Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011453.1 Corchorus capsularis cultivar CVL-1 contig11474, 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: 29335
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:3285 original size:217 final size:217
Alignment explanation
Indices: 2910--3344 Score: 861
Period size: 217 Copynumber: 2.0 Consensus size: 217
2900 GATTATGATG
2910 AAACTTTTGCTCCTGTTGCCAGGTTAGAGGCTATTCGTCTTTTACTTGCTTTTGCTTGTCATTTG
1 AAACTTTTGCTCCTGTTGCCAGGTTAGAGGCTATTCGTCTTTTACTTGCTTTTGCTTGTCATTTG
2975 AACTTTAAATTATTTCAGATGGATGTGAAAAGTGTTTTCCTGAATGGCAACATTCAAGAAGAAGT
66 AACTTTAAATTATTTCAGATGGATGTGAAAAGTGTTTTCCTGAATGGCAACATTCAAGAAGAAGT
3040 GTATGTGGAACAACCTCCTGGTTTTGAAGATTTCAAAAATCCAAACCATGTTTTCAGATTGCATA
131 GTATGTGGAACAACCTCCTGGTTTTGAAGATTTCAAAAATCCAAACCATGTTTTCAGATTGCATA
3105 AGGCTTTGTATGGACTCAAACA
196 AGGCTTTGTATGGACTCAAACA
*
3127 AAACTTTTGCTCCTGTTGCCAGGTTGGAGGCTATTCGTCTTTTACTTGCTTTTGCTTGTCATTTG
1 AAACTTTTGCTCCTGTTGCCAGGTTAGAGGCTATTCGTCTTTTACTTGCTTTTGCTTGTCATTTG
3192 AACTTTAAATTATTTCAGATGGATGTGAAAAGTGTTTTCCTGAATGGCAACATTCAAGAAGAAGT
66 AACTTTAAATTATTTCAGATGGATGTGAAAAGTGTTTTCCTGAATGGCAACATTCAAGAAGAAGT
3257 GTATGTGGAACAACCTCCTGGTTTTGAAGATTTCAAAAATCCAAACCATGTTTTCAGATTGCATA
131 GTATGTGGAACAACCTCCTGGTTTTGAAGATTTCAAAAATCCAAACCATGTTTTCAGATTGCATA
3322 AGGCTTTGTATGGACTCAAACA
196 AGGCTTTGTATGGACTCAAACA
3344 A
1 A
3345 GCTCCTAGAG
Statistics
Matches: 217, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
217 217 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (217 bp):
AAACTTTTGCTCCTGTTGCCAGGTTAGAGGCTATTCGTCTTTTACTTGCTTTTGCTTGTCATTTG
AACTTTAAATTATTTCAGATGGATGTGAAAAGTGTTTTCCTGAATGGCAACATTCAAGAAGAAGT
GTATGTGGAACAACCTCCTGGTTTTGAAGATTTCAAAAATCCAAACCATGTTTTCAGATTGCATA
AGGCTTTGTATGGACTCAAACA
Found at i:9876 original size:24 final size:24
Alignment explanation
Indices: 9849--9899 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
9839 TTATTTTGCA
9849 TTGTTAGAAAATGTCGAAATACAT
1 TTGTTAGAAAATGTCGAAATACAT
9873 TTGTTAGAAAATGTCGAAATACAT
1 TTGTTAGAAAATGTCGAAATACAT
9897 TTG
1 TTG
9900 GTGGACAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (24 bp):
TTGTTAGAAAATGTCGAAATACAT
Found at i:13800 original size:14 final size:14
Alignment explanation
Indices: 13781--13809 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13771 ATAAAGTAGA
13781 ACTCAATCACATGC
1 ACTCAATCACATGC
13795 ACTCAATCACATGC
1 ACTCAATCACATGC
13809 A
1 A
13810 TATCATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.34, G:0.07, T:0.21
Consensus pattern (14 bp):
ACTCAATCACATGC
Found at i:15068 original size:11 final size:11
Alignment explanation
Indices: 15052--15111 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
15042 GAAGTTCGTG
15052 TTTGAAGATTA
1 TTTGAAGATTA
*
15063 TTTGAAGATAA
1 TTTGAAGATTA
15074 TTTGAAG---A
1 TTTGAAGATTA
*
15082 TTTGAAGACTA
1 TTTGAAGATTA
15093 -TTGAAGAATTA
1 TTTGAAG-ATTA
*
15104 TTTTAAGA
1 TTTGAAGA
15112 AGTAAAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
8 8 0.20
10 6 0.15
11 22 0.54
12 5 0.12
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:27866 original size:31 final size:31
Alignment explanation
Indices: 27825--27890 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
27815 AACTTTATGT
* * *
27825 TTTCCGATTGTACCCTTATT-TTTAAAACTTA
1 TTTCCAATTGTACCATT-TTCTTTAAAACATA
27856 TTTCCAATTGTACCATTTTCTTTAAAACATA
1 TTTCCAATTGTACCATTTTCTTTAAAACATA
27887 TTTC
1 TTTC
27891 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCATTTTCTTTAAAACATA
Found at i:28228 original size:19 final size:21
Alignment explanation
Indices: 28196--28238 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
28186 TTCTTTACTA
28196 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
28217 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
28236 TTA
1 TTA
28239 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:28660 original size:22 final size:21
Alignment explanation
Indices: 28631--28697 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
28621 TTCTTGTCTC
28631 TAAG-TGGTTATCAAATTTTCA
