Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019232.1 Corchorus olitorius cultivar O-4 contig19265, 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: 74630
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:902 original size:9 final size:9
Alignment explanation
Indices: 890--923 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
880 TAAAAATGAA
890 AAAAGAAAG
1 AAAAGAAAG
*
899 AAAAAAAAG
1 AAAAGAAAG
908 AAAA-AAAG
1 AAAAGAAAG
916 AAAAGAAA
1 AAAAGAAA
924 ATGTACCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:906 original size:13 final size:12
Alignment explanation
Indices: 888--924 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
878 TATAAAAATG
888 AAAAAAGAAAGAA
1 AAAAAAGAAA-AA
901 AAAAAAGAAAAA
1 AAAAAAGAAAAA
913 AAGAAAAGAAAA
1 AA-AAAAGAAAA
925 TGTACCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:11403 original size:21 final size:19
Alignment explanation
Indices: 11379--11436 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
11369 GCTGTTCTAT
11379 TAATCTCATCTGTACAGTACA
1 TAATCTCATCTGTACAGT--A
*
11400 TAATCTAATCTGTACAGTA
1 TAATCTCATCTGTACAGTA
* *
11419 TAATTTCATTTGTACAGT
1 TAATCTCATCTGTACAGT
11437 GACCAAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTA
Found at i:12840 original size:51 final size:51
Alignment explanation
Indices: 12759--12862 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
12749 GTTTGGATTT
*
12759 GTCGATTCAATCTGGATCGTGTCTGGGTTTGGTGGGTGAGTCTACCAATGA
1 GTCGATTCAATCTGGATCGTGTCTGGGTTTGATGGGTGAGTCTACCAATGA
*
12810 GTCGATTCAATCTGGATCGTGTCTGTGTTTGATGGGTGAGTCTACCAATGA
1 GTCGATTCAATCTGGATCGTGTCTGGGTTTGATGGGTGAGTCTACCAATGA
12861 GT
1 GT
12863 GGCGACTGCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.18, C:0.15, G:0.32, T:0.35
Consensus pattern (51 bp):
GTCGATTCAATCTGGATCGTGTCTGGGTTTGATGGGTGAGTCTACCAATGA
Found at i:17986 original size:36 final size:36
Alignment explanation
Indices: 17939--18041 Score: 144
Period size: 36 Copynumber: 3.0 Consensus size: 36
17929 AAAAGAAAAC
17939 ACACATATATACCAATCAATCATCATCAAATTTCTT
1 ACACATATATACCAATCAATCATCATCAAATTTCTT
17975 ACACATATATACCAATCAATCATCATCAAATTTC-T
1 ACACATATATACCAATCAATCATCATCAAATTTCTT
**
18010 -CACA-ACT-T-GGAATCAATCATCATCAAATTTCT
1 ACACATA-TATACCAATCAATCATCATCAAATTTCT
18042 CACAACTTGG
Statistics
Matches: 63, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
32 21 0.33
33 2 0.03
34 5 0.08
35 1 0.02
36 34 0.54
ACGTcount: A:0.41, C:0.25, G:0.02, T:0.32
Consensus pattern (36 bp):
ACACATATATACCAATCAATCATCATCAAATTTCTT
Found at i:18029 original size:32 final size:32
Alignment explanation
Indices: 17952--18053 Score: 134
Period size: 32 Copynumber: 3.1 Consensus size: 32
17942 CATATATACC
