Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008391.1 Hibiscus syriacus cultivar Beakdansim tig00111156_pilon, 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: 685102
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:406510 original size:31 final size:31
Alignment explanation
Indices: 406470--406529 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
406460 GAAAAGAACC
*
406470 ATAGGTACAAGCCATTGTAAAACAAGTATTT
1 ATAGATACAAGCCATTGTAAAACAAGTATTT
406501 ATAGATACAAGCCATTGTAAAACAAGTAT
1 ATAGATACAAGCCATTGTAAAACAAGTAT
406530 AGCACAACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (31 bp):
ATAGATACAAGCCATTGTAAAACAAGTATTT
Found at i:408637 original size:29 final size:30
Alignment explanation
Indices: 408577--408638 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
408567 AATTTTATAT
*
408577 AATTTATATGTTAAAAATTAAAATTTAAAA
1 AATTTATATGTTAAAAATTAAAATTAAAAA
408607 AATTTATACT-TT-AAAATTAAAA-TAAATAA
1 AATTTATA-TGTTAAAAATTAAAATTAAA-AA
408636 AAT
1 AAT
408639 CATAGAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.10
29 15 0.52
30 10 0.34
31 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (30 bp):
AATTTATATGTTAAAAATTAAAATTAAAAA
Found at i:410251 original size:64 final size:64
Alignment explanation
Indices: 410140--410368 Score: 186
Period size: 64 Copynumber: 3.5 Consensus size: 64
410130 TTAAATGGTT
* * *
410140 AATA-ATATT-TTTTAATTTAAAATATTCAAAAGATATAGA-TA-CATTTTACTATACAAACTTA
1 AATAGATATTATTTTAATTTGAGATATTCAAAAGATATA-ATTATCATTTTAATATACAAACTTA
* * *
410201 AATAGATATTATTTTAATTTGAGATATTAAGAAAGATATAATTATC-TTTTAATATTCAAAGTTA
1 AATAGATATTATTTTAATTTGAGATATTCA-AAAGATATAATTATCATTTTAATATACAAACTTA
* ** *
410265 AATAGATAATAAATACCTTTTAATTTGAGATATTCAAAAGA-ATAATTATCCTACTAATATTCAA
1 AATAGAT-AT---TA--TTTTAATTTGAGATATTCAAAAGATATAATTATCATTTTAATATACAA
410329 A-TTA
60 ACTTA
* *
410333 AAGAGATAAATATATTTGAATTTGTA-ATATTCAAAA
1 AATAGAT--AT-TATTTTAATTTG-AGATATTCAAAA
410369 AGAATATGAA
Statistics
Matches: 143, Mismatches: 11, Indels: 24
0.80 0.06 0.13
Matches are distributed among these distances:
61 4 0.03
62 5 0.03
63 17 0.12
64 33 0.23
65 22 0.15
66 1 0.01
67 3 0.02
68 20 0.14
69 20 0.14
70 18 0.13
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (64 bp):
AATAGATATTATTTTAATTTGAGATATTCAAAAGATATAATTATCATTTTAATATACAAACTTA
Found at i:410252 original size:35 final size:34
Alignment explanation
Indices: 410212--410314 Score: 104
Period size: 35 Copynumber: 3.0 Consensus size: 34
410202 ATAGATATTA
410212 TTTTAATTTGAGATATTAAGAAAGATATAATTATC
1 TTTTAATTTGAGATATTAA-AAAGATATAATTATC
* * * *
410247 TTTTAATATTCA-A-AGTTAAATAGATAATAAATACC
1 TTTTAAT-TTGAGATA-TTAAAAAGAT-ATAATTATC
*
410282 TTTTAATTTGAGATATTCAAAAGA-ATAATTATC
1 TTTTAATTTGAGATATTAAAAAGATATAATTATC
410315 CTACTAATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
33 7 0.13
34 9 0.17
35 34 0.63
36 4 0.07
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.41
Consensus pattern (34 bp):
TTTTAATTTGAGATATTAAAAAGATATAATTATC
Found at i:410365 original size:65 final size:66
Alignment explanation
Indices: 410210--410374 Score: 192
Period size: 68 Copynumber: 2.4 Consensus size: 66
410200 AAATAGATAT
* ** *
410210 TATTTTAATTTGAGATATTAAGAAAGATATAATTATCTTTTAATATTCAAAGTTAAATAGATAAT
1 TATTTTAATTTGAGATATTCA-AAAGA-ATAATTATCTACTAATATTCAAAGTTAAAGAGATAAT
410275 AAA
64 AAA
410278 TACCTTTTAATTTGAGATATTCAAAAGAATAATTATCCTACTAATATTCAAA-TTAAAGAGATAA
1 TA--TTTTAATTTGAGATATTCAAAAGAATAATTAT-CTACTAATATTCAAAGTTAAAGAGATAA
*
410342 -ATA
63 TAAA
*
410345 TATTTGAATTTGTA-ATATTCAAAAAGAATA
1 TATTTTAATTTG-AGATATTC-AAAAGAATA
410375 TGAAGTTAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
65 15 0.17
66 10 0.12
67 4 0.05
68 21 0.24
69 18 0.21
70 18 0.21
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (66 bp):
TATTTTAATTTGAGATATTCAAAAGAATAATTATCTACTAATATTCAAAGTTAAAGAGATAATAA
A
Found at i:411935 original size:13 final size:13
Alignment explanation
Indices: 411917--411995 Score: 113
Period size: 13 Copynumber: 6.1 Consensus size: 13
411907 AAACAATTAA
**
411917 TCAAATCAGTTTC
1 TCAAATCAACTTC
411930 TCAAATCAACTTC
1 TCAAATCAACTTC
411943 TCAAATCAACTTC
1 TCAAATCAACTTC
411956 TCAAATCAACTTC
1 TCAAATCAACTTC
* *
411969 TTAAATCAGCTTC
1 TCAAATCAACTTC
*
411982 TCAAATCAGCTTC
1 TCAAATCAACTTC
411995 T
1 T
411996 ATACAATTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 61 1.00
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (13 bp):
TCAAATCAACTTC
Found at i:412489 original size:106 final size:106
Alignment explanation
Indices: 412304--412512 Score: 323
Period size: 106 Copynumber: 2.0 Consensus size: 106
412294 TGTTACCCGC
* * *
412304 AGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACATTTCCCCAATTT
1 AGACAACACAAGCTCAACTTCACGGCAAAGGGGCGGCTGACTGTCAACAAAAATTTCCCCAATTC
* *
412369 CATATCCAATTTCAACTTCAC-AGCGAAGGATATTGGACCCA
66 CAGAACCAATTTCAACTTCACGA-CGAAGGATATTGGACCCA
* *
412410 AGACAGCACAAGCTCAACTTCACGGCAAAGGGGCGGCTGACTGTCAACAAATAATTT-CCCAGTT
1 AGACAACACAAGCTCAACTTCACGGCAAAGGGGCGGCTGACTGTCAACAAA-AATTTCCCCAATT
412474 CCAGAACCAATTTCAACTTCACGACGAAGGATATTGGAC
65 CCAGAACCAATTTCAACTTCACGACGAAGGATATTGGAC
412513 TCGGAGCAAT
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
106 89 0.95
107 5 0.05
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.20
Consensus pattern (106 bp):
AGACAACACAAGCTCAACTTCACGGCAAAGGGGCGGCTGACTGTCAACAAAAATTTCCCCAATTC
CAGAACCAATTTCAACTTCACGACGAAGGATATTGGACCCA
Found at i:414661 original size:25 final size:25
Alignment explanation
Indices: 414633--414689 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
414623 ATTTTTCTAT
414633 TTATATTATAT-TATATTACTTATTC
1 TTATATTATATGTAT-TTACTTATTC
* * *
414658 TTATATTCTATGTATTTATTTATTT
1 TTATATTATATGTATTTACTTATTC
414683 TTATATT
1 TTATATT
414690 TTTTCTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (25 bp):
TTATATTATATGTATTTACTTATTC
Found at i:420041 original size:16 final size:15
Alignment explanation
Indices: 420010--420054 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
420000 TAGTTAATGT
*
420010 TACGTGAAACTGTTC
1 TACGTGAAAATGTTC
420025 TACGTGAAAAATGTTC
1 TACGTG-AAAATGTTC
*
420041 TACCTGAAAATGTT
1 TACGTGAAAATGTT
420055 ATATATATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (15 bp):
TACGTGAAAATGTTC
Found at i:421217 original size:2 final size:2
Alignment explanation
Indices: 421210--421249 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
421200 CTTATAACGG
421210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
421250 CAAAAATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:421328 original size:24 final size:24
Alignment explanation
Indices: 421290--421359 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
421280 TAAATCAGAG
* *
421290 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
421314 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* *
421338 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
421360 CTATATATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:421359 original size:48 final size:47
Alignment explanation
Indices: 421265--421359 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 47
421255 ATTAAAACAT
* * * ** *
421265 AATTCAGGTCAAGTATAAATCAGAGTCCATGTCAAGTATCATATAAA
1 AATTCAGGTCAAATATAAATCAGAATCCAGGTCAAAAATCAGATAAA
*
421312 AATTCAGGTCAAATATCATATCAGAATCCAGGTCAAAAATCAGATAAA
1 AATTCAGGTCAAATAT-AAATCAGAATCCAGGTCAAAAATCAGATAAA
421360 CTATATATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 15 0.38
48 25 0.62
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (47 bp):
AATTCAGGTCAAATATAAATCAGAATCCAGGTCAAAAATCAGATAAA
Found at i:422138 original size:30 final size:30
Alignment explanation
Indices: 422078--422177 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 30
422068 CTTTTAAAAT
* * * *
422078 AATTACCAAAATAACA-CCTTTTCAAATTA
1 AATTCCCAAAATAGCACCCATTTCGAATTA
*
422107 AATTCCCAAAATAGTACCCATTTCGAATTA
1 AATTCCCAAAATAGCACCCATTTCGAATTA
422137 AATTCCCAAAATAGCACCCATTTCGAATT-
1 AATTCCCAAAATAGCACCCATTTCGAATTA
422166 AATTCCCAAAAT
1 AATTCCCAAAAT
422178 GTCACCCGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 25 0.39
30 39 0.61
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.29
Consensus pattern (30 bp):
AATTCCCAAAATAGCACCCATTTCGAATTA
Found at i:428542 original size:24 final size:24
Alignment explanation
Indices: 428504--428573 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
