Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014849.1 Corchorus capsularis cultivar CVL-1 contig14870, 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: 30878
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:194 original size:79 final size:76
Alignment explanation
Indices: 11--250 Score: 341
Period size: 70 Copynumber: 3.2 Consensus size: 76
1 TTTTTTTAAC
*
11 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGAATTTAATTATATAAAAATTG
1 TAAAATAGTAAAA-TGTAAAATATAATAG-TATAAGGATATTAG-ATTTAATTATATAAAAATAG
76 AGTTTTTAGTTGAG
63 AGTTTTTAGTTGAG
90 TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAG-TATAAGGATATTAGATTTAATTATATAAAAATAGA
155 GTTTTTAGTTGAG
64 GTTTTTAGTTGAG
* * *
168 TAAAATAGTAAAA--T-AAA-ATAAT--TATAAAGATATTATATTTAATTAAATAAAAATAGAGT
1 TAAAATAGTAAAATGTAAAATATAATAGTATAAGGATATTAGATTTAATTATATAAAAATAGAGT
227 TTTTAGTTGAG
66 TTTTAGTTGAG
238 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
251 ACCTAAACAA
Statistics
Matches: 154, Mismatches: 5, Indels: 13
0.90 0.03 0.08
Matches are distributed among these distances:
70 55 0.36
71 2 0.01
73 5 0.03
74 3 0.02
75 1 0.01
78 47 0.31
79 41 0.27
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (76 bp):
TAAAATAGTAAAATGTAAAATATAATAGTATAAGGATATTAGATTTAATTATATAAAAATAGAGT
TTTTAGTTGAG
Found at i:450 original size:12 final size:12
Alignment explanation
Indices: 433--458 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
423 AGATTCTCCC
433 ATTATAATTAGT
1 ATTATAATTAGT
445 ATTATAATTAGT
1 ATTATAATTAGT
457 AT
1 AT
459 AGATAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTATAATTAGT
Found at i:11053 original size:66 final size:64
Alignment explanation
Indices: 10947--11135 Score: 256
Period size: 66 Copynumber: 2.9 Consensus size: 64
10937 GCTGCAGCCT
10947 TTTCTTCTAGGATCTCTTCTGGCATATCCAAAACCTGATCAGTTTCCTCCACTGTTTCAAACCGA
1 TTTCTTCT-GGATCTCTTCTGGCATATCCAAAA-CTGATCAGTTTCCTCCACTGTTTCAAACCGA
11012 G
64 G
* *
11013 TTTCTTCTGCGATCTCTTCTGGCATATCCAAAACTTGATCAGTTTCCTCCACTGTTTCAATCTGA
1 TTTCTTCTG-GATCTCTTCTGGCATATCCAAAAC-TGATCAGTTTCCTCCACTGTTTCAAACCGA
11078 G
64 G
* * * * *
11079 GTTCTTCTGAGATATCTTCTGGCATGTCC--GACTGATCAGTTTCCTCCACCGTTTCAA
1 TTTCTTCTG-GATCTCTTCTGGCATATCCAAAACTGATCAGTTTCCTCCACTGTTTCAA
11136 TCTCACCCTG
Statistics
Matches: 113, Mismatches: 8, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
63 24 0.21
64 2 0.02
65 2 0.02
66 85 0.75
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (64 bp):
TTTCTTCTGGATCTCTTCTGGCATATCCAAAACTGATCAGTTTCCTCCACTGTTTCAAACCGAG
Found at i:11415 original size:45 final size:45
Alignment explanation
Indices: 11365--11464 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
11355 CTTCCAGCAT
* * *
11365 TGCCTCTTCAACCTTTTGAGGCTCCTCA-AAATCTAAATTTTCCGC
1 TGCCTCTTCAACCTCTTCAGGCTCCTCATAAA-CTAAATTTTCCAC
* ** *
11410 TGCCTCCTCAACCTCTTCAGGCTCCTCATAAACTGCATTTTCCAT
1 TGCCTCTTCAACCTCTTCAGGCTCCTCATAAACTAAATTTTCCAC
11455 TGCCTCTTCA
1 TGCCTCTTCA
