Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021110.1 Corchorus olitorius cultivar O-4 contig21143, 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: 57510
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3027 original size:19 final size:18
Alignment explanation
Indices: 3003--3039 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
2993 TTTTTTACAC
3003 AAAAAAAAGGGGTCTCTTG
1 AAAAAAAAGGGGT-TCTTG
3022 AAAAAAAAGGGGTTCTTG
1 AAAAAAAAGGGGTTCTTG
3040 GTGGGCGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.43, C:0.08, G:0.27, T:0.22
Consensus pattern (18 bp):
AAAAAAAAGGGGTTCTTG
Found at i:4400 original size:7 final size:7
Alignment explanation
Indices: 4388--4421 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
4378 GCATTAGATA
4388 ATTAATT
1 ATTAATT
4395 ATTAATT
1 ATTAATT
4402 ATTAATT
1 ATTAATT
4409 ATTAATT
1 ATTAATT
4416 ATTAAT
1 ATTAAT
4422 CACATGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTAATT
Found at i:12250 original size:12 final size:11
Alignment explanation
Indices: 12218--12257 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
12208 TGCATGTGAT
12218 TATATATATCA
1 TATATATATCA
12229 TATATCATATCA
1 TATAT-ATATCA
12241 TATA-ATAT-A
1 TATATATATCA
12250 TAT-TATAT
1 TATATATAT
12258 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.30
10 4 0.15
11 5 0.19
12 10 0.37
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (11 bp):
TATATATATCA
Found at i:21581 original size:273 final size:262
Alignment explanation
Indices: 21090--21584 Score: 692
Period size: 263 Copynumber: 1.8 Consensus size: 262
21080 ATATGGTACT
* *
21090 TACCCTTATTGATGCTGTTTAGGAATAGGCGAATTTCAAATACGAGTTACATGTGTTCAAATATA
1 TACCCTTATTGATGCTATTTAGGAATAGGCGAATTTCAAATACAAGTTACATGTGTTCAAATATA
** *
21155 ATAGAGTGGGATTATGGAAATGTGTAAATAGAAAAACAAATTGAGTTGTGCATCATTTAATTACA
66 ATAGAGTCAGATTATGGAAATGTGTAAATAGAAAAACAAATTGAGTTGTGCATCATTTAATTAAA
* * *
21220 TATGCAATAATGTTTGTGTTTCTTTCATCTGTATTTATAGTTTTGCAAAGTTGCAAGACTCAAGT
131 CATGCAATAATGTTTGTGTTTCTTTCATCTGTATTTATAGTTTTGCAAAGCTGCAAGACTC-AGG
21285 GAAGAAAAATATCAGTGGACCAATTGATGTTGACGCAGAAGGTATATGATACCAGTCTATTTCTT
195 GAAGAAAAATATCAGTGGACCAATTGATGTTGACGCAGAAGGTATATGATACCAGTCTATTTCTT
21350 CCC
260 CCC
*
21353 TACCCTTATTGATGCTATTTAGGAATAGGTGAATTTCAAATACAAGTTACATGATGTTCAAATAT
1 TACCCTTATTGATGCTATTTAGGAATAGGCGAATTTCAAATACAAGTTACATG-TGTTCAAATAT
*
21418 AATAGAGTCAGATTATGGAAATGTGTAAATAG-AAAA-AAATTGAGTTGTTCATCATTTAATTAA
65 AATAGAGTCAGATTATGGAAATGTGTAAATAGAAAAACAAATTGAGTTGTGCATCATTTAATTAA
* *
21481 ACATTCAATAATGCTTATGTGAAACTTATCTTTCTTTCATCTTTATTTATAGTTTTGCAAAGCTG
130 ACATGCAATAATG-TT-TGTG---------TTTCTTTCATCTGTATTTATAGTTTTGCAAAGCTG
* *
21546 CAAGACTC-GGGAA-AAGAAGATTTCTGATGGACCAATTGA
184 CAAGACTCAGGGAAGAA-AA-ATATCAG-TGGACCAATTGA
