Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020637.1 Corchorus olitorius cultivar O-4 contig20670, 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: 27583
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:2923 original size:21 final size:21
Alignment explanation
Indices: 2899--2971 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
2889 GGCTTGGAAT
2899 GGTGATGGCACGGGCATGGCC
1 GGTGATGGCACGGGCATGGCC
* * **
2920 GGTGGTGGCACGGGCTTAACC
1 GGTGATGGCACGGGCATGGCC
* * *
2941 GGTGGTGTCACGGTGAATGGCC
1 GGTGATGGCACGG-GCATGGCC
*
2963 GGTAATGGC
1 GGTGATGGC
2972 TTGGTAGTGG
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
21 29 0.74
22 10 0.26
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19
Consensus pattern (21 bp):
GGTGATGGCACGGGCATGGCC
Found at i:3274 original size:21 final size:21
Alignment explanation
Indices: 3248--3298 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
3238 CCGGTCCCGT
3248 CCGGGCCATGTGCGAGGATGG
1 CCGGGCCATGTGCGAGGATGG
3269 CCGGGCCATGTGCGAGGATGG
1 CCGGGCCATGTGCGAGGATGG
3290 CCGGGCCAT
1 CCGGGCCAT
3299 ATCCGCGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (21 bp):
CCGGGCCATGTGCGAGGATGG
Found at i:6204 original size:23 final size:25
Alignment explanation
Indices: 6157--6208 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 25
6147 AAAAACTTTT
6157 TTTTATGACGCAGAAACAAAAAAAA
1 TTTTATGACGCAGAAACAAAAAAAA
6182 TTTTATGACGCA-AAA-AAAAAAAA
1 TTTTATGACGCAGAAACAAAAAAAA
6205 TTTT
1 TTTT
6209 TTTTCGACGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 12 0.44
24 3 0.11
25 12 0.44
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (25 bp):
TTTTATGACGCAGAAACAAAAAAAA
Found at i:6210 original size:25 final size:26
Alignment explanation
Indices: 6155--6223 Score: 90
Period size: 25 Copynumber: 2.7 Consensus size: 26
6145 GCAAAAACTT
6155 TTTTTTATGACGCAGAAACAAAAAAAA
1 TTTTTTATGACGCA-AAACAAAAAAAA
6182 --TTTTATGACGCAAAA-AAAAAAAA
1 TTTTTTATGACGCAAAACAAAAAAAA
*
6205 TTTTTTTTCGACGCAAAAC
1 TTTTTTAT-GACGCAAAAC
6224 GCAAAACAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 8 0.22
24 3 0.08
25 17 0.46
26 9 0.24
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (26 bp):
TTTTTTATGACGCAAAACAAAAAAAA
Found at i:6229 original size:26 final size:25
Alignment explanation
Indices: 6140--6229 Score: 65
Period size: 25 Copynumber: 3.4 Consensus size: 25
6130 TTTTATAGAA
*
6140 AAAACGCAAAAACTTTTTTTTATGACGC
1 AAAACG-AAAAA-ATTTTTTT-TGACGC
** *
6168 AGAAAC-AAAAAAAATTTTATGACGC
1 A-AAACGAAAAAATTTTTTTTGACGC
**
6193 AAAAAAAAAAAATTTTTTTTCGACGC
1 AAAACGAAAAAATTTTTTTT-GACGC
*
6219 AAAACGCAAAA
1 AAAACGAAAAA
6230 CAAACTTTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
24 3 0.06
25 18 0.38
26 17 0.35
27 5 0.10
28 1 0.02
29 4 0.08
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.24
Consensus pattern (25 bp):
AAAACGAAAAAATTTTTTTTGACGC
Found at i:6618 original size:16 final size:16
Alignment explanation
Indices: 6580--6619 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
6570 AGAGATTGAC
*
6580 AGAAAGCAATTAAACT
1 AGAAAACAATTAAACT
6596 A-AAAACAATTAAACT
1 AGAAAACAATTAAACT
6611 AGAAAACAA
1 AGAAAACAA
6620 AGTAAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:7395 original size:11 final size:11
Alignment explanation
Indices: 7379--7404 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7369 CCTTTGCCTA
7379 AAAACTAGAAG
1 AAAACTAGAAG
7390 AAAACTAGAAG
1 AAAACTAGAAG
7401 AAAA
1 AAAA
7405 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:9408 original size:25 final size:24
Alignment explanation
Indices: 9360--9428 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 24
9350 TTTGGTGGGT
*
