Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014289.1 Kokia drynarioides strain JFW-HI SEQ_129323, 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: 627727
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:261106 original size:18 final size:17
Alignment explanation
Indices: 261074--261107 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
261064 AAAAGTTGTG
261074 AGAAAAGAGAATGAAAA
1 AGAAAAGAGAATGAAAA
*
261091 AGAAAGAGAGACTGAAA
1 AGAAA-AGAGAATGAAA
261108 GAAATTGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.03, G:0.26, T:0.06
Consensus pattern (17 bp):
AGAAAAGAGAATGAAAA
Found at i:261170 original size:21 final size:21
Alignment explanation
Indices: 261146--261187 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
261136 AAAAGAGTGC
*
261146 AAGAGAGAAGAAGAAGAAAGT
1 AAGAGAGAAAAAGAAGAAAGT
**
261167 AAGATTGAAAAAGAAGAAAGT
1 AAGAGAGAAAAAGAAGAAAGT
261188 GATCAAGCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.29, T:0.10
Consensus pattern (21 bp):
AAGAGAGAAAAAGAAGAAAGT
Found at i:273490 original size:17 final size:17
Alignment explanation
Indices: 273468--273508 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
273458 TAATAAAAAT
*
273468 ATAATTTTATTATTTTA
1 ATAATTTTAATATTTTA
*
273485 ATAA-TTTAATATTTTT
1 ATAATTTTAATATTTTA
273501 ATAATTTT
1 ATAATTTT
273509 TAAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATAATTTTAATATTTTA
Found at i:274501 original size:24 final size:23
Alignment explanation
Indices: 274473--274532 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
274463 AAAATTATTT
274473 ATTTTTCAAACAAGTTTTAAATTC
1 ATTTTT-AAACAAGTTTTAAATTC
* * *
274497 ATTTTTTAAAAAATTTTTATATTC
1 A-TTTTTAAACAAGTTTTAAATTC
*
274521 ATCTTTAAACAA
1 ATTTTTAAACAA
274533 AGGTTTGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 9 0.30
24 16 0.53
25 5 0.17
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTTTAAACAAGTTTTAAATTC
Found at i:274799 original size:3 final size:3
Alignment explanation
Indices: 274791--274819 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
274781 TCCTATTGGC
274791 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
274820 GTTTCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:287431 original size:11 final size:11
Alignment explanation
Indices: 287412--287457 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
287402 CCACGTCAAC
287412 AAATGATTTTA
1 AAATGATTTTA
*
287423 AAATTATTTTA
1 AAATGATTTTA
287434 AAATGA--TTA
1 AAATGATTTTA
*
287443 AAATGATTTTT
1 AAATGATTTTA
287454 AAAT
1 AAAT
287458 CATTATCATC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 9 0.30
11 21 0.70
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (11 bp):
AAATGATTTTA
Found at i:287445 original size:20 final size:20
Alignment explanation
Indices: 287420--287462 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
287410 ACAAATGATT
* *
287420 TTAAAATTATTTTAAAATGA
1 TTAAAATGATTTTAAAATCA
*
287440 TTAAAATGATTTTTAAATCA
1 TTAAAATGATTTTAAAATCA
287460 TTA
1 TTA
287463 TCATCCCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (20 bp):
TTAAAATGATTTTAAAATCA
Found at i:297539 original size:17 final size:18
Alignment explanation
Indices: 297499--297534 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
297489 GAGAACGAAG
297499 AAGAAGAGAAAGAAGAAA
1 AAGAAGAGAAAGAAGAAA
297517 AAGAAGA-AAAGAATGAAA
1 AAGAAGAGAAAGAA-GAAA
297535 TGAAGGAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (18 bp):
AAGAAGAGAAAGAAGAAA
Found at i:297900 original size:6 final size:6
Alignment explanation
Indices: 297889--297914 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
297879 GTGAGCGCCC
297889 AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA
297915 CAAAGGCAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:302150 original size:21 final size:22
Alignment explanation
Indices: 302121--302163 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
302111 GTTGGTCTCG
302121 ATGTCGCGACAA-ACATACCCA
1 ATGTCGCGACAACACATACCCA
*
302142 ATGTTGCGACAACCACATACCC
1 ATGTCGCGACAA-CACATACCC
302164 GAGCAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.35, C:0.35, G:0.14, T:0.16
Consensus pattern (22 bp):
ATGTCGCGACAACACATACCCA
Found at i:303483 original size:22 final size:23
Alignment explanation
Indices: 303439--303483 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
303429 TTGAGACAAT
* *
303439 TTTTATTTTTAAATAATTTTATA
1 TTTTATTCTTAAATAATTATATA
*
303462 TTTTATTCTT-AATACTTATATA
1 TTTTATTCTTAAATAATTATATA
303484 ATTTGTAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTATTCTTAAATAATTATATA
Found at i:303780 original size:29 final size:29
Alignment explanation
Indices: 303725--303785 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
303715 CATAAGAATA
*
303725 TTTGGCATGTAGTTTTTATTTTTTAAAATT
1 TTTGGCATATAGTTTTTATTTTTT-AAATT
303755 TTTGGCATATAGTTTTTA-TTTTTAAATT
1 TTTGGCATATAGTTTTTATTTTTTAAATT
303783 TTT
1 TTT
303786 ATGAGTGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 8 0.27
29 5 0.17
30 17 0.57
ACGTcount: A:0.23, C:0.03, G:0.11, T:0.62
Consensus pattern (29 bp):
TTTGGCATATAGTTTTTATTTTTTAAATT
Found at i:319326 original size:18 final size:17
Alignment explanation
Indices: 319303--319345 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
319293 ATCATTTGAC
319303 AAAGAA-AAAAATGAGAAA
1 AAAGAAGAAAAA-GA-AAA
319321 AAAGAAGAAAAAGAAAA
1 AAAGAAGAAAAAGAAAA
*
319338 AAAAAAGA
1 AAAGAAGA
319346 TTTTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 8 0.35
19 5 0.22
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAGAAGAAAAAGAAAA
Found at i:334149 original size:34 final size:34
Alignment explanation
Indices: 334102--334168 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
334092 GAAAACTCAT
*
334102 AGTTAGCTTGCCTTACTGCACATCAATCAAAGTG
1 AGTTAGCTCGCCTTACTGCACATCAATCAAAGTG
334136 AGTTAGCTCGCCTTACTGCACATCAATCAAAGT
1 AGTTAGCTCGCCTTACTGCACATCAATCAAAGT
334169 CCTTCTAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (34 bp):
AGTTAGCTCGCCTTACTGCACATCAATCAAAGTG
Found at i:340173 original size:39 final size:39
Alignment explanation
Indices: 340127--340201 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
340117 ATCTAAGTTA
*
340127 TCCACAATTAGTAATGAAGTTGAAGTGGAGACTAAGCTG
1 TCCACAATTAGTAACGAAGTTGAAGTGGAGACTAAGCTG
