Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005740.1 Corchorus capsularis cultivar CVL-1 contig05758, 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: 18044
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Found at i:1066 original size:22 final size:22
Alignment explanation
Indices: 1041--1701 Score: 251
Period size: 22 Copynumber: 30.6 Consensus size: 22
1031 ATGACATCCT
1041 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
*
1063 TATGAAATTATGATAA--TTACAC
1 TATGAAATTTTGATAACCTT-C-C
* * *
1085 TAT----TTTTTATGA-CGTCC
1 TATGAAATTTTGATAACCTTCC
1102 TTATGAAATTTTGATAACCTTCC
1 -TATGAAATTTTGATAACCTTCC
** ** *
1125 TATGAAATTTCAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
1147 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
**
1169 TAT-AAATTTTTTTTAACC-T--
1 TATGAAA-TTTTGATAACCTTCC
* *
1188 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
1210 TAAGGAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATA-ACCTTC-C
1232 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
* * *
1253 AAATGAAATTTTGATAACCAATAC
1 -TATGAAATTTTGATAACC-TTCC
*
1277 TAT-AAGATGTTGATAACC-TCC
1 TATGAA-ATTTTGATAACCTTCC
* * * *
1298 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
1321 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
1342 ATATG-AATTGTCAGTAATC-ACAC
1 -TATGAAATTTTGA-TAACCTTC-C
* * *
1365 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
1387 TATGAAATTGTGATAA-CTTCGC
1 TATGAAATTTTGATAACCTTC-C
1409 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
1432 TATAAAATTTTGAT-A-CTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
1452 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTTCC
*
1475 TATAAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
1496 TTATGAAAATCTTGGTAA-----C
1 -TATG-AAATTTTGATAACCTTCC
* *
1515 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
1536 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
** * * *
1558 TATGGGATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
1580 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
1602 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
1624 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
1646 TATGAAATTTTGATAACTTTCA
1 TATGAAATTTTGATAACCTTCC
*
1668 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
1689 -ATGAAATTTTGAT
1 TATGAAATTTTGAT
1702 TACTCCATAA
Statistics
Matches: 480, Mismatches: 110, Indels: 100
0.70 0.16 0.14
Matches are distributed among these distances:
16 10 0.02
17 1 0.00
18 12 0.03
19 15 0.03
20 36 0.08
21 29 0.06
22 294 0.61
23 77 0.16
24 6 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:1103 original size:62 final size:62
Alignment explanation
Indices: 1005--1133 Score: 249
Period size: 62 Copynumber: 2.1 Consensus size: 62
995 ATTAAATTAA
1005 AAATTATGATAATTACACTATTTTTTATGACATCCTTATGAAATTTTGATAACCTTCCTATG
1 AAATTATGATAATTACACTATTTTTTATGACATCCTTATGAAATTTTGATAACCTTCCTATG
*
1067 AAATTATGATAATTACACTATTTTTTATGACGTCCTTATGAAATTTTGATAACCTTCCTATG
1 AAATTATGATAATTACACTATTTTTTATGACATCCTTATGAAATTTTGATAACCTTCCTATG
1129 AAATT
1 AAATT
1134 TCAATAACGA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (62 bp):
AAATTATGATAATTACACTATTTTTTATGACATCCTTATGAAATTTTGATAACCTTCCTATG
Found at i:1149 original size:62 final size:62
Alignment explanation
Indices: 1005--1149 Score: 202
Period size: 62 Copynumber: 2.3 Consensus size: 62
995 ATTAAATTAA
* **
1005 AAATTATGATAATTACACTATTTTTTATGACATCCTTATGAAATTTTGATAACCTTCCTATG
