Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013174.1 Corchorus olitorius cultivar O-4 contig13207, 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: 47350
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:687 original size:45 final size:42
Alignment explanation
Indices: 638--731 Score: 136
Period size: 45 Copynumber: 2.2 Consensus size: 42
628 AGCAACAATT
*
638 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT--A-GAGTAG
*
683 AATATCAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
725 AAT-TTAG
1 AATATTAG
732 ATAATAGACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 9 0.20
43 1 0.02
45 33 0.72
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
Found at i:2258 original size:41 final size:44
Alignment explanation
Indices: 2222--2308 Score: 129
Period size: 45 Copynumber: 2.0 Consensus size: 44
2212 TACCTAAATT
*
2222 CTACTCCATCTCTAGGTAATTCATCAAAATAAACCTAATATTTTA
1 CTACTCCATCTCTAGATAATTCATCAAAATAAACCTAATA-TTTA
* **
2267 CTCCTCCATCTCTAGATAATTCATCAAAATAAAATTAATATT
1 CTACTCCATCTCTAGATAATTCATCAAAATAAACCTAATATT
2309 AATTGTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
44 2 0.05
45 36 0.95
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (44 bp):
CTACTCCATCTCTAGATAATTCATCAAAATAAACCTAATATTTA
Found at i:4972 original size:204 final size:203
Alignment explanation
Indices: 4614--5008 Score: 614
Period size: 204 Copynumber: 1.9 Consensus size: 203
4604 TTTAATATTT
* *
4614 AAAAAGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAGT
1 AAAAAGGGTAATCATTTGATACACCGGCGGTGTAAATTTTGAACTCCACAAGCGGGTTGTGAAGT
* * * *
4679 TGACACATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCTCTAGAGGACAC
66 TGACACATGTCCATTTTCTGAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGAGGACAC
* * * *
4744 ATGTCACCCTTCAGGATCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGGTGTATTGTATAATTT
131 ATGTCACCCTTCAAGATCCGCTTGTGCAGTCTGCTAAACTCCACCGACGGTGTATTATATAATTT
4809 TCCATTAA
196 TCCATTAA
* *
4817 AAAATAGGGTAATCATTTGATACACCTGCGGTGTAAATTTTGAACTCCACAAGCGGGTTGTGGAG
1 AAAA-AGGGTAATCATTTGATACACCGGCGGTGTAAATTTTGAACTCCACAAGCGGGTTGTGAAG
*
4882 TTGACACATGTCTATTTTCTGAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTA-AGGGAC
65 TTGACACATGTCCATTTTCTGAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGA-GGAC
* *
4946 ACATGTCACCCTTCAAGA-CTCGCTTGTGCAGTCTGCTAAACTCCGCTGACGGTGTATTATATA
129 ACATGTCACCCTTCAAGATC-CGCTTGTGCAGTCTGCTAAACTCCACCGACGGTGTATTATATA
5009 TAAACTCTAA
Statistics
Matches: 174, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
203 6 0.03
204 168 0.97
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (203 bp):
AAAAAGGGTAATCATTTGATACACCGGCGGTGTAAATTTTGAACTCCACAAGCGGGTTGTGAAGT
TGACACATGTCCATTTTCTGAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGAGGACAC
ATGTCACCCTTCAAGATCCGCTTGTGCAGTCTGCTAAACTCCACCGACGGTGTATTATATAATTT
TCCATTAA
Found at i:11567 original size:37 final size:37
Alignment explanation
Indices: 11472--11567 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 37
11462 CAGTGCTTTG
*
11472 GGAGAGCTCTGCGGTGAAGATGGGAGCCGCCGCAGTAA
1 GGAGAGCTCTGCGGTGAAGA-GGGAGCCACCGCAGTAA
* * * *
11510 GGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCGGTAA
1 GGAGAGCTCTGCGGTGAAGAGGGAGCCACCGCAGTAA
*
11547 GGAGAGCTCTGCGATGAAGAG
1 GGAGAGCTCTGCGGTGAAGAG
11568 TGCTATCGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 32 0.63
