Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015609.1 Corchorus olitorius cultivar O-4 contig15642, 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: 46855
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:890 original size:20 final size:20
Alignment explanation
Indices: 865--910 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
855 TCCTAATTTC
865 AATGGGAGTTAAATGAAAGA
1 AATGGGAGTTAAATGAAAGA
885 AATGGGAGTTAAATGAAAGA
1 AATGGGAGTTAAATGAAAGA
905 AATGGG
1 AATGGG
911 CTCTTCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.20
Consensus pattern (20 bp):
AATGGGAGTTAAATGAAAGA
Found at i:2007 original size:11 final size:11
Alignment explanation
Indices: 1993--2030 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1983 ATTCATAACA
1993 AATTTATAATT
1 AATTTATAATT
2004 AATTTATAATT
1 AATTTATAATT
2015 -ATTTGATAATT
1 AATTT-ATAATT
*
2026 TATTT
1 AATTT
2031 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:6370 original size:47 final size:47
Alignment explanation
Indices: 6316--6412 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
6306 TGCAGAATAA
6316 AAGGTTTCTAAGTTACAAAAGAAACAACAATGCAACAGGATGGAGCT
1 AAGGTTTCTAAGTTACAAAAGAAACAACAATGCAACAGGATGGAGCT
6363 AAGGTTTCTAAGTTACAAAAGAAACAACAATGCAACAGGATGGAGCT
1 AAGGTTTCTAAGTTACAAAAGAAACAACAATGCAACAGGATGGAGCT
6410 AAG
1 AAG
6413 CTAATTATCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (47 bp):
AAGGTTTCTAAGTTACAAAAGAAACAACAATGCAACAGGATGGAGCT
Found at i:6493 original size:24 final size:25
Alignment explanation
Indices: 6461--6510 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
6451 TTTGCCTGAG
*
6461 TTCCTTGGCAACC-CCAATAATCTC
1 TTCCTTGGCAACCTCAAATAATCTC
6485 TTCCTTGGCAACCTCAAATAATCTC
1 TTCCTTGGCAACCTCAAATAATCTC
6510 T
1 T
6511 GCTTTTCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.26, C:0.34, G:0.08, T:0.32
Consensus pattern (25 bp):
TTCCTTGGCAACCTCAAATAATCTC
Found at i:8906 original size:14 final size:13
Alignment explanation
Indices: 8888--8913 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8878 AAACCTGATT
8888 TTTTTTTTTAAAC
1 TTTTTTTTTAAAC
8901 TTTTTTTTTAAAC
1 TTTTTTTTTAAAC
8914 ATTGATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTTTAAAC
Found at i:18511 original size:18 final size:18
Alignment explanation
Indices: 18488--18523 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
18478 ATGAAGCATA
18488 AGAGACTAGACTGACTCT
1 AGAGACTAGACTGACTCT
18506 AGAGACTAGACTGACTCT
1 AGAGACTAGACTGACTCT
18524 CAAGATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
AGAGACTAGACTGACTCT
Found at i:19126 original size:19 final size:20
Alignment explanation
Indices: 19075--19127 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
19065 ACAAATATTC
19075 AAATGCAAG-AGAATGAGATG
1 AAATGCAAGAAG-ATGAGATG
*
19095 AAAGTGCATGAAGATGA-ATG
1 AAA-TGCAAGAAGATGAGATG
19115 AAATGCAAGAAGA
1 AAATGCAAGAAGA
19128 GTTAAGTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 9 0.31
20 9 0.31
21 9 0.31
22 2 0.07
ACGTcount: A:0.51, C:0.06, G:0.28, T:0.15
Consensus pattern (20 bp):
AAATGCAAGAAGATGAGATG
Found at i:26767 original size:9 final size:9
Alignment explanation
Indices: 26727--26766 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
26717 GGAATTAAAC
26727 AATTCACCA
1 AATTCACCA
26736 AATTCACCA
1 AATTCACCA
26745 AATTCACCA
1 AATTCACCA
26754 AATT-ACCA
1 AATTCACCA
26762 GAATT
1 -AATT
26767 AATCTCCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 4 0.13
9 26 0.87
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.25
Consensus pattern (9 bp):
AATTCACCA
Found at i:32356 original size:3 final size:3
Alignment explanation
Indices: 32348--32379 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
32338 CCCAAAAACC
32348 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
32380 AGGGTTGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35327 original size:21 final size:18
Alignment explanation
Indices: 35292--35330 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
35282 AATTTCAGAA
35292 AAAAAAAAACGTAATAAT
1 AAAAAAAAACGTAATAAT
*
35310 AAAAAAAAACGCAATAAT
1 AAAAAAAAACGTAATAAT
35328 AAA
1 AAA
35331 TTTTTTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (18 bp):
AAAAAAAAACGTAATAAT
Found at i:37490 original size:30 final size:30
Alignment explanation
