Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006503.1 Hibiscus syriacus cultivar Beakdansim tig00015826_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: 108824
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5646 original size:24 final size:24
Alignment explanation
Indices: 5614--5662 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5604 TTTTATCTGG
5614 TTTCTGATTTGAAATATGTTATGA
1 TTTCTGATTTGAAATATGTTATGA
* *
5638 TTTCTGATTTGAATTCTGTTATGA
1 TTTCTGATTTGAAATATGTTATGA
5662 T
1 T
5663 ATATGATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.53
Consensus pattern (24 bp):
TTTCTGATTTGAAATATGTTATGA
Found at i:5668 original size:31 final size:31
Alignment explanation
Indices: 5633--5702 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
5623 TGAAATATGT
* * *
5633 TATGATTTCTGATTTGAATTCTGTTATGATA
1 TATGATATATGATATGAATTCTGTTATGATA
* *
5664 TATGATATATGATATGAATTCTGTTTTGATT
1 TATGATATATGATATGAATTCTGTTATGATA
*
5695 TCTGATAT
1 TATGATAT
5703 CTCCATTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (31 bp):
TATGATATATGATATGAATTCTGTTATGATA
Found at i:5669 original size:24 final size:24
Alignment explanation
Indices: 5618--5669 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5608 ATCTGGTTTC
* *
5618 TGATTTGAAATATGTTATGATTTC
1 TGATTTGAAATATGTTATGATATA
* *
5642 TGATTTGAATTCTGTTATGATATA
1 TGATTTGAAATATGTTATGATATA
5666 TGAT
1 TGAT
5670 ATATGATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.50
Consensus pattern (24 bp):
TGATTTGAAATATGTTATGATATA
Found at i:6006 original size:155 final size:154
Alignment explanation
Indices: 5721--6175 Score: 662
Period size: 155 Copynumber: 2.9 Consensus size: 154
5711 ATTGACGGAA
* * *
5721 AAATGTTTTATTT-GGGGG-TATTGTTGGAGGAAGAAAATATGAAGGCTCCTCAGCTTTGTGCTC
1 AAATGTTTTATTTGGGGGGTTATTGTTGGAGGAAGAATATATGAAGGCTCCTCGGCTGTGTGCTC
* * * *
5784 AGGGCCTAACTGTTGTGCTGGGGTTGTATGGTTCTCGGGAACCTACACATTATGATGTGTTCAGT
66 AGGGCCTTACTGTTGTGC-CGGGTTGTATGGTTCTGGGGAACCTACACATTATGATGTGTTCGGT
5849 TGGGGGATTTACTATGGTTTTTAAT
130 TGGGGGATTTACTATGGTTTTTAAT
* *
5874 AAATGTTTTATTTGGGGGGTTATTATTGGAGGAAGAATATATGAAGGCTCCTTGGCTGTGTGCTC
1 AAATGTTTTATTTGGGGGGTTATTGTTGGAGGAAGAATATATGAAGGCTCCTCGGCTGTGTGCTC
* *
5939 AGGGCCTTACTGTTGTGCCGAGGTTGTATGGTTATGGGGAACCTACATATTATGATGTGTTCGGT
66 AGGGCCTTACTGTTGTGCCG-GGTTGTATGGTTCTGGGGAACCTACACATTATGATGTGTTCGGT
* *
6004 TGGGGGATTTAATATGGTTTTTGAT
130 TGGGGGATTTACTATGGTTTTTAAT
* *
6029 AAATGTTTTATTTGGGGGGTTATTGTTGGAGGAAGAATATATGAAAGCTCCTCGGCTGTGTTCTC
1 AAATGTTTTATTTGGGGGGTTATTGTTGGAGGAAGAATATATGAAGGCTCCTCGGCTGTGTGCTC
* * * * *
6094 AGGGCCTTACTATTGTGTCGGAGTTGTATGGTTCTGGGGAATCTACACATTATGGACGTGTGCGG
66 AGGGCCTTACTGTTGTGCCGG-GTTGTATGGTTCTGGGGAACCTACACATTAT-GATGTGTTCGG
* *
6159 TTGAGGGAATTACTATG
129 TTGGGGGATTTACTATG
6176 ATTTCTGAAT
Statistics
Matches: 270, Mismatches: 27, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
153 13 0.05
154 7 0.03
155 227 0.84
156 23 0.09
ACGTcount: A:0.21, C:0.11, G:0.31, T:0.36
Consensus pattern (154 bp):
AAATGTTTTATTTGGGGGGTTATTGTTGGAGGAAGAATATATGAAGGCTCCTCGGCTGTGTGCTC
AGGGCCTTACTGTTGTGCCGGGTTGTATGGTTCTGGGGAACCTACACATTATGATGTGTTCGGTT
GGGGGATTTACTATGGTTTTTAAT
Found at i:8080 original size:18 final size:18
Alignment explanation
Indices: 8057--8120 Score: 101
Period size: 18 Copynumber: 3.6 Consensus size: 18
8047 ACCGGTTACA
*
8057 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
8075 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
8093 ACCCGACCCGACTCGATG
1 ACCCGACCCGACCCGTTG
8111 ACCCGACCCG
1 ACCCGACCCG
