Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007981.1 Hibiscus syriacus cultivar Beakdansim tig00110422_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: 1405786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:404939 original size:17 final size:18
Alignment explanation
Indices: 404898--404936 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
404888 AATATATAAG
404898 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
404915 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
404933 TAAA
1 TAAA
404937 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:404998 original size:10 final size:10
Alignment explanation
Indices: 404975--405024 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
404965 TACCTTAAAC
* *
404975 AGAGAATATA
1 AGAGAATTTG
*
404985 AGAGTATTTG
1 AGAGAATTTG
*
404995 AGAGAAGTTG
1 AGAGAATTTG
*
405005 AGAGAAATTG
1 AGAGAATTTG
405015 AGAGAATTTG
1 AGAGAATTTG
405025 GTGTGATGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:410072 original size:14 final size:14
Alignment explanation
Indices: 410055--410095 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
410045 GTTTGGTTAT
410055 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
410069 GTTCGGTTATGTTC
1 GTTCGTTTATGTTC
* *
410083 ATTCATTTATGTT
1 GTTCGTTTATGTT
410096 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.56
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:416395 original size:17 final size:17
Alignment explanation
Indices: 416373--416414 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
416363 TAATTTATCA
416373 ACTATTAA-TCGAGGGTT
1 ACTATTAACT-GAGGGTT
416390 ACTATTAACTGAGGGTT
1 ACTATTAACTGAGGGTT
*
416407 AGTATTAA
1 ACTATTAA
416415 ACCAAATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (17 bp):
ACTATTAACTGAGGGTT
Found at i:429405 original size:80 final size:80
Alignment explanation
Indices: 429317--429469 Score: 279
Period size: 80 Copynumber: 1.9 Consensus size: 80
429307 TTTATTTAAT
*
429317 TTTTTTATTATCGGCAACCTATACACTTTATATGTTTAAATTTATTTTTTTTAAATAATACTTTG
1 TTTTTTATTATCGGCAACCTATACACTTTATATGTTTAAATTTATTTTTTTTAAATAATACTCTG
429382 TTTTACTTTTTAAAA
66 TTTTACTTTTTAAAA
* *
429397 TTTTTTATTATCGGTAACCTGTACACTTTATATGTTTAAATTTATTTTTTTTAAATAATACTCTG
1 TTTTTTATTATCGGCAACCTATACACTTTATATGTTTAAATTTATTTTTTTTAAATAATACTCTG
429462 TTTTACTT
66 TTTTACTT
429470 AAAGCAATAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.28, C:0.10, G:0.06, T:0.56
Consensus pattern (80 bp):
TTTTTTATTATCGGCAACCTATACACTTTATATGTTTAAATTTATTTTTTTTAAATAATACTCTG
TTTTACTTTTTAAAA
Found at i:429654 original size:25 final size:25
Alignment explanation
Indices: 429615--429663 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
429605 GACCGACTCG
*
429615 AAAATATTAATATTTTAAAAATAATT
1 AAAATAATAATATTTT-AAAATAATT
429641 AAAATAAT-ATATTTTAAAATAAT
1 AAAATAATAATATTTTAAAATAAT
429664 ATATTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 7 0.32
26 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATAATAATATTTTAAAATAATT
Found at i:429659 original size:15 final size:15
Alignment explanation
Indices: 429639--429669 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
429629 TTAAAAATAA
429639 TTAAAATAATATATT
1 TTAAAATAATATATT
429654 TTAAAATAATATATT
1 TTAAAATAATATATT
429669 T
1 T
429670 ATAATTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAAATAATATATT
Found at i:434725 original size:289 final size:289
Alignment explanation
Indices: 434206--434783 Score: 1138
Period size: 289 Copynumber: 2.0 Consensus size: 289
434196 TCATCTGCCC
434206 TTACTCCTAACTAAGAGTGTAGTCTGCTAAGTGTGTTGTCACGGCATAAGAGAGCATTATGATAG
1 TTACTCCTAACTAAGAGTGTAGTCTGCTAAGTGTGTTGTCACGGCATAAGAGAGCATTATGATAG
434271 ATGATGGCATATCTGAAGGGAATAAGTCCAACTATTTGCATGCATAAAATCCTGATGGAAGAATG
66 ATGATGGCATATCTGAAGGGAATAAGTCCAACTATTTGCATGCATAAAATCCTGATGGAAGAATG
434336 TCATGGCAAATCCATAGAACCACAGTGAAGATTAAACCCAATCATGTGATGAAAGAAATTCTCAA
131 TCATGGCAAATCCATAGAACCACAGTGAAGATTAAACCCAATCATGTGATGAAAGAAATTCTCAA
* *
434401 GTGGCTTGACGTTGAGGTGATTTACCCTATTTCTGATAGTTCTTGGGTGAGTCCTGTCCAATGTA
196 GTGGCTTGACGTTGAGGTGATTTACCCTATTTCTGATAGTTCTTGGGTGAATCCCGTCCAATGTA
434466 TGCCAAAGAAGGGAGGCACGACCGTGGTG
261 TGCCAAAGAAGGGAGGCACGACCGTGGTG
434495 TTACTCCTAACTAAGAGTGTAGTCTGCTAAGTGTGTTGTCACGGCATAAGAGAGCATTATGATAG
1 TTACTCCTAACTAAGAGTGTAGTCTGCTAAGTGTGTTGTCACGGCATAAGAGAGCATTATGATAG
434560 ATGATGGCATATCTGAAGGGAATAAGTCCAACTATTTGCATGCATAAAATCCTGATGGAAGAATG
66 ATGATGGCATATCTGAAGGGAATAAGTCCAACTATTTGCATGCATAAAATCCTGATGGAAGAATG
434625 TCATGGCAAATCCATAGAACCACAGTGAAGATTAAACCCAATCATGTGATGAAAGAAATTCTCAA
131 TCATGGCAAATCCATAGAACCACAGTGAAGATTAAACCCAATCATGTGATGAAAGAAATTCTCAA
434690 GTGGCTTGACGTTGAGGTGATTTACCCTATTTCTGATAGTTCTTGGGTGAATCCCGTCCAATGTA
196 GTGGCTTGACGTTGAGGTGATTTACCCTATTTCTGATAGTTCTTGGGTGAATCCCGTCCAATGTA
434755 TGCCAAAGAAGGGAGGCACGACCGTGGTG
261 TGCCAAAGAAGGGAGGCACGACCGTGGTG
434784 ACAAGTGAAG
Statistics
Matches: 287, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
289 287 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (289 bp):
TTACTCCTAACTAAGAGTGTAGTCTGCTAAGTGTGTTGTCACGGCATAAGAGAGCATTATGATAG
ATGATGGCATATCTGAAGGGAATAAGTCCAACTATTTGCATGCATAAAATCCTGATGGAAGAATG
TCATGGCAAATCCATAGAACCACAGTGAAGATTAAACCCAATCATGTGATGAAAGAAATTCTCAA
GTGGCTTGACGTTGAGGTGATTTACCCTATTTCTGATAGTTCTTGGGTGAATCCCGTCCAATGTA
TGCCAAAGAAGGGAGGCACGACCGTGGTG
Found at i:440280 original size:20 final size:20
Alignment explanation
Indices: 440247--440289 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
440237 CCTAAGAGCC
*
440247 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
* *
440267 CATTTTGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
440287 CAT
1 CAT
440290 GTGGTGGAAT
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:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:441992 original size:21 final size:21
Alignment explanation
Indices: 441968--442012 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
441958 TAATATTTTT
*
441968 ATATTTTTTAATAAT-TAAATA
1 ATATATTTTAATAATATAAA-A
441989 ATATATTTTAATAATATAAAA
1 ATATATTTTAATAATATAAAA
442010 ATA
1 ATA
442013 AAAAATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATATTTTAATAATATAAAA
Found at i:442028 original size:2 final size:2
Alignment explanation
Indices: 442023--442047 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
442013 AAAAATCTTA
442023 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
442048 ATAACCGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:444307 original size:21 final size:22
Alignment explanation
Indices: 444283--444323 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
444273 TCATAATTAT
444283 TCAAAAA-ATTAAATAAAAATA
1 TCAAAAATATTAAATAAAAATA
*
444304 TCAAAAATATTTAATAAAAA
1 TCAAAAATATTAAATAAAAA
444324 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
TCAAAAATATTAAATAAAAATA
Found at i:451152 original size:2 final size:2
Alignment explanation
Indices: 451145--451211 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
451135 TTTTATCAAT
451145 TA TA TA TA TA TA 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 TA TA TA TA TA TA
*
451187 TA TA TA TA TA TA TA TA -A TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
451212 GGTTATGGAA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:453335 original size:243 final size:242
Alignment explanation
Indices: 452882--453341 Score: 638
Period size: 243 Copynumber: 1.9 Consensus size: 242
452872 TTTGACTCAC
* *
452882 AACCAATGTGGTGATGACGCATGTCATCACCCCATTGCACATAAAATATTAAATAAAAATATATA
1 AACCAATGTGGTGATAACACATGTCATCACCCCATTGCACATAAAATATTAAATAAAAATATATA
* *
452947 AAATTAATTTTAAAATTGATGACATGTCATTGTTGCCATATCACATTTTTTTATACATGGCACTG
66 AAATTAATTTGAAAATTGATGACATGTCATTGTTGCCACATCACATTTTTTTATACATGGCACTG
* * * * *
453012 GCACTCATCATTATTGCCATGTGAGTCTGTCACGTCATCTCAAGAAGTTAACCGTGAGTTGACTA
131 ACACTCAGCACTAGTGCCATGCGAGTCTGTCACGTCATCTCAAGAAGTTAACCGTGAGTTGACTA
*
453077 ACGGTTTTCATCCAATGAGGGGTCGTATATTTTTTGGTTTAAATTTA
196 ACAGTTTTCATCCAATGAGGGGTCGTATATTTTTTGGTTTAAATTTA
** * *
453124 AACCAATGTGGTGATAACATGTGTCATCACCCTATTGTACATAAAATATTAAATAAAAATATATA
1 AACCAATGTGGTGATAACACATGTCATCACCCCATTGCACATAAAATATTAAATAAAAATATATA
* * **
453189 AAATTAATTTGAAAATTTGATGACATGTCATT-TTGGCCACGTTAGCA-TTTTTTATATGTGGCA
66 AAATTAATTTGAAAA-TTGATGACATGTCATTGTT-GCCACATCA-CATTTTTTTATACATGGCA
* * * *
453252 CTGACACATCAGCACTAGTGTCATGCGAGT-TGTCACGTTATCTCAAGATGTTGACCGTGAGTTG
128 CTGACAC-TCAGCACTAGTGCCATGCGAGTCTGTCACGTCATCTCAAGAAGTTAACCGTGAGTTG
* * *
453316 ATTAACATTTTTTATCCAATGAGGGG
192 ACTAACAGTTTTCATCCAATGAGGGG
453342 GATTTTTGAC
Statistics
Matches: 189, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
242 75 0.40
243 95 0.50
244 19 0.10
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (242 bp):
AACCAATGTGGTGATAACACATGTCATCACCCCATTGCACATAAAATATTAAATAAAAATATATA
AAATTAATTTGAAAATTGATGACATGTCATTGTTGCCACATCACATTTTTTTATACATGGCACTG
ACACTCAGCACTAGTGCCATGCGAGTCTGTCACGTCATCTCAAGAAGTTAACCGTGAGTTGACTA
ACAGTTTTCATCCAATGAGGGGTCGTATATTTTTTGGTTTAAATTTA
Found at i:453639 original size:21 final size:21
Alignment explanation
Indices: 453615--453659 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
453605 TGGTTTTAAA
453615 AAAATTAAAAGTTTAGATACT
1 AAAATTAAAAGTTTAGATACT
* * *
453636 AAAATTGATAGTTTAGATATT
1 AAAATTAAAAGTTTAGATACT
453657 AAA
1 AAA
453660 TGCATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (21 bp):
AAAATTAAAAGTTTAGATACT
Found at i:463634 original size:24 final size:25
Alignment explanation
Indices: 463590--463637 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
463580 ATAAAATTTT
463590 AAGATAGAATTGAAATATAAAATAA
1 AAGATAGAATTGAAATATAAAATAA
*
463615 AAGATA-AATT-AATATTTAAAATA
