Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001778.1 Kokia drynarioides strain JFW-HI SEQ_113502, 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: 250292
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:239 original size:80 final size:78
Alignment explanation
Indices: 145--305 Score: 225
Period size: 80 Copynumber: 2.0 Consensus size: 78
135 TTATTAAGGA
* *
145 GAAATGCCATGCCTTTTTAGCTACATCAGATCCTAATGAAGAGACATGACTCATTGGCTTTCC-T
1 GAAATGCCATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGC-TTCCTT
209 ACAAGAGTTAAAAAT
65 ACAAGAGTT-AAAAT
* * **
224 GAAATTGCCATGCCTTTTTAACTACATTAGATCCTATTGAAGAGACATGACTTTTTAGCTTCCTT
1 GAAA-TGCCATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCTT
*
289 AGAAGAGTTAAAAT
65 ACAAGAGTTAAAAT
303 GAA
1 GAA
306 GTTAGTGCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
79 16 0.22
80 57 0.78
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (78 bp):
GAAATGCCATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCTTA
CAAGAGTTAAAAT
Found at i:3709 original size:38 final size:38
Alignment explanation
Indices: 3658--3733 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3648 AGATGGAGAT
3658 AGTTATGGTACGTGCTAATGTCGAGGAAGATCGAGAGG
1 AGTTATGGTACGTGCTAATGTCGAGGAAGATCGAGAGG
3696 AGTTATGGTACGTGCTAATGTCGAGGAAGATCGAGAGG
1 AGTTATGGTACGTGCTAATGTCGAGGAAGATCGAGAGG
3734 CTACCATGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.24
Consensus pattern (38 bp):
AGTTATGGTACGTGCTAATGTCGAGGAAGATCGAGAGG
Found at i:18241 original size:20 final size:20
Alignment explanation
Indices: 18214--18267 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
18204 TCTCAAGTTA
18214 TTTTCTCTCATTTCTTTT-T
1 TTTTCTCTCATTTCTTTTAT
18233 TTCTTCTCTCTATTTCTTTTAT
1 TT-TTCTCTC-ATTTCTTTTAT
*
18255 TTTTCACTCATTT
1 TTTTCTCTCATTT
18268 TCTCTCATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 2 0.06
20 11 0.35
21 15 0.48
22 3 0.10
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTCTCTCATTTCTTTTAT
Found at i:18259 original size:96 final size:95
Alignment explanation
Indices: 18159--18417 Score: 310
Period size: 96 Copynumber: 2.7 Consensus size: 95
18149 ACTCTTTGAA
*
18159 TTTTCTCTCATTTTCTCTTATCAACAACTCTTCTCTTT-TTTCTTCTCTCAAG-TT-ATTTTCTC
1 TTTTCACTCATTTTCTCTTATCAACAACTCTTCTCTTTCTTTCTT-T-T--AGCTTCATTTTCTC
*
18221 TCATTTCTTTTTTTCTTCTCTCTATTTCTTTTAT
62 TCATTTATTTTTTTCTTCTCTCTATTTCTTTTAT
* * * * *
18255 TTTTCACTCATTTTCTCTCATTATCAACTCTTGTCTTTCCTTTCTTTTAGCTTCTTTTTCTCTCA
1 TTTTCACTCATTTTCTCTTATCAACAACTCTTCTCTTT-CTTTCTTTTAGCTTCATTTTCTCTCA
18320 TTTATTTTTTTCTTCTCTCTATTTCTTTTAT
65 TTTATTTTTTTCTTCTCTCTATTTCTTTTAT
* ** * * *
18351 TTTT-AGCTCATTTTCTCTTATTATTAACTCTTGTCTTTCTTTTCTTTTAGCTGCTTTTTCTCTC
1 TTTTCA-CTCATTTTCTCTTATCAACAACTCTTCTCTTTC-TTTCTTTTAGCTTCATTTTCTCTC
18415 ATT
64 ATT
18418 CTTTCATTAC
Statistics
Matches: 147, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
94 2 0.01
95 4 0.03
96 134 0.91
97 1 0.01
98 6 0.04
ACGTcount: A:0.12, C:0.24, G:0.03, T:0.62
Consensus pattern (95 bp):
TTTTCACTCATTTTCTCTTATCAACAACTCTTCTCTTTCTTTCTTTTAGCTTCATTTTCTCTCAT
TTATTTTTTTCTTCTCTCTATTTCTTTTAT
Found at i:18316 original size:45 final size:45
Alignment explanation
Indices: 18265--18417 Score: 146
Period size: 45 Copynumber: 3.3 Consensus size: 45
18255 TTTTCACTCA
* *
18265 TTTTCTCTCATTATCAACTCTTGTCTTTCCTTTCTTTTAGCTTCT
1 TTTTCTCTCATTATTAACTCTTGTCTTTCTTTTCTTTTAGCTTCT
** * * * *
18310 TTTTCTCTCATTTATTTTTTTCTTCTCTCTATTTCTTTTATTTTTAGC-TCA
1 TTTTCTCTCA-TTA---TTAAC-TCT-TGTCTTTCTTTT-CTTTTAGCTTCT
* *
18361 TTTTCTCTTATTATTAACTCTTGTCTTTCTTTTCTTTTAGCTGCT
1 TTTTCTCTCATTATTAACTCTTGTCTTTCTTTTCTTTTAGCTTCT
18406 TTTTCTCTCATT
1 TTTTCTCTCATT
18418 CTTTCATTAC
Statistics
Matches: 83, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
44 7 0.08
45 32 0.39
46 6 0.07
47 3 0.04
49 2 0.02
50 6 0.07
51 20 0.24
52 7 0.08
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (45 bp):
TTTTCTCTCATTATTAACTCTTGTCTTTCTTTTCTTTTAGCTTCT
Found at i:18328 original size:26 final size:26
Alignment explanation
Indices: 18299--18368 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 26
18289 CTTTCCTTTC
18299 TTTTAGCTTCTTTTTCTCTCATTTAT
1 TTTTAGCTTCTTTTTCTCTCATTTAT
** * * * * *
18325 TTTTTTCTTCTCTCTATTTCTTTTAT
1 TTTTAGCTTCTTTTTCTCTCATTTAT
*
18351 TTTTAGC-TCATTTTCTCT
1 TTTTAGCTTCTTTTTCTCT
18369 TATTATTAAC
Statistics
Matches: 30, Mismatches: 14, Indels: 1
0.67 0.31 0.02
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTTAGCTTCTTTTTCTCTCATTTAT
Found at i:19175 original size:3 final size:3
Alignment explanation
Indices: 19162--19222 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
19152 TTCAACTAGC
*
19162 TCT TGT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
19210 TCG TCT TCT TCT T
1 TCT TCT TCT TCT T
19223 AATTTCAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:20322 original size:17 final size:17
Alignment explanation
Indices: 20302--20334 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20292 TTTAAGGACT
20302 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
20319 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
20335 TAAATGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:20577 original size:47 final size:49
Alignment explanation
Indices: 20516--20613 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 49
20506 ATGCATTATG
* * *
20516 TAATGACATTCATTAACT-C-T-CATGATTAGTTAAGTTTGCATCATAAA
1 TAATGACATCCATTAACTACTTACATG-TTAGTTAAATATGCATCATAAA
*
20563 TAATGACATCCATTAAGTAACTTACATGTTAGTTAAATATGCATCATAAA
1 TAATGACATCCATTAACT-ACTTACATGTTAGTTAAATATGCATCATAAA
20613 T
1 T
20614 CCTATCATGC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
47 16 0.37
49 1 0.02
50 22 0.51
51 4 0.09
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (49 bp):
TAATGACATCCATTAACTACTTACATGTTAGTTAAATATGCATCATAAA
Found at i:20608 original size:50 final size:50
Alignment explanation
Indices: 20529--20665 Score: 150
Period size: 50 Copynumber: 2.7 Consensus size: 50
20519 TGACATTCAT
* *
20529 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGA-CATCCATTAAG
1 TAACTCACATG-TTAGTTAAATTTGCATCATAAATAAT-ATCATCCATTAAG
* * ** * *
20580 TAACTTACATGTTAGTTAAATATGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAATTTGCATCATAAATAATATCATCCATTAAG
