Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016616.1 Corchorus olitorius cultivar O-4 contig16649, 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: 49651
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:60 original size:2 final size:2
Alignment explanation
Indices: 53--90 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
43 CTCCTTGCCC
*
53 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
91 TGAACAACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3223 original size:121 final size:119
Alignment explanation
Indices: 2903--3282 Score: 543
Period size: 120 Copynumber: 3.2 Consensus size: 119
2893 TAATGAAAAA
* *
2903 TTTCCTCATATTTTGTGACAATCAACAATTGTAAGTGACGTTATATTTTAGTATTTTGTGACACA
1 TTTCCTCATTTTTTGTGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGACACA
*
2968 CATTCCGTCACCTATACATGTGATGTTGCAATTTTCGTCACAAATAATGGAACAT
66 CATTCCGTCACCTATACATGTGACGTT-CAATTTTCGTCACAAATAATGGAACAT
*
3023 TTTCCTCATTTTTTGTGACAATCAACAATTGTTAGTGACGTTATATTGTAGTATTTTGTGACACA
1 TTTCCTCATTTTTTGTGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGACACA
*
3088 CATTCCGTCACCTATAGATGTGACGTTCCAATTTTCGTCACAAATAATGGAACAT
66 CATTCCGTCACCTATACATGTGACGTT-CAATTTTCGTCACAAATAATGGAACAT
* * * *
3143 TTTCCTCATTTTTTTGTGACAATCAACAATTGTTAGTGGCGTCATATTTTAATATTTTATGACGA
1 TTTCCTCA-TTTTTTGTGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGAC-A
* *
3208 -A-ATTGGCGTCACCTATACATGTGACGTTCACATTTTCGTCACATATAACT--AAGCAT
64 CACATT-CCGTCACCTATACATGTGACGTTCA-ATTTTCGTCACAAATAA-TGGAA-CAT
* *
3264 TTTCCTCATATTTGGTGAC
1 TTTCCTCATTTTTTGTGAC
3283 GACCCATGAT
Statistics
Matches: 238, Mismatches: 16, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
120 138 0.58
121 98 0.41
122 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (119 bp):
TTTCCTCATTTTTTGTGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGACACA
CATTCCGTCACCTATACATGTGACGTTCAATTTTCGTCACAAATAATGGAACAT
Found at i:11178 original size:44 final size:44
Alignment explanation
Indices: 11114--11198 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
11104 TAAATTTCAT
* * * *
11114 AATTATAGTGGATCTAGAATATCTTTTCATAATTTAAAAAATAC
1 AATTAAAGTAGATCTAGAATATCTTTCCATAATTGAAAAAATAC
*
11158 AATTAAAGTAGATGTAGAATATCTTTCCATAATTGAAAAAA
1 AATTAAAGTAGATCTAGAATATCTTTCCATAATTGAAAAAA
11199 CAAAGTGGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (44 bp):
AATTAAAGTAGATCTAGAATATCTTTCCATAATTGAAAAAATAC
Found at i:14447 original size:19 final size:19
Alignment explanation
Indices: 14423--14477 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
14413 AGGAAACATT
*
14423 AGGTCCTTATTGAGTCATC
1 AGGTCCTTATTGAGCCATC
*
14442 AGGTCCTTATTGTGCCATC
1 AGGTCCTTATTGAGCCATC
* *
14461 AGGTTCTTATTGTGCCA
1 AGGTCCTTATTGAGCCA
14478 AAATTGAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
AGGTCCTTATTGAGCCATC
Found at i:14771 original size:15 final size:15
Alignment explanation
Indices: 14727--14774 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
14717 TTCCTAGGAG
*
14727 AGTGATTCTAGGGAG
1 AGTGATTCTAGGGAA
* *
14742 TGTGATT-TCAAGGAA
1 AGTGATTCT-AGGGAA
14757 AGTGATTCTAGGGAA
1 AGTGATTCTAGGGAA
14772 AGT
1 AGT
14775 AACAATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.29
Consensus pattern (15 bp):
AGTGATTCTAGGGAA
Found at i:19683 original size:9 final size:9
Alignment explanation
