Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014826.1 Kokia drynarioides strain JFW-HI SEQ_129868, 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: 591985
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 238 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:302462 original size:12 final size:12
Alignment explanation
Indices: 302434--302477 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
302424 ACACATTACA
302434 TTTCTTTCCTTC
1 TTTCTTTCCTTC
*
302446 -TTCTTTCTTTC
1 TTTCTTTCCTTC
*
302457 CTTCTTTCCTTC
1 TTTCTTTCCTTC
302469 TTTCTTTCC
1 TTTCTTTCC
302478 CGTTTATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTCTTTCCTTC
Found at i:303270 original size:30 final size:33
Alignment explanation
Indices: 303214--303273 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
303204 GTGTTGTATG
*
303214 AAATTGAAGAAAGAGGGAAGAAGGAGAAAGACC
1 AAATTGAAGAAAGAAGGAAGAAGGAGAAAGACC
303247 AAATTGAAGAAA-AAGG-A-AAGGAGAAAG
1 AAATTGAAGAAAGAAGGAAGAAGGAGAAAG
303274 CTAAGGTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.38
31 1 0.04
32 3 0.12
33 12 0.46
ACGTcount: A:0.58, C:0.03, G:0.32, T:0.07
Consensus pattern (33 bp):
AAATTGAAGAAAGAAGGAAGAAGGAGAAAGACC
Found at i:304377 original size:6 final size:6
Alignment explanation
Indices: 304366--304404 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
304356 TGATCAAAAT
* * *
304366 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
304405 TAAGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:305772 original size:16 final size:17
Alignment explanation
Indices: 305743--305777 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
305733 TTATTTTTTT
305743 AATATATAAAAATAATA
1 AATATATAAAAATAATA
*
305760 AATA-ATAATAATAATA
1 AATATATAAAAATAATA
305776 AA
1 AA
305778 ATTCGTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATATAAAAATAATA
Found at i:308484 original size:16 final size:16
Alignment explanation
Indices: 308463--308497 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
308453 AGGGAATCTA
308463 TATATATATATATGCT
1 TATATATATATATGCT
308479 TATATATATATATGCT
1 TATATATATATATGCT
308495 TAT
1 TAT
308498 CTTACACGAG
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:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (16 bp):
TATATATATATATGCT
Found at i:314774 original size:19 final size:18
Alignment explanation
Indices: 314747--314786 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
314737 AAAATTTAGG
*
314747 AAAATATATATAATATAGA
1 AAAACATATATAATATA-A
*
314766 AAAACATATATATTATAA
1 AAAACATATATAATATAA
314784 AAA
1 AAA
314787 TTATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (18 bp):
AAAACATATATAATATAA
Found at i:314899 original size:25 final size:24
Alignment explanation
Indices: 314871--314960 Score: 55
Period size: 25 Copynumber: 3.8 Consensus size: 24
314861 AATGTAAAAG
314871 AATTATTAAAATTATAAAAATTTAT
1 AATT-TTAAAATTATAAAAATTTAT
*
314896 AATTTAAAAAATTA-AAAATATTT-T
1 AATTT-TAAAATTATAAAA-ATTTAT
* * *
314920 --TTAATAAAATT-TTAAAATATAT
1 AATT-TTAAAATTATAAAAATTTAT
* *
314942 AATTCTAAAATTTTAAAAA
1 AATTTTAAAATTATAAAAA
314961 GGTATTTCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
21 3 0.06
22 12 0.24
23 7 0.14
24 13 0.26
25 15 0.30
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTTTAAAATTATAAAAATTTAT
Found at i:314903 original size:23 final size:23
Alignment explanation
Indices: 314876--314960 Score: 61
Period size: 24 Copynumber: 3.7 Consensus size: 23
314866 AAAAGAATTA
314876 TTAAAATTATAAAAATTTATAAT
1 TTAAAATTATAAAAATTTATAAT
*
314899 TTAAAAAATTA-AAAATATTTTTTAA-
1 TT--AAAATTATAAAA-A-TTTATAAT
* *
314924 -TAAAATT-TTAAAATATATAAT
1 TTAAAATTATAAAAATTTATAAT
*
314945 TCTAAAATTTTAAAAA
1 T-TAAAATTATAAAAA
314961 GGTATTTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
20 5 0.10
21 1 0.02
22 9 0.19
23 9 0.19
24 10 0.21
25 8 0.17
26 6 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAAAATTATAAAAATTTATAAT
Found at i:315054 original size:19 final size:21
Alignment explanation
Indices: 315011--315063 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
315001 TTAAATACCT
315011 TTTTAAATTTTTATAACAAT-
1 TTTTAAATTTTTATAACAATA
* *
315031 TTTTTAATTTTTAT-ATAATA
1 TTTTAAATTTTTATAACAATA
* *
315051 TTTTGACTTTTTA
1 TTTTAAATTTTTA
315064 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTAAATTTTTATAACAATA
Found at i:315123 original size:21 final size:22
Alignment explanation
Indices: 315075--315124 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
315065 AATTTAAAAT
315075 TATA-TATTTTATAATTTTGTA
1 TATATTATTTTATAATTTTGTA
* * *
315096 AAAATTATTTT-TAATTTTTTA
1 TATATTATTTTATAATTTTGTA
315117 TATATTAT
1 TATATTAT
315125 ATATATTACA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATATTATTTTATAATTTTGTA
Found at i:315531 original size:22 final size:21
Alignment explanation
Indices: 315481--315531 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
315471 GAAAAAAATG
* * *
315481 TTTAAAAATATTTTTATAACA
1 TTTAAAAACATTATTATAAAA
315502 TTCT-AAAACATATATTATAAAA
1 TT-TAAAAACAT-TATTATAAAA
315524 TTTAAAAA
1 TTTAAAAA
315532 GTAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTAAAAACATTATTATAAAA
Found at i:316214 original size:18 final size:19
Alignment explanation
Indices: 316174--316234 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
316164 AAATGTTTTT
* *
316174 TTTTTCTATATTTTATATAA
1 TTTTTCAATTTTTTATAT-A
316194 TTTTT-AATTTTTTATATA
1 TTTTTCAATTTTTTATATA
*
316212 TTTTTCCATTTTTATATATA
1 TTTTTCAATTTTT-TATATA
316232 TTT
1 TTT
316235 AAAATGTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 6 0.17
19 16 0.44
20 14 0.39
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTCAATTTTTTATATA
Found at i:319282 original size:20 final size:20
Alignment explanation
Indices: 319245--319282 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
319235 TTCGTATACC
*
319245 TTAATTAGTTTTAGTTTAAT
1 TTAATTAATTTTAGTTTAAT
319265 TTAATTAATCTTTA-TTTA
1 TTAATTAAT-TTTAGTTTA
319283 TTAGTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (20 bp):
TTAATTAATTTTAGTTTAAT
Found at i:324519 original size:29 final size:29
Alignment explanation
Indices: 324456--324521 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
324446 TTTTAGTCTT
* *
324456 AATTA-TAAAAATTATAAAATATATTTAA
1 AATTATTAAAAATTATAAAATAAATATAA
* *
324484 AAATATTAAAAATTTATAAAGTAAATAT-A
1 AATTATTAAAAA-TTATAAAATAAATATAA
324513 AATTATTAA
1 AATTATTAA
324522 TTTTTTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.13
29 15 0.48
30 12 0.39
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
AATTATTAAAAATTATAAAATAAATATAA
Found at i:330177 original size:3 final size:3
Alignment explanation
Indices: 330171--330203 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
330161 TGCCATGTGT
330171 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
330204 CTTAAATGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:331744 original size:44 final size:45
Alignment explanation
Indices: 331681--331772 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
331671 CTCCCAACTT
331681 ACTCAAAATTATTTAGTTC-ACTATAAATAACTTGTTATACATTA
