Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007732.1 Corchorus capsularis cultivar CVL-1 contig07753, 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: 49539
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:1370 original size:33 final size:33
Alignment explanation
Indices: 1330--1411 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
1320 CCTGGCCAGA
1330 GGGTTATAGTA-TCT-GGAAAACGGCCCTGCTAAC
1 GGGTTATAGTAGT-TAGGAAAA-GGCCCTGCTAAC
* ***
1363 GGGTTATAATAGTTAGTTTAAGGCCCTGCTAAC
1 GGGTTATAGTAGTTAGGAAAAGGCCCTGCTAAC
1396 GGGTTATAGTAGTTAG
1 GGGTTATAGTAGTTAG
1412 CAATATGTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 38 0.90
34 4 0.10
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (33 bp):
GGGTTATAGTAGTTAGGAAAAGGCCCTGCTAAC
Found at i:9910 original size:47 final size:47
Alignment explanation
Indices: 9841--9930 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
9831 AAGAAAATTC
*
9841 AGTTAACGAATGGAATTTTGTTGTGAAATGATAACAAAACAAAACAA
1 AGTTAACGAATGAAATTTTGTTGTGAAATGATAACAAAACAAAACAA
9888 AGTTAA-GAAATGAAATTTTGTTGTGAAATGATAACAAAACAAA
1 AGTTAACG-AATGAAATTTTGTTGTGAAATGATAACAAAACAAA
9931 GCAATAGAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
46 1 0.02
47 40 0.98
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.27
Consensus pattern (47 bp):
AGTTAACGAATGAAATTTTGTTGTGAAATGATAACAAAACAAAACAA
Found at i:10224 original size:11 final size:11
Alignment explanation
Indices: 10210--10247 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
10200 ATTCATAACA
10210 AATTTATAATT
1 AATTTATAATT
10221 AATTTATAATT
1 AATTTATAATT
10232 -ATTTGATAATT
1 AATTT-ATAATT
*
10243 TATTT
1 AATTT
10248 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:11898 original size:29 final size:30
Alignment explanation
Indices: 11872--11927 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
11862 AACGTAAGGA
11872 ATTAATTTGTACCAA-A-AAAAACATAAGAG
1 ATTAATTTGT-CCAAGACAAAAACATAAGAG
*
11901 ATTATTTTGTCCAAGACAAAAACATAA
1 ATTAATTTGTCCAAGACAAAAACATAA
11928 ACGATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 4 0.17
29 10 0.42
30 10 0.42
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (30 bp):
ATTAATTTGTCCAAGACAAAAACATAAGAG
Found at i:12011 original size:19 final size:20
Alignment explanation
Indices: 11973--12014 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
11963 GTAAATATAC
11973 AAAGTAAAAAGTTAAAGAAA
1 AAAGTAAAAAGTTAAAGAAA
* *
11993 AAAGTAATAAG-TCAAGAAA
1 AAAGTAAAAAGTTAAAGAAA
12012 AAA
1 AAA
12015 AAATGTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAGTAAAAAGTTAAAGAAA
Found at i:21030 original size:93 final size:93
Alignment explanation
Indices: 20871--21056 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 93
20861 ATGTCCTTAT
* * *
20871 TTCATACTTCAGGGAGCAAAGTTGGATAAAAAAAGATTAGGAGGTAAAATGTCATTTTTGTGATA
1 TTCATACTTCAGGGAGCAAAGTTGGATAAAAAAAAATAAGGAGGCAAAATGTCATTTTTGTGATA
20936 CTTCAGAGGGGATTTTGGGCATTAAGCC
66 CTTCAGAGGGGATTTTGGGCATTAAGCC
* *
20964 TTCATACTTCAGGGAGCAAAGTTGGATAAAAAAAAATAAGGATGCAAAATGTCCTTTTTGTGATA
