Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 23 of 97
Found at i:9818861 original size:12 final size:12
Alignment explanation
Indices: 9818823--9818874 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
9818813 AAGGAAATGG
*
9818823 AGAAGGAAAAAA
1 AGAAAGAAAAAA
* *
9818835 GAGAGAGAAAGAA
1 -AGAAAGAAAAAA
9818848 AGAAAGAAAAAA
1 AGAAAGAAAAAA
*
9818860 AGAAAAAAGAAAA
1 AGAAAGAA-AAAA
9818873 AG
1 AG
9818875 CAGAAAGGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 17 0.53
13 15 0.47
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:9818880 original size:16 final size:16
Alignment explanation
Indices: 9818842--9818873 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
9818832 AAAGAGAGAG
9818842 AAAGAAAGAAAGAAAA
1 AAAGAAAGAAAGAAAA
9818858 AAAGAAA-AAAGAAAA
1 AAAGAAAGAAAGAAAA
9818873 A
1 A
9818874 GCAGAAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAAGAAAA
Found at i:9819279 original size:11 final size:11
Alignment explanation
Indices: 9819227--9819270 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
9819217 TAAATATTTG
9819227 ATAAAAAATAGAT
1 ATAAAAAA-A-AT
*
9819240 AT-AAACAAAT
1 ATAAAAAAAAT
9819250 ATAAAAAAAAT
1 ATAAAAAAAAT
9819261 ATAAAAAAAA
1 ATAAAAAAAA
9819271 AACTAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.14
11 18 0.64
12 4 0.14
13 2 0.07
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (11 bp):
ATAAAAAAAAT
Found at i:9831658 original size:32 final size:32
Alignment explanation
Indices: 9831622--9831685 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
9831612 ACTAAATGAA
* *
9831622 TATCCTCCATATATCAGATAATAAAAAGAATT
1 TATCCTCCATACATAAGATAATAAAAAGAATT
*
9831654 TATCCTCCATACATAAGATAATAATAAGAATT
1 TATCCTCCATACATAAGATAATAAAAAGAATT
9831686 GAAACTTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (32 bp):
TATCCTCCATACATAAGATAATAAAAAGAATT
Found at i:9833030 original size:10 final size:10
Alignment explanation
Indices: 9833015--9833041 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9833005 GGATCGAATA
9833015 ATTCTTGGTG
1 ATTCTTGGTG
9833025 ATTCTTGGTG
1 ATTCTTGGTG
9833035 ATTCTTG
1 ATTCTTG
9833042 ATCACCGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.11, G:0.26, T:0.52
Consensus pattern (10 bp):
ATTCTTGGTG
Found at i:9841404 original size:19 final size:20
Alignment explanation
Indices: 9841377--9841422 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
9841367 AGGAGACAAG
*
9841377 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
9841396 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
9841415 ATAATATT
1 ATAATATT
9841423 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:9844970 original size:15 final size:15
Alignment explanation
Indices: 9844944--9844985 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
9844934 AGATAAGATA
9844944 TTTTGG-TTTTAAAG
1 TTTTGGATTTTAAAG
9844958 TTTTGGATTTTAAAG
1 TTTTGGATTTTAAAG
*
9844973 TTTTTGATTTTAA
1 TTTTGGATTTTAA
9844986 GGTTGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.24, C:0.00, G:0.17, T:0.60
Consensus pattern (15 bp):
TTTTGGATTTTAAAG
Found at i:9853736 original size:27 final size:27
Alignment explanation
Indices: 9853685--9853736 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
9853675 ATGTCCTGAT
*
9853685 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATTTTGACCCTAG
9853712 GGTGGCAAAATTATC-ATTTT-ACCCT
1 GGTGG-AAAATTA-CAATTTTGACCCT
9853737 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.41
28 12 0.55
29 1 0.05
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAG
Found at i:9853807 original size:20 final size:20
Alignment explanation
Indices: 9853790--9853827 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9853780 CCTCAAATCT
9853790 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
9853810 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
9853828 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:9857453 original size:24 final size:24
Alignment explanation
Indices: 9857426--9857517 Score: 69
Period size: 24 Copynumber: 3.6 Consensus size: 24
9857416 ATATCGTATC
*
9857426 AATTTTATTGGAAATTTGCAACGA
1 AATTCTATTGGAAATTTGCAACGA
*
9857450 AATTTTCTATTTGAGAAGTATTTCCAACGA
1 AA--TTCTA-TTG-GAA--ATTTGCAACGA
** *
9857480 AATTCCGTTGGATATTTGCAAC-A
1 AATTCTATTGGAAATTTGCAACGA
9857503 GAATTCTATTGGAAA
1 -AATTCTATTGGAAA
9857518 AGCATTTCCC
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
23 1 0.02
24 21 0.40
26 6 0.12
27 6 0.12
28 6 0.12
30 12 0.23
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (24 bp):
AATTCTATTGGAAATTTGCAACGA
Found at i:9860622 original size:25 final size:26
Alignment explanation
Indices: 9860573--9860623 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
9860563 ATGTATATGG
**
9860573 TTAATATAATATGTATGAATGATATA
1 TTAATATAATATGTACAAATGATATA
*
9860599 TTAATAT-ATATGTACAAATTATATA
1 TTAATATAATATGTACAAATGATATA
9860624 ATAACAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (26 bp):
TTAATATAATATGTACAAATGATATA
Found at i:9863229 original size:14 final size:16
Alignment explanation
Indices: 9863210--9863242 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
9863200 AAAAAAATTC
9863210 ATTTTATT-T-TAATA
1 ATTTTATTATCTAATA
9863224 ATTTTATTATCTAATA
1 ATTTTATTATCTAATA
9863240 ATT
1 ATT
9863243 ATGTAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTATTATCTAATA
Found at i:9865679 original size:19 final size:20
Alignment explanation
Indices: 9865652--9865697 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
9865642 AGGAGACAAG
*
9865652 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
9865671 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
9865690 ATAATATT
1 ATAATATT
9865698 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:9872116 original size:18 final size:19
Alignment explanation
Indices: 9872093--9872132 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
9872083 CTAATTAGTA
*
9872093 AAGAC-TTTCCATACATGG
1 AAGACGTTTCCATACACGG
9872111 AAGACTGTTTCCATACACGG
1 AAGAC-GTTTCCATACACGG
9872131 AA
1 AA
9872133 TTAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
20 14 0.74
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (19 bp):
AAGACGTTTCCATACACGG
Found at i:9880012 original size:22 final size:22
Alignment explanation
Indices: 9879987--9880029 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
9879977 TTAGTATGTA
*
9879987 TTTAAAGTATTATTAGTTTTTG
1 TTTAAAGTATTATTAGATTTTG
**
9880009 TTTAATTTATTATTAGATTTT
1 TTTAAAGTATTATTAGATTTT
9880030 ATCATCTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (22 bp):
TTTAAAGTATTATTAGATTTTG
Found at i:9882385 original size:27 final size:27
Alignment explanation
Indices: 9882351--9882404 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
9882341 GTATTATCGT
** *
9882351 TTTATTTTCTTAATT-TATTATTTTTA
1 TTTATTTTAATAATTCTATAATTTTTA
9882377 TTTATTTTTAATAATTCTATAATTTTTA
1 TTTA-TTTTAATAATTCTATAATTTTTA
9882405 ACCTATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.17
27 9 0.39
28 10 0.43
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTATTTTAATAATTCTATAATTTTTA
Found at i:9885474 original size:15 final size:15
Alignment explanation
Indices: 9885431--9885468 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
9885421 TCCCATGATA
**
9885431 AATGTGTTCTTCCCC
1 AATGTGTTCTTCCTT
9885446 AATGTGTTCTTCCTT
1 AATGTGTTCTTCCTT
9885461 AATGTGTT
1 AATGTGTT
9885469 ACTCCTATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (15 bp):
AATGTGTTCTTCCTT
Found at i:9906266 original size:25 final size:25
Alignment explanation
Indices: 9906238--9906288 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
9906228 ATTTTTACTG
*
9906238 GACACCTAAAGTTGTTAATACAAGT
1 GACACCTAAAGTTGTCAATACAAGT
*
9906263 GACACCTAAAGTTGTCAATATAAGT
1 GACACCTAAAGTTGTCAATACAAGT
9906288 G
