Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008573.1 Corchorus capsularis cultivar CVL-1 contig08594, 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: 33582
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:628 original size:20 final size:20
Alignment explanation
Indices: 603--652 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
593 TTATGGAGTA
603 ATCAAAATTTCAAGGAGCAT
1 ATCAAAATTTCAAGGAGCAT
* *
623 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGCAT
*
643 ATTAAAATTT
1 ATCAAAATTT
653 AATAGTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGCAT
Found at i:691 original size:22 final size:21
Alignment explanation
Indices: 666--893 Score: 121
Period size: 22 Copynumber: 10.5 Consensus size: 21
656 AGTTTAGTTT
666 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCAT-AGAGGGTTA
688 TCAAAATTTCATAG-GGAGATTA
1 TCAAAATTTCATAGAGG-G-TTA
*
710 ACAAAATTTCCATA-ATGAGGTTA
1 TCAAAATTT-CATAGA-G-GGTTA
** *
733 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAGAG-GGTTA
*
755 TCAAAATTT-GT--A--GTTA
1 TCAAAATTTCATAGAGGGTTA
* **
771 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCAT-AGAGGGTTA
* *
793 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATA--GAGGGTTA
* **
816 TCAAAATTTTATAGGATGATTTA
1 TCAAAATTTCATA-GA-GGGTTA
*
839 TCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATAGAG-GGTTA
* *
861 TCACAAA-TTCATAGTGTGATTA
1 TCA-AAATTTCATAGAG-GGTTA
883 TCAAAATTTCA
1 TCAAAATTTCA
894 GAGTGCGATT
Statistics
Matches: 163, Mismatches: 24, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
16 12 0.07
17 1 0.01
20 3 0.02
21 9 0.06
22 84 0.52
23 51 0.31
24 2 0.01
25 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
TCAAAATTTCATAGAGGGTTA
Found at i:738 original size:45 final size:44
Alignment explanation
Indices: 667--763 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 44
657 GTTTAGTTTT
**
667 CAAAATTTCATAAGAGGGTTATCAAAATTTCATAGGGAGATTAA
1 CAAAATTTCATAAGAGGGTTATCAAAAAATCATAGGGAGATTAA
* *
711 CAAAATTTCCATAATGA-GGTTATCAAAAAATCATAGGGAGGTTAT
1 CAAAATTT-CATAA-GAGGGTTATCAAAAAATCATAGGGAGATTAA
756 CAAAATTT
1 CAAAATTT
764 GTAGTTATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
44 8 0.17
45 37 0.79
46 2 0.04
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.30
Consensus pattern (44 bp):
CAAAATTTCATAAGAGGGTTATCAAAAAATCATAGGGAGATTAA
Found at i:818 original size:23 final size:23
Alignment explanation
Indices: 790--869 Score: 101
Period size: 23 Copynumber: 3.5 Consensus size: 23
780 CATAAGAAAG
790 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
813 TTATCAAAATTTTATA-GGATGAT
1 TTATCAAAATTTTATAGGGA-GGT
* *
836 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
858 TTATCACAAATT
1 TTATCA-AAATT
870 CATAGTGTGA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.18
23 39 0.78
24 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:830 original size:128 final size:127
Alignment explanation
Indices: 661--891 Score: 304
Period size: 128 Copynumber: 1.8 Consensus size: 127
651 TTAATAGTTT
*
661 AGTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGGGA-GA-TTAACAAAATTTCCATA
1 AGTTATCAAAATTTCATAAGAGGGTTATCAAAATTTCATA-GGATGATTTAACAAAATTT-CATA
* *
724 ATGAGGTTATCAAAAAATCATAGGGAGGTTATCAAAATTTGTAGTTATCAAGATTTCATAAGAA
64 ACGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTTGTAGTTATCAAGATTTCATAAGAA
* * * * * *
