Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019010.1 Corchorus olitorius cultivar O-4 contig19043, 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: 76783
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1249 original size:15 final size:15
Alignment explanation
Indices: 1204--1253 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
1194 TGCACCGTTT
* *
1204 CCATTATTGTTCACA
1 CCATTGTTGTTCGCA
1219 CCATTGTTGTTCGCA
1 CCATTGTTGTTCGCA
*
1234 CCATTGTTGTTTGCA
1 CCATTGTTGTTCGCA
1249 CCATT
1 CCATT
1254 CACCCTAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (15 bp):
CCATTGTTGTTCGCA
Found at i:2178 original size:49 final size:47
Alignment explanation
Indices: 2077--2218 Score: 151
Period size: 49 Copynumber: 3.0 Consensus size: 47
2067 GAGCGTGCCA
* * * *
2077 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
*
2124 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAT
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * * *
2173 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGTAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
2219 GGATTGCTTG
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
47 12 0.15
48 27 0.34
49 41 0.51
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:3514 original size:9 final size:9
Alignment explanation
Indices: 3496--3524 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3486 TTAATTCATT
3496 TAATTT-CA
1 TAATTTCCA
3504 TAATTTCCA
1 TAATTTCCA
3513 TAATTTCCA
1 TAATTTCCA
3522 TAA
1 TAA
3525 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:4920 original size:20 final size:19
Alignment explanation
Indices: 4895--4936 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4885 AGTAGTCATA
4895 TAAGTAACTTTCAAAGTAAT
1 TAAGTAAC-TTCAAAGTAAT
* *
4915 TAAGTAGCTTCAAGGTAAT
1 TAAGTAACTTCAAAGTAAT
4934 TAA
1 TAA
4937 TTTTCTCCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (19 bp):
TAAGTAACTTCAAAGTAAT
Found at i:12424 original size:13 final size:14
Alignment explanation
Indices: 12403--12435 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
12393 ACTCAACACT
*
12403 AACTAACTCAA-AA
1 AACTGACTCAATAA
12416 AACTGACTCAATAA
1 AACTGACTCAATAA
12430 AACTGA
1 AACTGA
12436 TTAAAACCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (14 bp):
AACTGACTCAATAA
Found at i:13759 original size:2 final size:2
Alignment explanation
Indices: 13748--13782 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
13738 GTCTTGCCTG
13748 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13783 CACTACATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14153 original size:42 final size:42
Alignment explanation
Indices: 14094--14174 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
14084 TAAGGATCAA
* *
14094 GATTTGAGTTGAGTATTTCTTAGTTTACAAATAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
14136 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
14175 AAGACTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:15196 original size:29 final size:29
Alignment explanation
Indices: 15135--15206 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
15125 TGTATATATA
* *
15135 AATTATATATATATATATATTAATTGAGT
1 AATTATATATATATATATATAAATTGAGC
* *
15164 AATTATATTTATATATA-ATAAATTTGTGC
1 AATTATATATATATATATATAAA-TTGAGC
*
15193 AATT-TATATGTATA
1 AATTATATATATATA
15207 CCTTAATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 12 0.33
29 24 0.67
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (29 bp):
AATTATATATATATATATATAAATTGAGC
Found at i:15725 original size:83 final size:83
Alignment explanation
Indices: 15638--15798 Score: 304
Period size: 83 Copynumber: 1.9 Consensus size: 83
15628 CAAAAAAAAA
* *
15638 TATACTATATATAAAAGTACGAGTTTTGTAAAACTTTTTAATCGTTTATACCCTTATTTTTTGAA
1 TATACTATATATAAAAGTACGAGTTTTGTAAAACTTTTGAATCGTTTATACCCTTATTTTTCGAA
15703 CATATTTCTTTTTTTGTC
66 CATATTTCTTTTTTTGTC
15721 TATACTATATATAAAAGTACGAGTTTTGTAAAACTTTTGAATCGTTTATACCCTTATTTTTCGAA
1 TATACTATATATAAAAGTACGAGTTTTGTAAAACTTTTGAATCGTTTATACCCTTATTTTTCGAA
15786 CATATTTCTTTTT
66 CATATTTCTTTTT
15799 CTTTTTTTGA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (83 bp):
