Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016790.1 Corchorus olitorius cultivar O-4 contig16823, 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: 27264
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:12301 original size:29 final size:29
Alignment explanation
Indices: 12259--12314 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
12249 CCTTGCACGG
*
12259 TGTTGAAAGCTTGTAATTGTGGGGTTGAT
1 TGTTGAAAACTTGTAATTGTGGGGTTGAT
*
12288 TGTTGAAAACTTGTAATTGTGGTGTTG
1 TGTTGAAAACTTGTAATTGTGGGGTTG
12315 TAAACTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.04, G:0.32, T:0.43
Consensus pattern (29 bp):
TGTTGAAAACTTGTAATTGTGGGGTTGAT
Found at i:13117 original size:30 final size:30
Alignment explanation
Indices: 13082--13161 Score: 142
Period size: 30 Copynumber: 2.7 Consensus size: 30
13072 CACATTCCGA
13082 TAACGTTAGATCCTAAATTGACATAAGAGC
1 TAACGTTAGATCCTAAATTGACATAAGAGC
13112 TAACGTTAGATCCTAAATTGACATAAGAGC
1 TAACGTTAGATCCTAAATTGACATAAGAGC
* *
13142 TAACGTTAGAACCTGAATTG
1 TAACGTTAGATCCTAAATTG
13162 TCGTTTGCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (30 bp):
TAACGTTAGATCCTAAATTGACATAAGAGC
Found at i:15512 original size:294 final size:293
Alignment explanation
Indices: 14980--15567 Score: 921
Period size: 294 Copynumber: 2.0 Consensus size: 293
14970 AATCTTGATT
* * * *
14980 GCAATTGTTAAATTAATGAATTCGGGTAGACACATTTACAGCACTAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGATAGACACATTTACAGCACCAATCCTTAGGAATTCCGGCA
* *
15045 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAAAATGTAACTAAAACACATTTAAT
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAAAATATAACTAAAACACACTTAAT
** * *
15110 CATAAATATTAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAGGTAAGGGAGGAAATTCATCG
131 CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCATCA
* * *
15175 AGGGCCTTTTTAGTCACCCGAACAGTGAGAAAAGACAAAAAAAAAGCCAAAATGAGGCACCGCAT
196 AGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGAC-AAAAAAAAGCCAAAAGGAGGCACCACAT
15240 TAATCCTCAATTTGGCCTTTTAAG-AATTTCCATA
260 TAATCCTCAATTTGGCC-TTTAAGTAATTTCCATA
* *
15274 GCAATTGTTAAATTAATGAACTCGGATAGATACATTTATAGCACCAATCCTTAGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGATAGACACATTTACAGCACCAATCCTTAGGAATTCCGGCA
* * * *
15339 GAGGAGTTGAACCGGTAAATCCTAATATCCGCACACAATTAATATATAATTAAAACACACTTAAT
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAAAATATAACTAAAACACACTTAAT
*
15404 CATAAATACAAAAATAGTAAATTACAAAAAAGGG-AGAGAGAGAAAAGTAAGGGAGGAAA-TCAT
131 CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAG-CAG-GAAAAGTAAGGGAGGAAATTCAT
*
15467 CAAGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACA
194 CAAGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAGGCACCACA
*
15532 TTAATCCTTAATTTGGCCTTTAAGTAATTTCCATA
259 TTAATCCTCAATTTGGCCTTTAAGTAATTTCCATA
15567 G
1 G
15568 TCACTAAAAA
Statistics
Matches: 269, Mismatches: 22, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
292 6 0.02
293 54 0.20
294 192 0.71
295 17 0.06
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (293 bp):
GCAATTGTTAAATTAATGAACTCGGATAGACACATTTACAGCACCAATCCTTAGGAATTCCGGCA
GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAAAATATAACTAAAACACACTTAAT
CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCATCA
AGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAGGCACCACATT
AATCCTCAATTTGGCCTTTAAGTAATTTCCATA
Found at i:20954 original size:5 final size:5
Alignment explanation
Indices: 20944--21020 Score: 66
Period size: 5 Copynumber: 17.4 Consensus size: 5
20934 TTTTCTTATA
*
20944 ATCTT ATCTT ATCTT A-C-T ATCTT ATCTT ATCTT A-C-G ATCTT ATCTT
1 ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT
*
20990 A-C-T ATCTT ATTTT A-C-T ATCTT A-C-T ATCTT AT
1 ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT AT
21021 TACTATATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
3 9 0.16
4 9 0.16
5 40 0.69
ACGTcount: A:0.23, C:0.21, G:0.01, T:0.55
Consensus pattern (5 bp):
ATCTT
Found at i:20964 original size:8 final size:8
Alignment explanation
Indices: 20953--21019 Score: 65
Period size: 8 Copynumber: 8.9 Consensus size: 8
20943 AATCTTATCT
20953 TATCTTAC
1 TATCTTAC
20961 TATCTTATC
1 TATCTTA-C
20970 TTATCTTAC
1 -TATCTTAC
*
20979 GATC-T--
1 TATCTTAC
20984 TATCTTAC
1 TATCTTAC
20992 TATCTTA-
1 TATCTTAC
20999 T-T-TTAC
1 TATCTTAC
21005 TATCTTAC
1 TATCTTAC
21013 TATCTTA
1 TATCTTA
21020 TTACTATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
5 6 0.12
6 3 0.06
7 3 0.06
8 28 0.57
9 2 0.04
10 7 0.14
ACGTcount: A:0.24, C:0.21, G:0.01, T:0.54
Consensus pattern (8 bp):
TATCTTAC
Found at i:20964 original size:13 final size:13
Alignment explanation
Indices: 20948--21011 Score: 74
Period size: 13 Copynumber: 4.5 Consensus size: 13
20938 CTTATAATCT
20948 TATCTTATCTTAC
1 TATCTTATCTTAC
20961 TATCTTATCTTATC
1 TATCTTATCTTA-C
20975 TTACGATCTTATCTTAC
1 -T---ATCTTATCTTAC
*
20992 TATCTTATTTTAC
1 TATCTTATCTTAC
21005 TATCTTA
1 TATCTTA
21012 CTATCTTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
13 30 0.67
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.24
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.55
Consensus pattern (13 bp):
TATCTTATCTTAC
Found at i:20965 original size:18 final size:18
Alignment explanation
Indices: 20944--21020 Score: 90
Period size: 18 Copynumber: 4.4 Consensus size: 18
20934 TTTTCTTATA
20944 ATCTTATCTTATCTTACT
1 ATCTTATCTTATCTTACT
*
20962 ATCTTATCTTATCTTACG
1 ATCTTATCTTATCTTACT
20980 ATCTTATCTTA-C-TATCTT
1 ATCTTATCTTATCTTA-C-T
*
20998 ATTTTA-C-TATCTTACT
1 ATCTTATCTTATCTTACT
21014 ATCTTAT
1 ATCTTAT
21021 TACTATATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
16 10 0.20
17 5 0.10
18 35 0.70
ACGTcount: A:0.23, C:0.21, G:0.01, T:0.55
Consensus pattern (18 bp):
ATCTTATCTTATCTTACT
Found at i:22817 original size:2 final size:2
Alignment explanation
Indices: 22810--22861 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
22800 GCAATTAAAC
* * *
22810 AT AT AT AT AT AT AT AT GT AT AT AC AT AT AC 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
* *
22852 GT GT AT AT AT
1 AT AT AT AT AT
22862 GATACTAATG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Done.