Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold14
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: 2879421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 64274 characters in sequence are not A, C, G, or T
File 3 of 17
Found at i:376352 original size:15 final size:15
Alignment explanation
Indices: 376332--376372 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
376322 GTTCATCAAT
376332 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
376347 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
376362 CTCAATTTGGA
1 TTC-ATTTGGA
376373 CATTCTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:380473 original size:19 final size:20
Alignment explanation
Indices: 380430--380480 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
380420 TACAAGCCAA
*
380430 TGTATCGATACATTTTATGG
1 TGTATCGATACATCTTATGG
380450 TGTATCGATACATACTT-T-G
1 TGTATCGATACAT-CTTATGG
380469 TGTATCGATACA
1 TGTATCGATACA
380481 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.45
20 14 0.48
21 2 0.07
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATCTTATGG
Found at i:382540 original size:21 final size:20
Alignment explanation
Indices: 382511--382549 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
382501 GGCTAGTGTG
*
382511 GGGACTGCCCGGTTGCGACTT
1 GGGACTG-CCGGTCGCGACTT
*
382532 GGGAGTGCCGGTCGCGAC
1 GGGACTGCCGGTCGCGAC
382550 CTGGTGGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.10, C:0.28, G:0.44, T:0.18
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACTT
Found at i:385092 original size:15 final size:15
Alignment explanation
Indices: 385072--385112 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
385062 GTTCATCAAT
385072 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
385087 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
385102 CTCAATTTGGA
1 TTC-ATTTGGA
385113 CATTCTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:389209 original size:13 final size:13
Alignment explanation
Indices: 389191--389215 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
389181 CATTTTATGG
389191 TGTATCGATACAA
1 TGTATCGATACAA
389204 TGTATCGATACA
1 TGTATCGATACA
389216 TACTTTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:389231 original size:32 final size:33
Alignment explanation
Indices: 389168--389235 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
389158 CGTTACAAGC
*
389168 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATCTTATGGTGTATCGATA
389201 CAATGTATCGATACATACTT-T-GTGTATCGATA
1 CAATGTATCGATACAT-CTTATGGTGTATCGATA
389233 CAA
1 CAA
389236 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATCTTATGGTGTATCGATA
Found at i:392242 original size:105 final size:104
Alignment explanation
Indices: 391829--392243 Score: 306
Period size: 105 Copynumber: 3.9 Consensus size: 104
391819 CTCCAAAGAT
* * * *
391829 AAAATTGTGAAAATATTTAAGAACAAAGAGAAAATATGA-TTTTTTATGAAGAACAGGGCTAAAG
1 AAAATTATGAAAATATTTAAGAACAAAGAGAAAATTTGATTTTTTTATGAAGAACAGGGAT-TAG
* * * * *
391893 TGTTTCCTC--AGAGTAATGAGATTGGAGTTTTTCCCGAAG
65 AGTATCCTCTTAGAGTAGTGAGGTTGGAG-TTTTCCAGAAG
** * * * *
391932 ATAAAATTATGAAAATACCTATGGACAAAGAGAGAATTTAATTCGATTTTTTTATGAAGAA-TGG
1 --AAAATTATGAAAATATTTAAGAAC-AA-AGAGAA---AATTTGATTTTTTTATGAAGAACAGG
* * * * *
391996 GATTAGAGTATTCTCTTATACTAGTGAGGTTGGACTTTTTCCAGAGG
59 GATTAGAGTATCCTCTTAGAGTAGTGAGGTTGGA-GTTTTCCAGAAG
* * * *
392043 TAAAATTATGAAAATATTTAAGAACAAAGAGAAAATCTGATTCTTTTATAAAGAAC-GAGG-TTG
1 -AAAATTATGAAAATATTTAAGAACAAAGAGAAAATTTGATTTTTTTATGAAGAACAG-GGATTA
* * * * * * **
392106 GCGTATCC-CCTCGAAGGAGTAAGGTTAGAGTTTTCTTGAAG
64 GAGTATCCTCTTAG-AGTAGTGAGGTTGGAGTTTTCCAGAAG
* * * *
392147 ACAAACTTATGAAAACATTTAGGGACAAAGAGAAAATTTGATTTTTTTATGAAGAACAGGG-TTG
1 A-AAA-TTATGAAAATATTTAAGAACAAAGAGAAAATTTGATTTTTTTATGAAGAACAGGGATTA
*
392211 GAGTATCCTCTTAGAGTAGTGGGGTTGGAGTTT
64 GAGTATCCTCTTAGAGTAGTGAGGTTGGAGTTT
392244 CCCCGAAGTC
Statistics
Matches: 239, Mismatches: 55, Indels: 32
0.73 0.17 0.10
Matches are distributed among these distances:
103 1 0.00
104 13 0.05
105 129 0.54
106 8 0.03
107 6 0.03
108 6 0.03
109 10 0.04
110 30 0.13
111 36 0.15
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (104 bp):
AAAATTATGAAAATATTTAAGAACAAAGAGAAAATTTGATTTTTTTATGAAGAACAGGGATTAGA
GTATCCTCTTAGAGTAGTGAGGTTGGAGTTTTCCAGAAG
Found at i:393243 original size:378 final size:375
Alignment explanation
Indices: 392664--393397 Score: 904
Period size: 378 Copynumber: 1.9 Consensus size: 375
392654 AGCATATGCA
392664 GAAAAAAAAGAACCAAAATTTAAAAAAACATTTTGGGCTCACCTAAAACATTAAATAAAAAACCA
1 GAAAAAAAAGAACCAAAATTTAAAAAAACATTTTGGGCTCACCTAAAACATTAAATAAAAAACCA
* ** * ** * * * *
392729 TACCTTTTTGGAAAGAGAACTTTGTAAACTTTTTAAGAAAATATTTGAAAGTTTTGGAAAGTCGT
66 CACCTTTTCAGAAAGAGAAATTCATAAACTATTTAAGAAAATATTTCAAAATTTTGGAAAATCGT
* * *
392794 TTGATGGGCCCAAATGGCCTAAACAAAATATCGCATGCTAATTCTAGAGGTTTCAAACAGTAAAT
131 TTGATGGGCCCAAATGGCCTAAACAAAATATCGCATGCTAACTCTAGAGGTTCCAAACAGTAAAG
* *
392859 GTTTGAAAAATTATAACTCTCTCATCCGGAATGATCCAAGGGAGAACGAGACACCTTTGGAAAGG
196 GTTTGAAAAATTATAACTCCCTCATCCGGAATGATCCAAGGGAGAACGAGACAACTTTGGAAAGG
392924 TATTTCAATGCCCTTTAAGGAAAAAATAT-ATAAAAAGTCAAGAAAATATTTTGTGGTTCAAAAA
261 TATTTCAATGCCCTTTAAGG--AAAATATCAT-AAAAGTCAAGAAAATATTTTGTGGTTCAAAAA
**
392988 -TTTTTTCCAACCTTAGGCTACAATACTGCCAGACATTGGCAGCATATGTAAG
323 GGATTTTCCAACCTTAGGCTACAATACTGCCAGACATTGGCAGCATATGTAAG
* * * * * * ***
393040 GAAAAAAACA-AATCAAAATTTGAAAAATCATTTTGGGCTTATCTAGAATCATTAAATCGTAAAC
1 GAAAAAAA-AGAACCAAAATTTAAAAAAACATTTTGGGCTCACCTA-AAACATTAAATAAAAAAC
*
393104 CACACCTTTTCAGAAAGCA-AAATTCATAAACTATTTGAGAAAA-ATATTCAAAATTTTGGAAAA
64 CACACCTTTTCAGAAAG-AGAAATTCATAAACTATTTAAGAAAATAT-TTCAAAATTTTGG-AAA
* * * * * * * * **
393167 ATCTTTTGGTGGGCCGAAATGG-CTCGAACAAAATATTGTATGCTAGCTCTAGAGGTTCCGATTA
126 ATCGTTTGATGGGCCCAAATGGCCT-AAACAAAATATCGCATGCTAACTCTAGAGGTTCCAAACA
* * * * * * *
393231 GTAAAGGTTTGAAAAATTATAACTCCCTTATCCGTAATGATCCAATGGTGAAGGGGATAACTTTG
190 GTAAAGGTTTGAAAAATTATAACTCCCTCATCCGGAATGATCCAAGGGAGAACGAGACAACTTTG
* * *
393296 GAAAGTTATTTCGATGCCCTTTAAGGAAAATATCATAAAAGTCAAGAAGATATTTTGTGGTTCAA
255 GAAAGGTATTTCAATGCCCTTTAAGGAAAATATCATAAAAGTCAAGAAAATATTTTGTGGTTCAA
* *
393361 AAAGGATTTTCCAACCTTAGGCTATAATGCTGCCAGA
320 AAAGGATTTTCCAACCTTAGGCTACAATACTGCCAGA
393398 GCAAAATAGG
Statistics
Matches: 301, Mismatches: 49, Indels: 15
0.82 0.13 0.04
Matches are distributed among these distances:
376 78 0.26
377 92 0.31
378 131 0.44
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (375 bp):
GAAAAAAAAGAACCAAAATTTAAAAAAACATTTTGGGCTCACCTAAAACATTAAATAAAAAACCA
CACCTTTTCAGAAAGAGAAATTCATAAACTATTTAAGAAAATATTTCAAAATTTTGGAAAATCGT
TTGATGGGCCCAAATGGCCTAAACAAAATATCGCATGCTAACTCTAGAGGTTCCAAACAGTAAAG
GTTTGAAAAATTATAACTCCCTCATCCGGAATGATCCAAGGGAGAACGAGACAACTTTGGAAAGG
TATTTCAATGCCCTTTAAGGAAAATATCATAAAAGTCAAGAAAATATTTTGTGGTTCAAAAAGGA
TTTTCCAACCTTAGGCTACAATACTGCCAGACATTGGCAGCATATGTAAG
Found at i:408532 original size:20 final size:20
Alignment explanation
Indices: 408509--408562 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
408499 CATTTCAAGC
*
408509 ATGTATTGATACATTCACTT
1 ATGTATCGATACATTCACTT
* *
408529 ATGTATCAATACATTCAGTT
1 ATGTATCGATACATTCACTT
408549 ATTGTATCGATACA
1 A-TGTATCGATACA
408563 AATTATAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:411864 original size:108 final size:108
Alignment explanation
Indices: 411675--411892 Score: 321
Period size: 108 Copynumber: 2.0 Consensus size: 108
411665 TATAGTTGTC
* * * * *
411675 TTTCTTTAGCTATTGCTAAGTTTAGAAATAAGGAAAAACCATAGACACCATTTTTTTTCGGGGTA
1 TTTCTTTAGCTATTGCTAAGTTTAGAAATAAGGAAAAACCATAAACACCATTTTGTCTCAGAGTA
* * *
411740 TGATAAAGTCCCTTGAGATCTCATAAAGAAAATGGAAACAAAG
66 TAATAAAGTCCATTGAGATCTCATAAAGAAAAGGGAAACAAAG
*
411783 TTTCTTTAGCTATTGCTAAGTATTAGGAATAAGGAAAAACCATAAACACCATTTTGTCT-AGAGT
1 TTTCTTTAGCTATTGCTAAGT-TTAGAAATAAGGAAAAACCATAAACACCATTTTGTCTCAGAGT
**
411847 ATAATAAAGTCCATTGAGATCTGGTAAAGAAAAGGGAAACAAAG
65 ATAATAAAGTCCATTGAGATCTCATAAAGAAAAGGGAAACAAAG
411891 TT
1 TT
411893 AATTAATTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
108 65 0.66
109 33 0.34
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (108 bp):
TTTCTTTAGCTATTGCTAAGTTTAGAAATAAGGAAAAACCATAAACACCATTTTGTCTCAGAGTA
TAATAAAGTCCATTGAGATCTCATAAAGAAAAGGGAAACAAAG
Found at i:417563 original size:35 final size:34
Alignment explanation
Indices: 417499--417597 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 34
417489 GACTGGAACA
**
417499 AAACCAATAGTCTTAGAATAACTCAATGACCTAGGCG
1 AAACCAATAGT-TTA-AATAACTTGATGACCT-GGCG
*
417536 -AACCAATAGTTTGAAATAACTTGATGACCTGGTG
1 AAACCAATAGTTT-AAATAACTTGATGACCTGGCG
* * *
417570 AAACCAATAGTCTAAAAAAATTGATGAC
1 AAACCAATAGTTTAAATAACTTGATGAC
417598 TTAGATGGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
34 16 0.30
35 27 0.50
36 11 0.20
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.24
Consensus pattern (34 bp):
AAACCAATAGTTTAAATAACTTGATGACCTGGCG
Found at i:418526 original size:18 final size:19
Alignment explanation
Indices: 418491--418530 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
418481 TTGAACATTT
418491 AAAATTTAAATTTCTAAAA
1 AAAATTTAAATTTCTAAAA
**
418510 AAAATTTATCTTT-TAAAA
1 AAAATTTAAATTTCTAAAA
418528 AAA
1 AAA
418531 TGATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTTAAATTTCTAAAA
Found at i:419108 original size:25 final size:26
Alignment explanation
Indices: 419059--419110 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
419049 ATTTAGTGAT
*
419059 TTCATGTCAACAGATATTATATTTTA
1 TTCATGTCAACAGATATAATATTTTA
* *
419085 TTCATGTTAA-AGATATAATTTTTTA
1 TTCATGTCAACAGATATAATATTTTA
419110 T
1 T
419111 CTATAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (26 bp):
TTCATGTCAACAGATATAATATTTTA
Found at i:420912 original size:32 final size:32
Alignment explanation
Indices: 420876--420939 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
420866 TAGTAAAGAA
* *
420876 AATGGAAACACAGTT-GTTCAATTTTGCCAAGT
1 AATGGAAACAAAGTTAATT-AATTTTGCCAAGT
*
420908 AATGGGAACAAAGTTAATTAATTTTGCCAAGT
1 AATGGAAACAAAGTTAATTAATTTTGCCAAGT
420940 TTTAGTGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (32 bp):
AATGGAAACAAAGTTAATTAATTTTGCCAAGT
Found at i:422920 original size:16 final size:16
Alignment explanation
Indices: 422882--422920 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
422872 TAAAATTTAA
* *
422882 ATTTCTAAAAAAAATT
1 ATTTTTAAAAAAAATG
422898 ATCTTTTAAAAAAAATG
1 AT-TTTTAAAAAAAATG
422915 ATTTTT
1 ATTTTT
422921 TTTAGAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (16 bp):
ATTTTTAAAAAAAATG
Found at i:422921 original size:17 final size:17
Alignment explanation
Indices: 422887--422920 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
422877 TTTAAATTTC
*
422887 TAAAAAAAATTATCTTT
1 TAAAAAAAATGATCTTT
422904 TAAAAAAAATGAT-TTT
1 TAAAAAAAATGATCTTT
422920 T
1 T
422921 TTTAGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAAAAAAATGATCTTT
Found at i:423243 original size:59 final size:59
Alignment explanation
Indices: 423178--423296 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
423168 ATTCATCACC
*
423178 AAAAAATAACAAAAAGGGAAGGAAAAACCTTCAAGCATGAATCCATCATTAGCAATAGT
1 AAAAAATAACAAAAAAGGAAGGAAAAACCTTCAAGCATGAATCCATCATTAGCAATAGT
*
423237 AAAAAATAACAAAAAAGGAAGGAAAAACCTTCAAGCATGAATCCATCATTAGTAATAGT
1 AAAAAATAACAAAAAAGGAAGGAAAAACCTTCAAGCATGAATCCATCATTAGCAATAGT
423296 A
1 A
423297 TCTAGTAGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.18
Consensus pattern (59 bp):
AAAAAATAACAAAAAAGGAAGGAAAAACCTTCAAGCATGAATCCATCATTAGCAATAGT
Found at i:425271 original size:6 final size:6
Alignment explanation
Indices: 425262--425305 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
425252 TTTTATTCTT
* *
425262 TTTTTG TTTTTG TTTTTG CTTTTTTG TTTTTT TTTTTT TTTTTG
1 TTTTTG TTTTTG TTTTTG --TTTTTG TTTTTG TTTTTG TTTTTG
425306 CTTTCCTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 28 0.82
8 6 0.18
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:425285 original size:14 final size:14
Alignment explanation
Indices: 425268--425309 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
425258 TCTTTTTTTG
425268 TTTTTGTTTTTGCT
1 TTTTTGTTTTTGCT
425282 TTTTTGTTTTT--T
1 TTTTTGTTTTTGCT
*
425294 TTTTTTTTTTTGCT
1 TTTTTGTTTTTGCT
425308 TT
1 TT
425310 CCTTATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 11 0.44
14 14 0.56
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.86
Consensus pattern (14 bp):
TTTTTGTTTTTGCT
Found at i:425304 original size:20 final size:20
Alignment explanation