428494 TAAATCAGAG
* *
428504 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
428528 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
*
428552 TCCAGGTCAAAAATCATATAAA
1 TCCAGGTCAAATATCATATAAA
428574 CTATTTATAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:429368 original size:29 final size:30
Alignment explanation
Indices: 429297--429361 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
429287 AAAATAATGA
*
429297 CCAAAATAGCA-CCTTTTCGAATTAAATTC
1 CCAAAATAGCACCCATTTCGAATTAAATTC
429326 CCAAAATAGCACCCATTTCGAATT-AATTC
1 CCAAAATAGCACCCATTTCGAATTAAATTC
429355 CCAAAAT
1 CCAAAAT
429362 GTCACCCGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.40, C:0.26, G:0.06, T:0.28
Consensus pattern (30 bp):
CCAAAATAGCACCCATTTCGAATTAAATTC
Found at i:430682 original size:10 final size:11
Alignment explanation
Indices: 430654--430683 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
430644 TTTATAGTTC
430654 TTTCCTTTTTA
1 TTTCCTTTTTA
430665 TTTCCTTTTTA
1 TTTCCTTTTTA
430676 TTT-CTTTT
1 TTTCCTTTT
430684 AGAAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCCTTTTTA
Found at i:430932 original size:12 final size:12
Alignment explanation
Indices: 430915--430941 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
430905 GAATCGGGTT
430915 TTTAAATTTTAA
1 TTTAAATTTTAA
430927 TTTAAATTTTAA
1 TTTAAATTTTAA
430939 TTT
1 TTT
430942 TTGCGATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTAAATTTTAA
Found at i:433401 original size:13 final size:13
Alignment explanation
Indices: 433385--433409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
433375 ACAGTTAATT
433385 AAATCAGTTTCTC
1 AAATCAGTTTCTC
433398 AAATCAGTTTCT
1 AAATCAGTTTCT
433410 ATACAATTTG
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:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (13 bp):
AAATCAGTTTCTC
Found at i:434771 original size:17 final size:18
Alignment explanation
Indices: 434751--434784 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
434741 ATTTTATAAA
*
434751 TTTAT-AAATTATAATTT
1 TTTATCAAAATATAATTT
434768 TTTATCAAAATATAATT
1 TTTATCAAAATATAATT
434785 ATAGATTGAA
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:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTATCAAAATATAATTT
Found at i:438182 original size:24 final size:24
Alignment explanation
Indices: 438150--438316 Score: 92
Period size: 24 Copynumber: 7.5 Consensus size: 24
438140 ATCATGACCG
438150 GTATCGATACTACTTTACATAGTA
1 GTATCGATACTACTTTACATAGTA
* **
438174 GTATCGATACT-CCTTGGAT-G--
1 GTATCGATACTACTTTACATAGTA
* *
438194 GTATAGATATTACTTTACATAGTA
1 GTATCGATACTACTTTACATAGTA
* *
438218 GTATCGATACTCCTTGGAC--A--A
1 GTATCGATACTACTT-TACATAGTA
**
438239 -TATCGATACTTTTTTACATAGTA
1 GTATCGATACTACTTTACATAGTA
* * *
438262 GTATCGATAGTCCTTGGAC--A--A
1 GTATCGATACTACTT-TACATAGTA
**
438283 -TATCGATACTACTACACATAGTA
1 GTATCGATACTACTTTACATAGTA
438306 GTATCGATACT
1 GTATCGATACT
438317 CATTGAGAGG
Statistics
Matches: 104, Mismatches: 23, Indels: 32
0.65 0.14 0.20
Matches are distributed among these distances:
19 4 0.04
20 32 0.31
21 9 0.09
22 2 0.02
23 9 0.09
24 44 0.42
25 4 0.04
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (24 bp):
GTATCGATACTACTTTACATAGTA
Found at i:438208 original size:44 final size:44
Alignment explanation
Indices: 438148--438336 Score: 245
Period size: 44 Copynumber: 4.3 Consensus size: 44
438138 ATATCATGAC
438148 CGGTATCGATACTACTTTACATAGTAGTATCGATACTCCTTGGA
1 CGGTATCGATACTACTTTACATAGTAGTATCGATACTCCTTGGA
* * *
438192 TGGTATAGATATTACTTTACATAGTAGTATCGATACTCCTTGGA
1 CGGTATCGATACTACTTTACATAGTAGTATCGATACTCCTTGGA
** ** *
438236 CAATATCGATACTTTTTTACATAGTAGTATCGATAGTCCTTGGA
1 CGGTATCGATACTACTTTACATAGTAGTATCGATACTCCTTGGA
** ** *
438280 CAATATCGATACTACTACACATAGTAGTATCGATACTCATTGAGA
1 CGGTATCGATACTACTTTACATAGTAGTATCGATACTCCTTG-GA
438325 -GGTATCGATACT
1 CGGTATCGATACT
438337 GTTGGGTTGC
Statistics
Matches: 125, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
44 123 0.98
45 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (44 bp):
CGGTATCGATACTACTTTACATAGTAGTATCGATACTCCTTGGA
Found at i:443862 original size:20 final size:20
Alignment explanation
Indices: 443837--443912 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
443827 TGTGCACTTG
*
443837 GTATCGATACTACTCATATT
1 GTATCGATACTACTCATATA
* *
443857 GTATCGATACTACTCTTGCTA
1 GTATCGATACTACTCAT-ATA
* *
443878 GGTATCGATACTACTAACATA
1 -GTATCGATACTACTCATATA
443899 GTATCGATACTACT
1 GTATCGATACTACT
443913 TGAATGAGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 30 0.64
21 3 0.06
22 14 0.30
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
GTATCGATACTACTCATATA
Found at i:446795 original size:44 final size:44
Alignment explanation
Indices: 446722--446839 Score: 152
Period size: 44 Copynumber: 2.7 Consensus size: 44
446712 TTCAAATATG
* * ** *
446722 GTATCGATAC-CATT-GACCGGTATCCATACTACTTTATATAGTA
1 GTATCGATACTCCTTGGA-CGGTATCGATACTACTACACATAGTA
446765 GTATCGATACTCCTTGGACGGTATCGATACTACTACACATAGTA
1 GTATCGATACTCCTTGGACGGTATCGATACTACTACACATAGTA
446809 GTATCGATACTCCTTGAGA-GGTATCGATACT
1 GTATCGATACTCCTTG-GACGGTATCGATACT
446840 TTTGGGTTGC
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
43 10 0.15
44 53 0.79
45 4 0.06
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
GTATCGATACTCCTTGGACGGTATCGATACTACTACACATAGTA
Found at i:446910 original size:21 final size:21
Alignment explanation
Indices: 446881--446937 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
446871 TATAACAGGT
*
446881 AGTATCGATACCCATGAGTGG
1 AGTACCGATACCCATGAGTGG
446902 AGTACCGATACCCATGAGTGG
1 AGTACCGATACCCATGAGTGG
446923 AGTACCGATACCCAT
1 AGTACCGATACCCAT
446938 ACGCTCCCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (21 bp):
AGTACCGATACCCATGAGTGG
Found at i:449491 original size:20 final size:20
Alignment explanation
Indices: 449466--449518 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
449456 ACGATGAACA
*
449466 GTATCGATACTGATA-TAGAG
1 GTATCGATACTGAGAGTA-AG
**
449486 GTATCGATACCAAGAGTAAG
1 GTATCGATACTGAGAGTAAG
449506 GTATCGATACTGA
1 GTATCGATACTGA
449519 AAGTGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (20 bp):
GTATCGATACTGAGAGTAAG
Found at i:450434 original size:24 final size:23
Alignment explanation
Indices: 450355--450457 Score: 125
Period size: 23 Copynumber: 4.4 Consensus size: 23
450345 AGTCAAGGGT
* * *
450355 TCTACGTGATCCTTTGGGAAAAA
1 TCTACGTGGTCCTTCGGGACAAA
*
450378 TCTATGTGGTCCTTCGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* * *
450401 CCTACGTGGTCCTTCGTGACATAT
1 TCTACGTGGTCCTTCGGGACA-AA
*
450425 TCTACGTGGTCCTTAGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
450448 TCTACGTGGT
1 TCTACGTGGT
450458 ACTTTAGTAC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
23 48 0.72
24 19 0.28
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAA
Found at i:450474 original size:47 final size:47
Alignment explanation
Indices: 450356--450475 Score: 127
Period size: 47 Copynumber: 2.6 Consensus size: 47
450346 GTCAAGGGTT
* * * * * *
450356 CTACGTGATCCTTTGGGA-AAAATCTATGTGGTCCTTCGGGACAAAC
1 CTACGTGGTCCTTAGTGACAAATTCTACGTGGTCCTTAGGGACAAAC
* * *
450402 CTACGTGGTCCTTCGTGACATATTCTACGTGGTCCTTAGGGACAAAT
1 CTACGTGGTCCTTAGTGACAAATTCTACGTGGTCCTTAGGGACAAAC
*
450449 CTACGTGGTACTTTAGT-ACAAATTCTA
1 CTACGTGGT-CCTTAGTGACAAATTCTA
450476 TATGGCACTT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
46 15 0.25
47 41 0.67
48 5 0.08
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (47 bp):
CTACGTGGTCCTTAGTGACAAATTCTACGTGGTCCTTAGGGACAAAC
Found at i:450475 original size:24 final size:24
Alignment explanation
Indices: 450354--450475 Score: 108
Period size: 23 Copynumber: 5.2 Consensus size: 24
450344 GAGTCAAGGG
* *
450354 TTCTACGTGATCCTTTGGGA-AAA
1 TTCTACGTGGTCCTTAGGGACAAA
* * *
450377 ATCTATGTGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTAGGGACAAA
* * * *
450401 -CCTACGTGGTCCTTCGTGACATA
1 TTCTACGTGGTCCTTAGGGACAAA
450424 TTCTACGTGGTCCTTAGGGACAAA
1 TTCTACGTGGTCCTTAGGGACAAA
* *
450448 -TCTACGTGGTACTTTA-GTACAAA
1 TTCTACGTGGT-CCTTAGGGACAAA
450471 TTCTA
1 TTCTA
450476 TATGGCACTT
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
23 51 0.63
24 30 0.37
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (24 bp):
TTCTACGTGGTCCTTAGGGACAAA
Found at i:461979 original size:21 final size:21
Alignment explanation
