Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009433.1 Corchorus capsularis cultivar CVL-1 contig09454, 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: 49293
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:7812 original size:26 final size:26
Alignment explanation
Indices: 7774--7847 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 26
7764 TAGGGTCACC
*
7774 TAGGGGTATTTTGGTCATTTTACA-T
1 TAGGGGCATTTTGGTCATTTTACATT
* * *
7799 TATGGGCATTTTTGTCATTTTTGCATT
1 TAGGGGCATTTTGGTCA-TTTTACATT
7826 TAGGGGCATTTTGGTCATTTTA
1 TAGGGGCATTTTGGTCATTTTA
7848 TGTCCACTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 14 0.35
26 10 0.25
27 16 0.40
ACGTcount: A:0.18, C:0.09, G:0.23, T:0.50
Consensus pattern (26 bp):
TAGGGGCATTTTGGTCATTTTACATT
Found at i:22319 original size:267 final size:267
Alignment explanation
Indices: 21844--22369 Score: 989
Period size: 267 Copynumber: 2.0 Consensus size: 267
21834 TACATAATTG
*
21844 TTTTCTAATTTAGTTTTCCTATTTCGAAAATCCTAAATATCCCCTTTTGGTAAGACTTTCTTTTG
1 TTTTCTAATTTAGTTTTCCTATTTCGAAAATCCTAAAAATCCCCTTTTGGTAAGACTTTCTTTTG
*
21909 TACGAGTTGCCTTTGATTTGCTCCTTCCTTCTCTGTGGATTCGACCCCTACTTGCCCTAGCTAAT
66 TACGAGTTGCCTTTGATTTGCTCCTACCTTCTCTGTGGATTCGACCCCTACTTGCCCTAGCTAAT
21974 AGTTATAGGTTTGTGGGGATTATTTTGTGATTTGTTCAACGACCGATCAAGTCCATTGAAGACCA
131 AGTTATAGGTTTGTGGGGATTATTTTGTGATTTGTTCAACGACCGATCAAGTCCATTGAAGACCA
* *
22039 ATTAGAGAGCATTGAATTCGACATCACCAAGAATATTCCCATTGATTCCAAGGTGTTCACCTTAT
196 ATTAGAGAGCATTGAAGTCGACATCACCAAGAATATTCCCATCGATTCCAAGGTGTTCACCTTAT
22104 TTTGTGA
261 TTTGTGA
*
22111 TTTTCTAATTTAGTTTTCCTATTTCGAATATCCTAAAAATCCCCTTTTGGTAAGACTTTCTTTTG
1 TTTTCTAATTTAGTTTTCCTATTTCGAAAATCCTAAAAATCCCCTTTTGGTAAGACTTTCTTTTG
*
22176 TACGATTTGCCTTTGATTTGCTCCTACCTTCTCTGTGGATTCGACCCCTACTTGCCCTAGCTAAT
66 TACGAGTTGCCTTTGATTTGCTCCTACCTTCTCTGTGGATTCGACCCCTACTTGCCCTAGCTAAT
22241 AGTTATAGGTTTGTGGGGATTATTTTGTGATTTGTTCAACGACCGATCAAGTCCATTGAAGACCA
131 AGTTATAGGTTTGTGGGGATTATTTTGTGATTTGTTCAACGACCGATCAAGTCCATTGAAGACCA
*
22306 ATTGGAGAGCATTGAAGTCGACATCACCAAGAATATTCCCATCGATTCCAAGGTGTTCACCTTA
196 ATTAGAGAGCATTGAAGTCGACATCACCAAGAATATTCCCATCGATTCCAAGGTGTTCACCTTA
22370 CTTGAAATCG
Statistics
Matches: 252, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
267 252 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (267 bp):
TTTTCTAATTTAGTTTTCCTATTTCGAAAATCCTAAAAATCCCCTTTTGGTAAGACTTTCTTTTG
TACGAGTTGCCTTTGATTTGCTCCTACCTTCTCTGTGGATTCGACCCCTACTTGCCCTAGCTAAT
AGTTATAGGTTTGTGGGGATTATTTTGTGATTTGTTCAACGACCGATCAAGTCCATTGAAGACCA
ATTAGAGAGCATTGAAGTCGACATCACCAAGAATATTCCCATCGATTCCAAGGTGTTCACCTTAT
TTTGTGA
Found at i:24634 original size:13 final size:13
Alignment explanation
Indices: 24616--24650 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
24606 AATCTAAATC
*
24616 TAAAGCAGATTAA
1 TAAAGCAAATTAA
24629 TAAAGCAAATTAA
1 TAAAGCAAATTAA
24642 TAAAGCAAA
1 TAAAGCAAA
24651 CAATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:33342 original size:24 final size:25
Alignment explanation
Indices: 33290--33342 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
33280 CATGCAACAT
*
33290 TTTTATATATACATTTTTGTATTAT
