Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013716.1 Corchorus olitorius cultivar O-4 contig13749, 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: 7200
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Found at i:1776 original size:41 final size:41
Alignment explanation
Indices: 1638--1920 Score: 329
Period size: 41 Copynumber: 6.9 Consensus size: 41
1628 GTTTGATTTG
* * *
1638 ATTTGATTCAAGGG--TCGAATGACTTGGTCTTGAAATGATA
1 ATTTAATTCAAGGGTCTCG-ATGACTTGATCTTGAATTGATA
* ** * * * * * *
1678 ATCTCCTCCAAAGGTATTGACGACTTGGTCTTGAATTGATAATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTG---ATA
* *
1722 ATTTGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
1763 ATTTAATTCAAGGGTCTCGATGACTCT-ATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACT-TGATCTTGAATTGATA
* * *
1804 ATTTAATTCAAGGGTCTCGATGACTTGTTTTTAAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
1845 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
1886 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
1921 CAAACGAAAA
Statistics
Matches: 207, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
40 10 0.05
41 162 0.78
42 3 0.01
44 32 0.15
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
Found at i:2035 original size:14 final size:16
Alignment explanation
Indices: 2016--2048 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2006 TCTGAAAATA
2016 CTTCAGAG-TTTT-TG
1 CTTCAGAGCTTTTCTG
2030 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
2046 CTT
1 CTT
2049 TCGGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.48
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:2849 original size:73 final size:74
Alignment explanation
Indices: 2772--2914 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 74
2762 AGCGAGACTT
*
2772 TTTTTTTTCGCTCTAACTTTTGCC-TAAGCCATCCTTTACAGGA-TTTCAACATAGCGAGC-CTT
1 TTTTTTTTCGCTCTAACTTTTGCCTTAAGCCATCCTTTACAGGATTTTCAACATAGCAAGCTCTT
2834 TTTTTTTCC
66 TTTTTTTCC
* * * *
2843 TTTTTTTTCGCTCTAACTTTTGCCTTTAGCCGTCCTTTATAGGATTTTCAACTTAGCAAGCTCTT
1 TTTTTTTTCGCTCTAACTTTTGCCTTAAGCCATCCTTTACAGGATTTTCAACATAGCAAGCTCTT
2908 TTTTTTT
66 TTTTTTT
2915 TTTGTTGGGC
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 24 0.38
72 16 0.25
73 14 0.22
74 10 0.16
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (74 bp):
TTTTTTTTCGCTCTAACTTTTGCCTTAAGCCATCCTTTACAGGATTTTCAACATAGCAAGCTCTT
TTTTTTTCC
Found at i:4787 original size:41 final size:41
Alignment explanation
Indices: 4710--4931 Score: 329
Period size: 41 Copynumber: 5.3 Consensus size: 41
4700 AGGTATTGAC
* *
4710 GACTTGGTCTTGAATTGATAATAATTTGATTCAAGGGTCTCGAT
1 GACTTGATCTTGAATTG---ATAATTTAATTCAAGGGTCTCGAT
*
4754 GACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
4795 GACTCT-ATCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
1 GACT-TGATCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
* * *
4836 GACTTGTTTTTAAATTGATAATTTAATTCAAGGGTCTCGAT
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
**
4877 GACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
4918 GACTTGATCTTGAA
1 GACTTGATCTTGAA
4932 CAAATGAAAA
Statistics
Matches: 163, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
40 1 0.01
41 145 0.89
42 1 0.01
44 16 0.10
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.40
Consensus pattern (41 bp):
GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
Found at i:5048 original size:16 final size:16
Alignment explanation
Indices: 5027--5061 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5017 TCTGAAAATA
5027 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
5043 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
5059 CTT
1 CTT
5062 TCGGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:6259 original size:4 final size:4
Alignment explanation
Indices: 6250--6439 Score: 82
Period size: 4 Copynumber: 49.0 Consensus size: 4
6240 GGATATTTAC
* * * *
6250 TATT TATT TATT T-TT AATAT TATC TATT TATT TA-C TATT TATC TATT
1 TATT TATT TATT TATT TAT-T TATT TATT TATT TATT TATT TATT TATT
