Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019996.1 Corchorus olitorius cultivar O-4 contig20029, 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: 73632
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:10536 original size:17 final size:17
Alignment explanation
Indices: 10514--10568 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
10504 GATTACCCCC
*
10514 AGATCACTAGTGATCTA
1 AGATCACCAGTGATCTA
*
10531 AGATCACCAGTGATGTA
1 AGATCACCAGTGATCTA
* * *
10548 AAATCACCGGTGATCAA
1 AGATCACCAGTGATCTA
10565 AGAT
1 AGAT
10569 TACATGGGTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (17 bp):
AGATCACCAGTGATCTA
Found at i:13734 original size:2 final size:2
Alignment explanation
Indices: 13729--13758 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13719 GAGATGGCAG
13729 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13759 GATACAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15909 original size:17 final size:17
Alignment explanation
Indices: 15887--15921 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
15877 TTTTCATTTT
*
15887 TAATCTTGATTGCAACG
1 TAATCTTGATCGCAACG
15904 TAATCTTGATCGCAACG
1 TAATCTTGATCGCAACG
15921 T
1 T
15922 TGCGGTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (17 bp):
TAATCTTGATCGCAACG
Found at i:19532 original size:20 final size:21
Alignment explanation
Indices: 19507--19545 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
19497 GCCCAATTTT
*
19507 AAAGAAAAG-TAAAAGAAATA
1 AAAGAAAAGAGAAAAGAAATA
19527 AAAGAAAAGAGAAAAGAAA
1 AAAGAAAAGAGAAAAGAAA
19546 AGTAAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (21 bp):
AAAGAAAAGAGAAAAGAAATA
Found at i:20539 original size:27 final size:27
Alignment explanation
Indices: 20480--20539 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
20470 CTAGTATGTA
* **
20480 TAAATTACCGTTTTACCCCTAGTGGGC
1 TAAATTACAGTTTTACCCCTAGAAGGC
20507 TAAATTACAGTTTTACCCCTA-AAGGC
1 TAAATTACAGTTTTACCCCTAGAAGGC
20533 TAGAATT
1 TA-AATT
20540 GATAAATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (27 bp):
TAAATTACAGTTTTACCCCTAGAAGGC
Found at i:22385 original size:19 final size:19
Alignment explanation
Indices: 22363--22413 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
22353 GGGCTGAAAT
22363 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
22382 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
22401 TAATT-ATTATTAA
1 TAATTAATTATTAA
22414 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:29496 original size:12 final size:12
Alignment explanation
Indices: 29479--29503 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29469 ATTATGCGCA
29479 TCTTTTTGTTAG
1 TCTTTTTGTTAG
29491 TCTTTTTGTTAG
1 TCTTTTTGTTAG
29503 T
1 T
29504 TCATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (12 bp):
TCTTTTTGTTAG
Found at i:55226 original size:1 final size:1
Alignment explanation
Indices: 55220--55288 Score: 84
Period size: 1 Copynumber: 69.0 Consensus size: 1
55210 TTCCTGAAGG
* * * * * *
55220 AAAAAAAAAAAAAAACAAAAAAACAAAAAAAAAACAAAAAACAAAAAACAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
55285 AAAA
1 AAAA
55289 TAGTAGAAAG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:55266 original size:33 final size:32
Alignment explanation
Indices: 55222--55283 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
55212 CCTGAAGGAA
55222 AAAAAAAAAAAAACAAAAAAACAAAAAAAAAAC
1 AAAAAAAAAAAAACAAAAAAA-AAAAAAAAAAC
*
55255 AAAAAACAAAAAACAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAACAAAAAAAAAAAAAAA
55284 CAAAATAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (32 bp):
AAAAAAAAAAAAACAAAAAAAAAAAAAAAAAC
Found at i:57989 original size:8 final size:8
Alignment explanation
Indices: 57976--58000 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
57966 TTTACGCCTT
57976 TTTTTATA
1 TTTTTATA
57984 TTTTTATA
1 TTTTTATA
57992 TTTTTATA
1 TTTTTATA
58000 T
1 T
58001 CTACAGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTATA
Found at i:63377 original size:22 final size:23
Alignment explanation
Indices: 63351--63404 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
63341 ATAAATGTTG
* * *
63351 TTGATAATCTTTTCTTTTATCTC
1 TTGATAATCTCTCCTTTTATCAC
63374 -TGATAATTCTCTCCTTTTATCAC
1 TTGATAA-TCTCTCCTTTTATCAC
63397 TTGATAAT
1 TTGATAAT