8121 TTGACCAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.19, C:0.50, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:8095 original size:13 final size:13
Alignment explanation
Indices: 8079--8126 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
8069 CCGTTTACCC
8079 GACCCGACCCGTT
1 GACCCGACCCGTT
8092 GACCCGACCCGACTCGAT
1 GACCCGACCCG--T---T
8110 GACCCGACCCGTT
1 GACCCGACCCGTT
8123 GACC
1 GACC
8127 AAAGTTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 16 0.53
15 1 0.03
16 1 0.03
18 12 0.40
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:10603 original size:24 final size:24
Alignment explanation
Indices: 10552--10603 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
10542 ATCTGGTTTC
* *
10552 TGATTTGAAATATATTCTGATTTC
1 TGATTTGAAATATATTCTGATATA
* * *
10576 TGATTTGAATTCTGTTCTGATATA
1 TGATTTGAAATATATTCTGATATA
10600 TGAT
1 TGAT
10604 ATCTGATATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (24 bp):
TGATTTGAAATATATTCTGATATA
Found at i:10610 original size:14 final size:14
Alignment explanation
Indices: 10591--10619 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10581 TGAATTCTGT
10591 TCTGATATATGATA
1 TCTGATATATGATA
10605 TCTGATATATGATA
1 TCTGATATATGATA
10619 T
1 T
10620 GAATTATGTT
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:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (14 bp):
TCTGATATATGATA
Found at i:10623 original size:38 final size:38
Alignment explanation
Indices: 10567--10645 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
10557 TGAAATATAT
* * * *
10567 TCTGATTTCTGATTTGAATTCTGTTCTGATATATGATA
1 TCTGATATATGATATGAATTATGTTCTGATATATGATA
* * *
10605 TCTGATATATGATATGAATTATGTTTTGATTTCTGATA
1 TCTGATATATGATATGAATTATGTTCTGATATATGATA
10643 TCT
1 TCT
10646 CCATTTATTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (38 bp):
TCTGATATATGATATGAATTATGTTCTGATATATGATA
Found at i:15049 original size:24 final size:24
Alignment explanation
Indices: 14971--15065 Score: 75
Period size: 24 Copynumber: 4.0 Consensus size: 24
14961 ATTTTCGACT
* ** *
14971 TGAATTCTATTCTGATACATGACC
1 TGAATTCTGTTCTGATATTTGATC
* *
14995 TGAATTCTGTTCTAAT-TTCTGATA
1 TGAATTCTGTTCTGATATT-TGATC
* *
15019 TGGATTCTGTTCTGATATTTGTTC
1 TGAATTCTGTTCTGATATTTGATC
* * *
15043 TGAATTCTATTTTGATTTTTGAT
1 TGAATTCTGTTCTGATATTTGAT
15066 ATCTCCATTT
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
24 52 0.96
25 2 0.04
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATTTGATC
Found at i:21681 original size:20 final size:20
Alignment explanation
Indices: 21658--21713 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
21648 GTTCACAGAG
21658 TATCGGTACTATTCATACAA
1 TATCGGTACTATTCATACAA
*
21678 TATCGGTACTGTTCATACAA
1 TATCGGTACTATTCATACAA
**
21698 TA-CAATACTATTCATA
1 TATCGGTACTATTCATA
21714 AAAAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 11 0.34
20 21 0.66
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (20 bp):
TATCGGTACTATTCATACAA
Found at i:23611 original size:20 final size:20
Alignment explanation
Indices: 23583--23622 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
23573 CGTTGGGCTT
*
23583 GATATTACTGTAGCAGTATC
1 GATAGTACTGTAGCAGTATC
23603 GATAGTACTGTAGCAGTATC
1 GATAGTACTGTAGCAGTATC
23623 AGTACTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (20 bp):
GATAGTACTGTAGCAGTATC
Found at i:23628 original size:17 final size:18
Alignment explanation
Indices: 23588--23628 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
23578 GGCTTGATAT
23588 TACTGTAGCAGTATCGATAG
1 TACTGTAGCAGTATC-A-AG
23608 TACTGTAGCAGTATC-AG
1 TACTGTAGCAGTATCAAG
23625 TACT
1 TACT
