Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015252.1 Corchorus olitorius cultivar O-4 contig15285, 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: 61497
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Found at i:1145 original size:15 final size:15
Alignment explanation
Indices: 1121--1187 Score: 54
Period size: 16 Copynumber: 4.7 Consensus size: 15
1111 TATCATCCAT
1121 AATAATATCCTTCAAA
1 AATAA-ATCCTTCAAA
*
1137 AATAAATCCTTTAAAA
1 AATAAATCC-TTCAAA
* *
1153 AATACATTCTT---A
1 AATAAATCCTTCAAA
1165 AAT--ATCCTTCAAA
1 AATAAATCCTTCAAA
1178 AATAAATCCT
1 AATAAATCCT
1188 AGGAATGCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
10 5 0.12
12 4 0.10
13 4 0.10
15 11 0.27
16 17 0.41
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAATCCTTCAAA
Found at i:1398 original size:19 final size:19
Alignment explanation
Indices: 1380--1416 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1370 TATTAATTAT
*
1380 TTTA-ATATTATATTTTTA
1 TTTATATATTACATTTTTA
1398 TTTATATATTACATTTTTA
1 TTTATATATTACATTTTTA
1417 CTTAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTACATTTTTA
Found at i:1714 original size:13 final size:13
Alignment explanation
Indices: 1696--1721 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1686 TATGTAGAAT
1696 ATATGATTTATGA
1 ATATGATTTATGA
1709 ATATGATTTATGA
1 ATATGATTTATGA
1722 GGTTATAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
ATATGATTTATGA
Found at i:1815 original size:169 final size:169
Alignment explanation
Indices: 1536--1857 Score: 527
Period size: 169 Copynumber: 1.9 Consensus size: 169
1526 TTTAAATATA
* * *
1536 ATGAATATGATTTTTGAGGTTATAGAGAGATGGAATACGAATCGATTCAGTGTAACTGCATGTGA
1 ATGAATATGATTTATGAGGTTATAGAGAGATGGAATACGAATCGATTCAGTGTAACCGCATGTAA
*
1601 GAAATGACTAAAACAGGGCGATAAGGTCGTCCCAGGTTAAAAGTTAGAAGGAGCATTTAGTAATT
66 GAAATGACTAAAACAGGGCAATAAGGTCGTCCCAGGTTAAAAGTTAGAAGGAGCATTTAGTAATT
* *
1666 TCACTTGGTTACAAAAATAATATGTAGAATATATGATTT
131 TCACCTGATTACAAAAATAATATGTAGAATATATGATTT
1705 ATGAATATGATTTATGAGGTTATAGAGAGATGGAATACGAATCGATTCAGTGTAACCGCATGTAA
1 ATGAATATGATTTATGAGGTTATAGAGAGATGGAATACGAATCGATTCAGTGTAACCGCATGTAA
* * * * * * *
1770 GAAATGATTAAAACGGGGTAATAAGGTTGTCTCAGGTTAAAAGTTAGAATGATCATTTAGTAATT
66 GAAATGACTAAAACAGGGCAATAAGGTCGTCCCAGGTTAAAAGTTAGAAGGAGCATTTAGTAATT
1835 TCACCTGATTACAAAAATAATAT
131 TCACCTGATTACAAAAATAATAT
1858 ATAGGATAAT
Statistics
Matches: 140, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
169 140 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.30
Consensus pattern (169 bp):
ATGAATATGATTTATGAGGTTATAGAGAGATGGAATACGAATCGATTCAGTGTAACCGCATGTAA
GAAATGACTAAAACAGGGCAATAAGGTCGTCCCAGGTTAAAAGTTAGAAGGAGCATTTAGTAATT
TCACCTGATTACAAAAATAATATGTAGAATATATGATTT
Found at i:4604 original size:42 final size:41
Alignment explanation
Indices: 4557--4678 Score: 122
Period size: 42 Copynumber: 3.2 Consensus size: 41
4547 TGACCCAATT
4557 ACAGATCATAAACATATTAGGTTCTTGTGATGGTGACTCAAA
1 ACAGATCATAAACA-ATTAGGTTCTTGTGATGGTGACTCAAA
*
4599 ACAGATC----AC--TTA-G----TGTGATGGTGACCCAAA
1 ACAGATCATAAACAATTAGGTTCTTGTGATGGTGACTCAAA
* *
4629 ACAGATCATAAACAGATTAGGTTCTTGTGATGATAACTCAAA
1 ACAGATCATAAACA-ATTAGGTTCTTGTGATGGTGACTCAAA
4671 ACAGATCA
1 ACAGATCA
4679 CTTACTGTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
30 23 0.36
34 3 0.05
35 3 0.05
37 3 0.05
38 3 0.05
42 29 0.45
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (41 bp):
ACAGATCATAAACAATTAGGTTCTTGTGATGGTGACTCAAA
Found at i:4668 original size:72 final size:72
Alignment explanation
Indices: 4519--4703 Score: 280
Period size: 72 Copynumber: 2.6 Consensus size: 72
4509 TCTGATGGTG
* * * *
4519 ACTCAAAACAGATCACTTACTGTAATGCTGACCCAATTACAGATCATAAACATATTAGGTTCTTG
1 ACTCAAAACAGATCACTTACTGTGATGATGACCCAA-AACAGATCATAAACAGATTAGGTTCTTG
* *
4584 TGATGGTG
65 TGATGATA
* *
4592 ACTCAAAACAGATCACTTAGTGTGATGGTGACCCAAAACAGATCATAAACAGATTAGGTTCTTGT
1 ACTCAAAACAGATCACTTACTGTGATGATGACCCAAAACAGATCATAAACAGATTAGGTTCTTGT
4657 GATGATA
66 GATGATA
*
4664 ACTCAAAACAGATCACTTACTGTGATGATGACCAAAAACA
1 ACTCAAAACAGATCACTTACTGTGATGATGACCCAAAACA
4704 AATTACTTAC
Statistics
Matches: 102, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 69 0.68
73 33 0.32