340166 TCCACAATTAGTAACGAAGTTGAAGTGGAGACTAAG
1 TCCACAATTAGTAACGAAGTTGAAGTGGAGACTAAG
340202 GAGAAAGTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.24
Consensus pattern (39 bp):
TCCACAATTAGTAACGAAGTTGAAGTGGAGACTAAGCTG
Found at i:340408 original size:25 final size:25
Alignment explanation
Indices: 340374--340425 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
340364 TCATGGGTAA
340374 ACTTAGTTTTTCGGTTAGCAAATTG
1 ACTTAGTTTTTCGGTTAGCAAATTG
340399 ACTTAGTTTTTCGGTTAGCAAATTG
1 ACTTAGTTTTTCGGTTAGCAAATTG
340424 AC
1 AC
340426 CAGATGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (25 bp):
ACTTAGTTTTTCGGTTAGCAAATTG
Found at i:344196 original size:55 final size:54
Alignment explanation
Indices: 344100--344258 Score: 214
Period size: 55 Copynumber: 2.9 Consensus size: 54
344090 TCAACTTCTT
**
344100 CCATATGATGCCAT-GTCCATTATGA-TAGGTCTTACACTATATGGTCTTCTTTCC
1 CCATATGATGCCATAG-CCACCATGACTA-GTCTTACACTATATGGTCTTCTTTCC
* * *
344154 CCATATGTTGCCATAGCCACCATGACTAAGTCTTATACTATATGGTCTTATTTCC
1 CCATATGATGCCATAGCCACCATGACT-AGTCTTACACTATATGGTCTTCTTTCC
*
344209 CCATATGATGCTATAGCCACCATGACTAGTTCTTACACTATATGGTCTTC
1 CCATATGATGCCATAGCCACCATGACTAG-TCTTACACTATATGGTCTTC
344259 AATAGCCATG
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
54 22 0.24
55 69 0.75
56 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (54 bp):
CCATATGATGCCATAGCCACCATGACTAGTCTTACACTATATGGTCTTCTTTCC
Found at i:345590 original size:29 final size:29
Alignment explanation
Indices: 345554--345678 Score: 151
Period size: 29 Copynumber: 4.3 Consensus size: 29
345544 GCGAAATCAA
* * *
345554 CCACAAAGGCCCACATATAACAAATTTAG
1 CCACAAAGGCTCACATATAACAGATTCAG
* * * *
345583 TCACAAAGGTTCTCATTTAACAGATTCAG
1 CCACAAAGGCTCACATATAACAGATTCAG
* *
345612 CCACAAAGGCTCTCATATAACAGATTCCG
1 CCACAAAGGCTCACATATAACAGATTCAG
* *
345641 CCACAAAGGCTCACATATAATAGATTCAA
1 CCACAAAGGCTCACATATAACAGATTCAG
345670 CCACAAAGG
1 CCACAAAGG
345679 TTCTTTTTTT
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.40, C:0.26, G:0.13, T:0.21
Consensus pattern (29 bp):
CCACAAAGGCTCACATATAACAGATTCAG
Found at i:357328 original size:37 final size:37
Alignment explanation
Indices: 357277--357350 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
357267 ATTGTGGTAA
*
357277 TGTAAAATGAATGTATAGAATTTAGAAACACGCTAGG
1 TGTAAAAAGAATGTATAGAATTTAGAAACACGCTAGG
*
357314 TGTAAAAAGGATGTATAGAATTTAGAAACACGCTAGG
1 TGTAAAAAGAATGTATAGAATTTAGAAACACGCTAGG
357351 CTTTTTAGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.26
Consensus pattern (37 bp):
TGTAAAAAGAATGTATAGAATTTAGAAACACGCTAGG
Found at i:367140 original size:13 final size:13
Alignment explanation
Indices: 367122--367146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
367112 CAATACAACA
367122 TTTATTTTTATTT
1 TTTATTTTTATTT
367135 TTTATTTTTATT
1 TTTATTTTTATT
367147 AATGATTGAG
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:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTATTTTTATTT
Found at i:369661 original size:12 final size:12
Alignment explanation
Indices: 369640--369668 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
369630 GAGATAAATG
369640 TTTT-GGAGTGT
1 TTTTGGGAGTGT
369651 TTTTGGGAGTGT
1 TTTTGGGAGTGT
369663 TTTTGG
1 TTTTGG
369669 ATGCACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (12 bp):
TTTTGGGAGTGT
Found at i:370087 original size:15 final size:16
Alignment explanation
Indices: 370058--370087 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
370048 AACAACACGA
370058 TGAAAAGTGAAATAAT
1 TGAAAAGTGAAATAAT
370074 TGAAAAGT-AAATAA
1 TGAAAAGTGAAATAA
370088 AAAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (16 bp):
TGAAAAGTGAAATAAT
Found at i:378036 original size:21 final size:22
Alignment explanation
Indices: 378010--378051 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
378000 AATCAAAAAG
378010 AAAAGAAAAATGAGT-AGAAAC
1 AAAAGAAAAATGAGTAAGAAAC
**
378031 AAAAGAATCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
378052 ATATGTGAAT
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:396475 original size:23 final size:23
Alignment explanation
Indices: 396441--396512 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
396431 GTGTCATAAG
*
396441 ACAAAAACGTGCCACAAGGCAAA
1 ACAAAAGCGTGCCACAAGGCAAA
* * *
396464 AGAAAAGTGTGCCACAAGGTAAAGA
1 ACAAAAGCGTGCCACAAGG-CAA-A
396489 ACAAAAGCGTGCCACAAAGGCAAA
1 ACAAAAGCGTGCCAC-AAGGCAAA
396513 TAAAAATTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
23 16 0.41
24 3 0.08
25 16 0.41
26 4 0.10
ACGTcount: A:0.50, C:0.21, G:0.22, T:0.07
Consensus pattern (23 bp):
ACAAAAGCGTGCCACAAGGCAAA
Found at i:403571 original size:18 final size:18
Alignment explanation
Indices: 403548--403588 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
403538 CGGAAGGATT
* *
403548 AGCATACTGACTCGTTTG
1 AGCATACTGACTCATTAG
*
403566 AGCATACTGGCTCATTAG
1 AGCATACTGACTCATTAG
403584 AGCAT
1 AGCAT
403589 TATTAGATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (18 bp):
AGCATACTGACTCATTAG
Found at i:404291 original size:21 final size:21
Alignment explanation
Indices: 404267--404316 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
404257 TAGAAGTAAA
* *
404267 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
404288 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
404309 ACTTGTAT
1 ACTTGTAT
404317 TGATAGAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:404323 original size:21 final size:21
Alignment explanation
Indices: 404267--404324 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
404257 TAGAAGTAAA
* * **
404267 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGATAGAACTGTC
*
404288 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGATAGAACTGTC
*
404309 ACTTGTATTGATAGAA
1 ACTTGTATCGATAGAA
404325 GTCTACACTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (21 bp):
ACTTGTATCGATAGAACTGTC
Found at i:410497 original size:19 final size:18
Alignment explanation
Indices: 410453--410497 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
410443 GAAGGATTAA
* *
410453 CATACTGACTCGTTTGAG
1 CATACTGGCTCGTTAGAG
410471 CATACTGGCTCGTTAGAG
1 CATACTGGCTCGTTAGAG
410489 CATTACTGG
1 CA-TACTGG
410498 ATCGCAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (18 bp):