**
17952 AATCAATCATCATCAAATTTCTTACACATA-TATACC
1 AATCAATCATCATCAAATTTC-T-CACA-ACT-T-GG
17988 AATCAATCATCATCAAATTTCTCACAACTTGG
1 AATCAATCATCATCAAATTTCTCACAACTTGG
18020 AATCAATCATCATCAAATTTCTCACAACTTGG
1 AATCAATCATCATCAAATTTCTCACAACTTGG
18052 AA
1 AA
18054 ATACAAAATG
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
32 34 0.54
33 2 0.03
34 5 0.08
35 1 0.02
36 21 0.33
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.31
Consensus pattern (32 bp):
AATCAATCATCATCAAATTTCTCACAACTTGG
Found at i:18580 original size:7 final size:7
Alignment explanation
Indices: 18568--18595 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
18558 TGGAGACTGC
18568 CGAGAGG
1 CGAGAGG
18575 CGAGAGG
1 CGAGAGG
18582 CGAGAGG
1 CGAGAGG
18589 CGAGAGG
1 CGAGAGG
18596 GAAAGAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.57, T:0.00
Consensus pattern (7 bp):
CGAGAGG
Found at i:19718 original size:16 final size:16
Alignment explanation
Indices: 19675--19725 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 16
19665 TTGATGAGAT
* * *
19675 ATCTCTGTAGAGACAT
1 ATCTCTTTAGAAACAC
19691 ATCTCTTT--AAACAC
1 ATCTCTTTAGAAACAC
19705 ATCTCTTTAGAAACAAC
1 ATCTCTTTAGAAAC-AC
19722 ATCT
1 ATCT
19726 ATTCACTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 12 0.41
16 11 0.38
17 6 0.21
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (16 bp):
ATCTCTTTAGAAACAC
Found at i:22461 original size:16 final size:16
Alignment explanation
Indices: 22418--22468 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 16
22408 TTGATGAGAT
* * *
22418 ATCTCTGTAGAGACAT
1 ATCTCTTTAGAAACAC
22434 ATCTCTTT--AAACAC
1 ATCTCTTTAGAAACAC
22448 ATCTCTTTAGAAACAAC
1 ATCTCTTTAGAAAC-AC
22465 ATCT
1 ATCT
22469 ATCCACTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 12 0.41
16 11 0.38
17 6 0.21
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (16 bp):
ATCTCTTTAGAAACAC
Found at i:22538 original size:23 final size:23
Alignment explanation
Indices: 22512--22559 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
22502 TTGAACAAAC
*
22512 CTCTCAAATAAACCAAACGGTTT
1 CTCTCAAATAAACCAAACGATTT
22535 CTCTCAAATAAACCAAACGATTT
1 CTCTCAAATAAACCAAACGATTT
22558 CT
1 CT
22560 ATTAGTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.27, G:0.06, T:0.27
Consensus pattern (23 bp):
CTCTCAAATAAACCAAACGATTT
Found at i:31382 original size:23 final size:23
Alignment explanation
Indices: 31352--31395 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
31342 CGAACTTCAT
*
31352 AGGATTAGGGGTTAAAAATCTAA
1 AGGATTAGGGGGTAAAAATCTAA
*
31375 AGGATTAGGGGGTAAATATCT
1 AGGATTAGGGGGTAAAAATCT
31396 TTTATTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.30, T:0.27
Consensus pattern (23 bp):
AGGATTAGGGGGTAAAAATCTAA
