Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022619.1 Corchorus olitorius cultivar O-4 contig22652, 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: 38432
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1290 original size:31 final size:31
Alignment explanation
Indices: 1255--1358 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 31
1245 GATTAAACTC
* *
1255 AATTGAC-CTAATTTGACAAGTAGAGGGATTA
1 AATTGACACTAAATTG-CAAGTAGAGGGACTA
*
1286 AATTGACACTAAATTGCAAGTAGAGGGACTC
1 AATTGACACTAAATTGCAAGTAGAGGGACTA
* ** * *
1317 AATTGACAAT-TTTTG-TAGTAGAGGGACCA
1 AATTGACACTAAATTGCAAGTAGAGGGACTA
1346 AATTGACACTAAA
1 AATTGACACTAAA
1359 ATGTAAATTA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
29 20 0.34
30 3 0.05
31 29 0.49
32 7 0.12
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.27
Consensus pattern (31 bp):
AATTGACACTAAATTGCAAGTAGAGGGACTA
Found at i:1384 original size:18 final size:18
Alignment explanation
Indices: 1363--1416 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
1353 ACTAAAATGT
1363 AAATTATTTTTTTTTTCA
1 AAATTATTTTTTTTTTCA
*
1381 AAATTAATTTTTTATTTTCG
1 AAATT-ATTTTTT-TTTTCA
*
1401 AAATT-TTTTTATTTTC
1 AAATTATTTTTTTTTTC
1417 CACGTGTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 5 0.16
18 10 0.31
19 7 0.22
20 10 0.31
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (18 bp):
AAATTATTTTTTTTTTCA
Found at i:1518 original size:31 final size:31
Alignment explanation
Indices: 1475--1542 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1465 TCCCACCGTT
* *
1475 AGTAGAGGGACTCAATTGACA-CAATTTGTAA
1 AGTAAAGGGACTCAATTGACACCAAATTGT-A
*
1506 AGTAAAGGGACTCAATTGATACCAAATTGTA
1 AGTAAAGGGACTCAATTGACACCAAATTGTA
1537 AGTAAA
1 AGTAAA
1543 TGGTTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.25
Consensus pattern (31 bp):
AGTAAAGGGACTCAATTGACACCAAATTGTA
Found at i:10105 original size:2 final size:2
Alignment explanation
Indices: 10098--10137 Score: 62
Period size: 2 Copynumber: 19.0 Consensus size: 2
10088 CATTGTTACC
10098 AT AT AT AT AT AT GAT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT -AT AT
10138 CAACATGAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 32 0.89
3 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12389 original size:21 final size:20
Alignment explanation
Indices: 12351--12389 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12341 CCATGAACCT
*
12351 AAATTGGTCAAGATTATCCA
1 AAATTAGTCAAGATTATCCA
*
12371 AAATTAGTCTAAGTTTATC
1 AAATTAGTC-AAGATTATC
12390 AATTACTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
AAATTAGTCAAGATTATCCA
Found at i:14299 original size:39 final size:39
Alignment explanation
Indices: 14245--14323 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
14235 ACCACCAAAC
14245 TAATTGGACTAAATAAAGGCCAATCAATTATACAAAGAT
1 TAATTGGACTAAATAAAGGCCAATCAATTATACAAAGAT
*
14284 TAATTGGACTAAATAAAGGCCACTCAATTATACAAAGAT
1 TAATTGGACTAAATAAAGGCCAATCAATTATACAAAGAT
14323 T
1 T
14324 GAGTAGTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (39 bp):
