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* *
29411524 AGCAGATCAAAGTCCCCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTG-AAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
*
29411588 TTATCTCCCTAAGTAGTAGTGGG
66 TTATCTCCCTAAGCAGTAGT-GG
* *
29411611 AGCAGATTGAAGTCCCCAGCC-TGTCT-CCTGAGCAGCAGTGTAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
* *
29411674 TTATCTCCTTAAGCGGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* *
29411696 AGCAGATCGAAATCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACCGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
29411761 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
29411783 AGCAGATCGA
1 AGCAGATCGA
29411793 GGATGTGGAG
Statistics
Matches: 739, Mismatches: 48, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
85 43 0.06
86 70 0.09
87 626 0.85
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (87 bp):
AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
TTATCTCCCTAAGCAGTAGTGG
Found at i:29414606 original size:3 final size:3
Alignment explanation
Indices: 29414600--29414658 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
29414590 GGTTTCGACA
* * *
29414600 ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29414648 ATT ATT ATT AT
1 ATT ATT ATT AT
29414659 CACCGAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:29415397 original size:9 final size:9
Alignment explanation
Indices: 29415366--29415588 Score: 62
Period size: 9 Copynumber: 23.3 Consensus size: 9
29415356 AAAAATACTG
29415366 AAATTGATACA
1 AAATT-ATA-A
* *
29415377 AAGTTATTA
1 AAATTATAA
29415386 AAATTATAAA
1 AAATTAT-AA
*
29415396 AAATAATAA
1 AAATTATAA
**
29415405 TAACCTATAA
1 -AAATTATAA
*
29415415 ATATTATAA
1 AAATTATAA
*
29415424 AAA-TACAA
1 AAATTATAA
29415432 TAAA-TATAA
1 -AAATTATAA
29415441 TAAATTATTAA
1 -AAATTA-TAA
*
29415452 AAATTTTATA
1 AAATTATA-A
29415462 AAATTAATAA
1 AAATT-ATAA
*
29415472 AACTTATTTAA
1 AAATTA--TAA
29415483 AATATT-T-A
1 AA-ATTATAA
*
29415491 AAATTAAAA
1 AAATTATAA
*
29415500 AAATGTATTA
1 AAAT-TATAA
* *
29415510 GAATTCTTAAA
1 AAATT-AT-AA
**
29415521 AAAGAATAA
1 AAATTATAA
*
29415530 AAATTGTAA
1 AAATTATAA
*
29415539 AAA-AATATA
1 AAATTATA-A
*
29415548 AAATATATTA
1 AAAT-TATAA
29415558 AAATTGATATA
1 AAATT-ATA-A
*
29415569 AACTT-TAA
1 AAATTATAA
29415577 AAATTATAA
1 AAATTATAA
29415586 AAA
1 AAA
29415589 AAATCATTAA
Statistics
Matches: 153, Mismatches: 38, Indels: 44
0.65 0.16 0.19
Matches are distributed among these distances:
7 3 0.02
8 14 0.09
9 62 0.41
10 48 0.31
11 24 0.16
12 2 0.01
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Found at i:29415447 original size:27 final size:28
Alignment explanation
Indices: 29415385--29415455 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
29415375 CAAAGTTATT
* *
29415385 AAAATTATAAAAAATAATAATAACCTATA
1 AAAATTAT-AAAAATAACAATAACATATA
*
29415414 AATATTATAAAAAT-ACAATAA-ATATA
1 AAAATTATAAAAATAACAATAACATATA
29415440 ATAAATTATTAAAAAT
1 A-AAATTA-TAAAAAT
29415456 TTTATAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 5 0.14
27 11 0.31
28 13 0.36
29 7 0.19
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAATTATAAAAATAACAATAACATATA
Found at i:29415467 original size:20 final size:20
Alignment explanation
Indices: 29415442--29415496 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
29415432 TAAATATAAT
29415442 AAATTATTAAAAATT-TTATA
1 AAATTATTAAAAATTATT-TA
* *
29415462 AAATTAATAAAACTTATTTA
1 AAATTATTAAAAATTATTTA
*
29415482 AAA-TATTTAAAATTA
1 AAATTATTAAAAATTA
29415497 AAAAAATGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 9 0.31
20 18 0.62
21 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATTATTAAAAATTATTTA
Found at i:29415508 original size:29 final size:30
Alignment explanation
Indices: 29415437--29415560 Score: 87
Period size: 29 Copynumber: 4.2 Consensus size: 30
29415427 TACAATAAAT
*
29415437 ATAATAAATTATTAAAAATTTTATAAAATTA
1 ATAA-AAATTATTAAAAATATTATAAAATTA
* *
29415468 ATAAAACTTATTTAAAATATT-TAAAATTA
1 ATAAAAATTATTAAAAATATTATAAAATTA
* * * **
29415497 A-AAAAATGTATTAGAATTCTTA-AAAAAGA
1 ATAAAAAT-TATTAAAAATATTATAAAATTA
* *
29415526 ATAAAAATT-GTAAAAA-AATATAAAATATA
1 ATAAAAATTATTAAAAATATTATAAAAT-TA
*
29415555 TTAAAA
1 ATAAAA
29415561 TTGATATAAA
Statistics
Matches: 70, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
27 2 0.03
28 13 0.19
29 31 0.44
30 20 0.29
31 4 0.06
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (30 bp):
ATAAAAATTATTAAAAATATTATAAAATTA
Found at i:29415860 original size:3 final size:3
Alignment explanation
Indices: 29415847--29415902 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
29415837 AGTTCAATTA
29415847 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29415894 AAT AAT AAT
1 AAT AAT AAT
29415903 TGATTCAACC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29416188 original size:8 final size:9
Alignment explanation
Indices: 29416014--29416294 Score: 98
Period size: 10 Copynumber: 30.4 Consensus size: 9
29416004 CCAATTCAAG
*
29416014 TTTTATGAT
1 TTTTATAAT
*
29416023 TTTT-TTAT
1 TTTTATAAT
29416031 TTTTATAAGT
1 TTTTATAA-T
*
29416041 TTATATCAAT
1 TTTTAT-AAT
* *
29416051 TTTAATACT
1 TTTTATAAT
**
29416060 TTTGATATTTT
1 TTT--TATAAT
29416071 TTTTATAA-
1 TTTTATAAT
*
29416079 TTTTATGACT
1 TTTTAT-AAT
*
29416089 TTTATAGAAT
1 TTT-TATAAT
* *
29416099 TTTAATATGT
1 TTTTATA-AT
*
29416109 TTTTATAAAA
1 TTTTAT-AAT
29416119 TTTTA-AAT
1 TTTTATAAT
*
29416127 ATTTTAAAAAT
1 -TTTT-ATAAT
*
29416138 GTTTTGTTAA-
1 -TTTT-ATAAT
29416148 TTTTATATAT
1 TTTTATA-AT
29416158 TTTTATAAT
1 TTTTATAAT
*
29416167 TTATTAGAAT
1 TT-TTATAAT
29416177 TTTTAT-AT
1 TTTTATAAT
29416185 TTTT-TAAT
1 TTTTATAAT
29416193 TTTT-TAAT
1 TTTTATAAT
*
29416201 TTTTTTAAT
1 TTTTATAAT
*
29416210 TTTTA-AGT
1 TTTTATAAT
*
29416218 TTATATCAAT
1 TTTTAT-AAT
*
29416228 TTTCAT-A-
1 TTTTATAAT
*
29416235 TTTTCTAAT
1 TTTTATAAT
* *
29416244 ATTTAATATT
1 -TTTTATAAT
29416254 TTTTAT-AT
1 TTTTATAAT
* *
29416262 TTTTCTGAT
1 TTTTATAAT
29416271 TTTTGATAAT
1 TTTT-ATAAT
*
29416281 TTATTATGAT
1 TT-TTATAAT
29416291 TTTT
1 TTTT
29416295 TAAACATTTT
Statistics
Matches: 201, Mismatches: 45, Indels: 52
0.67 0.15 0.17
Matches are distributed among these distances:
7 5 0.02
8 51 0.25
9 54 0.27
10 69 0.34
11 22 0.11
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:29416258 original size:10 final size:9
Alignment explanation
Indices: 29416148--29416296 Score: 76
Period size: 9 Copynumber: 16.6 Consensus size: 9
29416138 GTTTTGTTAA
29416148 TTTTATATAT
1 TTTTATAT-T
29416158 TTTTATAATT
1 TTTTAT-ATT
* * *
29416168 TATTAGAAT
