Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001214.1 Corchorus capsularis cultivar CVL-1 contig01214, 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, 622
Length: 1038
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Found at i:33 original size:22 final size:21
Alignment explanation
Indices: 1--272 Score: 162
Period size: 22 Copynumber: 12.5 Consensus size: 21
*
1 GAAATTGTGATAACCTCGCTAT
1 GAAATTTTGATAACCTC-CTAT
*
23 GAAATTTTGATAAATCTTCCTAT
1 GAAATTTTGAT-AA-CCTCCTAT
*
46 AAAATTTTGATAAACCTCCCTAT
1 GAAATTTTGAT-AACCT-CCTAT
* * *
69 AAAATTTTGATAACTTTCTTAT
1 GAAATTTTGATAAC-CTCCTAT
*
91 GAAATCTTGATAA--T--TA-
1 GAAATTTTGATAACCTCCTAT
*
107 CAAATTTTGATAACCTCCCTAT
1 GAAATTTTGATAACCT-CCTAT
** *
129 GATTTTTTGATAACCTCATTAT
1 GAAATTTTGATAACCTC-CTAT
*
151 GAAATTTT-ATTAATCTCCCTAT
1 GAAATTTTGA-TAACCT-CCTAT
* * *
173 GAAATTTTGATCTACATACTAT
1 GAAATTTTGAT-AACCTCCTAT
* *
195 GAAATTTTGATAACCCTCTTGT
1 GAAATTTTGATAA-CCTCCTAT
* *
217 GAAATTTTGA-AAACTAAACTAT
1 GAAATTTTGATAACCT--CCTAT
* *
239 GAAGTTTTTGATAACCTTCATAT
1 GAA-ATTTTGATAACC-TCCTAT
262 GAAATTTTGAT
1 GAAATTTTGAT
273 TATTTCATAA
Statistics
Matches: 193, Mismatches: 36, Indels: 42
0.71 0.13 0.15
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
18 1 0.01
19 1 0.01
20 2 0.01
21 7 0.04
22 110 0.57
23 52 0.27
24 6 0.03
25 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (21 bp):
GAAATTTTGATAACCTCCTAT
Found at i:50 original size:23 final size:23
Alignment explanation
Indices: 19--103 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
9 GATAACCTCG
*
19 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
42 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
65 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
87 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
104 TTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:102 original size:45 final size:46
Alignment explanation
Indices: 8--103 Score: 124
Period size: 46 Copynumber: 2.1 Consensus size: 46
1 GAAATTG
* * *
8 TGAT-AACCTCGCTATGAAATTTTGATAAATCTTCCTATAAAATTT
1 TGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTATAAAATCT
* * *
53 TGATAAACCTCCCTATAAAATTTTGATAACT-TTCTTATGAAATCT
1 TGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTATAAAATCT
98 TGATAA
1 TGATAA
104 TTACAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
45 21 0.48
46 23 0.52
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (46 bp):
TGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTATAAAATCT
Found at i:220 original size:44 final size:43
Alignment explanation
Indices: 170--272 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 43
160 TTAATCTCCC
*
170 TATGAAATTTTGATCTACATACTATGAA-ATTTTGATAACCCTCT
1 TATGAAATTTTGATCTA-A-ACTATGAAGATTTTGATAACCCTCA
* * * *
214 TGTGAAATTTTGAAAACTAAACTATGAAGTTTTTGATAACCTTCA
1 TATGAAATTTTG--ATCTAAACTATGAAGATTTTGATAACCCTCA
259 TATGAAATTTTGAT
1 TATGAAATTTTGAT
273 TATTTCATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
43 1 0.02
44 19 0.39
45 25 0.51
46 4 0.08
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (43 bp):
TATGAAATTTTGATCTAAACTATGAAGATTTTGATAACCCTCA
Found at i:562 original size:21 final size:22
Alignment explanation
Indices: 352--579 Score: 111
Period size: 22 Copynumber: 10.5 Consensus size: 22
342 AAAAATATCA
352 CTATGAAATTTTTG-TAATCACATT
1 CTATGAAA-TTTTGATAATC-C-TT
*
376 -T-TGAAAATTTGATAA-CCTCT
1 CTATGAAATTTTGATAATCCT-T
* *
396 TTATGAAATTTTCATAA-CCTCT
1 CTATGAAATTTTGATAATCCT-T
* * ** * * *
418 TTATAAAATTTTTTTGACCCCT
1 CTATGAAATTTTGATAATCCTT
* *
440 CTATGAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAATC-CTT
* *
463 -TATGTAATTTTGATAATCTTT
1 CTATGAAATTTTGATAATCCTT
484 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAATCC--T-T
*
508 CTATGAAATTTCGATAATCAC-T
1 CTATGAAATTTTGATAATC-CTT
*
530 CTATGAGA-TTTGATAA-CCTT
1 CTATGAAATTTTGATAATCCTT