1 TTTTATATATACATTTTTGTATTAG
*
33315 TTTTGTAT-TACATTTTTGT-TTAAG
1 TTTTATATATACATTTTTGTATT-AG
33339 TTTT
1 TTTT
33343 TTACCTTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 2 0.08
24 16 0.64
25 7 0.28
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.66
Consensus pattern (25 bp):
TTTTATATATACATTTTTGTATTAG
Found at i:33343 original size:12 final size:13
Alignment explanation
Indices: 33286--33333 Score: 64
Period size: 11 Copynumber: 3.8 Consensus size: 13
33276 GGCACATGCA
*
33286 ACATTTTTATATAT
1 ACATTTTTGTAT-T
33300 ACATTTTTGTATT
1 ACATTTTTGTATT
33313 --ATTTTTGTATT
1 ACATTTTTGTATT
33324 ACATTTTTGT
1 ACATTTTTGT
33334 TTAAGTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 11 0.35
13 9 0.29
14 11 0.35
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (13 bp):
ACATTTTTGTATT
Found at i:33553 original size:18 final size:18
Alignment explanation
Indices: 33530--33567 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
33520 GTATCAACAA
33530 TAAGACCCTAAAACATAT
1 TAAGACCCTAAAACATAT
33548 TAAGACCCTAAAACATAT
1 TAAGACCCTAAAACATAT
33566 TA
1 TA
33568 TTCTTTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (18 bp):
TAAGACCCTAAAACATAT
Found at i:38903 original size:20 final size:20
Alignment explanation
Indices: 38878--38916 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38868 AAAAAGAGCA
*
38878 CCAATTTGCAAATCAAATGT
1 CCAATTCGCAAATCAAATGT
*
38898 CCAATTCGTAAATCAAATG
1 CCAATTCGCAAATCAAATG
38917 CCTTGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (20 bp):
CCAATTCGCAAATCAAATGT
Found at i:39080 original size:14 final size:14
Alignment explanation
Indices: 39057--39090 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
39047 TAAATATGAT
*
39057 ACTAATCTAAATGG
1 ACTAAACTAAATGG
39071 ACTAAACTAAATGG
1 ACTAAACTAAATGG
39085 ACTAAA
1 ACTAAA
39091 GTTAATATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.24
Consensus pattern (14 bp):
ACTAAACTAAATGG
Found at i:39469 original size:27 final size:28
Alignment explanation
Indices: 39428--39500 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
39418 GAGTGTACTC
* *
39428 AAAATGACGATAATGCCCC-TAAATG-A
1 AAAATGACAAAAATGCCCCTTAAATGTA
*
39454 AAGAATGACAAAAATGCCCCTTGAATGTA
1 AA-AATGACAAAAATGCCCCTTAAATGTA
*
39483 AAAATGACCAAAATGCCC
1 AAAATGACAAAAATGCCC
39501 TTGGTGACCC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 2 0.05
27 15 0.38
28 20 0.50
29 3 0.08
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.18
Consensus pattern (28 bp):
AAAATGACAAAAATGCCCCTTAAATGTA
Found at i:42933 original size:28 final size:27
Alignment explanation
Indices: 42853--42949 Score: 126
Period size: 27 Copynumber: 3.6 Consensus size: 27
42843 GCCCAAGGGT
42853 ATTTTGGTCATTTTTT-A-TCCAGGGGC
1 ATTTTGGTCATTTTTTCACT-CAGGGGC
** *
42879 ATTTTGGTCATTTTCGCACCCAGGGGC
1 ATTTTGGTCATTTTTTCACTCAGGGGC
42906 ATTTTGGTCATTTTTTCACTCAGGGGGC
1 ATTTTGGTCATTTTTTCACTCA-GGGGC
*
42934 ATTTTAGTCATTTTTT
1 ATTTTGGTCATTTTTT
42950 TAAGATCACC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
26 14 0.23
27 27 0.44
28 20 0.33
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (27 bp):