1 TTTTATATT
29416177 TTTTATATT
1 TTTTATATT
29416186 TTTTA-ATT
1 TTTTATATT
29416194 TTTTA-ATT
1 TTTTATATT
*
29416202 TTTT-TAAT
1 TTTTATATT
*
29416210 TTTTA-AGT
1 TTTTATATT
* *
29416218 TTATATCAAT
1 TTTTAT-ATT
*
29416228 TTTCATATT
1 TTTTATATT
* *
29416237 TTCTA-ATA
1 TTTTATATT
*
29416245 TTTAATATT
1 TTTTATATT
29416254 TTTTATATT
1 TTTTATATT
*
29416263 TTTCT-GATT
1 TTT-TATATT
*
29416272 TTTGATAATT
1 TTTTAT-ATT
*
29416282 TATTATGATT
1 TTTTAT-ATT
29416292 TTTTA
1 TTTTA
29416297 AACATTTTAA
Statistics
Matches: 103, Mismatches: 27, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
8 32 0.31
9 37 0.36
10 32 0.31
11 2 0.02
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTATATT
Found at i:29418255 original size:20 final size:20
Alignment explanation
Indices: 29418232--29418279 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
29418222 TTTAGCTCGG
*
29418232 TTCAGCTCACATGAGTTTAA
1 TTCAGCTCACATGAGCTTAA
29418252 TTCAGCTCACATGAGCTTAA
1 TTCAGCTCACATGAGCTTAA
*
29418272 TTTAGCTC
1 TTCAGCTC
29418280 GTTTGAGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (20 bp):
TTCAGCTCACATGAGCTTAA
Found at i:29419900 original size:70 final size:70
Alignment explanation
Indices: 29419781--29420115 Score: 292
Period size: 70 Copynumber: 4.9 Consensus size: 70
29419771 CCAGATCGCA
* * * ** *
29419781 TCAAGCTCCCAGCTGTACTCTTAAGGCTCGCTGATTTAATATCATGGCCTCCAAAATAGTTAGTG
1 TCAAGCTCTCAACTGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTAGCG
29419846 TGAGC
66 TGAGC
* ** *
29419851 TCAAGCTCTCAATTGTACTCTTAAGGCTCATTGATTCAATATCGCGGCCTCCAAAATTGTTAGC-
1 TCAAGCTCTCAACTGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTAGCG
29419915 --A--
66 TGAGC
* * * * * * *
29419916 -CAAG--CTCAAGTTGTACCCTTAAGGCTTGCTAATTCAATATTGCGGCCTCTAAAATTGTTAGC
1 TCAAGCTCTCAA-CTGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTAGC
***
29419978 ACAAGC
65 GTGAGC
* * * * * *
29419984 TCAAGCTCCCAACTGTACTCTTAAGGCTCGTTGATTCAATATCGCAGCCCCCAAAACAGTTACCG
1 TCAAGCTCTCAACTGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTAGCG
*
29420049 GGAGC
66 TGAGC
* * * * **
29420054 TCAAGCTGC-CAGCTATATTCTTAAGGCTCGCTAATTCAATATTACGGCCTCCAAAATAGTTA
1 TCAAGCT-CTCAACTGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTA
29420116 ACCAACAGTA
Statistics
Matches: 212, Mismatches: 43, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
62 5 0.02
63 45 0.21
64 4 0.02
66 1 0.00
67 1 0.00
69 4 0.02
70 147 0.69
71 5 0.02
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (70 bp):
TCAAGCTCTCAACTGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTAGCG
TGAGC
Found at i:29419952 original size:63 final size:63
Alignment explanation
Indices: 29419858--29419988 Score: 192
Period size: 63 Copynumber: 2.1 Consensus size: 63
29419848 AGCTCAAGCT
* * *
29419858 CTCAA-TTGTACTCTTAAGGCTCATTGATTCAATATCGCGGCCTCCAAAATTGTTAGCACAAG
1 CTCAAGTTGTACCCTTAAGGCTCACTAATTCAATATCGCGGCCTCCAAAATTGTTAGCACAAG
** * *
29419920 CTCAAGTTGTACCCTTAAGGCTTGCTAATTCAATATTGCGGCCTCTAAAATTGTTAGCACAAG
1 CTCAAGTTGTACCCTTAAGGCTCACTAATTCAATATCGCGGCCTCCAAAATTGTTAGCACAAG
29419983 CTCAAG
1 CTCAAG
29419989 CTCCCAACTG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
62 5 0.08
63 56 0.92
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (63 bp):
CTCAAGTTGTACCCTTAAGGCTCACTAATTCAATATCGCGGCCTCCAAAATTGTTAGCACAAG
Found at i:29423185 original size:16 final size:17
Alignment explanation
Indices: 29423153--29423187 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29423143 AATTTAGTCG
29423153 AAGTATAAACGATGTAT
1 AAGTATAAACGATGTAT
*
29423170 AAGTATATAC-ATGTAT
1 AAGTATAAACGATGTAT
29423186 AA
1 AA
29423188 ATTATTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (17 bp):
AAGTATAAACGATGTAT
Found at i:29429293 original size:41 final size:41
Alignment explanation
Indices: 29429236--29429394 Score: 214
Period size: 41 Copynumber: 3.9 Consensus size: 41
29429226 AAATAAGATG
*
29429236 TTTCAGACTTTACGTCTAGTAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
29429277 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
* * * *
29429318 CTTCAGACTTTATGTCTAGCAGGCTT-AGTGCCGGTGAAATG
1 TTTCAGACTTTACGTCTAGCAGGCTTGA-TGCCGGTGAATTA
* * *
29429359 TATCAGACCTTATGTCTAGCAGGCTTTG-TGCCGGTG
1 TTTCAGACTTTACGTCTAGCAGGC-TTGATGCCGGTG
29429395 GAATGTATCG
Statistics
Matches: 107, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.01
41 104 0.97
42 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (41 bp):
TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
Found at i:29429400 original size:41 final size:41
Alignment explanation
Indices: 29429233--29429435 Score: 202
Period size: 41 Copynumber: 5.0 Consensus size: 41
29429223 TGAAAATAAG
* * *
29429233 ATGTTTCAGACTTTACGTCTAGTAGGC-TTGATGCCGGT-GA
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGGA
*
29429273 AT-TATTTCAGACTTTACGTCTAGCAGGC-TTGATGCCGGT-GA
1 ATGTA--TCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGGA
* *
29429314 AT-TACTTCAGACTTTATGTCTAGCAGGCTTAGTGCCGGTGAA
1 ATGTA--TCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGGA
*
29429356 ATGTATCAGACCTTATGTCTAGCAGGCTTTGTGCCGGTGGA
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGGA
* * * * *
29429397 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTG
29429436 TTTTATACAA
Statistics
Matches: 143, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 2 0.01
41 133 0.93
42 5 0.03
43 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (41 bp):
ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGGA
Found at i:29431487 original size:21 final size:21
Alignment explanation
Indices: 29431461--29431501 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29431451 ATTCACAATT
29431461 TTAGGTAGGTTGTT-TTTAAAG
1 TTAGGTA-GTTGTTATTTAAAG
29431482 TTAGGTAGTTGTTATTTAAA
1 TTAGGTAGTTGTTATTTAAA
29431502 CACTAATCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (21 bp):
TTAGGTAGTTGTTATTTAAAG
Found at i:29432658 original size:30 final size:31
Alignment explanation
Indices: 29432609--29432669 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
29432599 AAGAACACAG
29432609 AACCATCACCGGAACTCCATATCATTACATA
1 AACCATCACCGGAACTCCATATCATTACATA
29432640 AACCATCA-CGCG-ACTCCATATCATTACATA
1 AACCATCACCG-GAACTCCATATCATTACATA
29432670 GTCATTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.38, C:0.33, G:0.07, T:0.23
Consensus pattern (31 bp):
AACCATCACCGGAACTCCATATCATTACATA
Found at i:29437409 original size:16 final size:17
Alignment explanation
Indices: 29437388--29437420 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29437378 GGGTATGCTT