1 AAGATAGAATTGAA-ATATAAAATA
463638 TATAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 13 0.62
25 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.29
Consensus pattern (25 bp):
AAGATAGAATTGAAATATAAAATAA
Found at i:470402 original size:19 final size:19
Alignment explanation
Indices: 470356--470402 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
470346 TATAATATTT
*
470356 AATAAGTAAAAAAATAAAA
1 AATAAATAAAAAAATAAAA
* *
470375 TATAAATAAAAAACTAAAA
1 AATAAATAAAAAAATAAAA
*
470394 AATATATAA
1 AATAAATAA
470403 CGTATTTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAATAAAAAAATAAAA
Found at i:470517 original size:42 final size:37
Alignment explanation
Indices: 470429--470528 Score: 98
Period size: 42 Copynumber: 2.6 Consensus size: 37
470419 AAAAATAATG
* *
470429 ATAAA-AAATAAAAATATATACAAAAATGTTAGGTAA
1 ATAAATAAATAAAAATATATAAAAAAACGTTAGGTAA
470465 A-AAATAAAATAAAATATATATATAAGTAAAACGTTAGGTTAA
1 ATAAAT-AAATAAAA-ATATATA-AA--AAAACGTTAGG-TAA
470507 ATAAATAAATAAATAATA-ATAA
1 ATAAATAAATAAA-AATATATAA
470529 TGATTAAAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
35 3 0.06
36 1 0.02
37 8 0.15
38 7 0.13
39 1 0.02
40 1 0.02
41 13 0.25
42 14 0.26
43 5 0.09
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (37 bp):
ATAAATAAATAAAAATATATAAAAAAACGTTAGGTAA
Found at i:470521 original size:41 final size:37
Alignment explanation
Indices: 470429--470528 Score: 100
Period size: 41 Copynumber: 2.6 Consensus size: 37
470419 AAAAATAATG
*
470429 ATAAA-AAATAAA-AATATATACAAAAATGTTAGGTAA
1 ATAAATAAATAAATAATATATA-AAAAACGTTAGGTAA
470465 A-AAATAAAATAAAATATATATATAAGTAAAACGTTAGGTTAA
1 ATAAAT-AAAT-AAATA-ATATATAA--AAAACGTTAGG-TAA
470507 ATAAATAAATAAATAATA-ATAA
1 ATAAATAAATAAATAATATATAA
470529 TGATTAAAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
35 3 0.06
36 1 0.02
37 4 0.07
38 3 0.06
39 6 0.11
40 10 0.19
41 15 0.28
42 8 0.15
43 4 0.07
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (37 bp):
ATAAATAAATAAATAATATATAAAAAACGTTAGGTAA
Found at i:471642 original size:2 final size:2
Alignment explanation
Indices: 471637--471681 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
471627 AGTAAAAAAC
471637 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
471677 A- AT AT
1 AT AT AT
471682 GTATGGACGA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:471661 original size:17 final size:17
Alignment explanation
Indices: 471639--471681 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
471629 TAAAAAACAT
471639 ATATATATATATATATA
1 ATATATATATATATATA
471656 ATATATATATATATATA
1 ATATATATATATATATA
471673 ATATA-ATAT
1 ATATATATAT
471682 GTATGGACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:472397 original size:85 final size:85
Alignment explanation
Indices: 472158--472611 Score: 469
Period size: 85 Copynumber: 5.4 Consensus size: 85
472148 ATGTGTCATC
* * * * * * * ** *
472158 GAGCTGAATGGAATCGAACTCGACA-TTTTTTGTTGACAGATAG-CTTTTTAGACTCAAGCTAAG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* *
472221 CTGTAAATTTGACATGGCC-TT
65 CTGAAAATTTGATAT-GCCTTT
* *
472242 GAGCTGAATAG-AATCGAACTCAAAGG--TTTATTGACAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAAT-GTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* * *
472304 TTGTAAATTTGTTATGCCTTT
65 CTGAAAATTTGATATGCCTTT
* * **
472325 GAGCTGAATGTAATCGAAC-CTGAAGGTCTTTGTTGGCAGATCGCCCTTCTTTCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTC-GAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
472389 CTGAAAATTTGA-ATGCCTTT
65 CTGAAAATTTGATATGCCTTT
* * * * *
472409 GAGTTGAACGTAATCAAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGATCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* *
472474 TGCAAATTTGATATGCTTTT
66 TGAAAATTTGATATGCCTTT
* * ** *
472494 GAGCTGAATGTAATCGAACTCGAAGGTC-TTGCTTGACAGATAACACTTCTTACCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTG-TTGACAGATAGCCCTTCTCGCCTTGAGCTATG
472558 CTGCAAAA-TTGATATGCCTTT
65 CTG-AAAATTTGATATGCCTTT
* *
472579 AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGT
472612 AACACCCCAA
Statistics
Matches: 310, Mismatches: 47, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
82 19 0.06
83 49 0.16
84 94 0.30
85 142 0.46
86 6 0.02
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
TGAAAATTTGATATGCCTTT
Found at i:472465 original size:169 final size:170
Alignment explanation
Indices: 472272--472608 Score: 475
Period size: 169 Copynumber: 2.0 Consensus size: 170
472262 CAAAGGTTTA
* * *
472272 TTGACAGATAGCCCTTCTCGCCTTGAGCTATGTTGTAAATTTGTTATGCCTTTGAGCTGAATGTA
1 TTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTTGATATGCCTTTGAGCTGAATGTA
* ** * *
472337 ATCGAAC-CTGAAGGTCTTTG-TTGGCAGATCGCCCTTCTTTCCTTGAGCTATGCTG-AAAATTT
66 ATCGAACTC-GAAGGTC-TTGCTTGACAGATAACACTTCTTACCTTGAGCTATGCTGCAAAA-TT
* *
472399 GA-ATGCCTTTGAGTTGAACGTAATCAAACTCGAAGGTCTTGG
128 GATATGCCTTTAAGCTGAACGTAATCAAACTCGAAGGTCTTGG
* *
472441 TTGACAGATAGCCCTTCTCGCCTTGATCTATGCTGCAAATTTGATATGCTTTTGAGCTGAATGTA
1 TTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTTGATATGCCTTTGAGCTGAATGTA
*
472506 ATCGAACTCGAAGGTCTTGCTTGACAGATAACACTTCTTACCTTGAGTTATGCTGCAAAATTGAT
66 ATCGAACTCGAAGGTCTTGCTTGACAGATAACACTTCTTACCTTGAGCTATGCTGCAAAATTGAT
** *
472571 ATGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGTCTT
131 ATGCCTTTAAGCTGAACGTAATCAAACTCGAAGGTCTT
472609 TGTAACACCC
Statistics
Matches: 148, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
168 3 0.02
169 107 0.72
170 38 0.26
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (170 bp):
TTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTTGATATGCCTTTGAGCTGAATGTA
ATCGAACTCGAAGGTCTTGCTTGACAGATAACACTTCTTACCTTGAGCTATGCTGCAAAATTGAT
ATGCCTTTAAGCTGAACGTAATCAAACTCGAAGGTCTTGG
Found at i:472874 original size:21 final size:21
Alignment explanation
Indices: 472850--472890 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
472840 CAATGAGCAG
472850 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
472871 TGCTACAGTGCATCGATGCA
1 TGCTACAGTGCATCGATGCA
472891 CCAAAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGCAT
Found at i:473675 original size:30 final size:31
Alignment explanation
Indices: 473636--473702 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
473626 GAATGACTTA
* *
473636 TCCAGAGGTCATAAAGAACCT-CGAAAACTG
1 TCCATAGGTCACAAAGAACCTACGAAAACTG
* * *
473666 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTACGAAAACTG
473697 TCCATA
1 TCCATA
473703 TGTTCCTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTACGAAAACTG
Found at i:473771 original size:32 final size:32
Alignment explanation
Indices: 473664--473849 Score: 154
Period size: 32 Copynumber: 5.9 Consensus size: 32
473654 CCTCGAAAAC
* *
473664 TGTCCATAGGTCCC-AAAGAACCTAGGTAA--A
1 TGTCCATATGTCCCGAAAG-ACATAGGTAATTA
* **
473694 CTGTCCATATGTTCC-TTAGAACATAGGT-A-TA
1 -TGTCCATATGTCCCGAAAG-ACATAGGTAATTA
473725 CTGTCCATATGTCCCGAAAGACACT-GGTAATTA
1 -TGTCCATATGTCCCGAAAGACA-TAGGTAATTA
* *
473758 TGTTCATATGTCCCGAAAGACATATGTAATTA
1 TGTCCATATGTCCCGAAAGACATAGGTAATTA
* * *
473790 TGTCCATATTTCCCGAACGACATAGGTAATTC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTA
* *
473822 TGTCCATATGTTCC-ATAGAACATAGGTA
1 TGTCCATATGTCCCGAAAG-ACATAGGTA
473850 GACCCTCAAC
Statistics
Matches: 129, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.01
31 46 0.36
32 80 0.62
33 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAAGACATAGGTAATTA
Found at i:473845 original size:64 final size:64
Alignment explanation
Indices: 473662--473849 Score: 201
Period size: 64 Copynumber: 3.0 Consensus size: 64
473652 AACCTCGAAA
* * *
473662 ACTGTCCATAGGTCCC-AAAGA-ACCTAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAAGACA-CTAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTAT
* * * * *
473724 ACTGTCCATATGTCCCGAAAGACACT-GGTAATTATGTTCATATGTCCCGAAAG-ACATATGTAA
1 ACTGTCCATATGTCCCGAAAGACACTAGGTAATTCTGTCCATATGTTCC-ATAGAACATAGGT-A
473787 TT
64 -T
* *
473789 A-TGTCCATATTTCCCGAACGACA-TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTA
1 ACTGTCCATATGTCCCGAAAGACACTAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTA
473850 GACCCTCAAC
Statistics
Matches: 103, Mismatches: 15, Indels: 15
0.77 0.11 0.11
Matches are distributed among these distances:
62 20 0.19
63 31 0.30
64 50 0.49
65 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (64 bp):
ACTGTCCATATGTCCCGAAAGACACTAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTAT
Found at i:475641 original size:85 final size:85
Alignment explanation
Indices: 475497--476134 Score: 677
Period size: 85 Copynumber: 7.5 Consensus size: 85
475487 GGATGTTACA
* * * * *
475497 GTCTTGGTTGATAGATAACCCTTCTTG-CTTGAGTTATACTGCAAATTTGATATGTCTTTGAGCT
1 GTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCT
*
475561 GAGTGTAATCGAACTCAAAG
66 GAGTGTAATCGAACTCGAAG
* *
475581 GTCTTGGTTGACAGATAACCTTTCTCGCCTTGAGTTATGCTGTAAATGTGATATGCCTTTGAGCT
1 GTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCT
*
475646 GAGTGTAATCGAACTTGAAG
66 GAGTGTAATCGAACTCGAAG
* ** ** * * * * * *
475666 GTCTTAGTTGACAGATAGTCCTTCTCTTCTTGAGCTGTGTTGCAAATTTAATATGCCTTTGAGAT
1 GTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCT
* *
475731 GAGTGTAATTGAACTTGAAG
66 GAGTGTAATCGAACTCGAAG
* * * * * * * *
475751 GTCTTTTGTTAACAGATAACCCTTCTTGCCTTAAGTTATTCTATAAATTTGATGTTCCTTTGAGC
1 GTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGC
** * *
475816 TGAAAGTAATCGATCTTGAAG
65 TGAGTGTAATCGAACTCGAAG
* * * * * * *
475837 GTCTTGGTTGACAAATAGCCCTTCTCGCCTTAAGCTATGTTGTAAATTTGTTATGCCTTTGAACT
1 GTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCT
* *
475902 GAATGTAATCGAACCCGAAG
66 GAGTGTAATCGAACTCGAAG
* * * * * * * * *