*
20630 TAACTCCCATGTTAGTTAAAGTTTGCATCATTAAAT
1 TAACTCACATGTTAGTTAAA-TTTGCATCA-TAAAT
20666 CAAGTCATGC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
49 1 0.01
50 49 0.68
51 17 0.24
52 5 0.07
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATTTGCATCATAAATAATATCATCCATTAAG
Found at i:25546 original size:50 final size:52
Alignment explanation
Indices: 25460--25557 Score: 146
Period size: 50 Copynumber: 1.9 Consensus size: 52
25450 TGCATGACTT
*
25460 GATTTAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGATAA
1 GATTTAATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGATAA
* * *
25512 GATTT-ATGATGCATA-TTTAACTAACATGTAAGTTACTTAATGCATG
1 GATTTAATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATG
25558 TCATATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 28 0.67
51 9 0.21
52 5 0.12
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (52 bp):
GATTTAATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGATAA
Found at i:25728 original size:17 final size:17
Alignment explanation
Indices: 25697--25729 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25687 CAAACACTTA
25697 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
25714 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
25730 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:28983 original size:30 final size:30
Alignment explanation
Indices: 28949--29078 Score: 206
Period size: 30 Copynumber: 4.3 Consensus size: 30
28939 GTGTGTTTGT
* * **
28949 AACATGAGTGTTCACAACTCCAATGTTCGC
1 AACATGAGTGTACACAGCTCCGGTGTTCGC
*
28979 AACATGAGTGGACACAGCTCCGGTGTTCGC
1 AACATGAGTGTACACAGCTCCGGTGTTCGC
*
29009 AACATGAGTGTACACAGCTCCGGTGTTCGT
1 AACATGAGTGTACACAGCTCCGGTGTTCGC
29039 AACATGAGTGTACACAGCTCCGGTGTTCGC
1 AACATGAGTGTACACAGCTCCGGTGTTCGC
29069 AACATGAGTG
1 AACATGAGTG
29079 CTCACAACAC
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 92 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (30 bp):
AACATGAGTGTACACAGCTCCGGTGTTCGC
Found at i:33459 original size:24 final size:24
Alignment explanation
Indices: 33432--33487 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
33422 GGAGAGTTCT
* *
33432 CAAGAGGAAAAAGTAAATGA-AAAA
1 CAAGAAGAAAAAGAAAAT-ACAAAA
*
33456 CAAGAAGAAAATGAAAATACAAAA
1 CAAGAAGAAAAAGAAAATACAAAA
33480 CAAGAAGA
1 CAAGAAGA
33488 TACTCATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.68, C:0.07, G:0.18, T:0.07
Consensus pattern (24 bp):
CAAGAAGAAAAAGAAAATACAAAA
Found at i:35392 original size:21 final size:21
Alignment explanation
Indices: 35350--35394 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35340 AATTAAAATT
** * *
35350 AATAAAATAAACGAGTAGTAA
1 AATAAAATAAAAAACTAATAA
35371 AATAAAATAAAAAACTAATAA
1 AATAAAATAAAAAACTAATAA
35392 AAT
1 AAT
35395 TTAATTTAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (21 bp):
AATAAAATAAAAAACTAATAA
Found at i:38165 original size:15 final size:17
Alignment explanation
Indices: 38145--38179 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
38135 AACTCTTGTT
38145 TTTCTTTTTG-CTCA-A
1 TTTCTTTTTGTCTCATA
38160 TTTCTTTTTGTCTCATA
1 TTTCTTTTTGTCTCATA
38177 TTT
1 TTT
38180 TCTTAAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.11, C:0.17, G:0.06, T:0.66
Consensus pattern (17 bp):
TTTCTTTTTGTCTCATA
Found at i:39689 original size:36 final size:36
Alignment explanation
Indices: 39633--39709 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
39623 GCTCAAAAAG
* *
39633 CATGTCTCTCCATTTGTCTTTGAGGATATGAAAGGA
1 CATGTCTCTCCATTTATCTTTGAGGAGATGAAAGGA
* * * *
39669 CATGTCTCTTCGTTTATCTTTGAGTAGATGAAAGGG
1 CATGTCTCTCCATTTATCTTTGAGGAGATGAAAGGA
39705 CATGT
1 CATGT
39710 TTTTTCATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (36 bp):
CATGTCTCTCCATTTATCTTTGAGGAGATGAAAGGA
Found at i:40126 original size:17 final size:19
Alignment explanation
Indices: 40106--40150 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
40096 AACAATCAAA
40106 TTAAATAACTC-A-CATAT
1 TTAAATAACTCAAGCATAT
*
40123 TTAATTAACTCAAGCATAT
1 TTAAATAACTCAAGCATAT
40142 TT-AATAACT
1 TTAAATAACT
40151 AAGATGCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.42
18 7 0.29
19 7 0.29
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (19 bp):
TTAAATAACTCAAGCATAT
Found at i:40142 original size:19 final size:16
Alignment explanation
Indices: 40109--40150 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 16
40099 AATCAAATTA
40109 AATAACTCACATATTT
1 AATAACTCACATATTT
40125 AATTAACTCAAGCATATTT
1 AA-TAACTC-A-CATATTT
40144 AATAACT
1 AATAACT
40151 AAGATGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.09
17 6 0.26
18 6 0.26
19 9 0.39
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (16 bp):
AATAACTCACATATTT
Found at i:40354 original size:101 final size:102
Alignment explanation
Indices: 40200--40424 Score: 280
Period size: 101 Copynumber: 2.2 Consensus size: 102
40190 AACTAATAGA
* *
40200 TTACTAAATGCATGAC-TTATTTCGAGGATGCAAACTTTAACTAACATGGGAGTTACATAATGCA
1 TTACTTAATGCATGACTTTATTTC-AGGATGCAAACTTTAACTAACATGAGAGTTACATAATGCA
* *
40264 TG--ATATAATTAGTGATGAATATTTAACTAACATGTAAG
65 TGTCAT-TAATTA-TGATGAATACTTAACTAACATGAAAG
* * *
40302 TTACTTAATGCATGTCTTTATTT-ATGATGCAAAC-TTAACTAATCATGAGAGTTATATAATGCA
1 TTACTTAATGCATGACTTTATTTCAGGATGCAAACTTTAACTAA-CATGAGAGTTACATAATGCA
* *
40365 TGTCATTATTTATGATGCATACTTAACTAACATGAAAG
65 TGTCATTAATTATGATGAATACTTAACTAACATGAAAG
* *
40403 TTACATATTGCATGACTTTATT
1 TTACTTAATGCATGACTTTATT
40425 AAATGCAGAA
Statistics
Matches: 107, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
100 8 0.07
101 72 0.67
102 19 0.18
103 8 0.07
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.37
Consensus pattern (102 bp):
TTACTTAATGCATGACTTTATTTCAGGATGCAAACTTTAACTAACATGAGAGTTACATAATGCAT
GTCATTAATTATGATGAATACTTAACTAACATGAAAG
Found at i:40424 original size:50 final size:50
Alignment explanation
Indices: 40206--40424 Score: 228
Period size: 50 Copynumber: 4.3 Consensus size: 50
40196 TAGATTACTA
* **
40206 AATGCATGAC-TTATTTCGAGGATGCAAACTTTAACTAACATGGGAGTTACAT
1 AATGCATGACTTTATTT--ATGATGCAAAC-TTAACTAACATGAAAGTTACAT
* * * * *
40258 AATGCATGA-TATAATTAGTGATG-AATATTTAACTAACATGTAAGTTACTT
1 AATGCATGACTTTATTTA-TGATGCAA-ACTTAACTAACATGAAAGTTACAT
* * *