29437388 GTAAATA-TGATTCGCA
1 GTAAATAGTGATTCGCA
*
29437404 GTAAATAGTGGTTCGCA
1 GTAAATAGTGATTCGCA
29437421 TGTGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (17 bp):
GTAAATAGTGATTCGCA
Found at i:29438004 original size:37 final size:37
Alignment explanation
Indices: 29437963--29438036 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
29437953 ACAGTGTTAA
29437963 AAAGAATGCTTATTAATCCTTTCTTTAAAAACTTGCT
1 AAAGAATGCTTATTAATCCTTTCTTTAAAAACTTGCT
29438000 AAAGAATGCTTATTAATCCTTTCTTTAAAAACTTGCT
1 AAAGAATGCTTATTAATCCTTTCTTTAAAAACTTGCT
29438037 TTAAAAAGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (37 bp):
AAAGAATGCTTATTAATCCTTTCTTTAAAAACTTGCT
Found at i:29440286 original size:7 final size:7
Alignment explanation
Indices: 29440274--29440312 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
29440264 GATGCCTCTT
29440274 CCCCTTC
1 CCCCTTC
29440281 CCCCTTC
1 CCCCTTC
29440288 CCCCTTC
1 CCCCTTC
29440295 CCCCTTC
1 CCCCTTC
29440302 CCCCTTC
1 CCCCTTC
29440309 CCCC
1 CCCC
29440313 ATCCTTGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (7 bp):
CCCCTTC
Found at i:29447847 original size:18 final size:18
Alignment explanation
Indices: 29447824--29447867 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29447814 GCTTATCTTG
*
29447824 CTCATTTGCCTTCTCATT
1 CTCATTTGCATTCTCATT
**
29447842 CTCATTTATATTCTCATT
1 CTCATTTGCATTCTCATT
*
29447860 CTCTTTTG
1 CTCATTTG
29447868 TCCATGACTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.14, C:0.27, G:0.05, T:0.55
Consensus pattern (18 bp):
CTCATTTGCATTCTCATT
Found at i:29448129 original size:27 final size:27
Alignment explanation
Indices: 29448099--29448155 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
29448089 GGTTCAACTA
*
29448099 GTTTAGCAATGTTTGGCTCCACTCTCG
1 GTTTAGCAATATTTGGCTCCACTCTCG
*** *
29448126 GTTTAGGGCTATTTGGTTCCACTCTCG
1 GTTTAGCAATATTTGGCTCCACTCTCG
29448153 GTT
1 GTT
29448156 CAAGACTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (27 bp):
GTTTAGCAATATTTGGCTCCACTCTCG
Found at i:29448167 original size:27 final size:27
Alignment explanation
Indices: 29448108--29448171 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
29448098 AGTTTAGCAA
* * * *
29448108 TGTTTGGCTCCACTCTCGGTTTAGGGC
1 TGTTTGGTTCCACTCTCGGTTCAAGAC
*
29448135 TATTTGGTTCCACTCTCGGTTCAAGAC
1 TGTTTGGTTCCACTCTCGGTTCAAGAC
29448162 TGTTTGGTTC
1 TGTTTGGTTC
29448172 TCCTTCAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.41
Consensus pattern (27 bp):
TGTTTGGTTCCACTCTCGGTTCAAGAC
Found at i:29456457 original size:42 final size:43
Alignment explanation
Indices: 29456390--29456685 Score: 335
Period size: 43 Copynumber: 7.1 Consensus size: 43
29456380 AGCGAGAAGA
* * * *
29456390 GCCGCTAAAGGT-TTGTTCTATAGCGGCTTTTGT-GAAAAAGT
1 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
* *
29456431 GCCGCTAAAGATCCTGATCTATAGCGGCGTTTGTCG-AAAAGC
1 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
* *
29456473 GCCGCTAAAGGTCTTGATCTATAGCGGTGTTTGTAGG--AAAGC
1 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGT-GGAAAAAGC
*
29456515 GCCGCTAAAGGT-CTAGATCTATAGCGGCGTTTGTAGAAAAAGC
1 GCCGCTAAAGGTCCT-GATCTATAGCGGCGTTTGTGGAAAAAGC
* * * *
29456558 GCCGCTAAAGATCTTGGTCTATAGCGGCGTTTGTGGTAAAAGC
1 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
* * * * *
29456601 ACCGCTAAAGGTCATGGTCTATAGCCGCGTTTGTGGGAAAAGC
1 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
29456644 GCCGCTAAAGGT-C---TCTATAGCGGCGTTTGTGG-AAAAGC
1 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
29456682 GCCG
1 GCCG
29456686 TTATATAGCG
Statistics
Matches: 223, Mismatches: 25, Indels: 17
0.84 0.09 0.06
Matches are distributed among these distances:
38 10 0.04
39 18 0.08
41 13 0.06
42 89 0.40
43 92 0.41
44 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (43 bp):
GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
Found at i:29456579 original size:43 final size:41
Alignment explanation
Indices: 29456390--29456685 Score: 341
Period size: 42 Copynumber: 7.1 Consensus size: 41
29456380 AGCGAGAAGA
* * *
29456390 GCCGCTAAAGGT-TTGTTCTATAGCGGCTTTTGTGAAAAAGT
1 GCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTG-AAAAGC
* *
29456431 GCCGCTAAAGATCCTGATCTATAGCGGCGTTTGTCGAAAAGC
1 GCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GAAAAGC
* *
29456473 GCCGCTAAAGGTCTTGATCTATAGCGGTGTTTGTAGGAAAGC
1 GCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GAAAAGC
*
29456515 GCCGCTAAAGGTCTAGATCTATAGCGGCGTTTGTAGAAAAAGC
1 GCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-G-AAAAGC
* *
29456558 GCCGCTAAAGATCTTGGTCTATAGCGGCGTTTGTGGTAAAAGC
1 GCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-G-AAAAGC
* * * *
29456601 ACCGCTAAAGGTCATGGTCTATAGCCGCGTTTGTGGGAAAAGC
1 GCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT--GAAAAGC
29456644 GCCGCTAAAGGTC----TCTATAGCGGCGTTTGTGGAAAAGC
1 GCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GAAAAGC
29456682 GCCG
1 GCCG
29456686 TTATATAGCG
Statistics
Matches: 227, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
38 12 0.05
39 16 0.07
41 11 0.05
42 94 0.41
43 92 0.41
44 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (41 bp):
GCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAGC
Found at i:29456946 original size:19 final size:19
Alignment explanation
Indices: 29456871--29456946 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
29456861 GTATGTGCAT
*
29456871 CAGGGGTACTGAAGTACAA
1 CAGGGGTACTAAAGTACAA
* *
29456890 TAGGGGCACTAAAGTACAA
1 CAGGGGTACTAAAGTACAA
* *
29456909 CA--GGTA-T---GTGCAT
1 CAGGGGTACTAAAGTACAA
29456922 CAGGGGTACTAAAGTACAA
1 CAGGGGTACTAAAGTACAA
29456941 CAGGGG
1 CAGGGG
29456947 CACGTATGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
13 6 0.14
15 4 0.10
16 2 0.05
17 3 0.07
19 27 0.64
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.17
Consensus pattern (19 bp):
CAGGGGTACTAAAGTACAA
Found at i:29459722 original size:13 final size:13
Alignment explanation
Indices: 29459704--29459728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29459694 ACTTTCATGA
29459704 TTGCTTACTTTCC
1 TTGCTTACTTTCC
29459717 TTGCTTACTTTC
1 TTGCTTACTTTC
29459729 TCTTCCATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.28, G:0.08, T:0.56
Consensus pattern (13 bp):
TTGCTTACTTTCC
Found at i:29460193 original size:18 final size:18
Alignment explanation
Indices: 29460148--29460182 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29460138 ATGAGTTTAC
29460148 AAATATTTTAAATTATTG
1 AAATATTTTAAATTATTG
29460166 AAATATTTTAAATTATT
1 AAATATTTTAAATTATT