38 19 0.37
ACGTcount: A:0.25, C:0.19, G:0.42, T:0.15
Consensus pattern (37 bp):
GGAGAGCTCTGCGGTGAAGAGGGAGCCACCGCAGTAA
Found at i:12747 original size:18 final size:19
Alignment explanation
Indices: 12724--12759 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
12714 AGGAAAAGAA
12724 ATGTGTTGGGCCT-TTTTC
1 ATGTGTTGGGCCTCTTTTC
12742 ATGTGTTGGGCCTCTTTT
1 ATGTGTTGGGCCTCTTTT
12760 GTGTGTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.06, C:0.17, G:0.28, T:0.50
Consensus pattern (19 bp):
ATGTGTTGGGCCTCTTTTC
Found at i:24267 original size:15 final size:15
Alignment explanation
Indices: 24243--24273 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24233 TTATATATAC
24243 AATAGAGATGGTCTT
1 AATAGAGATGGTCTT
*
24258 AATAGCGATGGTCTT
1 AATAGAGATGGTCTT
24273 A
1 A
24274 CATTCTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (15 bp):
AATAGAGATGGTCTT
Found at i:45644 original size:44 final size:43
Alignment explanation
Indices: 45596--46412 Score: 246
Period size: 44 Copynumber: 19.0 Consensus size: 43
45586 AATCACACTC
* * * *
45596 TGAAATTTTGATAATCACACTATGAAATTGTAATAACCTCGTTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTC-TTA
* * * *
45640 TGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AATCTCCCTATGAAATTTTGAT-AACCT-CTTA
* * * *
45686 TAAAATTTTGATAACCTCCTTATGAAATCTTGATAA---C-TA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCTTA
* * **
45725 -CAAATTTTTATAATCTCCCTATGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTC-TTA
*
45768 TGAAATTTTGTTAATCTCCCTATGAAATTTTGATAACCATCTTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACC-TCTTA
* ** *
45812 TGAAATTTTGA-AAACTAAACTATGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAATCT-CCCTATGAAATTTTGATAACC-TCTTA
* * * *
45856 TGAAATTTTGAT-ATCCTCCC--TCAAATTTTGATTACTTCATAA
1 TGAAATTTTGATAAT-CTCCCTATGAAATTTTGATAACCTC-TTA
* * * * * * * *
45898 TAAAAGTTTAATCACCTTCCT-T---A-TTTGGTAACCATATTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACC-TCTTA
* * *
45937 TGAAATTTTGATAACCTCCCCA-G-AA-----AT-ACCAC-TA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCTTA
* * ** * *
45971 TGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTC-TTA
* * * * *
46015 TGAAATTTTGATAA-C-CCATCGATAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAATCTCC--CTATGAAATTTTGATAACCTCT-TA
* ** ** *
46059 TGAAATTCTGATAATAACATTATGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCT--CTTA
* * * * *
46103 TGAAATTTTGATAA-CAACACTATGAAATTTTCATAATCTACCTA
1 TGAAATTTTGATAATC-TCCCTATGAAATTTTGATAACCT-CTTA
* * *
46147 T-AAATTTTGATAATTCGATCTCTATAAAATTTCGATAATCACTC-TA
1 TGAAATTTTGATAA-TC--TCCCTATGAAATTTTGATAA-C-CTCTTA
* ** * * * *
46193 TGAGA-TTTGAT-ATCTTTCTATCAAATTTTGGTACTCCTCATGAAA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATA-ACCTC-T--TA
* * * * * *
46238 TTGAGACTTTT-ATAACCTTCATATGAAATTTTGATAACCACACTA
1 -TGA-AATTTTGATAATCTCCCTATGAAATTTTGATAACCTC-TTA
** * * * * **
46283 AAAAATTTTGATAACCACACTATGAAATTTTAATAACCTCCCCA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCT-CTTA
* * * * *
46327 TGATATATT-AGTAACCTCCTTATGAAATTTT-ATTAACCACATTA
1 TGAAATTTTGA-TAATCTCCCTATGAAATTTTGA-TAACCTC-TTA
* * * *
46371 TGAAATTCTT-ATAACCTCGCTATGACATTTTGATAATCTCTT
1 TGAAATT-TTGATAATCTCCCTATGAAATTTTGATAACCTCTT
46413 TGATAACCTT
Statistics
Matches: 567, Mismatches: 145, Indels: 123
0.68 0.17 0.15
Matches are distributed among these distances:
34 17 0.03
35 1 0.00
36 5 0.01
37 1 0.00
38 28 0.05
39 26 0.05
40 3 0.01
41 9 0.02
42 48 0.08
43 34 0.06
44 267 0.47
45 47 0.08
46 49 0.09
47 10 0.02
48 22 0.04
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (43 bp):
TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCTTA
Found at i:45653 original size:22 final size:22
Alignment explanation
Indices: 45439--45876 Score: 259
Period size: 22 Copynumber: 20.0 Consensus size: 22
45429 TTAACATTCT
*
45439 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * **
45461 TAAGGAATTTTGA-AGACCTCAT
1 TATGAAATTTTGATA-ACCTCCC
* *
45483 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCCC
* * *
45506 TATGAGATGTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* * * * **
45528 AATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCC
* * * *
45550 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* * *
45572 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAACCTCCC
* * * *
45594 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCCC
* * **
45616 TATGAAATTGTAATAACCTCGT
1 TATGAAATTTTGATAACCTCCC
*
45638 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTCCC
*
45661 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCC
* *
45684 TATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCTCCC
*
45706 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTCCC
* * *
45723 TA-CAAATTTTTATAATCTCCC
1 TATGAAATTTTGATAACCTCCC
** **
45744 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCC
* *
45766 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCC
*
45788 TATGAAATTTTGATAACCAT-CT
1 TATGAAATTTTGATAACC-TCCC
* **
45810 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CCC
* *
45832 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTCCC
*
45854 TATGAAATTTTGATATCCTCCC
1 TATGAAATTTTGATAACCTCCC
45876 T
1 T
45877 CAAATTTTGA
Statistics
Matches: 315, Mismatches: 83, Indels: 36
0.73 0.19 0.08
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
20 1 0.00
21 11 0.03
22 222 0.70
23 69 0.22
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:45668 original size:23 final size:23
Alignment explanation
Indices: 45642--45721 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
45632 CCTCGTTATG
45642 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
45665 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
45688 AAATTTTGAT-AACC-TCCTTATG
1 AAATTTTGATAAACCTTCC-TATA
*
45710 AAATCTTGATAA
1 AAATTTTGATAA
45722 CTACAAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.04
22 16 0.31
23 33 0.65
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTTCCTATA
Found at i:46394 original size:22 final size:22
Alignment explanation
Indices: 45966--46406 Score: 159
Period size: 22 Copynumber: 19.9 Consensus size: 22
45956 CCAGAAATAC
* *
45966 CACTATGAAATTTTGGTAATCA
1 CACTATGAAATTTTGATAACCA
* * * *
45988 CATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAACCA
**
46010 CTTTATGAAATTTTGATAACC-
1 CACTATGAAATTTTGATAACCA
* * * * *
46031 CATCGATAAAATTTTGTTGACCC
1 CA-CTATGAAATTTTGATAACCA
* * **
46054 CTCTATGAAATTCTGATAATAA
1 CACTATGAAATTTTGATAACCA
* * *
46076 CATTATGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * *
46098 CGCTTTGAAATTTTGATAACAA
1 CACTATGAAATTTTGATAACCA
* *
46120 CACTATGAAATTTTCATAATCTA
1 CACTATGAAATTTTGATAA-CCA
*
46143 C-CTAT-AAATTTTGATAATTCGA
1 CACTATGAAATTTTGATAA--CCA
