Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024783.1 Corchorus olitorius cultivar O-4 contig24816, 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: 47743
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:521 original size:20 final size:20
Alignment explanation
Indices: 496--537 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
486 AAATAGTAAA
*
496 ATGGTAAAAATAAAATAGTT
1 ATGGTAAAAATAAAATAATT
516 ATGGTAAAAATAAAATAATT
1 ATGGTAAAAATAAAATAATT
536 AT
1 AT
538 AAGGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGGTAAAAATAAAATAATT
Found at i:1494 original size:14 final size:13
Alignment explanation
Indices: 1475--1513 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1465 AAATTGTAAA
1475 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
1488 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
1502 ATTTAAAAAATT
1 ATTTAAAAAATT
1514 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:1662 original size:127 final size:121
Alignment explanation
Indices: 1499--1749 Score: 362
Period size: 119 Copynumber: 2.0 Consensus size: 121
1489 ATTTAAGAAA
1499 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTC--ATATATATAAGTTTTTTAAATAAAATAGTAAAATGGT----A-AAAA
* *
1564 TAGATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
59 T-CATA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
1629 G
121 G
*
1630 TATATTT-AAAAATTC-TATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATCATAAA
1 TATATTTAAAAAATTCATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATCATAAA
*
1693 GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
1749 T
1 T
1750 TTAAACAATG
Statistics
Matches: 116, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
119 55 0.47
120 2 0.02
121 3 0.03
122 5 0.04
123 1 0.01
127 35 0.30
130 8 0.07
131 7 0.06
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (121 bp):
TATATTTAAAAAATTCATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATCATAAA
GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:4954 original size:18 final size:19
Alignment explanation
Indices: 4928--4963 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4918 AAACTAGTAA
*
4928 TAATAAATAATACTAATAT
1 TAATAAATAACACTAATAT
4947 TAAT-AATAACACTAATA
1 TAATAAATAACACTAATA
4964 ATTATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATAACACTAATAT
Found at i:5362 original size:32 final size:31
Alignment explanation
Indices: 5321--5380 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
5311 CAGACGCGGA
** *
5321 GGCGTCCCCAGGGGGCGTCTCGCCCATGGTGT
1 GGCGTCCCCAAAGGGCATCTC-CCCATGGTGT
5353 GGCGTCCCCAAAGGGCATCTCCCCATGG
1 GGCGTCCCCAAAGGGCATCTCCCCATGG
5381 GCGAGGCGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.12, C:0.37, G:0.35, T:0.17
Consensus pattern (31 bp):
GGCGTCCCCAAAGGGCATCTCCCCATGGTGT
Found at i:13056 original size:3 final size:3
Alignment explanation
Indices: 13048--13086 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
13038 ATTCTCTTTC
13048 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
13087 TCTTTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:25517 original size:21 final size:22
Alignment explanation
Indices: 25380--25606 Score: 108
Period size: 22 Copynumber: 10.8 Consensus size: 22
25370 AATTTACCTC
* *
25380 CCTATAAAATTTTGATGACC-T
1 CCTATGAAATTTTGATAACCAT
*
25401 CCATTTGAAATTTTGATAACC-T
1 CC-TATGAAATTTTGATAACCAT
25423 -C-ATGAAATTTTGATAACC-T
1 CCTATGAAATTTTGATAACCAT
* *
25442 --TAAGAAATTTTGAAAACCA-
1 CCTATGAAATTTTGATAACCAT
* *
25461 ACTCAAGAAATTTTGATAACCAT
1 CCT-ATGAAATTTTGATAACCAT
* *