Indices: 425260--425305 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
425250 CTTTTTATTC
425260 TTTTTTTGTTTTTGTTTTTG
1 TTTTTTTGTTTTTGTTTTTG
*
425280 CTTTTTTGTTTTT-TTTTT-
1 TTTTTTTGTTTTTGTTTTTG
425298 TTTTTTTG
1 TTTTTTTG
425306 CTTTCCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 5 0.21
20 12 0.50
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (20 bp):
TTTTTTTGTTTTTGTTTTTG
Found at i:441065 original size:2 final size:2
Alignment explanation
Indices: 441058--441085 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
441048 GGATCAGTTG
441058 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
441086 ATGCTTTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:445755 original size:57 final size:57
Alignment explanation
Indices: 445670--445794 Score: 148
Period size: 57 Copynumber: 2.2 Consensus size: 57
445660 AAAGTATTTG
* * * *
445670 AAATTGTATAAAAATCCTTATATCATGAAAAATAACTTAAATGATCC-AACATATATA
1 AAATTGCATAAAAATCCTTAGATCATGAAAAATAACCTAAATGA-CCTAACATAAATA
* * *
445727 AAATTGCATAAAAA-CCTTTAGATTATGAAAAATGACCTAAATGACCTAATATAAATA
1 AAATTGCATAAAAATCC-TTAGATCATGAAAAATAACCTAAATGACCTAACATAAATA
445784 AAATTGC-TAAA
1 AAATTGCATAAA
445795 GGTCCCTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
56 8 0.14
57 51 0.86
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (57 bp):
AAATTGCATAAAAATCCTTAGATCATGAAAAATAACCTAAATGACCTAACATAAATA
Found at i:445917 original size:47 final size:48
Alignment explanation
Indices: 445829--445928 Score: 141
Period size: 47 Copynumber: 2.1 Consensus size: 48
445819 TCGAAATAAC
* *
445829 CCTAGCATACATGAATTCACATAAAAGTCTTAAGATCATGAAAAATGA
1 CCTAACATAAATGAATTCACATAAAAGTCTTAAGATCATGAAAAATGA
* *
445877 CCTAACATAAATGAATT-GCATAAAAGTTCTT-AGATTATGAAAAATGA
1 CCTAACATAAATGAATTCACATAAAAG-TCTTAAGATCATGAAAAATGA
445924 CCTAA
1 CCTAA
445929 TGACCTCAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
47 28 0.60
48 19 0.40
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (48 bp):
CCTAACATAAATGAATTCACATAAAAGTCTTAAGATCATGAAAAATGA
Found at i:445969 original size:57 final size:57
Alignment explanation
Indices: 445871--445995 Score: 157
Period size: 57 Copynumber: 2.2 Consensus size: 57
445861 AGATCATGAA
* *
445871 AAATGACCT-AACATAAATGAATTGCATAAAAGTTCTTAGATTAT-GAAAAATGACCT
1 AAATGACCTCAACATAAATGAATTACATAAAAGTTCTCAGATTATAG-AAAATGACCT
* * *
445927 -AATGACCTCAACATTAATGAAATTACTTAAAAGTTCTCAGATTATAGAAAATTACCT
1 AAATGACCTCAACATAAATG-AATTACATAAAAGTTCTCAGATTATAGAAAATGACCT
*
445984 AAATGACATCAA
1 AAATGACCTCAA
445996 GAAAAATGCA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
55 8 0.14
56 9 0.15
57 31 0.53
58 11 0.19
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.29
Consensus pattern (57 bp):
AAATGACCTCAACATAAATGAATTACATAAAAGTTCTCAGATTATAGAAAATGACCT
Found at i:446058 original size:10 final size:10
Alignment explanation
Indices: 446036--446076 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
446026 AAGTCATAGG
446036 AAATAAC-TA
1 AAATAACATA
446045 AAATAACATA
1 AAATAACATA
*
446055 AAAT-GCATA
1 AAATAACATA
*
446064 AAATATCATA
1 AAATAACATA
446074 AAA
1 AAA
446077 ATTTTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 15 0.54
10 13 0.46
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (10 bp):
AAATAACATA
Found at i:446090 original size:57 final size:56
Alignment explanation
Indices: 445998--446126 Score: 152
Period size: 57 Copynumber: 2.2 Consensus size: 56
445988 GACATCAAGA
* * * *
445998 AAAATGCATGAAATGTCATGAAATCTCTAAGTCATAGGAAAT-AACTAAAATAACAT
1 AAAATGCATAAAATATCATAAAATCTCTAAGTCATAGAAAATGAA-TAAAATAACAT
* * *
446054 AAAATGCATAAAATATCATAAAAATTTTTAAGTCATAGAAAATGAATAAAATGACAT
1 AAAATGCATAAAATATCAT-AAAATCTCTAAGTCATAGAAAATGAATAAAATAACAT
446111 AGAAATGCATGAAAAT
1 A-AAATGCAT-AAAAT
446127 TACAAAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
56 17 0.27
57 30 0.48
58 10 0.16
59 5 0.08
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (56 bp):
AAAATGCATAAAATATCATAAAATCTCTAAGTCATAGAAAATGAATAAAATAACAT
Found at i:447790 original size:15 final size:15
Alignment explanation
Indices: 447766--447796 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
447756 CACCCCTATT
447766 TTATTATTATTTTTA
1 TTATTATTATTTTTA
*
447781 TTATTTTTATTTTTA
1 TTATTATTATTTTTA
447796 T
1 T
447797 AACTTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTATTATTTTTA
Found at i:449618 original size:25 final size:23
Alignment explanation
Indices: 449590--449652 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 23
449580 TTTATATAAG
*
449590 GATAAATTAATTAAAAAGATATTTT
1 GATAAATTAATTAAAAA-ATA-CTT
*
449615 GATAAGATT-ATCAAAAAATACTT
1 GATAA-ATTAATTAAAAAATACTT
*
449638 -ATAAATAAATTAAAA
1 GATAAATTAATTAAAA
449653 CTTTAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 2 0.06
22 10 0.31
23 2 0.06
24 3 0.09
25 12 0.38
26 3 0.09
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.33
Consensus pattern (23 bp):
GATAAATTAATTAAAAAATACTT
Found at i:451904 original size:2 final size:2
Alignment explanation
Indices: 451897--451921 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
451887 GATCACTTGT
451897 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
451922 TGATGCTTAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:454460 original size:5 final size:5
Alignment explanation
Indices: 454450--454475 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
454440 TTGGCCAAAA
454450 TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
454476 TTTTATGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:457540 original size:166 final size:164
Alignment explanation
Indices: 457185--457800 Score: 756
Period size: 166 Copynumber: 3.7 Consensus size: 164
457175 GACAAAATTT
*
457185 TTTTTCAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTTTAGAAGTAAAATCATCATTTTAGT
1 TTTTT-AAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGT
* * *
457250 CATTTTTCAAAGATTTCTATTATTCCTATGGCCTTCTATAGGGGTATAAAAATTTTCAAAATATT
65 CATTTTT-AAAGATTTCTATTATTCCTATGGCCTTCTTTAAGGGTATAAAAATTTTTAAAAT-TT
* * * * * * *
457315 TCGCT-TCCTCTTGGTATTCCATTGAGTACGAAATGAAA
128 TTG-TATCCTC-TAGTTTTTCATCGGGTATGAAATGAAA
* *
457353 TTTTTAAAAGTTTAAGGATTAAATAGCAAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTT
1 TTTTTAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTC
** *
457418 ATTTTTAAAGATTTCTATTATTATTATGGCCTTCTTTAAGAGTATAAAAATTTTTAAAACTTTTT
66 ATTTTTAAAGATTTCTATTATTCCTATGGCCTTCTTTAAGGGTATAAAAATTTTTAAAA-TTTTT
* *
457483 GTATCCTCTCAGTTTTTCGTCGGGTATGATATGAAA
130 GTATCCTCT-AGTTTTTCATCGGGTATGAAATGAAA
* ** *
457519 TTTTTAAGAGTTTAGGGATTAAATAAAAAATTTTAG-TTTTAGAGGTAAAATCATTATTTTAGTC
1 TTTTTAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTC
* * * *
457583 A-TTTTAAAGATTTCTATAATTCCTATAGCCTT-TTATAAGGGTATAAAAAATTTTAAGATTTTT
66 ATTTTTAAAGATTTCTATTATTCCTATGGCCTTCTT-TAAGGGTATAAAAATTTTTAAAATTTTT
* * * * *
457646 CGTATCATCTTGATTTCTCATCAGGTATGAAATAAAA
130 -GTATCCTCTAG-TTTTTCATCGGGTATGAAATGAAA
* * *
457683 TTTTGAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTTTAGAGGTAAGATCATCATTTTGGTC
1 TTTTTAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTC
* * * *
457748 ATTTTTAAAGTTTTTTATTATTCTTATGGCCTTTCGTTAA-GGTATAAAAATTT
66 ATTTTTAAAGATTTCTATTATTCCTATGGCC-TTCTTTAAGGGTATAAAAATTT
457801 GCAAGACTTT
Statistics
Matches: 386, Mismatches: 52, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
163 8 0.02
164 106 0.27
165 55 0.14
166 142 0.37
167 69 0.18
168 6 0.02
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (164 bp):
TTTTTAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTC
ATTTTTAAAGATTTCTATTATTCCTATGGCCTTCTTTAAGGGTATAAAAATTTTTAAAATTTTTG
TATCCTCTAGTTTTTCATCGGGTATGAAATGAAA
Found at i:457754 original size:330 final size:334
Alignment explanation
Indices: 457185--457800 Score: 899
Period size: 330 Copynumber: 1.9 Consensus size: 334
457175 GACAAAATTT
**
457185 TTTTTCAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTTTAGAAGTAAAATCATCATTTTAGT
1 TTTTTCAAAAGTTTAGGGATTAAATAAAAAATTTTAGTTTTTAGAAGTAAAATCATCATTTTAGT
* * *
457250 CATTTTTCAAAGATTTCTATTATTCCTATGGCCTTCTATAGGGGTATAAAAATTTTCAAAATATT
66 CATTTTTCAAAGATTTCTATAATTCCTATAGCCTTCTATAAGGGTATAAAAATTTTCAAAATATT
* * * * *
457315 TCGCTTCCTCTTGGTATTCCATTGAGTACGAAATGAAATTTTTAAAAGTTTAAGGATTAAATAGC
131 TCGCTTCATCTTGATATTCCATAGAGTACGAAATAAAATTTTGAAAAGTTTAAGGATTAAATAGC
*
457380 AAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTTATTTTTAAAGATTTCTATTATTATTAT
196 AAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTCATTTTTAAAGATTTCTATTATTATTAT
*
457445 GGCC-TTCTTTAAGAGTATAAAAATTTTTAAAACTTTTTGTATCCTCTCAGTTTTTCGTCGGGTA
261 GGCCTTTCGTTAAG-GTATAAAAATTTTTAAAACTTTTTGTATCCTCTCAGTTTTTCGTCGGGTA
457509 TGATATGAAA
325 TGATATGAAA
* * *
457519 TTTTT-AAGAGTTTAGGGATTAAATAAAAAATTTTAG-TTTTAGAGGTAAAATCATTATTTTAGT
1 TTTTTCAAAAGTTTAGGGATTAAATAAAAAATTTTAGTTTTTAGAAGTAAAATCATCATTTTAGT
* * *
457582 CA-TTTT-AAAGATTTCTATAATTCCTATAGCCTTTTATAAGGGTATAAAAAATTTT-AAGATTT
66 CATTTTTCAAAGATTTCTATAATTCCTATAGCCTTCTATAAGGGTAT-AAAAATTTTCAAAATAT
* *
457644 TTCG-TATCATCTTGAT-TTCTCATCAG-GTATGAAATAAAATTTTGAAAAGTTTAGGGATTAAA
130 TTCGCT-TCATCTTGATATTC-CAT-AGAGTACGAAATAAAATTTTGAAAAGTTTAAGGATTAAA
* * * * *
457706 TAGCAAATTTTAGTTTTTAGAGGTAAGATCATCATTTTGGTCATTTTTAAAGTTTTTTATTATTC
192 TAGCAAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTCATTTTTAAAGATTTCTATTATTA
457771 TTATGGCCTTTCGTTAAGGTATAAAAATTT
257 TTATGGCCTTTCGTTAAGGTATAAAAATTT
457801 GCAAGACTTT
Statistics
Matches: 252, Mismatches: 25, Indels: 14
0.87 0.09 0.05
Matches are distributed among these distances:
329 4 0.02
330 166 0.66
331 22 0.09
332 27 0.11
333 28 0.11
334 5 0.02
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (334 bp):
TTTTTCAAAAGTTTAGGGATTAAATAAAAAATTTTAGTTTTTAGAAGTAAAATCATCATTTTAGT
CATTTTTCAAAGATTTCTATAATTCCTATAGCCTTCTATAAGGGTATAAAAATTTTCAAAATATT
TCGCTTCATCTTGATATTCCATAGAGTACGAAATAAAATTTTGAAAAGTTTAAGGATTAAATAGC
AAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTCATTTTTAAAGATTTCTATTATTATTAT
GGCCTTTCGTTAAGGTATAAAAATTTTTAAAACTTTTTGTATCCTCTCAGTTTTTCGTCGGGTAT
GATATGAAA
Found at i:458789 original size:156 final size:154
Alignment explanation
Indices: 458037--459874 Score: 1575
Period size: 156 Copynumber: 11.8 Consensus size: 154
458027 TGATTCTTAA
* *
458037 GTTGTTACCAGGAT-CTTTTATGCC-AAGTGTGTGCATTTAGGATAGGTTCATCCCATTTATGAT
1 GTTGTCACCAAGATGCTTTTATGCCAAAG-GTGTGCATTTAGGATAGGTTCATCCCATTTATGAT
* * * * * ***
458100 CATTTTTAAGTCCTTTATGGTTACCATGATACTTTCACGTTGGAGGTAT-C-CTAAGCACATTTT
65 CATTTTTAAGTCCTTTAGGGTTACGA-GATACTTTCATGTTGAAGGTATACTTTAAGGGTATTTT
** * * *
458163 TGTAATTTTTTTAGCAGCGAGTCCTAA
129 CATAA-TTTTTTAGAATCGAGTCCTAG
* *
458190 GTTGTCACCAGGATG-TGTTTATGTCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGAT
1 GTTGTCACCAAGATGCT-TTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGAT
* * * * * * *
458254 TATTTTTAAGTCTTTTAGAGTTACTAAGATACTTTCATGTTGACA-ATATA-TCTCAAGGGCATT
65 CATTTTTAAGTCCTTTAGGGTTAC-GAGATACTTTCATGTTGA-AGGTATACT-TTAAGGGTATT
* * *
458317 TTTATAATTTTTTAAAATCGAGTCTTAG
127 TTCATAATTTTTTAGAATCGAGTCCTAG
* * * ** *
458345 GCTATCACCAAGATGCTTTTTTGTTAAAGGTGTGCATTTAGGATGGGTTCATCCCATTTATGA-C
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * ** **
458409 TATTTTTAAGTCTTTTAGGGTTATCGAAATGCTTTCATGTTGAAGGTATACCCTAAGGACATTTT
66 -ATTTTTAAGTCCTTTAGGGTTA-CGAGATACTTTCATGTTGAAGGTATACTTTAAGGGTATTTT
* * * *
458474 CATAATTTTCCTA-AAACCACGTCCTGG
129 CATAATTTT-TTAGAATCGA-GTCCTAG
* * * * *
458501 GATGTCACCAAGATACTTTTATGCCAAAAGTATGCATTTAGGAT-GATTTCAT-CCATTTATGA-
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAG-GTTCATCCCATTTATGAT
* * * * * * *
458563 -ATTTTTAAGCCCATTAGGGTTACCGAGATACTTTCATGTTGAAGGTATCCTTTATGGATCTTTC
65 CATTTTTAAGTCCTTTAGGGTTA-CGAGATACTTTCATGTTGAAGGTATACTTTAAGGGTATTTT
* *
458627 CATAATTTTCTTAAAATCAAGTCCTAG
129 CATAATTTT-TTAGAATCGAGTCCTAG
* *
458654 GTTGTCATCAAGATG-TATTTATGCCAAAGGTGTGCATTTAGGATAGGTTTATCCCATTTATGAT
1 GTTGTCACCAAGATGCT-TTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGAT
* * * *
458718 CATTTTTAAGTCCTTTAGGGTTATCGAGATACTTTAATATTGAAGGCATACTTTAAGGGTGTTTT
65 CATTTTTAAGTCCTTTAGGGTTA-CGAGATACTTTCATGTTGAAGGTATACTTTAAGGGTATTTT
* *
458783 CATAATTTTTCTAGAATTGAGTCCTGG
129 CATAATTTTT-TAGAATCGAGTCCTAG
* ** * * * *
458810 GTTTGT-AGTCGGGATGCTTTTATGCCAAAGGTGTGCATCTAGTATAGGTTCATCTCATTTATCA
1 G-TTGTCA-CCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGA
** * * * * * *
458874 TTGTTTTTAAGTTCTTTAGAGTTACCGAGATGCTTTCATGTCGAAGCTATACCTT-AGGGATATT
64 TCATTTTTAAGTCCTTTAGGGTTA-CGAGATACTTTCATGTTGAAGGTATACTTTAAGGG-TATT
* * *
458938 TTCATAATTTTTCTAAAATCGAGTCTTAC
