Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022562.1 Corchorus olitorius cultivar O-4 contig22595, 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: 94606
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1307 original size:25 final size:25
Alignment explanation
Indices: 1249--1298 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1239 AAGAAGATTA
1249 AAACATATAGGAAGATAAAACATATG
1 AAACATA-AGGAAGATAAAACATATG
*
1275 AAATATAAGGAAGATAAAACATAT
1 AAACATAAGGAAGATAAAACATAT
1299 AGGACATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (25 bp):
AAACATAAGGAAGATAAAACATATG
Found at i:1740 original size:18 final size:18
Alignment explanation
Indices: 1719--1757 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1709 ATAGCCAAAA
*
1719 CCACGACCACGGCCACGT
1 CCACGACCACGACCACGT
*
1737 CCACGTCCACGACCACGT
1 CCACGACCACGACCACGT
1755 CCA
1 CCA
1758 TAATTATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.51, G:0.18, T:0.08
Consensus pattern (18 bp):
CCACGACCACGACCACGT
Found at i:1754 original size:12 final size:12
Alignment explanation
Indices: 1719--1757 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1709 ATAGCCAAAA
*
1719 CCACGACCACGG
1 CCACGACCACGT
*
1731 CCACGTCCACGT
1 CCACGACCACGT
1743 CCACGACCACGT
1 CCACGACCACGT
1755 CCA
1 CCA
1758 TAATTATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.23, C:0.51, G:0.18, T:0.08
Consensus pattern (12 bp):
CCACGACCACGT
Found at i:2743 original size:33 final size:33
Alignment explanation
Indices: 2698--2766 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
2688 TTTAATAATA
* *
2698 AAAGAAAAGTAGAAGGAGGAGATTATGCATGAT
1 AAAGAAAAGTAGAAGAAGGAGATCATGCATGAT
*
2731 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
1 AAAGAAAAGTAGAAGAAGGAGATCATGCATGAT
2764 AAA
1 AAA
2767 TAAACTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.51, C:0.04, G:0.29, T:0.16
Consensus pattern (33 bp):
AAAGAAAAGTAGAAGAAGGAGATCATGCATGAT
Found at i:3891 original size:31 final size:31
Alignment explanation
Indices: 3856--3927 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
3846 TAAATTATTG
*
3856 CAAATTAAAACAAAT-TAAGTATTAAATTAAA
1 CAAATTAAAA-AAATAAAAGTATTAAATTAAA
* *
3887 CAAA-TAATTAAAATAAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATAAAAGTATTAAATTAAA
3918 CAAATTAAAA
1 CAAATTAAAA
3928 GCTTATAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 7 0.21
31 24 0.71
32 3 0.09
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (31 bp):
CAAATTAAAAAAATAAAAGTATTAAATTAAA
Found at i:4518 original size:7 final size:7
Alignment explanation
Indices: 4508--4548 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
4498 AGCGAAGATA
4508 AGAAATG
1 AGAAATG
4515 AGAAATG
1 AGAAATG
4522 AGAAATG
1 AGAAATG
4529 AGAAATG
1 AGAAATG
4536 AGAAATG
1 AGAAATG
4543 AGAAAT
1 AGAAAT
4549 CGATTGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.27, T:0.15
Consensus pattern (7 bp):
AGAAATG
Found at i:11365 original size:30 final size:30
Alignment explanation
Indices: 11329--11414 Score: 145
Period size: 30 Copynumber: 2.9 Consensus size: 30
11319 ATACACCGGA
*
11329 AGCACCGGCAGCGGAAGTGTTGGTGGTGGC
1 AGCACCGGCAGCGGAAGTATTGGTGGTGGC
*
11359 AGCACCGGCAGCGGAAGTCTTGGTGGTGGC
1 AGCACCGGCAGCGGAAGTATTGGTGGTGGC
*
11389 AGCACTGGCAGCGGAAGTATTGGTGG
1 AGCACCGGCAGCGGAAGTATTGGTGG
11415 CAGCCCTGGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.19, C:0.20, G:0.44, T:0.17
Consensus pattern (30 bp):
AGCACCGGCAGCGGAAGTATTGGTGGTGGC
