Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018095.1 Corchorus olitorius cultivar O-4 contig18128, 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: 14040
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Found at i:785 original size:29 final size:31
Alignment explanation
Indices: 725--793 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
715 CAAATAGATC
725 CCCGAACTTTGGCATAAATATCAAATAAGGG
1 CCCGAACTTTGGCATAAATATCAAATAAGGG
756 CCCGAACTTTGG-A-AAA-AGTCAAATAAGGG
1 CCCGAACTTTGGCATAAATA-TCAAATAAGGG
*
785 CCCCAACTT
1 CCCGAACTT
794 CGCTAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 1 0.03
29 22 0.61
30 1 0.03
31 12 0.33
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CCCGAACTTTGGCATAAATATCAAATAAGGG
Found at i:801 original size:29 final size:29
Alignment explanation
Indices: 745--813 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
735 GGCATAAATA
* * *
745 TCAAATAAGGGCCCGAACTTTGGAAAAAG
1 TCAAATAAGGGCCCCAACTTCGCAAAAAG
*
774 TCAAATAAGGGCCCCAACTTCGCTAAAAATC
1 TCAAATAAGGGCCCCAACTTCGC-AAAAA-G
805 TCAAATAAG
1 TCAAATAAG
814 TCCATTCCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 20 0.59
30 5 0.15
31 9 0.26
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (29 bp):
TCAAATAAGGGCCCCAACTTCGCAAAAAG
Found at i:2788 original size:24 final size:24
Alignment explanation
Indices: 2761--2831 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
2751 GAGGCACATG
* *
2761 TAGATGCTGTTAATGATGTTGGTT
1 TAGATGATGTTAATGATGCTGGTT
2785 TAGATGATGTTAATGATGCTGGTT
1 TAGATGATGTTAATGATGCTGGTT
* * *
2809 TAGATGTTGCTACTGATGCTGGT
1 TAGATGATGTTAATGATGCTGGT
2832 AAGGAAGGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.21, C:0.07, G:0.30, T:0.42
Consensus pattern (24 bp):
TAGATGATGTTAATGATGCTGGTT
Found at i:4471 original size:96 final size:96
Alignment explanation
Indices: 4353--4547 Score: 363
Period size: 96 Copynumber: 2.0 Consensus size: 96
4343 TTGGGCGATG
* *
4353 TACTTGAATTATTGCCATAAAACTGAATGCTTTTGTGACAATATTGTTACATACTTTCCATTCAT
1 TACTTGAAATATTGCCAAAAAACTGAATGCTTTTGTGACAATATTGTTACATACTTTCCATTCAT
4418 TTTGAATGTGAATTCATGTTACCATTTCAAT
66 TTTGAATGTGAATTCATGTTACCATTTCAAT
*
4449 TACTTGAAATATTGCCAAAAAACTGAATGCTTTTGTGACAATATTGTTACATATTTTCCATTCAT
1 TACTTGAAATATTGCCAAAAAACTGAATGCTTTTGTGACAATATTGTTACATACTTTCCATTCAT
4514 TTTGAATGTGAATTCATGTTACCATTTCAAT
66 TTTGAATGTGAATTCATGTTACCATTTCAAT
4545 TAC
1 TAC
4548 AGAGATCAAT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.42
Consensus pattern (96 bp):
TACTTGAAATATTGCCAAAAAACTGAATGCTTTTGTGACAATATTGTTACATACTTTCCATTCAT
TTTGAATGTGAATTCATGTTACCATTTCAAT
Found at i:6142 original size:33 final size:32
Alignment explanation
Indices: 6105--6168 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
6095 AAAGGAATTT
*
6105 AAATTAAATGAAAAAGAAATAAATACAAAAAAG
1 AAATTAAAAGAAAAAGAAATAAA-ACAAAAAAG
* **
6138 AAATTAAAAGGAAATTAAATAAAACAAAAAA
1 AAATTAAAAGAAAAAGAAATAAAACAAAAAA
6169 AGGGACTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 8 0.30
33 19 0.70
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (32 bp):
AAATTAAAAGAAAAAGAAATAAAACAAAAAAG
Found at i:7009 original size:21 final size:21
Alignment explanation
Indices: 6985--7053 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
6975 ACCAAAAATG
*
6985 CATATAGAGGTATCAAAACTT
1 CATATAGAGGTATCAAAATTT
*
7006 CATAGT-GTAGTTATCAAAATTT
1 CATA-TAG-AGGTATCAAAATTT
