Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005697.1 Hibiscus syriacus cultivar Beakdansim tig00013327_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: 123928
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3243 original size:51 final size:52
Alignment explanation
Indices: 3188--3295 Score: 130
Period size: 51 Copynumber: 2.1 Consensus size: 52
3178 AGTTGTGCAC
* * * * *
3188 TTCATTTAACT-AAGTACTTCATTGATTAAACTTGTTCATTGATTAAACTAG
1 TTCATTTAACTAAACTACTTCATTCATTAAACTAGTTCATTCATCAAACTAG
* * *
3239 TTCA-TTCATTAAACTAGTTCATTCATTAAACTAGTTCATTCATCAAACTAG
1 TTCATTTAACTAAACTACTTCATTCATTAAACTAGTTCATTCATCAAACTAG
3290 TTCATT
1 TTCATT
3296 CATGATTTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
50 4 0.09
51 42 0.89
52 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (52 bp):
TTCATTTAACTAAACTACTTCATTCATTAAACTAGTTCATTCATCAAACTAG
Found at i:3376 original size:17 final size:17
Alignment explanation
Indices: 3205--3375 Score: 180
Period size: 17 Copynumber: 9.9 Consensus size: 17
3195 AACTAAGTAC
* *
3205 TTCATTGATTAAACTTG
1 TTCATTCATTAAACTAG
*
3222 TTCATTGATTAAACTAG
1 TTCATTCATTAAACTAG
3239 TTCATTCATTAAACTAG
1 TTCATTCATTAAACTAG
3256 TTCATTCATTAAACTAG
1 TTCATTCATTAAACTAG
*
3273 TTCATTCATCAAACTAG
1 TTCATTCATTAAACTAG
* ** *
3290 TTCATTCATGATTTCAAG
1 TTCATTCATTA-AACTAG
* * *
3308 TTCATTGAATAAAGTTAG
1 TTCATTCATTAAA-CTAG
**
3326 TTCATAAATTAAACTAG
1 TTCATTCATTAAACTAG
* *
3343 TTCATTCATCAAACTAA
1 TTCATTCATTAAACTAG
*
3360 TTCATTTATTAAACTA
1 TTCATTCATTAAACTA
3376 ACTCTTAATT
Statistics
Matches: 128, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
17 105 0.82
18 23 0.18
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (17 bp):
TTCATTCATTAAACTAG
Found at i:4111 original size:21 final size:22
Alignment explanation
Indices: 4087--4131 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
4077 ATAAGGCTAA
* *
4087 ATTCAACCTC-AAATTATCTAG
1 ATTCAACCACAAAATAATCTAG
*
4108 ATTCATCCACAAAATAATCTAG
1 ATTCAACCACAAAATAATCTAG
4130 AT
1 AT
4132 ATTCAGCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.31
Consensus pattern (22 bp):
ATTCAACCACAAAATAATCTAG
Found at i:8459 original size:36 final size:35
Alignment explanation
Indices: 8360--8470 Score: 116
Period size: 35 Copynumber: 3.2 Consensus size: 35
8350 TTGGTGGTTA
** * * * *
8360 TATAGGCGTGAAATGGTGATAAAATATGGTTAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
* * * *
8395 TATAGGCGTGCAATAGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
8430 TATAGGCGTGAAAATGGTGATGGAAGATGGTAATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTAATGT
8466 T-TAGG
1 TATAGG
8471 TAGTATCTTA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
35 40 0.65
36 22 0.35
ACGTcount: A:0.33, C:0.04, G:0.34, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
Found at i:9190 original size:13 final size:13
Alignment explanation
Indices: 9172--9204 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
9162 ACCTCTAGCT
9172 AGCTCAAAAGTCC
1 AGCTCAAAAGTCC
9185 AGCTCAAAAGTCC
1 AGCTCAAAAGTCC
9198 AGCTCAA
1 AGCTCAA
9205 GTCAGCTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.30, G:0.15, T:0.15
Consensus pattern (13 bp):
AGCTCAAAAGTCC
Found at i:12353 original size:36 final size:35
Alignment explanation
Indices: 12247--12357 Score: 109
Period size: 35 Copynumber: 3.2 Consensus size: 35
12237 TTGGTGGTTA
** * * * *
12247 TATAGGCGTGAAATGGTGATAAAATATGGTTAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
* * *
12282 TATAGGCGTGCAATAGTAATGGAAGATGG-AGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTA-ATGT
12317 TATAGGCGTGAAAATGGTGATGGAAGATGGTAATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTAATGT
12353 T-TAGG
1 TATAGG
12358 TAGTATCTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
35 39 0.64
36 21 0.34
37 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.34, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
Found at i:16224 original size:36 final size:35
Alignment explanation
Indices: 16118--16228 Score: 109
Period size: 35 Copynumber: 3.2 Consensus size: 35
16108 TTGGTGGTAA
** * * * *
16118 TATAGGCGTGAAATGGTGATAAAATATGGTTAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
* * *
