Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019586.1 Corchorus olitorius cultivar O-4 contig19619, 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: 34548
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2368 original size:30 final size:30
Alignment explanation
Indices: 2312--2371 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2302 CAATTCTTGC
* **
2312 TCTTGAAATTATTCTTCAATGGTCTTCAAA
1 TCTTCAAATTATTCTTCAATAATCTTCAAA
2342 TCTTCAAATTA-TCTTCAATAAATCTTCAAA
1 TCTTCAAATTATTCTTCAAT-AATCTTCAAA
2372 CACGAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (30 bp):
TCTTCAAATTATTCTTCAATAATCTTCAAA
Found at i:11238 original size:27 final size:26
Alignment explanation
Indices: 11195--11273 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
11185 AAATGAACTT
** *
11195 AAAATGACCAACGTGCCCTTGATTATG
1 AAAATGACCAAAATGCCCTT-AGTATG
* *
11222 AAATTGACCAAAATGCCCTTAGTGTG
1 AAAATGACCAAAATGCCCTTAGTATG
*
11248 AAAATGACCAAAATGCCCCTAG-ATG
1 AAAATGACCAAAATGCCCTTAGTATG
11273 A
1 A
11274 CCCTAATGCC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 3 0.07
26 24 0.55
27 17 0.39
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCTTAGTATG
Found at i:11567 original size:50 final size:50
Alignment explanation
Indices: 11506--11784 Score: 325
Period size: 50 Copynumber: 5.6 Consensus size: 50
11496 TCCCAATCAA
* *
11506 CCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCTGCTTAT
1 CCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTAT
* *
11556 CCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGATTGTCTT-C-C-AAT
1 CCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTAT
*
11603 CGTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGATCGTCTTCCGCTTAT
1 CCTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGATCGTCTTCCGCTTAT
** * *
11654 CCTTTGAACTGTCTTCCAATTCAATCTT--CGGGAAATCGTCTTCCGAATCAACT
1 CCTTTGAACTGTCTTCCAATTCAATCTTAAAAGG--ATCGTCTTCCG-CT-TA-T
* * * * * *
11707 TCTTTGAATTGTCTTCCAATCCAATATTAAAAGGACCGTTTTCCGCTTAT
1 CCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTAT
*
11757 CCTTTGAACTGTCTTCCAATTCCATCTT
1 CCTTTGAACTGTCTTCCAATTCAATCTT
11785 GAGAAAATCA
Statistics
Matches: 191, Mismatches: 27, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
47 29 0.15
48 16 0.08
49 1 0.01
50 76 0.40
51 31 0.16
52 2 0.01
53 34 0.18
55 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (50 bp):
CCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTAT
Found at i:11793 original size:103 final size:100
Alignment explanation
Indices: 11490--11799 Score: 407
Period size: 103 Copynumber: 3.1 Consensus size: 100
11480 TTCGAAATGG
* *
11490 ATCGTCTCCCAATCAACCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCTGCTTA
1 ATCGTCTTCCAATCAACCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTA
11555 TCCTTTGAACTGTCTTCCAATTCAATCTT-A-AAA
66 TCCTTTGAACTGTCTTCCAATTCAATCTTGAGAAA
* * *
11588 GGATTGTCTTCCAAT---CGTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGATCGTCTTCCGC
1 --ATCGTCTTCCAATCAACCTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGC
*
11650 TTATCCTTTGAACTGTCTTCCAATTCAATCTTCG-GGAA
63 TTATCCTTTGAACTGTCTTCCAATTCAATCTT-GAGAAA
* * * *
11688 ATCGTCTTCCGAATCAACTTCTTTGAATTGTCTTCCAATCCAATATTAAAAGGACCGTTTTCCGC
1 ATCGTCTTCC-AATCAAC--CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGC
*
11753 TTATCCTTTGAACTGTCTTCCAATTCCATCTTGAGAAA
63 TTATCCTTTGAACTGTCTTCCAATTCAATCTTGAGAAA
*
11791 ATCATCTTC
1 ATCGTCTTC
11800 TGATACTCTT
Statistics
Matches: 183, Mismatches: 16, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
97 27 0.15
98 57 0.31
99 3 0.02
100 13 0.07
102 2 0.01
103 58 0.32
104 23 0.13
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.37
Consensus pattern (100 bp):
ATCGTCTTCCAATCAACCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTA
TCCTTTGAACTGTCTTCCAATTCAATCTTGAGAAA
Found at i:12128 original size:64 final size:64
Alignment explanation
Indices: 12045--12372 Score: 399
Period size: 64 Copynumber: 5.1 Consensus size: 64
12035 CAACTTCTGC
* * * * * * *
12045 AACTTTTGAGAAACTATCTTCTGGTGTACTTCCTAACAAAATCATCTTCCAATTCAT-TCCTAAA
1 AACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCATCTTCC-ACTCATCTCCTGAA
*
12109 AACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCGATTCA-CTCCTGAA
1 AACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCATCTTCC-ACTCATCTCCTGAA
* * *
12173 AACTCTTGAGAAACCAATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGCTCATCTTCTGAA
1 AACTCTTGAGAAACC-ATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCACTCATCTCCTGAA
* * * * * *
12238 AATTGTTGAGAAACCATCTTCTGGTGTACTTCTAGACAAGATCATCTACCGCTCATCTTCTGAA
1 AACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCACTCATCTCCTGAA
* * * * * *
12302 AATTGTTGAGAAACCATCTTCCGGTGTACTTCTTGACAAGATCGTCTTCCGCTCATCTTCTGAA
1 AACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCACTCATCTCCTGAA
*
12366 AATTCTT
1 AACTCTT
12373 TCTAGCAAAC
Statistics
Matches: 240, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
64 186 0.77
65 54 0.22
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (64 bp):
AACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCACTCATCTCCTGAA
Found at i:12247 original size:129 final size:127
Alignment explanation
Indices: 12012--12372 Score: 465
Period size: 129 Copynumber: 2.8 Consensus size: 127
12002 CCAGTGCATC
* * * * *
12012 TCTTAACAAGATCGTCTTCCGATCAACTTCTG-CAACTTTTGAGAAACTATCTTCTGGTGTACTT
1 TCTTGACAAGATCATCTTCCGATC-ACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTT
* * * * ** * * *
12076 CCTAACAAAATCATCTTCCAATTCAT-TCCTAAAAACTCTTGAGAAACCATCTTCTGGTGTACT
65 CTTGACAAGATCGTCTTCC-GCTCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
*
12139 TCTTGACAAGATCATCTTCCGATTCACTCCTGAAAACTCTTGAGAAACCAATCTTCTGGTGTACT
1 TCTTGACAAGATCATCTTCCGA-TCACTTCTGAAAACTCTTGAGAAACC-ATCTTCTGGTGTACT
*
12204 TCTTGACAAGATCGTCTTCCGCTCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
64 TCTTGACAAGATCGTCTTCCGCTCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
* * * * * *
12268 TCTAGACAAGATCATCTACCGCTCATCTTCTGAAAATTGTTGAGAAACCATCTTCCGGTGTACTT
1 TCTTGACAAGATCATCTTCCGATCA-CTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTT
12333 CTTGACAAGATCGTCTTCCGCTCATCTTCTGAAAATTCTT
65 CTTGACAAGATCGTCTTCCGCTCATCTTCTGAAAATTCTT
12373 TCTAGCAAAC
Statistics
Matches: 205, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
127 26 0.13
128 76 0.37
129 103 0.50
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (127 bp):
TCTTGACAAGATCATCTTCCGATCACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTC
TTGACAAGATCGTCTTCCGCTCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
