Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_pilon, whole genome shotgun sequence
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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 19
Found at i:3383722 original size:17 final size:17
Alignment explanation
Indices: 3383679--3383779 Score: 103
Period size: 18 Copynumber: 5.8 Consensus size: 17
3383669 ATTCTAAATG
**
3383679 TTTACAGTTATCAGGCA
1 TTTACAGTTATCAGATA
*
3383696 TTTCACAGTTATCATATA
1 TTT-ACAGTTATCAGATA
*
3383714 TTTACAGTTATTAGATGA
1 TTTACAGTTATCAGAT-A
*
3383732 TTTTCAGTTATCAGATA
1 TTTACAGTTATCAGATA
*
3383749 TTTACAGTTATTAGATGA
1 TTTACAGTTATCAGAT-A
**
3383767 TTTTTAGTTATCA
1 TTTACAGTTATCA
3383780 AATGATCTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
17 29 0.42
18 40 0.58
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.46
Consensus pattern (17 bp):
TTTACAGTTATCAGATA
Found at i:3383740 original size:35 final size:35
Alignment explanation
Indices: 3383701--3383779 Score: 140
Period size: 35 Copynumber: 2.3 Consensus size: 35
3383691 AGGCATTTCA
*
3383701 CAGTTATCATATATTTACAGTTATTAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATTAGATGATTTT
3383736 CAGTTATCAGATATTTACAGTTATTAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATTAGATGATTTT
*
3383771 TAGTTATCA
1 CAGTTATCA
3383780 AATGATCTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.47
Consensus pattern (35 bp):
CAGTTATCAGATATTTACAGTTATTAGATGATTTT
Found at i:3383776 original size:53 final size:53
Alignment explanation
Indices: 3383683--3383793 Score: 125
Period size: 53 Copynumber: 2.1 Consensus size: 53
3383673 TAAATGTTTA
* * * * *
3383683 CAGTTATCAGGCATTTCACAGTTATCATATATTTACAGTTATTAGATGATTTT
1 CAGTTATCAGACATTTCACAGTTATCAGATATTTACAGTTATCAAATGATCTT
* * **
3383736 CAGTTATCAGATATTT-ACAGTTATTAGATGATTTTTAGTTATCAAATGATCTT
1 CAGTTATCAGACATTTCACAGTTATCAGAT-ATTTACAGTTATCAAATGATCTT
3383789 CAGTT
1 CAGTT
3383794 GTCATATGGT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
52 11 0.23
53 37 0.77
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (53 bp):
CAGTTATCAGACATTTCACAGTTATCAGATATTTACAGTTATCAAATGATCTT
Found at i:3383784 original size:18 final size:18
Alignment explanation
Indices: 3383701--3383818 Score: 96
Period size: 18 Copynumber: 6.6 Consensus size: 18
3383691 AGGCATTTCA
* *
3383701 CAGTTATCATAT-ATTTA
1 CAGTTATCAAATGATTTT
* *
3383718 CAGTTATTAGATGATTTT
1 CAGTTATCAAATGATTTT
* *
3383736 CAGTTATCAGAT-ATTTA
1 CAGTTATCAAATGATTTT
* *
3383753 CAGTTATTAGATGATTTT
1 CAGTTATCAAATGATTTT
* *
3383771 TAGTTATCAAATGATCTT
1 CAGTTATCAAATGATTTT
* * *
3383789 CAGTTGTCATATGGTTTT
1 CAGTTATCAAATGATTTT
3383807 ACAGTTATCAAA
1 -CAGTTATCAAA
3383819 CGTAGATTAA
Statistics
Matches: 80, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
17 25 0.31
18 46 0.57
19 9 0.11
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (18 bp):
CAGTTATCAAATGATTTT
Found at i:3387991 original size:28 final size:28
Alignment explanation
Indices: 3387950--3388074 Score: 223
Period size: 28 Copynumber: 4.5 Consensus size: 28
3387940 TTCACATAAT
* *
3387950 AAATAAAATATTTACAATTTAACCATTA
1 AAATGAAATCTTTACAATTTAACCATTA
3387978 AAATGAAATCTTTACAATTTAACCATTA
1 AAATGAAATCTTTACAATTTAACCATTA
*
3388006 AAATGAAATATTTACAATTTAACCATTA
1 AAATGAAATCTTTACAATTTAACCATTA
3388034 AAATGAAATCTTTACAATTTAACCATTA
1 AAATGAAATCTTTACAATTTAACCATTA
3388062 AAATGAAATCTTT
1 AAATGAAATCTTT
3388075 TAGAATTCAT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 93 1.00
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (28 bp):
AAATGAAATCTTTACAATTTAACCATTA
Found at i:3393886 original size:22 final size:22
Alignment explanation
Indices: 3393843--3393886 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3393833 TAACATCCCT
* *
3393843 TCACTACATGCACAGCTGCACA
1 TCACCACATGCACAGCTACACA
*
3393865 TCACCACATGCACATCTACACA
1 TCACCACATGCACAGCTACACA
3393887 GCAGATCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.39, G:0.09, T:0.18
Consensus pattern (22 bp):
TCACCACATGCACAGCTACACA
Found at i:3398495 original size:22 final size:22
Alignment explanation
Indices: 3398465--3398530 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
3398455 TAACATCCCT
* *
3398465 TCACTACATGCACAACTATACA
1 TCACCACATGCACAACTACACA
*
3398487 TCACCACATGCACATCTACACA
1 TCACCACATGCACAACTACACA
*
3398509 TCACCACATGCACATCTACACA
1 TCACCACATGCACAACTACACA
3398531 GCAGATCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.38, C:0.38, G:0.05, T:0.20
Consensus pattern (22 bp):
TCACCACATGCACAACTACACA
Found at i:3405938 original size:20 final size:20
Alignment explanation
Indices: 3405915--3405952 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3405905 ACAGTTTCCA
* *
3405915 AATTCGCAACACTAATTTGG
1 AATTCACAACACGAATTTGG
3405935 AATTCACAACACGAATTT
1 AATTCACAACACGAATTT
3405953 CCCAAATTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (20 bp):
AATTCACAACACGAATTTGG
Found at i:3406101 original size:65 final size:65
Alignment explanation
Indices: 3405997--3406128 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
3405987 GCGAATTTGG
* * *
3405997 ATTTCACAACTCAATTACCGATATAGGTAAACACGGTAGAAAAAATCTGCAATTCGAATTCGCCA
1 ATTTCACAACTCAATTACCGACATAGGTAAACACGGTAGAAAAAATCTCCAACTCGAATTCGCCA
* *
3406062 ATTTCGCAACTCAATTACTGACATAGGTAAACACGGTAGAAAAAATCTCCAACTCGAATTCGCCA
1 ATTTCACAACTCAATTACCGACATAGGTAAACACGGTAGAAAAAATCTCCAACTCGAATTCGCCA
3406127 AT
1 AT
3406129 GTTTACCTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (65 bp):
ATTTCACAACTCAATTACCGACATAGGTAAACACGGTAGAAAAAATCTCCAACTCGAATTCGCCA
Found at i:3406175 original size:22 final size:22
Alignment explanation
Indices: 3406145--3406198 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3406135 CTATGGCGGT
3406145 AATT-GAGTTG-TGAAATTGGCG
1 AATTCGAGTTGTTG-AATTGGCG
*
3406166 AATTCGAGTTGTTGAATTTGCG
1 AATTCGAGTTGTTGAATTGGCG
*
3406188 AAATCGAGTTG
1 AATTCGAGTTG
3406199 CGGATTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 4 0.14
22 23 0.79
23 2 0.07
ACGTcount: A:0.28, C:0.07, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTCGAGTTGTTGAATTGGCG
Found at i:3406294 original size:22 final size:21
Alignment explanation
Indices: 3406250--3406359 Score: 77
Period size: 20 Copynumber: 5.4 Consensus size: 21
3406240 CGAAATCCGA
* * *
3406250 TTGCGAATTTGAAAACT-GAG
1 TTGCGAATTTGGAAATTCGTG
3406270 TTGCGAATTTGGGAAATTCGTG
1 TTGCGAATTT-GGAAATTCGTG
* *
3406292 TTGTGAATTTGGAAACT-GTG
1 TTGCGAATTTGGAAATTCGTG
** * * *
3406312 TTTTGAAATTGG-AGTTCATG
1 TTGCGAATTTGGAAATTCGTG
*
3406332 TTGCGAATTT-GAAA-TCGCG
1 TTGCGAATTTGGAAATTCGTG
3406351 TTGCGAATT
1 TTGCGAATT
3406360 CGTTGGTTAT
Statistics
Matches: 70, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
19 15 0.21
20 33 0.47
21 11 0.16
22 11 0.16
ACGTcount: A:0.26, C:0.09, G:0.27, T:0.37
Consensus pattern (21 bp):
TTGCGAATTTGGAAATTCGTG
Found at i:3406778 original size:123 final size:123
Alignment explanation
Indices: 3406616--3406858 Score: 486
Period size: 123 Copynumber: 2.0 Consensus size: 123
3406606 CATGTTTCAG
3406616 TTTAAAGCATGAGGTATGATGGATGAATATGAACATGAATAAATAAATAAAGCCTTAATATTTAG
1 TTTAAAGCATGAGGTATGATGGATGAATATGAACATGAATAAATAAATAAAGCCTTAATATTTAG
3406681 TTGCATGTACAGGTCACACAACCCAAGTCCAAATACAAAATCCCCGGAGCCCAAACAA
66 TTGCATGTACAGGTCACACAACCCAAGTCCAAATACAAAATCCCCGGAGCCCAAACAA
3406739 TTTAAAGCATGAGGTATGATGGATGAATATGAACATGAATAAATAAATAAAGCCTTAATATTTAG
1 TTTAAAGCATGAGGTATGATGGATGAATATGAACATGAATAAATAAATAAAGCCTTAATATTTAG
3406804 TTGCATGTACAGGTCACACAACCCAAGTCCAAATACAAAATCCCCGGAGCCCAAA
66 TTGCATGTACAGGTCACACAACCCAAGTCCAAATACAAAATCCCCGGAGCCCAAA
3406859 ACAACCCAGG
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 120 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (123 bp):
TTTAAAGCATGAGGTATGATGGATGAATATGAACATGAATAAATAAATAAAGCCTTAATATTTAG
TTGCATGTACAGGTCACACAACCCAAGTCCAAATACAAAATCCCCGGAGCCCAAACAA
Found at i:3407454 original size:32 final size:32
Alignment explanation
Indices: 3407412--3407484 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
3407402 ACTTTACTTT
*
3407412 ATTTTATTTTAT-TTTAGACACTAACATTCTAA
1 ATTTTATTTTATCATTAGA-ACTAACATTCTAA
*
3407444 CA-TTTATTTTATCATTCGAACTAACATTCTAA
1 -ATTTTATTTTATCATTAGAACTAACATTCTAA
3407476 ATTTTATTT
1 ATTTTATTT
3407485 ACTTTTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 1 0.03
32 30 0.83
33 5 0.14
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.51
Consensus pattern (32 bp):
ATTTTATTTTATCATTAGAACTAACATTCTAA
Found at i:3409258 original size:32 final size:34
Alignment explanation
Indices: 3409216--3409287 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
3409206 TTAAAACTTT
3409216 AAAATAATTT-AAGATTAA-AATAAATAATTT-A
1 AAAATAATTTAAAGATTAAGAATAAATAATTTGA
* *
3409247 AGAAATAATTTAAATATTAAGATTAAATAATTTGA
1 A-AAATAATTTAAAGATTAAGAATAAATAATTTGA
3409282 AAAATA
1 AAAATA
3409288 GAGATTTAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 1 0.03
32 9 0.26
33 7 0.20
34 16 0.46
35 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (34 bp):
AAAATAATTTAAAGATTAAGAATAAATAATTTGA
Found at i:3410916 original size:21 final size:20
Alignment explanation
Indices: 3410881--3410920 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
3410871 TTTATTGGTG
3410881 TTTTTGGTTTGGATTTGTTTC
1 TTTTTGGTTTGGA-TTGTTTC
3410902 TTTTTGG-TTGTGATTGTTT
1 TTTTTGGTTTG-GATTGTTT
3410921 ACTTGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.05, C:0.03, G:0.25, T:0.68
Consensus pattern (20 bp):
TTTTTGGTTTGGATTGTTTC
Found at i:3411188 original size:15 final size:15
Alignment explanation
Indices: 3411155--3411196 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3411145 AAAATAAAAT
*
3411155 AAATAA-AAT-ATAT
1 AAATAATAATAATAA
3411168 AAATAATAATAATAA
1 AAATAATAATAATAA
*
3411183 AAATAATATTAATA
1 AAATAATAATAATA
3411197 TAATATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 6 0.24
14 3 0.12
15 16 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAATAATAATAA
Found at i:3411320 original size:29 final size:28
Alignment explanation
Indices: 3411288--3411404 Score: 128
Period size: 28 Copynumber: 4.2 Consensus size: 28
3411278 AAAAACTATA
