Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012398.1 Corchorus olitorius cultivar O-4 contig12431, 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: 36725
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:1973 original size:14 final size:14
Alignment explanation
Indices: 1941--1972 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1931 TTTAATATCT
1941 CTTTTCTAGTTGGA
1 CTTTTCTAGTTGGA
1955 CTTTTCTAGTTGGA
1 CTTTTCTAGTTGGA
1969 -TTTT
1 CTTTT
1973 TAAGCATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.56
Consensus pattern (14 bp):
CTTTTCTAGTTGGA
Found at i:2280 original size:7 final size:7
Alignment explanation
Indices: 2244--2279 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
2234 GAGGAGGAAA
2244 CGCTGCC
1 CGCTGCC
2251 CGCTGCC
1 CGCTGCC
2258 CGCTGCC
1 CGCTGCC
2265 CGCTGCC
1 CGCTGCC
*
2272 CACTGCC
1 CGCTGCC
2279 C
1 C
2280 AGATTCCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.03, C:0.58, G:0.25, T:0.14
Consensus pattern (7 bp):
CGCTGCC
Found at i:7940 original size:33 final size:33
Alignment explanation
Indices: 7872--7997 Score: 150
Period size: 33 Copynumber: 3.9 Consensus size: 33
7862 TGATGGGCGT
* * *
7872 GGAGGCGTCCCCAGGGGGCACCCCA-CACGGGG
1 GGAGGCGTCCCCAGGGGGCGCCCAACCACGGAG
7904 GGAGGCGTCCCCAGGGTGG-GCCCAACCACGGAG
1 GGAGGCGTCCCCAGGG-GGCGCCCAACCACGGAG
* * *
7937 GGAGGCGTCCACAGGGGGTGCCCGACCACGGAG
1 GGAGGCGTCCCCAGGGGGCGCCCAACCACGGAG
* *
7970 GGAGGCGTCCCCA-AGGGCGCCCGACCAC
1 GGAGGCGTCCCCAGGGGGCGCCCAACCAC
7998 CGTGGTCGGG
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
32 35 0.42
33 48 0.58
ACGTcount: A:0.17, C:0.36, G:0.42, T:0.05
Consensus pattern (33 bp):
GGAGGCGTCCCCAGGGGGCGCCCAACCACGGAG
Found at i:7997 original size:65 final size:65
Alignment explanation
Indices: 7872--7997 Score: 164
Period size: 65 Copynumber: 1.9 Consensus size: 65
7862 TGATGGGCGT
* * * *
7872 GGAGGCGTCCCCAGGGGGCACCCCACACGGGGGGAGGCGTCCCCAGGGTGGGCCCAACCACGGAG
1 GGAGGCGTCCACAGGGGGCACCCCACACGGAGGGAGGCGTCCCCAAGGTGCGCCCAACCACGGAG
** * *
7937 GGAGGCGTCCACAGGGGGTGCCCGACCACGGAGGGAGGCGTCCCCAAGG-GCGCCCGACCAC
1 GGAGGCGTCCACAGGGGGCACCCCA-CACGGAGGGAGGCGTCCCCAAGGTGCGCCCAACCAC
7998 CGTGGTCGGG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 31 0.60
66 21 0.40
ACGTcount: A:0.17, C:0.36, G:0.42, T:0.05
Consensus pattern (65 bp):
GGAGGCGTCCACAGGGGGCACCCCACACGGAGGGAGGCGTCCCCAAGGTGCGCCCAACCACGGAG
Found at i:10847 original size:23 final size:23
Alignment explanation
Indices: 10815--10866 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
10805 AAGCAGGTTA
* *
10815 TGGGCCATCAAGGTTCTCCAATTT
1 TGGG-CATCAAAGTGCTCCAATTT
10839 TGGGCATCAAAGTGCTCCAATTT
1 TGGGCATCAAAGTGCTCCAATTT
10862 TGGGC
1 TGGGC
10867 CGTATAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGGCATCAAAGTGCTCCAATTT
Found at i:15277 original size:15 final size:15
Alignment explanation
Indices: 15257--15286 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15247 AATTATGTTT
15257 GATATGGATATCTTC
1 GATATGGATATCTTC
15272 GATATGGATATCTTC
1 GATATGGATATCTTC
15287 TGCACGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
GATATGGATATCTTC
Found at i:15809 original size:5 final size:5