127 TTCATAATTTTT-TAGAATCGAGTCCTAG
** * * * * * * *
458967 GTTGTCACCGGGATACTTTTAAGTCGAAGGTATGTATTTAGGGTAGGTTCATCCCATTTATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * * * *
459032 ATTTTTAAGTCTTTTGGGGTTACTGTGATACTTTCATATCGAAGGTATA-TCTTAGGGGTAGTTT
66 ATTTTTAAGTCCTTTAGGGTTAC-GAGATACTTTCATGTTGAAGGTATACT-TTAAGGGTA-TTT
* * *
459096 T-GTAATTTTTTTAGAATTGAGTCTTAG
128 TCATAA-TTTTTTAGAATCGAGTCCTAG
* * * * *
459123 GTTGTCACAAAGATGCTTTTATACCAAAAGTGTGCATTTAAGATAGGTTCATCTCATTTATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * * * *
459188 ATTTTTAAGTCCTTTATGGTTACCATGATACTTTCATGTTTAAGGTATA-TCCTAAAGGCATTTT
66 ATTTTTAAGTCCTTTAGGGTTACGA-GATACTTTCATGTTGAAGGTATACT-TTAAGGGTATTTT
** * *
459252 CGGAATTTTTTTAGAATTGAGTCCTAA
129 CATAA-TTTTTTAGAATCGAGTCCTAG
* ** ** * * * *
459279 GTTGTCACCGAGATATTTTTATGTTAAATGTATGCATTTAGGATAAGTTCATCCCATATATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * * * * *
459344 ATTTTTAAGTCTTTTAGGGTTACTAAGATATTTTCATGTCGAAGCTATACCTCAAGGGTATATTT
66 ATTTTTAAGTCCTTTAGGGTTAC-GAGATACTTTCATGTTGAAGGTATACTTTAAGGGTAT-TTT
* ** *
459409 -GTAATTTTTTAGAATCGAGTTTTTG
129 CATAATTTTTTAGAATCGAGTCCTAG
* * * ** * * * *
459434 GCTATCACCAAGATGCTTTTTTGTTAAAGGTGTGTATTTAGGATATGTTCATCCTATTTATGAGC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * * * **
459499 ATTTTTAAGTCTTTTAGGGTTATCGAGATGCTTTCATATTGAAGGTACACTCT-AGAGACATTTT
66 ATTTTTAAGTCCTTTAGGGTTA-CGAGATACTTTCATGTTGAAGGTATACTTTAAG-GGTATTTT
* *
459563 CATAATTTTTCTA-AAACTGCA-TCGTAG
129 CATAATTTTT-TAGAATC-G-AGTCCTAG
* * * *
459590 GATGTCACTAAGATGCTTTTACGCCAAAGGTGTGCATTTAGGATAGGTTTAT-CCATTTATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * *
459654 ATTTTTAAGCCCATTAGGGTTATCGAGATACTTTCATGTTGAAAGTATACCTT-AGGGATATTTT
66 ATTTTTAAGTCCTTTAGGGTTA-CGAGATACTTTCATGTTGAAGGTATACTTTAAGGG-TATTTT
*
459718 CATAATTTTTTTAAAATCGAGTCCTAG
129 CATAA-TTTTTTAGAATCGAGTCCTAG
* * * * *
459745 GTTGTCACCATGTTGCATTTATGCTAAAGGTGTGCATTTAGTATAGGTTCATCCCATTTATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * * *
459810 ATTTTTAAGTCCTTTAAGGTTACTAGGATACTTTAATATTGAAGGTATACTTTAAGGATATTTTC
66 ATTTTTAAGTCCTTTAGGGTTACGA-GATACTTTCATGTTGAAGGTATACTTTAAGGGTATTTTC
459875 GTAGAATCGA
Statistics
Matches: 1358, Mismatches: 276, Indels: 99
0.78 0.16 0.06
Matches are distributed among these distances:
152 1 0.00
153 124 0.09
154 102 0.08
155 397 0.29
156 590 0.43
157 143 0.11
158 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (154 bp):
GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
ATTTTTAAGTCCTTTAGGGTTACGAGATACTTTCATGTTGAAGGTATACTTTAAGGGTATTTTCA
TAATTTTTTAGAATCGAGTCCTAG
Found at i:459285 original size:312 final size:309
Alignment explanation
Indices: 458037--461403 Score: 2713
Period size: 311 Copynumber: 10.9 Consensus size: 309
458027 TGATTCTTAA
* *
458037 GTTGTTACCAGGAT-CTTTTATGCC-AAGTGTGTGCATTTAGGATAGGTTCATCCCATTTATGAT
1 GTTGTCACCAAGATGCTTTTATGCCAAAG-GTGTGCATTTAGGATAGGTTCATCCCATTTATGAT
* * * * * ***
458100 CATTTTTAAGTCCTTTATGGTTAC-CATGATACTTTCACGTTGGAGGTAT-CC-TAAGCACATTT
65 CATTTTTAAGTCTTTTAGGGTTACTGA-GATACTTTCATGTTGAAGGTATACCTTAAGGGTATTT
** * * * * *
458162 TTGTAATTTTTTTAGCAGCGAGTCCTAAGTTGTCACCAGGATG-TGTTTATGTCAAAGGTGTGCA
129 TCATAATTTTTTTAGAATCGAGTCCTAGGTTGTCACCAAGATGCT-TTTATGCCAAAGGTGTGCA
* * *
458226 TTTAGGATAGGTTCATCCCATTTATGATTATTTTTAAGTCTTTTAGAGTTACTAAGATACTTTCA
193 TTTAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTTAG-GTTAC-CAGATACTTTCA
* * * *
458291 TGTTGACA-ATATATCTCAAGGGCATTTTTATAA-TTTTTTAAAATCGAGTCTTAG
256 TGTTGA-AGGTATACCT-AAGGGCATTTTCATAATTTTTTTAAAATCGAGTCCTAG
* * * ** *
458345 GCTATCACCAAGATGCTTTTTTGTTAAAGGTGTGCATTTAGGATGGGTTCATCCCATTTATGA-C
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * **
458409 TATTTTTAAGTCTTTTAGGGTTA-TCGAAATGCTTTCATGTTGAAGGTATACCCTAAGGACATTT
66 -ATTTTTAAGTCTTTTAGGGTTACT-GAGATACTTTCATGTTGAAGGTATACCTTAAGGGTATTT
** * * * * * * *
458473 TCATAATTTTCCTA-AAACCACGTCCTGGGATGTCACCAAGATACTTTTATGCCAAAAGTATGCA
129 TCATAATTTTTTTAGAATCGA-GTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCA
* * *
458537 TTTAGGAT-GATTTCAT-CCATTTATGA--ATTTTTAAGCCCATTAGGGTTACCGAGATACTTTC
193 TTTAGGATAG-GTTCATCCCATTTATGATCATTTTTAAGTCCTTTA-GGTTACC-AGATACTTTC
* * * *
458598 ATGTTGAAGGTAT-CCTTTATGG-ATCTTTCCATAATTTTCTTAAAATCAAGTCCTAG
255 ATGTTGAAGGTATACC-TAAGGGCAT-TTT-CATAATTTTTTTAAAATCGAGTCCTAG
* *
458654 GTTGTCATCAAGATG-TATTTATGCCAAAGGTGTGCATTTAGGATAGGTTTATCCCATTTATGAT
1 GTTGTCACCAAGATGCT-TTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGAT
* * * * * *
458718 CATTTTTAAGTCCTTTAGGGTTA-TCGAGATACTTTAATATTGAAGGCATACTTTAAGGGTGTTT
65 CATTTTTAAGTCTTTTAGGGTTACT-GAGATACTTTCATGTTGAAGGTATACCTTAAGGGTATTT
* * * * **
458782 TCATAATTTTTCTAGAATTGAGTCCTGGGTTTGT-AGTCGGGATGCTTTTATGCCAAAGGTGTGC
129 TCATAATTTTTTTAGAATCGAGTCCTAGG-TTGTCA-CCAAGATGCTTTTATGCCAAAGGTGTGC
* * * * ** * *
458846 ATCTAGTATAGGTTCATCTCATTTATCATTGTTTTTAAGTTCTTTAGAGTTACCGAGATGCTTTC
192 ATTTAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTTAG-GTTACC-AGATACTTTC
* * * * * * *
458911 ATGTCGAAGCTATACCTTAGGGATATTTTCATAATTTTTCTAAAATCGAGTCTTAC
255 ATGTTGAAGGTATACCTAAGGG-CATTTTCATAATTTTTTTAAAATCGAGTCCTAG
** * * * * * * *
458967 GTTGTCACCGGGATACTTTTAAGTCGAAGGTATGTATTTAGGGTAGGTTCATCCCATTTATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * * * *
459032 ATTTTTAAGTCTTTTGGGGTTACTGTGATACTTTCATATCGAAGGTATATCTTAGGGGTAGTTTT
66 ATTTTTAAGTCTTTTAGGGTTACTGAGATACTTTCATGTTGAAGGTATACCTTAAGGGTA-TTTT
* * * * * *
459097 -GTAATTTTTTTAGAATTGAGTCTTAGGTTGTCACAAAGATGCTTTTATACCAAAAGTGTGCATT
130 CATAATTTTTTTAGAATCGAGTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATT
* *
459161 TAAGATAGGTTCATCTCATTTATGATCATTTTTAAGTCCTTTATGGTTACCATGATACTTTCATG
195 TAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTTA-GGTTACCA-GATACTTTCATG
* * ** * * *
459226 TTTAAGGTATATCCTAAAGGCATTTTCGGAATTTTTTTAGAATTGAGTCCTAA
258 TTGAAGGTATA-CCTAAGGGCATTTTCATAATTTTTTTAAAATCGAGTCCTAG
* ** ** * * * *
459279 GTTGTCACCGAGATATTTTTATGTTAAATGTATGCATTTAGGATAAGTTCATCCCATATATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * * *
459344 ATTTTTAAGTCTTTTAGGGTTACTAAGATATTTTCATGTCGAAGCTATACCTCAAGGGTATATTT
66 ATTTTTAAGTCTTTTAGGGTTACTGAGATACTTTCATGTTGAAGGTATACCTTAAGGGTAT-TTT
* ** * * * * ** *
459409 -GTAA-TTTTTTAGAATCGAGTTTTTGGCTATCACCAAGATGCTTTTTTGTTAAAGGTGTGTATT
130 CATAATTTTTTTAGAATCGAGTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATT
* * * * * * *
459472 TAGGATATGTTCATCCTATTTATGAGCATTTTTAAGTCTTTTAGGGTTATCGAGATGCTTTCATA
195 TAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTTA-GGTTA-CCAGATACTTTCATG
* * * *
459537 TTGAAGGTACACTCT-AGAGACATTTTCATAATTTTTCTAAAA-CTGCA-TCGTAG
258 TTGAAGGTATAC-CTAAG-GGCATTTTCATAATTTTTTTAAAATC-G-AGTCCTAG
* * * *
459590 GATGTCACTAAGATGCTTTTACGCCAAAGGTGTGCATTTAGGATAGGTTTAT-CCATTTATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* ** *
459654 ATTTTTAAGCCCATTAGGGTTA-TCGAGATACTTTCATGTTGAAAGTATACCTT-AGGGATATTT
66 ATTTTTAAGTCTTTTAGGGTTACT-GAGATACTTTCATGTTGAAGGTATACCTTAAGGG-TATTT
* * * * *
459717 TCATAATTTTTTTAAAATCGAGTCCTAGGTTGTCACCATGTTGCATTTATGCTAAAGGTGTGCAT
129 TCATAATTTTTTTAGAATCGAGTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCAT
* * *
459782 TTAGTATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTTAAGGTTACTAGGATACTTTAAT
194 TTAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTT-AGGTTACCA-GATACTTTCAT
* * ** *
459847 ATTGAAGGTATACTTTAA-GG-------AT-ATTTTCGTAGAATCGAGTCCTAG
257 GTTGAAGGTATAC-CTAAGGGCATTTTCATAATTTTTTTAAAATCGAGTCCTAG
* * * *
459892 GTTGTAATCGAGATGTTTTTATGCCATAA-GTGTGC-------AT---TT-AT--C-------AT
1 GTTGTCACCAAGATGCTTTTATGCCA-AAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGAT
* * * ** * * * *
459936 CATTTTTAAGT-TCTTTAGAGTTACTGAGATGCTTTTATGTCAAAGCTATACCCTAAAGGCATTT
65 CATTTTTAAGTCT-TTTAGGGTTACTGAGATACTTTCATGTTGAAGGTATACCTTAAGGGTATTT
** * * * ** *
460000 TCATAATTTTCCTAAAATTGAGTCTTAGGTTGTCACCGGGATGCTTTTATGCCAAAGGCGTGCAT
129 TCATAATTTTTTTAGAATCGAGTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCAT
* *
460065 TTA-GAGTAGGTTCATCCCATTTATGATCATTTTTAAGTCTTTTTAGGTTACTAGGATACTTTCA
194 TTAGGA-TAGGTTCATCCCATTTATGATCATTTTTAAGTC-CTTTAGGTTACCA-GATACTTTCA
* * * * * * * *
460129 TGTCGAAAGTATATCTTAGGGGTAGTTTT-GT-ATTTTTCTTAGAACCGAGTCCTAG
256 TGTTGAAGGTATA-CCTAAGGGCA-TTTTCATAATTTTT-TTAAAATCGAGTCCTAG
**** * *
460184 GTTGTCATTGGGATGCTTTTATACCAAAGGTGTGCATTTAGGATAGGTTCATCCGATTTATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * * * * *
460249 ATTTTTGAGTCCTTTATGGTTAC-CATGATATTTTCATGTTGAAGGTATATCC-TAAAGGCATTT
66 ATTTTTAAGTCTTTTAGGGTTACTGA-GATACTTTCATGTTGAAGGTATA-CCTTAAGGGTATTT
** * * * * ** * ** *
460312 TTGTAATTTTCTTAGCAGCGAGTCCTAAGTTGTCACCGGGATGTTTTTATGTTAAATGTGTGCAT
129 TCATAATTTTTTTAGAATCGAGTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCAT
* *
460377 TTAGGATAGGTTTATCCCATTTATGATCATTTTTAAGT-CTTTAAGGGTTACTAAGATACTTTCA
194 TTAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTT-A-GGTTAC-CAGATACTTTCA
* * * *
460441 TGTTAAAGATATACCTCAAGGGCATTTTCATAA-TTTTTTAGAATCGAGTCTTAG
256 TGTTGAAGGTATACCT-AAGGGCATTTTCATAATTTTTTTAAAATCGAGTCCTAG
* * * ** * * *
460495 GCTATCACCAAGATGCTTTTTTGTTAAAGGTGTGCATTTAGGATGGGTTCATCCCATTTATAAGC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * * * * * * **
460560 ATTTTTAAGTCCTTTAGGGTTATTGGGGTGCTTTCATGTTAAAGGTATACCCT-AGAGACATTTT
66 ATTTTTAAGTCTTTTAGGGTTACTGAGATACTTTCATGTTGAAGGTATACCTTAAG-GGTATTTT
** * * * *
460624 CATAATTTTCCTA-AAACTGCGTCCTAGGATGTCACCAAGATGCTTTTACGCCAAAGGTGTGCAT
130 CATAATTTTTTTAGAATC-GAGTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCAT
* * ** * * *
460688 TTAGGATGGGTTCA-CCCATTTATGATAATTTCCAAGCCCGTTACGGTTATCAAGATACTTTCAT
194 TTAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTTA-GGTTA-CCAGATACTTTCAT
* * *
460752 GTTGAAGGTATACCTCAGGGATATTTTCATATTTTTTTTAAAATCGAGTCCTAG
257 GTTGAAGGTATACCTAAGGG-CATTTTCATAATTTTTTTAAAATCGAGTCCTAG
* * * *
460806 ATTGTCACTAGGATGCATTTATGCCAAAGGTGTGCATTTAGGATAGG-T--T--C---TATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * ** *
460863 ATTTTTAAGTCTTTTAGGGTTA-TCGGGATACTTTAATGTTGAAGGTATATTTTAAAGGTATTTT
66 ATTTTTAAGTCTTTTAGGGTTACT-GAGATACTTTCATGTTGAAGGTATACCTTAAGGGTATTTT
* * * * *
460927 CGTTAA-TTTTCTAGAATCGAGTCCTAGGTTGTAATCGAGATGCTTTTATGCCAAAGGTGTGCAT
130 C-ATAATTTTTTTAGAATCGAGTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCAT
* * * * * * ** *
460991 TTAGCATAAGTTCATACGATTTATCATCATTTTAAAGTTTTTTAGAGTTACCGAGATGCTTTCAT
194 TTAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTTAG-GTTACC-AGATACTTTCAT
* * * * *
461056 GTTGATA-GTATACTTTAAAGGCATTTTTATAATTTTTCTAAAATCGAGTCTTAG
257 GTTGA-AGGTATAC-CTAAGGGCATTTTCATAATTTTTTTAAAATCGAGTCCTAG
* ** ** * *
461110 GTTGTCATCGGGATGCTTTTATGCCAAATATATGCATTTAGGATAGGTGCATCCCATTTATGATC
1 GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
* * *
461175 ATTTTTAAGTCTTTTAGGGTTACTGTGATACTTTTATGTTGAAGGTATACCTTAGGGGTAGTTTT
66 ATTTTTAAGTCTTTTAGGGTTACTGAGATACTTTCATGTTGAAGGTATACCTTAAGGGTA-TTTT
* * * ** * * **
461240 -ATAATTTTTTTAGAACCGACTCCTAAGTTGTCACCTGGATGCTTTTATACCAAAAGTACGCATT
130 CATAATTTTTTTAGAATCGAGTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATT
* *
461304 TAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTTTGAGTTACCGAGATACTTTCATA
195 TAGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTTAG-GTTACC-AGATACTTTCATG
* * ** *
461369 TTAAAGATATACTCTAAGAACATTTTGATAATTTT
258 TTGAAGGTATAC-CTAAGGGCATTTTCATAATTTT
461404 GCATTAGAGC
Statistics
Matches: 2444, Mismatches: 487, Indels: 252
0.77 0.15 0.08
Matches are distributed among these distances:
282 1 0.00
283 169 0.07
284 10 0.00
290 1 0.00
291 10 0.00
292 44 0.02
295 2 0.00
299 2 0.00
301 1 0.00
302 43 0.02
303 121 0.05
304 119 0.05
305 5 0.00
306 3 0.00
307 9 0.00
308 56 0.02
309 237 0.10
310 194 0.08
311 606 0.25
312 590 0.24
313 208 0.09
314 11 0.00
315 2 0.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (309 bp):
GTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTATGATC
ATTTTTAAGTCTTTTAGGGTTACTGAGATACTTTCATGTTGAAGGTATACCTTAAGGGTATTTTC
ATAATTTTTTTAGAATCGAGTCCTAGGTTGTCACCAAGATGCTTTTATGCCAAAGGTGTGCATTT
AGGATAGGTTCATCCCATTTATGATCATTTTTAAGTCCTTTAGGTTACCAGATACTTTCATGTTG
AAGGTATACCTAAGGGCATTTTCATAATTTTTTTAAAATCGAGTCCTAG
Found at i:460211 original size:156 final size:156
Alignment explanation
Indices: 459926--461380 Score: 1271
Period size: 156 Copynumber: 9.4 Consensus size: 156
459916 CATAAGTGTG
* * * * *
459926 CATTTATCATCATTTTTAAGT-TCTTTAGAGTTACT-GAGATGCTTTTATG-TCAAAGCTATACC
1 CATTTATGATCATTTTTAAGTCT-TTTAGGGTTACTAG-GATACTTTCATGTTGAAAG-TATACC
* * * * *
459988 CTAAAGGCATTTTCATAATTTTCCTAAAATTGAGTCTTAGGTTGTCACCGGGATGCTTTTATGCC
