Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023877.1 Corchorus olitorius cultivar O-4 contig23910, 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: 82755
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:586 original size:46 final size:46
Alignment explanation
Indices: 524--621 Score: 178
Period size: 46 Copynumber: 2.1 Consensus size: 46
514 CCAACAACCC
* *
524 ATCTCTTCATGATGTGGGATGTTCCCTTACATGTAAATCCTCAACA
1 ATCTCCTCATGATGTGGGATGTTCCCTCACATGTAAATCCTCAACA
570 ATCTCCTCATGATGTGGGATGTTCCCTCACATGTAAATCCTCAACA
1 ATCTCCTCATGATGTGGGATGTTCCCTCACATGTAAATCCTCAACA
616 ATCTCC
1 ATCTCC
622 CCCGATTTAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (46 bp):
ATCTCCTCATGATGTGGGATGTTCCCTCACATGTAAATCCTCAACA
Found at i:3768 original size:2 final size:2
Alignment explanation
Indices: 3761--3791 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3751 CCAACAGTAG
3761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3792 GAAGAATCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5956 original size:109 final size:109
Alignment explanation
Indices: 5765--5967 Score: 345
Period size: 109 Copynumber: 1.9 Consensus size: 109
5755 TAAATGGTGT
*
5765 CCACCCCAACTCGATCATGTGTTCCCACCCTTAATTGATTAATTCATTATTGTGTCCATAAATCA
1 CCACCCCAACTCGATCATGTGTTCCCACCCTTAATTGATTAATTCATCATTGTGTCCATAAATCA
*
5830 TAGTCCTCAATTCATCATTGTGCCCTTAAGTCATAGTTTGGAAG
66 TAATCCTCAATTCATCATTGTGCCCTTAAGTCATAGTTTGGAAG
* * *
5874 CCACCCCAACTCGATCATGTGTTCCCACCCTTAATTGATTGATTCATCATTGTG-CCCTTAATCC
1 CCACCCCAACTCGATCATGTGTTCCCACCCTTAATTGATTAATTCATCATTGTGTCCATAAAT-C
5938 ATAATCCTCAATTCATCATTGTGCCCTTAA
65 ATAATCCTCAATTCATCATTGTGCCCTTAA
5968 TTATAATAGA
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 6 0.07
109 82 0.93
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (109 bp):
CCACCCCAACTCGATCATGTGTTCCCACCCTTAATTGATTAATTCATCATTGTGTCCATAAATCA
TAATCCTCAATTCATCATTGTGCCCTTAAGTCATAGTTTGGAAG
Found at i:7240 original size:33 final size:33
Alignment explanation
Indices: 7198--7265 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
7188 AACTTATTGA
7198 ACTTTAGTTTCAAAGTTGAGGTGAGATCAGATG
1 ACTTTAGTTTCAAAGTTGAGGTGAGATCAGATG
7231 ACTTTAGTTTCAAAGTTGAGGTGAGATCAGATG
1 ACTTTAGTTTCAAAGTTGAGGTGAGATCAGATG
7264 AC
1 AC
7266 CACACTCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.32
Consensus pattern (33 bp):
ACTTTAGTTTCAAAGTTGAGGTGAGATCAGATG
Found at i:7423 original size:12 final size:12
Alignment explanation
Indices: 7402--7432 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
7392 GAAATCTTGG
7402 TTTTTCTTTTTTC
1 TTTTT-TTTTTTC
7415 TTTTTTTTTTTC
1 TTTTTTTTTTTC
7427 TTTTTT
1 TTTTTT
7433 GGTGAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:7814 original size:19 final size:20
Alignment explanation
Indices: 7790--7838 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
7780 CTGTTTAGCA
7790 ACTGTACAGATGAGATT-AT
1 ACTGTACAGATGAGATTAAT
*
7809 ACTGTACAGATTAGATTAGAT
1 ACTGTACAGATGAGATTA-AT
7830 ACTGTACAG
1 ACTGTACAG
7839 TACAGATGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 16 0.59
21 11 0.41
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAAT
Found at i:7845 original size:21 final size:21
Alignment explanation
Indices: 7790--7850 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
7780 CTGTTTAGCA
* *
7790 ACTGTACAGATGAGAT--TAT
1 ACTGTACAGATCAGATGAGAT
* *
7809 ACTGTACAGATTAGATTAGAT
1 ACTGTACAGATCAGATGAGAT
7830 ACTGTACAG-TACAGATGAGAT
1 ACTGTACAGAT-CAGATGAGAT
7851 TATTAGAGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 15 0.43
20 1 0.03
21 19 0.54
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (21 bp):
ACTGTACAGATCAGATGAGAT
Found at i:11476 original size:3 final size:3
Alignment explanation
