Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 33 of 335
Found at i:12136345 original size:26 final size:26
Alignment explanation
Indices: 12136308--12136391 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
12136298 TGATACAAAT
*
12136308 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
12136334 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
12136360 TGATAATGAGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
12136386 TGATAA
1 TGATAA
12136392 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:12137907 original size:25 final size:26
Alignment explanation
Indices: 12137865--12137916 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
12137855 TTTACAGTTT
12137865 TACCCCTAGGAGATAATT-ACCGAAA
1 TACCCCTAGGAGATAATTGACCGAAA
* *
12137890 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGAGAT-AATTGACCGAAA
12137916 T
1 T
12137917 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.09
25 14 0.61
26 7 0.30
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGAGATAATTGACCGAAA
Found at i:12138409 original size:137 final size:137
Alignment explanation
Indices: 12138164--12138586 Score: 794
Period size: 137 Copynumber: 3.1 Consensus size: 137
12138154 GAGTAGTCTC
*
12138164 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
12138228 TGTTATCTGAATAAGGGGCTAAGGTCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
12138293 ACTGTTA
131 ACTGTTA
12138300 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
12138365 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
12138430 ACTGTTA
131 ACTGTTA
12138437 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
12138502 TGTTATCTGAATAAGGGGCTAAGGCCTAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
12138567 ACTGTTA
131 ACTGTTA
**
12138574 CCTGAATGGGCTT
1 CCCAAATGGGCTT
12138587 AGGCCTAGGC
Statistics
Matches: 281, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
136 20 0.07
137 261 0.93
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:12140541 original size:5 final size:5
Alignment explanation
Indices: 12140487--12140533 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
12140477 TTATGTTTTA
12140487 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
12140534 AAATTAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:12141823 original size:15 final size:15
Alignment explanation
Indices: 12141803--12141859 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
12141793 CGATGAATTT
12141803 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
12141818 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
*
12141833 ATTGAATTTATATTA
1 ATTGAATTTATATTG
12141848 ATTGAA-TTATAT
1 ATTGAATTTATAT
12141860 AATATATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 6 0.16
15 31 0.84
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:12142252 original size:23 final size:22
Alignment explanation
Indices: 12142222--12142280 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
12142212 GCTTTATCGA
12142222 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGT-TT
* **
12142245 TCAGGCACCTCGTGTGTCGTTT
1 TCAGGCACTTTATGTGTCGTTT
12142267 T-AGGCACTTTATGT
1 TCAGGCACTTTATGT
12142281 AGCACCCCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 10 0.33
22 3 0.10
23 17 0.57
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (22 bp):
TCAGGCACTTTATGTGTCGTTT
Found at i:12144682 original size:23 final size:22
Alignment explanation
Indices: 12144628--12144686 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
12144618 TTGGGGTGCT
12144628 ACATAAAGTGCCT-AAAACGAC
1 ACATAAAGTGCCTGAAAACGAC
** *
12144649 ACACGAGGTGCCTGAAATACGAC
1 ACATAAAGTGCCTGAAA-ACGAC
12144672 ACATAAAGTGCCTGA
1 ACATAAAGTGCCTGA
12144687 TCGATAAAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 10 0.33
22 3 0.10
23 17 0.57
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (22 bp):
ACATAAAGTGCCTGAAAACGAC
Found at i:12145072 original size:15 final size:15
Alignment explanation
Indices: 12145047--12145104 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
12145037 TCATATATAT
12145047 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
12145063 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
12145078 AATAATTTCAATCAA
1 TATAAATTCAATCAA
12145093 TATAAATTCAAT
1 TATAAATTCAAT
12145105 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:12146374 original size:5 final size:5
Alignment explanation
Indices: 12146374--12146415 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
12146364 TCTTTAATTT
12146374 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
12146416 TAAAACATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:12151068 original size:28 final size:28
Alignment explanation
Indices: 12151028--12151083 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
12151018 CTTTGAGCAC
12151028 ACATTAATCTCTTGAATGAGAACAATCA
1 ACATTAATCTCTTGAATGAGAACAATCA
*
12151056 ACATTAATCTCTTGAATGAGAACGATCA
1 ACATTAATCTCTTGAATGAGAACAATCA
12151084 TCTCACTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (28 bp):
ACATTAATCTCTTGAATGAGAACAATCA
Found at i:12165019 original size:31 final size:31
Alignment explanation
Indices: 12164969--12165028 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
12164959 CTTTTTTGGC
12164969 AAATTTAGATGATTATGGTACATA-TTTTCA
1 AAATTTAGATGATTATGGTACATACTTTTCA
12164999 AAATCTTATGATG-TTATGGTACATACTTTT
1 AAAT-TTA-GATGATTATGGTACATACTTTT
12165029 TGATTCTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 4 0.15
31 15 0.56
32 8 0.30
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (31 bp):
AAATTTAGATGATTATGGTACATACTTTTCA
Found at i:12168829 original size:71 final size:69
Alignment explanation
Indices: 12168733--12168867 Score: 216
Period size: 71 Copynumber: 1.9 Consensus size: 69
12168723 CTTCCTCCAA
* *
12168733 CTTTTCGTCAAGGAAGTGTTCGATAAAATGCTTCACTGATGAAAAGGAAAGGCCTTTCAAATTCT
1 CTTTTCGTCAAGGAAGTGTTCGATAAAATGCTTCACTGATGAAAAAGAAA-GCCGTTCAAATTCT
12168798 TTCAT
65 TTCAT
* *
12168803 CTTTTCGTCGAGCGAAGTGTTCGATAAAATGCTTCACTGTTGAAAAAGAAAGCCGTTCAAATTCT
1 CTTTTCGTCAAG-GAAGTGTTCGATAAAATGCTTCACTGATGAAAAAGAAAGCCGTTCAAATTCT
12168868 AACGTTTGTG
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 24 0.40
71 36 0.60
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (69 bp):
CTTTTCGTCAAGGAAGTGTTCGATAAAATGCTTCACTGATGAAAAAGAAAGCCGTTCAAATTCTT
TCAT
Found at i:12182145 original size:15 final size:15
Alignment explanation
Indices: 12182125--12182153 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12182115 CTTATAATTC
12182125 ATAAAAATAAAAATA
1 ATAAAAATAAAAATA
12182140 ATAAAAATAAAAAT
1 ATAAAAATAAAAAT
12182154 CTAATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAAAATAAAAATA
Found at i:12193075 original size:30 final size:29
Alignment explanation
Indices: 12193022--12193079 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
12193012 TCAAATTAGA
12193022 AAAAGAAAAAAAATTACAACTAAAATAAC
1 AAAAGAAAAAAAATTACAACTAAAATAAC
*
12193051 AAAAGAAAAAAAGGTTA-AAGCTAAAATAA
1 AAAAGAAAAAAA-ATTACAA-CTAAAATAA
12193080 ACAACTGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.14
Consensus pattern (29 bp):
AAAAGAAAAAAAATTACAACTAAAATAAC
Found at i:12194290 original size:15 final size:15
Alignment explanation
Indices: 12194272--12194301 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12194262 ATTTGTTTCA
*
12194272 AATATATTTAATTTT
1 AATATATTAAATTTT
12194287 AATATATTAAATTTT
1 AATATATTAAATTTT
12194302 TTTATTCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATATATTAAATTTT
Found at i:12207132 original size:17 final size:18
Alignment explanation
Indices: 12207098--12207142 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
12207088 TATTTCAAGG
12207098 TAACAAATAAATAAATAA
1 TAACAAATAAATAAATAA
*
12207116 -AACGAATAAA-AAGATAA
1 TAACAAATAAATAA-ATAA
12207133 TAACAAATAA
1 TAACAAATAA
12207143 GCTAGGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 13 0.57
18 8 0.35
ACGTcount: A:0.71, C:0.07, G:0.04, T:0.18
Consensus pattern (18 bp):
TAACAAATAAATAAATAA
Found at i:12207659 original size:2 final size:2
Alignment explanation
Indices: 12207652--12207696 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
12207642 CAATATTAAG
* *
12207652 AT AT AT AT AT AT AT AT AT AT AT AT A- AT GT AT AC AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12207692 A- AT AT
1 AT AT AT
12207697 TAAAATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:12208324 original size:79 final size:79
Alignment explanation
Indices: 12208217--12208371 Score: 231
Period size: 79 Copynumber: 2.0 Consensus size: 79
12208207 TTGATTCCAC
* * * *
12208217 TCCCCCATGCTACTTTGTTTTATTATTAATTAAAACTACTCCTCCATACTATTTCG-TTTTATTA
1 TCCCCCATACTACTTTATTTTATTATTAATTAAAACCACTCCCCCATACTATTTCGTTTTTATTA
12208281 TTAATTAAAACTAT
66 TTAATTAAAACTAT
* * *
12208295 TCCCCCATACTATTTTATTTTCATTATTAATTAAAACCATTCCCCCATACTATTTTGTTTTTATT
1 TCCCCCATACTACTTTATTTT-ATTATTAATTAAAACCACTCCCCCATACTATTTCGTTTTTATT
12208360 ATTAATTAAAAC
65 ATTAATTAAAAC
12208372 CATACTTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
78 18 0.26
79 31 0.46
80 19 0.28
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.46
Consensus pattern (79 bp):
TCCCCCATACTACTTTATTTTATTATTAATTAAAACCACTCCCCCATACTATTTCGTTTTTATTA
TTAATTAAAACTAT
Found at i:12208337 original size:40 final size:39
Alignment explanation
Indices: 12208217--12208374 Score: 226
Period size: 39 Copynumber: 4.0 Consensus size: 39
12208207 TTGATTCCAC
* * * *
12208217 TCCCCCATGCTACTTTGTTTTATTATTAATTAAAACTAC
1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACCAT
* * *
12208256 TCCTCCATACTATTTCGTTTTATTATTAATTAAAACTAT
1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACCAT
*
12208295 TCCCCCATACTATTTTATTTTCATTATTAATTAAAACCAT
1 TCCCCCATACTATTTTGTTTT-ATTATTAATTAAAACCAT
12208335 TCCCCCATACTATTTTGTTTTTATTATTAATTAAAACCAT
1 TCCCCCATACTATTTTG-TTTTATTATTAATTAAAACCAT
12208375 ACTTTATTTT
Statistics
Matches: 107, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 52 0.49
40 51 0.48
41 4 0.04
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.46
Consensus pattern (39 bp):
TCCCCCATACTATTTTGTTTTATTATTAATTAAAACCAT
Found at i:12211220 original size:2 final size:2
Alignment explanation
Indices: 12211213--12211248 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12211203 AAAATCCTTC
12211213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12211249 CCATTTTAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12211875 original size:20 final size:18
Alignment explanation
Indices: 12211850--12211886 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
12211840 ATTGCTAAGT
12211850 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
12211870 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
12211887 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:12212495 original size:46 final size:46
Alignment explanation
Indices: 12212443--12212618 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
12212433 TGGTTGAGCA
12212443 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
12212489 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
12212534 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
12212582 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12212619 GCAGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 64 0.58
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:12212599 original size:93 final size:93
Alignment explanation
Indices: 12212440--12212610 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
12212430 GGATGGTTGA
* **
12212440 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
12212505 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
12212533 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
12212598 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
12212611 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:12220388 original size:2 final size:2
Alignment explanation
Indices: 12220334--12220372 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12220324 TTAATAAATG
12220334 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12220373 TTGTTTTCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12222050 original size:16 final size:16
Alignment explanation
Indices: 12222029--12222064 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
12222019 TGGTTAAACC
12222029 TACATCAATCTTTTTA
1 TACATCAATCTTTTTA
12222045 TACATCAATCTTTTTA
1 TACATCAATCTTTTTA
12222061 TACA
1 TACA
12222065 CACATAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TACATCAATCTTTTTA
Found at i:12224180 original size:23 final size:21
Alignment explanation
Indices: 12224151--12224233 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
12224141 TGATTAGTAT
*
12224151 ACGACACATAAAGTGCCTGAA
1 ACGACACACAAAGTGCCTGAA
* * *
12224172 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTGAA
* *
12224193 ACGACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCTG-AA
*
12224215 TACGACACATAAAGTGCCT
1 -ACGACACACAAAGTGCCT
12224234 AATCAGTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 36 0.69
22 1 0.02
23 15 0.29
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTGAA
Found at i:12236674 original size:36 final size:36
Alignment explanation
Indices: 12236627--12236698 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
12236617 AAAGAGATGA
12236627 AATATTGACAAAAAGTAATGCAAATGGCTTCAACTT
1 AATATTGACAAAAAGTAATGCAAATGGCTTCAACTT
12236663 AATATTGACAAAAAGTAATGCAAATGGCTTCAACTT
1 AATATTGACAAAAAGTAATGCAAATGGCTTCAACTT
12236699 TGATATGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
AATATTGACAAAAAGTAATGCAAATGGCTTCAACTT
Found at i:12238940 original size:15 final size:15
Alignment explanation
Indices: 12238922--12238965 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
12238912 TTAGAATAAT
*
12238922 CATATTTCAAAAACA
1 CATATTTAAAAAACA
12238937 CATATTTAAAATAACA
1 CATATTTAAAA-AACA
12238953 -AT-TTTAAAAAACA
1 CATATTTAAAAAACA
12238966 ACCATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 4 0.15
14 7 0.26
15 12 0.44
16 4 0.15
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (15 bp):
CATATTTAAAAAACA
Found at i:12241198 original size:30 final size:30
Alignment explanation
Indices: 12241163--12241232 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
12241153 AATTTTTGAC
* * *
12241163 TTTTTACAATTAATAAAATTACATTTTAAT
1 TTTTTAAAAATAATAAAATTACAATTTAAT
* **
12241193 TTTTTAAAAATGATAAAATTTTAATTTAA-
1 TTTTTAAAAATAATAAAATTACAATTTAAT
12241222 TTTTTAAAAAT
1 TTTTTAAAAAT
12241233 TATAGACATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 11 0.32
30 23 0.68
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (30 bp):
TTTTTAAAAATAATAAAATTACAATTTAAT
Found at i:12246420 original size:33 final size:33
Alignment explanation
Indices: 12246383--12246451 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
12246373 GTAGTCCACT
12246383 GAAGGAATATTTGAAGTTCATGAACTCGAGAGA
1 GAAGGAATATTTGAAGTTCATGAACTCGAGAGA
12246416 GAAGGAATATTTGAAGTTCATGAACTCGAGAGA
1 GAAGGAATATTTGAAGTTCATGAACTCGAGAGA
12246449 GAA
1 GAA