* * *
3411288 TATATGTTTTCAAAATACGTTTTTAAAAT
1 TATATGTTTTCAAAA-ATGTTTTCAAAAC
*
3411317 TATATG-TTTCCAAAATGTTTTCAAAAC
1 TATATGTTTTCAAAAATGTTTTCAAAAC
* **
3411344 CATACATTTTCAAAAATGTTTTCAAAAC
1 TATATGTTTTCAAAAATGTTTTCAAAAC
* * *
3411372 CACATGTTTTCAAAAATGTTTTCAAAAT
1 TATATGTTTTCAAAAATGTTTTCAAAAC
3411400 TATAT
1 TATAT
3411405 ATTATATACG
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
27 13 0.18
28 54 0.74
29 6 0.08
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (28 bp):
TATATGTTTTCAAAAATGTTTTCAAAAC
Found at i:3411380 original size:16 final size:15
Alignment explanation
Indices: 3411330--3411398 Score: 60
Period size: 12 Copynumber: 4.9 Consensus size: 15
3411320 ATGTTTCCAA
3411330 AATGTTTTCAAAACC
1 AATGTTTTCAAAACC
**
3411345 ATACATTTTC-AAA--
1 A-ATGTTTTCAAAACC
3411358 AATGTTTTCAAAACC
1 AATGTTTTCAAAACC
3411373 ACATGTTTTC-AAA--
1 A-ATGTTTTCAAAACC
3411386 AATGTTTTCAAAA
1 AATGTTTTCAAAA
3411399 TTATATATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
12 14 0.32
13 8 0.18
15 8 0.18
16 14 0.32
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (15 bp):
AATGTTTTCAAAACC
Found at i:3422216 original size:55 final size:55
Alignment explanation
Indices: 3422124--3422474 Score: 420
Period size: 55 Copynumber: 6.3 Consensus size: 55
3422114 CTAAGTGTAC
* * *
3422124 TACAGGCACTATGTGTGCAAATCCACGTAATTAATCATGAGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCG
* *
3422179 TACATGCACTATGTGTGTAAATCCACAAAATTCATCATGAGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCG
* * *
3422234 TACATGCACTATATGTGCAAATCCACATAATTCATCTTGAGTTGATGAATAATCG
1 TACATGCACTATGTGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCG
** * * *
3422289 TACATATATATTATGTGTGCAAATCCACATAATTCATCGTGA-TTGATGAATAACTG
1 TAC--ATGCACTATGTGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCG
* * * *
3422345 TACAAGCACTATGTGTGTGCAAATCCACAGAATTCATCATGAGTTAATGAATAACCA
1 TACATGCACTA--TGTGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCG
* * * * * *
3422402 TATAGGAACTATGTGTGC-AACCCACAGAATTCATCATGAGTTGATGAATTACCG
1 TACATGCACTATGTGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCG
*
3422456 TATATGCACTACT-TGTGCA
1 TACATGCACTA-TGTGTGCA
3422475 TTCTAATTAA
Statistics
Matches: 254, Mismatches: 35, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
54 50 0.20
55 111 0.44
56 42 0.17
57 51 0.20
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (55 bp):
TACATGCACTATGTGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCG
Found at i:3428641 original size:18 final size:19
Alignment explanation
Indices: 3428618--3428657 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3428608 AGTACCAATA
*
3428618 GGGGAT-TATCGATACTAT
1 GGGGATGTATCAATACTAT
3428636 GGGGATGGTATCAATACTAT
1 GGGGAT-GTATCAATACTAT
3428656 GG
1 GG
3428658 ATCACAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.28, C:0.10, G:0.33, T:0.30
Consensus pattern (19 bp):
GGGGATGTATCAATACTAT
Found at i:3429158 original size:55 final size:55
Alignment explanation
Indices: 3429074--3429474 Score: 567
Period size: 55 Copynumber: 7.3 Consensus size: 55
3429064 AAGTGTACTG
*
3429074 CAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTA
1 CAGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA
*
3429129 CAGGCACTATATGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA
1 CAGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA
* * *
3429184 CAGGCACTATGTGTGTAAATCCACATAATTCATCATGAGTTGATGAATAACCATA
1 CAGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA
* * * *
3429239 CAGGCACTATGCGTACAAATCCATATAATTCATCATGAGTTGATGAATAACCGTA
1 CAGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA
* * * *
3429294 CATGCACTATGTGTACAAATCCATAGAATTCATCATGAGTTGATGAATAACAGTA
1 CAGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA
* *
3429349 CAGGCACTATGTGTGCAAATCCACAGAATTCATCATGATTTGATGAATAACCATA
1 CAGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA
* * *
3429404 CAGGCACTATGTGTG--TATCCA-ACGAAATTCATAATGAGTTGATGAATTACCGTA
1 CAGGCACTATGTGTGCAAATCCACA-G-AATTCATCATGAGTTGATGAATAACCGTA
* *
3429458 TAGGAACTACT-TGTGCA
1 CAGGCACTA-TGTGTGCA
3429475 TTCTAATTAA
Statistics
Matches: 313, Mismatches: 28, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
52 1 0.00
53 6 0.02
54 36 0.12
55 270 0.86
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (55 bp):
CAGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA
Found at i:3429570 original size:20 final size:20
Alignment explanation
Indices: 3429534--3429571 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3429524 ACTAATGGTG
*
3429534 TAAATTTATAAGGTTTTCAA
1 TAAATTTATAAGATTTTCAA
3429554 TAAATTGTA-AAGATTTTC
1 TAAATT-TATAAGATTTTC
3429572 TCGATATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (20 bp):
TAAATTTATAAGATTTTCAA
Found at i:3433423 original size:28 final size:28
Alignment explanation
Indices: 3433343--3433431 Score: 117
Period size: 28 Copynumber: 3.2 Consensus size: 28
3433333 AAAAACCATA
* *
3433343 TATATGTTTTCAAAATACATTTTCAAAAT
1 TATATGTTTTCAAAA-ACGTTTTCAAAAC
*
3433372 TATTTGTTTTC-AAAACGTTTTCAAAAC
1 TATATGTTTTCAAAAACGTTTTCAAAAC
* *
3433399 CATATGTTTTCAAAAATGTTTTCAAAAC
1 TATATGTTTTCAAAAACGTTTTCAAAAC
3433427 TATAT
1 TATAT
3433432 ATTATATACG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 20 0.38
28 22 0.42
29 10 0.19
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (28 bp):
TATATGTTTTCAAAAACGTTTTCAAAAC
Found at i:3433881 original size:10 final size:10
Alignment explanation
Indices: 3433866--3433920 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
3433856 AGCTACTCAA
3433866 AACCTGATTT
1 AACCTGATTT
3433876 AACCTGATTT
1 AACCTGATTT
* *
3433886 GATCTGATTT
1 AACCTGATTT
**
3433896 AATTTGATTT
1 AACCTGATTT
* *
3433906 GACTTGATTT
1 AACCTGATTT
3433916 AACCT
1 AACCT
3433921 TACCCTCAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (10 bp):
AACCTGATTT
Found at i:3433894 original size:20 final size:19
Alignment explanation
Indices: 3433869--3433920 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
3433859 TACTCAAAAC
3433869 CTGATTTAACCTGATTTGA
1 CTGATTTAACCTGATTTGA
**
3433888 TCTGATTTAATTTGATTTGA
1 -CTGATTTAACCTGATTTGA
3433908 CTTGATTTAACCT
1 C-TGATTTAACCT
3433921 TACCCTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.48
Consensus pattern (19 bp):
CTGATTTAACCTGATTTGA
Found at i:3437420 original size:20 final size:20
Alignment explanation
Indices: 3437397--3437447 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
3437387 ACTTTTTTAT
3437397 TTAGTTATTGATGAATTTCA
1 TTAGTTATTGATGAATTTCA
*
3437417 TTAGTTGTTGATGAATTTCA
1 TTAGTTATTGATGAATTTCA
*
3437437 TTAGGTATTGA
1 TTAGTTATTGA
3437448 CCCTAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (20 bp):
TTAGTTATTGATGAATTTCA
Found at i:3438054 original size:40 final size:40
Alignment explanation
Indices: 3437964--3438077 Score: 165
Period size: 40 Copynumber: 2.8 Consensus size: 40
3437954 ATGACAACTT
* * * *
3437964 TAGTGGCGTTTCTTTATAAACGCCGCAATAGGTTTCATCTA
1 TAGTGGCGTTTTTTTATAAACGCCGTAATA-GATCCATCTA
*
3438005 TAGTGGCGTTTTTTTATAAACGTCGTAATAGATCCATCTA
1 TAGTGGCGTTTTTTTATAAACGCCGTAATAGATCCATCTA
*
3438045 TAGTGGCGTTTTTTAATAAACGCCGTAATAGAT
1 TAGTGGCGTTTTTTTATAAACGCCGTAATAGAT
3438078 TAGTACTTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
40 39 0.59
41 27 0.41
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (40 bp):
TAGTGGCGTTTTTTTATAAACGCCGTAATAGATCCATCTA
Found at i:3438171 original size:82 final size:82
Alignment explanation
Indices: 3438012--3438282 Score: 289
Period size: 82 Copynumber: 3.3 Consensus size: 82
3438002 CTATAGTGGC
* * * * * * *
3438012 GTTTTTTTATAAACGTCGTAATA-GATCCATCTATAGTGGCGTTTTTTAATAAACGCCGTAATAG
1 GTTTTTATATAAACGTCGTAATAGGGTTCACCTATAGTGGTGTTTTTCAATAAACGCCGCAATAG
*
3438076 ATTAGTACTTTAGCAGT
66 ATTAGAACTTTAGCAGT
* * *
3438093 GTTTTTATACAAACGTCGTAATAGGGTTCACCTATTA-TGGTGTTTTTCAATAAATGCCGCAAAA
1 GTTTTTATATAAACGTCGTAATAGGGTTCACCTA-TAGTGGTGTTTTTCAATAAACGCCGCAATA
* * *
3438157 AATTAGAACTTTAGCGGC
65 GATTAGAACTTTAGCAGT
* ** * *
3438175 GTTTTTATATTAACACCGCAATAGAGTTCACCTATAGTGGCAT-TTTTTCAATAAACGCCGCAAT
1 GTTTTTATATAAACGTCGTAATAGGGTTCACCTATAGTGG--TGTTTTTCAATAAACGCCGCAAT
*
3438239 AGATTAGAACTTTAG-TGAT
64 AGATTAGAACTTTAGCAG-T
*
3438258 GTTTTTATATAAACGTCATAATAGG
1 GTTTTTATATAAACGTCGTAATAGG
3438283 ATTTACCAAC
Statistics
Matches: 153, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
81 23 0.15
82 75 0.49
83 54 0.35
84 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (82 bp):
GTTTTTATATAAACGTCGTAATAGGGTTCACCTATAGTGGTGTTTTTCAATAAACGCCGCAATAG
ATTAGAACTTTAGCAGT
Found at i:3438255 original size:42 final size:41
Alignment explanation
Indices: 3437959--3438272 Score: 149
Period size: 41 Copynumber: 7.7 Consensus size: 41
3437949 ACAAAATGAC
* * **
3437959 AACTTTAGTGGCGTTTCTT-TATAAACGCCGCAATAGGTTTC
1 AACTTTAGTGGCGTTT-TTCAATAAACGCCGCAATAGATTAG
* * ** * * **
3438000 ATCTATAGTGGCGTTTTTTTATAAACGTCGTAATAGA-TCC
1 AACTTTAGTGGCGTTTTTCAATAAACGCCGCAATAGATTAG
* * * *
3438040 ATCTATAGTGGCGTTTTTTAATAAACGCCGTAATAGATTAG
1 AACTTTAGTGGCGTTTTTCAATAAACGCCGCAATAGATTAG
* ** * * * * * *
3438081 TACTTTAGCAGTGTTTTT-ATACAAACGTCGTAATAGGGTT-C
1 AACTTTAGTGGCGTTTTTCA-ATAAACGCCGCAATA-GATTAG
* * * * *
3438122 ACCTATTA-TGGTGTTTTTCAATAAATGCCGCAAAAAATTAG
1 AACT-TTAGTGGCGTTTTTCAATAAACGCCGCAATAGATTAG
* * * *
3438163 AACTTTAGCGGCGTTTTT-ATATTAACACCGCAATAGAGTT-C
1 AACTTTAGTGGCGTTTTTCA-ATAAACGCCGCAATAGA-TTAG
* * *
3438204 ACCTATAGTGGCATTTTTTCAATAAACGCCGCAATAGATTAG
1 AACTTTAGTGGC-GTTTTTCAATAAACGCCGCAATAGATTAG
**
3438246 AACTTTAGTGATGTTTTT-ATATAAACG
1 AACTTTAGTGGCGTTTTTCA-ATAAACG
3438273 TCATAATAGG
Statistics
Matches: 206, Mismatches: 53, Indels: 28
0.72 0.18 0.10
Matches are distributed among these distances:
40 47 0.23
41 121 0.59
42 37 0.18
43 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (41 bp):
AACTTTAGTGGCGTTTTTCAATAAACGCCGCAATAGATTAG
Found at i:3442146 original size:28 final size:28
Alignment explanation
Indices: 3442092--3442146 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
3442082 TTATTATGAA
* *
3442092 TTTCAAGTTTCTTGTTATGAATTTCAAG