TATACTATATATAAAAGTACGAGTTTTGTAAAACTTTTGAATCGTTTATACCCTTATTTTTCGAA
CATATTTCTTTTTTTGTC
Found at i:16649 original size:32 final size:33
Alignment explanation
Indices: 16608--16675 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
16598 TTACAGTTTT
*
16608 ATTCTAGTAAAAACTATATTTTTATTTAATTAA
1 ATTCTAGTAAAAACTATATTTGTATTTAATTAA
* *
16641 ATTC-AGTAAAAACTCTATTTGTATTTGATTAA
1 ATTCTAGTAAAAACTATATTTGTATTTAATTAA
16673 ATT
1 ATT
16676 TATAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (33 bp):
ATTCTAGTAAAAACTATATTTGTATTTAATTAA
Found at i:19771 original size:17 final size:18
Alignment explanation
Indices: 19749--19790 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
19739 AATTTCTATT
19749 AAAATATATATTTTA-AA
1 AAAATATATATTTTATAA
* *
19766 AAAATATTTTTTTTATAA
1 AAAATATATATTTTATAA
19784 AAAATAT
1 AAAATAT
19791 GACGTGGCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATATATATTTTATAA
Found at i:23260 original size:23 final size:22
Alignment explanation
Indices: 23091--23260 Score: 83
Period size: 22 Copynumber: 7.6 Consensus size: 22
23081 ATTAAATATT
*
23091 TTTATGAAATTTTGATAACCAC
1 TTTATGAAATTTTGATAACCTC
* * * *
23113 ATTATGAAATTTTGATGA-TTAT
1 TTTATGAAATTTTGATAACCT-C
* **
23135 TTTATGAAATTGTGATAAATTC
1 TTTATGAAATTTTGATAACCTC
*** ** * *
23157 CCAATGAAATACTGATAACTTA
1 TTTATGAAATTTTGATAACCTC
* * *
23179 ATTATGAAATTTTAATAAACAT-
1 TTTATGAAATTTTGAT-AACCTC
23201 TTCTATGAAATTTTGATAACCTC
1 TT-TATGAAATTTTGATAACCTC
** **
23224 CATATGATTTTTTTGATAACCCTC
1 TTTATGA-AATTTTGATAA-CCTC
23248 TTTATGAAATTTT
1 TTTATGAAATTTT
23261 ATTAATCTCC
Statistics
Matches: 107, Mismatches: 34, Indels: 13
0.69 0.22 0.08
Matches are distributed among these distances:
22 66 0.62
23 32 0.30
24 9 0.08
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (22 bp):
TTTATGAAATTTTGATAACCTC
Found at i:23260 original size:24 final size:23
Alignment explanation
Indices: 23204--23286 Score: 66
Period size: 22 Copynumber: 3.7 Consensus size: 23
23194 TAAACATTTC
23204 TATGAAA-TTTTGATAACCTCCA
1 TATGAAATTTTTGATAACCTCCA
** **
23226 TATGATTTTTTTGATAACCCTCTT
1 TATGAAATTTTTGATAA-CCTCCA
* *
23250 TATGAAA-TTTT-ATTAATCTCCC
1 TATGAAATTTTTGA-TAACCTCCA
23272 TAT-AAATTTTTGATA
1 TATGAAATTTTTGATA
23287 CCATAGTATG
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
21 3 0.06
22 18 0.38
23 17 0.36
24 9 0.19
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.47
Consensus pattern (23 bp):
TATGAAATTTTTGATAACCTCCA
Found at i:33757 original size:82 final size:82
Alignment explanation
Indices: 33613--33773 Score: 243
Period size: 82 Copynumber: 2.0 Consensus size: 82
33603 GGTTTTCACT
* * *
33613 AACGTTTCAAAAAATGTCTCTATTACTTGTCTCAACAACTATCTCTACCTAGAAATATAATCTGA
1 AACGTTTCAAAAAATGTCTCTATTACTCGTCTCAACAACTATCTCTACCTAGAAACAGAATCTGA
33678 GACGTACTATTGGCGGG
66 GACGTACTATTGGCGGG
* * *
33695 AACGTTTCAGAAAATGTCTCTATTAACTCGTCTCAGCAACTGTCTCTA-CTAGAAACAGAATCTG
1 AACGTTTCAAAAAATGTCTCTATT-ACTCGTCTCAACAACTATCTCTACCTAGAAACAGAATCTG
*
33759 AGACGTATTATTGGC
65 AGACGTACTATTGGC
33774 AGGATAAGCA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
82 51 0.72
83 20 0.28
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (82 bp):
AACGTTTCAAAAAATGTCTCTATTACTCGTCTCAACAACTATCTCTACCTAGAAACAGAATCTGA
GACGTACTATTGGCGGG
Found at i:39390 original size:19 final size:20
Alignment explanation
Indices: 39366--39413 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 20
39356 TTAGGTGTGG
39366 AAACAAGTATACACATGCA-
1 AAACAAGTATACACATGCAT
*
39385 AAACAA--ATA-ACATGTAT
1 AAACAAGTATACACATGCAT
39402 AAACAAGTATAC
1 AAACAAGTATAC
39414 CCACATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
19 9 0.38
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.19
Consensus pattern (20 bp):
AAACAAGTATACACATGCAT
Found at i:40297 original size:3 final size:3
Alignment explanation
Indices: 40278--40339 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
40268 ATTTTTGAGG
* * *
40278 TAT TA- TAT TAT TCT TAT TAT TAT TAT TAT CAT TA- TAT AAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
*
40325 TAT TAG TAT TAT TAT
1 TAT TAT TAT TAT TAT
40340 AATAATATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:40560 original size:2 final size:2
