Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018394.1 Corchorus olitorius cultivar O-4 contig18427, 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: 62855
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:14 original size:2 final size:2
Alignment explanation
Indices: 8--47 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 TAAGTAG
8 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48 CCAGTAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1608 original size:2 final size:2
Alignment explanation
Indices: 1601--1632 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1591 TTTTGCCTGG
1601 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1633 ATGTTCTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:18022 original size:22 final size:22
Alignment explanation
Indices: 17994--18950 Score: 272
Period size: 22 Copynumber: 43.6 Consensus size: 22
17984 TTCACTGCGG
* *
17994 GAAATTTTGAAAACCTCATTAT
1 GAAATTTTGATAACCTCACTAT
* * * *
18016 GAAATTTTAATAACTTCTCAAT
1 GAAATTTTGATAACCTCACTAT
* *
18038 GAAGTTTTGATAACCAACACTAT
1 GAAATTTTGATAACC-TCACTAT
*
18061 GAGATTTTGATAACCTTCA-TAT
1 GAAATTTTGATAACC-TCACTAT
* * * **
18083 GATATATTGATAACCACGTTAT
1 GAAATTTTGATAACCTCACTAT
* *
18105 GAAAATTTGAAAACCTC-CATAT
1 GAAATTTTGATAACCTCAC-TAT
* * *
18127 G-AATTATT-AGTAATCACACTCT
1 GAAATT-TTGA-TAACCTCACTAT
* * *
18149 AAAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCTCACTAT
* *
18171 GAAATTGTGATAACCTCGCTAT
1 GAAATTTTGATAACCTCACTAT
18193 GAAATTTTGATAAACCTTC-CTAT
1 GAAATTTTGAT-AACC-TCACTAT
*
18216 AAAATTTTGATAAACCTC-CTTAT
1 GAAATTTTGAT-AACCTCAC-TAT
*
18239 AAAATTTTGATAACCTC-CTTAT
1 GAAATTTTGATAACCTCAC-TAT
* *
18261 GAAATCTTCATAA-CT-AC---
1 GAAATTTTGATAACCTCACTAT
* *
18278 -AAATTTTGATAACATCCCTAT
1 GAAATTTTGATAACCTCACTAT
** * * *
18299 GATTTTTTTGTTAATCTCCCTAT
1 GA-AATTTTGATAACCTCACTAT
* * *
18322 AAAAATTTTGATCTATA-CTAATAGTAT
1 -GAAATTTTGA--TA-ACCT--CACTAT
*
18349 GAAATTTTGATAACCCTC-TTAT
1 GAAATTTTGATAA-CCTCACTAT
18371 GAAATTTTGATAACCTTCA-TAT
1 GAAATTTTGATAACC-TCACTAT
* * *
18393 GAAATTTTGATATCTTC-C-CT
1 GAAATTTTGATAACCTCACTAT
*
18413 GAAATTTTGATTA-CTC-CATAAT
1 GAAATTTTGATAACCTCAC-T-AT
* * * *
18435 AAAAGTTTAATAACCTC-C-CT
1 GAAATTTTGATAACCTCACTAT
*
18455 -AAA-TTTGGTAACCAT-ACTAT
1 GAAATTTTGATAACC-TCACTAT
* *
18475 GAAATTTTGATAACCTCCCCA-
1 GAAATTTTGATAACCTCACTAT
* **
18496 -AAA-----ATACCACT-ATGAT
1 GAAATTTTGATAAC-CTCACTAT
* * * * *
18512 GAAATTTTGGTAATCACATTTT
1 GAAATTTTGATAACCTCACTAT
* * **
18534 GAAAATTTGATAGCCTCTTTAT
1 GAAATTTTGATAACCTCACTAT
*
18556 GAAATTTTGATAACCTCTCTAT
1 GAAATTTTGATAACCTCACTAT
* * * * *
18578 AAAATTTTGTTGACCCCTCTAT
1 GAAATTTTGATAACCTCACTAT
* * *
18600 GAAATTTTGATAATCACATTAT
1 GAAATTTTGATAACCTCACTAT
** * *
18622 GTTATTTTGATAACCTCGCTTT
1 GAAATTTTGATAACCTCACTAT
* **
18644 GAAACTTTGATAACAACACTAT
1 GAAATTTTGATAACCTCACTAT
*
18666 GAAATTTTGATAATCTTC-CTAT
1 GAAATTTTGATAA-CCTCACTAT
* *
18688 -AAATTTTGATAATCAGATCTCTAT
1 GAAATTTTGATAA-C--CTCACTAT
* * * *
18712 GAAATTTCGATAATCACTCTAT
1 GAAATTTTGATAACCTCACTAT
*
18734 -AAGA-TTTGATAACCT-TCTAT
1 GAA-ATTTTGATAACCTCACTAT
