Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007340.1 Corchorus capsularis cultivar CVL-1 contig07361, 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: 18054
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1242 original size:22 final size:22
Alignment explanation
Indices: 1194--1246 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1184 CTTCCTATGA
*
1194 TTTTTGATAACCTCCCTGTAAG
1 TTTTTGATAACCTCCCTATAAG
* * * *
1216 ATTTTGTTAATCTCCCTATAAT
1 TTTTTGATAACCTCCCTATAAG
1238 TTTTTGATA
1 TTTTTGATA
1247 CTATAGTATG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.49
Consensus pattern (22 bp):
TTTTTGATAACCTCCCTATAAG
Found at i:12217 original size:37 final size:37
Alignment explanation
Indices: 12141--12220 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
12131 GTCCAAATAG
*
12141 AACAAAGACAAAAAGCAAAATTAAATACAACATTGGA
1 AACAAAGACAAAAAGCAAAATTAAATACAACATTAGA
* ** *
12178 AACAATGAC-AAAAGACAAAATTAAATAGGACGTTAGA
1 AACAAAGACAAAAAG-CAAAATTAAATACAACATTAGA
12215 AACAAA
1 AACAAA
12221 AGTAAAATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
36 5 0.14
37 31 0.86
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.14
Consensus pattern (37 bp):
AACAAAGACAAAAAGCAAAATTAAATACAACATTAGA
Found at i:12377 original size:31 final size:33
Alignment explanation
Indices: 12342--12414 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 33
12332 ATGACAATTT
***
12342 AGAAATATATTTTTTTAA-AAAGGGTACAATC-
1 AGAAATATATTTTAAAAATAAAGGGTACAATCG
*
12373 AGAAATATGTTTTAAAAATAAAGGGTACAATCG
1 AGAAATATATTTTAAAAATAAAGGGTACAATCG
*
12406 AAAAATATA
1 AGAAATATA
12415 AAGTTTCCCC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 14 0.41
32 13 0.38
33 7 0.21
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (33 bp):
AGAAATATATTTTAAAAATAAAGGGTACAATCG
Found at i:13237 original size:2 final size:2
Alignment explanation
Indices: 13232--13257 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13222 ACACACACAC
13232 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13258 TAACTATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14787 original size:16 final size:16
Alignment explanation
Indices: 14763--14802 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
14753 TATGCATGAG
*
14763 ATATATATATCTACCT
1 ATATCTATATCTACCT
*
14779 ATATCTATATCTATCT
1 ATATCTATATCTACCT
14795 ATA-CTATA
1 ATATCTATA
14803 CTAAAAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATCTATATCTACCT
Found at i:15479 original size:29 final size:31
Alignment explanation
Indices: 15447--15513 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
15437 ATGTAATTTG
*
15447 GGATATAACGTTAC-AAAA-TAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
* *
15476 GGATATAATGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
15507 GGATATA
1 GGATATA
15514 GTCCGGTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:15678 original size:31 final size:31
Alignment explanation
Indices: 15643--15752 Score: 143
Period size: 31 Copynumber: 3.6 Consensus size: 31
15633 TCCTAACTGA
15643 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
* *
15674 TTATATCCTTAATTGCTCGAAATCAAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
* ** * *
15705 TTATATTCTTAATTGCTTG-TTTTG-TAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
15734 TTATATCCTTAATTGCTTG
1 TTATATCCTTAATTGCTTG
15753 CGGCAGCAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
29 22 0.32
30 1 0.01
31 46 0.67
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACG
Found at i:15829 original size:3 final size:3
Alignment explanation
Indices: 15821--15861 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
15811 CCGTATTTTC
15821 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
15862 CCTAATTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:16098 original size:13 final size:14
Alignment explanation
Indices: 16080--16114 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
16070 ATATTGGAAC
16080 TTTTTAAAT-ATAT
1 TTTTTAAATGATAT
16093 TTTTTAAATGATAT
1 TTTTTAAATGATAT
*
16107 TGTTTAAA
1 TTTTTAAA
16115 CTTTTATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTTAAATGATAT
Found at i:16879 original size:31 final size:31
Alignment explanation
Indices: 16836--16916 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
16826 CGCTACAAAA
* **
16836 CAAGCAATTAAGGATATAACGTTTTTGATTT
1 CAAGCAATTAAGGATATAACATTTTCAATTT
* * *
16867 CGAGTAATTAAGGATATATCATTTTCAATTT
1 CAAGCAATTAAGGATATAACATTTTCAATTT
16898 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
16917 TCAGTTAGGG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACATTTTCAATTT
Found at i:17542 original size:12 final size:13
Alignment explanation
Indices: 17527--17560 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
17517 AATCTAAATC
*
17527 TAAAGCAGATT-A
1 TAAAGCAAATTAA
17539 TAAAGCAAATTAA
1 TAAAGCAAATTAA
17552 TAAAGCAAA
1 TAAAGCAAA
17561 CAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Done.