Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006238.1 Hibiscus syriacus cultivar Beakdansim tig00014865_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: 70177
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1770 original size:25 final size:25
Alignment explanation
Indices: 1742--1793 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1732 TGTAAGTTTC
1742 ATTTAT-AAATTTAAAAAAGATAAAA
1 ATTTATAAAATTT-AAAAAGATAAAA
*
1767 ATTTATAAAATTTTAAAAGATAAAA
1 ATTTATAAAATTTAAAAAGATAAAA
1792 AT
1 AT
1794 ATTTTATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATTTATAAAATTTAAAAAGATAAAA
Found at i:3765 original size:42 final size:41
Alignment explanation
Indices: 3695--3821 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 41
3685 CCGGAAGGTT
** *
3695 TCGGTGTTGGGTGGTAGTTACCATCGCTTCCATGCGATGGTG
1 TCGGT-TTGGGTGGTAGCCACCACCGCTTCCATGCGATGGTG
3737 TCGGTTTAGGGTGGTAGCCACCACCGCTTCCATGCGATGGTG
1 TCGGTTT-GGGTGGTAGCCACCACCGCTTCCATGCGATGGTG
* * * *
3779 TCGGTGTCGGGTCGTAGCCACCACCGCCTCCATGTGATGGTG
1 TCGGT-TTGGGTGGTAGCCACCACCGCTTCCATGCGATGGTG
3821 T
1 T
3822 TTCTTGAGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.03
42 73 0.96
43 1 0.01
ACGTcount: A:0.13, C:0.25, G:0.34, T:0.28
Consensus pattern (41 bp):
TCGGTTTGGGTGGTAGCCACCACCGCTTCCATGCGATGGTG
Found at i:7716 original size:23 final size:23
Alignment explanation
Indices: 7690--7742 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
7680 ATTGCACATA
7690 AGTGCCACGTAGAATTACACCGG
1 AGTGCCACGTAGAATTACACCGG
* * *
7713 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTACACCGG
7736 AGTGCCA
1 AGTGCCA
7743 TAAATAATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (23 bp):
AGTGCCACGTAGAATTACACCGG
Found at i:7890 original size:102 final size:103
Alignment explanation
Indices: 7764--7969 Score: 369
Period size: 103 Copynumber: 2.0 Consensus size: 103
7754 ATATGGACCA
*
7764 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATG-GTCTCACCAGACCTCA
1 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTATCTCACCAGACCTCA
*
7828 TACATGTTCCAAAAAATACATATATGTCCCGAAGAACC
66 CACATGTTCCAAAAAATACATATATGTCCCGAAGAACC
7866 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTATCTCACCAGACCTCA
1 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTATCTCACCAGACCTCA
* *
7931 CACATGTTCCAAAGAATACATATATGTCCCGAAGGACC
66 CACATGTTCCAAAAAATACATATATGTCCCGAAGAACC
7969 A
1 A
7970 AATAGACCCT
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 48 0.48
103 51 0.52
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTATCTCACCAGACCTCA
CACATGTTCCAAAAAATACATATATGTCCCGAAGAACC
Found at i:9127 original size:16 final size:16
Alignment explanation
Indices: 9103--9134 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9093 TAGATGTATG
*
9103 TTTATATGTTACATGA
1 TTTACATGTTACATGA
9119 TTTACATGTTACATGA
1 TTTACATGTTACATGA
9135 AAATGCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (16 bp):
TTTACATGTTACATGA
Found at i:9413 original size:31 final size:31
Alignment explanation
Indices: 9375--9497 Score: 203
Period size: 31 Copynumber: 4.0 Consensus size: 31
9365 GGGTCGAGGG
9375 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
9406 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
9437 TTACCTATGTTCTTCGGGACATATGGACTAT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
9468 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
9498 GTCATTCGGG
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:13776 original size:31 final size:31
Alignment explanation
Indices: 13738--13891 Score: 265
Period size: 31 Copynumber: 5.0 Consensus size: 31
13728 GGGTCGAGGG
13738 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
13769 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
13800 TTACTTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
13831 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
13862 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
13892 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:15294 original size:64 final size:67
Alignment explanation
Indices: 15184--15311 Score: 201
Period size: 64 Copynumber: 2.0 Consensus size: 67
15174 ATTTTCATCT
15184 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTG
15249 TA
66 TA
* *
15251 TTTAATGG-GG-ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCATATTCGATGTTT
15312 TCTTTTTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
63 1 0.02
64 32 0.55
65 15 0.26
66 2 0.03
67 8 0.14
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTG
TA
Found at i:15334 original size:64 final size:63
Alignment explanation
Indices: 15196--15356 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 63
15186 TAATGGAGGT
* * * * *
15196 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATACACTCCA-TATGCATCGATGCATAAATCATATTCGATGTTTCTATTTAAT-GGA
* * * * *
15261 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATACACTCCATATGCATCGATGCATAAATCATATTCGATG-TTTCTATTT-AATGGA
* * *
15325 ATGCTTCGATACACTGCATGTGCATCGATGCA
