Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014256.1 Corchorus capsularis cultivar CVL-1 contig14277, 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: 49005
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:689 original size:161 final size:165
Alignment explanation
Indices: 405--748 Score: 419
Period size: 161 Copynumber: 2.1 Consensus size: 165
395 CCAGACTTGC
* * * *
405 TTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTATCAAAGCTTG
1 TTGGTCATTTCTCAATGGAC-TT-ATAGACTAGTGGAATTAATAAAAGATCCCTATCAAAGATTG
* ** * * * * * *
470 TTTTTGGAGTTAGAGAACTTATTTTTTTCGTATTTTCATATTTGACAGATTACTTAAATGTCCTA
64 ATGATGGAGCTAGAAAACTAATCTTTTTCGTATTTACATACTTGACAGATTACTTAAATGTCCTA
* *
535 -ACTTTTAATGCATGACGGGATTAAATAAGTAATCTTT
129 CA-TTTTAATGCATGACGGGATTAAATAACTAAACTTT
*
572 TTGGTCATTTCTCAATGGAC-T-TAGACTAGTGGAATTAATAAAAGATCCC-ATCAAGGATTGAT
1 TTGGTCATTTCTCAATGGACTTATAGACTAGTGGAATTAATAAAAGATCCCTATCAAAGATTGAT
* * *
634 GAT-GAGCTAGAAAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTACA
66 GATGGAGCTAGAAAACTAATCTTTTTCGTATTTACATACTTGACAGATTACTTAAATGTCCTACA
* * * *
698 TTTTGATTCTTGAGGGGATTAAATAACTAAACTTT
131 TTTTAATGCATGACGGGATTAAATAACTAAACTTT
733 TTGGTCATTTCTCAAT
1 TTGGTCATTTCTCAAT
749 TGACAAATGA
Statistics
Matches: 153, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
161 95 0.62
162 12 0.08
163 26 0.17
165 1 0.01
167 19 0.12
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (165 bp):
TTGGTCATTTCTCAATGGACTTATAGACTAGTGGAATTAATAAAAGATCCCTATCAAAGATTGAT
GATGGAGCTAGAAAACTAATCTTTTTCGTATTTACATACTTGACAGATTACTTAAATGTCCTACA
TTTTAATGCATGACGGGATTAAATAACTAAACTTT
Found at i:8222 original size:45 final size:45
Alignment explanation
Indices: 8158--8247 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
8148 GATTTTTCGA
8158 AGGAGTTGAATTTTTAAACGTATAATCATACTATAAGAA-CTAAAC
1 AGGAGTTGAATTTTTAAACGTATAATCATACTATAA-AAGCTAAAC
8203 AGGAGTTGAATTTTTAAACGTATAATCATACTATAAAAGCTAAAC
1 AGGAGTTGAATTTTTAAACGTATAATCATACTATAAAAGCTAAAC
8248 CGGATTAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 2 0.05
45 42 0.95
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (45 bp):
AGGAGTTGAATTTTTAAACGTATAATCATACTATAAAAGCTAAAC
Found at i:9814 original size:22 final size:21
Alignment explanation
Indices: 9789--9973 Score: 153
Period size: 22 Copynumber: 8.6 Consensus size: 21
9779 GGAGATCTAA
*
9789 CAAAATCTCATAGAGAAGTTAT
1 CAAAATTTCATAG-GAAGTTAT
*
9811 CAAAA-ATCATAGGAAGGTTA-
1 CAAAATTTCATAGGAA-GTTAT
*
9831 CAAAATTTCATAGGATGGTTAT
1 CAAAATTTCATAGGA-AGTTAT
* * *
9853 CGAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAG-GAAGTTAT
*
9875 CAAAATTTCATATCG-AGTTTAT
1 CAAAATTTCATA-GGAAG-TTAT
*
9897 CATAATTTCATAGGTAA-TTAT
1 CAAAATTTCATAGG-AAGTTAT
* *
9918 CAAAATTTCATAGCATGATTAT
1 CAAAATTTCATAGGAAG-TTAT
* *
9940 CAAAATTTAATACGGTAGTTAT
1 CAAAATTTCATA-GGAAGTTAT