Indices: 461954--462012 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
461944 TCTACAAATA
*
461954 AAACCTAACACACTAAATATT
1 AAACCTAACCCACTAAATATT
461975 AAACCTAACCCACTAAATATT
1 AAACCTAACCCACTAAATATT
461996 AAACCTAACCCACTAAA
1 AAACCTAACCCACTAAA
462013 AATCCATGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACCTAACCCACTAAATATT
Found at i:464993 original size:79 final size:80
Alignment explanation
Indices: 464852--465066 Score: 308
Period size: 79 Copynumber: 2.7 Consensus size: 80
464842 CAGCAAAAAG
* * ** * *
464852 GGGAGCCAACCTAAGAATATACCTT-GGATCTACCCAAGGACATCCTTAGATCCGTAGGGTTACC
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
* *
464916 TTAAGCACACAGCTAA
65 TTAAGCACACAACAAA
*
464932 GGGAACCAACCTAAGGATATACCTTGGGGCCTA-CCGAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
*
464996 TATGCACACAACAAA
66 TAAGCACACAACAAA
*
465011 GGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTA
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTA
465067 ATGACTTACA
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
79 69 0.57
80 47 0.39
81 5 0.04
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.21
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TAAGCACACAACAAA
Found at i:468148 original size:22 final size:23
Alignment explanation
Indices: 468116--468164 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
468106 CCACATTCTA
468116 CAAATATTTAC-CAAACTAACACC
1 CAAATATTTACACAAA-TAACACC
*
468139 CAAAT-TTTACACAAATAGCACC
1 CAAATATTTACACAAATAACACC
468161 CAAA
1 CAAA
468165 CAGAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (23 bp):
CAAATATTTACACAAATAACACC
Found at i:470265 original size:80 final size:80
Alignment explanation
Indices: 470128--470343 Score: 317
Period size: 80 Copynumber: 2.7 Consensus size: 80
470118 CAGCAAAAAG
* ** * * *
470128 GGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGACATCTTTAGATCCGTAGGGTTACC
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
*
470192 TTAAGCACACAACTAA
65 TTAAGCACACAACAAA
* *
470208 GGGAACTAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCTGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
*
470273 TATGCACACAACAAA
66 TAAGCACACAACAAA
*
470288 GGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTA
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTA
470344 ATGACTTACA
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
80 112 0.92
81 10 0.08
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TAAGCACACAACAAA
Found at i:474193 original size:20 final size:20
Alignment explanation
Indices: 474164--474201 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
474154 CCCCTTCAAA
*
474164 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
474184 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
474202 TGTACCAAAA
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:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:480052 original size:22 final size:22
Alignment explanation
Indices: 480025--480080 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
480015 AAATAACTCA
480025 GGGGGGAATCGGTACCCCCTTG
1 GGGGGGAATCGGTACCCCCTTG
480047 GGGGGG-ATCGGTACCCCCTTG
1 GGGGGGAATCGGTACCCCCTTG
*
480068 GGAGGGAATCGGT
1 GGGGGGAATCGGT
480081 TCCCTCTAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCCCTTG
Found at i:481645 original size:18 final size:18
Alignment explanation
Indices: 481618--481664 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
481608 TTCATTCTAT
*
481618 CTTATTATTTAACTCCAA
1 CTTATCATTTAACTCCAA
481636 CTTATCATTTAACTCCAA
1 CTTATCATTTAACTCCAA
481654 CTTATCATTTA
1 CTTATCATTTA
481665 TTCCAGACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (18 bp):
CTTATCATTTAACTCCAA
Found at i:484857 original size:2 final size:2
Alignment explanation
Indices: 484850--484889 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
484840 AAAGAATGTA
484850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
484890 CTTATATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:486008 original size:23 final size:23
Alignment explanation
Indices: 485963--486028 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 23
485953 TAAATATTTT
*
485963 TTATTTTTATAATGTTAAAATATA
1 TTATTTTAATAAT-TTAAAATATA
*
485987 TTA-TTTAATTATTATAAAATATA
1 TTATTTTAATAATT-TAAAATATA
486010 TTATTTTAATAATTTAAAA
1 TTATTTTAATAATTTAAAA
486029 ATAATAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.03
23 24 0.65
24 12 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATTTTAATAATTTAAAATATA
Found at i:486057 original size:14 final size:15
Alignment explanation
Indices: 486040--486068 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
486030 TAATAAATGG
486040 TTAT-AAATATATTA
1 TTATAAAATATATTA
486054 TTATAAAATATATTA
1 TTATAAAATATATTA
486069 ATTTAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATAAAATATATTA
Found at i:494283 original size:28 final size:28
Alignment explanation
Indices: 494252--494311 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
494242 TAAATAAAAA
494252 TAAAAATAAAGATATGAACATTCATATC
1 TAAAAATAAAGATATGAACATTCATATC
* *** *
494280 TAAATATTGGGATATGAGCATTCATATC
1 TAAAAATAAAGATATGAACATTCATATC
494308 TAAA
1 TAAA
494312 TATTTTCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (28 bp):
TAAAAATAAAGATATGAACATTCATATC
Found at i:494312 original size:28 final size:28
Alignment explanation
Indices: 494262--494315 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
494252 TAAAAATAAA
494262 GATATGAACATTCATATCTAAATATTGG
1 GATATGAACATTCATATCTAAATATTGG
*
494290 GATATGAGCATTCATATCTAAATATT
1 GATATGAACATTCATATCTAAATATT
494316 TTCATTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (28 bp):
GATATGAACATTCATATCTAAATATTGG
Found at i:496540 original size:30 final size:30
Alignment explanation
Indices: 496506--496594 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 30
496496 ATAAATGAAT
496506 ATGAATAACTTCAAAAATAAATAAACAAAC
1 ATGAATAACTTCAAAAATAAATAAACAAAC
* *** * * *
496536 ATGAATACAATAGTAAAA-AATTAAATAAAT
1 ATGAATA-ACTTCAAAAATAAATAAACAAAC
*
496566 ATG-ATCACTTTCAAAAATAAATAAACAAA
1 ATGAATAAC-TTCAAAAATAAATAAACAAA
496595 AATAACCTTA
Statistics
Matches: 42, Mismatches: 14, Indels: 6
0.68 0.23 0.10
Matches are distributed among these distances:
28 1 0.02
29 7 0.17
30 28 0.67
31 6 0.14
ACGTcount: A:0.62, C:0.10, G:0.04, T:0.24
Consensus pattern (30 bp):
ATGAATAACTTCAAAAATAAATAAACAAAC
Found at i:502612 original size:31 final size:31
Alignment explanation
Indices: 502576--502636 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
502566 AAACTTAAAG
*
502576 TAGTTTTGTAATACTAAAATTTAAATAATTT
1 TAGTTTTATAATACTAAAATTTAAATAATTT
*
502607 TAGTTTTATAATATTAAAATTTAAATAATT
1 TAGTTTTATAATACTAAAATTTAAATAATT
502637 CATACAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (31 bp):
TAGTTTTATAATACTAAAATTTAAATAATTT
Found at i:502693 original size:22 final size:22
Alignment explanation
Indices: 502665--503180 Score: 721
Period size: 22 Copynumber: 23.4 Consensus size: 22
502655 ATTTTTTTAA
502665 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
502687 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
* *** *
502709 AAAATAATTTTTTTTCATATTTT
1 AAAATAA-ATCAATCCATATTTT
*
502732 AAAATAAATCAATCTATATTTT
1 AAAATAAATCAATCCATATTTT
502754 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
*
502776 AAAATAAATCAATTCATATTTT
1 AAAATAAATCAATCCATATTTT
502798 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
***
502820 AAAATAAATTTTTCCATATTTT
1 AAAATAAATCAATCCATATTTT
*
502842 AAAATAAATCAATCCATGTTTT
1 AAAATAAATCAATCCATATTTT
***
502864 AAAATAAATTTTTCCATATTTT
1 AAAATAAATCAATCCATATTTT
**
502886 AAAATAAAT-TTTCCCATATTTT
1 AAAATAAATCAAT-CCATATTTT
*
502908 AAAATAAATCAATCCATGTTTT
1 AAAATAAATCAATCCATATTTT
502930 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
502952 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
*** *
502974 AAAATAAATTTTTTCATATTTT
1 AAAATAAATCAATCCATATTTT
502996 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
503018 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
*
503040 AAAATAAATCAATCCATAATTT
1 AAAATAAATCAATCCATATTTT
** *
503062 AAAATAAAAT-TTTTCATATTTT
1 AAAAT-AAATCAATCCATATTTT
503084 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
*** *
503106 AAAATAAATTTTTCTATATTTT
1 AAAATAAATCAATCCATATTTT
*
503128 AAAATAAATCAATCTATATTTT
1 AAAATAAATCAATCCATATTTT