11465 GGTTCCCTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 43 0.93
46 3 0.07
ACGTcount: A:0.20, C:0.35, G:0.10, T:0.35
Consensus pattern (45 bp):
TGCCTCTTCAACCTCTTCAGGCTCCTCATAAACTAAATTTTCCAC
Found at i:13507 original size:6 final size:6
Alignment explanation
Indices: 13498--13522 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13488 CAAGAAAAAG
13498 AAATTC AAATTC AAATTC AAATTC A
1 AAATTC AAATTC AAATTC AAATTC A
13523 TGTATATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTC
Found at i:14189 original size:3 final size:3
Alignment explanation
Indices: 14181--14210 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
14171 ATCAAGTCAC
14181 ATA ATA ATAA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA AT
14211 GGATCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:15563 original size:282 final size:285
Alignment explanation
Indices: 15054--15623 Score: 1020
Period size: 282 Copynumber: 2.0 Consensus size: 285
15044 GGTGTGTAAA
* *
15054 TTTTAGCATACTAGGAATCTAAAAGTTTATCACGTATTTATATGTGAGTCTAGTCTTCTCATTGA
1 TTTTAGCATACTAGGAATCTAAAAGTTTATCACGTATTTATA-GT-AGTCGAGTCTTCTCATCGA
*
15119 AAGACTATCCTGGAAAATCCTAATTGATCACAAGCCCATTAATAAAAATATTTGGGCCACATTTA
64 AAGACTATCCTGGAAAACCCTAATTGATCACAAGCCCATTAATAAAAATATTTGGGCCACATTTA
*
15184 GCTATTGGATTTTAATTAAATTTTATTCCAAAAATCTTATTATCTATACTAATCTATTAATGTGA
129 GCTATTGGATCTTAATTAAATTTTATTCCAAAAATCTTATTATCTATACTAATCTATTAATGTGA
* * *
15249 GAATTTGAATTTGTTTCATGAGTTGGCTCGGAGAAAAATTTGATTTTGAAAAATCAAAAATAACT
194 GAATTTGAATTTGTCTCATGAGTTGGCTCGGAGAAAAATTCGATTTTGAAAAACCAAAAATAACT
15314 ACCTATCTAAAGGATAAATTTGATATC
259 ACCTATCTAAAGGATAAATTTGATATC
15341 TTTTAGCATACTAGGAATCTAAAAGTTTATCACGTATTTATA-T-G-CGAGTCTTCTCATCGAAA
1 TTTTAGCATACTAGGAATCTAAAAGTTTATCACGTATTTATAGTAGTCGAGTCTTCTCATCGAAA
15403 GACTATCCTGGAAAACCCTAATTGATCACAAGCCCATTAATAAAAATATTTGGGCCACATTTAGC
66 GACTATCCTGGAAAACCCTAATTGATCACAAGCCCATTAATAAAAATATTTGGGCCACATTTAGC
15468 TATTGGATCTTAATTAAATTTTATTCCAAAAATCTTATTATCTATACTAATCTATTAATGTGAGA
131 TATTGGATCTTAATTAAATTTTATTCCAAAAATCTTATTATCTATACTAATCTATTAATGTGAGA
* *
15533 ATTTGAATTTGTCTCATGAGTTGGCTCGGAGACAAATTCGATTTTGAAAAACCAAAAGTAACTAC
196 ATTTGAATTTGTCTCATGAGTTGGCTCGGAGAAAAATTCGATTTTGAAAAACCAAAAATAACTAC
15598 CTATCTAAAGGATAAATTTGATATC
261 CTATCTAAAGGATAAATTTGATATC
15623 T
1 T
15624 ATATCTTATT
Statistics
Matches: 274, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
282 230 0.84
283 1 0.00
285 1 0.00
287 42 0.15
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (285 bp):
TTTTAGCATACTAGGAATCTAAAAGTTTATCACGTATTTATAGTAGTCGAGTCTTCTCATCGAAA
GACTATCCTGGAAAACCCTAATTGATCACAAGCCCATTAATAAAAATATTTGGGCCACATTTAGC
TATTGGATCTTAATTAAATTTTATTCCAAAAATCTTATTATCTATACTAATCTATTAATGTGAGA
ATTTGAATTTGTCTCATGAGTTGGCTCGGAGAAAAATTCGATTTTGAAAAACCAAAAATAACTAC
CTATCTAAAGGATAAATTTGATATC
Found at i:15731 original size:136 final size:136
Alignment explanation
Indices: 15557--15810 Score: 481
Period size: 136 Copynumber: 1.9 Consensus size: 136
15547 CATGAGTTGG
* *