CATACTGGCTCGTTAGAG
Found at i:411732 original size:27 final size:28
Alignment explanation
Indices: 411666--411734 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 28
411656 TAAATCTCAA
* * *
411666 AATTATACATGAACTTTGATTTAATGTGC
1 AATTATACACGAACTTTAATTT-AGGTGC
411695 AACTGTATACACGAACTTTAATTT-GGTGC
1 AA-T-TATACACGAACTTTAATTTAGGTGC
411724 AATTATACACG
1 AATTATACACG
411735 TGAAACTCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 8 0.23
28 1 0.03
29 8 0.23
30 1 0.03
31 17 0.49
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (28 bp):
AATTATACACGAACTTTAATTTAGGTGC
Found at i:411967 original size:29 final size:30
Alignment explanation
Indices: 411934--412002 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
411924 ATCAAAATTA
*
411934 CATGTATAAAATTATACA-AAACCAAAGTT
1 CATGTATAAAATTACACATAAACCAAAGTT
* * *
411963 CATGTATATAATTGCACATTAAACCATAGTT
1 CATGTATAAAATTACACA-TAAACCAAAGTT
411994 CATGTATAA
1 CATGTATAA
412003 TTTTGATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 15 0.45
31 18 0.55
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (30 bp):
CATGTATAAAATTACACATAAACCAAAGTT
Found at i:412188 original size:21 final size:23
Alignment explanation
Indices: 412162--412204 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
412152 TGATTGTTTT
412162 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
412183 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
412205 TTATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:413688 original size:20 final size:20
Alignment explanation
Indices: 413663--413719 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
413653 TACAAAACAA
413663 TCAAAATAATTTTTAAAAAT
1 TCAAAATAATTTTTAAAAAT
*
413683 TGAAAATAATTTTT-AAAAT
1 TCAAAATAATTTTTAAAAAT
*
413702 TCAAAAT-ATTTATAAAAA
1 TCAAAATAATTTTTAAAAA
413720 ATCTTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.15
19 15 0.45
20 13 0.39
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (20 bp):
TCAAAATAATTTTTAAAAAT
Found at i:413700 original size:19 final size:19
Alignment explanation
Indices: 413663--413718 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
413653 TACAAAACAA
413663 TCAAAATAATTTTTAAAAAT
1 TCAAAATAATTTTT-AAAAT
*
413683 TGAAAATAATTTTTAAAAT
1 TCAAAATAATTTTTAAAAT
*
413702 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTTTTAAAA
413719 AATCTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 9 0.27
19 11 0.33
20 13 0.39
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (19 bp):
TCAAAATAATTTTTAAAAT
Found at i:418653 original size:12 final size:13
Alignment explanation
Indices: 418630--418668 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
418620 GCAAACATTT
418630 TTTTCTTCTTTTC
1 TTTTCTTCTTTTC
418643 TTTTC-TCTTTTC
1 TTTTCTTCTTTTC
418655 TTTTTCATTCTTTT
1 -TTTTC-TTCTTTT
418669 TCTCATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.30
13 10 0.43
15 6 0.26
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTCTTTTC
Found at i:419293 original size:19 final size:20
Alignment explanation
Indices: 419266--419309 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
419256 CTAAATTAAC
* *
419266 AAAAGAAATGTAATGACAA-
1 AAAAAAAATGGAATGACAAT
419285 AAAAAAAATGGAATGACAAT
1 AAAAAAAATGGAATGACAAT
419305 AAAAA
1 AAAAA
419310 TGCATACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.68, C:0.05, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAAAAAATGGAATGACAAT
Found at i:430527 original size:16 final size:15
Alignment explanation
Indices: 430497--430537 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
430487 TTTTCAACAT
430497 AAATTAAACTTAATTCA
1 AAATTAAA-TTAATT-A
430514 AAATTAAATTAATTA
1 AAATTAAATTAATTA
430529 AAA-TAAATT
1 AAATTAAATT
430538 TGGGTTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.25
15 4 0.17
16 6 0.25
17 8 0.33
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAAATTAATTA
Found at i:432690 original size:24 final size:24
Alignment explanation
Indices: 432651--433001 Score: 342
Period size: 24 Copynumber: 14.6 Consensus size: 24
432641 GTTGAATTAT
432651 GTAAACGTATATAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGC
* ** * *
432675 GTAAACGTGTGCAAGCTGACAATC
1 GTAAACGTATATAAGCTGACGAGC
* * * *
432699 ATAAACGTGTGTAAGCTGATGAGC
1 GTAAACGTATATAAGCTGACGAGC
432723 GTAAACGTATATAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGC
* * *
432747 GTAAACGTATATAAGCCGACAAGT
1 GTAAACGTATATAAGCTGACGAGC
* * ** *
432771 GTAAACATGTGCAAGCTGACGACC
1 GTAAACGTATATAAGCTGACGAGC
*
432795 GTAAACGTATATAAGCTAACGAGC
1 GTAAACGTATATAAGCTGACGAGC
* * ** *
432819 GTAAACATGTGCAAACTGACGAGC
1 GTAAACGTATATAAGCTGACGAGC
* *
432843 ATAAATGTATATAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGC
** * *
432867 GTAAACGTATGCAAGCTGACAAGT
1 GTAAACGTATATAAGCTGACGAGC
*
432891 GTAAATGTATATAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGC
* *
432915 ATAAATGTATATAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGC
* * * **
432939 ATAAATGTATATAAGCCGACGAAT
1 GTAAACGTATATAAGCTGACGAGC
**
432963 GTAAACGTATGCAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGC
*
432987 GTAAATGTATATAAG
1 GTAAACGTATATAAG
433002 TTGATAAGCA
Statistics
Matches: 258, Mismatches: 69, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 258 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (24 bp):
GTAAACGTATATAAGCTGACGAGC
Found at i:432704 original size:48 final size:48
Alignment explanation
Indices: 432651--433001 Score: 396
Period size: 48 Copynumber: 7.3 Consensus size: 48
432641 GTTGAATTAT
* * *
432651 GTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACAATC
1 GTAAACGTATATAAGCTGACGAGCGTAAACGTATGCAAGCTGACGAGC
* * * * **
432699 ATAAACGTGTGTAAGCTGATGAGCGTAAACGTATATAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGCGTAAACGTATGCAAGCTGACGAGC
* * * * * *
432747 GTAAACGTATATAAGCCGACAAGTGTAAACATGTGCAAGCTGACGACC
1 GTAAACGTATATAAGCTGACGAGCGTAAACGTATGCAAGCTGACGAGC
* * * *
432795 GTAAACGTATATAAGCTAACGAGCGTAAACATGTGCAAACTGACGAGC
1 GTAAACGTATATAAGCTGACGAGCGTAAACGTATGCAAGCTGACGAGC
* * * *
432843 ATAAATGTATATAAGCTGACGAGCGTAAACGTATGCAAGCTGACAAGT
1 GTAAACGTATATAAGCTGACGAGCGTAAACGTATGCAAGCTGACGAGC
* * * **
432891 GTAAATGTATATAAGCTGACGAGCATAAATGTATATAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGCGTAAACGTATGCAAGCTGACGAGC