Alignment explanation
Indices: 15801--15832 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
15791 TATTATTCAT
15801 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
15833 GATTGTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:16547 original size:6 final size:6
Alignment explanation
Indices: 16532--16576 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
16522 GATACGGCGT
* * * *
16532 GGTTTG GGTCTG GGTCTG GTTTTG GGTTTG GGTTTG GGATTG GGT
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGT
16577 GGATGTGGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.02, C:0.04, G:0.49, T:0.44
Consensus pattern (6 bp):
GGTTTG
Found at i:17152 original size:6 final size:6
Alignment explanation
Indices: 17106--17148 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
17096 AGAGCCAGAC
* *
17106 GAACCA GAACCA GAACCA GAACCA GAACCA GCACCA GCACCA G
1 GAACCA GAACCA GAACCA GAACCA GAACCA GAACCA GAACCA G
17149 CACCTGCACC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (6 bp):
GAACCA
Found at i:17157 original size:18 final size:18
Alignment explanation
Indices: 17106--17158 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
17096 AGAGCCAGAC
*
17106 GAACCAGAACCAGAACCA
1 GAACCAGAACCAGCACCA
17124 GAACCAGAACCAGCACCA
1 GAACCAGAACCAGCACCA
* * *
17142 GCACCAGCACCTGCACC
1 GAACCAGAACCAGCACC
17159 TTTCTTCTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.40, C:0.42, G:0.17, T:0.02
Consensus pattern (18 bp):
GAACCAGAACCAGCACCA
Found at i:17159 original size:6 final size:6
Alignment explanation
Indices: 17108--17158 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
17098 AGCCAGACGA
* * * * *
17108 ACCAGA ACCAGA ACCAGA ACCAGA ACCAGC ACCAGC ACCAGC ACCTGC
1 ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC
17156 ACC
1 ACC
17159 TTTCTTCTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.39, C:0.43, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCAGC
Found at i:17337 original size:6 final size:6
Alignment explanation
Indices: 17328--17357 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
17318 GCCGCCAATG
17328 CCATAC CCATAC CCATAC CCATAC CCATAC
1 CCATAC CCATAC CCATAC CCATAC CCATAC
17358 TCTGACGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
CCATAC
Found at i:28137 original size:63 final size:63
Alignment explanation
Indices: 28038--28166 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 63
28028 AAACTGTAAT
28038 TTGAAATGTTTAAGTAAATCCAATAATGATGTAATAAATCAATATTTGATTTGGGGGCAACTG
1 TTGAAATGTTTAAGTAAATCCAATAATGATGTAATAAATCAATATTTGATTTGGGGGCAACTG
*
28101 TTGAAATGTTTAAGTAAATCCAATAATGATGTAATAAATCAATATTTGATTTGGGGGCAATTG
1 TTGAAATGTTTAAGTAAATCCAATAATGATGTAATAAATCAATATTTGATTTGGGGGCAACTG
28164 TTG
1 TTG
28167 GAGTGCAAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.36
Consensus pattern (63 bp):
TTGAAATGTTTAAGTAAATCCAATAATGATGTAATAAATCAATATTTGATTTGGGGGCAACTG
Found at i:28427 original size:28 final size:28
Alignment explanation
Indices: 28387--28481 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 28
28377 ATTACTCCTT
*
28387 ATTTTGGTCATTTTTCGGATCCAAGGGC
1 ATTTTGGTCATTTTTCGGATCCAGGGGC
* *
28415 ATTTTGGTCATTTTGCAAGG--CTAGGGGC