29460183 TATGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATATTTTAAATTATTG
Found at i:29463957 original size:10 final size:10
Alignment explanation
Indices: 29463935--29463982 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
29463925 AGCTAATAAC
29463935 GAGCTGAATT
1 GAGCTGAATT
29463945 GAGCTCGAA-T
1 GAGCT-GAATT
*
29463955 GAGCTGACTT
1 GAGCTGAATT
* *
29463965 GAGCTCAAGT
1 GAGCTGAATT
29463975 GAGCTGAA
1 GAGCTGAA
29463983 CCACATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 26 0.84
11 3 0.10
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (10 bp):
GAGCTGAATT
Found at i:29463960 original size:20 final size:20
Alignment explanation
Indices: 29463935--29463982 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
29463925 AGCTAATAAC
29463935 GAGCTGAATTGAGCTCGAA-T
1 GAGCTGAATTGAGCTC-AAGT
*
29463955 GAGCTGACTTGAGCTCAAGT
1 GAGCTGAATTGAGCTCAAGT
29463975 GAGCTGAA
1 GAGCTGAA
29463983 CCACATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (20 bp):
GAGCTGAATTGAGCTCAAGT
Found at i:29475873 original size:33 final size:35
Alignment explanation
Indices: 29475831--29475895 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 35
29475821 CTTTTTGCCC
29475831 GTTAGGGTTTTGG-GTTATT-GGTTTAAGGTTAGG
1 GTTAGGGTTTTGGTGTTATTAGGTTTAAGGTTAGG
* *
29475864 GTTAGGGTTTTGGTGTTTTTAGGTTTAGGGTT
1 GTTAGGGTTTTGGTGTTATTAGGTTTAAGGTT
29475896 TTAGAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 13 0.46
34 5 0.18
35 10 0.36
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.49
Consensus pattern (35 bp):
GTTAGGGTTTTGGTGTTATTAGGTTTAAGGTTAGG
Found at i:29476048 original size:94 final size:93
Alignment explanation
Indices: 29475946--29476216 Score: 323
Period size: 93 Copynumber: 2.9 Consensus size: 93
29475936 GTTTGTTAAT
* * *
29475946 TAAATTAATTATAAATTTTTCAAAATTGGATTA-GGTTTCGTGTTTATTGTTTTTTAAGAAAAAT
1 TAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGTGTTTA-TG-TTTTTAAGAAAAAT
* * * *
29476010 CAATTAAATTAAGGTTTAGGGTTACTTGAG
64 CAAATAAATTAGGGTTTAGGATTACTTGAA
* ** * * *
29476040 TAATTTAATTA-ATTTTTTTTAAAATTAGATTAGGGTTTAGAG-TTAGGATTTTTAAGGAAAAAT
1 TAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGTGTTTATG-TTTTTAA-GAAAAAT
*
29476103 CAAATAAATTAGGGTTCAGGATTACTTGAA
64 CAAATAAATTAGGGTTTAGGATTACTTGAA
29476133 TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAGTGTTTTTAAGTAAAAA
1 TAAATTAATTATAAATTTTT-AAAAATTAGATTAGGGTTTAGTGTTTA-TGTTTTTAAG-AAAAA
29476198 CTCAAATAAATTAGGGTTT
63 -TCAAATAAATTAGGGTTT
29476217 GAGGTTTAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
92 8 0.05
93 62 0.42
94 23 0.16
95 22 0.15
96 15 0.10
97 18 0.12
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (93 bp):
TAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGTGTTTATGTTTTTAAGAAAAATCA
AATAAATTAGGGTTTAGGATTACTTGAA
Found at i:29476474 original size:126 final size:126
Alignment explanation
Indices: 29476249--29476666 Score: 639
Period size: 126 Copynumber: 3.3 Consensus size: 126
29476239 ATTTGTTAAT
*
29476249 TTAAAAAAGCTCTCACGTGGACGCGCTTTTGCTACAGTAGCTCCT-AAAAATATAATTTCGAGTT
1 TTAAAAAAGCTCTCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAA-ATAATTTCGAGTA
*
29476313 GACGTTTCTGAGTAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAATAGTAC
65 GACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAATAGTAC
* * *
29476375 TTAAAGAAGCTCTCACGTGGACGCGCTTTTACTACAGTAGTTCCTGAAAAAATAATTTCGTA-TA
1 TTAAAAAAGCTCTCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCG-AGTA
*
29476439 GACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAACAAGATGCTTTGTCAGCAATAGTAC
65 GACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAATAGTAC
* * *
29476501 TGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCAGAAAAAATAATTTCGAGTAG
1 TTAAAAAAGCTCTCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAG
* * * *
29476566 ACGTTTTTGAGCAAATGGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAGA-AGTA-
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCA-ATAGTAC
*
29476626 TTGAAAGAAGCTC-CACGTGGACGCGCTTTTGCTACAGTAGC
1 TT-AAAAAAGCTCTCACGTGGACGCGCTTTTGCTACAGTAGC
29476667 GCATGTTTGG
Statistics
Matches: 268, Mismatches: 19, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
125 30 0.11
126 231 0.86
127 7 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (126 bp):
TTAAAAAAGCTCTCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAG
ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAATAGTAC
Found at i:29480369 original size:18 final size:18
Alignment explanation
Indices: 29480343--29480385 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29480333 GACTAAAAAA
* * *
29480343 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
29480361 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
29480379 AGGATAC
1 AGGATAC
29480386 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:29480470 original size:30 final size:30
Alignment explanation
Indices: 29480436--29480519 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 30
29480426 TCGGTTGAAC
* * *
29480436 TGCTGGGTCGGGTGACTGTGTTGGTGCTGT
1 TGCTGGGTCGGGTGACTGTATGGGTGCTGA
* * *
29480466 TGCTGGGCCTGGTGATTGTATGGGTGCTGA
1 TGCTGGGTCGGGTGACTGTATGGGTGCTGA
* * * *
29480496 TGATGGGTTGGGTGATTGTCTGGG
1 TGCTGGGTCGGGTGACTGTATGGG
29480520 CCTCGTTGAT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.07, C:0.11, G:0.46, T:0.36
Consensus pattern (30 bp):
TGCTGGGTCGGGTGACTGTATGGGTGCTGA
Found at i:29481050 original size:7 final size:7
Alignment explanation
Indices: 29481040--29481128 Score: 169
Period size: 7 Copynumber: 12.7 Consensus size: 7
29481030 CATAATACAT
29481040 AATACTA
1 AATACTA
29481047 AATACTA
1 AATACTA
29481054 AATACTA
1 AATACTA
29481061 AATACTA
1 AATACTA
29481068 AATACTA
1 AATACTA
29481075 AATACTA
1 AATACTA
29481082 AATACTA
1 AATACTA
29481089 AATACTA
1 AATACTA
29481096 AATACTA
1 AATACTA
29481103 AATACTA
1 AATACTA
*
29481110 ATTACTA
1 AATACTA
29481117 AATACTA
1 AATACTA
29481124 AATAC
1 AATAC
29481129 CAATCGACTA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 80 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (7 bp):
AATACTA
Found at i:29482315 original size:11 final size:11
Alignment explanation
Indices: 29482301--29482346 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
29482291 TTTTTTAAAT
29482301 AGGAATTTGAG
1 AGGAATTTGAG
29482312 AGGAATTTGAG
1 AGGAATTTGAG
29482323 A-GAATATT-AG
1 AGGAAT-TTGAG
*
29482333 AGAGAAATTGAG
1 AG-GAATTTGAG
29482345 AG
1 AG
29482347 AAAGGATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.23
11 16 0.53
12 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24
