Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011935.1 Corchorus olitorius cultivar O-4 contig11968, 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: 56060
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Found at i:457 original size:10 final size:10
Alignment explanation
Indices: 442--499 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
432 GGAAGAAAAA
442 CTAATTAAAT
1 CTAATTAAAT
*
452 CTAATTAAGT
1 CTAATTAAAT
*
462 CTAATTAAAC
1 CTAATTAAAT
*
472 CTTAACT-AAT
1 C-TAATTAAAT
*
482 CTAAATAAAT
1 CTAATTAAAT
492 -T-ATTAAAT
1 CTAATTAAAT
500 ACTAGCCCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
8 6 0.15
9 5 0.13
10 24 0.62
11 4 0.10
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (10 bp):
CTAATTAAAT
Found at i:1947 original size:96 final size:94
Alignment explanation
Indices: 1785--1962 Score: 266
Period size: 96 Copynumber: 1.9 Consensus size: 94
1775 AAGACCATGG
* * *
1785 CCCAACGTGATGATCCAAGTGGAAACGAAAAGAAAAAAAGAAATGAACCCAACATGATGGCCCAA
1 CCCAACATGATGACCCAAGTGGAAACAAAAAGAAAAAAAGAAATGAACCCAACATGATGGCCCAA
*
1850 GTGTAAACAAAAAGAAAAAAAGAAATGAA
66 GTGGAAACAAAAAGAAAAAAAGAAATGAA
* * **
1879 CCCAACATGATGGCCCAAGTGTAAACAAAAAGAAATAGATGGAAATGAACCCAACATGATGGCCC
1 CCCAACATGATGACCCAAGTGGAAACAAAAAGAAA-A-AAAGAAATGAACCCAACATGATGGCCC
1944 AAGTGGAAACAAAAAGAAA
64 AAGTGGAAACAAAAAGAAA
1963 TAGTTGGAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
94 30 0.41
95 1 0.01
96 43 0.58
ACGTcount: A:0.52, C:0.17, G:0.20, T:0.11
Consensus pattern (94 bp):
CCCAACATGATGACCCAAGTGGAAACAAAAAGAAAAAAAGAAATGAACCCAACATGATGGCCCAA
GTGGAAACAAAAAGAAAAAAAGAAATGAA
Found at i:1983 original size:49 final size:47
Alignment explanation
Indices: 1785--1962 Score: 266
Period size: 47 Copynumber: 3.7 Consensus size: 47
1775 AAGACCATGG
* ** *
1785 CCCAACGTGATGATCCAAGTGGAAACGAAAAGAAAAAAAGAAATGAA
1 CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAAAAAAGAAATGAA
*
1832 CCCAACATGATGGCCCAAGTGTAAACAAAAAGAAAAAAAGAAATGAA
1 CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAAAAAAGAAATGAA
* **
1879 CCCAACATGATGGCCCAAGTGTAAACAAAAAGAAATAGATGGAAATGAA
1 CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAA-A-AAAGAAATGAA
1928 CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAA
1 CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAA
1963 TAGTTGGAAA
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
47 77 0.64
48 1 0.01
49 43 0.36
ACGTcount: A:0.52, C:0.17, G:0.20, T:0.11
Consensus pattern (47 bp):
CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAAAAAAGAAATGAA
Found at i:2356 original size:25 final size:25
Alignment explanation
Indices: 2328--2377 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2318 AGATCCTAAA
2328 CAGGTTTTTTCTTAAACGAAAACTC
1 CAGGTTTTTTCTTAAACGAAAACTC
*
2353 CAGGTTTTTTCTTAAATGAAAACTC
1 CAGGTTTTTTCTTAAACGAAAACTC
2378 TAAGTAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (25 bp):
CAGGTTTTTTCTTAAACGAAAACTC