1 AAATTATAATAACGACACTATTTTTTATGACATCCTTATGAAATTTTGATAACCTTCCTATG
* ** *
1067 AAATTATGATAATTACACTATTTTTTATGACGTCCTTATGAAATTTTGATAACCTTCCTATG
1 AAATTATAATAACGACACTATTTTTTATGACATCCTTATGAAATTTTGATAACCTTCCTATG
*
1129 AAATT-TCAATAACGATACTAT
1 AAATTAT-AATAACGACACTAT
1150 GGAATTTCGA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
61 1 0.01
62 76 0.99
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42
Consensus pattern (62 bp):
AAATTATAATAACGACACTATTTTTTATGACATCCTTATGAAATTTTGATAACCTTCCTATG
Found at i:1468 original size:43 final size:43
Alignment explanation
Indices: 1408--1489 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
1398 GATAACTTCG
* *
1408 CTATGAAATTTTGATAAACCTTCCTATAAAATTTTGATACTCC
1 CTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATACTCC
*
1451 CTATAAAATTTTGATAAATCTCCCTATAAAATTTTGATA
1 CTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATA
1490 ACCTCCTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (43 bp):
CTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATACTCC
Found at i:1832 original size:22 final size:22
Alignment explanation
Indices: 1783--1910 Score: 89
Period size: 22 Copynumber: 5.8 Consensus size: 22
1773 GAAATACCAC
* * *
1783 TATGAAATTTTGGTAATCACATT
1 TATGAAAATTTGATAACCAC-TT
*
1806 T-TGAAAATTTGATAACCTCTT
1 TATGAAAATTTGATAACCACTT
* *
1827 TATGAAATTTTGATAACCACTC
1 TATGAAAATTTGATAACCACTT
* * * *
1849 TAT-AAAATTTTGTTGACCCCTC
1 TATGAAAA-TTTGATAACCACTT
* * *
1871 TATGAAATTTTGATAATCACAT
1 TATGAAAATTTGATAACCACTT
* *
1893 TATGTAATTTTGATAACC
1 TATGAAAATTTGATAACC
1911 TCGTTTTAAA
Statistics
Matches: 82, Mismatches: 20, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
21 6 0.07
22 72 0.88
23 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAAATTTGATAACCACTT
Found at i:1833 original size:44 final size:44
Alignment explanation
Indices: 1783--1927 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 44
1773 GAAATACCAC
* *
1783 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
* * * * *
1827 TATGAAATTTTGATAACCAC-TCTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACAT-TATGAAAA-TTTGATAACCTCTT
* *
1871 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGTT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-TT
*
1916 T-TAAAATTTTGA
1 TATGAAATTTTGA
1928 AATTGGACCA
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
43 5 0.06
44 71 0.88
45 5 0.06
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
Found at i:3162 original size:2 final size:2
Alignment explanation
Indices: 3155--3194 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3145 AGTTTTAAGG
*
3155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3195 CACACACACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4609 original size:2 final size:2
Alignment explanation
Indices: 4602--4636 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4592 TTAATAGGTA
4602 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 A
4637 GTAATCTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8713 original size:40 final size:38
Alignment explanation
Indices: 8668--8746 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 38
8658 TGAGATTAGT
*
8668 TTTTGTAATTTGATATGTTTTAGTAGTTTTTAGTTTTATG
1 TTTTGTAATTTAATATG-TTTAGTAG-TTTTAGTTTTATG
*
8708 TTTTGTAGTTTAATATGTTTAGTAGTTTTAGTTTTATG
1 TTTTGTAATTTAATATGTTTAGTAGTTTTAGTTTTATG
8746 T
1 T
8747 ATGTTTTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 14 0.38
39 8 0.22
40 15 0.41
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.62