* * * *
46165 TCTCTATAAAATTTCGATAATCA
1 -CACTATGAAATTTTGATAACCA
* * * *
46188 CTCTATGAGA-TTTGAT-ATCT
1 CACTATGAAATTTTGATAACCA
** * * * *
46208 TTCTATCAAATTTTGGTACTCCT
1 CACTATGAAATTTTGATA-ACCA
* *
46231 CA-TGAAATTGAGACTTTT-ATAACCTT
1 CACT---A-TGA-AATTTTGATAACC-A
46257 CA-TATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
**
46278 CACTAAAAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
* *
46300 CACTATGAAATTTTAATAACCT
1 CACTATGAAATTTTGATAACCA
* * * * *
46322 CCCCATGATATATT-AGTAACCT
1 CACTATGAAATTTTGA-TAACCA
46344 C-CTTATGAAATTTT-ATTAACCA
1 CAC-TATGAAATTTTGA-TAACCA
* *
46366 CATTATGAAATTCTT-ATAACCT
1 CACTATGAAATT-TTGATAACCA
* *
46388 CGCTATGACATTTTGATAA
1 CACTATGAAATTTTGATAA
46407 TCTCTTTGAT
Statistics
Matches: 312, Mismatches: 84, Indels: 46
0.71 0.19 0.10
Matches are distributed among these distances:
20 10 0.03
21 33 0.11
22 226 0.72
23 12 0.04
24 4 0.01
25 14 0.04
26 8 0.03
27 5 0.02
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:46455 original size:22 final size:22
Alignment explanation
Indices: 46430--46644 Score: 106
Period size: 22 Copynumber: 9.8 Consensus size: 22
46420 CTTTCTATAT
*
46430 AATTGTGATAACCACACTATGA
1 AATTTTGATAACCACACTATGA
** * *
46452 AATTTCAATAACCTTC-CTAAGA
1 AATTTTGATAACC-ACACTATGA
* *
46474 AATTTTAATAACCTA-ATCCAATGA
1 AATTTTGATAACC-ACA--CTATGA
* * *
46498 AATTTAGGTAAGCACACTATGA
1 AATTTTGATAACCACACTATGA
* * *
46520 ATTTTTGATAACCTTC-CCATGA
1 AATTTTGATAACC-ACACTATGA
*
46542 AA-TTTGATAAGTTC-CA-TATGA
1 AATTTTGATAA--CCACACTATGA
*
46563 AATTTTG-TAACCACACTATGG
1 AATTTTGATAACCACACTATGA
*
46584 AATTTTGATAACCTC-CTCATGA
1 AATTTTGATAACCACACT-ATGA
* * * *
46606 AATTATAATAACCATC-TTACGA
1 AATTTTGATAACCA-CACTATGA
46628 AATTTTGATAACCACAC
1 AATTTTGATAACCACAC
46645 AGAGGCAAGA
Statistics
Matches: 142, Mismatches: 35, Indels: 32
0.68 0.17 0.15
Matches are distributed among these distances:
19 1 0.01
20 2 0.01
21 32 0.23
22 87 0.61
23 6 0.04
24 14 0.10
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
AATTTTGATAACCACACTATGA
Found at i:46593 original size:64 final size:66
Alignment explanation
Indices: 46438--46644 Score: 192
Period size: 64 Copynumber: 3.1 Consensus size: 66
46428 ATAATTGTGA
* ** * *
46438 TAACCACACTATGAAATTTCAATAACCTTCCTAAGAAATTTTAATAACCTAATCCAATGAAATTT
1 TAACCACACTATGGAATTTTGATAACCTTCCCATGAAA-TTTAATAACCT-ATCCAATGAAATTT
46503 AGG
64 AGG
* * *
46506 TAAGCACACTAT-GAATTTTTGATAACCTTCCCATGAAATTTGATAA-GT-TCCATATGAAATTT
1 TAACCACACTATGGAA-TTTTGATAACCTTCCCATGAAATTTAATAACCTATCCA-ATGAAATTT
*
46568 -TG
64 AGG
** *
46570 TAACCACACTATGGAATTTTGATAACC-TCCTCATGAAATTATAATAACC-ATCTTACGAAATTT
1 TAACCACACTATGGAATTTTGATAACCTTCC-CATGAAATT-TAATAACCTATCCAATGAAATTT
* *
46633 TGA
64 AGG
46636 TAACCACAC
1 TAACCACAC
46645 AGAGGCAAGA
Statistics
Matches: 114, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
63 3 0.03
64 36 0.32
65 25 0.22
66 12 0.11
67 9 0.08
68 29 0.25
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (66 bp):
TAACCACACTATGGAATTTTGATAACCTTCCCATGAAATTTAATAACCTATCCAATGAAATTTAG
G
Found at i:47037 original size:13 final size:13
Alignment explanation
Indices: 47019--47046 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47009 TCGTACTTTT
47019 ATATATAGTATAG
1 ATATATAGTATAG
47032 ATATATAGTATAG
1 ATATATAGTATAG
47045 AT
1 AT
47047 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
Done.