Found at i:2425 original size:39 final size:39
Alignment explanation
Indices: 2363--2876 Score: 439
Period size: 39 Copynumber: 13.2 Consensus size: 39
2353 CAGGTTTTTT
* * * * **
2363 CTTAAATGAAAACTCTAAGTAGAGATCTAAGCAAATTTA
1 CTTAAATGGAAACTTTAAATAGAGACCTAAGCAGGTTTA
* *
2402 CTTAAATGGAAACTATAAATAGAGATCTAAGCAGGTTTA
1 CTTAAATGGAAACTTTAAATAGAGACCTAAGCAGGTTTA
* * *
2441 CTTAAAATGG-AACTCTAAATAGAGATCTAGGCAGGTTTA
1 CTT-AAATGGAAACTTTAAATAGAGACCTAAGCAGGTTTA
* * *
2480 CTTAAATGGAAACTTTAGACACAGACCTAAGCAGGTTTA
1 CTTAAATGGAAACTTTAAATAGAGACCTAAGCAGGTTTA
* * * *
2519 CTTCAATGGAAACTTTAGACACAGACCTAAGCAGGTTTA
1 CTTAAATGGAAACTTTAAATAGAGACCTAAGCAGGTTTA
* *
2558 CTTAAATGGAAACTTTAGATACAGACCTAAGCAGGTTTA
1 CTTAAATGGAAACTTTAAATAGAGACCTAAGCAGGTTTA
* *
2597 CTTAAATGGAAACTTTAAACAGGGACCTAAGCAGGTTTA
1 CTTAAATGGAAACTTTAAATAGAGACCTAAGCAGGTTTA
* * *
2636 CTTAAATGGTTAA-TTTAGATAGAGACCTAAGCAGGTTTTT
1 CTTAAATGG-AAACTTTAAATAGAGACCTAAGCAGG-TTTA
* * * ** **
2676 CTTAAA-CGAAACTCTGAGCAGAGGGCTAAGCAGGTTTA
1 CTTAAATGGAAACTTTAAATAGAGACCTAAGCAGGTTTA
** * * *
2714 CTTAAAT-GACAACCCTAAATAGGGACTTAATCAGGTTTA
1 CTTAAATGGA-AACTTTAAATAGAGACCTAAGCAGGTTTA
* * * ** ** *
2753 -TTAGAT-CAAAGCTCTAAGCAGAGATCCTAAATAGGTTTT
1 CTTAAATGGAAA-CTTTAAATAGAGA-CCTAAGCAGGTTTA
* **
2792 CTTAAAT-GAAAATTCTAAGCAGAGACCTAAGCAGGTTTA
1 CTTAAATGGAAACTT-TAAATAGAGACCTAAGCAGGTTTA
* * * *
2831 TTTAAATGGAAACTTTAGACAAAGACCTAAGCAGGTTTA
1 CTTAAATGGAAACTTTAAATAGAGACCTAAGCAGGTTTA
*
2870 CGTAAAT
1 CTTAAAT
2877 AAAAACCCTA
Statistics
Matches: 395, Mismatches: 68, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
37 2 0.01
38 34 0.09
39 318 0.81
40 41 0.10
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (39 bp):
CTTAAATGGAAACTTTAAATAGAGACCTAAGCAGGTTTA
Found at i:2975 original size:11 final size:11
Alignment explanation
Indices: 2959--2988 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2949 TGTTGTTTGT
2959 TTTCTTTTCTC
1 TTTCTTTTCTC
2970 TTTCTTTTCTC
1 TTTCTTTTCTC
*
2981 TCTCTTTT
1 TTTCTTTT
2989 TTATTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTCTTTTCTC
Found at i:3929 original size:16 final size:17
Alignment explanation
Indices: 3898--3931 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3888 CTAACCTCTT
3898 TCTTTTTTTTGGTTAAGC
1 TCTTTTTTTT-GTTAAGC
3916 TCTTTTTTTT-TTAAGC
1 TCTTTTTTTTGTTAAGC
3932 ATAATACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (17 bp):
TCTTTTTTTTGTTAAGC
Found at i:8861 original size:96 final size:93
Alignment explanation
Indices: 8693--8869 Score: 282
Period size: 96 Copynumber: 1.9 Consensus size: 93
8683 AAGACCATGG
*
8693 CCCAACGTGATGACCCAAGTGGAAACAAAAAGAAAAAAGAAATGAACCCAACATGATGGCCCAAG
1 CCCAACATGATGACCCAAGTGGAAACAAAAAGAAAAAAGAAATGAACCCAACATGATGGCCCAAG
*
8758 TGTAAACAAAAAGAAAAAAAGAAATGAA
66 TGGAAACAAAAAGAAAAAAAGAAATGAA
* * *
8786 CCCAACATGATGGCCCAAGTGTAAACAAAAAGAAATAGATGGAAATGAACCCAACATGATGGCCC
1 CCCAACATGATGACCCAAGTGGAAACAAAAAGAAA-A-A-AGAAATGAACCCAACATGATGGCCC
8851 AAGTGGAAACAAAAAGAAA
