Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015206.1 Corchorus olitorius cultivar O-4 contig15239, 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: 11941
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Found at i:360 original size:21 final size:21
Alignment explanation
Indices: 335--377 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
325 CAAAAGTGTC
*
335 AAAAGGGGACGGTAATTAGCA
1 AAAAGGGGACGATAATTAGCA
* *
356 AAAAGGGGGCGATATTTAGCA
1 AAAAGGGGACGATAATTAGCA
377 A
1 A
378 TTCAGAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.09, G:0.33, T:0.16
Consensus pattern (21 bp):
AAAAGGGGACGATAATTAGCA
Found at i:5942 original size:11 final size:12
Alignment explanation
Indices: 5922--5946 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5912 TGGTGTCACC
5922 TTTTGTTTTTTT
1 TTTTGTTTTTTT
5934 TTTTGTTTTTTT
1 TTTTGTTTTTTT
5946 T
1 T
5947 GTCTTTTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:6336 original size:220 final size:222
Alignment explanation
Indices: 5939--6513 Score: 856
Period size: 220 Copynumber: 2.6 Consensus size: 222
5929 TTTTTTTTTG
* *
5939 TTTTTTT-TGTCTTTTCTCACTTTTTGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCCTTCC
1 TTTTTTTAGGTCTTTTCTCACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCCTTCC
* *
6003 TTTTTCTGCTACCTTCTTTTGTAATTACTCATTTCACTTCTTTAATTGC-TTTTAATTAATGTTT
66 TTTTCCTGCTACCTT-TTTTGTAATTACTCATTTCACTTCCTTAATTGCTTTTTAATTAATGTTT
* *
6067 CTCCCCCCTTTTCTTTTTTCCTCTCACAAACTCAGTACCCAGAGTAATTACTGAAAGGCCAAATT
130 CTCCCCCATTTTCTTTTTTCCTCTCACAAACTCAGTACCCAGAGTAATTACTAAAAGGCCAAATT
6132 GAGGATTAATG-CGTGCCACCTTTTGGC
195 GAGGATTAATGTCGTGCCACCTTTTGGC
*
6159 -TTTTTTAGGTCTTTTCTCACTATTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCCTTCC
1 TTTTTTTAGGTCTTTTCTCACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCCTTCC
* *
6223 TTTTCCTGCTACCTTTTTTGTAATTACTAATTTCACTTCCTCAATTGCTTTTTAATTAATGTTTC
66 TTTTCCTGCTACCTTTTTTGTAATTACTCATTTCACTTCCTTAATTGCTTTTTAATTAATGTTTC
* * * *
6288 TCCCCCATTTTCTTTTTTCCTTTCACCAACTCAGTACCTAGGGTAATTACTAAAAGGCCAAATTG
131 TCCCCCATTTTCTTTTTTCCTCTCACAAACTCAGTACCCAGAGTAATTACTAAAAGGCCAAATTG
* *
6353 AGGATTAATGTGGTGGCACCTTTTGGC
196 AGGATTAATGTCGTGCCACCTTTTGGC
** *
6380 TTTTTTTTTTTTTTGTCTTTTCTCACTTTTCGGATGACTAAAAAGCCCCTCCATGAG-TTCTCCC
1 -----TTTTTTTAGGTCTTTTCTCACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTC-CCC
* *
6444 CCTTCCTTTTCCTGCTACCCTTTTTTGTAATTACCCATTTCTCTTCCTTAATTG-TTTTTAATTA
60 CCTTCCTTTTCCTGCTA-CCTTTTTTGTAATTACTCATTTCACTTCCTTAATTGCTTTTTAATTA
6508 ATGTTT
124 ATGTTT
6514 AAGACTTTTA
Statistics
Matches: 321, Mismatches: 23, Indels: 15
0.89 0.06 0.04
Matches are distributed among these distances:
219 36 0.11
220 153 0.48
221 14 0.04
226 3 0.01
227 83 0.26
228 32 0.10
ACGTcount: A:0.19, C:0.25, G:0.11, T:0.45
Consensus pattern (222 bp):
TTTTTTTAGGTCTTTTCTCACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCCTTCC
TTTTCCTGCTACCTTTTTTGTAATTACTCATTTCACTTCCTTAATTGCTTTTTAATTAATGTTTC
TCCCCCATTTTCTTTTTTCCTCTCACAAACTCAGTACCCAGAGTAATTACTAAAAGGCCAAATTG
AGGATTAATGTCGTGCCACCTTTTGGC
Found at i:9241 original size:23 final size:22
Alignment explanation
Indices: 9212--9742 Score: 233
Period size: 22 Copynumber: 24.3 Consensus size: 22
9202 ATTTTTTGTG
9212 ACCTCCTTATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
* *
9234 ACCTTCC-TATGAAATTTTAATG
1 ACC-TCCTTATGAAATTTTGATA
* * * * * *