12246452 ATGTTACTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.09, G:0.28, T:0.23
Consensus pattern (33 bp):
GAAGGAATATTTGAAGTTCATGAACTCGAGAGA
Found at i:12249281 original size:55 final size:55
Alignment explanation
Indices: 12249216--12249324 Score: 218
Period size: 55 Copynumber: 2.0 Consensus size: 55
12249206 CTCCAAGGCA
12249216 CCAACTCGTACAGCGGAAGACTTCTTATGTCAAAAAAAGCTTACAAAGAACCATT
1 CCAACTCGTACAGCGGAAGACTTCTTATGTCAAAAAAAGCTTACAAAGAACCATT
12249271 CCAACTCGTACAGCGGAAGACTTCTTATGTCAAAAAAAGCTTACAAAGAACCAT
1 CCAACTCGTACAGCGGAAGACTTCTTATGTCAAAAAAAGCTTACAAAGAACCAT
12249325 AGAAAGGGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (55 bp):
CCAACTCGTACAGCGGAAGACTTCTTATGTCAAAAAAAGCTTACAAAGAACCATT
Found at i:12250621 original size:96 final size:96
Alignment explanation
Indices: 12250453--12250646 Score: 273
Period size: 96 Copynumber: 2.0 Consensus size: 96
12250443 TCGCATCTTT
* *
12250453 TTGCTCCTTTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
1 TTGCTCCTTTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCGT
* * * *
12250518 GTCTGCTCCATCGTTCCCTTCGATGACAGAC
66 ATCTGCTCCATCATTCCCATCGATAACAGAC
* * *
12250549 TTGCTCCTCTTT-GCCCTCTTGGCTTCGGGTTTTCTCTTGCTCGAACCAAGCTTCCTGGGCTCCG
1 TTGCTCCT-TTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCG
* *
12250613 TATTTGCTCGATCATTCCCATCGATAACAGAC
65 TATCTGCTCCATCATTCCCATCGATAACAGAC
12250645 TT
1 TT
12250647 CCTCGGACAC
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 83 0.97
97 3 0.03
ACGTcount: A:0.12, C:0.33, G:0.19, T:0.36
Consensus pattern (96 bp):
TTGCTCCTTTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCGT
ATCTGCTCCATCATTCCCATCGATAACAGAC
Found at i:12268482 original size:2 final size:2
Alignment explanation
Indices: 12268477--12268512 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12268467 AGAAGAAAAA
12268477 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12268513 TGACAATTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12274168 original size:30 final size:30
Alignment explanation
Indices: 12274134--12274196 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
12274124 ACTTATTTTA
* *
12274134 TTGTTCATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATGTTGTTATTATTTTAAAGACAT
*
12274164 TTGTTAATGTTGTTATTATTTTAGAGACAT
1 TTGTTAATGTTGTTATTATTTTAAAGACAT
12274194 TTG
1 TTG
12274197 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (30 bp):
TTGTTAATGTTGTTATTATTTTAAAGACAT
Found at i:12274298 original size:17 final size:19
Alignment explanation
Indices: 12274271--12274317 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
12274261 TTGTTAGGAA
* *
12274271 ATATTTATTTTGATGT-TT
1 ATATATATTTTCATGTATT
*
12274289 TTA-ATATTTTCATGTATT
1 ATATATATTTTCATGTATT
12274307 ATATATATTTT
1 ATATATATTTT
12274318 AAAATTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 10 0.43
18 6 0.26
19 7 0.30
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (19 bp):
ATATATATTTTCATGTATT
Found at i:12278359 original size:34 final size:34
Alignment explanation
Indices: 12278316--12278383 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
12278306 CATTTGATAA
12278316 AACTTAAATGGTGAACAGTCAAATTCATCATAGT
1 AACTTAAATGGTGAACAGTCAAATTCATCATAGT
12278350 AACTTAAATGGTGAACAGTCAAATTCATCATAGT
1 AACTTAAATGGTGAACAGTCAAATTCATCATAGT
12278384 CAGCTTCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (34 bp):
AACTTAAATGGTGAACAGTCAAATTCATCATAGT
Found at i:12286684 original size:7 final size:7
Alignment explanation
Indices: 12286662--12286699 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
12286652 AATCATAAAA
12286662 ACCCAAT
1 ACCCAAT
12286669 ACTCCAAT
1 AC-CCAAT
12286677 ACCCAAT
1 ACCCAAT
12286684 ACCCAAT
1 ACCCAAT
12286691 ACCCAAT
1 ACCCAAT
12286698 AC
1 AC
12286700 GGATGCGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (7 bp):
ACCCAAT
Found at i:12296689 original size:11 final size:11
Alignment explanation
Indices: 12296668--12296696 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12296658 GGTTCTGTCA
12296668 TTCTC-TTCTT
1 TTCTCTTTCTT
12296678 TTCTCTTTCTT
1 TTCTCTTTCTT
12296689 TTCTCTTT
1 TTCTCTTT
12296697 TGCACCATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCTCTTTCTT
Found at i:12298274 original size:37 final size:37
Alignment explanation
Indices: 12298233--12298308 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
12298223 AATGGTTACC
12298233 ATAAGTTGATTCATTAAGCAACAATGTTTGACTTTTA
1 ATAAGTTGATTCATTAAGCAACAATGTTTGACTTTTA
* * *
12298270 ATAAGTTGATTCATTAAGCAGCAATGTTTTATTTTTA
1 ATAAGTTGATTCATTAAGCAACAATGTTTGACTTTTA
12298307 AT
1 AT
12298309 CATTCTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.43
Consensus pattern (37 bp):
ATAAGTTGATTCATTAAGCAACAATGTTTGACTTTTA
Found at i:12308153 original size:25 final size:24
Alignment explanation
Indices: 12308103--12308155 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
12308093 TAGTCAAATA
*
12308103 AAAATATATAAAAAAATGTTATAT
1 AAAATATATAAAAAAATATTATAT
*
12308127 AAAATCATATAAACAAATA-TATAAT
1 AAAAT-ATATAAAAAAATATTAT-AT
12308152 AAAA
1 AAAA
12308156 CTAAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATATATAAAAAAATATTATAT
Found at i:12308847 original size:2 final size:2
Alignment explanation
Indices: 12308829--12308875 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
12308819 TACTAATTTC
* *
12308829 CT CT TT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12308871 CT CT C
1 CT CT C
12308876 AAACCACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:12312771 original size:17 final size:15
Alignment explanation
Indices: 12312735--12312774 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
12312725 AATTTACTGG
*
12312735 ATTTATTTTAATTTA
1 ATTTATTTTAATTAA
12312750 ATTTATTTCTATATTAA
1 ATTTATTT-TA-ATTAA
12312767 ATTTATTT
1 ATTTATTT
12312775 GTTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 2 0.09
17 12 0.55
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTATTTTAATTAA
Found at i:12317454 original size:24 final size:24
Alignment explanation
Indices: 12317422--12317481 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
12317412 TGATGAGAAA
*
12317422 ATTTATTAAATTAAAATAAAATAAT
1 ATTT-TTAAATTAAAACAAAATAAT
*
12317447 ATTTTTAAAAGTAAAACAAAATAAT
1 ATTTTT-AAATTAAAACAAAATAAT
* *
12317472 GTTTTCAAAT
1 ATTTTTAAAT
12317482 CAAGTGGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (24 bp):
ATTTTTAAATTAAAACAAAATAAT
Found at i:12334026 original size:47 final size:47
Alignment explanation
Indices: 12333917--12334027 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
12333907 CCGGGATAAG
* * *
12333917 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
12333964 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
12334011 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
12334028 ACTCAATGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:12334786 original size:4 final size:4
Alignment explanation
Indices: 12334768--12334805 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
12334758 CCTAAATTTC
* *
12334768 TCTT T-TT TATT TCTT TCTT TCTT TCCT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
12334806 AACGTTTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:12334879 original size:42 final size:43
Alignment explanation
Indices: 12334783--12334879 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 43
12334773 TTTATTTCTT
* * *
12334783 TCTTTCT-TTCCTTCTTTCTTTCTAACGTTTGCTCTCTGTTAG
1 TCTTTCTATTCTTTCTTTCTTTCTAACGTTTGCTCTCTGTAAC
* *
12334825 TCTTTCTA-TCTTTCTTTCTTTCTCACGTTTGCTCTTTGTAAC