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (72 bp):
ACTCAAAACAGATCACTTACTGTGATGATGACCCAAAACAGATCATAAACAGATTAGGTTCTTGT
GATGATA
Found at i:4690 original size:30 final size:30
Alignment explanation
Indices: 4654--4714 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
4644 ATTAGGTTCT
*
4654 TGTGATGATAACTC-AAAACAGATCACTTAC
1 TGTGATGATAAC-CAAAAACAAATCACTTAC
* *
4684 TGTGATGATGACCAAAAACAAATTACTTAC
1 TGTGATGATAACCAAAAACAAATCACTTAC
4714 T
1 T
4715 CATGACCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (30 bp):
TGTGATGATAACCAAAAACAAATCACTTAC
Found at i:32024 original size:18 final size:20
Alignment explanation
Indices: 31980--32025 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
31970 AGGCCTGTAC
31980 CAAAGAAAAATAAAAGGGAAA
1 CAAA-AAAAATAAAAGGGAAA
**
32001 TTAAAAAAA-AAAA-GGAAA
1 CAAAAAAAATAAAAGGGAAA
32019 CAAAAAA
1 CAAAAAA
32026 TTTTCCATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 10 0.48
19 4 0.19
20 5 0.24
21 2 0.10
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (20 bp):
CAAAAAAAATAAAAGGGAAA
Found at i:35963 original size:33 final size:33
Alignment explanation
Indices: 35926--36015 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
35916 CATCTAATGT
*
35926 TAATGTTAACATTTACAGAAATCTTCCATCACC
1 TAATGTTAACATTTACAGAAATCTACCATCACC
* *
35959 TAATGTTAACATTTCCAGAAATCTACTATCACC
1 TAATGTTAACATTTACAGAAATCTACCATCACC
* * **
35992 TAATTTTTACATTTGTAGAAATCT
1 TAATGTTAACATTTACAGAAATCT
36016 GCATTTCCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (33 bp):
TAATGTTAACATTTACAGAAATCTACCATCACC
Found at i:36499 original size:30 final size:30
Alignment explanation
Indices: 36465--36563 Score: 146
Period size: 30 Copynumber: 3.3 Consensus size: 30
36455 CCTCCTTGGT
*
36465 GGACCTTTGCTTGGTGCAGTGGCTTGTACA
1 GGACCTTTGCTTGGTGCAGTGGCTTGTGCA
* * *
36495 GGACCTTTGGTTGGTGCAATGGAGTT-TGCA
1 GGACCTTTGCTTGGTGCAGTGG-CTTGTGCA
36525 GGACCTTTGCTTGGTGCAGTGGCTTGTGCA
1 GGACCTTTGCTTGGTGCAGTGGCTTGTGCA
36555 GGACCTTTG
1 GGACCTTTG
36564 GTTGCTTGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
29 2 0.03
30 56 0.93
31 2 0.03
ACGTcount: A:0.13, C:0.18, G:0.35, T:0.33
Consensus pattern (30 bp):
GGACCTTTGCTTGGTGCAGTGGCTTGTGCA
Found at i:52448 original size:84 final size:84
Alignment explanation
Indices: 52284--52611 Score: 525
Period size: 84 Copynumber: 3.9 Consensus size: 84
52274 AATAACCAAA
* *
52284 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTTCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC-AAAGTCCTCAAACACATATATA
52349 ACACAGAGGCACCTATATCC
65 ACACAGAGGCACCTATATCC
*
52369 AAGTCCCCAAACACATATATAACACAGGGGCACCTT-TATTACAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTACAAAGTCCTCAAACACATATATA
* * *
52433 ACACAGATGCGCCTATATTC
65 ACACAGAGGCACCTATATCC
*
52453 AACTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
** *
52518 CACAGAGGCATTTATATCA
66 CACAGAGGCACCTATATCC
52537 AAGTCCCCAAACACATATATAACACAGGGGC-ATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAAGTCCTCAAACACATATATA
52601 ACACAGAGGCA
65 ACACAGAGGCA
52612 TTTCTCCTTA
Statistics
Matches: 225, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
83 4 0.02
84 182 0.81
85 37 0.16
86 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21
Consensus pattern (84 bp):
AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
CACAGAGGCACCTATATCC
Found at i:52612 original size:43 final size:43
Alignment explanation
Indices: 52283--52612 Score: 383
Period size: 43 Copynumber: 7.8 Consensus size: 43
52273 CAATAACCAA
* *
52283 AAAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC
* *
52326 AAAAGTTCTCAAACACATATATAACACAGAGGCA-C-CTA-TATC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
* * * *
52368 CAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * ** *
52411 AAAGTCCTCAAACACATATATAACACAGATGCGCCTATATT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
52453 -AACTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC
*
52495 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
*
52536 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
52579 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
52613 TTCTCCTTAT
Statistics