Alignment explanation
Indices: 40553--40593 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
40543 GATTACCCTA
40553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40594 CACCGTTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41092 original size:3 final size:3
Alignment explanation
Indices: 41084--41133 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
41074 TGGAAATGGT
41084 TTA TTA TTA TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41130 TTA T
1 TTA T
41134 ATAGGCTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:44710 original size:24 final size:24
Alignment explanation
Indices: 44678--44734 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
44668 CGCACATAAC
*
44678 TAGCAAACATATTATAATCAAATT
1 TAGCAAACATATTACAATCAAATT
44702 TAGCAAACATATTACAATCAAATT
1 TAGCAAACATATTACAATCAAATT
44726 TAGCTAAAC
1 TAGC-AAAC
44735 TATGAGCACA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (24 bp):
TAGCAAACATATTACAATCAAATT
Found at i:46058 original size:20 final size:19
Alignment explanation
Indices: 46021--46059 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
46011 AAATGTGAAA
* *
46021 TTTTTTAAAATTTTTATTT
1 TTTTTTAAAAATTGTATTT
46040 TTTTTTAAAAAATTGTATTT
1 TTTTTT-AAAAATTGTATTT
46060 ATTGAGGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTTTAAAAATTGTATTT
Found at i:52238 original size:1 final size:1
Alignment explanation
Indices: 52232--52266 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
52222 TCCTTTAAGC
52232 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
52267 GTCTGATAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:62045 original size:29 final size:29
Alignment explanation
Indices: 62010--62093 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 29
62000 ACAGAAATTA
*
62010 AAAGGTTTAGGACCAAATTGAGC-CGGTC
1 AAAGGTTTAGGACCAAATTGAGCACCGTC
* * *
62038 AGAAGGTTTAAGACCAAATCGAGCAGACCGTG
1 A-AAGGTTTAGGACCAAATTGAGC--ACCGTC
*
62070 AAAGGTTTAGAACCAAATTGAGCA
1 AAAGGTTTAGGACCAAATTGAGCA
62094 TTTAGCCCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.02
29 21 0.47
31 19 0.42
32 4 0.09
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (29 bp):
AAAGGTTTAGGACCAAATTGAGCACCGTC
Found at i:65618 original size:2 final size:2
Alignment explanation
Indices: 65611--65645 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
65601 TCACTTTTTG
65611 TA TA TA 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 TA TA TA T
65646 TTAATTATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68234 original size:22 final size:22
Alignment explanation
Indices: 68206--68282 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
68196 TATTTTTATG
*
68206 AAATTTTGATAATCACCCTATT
1 AAATTTTGATAATCACCCTATA
* * *
68228 AAATTTTGATAACCACCATATG
1 AAATTTTGATAATCACCCTATA
*
68250 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAATCACCCTATA
*
68271 AAATTGTGATAA
1 AAATTTTGATAA
68283 ACTCTATAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 15 0.32
22 32 0.68
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAATCACCCTATA
Found at i:71542 original size:33 final size:33
Alignment explanation
Indices: 71500--71565 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
71490 TAGTCACACC
*
71500 CTATAAGATTATGAATAGTATTTTGACCCATGT
1 CTATAAGATTATAAATAGTATTTTGACCCATGT
*
71533 CTATAAGATTATAAATCGTATTTTGACCCATGT
1 CTATAAGATTATAAATAGTATTTTGACCCATGT
71566 GCCATGTCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (33 bp):
CTATAAGATTATAAATAGTATTTTGACCCATGT
Found at i:72166 original size:47 final size:47
Alignment explanation
Indices: 72097--72220 Score: 212
Period size: 47 Copynumber: 2.6 Consensus size: 47
72087 CACAAAATCA
72097 TTAAAACTTCCAAAACGAGTTCAAGCATTGTTAATAGTAACAATAAT
1 TTAAAACTTCCAAAACGAGTTCAAGCATTGTTAATAGTAACAATAAT
* * *
72144 TTAAAACTTCTAAAACGAGTTCAAGCATTGTTAATAGTAATAGTAAT
1 TTAAAACTTCCAAAACGAGTTCAAGCATTGTTAATAGTAACAATAAT
*
72191 TTAAAACTTCCAAAACGAGTTCGAGCATTG
1 TTAAAACTTCCAAAACGAGTTCAAGCATTG
72221 ACAACTTACA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (47 bp):
TTAAAACTTCCAAAACGAGTTCAAGCATTGTTAATAGTAACAATAAT
Done.