Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002098.1 Hibiscus syriacus cultivar Beakdansim tig00004282_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: 62244
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:9532 original size:21 final size:21
Alignment explanation
Indices: 9508--9548 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9498 CGTTGTTGGA
*
9508 GGAGGAAGAGGAAGAGGAAGT
1 GGAGGAAGAAGAAGAGGAAGT
*
9529 GGAGGAAGAAGAGGAGGAAG
1 GGAGGAAGAAGAAGAGGAAG
9549 AGTCGGAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.54, T:0.02
Consensus pattern (21 bp):
GGAGGAAGAAGAAGAGGAAGT
Found at i:9544 original size:12 final size:12
Alignment explanation
Indices: 9505--9549 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
9495 CTCCGTTGTT
*
9505 GGAGGAGGAAGA
1 GGAGGAAGAAGA
* * *
9517 GGAAGAGGAAGT
1 GGAGGAAGAAGA
9529 GGAGGAAGAAGA
1 GGAGGAAGAAGA
9541 GGAGGAAGA
1 GGAGGAAGA
9550 GTCGGAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.53, T:0.02
Consensus pattern (12 bp):
GGAGGAAGAAGA
Found at i:10701 original size:105 final size:106
Alignment explanation
Indices: 10519--10825 Score: 516
Period size: 105 Copynumber: 3.0 Consensus size: 106
10509 TACATATTCA
10519 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
1 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
10584 TATGGGATTCTTTTTC-TTGCGAATTGTGATTTAGTTACTG
66 TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
10624 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
1 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
10689 TATGGGATTCTTTTTCTTTGCGAA-T-TGATTTAGTTACTG
66 TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
10728 TATCTGTTAC----TA----GGGA-TTATTGAGT-GGAGTCTAACAGAATAG-CTAGAAGCATAT
1 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
10782 TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
66 TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
10823 TAT
1 TAT
10826 GATTCTGTTG
Statistics
Matches: 199, Mismatches: 0, Indels: 16
0.93 0.00 0.07
Matches are distributed among these distances:
93 36 0.18
94 18 0.09
95 26 0.13
96 4 0.02
100 2 0.01
104 24 0.12
105 82 0.41
106 7 0.04
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.41
Consensus pattern (106 bp):
TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
Found at i:15894 original size:18 final size:18
Alignment explanation
Indices: 15868--15912 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
15858 TCACGGAATG
* *
15868 TAAGATTACCGGCGGTAA
1 TAAGATTACCGGAGGGAA
*
15886 TAGGATTACCGGAGGGAA
1 TAAGATTACCGGAGGGAA
15904 TAAGATTAC
1 TAAGATTAC
15913 TGGGAATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.22
Consensus pattern (18 bp):
TAAGATTACCGGAGGGAA
Found at i:18209 original size:14 final size:13
Alignment explanation
Indices: 18190--18233 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 13
18180 GGCAACTCAT
18190 TTTATTATTTTTTA
1 TTTATT-TTTTTTA
18204 TTTATTTTTTGGTTA
1 TTTATTTTTT--TTA
18219 TTTATTTTTCTTTA
1 TTTATTTTT-TTTA
18233 T
1 T
18234 ATTTTTAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.15
14 10 0.37
15 12 0.44
16 1 0.04
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTATTTTTTTTA
Found at i:19653 original size:30 final size:29
Alignment explanation
Indices: 19605--19689 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
19595 TTTTACCAAC
*
19605 ATTTTTTCTAACATTTGTTATTAAGGGTCT
1 ATTTTTTC-AATATTTGTTATTAAGGGTCT
* *
19635 AATTTTTTCAATACTTGTTA-TAATGGGCCT
1 -ATTTTTTCAATATTTGTTATTAA-GGGTCT
*
19665 -TTTTTT-AATATTTGTTATTAGGGGT
1 ATTTTTTCAATATTTGTTATTAAGGGT
19690 ATACTTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