Indices: 11457--11546 Score: 146
Period size: 3 Copynumber: 30.0 Consensus size: 3
11447 TAATCAAATC
* *
11457 TAT TAT TACT TAG TAT TAT TA- TGT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11502 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11547 AATATATGTT
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
2 1 0.01
3 77 0.95
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:11876 original size:8 final size:9
Alignment explanation
Indices: 11840--11877 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
11830 CCCAAATTAC
11840 TTATGGAAA
1 TTATGGAAA
*
11849 TTAAGGAAA
1 TTATGGAAA
11858 TTATGGAAA
1 TTATGGAAA
11867 TTAT-GAAA
1 TTATGGAAA
11875 TTA
1 TTA
11878 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Found at i:13239 original size:49 final size:48
Alignment explanation
Indices: 13150--13288 Score: 149
Period size: 49 Copynumber: 2.9 Consensus size: 48
13140 CAAGCAATCC
* **
13150 TTTACTTTTCA-CTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATC-GCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
* * * *
13198 TTTATTTTTTACTTGCA-TCTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TCGCACT-TTTTCTCAATTTTTAAGACAAAATTGAACT
* *
13247 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATT
1 TTTAATTTTCATCGCACTTTTTCTCAATTTTTAAGACAAAATT
13289 AATTGGCACG
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
47 9 0.12
48 27 0.36
49 40 0.53
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (48 bp):
TTTAATTTTCATCGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
Found at i:29517 original size:21 final size:21
Alignment explanation
Indices: 29491--29538 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
29481 CGGACAGCGC
*
29491 GGAGGCGGAGCG-GCGATTGCG
1 GGAGGCGGAG-GAGCGATTGAG
29512 GGAGGCGGAGGAGCGATTGAG
1 GGAGGCGGAGGAGCGATTGAG
29533 GGAGGC
1 GGAGGC
29539 CATAGAGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.19, C:0.15, G:0.58, T:0.08
Consensus pattern (21 bp):
GGAGGCGGAGGAGCGATTGAG
Found at i:57879 original size:47 final size:47
Alignment explanation
Indices: 57816--57921 Score: 194
Period size: 47 Copynumber: 2.3 Consensus size: 47
57806 AAGATCTTAG
* *
57816 ATTCGAGTCTTATGAATAAAGAAAATAGACACTTAGAGATCAGGGAA
1 ATTCGAGTCTTCTGAATAAAGAAAATAGACACTTAGAAATCAGGGAA
57863 ATTCGAGTCTTCTGAATAAAGAAAATAGACACTTAGAAATCAGGGAA
1 ATTCGAGTCTTCTGAATAAAGAAAATAGACACTTAGAAATCAGGGAA
57910 ATTCGAGTCTTC
1 ATTCGAGTCTTC
57922 AGCTTCCCGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (47 bp):
ATTCGAGTCTTCTGAATAAAGAAAATAGACACTTAGAAATCAGGGAA
Found at i:60840 original size:26 final size:26
Alignment explanation
Indices: 60810--60861 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
60800 GGTCATGCCC
*
60810 CATTGAAGTTCAGAGTTCCAATCTTT
1 CATTGAACTTCAGAGTTCCAATCTTT
60836 CATTGAACTTCAGAGTTCCAATCTTT
1 CATTGAACTTCAGAGTTCCAATCTTT
60862 TGAGGTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (26 bp):
CATTGAACTTCAGAGTTCCAATCTTT
Found at i:62441 original size:66 final size:66
Alignment explanation
Indices: 62356--62582 Score: 393
Period size: 66 Copynumber: 3.4 Consensus size: 66
62346 GATGGGAGCT
* **
62356 TCTCATCATCTAATAAATTCACCACACGAATAGGTATGTTCTCCTCACCTTGAGAAATATCATTC
1 TCTCATCATCCAACGAATTCACCACACGAATAGGTATGTTCTCCTCACCTTGAGAAATATCATTC
62421 C
66 C
*
62422 TCTCATCATCCAACGAATTCACCACACTG-ATAGGTATGTTCTCCTCACCTTGAGACATATCATT
1 TCTCATCATCCAACGAATTCACCACAC-GAATAGGTATGTTCTCCTCACCTTGAGAAATATCATT
62486 CC
65 CC
*
62488 TCTCATCATCCAACGAATTCACCACACGAATAGGCATGTTCTCCTCACCTTGAGAAATATCATTC
1 TCTCATCATCCAACGAATTCACCACACGAATAGGTATGTTCTCCTCACCTTGAGAAATATCATTC
62553 C
66 C
62554 TCTCATCATCCAACGAATTCACCACACGA
1 TCTCATCATCCAACGAATTCACCACACGA
62583 GCCAATCTAG
Statistics