1 TTCATACTTCAGGGAGCAAAGTTGGATAAAAAAAAATAAGGAGGCAAAATGTCATTTTTGTGATA
21029 CTTCAGAGGGGATTTTGGGCATTAAGCC
66 CTTCAGAGGGGATTTTGGGCATTAAGCC
21057 GTATTTAGGT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.30
Consensus pattern (93 bp):
TTCATACTTCAGGGAGCAAAGTTGGATAAAAAAAAATAAGGAGGCAAAATGTCATTTTTGTGATA
CTTCAGAGGGGATTTTGGGCATTAAGCC
Found at i:23603 original size:32 final size:30
Alignment explanation
Indices: 23567--23627 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
23557 TATTTTTAAT
23567 TAAAAGTAAATTATAAAAATATATATAATATA
1 TAAAAGTAAA--ATAAAAATATATATAATATA
* *
23599 TAAAATTAAAATTAAAATATATATAATAT
1 TAAAAGTAAAATAAAAATATATATAATAT
23628 GAAATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 18 0.67
32 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (30 bp):
TAAAAGTAAAATAAAAATATATATAATATA
Found at i:23618 original size:19 final size:19
Alignment explanation
Indices: 23564--23619 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
23554 TATTATTTTT
* *
23564 AATTAAAAGTAAATTATAA
1 AATTAAAATTAAAATATAA
* * *
23583 AAAT-ATATATAATATATAA
1 AATTAAAAT-TAAAATATAA
23602 AATTAAAATTAAAATATA
1 AATTAAAATTAAAATATA
23620 TATAATATGA
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
18 2 0.07
19 22 0.81
20 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AATTAAAATTAAAATATAA
Found at i:27129 original size:25 final size:25
Alignment explanation
Indices: 27098--27147 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27088 CCACTAATTG
27098 TTTTTGTCTCATACATCATCGAAAT
1 TTTTTGTCTCATACATCATCGAAAT
27123 TTTTTGTCTCATACATCATCGAAAT
1 TTTTTGTCTCATACATCATCGAAAT
27148 CAGATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.44
Consensus pattern (25 bp):
TTTTTGTCTCATACATCATCGAAAT
Found at i:32778 original size:14 final size:14
Alignment explanation
Indices: 32759--32788 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
32749 CACTTTTTGA
32759 TTAAAAAAATATAT
1 TTAAAAAAATATAT
32773 TTAAAAAAATATAT
1 TTAAAAAAATATAT
32787 TT
1 TT
32789 TTTTTAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAAAAAATATAT
Found at i:37988 original size:20 final size:20
Alignment explanation
Indices: 37951--37990 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
37941 TGGTTTTATA
**
37951 ATCTTGGTTTTGGATTGATT
1 ATCTTGGTTTTACATTGATT
*
37971 ATCTTGGTTTTACTTTGATT
1 ATCTTGGTTTTACATTGATT
37991 TATGATCATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.57
Consensus pattern (20 bp):
ATCTTGGTTTTACATTGATT
Found at i:41502 original size:67 final size:67
Alignment explanation
Indices: 41059--41709 Score: 572
Period size: 67 Copynumber: 9.8 Consensus size: 67
41049 AAAAGTTGAG
* * * *
41059 CTTAAATGCAAAAAGACAAAATTGACCCTTTGACCGAAAGGGTA-TTCTGGAAACGAAAATACTA
1 CTTAAATGCAAAAAGACTAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTA
41123 AA
66 AA
** * *
41125 CTTAAACACAAAAAGA-TGAAACTG-GCCTTTCGACCGAAAGGGTATTTCTGGAAA-GTAAAA-A
1 CTTAAATGCAAAAAGACT-AAACTGACCCTTT-GACCGAAAGGGTATTTTTGGAAATG-AAAATA
41186 CTAAA
63 CTAAA
* * * * *
41191 CTTAAATGCAATCAACCTGA-TGAAATTGA--TTTCTCGACCGGAAGGATATCTTTTGGAAA-GA