16153 TATAGGCGTGCAATAGTAATGGAAGATGG-AGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTA-ATGT
16188 TATAGGCGTGAAAATGGTGATGGAAGATGGTAATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTAATGT
16224 T-TAGG
1 TATAGG
16229 TAGTATCTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
35 39 0.64
36 21 0.34
37 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.34, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
Found at i:19568 original size:6 final size:6
Alignment explanation
Indices: 19557--19599 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
19547 ATTGTAGGAG
* *
19557 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TGTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
19600 TGTTGTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:20095 original size:36 final size:35
Alignment explanation
Indices: 19989--20099 Score: 109
Period size: 35 Copynumber: 3.2 Consensus size: 35
19979 TTGGTTGTTA
** * * * *
19989 TATAGGCGTGAAATGGTGATAAAATATGGTTAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
* * *
20024 TATAGGCGTGCAATAGTAATGGAAGATGG-AGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTA-ATGT
20059 TATAGGCGTGAAAATGGTGATGGAAGATGGTAATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTAATGT
20095 T-TAGG
1 TATAGG
20100 TAGTATCTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
35 39 0.64
36 21 0.34
37 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.34, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
Found at i:23410 original size:10 final size:10
Alignment explanation
Indices: 23376--23417 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
23366 GTCTTTTTCT
*
23376 TTTCTTTTTG
1 TTTCTTGTTG
* *
23386 TTT-TTCTTC
1 TTTCTTGTTG
23395 TTTCTTGTTG
1 TTTCTTGTTG
23405 TTTCTTGTTG
1 TTTCTTGTTG
23415 TTT
1 TTT
23418 TTGCTGCAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (10 bp):
TTTCTTGTTG
Found at i:23905 original size:36 final size:35
Alignment explanation
Indices: 23799--23909 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 35
23789 TTGGTGGTTA
** * * * *
23799 TATAGGCGTGAAATGGTGATAAAATATGGTTAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
* * * *
23834 TATAGGCATGCAATAGTAATGGAAGATGG-AGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTA-ATGT
23869 TATAGGCGTGAAAATGGTGATGGAAGATGGTAATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTAATGT
23905 T-TAGG
1 TATAGG
23910 TAGTATCTTA
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
35 37 0.63
36 21 0.36
37 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.33, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
Found at i:25625 original size:8 final size:8
Alignment explanation
Indices: 25612--25667 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
25602 ATTTTTTTTT
25612 CAAAAAAA
1 CAAAAAAA
25620 CAAAAAAA
1 CAAAAAAA
25628 CAAAAAAA
1 CAAAAAAA
25636 GGC-AAAAAA
1 --CAAAAAAA
**
25645 -AAAAAGG
1 CAAAAAAA
25652 CAAAAAAA
1 CAAAAAAA
25660 CAAAAAAA
1 CAAAAAAA
25668 AGAGCCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 4 0.10
8 29 0.73
9 6 0.15
10 1 0.03
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:25646 original size:14 final size:14
Alignment explanation
Indices: 25624--25664 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
25614 AAAAAACAAA
25624 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGGC
25639 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
25653 AAAAAAACAAAA
1 AAAAAAA-AAAA
25665 AAAAGAGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:25649 original size:22 final size:21
Alignment explanation
Indices: 25616--25686 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
25606 TTTTTTCAAA
25616 AAAACAAAAAAACAAAAAAAGGC
1 AAAA-AAAAAAACAAAAAAA-GC
25639 AAAAAAAAAAAGGCAAAAAAA-C
1 AAAAAAAAAAA--CAAAAAAAGC
* * *
25661 AAAAAAAAGAGCCAAAAAAGC
1 AAAAAAAAAAACAAAAAAAGC
*
25682 CAAAA
1 AAAAA
25687 TTTCAAACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 7 0.17
21 5 0.12
22 17 0.41
23 4 0.10
24 8 0.20
ACGTcount: A:0.77, C:0.13, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAACAAAAAAAGC
Found at i:25686 original size:21 final size:21
Alignment explanation
Indices: 25640--25679 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25630 AAAAAAGGCA
*
