Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003841.1 Hibiscus syriacus cultivar Beakdansim tig00008233_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: 89538
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:2559 original size:23 final size:25
Alignment explanation
Indices: 2545--2591 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2535 TAAAAATACA
2545 TATTTA-ATA-TTAAT--AAATACA
1 TATTTATATATTTAATAAAAATACA
2566 TATTTATATATTTAATAAAAATACA
1 TATTTATATATTTAATAAAAATACA
2591 T
1 T
2592 TAAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.27
22 3 0.14
23 5 0.23
25 8 0.36
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTTATATATTTAATAAAAATACA
Found at i:2564 original size:21 final size:23
Alignment explanation
Indices: 2538--2584 Score: 80
Period size: 21 Copynumber: 2.1 Consensus size: 23
2528 AACTAAATAA
2538 AAATACATATTTA-ATA-TTAAT
1 AAATACATATTTATATATTTAAT
2559 AAATACATATTTATATATTTAAT
1 AAATACATATTTATATATTTAAT
2582 AAA
1 AAA
2585 AATACATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.54
22 3 0.12
23 8 0.33
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATACATATTTATATATTTAAT
Found at i:4150 original size:3 final size:3
Alignment explanation
Indices: 4142--4217 Score: 125
Period size: 3 Copynumber: 25.3 Consensus size: 3
4132 TTCGTCCTGC
*
4142 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
4190 TAT TAT TAA TAT TAT TAA TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4218 TTTAATGCAG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:9126 original size:17 final size:16
Alignment explanation
Indices: 9095--9129 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
9085 AAGCTTTGAC
*
9095 TATATTATATTATATA
1 TATATTATATAATATA
9111 TATATATATATAATATA
1 TATAT-TATATAATATA
9128 TA
1 TA
9130 GTTTAGCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATTATATAATATA
Found at i:10098 original size:6 final size:5
Alignment explanation
Indices: 10063--10232 Score: 80
Period size: 6 Copynumber: 31.4 Consensus size: 5
10053 ATATATGTAA
* * * *
10063 TATAA TATAT TATGT TATAAT TATAT TATAT CTATA- TA-AT TATAT AACCACT
1 TATAT TATAT TATAT TAT-AT TATAT TATAT -TATAT TATAT TATAT TA-TA-T
*
10115 TATA- TATAT ATATAT ATATAT AATAT ATATAT ATATAT ATATAT ATATAT
1 TATAT TATAT -TATAT -TATAT TATAT -TATAT -TATAT -TATAT -TATAT
* *
10165 ATATAT ATATAT AATA- TATAT ATATAT ATATAT TATA- TATAT ATATAAC
1 -TATAT -TATAT TATAT TATAT -TATAT -TATAT TATAT TATAT -TAT-AT
10214 TATAT ATATAT ATATAT TA
1 TATAT -TATAT -TATAT TA
10233 GCTAAACTAA
Statistics
Matches: 137, Mismatches: 13, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
3 1 0.01
4 15 0.11
5 35 0.26
6 83 0.61
7 3 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.49
Consensus pattern (5 bp):
TATAT
Found at i:10120 original size:2 final size:2
Alignment explanation
Indices: 10115--10326 Score: 216
Period size: 2 Copynumber: 109.0 Consensus size: 2
10105 TATAACCACT
10115 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10156 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
**
10197 T- TA TA TA TA TA TA TA -A CTA TA TA TA TA TA TA TA T- TA GC TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
10237 AA CTA -A TA -A TA TA -A CTA CTA -A CTA TA TGA TA -A TA -A TA CTA
1 TA -TA TA TA TA TA TA TA -TA -TA TA -TA TA T-A TA TA TA TA TA -TA
* * *
10277 -A TA -A TA CA AA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10317 TA TA TA TA TA
1 TA TA TA TA TA
10327 GACAAGCATG
Statistics
Matches: 181, Mismatches: 10, Indels: 38
0.79 0.04 0.17