Consensus pattern (11 bp):
AGGAATTTGAG
Found at i:29482345 original size:10 final size:10
Alignment explanation
Indices: 29482307--29482349 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
29482297 AAATAGGAAT
*
29482307 TTGAGAGGAAT
1 TTGAGA-GAAA
29482318 TTGAGAGAATA
1 TTGAGAGAA-A
29482329 TTAGAGAGAAA
1 TT-GAGAGAAA
29482340 TTGAGAGAAA
1 TTGAGAGAAA
29482350 GGATTTCGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 11 0.38
11 11 0.38
12 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:29483820 original size:15 final size:16
Alignment explanation
Indices: 29483800--29483829 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29483790 CATATCAACA
29483800 AAAAATTAA-AAAAAT
1 AAAAATTAATAAAAAT
29483815 AAAAATTAATAAAAA
1 AAAAATTAATAAAAA
29483830 AATATATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAATTAATAAAAAT
Found at i:29485230 original size:78 final size:78
Alignment explanation
Indices: 29485100--29485244 Score: 202
Period size: 78 Copynumber: 1.9 Consensus size: 78
29485090 GACCACATTT
* * * *
29485100 GAGGTTCAAAGGAAATATGAAGAACTTCAGCAACAACTTAAAGCACAGGCGGCATGGAGAGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTACAGCAACAACTTAAAGAACAGGCGGCATCGAGAGAAGC
29485165 AGCGATAGAAGCA
66 AGCGATAGAAGCA
* * * *
29485178 GAGGTTCAAAAGAAATATGAAGAACTACAGCTACGACTTCAAA-AAGATGCGGCATCGAGAGAAG
1 GAGGTTCAAAAGAAATATGAAGAACTACAGCAACAACTT-AAAGAACAGGCGGCATCGAGAGAAG
29485242 CAG
65 CAG
29485245 AGCAGAGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
78 55 0.95
79 3 0.05
ACGTcount: A:0.43, C:0.17, G:0.27, T:0.14
Consensus pattern (78 bp):
GAGGTTCAAAAGAAATATGAAGAACTACAGCAACAACTTAAAGAACAGGCGGCATCGAGAGAAGC
AGCGATAGAAGCA
Found at i:29485672 original size:43 final size:41
Alignment explanation
Indices: 29485602--29485727 Score: 139
Period size: 43 Copynumber: 3.0 Consensus size: 41
29485592 TTTGTGAAAC
*
29485602 AAGCGCCGCTAAAGAACACT-A-CTTTTACAGGCGTTTTCTTCCA
1 AAGCGCCGCTAAAGAACA-TGATC-TTTACTGGCGTTTT-TT-CA
**
29485645 AAGCGCCGCTAAAGAACATGATCTTTACTGGCGTGTATTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTACTGGCGT-T-TTTTCA
* *
29485688 TAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTC
1 AAGCGCCGCTAAAGAACATGATCTTTACTGGCGTTTTTTC
29485728 TGTAAGCCCC
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
41 4 0.05
42 2 0.03
43 61 0.84
44 4 0.05
45 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGATCTTTACTGGCGTTTTTTCA
Found at i:29486717 original size:10 final size:9
Alignment explanation
Indices: 29486697--29486721 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29486687 TGCCCCTTTT
29486697 AAAAAATAA
1 AAAAAATAA
29486706 AAAAAATAA
1 AAAAAATAA
29486715 AAAAAAT
1 AAAAAAT
29486722 CAACTAAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:29488473 original size:29 final size:28
Alignment explanation
Indices: 29488409--29488473 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 28
29488399 TTTAATTCGG
* * *
29488409 CAAACTTTGGAAAATTACAGTCACGCCT
1 CAAACTTTGAAAAATTACAGTAACGCCC
* *
29488437 CAAACTTTGAAAAATTTATAGTAATGCCC
1 CAAACTTTGAAAAA-TTACAGTAACGCCC
29488466 CAAACTTT
1 CAAACTTT
29488474 TGTAAACCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (28 bp):
CAAACTTTGAAAAATTACAGTAACGCCC
Found at i:29495292 original size:13 final size:13
Alignment explanation
Indices: 29495274--29495300 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29495264 ATTTTTCAAG
29495274 TCATTTTCATTTT
1 TCATTTTCATTTT
29495287 TCATTTTCATTTT
1 TCATTTTCATTTT
29495300 T
1 T
29495301 GAGAAAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:29500742 original size:16 final size:17
Alignment explanation
Indices: 29500721--29500758 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
29500711 ATTCGCTTGC
29500721 TATGTAAACCACATT-A
1 TATGTAAACCACATTAA
29500737 TATGTAAACCACATTAA
1 TATGTAAACCACATTAA
29500754 TATGT
1 TATGT
29500759 TGTTACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (17 bp):
TATGTAAACCACATTAA
Found at i:29516720 original size:21 final size:21
Alignment explanation
Indices: 29516691--29516768 Score: 54
Period size: 21 Copynumber: 3.7 Consensus size: 21
29516681 GAATGAATCC
29516691 AAAATGAAATTGAGAAAAGAAG
1 AAAA-GAAATTGAGAAAAGAAG
*
29516713 AAAAGAAA-TAAGAGAAA-AAG
1 AAAAGAAATTGAGA-AAAGAAG
* * *
29516733 AAAAAGAGATCGA-AAAAGAGAA
1 -AAAAGAAATTGAGAAAAGA-AG
*
29516755 AAAAGAGATTGAGA
1 AAAAGAAATTGAGA
29516769 GCAAAAAAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
20 10 0.23
21 27 0.61
22 7 0.16
ACGTcount: A:0.67, C:0.01, G:0.23, T:0.09
Consensus pattern (21 bp):
AAAAGAAATTGAGAAAAGAAG
Found at i:29516730 original size:14 final size:13
Alignment explanation
Indices: 29516705--29516756 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 13
29516695 TGAAATTGAG
29516705 AAAAGAAGAAAAGA
1 AAAAG-AGAAAAGA
29516719 AATAAGAGAAAAAGA
1 AA-AAGAG-AAAAGA
**
29516734 AAAAGAG-ATCGA
1 AAAAGAGAAAAGA
29516746 AAAAGAGAAAA
1 AAAAGAGAAAA
29516757 AAGAGATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
12 10 0.32
13 1 0.03
14 9 0.29
15 11 0.35
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.04
Consensus pattern (13 bp):
AAAAGAGAAAAGA
Found at i:29524000 original size:25 final size:25
Alignment explanation
Indices: 29523968--29524037 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
29523958 CGTTCCAACC
*
29523968 CACAGCTCGTGTAAGCATACCGATT
1 CACAGCTCGTGTGAGCATACCGATT
* *
29523993 CATAGCTCCTGTGAGCATACCGATT
1 CACAGCTCGTGTGAGCATACCGATT
29524018 CACAGCTCGTGTGAGCATAC
1 CACAGCTCGTGTGAGCATAC
29524038 ATGTACAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (25 bp):
CACAGCTCGTGTGAGCATACCGATT
Found at i:29529528 original size:32 final size:32
Alignment explanation
Indices: 29529487--29529551 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
29529477 GTATGTTGCC
*
29529487 TTTGAGGCGTGGTCTATTTGACCCTTGTGGCA
1 TTTGAGGCGTGGTCTATTTGACCATTGTGGCA
29529519 TTTGAGGCGTGGTCTATTTGACCATTGTGGCA
1 TTTGAGGCGTGGTCTATTTGACCATTGTGGCA
29529551 T
1 T
29529552 ACTCTAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.14, C:0.17, G:0.31, T:0.38
Consensus pattern (32 bp):
TTTGAGGCGTGGTCTATTTGACCATTGTGGCA
Found at i:29529537 original size:16 final size:16
Alignment explanation
Indices: 29529487--29529539 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
29529477 GTATGTTGCC
29529487 TTTGAGGCGTGGTCTA
1 TTTGAGGCGTGGTCTA
**
29529503 TTTGACCCTTGTGG-C-A
1 TTTGAGGC--GTGGTCTA
29529519 TTTGAGGCGTGGTCTA
1 TTTGAGGCGTGGTCTA
29529535 TTTGA
1 TTTGA
29529540 CCATTGTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 4 0.14