Found at i:12437 original size:67 final size:67
Alignment explanation
Indices: 12362--12597 Score: 418
Period size: 67 Copynumber: 3.5 Consensus size: 67
12352 GCTCATCTTC
*
12362 TGAAAATTCTTTCTAGCAAACTGTCTTCCGATGTATTCCTTAATGAGATTGTCTTCCAATCAACA
1 TGAAAATTCTTTCTAGCAAACTGTCTTCCGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACA
12427 TT
66 TT
*
12429 TGAAAATTCTTTCTTGCAAACTGTCTTCCGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACA
1 TGAAAATTCTTTCTAGCAAACTGTCTTCCGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACA
12494 TT
66 TT
* * *
12496 TTAAAATTCTTTCTAGCAAACCGTCTTCAGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACA
1 TGAAAATTCTTTCTAGCAAACTGTCTTCCGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACA
12561 TT
66 TT
*
12563 TGAAAATTCTTTCCAGCAAACTGTCTTCCGGTGTA
1 TGAAAATTCTTTCTAGCAAACTGTCTTCCGGTGTA
12598 AACTTAAATC
Statistics
Matches: 159, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 159 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (67 bp):
TGAAAATTCTTTCTAGCAAACTGTCTTCCGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACA
TT
Found at i:16706 original size:44 final size:43
Alignment explanation
Indices: 16639--16727 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 43
16629 GCATGAACAC
** *
16639 ATATACAAAGGAATGGATGATGCATGATGGATGTATGAACATAT
1 ATATACAAAGGAATGGACAATGCATGAAGGATGTATG-ACATAT
*
16683 ATATACAAA-GACATGGACAATGCATGAAGGATGTTTGACATAT
1 ATATACAAAGGA-ATGGACAATGCATGAAGGATGTATGACATAT
16726 AT
1 AT
16728 TAATGGATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 10 0.25
44 30 0.75
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (43 bp):
ATATACAAAGGAATGGACAATGCATGAAGGATGTATGACATAT
Found at i:17602 original size:15 final size:14
Alignment explanation
Indices: 17573--17610 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
17563 AATAAAACAT
*
17573 CAAAGCAAACGAAA
1 CAAAACAAACGAAA
17587 CAAAACAAACCGAAA
1 CAAAACAAA-CGAAA
17602 CAAAACAAA
1 CAAAACAAA
17611 GCAACCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.68, C:0.24, G:0.08, T:0.00
Consensus pattern (14 bp):
CAAAACAAACGAAA
Found at i:22123 original size:21 final size:22
Alignment explanation
Indices: 22097--22137 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
22087 GCAGAATGAA
*
22097 TTCTTCAAGTTC-GCAAGGTTC
1 TTCTTCAAGATCTGCAAGGTTC
*
22118 TTCTTCCAGATCTGCAAGGT
1 TTCTTCAAGATCTGCAAGGT
22138 CGGCTTCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (22 bp):
TTCTTCAAGATCTGCAAGGTTC
Found at i:26584 original size:24 final size:24
Alignment explanation
Indices: 26538--26584 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
26528 TTTCAACTAC
* * *
26538 ATTTTCATCCATATTTTGCTCTAA
1 ATTTTCATCCACATTCTGATCTAA
*
26562 ATTTTCATCTACATTCTGATCTA
1 ATTTTCATCCACATTCTGATCTA
26585 CATTCTCAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTTTCATCCACATTCTGATCTAA
Found at i:26650 original size:24 final size:24
Alignment explanation
Indices: 26618--26666 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
26608 CCATTTTCAA
*
26618 CTTCTAAACCAT-CTAAATCATCAC
1 CTTCTAAACC-TGCCAAATCATCAC
26642 CTTCTAAACCTGCCAAATCATCAC
1 CTTCTAAACCTGCCAAATCATCAC
26666 C
1 C
26667 CTCAACTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.27
Consensus pattern (24 bp):
CTTCTAAACCTGCCAAATCATCAC
Done.