1 G
9906289 CAAATGGGAA
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:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (25 bp):
GACACCTAAAGTTGTCAATACAAGT
Found at i:9910361 original size:29 final size:28
Alignment explanation
Indices: 9910316--9910372 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
9910306 TTAGAAATAG
*
9910316 TGAGAAATGAATCAGAAGTTCTTCTCTCA
1 TGAGAAATAAATCAGAAGTT-TTCTCTCA
*
9910345 TGAGAAATAAA-CTAGAAGTTTTTTCTCA
1 TGAGAAATAAATC-AGAAGTTTTCTCTCA
9910373 ATTATTCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (28 bp):
TGAGAAATAAATCAGAAGTTTTCTCTCA
Found at i:9919980 original size:19 final size:20
Alignment explanation
Indices: 9919948--9919987 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
9919938 ACTTATCCTG
9919948 TTTTTCTATATTTCTC-TTT
1 TTTTTCTATATTTCTCATTT
* *
9919967 TTTTTGTATTTTTCTCATTT
1 TTTTTCTATATTTCTCATTT
9919987 T
1 T
9919988 GGCTGGGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.10, C:0.12, G:0.03, T:0.75
Consensus pattern (20 bp):
TTTTTCTATATTTCTCATTT
Found at i:9920490 original size:22 final size:22
Alignment explanation
Indices: 9920433--9920491 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
9920423 CCAGCCCTGT
* *
9920433 TTCTCACTGCAGCAAAAAAGAA
1 TTCTCGCTGCAGCGAAAAAGAA
* *
9920455 TTCTCGCTGCAGCGAAAATGGA
1 TTCTCGCTGCAGCGAAAAAGAA
9920477 TTCTCGCTGCAGCGA
1 TTCTCGCTGCAGCGA
9920492 GAAACTCTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (22 bp):
TTCTCGCTGCAGCGAAAAAGAA
Found at i:9927251 original size:17 final size:17
Alignment explanation
Indices: 9927218--9927251 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9927208 AAGGATGTGT
*
9927218 ACAAGACTCAACTAAAA
1 ACAAGACTCAACCAAAA
*
9927235 ACAAGACTTAACCAAAA
1 ACAAGACTCAACCAAAA
9927252 CAATAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.24, G:0.06, T:0.12
Consensus pattern (17 bp):
ACAAGACTCAACCAAAA
Found at i:9940618 original size:6 final size:6
Alignment explanation
Indices: 9940607--9940637 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
9940597 TATCATCATT
*
9940607 TCAATC TCAATC GCAATC TCAATC TCAATC T
1 TCAATC TCAATC TCAATC TCAATC TCAATC T
9940638 GCTGCATCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (6 bp):
TCAATC
Found at i:9956513 original size:16 final size:17
Alignment explanation
Indices: 9956479--9956519 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
9956469 TATGTATATC
9956479 TAGATTTGGATGTAAAT
1 TAGATTTGGATGTAAAT
9956496 TAGA-TTGGATG-AAGAT
1 TAGATTTGGATGTAA-AT
9956512 TAGGATTT
1 TA-GATTT
9956520 AATCCATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 11 0.52
17 6 0.29
18 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (17 bp):
TAGATTTGGATGTAAAT
Found at i:9957903 original size:15 final size:16
Alignment explanation
Indices: 9957878--9957909 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
9957868 TCTTCTTTGT
9957878 TAACATTATAAAATTA
1 TAACATTATAAAATTA
9957894 TAAC-TTATAAAATTA
1 TAACATTATAAAATTA
9957909 T
1 T
9957910 TAGTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
TAACATTATAAAATTA
Found at i:9958275 original size:21 final size:20
Alignment explanation
Indices: 9958227--9958284 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
9958217 GATATGCTAT
*
9958227 ATAAA-ATTAATATATAACTT
1 ATAAATATT-ATATATAACTA
* *
9958247 ATATATATTGATATATAAGTA
1 ATAAATATT-ATATATAACTA
9958268 ATAAATATTATTATATA
1 ATAAATATTA-TATATA
9958285 TTAATATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (20 bp):
ATAAATATTATATATAACTA
Found at i:9958316 original size:25 final size:25
Alignment explanation
Indices: 9958246--9958323 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
9958236 ATATATAACT
*
9958246 TATATA-TATTGATAT-ATAA-GTAA
1 TATATATTATT-ATATAATAATATAA
* *
9958269 TAAATATTATTATATATTAATATAA
1 TATATATTATTATATAATAATATAA
*
9958294 TATATATTATTTTATACAT-ATATAA
1 TATATATTATTATATA-ATAATATAA
*
9958319 CATAT
1 TATAT
9958324 TATGTATAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 9 0.20
24 7 0.16
25 27 0.61
26 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (25 bp):
TATATATTATTATATAATAATATAA
Found at i:9959198 original size:19 final size:20
Alignment explanation
Indices: 9959155--9959199 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
9959145 AATAGACCTA
* *
9959155 AGAAATAAATGAATGATGGT
1 AGAAATAAATGAATGAAGAT
9959175 A-AAATAAATGAA-GAAGAT
1 AGAAATAAATGAATGAAGAT
9959193 AGAAATA
1 AGAAATA
9959200 CTGATAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 16 0.73
20 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (20 bp):
AGAAATAAATGAATGAAGAT
Found at i:9960353 original size:43 final size:43
Alignment explanation
Indices: 9960248--9960373 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 43
9960238 TTTTGTGTGG
* *
9960248 TAATGATGACCCAACTATGTGC-ATGTAGGAGAGT--ACATGAGC
1 TAATGATGACCCAGCCATGTGCGA-GTAGG-GAGTGCACATGAGC
*
9960290 TAATGATGACCCAGCCATGTGCG-GTGTGGGAGTGCACATGAGC
1 TAATGATGACCCAGCCATGTGCGAGT-AGGGAGTGCACATGAGC
* * * *
9960333 TAATGATGACTCGGCTATGTGTGAGTAGGGAGTGCACATGA
1 TAATGATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGA
9960374 TGATGATATT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
41 6 0.08
42 22 0.31
43 41 0.58
44 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.24
Consensus pattern (43 bp):
TAATGATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGC
Found at i:9960456 original size:2 final size:2
Alignment explanation
Indices: 9960449--9960481 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9960439 ATGATGTATG
9960449 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9960482 GTTATTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9975793 original size:14 final size:15
Alignment explanation
Indices: 9975769--9975797 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9975759 TTTTGGAGAA
9975769 ATATCCAAGGAAATG
1 ATATCCAAGGAAATG
9975784 ATAT-CAAGGAAATG
1 ATATCCAAGGAAATG
9975798 TAATCTATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (15 bp):
ATATCCAAGGAAATG
Found at i:9976704 original size:19 final size:19
Alignment explanation
Indices: 9976664--9976705 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
9976654 AGACCTAAGG
* *
9976664 AATAAATGAATGATGGTAA
1 AATAAATGAATGAAGATAA
9976683 AATAAATGAA-GAAGATAGA
1 AATAAATGAATGAAGATA-A
9976702 AATA
1 AATA
9976706 TTGATAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (19 bp):
AATAAATGAATGAAGATAA
Found at i:9977827 original size:42 final size:42
Alignment explanation
Indices: 9977770--9977898 Score: 170
Period size: 43 Copynumber: 3.0 Consensus size: 42
9977760 TTGTGTGGTA
9977770 ATGATGACCCAACTATGCT-CGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAACTATG-TACGTGTGGGAGTGCACATGAGCTG
*
9977812 ATGATGACCCAACTATGTACGGTGTGGGAGTGCACATGAGCTC
1 ATGATGACCCAACTATGTAC-GTGTGGGAGTGCACATGAGCTG
** * * *
9977855 ATGATGACCTGACTATATGCGAGTAGGGAGTGCACATGAGCTG
1 ATGATGACCCAACTATGTACGTGT-GGGAGTGCACATGAGCTG
9977898 A
1 A
9977899 GTGTGGCGAG
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
41 1 0.01
42 21 0.27
43 55 0.71
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (42 bp):
ATGATGACCCAACTATGTACGTGTGGGAGTGCACATGAGCTG
Found at i:9984241 original size:11 final size:11
Alignment explanation
Indices: 9984212--9984244 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
9984202 GAGGCTGAAA
9984212 TTGATGATA-T
1 TTGATGATATT
*
9984222 TTCATGATATT
1 TTGATGATATT
9984233 TTGATGATATT
1 TTGATGATATT
9984244 T
1 T
9984245 AATGATTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (11 bp):
TTGATGATATT
Found at i:9994729 original size:18 final size:18
Alignment explanation
Indices: 9994698--9994735 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
9994688 CTTTTTGTTT
9994698 TATACATACAAACAAACA