40308 AATGCATGTCTTTATTTATGATGCAAACTTAACTAATCATGAGAGTTATAT
1 AATGCATGACTTTATTTATGATGCAAACTTAACTAA-CATGAAAGTTACAT
* * *
40359 AATGCATGTCATTATTTATGATGCATACTTAACTAACATGAAAGTTACAT
1 AATGCATGACTTTATTTATGATGCAAACTTAACTAACATGAAAGTTACAT
*
40409 ATTGCATGACTTTATT
1 AATGCATGACTTTATT
40425 AAATGCAGAA
Statistics
Matches: 139, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
50 69 0.50
51 57 0.41
52 13 0.09
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (50 bp):
AATGCATGACTTTATTTATGATGCAAACTTAACTAACATGAAAGTTACAT
Found at i:40512 original size:31 final size:31
Alignment explanation
Indices: 40404--40512 Score: 80
Period size: 31 Copynumber: 3.4 Consensus size: 31
40394 ACATGAAAGT
*
40404 TACATATTGCATGACTTTATTAAATGCAGAA
1 TACATAATGCATGACTTTATTAAATGCAGAA
* * * *
40435 TAATGTCATTATTCAT-ACTTAACTAACATG-A-AA
1 T-A---CATAATGCATGACTTTATTAA-ATGCAGAA
*
40468 GTTACATATTGCATGACTTTATTAAATGCAGAA
1 --TACATAATGCATGACTTTATTAAATGCAGAA
40501 TACATAATGCAT
1 TACATAATGCAT
40513 ATCTTAATTA
Statistics
Matches: 57, Mismatches: 11, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
31 22 0.39
32 10 0.18
33 4 0.07
34 10 0.18
35 11 0.19
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (31 bp):
TACATAATGCATGACTTTATTAAATGCAGAA
Found at i:41196 original size:87 final size:87
Alignment explanation
Indices: 41048--41221 Score: 339
Period size: 87 Copynumber: 2.0 Consensus size: 87
41038 TCATACCCGA
*
41048 GGTTGGAACATTCATCAATTCGATTTATTTTCTTTTATTTTGAAATTATTTTTTATTTATTGTTT
1 GGTTGGAACATTCATCAATTCGATTTATTTTCTTTTATTTTGAAATTATTTTTTATATATTGTTT
41113 TATTATCTTTTGATTTTAATTT
66 TATTATCTTTTGATTTTAATTT
41135 GGTTGGAACATTCATCAATTCGATTTATTTTCTTTTATTTTGAAATTATTTTTTATATATTGTTT
1 GGTTGGAACATTCATCAATTCGATTTATTTTCTTTTATTTTGAAATTATTTTTTATATATTGTTT
41200 TATTATCTTTTGATTTTAATTT
66 TATTATCTTTTGATTTTAATTT
41222 ATTTAATTTC
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.60
Consensus pattern (87 bp):
GGTTGGAACATTCATCAATTCGATTTATTTTCTTTTATTTTGAAATTATTTTTTATATATTGTTT
TATTATCTTTTGATTTTAATTT
Found at i:57834 original size:6 final size:6
Alignment explanation
Indices: 57825--57856 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
57815 CTTTTTCCCT
*
57825 TTGGTC TTGGTC TTGGTC TTGGTA TTGGTC TT
1 TTGGTC TTGGTC TTGGTC TTGGTC TTGGTC TT
57857 AACTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.12, G:0.31, T:0.53
Consensus pattern (6 bp):
TTGGTC
Found at i:58835 original size:13 final size:13
Alignment explanation
Indices: 58797--58840 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
58787 GGCACCGCTT
*
58797 TAATTTAAAAAAA
1 TAATTGAAAAAAA
58810 TAACTTGTCAAAAAAA
1 TAA-TTG--AAAAAAA
58826 TAATTGAAAAAAA
1 TAATTGAAAAAAA
58839 TA
1 TA
58841 TATATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 12 0.44
14 2 0.07
15 3 0.11
16 10 0.37
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (13 bp):
TAATTGAAAAAAA
Found at i:66930 original size:2 final size:2
Alignment explanation
Indices: 66923--66947 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
66913 CCAACATTCC
66923 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
66948 AAAGGTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70413 original size:96 final size:96
Alignment explanation
Indices: 70262--70456 Score: 390
Period size: 96 Copynumber: 2.0 Consensus size: 96
70252 AAATTCATAA
70262 AACAATTGATGCCAAAGACATGAAAAGAAAGAAAGAAAGAAAAACCCTTTGGAAGGAGGAATCAA
1 AACAATTGATGCCAAAGACATGAAAAGAAAGAAAGAAAGAAAAACCCTTTGGAAGGAGGAATCAA
70327 ATCTGCACCTTTCAATTTCCTCAACGCTTTT
66 ATCTGCACCTTTCAATTTCCTCAACGCTTTT
70358 AACAATTGATGCCAAAGACATGAAAAGAAAGAAAGAAAGAAAAACCCTTTGGAAGGAGGAATCAA
1 AACAATTGATGCCAAAGACATGAAAAGAAAGAAAGAAAGAAAAACCCTTTGGAAGGAGGAATCAA
70423 ATCTGCACCTTTCAATTTCCTCAACGCTTTT
66 ATCTGCACCTTTCAATTTCCTCAACGCTTTT
70454 AAC
1 AAC
70457 TACTCAGCTA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 99 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (96 bp):
AACAATTGATGCCAAAGACATGAAAAGAAAGAAAGAAAGAAAAACCCTTTGGAAGGAGGAATCAA
ATCTGCACCTTTCAATTTCCTCAACGCTTTT
Found at i:71759 original size:14 final size:15
Alignment explanation
Indices: 71723--71752 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
71713 CTCGTTTATG
71723 AAATTAAGGGTTGTA
1 AAATTAAGGGTTGTA
71738 AATATTAAGGGTTGT
1 AA-ATTAAGGGTTGT
71753 GAATTAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 2 0.14
16 12 0.86
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (15 bp):
AAATTAAGGGTTGTA
Found at i:73319 original size:18 final size:17
Alignment explanation
Indices: 73291--73360 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 17
73281 GAAAGTACTG
73291 TACTGGCTCGTTAGAGCA
1 TACT-GCTCGTTAGAGCA
* *
73309 AACTAGCTCGTTTGAGCA
1 TACT-GCTCGTTAGAGCA
*
73327 TACTGACTCGTTTGAGCA
1 TACTG-CTCGTTAGAGCA
*
73345 TACTGGCTCGTAAGAG
1 TACT-GCTCGTTAGAG
73361 TTAATTATTG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
17 1 0.02
18 42 0.95
19 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (17 bp):
TACTGCTCGTTAGAGCA
Found at i:77073 original size:19 final size:19
Alignment explanation
Indices: 77013--77083 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
77003 TCGAGCATAT
77013 TGGCTCGTAAGAGCGATAC
1 TGGCTCGTAAGAGCGATAC
* * * *
77032 TGGCTTGTACGAGTGGTAC
1 TGGCTCGTAAGAGCGATAC
*
77051 TGGCTCGTAAGAGCGATAT
1 TGGCTCGTAAGAGCGATAC
77070 TGGCTCGTAAGAGC
1 TGGCTCGTAAGAGC
77084 AAATTACTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (19 bp):
TGGCTCGTAAGAGCGATAC
Found at i:78870 original size:16 final size:16
Alignment explanation
Indices: 78849--78880 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
78839 GCCAGAATTC
78849 CTTCGTTCCCAAGCAA
1 CTTCGTTCCCAAGCAA
78865 CTTCGTTCCCAAGCAA
1 CTTCGTTCCCAAGCAA
78881 TTTCTGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.38, G:0.12, T:0.25
Consensus pattern (16 bp):
CTTCGTTCCCAAGCAA
Found at i:98752 original size:26 final size:28
Alignment explanation
Indices: 98716--98790 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 28
98706 CAAAAATTTA
* *
98716 GCTCATACGAGCCCAG-GT-AGAATATC
1 GCTCTTACGAGCCCAGAATCAGAATATC
98742 GCTCTTACGAG-CCAGAATCAGAATATC
1 GCTCTTACGAGCCCAGAATCAGAATATC
98769 GCTCCTT-CGAG-CCAGAATCAGA
1 GCT-CTTACGAGCCCAGAATCAGA
98791 TTGCTCCTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
