Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009805.1 Corchorus olitorius cultivar O-4 contig09837, 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: 18778
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1924 original size:2 final size:2
Alignment explanation
Indices: 1917--1944 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1907 TCTAGCTGGA
1917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1945 TATTAAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10499 original size:66 final size:65
Alignment explanation
Indices: 10393--10523 Score: 208
Period size: 66 Copynumber: 2.0 Consensus size: 65
10383 ACTATTAGTT
* * *
10393 AATGATTTGACTTAGAAATTGTTTTGTTTGTAGTAAAACTGGTTAAAAGAGGCACATTAAGAATG
1 AATGATTTGACTTAGAAATTGTTATATTTGTAGTAAAACTGGTT-AAAGAGGCACATCAAGAATG
10458 G
65 G
* *
10459 AATGATTTGATTTAGAAATTGTTATATTTGTAGTAAAACTGGTTAAAGAGGCACATCATGAATGG
1 AATGATTTGACTTAGAAATTGTTATATTTGTAGTAAAACTGGTTAAAGAGGCACATCAAGAATGG
10524 TTAGCTTGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
65 19 0.32
66 41 0.68
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (65 bp):
AATGATTTGACTTAGAAATTGTTATATTTGTAGTAAAACTGGTTAAAGAGGCACATCAAGAATGG
Found at i:10726 original size:51 final size:51
Alignment explanation
Indices: 10664--10766 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
10654 TAATACTCCC
* *
10664 TTTGTTCCATATTATCTATCCCTTTTTGAGATTTTTTTTAATCTCAAATTA
1 TTTGTCCCATATTATCTATCCCTTTTTGAGATTTTTTTTAATCCCAAATTA
* *
10715 TTTGTCCCATATTATCTGTCCCTTTTTTAGATTTTTTTTAATCCCAAATTA
1 TTTGTCCCATATTATCTATCCCTTTTTGAGATTTTTTTTAATCCCAAATTA
10766 T
1 T
10767 CTATCATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.54
Consensus pattern (51 bp):
TTTGTCCCATATTATCTATCCCTTTTTGAGATTTTTTTTAATCCCAAATTA
Found at i:16700 original size:18 final size:18
Alignment explanation
Indices: 16677--16735 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
16667 ATTAAGTCAT
16677 TTTCTTTTTATTCATCAC
1 TTTCTTTTTATTCATCAC
*
16695 TTTC-TTTTA--AATCA-
1 TTTCTTTTTATTCATCAC
*
16709 TTCTCTTTTTATTCATCCC
1 TT-TCTTTTTATTCATCAC
16728 TTTCTTTT
1 TTTCTTTT
16736 AAATCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 2 0.06
15 6 0.18
16 5 0.15
17 5 0.15
18 13 0.39
19 2 0.06
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTCTTTTTATTCATCAC
Found at i:16716 original size:33 final size:33
Alignment explanation
Indices: 16668--16743 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
16658 ATTTTATCCA
* *
16668 TTAAGTCATTTTCTTTTTATTCATCACTTTCTT
1 TTAAATCATTCTCTTTTTATTCATCACTTTCTT
*
16701 TTAAATCATTCTCTTTTTATTCATCCCTTTCTT
1 TTAAATCATTCTCTTTTTATTCATCACTTTCTT
16734 TTAAATCATT
1 TTAAATCATT
16744 TTGTGATTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.21, C:0.20, G:0.01, T:0.58
Consensus pattern (33 bp):
TTAAATCATTCTCTTTTTATTCATCACTTTCTT
Found at i:16742 original size:18 final size:17
Alignment explanation
Indices: 16677--16742 Score: 55
Period size: 18 Copynumber: 3.9 Consensus size: 17
16667 ATTAAGTCAT
* *
16677 TTTCTTTTTATTCATCAC
1 TTTCTTTTAAATCATC-C
16695 TTTCTTTTAAATCAT--
1 TTTCTTTTAAATCATCC
* * *
16710 TCTCTTTTTATTCATCCC
1 TTTCTTTTAAATCAT-CC
16728 TTTCTTTTAAATCAT
1 TTTCTTTTAAATCAT
16743 TTTGTGATTC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
15 12 0.32
18 25 0.68
ACGTcount: A:0.20, C:0.21, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTCTTTTAAATCATCC
Found at i:17031 original size:15 final size:15
Alignment explanation
Indices: 17013--17044 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
17003 ATTAAATTGG
17013 TGACGATTCAATTCA
1 TGACGATTCAATTCA
17028 TGACGATTCAATTCA
1 TGACGATTCAATTCA
17043 TG
1 TG
17045 GTTGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (15 bp):
TGACGATTCAATTCA
Found at i:17421 original size:13 final size:13
Alignment explanation
Indices: 17403--17427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17393 TTAGAATTCC
17403 AAATAATATTTAT
1 AAATAATATTTAT
17416 AAATAATATTTA
1 AAATAATATTTA
17428 GAAGATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:18440 original size:3 final size:3
Alignment explanation
Indices: 18427--18468 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
18417 ATATATATAT
18427 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT- ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA A
18469 GAACGAAGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18750 original size:5 final size:5
Alignment explanation
Indices: 18742--18777 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
18732 AGAAAGCAAG
18742 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
18778 T
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:18750 original size:15 final size:14
Alignment explanation
Indices: 18725--18777 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
18715 TTTTGTCGTT
*
18725 AAAGTAAAGAAAGCA
1 AAAGAAAAGAAAG-A
*
18740 AGAGAAAAGAAAAGA
1 AAAGAAAAG-AAAGA
18755 AAAGAAAAGAAAAGA
1 AAAGAAAAG-AAAGA
18770 AAAGAAAA
1 AAAGAAAA
18778 T
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAAGA
Done.