63405 ATCTAGCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 6 0.23
23 14 0.54
24 6 0.23
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.54
Consensus pattern (23 bp):
TTGATAATCTCTCCTTTTATCAC
Found at i:70079 original size:30 final size:30
Alignment explanation
Indices: 69947--70180 Score: 253
Period size: 30 Copynumber: 7.8 Consensus size: 30
69937 TTTGAAAGGT
69947 AAAATCATGACAACTTCTGGTGTCAATTG-
1 AAAATCATGACAACTTCTGGTGTCAATTGC
* * ** * *
69976 --AATTATGACATCTTCAAGTGTCTATTGG
1 AAAATCATGACAACTTCTGGTGTCAATTGC
*
70004 AAATTTATCATGACAACTTCT-G-GTCAATTGT
1 AAA---ATCATGACAACTTCTGGTGTCAATTGC
* * *
70035 AAGACCATTGACAACTTCTGGTGTCAATTGT
1 AAAATCA-TGACAACTTCTGGTGTCAATTGC
70066 AAAATCATGACAACTTCTGGTGTCAATTGC
1 AAAATCATGACAACTTCTGGTGTCAATTGC
* *
70096 AAGAGCATGACAACTTCTGGTGTCAATTGC
1 AAAATCATGACAACTTCTGGTGTCAATTGC
* *
70126 AAGAGCATGACAACTTCTGGTGTCAATTGC
1 AAAATCATGACAACTTCTGGTGTCAATTGC
* *
70156 AAGAGCATGACAACTTCTGGTGTCA
1 AAAATCATGACAACTTCTGGTGTCA
70181 TTTGGAGATT
Statistics
Matches: 179, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
27 22 0.12
28 3 0.02
29 11 0.06
30 107 0.60
31 23 0.13
32 1 0.01
33 12 0.07
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (30 bp):
AAAATCATGACAACTTCTGGTGTCAATTGC
Found at i:70091 original size:119 final size:119
Alignment explanation
Indices: 69945--70180 Score: 300
Period size: 119 Copynumber: 2.0 Consensus size: 119
69935 AATTTGAAAG
** * *
69945 GTAAAATCATGACAACTTCTGGTGTCAATTG-A-ATTATGACATCTTCAAGTGTCTATTGGAAAT
1 GTAAAATCATGACAACTTCTGGTGTCAATTGAAGAGCATGACAACTTCAAGTGTCAATT-GAAA-
* * *
70008 TTATCATGACAACTTCT-G-GTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATT
64 -GAGCATGACAACTTCTGGTGTCAATTGCAAGACCA-TGACAACTTCTGGTGTCAATT
** *
70064 GTAAAATCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTGCAAG
1 GTAAAATCATGACAACTTCTGGTGTCAATTG-AAGAGCATGACAACTTCAAGTGTCAATTGAAAG
*
70129 AGCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCA
65 AGCATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCA
70181 TTTGGAGATT
Statistics
Matches: 101, Mismatches: 11, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
119 45 0.45
120 19 0.19
121 18 0.18
122 19 0.19
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (119 bp):
GTAAAATCATGACAACTTCTGGTGTCAATTGAAGAGCATGACAACTTCAAGTGTCAATTGAAAGA
GCATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATT
Found at i:70120 original size:60 final size:60
Alignment explanation
Indices: 69945--70180 Score: 293
Period size: 60 Copynumber: 4.0 Consensus size: 60
69935 AATTTGAAAG
** * ** *
69945 GTAAAATCATGACAACTTCTGGTGTCAATTG--A-ATTATGACATCTTCAAGTGTCTATT
1 GTAAAATCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATT
* * *
70002 GGAAATTTATCATGACAACTTCT-G-GTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATT
1 GTAAA---ATCATGACAACTTCTGGTGTCAATTGCAAGAGCA-TGACAACTTCTGGTGTCAATT
70064 GTAAAATCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATT
1 GTAAAATCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATT
* * *
70124 GCAAGAGCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCA
1 GTAAAATCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCA
70181 TTTGGAGATT
Statistics
Matches: 157, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
57 4 0.03
58 8 0.05
59 16 0.10
60 92 0.59
61 16 0.10
62 21 0.13
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (60 bp):
GTAAAATCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATT
Found at i:72056 original size:85 final size:84
Alignment explanation
Indices: 71913--72086 Score: 303
Period size: 85 Copynumber: 2.1 Consensus size: 84
71903 AGTTTCATAC
*
71913 TGATTTAATGTCACCATTTAGATCACCTTCGTGATTAGATCACCATAGTAATAGTTTTTTTTTTA
1 TGATTTAATATCACCATTTAGATCACCTTCGTGATTAGATCACCATAGTAATAG-TTTTTTTTTA
*
71978 TTTATACCAAATTAATATGG
65 TTTATACCAAATTAACATGG
*
71998 TGATTTAATATCACCATTTAGATCACCTTCGTGATTAGATCACCATAGTAATAGTTTTTTTTTGT
1 TGATTTAATATCACCATTTAGATCACCTTCGTGATTAGATCACCATAGTAATAGTTTTTTTTTAT
*
72063 TTATATCAAATTAACATGG
66 TTATACCAAATTAACATGG
72082 TGATT
1 TGATT
72087 AAATCAGTAA
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
84 32 0.38
85 53 0.62
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (84 bp):
TGATTTAATATCACCATTTAGATCACCTTCGTGATTAGATCACCATAGTAATAGTTTTTTTTTAT
TTATACCAAATTAACATGG
Done.