25 4 0.09
26 11 0.25
27 26 0.59
28 3 0.07
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (28 bp):
GCTCTTACGAGCCCAGAATCAGAATATC
Found at i:98800 original size:27 final size:27
Alignment explanation
Indices: 98734--98790 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
98724 GAGCCCAGGT
98734 AGAATATCGCT-CTTACGAGCCAGAATC
1 AGAATATCGCTCCTT-CGAGCCAGAATC
98761 AGAATATCGCTCCTTCGAGCCAGAATC
1 AGAATATCGCTCCTTCGAGCCAGAATC
98788 AGA
1 AGA
98791 TTGCTCCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (27 bp):
AGAATATCGCTCCTTCGAGCCAGAATC
Found at i:109556 original size:26 final size:27
Alignment explanation
Indices: 109527--109585 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
109517 ATGCGGTGAT
* *
109527 AATTCTGGACCTGCTT-ATGCAGCGAC
1 AATTCTGGAACAGCTTCATGCAGCGAC
* *
109553 AATTCT-GAACAGGTTCTTGCAGCGAC
1 AATTCTGGAACAGCTTCATGCAGCGAC
109579 AATTCTG
1 AATTCTG
109586 AGCGCAATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (27 bp):
AATTCTGGAACAGCTTCATGCAGCGAC
Found at i:110079 original size:15 final size:15
Alignment explanation
Indices: 110055--110089 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
110045 TATACATATA
*
110055 TTTTTTTCTTTTCCC
1 TTTTTCTCTTTTCCC
*
110070 TTTTTCTCTTTTCTC
1 TTTTTCTCTTTTCCC
110085 TTTTT
1 TTTTT
110090 TTTCATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTCTTTTCCC
Found at i:123669 original size:23 final size:23
Alignment explanation
Indices: 123639--123686 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
123629 CTTTGAGATG
123639 TTTAACCTTGGCATCTCAATAAC
1 TTTAACCTTGGCATCTCAATAAC
*
123662 TTTAACCTTGGCATCTTAATAAC
1 TTTAACCTTGGCATCTCAATAAC
123685 TT
1 TT
123687 CTTTTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (23 bp):
TTTAACCTTGGCATCTCAATAAC
Found at i:126867 original size:15 final size:15
Alignment explanation
Indices: 126829--126870 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
126819 CGATGACGAC
126829 ATCTATGAAGATGAT
1 ATCTATGAAGATGAT
* *
126844 ATCTTTGAAGATGGGT
1 ATCTATGAAGAT-GAT
126860 A-CTATGAAGAT
1 ATCTATGAAGAT
126871 TGGGAGATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (15 bp):
ATCTATGAAGATGAT
Found at i:134779 original size:29 final size:29
Alignment explanation
Indices: 134746--134803 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
134736 AGTAATTAAT
*
134746 TCTATTTTTTGCAAGGATTTAATTCACTA
1 TCTATTCTTTGCAAGGATTTAATTCACTA
134775 TCTATTCTTTGCAAGGATTTAATTCACTA
1 TCTATTCTTTGCAAGGATTTAATTCACTA
134804 CCGCCTTACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.47
Consensus pattern (29 bp):
TCTATTCTTTGCAAGGATTTAATTCACTA
Found at i:136692 original size:19 final size:21
Alignment explanation
Indices: 136670--136715 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
136660 GAGTTTTTAC
136670 TTTTATTTTATTT-TTT-GTA
1 TTTTATTTTATTTCTTTCGTA
136689 TTTTA--TTATTTCTTTCGTA
1 TTTTATTTTATTTCTTTCGTA
136708 -TTTATTTT
1 TTTTATTTT
136716 TGGTTTATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 6 0.26
18 7 0.30
19 8 0.35
20 2 0.09
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTATTTTATTTCTTTCGTA
Found at i:138292 original size:13 final size:13
Alignment explanation
Indices: 138274--138298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
138264 CTCGAGCGGT
138274 GCGTGACGACGGC
1 GCGTGACGACGGC
138287 GCGTGACGACGG
1 GCGTGACGACGG
138299 GTGACAACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.48, T:0.08
Consensus pattern (13 bp):
GCGTGACGACGGC
Found at i:138964 original size:30 final size:30
Alignment explanation
Indices: 138928--139287 Score: 282
Period size: 30 Copynumber: 12.0 Consensus size: 30
138918 AAGAGGTCCC
* * *
138928 CAAACTTCTCAAAAATTATATTTTAACCCT
1 CAAACTTTTCCAAAATTACATTTTAACCCT
* *
138958 CAAACTTCTCAAAAATTACATTTTAA-CCT
1 CAAACTTTTCCAAAATTACATTTTAACCCT
* * * *
138987 CTAAACTTATCAAAAAATTAAATTTTAGCCC-
1 C-AAACTTTTC-CAAAATTACATTTTAACCCT
*
139018 CTAAAC-TTCCCAAAATTACATTTTAA-CCT
1 C-AAACTTTTCCAAAATTACATTTTAACCCT
*
139047 CTAACCTTTTCCAAAATTACATTTTAACCCT
1 C-AAACTTTTCCAAAATTACATTTTAACCCT
*
139078 TAAACTTTTCCAAAATTACATTTTAACCCT
1 CAAACTTTTCCAAAATTACATTTTAACCCT
* * * *
139108 TAAATTTTTCTAAAATTACATTTTAACCAT
1 CAAACTTTTCCAAAATTACATTTTAACCCT
* * **
139138 TAAACTTTTCCAAAATCACATTTCGACCC-
1 CAAACTTTTCCAAAATTACATTTTAACCCT
* * *
139167 CTAAACTTTCCCAAAATTACATTTTGA-TCT
1 C-AAACTTTTCCAAAATTACATTTTAACCCT
* *** ** *
139197 CAAAAAATTTTTTGAAATTGTATTTTGACCCT
1 C--AAACTTTTCCAAAATTACATTTTAACCCT
* * * *
139229 TAAACTTCTCCAAAATCACATTTTCACCCT
1 CAAACTTTTCCAAAATTACATTTTAACCCT
* **
139259 TAAACTTTTCCAAAATTATGTTTTAACCC
1 CAAACTTTTCCAAAATTACATTTTAACCC
139288 GAAATTCTCC
Statistics
Matches: 269, Mismatches: 51, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
28 2 0.01
29 23 0.09
30 199 0.74
31 41 0.15
32 4 0.01
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (30 bp):
CAAACTTTTCCAAAATTACATTTTAACCCT
Found at i:139398 original size:20 final size:19
Alignment explanation
Indices: 139356--139393 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
139346 GTATGTAAAA
139356 TTTAATTATTATCCTTTTTT
1 TTTAATTA-TATCCTTTTTT
139376 TTTAATTA-ATCCTTTTTT
1 TTTAATTATATCCTTTTTT
139394 ATTTTGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATTATATCCTTTTTT
Found at i:142392 original size:22 final size:21
Alignment explanation
Indices: 142367--142408 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
142357 GAGAGTCAAG
*
142367 CCGAGACAAATGAGTTAAAGGC
1 CCGA-ACAAAAGAGTTAAAGGC
*
142389 CCGAATAAAAGAGTTAAAGG
1 CCGAACAAAAGAGTTAAAGG
142409 GATCCTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.45, C:0.14, G:0.26, T:0.14
Consensus pattern (21 bp):
CCGAACAAAAGAGTTAAAGGC
Found at i:148006 original size:77 final size:78
Alignment explanation
Indices: 147920--148242 Score: 300
Period size: 77 Copynumber: 4.2 Consensus size: 78
147910 ACCTCGATCA
*
147920 TGGGGCAGATCACAGTCATTCGATCTTTTACCCCGAGCTT-GGGCAGATCACCATCAGCCAATCT
1 TGGGGCAGATCACAGTCATTCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCT
147984 CTTACCCTAAGCC
66 CTTACCCTAAGCC
* ** * * * * ** * *
147997 TGGGACAGATTGCAGCCATTCAATCTTTTACCCCGAGCCTAAGGCAGATCACCCTCAACCAATCT
1 TGGGGCAGATCACAGTCATTCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCT
* *
148062 CTTA-CCTCGAGCT
66 CTTACCCT-AAGCC
* * *
148075 TGGGGCAGATTGCA-ACT-ATCCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCAAT
1 TGGGGCAGA-T-CACAGTCATTCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAAT
* *
148138 CTTTTACCC-GAGCC
64 CTCTTACCCTAAGCC
* * * * * * *
148152 TGAGGTAGATTACAG-C-TATCTGATCTCTTACCCCGAGCTTGGGGCGGATCACCCTTAGCTAAT
1 TGGGGCAGATCACAGTCAT-TC-GATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAAT
*
148215 CTCTTACCCCAAGCC
64 CTCTTACCCTAAGCC
*
148230 TGGGGCAAATCAC
1 TGGGGCAGATCAC
148243 CATTAGCCAA
Statistics
Matches: 195, Mismatches: 41, Indels: 19
0.76 0.16 0.07
Matches are distributed among these distances:
75 2 0.01
76 3 0.02
77 95 0.49
78 91 0.47
79 4 0.02
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.25
Consensus pattern (78 bp):
TGGGGCAGATCACAGTCATTCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCT
CTTACCCTAAGCC
Found at i:148036 original size:39 final size:37
Alignment explanation
Indices: 147903--148492 Score: 245
Period size: 39 Copynumber: 15.2 Consensus size: 37
147893 AAAGATTCTG
* * * *
147903 ATCTCTTACCTCGATCATGGGGCAGA-TCACAGTCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCAC---CATTCA
* * *
147942 ATCTTTTACCCCGAG-CTTGGGCAGA-TCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCACCAT---TCA
** *
147980 ATCTCTTACCCTAAGCCTGGGACAGATTGCAGCCATTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CA-CCATTCA
* ** **
148019 ATCTTTTACCCCGAGCCTAAGGCAGA-TCACCCTCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCA--C-CATTCA
* * * * *
148058 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACTATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-C-ACCATTCA
*
148097 ATCTCTTACCCCGAGCTTGGGGCAGA-TCACCATTAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCACCATT---CA
* * * * *
148136 ATCTTTTA-CCCGAGCCTGAGGTAGATTACAGC-TATCTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CACCAT-TC-A
* * *
148174 ATCTCTTACCCCGAGCTTGGGGCGGA-TCACCCTTAGCTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCACCATT--C-A
* *
148213 ATCTCTTACCCCAAGCCTGGGGCA-AATCACCATTAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCACCATT---CA
* * * * *
148252 ATCTTTTACTCTGAGCCT-GGGCAGATTACAGC-TATCTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CACCAT-TC-A
* * *
148290 TTCTCTTACCTCGAGCCTGGGGCAGA-TCACCATCGACTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCACCAT--TC-A
* * * * *
148329 ATCTCTTACCTCAAGCCTGGGGCAGATTGTAGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CA-CCATTCA
*
148368 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATT-CA-CCATTCA
* * **
148407 ATCTTTTACCTCGAGCCTGGGGCAGA-TCACCGTCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTCA-C--CATTCA
* * *
148446 ATCTCTTACCCCGTG-ATAGGGGCAGATTGCAACCATCCA
1 ATCTCTTACCCCGAGCCT-GGGGCAGATT-C-ACCATTCA
148485 ATCTCTTA
1 ATCTCTTA
148493 AAAAAATCTT
Statistics
Matches: 422, Mismatches: 88, Indels: 82
0.71 0.15 0.14
Matches are distributed among these distances:
35 3 0.01
36 4 0.01
37 15 0.04
38 74 0.18
39 295 0.70
40 15 0.04
41 6 0.01
42 10 0.02
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.26
Consensus pattern (37 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTCACCATTCA
Found at i:148162 original size:155 final size:155
Alignment explanation
Indices: 147903--148242 Score: 384
Period size: 155 Copynumber: 2.2 Consensus size: 155
147893 AAAGATTCTG
* * * *
147903 ATCTCTTACCTCGATCATGGGGCAGATCACAGTCATTCGATCTTTTACCCCGAGCTTGGGCAGAT
1 ATCTCTTACCTCGAGCATGGGGCAGATCACACTCATCCGATCTCTTACCCCGAGCTTGGGCAGAT
* *
147968 CACCATCAGCCAATCTCTTACCCTAAGCCTGGGACAGATTGCAGCCAT-TCAATCTTTTACCCCG
66 CACCATCAGCCAATCTCTTACCCTAAGCCTGGGACAGATTACAGCCATCT-AATCTCTTACCCCG
148032 AGCCTAAGGCAGATCACCCTCAACCA
130 AGCCTAAGGCAGATCACCCTCAACCA
*
148058 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA-ACT-ATCCGATCTCTTACCCCGAGCTTGGGGCA
1 ATCTCTTACCTCGAGCATGGGGCAGA-T-CACACTCATCCGATCTCTTACCCCGAGCTT-GGGCA
* * * * * *
148121 GATCACCATTAGCCAATCTTTTACCC-GAGCCTGAGG-TAGATTACAGCTATCTGATCTCTTACC
63 GATCACCATCAGCCAATCTCTTACCCTAAGCCTG-GGACAGATTACAGCCATCTAATCTCTTACC
* ** * * * *
148184 CCGAGCTTGGGGCGGATCACCCTTAGCTA
127 CCGAGCCTAAGGCAGATCACCCTCAACCA
* * * *
148213 ATCTCTTACCCCAAGCCTGGGGCAAATCAC
1 ATCTCTTACCTCGAGCATGGGGCAGATCAC
148243 CATTAGCCAA
Statistics
Matches: 155, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
153 2 0.01
154 1 0.01
155 115 0.74
156 35 0.23
157 2 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (155 bp):
ATCTCTTACCTCGAGCATGGGGCAGATCACACTCATCCGATCTCTTACCCCGAGCTTGGGCAGAT
CACCATCAGCCAATCTCTTACCCTAAGCCTGGGACAGATTACAGCCATCTAATCTCTTACCCCGA
GCCTAAGGCAGATCACCCTCAACCA
Found at i:148192 original size:116 final size:117
Alignment explanation
Indices: 147941--148457 Score: 404
Period size: 116 Copynumber: 4.5 Consensus size: 117
147931 ACAGTCATTC
* * * * *
147941 GATCTTTTACCCCGAGCTT-GGGCAGA-TCAC-CATCAGCCAATCTCTTACCCTAAGCCTGGGAC
1 GATCTCTTACCTCGAGCTTGGGGCAGATTCACAC-TTAGCCAATCTCTTACCCCAAGCCTGGGGC
* * * * * * *
148003 AGATTGCAGCCATT---CAATCTTTTACCCCGAGCCTAAGGCAGATCAC-CCTCAACC
65 A-AAT-CA-CCATTAGCCAATCTTTTACTCCGAGCCT-GGGCAGATTACAGCT-ATCT
* * * * *
148057 AATCTCTTACCTCGAGCTTGGGGCAGATTGCA-AC-TATCCGATCTCTTACCCCGAGCTTGGGGC
1 GATCTCTTACCTCGAGCTTGGGGCAGATT-CACACTTAGCCAATCTCTTACCCCAAGCCTGGGGC
* *
148120 AGATCACCATTAGCCAATCTTTTAC-CCGAGCCTGAGGTAGATTACAGCTATCT
65 AAATCACCATTAGCCAATCTTTTACTCCGAGCCTG-GGCAGATTACAGCTATCT
* * * *
148173 GATCTCTTACCCCGAGCTTGGGGCGGA-TCACCCTTAGCTAATCTCTTACCCCAAGCCTGGGGCA
1 GATCTCTTACCTCGAGCTTGGGGCAGATTCACACTTAGCCAATCTCTTACCCCAAGCCTGGGGCA
*
148237 AATCACCATTAGCCAATCTTTTACTCTGAGCCTGGGCAGATTACAGCTATCT
66 AATCACCATTAGCCAATCTTTTACTCCGAGCCTGGGCAGATTACAGCTATCT
* * * * * *
148289 GTTCTCTTACCTCGAGCCTGGGGCAGA-TCAC-CATCGACTAATCTCTTACCTCAAGCCTGGGGC
1 GATCTCTTACCTCGAGCTTGGGGCAGATTCACACTTAG-CCAATCTCTTACCCCAAGCCTGGGGC
* * * * * * *
148352 AGATTGTAGCCA-T--CCGATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCC
65 A-AAT-CA-CCATTAGCCAATCTTTTACTCCGAGCCT-GGGCAGATTACAGCTATCT
* * * * *
148406 AATCTTTTACCTCGAGCCTGGGGCAGA-TCAC-CGTCAACCAATCTCTTACCCC
1 GATCTCTTACCTCGAGCTTGGGGCAGATTCACAC-TTAGCCAATCTCTTACCCC
148458 GTGATAGGGG
Statistics
Matches: 329, Mismatches: 54, Indels: 35
0.79 0.13 0.08