475922 GTCTTTGTTGGCATATAGCCCTTCTCGCATTGAGTTATGCTGCAAATTTTATATACCTTTGAGAT
1 GTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCT
*
475987 GAATGTAATCGAACTCGAAG
66 GAGTGTAATCGAACTCGAAG
* *
476007 GTCTTAGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCCT-TCAAATTTGATATGCCTTTGAG
1 GTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG-CTGT-AAATTTGATATGCCTTTGAG
*
476071 CTGAGTATAATCGAACTCGAAG
64 CTGAGTGTAATCGAACTCGAAG
* * * * *
476093 GTCTTTTGCTGGCATATAACCCTTTTCGCCTTGAGTTATGCT
1 GTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCT
476135 TTGAATTGTT
Statistics
Matches: 455, Mismatches: 94, Indels: 8
0.82 0.17 0.01
Matches are distributed among these distances:
84 24 0.05
85 294 0.65
86 107 0.24
87 30 0.07
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (85 bp):
GTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCT
GAGTGTAATCGAACTCGAAG
Found at i:475836 original size:171 final size:170
Alignment explanation
Indices: 475497--476134 Score: 708
Period size: 171 Copynumber: 3.7 Consensus size: 170
475487 GGATGTTACA
* * * * * ** * *
475497 GTCTTGGTTGATAGATAACCCTTCT-TGCTTGAGTTATACTGCAAATTTGATATGTCTTTGAGCT
1 GTCTTAGTTGACAGATAGCCCTTCTCTCCTTGAGCTATGTTGCAAATTTGATATGCCTTTGAGAT
* * *
475561 GAGTGTAATCGAACTCAAAGGTCTTGGTTGACAGATAACCTTTCTCGCCTTGAGTTATGCTGTAA
66 GAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAA
* * *
475626 ATGTGATATGCCTTTGAGCTGAGTGTAATCGAACTTGAAG
131 ATTTGATATACCTTTGAGCTGAATGTAATCGAACTTGAAG
* * * *
475666 GTCTTAGTTGACAGATAGTCCTTCTCTTCTTGAGCTGTGTTGCAAATTTAATATGCCTTTGAGAT
1 GTCTTAGTTGACAGATAGCCCTTCTCTCCTTGAGCTATGTTGCAAATTTGATATGCCTTTGAGAT
* * * * * * *
475731 GAGTGTAATTGAACTTGAAGGTCTTTTGTTAACAGATAACCCTTCTTGCCTTAAGTTATTCTATA
66 GAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTA
* * * *
475796 AATTTGATGTTCCTTTGAGCTGAAAGTAATCGATCTTGAAG
130 AATTTGATATACCTTTGAGCTGAATGTAATCGAACTTGAAG
* * * * * *
475837 GTCTTGGTTGACAAATAGCCCTTCTCGCCTTAAGCTATGTTGTAAATTTGTTATGCCTTTGA-AC
1 GTCTTAGTTGACAGATAGCCCTTCTCTCCTTGAGCTATGTTGCAAATTTGATATGCCTTTGAGA-
* * * * * * *
475901 TGAATGTAATCGAACCCGAAGGTCTTTGTTGGCATATAGCCCTTCTCGCATTGAGTTATGCTGCA
65 TGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTA
* * *
475966 AATTTTATATACCTTTGAGATGAATGTAATCGAACTCGAAG
130 AATTTGATATACCTTTGAGCTGAATGTAATCGAACTTGAAG
* *
476007 GTCTTAGTTGACAGATAACCCTTCT-TGCCTTGAGTTATGCCTT-CAAATTTGATATGCCTTTGA
1 GTCTTAGTTGACAGATAGCCCTTCTCT-CCTTGAGCTATG--TTGCAAATTTGATATGCCTTTGA
* * * * * *
476070 GCTGAGTATAATCGAACTCGAAGGTCTTTTGCTGGCATATAACCCTTTTCGCCTTGAGTTATGCT
63 GATGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCT
476135 TTGAATTGTT
Statistics
Matches: 386, Mismatches: 75, Indels: 13
0.81 0.16 0.03
Matches are distributed among these distances:
169 21 0.05
170 149 0.39
171 180 0.47
172 36 0.09
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (170 bp):
GTCTTAGTTGACAGATAGCCCTTCTCTCCTTGAGCTATGTTGCAAATTTGATATGCCTTTGAGAT
GAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAA
ATTTGATATACCTTTGAGCTGAATGTAATCGAACTTGAAG
Found at i:476009 original size:256 final size:254
Alignment explanation
Indices: 475509--476134 Score: 729
Period size: 256 Copynumber: 2.4 Consensus size: 254
475499 CTTGGTTGAT
* **
475509 AGATAACCCTTCTTG-CTTGAGTTATACTGCAAATTTGATATGT-CTTTGAGCTGAGTGTAATCG
1 AGATAACCCTTCTTGCCTTGAGTTATACT-TAAATTTGATAT-TCCTTTGAGCTGAAAGTAATCG
* * * * *
475572 AACTCAAAGGTCTTGGTTGACAGATAACCTTTCTCGCCTTGAGTTATGCTGTAAATGTGATATGC
64 AACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTAAGCTATGCTGTAAATGTGATATGC
* * ** * *
475637 CTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTAGTTGACAGATAGTCCTTCTCTTCTTGAGCT
129 CTTTGAACTGAATGTAATCGAACCCGAAGGTCTTAGTTGACAGATAGCCCTTCTCTGCTTGAGCT
* * * * * * *
475702 GTGTTGCAAATTTAATATGCCTTTGAGATGAGTGTAATTGAACTTGAAGGTCTTTTGTTAAC
194 ATGCTGCAAATTTAATATACCTTTGAGATGAATGTAATCGAACTCGAAGGTC-TTAGTTAAC
* * *
475764 AGATAACCCTTCTTGCCTTAAGTTATTCTATAAATTTGATGTTCCTTTGAGCTGAAAGTAATCGA
1 AGATAACCCTTCTTGCCTTGAGTTATACT-TAAATTTGATATTCCTTTGAGCTGAAAGTAATCGA
* * * * * *
475829 TCTTGAAGGTCTTGGTTGACAAATAGCCCTTCTCGCCTTAAGCTATGTTGTAAATTTGTTATGCC
65 ACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTAAGCTATGCTGTAAATGTGATATGCC
* * * *
475894 TTTGAACTGAATGTAATCGAACCCGAAGGTCTTTGTTGGCATATAGCCCTTCTC-GCATTGAGTT
130 TTTGAACTGAATGTAATCGAACCCGAAGGTCTTAGTTGACAGATAGCCCTTCTCTGC-TTGAGCT
* *
475958 ATGCTGCAAATTTTATATACCTTTGAGATGAATGTAATCGAACTCGAAGGTCTTAGTTGAC
194 ATGCTGCAAATTTAATATACCTTTGAGATGAATGTAATCGAACTCGAAGGTCTTAGTTAAC
* * *
476019 AGATAACCCTTCTTGCCTTGAGTTATGCCTTCAAATTTGATATGCCTTTGAGCTGAGTA-TAATC
1 AGATAACCCTTCTTGCCTTGAGTTAT-ACTT-AAATTTGATATTCCTTTGAGCTGA-AAGTAATC
* * * * * * *
476083 GAACTCGAAGGTCTTTTGCTGGCATATAACCCTTTTCGCCTTGAGTTATGCT
63 GAACTCGAAGGTC-TTGGTTGACAAATAACCCTTCTCGCCTTAAGCTATGCT
476135 TTGAATTGTT
Statistics
Matches: 311, Mismatches: 53, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
255 50 0.16
256 231 0.74
257 30 0.10
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (254 bp):
AGATAACCCTTCTTGCCTTGAGTTATACTTAAATTTGATATTCCTTTGAGCTGAAAGTAATCGAA
CTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTAAGCTATGCTGTAAATGTGATATGCCT
TTGAACTGAATGTAATCGAACCCGAAGGTCTTAGTTGACAGATAGCCCTTCTCTGCTTGAGCTAT
GCTGCAAATTTAATATACCTTTGAGATGAATGTAATCGAACTCGAAGGTCTTAGTTAAC
Found at i:477450 original size:95 final size:95
Alignment explanation
Indices: 477282--477475 Score: 302
Period size: 95 Copynumber: 2.0 Consensus size: 95
477272 AGACAGCTCA
477282 ATATTATAAATACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGTGTTTAACCAATT
1 ATATTATAAATACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGTGTTTAACCAATT
*
477347 GCTTTAGAGGGACAACTCAAGCTTTATTGT
66 GCTCTAGAGGGACAACTCAAGCTTTATTGT
*
477377 ATATTAT-AATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGGT-GGGGTGTTTAACCAA
1 ATATTATAAAT-ACCTTTATCAGGCTAGCTGAATATTATCCATAAA-GTCGGGGTGTTTAACCAA
** **
477440 TTGCTCTAGAGGGTTAGTTCAAGCTTTATTGT
64 TTGCTCTAGAGGGACAACTCAAGCTTTATTGT
477472 ATAT
1 ATAT
477476 ATCATATTAT
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
94 3 0.03
95 86 0.95
96 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (95 bp):
ATATTATAAATACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGTGTTTAACCAATT
GCTCTAGAGGGACAACTCAAGCTTTATTGT
Found at i:481788 original size:15 final size:16
Alignment explanation
Indices: 481760--481789 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
481750 TATATAGTAT
481760 ATATGAACAAAGGATG
1 ATATGAACAAAGGATG
481776 ATATGAA-AAAGGAT
1 ATATGAACAAAGGAT
481790 ATAAGAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.20
Consensus pattern (16 bp):
ATATGAACAAAGGATG
Found at i:482042 original size:18 final size:18
Alignment explanation
Indices: 482019--482054 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
482009 ATGGATTATC
482019 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
482037 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
482055 TTCATAGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:482064 original size:23 final size:23
Alignment explanation
Indices: 482034--482099 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
482024 TCCTTCGGGA
*
482034 CATAGTGGTCCTTCGGGACATTT
1 CATAGTGGTCCTTCAGGACATTT
*
482057 CATAGTGGTCCTTCTGGACATTT
1 CATAGTGGTCCTTCAGGACATTT
482080 CATAGTGGTCCTTCAGGACA
1 CATAGTGGTCCTTCAGGACA
482100 AATTCATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (23 bp):
CATAGTGGTCCTTCAGGACATTT
Found at i:486099 original size:64 final size:61
Alignment explanation
Indices: 485969--486123 Score: 154
Period size: 64 Copynumber: 2.5 Consensus size: 61
485959 CAAGGTGGAT
* * * * *
485969 CGATGCACATGAAGTGTATCGATGCACTCC-TTTAAAAAAACATCGAATGTCATCAGTGTAT
1 CGATGCACAAGTAGTGCATCGATGCAC-CCGCTTAAAAAAACATCGAATGTCATCAGTGTAC
* *
486030 CGATGCACAAGTAGTGCATCGATGCACCCGCTTAAAGTACAAACATCGAATGTGATTTA-TGTAC
1 CGATGCACAAGTAGTGCATCGATGCACCCGCTTAAA--A-AAACATCGAATGTCA-TCAGTGTAC
* *
486094 CGATGCA-TAGATAGTGCATCGATGTACCCG
1 CGATGCACAAG-TAGTGCATCGATGCACCCG
486124 TCAAGGAATG
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
60 2 0.03
61 29 0.37
63 3 0.04
64 43 0.54
65 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (61 bp):
CGATGCACAAGTAGTGCATCGATGCACCCGCTTAAAAAAACATCGAATGTCATCAGTGTAC
Found at i:489017 original size:14 final size:14
Alignment explanation
Indices: 488998--489044 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
488988 AGTAAAAAAT
488998 AAAATAGAAATAAA
1 AAAATAGAAATAAA
489012 AAAATAGAAATAGAA
1 AAAATAGAAATA-AA
489027 ATAAA-A-AAACTAAA
1 A-AAATAGAAA-TAAA
489041 AAAA
1 AAAA
489045 ACATATAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.10
14 18 0.60
15 6 0.20
16 3 0.10
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (14 bp):
AAAATAGAAATAAA
Found at i:489022 original size:20 final size:19
Alignment explanation
Indices: 488991--489041 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 19
488981 TTTAATAAGT
488991 AAAAAATAAAATAGAAATA
1 AAAAAATAAAATAGAAATA
489010 AAAAAATAGAAATAGAAATA
1 AAAAAATA-AAATAGAAATA
489030 AAAAAACTAAAA
1 AAAAAA-TAAAA
489042 AAAACATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.27
20 20 0.67
21 2 0.07
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (19 bp):
AAAAAATAAAATAGAAATA
Found at i:489128 original size:40 final size:43
Alignment explanation
Indices: 489084--489175 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 43
489074 AAAAATAATG
* *
489084 ATAAAAAATAAAA-ATATATACA-AAAATGTTAG-GTAAAAAA
1 ATAAAAAATAAAATATATATAAATAAAACGTTAGAGTAAAAAA
* *
489124 AT--AAAATAAAATATATATAAATAAAACGTTAGATTAAATAA
1 ATAAAAAATAAAATATATATAAATAAAACGTTAGAGTAAAAAA
*
489165 ATAAATAATAA
1 ATAAAAAATAA
489176 TAATGATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