25640 AAAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAAGCCAAAAAAAC
*
25661 AAAAAAAAGAGCCAAAAAA
1 AAAAAAAAAAGCCAAAAAA
25680 GCCAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAGCCAAAAAAAC
Found at i:33025 original size:6 final size:6
Alignment explanation
Indices: 33014--33057 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
33004 ATTGTAGGAG
*
33014 TCTTTT TC-TTT TCTTTT TCTTTT TCTTCTT TCTTGTT GCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTT-TT TCTTTT T
33058 GTTGTTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 5 0.15
6 17 0.52
7 11 0.33
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (6 bp):
TCTTTT
Found at i:33068 original size:19 final size:20
Alignment explanation
Indices: 33015--33071 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
33005 TTGTAGGAGT
*
33015 CTTTTTC-T-TTTCTT-TTT
1 CTTTTTCTTCTTTCTTGTTG
33032 CTTTTTCTTCTTTCTTGTTG
1 CTTTTTCTTCTTTCTTGTTG
* *
33052 CTTTTTGTTGTTT-TTGTTG
1 CTTTTTCTTCTTTCTTGTTG
33071 C
1 C
33072 AGCACTTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.21
18 1 0.03
19 13 0.38
20 13 0.38
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.74
Consensus pattern (20 bp):
CTTTTTCTTCTTTCTTGTTG
Found at i:35869 original size:24 final size:25
Alignment explanation
Indices: 35823--35877 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
35813 ATAGTTATGC
*
35823 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
35847 CACTTGAAGTGCCACAAGCTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
35872 CA-TTGA
1 CACTTGA
35878 GGCTTCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:37840 original size:20 final size:19
Alignment explanation
Indices: 37797--37846 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
37787 CGGCCAAGAG
*
37797 CATGTATTTTCATTAAAGT
1 CATGTATTTTCATTAAAAT
*
37816 CATGTTTTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
37836 CATGTCATTTT
1 CATGT-ATTTT
37847 AGGAAGGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 13 0.50
20 9 0.35
21 4 0.15
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:38780 original size:17 final size:17
Alignment explanation
Indices: 38731--38801 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
38721 ATTAAGAGTA
* *
38731 AGTTTAATAAATGAAAT
1 AGTTTAATTAATGAACT
* *
38748 AGTTTGATGAATGAACT
1 AGTTTAATTAATGAACT
38765 AGTTTAATTAATGAACT
1 AGTTTAATTAATGAACT
*
38782 AACTTT-ATTCAATGAACT
1 -AGTTTAATT-AATGAACT
38800 AG
1 AG
38802 AACTTTATGC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
17 33 0.73
18 12 0.27
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (17 bp):
AGTTTAATTAATGAACT
Found at i:38807 original size:20 final size:20
Alignment explanation
Indices: 38774--38822 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
38764 TAGTTTAATT
*
38774 AATGAACT--AACTTTATTC
1 AATGAACTAGAACTTTATGC
38792 AATGAACTAGAACTTTATGC
1 AATGAACTAGAACTTTATGC
38812 AATGAACTAGA
1 AATGAACTAGA
38823 TGCATAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 8 0.29
20 20 0.71
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (20 bp):
AATGAACTAGAACTTTATGC
Found at i:39665 original size:19 final size:20
Alignment explanation
Indices: 39637--39676 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
39627 GAATAATAAT
39637 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
39657 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
39676 A
1 A
39677 AGAAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:42718 original size:26 final size:26
Alignment explanation
Indices: 42671--42728 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 26
42661 AATGTGAACT
*
42671 ATAATATATTATGATAACTTAT-ATC
1 ATAATATATTATGACAACTTATCATC
*
42696 -TAATATATTAATGGACAAGTTATCATC
1 ATAATATATT-AT-GACAACTTATCATC
42723 ATAATA
1 ATAATA
42729 ACTATAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 9 0.33
25 2 0.07
26 8 0.30
27 3 0.11
28 5 0.19
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.40
Consensus pattern (26 bp):
ATAATATATTATGACAACTTATCATC
Found at i:44992 original size:18 final size:17
Alignment explanation
Indices: 44971--45050 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
44961 CCTTGTCTTG
44971 CTTTCTTTTTGAATTTTT
1 CTTTCTTTTTG-ATTTTT
44989 CTTT-TTCTTT--TCTTTT
1 CTTTCTT-TTTGAT-TTTT