Indices: 19669--19693 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19659 GATACTCGAA
19669 TCGAGCTAC
1 TCGAGCTAC
19678 TCGAGCTAC
1 TCGAGCTAC
19687 TCGAGCT
1 TCGAGCT
19694 CGACAAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.24
Consensus pattern (9 bp):
TCGAGCTAC
Found at i:29889 original size:12 final size:12
Alignment explanation
Indices: 29872--29896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29862 GTTTCACCAG
29872 AAAAAAAGAAAA
1 AAAAAAAGAAAA
29884 AAAAAAAGAAAA
1 AAAAAAAGAAAA
29896 A
1 A
29897 CTTAAGTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:33356 original size:15 final size:15
Alignment explanation
Indices: 33298--33357 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
33288 GGGTTGGTAT
*
33298 GGCATAGGTGGCAAC
1 GGCATAGGTGGAAAC
* * *
33313 GGCATACGCGGATAC
1 GGCATAGGTGGAAAC
* *
33328 GGCAAAGGTTGAAAC
1 GGCATAGGTGGAAAC
*
33343 GCCATAGGTGGAAAC
1 GGCATAGGTGGAAAC
33358 ATCATTGGTG
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.32, C:0.20, G:0.35, T:0.13
Consensus pattern (15 bp):
GGCATAGGTGGAAAC
Found at i:36271 original size:35 final size:35
Alignment explanation
Indices: 36232--36369 Score: 267
Period size: 35 Copynumber: 3.9 Consensus size: 35
36222 GCCAAAGCAG
36232 TGGGCCGCGCGGGCCAAGGCCAAGCGCTGGCCTAC
1 TGGGCCGCGCGGGCCAAGGCCAAGCGCTGGCCTAC
36267 TGGGCCGCGCGGGCCAAGGCCAAGCGCTGGCCTAC
1 TGGGCCGCGCGGGCCAAGGCCAAGCGCTGGCCTAC
*
36302 TGGGCCACGCGGGCCAAGGCCAAGCGCTGGCCTAC
1 TGGGCCGCGCGGGCCAAGGCCAAGCGCTGGCCTAC
36337 TGGGCCGCGCGGGCCAAGGCCAAGCGCTGGCCT
1 TGGGCCGCGCGGGCCAAGGCCAAGCGCTGGCCT
36370 GCGCAGGCCA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 101 1.00
ACGTcount: A:0.14, C:0.37, G:0.40, T:0.09
Consensus pattern (35 bp):
TGGGCCGCGCGGGCCAAGGCCAAGCGCTGGCCTAC
Found at i:36373 original size:27 final size:28
Alignment explanation
Indices: 36339--36399 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
36329 TGGCCTACTG
*
36339 GGCC-GCGCGGGCCAAGG-CCAAGCGCT-
1 GGCCTGCGCAGGCC-AGGCCCAAGCGCTA
*
36365 GGCCTGCGCAGGCCAGGCCCTAGCGCTA
1 GGCCTGCGCAGGCCAGGCCCAAGCGCTA
36393 GGCCTGC
1 GGCCTGC
36400 TTTCTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.23
27 16 0.53
28 7 0.23
ACGTcount: A:0.13, C:0.39, G:0.39, T:0.08
Consensus pattern (28 bp):
GGCCTGCGCAGGCCAGGCCCAAGCGCTA
Found at i:39292 original size:13 final size:12
Alignment explanation
Indices: 39262--39318 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
39252 CCCGTTGAGG
39262 AAATGTTT-TAT
1 AAATGTTTATAT
*
39273 AACTGCTTTATAT
1 AAATG-TTTATAT
39286 AAATGCTTTATA-
1 AAATG-TTTATAT
*
39298 AAATGTTTTTAAT
1 AAATGTTTAT-AT
39311 AAATGTTT
1 AAATGTTT
39319 TGGGTGCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
11 8 0.21
12 9 0.23
13 22 0.56
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (12 bp):
AAATGTTTATAT
Found at i:42133 original size:345 final size:341
Alignment explanation
Indices: 41551--42178 Score: 1010
Period size: 345 Copynumber: 1.8 Consensus size: 341
41541 TTTTATGATC
* * * *
41551 ATTATATAGATTTTTTAGTAACTTTTAAGAAAAAAATGGTAAATATTCACCATTGATTAAAGTTT
1 ATTATATAGATTTTTCAATAACTTTTAAGAAAAAAATGGTAAATATTCACCATTGATGAAAGATT
41616 ACTACTAATGTTATTAAGAATGTAAGAATTGATAAATACAATTTTAATAACTTTTATAGCTTTTT
66 A-TACTAATGTTATTAAGAATGTAAGAATTGATAAATACAATTTTAATAACTTTTATAGCTTTTT
* *
41681 TAGTAAACTTAAGTAATAAAATTGGTAACTTTTATTAATGATAAAAAGTTACTAAAATTAATATG