Matches are distributed among these distances:
1 13 0.07
2 157 0.87
3 11 0.06
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (2 bp):
TA
Found at i:11767 original size:18 final size:18
Alignment explanation
Indices: 11744--11778 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11734 GATTATATTT
11744 TATTTTGATTAATAAAAA
1 TATTTTGATTAATAAAAA
* *
11762 TATTTTTATTATTAAAA
1 TATTTTGATTAATAAAA
11779 TTTTAAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TATTTTGATTAATAAAAA
Found at i:15840 original size:77 final size:79
Alignment explanation
Indices: 15696--15848 Score: 204
Period size: 77 Copynumber: 2.0 Consensus size: 79
15686 TCGAATATAG
*
15696 TAAATAAACATTAAAATAATGTAATTCTGATTACAACTCTTTTAATGGATATTTAATTCGGAATA
1 TAAATAAACATTAAAATAATGTAATTCAGATTACAACTCTTTTAATGGATATTTAATTCGGAATA
15761 ATTAAATAAGAGTT
66 ATTAAATAAGAGTT
* * * * * * *
15775 TAAATAAACGTTAAAGT-GTGTAATTCAGATTATAATTC-TTTAATGGTTATTTAATT-TGAATT
1 TAAATAAACATTAAAATAATGTAATTCAGATTACAACTCTTTTAATGGATATTTAATTCGGAA-T
15837 AATTAAATAAGA
65 AATTAAATAAGA
15849 ATTTGATTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
76 3 0.05
77 30 0.46
78 17 0.26
79 15 0.23
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (79 bp):
TAAATAAACATTAAAATAATGTAATTCAGATTACAACTCTTTTAATGGATATTTAATTCGGAATA
ATTAAATAAGAGTT
Found at i:18902 original size:15 final size:16
Alignment explanation
Indices: 18866--18902 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
18856 TTTTAGTTAC
*
18866 ATAATGTGATATTAAT
1 ATAATGTGATATAAAT
18882 AT-ATGTGATA-AAAT
1 ATAATGTGATATAAAT
18896 ATAATGT
1 ATAATGT
18903 AGTCCACCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 12 0.63
16 2 0.11
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (16 bp):
ATAATGTGATATAAAT
Found at i:24140 original size:2 final size:2
Alignment explanation
Indices: 24087--24122 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24077 GTATTTGCAG
24087 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
24123 GAATAAGGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24654 original size:23 final size:23
Alignment explanation
Indices: 24621--24688 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
24611 AACCTTATAT
*
24621 GGCACTTCGGTGCATTTGTACGC
1 GGCACTTCGGTGCATTTATACGC
* * * *
24644 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTATACGC
24667 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTATACG
24689 AGTTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTATACGC
Found at i:26634 original size:15 final size:15
Alignment explanation
Indices: 26614--26646 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
26604 TGAAGTTTTG
26614 TATAAGTAAATGGGT
1 TATAAGTAAATGGGT
26629 TATAAGTAAATGGGT
1 TATAAGTAAATGGGT
26644 TAT
1 TAT
26647 CAAAGTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (15 bp):
TATAAGTAAATGGGT
Found at i:29604 original size:23 final size:23
Alignment explanation
Indices: 29578--29645 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
29568 AACCTTATAT
*
29578 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
29601 GGCACTACGGTGTAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
29624 GGCACTTCAGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
29646 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:33053 original size:2 final size:2
Alignment explanation
Indices: 33046--33091 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
33036 TTTTGGTGAC
*
33046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33088 AT AT
1 AT AT
33092 TATGTTTACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35281 original size:23 final size:22