38 9 0.21
39 8 0.19
40 11 0.26
41 8 0.19
43 6 0.14
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.26
Consensus pattern (43 bp):
ATAAAAAATAAAATATATATAAATAAAACGTTAGAGTAAAAAA
Found at i:490293 original size:64 final size:62
Alignment explanation
Indices: 490218--490376 Score: 167
Period size: 62 Copynumber: 2.5 Consensus size: 62
490208 ATTGTTCAAG
* *
490218 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATTGAATGCTATAA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCAC-CC-TTAAAATAAAAACATTGAATGCTATAA
* * * * * **
490282 GTGTATTGATGCACAAGTAGTGCATCGATGCACCCTTAAGATTAAAACATTGAA-GGTGATTT
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCTTAAAATAAAAACATTGAATGCT-ATAA
* * * *
490344 GTATACCGATGCACAGGTAGTGCATCGATGCAC
1 GTGTATCGATGCACAAGAAGTGCATCGATGCAC
490377 AGGTAGTGCA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
61 2 0.02
62 48 0.59
63 2 0.02
64 29 0.36
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (62 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCTTAAAATAAAAACATTGAATGCTATAA
Found at i:490374 original size:19 final size:19
Alignment explanation
Indices: 490350--490396 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
490340 ATTTGTATAC
490350 CGATGCACAGGTAGTGCAT
1 CGATGCACAGGTAGTGCAT
490369 CGATGCACAGGTAGTGCAT
1 CGATGCACAGGTAGTGCAT
490388 CGATGCACA
1 CGATGCACA
490397 CGTTATGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.19
Consensus pattern (19 bp):
CGATGCACAGGTAGTGCAT
Found at i:490410 original size:24 final size:22
Alignment explanation
Indices: 490383--490438 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
490373 GCACAGGTAG
*
490383 TGCATCGATGCACACGTTATGGAA
1 TGCATCGATGCACAC--TATAGAA
*
490407 TGCATCGAT--ACACTATAGAG
1 TGCATCGATGCACACTATAGAA
490427 TGCATCGATGCA
1 TGCATCGATGCA
490439 TACCTTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 14 0.50
22 5 0.18
24 9 0.32
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACACTATAGAA
Found at i:491082 original size:15 final size:17
Alignment explanation
Indices: 491051--491083 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
491041 GTAGTGCACA
491051 ACCTCTATGTACTCAAT
1 ACCTCTATGTACTCAAT
491068 ACCTCTAT-T-CTCAAT
1 ACCTCTATGTACTCAAT
491083 A
1 A
491084 ATGTACATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.36
Consensus pattern (17 bp):
ACCTCTATGTACTCAAT
Found at i:492466 original size:3 final size:3
Alignment explanation
Indices: 492458--492502 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
492448 AAATATCATG
* * *
492458 TAT TAT TAT AAT TAT TAC CAT GTAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
492503 AGTAAAAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 33 0.94
4 2 0.06
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:492482 original size:22 final size:22
Alignment explanation
Indices: 492454--492496 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
492444 AGACAAATAT
492454 CATGTATTATTATAATTATTAC
1 CATGTATTATTATAATTATTAC
*
492476 CATGTATTATTATTATTATTA
1 CATGTATTATTATAATTATTA
492497 TTATTAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (22 bp):
CATGTATTATTATAATTATTAC
Found at i:492518 original size:2 final size:2
Alignment explanation
Indices: 492513--492541 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
492503 AGTAAAAAAC
492513 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
492542 ATTTGCATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:499834 original size:31 final size:29
Alignment explanation
Indices: 499777--499834 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
499767 GATTGTTTTA
*
499777 TTTTTAAATTGAATTATTTAAATTTTACC
1 TTTTTAAATTGAATTATATAAATTTTACC
* *
499806 TTTTATAAATTTAATCTATATATATTTTA
1 TTTT-TAAATTGAAT-TATATAAATTTTA
499835 TTTATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.17
30 9 0.38
31 11 0.46
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTTAAATTGAATTATATAAATTTTACC
Found at i:500473 original size:13 final size:13
Alignment explanation
Indices: 500455--500479 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
500445 CTCGAGTATT
500455 GTTCATAAATTCG
1 GTTCATAAATTCG
500468 GTTCATAAATTC
1 GTTCATAAATTC
500480 AGAACTCCGA
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:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
GTTCATAAATTCG
Found at i:523621 original size:21 final size:21
Alignment explanation
Indices: 523506--523621 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
523496 GCGAAATAAA
**
523506 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
523526 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
523546 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
523567 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
523587 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
523609 AATCGCAACGCGA
1 AATCGCAACGCGA
523622 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:523681 original size:20 final size:20
Alignment explanation
Indices: 523609--523800 Score: 287
Period size: 20 Copynumber: 9.6 Consensus size: 20
523599 GATTTTCCAG
* ** *
523609 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
523629 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
523649 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
523669 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
523689 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
523709 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
523729 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
523749 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
523769 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
523789 AATCGCAACGCG
1 AATCGCAACGCG
523801 ATTTTTAAAG
Statistics
Matches: 157, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
19 1 0.01
20 154 0.98
21 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:524220 original size:33 final size:33
Alignment explanation
Indices: 524180--524250 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
524170 TTCACTTAGA
524180 TTTCATTTCACGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCACGTTACGATTCTCTCGTTGCGAT
* * *
524213 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCACGTTACGATTCTCTCGTTGCGAT
524246 TTTCA
1 TTTCA
524251 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.13, C:0.24, G:0.15, T:0.48
Consensus pattern (33 bp):
TTTCATTTCACGTTACGATTCTCTCGTTGCGAT
Found at i:524356 original size:21 final size:20
Alignment explanation
Indices: 524330--524436 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
524320 TGCAGAAGAG
524330 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
524351 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
524371 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAACGAGA-AAATGAAAA
524393 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
524407 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
524426 TCGCAACGAGA
1 TCGCAACGAGA
524437 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 26 0.37
22 9 0.13
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:524410 original size:14 final size:14
Alignment explanation
Indices: 524391--524447 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
524381 GAGAAATGAA
524391 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
524405 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
524424 AATCGCAACGAGAG
1 AATCGCAACGAGAG
524438 AATCGCAACG
1 AATCGCAACG
524448 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:524421 original size:33 final size:33
Alignment explanation
Indices: 524383--524463 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
524373 TGCAACGAGA
524383 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
524416 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
524449 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
524464 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:524515 original size:21 final size:21
Alignment explanation
Indices: 524489--524553 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
524479 CGCGTTGCGA
524489 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
524510 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
524530 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
524551 TTC
1 TTC
524554 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:524550 original size:20 final size:20
Alignment explanation
Indices: 524488--524551 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
524478 TCGCGTTGCG
524488 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
524508 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
524529 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
524549 ATT
1 ATT
524552 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:526394 original size:93 final size:93
Alignment explanation
Indices: 526235--526550 Score: 605
Period size: 93 Copynumber: 3.4 Consensus size: 93
526225 TAGATTGCTT
*
526235 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526300 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
526328 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526393 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
526421 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCCAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
526486 TTTGTCTTTATTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
526514 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
526551 AATACCCTGA
Statistics
Matches: 219, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 219 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:526685 original size:14 final size:14
Alignment explanation
