Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016198.1 Corchorus olitorius cultivar O-4 contig16231, 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: 15739
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1083 original size:31 final size:30
Alignment explanation
Indices: 1014--1084 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
1004 TTGCCATAAA
*
1014 TCTCAAATAAGGGCCCGAACTTTATAAAAG
1 TCTCAAATAAGGGCCCCAACTTTATAAAAG
*
1044 -GTCAAATAAGGGCCCCAAC-TTATCAGAAAG
1 TCTCAAATAAGGGCCCCAACTTTAT-A-AAAG
1074 TCTCAAATAAG
1 TCTCAAATAAG
1085 TCCATCCACT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 4 0.11
29 18 0.51
30 4 0.11
31 9 0.26
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (30 bp):
TCTCAAATAAGGGCCCCAACTTTATAAAAG
Found at i:2148 original size:42 final size:43
Alignment explanation
Indices: 2101--2183 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
2091 CGTGTTTGAC
*
2101 TTATCGTGTCTCGTGT-CTGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTGTCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA
*
2143 TTATCGTGTTTCGTGTCCTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAA
2184 CACGTTTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 24 0.65
43 13 0.35
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA
Found at i:2196 original size:20 final size:21
Alignment explanation
Indices: 2171--2213 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2161 TAATCGTGTC
*
2171 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
2191 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
2212 AA
1 AA
2214 TTAACGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:2554 original size:5 final size:5
Alignment explanation
Indices: 2544--2580 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
2534 CACGGCTTAA
2544 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TC
1 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TC
2581 TCGTGTACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.22, G:0.38, T:0.41
Consensus pattern (5 bp):
TCGTG
Found at i:2706 original size:12 final size:12
Alignment explanation
Indices: 2689--2719 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2679 TACCCTATGT
2689 AAACACGACACG
1 AAACACGACACG
2701 AAACACGACACG
1 AAACACGACACG
*
2713 GAACACG
1 AAACACG
2720 GATTGCCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.32, G:0.19, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:3250 original size:57 final size:57
Alignment explanation
Indices: 3162--3269 Score: 216
Period size: 57 Copynumber: 1.9 Consensus size: 57
3152 ATTGGTGTCA
3162 ATGTTAGAAAATGTAAATTCATGATTTGTATTGTTAGTGACACTGGTGTCAGTGTTT
1 ATGTTAGAAAATGTAAATTCATGATTTGTATTGTTAGTGACACTGGTGTCAGTGTTT
3219 ATGTTAGAAAATGTAAATTCATGATTTGTATTGTTAGTGACACTGGTGTCA
1 ATGTTAGAAAATGTAAATTCATGATTTGTATTGTTAGTGACACTGGTGTCA
3270 ATGATTTGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (57 bp):