1 TTTCAAGTTTCATGTTATGAATGTCAAG
* *
3442120 TTTCAAGTTTGATGTTATGGATGTCAA
1 TTTCAAGTTTCATGTTATGAATGTCAA
3442147 ATTTATTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.47
Consensus pattern (28 bp):
TTTCAAGTTTCATGTTATGAATGTCAAG
Found at i:3442346 original size:85 final size:85
Alignment explanation
Indices: 3442233--3442678 Score: 452
Period size: 85 Copynumber: 5.2 Consensus size: 85
3442223 GTTTTAATTC
* ** * ** *
3442233 GCGGCGTTTGTA-TAAAAAACGTTGCTATAGATTTGACCTTTTGTGGCGTTTATTCTAAAAACGC
1 GCGGCGTTTGTATTCAAAAACGCCGCTATAGATCTGACCTTTTACGGCGTTTGTTCTAAAAACGC
* *
3442297 CGCTCTAGATCTAACCTTTT
66 CGCTATAGATCTGACCTTTT
* * *
3442317 GCGGCGTTTGTATTCAAAAACGCCGCTATAGATATGACCTTTTACGGTGTTTGTTCTAAAAACGT
1 GCGGCGTTTGTATTCAAAAACGCCGCTATAGATCTGACCTTTTACGGCGTTTGTTCTAAAAACGC
*
3442382 CGTTATAGATCTGACCTTTT
66 CGCTATAGATCTGACCTTTT
* * * * * *
3442402 GTGGTGTTTGTATCCAAAAATGCAGCTATAGATCTGACCTTTTACGGCATTTGTATCTAAAAACG
1 GCGGCGTTTGTATTCAAAAACGCCGCTATAGATCTGACCTTTTACGGCGTTTGT-TCTAAAAACG
** *
3442467 TTGCTATAGATATGACCTTTT
65 CCGCTATAGATCTGACCTTTT
* * * *
3442488 GCGGCATTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACG
1 GCGGCGTTTGTATTCAAAAACGCCGCTATAGATCTGACCTTTTACGGCGTTTGT-TCTAAAAACG
**
3442552 CCGCTATAGATCTGATTTTTT
65 CCGCTATAGATCTGACCTTTT
* * ** * **
3442573 GCGGCG-TT-TATTCTGAAAACGCCGCTATAGATCTCGACCTTTTATGGTATTTATTCCGAAAAC
1 GCGGCGTTTGTATTC-AAAAACGCCGCTATAGATCT-GACCTTTTACGGCGTTTGTTCTAAAAAC
* *
3442636 GCCGCTATAGATATCGATCTTTT
64 GCCGCTATAGATCT-GACCTTTT
* * *
3442659 GCAGCATTTGT-TCCAAAAAC
1 GCGGCGTTTGTATTCAAAAAC
3442679 ATAGATCTTG
Statistics
Matches: 303, Mismatches: 51, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
83 1 0.00
84 16 0.05
85 215 0.71
86 66 0.22
87 4 0.01
88 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (85 bp):
GCGGCGTTTGTATTCAAAAACGCCGCTATAGATCTGACCTTTTACGGCGTTTGTTCTAAAAACGC
CGCTATAGATCTGACCTTTT
Found at i:3442465 original size:128 final size:128
Alignment explanation
Indices: 3442247--3442678 Score: 494
Period size: 128 Copynumber: 3.4 Consensus size: 128
3442237 CGTTTGTATA
* * * * * *
3442247 AAAAACGTTGCTATAGATTTGACCTTTTGTGGCGTTTAT-TCTAAAAACGCCGCTCTAGATCTAA
1 AAAAACGTCGCTATAGATCTGACCTTTTGTGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGA
** *
3442311 CCTTTTGCGGCGTTTGTAT-TCAAAAACGCCGCTATAGATATGACCTTTTACGGTGTTTGTTCT
66 CCTTTTGCGGCGTTTGTATCT-AAAAACGCCGCTATAGATATGACCTTTTACGGCATTTGTTCC
* * * *
3442374 AAAAACGTCGTTATAGATCTGACCTTTTGTGGTGTTTGTATCCAAAAATGCAGCTATAGATCTGA
1 AAAAACGTCGCTATAGATCTGACCTTTTGTGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGA
* * ** *
3442439 CCTTTTACGGCATTTGTATCTAAAAACGTTGCTATAGATATGACCTTTTGCGGCATTTGTTCC
66 CCTTTTGCGGCGTTTGTATCTAAAAACGCCGCTATAGATATGACCTTTTACGGCATTTGTTCC
* *
3442502 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGA
1 AAAAACGTCGCTATAGATCTGACCTTTTGTGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGA
** * * * * * *
3442567 TTTTTTGCGGCGTTTAT-TCTGAAAACGCCGCTATAGATCTCGACCTTTTATGGTATTTATTCC
66 CCTTTTGCGGCGTTTGTATCTAAAAACGCCGCTATAGATAT-GACCTTTTACGGCATTTGTTCC
* * * * ** *
3442630 GAAAACGCCGCTATAGATATCGATCTTTTGCAGCATTTGT-TCCAAAAAC
1 AAAAACGTCGCTATAGATCT-GACCTTTTGTGGCGTTTGTATCCAAAAAC
3442679 ATAGATCTTG
Statistics
Matches: 259, Mismatches: 42, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
127 53 0.20
128 189 0.73
129 17 0.07
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (128 bp):
AAAAACGTCGCTATAGATCTGACCTTTTGTGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGA
CCTTTTGCGGCGTTTGTATCTAAAAACGCCGCTATAGATATGACCTTTTACGGCATTTGTTCC
Found at i:3442640 original size:43 final size:42
Alignment explanation
Indices: 3442233--3442678 Score: 444
Period size: 43 Copynumber: 10.5 Consensus size: 42
3442223 GTTTTAATTC
* ** *
3442233 GCGGCGTTTGTAT-AAAAAACGTTGCTATAGATTTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * * *
3442275 GTGGCGTTTATTCTAAAAACGCCGCTCTAGATCTAACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
3442317 GCGGCGTTTGTATTCAAAAACGCCGCTATAGATATGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * * *
3442360 ACGGTGTTTGTTCTAAAAACGTCGTTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
3442402 GTGGTGTTTGTATCCAAAAATGCAGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * ** *
3442445 ACGGCATTTGTATCTAAAAACGTTGCTATAGATATGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
*
3442488 GCGGCATTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
**
3442530 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGATTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* **
3442573 GCGGCGTTTATTCTGAAAACGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
** ** * * * *
3442616 ATGGTATTTATTCCGAAAACGCCGCTATAGATATCGATCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
* *
3442659 GCAGCATTTGTTCCAAAAAC
1 GCGGCGTTTGTTCCAAAAAC
3442679 ATAGATCTTG
Statistics
Matches: 335, Mismatches: 64, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
41 1 0.00
42 134 0.40
43 200 0.60
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:3445417 original size:13 final size:14
Alignment explanation
Indices: 3445391--3445419 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3445381 TTGACCTAAC
3445391 CCGTTGACTGTTGA
1 CCGTTGACTGTTGA
3445405 CCGTTGACT-TTGA
1 CCGTTGACTGTTGA
3445418 CC
1 CC
3445420 AAAAAGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.14, C:0.28, G:0.24, T:0.34
Consensus pattern (14 bp):
CCGTTGACTGTTGA
Found at i:3445440 original size:16 final size:16
Alignment explanation
Indices: 3445419--3445450 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3445409 TGACTTTGAC
3445419 CAAAAAGTCAAATTTT
1 CAAAAAGTCAAATTTT
*
3445435 CAAAAAGTCATATTTT
1 CAAAAAGTCAAATTTT
3445451 ATGTTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (16 bp):
CAAAAAGTCAAATTTT
Found at i:3447718 original size:24 final size:24
Alignment explanation
Indices: 3447622--3447718 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 24
3447612 GAATATTTTA
* * *
3447622 TCTGATTTCCGATTTGAATTTTGT
1 TCTGATATCTGATCTGAATTTTGT
* * * *
3447646 TCTAACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTTTGT
* * * *
3447670 TCTTATTTCTGACCTGGATTTTGT
1 TCTGATATCTGATCTGAATTTTGT
*
3447694 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTTTGT
3447718 T
1 T
3447719 TTGTTTTCTG
Statistics
Matches: 54, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTTTGT
Found at i:3449240 original size:38 final size:38
Alignment explanation
Indices: 3449145--3449245 Score: 107
Period size: 38 Copynumber: 2.6 Consensus size: 38
3449135 AAGATAAGGT
*
3449145 TCTTAAATTCAAGAAGAAATAAAAAATGACGTAAGGAAGAA
1 TCTTAAATT-AAAAAGAAAT--AAAATGACGTAAGGAAGAA
* *
3449186 TCTTAAATTTAGAAAGAAATAAAGTGACGTAA-G-AGAAA
1 TCTTAAA-TTAAAAAGAAATAAAATGACGTAAGGAAG-AA
3449224 TCTTAAATCTAAAAAGAAATAA
1 TCTTAAAT-TAAAAAGAAATAA
3449246 GATGGAATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
37 3 0.06
38 22 0.42
39 11 0.21
41 15 0.28
42 2 0.04
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23
Consensus pattern (38 bp):
TCTTAAATTAAAAAGAAATAAAATGACGTAAGGAAGAA
Found at i:3449698 original size:14 final size:14
Alignment explanation
Indices: 3449687--3449716 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3449677 AAAATGAATT
3449687 ACATTTTCTGAAAA
1 ACATTTTCTGAAAA
*
3449701 ACATTTTCTGGAAA
1 ACATTTTCTGAAAA
3449715 AC
1 AC
3449717 GTATGTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (14 bp):
ACATTTTCTGAAAA
Found at i:3450013 original size:23 final size:22
Alignment explanation
Indices: 3449971--3450055 Score: 61
Period size: 23 Copynumber: 3.9 Consensus size: 22
3449961 AATATTGGTA
*
3449971 TATTATA-TTTAAAAATTATTAAT
1 TATTATATTTTAAATA-TATT-AT
3449994 TATTATATTTTAAATATATTTAT
1 TATTATATTTTAAATATA-TTAT
** *
3450017 TAAAATATTATTAGAT-TATTA-
1 TATTATATT-TTAAATATATTAT
*
3450038 TATTA-ATATTAAATATAT
1 TATTATATTTTAAATATAT
3450056 AAATAATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
19 5 0.10
20 5 0.10
21 3 0.06
22 3 0.06
23 20 0.40
24 14 0.28
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
TATTATATTTTAAATATATTAT
Found at i:3450025 original size:28 final size:23
Alignment explanation
Indices: 3449970--3450027 Score: 62
Period size: 28 Copynumber: 2.3 Consensus size: 23
3449960 TAATATTGGT
3449970 ATATTATATTTAAAAATTATTAA
1 ATATTATATTTAAAAATTATTAA
*
3449993 TTATTATATTTTAAATATATTTATTAAA
1 ATATTATA-TTTAAA-A-A-TTATT-AA
3450021 ATATTAT
1 ATATTAT
3450028 TAGATTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 7 0.25
24 6 0.21
25 1 0.04
26 1 0.04
27 5 0.18
28 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTATATTTAAAAATTATTAA
Found at i:3450081 original size:19 final size:19
Alignment explanation
Indices: 3450013--3450093 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
3450003 TTAAATATAT
3450013 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
3450032 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
3450051 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
3450071 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
3450089 -TATTA
1 TTATTA
3450094 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:3450226 original size:22 final size:22
Alignment explanation
Indices: 3450198--3450241 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3450188 TTGATTATTT
3450198 TATTATAATATTAAAAACATTA
1 TATTATAATATTAAAAACATTA
* * *
3450220 TATTATATTATTAGAAATATTA
1 TATTATAATATTAAAAACATTA
3450242 ATAAATGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTATAATATTAAAAACATTA
Found at i:3461854 original size:20 final size:20
Alignment explanation
Indices: 3461831--3461875 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
3461821 AAAAAATTAA
3461831 AATGAA-AATTTAAAATAATT
1 AATGAACAATTTAAAAT-ATT
*
3461851 AATGAACAATTTGAAATATT
1 AATGAACAATTTAAAATATT
3461871 AATGA
1 AATGA
3461876 CATTAACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (20 bp):
AATGAACAATTTAAAATATT
Found at i:3470734 original size:50 final size:50
Alignment explanation
Indices: 3470624--3470760 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
3470614 TGTGGGGTTG
* *
