Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000647.1 Hibiscus syriacus cultivar Beakdansim tig00001253_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: 75953
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:524 original size:21 final size:21
Alignment explanation
Indices: 480--524 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
470 TGATTCTGGG
* * *
480 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
501 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
522 CAA
1 CAA
525 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:597 original size:23 final size:22
Alignment explanation
Indices: 553--597 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
543 AATGCCAGAG
*
553 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
575 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
598 AAATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:896 original size:24 final size:24
Alignment explanation
Indices: 852--899 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
842 CCTATGTTTA
*
852 ATGCATGAATATGATTATATGTAT
1 ATGCATGAATATAATTATATGTAT
*
876 ATGCATGACATA-AATTGTATGTAT
1 ATGCATGA-ATATAATTATATGTAT
900 GCATGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (24 bp):
ATGCATGAATATAATTATATGTAT
Found at i:1437 original size:32 final size:32
Alignment explanation
Indices: 1396--1491 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
1386 GAGTCGAGGG
1396 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
* *
1428 TTTACCTATG-TCTTTC-GAGACATATAGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
1459 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
1491 T
1 T
1492 ACCGAGGATC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 25 0.47
32 28 0.53
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:1482 original size:31 final size:30
Alignment explanation
Indices: 1397--1494 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 30
1387 AGTCGAGGGT
*
1397 TTACCTATGTTCTACGGAACATATGGACAG
1 TTACCTATGTTCTAAGGAACATATGGACAG
*** *
1427 TTTTACCTATG-TCTTTCGAGACATATAGACAG
1 --TTACCTATGTTCTAAGGA-ACATATGGACAG
1459 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAAGGAACATATGGACAG
1490 TTACC
1 TTACC
1495 GAGGATCTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
30 5 0.09
31 25 0.45
32 25 0.45
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (30 bp):
TTACCTATGTTCTAAGGAACATATGGACAG
Found at i:1577 original size:29 final size:30
Alignment explanation
Indices: 1483--1574 Score: 134
Period size: 29 Copynumber: 3.1 Consensus size: 30
1473 AAGGAACATA
1483 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1513 TGGACAATTA-CGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
1542 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1571 TGGA
1 TGGA
1575 TAGGTTCGGG
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
29 45 0.80
30 11 0.20
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1847 original size:2 final size:2
Alignment explanation
Indices: 1842--1883 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1832 GTATGTGTGG
*