* * * **
432939 ATAAATGTATATAAGCCGACGAATGTAAACGTATGCAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGCGTAAACGTATGCAAGCTGACGAGC
*
432987 GTAAATGTATATAAG
1 GTAAACGTATATAAG
433002 TTGATAAGCA
Statistics
Matches: 252, Mismatches: 51, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 252 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (48 bp):
GTAAACGTATATAAGCTGACGAGCGTAAACGTATGCAAGCTGACGAGC
Found at i:435139 original size:12 final size:12
Alignment explanation
Indices: 435109--435146 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
435099 TTTTTATTTT
435109 ATAAAT-ATAAA
1 ATAAATAATAAA
435120 A-AAA-AATAAA
1 ATAAATAATAAA
435130 ATAAATAATAAA
1 ATAAATAATAAA
435142 ATAAA
1 ATAAA
435147 CTCATTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.38
11 4 0.17
12 11 0.46
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
ATAAATAATAAA
Found at i:435142 original size:17 final size:16
Alignment explanation
Indices: 435109--435146 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
435099 TTTTTATTTT
435109 ATAAATATAAAAAAAA
1 ATAAATATAAAAAAAA
435125 ATAAA-ATAAATAATAAA
1 ATAAATATAAA-AA-AAA
435142 ATAAA
1 ATAAA
435147 CTCATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
ATAAATATAAAAAAAA
Found at i:448405 original size:4 final size:4
Alignment explanation
Indices: 448396--448441 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
448386 GTGCCCCAAT
* * * *
448396 TTCA TTCA TTTA CTCA CTCA TTCA TTCA TTCA TTCA TTCA CTCA TT
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TT
448442 TGCTCATTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (4 bp):
TTCA
Found at i:459056 original size:20 final size:20
Alignment explanation
Indices: 459026--459079 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
459016 AACCCAATTA
*
459026 TTTTTATTTTTATTTTTATTT
1 TTTTTA-TTTTATTTCTATTT
459047 TTTTTATTTT-TTCTCTATTT
1 TTTTTATTTTATT-TCTATTT
*
459067 TATTTA-TTTATTT
1 TTTTTATTTTATTT
459080 ATTTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 6 0.21
20 17 0.59
21 6 0.21
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTATTTTATTTCTATTT
Found at i:459057 original size:6 final size:6
Alignment explanation
Indices: 459023--459048 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
459013 GGCAACCCAA
459023 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
459049 TTTATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:459057 original size:16 final size:16
Alignment explanation
Indices: 459032--459090 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
459022 ATTATTTTTA
459032 TTTTTA-TTTTTATTT
1 TTTTTATTTTTTATTT
* *
459047 TTTTTATTTTTTCTCT
1 TTTTTATTTTTTATTT
*
459063 ATTTTATTTATTTATTT
1 TTTTTATTT-TTTATTT
459080 ATTTATTATTT
1 -TTT-TTATTT
459091 GTCCAGGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 6 0.18
16 15 0.44
17 5 0.15
18 2 0.06
19 6 0.18
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTATTTTTTATTT
Found at i:459082 original size:12 final size:11
Alignment explanation
Indices: 459028--459090 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 11
459018 CCCAATTATT
459028 TTTATT-TTTA
1 TTTATTATTTA
459038 TTT-TTATTT-
1 TTTATTATTTA
459047 TTT-TTATTT-
1 TTTATTATTTA
*
459056 TTTCTCTATTTTA
1 TTTAT-TA-TTTA
459069 TTTATTTATTTA
1 TTTA-TTATTTA
459081 TTTATTATTT
1 TTTATTATTT
459091 GTCCAGGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
9 14 0.30
10 7 0.15
11 8 0.17
12 11 0.24
13 5 0.11
14 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:460627 original size:23 final size:24
Alignment explanation
Indices: 460601--460651 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
460591 ATTTAAGATA
460601 TTATTTATTATTTA-A-TTTTGTAT
1 TTATTTA-TATTTATATTTTTGTAT
460624 TTATTTATATTTATATTTTTGTAT
1 TTATTTATATTTATATTTTTGTAT
460648 TTAT
1 TTAT
460652 CTTTTAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 6 0.23
23 8 0.31
24 12 0.46
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (24 bp):
TTATTTATATTTATATTTTTGTAT
Found at i:461472 original size:22 final size:22
Alignment explanation
Indices: 461429--461489 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
461419 TGCGATTTCC
* *
461429 CTATTTTCTATTT-CTTTCAATT
1 CTATTTTCT-TTTATTTTTAATT
461451 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
*
461473 TTA-TTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
461490 CCTTAAATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:463984 original size:8 final size:8
Alignment explanation
Indices: 463971--464014 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
463961 CCCAATTATT
463971 TTTTTTTA
1 TTTTTTTA
463979 TTTTTTTA
1 TTTTTTTA
*
463987 TTTTTTTC
1 TTTTTTTA
*
463995 TCTATTTTA
1 T-TTTTTTA
*
464004 TTTATTTA
1 TTTTTTTA
464012 TTT
1 TTT
464015 ATTACTTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 24 0.80
9 6 0.20
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:463989 original size:18 final size:21
Alignment explanation
Indices: 463966--464010 Score: 69
Period size: 18 Copynumber: 2.3 Consensus size: 21
463956 GTAAACCCAA
463966 TTATTTTTTT-T-TATTTT-T
1 TTATTTTTTTCTCTATTTTAT
463984 TTATTTTTTTCTCTATTTTAT
1 TTATTTTTTTCTCTATTTTAT
464005 TTATTT
1 TTATTT
464011 ATTTATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.42
19 1 0.04
20 6 0.25
21 7 0.29
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.82
Consensus pattern (21 bp):
TTATTTTTTTCTCTATTTTAT
Found at i:465553 original size:12 final size:13
Alignment explanation
Indices: 465538--465585 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
465528 TATTATTTAT
465538 TATTTA-CTTTTG
1 TATTTATCTTTTG
*
465550 TATTTAT-TTATG
1 TATTTATCTTTTG
465562 --TTTATCTTTTTG
1 TATTTATC-TTTTG
465574 TATTTATCTTTT
1 TATTTATCTTTT
465586 AGAGTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 5 0.17
12 14 0.48
13 4 0.14
14 6 0.21
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (13 bp):
TATTTATCTTTTG
Found at i:465556 original size:23 final size:24
Alignment explanation
Indices: 465530--465580 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
465520 ATTTAAGATA
465530 TTATTTATTATTTA-C-TTTTGTAT
1 TTATTTA-TATTTATCTTTTTGTAT
*
465553 TTATTTATGTTTATCTTTTTGTAT
1 TTATTTATATTTATCTTTTTGTAT
465577 TTAT
1 TTAT