63 TTAAAGGCATTTTCATAATTTTCTTAGAATCGAGTCCTAGGTTGTCACCGGGATGCTTTTATGCC
*
460053 AAAGGCGTGCATTTA-GAGTAGGTTCATCC
128 AAAGGTGTGCATTTAGGA-TAGGTTCATCC
* *
460082 CATTTATGATCATTTTTAAGTCTTTTTA-GGTTACTAGGATACTTTCATGTCGAAAGTATATCTT
1 CATTTATGATCATTTTTAAGTC-TTTTAGGGTTACTAGGATACTTTCATGTTGAAAGTATACCTT
** * * * * ** *
460146 AGGGGTAGTTTT-GTATTTTTCTTAGAACCGAGTCCTAGGTTGTCATTGGGATGCTTTTATACCA
65 AAAGGCA-TTTTCATAATTTTCTTAGAATCGAGTCCTAGGTTGTCACCGGGATGCTTTTATGCCA
460210 AAGGTGTGCATTTAGGATAGGTTCATCC
129 AAGGTGTGCATTTAGGATAGGTTCATCC
* * * * * * * *
460238 GATTTATGATCATTTTTGAGTCCTTTATGGTTACCATGATATTTTCATGTTGAAGGTATATCC-T
1 CATTTATGATCATTTTTAAGTCTTTTAGGGTTACTAGGATACTTTCATGTTGAAAGTATA-CCTT
** * * * * **
460302 AAAGGCATTTTTGTAATTTTCTTAGCAGCGAGTCCTAAGTTGTCACCGGGATGTTTTTATGTTAA
65 AAAGGCATTTTCATAATTTTCTTAGAATCGAGTCCTAGGTTGTCACCGGGATGCTTTTATGCCAA
* *
460367 ATGTGTGCATTTAGGATAGGTTTATCC
130 AGGTGTGCATTTAGGATAGGTTCATCC
* * *
460394 CATTTATGATCATTTTTAAGTCTTTAAGGGTTACTAAGATACTTTCATGTT-AAAGATATACCTC
1 CATTTATGATCATTTTTAAGTCTTTTAGGGTTACTAGGATACTTTCATGTTGAAAG-TATACCTT
* * * * ** * **
460458 AAGGGCATTTTCATAATTTT-TTAGAATCGAGTCTTAGGCTATCACCAAGATGCTTTTTTGTTAA
65 AAAGGCATTTTCATAATTTTCTTAGAATCGAGTCCTAGGTTGTCACCGGGATGCTTTTATGCCAA
*
460522 AGGTGTGCATTTAGGATGGGTTCATCC
130 AGGTGTGCATTTAGGATAGGTTCATCC
* * * * * * * *
460549 CATTTATAAGCATTTTTAAGTCCTTTAGGGTTATTGGGGTGCTTTCATGTT-AAAGGTATACCCT
1 CATTTATGATCATTTTTAAGTCTTTTAGGGTTACTAGGATACTTTCATGTTGAAA-GTATACCTT
* * * * * * ** *
460613 AGAGACATTTTCATAATTTTCCTA-AAACTGCGTCCTAGGATGTCACCAAGATGCTTTTACGCCA
65 AAAGGCATTTTCATAATTTTCTTAGAATC-GAGTCCTAGGTTGTCACCGGGATGCTTTTATGCCA
*
460677 AAGGTGTGCATTTAGGATGGGTTCA-CC
129 AAGGTGTGCATTTAGGATAGGTTCATCC
* ** * ** * * *
460704 CATTTATGATAATTTCCAAGCCCGTTACGGTTA-TCAAGATACTTTCATGTTGAAGGTATACC-T
1 CATTTATGATCATTTTTAAGTCTTTTAGGGTTACT-AGGATACTTTCATGTTGAAAGTATACCTT
* * * * * * * ** *
460767 CAGGGATATTTTCATATTTTTTTTAAAATCGAGTCCTAGATTGTCACTAGGATGCATTTATGCCA
65 AAAGG-CATTTTCATAATTTTCTTAGAATCGAGTCCTAGGTTGTCACCGGGATGCTTTTATGCCA
460832 AAGGTGTGCATTTAGGATAGG-T--T--
129 AAGGTGTGCATTTAGGATAGGTTCATCC
* * * **
460855 C---TATGATCATTTTTAAGTCTTTTAGGGTTA-TCGGGATACTTTAATGTTGAAGGTATATTTT
1 CATTTATGATCATTTTTAAGTCTTTTAGGGTTACT-AGGATACTTTCATGTTGAAAGTATACCTT
* * * * *
460916 AAAGGTATTTTCGTTAATTTTC-TAGAATCGAGTCCTAGGTTGTAATCGAGATGCTTTTATGCCA
65 AAAGGCATTTTC-ATAATTTTCTTAGAATCGAGTCCTAGGTTGTCACCGGGATGCTTTTATGCCA
* * *
460980 AAGGTGTGCATTTAGCATAAGTTCATAC
129 AAGGTGTGCATTTAGGATAGGTTCATCC
* * * * * * * * *
461008 GATTTATCATCATTTTAAAGTTTTTTAGAGTTAC-CGAGATGCTTTCATGTTGATAGTATACTTT
1 CATTTATGATCATTTTTAAGTCTTTTAGGGTTACTAG-GATACTTTCATGTTGAAAGTATACCTT
* * * *
461072 AAAGGCATTTTTATAATTTT-TCTAAAATCGAGTCTTAGGTTGTCATCGGGATGCTTTTATGCCA
65 AAAGGCATTTTCATAATTTTCT-TAGAATCGAGTCCTAGGTTGTCACCGGGATGCTTTTATGCCA
** * *
461136 AATATATGCATTTAGGATAGGTGCATCC
129 AAGGTGTGCATTTAGGATAGGTTCATCC
* *
461164 CATTTATGATCATTTTTAAGTCTTTTAGGGTTACT-GTGATACTTTTATGTTGAAGGTATACCTT
1 CATTTATGATCATTTTTAAGTCTTTTAGGGTTACTAG-GATACTTTCATGTTGAAAGTATACCTT
** * * * * * * *
461228 AGGGGTAGTTTT-ATAATTTTTTTAGAACCGACTCCTAAGTTGTCACCTGGATGCTTTTATACCA
65 AAAGGCA-TTTTCATAATTTTCTTAGAATCGAGTCCTAGGTTGTCACCGGGATGCTTTTATGCCA
* **
461292 AAAGTACGCATTTAGGATAGGTTCATCC
129 AAGGTGTGCATTTAGGATAGGTTCATCC
* * *
461320 CATTTATGATCATTTTTAAGTCCTTTT-GAGTTAC-CGAGATACTTTCATATT-AAAGATATAC
1 CATTTATGATCATTTTTAAGT-CTTTTAGGGTTACTAG-GATACTTTCATGTTGAAAG-TATAC
461381 TCTAAGAACA
Statistics
Matches: 1051, Mismatches: 209, Indels: 78
0.79 0.16 0.06
Matches are distributed among these distances:
148 106 0.10
149 11 0.01
151 2 0.00
154 4 0.00
155 262 0.25
156 639 0.61
157 26 0.02
158 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (156 bp):
CATTTATGATCATTTTTAAGTCTTTTAGGGTTACTAGGATACTTTCATGTTGAAAGTATACCTTA
AAGGCATTTTCATAATTTTCTTAGAATCGAGTCCTAGGTTGTCACCGGGATGCTTTTATGCCAAA
GGTGTGCATTTAGGATAGGTTCATCC
Found at i:465037 original size:17 final size:17
Alignment explanation
Indices: 465008--465050 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
464998 AAGTAATAAA
465008 AAAATACAAAAAAAAGGG
1 AAAATA-AAAAAAAAGGG
*
465026 AAAGTAAAAAAAAAGGG
1 AAAATAAAAAAAAAGGG
465043 AAAATAAA
1 AAAATAAA
465051 GCTTTAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.07
Consensus pattern (17 bp):
AAAATAAAAAAAAAGGG
Found at i:465497 original size:113 final size:111
Alignment explanation
Indices: 465307--465530 Score: 283
Period size: 113 Copynumber: 2.0 Consensus size: 111
465297 ATGTAAAAAG
**
465307 AACATCAAATTTATCTGATTTTCAAAGAAATCATGTTTTATACAACCTAATCCATTTGTGCCTAG
1 AACATCAAATTTATCTGATTTTCAAAGAAATCATACTTTATACAACCTAATCCATTTGTGCCTAG
* * *
465372 GAAAATAGGGCATGTATCCTATCAGTTTTTGAAAATTTTT-AGCCAAC
66 GAAAATAGGGCATGCATCCTACCA-TTTCTG-AAATTTTTGAGCCAAC
* * * * * *
465419 AACATTAAATTTGTTTGATTTTCGAAGAAATTCATACTTTATACGACCTGATCCATTCT-TGCCT
1 AACATCAAATTTATCTGATTTTCAAAGAAA-TCATACTTTATACAACCTAATCCATT-TGTGCCT
465483 AGGAAAAT-GAGGCATGCATCCTACCATTTCTGAAATTTTTGAGCCAAC
64 AGGAAAATAG-GGCATGCATCCTACCATTTCTGAAATTTTTGAGCCAAC
465531 CAAAGTTTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
111 8 0.08
112 39 0.40
113 49 0.51
114 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.35
Consensus pattern (111 bp):
AACATCAAATTTATCTGATTTTCAAAGAAATCATACTTTATACAACCTAATCCATTTGTGCCTAG
GAAAATAGGGCATGCATCCTACCATTTCTGAAATTTTTGAGCCAAC
Found at i:466381 original size:13 final size:13
Alignment explanation
Indices: 466363--466392 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
466353 ACATTTTACT
466363 ATGTATCGATACA
1 ATGTATCGATACA
466376 ATGTATCGATACA
1 ATGTATCGATACA
466389 ATGT
1 ATGT
466393 CCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:466382 original size:33 final size:33
Alignment explanation
Indices: 466340--466407 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
466330 GCCGTTGGGC
* * *
466340 ACAATGTATCGATACATTTTACTATGTATCGAT
1 ACAATGTATCGATACAATGTACCATGTATCGAT
*
466373 ACAATGTATCGATACAATGTCCCATGTATCGAT
1 ACAATGTATCGATACAATGTACCATGTATCGAT
466406 AC
1 AC
466408 TAATAGTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTACCATGTATCGAT
Found at i:475253 original size:13 final size:13
Alignment explanation
Indices: 475235--475264 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
475225 ACTTTTTACT
475235 ATGTATCGATACA
1 ATGTATCGATACA
475248 ATGTATCGATACA
1 ATGTATCGATACA
475261 ATGT
1 ATGT
475265 CCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:476097 original size:20 final size:20
Alignment explanation
Indices: 476072--476124 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
476062 TCACATTGAT
476072 ATTTGCATCATTTCATATAC
1 ATTTGCATCATTTCATATAC
476092 ATTTGCATCATTTCATATAC
1 ATTTGCATCATTTCATATAC
*
476112 ATTTGCACCATTT
1 ATTTGCATCATTT
476125 GTATTGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (20 bp):
ATTTGCATCATTTCATATAC
Found at i:476297 original size:44 final size:44
Alignment explanation
Indices: 476249--476395 Score: 133
Period size: 44 Copynumber: 3.4 Consensus size: 44
476239 TTGATCCTCA
* *
476249 CATTTTCATCATTTCATGTGCACTGACACTTTAGATGACATTGG
1 CATTTTCATCATTTCATGTACATTGACACTTTAGATGACATTGG
* * * *
476293 CATTTACATCATTTCATATACATTTACCACTTTA-TTGATC-TT-G
1 CATTTTCATCATTTCATGTACATTGA-CACTTTAGATGA-CATTGG
* * *
476336 CATTTTCATCGTTTCATGCACATTTG-CATTTTAGATGACATTGG
1 CATTTTCATCATTTCATGTACA-TTGACACTTTAGATGACATTGG
*
476380 CATCTAT-ATCATTTCA
1 CAT-TTTCATCATTTCA
476396 CATACATTTG
Statistics
Matches: 81, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
42 7 0.09
43 24 0.30
44 40 0.49
45 10 0.12
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (44 bp):
CATTTTCATCATTTCATGTACATTGACACTTTAGATGACATTGG
Found at i:476479 original size:88 final size:87
Alignment explanation
Indices: 476278--476682 Score: 332
Period size: 88 Copynumber: 4.6 Consensus size: 87
476268 GCACTGACAC
* * *
476278 TTTAGATGACATTGGCATTTACATCATTTCATATACATTTACCACTTTATTGATCTTGCATTTTC
1 TTTAGATGACATTGGCATTTACATCATTTCATATACATTTGCCACTTTATTGATCTTGCAATTGC
*
476343 ATCGTTTCATGCACATTTGCAT
66 ATCGTTTCATGCACATCTGCAT
* * * * *
476365 TTTAGATGACATTGGCATCTATATCATTTCACATACATTTGCCCCCTTATTGATGCTTGCAATTG
1 TTTAGATGACATTGGCATTTACATCATTTCATATACATTTGCCACTTTATTGAT-CTTGCAATTG
* *
476430 CATTGTTT-TTGGCACATCTGCAT
65 CATCGTTTCAT-GCACATCTGCAT
* * * * * * * *
476453 TTTAGATGATATTGGTATTTGCATCATTTCATTTGCATTTGCCTCTTTATTGATCTTTACATTTG
1 TTTAGATGACATTGGCATTTACATCATTTCATATACATTTGCCACTTTATTGATC-TTGCAATTG
* * * * *
476518 CATCGTTTCACAG-ATATTTTCCT
65 CATCGTTTCA-TGCACATCTGCAT
* * * ** * *
476541 TTTAGATGACATTAGTATTTACATCATTTCA-AGTATATTTGCTTCTTTATTGATCTTTGTATTT
1 TTTAGATGACATTGGCATTTACATCATTTCATA-TACATTTGCCACTTTATTGATC-TTGCAATT
* * * *
476605 TCATCATTTCACGCACATATGCAT
64 GCATCGTTTCATGCACATCTGCAT
* ** ** * * *
476629 TTTAGAT-ACCTTTGGTGTTGGCATCGTTTCATATGCATTTACCACTTTATTGAT
1 TTTAGATGA-CATTGGCATTTACATCATTTCATATACATTTGCCACTTTATTGAT
476683 GTTTGCATTG
Statistics
Matches: 252, Mismatches: 57, Indels: 17
0.77 0.17 0.05
Matches are distributed among these distances:
87 52 0.21
88 198 0.79
89 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (87 bp):
TTTAGATGACATTGGCATTTACATCATTTCATATACATTTGCCACTTTATTGATCTTGCAATTGC
ATCGTTTCATGCACATCTGCAT
Found at i:476603 original size:44 final size:44
Alignment explanation
Indices: 476489--476616 Score: 127
Period size: 44 Copynumber: 2.9 Consensus size: 44
476479 TTTCATTTGC
** * *
476489 ATTTGCCTCTTTATTGATCTTTACATTTGCATCGTTTCACAGAT
1 ATTTGCCTCTTTATTGATCTTTGTATTTACATCATTTCACAGAT
* * *
476533 ATTTTCCT-TTTAGATGA-CATTAGTATTTACATCATTTCA-AGTAT
1 ATTTGCCTCTTTA-TTGATC-TTTGTATTTACATCATTTCACAG-AT
* *
476577 ATTTGCTTCTTTATTGATCTTTGTATTTTCATCATTTCAC
1 ATTTGCCTCTTTATTGATCTTTGTATTTACATCATTTCAC
476617 GCACATATGC
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
43 7 0.11
44 54 0.82
45 5 0.08
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (44 bp):
ATTTGCCTCTTTATTGATCTTTGTATTTACATCATTTCACAGAT
Found at i:476630 original size:176 final size:175
Alignment explanation
Indices: 476161--476691 Score: 507
Period size: 176 Copynumber: 3.0 Consensus size: 175
476151 ATGCTTGTGG
* * ** *
476161 TTGCATCATTTCACACATATTTGCATTTTAGACAACATTAGTGTATTTTGTATCATTTCAAGTAC
1 TTGCATCGTTTCACAGATATTTGCATTTTAGATGACATTA--GTA-TTTATATCATTTCAAGTAC
* ** * ** * *
476226 ATTTGCTTTTTTATTGATCCTCACATTTTCATCATTTCATGTGCA-CTGACACTTTAGATGACAT
63 ATTTGCTTCTTTATTGAT-CTTGCATTTTCATCATTTCACGCACATCTG-CATTTTAGATGATAT
* * *
476290 TGGCATTTACATCATTTCATATACATTTACCACTTTATTGATC-TTGCAT
126 TGGTATTTGCATCATTTCATATGCATTTACCACTTTATTGATCTTTGCAT
* * * * * *
476339 TTTCATCGTTTCA-TGCACATTTGCATTTTAGATGACATTGGCATCTATATCATTTCACA-TACA
1 TTGCATCGTTTCACAG-ATATTTGCATTTTAGATGACATTAGTATTTATATCATTTCA-AGTACA
** * * * ** ***
476402 TTTGCCCCCTTATTGATGCTTGCAATTGCATTGTTTTTGGCACATCTGCATTTTAGATGATATTG
64 TTTGCTTCTTTATTGAT-CTTGCATTTTCATCATTTCACGCACATCTGCATTTTAGATGATATTG
* * * *
476467 GTATTTGCATCATTTCATTTGCATTTGCCTCTTTATTGATCTTTACAT
128 GTATTTGCATCATTTCATATGCATTTACCACTTTATTGATCTTTGCAT
* * * *
476515 TTGCATCGTTTCACAGATATTTTCCTTTTAGATGACATTAGTATTTACATCATTTCAAGTATATT
1 TTGCATCGTTTCACAGATATTTGCATTTTAGATGACATTAGTATTTATATCATTTCAAGTACATT
* *
476580 TGCTTCTTTATTGATCTTTGTATTTTCATCATTTCACGCACATATGCATTTTAGAT-ACCT-TTG
66 TGCTTCTTTATTGATC-TTGCATTTTCATCATTTCACGCACATCTGCATTTTAGATGA--TATTG
* * * *
476643 GTGTTGGCATCGTTTCATATGCATTTACCACTTTATTGATGTTTGCAT
128 GTATTTGCATCATTTCATATGCATTTACCACTTTATTGATCTTTGCAT
476691 T
1 T
476692 GTTATTTGCC
Statistics
Matches: 278, Mismatches: 66, Indels: 20
0.76 0.18 0.05
Matches are distributed among these distances:
175 97 0.35
176 148 0.53
177 2 0.01
178 31 0.11
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (175 bp):
TTGCATCGTTTCACAGATATTTGCATTTTAGATGACATTAGTATTTATATCATTTCAAGTACATT
TGCTTCTTTATTGATCTTGCATTTTCATCATTTCACGCACATCTGCATTTTAGATGATATTGGTA
TTTGCATCATTTCATATGCATTTACCACTTTATTGATCTTTGCAT
Found at i:477233 original size:60 final size:60
Alignment explanation
Indices: 477103--477333 Score: 234
Period size: 60 Copynumber: 3.9 Consensus size: 60
477093 ATATGTAGTT
* ** * * * *
477103 ATTGTTTAGGCTTCTAATTTCATCTAAACCATTTAGTTGAATCTTGATTTTGCCCAAGTC
1 ATTGTTTAGGTTTCTGGTTTCATCTAAGCCATTTTGTTGAGTCTTGATTTTTCCCAAGTC
* *
477163 ATTGTTTAGGTTTCTGGTTTCATCTAGGCCATTTTGTTGAGTCTTGATTTTTCCCTAGTC
1 ATTGTTTAGGTTTCTGGTTTCATCTAAGCCATTTTGTTGAGTCTTGATTTTTCCCAAGTC
* ** * * * *
477223 ATTATTTAGGTTTCCAGTTTCGTC-CAGTCATTTTGTTGAGT-TTTAGTTTTGTCCCAAGTC
1 ATTGTTTAGGTTTCTGGTTTCATCTAAGCCATTTTGTTGAGTCTTGA-TTTT-TCCCAAGTC
** * *
477283 ATTGTTTAGGTTTCTGGTTTTGT-TCAAGCCATTTCGTTGAGTCTTGGTTTT
