Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013907.1 Corchorus capsularis cultivar CVL-1 contig13928, 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: 22940
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:72 original size:48 final size:48
Alignment explanation
Indices: 1--223 Score: 276
Period size: 48 Copynumber: 4.7 Consensus size: 48
* **
1 CTCTTCAACCCAAGTTGGTCTTTCCTCACTTCCATGTGAGTCAGAAAT
1 CTCTTCGACCCAAGTTGGTCTTTCCTCACTTCCACATGAGTCAGAAAT
* *
49 CTCTTCGACCCAGGTTGGTCTTTCCTCACTTCCGCGA-GAGTCAGAAAT
1 CTCTTCGACCCAAGTTGGTCTTTCCTCACTTCCAC-ATGAGTCAGAAAT
* * *
97 CTTTTCGACCCAGGTTGGTTTTTCCTCACTTCCACATGAGTCAGAAAT
1 CTCTTCGACCCAAGTTGGTCTTTCCTCACTTCCACATGAGTCAGAAAT
* * *
145 CTCTTCGACCCAACTTGGTCTTTCCTCACTT-C-TAT--GTCAGCAAT
1 CTCTTCGACCCAAGTTGGTCTTTCCTCACTTCCACATGAGTCAGAAAT
* * *
189 CTCTTCGACCAAAGTTCGTCTTTCCTCGCTTCCAC
1 CTCTTCGACCCAAGTTGGTCTTTCCTCACTTCCAC
224 GAGAGTCCCA
Statistics
Matches: 152, Mismatches: 19, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
44 35 0.23
45 1 0.01
46 2 0.01
47 2 0.01
48 112 0.74
ACGTcount: A:0.19, C:0.32, G:0.15, T:0.34
Consensus pattern (48 bp):
CTCTTCGACCCAAGTTGGTCTTTCCTCACTTCCACATGAGTCAGAAAT
Found at i:1107 original size:10 final size:12
Alignment explanation
Indices: 1068--1113 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
1058 TCCCATGTGA
1068 TGGCCGGTCATG
1 TGGCCGGTCATG
1080 TGGCCGGTCATG
1 TGGCCGGTCATG
1092 TGGCCGGTC-T-
1 TGGCCGGTCATG
1102 TGGCCGGTCATG
1 TGGCCGGTCATG
1114 GTTCCATGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.28
11 2 0.06
12 21 0.66
ACGTcount: A:0.07, C:0.26, G:0.41, T:0.26
Consensus pattern (12 bp):
TGGCCGGTCATG
Found at i:1108 original size:22 final size:24
Alignment explanation
Indices: 1068--1113 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
1058 TCCCATGTGA
1068 TGGCCGGTCATGTGGCCGGTCATG
1 TGGCCGGTCATGTGGCCGGTCATG
1092 TGGCCGGTC-T-TGGCCGGTCATG
1 TGGCCGGTCATGTGGCCGGTCATG
1114 GTTCCATGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 12 0.55
23 1 0.05
24 9 0.41
ACGTcount: A:0.07, C:0.26, G:0.41, T:0.26
Consensus pattern (24 bp):
TGGCCGGTCATGTGGCCGGTCATG
Found at i:1167 original size:21 final size:21
Alignment explanation
Indices: 1116--1170 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1106 CGGTCATGGT
**
1116 TCCATGCGATGGCGCGGCTAC
1 TCCATGCTTTGGCGCGGCTAC
* *
1137 TCCATACTTTGGCGCGGCTTC
1 TCCATGCTTTGGCGCGGCTAC
1158 TCCATGCTTTGGC
1 TCCATGCTTTGGC
1171 CGGTCATATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.11, C:0.33, G:0.27, T:0.29
Consensus pattern (21 bp):
TCCATGCTTTGGCGCGGCTAC
Found at i:12168 original size:201 final size:201
Alignment explanation
Indices: 11810--12209 Score: 739
Period size: 201 Copynumber: 2.0 Consensus size: 201
11800 GGTTGAACTG
*
11810 GAAATCGAGGTCCAGATCGGTATCGGTATATATAAAATATTGAAAGTCAATGAATTGGTGTTGAT
1 GAAATCGAGGTCCAGATCGGTATCGGTATATATAAAATATTGAAAGTCAATGAATCGGTGTTGAT
* * *
11875 CCGGTTCAATCGTGGTTGAACTGGCTGGTTTATCGGTTTTTTGATTGGTTTGGAATTTGGTCAAC