25484 CTTATGGAATTTTGATAA-CATT
1 CCTATGAAATTTTGATAACCA-T
*
25506 CCTAT-AAATTTTTTG-TAATC-T
1 CCTATGAAA--TTTTGATAACCAT
* *
25527 -C-ATAAAATTTTGTTAACC-T
1 CCTATGAAATTTTGATAACCAT
* * **
25546 CATACGAAATTTTGATAAAAAT
1 CCTATGAAATTTTGATAACCAT
* * * *
25568 ACTATTAAATTTTGATGACC-C
1 CCTATGAAATTTTGATAACCAT
*
25589 CCAATGAAATTTTGATAA
1 CCTATGAAATTTTGATAA
25607 TTAACTATAC
Statistics
Matches: 158, Mismatches: 32, Indels: 32
0.71 0.14 0.14
Matches are distributed among these distances:
18 5 0.03
19 39 0.25
20 4 0.03
21 35 0.22
22 68 0.43
23 7 0.04
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCAT
Found at i:25816 original size:22 final size:22
Alignment explanation
Indices: 25780--25824 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
25770 CCTCTGAAAT
*
25780 ACCACATTATAAAATTTTGATA
1 ACCACAATATAAAATTTTGATA
*
25802 ACCACAATATGAAATTTTGATA
1 ACCACAATATAAAATTTTGATA
25824 A
1 A
25825 TCTCCCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (22 bp):
ACCACAATATAAAATTTTGATA
Found at i:26126 original size:43 final size:44
Alignment explanation
Indices: 26056--26175 Score: 120
Period size: 43 Copynumber: 2.8 Consensus size: 44
26046 CAACCAGAGT
* * * * *
26056 ATGAAATTTTAGTAACCTCCCTGTGAAATTTTAATAACTTTTC-C
1 ATGAAACTTTAATAACCTCCTTATGAAATTTTAATAAC-CTTCAC
* *
26100 ATG-AA-TTTCAATAACCTCCTTATGAAATTTTGATAACCTTCAT
1 ATGAAACTTT-AATAACCTCCTTATGAAATTTTAATAACCTTCAC
* *
26143 ATGAAACTTTGATAACATCCTTATGAAATTTTA
1 ATGAAACTTTAATAACCTCCTTATGAAATTTTA
26176 TTTTAATAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
42 6 0.10
43 29 0.46
44 25 0.40
45 3 0.05
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (44 bp):
ATGAAACTTTAATAACCTCCTTATGAAATTTTAATAACCTTCAC
Found at i:26135 original size:22 final size:22
Alignment explanation
Indices: 25945--26228 Score: 141
Period size: 22 Copynumber: 12.8 Consensus size: 22
25935 TCTATCTCAC
* * *
25945 TATGTAATTTTTATAACCACAC-
1 TATGAAATTTTGATAACCTC-CT
* *
25967 TATGAAATTTTGTTAATCTTCC-
1 TATGAAATTTTGATAA-CCTCCT
* *
25989 TATAAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCT
* * * * *
26011 TATAAAATTTCGATAATCGCCC
1 TATGAAATTTTGATAACCTCCT
* * ****
26033 AATGAAATTTTGACAACCAGAG
1 TATGAAATTTTGATAACCTCCT
*
26055 TATGAAATTTT-AGTAACCTCCC
1 TATGAAATTTTGA-TAACCTCCT
* * *
26077 TGTGAAATTTTAATAA-CT-TT
1 TATGAAATTTTGATAACCTCCT
**
26097 TCCATG-AATTTCAATAACCTCCT
1 T--ATGAAATTTTGATAACCTCCT
* *
26120 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTCCT
* *
26142 TATGAAACTTTGATAACATCCT
1 TATGAAATTTTGATAACCTCCT
*
26164 TATGAAATTTTATTTTAATAACCTCCT
1 TATG-AA----ATTTTGATAACCTCCT
*
26191 TATGAAATTTTGATAA-CTTCT
1 TATGAAATTTTGATAACCTCCT
* *
26212 CATGAAATTGTGATAAC
1 TATGAAATTTTGATAAC
26229 TACACTATAA
Statistics
Matches: 199, Mismatches: 48, Indels: 30
0.72 0.17 0.11
Matches are distributed among these distances:
20 1 0.01
21 38 0.19
22 134 0.67
23 7 0.04
26 2 0.01
27 17 0.09
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCT
Found at i:26203 original size:49 final size:48
Alignment explanation
Indices: 26126--26220 Score: 127
Period size: 49 Copynumber: 2.0 Consensus size: 48
26116 TCCTTATGAA
* * *
26126 ATTTTGATAACCTTCATATGAAACTTTGATAACATCCTTATGAAATTTT
1 ATTTTAATAACCTCCATATGAAACTTTGATAAC-TCCTCATGAAATTTT
* * *
26175 ATTTTAATAACCTCCTTATGAAATTTTGATAACTTCTCATGAAATT
1 ATTTTAATAACCTCCATATGAAACTTTGATAACTCCTCATGAAATT
26221 GTGATAACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 11 0.28
49 29 0.73
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (48 bp):
ATTTTAATAACCTCCATATGAAACTTTGATAACTCCTCATGAAATTTT
Found at i:26243 original size:43 final size:43
