Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020017.1 Corchorus olitorius cultivar O-4 contig20050, 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: 39168
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:7898 original size:36 final size:37
Alignment explanation
Indices: 7834--7904 Score: 126
Period size: 36 Copynumber: 1.9 Consensus size: 37
7824 CATATCGAGC
7834 TCCATTCCTTCTAAATCAAAAAGGGTTCATCAATGCCA
1 TCCATTCCTTCTAAA-CAAAAAGGGTTCATCAATGCCA
7872 TCCATTCCTTCTAAA-AAAAAGGGTTCATCAATG
1 TCCATTCCTTCTAAACAAAAAGGGTTCATCAATG
7905 ACTCAAAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 18 0.55
38 15 0.45
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (37 bp):
TCCATTCCTTCTAAACAAAAAGGGTTCATCAATGCCA
Found at i:10539 original size:38 final size:38
Alignment explanation
Indices: 10487--10560 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
10477 ATAACCTTTT
10487 TTTAAGCAACTCCAAAAGAAGATTTTGGAAAATAAAAG
1 TTTAAGCAACTCCAAAAGAAGATTTTGGAAAATAAAAG
* *
10525 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAA
1 TTTAAGCAACTCCAAAAGAAGATTTTGGAAAATAAA
10561 GAAATCCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (38 bp):
TTTAAGCAACTCCAAAAGAAGATTTTGGAAAATAAAAG
Found at i:14196 original size:13 final size:13
Alignment explanation
Indices: 14168--14222 Score: 65
Period size: 14 Copynumber: 4.0 Consensus size: 13
14158 AGTGCATGGT
14168 GAAAAAAAGAAGAA
1 GAAAAAAAGAA-AA
*
14182 GAAAATAAGAAAA
1 GAAAAAAAGAAAA
*
14195 GAAAAGAAGAAAGA
1 GAAAAAAAGAAA-A
14209 GAAAAAGAAGAAAA
1 GAAAAA-AAGAAAA
14223 AGAGAGAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 13 0.36
14 17 0.47
15 6 0.17
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (13 bp):
GAAAAAAAGAAAA
Found at i:14200 original size:24 final size:23
Alignment explanation
Indices: 14169--14237 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 23
14159 GTGCATGGTG
14169 AAAAAAAGAAGAAGA-AAATAAGA
1 AAAAAAAGAAGAAGAGAAA-AAGA
14192 AAAGAAAAGAAGAAAGAGAAAAAGA
1 AAA-AAAAGAAG-AAGAGAAAAAGA
* *
14217 AGAAAAAGAGAGAAGATAAAA
1 AAAAAAAGA-AGAAGAGAAAA
14238 GCTCTAGGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 3 0.08
24 22 0.55
25 12 0.30
26 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (23 bp):
AAAAAAAGAAGAAGAGAAAAAGA
Found at i:14216 original size:12 final size:12
Alignment explanation
Indices: 14168--14222 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 12
14158 AGTGCATGGT
14168 GAAA-AAAAGAA
1 GAAAGAAAAGAA
*
14179 G-AAGAAAATAA
1 GAAAGAAAAGAA
14190 GAAAAGAAAAGAA
1 G-AAAGAAAAGAA
14203 GAAAGAGAAA-AA
1 GAAAGA-AAAGAA
14215 G-AAGAAAA
1 GAAAGAAAA
14223 AGAGAGAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 5 0.13
11 12 0.32
12 8 0.21
13 13 0.34
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (12 bp):
GAAAGAAAAGAA
Found at i:15988 original size:67 final size:67
Alignment explanation
Indices: 15880--16198 Score: 317
Period size: 67 Copynumber: 4.9 Consensus size: 67
15870 GGATTTTAGA
* *
15880 AGTACACCGGAAGACGGTTTCCTAGAAAGAATTTTCAAATGTTGATTGGACGACAATCTCATTAA
1 AGTACACCGGAAGACGGTTTACTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
15945 GG
66 GG
* * *
15947 AGTACACCGGAAGACGATTTGCTGGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
1 AGTACACCGGAAGACGGTTTACTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
16012 GG
66 GG
* * * * * * ** *
16014 AATACATCGGAAAACGGTTTACTAGAAAGAATTTTCAAATGTTGATCGAAAGACGATCTTGTCAA
1 AGTACACCGGAAGACGGTTTACTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
*
16079 GA
66 GG
* * * * * * * ** *
16081 AGTACACCGGAAGATGGTTT-CT--CAACAATTCTCAGATGTTGATCGGAAGACGATCTTGTCAA
1 AGTACACCGGAAGACGGTTTACTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
*
16143 GA
66 GG
* * * * *
16145 AGTACACCGGAAGATGGTTT-CT--CAACATTTTTCAGATGTTGATTGGAAGACAAT
1 AGTACACCGGAAGACGGTTTACTAGAAAGAATTTTCAAATGTTGATTGGAAGACAAT
16199 GTTGTTAAAA
Statistics
Matches: 222, Mismatches: 30, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
64 87 0.39
66 2 0.01
67 133 0.60
