Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017605.1 Corchorus olitorius cultivar O-4 contig17638, 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: 51594
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:6656 original size:42 final size:43
Alignment explanation
Indices: 6605--6698 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
6595 AGTGCATTAC
* *
6605 CTAA-ATTCTA-CTCTATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
6646 CTAATATTCTAGTCCTCCATCTCTAGATAATTCATCAAAATCAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
6691 CTAATATT
1 CTAATATT
6699 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:11289 original size:19 final size:19
Alignment explanation
Indices: 11265--11309 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
11255 ACCATATTTA
*
11265 GGCCTTTTAGTTG-TGTTTG
1 GGCCTTTGAGTTGTTG-TTG
*
11284 GGCCTTAGAGTTGTTGTTG
1 GGCCTTTGAGTTGTTGTTG
11303 GGCCTTT
1 GGCCTTT
11310 AGATTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.07, C:0.13, G:0.33, T:0.47
Consensus pattern (19 bp):
GGCCTTTGAGTTGTTGTTG
Found at i:11593 original size:15 final size:16
Alignment explanation
Indices: 11573--11602 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11563 AGGAAATGAA
11573 ACAGAAAG-AAGTAGC
1 ACAGAAAGAAAGTAGC
11588 ACAGAAAGAAAGTAG
1 ACAGAAAGAAAGTAG
11603 GAGGGAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.10, G:0.27, T:0.07
Consensus pattern (16 bp):
ACAGAAAGAAAGTAGC
Found at i:12807 original size:38 final size:38
Alignment explanation
Indices: 12765--12845 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
12755 TTAGAGAGCA
*
12765 ATTAAAATTATATCCAAATATATTACATCTATTTGTGT
1 ATTAAAATTATATCCAAATATATTACATCTATTAGTGT
12803 ATTAAAATTATATCCAAATATATTACATCTATTAGTGT
1 ATTAAAATTATATCCAAATATATTACATCTATTAGTGT
12841 ATTAA
1 ATTAA
12846 GGAAATGAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (38 bp):
ATTAAAATTATATCCAAATATATTACATCTATTAGTGT
Found at i:16499 original size:11 final size:11
Alignment explanation
Indices: 16483--16508 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16473 AGATAATTTC
16483 TTTTCTTCTAG
1 TTTTCTTCTAG
16494 TTTTCTTCTAG
1 TTTTCTTCTAG
16505 TTTT
1 TTTT
16509 TAGGCAAAGG
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:17298 original size:15 final size:15
Alignment explanation
Indices: 17268--17309 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
17258 TTACTCTGCT
17268 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
17284 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
17299 TTGCTTTCTGT
1 TTGTTTTCTGT
17310 CAATCTCTGT
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:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:18868 original size:56 final size:54
Alignment explanation
Indices: 18806--18911 Score: 167
Period size: 56 Copynumber: 1.9 Consensus size: 54
18796 TAAACTCAAA
18806 TAGACTATAATTTAAATCAAAAATAATTATTAAAAGATTATATACACTAAAGTGAG
1 TAGACTATAATTTAAATCAAAAATAATTATTAAAAGA-T-TATACACTAAAGTGAG
* * *
18862 TAGACTATAATTTAAATCAACAATGATTATTAATAGATTATACACTAAAG
1 TAGACTATAATTTAAATCAAAAATAATTATTAAAAGATTATACACTAAAG
18912 ATGCAAATCC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 12 0.26
55 1 0.02
56 34 0.72
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (54 bp):
TAGACTATAATTTAAATCAAAAATAATTATTAAAAGATTATACACTAAAGTGAG
Found at i:20182 original size:16 final size:16
Alignment explanation
Indices: 20157--20216 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
20147 TGTGACTTCC
* *
20157 TTTCCCTTCCTCCCTA
1 TTTCCTTTCCTCCTTA
**
20173 TTTCCTTTCCCTTGTTA
1 TTTCCTTT-CCTCCTTA
*
20190 TTTCCTTTCCTTCTTA
