Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012028.1 Corchorus olitorius cultivar O-4 contig12061, 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: 12435
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Found at i:723 original size:54 final size:54
Alignment explanation
Indices: 527--733 Score: 240
Period size: 54 Copynumber: 3.9 Consensus size: 54
517 GCCGTCAAGC
* * *
527 ACCCTGTGCGGTTTTTCATAGAAGTTTTCAGA-AGTTTAAGTTGATCTTTAGATA
1 ACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGA-TCTAAGTTGATCTTCAGATA
* * * *
581 ACCCTGTGTGGTCTTTCATAGAAG-TTTCAGAAATTTAAGTTGTTCTTCAGATA
1 ACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATA
* * * * * * *
634 ACCCTGTGCAGTCTTTCACAAAAGCTTTCAAAGATCTATGTTGATCATCAGATA
1 ACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATA
*
688 ACCCTGTGCGGTCTTTCATAGAAGTTTTTAGAGATC-AGAGTTGATC
1 ACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTA-AGTTGATC
734 CCTAGATGAT
Statistics
Matches: 129, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
53 46 0.36
54 83 0.64
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (54 bp):
ACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATA
Found at i:806 original size:107 final size:106
Alignment explanation
Indices: 693--893 Score: 302
Period size: 107 Copynumber: 1.9 Consensus size: 106
683 AGATAACCCT
*
693 GTGCGGTC-TTTCATAGAAGTTTTTAGAGATCAGAGTTGATC-CCTAGATGATCCAGTGCGG-TC
1 GTGCGGTCATTCCA-AGAAGTTTTTAGAGATCAGAGTTGATCTCC-AGATGATCCAGTGCGGTTC
* *
755 ATTTCAAGTAGTTCTCTT-TGATCAGAGTTGATCCCAGGTGATCCA
64 -TTCCAAGAAGTT-T-TTATGATCAGAGTTGATCCCAGGTGATCCA
800 GTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTTCTT
1 GTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTTCTT
865 CCAAGAAGTTTTTATGATCAGAGTTGATC
66 CCAAGAAGTTTTTATGATCAGAGTTGATC
894 TTGTTTCAAG
Statistics
Matches: 87, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
105 2 0.02
106 16 0.18
107 61 0.70
108 8 0.09
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (106 bp):
GTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTTCTT
CCAAGAAGTTTTTATGATCAGAGTTGATCCCAGGTGATCCA
Found at i:808 original size:53 final size:52
Alignment explanation
Indices: 693--893 Score: 255
Period size: 54 Copynumber: 3.8 Consensus size: 52
683 AGATAACCCT
* *
693 GTGCGGTC-TTTCATAGAAGTTTTTAGAGATCAGAGTTGATCCCTAGATGATCCA
1 GTGCGGTCATTCCA-AGAAGTTTTTA-TGATCAGAGTTGATCCC-AGATGATCCA
* * *
747 GTGCGGTCATTTCAAGTAGTTCTCTT-TGATCAGAGTTGATCCCAGGTGATCCA
1 GTGCGGTCATTCCAAGAAGTT-T-TTATGATCAGAGTTGATCCCAGATGATCCA
*
800 GTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCTCCAGATGATCCA
1 GTGCGGTCATTCCAAGAAGTTTTTA-TGATCAGAGTTGATC-CCAGATGATCCA
854 GTGCGGTTC-TTCCAAGAAGTTTTTATGATCAGAGTTGATC
1 GTGCGG-TCATTCCAAGAAGTTTTTATGATCAGAGTTGATC
894 TTGTTTCAAG
Statistics
Matches: 132, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
51 2 0.02
52 1 0.01
53 56 0.42
54 63 0.48
55 8 0.06
56 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (52 bp):
GTGCGGTCATTCCAAGAAGTTTTTATGATCAGAGTTGATCCCAGATGATCCA
Found at i:923 original size:35 final size:35
Alignment explanation
Indices: 866--1842 Score: 1246
Period size: 35 Copynumber: 27.8 Consensus size: 35
856 GCGGTTCTTC
* *
866 CAAGAAGTTTT-TATGATCAGAGTTGATCTTGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
*
900 CAAGAAGTTTTCGATGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * *
935 CAAGAAGTTTTCAATGATCATAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
*
970 CAAGGAAGTTTTCGATGATCAGAGTTGATCTCCTTT
1 CAA-GAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
1006 CAAGAAGTTTTCGTTGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
1041 CAAGAAGTTTT-TATGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
1075 CAAGAAGTTTTCGTTGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
** *
1110 CAAGAAGTTTTTTTTTATGTATCAGAGTTGATCTC-ATT
1 CAAGAAG---TTTTCGATG-ATCAGAGTTGATCTCGTTT
** *
1148 CGAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTT
1 C-AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
1184 CAATAAGTTTTCGATGATCAGAGTGGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
** *
1219 CAA-AAGTTTTTTTATGATCAGAGTTGATCTCCTTT
1 CAAGAAG-TTTTCGATGATCAGAGTTGATCTCGTTT
* *
1254 CAAGAAGTTTCCAATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* ** * *
1289 TAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * *
1324 CAAGAACTTTCCAATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
** **
1359 CAAGAAGTTTTTTATGATCAGAGTTGATCTTATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
1394 TAAGAAATTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1429 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1464 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
1499 CAAGAAGTTTTTGATGATCAGATTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
** * *
1534 CAAGAAGTTTTTTTATGATCAGAGTTTATCTCCTTT
1 CAAGAAG-TTTTCGATGATCAGAGTTGATCTCGTTT
1570 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * *
1605 CAAGAAATTTTTGATGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
1640 CAAGAAGTTTTCGATGACCAGAGTTGATGTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * **
1675 CAAGAAGTTATT--TTTATCAGAAATGATCTCGTTT
1 CAAGAAGTT-TTCGATGATCAGAGTTGATCTCGTTT
** * *
1709 CAAGAAGTTTTTTATGATCAGAGTTTATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1744 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* ** * * *
1779 CAAGAGGTTTTTTATGATCATAGTTGTTCTCTTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1814 CAAGAAGTTTTCGATGATCAGAGTTGATC
1 CAAGAAGTTTTCGATGATCAGAGTTGATC
1843 CCTAGATGAT
Statistics
Matches: 821, Mismatches: 107, Indels: 29
0.86 0.11 0.03
Matches are distributed among these distances:
33 2 0.00
34 70 0.09
35 639 0.78
36 80 0.10
38 9 0.01
39 21 0.03
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (35 bp):
CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
Found at i:1877 original size:54 final size:53
Alignment explanation
Indices: 1814--2108 Score: 355
Period size: 54 Copynumber: 5.5 Consensus size: 53
1804 GTTCTCTTTT
* *
1814 CAAGAAGTTTTCGATGATCAGAGTTGATCCCTAGATGATCTAGTGCGGTCATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGAT-CCTAGATGATCCAGTGCGGTCATTC
1868 CAAGAAGTTTTCAATGATCAGAGTTGATTCCTAGATGATCCAGTGCGGTCATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGA-TCCTAGATGATCCAGTGCGGTCATTC
* * *
1922 C-AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCCAGTGCAGTTATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGAT-CCTAGATGATCCAGTGCGGTCATTC
* * * * * *
1975 CAAGAAGTTTTTAGA-GATCAGAGCTGATCC-AGATGATCTAGTGCGTTCTTTT
1 CAAGAAGTTTTCA-ATGATCAGAGTTGATCCTAGATGATCCAGTGCGGTCATTC
* * * *
2027 CAAGAAATTTTCAATGATCAGAGTTGATCTTCA-ATTGATACAGTGCAGTCATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGATCCT-AGA-TGATCCAGTGCGGTCATTC
* *
2081 CAATAAGTTTTCGATGATCAGAGTTGAT
1 CAAGAAGTTTTCAATGATCAGAGTTGAT
2109 TTTCAATTTG
Statistics
Matches: 207, Mismatches: 26, Indels: 16
0.83 0.10 0.06
Matches are distributed among these distances:
51 1 0.00
52 41 0.20
53 51 0.25
54 112 0.54
55 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (53 bp):
CAAGAAGTTTTCAATGATCAGAGTTGATCCTAGATGATCCAGTGCGGTCATTC