1 ACTCAAAATTATTTAGTTCAACTATAAATAACTTGTTATACATTA
331725 ACTCAAAATTATTTAGTTCAACTATAAATAACTTGTTATACATTA
1 ACTCAAAATTATTTAGTTCAACTATAAATAACTTGTTATACATTA
331770 ACT
1 ACT
331773 GACGGTCCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 19 0.40
45 28 0.60
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.40
Consensus pattern (45 bp):
ACTCAAAATTATTTAGTTCAACTATAAATAACTTGTTATACATTA
Found at i:331772 original size:25 final size:25
Alignment explanation
Indices: 331700--331772 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
331690 TATTTAGTTC
331700 ACTATAAATAACTTGTTATACATTA
1 ACTATAAATAACTTGTTATACATTA
* * *
331725 AC--TCAA-AA-TTATT-TA-GTTCA
1 ACTATAAATAACTTGTTATACATT-A
331745 ACTATAAATAACTTGTTATACATTA
1 ACTATAAATAACTTGTTATACATTA
331770 ACT
1 ACT
331773 GACGGTCCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 4 0.11
22 5 0.14
23 5 0.14
24 4 0.11
25 8 0.23
26 2 0.06
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (25 bp):
ACTATAAATAACTTGTTATACATTA
Found at i:339581 original size:17 final size:18
Alignment explanation
Indices: 339548--339589 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
339538 ATTTACCAAT
339548 TTAATTATTTCATTTTAA
1 TTAATTATTTCATTTTAA
*
339566 TTAATTATTT-ATTTTAC
1 TTAATTATTTCATTTTAA
339583 TTAATTA
1 TTAATTA
339590 GAGTCATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATTATTTCATTTTAA
Found at i:341118 original size:21 final size:21
Alignment explanation
Indices: 341094--341133 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
341084 TGAAAACTAC
*
341094 ATGGTTTTGTCTTTTAACTCA
1 ATGGTTTTGACTTTTAACTCA
341115 ATGGTTTTGACTTTTAACT
1 ATGGTTTTGACTTTTAACT
341134 TTAAAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.53
Consensus pattern (21 bp):
ATGGTTTTGACTTTTAACTCA
Found at i:345448 original size:20 final size:20
Alignment explanation
Indices: 345423--345463 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
345413 GTGCCTAGCT
*
345423 TTACACTGTGTTAGCCCAGG
1 TTACACTATGTTAGCCCAGG
345443 TTACACTATGTTAGCCCAGG
1 TTACACTATGTTAGCCCAGG
345463 T
1 T
345464 AATAATGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (20 bp):
TTACACTATGTTAGCCCAGG
Found at i:353288 original size:22 final size:21
Alignment explanation
Indices: 353241--353288 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
353231 TCATATTACA
353241 TTTTAATTATTTTAAATAATT
1 TTTTAATTATTTTAAATAATT
* *
353262 ATTTATATTATGTTTTAAT-ATT
1 TTTTA-ATTAT-TTTAAATAATT
353284 TTTTA
1 TTTTA
353289 GAAAACAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.18
22 12 0.55
23 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTAATTATTTTAAATAATT
Found at i:353324 original size:18 final size:18
Alignment explanation
Indices: 353301--353347 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
353291 AAACAAATTG
353301 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
353319 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
353337 TTAA-TAAAAAA
1 TTAATTAAAAAA
353348 CAATAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:357236 original size:23 final size:22
Alignment explanation
Indices: 357194--357239 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
357184 ATTTGAATTT
*
357194 TTTTTAAATTTATTAAAAAATA
1 TTTTTAAATTTACTAAAAAATA
357216 TTTTTATAATTT-CTAAGAAAATA
1 TTTTTA-AATTTACTAA-AAAATA
357239 T
1 T
357240 ATATTTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTTAAATTTACTAAAAAATA
Found at i:379875 original size:31 final size:31
Alignment explanation
Indices: 379837--379895 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
379827 TTAATATAAT
* *
379837 ATTTGGTATCTGAACTTGACACTTTTTTCTG
1 ATTTGGTACCTAAACTTGACACTTTTTTCTG
*
379868 ATTTGGTACCTAAATTTGACACTTTTTT
1 ATTTGGTACCTAAACTTGACACTTTTTT
379896 TAAGTAGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.14, T:0.49
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTTCTG
Found at i:379906 original size:30 final size:31
Alignment explanation
Indices: 379852--379911 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
379842 GTATCTGAAC
* * *
379852 TTGACACTTTTTTCTGATTTGGTACCTAAAT
1 TTGACACTTTTTTCTAAGTAGGTACCTAAAT
*
379883 TTGACACTTTTTT-TAAGTAGGTACTTAAA
1 TTGACACTTTTTTCTAAGTAGGTACCTAAA
379912 CATTTTGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (31 bp):
TTGACACTTTTTTCTAAGTAGGTACCTAAAT
Found at i:380267 original size:30 final size:31
Alignment explanation
Indices: 380215--380280 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
380205 GTTTAGGTAT
380215 CAAATTAAGAAAAAGTGTCAAGTTCAAGTAC
1 CAAATTAAGAAAAAGTGTCAAGTTCAAGTAC
*
380246 CAAATTAAGTAAAAG-GTCAAGTTCAAGTAC
1 CAAATTAAGAAAAAGTGTCAAGTTCAAGTAC
380276 CAAAT
1 CAAAT
380281 ATTATATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 20 0.59
31 14 0.41
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (31 bp):
CAAATTAAGAAAAAGTGTCAAGTTCAAGTAC
Found at i:390120 original size:17 final size:17
Alignment explanation
Indices: 390068--390120 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
390058 TTTAGTAATC
*
390068 TTTATTTATTTTATGAT
1 TTTATTAATTTTATGAT
*
390085 TTT-TTAATTTGTAT-TT
1 TTTATTAATTT-TATGAT
390101 TTTATTAATTTTATGAT
1 TTTATTAATTTTATGAT
390118 TTT
1 TTT
390121 TAATAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 13 0.43
17 17 0.57
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTATTAATTTTATGAT
Found at i:390135 original size:33 final size:33
Alignment explanation
Indices: 390068--390144 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
390058 TTTAGTAATC
* **
390068 TTTATTTATTTTATGATTTTTTAATTTGTATTT
1 TTTATTAATTTTATGATTTTTTAAAATGTATTT
390101 TTTATTAATTTTATGATTTTTAATAAAAT-T-TTT
1 TTTATTAATTTTATGATTTTT--TAAAATGTATTT
390134 TTTA-TAATTTT
1 TTTATTAATTTT
390145 TAATAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.18
33 27 0.69
34 1 0.03
35 4 0.10
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (33 bp):
TTTATTAATTTTATGATTTTTTAAAATGTATTT
Found at i:393263 original size:2 final size:2
Alignment explanation
Indices: 393252--393284 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
393242 AGAAATTGTT
393252 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
393285 CAAAATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:397553 original size:17 final size:17
Alignment explanation
Indices: 397531--397566 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
397521 GAAACTTTTG
**
397531 TTTTTAAATCTTTTAAA
1 TTTTTAAAAATTTTAAA
397548 TTTTTAAAAATTTTAAA
1 TTTTTAAAAATTTTAAA
397565 TT
1 TT
397567 AGTAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTAAAAATTTTAAA
Found at i:400710 original size:22 final size:23
Alignment explanation
Indices: 400679--400721 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
400669 TATGTATTTT
* *
400679 AAATATTTTATTATATTTTTATA
1 AAATATTTTATCAAATTTTTATA
400702 AAATA-TTTATCAAATTTTTA
1 AAATATTTTATCAAATTTTTA
400722 ATGCTGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATATTTTATCAAATTTTTATA
Found at i:406008 original size:3 final size:3
Alignment explanation
Indices: 406000--406031 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
405990 ATTCCTCGAA
*