Consensus pattern (38 bp):
TTTTGTAATTTAATATGTTTAGTAGTTTTAGTTTTATG
Found at i:8726 original size:17 final size:15
Alignment explanation
Indices: 8693--8742 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 15
8683 TGTTTTAGTA
8693 GTTTT-TAGTTTTAT
1 GTTTTGTAGTTTTAT
8707 GTTTTGTAGTTTAATAT
1 GTTTTGTAGTTT--TAT
*
8724 GTTTAGTAGTTTTA-
1 GTTTTGTAGTTTTAT
8738 GTTTT
1 GTTTT
8743 ATGTATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 9 0.29
15 8 0.26
17 14 0.45
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (15 bp):
GTTTTGTAGTTTTAT
Found at i:9252 original size:2 final size:2
Alignment explanation
Indices: 9245--9284 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
9235 GAATACATAC
9245 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
9285 GATTAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9832 original size:14 final size:15
Alignment explanation
Indices: 9813--9841 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9803 TGACAATTGC
9813 GACTGTAAC-AAAAA
1 GACTGTAACGAAAAA
9827 GACTGTAACGAAAAA
1 GACTGTAACGAAAAA
9842 ACTATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (15 bp):
GACTGTAACGAAAAA
Found at i:10104 original size:17 final size:17
Alignment explanation
Indices: 10082--10116 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
10072 GTCCCGTGTC
10082 TCTGGTATTATATCTTA
1 TCTGGTATTATATCTTA
10099 TCTGGTATTATATCTTA
1 TCTGGTATTATATCTTA
10116 T
1 T
10117 TTGTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.54
Consensus pattern (17 bp):
TCTGGTATTATATCTTA
Found at i:12310 original size:48 final size:48
Alignment explanation
Indices: 12255--12350 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
12245 GTTGTTGCTT
12255 TGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGA
1 TGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGA
12303 TGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGA
1 TGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGA
12351 AAAACTTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (48 bp):
TGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGA
Found at i:14796 original size:7 final size:6
Alignment explanation
Indices: 14774--14827 Score: 58
Period size: 6 Copynumber: 8.8 Consensus size: 6
14764 AAAGAAGATG
*
14774 AGAAAA AGAAAA A-AAAA TGAAAA AGAAAA ACGAAAAA ACGAAAA A-AAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A-G-AAAA A-GAAAA AGAAAA
14823 AGAAA
1 AGAAA
14828 TATAAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 9 0.21
6 20 0.48
7 6 0.14
8 7 0.17
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:17203 original size:26 final size:26
Alignment explanation
Indices: 17167--17288 Score: 140
Period size: 26 Copynumber: 4.7 Consensus size: 26
17157 TCGCACGCGC
17167 GAGGTCACGTGTGGAGTTGTAC-TTCG
1 GAGGTCACGTGTGGAGTTGTACGTT-G
* * *
17193 GAGGTCACGTGTTGAAGGTGTCCGTTG
1 GAGGTCACGTG-TGGAGTTGTACGTTG
* *
17220 GAGGTCATGTGCGGAGTTGTAC-TTCG
1 GAGGTCACGTGTGGAGTTGTACGTT-G
* *
17246 GAGGTCACGTGTGGGGTCGTACGTTG
1 GAGGTCACGTGTGGAGTTGTACGTTG
17272 GAGGTCACGTGTGGAGT
1 GAGGTCACGTGTGGAGT
17289 GCCAGCTGGC
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.03
26 54 0.68
27 21 0.27
28 2 0.03
ACGTcount: A:0.15, C:0.15, G:0.42, T:0.29
Consensus pattern (26 bp):
GAGGTCACGTGTGGAGTTGTACGTTG
Found at i:17247 original size:53 final size:52
Alignment explanation
Indices: 17167--17288 Score: 183
Period size: 53 Copynumber: 2.3 Consensus size: 52
17157 TCGCACGCGC
*
17167 GAGGTCACGTGTGGAGTTGTACTTCGGAGGTCACGTGTTGAAGGT-GTCCGTTG