27 13 0.28
28 8 0.17
29 3 0.07
30 14 0.30
31 8 0.17
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (29 bp):
ATTTTTTCAATATTTGTTATTAAGGGTCT
Found at i:21794 original size:28 final size:29
Alignment explanation
Indices: 21737--21797 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
21727 TGAACATATA
* *
21737 AATAGTCGAGTGATCATTTTATATCTTTT
1 AATAGTCGAGAGATCATTTTATAACTTTT
*
21766 AATAGTTGAGAGATCA-TTTATAACTTTT
1 AATAGTCGAGAGATCATTTTATAACTTTT
21794 AATA
1 AATA
21798 CTCAGAGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.44
Consensus pattern (29 bp):
AATAGTCGAGAGATCATTTTATAACTTTT
Found at i:21994 original size:12 final size:12
Alignment explanation
Indices: 21977--22003 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21967 CTATTACCAT
21977 TTTAAGGTCAAA
1 TTTAAGGTCAAA
21989 TTTAAGGTCAAA
1 TTTAAGGTCAAA
22001 TTT
1 TTT
22004 TCATCATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (12 bp):
TTTAAGGTCAAA
Found at i:22253 original size:38 final size:38
Alignment explanation
Indices: 22207--22280 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
22197 CTATCTACAA
*
22207 TCCTAAAAAATCTCTAACCTCATAGTCCATTATTGTCG
1 TCCTAAAAAATCTCTAACCTCAAAGTCCATTATTGTCG
*
22245 TCCTAAAAAATCTCTATCCTCAAAGTCCATTATTGT
1 TCCTAAAAAATCTCTAACCTCAAAGTCCATTATTGT
22281 TGCCGATTGT
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:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (38 bp):
TCCTAAAAAATCTCTAACCTCAAAGTCCATTATTGTCG
Found at i:22609 original size:14 final size:15
Alignment explanation
Indices: 22578--22610 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22568 TTTACCGGAT
*
22578 AAAAAACCGGTTTGA
1 AAAAAACCGGTTTAA
22593 AAAAAACCGG-TTAA
1 AAAAAACCGGTTTAA
22607 AAAA
1 AAAA
22611 CTAGTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (15 bp):
AAAAAACCGGTTTAA
Found at i:24932 original size:21 final size:21
Alignment explanation
Indices: 24908--24949 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
24898 AGTTTACTTT
*
24908 TAAACTTTATTTTAATTATCG
1 TAAACTTTATTTCAATTATCG
*
24929 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
24950 AACTTGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:24998 original size:33 final size:32
Alignment explanation
Indices: 24938--25046 Score: 159
Period size: 33 Copynumber: 3.4 Consensus size: 32
24928 GTAAACTTTG
24938 TTTCAA-TTATCGAACTTGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGAAGTTTTTAAGTA
*
24969 TTTGAATTTATCGAACTTGAAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTG-AAGTTTTTAAGTA
* *
25002 TTTTAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAATTTATCGAACTT-GAAGTTTTTAAGTA
25035 TTTCAA-TTATCG
1 TTTCAATTTATCG
25047 TAAACTTTGT
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 5 0.07
32 18 0.25
33 47 0.66
34 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (32 bp):
TTTCAATTTATCGAACTTGAAGTTTTTAAGTA
Found at i:25143 original size:15 final size:15
Alignment explanation
Indices: 25088--25144 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
25078 TTTAATAATA
*
25088 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
25103 TTATAACCGGATTTTT
1 TTAAAACCGG-TTTTT
**
25119 AAAAAAAACCGGTTTTT
1 --TTAAAACCGGTTTTT
25136 TTAAAACCG
1 TTAAAACCG
25145 AAACCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
15 15 0.47
16 5 0.16
17 5 0.16
18 7 0.22
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:31297 original size:14 final size:14
Alignment explanation
Indices: 31280--31330 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
31270 TATTTTTAAT
*
31280 AAAATGATAATAAA
1 AAAATTATAATAAA