9256 ACGATAC-TATGGAATATCGAGA
1 AC-CTCCTTATGAAATTTTGATA
** * **
9278 ACCTTTTTAT-TAATTTTTTTA
1 ACCTCCTTATGAAATTTTGATA
* * *
9299 ACATTCTTATGAAATTTTGTTA
1 ACCTCCTTATGAAATTTTGATA
* * *
9321 ACCTCCCTAAGGAATTTTGA-A
1 ACCTCCTTATGAAATTTTGATA
9342 GACCTCAC-TATGAAATTTTGATA
1 -ACCTC-CTTATGAAATTTTGATA
** * *
9365 ACGAACAC-TATGAGATGTTGATA
1 AC-CTC-CTTATGAAATTTTGATA
** * *
9388 ACCTCCAAATGATATATTGATA
1 ACCTCCTTATGAAATTTTGATA
* * *
9410 ACCACGTTATGAAAATTT-ATAA
1 ACCTCCTTATGAAATTTTGAT-A
*
9432 ACCTCCATATG-AATTGTT-AGTA
1 ACCTCCTTATGAAATT-TTGA-TA
* * *
9454 ATCACAC-TCTGAAATTTTGATA
1 ACCTC-CTTATGAAATTTTGATA
* * * *
9476 ATCACAC-TATGAAATTGTAATA
1 ACCTC-CTTATGAAATTTTGATA
*
9498 ACCTCGTTATGAAATTTTGATAA
1 ACCTCCTTATGAAATTTTGAT-A
*
9521 ACCTTCC-TATAAAATTTTGATAA
1 ACC-TCCTTATGAAATTTTGAT-A
* *
9544 ACCTCCCTATAAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
9566 ACCTCCTTATGAAATTCTTGATA
1 ACCTCCTTATGAAATT-TTGATA
*
9589 A----C-TA-CAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
* * *
9605 ATCTCCCTATG-ATTCTTTGATA
1 ACCTCCTTATGAAAT-TTTGATA
* *
9627 ACCTCATTATGAAATTTTGTTA
1 ACCTCCTTATGAAATTTTGATA
* *
9649 ATCTCCCTATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
*
9671 ACCAT-CTTATGAAATTTTCA-A
1 ACC-TCCTTATGAAATTTTGATA
* *
9692 AACTAAAC-TATGAAATTTTGATA
1 ACCT--CCTTATGAAATTTTGATA
* *
9715 ACCTTCATATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
*
9737 TCCTCC
1 ACCTCC
9743 CTCAAATTTT
Statistics
Matches: 388, Mismatches: 87, Indels: 68
0.71 0.16 0.13
Matches are distributed among these distances:
16 7 0.02
17 5 0.01
18 2 0.01
19 1 0.00
20 2 0.01
21 29 0.07
22 259 0.67
23 81 0.21
24 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
ACCTCCTTATGAAATTTTGATA
Found at i:9657 original size:44 final size:44
Alignment explanation
Indices: 9463--10050 Score: 269
Period size: 44 Copynumber: 13.8 Consensus size: 44
9453 AATCACACTC
* * * *
9463 TGAAATTTTGATAATCACACTATGAAATTGTAATAACC-TCGTTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCATC-TTA
* * * *
9507 TGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACC-TCCCTA
1 TGAAATTTTGAT-AATCTCCCTATGAAATTTTGAT-AACCAT-CTTA
* * *
9553 TAAAATTTTGATAACCTCCTTATGAAATTCTTGAT-A--A-C-TA
1 TGAAATTTTGATAATCTCCCTATGAAATT-TTGATAACCATCTTA
* *
9593 -CAAATTTTGATAATCTCCCTATG-ATTCTTTGATAACC-TCATTA
1 TGAAATTTTGATAATCTCCCTATGAAAT-TTTGATAACCATC-TTA
*
9636 TGAAATTTTGTTAATCTCCCTATGAAATTTTGATAACCATCTTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCATCTTA
* * ** * *
9680 TGAAATTTTCA-AAACTAAACTATGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAATCT-CCCTATGAAATTTTGATAACCATCTTA
* * * *
9724 TGAAATTTTGAT-ATCCTCCC--TCAAATTTTGATTA-CTTCATAA
1 TGAAATTTTGATAAT-CTCCCTATGAAATTTTGATAACCATC-TTA
* * * * * * *
9766 TAAAAGTTTAATAACCTTCCT-T---A-TTTGGTAACCATATTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCATCTTA
* *
9805 TGAAATTTTGATAACCTCCCCA--AAA-----AT-ACCA-C-TA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCATCTTA
* * ** * *
9839 TGAAATTTTGGTAATCACATTTTGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCATC-TTA
* * * * * *
9883 TGAAATTTTGTTGA-CCCCTCTATGAAATTCTGATAA-TAACATTA
1 TGAAATTTTGATAATCTCC-CTATGAAATTTTGATAACCATC-TTA
* * * *
9927 TGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACA-C-TA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAAC--CATCTTA
*
9971 TGAAATTTTGATAATCTACCTAT-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAA-CC-ATCT-TA