Indices: 37454--37514 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
37444 TTAGTAAGAT
* *
37454 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
1 ATTAAAATTTGAGGGTATAAAAAGAAAGTC
37484 ATTAAAATTTGAGGGTATAAAAAGAAAGTC
1 ATTAAAATTTGAGGGTATAAAAAGAAAGTC
37514 A
1 A
37515 AGATAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.23, T:0.26
Consensus pattern (30 bp):
ATTAAAATTTGAGGGTATAAAAAGAAAGTC
Found at i:38163 original size:4 final size:4
Alignment explanation
Indices: 38154--38183 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
38144 AGTTACTCAG
38154 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
38184 TATATACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:39344 original size:55 final size:51
Alignment explanation
Indices: 39246--39350 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 51
39236 TCATAAAAAT
*
39246 AAATAAATAAATATAATAAATCACATATTAATTTGTAATCATAAATCATAA
1 AAATAAAAAAATATAATAAATCACATATTAATTTGTAATCATAAATCATAA
*
39297 AAATAAAAAAATATGATAAATCACATATTAATTTGTAAT-AT-AA-CATAA
1 AAATAAAAAAATATAATAAATCACATATTAATTTGTAATCATAAATCATAA
39345 AAATAA
1 AAATAA
39351 TATAATTTCC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
48 11 0.21
49 2 0.04
50 2 0.04
51 37 0.71
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (51 bp):
AAATAAAAAAATATAATAAATCACATATTAATTTGTAATCATAAATCATAA
Found at i:42164 original size:20 final size:19
Alignment explanation
Indices: 42130--42167 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
42120 ATATTTACTA
*
42130 AAAACAATTAGAGGTTATC
1 AAAACAATTAAAGGTTATC
42149 AAAACAATTATAAGGTTAT
1 AAAACAATTA-AAGGTTAT
42168 TAATAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAACAATTAAAGGTTATC
Found at i:43162 original size:45 final size:44
Alignment explanation
Indices: 43099--43189 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 44
43089 TTAGTTCTTC
43099 TTTTTTTATAGGTTATTCCTAACTACCAACTTCTTCCCTCTGTG
1 TTTTTTTATAGGTTATTCCTAACTACCAACTTCTTCCCTCTGTG
*
43143 TTTTATTTATAGGTTATTCCTAACTATCAACTTCTTCCCTCTGTG
1 TTTT-TTTATAGGTTATTCCTAACTACCAACTTCTTCCCTCTGTG
43188 TT
1 TT
43190 CATAGAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 4 0.09
45 41 0.91
ACGTcount: A:0.19, C:0.23, G:0.09, T:0.49
Consensus pattern (44 bp):
TTTTTTTATAGGTTATTCCTAACTACCAACTTCTTCCCTCTGTG
Found at i:43335 original size:27 final size:27
Alignment explanation
Indices: 43305--43385 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
43295 TACCAAAATA
43305 TTATGAGATTAGAGAAAATCATAACAC
1 TTATGAGATTAGAGAAAATCATAACAC
* * * *
43332 TTATGA-ATCA-ATACAA--A-AATA-
1 TTATGAGATTAGAGAAAATCATAACAC
*
43353 TTATGAGATTAGAGCAAATCATAACAC
1 TTATGAGATTAGAGAAAATCATAACAC
*
43380 TCATGA
1 TTATGA
43386 ATCAAAATAG
Statistics
Matches: 38, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
21 6 0.16
22 6 0.16
23 4 0.11
25 5 0.13
26 6 0.16
27 11 0.29
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (27 bp):
TTATGAGATTAGAGAAAATCATAACAC
Found at i:43345 original size:48 final size:48
Alignment explanation
Indices: 43293--43390 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
43283 ACGTTAATTT
* *
43293 AATACCAAAATATTATGAGATTAGAGAAAATCATAACACTTATGAATC
1 AATACAAAAATATTATGAGATTAGAGAAAATCATAACACTCATGAATC
*
43341 AATACAAAAATATTATGAGATTAGAGCAAATCATAACACTCATGAATC
1 AATACAAAAATATTATGAGATTAGAGAAAATCATAACACTCATGAATC
43389 AA
1 AA
43391 AATAGTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (48 bp):
AATACAAAAATATTATGAGATTAGAGAAAATCATAACACTCATGAATC
Found at i:45820 original size:72 final size:75
Alignment explanation
Indices: 45692--45830 Score: 230
Period size: 72 Copynumber: 1.9 Consensus size: 75
45682 GACTCGATCA
*
45692 GTTGTTTAACGTAATATCTCAAAAAAAAAAAGAGAGATGTACTTTAACTTAAAAATAATGAGTAT
1 GTTGTTCAACGTAATATCTC--AAAAAAAAAGAGAGATGTACTTTAACTTAAAAATAATGAGTAT
45757 TACTAATAATTT
64 TACTAATAATTT
45769 GTTGTTCAACGTAATATCTC-AAAAAAAA-A-AGATGTACTTTAACTTAAAAATAATGAGTATTA
1 GTTGTTCAACGTAATATCTCAAAAAAAAAGAGAGATGTACTTTAACTTAAAAATAATGAGTATTA
45831 TTTTAGACTT
Statistics
Matches: 61, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
72 33 0.54
73 1 0.02
74 8 0.13
77 19 0.31
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.33
Consensus pattern (75 bp):
GTTGTTCAACGTAATATCTCAAAAAAAAAGAGAGATGTACTTTAACTTAAAAATAATGAGTATTA
CTAATAATTT
Done.