1 ATTTTGGTCATTTTTC--GGATCCAGGGGC
* *
28443 ATTTTGGTCATTTCTC-AAGTCCAGGGGC
1 ATTTTGGTCATTTTTCGGA-TCCAGGGGC
28471 ATTTTGGTCAT
1 ATTTTGGTCAT
28482 CTTGCACGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
28 53 0.96
30 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (28 bp):
ATTTTGGTCATTTTTCGGATCCAGGGGC
Found at i:28448 original size:56 final size:56
Alignment explanation
Indices: 28387--28512 Score: 155
Period size: 56 Copynumber: 2.2 Consensus size: 56
28377 ATTACTCCTT
* * * *
28387 ATTTTGGTCATTTTTC-GGATCCAAGGGCATTTTGGTCATTTTGCAAGGCTAGGGGC
1 ATTTTGGTCATTTCTCAAG-TCCAAGGGCATTTTGGTCATCTTGCAAGGCCAGGGGC
* * * *
28443 ATTTTGGTCATTTCTCAAGTCCAGGGGCATTTTGGTCATCTTGCACGTCCAGGGGT
1 ATTTTGGTCATTTCTCAAGTCCAAGGGCATTTTGGTCATCTTGCAAGGCCAGGGGC
*
28499 ATTTTGATCATTTC
1 ATTTTGGTCATTTC
28513 AGGGACACCA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
56 59 0.98
57 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.39
Consensus pattern (56 bp):
ATTTTGGTCATTTCTCAAGTCCAAGGGCATTTTGGTCATCTTGCAAGGCCAGGGGC
Found at i:28492 original size:28 final size:27
Alignment explanation
Indices: 28406--28511 Score: 122
Period size: 28 Copynumber: 3.8 Consensus size: 27
28396 ATTTTTCGGA
*
28406 TCCAAGGGCATTTTGGTCATTTTGCAAG
1 TCCAGGGGCATTTTGGTCA-TTTGCAAG
* * *
28434 GCTAGGGGCATTTTGGTCATTTCTCAAG
1 TCCAGGGGCATTTTGGTCATTT-GCAAG
*
28462 TCCAGGGGCATTTTGGTCATCTTGCACG
1 TCCAGGGGCATTTTGGTCAT-TTGCAAG
* *
28490 TCCAGGGGTATTTTGATCATTT
1 TCCAGGGGCATTTTGGTCATTT
28512 CAGGGACACC
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
27 5 0.08
28 59 0.89
29 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (27 bp):
TCCAGGGGCATTTTGGTCATTTGCAAG
Found at i:33666 original size:9 final size:9
Alignment explanation
Indices: 33652--33678 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
33642 AAACGGTTGC
33652 TTTGTTTTG
1 TTTGTTTTG
33661 TTTGTTTTG
1 TTTGTTTTG
33670 TTTGTTTTG
1 TTTGTTTTG
33679 ATGTTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (9 bp):
TTTGTTTTG
Found at i:35751 original size:15 final size:15
Alignment explanation
Indices: 35731--35762 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
35721 CCTTGGGGGT
35731 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
35746 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
35761 TC
1 TC
35763 CACTTAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (15 bp):
TCAAAATCAACAAGC
Found at i:36453 original size:33 final size:31
Alignment explanation
Indices: 36347--36492 Score: 123
Period size: 33 Copynumber: 4.5 Consensus size: 31
36337 GAGTAATTCT
* *
36347 AAATCTGTTTTAGATGTTGTTTGCGAT-AATAC
1 AAATCTGTTTT-GGTGTTGTTTGTGATGAA-AC
* ** *
36379 TAAACCTAATTTGAGTGTTGTTTGTGATGACAC
1 -AAATCTGTTTTG-GTGTTGTTTGTGATGAAAC
36412 TAAATCTGTTTTAGGTGTTGTTTGTGATGAAAC
1 -AAATCTGTTTT-GGTGTTGTTTGTGATGAAAC
* **
36445 AAATTCTGTTTTGGATGCTAATTGTGATGTAAAC
1 AAA-TCTGTTTTGG-TGTTGTTTGTGATG-AAAC
36479 AAATCTGTTTTGGT
1 AAATCTGTTTTGGT
36493 TGATCATAGC
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
32 7 0.07
33 78 0.83
34 9 0.10
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (31 bp):
AAATCTGTTTTGGTGTTGTTTGTGATGAAAC
Done.