* * ** *
18754 CAAATTTTGGTTTTCCTTA-TGAAATT
1 GAAATTTT-GATAACCTCACT---A-T
*
18780 GAGACTTTT-ATAACCTTCA-TAT
1 GA-AATTTTGATAACC-TCACTAT
* * *
18802 GAAATCTTGATAACCACACTAA
1 GAAATTTTGATAACCTCACTAT
* *
18824 AAAATTTTGATAACTAACCACACTAT
1 GAAATTTTG---A-TAACCTCACTAT
* * *
18850 GAAATTTTGATAATCTCCCCAT
1 GAAATTTTGATAACCTCACTAT
* * *
18872 GAAATATTAATAGCCTC-CTTAT
1 GAAATTTTGATAACCTCAC-TAT
* *
18894 GAAATTTTGTTAACCACACTAT
1 GAAATTTTGATAACCTCACTAT
**
18916 GAAATTCTT-ATAACCTCGTTAT
1 GAAATT-TTGATAACCTCACTAT
*
18938 GACATTTTGATAA
1 GAAATTTTGATAA
18951 TCTCTTTGAT
Statistics
Matches: 687, Mismatches: 173, Indels: 150
0.68 0.17 0.15
Matches are distributed among these distances:
15 5 0.01
16 12 0.02
17 4 0.01
18 9 0.01
19 8 0.01
20 23 0.03
21 55 0.08
22 402 0.59
23 96 0.14
24 9 0.01
25 22 0.03
26 34 0.05
27 8 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
GAAATTTTGATAACCTCACTAT
Found at i:18254 original size:45 final size:45
Alignment explanation
Indices: 18148--18254 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 45
18138 AATCACACTC
* *
18148 TAAAATTTTGATAATC-ACACTATGAAATTGTGATAACCTCGCTA
1 TAAAATTTTGATAACCTACACTATAAAATTGTGATAACCTCGCTA
* * *
18192 TGAAATTTTGATAAACCTTC-CTATAAAATTTTGATAAACCTC-CTTA
1 TAAAATTTTGAT-AACCTACACTATAAAATTGTGAT-AACCTCGC-TA
18238 TAAAATTTTGATAACCT
1 TAAAATTTTGATAACCT
18255 CCTTATGAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 11 0.21
45 22 0.42
46 20 0.38
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (45 bp):
TAAAATTTTGATAACCTACACTATAAAATTGTGATAACCTCGCTA
Found at i:18760 original size:20 final size:21
Alignment explanation
Indices: 18662--18745 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 21
18652 GATAACAACA
* *
18662 CTATGAAATTTTGATAATC-TT
1 CTAT-AAATTTCGATAATCACT
*
18683 CCTATAAATTTTGATAATCAGATCT
1 -CTATAAATTTCGATAATC--A-CT
18708 CTATGAAATTTCGATAATCACT
1 CTAT-AAATTTCGATAATCACT
18730 CTATAAGATTT-GATAA
1 CTATAA-ATTTCGATAA
18746 CCTTCTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
21 21 0.39
22 14 0.26
23 1 0.02
24 4 0.07
25 14 0.26
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (21 bp):
CTATAAATTTCGATAATCACT
Found at i:18848 original size:26 final size:26
Alignment explanation
Indices: 18812--18862 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
18802 GAAATCTTGA
18812 TAACCACACTAAAAAATTTTGATAAC
1 TAACCACACTAAAAAATTTTGATAAC
**
18838 TAACCACACTATGAAATTTTGATAA
1 TAACCACACTAAAAAATTTTGATAA
18863 TCTCCCCATG
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:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (26 bp):
TAACCACACTAAAAAATTTTGATAAC
Found at i:19065 original size:22 final size:22
Alignment explanation
Indices: 18982--19191 Score: 130
Period size: 22 Copynumber: 9.5 Consensus size: 22
18972 AAAATTGTAT
**
18982 ATAACCACACTATGAAATTTCA
1 ATAACCACACTATGAAATTTTG
* * *
19004 ATAACCTTCA-TAAGAAATTTTA
1 ATAACC-ACACTATGAAATTTTG
*
19026 ATAA-CATGATCCTATGAAATTTTG
1 ATAACCA-CA--CTATGAAATTTTG
*
19050 GTAACCACACTATGAAATTTTG
1 ATAACCACACTATGAAATTTTG
* *
19072 ATAACCTTC-CCATGAAATTTTG
1 ATAACC-ACACTATGAAATTTTG