9962 CAAAATTTCATA
1 CAAAATTTCATA
9974 AAAATATTCA
Statistics
Matches: 132, Mismatches: 19, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
20 9 0.07
21 40 0.30
22 79 0.60
23 4 0.03
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (21 bp):
CAAAATTTCATAGGAAGTTAT
Found at i:9820 original size:21 final size:20
Alignment explanation
Indices: 9796--9851 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
9786 TAACAAAATC
9796 TCATAGAGAA-GTTATCAAAAA
1 TCATAG-GAAGGTTA-CAAAAA
*
9817 TCATAGGAAGGTTACAAAATT
1 TCATAGGAAGGTTACAAAA-A
*
9838 TCATAGGATGGTTA
1 TCATAGGAAGGTTA
9852 TCGAAATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.26
21 23 0.74
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.29
Consensus pattern (20 bp):
TCATAGGAAGGTTACAAAAA
Found at i:9886 original size:44 final size:42
Alignment explanation
Indices: 9789--9973 Score: 169
Period size: 44 Copynumber: 4.3 Consensus size: 42
9779 GGAGATCTAA
* * ** *
9789 CAAAATCTCATAGAGAAG-TTATCAAAAATCATAGGAAGGTTA-
1 CAAAATTTCATAG-GATGATTATCAAATTTCATAGGTA-GTTAT
* *
9831 CAAAATTTCATAGGATGGTTATCGAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGATGATTATC-AAATTTCATAGGTA-GTTAT
* * *
9875 CAAAATTTCATATCGA-GTTTATCATAATTTCATAGGTAATTAT
1 CAAAATTTCATA-GGATGATTATCA-AATTTCATAGGTAGTTAT
* *
9918 CAAAATTTCATAGCATGATTATCAAAATTTAATACGGTAGTTAT
1 CAAAATTTCATAGGATGATTATC-AAATTTCATA-GGTAGTTAT
9962 CAAAATTTCATA
1 CAAAATTTCATA
9974 AAAATATTCA
Statistics
Matches: 120, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
41 3 0.03
42 18 0.15
43 46 0.38
44 51 0.43
45 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (42 bp):
CAAAATTTCATAGGATGATTATCAAATTTCATAGGTAGTTAT
Found at i:9925 original size:65 final size:65
Alignment explanation
Indices: 9831--9973 Score: 166
Period size: 65 Copynumber: 2.2 Consensus size: 65
9821 AGGAAGGTTA
** * * * *
9831 CAAAATTTCATAGGATGGTTATCGAAATTTCATAG-TTAGGTTATCAAAATTTCATATCGAGT-T
1 CAAAATTTCATAGGATAATTATCAAAATTTCATAGCAT-GATTATCAAAATTTAATA-CG-GTAT
9894 TAT
63 TAT
*
9897 CATAATTTCATAGG-TAATTATCAAAATTTCATAGCATGATTATCAAAATTTAATACGGTAGTTA
1 CAAAATTTCATAGGATAATTATCAAAATTTCATAGCATGATTATCAAAATTTAATACGGTA-TTA
9961 T
65 T
9962 CAAAATTTCATA
1 CAAAATTTCATA
9974 AAAATATTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
63 2 0.03
64 2 0.03
65 48 0.73
66 14 0.21
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (65 bp):
CAAAATTTCATAGGATAATTATCAAAATTTCATAGCATGATTATCAAAATTTAATACGGTATTAT
Found at i:12090 original size:13 final size:13
Alignment explanation
Indices: 12059--12097 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
12049 CTGTTTTCTT
* *
12059 TTTTTTTTTTGAT
1 TTTTTTTTTTAAG
12072 TGTTTTTTTTTAAG
1 T-TTTTTTTTTAAG
12086 TTTTTTTTTTAA
1 TTTTTTTTTTAA
12098 TGTTGGTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTTAAG
Found at i:14463 original size:20 final size:20
Alignment explanation
Indices: 14426--14463 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
14416 ACAGGCAAAC
*
14426 TACTTCACAAATACATAAAA
1 TACTTCAAAAATACATAAAA
14446 TACTTCAAACAATA-ATAA
1 TACTTCAAA-AATACATAA
14464 CAGAATCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.26
Consensus pattern (20 bp):
TACTTCAAAAATACATAAAA
Found at i:17212 original size:41 final size:44
Alignment explanation
Indices: 17140--17265 Score: 125
Period size: 50 Copynumber: 2.8 Consensus size: 44
17130 TATTTATGGA
*
17140 ATAATTATGGTGATTATA-TAATTAACCATATTATC-C-A-TAGAG
1 ATAATTAT-G-GATTATATTTATTAACCATATTATCACAATTAGAG
17182 ATAATTATGGATTATATTTATTAACCATATTATCTACATAAATATTAGAG
1 ATAATTATGGATTATATTTATTAACCATATTATC-AC----A-ATTAGAG
**
17232 ATAATTATGGATTATATTTATTATTCATATTATC
1 ATAATTATGGATTATATTTATTAACCATATTATC
17266 TTTAAAGATA
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
40 7 0.10
41 17 0.24
42 8 0.11
43 1 0.01
49 1 0.01
50 37 0.52
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.44
Consensus pattern (44 bp):
ATAATTATGGATTATATTTATTAACCATATTATCACAATTAGAG
Found at i:20072 original size:6 final size:5
Alignment explanation
Indices: 20061--20111 Score: 75
Period size: 5 Copynumber: 9.6 Consensus size: 5
20051 AAGTTCAGTC
20061 ACAAA ACAAAA ACAAA ACAAAA ACAAAA ACAAA ACAAA ACAAA ACAAA
1 ACAAA AC-AAA ACAAA AC-AAA AC-AAA ACAAA ACAAA ACAAA ACAAA
20109 ACA
1 ACA
20112 TATGTTTACA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
5 28 0.64
6 16 0.36
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
ACAAA
Found at i:20077 original size:11 final size:11
Alignment explanation
Indices: 20061--20111 Score: 79
Period size: 11 Copynumber: 4.7 Consensus size: 11
20051 AAGTTCAGTC
20061 ACAAAACAAAA
1 ACAAAACAAAA
20072 ACAAAACAAAA
1 ACAAAACAAAA
20083 ACAAAA-ACAAA
1 ACAAAACA-AAA
20094 ACAAAAC-AAA
1 ACAAAACAAAA
20104 ACAAAACA
1 ACAAAACA
20112 TATGTTTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 11 0.30
11 26 0.70
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (11 bp):
ACAAAACAAAA
Found at i:20355 original size:29 final size:29
Alignment explanation
Indices: 20289--20369 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
20279 GACGCCATTC
*
20289 CATATATACAAAAATGGCCTATGATGCCA
1 CATATATATAAAAATGGCCTATGATGCCA
* * *
20318 CACATATATAACATTGGCCTATGATGCCA
1 CATATATATAAAAATGGCCTATGATGCCA
* * *
20347 CATATATATGATAATGGCTTATG
1 CATATATATAAAAATGGCCTATG
20370 TCGCCAAACA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (29 bp):
CATATATATAAAAATGGCCTATGATGCCA
Found at i:21049 original size:154 final size:154
Alignment explanation
Indices: 20769--21076 Score: 607
Period size: 154 Copynumber: 2.0 Consensus size: 154
20759 GAAACAGTCT
20769 GCCAAACATGTTTTCACTGTTTTGTTTCCAAAAACAGGAAATTGGCAACAGAAAACAAAAAACAA