1 TTTCCTTTCCTCCTTA
20206 TTT-CTTTCCTC
1 TTTCCTTTCCTC
20217 TCTACCAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 7 0.19
16 17 0.46
17 13 0.35
ACGTcount: A:0.05, C:0.37, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTCCTTTCCTCCTTA
Found at i:20193 original size:17 final size:17
Alignment explanation
Indices: 20171--20214 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
20161 CCTTCCTCCC
*
20171 TATTTCCTTTCCCTTGT
1 TATTTCCTTTCCCTTCT
20188 TATTTCCTTT-CCTTCT
1 TATTTCCTTTCCCTTCT
20204 TATTT-CTTTCC
1 TATTTCCTTTCC
20215 TCTCTACCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.16
16 11 0.44
17 10 0.40
ACGTcount: A:0.07, C:0.30, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTTCCTTTCCCTTCT
Found at i:25090 original size:29 final size:29
Alignment explanation
Indices: 25057--25135 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
25047 CAGACCCCTA
25057 ATGATATCAGAGCCCAAATATATAGTTAT
1 ATGATATCAGAGCCCAAATATATAGTTAT
* *
25086 ATGATATTAGAGCCCAAATACATAGTTAT
1 ATGATATCAGAGCCCAAATATATAGTTAT
*
25115 ATGATATCAGAACCCAAATAT
1 ATGATATCAGAGCCCAAATAT
25136 TTATTTTAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (29 bp):
ATGATATCAGAGCCCAAATATATAGTTAT
Found at i:25304 original size:2 final size:2
Alignment explanation
Indices: 25299--25339 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
25289 TCTGTGTGTT
25299 TA TA TA TA TA 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 TA TA TA TA TA T
25340 GGATATAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27411 original size:29 final size:29
Alignment explanation
Indices: 27378--27459 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
27368 TAGACCCCTA
*
27378 ATGATATCAAAGCCCAAATATATAGTTAT
1 ATGATATCAGAGCCCAAATATATAGTTAT
* *
27407 ATGATATTAGAGCCCAAATACATAGTTAT
1 ATGATATCAGAGCCCAAATATATAGTTAT
27436 ATGATATCAGAGCCCAAATATATA
1 ATGATATCAGAGCCCAAATATATA
27460 TTTTAAGCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (29 bp):
ATGATATCAGAGCCCAAATATATAGTTAT
Found at i:27566 original size:25 final size:23
Alignment explanation
Indices: 27513--27565 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
27503 CATATGTAGT
*
27513 TTATACAAATATTGGAAGAAATG
1 TTATATAAATATTGGAAGAAATG
27536 TTATATAAATATTGGAAGAAATG
1 TTATATAAATATTGGAAGAAATG
27559 TTATATA
1 TTATATA
27566 TAATTATCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.36
Consensus pattern (23 bp):
TTATATAAATATTGGAAGAAATG
Found at i:27646 original size:2 final size:2
Alignment explanation
Indices: 27641--27671 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27631 TGTGTGTGTT
27641 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
27672 TGGATATAGT
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:31507 original size:6 final size:6
Alignment explanation
Indices: 31496--31528 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
31486 ATGTATGTTT
*
31496 CTTTAG CTTTAG CTTTAG CTTCAG C-TTAG CTTT
1 CTTTAG CTTTAG CTTTAG CTTTAG CTTTAG CTTT
31529 TTCACGTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.48
Consensus pattern (6 bp):
CTTTAG
Found at i:32321 original size:48 final size:47
Alignment explanation
Indices: 32265--32360 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 47
32255 TCAGAGTAAT
*
32265 ATTTGGGTAGGTGGGCTACAAGGTGGGGAAATTGTTTTTTGTATTTTA
1 ATTTGGGTAGGTGGGCTACAAGGTGGGGAAATT-TTTGTTGTATTTTA
***
32313 ATTTGGGTAGGTGGGCTACAAGGTGTTTAAATTTTTGTTGTATTTTA
1 ATTTGGGTAGGTGGGCTACAAGGTGGGGAAATTTTTGTTGTATTTTA
32360 A
1 A
32361 GTGAAATACC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 14 0.32
48 30 0.68
ACGTcount: A:0.22, C:0.04, G:0.30, T:0.44
