Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013080.1 Corchorus olitorius cultivar O-4 contig13113, 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: 22883
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4516 original size:30 final size:29
Alignment explanation
Indices: 4480--4638 Score: 162
Period size: 28 Copynumber: 5.5 Consensus size: 29
4470 AATAAACTTG
*
4480 AAATGACTAAAATGCCCCCCTGAACATGAA
1 AAATGACCAAAATG-CCCCCTGAACATGAA
*
4510 AAATGACCAAAATG-CCCCTGGACATGAA
1 AAATGACCAAAATGCCCCCTGAACATGAA
4538 AAATGACCAAAATGCCCCC-GAACATGAA
1 AAATGACCAAAATGCCCCCTGAACATGAA
* * * * * *
4566 TAATGATCACAATTCCCCTCTGGACCTAGAA
1 AAATGACCAAAATGCCCC-CTGAACAT-GAA
* * *
4597 GAATGACCAGAATG-CCCCTGAACATGTA
1 AAATGACCAAAATGCCCCCTGAACATGAA
*
4625 AAATAACCAAAATG
1 AAATGACCAAAATG
4639 AGAAGCAAAG
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
28 62 0.58
29 11 0.10
30 20 0.19
31 13 0.12
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (29 bp):
AAATGACCAAAATGCCCCCTGAACATGAA
Found at i:4620 original size:59 final size:56
Alignment explanation
Indices: 4480--4637 Score: 172
Period size: 59 Copynumber: 2.7 Consensus size: 56
4470 AATAAACTTG
* *
4480 AAATGACTAAAATGCCCCCCTGAACATGAAAAATGACCAAAATGCCCCTGGACATGAA
1 AAATGACCAAAATG--CCCCTGAACATGAAAAATGACCAAAATCCCCCTGGACATGAA
* * * * *
4538 AAATGACCAAAATGCCCCCGAACATGAATAATGATCACAATTCCCCTCTGGACCTAGAA
1 AAATGACCAAAATGCCCCTGAACATGAAAAATGACCA-AAATCCCC-CTGGACAT-GAA
* * * *
4597 GAATGACCAGAATGCCCCTGAACATGTAAAATAACCAAAAT
1 AAATGACCAAAATGCCCCTGAACATGAAAAATGACCAAAAT
4638 GAGAAGCAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
56 20 0.24
57 6 0.07
58 23 0.28
59 33 0.40
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (56 bp):
AAATGACCAAAATGCCCCTGAACATGAAAAATGACCAAAATCCCCCTGGACATGAA
Found at i:6594 original size:9 final size:9
Alignment explanation
Indices: 6574--6602 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
6564 TTAATTCATT
6574 TAATTTCC-
1 TAATTTCCA
6582 TAATTTCCA
1 TAATTTCCA
6591 TAATTTCCA
1 TAATTTCCA
6600 TAA
1 TAA
6603 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:7928 original size:45 final size:45
Alignment explanation
Indices: 7864--8062 Score: 317
Period size: 45 Copynumber: 4.4 Consensus size: 45
7854 TCACTGTTAT
* * ***
7864 ACCCATCCAGATTTTCACCCCCATTATTGGCTCTAACTCCCTCAA
1 ACCCATCCAGATTTTCACCCTCATTCTCCTCTCTAACTCCCTCAA
*
7909 ACCCATCAAGATTTTCACCCTCATTCTCCTCTCTAACTCCCTCAA
1 ACCCATCCAGATTTTCACCCTCATTCTCCTCTCTAACTCCCTCAA
*
7954 ACCCATCAAGATTTTCACCCTCATTCTCCTCTCTAACTCCCTCAA
1 ACCCATCCAGATTTTCACCCTCATTCTCCTCTCTAACTCCCTCAA
*
7999 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCCTCAA
1 ACCCATCCAGATTTTCACCCTCATTCTCCTCTCTAACTCCCTCAA
*
8044 ACCCATCCACATTTTCACC
1 ACCCATCCAGATTTTCACC
8063 TTCTGCAGCA
Statistics
Matches: 146, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 146 1.00
ACGTcount: A:0.24, C:0.43, G:0.03, T:0.30
Consensus pattern (45 bp):
ACCCATCCAGATTTTCACCCTCATTCTCCTCTCTAACTCCCTCAA