ATGTTAGAAAATGTAAATTCATGATTTGTATTGTTAGTGACACTGGTGTCAGTGTTT
Found at i:5600 original size:31 final size:30
Alignment explanation
Indices: 5562--5667 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 30
5552 ACGAAATGGA
5562 CTTATTTGAGACTTTCTGACAAGTTGGGGCC
1 CTTATTTGAGA-TTTCTGACAAGTTGGGGCC
** * *
5593 CTTATTTGACCTTT-T-ATAAAGTTCGGGCC
1 CTTATTTGAGATTTCTGA-CAAGTTGGGGCC
* * *
5622 CTTATTTGAGATTTATGGCAAAGTTCGGGGAC
1 CTTATTTGAGATTTCTGAC-AAGTT-GGGGCC
5654 C-TATTTGAGATTTC
1 CTTATTTGAGATTTC
5668 AGCCGAAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.02
29 23 0.39
30 4 0.07
31 26 0.44
32 5 0.08
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (30 bp):
CTTATTTGAGATTTCTGACAAGTTGGGGCC
Found at i:6314 original size:22 final size:23
Alignment explanation
Indices: 6257--6334 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 23
6247 AACCACACTG
6257 TGAAAATTTGAT-AATCTCATTA
1 TGAAAATTTGATAAATCTCATTA
*
6279 T-AAAATTTCTATAACAT-TC-TTA
1 TGAAAATTT-GATAA-ATCTCATTA
*
6301 TGAAAATTTGAT-AATCACA--A
1 TGAAAATTTGATAAATCTCATTA
*
6321 TGAAATTTTGATAA
1 TGAAAATTTGATAA
6335 CCACACTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
20 14 0.31
21 10 0.22
22 9 0.20
23 10 0.22
24 2 0.04
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.40
Consensus pattern (23 bp):
TGAAAATTTGATAAATCTCATTA
Found at i:6325 original size:20 final size:20
Alignment explanation
Indices: 6300--6339 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6290 TAACATTCTT
*
6300 ATGAAAATTTGATAATCACA
1 ATGAAAATTTGATAACCACA
*
6320 ATGAAATTTTGATAACCACA
1 ATGAAAATTTGATAACCACA
6340 CTATTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (20 bp):
ATGAAAATTTGATAACCACA
Found at i:6352 original size:22 final size:22
Alignment explanation
Indices: 6237--6393 Score: 90
Period size: 22 Copynumber: 7.2 Consensus size: 22
6227 TCAAATGTGG
* * * *
6237 AAATATTGATAACCACACTGTG
1 AAATTTTGATAATCACACTATT
* * * *
6259 AAAATTTGATAATCTCATTATA
1 AAATTTTGATAATCACACTATT
** *
6281 AAATTTCT-ATAA-CATTCTTATG
1 AAATTT-TGATAATCACAC-TATT
* *
6303 AAAATTTGATAATCACA--ATG
1 AAATTTTGATAATCACACTATT
*
6323 AAATTTTGATAACCACACTATT
1 AAATTTTGATAATCACACTATT
* * *
6345 TAATTTTGATAATCTCCCTATT
1 AAATTTTGATAATCACACTATT
*
6367 AAATTCTT-ATAATCACACTATA
1 AAATT-TTGATAATCACACTATT
6389 AAATT
1 AAATT
6394 AATAACTGCA
Statistics
Matches: 101, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
20 18 0.18
21 2 0.02
22 76 0.75
23 5 0.05
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAATCACACTATT
Found at i:6529 original size:22 final size:22
Alignment explanation
Indices: 6504--6653 Score: 122
Period size: 22 Copynumber: 6.6 Consensus size: 22
6494 CTCTCTATGT
*
6504 AATTTTGATAACCTCCCCATAA
1 AATTTTGATAACCTCCCTATAA
* * *
6526 AATTTTCATAACCTCCTTATGA
1 AATTTTGATAACCTCCCTATAA
* **
6548 AATTTTGTTAACCTCCCTAGGA
1 AATTTTGATAACCTCCCTATAA
*
6570 AATTTTGATAACTTCCCTCCATATGA
1 AATTTTGATAACCTCCCT--ATA--A