406000 TGG TGG TGG TGG TGG TGG TGC TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
406032 AGCAAGTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.62, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:411772 original size:3 final size:3
Alignment explanation
Indices: 411764--411804 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
411754 GCGAGATGAC
* * *
411764 GTT GTT GTT GTT GTT GTT GTT GTC GTC GTC GTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GT
411805 CGTGGAGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.07, G:0.34, T:0.59
Consensus pattern (3 bp):
GTT
Found at i:415420 original size:20 final size:20
Alignment explanation
Indices: 415397--415517 Score: 134
Period size: 20 Copynumber: 6.0 Consensus size: 20
415387 CCTGAATCAT
415397 CGGCACAAAGCCTGATACAC
1 CGGCACAAAGCCTGATACAC
* * * *
415417 CGGCATAAAACCTGTTTCAC
1 CGGCACAAAGCCTGATACAC
415437 CGGCACAAAGCCTGATACAC
1 CGGCACAAAGCCTGATACAC
* * * *
415457 CGACATAAAACCTGATTCAC
1 CGGCACAAAGCCTGATACAC
415477 CGGCACAAAGCCTGATACAC
1 CGGCACAAAGCCTGATACAC
* * * *
415497 CGACATAAAGTCTGATTCAC
1 CGGCACAAAGCCTGATACAC
415517 C
1 C
415518 CGTAGTTTTC
Statistics
Matches: 81, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.35, C:0.32, G:0.17, T:0.17
Consensus pattern (20 bp):
CGGCACAAAGCCTGATACAC
Found at i:415452 original size:40 final size:40
Alignment explanation
Indices: 415387--415517 Score: 208
Period size: 40 Copynumber: 3.3 Consensus size: 40
415377 TATATTAGTT
* * *
415387 CCTGAATCATCGGCACAAAGCCTGATACACCGGCATAAAA
1 CCTGATTCACCGGCACAAAGCCTGATACACCGACATAAAA
*
415427 CCTGTTTCACCGGCACAAAGCCTGATACACCGACATAAAA
1 CCTGATTCACCGGCACAAAGCCTGATACACCGACATAAAA
*
415467 CCTGATTCACCGGCACAAAGCCTGATACACCGACATAAAG
1 CCTGATTCACCGGCACAAAGCCTGATACACCGACATAAAA
*
415507 TCTGATTCACC
1 CCTGATTCACC
415518 CGTAGTTTTC
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (40 bp):
CCTGATTCACCGGCACAAAGCCTGATACACCGACATAAAA
Found at i:418571 original size:17 final size:17
Alignment explanation
Indices: 418549--418586 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
418539 ATATTTTATT
*
418549 ATTAATAATTTTTGTTA
1 ATTAATAATTTCTGTTA
*
418566 ATTAATTATTTCTGTTA
1 ATTAATAATTTCTGTTA
418583 ATTA
1 ATTA
418587 CTTGATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (17 bp):
ATTAATAATTTCTGTTA
Found at i:427407 original size:38 final size:38
Alignment explanation
Indices: 427364--427436 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
427354 AAATTCATTG
427364 TAACATTTTACCAATAAAAATATTCAATATAAATATTT
1 TAACATTTTACCAATAAAAATATTCAATATAAATATTT
*
427402 TAACATTTTACCATTAAAAATATTCAATATAAATA
1 TAACATTTTACCAATAAAAATATTCAATATAAATA
427437 GAAGAAGCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (38 bp):
TAACATTTTACCAATAAAAATATTCAATATAAATATTT
Found at i:441819 original size:47 final size:46
Alignment explanation
Indices: 441752--441843 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 46
441742 ATCTTCATCT
*
441752 TCTTTGTCTGAACCATCTTACTCCACTTCCATAACCAGCAATTCAA
1 TCTTTGTCTGAACCATCTTACTCCACTTCCATAACCAACAATTCAA
* *
441798 TCTTTGTGTGAAACCATCTTACTCCACTTTCATAACCAACAATTCA
1 TCTTTGTCTG-AACCATCTTACTCCACTTCCATAACCAACAATTCA
441844 GTTCTTTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 9 0.21
47 33 0.79
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.34
Consensus pattern (46 bp):
TCTTTGTCTGAACCATCTTACTCCACTTCCATAACCAACAATTCAA
Found at i:442232 original size:41 final size:42
Alignment explanation
Indices: 442187--442273 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
442177 ACTTCGAAAT
* * *
442187 AAAA-TAGTT-GTGGGATTAAAAATTGAAAGAAAAATAAAAGA
1 AAAATTAGTTGGT-GGATTAAAAATTGAAAAAAAAAAAAAAAA
* *
442228 AAAATTAGTTGGTGGATTGAAATTTGAAAAAAAAAAAAAAAA
1 AAAATTAGTTGGTGGATTAAAAATTGAAAAAAAAAAAAAAAA
442270 AAAA
1 AAAA
442274 ANNNNNNNNN
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 4 0.10
42 33 0.85
43 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (42 bp):
AAAATTAGTTGGTGGATTAAAAATTGAAAAAAAAAAAAAAAA
Found at i:442783 original size:55 final size:55
Alignment explanation
Indices: 442717--442820 Score: 190
Period size: 55 Copynumber: 1.9 Consensus size: 55
442707 TAAGAATTAT
*
442717 ATATTTAACGTTAATGAACCTTGTAAGATATAATATATTTGAGCTTAAAATATAG
1 ATATCTAACGTTAATGAACCTTGTAAGATATAATATATTTGAGCTTAAAATATAG
*
442772 ATATCTAACGTTAATGAACCTTGTAAGATATGATATATTTGAGCTTAAA
1 ATATCTAACGTTAATGAACCTTGTAAGATATAATATATTTGAGCTTAAA
442821 GGCGACATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (55 bp):
ATATCTAACGTTAATGAACCTTGTAAGATATAATATATTTGAGCTTAAAATATAG
Found at i:459260 original size:129 final size:129
Alignment explanation
Indices: 459030--459287 Score: 426
Period size: 129 Copynumber: 2.0 Consensus size: 129
459020 GTTAGAAATG
* * *
459030 ATCATGGTAGAGGCAGAATTCCTTGAAGGAAAGAAGAAATTATAGTAAGAGAACGAGCTAGTTTG
1 ATCATGGTAGAGGCAGAACTCCTTGAAGGAAAGAAGAAATCATAGTAAGAGAACGAGCTAGTTGG
* *
459095 TAGCTTGGAACTAAATGGCCTGCGTCTCTCACTGTCACCAATGTCAGCCTCTCATATTCCTCCA
66 TAGCTTGGAACGAAATGGCCTGCGTCTCTCACTGTCACCAATGTCAGCCCCTCATATTCCTCCA
* * * *
459159 ATCATGGTGGAGGCAGAACTCCTTGAAGGAAAGAGGAAATCATGGTAAGAGAACGAGCTGGTTGG
1 ATCATGGTAGAGGCAGAACTCCTTGAAGGAAAGAAGAAATCATAGTAAGAGAACGAGCTAGTTGG
*
459224 TAGCTTGGAACGAAATGGCCTGCGTTTCTCACTGTCACCAATGTCAGCCCCTCATATTCCTCCA
66 TAGCTTGGAACGAAATGGCCTGCGTCTCTCACTGTCACCAATGTCAGCCCCTCATATTCCTCCA
459288 CATATCCTCC
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 119 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (129 bp):
ATCATGGTAGAGGCAGAACTCCTTGAAGGAAAGAAGAAATCATAGTAAGAGAACGAGCTAGTTGG
TAGCTTGGAACGAAATGGCCTGCGTCTCTCACTGTCACCAATGTCAGCCCCTCATATTCCTCCA
Found at i:462998 original size:17 final size:17
Alignment explanation
Indices: 462978--463062 Score: 118
Period size: 17 Copynumber: 5.0 Consensus size: 17
462968 TTTTAGATTG
462978 TTTTAAACTTT-AATTTA
1 TTTTAAA-TTTAAATTTA
*
462995 TTTTAACTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
463012 TTTTAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
* *
463029 CTTTGAATTTAAATTTA
1 TTTTAAATTTAAATTTA
463046 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
463063 ATTAAAAGTG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
16 3 0.05
17 56 0.95
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:463011 original size:6 final size:6
Alignment explanation
Indices: 462979--463063 Score: 63
Period size: 6 Copynumber: 14.8 Consensus size: 6
462969 TTTAGATTGT
* * *
462979 TTTAAA CTTT-AA TTT-AT TTTAAC TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
463025 CTT-AC TTTGAA TTTAAA TTT-AT TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
463064 TTAAAAGTGT
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
5 18 0.29
6 41 0.66
7 3 0.05
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:463016 original size:11 final size:11
Alignment explanation
Indices: 462979--463063 Score: 66
Period size: 11 Copynumber: 7.5 Consensus size: 11
462969 TTTAGATTGT
462979 TTTAAACTTTAA
1 TTTAAA-TTTAA
*
462991 TTT-ATTTTAA
1 TTTAAATTTAA
*
463001 CTTTAAATTTAT
1 -TTTAAATTTAA
463013 TTTAAATTTAAA
1 TTTAAATTT-AA
* *
463025 CTT-ACTTTGAA