Alignment explanation
Indices: 35236--35281 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
35226 GGGTTTATAG
**
35236 TTTGGTTAATTTTTCATTCGTT
1 TTTGGTTAATTTTGAATTCGTT
*
35258 TTTGGTTAAATTTTGAATTGGTT
1 TTTGGTT-AATTTTGAATTCGTT
35281 T
1 T
35282 GGATTGTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.61
Consensus pattern (22 bp):
TTTGGTTAATTTTGAATTCGTT
Found at i:36900 original size:13 final size:13
Alignment explanation
Indices: 36863--36901 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
36853 GTCAATCCAC
36863 ACTGAGTCAACTT
1 ACTGAGTCAACTT
36876 AGCTGAGTCAACTT
1 A-CTGAGTCAACTT
*
36890 ACTGGGTCAACT
1 ACTGAGTCAACT
36902 CGTTGACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (13 bp):
ACTGAGTCAACTT
Found at i:40002 original size:30 final size:30
Alignment explanation
Indices: 39968--40026 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
39958 TGTATTCAAC
* **
39968 ACCTAGCATATTTGGAATAAAATAATCATT
1 ACCTAACATATTAAGAATAAAATAATCATT
*
39998 ACCTAACATATTAAGAATAAAGTAATCAT
1 ACCTAACATATTAAGAATAAAATAATCAT
40027 ATGAAAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (30 bp):
ACCTAACATATTAAGAATAAAATAATCATT
Found at i:41950 original size:5 final size:5
Alignment explanation
Indices: 41940--41973 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
41930 AACGGTCAAC
* *
41940 GGTCG GGTCG GGTCA GGTCG GGTCG GGTCA GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
41974 TGTTCAGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.06, C:0.21, G:0.53, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:41960 original size:15 final size:15
Alignment explanation
Indices: 41940--41973 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
41930 AACGGTCAAC
41940 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
41955 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
41970 GGTC
1 GGTC
41974 TGTTCAGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.21, G:0.53, T:0.21
Consensus pattern (15 bp):
GGTCGGGTCGGGTCA
Found at i:41995 original size:9 final size:10
Alignment explanation
Indices: 41981--42025 Score: 58
Period size: 9 Copynumber: 4.6 Consensus size: 10
41971 GTCTGTTCAG
41981 ACCGGTC-AA
1 ACCGGTCAAA
41990 ACCGGTCAAA
1 ACCGGTCAAA
*
42000 ACAGGTTCAAA
1 ACCGG-TCAAA
42011 ACCGGTC-AA
1 ACCGGTCAAA
42020 ACCGGT
1 ACCGGT
42026 TTTCCAACTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 15 0.47
10 8 0.25
11 9 0.28
ACGTcount: A:0.36, C:0.29, G:0.22, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:48365 original size:19 final size:19
Alignment explanation
Indices: 48343--48452 Score: 116
Period size: 19 Copynumber: 5.7 Consensus size: 19
48333 TCAACGGTCA
*
48343 GGTCAGACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
48362 GGTCAAACCAGTTCAGACC
1 GGTCAAACCGGTTCAGACC
48381 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
48400 GGTCGAAACC-GATCAAACC
1 GGTC-AAACCGGTTCAGACC
* *
48419 GGTCAAAACAGGTTCAAAACC
1 GGTC-AAACCGGTTC-AGACC
48440 GGTCAAACCGGTT
1 GGTCAAACCGGTT
48453 TTCTAACTGC
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.01
19 51 0.66
20 16 0.21
21 9 0.12
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:48399 original size:29 final size:29
Alignment explanation
Indices: 48349--48451 Score: 102
Period size: 29 Copynumber: 3.5 Consensus size: 29
48339 GTCAGGTCAG
* *
48349 ACCGGTTCAGACCGGTCAAACCAGTTC-AG
1 ACCGG-TCAAACCGGTCAAACCAGTTCAAA
* * *
48378 ACCGGTCAAACCGGTTCGAACC-GGTCGAA
1 ACCGGTCAAACCGG-TCAAACCAGTTCAAA
* *
48407 ACCGATCAAACCGGTCAAAACAGGTTCAAA