503150 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
503172 AAAATAAAT
1 AAAATAAAT
503181 TTTAAAATAG
Statistics
Matches: 436, Mismatches: 53, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
21 7 0.02
22 407 0.93
23 22 0.05
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATAAATCAATCCATATTTT
Found at i:503197 original size:11 final size:12
Alignment explanation
Indices: 503167--503206 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
503157 ATCAATCCAT
503167 ATTTTAAAATAA
1 ATTTTAAAATAA
*
503179 ATTTTAAAATAG
1 ATTTTAAAATAA
503191 A-TTT-AAA-AA
1 ATTTTAAAATAA
503200 ATTTTAA
1 ATTTTAA
503207 TTTCTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 2 0.08
10 6 0.25
11 4 0.17
12 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:511441 original size:23 final size:24
Alignment explanation
Indices: 511405--511450 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
511395 ATCATTAAAT
511405 TTATTATTTTAATT-TATATATTTG
1 TTATTATTTTAATTATA-ATATTTG
511429 TTATT-TTTTAATTATAATATTT
1 TTATTATTTTAATTATAATATTT
511451 TTAAGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTATTATTTTAATTATAATATTTG
Found at i:511459 original size:22 final size:23
Alignment explanation
Indices: 511411--511460 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
511401 AAATTTATTA
**
511411 TTTTAATTTATATATTTGTTATT
1 TTTTAATTTATATATTTGTTAAG
511434 TTTTAA-TTATAATATTT-TTAAG
1 TTTTAATTTAT-ATATTTGTTAAG
511456 TTTTA
1 TTTTA
511461 TTTTGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTTAATTTATATATTTGTTAAG
Found at i:511459 original size:23 final size:23
Alignment explanation
Indices: 511411--511459 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
511401 AAATTTATTA
*
511411 TTTTAATTTATATATTTGTTATT
1 TTTTAATTTATATATTTGTTAGT
511434 TTTTAA-TTATAATATTT-TTAAGT
1 TTTTAATTTAT-ATATTTGTT-AGT
511457 TTT
1 TTT
511460 ATTTTGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTAATTTATATATTTGTTAGT
Found at i:512691 original size:39 final size:40
Alignment explanation
Indices: 512648--512725 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
512638 ACATGGCTTA
*
512648 CACGT-GGGTATAGCG-CGCCCCTTGTTCCGCGCTATACGC
1 CACGTAGGGTATAGCGTCGCCCC-TGTTCAGCGCTATACGC
512687 CACGTAGGGGTATAGCGTCGCCCCTGTTCAGCGCTATAC
1 CACGTA-GGGTATAGCGTCGCCCCTGTTCAGCGCTATAC
512726 CTTGGTACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
39 5 0.14
41 24 0.69
42 6 0.17
ACGTcount: A:0.15, C:0.33, G:0.28, T:0.23
Consensus pattern (40 bp):
CACGTAGGGTATAGCGTCGCCCCTGTTCAGCGCTATACGC
Found at i:515271 original size:9 final size:9
Alignment explanation
Indices: 515257--515298 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
515247 ACTCCTCGCT
515257 GTCATCATC
1 GTCATCATC
*
515266 GTCATCGTC
1 GTCATCATC
515275 GTCATCATC
1 GTCATCATC
*
515284 GTCGTCATC
1 GTCATCATC
515293 GTCATC
1 GTCATC
515299 GTCCTGAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (9 bp):
GTCATCATC
Found at i:515284 original size:12 final size:12
Alignment explanation
Indices: 515267--515292 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
515257 GTCATCATCG
515267 TCATCGTCGTCA
1 TCATCGTCGTCA
515279 TCATCGTCGTCA
1 TCATCGTCGTCA
515291 TC
1 TC
515293 GTCATCGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.15, T:0.35
Consensus pattern (12 bp):
TCATCGTCGTCA
Found at i:517093 original size:17 final size:18
Alignment explanation
Indices: 517073--517113 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
517063 AAATTATATT
517073 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
517090 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
517108 ATTAAA
1 AGTAAA
517114 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:517401 original size:51 final size:50
Alignment explanation
Indices: 517295--517406 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 50
517285 GATAAACAAC
** * *
517295 TATAGCGCGGAACAAGGGGCGCGCTATACCCACGTGTAAGCCATGTTAGCG
1 TATAGCGCGGAACAAGGGGCGCGCTATACCCACGTG-AAGCCAAATCAGCA
* *
517346 TATAGCGCGGTACATA-GGGCGCGCTATACCCCACGT-AGCGCCAAATCAGCA
1 TATAGCGCGGAACA-AGGGGCGCGCTATA-CCCACGTGA-AGCCAAATCAGCA
517397 TATAGCGCGG
1 TATAGCGCGG
517407 GGAAGGGAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
50 1 0.02
51 43 0.83
52 8 0.15
ACGTcount: A:0.26, C:0.28, G:0.29, T:0.17
Consensus pattern (50 bp):
TATAGCGCGGAACAAGGGGCGCGCTATACCCACGTGAAGCCAAATCAGCA
Found at i:519849 original size:13 final size:15
Alignment explanation
Indices: 519831--519863 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
519821 TCATCCACCA
519831 TATTTTA-A-TTAGG
1 TATTTTAGATTTAGG
519844 TATTTTAGATTTAGG
1 TATTTTAGATTTAGG
519859 TATTT
1 TATTT
519864 AAGTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 1 0.06
15 10 0.56
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (15 bp):
TATTTTAGATTTAGG
Found at i:519929 original size:70 final size:67
Alignment explanation
Indices: 519853--520026 Score: 194
Period size: 70 Copynumber: 2.6 Consensus size: 67
519843 GTATTTTAGA
* * *
519853 TTTAGGTATTTAAGTTTAAATAGGTTTTATTA-TTTAATTAAG-TTTAGGAATTATTTTATATTT
1 TTTAGGTATTT-AGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAAATTATTTTA-A-AT
*
519916 ATCTTT
63 AT-TAT
* *
519922 GTTTAGGTTTTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAAATTATTTTAAATA
1 -TTTAGG-TATTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAAATTATTTTAAATA
519987 TTAT
64 TTAT
*
519991 TTTAGGTATTTAG-TTAAATA-GTTTTAAGTGTTTTAA
1 TTTAGGTATTTAGTTTAAATAGGTTTT-AGTATTTTAA
520027 CCCGGATTAA
Statistics
Matches: 92, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
65 5 0.05
66 16 0.17
67 6 0.07
68 6 0.07
69 2 0.02
70 28 0.30
71 14 0.15
72 15 0.16
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (67 bp):
TTTAGGTATTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAAATTATTTTAAATATT
AT
Found at i:519965 original size:19 final size:19
Alignment explanation
Indices: 519924--519971 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
519914 TTATCTTTGT
*
519924 TTAGGTTTT-TTAGTTTAA
1 TTAGGTTTTAGTAGTTTAA
* *
519942 ATAGGTTTTAGTATTTTAA
1 TTAGGTTTTAGTAGTTTAA
*
519961 TTAGGATTTAG
1 TTAGGTTTTAG
519972 AAATTATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (19 bp):
TTAGGTTTTAGTAGTTTAA
Found at i:520649 original size:18 final size:18
Alignment explanation
Indices: 520626--520668 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
520616 TCTTAGATTA
520626 TTTATTTAATTATTT-TCT
1 TTTATTTAATT-TTTATCT
520644 TTTATTTAATTTTTATCT
1 TTTATTTAATTTTTATCT
520662 TTTATTT
1 TTTATTT
520669 TAAAAACCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTTTTATCT
Found at i:528485 original size:16 final size:17
Alignment explanation
Indices: 528451--528493 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
528441 TTATATATGA
528451 TAAAAAATAAATGTCAT
1 TAAAAAATAAATGTCAT
*
528468 TAAAAAATAAAT-TTAT
1 TAAAAAATAAATGTCAT
528484 TAAAACAATA
1 TAAAA-AATA
528494 TGACTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAAAATAAATGTCAT
Found at i:529321 original size:29 final size:28
Alignment explanation
Indices: 529289--529344 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
529279 TAGCAAATAG
*
529289 ATTTATCAAATTATTATAATATTAATTAC
1 ATTTATCAAATTATTATAA-AATAATTAC
**
529318 ATTTATTGAATTATTATAAAATAATTA
1 ATTTATCAAATTATTATAAAATAATTA
529345 TTAAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (28 bp):
ATTTATCAAATTATTATAAAATAATTAC
Found at i:532648 original size:26 final size:26
Alignment explanation
Indices: 532619--532676 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
532609 TAATTCGAGG
532619 ACGAATTGAGGTAAAACATATGAATT
1 ACGAATTGAGGTAAAACATATGAATT
532645 ACGAATTGAGGTAAAACATATGAATT
1 ACGAATTGAGGTAAAACATATGAATT
532671 ACGAAT
1 ACGAAT
532677 AGAGCATCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (26 bp):
ACGAATTGAGGTAAAACATATGAATT
Found at i:534123 original size:26 final size:26
Alignment explanation
Indices: 534087--534139 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
534077 ACTGTCTGAC
*
534087 GTGGCAGTTTCTAGAAGGTCCAGTCA
1 GTGGCAGTTTCTAGAAGATCCAGTCA
*
534113 GTGGCAGTTTCTAGAAGATCTAGTCA
1 GTGGCAGTTTCTAGAAGATCCAGTCA
534139 G
1 G
534140 CGCGCATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (26 bp):
GTGGCAGTTTCTAGAAGATCCAGTCA
Found at i:544332 original size:26 final size:25
Alignment explanation
Indices: 544297--544345 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