1842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1884 GAAAGGTGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4752 original size:22 final size:22
Alignment explanation
Indices: 4709--4752 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4699 AATGCCAGAG
*
4709 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
4731 GGGAACCGATTCCCCTAAAGGA
1 GGGAACCGATACCCCCAAAGGA
4753 AAATGTTAAT
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:0.32, C:0.32, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:5615 original size:32 final size:32
Alignment explanation
Indices: 5574--5669 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
5564 GAGTCGAGGG
5574 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
5606 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* * *
5637 TATACCTATGTTCTAAGGAACATATGGATAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
5669 T
1 T
5670 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
31 25 0.46
32 29 0.54
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:5750 original size:29 final size:30
Alignment explanation
Indices: 5661--5756 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
5651 AAGGAACATA
5661 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
5691 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
* *
5721 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
5750 TGGATAG
1 TGGATAG
5757 GTCCTTCGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 21 0.34
30 41 0.66
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:6036 original size:2 final size:2
Alignment explanation
Indices: 6026--6061 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6016 GTATGTGTGG
* *
6026 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6062 GAAAGGTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11605 original size:13 final size:12
Alignment explanation
Indices: 11576--11640 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
11566 TTTACTGTTC
11576 ACTGCTACAATA
1 ACTGCTACAATA
11588 ACTGCTACAATAA
1 ACTGCTACAAT-A
*
11601 ACTG---CAGTA
1 ACTGCTACAATA
*
11610 ACTGCTACAGTA
1 ACTGCTACAATA
*
11622 A--GCTACATTA
1 ACTGCTACAATA
11632 ACTGCTACA
1 ACTGCTACA
11641 GTAAGATGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
9 5 0.11
10 12 0.27
12 23 0.51
13 5 0.11
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (12 bp):
ACTGCTACAATA
Found at i:11612 original size:22 final size:22
Alignment explanation
Indices: 11586--11665 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
11576 ACTGCTACAA
*
11586 TAACTGCTACAATAAACTGCAG
1 TAACTGCTACAGTAAACTGCAG
* * *
11608 TAACTGCTACAGTAAGCTACAT
1 TAACTGCTACAGTAAACTGCAG
11630 TAACTGCTACAGTAAGA-TGCAG
1 TAACTGCTACAGTAA-ACTGCAG
*
11652 TATCTGCTACAGTA
1 TAACTGCTACAGTA
11666 CTTTCGAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (22 bp):
TAACTGCTACAGTAAACTGCAG
Found at i:11651 original size:44 final size:44
Alignment explanation
Indices: 11579--11665 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
11569 ACTGTTCACT
11579 GCTACAATAACTGCTACAATAAACTGCAGTAACTGCTACAGTAA
1 GCTACAATAACTGCTACAATAAACTGCAGTAACTGCTACAGTAA
* * *
11623 GCTACATTAACTGCTACAGTAAGA-TGCAGTATCTGCTACAGTA
1 GCTACAATAACTGCTACAATAA-ACTGCAGTAACTGCTACAGTA
