Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021537.1 Corchorus olitorius cultivar O-4 contig21570, 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: 32280
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:2936 original size:29 final size:29
Alignment explanation
Indices: 2904--2965 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
2894 TATAAGGATA
2904 TTAGATTTAATTA-AATAAAAATAGAGTTT
1 TTAGATTTAATTACAA-AAAAATAGAGTTT
* ** *
2933 TTAGTTTTTTTTACCAAAAAATAGAGTTT
1 TTAGATTTAATTACAAAAAAATAGAGTTT
2962 TTAG
1 TTAG
2966 TTGAGTAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.45
Consensus pattern (29 bp):
TTAGATTTAATTACAAAAAAATAGAGTTT
Found at i:3888 original size:29 final size:30
Alignment explanation
Indices: 3853--3912 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
3843 TATATAAATA
* *
3853 ATATAATATAATTAAATAA-TTATATTTAT
1 ATATAATAAAATTAAATAATTTATATGTAT
*
3882 ATATAATAAAATTGAATAATTTATATGTAT
1 ATATAATAAAATTAAATAATTTATATGTAT
3912 A
1 A
3913 CAGTAATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
ATATAATAAAATTAAATAATTTATATGTAT
Found at i:4040 original size:26 final size:26
Alignment explanation
Indices: 4015--4063 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
4005 TTAATGTTTA
4015 AATT-TTATTTT-TTATTAAAAAATTT
1 AATTATTATTTTATT-TTAAAAAATTT
4040 AATTATTATTTTATTTTAAAAAAT
1 AATTATTATTTTATTTTAAAAAAT
4064 AAATATGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 16 0.73
27 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTATTATTTTATTTTAAAAAATTT
Found at i:6937 original size:25 final size:26
Alignment explanation
Indices: 6884--6939 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
6874 TTTAGACCTC
**
6884 ATAAAAAAATGGAGTAAATTTTTGAA
1 ATAAAAAAATGGAGTAAATTTTAAAA
6910 ATAAAAAAATGGAGT-AA-TTTAAATA
1 ATAAAAAAATGGAGTAAATTTTAAA-A
6935 ATAAA
1 ATAAA
6940 GAAAGACCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 8 0.30
26 15 0.56
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (26 bp):
ATAAAAAAATGGAGTAAATTTTAAAA
Found at i:12487 original size:14 final size:14
Alignment explanation
Indices: 12468--12498 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12458 TTGACAAATC
12468 TCGCTTCTCTCTCG
1 TCGCTTCTCTCTCG
*
12482 TCGCTTCTCTCTTG
1 TCGCTTCTCTCTCG
12496 TCG
1 TCG
12499 AACAGAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.39, G:0.16, T:0.45
Consensus pattern (14 bp):
TCGCTTCTCTCTCG
Found at i:12711 original size:42 final size:42
Alignment explanation
Indices: 12643--12728 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 42
12633 ATTTCCATTC
12643 TCTATTTTCTTCTTCTTCCTCGTTTTAATCGATAAATTTCAA
1 TCTATTTTCTTCTTCTTCCTCGTTTTAATCGATAAATTTCAA
* *
12685 TCTACTTTT-TTCTTCTTCTTCGTTTTAGTCGATAAATTTCAA
1 TCTA-TTTTCTTCTTCTTCCTCGTTTTAATCGATAAATTTCAA
12727 TC
1 TC
12729 AAGACGCCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 37 0.90
43 4 0.10
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.53
Consensus pattern (42 bp):
TCTATTTTCTTCTTCTTCCTCGTTTTAATCGATAAATTTCAA
Found at i:22423 original size:14 final size:14
Alignment explanation
Indices: 22404--22459 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
22394 CATTTAGGGG
22404 TCGTTTTCGTTTTT
1 TCGTTTTCGTTTTT
*
22418 TCGTTTTTTGTTTTT
1 TCG-TTTTCGTTTTT
*
22433 T-GTTTT--TTGTT
1 TCGTTTTCGTTTTT
22444 TCGTTTTCGGTTTTT
1 TCGTTTTC-GTTTTT
22459 T
1 T
22460 TTTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 4 0.12
14 4 0.12
15 16 0.47
ACGTcount: A:0.00, C:0.09, G:0.16, T:0.75
Consensus pattern (14 bp):
TCGTTTTCGTTTTT
Found at i:22431 original size:6 final size:7
Alignment explanation
Indices: 22407--22472 Score: 59
Period size: 7 Copynumber: 9.9 Consensus size: 7
22397 TTAGGGGTCG
*
22407 TTTTCGT
1 TTTTTGT
22414 TTTTTCGT
1 TTTTT-GT
22422 TTTTTGT
1 TTTTTGT
22429 TTTTTGT
1 TTTTTGT
22436 TTTTTG-
1 TTTTTGT
*
22442 -TTTCGT
1 TTTTTGT
**
22448 TTTCGGT
1 TTTTTGT
22455 TTTTT-T
1 TTTTTGT
22461 TTTTT-T
1 TTTTTGT
22467 TTTTTG
1 TTTTTG
22473 CGCTGTCAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
5 4 0.08
6 12 0.24
7 26 0.53
8 7 0.14
ACGTcount: A:0.00, C:0.06, G:0.14, T:0.80
Consensus pattern (7 bp):
TTTTTGT
Found at i:22450 original size:26 final size:26
Alignment explanation
Indices: 22416--22466 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
22406 GTTTTCGTTT
**
22416 TTTCGTTTTTTGTTTTTTGTTTTTTG
1 TTTCGTTTTCGGTTTTTTGTTTTTTG
*
22442 TTTCGTTTTCGGTTTTTTTTTTTTT
1 TTTCGTTTTCGGTTTTTTGTTTTTT
22467 TTTTTGCGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.00, C:0.06, G:0.14, T:0.80
Consensus pattern (26 bp):
TTTCGTTTTCGGTTTTTTGTTTTTTG
Done.