ATTTTGGTCATTTTTTCACTCAGGGGC
Found at i:44743 original size:51 final size:50
Alignment explanation
Indices: 44654--44843 Score: 188
Period size: 51 Copynumber: 3.8 Consensus size: 50
44644 AGATTTATCA
* * * *
44654 TTTGAATGAAAGATTGAATTTTTAAGTAATTGGAAAATAAAAATGTCATC
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCACC
** * * * *
44704 TTTGGGTAAAAGATTGAATTTTTAGAGTAACTAGTAAATAAAGATTTAACC
1 TTTGAATAAAAGATTGAATTTTTA-AGTAATTAGTAAATAAAAATGTCACC
*
44755 TTTGAATAAAAGATTGAATTTTTAAGT--TTAGTAAAT-AAAATGTCACA
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCACC
* * * * **
44802 TTTGAATTAGAAGTTTGAACTTTTAGGCCATTAGTAAATAAA
1 TTTGAA-TAAAAGATTGAATTTTTAAGTAATTAGTAAATAAA
44844 TTGATGTTTG
Statistics
Matches: 113, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
47 13 0.12
48 24 0.21
50 33 0.29
51 43 0.38
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (50 bp):
TTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCACC
Found at i:45508 original size:55 final size:55
Alignment explanation
Indices: 45443--45767 Score: 369
Period size: 55 Copynumber: 6.2 Consensus size: 55
45433 AAAAGGGGGC
*
45443 AATCAGTAATTAAGT-AAAAGGAGATTAACCAGAGTTAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGG-GATTAACCAGAGTCAAAGTAATAGTAATCAGTA
* * * *
45498 AATCAATAATTGAGTAAAAAGAGATT------AGTCAAAGTTAATAGTGATCAGTA
1 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAAAG-TAATAGTAATCAGTA
* * *
45548 AGTCAGTAATTAAGTAAAAAGGGATTAATCAGAGTCAATGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAAAGTAATAGTAATCAGTA
*
45603 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTC-AAG-----GCAAT-AG-A
1 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAAAGTAATAGTAATCAGTA
* *
45650 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTGAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAAAGTAATAGTAATCAGTA
* * * *
45705 AATCAGTAATTAAGT-AAAAGAGATTAATCAGAGTCAAGGTAATA-AAAGTCAGTA
1 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAAAGTAATAGTAA-TCAGTA
45759 AATCAGTAA
1 AATCAGTAA
45768 AAGGATATTA
Statistics
Matches: 231, Mismatches: 22, Indels: 35
0.80 0.08 0.12
Matches are distributed among these distances:
47 36 0.16
48 4 0.02
49 11 0.05
50 36 0.16
53 6 0.03
54 45 0.19
55 81 0.35
56 12 0.05
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAAAGTAATAGTAATCAGTA
Found at i:45656 original size:47 final size:47
Alignment explanation
Indices: 45443--45815 Score: 223
Period size: 55 Copynumber: 7.4 Consensus size: 47
45433 AAAAGGGGGC
*
45443 AATCAGTAATTAAGT-AAAAGGAGATTAACCAGAGTTAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGG-GATTAACCAGAG-TCAAG-----GTAAT-AG-A
* * * ** * * * *
45498 AATCAATAATTGAGTAAAAAGAGATTAGTCAAAGTTAATAGTGATCAGTA
1 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAA-GGTAAT-AG-A
* *
45548 AGTCAGTAATTAAGTAAAAAGGGATTAATCAGAGTCAATGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAA-G-----GTAAT-AG-A
*
45603 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAAGGCAATAGA
1 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAAGGTAATAGA
*
45650 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTGAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAA-G-----GTAAT-AG-A