1 CTTAAATGCAA--AA--AGACT-AAACTGACCCTT-T-GACCGAAAGGGTAT-TTTTGGAAATGA
*
41252 AAGGT--TAAA
58 AA-ATACTAAA
* * * * * * *
41261 CCTAAATGCAAAAAGACGAAACTGACCCTTCGACCGAAAGAGCATTATTGG--A-GAACAAAACT
1 CTTAAATGCAAAAAGACTAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAA-AATACT
41323 AAA
65 AAA
* *
41326 CTTAAATG-AGAAAAGACGAAACTGACCGTTTGACCGAAAGGGTATTTTTGGAAATGAAAAT--T
1 CTTAAATGCA-AAAAGACTAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACT
41388 ---
65 AAA
* * * * * *
41388 -TAAAATGCAAGAAGACTAGACTGGCCCTTTGACTGAAAGGGTGTTTTTGGAAATGAAAATACTA
1 CTTAAATGCAAAAAGACTAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTA
41452 AA
66 AA
* * *
41454 CTTAAATGCAAGAAGACTAGACTGACCCTTTAACCGAAAGGGTATTTTTGGAAATGAAAATACTA
1 CTTAAATGCAAAAAGACTAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTA
41519 AA
66 AA
* * * * * *
41521 CTTAAATGTAAGAAGATTAGACTGACCCTTTAACCGAAAGTGTATTTTTGGAAATGAAAATACTA
1 CTTAAATGCAAAAAGACTAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTA
41586 AA
66 AA
* * * * * *
41588 CTTAAATACAAGAAGACTAGACTTACCCTTTGACCGAAAGAGTATTTCTGGAAAACT-AAAATAC
1 CTTAAATGCAAAAAGACTAAACTGACCCTTTGACCGAAAGGGTATTTTTGG-AAA-TGAAAATAC
41652 TAAA
64 TAAA
* * * *
41656 CTTAAATGCAAAAAGCCTAGACTGACCCTTTGACTGAAAGGGTATTTCTGGAAA
1 CTTAAATGCAAAAAGACTAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAA
41710 ACTAACCTAA
Statistics
Matches: 490, Mismatches: 63, Indels: 63
0.80 0.10 0.10
Matches are distributed among these distances:
61 50 0.10
62 1 0.00
63 5 0.01
64 2 0.00
65 58 0.12
66 66 0.13
67 188 0.38
68 68 0.14
69 3 0.01
70 40 0.08
71 9 0.02
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (67 bp):
CTTAAATGCAAAAAGACTAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTA
AA
Found at i:41800 original size:13 final size:13
Alignment explanation
Indices: 41782--41806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41772 ATTTCATCTC
41782 TTTTTTATTTTTA
1 TTTTTTATTTTTA
41795 TTTTTTATTTTT
1 TTTTTTATTTTT
41807 TTTGAATTTC
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:45447 original size:21 final size:21
Alignment explanation
Indices: 45409--45448 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45399 GGTGCCCACA
* *
45409 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAACACCCATG
*
45430 TGGTTTGCCTGATCACCCA
1 TGGTTTGCCTGAACACCCA
45449 GGTAGGCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TGGTTTGCCTGAACACCCATG
Found at i:48648 original size:109 final size:108
Alignment explanation
Indices: 48457--49006 Score: 771
Period size: 109 Copynumber: 5.0 Consensus size: 108
48447 TCGAATTTTA
*
48457 CTTTTAATTTGGCATAAAAAAAAGTTTTGACATAAT-AGAATTTTTTACTAAAATCCTATTGGTT
1 CTTTTAATTTGGCATAAAAAAAAGTTTTGATATAATCA-AA-TTTTTACTAAAATCCTATTGGTT
* *
48521 TAAGATGGAGCACATGGATCGTCATACCAACCGTTGGATTGAATC
64 CAAGATGAAGCACATGGATCGTCATACCAACCGTTGGATTGAATC
*
48566 CTTTTAATTTGGCATCAAAAAAAAGTTTTGATATAATCAAATTTTTACTAAAATCCTATTAGTTC
1 CTTTTAATTTGGCAT-AAAAAAAAGTTTTGATATAATCAAATTTTTACTAAAATCCTATTGGTTC
* *
48631 AAGATGAAGCACATGGATAGTCATACCAATCGTTGGATTGAATC
65 AAGATGAAGCACATGGATCGTCATACCAACCGTTGGATTGAATC
* * *