1 TCTTTCTATTCTTTCTTTCTTTCTAACGTTTGCTCTCTGTAAC
12334867 T-TTTCTATTCTTT
1 TCTTTCTATTCTTT
12334880 ACTATTATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
41 6 0.12
42 42 0.88
ACGTcount: A:0.08, C:0.25, G:0.07, T:0.60
Consensus pattern (43 bp):
TCTTTCTATTCTTTCTTTCTTTCTAACGTTTGCTCTCTGTAAC
Found at i:12335754 original size:31 final size:30
Alignment explanation
Indices: 12335701--12335774 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 30
12335691 TTTGGACAGG
* *
12335701 ATTAAATCTTTTAATGTGTTTAGGAGGTTTA
1 ATTAAATATTTCAATGTGTTTAGG-GGTTTA
* * * *
12335732 ATTAAATGTTTCAATTTTTTTAGGGTTTTA
1 ATTAAATATTTCAATGTGTTTAGGGGTTTA
12335762 A-TAAATATTTCAA
1 ATTAAATATTTCAA
12335775 AAATCCTAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 11 0.30
30 6 0.16
31 20 0.54
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.50
Consensus pattern (30 bp):
ATTAAATATTTCAATGTGTTTAGGGGTTTA
Found at i:12335895 original size:18 final size:18
Alignment explanation
Indices: 12335874--12335913 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
12335864 TTTGAGCGGC
*
12335874 TAATTAAGTTTTTTAAAA
1 TAATTAAATTTTTTAAAA
*
12335892 TAA-TAAATTTTTTTAAA
1 TAATTAAATTTTTTAAAA
12335909 TAATT
1 TAATT
12335914 CTTTGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TAATTAAATTTTTTAAAA
Found at i:12336024 original size:22 final size:21
Alignment explanation
Indices: 12335982--12336037 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
12335972 TATACTCTTC
12335982 ATATT-TTAACATTTAAGTTT
1 ATATTGTTAACATTTAAGTTT
*
12336002 A-ATTGTTAACTATATTAATTTT
1 ATATTGTTAAC-AT-TTAAGTTT
*
12336024 ATTTTGTTAA-ATTT
1 ATATTGTTAACATTT
12336038 GTTGGTGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
19 3 0.10
20 8 0.27
21 4 0.13
22 8 0.27
23 7 0.23
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (21 bp):
ATATTGTTAACATTTAAGTTT
Found at i:12338838 original size:2 final size:2
Alignment explanation
Indices: 12338831--12338859 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12338821 TTAACTTTTG
12338831 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12338860 TTTCAATCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12348415 original size:14 final size:15
Alignment explanation
Indices: 12348385--12348418 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12348375 ATTGTAATGT
*
12348385 ATATTTATTATTAAA
1 ATATTTATTAATAAA
12348400 ATATTT-TTAATAAA
1 ATATTTATTAATAAA
12348414 ATATT
1 ATATT
12348419 AAGAAAATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTATTAATAAA
Found at i:12348439 original size:2 final size:2
Alignment explanation
Indices: 12348432--12348465 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12348422 AAAATGCAAA
12348432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12348466 TTAGGATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12351337 original size:46 final size:46
Alignment explanation
Indices: 12351272--12351541 Score: 319
Period size: 46 Copynumber: 5.9 Consensus size: 46
12351262 TTATCTTCGA
* * * *
12351272 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
* ** * *
12351318 CATGTTGCCATGGTATCTTTCGACCATGGTCTTTTTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
* * *
12351364 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
** *
12351409 CATGTTGCCACAGTATCTTTCAACCATGGTCTTATTC-TTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTC-TGT
** * * * *
12351455 CACATTGCCATGGTATCTTTCAACTATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
*
12351501 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTT
12351542 CATTTCAGAA
Statistics
Matches: 194, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
45 45 0.23
46 145 0.75
47 4 0.02
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
Found at i:12351504 original size:137 final size:137
Alignment explanation
Indices: 12351272--12351534 Score: 366
Period size: 137 Copynumber: 1.9 Consensus size: 137
12351262 TTATCTTCGA
* * * **
12351272 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTT
1 CATGATGCCACAGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCACATTGCCATGGTATCTT
* *** * *
12351337 TCGACCATGGTCTTTTTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA
66 TCAACCATGGTCTTACACATTTCACATCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA
12351402 TTCCCGT
131 TTCCCGT
* *
12351409 CATGTTGCCACAGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACATTGCCATGGTATCT
1 CATGATGCCACAGTATCTTTCAACCATGGTCTTACTCATTTTC-TGTCACATTGCCATGGTATCT
* * *
12351473 TTCAACTATGGTCTTACACATTTTATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
65 TTCAACCATGGTCTTACACATTTCACATCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
12351535 CACATTTCAT
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
136 5 0.05
137 104 0.95
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.42
Consensus pattern (137 bp):
CATGATGCCACAGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCACATTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTCACATCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA
TTCCCGT
Found at i:12353599 original size:11 final size:11
Alignment explanation
Indices: 12353583--12353630 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
12353573 CTTTATATAC
12353583 TAATAAAATAA
1 TAATAAAATAA
*
12353594 TAATAAAATATCT
1 TAATAAAATA--A
* *
12353607 TATTAAAATAT
1 TAATAAAATAA
12353618 TAATAAAATAA
1 TAATAAAATAA
12353629 TA
1 TA
12353631 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:12354592 original size:9 final size:9
Alignment explanation
Indices: 12354580--12354670 Score: 56
Period size: 9 Copynumber: 9.6 Consensus size: 9
12354570 AAATATTACA
12354580 AAAAAAATT
1 AAAAAAATT
*
12354589 AAAATAATT
1 AAAAAAATT
***
12354598 TTTAAAATT
1 AAAAAAATT
*
12354607 AAAAATATTT
1 AAAAA-AATT
*
12354617 ATAAAAATTT
1 A-AAAAAATT
12354627 AAAAAAATCT
1 AAAAAAAT-T
12354637 AAAAAATATAT
1 AAAAAA-AT-T
* *
12354648 AAAGAAAGT
1 AAAAAAATT
*
12354657 AAAAAATTT
1 AAAAAAATT
12354666 AAAAA
1 AAAAA
12354671 TTTTCTAGAA
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
9 33 0.53
10 17 0.27
11 12 0.19
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAAAATT
Found at i:12354634 original size:29 final size:30
Alignment explanation
Indices: 12354601--12354671 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
12354591 AATAATTTTT
* **
12354601 AAAATTAAAAATATTTATAAA-AATTTAAA
1 AAAATTAAAAATATATATAAAGAAAGTAAA
12354630 AAAATCTAAAAA-ATATATAAAGAAAGTAAA
1 AAAAT-TAAAAATATATATAAAGAAAGTAAA
*
12354660 AAATTTAAAAAT
1 AAAATTAAAAAT
12354672 TTTCTAGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (30 bp):
AAAATTAAAAATATATATAAAGAAAGTAAA
Found at i:12354642 original size:20 final size:20
Alignment explanation
Indices: 12354601--12354670 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
12354591 AATAATTTTT
* * *
12354601 AAAA-TTAAAAATATTTATA
1 AAAATTTAAAAAAATCTAAA
12354620 AAAATTTAAAAAAATCTAAA
1 AAAATTTAAAAAAATCTAAA
* * *
12354640 AAATATATAAAGAAA-GT-AA
1 AAA-ATTTAAAAAAATCTAAA
12354659 AAAATTTAAAAA
1 AAAATTTAAAAA
12354671 TTTTCTAGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
18 7 0.17
19 9 0.22
20 16 0.39
21 9 0.22
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (20 bp):
AAAATTTAAAAAAATCTAAA
Found at i:12355960 original size:26 final size:27
Alignment explanation
Indices: 12355930--12355984 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
12355920 CATTATAAAG
*
12355930 ATGTAATTATA-ATGTATTAATAAAAC
1 ATGTAATTAAATATGTATTAATAAAAC
12355956 ATGTAATTAAATATGTATTAATAAAAC
1 ATGTAATTAAATATGTATTAATAAAAC