23629 TACATTCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
20 15 0.71
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (18 bp):
TACTGTAGCAGTATCAAG
Found at i:23713 original size:20 final size:21
Alignment explanation
Indices: 23668--23733 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 21
23658 GTTCATTAAT
*
23668 GTTCACACAGTATCGATACTA
1 GTTCATACAGTATCGATACTA
* *
23689 -CTCATACAGTATCGGTAC-A
1 GTTCATACAGTATCGATACTA
* *
23708 GTTCATACAATA-CAATACTA
1 GTTCATACAGTATCGATACTA
23728 -TTCATA
1 GTTCATA
23734 AAACAATTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
19 11 0.31
20 25 0.69
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (21 bp):
GTTCATACAGTATCGATACTA
Found at i:29231 original size:22 final size:21
Alignment explanation
Indices: 29189--29228 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29179 GAGTTTATTT
*
29189 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
29210 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
29229 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:31212 original size:18 final size:17
Alignment explanation
Indices: 31158--31206 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
31148 TTGGAACCTT
* *
31158 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
31176 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
31194 AGTGCATTCGATG
1 AGTGCA-TCGATG
31207 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:31310 original size:64 final size:64
Alignment explanation
Indices: 31158--31367 Score: 182
Period size: 64 Copynumber: 3.3 Consensus size: 64
31148 TTGGAACCTT
* * * *
31158 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCAA--AATAGCC
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAA-A-TC
*
31220 CG
63 AG
* * * ** *
31222 ACTGCATCGATTCATGGCTG-GTGCATCGATGCATCAAATGCATTAAATGTTTTAATTAAATCAG
1 AGTGCATCGATGCATGG-AGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCAG
* *
31286 AGTGCATCGATGCATGGAGAGTGCATC-AGTGCAT-AGAATGCATTCGATGTTTCAATTTATTCA
1 AGTGCATCGATGCATGGAGAGTGCATCGA-TGCATCA-AATGCATTCGATGTTTCAATTAAATCA
31349 TTG
64 --G
31352 A-TGCATCGATGCATGG
1 AGTGCATCGATGCATGG
31368 TATTGATGCA
Statistics
Matches: 118, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
63 4 0.03
64 93 0.79
65 17 0.14
66 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (64 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCAG
Found at i:31372 original size:21 final size:21
Alignment explanation
Indices: 31348--31387 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31338 CAATTTATTC
31348 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
31369 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
31388 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:33609 original size:20 final size:20
Alignment explanation
Indices: 33581--33620 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
33571 CGTTGGGCTT
*
33581 GATATTACTATAGCAGTATC
1 GATAGTACTATAGCAGTATC
*
33601 GATAGTACTGTAGCAGTATC
1 GATAGTACTATAGCAGTATC
33621 AGTACTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (20 bp):
GATAGTACTATAGCAGTATC
Found at i:33695 original size:20 final size:20
Alignment explanation
Indices: 33667--33731 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
33657 TTCATTAATG
*
33667 TTCACACAGTATCAATACTA
1 TTCATACAGTATCAATACTA
**
33687 TTCATACAGTATCGGTAC-A
1 TTCATACAGTATCAATACTA
*
33706 GTTCATACAATA-CAATACTA
1 -TTCATACAGTATCAATACTA
33726 TTCATA
1 TTCATA
33732 AAACAATTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
19 11 0.30
20 26 0.70
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (20 bp):