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (67 bp):
AGTACACCGGAAGACGGTTTACTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
GG
Found at i:16131 original size:64 final size:64
Alignment explanation
Indices: 16043--16551 Score: 698
Period size: 64 Copynumber: 8.0 Consensus size: 64
16033 TACTAGAAAG
* *
16043 AATTTTCA-AATGTTGATCGAAAGACGATCTTGTCAAGAAGTACACCGGAAGATGGTTTCTCAAC
1 AATTTTCAGAA-GTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * *
16107 AATTCTCAGATGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCGGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * * * * * *
16171 ATTTTTCAGATGTTGATTGGAAGACAATGTTGTTAAAAAGTACACCAGAAGATGGTTTCTCAAT
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* *
16235 AGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTCCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* *
16299 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTATCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * ***
16363 AGTTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAGAAGTACACCAGAAGATGGTTTCTCGGG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
** * * * * *
16427 AGCTTTCAGGAGTTGATCGGAAGACGATCTTATCAAGAAGTACGCCAGAAGATGGTTTTTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * *
16491 AATTTGCAGAAGTTGATCGGAAGACGATCTTGTTGAA-AAGTACACCAGAAGATAGTTTCTC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTG-TCAAGAAGTACACCAGAAGATGGTTTCTC
16552 GAAAAGGTTT
Statistics
Matches: 395, Mismatches: 48, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
64 391 0.99
65 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
Found at i:17846 original size:20 final size:20
Alignment explanation
Indices: 17821--17863 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
17811 TGAATTAGAC
17821 AGCCAAATTTCCAGCAAACA
1 AGCCAAATTTCCAGCAAACA
17841 AGCCAAATTTCCAGCAAACA
1 AGCCAAATTTCCAGCAAACA
17861 AGC
1 AGC
17864 ATTTAGATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.30, G:0.12, T:0.14
Consensus pattern (20 bp):
AGCCAAATTTCCAGCAAACA
Found at i:17974 original size:36 final size:36
Alignment explanation
Indices: 17927--17997 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
17917 AAAATAAAAC
17927 ACACATATATACCAATCAATCATCATCAAATTTCTT
1 ACACATATATACCAATCAATCATCATCAAATTTCTT
*
17963 ACACATATATACCAATCACTCATCATCAAATTTCT
1 ACACATATATACCAATCAATCATCATCAAATTTCT
17998 CACAACTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (36 bp):
ACACATATATACCAATCAATCATCATCAAATTTCTT
Found at i:22387 original size:23 final size:26
Alignment explanation
Indices: 22330--22398 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 26
22320 TTTAAGCAAC
22330 TCAAAGAGATTTGGAAATAAAGTTAGTAA
1 TCAAAGAGATTTGGAAAT-AA--TAGTAA
22359 TCAAAGAGATTTGGAAAT-A-AG-AA
1 TCAAAGAGATTTGGAAATAATAGTAA
*
22382 TCAAAGAAGGTTTGGAA
1 TCAAAG-AGATTTGGAA
22399 TTATAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 8 0.21
24 11 0.29
27 1 0.03
29 18 0.47
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.25
Consensus pattern (26 bp):
TCAAAGAGATTTGGAAATAATAGTAA
Found at i:23491 original size:22 final size:22
Alignment explanation
Indices: 23459--23695 Score: 156
Period size: 22 Copynumber: 10.8 Consensus size: 22
23449 GGTTTTGTGT
23459 GGTTATCAAAATTTCATAGTGA
1 GGTTATCAAAATTTCATAGTGA
* * * *
23481 GATTATAAAAAATTCATAGGGA
1 GGTTATCAAAATTTCATAGTGA
*
23503 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGA
* * *
23525 GGTTATCAAAATGTCATAGCGT
1 GGTTATCAAAATTTCATAGTGA
* * * *
23547 GGTTATCACAATTTTATAATGT
1 GGTTATCAAAATTTCATAGTGA
* *
23569 GGTTATTAAAATTTTATAAG-GA
1 GGTTATCAAAATTTCAT-AGTGA
** * * * *
23591 AATTGTCAGAATTTTATACTGA
1 GGTTATCAAAATTTCATAGTGA
** * *
23613 TTTTATCAAAAGTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGA
* * *
23635 GGTTATAAAAAATTTCATACTAA
1 GGTTAT-CAAAATTTCATAGTGA
* *
23658 GGTTATCATAATATCATAGT--
1 GGTTATCAAAATTTCATAGTGA
* *
23678 GGATATCACAATTTCATA
1 GGTTATCAAAATTTCATA
23696 ATACCAAAAT
Statistics
Matches: 164, Mismatches: 48, Indels: 8