11666 CTTTCGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (44 bp):
GCTACAATAACTGCTACAATAAACTGCAGTAACTGCTACAGTAA
Found at i:14036 original size:19 final size:19
Alignment explanation
Indices: 14012--14061 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
14002 CGTTGAACAG
14012 TGGGGGGAATCGATACCCC
1 TGGGGGGAATCGATACCCC
14031 TGGGGGGAATCGATACCCC
1 TGGGGGGAATCGATACCCC
14050 TGGGGGGAATCG
1 TGGGGGGAATCG
14062 GTTCCCTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.16
Consensus pattern (19 bp):
TGGGGGGAATCGATACCCC
Found at i:14131 original size:21 final size:21
Alignment explanation
Indices: 14106--14145 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14096 AAACCATTCA
14106 GGGGGAATCGATACCCTCTTG
1 GGGGGAATCGATACCCTCTTG
* *
14127 GGGGGAATCGTTTCCCTCT
1 GGGGGAATCGATACCCTCT
14146 GGACAATCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.28
Consensus pattern (21 bp):
GGGGGAATCGATACCCTCTTG
Found at i:14398 original size:38 final size:38
Alignment explanation
Indices: 14355--14428 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
14345 TTTATCTTAA
14355 TTTGTTATATCAAAAAATCAAAATGTTTTCAACAATTT
1 TTTGTTATATCAAAAAATCAAAATGTTTTCAACAATTT
* *
14393 TTTGTTATATCGAAATATCAAAATGTTTTCAACAAT
1 TTTGTTATATCAAAAAATCAAAATGTTTTCAACAAT
14429 CTCCCCCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.42
Consensus pattern (38 bp):
TTTGTTATATCAAAAAATCAAAATGTTTTCAACAATTT
Found at i:14490 original size:13 final size:14
Alignment explanation
Indices: 14466--14495 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
14456 TTTAGTAATT
14466 TTAAGATTTTGAAA
1 TTAAGATTTTGAAA
14480 TTAAG-TTTTGAAA
1 TTAAGATTTTGAAA
14493 TTA
1 TTA
14496 CTCCCCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TTAAGATTTTGAAA
Found at i:21839 original size:76 final size:77
Alignment explanation
Indices: 21730--21916 Score: 301
Period size: 76 Copynumber: 2.5 Consensus size: 77
21720 TTGAACAGTG
*
21730 GGGGGAATCGATA-CCCC-T-GGGGGGAATCGGTTCCCTTCGAGCATACTAGAATTTCTCAGAGC
1 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTTCGAGCATACTAGAATTTCTCAGAGC
21792 CAAACCATTC-A
66 CAAACCATTCGA
* *
21803 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTTCGAGCATACTGGAATTTCTCGGAGC
1 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTTCGAGCATACTAGAATTTCTCAGAGC
*
21868 CAAACCATTCGG
66 CAAACCATTCGA
*
21880 GGGGGAATTGGTACCCCCTTGGGGGGGAATCGGTTCC
1 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCC
21917 ATCTGGACAA
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
73 12 0.11
74 4 0.04
75 1 0.01
76 52 0.50
77 36 0.34
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.22
Consensus pattern (77 bp):
GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTTCGAGCATACTAGAATTTCTCAGAGC
CAAACCATTCGA
Found at i:22173 original size:38 final size:38
Alignment explanation
Indices: 22131--22203 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
22121 TTTATCTTAA
22131 TTTGTTATATCGAAATATCAAAATGTTTTCAACAATCT
1 TTTGTTATATCGAAATATCAAAATGTTTTCAACAATCT
22169 TTTGTTATATCGAAATATCAAAATGTTTTCAACAA
1 TTTGTTATATCGAAATATCAAAATGTTTTCAACAA
22204 GAACACTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.41