1 ATGCATCGATACACTCCATATGCATCGATGCA
15357 CCTTAAACAA
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 55 0.68
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (63 bp):
ATGCATCGATACACTCCATATGCATCGATGCATAAATCATATTCGATGTTTCTATTTAATGGA
Found at i:16611 original size:42 final size:42
Alignment explanation
Indices: 16556--16701 Score: 192
Period size: 42 Copynumber: 3.5 Consensus size: 42
16546 GCGATTTTGA
* * *
16556 ACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTTG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
16598 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
*
16640 ACTATCGCAACGCGAACTTGGACT--ATCGCAA--CGAACTTGG
1 ACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTGG
16680 ACTATCGCAACGCGAACTTGGA
1 ACTATCGCAA--CGAACTTGGA
16702 CTATCGCAAC
Statistics
Matches: 98, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
40 31 0.32
42 56 0.57
44 11 0.11
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (42 bp):
ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
Found at i:16613 original size:19 final size:20
Alignment explanation
Indices: 16580--16720 Score: 180
Period size: 21 Copynumber: 6.9 Consensus size: 20
16570 TTTGGAATAA
*
16580 ATCGCAACGCGAACTTTGACT
1 ATCGCAAC-CGAACTTGGACT
*
16601 ATCGCAA-CGAACTTGGAAT
1 ATCGCAACCGAACTTGGACT
16620 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAAC-CGAACTTGGACT
16643 ATCGCAACGCGAACTTGGACT
1 ATCGCAAC-CGAACTTGGACT
16664 ATCGCAA-CGAACTTGGACT
1 ATCGCAACCGAACTTGGACT
16683 ATCGCAACGCGAACTTGGACT
1 ATCGCAAC-CGAACTTGGACT
*
16704 ATCGCAA-CGAATTTGGA
1 ATCGCAACCGAACTTGGA
16721 AAATCGCATT
Statistics
Matches: 110, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
19 38 0.35
21 61 0.55
23 11 0.10
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (20 bp):
ATCGCAACCGAACTTGGACT
Found at i:16664 original size:63 final size:61
Alignment explanation
Indices: 16580--16712 Score: 230
Period size: 63 Copynumber: 2.1 Consensus size: 61
16570 TTTGGAATAA
*
16580 ATCGCAACGCGAACTTTGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
*
16643 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATATCGCAACGCGAACTTGGACT
16704 ATCGCAACG
1 ATCGCAACG
16713 AATTTGGAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 30 0.44
63 38 0.56
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.20
Consensus pattern (61 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATATCGCAACGCGAACTTGGACT
Found at i:16686 original size:40 final size:41
Alignment explanation
Indices: 16580--16720 Score: 191
Period size: 40 Copynumber: 3.4 Consensus size: 41
16570 TTTGGAATAA
* *
16580 ATCGCAACGCGAACTTTGACTATCGCAA--CGAACTTGGAAT
1 ATCGCAAC-CGAACTTGGACTATCGCAACGCGAACTTGGACT
16620 AAATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTGGACT
1 --ATCGCAAC-CGAACTTGGACTATCGCAACGCGAACTTGGACT
16664 ATCGCAA-CGAACTTGGACTATCGCAACGCGAACTTGGACT
1 ATCGCAACCGAACTTGGACTATCGCAACGCGAACTTGGACT
*
16704 ATCGCAA-CGAATTTGGA
1 ATCGCAACCGAACTTGGA
16721 AAATCGCATT
Statistics
Matches: 94, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
40 49 0.52
42 34 0.36
44 11 0.12
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (41 bp):
ATCGCAACCGAACTTGGACTATCGCAACGCGAACTTGGACT
Found at i:16753 original size:21 final size:21
Alignment explanation
Indices: 16724--16776 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
16714 ATTTGGAAAA
16724 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
16745 TCGCGTTGCGATAGTCGATGT
1 TCGCATTGCGATAGTCGAAGT
16766 TCGCATTGCGA
1 TCGCATTGCGA
16777 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:16934 original size:2 final size:2
Alignment explanation
Indices: 16927--16990 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
16917 TTCTCTTTAA
16927 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
16969 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
16991 GTTTAAATAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19016 original size:42 final size:42
Alignment explanation
Indices: 18886--18995 Score: 202
Period size: 42 Copynumber: 2.6 Consensus size: 42
18876 TTCCCCACCG
18886 GATGGTGTCGGTGTTGGGTGGTAGCCATCACGGCTTCCATGC
1 GATGGTGTCGGTGTTGGGTGGTAGCCATCACGGCTTCCATGC
*
18928 GATGGTATCGGTGTTGGGTGGTAGCCATCACGGCTTCCATGC
1 GATGGTGTCGGTGTTGGGTGGTAGCCATCACGGCTTCCATGC
*
18970 GATGGTGTCGGTGTTGGGTCGTAGCC
1 GATGGTGTCGGTGTTGGGTGGTAGCC
18996 GCCATCGCTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.12, C:0.20, G:0.39, T:0.29
Consensus pattern (42 bp):
GATGGTGTCGGTGTTGGGTGGTAGCCATCACGGCTTCCATGC
Found at i:21710 original size:21 final size:21
Alignment explanation
Indices: 21686--21760 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
21676 ATTCTTAATT
*
21686 TAAATAATTTTTTAATTTAAA
1 TAAATAATTTATTAATTTAAA
* * *
21707 TAAATAAATTATTATTTTTAA
1 TAAATAATTTATTAATTTAAA
*
21728 TAAA-AAATTA-TAA-TTAAA
1 TAAATAATTTATTAATTTAAA
*
21746 T-TATAATTCTATTAA
1 TAAATAATT-TATTAA
21761 AAGTAGAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