3470624 CACATAGTGCCAATA-AGGAAATTCATAAACTCATTATGAATTTTGTGAGGTTGCA
1 CACATAGTACCAATACA-GAAATTCATAAACTC-----GAATTTTGTGAGGTTACA
*
3470679 CACATAGTACCATTACAGAAATTCATAAACTCGAATTTTGTGAGGTTACA
1 CACATAGTACCAATACAGAAATTCATAAACTCGAATTTTGTGAGGTTACA
* **
3470729 CACATAGTGCCAATATGGAAATTCATAAACTC
1 CACATAGTACCAATACAGAAATTCATAAACTC
3470761 ATTATAAATT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
50 45 0.61
55 28 0.38
56 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (50 bp):
CACATAGTACCAATACAGAAATTCATAAACTCGAATTTTGTGAGGTTACA
Found at i:3470796 original size:55 final size:54
Alignment explanation
Indices: 3470543--3470807 Score: 231
Period size: 55 Copynumber: 4.9 Consensus size: 54
3470533 TGAATATTTC
* * * *** *
3470543 AACTCATTATAAATTCCGTG-GTTTTGCACACGTAGTGCCAATACATTAATTCACA
1 AACTCATTATAAATT-TGTGAG-GTTGCACACATAGTGCCAATACGGAAATTCATA
* * *
3470598 AACTCATTATGAATTATGTGGGGTTG--CACATAGTGCCAATAAGGAAATTCATA
1 AACTCATTATAAATT-TGTGAGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * * *
3470651 AACTCATTATGAATTTTGTGAGGTTGCACACATAGTACCATTACAGAAATTCATA
1 AACTCATTAT-AAATTTGTGAGGTTGCACACATAGTGCCAATACGGAAATTCATA
* *
3470706 AACTCGA--AT---TTTGTGAGGTTACACACATAGTGCCAATATGGAAATTCATA
1 AACTC-ATTATAAATTTGTGAGGTTGCACACATAGTGCCAATACGGAAATTCATA
* ** * *
3470756 AACTCATTATAAATTTCGTGATGTTGCACTTATAGTGCCAATATGAAAATTC
1 AACTCATTATAAATTT-GTGAGGTTGCACACATAGTGCCAATACGGAAATTC
3470808 CAACATATAA
Statistics
Matches: 172, Mismatches: 27, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
49 1 0.01
50 41 0.24
51 2 0.01
53 40 0.23
54 8 0.05
55 78 0.45
56 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (54 bp):
AACTCATTATAAATTTGTGAGGTTGCACACATAGTGCCAATACGGAAATTCATA
Found at i:3480309 original size:55 final size:55
Alignment explanation
Indices: 3480250--3480828 Score: 759
Period size: 55 Copynumber: 10.5 Consensus size: 55
3480240 TTCCACGGTT
* * * * * *
3480250 TTGCACACATAGTGTCGATA-TGATAATTCAAAAACTCATTATGAATTACGTGGGG
1 TTGCACACATAGTGCCAATACGGA-AATTCATAAACTCATTATGAATTTCGTGAGG
* * *
3480305 TTGCACACATAGTGCCAATACTGAAATTCATAAACTCATTTTTGAATTTCTTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCA-TTATGAATTTCGTGAGG
* * *
3480361 TTGCACACATAATGCTAATACGGAAATTCATAAACACATTATGAATTTCGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* * *
3480416 TTGCACACATAGTGCCAATATGTAAATTCATAAACTCATTATGAATTTAGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* *
3480471 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCGTTAT-AATTTTCATGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAA-TTTCGTGAGG
* * * *
3480526 TTCCACACATAATACCAATACGGAAATTCATAAACTCATTATGAATTTTGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* * ** * *
3480581 TTGCACATATAGTTCCAATACAAAAATTCATAAACTCATTATAAATTTTGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* * * * *
3480636 TTACACACATAGTTCCAATAGGGAAATTCATAAACTCATTATGAATTTTGTGTGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
*
3480691 TTGCACACATAGTGCCAATA-GAGAAATTCATAAACTCATTATGAATTTCTTGAGG
1 TTGCACACATAGTGCCAATACG-GAAATTCATAAACTCATTATGAATTTCGTGAGG
* ** * *
3480746 TTCCACACATAGTGCCAATACAAAAATTCATAAACTTATTATGAATTTTGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
3480801 TTGCACACATAGTGCCAATACGGAAATT
1 TTGCACACATAGTGCCAATACGGAAATT
3480829 TCCAACATAT
Statistics
Matches: 460, Mismatches: 58, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
54 3 0.01
55 405 0.88
56 52 0.11
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (55 bp):
TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
Found at i:3491020 original size:24 final size:23
Alignment explanation
Indices: 3490993--3491041 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3490983 TAGGGGCACG
*
3490993 TAGAAATTATCCTGAAAGACCACA
1 TAGAAA-TATCCCGAAAGACCACA
* *
3491017 TAGAAATGTCCCGAAGGACCACA
1 TAGAAATATCCCGAAAGACCACA
3491040 TA
1 TA
3491042 TAACACATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.18
Consensus pattern (23 bp):
TAGAAATATCCCGAAAGACCACA
Found at i:3496951 original size:22 final size:21
Alignment explanation
Indices: 3496899--3496951 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
3496889 AAGTTACCTG
3496899 GGTATTGATACCCTTCACATA
1 GGTATTGATACCCTTCACATA
*
3496920 GATATTGATACCCCTTTCACAT-
1 GGTATTGATA-CCC-TTCACATA
*
3496942 GGTATCGATA
1 GGTATTGATA
3496952 TTGTTCAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.33
22 11 0.41
23 7 0.26
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (21 bp):
GGTATTGATACCCTTCACATA
Found at i:3498582 original size:66 final size:66
Alignment explanation
Indices: 3498449--3498609 Score: 222
Period size: 66 Copynumber: 2.5 Consensus size: 66
3498439 TGCACTAAGA
* * * *
3498449 GTGCATCAATGCATGAAGTGCATTCGATG--TTTCAAAATAGCCTGAGTGCATCGATGCATGACT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTTCAAAATACCCTGAGTGCATCGATGCATGACT
3498512 T
66 T
* *
3498513 GTGCATCGATGCATCAAATGCATTCGATGTTTTTCATAAA-ACCCTGAGTGCATCGATGCATG-G
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTTCA-AAATACCCTGAGTGCATCGATGCATGAC
3498576 TAT
65 T-T
3498579 GTGCATCGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
3498610 CAATTTATTC
Statistics
Matches: 87, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
64 26 0.30
65 1 0.01
66 57 0.66
67 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (66 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTTCAAAATACCCTGAGTGCATCGATGCATGACT
T
Found at i:3508497 original size:17 final size:17
Alignment explanation
Indices: 3508475--3508517 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3508465 TTAAGGTTAG
3508475 AGAAGATGAACAGAGAT
1 AGAAGATGAACAGAGAT
3508492 AGAAGATGAACAGAGAT
1 AGAAGATGAACAGAGAT
*
3508509 AGAATATGA
1 AGAAGATGA
3508518 GGAGGCTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.53, C:0.05, G:0.28, T:0.14
Consensus pattern (17 bp):
AGAAGATGAACAGAGAT
Found at i:3509068 original size:111 final size:111
Alignment explanation
Indices: 3508856--3509059 Score: 241
Period size: 111 Copynumber: 1.8 Consensus size: 111
3508846 GTTTGGGGAA
* * *
3508856 GAACACGGATGAACATGATTTAATTTTTGGGTGTTAGATCGAAAAAGCATGAATGAGTTTAGGTT
1 GAACACGGATGAACAGGATTGAATTTTTGGGTGTTAGATCGAAAAAGCAGGAATGAGTTTAGGTT
* * * * * *
3508921 TTTGTGTTTGTGAATATCGAATAATGGTTTAGGGAATAACTGATAC
66 TTTATGTTTGTAAAGATCAAAGAAGGGTTTAGGGAATAACTGATAC
* * * * *
3508967 GAACACGGATGAACAAGGGTTGAATTTTTGGGTGTTTGATCGAAAAA-TAGGAAAT-TGTTTGGG
1 GAACACGGATGAAC-AGGATTGAATTTTTGGGTGTTAGATCGAAAAAGCAGG-AATGAGTTTAGG
*
3509030 TTTTTATGTTTGTAAAGATCAAAGGAGGGT
64 TTTTTATGTTTGTAAAGATCAAAGAAGGGT
3509060 ATTTGGAATG
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
111 45 0.59
112 31 0.41
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.34
Consensus pattern (111 bp):
GAACACGGATGAACAGGATTGAATTTTTGGGTGTTAGATCGAAAAAGCAGGAATGAGTTTAGGTT
TTTATGTTTGTAAAGATCAAAGAAGGGTTTAGGGAATAACTGATAC
Found at i:3509331 original size:61 final size:61
Alignment explanation
Indices: 3509261--3509396 Score: 247
Period size: 61 Copynumber: 2.2 Consensus size: 61
3509251 CCTAGTTTTT
3509261 AATTTGTTCAATTTAGTCCAAATTTAATGATT-CAATTCATTAATTTAAGCTTCATATTTAA
1 AATTTGTTCAATTTAGTCCAAATTTAATG-TTGCAATTCATTAATTTAAGCTTCATATTTAA
*
3509322 AATTTGTTCAATTTAGTCCAAATTTAATGTTGCAATTTATTAATTTAAGCTTCATATTTAA
1 AATTTGTTCAATTTAGTCCAAATTTAATGTTGCAATTCATTAATTTAAGCTTCATATTTAA
3509383 AATTTGTTCAATTT
1 AATTTGTTCAATTT
3509397 GATACTTATA
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
60 2 0.03
61 71 0.97
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (61 bp):
AATTTGTTCAATTTAGTCCAAATTTAATGTTGCAATTCATTAATTTAAGCTTCATATTTAA
Found at i:3509348 original size:27 final size:28
Alignment explanation
Indices: 3509260--3509349 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 28
3509250 CCCTAGTTTT
3509260 TAATTTGTTCAATTTAGTCCAAATTTAA
1 TAATTTGTTCAATTTAGTCCAAATTTAA
* ** * *
3509288 TGATTCAATTCATTAATTTAAGCTTCATATTTAA
1 TAATT-TGTTC---AATTT-AG-TCCAAATTTAA
3509322 -AATTTGTTCAATTTAGTCCAAATTTAA
1 TAATTTGTTCAATTTAGTCCAAATTTAA
3509349 T
1 T
3509350 GTTGCAATTT
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
27 9 0.20
28 6 0.13
29 8 0.18
32 8 0.18
33 5 0.11
34 9 0.20
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (28 bp):
TAATTTGTTCAATTTAGTCCAAATTTAA
Found at i:3509380 original size:21 final size:19
Alignment explanation
Indices: 3509266--3509396 Score: 67
Period size: 21 Copynumber: 6.5 Consensus size: 19
3509256 TTTTTAATTT
3509266 GTTCAATTTAGTCCAAATTTAA
1 GTTCAATTTA-T--AAATTTAA
* *
3509288 TGATTCAATTCATTAATTTAA
1 -G-TTCAATTTATAAATTTAA
3509309 GCTTCATATTTA-AAATTT--
1 G-TTCA-ATTTATAAATTTAA
3509327 GTTCAATTTAGTCCAAATTTAA
1 GTTCAATTTA-T--AAATTTAA
*
3509349 TGTTGCAATTTATTAATTTAA
1 -GTT-CAATTTATAAATTTAA
3509370 GCTTCATATTTA-AAATTT--
1 G-TTCA-ATTTATAAATTTAA
3509388 GTTCAATTT
1 GTTCAATTT
3509397 GATACTTATA
Statistics
Matches: 89, Mismatches: 7, Indels: 31
0.70 0.06 0.24
Matches are distributed among these distances:
16 9 0.10
17 8 0.09
18 2 0.02
20 24 0.27
21 25 0.28
23 6 0.07
24 15 0.17
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (19 bp):
GTTCAATTTATAAATTTAA
Found at i:3509500 original size:33 final size:32
Alignment explanation
Indices: 3509453--3509551 Score: 114
Period size: 33 Copynumber: 3.1 Consensus size: 32
3509443 ATTAATAAAT
3509453 TAATAT-TAGTTTATATATACTA-ATGAAGTATA
1 TAATATATAGTTTATATATACTATAT--AGTATA
*
3509485 TAATATATAGTTTATATATACTATATAGTTTA
1 TAATATATAGTTTATATATACTATATAGTATA
* *
3509517 T-ATATATAGTTCATATGTAAACTATATAGTATA
1 TAATATATAGTT--TATATATACTATATAGTATA
3509550 TA
1 TA
3509552 TAGTTTATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
31 10 0.17
32 12 0.21
33 34 0.59
34 2 0.03
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (32 bp):
TAATATATAGTTTATATATACTATATAGTATA
Found at i:3509504 original size:18 final size:18
Alignment explanation
Indices: 3509481--3509522 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
3509471 ACTAATGAAG
3509481 TATATAATATATAGTTTA
1 TATATAATATATAGTTTA
*
3509499 TATATACTATATAGTTTA
1 TATATAATATATAGTTTA
3509517 TATATA
1 TATATA