15557 CTCGGAGACAAATTCGATTTTGAAAAACCAAAAGTAACTACCTATCTAAAGGATAAATTTGATAT
1 CTCGGAGACAAATTCGATTCTGAAAAACCAAAAATAACTACCTATCTAAAGGATAAATTTGATAT
*
15622 CTATATCTTATTATTTTACCTATATATATTAGAGTTATCCTCAAACTGCTGTACGTTCAGAATTT
66 CTATATCTTATTATTTTACCTATATACATTAGAGTTATCCTCAAACTGCTGTACGTTCAGAATTT
15687 GACTCA
131 GACTCA
15693 CTCGGAGACAAATTCGATTCTGAAAAACCAAAAATAACTACCTATCTAAAGGATAAATTTGATAT
1 CTCGGAGACAAATTCGATTCTGAAAAACCAAAAATAACTACCTATCTAAAGGATAAATTTGATAT
15758 CTATATCTTATTATTTTACCTATATACATTAGAGTTATCCTCAAACTGCTGTA
66 CTATATCTTATTATTTTACCTATATACATTAGAGTTATCCTCAAACTGCTGTA
15811 TGCTTAAGAT
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 115 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (136 bp):
CTCGGAGACAAATTCGATTCTGAAAAACCAAAAATAACTACCTATCTAAAGGATAAATTTGATAT
CTATATCTTATTATTTTACCTATATACATTAGAGTTATCCTCAAACTGCTGTACGTTCAGAATTT
GACTCA
Found at i:18120 original size:5 final size:5
Alignment explanation
Indices: 18109--18150 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
18099 GCTTACTGCT
* *
18109 TAGCC GAGCC GAGCC TAGCC TAGCC TAGCC TAGCC TAGCC TA
1 TAGCC TAGCC TAGCC TAGCC TAGCC TAGCC TAGCC TAGCC TA
18151 CTAGTTCTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (5 bp):
TAGCC
Found at i:19817 original size:21 final size:21
Alignment explanation
Indices: 19792--19875 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 21
19782 ATACTGTTTT
19792 TTCAATTCTGTTTTTGTTTAG
1 TTCAATTCTGTTTTTGTTTAG
*
19813 TTCAATTCTGTTTTTTAATTCTGTTT-T
1 TTCAATTCTG----TT--TT-TGTTTAG
*
19840 TTCAATTCTATTTTTGTTTAG
1 TTCAATTCTGTTTTTGTTTAG
19861 TTCAATTCTGTTTTT
1 TTCAATTCTGTTTTT
19876 AATATGCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
20 5 0.10
21 26 0.51
23 2 0.04
25 2 0.04
27 11 0.22
28 5 0.10
ACGTcount: A:0.15, C:0.11, G:0.10, T:0.64
Consensus pattern (21 bp):
TTCAATTCTGTTTTTGTTTAG
Found at i:19820 original size:48 final size:47
Alignment explanation
Indices: 19768--19879 Score: 188
Period size: 48 Copynumber: 2.3 Consensus size: 47
19758 ATATTTTGTA
*
19768 AATTCTGTTTTTCAATACTGTTTTTTCAATTCTGTTTTTGTTTAGTTC
1 AATTCTGTTTTT-AATACTGTTTTTTCAATTCTATTTTTGTTTAGTTC
*
19816 AATTCTGTTTTTTAATTCTGTTTTTTCAATTCTATTTTTGTTTAGTTC
1 AATTCTG-TTTTTAATACTGTTTTTTCAATTCTATTTTTGTTTAGTTC
19864 AATTCTGTTTTTAATA
1 AATTCTGTTTTTAATA
19880 TGCAAAGTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
47 8 0.13
48 47 0.78
49 5 0.08
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.62
Consensus pattern (47 bp):
AATTCTGTTTTTAATACTGTTTTTTCAATTCTATTTTTGTTTAGTTC
Found at i:19834 original size:13 final size:14
Alignment explanation
Indices: 19813--19854 Score: 68
Period size: 13 Copynumber: 3.1 Consensus size: 14
19803 TTTTGTTTAG
19813 TTCAATTCTGTTTT
1 TTCAATTCTGTTTT
19827 TT-AATTCTGTTTT
1 TTCAATTCTGTTTT
*
19840 TTCAATTCTATTTT
1 TTCAATTCTGTTTT
19854 T
1 T
19855 GTTTAGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.67
Consensus pattern (14 bp):
TTCAATTCTGTTTT
Found at i:19846 original size:14 final size:14
Alignment explanation