1 ACCGGTCAAACCGGTCAAACCA-GTTCAAA
48437 ACCGGTCAAACCGGT
1 ACCGGTCAAACCGGT
48452 TTTCTAACTG
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
28 16 0.27
29 25 0.42
30 19 0.32
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (29 bp):
ACCGGTCAAACCGGTCAAACCAGTTCAAA
Found at i:48427 original size:10 final size:9
Alignment explanation
Indices: 48343--48451 Score: 92
Period size: 10 Copynumber: 11.3 Consensus size: 9
48333 TCAACGGTCA
*
48343 GGTCAGACC
1 GGTCAAACC
*
48352 GGTTCAGACC
1 GG-TCAAACC
48362 GGTCAAACC
1 GGTCAAACC
* *
48371 AGTTCAGACC
1 -GGTCAAACC
48381 GGTCAAACC
1 GGTCAAACC
*
48390 GGTTCGAACC
1 GG-TCAAACC
48400 GGTCGAAACC
1 GGTC-AAACC
*
48410 GATCAAACC
1 GGTCAAACC
*
48419 GGTCAAAACA
1 GGTC-AAACC
48429 GGTTCAAAACC
1 GG-TC-AAACC
48440 GGTCAAACC
1 GGTCAAACC
48449 GGT
1 GGT
48452 TTTCTAACTG
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
9 35 0.42
10 39 0.47
11 9 0.11
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:50695 original size:30 final size:30
Alignment explanation
Indices: 50661--50724 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
50651 ATGTTTTTAT
50661 TGATATCGCATGCCACATTACTTCTTTAAC
1 TGATATCGCATGCCACATTACTTCTTTAAC
50691 TGATATCGCATGCCACATTACTTCTTTAAC
1 TGATATCGCATGCCACATTACTTCTTTAAC
50721 -GATA
1 TGATA
50725 AATAATGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (30 bp):
TGATATCGCATGCCACATTACTTCTTTAAC
Found at i:53247 original size:3 final size:3
Alignment explanation
Indices: 53239--53309 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
53229 ATTTTATTTA
53239 TAT TAT TAT TAT TAT TA- TAT TAT TA- TAT TAT TATT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT -TAT
* *
53284 TTT TAT TAT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
53310 CAAGCAGACT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.07
3 50 0.83
4 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:53265 original size:25 final size:25
Alignment explanation
Indices: 53236--53307 Score: 101
Period size: 25 Copynumber: 2.8 Consensus size: 25
53226 CCGATTTTAT
53236 TTATATTATTATTATTATTATATTA
1 TTATATTATTATTATTATTATATTA
*
53261 TTATATTATTATTTATTA-TATATTT
1 TTATATTATTA-TTATTATTATATTA
*
53286 TTATTATTAATATTATTATTAT
1 TTA-TATTATTATTATTATTAT
53308 TACAAGCAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
25 26 0.62
26 16 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATATTATTATTATTATTATATTA
Found at i:53688 original size:21 final size:21
Alignment explanation
Indices: 53654--53707 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
53644 TGAGGGCTAC
* *
53654 GGTGAGTCATCACTATAGTTT
1 GGTGACTCACCACTATAGTTT
53675 GGTGACTCACCACTATAGTTT
1 GGTGACTCACCACTATAGTTT
53696 GGTGACTCACCA
1 GGTGACTCACCA
53708 TAATACAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (21 bp):
GGTGACTCACCACTATAGTTT
Found at i:54106 original size:27 final size:27
Alignment explanation
Indices: 54076--54138 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
54066 AGAGAGAGGC
54076 GAGAGAGAAATCTATCTCTCAGTTTAA
1 GAGAGAGAAATCTATCTCTCAGTTTAA
*
54103 GAGAGAGAAATCTCTCTCTCAGTTTAA
1 GAGAGAGAAATCTATCTCTCAGTTTAA
54130 GAGAGAGAA
1 GAGAGAGAA
54139 GAGAAATGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (27 bp):
GAGAGAGAAATCTATCTCTCAGTTTAA
Found at i:54643 original size:15 final size:14
Alignment explanation
Indices: 54622--54660 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
54612 TTGCAATATT
54622 ATTATTATTATTTC
1 ATTATTATTATTTC
*
54636 TTTAATTATTATTTC
1 ATT-ATTATTATTTC
54651 ATTATTATTA
1 ATTATTATTA