3509523 TAGTTCATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (18 bp):
TATATAATATATAGTTTA
Found at i:3509504 original size:20 final size:20
Alignment explanation
Indices: 3509481--3509573 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
3509471 ACTAATGAAG
3509481 TATATAATATATAG-TT-TA
1 TATATAATATATAGTTTATA
*
3509499 TATATACTATATAGTTTATA
1 TATATAATATATAGTTTATA
* * *
3509519 TATATAGT-TCATA-TGTAAA
1 TATATAATAT-ATAGTTTATA
3509538 CTATATAGTATATATAGTTTATA
1 -TATATA--ATATATAGTTTATA
*
3509561 TATGTAATATATA
1 TATATAATATATA
3509574 CTATATAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
18 13 0.22
19 7 0.12
20 25 0.42
22 9 0.15
23 5 0.08
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (20 bp):
TATATAATATATAGTTTATA
Found at i:3509522 original size:31 final size:30
Alignment explanation
Indices: 3509429--3509593 Score: 111
Period size: 33 Copynumber: 5.6 Consensus size: 30
3509419 GTTTCAATTA
*
3509429 ATATATAT-GTTTATAT-TA--ATA-AATT
1 ATATATATAGTTTATATATACTATATAGTT
3509454 A-ATAT-TAGTTTATATATACTA-ATGAAGTAT
1 ATATATATAGTTTATATATACTATAT--AGT-T
3509484 ATAATATATAGTTTATATATACTATATAGTTT
1 AT-ATATATAGTTTATATATACTATATAG-TT
* *
3509516 ATATATATAGTTCATATGTAAACTATATAG--
1 ATATATATAGTT--TATATATACTATATAGTT
* *
3509546 -TATATATAGTTTATATATGTAATATATA-CT
1 ATATATATAGTTTATATA--TACTATATAGTT
*
3509576 ATATAAATAGTTTATATA
1 ATATATATAGTTTATATA
3509594 GTTCATTAAT
Statistics
Matches: 113, Mismatches: 7, Indels: 34
0.73 0.05 0.22
Matches are distributed among these distances:
23 1 0.01
24 12 0.11
25 3 0.03
26 1 0.01
27 6 0.05
29 20 0.18
30 2 0.02
31 26 0.23
32 9 0.08
33 31 0.27
34 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (30 bp):
ATATATATAGTTTATATATACTATATAGTT
Found at i:3509551 original size:9 final size:9
Alignment explanation
Indices: 3509539--3509595 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
3509529 ATATGTAAAC
3509539 TATATAGTA
1 TATATAGTA
*
3509548 TATATAGTT
1 TATATAGTA
3509557 TATATATGTAA
1 TATATA-GT-A
*
3509568 TATATACTA
1 TATATAGTA
*
3509577 TATAAATAGTT
1 TAT--ATAGTA
3509588 TATATAGT
1 TATATAGT
3509596 TCATTAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
9 23 0.59
10 3 0.08
11 13 0.33
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (9 bp):
TATATAGTA
Found at i:3509619 original size:33 final size:31
Alignment explanation
Indices: 3509487--3509625 Score: 92
Period size: 31 Copynumber: 4.5 Consensus size: 31
3509477 GAAGTATATA
* ***
3509487 ATATATAGTTTATATATACT-ATATAGTTTAT
1 ATATATAGTTTATATAT-GTAATATAAACTAT
* *
3509518 ATATATAG-TT-CATATGTAA-ACTATA-TAGT
1 ATATATAGTTTATATATGTAATA-TAAACTA-T
*
3509547 ATATATAGTTTATATATGTAATATATACTAT
1 ATATATAGTTTATATATGTAATATAAACTAT
* *
3509578 ATAAATAGTTTATATA-GTTCATTAATAAACTAT
1 ATATATAGTTTATATATG-T-AAT-ATAAACTAT
*
3509611 ATATATAGTTCATAT
1 ATATATAGTTTATAT
3509626 GAAACTGCTA
Statistics
Matches: 88, Mismatches: 10, Indels: 18
0.76 0.09 0.16
Matches are distributed among these distances:
28 4 0.05
29 16 0.18
30 5 0.06
31 37 0.42
32 5 0.06
33 21 0.24
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (31 bp):
ATATATAGTTTATATATGTAATATAAACTAT
Found at i:3509680 original size:22 final size:22
Alignment explanation
Indices: 3509643--3509699 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
3509633 CTAAACTATA
3509643 TATATTATATAATTTACATAATT
1 TATA-TATATAATTTACATAATT
* * *
3509666 TATATATATAGTTTATATAGTT
1 TATATATATAATTTACATAATT
*
3509688 TATACATATAAT
1 TATATATATAAT
3509700 ATATATGTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
TATATATATAATTTACATAATT
Found at i:3509691 original size:20 final size:20
Alignment explanation
Indices: 3509648--3510266 Score: 147
Period size: 20 Copynumber: 31.9 Consensus size: 20
3509638 CTATATATAT
* * *
3509648 TATATAATTTACATAATTTA
1 TATATAATATATATAGTTTA
*
3509668 TATATATAGTTTATATAGTTTA
1 TATATA-A-TATATATAGTTTA
**
3509690 TACATATAATATATAT-GTAAA
1 T--ATATAATATATATAGTTTA
3509711 CTATATAATATATATAGTTTA
1 -TATATAATATATATAGTTTA
* *
3509732 CATATAATATATAT-GATTTT
1 TATATAATATATATAG-TTTA
* * * *
3509752 TATATAGTTTATATACTACTA
1 TATATAATATATATAGT-TTA
*
3509773 TCTATAA-ACTATATAGTTTA
1 TATATAATA-TATATAGTTTA
* *
3509793 TATATAAACTACATATA-ATTA
1 TATAT-AA-TATATATAGTTTA
* ****
3509814 CATA-AAT-TA-ACCCTAAACCA
1 TATATAATATATA---TAGTTTA
**
3509834 TATATGCTATATATA---TA
1 TATATAATATATATAGTTTA
* *
3509851 TATATAATTATAAATAATTTA
1 TATATAA-TATATATAGTTTA
3509872 TA-AT--TATATATAGTTTA
1 TATATAATATATATAGTTTA
*
3509889 TATATATAAACTATATAGTTTA
1 TATATA-ATA-TATATAGTTTA
*
3509911 TATAT-ACATA-A-A--TTA
1 TATATAATATATATAGTTTA
**
3509926 -ACCCTAA-ACTATATAGTTTA
1 TA-TATAATA-TATATAGTTTA
*
3509946 TAT-TAATAAGCTATATAATTTA
1 TATATAAT-A--TATATAGTTTA
3509968 TATATAATATATA-A-TTTA
1 TATATAATATATATAGTTTA
* * *
3509986 TA-ATTATACATGATA-TATA
1 TATATAATATAT-ATAGTTTA
* *
3510005 AATATAAGT-TGTATAGTTTA
1 TATATAA-TATATATAGTTTA
3510025 TATATAATTCATATATA-TTTCA
1 TATATAA-T-ATATATAGTTT-A
* *
3510047 TATATAATTTATATAATTTA
1 TATATAATATATATAGTTTA
*
3510067 TAT-TAATAAACTATATAATTTA
1 TATATAAT--A-TATATAGTTTA
*
3510089 TATATAGT-T-TATA-TTTA
1 TATATAATATATATAGTTTA
*
3510106 TA-A-ACTATATAT--TTTA
1 TATATAATATATATAGTTTA
* * *
3510122 TACATAATATATACAGTTCA
1 TATATAATATATATAGTTTA
3510142 TATATAATA-ATATA----A
1 TATATAATATATATAGTTTA
3510157 -ATATAA-ACTATATAG-TT-
1 TATATAATA-TATATAGTTTA
* *
3510174 TATAT-ATATACATAGTTCA
1 TATATAATATATATAGTTTA
*
3510193 TATATAGTATATA-A----A
1 TATATAATATATATAGTTTA
*
3510208 TATA-AA-CTATATAGTTTA
1 TATATAATATATATAGTTTA
*
3510226 TATATATATATATATA-TATA
1 TATATA-ATATATATAGTTTA
3510246 TATATATATATATATATGTTT
1 TATATA-ATATATATA-GTTT
3510267 CAATTTTTTC
Statistics
Matches: 448, Mismatches: 71, Indels: 158
0.66 0.10 0.23
Matches are distributed among these distances:
13 5 0.01
14 9 0.02
15 18 0.04
16 12 0.03
17 46 0.10
18 41 0.09
19 35 0.08
20 131 0.29
21 50 0.11
22 86 0.19
23 10 0.02
24 5 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (20 bp):
TATATAATATATATAGTTTA
Found at i:3509873 original size:17 final size:17
Alignment explanation
Indices: 3509853--3509890 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3509843 TATATATATA
3509853 TATAATTATAAATAATT
1 TATAATTATAAATAATT
* *
3509870 TATAATTATATATAGTT
1 TATAATTATAAATAATT
3509887 TATA
1 TATA
3509891 TATATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATAATTATAAATAATT
Found at i:3509889 original size:11 final size:11
Alignment explanation
Indices: 3509875--3509916 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
3509865 TAATTTATAA
3509875 TTATATATAGT
1 TTATATATAGT
3509886 TTATATATA-T
1 TTATATATAGT
**
3509896 AAACTATATAGT
1 TTA-TATATAGT
3509908 TTATATATA
1 TTATATATA
3509917 CATAAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.08
11 21 0.84
12 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (11 bp):
TTATATATAGT
Found at i:3509959 original size:22 final size:23
Alignment explanation
Indices: 3509934--3509976 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3509924 TAACCCTAAA
*
3509934 CTATATAGTTTATAT-TAATAAG
1 CTATATAATTTATATATAATAAG
3509956 CTATATAATTTATATATAATA
1 CTATATAATTTATATATAATA
3509977 TATAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (23 bp):
CTATATAATTTATATATAATAAG
Found at i:3509971 original size:2 final size:2
Alignment explanation
Indices: 3509957--3510262 Score: 103
Period size: 2 Copynumber: 154.5 Consensus size: 2
3509947 ATTAATAAGC
* *
3509957 TA TA TA -A TT TA TA TA TA -A TA TA TA -A TT TA TA -A T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
3509994 CA TGA TA TA TA AA TA TA -A GT- TG TA TA GTT TA TA TA TA -A T-
1 TA T-A TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA
* * *
3510033 TCA TA TA TA TT TCA TA TA TA -A TT TA TA TA -A TT TA TA T- TA -A
1 T-A TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
3510073 TA AA CTA TA TA -A TT TA TA TA TA GTT TA TA TT TA TA AA CTA TA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * *
3510115 TA T- TT TA TA CA TA -A TA TA TA CA GT- TCA TA TA TA -A TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA
* * * *
3510154 TA AA TA TA AA CTA TA TA GTT TA TA TA TA TA CA TA GT- TCA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA T-A TA TA
* * *
3510197 TA GTA TA TA AA TA TA AA CTA TA TA GTT 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
3510240 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
3510263 GTTTCAATTT
Statistics
Matches: 221, Mismatches: 46, Indels: 74
0.65 0.13 0.22
Matches are distributed among these distances:
1 20 0.09
2 184 0.83
3 17 0.08
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3509973 original size:11 final size:11
Alignment explanation
Indices: 3509957--3510261 Score: 95
Period size: 11 Copynumber: 27.5 Consensus size: 11
3509947 ATTAATAAGC
*
3509957 TATATAATTTA
1 TATATAATATA
3509968 TATATAATATA
1 TATATAATATA
*
3509979 TA-AT-TTATA
1 TATATAATATA
3509988 -ATTATACATGATA
1 TA-TATA-AT-ATA
3510001 TATA-AATATAA
1 TATATAATAT-A
* * *
3510012 GTTGTATAGTTTA
1 --TATATAATATA
3510025 TATATAAT-TCA
1 TATATAATAT-A
*
3510036 TATAT-ATTTCA
1 TATATAATAT-A
3510047 TATATAAT-T-
1 TATATAATATA
*
3510056 TATATAATTTA
1 TATATAATATA
*
3510067 TAT-TAATAAA
1 TATATAATATA
*
3510077 CTATATAATTTA
1 -TATATAATATA
* *
3510089 TATATAGTTTA
1 TATATAATATA
* *
3510100 TAT-TTATAAA
1 TATATAATATA
* *
3510110 CTATATATTTTA
1 -TATATAATATA
*
3510122 TACATAATATA
1 TATATAATATA
* *
3510133 TACAGTTCATATA
1 TATA--TAATATA
3510146 TA-ATAATATA
1 TATATAATATA
*
3510156 AATATAA-ACTA
1 TATATAATA-TA
*
3510167 TATAGT-TTATA
1 TATA-TAATATA
3510178 TATATACATAGTTCA
1 TATATA-ATA--T-A
*
3510193 TATATAGTATA
1 TATATAATATA
* *
3510204 TAAAT-ATAAA
1 TATATAATATA
* *
3510214 CTATATAGTTTA
1 -TATATAATATA
3510226 TATAT-ATATA
1 TATATAATATA
3510236 TATAT-ATATA
1 TATATAATATA
3510246 TATAT-ATATA
1 TATATAATATA
3510256 TATATA
1 TATATA
3510262 TGTTTCAATT
Statistics
Matches: 221, Mismatches: 40, Indels: 66
0.68 0.12 0.20
Matches are distributed among these distances:
8 1 0.00
9 12 0.05
10 58 0.26
11 99 0.45
12 20 0.09
13 17 0.08
14 7 0.03
15 7 0.03
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (11 bp):
TATATAATATA