Matches: 153, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
65 1 0.01
66 151 0.99
67 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.10, T:0.29
Consensus pattern (66 bp):
TCTCATCATCCAACGAATTCACCACACGAATAGGTATGTTCTCCTCACCTTGAGAAATATCATTC
C
Found at i:64288 original size:149 final size:145
Alignment explanation
Indices: 64020--64319 Score: 406
Period size: 149 Copynumber: 2.0 Consensus size: 145
64010 CGCATAATAG
* * *
64020 CTCCCAATTTATCAGTTAAACTCAAGAAATTTCCAGAATTTCCAAACAATAGGTATCCAATTAAA
1 CTCCCAATTTATCAGTTAAACTCAAGAAATTTCCA-AAGTTCAAAACAATAGATATCCAATTAAA
* * * * *
64085 GGTTCAATATATATATATATAAAACTTTCTTTCTTCCCATGAGGGGATTCGGAAAGAAAATAGTA
65 GGTTCAAAATATAAAAAAAAAAAACTTTCTTTCTTCCCATGAGGGGATTCGGAAAGAAAATAGTA
*
64150 AGTAATAACAATGTCA
130 AGCAATAACAATGTCA
* *
64166 CTCCCAATTTTTCAGTTAAACTCAAGAAATTTCC-AAGTTCAAAATCTCATTCA-ATATCCAATT
1 CTCCCAATTTATCAGTTAAACTCAAGAAATTTCCAAAGTTCAAAA---CAAT-AGATATCCAATT
64229 AAAGGTTCAAAATATTCAAAAAAAAAAAACTTTCTTTCTTCCCATGAGGGGATTCGGAAAGAAAA
62 AAAGGTTCAAAATA-T-AAAAAAAAAAAACTTTCTTTCTTCCCATGAGGGGATTCGGAAAGAAAA
*
64294 TCGTAAGCAATAACAATGTCA
125 TAGTAAGCAATAACAATGTCA
*
64315 ATCCC
1 CTCCC
64320 CTTTACCTTT
Statistics
Matches: 135, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
144 8 0.06
146 33 0.24
147 25 0.19
148 2 0.01
149 67 0.50
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (145 bp):
CTCCCAATTTATCAGTTAAACTCAAGAAATTTCCAAAGTTCAAAACAATAGATATCCAATTAAAG
GTTCAAAATATAAAAAAAAAAAACTTTCTTTCTTCCCATGAGGGGATTCGGAAAGAAAATAGTAA
GCAATAACAATGTCA
Found at i:64501 original size:14 final size:14
Alignment explanation
Indices: 64482--64515 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
64472 TCAAACTATA
64482 TTCACTATAAAGCG
1 TTCACTATAAAGCG
*
64496 TTCACTATAAAGCT
1 TTCACTATAAAGCG
64510 TTCACT
1 TTCACT
64516 GATCAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (14 bp):
TTCACTATAAAGCG
Found at i:70977 original size:22 final size:22
Alignment explanation
Indices: 70952--70995 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
70942 GTCCTTTTTT
70952 TTTGCATC-AATGTACAGTCCCC
1 TTTG-ATCAAATGTACAGTCCCC
70974 TTTGATCAAAATGTACAGTCCC
1 TTTGATC-AAATGTACAGTCCC
70996 TTTAGTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.15
22 4 0.20
23 13 0.65
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (22 bp):
TTTGATCAAATGTACAGTCCCC
Found at i:71641 original size:2 final size:2
Alignment explanation
Indices: 71634--71663 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
71624 ATTAAAACTC
71634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71664 GCAATAAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72508 original size:3 final size:3
Alignment explanation
Indices: 72500--72526 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
72490 ACATAGGCAC
72500 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
72527 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:77389 original size:24 final size:24
Alignment explanation
Indices: 77362--77411 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
77352 AATATATGAC
77362 ACTATAAAACCTACAATCATATTT
1 ACTATAAAACCTACAATCATATTT
*
77386 ACTATAAAACCTGCAATCATATTT
1 ACTATAAAACCTACAATCATATTT
77410 AC
1 AC
77412 GAGTGCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.32
Consensus pattern (24 bp):
ACTATAAAACCTACAATCATATTT
Found at i:81003 original size:28 final size:28
Alignment explanation
Indices: 80971--81026 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
80961 GTAAGACTTA
80971 GAATGATCATTTACAAGAAGAAGGATCT
1 GAATGATCATTTACAAGAAGAAGGATCT
80999 GAATGATCATTTACAAGAAGAAGGATCT
1 GAATGATCATTTACAAGAAGAAGGATCT
81027 TCTTACCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (28 bp):
GAATGATCATTTACAAGAAGAAGGATCT
Done.