Indices: 19768--19854 Score: 79
Period size: 14 Copynumber: 5.9 Consensus size: 14
19758 ATATTTTGTA
19768 AATTCTG-TTTTTC
1 AATTCTGTTTTTTC
*
19781 AATACTGTTTTTTC
1 AATTCTGTTTTTTC
19795 AATTCTGTTTTTGTTTAGTTC
1 AATTCTG----T-TTT--TTC
19816 AATTCTGTTTTTT-
1 AATTCTGTTTTTTC
19829 AATTCTGTTTTTTC
1 AATTCTGTTTTTTC
*
19843 AATTCTATTTTT
1 AATTCTGTTTTT
19855 GTTTAGTTCA
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
13 19 0.31
14 25 0.40
16 3 0.05
17 1 0.02
18 1 0.02
19 3 0.05
21 10 0.16
ACGTcount: A:0.17, C:0.11, G:0.08, T:0.63
Consensus pattern (14 bp):
AATTCTGTTTTTTC
Found at i:25778 original size:164 final size:166
Alignment explanation
Indices: 25468--25780 Score: 443
Period size: 166 Copynumber: 1.9 Consensus size: 166
25458 GAGTCATTTG
* * *
25468 TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTGAAGAATAAAAAGTAAGGACATT
1 TCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATAAAAAGTAAGGACATT
** * * * *
25533 TAAGTAATCTGCCAAGTAGGTAAATACGAAAAAGATTAGTTCTCCAGCTCATCATTAATCCGGGG
66 TAAGTAATAGGCCAAATAGGAAAAGACGAAAAAGAATAGTTCTCCAGCTCATCATTAATCCGGGG
*
25598 TATGGATCTTTTAGTAATTCCACTACTTTATTAAAT
131 TAGGGATCTTTTAGTAATTCCACTACTTTATTAAAT
* * *
25634 TCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTA-GATATT
1 TCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATAAAAAGTAAGGACATT
* * * *
25698 TAAGTAATAGGTCAAATGGGAAAAGACGAAAAA-AATAGTTCTTTC-GCTCCTCATTAATCCGGG
66 TAAGTAATAGGCCAAATAGGAAAAGACGAAAAAGAATAGTTC-TCCAGCTCATCATTAATCCGGG
25761 GTAGGGATCTTTTAGTAATT
130 GTAGGGATCTTTTAGTAATT
25781 TTCATATATT
Statistics
Matches: 129, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
164 43 0.33
165 33 0.26
166 53 0.41
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (166 bp):
TCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATAAAAAGTAAGGACATT
TAAGTAATAGGCCAAATAGGAAAAGACGAAAAAGAATAGTTCTCCAGCTCATCATTAATCCGGGG
TAGGGATCTTTTAGTAATTCCACTACTTTATTAAAT
Found at i:27279 original size:30 final size:29
Alignment explanation
Indices: 27245--27311 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
27235 GGTAAAGGAG
*
27245 GGTGCAAAATGTACGCAAAATAAAACA-TTA
1 GGTGCAAAATG-A-GCAAAATAAAAAAGTTA
* * *
27275 GGTGCAATATGATCAAAATAAAAAAGTTG
1 GGTGCAAAATGAGCAAAATAAAAAAGTTA
27304 GGTGCAAA
1 GGTGCAAA
27312 GTGATAGTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 11 0.35
29 10 0.32
30 10 0.32
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (29 bp):
GGTGCAAAATGAGCAAAATAAAAAAGTTA
Found at i:30644 original size:3 final size:3
Alignment explanation
Indices: 30638--30705 Score: 88
Period size: 3 Copynumber: 23.3 Consensus size: 3
30628 ATTTGAACAA
* *
30638 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -TT GAAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
30686 AA- AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
30706 TACAAATGTC
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
2 5 0.09
3 53 0.91
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Done.