9360 GTGTTTATGGTATACCTTTGATGG
1 GTGTTTACGGTATACCTTTGATGG
9384 GTGTTTACGGTATACCCTTTGATGG
1 GTGTTTACGGTATA-CCTTTGATGG
9409 GTGTTTACGGTATACCTTTG
1 GTGTTTACGGTATACCTTTG
9429 GTTGGTACTC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
24 19 0.44
25 24 0.56
ACGTcount: A:0.16, C:0.13, G:0.28, T:0.43
Consensus pattern (24 bp):
GTGTTTACGGTATACCTTTGATGG
Found at i:9898 original size:22 final size:22
Alignment explanation
Indices: 9877--9962 Score: 113
Period size: 23 Copynumber: 3.9 Consensus size: 22
9867 TCACATTATG
* *
9877 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTC-CTATA
9899 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACC-TCCTATA
9922 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCT-CCTATA
9945 AAATTTTGAT-AACCTCCT
1 AAATTTTGATAAACCTCCT
9963 TATGATAAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
21 3 0.05
22 15 0.25
23 39 0.66
24 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAAACCTCCTATA
Found at i:10125 original size:22 final size:22
Alignment explanation
Indices: 10098--10465 Score: 193
Period size: 22 Copynumber: 16.6 Consensus size: 22
10088 AATCATATTT
10098 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
10120 TAAAATTTTGTTGACC-CTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
10141 TGAAATTTTGATAATCACAT-TG
1 TGAAATTTTGATAACCTC-TCTA
* * *
10163 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
* * ** *
10185 TGAAGTTTCGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
10207 TAAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
*
10229 T-AAATTTTGATAATCCGATCTTTA
1 TGAAATTTTGATAA-CC--TCTCTA
* *
10253 TGAAATTTCGATAA-TTACTCTA
1 TGAAATTTTGATAACCT-CTCTA
*
10275 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
10295 TTAAATTTTGGT-ACTTCT-TA
1 TGAAATTTTGATAACCTCTCTA
* * *
10315 TGAAATTGAGACTTTTATAACCTTTATA
1 TGAAA-T-----TTTGATAACCTCTCTA
* *
10343 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
10365 TAAAATTTTGATAACCTCTCCA
1 TGAAATTTTGATAACCTCTCTA
*
10387 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* * *
10409 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
10431 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCTCTA
*
10453 TGACATTTTGATA
1 TGAAATTTTGATA
10466 TTCTCTTTGA
Statistics
Matches: 256, Mismatches: 63, Indels: 54
0.69 0.17 0.14
Matches are distributed among these distances:
20 16 0.06
21 48 0.19
22 156 0.61
23 4 0.02
24 4 0.02
25 12 0.05
26 4 0.02
27 5 0.02
28 7 0.03
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:10580 original size:46 final size:44
Alignment explanation
Indices: 10530--10618 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
10520 TCTTCCTAAG
*
10530 AAATTTTAATAACTTGATCC-TATGAAATTTTGGTAAGCACACTATA
1 AAATTTTAATAAC-T--TCCATATGAAATTTTGGTAACCACACTATA
* *
10576 AAATTTTGATAACTTCCATATGCAATTTTGGTAACCACACTAT
1 AAATTTTAATAACTTCCATATGAAATTTTGGTAACCACACTAT
10619 GCAATTTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 3 0.08
44 23 0.59
45 1 0.03
46 12 0.31
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (44 bp):
AAATTTTAATAACTTCCATATGAAATTTTGGTAACCACACTATA
Found at i:10602 original size:22 final size:22
Alignment explanation
Indices: 10549--10681 Score: 76
Period size: 22 Copynumber: 6.0 Consensus size: 22
10539 TAACTTGATC
* * *
10549 CTATGAAATTTTGGTAAGCACA
1 CTATGCAATTTTGATAACCACA
**
10571 CTATAAAATTTTGATAACTTC-CA
1 CTATGCAATTTTGATAAC--CACA
*
10594 -TATGCAATTTTGGTAACCACA
1 CTATGCAATTTTGATAACCACA
* *
10615 CTATGCAATTTTGATCACCTC-
1 CTATGCAATTTTGATAACCACA
* * * *
10636 CTCATGAAACTATAATAACCATC-
1 CT-ATGCAATTTTGATAACCA-CA
* *
10659 TTATGAAATTTTGATAACCACA
1 CTATGCAATTTTGATAACCACA
10681 C
1 C