544287 ATGATGTGGC
544297 AGTTTTAGAA-AGTCCAGTCAGCGGT
1 AGTTTTAGAAGA-TCCAGTCAGCGGT
*
544322 AGTTTCTAGAAGATCTAGTCAGCG
1 AGTTT-TAGAAGATCCAGTCAGCG
544346 CTCTTTCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 15 0.71
27 1 0.05
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (25 bp):
AGTTTTAGAAGATCCAGTCAGCGGT
Found at i:545224 original size:20 final size:19
Alignment explanation
Indices: 545195--545242 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
545185 ATCTTTATTT
*
545195 TCTTTATTATTCCTTTAAAT-
1 TCTTT-TTATTAC-TTAAATA
545215 TGCTTTTTATTACTTAAATA
1 T-CTTTTTATTACTTAAATA
545235 TCTTTTTA
1 TCTTTTTA
545243 CCAAAACCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 13 0.52
20 8 0.32
21 4 0.16
ACGTcount: A:0.25, C:0.12, G:0.02, T:0.60
Consensus pattern (19 bp):
TCTTTTTATTACTTAAATA
Found at i:548373 original size:23 final size:23
Alignment explanation
Indices: 548330--548374 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
548320 AGATTGGATA
*
548330 TTCTAGAAGCTACTGACTGGGCC
1 TTCTAGAAGCTACTGAATGGGCC
**
548353 TTCTAGAAGCTGTTGAATGGGC
1 TTCTAGAAGCTACTGAATGGGC
548375 GCCATGTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (23 bp):
TTCTAGAAGCTACTGAATGGGCC
Found at i:554152 original size:2 final size:2
Alignment explanation
Indices: 554147--554176 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
554137 AATAACTAAT
554147 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
554177 AGACCAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:554674 original size:32 final size:32
Alignment explanation
Indices: 554615--554690 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
554605 AGATTTATCA
* *
554615 AATTATTATAAATTATTAATTACATTTTATTG
1 AATTATTATAAATTAATAATTAAATTTTATTG
* **
554647 AATTATTATAGAA-TAATCATTAAATTTTATCA
1 AATTATTATA-AATTAATAATTAAATTTTATTG
*
554679 AAATATTATAAA
1 AATTATTATAAA
554691 AGTCTCATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 2 0.05
32 33 0.89
33 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (32 bp):
AATTATTATAAATTAATAATTAAATTTTATTG
Found at i:559097 original size:214 final size:214
Alignment explanation
Indices: 558855--559420 Score: 877
Period size: 214 Copynumber: 2.6 Consensus size: 214
558845 TTTTAAAAAA
*
558855 TGTGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACTTCATTTTCC
1 TGTGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTCC
* *
558920 ATTTTCAAATTCATTTGAAAACATCTTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCAT
66 ATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCAT
* * * * *
558985 CTTGCTCTAATGGCTTACAGATGACCCAAAGGATTTAAGCATTATGCTCGAGAGACTTACTGATG
131 CATGCTCTAAAGGCTTACAGATGACCCAAAGGATTTAAACATCATGCTCGAAAGACTTACTGATG
559050 GCCCGAAGGACTTATAAAT
196 GCCCGAAGGACTTATAAAT
* *
559069 TGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAA-TTCATCTTCTTAAAACAT-AATTTCC
1 TGTGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTCC
* *
559132 TTATCTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCTGAAGGACTTATC
66 --ATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATC
** *
559197 ATCATGCTCTAAAGGCTTACAGATGACCCGGAGGATTTAAACATCATGCTTGAAAGACTTACTGA
129 ATCATGCTCTAAAGGCTTACAGATGACCCAAAGGATTTAAACATCATGCTCGAAAGACTTACTGA
*
559262 TGGCCCGGAGGACTTATAAAT
194 TGGCCCGAAGGACTTATAAAT
* * *
559283 TGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTC
1 TGTGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTCC
* * *
559348 ATTTTCAATTTC-TTGTGAAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGATTTAATC
66 ATTTTCAAATTCATT-TGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTT-ATC
559412 ATCATGCTC
129 ATCATGCTC
559421 GGAAGACTTA
Statistics
Matches: 320, Mismatches: 26, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
212 6 0.02
213 19 0.06
214 261 0.82
215 29 0.09
216 5 0.02
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (214 bp):
TGTGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTCC
ATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCAT
CATGCTCTAAAGGCTTACAGATGACCCAAAGGATTTAAACATCATGCTCGAAAGACTTACTGATG
GCCCGAAGGACTTATAAAT
Found at i:559613 original size:116 final size:116
Alignment explanation
Indices: 559401--560438 Score: 1819
Period size: 116 Copynumber: 9.0 Consensus size: 116
559391 GATGACCCGA
* *
559401 AGGATTTAATCATCATGCTCGGAAGACTTACTGATGGATTTGCTTCACTACTCT-TCGGTGAAGG
1 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCT-GGTGAAGG
* *
559465 CTTAAAATTGATTTGCTTCACTATTCTTAGGTGAAGGCTTAAGATTGCCCTG
65 CTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
* *
559517 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGATTTACTACTCTCTGGTGAAGGC
1 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCTGGTGAAGGC
559582 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
66 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
*
559633 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCCGGTGAAGGC
1 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCTGGTGAAGGC
559698 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
66 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
*
559749 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCCGGTGAAGGC
1 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCTGGTGAAGGC
*
559814 TTAAGATTGATTTGATTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
66 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
*
559865 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTTTGGTGAAGGC
1 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCTGGTGAAGGC
*
559930 TTAAAATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
66 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
*
559981 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTTTGGTGAAGGC
1 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCTGGTGAAGGC
* *
560046 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAAATTACCCTG
66 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
*
560097 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCCGGTGAAGGC
1 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCTGGTGAAGGC
* *
560162 TTAAGATTGATTTGCTTCAATATTCTCAGGTGAAGGGTTAAGATTGCCCTG
66 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
* *
560213 AGGACTTAATCATCATGCTCGGAAGGCTTACCGATGGATTTGCTTCACTACTCTTTGGTGAAGGC
1 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCTGGTGAAGGC
* *
560278 TTAAAATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTTCCCTG
66 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
* *
560329 AGGACTTAATTATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTTTGGTGAAGGC
1 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCTGGTGAAGGC
* * *
560394 TTAAAATAG-TTTGCTTCACTATTCTCAAGTGAAGGCTTAAGATTG
66 TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTG
560439 ATTGCTTCAC
Statistics
Matches: 886, Mismatches: 35, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
115 34 0.04
116 851 0.96
117 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (116 bp):
AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTCTGGTGAAGGC
TTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG
Found at i:560414 original size:36 final size:36
Alignment explanation
Indices: 560367--560469 Score: 134
Period size: 36 Copynumber: 2.9 Consensus size: 36
560357 TACTGATGGA
*
560367 TTTGCTTCACTACTCTTTGGTGAAGGCTTAAAATAG
1 TTTGCTTCACTACTCTTAGGTGAAGGCTTAAAATAG
* * * * *
560403 TTTGCTTCACTATTCTCAAGTGAAGGCTTAAGATTG
1 TTTGCTTCACTACTCTTAGGTGAAGGCTTAAAATAG
* *
560439 ATTGCTTCACTACTCTTCGGTGAAGGCTTAA
1 TTTGCTTCACTACTCTTAGGTGAAGGCTTAA
560470 GATTGACTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (36 bp):
TTTGCTTCACTACTCTTAGGTGAAGGCTTAAAATAG
Found at i:563074 original size:12 final size:11
Alignment explanation
Indices: 563054--563094 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
563044 TAGTTTCAAT
563054 TTTTTCTTTTC
1 TTTTTCTTTTC
563065 TTTCTTCTTTTC
1 TTT-TTCTTTTC
*
563077 TTTTCCTTTTC
1 TTTTTCTTTTC
*
563088 TCTTTCT
1 TTTTTCT
563095 ACATTTCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:563075 original size:17 final size:16
Alignment explanation
Indices: 563055--563094 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
563045 AGTTTCAATT
*
563055 TTTTCTTTTCTTTCTTC
1 TTTTCTTTTCCTT-TTC
563072 TTTTCTTTTCCTTTTC
1 TTTTCTTTTCCTTTTC
563088 TCTTTCT
1 T-TTTCT
563095 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTCTTTTCCTTTTC
Found at i:563101 original size:25 final size:23
Alignment explanation
Indices: 563057--563114 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 23
563047 TTTCAATTTT
* * *
563057 TTCTTT-TCTTTCTTCTTTTCTT
1 TTCTTTCTCTTTCTACATTTCTC
563079 TTCCTTTTCTCTTTCTACATTTCTC
1 TT-C-TTTCTCTTTCTACATTTCTC
563104 TTCTTTCTCTT
1 TTCTTTCTCTT
563115 AATGATGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.07
23 9 0.30
24 4 0.13
25 15 0.50
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (23 bp):
TTCTTTCTCTTTCTACATTTCTC
Found at i:565404 original size:6 final size:6
Alignment explanation
Indices: 565387--565425 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
565377 TTAAACAAAT
565387 AAATGC -AATGC AAATGC AAATGC TAAATGC AAATGC AAA
1 AAATGC AAATGC AAATGC AAATGC -AAATGC AAATGC AAA
565426 AGGTGTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
7 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (6 bp):
AAATGC
Found at i:565416 original size:13 final size:13
Alignment explanation
Indices: 565386--565422 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
565376 CTTAAACAAA
565386 TAAATGC-AATGC
1 TAAATGCAAATGC
565398 -AAATGCAAATGC
1 TAAATGCAAATGC
565410 TAAATGCAAATGC
1 TAAATGCAAATGC
565423 AAAAGGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.26
12 5 0.22
13 12 0.52
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (13 bp):
TAAATGCAAATGC
Found at i:565698 original size:22 final size:22
Alignment explanation
Indices: 565673--565723 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
565663 ACTCTCCATA
*
565673 TCTTTGGTGAATGGTCTTCTCG
1 TCTTTGGTGAACGGTCTTCTCG
*
565695 TCTTT-ATGAACGGTCTTCTCG
1 TCTTTGGTGAACGGTCTTCTCG
*
565716 TCCTTGGT
1 TCTTTGGT
565724 ATGATTGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.45
Consensus pattern (22 bp):
TCTTTGGTGAACGGTCTTCTCG
Found at i:571234 original size:32 final size:32
Alignment explanation
Indices: 571198--571274 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
571188 TATTAATGAC
** * *
571198 ATTTTATTGAATTATTATAGAATAATCATTAA
1 ATTTTATCAAATTATTACAAAATAATCATTAA
**
571230 ATTTTATCAAATTATTACAAAATTTTCATTAA
1 ATTTTATCAAATTATTACAAAATAATCATTAA
*
571262 A-TTTATCATATTA
1 ATTTTATCAAATTA
571275 AAAACTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 11 0.29
32 27 0.71
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (32 bp):
ATTTTATCAAATTATTACAAAATAATCATTAA
Found at i:572170 original size:32 final size:31
Alignment explanation
Indices: 572075--572176 Score: 80
Period size: 32 Copynumber: 3.2 Consensus size: 31
572065 AAACAACCAA
* *
572075 TACA-TTTATCAAATTATTATAAATTATTAAT
1 TACATTTTATCAAATTATTAAAAATT-TTCAT
* ** * * **
572106 TACAATTTATTGAATTGTTATAGAATAATCAT
1 TACATTTTATCAAATTATTA-AAAATTTTCAT
572138 TACATTTTATCAAATTATTACAAAATTTTCAT
1 TACATTTTATCAAATTATTA-AAAATTTTCAT
*
572170 TAAATTT
1 TACATTT
572177 GTCATATTAA
Statistics
Matches: 52, Mismatches: 17, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
31 4 0.08
32 45 0.87
33 3 0.06
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (31 bp):
TACATTTTATCAAATTATTAAAAATTTTCAT
Found at i:572567 original size:915 final size:910
Alignment explanation
Indices: 570783--572595 Score: 2687
Period size: 915 Copynumber: 2.0 Consensus size: 910
570773 AACTTAATCT
* *
570783 AAATTACGAAAGAAAATAAAAGAGAGGAAAGCTTACCAATATGACTTGGGATCGATGTTACAAAA
1 AAATTACGAAAGAAAAGAAAAGAGAGGAAAGCTGACCAATATGACTTGGGATCGATGTTACAAAA
* * * *
570848 ATTGGCGTAAGAAAAACCCACTCATTCCAACTAGAAGAGAAAAAATGCCTTTTTTTTATTTAATC
66 ATTGGCGAAAGAAAAACCCACTCATTCCAACTAGAAGAGAAAAAATGCCTTGTATTGATTTAATC
*** *
570913 GAAGAGAATTGTTGTAATTCACCTTTCAAAGAAGACGAGGAAAAAGACCCTTGTGAGTTTCTGTT
131 GAAGAGAATTGTTGTAATTCACCAAGCAAAGAAAACGAGGAAAAAGACCCTTGTGAGTTTCTGTT
* * *
570978 TTGGAGTTTGATCCTTATAAAGCACAACAATTAATGTTAGTTTTGAAAATATCTTCTCCTTTACT
196 TTGGAGTTTGATCCTTATAAAGCACAACAATTAATGTTAGTTTTAAAAATATATTCTCCTTCACT
* *
571043 CCTAAAGTTTCAATGTCATTGGTTTACAATTTAAAACGATGGGTAAAGTAAATCAGAGGATTGAA
261 CCTAAAGTTTCAATGCCATTGGTTTACAATTTAAAACGATGGGTAAAGTAAATCAGAGCATTGAA
* *
571108 CTATGTTTAAACAAATGTTTTGGTCATTCAATTTTTTACAGATACAAAACAACCAATAGATTCAT
326 CTATGTTTAAACAAATGTTTTGGTCATTCAATTTTATACAGATACAAAACAACCAATACATTCAT
*
571173 CAAAATATTATAAATTATTAATGACATTTTATTGAATTATTATAGAATAATCATTAAATTTTATC
391 CAAAATATTATAAATTATTAATGACAATTTATTGAATTATTATAGAATAATCATTAAATTTTATC
571238 AAATTATTACAAAATTTTCATTAAATTTATCATATTAAAAACTTTATATAATACCACAATGATTA
456 AAATTATTACAAAATTTTCATTAAATTTATCATATTAAAAACTTTATATAATACCACAATGATTA
* *
571303 TTAAAAAATTGTCACTAAATAAATTTTTATTAAAATTTTAAAAGAGAGCCATGATTTTTTATTTA
521 TTAAAAAAATGTCACTAAATAAATTGTTATTAAAATTTTAAAAGAGAGCCATGATTTTTTATTTA
* * *
571368 AAAAAAGAAACATTAATTCTCTATGAGTGTCATTCCACTAGAGGAGTTGTAGGTCTAGACTCAGT
586 AAAAAAGAAACATTAATGCTCTATGAGTGCCATTCCACTAGAGGAGTTGTAGGTCCAGACTCAGT
* * * *
571433 GTAGTTAATTGTGTGATAATAGTTAACAGGTCTTCGCCTCTCTGACCACCCCACCATGCTGATTC
651 GCAATTAATTGTGTGATAACAGTTAACAGGTCTTCGCCTCTCTGACCACCCCACCATCCTGATTC
* * * ** *
571498 CCGTACATGCCATCAAATAATAAGAAGGAGCGGCGACTACTCTTTGGAAACTATAAGATATCTGT
716 CCGCACATGCCATCAAACAATAAGAAGAAGCAACGACTACTCTTTGAAAACTATAAGATATCTGT
*
571563 AATAATATATTTTGTCTAACTATTTGAGCTTTACCAGTAATAAAGTTTAGGATCAAATTTGGGTC
781 AATAATATATTTTGTCTAACTATTTGAACTTTACCAGTAATAAAGTTTAGGATCAAATTTGGGTC
* * *
571628 ATCATCTTTAGATCTCGAATCAAATAGATCAATTCAGATAATCATATTTGAATCAATTTCGATCC
846 ATCATCTTCAGATCTCGAATCAAATAGATCAATTCAAATAATAATATTTGAATCAATTTCGATCC
* *
571693 AAATTACGAAAGAAAAGAAAAGAGAGGATAA-CTGACCAGA-ATTA-TTGGGGATCGATGTTGCA
1 AAATTACGAAAGAAAAGAAAAGAGAGGA-AAGCTGACCA-ATATGACTT-GGGATCGATGTTACA
*
571755 AAAATTGGCGAAAGAAAAACCCATTCATTCCAACTAGAAGA-AAAAAATTG-CTTGTATTGATTT
63 AAAATTGGCGAAAGAAAAACCCACTCATTCCAACTAGAAGAGAAAAAA-TGCCTTGTATTGATTT
* * * *
571818 AATCGAATAGAATTTTTGTAATTCACCAAGCAAAGAAAATGAGGAAAAAGACCCTTGTGAGTTTT
127 AATCGAAGAGAATTGTTGTAATTCACCAAGCAAAGAAAACGAGGAAAAAGACCCTTGTGAGTTTC
*
571883 TGTTTTGGAGTTTGATCCTTATAAAGTACAACAATTAATGTTAGGTTTTAAAAATATATTCTCCT
192 TGTTTTGGAGTTTGATCCTTATAAAGCACAACAATTAATGTTA-GTTTTAAAAATATATTCTCCT
* *
571948 TCACTCCTAAGGTTTCAATGCCATTGGTTTACAATTTAAAATGATGGGTAAAGTAAATCAGAGCA
256 TCACTCCTAAAGTTTCAATGCCATTGGTTTACAATTTAAAACGATGGGTAAAGTAAATCAGAG--
* *
572013 CATTTAACTATGTTTAAACAAATGTTTTGTTCATTCAATTTTATA-ATG-TACAAAACAACCAAT
319 CATTGAACTATGTTTAAACAAATGTTTTGGTCATTCAATTTTATACA-GATACAAAACAACCAAT
* * * * *
572076 ACATTTATCAAATTATTATAAATTATTAATTACAATTTATTGAATTGTTATAGAATAATCATTAC
383 ACATTCATCAAAATATTATAAATTATTAATGACAATTTATTGAATTATTATAGAATAATCATTAA
* ** *
572141 ATTTTATCAAATTATTACAAAATTTTCATTAAATTTGTCATATTAAAGGCTTTATATAATACCAT
448 ATTTTATCAAATTATTACAAAATTTTCATTAAATTTATCATATTAAAAACTTTATATAATACCAC
* *
572206 AATGATTATTAAAAACAAT-TCAGTAAATAAATTGTTATTTAAAA-TTTCAAAGAGAGCCATGAT
513 AATGATTATTAAAAA-AATGTCACTAAATAAATTGTTA-TTAAAATTTTAAAAGAGAGCCATGAT
* * *
572269 TTTTTATACTTAAAAAAAAAGAAATATTAATGCTTTATGAGTGCCATTCCGCTAGAGGAGTTGTA
576 TTTTTAT--TT--AAAAAAAGAAACATTAATGCTCTATGAGTGCCATTCCACTAGAGGAGTTGTA
** * *
572334 GGTCCAGACTGGGTGCAATTAATTGTGTGCTAACAGTTATCAGGTCCTT-GCCTCT-TAGACCAC
637 GGTCCAGACTCAGTGCAATTAATTGTGTGATAACAGTTAACAGGT-CTTCGCCTCTCT-GACCAC
* ** * *
572397 CCGACCATCCTGATTCTTGCACATGCCATCCAACAATAAGAAGAAGCAACGACTA-TTTTTAGAA
700 CCCACCATCCTGATTCCCGCACATGCCATCAAACAATAAGAAGAAGCAACGACTACTCTTT-GAA
* ** *
572461 AACTCTAAGATATCTGTAATAATATATTTTGTCTAACTATTTGAACTTTACTTGTAATCAAGTTT
764 AACTATAAGATATCTGTAATAATATATTTTGTCTAACTATTTGAACTTTACCAGTAATAAAGTTT
* *
572526 AGGATCAAATTTGGGTCATCATCTTCATATCTGGAATCAAATAGATCAATTCAAATAATAATATT
829 AGGATCAAATTTGGGTCATCATCTTCAGATCTCGAATCAAATAGATCAATTCAAATAATAATATT
572591 TGAAT
894 TGAAT
572596 TAAATTTGTC
Statistics
Matches: 808, Mismatches: 78, Indels: 29
0.88 0.09 0.03
Matches are distributed among these distances:
909 117 0.14
910 169 0.21
911 194 0.24
912 50 0.06
913 2 0.00
914 5 0.01
915 268 0.33
916 3 0.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (910 bp):
AAATTACGAAAGAAAAGAAAAGAGAGGAAAGCTGACCAATATGACTTGGGATCGATGTTACAAAA
ATTGGCGAAAGAAAAACCCACTCATTCCAACTAGAAGAGAAAAAATGCCTTGTATTGATTTAATC
GAAGAGAATTGTTGTAATTCACCAAGCAAAGAAAACGAGGAAAAAGACCCTTGTGAGTTTCTGTT
TTGGAGTTTGATCCTTATAAAGCACAACAATTAATGTTAGTTTTAAAAATATATTCTCCTTCACT
CCTAAAGTTTCAATGCCATTGGTTTACAATTTAAAACGATGGGTAAAGTAAATCAGAGCATTGAA
CTATGTTTAAACAAATGTTTTGGTCATTCAATTTTATACAGATACAAAACAACCAATACATTCAT
CAAAATATTATAAATTATTAATGACAATTTATTGAATTATTATAGAATAATCATTAAATTTTATC
