Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015780.1 Corchorus olitorius cultivar O-4 contig15813, 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: 42017
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--32 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33 ATAATGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1842 original size:20 final size:20
Alignment explanation
Indices: 1780--1844 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 20
1770 ATATATATAT
*
1780 ATATATATTATGTTTATTAATA
1 ATATATATTATGTTAATT--TA
* *
1802 ATTTGATATT-TG-TATTATTA
1 ATAT-ATATTATGTTAAT-TTA
1822 ATATATATTATGTTAATTTA
1 ATATATATTATGTTAATTTA
1842 ATA
1 ATA
1845 GTGTTGTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
19 5 0.15
20 13 0.38
21 5 0.15
22 6 0.18
23 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (20 bp):
ATATATATTATGTTAATTTA
Found at i:8503 original size:19 final size:19
Alignment explanation
Indices: 8479--8524 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
8469 GTGAGATTTG
*
8479 GAGATGGTACCTTAAGAGA
1 GAGATGGTACATTAAGAGA
*
8498 GAGATGGTTCATTAAGAGA
1 GAGATGGTACATTAAGAGA
8517 GAGATGGT
1 GAGATGGT
8525 GGTTTAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.24
Consensus pattern (19 bp):
GAGATGGTACATTAAGAGA
Found at i:11748 original size:21 final size:21
Alignment explanation
Indices: 11724--11769 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
11714 CTAAGATGCA
*
11724 TAAAAA-AATAAATCTTAAATC
1 TAAAAACAAGAAAT-TTAAATC
11745 TAAAAACAAGAAATTTAAATC
1 TAAAAACAAGAAATTTAAATC
11766 TAAA
1 TAAA
11770 CCTAAATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAAACAAGAAATTTAAATC
Found at i:18677 original size:19 final size:18
Alignment explanation
Indices: 18639--18678 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
18629 AGAAAACAAT
*
18639 TAATAAGAAAGCAGTGAA
1 TAATAAGAAAGCAATGAA
*
18657 TAATCAAGAAAGCAATTAA
1 TAAT-AAGAAAGCAATGAA
18676 TAA
1 TAA
18679 AAACCTCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.20
Consensus pattern (18 bp):
TAATAAGAAAGCAATGAA
Found at i:33352 original size:2 final size:2
Alignment explanation
Indices: 33345--33374 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33335 TTCCTCACAA
33345 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
33375 ATACCTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:35322 original size:170 final size:170
Alignment explanation
Indices: 35040--35380 Score: 603
Period size: 170 Copynumber: 2.0 Consensus size: 170
35030 GTGCTTGGAA
* * *
35040 CATGTTGTGCACAATTTCCTTGATCTTCATGCTTCTTCTTGCTTCCTTGCACTCCATGCTCATCC
1 CATGTTGTGCACAATCTCCTTGATCTTCATGCTTCTTCATGCTTCATTGCACTCCATGCTCATCC
35105 TCTCCATGATCTCCATTGTCATCTTGATGTCCTTGATAAGCCCTTGGCGCATCAACGA-CTGGTA
66 TCTCCATGATCTCCATTGTCATCTTGATGTCCTTGATAAGCCCTTGGCGCATCAACGATC-GGTA
*
35169 TTAAAGTTTCTGCCACCCCTAATTGCTTGATTATGTGTGCT
130 TTAAAGTTTCTGCCACCCCTAATTGATTGATTATGTGTGCT
* *
35210 CATGTTGTGCGCAATCTCCTTGATCTTCATGCTTCTTCATGCTTTATTGCACTCCATGCTCATCC
1 CATGTTGTGCACAATCTCCTTGATCTTCATGCTTCTTCATGCTTCATTGCACTCCATGCTCATCC
35275 TCTCCATGATCTCCATTGTCATCTTGATGTCCTTGATAAGCCCTTGGCGCATCAACGATCGGTAT
66 TCTCCATGATCTCCATTGTCATCTTGATGTCCTTGATAAGCCCTTGGCGCATCAACGATCGGTAT
*
35340 TAAAGTTTCTGCCACCCCTAATTGATTGATTTTGTGTGCT
131 TAAAGTTTCTGCCACCCCTAATTGATTGATTATGTGTGCT
35380 C
1 C
35381 TGGCAATACG
Statistics
Matches: 163, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
170 162 0.99
171 1 0.01
ACGTcount: A:0.18, C:0.28, G:0.16, T:0.38
Consensus pattern (170 bp):
CATGTTGTGCACAATCTCCTTGATCTTCATGCTTCTTCATGCTTCATTGCACTCCATGCTCATCC
TCTCCATGATCTCCATTGTCATCTTGATGTCCTTGATAAGCCCTTGGCGCATCAACGATCGGTAT
TAAAGTTTCTGCCACCCCTAATTGATTGATTATGTGTGCT
Found at i:38477 original size:2 final size:2
Alignment explanation
Indices: 38470--38503 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38460 AGAAAAGCCA
38470 AT AT AT 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 AT AT AT
38504 CTTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39362 original size:142 final size:142
Alignment explanation
Indices: 39106--39388 Score: 469
Period size: 142 Copynumber: 2.0 Consensus size: 142
39096 GCACATGTGC
* *
39106 AAACATCTTGGCATTTCATATAAGCTGCATTCATCTTAGAATTATCACGCATTTTAAATCACTTG
1 AAACATCATGGCATTTCATATAAGCTGCATTCATCTTAGAATTATCACGCATGTTAAATCACTTG
* * *
39171 ACTTCCCCACCAAAATCATATCATATATTCAAAATTCAGTTCTTGTACACTAAAAATACCAAGAA
66 ACTTCCCCACCAAAATCATATCATACATTCAAAATTCAGTTCATGTACACTAAAAATACCAAAAA
39236 CAGAGCATACAA
131 CAGAGCATACAA
*
39248 AAACATCATGGCATTTCATATAAGCTGCATTCATCTTAGAATTATCACGCATAGTT-AATTACTT
1 AAACATCATGGCATTTCATATAAGCTGCATTCATCTTAGAATTATCACGCAT-GTTAAATCACTT
* * *
39312 GACTTCCCCATCAAAATCATATCATACATTCATAATTCAGTTCATGTACACTCAAAATACCAAAA
65 GACTTCCCCACCAAAATCATATCATACATTCAAAATTCAGTTCATGTACACTAAAAATACCAAAA
39377 ACAGAGCATACA
130 ACAGAGCATACA
39389 CACATATAGT
Statistics
Matches: 131, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
142 129 0.98
143 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (142 bp):
AAACATCATGGCATTTCATATAAGCTGCATTCATCTTAGAATTATCACGCATGTTAAATCACTTG
ACTTCCCCACCAAAATCATATCATACATTCAAAATTCAGTTCATGTACACTAAAAATACCAAAAA
CAGAGCATACAA
Found at i:41929 original size:2 final size:2
Alignment explanation
Indices: 41922--42017 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
41912 TAAAATTAAA
41922 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41964 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
42006 AG AG AG AG AG AG
1 AG AG AG AG AG AG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.