Found at i:11423 original size:27 final size:29
Alignment explanation
Indices: 11335--11423 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 29
11325 CGGAAGCACC
**
11335 GGCAGCGGAAGTGTTGGTGGTGGCAGCACC-
1 GGCAGCGGAAGTCAT-GTGGTGGCAGC-CCT
* *
11365 GGCAGCGGAAGTCTTGGTGGTGGCAGCACT
1 GGCAGCGGAAGTCAT-GTGGTGGCAGCCCT
11395 GGCAGCGGAAGT-AT-TGGTGGCAGCCCT
1 GGCAGCGGAAGTCATGTGGTGGCAGCCCT
11422 GG
1 GG
11424 TGGAGCTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 14 0.26
29 2 0.04
30 38 0.70
ACGTcount: A:0.17, C:0.20, G:0.45, T:0.18
Consensus pattern (29 bp):
GGCAGCGGAAGTCATGTGGTGGCAGCCCT
Found at i:13935 original size:21 final size:20
Alignment explanation
Indices: 13909--13948 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13899 TTATCAAAAG
*
13909 ATTATTTTAATTATAAAGATA
1 ATTATTATAATT-TAAAGATA
*
13930 ATTATTATGATTTAAAGAT
1 ATTATTATAATTTAAAGAT
13949 CTTTTCAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
ATTATTATAATTTAAAGATA
Found at i:26021 original size:29 final size:29
Alignment explanation
Indices: 25979--26037 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
25969 CTTAAAATTC
25979 ACATGAATATATGATCATACGTGTGATTT
1 ACATGAATATATGATCATACGTGTGATTT
26008 ACATGAATATATGATCATACGTGTGATTT
1 ACATGAATATATGATCATACGTGTGATTT
26037 A
1 A
26038 GCCTCGAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (29 bp):
ACATGAATATATGATCATACGTGTGATTT
Found at i:38104 original size:1 final size:1
Alignment explanation
Indices: 38100--38126 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
38090 GTTCTGCCTG
38100 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
38127 AATTTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40632 original size:11 final size:10
Alignment explanation
Indices: 40616--40663 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
40606 TGCAACCTCA
40616 TTCTTTTTCTT
1 TTCTTTTT-TT
40627 TTCTTTTTTT
1 TTCTTTTTTT
**
40637 ACCTTTTTTT
1 TTCTTTTTTT
40647 TT-TTTTTTT
1 TTCTTTTTTT
40656 TT-TTTTTT
1 TTCTTTTTT
40664 AATTTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 15 0.45
10 10 0.30
11 8 0.24
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:40644 original size:21 final size:21
Alignment explanation
Indices: 40618--40657 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40608 CAACCTCATT
40618 CTTTTTCTTTTCTTTTTTTAC
1 CTTTTTCTTTTCTTTTTTTAC
* *
40639 CTTTTTTTTTTTTTTTTTT
1 CTTTTTCTTTTCTTTTTTT
40658 TTTTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (21 bp):
CTTTTTCTTTTCTTTTTTTAC
Found at i:40648 original size:15 final size:14
Alignment explanation
Indices: 40619--40664 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 14
40609 AACCTCATTC
*
40619 TTTTT-CTTTTCTT
1 TTTTTACTTTTTTT
40632 TTTTTACCTTTTTTT
1 TTTTTA-CTTTTTTT
40647 TTTTT--TTTTTTT
1 TTTTTACTTTTTTT
40659 TTTTTA
1 TTTTTA
40665 ATTTAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 12 0.41
13 5 0.17
15 12 0.41
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTACTTTTTTT
Found at i:47402 original size:16 final size:15
Alignment explanation
Indices: 47364--47405 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
47354 ACAGAGATTG
*
47364 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
47379 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
47394 ACTAGAAAACAA
1 AC-AGAAAACAA
47406 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:48170 original size:11 final size:11
Alignment explanation
Indices: 48154--48179 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48144 CCTTTGCCTA