* * *
550 CTATCAAATTTTGGTACTCC-T
1 CTATGAAATTTTGATAATCCTT
571 -TATGAAATT
1 CTATGAAATT
580 GAGACTTTTA
Statistics
Matches: 159, Mismatches: 30, Indels: 34
0.71 0.13 0.15
Matches are distributed among these distances:
19 2 0.01
20 18 0.11
21 34 0.21
22 80 0.50
23 6 0.04
24 5 0.03
25 13 0.08
26 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCCTT
Found at i:614 original size:22 final size:22
Alignment explanation
Indices: 441--650 Score: 75
Period size: 22 Copynumber: 9.4 Consensus size: 22
431 TTGACCCCTC
* * *
441 TATGAAATTCTGATAATC-ACA
1 TATGAAATTTTGATAACCTTCA
* *
462 TTATGTAATTTTGATAATCTTTC-
1 -TATGAAATTTTGATAA-CCTTCA
485 TAT-AAATTTTGATAATCCGATCTC-
1 TATGAAATTTTGATAA-CC--T-TCA
*
509 TATGAAATTTCGATAATCAC-TC-
1 TATGAAATTTTGATAA-C-CTTCA
*
531 TATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAACCTTCA
* * *
551 TATCAAATTTTGGTACTCCTT-A
1 TATGAAATTTTGATA-ACCTTCA
*
573 TGAAATTGAGACTTTT-ATAACCTTCA
1 T---A-TGA-AATTTTGATAACCTTCA
*
599 TATGAAATTTTGATAACC-ACA
1 TATGAAATTTTGATAACCTTCA
*
620 CTATAAAATTTTGATAACC-TCA
1 -TATGAAATTTTGATAACCTTCA
642 TCATGAAAT
1 T-ATGAAAT
651 ATTTAATGAA
Statistics
Matches: 145, Mismatches: 23, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
19 1 0.01
20 8 0.06
21 34 0.23
22 64 0.44
23 2 0.01
24 6 0.04
25 18 0.12
26 7 0.05
27 5 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:714 original size:22 final size:22
Alignment explanation
Indices: 656--714 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
646 GAAATATTTA
*
656 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCACACT
* *
678 ATGAAATTCTT-ATAACCTCGCT
1 ATGAAATT-TTGATAACCACACT
*
700 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
715 TCTCTTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACT
Found at i:782 original size:22 final size:22
Alignment explanation
Indices: 750--798 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
740 TTGTGATAAT
* *
750 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTAAGAAATTTCAA
* *
772 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTAAGAAATTTCAA
794 TAACC
1 TAACC
799 TGATCCTATA
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:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTCAA
Found at i:834 original size:22 final size:22
Alignment explanation
Indices: 804--879 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
794 TAACCTGATC
*
804 CTATAAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
826 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
* *
848 CTATGAAATTTTGATAACCTC-
1 CTATGAAATTTTGGTAACCACA
869 CTCATGAAATT
1 CT-ATGAAATT
880 ATAATAATCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 2 0.04
22 46 0.96
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:866 original size:44 final size:44
Alignment explanation
Indices: 804--913 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 44
794 TAACCTGATC
* * * **
804 CTATAAAATTTTGGTAACCACACT-ATGAAATTTTGGTAACTACA-
1 CTATGAAATTTTGATAACCACACTCATGAAATTATAATAA-T-CAT
*
848 CTATGAAATTTTGATAACCTC-CTCATGAAATTATAATAATCAT
1 CTATGAAATTTTGATAACCACACTCATGAAATTATAATAATCAT
*
891 CTTATGAAATTCTGATAACCACA
1 C-TATGAAATTTTGATAACCACA
914 TAAAGACAAG
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
42 2 0.04
43 4 0.07
44 48 0.89
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCACACTCATGAAATTATAATAATCAT
Found at i:908 original size:22 final size:22
Alignment explanation
Indices: 849--909 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
839 GTAACTACAC
* *
849 TATGAAATTTTGATAACCTCCT
1 TATGAAATTATGATAACATCCT
* *
871 CATGAAATTATAATAATCAT-CT
1 TATGAAATTATGATAA-CATCCT
*
893 TATGAAATTCTGATAAC
1 TATGAAATTATGATAAC
910 CACATAAAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 1 0.03
22 28 0.90
23 2 0.06
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (22 bp):
TATGAAATTATGATAACATCCT
Done.