1 TATACATACAAACAAACA
9994716 TATACCATAC-AACAAACA
1 TATA-CATACAAACAAACA
9994734 TA
1 TA
9994736 CAACATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.18
Consensus pattern (18 bp):
TATACATACAAACAAACA
Found at i:9994742 original size:18 final size:19
Alignment explanation
Indices: 9994701--9994742 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
9994691 TTTGTTTTAT
*
9994701 ACATACAAACAAACATATA
1 ACATACAAACAAACATACA
*
9994720 CCATAC-AACAAACATACA
1 ACATACAAACAAACATACA
9994738 ACATA
1 ACATA
9994743 AGTAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.60, C:0.26, G:0.00, T:0.14
Consensus pattern (19 bp):
ACATACAAACAAACATACA
Found at i:9997257 original size:37 final size:37
Alignment explanation
Indices: 9997216--9997291 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
9997206 TAGTTACTTA
9997216 TGACATTCTGCTGTGATAATTGCTGATGGTTAGGATT
1 TGACATTCTGCTGTGATAATTGCTGATGGTTAGGATT
* *
9997253 TGACATTCTGTTGTGATAATTGCTTATGGTTAGGATT
1 TGACATTCTGCTGTGATAATTGCTGATGGTTAGGATT
9997290 TG
1 TG
9997292 GATGTTGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.43
Consensus pattern (37 bp):
TGACATTCTGCTGTGATAATTGCTGATGGTTAGGATT
Found at i:9997961 original size:73 final size:73
Alignment explanation
Indices: 9997842--9998039 Score: 252
Period size: 73 Copynumber: 2.7 Consensus size: 73
9997832 TGGTTGGCTT
* * * * * *
9997842 AGAAATAGAGACAACTTAATCAACTAAAAAGCATTATTAGTCGACTAAGATCTTATTGCCAGAAA
1 AGAAATAGAGATAACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGCTTACTGCCAGAAA
* *
9997907 TTGGGTTC
66 CTAGGTTC
* *
9997915 AGAAATAGAGATAACTTAATCGACTAAGAAGCATTGTAAGTCGACTAAGAGCTTACTGTCAGAAA
1 AGAAATAGAGATAACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGCTTACTGCCAGAAA
9997980 CTAGGTTC
66 CTAGGTTC
* * * * * *
9997988 ATAGACAGAGATGACTTAATCGACTAAGAAGCATAGTTAGTCAACTAAGAGC
1 AGAAATAGAGATAACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGC
9998040 ACACTGTTGA
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 108 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (73 bp):
AGAAATAGAGATAACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGCTTACTGCCAGAAA
CTAGGTTC
Found at i:10004456 original size:17 final size:17
Alignment explanation
Indices: 10004421--10004463 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
10004411 TTTTATTAAT
*
10004421 TATTTTTTACTTTTATA
1 TATTTTTTAATTTTATA
10004438 TATTGTTTTAATTTTTATA
1 TATT-TTTTAA-TTTTATA
10004457 TATTTTT
1 TATTTTT
10004464 AATATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TATTTTTTAATTTTATA
Found at i:10005795 original size:2 final size:2
Alignment explanation
Indices: 10005788--10005827 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
10005778 AAATTTTTAT
10005788 TA TA TA TA T- TA TA TA -A T- TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10005826 TA
1 TA
10005828 GCGTTCTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.12
2 30 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:10005823 original size:15 final size:15
Alignment explanation
Indices: 10005788--10005824 Score: 60
Period size: 13 Copynumber: 2.6 Consensus size: 15
10005778 AAATTTTTAT
10005788 TATATATATTATATA
1 TATATATATTATATA
10005803 -AT-TATATTATATA
1 TATATATATTATATA
10005816 TATATATAT
1 TATATATAT
10005825 ATAGCGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 11 0.55
14 4 0.20
15 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATATATTATATA
Found at i:10005825 original size:17 final size:16
Alignment explanation
Indices: 10005785--10005826 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 16
10005775 TGAAAATTTT
10005785 TATTATATATATTATA
1 TATTATATATATTATA
10005801 TA--AT-TATATTATA
1 TATTATATATATTATA
10005814 TATATATATATAT
1 TAT-TATATATAT
10005827 AGCGTTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.50
14 2 0.09
16 4 0.18
17 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATATATATTATA
Found at i:10005951 original size:49 final size:48
Alignment explanation
Indices: 10005864--10005969 Score: 167
Period size: 49 Copynumber: 2.2 Consensus size: 48
10005854 ATATAGCCCT
*
10005864 TTCAAAATTTTTGAAATTTTTATGTATTATATATTTTTTAATGGTCTTC
1 TTCAAAATTTATGAAATTTTTATGTATTATATATTTTTTAATGGT-TTC
*
10005913 TTCAAAATTTATGAAATTATTTATTTATTATATATTTTTTAATGGTTTC
1 TTCAAAATTTATGAAATT-TTTATGTATTATATATTTTTTAATGGTTTC
*
10005962 CTCAAAAT
1 TTCAAAAT
10005970 AATTTTTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
49 27 0.51
50 26 0.49
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (48 bp):
TTCAAAATTTATGAAATTTTTATGTATTATATATTTTTTAATGGTTTC
Found at i:10012067 original size:13 final size:13
Alignment explanation
Indices: 10012049--10012073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10012039 GGAAAATGGG
10012049 ATTTTATAAAATA
1 ATTTTATAAAATA
10012062 ATTTTATAAAAT
1 ATTTTATAAAAT
10012074 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:10017810 original size:17 final size:16
Alignment explanation
Indices: 10017782--10017814 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
10017772 CACACAATGA
10017782 TTAAATATATAAATAG
1 TTAAATATATAAATAG
10017798 TTAAATAATATAAATAG
1 TTAAAT-ATATAAATAG
10017815 AAAGATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
TTAAATATATAAATAG
Found at i:10018220 original size:2 final size:2
Alignment explanation
Indices: 10018213--10018300 Score: 87
Period size: 2 Copynumber: 45.0 Consensus size: 2
10018203 TTGAAGGGGC
* *
10018213 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA NTGC TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA
*
10018256 -A T- TA AA CTA TA TA TA TA -A TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10018295 TA TA TA
1 TA TA TA
10018301 GAATAATTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
1 5 0.07
2 65 0.89
3 3 0.04
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10019023 original size:12 final size:12
Alignment explanation
Indices: 10019002--10019044 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
10018992 GCAAATCAGA
10019002 AAAT-AAAATTC
1 AAATAAAAATTC
10019013 AAATAAAAATTTTC
1 AAATAAAAA--TTC
*
10019027 AAAAAAAAATTC
1 AAATAAAAATTC
10019039 AAATAA
1 AAATAA
10019045 TGCCCCTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 4 0.15
12 12 0.44
14 11 0.41
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATAAAAATTC
Found at i:10020371 original size:45 final size:45
Alignment explanation
Indices: 10020265--10020354 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
10020255 TGAAAAACTA
* * * * *
10020265 AATCATCATCCAGAATAATCTACCGACAGATGGTATCATCAACAT
1 AATCATCATCTAGAGTAATCTCCCAACAGATGGTATCATAAACAT
*
10020310 AATCATCATCTAGAGTAATCTCCCAACAGATGGTATCGTAAACAT
1 AATCATCATCTAGAGTAATCTCCCAACAGATGGTATCATAAACAT
10020355 GCTCATCACT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (45 bp):
AATCATCATCTAGAGTAATCTCCCAACAGATGGTATCATAAACAT
Found at i:10020429 original size:13 final size:13
Alignment explanation
Indices: 10020411--10020437 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10020401 ATCATCCAGA
10020411 GTAATCTCCCAAT
1 GTAATCTCCCAAT
10020424 GTAATCTCCCAAT
1 GTAATCTCCCAAT
10020437 G
1 G
10020438 GATGATAACA
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:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (13 bp):
GTAATCTCCCAAT
Found at i:10023667 original size:18 final size:19
Alignment explanation
Indices: 10023644--10023687 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
10023634 GATGAGAGAG
10023644 AAAAGAAAAAAAA-AAGGA
1 AAAAGAAAAAAAAGAAGGA
10023662 AAAAGAAAAAAAAAGAAGGA
1 AAAAG-AAAAAAAAGAAGGA
10023682 AAAAGA
1 AAAAGA
10023688 GGAGTGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 9 0.38
20 10 0.42
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAAAGAAGGA
Found at i:10035452 original size:42 final size:42