Found at i:8289 original size:15 final size:15
Alignment explanation
Indices: 8271--8299 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8261 AACATCAAAA
8271 ACATTATCAGTGGTG
1 ACATTATCAGTGGTG
8286 ACATTATCAGTGGT
1 ACATTATCAGTGGT
8300 CACAGTGGGC
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:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (15 bp):
ACATTATCAGTGGTG
Found at i:9836 original size:20 final size:20
Alignment explanation
Indices: 9807--9849 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9797 TATGACGTGT
* *
9807 CCTCTGATAATTTCACATGG
1 CCTCTCATAATTCCACATGG
*
9827 CCTCTCATAATTCCACGTGG
1 CCTCTCATAATTCCACATGG
9847 CCT
1 CCT
9850 ATATTCACGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.33
Consensus pattern (20 bp):
CCTCTCATAATTCCACATGG
Found at i:16070 original size:14 final size:14
Alignment explanation
Indices: 16051--16078 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16041 TCTGCTATCC
16051 TCTTACAATTTTGA
1 TCTTACAATTTTGA
16065 TCTTACAATTTTGA
1 TCTTACAATTTTGA
16079 AGGGGCATTG
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:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
TCTTACAATTTTGA
Found at i:19630 original size:34 final size:33
Alignment explanation
Indices: 19581--19697 Score: 129
Period size: 34 Copynumber: 3.6 Consensus size: 33
19571 GTCATGAAAA
*
19581 TTGACACCAGCAGTTGTCATATCAAATTATTATC
1 TTGACACCA-AAGTTGTCATATCAAATTATTATC
*
19615 TTGACACCATAAGTTGTC--ATGAAA--ATTA--
1 TTGACACCA-AAGTTGTCATATCAAATTATTATC
19643 TTGACACCGGAAAGTTGTCATATCAAATTATTATC
1 TTGACACC--AAAGTTGTCATATCAAATTATTATC
19678 TTGACACCAAAAGTTGTCAT
1 TTGACACC-AAAGTTGTCAT
19698 GCTGAGGAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
28 8 0.11
29 8 0.11
30 5 0.07
31 5 0.07
32 5 0.07
33 4 0.06
34 27 0.39
35 8 0.11
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (33 bp):
TTGACACCAAAGTTGTCATATCAAATTATTATC
Found at i:19669 original size:63 final size:62
Alignment explanation
Indices: 19520--19730 Score: 284
Period size: 63 Copynumber: 3.3 Consensus size: 62
19510 TTTAAATTTA
* * *
19520 ATTGACACCAGAAGTTGTCATATTATATTATTATCTTTGACACCAGAAGTTGTCATG-AAA--
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATC-TTGACACCAAAAGTTGTCATGAAAATT
* *
19580 ATTGACACCAGCAGTTGTCATATCAAATTATTATCTTGACACCATAAGTTGTCATGAAAATT
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAAAAGTTGTCATGAAAATT
*
19642 ATTGACACCGGAAAGTTGTCATATCAAATTATTATCTTGACACCAAAAGTTGTCATGCTGAGGAA
1 ATTGACACCAG-AAGTTGTCATATCAAATTATTATCTTGACACCAAAAGTTGTCA---TGA--AA
19707 ATT
60 ATT
19710 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
19731 CCCGAGATTG
Statistics
Matches: 134, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
59 20 0.15
60 35 0.26
62 10 0.07
63 41 0.31
66 3 0.02
67 10 0.07
68 15 0.11
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (62 bp):
ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAAAAGTTGTCATGAAAATT
Done.