54661 CTATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATTATTTC
Found at i:54866 original size:17 final size:19
Alignment explanation
Indices: 54827--54866 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
54817 CCGTTTTCTG
*
54827 ATATTTTTACTAAATATCT
1 ATATTTTTACTAAATACCT
54846 -TATTTTTA-TAAAT-CCT
1 ATATTTTTACTAAATACCT
54862 ATATT
1 ATATT
54867 AACTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTTTACTAAATACCT
Found at i:55524 original size:26 final size:27
Alignment explanation
Indices: 55472--55529 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
55462 TAATTCTTTC
*
55472 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
55500 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
55526 TTTT
1 TTTT
55530 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:56673 original size:14 final size:14
Alignment explanation
Indices: 56635--56688 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
56625 ATTTTAAATA
*
56635 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
56649 TTTTACATTTGCAT
1 ATTTACATTTGCAT
56663 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
56678 CTTTGCATTTG
1 ATTTACATTTG
56689 TATTTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:59673 original size:2 final size:2
Alignment explanation
Indices: 59666--59713 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
59656 TTATCCTTTA
59666 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
59708 AT AT AT
1 AT AT AT
59714 CCTTTGTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60042 original size:31 final size:27
Alignment explanation
Indices: 60007--60090 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 27
59997 CTCATCCAGC
60007 AAAGAAAGAAGAAGGAAAAAAGAAAAATGGA
1 AAAGAAAGAAGAA-GAAAAAAGAAAAA---A
*
60038 AAAGAAAGAAAAAGAAAAAGAGAACAAAA
1 AAAGAAAGAAGAAGAAAAA-AGAA-AAAA
*
60067 AAAG-AAGAAGAAGAAAAAGGAAAA
1 AAAGAAAGAAGAAGAAAAAAGAAAA
60091 TTGAATCAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 13 0.27
29 5 0.10
30 6 0.12
31 16 0.33
32 3 0.06
ACGTcount: A:0.75, C:0.01, G:0.23, T:0.01
Consensus pattern (27 bp):
AAAGAAAGAAGAAGAAAAAAGAAAAAA
Found at i:60346 original size:22 final size:22
Alignment explanation
Indices: 60321--60366 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
60311 CCTTAAACAC
60321 TTATTTGGGCCTTTTTATCCCT
1 TTATTTGGGCCTTTTTATCCCT
60343 TTATTTGGGCCTTTTTATCCCT
1 TTATTTGGGCCTTTTTATCCCT
60365 TT
1 TT
60367 CTTTCGTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.09, C:0.22, G:0.13, T:0.57
Consensus pattern (22 bp):
TTATTTGGGCCTTTTTATCCCT
Found at i:65000 original size:22 final size:22
Alignment explanation
Indices: 64972--65048 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
64962 ATCTACACTT
**
64972 TTCAAAGATGATAGGTTCTCTC
1 TTCAAAGATGATATATTCTCTC
* *
64994 TTCAAAGCTGATATACTCTCTC
1 TTCAAAGATGATATATTCTCTC
* *
65016 TTTAAAGATGATATATTCTCTT
1 TTCAAAGATGATATATTCTCTC
65038 TTCAAAGATGA
1 TTCAAAGATGA
65049 AAGCTTTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATATATTCTCTC
Found at i:65796 original size:36 final size:36
Alignment explanation
Indices: 65755--65954 Score: 202
Period size: 36 Copynumber: 5.5 Consensus size: 36
65745 TTCAAATAGC
65755 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* * ** ** *
65791 AATTTATCTCGCTCGAGACAGTTTCACTTGAAACAGA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACA-A
*
65828 ACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* * * ** ** **
65864 AATTTGTCTCGCTCGAGACAGTTTCACTCGAAACAGA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACA-A
*
