Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024422.1 Corchorus olitorius cultivar O-4 contig24455, 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: 12734
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Found at i:121 original size:27 final size:28
Alignment explanation
Indices: 71--123 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
61 AAATCAATTA
*
71 GAAATCATAAAAACATAAAGATAAATCT
1 GAAATCATAAAAACACAAAGATAAATCT
99 GAAATCATAAAATAC-CAAA-ATAAAT
1 GAAATCATAAAA-ACACAAAGATAAAT
124 AATCAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 15 0.65
29 2 0.09
ACGTcount: A:0.62, C:0.11, G:0.06, T:0.21
Consensus pattern (28 bp):
GAAATCATAAAAACACAAAGATAAATCT
Found at i:578 original size:22 final size:22
Alignment explanation
Indices: 553--594 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
543 ACGTTCCTGA
553 GGGTACCCGAGGCCGGGTAGGG
1 GGGTACCCGAGGCCGGGTAGGG
*
575 GGGTACCCGGGGCCGGGTAG
1 GGGTACCCGAGGCCGGGTAG
595 CCTCAGAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.55, T:0.10
Consensus pattern (22 bp):
GGGTACCCGAGGCCGGGTAGGG
Found at i:1575 original size:2 final size:2
Alignment explanation
Indices: 1570--1594 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1560 ACATATACAA
1570 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1595 AAGTAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2666 original size:40 final size:40
Alignment explanation
Indices: 2586--2668 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 40
2576 TTTCTATCTT
* *
2586 AAAAATCTGGACAGAAAGCATCTTTTGCATTATTAGAAGAA
1 AAAAATCTGGACAGAAAGCATCTTTT-CATAATTAAAAGAA
2627 AAAAATCTGGACAGAAAGCATCGTGTTT-A-AATTAAAAGAA
1 AAAAATCTGGACAGAAAGCATC-T-TTTCATAATTAAAAGAA
2667 AA
1 AA
2669 TTAAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
40 11 0.29
41 23 0.61
42 1 0.03
43 3 0.08
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (40 bp):
AAAAATCTGGACAGAAAGCATCTTTTCATAATTAAAAGAA
Found at i:3563 original size:42 final size:43
Alignment explanation
Indices: 3512--3605 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
3502 AGTGCATTAC
*
3512 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
* *
3553 CTAATATTCTACTCCTCCATCTTTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
3598 CTAATATT
1 CTAATATT
3606 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:5101 original size:15 final size:16
Alignment explanation
Indices: 5068--5105 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
5058 CCAAGCCCTG
5068 AACCCGAAAAACCCAA
1 AACCCGAAAAACCCAA
5084 AACCCGAAAAACCC-A
1 AACCCGAAAAACCCAA
5099 AACCCGA
1 AACCCGA
5106 GGGAAAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.53, C:0.39, G:0.08, T:0.00
Consensus pattern (16 bp):
AACCCGAAAAACCCAA
Found at i:6218 original size:31 final size:31
Alignment explanation
Indices: 6180--6241 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
6170 GAGTTTTGTA
*
6180 AAACTTTTGAATAGTCTATTATACCCTTATT
1 AAACTTTTGAATAGCCTATTATACCCTTATT
*
6211 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATAGCCTATTATACCCTTATT
6242 TTTTGAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (31 bp):
AAACTTTTGAATAGCCTATTATACCCTTATT
Found at i:6411 original size:93 final size:94
Alignment explanation
Indices: 6277--6446 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 94
6267 TTATTTAAAT
* *
6277 TTTTATAGTTTTAGTCAACTAAAAACACTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGATTTACTCAACTAAAAACACTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
6342 -TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTTATTTTTACCATTTTACTATTTTAC
* *
6370 TTTTATAGATTTACTCAACTAAAAA-ATCTGTTTTTATTTAATTAAATCTAATATCCTTATACCT
1 TTTTATAGATTTACTCAACTAAAAACA-CTATTTTTATTTAATTAAATCTAATATCCTTATAACT
6434 ATTTTTATTTTTA
65 ATTTTTATTTTTA
6447 AGATATTACT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
92 1 0.01
93 59 0.83
94 11 0.15
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (94 bp):
TTTTATAGATTTACTCAACTAAAAACACTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTTATTTTTACCATTTTACTATTTTAC
Found at i:7118 original size:17 final size:17
Alignment explanation
Indices: 7096--7130 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
7086 TGGCCTCAGG
7096 TCATTTGGGTTTTGGGT
1 TCATTTGGGTTTTGGGT
7113 TCATTTGGGTTTTGGGT
1 TCATTTGGGTTTTGGGT
7130 T
1 T
7131 TTTCGGCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.34, T:0.54
Consensus pattern (17 bp):
TCATTTGGGTTTTGGGT
Found at i:7961 original size:17 final size:18
Alignment explanation
Indices: 7939--7972 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7929 ATTTTCGACA
*
7939 CATGCT-TTCATTTATTC
1 CATGCTCTTAATTTATTC
7956 CATGCTCTTAATTTATT
1 CATGCTCTTAATTTATT
7973 ATTTATCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (18 bp):
CATGCTCTTAATTTATTC
Found at i:8696 original size:9 final size:9
Alignment explanation
Indices: 8682--8729 Score: 87
Period size: 9 Copynumber: 5.3 Consensus size: 9
8672 GGTGCGGTCA
8682 GTTATGGCG
1 GTTATGGCG
8691 GTTATGGCG
1 GTTATGGCG
8700 GTTATGGCG
1 GTTATGGCG
8709 GTTATGGCG
1 GTTATGGCG
*
8718 GTTATGTCG
1 GTTATGGCG
8727 GTT
1 GTT
8730 TTTCAATTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.10, C:0.10, G:0.42, T:0.38
Consensus pattern (9 bp):
GTTATGGCG
Found at i:9121 original size:14 final size:14
Alignment explanation
Indices: 9102--9149 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
9092 ACCTCCTATC
9102 TATGCACTTGCACA
1 TATGCACTTGCACA
* *
9116 TATGCA-TT-AACC
1 TATGCACTTGCACA
*
9128 TATTCACTTGCACA
1 TATGCACTTGCACA
9142 TATGCACT
1 TATGCACT
9150 AAATATACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 15 0.58
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.33
Consensus pattern (14 bp):
TATGCACTTGCACA
Found at i:11146 original size:28 final size:26
Alignment explanation
Indices: 11106--11177 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 26
11096 ATTTACTTTT
11106 ATTTTGGTCATTTTGCATGACCAAGGGC
1 ATTTTGGTCATTTTGCAT--CCAAGGGC
*
11134 ATTTTGGTCATTTTGTACATCCATGGGC
1 ATTTTGGTCATTTTG--CATCCAAGGGC
*
11162 CTTTTGGTCATTTTGC
1 ATTTTGGTCATTTTGC
11178 TAGGCTAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 1 0.03
28 36 0.90
30 3 0.08
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (26 bp):
ATTTTGGTCATTTTGCATCCAAGGGC
Done.