AAATTATTACAAAATTTTCATTAAATTTATCATATTAAAAACTTTATATAATACCACAATGATTA
TTAAAAAAATGTCACTAAATAAATTGTTATTAAAATTTTAAAAGAGAGCCATGATTTTTTATTTA
AAAAAAGAAACATTAATGCTCTATGAGTGCCATTCCACTAGAGGAGTTGTAGGTCCAGACTCAGT
GCAATTAATTGTGTGATAACAGTTAACAGGTCTTCGCCTCTCTGACCACCCCACCATCCTGATTC
CCGCACATGCCATCAAACAATAAGAAGAAGCAACGACTACTCTTTGAAAACTATAAGATATCTGT
AATAATATATTTTGTCTAACTATTTGAACTTTACCAGTAATAAAGTTTAGGATCAAATTTGGGTC
ATCATCTTCAGATCTCGAATCAAATAGATCAATTCAAATAATAATATTTGAATCAATTTCGATCC
Found at i:574259 original size:15 final size:14
Alignment explanation
Indices: 574239--574269 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
574229 TATTTAAGAC
574239 CTAGTCAATTTAGAG
1 CTAGTCAATTTA-AG
574254 CTAGTCAATTTAAG
1 CTAGTCAATTTAAG
574268 CT
1 CT
574270 CTACAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (14 bp):
CTAGTCAATTTAAG
Found at i:579286 original size:24 final size:24
Alignment explanation
Indices: 579259--579309 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
579249 TCTGATTTCC
579259 GTTCTAATTTCTAATATGGATTAT
1 GTTCTAATTTCTAATATGGATTAT
* * *
579283 GTTCTGATTTCTTATATGGATTTT
1 GTTCTAATTTCTAATATGGATTAT
579307 GTT
1 GTT
579310 ATGATATCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.55
Consensus pattern (24 bp):
GTTCTAATTTCTAATATGGATTAT
Found at i:579314 original size:24 final size:24
Alignment explanation
Indices: 579265--579347 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 24
579255 TTCCGTTCTA
* *
579265 ATTTCTAATATGGATTATGTTCTG
1 ATTTCTGATATGGATTATGTTATG
* *
579289 ATTTCTTATATGGATTTTGTTATG
1 ATTTCTGATATGGATTATGTTATG
* * * *
579313 ATATCTGATATGAATTCTGTTTTG
1 ATTTCTGATATGGATTATGTTATG
579337 ATTTCTGATAT
1 ATTTCTGATAT
579348 CTCTGTTTAC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.53
Consensus pattern (24 bp):
ATTTCTGATATGGATTATGTTATG
Found at i:584603 original size:20 final size:19
Alignment explanation
Indices: 584555--584604 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
584545 ACCCAGTTTT
* *
584555 GACCCTACCCGTTTGACCT
1 GACCCAACCCGTTTGACCC
**
584574 GACCTGACCCAGTTTGACCC
1 GACCCAACCC-GTTTGACCC
584594 GACCCAACCCG
1 GACCCAACCCG
584605 ACCCGTTAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.20, C:0.44, G:0.18, T:0.18
Consensus pattern (19 bp):
GACCCAACCCGTTTGACCC
Found at i:587007 original size:12 final size:13
Alignment explanation
Indices: 586986--587028 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
586976 CCGATTTGAA
586986 TTTTATTCTGATT
1 TTTTATTCTGATT
*
586999 TTTTA-TCTGA-A
1 TTTTATTCTGATT
587010 TTTTATTCTGATT
1 TTTTATTCTGATT
*
587023 TCTTAT
1 TTTTAT
587029 ATGGACTCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 5 0.20
12 10 0.40
13 10 0.40
ACGTcount: A:0.19, C:0.09, G:0.07, T:0.65
Consensus pattern (13 bp):
TTTTATTCTGATT
Found at i:587023 original size:11 final size:11
Alignment explanation
Indices: 586985--587023 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
586975 TCCGATTTGA
586985 ATTTTATTCTG
1 ATTTTATTCTG
*
586996 ATTTTTTATCTG
1 ATTTTAT-TCTG
587008 AATTTTATTCTG
1 -ATTTTATTCTG
587020 ATTT
1 ATTT
587024 CTTATATGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.64
Consensus pattern (11 bp):
ATTTTATTCTG
Found at i:587028 original size:24 final size:24
Alignment explanation
Indices: 586963--587076 Score: 95
Period size: 24 Copynumber: 4.8 Consensus size: 24
586953 TATATGAATG
** *
586963 TTTTA-TCTGATTTCCGATTTGAA
1 TTTTATTCTGATTTCTTATCTGAA
*
586986 TTTTATTCTGATTTTTTATCTGAA
1 TTTTATTCTGATTTCTTATCTGAA
* *
587010 TTTTATTCTGATTTCTTATATGGA
1 TTTTATTCTGATTTCTTATCTGAA
* * * * *
587034 CTCTGTTCTGATATCTGATCTGAA
1 TTTTATTCTGATTTCTTATCTGAA
* * *
587058 TTCTGTTTTGATTTCTTAT
1 TTTTATTCTGATTTCTTAT
587077 ATCTCCGTTT
Statistics
Matches: 72, Mismatches: 18, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
23 5 0.07
24 67 0.93
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (24 bp):
TTTTATTCTGATTTCTTATCTGAA
Found at i:589594 original size:12 final size:12
Alignment explanation
Indices: 589577--589605 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
589567 TCTGGAATGG
589577 GTGTTGTTAATT
1 GTGTTGTTAATT
589589 GTGTTGTTAATT
1 GTGTTGTTAATT
589601 GTGTT
1 GTGTT
589606 CTGACAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.59
Consensus pattern (12 bp):
GTGTTGTTAATT
Found at i:592351 original size:32 final size:31
Alignment explanation
Indices: 592259--592361 Score: 93
Period size: 32 Copynumber: 3.3 Consensus size: 31
592249 CAACCAATAC
*
592259 ATTTATCAAATTA-TA-ATAAATTATTAATTAAA
1 ATTTATCAAATTATTACA-AAATT-TTCATT-AA
** * **
592291 ATTTATTGAATTGTTACAAAATAATCATTAA
1 ATTTATCAAATTATTACAAAATTTTCATTAA
*
592322 ATTTTATCAAATTATTACAAAATTTTCATTAT
1 A-TTTATCAAATTATTACAAAATTTTCATTAA
592354 ATTTATCA
1 ATTTATCA
592362 TAGTAACGAC
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
31 10 0.18
32 39 0.70
33 6 0.11
34 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (31 bp):
ATTTATCAAATTATTACAAAATTTTCATTAA
Found at i:593839 original size:31 final size:31
Alignment explanation
Indices: 593804--593904 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 31
593794 TAACCAATAT
*
593804 ATTTATCAAATTATATA-AATTATTAATTACA
1 ATTTATCAAATTATATACAATTATTCATTA-A
* * * * *
593835 ATTTATGAATTTTTATAGAA-TAATCATTAA
1 ATTTATCAAATTATATACAATTATTCATTAA
*
593865 ATTTTATCAAATTAT-TACAATTTTTTCATTAA
1 A-TTTATCAAATTATATACAA-TTATTCATTAA
593897 ATTTATCA
1 ATTTATCA
593905 TACCATAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
30 6 0.11
31 38 0.69
32 11 0.20
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.49
Consensus pattern (31 bp):
ATTTATCAAATTATATACAATTATTCATTAA
Found at i:595240 original size:32 final size:31
Alignment explanation
Indices: 595159--595266 Score: 81
Period size: 32 Copynumber: 3.4 Consensus size: 31
595149 CAACCAATAC
* * * * *
595159 ATTTATCAAAATATTATAAATTATTAATTACA
1 ATTTATCAAATTATTACAAAATAATCATTA-A
** * *
595191 ATTTATTGAATTCTTACAGAATAATCATTAA
1 ATTTATCAAATTATTACAAAATAATCATTAA
** *
595222 ATTTTATCAAATTATTACAAAATTGTCTTTAA
1 A-TTTATCAAATTATTACAAAATAATCATTAA
*
595254 ATTTATCATATTA
1 ATTTATCAAATTA
595267 AAGACTTTAT
Statistics
Matches: 58, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
31 13 0.22
32 45 0.78
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (31 bp):
ATTTATCAAATTATTACAAAATAATCATTAA
Found at i:598138 original size:21 final size:21
Alignment explanation
Indices: 598114--598204 Score: 55
Period size: 21 Copynumber: 4.4 Consensus size: 21
598104 AAAATAACCA
598114 AAATATTTATCAAATTATTAT
1 AAATATTTATCAAATTATTAT
* * *
598135 AAATTATTAATTAAAAT-TTAT
1 AAA-TATTTATCAAATTATTAT
* * * *
598156 GAATTTTTAT-AGAATAATCATT
1 AAATATTTATCA-AATTATTA-T
*
598178 AAAT-TTTATCAAATTATTAC
1 AAATATTTATCAAATTATTAT
598198 AAA-ATTT
1 AAATATTT
598205 TCATTAAATT
Statistics
Matches: 51, Mismatches: 13, Indels: 13
0.66 0.17 0.17
Matches are distributed among these distances:
19 1 0.02
20 13 0.25
21 22 0.43
22 15 0.29
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
AAATATTTATCAAATTATTAT
Found at i:598692 original size:15 final size:14
Alignment explanation
Indices: 598672--598701 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
598662 ATTTGAGACG
598672 TAGTCAATTTAGAGC
1 TAGTCAATTTA-AGC
598687 TAGTCAATTTAAGC
1 TAGTCAATTTAAGC
598701 T
1 T
598702 CCAAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (14 bp):
TAGTCAATTTAAGC
Found at i:600228 original size:15 final size:14
Alignment explanation
Indices: 600208--600238 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
600198 CATTTAAGAT
600208 CTAGTCAATTTAGAG
1 CTAGTCAATTTA-AG
600223 CTAGTCAATTTAAG
1 CTAGTCAATTTAAG
600237 CT
1 CT
600239 CTAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (14 bp):
CTAGTCAATTTAAG
Found at i:604346 original size:15 final size:14
Alignment explanation
Indices: 604326--604356 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
604316 CATTTAAGAT
604326 CTAGTCAATTTAGAG
1 CTAGTCAATTTA-AG
604341 CTAGTCAATTTAAG
1 CTAGTCAATTTAAG
604355 CT
1 CT
604357 CTAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (14 bp):
CTAGTCAATTTAAG
Found at i:605831 original size:15 final size:14
Alignment explanation
Indices: 605811--605841 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
605801 CCTTTAAGAT
605811 CTAGTCAATTTAGAG
1 CTAGTCAATTTA-AG
605826 CTAGTCAATTTAAG
1 CTAGTCAATTTAAG
605840 CT
1 CT
605842 CTAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (14 bp):
