Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020965.1 Corchorus olitorius cultivar O-4 contig20998, 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: 30705
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:329 original size:22 final size:22
Alignment explanation
Indices: 298--341 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
288 TTCTTTCCGC
*
298 AACAACTTCTGTCCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
* *
320 AACAAGTTCTGGGCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
342 TCCTGCGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
AACAACTTCTGGCCCGAAGTTG
Found at i:373 original size:52 final size:52
Alignment explanation
Indices: 295--395 Score: 177
Period size: 52 Copynumber: 1.9 Consensus size: 52
285 TTTTTCTTTC
*
295 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTGCCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
347 CGCAACAACCTT-TGCCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTC
1 CGCAACAA-CTTCTGCCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTC
396 TTGCAAATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 44 0.94
53 3 0.06
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.24
Consensus pattern (52 bp):
CGCAACAACTTCTGCCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
Found at i:449 original size:21 final size:21
Alignment explanation
Indices: 425--465 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
415 TTCGACAGGC
*
425 CAACTTCTGGGCAGAAGTTGA
1 CAACATCTGGGCAGAAGTTGA
*
446 CAACATCTGGGCTGAAGTTG
1 CAACATCTGGGCAGAAGTTG
466 TCTTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (21 bp):
CAACATCTGGGCAGAAGTTGA
Found at i:5697 original size:21 final size:21
Alignment explanation
Indices: 5672--5712 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5662 TTAGAAACCC
5672 TAGTACCACTTAG-ATCCAATT
1 TAGTACCACTT-GTATCCAATT
5693 TAGTACCACTTGTATCCAAT
1 TAGTACCACTTGTATCCAAT
5713 AGGGCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (21 bp):
TAGTACCACTTGTATCCAATT
Found at i:6628 original size:21 final size:21
Alignment explanation
Indices: 6602--6643 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6592 TAAGGAAGAA
6602 GTTTCAAGCTCATCAGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
*
6623 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
6644 CCTAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCAGAGTTG
Found at i:7828 original size:22 final size:22
Alignment explanation
Indices: 7797--7839 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
7787 TTCTTTCCGC
*
7797 AACAACTTCTGTCCCGAAGTTA
1 AACAACTTCTGGCCCGAAGTTA
* *
7819 AACAAGTTCTGGGCCGAAGTT
1 AACAACTTCTGGCCCGAAGTT
7840 GTCCTGCGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (22 bp):
AACAACTTCTGGCCCGAAGTTA
Found at i:7850 original size:52 final size:52
Alignment explanation
Indices: 7794--7898 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
7784 TTTTTCTTTC
*
7794 CGCAACAACTTCTGTCCCGAAGTTAAACAAGTTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTGCCCCGAAGTTAAACAAGTTCTGGGCCGAAGTTGTCCTG
* * *
7846 CGCAACAACTTTTGCCCCGAAGTTGAATAAGTTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTGCCCCGAAGTTAAACAAGTTCTGGGCCGAAGTTGTCCTG
7898 C
1 C
7899 AATTCTTGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.26
Consensus pattern (52 bp):
CGCAACAACTTCTGCCCCGAAGTTAAACAAGTTCTGGGCCGAAGTTGTCCTG
Found at i:7948 original size:21 final size:21
Alignment explanation
Indices: 7924--7964 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7914 TTCGACAGGC
*
7924 CAACTTCTGGG-CAGAAGTTGA
1 CAACATCTGGGTC-GAAGTTGA
7945 CAACATCTGGGTCGAAGTTG