48675 CTTTTAATTTGGCATAAAAAACAGTTTTTGATATAATTGAATTTTTTACTAAAATCCTATTGGTT
1 CTTTTAATTTGGCATAAAAAAAAG-TTTTGATATAA-TCAAATTTTTACTAAAATCCTATTGGTT
* * * *
48740 CAAGATGAAGTACATGGGTCGTCATACCAACCGTTGGATTAAATA
64 CAAGATGAAGCACATGGATCGTCATACCAACCGTTGGATTGAATC
* *
48785 ATTTTAATTTGGCAT-AAAAAAAGTTTTGATATAATCGAATTTTTACTAAAATCCTATTGGTTCA
1 CTTTTAATTTGGCATAAAAAAAAGTTTTGATATAATCAAATTTTTACTAAAATCCTATTGGTTCA
48849 AGATGAAGCACATGGATCGTCATACCAACCGTTGGATTGAATC
66 AGATGAAGCACATGGATCGTCATACCAACCGTTGGATTGAATC
* *
48892 CTTTTCATTTGGCATTAAAAAGAAGTTTTGATATAATCGAATTTTCGAATTTTTTACTAAAATCC
1 CTTTTAATTTGGCA-TAAAAAAAAGTTTTGATATAATC--A------AA-TTTTTACTAAAATCC
* * *
48957 TATTGGTTTAAGATGAAGGACATGGGTCGTCATACCAACCGTTGGATTGA
56 TATTGGTTCAAGATGAAGCACATGGATCGTCATACCAACCGTTGGATTGA
49007 GATTCAATCC
Statistics
Matches: 394, Mismatches: 32, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
107 78 0.20
108 20 0.05
109 131 0.33
110 100 0.25
111 1 0.00
117 2 0.01
118 62 0.16
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (108 bp):
CTTTTAATTTGGCATAAAAAAAAGTTTTGATATAATCAAATTTTTACTAAAATCCTATTGGTTCA
AGATGAAGCACATGGATCGTCATACCAACCGTTGGATTGAATC
Found at i:48864 original size:217 final size:216
Alignment explanation
Indices: 48457--49004 Score: 828
Period size: 217 Copynumber: 2.5 Consensus size: 216
48447 TCGAATTTTA
* *
48457 CTTTTAATTTGGCATAAAAAAAAGTTTTGACATAATAGAATTTTTTACTAAAATCCTATTGGTTT
1 CTTTTAATTTGGCAT-AAAAAAAGTTTTGATATAATTGAATTTTTTACTAAAATCCTATTGGTTT
* * * **
48522 AAGATGGAGCACATGGATCGTCATACCAACCGTTGGATTGAATCCTTTTAATTTGGCATCAAAAA
65 AAGATGAAGCACATGGGTCGTCATACCAACCGTTGGATTAAATAATTTTAATTTGGCAT-AAAAA
48587 AAAGTTTTGATATAATCAAATTTTTACTAAAATCCTATTAGTTCAAGATGAAGCACATGGATAGT
129 AAAGTTTTGATATAATCAAATTTTTACTAAAATCCTATTAGTTCAAGATGAAGCACATGGATAGT
*
48652 CATACCAATCGTTGGATTGAATC
194 CATACCAACCGTTGGATTGAATC
48675 CTTTTAATTTGGCATAAAAAACAGTTTTTGATATAATTGAATTTTTTACTAAAATCCTATTGGTT
1 CTTTTAATTTGGCATAAAAAA-AG-TTTTGATATAATTGAATTTTTTACTAAAATCCTATTGGTT
* *
48740 CAAGATGAAGTACATGGGTCGTCATACCAACCGTTGGATTAAATAATTTTAATTTGGCAT-AAAA
64 TAAGATGAAGCACATGGGTCGTCATACCAACCGTTGGATTAAATAATTTTAATTTGGCATAAAAA
* * *
48804 AAAGTTTTGATATAATCGAATTTTTACTAAAATCCTATTGGTTCAAGATGAAGCACATGGATCGT
129 AAAGTTTTGATATAATCAAATTTTTACTAAAATCCTATTAGTTCAAGATGAAGCACATGGATAGT
48869 CATACCAACCGTTGGATTGAATC
194 CATACCAACCGTTGGATTGAATC
*
48892 CTTTTCATTTGGCATTAAAAAGAAGTTTTGATATAATCGAATTTTCGAATTTTTTACTAAAATCC
1 CTTTTAATTTGGCA-TAAAAA-AAGTTTTG--AT-AT--AA--TT-GAATTTTTTACTAAAATCC
*
48957 TATTGGTTTAAGATGAAGGACATGGGTCGTCATACCAACCGTTGGATT
56 TATTGGTTTAAGATGAAGCACATGGGTCGTCATACCAACCGTTGGATT
49005 GAGATTCAAT
Statistics
Matches: 302, Mismatches: 16, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
217 112 0.37
218 25 0.08
219 94 0.31
220 2 0.01
222 2 0.01
224 2 0.01
225 65 0.22
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (216 bp):
CTTTTAATTTGGCATAAAAAAAGTTTTGATATAATTGAATTTTTTACTAAAATCCTATTGGTTTA
AGATGAAGCACATGGGTCGTCATACCAACCGTTGGATTAAATAATTTTAATTTGGCATAAAAAAA
AGTTTTGATATAATCAAATTTTTACTAAAATCCTATTAGTTCAAGATGAAGCACATGGATAGTCA
TACCAACCGTTGGATTGAATC
Done.