*
19094 ATATCTTC-CA-TATGAAATTTTG
1 ATAAC--CACACTATGAAATTTTG
* *
19116 GTAACCACACTATGGAATTTTG
1 ATAACCACACTATGAAATTTTG
* * * *
19138 ATAACCTC-CTCAAGAAATTATA
1 ATAACCACACT-ATGAAATTTTG
19160 ATAA-CA-ATCTTATGAAATTTTG
1 ATAACCACA-C-TATGAAATTTTG
19182 ATAACCACAC
1 ATAACCACAC
19192 AGAGACAAGA
Statistics
Matches: 143, Mismatches: 27, Indels: 35
0.70 0.13 0.17
Matches are distributed among these distances:
20 1 0.01
21 7 0.05
22 110 0.77
23 7 0.05
24 16 0.11
25 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (22 bp):
ATAACCACACTATGAAATTTTG
Found at i:19137 original size:66 final size:67
Alignment explanation
Indices: 18983--19191 Score: 262
Period size: 66 Copynumber: 3.1 Consensus size: 67
18973 AAATTGTATA
** *
18983 TAACCACACTATGAAATTTCAATAACCTTCATAAGAAATTTTAATAACATGATCCTATGAAATTT
1 TAACCACACTATGAAATTTTGATAACCTTCACAAGAAATTTTAATAACAT-ATCCTATGAAATTT
19048 TGG
65 TGG
* * * *
19051 TAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATATC-T-TCCATATGAAATTT
1 TAACCACACTATGAAATTTTGATAACCTTCACAAGAAATTTTAATAACATATCC-TATGAAATTT
19114 TGG
65 TGG
* * * * *
19117 TAACCACACTATGGAATTTTGATAACCTCCTCAAGAAATTATAATAACA-ATCTTATGAAATTTT
1 TAACCACACTATGAAATTTTGATAACCTTCACAAGAAATTTTAATAACATATCCTATGAAATTTT
*
19181 GA
66 GG
19183 TAACCACAC
1 TAACCACAC
19192 AGAGACAAGA
Statistics
Matches: 122, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
65 3 0.02
66 75 0.61
67 3 0.02
68 41 0.34
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (67 bp):
TAACCACACTATGAAATTTTGATAACCTTCACAAGAAATTTTAATAACATATCCTATGAAATTTT
GG
Found at i:22371 original size:21 final size:23
Alignment explanation
Indices: 22342--22398 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 23
22332 TTTTGAACTC
22342 ATTATTTATAATTTAA-AATATAT
1 ATTA-TTATAATTTAATAATATAT
* *
22365 -TTATTATTTATTTAATAGTATAT
1 ATTATTA-TAATTTAATAATATAT
22388 ATTATATATAA
1 ATTAT-TATAA
22399 GATAGTAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
21 3 0.11
22 10 0.37
23 6 0.22
24 6 0.22
25 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTATTATAATTTAATAATATAT
Found at i:24637 original size:32 final size:32
Alignment explanation
Indices: 24567--24637 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
24557 TTTGAATTAG
* *
24567 CCAAATTGGATTAGGATTTGATGTATTCCTCA
1 CCAAATTGGATTAGGATTAGATGTATTCCTAA
**
24599 TGAAATTAGG-TTAGGATTAGATG-ATTCCTAAA
1 CCAAATT-GGATTAGGATTAGATGTATTCCT-AA
24631 CCAAATT
1 CCAAATT
24638 TAACAAGGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
31 6 0.19
32 23 0.74
33 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
CCAAATTGGATTAGGATTAGATGTATTCCTAA
Found at i:40115 original size:15 final size:16
Alignment explanation
Indices: 40090--40119 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40080 CTTTGCTTTG
40090 TTTTCTAGTTTAATTT
1 TTTTCTAGTTTAATTT
40106 TTTTCT-GTTTAATT
1 TTTTCTAGTTTAATT
40120 GCTTTCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (16 bp):
TTTTCTAGTTTAATTT
Found at i:43062 original size:12 final size:13
Alignment explanation
Indices: 43034--43063 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