* * *
7028 TATACAGAGGTTACCAAAATTT
1 CATATAGAGG-TATCAAAATTT
7050 CATA
1 CATA
7054 AAAAATGTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
21 7 0.19
22 30 0.81
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (21 bp):
CATATAGAGGTATCAAAATTT
Found at i:7199 original size:22 final size:22
Alignment explanation
Indices: 7147--7473 Score: 87
Period size: 22 Copynumber: 14.6 Consensus size: 22
7137 AAATTTGTGC
**
7147 TTATCAAAATTTCCTAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
*
7169 TTAACAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
* * *
7191 TTATGAAAAATTTAT-GAAGAGG
1 TTATCAAAATTTTATAG-GGAGG
** **
7213 TTATCGAAAA-TACATAGAAAGG
1 TTATC-AAAATTTTATAGGGAGG
* *
7235 ATATCACAATTTCATCCTCATAGGGAGG
1 TTATCA-AAATT--T--T-ATAGGGAGG
* *
7263 TTATCAAAATTTCAT-GGTGTGG
1 TTATCAAAATTTTATAGG-GAGG
* *
7285 TTATCAAAATTTTCATAGTGCGG
1 TTATCAAAATTTT-ATAGGGAGG
* ** * *
7308 TTA-C-CAATTTTATTTATTGTGA
1 TTATCAAAATTTTA--TAGGGAGG
* *
7330 TTA-CTAAAATTTTATAGGCAGA
1 TTATC-AAAATTTTATAGGGAGG
* **
7352 TTATCAAAATTTTAAACTGAGG
1 TTATCAAAATTTTATAGGGAGG
** * *
7374 TTATTGAAATTTCAT-GGTGCGG
1 TTATCAAAATTTTATAGG-GAGG
* * * ** *
7396 TTACCAAAATTTCACATTGTGG
1 TTATCAAAATTTTATAGGGAGG
7418 TTATC-AAATTTTCATAGGGAGG
1 TTATCAAAATTTT-ATAGGGAGG
* * **
7440 TTATCGAAATTTCATAATGAGG
1 TTATCAAAATTTTATAGGGAGG
*
7462 TTCTC-AAATTTT
1 TTATCAAAATTTT
7474 CAAAATGTGG
Statistics
Matches: 220, Mismatches: 63, Indels: 45
0.67 0.19 0.14
Matches are distributed among these distances:
20 1 0.00
21 22 0.10
22 151 0.69
23 21 0.10
24 8 0.04
25 1 0.00
27 4 0.02
28 12 0.05
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGG
Found at i:7422 original size:66 final size:67
Alignment explanation
Indices: 7352--7495 Score: 159
Period size: 66 Copynumber: 2.2 Consensus size: 67
7342 TATAGGCAGA
* * ** * * *
7352 TTATCAAAATTTT-AAACTGAGGTTATTGAAATTTCATGGTGCGGTTAC-CAAAATTTCACATTG
1 TTATCAAAATTTTCAAACGGAGGTTATCGAAATTTCATAATGAGGTT-CTCAAAATTTCAAAATG
7415 TGG
65 TGG
* * *
7418 TTATC-AAATTTTCATAGGGAGGTTATCGAAATTTCATAATGAGGTTCTCAAATTTTCAAAATGT
1 TTATCAAAATTTTCAAACGGAGGTTATCGAAATTTCATAATGAGGTTCTCAAAATTTCAAAATGT
7482 GG
66 GG
*
7484 TTATCAATATTT
1 TTATCAAAATTT
7496 CTACATTGGA
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
65 8 0.12
66 51 0.80
67 5 0.08
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (67 bp):
TTATCAAAATTTTCAAACGGAGGTTATCGAAATTTCATAATGAGGTTCTCAAAATTTCAAAATGT
GG
Found at i:7431 original size:44 final size:43
Alignment explanation
Indices: 7252--7475 Score: 141
Period size: 44 Copynumber: 5.1 Consensus size: 43
7242 AATTTCATCC
* **
7252 TCATAGGGAGGTTATCAAAATTTCATGGTGTGGTTATCAAAATTT
1 TCATA-GGCGGTTATCAAAATTTCATATTGTGGTTATC-AAATTT
* * * *
7297 TCATAGTGCGGTTA-C-CAATTTTATTTATTGTGATTACTAAAATTT
1 TCATAG-GCGGTTATCAAAATTTCA--TATTGTGGTTA-TCAAATTT
* * * * * *
7342 T-ATAGGCAGATTATCAAAATTTTAAACTGAGGTTATTGAAA-TT
1 TCATAGGC-GGTTATCAAAATTTCATATTGTGGTTA-TCAAATTT
* * *
7385 TCATGGTGCGGTTACCAAAATTTCACATTGTGGTTATCAAATTT
1 TCATAG-GCGGTTATCAAAATTTCATATTGTGGTTATCAAATTT
* * * * *
7429 TCATAGGGAGGTTATCGAAATTTCATAATGAGGTTCTCAAATTT
1 TCATA-GGCGGTTATCAAAATTTCATATTGTGGTTATCAAATTT
7473 TCA
1 TCA
7476 AAATGTGGTT
Statistics
Matches: 137, Mismatches: 31, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
43 15 0.11
44 84 0.61
45 30 0.22
46 8 0.06
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (43 bp):