17 1 0.02
18 8 0.19
19 4 0.09
20 9 0.21
21 21 0.49
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATAATTTATTAATTTAAA
Found at i:24696 original size:20 final size:21
Alignment explanation
Indices: 24671--24722 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
24661 TTTTCCCAAT
*
24671 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
24691 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
24712 TCGCAATGCGA
1 TCGCAATGCGA
24723 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:24801 original size:20 final size:20
Alignment explanation
Indices: 24753--24805 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
24743 TAATACAAAA
* *
24753 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
24773 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
24793 TCGCAACGCGATT
1 TCGCAACGCGATT
24806 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:25357 original size:19 final size:19
Alignment explanation
Indices: 25319--25386 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
25309 TTCGAGAATG
25319 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
25339 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
25358 AAAATTCGCAACGCGAAACC
1 AAAA-TCGCAACGCGAAATA
25378 AAAATCGCA
1 AAAATCGCA
25387 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.32
20 28 0.68
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:25404 original size:19 final size:19
Alignment explanation
Indices: 25382--25452 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
25372 GAAACCAAAA
25382 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
25401 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
25420 TCGCAGTTGCGATTTTCATT
1 TCGCA-TTGCGATTTTCATT
*
25440 TCGCGTTGCGATT
1 TCGCATTGCGATT
25453 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 30 0.62
20 18 0.38
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:25462 original size:19 final size:19
Alignment explanation
Indices: 25382--25547 Score: 145
Period size: 20 Copynumber: 9.1 Consensus size: 19
25372 GAAACCAAAA
*
25382 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
25401 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
25420 TCGCAGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
25440 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
25456 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
25473 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
25487 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
25506 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
25526 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
25546 TC
1 TC
25548 AACCAAAAGA
Statistics
Matches: 121, Mismatches: 13, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 42 0.35
20 50 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:25472 original size:33 final size:33
Alignment explanation
Indices: 25435--25522 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
25425 GTTGCGATTT
* *
25435 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
25468 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
25501 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
25523 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:27616 original size:42 final size:42
Alignment explanation
Indices: 27570--27658 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
27560 CCTATTGTTG
* * *
27570 AAGAGGCCCCTATCATTCCTCG-AGA-GTCTCCTCCCACCGTTC
1 AAGAGGCCACTATCA-TCATCGAAGAGGTC-CCTCCCACCATTC
* *
27612 AAGAGGCCACTGTCATCATTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCATCGAAGAGGTCCCTCCCACCATTC
27654 AAGAG
1 AAGAG
27659 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 33 0.82
43 3 0.08
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (42 bp):
AAGAGGCCACTATCATCATCGAAGAGGTCCCTCCCACCATTC
Found at i:29041 original size:14 final size:14
Alignment explanation
Indices: 29022--29057 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
29012 TTTGTTTAAT
29022 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
29036 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
29050 TGATTTGT
1 TGATTTGT
29058 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:29258 original size:19 final size:19
Alignment explanation
Indices: 29236--29386 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
29226 CGAAATTAAA
29236 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
29255 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
29270 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
29288 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
29302 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
29321 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
29336 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
29354 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
29373 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
29387 GGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:29282 original size:33 final size:32
