Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017528.1 Corchorus olitorius cultivar O-4 contig17561, 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: 50652
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:8260 original size:151 final size:151
Alignment explanation
Indices: 7979--8265 Score: 468
Period size: 151 Copynumber: 1.9 Consensus size: 151
7969 GATCAACTTG
* *
7979 TTTATATTAATTATAATGTGAAATCCTGAATTTGTGTCACGAGTTGACTTAGTGACAAACTCAGT
1 TTTATACTAATTATAATGTGAAATCCTGAATTTGTGTCACGAGTTGACTCAGTGACAAACTCAGT
*
8044 TTTAAAAAAATTGAAAACAAAATTAAAACTATCCATTTTAAATAAAACTACCCATTGCAGAATAA
66 TTTAAAAAAATTGAAAACAAAATAAAAACTATCCATTTTAAATAAAACTACCCATTGCAGAATAA
8109 ATATAAGGATAAATATAATAA
131 ATATAAGGATAAATATAATAA
* * * *
8130 TTTATACTAATTATAATGTGAAGTCCTGAGTTTGTGTCATGAGTTGACTCGGTGACAAACTCAGT
1 TTTATACTAATTATAATGTGAAATCCTGAATTTGTGTCACGAGTTGACTCAGTGACAAACTCAGT
* * *
8195 TTTAAAAAAATTGAAAACAAAATAAAAACTA-CACATTTTAAATAATACTACCCATTGGAGTATA
66 TTTAAAAAAATTGAAAACAAAATAAAAACTATC-CATTTTAAATAAAACTACCCATTGCAGAATA
8259 AATATAA
130 AATATAA
8266 TAATTACAAG
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
150 1 0.01
151 124 0.99
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (151 bp):
TTTATACTAATTATAATGTGAAATCCTGAATTTGTGTCACGAGTTGACTCAGTGACAAACTCAGT
TTTAAAAAAATTGAAAACAAAATAAAAACTATCCATTTTAAATAAAACTACCCATTGCAGAATAA
ATATAAGGATAAATATAATAA
Found at i:8522 original size:42 final size:44
Alignment explanation
Indices: 8471--8564 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
8461 AGTGCATTAT
*
8471 CTAA-ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
*
8512 CTGATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCT-CATCTCTAGATAATTCATCAAAATAAAG
8557 CTAATATT
1 CTAATATT
8565 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 8 0.17
43 2 0.04
45 33 0.72
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
Found at i:11989 original size:18 final size:17
Alignment explanation
Indices: 11964--12005 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
11954 ACTTATAATA
11964 AATCTTGGTTTGATACT
1 AATCTTGGTTTGATACT
*
11981 AACTCTTGGTTTGATAGT
1 AA-TCTTGGTTTGATACT
11999 AATCTTG
1 AATCTTG
12006 TTGAATTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (17 bp):
AATCTTGGTTTGATACT
Found at i:14367 original size:2 final size:2
Alignment explanation
Indices: 14360--14556 Score: 394
Period size: 2 Copynumber: 98.5 Consensus size: 2
14350 CACAATTTAA
14360 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
14402 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
14444 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
14486 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
14528 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
14557 TAAAACCTGA
Statistics
Matches: 195, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 195 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:17661 original size:40 final size:39
Alignment explanation
Indices: 17599--17677 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 39
17589 ATCAGAACAG
* *
17599 GTATGCAATATTCCTATTAACTACCAGCAAGCAAAACCAA
1 GTATGCAATATTCATATAAACTACCAGCAAGC-AAACCAA
*
17639 GTATGCAATATTCATCTAAACTACCAGCAAGCAAACCAA
1 GTATGCAATATTCATATAAACTACCAGCAAGCAAACCAA
17678 TAACATTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 7 0.19
40 29 0.81
ACGTcount: A:0.43, C:0.25, G:0.10, T:0.22
Consensus pattern (39 bp):
GTATGCAATATTCATATAAACTACCAGCAAGCAAACCAA
Found at i:18987 original size:2 final size:2
Alignment explanation
Indices: 18980--19022 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
18970 CGGCCATTAC
18980 AT AT AT AT 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 AT AT AT AT
19022 A
1 A
19023 ACTAATTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23611 original size:18 final size:18
Alignment explanation
Indices: 23588--23633 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
23578 TATCATTTTA
*
23588 AAAAAAAACTACCTATTT
1 AAAAAAAACTACCCATTT
*