CTAGTCAATTTAAG
Found at i:609761 original size:15 final size:14
Alignment explanation
Indices: 609741--609771 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
609731 CATTTAAGAT
609741 CTAGTCAATTTAGAG
1 CTAGTCAATTTA-AG
609756 CTAGTCAATTTAAG
1 CTAGTCAATTTAAG
609770 CT
1 CT
609772 CTAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (14 bp):
CTAGTCAATTTAAG
Found at i:612399 original size:15 final size:14
Alignment explanation
Indices: 612379--612409 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
612369 CATTTGAGAC
612379 CTAGTCAATTTAGAG
1 CTAGTCAATTTA-AG
612394 CTAGTCAATTTAAG
1 CTAGTCAATTTAAG
612408 CT
1 CT
612410 CCACAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (14 bp):
CTAGTCAATTTAAG
Found at i:613938 original size:15 final size:14
Alignment explanation
Indices: 613918--613948 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
613908 CATTTAAGAT
613918 CTAGTCAATTTAGAG
1 CTAGTCAATTTA-AG
613933 CTAGTCAATTTAAG
1 CTAGTCAATTTAAG
613947 CT
1 CT
613949 CTAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (14 bp):
CTAGTCAATTTAAG
Found at i:614543 original size:27 final size:27
Alignment explanation
Indices: 614475--614531 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
614465 AATTGGAAGA
614475 AAAAAAAATTCTTGTTTTGATTAAATC
1 AAAAAAAATTCTTGTTTTGATTAAATC
614502 AAAAAAAATTCTTGTTTTGATTAAATC
1 AAAAAAAATTCTTGTTTTGATTAAATC
614529 AAA
1 AAA
614532 TAGAATTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (27 bp):
AAAAAAAATTCTTGTTTTGATTAAATC
Found at i:623796 original size:15 final size:14
Alignment explanation
Indices: 623776--623806 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
623766 CATTTGAGAC
623776 CTAGTCAATTTAGAG
1 CTAGTCAATTTA-AG
623791 CTAGTCAATTTAAG
1 CTAGTCAATTTAAG
623805 CT
1 CT
623807 CCACAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (14 bp):
CTAGTCAATTTAAG
Found at i:629219 original size:16 final size:17
Alignment explanation
Indices: 629180--629223 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
629170 TTATTTAGGC
*
629180 AATATATTT-TAT-CAA
1 AATATATTTAAATCCAA
629195 AATATATTTAAATCCAA
1 AATATATTTAAATCCAA
629212 AA-ATATTTAAAT
1 AATATATTTAAAT
629224 TTGTACTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.35
16 12 0.46
17 5 0.19
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATATTTAAATCCAA
Found at i:633519 original size:15 final size:14
Alignment explanation
Indices: 633499--633528 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
633489 ATTTATGACT
633499 TAGTCAATTTAGAGC
1 TAGTCAATTTA-AGC
633514 TAGTCAATTTAAGC
1 TAGTCAATTTAAGC
633528 T
1 T
633529 CTAAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (14 bp):
TAGTCAATTTAAGC
Found at i:635070 original size:16 final size:15
Alignment explanation
Indices: 635058--635088 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
635048 CATTTAGGAT
635058 CTAGTCAATTTAGAG
1 CTAGTCAATTTAGAG
635073 CTAGTCAATTTA-AG
1 CTAGTCAATTTAGAG
635087 CT
1 CT
635089 CTAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (15 bp):
CTAGTCAATTTAGAG
Found at i:652037 original size:15 final size:14
Alignment explanation
Indices: 652017--652047 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
652007 CATTTATGAT
652017 CTAGTCAATTTAGAG
1 CTAGTCAATTTA-AG
652032 CTAGTCAATTTAAG
1 CTAGTCAATTTAAG
652046 CT
1 CT
652048 CTAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (14 bp):
CTAGTCAATTTAAG
Found at i:653020 original size:32 final size:32
Alignment explanation
Indices: 652966--653043 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
652956 ACATTTGTCA
* *
652966 AATTATTATAAATTATTAATTACAATTTATTG
1 AATTATTATAAAATAATAATTACAATTTATTG
* * * **
652998 AATTGTTATAAAATAATCATTACATTTTATCA
1 AATTATTATAAAATAATAATTACAATTTATTG
*
653030 AATTATTACAAAAT
1 AATTATTATAAAAT
653044 TTTCATTATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (32 bp):
AATTATTATAAAATAATAATTACAATTTATTG
Found at i:653050 original size:32 final size:30
Alignment explanation
Indices: 652955--653051 Score: 77
Period size: 32 Copynumber: 3.1 Consensus size: 30
652945 AAACAACCAA
* * *
652955 TACATTTGTCAAATTATTATAAATTATTAAT
1 TACATTTATCAAATTATTAAAAATT-TTCAT
** * **
652986 TACAATTTATTGAATTGTTATAAAATAATCAT
1 TAC-ATTTATCAAATTATTA-AAAATTTTCAT
653018 TACATTTTATCAAATTATTACAAAATTTTCAT
1 TACA-TTTATCAAATTATTA-AAAATTTTCAT
653050 TA
1 TA
653052 TTAAATTTAT
Statistics
Matches: 49, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
31 4 0.08
32 41 0.84
33 4 0.08
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.46
Consensus pattern (30 bp):
TACATTTATCAAATTATTAAAAATTTTCAT
Found at i:654889 original size:25 final size:25
Alignment explanation
Indices: 654831--654890 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
654821 AAATTTCACC
654831 CCGACCCGACATATAACTTAGAAAT
1 CCGACCCGACATATAACTTAGAAAT
* *
654856 TCAACCCGACATATAACTTAGAAAT
1 CCGACCCGACATATAACTTAGAAAT
*
654881 CCGATCCGAC
1 CCGACCCGAC
654891 CCGACCCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (25 bp):
CCGACCCGACATATAACTTAGAAAT
Found at i:659670 original size:24 final size:25
Alignment explanation
Indices: 659643--659693 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
659633 AATTCAATGA
* *
659643 ATGAAATATGAATAAATATAAA-AT
1 ATGAAAAATAAATAAATATAAATAT
*
659667 ATGAAAAATAAATAACTATAAATAT
1 ATGAAAAATAAATAAATATAAATAT
659692 AT
1 AT
659694 ATACATATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (25 bp):
ATGAAAAATAAATAAATATAAATAT
Found at i:661937 original size:32 final size:31
Alignment explanation
Indices: 661896--661967 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
661886 ATTATTATAA
* * *
661896 ATTACATTTTATTGAATTATTATAGAATAATC
1 ATTAAATTTTATTAAATTATTACA-AATAATC
**
661928 ATTAAATTTTATTAAATTATTACAAATTTTC
1 ATTAAATTTTATTAAATTATTACAAATAATC
661959 ATTAAATTT
1 ATTAAATTT
661968 ATCATATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 14 0.40
32 21 0.60
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (31 bp):
ATTAAATTTTATTAAATTATTACAAATAATC
Found at i:671881 original size:20 final size:20
Alignment explanation
Indices: 671843--671881 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
671833 TCCTGCACCA
* **
671843 TTGAACAAGAAAATTAAAAT
1 TTGAAAAAGAAAACAAAAAT
671863 TTGAAAAAGAAAACAAAAA
1 TTGAAAAAGAAAACAAAAA
671882 CAAAAACAAA
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:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (20 bp):
TTGAAAAAGAAAACAAAAAT
Found at i:672622 original size:36 final size:36
Alignment explanation
Indices: 672570--672641 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
672560 AAATTTAAAG
672570 TACAATGAGTAAAATAAAAGAGAATAAAGTTCAGTT
1 TACAATGAGTAAAATAAAAGAGAATAAAGTTCAGTT
* * *
672606 TACAGTGAGTAAAATAAGAGAGAGTAAAGTTCAGTT
1 TACAATGAGTAAAATAAAAGAGAATAAAGTTCAGTT
672642 ACCAAATTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.21, T:0.25
Consensus pattern (36 bp):
TACAATGAGTAAAATAAAAGAGAATAAAGTTCAGTT
Found at i:678588 original size:17 final size:17
Alignment explanation
Indices: 678566--678604 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
678556 AACGGTCAAC
678566 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
678583 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
678600 GGTCA
1 GGTCA
678605 GACCGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:678618 original size:9 final size:9
Alignment explanation
Indices: 678600--678679 Score: 70
Period size: 9 Copynumber: 8.3 Consensus size: 9
678590 GGTCGGGTCG
*
678600 GGTCAGACC
1 GGTCAAACC
678609 GGTCAAACC
1 GGTCAAACC
*
678618 GGTTCGAACC
1 GG-TCAAACC
*
678628 GGTTGAAACC
1 GG-TCAAACC
678638 GGTCAAACC
1 GGTCAAACC
678647 GGTCAGAACC
1 GGTCA-AACC
*
678657 GGTTGAAAACC
1 GG-T-CAAACC
*
678668 GGTTAAACC
1 GGTCAAACC
678677 GGT
1 GGT
678680 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 29 0.48
10 23 0.38
11 7 0.12
12 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:678640 original size:29 final size:31
Alignment explanation
Indices: 678606--678680 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
678596 GTCGGGTCAG
678606 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
678635 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
678665 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
678681 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Done.