1 CAACATCTGGGTCGAAGTTG
7965 TCTTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (21 bp):
CAACATCTGGGTCGAAGTTGA
Found at i:9175 original size:50 final size:50
Alignment explanation
Indices: 9116--9229 Score: 201
Period size: 50 Copynumber: 2.3 Consensus size: 50
9106 GTCCAAATCC
*
9116 TGGGCAGGACTTGTTCTGAATTTTCTTCCTTCTTTCACCAAACCATGTCT
1 TGGGCAGGACTTGTTCTGAATTTTCTTCCCTCTTTCACCAAACCATGTCT
* *
9166 TGGGTAGGACTTGTTCTGAATTTTCTTCCCTCTTTCACCAGACCATGTCT
1 TGGGCAGGACTTGTTCTGAATTTTCTTCCCTCTTTCACCAAACCATGTCT
9216 TGGGCAGGACTTGT
1 TGGGCAGGACTTGT
9230 CCTCTTTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.39
Consensus pattern (50 bp):
TGGGCAGGACTTGTTCTGAATTTTCTTCCCTCTTTCACCAAACCATGTCT
Found at i:9787 original size:685 final size:689
Alignment explanation
Indices: 8472--9798 Score: 2356
Period size: 685 Copynumber: 1.9 Consensus size: 689
8462 AGTCGTCCAA
*
8472 GTCTTGGGCAGGACTTGTTCTGAATTTTATTCCTTCTTTCAACAGACCACGTCCTGGGCAGGACT
1 GTCTTGGGCAGGACTTGTTCTGAATTTTATTCCCTCTTTCAACAGACCACGTCCTGGGCAGGACT
* *
8537 TGTCCTGTTATTAGGCTTCAATAACAAGCAAATTAATGAGTTTTTCATTGCTCAAATCATCTTCA
66 TGTCCTCTTATTAGGCTTCAATAACAAGCAAATTAATGAGTTTTTCATTGCTCAAATCATCTGCA
8602 AAGGTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCGAACAAGGCCCATTAA
131 AAGGTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCGAACAAGGCCCATTAA
*
8667 TGCATCCTTGAATCTCTTTGCTCTTGCTCTTGTCATTGGACCTAATGGCATCTTCAATGGATCAA
196 TGCATCCTTGAATCTCTTTGCTC-T-CTCTTGTCATTGGACCTAATGGCATCTTCAATGGATAAA
* *
8732 ATGACATCTTTGGCATATTCTTGGTGTTTGAAACATGTTGTGCGATATCTCCTTGATCTTCATGC
259 ATGACATCTTTGGCATATCCTTGGTGTTTGAAACATGTTGTGCGATATCTCCGTGATCTTCATGC
8797 TTCTCCATGCTTCCTTCCACTCCATGCTCATCCTCTCCATGATATCCAATGTCATCTTGATATCC
324 TTCTCCATGCTTCCTTCCACTCCATGCTCATCCTCTCCATGATATCCAATGTCATCTTGATATCC
* *
8862 TTGATAAGCCCTTGGCGCATCATTCCCTCCCCGTTGAGAAGGATTTGTCCTCAAATCTGAATCAT
389 TTGAGAAGCCCTTGGCGCATCATTCCCTCCCCGTTGAAAAGGATTTGTCCTCAAATCTGAATCAT
*
8927 TATCAAACAAAGACAAATCAGAAACATTAAAGGTAGCACTCACATTACCATACTCACTAGGAAGA
454 TATCAAACAAAGACAAATCAGAAACATTAAAGGTAGCACGCACATTACCATACTCACTAGGAAGA
8992 TCTAGCTTGTATTCCACAACAATGCCTACACCAAATGCATCACATTCAATCTCAAAAGTAGAATT
519 TCTAGCTTGTATTCCACAACAATGCCTACACCAAATGCATCACATTCAATCTCAAAAGTAGAATT
*
9057 AAAGTTAGGTAAAACAAGTAAAGGGGCATTAGAAAGCTTAGTCTTTAATGTC-CAAATCCTGGGC
584 AAAATTAGGTAAAACAAGTAAAGGGGCATTAGAAAGCTTAGTCTTTAATGTCTCAAATCCTGGGC
9121 AGGACTTGTTCTGAATTTTCTTCCTTCTTTCACCAAACCAT
649 AGGACTTGTTCTGAATTTTCTTCCTTCTTTCACCAAACCAT
* * * * *
9162 GTCTTGGGTAGGACTTGTTCTGAATTTTCTTCCCTCTTTCACCAGACCATGTCTTGGGCAGGACT
1 GTCTTGGGCAGGACTTGTTCTGAATTTTATTCCCTCTTTCAACAGACCACGTCCTGGGCAGGACT
* *
9227 TGTCCTCTTTTTAGGCTTCAATAACAAGCAAATTAATGAGTTTTTCTTTGCTCAAATCATCTGCA
66 TGTCCTCTTATTAGGCTTCAATAACAAGCAAATTAATGAGTTTTTCATTGCTCAAATCATCTGCA
9292 AAGGTCTTC-ATTGAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCGAACAAGGCCCATTAA
131 AAGGTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCGAACAAGGCCCATTAA
*
9356 TGGATCCTTGAATCTCTTTGCTC-CTCTTGTCATTGGACCTAATGGCATCTTCAATGGATAAAAT
196 TGCATCCTTGAATCTCTTTGCTCTCTCTTGTCATTGGACCTAATGGCATCTTCAATGGATAAAAT
* *
9420 GGCATCTTTGGCATCTCCTTGGTGTTTGAAACATGTTGTGCGATATCTCCGTGATCTTCATGCTT
261 GACATCTTTGGCATATCCTTGGTGTTTGAAACATGTTGTGCGATATCTCCGTGATCTTCATGCTT
* * * * *
9485 CTCCATTCTTCCTTGCAC-GCATGCTCATCCTTTCCATGATCTCCAATGTCATCTTGATATCCTT
326 CTCCATGCTTCCTTCCACTCCATGCTCATCCTCTCCATGATATCCAATGTCATCTTGATATCCTT
9549 GAGAAGCCCTTGGCGCATCATTCCCTCCCCGTTGAAAAGGATTTGTCCTCAAATCTGAATCATTA
391 GAGAAGCCCTTGGCGCATCATTCCCTCCCCGTTGAAAAGGATTTGTCCTCAAATCTGAATCATTA
*
9614 TCAAACAAAGACAAATCAGAAACATTAAAGGTAGTACGCACATTACCATACTCACTAGGAAGATC
456 TCAAACAAAGACAAATCAGAAACATTAAAGGTAGCACGCACATTACCATACTCACTAGGAAGATC