Matches are distributed among these distances:
114 7 0.02
115 7 0.02
116 194 0.59
117 112 0.34
118 3 0.01
119 6 0.02
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (117 bp):
GATCTCTTACCTCGAGCTTGGGGCAGATTCACACTTAGCCAATCTCTTACCCCAAGCCTGGGGCA
AATCACCATTAGCCAATCTTTTACTCCGAGCCTGGGCAGATTACAGCTATCT
Found at i:148468 original size:78 final size:78
Alignment explanation
Indices: 147903--148488 Score: 420
Period size: 78 Copynumber: 7.6 Consensus size: 78
147893 AAAGATTCTG
* * * * * * * *
147903 ATCTCTTACCTCGATCATGGGGCAGATCACAGTCATTCGATCTTTTACCCCGAG-CTTGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCCAATCTTTTACCCCGAGCCTGGGGCAGA
*
147967 TCACCATCAGCCA
66 TCACCGTCAGCCA
** * * * **
147980 ATCTCTTACCCTAAGCCTGGGACAGATTGCAGCCATTCAATCTTTTACCCCGAGCCTAAGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCCAATCTTTTACCCCGAGCCTGGGGCAGA
* *
148045 TCACCCTCAACCA
66 TCACCGTCAGCCA
* * * * * * * *
148058 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACTATCCGATCTCTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCCAATCTTTTACCCCGAGCCTGGGGCAGA
* *
148123 TCACCATTAGCCA
66 TCACCGTCAGCCA
* * * * ** * * *
148136 ATCTTTTA-CCCGAGCCTGAGGTAGATTACAGCTATCTGATCTCTTACCCCGAGCTTGGGGCGGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCCAATCTTTTACCCCGAGCCTGGGGCAGA
* * *
148200 TCACCCTTAGCTA
66 TCACCGTCAGCCA
* * * *
148213 ATCTCTTACCCCAAGCCTGGGGCA-AAT-CA-CCATTAGCCAATCTTTTACTCTGAGCCT-GGGC
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCA-T--CCAATCTTTTACCCCGAGCCTGGGGC
* * * **
148274 AGATTACAG-CTATCTG
63 AGATCACCGTC-AGCCA
* * * * *
148290 TTCTCTTACCTCGAGCCTGGGGCAGA-T-CA-CCATCGACTAATCTCTTACCTCAAGCCTGGGGC
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATC--C-AATCTTTTACCCCGAGCCTGGGGC
**** * * *
148352 AGATTGTAGCCATCCG
63 AGATCACCGTCAGCCA
*
148368 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCCAATCTTTTACCTCGAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCCAATCTTTTACCCCGAGCCTGGGGCAGA
*
148433 TCACCGTCAACCA
66 TCACCGTCAGCCA
* * * *
148446 ATCTCTTACCCCGTG-ATAGGGGCAGATTGCAACCATCCAATCT
1 ATCTCTTACCCCGAGCCT-GGGGCAGATTACAGCCATCCAATCT
148489 CTTAAAAAAA
Statistics
Matches: 407, Mismatches: 86, Indels: 31
0.78 0.16 0.06
Matches are distributed among these distances:
74 1 0.00
75 2 0.00
76 5 0.01
77 166 0.41
78 223 0.55
79 3 0.01
80 2 0.00
81 5 0.01
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCCAATCTTTTACCCCGAGCCTGGGGCAGA
TCACCGTCAGCCA
Found at i:150720 original size:29 final size:29
Alignment explanation
Indices: 150639--150929 Score: 221
Period size: 29 Copynumber: 9.9 Consensus size: 29
150629 GAGGTCCTCG
* * * * *
150639 AACTTCTCAAAAATTATATTTTGACCCATG
1 AACTTTTC-AAAATTACATTTTAACCCCTA
* * *
150669 AACTTCTCAAAAATTACATTTTAACACTTA
1 AACTTTTC-AAAATTACATTTTAACCCCTA
*
150699 AACTTTTCAAAATTACATTTTAACCCCAA
1 AACTTTTCAAAATTACATTTTAACCCCTA
*
150728 AACTTTTCAAAATTACA-TTTAACCCTTA
1 AACTTTTCAAAATTACATTTTAACCCCTA
* *
150756 AACTTCTCCAAAATTACATTTTAA-CACTA
1 AACTT-TTCAAAATTACATTTTAACCCCTA
* *
150785 AACTTTCTCAAAATTGCATTTTGACCCCT-
1 AACTTT-TCAAAATTACATTTTAACCCCTA
* * * * **
150814 AACTTTCCTAAAATCACATTTCAATCTCAAA
1 AACTTTTC-AAAATTACATTTTAA-CCCCTA
* * *
150845 AAATTTACCAAAATTACATTTTGACCCCTA
1 AACTTT-TCAAAATTACATTTTAACCCCTA
* * *
150875 AACTTCTCCAAAATCACATTTT-ATCCCTA
1 AACTT-TTCAAAATTACATTTTAACCCCTA
**
150904 AACTTTTCTAAAATTATGTTTTAACC
1 AACTTTTC-AAAATTACATTTTAACC
150930 TTGAATTCTC
Statistics
Matches: 209, Mismatches: 41, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
28 18 0.09
29 106 0.51
30 65 0.31
31 18 0.09
32 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (29 bp):
AACTTTTCAAAATTACATTTTAACCCCTA
Found at i:150769 original size:87 final size:85
Alignment explanation
Indices: 150669--150944 Score: 263
Period size: 87 Copynumber: 3.2 Consensus size: 85
150659 TTGACCCATG
*
150669 AACTTCTCAAAAATTACATTTTAACACTTAAACTTTTCAAAATTACATTTTAACCCCAAAACTTT
1 AACTTCTCCAAAATTACATTTTAACAC-TAAACTTTTCAAAATTACATTTT-ACCCC-AAACTTT
150734 TC-AAAATTACATTTAACCCTTA
63 TCTAAAATTACATTTAACCCTTA
* * *
150756 AACTTCTCCAAAATTACATTTTAACACTAAACTTTCTCAAAATTGCATTTTGACCCCTAACTTTC
1 AACTTCTCCAAAATTACATTTTAACACTAAACTTT-TCAAAATTACATTTT-ACCCCAAACTTTT
* * **
150821 CTAAAATCACATTTCAATCTCAAA
64 CTAAAATTACATTT-AA-CCCTTA
* * * * * *
150845 AAATT-TACCAAAATTACATTTTGACCCCTAAACTTCTCCAAAATCACATTTTATCCCTAAACTT
1 AACTTCT-CCAAAATTACATTTT-AACACTAAACTT-TTCAAAATTACATTTTA-CCCCAAACTT
** *
150909 TTCTAAAATTATGTTTTAA-CCTTG
62 TTCTAAAATTA-CATTTAACCCTTA
150933 AA-TTCTCCAAAA
1 AACTTCTCCAAAA
150945 CTTCATTCTT
Statistics
Matches: 154, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
86 15 0.10
87 64 0.42
88 7 0.05
89 23 0.15
90 41 0.27
91 4 0.03
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (85 bp):
AACTTCTCCAAAATTACATTTTAACACTAAACTTTTCAAAATTACATTTTACCCCAAACTTTTCT
AAAATTACATTTAACCCTTA
Found at i:151042 original size:20 final size:22
Alignment explanation
Indices: 150997--151042 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
150987 GTATATAAAA
*
150997 TTTAATTATTATCCTTTGTTTTT
1 TTTAATTA-TATCCTTTGTTTAT
151020 TTTAATTA-ATCCTTT-TTTAT
1 TTTAATTATATCCTTTGTTTAT
151040 TTT
1 TTT
151043 GATTCGCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
23 8 0.36
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTAATTATATCCTTTGTTTAT
Found at i:156517 original size:21 final size:22
Alignment explanation
Indices: 156493--156534 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
156483 AAAAAAAATG
156493 AAAAGAAAAATGAGT-AGAAAC
1 AAAAGAAAAATGAGTAAGAAAC
**
156514 AAAAGAATCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
156535 ATAGATAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.05, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAGAAAAATGAGTAAGAAAC
Found at i:157960 original size:55 final size:55
Alignment explanation
Indices: 157876--157988 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
157866 AGATGAAAAG
157876 AAAGAATTTGAACTATGAGTTCTTTAACAAAACCCCATTCAATAATTTTTATATC
1 AAAGAATTTGAACTATGAGTTCTTTAACAAAACCCCATTCAATAATTTTTATATC
*
157931 AAAGATTTTGAACTATGAGTTCTTTAACAAAACCCCATTCAATAATTTTTATATC
1 AAAGAATTTGAACTATGAGTTCTTTAACAAAACCCCATTCAATAATTTTTATATC
157986 AAA
1 AAA