Alignment explanation
Indices: 29240--29366 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
29230 ATTAAATTCG
*
29240 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
29273 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
29306 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
29339 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
29367 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:29335 original size:66 final size:66
Alignment explanation
Indices: 29233--29365 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
29223 ACGCGAAATT
* *
29233 AAATTCGCGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
29298 G
66 G
* *
29299 AAATTAGCGTTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
29364 G
66 G
29365 A
1 A
29366 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:29593 original size:18 final size:18
Alignment explanation
Indices: 29570--29604 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29560 AAGCCAGTTG
29570 TGATTGGGATTTTAAAGA
1 TGATTGGGATTTTAAAGA
29588 TGATTGGGATTTTAAAG
1 TGATTGGGATTTTAAAG
29605 CTGAAACATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (18 bp):
TGATTGGGATTTTAAAGA
Found at i:30755 original size:20 final size:20
Alignment explanation
Indices: 30730--30787 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
30720 ATTCATTTGA
30730 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
30750 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
30770 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
30788 TGTAATGACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:30830 original size:14 final size:16
Alignment explanation
Indices: 30810--30883 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
30800 TGAAAATCGC
30810 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
30825 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
30842 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
30861 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
30877 -TTGCGAT
1 ATTGCGAT
30884 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:30847 original size:19 final size:19
Alignment explanation
Indices: 30806--30873 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
30796 CAAATGAAAA
30806 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
30822 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
30839 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
30858 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
30874 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:31009 original size:14 final size:14
Alignment explanation
Indices: 30990--31026 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
30980 CATCAATTAA
30990 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
31004 ACAAATCATCTTTT
1 ACAAATCAACATTT
31018 ACAAATCAA
1 ACAAATCAA
31027 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:31414 original size:20 final size:20
Alignment explanation
Indices: 31389--31446 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
31379 ATTCATTTGA
31389 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
31409 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
31429 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
31447 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:31495 original size:19 final size:19
Alignment explanation
Indices: 31473--31521 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
31463 GATTTTCTCC
31473 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31492 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31511 TTGCGATTTTC
1 TTGCGATTTTC
31522 TCGTTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:31657 original size:14 final size:14
Alignment explanation
Indices: 31638--31674 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
31628 CATCAATTAA
31638 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
31652 ACAAATCATCTTTT
1 ACAAATCAACATTT
31666 ACAAATCAA
1 ACAAATCAA
31675 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:31840 original size:648 final size:654
Alignment explanation
Indices: 30542--31923 Score: 2571
Period size: 648 Copynumber: 2.1 Consensus size: 654
30532 TTTAACAATT
30542 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAG-ATATATGTTAACAAAA
30607 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
65 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
*
30672 GAGTTTGAACATTTCTATGATATGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
130 GAGTTTGAACATTGCTATGATATGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
* *
30737 AACGCGAAAATGGCTATCGCAACGCGAAAATGGTTATCGCAACGAGAAAATTGTAATGACAAATG
195 AACGCGAAAATGGCTATCGCAACGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGAC--A-G
*
30802 AAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
257 AAAA---CATTGCGATTTTCTCCTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
30867 GATTTTCTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGA
319 GATTTTCTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGA
30932 TTAAAAATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATC
384 TTAAAAATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATC
30997 AACATTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTC
449 AACATTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTC
*
31062 TTCATCAATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCTATTTCACGCAGCTC
514 TTCATCAATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTC
31127 ACTTAAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAACCT
579 ACTTAAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAACCT
31192 ACAAACAGCAA
644 ACAAACAGCAA
31203 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAG-TATATGTTAACAAAAC
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGATATATGTTAACAAAAC
31267 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
66 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
31332 AGTTTGAACATTGCTATGATATGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
131 AGTTTGAACATTGCTATGATATGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
31397 ACGCGAAAATGGCTATCGCAACGCGAAAATGGTTATCGCAACGAGAAAATCGCAATG-C-G-AAA
196 ACGCGAAAATGGCTATCGCAACGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGACAGAAAA
31459 -A-TGCGATTTTCTCCTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
261 CATTGCGATTTTCTCCTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
*
31522 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
326 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTAAAAA
31587 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
391 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
31652 ACAAATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCA
456 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
31716 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
521 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
31781 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
586 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCT-AAACCTACAAAC
*
31846 ATCAA
650 AGCAA
31851 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAG-ATATATGTTAACAAAA
31916 CTTGCATT
65 CTTGCATT
31924 TGACTTACCA
Statistics
Matches: 711, Mismatches: 7, Indels: 17
0.97 0.01 0.02
Matches are distributed among these distances:
647 147 0.21
648 287 0.40
649 1 0.00
650 23 0.03
653 3 0.00
654 1 0.00
658 1 0.00
659 200 0.28
661 48 0.07
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (654 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGATATATGTTAACAAAAC
TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
AGTTTGAACATTGCTATGATATGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
ACGCGAAAATGGCTATCGCAACGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGACAGAAAA
CATTGCGATTTTCTCCTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTAAAAA
TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAACCTACAAACA
GCAA
Found at i:33571 original size:20 final size:19
Alignment explanation
Indices: 33536--33602 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
33526 GAAACTTAAA
33536 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
33555 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
33575 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
33594 ATCGCAACG
1 ATCGCAACG
33603 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:33610 original size:14 final size:14
Alignment explanation
Indices: 33591--33694 Score: 109
Period size: 14 Copynumber: 6.9 Consensus size: 14
33581 ATGCGAAATG
33591 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
33605 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
33621 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
* *
33637 AAAATCGTAACGCGAA
1 AAAATCGCAA--CGAC
33653 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
33669 AAAATCGCAACGAC
1 AAAATCGCAACGAC
33683 AAAATCGCAACG
1 AAAATCGCAACG
33695 CGAAACACAA
Statistics
Matches: 76, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
14 43 0.57
16 16 0.21
18 17 0.22
ACGTcount: A:0.48, C:0.25, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:33633 original size:32 final size:32
Alignment explanation
Indices: 33575--33680 Score: 185
Period size: 32 Copynumber: 3.3 Consensus size: 32
33565 GGAAATGGCT
*
33575 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
33608 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
*
33640 ATCGTAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
33672 ATCGCAACG
1 ATCGCAACG
33681 ACAAAATCGC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 55 0.79
33 15 0.21
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:33728 original size:19 final size:17
Alignment explanation
Indices: 33706--33800 Score: 85
Period size: 18 Copynumber: 5.6 Consensus size: 17
33696 GAAACACAAA
33706 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
33725 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