* * * *
10017 TGAAATTTCGATAATCACTCTATGAGA-TTTGATA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATA
10051 TCTTTCTATC
Statistics
Matches: 409, Mismatches: 87, Indels: 94
0.69 0.15 0.16
Matches are distributed among these distances:
34 17 0.04
36 7 0.02
37 1 0.00
38 7 0.02
39 46 0.11
40 5 0.01
41 9 0.02
42 31 0.08
43 23 0.06
44 170 0.42
45 37 0.09
46 52 0.13
47 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (44 bp):
TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCATCTTA
Found at i:9942 original size:66 final size:66
Alignment explanation
Indices: 9834--9985 Score: 180
Period size: 66 Copynumber: 2.3 Consensus size: 66
9824 CCAAAAATAC
* * * * * *
9834 CACTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTC-TTTATGAAATTTTGTTGAC
1 CACTATGAAATTTTGATAATAACATTATGAAAATTTGATAACCTCGCTT-TGAAATTTTGATAAC
**
9898 CC
65 AA
* * * *
9900 CTCTATGAAATTCTGATAATAACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACA
1 CACTATGAAATTTTGATAATAACATTATGAAAATTTGATAACCTCGCTTTGAAATTTTGATAACA
9965 A
66 A
9966 CACTATGAAATTTTGATAAT
1 CACTATGAAATTTTGATAAT
9986 CTACCTATAA
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
66 69 0.97
67 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (66 bp):
CACTATGAAATTTTGATAATAACATTATGAAAATTTGATAACCTCGCTTTGAAATTTTGATAACA
A
Found at i:10040 original size:22 final size:23
Alignment explanation
Indices: 9836--10050 Score: 121
Period size: 22 Copynumber: 9.7 Consensus size: 23
9826 AAAAATACCA
*
9836 CTATGAAATTTTGGTAATC-ACAT
1 CTATGAAATTTTGATAATCAAC-T
* * **
9859 -TTTGAAAATTTGATAA-CCTCT
1 CTATGAAATTTTGATAATCAACT
* * * **
9880 TTATGAAATTTTGTTGA-CCCCT
1 CTATGAAATTTTGATAATCAACT
*
9902 CTATGAAATTCTGATAAT-AACAT
1 CTATGAAATTTTGATAATCAAC-T
* ** *
9925 -TATGTAATTTTGATAA-CCTCG
1 CTATGAAATTTTGATAATCAACT
* *
9946 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATCAACT
*
9968 CTATGAAATTTTGATAATCTAC-
1 CTATGAAATTTTGATAATCAACT
*
9990 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAAT-C-AACT
*
10014 CTATGAAATTTCGATAATC-ACT
1 CTATGAAATTTTGATAATCAACT
*
10036 CTATGAGA-TTTGATA
1 CTATGAAATTTTGATA
10051 TCTTTCTATC
Statistics
Matches: 148, Mismatches: 33, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
21 21 0.14
22 105 0.71
23 5 0.03
24 5 0.03
25 12 0.08
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCAACT
Found at i:10120 original size:22 final size:22
Alignment explanation
Indices: 9861--10167 Score: 70
Period size: 22 Copynumber: 13.8 Consensus size: 22
9851 AATCACATTT
* *
9861 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
* * *
9883 TGAAATTTTGTTGACCCCTC-TA
1 TGAAATTTTGAT-AACCTTCATA
* *
9905 TGAAATTCTGATAA--TAACATTA
1 TGAAATTTTGATAACCT-TCA-TA
* * *
9927 TGTAATTTTGATAACC-TCGCTT
1 TGAAATTTTGATAACCTTC-ATA
**
9949 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * *
9971 TGAAATTTTGATAATCTACCTA
1 TGAAATTTTGATAACCTTCATA
9993 T-AAATTTTGATAATCCGATCTC-TA
1 TGAAATTTTGATAA-CC--T-TCATA
*
10017 TGAAATTTCGATAATCAC-TC-TA
1 TGAAATTTTGATAA-C-CTTCATA
* * *
10039 TGAGA-TTTGATATCTTTC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
10059 TCAAATTTTGGT-ACTCCTCATGAAA
1 TGAAATTTTGATAAC-CTTCAT---A
*
10084 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
*
10107 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
** *
10129 AAAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
