Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014098.1 Corchorus olitorius cultivar O-4 contig14131, 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: 48412
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1771 original size:10 final size:11
Alignment explanation
Indices: 1747--1777 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
1737 ACGGTCATAA
1747 TTTTACAAAGT
1 TTTTACAAAGT
1758 TTTTACAAAG-
1 TTTTACAAAGT
1768 TTTTACAAAG
1 TTTTACAAAG
1778 ACGGAGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (11 bp):
TTTTACAAAGT
Found at i:2194 original size:49 final size:50
Alignment explanation
Indices: 2093--2226 Score: 143
Period size: 49 Copynumber: 2.7 Consensus size: 50
2083 CGTGTCAAAT
* *
2093 AATTTTGTCA-AAAAATTGATAAAAA-GTGCAATAAAAAGTAAATGATCA
1 AATTTTGTCATAAAAATTGAGAAAAAGGTGCAAGAAAAAGTAAATGATCA
* *
2141 AA-TTTGTCATAAAAATTTGAGAAAAAGGTGCAAGGAAAATTAAA-GATTC-
1 AATTTTGTCATAAAAA-TTGAGAAAAAGGTGCAAGAAAAAGTAAATGA-TCA
** * *
2190 AATTTTGTTGTAAAAATTGAGAAAAAGATGCATGAAA
1 AATTTTGTCATAAAAATTGAGAAAAAGGTGCAAGAAA
2227 TGTAAAATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
47 7 0.10
48 7 0.10
49 31 0.43
50 27 0.38
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (50 bp):
AATTTTGTCATAAAAATTGAGAAAAAGGTGCAAGAAAAAGTAAATGATCA
Found at i:4416 original size:22 final size:22
Alignment explanation
Indices: 4388--4430 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4378 GCAGCCATGT
*
4388 TTCGACCCTGTCAG-AGGTCGAG
1 TTCGACCC-GACAGAAGGTCGAG
4410 TTCGACCCGACAGAAGGTCGA
1 TTCGACCCGACAGAAGGTCGA
4431 AAAGTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (22 bp):
TTCGACCCGACAGAAGGTCGAG
Found at i:8657 original size:29 final size:28
Alignment explanation
Indices: 8560--8666 Score: 106
Period size: 29 Copynumber: 3.8 Consensus size: 28
8550 AGGATCACCT
* * *
8560 AGGGGCATTTTGGTTATTTTTAAAAACCC
1 AGGGGCATTTTGGTCA-TTTTACAAATCC
* * * *
8589 AGGGGTATTTTGGTCATTTTTCACATTC
1 AGGGGCATTTTGGTCATTTTACAAATCC
* *
8617 AGGGGCATTTTGGTCATTTCTGCATATCC
1 AGGGGCATTTTGGTCATTT-TACAAATCC
*
8646 AGGGGCATTTTGATCATTTTA
1 AGGGGCATTTTGGTCATTTTA
8667 AGTTCATTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
28 26 0.41
29 38 0.59
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.41
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTACAAATCC
Found at i:23925 original size:50 final size:47
Alignment explanation
Indices: 23822--23946 Score: 137
Period size: 50 Copynumber: 2.6 Consensus size: 47
23812 GAGCGTGCCA
* *
23822 ATCAATTTTGTC-AAAAATTGATAAAAAGTGCAATAAAAAGTAAATG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGAAAAAGTAAATG
* * *
23868 ATCAATTTTGTCATAAAAATTTGAGAAAACGGTGCAAGGAAAATTAAA-G
1 ATCAATTTTGTC-TAAAAA-TTGAGAAAA-AGTGCAAGAAAAAGTAAATG
*
23917 ATTCAATTTTGTTGTAAAAATTGAGAAAAA
1 A-TCAATTTTG-TCTAAAAATTGAGAAAAA
23947 AAGGTGCATG
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
46 12 0.18
48 5 0.08
49 19 0.29
50 29 0.44
51 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.30
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGAAAAAGTAAATG
Found at i:26205 original size:49 final size:49
Alignment explanation
Indices: 26133--26229 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
26123 ATAATTGGCA
26133 CCTACATCACACGTAACATGTGCCAAATTATGAGCCAATTTATTTGCTT
1 CCTACATCACACGTAACATGTGCCAAATTATGAGCCAATTTATTTGCTT
26182 CCTACATCACACGTAACATGTGCCAAATTATGAGCCAATTTATTTGCT
1 CCTACATCACACGTAACATGTGCCAAATTATGAGCCAATTTATTTGCT
26230 ACTCTATGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (49 bp):
CCTACATCACACGTAACATGTGCCAAATTATGAGCCAATTTATTTGCTT
Found at i:32175 original size:3 final size:3
Alignment explanation
Indices: 32167--32229 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
32157 CTAGAACCAC
*
32167 TAT TAT TAT TAT TAT TAT TAT TAC TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
32214 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
32230 TGTTCTAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:32803 original size:41 final size:41
Alignment explanation