1 TTTAAATTT-AA
*
463036 TTTAAATTTAT
1 TTTAAATTTAA
463047 TTTAAATTTAAA
1 TTTAAATTT-AA
463059 TTTAA
1 TTTAA
463064 TTAAAAGTGT
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
10 5 0.09
11 31 0.54
12 21 0.37
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:463710 original size:17 final size:18
Alignment explanation
Indices: 463676--463712 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
463666 CCTTATTGTT
463676 ATTTATTAATATATAATA
1 ATTTATTAATATATAATA
*
463694 ATTTTTTAATA-ATAATA
1 ATTTATTAATATATAATA
463711 AT
1 AT
463713 AATAATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTATTAATATATAATA
Found at i:463713 original size:20 final size:21
Alignment explanation
Indices: 463677--463715 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
463667 CTTATTGTTA
*
463677 TTTATTAATATATAATAATTT
1 TTTAATAATATATAATAATTT
463698 TTTAATAATA-ATAATAAT
1 TTTAATAATATATAATAAT
463716 AATAACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATAATATATAATAATTT
Found at i:463743 original size:13 final size:13
Alignment explanation
Indices: 463699--463783 Score: 79
Period size: 13 Copynumber: 6.8 Consensus size: 13
463689 TAATAATTTT
463699 TTAATAAT-AATA
1 TTAATAATAAATA
* *
463711 ATAATAAT-AACA
1 TTAATAATAAATA
463723 TTAATAATAAATA
1 TTAATAATAAATA
* *
463736 TTAGTAATAAAAA
1 TTAATAATAAATA
** *
463749 GCATTAATAAATA
1 TTAATAATAAATA
463762 TTAA-AA-AAATA
1 TTAATAATAAATA
463773 TTAATAATAAA
1 TTAATAATAAA
463784 GTAATAAATA
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
11 9 0.16
12 21 0.37
13 27 0.47
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (13 bp):
TTAATAATAAATA
Found at i:465847 original size:6 final size:6
Alignment explanation
Indices: 465836--465874 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
465826 TGATCAAAAT
* * *
465836 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
465875 TATGAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:474400 original size:18 final size:18
Alignment explanation
Indices: 474373--474416 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
474363 CAGATGTGAA
474373 GGAAAAGAAGAAAGAGAT
1 GGAAAAGAAGAAAGAGAT
* **
474391 GGAAAGGAAGCGAGAGAT
1 GGAAAAGAAGAAAGAGAT
474409 GAGAAAAG
1 G-GAAAAG
474417 CACGACTGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.39, T:0.05
Consensus pattern (18 bp):
GGAAAAGAAGAAAGAGAT
Found at i:479110 original size:49 final size:49
Alignment explanation
Indices: 479057--479510 Score: 383
Period size: 49 Copynumber: 9.3 Consensus size: 49
479047 GTACCACGAA
* * * *
479057 ACATGGAGGGAAAGGTTTAAGTCGCAATGGAGAACCTTA-TACCTCAGAG
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAACC-TAGTACCTCAGAG
* *
479106 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCC-AGTACCACAAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAA-CCTAGTACCTCAGAG
* * * * * * * *
479155 AAACGAGGGGAAAGGTTTAAGTCGCAACGGCGAACCTAGTACCTTAAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAACCTAGTACCTCAGAG
* *
479204 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAA-CCTAGTACCTCAG-AG
** * * *
479253 ACACAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTAGTACCTCAGAG
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAACCTAGTACCTCAGAG
* * *
479302 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTTCCAC-GAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAA-CCTAGTACCTCAG-AG
** * * *
479351 ACACAAAGGGAAA-AGTTTAAGTCGCAATGACGAACCTAGTACCTCAGAC
1 ACATGAAGGGAAAGA-TTTAAGCCGCAATGGCGAACCTAGTACCTCAGAG
* *
479400 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCGC-GA-
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAA-CCTAGTACCTCAGAG
* * ** *
479447 AAATACGAATGGAAAGATTTAAGTTGTAATGGCGAACCTTA-TACCTCAG-G
1 ACAT--GAAGGGAAAGATTTAAGCCGCAATGGCGAACC-TAGTACCTCAGAG
*
479497 AGCATGAAAGGAAA
1 A-CATGAAGGGAAA
479511 TTTAAGTAAC
Statistics
Matches: 324, Mismatches: 60, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
47 3 0.01
48 13 0.04
49 292 0.90
50 14 0.04
51 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.16
Consensus pattern (49 bp):
ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAACCTAGTACCTCAGAG
Found at i:479198 original size:98 final size:98
Alignment explanation
Indices: 479063--479510 Score: 625
Period size: 98 Copynumber: 4.6 Consensus size: 98
479053 CGAAACATGG
*
479063 AGGGAAAGGTTTAAGTCGCAATGGAGAACCTTA-TACCTCAGAGACATGAAGGGAAAGATTTAAG
1 AGGGAAAGGTTTAAGTCGCAATGGCGAACC-TAGTACCTCAGAGACATGAAGGGAAAGATTTAAG
* * *
479127 CCGCAATGGCGAATCCAGTACCACAAAGAAACGA
65 CCGCAACGGCGAATCCAGTACCACAAAGACACAA
* * * *
479161 GGGGAAAGGTTTAAGTCGCAACGGCGAACCTAGTACCTTAAAGACATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATTTAAGC
*
479226 CGCAACGGCGAATCCAGTACCACGAAGACACAA
66 CGCAACGGCGAATCCAGTACCACAAAGACACAA
*
479259 AGGGAAAGGTTTAAGTCGCAATGACGAACCTAGTACCTCAGAGACATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATTTAAGC
* *
479324 CGCAACGGCGAATCCAGTTCCACGAAGACACAA
66 CGCAACGGCGAATCCAGTACCACAAAGACACAA
* * *
479357 AGGGAAAAGTTTAAGTCGCAATGACGAACCTAGTACCTCAGACACATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATTTAAGC
* * *
479422 CGCAACGGCGAATCCAGTACCGCGAAA-ATACGA
66 CGCAACGGCGAATCCAGTACCAC-AAAGACACAA
* * * * *
479455 ATGGAAAGATTTAAGTTGTAATGGCGAACCTTA-TACCTCAG-GAGCATGAAAGGAAA
1 AGGGAAAGGTTTAAGTCGCAATGGCGAACC-TAGTACCTCAGAGA-CATGAAGGGAAA
479511 TTTAAGTAAC
Statistics
Matches: 316, Mismatches: 30, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
97 3 0.01
98 309 0.98
99 4 0.01
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (98 bp):
AGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATTTAAGC
CGCAACGGCGAATCCAGTACCACAAAGACACAA
Found at i:479982 original size:17 final size:17
Alignment explanation
Indices: 479961--480063 Score: 118
Period size: 17 Copynumber: 6.0 Consensus size: 17
479951 TTTTAGATTG
479961 TTTTAAACTTT-AATTTA
1 TTTTAAA-TTTAAATTTA
* *
479978 ATTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
479995 TTTTAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
* * *
480012 CTTTGAACTTAAATTTA
1 TTTTAAATTTAAATTTA
480029 TTTTAAAATTTAAATTTA
1 TTTT-AAATTTAAATTTA
*
480047 TTTTAAATTAAAATTTA
1 TTTTAAATTTAAATTTA
480064 ATTAAAAGTG
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
16 3 0.04
17 53 0.75
18 15 0.21
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:479988 original size:23 final size:23
Alignment explanation
Indices: 479962--480066 Score: 65
Period size: 23 Copynumber: 4.6 Consensus size: 23
479952 TTTAGATTGT
479962 TTTAAACTTTAATTT-AATTTAAG
1 TTTAAA-TTTAATTTAAATTTAAG
* *
479985 TTTAAATTTATTTTAAATTTAAA
1 TTTAAATTTAATTTAAATTTAAG
* * * *
480008 CTT-ACTTTGAACTTAAATTT-AT
1 TTTAAATTT-AATTTAAATTTAAG
* *
480030 TTTAAAATTTAAATTT-ATTTTAAA
1 TTT-AAATTT-AATTTAAATTTAAG
*
480054 TTAAAATTTAATT
1 TTTAAATTTAATT
480067 AAAAGTGTCC
Statistics
Matches: 63, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
22 18 0.29
23 34 0.54
24 11 0.17
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTAAATTTAATTTAAATTTAAG
Found at i:480709 original size:3 final size:3
Alignment explanation
Indices: 480703--480741 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