788 AGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGATGATTTATCAAAATTTCATAG
1 AGTTATCAAAATTTCATA-AGAGGGTTATCAAAATTTCATAGGATGATTTAACAAAATTTCATAA
* * * *
853 CGAGGTTATCACAAATTCATAGTGTGATTATCAAAATTT
65 CGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTT
892 CAGAGTGCGA
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
127 19 0.22
128 58 0.66
129 11 0.12
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (127 bp):
AGTTATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGGATGATTTAACAAAATTTCATAAC
GAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTTGTAGTTATCAAGATTTCATAAGAA
Found at i:842 original size:46 final size:44
Alignment explanation
Indices: 790--893 Score: 131
Period size: 46 Copynumber: 2.3 Consensus size: 44
780 CATAAGAAAG
* * *
790 TTATCAAAATTTTATAGGGAGGTTTATCA-AAATTTTATAG-GATGA
1 TTATCAAAATTTCATAGCGAGG-TTATCACAAA-TTCATAGTG-TGA
835 TTTATCAAAATTTCATAGCGAGGTTATCACAAATTCATAGTGTGA
1 -TTATCAAAATTTCATAGCGAGGTTATCACAAATTCATAGTGTGA
880 TTATCAAAATTTCA
1 TTATCAAAATTTCA
894 GAGTGCGATT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
44 14 0.26
45 15 0.28
46 24 0.45
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATAGCGAGGTTATCACAAATTCATAGTGTGA
Found at i:1096 original size:21 final size:22
Alignment explanation
Indices: 1056--1103 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1046 TTCCTTAGAG
* * *
1056 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTCATAAAA
1078 AGGTTAAAAAAAATT-ATAAAA
1 AGGTTAAAAAAAATTCATAAAA
1099 AGGTT
1 AGGTT
1104 CTCGAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.27
Consensus pattern (22 bp):
AGGTTAAAAAAAATTCATAAAA
Found at i:1820 original size:13 final size:13
Alignment explanation
Indices: 1802--1826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1792 CTATAACCTT
1802 ATAAATCATATTC
1 ATAAATCATATTC
1815 ATAAATCATATT
1 ATAAATCATATT
1827 TATTATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAAATCATATTC
Found at i:1968 original size:19 final size:18
Alignment explanation
Indices: 1939--1980 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1929 TGAGTAGTTT
* *
1939 TTAAGTAAAAATGTAATA
1 TTAAATAAAAATATAATA
1957 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
1976 TTAAA
1 TTAAA
1981 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:1984 original size:19 final size:19
Alignment explanation
Indices: 1944--1980 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1934 AGTTTTTAAG
*
1944 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
1963 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
1981 ATAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:3193 original size:76 final size:76
Alignment explanation
Indices: 3067--3220 Score: 281
Period size: 76 Copynumber: 2.0 Consensus size: 76
3057 CATTCCCTTA
* *
3067 TGATGTGCGATGTTTATTCACAAGTGAATCCTCAACATTCTCCCCCGATTCACTTATAAGTTCTC
1 TGATGTGCGATGTTTATTCACAAGTGAATCATCAACATTCACCCCCGATTCACTTATAAGTTCTC
3132 ATCTCTCCCAG
66 ATCTCTCCCAG
*
3143 TGATGTGCGATGTTTATTCACAAGTGAATCATCAACATTCACCCCCGATTCACTTGTAAGTTCTC
1 TGATGTGCGATGTTTATTCACAAGTGAATCATCAACATTCACCCCCGATTCACTTATAAGTTCTC
3208 ATCTCTCCCAG
66 ATCTCTCCCAG
3219 TG
1 TG
3221 CAGCCCAACC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (76 bp):
TGATGTGCGATGTTTATTCACAAGTGAATCATCAACATTCACCCCCGATTCACTTATAAGTTCTC
ATCTCTCCCAG
Found at i:9914 original size:29 final size:29
Alignment explanation