48154 AAAACTAGAAG
1 AAAACTAGAAG
48165 AAAACTAGAAG
1 AAAACTAGAAG
48176 AAAA
1 AAAA
48180 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:54304 original size:16 final size:15
Alignment explanation
Indices: 54266--54307 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
54256 ACAGAGATTG
*
54266 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
54281 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
54296 ACTAGAAAACAA
1 AC-AGAAAACAA
54308 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:55071 original size:11 final size:11
Alignment explanation
Indices: 55055--55080 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55045 CCTTTGCCTA
55055 AAAACTAGAAG
1 AAAACTAGAAG
55066 AAAACTAGAAG
1 AAAACTAGAAG
55077 AAAA
1 AAAA
55081 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:58664 original size:13 final size:13
Alignment explanation
Indices: 58646--58671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58636 GAACATACTT
58646 GAAAACACTTTTG
1 GAAAACACTTTTG
58659 GAAAACACTTTTG
1 GAAAACACTTTTG
58672 ATTTTTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
GAAAACACTTTTG
Found at i:59497 original size:41 final size:41
Alignment explanation
Indices: 59226--59519 Score: 174
Period size: 40 Copynumber: 7.2 Consensus size: 41
59216 TAACATCAAT
* * * *
59226 TCCTAAAATCAGGGATTAAATTGCAT-AAAAAATAAATAAAA
1 TCCT-AAATCAGGGATCAAATTGAATCAAATAGTAAATAAAA
* * * ** * *
59267 TCCTAAAACAGGGACCAAATTGCATTTAATCAGGAAATAAAG
1 TCCTAAATCAGGGATCAAATTGAATCAAAT-AGTAAATAAAA
* *** * * *
59309 TCTTAAATCAGGGA-CTAGGCTGCA-GAAATCA-AAAATAAAA
1 TCCTAAATCAGGGATC-AAATTGAATCAAAT-AGTAAATAAAA
* * * **
59349 TCTTAAATCAGGGGTGAAATTGAATC-AATAGTAAATATTA
1 TCCTAAATCAGGGATCAAATTGAATCAAATAGTAAATAAAA
* * *
59389 TCCTAAATCAGGGACCAAATTGCATCATAA-A-TAAATATTAA
1 TCCTAAATCAGGGATCAAATTGAATCA-AATAGTAAATA-AAA
*
59430 -CCTAAATCAGGGA-CAAAATTGCATCAAATAGTAAATAAAA
1 TCCTAAATCAGGGATC-AAATTGAATCAAATAGTAAATAAAA
* * * *
59470 TCCAAAATAAGGGATCAAATTGAATCAAATAGTAAGTAAGA
1 TCCTAAATCAGGGATCAAATTGAATCAAATAGTAAATAAAA
*
59511 TACTAAATC
1 TCCTAAATC
59520 GAGGACTAAT
Statistics
Matches: 197, Mismatches: 42, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
39 4 0.02
40 105 0.53
41 60 0.30
42 28 0.14
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (41 bp):
TCCTAAATCAGGGATCAAATTGAATCAAATAGTAAATAAAA
Found at i:61920 original size:27 final size:27
Alignment explanation
Indices: 61854--61953 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 27
61844 AGCGAACTTA
* * *
61854 AAATGACCAACATGCCCTTGAATGTGC
1 AAATGACCAAAATGCCCCTGAACGTGC
*
61881 AAAATGACCAAAATGCCCCTGGACGTGC
1 -AAATGACCAAAATGCCCCTGAACGTGC
* *
61909 AAATGACTAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACGTGC
*
61936 AAATGACTAAAATGCCCC
1 AAATGACCAAAATGCCCC
61954 ATAGGTGACC
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 42 0.65
28 23 0.35
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACGTGC
Found at i:65083 original size:19 final size:19
Alignment explanation
Indices: 65059--65108 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
65049 ACCCAATACA
* *
65059 ATACTCACTTACAAAGGCT
1 ATACTCACTTACAAAGACC
65078 ATACTCACTTACAAAGACC
1 ATACTCACTTACAAAGACC
65097 ATACTCACTTAC
1 ATACTCACTTAC
65109 CATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.38, C:0.30, G:0.06, T:0.26
Consensus pattern (19 bp):
ATACTCACTTACAAAGACC
Found at i:71040 original size:11 final size:11
Alignment explanation