* *
45705 AATCAGTAATTAAGT-AAAAGAGATTAATCAGAGTCAAGGTAATA-A
1 AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAAGGTAATAGA
* * * * ** *
45750 AAGTCAGTAAATCAGT-AAAAGGATATTAATCAGAAACAAGGTAATAGC
1 AA-TCAGTAATTAAGTAAAAAGG-GATTAACCAGAGTCAAGGTAATAGA
* *
45798 AATCAGTAAATCAGTAAA
1 AATCAGTAATTAAGTAAA
45816 TAAGCAAAAA
Statistics
Matches: 266, Mismatches: 33, Indels: 45
0.77 0.10 0.13
Matches are distributed among these distances:
45 3 0.01
46 16 0.06
47 72 0.27
48 12 0.05
49 4 0.02
50 41 0.15
53 5 0.02
54 25 0.09
55 83 0.31
56 5 0.02
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (47 bp):
AATCAGTAATTAAGTAAAAAGGGATTAACCAGAGTCAAGGTAATAGA
Found at i:46064 original size:24 final size:24
Alignment explanation
Indices: 46036--46082 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
46026 GAGATTGGTA
46036 ATTAAAGTAGTAATTAAGATTCAT
1 ATTAAAGTAGTAATTAAGATTCAT
* *
46060 ATTAAAGTGGTAATTGAGATTCA
1 ATTAAAGTAGTAATTAAGATTCA
46083 AGGTAAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (24 bp):
ATTAAAGTAGTAATTAAGATTCAT
Found at i:46296 original size:16 final size:16
Alignment explanation
Indices: 46275--46329 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
46265 GGGTAAAAAA
46275 GAGTAAAAATGGTATT
1 GAGTAAAAATGGTATT
46291 GAGTAAAAA-GG-A--
1 GAGTAAAAATGGTATT
46303 GAGTAAAAAATGGTAATT
1 GAGT-AAAAATGGT-ATT
*
46321 AAGTAAAAA
1 GAGTAAAAA
46330 GACTAAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
12 4 0.12
13 5 0.16
14 3 0.09
15 2 0.06
16 10 0.31
17 5 0.16
18 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.22
Consensus pattern (16 bp):
GAGTAAAAATGGTATT
Found at i:46299 original size:26 final size:26
Alignment explanation
Indices: 46267--46433 Score: 110
Period size: 26 Copynumber: 6.2 Consensus size: 26
46257 GAAGTAAAGG
*
46267 GTAAAAAAGAGTAAAAATGGTATTGA
1 GTAAAAAAGAGTAAAAATGGTATTCA
*
46293 GTAAAAAGGAGAGTAAAAAATGGTAATTAA
1 GTAAAAA--AGAGT-AAAAATGGT-ATTCA
*
46323 GT-AAAAAGACTAAAAAGTGGTATTCA
1 GTAAAAAAGAGTAAAAA-TGGTATTCA
* * ** *
46349 GCCAAAATAGAAAG-AAAAGGGGTAATCA
1 G-TAAAA-A-AGAGTAAAAATGGTATTCA
*
46377 GT-AAAAAGAGTAAAATATGGTAATCA
1 GTAAAAAAGAGTAAAA-ATGGTATTCA
*
46403 GT-ATAAAGAGTAAAAATTGGTAATT-A
1 GTAAAAAAGAGTAAAAA-TGGT-ATTCA
46429 GTAAA
1 GTAAA
46434 TCAAAAATAA
Statistics
Matches: 111, Mismatches: 16, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
24 3 0.03
25 6 0.05
26 49 0.44
27 11 0.10
28 16 0.14
29 18 0.16
30 8 0.07
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.22
Consensus pattern (26 bp):
GTAAAAAAGAGTAAAAATGGTATTCA
Found at i:46328 original size:30 final size:27
Alignment explanation
Indices: 46267--46331 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 27
46257 GAAGTAAAGG
*
46267 GTAAAAA-AGAGTAAAAATGGTATTGA
1 GTAAAAAGAGAGTAAAAATGGTATTAA
46293 GTAAAAAGGAGAGTAAAAAATGGTAATTAA
1 GTAAAAA-GAGAGT-AAAAATGGT-ATTAA
46323 GTAAAAAGA
1 GTAAAAAGA
46332 CTAAAAAGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.21
28 5 0.15
29 11 0.32
30 11 0.32
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (27 bp):
GTAAAAAGAGAGTAAAAATGGTATTAA
Done.