65901 ACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* *
65937 AATTTGTCTCGCTTGAGA
1 AATTTATCTCACTTGAGA
65955 CAGTCTCATT
Statistics
Matches: 124, Mismatches: 38, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
36 70 0.56
37 54 0.44
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (36 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:65836 original size:37 final size:36
Alignment explanation
Indices: 65755--65978 Score: 171
Period size: 36 Copynumber: 6.1 Consensus size: 36
65745 TTCAAATAGC
* ** ** *
65755 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCGCTTGAGACAGTTTCACTTGAAACAA
*
65791 AATTTATCTCGCTCGAGACAGTTTCACTTGAAACAGA
1 AATTTATCTCGCTTGAGACAGTTTCACTTGAAACA-A
* * ** ** *
65828 ACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCGCTTGAGACAGTTTCACTTGAAACAA
* * *
65864 AATTTGTCTCGCTCGAGACAGTTTCACTCGAAACAGA
1 AATTTATCTCGCTTGAGACAGTTTCACTTGAAACA-A
* * ** ** *
65901 ACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCGCTTGAGACAGTTTCACTTGAAACAA
* *
65937 AATTTGTCTCGCTTGAGACAGTCTCA-TTCGAAACAGA
1 AATTTATCTCGCTTGAGACAGTTTCACTT-GAAACA-A
65974 AATTT
1 AATTT
65979 CCATCACTTG
Statistics
Matches: 140, Mismatches: 44, Indels: 7
0.73 0.23 0.04
Matches are distributed among these distances:
35 2 0.01
36 78 0.56
37 60 0.43
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (36 bp):
AATTTATCTCGCTTGAGACAGTTTCACTTGAAACAA
Found at i:65989 original size:73 final size:73
Alignment explanation
Indices: 65757--65974 Score: 384
Period size: 73 Copynumber: 3.0 Consensus size: 73
65747 CAAATAGCAA
*
65757 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTCGAGACAGTTTCACTT-G
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGTTTCA-TTCG
65821 AAACAGAAC
65 AAACAGAAC
*
65830 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGTTTCACTCGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGTTTCATTCGA
65895 AACAGAAC
66 AACAGAAC
* *
65903 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTCTCATTCGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGTTTCATTCGA
65968 AACAGAA
66 AACAGAA
65975 ATTTCCATCA
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
72 1 0.01
73 138 0.99
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (73 bp):
TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGTTTCATTCGA
AACAGAAC
Found at i:66136 original size:114 final size:113
Alignment explanation
Indices: 65980--66424 Score: 614
Period size: 114 Copynumber: 3.9 Consensus size: 113
65970 CAGAAATTTC
* * * * *
65980 CATCACTTGATGGATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCACTCGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G
* *
66044 AAGAATAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTCGAATT
64 AAGAAGAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTTGAATT
* * **
66094 CATCACTTGATGGATC-AGTATTTCCAG-GCCGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 CATCACTCGATGGATCAACT-TTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAA-
* * *
66157 GAATAAGAAATTCATAATGAGAAGAATTTGTTCCAACTTTTTGTTTGAATT
63 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTTGAATT
66208 CATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-A-AA
1 CATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
* *
66271 GAATAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGTTTGAATT
66 GAAGAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTTGAATT
*
66319 CATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGCAATA
1 CATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGA
* **
66384 AGAAGAAGTTCATAATGAGAAGAGCTTGTT-CAACCTTTTGC