TAATTGGACTAAATAAAGGCCAATCAATTATACAAAGAT
Found at i:15512 original size:2 final size:2
Alignment explanation
Indices: 15505--15538 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15495 ACAATTGGAG
15505 AT AT 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 AT AT
15539 GCAGAATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21233 original size:19 final size:18
Alignment explanation
Indices: 21211--21246 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21201 AGGGTAGTTA
*
21211 AAAAAAAATTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
*
21229 AAAAAGAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
21247 GCAAGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAAAAAGTGTTTTCAT
Found at i:22865 original size:2 final size:2
Alignment explanation
Indices: 22858--22891 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22848 GGACAATTGG
22858 AT AT 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 AT AT
22892 GCAGAATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29876 original size:27 final size:27
Alignment explanation
Indices: 29840--29927 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
29830 TGAGTATGCA
*
29840 AAATGACCAAAATGCCCCTAGGTTTGC
1 AAATGACCAAAATGCCCCTAGGTGTGC
* *
29867 AAATGACCAAAATGCCCCTTA-ATGTGT
1 AAATGACCAAAATGCCCC-TAGGTGTGC
29894 AAATGACCAAAATGCCCCT-GAGTGTGC
1 AAATGACCAAAATGCCCCTAG-GTGTGC
29921 AAATGAC
1 AAATGAC
29928 TAATTAAGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
26 1 0.02
27 50 0.94
28 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTAGGTGTGC
Found at i:32441 original size:58 final size:58
Alignment explanation
Indices: 32259--32475 Score: 285
Period size: 59 Copynumber: 3.7 Consensus size: 58
32249 CAGGGTTCTA
** * *
32259 GAAAACTCTCTACCAGAGACCCCGAACAGGGTTTTTAAAACAAGACAAGATTTTGAATT
1 GAAAACTCTCCCCCAGAGACCTCGAACA-GGATTTTAAAACAAGACAAGATTTTGAATT
*
32318 GAGAACTC-CCCACCAGAGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATT
1 GAAAACTCTCCC-CCAGAGACCTCGAACAGGATTTT-AAAACAAGACAAGATTTTGAATT
* *
32377 GAAAACTCTCCCCCAGAGACCTTGAACAAGATTTTAAAACAAGACAAGATTTTGAATT
1 GAAAACTCTCCCCCAGAGACCTCGAACAGGATTTTAAAACAAGACAAGATTTTGAATT
* * * *
32435 GAAAACTTTCTACCC-GAGACCTCGAACAGGACTTTGAAACA
1 GAAAACTCTC-CCCCAGAGACCTCGAACAGGATTTTAAAACA
32476 GAAGGGGGAA
Statistics
Matches: 140, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
58 61 0.44
59 76 0.54
60 3 0.02
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (58 bp):
GAAAACTCTCCCCCAGAGACCTCGAACAGGATTTTAAAACAAGACAAGATTTTGAATT
Found at i:32490 original size:117 final size:117
Alignment explanation
Indices: 32259--32473 Score: 288
Period size: 117 Copynumber: 1.8 Consensus size: 117
32249 CAGGGTTCTA
* * * *
32259 GAAAACTCTCTACCAGAGACCCCGAACAGGGTTTTTAAAACAAGACAAGATTTTGAATTGAGAAC
1 GAAAACTCTCCACCAGAGACCCCGAACAGAGATTTTAAAACAAGACAAGATTTTGAATTGAAAAC
* *
32324 TCCCCACCAGAGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATT
66 TCCCCACCAGAGACCTCGAACAGGATTTGAAAAACAAGACAAGAATTTG-ATT
