Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020779.1 Corchorus olitorius cultivar O-4 contig20812, 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: 112636
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:2146 original size:67 final size:65
Alignment explanation
Indices: 2043--2176 Score: 196
Period size: 67 Copynumber: 2.0 Consensus size: 65
2033 TGAAAAACGG
* *
2043 AAAAAAATGGCACTTATTTCCTCTCCACACAAACACTTATTTCCCTTCTCTTTCTTTGATCTAAA
1 AAAAAAATGGCACTTATTTCCACTCCACACAAACACTTATTTCCCTTCTCTTTCTTTGAACTAAA
* * * *
2108 AAAAAAAGTGGACCCTTATTTCCACTCTATACAAACACTTATTTCCCTTCTCTTTCTTTTAACTA
1 AAAAAAA-TGG-CACTTATTTCCACTCCACACAAACACTTATTTCCCTTCTCTTTCTTTGAACTA
2173 AA
64 AA
2175 AA
1 AA
2177 TCAAACACAC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 7 0.11
66 3 0.05
67 51 0.84
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (65 bp):
AAAAAAATGGCACTTATTTCCACTCCACACAAACACTTATTTCCCTTCTCTTTCTTTGAACTAAA
Found at i:3078 original size:71 final size:71
Alignment explanation
Indices: 2989--3129 Score: 255
Period size: 71 Copynumber: 2.0 Consensus size: 71
2979 CACGTTAGCA
* *
2989 GAGTTGATGAGGTCACTGCCACGTAGGCCAATTTAACAGATCCTCTGACGGCTTGTAACGAAACG
1 GAGTTGACGAGGTCACTGCCACGTAGGCCAATTTAACAGATCCTCTGACGGCTTGTAACGAAACA
3054 GACCTG
66 GACCTG
*
3060 GAGTTGACGAGTTCACTGCCACGTAGGCCAATTTAACAGATCCTCTGACGGCTTGTAACGAAACA
1 GAGTTGACGAGGTCACTGCCACGTAGGCCAATTTAACAGATCCTCTGACGGCTTGTAACGAAACA
3125 GACCT
66 GACCT
3130 ATTGCTCGGT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (71 bp):
GAGTTGACGAGGTCACTGCCACGTAGGCCAATTTAACAGATCCTCTGACGGCTTGTAACGAAACA
GACCTG
Found at i:5493 original size:98 final size:95
Alignment explanation
Indices: 5327--5514 Score: 245
Period size: 98 Copynumber: 1.9 Consensus size: 95
5317 TTTTATATTA
* *
5327 ACTTCAACTGAAGTTAACTTTTATTTTGATTCAATCAAAATTGATCATTAAGGGACAAAACTGCA
1 ACTTCAACTGAAGTTAACTTTTATTTCGATTCAATCAAAATTGATCATTAAGGGACAAAACTACA
*
5392 ATTG-TGAATAATCTTTTAGAAATATGGTGC
66 ATTGCT-AATAATCTATTAGAAATATGGTGC
* * * *
5422 ACTTCAATTGAATTTAA-TCTTTATTTCGATTTAATCAATATACTTGATCATTAATGGACAAAAC
1 ACTTCAACTGAAGTTAACT-TTTATTTCGATTCAATCAA-A-A-TTGATCATTAAGGGACAAAAC
*
5486 TACAATTGCTACTAATCTATTAGAAATAT
62 TACAATTGCTAATAATCTATTAGAAATAT
5515 TATGCTTCCT
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
94 1 0.01
95 32 0.40
96 1 0.01
97 1 0.01
98 44 0.55
99 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (95 bp):
ACTTCAACTGAAGTTAACTTTTATTTCGATTCAATCAAAATTGATCATTAAGGGACAAAACTACA
ATTGCTAATAATCTATTAGAAATATGGTGC
Found at i:7275 original size:85 final size:85
Alignment explanation
Indices: 7174--7344 Score: 279
Period size: 85 Copynumber: 2.0 Consensus size: 85
7164 TAATTAAATT
* * *
7174 AGTAATATTGTAAAAATAAAATAGGCATAAGGATATTAGATTTAATCAAATAAAAATAGAGTTTT
1 AGTAAAATGGTAAAAATAAAATAGGCATAAGGATATTAGATGTAATCAAATAAAAATAGAGTTTT
*
7239 TAGTTGAGTAAAACTATAAA
66 TAGTTGACTAAAACTATAAA
** *
7259 AGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATGTAATTAAATAAAAATAGAGTTTT
1 AGTAAAATGGTAAAAATAAAATAGGCATAAGGATATTAGATGTAATCAAATAAAAATAGAGTTTT
7324 TAGTTGACTAAAACTATAAA
66 TAGTTGACTAAAACTATAAA
7344 A
1 A
7345 ATTTAAATAA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (85 bp):
AGTAAAATGGTAAAAATAAAATAGGCATAAGGATATTAGATGTAATCAAATAAAAATAGAGTTTT
TAGTTGACTAAAACTATAAA
Found at i:7404 original size:27 final size:28
Alignment explanation