1 GAGGTCACGTGTGGAGTTGTACTTCGGAGGTCACGTG-TG-AGGTCGTACGTTG
* * *
17220 GAGGTCATGTGCGGAGTTGTACTTCGGAGGTCACGTGTGGGGTCGTACGTTG
1 GAGGTCACGTGTGGAGTTGTACTTCGGAGGTCACGTGTGAGGTCGTACGTTG
17272 GAGGTCACGTGTGGAGT
1 GAGGTCACGTGTGGAGT
17289 GCCAGCTGGC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
51 3 0.05
52 24 0.39
53 35 0.56
ACGTcount: A:0.15, C:0.15, G:0.42, T:0.29
Consensus pattern (52 bp):
GAGGTCACGTGTGGAGTTGTACTTCGGAGGTCACGTGTGAGGTCGTACGTTG
Found at i:17281 original size:12 final size:13
Alignment explanation
Indices: 17245--17287 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
17235 GTTGTACTTC
17245 GGAGGTCACGTGT
1 GGAGGTCACGTGT
17258 GG-GGTCGTACGT-T
1 GGAGGTC--ACGTGT
17271 GGAGGTCACGTGT
1 GGAGGTCACGTGT
17284 GGAG
1 GGAG
17288 TGCCAGCTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 8 0.31
13 10 0.38
14 8 0.31
ACGTcount: A:0.14, C:0.14, G:0.49, T:0.23
Consensus pattern (13 bp):
GGAGGTCACGTGT
Found at i:17354 original size:23 final size:23
Alignment explanation
Indices: 17328--17460 Score: 176
Period size: 23 Copynumber: 5.7 Consensus size: 23
17318 CTTGTGGTCA
*
17328 TAAGTGGTCGGGCGCCAGGCTTG
1 TAAGTGGTCGGGCGCTAGGCTTG
*
17351 TAAGTGGTCGGTCGCTAGGCTTTG
1 TAAGTGGTCGGGCGCTAGGC-TTG
*
17375 TAAGTGGTCGGTCGCTAGGCTTG
1 TAAGTGGTCGGGCGCTAGGCTTG
* *
17398 TAAGTGGTCGGTCGTTAGGCTTG
1 TAAGTGGTCGGGCGCTAGGCTTG
* **
17421 TAAGTGGTCGGGCGTTAATCTTG
1 TAAGTGGTCGGGCGCTAGGCTTG
*
17444 GAAGTGGTCGGGCGCTA
1 TAAGTGGTCGGGCGCTA
17461 AGCCATTGTG
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
23 78 0.77
24 23 0.23
ACGTcount: A:0.14, C:0.17, G:0.40, T:0.29
Consensus pattern (23 bp):
TAAGTGGTCGGGCGCTAGGCTTG
Found at i:17495 original size:108 final size:109
Alignment explanation
Indices: 17361--17580 Score: 379
Period size: 108 Copynumber: 2.0 Consensus size: 109
17351 TAAGTGGTCG
* *
17361 GTCGCTAGGCTTTGTAAGTGGTCGGTCGCTAGGCTTGTAAGTGGTCGGTCGTTAGGCTTGTAAGT
1 GTCGCTAGGCTTTGTAAGTGGTCGGTCGCTAGGCTTGTAAGTGGTCGGTCGTTAGGCTCGCAAGT
* *
17426 GGTCGGGCGTTAATCTTGGAAGTGGTCGGGCGCTAAGCCATTGT
66 GGTCAGGCGTTAATCTTGGAAGTGGTCGGGCACTAAGCCATTGT
17470 GTCGCTAGGC-TTGTAAGTGGTCGGTCGCTAGGCTTGTAAGTGGTCGGTCGTTAGGCTCGCAAGT
1 GTCGCTAGGCTTTGTAAGTGGTCGGTCGCTAGGCTTGTAAGTGGTCGGTCGTTAGGCTCGCAAGT
* *
17534 GGTTAGGTGTTAATCTTGGAAGTGGTCGGGCACTAAGCCATTGT
66 GGTCAGGCGTTAATCTTGGAAGTGGTCGGGCACTAAGCCATTGT
17578 GTC
1 GTC
17581 ATGCTCAACA
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
108 95 0.90
109 10 0.10
ACGTcount: A:0.15, C:0.17, G:0.37, T:0.31
Consensus pattern (109 bp):
GTCGCTAGGCTTTGTAAGTGGTCGGTCGCTAGGCTTGTAAGTGGTCGGTCGTTAGGCTCGCAAGT
GGTCAGGCGTTAATCTTGGAAGTGGTCGGGCACTAAGCCATTGT
Found at i:17496 original size:23 final size:23
Alignment explanation
Indices: 17470--17536 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
17460 AAGCCATTGT
17470 GTCGCTAGGCTTGTAAGTGGTCG
1 GTCGCTAGGCTTGTAAGTGGTCG
17493 GTCGCTAGGCTTGTAAGTGGTCG
1 GTCGCTAGGCTTGTAAGTGGTCG
* * *
17516 GTCGTTAGGCTCGCAAGTGGT
1 GTCGCTAGGCTTGTAAGTGGT
17537 TAGGTGTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.13, C:0.18, G:0.39, T:0.30
Consensus pattern (23 bp):
GTCGCTAGGCTTGTAAGTGGTCG
Found at i:18023 original size:18 final size:19
Alignment explanation
Indices: 17988--18023 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17978 TACACCCTTC
*
17988 CTTTTTTTTTTTGGGAATT
1 CTTTTTTTTTTTGAGAATT
18007 CTTTTTTTTTTT-AGAAT
1 CTTTTTTTTTTTGAGAAT
18024 CAAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (19 bp):
CTTTTTTTTTTTGAGAATT
Done.