Indices: 32745--32823 Score: 142
Period size: 41 Copynumber: 1.9 Consensus size: 41
32735 TGCTGACACT
32745 AGAAGTTGTCATCTTGGTAAATTAAAATTACCTTTGACGCC
1 AGAAGTTGTCATCTTGGTAAATTAAAATTACCTTTGACGCC
32786 AGAAGTTGTCA-CTTTGGTAAATTAAAATTACCTTTGAC
1 AGAAGTTGTCATC-TTGGTAAATTAAAATTACCTTTGAC
32824 ACCGTAAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (41 bp):
AGAAGTTGTCATCTTGGTAAATTAAAATTACCTTTGACGCC
Found at i:35043 original size:25 final size:25
Alignment explanation
Indices: 35015--35071 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
35005 GATCTAAAGG
35015 AAAAAAAAAGTTTTGGCAGACGGAA
1 AAAAAAAAAGTTTTGGCAGACGGAA
35040 AAAAAAAAAGTTTTGGCAGACGGAA
1 AAAAAAAAAGTTTTGGCAGACGGAA
35065 AAAAAAA
1 AAAAAAA
35072 GGAAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.58, C:0.07, G:0.21, T:0.14
Consensus pattern (25 bp):
AAAAAAAAAGTTTTGGCAGACGGAA
Found at i:36063 original size:13 final size:13
Alignment explanation
Indices: 36045--36077 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
36035 ATAATTTGAT
36045 TTTGCATTCATCA
1 TTTGCATTCATCA
36058 TTTGCATTCATCA
1 TTTGCATTCATCA
36071 TTTGCAT
1 TTTGCAT
36078 ACATGCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.48
Consensus pattern (13 bp):
TTTGCATTCATCA
Found at i:43371 original size:3 final size:3
Alignment explanation
Indices: 43331--43356 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43321 GTTTTGTAAC
43331 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
43357 ATACTACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:43644 original size:56 final size:56
Alignment explanation
Indices: 43547--43658 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 56
43537 TTCGTTTCCC
* * *
43547 TTCACACAATAAATGTTGTAATAAATCATATCCCTCTATCTCTACTTAATTATTCT
1 TTCACACAATAAATATTATAATAAATCATATCCCTCCATCTCTACTTAATTATTCT
*
43603 TTCACACAATAAATATTATAATAAATCTTATTCCC-CCATCTCTACTTAATTATTCT
1 TTCACACAATAAATATTATAATAAATCATA-TCCCTCCATCTCTACTTAATTATTCT
43659 ACAAAATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 47 0.92
57 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (56 bp):
TTCACACAATAAATATTATAATAAATCATATCCCTCCATCTCTACTTAATTATTCT
Found at i:43675 original size:56 final size:55
Alignment explanation
Indices: 43546--43670 Score: 157
Period size: 56 Copynumber: 2.3 Consensus size: 55
43536 ATTCGTTTCC
* * * *
43546 CTTCACACAATAAATGTTGTAATAAATCATATCCCTCTATCTCTACTTAATTATT
1 CTTCACAAAATAAATATTATAATAAATCATATCCCTCCATCTCTACTTAATTATT
* *
43601 CTTTCACACAATAAATATTATAATAAATCTTATTCCC-CCATCTCTACTTAATTATT
1 C-TTCACAAAATAAATATTATAATAAATCATA-TCCCTCCATCTCTACTTAATTATT
43657 C-T-ACAAAATAAATA
1 CTTCACAAAATAAATA
43671 ATATTTTCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
53 11 0.17
54 1 0.02
55 1 0.02
56 46 0.73
57 4 0.06
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (55 bp):
CTTCACAAAATAAATATTATAATAAATCATATCCCTCCATCTCTACTTAATTATT
Found at i:43784 original size:42 final size:42
Alignment explanation
Indices: 43724--43804 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
43714 TAAGGATCGG
43724 GATTTGAGTTGAGCATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGCATTTCTTAATTTACAAAGAATTTTCTAT
* *
43766 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGCATTTCTTAATTTACAAAGAATTTTC
43805 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.46
Consensus pattern (42 bp):
GATTTGAGTTGAGCATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:44527 original size:3 final size:3
Alignment explanation
Indices: 44519--44570 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
44509 GCCGATACAC
44519 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44567 TTA T
1 TTA T
44571 GTGTGTATGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:47504 original size:15 final size:16
Alignment explanation
Indices: 47479--47508 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47469 AATTTGCTAA
47479 AATTCATTATATGAAC
1 AATTCATTATATGAAC
47495 AATT-ATTATATGAA
1 AATTCATTATATGAA
47509 TAAATACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
AATTCATTATATGAAC
Done.