Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017469.1 Corchorus olitorius cultivar O-4 contig17502, 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: 38515
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:311 original size:39 final size:40
Alignment explanation
Indices: 255--335 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
245 TTTAATTCCT
* *
255 ATGTAATATATATAATAACTAAAATACTTAGATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATGAATTAA
* *
295 ATGTAATA-CTATAATAACTGAAATACTTACATGAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATGAATTAA
334 AT
1 AT
336 TCTTAGGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATGAATTAA
Found at i:3200 original size:58 final size:58
Alignment explanation
Indices: 3102--3211 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
3092 ATCATGCCTC
* *
3102 GGTCCTAAAACGTCTTTTTTAGACATTTAATAAAAAAACATGTCACTCGATAAGTCTT
1 GGTCCGAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGTCTT
* *
3160 GGTCCGAAAACGTCTTTCTTTATG-CATCTAAT-AAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTCTTT-TTTA-GACATCTAATAAAAAAACATGTCACTCGATA
3212 TTTGATTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 34 0.74
59 11 0.24
60 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGTCTT
Found at i:6868 original size:22 final size:22
Alignment explanation
Indices: 6839--6896 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
6829 TAAATATCTT
*
6839 TATGAAATTTTGATAACTATC-C
1 TATGAAATTTTGATAACCA-CGC
*
6861 TATTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACCACGC
6883 TATGAAATTTTGAT
1 TATGAAATTTTGAT
6897 GATTTATCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACGC
Found at i:6997 original size:44 final size:44
Alignment explanation
Indices: 6839--7013 Score: 150
Period size: 44 Copynumber: 4.0 Consensus size: 44
6829 TAAATATCTT
* *
6839 TATGAAATTTTGATAACTATCCTATTAAATTTTGAT-AACCACGC
1 TATGAAATTTTGATAACTATCCTATGAAATTTTGATAAACCTC-C
** * *
6883 TATGAAATTTTGATGATTTAT-CTATAAAATTGTGATAAA-CTCC
1 TATGAAATTTTGAT-AACTATCCTATGAAATTTTGATAAACCTCC
* *
6926 ATATGAAACTTTGATAATCTAAT--TATGAAATTTTAATAAACCTTCC
1 -TATGAAATTTTGATAA-CT-ATCCTATGAAATTTTGATAAACC-TCC
* *
6972 TATGAAATTTTG-TAACTTTCCTATG-ATTTTTGAT-AACCTCC
1 TATGAAATTTTGATAACTATCCTATGAAATTTTGATAAACCTCC
7013 T
1 T
7014 TGTGAGATTT
Statistics
Matches: 107, Mismatches: 15, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
41 4 0.04
42 5 0.05
43 11 0.10
44 64 0.60
45 20 0.19
46 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (44 bp):
TATGAAATTTTGATAACTATCCTATGAAATTTTGATAAACCTCC
Found at i:7008 original size:21 final size:21
Alignment explanation
Indices: 6949--6997 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
6939 ATAATCTAAT
* *
6949 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTT-GT-AACTTTCC
6972 TATGAAATTTTGTAACTTTCC
1 TATGAAATTTTGTAACTTTCC
6993 TATGA
1 TATGA
6998 TTTTTGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.50
22 1 0.04
23 11 0.46
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (21 bp):
TATGAAATTTTGTAACTTTCC
Found at i:8751 original size:25 final size:26
Alignment explanation
Indices: 8714--8764 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
8704 TTAATAATAG
*
8714 AATAATTAAAA-TTA-AAATATTATTT