1 GCCAAACATGTTTTCACTGTTTTGTTTCCAAAAACAGGAAATTGGCAACAGAAAACAAAAAACAA
20834 AAACGATGCCAAACAAGCTCTAAATGTTCCTTCCAAGTAGCAGAATCTTTTCTCCTTGTAGAGGT
66 AAACGATGCCAAACAAGCTCTAAATGTTCCTTCCAAGTAGCAGAATCTTTTCTCCTTGTAGAGGT
20899 CAAAAGCACTCTCATTGCTGCTAA
131 CAAAAGCACTCTCATTGCTGCTAA
20923 GCCAAACATGTTTTCACTGTTTTGTTTCCAAAAACAGGAAATTGGCAACAGAAAACAAAAAACAA
1 GCCAAACATGTTTTCACTGTTTTGTTTCCAAAAACAGGAAATTGGCAACAGAAAACAAAAAACAA
*
20988 AAACGATGCTAAACAAGCTCTAAATGTTCCTTCCAAGTAGCAGAATCTTTTCTCCTTGTAGAGGT
66 AAACGATGCCAAACAAGCTCTAAATGTTCCTTCCAAGTAGCAGAATCTTTTCTCCTTGTAGAGGT
21053 CAAAAGCACTCTCATTGCTGCTAA
131 CAAAAGCACTCTCATTGCTGCTAA
21077 CAAAGGCAAG
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 153 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (154 bp):
GCCAAACATGTTTTCACTGTTTTGTTTCCAAAAACAGGAAATTGGCAACAGAAAACAAAAAACAA
AAACGATGCCAAACAAGCTCTAAATGTTCCTTCCAAGTAGCAGAATCTTTTCTCCTTGTAGAGGT
CAAAAGCACTCTCATTGCTGCTAA
Found at i:21158 original size:88 final size:88
Alignment explanation
Indices: 21006--21329 Score: 488
Period size: 88 Copynumber: 3.6 Consensus size: 88
20996 CTAAACAAGC
* * * * *
21006 TCTAAATGTTCCTTCCAAGTAGCAGAATCTTTTCTCCTTGTAGAGGTCAAAAGCACTCTCATTGC
1 TCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCTCCTTGTAGAGGTCGAAAGCACTCTTATTGC
21071 TGCTAACAAAGGCAAGCTCAATA
66 TGCTAACAAAGGCAAGCTCAATA
*
21094 TCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCTCCTTGTAGAGGTCGAGAGCACTCTTATTGC
1 TCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCTCCTTGTAGAGGTCGAAAGCACTCTTATTGC
*
21159 TGCTAACAAAGGTAAGCTCAATA
66 TGCTAACAAAGGCAAGCTCAATA
*
21182 TCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCTCCTTGTAGAGGTTGAAAGCACTCTTATTGC
1 TCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCTCCTTGTAGAGGTCGAAAGCACTCTTATTGC
* *
21247 CGCTAATCAAA-GCAAGCTTAATA
66 TGCTAA-CAAAGGCAAGCTCAATA
* * *
21270 TCTATATGCTCCCTCCAAGCAGTAGAATCCTTTTTTCTCCTTGTAGAGGTTGAAAGCACT
1 TCTAAATGCTCCCTCCAAGTAGTAGAAT-C--TTTTCTCCTTGTAGAGGTCGAAAGCACT
21330 TTCCTTGCAG
Statistics
Matches: 218, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
88 185 0.85
89 5 0.02
91 28 0.13
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (88 bp):
TCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCTCCTTGTAGAGGTCGAAAGCACTCTTATTGC
TGCTAACAAAGGCAAGCTCAATA
Found at i:22135 original size:27 final size:27
Alignment explanation
Indices: 22095--22146 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
22085 CAATCACTGT
*
22095 TATCGCAGCTTGCCAAGACAGGGTTGA
1 TATCGCAGCCTGCCAAGACAGGGTTGA
22122 TATCGCAGCCTGCCAAGACAGGGTT
1 TATCGCAGCCTGCCAAGACAGGGTT
22147 ACAGCTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.21
Consensus pattern (27 bp):
TATCGCAGCCTGCCAAGACAGGGTTGA
Found at i:28885 original size:16 final size:16
Alignment explanation
