Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023587.1 Corchorus olitorius cultivar O-4 contig23620, 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: 13086
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Found at i:207 original size:22 final size:23
Alignment explanation
Indices: 159--210 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
149 TAATAAAATT
*
159 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACACTATGAGATA
** *
182 TTGATAACCTTCA-TATGATATA
1 TTGATAACCAACACTATGAGATA
204 TTGATAA
1 TTGATAA
211 ACACGTTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
TTGATAACCAACACTATGAGATA
Found at i:277 original size:22 final size:22
Alignment explanation
Indices: 252--552 Score: 112
Period size: 22 Copynumber: 14.0 Consensus size: 22
242 GAATTGTTAG
*
252 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
274 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* **
296 TAATCTCGTTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
318 TAAGC-CTTCCTATAAAAATTTTGA
1 TAATCAC--ACTAT-GAAATTTTGA
* * * * *
342 TAAACCTCCCTATAAAAATTTGA
1 T-AATCACACTATGAAATTTTGA
* *
365 TAA-C-CTC-ATGAAATCTTGA
1 TAATCACACTATGAAATTTTGA
384 TAA-CA-AC----AAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
400 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * * * *
422 TAACCTCATTAAGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
444 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
466 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
488 TAA-CCCTCTTATGAAATTTTAA
1 TAATCACAC-TATGAAATTTTGA
* *
510 TAACCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
532 T-ATCATC-C-ATGAAATTTTGA
1 TAATCA-CACTATGAAATTTTGA
552 T
1 T
553 TACTCAATAA
Statistics
Matches: 213, Mismatches: 47, Indels: 40
0.71 0.16 0.13
Matches are distributed among these distances:
16 11 0.05
17 1 0.00
18 1 0.00
19 14 0.07
20 15 0.07
21 8 0.04
22 129 0.61
23 14 0.07
24 16 0.08
25 3 0.01
26 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:363 original size:23 final size:24
Alignment explanation
Indices: 309--371 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
299 TCTCGTTATG
* *
309 AAATTTTGATAAGCCTTCCTATAA
1 AAATTTTGATAAACCTCCCTATAA
333 AAATTTTGATAAACCTCCCTATAA
1 AAATTTTGATAAACCTCCCTATAA
357 AAA-TTTGAT-AACCTC
1 AAATTTTGATAAACCTC
372 ATGAAATCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.16
23 6 0.16
24 25 0.68
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATTTTGATAAACCTCCCTATAA
Found at i:504 original size:66 final size:64
Alignment explanation
Indices: 416--552 Score: 168
Period size: 66 Copynumber: 2.1 Consensus size: 64
406 CCCTATGATT
** * * * *
416 TTTTGATAACCTCATTAAGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATACTATGAA
1 TTTTGATAACCTCATTAAGAAATTTTAATAACCTCCATATGAAATTTTGATAT-CAT-CCATGAA
481 A
64 A
* *
482 TTTTGATAACCCTC-TTATGAAATTTTAATAACCTTCATATGAAATTTTGATATCATCCATGAAA
1 TTTTGATAA-CCTCATTAAGAAATTTTAATAACCTCCATATGAAATTTTGATATCATCCATGAAA
546 TTTTGAT
1 TTTTGAT
553 TACTCAATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 14 0.23
65 3 0.05
66 41 0.66
67 4 0.06
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (64 bp):
TTTTGATAACCTCATTAAGAAATTTTAATAACCTCCATATGAAATTTTGATATCATCCATGAAA
Found at i:576 original size:64 final size:66
Alignment explanation
Indices: 453--581 Score: 154
Period size: 64 Copynumber: 2.0 Consensus size: 66
443 TTAATCTCCC
* * ** * * * *
453 TATGAAATTTTGATCTACATACTATGAAATTTTGATAACCCTCTTATGAAATTTTAATAACCTTC
1 TATGAAATTTTGATATACATACCATGAAATTTTGATAACCCAATAATAAAAGTTCAATAACCTTC
518 A
66 A
* *
519 TATGAAATTTTGATAT-CAT-CCATGAAATTTTGATTACTCAATAATAAAAGTTCAATAACCTTC
1 TATGAAATTTTGATATACATACCATGAAATTTTGATAACCCAATAATAAAAGTTCAATAACCTTC
582 CTAATTTGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 35 0.66
65 3 0.06
66 15 0.28
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (66 bp):
TATGAAATTTTGATATACATACCATGAAATTTTGATAACCCAATAATAAAAGTTCAATAACCTTC
A
Found at i:660 original size:22 final size:22
Alignment explanation
Indices: 633--925 Score: 124