66 CCGGTTCAATCGTGGTTGAACCGGCCGGTTTATCGGTTTTTTGATCGGTTTGGAATTTGGTCAAC
*
11940 TTTTTCAATTTTGAAAAATTTAAAAAAAACAATTGCAAATGGTAAGAATCGAATCCCACACACTT
131 TTTTTCAATTTTGAAAAATTAAAAAAAAACAATTGCAAATGGTAAGAATCGAATCCCACACACTT
12005 TGAATA
196 TGAATA
*
12011 GAAATCGAGGTCCAGTTCGGTATCGGTATATATAAAATATTGAAAGTCAATGAATCGGTGTTGAT
1 GAAATCGAGGTCCAGATCGGTATCGGTATATATAAAATATTGAAAGTCAATGAATCGGTGTTGAT
12076 CCGGTTCAATCGTGGTTGAACCGGCCGGTTTATCGGTTTTTT-ATCGGTTTGGAATTTGGTCAAC
66 CCGGTTCAATCGTGGTTGAACCGGCCGGTTTATCGGTTTTTTGATCGGTTTGGAATTTGGTCAAC
12140 TTTTTCAATTTTGAAAAATTAAAAAAAAACAATTGCAAATGGTAAGAATCGAATCCCACACACTT
131 TTTTTCAATTTTGAAAAATTAAAAAAAAACAATTGCAAATGGTAAGAATCGAATCCCACACACTT
12205 TGAAT
196 TGAAT
12210 GAAGACAAAA
Statistics
Matches: 193, Mismatches: 6, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
200 90 0.47
201 103 0.53
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.34
Consensus pattern (201 bp):
GAAATCGAGGTCCAGATCGGTATCGGTATATATAAAATATTGAAAGTCAATGAATCGGTGTTGAT
CCGGTTCAATCGTGGTTGAACCGGCCGGTTTATCGGTTTTTTGATCGGTTTGGAATTTGGTCAAC
TTTTTCAATTTTGAAAAATTAAAAAAAAACAATTGCAAATGGTAAGAATCGAATCCCACACACTT
TGAATA
Found at i:12674 original size:23 final size:23
Alignment explanation
Indices: 12644--12690 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
12634 TAACTACAAA
12644 CTAGTTCATAGACTTAAAATTCC
1 CTAGTTCATAGACTTAAAATTCC
12667 CTAGTTCATAGACTTAAAATTCC
1 CTAGTTCATAGACTTAAAATTCC
12690 C
1 C
12691 AGATGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (23 bp):
CTAGTTCATAGACTTAAAATTCC
Found at i:13751 original size:2 final size:2
Alignment explanation
Indices: 13746--13791 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
13736 CCCCGTACAA
*
13746 AT AT AT AGT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13789 AT A
1 AT A
13792 ATGCTCTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 40 0.98
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17120 original size:12 final size:12
Alignment explanation
Indices: 17105--17129 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17095 ACCTGGCAAT
17105 TCGTGTTTCGTG
1 TCGTGTTTCGTG
17117 TCGTGTTTCGTG
1 TCGTGTTTCGTG
17129 T
1 T
17130 ATAATTTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:21177 original size:33 final size:33
Alignment explanation
Indices: 21098--21235 Score: 127
Period size: 33 Copynumber: 4.2 Consensus size: 33
21088 TTGCAAAGAG
* *
21098 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAGATGTTGTTTGCGATGAAACTAAATC
** *
21131 TAATTT-GACTGTTGTTTGCGATGACACTAAATC
1 TGTTTTAGA-TGTTGTTTGCGATGAAACTAAATC
* * *
21164 TGTTTTAGGTGTTGTTTGTGATGAAACAAAATC
1 TGTTTTAGATGTTGTTTGCGATGAAACTAAATC
* * ** *
21197 TGTTTTGGATGCTAATTGTGATGAAAAC-AAATC
1 TGTTTTAGATGTTGTTTGCGATG-AAACTAAATC
21230 TGTTTT
1 TGTTTT
21236 GGTTGATCAT
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
32 2 0.02
33 80 0.92
34 5 0.06
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (33 bp):
TGTTTTAGATGTTGTTTGCGATGAAACTAAATC
Done.