157989 CGGTTCATGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (55 bp):
AAAGAATTTGAACTATGAGTTCTTTAACAAAACCCCATTCAATAATTTTTATATC
Found at i:161743 original size:18 final size:18
Alignment explanation
Indices: 161730--161773 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
161720 AATTCATATA
161730 ATATTTCTTCTTCAGGAT
1 ATATTTCTTCTTCAGGAT
* * *
161748 TTATTTCTTCTTCAAGAC
1 ATATTTCTTCTTCAGGAT
161766 ATATTTCT
1 ATATTTCT
161774 ATATTTTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.07, T:0.52
Consensus pattern (18 bp):
ATATTTCTTCTTCAGGAT
Found at i:163957 original size:11 final size:11
Alignment explanation
Indices: 163941--163966 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
163931 AGGGAAGCTA
163941 TATTACAAAAG
1 TATTACAAAAG
163952 TATTACAAAAG
1 TATTACAAAAG
163963 TATT
1 TATT
163967 TTACAGAGAA
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:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (11 bp):
TATTACAAAAG
Found at i:164863 original size:21 final size:21
Alignment explanation
Indices: 164828--164887 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
164818 AAGGGTGCAG
* *
164828 ACTTTTACTGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* * *
164849 AGTTCTATCGATACAAATGAC
1 ACTTCTACCGATACAAGTGAC
* *
164870 TCTTCTACCGAAACAAGT
1 ACTTCTACCGATACAAGT
164888 CTTACTTCTA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:165617 original size:36 final size:35
Alignment explanation
Indices: 165570--165673 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 35
165560 TGTTCATTAT
*
165570 TCATTTTACTCCCTATTGATCCAAAGGTCATGATGC
1 TCATTTTACTCCCTATTGA-CCAAAGGTCATGACGC
* *
165606 TCATTTTACTCCCTATTGACCCAAAGGTTATTACGC
1 TCATTTTACTCCCTATTGA-CCAAAGGTCATGACGC
*
165642 TCATTTTACTCCCTGTTGACCTAAAGGTCATG
1 TCATTTTACTCCCTATTGACC-AAAGGTCATG
165674 CCTGTTACCA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 2 0.03
36 58 0.97
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (35 bp):
TCATTTTACTCCCTATTGACCAAAGGTCATGACGC
Found at i:166455 original size:14 final size:14
Alignment explanation
Indices: 166436--166488 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
166426 CAAATCTATC
166436 ACAAGCTTTCAAGA
1 ACAAGCTTTCAAGA
*
166450 ACAAGCATATTCAACA
1 ACAAGC-T-TTCAAGA
166466 ATGGCAAGCTTTCAAGA
1 A---CAAGCTTTCAAGA
166483 ACAAGC
1 ACAAGC
166489 ATATTCAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 11 0.34
15 1 0.03
16 7 0.22
17 7 0.22
18 1 0.03
19 5 0.16
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (14 bp):
ACAAGCTTTCAAGA
Found at i:166475 original size:33 final size:33
Alignment explanation
Indices: 166437--166506 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
166427 AAATCTATCA
166437 CAAGCTTTCAAGAACAAGCATATTCAACAATGG
1 CAAGCTTTCAAGAACAAGCATATTCAACAATGG
166470 CAAGCTTTCAAGAACAAGCATATTCAACAATGG
1 CAAGCTTTCAAGAACAAGCATATTCAACAATGG
166503 CAAG
1 CAAG
166507 TTTTATAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (33 bp):
CAAGCTTTCAAGAACAAGCATATTCAACAATGG
Found at i:174147 original size:44 final size:46
Alignment explanation
Indices: 174084--174178 Score: 124
Period size: 46 Copynumber: 2.1 Consensus size: 46
174074 TATTACAACA
*
174084 CCATTCCATTCAACCAAAC-AC-AAGAATACT-ATTACAGCTCTATT
1 CCATTCCATTCAACCAAACAACTAA-AATACTGATTACAGCCCTATT
* * *
174128 CCATTTCATTCAACCAAACAACTAAATTATTGATTACAGCCCTATT
1 CCATTCCATTCAACCAAACAACTAAAATACTGATTACAGCCCTATT
174174 CCATT
1 CCATT
174179 ACAGCTATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 18 0.41
45 6 0.14
46 20 0.45
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (46 bp):
CCATTCCATTCAACCAAACAACTAAAATACTGATTACAGCCCTATT
Found at i:174181 original size:16 final size:16
Alignment explanation
Indices: 174160--174231 Score: 92
Period size: 16 Copynumber: 4.5 Consensus size: 16
174150 TAAATTATTG
*
174160 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
* *
174176 ATTACAGCTATATTAC
1 ATTACAGCTCTATTCC
174192 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
174208 ATTACAACAT-TATTCC
1 ATTACAGC-TCTATTCC
174224 ATTACAGC
1 ATTACAGC
174232 GAACCACACG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
16 47 0.98
17 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:174388 original size:11 final size:11
Alignment explanation
Indices: 174372--174398 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
174362 AAGGTCATAT
174372 ATTATCATTTA
1 ATTATCATTTA
174383 ATTATCATTTA
1 ATTATCATTTA
174394 ATTAT
1 ATTAT
174399 AATCACAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATCATTTA
Found at i:175281 original size:36 final size:35
Alignment explanation
Indices: 175234--175336 Score: 125
Period size: 36 Copynumber: 2.9 Consensus size: 35
175224 TGTTCGTTAT
175234 TCATTTTACTCCCTGTTGACCCAAAGGTCATGATGC
1 TCATTTTACTCCCT-TTGACCCAAAGGTCATGATGC
* * * *
175270 TCATTTTACTCCTTATTAAACCAAAGGTCATTATGC
1 TCATTTTACTCCCT-TTGACCCAAAGGTCATGATGC
* * *
175306 TAATTTTACTCCCTATGACCTAAAGGTCATG
1 TCATTTTACTCCCTTTGACCCAAAGGTCATG
175337 CTTGTTACTA
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
35 12 0.22
36 43 0.78
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (35 bp):
TCATTTTACTCCCTTTGACCCAAAGGTCATGATGC
Found at i:178442 original size:22 final size:23
Alignment explanation
Indices: 178413--178474 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
178403 TTGTACGAAG
*
178413 CACTAGAAGGAGCTACCTT-ATA
1 CACTAGAAGGATCTACCTTGATA
* * *
178435 TACTAGAAAGATCTA-CTTGATG
1 CACTAGAAGGATCTACCTTGATA
178457 CACTAGAAGGATCTACCT
1 CACTAGAAGGATCTACCT
178475 AAAAATGAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.09
22 27 0.84
23 2 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (23 bp):
CACTAGAAGGATCTACCTTGATA
Found at i:191222 original size:55 final size:58
Alignment explanation
Indices: 191162--191314 Score: 167
Period size: 55 Copynumber: 2.7 Consensus size: 58
191152 TTATTATTAA
*
191162 ATTTTAATAAGATTATTATTAAATATAATTTAATAAAAAATAAT-TA-TTTAAT-CAT
1 ATTTTAATAAGATTATTATTAAATATAATTTAATAAAAAAGAATATATTTTAATACAT
* * * *
191217 ATTTTAA-AATGATTATTGTTAAATACAATTTAATGAAATAGAATATATTTTAATAACAT
1 ATTTTAATAA-GATTATTATTAAATATAATTTAATAAAAAAGAATATATTTTAAT-ACAT
191276 -TTTTAATATA-ATTATTATTAAAATATGAA-TTAATAAAAA
1 ATTTTAATA-AGATTATTATT-AAATAT-AATTTAATAAAAA
191315 TTATAAAATA