465581 CTTTTAGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 8 0.32
24 12 0.48
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.71
Consensus pattern (24 bp):
TTATTTATATTTATCTTTTTGTAT
Found at i:466994 original size:6 final size:6
Alignment explanation
Indices: 466983--467008 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
466973 GGCAACCCAA
466983 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
467009 TCTCTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:467036 original size:20 final size:20
Alignment explanation
Indices: 467000--467037 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
466990 TATTTTTATT
*
467000 TTTATTTTTTCTCTATTTTA
1 TTTATTTTTTATCTATTTTA
467020 TTTATTTATTTAT-TATTT
1 TTTATTT-TTTATCTATTT
467038 GTCCAGGAAA
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:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTTTTATCTATTTTA
Found at i:468586 original size:14 final size:14
Alignment explanation
Indices: 468563--468592 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
468553 TTTGTATTTA
*
468563 TTTATGTTTATCTT
1 TTTATATTTATCTT
468577 TTTATATTTATCTT
1 TTTATATTTATCTT
468591 TT
1 TT
468593 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:470296 original size:134 final size:133
Alignment explanation
Indices: 470019--470514 Score: 532
Period size: 134 Copynumber: 3.6 Consensus size: 133
470009 TTGTTTGGAA
* * * * *
470019 AAAGTTTTGGTTTTTTTTAAACAATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATT
1 AAAGTTTTGATTTTTTTT-AACTATTTCAAAAAAAAAGTTTGGATTTTTAAGTAAAATAGTGA--
* *
470084 TTTTTTTTTAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGAAAAGTTTAAAT
63 TTTTCTTTAAAAAAGAAAGTTT--ATTTTTAAAAATAAAAATCTATTTTTTAGAAAAGTTTAAAT
*
470149 TTTTAAAC
126 TTTTAAAT
* * *
470157 AAAGTTTTTATTTTTTTTAACTATTTCAAAAAAAAAGTTTGGATTTTTATGTAAAATAATGATTT
1 AAAGTTTTGATTTTTTTTAACTATTTCAAAAAAAAAGTTTGGATTTTTAAGTAAAATAGTGATTT
* *
470222 TCTTTAAAGAAGAGAAAGTTT-TTTTTTAAAATAAAAATCTATTGTTTT-GAAAAGTTTAAAATT
66 TCTTTAAA-AA-AGAAAGTTTATTTTTAAAAATAAAAATCTATT-TTTTAGAAAAGTTTAAATTT
470285 TTAAAT
128 TTAAAT
* * * *
470291 AAAGTTTTGATTTTTTTTAACTATTTCGAAATATAAGTTTGGATTTTTAAATAAAATAGTGATTT
1 AAAGTTTTGATTTTTTTTAACTATTTCAAAAAAAAAGTTTGGATTTTTAAGTAAAATAGTGATTT
*
470356 TCTTTAAAAAAATAGAAAGTTTATATTTTAAAAATAAAATTCTGTTTTTTAGTTATTTTAAAGAA
66 TCTTT--AAAAA-AGAAAGTTTAT-TTTTAAAAATAAAAATC-------TA-TT-TTTT--AG-A
*
470421 AAATTTTAAATTTTTAAAT
115 AAAGTTTAAATTTTTAAAT
* * *
470440 AAAGTTTTGA-TTTTTTTAACTATTTCGAAATAAAAA-TTTAGATTTTTAAGTAAAGTAGTGATT
1 AAAGTTTTGATTTTTTTTAACTATTTC-AAAAAAAAAGTTTGGATTTTTAAGTAAAATAGTGATT
*
470503 TTCATTAAAAAA
65 TTCTTTAAAAAA
470515 AAAAAGAAGG
Statistics
Matches: 304, Mismatches: 34, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
134 103 0.34
135 24 0.08
136 6 0.02
137 62 0.20
138 16 0.05
144 2 0.01
145 7 0.02
146 5 0.02
148 46 0.15
149 33 0.11
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (133 bp):
AAAGTTTTGATTTTTTTTAACTATTTCAAAAAAAAAGTTTGGATTTTTAAGTAAAATAGTGATTT
TCTTTAAAAAAGAAAGTTTATTTTTAAAAATAAAAATCTATTTTTTAGAAAAGTTTAAATTTTTA
AAT
Found at i:478106 original size:24 final size:25
Alignment explanation
Indices: 478051--478108 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
478041 GAGAGAACTC
478051 TAAAATTTAGAATTTGAAGATATAT
1 TAAAATTTAGAATTTGAAGATATAT
*
478076 T--ATTTTAGAATTTTGAAGA-AT-T
1 TAAAATTTAGAA-TTTGAAGATATAT
478098 TAAAATTTAGA
1 TAAAATTTAGA
478109 TCAAGAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 2 0.07
23 10 0.36
24 15 0.54
25 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (25 bp):
TAAAATTTAGAATTTGAAGATATAT
Found at i:478129 original size:20 final size:20
Alignment explanation
Indices: 478091--478129 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
478081 TAGAATTTTG
* *
478091 AAGAATTTAAAATTTAGATC
1 AAGAATTTAAAAGTAAGATC
*
478111 AAGAATTTTAAAGTAAGAT
1 AAGAATTTAAAAGTAAGAT
478130 AAATCATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (20 bp):
AAGAATTTAAAAGTAAGATC
Found at i:478634 original size:239 final size:236
Alignment explanation
Indices: 478210--478684 Score: 815
Period size: 239 Copynumber: 2.0 Consensus size: 236
478200 AAAATAATAA
*
478210 TAATGATAAAAGATTGAATAAGTTGTAGATGAATTTTAATATTTCTCTGAATTAATTAGTAACTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTGAATTAATTAGTAACTT
478275 TTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAGGTATTTTACTAGAATTAT
66 TTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAGGTATTTTACTAGAATTAT
* *
478340 TTAAGTATCTTTTAGGGTTCTCATTAGAAGTAAAAATCTCTAATTTAATTTTTAAATTAGATAAG
131 TTAAGTATCCTTTAGGGTTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAAG
478405 TTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
196 TTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
* * **
478446 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTATTTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTGAATTAATTAGTAACTT
478511 TTAAAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTACTAGAAT
66 TT--AGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTG-AGGTATTTTACTAGAAT
* * *
478576 TATTTAGGTATCCTTTAGGTTTCTTATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGAT
128 TATTTAAGTATCCTTTAGGGTTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGAT
* *
478641 AAGTTTGGTGAACACGTCTTAGTTAAGTTACAAGTAAATTGGAG
193 AAGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
478685 GCATTGTTTA
Statistics
Matches: 224, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
236 62 0.28
238 43 0.19
239 119 0.53
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.42
Consensus pattern (236 bp):
TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTGAATTAATTAGTAACTT
TTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAGGTATTTTACTAGAATTAT
TTAAGTATCCTTTAGGGTTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAAG
TTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
Found at i:479320 original size:50 final size:49
Alignment explanation
Indices: 479266--479403 Score: 150
Period size: 50 Copynumber: 2.8 Consensus size: 49
479256 AGATAAATGA
* * *
479266 ATTGAAGTCGTAATGGTGAATCTTATACACCTAAAGCTGTAGACGGGTAG
1 ATTGAAG-CGCAATGGTGAATCTTATACACCTAAAGCTGTAAACGGGCAG
* ** * *
479316 ATTGAAGCCACAATGACGAATCTCATACACCTAAAGCTGTAAAGGGGCAG