33741 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
33757 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
33773 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
33789 TCGCATTGCGAT
1 TCGC-TTGCGAT
33801 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
14 18 0.29
16 16 0.25
18 19 0.30
19 10 0.16
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:33747 original size:14 final size:14
Alignment explanation
Indices: 33728--33784 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
33718 TTTCATTTCG
33728 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
33742 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
33758 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
33774 CGTTGCGATTT
1 CGTTGCGATTT
33785 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:33758 original size:32 final size:32
Alignment explanation
Indices: 33711--33800 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
33701 ACAAATCGCA
33711 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
33744 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
*
33776 TTGCGATTTCATTTCGCATTGCGAT
1 TTGCGATTTCATTTCGCGTTGCGAT
33801 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 50 0.89
33 6 0.11
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:33819 original size:20 final size:19
Alignment explanation
Indices: 33785--33839 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
33775 GTTGCGATTT
*
33785 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
33804 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
33824 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
33840 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:34346 original size:18 final size:18
Alignment explanation
Indices: 34320--34364 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
34310 GTCGATCAGA
*
34320 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
34338 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
34356 TGATGGCTC
1 TGATGGCTC
34365 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:36012 original size:22 final size:22
Alignment explanation
Indices: 35985--36028 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
35975 GATGGAGATA
35985 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
36007 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
36029 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:36241 original size:20 final size:20
Alignment explanation
Indices: 36216--36309 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
36206 GATTATGTAT
36216 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
36236 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
** *** * *
36256 TATATCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
36277 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
36297 TATCGCATTGCGA
1 TATCGCGTTGCGA
36310 TTTTCCCAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 46 0.79
21 12 0.21
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:36281 original size:41 final size:41
Alignment explanation
Indices: 36236--36313 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
36226 CGAAAGTCAG
* * *
36236 TATCGCGTTGCGAAAGTAAGTATATCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATAGCATTGCGATTTTTTAT
* * *
36277 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATAGCATTGCGATTTT
36314 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATAGCATTGCGATTTTTTAT
Found at i:36310 original size:20 final size:20
Alignment explanation
Indices: 36196--36310 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
36186 CGCTTTGAAA
*
36196 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
36217 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
36237 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
** * ** * *
36257 ATATCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
36278 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
36298 ATCGCATTGCGAT
1 ATCGCATTGCGAT
36311 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.66
21 23 0.31
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:36328 original size:21 final size:21
Alignment explanation
Indices: 36299--36391 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
36289 ATAGTCAGTA
36299 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
36320 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
36340 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
36361 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
36381 TCGCATTGCGA
1 TCGCATTGCGA
36392 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:36329 original size:41 final size:41
Alignment explanation
Indices: 36299--36391 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
36289 ATAGTCAGTA
* *
36299 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
36340 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
36381 TCGCATTGCGA
1 TCGCATTGCGA