21585 CATTGAATCT
Statistics
Matches: 203, Mismatches: 14, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
262 36 0.18
263 56 0.28
264 45 0.22
270 2 0.01
271 6 0.03
272 5 0.02
273 53 0.26
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (262 bp):
TACCCTTATTGATGCTATTTAGGAATAGGCGAATTTCAAATACAAGTTACATGTGTTCAAATATA
ATAGAGTCAGATTATGGAAATGTGTAAATAGAAAAACAAATTGAGTTGTGCATCATTTAATTAAA
CATGCAATAATGTTTGTGTTTCTTTCATCTGTATTTATAGTTTTGCAAAGCTGCAAGACTCAGGG
AAGAAAAATATCAGTGGACCAATTGATGTTGACGCAGAAGGTATATGATACCAGTCTATTTCTTC
CC
Found at i:21601 original size:273 final size:262
Alignment explanation
Indices: 21090--21605 Score: 689
Period size: 273 Copynumber: 1.9 Consensus size: 262
21080 ATATGGTACT
* *
21090 TACCCTTATTGATGCTGTTTAGGAATAGGCGAATTTCAAATACGAGTTACATGTGTTCAAATATA
1 TACCCTTATTGATGCTATTTAGGAATAGGCGAATTTCAAATACAAGTTACATGTGTTCAAATATA
** *
21155 ATAGAGTGGGATTATGGAAATGTGTAAATAGAAAAACAAATTGAGTTGTGCATCATTTAATTACA
66 ATAGAGTCAGATTATGGAAATGTGTAAATAGAAAAACAAATTGAGTTGTGCATCATTTAATTAAA
* * *
21220 TATGCAATAATGTTTGTGTTTCTTTCATCTGTATTTATAGTTTTGCAAAGTTGCAAGACTCAAGT
131 CATGCAATAATGTTTGTGTTTCTTTCATCTGTATTTATAGTTTTGCAAAGCTGCAAGACTC-AGG
** *
21285 GAAGAAAAATATCAGTGGACCAATTGATGTTGACGCAGAAGGTATATGATACCAGTCTATTTCTT
195 GAAGAAAAATATCAGTGGACCAATTGACATTGAAGCAGAAGGTATATGATACCAGTCTATTTCTT
21350 CCC
260 CCC
*
21353 TACCCTTATTGATGCTATTTAGGAATAGGTGAATTTCAAATACAAGTTACATGATGTTCAAATAT
1 TACCCTTATTGATGCTATTTAGGAATAGGCGAATTTCAAATACAAGTTACATG-TGTTCAAATAT
*
21418 AATAGAGTCAGATTATGGAAATGTGTAAATAG-AAAA-AAATTGAGTTGTTCATCATTTAATTAA
65 AATAGAGTCAGATTATGGAAATGTGTAAATAGAAAAACAAATTGAGTTGTGCATCATTTAATTAA
* *
21481 ACATTCAATAATGCTTATGTGAAACTTATCTTTCTTTCATCTTTATTTATAGTTTTGCAAAGCTG
130 ACATGCAATAATG-TT-TGTG---------TTTCTTTCATCTGTATTTATAGTTTTGCAAAGCTG
* * * *
21546 CAAGACTC-GGGAA-AAGAAGATTTCTGATGGACCAATTGACATTGAATCTGAAGGTATATG
184 CAAGACTCAGGGAAGAA-AA-ATATCAG-TGGACCAATTGACATTGAAGCAGAAGGTATATG
21606 GTATCAGTGT
Statistics
Matches: 219, Mismatches: 19, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
262 36 0.16
263 56 0.26
264 45 0.21
270 2 0.01
271 6 0.03
272 5 0.02
273 69 0.32
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (262 bp):
TACCCTTATTGATGCTATTTAGGAATAGGCGAATTTCAAATACAAGTTACATGTGTTCAAATATA
ATAGAGTCAGATTATGGAAATGTGTAAATAGAAAAACAAATTGAGTTGTGCATCATTTAATTAAA
CATGCAATAATGTTTGTGTTTCTTTCATCTGTATTTATAGTTTTGCAAAGCTGCAAGACTCAGGG
AAGAAAAATATCAGTGGACCAATTGACATTGAAGCAGAAGGTATATGATACCAGTCTATTTCTTC
CC
Found at i:23943 original size:8 final size:8
Alignment explanation
Indices: 23930--23959 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
23920 AGAAGATATT
23930 TTTTTTTA
1 TTTTTTTA
23938 TTTTTTTA
1 TTTTTTTA
23946 -TTTTTTA
1 TTTTTTTA
23953 TTTTTTT
1 TTTTTTT