Indices: 71009--71041 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
70999 TAAGGGGTAA
71009 CTAAATCTTTT
1 CTAAATCTTTT
*
71020 ATAAAT-TTTT
1 CTAAATCTTTT
71030 CTAAATCTTTT
1 CTAAATCTTTT
71041 C
1 C
71042 ATTTATCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (11 bp):
CTAAATCTTTT
Found at i:72393 original size:27 final size:27
Alignment explanation
Indices: 72355--72435 Score: 162
Period size: 27 Copynumber: 3.0 Consensus size: 27
72345 CTTGACGAGG
72355 AAACGATACACAATTACGGGGTGCCAC
1 AAACGATACACAATTACGGGGTGCCAC
72382 AAACGATACACAATTACGGGGTGCCAC
1 AAACGATACACAATTACGGGGTGCCAC
72409 AAACGATACACAATTACGGGGTGCCAC
1 AAACGATACACAATTACGGGGTGCCAC
72436 TCACAATTCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (27 bp):
AAACGATACACAATTACGGGGTGCCAC
Found at i:75445 original size:11 final size:11
Alignment explanation
Indices: 75411--75458 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
75401 TCTTTCAAAA
75411 TCTTTTTTT-T
1 TCTTTTTTTAT
*
75421 TC-TATTTTA-
1 TCTTTTTTTAT
75430 T-TTTTTTTAT
1 TCTTTTTTTAT
75440 TCTTTTTTTAT
1 TCTTTTTTTAT
75451 TCTTTTTT
1 TCTTTTTT
75459 ATAAAATAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 12 0.38
10 3 0.09
11 17 0.53
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (11 bp):
TCTTTTTTTAT
Found at i:75480 original size:23 final size:24
Alignment explanation
Indices: 75449--75520 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
75439 TTCTTTTTTT
*
75449 ATTCTTTTTTATAAAATAAGTTAC
1 ATTCATTTTTATAAAATAAGTTAC
* *
75473 ATT-ATTTTTA-GAAGTCAAGTTAC
1 ATTCATTTTTATAAAAT-AAGTTAC
* *
75496 ATTCTTTTTTATCAAATAAGTTAC
1 ATTCATTTTTATAAAATAAGTTAC
75520 A
1 A
75521 CCAATAAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 3 0.08
23 16 0.41
24 17 0.44
25 3 0.08
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (24 bp):
ATTCATTTTTATAAAATAAGTTAC
Found at i:75480 original size:24 final size:24
Alignment explanation
Indices: 75453--75520 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
75443 TTTTTTATTC
75453 TTTTTTATAAAATAAGTTACATTA
1 TTTTTTATAAAATAAGTTACATTA
* * *
75477 -TTTTTA-GAAGTCAAGTTACATTC
1 TTTTTTATAAAAT-AAGTTACATTA
*
75500 TTTTTTATCAAATAAGTTACA
1 TTTTTTATAAAATAAGTTACA
75521 CCAATAAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 3 0.08
23 16 0.44
24 14 0.39
25 3 0.08
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (24 bp):
TTTTTTATAAAATAAGTTACATTA
Found at i:84835 original size:19 final size:18
Alignment explanation
Indices: 84811--84846 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
84801 TGAAGACTTA
84811 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
84830 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
84847 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:92520 original size:13 final size:13
Alignment explanation
Indices: 92494--92527 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
92484 TCTTTCAACA
92494 TCTTTTTTTCTTT
1 TCTTTTTTTCTTT
92507 TCTGTTTTTT-TTT
1 TCT-TTTTTTCTTT
92520 TCTTTTTT
1 TCTTTTTT
92528 ATCAAATGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 9 0.45
14 6 0.30
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (13 bp):
TCTTTTTTTCTTT
Found at i:93214 original size:12 final size:12
Alignment explanation
Indices: 93197--93223 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
93187 TAAAAAAGTA
93197 TTTCTCATACTT
1 TTTCTCATACTT
93209 TTTCTCATACTT
1 TTTCTCATACTT
93221 TTT
1 TTT
93224 TTTTTGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTCTCATACTT
Done.