12355983 AT
1 AT
12355985 AAAATAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (27 bp):
ATGTAATTAAATATGTATTAATAAAAC
Found at i:12357555 original size:78 final size:78
Alignment explanation
Indices: 12357438--12357652 Score: 308
Period size: 78 Copynumber: 2.8 Consensus size: 78
12357428 TAATTGTAGT
* * *
12357438 GAATCAGGATTACCTTTTCAAGTCAAATCCTACCCACCTTAAGTTATCATAAGGAATCATATATC
1 GAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCATAAGGAATCATATATC
*
12357503 GTGT-AATCTAGC
66 ATGTAAATCTAGC
* * *
12357515 GAATCAAGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAGGTTACCATAATGAATCATATAT
1 GAATCAGGATTA-CCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCATAAGGAATCATATAT
* *
12357580 CATTTAAATGTAGC
65 CATGTAAATCTAGC
*
12357594 GAATCAGGATTACCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCAT-AGTGAATCA
1 GAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCATAAG-GAATCA
12357653 GGAATAAATC
Statistics
Matches: 122, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
77 12 0.10
78 92 0.75
79 18 0.15
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (78 bp):
GAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCATAAGGAATCATATATC
ATGTAAATCTAGC
Found at i:12357674 original size:39 final size:39
Alignment explanation
Indices: 12357617--12357750 Score: 153
Period size: 39 Copynumber: 3.4 Consensus size: 39
12357607 CTTTTCAGGT
* *
12357617 CAAATCCTATCCGCCTTAAGTTACCATAGTGAATCAGGAA
1 CAAATCCTATTC-ACTTAAGTTACCATAGTGAATCAGGAA
* *
12357657 TAAATCCTATTCACTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATTCACTTAAGTTACCATAGTGAATCAGGAA
* * **
12357696 CAAATCCTA-TCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATTCAC-TTAAGTTACCATAGTGAATCAGGAA
* *
12357735 CGAATCCTATCCACTT
1 CAAATCCTATTCACTT
12357751 TATATTCTCG
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
38 4 0.05
39 63 0.79
40 13 0.16
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (39 bp):
CAAATCCTATTCACTTAAGTTACCATAGTGAATCAGGAA
Found at i:12362730 original size:35 final size:35
Alignment explanation
Indices: 12362703--12362868 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
12362693 CATGGCAAAG
*
12362703 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
12362738 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
12362773 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
12362813 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
12362848 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
12362869 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:12362822 original size:75 final size:75
Alignment explanation
Indices: 12362703--12362873 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
12362693 CATGGCAAAG
** *
12362703 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
12362762 CCATACTGAGC
65 CCATACCGAGC
12362773 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
12362838 CATACCGAGT
66 CATACCGAGC
**
12362848 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
12362874 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:12370224 original size:35 final size:35
Alignment explanation
Indices: 12370197--12370362 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
12370187 CATGGCAAAG
*
12370197 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
12370232 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
12370267 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
12370307 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
12370342 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
12370363 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:12370316 original size:75 final size:75
Alignment explanation
Indices: 12370197--12370367 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
12370187 CATGGCAAAG
** *
12370197 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
12370256 CCATACTGAGC
65 CCATACCGAGC
12370267 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
12370332 CATACCGAGT
66 CATACCGAGC
**
12370342 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
12370368 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:12372798 original size:48 final size:48
Alignment explanation
Indices: 12372727--12372824 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
12372717 ATCTTAAATG
12372727 AACAAATATTTTAATTTTTCAACAAATTAATAGCATCCATTTAACTTT
1 AACAAATATTTTAATTTTTCAACAAATTAATAGCATCCATTTAACTTT
12372775 AACAAATATTTTAATTTTTCAACAAATTAATAGCATCCATTTAACTTT
1 AACAAATATTTTAATTTTTCAACAAATTAATAGCATCCATTTAACTTT
12372823 AA
1 AA
12372825 TATCATATCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (48 bp):
AACAAATATTTTAATTTTTCAACAAATTAATAGCATCCATTTAACTTT
Found at i:12377397 original size:6 final size:6
Alignment explanation
Indices: 12377386--12377411 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12377376 GTGCCTGTCT
12377386 TGCACA TGCACA TGCACA TGCACA TG
1 TGCACA TGCACA TGCACA TGCACA TG
12377412 GTTAATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (6 bp):
TGCACA
Found at i:12378774 original size:20 final size:20
Alignment explanation
Indices: 12378749--12378788 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12378739 CGGAAAATGA
12378749 TTTTTGAAAAATGATTTACT
1 TTTTTGAAAAATGATTTACT
*
12378769 TTTTTGGAAAATGATTTACT
1 TTTTTGAAAAATGATTTACT
12378789 GAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTTTGAAAAATGATTTACT
Found at i:12378864 original size:32 final size:32
Alignment explanation
Indices: 12378779--12378865 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
12378769 TTTTTGGAAA
*
12378779 ATGATTTACTGAAAATATTTTCTGATGTTTGG
1 ATGATTTTCTGAAAATATTTTCTGATGTTTGG
*** * *
12378811 ATGAAACTGTGTAAAATATTTTCTGTTGTTTGG
1 ATGATTTTCTG-AAAATATTTTCTGATGTTTGG
12378844 CA-GATTTTCTGAAAATATTTTC
1 -ATGATTTTCTGAAAATATTTTC
12378866 CGTAAAAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
32 17 0.40
33 25 0.58
34 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (32 bp):
ATGATTTTCTGAAAATATTTTCTGATGTTTGG
Found at i:12380568 original size:2 final size:2
Alignment explanation
Indices: 12380561--12380589 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12380551 TGTTGTTAAG
12380561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12380590 AACCAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12389171 original size:21 final size:19
Alignment explanation
Indices: 12389135--12389176 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
12389125 TATTATATAT
12389135 AAAGAAATAAAAGAAAGAA
1 AAAGAAATAAAAGAAAGAA
*
12389154 AAAGAGAATAGAATGAAAGAA
1 AAAGA-AATA-AAAGAAAGAA
12389175 AA
1 AA
12389177 GAGGGAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (19 bp):
AAAGAAATAAAAGAAAGAA
Found at i:12389621 original size:33 final size:35
Alignment explanation
Indices: 12389584--12389677 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
12389574 AACATTTGTT
12389584 AATATA-AAG-TGAATTGAAATATATTGAATTGAG
1 AATATATAAGATGAATTGAAATATATTGAATTGAG
** *
12389617 AATATATCTGATTAATTGAAATATATTGAATTGAG
1 AATATATAAGATGAATTGAAATATATTGAATTGAG
** * *
12389652 AATATATCTGATTAGTTGAAATATAT
1 AATATATAAGATGAATTGAAATATAT
12389678 ACTGATTGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 6 0.11
34 1 0.02
35 48 0.87
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (35 bp):
AATATATAAGATGAATTGAAATATATTGAATTGAG
Found at i:12389622 original size:16 final size:15
Alignment explanation
Indices: 12389593--12389677 Score: 80
Period size: 19 Copynumber: 5.0 Consensus size: 15
12389583 TAATATAAAG
