Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024061.1 Corchorus olitorius cultivar O-4 contig24094, 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: 27676
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Found at i:2493 original size:18 final size:15
Alignment explanation
Indices: 2448--2499 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
2438 TGCTAGGGTG
2448 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
2463 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
* *
2478 AATGGTGCGAATAAC
1 AATGGTGCAAACAAC
2493 AATGGTG
1 AATGGTG
2500 TGAACAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.17
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:14395 original size:125 final size:124
Alignment explanation
Indices: 14243--14652 Score: 583
Period size: 125 Copynumber: 3.3 Consensus size: 124
14233 TTCTAAATAC
* *
14243 AATAGCGGCGTTTCTGATG-CATAACGCCGCTAAATAGTGGCGTTTCTAAAGTAAACGCCGCTAT
1 AATAGCGGCGTTTCTCATGACA-GACGCCGCTAAATAGTGGCGTTTCTAAA-TAAACGCCGCTAT
14307 ATATAATGTTTTCCAAAGAATAGAAATTTGGTGAAACTAAAAACACAATTTCTTTGTTATG
64 ATATAATGTTTTCCAAAGAATAGAAATTTGGTGAAACTAAAAACACAATTTCTTTGTTATG
* * *
14368 AATAGCAGCGTTTCTCATGACAGACGCCGCTAAATAGTGGCGTTTCTAAAATAAACACTGCTATA
1 AATAGCGGCGTTTCTCATGACAGACGCCGCTAAATAGTGGCGTTTCT-AAATAAACGCCGCTATA
*
14433 TATAATGTTTTCCGAAA-AATAGAAATTTGGTGAAACTAAAAACGCAATTTCTTTGTTATG
65 TATAATGTTTTCC-AAAGAATAGAAATTTGGTGAAACTAAAAACACAATTTCTTTGTTATG
* * * * * *
14493 AATAGCGGCGTTTCTCATGACAGACTCCACTAAATAGTGACATTTTTATAAAAAACGCCGCTA-A
1 AATAGCGGCGTTTCTCATGACAGACGCCGCTAAATAGTGGCGTTTCTA-AATAAACGCCGCTATA
* * * * *
14557 TATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTTGATATG
65 TATAATGTTTTCCAAAGAATAGAAATTTGGTGAAACTAAAAACACAATTTCTTTGTTATG
* *
14617 AATCGCGGCGTTTCTCATGACGGACGCCGCTAAATA
1 AATAGCGGCGTTTCTCATGACAGACGCCGCTAAATA
14653 TAATCTTCTA
Statistics
Matches: 255, Mismatches: 25, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
123 3 0.01
124 84 0.33
125 160 0.63
126 8 0.03
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (124 bp):
AATAGCGGCGTTTCTCATGACAGACGCCGCTAAATAGTGGCGTTTCTAAATAAACGCCGCTATAT
ATAATGTTTTCCAAAGAATAGAAATTTGGTGAAACTAAAAACACAATTTCTTTGTTATG
Found at i:14719 original size:94 final size:93
Alignment explanation
Indices: 14547--14724 Score: 329
Period size: 94 Copynumber: 1.9 Consensus size: 93
14537 TTTATAAAAA
14547 ACGCCGCTAATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTTG
1 ACGCCGCTAATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTTG
*
14612 ATATGAATCGCGGCGTTTCTCATGACGG
66 ATATGAATAGCGGCGTTTCTCATGACGG
14640 ACGCCGCTAAATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTT
1 ACGCCGCT-AATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTT
*
14705 GTTATGAATAGCGGCGTTTC
65 GATATGAATAGCGGCGTTTC
14725 AGTACAGAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
93 8 0.10
94 74 0.90
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (93 bp):
ACGCCGCTAATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTTG
ATATGAATAGCGGCGTTTCTCATGACGG
Found at i:14829 original size:32 final size:32
Alignment explanation
Indices: 14793--14917 Score: 97
Period size: 32 Copynumber: 3.8 Consensus size: 32
14783 TTTAAGTTCA
14793 GAAACGCCACTAAATAGCGGCGTTTCTGTACG
1 GAAACGCCACTAAATAGCGGCGTTTCTGTACG
** *
14825 GAAACGCCACTATTTTTAGCGGCGTTTCGGTACAG
1 GAAACGCCACTA--AATAGCGGCGTTTCTGTAC-G
* * ** * * *
14860 AAAACGCCGCTATTTAGTGGCGTTTCTGAACA
1 GAAACGCCACTAAATAGCGGCGTTTCTGTACG
* * * *
14892 TAAACGCCGCTAAACAGTGGCGTTTC
1 GAAACGCCACTAAATAGCGGCGTTTC
14918 GGTAAAAAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
32 34 0.44
33 16 0.21
34 16 0.21
35 11 0.14
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (32 bp):
GAAACGCCACTAAATAGCGGCGTTTCTGTACG
Found at i:14850 original size:34 final size:33
Alignment explanation
Indices: 14794--14887 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 33
14784 TTAAGTTCAG
** *
14794 AAACGCCACTAAATAGCGGCGTTTCTGTAC-GG
1 AAACGCCACTATTTAGCGGCGTTTCTGTACAGA