10682 AGAGACAAGA
Statistics
Matches: 84, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
20 1 0.01
21 5 0.06
22 73 0.87
23 4 0.05
24 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (22 bp):
CTATGCAATTTTGATAACCACA
Found at i:10882 original size:20 final size:20
Alignment explanation
Indices: 10844--10882 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10834 TATCGACATT
10844 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
10864 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
10883 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:13664 original size:69 final size:69
Alignment explanation
Indices: 13541--13673 Score: 207
Period size: 69 Copynumber: 1.9 Consensus size: 69
13531 CAAATACATT
** *
13541 GTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGCTTCTATCATTTTTTCCTTAGTG
1 GTCTTTATATGTAATTTTAGCATTAAGATGTAATTAATGGTGCTTCCATCATTTTTTCCTTAGTG
13606 TATC
66 TATC
13610 GTCTTTATATGTAATTTTAGCATTAAGATGTAATTAATGGTG-TTCCCA-CAATTTTTTCCTTAG
1 GTCTTTATATGTAATTTTAGCATTAAGATGTAATTAATGGTGCTT-CCATC-ATTTTTTCCTTAG
13673 T
64 T
13674 TGTTAGTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
68 3 0.05
69 56 0.95
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (69 bp):
GTCTTTATATGTAATTTTAGCATTAAGATGTAATTAATGGTGCTTCCATCATTTTTTCCTTAGTG
TATC
Found at i:19361 original size:16 final size:18
Alignment explanation
Indices: 19340--19375 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
19330 TAGAAAAATA
19340 TTACTAAAT-TTT-TAAT
1 TTACTAAATCTTTATAAT
19356 TTACTAAATCTTTATAAT
1 TTACTAAATCTTTATAAT
19374 TT
1 TT
19376 GTAAAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 3 0.17
18 6 0.33
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (18 bp):
TTACTAAATCTTTATAAT
Found at i:19892 original size:21 final size:21
Alignment explanation
Indices: 19849--19999 Score: 77
Period size: 21 Copynumber: 7.4 Consensus size: 21
19839 TTTTGGTCAT
* *
19849 CTTATTAAAGTTTTTTATCTAAC
1 CTTATT-AAGATTTTTA-GTAAC
19872 CTTATTAAGATTTTTAGTAAC
1 CTTATTAAGATTTTTAGTAAC
** * *
19893 CTTATTGTGAATTTTA-TAAGT
1 CTTATTAAGATTTTTAGTAA-C
* *
19914 CTTATTAAGCTTTTTAATAAC
1 CTTATTAAGATTTTTAGTAAC
* *
19935 TTTA-TAAG-TTTTTCAGTAAT
1 CTTATTAAGATTTTT-AGTAAC
* *
19955 CTTA--GAGATTTTTAATAA-
1 CTTATTAAGATTTTTAGTAAC
19973 CTTGA-TAA-A-TTTTAGTAAC
1 CTT-ATTAAGATTTTTAGTAAC
*
19992 TTTATTAA
1 CTTATTAA
20000 ACTTTAAGTA
Statistics
Matches: 100, Mismatches: 20, Indels: 20
0.71 0.14 0.14
Matches are distributed among these distances:
18 12 0.12
19 18 0.18
20 20 0.20
21 32 0.32
22 12 0.12
23 6 0.06
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (21 bp):
CTTATTAAGATTTTTAGTAAC
Found at i:19984 original size:19 final size:18
Alignment explanation
Indices: 19924--20067 Score: 58
Period size: 20 Copynumber: 7.3 Consensus size: 18
19914 CTTATTAAGC
*
19924 TTTTTAATAACTTTATAAG
1 TTTTTAATAAC-TTATAAA
* * *
19943 TTTTTCAGTAATCTTAGAGA
1 TTTTT-AATAA-CTTATAAA
19963 TTTTTAATAACTTGATAAA
1 TTTTTAATAACTT-ATAAA
*
19982 -TTTTAGTAACTTTATTAAA
1 TTTTTAATAAC-TTA-TAAA
* *
20001 -CTTTAAGTAACATTACTAATT
1 TTTTTAA-TAAC-TTA-TAA-A
*
20022 TATTTTAATAATTTTATAAA
1 T-TTTTAATAA-CTTATAAA
*
20042 CTTTTTACTAACATTATAAA
1 -TTTTTAATAAC-TTATAAA
20062 GTTTTT
1 -TTTTT
20068 TTAATACTTG
Statistics
Matches: 94, Mismatches: 19, Indels: 23
0.69 0.14 0.17
Matches are distributed among these distances:
18 13 0.14
19 22 0.23
20 43 0.46
21 5 0.05
22 6 0.06
23 5 0.05
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTTAATAACTTATAAA
Found at i:20054 original size:42 final size:43
Alignment explanation
Indices: 19981--20083 Score: 108
Period size: 42 Copynumber: 2.5 Consensus size: 43
19971 AACTTGATAA