65 AGAAGAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGC
66425 ATGACTCTAT
Statistics
Matches: 302, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
111 107 0.35
113 12 0.04
114 180 0.60
115 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (113 bp):
CATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
GAAGAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTTGAATT
Found at i:66374 original size:225 final size:226
Alignment explanation
Indices: 65980--66423 Score: 639
Period size: 225 Copynumber: 2.0 Consensus size: 226
65970 CAGAAATTTC
* * *
65980 CATCACTTGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GA
*
66045 AGAATAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTCGAATTCATCACTTGATGGATC
65 AGAATAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTCGAATTCATCACTCGATGGATC
* ** *
66110 AGTATTTCCAGGCCGAGTTCATAATGAGAAGAACTCATCTGAAG-AAGGAATAAGAAATTCATAA
130 ACTATTTCCAGGCAAAGTTCATAATGAGAAGAACTCATCTGAAGCAA-GAAGAAGAAATTCATAA
* *
66174 TGAGAAGAATTTGTTCCAACTTTTTGTTTGAATT
194 TGAGAAGAACTTGTT-CAACCTTTTGTTTGAATT
* *
66208 CATCACTCGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG-A-A
1 CATCACTCGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
* *
66270 AGAATAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGTTTGAATTCATCACTCGATGGATC
65 AGAATAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTCGAATTCATCACTCGATGGATC
* *
66335 AACT-TTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGCAATAAGAAGAAGTTCATA
130 -ACTATTTCCAG-GCAAAGTTCATAATGAGAAGAACTCATCTGAAGCAAGAAGAAGAAATTCATA
*
66398 ATGAGAAGAGCTTGTTCAACCTTTTG
193 ATGAGAAGAACTTGTTCAACCTTTTG
66424 CATGACTCTA
Statistics
Matches: 195, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
224 9 0.05
225 126 0.65
226 5 0.03
227 1 0.01
228 53 0.27
229 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (226 bp):
CATCACTCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
GAATAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTCGAATTCATCACTCGATGGATCA
CTATTTCCAGGCAAAGTTCATAATGAGAAGAACTCATCTGAAGCAAGAAGAAGAAATTCATAATG
AGAAGAACTTGTTCAACCTTTTGTTTGAATT
Found at i:66660 original size:3 final size:3
Alignment explanation
Indices: 66652--66703 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
66642 ATTTTATTTA
* *
66652 TAT TAT TA- TAT TAT TAT TAT TAT ATAT T-T TAT TAT TAA TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
66696 TAT TAT TA
1 TAT TAT TA
66704 CAAACAGGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:66662 original size:8 final size:8
Alignment explanation
Indices: 66649--66703 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 8
66639 CCGATTTTAT
66649 TTATATTA
1 TTATATTA
66657 TTATATTA
1 TTATATTA
66665 -T-TATTA
1 TTATATTA
66671 TTATA-TA
1 TTATATTA
*
66678 TTTTATTA
1 TTATATTA
66686 TTAATATT-
1 TT-ATATTA
66694 TT-TATTA
1 TTATATTA
66701 TTA
1 TTA
66704 CAAACAGGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
6 9 0.23
7 10 0.26
8 16 0.41
9 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATATTA
Found at i:66693 original size:30 final size:30
Alignment explanation
Indices: 66646--66703 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
66636 GTCCCGATTT
66646 TATTTATATTATTATATTATTATTATTATA
1 TATTTATATTATTATATTATTATTATTATA
*
66676 TATTT-TATTATTAATATTTTTATTATTA
1 TATTTATATTATT-ATATTATTATTATTA
66704 CAAACAGGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (30 bp):
TATTTATATTATTATATTATTATTATTATA
Found at i:68052 original size:3 final size:3
Alignment explanation
Indices: 68044--68093 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