Indices: 7372--7437 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 28
7362 TAAGAAATAT
*
7372 ATTCAAAA-AATAAGGATACGATAGGCG
1 ATTCAAAATAATAAGGATACAATAGGCG
*
7399 ATTCAAAAGTTTAATAAGGATATAATAGGCG
1 ATTCAAAA---TAATAAGGATACAATAGGCG
7430 ATTCAAAA
1 ATTCAAAA
7438 GTTTTACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 8 0.24
31 25 0.76
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.24
Consensus pattern (28 bp):
ATTCAAAATAATAAGGATACAATAGGCG
Found at i:7418 original size:31 final size:31
Alignment explanation
Indices: 7380--7441 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
7370 ATATTCAAAA
*
7380 AATAAGGATACGATAGGCGATTCAAAAGTTT
1 AATAAGGATACAATAGGCGATTCAAAAGTTT
*
7411 AATAAGGATATAATAGGCGATTCAAAAGTTT
1 AATAAGGATACAATAGGCGATTCAAAAGTTT
7442 TACAAAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (31 bp):
AATAAGGATACAATAGGCGATTCAAAAGTTT
Found at i:9043 original size:31 final size:31
Alignment explanation
Indices: 9005--9108 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 31
8995 AACTTACGCC
*
9005 AGGCCCTTATTTGAGTATTTTCGATAACATT
1 AGGCCCTTATTTGAGTAATTTCGATAACATT
* * ** *
9036 AGGCCCTTATTTG-GTCAAATT--AAAAGGTC
1 AGGCCCTTATTTGAGT-AATTTCGATAACATT
* * *
9065 GGGCCCTTATTTGAGCAGTTTCGATAACATT
1 AGGCCCTTATTTGAGTAATTTCGATAACATT
*
9096 AGGCTCTTATTTG
1 AGGCCCTTATTTG
9109 GCCAAATTAA
Statistics
Matches: 53, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
29 19 0.36
30 3 0.06
31 31 0.58
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (31 bp):
AGGCCCTTATTTGAGTAATTTCGATAACATT
Found at i:9099 original size:60 final size:60
Alignment explanation
Indices: 9006--9168 Score: 222
Period size: 60 Copynumber: 2.7 Consensus size: 60
8996 ACTTACGCCA
* * **
9006 GGCCCTTATTTGAGTATTTTCGATAACATTAGGCCCTTATTTGGTCAAATTAAAAGGTCG
1 GGCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGACCG
* *
9066 GGCCCTTATTTGAGCAGTTTCGATAACATTAGGCTCTTATTTGGCCAAATTAAAAGACCG
1 GGCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGACCG
* *
9126 GGCCCTTATTTGAACATTTTAGCA-AA-AGTTAGGCCCTTATTTG
1 GGCCCTTATTTGAGCATTTTCG-ATAACA-TTAGGCCCTTATTTG
9169 AGGAATTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
59 1 0.01
60 89 0.98
61 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGACCG
Found at i:9238 original size:22 final size:22
Alignment explanation
Indices: 9212--9260 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
9202 GAATTTCGAA
* *
9212 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTCTTATGAAA-TTTTGTT
9234 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
9256 AACCT
1 AACCT
9261 CTCTAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:9435 original size:22 final size:22
Alignment explanation
Indices: 9397--9471 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
9387 AAAACCTCCA
* *
9397 TATG-AATTGTTAGTAATCACAT
1 TATGAAATTGTGA-TAATCACAC
* * *
9419 TCTGAAATTTTGATAATCATAC
1 TATGAAATTGTGATAATCACAC
* * *
9441 TATGAAATTGTGATAACCTCGC
1 TATGAAATTGTGATAATCACAC
9463 TATGAAATT
1 TATGAAATT
9472 TTAATAAACC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 35 0.85
23 6 0.15
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:9488 original size:23 final size:22
Alignment explanation
Indices: 9423--9523 Score: 105
Period size: 22 Copynumber: 4.5 Consensus size: 22
9413 TCACATTCTG
* * * *