130 TAGTAAACTTAAGTAATAAAATTGGTAACTTTCATTAATGATAAAAAGTTACTAAAATTAATAAG
* * *
41746 GATGTAAGGTTATTTCAATCTAGATAGTATTATAATGTTTTCCATAACCTTTATAACCTTTTAAG
195 GATGTAAGATTACTTCAATCTAGATAGTATTATAAAGTTTTCCATAACCTTTATAACCTTTTAAG
41811 AAATCTTAGATAAGAAAATCAGTATTATACCTTTATAATGTAAGGTCAGTGAAAAAGTTGATAAT
260 AAATCTTAGATAAGAAAATCAGTATTATACCTTTATAATGTAAGGTCAGTGAAAAAGTTGATAAT
41876 ATCGTACCTTTTTTATG
325 ATCGTACCTTTTTTATG
* * * *
41893 ATTATCATAGGTTTTTCAATAACTTTTGAGGAAAAAAATGGTAAATCTTTTACCATTGATGAAA-
1 ATTAT-ATAGATTTTTCAATAACTTTT-AAGAAAAAAATGGTAAAT-ATTCACCATTGATGAAAG
*
41957 ATT-TACTAATGTTATTAAGAATGTAAGGAA-TGGTAAATACAATTTTAATAACTTTTATAGCTT
63 ATTATACTAATGTTATTAAGAATGTAA-GAATTGATAAATACAATTTTAATAACTTTTATAGCTT
* *
42020 TTTTAGTAGATTACTTAAGTAATATAATTGGTAACTTTCATTATTGATAAAAAGTTACTAAAATT
127 TTTTAGTA-A--ACTTAAGTAATAAAATTGGTAACTTTCATTAATGATAAAAAGTTACTAAAATT
*
42085 AATAAGGATGTAAGATTACTTGAATCTAGATAGTATTATAAAGTTTTCCATAACCTTTATAACCT
189 AATAAGGATGTAAGATTACTTCAATCTAGATAGTATTATAAAGTTTTCCATAACCTTTATAACCT
42150 TTTAAGAAATCTTAGATAAGAAAATCAGT
254 TTTAAGAAATCTTAGATAAGAAAATCAGT
42179 GACCAATATT
Statistics
Matches: 262, Mismatches: 17, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
342 68 0.26
343 22 0.08
344 19 0.07
345 153 0.58
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (341 bp):
ATTATATAGATTTTTCAATAACTTTTAAGAAAAAAATGGTAAATATTCACCATTGATGAAAGATT
ATACTAATGTTATTAAGAATGTAAGAATTGATAAATACAATTTTAATAACTTTTATAGCTTTTTT
AGTAAACTTAAGTAATAAAATTGGTAACTTTCATTAATGATAAAAAGTTACTAAAATTAATAAGG
ATGTAAGATTACTTCAATCTAGATAGTATTATAAAGTTTTCCATAACCTTTATAACCTTTTAAGA
AATCTTAGATAAGAAAATCAGTATTATACCTTTATAATGTAAGGTCAGTGAAAAAGTTGATAATA
TCGTACCTTTTTTATG
Found at i:43109 original size:21 final size:20
Alignment explanation
Indices: 43076--43119 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
43066 GTGGAAAGCA
*
43076 TTATAGCAATTTTAATAACTT
1 TTATAACAATTTTAATAA-TT
* *
43097 TTATAACACTTTTAGTAATT
1 TTATAACAATTTTAATAATT
43117 TTA
1 TTA
43120 GATTACAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (20 bp):
TTATAACAATTTTAATAATT
Found at i:43329 original size:8 final size:8
Alignment explanation
Indices: 43316--43345 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
43306 TTAGGTTACT
43316 AATTTATG
1 AATTTATG
43324 AATTTATG
1 AATTTATG
43332 AATTTATG
1 AATTTATG
43340 AATTTA
1 AATTTA
43346 AATATTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (8 bp):
AATTTATG
Found at i:44863 original size:13 final size:13
Alignment explanation
Indices: 44845--44869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44835 TTGGAATTCC
44845 AAATAATATTTAT
1 AAATAATATTTAT
44858 AAATAATATTTA
1 AAATAATATTTA
44870 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:46662 original size:13 final size:13
Alignment explanation
Indices: 46644--46668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46634 TTATTGAATA
46644 ATAATTATTATTT
1 ATAATTATTATTT
46657 ATAATTATTATT
1 ATAATTATTATT
46669 ATTAGCTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATAATTATTATTT
Found at i:46666 original size:16 final size:16
Alignment explanation
Indices: 46641--46671 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46631 TAATTATTGA
46641 ATAATAATTATTATTT
1 ATAATAATTATTATTT
*
46657 ATAATTATTATTATT
1 ATAATAATTATTATT
46672 AGCTCAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAATAATTATTATTT
Done.