* *
19981 ATTTTAGTAACTTTATTAAACTTTAAGTAACATTACT-AA-TTT
1 ATTTTAATAACTTTATTAAACTTTAACTAACATTA-TAAAGTTT
* *
20023 ATTTTAATAATTTTA-TAAACTTTTTACTAACATTATAAAGTTT
1 ATTTTAATAACTTTATTAAAC-TTTAACTAACATTATAAAGTTT
*
20066 -TTTTAAT-ACTTGATTAAA
1 ATTTTAATAACTTTATTAAA
20084 TTTTTTGGGA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
41 10 0.20
42 38 0.75
43 3 0.06
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.50
Consensus pattern (43 bp):
ATTTTAATAACTTTATTAAACTTTAACTAACATTATAAAGTTT
Found at i:20474 original size:21 final size:20
Alignment explanation
Indices: 20450--20494 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
20440 TCTAGCTTTT
*
20450 TTAAGCAATTTAGTAACTGTA
1 TTAAGCAATTTAGCAACT-TA
* *
20471 TTAAGTATTTTAGCAACTTA
1 TTAAGCAATTTAGCAACTTA
20491 TTAA
1 TTAA
20495 ACTTTCATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (20 bp):
TTAAGCAATTTAGCAACTTA
Found at i:21155 original size:21 final size:20
Alignment explanation
Indices: 21122--21161 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
21112 CCAAAATTTC
21122 TTAAAACTCCAC-TTAAAAT
1 TTAAAACTCCACTTTAAAAT
21141 TTAATAACATCCACTTTAAAA
1 TTAA-AAC-TCCACTTTAAAA
21162 AGGATAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 3 0.17
21 5 0.28
22 6 0.33
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAACTCCACTTTAAAAT
Found at i:21573 original size:123 final size:123
Alignment explanation
Indices: 21434--21688 Score: 483
Period size: 123 Copynumber: 2.1 Consensus size: 123
21424 TTGCATAATT
*
21434 TTACAAAAATAGGTAATGTGTTACCAAAAACTCTACATATTTTCTATTAAATTAGTAATCTCACA
1 TTAC-AAAATAGGTAATGTGTTACCAAAAACTCTACATATTTTCTATTAAATTAGTAACCTCACA
21499 TCTTTAAAACTTTTAGTAATCTTGTATTGAAATTTTAGTAACATCTTATCAATTGAAGG
65 TCTTTAAAACTTTTAGTAATCTTGTATTGAAATTTTAGTAACATCTTATCAATTGAAGG
21558 TTACAAAATAGGTAATGTGTTACCAAAAACTCTACATATTTTCTATTAAATTAGTAACCTCACAT
1 TTACAAAATAGGTAATGTGTTACCAAAAACTCTACATATTTTCTATTAAATTAGTAACCTCACAT
21623 CTTTAAAACTTTTAGTAATCTTGTATTGAAATTTTAGTAACATCTTATCAATTGAAGG
66 CTTTAAAACTTTTAGTAATCTTGTATTGAAATTTTAGTAACATCTTATCAATTGAAGG
21681 TTATCAAA
1 TTA-CAAA
21689 CTGATTGCAT
Statistics
Matches: 129, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
123 121 0.94
124 8 0.06
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.39
Consensus pattern (123 bp):
TTACAAAATAGGTAATGTGTTACCAAAAACTCTACATATTTTCTATTAAATTAGTAACCTCACAT
CTTTAAAACTTTTAGTAATCTTGTATTGAAATTTTAGTAACATCTTATCAATTGAAGG
Found at i:23313 original size:12 final size:12
Alignment explanation
Indices: 23283--23316 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
23273 AAATCAATAT
* *
23283 ATATTAATAATA
1 ATATTATTATTA
23295 ATATTATTATTA
1 ATATTATTATTA
23307 ATATTATTAT
1 ATATTATTAT
23317 ACATACACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTATTATTA
Found at i:24070 original size:38 final size:38
Alignment explanation
Indices: 23981--24058 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
23971 TCAATAGTTG
*
23981 TAAAAAAATTTTAATTTTAATAAAGAGAATGTAAGAGA
1 TAAAAAAATTTTAATTTTAATAAAGAAAATGTAAGAGA
* *
24019 TAAAAAAAATTTAATTTTAATAAGGAAAATGTAAGAGA
1 TAAAAAAATTTTAATTTTAATAAAGAAAATGTAAGAGA
24057 TA
1 TA
24059 TAAGGGTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (38 bp):
TAAAAAAATTTTAATTTTAATAAAGAAAATGTAAGAGA
Found at i:24481 original size:16 final size:18
Alignment explanation
Indices: 24450--24482 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
24440 GTCAATGGAG
24450 AAAACCAAAAATCGAGGT
1 AAAACCAAAAATCGAGGT
24468 AAAA-CAAAAA-CGAGG
1 AAAACCAAAAATCGAGG
24483 AGCAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.61, C:0.15, G:0.18, T:0.06
Consensus pattern (18 bp):
AAAACCAAAAATCGAGGT
Done.