1 ATTGAAG-CGCAATGGTGAATCTTATACACCTAAAGCTGTAAACGGGCAG
* * *
479366 ATTGAAGCTGCAAGGGTGAATCTTATACTCTTAAAGCT
1 ATTGAAGC-GCAATGGTGAATCTTATACACCTAAAGCT
479404 AGAAAAGGGT
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
49 1 0.01
50 70 0.99
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25
Consensus pattern (49 bp):
ATTGAAGCGCAATGGTGAATCTTATACACCTAAAGCTGTAAACGGGCAG
Found at i:479464 original size:100 final size:100
Alignment explanation
Indices: 479280--479466 Score: 218
Period size: 100 Copynumber: 1.9 Consensus size: 100
479270 AAGTCGTAAT
* * * * *
479280 GGTGAATCTTATACACCTAAAGCTGTAGACGGGTAGATTGAAGCCACAATGACGAATCTCATACA
1 GGTGAATCTTATACACCTAAAGCTGTAAAAGGGTAAATTGAAGCCACAATGACAAATCCCATACA
479345 CCTAAAGCTGTAAAGGGGCAGATTGAAGCTGCAAG
66 CCTAAAGCTGTAAAGGGGCAGATTGAAGCTGCAAG
* * *
479380 GGTGAATCTTATACTCTTAAAGCTAG-AAAAGGGTAAATTGAAGCTACAA-GAGCAAATCCCTAT
1 GGTGAATCTTATACACCTAAAGCT-GTAAAAGGGTAAATTGAAGCCACAATGA-CAAATCCC-AT
* * * *
479443 ACCCCTGAAGTTGTAGA-GGGCAGA
63 ACACCTAAAGCTGTAAAGGGGCAGA
479467 ATAAAACTCG
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
99 2 0.03
100 54 0.75
101 16 0.22
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (100 bp):
GGTGAATCTTATACACCTAAAGCTGTAAAAGGGTAAATTGAAGCCACAATGACAAATCCCATACA
CCTAAAGCTGTAAAGGGGCAGATTGAAGCTGCAAG
Found at i:480340 original size:24 final size:23
Alignment explanation
Indices: 480309--480382 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 23
480299 AGGCCAATTT
* *
480309 TTTTTTTTTTTTTACCAGCCTAA
1 TTTTTTTTTTTTTACAAGCCCAA
*
480332 TTTTATTTTTTTTTACAATCCCAA
1 TTTT-TTTTTTTTTACAAGCCCAA
*
480356 -TTTTTTTTTCTTACAAGCCCAA
1 TTTTTTTTTTTTTACAAGCCCAA
*
480378 ATTTT
1 TTTTT
480383 AAAAGAACCC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 17 0.39
23 11 0.25
24 16 0.36
ACGTcount: A:0.22, C:0.18, G:0.03, T:0.58
Consensus pattern (23 bp):
TTTTTTTTTTTTTACAAGCCCAA
Found at i:480746 original size:21 final size:20
Alignment explanation
Indices: 480708--480757 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
480698 TGTTACAATA
480708 TATTTATTTTATATTTTATT
1 TATTTATTTTATATTTTATT
480728 TATTTATTATTAT-TATTTATT
1 TATTTATT-TTATAT-TTTATT
*
480749 TTTTTATTT
1 TATTTATTT
480758 CAAAACAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTATTTTATATTTTATT
Found at i:484030 original size:25 final size:25
Alignment explanation
Indices: 484002--484060 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
483992 TCCCACTTAC
*
484002 TAAAATAAAAGAAATAT-AAACAAAA
1 TAAAATAAAAAAAATATCAAA-AAAA
*
484027 TAAAATAAAAAAAATATCAAAGAAA
1 TAAAATAAAAAAAATATCAAAAAAA
484052 T-AAATAAAA
1 TAAAATAAAA
484061 TCTGATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 8 0.26
25 20 0.65
26 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (25 bp):
TAAAATAAAAAAAATATCAAAAAAA
Found at i:489540 original size:14 final size:14
Alignment explanation
Indices: 489517--489565 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 14
489507 AATTATTTCA
489517 TTAA-TAAATTGGG
1 TTAATTAAATTGGG
489530 TTAATTAAATT--G
1 TTAATTAAATTGGG
489542 TTAATT-AATTGGG
1 TTAATTAAATTGGG
*
489555 TTAATTTAATT
1 TTAATTAAATT
489566 AATTTGACCC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.12
12 7 0.22
13 11 0.34
14 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (14 bp):
TTAATTAAATTGGG
Found at i:489545 original size:25 final size:25
Alignment explanation
Indices: 489517--489565 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
489507 AATTATTTCA
489517 TTAATAAATTGGGTTAATTAAATTG
1 TTAATAAATTGGGTTAATTAAATTG
* *
489542 TTAATTAATTGGGTTAATTTAATT
1 TTAATAAATTGGGTTAATTAAATT
489566 AATTTGACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (25 bp):
TTAATAAATTGGGTTAATTAAATTG
Found at i:497957 original size:147 final size:147
Alignment explanation
Indices: 497678--497968 Score: 449
Period size: 147 Copynumber: 2.0 Consensus size: 147
497668 CGTGTTAACA
* * * * *
497678 TTTAGGGCCTTGGTAACGAAGTCTTGGATGGTCCTGTTCAATCTTGCTCGAATTTGCTTGGCCTT
1 TTTAAGGCCTTGGTAACAAAGTCTTGGACGGTCCTATTCAATCTTGCTCAAATTTGCTTGGCCTT
* * * * *
497743 CGACCTCGTTATTGGGCCTTGAGAAACTTTGATCCCATCACATTTATGAGCTTGAATTTGGGTCT
66 CGACCTCGTTATTGGACCTTGAGAAACTTTAATCCCATCACATTTATAAGCTTGAATTTAGGCCT
497808 TACGACTCATATCATTC
131 TACGACTCATATCATTC
* *
497825 TTTAAGGCCTTGGTAACAAAGTCTTGGACGGTCTTATTCAATCTTGCTCAAATTTGCTTGGGCTT
1 TTTAAGGCCTTGGTAACAAAGTCTTGGACGGTCCTATTCAATCTTGCTCAAATTTGCTTGGCCTT
*
497890 CGACCTCGTTATTGGACCTTGA-ACAACTTTAATCTCATCACATTTATAAGCTTGAATTTAGGCC
66 CGACCTCGTTATTGGACCTTGAGA-AACTTTAATCCCATCACATTTATAAGCTTGAATTTAGGCC
497954 TTACGACTCATATCA
130 TTACGACTCATATCA
497969 CACAATAATT
Statistics
Matches: 130, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
146 1 0.01
147 129 0.99
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (147 bp):
TTTAAGGCCTTGGTAACAAAGTCTTGGACGGTCCTATTCAATCTTGCTCAAATTTGCTTGGCCTT
CGACCTCGTTATTGGACCTTGAGAAACTTTAATCCCATCACATTTATAAGCTTGAATTTAGGCCT
TACGACTCATATCATTC
Found at i:501016 original size:3 final size:3
Alignment explanation
Indices: 501008--501077 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
500998 ATCGAGACAA
* *
501008 CTT CTT CTT CTT CTT CTT CTT TTT CTTT CTAT -TC CTT -TT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT C-TT CT-T CTT CTT CTT CTT CTT
*
501053 CTT -TT CTT -TT C-T CTT CTT CTG CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
501078 AATACCCACA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
2 8 0.15
3 42 0.78
4 4 0.07
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:501077 original size:27 final size:27
Alignment explanation
Indices: 501010--501077 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
501000 CGAGACAACT
501010 TCTTCTTCTTCTTCTTCTTTTTCTTTC
1 TCTTCTTCTTCTTCTTCTTTTTCTTTC
*
501037 TATTCCTT-TTCTTCTTC-TTTTCTTTTC
1 TCTT-CTTCTTCTTCTTCTTTTTC-TTTC
*
501064 TCTTCTTCTGCTTC
1 TCTTCTTCTTCTTC
501078 AATACCCACA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 8 0.23
27 24 0.69
28 3 0.09
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.68
Consensus pattern (27 bp):
TCTTCTTCTTCTTCTTCTTTTTCTTTC
Found at i:502883 original size:24 final size:24
Alignment explanation
Indices: 502838--502884 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
502828 TGCAAAAACT
* *
502838 AAAGAAACAAATTAAAGTAAAATA