TTCATACAGTATCAATACTA
Found at i:37053 original size:20 final size:20
Alignment explanation
Indices: 37025--37070 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
37015 CGTTGGGCTT
* *
37025 GATATTACTGTAGCAACATC
1 GATACTACTATAGCAACATC
*
37045 GATACTACTATAGCAATATC
1 GATACTACTATAGCAACATC
*
37065 GGTACT
1 GATACT
37071 TACATTCGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (20 bp):
GATACTACTATAGCAACATC
Found at i:37459 original size:13 final size:13
Alignment explanation
Indices: 37424--37461 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
37414 TTTCCTTCAT
37424 TTCCTCTTTCTTA
1 TTCCTCTTTCTTA
*
37437 TTCTTCTTTCTTA
1 TTCCTCTTTCTTA
37450 TATCCT-TTTCTT
1 T-TCCTCTTTCTT
37462 TTTATCAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 19 0.86
14 3 0.14
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (13 bp):
TTCCTCTTTCTTA
Found at i:42657 original size:22 final size:21
Alignment explanation
Indices: 42632--42672 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
42622 TGATTATACC
*
42632 AACAATTAAGCATAATAATTTG
1 AACAACTAAGCAT-ATAATTTG
*
42654 AACAACTGAGCATATAATT
1 AACAACTAAGCATATAATT
42673 ATACTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (21 bp):
AACAACTAAGCATATAATTTG
Found at i:54395 original size:39 final size:39
Alignment explanation
Indices: 54292--54387 Score: 111
Period size: 39 Copynumber: 2.5 Consensus size: 39
54282 CCTGTACACC
* * * * *
54292 CAGTAAGGGCTTACCCTGTGCAGAAAGCATAAGAGCCTG
1 CAGTAAGGACTTACCCTGTGCACAAACCACAAGAGACTG
* * * *
54331 CAATAAGGTCTTATCCTGTGCACAAACCACAGGAGACTG
1 CAGTAAGGACTTACCCTGTGCACAAACCACAAGAGACTG
54370 CAGTAAGGACTTACCCTG
1 CAGTAAGGACTTACCCTG
54388 AGTACAAAGC
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGTGCACAAACCACAAGAGACTG
Found at i:54416 original size:39 final size:39
Alignment explanation
Indices: 54373--54449 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 39
54363 GAGACTGCAG
* * *
54373 TAAGGACTTACCCTGAGTACAAAGCCGATGAGCATGCGT
1 TAAGGACTTACCATGAGCACAAAGCCGAGGAGCATGCGT
* * * *
54412 TAAGGTCTTATCATGTGCACAAAGCCGAGGAGCTTGCG
1 TAAGGACTTACCATGAGCACAAAGCCGAGGAGCATGCG
54450 AAAAGCGGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (39 bp):
TAAGGACTTACCATGAGCACAAAGCCGAGGAGCATGCGT
Found at i:56010 original size:23 final size:23
Alignment explanation
Indices: 55951--56016 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
55941 CAGTTAAACC
*
55951 GTTGAATCGAACTCCCTAAAATT
1 GTTGAATCGAACTGCCTAAAATT
55974 GTTGAATCGAACTGCCTAAAATT
1 GTTGAATCGAACTGCCTAAAATT
*
55997 GTTGAATCGAACTGACTAAA
1 GTTGAATCGAACTGCCTAAA
56017 CTGAACCGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (23 bp):
GTTGAATCGAACTGCCTAAAATT
Found at i:56072 original size:14 final size:15
Alignment explanation
Indices: 56046--56078 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
56036 ATGACTCGAC
56046 TTGACTGTTGACTCA
1 TTGACTGTTGACTCA
56061 TTGACT-TTGACTCA
1 TTGACTGTTGACTCA
56075 TTGA
1 TTGA
56079 TCGTTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (15 bp):
TTGACTGTTGACTCA
Found at i:56756 original size:46 final size:46
Alignment explanation
Indices: 56635--56784 Score: 137
Period size: 46 Copynumber: 3.3 Consensus size: 46
56625 AAATACATGT
* * *
56635 TGGTGCATCCTTACTGGATGAAAATCC-AATTATCGATTTAGAGGC
1 TGGTGCATCCTTACTGGATGATAATCCTAATTAACGATTTACAGGC
* * * * *
56680 CGGTGTATCTTTACTAGATGATAAAT-CTAATTAACGATTTATAGGC
1 TGGTGCATCCTTACTGGATGAT-AATCCTAATTAACGATTTACAGGC
* * *
56726 TGGTGCATCCTTAGC-GGATGGTAATCCTAATTAGC-ATATTACAAGC
1 TGGTGCATCCTTA-CTGGATGATAATCCTAATTAACGAT-TTACAGGC