9423 AAATTTTGATAATCATACTATG
1 AAATTTTGATAACCTTCCTATA
* *
9445 AAATTGTGATAACC-TCGCTATG
1 AAATTTTGATAACCTTC-CTATA
*
9467 AAATTTTAATAAACCTTCCTATA
1 AAATTTTGAT-AACCTTCCTATA
*
9490 AAATTTTGATAACCTCCCTATA
1 AAATTTTGATAACCTTCCTATA
9512 AAATTTTGATAA
1 AAATTTTGATAA
9524 TGCCCTTATG
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.01
22 48 0.71
23 17 0.25
24 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTTCCTATA
Found at i:9537 original size:22 final size:21
Alignment explanation
Indices: 9423--9547 Score: 83
Period size: 22 Copynumber: 5.7 Consensus size: 21
9413 TCACATTCTG
* *
9423 AAATTTTGATAA-TCATACTATG
1 AAATTTTGATAACTC--CCTATA
* * *
9445 AAATTGTGATAACCTCGCTATG
1 AAATTTTGATAA-CTCCCTATA
* *
9467 AAATTTTAATAAACCTTCCTATA
1 AAATTTTGAT-AA-CTCCCTATA
9490 AAATTTTGATAACCTCCCTATA
1 AAATTTTGATAA-CTCCCTATA
*
9512 AAATTTTGATAA-TGCCCTTATG
1 AAATTTTGATAACT-CCC-TATA
*
9534 AAATCTTGATAACT
1 AAATTTTGATAACT
9548 ACAAATTTTG
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 61 0.71
23 19 0.22
24 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
AAATTTTGATAACTCCCTATA
Found at i:11226 original size:47 final size:47
Alignment explanation
Indices: 11157--11246 Score: 180
Period size: 47 Copynumber: 1.9 Consensus size: 47
11147 CTGCCAAACA
11157 AAAAAAAATTAACAAAGAACCAAAGAAATATAGAGGGAAAATAGATT
1 AAAAAAAATTAACAAAGAACCAAAGAAATATAGAGGGAAAATAGATT
11204 AAAAAAAATTAACAAAGAACCAAAGAAATATAGAGGGAAAATA
1 AAAAAAAATTAACAAAGAACCAAAGAAATATAGAGGGAAAATA
11247 TATCAGAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.13
Consensus pattern (47 bp):
AAAAAAAATTAACAAAGAACCAAAGAAATATAGAGGGAAAATAGATT
Found at i:14228 original size:15 final size:16
Alignment explanation
Indices: 14200--14229 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14190 TTTTTTTTTC
14200 CTATACTCATATATAT
1 CTATACTCATATATAT
14216 CTATACT-ATATATA
1 CTATACTCATATATA
14230 AAAGTACGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (16 bp):
CTATACTCATATATAT
Found at i:15328 original size:25 final size:24
Alignment explanation
Indices: 15278--15329 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
15268 CCTTGAATTT
* *
15278 TTTAATGTTTAATTCTTAAATTTA
1 TTTAATGTTTAATTATTAAATCTA
*
15302 TTTAATGTCTTAATTATTCAATCTA
1 TTTAATGT-TTAATTATTAAATCTA
15327 TTT
1 TTT
15330 TACAATTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTAATGTTTAATTATTAAATCTA
Found at i:16563 original size:15 final size:16
Alignment explanation
Indices: 16543--16574 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16533 CCTTGATATG
16543 TTATACT-AAAATACA
1 TTATACTAAAAATACA
16558 TTATACTAAAAATACA
1 TTATACTAAAAATACA
16574 T
1 T
16575 AATTTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (16 bp):
TTATACTAAAAATACA
Found at i:17786 original size:13 final size:13
Alignment explanation
Indices: 17768--17796 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17758 CAAAACTTTA
17768 TCTTCTAAAGTTT
1 TCTTCTAAAGTTT
17781 TCTTCTAAAGTTT
1 TCTTCTAAAGTTT
17794 TCT
1 TCT
17797 CTTACCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.55
Consensus pattern (13 bp):
TCTTCTAAAGTTT
Found at i:19921 original size:59 final size:59
Alignment explanation
Indices: 19772--19940 Score: 207
Period size: 59 Copynumber: 2.8 Consensus size: 59
19762 CTTACACCAT
* * * * *