* *
31294 AAAATTATATTACA
1 AAAATTATAATAAA
31308 AAAATTATTAATAAA
1 AAAATTA-TAATAAA
31323 ATAAATTA
1 A-AAATTA
31331 GAGTGATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 18 0.60
15 6 0.20
16 6 0.20
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
AAAATTATAATAAA
Found at i:34385 original size:27 final size:27
Alignment explanation
Indices: 34350--34407 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
34340 ATAAATAACT
34350 ATTATAATGAAATTTAATTTATATCAA
1 ATTATAATGAAATTTAATTTATATCAA
34377 ATTATAATGAAATTTAATTTATATCAA
1 ATTATAATGAAATTTAATTTATATCAA
34404 ATTA
1 ATTA
34408 AATTAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (27 bp):
ATTATAATGAAATTTAATTTATATCAA
Found at i:34405 original size:16 final size:16
Alignment explanation
Indices: 34359--34411 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
34349 TATTATAATG
34359 AAATTTAATTTATATC
1 AAATTTAATTTATATC
*
34375 AAA-TT-A--TA-ATG
1 AAATTTAATTTATATC
34386 AAATTTAATTTATATC
1 AAATTTAATTTATATC
*
34402 AAATTAAATT
1 AAATTTAATT
34412 AAAAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
11 5 0.17
12 4 0.14
13 1 0.03
14 1 0.03
15 4 0.14
16 14 0.48
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATTTAATTTATATC
Found at i:34706 original size:31 final size:29
Alignment explanation
Indices: 34668--34732 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
34658 GATCCAATGG
34668 TATAATTGAAATAAAAATCAAAGTTCAGTGC
1 TATAATTG-AA-AAAAATCAAAGTTCAGTGC
* * * *
34699 TATAATTGGAAAAATTGAAAGTTCAGTGG
1 TATAATTGAAAAAAATCAAAGTTCAGTGC
34728 TATAA
1 TATAA
34733 ATGATACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 21 0.70
30 1 0.03
31 8 0.27
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (29 bp):
TATAATTGAAAAAAATCAAAGTTCAGTGC
Found at i:34785 original size:30 final size:31
Alignment explanation
Indices: 34716--34791 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
34706 GGAAAAATTG
* * *
34716 AAAGTTCAGTGGTATAAATGATACAATACCT
1 AAAGTTTAGTGGTATAAACGATACAACACCT
* *
34747 AAATTTTAGTGGTATAAACGATA-AACATCT
1 AAAGTTTAGTGGTATAAACGATACAACACCT
34777 AAAGTTTAGTGGTAT
1 AAAGTTTAGTGGTAT
34792 CTGATTTAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 19 0.49
31 20 0.51
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (31 bp):
AAAGTTTAGTGGTATAAACGATACAACACCT
Found at i:37305 original size:31 final size:30
Alignment explanation
Indices: 37270--37328 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
37260 TTATTACAAG
*
37270 TGATGACAAAAATGAATTACACATCAAAATA
1 TGATGACAAAAATAAATTACACAT-AAAATA
*
37301 TGATGACCAAAATAAATTACACATAAAA
1 TGATGACAAAAATAAATTACACATAAAA
37329 GTAAAAGGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.56, C:0.14, G:0.08, T:0.22
Consensus pattern (30 bp):
TGATGACAAAAATAAATTACACATAAAATA
Found at i:43590 original size:2 final size:2
Alignment explanation
Indices: 43546--43579 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
43536 GACCGTCGCA
43546 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43580 GAATTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:43623 original size:2 final size:2
Alignment explanation
Indices: 43616--43641 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43606 CCTCACCACA
43616 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
43642 CAACGACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43639 original size:49 final size:49
Alignment explanation
Indices: 43565--43690 Score: 198
Period size: 49 Copynumber: 2.5 Consensus size: 49
43555 TAATATATAT
* * *
43565 ATATATATATATATAGAATTATATATCTCAACGACTATGTGCCTCACCACA
1 ATATATATATATATA-TA-TATATATATCAACGACTATATGCCTCACCACA