Found at i:3510947 original size:90 final size:90
Alignment explanation
Indices: 3510842--3511032 Score: 373
Period size: 90 Copynumber: 2.1 Consensus size: 90
3510832 TGAAGTCCAT
*
3510842 CTAAACCTGAATTAACTTGGTCTTTAACTCCTCCGAACCTGAATTGTTTTGACCTAAACTAAAAT
1 CTAAACCCGAATTAACTTGGTCTTTAACTCCTCCGAACCTGAATTGTTTTGACCTAAACTAAAAT
3510907 CGATCCAAACTGAAAGTAATCCAAC
66 CGATCCAAACTGAAAGTAATCCAAC
3510932 CTAAACCCGAATTAACTTGGTCTTTAACTCCTCCGAACCTGAATTGTTTTGACCTAAACTAAAAT
1 CTAAACCCGAATTAACTTGGTCTTTAACTCCTCCGAACCTGAATTGTTTTGACCTAAACTAAAAT
3510997 CGATCCAAACTGAAAGTAATCCAAC
66 CGATCCAAACTGAAAGTAATCCAAC
3511022 CTAAACCCGAA
1 CTAAACCCGAA
3511033 CTGAAACTGG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 100 1.00
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (90 bp):
CTAAACCCGAATTAACTTGGTCTTTAACTCCTCCGAACCTGAATTGTTTTGACCTAAACTAAAAT
CGATCCAAACTGAAAGTAATCCAAC
Found at i:3513348 original size:17 final size:16
Alignment explanation
Indices: 3513300--3513348 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
3513290 ACAAATTTAT
3513300 AAAAT-TTTAAAAGATA
1 AAAATATTTAAAA-ATA
**
3513316 AAAATATTTATTAATA
1 AAAATATTTAAAAATA
3513332 AAACATATTTAAAAATA
1 AAA-ATATTTAAAAATA
3513349 TTTAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAATATTTAAAAATA
Found at i:3513361 original size:17 final size:17
Alignment explanation
Indices: 3513348--3513390 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
3513338 ATTTAAAAAT
3513348 ATTTAAAATATAAAAGA
1 ATTTAAAATATAAAAGA
3513365 ATTTAAAATATAAAAGA
1 ATTTAAAATATAAAAGA
3513382 ATTTAAAAT
1 ATTTAAAAT
3513391 TTATCACAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
ATTTAAAATATAAAAGA
Found at i:3513368 original size:27 final size:27
Alignment explanation
Indices: 3513314--3513372 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
3513304 TTTTAAAAGA
**
3513314 TAAAAATATTTATTAATAAAACATATT
1 TAAAAATATTTAAAAATAAAACATATT
*
3513341 TAAAAATATTTAAAATATAAAAGA-ATT
1 TAAAAATATTTAAAA-ATAAAACATATT
3513368 TAAAA
1 TAAAA
3513373 TATAAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
TAAAAATATTTAAAAATAAAACATATT
Found at i:3513386 original size:44 final size:42
Alignment explanation
Indices: 3513293--3513389 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 42
3513283 TAGAATAACA
**
3513293 AATTTATAAAATTTTAAAAGATAAAAATATTTATTAATAAAAC
1 AATTTA-AAAATTTTAAAAGATAAAAATATTTAAAAATAAAAC
* *
3513336 ATATTTAAAAATATTTAAAATATAAAAGA-ATTTAAAATATAAAAG
1 A-ATTTAAAAAT-TTTAAAAGATAAAA-ATATTTAAAA-ATAAAAC
3513381 AATTTAAAA
1 AATTTAAAA
3513390 TTTATCACAG
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 6 0.13
44 32 0.70
45 8 0.17
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (42 bp):
AATTTAAAAATTTTAAAAGATAAAAATATTTAAAAATAAAAC
Found at i:3525727 original size:29 final size:30
Alignment explanation
Indices: 3525670--3525735 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
3525660 GGCTGCTGGA
3525670 AACCGG-TTTAACCGGTTTAACCGGTTTTC
1 AACCGGTTTTAACCGGTTTAACCGGTTTTC
* *
3525699 AACCGGTTTTGACCGGTTTGACCGG-TTTC
1 AACCGGTTTTAACCGGTTTAACCGGTTTTC
3525728 AACCGGTT
1 AACCGGTT
3525736 CGAACTAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.33
Consensus pattern (30 bp):
AACCGGTTTTAACCGGTTTAACCGGTTTTC
Found at i:3525732 original size:10 final size:9
Alignment explanation
Indices: 3525670--3525735 Score: 78
Period size: 9 Copynumber: 6.9 Consensus size: 9
3525660 GGCTGCTGGA
3525670 AACCGGTTT
1 AACCGGTTT
3525679 AACCGGTTT
1 AACCGGTTT
3525688 AACCGGTTTT
1 AACCGG-TTT
3525698 CAACCGGTTTT
1 -AACCGG-TTT
*
3525709 GACCGGTTT
1 AACCGGTTT
*
3525718 GACCGGTTT
1 AACCGGTTT
3525727 CAACCGGTT
1 -AACCGGTT
3525736 CGAACTAGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
9 27 0.52
10 15 0.29
11 10 0.19
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.33
Consensus pattern (9 bp):
AACCGGTTT
Found at i:3525777 original size:17 final size:17
Alignment explanation
Indices: 3525755--3525793 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
3525745 TTGACCGGTC
3525755 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
3525772 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
3525789 TGACC
1 TGACC
3525794 GTTGACTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:3525793 original size:7 final size:7
Alignment explanation
Indices: 3525783--3525813 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3525773 GACCCGACCC
3525783 GACCGTT
1 GACCGTT
3525790 GACCGTT
1 GACCGTT
*
3525797 GACTGTT
1 GACCGTT
3525804 GACCGTT
1 GACCGTT
3525811 GAC
1 GAC
3525814 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:3533017 original size:10 final size:9
Alignment explanation
Indices: 3532982--3533080 Score: 72
Period size: 10 Copynumber: 10.3 Consensus size: 9
3532972 GCTGCTGGAA
*
3532982 ACCGGTTTA
1 ACCGGTTTG
*
3532991 ACCGGTTTTCA
1 ACCGG-TTT-G
3533002 ACCGGTTCTG
1 ACCGGTT-TG
3533012 ACCGGTTTG
1 ACCGGTTTG
*
3533021 ACCGGTTTCA
1 ACCGGTTT-G
*
3533031 ACCGGTTCG
1 ACCGGTTTG
*
3533040 AACCAGTTTG
1 -ACCGGTTTG
* *
3533050 ACCGATCTG
1 ACCGGTTTG
3533059 AACCGGTTTG
1 -ACCGGTTTG
*
3533069 ACCGGTCTG
1 ACCGGTTTG
3533078 ACC
1 ACC
3533081 CTACCCGACC
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
9 32 0.44
10 33 0.46
11 7 0.10
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3533018 original size:30 final size:29
Alignment explanation
Indices: 3532982--3533074 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
3532972 GCTGCTGGAA
3532982 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTAACCGG-TTTCAACCGGTTCTG
*
3533012 ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 ACCGGTTTAACCGGTTTCAACCGGTTCTG
* * * * *
3533040 AACCAGTTTGACCGATCTGAACCGGTT-TG
1 -ACCGGTTTAACCGGTTTCAACCGGTTCTG
3533069 ACCGGT
1 ACCGGT
3533075 CTGACCCTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.11
29 36 0.65
30 13 0.24
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTAACCGGTTTCAACCGGTTCTG
Found at i:3533026 original size:19 final size:19
Alignment explanation
Indices: 3532983--3533080 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
3532973 CTGCTGGAAA
* * *
3532983 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
3533003 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
3533022 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
* *
3533042 CCAGTTTGACC-GATCTGAA
1 CCGGTTTGACCGGTTCTG-A
3533061 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
3533079 CC
1 CC
3533081 CTACCCGACC
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
18 7 0.11
19 35 0.54
20 15 0.23
21 8 0.12
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.29
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:3533100 original size:12 final size:12
Alignment explanation
Indices: 3533083--3533124 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
3533073 GTCTGACCCT
3533083 ACCCGACCGTTG
1 ACCCGACCGTTG
*
3533095 ACCCGACC--CG
1 ACCCGACCGTTG
*
3533105 ATCCGACCGTTG
1 ACCCGACCGTTG
3533117 ACCCGACC
1 ACCCGACC
3533125 CGATCCGACC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.33
12 16 0.67
ACGTcount: A:0.19, C:0.48, G:0.21, T:0.12
Consensus pattern (12 bp):
ACCCGACCGTTG
Found at i:3533103 original size:22 final size:22
Alignment explanation
Indices: 3533085--3533140 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
3533075 CTGACCCTAC
3533085 CCGACCGTTGACCCGACCCGAT
1 CCGACCGTTGACCCGACCCGAT
3533107 CCGACCGTTGACCCGACCCGAT
1 CCGACCGTTGACCCGACCCGAT
3533129 CCGACCGTTGAC
1 CCGACCGTTGAC
3533141 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (22 bp):
CCGACCGTTGACCCGACCCGAT
Found at i:3539784 original size:15 final size:15
Alignment explanation
Indices: 3539766--3539797 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3539756 TGTATGCCTA
3539766 TCCTTAAGTCGGCTT
1 TCCTTAAGTCGGCTT
3539781 TCCTTAAGTCGGCTT
1 TCCTTAAGTCGGCTT
3539796 TC
1 TC
3539798 TTTTTGCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.28, G:0.19, T:0.41
Consensus pattern (15 bp):
TCCTTAAGTCGGCTT
Found at i:3546053 original size:9 final size:9
Alignment explanation
Indices: 3546039--3546094 Score: 58
Period size: 10 Copynumber: 5.8 Consensus size: 9
3546029 GGCTGCTGGA
3546039 AACCGGTTT
1 AACCGGTTT
3546048 AACCGGTTTT
1 AACCGG-TTT
3546058 CAACCGGTTT
1 -AACCGGTTT
*
3546068 CAACCGGTTCG
1 -AACCGGTT-T
3546079 AACCGGTTT
1 AACCGGTTT
*
3546088 GACCGGT
1 AACCGGT
3546095 CTGACCCAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 12 0.29
10 23 0.56
11 6 0.15
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:3546064 original size:20 final size:20
Alignment explanation
Indices: 3546039--3546094 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
3546029 GGCTGCTGGA
3546039 AACCGGTTTAACCGGTTTTC-
1 AACCGGTTTAACCGG-TTTCG
3546059 AACCGGTTTCAACCGG-TTCG
1 AACCGGTTT-AACCGGTTTCG
*
3546079 AACCGGTTTGACCGGT
1 AACCGGTTTAACCGGT
3546095 CTGACCCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.25
20 18 0.56
21 6 0.19
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTTCG
Found at i:3546070 original size:10 final size:10
Alignment explanation
Indices: 3546039--3546087 Score: 66
Period size: 10 Copynumber: 4.9 Consensus size: 10
3546029 GGCTGCTGGA
3546039 AACCGGTTT-
1 AACCGGTTTC
3546048 AACCGGTTTTC
1 AACCGG-TTTC
3546059 AACCGGTTTC
1 AACCGGTTTC
3546069 AACCGG-TTC
1 AACCGGTTTC
3546078 GAACCGGTTT
1 -AACCGGTTT
3546088 GACCGGTCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.25
10 19 0.53
11 8 0.22
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (10 bp):
AACCGGTTTC
Found at i:3546129 original size:22 final size:23
Alignment explanation
Indices: 3546103--3546166 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 23
3546093 GTCTGACCCA
3546103 ACCCGACCGTTGACCCGACTCGACCCG
1 ACCCGACCGTTGACCCGA--C--CCCG
3546130 ACCCGACCGTTGACCCGA-CCCG
1 ACCCGACCGTTGACCCGACCCCG
3546152 ACCCGACCGTTGACC
1 ACCCGACCGTTGACC
3546167 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
22 19 0.51
27 18 0.49
ACGTcount: A:0.19, C:0.48, G:0.22, T:0.11
Consensus pattern (23 bp):
ACCCGACCGTTGACCCGACCCCG
Found at i:3546131 original size:5 final size:5
Alignment explanation