*
9679 TAGCTTGTATTCCACAACAATGCCTACACCAAATGCATCACATTCAATCTCAAAAGTATAATTAA
521 TAGCTTGTATTCCACAACAATGCCTACACCAAATGCATCACATTCAATCTCAAAAGTAGAATTAA
*
9744 AATTAGGTAAAACAAGTAAAGGGGCATTAGAAAGCTTAGTCTTTTATGTCTCAAA
586 AATTAGGTAAAACAAGTAAAGGGGCATTAGAAAGCTTAGTCTTTAATGTCTCAAA
9799 CGCCTCTTGT
Statistics
Matches: 608, Mismatches: 28, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
685 281 0.46
686 121 0.20
689 77 0.13
690 129 0.21
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (689 bp):
GTCTTGGGCAGGACTTGTTCTGAATTTTATTCCCTCTTTCAACAGACCACGTCCTGGGCAGGACT
TGTCCTCTTATTAGGCTTCAATAACAAGCAAATTAATGAGTTTTTCATTGCTCAAATCATCTGCA
AAGGTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCGAACAAGGCCCATTAA
TGCATCCTTGAATCTCTTTGCTCTCTCTTGTCATTGGACCTAATGGCATCTTCAATGGATAAAAT
GACATCTTTGGCATATCCTTGGTGTTTGAAACATGTTGTGCGATATCTCCGTGATCTTCATGCTT
CTCCATGCTTCCTTCCACTCCATGCTCATCCTCTCCATGATATCCAATGTCATCTTGATATCCTT
GAGAAGCCCTTGGCGCATCATTCCCTCCCCGTTGAAAAGGATTTGTCCTCAAATCTGAATCATTA
TCAAACAAAGACAAATCAGAAACATTAAAGGTAGCACGCACATTACCATACTCACTAGGAAGATC
TAGCTTGTATTCCACAACAATGCCTACACCAAATGCATCACATTCAATCTCAAAAGTAGAATTAA
AATTAGGTAAAACAAGTAAAGGGGCATTAGAAAGCTTAGTCTTTAATGTCTCAAATCCTGGGCAG
GACTTGTTCTGAATTTTCTTCCTTCTTTCACCAAACCAT
Found at i:12959 original size:19 final size:18
Alignment explanation
Indices: 12917--12959 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12907 TTTAGGGTTT
* * *
12917 CTAATTTGTGCAATTGAG
1 CTAATTTCTGCAATTAAC
12935 CTAATTTCTGCAATTAACC
1 CTAATTTCTGCAATTAA-C
12954 CTAATT
1 CTAATT
12960 GGAGGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (18 bp):
CTAATTTCTGCAATTAAC
Found at i:13429 original size:22 final size:21
Alignment explanation
Indices: 13404--13456 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
13394 AAATCAAACC
*
13404 AACAATTTAAAAATTCTAAGAA
1 AACAATTTAAAAATT-AAAGAA
**
13426 AACAATCAAGAAAATTAAAGAA
1 AACAATTTA-AAAATTAAAGAA
13448 AAC-ATTTAA
1 AACAATTTAA
13457 TAAGAAAGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 1 0.04
21 3 0.12
22 15 0.60
23 6 0.24
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.23
Consensus pattern (21 bp):
AACAATTTAAAAATTAAAGAA
Found at i:18754 original size:13 final size:13
Alignment explanation
Indices: 18736--18761 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18726 CAAATCAAAT
18736 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
18749 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
18762 TAATACACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Found at i:20300 original size:22 final size:21
Alignment explanation
Indices: 20248--20301 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
20238 TGCTTCTTGA
20248 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
20269 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
20288 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
20302 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:21720 original size:25 final size:24
Alignment explanation
Indices: 21684--21730 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
21674 TCCTTCTATT
21684 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
21707 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
21731 AATTTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:22184 original size:21 final size:21
Alignment explanation
Indices: 22158--22198 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22148 TTTAAAACCT
22158 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
22179 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
22199 GGGTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Done.