12389593 TGAATTGAAATATAT
1 TGAATTGAAATATAT
12389608 TGAATTGAGAATATAT
1 TGAATTGA-AATATAT
12389624 CTGATTAATTGAAATATAT
1 -TG---AATTGAAATATAT
12389643 TGAATTGAGAATATAT
1 TGAATTGA-AATATAT
12389659 CTGATTAGTTGAAATATAT
1 -TGA--A-TTGAAATATAT
12389678 ACTGATTGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
15 14 0.23
16 14 0.23
17 5 0.08
18 2 0.03
19 15 0.25
20 10 0.17
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.40
Consensus pattern (15 bp):
TGAATTGAAATATAT
Found at i:12389635 original size:20 final size:19
Alignment explanation
Indices: 12389595--12389684 Score: 88
Period size: 20 Copynumber: 5.0 Consensus size: 19
12389585 ATATAAAGTG
12389595 AATTGAAATATAT-TG---
1 AATTGAAATATATCTGATT
12389610 AATTGAGAATATATCTGATT
1 AATTGA-AATATATCTGATT
12389630 AATTGAAATATAT-TG---
1 AATTGAAATATATCTGATT
12389645 AATTGAGAATATATCTGATT
1 AATTGA-AATATATCTGATT
*
12389665 AGTTGAAATATATACTGATT
1 AATTGAAATATAT-CTGATT
12389685 GAAAACTAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 17
0.78 0.01 0.21
Matches are distributed among these distances:
15 12 0.19
16 14 0.22
17 4 0.06
18 2 0.03
19 14 0.22
20 17 0.27
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.40
Consensus pattern (19 bp):
AATTGAAATATATCTGATT
Found at i:12389636 original size:35 final size:35
Alignment explanation
Indices: 12389595--12389677 Score: 157
Period size: 35 Copynumber: 2.4 Consensus size: 35
12389585 ATATAAAGTG
12389595 AATTGAAATATATTGAATTGAGAATATATCTGATT
1 AATTGAAATATATTGAATTGAGAATATATCTGATT
12389630 AATTGAAATATATTGAATTGAGAATATATCTGATT
1 AATTGAAATATATTGAATTGAGAATATATCTGATT
*
12389665 AGTTGAAATATAT
1 AATTGAAATATAT
12389678 ACTGATTGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.40
Consensus pattern (35 bp):
AATTGAAATATATTGAATTGAGAATATATCTGATT
Found at i:12390076 original size:18 final size:18
Alignment explanation
Indices: 12390039--12390097 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
12390029 ACTAACTGCC
* * *
12390039 ACTGAATAAACGACTGTT
1 ACTGAATAAATGATTATT
12390057 ACTGAATAAATGATTATT
1 ACTGAATAAATGATTATT
* *
12390075 ACTGAATAACTGATTAAT
1 ACTGAATAAATGATTATT
12390093 ACTGA
1 ACTGA
12390098 TGACTGAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (18 bp):
ACTGAATAAATGATTATT
Found at i:12394009 original size:2 final size:2
Alignment explanation
Indices: 12394002--12394049 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
12393992 CACTCACTCA
12394002 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12394044 CT CT CT
1 CT CT CT
12394050 TTATTTGTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12397355 original size:27 final size:27
Alignment explanation
Indices: 12397323--12397388 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
12397313 TAGTTGAACT
*
12397323 ATGGCAAAGTGATAAAGTGTGTCAAAC
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
*
12397350 ATGGCAAAGTGATAAAGTGTGCCAAAT
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
12397377 ATGGCAAAGTGA
1 ATGGCAAAGTGA
12397389 AATGTGACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.21
Consensus pattern (27 bp):
ATGGCAAAGTGATAAAGTGTGCCAAAC
Found at i:12398825 original size:12 final size:13
Alignment explanation
Indices: 12398808--12398848 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
12398798 ATTAAGTCCC
12398808 TTTTATTTTT-AT
1 TTTTATTTTTCAT
12398820 TTTTATTTTTCA-
1 TTTTATTTTTCAT
**
12398832 TTTTATGATTCAT
1 TTTTATTTTTCAT
12398845 TTTT
1 TTTT
12398849 TTATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTCAT
Found at i:12399548 original size:22 final size:22
Alignment explanation
Indices: 12399501--12399551 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
12399491 TATTTAGCGC
* *
12399501 ATTATATCTTGTCATATATCTTT
1 ATTAT-TCTTGTCATATATATAT
12399524 ATTATTCTT-TCATATTATATAT
1 ATTATTCTTGTCATA-TATATAT
12399546 ATTATT
1 ATTATT
12399552 TAAATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.20
22 15 0.60
23 5 0.20
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTATTCTTGTCATATATATAT
Found at i:12400360 original size:131 final size:132
Alignment explanation
Indices: 12400113--12400363 Score: 380
Period size: 131 Copynumber: 1.9 Consensus size: 132
12400103 TCATTCATTC
** * * *
12400113 AAAAGTTCTTCAAAACGAAGACGAGATTCGATGTTTGGCAATTGGCGGAATCGTGCCCTAACGTG
1 AAAAGTTCTTCAAAACGAAGACGAGATTCGATACTTAGCAATTCGCGAAATCGTGCCCTAACGTG
* *
12400178 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCGAAATTTCACTCGCGTCTT
66 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAACATCACTTCAAAATTTCACTCGCGTCTT
12400243 TT
131 TT
12400245 AAAA-TTCTTCAAAACGAAGACGAGATTCGATACTTAGCAATTCGCGAAATCGTGCCCTAACGTG
1 AAAAGTTCTTCAAAACGAAGACGAGATTCGATACTTAGCAATTCGCGAAATCGTGCCCTAACGTG
* * * *
12400309 TTGGGTTGCAATTTTGCGTTTG-TCCAAAGTAATCGAGCATCCCTTCAAAATTTCA
66 TTGGGTTGCAATTTCGCGTTTGCT-CAAAATAATCGAACATCACTTCAAAATTTCA
12400364 TTCATATCTT
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
130 1 0.01
131 102 0.95
132 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (132 bp):
AAAAGTTCTTCAAAACGAAGACGAGATTCGATACTTAGCAATTCGCGAAATCGTGCCCTAACGTG
TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAACATCACTTCAAAATTTCACTCGCGTCTT
TT
Found at i:12400379 original size:131 final size:132
Alignment explanation
Indices: 12400113--12400394 Score: 370
Period size: 131 Copynumber: 2.1 Consensus size: 132
12400103 TCATTCATTC
* ** * * *
12400113 AAAAGTTCTTCAAAACGAAGACGAGATTCGATGTTTGGCAATTGGCGGAATCGTGCCCTAACGTG
1 AAAAATTCTTCAAAACGAAGACGAGATTCGATACTTAGCAATTCGCGAAATCGTGCCCTAACGTG
* * * *
12400178 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCGAAATTTCACTCGCGTCTT
66 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAACATCACTTCAAAATTTCACTCACATCTT
12400243 -T
131 CT
*
12400244 TAAAATTCTTCAAAACGAAGACGAGATTCGATACTTAGCAATTCGCGAAATCGTGCCCTAACGTG
1 AAAAATTCTTCAAAACGAAGACGAGATTCGATACTTAGCAATTCGCGAAATCGTGCCCTAACGTG
* * * * * *
12400309 TTGGGTTGCAATTTTGCGTTTG-TCCAAAGTAATCGAGCATCCCTTCAAAATTTCATTCATATCT
66 TTGGGTTGCAATTTCGCGTTTGCT-CAAAATAATCGAACATCACTTCAAAATTTCACTCACATCT
12400373 TCT
130 TCT
* *
12400376 AAAAATTATTTAAAACGAA
1 AAAAATTCTTCAAAACGAA
12400395 AGCTATATTC
Statistics
Matches: 129, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
130 1 0.01
131 111 0.86
132 17 0.13
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (132 bp):
AAAAATTCTTCAAAACGAAGACGAGATTCGATACTTAGCAATTCGCGAAATCGTGCCCTAACGTG
TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAACATCACTTCAAAATTTCACTCACATCTT
CT
Found at i:12402691 original size:57 final size:57
Alignment explanation
Indices: 12402618--12402739 Score: 147
Period size: 57 Copynumber: 2.2 Consensus size: 57
12402608 TTAGTCCAAG
* * * * *
12402618 ATATTAATAAAAATTTATACTTAATACATGCATCAATGTATAATAAATTTAATTAAA
1 ATATTAATAAAAATTTATACTTAACACAAGCATAAATATATAATAAAATTAATTAAA
* * * * *
12402675 ATATTAATAAATATTTATATTTAACATAAGGATAAATATATAATAAAATTAATTAAT
1 ATATTAATAAAAATTTATACTTAACACAAGCATAAATATATAATAAAATTAATTAAA
12402732 ATA-TAATA
1 ATATTAATA
12402740 TATGAGTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
56 5 0.09
57 50 0.91
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (57 bp):
ATATTAATAAAAATTTATACTTAACACAAGCATAAATATATAATAAAATTAATTAAA
Found at i:12402811 original size:10 final size:10
Alignment explanation
Indices: 12402796--12402829 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
12402786 AATATATTAT
12402796 TTTTATTTAA
1 TTTTATTTAA
*
12402806 TTTTATATAA
1 TTTTATTTAA
*
12402816 TTTTATTAAA
1 TTTTATTTAA
12402826 TTTT
1 TTTT