*
10151 TGAAATTTTAATAACCT
1 TGAAATTTTGATAACCT
10168 CCCCATGATA
Statistics
Matches: 212, Mismatches: 43, Indels: 59
0.68 0.14 0.19
Matches are distributed among these distances:
20 10 0.05
21 34 0.16
22 124 0.58
23 7 0.03
24 6 0.03
25 15 0.07
26 9 0.04
27 7 0.03
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:10175 original size:22 final size:22
Alignment explanation
Indices: 10131--10191 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
10121 CCACACTAAA
* * * *
10131 AAATTTTGATAACCACACTATG
1 AAATTTTAATAACCTCCCCATG
10153 AAATTTTAATAACCTCCCCATG
1 AAATTTTAATAACCTCCCCATG
* * *
10175 ATATATTAGTAACCTCC
1 AAATTTTAATAACCTCC
10192 TTATAAAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (22 bp):
AAATTTTAATAACCTCCCCATG
Found at i:10300 original size:22 final size:21
Alignment explanation
Indices: 10275--10489 Score: 135
Period size: 22 Copynumber: 9.7 Consensus size: 21
10265 CTTTCTATAT
*
10275 AATTGTGATAACCACACTATGA
1 AATTTTGATAACCAC-CTATGA
** * *
10297 AATTTCAATAACCGTCCTAAGA
1 AATTTTGATAACC-ACCTATGA
*
10319 AATTTTAATAACCTGATCCTATGA
1 AATTTTGATAACC--A-CCTATGA
* * *
10343 AATTTAGGTAAGCACACTATGA
1 AATTTTGATAACCAC-CTATGA
* * *
10365 ATTTTTGATAACCTTCCCATGA
1 AATTTTGATAACC-ACCTATGA
***
10387 AATTTTGATAAGTTCCATATGA
1 AATTTTGATAACCACC-TATGA
*
10409 AATTTTTG-TAACCACACTATGG
1 AA-TTTTGATAACCAC-CTATGA
*
10431 AATTTTGATAACCTCCTCATGA
1 AATTTTGATAACCACCT-ATGA
* * *
10453 AATTATAATAACCATCTTATGA
1 AATTTTGATAACCA-CCTATGA
10475 AATTTTGATAACCAC
1 AATTTTGATAACCAC
10490 ACAGAGACAA
Statistics
Matches: 148, Mismatches: 34, Indels: 23
0.72 0.17 0.11
Matches are distributed among these distances:
21 12 0.08
22 110 0.74
23 11 0.07
24 15 0.10
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (21 bp):
AATTTTGATAACCACCTATGA
Found at i:10437 original size:66 final size:65
Alignment explanation
Indices: 10283--10491 Score: 206
Period size: 66 Copynumber: 3.1 Consensus size: 65
10273 ATAATTGTGA
* ** * *
10283 TAACCACACTATGAAATTTCAATAACCGTCCTAAGAAATTTTAATAACCTGATCCTATGAAATTT
1 TAACCACACTATGGAATTTTGATAACC-TCCCATGAAATTTTAATAA-C-GATCCTATGAAATTT
10348 AGG
63 AGG
* * *
10351 TAAGCACACTAT-GAATTTTTGATAACCTTCCCATGAAATTTTGATAA-GTTCCATATGAAATTT
1 TAACCACACTATGGAA-TTTTGATAACC-TCCCATGAAATTTTAATAACGATCC-TATGAAATTT
**
10414 TTG
63 AGG
* * * *
10417 TAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTG
1 TAACCACACTATGGAATTTTGATAACCTCC-CATGAAATTTTAATAACGATCCTATGAAATTTAG
*
10482 A
65 G
10483 TAACCACAC
1 TAACCACAC
10492 AGAGACAAGG
Statistics
Matches: 117, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
65 7 0.06
66 67 0.57
67 7 0.06
68 36 0.31
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (65 bp):
TAACCACACTATGGAATTTTGATAACCTCCCATGAAATTTTAATAACGATCCTATGAAATTTAGG
Found at i:10884 original size:13 final size:13
Alignment explanation
Indices: 10866--10893 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10856 TCGTACTTTT
10866 ATATATAGTATAG
1 ATATATAGTATAG
10879 ATATATAGTATAG
1 ATATATAGTATAG
10892 AT
1 AT
10894 TTGGAGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (13 bp):
ATATATAGTATAG
Found at i:11904 original size:2 final size:2
Alignment explanation
Indices: 11897--11925 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11887 AGGCAAATAC
11897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11926 CACACAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.