63 AAGTGGAAACAAAAAGAAA
8870 TAGTTGGAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
93 32 0.42
94 1 0.01
95 1 0.01
96 42 0.55
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (93 bp):
CCCAACATGATGACCCAAGTGGAAACAAAAAGAAAAAAGAAATGAACCCAACATGATGGCCCAAG
TGGAAACAAAAAGAAAAAAAGAAATGAA
Found at i:8890 original size:49 final size:47
Alignment explanation
Indices: 8693--8869 Score: 275
Period size: 47 Copynumber: 3.7 Consensus size: 47
8683 AAGACCATGG
* *
8693 CCCAACGTGATGACCCAAGTGGAAACAAAAAG-AAAAAAGAAATGAA
1 CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAAAAAAGAAATGAA
*
8739 CCCAACATGATGGCCCAAGTGTAAACAAAAAGAAAAAAAGAAATGAA
1 CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAAAAAAGAAATGAA
* **
8786 CCCAACATGATGGCCCAAGTGTAAACAAAAAGAAATAGATGGAAATGAA
1 CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAA-A-AAAGAAATGAA
8835 CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAA
1 CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAA
8870 TAGTTGGAAA
Statistics
Matches: 122, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
46 29 0.24
47 49 0.40
48 1 0.01
49 43 0.35
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (47 bp):
CCCAACATGATGGCCCAAGTGGAAACAAAAAGAAAAAAAGAAATGAA
Found at i:16950 original size:18 final size:18
Alignment explanation
Indices: 16927--16961 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16917 AAATGAGTTT
16927 TTCAAAAATCCAAAAAAA
1 TTCAAAAATCCAAAAAAA
*
16945 TTCAAAAATTCAAAAAA
1 TTCAAAAATCCAAAAAA
16962 CCAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (18 bp):
TTCAAAAATCCAAAAAAA
Found at i:20866 original size:12 final size:12
Alignment explanation
Indices: 20849--20882 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
20839 AATTCTGAGA
20849 ATATGCATAAGT
1 ATATGCATAAGT
*
20861 ATATGCATCAGT
1 ATATGCATAAGT
20873 ATATGCATAA
1 ATATGCATAA
20883 CAGCATCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (12 bp):
ATATGCATAAGT
Found at i:21711 original size:11 final size:11
Alignment explanation
Indices: 21695--21736 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
21685 AAATAATTGA
21695 TTATATATATT
1 TTATATATATT
*
21706 TTATATAGATT
1 TTATATATATT
* *
21717 ATAAATATATT
1 TTATATATATT
21728 TTATATATA
1 TTATATATA
21737 ATATATAATC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
TTATATATATT
Found at i:21741 original size:22 final size:22
Alignment explanation
Indices: 21699--21741 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21689 AATTGATTAT
*
21699 ATATATTTTATATAGATTATAA
1 ATATATTTTATATAGAATATAA
*
21721 ATATATTTTATATATAATATA
1 ATATATTTTATATAGAATATA
21742 TAATCGGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATATTTTATATAGAATATAA
Found at i:21743 original size:11 final size:11
Alignment explanation
Indices: 21696--21743 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
21686 AATAATTGAT
*
21696 TATATATATTT
1 TATATATATTA
*
21707 TATATAGATTA
1 TATATATATTA
* *