Alignment explanation
Indices: 10035366--10035491 Score: 153
Period size: 42 Copynumber: 3.0 Consensus size: 42
10035356 TCTTCCAACG
* * * * ** *
10035366 TCATCAGCTCATGTGCACTCCCTACTAGCACATGGCTGGGTCA
1 TCATCGGCTTATGTGCACTCTC-ACTCGCACATAACCGGGTCA
10035409 TCATCGGCTTATGTGCACTCTCACTCGCACATAACCGGGTCA
1 TCATCGGCTTATGTGCACTCTCACTCGCACATAACCGGGTCA
* * *
10035451 TCATCGGCTTATGTACACTCTTACTCGCACATAACCAGGTC
1 TCATCGGCTTATGTGCACTCTCACTCGCACATAACCGGGTC
10035492 CACACCAACA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 54 0.74
43 19 0.26
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (42 bp):
TCATCGGCTTATGTGCACTCTCACTCGCACATAACCGGGTCA
Found at i:10049790 original size:4 final size:4
Alignment explanation
Indices: 10049771--10049823 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
10049761 GTCTTATCCT
* * *
10049771 TTTA TTTTA TTTTA TTTA TTTA TTTA TTTA TTCA TTTA TTCA TTGA TTT-
1 TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
10049820 TTTA
1 TTTA
10049824 GACCAAACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
3 3 0.07
4 30 0.71
5 9 0.21
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:10058858 original size:2 final size:2
Alignment explanation
Indices: 10058851--10058890 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
10058841 ATACAATTAA
10058851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
10058891 AATAAAGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10060192 original size:15 final size:15
Alignment explanation
Indices: 10060164--10060197 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10060154 TATACATTTG
10060164 ATATAAATATTTAAT
1 ATATAAATATTTAAT
10060179 ATATATAATA-TTAAT
1 ATATA-AATATTTAAT
10060194 ATAT
1 ATAT
10060198 TAGAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATAAATATTTAAT
Found at i:10060228 original size:16 final size:16
Alignment explanation
Indices: 10060204--10060237 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10060194 ATATTAGAAA
*
10060204 AATTGATAGTAAACTT
1 AATTAATAGTAAACTT
*
10060220 AATTAATAGTATACTT
1 AATTAATAGTAAACTT
10060236 AA
1 AA
10060238 AATATATTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (16 bp):
AATTAATAGTAAACTT
Found at i:10060478 original size:18 final size:17
Alignment explanation
Indices: 10060457--10060490 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
10060447 AATGTTATGA
10060457 ATATATGTAATTGTATAT
1 ATATATGTAATT-TATAT
*
10060475 ATATATTTAATTTATA
1 ATATATGTAATTTATA
10060491 CATAAGCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATATATGTAATTTATAT
Found at i:10061984 original size:20 final size:23
Alignment explanation
Indices: 10061947--10061991 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
10061937 TATTTAACTA
10061947 TTTATATATTATGAATTAT-AGT
1 TTTATATATTATGAATTATAAGT
*
10061969 TTTATAT-TTA-GTATTATAAGT
1 TTTATATATTATGAATTATAAGT
10061990 TT
1 TT
10061992 AAATAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 8 0.38
22 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (23 bp):
TTTATATATTATGAATTATAAGT
Found at i:10075832 original size:16 final size:16
Alignment explanation
Indices: 10075808--10075838 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10075798 GCCACAGGAA
*
10075808 ATATTAATGAGTGAAC
1 ATATAAATGAGTGAAC
10075824 ATATAAATGAGTGAA
1 ATATAAATGAGTGAA
10075839 AAAAGGAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.29
Consensus pattern (16 bp):
ATATAAATGAGTGAAC
Found at i:10077787 original size:17 final size:17
Alignment explanation
Indices: 10077765--10077800 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
10077755 AATGATAATC
10077765 ATATATA-ATAATATATT
1 ATATATATAT-ATATATT
10077782 ATATATATATATATATT
1 ATATATATATATATATT
10077799 AT
1 AT
10077801 TTCTCTNTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:10077876 original size:2 final size:2
Alignment explanation
Indices: 10077869--10077902 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10077859 AATGATAATC
10077869 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10077903 TAATAATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10077884 original size:104 final size:104
Alignment explanation
Indices: 10077704--10077904 Score: 370
Period size: 104 Copynumber: 1.9 Consensus size: 104
10077694 CTAGAACTAG
10077704 TTAATTCGATTGTGTTCTTTCAATCCATTTGATTGGATGACTCTTTTCACAAATGATAATCATAT
1 TTAATTCGATTGTGTTCTTTCAATCCATTTGATTGGATGACTCTTTTCACAAATGATAATCATAT
10077769 ATAATAATATAT-TATATATATATATATATTATTTCTCT
66 ATAATAATATATATATATATATATATATATTATTTCTCT
10077807 NTTAATTCGATTGTGTTCTTTCAATCCATTTGATTGGATGACTCTTTTCACAAATGATAATCATA
1 -TTAATTCGATTGTGTTCTTTCAATCCATTTGATTGGATGACTCTTTTCACAAATGATAATCATA
10077872 TAT-ATATATATATATATATATATATATATATTA
65 TATAATA-ATATATATATATATATATATATATTA
10077905 ATAATTTCTC
Statistics
Matches: 95, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
103 3 0.03
104 73 0.77
105 19 0.20
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (104 bp):
TTAATTCGATTGTGTTCTTTCAATCCATTTGATTGGATGACTCTTTTCACAAATGATAATCATAT
ATAATAATATATATATATATATATATATATTATTTCTCT
Found at i:10081290 original size:19 final size:19
Alignment explanation
Indices: 10081266--10081302 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10081256 CCATTTGACT
10081266 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
*
10081285 TATTGGAGTATGATTTGA
1 TATTGGAGTATAATTTGA
10081303 AGTTTAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:10088556 original size:60 final size:60
Alignment explanation
Indices: 10088484--10088600 Score: 175
Period size: 60 Copynumber: 1.9 Consensus size: 60
10088474 ACAACTAGAT
* *
10088484 TCAATCTTGCTGCAGCGAAATT-GTAACCCAGAAACAG-AATGTTTCTTGCTGCAGCGAAAG
1 TCAATCTCGCTGCAGCGAAATTACT-ACCCAGAAACAGAAAT-TTTCTTGCTGCAGCGAAAG
*
10088544 TCAATCTCGCTGCAGTGAAATTACTACCCAGAAACAGAAATTTTCTTGCTGCAGCGA
1 TCAATCTCGCTGCAGCGAAATTACTACCCAGAAACAGAAATTTTCTTGCTGCAGCGA
10088601 GAATGTATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 48 0.92
61 4 0.08
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (60 bp):
TCAATCTCGCTGCAGCGAAATTACTACCCAGAAACAGAAATTTTCTTGCTGCAGCGAAAG
Found at i:10088909 original size:2 final size:2
Alignment explanation
Indices: 10088899--10088939 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
10088889 ACATATTTAC
*
10088899 AT AT GT 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 AT A
10088940 CACTACTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10089125 original size:43 final size:44
Alignment explanation
Indices: 10089050--10089159 Score: 152
Period size: 43 Copynumber: 2.5 Consensus size: 44
10089040 NNNNNAGCTC
** **
10089050 ATGCACACTCCCTACTCGCACAT-GGCTGGGTCATCATCGGGTT
1 ATGCACACTCCCTACTCGCACATAACCTGGGTCATCATCGACTT
* *
10089093 ATGCGCACTCCCTACTCGCACATAACCT-GGTCATCCTCGACTT
1 ATGCACACTCCCTACTCGCACATAACCTGGGTCATCATCGACTT
10089136 ATGCACACTCCCTACTCGCACATA
1 ATGCACACTCCCTACTCGCACATA
10089160 GCCGAGTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 57 0.97
44 2 0.03
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.25
Consensus pattern (44 bp):
ATGCACACTCCCTACTCGCACATAACCTGGGTCATCATCGACTT
Found at i:10092152 original size:21 final size:19
Alignment explanation
Indices: 10092126--10092166 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
10092116 AATTTAAAAC
10092126 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
10092147 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
10092166 A
1 A
10092167 CTTAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:10096826 original size:16 final size:15
Alignment explanation
Indices: 10096807--10096849 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
10096797 TTATTTATTT
10096807 TTAGTTTTTTTTATAA
1 TTAGTTTTTTTTA-AA
10096823 TTAGTTTATTTTTAAA
1 TTAGTTT-TTTTTAAA
*