43024 ACTCCTAATC
43034 TTTTAAGCCAAGT
1 TTTTAAGCCAAGT
43047 TTTTAAGCCAAGT
1 TTTTAAGCCAAGT
43060 TTTT
1 TTTT
43064 CTTTGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (13 bp):
TTTTAAGCCAAGT
Found at i:49831 original size:297 final size:294
Alignment explanation
Indices: 49273--49843 Score: 946
Period size: 297 Copynumber: 1.9 Consensus size: 294
49263 CATTATTTTT
* *
49273 ATTGACTATGCAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGTCTCTTTTTGGCTTTTT
1 ATTGACTATGCAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCTTTTT
* * *
49338 TTGGTCTTTTCTTACTTTTCGGGTGACTAAAAAGGCCCTTGATGAATTTCATCTCTTACTTTTCC
66 TTGGTCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCATCCCTTACTTTTCC
*
49403 TCCTGCCCTTTTTTGTAATTTACTATTTTTGTATTTATGATTAAGTGTGTTTTAATTACATATTA
131 TCCTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTA
* * *
49468 ATTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGAATTGGTGCT
196 ATCGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATCCCAAAGAATTAGTGCT
49533 ATAAATGTATCTACCTGAATTCATTAATTTAACA
261 ATAAATGTATCTACCTGAATTCATTAATTTAACA
*
49567 ATTG-CTATGGAAATTACTTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCTTTT
1 ATTGACTATGCAAATTACTT-AAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGC--TT
*
49631 TTTTTGGTCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTT
63 TTTTTGGTCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCATCCCTTACTTT
*
49696 TCCTGCTGCCCTTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACAT
128 TCCTCCTGCCC-TTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACAT
* * **
49761 ATTGATCGTGTGTGGATATTAGGATTTACTGGTTCAACTCCTCTGCCGGAATCCCAAAGGGTTAG
192 ATTAATCGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATCCCAAAGAATTAG
*
49826 TGCTATAAATGTGTCTAC
257 TGCTATAAATGTATCTAC
49844 TCGAGTTCAA
Statistics
Matches: 256, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
293 14 0.05
294 42 0.16
296 73 0.29
297 127 0.50
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (294 bp):
ATTGACTATGCAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCTTTTT
TTGGTCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCATCCCTTACTTTTCC
TCCTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTA
ATCGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATCCCAAAGAATTAGTGCT
ATAAATGTATCTACCTGAATTCATTAATTTAACA
Found at i:51736 original size:14 final size:14
Alignment explanation
Indices: 51717--51745 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
51707 TAATTAGTTG
51717 TTCTTTTTCTTTTT
1 TTCTTTTTCTTTTT
51731 TTCTTTTTCTTTTT
1 TTCTTTTTCTTTTT
51745 T
1 T
51746 ACCTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTCTTTTTCTTTTT
Found at i:62156 original size:22 final size:23
Alignment explanation
Indices: 62131--62178 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
62121 TTAAGTAAAT
*
62131 AAAAAATATTTTTTAATTA-TTA
1 AAAAAATAATTTTTAATTACTTA
*
62153 AAAAAGTAATTTTTAATTACTTA
1 AAAAAATAATTTTTAATTACTTA
62176 AAA
1 AAA
62179 TAAAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
AAAAAATAATTTTTAATTACTTA
Done.