Indices: 526666--526722 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
526656 CGAAACTTAA
526666 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
526680 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
526699 AATCGCAACGACAG
1 AATCGCAACGAGAG
526713 AATCGCAACG
1 AATCGCAACG
526723 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:526704 original size:19 final size:18
Alignment explanation
Indices: 526680--526771 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
526670 GCAACGAGAG
526680 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
526699 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
526713 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
526732 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
526746 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
526765 AATCGCA
1 AATCGCA
526772 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:526706 original size:33 final size:33
Alignment explanation
Indices: 526648--526771 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
526638 TAGTTTACTT
* * *
526648 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
526682 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
526715 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
526748 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
526772 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:526748 original size:14 final size:14
Alignment explanation
Indices: 526697--526755 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
526687 ACGCGAAATG
526697 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
526711 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
526730 AAAATCGCAACGAC
1 AAAATCGCAACGAC
526744 AAAATCGCAACG
1 AAAATCGCAACG
526756 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:526789 original size:19 final size:19
Alignment explanation
Indices: 526767--526939 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
526757 GAAACCAAAA
* *
526767 TCGCATTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
526786 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
526800 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
526819 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
526835 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
526852 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
526871 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
526890 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
526909 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
526929 TCGTGTTGCGA
1 TCGCGTTGCGA
526940 AAGTAAACTA
Statistics
Matches: 125, Mismatches: 18, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
14 17 0.14
16 8 0.06
17 7 0.06
19 81 0.65
20 12 0.10
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:526808 original size:14 final size:14
Alignment explanation
Indices: 526789--526845 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
526779 TTTAATTTCG
526789 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
526803 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
526820 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
526836 CGTTGCGATT
1 CGTTGCGATT
526846 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:526897 original size:38 final size:38
Alignment explanation
Indices: 526767--526939 Score: 159
Period size: 33 Copynumber: 4.8 Consensus size: 38
526757 GAAACCAAAA
* *
526767 TCGCATTGCGATTTTAATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
526802 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
526835 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
526871 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
526909 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
526940 AAGTAAACTA
Statistics
Matches: 114, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 51 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.39
39 11 0.10
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:528870 original size:14 final size:14
Alignment explanation
Indices: 528851--528886 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
528841 ATTGTTTAAT
528851 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
528865 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
528879 TGATTTGT
1 TGATTTGT
528887 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:529069 original size:20 final size:19
Alignment explanation
Indices: 528993--529091 Score: 136
Period size: 20 Copynumber: 5.4 Consensus size: 19
528983 AAAAATGACT
528993 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
529012 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
529031 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
529045 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
529065 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
529085 ATCGCAA
1 ATCGCAA
529092 CGAGAGAATC
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 3 0.04
19 27 0.38
20 30 0.42
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:529095 original size:54 final size:53
Alignment explanation
Indices: 528993--529109 Score: 218
Period size: 54 Copynumber: 2.2 Consensus size: 53
528983 AAAAATGACT
528993 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
529045 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
529099 ATCGCAATGCG
1 ATCGCAATGCG
529110 ATTTTCATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 10 0.16
53 19 0.30
54 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:529128 original size:19 final size:19
Alignment explanation
Indices: 529100--529256 Score: 190
Period size: 19 Copynumber: 8.7 Consensus size: 19
529090 AACGAGAGAA
*
529100 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
529119 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
529138 TCCGTATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
529155 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
529172 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
529191 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
529210 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
529228 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
529244 TCGCATTGCGATT
1 TCGCATTGCGATT
529257 CTCTCGTTGC
Statistics
Matches: 120, Mismatches: 6, Indels: 24
0.80 0.04 0.16
Matches are distributed among these distances:
14 17 0.14
16 7 0.06
17 7 0.06
18 4 0.03
19 60 0.50
20 25 0.21
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:529169 original size:53 final size:52
Alignment explanation
Indices: 529106--529270 Score: 205
Period size: 53 Copynumber: 3.1 Consensus size: 52
529096 AGAATCGCAA
*
529106 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGTATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
529159 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
529217 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
529264 TGCGATT
1 TGCGATT
529271 GTAATTTCCG
Statistics
Matches: 102, Mismatches: 4, Indels: 18
0.82 0.03 0.15
Matches are distributed among these distances:
47 8 0.08
49 2 0.02
50 2 0.02
51 3 0.03
52 9 0.09
53 57 0.56
54 3 0.03
55 3 0.03
56 3 0.03
58 12 0.12
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:529219 original size:72 final size:72
Alignment explanation
Indices: 529100--529256 Score: 262
Period size: 72 Copynumber: 2.2 Consensus size: 72
529090 AACGAGAGAA
* *
529100 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGTATTGCGATTCTC-TCGTTGCGA
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCAT-GTTGCGA
529164 TTTTCATT
65 TTTTCATT
* *
529172 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATGTTGCGAT
529237 TTTCATT
66 TTTCATT
529244 TCGCATTGCGATT
1 TCGCATTGCGATT
529257 CTCTCGTTGC
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
72 79 0.99
73 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (72 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATGTTGCGAT
TTTCATT
Found at i:529285 original size:53 final size:52
Alignment explanation
Indices: 529106--529289 Score: 174
Period size: 53 Copynumber: 3.5 Consensus size: 52
529096 AGAATCGCAA
* * ** *
529106 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGTATTGCGATTCTCTCGT
1 TGCGATTGTAATTTCGTGTTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
* * ** *
529159 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATT
1 TGCGATTGTAATTTCGTGTTGCGATTTTCATTTCGCATTGCGATTCTCTC-GT
* * * * *
529210 TCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCG-ATTG-TAATTTCGTGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
529264 TGCGATTGTAATTTCCGTGTTGCGAT
1 TGCGATTGTAATTT-CGTGTTGCGAT
529290 AGTCAAATGC
Statistics
Matches: 108, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
50 2 0.02
51 5 0.05
52 18 0.17
53 76 0.70
54 5 0.05
55 2 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (52 bp):
TGCGATTGTAATTTCGTGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:531565 original size:12 final size:12
Alignment explanation
Indices: 531548--531572 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
531538 TCTTCGGGGA
531548 CTTTTTCTTCTT
1 CTTTTTCTTCTT
531560 CTTTTTCTTCTT
1 CTTTTTCTTCTT
531572 C
1 C
531573 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:531781 original size:24 final size:24
Alignment explanation
Indices: 531747--531793 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
531737 CTGAAACATC
531747 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
531771 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
531794 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:532514 original size:20 final size:20
Alignment explanation
Indices: 532486--532676 Score: 224