10096839 TGAGTTATTTT
1 TTAGTT-TTTT
10096850 AATTTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (15 bp):
TTAGTTTTTTTTAAA
Found at i:10103525 original size:26 final size:26
Alignment explanation
Indices: 10103470--10103525 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
10103460 CAATTTTCAA
** **
10103470 TTATAATTTATTTATTTTTAGTTGTT
1 TTATAATTTATTTATTTTTAAATGAG
10103496 TTATAA-TTAGTTTATTTTTAAATGAG
1 TTATAATTTA-TTTATTTTTAAATGAG
10103522 TTAT
1 TTAT
10103526 TTTAATTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (26 bp):
TTATAATTTATTTATTTTTAAATGAG
Found at i:10122513 original size:13 final size:13
Alignment explanation
Indices: 10122495--10122520 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10122485 GATGCTCCCT
10122495 TTTTTATTTTTTA
1 TTTTTATTTTTTA
10122508 TTTTTATTTTTTA
1 TTTTTATTTTTTA
10122521 AAATTTAATA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:10127121 original size:21 final size:22
Alignment explanation
Indices: 10127097--10127139 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
10127087 AATACCTTTT
10127097 ATTATAATATTTAAT-TTTTAA
1 ATTATAATATTTAATCTTTTAA
*
10127118 ATTATAATATTTATTCTTTTAA
1 ATTATAATATTTAATCTTTTAA
10127140 TAATTTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATAATATTTAATCTTTTAA
Found at i:10127220 original size:24 final size:26
Alignment explanation
Indices: 10127193--10127250 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
10127183 ACGATTATTT
10127193 ATTT-TAGTT-TGTAAAATATTAATA
1 ATTTATAGTTATGTAAAATATTAATA
* *
10127217 ATTTATATTTCATTTAAAATATTAATA
1 ATTTATAGTT-ATGTAAAATATTAATA
*
10127244 ATATATA
1 ATTTATA
10127251 ATTAAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 4 0.14
27 20 0.71
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (26 bp):
ATTTATAGTTATGTAAAATATTAATA
Found at i:10127481 original size:21 final size:21
Alignment explanation
Indices: 10127450--10127496 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
10127440 TTTAATTATT
10127450 TTAAT-AATTTT-TTTCAAATA
1 TTAATAAATTTTATTT-AAATA
*
10127470 TTAATAAATTTTATTTAAATT
1 TTAATAAATTTTATTTAAATA
10127491 TTAATA
1 TTAATA
10127497 TGATTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 16 0.67
22 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATAAATTTTATTTAAATA
Found at i:10127550 original size:27 final size:29
Alignment explanation
Indices: 10127502--10127568 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 29
10127492 TAATATGATT
10127502 ATTTAT-TTTAATTTACATAATATTAAAA
1 ATTTATATTTAATTTACATAATATTAAAA
* *
10127530 ATTTATATTTCATTTA-A-AATATTAATA
1 ATTTATATTTAATTTACATAATATTAAAA
*
10127557 ATTTATAATTAA
1 ATTTATATTTAA
10127569 AAAACTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.56
28 7 0.21
29 8 0.24
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTATATTTAATTTACATAATATTAAAA
Found at i:10127676 original size:21 final size:21
Alignment explanation
Indices: 10127647--10127725 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 21
10127637 AAATTTTAAT
*
10127647 TTAATTTTTAAGTTTAAAATA
1 TTAACTTTTAAGTTTAAAATA
* *
10127668 TTAACTTTTTATAATTTATAATNTTTTA
1 TTAAC-TTTTA-AGTTTA-AA----ATA
*
10127696 TTAATTTTTAAGTTTAAAATA
1 TTAACTTTTAAGTTTAAAATA
10127717 TTAACTTTT
1 TTAACTTTT
10127726 TATAATTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
21 14 0.32
22 5 0.11
23 5 0.11
24 2 0.05
25 2 0.05
26 5 0.11
27 5 0.11
28 6 0.14
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TTAACTTTTAAGTTTAAAATA
Found at i:10127686 original size:313 final size:313
Alignment explanation
Indices: 10127118--10127689 Score: 907
Period size: 313 Copynumber: 1.8 Consensus size: 313
10127108 TAATTTTTAA
*
10127118 ATTATAATATTTATTCTTTTAATAATTTATTGTAAATATTAATAAATTGTTATTTAAATGCTAAT
1 ATTATAATATTTATTATTTTAATAATTTATTGTAAATATTAATAAATTGTTATTTAAATGCTAAT
* ** *
10127183 ACGATTATTTATTTTAGTTTGTAAAATATTAATAATTTATATTTCATTTAAAATATTAATAATAT
66 ACGATTATTTATTTTAATTTACAAAATATTAAAAATTTATATTTCATTTAAAATATTAATAATAT
* * * * * *
10127248 ATAATTAAAACATTAATTTTATTGTTTTATTTTATTCTTTATTTTGAAAATATTAAAATATAACA
131 ATAATTAAAAAACTAATATTAATATTTTATTTTATTCTTTATTTTGAAAATATTAAAATATAAAA
* *
10127313 AGTTTATAATTAAAATTTTAATTTAGTTTTAAGTTTAAAATATTAACTTTTTATAATTTATAATT
196 AATTTATAATCAAAATTTTAATTTAGTTTTAAGTTTAAAATATTAACTTTTTATAATTTATAATT
10127378 AAAACTGAAACCTTTTTATTTTAACTTAATTTTAATTTTTCTTTTTTATTTTT
261 AAAACTGAAACCTTTTTATTTTAACTTAATTTTAATTTTTCTTTTTTATTTTT
* **
10127431 ATTATAATATTTAATTATTTTAATAATTT-TTTTCAAATATTAATAAATT-TTATTTAAATTTTA
1 ATTATAATATTT-ATTATTTTAATAATTTATTGT-AAATATTAATAAATTGTTATTTAAATGCTA
* *
10127494 ATATGATTATTTATTTTAATTTACATAATATTAAAAATTTATATTTCATTTAAAATATTAATAAT
64 ATACGATTATTTATTTTAATTTACAAAATATTAAAAATTTATATTTCATTTAAAATATTAATAAT
* *
10127559 TTATAATTAAAAAACTAATATTAATATTTTATTTTATTCTTTATTTT-AATATATTAAAATATAA
129 ATATAATTAAAAAACTAATATTAATATTTTATTTTATTCTTTATTTTGAAAATATTAAAATATAA
*
10127623 AAAATTTATAATCAAAATTTTAATTTAATTTTTAAGTTTAAAATATTAACTTTTTATAATTTATA
194 AAAATTTATAATCAAAATTTTAATTT-AGTTTTAAGTTTAAAATATTAACTTTTTATAATTTATA
10127688 AT
258 AT
10127690 NTTTTATTAA
Statistics
Matches: 235, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
312 39 0.17
313 166 0.71
314 30 0.13
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (313 bp):
ATTATAATATTTATTATTTTAATAATTTATTGTAAATATTAATAAATTGTTATTTAAATGCTAAT
ACGATTATTTATTTTAATTTACAAAATATTAAAAATTTATATTTCATTTAAAATATTAATAATAT
ATAATTAAAAAACTAATATTAATATTTTATTTTATTCTTTATTTTGAAAATATTAAAATATAAAA
AATTTATAATCAAAATTTTAATTTAGTTTTAAGTTTAAAATATTAACTTTTTATAATTTATAATT
AAAACTGAAACCTTTTTATTTTAACTTAATTTTAATTTTTCTTTTTTATTTTT
Found at i:10127782 original size:15 final size:16
Alignment explanation
Indices: 10127752--10127809 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
10127742 AACTTAAACC
*
10127752 TTTTTATTTTAATTTCA
1 TTTTAATTTT-ATTTCA
*
10127769 TTTTAATTTT-TTTCC
1 TTTTAATTTTATTTCA
*
10127784 TTTTAATTTTAACTTCA
1 TTTTAATTTT-ATTTCA
10127801 TTTTAATTT
1 TTTTAATTT
10127810 ATTGAGAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 14 0.40
17 21 0.60
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTAATTTTATTTCA
Found at i:10133073 original size:38 final size:39
Alignment explanation
Indices: 10132974--10133079 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 39
10132964 CACTCCCGGC
*
10132974 TCATGTACATCCCCCCACATCGTGCACATAGCCGGCACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGG-ACCA
* * * *
10133014 TCATGTGCATCCCCCCTCATCGTGCACA-ATCAGTG-CTA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAG-GACCA
*
10133052 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
10133080 CGGGCACTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
38 27 0.47
39 3 0.05
40 27 0.47
ACGTcount: A:0.23, C:0.41, G:0.15, T:0.22
Consensus pattern (39 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGGACCA
Found at i:10139171 original size:59 final size:59
Alignment explanation
Indices: 10139091--10139212 Score: 140
Period size: 60 Copynumber: 2.1 Consensus size: 59
10139081 ATTACATCTG
* *
10139091 AAGCAGCATCCATGTAGACA-TCAAAAAGTTTAAAACATCAAG-CATGTAAATACATCCAA
1 AAGCAACAACCATGTAGACACTCAAAAAG-TTAAAACAT-AAGACATGTAAATACATCCAA
* * ** *
10139150 AAGCAACAACCATGTATACATCTCGAAAAGTTAAAACATTTGACATTTAAATACATCCAA
1 AAGCAACAACCATGTAGACA-CTCAAAAAGTTAAAACATAAGACATGTAAATACATCCAA
10139210 AAG
1 AAG
10139213 ATTGAAAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
59 18 0.34
60 28 0.53
61 7 0.13
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.22
Consensus pattern (59 bp):
AAGCAACAACCATGTAGACACTCAAAAAGTTAAAACATAAGACATGTAAATACATCCAA
Found at i:10140994 original size:20 final size:20
Alignment explanation
Indices: 10140949--10140994 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
10140939 ACATGTTGAG
*
10140949 TAGTTTAATTTAAGTTATTT
1 TAGTTTAATTTAAGTTAATT