1 ATTGTTTAGGTTTCTGGTTTCATCT-AAGCCATTTTGTTGAGTCTTGATTTT
477334 GCCTAAGTTA
Statistics
Matches: 139, Mismatches: 27, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
58 3 0.02
59 18 0.13
60 98 0.71
61 18 0.13
62 2 0.01
ACGTcount: A:0.17, C:0.16, G:0.19, T:0.48
Consensus pattern (60 bp):
ATTGTTTAGGTTTCTGGTTTCATCTAAGCCATTTTGTTGAGTCTTGATTTTTCCCAAGTC
Found at i:478192 original size:33 final size:33
Alignment explanation
Indices: 478152--478220 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
478142 CCATTACAAG
* *
478152 CAATGTATTAATATAAT-TCATCATATATCGATA
1 CAATGTATCAATACAATGT-ATCATATATCGATA
* *
478185 CAATGTATCGATACAATGTATCATGTATCGATA
1 CAATGTATCAATACAATGTATCATATATCGATA
478218 CAA
1 CAA
478221 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (33 bp):
CAATGTATCAATACAATGTATCATATATCGATA
Found at i:478195 original size:13 final size:13
Alignment explanation
Indices: 478177--478206 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
478167 ATTCATCATA
478177 TATCGATACAATG
1 TATCGATACAATG
478190 TATCGATACAATG
1 TATCGATACAATG
478203 TATC
1 TATC
478207 ATGTATCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:478293 original size:19 final size:19
Alignment explanation
Indices: 478249--478303 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
478239 CTGCCAGTTT
**
478249 CATGTATCGATACAAGTGTC
1 CATGTATCGATACAA-TGAA
478269 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
478288 CATGTATCGATACAAT
1 CATGTATCGATACAAT
478304 ATATCGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:478334 original size:33 final size:32
Alignment explanation
Indices: 478273--478334 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
478263 AGTGTCCATG
* *
478273 TATCGATACAATGAACATGTATCGATACAATA
1 TATCGATACAAAGAACATGTATCAATACAATA
478305 TATCGATACAAAGCATA-ATGTATCAATACA
1 TATCGATACAAAG-A-ACATGTATCAATACA
478335 TCTGGGTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 12 0.46
33 13 0.50
34 1 0.04
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (32 bp):
TATCGATACAAAGAACATGTATCAATACAATA
Found at i:478938 original size:22 final size:22
Alignment explanation
Indices: 478919--478987 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
478909 TATTTTTAAT
478919 AAAATATTTCTCCCCCTTTATC
1 AAAATATTTCTCCCCCTTTATC
*
478941 AAAATATTTTTCCCCCTTTATC
1 AAAATATTTCTCCCCCTTTATC
* *
478963 AAAGTATTTCTCCCCCTTTGTC
1 AAAATATTTCTCCCCCTTTATC
478985 AAA
1 AAA
478988 TCAAAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.28, C:0.29, G:0.03, T:0.41
Consensus pattern (22 bp):
AAAATATTTCTCCCCCTTTATC
Found at i:479013 original size:89 final size:90
Alignment explanation
Indices: 478857--479026 Score: 306
Period size: 89 Copynumber: 1.9 Consensus size: 90
478847 AAGTTTTCAT
*
478857 TTTTCTCCCCCTTAATCAAAGCATTTCTCCCCCTTTGTCAAATCAAAAAATTTATTTTTAATAAA
1 TTTTCTCCCCCTTAATCAAAGCATTTCTCCCCCTTTGTCAAATCAAAAAATTTATTTTCAATAAA
478922 ATATTTCTCCCCCTTTATCAAAATA
66 ATATTTCTCCCCCTTTATCAAAATA
* *
478947 TTTT-TCCCCCTTTATCAAAGTATTTCTCCCCCTTTGTCAAATCAAAAAATTTATTTTCAATAAA
1 TTTTCTCCCCCTTAATCAAAGCATTTCTCCCCCTTTGTCAAATCAAAAAATTTATTTTCAATAAA
479011 ATATTTCTCCCCCTTT
66 ATATTTCTCCCCCTTT
479027 TTGTTATAAC
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 73 0.95
90 4 0.05
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.42
Consensus pattern (90 bp):
TTTTCTCCCCCTTAATCAAAGCATTTCTCCCCCTTTGTCAAATCAAAAAATTTATTTTCAATAAA
ATATTTCTCCCCCTTTATCAAAATA
Found at i:484796 original size:20 final size:21
Alignment explanation
Indices: 484764--484806 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
484754 GAATCATGCA
484764 AATTCTTATTTTTC-TTAGCT
1 AATTCTTATTTTTCATTAGCT
484784 AATTCATTA-TTTTCATTAGCT
1 AATTC-TTATTTTTCATTAGCT
484805 AA
1 AA
484807 CTTTTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (21 bp):
AATTCTTATTTTTCATTAGCT
Found at i:487337 original size:13 final size:13
Alignment explanation
Indices: 487319--487343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
487309 ATTTTGCTTA
487319 GTATCGATACATT
1 GTATCGATACATT
487332 GTATCGATACAT
1 GTATCGATACAT
487344 AAAACTGACA
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:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:487413 original size:32 final size:32
Alignment explanation
Indices: 487372--487468 Score: 167
Period size: 32 Copynumber: 3.0 Consensus size: 32
487362 ATCTCATTTT
*
487372 TCACTGTTCATCATTGTTCATGTATCGATACA
1 TCACTGTTCATCACTGTTCATGTATCGATACA
*
487404 TCACTGTTCATCACTATTCATGTATCGATACA
1 TCACTGTTCATCACTGTTCATGTATCGATACA
*
487436 TCATTGTTCATCACTGTTCATGTATCGATACA
1 TCACTGTTCATCACTGTTCATGTATCGATACA
487468 T
1 T
487469 TGTATCGATA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (32 bp):
TCACTGTTCATCACTGTTCATGTATCGATACA
Found at i:487474 original size:13 final size:13
Alignment explanation
Indices: 487456--487497 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
487446 TCACTGTTCA
487456 TGTATCGATACAT
1 TGTATCGATACAT
* *
487469 TGTATCGATATAG
1 TGTATCGATACAT
487482 TGTATCGATACAT
1 TGTATCGATACAT
487495 TGT
1 TGT
487498 GAATAGTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:488003 original size:36 final size:32
Alignment explanation
Indices: 487956--488052 Score: 108
Period size: 36 Copynumber: 2.9 Consensus size: 32
487946 AATGATTGTG
487956 AGGTTCTATCTTAGCCTTTGAAAAAGATAGAGAGAA
1 AGGTTCTATCTTAGCC-TTG-AAAAGATAGAG-G-A
*
487992 AGGTTCTATCTTAGCCCGTGAAAAGATAG-GGA
1 AGGTTCTATCTTAG-CCTTGAAAAGATAGAGGA
* *
488024 CGTTTCTATCTTAGCCTTG-AAAGATAGAG
1 AGGTTCTATCTTAGCCTTGAAAAGATAGAG
488053 TTGTAAGGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
30 8 0.15
31 5 0.09
32 13 0.24
33 1 0.02
34 1 0.02
35 9 0.16
36 16 0.29
37 2 0.04
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (32 bp):
AGGTTCTATCTTAGCCTTGAAAAGATAGAGGA
Found at i:488907 original size:76 final size:76
Alignment explanation
Indices: 488778--489303 Score: 484
Period size: 76 Copynumber: 6.9 Consensus size: 76
488768 ATCATTACTC
* * *
488778 TTATCAGTTTGTTTCGGCTGTTGATGGAAATTTTAAAAATCACATATTCCCCATCATGTTCTTTT
1 TTATCAGTTTATTTCGGCTGTTGATGGAAATTTTAGAAATCACATATTTCCCATCATGTTCTTTT
488843 CCTTCAACCCG
66 CCTTCAACCCG
* * * ** * *
488854 TTATCAGTTTCTTTTGGCTGTTAATTAAAATTTTAGAAATCACATTTTTCCCATCATGTTCCTTT
1 TTATCAGTTTATTTCGGCTGTTGATGGAAATTTTAGAAATCACATATTTCCCATCATGTTCTTTT
* * *
488919 CTTTCAGCTCG
66 CCTTCAACCCG
* * *
488930 TTATAAGTTTATTTTGGTTGTTGATGGAAATTTTAGAAATCACATA-TTCCCTATCATGTTGC-T
1 TTATCAGTTTATTTCGGCTGTTGATGGAAATTTTAGAAATCACATATTTCCC-ATCATGTT-CTT
* *
488993 TTCCTTTAACCCA
64 TTCCTTCAACCCG
* * ** * * * * *
489006 TTATCAATTTGTTTCAACTGTTGATAAGAAATTATAG-AATCACATATTTCCCATTATGATCTTC
1 TTATCAGTTTATTTCGGCTGTTGAT-GGAAATTTTAGAAATCACATATTTCCCATCATGTTCTTT
* ** **
489070 TACTTCGGCTTG
65 TCCTTCAACCCG
** * * * *
489082 TTATCAGTTTATTTCGATTGTTGAAGGAAATTTTAGAAATAACATATTTCCTATCATGTTTTTTT
1 TTATCAGTTTATTTCGGCTGTTGATGGAAATTTTAGAAATCACATATTTCCCATCATGTTCTTTT
* * **
489147 CTTTCAGCCTA
66 CCTTCAACCCG
** * *
489158 TTATCAGTTTATTTCAACTGTTGAAGGAAATTTTAGAAATCACATATTCCCTCATCATGTTCCTT
1 TTATCAGTTTATTTCGGCTGTTGATGGAAATTTTAGAAATCACATATTTCC-CATCATGTT-CTT
* *
489223 TT-TTTCAACCTG
64 TTCCTTCAACCCG
* ** * * * *
489235 TTATCAGTTTGTTTTAGTTATTGATGAAAATTTTAGAAATCACATATTCCCCATCATGTTCTTTT
1 TTATCAGTTTATTTCGGCTGTTGATGGAAATTTTAGAAATCACATATTTCCCATCATGTTCTTTT
489300 CCTT
66 CCTT
489304 TCTTTCCAAT
Statistics
Matches: 364, Mismatches: 77, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
75 20 0.05
76 265 0.73
77 75 0.21
78 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.45
Consensus pattern (76 bp):
TTATCAGTTTATTTCGGCTGTTGATGGAAATTTTAGAAATCACATATTTCCCATCATGTTCTTTT
CCTTCAACCCG
Found at i:489059 original size:152 final size:153
Alignment explanation
Indices: 488778--489304 Score: 593
Period size: 152 Copynumber: 3.5 Consensus size: 153
488768 ATCATTACTC
* * *
488778 TTATCAGTTTGTTTCGGCTGTTGATGGAAATTTTAAAAATCACATATTCCCCATCATGTTCTTTT
1 TTATCAGTTTATTTCGGTTGTTGATGGAAATTTTAGAAATCACATATTCCCCATCATGTTCTTTT
* * * *** * * *
488843 CCTTCAACCCGTTATCAGTTTCTTTTGGCTGTTAATTA-AAATTTTAGAAATCACATTTTTCCCA
66 CCTTTAACCCATTATCAGTTTATTTCAACTGTTGATAAGAAATTTTAGAAATCACATATTTCCCA
488907 TCATGTTCCTTTCTTTCAGCTCG
131 TCATGTTCCTTTCTTTCAGCTCG
* * *
488930 TTATAAGTTTATTTTGGTTGTTGATGGAAATTTTAGAAATCACATATTCCCTATCATGTTGC-TT
1 TTATCAGTTTATTTCGGTTGTTGATGGAAATTTTAGAAATCACATATTCCCCATCATGTT-CTTT
* * *
488994 TCCTTTAACCCATTATCAATTTGTTTCAACTGTTGATAAGAAATTATAG-AATCACATATTTCCC
65 TCCTTTAACCCATTATCAGTTTATTTCAACTGTTGATAAGAAATTTTAGAAATCACATATTTCCC
* * * *
489058 ATTATGAT-C-TTCTACTTCGGCTTG
130 ATCATGTTCCTTTCT--TTCAGCTCG
* * * * *
489082 TTATCAGTTTATTTCGATTGTTGAAGGAAATTTTAGAAATAACATATTTCCTATCATGTT-TTTT
1 TTATCAGTTTATTTCGGTTGTTGATGGAAATTTTAGAAATCACATATTCCCCATCATGTTCTTTT
* * * * *
489146 TCTTTCAGCCTATTATCAGTTTATTTCAACTGTTGA-AGGAAATTTTAGAAATCACATATTCCCT
66 CCTTT-AACCCATTATCAGTTTATTTCAACTGTTGATAAGAAATTTTAGAAATCACATATTTCC-
* *
489210 CATCATGTTCCTTTTTTTCAAC-CTG
129 CATCATGTTCCTTTCTTTCAGCTC-G
* ** * *
489235 TTATCAGTTTGTTTTAGTTATTGATGAAAATTTTAGAAATCACATATTCCCCATCATGTTCTTTT
1 TTATCAGTTTATTTCGGTTGTTGATGGAAATTTTAGAAATCACATATTCCCCATCATGTTCTTTT
489300 CCTTT
66 CCTTT
489305 CTTTCCAATC
Statistics
Matches: 311, Mismatches: 52, Indels: 22
0.81 0.14 0.06
Matches are distributed among these distances:
150 4 0.01
151 18 0.06
152 206 0.66
153 71 0.23
154 9 0.03
155 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.45
Consensus pattern (153 bp):
TTATCAGTTTATTTCGGTTGTTGATGGAAATTTTAGAAATCACATATTCCCCATCATGTTCTTTT
CCTTTAACCCATTATCAGTTTATTTCAACTGTTGATAAGAAATTTTAGAAATCACATATTTCCCA
TCATGTTCCTTTCTTTCAGCTCG
Found at i:490082 original size:66 final size:66
Alignment explanation
Indices: 489973--490285 Score: 274
Period size: 66 Copynumber: 4.7 Consensus size: 66
489963 CTTTAAACTT
* * * * * * ** *
489973 GTTGACTTTATTGATTTCACCCTGGTCAACCTCTTTTCAACTTAGGTTTTTCTTTGGTCACCCTT
1 GTTGACTTTATCGATTTCGCCTTAGTCAATCTCTTTTCGACTTAGGTTTTTCCCTAGTCACCCTT
490038 A
66 A
* * * *
490039 GTTGACTTTATCGGTTTCGCAC-TAGTTAATCTTTTTTCGACTTAGGTTTTACCCTAGTCACCCT
1 GTTGACTTTATCGATTTCGC-CTTAGTCAATCTCTTTTCGACTTAGGTTTTTCCCTAGTCACCCT
490103 TA
65 TA
* * ** * *
490105 GTTGACTTTATCGATTTTGCCTTAGTCAA-CTGCTCTTCGACTTAGGCTTCAT-CTTGGTCACCC
1 GTTGACTTTATCGATTTCGCCTTAGTCAATCT-CTTTTCGACTTAGG-TTTTTCCCTAGTCACCC
490168 TTA
64 TTA
** * * * * * * * *
490171 GTTGACTTTATCGATTTTACCATGGTCAATC-CTTTTTCAACCTAAGTTATGCCCTAGTCACCTT
1 GTTGACTTTATCGATTTCGCCTTAGTCAATCTC-TTTTCGACTTAGGTTTTTCCCTAGTCACCCT
490235 TA
65 TA
* * *
490237 GTTGACTTTATCTATTTCGCCTTAGTTAACCTCTTTTCGACTTAGGTTT
1 GTTGACTTTATCGATTTCGCCTTAGTCAATCTCTTTTCGACTTAGGTTT
490286 ACCCTTTTAC
Statistics
Matches: 193, Mismatches: 46, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
65 6 0.03
66 182 0.94
67 5 0.03
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.44
Consensus pattern (66 bp):
GTTGACTTTATCGATTTCGCCTTAGTCAATCTCTTTTCGACTTAGGTTTTTCCCTAGTCACCCTT
A
Found at i:490164 original size:132 final size:132
Alignment explanation
Indices: 489973--490282 Score: 358
Period size: 132 Copynumber: 2.3 Consensus size: 132
489963 CTTTAAACTT
* * * * * * **
489973 GTTGACTTTATTGATTTCACCCTGGTCAACCTCTTTTCAACTTAGG-TTTTTCTTTGGTCACCCT
1 GTTGACTTTATCGATTTCGCCTTAGTCAACCTCTCTTCGACTTAGGCTTCATC-TTGGTCACCCT
* * * * * *
490037 TAGTTGACTTTATCG-GTTT-CGCACTAGTTAATCTTTTTTCGACTTAGGTTTTACCCTAGTCAC
65 TAGTTGACTTTATCGAGTTTAC-CA-TAGTCAATCCTTTTTCAACCTAAGTTATACCCTAGTCAC
490100 CCTTA
128 CCTTA
*
490105 GTTGACTTTATCGATTTTGCCTTAGTCAA-CTGCTCTTCGACTTAGGCTTCATCTTGGTCACCCT
1 GTTGACTTTATCGATTTCGCCTTAGTCAACCT-CTCTTCGACTTAGGCTTCATCTTGGTCACCCT
* * * *
490169 TAGTTGACTTTATCGATTTTACCATGGTCAATCCTTTTTCAACCTAAGTTATGCCCTAGTCACCT
65 TAGTTGACTTTATCGAGTTTACCATAGTCAATCCTTTTTCAACCTAAGTTATACCCTAGTCACCC
490234 TTA
130 TTA
* * *
490237 GTTGACTTTATCTATTTCGCCTTAGTTAACCTCTTTTCGACTTAGG
1 GTTGACTTTATCGATTTCGCCTTAGTCAACCTCTCTTCGACTTAGG
490283 TTTACCCTTT
Statistics
Matches: 150, Mismatches: 23, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
131 2 0.01
132 136 0.91
133 11 0.07
134 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (132 bp):
GTTGACTTTATCGATTTCGCCTTAGTCAACCTCTCTTCGACTTAGGCTTCATCTTGGTCACCCTT
AGTTGACTTTATCGAGTTTACCATAGTCAATCCTTTTTCAACCTAAGTTATACCCTAGTCACCCT
TA
Found at i:490661 original size:64 final size:64
Alignment explanation
Indices: 490564--490729 Score: 192
Period size: 64 Copynumber: 2.6 Consensus size: 64
490554 ACTTCGCCGA
* * * * * * *
490564 TTTTGCCTTGGTCAAGACCCTTTTCGACGTAGGTTTTA-CCTTGGTCTCTTTTAGTTGACTTAAC
1 TTTTACCTTGGTC-A-ACCCTTTTTGACTTAGGTTTCATCC-TAGTCACCTTTAGTTGACTT-AC
490628 -GG