*
56772 TGATGCATCCTTA
1 TGGTGCATCCTTA
56785 TAGGATGCAA
Statistics
Matches: 84, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
45 23 0.27
46 60 0.71
47 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (46 bp):
TGGTGCATCCTTACTGGATGATAATCCTAATTAACGATTTACAGGC
Found at i:58247 original size:14 final size:15
Alignment explanation
Indices: 58228--58256 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58218 TACATGATCT
58228 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
58242 GCATAAAACATAAGA
1 GCATAAAACATAAGA
58257 TATAGGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:58290 original size:24 final size:23
Alignment explanation
Indices: 58263--58307 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
58253 AAGATATAGG
58263 ATATG-ATATACATGATGATATGCA
1 ATATGTAT-TACAT-ATGATATGCA
*
58287 ATATGTATTACATATTATATG
1 ATATGTATTACATATGATATG
58308 AAATGACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (23 bp):
ATATGTATTACATATGATATGCA
Found at i:58363 original size:21 final size:23
Alignment explanation
Indices: 58339--58380 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
58329 ATACATGTGG
*
58339 TATGTGA-CATAAGA-AAATGTA
1 TATGTGATCACAAGAGAAATGTA
58360 TATGTGATCACAAGAGAAATG
1 TATGTGATCACAAGAGAAATG
58381 ACATGAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.26
Consensus pattern (23 bp):
TATGTGATCACAAGAGAAATGTA
Found at i:70999 original size:20 final size:20
Alignment explanation
Indices: 70957--71000 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
70947 ATATAATTTA
** * *
70957 AAAAAATAAATTGCTATGTT
1 AAAAAATAAATTGAAAAGCT
70977 AAAAAATAAATTGAAAAGCT
1 AAAAAATAAATTGAAAAGCT
70997 AAAA
1 AAAA
71001 TAAATTAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.25
Consensus pattern (20 bp):
AAAAAATAAATTGAAAAGCT
Found at i:75340 original size:2 final size:2
Alignment explanation
Indices: 75333--75363 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
75323 ATAGAAAAAC
*
75333 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75364 GGTTATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:77713 original size:21 final size:21
Alignment explanation
Indices: 77689--77750 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
77679 AGAAACTATC
77689 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
* *
77710 TCAAGGAAGAC------TGTC
1 TCAAGGGAGACAAAATTTGTT
*
77725 TCAAGAGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
77746 TCAAG
1 TCAAG
77751 AGAAACTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 12 0.40
21 18 0.60
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:77727 original size:36 final size:36
Alignment explanation
Indices: 77669--77791 Score: 185
Period size: 36 Copynumber: 3.4 Consensus size: 36
77659 GCAAATTGTG
* * *
77669 TTGTTTCGAGAGAAACTATCTCAAGGGAGACAAAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
77705 TTGTTTCAAG-GAAGACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGAGAA-ACTGTCTCAAGAGAGACAAAAT
*
77741 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
*
77777 TTATTTCAAGAGAAA
1 TTGTTTCAAGAGAAA
77792 ACATATTCAA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
35 3 0.04
36 74 0.93
37 3 0.04
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
Found at i:77814 original size:30 final size:30
Alignment explanation
Indices: 77780--77851 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
77770 ACAAAACTTA
77780 TTTCAAGAGAAAACATATTCAAAGATTT-TG
1 TTTCAAGAGAAAACATATTCAAAG-TTTATG
* *** *
77810 TTTCAAGGGAAATTGTTTTCAAAGTTTATG
1 TTTCAAGAGAAAACATATTCAAAGTTTATG
77840 TTTCAAGAGAAA