Indices: 28864--28920 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
28854 GATGTATAAT
28864 TGGTAATACATGTTGA
1 TGGTAATACATGTTGA
*
28880 TGGTAATAC-TTTGTGA
1 TGGTAATACATGT-TGA
* *
28896 CTAGTAATACATGTTGT
1 -TGGTAATACATGTTGA
28913 TGGTAATA
1 TGGTAATA
28921 TCCTGTGAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 2 0.06
16 19 0.58
17 10 0.30
18 2 0.06
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (16 bp):
TGGTAATACATGTTGA
Found at i:28928 original size:33 final size:33
Alignment explanation
Indices: 28866--28928 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
28856 TGTATAATTG
*
28866 GTAATACATGTTGATGGTAATACTTTGTGACTA
1 GTAATACATGTTGATGGTAATACTCTGTGACTA
*
28899 GTAATACATGTTGTTGGTAATA-TCCTGTGA
1 GTAATACATGTTGATGGTAATACT-CTGTGA
28929 ACTGGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.40
Consensus pattern (33 bp):
GTAATACATGTTGATGGTAATACTCTGTGACTA
Found at i:31092 original size:14 final size:13
Alignment explanation
Indices: 31060--31102 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
31050 AATAAGCACC
31060 TATATATTTTTAA
1 TATATATTTTTAA
31073 TA-ATATTTTTAA
1 TATATATTTTTAA
*
31085 TAATATATATGTTAA
1 T-ATATAT-TTTTAA
31100 TAT
1 TAT
31103 TTAAATTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 11 0.42
13 3 0.12
14 6 0.23
15 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TATATATTTTTAA
Found at i:31101 original size:15 final size:12
Alignment explanation
Indices: 31063--31090 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
31053 AAGCACCTAT
31063 ATATTTTTAATA
1 ATATTTTTAATA
31075 ATATTTTTAATA
1 ATATTTTTAATA
31087 ATAT
1 ATAT
31091 ATATGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATTTTTAATA
Found at i:32491 original size:6 final size:6
Alignment explanation
Indices: 32476--32525 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
32466 AAAACAAGCC
* * *
32476 CAACAA CAACAG CAACAT CAACAT C-A-A- CAACAG CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
32521 CAACA
1 CAACA
32526 ACAAGCGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 1 0.03
4 2 0.05
5 2 0.05
6 34 0.87
ACGTcount: A:0.54, C:0.34, G:0.08, T:0.04
Consensus pattern (6 bp):
CAACAG
Found at i:32491 original size:12 final size:12
Alignment explanation
Indices: 32476--32529 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
32466 AAAACAAGCC
32476 CAACAACAACAG
1 CAACAACAACAG
*
32488 CAACATC-A-A-
1 CAACAACAACAG
*
32497 CATCAACAACAG
1 CAACAACAACAG
*
32509 CAACAGCAACAG
1 CAACAACAACAG
32521 CAACAACAA
1 CAACAACAA
32530 GCGATTTCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
9 5 0.15
10 2 0.06
11 2 0.06
12 24 0.73
ACGTcount: A:0.56, C:0.33, G:0.07, T:0.04
Consensus pattern (12 bp):
CAACAACAACAG
Found at i:32497 original size:15 final size:15
Alignment explanation
Indices: 32479--32528 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