1 AAAGAAACAAAATAAAGAAAAATA
502862 AAAGAAA-AAAATAATAGAAAAAT
1 AAAGAAACAAAATAA-AGAAAAAT
502885 TACAATGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (24 bp):
AAAGAAACAAAATAAAGAAAAATA
Found at i:525535 original size:18 final size:18
Alignment explanation
Indices: 525514--525549 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
525504 CGTTATGACA
525514 ATGATATCTACAAAGACG
1 ATGATATCTACAAAGACG
* *
525532 ATGATATTTACGAAGACG
1 ATGATATCTACAAAGACG
525550 GGTAATATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (18 bp):
ATGATATCTACAAAGACG
Found at i:530622 original size:23 final size:23
Alignment explanation
Indices: 530586--530629 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
530576 AAGAATCGAC
530586 TAAATCTAAAGCTCTGATACCAA
1 TAAATCTAAAGCTCTGATACCAA
* * *
530609 TAAATGTAACGCTCTTATACC
1 TAAATCTAAAGCTCTGATACC
530630 TGACCCGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (23 bp):
TAAATCTAAAGCTCTGATACCAA
Found at i:535054 original size:6 final size:6
Alignment explanation
Indices: 535043--535081 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
535033 CTGTTTTCAT
535043 CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC CCC
1 CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC CCC
535082 TCTGATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.69, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCATC
Found at i:537418 original size:20 final size:20
Alignment explanation
Indices: 537393--537430 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
537383 TTAACCGTTA
*
537393 GATTTAGTGGTCGACCATTG
1 GATTTAATGGTCGACCATTG
*
537413 GATTTAATGGTTGACCAT
1 GATTTAATGGTCGACCAT
537431 CAAGTCTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (20 bp):
GATTTAATGGTCGACCATTG
Found at i:546205 original size:14 final size:14
Alignment explanation
Indices: 546186--546218 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
546176 TCACCAAAAT
*
546186 TATTTTTTTTGACG
1 TATTTTTTGTGACG
546200 TATTTTTTGTGACG
1 TATTTTTTGTGACG
546214 T-TTTT
1 TATTTT
546219 AAACGTCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.12, C:0.06, G:0.15, T:0.67
Consensus pattern (14 bp):
TATTTTTTGTGACG
Found at i:546254 original size:48 final size:48
Alignment explanation
Indices: 546151--546256 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
546141 ATGTTTACTA
* * * ** *
546151 ATATTATTTGTGATGTTTTTAAACGTCACCAAAATTATTTTTTTTGAC
1 ATATTTTTTGTGACGTTTTTAAACGTCACCAAAACTATTTTTCGTAAC
* *
546199 GTATTTTTTGTGACGTTTTTAAACGTCACCATAACTACTTTTTCGTAAC
1 ATATTTTTTGTGACGTTTTTAAACGTCACCAAAACTA-TTTTTCGTAAC
*
546248 ATTTTTTTT
1 ATATTTTTT
546257 ATATTTTTTG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
48 32 0.68
49 15 0.32
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.51
Consensus pattern (48 bp):
ATATTTTTTGTGACGTTTTTAAACGTCACCAAAACTATTTTTCGTAAC
Found at i:549326 original size:25 final size:25
Alignment explanation
Indices: 549298--549347 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
549288 TTAAAGGAAG
549298 AAAGCTTAACATAAGCCATTTTCAT
1 AAAGCTTAACATAAGCCATTTTCAT
549323 AAAGCTTAACATAAGCCATTTTCAT
1 AAAGCTTAACATAAGCCATTTTCAT
549348 CCTTTTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (25 bp):
AAAGCTTAACATAAGCCATTTTCAT
Found at i:551927 original size:2 final size:2
Alignment explanation
Indices: 551915--551988 Score: 53
Period size: 2 Copynumber: 37.5 Consensus size: 2
551905 TTGTATATTT
* * * * *
551915 TA TA CA TA TA TA TT TT TA TA CA TA TA TA CTG T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
551957 TA TA TA TA TA CA TA TA TA T- TT TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
551989 CTTTAATTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.04
2 54 0.95
3 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:551933 original size:16 final size:16
Alignment explanation
Indices: 551887--551988 Score: 109
Period size: 16 Copynumber: 6.4 Consensus size: 16
551877 GTAATTTTAG
551887 ATATAT-TTTTTATAC
1 ATATATATTTTTATAC
* *
551902 AAATTGTATATTTTATAC
1 ATA-TATAT-TTTTATAC
551920 ATATATATTTTTATAC
1 ATATATATTTTTATAC
* * *
551936 ATATATACTGTTATAT
1 ATATATATTTTTATAC
* *
551952 ATATATATATATATAC
1 ATATATATTTTTATAC
551968 ATATATA-TTTTATAC
1 ATATATATTTTTATAC
551983 ATATAT
1 ATATAT
551989 CTTTAATTAA
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
15 14 0.20
16 41 0.59
17 5 0.07
18 10 0.14
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATATTTTTATAC
Found at i:553702 original size:196 final size:196
Alignment explanation
Indices: 553368--553765 Score: 708
Period size: 196 Copynumber: 2.0 Consensus size: 196
553358 GTTCTACATG
* *
553368 TTTTTGGTTGGATTATATTACGATTTTGAATTTTTTGGTTGTCTTTCTTAAGGTATTAATTTTTT
1 TTTTTGGTTGGATTACATTACGATTTTGAATTGTTTGGTTGTCTTTCTTAAGGTATTAATTTTTT
* *
553433 TTTATCAATTGAATATTTGTTTGCTTTGGGATGTTCTTACTTTCATTGCTTTTGAATGTTTTTGG
66 TTTATCAATTAAATATTTGGTTGCTTTGGGATGTTCTTACTTTCATTGCTTTTGAATGTTTTTGG
* *
553498 TTCAAATGTACTACCAGTATATGTATGCTATTTAATTGTTTATGCATCATTTTTCTTTAATTGTT
131 TTCAAATGTACTACCAGTATATGTATGCTATCTAATAGTTTATGCATCATTTTTCTTTAATTGTT
553563 A
196 A
553564 TTTTTGGTTGGATTACATTACGATTTTGAATTGTTTGGTTGTCTTTCTT-AGGTATTAATTTTAT
1 TTTTTGGTTGGATTACATTACGATTTTGAATTGTTTGGTTGTCTTTCTTAAGGTATTAATTTT-T
*
553628 TTTTATCAATTAAATATTTGGTTGCTTTGGGATTTTCTTACTTTCATTGCTTTTGAATGTTTTTG
65 TTTTATCAATTAAATATTTGGTTGCTTTGGGATGTTCTTACTTTCATTGCTTTTGAATGTTTTTG
*
553693 GTTCAAATGTACTACCAGTATATGTATGCTATCTACTAGTTTATGCATCATTTTTCTTTAATTGT
130 GTTCAAATGTACTACCAGTATATGTATGCTATCTAATAGTTTATGCATCATTTTTCTTTAATTGT
553758 TA
195 TA
553760 TTTTTG
1 TTTTTG
553766 TTTCTTCTTT
Statistics
Matches: 193, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
195 13 0.07
196 180 0.93
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.55
Consensus pattern (196 bp):
TTTTTGGTTGGATTACATTACGATTTTGAATTGTTTGGTTGTCTTTCTTAAGGTATTAATTTTTT
TTTATCAATTAAATATTTGGTTGCTTTGGGATGTTCTTACTTTCATTGCTTTTGAATGTTTTTGG
TTCAAATGTACTACCAGTATATGTATGCTATCTAATAGTTTATGCATCATTTTTCTTTAATTGTT
A
Found at i:563794 original size:15 final size:16
Alignment explanation
Indices: 563764--563795 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
563754 AATTTTGCCA
563764 TGTTTTTCATTATTTT
1 TGTTTTTCATTATTTT
563780 TGTTTTT-ATT-TTTT
1 TGTTTTTCATTATTTT