1 TTTCAAGAGAAA
77852 CTGTCTCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 3 0.09
30 32 0.91
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (30 bp):
TTTCAAGAGAAAACATATTCAAAGTTTATG
Found at i:77889 original size:37 final size:37
Alignment explanation
Indices: 77829--77931 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 37
77819 AAATTGTTTT
* * *
77829 CAAAGTTTATGTTTCAAGAGAAACTGTCTCAAAG-GAGA
1 CAAAATTT-TGTTTTAAGAGAAACTATCTC-AAGCGAGA
*
77867 CAAAATTTTGTTTTAAGGGAAACTATCTCAAGCGAGA
1 CAAAATTTTGTTTTAAGAGAAACTATCTCAAGCGAGA
* * * *
77904 TAAAATCTTGTTTTAAGAAAAACAATCT
1 CAAAATTTTGTTTTAAGAGAAACTATCT
77932 TGAGTGAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
36 3 0.05
37 45 0.82
38 7 0.13
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (37 bp):
CAAAATTTTGTTTTAAGAGAAACTATCTCAAGCGAGA
Found at i:81081 original size:18 final size:18
Alignment explanation
Indices: 81058--81092 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
81048 TTCCATCCGG
*
81058 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
81076 TCTTATCATTTATTTCA
1 TCTTATCATTTAATTCA
81093 GTCCTTTCGA
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:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:82411 original size:12 final size:13
Alignment explanation
Indices: 82386--82456 Score: 83
Period size: 12 Copynumber: 5.3 Consensus size: 13
82376 GCGGGACAAC
82386 GGTCAACGGGTCG
1 GGTCAACGGGTCG
82399 GGTCAACGGTCGGGTCG
1 GGTCAA----CGGGTCG
*
82416 GGTC-ACTGGTCG
1 GGTCAACGGGTCG
82428 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
82440 GGTCAACGGGTCG
1 GGTCAACGGGTCG
82453 GGTC
1 GGTC
82457 GGGTGGGGTT
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
12 22 0.43
13 17 0.33
16 1 0.02
17 11 0.22
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:82414 original size:17 final size:17
Alignment explanation
Indices: 82392--82443 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
82382 CAACGGTCAA
82392 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
82409 CGGGTCGGGTC-AC--T
1 CGGGTCGGGTCAACGGT
82423 --GGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
82438 CGGGTC
1 CGGGTC
82444 AACGGGTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
12 9 0.30
13 2 0.07
14 1 0.03
15 1 0.03
16 2 0.07
17 15 0.50
ACGTcount: A:0.10, C:0.25, G:0.46, T:0.19
Consensus pattern (17 bp):
CGGGTCGGGTCAACGGT
Found at i:83381 original size:22 final size:22
Alignment explanation
Indices: 83355--83409 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
83345 ATCGTGTTGG
83355 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
83377 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
83399 TCAAAGGTTTG
1 TCAAAGGTTTG
83410 ATGGGGTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:84042 original size:32 final size:30
Alignment explanation
Indices: 84006--84074 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 30
83996 TTTGCATGTG
84006 CTTTTTGTCCCTT-TTTCT-TTTTGATTCCTTTT
1 CTTTTTGT-CCTTGTTTCTCTTTT--TTCC-TTT
*
84038 CTTTTTGTTCTTGTTTCTCTTTTTTCCTTT
1 CTTTTTGTCCTTGTTTCTCTTTTTTCCTTT
84068 CTTTTTG
1 CTTTTTG
84075 CTTTTTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
30 10 0.29
31 7 0.21
32 13 0.38
33 4 0.12
ACGTcount: A:0.01, C:0.20, G:0.07, T:0.71
Consensus pattern (30 bp):
CTTTTTGTCCTTGTTTCTCTTTTTTCCTTT
Found at i:84054 original size:16 final size:15
Alignment explanation
Indices: 84006--84097 Score: 66
Period size: 16 Copynumber: 6.0 Consensus size: 15
83996 TTTGCATGTG
*
84006 CTTTTTGTCCCTTTTT
1 CTTTTTGT-TCTTTTT
*
84022 CTTTTTGATTCCTTTT
1 CTTTTTG-TTCTTTTT