480693 AATAAATTTT
480703 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
480742 ACATTAGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:480713 original size:17 final size:19
Alignment explanation
Indices: 480679--480714 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
480669 CCTTATTGTT
480679 ATTTATTAATATATAATAA
1 ATTTATTAATATATAATAA
480698 ATTT-TTAATA-ATAATAA
1 ATTTATTAATATATAATAA
480715 TAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTATTAATATATAATAA
Found at i:480783 original size:12 final size:13
Alignment explanation
Indices: 480704--480800 Score: 92
Period size: 12 Copynumber: 7.6 Consensus size: 13
480694 ATAAATTTTT
480704 AATAATAATAAT-
1 AATAATAATAATA
480716 AATAATAATAAT-
1 AATAATAATAATA
480728 AATAATAATAATA
1 AATAATAATAATA
* * *
480741 AACATTAGTAATA
1 AATAATAATAATA
** *
480754 AATAGCATTAATA
1 AATAATAATAATA
*
480767 AATATTAATAA-A
1 AATAATAATAATA
*
480779 AATATTAATAATA
1 AATAATAATAATA
480792 AAGTAATAA
1 AA-TAATAA
480801 ATAAAGAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
12 36 0.51
13 30 0.42
14 5 0.07
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:481943 original size:29 final size:30
Alignment explanation
Indices: 481877--482130 Score: 156
Period size: 29 Copynumber: 8.7 Consensus size: 30
481867 CATTATTGAT
**
481877 TTTTCC-AAAATTCCA-TTTTTACCCCAAA
1 TTTTCCAAAAATTCCATTTTTTACCCTTAA
*
481905 CTTTCC-AAAATTCCATTTTTTA-CCTTAA
1 TTTTCCAAAAATTCCATTTTTTACCCTTAA
* * *
481933 TTTTCCAAAAATTAC-TATTTTACCCTCGAA
1 TTTTCCAAAAATTCCATTTTTTACCCT-TAA
* * *
481963 -CTTCCAAAAATTTCATTTTTGA-CCTTAA
1 TTTTCCAAAAATTCCATTTTTTACCCTTAA
*
481991 TTTTTTCAAAAATTACCA--TTTTACCCTTAA
1 -TTTTCCAAAAATT-CCATTTTTTACCCTTAA
** * * *
482021 ACTTCCAAAAATTCCA-TTTTGA-CCTCGAT
1 TTTTCCAAAAATTCCATTTTTTACCCT-TAA
* * *
482050 TTTTCTAAAAAATACCA--TTTTACCCTCAA
1 TTTTC-CAAAAATTCCATTTTTTACCCTTAA
** *
482079 GCTTCCAAAAAATTCCATTTTTTACCCTTAT
1 TTTTCC-AAAAATTCCATTTTTTACCCTTAA
*
482110 TTTTCCAAAAAATACCATTTT
1 TTTTCC-AAAAATTCCATTTT
482131 ACCCTCGAGC
Statistics
Matches: 172, Mismatches: 38, Indels: 29
0.72 0.16 0.12
Matches are distributed among these distances:
28 37 0.22
29 70 0.41
30 35 0.20
31 30 0.17
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (30 bp):
TTTTCCAAAAATTCCATTTTTTACCCTTAA
Found at i:481981 original size:58 final size:58
Alignment explanation
Indices: 481875--482221 Score: 395
Period size: 58 Copynumber: 6.0 Consensus size: 58
481865 TACATTATTG
* *
481875 ATTTTTCC-AAAATT-CCATTTTTACCC-CAAACTTTCC-AAAATTCCATTTTTTACCTT
1 ATTTTTCCAAAAATTACCA-TTTTACCCTCGAAC-TTCCAAAAATTCCATTTTTGACCTT
* * *
481931 AATTTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATTTCATTTTTGACCTT
1 ATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTT
* ** *
481989 AATTTTTTCAAAAATTACCATTTTACCCTTAAACTTCCAAAAATTCCA-TTTTGACCTCG
1 -ATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCT-T
* * *
482048 ATTTTTCTAAAAAATACCATTTTACCCTC-AAGCTTCCAAAAAATTCCATTTTTTACCCTT
1 ATTTTTCCAAAAATTACCATTTTACCCTCGAA-CTTCC-AAAAATTCCATTTTTGA-CCTT
* * * *
482108 ATTTTTCCAAAAAATACCATTTTACCCTCGAGCTTCTAAAAATTCCATTTTTGACCTCG
1 ATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCT-T
* *
482167 ATTTTTTC-AAAATTACCATTTTACCCTCGAA-TGTCTAAAAATTCCATTTTTGACC
1 ATTTTTCCAAAAATTACCATTTTACCCTCGAACT-TCCAAAAATTCCATTTTTGACC
482222 CTAAACTTTC
Statistics
Matches: 252, Mismatches: 26, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
56 7 0.03
57 21 0.08
58 109 0.43
59 74 0.29
60 37 0.15
61 4 0.02
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (58 bp):
ATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTT
Found at i:482207 original size:29 final size:28
Alignment explanation
Indices: 481883--482216 Score: 139
Period size: 29 Copynumber: 11.5 Consensus size: 28
481873 TGATTTTTCC
* *
481883 AAAATTCCATTTTTACCC-CAAACTTTC-C
1 AAAATTCCA-TTTTACCCTCGAA-TTTCTA
* *
481911 AAAATTCCATTTTTTA-CCT-TAATTTTCCA
1 AAAATTCCA--TTTTACCCTCGAA-TTTCTA
* * *
481940 AAAATTACTATTTTACCCTCGAACTTCCA
1 AAAATT-CCATTTTACCCTCGAATTTCTA
* * *
481969 AAAATTTCATTTTTGA-CCT-TAATTTTTTCA
1 AAAATTCCA-TTTT-ACCCTCGAA-TTTCT-A
** * *
481999 AAAATTACCATTTTACCCTTAAACTTCCA
1 AAAATT-CCATTTTACCCTCGAATTTCTA
*
482028 AAAATTCCATTTTGA-CCTCGATTTTTCTAA
1 AAAATTCCATTTT-ACCCTCGA-ATTTCT-A
* * *
482058 AAAATACCATTTTACCCTC-AAGCTTCCAA
1 AAAATTCCATTTTACCCTCGAA--TTTCTA
* * *
482087 AAAATTCCATTTTTTACCCT-TATTTTTCCAA
1 AAAATTCCA--TTTTACCCTCGA-ATTT-CTA
* **
482118 AAAATACCATTTTACCCTCGAGCTTCTA
1 AAAATTCCATTTTACCCTCGAATTTCTA
* * *
482146 AAAATTCCATTTTTGA-CCTCGATTTTTTC
1 AAAATTCCA-TTTT-ACCCTCGAATTTCTA
*
482175 AAAATTACCATTTTACCCTCGAATGTCTA
1 AAAATT-CCATTTTACCCTCGAATTTCTA
482204 AAAATTCCATTTT
1 AAAATTCCATTTT
482217 TGACCCTAAA
Statistics
Matches: 234, Mismatches: 43, Indels: 58
0.70 0.13 0.17
Matches are distributed among these distances:
28 54 0.23
29 107 0.46
30 48 0.21
31 25 0.11
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.40
Consensus pattern (28 bp):
AAAATTCCATTTTACCCTCGAATTTCTA
Found at i:482292 original size:28 final size:29
Alignment explanation
Indices: 482235--482304 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
482225 AACTTTCTCG
*
482235 AAATTACCATTTTGCCCCCCGAGTGACCA
1 AAATTATCATTTTGCCCCCCGAGTGACCA
482264 AAATTATCATTTTG-CCCCCGAGT-ATCCA
1 AAATTATCATTTTGCCCCCCGAGTGA-CCA
* *
482292 AAAATCTCATTTT
1 AAATTATCATTTT
482305 CAACTCCGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.03
28 23 0.62
29 13 0.35
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.31
Consensus pattern (29 bp):
AAATTATCATTTTGCCCCCCGAGTGACCA
Found at i:489895 original size:21 final size:18
Alignment explanation
Indices: 489860--489903 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
489850 TTTTTTAAAT
489860 AATTATTAAAAATAAAAA
1 AATTATTAAAAATAAAAA
* *
489878 AATTATTTAAAATTATAAA
1 AATTA-TTAAAAATAAAAA
489897 AA-TATTA
1 AATTATTA
489904 GAATTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 7 0.30
19 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTATTAAAAATAAAAA
Found at i:489898 original size:27 final size:28
Alignment explanation
Indices: 489860--489917 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
489850 TTTTTTAAAT
489860 AATTATTAAAAATAAAAAAATTATTTAA
1 AATTATTAAAAATAAAAAAATTATTTAA
** *
489888 AATTA-TAAAAATATTAGAATTATTTAA
1 AATTATTAAAAATAAAAAAATTATTTAA
489915 AAT
1 AAT
489918 AAAGTCTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
AATTATTAAAAATAAAAAAATTATTTAA
Found at i:490250 original size:19 final size:18
Alignment explanation
Indices: 490208--490276 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 18
490198 TTTTTATAAA
*
490208 TTTTAAAATTA-AAAAAGT
1 TTTTAAAATTATTAAAA-T
* *
490226 TGTTTATAATTATTAATATT
1 T-TTTAAAATTATTAA-AAT
490246 TTTTAAAAATT-TTAAAAT
1 TTTT-AAAATTATTAAAAT
490264 TTTTAAAATTATT
1 TTTTAAAATTATT
490277 TAATCATTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 6 0.15
18 9 0.22
19 16 0.39
20 9 0.22
21 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
TTTTAAAATTATTAAAAT
Found at i:490272 original size:9 final size:9
Alignment explanation