Found at i:47710 original size:47 final size:47
Alignment explanation
Indices: 47658--47799 Score: 275
Period size: 47 Copynumber: 3.0 Consensus size: 47
47648 ACTGCCCCTC
*
47658 TACTGCTTCTTTTTGGTCATTTTTTTACTCTCTCGGTTTTGCCTCTG
1 TACTGCTTCTTTTTGGTCATTTCTTTACTCTCTCGGTTTTGCCTCTG
47705 TACTGCTTCTTTTTGGTCATTTCTTTACTCTCTCGGTTTTGCCTCTG
1 TACTGCTTCTTTTTGGTCATTTCTTTACTCTCTCGGTTTTGCCTCTG
47752 TACTGCTTCTTTTTGGTCATTTCTTTACTCTCTCGGTTTTGCCTCTG
1 TACTGCTTCTTTTTGGTCATTTCTTTACTCTCTCGGTTTTGCCTCTG
47799 T
1 T
47800 TATCATTATG
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 94 1.00
ACGTcount: A:0.06, C:0.25, G:0.15, T:0.54
Consensus pattern (47 bp):
TACTGCTTCTTTTTGGTCATTTCTTTACTCTCTCGGTTTTGCCTCTG
Found at i:52307 original size:40 final size:40
Alignment explanation
Indices: 52226--52307 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
52216 TGTAAGGATA
* ** *
52226 CACATAAAAGAAATCTATAATTATCAAGATTGTGCGCATG
1 CACATAAAAGAAATCTATAATTATCAAGAGTGCACGAATG
52266 CACATAAAAGAAATCTATAATTATCAAGAGTGCACGAATG
1 CACATAAAAGAAATCTATAATTATCAAGAGTGCACGAATG
52306 CA
1 CA
52308 TGCGCACACT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (40 bp):
CACATAAAAGAAATCTATAATTATCAAGAGTGCACGAATG
Found at i:55896 original size:15 final size:16
Alignment explanation
Indices: 55876--55905 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55866 AGTTTCTTCA
55876 TCAATTTCTT-TTCTC
1 TCAATTTCTTCTTCTC
55891 TCAATTTCTTCTTCT
1 TCAATTTCTTCTTCT
55906 TATCTTGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (16 bp):
TCAATTTCTTCTTCTC
Found at i:56845 original size:42 final size:42
Alignment explanation
Indices: 56786--56870 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
56776 GTTAATTTAT
56786 GGGCCTTTAGATTAAAGGCCCAAACCGTTAAAAAATTGGACC
1 GGGCCTTTAGATTAAAGGCCCAAACCGTTAAAAAATTGGACC
* *
56828 GGGCCTTTAGATTAAAGGCCCAAACTGTTAAAAAGTTGGACC
1 GGGCCTTTAGATTAAAGGCCCAAACCGTTAAAAAATTGGACC
56870 G
1 G
56871 AGTCGTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (42 bp):
GGGCCTTTAGATTAAAGGCCCAAACCGTTAAAAAATTGGACC
Found at i:67249 original size:281 final size:276
Alignment explanation
Indices: 66744--67264 Score: 696
Period size: 281 Copynumber: 1.9 Consensus size: 276
66734 TCAATACATG
*
66744 CAATGCAACCCCAAAACTTTGTTTGGACTTTGAAGTACAAGAATCAGAACCACCAAACATAATAC
1 CAATGCAACCCCAAAACCTTGTTTGGACTTTGAAGTACAAGAATCAGAACCACCAAACATAATAC
*
66809 TAAGGTAGGATGGAAGACAGAAACAGATGACTATTTTAAAATTAATAGATAAATAAAATAAACAT
66 TAAGGTAGGATGGAAGACAGAAACAGATGACTA-TTTAAAATCAATAGATAAATAAAATAAACAT
** ** * *
66874 ACGCTGCAAATTTTTAATTTAATTTAAAGTAATTTATAGTAGGCTAGGTTTTAATAGTCTGCAAT
130 AAACTGCAAAGCTGTAA--TAATTT--AGTAATTTAAAGTAGGCTAGGTTTTAATAGTCTGCAAT
* *