563794 TG
1 TG
563796 CTTTCGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.78
Consensus pattern (16 bp):
TGTTTTTCATTATTTT
Found at i:568732 original size:18 final size:18
Alignment explanation
Indices: 568698--568735 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
568688 ATTTTGAAAT
*
568698 AAAACATAAAATTTTGGA
1 AAAACATAAAATATTGGA
568716 AAAACATGAAAA-ATTGGA
1 AAAACAT-AAAATATTGGA
568734 AA
1 AA
568736 CAAGAGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (18 bp):
AAAACATAAAATATTGGA
Found at i:579854 original size:18 final size:18
Alignment explanation
Indices: 579814--579861 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
579804 AGGTAGTATA
579814 TAATAAATACAATTTAAATT
1 TAAT-AATA-AATTTAAATT
579834 TAATAATAAATTGTAAA-T
1 TAATAATAAATT-TAAATT
579852 TAATAA-AAAT
1 TAATAATAAAT
579862 CAAATAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.15
18 11 0.41
19 8 0.30
20 4 0.15
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
TAATAATAAATTTAAATT
Found at i:580251 original size:23 final size:23
Alignment explanation
Indices: 580223--580278 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
580213 GTAATTTAAA
580223 ACAAACATAATGATAGAAGAGTT
1 ACAAACATAATGATAGAAGAGTT
* *
580246 ACAAACATAATGGTAGGAGAGTT
1 ACAAACATAATGATAGAAGAGTT
580269 ACAAA-ATAAT
1 ACAAACATAAT
580279 AATAACTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.21
Consensus pattern (23 bp):
ACAAACATAATGATAGAAGAGTT
Found at i:589225 original size:35 final size:35
Alignment explanation
Indices: 589186--589277 Score: 141
Period size: 36 Copynumber: 2.5 Consensus size: 35
589176 CTTTTTCTCC
589186 CTTTTTTTTTCTTTTTTTTCTTTTCGAACCTTTTG
1 CTTTTTTTTTCTTTTTTTTCTTTTCGAACCTTTTG
589221 CTTTTTTTCTT-TGTTTTTTTCTTTTCGAACCTTTTG
1 CTTTTTTT-TTCT-TTTTTTTCTTTTCGAACCTTTTG
589257 CTTTTTTCTTCTCTTTTTTTT
1 CTTTTTT-TT-TCTTTTTTTT
589278 TTTGCTGTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
35 9 0.17
36 33 0.63
37 9 0.17
38 1 0.02
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.73
Consensus pattern (35 bp):
CTTTTTTTTTCTTTTTTTTCTTTTCGAACCTTTTG
Found at i:590196 original size:16 final size:15
Alignment explanation
Indices: 590175--590212 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
590165 CTAAAATACC
590175 AAAAATAAAAATAAGT
1 AAAAATAAAAATAA-T
590191 AAAAAT-AAAATAAT
1 AAAAATAAAAATAAT
*
590205 ATAAATAA
1 AAAAATAA
590213 TTGAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 8 0.40
16 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAAATAAAAATAAT
Found at i:591592 original size:93 final size:93
Alignment explanation
Indices: 591428--591613 Score: 345
Period size: 93 Copynumber: 2.0 Consensus size: 93
591418 TTTAGAATTG
591428 AATTTACCTCATCTTCAGCGACACGTCACCGAATTACCTGATCCGAGCAGTGTTTCCAAAGGTAC
1 AATTTACCTCATCTTCAGCGACACGTCACCGAATTACCTGATCCGAGCAGTGTTTCCAAAGGTAC
*
591493 GGATCATCCCAAATATAAAATCGAGACT
66 GAATCATCCCAAATATAAAATCGAGACT
* *
591521 AATTTACCTCATCTTCAGTGACACGTCACTGAATTACCTGATCCGAGCAGTGTTTCCAAAGGTAC
1 AATTTACCTCATCTTCAGCGACACGTCACCGAATTACCTGATCCGAGCAGTGTTTCCAAAGGTAC
591586 GAATCATCCCAAATATAAAATCGAGACT
66 GAATCATCCCAAATATAAAATCGAGACT
591614 CTCGCTTTAT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (93 bp):
AATTTACCTCATCTTCAGCGACACGTCACCGAATTACCTGATCCGAGCAGTGTTTCCAAAGGTAC
GAATCATCCCAAATATAAAATCGAGACT
Found at i:602266 original size:16 final size:16
Alignment explanation
Indices: 602245--602278 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
602235 AGAGAGAGAT
*
602245 AACAACTAGAAAATAA
1 AACAACCAGAAAATAA
*
602261 AACAACCATAAAATAA
1 AACAACCAGAAAATAA
602277 AA
1 AA
602279 ATAAAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.15, G:0.03, T:0.12
Consensus pattern (16 bp):
AACAACCAGAAAATAA
Found at i:604085 original size:20 final size:20
Alignment explanation
Indices: 604056--604093 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
604046 AAATAGTAAT
*
604056 AATAACAATAATCATAAATA
1 AATAACAATAATAATAAATA
*
604076 AATAATAATAATAATAAA
1 AATAACAATAATAATAAA
604094 GGTAAAAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAACAATAATAATAAATA
Found at i:609328 original size:32 final size:32
Alignment explanation
Indices: 609287--609350 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
609277 AGATATTAAA
*
609287 AAGATCCAAGTAAGTTTATTTTTTAATTCTGT
1 AAGATCCAAGTAAGTTTATTATTTAATTCTGT
609319 AAGATCCAAGTAAGTTTATTATTTAATTCTGT
1 AAGATCCAAGTAAGTTTATTATTTAATTCTGT
609351 GACATCATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (32 bp):
AAGATCCAAGTAAGTTTATTATTTAATTCTGT
Found at i:610106 original size:22 final size:23
Alignment explanation
Indices: 610081--610130 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
610071 CAAAACCCGA
*
610081 AAACAAAAAACCCT-CAAAATGT
1 AAACAAAAAACCCTCCAAAACGT
* **
610103 AAACACAAAATTCTCCAAAACGT
1 AAACAAAAAACCCTCCAAAACGT
610126 AAACA
1 AAACA
610131 CCGAGTCTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.58, C:0.24, G:0.04, T:0.14
Consensus pattern (23 bp):
AAACAAAAAACCCTCCAAAACGT
Found at i:620453 original size:38 final size:37
Alignment explanation
Indices: 620396--620517 Score: 106
Period size: 37 Copynumber: 3.3 Consensus size: 37
620386 ATTCTTGGGC
* * *
620396 GCAA-TTGAAGAATACTTATGCAGCGATAGTTTTGGAT
1 GCAATTTGGAGAATATTTATGCAGTGATAGTTTTGG-T
* *
620433 GCAATTTGGAGAATATTTATGCAGTGACAGTCTTAGGT
1 GCAATTTGGAGAATATTTATGCAGTGATAGT-TTTGGT
** *
620471 GC-ATTCTGGA-AATATTCCTACAGTGATAGTTTTGGGT
1 GCAATT-TGGAGAATATTTATGCAGTGATAGTTTT-GGT
*
620508 GCAATCTGGA
1 GCAATTTGGA
620518 AGTGCTCATG
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
36 2 0.03
37 32 0.46
38 31 0.45
39 4 0.06
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (37 bp):
GCAATTTGGAGAATATTTATGCAGTGATAGTTTTGGT
Found at i:620534 original size:37 final size:37
Alignment explanation
Indices: 620492--620570 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
620482 ATATTCCTAC
* *
620492 AGTGATAGTTTTGGGTGCAATCTGGAAGTGCTCATGT
1 AGTGATAGTTTTGGGCGCAATCTAGAAGTGCTCATGT
* *
620529 GGTGATAGTTTTGGGCGCAATCTAGAATTGCTCATGT
1 AGTGATAGTTTTGGGCGCAATCTAGAAGTGCTCATGT
620566 AGTGA
1 AGTGA
620571 CATTAGTAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.23, C:0.11, G:0.32, T:0.34
Consensus pattern (37 bp):
AGTGATAGTTTTGGGCGCAATCTAGAAGTGCTCATGT
Done.