Consensus pattern (38 bp):
TTTGTTATATCGAAATATCAAAATGTTTTCAACAATCT
Found at i:33648 original size:23 final size:23
Alignment explanation
Indices: 33579--33659 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 23
33569 ACACCTAACA
* *
33579 GTGCATCAATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
33601 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
33622 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
*
33645 GTGCATCAATGCACA
1 GTGCATCGATGCACA
33660 AGGCCATGCA
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.33
22 9 0.20
23 20 0.44
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:34368 original size:21 final size:21
Alignment explanation
Indices: 34326--34369 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
34316 ACTCTGGGAG
* *
34326 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
34347 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
34368 CT
1 CT
34370 CCTCTTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:35490 original size:81 final size:82
Alignment explanation
Indices: 35378--35558 Score: 240
Period size: 81 Copynumber: 2.2 Consensus size: 82
35368 TTCAGGGTGA
* *
35378 TGCACCGATGCACCAATCCATGCATCGATGCACCATGGATTAAATTG-AACATCGAATGCATTTC
1 TGCACCGATGCA-CAAACCATGCATCGATGCACCATGG-CTAAATTGAAACATCGAATGCATTTC
35442 ATGCATCGATGCACTC-AG
64 ATGCATCGATGCACTCTAG
* ** ** *
35460 TGCATCGATGCACAAACCATGCATCGATGCACTTTGGCTATTTTGAAACATCGAATGCATTTTAT
1 TGCACCGATGCACAAACCATGCATCGATGCACCATGGCTAAATTGAAACATCGAATGCATTTCAT
*
35525 GCATCGTTGCACTCTTAG
66 GCATCGATGCACTC-TAG
35543 TGCACCGATGCACAAA
1 TGCACCGATGCACAAA
35559 GGGTCCAACG
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 5 0.06
81 53 0.62
82 11 0.13
83 17 0.20
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (82 bp):
TGCACCGATGCACAAACCATGCATCGATGCACCATGGCTAAATTGAAACATCGAATGCATTTCAT
GCATCGATGCACTCTAG
Found at i:36524 original size:23 final size:23
Alignment explanation
Indices: 36498--36543 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
36488 AAGAACCAAG
36498 ATAAA-CTTAAATATACCATTAAA
1 ATAAAGCTTAAATAT-CCATTAAA
*
36521 ATAAAGTTTAAATATCCATTAAA
1 ATAAAGCTTAAATATCCATTAAA
36544 CCAACCACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (23 bp):
ATAAAGCTTAAATATCCATTAAA
Found at i:37434 original size:12 final size:12
Alignment explanation
Indices: 37417--37450 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
37407 TTTACAAGAG
37417 AGAATGAAAATA
1 AGAATGAAAATA
*
37429 AGAATGTAAATA
1 AGAATGAAAATA
37441 AGAATGAAAA
1 AGAATGAAAA
37451 ACTTCTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (12 bp):
AGAATGAAAATA
Found at i:37713 original size:20 final size:20
Alignment explanation
Indices: 37688--37747 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
37678 CCGTTGCAGA
* *
37688 CAGGGTTTATGGATACACTG
1 CAGGGTGTATCGATACACTG
37708 CAGGGTGTATCGATACACT-
1 CAGGGTGTATCGATACACTG
* *
37727 CATAGGTGTATCGGTACACTG
1 CA-GGGTGTATCGATACACTG
37748 TTTGCATTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.06
20 32 0.94
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (20 bp):
CAGGGTGTATCGATACACTG
Found at i:40757 original size:2 final size:2