Indices: 490245--490279 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
490235 TTATTAATAT
490245 TTTTTAAAA
1 TTTTTAAAA
*
490254 ATTTTAAAA
1 TTTTTAAAA
490263 TTTTTAAAA
1 TTTTTAAAA
490272 TTATTTAA
1 TT-TTTAA
490280 TCATTGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:490326 original size:10 final size:10
Alignment explanation
Indices: 490311--490369 Score: 59
Period size: 10 Copynumber: 5.9 Consensus size: 10
490301 TTAGATGTTG
*
490311 TTTTTAATCA
1 TTTTTAATAA
490321 TTTTT-ATAA
1 TTTTTAATAA
490330 TTTATT-ATAA
1 TTT-TTAATAA
*
490340 TTCTTAATAA
1 TTTTTAATAA
*
490350 TTTTAAATACA
1 TTTTTAATA-A
490361 TTTTTAATA
1 TTTTTAATA
490370 TTTATTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.20
10 24 0.59
11 9 0.22
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:490587 original size:15 final size:15
Alignment explanation
Indices: 490567--490612 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
490557 TTAAGTTACA
490567 TTTTAATCACTTATG
1 TTTTAATCACTTATG
*
490582 TTTTAA--ATGTTATG
1 TTTTAATCA-CTTATG
*
490596 TTTTAGTCACTTATG
1 TTTTAATCACTTATG
490611 TT
1 TT
490613 AATATTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.40
15 13 0.52
16 1 0.04
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.57
Consensus pattern (15 bp):
TTTTAATCACTTATG
Found at i:497413 original size:11 final size:11
Alignment explanation
Indices: 497397--497422 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
497387 TTCAAGTACC
497397 ATTATAGAAAT
1 ATTATAGAAAT
497408 ATTATAGAAAT
1 ATTATAGAAAT
497419 ATTA
1 ATTA
497423 AAAATTATAT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
ATTATAGAAAT
Found at i:500355 original size:28 final size:33
Alignment explanation
Indices: 500298--500367 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 33
500288 GCTATTATAT
*
500298 TACTATTATTTTGTTGTTATTGTTTGAATTTTG-
1 TACTATT-TCTTGTTGTTATTGTTTGAATTTTGC
500331 TA-TATTTCTTGTT-TTATTG-TT-AATTTTGC
1 TACTATTTCTTGTTGTTATTGTTTGAATTTTGC
500360 TACTATTT
1 TACTATTT
500368 TTAAGACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 7 0.21
29 4 0.12
30 11 0.32
31 6 0.18
32 4 0.12
33 2 0.06
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (33 bp):
TACTATTTCTTGTTGTTATTGTTTGAATTTTGC
Found at i:506447 original size:33 final size:33
Alignment explanation
Indices: 506405--506470 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
506395 GTTGAACAAG
506405 AACAAGTATAAATGTTTTGTAATTATGACTTCT
1 AACAAGTATAAATGTTTTGTAATTATGACTTCT
506438 AACAAGTATAAATGTTTTGTAATTATGACTTCT
1 AACAAGTATAAATGTTTTGTAATTATGACTTCT
506471 GATCATACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (33 bp):
AACAAGTATAAATGTTTTGTAATTATGACTTCT
Found at i:509409 original size:21 final size:21
Alignment explanation
Indices: 509383--509422 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
509373 AAACGATATA
* *
509383 GTTTTGCCTTTTAATTTAATG
1 GTTTTGACTTTTAACTTAATG
509404 GTTTTGACTTTTAACTTAA
1 GTTTTGACTTTTAACTTAA
509423 AAAAGGTAAA
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:0.23, C:0.10, G:0.12, T:0.55
Consensus pattern (21 bp):
GTTTTGACTTTTAACTTAATG
Found at i:516127 original size:47 final size:47
Alignment explanation
Indices: 516063--516186 Score: 134
Period size: 41 Copynumber: 2.8 Consensus size: 47
516053 TTATTCCAAC
* * * *
516063 TGGTGATAAGGTGTTGTTGTAAAATGTCAAGGGGAGCTTACTCGACG
1 TGGTGATAAGTTTTTGTTCTAAAATGTCAAGGGGAGCCTACTCGACG
* *
516110 TGTTGATAAGTTTTTGTTCTAAAA--T----GGGAGCCTACTTGACG
1 TGGTGATAAGTTTTTGTTCTAAAATGTCAAGGGGAGCCTACTCGACG
* *
516151 TGGTGATAATTTTTTGTTCTAAAATGCCAAGGGGAG
1 TGGTGATAAGTTTTTGTTCTAAAATGTCAAGGGGAG
516187 TGTTAATGCT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
41 36 0.58
45 1 0.02
47 25 0.40
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (47 bp):
TGGTGATAAGTTTTTGTTCTAAAATGTCAAGGGGAGCCTACTCGACG
Found at i:516842 original size:30 final size:27
Alignment explanation
Indices: 516784--516847 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 27
516774 AATATATTTG
**
516784 AAATTTAATCTCTATTTTTACTTTTAA
1 AAATTTAATCTCTATTTTTAAATTTAA
516811 AAATTTAATTCTTCTATTTTTCAAATTTAA
1 AAATTTAA-TC-TCTATTTTT-AAATTTAA
516841 AAATTTA
1 AAATTTA
516848 CTTTCAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 8 0.25
28 2 0.06
29 9 0.28
30 13 0.41
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (27 bp):
AAATTTAATCTCTATTTTTAAATTTAA
Found at i:517600 original size:24 final size:24
Alignment explanation
Indices: 517560--517608 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
517550 TGAGGGAGGT
517560 AATAAAATATGCATATTAAATTAA
1 AATAAAATATGCATATTAAATTAA
*
517584 AATATAAATA-GCGTATTAAATTAA
1 AATA-AAATATGCATATTAAATTAA
517608 A
1 A
517609 GCTTTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (24 bp):
AATAAAATATGCATATTAAATTAA
Found at i:523028 original size:59 final size:58
Alignment explanation
Indices: 522926--523128 Score: 180
Period size: 59 Copynumber: 3.5 Consensus size: 58
522916 AGTTCGGGGT
* * * *
522926 TAAAAATAGAATTTTT--ACA-CCCGAGGGTAAAATGATAACTTTTAAAAAAATCGGGA
1 TAAAAATGGAATTTTTGGACATCCAG-GGGTAAAACGATAATTTTTAAAAAAATCGGGA
* ** *
522982 TCAAAAACGGAATTTTTGGACATCCAGGGGTAAAACGATAATTTTTAGGAAAATCAGGA
1 T-AAAAATGGAATTTTTGGACATCCAGGGGTAAAACGATAATTTTTAAAAAAATCGGGA
* * * * *** *
523041 TAAAAAATGGAATTTTTGGACATTC-GGGGATAAAAGGGTAATTTTTGAAAGTTTCGGGG
1 T-AAAAATGGAATTTTTGGACATCCAGGGG-TAAAACGATAATTTTTAAAAAAATCGGGA
*
523100 TTAAAATGGAATTTTTGGACATCCGAGGG
1 TAAAAATGGAATTTTTGGACATCC-AGGG
523129 CAAAATGATA
Statistics
Matches: 117, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
56 1 0.01
57 13 0.11
58 25 0.21
59 72 0.62
60 6 0.05
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (58 bp):
TAAAAATGGAATTTTTGGACATCCAGGGGTAAAACGATAATTTTTAAAAAAATCGGGA
Found at i:523072 original size:30 final size:29
Alignment explanation
Indices: 522978--523121 Score: 86
Period size: 30 Copynumber: 4.9 Consensus size: 29
522968 TAAAAAAATC
* *
522978 GGGATCAAAAACGGAATTTTTGGACATCCAG
1 GGGAT-AAAAATGGAATTTTTGGACATTC-G
* *
523009 GGG-TAAAACGAT--AATTTTTAGGAAAATC-
1 GGGATAAAA--ATGGAATTTTT-GGACATTCG
*
523037 AGGATAAAAAATGGAATTTTTGGACATTCG
1 GGGAT-AAAAATGGAATTTTTGGACATTCG
* *
523067 GGGAT-AAAAGGGTAATTTTT-GAAAGTTTCG
1 GGGATAAAAATGG-AATTTTTGGACA--TTCG
*
523097 GGG-TTAAAATGGAATTTTTGGACAT
1 GGGATAAAAATGGAATTTTTGGACAT
523122 CCGAGGGCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 29
0.68 0.09 0.22
Matches are distributed among these distances:
28 14 0.16
29 33 0.38
30 37 0.42
31 4 0.05
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.30
Consensus pattern (29 bp):
GGGATAAAAATGGAATTTTTGGACATTCG
Found at i:523144 original size:58 final size:58
Alignment explanation
Indices: 522985--523163 Score: 152
Period size: 58 Copynumber: 3.1 Consensus size: 58
522975 ATCGGGATCA
* * * * *
522985 AAAACGGAATTTTTGGACATCCAGGGG-TAAAACGATAATTTTTAGGAAA--ATC-AGGATAA
1 AAAATGGAATTTTTGGACATCC-GGGGACAAAAGGATAATTTTT--GAAAGTTTCGAGG-T-C
* * * * *
523044 AAAATGGAATTTTTGGACATTCGGGGATAAAAGGGTAATTTTTGAAAGTTTCGGGGTT
1 AAAATGGAATTTTTGGACATCCGGGGACAAAAGGATAATTTTTGAAAGTTTCGAGGTC
* * *
523102 AAAATGGAATTTTTGGACATCCGAGGG-CAAAATGATATTTTTTGGAAGTTTCGAGGTC