84038 CTTTTTGTTCTTGTTT
1 CTTTTTGTTCTT-TTT
*
84054 CTCTTTT-TTC-CTTT
1 CT-TTTTGTTCTTTTT
84068 CTTTTTGCTT-TTTTT
1 CTTTTTG-TTCTTTTT
*
84083 ACTTCTT-TTCTTTTT
1 -CTTTTTGTTCTTTTT
84098 GTCTTGATTG
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
13 4 0.06
14 7 0.11
15 14 0.23
16 32 0.52
17 5 0.08
ACGTcount: A:0.02, C:0.20, G:0.05, T:0.73
Consensus pattern (15 bp):
CTTTTTGTTCTTTTT
Found at i:87201 original size:61 final size:63
Alignment explanation
Indices: 87116--87237 Score: 153
Period size: 61 Copynumber: 2.0 Consensus size: 63
87106 ACCTAAGGGA
** *
87116 ACATCTTAGGGCTTGAGAGCCTACCCAAGAAAG-T-TCGGGGCCAC-GAGGCCTACCTAAGAAC
1 ACATCTTAGGGCGCGAGAGCCTACCCAAGAAAGATCTCAGGGCCACAGA-GCCTACCTAAGAAC
* *
87177 ACATCTTAGGGCCGCGAG-GCCTACCCGAGAATGATCTCAGGGCCACAGAGCCTACCTAAGA
1 ACATCTTAGGG-CGCGAGAGCCTACCCAAGAAAGATCTCAGGGCCACAGAGCCTACCTAAGA
87238 GTCACATTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
61 24 0.46
62 5 0.10
63 21 0.40
64 2 0.04
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.16
Consensus pattern (63 bp):
ACATCTTAGGGCGCGAGAGCCTACCCAAGAAAGATCTCAGGGCCACAGAGCCTACCTAAGAAC
Found at i:90725 original size:2 final size:2
Alignment explanation
Indices: 90718--90756 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
90708 TAAAGTATGA
90718 AT 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 AT A
90757 CCAACAACTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:95971 original size:2 final size:2
Alignment explanation
Indices: 95964--95996 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
95954 TAAATTAGGA
95964 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 A
95997 CCAACAACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:98747 original size:27 final size:27
Alignment explanation
Indices: 98684--98747 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
98674 AAGGCAAAAG
*
98684 AATAATAAAAAAATGAAAATAGTATGA
1 AATAATAAAAAAATGAAAATAGTATAA
*
98711 TATAATAAAAAAATGAAAATAG-A-AA
1 AATAATAAAAAAATGAAAATAGTATAA
*
98736 AATAATAGAAAA
1 AATAATAAAAAA
98748 CACATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 11 0.33
26 1 0.03
27 21 0.64
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (27 bp):
AATAATAAAAAAATGAAAATAGTATAA
Found at i:98758 original size:2 final size:2
Alignment explanation
Indices: 98751--98856 Score: 110
Period size: 2 Copynumber: 52.5 Consensus size: 2
98741 TAGAAAACAC
* * *
98751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AGG AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
98794 A- AGT AT AT AT AC A- AT GCT A- AT GAT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT AT
98834 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
98857 AAAATTAATA
Statistics
Matches: 89, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
1 3 0.03
2 81 0.91
3 5 0.06
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:102447 original size:2 final size:2
Alignment explanation
Indices: 102440--102476 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
102430 ACTTTTTCAG
102440 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
102477 CAGAGTGTGA
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:107354 original size:23 final size:23
Alignment explanation
Indices: 107328--107371 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
107318 CACGTATTCT
* * *
107328 TCTGCCTTTATGGCATGTTTTTC
1 TCTGCCTCTATGACATATTTTTC
107351 TCTGCCTCTATGACATATTTT
1 TCTGCCTCTATGACATATTTT
107372 CTGTTGTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.50
Consensus pattern (23 bp):
TCTGCCTCTATGACATATTTTTC
Done.