Alignment explanation
Indices: 40750--40786 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40740 TCGGATACAA
40750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40787 ATTCAATGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45466 original size:3 final size:3
Alignment explanation
Indices: 45458--45482 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45448 TAATTTACCC
45458 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
45483 ATAATAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55759 original size:2 final size:2
Alignment explanation
Indices: 55754--55803 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
55744 ATTTCCTACA
55754 AT AT AT AT 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 AT AT AT AT
55796 AT A- AT AT A
1 AT AT AT AT A
55804 AAAGAAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62654 original size:60 final size:59
Alignment explanation
Indices: 62519--62635 Score: 198
Period size: 60 Copynumber: 2.0 Consensus size: 59
62509 ATAGTCATGC
*
62519 AACTATTTTGTAACTTTTAATAGTCGATGACTCAACAAAGCAACACCCTATAGTTGAAT
1 AACTATTTTGTAACTTTTAATAGTCGATGACTCAACAAAGCAACACCCTATAGTCGAAT
* *
62578 AACCATTTTGTAACTTTTAATAGTCGAGTGACTCAACAAAGCATCACCCTATAGTCGA
1 AACTATTTTGTAACTTTTAATAGTCGA-TGACTCAACAAAGCAACACCCTATAGTCGA
62636 TGGACTATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
59 26 0.48
60 28 0.52
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (59 bp):
AACTATTTTGTAACTTTTAATAGTCGATGACTCAACAAAGCAACACCCTATAGTCGAAT
Found at i:70333 original size:95 final size:96
Alignment explanation
Indices: 70155--70378 Score: 310
Period size: 95 Copynumber: 2.4 Consensus size: 96
70145 TCATGCAACA
* * *
70155 GCCTCCG-AAGAGACGCAAACTCT-TTTAATGCAACCACCAGCGCCTCCGCCTCCTAAAGAAACG
1 GCCTCCGAAAGAAACGCAAACTCTGTTT-ATGCAACCACCAGCGCCTCCGCATCATAAAGAAACG
* *
70218 CAGACGCTGTTTATGCAACCGCCGACGCATCC
65 CAGACGCTATTTATGCAACCGCCGACACATCC
* * *
70250 GCCTCCGAAAGAAACGCAACCTCTGTTTATGCAGCCACCGGCGCCTCCGCATCATAAAG-AACGC
1 GCCTCCGAAAGAAACGCAAACTCTGTTTATGCAACCACCAGCGCCTCCGCATCATAAAGAAACGC
* *
70314 AGACGCTATTTATGCAACCGCCGGCACCTCC
66 AGACGCTATTTATGCAACCGCCGACACATCC
* *
70345 ACCTCCGAAAGAAACGCAAACGCTGTTTATGCAA
1 GCCTCCGAAAGAAACGCAAACTCTGTTTATGCAA
70379 ACGCCGCCCA
Statistics
Matches: 113, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
95 69 0.61
96 41 0.36
97 3 0.03
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.17
Consensus pattern (96 bp):
GCCTCCGAAAGAAACGCAAACTCTGTTTATGCAACCACCAGCGCCTCCGCATCATAAAGAAACGC
AGACGCTATTTATGCAACCGCCGACACATCC
Found at i:70384 original size:48 final size:48
Alignment explanation
Indices: 70155--70384 Score: 250
Period size: 48 Copynumber: 4.8 Consensus size: 48
70145 TCATGCAACA
* * * *
70155 GCCTCCG-AAGAGACGCAAACTCT-TTTAATGCAACCACCAGCGCCTCC
1 GCCTCCGAAAGAAACGCAAACGCTGTTT-ATGCAACCGCCGGCGCCTCC
* * * *
70202 GCCTCCTAAAGAAACGCAGACGCTGTTTATGCAACCGCCGACGCATCC
1 GCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACCGCCGGCGCCTCC
* * * *
70250 GCCTCCGAAAGAAACGCAACCTCTGTTTATGCAGCCACCGGCGCCTCC
1 GCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACCGCCGGCGCCTCC
* ** * * *