21718 TAAATATATTT
1 TATATATATTA
*
21729 TATATATAATA
1 TATATATATTA
21740 TATA
1 TATA
21744 ATCGGTCGGT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (11 bp):
TATATATATTA
Found at i:25804 original size:21 final size:21
Alignment explanation
Indices: 25780--25830 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
25770 AATTAGTGCG
* *
25780 CCGAGACGAAGAGGCGAAACA
1 CCGAGAAGAAGAGGCAAAACA
*
25801 CCGAGAAGAAGAGGCAAAACG
1 CCGAGAAGAAGAGGCAAAACA
25822 CCGAGAAGA
1 CCGAGAAGA
25831 GGCTACAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.22, G:0.33, T:0.00
Consensus pattern (21 bp):
CCGAGAAGAAGAGGCAAAACA
Found at i:29532 original size:2 final size:2
Alignment explanation
Indices: 29527--29557 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29517 TCTATGTGTG
29527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29558 CTCTTCAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34176 original size:39 final size:39
Alignment explanation
Indices: 34133--34412 Score: 447
Period size: 39 Copynumber: 7.2 Consensus size: 39
34123 AGACAGATCG
* *
34133 TCTTTTCAACATTTATCAAAGTTGACTAGAAACAGGTCA
1 TCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCA
* *
34172 TCTTTTCAGCATTTATCAATGTTGACTGGGAACAGGTCA
1 TCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCA
34211 TCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCA
1 TCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCA
* *
34250 TATTTTCAGTATTTATCAAAGTTGACTGGAAACAGGTCA
1 TCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCA
*
34289 TCTTTTCAGCATTTATCAAAGTTGACTGGAAACAAGTCA
1 TCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCA
34328 TCTTTTCAGCATTTATCAAAGTTGA-TAGGAAA-ACGGTCA
1 TCTTTTCAGCATTTATCAAAGTTGACT-GGAAACA-GGTCA
*
34367 TCTTTTCAGCATTTATCAAAGTTGACTAGAAACAGGTCA
1 TCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCA
*
34406 TCCTTTC
1 TCTTTTC
34413 TCAGTTTTAT
Statistics
Matches: 223, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
38 2 0.01
39 219 0.98
40 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (39 bp):
TCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCA
Found at i:34453 original size:78 final size:72
Alignment explanation
Indices: 34090--34446 Score: 276
Period size: 78 Copynumber: 4.7 Consensus size: 72
34080 TCCGGACCTC
* * * *
34090 AAACAGGTC-T-TTCTCAGTTTTATTTTCGACCTCAGAC-AGATCGTCTTTTCAACATTTATCAA
1 AAACAGGTCATCTTTTCAGTTTTATGTT-GA-CTCAGACAAG-TCATCTTTTCAGCATTTATCAA
34152 AGTTGACTAG
63 AGTTGACTAG
** *
34162 AAACAGGTCATCTTTTCAGCATTTATCAATGTTGACTGGGAACAGGTCATCTTTTCAGCATTTAT
1 AAACAGGTCATCTTTTCAG--TTT-T--ATGTTGACTCAG-ACAAGTCATCTTTTCAGCATTTAT
*
34227 CAAAGTTGACTGG
60 CAAAGTTGACTAG
* * * *
34240 AAACAGGTCATATTTTCAGTATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTAT
1 AAACAGGTCATCTTTTCAGT-TTTAT----GTTGACT-CAGACAAGTCATCTTTTCAGCATTTAT
*
34305 CAAAGTTGACTGG
60 CAAAGTTGACTAG
* * *
34318 AAACAAGTCATCTTTTCAGCATTTATCAAAGTTGA-T-AGGAAAACGGTCATCTTTTCAGCATTT