66939 TGCAATCTAATTAACGCTTAAATTACATAAAACTTTGACAGCAATCTAATTAACCCTTAAAATAC
191 CGCAATCTAATTAACGCTTAAAATACATAAAACTTTGACAGCAATCTAATTAACCCTTAAAATAC
67004 ATAAAACTTTCACTGTCAAAT
256 ATAAAACTTTCACTGTCAAAT
*
67025 CAATGCAGCCCCAAAACCTTGTTTGGACTTTGAAGTACAAGAATCAGAACACCAAACAGGCAAAC
1 CAATGCAACCCCAAAACCTTGTTTGGACTTTGAAGTACAAGAATCAG-A-ACC--AC---CAAAC
67090 ATATATATACTAAGGTAGGATGGAAGACAGAAACAGATGACTA-TTAAAATCAATAGATAAATAA
59 --ATA-ATACTAAGGTAGGATGGAAGACAGAAACAGATGACTATTTAAAATCAATAGATAAAT-A
* * * *
67154 TAAATAAA-ATAAAC-G-TACGCTGTCA-AATTT-TTAATTTAAAGTA-GCTAGGTTTTAATAGT
120 -AAATAAACATAAACTGCAAAGCTGTAATAATTTAGTAATTTAAAGTAGGCTAGGTTTTAATAGT
*
67213 CTGCAATCGCAATCTAATTAACGCTTAAAATACATAAATCTTTGACAGCAAT
184 CTGCAATCGCAATCTAATTAACGCTTAAAATACATAAAACTTTGACAGCAAT
67265 TGCAATCTAA
Statistics
Matches: 212, Mismatches: 16, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
281 110 0.52
282 12 0.06
283 3 0.01
285 7 0.03
288 9 0.04
289 19 0.09
290 8 0.04
291 44 0.21
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (276 bp):
CAATGCAACCCCAAAACCTTGTTTGGACTTTGAAGTACAAGAATCAGAACCACCAAACATAATAC
TAAGGTAGGATGGAAGACAGAAACAGATGACTATTTAAAATCAATAGATAAATAAAATAAACATA
AACTGCAAAGCTGTAATAATTTAGTAATTTAAAGTAGGCTAGGTTTTAATAGTCTGCAATCGCAA
TCTAATTAACGCTTAAAATACATAAAACTTTGACAGCAATCTAATTAACCCTTAAAATACATAAA
ACTTTCACTGTCAAAT
Found at i:72711 original size:107 final size:107
Alignment explanation
Indices: 72525--72751 Score: 375
Period size: 107 Copynumber: 2.1 Consensus size: 107
72515 AAAGCTAATG
*
72525 AGCCCCAAATTAAAATTTTAATACAATTTTAAGGGTAAGTTCCAAAATTAATAATTTATTGTTAT
1 AGCCCCAAATTAAAATTTTAATACAATTTTAAGGGTAAATTCCAAAATTAATAATTTATTGTTAT
* *
72590 TGGGTTTTAGAATTAAA-ATATAACATTAATGTCACTAAGTTT
66 AGGGTTTTAGAATTAAAGA-ATAAAATTAATGTCACTAAGTTT
**
72632 AGCCCCAAATTAAAATTTTAATTTAATTTTAAGGGTAAATTCCAAAATTAATAATTTATTGTTAT
1 AGCCCCAAATTAAAATTTTAATACAATTTTAAGGGTAAATTCCAAAATTAATAATTTATTGTTAT
72697 AGGGTTTTAGAATTAAAGAATAAAATTAATGTCACTAAGTTT
66 AGGGTTTTAGAATTAAAGAATAAAATTAATGTCACTAAGTTT
* *
72739 AACCCTAAATTAA
1 AGCCCCAAATTAA
72752 TATATTTTTA
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
107 111 0.99
108 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (107 bp):
AGCCCCAAATTAAAATTTTAATACAATTTTAAGGGTAAATTCCAAAATTAATAATTTATTGTTAT
AGGGTTTTAGAATTAAAGAATAAAATTAATGTCACTAAGTTT
Found at i:73906 original size:21 final size:21
Alignment explanation
Indices: 73882--73931 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
73872 ATTCTTTCAG
73882 CAACATCACCTGACTCTTCCA
1 CAACATCACCTGACTCTTCCA
* *
73903 CAACATCACTTGACTCTTCCT
1 CAACATCACCTGACTCTTCCA
*
73924 TAACATCA
1 CAACATCA
73932 AGAATGACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.28
Consensus pattern (21 bp):
CAACATCACCTGACTCTTCCA
Done.