*
10140969 TAGTTTAATTTTATGTTAATT
1 TAGTTTAA-TTTAAGTTAATT
10140990 T-GTTT
1 TAGTTT
10140995 TATATTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (20 bp):
TAGTTTAATTTAAGTTAATT
Found at i:10150360 original size:20 final size:21
Alignment explanation
Indices: 10150337--10150383 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
10150327 TACATGTTAA
10150337 TTAGTTTAA-TTTAAGTTATT
1 TTAGTTTAATTTTAAGTTATT
* *
10150357 TTAGTTAAATTTTATGTTATT
1 TTAGTTTAATTTTAAGTTATT
10150378 TT-GTTT
1 TTAGTTT
10150384 TAAATTACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.64
Consensus pattern (21 bp):
TTAGTTTAATTTTAAGTTATT
Found at i:10153778 original size:43 final size:43
Alignment explanation
Indices: 10153706--10153863 Score: 176
Period size: 43 Copynumber: 3.7 Consensus size: 43
10153696 CAGCTCATGT
** *
10153706 GCACTCCCTACTCGCACAT-GGCTAGGTCATCA-CTGGGTTATGC
1 GCACTCCCTACTCGCACATAACCGA-GTCATCATC-GGGTTATGC
** *
10153749 ATACTCCTTACTCGCACATAACCGAGTCATCATCGGGTTATGC
1 GCACTCCCTACTCGCACATAACCGAGTCATCATCGGGTTATGC
* * * *
10153792 GCACTCCCTACTAGCACATAACTGGGTCATCATCGGCTTATGC
1 GCACTCCCTACTCGCACATAACCGAGTCATCATCGGGTTATGC
* *
10153835 GCACTCCCTACTCTCACATAGCCGAGTCA
1 GCACTCCCTACTCGCACATAACCGAGTCA
10153864 ATATCATTAC
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
43 92 0.97
44 3 0.03
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (43 bp):
GCACTCCCTACTCGCACATAACCGAGTCATCATCGGGTTATGC
Found at i:10153809 original size:86 final size:86
Alignment explanation
Indices: 10153706--10153863 Score: 210
Period size: 86 Copynumber: 1.8 Consensus size: 86
10153696 CAGCTCATGT
* ** * * *
10153706 GCACTCCCTACTCGCACATGGCTAGGTCATCA-CTGGGTTATGCATACTCCTTACTCGCACATAA
1 GCACTCCCTACTAGCACATAACTAGGTCATCATC-GGCTTATGCACACTCCCTACTCGCACATAA
10153770 CCGAGTCATCATCGGGTTATGC
65 CCGAGTCATCATCGGGTTATGC
* * * *
10153792 GCACTCCCTACTAGCACATAACTGGGTCATCATCGGCTTATGCGCACTCCCTACTCTCACATAGC
1 GCACTCCCTACTAGCACATAACTAGGTCATCATCGGCTTATGCACACTCCCTACTCGCACATAAC
10153857 CGAGTCA
66 CGAGTCA
10153864 ATATCATTAC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
86 60 0.98
87 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (86 bp):
GCACTCCCTACTAGCACATAACTAGGTCATCATCGGCTTATGCACACTCCCTACTCGCACATAAC
CGAGTCATCATCGGGTTATGC
Found at i:10171088 original size:2 final size:2
Alignment explanation
Indices: 10171071--10171114 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
10171061 GTTGGAGAAC
* *
10171071 TA TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10171113 TA
1 TA
10171115 ATTGCCTAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10181711 original size:20 final size:20
Alignment explanation
Indices: 10181672--10181711 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
10181662 ATTCAAGTTA
**
10181672 ATCTATCAATAGATGTAAGT
1 ATCTATCAATAGATACAAGT
*
10181692 ATCTATCGATAGATACAAGT
1 ATCTATCAATAGATACAAGT
10181712 CAAGGTCCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (20 bp):
ATCTATCAATAGATACAAGT
Found at i:10181927 original size:15 final size:15
Alignment explanation
Indices: 10181907--10181937 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10181897 GCTGTTCTTC
*
10181907 ATCTATTGATAGATA
1 ATCTATTAATAGATA
10181922 ATCTATTAATAGATA
1 ATCTATTAATAGATA
10181937 A
1 A
10181938 GCCTATCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (15 bp):
ATCTATTAATAGATA
Found at i:10184878 original size:30 final size:30
Alignment explanation
Indices: 10184835--10184940 Score: 151
Period size: 30 Copynumber: 3.5 Consensus size: 30
10184825 TAAATCTAAG
*
10184835 GCCTC-AAGAAGGAAGATTTTGAAGCTCAAA
1 GCCTCTAA-AAGGAAGATTTTGAAGATCAAA
** *
10184865 GCCTCTACGAGGAAGATTTTGAATATCAAA
1 GCCTCTAAAAGGAAGATTTTGAAGATCAAA
*
10184895 GCCTCCAAAAGGAAGATTTTGAAGATCAAA
1 GCCTCTAAAAGGAAGATTTTGAAGATCAAA
10184925 GCCTCTAAAAGGAAGA
1 GCCTCTAAAAGGAAGA
10184941 GAAAAATCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
30 65 0.98
31 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.21
Consensus pattern (30 bp):
GCCTCTAAAAGGAAGATTTTGAAGATCAAA
Found at i:10192780 original size:21 final size:21
Alignment explanation
Indices: 10192739--10192780 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10192729 AAACAGAAGG
*
10192739 TTTCTCGCTGCAACGAGATTC
1 TTTCTCGCTGCAACGAAATTC
**
10192760 TTTCTCGCTGCAGTGAAATTC
1 TTTCTCGCTGCAACGAAATTC
10192781 AACTGATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
TTTCTCGCTGCAACGAAATTC
Found at i:10193210 original size:43 final size:43
Alignment explanation
Indices: 10193157--10193275 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
10193147 TCACCAGCTC
** * **
10193157 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGACTT
*
10193200 ATGCGTACTCCCTACTCGCACATAACCGGGTCATCCTCGACTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGACTT
* *
10193243 ATGCACACTCCCTACTCGCACATAACCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
10193276 ATATAATTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 65 0.98
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGACTT
Found at i:10201433 original size:28 final size:28
Alignment explanation
Indices: 10201374--10201444 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 28
10201364 CCATGTCATT
*** * *
10201374 CAACTTTGTTGTGTTTTGTCAAGATTTT
1 CAACTTTGTTGTGTTTCACCAAGATATG
*
10201402 CAACTTTGTTGTGTTTCACCATGATATG
1 CAACTTTGTTGTGTTTCACCAAGATATG
*
10201430 CAAC-TTGTTATGTTT
1 CAACTTTGTTGTGTTT
10201445 TGCTGTGTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 10 0.28
28 26 0.72
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (28 bp):
CAACTTTGTTGTGTTTCACCAAGATATG
Found at i:10201461 original size:37 final size:37
Alignment explanation
Indices: 10201406--10201509 Score: 172
Period size: 37 Copynumber: 2.8 Consensus size: 37
10201396 GATTTTCAAC
* *
10201406 TTTGTTGTGTTTCACCATGATATGCAACTTGTTATGT
1 TTTGCTGTGTTTCACCATGATATGCAACTTGTTATCT
10201443 TTTGCTGTGTTTCACCATGATATGCAACTTGTTATCT
1 TTTGCTGTGTTTCACCATGATATGCAACTTGTTATCT
* *
10201480 TTTGCTGTGTTTCACCATGACATTCAACTT
1 TTTGCTGTGTTTCACCATGATATGCAACTT
10201510 CAACTTGTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.46
Consensus pattern (37 bp):
TTTGCTGTGTTTCACCATGATATGCAACTTGTTATCT
Found at i:10201564 original size:40 final size:40
Alignment explanation
Indices: 10201507--10201584 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
10201497 TGACATTCAA
10201507 CTTCAACTTGTCATGTTTCACCACAACGTTCAACTTCATT
1 CTTCAACTTGTCATGTTTCACCACAACGTTCAACTTCATT
** * *
10201547 CTTCAACTTGTTGTGTTTCACCACGATGTTCAACTTCA
1 CTTCAACTTGTCATGTTTCACCACAACGTTCAACTTCA
10201585 ATTTGTCGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.38
Consensus pattern (40 bp):
CTTCAACTTGTCATGTTTCACCACAACGTTCAACTTCATT
Found at i:10201612 original size:33 final size:33
Alignment explanation
Indices: 10201547--10201614 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
10201537 CAACTTCATT
* *
10201547 CTTCAACTTGTTGTGTTTCACCACGATGTTCAA
1 CTTCAACTTGTCGTGTTTCACCACGATATTCAA
*
10201580 CTTCAATTTGTCGTGTTTCACCAC-ATCATTCAA
1 CTTCAACTTGTCGTGTTTCACCACGAT-ATTCAA
10201613 CT
1 CT
10201615 CATGCCATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (33 bp):
CTTCAACTTGTCGTGTTTCACCACGATATTCAA
Found at i:10208541 original size:17 final size:17
Alignment explanation
Indices: 10208521--10208554 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10208511 AATTGATGTT
*
10208521 AAAAATAATTAAATCTC
1 AAAAATAACTAAATCTC
*
10208538 AAAATTAACTAAATCTC
1 AAAAATAACTAAATCTC
10208555 GTAATTTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATAACTAAATCTC
Found at i:10212294 original size:17 final size:17
Alignment explanation
Indices: 10212254--10212303 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
10212244 ACCATATTAT
*
10212254 ATATATACTAATACTTTTA