*
43616 ATATATATATATATATATATATATATCAACGACTATATTCCTCACCACA
1 ATATATATATATATATATATATATATCAACGACTATATGCCTCACCACA
43665 ATATATATATATATATATATATATAT
1 ATATATATATATATATATATATATAT
43691 ATATATATAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
49 55 0.77
50 1 0.01
51 15 0.21
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (49 bp):
ATATATATATATATATATATATATATCAACGACTATATGCCTCACCACA
Found at i:43672 original size:2 final size:2
Alignment explanation
Indices: 43665--43710 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
43655 CCTCACCACA
43665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43705 AT AT AT
1 AT AT AT
43711 CTCAACGACT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48180 original size:40 final size:41
Alignment explanation
Indices: 48113--48459 Score: 323
Period size: 41 Copynumber: 8.5 Consensus size: 41
48103 TGATTGAATT
* * * *
48113 GAATTGTGAATTATTGAATGATGCCATGATCGAATTAAGTA
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAATTAAGTC
*
48154 GAATTGTGAA-TATTGCATGCTTCCATGATCTAATTAAGTC
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAATTAAGTC
* * * *
48194 GAA-TGTGAATTATCGCATGCTTTCATGATCGAATTCAGTT
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAATTAAGTC
* *
48234 GAATTGTAAATTATTGCATG-TTGCCATGATCGAATTAAGTT
1 GAATTGTGAATTATTGCATGCTT-CCATGATCGAATTAAGTC
* * * * *
48275 GAATTGTGAATTA-TACATGATGCCATAATTGAATTGAA-TC
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAATT-AAGTC
* * * *
48315 GAATTGTGTATTATTGCATTCTAT-CATGATTGAATTGAA-TG
1 GAATTGTGAATTATTGCATGCT-TCCATGATCGAATT-AAGTC
* * *
48356 GAATTGTGAATTATTGAATGTTTCCATGATCGAATTGAGTC
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAATTAAGTC
* * * * *
48397 GAATGGTGAATTATTGCACGTTTCCATGATTGAACTGAA-TC
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAA-TTAAGTC
* *
48438 GAATTTTGAATTAGTGCATGCT
1 GAATTGTGAATTATTGCATGCT
48460 GCAAAGATCG
Statistics
Matches: 251, Mismatches: 45, Indels: 20
0.79 0.14 0.06
Matches are distributed among these distances:
39 6 0.02
40 89 0.35
41 154 0.61
42 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (41 bp):
GAATTGTGAATTATTGCATGCTTCCATGATCGAATTAAGTC
Found at i:48309 original size:81 final size:81
Alignment explanation
Indices: 48111--48426 Score: 279
Period size: 81 Copynumber: 3.9 Consensus size: 81
48101 CATGATTGAA
*
48111 TTGAATTGTGAATTATTGA-ATGATGCCATGATCGAATTAAGTAGAATTGTGAA-TATTGCATGC
1 TTGAATTGTGAATTA-TCACATGATGCCATGATCGAATTAAGTAGAATTGTGAATTATTGCATG-
*
48174 TTCCATGATCTAATTAAG
64 TTCCATGATCGAATTAAG
* * * ** * * *
48192 TCGAA-TGTGAATTATCGCATGCTTTCATGATCGAATTCAGTTGAATTGTAAATTATTGCATGTT
1 TTGAATTGTGAATTATCACATGATGCCATGATCGAATTAAGTAGAATTGTGAATTATTGCATGTT
48256 GCCATGATCGAATTAAG
66 -CCATGATCGAATTAAG
* * * *
48273 TTGAATTGTGAATTAT-ACATGATGCCATAATTGAATTGAA-TCGAATTGTGTATTATTGCAT-T
1 TTGAATTGTGAATTATCACATGATGCCATGATCGAATT-AAGTAGAATTGTGAATTATTGCATGT
* *
48335 CTATCATGATTGAATTGAA-
65 -T-CCATGATCGAATT-AAG
* * * * * * * *
48354 TGGAATTGTGAATTATTGA-ATGTTTCCATGATCGAATTGAGTCGAATGGTGAATTATTGCACGT
1 TTGAATTGTGAATTA-TCACATGATGCCATGATCGAATTAAGTAGAATTGTGAATTATTGCATG-
48418 TTCCATGAT
64 TTCCATGAT
48427 TGAACTGAAT
Statistics
Matches: 189, Mismatches: 34, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
79 1 0.01
80 40 0.21
81 92 0.49
82 53 0.28
83 2 0.01
84 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (81 bp):
TTGAATTGTGAATTATCACATGATGCCATGATCGAATTAAGTAGAATTGTGAATTATTGCATGTT
CCATGATCGAATTAAG
Found at i:49273 original size:36 final size:36
Alignment explanation
Indices: 49226--49299 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