45005 C-TTCTTTTCTGATTTTT
1 CTTTCTTTT-TGATTTTT
*
45022 CTCTTC-TTTTGTCTTTTT
1 CT-TTCTTTTTG-ATTTTT
45040 CTTTCTTTTTG
1 CTTTCTTTTTG
45051 CACTCCAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 20
0.71 0.01 0.28
Matches are distributed among these distances:
15 5 0.10
16 8 0.16
17 12 0.24
18 23 0.45
19 3 0.06
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.74
Consensus pattern (17 bp):
CTTTCTTTTTGATTTTT
Found at i:45009 original size:13 final size:12
Alignment explanation
Indices: 44985--45043 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
44975 CTTTTTGAAT
44985 TTTTC-TTTTTC
1 TTTTCTTTTTTC
44996 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
45009 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
45023 TCTTCTTTTGTC
1 TTTTCTTTTTTC
45035 TTTTTCTTT
1 -TTTTCTTT
45044 CTTTTTGCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 16 0.40
14 8 0.20
15 3 0.08
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:45009 original size:19 final size:19
Alignment explanation
Indices: 44987--45043 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
44977 TTTTGAATTT
44987 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
*
45006 TTC-TTTTCTGATTT-TTCTC
1 TTCTTTTTCT--TTTCTTTTC
45025 TTCTTTTGTCTTTTTCTTT
1 TTCTTTT-TC-TTTTCTTT
45044 CTTTTTGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 9 0.30
21 4 0.13
22 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:55714 original size:24 final size:21
Alignment explanation
Indices: 55680--55722 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
55670 TGCACAAGAT
*
55680 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
55702 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
55723 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:76007 original size:2 final size:2
Alignment explanation
Indices: 76000--76035 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
75990 TGTCACCAAC
76000 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
76036 TCTGCTTCCA
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:80413 original size:30 final size:33
Alignment explanation
Indices: 80354--80414 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 33
80344 TTGATAACAT
80354 TTCTATCCATTTCCTTTCTTATCATTTCCATTA
1 TTCTATCCATTTCCTTTCTTATCATTTCCATTA
80387 TTCT-TCCATTT-CTTAT-TTAT-ATTTCCAT
1 TTCTATCCATTTCCTT-TCTTATCATTTCCAT
80415 CTTAATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.30
31 7 0.26
32 8 0.30
33 4 0.15
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (33 bp):
TTCTATCCATTTCCTTTCTTATCATTTCCATTA
Found at i:80626 original size:24 final size:21
Alignment explanation
Indices: 80599--80646 Score: 51
Period size: 21 Copynumber: 2.1 Consensus size: 21
80589 TGTTGCAACA
80599 AAAGTAACAAAAAGAGAAAAAAAT
1 AAAG-AACAAAAA-A-AAAAAAAT
* *
80623 AAAGAAGAAAAAATAAAAAAT
1 AAAGAACAAAAAAAAAAAAAT
80644 AAA
1 AAA
80647 AAAAAAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 10 0.45
22 1 0.05
23 7 0.32
24 4 0.18
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.08
Consensus pattern (21 bp):
AAAGAACAAAAAAAAAAAAAT
Found at i:80633 original size:14 final size:14
Alignment explanation
Indices: 80616--80654 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
80606 CAAAAAGAGA
80616 AAAAAATAAAGAAG
1 AAAAAATAAAGAAG
* *
80630 AAAAAATAAAAAAT
1 AAAAAATAAAGAAG
80644 AAAAAA-AAAGA
1 AAAAAATAAAGA
80655 TAAAGAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (14 bp):
AAAAAATAAAGAAG
Found at i:80633 original size:15 final size:15
Alignment explanation
Indices: 80609--80650 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
80599 AAAGTAACAA
80609 AAAG-AGAAAAAAAT
1 AAAGAAGAAAAAAAT
80623 AAAGAAG-AAAAAAT
1 AAAGAAGAAAAAAAT
* *
80637 AAAAAATAAAAAAA
1 AAAGAAGAAAAAAA
80651 AAGATAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAGAAGAAAAAAAT
Found at i:80650 original size:8 final size:7
Alignment explanation
Indices: 80616--80649 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
80606 CAAAAAGAGA
80616 AAAAAAT
1 AAAAAAT
* *
80623 AAAGAAG
1 AAAAAAT
80630 AAAAAAT
1 AAAAAAT
80637 AAAAAAT
1 AAAAAAT
80644 AAAAAA
1 AAAAAA
80650 AAAGATAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (7 bp):
AAAAAAT