23960 TAAATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:23951 original size:15 final size:15
Alignment explanation
Indices: 23931--23959 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
23921 GAAGATATTT
23931 TTTTTTATTTTTTTA
1 TTTTTTATTTTTTTA
23946 TTTTTTATTTTTTT
1 TTTTTTATTTTTTT
23960 TAAATTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTATTTTTTTA
Found at i:31827 original size:6 final size:6
Alignment explanation
Indices: 31818--31856 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
31808 AAACAGAAGC
* **
31818 AGAAAG AGAAAG AGAAAG AGAAAC TTAAAG AGAAAG AGA
1 AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AGA
31857 GGGAAGAGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.64, C:0.03, G:0.28, T:0.05
Consensus pattern (6 bp):
AGAAAG
Found at i:44563 original size:11 final size:11
Alignment explanation
Indices: 44547--44572 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44537 TCAAGTTATA
44547 GTTAGTCTATG
1 GTTAGTCTATG
44558 GTTAGTCTATG
1 GTTAGTCTATG
44569 GTTA
1 GTTA
44573 AGTAATAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.08, G:0.27, T:0.46
Consensus pattern (11 bp):
GTTAGTCTATG
Found at i:45685 original size:21 final size:21
Alignment explanation
Indices: 45661--45716 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 21
45651 CTTTACAAAC
45661 TGCAACTTGATTCTTCTGCTA
1 TGCAACTTGATTCTTCTGCTA
*
45682 TGCAA---AATTCTTCTGCTA
1 TGCAACTTGATTCTTCTGCTA
45700 TGACTGAACTTGATTCT
1 TG-C--AACTTGATTCT
45717 ACTATGTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
18 14 0.52
19 1 0.04
21 7 0.26
24 5 0.19
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.41
Consensus pattern (21 bp):
TGCAACTTGATTCTTCTGCTA
Found at i:48764 original size:22 final size:22
Alignment explanation
Indices: 48739--48782 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
48729 TATTATTAAC
48739 CTATGGTCAAGCT-ATAGTTAGT
1 CTATGGTCAAG-TAATAGTTAGT
*
48761 CTATGGTTAAGTAATAGTTAGT
1 CTATGGTCAAGTAATAGTTAGT
48783 TATAGATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.39
Consensus pattern (22 bp):
CTATGGTCAAGTAATAGTTAGT
Found at i:54805 original size:72 final size:72
Alignment explanation
Indices: 54696--54837 Score: 284
Period size: 72 Copynumber: 2.0 Consensus size: 72
54686 TAGGAGGAGG
54696 AATTCGCCTTCTTCAGCAAGGCAAGCCCATTAATGCCAAATCCCATGCCGCCCCCTATATAAAGG
1 AATTCGCCTTCTTCAGCAAGGCAAGCCCATTAATGCCAAATCCCATGCCGCCCCCTATATAAAGG
54761 GAGGCGA
66 GAGGCGA
54768 AATTCGCCTTCTTCAGCAAGGCAAGCCCATTAATGCCAAATCCCATGCCGCCCCCTATATAAAGG
1 AATTCGCCTTCTTCAGCAAGGCAAGCCCATTAATGCCAAATCCCATGCCGCCCCCTATATAAAGG
54833 GAGGC
66 GAGGC
54838 CATTCTCAGG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (72 bp):
AATTCGCCTTCTTCAGCAAGGCAAGCCCATTAATGCCAAATCCCATGCCGCCCCCTATATAAAGG
GAGGCGA
Done.