TCATAGGCGGTTATCAAAATTTCATATTGTGGTTATCAAATTT
Found at i:7461 original size:88 final size:89
Alignment explanation
Indices: 7252--7475 Score: 235
Period size: 88 Copynumber: 2.5 Consensus size: 89
7242 AATTTCATCC
** *
7252 TCATAGGGAGGTTATCAAAATTTCATGGTGTGGTTATCAAAATTTTCATAGTGCGGTTACCAATT
1 TCATAGGGAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTTCATAGTGCGGTTACCAATT
* *
7317 TTATTTATTGTGATTACTAAAATTT
66 TCA-TCATTGTGATTACTAAAATTT
* * * ** *
7342 T-ATAGGCAGATTATCAAAATTTTA-AACTGAGGTTATTGAAA-TTTCATGGTGCGGTTACCAAA
1 TCATAGGGAGGTTATCAAAATTTCATAA-TGAGGTTATCAAAATTTTCATAGTGCGGTTACC--A
* *
7404 ATTTCA-CATTGTGGTTA-TCAAATTT
63 ATTTCATCATTGTGATTACTAAAATTT
* *
7429 TCATAGGGAGGTTATCGAAATTTCATAATGAGGTTCTC-AAATTTTCA
1 TCATAGGGAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTTCA
7476 AAATGTGGTT
Statistics
Matches: 109, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
87 11 0.10
88 58 0.53
89 33 0.30
90 7 0.06
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (89 bp):
TCATAGGGAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTTCATAGTGCGGTTACCAATT
TCATCATTGTGATTACTAAAATTT
Found at i:7474 original size:22 final size:22
Alignment explanation
Indices: 7416--7495 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
7406 TTCACATTGT
**
7416 GGTTATCAAATTTTCATAGGGA
1 GGTTATCAAATTTTCATAATGA
7438 GGTTATCGAAA-TTTCATAATGA
1 GGTTATC-AAATTTTCATAATGA
* * *
7460 GGTTCTCAAATTTTCAAAATGT
1 GGTTATCAAATTTTCATAATGA
7482 GGTTATCAATATTT
1 GGTTATCAA-ATTT
7496 CTACATTGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.06
22 39 0.80
23 7 0.14
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (22 bp):
GGTTATCAAATTTTCATAATGA
Found at i:7486 original size:44 final size:43
Alignment explanation
Indices: 7402--7496 Score: 100
Period size: 44 Copynumber: 2.2 Consensus size: 43
7392 GCGGTTACCA
* * * *
7402 AAATTTCACATTGTGGTTATCAAATTTTCATAGGGAGGTTATC
1 AAATTTCACAATGAGGTTATCAAATTTTCAAAAGGAGGTTATC
* * * *
7445 GAAATTTCATAATGAGGTTCTCAAATTTTCAAAATGTGGTTATC
1 -AAATTTCACAATGAGGTTATCAAATTTTCAAAAGGAGGTTATC
7489 AATATTTC
1 AA-ATTTC
7497 TACATTGGAG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (43 bp):
AAATTTCACAATGAGGTTATCAAATTTTCAAAAGGAGGTTATC
Found at i:7496 original size:22 final size:21
Alignment explanation
Indices: 7352--7496 Score: 85
Period size: 22 Copynumber: 6.6 Consensus size: 21
7342 TATAGGCAGA
*
7352 TTATCAAAATTTTA-AACTGAGG
1 TTATC-AAATTTCATAA-TGAGG
* ** *
7374 TTATTGAAATTTCATGGTGCGG
1 TTA-TCAAATTTCATAATGAGG
* * * *
7396 TTACCAAAATTTCACATTGTGG
1 TTATC-AAATTTCATAATGAGG
**
7418 TTATCAAATTTTCATAGGGAGG
1 TTATCAAA-TTTCATAATGAGG
7440 TTATCGAAATTTCATAATGAGG
1 TTATC-AAATTTCATAATGAGG
* * *
7462 TTCTCAAATTTTCAAAATGTGG
1 TTATCAAA-TTTCATAATGAGG
7484 TTATCAATATTTC
1 TTATCAA-ATTTC
7497 TACATTGGAG
Statistics
Matches: 94, Mismatches: 22, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
21 6 0.06
22 83 0.88
23 5 0.05
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (21 bp):
TTATCAAATTTCATAATGAGG
Found at i:8332 original size:13 final size:14
Alignment explanation
Indices: 8312--8339 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8302 TACAATGGAC
8312 CAAAAAAAACCCAA
1 CAAAAAAAACCCAA
8326 CAAAAAAAACCCAA
1 CAAAAAAAACCCAA
8340 ATAGCTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (14 bp):
CAAAAAAAACCCAA
Found at i:8550 original size:2 final size:2