62 TGG
490630 TTTTACCTTGGTCAACCCTTTTTGACTTAGGTTTCATCCTAGTCACCTTTAGTTGACTTACTGG
1 TTTTACCTTGGTCAACCCTTTTTGACTTAGGTTTCATCCTAGTCACCTTTAGTTGACTTACTGG
* * *
490694 TTTCACCATGGTCAACCCTTTCTGACTTAGGTTTCA
1 TTTTACCTTGGTCAACCCTTTTTGACTTAGGTTTCA
490730 CTTTAGTCAC
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
63 2 0.02
64 71 0.81
65 3 0.03
66 12 0.14
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (64 bp):
TTTTACCTTGGTCAACCCTTTTTGACTTAGGTTTCATCCTAGTCACCTTTAGTTGACTTACTGG
Found at i:490730 original size:31 final size:31
Alignment explanation
Indices: 490618--490730 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 31
490608 TCTCTTTTAG
*
490618 TTGACTTAACGGTTTTACCTTGGTCAACCCTTT
1 TTGACTT-ACGGTTTCACC-TGGTCAACCCTTT
*
490651 TTGACTTA-GGTTTCATCCTAGTC-A-CCTTT
1 TTGACTTACGGTTTCA-CCTGGTCAACCCTTT
490680 AGTTGACTTACTGGTTTCACCATGGTCAACCCTTT
1 --TTGACTTAC-GGTTTCACC-TGGTCAACCCTTT
*
490715 CTGACTTA-GGTTTCAC
1 TTGACTTACGGTTTCAC
490731 TTTAGTCACC
Statistics
Matches: 68, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
29 5 0.07
30 1 0.01
31 26 0.38
32 5 0.07
33 25 0.37
34 1 0.01
35 5 0.07
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.41
Consensus pattern (31 bp):
TTGACTTACGGTTTCACCTGGTCAACCCTTT
Found at i:493336 original size:13 final size:13
Alignment explanation
Indices: 493318--493343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
493308 TACAGCAAGT
493318 ATGTATCGATACA
1 ATGTATCGATACA
493331 ATGTATCGATACA
1 ATGTATCGATACA
493344 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:494588 original size:163 final size:163
Alignment explanation
Indices: 494365--494795 Score: 462
Period size: 163 Copynumber: 2.6 Consensus size: 163
494355 AAATTTTAAT
* * * * *
494365 TTTTAGA-GTCAATATCATCATTTTAGTCATTTTTAAAGATTTGTATTATTTTTATGGCCTTTTG
1 TTTTAGAGGT-AAAATCATCATTTTAGTCA-TTTTAAAAATTTATATTATTCTTATGGCCTTCTG
* * * * *
494429 TAGGGGTATAAAATTTTTTAAAACTTTTTGTATCCTCTC-AGTATTGCATT-GGGTATGAAATGG
64 TAGAGATATAAAA-TTTTTAAAACTTTTCGTATCCTCTCGA-T-TTGCATTCAGGCATGAAAT-G
*
494492 AAATTTT-AAAAGTTTAGGGATTAAATAG-AAAGTTTAG
125 AAATTTTCAAAAGTTTAGGAATTAAATAGCAAAGTTTAG
* * * *
494529 -TTTAGAGGTAAAA-CTATCATGTTAATCATTTTAAAAAATTTCTATTATTCCTATGGCCTTCTG
1 TTTTAGAGGTAAAATC-ATCATTTTAGTCATTTT-AAAAATTTATATTATTCTTATGGCCTTCTG
* * ***
494592 TAGAGCTATAGAAATTTTTAAAACTTTTCGTATCTTCTCGATTTTTTTTCAGGCATGAAATGAAA
64 TAGAGATATA-AAATTTTTAAAACTTTTCGTATCCTCTCGATTTGCATTCAGGCATGAAATGAAA
*
494657 TTTTCAAAAGTTTAGGAATTAAATAGCAAATTTTAG
128 TTTTCAAAAGTTTAGGAATTAAATAGCAAAGTTTAG
* * *
494693 TTTTTAGAGGTAAAATCATCATTTTAGTTATTGTTAAATATTTATATTATTCTTATGGCCTTCCG
1 -TTTTAGAGGTAAAATCATCATTTTAGTCATT-TTAAAAATTTATATTATTCTTATGGCCTTCTG
* * *
494758 TATAGATATAAAAATTTTCAAGACTTTTCGTATCCTCT
64 TAGAGATAT-AAAATTTTTAAAACTTTTCGTATCCTCT
494796 TAGTTTTTCG
Statistics
Matches: 223, Mismatches: 31, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
162 17 0.08
163 106 0.48
164 14 0.06
166 82 0.37
167 4 0.02
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (163 bp):
TTTTAGAGGTAAAATCATCATTTTAGTCATTTTAAAAATTTATATTATTCTTATGGCCTTCTGTA
GAGATATAAAATTTTTAAAACTTTTCGTATCCTCTCGATTTGCATTCAGGCATGAAATGAAATTT
TCAAAAGTTTAGGAATTAAATAGCAAAGTTTAG
Found at i:494826 original size:166 final size:164
Alignment explanation
Indices: 494297--494838 Score: 513
Period size: 166 Copynumber: 3.3 Consensus size: 164
494287 CCTTCATATT
* * * * ** * * *
494297 CTCTTAGTTTTTTAACATGTATGAAATGAAATTTTAAAAAAATTA-AAGATTTAATCGTAAATTT
1 CTCTTAGTTTTTCATCAGGTATGAAATGAAATTTTCAAAAGTTTAGGA-ATTAAATAG-AAATTT
* * * * *
494361 TAATTTTTAGA-GTCAATATCATCATTTTAGTCATTTTTAAAGATTTGTATTATTTTTATGGCCT
64 TAGTTTTTAGAGGT-AAAATCATCATTTTAGTCA-TTTTAAAAATTTATATTATTCTTATGGCCT
* * * * *
494425 TTTGTAGGGGTATAAAATTTTTTAAAACTTTTTGTATC
127 TCTGTAGAGATATAAAAATTTTTAAAACTTTTCGTATC
* * * ** * *
494463 CTCTCAGTATTGCATTGGGTATGAAATGGAAATTTT-AAAAGTTTAGGGATTAAATAGAAAGTTT
1 CTCTTAGTTTTTCATCAGGTATGAAAT-GAAATTTTCAAAAGTTTAGGAATTAAATAGAAATTTT
* * * *
494527 AG--TTTAGAGGTAAAA-CTATCATGTTAATCATTTTAAAAAATTTCTATTATTCCTATGGCCTT
65 AGTTTTTAGAGGTAAAATC-ATCATTTTAGTCATTTT-AAAAATTTATATTATTCTTATGGCCTT
* *
494589 CTGTAGAGCTATAGAAATTTTTAAAACTTTTCGTATC
128 CTGTAGAGATATAAAAATTTTTAAAACTTTTCGTATC
* * ** *
494626 TTC-TCGATTTTTTTTCAGGCATGAAATGAAATTTTCAAAAGTTTAGGAATTAAATAGCAAATTT
1 CTCTTAG-TTTTTCATCAGGTATGAAATGAAATTTTCAAAAGTTTAGGAATTAAATAG-AAATTT
* *
494690 TAGTTTTTAGAGGTAAAATCATCATTTTAGTTATTGTTAAATATTTATATTATTCTTATGGCCTT
64 TAGTTTTTAGAGGTAAAATCATCATTTTAGTCATT-TTAAAAATTTATATTATTCTTATGGCCTT
* * * *
494755 CCGTATAGATATAAAAATTTTCAAGACTTTTCGTATC
128 CTGTAGAGATATAAAAATTTTTAAAACTTTTCGTATC
* * * * *
494792 CTCTTAGTTTTTCGTCAAGTATCAAATAAAATTTTCAAAGGTTTAGG
1 CTCTTAGTTTTTCATCAGGTATGAAATGAAATTTTCAAAAGTTTAGG
494839 GGCTTAATTG
Statistics
Matches: 301, Mismatches: 62, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
162 14 0.05
163 109 0.36
164 10 0.03
165 7 0.02
166 148 0.49
167 13 0.04
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (164 bp):
CTCTTAGTTTTTCATCAGGTATGAAATGAAATTTTCAAAAGTTTAGGAATTAAATAGAAATTTTA
GTTTTTAGAGGTAAAATCATCATTTTAGTCATTTTAAAAATTTATATTATTCTTATGGCCTTCTG
TAGAGATATAAAAATTTTTAAAACTTTTCGTATC
Found at i:495659 original size:156 final size:155
Alignment explanation
Indices: 494947--496071 Score: 784
Period size: 156 Copynumber: 7.2 Consensus size: 155
494937 AGGGTTATCG
* * * * * * *
494947 AGATACTTTCATGTCAAAAGCATACCCAATGGTATTTTCATAATTTTCCTAAAATCGAAT-ATGA
1 AGATACTTTTATGTCGAAAGTATACCCAAAGGTATTTTCATAATTTTCCTAGAATCGAGTCCT-A
* * * * * * * *
495011 GGTTTTCATCGGGATGGTTTTTATGCCAAAAGTGGGCATTTAGGATAGATTCATCACATTTATTA
65 GGTTGTCATCGGGAT-GCTTTTATGTCAAAGGTGTGCATTTAGGATAGGTTTATCACATTTATGA
* ** * *
495076 TTATTTTTAAGTCTTTTAGGGTT-TCG
129 TCATTTTTAAGTCTTTTAAAGTTACCA
* * * * * * * *
495102 AGATACTTTTATGTCGAAGGTATACCCTAGGAGCATTTCCATAATTTTCTTAGAACCGAATCCTA
1 AGATACTTTTATGTCGAAAGTATACCCAAAG-GTATTTTCATAATTTTCCTAGAATCGAGTCCTA
* * ** *
495167 GGTTATCA-CTGGGATGCTTTTATGCCAAAGGTGTGCATTTAAAATAGGCTTATC-CTATTTATG
65 GGTTGTCATC-GGGATGCTTTTATGTCAAAGGTGTGCATTTAGGATAGGTTTATCAC-ATTTATG
* *
495230 ATCATTTTTAAGTCTTTT-AGGATTATCA
128 ATCATTTTTAAGTCTTTTAAAG-TTACCA
* * * **
495258 GGATA-TTTTCATGTC-AAAGGTATA-CCTAAGGGATTTTTGTAATTTTCCTAGAATCGAGTCCT
1 AGATACTTTT-ATGTCGAAA-GTATACCCAAAGGTATTTTCATAATTTTCCTAGAATCGAGTCCT
* * ** * ** *
495320 AGGTTGTTA-CGAGATAATTTTATGCCAAAGGCATGCATTTAGGATAGGTTTATCTCATTTATGA
64 AGGTTGTCATCGGGATGCTTTTATGTCAAAGGTGTGCATTTAGGATAGGTTTATCACATTTATGA
495384 TCA--TTTAAGTCTTTTAAAGTTACCA
129 TCATTTTTAAGTCTTTTAAAGTTACCA
* * * * ** * * *
495409 AGATACTTTCATGTCGAAGGTATACCTAAGGGTATTTTCATAATTTTTTTAGAACCAAGTCTTAG
1 AGATACTTTTATGTCGAAAGTATACCCAAAGGTATTTTCATAATTTTCCTAGAATCGAGTCCTAG
* * *
495474 GTTGTCATCGGGATGCTTTTATGTCAAAGGTATGCATATAGGATAGGTTTATCCCATTTATGATC
66 GTTGTCATCGGGATGCTTTTATGTCAAAGGTGTGCATTTAGGATAGGTTTATCACATTTATGATC
*
495539 ATTTTTAAGTCTTTTAAAGTTACCG
131 ATTTTTAAGTCTTTTAAAGTTACCA
* * * * *
495564 GGATACTTTTATGTCGAAAGTATACCCCAAAAGTATTTTAATAATTTTCCTAAAATCTAGTCCTA
1 AGATACTTTTATGTCGAAAGTATA-CCCAAAGGTATTTTCATAATTTTCCTAGAATCGAGTCCTA
* * * * *
495629 AGTTGTCATCGGGATGCTTTTATATCAAAGGCGTGTATTTAGGATAGGTTTATCACATTCATGAT
65 GGTTGTCATCGGGATGCTTTTATGTCAAAGGTGTGCATTTAGGATAGGTTTATCACATTTATGAT
* ** *
495694 CATTTTT-AGATCCTTTAGGGTTAACA
130 CATTTTTAAG-TCTTTTAAAGTTACCA
* * ** * * *
495720 AGATA-TTTTCATATC-AAAGGTATACCTTAGGGGTATTTTCATAATTTTTCTA-AAACTAAGTC
1 AGATACTTTT-ATGTCGAAA-GTATACC-CAAAGGTATTTTCATAATTTTCCTAGAATC-GAGTC
* * * * *
495782 ATAGTTTGTCACCAGGATGCTTTTATG-CTAAAGGTTTGCATTTAGGATAAGTTCGCATTTAGGA
62 CTAGGTTGTCATCGGGATGCTTTTATGTC-AAAGGTGTGCATTTAGGAT-AG---G---TT----
* ** *
495846 TAGGTTCATCCAATTCATGATCATTTTTAAGTCTTTTAGGGTTGCCGA
115 TA---TCA--C-ATTTATGATCATTTTTAAGTCTTTTAAAGTTACC-A
* ** * * ** * *
495894 A-ATATTTTTATGTC-AAATGTATACCTTAAGATTTTTTTTGTAATTTGT-TTAAAATAC-AGTC
1 AGATACTTTTATGTCGAAA-GTATACCCAAAG-GTATTTTCATAATTT-TCCTAGAAT-CGAGTC
* * * *
495955 CTAGGTTGCCA-CTGGGATGCTTTTATGCCAAA-GTGTGCATTTAGGATAGGTTCATCTCATTTA
62 CTAGGTTGTCATC-GGGATGCTTTTATGTCAAAGGTGTGCATTTAGGATAGGTTTATCACATTTA
* *
496018 TGATTATTTTTAAGTCTTTTAGAGTTACCA
126 TGATCATTTTTAAGTCTTTTAAAGTTACCA
496048 AGATA-TTTTCATGTCGAAAGTATA
1 AGATACTTTT-ATGTCGAAAGTATA
496072 TACTAAGGAC
Statistics
Matches: 778, Mismatches: 140, Indels: 104
0.76 0.14 0.10
Matches are distributed among these distances:
151 31 0.04
152 42 0.05
153 98 0.13
154 43 0.06
155 193 0.25
156 235 0.30
157 3 0.00
158 2 0.00
160 1 0.00
161 1 0.00
163 2 0.00
165 2 0.00
167 2 0.00
168 1 0.00
170 3 0.00
171 2 0.00
172 18 0.02
173 86 0.11
174 12 0.02
175 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (155 bp):
AGATACTTTTATGTCGAAAGTATACCCAAAGGTATTTTCATAATTTTCCTAGAATCGAGTCCTAG
GTTGTCATCGGGATGCTTTTATGTCAAAGGTGTGCATTTAGGATAGGTTTATCACATTTATGATC
ATTTTTAAGTCTTTTAAAGTTACCA
Found at i:495841 original size:17 final size:17
Alignment explanation
Indices: 495819--495852 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
495809 CTAAAGGTTT
495819 GCATTTAGGATAAGTTC
1 GCATTTAGGATAAGTTC
*
495836 GCATTTAGGATAGGTTC
1 GCATTTAGGATAAGTTC
495853 ATCCAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (17 bp):
GCATTTAGGATAAGTTC
Found at i:495975 original size:173 final size:172
Alignment explanation
Indices: 495665--496007 Score: 408
Period size: 173 Copynumber: 2.0 Consensus size: 172
495655 AAAGGCGTGT
*
495665 ATTTAGGATAGGTTTATCACATTCATGATCATTTTTAGATCCTTTAGGGTTAACAAGATATTTTC
1 ATTTAGGATAGGTTCATCACATTCATGATCATTTTTAGATCCTTTAGGGTTAACAAGATATTTTC
* * * *
495730 ATATCAAAGGTATACCTTAGGGGTATTTTCATAATTTTTCTAAAACTAAGTCATAGTTTGTCACC
66 ATATCAAAGGTATACCTTAAGAGTATTTTCATAATTTTTCTAAAACTAAGTCATAGGTTGCCACC
* *
495795 AGGATGCTTTTATGCTAAAGGTTTGCATTTAGGATAAGTTCGC
131 AGGATGCTTTTATGCCAAA-GTGTGCATTTAGGATAAGTTCGC
* **
495838 ATTTAGGATAGGTTCATC-CAATTCATGATCATTTTTA-AGTCTTTTAGGGTTGCCGAA-ATATT
1 ATTTAGGATAGGTTCATCAC-ATTCATGATCATTTTTAGA-TCCTTTAGGGTTAAC-AAGATATT
* * * * * ** *
495900 TTTATGTCAAATGTATACCTTAAGATTTTTTTTGTAATTTGTT-TAAAA-TACAGTCCTAGGTTG
63 TTCATATCAAAGGTATACCTTAAGAGTATTTTCATAATTT-TTCTAAAACTA-AGTCATAGGTTG
** *
495963 CCACTGGGATGCTTTTATGCCAAAGTGTGCATTTAGGATAGGTTC
126 CCACCAGGATGCTTTTATGCCAAAGTGTGCATTTAGGATAAGTTC
496008 ATCTCATTTA
Statistics
Matches: 144, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
172 23 0.16
173 117 0.81
174 4 0.03
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (172 bp):
ATTTAGGATAGGTTCATCACATTCATGATCATTTTTAGATCCTTTAGGGTTAACAAGATATTTTC
ATATCAAAGGTATACCTTAAGAGTATTTTCATAATTTTTCTAAAACTAAGTCATAGGTTGCCACC
AGGATGCTTTTATGCCAAAGTGTGCATTTAGGATAAGTTCGC
Found at i:496983 original size:32 final size:33
Alignment explanation
Indices: 496923--496986 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
496913 CACACCCAGA
* *
496923 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCAATACATATTGCATAGTATCGATACAT
*
496956 TGTATCAATACATGTT-CATAGTATCGATACA
1 TGTATCAATACATATTGCATAGTATCGATACA
496987 CCTTGAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (33 bp):
TGTATCAATACATATTGCATAGTATCGATACAT
Found at i:497069 original size:20 final size:20
Alignment explanation
Indices: 497040--497100 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
497030 CACTTAGTAT
*
497040 TGATACATTGTATCGATACA
1 TGATAAATTGTATCGATACA
*
497060 TGATGAATTGTATCGATACA
1 TGATAAATTGTATCGATACA
* * *
497080 TGGTAAAATGTATCAATACA
1 TGATAAATTGTATCGATACA
497100 T
1 T
497101 TGAGATCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
TGATAAATTGTATCGATACA
Found at i:499179 original size:20 final size:20
Alignment explanation
Indices: 499154--499231 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
499144 ATTGCCAAGG
499154 AAATGTATCAATACATTAAT
1 AAATGTATCAATACATTAAT
* ***
499174 AAATGTATCGATACATGCTT
1 AAATGTATCAATACATTAAT
* *
499194 CAAATTGTATCGATACATTTAT
1 -AAA-TGTATCAATACATTAAT
* *
499216 CATTGTATCAATACAT
1 AAATGTATCAATACAT
499232 CTGGGTTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
20 28 0.61
21 4 0.09
22 14 0.30
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (20 bp):
AAATGTATCAATACATTAAT
Found at i:500447 original size:21 final size:21
Alignment explanation
Indices: 500421--500467 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
500411 TACATGTTTG
500421 AAAAGTGTCAAAACTGATTTC
1 AAAAGTGTCAAAACTGATTTC
500442 AAAAGTGTCAAAACTGATTTC
1 AAAAGTGTCAAAACTGATTTC
500463 AAAAG
1 AAAAG
500468 ATCTCCCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.26
Consensus pattern (21 bp):
AAAAGTGTCAAAACTGATTTC
Found at i:503018 original size:23 final size:23
Alignment explanation