*
14826 AAACGCCACTATTTTTAGCGGCGTTTCGGTACAGA
1 AAACGCCACTA--TTTAGCGGCGTTTCTGTACAGA
* *
14861 AAACGCCGCTATTTAGTGGCGTTTCTG
1 AAACGCCACTATTTAGCGGCGTTTCTG
14888 AACATAAACG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 11 0.21
33 14 0.27
34 16 0.31
35 11 0.21
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.28
Consensus pattern (33 bp):
AAACGCCACTATTTAGCGGCGTTTCTGTACAGA
Found at i:14882 original size:33 final size:33
Alignment explanation
Indices: 14811--14921 Score: 100
Period size: 32 Copynumber: 3.4 Consensus size: 33
14801 ACTAAATAGC
* * * *
14811 GGCGTTTCTGTAC-GGAAACGCCACTATTTTTAGC
1 GGCGTTTCGGTACAGAAAACGCCGCTA--TTTAGT
14845 GGCGTTTCGGTACAGAAAACGCCGCTATTTAGT
1 GGCGTTTCGGTACAGAAAACGCCGCTATTTAGT
* * * ***
14878 GGCGTTTCTGAACA-TAAACGCCGCTAAACAGT
1 GGCGTTTCGGTACAGAAAACGCCGCTATTTAGT
14910 GGCGTTTCGGTA
1 GGCGTTTCGGTA
14922 AAAAATGCCA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 24 0.38
33 17 0.27
34 12 0.19
35 11 0.17
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (33 bp):
GGCGTTTCGGTACAGAAAACGCCGCTATTTAGT
Found at i:17864 original size:51 final size:51
Alignment explanation
Indices: 17798--17894 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
17788 AATTTTTACT
* *
17798 ACAAAATTGAACTTTTATTTTTAC-TTGCATCTTTTTCT-AATTTTTTTTAAG
1 ACAAAATTGAACTTTTAATTTT-CTTTGCA-CTTTTTATCAATTTTTTTTAAG
*
17849 ACAAAATTGATCTTTTAATTTTCTTTGCACTTTTTATCAATTTTTT
1 ACAAAATTGAACTTTTAATTTTCTTTGCACTTTTTATCAATTTTTT
17895 GACAAAATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
50 8 0.20
51 33 0.80
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (51 bp):
ACAAAATTGAACTTTTAATTTTCTTTGCACTTTTTATCAATTTTTTTTAAG
Found at i:21651 original size:29 final size:29
Alignment explanation
Indices: 21605--21665 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
21595 TGTCATGGCA
* *
21605 TAATTAGCAACATGAAGAAGTATAAAATT
1 TAATTAACAACATAAAGAAGTATAAAATT
21634 TAATTAACAACATAAAGAAGTATAAAATT
1 TAATTAACAACATAAAGAAGTATAAAATT
21663 TAA
1 TAA
21666 ACATGGATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.28
Consensus pattern (29 bp):
TAATTAACAACATAAAGAAGTATAAAATT
Found at i:26008 original size:54 final size:53
Alignment explanation
Indices: 25889--26329 Score: 437
Period size: 54 Copynumber: 8.2 Consensus size: 53
25879 ACGAAAACCT
* * *
25889 TTCTTGGAGTGACCATACTGGATCAAAT-TGGAGATCAACTCTGATCATTGGAAAC
1 TTCTTGGAATGACCACACTGGATC--ATCTGGAGATCAACTCTGATC-TTGAAAAC
*
25944 TTCTT-GAACGACCACACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTT-GAAAAC
** * * * * *
25997 TTCTTAAAACGACCATACCGGATCATCTGAAGATCAACTCTGATCTTCGAAAAT
1 TTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTT-GAAAAC
* * *
26051 TTCTTGAAATGA-CAGCACCGGATCATCTGGAGATCAACTTTGATCTTTGAAAAC
1 TTCTTGGAATGACCA-CACTGGATCATCTGGAGATCAACTCTGATC-TTGAAAAC
* * **
26105 TTCTAGGAA-GAACCGCACTGGATCATCTGGAGATCAACTCTGATCATCAAAAAC
1 TTCTTGGAATG-ACCACACTGGATCATCTGGAGATCAACTCTGATC-TTGAAAAC
** * *
26159 TTCTTGGAATGACGGCACGGGATCATCT-GAGGATCAACTCTGATCAT-AAAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGA-GATCAACTCTGATCTTGAAAAC
* * * * *
26211 TTCTTGGAATGACCGCATTGGATC-TTTGGCGATCAACTCTGACCATTGAAAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATC-TTGAAAAC
* * * * *
26264 TTCTTGGAATGACCACACTGGATCTTTTGGGGATCAACTTTGACCATTGAAAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATC-TTGAAAAC
26318 TTCTTGGAATGA
1 TTCTTGGAATGA
26330 GATCAACTCT
Statistics
Matches: 334, Mismatches: 39, Indels: 27
0.83 0.10 0.07
Matches are distributed among these distances:
51 15 0.04
52 32 0.10
53 60 0.18
54 218 0.65
55 9 0.03
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (53 bp):
TTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTTGAAAAC
Found at i:26335 original size:35 final size:35
Alignment explanation
Indices: 26295--26810 Score: 642
Period size: 35 Copynumber: 14.4 Consensus size: 35
26285 ATCTTTTGGG
* * ** *
26295 GATCAACTTTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
26330 GATCAACTCTGATTATAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAATGA
*
26366 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* * *
26401 GATCAACTCTGATAATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* *
26436 GATCAACTCTGATCATCAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* *
26471 GAACAACTCTGATCATAAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* **
26506 GAACAACTCTGATCATCGAAAACTTCTT-AGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGA-AATGA
* *
26541 GATCAACTCTGATCA-ACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATA-AAAAACTTCTTGAAATGA
*
26576 GATCAACTCTGATCATAAAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
26611 GATCAACTCTGATCAATAAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATC-AT----AAAAAACTTCTTGAAATGA
**
26651 GATCAACTCTGATCATAAAAAAGAACTTCTTGAAACAA
1 GATCAACTCTGATCAT--AAAA-AACTTCTTGAAATGA
*
26689 GATCAACTCTGATCATAAAAAGAACTTCTTGAAAGGA
1 GATCAACTCTGATCAT-AAAA-AACTTCTTGAAATGA
*
26726 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
**
26761 GATCAACTCTGATCATCGAAAACTTCTT-AGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGA-AATGA
26796 GATCAACTCTGATCA
1 GATCAACTCTGATCA
26811 CCGGTTCATC
Statistics
Matches: 437, Mismatches: 32, Indels: 24
0.89 0.06 0.05
Matches are distributed among these distances:
34 2 0.00
35 292 0.67
36 39 0.09
37 41 0.09
38 30 0.07
39 2 0.00
40 31 0.07
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
Found at i:26908 original size:52 final size:53
Alignment explanation
Indices: 26828--27027 Score: 251
Period size: 54 Copynumber: 3.7 Consensus size: 53
26818 ATCTGAAAGG
* **
26828 AGATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACATCGAGTCATCTGA
1 AGATCAACT-TGATCTCTGAAAACTTCTATGAAAGACCGCATCGAGTCATCTGA
* * *
26882 AGATCAACTT-ATCTCTGAAAGCTTCTATGAAAGACCGCA-CAAGGTCATCTTA
1 AGATCAACTTGATCTCTGAAAACTTCTATGAAAGACCGCATCGA-GTCATCTGA
* * * *
26934 AAATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGGATTGGGTCATCTGA
1 AGATCAACTT-GATCTCTGAAAACTTCTATGAAAGACCGCATCGAGTCATCTGA
*
26988 AGATCAACTTAGATCTCTGAAAGCTTCTATGAAAGACCGC
1 AGATCAACTT-GATCTCTGAAAACTTCTATGAAAGACCGC
27028 CCAGGGCTTA
Statistics
Matches: 126, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
51 2 0.02
52 42 0.33
53 1 0.01
54 81 0.64
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (53 bp):
AGATCAACTTGATCTCTGAAAACTTCTATGAAAGACCGCATCGAGTCATCTGA
Found at i:26949 original size:106 final size:107
Alignment explanation
Indices: 26830--27027 Score: 310
Period size: 106 Copynumber: 1.9 Consensus size: 107
26820 CTGAAAGGAG
26830 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACATCGAGTCATCTGAAGATCAACTT-AT
1 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACATCGAGTCATCTGAAGATCAACTTAAT
26894 CTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCTTAAA
66 CTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCTTAAA
* *** * *
26936 ATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCGGATTGGGTCATCTGAAGATCAACTTAG
1 ATCAACTCT-GATCTCTAAAAACTTCTATGAAAGACAACATCGAGTCATCTGAAGATCAACTTA-
27000 ATCTCTGAAAGCTTCTATGAAAGACCGC
64 ATCTCTGAAAGCTTCTATGAAAGACCGC
27028 CCAGGGCTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
105 1 0.01
106 54 0.65
108 28 0.34
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (107 bp):
ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACATCGAGTCATCTGAAGATCAACTTAAT
CTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCTTAAA
Found at i:27044 original size:39 final size:39
Alignment explanation
Indices: 26995--27105 Score: 204
Period size: 39 Copynumber: 2.8 Consensus size: 39
26985 TGAAGATCAA
26995 CTTAGATCTCTGAAAGCTTCTATGAAAGACCGCCCAGGG
1 CTTAGATCTCTGAAAGCTTCTATGAAAGACCGCCCAGGG
* *
27034 CTTACATCTCTGGAAGCTTCTATGAAAGACCGCCCAGGG
1 CTTAGATCTCTGAAAGCTTCTATGAAAGACCGCCCAGGG
27073 CTTAGATCTCTGAAAGCTTCTATGAAAGACCGC
1 CTTAGATCTCTGAAAGCTTCTATGAAAGACCGC
27106 AAAGGGTCTC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (39 bp):
CTTAGATCTCTGAAAGCTTCTATGAAAGACCGCCCAGGG
Done.