Period size: 20 Copynumber: 9.6 Consensus size: 20
532476 AAATTTCAGT
* * * *
532486 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
532506 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
** *
532526 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACGGATACGC
*
532546 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
532566 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
532586 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
532606 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
532626 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
532646 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
532666 GTTGCGATTTA
1 GTTGCGATTTA
532677 TGTGTTCGCG
Statistics
Matches: 145, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
19 3 0.02
20 140 0.97
21 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:532686 original size:20 final size:20
Alignment explanation
Indices: 532663--532714 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
532653 TTTACGGATA
* *
532663 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
*
532683 CGCGTTGTGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
532703 CGCGTTGCGATT
1 CGCGTTGCGATT
532715 CTTGAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.12, C:0.17, G:0.27, T:0.44
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:534968 original size:23 final size:22
Alignment explanation
Indices: 534942--534994 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
534932 TATAATTGAG
*
534942 TATATTATTATAGATATTAAAAA
1 TATAATATTATA-ATATTAAAAA
* *
534965 TATAATATTATATTATTATAAA
1 TATAATATTATAATATTAAAAA
534987 TATTAATA
1 TA-TAATA
534995 AATATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATAATATTATAATATTAAAAA
Found at i:545484 original size:18 final size:18
Alignment explanation
Indices: 545457--545491 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
545447 ATATTTTATT
545457 TAATTATTTAG-ATTACA
1 TAATTATTTAGAATTACA
545474 TAATATATTTAGAATTAC
1 TAAT-TATTTAGAATTAC
545492 CTAAAGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
TAATTATTTAGAATTACA
Found at i:556414 original size:55 final size:55
Alignment explanation
Indices: 556330--556446 Score: 207
Period size: 55 Copynumber: 2.1 Consensus size: 55
556320 TTAAGGGAGA
* *
556330 TCGATATAGTGCCGTGTGCGAGGTTTACACACCTGCACATAATGGGGCTGAAGGT
1 TCGATATAGTGCCGTCTGCGAGGTTTACACACCTGCACATAACGGGGCTGAAGGT
*
556385 TCGATATAGTGCCGTCTGCGAGGTTTACACACCTGCACATAACGGGGTTGAAGGT
1 TCGATATAGTGCCGTCTGCGAGGTTTACACACCTGCACATAACGGGGCTGAAGGT
556440 TCGATAT
1 TCGATAT
556447 GGATGCTGGC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (55 bp):
TCGATATAGTGCCGTCTGCGAGGTTTACACACCTGCACATAACGGGGCTGAAGGT
Found at i:559140 original size:17 final size:17
Alignment explanation
Indices: 559118--559171 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
559108 AATGTTAATA
559118 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
559135 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
559152 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
559169 TTT
1 TTT
559172 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:560732 original size:21 final size:21
Alignment explanation
Indices: 560702--560749 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
560692 GCAGGGGTAC
* *
560702 ATGCCCAGCCCTCCACTTTAT
1 ATGCCAAGCCCACCACTTTAT
*
560723 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTTAT
560744 ATGCCA
1 ATGCCA
560750 TCTCCGCAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.38, G:0.12, T:0.25
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTTAT
Found at i:560779 original size:21 final size:21
Alignment explanation
Indices: 560753--560825 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
560743 TATGCCATCT
*
560753 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
560774 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
560795 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
560816 CCGCAGGGTT
1 CCGCAGGGTT
560826 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:569446 original size:3 final size:3
Alignment explanation
Indices: 569438--569472 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
569428 TTCCAATGAA
569438 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
569473 ATCATCTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:569916 original size:4 final size:4
Alignment explanation
Indices: 569907--569967 Score: 83
Period size: 4 Copynumber: 16.0 Consensus size: 4
569897 ATGAGGATCC
*
569907 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG --TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
569953 TATA TATG TAT- TATG
1 TATG TATG TATG TATG
569968 ATGATGCAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.04
3 3 0.06
4 46 0.90
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:570654 original size:26 final size:26
Alignment explanation
Indices: 570618--570710 Score: 122
Period size: 26 Copynumber: 3.7 Consensus size: 26
570608 ATTTTGATTG
*
570618 ACTCTTCTTCTTCTTCTTAAACCCAA
1 ACTCATCTTCTTCTTCTTAAACCCAA
570644 ACTCATCTTCTTCTTCTTAAACCC-A
1 ACTCATCTTCTTCTTCTTAAACCCAA
*
570669 AC-C--CTATCTTCTTCTTCAACCCAA
1 ACTCATCT-TCTTCTTCTTAAACCCAA
*
570693 CCTCATCTTCTTCTTCTT
1 ACTCATCTTCTTCTTCTT
570711 TCTTTCTCTT
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
22 2 0.03
23 15 0.25
24 3 0.05
25 4 0.07
26 33 0.56
27 2 0.03
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (26 bp):
ACTCATCTTCTTCTTCTTAAACCCAA
Found at i:570708 original size:23 final size:23
Alignment explanation
Indices: 570626--570708 Score: 105
Period size: 23 Copynumber: 3.5 Consensus size: 23
570616 TGACTCTTCT
* *
570626 TCTTCTTCTTAAACCCAAACTCA
1 TCTTCTTCTTCAACCCAACCTCA
570649 TCTTCTTCTTCTTAAACCCAACC-CTA
1 TCTTCTTCTTC---AACCCAACCTC-A
570675 TCTTCTTCTTCAACCCAACCTCA
1 TCTTCTTCTTCAACCCAACCTCA
570698 TCTTCTTCTTC
1 TCTTCTTCTTC
570709 TTTCTTTCTC
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
23 31 0.58
24 1 0.02
25 1 0.02
26 20 0.38
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.40
Consensus pattern (23 bp):
TCTTCTTCTTCAACCCAACCTCA
Found at i:571599 original size:23 final size:23
Alignment explanation
Indices: 571543--571599 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
571533 AGAGAAAGAA
* *
571543 GAAGATGAAGATAGGGTTGGGTT
1 GAAGAAGAAGATAGGGTGGGGTT
* *
571566 -AATGAATAAGATGGGGTGGGGTT
1 GAA-GAAGAAGATAGGGTGGGGTT
571589 GAAGAAGAAGA
1 GAAGAAGAAGA
571600 AGAGTCAGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
22 2 0.07
23 23 0.85
24 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.42, T:0.21
Consensus pattern (23 bp):
GAAGAAGAAGATAGGGTGGGGTT
Found at i:572843 original size:42 final size:42
Alignment explanation
Indices: 572796--572944 Score: 226
Period size: 42 Copynumber: 3.5 Consensus size: 42
572786 CAAGAACTCT
*
572796 TCAAACTTTCAACTTAATTAGCATATTAATTAGCTAAACCTC
1 TCAAACTTTCAACTTAATAAGCATATTAATTAGCTAAACCTC
* *
572838 TCAAACTTTCAACTTAATAATCCTATTAATTAGCTAAACCTC
1 TCAAACTTTCAACTTAATAAGCATATTAATTAGCTAAACCTC
* * *
572880 TCAAACTTTCAACTTAATAATCCTATTAATTAGCTAAACCTT
1 TCAAACTTTCAACTTAATAAGCATATTAATTAGCTAAACCTC
* *
572922 TAAAACTTTCAACTTAATTAGCA
1 TCAAACTTTCAACTTAATAAGCA
572945 CATAACTTTG
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 99 1.00
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (42 bp):
TCAAACTTTCAACTTAATAAGCATATTAATTAGCTAAACCTC
Found at i:576094 original size:3 final size:3
Alignment explanation
Indices: 576086--576140 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
576076 ACCCGTCTTT
* *
576086 TTA TTA TTA TTTA ATA TTA TTA ATA TTA TTTA TTA TTA TTA TTA TT-
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
576132 TTGA TTA TT
1 TT-A TTA TT
576141 TTAATTACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 2 0.05
3 34 0.77
4 8 0.18
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:576103 original size:10 final size:10
Alignment explanation
Indices: 576085--576125 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
576075 CACCCGTCTT
*
576085 TTTATTATTA
1 TTTAATATTA
576095 TTTAATATTA
1 TTTAATATTA
576105 -TTAATATTA
1 TTTAATATTA
*
576114 TTTATTATTA
1 TTTAATATTA
576124 TT
1 TT
576126 ATTATTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTAATATTA
Found at i:576107 original size:16 final size:16
Alignment explanation
Indices: 576086--576132 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 16
576076 ACCCGTCTTT
576086 TTATTATTATTTAATA
1 TTATTATTATTTAATA
*
576102 TTATTAATATTATTTATTA
1 TTA-T--TATTATTTAATA
576121 TTATTATTATTT
1 TTATTATTATTT
576133 TGATTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 11 0.41
17 1 0.04
18 1 0.04
19 14 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTATTATTTAATA
Found at i:576114 original size:19 final size:19
Alignment explanation
Indices: 576090--576131 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
576080 GTCTTTTTAT
576090 TATTATTTAATATTATTAA
1 TATTATTTAATATTATTAA
* *
576109 TATTATTTATTATTATTAT
1 TATTATTTAATATTATTAA
576128 TATT
1 TATT
576132 TTGATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTATTTAATATTATTAA
Found at i:576147 original size:9 final size:10
Alignment explanation
Indices: 576088--576147 Score: 58
Period size: 9 Copynumber: 6.4 Consensus size: 10
576078 CCGTCTTTTT
576088 ATTATTATTTA
1 ATTATTA-TTA
576099 A-TATTATTA
1 ATTATTATTA
*
576108 A-TATTATTT
1 ATTATTATTA
576117 ATTATTATT-
1 ATTATTATTA
*
576126 ATTATT-TTG
1 ATTATTATTA
576135 ATTATT-TTA
1 ATTATTATTA
576144 ATTA
1 ATTA
576148 CATTTTGCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
8 2 0.04
9 30 0.67
10 12 0.27
11 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
ATTATTATTA