32469 ACAAGCCCAA
*
32479 CAACAACAGCAACAT
1 CAACAACAGCAACAG
* *
32494 CAACATCAACAACAG
1 CAACAACAGCAACAG
32509 ---CAACAGCAACAG
1 CAACAACAGCAACAG
32521 CAACAACA
1 CAACAACA
32529 AGCGATTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
12 10 0.37
15 17 0.63
ACGTcount: A:0.54, C:0.34, G:0.08, T:0.04
Consensus pattern (15 bp):
CAACAACAGCAACAG
Found at i:32503 original size:21 final size:21
Alignment explanation
Indices: 32479--32528 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
32469 ACAAGCCCAA
* *
32479 CAACAACAGCAACATCAACAT
1 CAACAACAGCAACAGCAACAG
32500 CAACAACAGCAACAGCAACAG
1 CAACAACAGCAACAGCAACAG
32521 CAACAACA
1 CAACAACA
32529 AGCGATTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.54, C:0.34, G:0.08, T:0.04
Consensus pattern (21 bp):
CAACAACAGCAACAGCAACAG
Found at i:32687 original size:18 final size:18
Alignment explanation
Indices: 32664--32702 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
32654 CTTCTAATTT
*
32664 ACAACCACCACCACAACA
1 ACAACCACCACAACAACA
* *
32682 ACAACCCCCGCAACAACA
1 ACAACCACCACAACAACA
32700 ACA
1 ACA
32703 GCAGCAACAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.49, G:0.03, T:0.00
Consensus pattern (18 bp):
ACAACCACCACAACAACA
Found at i:32710 original size:12 final size:12
Alignment explanation
Indices: 32695--32783 Score: 54
Period size: 12 Copynumber: 7.2 Consensus size: 12
32685 ACCCCCGCAA
32695 CAACAACAGCAG
1 CAACAACAGCAG
* *
32707 CAACAGCCTCCGCAG
1 CAACA---ACAGCAG
*
32722 CAGCAACAGCAG
1 CAACAACAGCAG
* *
32734 CCACAACAGCAA
1 CAACAACAGCAG
**
32746 CAACAACAGCCT
1 CAACAACAGCAG
*
32758 CAA-AATCAGCAA
1 CAACAA-CAGCAG
*
32770 CAGCAACAGCAG
1 CAACAACAGCAG
32782 CA
1 CA
32784 GCAGCAGAAG
Statistics
Matches: 57, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
11 2 0.04
12 44 0.77
13 2 0.04
15 9 0.16
ACGTcount: A:0.44, C:0.37, G:0.16, T:0.03
Consensus pattern (12 bp):
CAACAACAGCAG
Found at i:32752 original size:24 final size:26
Alignment explanation
Indices: 32725--32782 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 26
32715 TCCGCAGCAG
*
32725 CAACAGCAGC-CACAA-CAGCAACAA
1 CAACAGCAGCTCAAAATCAGCAACAA
*
32749 CAACAGC--CTCAAAATCAGCAACAG
1 CAACAGCAGCTCAAAATCAGCAACAA
32773 CAACAGCAGC
1 CAACAGCAGC
32783 AGCAGCAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 4 0.14
24 22 0.79
26 1 0.04
ACGTcount: A:0.47, C:0.36, G:0.14, T:0.03
Consensus pattern (26 bp):
CAACAGCAGCTCAAAATCAGCAACAA
Found at i:32770 original size:21 final size:21
Alignment explanation
Indices: 32720--32771 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
32710 CAGCCTCCGC
* *
32720 AGCAGCAACAGCAGCCACAAC
1 AGCAGCAACAACAGCCACAAA
* *
32741 AGCAACAACAACAGCCTCAAA
1 AGCAGCAACAACAGCCACAAA
*
32762 ATCAGCAACA
1 AGCAGCAACA
32772 GCAACAGCAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.35, G:0.13, T:0.04