0.75 0.22 0.04
Matches are distributed among these distances:
20 15 0.09
21 1 0.01
22 130 0.79
23 18 0.11
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGA
Found at i:26922 original size:3 final size:3
Alignment explanation
Indices: 26914--26941 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
26904 TTAACCAAAT
26914 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
26942 ATGAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:27602 original size:12 final size:14
Alignment explanation
Indices: 27585--27621 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
27575 CAATTAATTA
27585 TAACCCAAT-AC-T
1 TAACCCAATAACTT
27597 TAACCCAATAACTT
1 TAACCCAATAACTT
*
27611 TAACCCCATAA
1 TAACCCAATAA
27622 AAATTATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 11 0.50
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.24
Consensus pattern (14 bp):
TAACCCAATAACTT
Found at i:28162 original size:23 final size:23
Alignment explanation
Indices: 28119--28165 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
28109 CTTATCCCAA
28119 ATAACCCAAAATCTTAAAGAACCC
1 ATAACCCAAAA-CTTAAAGAACCC
28143 ATAACCCAGAAA-TTAAAGAACCC
1 ATAACCCA-AAACTTAAAGAACCC
28166 TTATAACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.50
24 8 0.36
25 3 0.14
ACGTcount: A:0.51, C:0.28, G:0.06, T:0.15
Consensus pattern (23 bp):
ATAACCCAAAACTTAAAGAACCC
Found at i:28223 original size:17 final size:17
Alignment explanation
Indices: 28201--28240 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28191 TAACCAAGAA
28201 AACCCTG-AATCTTAAAG
1 AACCCTGAAAT-TTAAAG
*
28218 AACCCTGAAATTTAATG
1 AACCCTGAAATTTAAAG
28235 AACCCT
1 AACCCT
28241 TATAACCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (17 bp):
AACCCTGAAATTTAAAG
Found at i:31669 original size:81 final size:81
Alignment explanation
Indices: 31534--31695 Score: 315
Period size: 81 Copynumber: 2.0 Consensus size: 81
31524 GGTACCAGCA
31534 CTGGTGGACTGGTGAGGTACCCTTTAATTTTCTCAAATGTTGTTTGGCATTCTTCATCCCACTCT
1 CTGGTGGACTGGTGAGGTACCCTTTAATTTTCTCAAATGTTGTTTGGCATTCTTCATCCCACTCT
*
31599 CTTGAGTCGTGCTTCC
66 CTTGAATCGTGCTTCC
31615 CTGGTGGACTGGTGAGGTACCCTTTAATTTTCTCAAATGTTGTTTGGCATTCTTCATCCCACTCT
1 CTGGTGGACTGGTGAGGTACCCTTTAATTTTCTCAAATGTTGTTTGGCATTCTTCATCCCACTCT
31680 CTTGAATCGTGCTTCC
66 CTTGAATCGTGCTTCC
31696 GAAGAAGTTC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (81 bp):
CTGGTGGACTGGTGAGGTACCCTTTAATTTTCTCAAATGTTGTTTGGCATTCTTCATCCCACTCT
CTTGAATCGTGCTTCC
Found at i:31999 original size:27 final size:27
Alignment explanation
Indices: 31969--32041 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
31959 AGGGTCACAT
*
31969 AGGGGCATTTTGGTCATTTTTACACTA
1 AGGGGCAATTTGGTCATTTTTACACTA
* *** *
31996 A-GGGCAATTTGGTCATTTGTATGTTC
1 AGGGGCAATTTGGTCATTTTTACACTA
32022 AGGGGCAATTTGGTCATTTT
1 AGGGGCAATTTGGTCATTTT
32042 AAGTCCAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 20 0.53
27 18 0.47
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (27 bp):
AGGGGCAATTTGGTCATTTTTACACTA
Found at i:37211 original size:40 final size:41
Alignment explanation
Indices: 37158--37271 Score: 128
Period size: 40 Copynumber: 2.9 Consensus size: 41
37148 ACGTATAGCC
*
37158 TCCTAAATCAGGGACTAAATTGCATCAAAT-AGTAAAT-AAA
1 TCCTAAATCAGGGACTAAATTGCATCAAATCA-AAAATAAAA
* * ***
37198 TCTTGAATCAGGGACTAAGCCGCAT-AAATCAAAAATAAAA
1 TCCTAAATCAGGGACTAAATTGCATCAAATCAAAAATAAAA
*
37238 TCCTAAATCAGGGACAAAATTGCATCAAA-CAAAA
1 TCCTAAATCAGGGACTAAATTGCATCAAATCAAAA
37272 GGTAGTATCC
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
39 8 0.14
40 48 0.81
41 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (41 bp):
TCCTAAATCAGGGACTAAATTGCATCAAATCAAAAATAAAA
Found at i:38450 original size:13 final size:13
Alignment explanation
Indices: 38432--38457 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38422 CTCTTGTGCT
38432 CTTATGCAGGTCA
1 CTTATGCAGGTCA
38445 CTTATGCAGGTCA
1 CTTATGCAGGTCA
38458 ATTCTGTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
CTTATGCAGGTCA
Done.