Found at i:80710 original size:9 final size:10
Alignment explanation
Indices: 80689--80721 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
80679 TTTGGAGTGC
80689 AAAAGAAAGA
1 AAAAGAAAGA
80699 AAAAGAAA-A
1 AAAAGAAAGA
*
80708 AAAATAAAGA
1 AAAAGAAAGA
80718 AAAA
1 AAAA
80722 CAGAAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:86159 original size:19 final size:20
Alignment explanation
Indices: 86118--86166 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
86108 GTAACCCCTT
*
86118 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
86138 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
86157 TGAACATACA
1 TGAAAATACA
86167 CGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:87644 original size:11 final size:13
Alignment explanation
Indices: 87612--87641 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
87602 TGGCCAAAGA
87612 TGAAAAGGTATGT
1 TGAAAAGGTATGT
87625 TGAAAAGGTATG-
1 TGAAAAGGTATGT
87637 TGAAA
1 TGAAA
87642 GGTGCTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:89498 original size:13 final size:14
Alignment explanation
Indices: 89470--89502 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
89460 ATACTATTTT
*
89470 CATCACCATCTTTC
1 CATCACCATCTCTC
89484 CATCACCATC-CTC
1 CATCACCATCTCTC
89497 CATCAC
1 CATCAC
89503 TTTCACGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.27
Consensus pattern (14 bp):
CATCACCATCTCTC
Found at i:90900 original size:6 final size:6
Alignment explanation
Indices: 90891--90923 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
90881 GTTTCAATTC
*
90891 TTTCCA TTTCCT TTTCCA TTTCCA TTTCC- TTTC
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTC
90924 TTAATTATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTCCA
Found at i:94355 original size:19 final size:21
Alignment explanation
Indices: 94312--94363 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
94302 GAAACCCCTT
94312 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
94333 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
94352 TGAAGATACATG
1 TGAAAATACATG
94364 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:98458 original size:19 final size:21
Alignment explanation
Indices: 98415--98466 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
98405 GAAACCCCTT
98415 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
98436 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
98455 TGAAGATACATG
1 TGAAAATACATG
98467 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:103943 original size:19 final size:20
Alignment explanation
Indices: 103902--103952 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
103892 GAAACCCCTT
*
103902 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
103922 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
103941 TGAAGATACATG
1 TGAAAATACATG
103953 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:108082 original size:19 final size:20
Alignment explanation
Indices: 108041--108091 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
108031 GAAACCCCTT
*
108041 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
108061 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
108080 TGAAGATACATG
1 TGAAAATACATG
108092 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:114232 original size:105 final size:105
Alignment explanation
Indices: 114107--114305 Score: 344
Period size: 105 Copynumber: 1.9 Consensus size: 105
114097 GATGTAGCTC
* *
114107 AACCTAGCCTCACTTCGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTTTCGATCTAGGAA
1 AACCTAGCCTCACTTCGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTTTCAATCTAGAAA
*
114172 AGCAACAAGGATCCTGCACAAATAAGAAATGATACAGTTA
66 AGCAACAAGGATCCTGCACAAACAAGAAATGATACAGTTA
* * *
114212 AACCTAGCCTCACTTGGATGGATGGTGAAGTTAAGGTTGTACCTTTGATTGTTTCAATCTAGAAA
1 AACCTAGCCTCACTTCGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTTTCAATCTAGAAA
114277 AGCAACAAGGATCCTGCACAAACAAGAAA
66 AGCAACAAGGATCCTGCACAAACAAGAAA
114306 GCTCAAAAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 88 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (105 bp):
AACCTAGCCTCACTTCGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTTTCAATCTAGAAA
AGCAACAAGGATCCTGCACAAACAAGAAATGATACAGTTA
Done.