Alignment explanation
Indices: 8543--8587 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
8533 ATAACCAAAC
8543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
8586 AT
1 AT
8588 TATTTTTAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9826 original size:20 final size:20
Alignment explanation
Indices: 9801--9844 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
9791 TTTATCAATT
*
9801 ATTAATTCTAATAATTCATA
1 ATTAATTCCAATAATTCATA
9821 ATTAATTCCAATAATTCATA
1 ATTAATTCCAATAATTCATA
9841 ATTA
1 ATTA
9845 GAATACATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTAATTCCAATAATTCATA
Found at i:9885 original size:13 final size:12
Alignment explanation
Indices: 9863--9910 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
9853 GATTAACAAA
9863 ATAATCAAAAATC
1 ATAAT-AAAAATC
*
9876 ATAATTAAAAATA
1 ATAA-TAAAAATC
*
9889 ATAA-AAAATTC
1 ATAATAAAAATC
9900 ATAATAAAAAT
1 ATAATAAAAAT
9911 TACATGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 9 0.31
12 5 0.17
13 14 0.48
14 1 0.03
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAATAAAAATC
Found at i:9890 original size:23 final size:23
Alignment explanation
Indices: 9860--9910 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
9850 CATGATTAAC
*
9860 AAAATAATCAAAAA-TCATAATTA
1 AAAATAATAAAAAATTCATAA-TA
9883 AAAATAATAAAAAATTCATAATA
1 AAAATAATAAAAAATTCATAATA
9906 AAAAT
1 AAAAT
9911 TACATGATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAATAATAAAAAATTCATAATA
Found at i:13650 original size:22 final size:22
Alignment explanation
Indices: 13192--13651 Score: 191
Period size: 22 Copynumber: 20.5 Consensus size: 22
13182 CAGATTATTG
* * *
13192 AAATTTCATAGTGTGGCTACCA
1 AAATTTCATAGTGAGGTTATCA
* *
13214 AAATTTCATAATGTGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* * *
13236 AATTTTCATAATGTA-ATTA-CAA
1 AAATTTCATAGTG-AGGTTATC-A
* * *
13258 AAATTTCATAG-AAGATAATCA
1 AAATTTCATAGTGAGGTTATCA
* * * *
13279 AAGTTTCATATTGTGCTTATCA
1 AAATTTCATAGTGAGGTTATCA
* * *
13301 AAATTTCATAGTGAGATTAACG
1 AAATTTCATAGTGAGGTTATCA
* *
13323 AAA-TTCTATAGGGAAGTTATCA
1 AAATTTC-ATAGTGAGGTTATCA
* * *
13345 ACATTCCATAGGGAGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
*
13367 AAATTTCATAGT-ATGGTTATCC
1 AAATTTCATAGTGA-GGTTATCA
****
13389 AAATTTCATAGTGTACCAAATCA
1 AAATTTCATAGTG-AGGTTATCA
** * * * * *
13412 ACCTTTCACAATTAATGTAAAATTCA
1 AAATTTCA-TAGTGAGGT--TA-TCA
* * * *
13438 AAATTTTATATTTAGGTCATCA
1 AAATTTCATAGTGAGGTTATCA
*
13460 AAATTAATATCATA-TAGAGGTTCTCA
1 AAA-T--T-TCATAGT-GAGGTTATCA
* * * *
13486 CAATTTTATAGTGTGATTATCA
1 AAATTTCATAGTGAGGTTATCA
* *
13508 AAATTTCATAGTGTGGTGA-CTA
1 AAATTTCATAGTGAGGTTATC-A
*
13530 AAATTTCATAG-GATGGTTATCG
1 AAATTTCATAGTGA-GGTTATCA
*
13552 AAATTTCATAGTGTGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* * *
13574 AAGTTTCACAGGGAGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* *
13596 CAATTTCTTAGTGAGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* * * *
13618 AAATAAT-ATAGCGAGATTACCA
1 AAAT-TTCATAGTGAGGTTATCA
13640 AAATTTCATAGT
1 AAATTTCATAGT
13652 AAGACTATGT
Statistics
Matches: 323, Mismatches: 89, Indels: 52
0.70 0.19 0.11
Matches are distributed among these distances:
20 1 0.00
21 21 0.07
22 247 0.76
23 19 0.06
24 3 0.01
25 11 0.03
26 21 0.07
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (22 bp):
AAATTTCATAGTGAGGTTATCA
Done.