1 ATATATA-T-ATACTTTAA
*
10212273 GTATATATATACTTTAA
1 ATATATATATACTTTAA
10212290 ATATA-ATATA-TTTA
1 ATATATATATACTTTA
10212304 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 4 0.14
16 5 0.18
17 12 0.43
18 1 0.04
19 6 0.21
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (17 bp):
ATATATATATACTTTAA
Found at i:10212640 original size:18 final size:18
Alignment explanation
Indices: 10212619--10212663 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
10212609 TCATATAATT
10212619 AATTA-AATTAATTAATAA
1 AATTATAATT-ATTAATAA
*
10212637 AATTATAATTATTAATTA
1 AATTATAATTATTAATAA
*
10212655 AATTGTAAT
1 AATTATAAT
10212664 GTCTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
AATTATAATTATTAATAA
Found at i:10213039 original size:6 final size:6
Alignment explanation
Indices: 10213028--10213053 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
10213018 AAAAATGTAA
10213028 TAGGGT TAGGGT TAGGGT TAGGGT TA
1 TAGGGT TAGGGT TAGGGT TAGGGT TA
10213054 TGGTAGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.46, T:0.35
Consensus pattern (6 bp):
TAGGGT
Found at i:10214100 original size:85 final size:85
Alignment explanation
Indices: 10213957--10214127 Score: 342
Period size: 85 Copynumber: 2.0 Consensus size: 85
10213947 CCCTGTTGTG
10213957 TTTTTGTCCAAAAACAACTAAACAAAAGCAATAAACTTTGCTTATTAATTGTGGACTTCTCTTAG
1 TTTTTGTCCAAAAACAACTAAACAAAAGCAATAAACTTTGCTTATTAATTGTGGACTTCTCTTAG
10214022 TTCCAGATTGTGCTAAATAT
66 TTCCAGATTGTGCTAAATAT
10214042 TTTTTGTCCAAAAACAACTAAACAAAAGCAATAAACTTTGCTTATTAATTGTGGACTTCTCTTAG
1 TTTTTGTCCAAAAACAACTAAACAAAAGCAATAAACTTTGCTTATTAATTGTGGACTTCTCTTAG
10214107 TTCCAGATTGTGCTAAATAT
66 TTCCAGATTGTGCTAAATAT
10214127 T
1 T
10214128 AACTGTCTGA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (85 bp):
TTTTTGTCCAAAAACAACTAAACAAAAGCAATAAACTTTGCTTATTAATTGTGGACTTCTCTTAG
TTCCAGATTGTGCTAAATAT
Found at i:10219559 original size:45 final size:45
Alignment explanation
Indices: 10219503--10219589 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
10219493 ATGAGCACAC
* * * *
10219503 ACACCCTTTCGCATATGGATTCACATACATATAATGCAGGCAGAG
1 ACACCCATTCGCACATGGATTCACATAAACATAATGCAGGCAGAG
10219548 ACACCCATTCGCACATGGATTCACATAAACATAATGCAGGCA
1 ACACCCATTCGCACATGGATTCACATAAACATAATGCAGGCA
10219590 TAAATGGGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (45 bp):
ACACCCATTCGCACATGGATTCACATAAACATAATGCAGGCAGAG
Found at i:10220640 original size:17 final size:18
Alignment explanation
Indices: 10220606--10220642 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10220596 TAATTTTTCA
10220606 TTATTTTTTCACTGTCTT
1 TTATTTTTTCACTGTCTT
*
10220624 TTATTTTTTCTCT-TCTT
1 TTATTTTTTCACTGTCTT
10220641 TT
1 TT
10220643 CGTATTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.73
Consensus pattern (18 bp):
TTATTTTTTCACTGTCTT
Found at i:10258018 original size:20 final size:20
Alignment explanation
Indices: 10257977--10258018 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
10257967 TGTTGAGTAG
*
10257977 TTAATTTAAATTATTTTAGT
1 TTAATTTAAATTAGTTTAGT
*
10257997 TTAATTTTATATTAGTTT-GT
1 TTAA-TTTAAATTAGTTTAGT
10258017 TT
1 TT
10258019 TAAATTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
TTAATTTAAATTAGTTTAGT
Found at i:10261234 original size:20 final size:21
Alignment explanation
Indices: 10261189--10261235 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
10261179 AGATGTCTAA
*
10261189 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
10261210 TATAATTGTTTG-AATAAAAT
1 AATAATTATTTGAAATAAAAT
10261230 AATAAT
1 AATAAT
10261236 ATTCAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:10272892 original size:68 final size:68
Alignment explanation
Indices: 10272778--10272975 Score: 261
Period size: 68 Copynumber: 2.9 Consensus size: 68
10272768 AAGATGTTAT
* * * * * * * *
10272778 ATTATGTATATGATGTATATACCATATACTACATGAGATCATTGAGAAAGCTTGACGAATGCCAT
1 ATTAAGTATATGATGCACATTCCATATACTACTTGAGATGATTGAGAAAGCATGATGAATGCCAT
10272843 GAA
66 GAA
* *
10272846 ATTAAGTATATGATGCACATTTCGTATACTACTTGAGATGATTGAGAAAGCATGATGAATGCCAT
1 ATTAAGTATATGATGCACATTCCATATACTACTTGAGATGATTGAGAAAGCATGATGAATGCCAT
10272911 GAA
66 GAA
** * * *
10272914 ATTAAGTATATGATGTGCATTCCATATACTACTTGAAATGGTTGAGAAGGCATGATGAATGC
1 ATTAAGTATATGATGCACATTCCATATACTACTTGAGATGATTGAGAAAGCATGATGAATGC
10272976 ATAAGATTAT
Statistics
Matches: 113, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 113 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (68 bp):
ATTAAGTATATGATGCACATTCCATATACTACTTGAGATGATTGAGAAAGCATGATGAATGCCAT
GAA
Found at i:10274515 original size:35 final size:36
Alignment explanation
Indices: 10274464--10274543 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 36
10274454 TCAACCAAAA
* * *
10274464 CACAAAAATTACCTTTTCACGAGAGCAAGCACAACC
1 CACAACAATTACCTTTTAACGAGAACAAGCACAACC
* * * *
10274500 CTCAACAATT-CCTTTTAATGAGAACAAGCATAATC
1 CACAACAATTACCTTTTAACGAGAACAAGCACAACC
10274535 CACAACAAT
1 CACAACAAT
10274544 GCCTATTAAC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
35 28 0.78
36 8 0.22
ACGTcount: A:0.42, C:0.28, G:0.09, T:0.21
Consensus pattern (36 bp):
CACAACAATTACCTTTTAACGAGAACAAGCACAACC
Found at i:10278625 original size:18 final size:18
Alignment explanation
Indices: 10278602--10278645 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
10278592 ACTACAACAA
*
10278602 CCATAATTGTTTATGCAT
1 CCATAACTGTTTATGCAT
10278620 CCATAACTGTTTATGCAT
1 CCATAACTGTTTATGCAT
10278638 CCATAACT
1 CCATAACT
10278646 ACTGCAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (18 bp):
CCATAACTGTTTATGCAT
Found at i:10286807 original size:32 final size:30
Alignment explanation
Indices: 10286769--10286827 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
10286759 ACTTCATTTA
*
10286769 ATTTTAATATATCAAATATTAATATAAAATAT
1 ATTTTAATATATC-AATAATAA-ATAAAATAT
*
10286801 ATTTTAATATTTCAATAATAAATAAAA
1 ATTTTAATATATCAATAATAAATAAAA
10286828 GTAACTAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 7 0.28
32 12 0.48
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
ATTTTAATATATCAATAATAAATAAAATAT
Found at i:10288787 original size:26 final size:26
Alignment explanation
Indices: 10288754--10288809 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
10288744 GATTGCAATA
* ** *
10288754 TTTTCAACACAATGTGTAATAATTTT
1 TTTTCAACAAAACATGTAACAATTTT
10288780 TTTTCAACAAAACATGTAACAATTTT
1 TTTTCAACAAAACATGTAACAATTTT
10288806 TTTT
1 TTTT
10288810 TTCAACATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.46
Consensus pattern (26 bp):
TTTTCAACAAAACATGTAACAATTTT
Found at i:10288822 original size:28 final size:27
Alignment explanation
Indices: 10288776--10288917 Score: 96
Period size: 28 Copynumber: 5.3 Consensus size: 27
10288766 TGTGTAATAA
** *
10288776 TTTTTTTTCAACAAAACATGTAACAATT
1 TTTTTTTTCAACATGACATATAACAA-T
*
10288804 TTTTTTTTCAACATGACATATAGCAA-
1 TTTTTTTTCAACATGACATATAACAAT
* * *
10288830 --CTTTTTGAACATGACGTATAAC-AT
1 TTTTTTTTCAACATGACATATAACAAT
** * *
10288854 CATTTTTTCAACATGGCATGTAACAACTT
1 TTTTTTTTCAACATGACATATAACAA--T
* *
10288883 TTTTTTTTCAACAT-AGCATATAATAAC
1 TTTTTTTTCAACATGA-CATATAACAAT
10288910 TTTTTTTT
1 TTTTTTTT
10288918 GACATGGCGT
Statistics
Matches: 88, Mismatches: 19, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
23 1 0.01
24 18 0.20
26 17 0.19
27 9 0.10
28 22 0.25
29 21 0.24
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (27 bp):
TTTTTTTTCAACATGACATATAACAAT
Found at i:10288834 original size:26 final size:26
Alignment explanation
Indices: 10288777--10288916 Score: 97
Period size: 26 Copynumber: 5.3 Consensus size: 26
10288767 GTGTAATAAT
** * *
10288777 TTTTTTTCAACAAAACATGTAACAATTT
1 TTTTTTTCAACATGACATATAACAA--C
*
10288805 TTTTTTTCAACATGACATATAGCAAC
1 TTTTTTTCAACATGACATATAACAAC
* * *
10288831 --TTTTTGAACATGACGTATAACATC