* * *
6596 AATTTT-ATTAACCTTCTTATGA
1 AATTTTGA-TAACCTCCCTATAA
* *
6618 AATTTTGATAACCACACTATAA
1 AATTTTGATAACCTCCCTATAA
*
6640 AATGTTGATAACCT
1 AATTTTGATAACCT
6654 TCGTATGTTG
Statistics
Matches: 99, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
22 80 0.81
23 1 0.01
24 3 0.03
25 1 0.01
26 14 0.14
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTCCCTATAA
Found at i:6607 original size:48 final size:48
Alignment explanation
Indices: 6537--6629 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
6527 ATTTTCATAA
* *
6537 CCTCCTTATGAAATTTTGTTAACCTCCCTAGGAAATTTTGATAACTTC
1 CCTCCATATGAAATTTTATTAACCTCCCTAGGAAATTTTGATAACTTC
* * *
6585 CCTCCATATGAAATTTTATTAACCTTCTTATGAAATTTTGATAAC
1 CCTCCATATGAAATTTTATTAACCTCCCTAGGAAATTTTGATAAC
6630 CACACTATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (48 bp):
CCTCCATATGAAATTTTATTAACCTCCCTAGGAAATTTTGATAACTTC
Found at i:6609 original size:70 final size:66
Alignment explanation
Indices: 6504--6653 Score: 176
Period size: 70 Copynumber: 2.2 Consensus size: 66
6494 CTCTCTATGT
*
6504 AATTTTGATAACCTCCCCATAAAATTTTCATAACCTCCTTATGAAATTTTGTTAACCTCCCTAGG
1 AATTTTGATAACCTCCCCATAAAATTTTCATAACCTCCTTATGAAATTTTGATAACCTCCCTAGG
6569 A
66 A
* * * *
6570 AATTTTGATAACTTCCCTCCATATGAAATTTT-ATTAACCTTCTTATGAAATTTTGATAACCACA
1 AATTTTGATAACCT-CC-CCATA--AAATTTTCA-TAACCTCCTTATGAAATTTTGATAACCTCC
**
6634 CTATAA
61 CTAGGA
*
6640 AATGTTGATAACCT
1 AATTTTGATAACCT
6654 TCGTATGTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
66 13 0.19
67 2 0.03
68 5 0.07
69 1 0.01
70 49 0.70
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (66 bp):
AATTTTGATAACCTCCCCATAAAATTTTCATAACCTCCTTATGAAATTTTGATAACCTCCCTAGG
A
Found at i:6693 original size:22 final size:22
Alignment explanation
Indices: 6504--6773 Score: 102
Period size: 22 Copynumber: 12.3 Consensus size: 22
6494 CTCTCTATGT
* *
6504 AATTTTGATAACCTCCCCATA-A
1 AATTTTGATAACCTTCCTA-AGA
* *
6526 AATTTTCATAACC-TCCTTATGA
1 AATTTTGATAACCTTCC-TAAGA
* * *
6548 AATTTTGTTAACCTCCCTAGGA
1 AATTTTGATAACCTTCCTAAGA
6570 AATTTTGATAA-CTTCCCTCCATATGA
1 AATTTTGATAACCTT-CCT--A-A-GA
* *
6596 AATTTT-ATTAACCTTCTTATGA
1 AATTTTGA-TAACCTTCCTAAGA
*
6618 AATTTTGATAACC-ACACTATA-A
1 AATTTTGATAACCTTC-CTA-AGA
*
6640 AATGTTGATAACCTT-C---G-
1 AATTTTGATAACCTTCCTAAGA
* * *
6657 TATGTTGTTAACCTTCCTAAGA
1 AATTTTGATAACCTTCCTAAGA
*
6679 AATTTTGATAACCTT-TTAATGA
1 AATTTTGATAACCTTCCTAA-GA
* * *
6701 AATTTTGGT-ACCTTCTGTATGA
1 AATTTTGATAACCTTC-CTAAGA
* * *
6723 AATTTTAATAA-CTACACTATGA
1 AATTTTGATAACCTTC-CTAAGA
* *
6745 AGTTTTGATAACC-TCCATATGA
1 AATTTTGATAACCTTCC-TAAGA
6767 AATTTTG
1 AATTTTG
6774 GTAGCAACAC
Statistics
Matches: 186, Mismatches: 36, Indels: 52
0.68 0.13 0.19
Matches are distributed among these distances:
17 13 0.07
18 1 0.01
21 16 0.09
22 130 0.70
23 7 0.04
24 2 0.01
25 1 0.01
26 13 0.07
27 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.40
Consensus pattern (22 bp):