12402830 TAAACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:12403157 original size:18 final size:17
Alignment explanation
Indices: 12403134--12403167 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
12403124 TTTTAAAAAT
12403134 TATAAAAATATAAATTAA
1 TATAAAAATA-AAATTAA
12403152 TATAAAAATAAAATTA
1 TATAAAAATAAAATTA
12403168 CATTGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TATAAAAATAAAATTAA
Found at i:12412443 original size:9 final size:9
Alignment explanation
Indices: 12412429--12412479 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
12412419 TTTTTTTAAA
12412429 TTTAAAAAT
1 TTTAAAAAT
12412438 TTTAAAAA-
1 TTTAAAAAT
12412446 -TTAAAAAT
1 TTTAAAAAT
*
12412454 TATTTAAAAT
1 T-TTAAAAAT
*
12412464 ATTAAAAAT
1 TTTAAAAAT
*
12412473 TATAAAA
1 TTTAAAA
12412480 TATATTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 7 0.21
9 20 0.59
10 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:12412467 original size:19 final size:19
Alignment explanation
Indices: 12412426--12412475 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
12412416 TTATTTTTTT
12412426 AAAT-TTAAAAA-T-TTTA
1 AAATATTAAAAATTATTTA
12412442 AAA-ATTAAAAATTATTTA
1 AAATATTAAAAATTATTTA
12412460 AAATATTAAAAATTAT
1 AAATATTAAAAATTAT
12412476 AAAATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.33
17 1 0.03
18 7 0.23
19 12 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATTAAAAATTATTTA
Found at i:12412469 original size:26 final size:29
Alignment explanation
Indices: 12412428--12412486 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 29
12412418 ATTTTTTTAA
*
12412428 ATTTAAAAATTTTAAAAATTA-AAAAT-T
1 ATTTAAAAATATTAAAAATTATAAAATAT
12412455 ATTT-AAAATATTAAAAATTATAAAATAT
1 ATTTAAAAATATTAAAAATTATAAAATAT
12412483 ATTT
1 ATTT
12412487 TTATACTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 15 0.52
27 9 0.31
28 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
ATTTAAAAATATTAAAAATTATAAAATAT
Found at i:12412480 original size:17 final size:17
Alignment explanation
Indices: 12412426--12412482 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 17
12412416 TTATTTTTTT
*
12412426 AAAT-TTAAAAATTTTA
1 AAATATTAAAAATTATA
12412442 AAA-ATTAAAAATTATTTA
1 AAATATTAAAAATTA--TA
12412460 AAATATTAAAAATTATA
1 AAATATTAAAAATTATA
12412477 AAATAT
1 AAATAT
12412483 ATTTTTATAC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 12 0.33
17 8 0.22
18 5 0.14
19 11 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATTAAAAATTATA
Found at i:12412484 original size:19 final size:19
Alignment explanation
Indices: 12412426--12412485 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
12412416 TTATTTTTTT
12412426 AAAT-TTAAAAATT-TT-A
1 AAATATTAAAAATTATTAA
*
12412442 AAA-ATTAAAAATTATTTA
1 AAATATTAAAAATTATTAA
12412460 AAATATTAAAAATTA-TAA
1 AAATATTAAAAATTATTAA
12412478 AATATATT
1 AA-ATATT
12412486 TTTATACTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 12 0.32
17 2 0.05
18 8 0.21
19 16 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATTAAAAATTATTAA
Found at i:12413345 original size:13 final size:13
Alignment explanation
Indices: 12413327--12413353 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12413317 AAGAATGCAG
12413327 TGGTAGCACCAAC
1 TGGTAGCACCAAC
12413340 TGGTAGCACCAAC
1 TGGTAGCACCAAC
12413353 T
1 T
12413354 AGTGCTCTTG
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:0.30, G:0.22, T:0.19
Consensus pattern (13 bp):
TGGTAGCACCAAC
Found at i:12413755 original size:12 final size:12
Alignment explanation
Indices: 12413738--12413762 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12413728 TAAGCTCTCT
12413738 AAATTTTATTAA
1 AAATTTTATTAA
12413750 AAATTTTATTAA
1 AAATTTTATTAA
12413762 A
1 A
12413763 CAACTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTTTATTAA
Found at i:12419018 original size:5 final size:5
Alignment explanation
Indices: 12418977--12419017 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
12418967 AACAAGACTT
*
12418977 TCTAA TCTAA TCTAA TCTAA TCTAA TCTAA TCTAA TTTAA T
1 TCTAA TCTAA TCTAA TCTAA TCTAA TCTAA TCTAA TCTAA T
12419018 TCCATTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (5 bp):
TCTAA
Found at i:12422125 original size:13 final size:13
Alignment explanation
Indices: 12422103--12422166 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
12422093 TTTGGCAATA
12422103 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
12422116 CTTTTAAAAAGTG
1 CTTTTGAAAAGTG
*
12422129 C-TGTGAAAAAGTG
1 CTTTTG-AAAAGTG
* *
12422142 TTTTTGAGAAGTG
1 CTTTTGAAAAGTG
12422155 CTTTTGAAAAGT
1 CTTTTGAAAAGT
12422167 TTGATTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 2 0.05
13 36 0.88
14 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:12424300 original size:28 final size:30
Alignment explanation
Indices: 12424264--12424329 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
12424254 ATAATCGTTG
*
12424264 ATAT-TATATT-TTTTTAGAA-ATTTAAACT
1 ATATATATATTCTTTTT-GAAGATTTAAAAT
*
12424292 A-ATATATATTCTTTTTGAAGTTTTAAAAT
1 ATATATATATTCTTTTTGAAGATTTAAAAT
12424321 ATATATATA
1 ATATATATA
12424330 GATAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 2 0.06
28 10 0.31
29 13 0.41
30 7 0.22
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (30 bp):
ATATATATATTCTTTTTGAAGATTTAAAAT
Found at i:12442517 original size:27 final size:27
Alignment explanation
Indices: 12442460--12442517 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
12442450 TAATTTGAAT
**
12442460 ATTTTATTTTTTATAAAAAGATAATTT
1 ATTTTATTTTTTATAAAAAGATAATAA
12442487 ATTTTATTTTTTAATAAAATA-A-AATAA
1 ATTTTATTTTTT-ATAAAA-AGATAATAA
12442514 ATTT
1 ATTT
12442518 AATATTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 19 0.70
28 7 0.26
29 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTTATTTTTTATAAAAAGATAATAA
Found at i:12450404 original size:23 final size:25
Alignment explanation
Indices: 12450378--12450424 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12450368 TATCATTCAT
*
12450378 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
12450401 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
12450425 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:12450744 original size:46 final size:46
Alignment explanation
Indices: 12450684--12451087 Score: 619
Period size: 46 Copynumber: 9.0 Consensus size: 46
12450674 TTTGACGTGA
* * * * * *
12450684 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
12450730 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
12450776 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
12450822 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
12450868 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
12450914 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
12450960 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
12451006 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
12451044 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
12451088 AGAGCACACT
Statistics
Matches: 334, Mismatches: 15, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
38 33 0.10
39 1 0.00
40 3 0.01
41 1 0.00
43 1 0.00
44 3 0.01
45 5 0.01
46 287 0.86
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:12451052 original size:38 final size:38
Alignment explanation
Indices: 12451001--12451076 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
12450991 CATTTCATAT
12451001 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
12451039 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