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
54 2 0.03
55 36 0.45
56 2 0.03
57 6 0.08
58 14 0.17
59 17 0.21
60 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (58 bp):
ATTTTAATAAGATTATTATTAAATATAATTTAATAAAAAAGAATATATTTTAATACAT
Found at i:194118 original size:16 final size:16
Alignment explanation
Indices: 194097--194131 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
194087 ATATAATGCT
194097 TATTTCAACTTTCTTC
1 TATTTCAACTTTCTTC
194113 TATTTCAACTTTCTTC
1 TATTTCAACTTTCTTC
194129 TAT
1 TAT
194132 CCATAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTCAACTTTCTTC
Found at i:195224 original size:31 final size:31
Alignment explanation
Indices: 195189--195270 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
195179 TAAAATGAAG
*
195189 TTTTAGGTTCTTTAAAAGTTAG-AGAAAAAAA
1 TTTTAGGATCTTTAAAAGTTAGTA-AAAAAAA
* *
195220 TTTTA-AATCTCTTATAAGTTAGTAAAAAAAA
1 TTTTAGGATCT-TTAAAAGTTAGTAAAAAAAA
*
195251 TTTT-GGATCCTTAAAAGTTA
1 TTTTAGGATCTTTAAAAGTTA
195271 AAATAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
30 12 0.29
31 29 0.69
32 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (31 bp):
TTTTAGGATCTTTAAAAGTTAGTAAAAAAAA
Found at i:195269 original size:30 final size:31
Alignment explanation
Indices: 195200--195270 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
195190 TTTAGGTTCT
195200 TTAAAAGTTAGAGAAAAAAATTTTAAATCTC
1 TTAAAAGTTAGAGAAAAAAATTTTAAATCTC
* **
195231 TTATAAGTTAGTA-AAAAAAATTTTGGATC-C
1 TTAAAAGTTAG-AGAAAAAAATTTTAAATCTC
195261 TTAAAAGTTA
1 TTAAAAGTTA
195271 AAATAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.29
31 24 0.69
32 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (31 bp):
TTAAAAGTTAGAGAAAAAAATTTTAAATCTC
Found at i:195342 original size:25 final size:26
Alignment explanation
Indices: 195314--195364 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
195304 GTAAATTTTT
* *
195314 TTTTTTTAACTT-TTAAAAGTTAAAA
1 TTTTTTGAACTTCTTAAAAATTAAAA
195339 TTTTTTGAACTTCTTAAAAATTAAAA
1 TTTTTTGAACTTCTTAAAAATTAAAA
195365 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (26 bp):
TTTTTTGAACTTCTTAAAAATTAAAA
Found at i:201648 original size:14 final size:14
Alignment explanation
Indices: 201629--201657 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
201619 AAAAAAATTG
201629 TATAACAGTATATA
1 TATAACAGTATATA
201643 TATAACAGTATATA
1 TATAACAGTATATA
201657 T
1 T
201658 GTAAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (14 bp):
TATAACAGTATATA
Found at i:223958 original size:21 final size:20
Alignment explanation
Indices: 223933--223973 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
223923 AGAGAAGGAT
*
223933 GAAGAAAAAGAAAAAGGAAAG
1 GAAG-AAAAGAAAAAAGAAAG
*
223954 GAAGAAGAGAAAAAAGAAAG
1 GAAGAAAAGAAAAAAGAAAG
223974 AAAACCTGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
GAAGAAAAGAAAAAAGAAAG
Found at i:223976 original size:24 final size:23
Alignment explanation
Indices: 223922--223976 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
223912 GGAGGTGATC
*
223922 AAGAGAAGGATGAAGAAAAAGAAA
1 AAGA-AAGGAAGAAGAAAAAGAAA
223946 AAGGAAAGGAAGAAGAGAAAA-AAGA
1 AA-GAAAGGAAGAAGA-AAAAGAA-A
223971 AAGAAA
1 AAGAAA
223977 ACCTGGCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (23 bp):
AAGAAAGGAAGAAGAAAAAGAAA
Found at i:235802 original size:39 final size:39
Alignment explanation
Indices: 235759--235838 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
235749 AAATAATAAA
235759 TTATTAAATAATTTTAATTTCCAATTTCATCATCTCTTC
1 TTATTAAATAATTTTAATTTCCAATTTCATCATCTCTTC
*
235798 TTATTAAATAATTTTAATTTTCAATTTCATCATCTCTTC
1 TTATTAAATAATTTTAATTTCCAATTTCATCATCTCTTC
235837 TT
1 TT
235839 TTCTCTTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (39 bp):
TTATTAAATAATTTTAATTTCCAATTTCATCATCTCTTC
Found at i:236875 original size:12 final size:12
Alignment explanation
Indices: 236858--236908 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 12
236848 AATTTTTTAT
236858 TTTAAAAAATAA
1 TTTAAAAAATAA
236870 TTTAAAAAATTTTATA
1 TTTAAAAAA---TA-A
236886 TTTAAAAAAATAA
1 TTT-AAAAAATAA
236899 TTTAAAAAAT
1 TTTAAAAAAT
236909 TTATATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 16 0.47
13 4 0.12
14 2 0.06
15 2 0.06
16 4 0.12
17 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TTTAAAAAATAA
Found at i:236880 original size:29 final size:29
Alignment explanation
Indices: 236804--236940 Score: 161
Period size: 29 Copynumber: 4.7 Consensus size: 29
236794 ATTGGAAATT
*
236804 AAAATTATTT-AATAATTTTATTATTTCAAA
1 AAAATAATTTAAATAATTTTA-TATTT-AAA
* * *
236834 AAAATAATTTTAATAATTTTTTATTTTAA
1 AAAATAATTTAAATAATTTTATATTTAAA
*
236863 AAAATAATTTAAAAAATTTTATATTTAAA
1 AAAATAATTTAAATAATTTTATATTTAAA
* *
236892 AAAATAATTTAAA-AAATTTATATTTTAA
1 AAAATAATTTAAATAATTTTATATTTAAA
* *
236920 ACAATAATTTTAATAATTTTA
1 AAAATAATTTAAATAATTTTA
236941 AAATTATTTG
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
28 24 0.26
29 46 0.49
30 14 0.15
31 9 0.10
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (29 bp):
AAAATAATTTAAATAATTTTATATTTAAA
Found at i:236916 original size:57 final size:59
Alignment explanation
Indices: 236804--236940 Score: 181
Period size: 57 Copynumber: 2.3 Consensus size: 59
236794 ATTGGAAATT
* * * *
236804 AAAATTATTTAATAATTTTATTATTTCAAAAAAATAATTTTAATAATTTTTTATTTTAA
1 AAAATAATTTAATAATTTTATTATTTCAAAAAAATAATTTTAAAAAATTTATATTTTAA
*
236863 AAAATAATTTAAAAAATTTTA-TATTT-AAAAAAATAA-TTTAAAAAATTTATATTTTAA
1 AAAATAATTT-AATAATTTTATTATTTCAAAAAAATAATTTTAAAAAATTTATATTTTAA
*
236920 ACAATAATTTTAATAATTTTA
1 AAAATAA-TTTAATAATTTTA
236941 AAATTATTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
57 33 0.48
58 13 0.19
59 14 0.20
60 9 0.13
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (59 bp):
AAAATAATTTAATAATTTTATTATTTCAAAAAAATAATTTTAAAAAATTTATATTTTAA
Found at i:240122 original size:33 final size:33
Alignment explanation
Indices: 240080--240142 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
240070 TTGTCCATTG
240080 ATAGTACTAGAAAGAACATATGTTTTTTCCCTA
1 ATAGTACTAGAAAGAACATATGTTTTTTCCCTA
240113 ATAGTACTAGAAAGAACATATGTTTTTTCC
1 ATAGTACTAGAAAGAACATATGTTTTTTCC
240143 TACTTATTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (33 bp):
ATAGTACTAGAAAGAACATATGTTTTTTCCCTA
Done.