49216 TGCATTGGTG
49226 CACTATCATGGTGCATCGATACCCCTTCATTAAATT
1 CACTATCATGGTGCATCGATACCCCTTCATTAAATT
49262 CACTATCATGGTGCATCGATACCCCTTCATTAAATT
1 CACTATCATGGTGCATCGATACCCCTTCATTAAATT
49298 CA
1 CA
49300 AATAAACTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.32
Consensus pattern (36 bp):
CACTATCATGGTGCATCGATACCCCTTCATTAAATT
Found at i:49357 original size:12 final size:12
Alignment explanation
Indices: 49340--49379 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
49330 CTTGATGCAT
49340 GGATGCATGGCA
1 GGATGCATGGCA
49352 GGATGCAT--C-
1 GGATGCATGGCA
49361 -GATGCATGGCA
1 GGATGCATGGCA
49372 GGATGCAT
1 GGATGCAT
49380 CGATGCATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
8 7 0.29
10 2 0.08
12 15 0.62
ACGTcount: A:0.25, C:0.17, G:0.38, T:0.20
Consensus pattern (12 bp):
GGATGCATGGCA
Found at i:49358 original size:20 final size:20
Alignment explanation
Indices: 49333--49427 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
49323 TTGCAGCCTT
*
49333 GATGCATGGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
49353 GATGCATCGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
**
49373 GATGCATCGATGCATGGCCTT
1 GATGCATCGATGCATGG-CAG
** *
49394 GATGCATCGATGCACAGAAG
1 GATGCATCGATGCATGGCAG
49414 GATGCATCGATGCA
1 GATGCATCGATGCA
49428 CTAATTGCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 50 0.76
21 16 0.24
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:49416 original size:41 final size:40
Alignment explanation
Indices: 49333--49427 Score: 127
Period size: 41 Copynumber: 2.4 Consensus size: 40
49323 TTGCAGCCTT
* ** *
49333 GATGCATGGATGCATGGCAGGATGCATCGATGCATGGCAG
1 GATGCATCGATGCATGGCAGGATGCATCGATGCACAGAAG
**
49373 GATGCATCGATGCATGGCCTTGATGCATCGATGCACAGAAG
1 GATGCATCGATGCATGG-CAGGATGCATCGATGCACAGAAG
49414 GATGCATCGATGCA
1 GATGCATCGATGCA
49428 CTAATTGCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 16 0.33
41 32 0.67
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (40 bp):
GATGCATCGATGCATGGCAGGATGCATCGATGCACAGAAG
Found at i:49615 original size:29 final size:29
Alignment explanation
Indices: 49594--49651 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
49584 AAACTTTGAA
49594 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
49623 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
49652 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:49641 original size:30 final size:30
Alignment explanation
Indices: 49594--49653 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
49584 AAACTTTGAA
49594 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
49623 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
49654 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:49788 original size:21 final size:21
Alignment explanation
Indices: 49764--49803 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49754 ATGTTTAATG
*
49764 AAAAAGATATCAATTGTTAAC
1 AAAAAGATAACAATTGTTAAC
*
49785 AAAATGATAACAATTGTTA
1 AAAAAGATAACAATTGTTA
49804 CCAATTGTTG
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:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATAACAATTGTTAAC
Found at i:57532 original size:20 final size:22
Alignment explanation
Indices: 57507--57546 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
57497 TGTTGTATAT
57507 AGTCG-TTGGGGATG-TTTTGG
1 AGTCGTTTGGGGATGATTTTGG
57527 AGTCGTTTGGGGATGATTTT
1 AGTCGTTTGGGGATGATTTT
57547 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.05, G:0.40, T:0.42
Consensus pattern (22 bp):
AGTCGTTTGGGGATGATTTTGG
Found at i:57661 original size:20 final size:20
Alignment explanation