Indices: 3546114--3546159 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
3546104 CCCGACCGTT
* *
3546114 GACCC GACTC GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
3546160 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 31 0.89
7 4 0.11
ACGTcount: A:0.20, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:3546133 original size:27 final size:27
Alignment explanation
Indices: 3546097--3546173 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
3546087 TGACCGGTCT
* *
3546097 GACCCAACCCGACCGTTGACCCGACTC
1 GACCCGACCCGACCGTTGACCCGACCC
3546124 GACCCGACCCGACCGTTGACCCGACCC
1 GACCCGACCCGACCGTTGACCCGACCC
*
3546151 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
3546174 GTTGACTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 34 0.76
29 11 0.24
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.12
Consensus pattern (27 bp):
GACCCGACCCGACCGTTGACCCGACCC
Found at i:3547100 original size:14 final size:14
Alignment explanation
Indices: 3547081--3547109 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3547071 ATCCTTAAGT
3547081 CGGCTTTCTTTTTG
1 CGGCTTTCTTTTTG
3547095 CGGCTTTCTTTTTG
1 CGGCTTTCTTTTTG
3547109 C
1 C
3547110 TATGTGCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.21, T:0.55
Consensus pattern (14 bp):
CGGCTTTCTTTTTG
Found at i:3549478 original size:45 final size:45
Alignment explanation
Indices: 3549388--3549598 Score: 361
Period size: 45 Copynumber: 4.7 Consensus size: 45
3549378 GGTAAACATG
* *
3549388 AAAATAAGCTTACGAGCTTATGGAAT-AATGGAAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTACATTGGT
3549432 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTACATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTACATTGGT
3549477 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTACATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTACATTGGT
* * *
3549522 AAAATAAGCTTACGAGCTTATGGATTAAATAGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTACATTGGT
*
3549567 AAAATAAGCTTACGAGCTTATGGGATAAATGG
1 AAAATAAGCTTACGAGCTTATGGAATAAATGG
3549599 AAAATAAATG
Statistics
Matches: 158, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
44 26 0.16
45 132 0.84
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTACATTGGT
Found at i:3557008 original size:36 final size:35
Alignment explanation
Indices: 3556958--3557063 Score: 151
Period size: 35 Copynumber: 3.0 Consensus size: 35
3556948 ATTTAAGTTT
*
3556958 TCTTATGTATGCATATTTACTTATGTTTCATTTCA
1 TCTTATGCATGCATATTTACTTATGTTTCATTTCA
*
3556993 TCTTATGCCATGCATA-TTAGTTATGTTTCATTTCA
1 TCTTATG-CATGCATATTTACTTATGTTTCATTTCA
* *
3557028 TCTTAAGTCATGTATATTTACTTATGTTTCATTTCA
1 TCTTATG-CATGCATATTTACTTATGTTTCATTTCA
3557064 AACTATGCAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
35 38 0.60
36 25 0.40
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (35 bp):
TCTTATGCATGCATATTTACTTATGTTTCATTTCA
Found at i:3557076 original size:31 final size:31
Alignment explanation
Indices: 3556965--3557090 Score: 110
Period size: 31 Copynumber: 3.8 Consensus size: 31
3556955 TTTTCTTATG
*
3556965 TATGCATATTTACTTATGTTTCATTTC-ATC
1 TATGCATATTTACTTATGTTTCATTTCAAAC
* *
3556995 TTATGCCATGCATATTAGTTATGTTTCATTTCATCTTAAG
1 -TATG-CAT--AT-TTACTTATGTTTCATTTCA----AAC
*
3557035 TCATGTATATTTACTTATGTTTCATTTCAAAC
1 T-ATGCATATTTACTTATGTTTCATTTCAAAC
*
3557067 TATGCATATTTATTTATGTTTCAT
1 TATGCATATTTACTTATGTTTCAT
3557091 ATTTATCCTA
Statistics
Matches: 77, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
31 25 0.32
32 6 0.08
34 2 0.03
35 17 0.22
36 18 0.23
37 2 0.03
39 3 0.04
40 4 0.05
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (31 bp):
TATGCATATTTACTTATGTTTCATTTCAAAC
Found at i:3570596 original size:55 final size:55
Alignment explanation
Indices: 3570531--3570689 Score: 205
Period size: 55 Copynumber: 2.9 Consensus size: 55
3570521 TGACACTAAG
* * * * * *
3570531 TGTGTA-AAAACTAAGAAATTCATAATAAGTGTGTGAATTTCTGTATTGGTACTT
1 TGTGTACAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTA
* *
3570585 TGTGTACAAAACTAAGAAATTCATTCTAAGTGTATGGATTTCCGTATGGGCACTA
1 TGTGTACAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTA
* *
3570640 TGTGTGC-AAACTAAGAAAATTCATACTAAGTGTATGAAGTTCCGTATGGG
1 TGTGTACAAAACTAAG-AAATTCATACTAAGTGTATGAATTTCCGTATGGG
3570690 AAATATATGT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
54 14 0.15
55 77 0.85
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (55 bp):
TGTGTACAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTA
Found at i:3571056 original size:67 final size:67
Alignment explanation
Indices: 3570911--3571086 Score: 271
Period size: 67 Copynumber: 2.6 Consensus size: 67
3570901 GGACTAGTTA
* * * *
3570911 TGCATATGGCAAAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAG
1 TGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATG-AAGACTAAGTGCCTTTGAGGCCTAA
3570976 CTG
65 CTG
* *
3570979 TGCATATGACAGAAATGTTTCATTTATGCCAGTTAGATGAAGACTAAGTGCCTTTGAGTCCTAAC
1 TGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAGACTAAGTGCCTTTGAGGCCTAAC
3571044 TG
66 TG
* *
3571046 TGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
1 TGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAA
3571087 TGGTTAAGTA
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 63 0.64
68 36 0.36
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (67 bp):
TGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAGACTAAGTGCCTTTGAGGCCTAAC
TG
Found at i:3571178 original size:81 final size:81
Alignment explanation
Indices: 3571043--3571266 Score: 313
Period size: 81 Copynumber: 2.8 Consensus size: 81
3571033 TGAGTCCTAA
* * *
3571043 CTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAATGGTTAAGTACCGTTGAGTAA
1 CTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTTAGATGAAAGGTTAAGTACCATTGAGTAA
* **
3571108 AAGATTAATGGTCTAG
66 AAGAATAATGAACTAG
* *
3571124 CTGTGCATTTGACAGAAAAGTGTCATTTATGCTAGTTAGATGAACGGTTAAGTACCATTGAGTAA
1 CTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTTAGATGAAAGGTTAAGTACCATTGAGTAA
3571189 AAGAATAATGAACTAG
66 AAGAATAATGAACTAG
* * * * * * *
3571205 TTGTACATTTGATAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 CTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTTAGATGAAAGGTTAAGTACCATTGAG
3571267 GCCTAGCTGT
Statistics
Matches: 127, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 127 1.00
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (81 bp):
CTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTTAGATGAAAGGTTAAGTACCATTGAGTAA
AAGAATAATGAACTAG
Found at i:3571538 original size:68 final size:68
Alignment explanation
Indices: 3571218--3571529 Score: 480
Period size: 68 Copynumber: 4.6 Consensus size: 68
3571208 TACATTTGAT
*
3571218 AGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGCTGTGCATAC
1 AGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGCTGTGCATAT
3571283 GAA
66 GAA
* *
3571286 ATAAATGTGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCCTTTGAGGCCTAGCTGTGCATAT
1 AGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGCTGTGCATAT
3571351 GAA
66 GAA
* * * * * * *
3571354 ACAAAGGTGTTATTTATACCAGTTAGATGAAAGGCTAAGTGGCTTTGAGGCCTAGCCGTGCAAAT
1 AGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGCTGTGCATAT
3571419 GAA
66 GAA
* * *
3571422 AGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTGAGGCCTAACTGTGCATTT
1 AGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGCTGTGCATAT
*
3571487 GAC
66 GAA
* *
3571490 AGAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAGT
1 AGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
3571530 ACTGTTGAGT
Statistics
Matches: 221, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 221 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (68 bp):
AGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGCTGTGCATAT
GAA
Found at i:3571618 original size:81 final size:82
Alignment explanation
Indices: 3571472--3571690 Score: 325
Period size: 81 Copynumber: 2.7 Consensus size: 82
3571462 GTCTTTGAGG
* *
3571472 CCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAGTACTGTTG
1 CCTAGCTGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAGTACTGTTG
*
3571537 AGTAAAAGAAT-AATGT
66 AGTAAAAGAATAAATGA
*
3571553 CCTAGCTGTGTATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAGTA-TCGTT
1 CCTAGCTGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAGTACT-GTT
*
3571617 GAGTAAAATAATAAATGA
65 GAGTAAAAGAATAAATGA
* * * * *
3571635 ACTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGACAGTTAAATGAACGGTTAA
1 CCTAGCTGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAA
3571691 ACATTATTAA
Statistics
Matches: 125, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
80 1 0.01
81 70 0.56
82 54 0.43
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (82 bp):
CCTAGCTGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAGTACTGTTG
AGTAAAAGAATAAATGA
Found at i:3571734 original size:29 final size:29
Alignment explanation
Indices: 3571679--3571737 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
3571669 TGACAGTTAA
*
3571679 ATGAACGGTTAAACATTATTAAGTAAAAG
1 ATGAACGGTTAAACACTATTAAGTAAAAG
*
3571708 ATGAACGGTTAAACACTGTTGAA-TAAAAG
1 ATGAACGGTTAAACACTATT-AAGTAAAAG
3571737 A
1 A
3571738 ATAATGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.25
Consensus pattern (29 bp):
ATGAACGGTTAAACACTATTAAGTAAAAG
Found at i:3571818 original size:110 final size:111
Alignment explanation
Indices: 3571595--3571801 Score: 271
Period size: 110 Copynumber: 1.9 Consensus size: 111
3571585 TATGCCAGTT
** * * *
3571595 AGATGAACGGTTAAGTATCGTTGAGTAAAATAATAAATGAACTAGCTGTGCATTTGACAAAAAGG
1 AGATGAACGGTTAAACATCGTTGAATAAAAGAATAAATGAACTAGCTGTGCATTTGACAAAAAAG
* *
3571660 TGTCAATTATGACAGTTAAATGAACGGTTAAACATTATTAAGTAAA
66 TGTCAAATATGACAGTTAAATGAAAGGTTAAACATTATTAAGTAAA
3571706 AGATGAACGGTTAAACA-CTGTTGAATAAAAGAAT-AATGATA-TAGCTGTGCATTTGA-AAGAA
1 AGATGAACGGTTAAACATC-GTTGAATAAAAGAATAAATGA-ACTAGCTGTGCATTTGACAA-AA
*
3571767 AAGTGTCAAATATG-CAAGTTAGATGAAAGGTTAAA
63 AAGTGTCAAATATGAC-AGTTAAATGAAAGGTTAAA
3571802 TATCTTTGGG