AATTTTGATAACCTTCCTAAGA
Found at i:6740 original size:105 final size:107
Alignment explanation
Indices: 6552--6758 Score: 260
Period size: 105 Copynumber: 1.9 Consensus size: 107
6542 TTATGAAATT
* *
6552 TTGTTAACCTCCCTAGGAAATTTTGATAACTTCCCTCCATATGAAATTTTATTAACCTTCTTATG
1 TTGTTAACCTCCCTAAGAAATTTTGATAACTT--CTCCATATGAAATTTTAGTAACCTTCTTATG
*
6617 AAATTTTGATAACCACACTATAAAATGTTGATAACCTTCGTATG
64 AAATTTTAATAACCACACTATAAAATGTTGATAACCTTCGTATG
* * *
6661 TTGTTAACCTTCCTAAGAAATTTTGATAACCTT-T-TA-ATGAAATTTTGGT-ACCTTCTGTATG
1 TTGTTAACCTCCCTAAGAAATTTTGATAA-CTTCTCCATATGAAATTTTAGTAACCTTCT-TATG
* * * *
6722 AAATTTTAATAACTACACTATGAAGTTTTGATAACCT
64 AAATTTTAATAACCACACTATAAAATGTTGATAACCT
6759 CCATATGAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
104 7 0.08
105 47 0.55
106 1 0.01
107 1 0.01
109 27 0.31
110 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (107 bp):
TTGTTAACCTCCCTAAGAAATTTTGATAACTTCTCCATATGAAATTTTAGTAACCTTCTTATGAA
ATTTTAATAACCACACTATAAAATGTTGATAACCTTCGTATG
Found at i:14042 original size:30 final size:30
Alignment explanation
Indices: 13994--14075 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
13984 ATACCGTACA
13994 GGTCCCTCTACTTACAAAAAGGGATCAATTT
1 GGTCCCTCTACTTACAAAAAGGG-TCAATTT
* **
14025 GGTCCCCCTAC-TACAAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAAGGGTCAATTT
*
14054 GGTCCCTTTACTTACAAAAAGG
1 GGTCCCTCTACTTACAAAAAGG
14076 TTGCTTATGT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 16 0.37
30 17 0.40
31 10 0.23
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.28
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAAGGGTCAATTT
Found at i:14288 original size:31 final size:30
Alignment explanation
Indices: 14255--14375 Score: 120
Period size: 31 Copynumber: 4.0 Consensus size: 30
14245 ATATATAATC
14255 AATTGACAGATTTTGTTAAGTAGAGGGACTC-
1 AATTGACAGATTTTG-TAAGTAGAGGGAC-CA
* * **
14286 AATCGACACCAAATTGTAAGTAGAGGGACCA
1 AATTGACA-GATTTTGTAAGTAGAGGGACCA
* *
14317 AATTGACAGCTTTTAT-AGTAGAGGGACCA
1 AATTGACAGATTTTGTAAGTAGAGGGACCA
**
14346 AATTGATCATTTTTTGTAAGTAGAGGGACC
1 AATTGA-CAGATTTTGTAAGTAGAGGGACC
14376 TGTACGGTAT
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
29 19 0.26
30 11 0.15
31 39 0.53
32 4 0.05
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (30 bp):
AATTGACAGATTTTGTAAGTAGAGGGACCA
Found at i:14346 original size:29 final size:31
Alignment explanation
Indices: 14302--14375 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 31
14292 CACCAAATTG
14302 TAAGTAGAGGGACCAAATTGA-CAGCTTTTA
1 TAAGTAGAGGGACCAAATTGATCAGCTTTTA
** *
14332 T-AGTAGAGGGACCAAATTGATCATTTTTTG
1 TAAGTAGAGGGACCAAATTGATCAGCTTTTA
14362 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
14376 TGTACGGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 19 0.49
30 8 0.21
31 12 0.31
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (31 bp):
TAAGTAGAGGGACCAAATTGATCAGCTTTTA
Done.