Consensus pattern (21 bp):
AGCAGCAACAACAGCCACAAA
Found at i:32785 original size:12 final size:12
Alignment explanation
Indices: 32718--32796 Score: 54
Period size: 12 Copynumber: 6.6 Consensus size: 12
32708 AACAGCCTCC
32718 GCAGCAGCAACA
1 GCAGCAGCAACA
32730 GCAGCCA-CAACA
1 GCAG-CAGCAACA
* *
32742 GCAACAACAACA
1 GCAGCAGCAACA
** *
32754 GCCTCA-AAATCA
1 GCAGCAGCAA-CA
*
32766 GCAACAGCAACA
1 GCAGCAGCAACA
*
32778 GCAGCAGCAGCA
1 GCAGCAGCAACA
*
32790 GAAGCAG
1 GCAGCAG
32797 ATTCGACCGT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
11 4 0.08
12 45 0.85
13 4 0.08
ACGTcount: A:0.44, C:0.33, G:0.20, T:0.03
Consensus pattern (12 bp):
GCAGCAGCAACA
Found at i:35161 original size:132 final size:132
Alignment explanation
Indices: 34924--35191 Score: 509
Period size: 132 Copynumber: 2.0 Consensus size: 132
34914 TTATAACAGT
34924 TAATATGAAGCATTGTTCTGGAAGTTTGAGAGGGATGTTTTACAAAGTTTGTGTGCTTTTGACAT
1 TAATATGAAGCATTGTTCTGGAAGTTTGAGAGGGATGTTTTACAAAGTTTGTGTGCTTTTGACAT
*
34989 AAATCACTTAGTTCTTTGGTTGACATCAATAGGATAATTTGAGCTCTCACCCTTCTTGACTCTTG
66 AAATCACTTAGTTCTATGGTTGACATCAATAGGATAATTTGAGCTCTCACCCTTCTTGACTCTTG
35054 AG
131 AG
**
35056 TAATATGAAGCATTGTTCTGGAAGTTTGAGAGGGATGTTTTACACGGTTTGTGTGCTTTTGACAT
1 TAATATGAAGCATTGTTCTGGAAGTTTGAGAGGGATGTTTTACAAAGTTTGTGTGCTTTTGACAT
35121 AAATCACTTAGTTCTATGGTTGACATCAATAGGATAATTTGAGCTCTCACCCTTCTTGACTCTTG
66 AAATCACTTAGTTCTATGGTTGACATCAATAGGATAATTTGAGCTCTCACCCTTCTTGACTCTTG
35186 AG
131 AG
35188 TAAT
1 TAAT
35192 TTCCATGATG
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (132 bp):
TAATATGAAGCATTGTTCTGGAAGTTTGAGAGGGATGTTTTACAAAGTTTGTGTGCTTTTGACAT
AAATCACTTAGTTCTATGGTTGACATCAATAGGATAATTTGAGCTCTCACCCTTCTTGACTCTTG
AG
Found at i:40505 original size:6 final size:6
Alignment explanation
Indices: 40473--40504 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
40463 CACTCCCTCC
*
40473 CTTTCT CTTTCT CTTTCT CTTTCT CTCTCT CT
1 CTTTCT CTTTCT CTTTCT CTTTCT CTTTCT CT
40505 CGAATGACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (6 bp):
CTTTCT
Found at i:47180 original size:70 final size:72
Alignment explanation
Indices: 47080--47223 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 72
47070 ATTTATTTAA
*
47080 TATAAAAAGAAATATCTAAAATGTATCTTCTTAAACATTTATTTAAATTCAACTTTTAAACTTTA
1 TATAAAAAGAAATA-CTAAAATATATCTTCTTAAACATTTATTTAAATTCAACTTTTAAACTTTA
47145 ACTTTGAT
65 ACTTTGAT
*
47153 TATAAAAA-AAATA-TAAAATATATCTTCTTAAACTTTTATTTAAATTCAACTTTTAAACTTTAA
1 TATAAAAAGAAATACTAAAATATATCTTCTTAAACATTTATTTAAATTCAACTTTTAAACTTTAA
47216 CTTTGAT
66 CTTTGAT
47223 T
1 T
47224 GGCCAAAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
70 56 0.81
72 5 0.07
73 8 0.12
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (72 bp):
TATAAAAAGAAATACTAAAATATATCTTCTTAAACATTTATTTAAATTCAACTTTTAAACTTTAA
CTTTGAT
Done.