36392 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:37817 original size:37 final size:37
Alignment explanation
Indices: 37776--37853 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
37766 TTCATTTATT
37776 AATATAATAATAATATGTGTTATTATTGTATTGGTGA
1 AATATAATAATAATATGTGTTATTATTGTATTGGTGA
*
37813 AATATAATAATAATGTGTGTTATTATTGTATTGGTGA
1 AATATAATAATAATATGTGTTATTATTGTATTGGTGA
37850 AATA
1 AATA
37854 CAGTGTGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (37 bp):
AATATAATAATAATATGTGTTATTATTGTATTGGTGA
Found at i:39260 original size:16 final size:18
Alignment explanation
Indices: 39225--39261 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
39215 CGAAAAATCG
*
39225 AAAAACTCGAACCGTTAA
1 AAAAACTCGAACCGTAAA
39243 AAAAAC-CGAACCG-AAA
1 AAAAACTCGAACCGTAAA
39259 AAA
1 AAA
39262 CTAGTTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 7 0.39
18 6 0.33
ACGTcount: A:0.59, C:0.22, G:0.11, T:0.08
Consensus pattern (18 bp):
AAAAACTCGAACCGTAAA
Found at i:42635 original size:2 final size:2
Alignment explanation
Indices: 42628--42698 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
42618 TTAAGATGAG
42628 TA TA TA TA TA TA TA 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
42670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42699 TTGCTGGTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44575 original size:30 final size:30
Alignment explanation
Indices: 44521--44597 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
44511 TGTGATCAAT
* * * *
44521 TGATAACGTAACATATGTCTTATCATCTAAAG
1 TGATGACGTAAC--ATGTCATATCATCCAAAA
44553 TGATGACGTAACATGTCATATCATCCAAAA
1 TGATGACGTAACATGTCATATCATCCAAAA
* *
44583 TGATGATGTGACATG
1 TGATGACGTAACATG
44598 AATCATGCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 28 0.72
32 11 0.28
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (30 bp):
TGATGACGTAACATGTCATATCATCCAAAA
Found at i:46581 original size:2 final size:2
Alignment explanation
Indices: 46574--46605 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46564 AGTGCCCCCA
46574 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
46606 GTATGTGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49169 original size:2 final size:2
Alignment explanation
Indices: 49162--49198 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
49152 TGAAACAAAT
49162 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
49199 AGCACACAGA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:63481 original size:31 final size:30
Alignment explanation
Indices: 63435--63518 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 30
63425 ATTTAGGTAT
63435 CTAAAG-TATTTTTTGGTCAAAATA-AGTAC
1 CTAAAGTTATTTTTTGGTCAAAATAGA-TAC
* *
63464 CTAAAGTTATTTTTTTGGTCAATATAGATAT
1 CTAAAGTTA-TTTTTTGGTCAAAATAGATAC
* *
63495 CTAAAGTT-TTCTAT-GTCAAAATAG
1 CTAAAGTTATTTTTTGGTCAAAATAG
63519 GTACATGAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 9 0.19
29 10 0.21
30 2 0.04
31 25 0.53
32 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.42
Consensus pattern (30 bp):
CTAAAGTTATTTTTTGGTCAAAATAGATAC
Found at i:63496 original size:60 final size:58
Alignment explanation
Indices: 63394--63522 Score: 138
Period size: 60 Copynumber: 2.2 Consensus size: 58
63384 CTTATATCAC
* * *
63394 AAATAAGTACCTAAAGTATATTCACTTTTTCATTTAGGTATCTAAAGTATTT-TTTGGTCA
1 AAATAAGTACCTAAAGTATATT-ACTTTTTCATATAGATATCTAAAGT-TTTCTAT-GTCA
*
63454 AAATAAGTACCTAAAGT-TATT-TTTTTGGTCAATATAGATATCTAAAGTTTTCTATGTCA
1 AAATAAGTACCTAAAGTATATTACTTTT--TC-ATATAGATATCTAAAGTTTTCTATGTCA
*
63513 AAATAGGTAC
1 AAATAAGTAC
63523 ATGAACTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
57 4 0.07
59 22 0.37
60 34 0.57
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (58 bp):
AAATAAGTACCTAAAGTATATTACTTTTTCATATAGATATCTAAAGTTTTCTATGTCA
Found at i:63690 original size:30 final size:29
Alignment explanation
Indices: 63617--63690 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
63607 AAATAAATAT
* *
63617 TTTATGTACTTATTTTGACCAAAAGATAA
1 TTTAGGTACTTATTTTGACAAAAAGATAA
* *
63646 TTTAGGT-GTATATTTTGACAAAAATATAA
1 TTTAGGTACT-TATTTTGACAAAAAGATAA
63675 CTTTAGGTACTTATTT
1 -TTTAGGTACTTATTT
63691 ATTATATAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 23 0.62
30 12 0.32
31 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (29 bp):
TTTAGGTACTTATTTTGACAAAAAGATAA
Found at i:64089 original size:14 final size:14
Alignment explanation
Indices: 64070--64100 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
64060 GCCGCGGGTG
64070 CTCGAACTCGTGAC
1 CTCGAACTCGTGAC
*
64084 CTCGAACTTGTGAC
1 CTCGAACTCGTGAC
64098 CTC
1 CTC
64101 TATGAACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.26
Consensus pattern (14 bp):
CTCGAACTCGTGAC
Found at i:64840 original size:2 final size:2
Alignment explanation
Indices: 64833--64871 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
64823 TTTTCTGATA
64833 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
64872 AAAAAAGAGA
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
Done.