1 AATAATGAAAATTTAGAAATA-TATTT
*
8739 AATAATGATAATTTAGAAATATATTT
1 AATAATGAAAATTTAGAAATATATTT
8765 GAAAAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 9 0.41
26 8 0.36
27 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (26 bp):
AATAATGAAAATTTAGAAATATATTT
Found at i:10670 original size:33 final size:33
Alignment explanation
Indices: 10633--10695 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
10623 CGATTTTATT
10633 AATTTAACAATTACAATCAAGATTAAAAAAATG
1 AATTTAACAATTACAATCAAGATTAAAAAAATG
*
10666 AATTTAACAATTGCAATCAAGATTAAAAAA
1 AATTTAACAATTACAATCAAGATTAAAAAA
10696 TGACCACAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (33 bp):
AATTTAACAATTACAATCAAGATTAAAAAAATG
Found at i:11449 original size:29 final size:29
Alignment explanation
Indices: 11409--11518 Score: 125
Period size: 31 Copynumber: 3.7 Consensus size: 29
11399 GGCGAAAATC
**
11409 TCAATTTG-GTCCCTCTACAAAATAAC-TG
1 TCAA-TTGAGTCCCTCTACTTAATAACTTG
11437 ATCAATTGAGTCCCTCTACTTAATAACACTTG
1 -TCAATTGAGTCCCTCTACTTAAT-A-ACTTG
11469 TCAATTGAGTCCCTCTACTTAATAACATTTG
1 TCAATTGAGTCCCTCTACTTAATAAC--TTG
*
11500 TCAACTGAGTCCCTCTACT
1 TCAATTGAGTCCCTCTACT
11519 ACAGGATTGT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
28 3 0.04
29 19 0.26
30 2 0.03
31 46 0.64
32 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (29 bp):
TCAATTGAGTCCCTCTACTTAATAACTTG
Found at i:11476 original size:31 final size:31
Alignment explanation
Indices: 11438--11518 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
11428 AAATAACTGA
11438 TCAATTGAGTCCCTCTACTTAATAACACTTG
1 TCAATTGAGTCCCTCTACTTAATAACACTTG
*
11469 TCAATTGAGTCCCTCTACTTAATAACATTTG
1 TCAATTGAGTCCCTCTACTTAATAACACTTG
*
11500 TCAACTGAGTCCCTCTACT
1 TCAATTGAGTCCCTCTACT
11519 ACAGGATTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (31 bp):
TCAATTGAGTCCCTCTACTTAATAACACTTG
Found at i:11539 original size:30 final size:31
Alignment explanation
Indices: 11438--11540 Score: 129
Period size: 31 Copynumber: 3.4 Consensus size: 31
11428 AAATAACTGA
* *
11438 TCAATTGAGTCCCTCTACTTAATAACACTTG
1 TCAATTGAGTCCCTCTACTTAACAACATTTG
*
11469 TCAATTGAGTCCCTCTACTTAATAACATTTG
1 TCAATTGAGTCCCTCTACTTAACAACATTTG
* **
11500 TCAACTGAGTCCCTCTAC-T-ACAGGATTGTG
1 TCAATTGAGTCCCTCTACTTAACAACATT-TG
11530 TCAATTGAGTC
1 TCAATTGAGTC
11541 AAATCACTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
29 5 0.08
30 13 0.20
31 47 0.72
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (31 bp):
TCAATTGAGTCCCTCTACTTAACAACATTTG
Found at i:12296 original size:29 final size:31
Alignment explanation
Indices: 12263--12320 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
12253 TCTCCATCTG
*
12263 GTCCCGCTACCTAAT-ATAAC-GTCAATTTA
1 GTCCCGATACCTAATAATAACTGTCAATTTA
* *
12292 GTCCCTATACTTAATAATAACTGTCAATT
1 GTCCCGATACCTAATAATAACTGTCAATT
12321 GAAGGCCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.50
30 5 0.21
31 7 0.29
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (31 bp):
GTCCCGATACCTAATAATAACTGTCAATTTA
Found at i:14425 original size:10 final size:11
Alignment explanation
Indices: 14400--14428 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
14390 TTTATATAAA
14400 AAAAATAATAT
1 AAAAATAATAT
14411 AAAAATAATAT
1 AAAAATAATAT
14422 AAAAATA
1 AAAAATA