19772 GCCCTTATTTGAGCATTTTCGATAACATTAGACCCTTATTTGGTCAAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGG-CCAATTAAAAGACCGA
* *
19832 GTCCTTATTTGAGCATTTTCGATAAAGTTAGGCCCTTATTTGGCCAATTAAAAGACCGA
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAATTAAAAGACCGA
** *
19891 GCCCTTATTTGAAAATTTTGGCA-AACGTTAGGCCCTTATTTGAG-CAATTA
1 GCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG-GCCAATTA
19941 GCCAAATTTT
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
59 54 0.57
60 41 0.43
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (59 bp):
GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAATTAAAAGACCGA
Found at i:20005 original size:22 final size:22
Alignment explanation
Indices: 19967--20023 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
19957 GACACTATTG
**
19967 AATTTTGAGAACCTTTTTAT-A
1 AATTTTGTTAACCTTTTTATGA
*
19988 AATTTTTTTAACCTTTTTATGA
1 AATTTTGTTAACCTTTTTATGA
20010 AATTTTGTTAACCT
1 AATTTTGTTAACCT
20024 CCCTAAGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (22 bp):
AATTTTGTTAACCTTTTTATGA
Found at i:20239 original size:22 final size:22
Alignment explanation
Indices: 20005--20347 Score: 178
Period size: 22 Copynumber: 15.8 Consensus size: 22
19995 TTAACCTTTT
* *
20005 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
20027 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTCAC
*
20049 TATGAAATTTTGATAA-CTTACC
1 TATGAAATTTTGATAACCTCA-C
* * *
20071 AATGAAAATTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* * *
20094 TATGAGATGTCGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * **
20115 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCAC
* * *
20138 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * *
20159 ATATG-AATTGTTAATAATCACAC
1 -TATGAAATT-TTGATAACCTCAC
* *
20182 TTTGAAATTTTGATAATCAT-AC
1 TATGAAATTTTGATAA-CCTCAC
*
20204 TATGAAATTGTGATAACCTCAC
1 TATGAAATTTTGATAACCTCAC
*
20226 TATGAAATTTTGATAAACATTC-C
1 TATGAAATTTTGAT-AAC-CTCAC
*
20249 TAT-AAATTTTTGATAACCTCCC
1 TATGAAA-TTTTGATAACCTCAC
* *
20271 TATAAAATTTTGAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
*
20292 TTATGAAATCTTGATAA-CT-AC
1 -TATGAAATTTTGATAACCTCAC
20313 ----AAATTTTGATAACCTTC-C
1 TATGAAATTTTGATAACC-TCAC
**
20331 TATGATTTTTTGATAAC
1 TATGAAATTTTGATAAC
20348 TTCCCTCAAA
Statistics
Matches: 243, Mismatches: 51, Indels: 54
0.70 0.15 0.16
Matches are distributed among these distances:
16 11 0.05
17 1 0.00
18 2 0.01
21 16 0.07
22 172 0.71
23 38 0.16
24 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:20279 original size:45 final size:44
Alignment explanation
Indices: 20186--20309 Score: 128
Period size: 45 Copynumber: 2.8 Consensus size: 44
20176 TCACACTTTG
* *
20186 AAATTTTGATAATCATACTATGAAATTGTGATAACCTCACTATG
1 AAATTTTGATAAACATACTATGAAATTGTGATAACCTCACTATA
* * *
20230 AAATTTTGATAAACATTCCTAT-AAATTTTTGATAACCTCCCTATA
1 AAATTTTGATAAACA-TACTATGAAA-TTGTGATAACCTCACTATA
* *
20275 AAATTTTGA-AAACCTCCTTATGAAATCT-TGATAAC
1 AAATTTTGATAAACATAC-TATGAAAT-TGTGATAAC
20310 TACAAATTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
43 3 0.04
44 32 0.46
45 34 0.49
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (44 bp):
AAATTTTGATAAACATACTATGAAATTGTGATAACCTCACTATA
Found at i:28564 original size:10 final size:10
Alignment explanation
Indices: 28549--28575 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
28539 CGAGAGAAAG
28549 AAAAAAAGAA
1 AAAAAAAGAA