Alignment explanation
Indices: 26181--26293 Score: 108
Period size: 43 Copynumber: 2.6 Consensus size: 43
26171 TTTTATTTTA
*
26181 ATAACCTC-CTTATGAAATTTTGATAACTT-CTC-ATGAAATTGTG
1 ATAACCTCAC-TATAAAATTTTGATAACTTAC-CAAT-AAATTGTG
* * *
26224 ATAA-CTACACTATAAAATTTTAATATCTTACCAATAAATTTTG
1 ATAACCT-CACTATAAAATTTTGATAACTTACCAATAAATTGTG
* *
26267 GTAACCTCACTGTAAAATTTTGATAAC
1 ATAACCTCACTATAAAATTTTGATAAC
26294 CACACTATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.04
43 49 0.86
44 6 0.11
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (43 bp):
ATAACCTCACTATAAAATTTTGATAACTTACCAATAAATTGTG
Found at i:26286 original size:22 final size:22
Alignment explanation
Indices: 26259--26359 Score: 107
Period size: 22 Copynumber: 4.6 Consensus size: 22
26249 TCTTACCAAT
* * *
26259 AAATTTTGGTAACCTCACTGTA
1 AAATTTTGATAACCACACTATA
26281 AAATTTTGATAACCACACTATA
1 AAATTTTGATAACCACACTATA
* * *
26303 AAATTTCGAGAACCACAATATA
1 AAATTTTGATAACCACACTATA
*
26325 AAATTTT-AGTAACCACACAAT-
1 AAATTTTGA-TAACCACACTATA
*
26346 GAATTTTGATAACC
1 AAATTTTGATAACC
26360 TGCAAAATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
21 12 0.18
22 54 0.82
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:30684 original size:30 final size:31
Alignment explanation
Indices: 30650--30721 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
30640 ATTGAATTGT
** *
30650 TCAAATCCT-TTGGTTTGAATCTAAGCCTTA
1 TCAAATCCTGTTAATTTGAACCTAAGCCTTA
30680 TCAAAT-CTGTTAATTTGAACCTAAGCCTTA
1 TCAAATCCTGTTAATTTGAACCTAAGCCTTA
30710 TCAAAT-CTGTTA
1 TCAAATCCTGTTA
30722 CTAGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 2 0.05
30 36 0.95
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (31 bp):
TCAAATCCTGTTAATTTGAACCTAAGCCTTA
Found at i:35154 original size:30 final size:30
Alignment explanation
Indices: 35120--35179 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
35110 AAACCCTTTG
35120 GTTTGAACCTAAGCCTTATCAAATCTGTTA
1 GTTTGAACCTAAGCCTTATCAAATCTGTTA
35150 GTTTGAACCTAAGCCTTATCAAATCTGTTA
1 GTTTGAACCTAAGCCTTATCAAATCTGTTA
35180 CTAGTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (30 bp):
GTTTGAACCTAAGCCTTATCAAATCTGTTA
Found at i:39204 original size:26 final size:26
Alignment explanation
Indices: 39141--39191 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
39131 ATATTGATGA
* *
39141 AAGATTACTAAAATTTGTAAGAATGC
1 AAGATTACTAAAAATTCTAAGAATGC
39167 AAGATTACTAAAAATTCTAAGAATG
1 AAGATTACTAAAAATTCTAAGAATG
39192 TGAGGTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (26 bp):
AAGATTACTAAAAATTCTAAGAATGC
Found at i:39747 original size:21 final size:20
Alignment explanation
Indices: 39713--39764 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
39703 TAATGAAAGT
*
39713 TTAATAAGTTACTAAAATAC
1 TTAATAAATTACTAAAATAC
* *
39733 TTAATACAATTACTAAATTGC
1 TTAATA-AATTACTAAAATAC
39754 TTAATAAATTA
1 TTAATAAATTA
39765 TAGATAAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (20 bp):
TTAATAAATTACTAAAATAC
Found at i:39829 original size:4 final size:4
Alignment explanation
Indices: 39820--39861 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
39810 AATAAGAATT
39820 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
39862 TATATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:46766 original size:2 final size:2
Alignment explanation
Indices: 46759--46788 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46749 GTTATAATCC
46759 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
46789 GATAGTTCAT
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
Done.