Period size: 22 Copynumber: 13.4 Consensus size: 22
623 ATAATACCAC
*
633 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAATCAC-TT
* *
656 T-TGAAAATTTGATAATCTCTT
1 TATGAAATTTTGATAATCACTT
* * *
677 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAATCACTT
* * * * * *
699 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACTT
* * * * *
721 TATGAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACTT
* *
743 TATGAGATTTTGATAATCACAT
1 TATGAAATTTTGATAATCACTT
* * *
765 TATGTAATTTTGATAGCCTCGC-T
1 TATGAAATTTTGATA--ATCACTT
* *
788 T-TGAAATTTTGATAA-CAATAC
1 TATGAAATTTTGATAATCACT-T
*
809 TATGAAATTTTTATAAT--CTT
1 TATGAAATTTTGATAATCACTT
* *
829 CCTAT-AAATTTTGATGATCCGATCTC
1 --TATGAAATTTTGATAAT-C-A-CTT
*
855 TATGAAATTTTGATAATCACTC
1 TATGAAATTTTGATAATCACTT
*
877 TATGAGA-TTTGATAA-C-CTT
1 TATGAAATTTTGATAATCACTT
* * *
896 CTATCAAATTTTGGTACTC-C-T
1 -TATGAAATTTTGATAATCACTT
917 TATGAAATT
1 TATGAAATT
926 GAGACTTTTA
Statistics
Matches: 211, Mismatches: 41, Indels: 39
0.73 0.14 0.13
Matches are distributed among these distances:
19 3 0.01
20 14 0.07
21 31 0.15
22 138 0.65
23 4 0.02
24 7 0.03
25 12 0.06
26 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACTT
Found at i:960 original size:22 final size:21
Alignment explanation
Indices: 931--1047 Score: 64
Period size: 22 Copynumber: 5.4 Consensus size: 21
921 AAATTGAGAC
931 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTC-TATGAAA
*
952 TTTTGATAACCTCCCTATGAAA
1 TTTTGATAACCT-TCTATGAAA
* *
974 TATT-AGTAACCTCCTTATGAAA
1 TTTTGA-TAACCTTC-TATGAAA
*
996 TTTTGTTAA--TTACACTATGAAA
1 TTTTGATAACCTT---CTATGAAA
* *
1018 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCT-TCTATGAAA
1040 TTTTGATA
1 TTTTGATA
1048 TTCTCTTTGA
Statistics
Matches: 75, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
20 1 0.01
21 9 0.12
22 60 0.80
23 4 0.05
24 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
TTTTGATAACCTTCTATGAAA
Found at i:993 original size:44 final size:43
Alignment explanation
Indices: 933--1047 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 43
923 ATTGAGACTT
* *
933 TTATAACCTTCATATGAAATTTTGATAACCT-CCCTATGAAA-TA
1 TTATAACC-TCCTATGAAATTTTGATAA-CTACACTATGAAATTA
* * *
976 TTAGTAACCTCCTTATGAAATTTTGTTAATTACACTATGAAATTC
1 TTA-TAACCTCC-TATGAAATTTTGATAACTACACTATGAAATTA
*
1021 TTATAACCTCGCTATGACATTTTGATA
1 TTATAACCTC-CTATGAAATTTTGATA
1048 TTCTCTTTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
43 6 0.10
44 49 0.82
45 5 0.08
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (43 bp):
TTATAACCTCCTATGAAATTTTGATAACTACACTATGAAATTA
Found at i:1104 original size:22 final size:22
Alignment explanation
Indices: 1071--1265 Score: 116
Period size: 22 Copynumber: 8.8 Consensus size: 22
1061 CCTTTCCATA
1071 AAATTGTT-ATAACCACACTATG
1 AAATT-TTAATAACCACACTATG
* * *
1093 AAATTTCAATAACCTTC-CTAAG
1 AAATTTTAATAACC-ACACTATG
*
1115 AAATTTTAATTACCTTATC-CTATG
1 AAATTTTAATAACC--A-CACTATG
** *
1139 AAATTTTGGTAACCACACTGTG
1 AAATTTTAATAACCACACTATG
* *
1161 ATATTTTGATAACTTC-CA-TATG
1 AAATTTTAATAAC--CACACTATG
**
1183 AAATTTTGGTAACCACACTATG
1 AAATTTTAATAACCACACTATG
* *
1205 GAATTTTAATAACCTC-CTCATG
1 AAATTTTAATAACCACACT-ATG
* *
1227 AAATTATAATAACCATC-TTATG
1 AAATTTTAATAACCA-CACTATG
*
1249 AAATTTTGATAACCACA
1 AAATTTTAATAACCACA
1266 TAGAGACAAG
Statistics
Matches: 135, Mismatches: 26, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
20 1 0.01
21 7 0.05
22 104 0.77
23 6 0.04
24 17 0.13
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTTTAATAACCACACTATG
Found at i:1190 original size:44 final size:43
Alignment explanation
Indices: 1132--1231 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 43
1122 AATTACCTTA
* * *
1132 TCCTATGAAATTTTGGTAACCACACTGT-GATATTTTGATAACT
1 TCCTATGAAATTTTGGTAACCACACTATGGA-ATTTTAATAACC
1175 TCCATATGAAATTTTGGTAACCACACTATGGAATTTTAATAACC
1 TCC-TATGAAATTTTGGTAACCACACTATGGAATTTTAATAACC
1219 TCCTCATGAAATT
1 TCCT-ATGAAATT
1232 ATAATAACCA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
43 4 0.08
44 45 0.88