28559 AAAAAAAGAA
1 AAAAAAAGAA
28569 AAAAAAA
1 AAAAAAA
28576 TTAAGGCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:32205 original size:29 final size:29
Alignment explanation
Indices: 32170--32228 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
32160 AAATTCATGA
32170 GGCAAAGTGGCACAATTTAAAGTTCAGGG
1 GGCAAAGTGGCACAATTTAAAGTTCAGGG
*
32199 GGCAAAGTGGCACAATTTAAAGTTTAGGG
1 GGCAAAGTGGCACAATTTAAAGTTCAGGG
32228 G
1 G
32229 ACAACTTGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (29 bp):
GGCAAAGTGGCACAATTTAAAGTTCAGGG
Found at i:44783 original size:60 final size:60
Alignment explanation
Indices: 44715--44835 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
44705 TGAACGATTT
*
44715 GAAAACGGTTTTTGTAGATTTTGATTTGGGAAGTTGTGTTGAGGCAAATGTAGATGCATG
1 GAAAACGGTTTTTGTAGATTTTGATTTGGGAAGTGGTGTTGAGGCAAATGTAGATGCATG
44775 GAAAACGGTTTTTGTAGATTTTGATTTGGGAAGTGGTGTTGAGGCAAATGTAGATGCATG
1 GAAAACGGTTTTTGTAGATTTTGATTTGGGAAGTGGTGTTGAGGCAAATGTAGATGCATG
44835 G
1 G
44836 TATGAAATTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.36
Consensus pattern (60 bp):
GAAAACGGTTTTTGTAGATTTTGATTTGGGAAGTGGTGTTGAGGCAAATGTAGATGCATG
Found at i:64182 original size:37 final size:37
Alignment explanation
Indices: 64132--64208 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
64122 TGATGGAATC
*
64132 ACTCAAGGCCCAAAGAAACGATCGCTTTTCATGGCAA
1 ACTCAAGGCCCAAAGAAACGATCGATTTTCATGGCAA
*
64169 ACTCAAGGCCCAAAGAAACGATCGATTTTCATGGTAA
1 ACTCAAGGCCCAAAGAAACGATCGATTTTCATGGCAA
64206 ACT
1 ACT
64209 TTCAAGAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (37 bp):
ACTCAAGGCCCAAAGAAACGATCGATTTTCATGGCAA
Found at i:94988 original size:77 final size:77
Alignment explanation
Indices: 94861--95014 Score: 245
Period size: 77 Copynumber: 2.0 Consensus size: 77
94851 GGATTCGAAG
** * *
94861 GTCTGCTAAACCAATCTTGTTCTCCATATATCTTAAATATTGTTGGTTGCTTTTTATGTGCATCT
1 GTCTGCTAAACCAATCCCGTTCTCCATATATCTTAAATATTGTTAGTTGCTTTTTACGTGCATCT
94926 TGATCATTTGTT
66 TGATCATTTGTT
* * *
94938 GTCTGCTAAACCAATCCCGTTCTCCATATATCTTAAGTATTGTTAGTTGCTTTTTCCGTGCTTCT
1 GTCTGCTAAACCAATCCCGTTCTCCATATATCTTAAATATTGTTAGTTGCTTTTTACGTGCATCT
95003 TGATCATTTGTT
66 TGATCATTTGTT
95015 CATTTGGACT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (77 bp):
GTCTGCTAAACCAATCCCGTTCTCCATATATCTTAAATATTGTTAGTTGCTTTTTACGTGCATCT
TGATCATTTGTT
Found at i:99182 original size:20 final size:20
Alignment explanation
Indices: 99157--99194 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
99147 GTTTTGTGGG
*
99157 TTTCATATTTGTGCATTACA
1 TTTCATATTGGTGCATTACA
*
99177 TTTCATGTTGGTGCATTA
1 TTTCATATTGGTGCATTA
99195 TGGGAGCAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTCATATTGGTGCATTACA
Found at i:102025 original size:11 final size:11
Alignment explanation
Indices: 102009--102033 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
101999 TAAAGCTATC
102009 ATTGCTTTATG
1 ATTGCTTTATG
102020 ATTGCTTTATG
1 ATTGCTTTATG
102031 ATT
1 ATT
102034 AAATTGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (11 bp):
ATTGCTTTATG
Found at i:107599 original size:5 final size:5
Alignment explanation
Indices: 107591--107615 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
107581 CTTATGCCTT
107591 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
107616 AACTTTGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Done.