15 1 0.03
16 19 0.66
17 1 0.03
18 4 0.14
ACGTcount: A:0.13, C:0.15, G:0.32, T:0.40
Consensus pattern (16 bp):
TTTGAGGCGTGGTCTA
Found at i:29533628 original size:20 final size:19
Alignment explanation
Indices: 29533601--29533639 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
29533591 TTCAAATAAT
*
29533601 CATTAAAAGTATCAATATC
1 CATTAAAAATATCAATATC
*
29533620 CATTCAAAAATATCGATATC
1 CATT-AAAAATATCAATATC
29533640 TTTTACCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (19 bp):
CATTAAAAATATCAATATC
Found at i:29536297 original size:20 final size:20
Alignment explanation
Indices: 29536272--29536340 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
29536262 TGCAAACTAA
29536272 AATGAGCTTAAGATGAGCTG
1 AATGAGCTTAAGATGAGCTG
*
29536292 AATGAGC-TAAGAATGATCTTG
1 AATGAGCTTAAG-ATGAGC-TG
* * *
29536313 -TTGAGCTAAAGTTGAGCTG
1 AATGAGCTTAAGATGAGCTG
*
29536332 AGTGAGCTT
1 AATGAGCTT
29536341 GTAGTAGAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 6 0.16
20 27 0.71
21 5 0.13
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (20 bp):
AATGAGCTTAAGATGAGCTG
Found at i:29542953 original size:20 final size:20
Alignment explanation
Indices: 29542928--29542966 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29542918 TGCAAACTAA
29542928 AATGAGCTTAAG-ATGAGCTG
1 AATGAGC-TAAGAATGAGCTG
29542948 AATGAGCTAAGAATGAGCT
1 AATGAGCTAAGAATGAGCT
29542967 CGTTGAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.23
Consensus pattern (20 bp):
AATGAGCTAAGAATGAGCTG
Found at i:29549123 original size:151 final size:151
Alignment explanation
Indices: 29548867--29549142 Score: 453
Period size: 151 Copynumber: 1.8 Consensus size: 151
29548857 AAGTGGATCT
* *
29548867 GGGTGCTGGTCATAAGTTCTACCAGTGGCTGGGTATACCGACATATGTTGTGGATACTTGACAGC
1 GGGTGCTGGTCATAAGTTCTACCAGTGGCTGGGTATACCGACATATGTTGCGGATACCTGACAGC
* * * * *
29548932 TTGTGTGAGCAGCACTGAGTAGTAACGAATGACTGACAGCTTGTGTGAGTAGGCCCGTGATGCGA
66 TTGTGTGAGCAACACTGAGTAGTAACAAAAGACTGACAGCTTGTGTGAGCAGACCCGTGATGCGA
29548997 AACTGTGATTAATGTGAACTC
131 AACTGTGATTAATGTGAACTC
* * * *
29549018 GGGTGCTGGTCTTAAGTTCTATCAGTGGCTGGGTATGCCGGCATATGTTGCGGATACCTGACAGC
1 GGGTGCTGGTCATAAGTTCTACCAGTGGCTGGGTATACCGACATATGTTGCGGATACCTGACAGC
29549083 TTGTGTGAGCAACACTGAGTAGTAACAAAAGACTGACAGCTTGTGTGAGCAGACCCGTGA
66 TTGTGTGAGCAACACTGAGTAGTAACAAAAGACTGACAGCTTGTGTGAGCAGACCCGTGA
29549143 AAGTGAATAG
Statistics
Matches: 114, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
151 114 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (151 bp):
GGGTGCTGGTCATAAGTTCTACCAGTGGCTGGGTATACCGACATATGTTGCGGATACCTGACAGC
TTGTGTGAGCAACACTGAGTAGTAACAAAAGACTGACAGCTTGTGTGAGCAGACCCGTGATGCGA
AACTGTGATTAATGTGAACTC
Found at i:29562459 original size:21 final size:21
Alignment explanation
Indices: 29562435--29562475 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29562425 AATAAACTTT
*
29562435 CAATTCGTTGTATAAAACAAA
1 CAATACGTTGTATAAAACAAA
*
29562456 CAATAGGTTGTATAAAACAA
1 CAATACGTTGTATAAAACAA
29562476 TATACTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (21 bp):
CAATACGTTGTATAAAACAAA
Found at i:29563369 original size:21 final size:22
Alignment explanation
Indices: 29563345--29563398 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
29563335 GCAGTAGACG
*
29563345 TTGGGGAAAAAAGTAAGGGA-T
1 TTGGGGAAAAAAATAAGGGATT
*
29563366 TTGGGGAAAAAAATTAGGGATT
1 TTGGGGAAAAAAATAAGGGATT
*
29563388 TTAGGGAAAAA
1 TTGGGGAAAAA
29563399 CTAAGGCCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (22 bp):
TTGGGGAAAAAAATAAGGGATT
Found at i:29563562 original size:41 final size:40
Alignment explanation
Indices: 29563462--29563579 Score: 141
Period size: 41 Copynumber: 3.0 Consensus size: 40
29563452 TTTTAAGGGT
*
29563462 AAAACGCTGCTATTGC-TTACCTTTTGCGGCGTTTATTCA
1 AAAACGCTGCTATTGCTTTACCTTTTGCGGCGTTTTTTCA
*** * *
29563501 AAAACGCCATTACTGTTTTACCTTTTGCGGCGTTTTTCTCA
1 AAAACGCTGCTATTGCTTTACCTTTTGCGGCGTTTTT-TCA
*
29563542 AAAACGCTGCTATTGCTTTA-CTTATTGCGGCATTTTTT
1 AAAACGCTGCTATTGCTTTACCTT-TTGCGGCGTTTTTT
29563580 GGTTAGCGCC
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
39 11 0.17
40 23 0.36
41 30 0.47
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (40 bp):
AAAACGCTGCTATTGCTTTACCTTTTGCGGCGTTTTTTCA
Found at i:29564322 original size:6 final size:6
Alignment explanation
Indices: 29564311--29564339 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29564301 TTTTTAAATA
29564311 ATATTT ATATTT ATATTT ATATTT ATATT
1 ATATTT ATATTT ATATTT ATATTT ATATT
29564340 AATTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:29564812 original size:22 final size:21
Alignment explanation
Indices: 29564786--29564827 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29564776 GTTAATTTAT
*
29564786 TTTAAATTATTTTATTTAAAAG
1 TTTAAATT-TTTCATTTAAAAG
*
29564808 TTTAAGTTTTTCATTTAAAA
1 TTTAAATTTTTCATTTAAAA
29564828 TAATAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAAATTTTTCATTTAAAAG
Found at i:29564920 original size:2 final size:2
Alignment explanation
Indices: 29564913--29564947 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29564903 AAAGTTTGTA
29564913 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 A
29564948 ATTTTCTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29565161 original size:26 final size:25
Alignment explanation
Indices: 29565116--29565166 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29565106 CTGAAAGATG
29565116 ATTTTTTAGAACAAATAAAAATGAT
1 ATTTTTTAGAACAAATAAAAATGAT
**
29565141 ATTTTTTAGAATGAATAAAAATGAT
1 ATTTTTTAGAACAAATAAAAATGAT
29565166 A
1 A
29565167 GGATCTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (25 bp):
ATTTTTTAGAACAAATAAAAATGAT
Found at i:29565935 original size:3 final size:3
Alignment explanation
Indices: 29565927--29565976 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
29565917 GGAACCAAAC
29565927 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29565975 TA
1 TA
29565977 CGCACCACTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29567228 original size:19 final size:19
Alignment explanation
Indices: 29567197--29567249 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
29567187 TTATGTTAAT
*
29567197 AAATAAATTAAAAAATATAA
1 AAATATATTAAAAAATA-AA
29567217 AAATAT-TT-AAAAATAAA
1 AAATATATTAAAAAATAAA
29567234 AAATATATTATAAAAA
1 AAATATATTA-AAAAA
29567250 AATTATAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 8 0.28
18 9 0.31
19 2 0.07
20 10 0.34
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATATATTAAAAAATAAA
Found at i:29567251 original size:17 final size:17
Alignment explanation