Found at i:577496 original size:38 final size:38
Alignment explanation
Indices: 577452--577527 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
577442 TTTAGTCCTC
577452 CATGTTTCTTGTTTATTTTATTTTAATATGTAAACATT
1 CATGTTTCTTGTTTATTTTATTTTAATATGTAAACATT
*
577490 CATGTTTCTTGTTTATTTTATTTTAATCTGTAAACATT
1 CATGTTTCTTGTTTATTTTATTTTAATATGTAAACATT
577528 ATTTAGGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.58
Consensus pattern (38 bp):
CATGTTTCTTGTTTATTTTATTTTAATATGTAAACATT
Found at i:577686 original size:29 final size:30
Alignment explanation
Indices: 577649--577821 Score: 128
Period size: 30 Copynumber: 5.9 Consensus size: 30
577639 TTAAACCCTT
* *
577649 TAAGATTCTATTTTTAT-TGTTTTAGTCCC
1 TAAGTTTCTATTTTTATCTATTTTAGTCCC
* **
577678 TAAGTTTCTA-TTTT-GCTATTTTAGTTCTT
1 TAAGTTTCTATTTTTATCTATTTTAG-TCCC
* * *
577707 TAAG-TT-TATGTTTTATCCATTTTGGTCCT
1 TAAGTTTCTAT-TTTTATCTATTTTAGTCCC
*
577736 TGAAGTTTCTA-TTTTATCTATTTTGGTCCC
1 T-AAGTTTCTATTTTTATCTATTTTAGTCCC
* *
577766 TGAAGTTTCT-TTTTTATATATTTTAGACCC
1 T-AAGTTTCTATTTTTATCTATTTTAGTCCC
* *
577796 TTAAGTTTTTGTTTTTA-CTATTTTAG
1 -TAAGTTTCTATTTTTATCTATTTTAG
577822 CCATTTAAGT
Statistics
Matches: 117, Mismatches: 16, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.02
28 13 0.11
29 23 0.20
30 68 0.58
31 9 0.08
32 2 0.02
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.57
Consensus pattern (30 bp):
TAAGTTTCTATTTTTATCTATTTTAGTCCC
Found at i:577773 original size:60 final size:59
Alignment explanation
Indices: 577668--577916 Score: 159
Period size: 60 Copynumber: 4.2 Consensus size: 59
577658 ATTTTTATTG
* * * * *
577668 TTTTAGTCCCTAAGTTTCTATTTTGCTATTTTAGTTC-TTTAAGTTTATGTTTTATCCA
1 TTTTGGTCCTTAAGTTTCTATTTTTCTATTTTAGTCCATTGAAGTTTATGTTTTATCCA
* * * * **
577726 TTTTGGTCCTTGAAGTTTCTATTTTATCTATTTTGGTCC-CTGAAGTTTCTTTTTTATATA
1 TTTTGGTCCTT-AAGTTTCTATTTT-TCTATTTTAGTCCATTGAAGTTTATGTTTTATCCA
** * * * **
577786 TTTTAGACCCTTAAGTTTTTGTTTTTACTATTTTAG-CCATTTAAGTTTATGTTTTGGCCA
1 TTTT-GGTCCTTAAGTTTCTATTTTT-CTATTTTAGTCCATTGAAGTTTATGTTTTATCCA
* * * * * * *
577846 TATTAGTCCTTTAAATTCCTATTTGTACTATTTT-GATCCTTTG-AGTTTATGTGTTTA-CTA
1 TTTTGGTCC-TTAAGTTTCTATTT-TTCTATTTTAG-TCCATTGAAGTTTATGT-TTTATCCA
577906 TTTTGGTCCTT
1 TTTTGGTCCTT
577917 TATAATTTCA
Statistics
Matches: 142, Mismatches: 39, Indels: 19
0.71 0.19 0.09
Matches are distributed among these distances:
58 9 0.06
59 21 0.15
60 99 0.70
61 13 0.09
ACGTcount: A:0.18, C:0.14, G:0.12, T:0.55
Consensus pattern (59 bp):
TTTTGGTCCTTAAGTTTCTATTTTTCTATTTTAGTCCATTGAAGTTTATGTTTTATCCA
Found at i:577820 original size:30 final size:29
Alignment explanation
Indices: 577747--577840 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 29
577737 GAAGTTTCTA
* *
577747 TTTTATCTATTTTGGTCCCTGAAGTTTCTT-T
1 TTTTA-CTATTTTAG-CCCTTAAGTTT-TTGT
577778 TTTATA-TATTTTAGACCCTTAAGTTTTTGT
1 TTT-TACTATTTTAG-CCCTTAAGTTTTTGT
* *
577808 TTTTACTATTTTAGCCATTTAAGTTTATGT
1 TTTTACTATTTTAGCC-CTTAAGTTTTTGT
577838 TTT
1 TTT
577841 GGCCATATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
29 6 0.11
30 43 0.80
31 3 0.06
32 2 0.04
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.59
Consensus pattern (29 bp):
TTTTACTATTTTAGCCCTTAAGTTTTTGT
Found at i:577831 original size:120 final size:118
Alignment explanation
Indices: 577654--577880 Score: 271
Period size: 120 Copynumber: 1.9 Consensus size: 118
577644 CCCTTTAAGA
* * * *
577654 TTCTATTTTTATTGTTTTAGTCCCTAAGTTTCTATTTTGCTATTTTAGTTCTTTAAGTTTATGTT
1 TTCTATTTTTATTATTTTAGACCCTAAGTTTCTATTTTACTATTTTAGTCCTTTAAGTTTATGTT
* * * * *
577719 TTATCCATTTTGGTCCTTGAAGTTTCTATTT-TATCTATTTTGGTCCCTGAAGT
66 TTAGCCATATTAGTCCTTGAAATTCCTATTTGTA-CTATTTTGGTCCCTGAAGT
* *
577772 TTCT-TTTTTATATATTTTAGACCCTTAAGTTTTTGTTTTTACTATTTTAG-CCATTTAAGTTTA
1 TTCTATTTTTAT-TATTTTAGACCC-TAAGTTTCT-ATTTTACTATTTTAGTCC-TTTAAGTTTA
* *
577835 TGTTTTGGCCATATTAGTCCTTTAAATTCCTATTTGTACTATTTTG
62 TGTTTTAGCCATATTAGTCCTTGAAATTCCTATTTGTACTATTTTG
577881 ATCCTTTGAG
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
117 7 0.08
118 14 0.15
119 9 0.10
120 59 0.65
121 2 0.02
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.56
Consensus pattern (118 bp):
TTCTATTTTTATTATTTTAGACCCTAAGTTTCTATTTTACTATTTTAGTCCTTTAAGTTTATGTT
TTAGCCATATTAGTCCTTGAAATTCCTATTTGTACTATTTTGGTCCCTGAAGT
Found at i:583341 original size:4 final size:4
Alignment explanation
Indices: 583332--584532 Score: 2351
Period size: 4 Copynumber: 301.8 Consensus size: 4
583322 ATCGAGAAAA
583332 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583380 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583428 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583476 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583524 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583570 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583618 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583666 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
583714 ACAT ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583762 ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583808 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583856 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583904 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583952 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
583999 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584047 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584095 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584143 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584191 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584239 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584287 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584335 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584383 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584431 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584479 ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
584526 ACAT ACA
1 ACAT ACA
584533 GTATATTAAG
Statistics
Matches: 1189, Mismatches: 2, Indels: 12
0.99 0.00 0.01
Matches are distributed among these distances:
2 4 0.00
3 6 0.01
4 1179 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:584997 original size:104 final size:101
Alignment explanation
Indices: 584871--585171 Score: 366
Period size: 103 Copynumber: 3.0 Consensus size: 101
584861 ATTTAAGATA
*
584871 ATTTCTCTT-AAAACAAACTTCGTCTCGCTTGAGACATTTTTCTTTGAGATACGAATTTTGAATT
1 ATTTCT-TTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCTTTGAGATAC-AATTTT-AATT
584935 TGATTCACTTGAAACAAAATTAATCTCACTTGAGATTGTT
63 TG-TTCACTTGAAACAAAATTAATCTCACTTGAGATTGTT
* *
584975 ATTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGATATACATATTTCAAATT
1 ATTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTT-CTTTGAGATACA-ATTT-TAATT
585040 TGCTTCACTTG-AA-AAAATTAATCTCACTTGAGATTGTT
63 TG-TTCACTTGAAACAAAATTAATCTCACTTGAGATTGTT
* * * * ** * *
585078 GTTTATTTCAAAACAAATTTCGTCTCACTTGAGATA-TTTTCCCTCAGAATACAAATTT-A-TT-
1 ATTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCTTTGAG-ATACAATTTTAATTTG
585139 TT-ACTTGAAACAAAATTAATCTCACTTGAGATT
65 TTCACTTGAAACAAAATTAATCTCACTTGAGATT
585172 TTCAAAACTG
Statistics
Matches: 176, Mismatches: 14, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
95 5 0.03
96 4 0.02
97 22 0.12
98 2 0.01
99 1 0.01
101 6 0.03
102 9 0.05
103 59 0.34
104 40 0.23
105 28 0.16
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (101 bp):
ATTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCTTTGAGATACAATTTTAATTTGT
TCACTTGAAACAAAATTAATCTCACTTGAGATTGTT
Found at i:586797 original size:13 final size:13
Alignment explanation
Indices: 586775--586808 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
586765 TATGTAATTC
* *
586775 TGTGGAACATATG
1 TGTGGTACATATA
586788 TGTGGTACATATA
1 TGTGGTACATATA
586801 TGTGGTAC
1 TGTGGTAC
586809 TTCGGTACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.35
Consensus pattern (13 bp):
TGTGGTACATATA
Found at i:587203 original size:13 final size:12
Alignment explanation
Indices: 587164--587205 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
587154 TATGCGTGCA
587164 TGTATAT-AATT
1 TGTATATGAATT
*
587175 TGTTATATGAACT
1 TG-TATATGAATT
587188 TGTATATGATATT
1 TGTATATGA-ATT
587201 TGTAT
1 TGTAT
587206 TATATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 2 0.08
12 12 0.46
13 12 0.46
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.52
Consensus pattern (12 bp):
TGTATATGAATT
Found at i:587935 original size:27 final size:27
Alignment explanation
Indices: 587879--587935 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
587869 GTTGTCTCTC
* *
587879 TTGAGACGTTTCTATTAAAAACAACCT
1 TTGAGACGTTTCCATTAAAAACAAACT
* *
587906 TTGAGATCGTTTCCATT-GAAACAAATT
1 TTGAGA-CGTTTCCATTAAAAACAAACT
587933 TTG
1 TTG
587936 TCTGCCTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (27 bp):
TTGAGACGTTTCCATTAAAAACAAACT
Found at i:587985 original size:31 final size:31
Alignment explanation
Indices: 587950--588027 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
587940 CCTTGAGGCA
* *
587950 GTTTCTTTGGAAACACAAA-ATCTTTGAGTCT
1 GTTTCTCTAGAAACA-AAACATCTTTGAGTCT
587981 GTTTCTCTAGAAACAAAACCATCTTTGAGTC-
1 GTTTCTCTAGAAACAAAA-CATCTTTGAGTCT
* *
588012 ATTTC-CTTGAAACAAA
1 GTTTCTCTAGAAACAAA
588028 TTTTGTCTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 13 0.32
31 17 0.41
32 11 0.27
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (31 bp):
GTTTCTCTAGAAACAAAACATCTTTGAGTCT
Found at i:588026 original size:30 final size:32
Alignment explanation
Indices: 587969--588027 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