1 AAAATGGAATTTTTGGACATCCG-GGGACAAAAGGATAATTTTTGAAAGTTTCGAGGTC
523160 AAAA
1 AAAA
523164 ATCGATCGAG
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
57 4 0.04
58 54 0.54
59 40 0.40
60 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.30
Consensus pattern (58 bp):
AAAATGGAATTTTTGGACATCCGGGGACAAAAGGATAATTTTTGAAAGTTTCGAGGTC
Found at i:523199 original size:47 final size:46
Alignment explanation
Indices: 523123--523214 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 46
523113 TTTGGACATC
*
523123 CGAGGGCAAAATGATATTTTTTGGAAGTTTCGAGGTCAAAAATCGAT
1 CGAGGGCAAAATGATATTTTTTAGAAGTTTCGAGGTC-AAAATCGAT
* *
523170 CGAGGGTAAAATGGTAATTTTTTAG-AGTTTCGAGGTCAAAATCGA
1 CGAGGGCAAAATGAT-ATTTTTTAGAAGTTTCGAGGTCAAAATCGA
523215 GACTTTTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
46 8 0.20
47 25 0.61
48 8 0.20
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (46 bp):
CGAGGGCAAAATGATATTTTTTAGAAGTTTCGAGGTCAAAATCGAT
Found at i:523211 original size:30 final size:28
Alignment explanation
Indices: 523169--523323 Score: 98
Period size: 30 Copynumber: 5.2 Consensus size: 28
523159 CAAAAATCGA
* *
523169 TCGAGGGTAAAATGGTAATTTTTTAGAGTT
1 TCGA-GGTAAAAT-GTAATTTTTGAAAGTT
*
523199 TCGAGGTCAAAATCG-AGACTTTTGAAAGTT
1 TCGAGGT-AAAAT-GTA-ATTTTTGAAAGTT
* *
523229 TGGAGGTAAAAATGTAATTTTTGGAAGTT
1 TCGAGGT-AAAATGTAATTTTTGAAAGTT
* * * *
523258 TTGGGGTTAAAAATGGAATTTTTGGAAG-T
1 TCGAGG-T-AAAATGTAATTTTTGAAAGTT
* *
523287 TCGGGGGTAAAAATGTAATTTTTGGAAGTT
1 TC-GAGGT-AAAATGTAATTTTTGAAAGTT
*
523317 TCAAGGT
1 TCGAGGT
523324 GTTTGGGGTC
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
29 45 0.43
30 59 0.57
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.36
Consensus pattern (28 bp):
TCGAGGTAAAATGTAATTTTTGAAAGTT
Found at i:523246 original size:59 final size:60
Alignment explanation
Indices: 523177--523323 Score: 149
Period size: 59 Copynumber: 2.5 Consensus size: 60
523167 GATCGAGGGT
* *
523177 AAAATGGTAATTTTTTAG-AGTTTCGAGG-TCAAAATCGAGACTTTTGAAAGTTTGGAGGTA
1 AAAAT-GTAATTTTTTAGAAGTTTCGAGGTTAAAAATCGA-ACTTTTGAAAGTTCGGAGGTA
* * * * * * *
523237 AAAATGTAA-TTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGTAATTTTTTAGAAGTTTCGAGGTTAAAAATCGAACTTTTGAAAGTTCGGAGGTA
* *
523296 AAAATGTAA-TTTTTGGAAGTTTCAAGGT
1 AAAATGTAATTTTTTAGAAGTTTCGAGGT
523324 GTTTGGGGTC
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 6 0.08
59 54 0.74
60 13 0.18
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.37
Consensus pattern (60 bp):
AAAATGTAATTTTTTAGAAGTTTCGAGGTTAAAAATCGAACTTTTGAAAGTTCGGAGGTA
Found at i:523251 original size:29 final size:29
Alignment explanation
Indices: 523218--523317 Score: 139
Period size: 29 Copynumber: 3.4 Consensus size: 29
523208 AAATCGAGAC
*
523218 TTTTGAAAGTTTGGAGGTAAAAATGTAAT
1 TTTTGGAAGTTTGGAGGTAAAAATGTAAT
*
523247 TTTTGGAAGTTTTGG-GGTTAAAAATGGAAT
1 TTTTGGAAG-TTTGGAGG-TAAAAATGTAAT
* *
523277 TTTTGGAAGTTCGGGGGTAAAAATGTAAT
1 TTTTGGAAGTTTGGAGGTAAAAATGTAAT
523306 TTTTGGAAGTTT
1 TTTTGGAAGTTT
523318 CAAGGTGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
29 36 0.57
30 27 0.43
ACGTcount: A:0.31, C:0.01, G:0.28, T:0.40
Consensus pattern (29 bp):
TTTTGGAAGTTTGGAGGTAAAAATGTAAT
Found at i:525270 original size:17 final size:17
Alignment explanation
Indices: 525242--525304 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
525232 ATTTTAAAGT
* *
525242 TTTAAGTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
*
525258 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
*
525276 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
525293 TTTAAATTTAAA
1 TTTAAATTTAAA
525305 TTTAGAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
16 3 0.08
17 33 0.82
18 4 0.10
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:525322 original size:6 final size:6
Alignment explanation
Indices: 525257--525308 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
525247 GTTTAAAATT
* **
525257 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-ACAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
525304 ATTTA
1 ATTTA
525309 GAAATAAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
5 7 0.19
6 26 0.70
7 4 0.11
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:531250 original size:22 final size:23
Alignment explanation
Indices: 531225--531288 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
531215 TTATAAACAA
531225 TATATTATACTATTAAAT-ATAT
1 TATATTATACTATTAAATAATAT
* * *
531247 TATAATATATTACTAAATAATAT
1 TATATTATACTATTAAATAATAT
*
531270 TTTAATTATAAC-ATTAAAT
1 TAT-ATTAT-ACTATTAAAT
531289 TTTTTACATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
22 15 0.47
23 6 0.19
24 10 0.31
25 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
TATATTATACTATTAAATAATAT
Found at i:532454 original size:20 final size:21
Alignment explanation
Indices: 532414--532459 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
532404 TATTCATTTA
* *
532414 TTTATAAATATTTTGTATGTT
1 TTTATAAATATCTTATATGTT
532435 TTTATAAA-ATCTTATATGTT
1 TTTATAAATATCTTATATGTT
532455 TTTAT
1 TTTAT
532460 TGAAAAGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (21 bp):
TTTATAAATATCTTATATGTT
Found at i:532579 original size:25 final size:25
Alignment explanation
Indices: 532542--532592 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
532532 AACTTGATTT
*
532542 AATTTGTAAAATT-GAAAGTTAATTG
1 AATTTGTAAAATTAGAAA-TAAATTG
* *
532567 AATTTTTAGAATTAGAAATAAATTG
1 AATTTGTAAAATTAGAAATAAATTG
532592 A
1 A
532593 TAGAATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (25 bp):
AATTTGTAAAATTAGAAATAAATTG
Found at i:533158 original size:18 final size:19
Alignment explanation
Indices: 533123--533158 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
533113 CTTTAGATCA
*
533123 TCCATCGTAATCAAATTTG
1 TCCACCGTAATCAAATTTG
533142 TCCACCGTAAT-AAATTT
1 TCCACCGTAATCAAATTT
533159 TTTATTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.36
Consensus pattern (19 bp):
TCCACCGTAATCAAATTTG
Found at i:533279 original size:20 final size:20
Alignment explanation
Indices: 533254--533293 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
533244 TCTTGTCATC
*
533254 ATATATTTTGAAAT-TAAAAA
1 ATATATATT-AAATGTAAAAA
533274 ATATATATTAAATGTAAAAA
1 ATATATATTAAATGTAAAAA
533294 TGTGATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
ATATATATTAAATGTAAAAA
Found at i:533486 original size:17 final size:17
Alignment explanation
Indices: 533426--533486 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
533416 TCAGCATGAT
*
533426 TAAACAATTCAATAATA
1 TAAATAATTCAATAATA
* *
533443 TAAATAGTACAA-AATA
1 TAAATAATTCAATAATA
533459 TAAAATTTAATTCAATAATA
1 T-AAA--TAATTCAATAATA
533479 TAAATAAT
1 TAAATAAT
533487 AGACACATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 5 0.14
17 16 0.46
19 9 0.26
20 5 0.14
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:533850 original size:17 final size:17
Alignment explanation
Indices: 533818--533853 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
533808 ACCCCTAGAT
533818 TTAAGCTTTTAAAAGTA
1 TTAAGCTTTTAAAAGTA
533835 TTAAG-TTTTAATAAGTA
1 TTAAGCTTTTAA-AAGTA
533852 TT
1 TT