Indices: 29567194--29567239 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
29567184 ATGTTATGTT
* *
29567194 AATAAATAA-ATTAAAA
1 AATAAAAAATATTTAAA
29567210 AATATAAAAATATTTAAA
1 AATA-AAAAATATTTAAA
29567228 AATAAAAAATAT
1 AATAAAAAATAT
29567240 ATTATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 4 0.15
17 12 0.46
18 10 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAAAAAATATTTAAA
Found at i:29567265 original size:16 final size:16
Alignment explanation
Indices: 29567194--29567267 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 16
29567184 ATGTTATGTT
29567194 AATAAATAAATTA-AAA
1 AATAAA-AAATTATAAA
*
29567210 AATATAAAAATATTTAAA
1 AATA-AAAAAT-TATAAA
*
29567228 AATAAAAAA-TAT-AT
1 AATAAAAAATTATAAA
* *
29567242 TATAAAAAAATTATAGA
1 AAT-AAAAAATTATAAA
29567259 AATAAAAAA
1 AATAAAAAA
29567268 ATTAACATGA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
14 3 0.07
15 8 0.18
16 17 0.38
17 10 0.22
18 7 0.16
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (16 bp):
AATAAAAAATTATAAA
Found at i:29567279 original size:19 final size:17
Alignment explanation
Indices: 29567243--29567281 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
29567233 AAAATATATT
*
29567243 ATAAAAAAATTATAGAA
1 ATAAAAAAATTACAGAA
29567260 ATAAAAAAATTAACATGAA
1 ATAAAAAAATT-ACA-GAA
29567279 ATA
1 ATA
29567282 CATATAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (17 bp):
ATAAAAAAATTACAGAA
Found at i:29568632 original size:111 final size:111
Alignment explanation
Indices: 29568483--29568686 Score: 408
Period size: 111 Copynumber: 1.8 Consensus size: 111
29568473 ATAACTTTCC
29568483 TAAAGTATAGGGACTAATAGCAGAATTTAACCTTTATACTATTTAATTTAAACTTCAAAACATAT
1 TAAAGTATAGGGACTAATAGCAGAATTTAACCTTTATACTATTTAATTTAAACTTCAAAACATAT
29568548 AAGCTGCTTCCACAATCAAATGTTTTAACCTTTATACTATTTAATT
66 AAGCTGCTTCCACAATCAAATGTTTTAACCTTTATACTATTTAATT
29568594 TAAAGTATAGGGACTAATAGCAGAATTTAACCTTTATACTATTTAATTTAAACTTCAAAACATAT
1 TAAAGTATAGGGACTAATAGCAGAATTTAACCTTTATACTATTTAATTTAAACTTCAAAACATAT
29568659 AAGCTGCTTCCACAATCAAATGTTTTAA
66 AAGCTGCTTCCACAATCAAATGTTTTAA
29568687 TCGATGAATC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 93 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (111 bp):
TAAAGTATAGGGACTAATAGCAGAATTTAACCTTTATACTATTTAATTTAAACTTCAAAACATAT
AAGCTGCTTCCACAATCAAATGTTTTAACCTTTATACTATTTAATT
Found at i:29575558 original size:36 final size:36
Alignment explanation
Indices: 29575511--29575584 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
29575501 GTCCAAAGGG
29575511 AAGTTGTCATCTCAAACAGGTTTGAATCCACGAAAA
1 AAGTTGTCATCTCAAACAGGTTTGAATCCACGAAAA
29575547 AAGTTGTCATCTCAAACAGGTTTGAATCCACGAAAA
1 AAGTTGTCATCTCAAACAGGTTTGAATCCACGAAAA
29575583 AA
1 AA
29575585 ATACAAGTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (36 bp):
AAGTTGTCATCTCAAACAGGTTTGAATCCACGAAAA
Found at i:29595778 original size:18 final size:19
Alignment explanation
Indices: 29595738--29595778 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
29595728 GGGAACTTAG
*
29595738 AAAAAGATGTTAGGGGTTA
1 AAAAAAATGTTAGGGGTTA
29595757 AAAAAAATGTTAGGGGTTA
1 AAAAAAATGTTAGGGGTTA
29595776 AAA
1 AAA
29595779 TTAAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (19 bp):
AAAAAAATGTTAGGGGTTA
Found at i:29597066 original size:3 final size:3
Alignment explanation
Indices: 29597058--29597108 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
29597048 GTTATACCAA
29597058 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29597106 AAT
1 AAT
29597109 TGAATCTTTT
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):
AAT
Found at i:29600705 original size:26 final size:26
Alignment explanation
Indices: 29600676--29600736 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
29600666 AAATAATTGA
*
29600676 ACATATGTGGTAAATTTGACTTAGTC
1 ACATATGTAGTAAATTTGACTTAGTC
29600702 ACATATGTAGTAAATTTGACTTAGTC
1 ACATATGTAGTAAATTTGACTTAGTC
29600728 A-ATA-GTAGT
1 ACATATGTAGT
29600737 TGAAAGAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 5 0.15
25 3 0.09
26 26 0.76
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (26 bp):
ACATATGTAGTAAATTTGACTTAGTC
Found at i:29601444 original size:41 final size:40
Alignment explanation
Indices: 29601382--29601517 Score: 209
Period size: 41 Copynumber: 3.3 Consensus size: 40
29601372 CCATCCGGGG
*
29601382 CTTTAGCGGCGTTTCTAAAAAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTT-TGAAAAAGCGCCGCTAATGCTCAGAT
*
29601423 CTTTAGCGGCATTCTTGAAAAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTT-TTGAAAAAGCGCCGCTAATGCTCAGAT
* *
29601464 CTTTAGCGGCGTTTTTGGAAAAGCACCGCTAATGCTCAGAT
1 CTTTAGCGGCG-TTTTGAAAAAGCGCCGCTAATGCTCAGAT
29601505 CTTTAGCGGCGTT
1 CTTTAGCGGCGTT
29601518 AGCGCTGCTA
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
40 2 0.02
41 83 0.94
42 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTGAAAAAGCGCCGCTAATGCTCAGAT
Found at i:29602185 original size:89 final size:89
Alignment explanation
Indices: 29602076--29602246 Score: 252
Period size: 89 Copynumber: 1.9 Consensus size: 89
29602066 TAGGGTTTAT
* * *
29602076 GGATTCGGTGTCAGGTTAGGGTTTAGGGTTTAGATTAATTAATGTGTTTTAATTTATATATTAAA
1 GGATTCGGGGTCAGGTTAGGGTTTAAGATTTAGATTAATTAATGTGTTTTAATTTATATATTAAA
* *
29602141 TAATATTTAGGGTTTAGGAGTTAG
66 TAAGATTTAGGGGTTAGGAGTTAG
* * * *
29602165 GGATTCGGGGTCGGGTTAGGGTTTAAGATTTAGATTAATTAGTGTTTTTTAATTTATATATTCAA
1 GGATTCGGGGTCAGGTTAGGGTTTAAGATTTAGATTAATTAATGTGTTTTAATTTATATATTAAA
*
29602230 TAAGGTTTAGGGGTTAG
66 TAAGATTTAGGGGTTAG
29602247 TGTTTAGGGG
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 72 1.00
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (89 bp):
GGATTCGGGGTCAGGTTAGGGTTTAAGATTTAGATTAATTAATGTGTTTTAATTTATATATTAAA
TAAGATTTAGGGGTTAGGAGTTAG
Found at i:29602254 original size:89 final size:88
Alignment explanation
Indices: 29602069--29602264 Score: 248
Period size: 89 Copynumber: 2.2 Consensus size: 88
29602059 ATGGATTTAG
* * * *
29602069 GGTTTATGGATTCGGTGTCAGGTTAGGGTTTAGGGTTTAGATTAATTAATGTGTTTTAATTTATA
1 GGTTTAGGGATTCGGGGTCAGGTTAGGGTTTAAGATTTAGATTAATTAATGTGTTTTAATTTATA
* *
29602134 TATTAAATAATATTTAGGGTTTA
66 TATTAAATAAGATTTAGGGGTTA
* * * *
29602157 GGAGTTAGGGATTCGGGGTCGGGTTAGGGTTTAAGATTTAGATTAATTAGTGTTTTTTAATTTAT
1 GG-TTTAGGGATTCGGGGTCAGGTTAGGGTTTAAGATTTAGATTAATTAATGTGTTTTAATTTAT
* *
29602222 ATATTCAATAAGGTTTAGGGGTTA
65 ATATTAAATAAGATTTAGGGGTTA
* *
29602246 GTGTTTAGGGGTTTGGGGT
1 G-GTTTAGGGATTCGGGGT
29602265 TTGGGGTTAA
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
88 2 0.02
89 88 0.97
90 1 0.01
ACGTcount: A:0.24, C:0.03, G:0.29, T:0.44