587959 GAAACACAAA
*
587969 ATCTTTGAGTCTGTTTCTCTAGAAACAAAACC
1 ATCTTTGAGTCTATTTCTCTAGAAACAAAACC
*
588001 ATCTTTGAGTC-ATTTC-CTTGAAACAAA
1 ATCTTTGAGTCTATTTCTCTAGAAACAAA
588028 TTTTGTCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 10 0.40
31 4 0.16
32 11 0.44
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (32 bp):
ATCTTTGAGTCTATTTCTCTAGAAACAAAACC
Found at i:588095 original size:28 final size:28
Alignment explanation
Indices: 588064--588129 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
588054 TCGAAGCATC
*
588064 ATCTTTGAGTTT-TTTTTTCTTGAAACAA
1 ATCTTTGAGTTTGTTTCTT-TTGAAACAA
588092 ATCTTTGAGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAGTTTGTTTCTTTTGAAACAA
588120 ATCTTTGAGT
1 ATCTTTGAGT
588130 CGGTTACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 31 0.86
29 5 0.14
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.52
Consensus pattern (28 bp):
ATCTTTGAGTTTGTTTCTTTTGAAACAA
Found at i:588142 original size:28 final size:28
Alignment explanation
Indices: 588082--588145 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
588072 GTTTTTTTTT
** * *
588082 CTTGAAACAAATCTTTGAGTTTGTTTCT
1 CTTGAAACAAATCTTTGAGTCGGTTACC
*
588110 TTTGAAACAAATCTTTGAGTCGGTTACC
1 CTTGAAACAAATCTTTGAGTCGGTTACC
588138 CTTGAAAC
1 CTTGAAAC
588146 CAAAATCCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (28 bp):
CTTGAAACAAATCTTTGAGTCGGTTACC
Found at i:588397 original size:134 final size:134
Alignment explanation
Indices: 588153--588400 Score: 299
Period size: 134 Copynumber: 1.9 Consensus size: 134
588143 AACCAAAATC
588153 CCTAAAGATGGATAACCGTCCTCATCACGTAAGAACCGTGTCATCCCCCGACCAGATCTCTTCAT
1 CCTAAAGATGGATAACCGTCCTCATCACGTAAGAACCGTGTCATCCCCCGACCAGATCTCTTCAT
* * * * * *
588218 TACGTAAGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACATAGGAACCGAGTTATAAC
66 CACGTAAGAGCCATGTCACCCCTAGACAACCAGACGTACTAATCACATAGGAACCGAGTTATAAC
588283 CCTT
131 CCTT
* * * *
588287 CCTAAAGATGGCCATAA-C-TCTTCATCACGTATGAGCCGTGTCATCCCCCGACTAGATCT-TCT
1 CCTAAAGATGG--ATAACCGTCCTCATCACGTAAGAACCGTGTCATCCCCCGACCAGATCTCT-T
* * *
588349 CATCACGT-AGAAGCCATGTCACCCTTAGACAACCCGAAC-TATTAATCACATA
63 CATCACGTAAG-AGCCATGTCACCCCTAGACAACCAG-ACGTACTAATCACATA
588401 TGAGCAGTGT
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
133 3 0.03
134 87 0.91
135 2 0.02
136 4 0.04
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.23
Consensus pattern (134 bp):
CCTAAAGATGGATAACCGTCCTCATCACGTAAGAACCGTGTCATCCCCCGACCAGATCTCTTCAT
CACGTAAGAGCCATGTCACCCCTAGACAACCAGACGTACTAATCACATAGGAACCGAGTTATAAC
CCTT
Found at i:590157 original size:31 final size:31
Alignment explanation
Indices: 590094--590176 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
590084 TTAGTTCTTT
* *
590094 AAGTTTCTGTTTTATCCA-TTTTGGTTCCTG
1 AAGTTTCTATTTTATCTATTTTTGGTTCCTG
590124 AAGTTTCTATTTTATCTATTTTTGG-TCCGTG
1 AAGTTTCTATTTTATCTATTTTTGGTTCC-TG
*
590155 AAGTTTCTATTTTATGTATTTT
1 AAGTTTCTATTTTATCTATTTT
590177 AGACTCTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
30 19 0.40
31 29 0.60
ACGTcount: A:0.17, C:0.12, G:0.14, T:0.57
Consensus pattern (31 bp):
AAGTTTCTATTTTATCTATTTTTGGTTCCTG
Found at i:598693 original size:12 final size:12
Alignment explanation
Indices: 598678--598748 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
598668 ATAGTTTAGC
598678 ATATATTATAAT
1 ATATATTATAAT
598690 ATAT-TATATAGTAT
1 ATATAT-TATA--AT
*
598704 ATTATATTATAGT
1 A-TATATTATAAT
598717 ATATATTAT-AT
1 ATATATTATAAT
*
598728 -TATATCAT-AT
1 ATATATTATAAT
598738 ATTATATTATA
1 A-TATATTATA
598749 GAGAAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
10 9 0.19
11 2 0.04
12 23 0.49
13 2 0.04
14 3 0.06
15 7 0.15
16 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (12 bp):
ATATATTATAAT
Found at i:598698 original size:17 final size:16
Alignment explanation
Indices: 598678--598748 Score: 97
Period size: 17 Copynumber: 4.2 Consensus size: 16
598668 ATAGTTTAGC
*
598678 ATATATTATAATATATT
1 ATATA-TATATTATATT
598695 ATATAGTATATTATATT
1 ATATA-TATATTATATT
598712 ATAGTATATATTATATT
1 ATA-TATATATTATATT
598729 ATATCATATATTATATT
1 ATAT-ATATATTATATT
598746 ATA
1 ATA
598749 GAGAAAATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
16 1 0.02
17 47 0.94
18 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (16 bp):
ATATATATATTATATT
Found at i:598937 original size:19 final size:19
Alignment explanation
Indices: 598913--599017 Score: 102
Period size: 19 Copynumber: 5.2 Consensus size: 19
598903 GCGATTTTGA
*
598913 AAAATGTGTTGTGATAGTT
1 AAAATGTGTTGCGATAGTT
598932 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
598951 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
* *
598971 GAAAAACGTGTTGTTGTGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
598995 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
599014 AAAA
1 AAAA
599018 ATCCAAAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
19 50 0.68
20 3 0.04
22 8 0.11
24 3 0.04
25 9 0.12
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:599331 original size:5 final size:5
Alignment explanation
Indices: 599323--599363 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
599313 TCGTCCCGTC
599323 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
599364 TGGTAATACG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:599352 original size:6 final size:6
Alignment explanation
Indices: 599326--599367 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
599316 TCCCGTCTCG
599326 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
599368 AATACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:599581 original size:5 final size:5
Alignment explanation
Indices: 599571--599632 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
599561 TTATTTTCTC
* * * *
599571 TATAT TATAT TATAT TGT-T TATAT TATAAA AATAT TATAG TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TA-TAT TATAT
599622 TATTAT TATAT
1 TA-TAT TATAT
599633 ATTAATTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
4 3 0.07
5 30 0.67
6 12 0.27
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:599582 original size:19 final size:19
Alignment explanation
Indices: 599560--599598 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
599550 GGTCACTGAG
*
599560 ATTATTTTCTCTATATTAT
1 ATTATATTCTCTATATTAT
* *
599579 ATTATATTGTTTATATTAT
1 ATTATATTCTCTATATTAT
599598 A
1 A
599599 AAAATATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTATATTCTCTATATTAT
Found at i:599617 original size:11 final size:10
Alignment explanation
Indices: 599603--599636 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
599593 ATTATAAAAA
599603 TATTATAGTAT
1 TATTATA-TAT
599614 TATTATATTAT
1 TATTATA-TAT
599625 TATTATATAT
1 TATTATATAT
599635 TA
1 TA
599637 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
TATTATATAT
Found at i:601670 original size:26 final size:26
Alignment explanation
Indices: 601619--601672 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
601609 ATTCAAAACC
*
601619 TAGGACGCTTGATTTATTTCATGTCT
1 TAGGACGCTTGATTTATTTCACGTCT
*
601645 TAGGACGCTTGATTTATTTCCCGTCT
1 TAGGACGCTTGATTTATTTCACGTCT
601671 TA
1 TA
601673 CTTTAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (26 bp):
TAGGACGCTTGATTTATTTCACGTCT
Found at i:606511 original size:24 final size:23
Alignment explanation
Indices: 606478--606544 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 23
606468 CCATATACAT
606478 TTTTAACTTTAAAATCTTTTCTTTA
1 TTTT-ACTTTAAAATCTTTT-TTTA
*
606503 TTTTACTTT-AAAT-TATTTTTA
1 TTTTACTTTAAAATCTTTTTTTA
606524 TTATTA-TTTAAATATCTTTTT
1 TT-TTACTTTAAA-ATCTTTTT
606545 ACCTAACCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 9 0.25
22 8 0.22
23 6 0.17
24 9 0.25
25 4 0.11
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTACTTTAAAATCTTTTTTTA
Found at i:612261 original size:19 final size:19
Alignment explanation
Indices: 612239--612277 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
612229 TGGAAATATA
612239 ACCAAAAAATGGTATCGAT
1 ACCAAAAAATGGTATCGAT
**
612258 ACCATTAAATGGTATCGAT
1 ACCAAAAAATGGTATCGAT
612277 A
1 A
612278 GTACTCTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (19 bp):
ACCAAAAAATGGTATCGAT
Found at i:615172 original size:41 final size:43
Alignment explanation
Indices: 615117--615236 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 43
615107 AAATGGTAAG
*
615117 TATG-AAAATAAGCTTATGAGCTTATGGAATAATGGAAAGTA-
1 TATGTAAAATAAGCTTACGAGCTTATGGAATAATGGAAAGTAT
* *
615158 TAT-TAAAATAAGCTTACGAGCTTATGGAAATTAAATGGTAGGTAT
1 TATGTAAAATAAGCTTACGAGCTTATGG-AA-T-AATGGAAAGTAT
* *
615203 TTTGGTAAAATAAGCTTACGAGCTTATGGGATAA
1 TAT-GTAAAATAAGCTTACGAGCTTATGGAATAA
615237 ATGGTAAGAG
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
41 25 0.37
42 2 0.03
43 1 0.01
44 11 0.16
45 3 0.04
46 1 0.01
47 24 0.36
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.32
Consensus pattern (43 bp):
TATGTAAAATAAGCTTACGAGCTTATGGAATAATGGAAAGTAT
Found at i:615215 original size:47 final size:41
Alignment explanation
Indices: 615121--615236 Score: 133
Period size: 47 Copynumber: 2.7 Consensus size: 41
615111 GGTAAGTATG
*
615121 AAAATAAGCTTATGAGCTTATGGAATAATGGAAAGTATATT
1 AAAATAAGCTTACGAGCTTATGGAATAATGGAAAGTATATT
* * *
615162 AAAATAAGCTTACGAGCTTATGGAAATTAAATGGTAGGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGG-AA-T-AATGGAAAGTA-TAT--T
*
615209 AAAATAAGCTTACGAGCTTATGGGATAA
1 AAAATAAGCTTACGAGCTTATGGAATAA
615237 ATGGTAAGAG
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
41 22 0.34
42 2 0.03
43 1 0.02
44 11 0.17
45 3 0.05
46 1 0.02
47 24 0.38
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.31
Consensus pattern (41 bp):
AAAATAAGCTTACGAGCTTATGGAATAATGGAAAGTATATT
Done.