Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015537.1 Corchorus olitorius cultivar O-4 contig15570, 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: 48574
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:764 original size:21 final size:22
Alignment explanation
Indices: 739--818 Score: 69
Period size: 21 Copynumber: 3.7 Consensus size: 22
729 ACTATAGTAT
*
739 CAAAAATTATAGGGAGATTA-A
1 CAAAAATTATAGGAAGATTATA
760 C-AAAATCTCATAGGAAGATTATA
1 CAAAAAT-T-ATAGGAAGATTATA
* *
783 -AAAAATCATAGGAAGGTTATA
1 CAAAAATTATAGGAAGATTATA
**
804 -AAATTTTATAGGAAG
1 CAAAAATTATAGGAAG
819 GTAAAATTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
20 5 0.10
21 27 0.55
22 11 0.22
23 6 0.12
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.26
Consensus pattern (22 bp):
CAAAAATTATAGGAAGATTATA
Found at i:773 original size:22 final size:23
Alignment explanation
Indices: 740--806 Score: 72
Period size: 21 Copynumber: 3.1 Consensus size: 23
730 CTATAGTATC
*
740 AAAAAT-T-ATAGGGAGATTA-A
1 AAAAATCTCATAGGAAGATTATA
*
760 CAAAATCTCATAGGAAGATTATA
1 AAAAATCTCATAGGAAGATTATA
*
783 AAAAA--TCATAGGAAGGTTATA
1 AAAAATCTCATAGGAAGATTATA
804 AAA
1 AAA
807 TTTTATAGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 5 0.12
21 19 0.47
22 11 0.28
23 5 0.12
ACGTcount: A:0.54, C:0.06, G:0.16, T:0.24
Consensus pattern (23 bp):
AAAAATCTCATAGGAAGATTATA
Found at i:819 original size:21 final size:21
Alignment explanation
Indices: 767--820 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
757 TAACAAAATC
*
767 TCATAGGAAGATTATAAAAAA
1 TCATAGGAAGGTTATAAAAAA
**
788 TCATAGGAAGGTTATAAAATT
1 TCATAGGAAGGTTATAAAAAA
*
809 TTATAGGAAGGT
1 TCATAGGAAGGT
821 AAAATTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (21 bp):
TCATAGGAAGGTTATAAAAAA
Found at i:851 original size:22 final size:22
Alignment explanation
Indices: 821--940 Score: 131
Period size: 22 Copynumber: 5.5 Consensus size: 22
811 ATAGGAAGGT
* *
821 AAAATTTCATAGTTAGCTTATC
1 AAAATTTCATAGGTAGATTATC
* *
843 AAAAATTCATATGG-AGTTTATC
1 AAAATTTCATA-GGTAGATTATC
*
865 ACAATTTCATAGGTA-ATTATC
1 AAAATTTCATAGGTAGATTATC
886 AAAATTTCATAGCGT-GATTATC
1 AAAATTTCATAG-GTAGATTATC
*
908 AAAATTTAATAGGGTAG-TTATC
1 AAAATTTCATA-GGTAGATTATC
930 AAAATTTCATA
1 AAAATTTCATA
941 AAAATATTCT
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
21 18 0.22
22 62 0.75
23 3 0.04
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.38
Consensus pattern (22 bp):
AAAATTTCATAGGTAGATTATC
Found at i:1138 original size:23 final size:23
Alignment explanation
Indices: 1101--1152 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1091 ACTATTGTAG
*
1101 TTTTATTCTACTAAAAACT-ATAT
1 TTTTATTCAACT-AAAACTAATAT
* *
1124 TTTTATTCAATTAAATCTAATAT
1 TTTTATTCAACTAAAACTAATAT
1147 TTTTAT
1 TTTTAT
1153 AATTACTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTATTCAACTAAAACTAATAT
Found at i:10525 original size:25 final size:24
Alignment explanation
Indices: 10474--10530 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
10464 GTCAGTCTTG
*
10474 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
10497 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
10522 AATTTATTT
1 AATTTATTT
10531 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:17032 original size:20 final size:20
Alignment explanation
Indices: 17007--17046 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
16997 CATTCCAATT
17007 TTATCGGATATCCCCGAAGG
1 TTATCGGATATCCCCGAAGG
*
17027 TTATCGGATGTCCCCGAAGG
1 TTATCGGATATCCCCGAAGG
17047 GACAATACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (20 bp):
TTATCGGATATCCCCGAAGG
Found at i:19267 original size:29 final size:28
Alignment explanation
Indices: 19228--19325 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 28
19218 TCAAAATGTT
19228 CAAATAAGGGCCCGATCTTTTAATTTAGC
1 CAAATAAGGGCCCGATCTTTTAATTT-GC
* * ** **
19257 CAAATAAGGG-CCTAACGTTAGCCAAAATGC
1 CAAATAAGGGCCCGATC-TT--TTAATTTGC
19287 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTT-GC
19317 CAAATAAGG
1 CAAATAAGG
19326 ACCTAATGTT
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 4 0.08
29 24 0.47
30 4 0.08
31 15 0.29
32 4 0.08
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (28 bp):
CAAATAAGGGCCCGATCTTTTAATTTGC
Found at i:19283 original size:60 final size:60
Alignment explanation
Indices: 19197--19358 Score: 261
Period size: 60 Copynumber: 2.7 Consensus size: 60
19187 GCTAATTGCT
* *
19197 CAAATAAGGGTCTAATGTTTGTCAAAATGTTCAAATAAGGGCCCGATCTTTTAATTTAGC
1 CAAATAAGGGCCTAATGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTAGC
* * * *
19257 CAAATAAGGGCCTAACGTTAGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTAGC
*