* **
32377 GAAAACTCTCCCCCAGAGACCTTGAACA-AGATTTTAAAACAAGACAAGATTTTGAATTGAAAAC
1 GAAAACTCTCCACCAGAGACCCCGAACAGAGATTTTAAAACAAGACAAGATTTTGAATTGAAAAC
** * *
32441 TTTCTACCCGAGACCTCGAACAGGACTTTGAAA
66 TCCCCACCAGAGACCTCGAACAGGA-TTTGAAA
32474 CAGAAGGGGG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
117 54 0.64
118 30 0.36
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (117 bp):
GAAAACTCTCCACCAGAGACCCCGAACAGAGATTTTAAAACAAGACAAGATTTTGAATTGAAAAC
TCCCCACCAGAGACCTCGAACAGGATTTGAAAAACAAGACAAGAATTTGATT
Found at i:33380 original size:36 final size:36
Alignment explanation
Indices: 33325--33444 Score: 127
Period size: 41 Copynumber: 3.2 Consensus size: 36
33315 TATTTATTTC
*
33325 TTTTTTTCTGACCTCTTTCTATTTTAGGCTAAGTTT
1 TTTTTTTCTGACCTCTTTCTATTTTAGGCCAAGTTT
* *
33361 TTCTTTTTC-GACCTGTTTCTATTTTAGGCCCAGTTT
1 TT-TTTTTCTGACCTCTTTCTATTTTAGGCCAAGTTT
*
33397 TTTTTTTCTTTTTCGACCTCTCTCTATTTTAGGTCC-AGTTT
1 TTTTTTTC----T-GACCTCTTTCTATTTTAGG-CCAAGTTT
33438 TTTTTTT
1 TTTTTTT
33445 TAGCTCCTCT
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
35 6 0.08
36 28 0.39
37 6 0.08
41 29 0.41
42 2 0.03
ACGTcount: A:0.11, C:0.19, G:0.11, T:0.59
Consensus pattern (36 bp):
TTTTTTTCTGACCTCTTTCTATTTTAGGCCAAGTTT
Found at i:33411 original size:41 final size:41
Alignment explanation
Indices: 33358--33444 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
33348 TTAGGCTAAG
* *
33358 TTTTTCTTTTTCGACCTGTTTCTATTTTAGGCCCAGTTTTT
1 TTTTTCTTTTTCGACCTCTCTCTATTTTAGGCCCAGTTTTT
*
33399 TTTTTCTTTTTCGACCTCTCTCTATTTTAGGTCCAGTTTTT
1 TTTTTCTTTTTCGACCTCTCTCTATTTTAGGCCCAGTTTTT
33440 TTTTT
1 TTTTT
33445 TAGCTCCTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.09, C:0.20, G:0.10, T:0.61
Consensus pattern (41 bp):
TTTTTCTTTTTCGACCTCTCTCTATTTTAGGCCCAGTTTTT
Found at i:35585 original size:41 final size:41
Alignment explanation
Indices: 35524--35844 Score: 316
Period size: 42 Copynumber: 7.9 Consensus size: 41
35514 AAAATCTTTA
35524 ATGGGATCTTTCCCCT-AATTGAAAACTTTGAAAAAGACTAG
1 ATGGGATCTTT-CCCTAAATTGAAAACTTTGAAAAAGACTAG
*
35565 ATGGGATCTTTCCCTAAATTGAAAAC-TTG--AAA-ACTCG
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTAG
* * * *
35602 ACGGGATCTTTCCCTAAATTTAAAATTTTGAAGAAGACTAG
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTAG
*
35643 ATGGGATCTTTCCCTAAATT-AAAACTCTGAAAAAGAC-AGG
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTA-G
* * ** *
35683 ATGTGATCTTTCCCTAAATT-AAAGGCTTTTGAAAACTACTTG
1 ATGGGATCTTTCCCTAAATTGAAA-AC-TTTGAAAAAGACTAG
* * * *
35725 AAGGGAGCTTTCCCTAAATTGAAAACTTTGAAAAATACTTTG
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGAC-TAG
* * * * * *
35767 GTGGGATCTTTCCCTAATTTGAAATCTTTAAAAAAATACTTTG
1 ATGGGATCTTTCCCTAAATTGAAAACTTT-GAAAAAGAC-TAG
* *
35810 GTGGGATCTTTCCCTAAATTGATAACTTTGAAAAA
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAA
35845 ACTTGTTTTT
Statistics
Matches: 237, Mismatches: 31, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
37 27 0.11
38 6 0.03
39 1 0.00
40 46 0.19