45 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (43 bp):
TCCTATGAAATTTTGGTAACCACACTATGGAATTTTAATAACC
Found at i:2202 original size:19 final size:18
Alignment explanation
Indices: 2166--2207 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2156 TGAGTAATTT
*
2166 TTAAGTAAAAATATAATA
1 TTAAATAAAAATATAATA
2184 TATAAATAAAAAT-TCAATA
1 T-TAAATAAAAATAT-AATA
2203 TTAAA
1 TTAAA
2208 ATAATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:3179 original size:21 final size:21
Alignment explanation
Indices: 3142--3190 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3132 TATGCCAAAA
*
3142 ATTATTAAATAAATAATAAAT
1 ATTATTTAATAAATAATAAAT
*
3163 ATTTATTTAAT-AATAATAATT
1 A-TTATTTAATAAATAATAAAT
3184 ATTATTT
1 ATTATTT
3191 TCCCATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 11 0.44
22 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATTTAATAAATAATAAAT
Found at i:3956 original size:48 final size:48
Alignment explanation
Indices: 3904--4000 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
3894 TATGGCTTTC
3904 TCACCCCGGTTTTAGCCATTTTCTTGACTAAGTATTATTTTTATGTTT
1 TCACCCCGGTTTTAGCCATTTTCTTGACTAAGTATTATTTTTATGTTT
3952 TCACCCCGGTTTTAGCCATTTTCTTGACTAAGTATTATTTTTATGTTT
1 TCACCCCGGTTTTAGCCATTTTCTTGACTAAGTATTATTTTTATGTTT
4000 T
1 T
4001 GATGAGCTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.51
Consensus pattern (48 bp):
TCACCCCGGTTTTAGCCATTTTCTTGACTAAGTATTATTTTTATGTTT
Found at i:4672 original size:19 final size:19
Alignment explanation
Indices: 4632--4668 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4622 AATTTTTAAG
4632 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
4651 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
4669 ATAATTAATT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:5363 original size:43 final size:43
Alignment explanation
Indices: 5120--5363 Score: 347
Period size: 43 Copynumber: 5.8 Consensus size: 43
5110 CAATAACCAG
*
5120 AAGTCCCCAAACACATATATAACACATG-GGCAACTCTATTACA
1 AAGTCCCCAAACACATATATAACACA-GAGGCATCTCTATTACA
* *
5163 AAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-CA
1 AAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTACA
* *
5204 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACA
1 AAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTACA
* *
5247 AAGTCCTCAAACACATATATAACACATAGGCAT-T-TA-TATCA
1 AAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-CA
*
5288 AAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACA
1 AAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTACA
*
5331 AAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAGTCCCCAAACACATATATAACACAGAGGCAT
5364 TTCTCCTTAT
Statistics
Matches: 178, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
40 2 0.01
41 70 0.39
42 5 0.03
43 99 0.56
44 2 0.01
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (43 bp):
AAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTACA
Found at i:5364 original size:84 final size:84
Alignment explanation
Indices: 5120--5365 Score: 456
Period size: 84 Copynumber: 2.9 Consensus size: 84
5110 CAATAACCAG
*
5120 AAGTCCCCAAACACATATATAACACATGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
*
5185 CACAGAGGCATCTATATCA
66 CACAGAGGCATTTATATCA
5204 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
*
5269 CACATAGGCATTTATATCA
66 CACAGAGGCATTTATATCA
*
5288 AAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
5353 CACAGAGGCATTT
66 CACAGAGGCATTT
5366 CTCCTTATGG
Statistics
Matches: 157, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 157 1.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (84 bp):
AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAA
CACAGAGGCATTTATATCA
Found at i:11733 original size:18 final size:18
Alignment explanation
Indices: 11698--11732 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11688 CTCCTCTATC
*
11698 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
11716 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
11733 TTGTAATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Done.