* * * * *
6297 TATT TA-T T-TT TAAT TA-T TATC TATC TATT TA-C TATT TATC TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
* * * *
6341 CATT TA-T T-TT TAAT TA-T TATC TATT TATT TA-C TATT TATCT T-TT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT-T TATT
* **
6385 TAGTGT CTAATT T-TGC TA-T TACC TATT TATT TATT TATT TATT TATT
1 TA-T-T -T-ATT TAT-T TATT TATT TATT TATT TATT TATT TATT TATT
6432 TATT TATT
1 TATT TATT
6440 ATTATTATTA
Statistics
Matches: 139, Mismatches: 27, Indels: 40
0.67 0.13 0.19
Matches are distributed among these distances:
3 27 0.19
4 100 0.72
5 7 0.05
6 2 0.01
7 2 0.01
8 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.65
Consensus pattern (4 bp):
TATT
Found at i:6259 original size:11 final size:11
Alignment explanation
Indices: 6243--6379 Score: 86
Period size: 11 Copynumber: 12.3 Consensus size: 11
6233 AAGGAATGGA
6243 TATTTACTATT
1 TATTTACTATT
*
6254 TATTTA-TTTT
1 TATTTACTATT
6264 TAATATTATCTATT
1 T-AT-TTA-CTATT
6278 TATTTACTATT
1 TATTTACTATT
* *
6289 TATCTATTTATT
1 TATTTA-CTATT
* *
6301 TATTT-TTAAT
1 TATTTACTATT
*
6311 TA-TTATCTATC
1 TATTTA-CTATT
6322 TATTTACTATT
1 TATTTACTATT
* *
6333 TATCTATTCATT
1 TATTTACT-ATT
* *
6345 TATTT-TTAAT
1 TATTTACTATT
6355 TA-TTATCTATT
1 TATTTA-CTATT
6366 TATTTACTATT
1 TATTTACTATT
6377 TAT
1 TAT
6380 CTTTTTAGTG
Statistics
Matches: 98, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
9 4 0.04
10 14 0.14
11 47 0.48
12 27 0.28
13 2 0.02
14 4 0.04
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTACTATT
Found at i:6330 original size:44 final size:44
Alignment explanation
Indices: 6243--6454 Score: 263
Period size: 44 Copynumber: 4.8 Consensus size: 44
6233 AAGGAATGGA
6243 TATTTA-CTATTTATTTATTTTTAA-TATTATCTATTTATTTAC
1 TATTTATCTATTTATTTATTTTTAATTATTATCTATTTATTTAC
*
6285 TATTTATCTATTTATTTATTTTTAATTATTATCTATCTATTTAC
1 TATTTATCTATTTATTTATTTTTAATTATTATCTATTTATTTAC
*
6329 TATTTATCTATTCATTTATTTTTAATTATTATCTATTTATTTAC
1 TATTTATCTATTTATTTATTTTTAATTATTATCTATTTATTTAC
* * ** * *
6373 TATTTATCTTTTTAGTGTCTAATTTT-GCTATTACCTATTTATTTATT
1 TATTTATCTATTTA-T-T-TATTTTTAATTATTATCTATTTATTTA-C
* *
6420 TATTTATTTATTTATTTATTATT-ATTATTAT-TATT
1 TATTTATCTATTTATTTATTTTTAATTATTATCTATT
6455 ATTATTATTA
Statistics
Matches: 147, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
42 6 0.04
43 22 0.15
44 81 0.55
45 2 0.01
46 18 0.12
47 18 0.12
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.65
Consensus pattern (44 bp):
TATTTATCTATTTATTTATTTTTAATTATTATCTATTTATTTAC
Found at i:6443 original size:3 final size:3
Alignment explanation
Indices: 6435--6472 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6425 ATTTATTTAT
6435 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6473 TAGCTACCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6511 original size:24 final size:22
Alignment explanation
Indices: 6460--6539 Score: 65
Period size: 24 Copynumber: 3.5 Consensus size: 22
6450 TTATTATTAT
***
6460 TATTA-TTATTATTTAGCTACC
1 TATTATTTATTATTTCTATACC
*
6481 TAATTATTTATTATTCTCTGTACC
1 T-ATTATTTATTATT-TCTATACC
*
6505 TATTTATCTATTTATTTCTATACC
1 TA-TTATTTA-TTATTTCTATACC
6529 TATTA-TTATTA
1 TATTATTTATTA
6540 CTTTTTTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
21 4 0.08
22 6 0.12
23 12 0.25
24 21 0.44
25 5 0.10
ACGTcount: A:0.28, C:0.14, G:0.03, T:0.56
Consensus pattern (22 bp):
TATTATTTATTATTTCTATACC
Found at i:6613 original size:44 final size:42
Alignment explanation
Indices: 6527--6613 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 42
6517 TATTTCTATA
**
6527 CCTATTATTATTACTTTTTTTAATTTTTTTTAAACTTGTTTT
1 CCTATTATTATTACTTTTTTTAATTTTTTTTAAACTAATTTT
6569 CCTATTTATCTATTACTTTTTTTAATATTTATTTT-AA-TAATTTT
1 CCTA-TTAT-TATTACTTTTTTTAAT-TTT-TTTTAAACTAATTTT
6613 C
1 C
6614 TTAATCAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
42 4 0.10
43 4 0.10
44 22 0.56
45 5 0.13
46 4 0.10
ACGTcount: A:0.24, C:0.10, G:0.01, T:0.64
Consensus pattern (42 bp):
CCTATTATTATTACTTTTTTTAATTTTTTTTAAACTAATTTT
Done.