41 56 0.24
42 60 0.25
43 41 0.17
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (41 bp):
ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTAG
Found at i:35736 original size:42 final size:42
Alignment explanation
Indices: 35514--35848 Score: 214
Period size: 41 Copynumber: 8.2 Consensus size: 42
35504 ACTCAATTTT
*
35514 AAAAT-CTTT-AATGGGATCTTTCCCCT-AATTGAAAACTTTGA
1 AAAATACTTTGAA-GGGAGCTTT-CCCTAAATTGAAAACTTTGA
* * * *
35555 AAAAGAC-TAGATGGGATCTTTCCCTAAATTGAAAAC-TTG-
1 AAAATACTTTGAAGGGAGCTTTCCCTAAATTGAAAACTTTGA
* * * * *
35594 -AAA-AC-TCGACGGGATCTTTCCCTAAATTTAAAATTTTGA
1 AAAATACTTTGAAGGGAGCTTTCCCTAAATTGAAAACTTTGA
* * * * * *
35633 AGAAGAC-TAGATGGGATCTTTCCCTAAATT-AAAACTCTGA
1 AAAATACTTTGAAGGGAGCTTTCCCTAAATTGAAAACTTTGA
* ** * * * *
35673 AAAAGAC-AGGATGTGATCTTTCCCTAAATT-AAAGGCTTTTGA
1 AAAATACTTTGAAGGGAGCTTTCCCTAAATTGAAA-AC-TTTGA
*
35715 AAACTAC-TTGAAGGGAGCTTTCCCTAAATTGAAAACTTTGA
1 AAAATACTTTGAAGGGAGCTTTCCCTAAATTGAAAACTTTGA
** * * * *
35756 AAAATACTTTGGTGGGATCTTTCCCTAATTTGAAATCTTTAAA
1 AAAATACTTTGAAGGGAGCTTTCCCTAAATTGAAAACTTT-GA
** * *
35799 AAAATACTTTGGTGGGATCTTTCCCTAAATTGATAACTTTGA
1 AAAATACTTTGAAGGGAGCTTTCCCTAAATTGAAAACTTTGA
35841 AAAA-ACTT
1 AAAATACTT
35849 GTTTTTTGAT
Statistics
Matches: 245, Mismatches: 37, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
37 27 0.11
38 6 0.02
40 46 0.19
41 63 0.26
42 62 0.25
43 41 0.17
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (42 bp):
AAAATACTTTGAAGGGAGCTTTCCCTAAATTGAAAACTTTGA
Found at i:35740 original size:82 final size:82
Alignment explanation
Indices: 35528--35759 Score: 237
Period size: 78 Copynumber: 2.9 Consensus size: 82
35518 TCTTTAATGG
* * * * *
35528 GATCTTTCCCCT-AATTGAAAACTTTGAAAAAGACTAGATGGGATCTTTCCCTAAATTGAAAACT
1 GATCTTT-CCCTAAATTTAAAATTTTGAAGAAGACTAGAAGGGAGCTTTCCCTAAATTGAAAACT
** * *
35592 -TG--AAA-ACTCGACGG
65 CTGAAAAAGACAGGATGT
* *
35606 GATCTTTCCCTAAATTTAAAATTTTGAAGAAGACTAGATGGGATCTTTCCCTAAATT-AAAACTC
1 GATCTTTCCCTAAATTTAAAATTTTGAAGAAGACTAGAAGGGAGCTTTCCCTAAATTGAAAACTC
35670 TGAAAAAGACAGGATGT
66 TGAAAAAGACAGGATGT
* * *
35687 GATCTTTCCCTAAA-TTAAAGGCTTTTGAA-AACTACTTGAAGGGAGCTTTCCCTAAATTGAAAA
1 GATCTTTCCCTAAATTTAAA--ATTTTGAAGAA-GACTAGAAGGGAGCTTTCCCTAAATTGAAAA
*
35750 CTTTGAAAAA
63 CTCTGAAAAA
35760 TACTTTGGTG
Statistics
Matches: 132, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
77 10 0.08
78 51 0.39
80 8 0.06
81 21 0.16
82 29 0.22
83 13 0.10
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (82 bp):
GATCTTTCCCTAAATTTAAAATTTTGAAGAAGACTAGAAGGGAGCTTTCCCTAAATTGAAAACTC
TGAAAAAGACAGGATGT
Found at i:36448 original size:22 final size:21
Alignment explanation
Indices: 36405--36448 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
36395 AAATAACTAA
*
36405 AACAAACAAAGCCCAAATTAT
1 AACAAACAAAGCCCAAAGTAT
* *
36426 AACAAAGCCAAGCCTAAAGTAT
1 AACAAA-CAAAGCCCAAAGTAT
36448 A
1 A
36449 TATGTTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.55, C:0.23, G:0.09, T:0.14
Consensus pattern (21 bp):
AACAAACAAAGCCCAAAGTAT
Done.