Found at i:2114 original size:54 final size:51
Alignment explanation
Indices: 1814--2141 Score: 315
Period size: 54 Copynumber: 6.1 Consensus size: 51
1804 GTTCTCTTTT
* *
1814 CAAGAAGTTTTCGATGATCAGAGTTGATCCCTAGATGATCTAGTGCGGTCATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGATTCC-AGATGATC-AGTGC-GTCATTC
1868 CAAGAAGTTTTCAATGATCAGAGTTGATTCCTAGATGATCCAGTGCGGTCATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGATTCC-AGATGAT-CAGTGC-GTCATTC
* *
1922 C-AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCCAGTGCAGTTATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGAT-TCCAGATGAT-CAGTGC-GTCATTC
* * * *
1975 CAAGAAGTTTTTAGA-GATCAGAGCTGA-TCCAGATGATCTAGTGCGTTCTTTT
1 CAAGAAGTTTTCA-ATGATCAGAGTTGATTCCAGATGATC-AGTGCG-TCATTC
* *
2027 CAAGAAATTTTCAATGATCAGAGTTGATCTTCA-ATTGATACAGTGCAGTCATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGAT-TCCAGA-TGAT-CAGTGC-GTCATTC
* * *
2081 CAATAAGTTTTCGATGATCAGAGTTGATTTTCA-ATTTGATTCAGTGCGATCATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGA-TTCCAGA--TGA-TCAGTGCG-TCATTC
2136 CAAGAA
1 CAAGAA
2142 AGGTTTACAT
Statistics
Matches: 237, Mismatches: 21, Indels: 31
0.82 0.07 0.11
Matches are distributed among these distances:
51 3 0.01
52 39 0.16
53 48 0.20
54 120 0.51
55 26 0.11
56 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (51 bp):
CAAGAAGTTTTCAATGATCAGAGTTGATTCCAGATGATCAGTGCGTCATTC
Found at i:2710 original size:19 final size:18
Alignment explanation
Indices: 2686--2721 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2676 TGAAGACTTA
2686 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
2705 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
2722 ATAATTTCAA
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:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:2728 original size:30 final size:30
Alignment explanation
Indices: 2674--2733 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2664 GAAGTTCGTG
* *
2674 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
2704 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
2734 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:4973 original size:10 final size:10
Alignment explanation
Indices: 4958--4988 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
4948 TTTCTATGTC
4958 CTGAAGATGA
1 CTGAAGATGA
4968 CTGAAGATGA
1 CTGAAGATGA
4978 CTGAAGATGA
1 CTGAAGATGA
4988 C
1 C
4989 CTTCATCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.19
Consensus pattern (10 bp):
CTGAAGATGA
Found at i:8454 original size:18 final size:18
Alignment explanation
Indices: 8411--8454 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
8401 ATAATTAATT
8411 CTAATTTTAATTTTATTA
1 CTAATTTTAATTTTATTA
* *
8429 TTATTTTTAA-TTTATATA
1 CTAATTTTAATTTTAT-TA
8447 CTAATTTT
1 CTAATTTT
8455 TCTTTGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (18 bp):
CTAATTTTAATTTTATTA
Found at i:11234 original size:12 final size:13
Alignment explanation
Indices: 11217--11246 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
11207 GTTTTCTTTA
11217 ATTTTCTTGATT-
1 ATTTTCTTGATTG
11229 ATTTTCTTGATTG
1 ATTTTCTTGATTG
11242 ATTTT
1 ATTTT
11247 AATTGTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:11477 original size:16 final size:17
Alignment explanation
Indices: 11456--11487 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11446 GAGATTGTGT
11456 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
11472 TTTATTTTTCTATTTT
1 TTTATTTTTCTATTTT
11488 AATTTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Done.