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
109 3 0.04
110 52 0.62
111 29 0.35
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (111 bp):
AGATGAACGGTTAAACATCGTTGAATAAAAGAATAAATGAACTAGCTGTGCATTTGACAAAAAAG
TGTCAAATATGACAGTTAAATGAAAGGTTAAACATTATTAAGTAAA
Found at i:3574399 original size:17 final size:17
Alignment explanation
Indices: 3574377--3574411 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3574367 CTTGGCTCAT
3574377 TAAATTTAAGATTTTTA
1 TAAATTTAAGATTTTTA
3574394 TAAATTTAAGATTTTTA
1 TAAATTTAAGATTTTTA
3574411 T
1 T
3574412 TGTTAGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TAAATTTAAGATTTTTA
Found at i:3574985 original size:20 final size:20
Alignment explanation
Indices: 3574945--3574985 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3574935 CTCAACCAAT
*
3574945 AATCAATCAATGCAACTACA
1 AATCAATCAATGCAACAACA
*
3574965 AATCAATCAATGTAACAACA
1 AATCAATCAATGCAACAACA
3574985 A
1 A
3574986 CGCAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.22, G:0.05, T:0.20
Consensus pattern (20 bp):
AATCAATCAATGCAACAACA
Found at i:3586610 original size:27 final size:27
Alignment explanation
Indices: 3586580--3586669 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
3586570 AGATTTTTCT
* * *
3586580 ATTTTTTGAAAAATTCGGATAAACACG
1 ATTTTTGGCAAAATTCAGATAAACACG
*
3586607 ATTTTTGGCAAAATCCAGATAAACACG
1 ATTTTTGGCAAAATTCAGATAAACACG
3586634 ATTTTTGGCAAAATTCAGATAAACACG
1 ATTTTTGGCAAAATTCAGATAAACACG
3586661 ATTTTTGGC
1 ATTTTTGGC
3586670 TATAACAATC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (27 bp):
ATTTTTGGCAAAATTCAGATAAACACG
Found at i:3587346 original size:18 final size:18
Alignment explanation
Indices: 3587323--3587369 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
3587313 ATTATAAAAA
3587323 GAAGGAAGAAATAGTTAG
1 GAAGGAAGAAATAGTTAG
3587341 GAAGGAAGAAATAGTTAG
1 GAAGGAAGAAATAGTTAG
*
3587359 GAAGAAAGAAA
1 GAAGGAAGAAA
3587370 GAATTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.32, T:0.13
Consensus pattern (18 bp):
GAAGGAAGAAATAGTTAG
Found at i:3587880 original size:17 final size:18
Alignment explanation
Indices: 3587853--3587886 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3587843 AATTATAATA
3587853 TTTTAAAATAAAAATCAG
1 TTTTAAAATAAAAATCAG
3587871 TTTT-AAATAAAAATCA
1 TTTTAAAATAAAAATCA
3587887 AATTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
TTTTAAAATAAAAATCAG
Found at i:3587892 original size:17 final size:17
Alignment explanation
Indices: 3587858--3587893 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3587848 TAATATTTTA
**
3587858 AAATAAAAATCAGTTTT
1 AAATAAAAATCAAATTT
3587875 AAATAAAAATCAAATTT
1 AAATAAAAATCAAATTT
3587892 AA
1 AA
3587894 TTTTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
AAATAAAAATCAAATTT
Found at i:3596112 original size:78 final size:78
Alignment explanation
Indices: 3595983--3596138 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
3595973 TCTTGGTGGG
3595983 GGAAGAATTGTAATACCCCAAAATTTTGGCTAGTGACCAAAATATAAATTTTGAAAGTTTGGTTC
1 GGAAGAATTGTAATACCCCAAAATTTTGGCTAGTGACCAAAATATAAATTTTGAAAGTTTGGTTC
3596048 CCAAAGTAGAAAA
66 CCAAAGTAGAAAA
3596061 GGAAGAATTGTAATACCCCAAAATTTTGGCTAGTGACCAAAATATAAATTTTGAAAGTTTGGTTC
1 GGAAGAATTGTAATACCCCAAAATTTTGGCTAGTGACCAAAATATAAATTTTGAAAGTTTGGTTC
3596126 CCAAAGTAGAAAA
66 CCAAAGTAGAAAA
3596139 TTAGGAAAAG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (78 bp):
GGAAGAATTGTAATACCCCAAAATTTTGGCTAGTGACCAAAATATAAATTTTGAAAGTTTGGTTC
CCAAAGTAGAAAA
Found at i:3597158 original size:22 final size:23
Alignment explanation
Indices: 3597133--3597177 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3597123 TGATTTGGAG
*
3597133 GTATATG-AAAAAACTATGAATT
1 GTATATGCAAAAAAATATGAATT
3597155 GTATATGCAAAAAAATATGAATT
1 GTATATGCAAAAAAATATGAATT
3597178 TTTAATCGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.31
Consensus pattern (23 bp):
GTATATGCAAAAAAATATGAATT
Found at i:3604640 original size:15 final size:16
Alignment explanation
Indices: 3604620--3604651 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3604610 ACTGTTTTAA
3604620 TCAAAACCTT-AATTT
1 TCAAAACCTTCAATTT
3604635 TCAAAACCTTCAATTT
1 TCAAAACCTTCAATTT
3604651 T
1 T
3604652 AATTTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (16 bp):
TCAAAACCTTCAATTT
Found at i:3607147 original size:30 final size:29
Alignment explanation
Indices: 3607105--3607167 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
3607095 AAGCCTAATA
*
3607105 AAAATTTGGGGACC-ATTAT-GTAAATTTTG
1 AAAAGTTGGGGACCAATT-TGGT-AATTTTG
3607134 AAAAGTTGAGGGACCAATTTGGTAATTTTG
1 AAAAGTTG-GGGACCAATTTGGTAATTTTG
3607164 AAAA
1 AAAA
3607168 ATAGTGGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 7 0.23
30 18 0.60
31 5 0.17
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.33
Consensus pattern (29 bp):
AAAAGTTGGGGACCAATTTGGTAATTTTG
Found at i:3612096 original size:20 final size:20
Alignment explanation
Indices: 3612069--3612106 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3612059 CTAAAAGAAG
3612069 AAATAATATTT-CAAAAATT
1 AAATAATATTTACAAAAATT
3612088 AAATGAATATTTACAAAAA
1 AAAT-AATATTTACAAAAA
3612107 AGAGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATAATATTTACAAAAATT
Found at i:3612534 original size:18 final size:20
Alignment explanation
Indices: 3612488--3612534 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
3612478 TTAAAATATA
3612488 ATTTAATA-TAGTAATATTT
1 ATTTAATACTAGTAATATTT
3612507 ATTT-ATACTA-TAA-ATTT
1 ATTTAATACTAGTAATATTT
3612524 ATTTAATACTA
1 ATTTAATACTA
3612535 ACAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.31
18 12 0.46
19 6 0.23
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTAATACTAGTAATATTT
Found at i:3613053 original size:30 final size:30
Alignment explanation
Indices: 3613017--3613114 Score: 133
Period size: 30 Copynumber: 3.3 Consensus size: 30
3613007 TATACATTGG
* * *
3613017 GTGTCCTTACACACCATAGTGTTGCACTGA
1 GTGTCCTTACACACTATAGTGTTGTACTAA
* *
3613047 GTGTCCTTACACACTACAATGTTGTACTAA
1 GTGTCCTTACACACTATAGTGTTGTACTAA
**
3613077 GTGTCCTTACACACTATAGTAATGTACTAA
1 GTGTCCTTACACACTATAGTGTTGTACTAA
3613107 GTGTCCTT
1 GTGTCCTT
3613115 GATAATATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (30 bp):
GTGTCCTTACACACTATAGTGTTGTACTAA
Found at i:3617835 original size:3 final size:3
Alignment explanation
Indices: 3617822--3617860 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
3617812 TTGAAAAAAC
3617822 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3617861 GGTATAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3618142 original size:37 final size:38
Alignment explanation
Indices: 3618095--3618182 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 38
3618085 ATAGACTAGC
* *
3618095 CTTTTGTCATTTT-AAATATTGCTTTGAATTATTATAA
1 CTTTAGTCATTTTCAAATATTGCTTTGAATTATTACAA
** *
3618132 CTTTAGTCATTTTCCATGTATTGCTTTGAATTATTGCAA
1 CTTTAGTCATTTT-CAAATATTGCTTTGAATTATTACAA
3618171 CTTTAGTCATTT
1 CTTTAGTCATTT
3618183 CCATTAGTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 12 0.27
39 32 0.73
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.52
Consensus pattern (38 bp):
CTTTAGTCATTTTCAAATATTGCTTTGAATTATTACAA
Found at i:3618157 original size:39 final size:38
Alignment explanation
Indices: 3618111--3618186 Score: 125
Period size: 39 Copynumber: 2.0 Consensus size: 38
3618101 TCATTTTAAA
*
3618111 TATTGCTTTGAATTATTATAACTTTAGTCATTTTCCATG
1 TATTGCTTTGAATTATTACAACTTTAGTCA-TTTCCATG
*
3618150 TATTGCTTTGAATTATTGCAACTTTAGTCATTTCCAT
1 TATTGCTTTGAATTATTACAACTTTAGTCATTTCCAT
3618187 TAGTTGGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 7 0.20
39 28 0.80
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (38 bp):
TATTGCTTTGAATTATTACAACTTTAGTCATTTCCATG
Found at i:3621874 original size:17 final size:17
Alignment explanation
Indices: 3621852--3621886 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3621842 ACTTTGACCC
*
3621852 AAAAAGTTAAATTTTAT
1 AAAAAGTCAAATTTTAT
*
3621869 AAAAAGTCATATTTTAT
1 AAAAAGTCAAATTTTAT
3621886 A
1 A
3621887 TTTCTCGACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (17 bp):
AAAAAGTCAAATTTTAT
Found at i:3622757 original size:26 final size:27
Alignment explanation
Indices: 3622710--3622761 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3622700 GAAAATGAAT
* *
3622710 AAATACCCTTGAACTGTAAAATGACCA
1 AAATACCCCTAAACTGTAAAATGACCA
*
3622737 AAATACCCCTAAAGTGT-AAATGACC
1 AAATACCCCTAAACTGTAAAATGACC
3622762 TAAGGTAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (27 bp):
AAATACCCCTAAACTGTAAAATGACCA
Found at i:3624715 original size:9 final size:9
Alignment explanation
Indices: 3624701--3624728 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3624691 ATAAAATATT
3624701 ATTTAATTA
1 ATTTAATTA
3624710 ATTTAATTA
1 ATTTAATTA
3624719 ATTTAATTA
1 ATTTAATTA
3624728 A
1 A
3624729 ATATACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTTAATTA
Found at i:3628033 original size:31 final size:31
Alignment explanation
Indices: 3627995--3628056 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3627985 CTGGTAGGAA
3627995 GTCTCTACAAGTTCAGCTCGATCAAACTGGT
1 GTCTCTACAAGTTCAGCTCGATCAAACTGGT
3628026 GTCTCTACAAGTTCAGCTCGATCAAACTGGT
1 GTCTCTACAAGTTCAGCTCGATCAAACTGGT
3628057 AATTCCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (31 bp):
GTCTCTACAAGTTCAGCTCGATCAAACTGGT
Found at i:3628084 original size:35 final size:36
Alignment explanation
Indices: 3628036--3628171 Score: 118
Period size: 35 Copynumber: 3.9 Consensus size: 36
3628026 GTCTCTACAA
3628036 GTTCAG-CTCGATCAAACTGGTAATTCCTTATATAG
1 GTTCAGACTCGATCAAACTGGTAATTCCTTATATAG
* * ** *
3628071 GTTCAGACT-GATCAAATTGGTATTTCCTTATGGCAA
1 GTTCAGACTCGATCAAACTGGTAATTCCTTAT-ATAG
* * *
3628107 ATTCA-ACTCGATGAAATTGGTAATTCCTTATATAG
1 GTTCAGACTCGATCAAACTGGTAATTCCTTATATAG
* * * * *
3628142 CTTTAGAC-CGATCGAGCTGATAATTCCTTA
1 GTTCAGACTCGATCAAACTGGTAATTCCTTA
3628172 CAGATCTAAG
Statistics
Matches: 79, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
35 50 0.63
36 29 0.37
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (36 bp):
GTTCAGACTCGATCAAACTGGTAATTCCTTATATAG
Done.