Matches: 245, Mismatches: 29, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
40 2 0.01
41 97 0.40
42 11 0.04
43 102 0.42
44 33 0.13
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:59418 original size:72 final size:72
Alignment explanation
Indices: 59337--59806 Score: 665
Period size: 72 Copynumber: 6.5 Consensus size: 72
59327 ATTGAAGGCA
*
59337 AGGCAGTTCCCACATTTGGCAGTCCTTCGCATAATCCTTACGTGATAATCTTCCATATTGCGGTT
1 AGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAATCTTCCATATTGCGGTT
59402 GTAGCCG
66 GTAGCCG
* * * *
59409 AGGCAGTTCCCACATTTGGTAGTCCTTCGCACAATCCTTATGTGATTATCTTCCGTATTGCGGTT
1 AGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAATCTTCCATATTGCGGTT
59474 GTAGCCG
66 GTAGCCG
* * * * *
59481 AGGCAGTTCCAACGTTTGGCAGTCCTTCGCACAATCCTTACGTGATAATTTTCCATGTTGCAGTT
1 AGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAATCTTCCATATTGCGGTT
*
59546 GTAGTCG
66 GTAGCCG
* * * * *
59553 AGGCAGTTCCCACATTGGGCAGTCCTTCGCACAATCCTTATGTGATTATCTTCCGTATTACGGTT
1 AGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAATCTTCCATATTGCGGTT
59618 GTAGCCG
66 GTAGCCG
* * * * *
59625 AGGCAGCTCCAACGTTTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCATATTGCGATT
1 AGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAATCTTCCATATTGCGGTT
59690 GTAGCCG
66 GTAGCCG
* * * * **
59697 AGGCAGTTCCCACATTTGGCAGTCCATCGCACAATCCTTATGTGATTATCTTCC-TCATTTCAAT
1 AGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAATCTTCCAT-ATTGCGGT
59761 TGTAGCCG
65 TGTAGCCG
*
59769 AGGCAGTGCCCACA-TTGGCAGTCCTTCGCACAATCCTT
1 AGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
59807 GCTACTAATC
Statistics
Matches: 350, Mismatches: 47, Indels: 3
0.88 0.12 0.01
Matches are distributed among these distances:
71 24 0.07
72 326 0.93
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.32
Consensus pattern (72 bp):
AGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAATCTTCCATATTGCGGTT
GTAGCCG
Found at i:61161 original size:84 final size:84
Alignment explanation
Indices: 61008--61335 Score: 516
Period size: 84 Copynumber: 3.9 Consensus size: 84
60998 AATAACCAAA
* *
61008 AAGTCCCCAAACACATATATAACACAGTGGCAATTCTATTCCAAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC-AAAGTCCTCAAACACATATATA
61073 ACACAGAGGCACCTATATCC
65 ACACAGAGGCACCTATATCC
* *
61093 AAGTCCCCAAACACATATATAACACAGGGACACCTT-TATTACAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTACAAAGTCCTCAAACACATATATA
* * *
61157 ACACAGATGCGCCTATATTC
65 ACACAGAGGCACCTATATCC
*
61177 AACTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
** *
61242 CACAGAGGCATTTATATCA
66 CACAGAGGCACCTATATCC
61261 AAGTCCCCAAACACATATATAACACAGGGGC-ATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAAGTCCTCAAACACATATATA
61325 ACACAGAGGCA
65 ACACAGAGGCA
61336 TTTCTCCTTA
Statistics
Matches: 223, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
83 4 0.02
84 182 0.82
85 35 0.16
86 2 0.01
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (84 bp):
AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
CACAGAGGCACCTATATCC
Found at i:61336 original size:43 final size:43
Alignment explanation
Indices: 61007--61336 Score: 385
Period size: 43 Copynumber: 7.8 Consensus size: 43
60997 CAATAACCAA
* *
61007 AAAGTCCCCAAACACATATATAACACAGTGGCAAT-TCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC
*
61050 AAAAGTCCTCAAACACATATATAACACAGAGGCA-C-CTA-TATC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
* * *
61092 CAAGTCCCCAAACACATATATAACACAG-GGACACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGG-CATCTCTATTAC
* * ** *
61135 AAAGTCCTCAAACACATATATAACACAGATGCGCCTATATT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
61177 -AACTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC
*
61219 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
*
61260 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
61303 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
61337 TTCTCCTTAT
Statistics
Matches: 247, Mismatches: 25, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
40 4 0.02
41 96 0.39
42 11 0.04
43 101 0.41
44 35 0.14
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.22
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Done.