Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016411.1 Corchorus capsularis cultivar CVL-1 contig16432, 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: 12146
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Found at i:1314 original size:19 final size:19
Alignment explanation
Indices: 1290--1329 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1280 CTCTTCTCCT
1290 CCACCGTCACCGCTGTCTG
1 CCACCGTCACCGCTGTCTG
1309 CCACCGTCACCGCTGTCTG
1 CCACCGTCACCGCTGTCTG
1328 CC
1 CC
1330 TCCGACGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.50, G:0.20, T:0.20
Consensus pattern (19 bp):
CCACCGTCACCGCTGTCTG
Found at i:1707 original size:18 final size:17
Alignment explanation
Indices: 1683--1723 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1673 TTTATACTTC
1683 CTTGTTTTATGCCATTT
1 CTTGTTTTATGCCATTT
*
1700 CTT-TGTTTATGCCCTTT
1 CTTGT-TTTATGCCATTT
1717 CTTGTTT
1 CTTGTTT
1724 CTTCTGCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.07, C:0.20, G:0.12, T:0.61
Consensus pattern (17 bp):
CTTGTTTTATGCCATTT
Found at i:5370 original size:14 final size:14
Alignment explanation
Indices: 5321--5377 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
5311 TGCTTTTAAT
5321 TTGCTGTTTTGAAG
1 TTGCTGTTTTGAAG
*
5335 TTCCTGTTTTGAAG
1 TTGCTGTTTTGAAG
* * *
5349 TTGTTGTTTTGTAC
1 TTGCTGTTTTGAAG
5363 TTGCTGTTTTTGAAG
1 TTGCTG-TTTTGAAG
5378 GAAAAATGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
14 28 0.82
15 6 0.18
ACGTcount: A:0.12, C:0.09, G:0.25, T:0.54
Consensus pattern (14 bp):
TTGCTGTTTTGAAG
Found at i:5460 original size:21 final size:21
Alignment explanation
Indices: 5414--5469 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
5404 CTGTATGTAC
* *
5414 TTTCTGTTTTTGAGTAATTGCG
1 TTTCTGTTTTT-AGTGATTGAG
*
5436 -TTCTGTTTTTAGTGCTTGAG
1 TTTCTGTTTTTAGTGATTGAG
*
5456 TTTCTG-ATTTAGTG
1 TTTCTGTTTTTAGTG
5470 TTTTTGCTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.12, C:0.09, G:0.23, T:0.55
Consensus pattern (21 bp):
TTTCTGTTTTTAGTGATTGAG
Found at i:6784 original size:31 final size:31
Alignment explanation
Indices: 6730--6887 Score: 127
Period size: 31 Copynumber: 5.4 Consensus size: 31
6720 TTTTGTGCAC
* * * * **
6730 GTGGCATGCTACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCACATGTCACTTTTTGGTACAT
*
6761 GTGGCATGCCACATGTCACTTTTTGGTACAC
1 GTGGCATGCCACATGTCACTTTTTGGTACAT
* * ** *
6792 GTGGCGTGACATGTGTCACTTTTTGATACAT
1 GTGGCATGCCACATGTCACTTTTTGGTACAT
6823 GT-G---G-CAC--G--ACTTTTTGGTACAT
1 GTGGCATGCCACATGTCACTTTTTGGTACAT
* *
6845 GTGGCGTGCCACATGTCACTTTTTGGTACAC
1 GTGGCATGCCACATGTCACTTTTTGGTACAT
6876 GTGGCATGCCAC
1 GTGGCATGCCAC
6888 GTCAGACACC
Statistics
Matches: 101, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
22 15 0.15
23 1 0.01
24 1 0.01
26 3 0.03
27 4 0.04
29 1 0.01
30 1 0.01
31 75 0.74
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCACATGTCACTTTTTGGTACAT
Found at i:6836 original size:53 final size:53
Alignment explanation
Indices: 6778--6881 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 53
6768 GCCACATGTC
** *
6778 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGATACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGATACACGTGGCACG
* * *
6831 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCA
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGATACACGTGGCA
6882 TGCCACGTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGATACACGTGGCACG
Found at i:10715 original size:22 final size:20
Alignment explanation
Indices: 10689--10746 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 20
10679 TATTTGTTCT
10689 ATTGAACGGCTCAATATTCA
1 ATTGAACGGCTCAATATTCA
* *
10709 AGTTTGAATGGCTCAATATTCT
1 A--TTGAACGGCTCAATATTCA
10731 ATTGAACGGCTCAATA
1 ATTGAACGGCTCAATA
10747 GAACTATTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.45
22 18 0.55
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (20 bp):
ATTGAACGGCTCAATATTCA
Found at i:10741 original size:20 final size:20
Alignment explanation
Indices: 10685--10746 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
10675 AAACTATTTG
10685 TTCTATTGAACGGCTCAATA
1 TTCTATTGAACGGCTCAATA
* *
10705 TTCAAGTTTGAATGGCTCAATA
1 TTCTA--TTGAACGGCTCAATA
10727 TTCTATTGAACGGCTCAATA
1 TTCTATTGAACGGCTCAATA
10747 GAACTATTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 18 0.50
22 18 0.50
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (20 bp):
TTCTATTGAACGGCTCAATA
Found at i:11080 original size:356 final size:356
Alignment explanation
Indices: 10421--11080 Score: 1178
Period size: 356 Copynumber: 1.9 Consensus size: 356
10411 TAATTCTTTC
*
10421 TTCAAACACAACATATTAATAATCGATTTTGACATATAAATCGACTCCAACTTATCCATCAACTC
1 TTCAAACACAACATATTAATAATCGATTTTGACATATAAATCAACTCCAACTTATCCATCAACTC
*
10486 TTTTGGAGTTTTCACATCTAACACATCGTATTTAATTTCAGTAGCGAGAGACAAACGAATTATAC
66 TTTTGGAGTTTTCACATCTAACACATCATATTTAATTTCAGTAGCGAGAGACAAACGAATTATAC
* *
10551 TTACTTCTTTTCGTTGAATATCTCTCCAGTTGTTCTCATTCACAGCTACAGGCTTATCAGTTTCA
131 TTACTTCTTTTCGTTCAATATCTCTCCAATTGTTCTCATTCACAGCTACAGGCTTATCAGTTTCA
*
10616 AACGCATCTCCCAATCCTTGTTGTACTAATACATATGTTATCTTACTCTGCCACATCTGAAACTA
196 AACGCATCTCCCAATCCTTGTTGTACTAATACATATGTTATCGTACTCTGCCACATCTGAAACTA
** * *
10681 TTTGTTCTATTGAACGGCTCAATATTCAAGTTTGAATGGCTCAATATTCTATTGAACGGCTCAAT
261 TCCGTTCTATTGAACGACTCAATATTCAAGTTTGAACGGCTCAATATTCTATTGAACGGCTCAAT
10746 AGAACTATTCGTTCTATTGAACGGCTCAATA
326 AGAACTATTCGTTCTATTGAACGGCTCAATA
*
10777 TTCAAACACAACATATTAATAATCGATTTTGACATATAAATCAACTCCAACTTATCTATCAACTC
1 TTCAAACACAACATATTAATAATCGATTTTGACATATAAATCAACTCCAACTTATCCATCAACTC
* *
10842 TTTTGGGGTTTTCACATCTAACACATCATATTTAATTTTAGTAGCGAGAGACAAACGAATTATAC
66 TTTTGGAGTTTTCACATCTAACACATCATATTTAATTTCAGTAGCGAGAGACAAACGAATTATAC
*
10907 TTACTTCTTTTCGTTCAATATCTCTCCAATTGTTCTCATTCAGC-GCTGCAGGCTTATCAGTTTC
131 TTACTTCTTTTCGTTCAATATCTCTCCAATTGTTCTCATTCA-CAGCTACAGGCTTATCAGTTTC
*
10971 AAACGCATCTCCCAATCCTTGTTGTACTAATACATATGTTATCGTACTCTGCCACATTTGAAACT
195 AAACGCATCTCCCAATCCTTGTTGTACTAATACATATGTTATCGTACTCTGCCACATCTGAAACT
11036 ATCCGTTCTATTGAACGACTCAATATTCAAGTTTGAACGGCTCAA
260 ATCCGTTCTATTGAACGACTCAATATTCAAGTTTGAACGGCTCAA
11081 ACTTCAAAGC
Statistics
Matches: 289, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
356 288 1.00
357 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (356 bp):
TTCAAACACAACATATTAATAATCGATTTTGACATATAAATCAACTCCAACTTATCCATCAACTC
TTTTGGAGTTTTCACATCTAACACATCATATTTAATTTCAGTAGCGAGAGACAAACGAATTATAC
TTACTTCTTTTCGTTCAATATCTCTCCAATTGTTCTCATTCACAGCTACAGGCTTATCAGTTTCA
AACGCATCTCCCAATCCTTGTTGTACTAATACATATGTTATCGTACTCTGCCACATCTGAAACTA
TCCGTTCTATTGAACGACTCAATATTCAAGTTTGAACGGCTCAATATTCTATTGAACGGCTCAAT
AGAACTATTCGTTCTATTGAACGGCTCAATA
Done.