Indices: 9840--9916 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
9830 CTTGTATCGT
* *
9840 TTGGACGTTTTGTCCCCTGAACTTCAATC
1 TTGGACGATTTGCCCCCTGAACTTCAATC
* *
9869 TTAGAC-ATTCTGCCCCCTGAACTTCAATT
1 TTGGACGATT-TGCCCCCTGAACTTCAATC
*
9898 TTGGGACGGTTTGCCCCCT
1 TT-GGACGATTTGCCCCCT
9917 CAACCTAACG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.05
29 24 0.62
30 11 0.28
31 2 0.05
ACGTcount: A:0.17, C:0.30, G:0.18, T:0.35
Consensus pattern (29 bp):
TTGGACGATTTGCCCCCTGAACTTCAATC
Found at i:10111 original size:30 final size:29
Alignment explanation
Indices: 10070--10147 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
10060 CGTTAGGTTG
* *
10070 AGGGGGTAAAATGTCCCAAAATTTAAGTTC
1 AGGGGGCAAAATGT-CCAAAATTGAAGTTC
*
10100 AGGGGGCAAAATGTCCAAGATTGAAGTTC
1 AGGGGGCAAAATGTCCAAAATTGAAGTTC
*** *
10129 ATAAGGCAAAACGTCCAAA
1 AGGGGGCAAAATGTCCAAA
10148 CGATACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (29 bp):
AGGGGGCAAAATGTCCAAAATTGAAGTTC
Found at i:10126 original size:29 final size:30
Alignment explanation
Indices: 10070--10129 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
10060 CGTTAGGTTG
* *
10070 AGGGGGTAAAATGTCCCAAAATTTAAGTTC
1 AGGGGGCAAAATGTCCCAAAATTGAAGTTC
*
10100 AGGGGGCAAAATGT-CCAAGATTGAAGTTC
1 AGGGGGCAAAATGTCCCAAAATTGAAGTTC
10129 A
1 A
10130 TAAGGCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (30 bp):
AGGGGGCAAAATGTCCCAAAATTGAAGTTC
Found at i:18704 original size:14 final size:14
Alignment explanation
Indices: 18685--18715 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18675 TTATATGTTT
18685 ATATAATAACTATC
1 ATATAATAACTATC
18699 ATATAATAACTATC
1 ATATAATAACTATC
18713 ATA
1 ATA
18716 CATAAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATAATAACTATC
Found at i:26679 original size:31 final size:31
Alignment explanation
Indices: 26641--26699 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
26631 TTTGTAAAAC
*
26641 TTTTGAAACT-TCTATTGTACCCTTATTTAAT
1 TTTTGAAA-TGTCTATTATACCCTTATTTAAT
*
26672 TTTTGAAATGTCTATTATATCCTTATTT
1 TTTTGAAATGTCTATTATACCCTTATTT
26700 GTTTTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (31 bp):
TTTTGAAATGTCTATTATACCCTTATTTAAT
Found at i:27436 original size:56 final size:57
Alignment explanation
Indices: 27343--27453 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 57
27333 CAACGTAATA
*
27343 GATAAATTTGCTTGCTTTTAGCTGTCTTAACGAAAGACGAAGACAA-GCTATGTCATG
1 GATAAATTTGCTTGCTTTTAGCTGCCTTAACGAAAGACGAAGACAATG-TATGTCATG
*
27400 GATAAATTTGCTTGC-TTTAGCTGCCTTAACGGAAGACGAAGACAATGTATGTCA
1 GATAAATTTGCTTGCTTTTAGCTGCCTTAACGAAAGACGAAGACAATGTATGTCA
27454 GCTGCTTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
56 35 0.69
57 16 0.31
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (57 bp):
GATAAATTTGCTTGCTTTTAGCTGCCTTAACGAAAGACGAAGACAATGTATGTCATG
Found at i:27667 original size:2 final size:2
Alignment explanation
Indices: 27660--27688 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27650 AATCATGTTT
27660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27689 CTAGAACCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30557 original size:2 final size:2
Alignment explanation
Indices: 30550--30587 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
30540 AACTAACTCT
30550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
30588 TATTTTTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.