Indices: 502986--503057 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
502976 TTTTTTTTGT
* *
502986 TTTAATTGGGCTTTTAGTTTAGG
1 TTTAAATGGGCTTTTAGTTTAGA
*
503009 TTTAGATGGGCTTTTAGTTTAGA
1 TTTAAATGGGCTTTTAGTTTAGA
* * *
503032 TTTAAAT-GGATTTAAGTTTAAA
1 TTTAAATGGGCTTTTAGTTTAGA
503054 TTTA
1 TTTA
503058 TATTTTATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.38
23 26 0.62
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (23 bp):
TTTAAATGGGCTTTTAGTTTAGA
Found at i:504048 original size:128 final size:128
Alignment explanation
Indices: 503820--504077 Score: 480
Period size: 128 Copynumber: 2.0 Consensus size: 128
503810 TGAGTAATAG
*
503820 AATCAATCCTTAAAAACTAAAAAGTTAAAACCTTCTTAAAATATAAAGCTAAGGAATTAATAATC
1 AATCAATCCTTAAAAACTAAAAAGTTAAAACCTTCTTAAAATATAAAGCTAAAGAATTAATAATC
503885 AATTAAAACTCAAAAAAGAATTAAAAGTCAAATAAAATACTAAAAGGAATTAAAAGTCAGCTA
66 AATTAAAACTCAAAAAAGAATTAAAAGTCAAATAAAATACTAAAAGGAATTAAAAGTCAGCTA
* * *
503948 AATCAATCCTTACAAACTAAAAATTTAAAACCTTTTTAAAATATAAAGCTAAAGAATTAATAATC
1 AATCAATCCTTAAAAACTAAAAAGTTAAAACCTTCTTAAAATATAAAGCTAAAGAATTAATAATC
504013 AATTAAAACTCAAAAAAGAATTAAAAGTCAAATAAAATACTAAAAGGAATTAAAAGTCAGCTA
66 AATTAAAACTCAAAAAAGAATTAAAAGTCAAATAAAATACTAAAAGGAATTAAAAGTCAGCTA
504076 AA
1 AA
504078 ACACTAAAAT
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 126 1.00
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.25
Consensus pattern (128 bp):
AATCAATCCTTAAAAACTAAAAAGTTAAAACCTTCTTAAAATATAAAGCTAAAGAATTAATAATC
AATTAAAACTCAAAAAAGAATTAAAAGTCAAATAAAATACTAAAAGGAATTAAAAGTCAGCTA
Found at i:504057 original size:29 final size:29
Alignment explanation
Indices: 503998--504107 Score: 118
Period size: 29 Copynumber: 3.8 Consensus size: 29
503988 ATATAAAGCT
* *
503998 AAAGAATTAATAA-TCAATTAAAACT-CAAA
1 AAAGAATTAA-AAGTCAACTAAAA-TACTAA
*
504027 AAAGAATTAAAAGTCAAATAAAATACTAA
1 AAAGAATTAAAAGTCAACTAAAATACTAA
* * *
504056 AAGGAATTAAAAGTCAGCTAAAACACTAA
1 AAAGAATTAAAAGTCAACTAAAATACTAA
504085 AATA-AATTAAAAGTCAACTAAAA
1 AA-AGAATTAAAAGTCAACTAAAA
504108 ACACTAGAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.04
29 67 0.96
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (29 bp):
AAAGAATTAAAAGTCAACTAAAATACTAA
Found at i:508158 original size:28 final size:28
Alignment explanation
Indices: 508085--508193 Score: 121
Period size: 29 Copynumber: 3.8 Consensus size: 28
508075 TAAAGCTAAG
* * * *
508085 GAATTAAAAGTAAACTAAAACTCCAAAA
1 GAATTAAAAATCAACTAAAACACTAAAA
* * *
508113 GAAAATAAAAGTCAACTAGAACACTAAAA
1 G-AATTAAAAATCAACTAAAACACTAAAA
508142 GAATTAAAAATCAACTAAAACACTAAAAA
1 GAATTAAAAATCAACTAAAACACT-AAAA
508171 GAATT-AAAATCAAACTAAAACAC
1 GAATTAAAAATC-AACTAAAACAC
508194 CAGAACTTCC
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
28 27 0.39
29 43 0.61
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.17
Consensus pattern (28 bp):
GAATTAAAAATCAACTAAAACACTAAAA
Found at i:508179 original size:57 final size:57
Alignment explanation
Indices: 508085--508193 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 57
508075 TAAAGCTAAG
* * * *
508085 GAATTAAAAGTAAACTAAAACTCCAAAAGAAAATAAAAGTC-AACTAGAACACTAAAA
1 GAATTAAAAATAAACTAAAACACAAAAAGAAAATAAAA-TCAAACTAAAACACTAAAA
* *
508142 GAATTAAAAATCAACTAAAACACTAAAAAG-AATTAAAATCAAACTAAAACAC
1 GAATTAAAAATAAACTAAAACAC-AAAAAGAAAATAAAATCAAACTAAAACAC
508194 CAGAACTTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
56 2 0.05
57 37 0.84
58 5 0.11
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.17
Consensus pattern (57 bp):
GAATTAAAAATAAACTAAAACACAAAAAGAAAATAAAATCAAACTAAAACACTAAAA
Found at i:509936 original size:43 final size:43
Alignment explanation
Indices: 509875--509973 Score: 198
Period size: 43 Copynumber: 2.3 Consensus size: 43
509865 TACTTTTCAT
509875 AATGTATCGATACATGTGTTTGAAATTTATAGCCGTTGGGCAC
1 AATGTATCGATACATGTGTTTGAAATTTATAGCCGTTGGGCAC
509918 AATGTATCGATACATGTGTTTGAAATTTATAGCCGTTGGGCAC
1 AATGTATCGATACATGTGTTTGAAATTTATAGCCGTTGGGCAC
509961 AATGTATCGATAC
1 AATGTATCGATAC
509974 TTTTCACCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (43 bp):
AATGTATCGATACATGTGTTTGAAATTTATAGCCGTTGGGCAC
Found at i:509987 original size:20 final size:19
Alignment explanation
Indices: 509962--510017 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
509952 GTTGGGCACA
509962 ATGTATCGATACTTTTCACC
1 ATGTATCGATACTTTTC-CC
* * *
509982 ATGTATCAATACAATGTCCC
1 ATGTATCGATAC-TTTTCCC
510002 ATGTATCGATACTTTT
1 ATGTATCGATACTTTT
510018 TACTTAGGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACTTTTCCC
Found at i:516580 original size:19 final size:19
Alignment explanation
Indices: 516536--516591 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
516526 CTGCCAGTTT
* **
516536 CATGTATCGATATAATTGTG
1 CATGTATCGATACAA-TGAA
516556 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
516575 CATGTATCGATACAATG
1 CATGTATCGATACAATG
516592 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:516594 original size:13 final size:13
Alignment explanation
Indices: 516576--516602 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
516566 TACAATGAAC
516576 ATGTATCGATACA
1 ATGTATCGATACA
516589 ATGTATCGATACA
1 ATGTATCGATACA
516602 A
1 A
516603 AGCATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:518972 original size:13 final size:13
Alignment explanation
Indices: 518950--518987 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
518940 TATAACCTAC
* *
518950 GTATCAATACATT
1 GTATCGATACAAT
518963 GTATCGATACAAT
1 GTATCGATACAAT
518976 GTATCGATACAA
1 GTATCGATACAA
518988 AGAACATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:520423 original size:16 final size:16
Alignment explanation
Indices: 520398--520434 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
520388 TTTTATCAAT
520398 ATTTTCTCTATTAAAA
1 ATTTTCTCTATTAAAA
* *
520414 GTTTTTTCTATTAAAA
1 ATTTTCTCTATTAAAA
520430 ATTTT
1 ATTTT
520435 GAAAGCCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTTCTCTATTAAAA
Found at i:523584 original size:13 final size:13
Alignment explanation
Indices: 523566--523592 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
523556 ACATTATGCT
523566 TTGTATCGATACA
1 TTGTATCGATACA
523579 TTGTATCGATACA
1 TTGTATCGATACA
523592 T
1 T
523593 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:523602 original size:32 final size:33
Alignment explanation
Indices: 523543--523611 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
523533 AATACACACC
* *
523543 TACA-TGTATCGATACATTATGCTTTGTATCGA
1 TACATTGTATCGATACATTATGCATTGTATCAA
523575 TACATTGTATCGATACATGT-T-CATTGTATCAA
1 TACATTGTATCGATACAT-TATGCATTGTATCAA
523607 TACAT
1 TACAT
523612 GGACAATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 18 0.55
33 14 0.42
34 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (33 bp):
TACATTGTATCGATACATTATGCATTGTATCAA
Found at i:523622 original size:20 final size:19
Alignment explanation
Indices: 523576--523632 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
523566 TTGTATCGAT
*
523576 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
523595 TCATTGTATCAATACATGG
1 ACATTGTATCGATACATGG
523614 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
523633 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:523714 original size:19 final size:19
Alignment explanation
Indices: 523690--523779 Score: 102
Period size: 19 Copynumber: 5.0 Consensus size: 19
523680 ATTGTATCGA
523690 TTCATTGTATCGATACATG
1 TTCATTGTATCGATACATG
523709 TTCATTGTATCGAT--A--
1 TTCATTGTATCGATACATG
523724 --CATTGTATCGATACATG
1 TTCATTGTATCGATACATG
*
523741 TTCATTGTATCGATACACG
1 TTCATTGTATCGATACATG
**
523760 GACAATTGTATCGATACATG
1 TTC-ATTGTATCGATACATG
523780 AAATTGGCAG
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
13 12 0.20
15 1 0.02
17 1 0.02
19 31 0.52
20 15 0.25
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (19 bp):
TTCATTGTATCGATACATG
Found at i:523720 original size:32 final size:32
Alignment explanation
Indices: 523661--523757 Score: 167
Period size: 32 Copynumber: 3.0 Consensus size: 32
523651 CTACCACTGT
* *
523661 TTGTATCGATACATGGTACATTGTATCGATTCA
1 TTGTATCGATACAT-GTTCATTGTATCGATACA
523694 TTGTATCGATACATGTTCATTGTATCGATACA
1 TTGTATCGATACATGTTCATTGTATCGATACA
523726 TTGTATCGATACATGTTCATTGTATCGATACA
1 TTGTATCGATACATGTTCATTGTATCGATACA
523758 CGGACAATTG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 48 0.77
33 14 0.23
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.40
Consensus pattern (32 bp):
TTGTATCGATACATGTTCATTGTATCGATACA
Found at i:523734 original size:147 final size:147
Alignment explanation
Indices: 523543--523876 Score: 537
Period size: 147 Copynumber: 2.3 Consensus size: 147
523533 AATACACACC
*
523543 TACA-TGTATCGATACAT-TATGCTTTGTATCGATACATTGTATCGATACATGTTCATTGTATCA
1 TACATTGTATCGATACATGT-T-CATTGTATCGATACATTGTATCGATACATGTTCATTGTATCA
* *
523606 ATACATGGACAATTGTATCGATACATGAAACTGGCAGTAGCTACCCTACCACTGTTTGTATCGAT
64 ATACACGGACAATTGTATCGATACATGAAACTGGCAGTAACTACCCTACCACTGTTTGTATCGAT
523671 ACATGGTACATTGTATCGA
129 ACATGGTACATTGTATCGA
* *
523690 TTCATTGTATCGATACATGTTCATTGTATCGATACATTGTATCGATACATGTTCATTGTATCGAT
1 TACATTGTATCGATACATGTTCATTGTATCGATACATTGTATCGATACATGTTCATTGTATCAAT
* *
523755 ACACGGACAATTGTATCGATACATGAAATTGGCAGTAACTACCCTACTACTGTTTGTATCGATAC
66 ACACGGACAATTGTATCGATACATGAAACTGGCAGTAACTACCCTACCACTGTTTGTATCGATAC
523820 ATGGTACATTGTATCGA
131 ATGGTACATTGTATCGA
* **
523837 TACATTATATCGATACATGATGAATTGTATCGATACATTG
1 TACATTGTATCGATACATG-TTCATTGTATCGATACATTG
523877 CTTCTAACGG
Statistics
Matches: 173, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
147 140 0.81
148 32 0.18
149 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (147 bp):
TACATTGTATCGATACATGTTCATTGTATCGATACATTGTATCGATACATGTTCATTGTATCAAT
ACACGGACAATTGTATCGATACATGAAACTGGCAGTAACTACCCTACCACTGTTTGTATCGATAC
ATGGTACATTGTATCGA
Found at i:523736 original size:13 final size:13
Alignment explanation
Indices: 523677--523739 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 13
523667 CGATACATGG
523677 TACATTGTATCGA
1 TACATTGTATCGA
*
523690 TTCATTGTATCGA
1 TACATTGTATCGA
523703 TACA-TG--T---
1 TACATTGTATCGA
523710 T-CATTGTATCGA
1 TACATTGTATCGA
523722 TACATTGTATCGA
1 TACATTGTATCGA
523735 TACAT
1 TACAT
523740 GTTCATTGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
6 2 0.05
7 3 0.07
9 1 0.02
10 1 0.02
12 3 0.07
13 31 0.76
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:523842 original size:13 final size:13
Alignment explanation
Indices: 523824--523876 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
523814 CGATACATGG
523824 TACATTGTATCGA
1 TACATTGTATCGA
*
523837 TACATTATATCGA
1 TACATTGTATCGA
523850 TACA-TG-AT-G-
1 TACATTGTATCGA
523859 -A-ATTGTATCGA
1 TACATTGTATCGA
523870 TACATTG
1 TACATTG
523877 CTTCTAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 2 0.06
13 20 0.62
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:523853 original size:33 final size:33
Alignment explanation
Indices: 523811--523875 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
523801 CTACTGTTTG
*
523811 TATCGATACATGGT-ACATTGTATCGATACATTA
1 TATCGATACATGATGA-ATTGTATCGATACATTA
523844 TATCGATACATGATGAATTGTATCGATACATT
1 TATCGATACATGATGAATTGTATCGATACATT
523876 GCTTCTAACG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (33 bp):
TATCGATACATGATGAATTGTATCGATACATTA
Found at i:529984 original size:22 final size:22
Alignment explanation
Indices: 529956--529997 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
529946 TTTTTTAGAA
529956 ATTTTCTAGAATGCATCGATAC
1 ATTTTCTAGAATGCATCGATAC
*
529978 ATTTTCTAGAATGTATCGAT
1 ATTTTCTAGAATGCATCGAT
529998 CGATTGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (22 bp):
ATTTTCTAGAATGCATCGATAC
Found at i:531016 original size:33 final size:33
Alignment explanation
Indices: 530978--531045 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
530968 GTCGTTGGGC
* *
530978 ACAATGTATACATAC-TTTTCACCATGTATCGAT
1 ACAATGTATACATACAATGTC-CCATGTATCGAT
**
531011 ACAATGTATGGATACAATGTCCCATGTATCGAT
1 ACAATGTATACATACAATGTCCCATGTATCGAT
531044 AC
1 AC
531046 TTTTTACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (33 bp):
ACAATGTATACATACAATGTCCCATGTATCGAT
Found at i:531019 original size:13 final size:13
Alignment explanation
Indices: 531001--531030 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
530991 ACTTTTCACC
531001 ATGTATCGATACA
1 ATGTATCGATACA
*
531014 ATGTATGGATACA
1 ATGTATCGATACA
531027 ATGT
1 ATGT
531031 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:531759 original size:59 final size:59
Alignment explanation
Indices: 531471--531766 Score: 314