Consensus pattern (88 bp):
GGTTTAGGGATTCGGGGTCAGGTTAGGGTTTAAGATTTAGATTAATTAATGTGTTTTAATTTATA
TATTAAATAAGATTTAGGGGTTA
Found at i:29602281 original size:28 final size:29
Alignment explanation
Indices: 29602233--29602301 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
29602223 TATTCAATAA
* * *
29602233 GGTTTAGGGGTTAGTGTTTAGGGGTTTGG
1 GGTTTAGGGGTTAGAGTTTAGGGATTTAG
*
29602262 GGTTT-GGGGTTAAGAG-TTAGTGATTTAG
1 GGTTTAGGGGTT-AGAGTTTAGGGATTTAG
29602290 GGTTTAGGGGTT
1 GGTTTAGGGGTT
29602302 TGGGGTCAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 20 0.59
29 14 0.41
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (29 bp):
GGTTTAGGGGTTAGAGTTTAGGGATTTAG
Found at i:29603027 original size:148 final size:148
Alignment explanation
Indices: 29602875--29603309 Score: 655
Period size: 154 Copynumber: 2.9 Consensus size: 148
29602865 AATGTTTTAT
* * *
29602875 AAAACAATGTCATTTTATTCCAAATGAAATAATTTTTTGCGGCGTTTTT-ATGAAAAACGCCGCA
1 AAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCGGCGTTTTTCAT-AAAAACGCCTCA
*
29602939 AAAGGTAAGCAATAGCGGCGTTTTTT-TAAAAAACGCCACAAAAAGTAATTTTACTTTTAAAAAA
65 AAATGTAAGCAATAGCGGCGTTTTTTATAAAAAACGCCACAAAAA-TAATTTTACTTTTAAAAAA
29603003 TAGCACCCTTTTAGCATAGC
129 TAGCACCCTTTTAGCATAGC
29603023 AAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCGGCGTTTTTCATAAAAACGCCTCAA
1 AAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCGGCGTTTTTCATAAAAACGCCTCAA
* * *
29603088 AATGTAAGCAATAGCGGCGTTTTTCGTTTTTATAAAAAATGCCGCAAAAATAATTTTACTTTAAA
66 AATGTAAGCAATAGCGGCG----T--TTTTTATAAAAAACGCCACAAAAATAATTTTACTTTTAA
*
29603153 AAAATAGCGCCCTTTTAGCATAGC
125 AAAATAGCACCCTTTTAGCATAGC
29603177 AAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCGGCGTTTTTCATAAAAACGCCTCAA
1 AAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCGGCGTTTTTCATAAAAACGCCTCAA
29603242 AATGTAAGCAATAGCGGCGTTTTTTATAAAAAAAACGCCACTAAAAA-AA--TTACTTTTAAAAA
66 AATGTAAGCAATAGCGGCGTTTTTTAT--AAAAAACGCCAC-AAAAATAATTTTACTTTTAAAAA
29603304 ACTAGC
128 A-TAGC
29603310 GCCATTTTGT
Statistics
Matches: 264, Mismatches: 11, Indels: 23
0.89 0.04 0.08
Matches are distributed among these distances:
148 97 0.37
149 6 0.02
150 13 0.05
151 5 0.02
152 1 0.00
154 126 0.48
155 16 0.06
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (148 bp):
AAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCGGCGTTTTTCATAAAAACGCCTCAA
AATGTAAGCAATAGCGGCGTTTTTTATAAAAAACGCCACAAAAATAATTTTACTTTTAAAAAATA
GCACCCTTTTAGCATAGC
Found at i:29603355 original size:21 final size:21
Alignment explanation
Indices: 29603329--29603374 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
29603319 TAAAATTCCC
29603329 TCCCCCC-AAAATCCCCAACTT
1 TCCCCCCTAAAATCCCCAA-TT
*
29603350 TCCCCCCTAAAATCCCTAATT
1 TCCCCCCTAAAATCCCCAATT
29603371 TCCC
1 TCCC
29603375 ACATCCAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.26, C:0.50, G:0.00, T:0.24
Consensus pattern (21 bp):
TCCCCCCTAAAATCCCCAATT
Found at i:29605653 original size:17 final size:17
Alignment explanation
Indices: 29605631--29605663 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29605621 ACCTGGTAAG
29605631 TTTGATGAATGGTTGTT
1 TTTGATGAATGGTTGTT
29605648 TTTGATGAATGGTTGT
1 TTTGATGAATGGTTGT
29605664 GTTATGTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.30, T:0.52
Consensus pattern (17 bp):
TTTGATGAATGGTTGTT
Found at i:29607118 original size:43 final size:42
Alignment explanation
Indices: 29607008--29607226 Score: 201
Period size: 43 Copynumber: 5.1 Consensus size: 42
29606998 AAGTTATGTT
* *
29607008 TTTAGCGGCGTTTGTG-AAAAGGCGTCGCTAAAAGTC--AATC
1 TTTAGCGGCGTTTGTGTAAAA-GCGTCGCTAAAGGTCTTGATC
* * *
29607048 TTATAGCGGCGTTTGTAATAGACGCGTCGCTAAAGGTCTTGATC
1 TT-TAGCGGCGTTTGT-GTAAAAGCGTCGCTAAAGGTCTTGATC
* * *
29607092 TTTAGTGGCGTTTGTGGTAAAAGCGTCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGT-GTAAAAGCGTCGCTAAAGGTCTTGATC
* ** * * *
29607135 TTTAGCGCCAATTGTGTAAACGGCGCCGCTAAAGGTCTTGCTC
1 TTTAGCGGCGTTTGTGTAAA-AGCGTCGCTAAAGGTCTTGATC
* * * *
29607178 TTTAGCGACGTTTGTGGGAAAAGCGTCGCTAATGGTCTTGGTC
1 TTTAGCGGCGTTTGT-GTAAAAGCGTCGCTAAAGGTCTTGATC
29607221 TTTAGC
1 TTTAGC
29607227 TTTCGTGGTC
Statistics
Matches: 144, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
40 2 0.01
41 13 0.09
42 19 0.13
43 101 0.70
44 9 0.06
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGTAAAAGCGTCGCTAAAGGTCTTGATC
Found at i:29607370 original size:22 final size:22
Alignment explanation
Indices: 29607342--29607384 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29607332 TAGCGGCGCT
* *
29607342 AAAAAGCGTCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
29607364 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
29607385 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:29608172 original size:13 final size:13
Alignment explanation
Indices: 29608156--29608181 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29608146 TAAATATATA
29608156 ATAATGTTATTAT
1 ATAATGTTATTAT
29608169 ATAATGTTATTAT
1 ATAATGTTATTAT
29608182 TAAATACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATAATGTTATTAT
Found at i:29608598 original size:32 final size:32
Alignment explanation
Indices: 29608557--29608623 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
29608547 TAGAAATAAG
*
29608557 TATAAATGAAGTAGAGATCTACTTCTAATGAC
1 TATAAATGAAGTAGAGATCTACTTCCAATGAC
29608589 TATAAATGAAGTAGAGATCTACTTCCAATGAC
1 TATAAATGAAGTAGAGATCTACTTCCAATGAC
29608621 TAT
1 TAT
29608624 TAGAATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (32 bp):
TATAAATGAAGTAGAGATCTACTTCCAATGAC
Found at i:29610805 original size:3 final size:3
Alignment explanation
Indices: 29610797--29610840 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
29610787 TTATAATAGA
29610797 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29610841 ATGGACAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29612907 original size:41 final size:42
Alignment explanation
Indices: 29612845--29612971 Score: 170
Period size: 43 Copynumber: 3.0 Consensus size: 42
29612835 TAACCGTTAC
29612845 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
* *
29612887 ACGG-GGAATCAGCACATAGCAACC-CCTT-TCACAGTCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTAT-A-A-TCAATGAT
*
29612929 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC-TTATAATCAATGAT
29612972 GCGGATTCAC
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
39 1 0.01
40 5 0.07
41 20 0.27
42 15 0.21
43 26 0.36
44 2 0.03
45 3 0.04
46 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (42 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
Done.