68034 TTATTTGCAA
* * *
68044 TAT TAT TAT TAT TAT TGCT T-T AAT TAT TAT T-T CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
68088 TAT TAT
1 TAT TAT
68094 ATAAATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:68090 original size:35 final size:36
Alignment explanation
Indices: 68026--68093 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
68016 TTCCTTTTAT
68026 TTTAATCATTATTTGCAATATTATTATTATTATTGC
1 TTTAATCATTATTTGCAATATTATTATTATTATTGC
* *
68062 TTTAATTATTATTT-CATTATTATTATTATTAT
1 TTTAATCATTATTTGCAATATTATTATTATTAT
68094 ATAAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (36 bp):
TTTAATCATTATTTGCAATATTATTATTATTATTGC
Found at i:72637 original size:60 final size:60
Alignment explanation
Indices: 72547--72671 Score: 232
Period size: 60 Copynumber: 2.1 Consensus size: 60
72537 TTCGTTTTTG
72547 AAAATTCAAGTTTAAATTAGGTTGGGAATTTTCTGAAGGATGAGGTTGGGTTCAAGATGA
1 AAAATTCAAGTTTAAATTAGGTTGGGAATTTTCTGAAGGATGAGGTTGGGTTCAAGATGA
* *
72607 AAAATTCAAGTTTAAATTGGGTTGGGAATTTTTTGAAGGATGAGGTTGGGTTCAAGATGA
1 AAAATTCAAGTTTAAATTAGGTTGGGAATTTTCTGAAGGATGAGGTTGGGTTCAAGATGA
72667 AAAAT
1 AAAAT
72672 CTTACTTAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (60 bp):
AAAATTCAAGTTTAAATTAGGTTGGGAATTTTCTGAAGGATGAGGTTGGGTTCAAGATGA
Found at i:72792 original size:32 final size:32
Alignment explanation
Indices: 72742--72861 Score: 186
Period size: 32 Copynumber: 3.8 Consensus size: 32
72732 GATTATGGTA
* * *
72742 AGTTTAAGATGAAAAATCTTACTTTAAGGTCG
1 AGTTTATGGTGAAAAATCTTACTTTAACGTCG
* * *
72774 AATTTATTGTGAAAAATCTTACTTTAACGTCT
1 AGTTTATGGTGAAAAATCTTACTTTAACGTCG
72806 AGTTTATGGTGAAAAATCTTACTTTAACGTCG
1 AGTTTATGGTGAAAAATCTTACTTTAACGTCG
72838 AGTTTATGGTGAAAAATCTTACTT
1 AGTTTATGGTGAAAAATCTTACTT
72862 AAGATAATAT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 79 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (32 bp):
AGTTTATGGTGAAAAATCTTACTTTAACGTCG
Found at i:72953 original size:20 final size:19
Alignment explanation
Indices: 72915--72955 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
72905 TCATTATATA
**
72915 AATTTTTTTATAATTAAAT
1 AATTTTTTTATAAACAAAT
72934 AATTATTTTTATAAACAAAT
1 AATT-TTTTTATAAACAAAT
72954 AA
1 AA
72956 CAAGGTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTTTTTTATAAACAAAT
Found at i:82714 original size:2 final size:2
Alignment explanation
Indices: 82707--82749 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
82697 TTATTTTTCA
82707 AT AT AT AT AT AT AT AT AT AT AT A- 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
82748 AT
1 AT
82750 TAATATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82755 original size:6 final size:7
Alignment explanation
Indices: 82706--82759 Score: 58
Period size: 8 Copynumber: 7.4 Consensus size: 7
82696 TTTATTTTTC
82706 AATATAT
1 AATATAT
82713 ATATATAT
1 A-ATATAT
82721 ATATATAT
1 A-ATATAT
82729 AATATAT
1 AATATAT
82736 -ATATAT
1 AATATAT
82742 ATATATATT
1 A-ATATA-T
82751 AATAT-T
1 AATATAT
82757 AAT
1 AAT
82760 TAATATTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
6 10 0.23
7 7 0.16
8 24 0.56
9 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
AATATAT
Found at i:85128 original size:29 final size:29
Alignment explanation
Indices: 85094--85152 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
85084 CCTAAATTAA
*
85094 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
* *
85123 TTTGATGTCATTATTTACATTAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
85152 T
1 T
85153 AGGTGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Done.