Indices: 57636--57710 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
57626 TTGCAACCTT
*
57636 GATGCATGGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
**
57656 GATGCATCGATGCATGGCCTT
1 GATGCATCGATGCATGG-CAG
* **
57677 GATGCATAGATGCA-CACAAG
1 GATGCATCGATGCATGGC-AG
57697 GATGCATCGATGCA
1 GATGCATCGATGCA
57711 CTAATTGCAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 29 0.66
21 14 0.32
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:57689 original size:41 final size:41
Alignment explanation
Indices: 57632--57710 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
57622 GCCGTTGCAA
* **
57632 CCTTGATGCATGGATGCATGGC-AGGATGCATCGATGCATGG
1 CCTTGATGCATAGATGCA-CACAAGGATGCATCGATGCATGG
57673 CCTTGATGCATAGATGCACACAAGGATGCATCGATGCA
1 CCTTGATGCATAGATGCACACAAGGATGCATCGATGCA
57711 CTAATTGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (41 bp):
CCTTGATGCATAGATGCACACAAGGATGCATCGATGCATGG
Found at i:57756 original size:12 final size:13
Alignment explanation
Indices: 57733--57828 Score: 52
Period size: 13 Copynumber: 7.9 Consensus size: 13
57723 GGTGTTTGAG
57733 TGCATGGATGCAC
1 TGCATGGATGCAC
57746 TGCAT-GATGCATC
1 TGCATGGATGCA-C
*
57759 GATGCATCGATGCAC
1 --TGCATGGATGCAC
*
57774 T--A--G-TGCAGG
1 TGCATGGATGCA-C
57783 TGCATGGATGCAC
1 TGCATGGATGCAC
57796 TGCA-GG--G-A-
1 TGCATGGATGCAC
57804 TGCATGGATGCAC
1 TGCATGGATGCAC
*
57817 TGCAGGGATGCA
1 TGCATGGATGCA
57829 GGGATGCACT
Statistics
Matches: 65, Mismatches: 3, Indels: 30
0.66 0.03 0.31
Matches are distributed among these distances:
8 8 0.12
9 5 0.08
10 1 0.02
11 3 0.05
12 9 0.14
13 23 0.35
14 4 0.06
15 6 0.09
16 6 0.09
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (13 bp):
TGCATGGATGCAC
Found at i:57809 original size:21 final size:21
Alignment explanation
Indices: 57783--57838 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
57773 CTAGTGCAGG
57783 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
57804 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
57825 TGCAGGGATGCACT
1 TGCATGGATGCACT
57839 TTGACACCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.38, T:0.20
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:57939 original size:29 final size:30
Alignment explanation
Indices: 57907--57975 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
57897 GAAACCTTTT
57907 AAAAC-TTTGAATAAATTCAATT-AAGTCCA
1 AAAACATTT-AATAAATTCAATTCAAGTCCA
*
57936 AAAACATTTTATAAATTCAATTCAAGTCCA
1 AAAACATTTAATAAATTCAATTCAAGTCCA
57966 AAAACCATTT
1 AAAA-CATTT
57976 TGCCTTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 17 0.47
30 14 0.39
31 5 0.14
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAACATTTAATAAATTCAATTCAAGTCCA
Found at i:57965 original size:30 final size:30
Alignment explanation
Indices: 57917--57976 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
57907 AAAACTTTGA
57917 ATAAATTCAATTAAGTCCAAAAA-CATTTT
1 ATAAATTCAATTAAGTCCAAAAACCATTTT
57946 ATAAATTCAATTCAAGTCCAAAAACCATTTT
1 ATAAATTCAATT-AAGTCCAAAAACCATTTT
57977 GCCTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 12 0.41
30 11 0.38
31 6 0.21
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (30 bp):
ATAAATTCAATTAAGTCCAAAAACCATTTT
Found at i:58299 original size:31 final size:31
Alignment explanation
Indices: 58264--58327 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
58254 TGTATATGCA
*
58264 TGAATTG-TTCAAATCGAATTGCTATATAGAT
1 TGAATTGCTT-AAATCGAAATGCTATATAGAT
* *
58295 TGAATTGCTTAATTCGAAATGCTATGTAGAT
1 TGAATTGCTTAAATCGAAATGCTATATAGAT
58326 TG
1 TG
58328 TGTGTTGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (31 bp):
TGAATTGCTTAAATCGAAATGCTATATAGAT
Done.