23606 AAAAAAAACTTCCCATTT
1 AAAAAAAACTACCCATTT
*
23624 AGAAAAAACT
1 AAAAAAAACT
23634 GCCACAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAAAAACTACCCATTT
Found at i:25274 original size:8 final size:8
Alignment explanation
Indices: 25261--25291 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
25251 CACATGCAGC
25261 AAAAAAAT
1 AAAAAAAT
25269 AAAAAAAT
1 AAAAAAAT
*
25277 AAAAAGAT
1 AAAAAAAT
25285 AAAAAAA
1 AAAAAAA
25292 AACAACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:27825 original size:11 final size:11
Alignment explanation
Indices: 27809--27847 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
27799 ACTAAAAATA
27809 ATATATAGTAT
1 ATATATAGTAT
27820 ATATATAGTAT
1 ATATATAGTAT
27831 AGTAT-TA-TAT
1 A-TATATAGTAT
27841 ATATATA
1 ATATATA
27848 TTTTTGGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.12
10 6 0.23
11 14 0.54
12 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
ATATATAGTAT
Found at i:28330 original size:41 final size:41
Alignment explanation
Indices: 28273--28353 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
28263 AGGAAATGGG
28273 AGGAAAGGGGCATCCCTTCACTTGTTTGGATTAGATTTTTT
1 AGGAAAGGGGCATCCCTTCACTTGTTTGGATTAGATTTTTT
*
28314 AGGAAAGGGGCATCCCTTCATTTGTTTGGATTAGATTTTT
1 AGGAAAGGGGCATCCCTTCACTTGTTTGGATTAGATTTTT
28354 AATTTTTAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.40
Consensus pattern (41 bp):
AGGAAAGGGGCATCCCTTCACTTGTTTGGATTAGATTTTTT
Found at i:32871 original size:12 final size:12
Alignment explanation
Indices: 32851--32886 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
32841 AACATGTTAA
32851 TTTTCTTTTTAG
1 TTTTCTTTTTAG
* *
32863 TTTTGTTTTTAT
1 TTTTCTTTTTAG
32875 TTTTCTTTTTAG
1 TTTTCTTTTTAG
32887 GATTTCAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.08, C:0.06, G:0.08, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTTAG
Found at i:36340 original size:20 final size:21
Alignment explanation
Indices: 36304--36350 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
36294 TAGATTTAGA
*
36304 TTTAATTTAATTTGCTTTGTT
1 TTTAATTTAATTTGCTTTCTT
*
36325 TTTAGTTTAA-TTGCTTTC-T
1 TTTAATTTAATTTGCTTTCTT
36344 TTTAATT
1 TTTAATT
36351 GTTATTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 7 0.30
21 9 0.39
ACGTcount: A:0.19, C:0.06, G:0.09, T:0.66
Consensus pattern (21 bp):
TTTAATTTAATTTGCTTTCTT
Found at i:37540 original size:30 final size:30
Alignment explanation
Indices: 37500--37561 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
37490 AAAGAGAGTT
* *
37500 TCTTTCAAAGGCTATGTATCCCGGATCAAA
1 TCTTTAAAAGGCTATGGATCCCGGATCAAA
37530 TCTTTAAAAGGCTATGGATCCCGGATCAAA
1 TCTTTAAAAGGCTATGGATCCCGGATCAAA
37560 TC
1 TC
37562 AACAATTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (30 bp):
TCTTTAAAAGGCTATGGATCCCGGATCAAA
Found at i:40741 original size:11 final size:11
Alignment explanation
Indices: 40725--40749 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40715 AGAAAATTGT
40725 TTGTTTTTGGA
1 TTGTTTTTGGA
40736 TTGTTTTTGGA
1 TTGTTTTTGGA
40747 TTG
1 TTG
40750 ATTATTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Found at i:43798 original size:2 final size:2
Alignment explanation
Indices: 43791--43834 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
43781 CGTGTTCGTC
43791 TA TA TA TA TA 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 TA TA TA TA TA
43833 TA
1 TA
43835 GCAAGATAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46325 original size:26 final size:27
Alignment explanation
Indices: 46259--46332 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 27
46249 TAAGGTCATT
*
46259 CAGGGCATTTTGGTCATTTTTCAATTA
1 CAGGGCATTTTGGTCATTTTTCAACTA
46286 CAGGGGCATTTTGGTCATTTTT-ACACTA
1 CA-GGGCATTTTGGTCATTTTTCA-ACTA
46314 -AGGGCATTTTGGTCATTTT
1 CAGGGCATTTTGGTCATTTT
46333 AAGCTCACTT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 18 0.41
27 4 0.09
28 22 0.50
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (27 bp):
CAGGGCATTTTGGTCATTTTTCAACTA
Done.