70298 GCATCATAAAG-AACGCAGACGCTATTTATGCAACCGCCGGCACCTCC
1 GCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACCGCCGGCGCCTCC
* *
70345 ACCTCCGAAAGAAACGCAAACGCTGTTTATGCAAACGCCG
1 GCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACCGCCG
70385 CCCAAAGAAA
Statistics
Matches: 147, Mismatches: 33, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
47 42 0.29
48 102 0.69
49 3 0.02
ACGTcount: A:0.28, C:0.36, G:0.20, T:0.17
Consensus pattern (48 bp):
GCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACCGCCGGCGCCTCC
Found at i:70649 original size:33 final size:32
Alignment explanation
Indices: 70627--70738 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 32
70617 TACACGGACA
70627 AGCCAGGTTAATCGACCGGAGCCTACCCAGGCG
1 AGCCAGGTTAATCG-CCGGAGCCTACCCAGGCG
* * *
70660 AGCCAGGTTAATTGGCCGGAACGTACCCAGGCG
1 AGCCAGGTTAA-TCGCCGGAGCCTACCCAGGCG
* * *
70693 AGCCAGGTTAATCTGCCTGAGCCTACGC-GGACT
1 AGCCAGGTTAATC-GCCGGAGCCTACCCAGG-CG
70726 AGCCAGGTTAATC
1 AGCCAGGTTAATC
70739 AGGTAGGAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
32 3 0.04
33 62 0.93
34 2 0.03
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.17
Consensus pattern (32 bp):
AGCCAGGTTAATCGCCGGAGCCTACCCAGGCG
Found at i:74532 original size:33 final size:33
Alignment explanation
Indices: 74476--74570 Score: 118
Period size: 33 Copynumber: 2.9 Consensus size: 33
74466 TTTCAAAACT
* * * *
74476 TGAAATACCTAAAATACCTGAGTTGCCTAAGCC
1 TGAATTACCTAAAGTTCCTGAGTTGCCAAAGCC
*
74509 TGAATTACCTAAAGTTCCAGAGTTGCCAAAGCC
1 TGAATTACCTAAAGTTCCTGAGTTGCCAAAGCC
* * *
74542 TGAATTGCCTAAGGTTCCTGAGTTTCCAA
1 TGAATTACCTAAAGTTCCTGAGTTGCCAA
74571 CAGTGCCAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (33 bp):
TGAATTACCTAAAGTTCCTGAGTTGCCAAAGCC
Found at i:74584 original size:51 final size:51
Alignment explanation
Indices: 74525--74621 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
74515 ACCTAAAGTT
* * *
74525 CCAGAGTTGCCAAAGCCTGAA-TTGCCTAAGGTTCCTGAGTTTCCAACAGTG
1 CCAGAGTTGCCAAAGCCTGAACTT-CCTAAAGTTCATGAGTTGCCAACAGTG
74576 CCAGAGTTGCCAAAGCCTGAACTTCCTAAAGTTCATGAGTTGCCAA
1 CCAGAGTTGCCAAAGCCTGAACTTCCTAAAGTTCATGAGTTGCCAA
74622 AGCTAGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
51 40 0.95
52 2 0.05
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (51 bp):
CCAGAGTTGCCAAAGCCTGAACTTCCTAAAGTTCATGAGTTGCCAACAGTG
Found at i:74637 original size:33 final size:33
Alignment explanation
Indices: 74579--74655 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
74569 AACAGTGCCA
*
74579 GAGTTGCCAAAGCCTGAACTTCCTAAAGTTCAT
1 GAGTTGCCAAAGCCTGAACTTCCTAAAGTACAT
* *
74612 GAGTTGCCAAAG-CTAGAA-TTACCTAAGGTACCT
1 GAGTTGCCAAAGCCT-GAACTT-CCTAAAGTACAT
*
74645 GAGTTTCCAAA
1 GAGTTGCCAAA
74656 AGTGCCCGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 4 0.11
33 34 0.89
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (33 bp):
GAGTTGCCAAAGCCTGAACTTCCTAAAGTACAT
Found at i:74637 original size:84 final size:84
Alignment explanation
Indices: 74495--74701 Score: 287
Period size: 84 Copynumber: 2.5 Consensus size: 84
74485 TAAAATACCT
* * *
74495 GAGTTGCCTAAGCCTGAA-TTACCTAAAGTTCCA-GAGTTGCCAAAGCCTGAATTGCCTAAGGTT