1 TAAGATGGTTATCAAA-TTTCA
*
28652 TAAGATGGTTATTATAATTTCA
1 TAAGATGGTTATCA-AATTTCA
* *
28674 TGAGGA-GGTTACCAAAATTTCA
1 T-AAGATGGTTATC-AAATTTCA
28696 TA
1 TA
28698 GTGTAGTTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 5 0.13
22 27 0.71
23 6 0.16
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (21 bp):
TAAGATGGTTATCAAATTTCA
Found at i:28754 original size:22 final size:22
Alignment explanation
Indices: 28726--28774 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
28716 CATAGGATCA
* *
28726 GGTTATTAAAATCTCTTAGGTT
1 GGTTATTAAAATCTCATAGGGT
* *
28748 GGTTATTGAAATTTCATAGGGT
1 GGTTATTAAAATCTCATAGGGT
28770 GGTTA
1 GGTTA
28775 ATTATCACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (22 bp):
GGTTATTAAAATCTCATAGGGT
Found at i:28869 original size:22 final size:23
Alignment explanation
Indices: 28810--28870 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
28800 ATCAAAGAGA
*
28810 TTAT-CAAAATGTCATAGCGAGG
1 TTATACAAAATTTCATAGCGAGG
* * *
28832 TTATATAAGAATTTCATAGTGTGG
1 TTATACAA-AATTTCATAGCGAGG
28856 TTA-ACAAAATTTCAT
1 TTATACAAAATTTCAT
28871 TAAATATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 12 0.38
23 5 0.16
24 15 0.47
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (23 bp):
TTATACAAAATTTCATAGCGAGG
Found at i:28906 original size:56 final size:56
Alignment explanation
Indices: 28841--28982 Score: 266
Period size: 56 Copynumber: 2.5 Consensus size: 56
28831 GTTATATAAG
*
28841 AATTTCATAGTGTGGTTAACAAAATTTCATTAAATATTTAATGGGGAGGTCATCAA
1 AATTTCATAGTGTGGTTATCAAAATTTCATTAAATATTTAATGGGGAGGTCATCAA
28897 AATTTCATAGTGTGGTTATCAAAATTTCATTAAATATTTAATGGGGAGGTCATCAA
1 AATTTCATAGTGTGGTTATCAAAATTTCATTAAATATTTAATGGGGAGGTCATCAA
*
28953 AATTTTATAGTGTGGTTATCAAAATTTCAT
1 AATTTCATAGTGTGGTTATCAAAATTTCAT
28983 ATGAAGGTTA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 84 1.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (56 bp):
AATTTCATAGTGTGGTTATCAAAATTTCATTAAATATTTAATGGGGAGGTCATCAA
Found at i:29072 original size:22 final size:23
Alignment explanation
Indices: 29020--29274 Score: 139
Period size: 22 Copynumber: 11.6 Consensus size: 23
29010 TAGGGAGTAC
* *
29020 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
29041 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
29062 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
*
29087 CAAAATTT-ATAGA-AAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
29108 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* *
29130 CAAAATTTCA-AAACGA-GGTTAT
1 CAAAATTTCATAGA-GATGATTAT
* *
29152 CAAAACTGCATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * * *
29174 CAGAATTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* * *
29196 CAAAATTTTATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
29218 CAAAATTTCATAAAGATG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* *
29240 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
29261 CAAAAGTTTCATAG
1 CAAAA-TTTCATAG
29275 TGGTATTTCT
Statistics
Matches: 183, Mismatches: 32, Indels: 36
0.73 0.13 0.14
Matches are distributed among these distances:
20 10 0.05
21 32 0.17
22 116 0.63
23 7 0.04
24 5 0.03
25 13 0.07
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:29249 original size:66 final size:66
Alignment explanation
Indices: 29083--29246 Score: 169
Period size: 66 Copynumber: 2.5 Consensus size: 66
29073 AGAGATCGGA
* ** * *
29083 TTATCAAAATTT-ATAGAA-A-GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAACG
1 TTATCAAAATTTCATA-AAGATGATTATC-AAATTTCATAGAGGGGTCAACAAAATTTCAAAACG
29145 AGG
64 AGG
* * * *
29148 TTATCAAAACTGCATAATG-TGATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAA-G
1 TTATCAAAATTTCATAAAGATGATTATCA-AATTTCATAGAGGGGTCAACAAAATTTCA-AAACG
29211 AGG
64 AGG
29214 TTATCAAAATTTCATAAAGATG-TTATCAAATTT
1 TTATCAAAATTTCATAAAGATGATTATCAAATTT
29247 TCAAAATGTG
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
65 17 0.21
66 59 0.73
67 5 0.06
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (66 bp):
TTATCAAAATTTCATAAAGATGATTATCAAATTTCATAGAGGGGTCAACAAAATTTCAAAACGAG
G
Done.