Consensus pattern (47 bp):
ATTTGGGTAGGTGGGCTACAAGGTGGGGAAATTTTTGTTGTATTTTA
Found at i:37708 original size:31 final size:32
Alignment explanation
Indices: 37673--37771 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 32
37663 AGTACCTAAA
* *
37673 TAGTCCCTGTACTATTGAAAAAAC-ATCATTT
1 TAGTCCCTATACTATTGAAAAAACGATCAATT
** * *
37704 TAGTCCCTCCATTA-TG--AAATCTG-TCAATT
1 TAGTCCCTATACTATTGAAAAAAC-GATCAATT
37733 TAGTCCCTATACTATT-AAAAAACGATCAATT
1 TAGTCCCTATACTATTGAAAAAACGATCAATT
37764 TAGTCCCT
1 TAGTCCCT
37772 CTTTGAAATG
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 4 0.08
29 16 0.30
30 4 0.08
31 29 0.55
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.35
Consensus pattern (32 bp):
TAGTCCCTATACTATTGAAAAAACGATCAATT
Found at i:41579 original size:30 final size:29
Alignment explanation
Indices: 41545--41635 Score: 91
Period size: 29 Copynumber: 3.1 Consensus size: 29
41535 TTTCACGGAG
41545 GGACTAAATTGATCGTTTGTTAATAGTACA
1 GGACTAAATTGATCGTTT-TTAATAGTACA
*
41575 GGACTAAATTGA-CAGATTTCTTAATAG-A-G
1 GGACTAAATTGATC-G-TTT-TTAATAGTACA
*
41604 GGACTAAAATGATC-TTTTTCAATAGTACA
1 GGACTAAATTGATCGTTTTT-AATAGTACA
41633 GGA
1 GGA
41636 ACTATTTAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
26 2 0.04
27 8 0.16
28 1 0.02
29 15 0.29
30 15 0.29
31 10 0.20
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (29 bp):
GGACTAAATTGATCGTTTTTAATAGTACA
Found at i:45071 original size:62 final size:62
Alignment explanation
Indices: 44993--45159 Score: 334
Period size: 62 Copynumber: 2.7 Consensus size: 62
44983 AGTTATAACG
44993 CATACGATTAGTAATACTAATACAAACATATAAGTTATAACGCTATTAAAGCACTAAGAACC
1 CATACGATTAGTAATACTAATACAAACATATAAGTTATAACGCTATTAAAGCACTAAGAACC
45055 CATACGATTAGTAATACTAATACAAACATATAAGTTATAACGCTATTAAAGCACTAAGAACC
1 CATACGATTAGTAATACTAATACAAACATATAAGTTATAACGCTATTAAAGCACTAAGAACC
45117 CATACGATTAGTAATACTAATACAAACATATAAGTTATAACGC
1 CATACGATTAGTAATACTAATACAAACATATAAGTTATAACGC
45160 GTGCCTGAGA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 105 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (62 bp):
CATACGATTAGTAATACTAATACAAACATATAAGTTATAACGCTATTAAAGCACTAAGAACC
Found at i:46879 original size:63 final size:63
Alignment explanation
Indices: 46780--46905 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
46770 CCGATACGTT
46780 ACACCGTTATACGAGTTGCATGTGCCACGACCGTGACCGTTACATAACGGCCGCGACAGAGGC
1 ACACCGTTATACGAGTTGCATGTGCCACGACCGTGACCGTTACATAACGGCCGCGACAGAGGC
* * * *
46843 ACACCGTTATAGGAGTTGCATGTGTCACGGCCGTGACCGTTACATAACGGCCGCGACGGAGGC
1 ACACCGTTATACGAGTTGCATGTGCCACGACCGTGACCGTTACATAACGGCCGCGACAGAGGC
46906 CAAAAAACGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (63 bp):
ACACCGTTATACGAGTTGCATGTGCCACGACCGTGACCGTTACATAACGGCCGCGACAGAGGC
Found at i:50180 original size:334 final size:328
Alignment explanation
Indices: 49663--50747 Score: 1053
Period size: 334 Copynumber: 3.3 Consensus size: 328
49653 CGATACTCAT
* * * * * * *
49663 AAAAAATAAATAATTCAATGCCAAAAATATTGAAAGGCTTTTCACACTTCTAATATCGATTTTCC
1 AAAAAATATATAAATCAATACCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTTC
49728 TATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAAT
66 TAT-TTTTTT-CGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAAT
* * *
49793 CTTTAAATCCAATGTGGTTGAGATTTAGTTTGATGGATATAGATATATCAATGAGACTTGGCGCC
129 CTTTAAATCCAATGTGGCTGAGATTT-GTTAGATGGATATAGATATTTCAATGAGACTTGGCGCC
* * * *
49858 AAAAATCATGCAAAATAGAGCCGGCACCCAGAAACACGTTTTTAGTCAAAAATTGTGATGGTTAG
193 AAAAATCATGCAAAATAGAGTCGG-ACCC-GGAACGCGTTTTTAGTCAAAAACTGTGATGGTTAG
* ** * *
49923 TACACGATTTCTGCTAAAATTTTACAAAATTTGACACGAAACATTTCTCCTTAATTTCCGGCTAC