14429 GATCAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:23602 original size:11 final size:10
Alignment explanation
Indices: 23542--23615 Score: 66
Period size: 10 Copynumber: 7.7 Consensus size: 10
23532 TTTTTGTTTT
*
23542 TAATTATTAA
1 TAATTAATAA
* *
23552 TTATTAATTA
1 TAATTAATAA
23562 TAATTAATAA
1 TAATTAATAA
* *
23572 TAA-CAAT-T
1 TAATTAATAA
23580 TAAATTAATAA
1 T-AATTAATAA
23591 TAATT-A-AA
1 TAATTAATAA
23599 TAATTAATAA
1 TAATTAATAA
23609 TAATTAA
1 TAATTAA
23616 AAAAAATTGG
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
8 8 0.16
9 7 0.14
10 34 0.68
11 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (10 bp):
TAATTAATAA
Found at i:23609 original size:7 final size:7
Alignment explanation
Indices: 23542--23609 Score: 52
Period size: 7 Copynumber: 9.6 Consensus size: 7
23532 TTTTTGTTTT
*
23542 TAATTAT
1 TAATTAA
*
23549 TAATTAT
1 TAATTAA
23556 TAATT-A
1 TAATTAA
23562 TAATTAA
1 TAATTAA
23569 TAA-TAA
1 TAATTAA
*
23575 CAATTTAAA
1 TAA-TT-AA
23584 TTAA-TAA
1 -TAATTAA
23591 TAATTAAA
1 TAATT-AA
23599 TAATTAA
1 TAATTAA
23606 TAAT
1 TAAT
23610 AATTAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
6 13 0.25
7 25 0.49
8 9 0.18
9 2 0.04
10 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATTAA
Found at i:28740 original size:10 final size:10
Alignment explanation
Indices: 28725--28758 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
28715 ATACCTCGAT
28725 ATATCCGTAA
1 ATATCCGTAA
28735 ATATCCGTAA
1 ATATCCGTAA
*
28745 ATATCCGTAT
1 ATATCCGTAA
28755 ATAT
1 ATAT
28759 TCATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:29682 original size:45 final size:45
Alignment explanation
Indices: 29613--29707 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
29603 TCGAAAATGA
*
29613 AATAAATGTATGATTAAATTAGTGTATTTGATTTATACATAATAT
1 AATATATGTATGATTAAATTAGTGTATTTGATTTATACATAATAT
29658 AATATATGTATGATTAAATTAGTGTATTTGATTTATACATAATAT
1 AATATATGTATGATTAAATTAGTGTATTTGATTTATACATAATAT
29703 AATAT
1 AATAT
29708 TTTATCGCAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (45 bp):
AATATATGTATGATTAAATTAGTGTATTTGATTTATACATAATAT
Found at i:30288 original size:19 final size:20
Alignment explanation
Indices: 30264--30302 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
30254 GTTAACCCAA
30264 ATTCTGCAGAA-GAAAATTT
1 ATTCTGCAGAAGGAAAATTT
*
30283 ATTCTGCGGAAGGAAAATTT
1 ATTCTGCAGAAGGAAAATTT
30303 TGGGATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
ATTCTGCAGAAGGAAAATTT
Found at i:32019 original size:15 final size:15
Alignment explanation
Indices: 31999--32041 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
31989 TAGACGAGTC
31999 TTTTTTTTGGGG--T
1 TTTTTTTTGGGGTTT
32012 TTTTTTTTGGGGTTT
1 TTTTTTTTGGGGTTT
*
32027 TTTTTTTTTGGGTTT
1 TTTTTTTTGGGGTTT
32042 AACCAAGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 12 0.44
15 15 0.56
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (15 bp):
TTTTTTTTGGGGTTT
Found at i:32033 original size:14 final size:13
Alignment explanation
Indices: 31999--32032 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
31989 TAGACGAGTC
31999 TTTTTTTTGGGGT
1 TTTTTTTTGGGGT
32012 TTTTTTTTGGGGT
1 TTTTTTTTGGGGT
32025 TTTTTTTT
1 TTTTTTTT
32033 TTTGGGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (13 bp):
TTTTTTTTGGGGT
Done.