Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016823.1 Corchorus olitorius cultivar O-4 contig16856, 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: 20213
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:549 original size:21 final size:21
Alignment explanation
Indices: 525--594 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
515 GGCTTGGAAT
* *
525 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATAGCC
*
546 GGTGGTGGCACGGGCTTAGCC
1 GGTGGTGGCACGGGCATAGCC
* *
567 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAGCC
588 GGTGGTG
1 GGTGGTG
595 TGGCAATCGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.11, C:0.21, G:0.49, T:0.19
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAGCC
Found at i:3632 original size:15 final size:16
Alignment explanation
Indices: 3612--3643 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3602 GATTCCTAAT
3612 AAAACTCAAAA-AAAA
1 AAAACTCAAAAGAAAA
3627 AAAACTCAAAAGAAAA
1 AAAACTCAAAAGAAAA
3643 A
1 A
3644 TTGATTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.78, C:0.12, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAACTCAAAAGAAAA
Found at i:4150 original size:15 final size:16
Alignment explanation
Indices: 4128--4167 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
4118 AGAGGTTGAC
4128 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
*
4143 ATAAAACAATTAAACT
1 AGAAAACAATTAAACT
4159 AGAAAACAA
1 AGAAAACAA
4168 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.68, C:0.12, G:0.05, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:10599 original size:38 final size:38
Alignment explanation
Indices: 10542--10646 Score: 142
Period size: 38 Copynumber: 2.8 Consensus size: 38
10532 TTTTTTTCAT
*
10542 TAAGTAATTCCAAATGAAGATTTTGG-AAAATAAAAGTC
1 TAAGTAATTCCAAAAGAAGATTTTGGAAAAAT-AAAGTC
* *
10580 TAGGTAATTCCAAAAGAAGATTTTGGAAAAATAAAGTT
1 TAAGTAATTCCAAAAGAAGATTTTGGAAAAATAAAGTC
*
10618 TAAG-ATATCCCAAAAGAAGATTTTGGAAA
1 TAAGTA-ATTCCAAAAGAAGATTTTGGAAA
10647 TTAATAAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
37 1 0.02
38 54 0.90
39 5 0.08
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.28
Consensus pattern (38 bp):
TAAGTAATTCCAAAAGAAGATTTTGGAAAAATAAAGTC
Found at i:11553 original size:19 final size:18
Alignment explanation
Indices: 11516--11555 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
11506 TTCTTGAAAT
*
11516 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
11534 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
11553 AAT
1 AAT
11556 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:11936 original size:22 final size:23
Alignment explanation
Indices: 11868--11995 Score: 101
Period size: 22 Copynumber: 5.8 Consensus size: 23
11858 TGAATCTTTT
11868 TATGAAATTTTGATAA-CTACTC
1 TATGAAATTTTGATAACCTACTC
* * *
11890 TATTAAATTTTGATAATC-ACGC
1 TATGAAATTTTGATAACCTACTC
* *
11912 TATAAAATTTTGATAACCTA-AC
1 TATGAAATTTTGATAACCTACTC
*
11934 TATGAAATTTTAATAAACCT--TC
1 TATGAAATTTTGAT-AACCTACTC
*
11956 ATATGAAATTTTG-TAACCTTC-C
1 -TATGAAATTTTGATAACCTACTC
* *
11978 TATG-ATTTTTTATAACCT
1 TATGAAATTTTGATAACCT
11996 CCCCATAACA
Statistics
Matches: 88, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.06
21 15 0.17
22 50 0.57
23 18 0.20
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (23 bp):
TATGAAATTTTGATAACCTACTC
Found at i:11975 original size:21 final size:21
Alignment explanation
Indices: 11916--11982 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 21
11906 TCACGCTATA
*
11916 AAATTTTGATAACC-TAACTATG
1 AAATTTTG-TAACCTTCA-TATG
*
11938 AAATTTTAATAAACCTTCATATG
1 AAATTTT-GT-AACCTTCATATG
*
11961 AAATTTTGTAACCTTCCTATG
1 AAATTTTGTAACCTTCATATG
11982 A
1 A
11983 TTTTTTATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 12 0.32
22 9 0.24
23 15 0.39
24 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (21 bp):
AAATTTTGTAACCTTCATATG
Found at i:11988 original size:21 final size:21
Alignment explanation
Indices: 11916--11995 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
11906 TCACGCTATA
*
11916 AAATTTTGATAACC-TAACTATG
1 AAATTTT-ATAACCTTCA-TATG
11938 AAATTTTAATAAACCTTCATATG
1 AAATTTT-AT-AACCTTCATATG
* *
11961 AAATTTTGTAACCTTCCTATG
1 AAATTTTATAACCTTCATATG
**
11982 ATTTTTTATAACCT
1 AAATTTTATAACCT
11996 CCCCATAACA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
21 22 0.45
22 10 0.20
23 15 0.31
24 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (21 bp):
AAATTTTATAACCTTCATATG
Found at i:12323 original size:45 final size:45
Alignment explanation
Indices: 12259--12348 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
12249 GGCAATCTAA
* * *
12259 TCCGGTTTAGCTCTTATAGTATGTTTATACGTTTAAAAATTCAAC
1 TCCGGTTTAGCTCTCATAGTATGATTATACATTTAAAAATTCAAC
*
12304 TCCGGTTTAGTTCTCATAGTATGATTATACATTTAAAAATTCAAC
1 TCCGGTTTAGCTCTCATAGTATGATTATACATTTAAAAATTCAAC
12349 ACCTTTGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (45 bp):
TCCGGTTTAGCTCTCATAGTATGATTATACATTTAAAAATTCAAC
Found at i:13752 original size:32 final size:32
Alignment explanation
Indices: 13715--13786 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
13705 CAAAAATAAT
* *
13715 TTGAAGATTCGTAGTTAGTGTTTTAAGATTTA
1 TTGAAGATTCGAAGTTAGTGTTTTAAGACTTA
13747 TTGAAGATTCGAAGTTAGTGTTTTAAGACTTA
1 TTGAAGATTCGAAGTTAGTGTTTTAAGACTTA
13779 TTGAAGAT
1 TTGAAGAT
13787 AATTTGAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (32 bp):
TTGAAGATTCGAAGTTAGTGTTTTAAGACTTA
Found at i:13803 original size:19 final size:18
Alignment explanation
Indices: 13779--13814 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13769 TTAAGACTTA
*
13779 TTGAAGATAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
13798 TTGAAGACAATTGAAGA
1 TTGAAGACAATTGAAGA
13815 ATTATCTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.