19317 CAAATAAGGACCTAATGTTTGTCAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAATGTTTGTCAAAATGCTCAAATAAGGGC
19359 ATGCCATCAG
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAATGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTAGC
Found at i:19355 original size:31 final size:31
Alignment explanation
Indices: 19193--19358 Score: 128
Period size: 31 Copynumber: 5.5 Consensus size: 31
19183 TAAGGCTAAT
*
19193 TGCTCAAATAAGGGTCTAATGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
* ** * **
19224 TGTTCAAATAAGGGCCCGATCTTT-T-AATT
1 TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
* * *
19253 TAGC-CAAATAAGGGCCTAACGTTAGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTGTCAAAA
** * **
19284 TGCTCAAATAAGGGCCCGATCTTT-T-AATT
1 TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
*
19313 TGGC-CAAATAAGGACCTAATGTTTGTCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTGTCAAAA
19344 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
19359 ATGCCATCAG
Statistics
Matches: 96, Mismatches: 31, Indels: 16
0.67 0.22 0.11
Matches are distributed among these distances:
29 37 0.39
30 9 0.09
31 50 0.52
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
Found at i:19477 original size:29 final size:29
Alignment explanation
Indices: 19443--19539 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
19433 CCCTTATTAA
19443 CTTATTTGGCCAAATTAAAAGATCGGGCC
1 CTTATTTGGCCAAATTAAAAGATCGGGCC
** * * **
19472 CTTATTTGAG-CATTTTGGCTAATG-TTAGGCC
1 CTTATTTG-GCCAAATT---AAAAGATCGGGCC
19503 CTTATTTGGCCAAATTAAAAGATCGGGCC
1 CTTATTTGGCCAAATTAAAAGATCGGGCC
19532 CTTATTTG
1 CTTATTTG
19540 AGCATTTTGG
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 3 0.06
29 25 0.50
30 2 0.04
31 17 0.34
32 3 0.06
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (29 bp):
CTTATTTGGCCAAATTAAAAGATCGGGCC
Found at i:19506 original size:31 final size:31
Alignment explanation
Indices: 19468--19574 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 31
19458 TAAAAGATCG
* *
19468 GGCCCTTATTTGAGCATTTTGGCTAATGTTA
1 GGCCCTTATTTGAGCATTTTGGCAAAAGTTA
** **
19499 GGCCCTTATTTG-GCCAAATT---AAAAGATCG
1 GGCCCTTATTTGAG-CATTTTGGCAAAAG-TTA
*
19528 GGCCCTTATTTGAGCATTTTGGCAAACGTTA
1 GGCCCTTATTTGAGCATTTTGGCAAAAGTTA
*
19559 GACCCTTATTTGAGCA
1 GGCCCTTATTTGAGCA
19575 ATTAGCCTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
28 3 0.05
29 17 0.29
30 2 0.03
31 32 0.55
32 4 0.07
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (31 bp):
GGCCCTTATTTGAGCATTTTGGCAAAAGTTA
Found at i:19536 original size:60 final size:60
Alignment explanation
Indices: 19443--19570 Score: 229
Period size: 60 Copynumber: 2.1 Consensus size: 60
19433 CCCTTATTAA
* * *
19443 CTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTGGCTAATGTTAGGCC
1 CTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACC
19503 CTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACC
1 CTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACC
19563 CTTATTTG
1 CTTATTTG
19571 AGCAATTAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (60 bp):
CTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACC
Found at i:22167 original size:3 final size:3
Alignment explanation
Indices: 22150--22187 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
22140 AAAAAAGATG
22150 GAA GAA -AA TGAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
22188 TGAAAATGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:22794 original size:21 final size:21
Alignment explanation
Indices: 22770--22811 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
22760 TTCTGTTTTC
22770 TGTGTCTATTGAGTCGAGTGG
1 TGTGTCTATTGAGTCGAGTGG
22791 TGTGTCTATTGAGTCGAGTGG
1 TGTGTCTATTGAGTCGAGTGG
22812 AATAAACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
TGTGTCTATTGAGTCGAGTGG
Found at i:24756 original size:49 final size:49
Alignment explanation
Indices: 24697--24801 Score: 156
Period size: 49 Copynumber: 2.1 Consensus size: 49
24687 AAAGACAGAT
*
24697 AAGAAAAGAATCTCAACAGTACAAGAACTGGGTGAATAGAATACTCATG
1 AAGAAAAGAATCTCAACAGCACAAGAACTGGGTGAATAGAATACTCATG
* * * * *
24746 AAGAGAAGAATCTCTACAGCAGAAGAATTGGGTGAATAGAATACTGATG
1 AAGAAAAGAATCTCAACAGCACAAGAACTGGGTGAATAGAATACTCATG
24795 AAGAAAA
1 AAGAAAA
24802 AGAAGGGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (49 bp):
AAGAAAAGAATCTCAACAGCACAAGAACTGGGTGAATAGAATACTCATG
Found at i:45642 original size:17 final size:17
Alignment explanation
Indices: 45620--45655 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
45610 GACAAAAAGC
45620 AATCAATTTAGTCAATT
1 AATCAATTTAGTCAATT
45637 AATCAATTTAGTCAATT
1 AATCAATTTAGTCAATT
45654 AA
1 AA
45656 ATTAACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (17 bp):
AATCAATTTAGTCAATT
Done.