1 GAGTTGCCAAAGCCTGAACTT-CCTAAAGTT-CATGAGTTGCCAAAGCCTGAATTACCTAAGGTA
*
74558 CCTGAGTTTCCAACAGTGCCA
64 CCTGAGTTTCCAAAAGTGCCA
74579 GAGTTGCCAAAGCCTGAACTTCCTAAAGTTCATGAGTTGCCAAAG-CTAGAATTACCTAAGGTAC
1 GAGTTGCCAAAGCCTGAACTTCCTAAAGTTCATGAGTTGCCAAAGCCT-GAATTACCTAAGGTAC
*
74643 CTGAGTTTCCAAAAGTGCCC
65 CTGAGTTTCCAAAAGTGCCA
* *
74663 GAGTTGCCAAAGCCAGAACTTCC-AAAGGTTCCTGAGTTG
1 GAGTTGCCAAAGCCTGAACTTCCTAAA-GTTCATGAGTTG
74702 ACTAAGTTGC
Statistics
Matches: 112, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
83 7 0.06
84 103 0.92
85 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (84 bp):
GAGTTGCCAAAGCCTGAACTTCCTAAAGTTCATGAGTTGCCAAAGCCTGAATTACCTAAGGTACC
TGAGTTTCCAAAAGTGCCA
Found at i:74646 original size:51 final size:51
Alignment explanation
Indices: 74591--74697 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 51
74581 GTTGCCAAAG
* * * * *
74591 CCTGAACTTCCTAAAGTTCATGAGTTGCCAAAGCTAGAA-TTACCTAAGGTA
1 CCTGAACTTCCAAAAGTGCACGAGTTGCCAAAGCCAGAACTT-CCAAAGGTA
** * *
74642 CCTGAGTTTCCAAAAGTGCCCGAGTTGCCAAAGCCAGAACTTCCAAAGGTT
1 CCTGAACTTCCAAAAGTGCACGAGTTGCCAAAGCCAGAACTTCCAAAGGTA
74693 CCTGA
1 CCTGA
74698 GTTGACTAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
51 44 0.96
52 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (51 bp):
CCTGAACTTCCAAAAGTGCACGAGTTGCCAAAGCCAGAACTTCCAAAGGTA
Found at i:74817 original size:33 final size:33
Alignment explanation
Indices: 74775--75130 Score: 339
Period size: 33 Copynumber: 10.9 Consensus size: 33
74765 GATCCTAAGC
* * * ***
74775 TACCAAAAGTTCATGAATTACCGAAGTTAGAAT
1 TACCTAAAGTTCCTGAATTACCAAAACCAGAAT
* * * * * *
74808 TACCTAAAGTTTCTGAGGTGACCAAACTCCTGAAA
1 TACCTAAAGTTCCTGA-ATTACCAAA-ACCAGAAT
74843 TACCTAAAGTTCCTGAATTACCAAAACCAGAAT
1 TACCTAAAGTTCCTGAATTACCAAAACCAGAAT
*
74876 TACCTAAAGTTCATGAATTACCAAAACCAGAAT
1 TACCTAAAGTTCCTGAATTACCAAAACCAGAAT
* ** *
74909 TACC-AAATGTT-CTGAGTTA-CAAAGGCAAAAT
1 TACCTAAA-GTTCCTGAATTACCAAAACCAGAAT
* * *
74940 TACCTAAAATTCCCGAGTTACCAAAACCAGAAT
1 TACCTAAAGTTCCTGAATTACCAAAACCAGAAT
74973 TACCTAAA-TTCCTGAATTACCAAAACCAGAAT
1 TACCTAAAGTTCCTGAATTACCAAAACCAGAAT
*
75005 TACCTAAAATTCCTGAATTACC-AAACCAGAAT
1 TACCTAAAGTTCCTGAATTACCAAAACCAGAAT
* * * * *
75037 TACCAAAAGTTCCAGAGTTATCAAAGCCAGAAT
1 TACCTAAAGTTCCTGAATTACCAAAACCAGAAT
* *
75070 TACCTAAAATTCCCGAGA-TACC-AAACCAGAAT
1 TACCTAAAGTTCCTGA-ATTACCAAAACCAGAAT
* ** *
75102 TACCCAAAACTCCTGAATTAACAAAACCA
1 TACCTAAAGTTCCTGAATTACCAAAACCA
75131 TAATCAACTG
Statistics
Matches: 266, Mismatches: 46, Indels: 22
0.80 0.14 0.07
Matches are distributed among these distances:
31 16 0.06
32 101 0.38
33 118 0.44
34 13 0.05
35 18 0.07
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (33 bp):
TACCTAAAGTTCCTGAATTACCAAAACCAGAAT
Found at i:74974 original size:97 final size:96
Alignment explanation
Indices: 74843--75126 Score: 335
Period size: 97 Copynumber: 2.9 Consensus size: 96
74833 ACTCCTGAAA
* * * *
74843 TACCTAAAGTTCCTGAATTACCAAAACCAGAATTACCTAAAGTTCATGAATTACCAAAACCAGAA
1 TACCTAAAATTCCAGAGTTACCAAAACCAGAATTACCTAAA-TTCCTGAATTACCAAAACCAGAA
* * *
74908 TTACC-AAATGTTCTGAGTTA-CAAAGGCAAAAT
65 TTACCAAAAT-TCCTGAATTACCAAA-CCAAAAT
*
74940 TACCTAAAATTCCCGAGTTACCAAAACCAGAATTACCTAAATTCCTGAATTACCAAAACCAGAAT