1 TTTTTTTCAACATGACATATAACAAC
* * *
10288855 ATTTTTTCAACATGGCATGTAACAAC
1 TTTTTTTCAACATGACATATAACAAC
*
10288881 TTTTTTTTTTCAACAT-AGCATATAATAAC
1 ---TTTTTTTCAACATGA-CATATAACAAC
10288910 TTTTTTT
1 TTTTTTT
10288917 TGACATGGCG
Statistics
Matches: 88, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
24 20 0.23
26 26 0.30
28 21 0.24
29 21 0.24
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.44
Consensus pattern (26 bp):
TTTTTTTCAACATGACATATAACAAC
Found at i:10288834 original size:29 final size:29
Alignment explanation
Indices: 10288776--10288917 Score: 106
Period size: 29 Copynumber: 5.2 Consensus size: 29
10288766 TGTGTAATAA
** *
10288776 TTTTTTTTCAACAAAACATGTAACAA-TT
1 TTTTTTTTCAACATGACATATAACAACTT
*
10288804 TTTTTTTTCAACATGACATATAGCAAC--
1 TTTTTTTTCAACATGACATATAACAACTT
* *
10288831 ---TTTTTGAACATGACGTATAAC-A--T
1 TTTTTTTTCAACATGACATATAACAACTT
** * *
10288854 CATTTTTTCAACATGGCATGTAACAACTT
1 TTTTTTTTCAACATGACATATAACAACTT
*
10288883 TTTTTTTTCAACAT-AGCATATAATAACTT
1 TTTTTTTTCAACATGA-CATATAACAACTT
10288912 TTTTTT
1 TTTTTT
10288918 GACATGGCGT
Statistics
Matches: 89, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
23 1 0.01
24 18 0.20
26 17 0.19
27 1 0.01
28 22 0.25
29 30 0.34
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (29 bp):
TTTTTTTTCAACATGACATATAACAACTT
Found at i:10288840 original size:24 final size:24
Alignment explanation
Indices: 10288807--10288885 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
10288797 AACAATTTTT
*
10288807 TTTTTCAACATGACATATAGCAAC
1 TTTTTCAACATGACATATAACAAC
* * *
10288831 TTTTTGAACATGACGTATAACATCAT
1 TTTTTCAACATGACATATAACA--AC
* *
10288857 TTTTTCAACATGGCATGTAACAAC
1 TTTTTCAACATGACATATAACAAC
10288881 TTTTT
1 TTTTT
10288886 TTTTTCAACA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
24 25 0.57
26 19 0.43
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (24 bp):
TTTTTCAACATGACATATAACAAC
Found at i:10290219 original size:34 final size:34
Alignment explanation
Indices: 10290175--10290244 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
10290165 ATAAACATAT
* *
10290175 TTTAATATTAACTTCACATGAATGATCCATGATC
1 TTTAAAATTAACTTCACATGAATAATCCATGATC
* *
10290209 TTTAAAATTAATTTCACATGAATAATCGATGATC
1 TTTAAAATTAACTTCACATGAATAATCCATGATC
10290243 TT
1 TT
10290245 AATTTTACAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (34 bp):
TTTAAAATTAACTTCACATGAATAATCCATGATC
Found at i:10292090 original size:22 final size:22
Alignment explanation
Indices: 10292065--10292106 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10292055 AAATCTCAAT
* * *
10292065 ATTATAAATCCATCAAAAATCG
1 ATTAAAAATACATAAAAAATCG
10292087 ATTAAAAATACATAAAAAAT
1 ATTAAAAATACATAAAAAAT
10292107 AAGTCAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (22 bp):
ATTAAAAATACATAAAAAATCG
Found at i:10293175 original size:15 final size:15
Alignment explanation
Indices: 10293142--10293175 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
10293132 CAATTACTAC
* *
10293142 TATATATACTTTTAG
1 TATATATACTTTAAA
10293157 TATATATACTTTAAA
1 TATATATACTTTAAA
10293172 TATA
1 TATA
10293176 AACATACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (15 bp):
TATATATACTTTAAA
Found at i:10293229 original size:15 final size:17
Alignment explanation
Indices: 10293201--10293233 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
10293191 TATTTTATAT
10293201 TAACGTTATAAAAATTA
1 TAACGTTATAAAAATTA
10293218 TAAC-TTAT-AAAATTA
1 TAACGTTATAAAAATTA
10293233 T
1 T
10293234 TAATTAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (17 bp):
TAACGTTATAAAAATTA
Found at i:10294015 original size:91 final size:91
Alignment explanation
Indices: 10293860--10294053 Score: 379
Period size: 91 Copynumber: 2.1 Consensus size: 91
10293850 TGACCTCAAA
10293860 AGTCGATCCTAGTGCATAAAGGATCGAATTTGCAAAGTAAAATGCTGAAGACGAAAGTGCACTGG
1 AGTCGATCCTAGTGCATAAAGGATCGAATTTGCAAAGTAAAATGCTGAAGACGAAAGTGCACTGG
*
10293925 CCTAGGATTGAGTATAGACCCCTTGT
66 CCTAAGATTGAGTATAGACCCCTTGT
10293951 AGTCGATCCTAGTGCATAAAGGATCGAATTTGCAAAGTAAAATGCTGAAGACGAAAGTGCACTGG
1 AGTCGATCCTAGTGCATAAAGGATCGAATTTGCAAAGTAAAATGCTGAAGACGAAAGTGCACTGG
10294016 CCTAAGATTGAGTATAGACCCCTTGT
66 CCTAAGATTGAGTATAGACCCCTTGT
10294042 AGTCGATCCTAG
1 AGTCGATCCTAG
10294054 GGCAGGAAAT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 102 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (91 bp):
AGTCGATCCTAGTGCATAAAGGATCGAATTTGCAAAGTAAAATGCTGAAGACGAAAGTGCACTGG
CCTAAGATTGAGTATAGACCCCTTGT
Found at i:10300878 original size:32 final size:31
Alignment explanation
Indices: 10300842--10300949 Score: 112
Period size: 32 Copynumber: 3.3 Consensus size: 31
10300832 CCTTTAGTAA
10300842 TGGTTTTTCACGAGATCAACCAAAACCCAAAG
1 TGGTTTTTCA-GAGATCAACCAAAACCCAAAG
* *
10300874 TGGTTTTTCA-AGACTCAACCACAACCTTTAGCAA-
1 TGGTTTTTCAGAGA-TCAACCAAAACC--CA--AAG
*
10300908 TGGTTTTTCATGGGATCAACCAAAACCCAAAG
1 TGGTTTTTCA-GAGATCAACCAAAACCCAAAG
10300940 TGGTTTTTCA
1 TGGTTTTTCA
10300950 AGGCTTAACC
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
30 3 0.05
31 13 0.21
32 20 0.32
33 2 0.03
34 10 0.16
35 13 0.21
36 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (31 bp):
TGGTTTTTCAGAGATCAACCAAAACCCAAAG
Found at i:10300898 original size:66 final size:66
Alignment explanation
Indices: 10300818--10301033 Score: 292
Period size: 66 Copynumber: 3.3 Consensus size: 66
10300808 GACTTTTCGT
* *
10300818 AGGCTCAGCCACAACCTTTAGTAATGGTTTTTCACGAGATCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTCAACCACAACCTTTAGTAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
10300883 A
66 A
* * *
10300884 AGACTCAACCACAACCTTTAGCAATGGTTTTTCATGGGATCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTCAACCACAACCTTTAGTAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
10300949 A
66 A
* * * * * *
10300950 AGGCTTAACCACAACCTTT--TACACTAGTTTTTTACGGGCTAAACTAAAACCCAAAGTGGTTTT
1 AGGCTCAACCACAACCTTTAGTA-A-TGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTT
10301013 TCTA
64 TC-A
10301017 AGGCTCAACCACAACCT
1 AGGCTCAACCACAACCT
10301034 ACAACAATCA
Statistics
Matches: 132, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
64 1 0.01
65 1 0.01
66 113 0.86
67 17 0.13
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (66 bp):
AGGCTCAACCACAACCTTTAGTAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
A
Found at i:10301593 original size:21 final size:22
Alignment explanation
Indices: 10301569--10301611 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
10301559 AGCTTGGTCA
10301569 ACCAATA-TTCTTCCTTATTTC
1 ACCAATAGTTCTTCCTTATTTC
10301590 ACCAATAGGCTTCTTCCTTATT
1 ACCAATA-G-TTCTTCCTTATT
10301612 AGATAGTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
24 12 0.63
ACGTcount: A:0.23, C:0.28, G:0.05, T:0.44
Consensus pattern (22 bp):
ACCAATAGTTCTTCCTTATTTC
Found at i:10301932 original size:16 final size:16
Alignment explanation
Indices: 10301911--10301951 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
10301901 TAGTATGGCT
10301911 GCCATGATTATGATAG
1 GCCATGATTATGATAG
10301927 GCCATGATTATGATAG
1 GCCATGATTATGATAG
*
10301943 ACCATGATT
1 GCCATGATT
10301952 TATAGGTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (16 bp):
GCCATGATTATGATAG
Found at i:10310512 original size:23 final size:25
Alignment explanation
Indices: 10310486--10310547 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
10310476 TCCATTCTCG
*
10310486 TTTTCTTCTTTTTGCC-ATTACCTT
1 TTTTCTTCTTTTTGCCAATGACCTT
* *
10310510 TTTT-TTCTTATTTTCCAATGGCCTT
1 TTTTCTTCTT-TTTGCCAATGACCTT
10310535 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
10310548 CTATTTATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.16
24 9 0.28
25 13 0.41
26 5 0.16
ACGTcount: A:0.08, C:0.21, G:0.05, T:0.66
Consensus pattern (25 bp):
TTTTCTTCTTTTTGCCAATGACCTT
Done.