256 TACACGATTTCAGCTAAAATTTTGTAAAATTTGAC-CGAAA-ATTTCTCCTAAATTT-TGGCTAC
49988 CATATTCATAA
318 CATATTCATAA
* * * **
49999 AAAAAATATATAAATCAATGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATATTTTTTTTTC
1 AAAAAATATATAAATCAATACCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTTC
* * * * *
50064 TATTTTTTTCGAGTTAATTTCTAATTAAATCAAAAC-CGAATTGAGATACTCGTAAAAACAAATC
66 TATTTTTTTCGAATTAATTTCTAATTAAATCGAAACATG-ATTCAGATGCTCGTAAAAACAAATC
** *
50128 TTTAAATCCAATGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGGCGCCA
130 TTTAAATCCAATGTGGCTGAGATTT-GTTAGATGGATATAGATATTTCAATGAGACTTGGCGCCA
* * * *
50193 AAGATCATGC-AAATCTGAGTCGGAGTCCCGGAACGCGTTTTTAGCCAAAAACCT-TGATAGTTA
194 AAAATCATGCAAAAT-AGAGTCGGA--CCCGGAACGCGTTTTTAGTCAAAAA-CTGTGATGGTTA
* * *
50256 GTACACGATTTCGGCTAAAATTTTGTAAAAATTGATCCGAAAGAATTT-TCCTAAATTTTTGGCC
255 GTACACGATTTCAGCTAAAATTTTGTAAAATTTGA-CCG-AA-AATTTCTCCTAAA-TTTTGGCT
** *
50320 ATGATACTCAT--
316 ACCATATTCATAA
* * * * * *
50331 AAAAAATATATAAGTCAACACCAAAAATATTGAAAGGCTATTCATGCTTCTAATATCGTATTTTC
1 AAAAAATATATAAATCAATACCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTTC
* * * *
50396 TA-TTTTTTCTGAATTAATTCCTAATTGAATCGAAACATGATTCATATGCTCGTAGAAAC--A--
66 TATTTTTTTC-GAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATC
* * * * * *
50456 --T-GATTCAATGCGGGTAAGATTTGCTTAGATGGATATAGATATTTCAATGAGACTTGGTGCCA
130 TTTAAATCCAATGTGGCTGAGATTTG-TTAGATGGATATAGATATTTCAATGAGACTTGGCGCCA
* * * * * *
50518 AAAATCTTGCAAAA-ATGAATCGGGGCTTCGGAACGCG--GTTAGTCAAAAACCGTGATGGTTAG
194 AAAATCATGCAAAATA-GAGTC-GGAC-CCGGAACGCGTTTTTAGTCAAAAACTGTGATGGTTAG
* * *
50580 TACATGATTTCAGCTAAAATTTTGTAAAATTTGACCCGAGAAATTTCTCCTCAATTTTGGGT-CA
256 TACACGATTTCAGCTAAAATTTTGTAAAATTTGA-CCGA-AAATTTCTCCTAAATTTTGGCTAC-
*
50644 CA-ATAC-TAA
318 CATATTCATAA
* * * * ***
50653 TAAAAAATATTTAACTCAATACCAAAAAGACTG-AAGGACTTCTCACGCTTCTAATA-CCACTTT
1 -AAAAAATATATAAATCAATACCAAAAAGATTGAAAGG-CTTTTCACGCTTCTAATATCGTTTTT
* * *
50716 CCTACCTTTTTCCGAATTAATTTCTAATTAAA
64 TCTA-TTTTTTTCGAATTAATTTCTAATTAAA
50748 AAATGATATT
Statistics
Matches: 620, Mismatches: 103, Indels: 65
0.79 0.13 0.08
Matches are distributed among these distances:
320 1 0.00
321 2 0.00
322 25 0.04
323 119 0.19
324 8 0.01
325 71 0.11
326 6 0.01
330 1 0.00
331 7 0.01
332 96 0.15
333 7 0.01
334 198 0.32
335 20 0.03
336 59 0.10
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (328 bp):
AAAAAATATATAAATCAATACCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTTC
TATTTTTTTCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCT
TTAAATCCAATGTGGCTGAGATTTGTTAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAA
AATCATGCAAAATAGAGTCGGACCCGGAACGCGTTTTTAGTCAAAAACTGTGATGGTTAGTACAC
GATTTCAGCTAAAATTTTGTAAAATTTGACCGAAAATTTCTCCTAAATTTTGGCTACCATATTCA
TAA
Found at i:50984 original size:96 final size:94
Alignment explanation
Indices: 50789--50967 Score: 243
Period size: 94 Copynumber: 1.9 Consensus size: 94
50779 AAATATATTT
* *** * *
50789 GAAAAAAATACACAAATTATATTTTAATAATGGTATAGTTAAAATATATTTTAATAGTAAAAATT
1 GAAAAAAATACAAAAATTATATTTTAATAATAACATAATTAAAATATA-TTTAATAATAAAAATT
50854 TAAAAATATATTTGAAAAAATAGTACAATC
65 TAAAAATATATTTGAAAAAATAGTACAATC
* * *
50884 GAAAAATATACATAAAATTATATTTTAATAATAACATAATTAAAATATA-TTAATAATGATAATT
1 GAAAAAAATACA-AAAATTATATTTTAATAATAACATAATTAAAATATATTTAATAATAAAAATT
*
50948 TAGAAATATATTTGAAAAAA
65 TAAAAATATATTTGAAAAAA
50968 AGGGTATAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 31 0.42
95 11 0.15
96 31 0.42
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (94 bp):
GAAAAAAATACAAAAATTATATTTTAATAATAACATAATTAAAATATATTTAATAATAAAAATTT
AAAAATATATTTGAAAAAATAGTACAATC
Done.