1 TACCTAAAATTCCAGAGTTACCAAAACCAGAATTACCTAAATTCCTGAATTACCAAAACCAGAAT
*
75005 TACCTAAAATTCCTGAATTACCAAACCAGAAT
66 TACC-AAAATTCCTGAATTACCAAACCAAAAT
* * *
75037 TACC-AAAAGTTCCAGAGTTATCAAAGCCAGAATTACCTAAAATTCCCGAGA-TACC-AAACCAG
1 TACCTAAAA-TTCCAGAGTTACCAAAACCAGAATTACCT-AAATTCCTGA-ATTACCAAAACCAG
* *
75099 AATTACCCAAAACTCCTGAATTAACAAA
63 AATTA-CCAAAATTCCTGAATTACCAAA
75127 ACCATAATCA
Statistics
Matches: 166, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
96 31 0.19
97 111 0.67
98 23 0.14
99 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.23
Consensus pattern (96 bp):
TACCTAAAATTCCAGAGTTACCAAAACCAGAATTACCTAAATTCCTGAATTACCAAAACCAGAAT
TACCAAAATTCCTGAATTACCAAACCAAAAT
Found at i:75026 original size:65 final size:64
Alignment explanation
Indices: 74843--75130 Score: 330
Period size: 65 Copynumber: 4.4 Consensus size: 64
74833 ACTCCTGAAA
* * **
74843 TACCTAAAGTTCCTGAATTACCAAAACCAGAATTACCTAAAGTTCATGAATTACCAAAACCAGAA
1 TACC-AAAATTCCTGAATTACCAAAACCAGAATTACCTAAAATTCCCGAATTACC-AAACCAGAA
74908 T
64 T
* * ** * *
74909 TACC-AAATGTTCTGAGTTA-CAAAGGCAAAATTACCTAAAATTCCCGAGTTACCAAAACCAGAA
1 TACCAAAAT-TCCTGAATTACCAAAACCAGAATTACCTAAAATTCCCGAATTACC-AAACCAGAA
74972 T
64 T
* *
74973 TACCTAAATTCCTGAATTACCAAAACCAGAATTACCTAAAATTCCTGAATTACCAAACCAGAAT
1 TACCAAAATTCCTGAATTACCAAAACCAGAATTACCTAAAATTCCCGAATTACCAAACCAGAAT
* * * *
75037 TACCAAAAGTTCCAGAGTTATCAAAGCCAGAATTACCTAAAATTCCCGAGA-TACCAAACCAGAA
1 TACCAAAA-TTCCTGAATTACCAAAACCAGAATTACCTAAAATTCCCGA-ATTACCAAACCAGAA
75101 T
64 T
* *
75102 TACCCAAAACTCCTGAATTAACAAAACCA
1 TA-CCAAAATTCCTGAATTACCAAAACCA
75131 TAATCAACTG
Statistics
Matches: 188, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
64 70 0.37
65 107 0.57
66 11 0.06
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (64 bp):
TACCAAAATTCCTGAATTACCAAAACCAGAATTACCTAAAATTCCCGAATTACCAAACCAGAAT
Found at i:75168 original size:97 final size:96
Alignment explanation
Indices: 74848--75176 Score: 254
Period size: 97 Copynumber: 3.4 Consensus size: 96
74838 TGAAATACCT
* * * **
74848 AAAGTTCCTGAATTACCAAAACCAGAATTACCTAAAGTTCATGAATTACCAAAACCAGAATTA-C
1 AAAGTTCCAGAACTATC-AAACCAGAATTACCTAAA-TTCCCGAATTACCAAAACCAGAATTACC
** * * ** * * *
74912 CAAATGTTCTGAGTTACAAAGGCAAAATTACCTA
64 CAAAACTCCTGAATTACAAAACCAGAATCAAC-A
* ** * * *
74946 AAA-TTCCCGAGTTACCAAAACCAGAATTACCTAAATTCCTGAATTACCAAAACCAGAATTACCT
1 AAAGTTCCAGAACTATC-AAACCAGAATTACCTAAATTCCCGAATTACCAAAACCAGAATTACCC
* * * *
75010 AAAATTCCTGAATTACCAAACCAGAATTACCA
65 AAAACTCCTGAATTACAAAACCAGAATCAACA
**
75042 AAAGTTCCAGAGTTATCAAAGCCAGAATTACCTAAAATTCCCGAGA-TACC-AAACCAGAATTAC
1 AAAGTTCCAGAACTATCAAA-CCAGAATTACCT-AAATTCCCGA-ATTACCAAAACCAGAATTAC
* *
75105 CCAAAACTCCTGAATTAACAAAACCATAATCAACT
63 CCAAAACTCCTGAATT-ACAAAACCAGAATCAACA
* * * *
75140 GATGTTCCA-AACTATCCAAACCATAATTACCCAAATT
1 AAAGTTCCAGAACTAT-CAAACCAGAATTACCTAAATT
75177 ATTAAAATGC
Statistics
Matches: 196, Mismatches: 28, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
96 37 0.19
97 118 0.60
98 40 0.20
99 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (96 bp):
AAAGTTCCAGAACTATCAAACCAGAATTACCTAAATTCCCGAATTACCAAAACCAGAATTACCCA
AAACTCCTGAATTACAAAACCAGAATCAACA
Done.