Period size: 58 Copynumber: 5.1 Consensus size: 59
531461 GAAAAAAACT
** ** * * *
531471 TAAATGATTCCAACATATGTGAAATTGCATAAAAG-CCCTTAGATCAAAAAAAATGACC
1 TAAATGACCCCAACATACATGAAATTACATAAAAGTCTCTTAGATCATAAAAAATGACC
* * * * * *
531529 TAAATGACCTCTACATATATGAAATTACATAAAA-ACCCTTAGATCATGAAAAATGACC
1 TAAATGACCCCAACATACATGAAATTACATAAAAGTCTCTTAGATCATAAAAAATGACC
* * * * *
531587 TGAATGACCCCAACATACATGAATTTACATAAAAGTCTC-TAGATCATGAAAAATAAGC
1 TAAATGACCCCAACATACATGAAATTACATAAAAGTCTCTTAGATCATAAAAAATGACC
* * * * *
531645 TAAATGACCCCAACATACATGAATTTGCAAAAAAGT-TCTTAAATCATAAACAATGACC
1 TAAATGACCCCAACATACATGAAATTACATAAAAGTCTCTTAGATCATAAAAAATGACC
* * *
531703 AAAATGACCCCAACATACATGGAAATTATATAAAAGTTTC-TAGATCATAAAAAATGACC
1 TAAATGACCCCAACATACAT-GAAATTACATAAAAGTCTCTTAGATCATAAAAAATGACC
531762 TAAAT
1 TAAAT
531767 AACATCAAGA
Statistics
Matches: 200, Mismatches: 33, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
57 2 0.01
58 161 0.81
59 35 0.17
60 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.25
Consensus pattern (59 bp):
TAAATGACCCCAACATACATGAAATTACATAAAAGTCTCTTAGATCATAAAAAATGACC
Found at i:532684 original size:33 final size:33
Alignment explanation
Indices: 532646--532712 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
532636 GTTACAAGCT
532646 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTATAC--CATGTATCGATACA
532679 ATGTATCGATACATTATACCATGTATCGATACA
1 ATGTATCGATACATTATACCATGTATCGATACA
532712 A
1 A
532713 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTATACCATGTATCGATACA
Found at i:532697 original size:20 final size:20
Alignment explanation
Indices: 532674--532711 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
532664 TCATGTATCG
532674 ATACAATGTATCGATACATT
1 ATACAATGTATCGATACATT
*
532694 ATACCATGTATCGATACA
1 ATACAATGTATCGATACA
532712 AATAGTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCGATACATT
Found at i:532710 original size:13 final size:13
Alignment explanation
Indices: 532666--532691 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
532656 ACATTTCTTC
532666 ATGTATCGATACA
1 ATGTATCGATACA
532679 ATGTATCGATACA
1 ATGTATCGATACA
532692 TTATACCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:532786 original size:19 final size:19
Alignment explanation
Indices: 532741--532797 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
532731 CTGCCAGTTT
**
532741 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
532762 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
532781 CATGTATCGATATAATG
1 CATGTATCGATACAATG
532798 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
21 15 0.45
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:532804 original size:32 final size:33
Alignment explanation
Indices: 532763--532825 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
532753 CAATTTGTCC
*
532763 ATGTATCGATACAATG-AACATGTATCGATATA
1 ATGTATCGATACAAAGCAACATGTATCGATATA
*
532795 ATGTATCGATACAAAGCAGCATGTATCGATA
1 ATGTATCGATACAAAGCAACATGTATCGATA
532826 CATCTGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAACATGTATCGATATA
Found at i:539175 original size:13 final size:13
Alignment explanation
Indices: 539157--539187 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
539147 ACATTTCTTC
539157 ATGTATCGATACA
1 ATGTATCGATACA
539170 ATGTATCGATACA
1 ATGTATCGATACA
*
539183 TTGTA
1 ATGTA
539188 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:539175 original size:33 final size:33
Alignment explanation
Indices: 539137--539203 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
539127 GTTACAAGCT
539137 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
539170 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
539203 A
1 A
539204 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:541111 original size:20 final size:19
Alignment explanation
Indices: 541083--541134 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
541073 GGGCATATTT
*
541083 TATCGATACAATGGGCACTG
1 TATCAATACAAT-GGCACTG
*
541103 TATCAATACATTATGGCCCTG
1 TATCAATACA--ATGGCACTG
*
541124 TACCAATACAA
1 TATCAATACAA
541135 ATACATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.04
20 9 0.33
21 15 0.56
22 2 0.07
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (19 bp):
TATCAATACAATGGCACTG
Found at i:541821 original size:12 final size:12
Alignment explanation
Indices: 541804--541857 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
541794 TTTTACCCAA
541804 ATGTATCGATAC
1 ATGTATCGATAC
541816 ATGTAT-G--A-
1 ATGTATCGATAC
541824 ATGTATCGATAC
1 ATGTATCGATAC
541836 ATGTAT-G--A-
1 ATGTATCGATAC
541844 ATGTATCGATAC
1 ATGTATCGATAC
541856 AT
1 AT
541858 TCTTCAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
8 12 0.35
9 4 0.12
11 4 0.12
12 14 0.41
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:541880 original size:20 final size:20
Alignment explanation
Indices: 541803--541877 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
541793 TTTTTACCCA
541803 AATGTATCGATACATGTATG
1 AATGTATCGATACATGTATG
541823 AATGTATCGATACATGTATG
1 AATGTATCGATACATGTATG
* *
541843 AATGTATCGATACAT-TCTTC
1 AATGTATCGATACATGT-ATG
541863 AATGTATCGATACAT
1 AATGTATCGATACAT
541878 TCTGTCTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 1 0.02
20 51 0.98
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATGTATG
Found at i:544494 original size:13 final size:13
Alignment explanation
Indices: 544476--544532 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
544466 TTCAACAATT
544476 TGTATCGATACAA
1 TGTATCGATACAA
*
544489 TGTATCGACACATAA
1 TGTATCGATAC--AA
544504 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
544521 TGTATCGATACA
1 TGTATCGATACA
544533 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:544516 original size:32 final size:32
Alignment explanation
Indices: 544475--544559 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
544465 TTTCAACAAT
544475 TTGTATCGATACAATGTATCGACACATAAGTG
1 TTGTATCGATACAATGTATCGACACATAAGTG
* *
544507 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGACACATAAGTG
544539 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
544560 CTACGAAGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGACACATAAGTG
Found at i:544545 original size:19 final size:18
Alignment explanation
Indices: 544489--544551 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
544479 ATCGATACAA
*
544489 TGTATCGACACATAAGTGT
1 TGTATCGATACATAAGT-T
544508 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
544521 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
544540 TGTATCGATACA
1 TGTATCGATACA
544552 ATGTATCGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:553971 original size:165 final size:165
Alignment explanation
Indices: 553784--554276 Score: 959
Period size: 165 Copynumber: 3.0 Consensus size: 165
553774 ACCCACCCCC
**
553784 ACTCCACCAAAAGCTGAAAATAAATAAATAAATAAATAAAATCCCTACTCCATATTGTTGTTATT
1 ACTCCACCAAAAGCCAAAAATAAATAAATAAATAAATAAAATCCCTACTCCATATTGTTGTTATT
553849 CTCATGCCATACAATCAAGAATGAAGTTTTCATTGTTTATGCATCAAGTATAGCATGACTGCGAT
66 CTCATGCCATACAATCAAGAATGAAGTTTTCATTGTTTATGCATCAAGTATAGCATGACTGCGAT
553914 AAATGGAGCAAACACAGGACAATATCCAATATCAA
131 AAATGGAGCAAACACAGGACAATATCCAATATCAA
553949 ACTCCACCAAAAGCCAAAAATAAATAAATAAATAAATAAAATCCCTACTCCATATTGTTGTTATT
1 ACTCCACCAAAAGCCAAAAATAAATAAATAAATAAATAAAATCCCTACTCCATATTGTTGTTATT
554014 CTCATGCCATACAATCAAGAATGAAGTTTTCATTGTTTATGCATCAAGTATAGCATGACTGCGAT
66 CTCATGCCATACAATCAAGAATGAAGTTTTCATTGTTTATGCATCAAGTATAGCATGACTGCGAT
554079 AAATGGAGCAAACACAGGACAATATCCAATATCAA
131 AAATGGAGCAAACACAGGACAATATCCAATATCAA
554114 ACTCCACCAAAAGCCAAAAATAAATAAATAAATAAATAAAATCCCTACTCCATATTGTTGTTATT
1 ACTCCACCAAAAGCCAAAAATAAATAAATAAATAAATAAAATCCCTACTCCATATTGTTGTTATT
*
554179 CTCATGCCATACAATCAAGAATGAAGTTTTCATTGTTTATGCATCAAGTATAGCATGACTGCAAT
66 CTCATGCCATACAATCAAGAATGAAGTTTTCATTGTTTATGCATCAAGTATAGCATGACTGCGAT
554244 AAATGGAGCAAACACAGGACAATATCCAATATC
131 AAATGGAGCAAACACAGGACAATATCCAATATC
554277 TAATGGGTAG
Statistics
Matches: 325, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 325 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (165 bp):
ACTCCACCAAAAGCCAAAAATAAATAAATAAATAAATAAAATCCCTACTCCATATTGTTGTTATT
CTCATGCCATACAATCAAGAATGAAGTTTTCATTGTTTATGCATCAAGTATAGCATGACTGCGAT
AAATGGAGCAAACACAGGACAATATCCAATATCAA
Found at i:556966 original size:16 final size:18
Alignment explanation
Indices: 556945--556987 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
556935 AAGGTGAACG
556945 AAAAAAATA-TTT-TTTA
1 AAAAAAATATTTTATTTA
*
556961 AAAAAATTATTTTATTTA
1 AAAAAAATATTTTATTTA
*
556979 AAAATAATA
1 AAAAAAATA
556988 AGTTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAAAATATTTTATTTA
Found at i:557021 original size:21 final size:21
Alignment explanation
Indices: 556990--557043 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
556980 AAATAATAAG
*
556990 TTAAAAATAAAAAGATAATTTT
1 TTAAAATTAAAAAG-TAATTTT
* * *
557012 TT-TAATTAAATAGTTATTTT
1 TTAAAATTAAAAAGTAATTTT
557032 TTAAAATTAAAA
1 TTAAAATTAAAA
557044 TATAAAATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
20 8 0.32
21 15 0.60
22 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
TTAAAATTAAAAAGTAATTTT
Found at i:558077 original size:16 final size:16
Alignment explanation
Indices: 558058--558096 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
558048 AAAAATATAA
* *
558058 TAAATTTTTTTAAGTT
1 TAAATTATTTTAAATT
558074 TAAATTATTTTAAATT
1 TAAATTATTTTAAATT
*
558090 TATATTA
1 TAAATTA
558097 ATTGATTCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TAAATTATTTTAAATT
Found at i:558600 original size:29 final size:27
Alignment explanation
Indices: 558548--558616 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
558538 TGCTTAAATT
558548 TAATATTTTATAATTTAATTAATA-AAA
1 TAATATTTT-TAATTTAATTAATATAAA
*
558575 TAATATTTTTTATTTAAATATAAATATAAA
1 TAATATTTTTAATTT-AAT-T-AATATAAA
*
558605 -ATTATTTTTAAT
1 TAATATTTTTAAT
558617 ATGTTAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 5 0.14
27 12 0.34
28 1 0.03
29 14 0.40
30 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATATTTTTAATTTAATTAATATAAA
Found at i:558603 original size:26 final size:27
Alignment explanation
Indices: 558542--558612 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
558532 ACGTCATGCT
* * *
558542 TAAATTTAATATTTTATAATTTAATTAA
1 TAAATATAATATTTT-TTATTTAAATAA
558570 TAAA-ATAATATTTTTTATTTAAAT-A
1 TAAATATAATATTTTTTATTTAAATAA
*
558595 TAAATATAAAATTATTTT
1 TAAATATAATATT-TTTT
558613 TAATATGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 5 0.14
26 15 0.41
27 13 0.35
28 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAAATATAATATTTTTTATTTAAATAA
Found at i:559002 original size:31 final size:32
Alignment explanation
Indices: 558967--559032 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
558957 TTATTATGAT
* *
558967 TATATTAGTTATATATTTTATAT-AAATTTAA
1 TATATTAATAATATATTTTATATAAAATTTAA
* *
558998 TATATTAATAATTTATTTTATATAAAATTTTA
1 TATATTAATAATATATTTTATATAAAATTTAA
559030 TAT
1 TAT
559033 CTATAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
TATATTAATAATATATTTTATATAAAATTTAA
Found at i:559026 original size:16 final size:16
Alignment explanation
Indices: 558980--559027 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
558970 ATTAGTTATA
558980 TATTTTATAT-AAATT
1 TATTTTATATAAAATT
* *
558995 TAATATAT-TAATAATT
1 TATTTTATATAA-AATT
559011 TATTTTATATAAAATT
1 TATTTTATATAAAATT
559027 T
1 T
559028 TATATCTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 1 0.04
15 7 0.27
16 15 0.58
17 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTATATAAAATT
Found at i:559039 original size:30 final size:30
Alignment explanation
Indices: 558980--559043 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
558970 ATTAGTTATA
558980 TATTTTATATAAATTTAATATATTAATAATT
1 TATTTTATATAAATTT-ATATATTAATAATT
559011 TATTTTATATAAAATTT-TATATCT-ATAATT
1 TATTTTATAT-AAATTTATATAT-TAATAATT
559041 TAT
1 TAT
559044 AATAATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 14 0.45
31 11 0.35
32 6 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (30 bp):
TATTTTATATAAATTTATATATTAATAATT
Found at i:559298 original size:18 final size:18
Alignment explanation
Indices: 559263--559304 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
559253 ATATCGTATC
*
559263 TATATTTTTATATCTTTT
1 TATATTTTAATATCTTTT
559281 TATATTTTAATTAT-TTTT
1 TATATTTTAA-TATCTTTT
*
559299 AATATT
1 TATATT
559305 ATTTCATGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TATATTTTAATATCTTTT
Done.