1 AAACAGGTCATCTTTTCAG--TTT-T--ATGTTGACTCA-GACAA--GTCATCTTTTCAGCATTT
34381 ATCAAAGTTGACTAG
58 ATCAAAGTTGACTAG
*
34396 AAACAGGTCATCCTTTCTCAGTTTTATTTTCGACCTCAGACAAGTCA-CTTT
1 AAACAGGTCAT-CTTT-TCAGTTTTATGTT-GA-CTCAGACAAGTCATCTTT
34447 CTTTCAGTTT
Statistics
Matches: 234, Mismatches: 22, Indels: 55
0.75 0.07 0.18
Matches are distributed among these distances:
72 9 0.04
73 1 0.00
74 8 0.03
75 8 0.03
76 13 0.06
77 8 0.03
78 167 0.71
79 13 0.06
80 6 0.03
82 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (72 bp):
AAACAGGTCATCTTTTCAGTTTTATGTTGACTCAGACAAGTCATCTTTTCAGCATTTATCAAAGT
TGACTAG
Found at i:43592 original size:21 final size:21
Alignment explanation
Indices: 43549--43592 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43539 CCAATTTAGG
*
43549 TTTAGATTTAAATTTCTTGTT
1 TTTAGATTTAAATTTATTGTT
43570 TTTAGATTTAAGATTTATT-TT
1 TTTAGATTTAA-ATTTATTGTT
43591 TT
1 TT
43593 ATGCATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTAGATTTAAATTTATTGTT
Found at i:44899 original size:15 final size:16
Alignment explanation
Indices: 44870--44899 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44860 GTATGAATTC
44870 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
44886 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
44900 TTAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:49484 original size:18 final size:18
Alignment explanation
Indices: 49461--49495 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49451 AATTGAGTTT
49461 TTCAAAAATCCAAAAAAA
1 TTCAAAAATCCAAAAAAA
*
49479 TTCAAAAATTCAAAAAA
1 TTCAAAAATCCAAAAAA
49496 CCAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (18 bp):
TTCAAAAATCCAAAAAAA
Found at i:49646 original size:35 final size:33
Alignment explanation
Indices: 49520--49689 Score: 142
Period size: 35 Copynumber: 4.9 Consensus size: 33
49510 TTTCATCAAC
* * * *
49520 TTAGTTTTCAAATTGAGAAAATTCCTACCAGTCT
1 TTAGTTTTCAAATTGGGAAAGTTCCCATCAG-CT
* * *
49554 TTAAGTTTTCAAATCGAGAAAGTTTCCATTCAGTCT
1 TT-AGTTTTCAAATTGGGAAAGTTCCCA-TCAG-CT
* * * * *
49590 TCAAAGTTTTTAAGTTGGGAAAGATCCCATCAGGTT
1 T--TAGTTTTCAAATTGGGAAAGTTCCCATCA-GCT
*
49626 TTAGTTTTCAATTTAGGGAAAGTTCCCATCAGCT
1 TTAGTTTTCAAATT-GGGAAAGTTCCCATCAGCT
*
49660 TTAGTTTTTAAATTGGGAAAGTTCCCATCA
1 TTAGTTTTCAAATTGGGAAAGTTCCCATCA
49690 AAAACATTTT
Statistics
Matches: 110, Mismatches: 20, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
33 16 0.15
34 26 0.24
35 36 0.33
36 12 0.11
37 20 0.18
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (33 bp):
TTAGTTTTCAAATTGGGAAAGTTCCCATCAGCT
Found at i:51535 original size:21 final size:21
Alignment explanation
Indices: 51509--51558 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
51499 TGCTAGGAGT
51509 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
51530 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
51551 TCATTGGA
1 TCATTGGA
51559 ATTGCCTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.