533854 TAGATCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (17 bp):
TTAAGCTTTTAAAAGTA
Found at i:541251 original size:31 final size:33
Alignment explanation
Indices: 541200--541264 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 33
541190 AAATGATTAT
541200 TTTAATATAATAATTAAT-AAA-ATTTAAATAA
1 TTTAATATAATAATTAATAAAATATTTAAATAA
541231 TTTAATATAA-AGA-TACATAAAATATTTAAATAA
1 TTTAATATAATA-ATTA-ATAAAATATTTAAATAA
541264 T
1 T
541265 AAATGTTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
30 3 0.10
31 13 0.43
32 3 0.10
33 11 0.37
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (33 bp):
TTTAATATAATAATTAATAAAATATTTAAATAA
Found at i:544906 original size:21 final size:21
Alignment explanation
Indices: 544881--544925 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
544871 CAAACAGTCC
*
544881 AAACAG-ATAAAAAAATACCAA
1 AAACAGCA-AAAAAAACACCAA
*
544902 AAACAGCAAAAAATACACCAA
1 AAACAGCAAAAAAAACACCAA
544923 AAA
1 AAA
544926 ATGTAAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.71, C:0.18, G:0.04, T:0.07
Consensus pattern (21 bp):
AAACAGCAAAAAAAACACCAA
Found at i:545562 original size:26 final size:26
Alignment explanation
Indices: 545533--545586 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
545523 TCAAATAAGG
545533 TAATTGCTTCATAAATTCTTCTTGTT
1 TAATTGCTTCATAAATTCTTCTTGTT
545559 TAATTGCTTCATAAATTCTTCTTGTT
1 TAATTGCTTCATAAATTCTTCTTGTT
545585 TA
1 TA
545587 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (26 bp):
TAATTGCTTCATAAATTCTTCTTGTT
Found at i:548832 original size:6 final size:6
Alignment explanation
Indices: 548821--548850 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
548811 AAAAATGAGT
548821 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
548851 AAAAGCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:556062 original size:9 final size:9
Alignment explanation
Indices: 556048--556075 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
556038 TGGTATTTCA
556048 CATTTTAAT
1 CATTTTAAT
556057 CATTTTAAT
1 CATTTTAAT
556066 CATTTTAAT
1 CATTTTAAT
556075 C
1 C
556076 CCCCCACTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (9 bp):
CATTTTAAT
Found at i:559509 original size:24 final size:24
Alignment explanation
Indices: 559482--559534 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
559472 TCACTAAATG
559482 ATTAAAAATA-TAAAAAATCAATAA
1 ATTAAAAATAGTAAAAAATC-ATAA
*
559506 ATT-AAAATAGTTAAAAATCATAA
1 ATTAAAAATAGTAAAAAATCATAA
559529 A-TAAAA
1 ATTAAAA
559535 TTTTATGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.04
23 14 0.54
24 11 0.42
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (24 bp):
ATTAAAAATAGTAAAAAATCATAA
Found at i:559736 original size:15 final size:15
Alignment explanation
Indices: 559716--559744 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
559706 AATATTAAAA
559716 AGTGATAAATTTTGT
1 AGTGATAAATTTTGT
559731 AGTGATAAATTTTG
1 AGTGATAAATTTTG
559745 AAATAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
AGTGATAAATTTTGT
Found at i:559793 original size:22 final size:22
Alignment explanation
Indices: 559768--559818 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
559758 ATATTTTTAT
559768 AAATTTTTTTGAATGAGTTTGA
1 AAATTTTTTTGAATGAGTTTGA
559790 AAATTTTTTTGAATGAGTTTGA
1 AAATTTTTTTGAATGAGTTTGA
559812 AAATTTT
1 AAATTTT
559819 GAAATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
AAATTTTTTTGAATGAGTTTGA
Found at i:560599 original size:17 final size:17
Alignment explanation
Indices: 560567--560600 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
560557 TAGATGAATT
**
560567 GAATTTTAATTTTAATA
1 GAATTTTAATCATAATA
560584 GAATTTTAATCATAATA
1 GAATTTTAATCATAATA
560601 TAGAAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (17 bp):
GAATTTTAATCATAATA
Found at i:566330 original size:33 final size:34
Alignment explanation
Indices: 566293--566360 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
566283 ACAAGTTTTA
566293 TTATTATTTAATAT-AAAATAA-TTTAAATATATT
1 TTATTATTTAATATGAAAATAATTTTAAA-ATATT
* *
566326 TTATTATTTATTATGAATATAATTTTAAAATATT
1 TTATTATTTAATATGAAAATAATTTTAAAATATT
566360 T
1 T
566361 AAATTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 13 0.42
34 12 0.39
35 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (34 bp):
TTATTATTTAATATGAAAATAATTTTAAAATATT
Found at i:566393 original size:31 final size:30
Alignment explanation
Indices: 566310--566410 Score: 80
Period size: 31 Copynumber: 3.2 Consensus size: 30
566300 TTAATATAAA
*
566310 ATAA-TTTAAATATATTTTATTATTTATTATGAAT
1 ATAATTTTAAA-ATA-TTTAAT-TTTATTAT--AT
566344 ATAATTTTAAAATATTTAAATTTTATTATAT
1 ATAATTTTAAAATATTT-AATTTTATTATAT
* * *
566375 ATGATTTTAATATTTTTAATTATTATT-TAT
1 ATAATTTTAAAATATTTAATT-TTATTATAT
*
566405 AAAATT
1 ATAATT
566411 ATAATTATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 11 0.19
31 21 0.36
33 11 0.19
34 9 0.16
35 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
ATAATTTTAAAATATTTAATTTTATTATAT
Found at i:566519 original size:20 final size:20
Alignment explanation
Indices: 566463--566520 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
566453 TATGTCATAT
*
566463 AAGAGTTTAAATCGATTTAA
1 AAGAGTTTGAATCGATTTAA
* *
566483 AAGACTTTGAGTCGATTTAA
1 AAGAGTTTGAATCGATTTAA
*
566503 AAGAGTTTGAATTGATTT
1 AAGAGTTTGAATCGATTT
566521 CGAAGAAACC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (20 bp):
AAGAGTTTGAATCGATTTAA
Found at i:567061 original size:17 final size:18
Alignment explanation
Indices: 567031--567064 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
567021 TTATCATTGT
567031 TATAAAAGAATAATTAAC
1 TATAAAAGAATAATTAAC
567049 TATAAAA-AATAATTAA
1 TATAAAAGAATAATTAA
567065 AATAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
TATAAAAGAATAATTAAC
Found at i:576916 original size:29 final size:29
Alignment explanation
Indices: 576836--576908 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
576826 AAACTTTATT
576836 TTAAAAGTCATCTTTCTTTTTGTCCCAAC
1 TTAAAAGTCATCTTTCTTTTTGTCCCAAC
*
576865 TTAAAAGTCGTCTTTCTTTTTGTCCCAAC
1 TTAAAAGTCATCTTTCTTTTTGTCCCAAC
576894 TTAAAAGTCATCTTT
1 TTAAAAGTCATCTTT
576909 TGACTTGTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (29 bp):
TTAAAAGTCATCTTTCTTTTTGTCCCAAC
Found at i:584426 original size:5 final size:5
Alignment explanation
Indices: 584413--584465 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
584403 CAATCCAATG
* *
584413 GAAAA -AAAA GAAAA GAAAA GAAAA GAAGAG GAGAA -AAAA G-AAA G-AAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAA-AA GAAAA GAAAA GAAAA GAAAA
584460 GAAAA G
1 GAAAA G
584466 GAATTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 15 0.38
5 22 0.55
6 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:586426 original size:25 final size:25
Alignment explanation
Indices: 586392--586442 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
586382 TGTTGTTTTT
586392 TGGTAGAGTGCTGAACTCTTAGTTC
1 TGGTAGAGTGCTGAACTCTTAGTTC
586417 TGGTAGAGTGCTGAACTCTTAGTTC
1 TGGTAGAGTGCTGAACTCTTAGTTC
586442 T
1 T
586443 AGCGAGTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (25 bp):
TGGTAGAGTGCTGAACTCTTAGTTC
Done.