12451077 TTTCATATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:12460503 original size:60 final size:60
Alignment explanation
Indices: 12460433--12460548 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
12460423 TAAATAATTA
* * *
12460433 AATGATTATTTTATAATT-TTTTATAATCAGATGATCAAAAAATAAATTTATTAATAGTTT
1 AATGATTATTTTATAATTATTTTACAATCAAATAAT-AAAAAATAAATTTATTAATAGTTT
* *
12460493 AATGATTATTTTATAATTATTTTACAATTAAATAATTAAAAATAAATTTATTAATA
1 AATGATTATTTTATAATTATTTTACAATCAAATAATAAAAAATAAATTTATTAATA
12460549 ATTGAGTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 37 0.74
61 13 0.26
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (60 bp):
AATGATTATTTTATAATTATTTTACAATCAAATAATAAAAAATAAATTTATTAATAGTTT
Found at i:12462353 original size:17 final size:16
Alignment explanation
Indices: 12462322--12462358 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
12462312 TTCCAGCATG
*
12462322 CAATAAATGCATAAAT
1 CAATAAATACATAAAT
12462338 CAATAAGATACATAAAT
1 CAATAA-ATACATAAAT
12462355 CAAT
1 CAAT
12462359 TAGAAGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (16 bp):
CAATAAATACATAAAT
Found at i:12469199 original size:17 final size:17
Alignment explanation
Indices: 12469177--12469212 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
12469167 AACCATCCAT
*
12469177 TTTTGTTTAGAAGTGGG
1 TTTTGTTTACAAGTGGG
12469194 TTTTGTTTACAAGTGGG
1 TTTTGTTTACAAGTGGG
12469211 TT
1 TT
12469213 AGTACACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.31, T:0.50
Consensus pattern (17 bp):
TTTTGTTTACAAGTGGG
Found at i:12475942 original size:16 final size:17
Alignment explanation
Indices: 12475921--12475956 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
12475911 ACAAGTAAGA
12475921 TTTAAATATT-TCATTT
1 TTTAAATATTATCATTT
12475937 TTTAAATATTATCATTT
1 TTTAAATATTATCATTT
12475954 TTT
1 TTT
12475957 TAATTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAAATATTATCATTT
Found at i:12476018 original size:14 final size:14
Alignment explanation
Indices: 12476001--12476028 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12475991 AACTCTATTT
12476001 TTATAATACAAAAG
1 TTATAATACAAAAG
12476015 TTATAATACAAAAG
1 TTATAATACAAAAG
12476029 CGTGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
TTATAATACAAAAG
Found at i:12478108 original size:28 final size:28
Alignment explanation
Indices: 12478077--12478174 Score: 68
Period size: 30 Copynumber: 3.6 Consensus size: 28
12478067 ATAGAAACTT
12478077 TTTTATTTAAATTTTAAAAAAATTAAAA
1 TTTTATTTAAATTTTAAAAAAATTAAAA
12478105 ---T-TTTAAA--TTAATAAAAA-TAAAA
1 TTTTATTTAAATTTTAA-AAAAATTAAAA
* *
12478127 TTATATTTAAATTCCTT-TAAAAATATAAAA
1 TTTTATTTAAATT--TTAAAAAAAT-TAAAA
*
12478157 TTTAATTTAATATTTTAA
1 TTTTATTTAA-ATTTTAA
12478175 GAATTATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 24
0.65 0.05 0.30
Matches are distributed among these distances:
22 9 0.17
23 5 0.09
24 6 0.11
25 2 0.04
26 6 0.11
28 5 0.09
29 2 0.04
30 15 0.28
31 3 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
TTTTATTTAAATTTTAAAAAAATTAAAA
Found at i:12479446 original size:19 final size:18
Alignment explanation
Indices: 12479395--12479448 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
12479385 TAAAATAATT
*
12479395 TAATTTTTATATAATTCTA
1 TAATTTTTATA-ATTTCTA
* *
12479414 TCATTTTAATTAATTTCTAA
1 TAATTTTTA-TAATTTCT-A
12479434 TAATTTTTATAATTT
1 TAATTTTTATAATTT
12479449 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TAATTTTTATAATTTCTA
Found at i:12484926 original size:46 final size:49
Alignment explanation
Indices: 12484820--12484935 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 49
12484810 TGTCTTCAAC
** * *
12484820 ATGGACTTACATGAATTATTCGTGTCTCCAATGCCCTATATATATCTAAT
1 ATGGACTTACATGGCTCATTCGTGTCTCCAAAGCCCTATATATA-CTAAT
* * *
12484870 ATGGGCTTACATGGCTCATTCTTGTCTCCAAAG-CC-ATATATA-TGAT
1 ATGGACTTACATGGCTCATTCGTGTCTCCAAAGCCCTATATATACTAAT
12484916 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
12484936 TCTGTCCTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 22 0.38
48 7 0.12
49 2 0.03
50 27 0.47
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (49 bp):
ATGGACTTACATGGCTCATTCGTGTCTCCAAAGCCCTATATATACTAAT
Found at i:12492484 original size:12 final size:13
Alignment explanation
Indices: 12492469--12492502 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
12492459 TAATTGACAG
12492469 TTTAATTAATTT-
1 TTTAATTAATTTA
*
12492481 TTTAAATAATTTA
1 TTTAATTAATTTA
12492494 TTTAATTAA
1 TTTAATTAA
12492503 AAATAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAATTAATTTA
Found at i:12494991 original size:12 final size:12
Alignment explanation
Indices: 12494966--12495025 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 12
12494956 TTTAAATTTT
*
12494966 AAAAATTAT-TA
1 AAAAATTATAAA
*
12494977 AAAAATCAT-AA
1 AAAAATTATAAA
12494988 AAAAA-TATAAA
1 AAAAATTATAAA
*
12494999 CAAAATTTATAAA
1 -AAAAATTATAAA
*
12495012 AATAATTATAAA
1 AAAAATTATAAA
12495024 AA
1 AA
12495026 TTTTAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 2 0.05
11 16 0.40
12 16 0.40
13 6 0.15
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:12501674 original size:27 final size:27
Alignment explanation
Indices: 12501623--12501676 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
12501613 TTCTTGAATA
*
12501623 ATTTTAGGTTTATATTTTATCATATTC
1 ATTTTAGGTTTATATTTTATAATATTC
12501650 ATTTGTAGGTTT-TA-TTTATTAATATTC
1 ATTT-TAGGTTTATATTTTA-TAATATTC
12501677 CGATTTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 13 0.54
28 7 0.29
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (27 bp):
ATTTTAGGTTTATATTTTATAATATTC
Found at i:12503168 original size:3 final size:3
Alignment explanation
Indices: 12503160--12503193 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12503150 AAGTCAGGGT
12503160 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12503194 AGTAAGAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12515691 original size:25 final size:25
Alignment explanation
Indices: 12515663--12515720 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
12515653 AATTTGATAT
*
12515663 TTCAGTAAAGAAGGCATTGTTGAGA
1 TTCAGCAAAGAAGGCATTGTTGAGA
*
12515688 TTCAGCAGAGAAGGCATTGTTGAGA
1 TTCAGCAAAGAAGGCATTGTTGAGA
12515713 TTC-GCAAA
1 TTCAGCAAA
12515721 CTCAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (25 bp):
TTCAGCAAAGAAGGCATTGTTGAGA
Found at i:12516538 original size:16 final size:16
Alignment explanation
Indices: 12516517--12516594 Score: 51
Period size: 16 Copynumber: 5.2 Consensus size: 16
12516507 ATCTTTATTA
12516517 AATTATATTTAATAAT
1 AATTATATTTAATAAT
*
12516533 AATTATATTAAAGT-AT
1 AATTATATTTAA-TAAT
* * *
12516549 AATTA-AATTATTTAT
1 AATTATATTTAATAAT
* *
12516564 TATT-TA-TT-ATTA-
1 AATTATATTTAATAAT
12516576 AATTATATTTAATAAT
1 AATTATATTTAATAAT
12516592 AAT
1 AAT
12516595 CCTATTATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
12 3 0.06
13 5 0.11
14 5 0.11
15 12 0.26
16 21 0.45
17 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (16 bp):
AATTATATTTAATAAT
Found at i:12516538 original size:24 final size:23
Alignment explanation
Indices: 12516471--12516538 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
12516461 TTTTAATAAT
* *
12516471 AATTATA-TTAAGAATGTTATTA
1 AATTATATTTAATAATATTATTA
* *
12516493 AATTATATATT-ATTATCTTTATTA
1 AATTATAT-TTAATAAT-ATTATTA
12516517 AATTATATTTAATAATAATTAT
1 AATTATATTTAATAAT-ATTAT
12516539 ATTAAAGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 7 0.19
23 5 0.14
24 24 0.67
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (23 bp):
AATTATATTTAATAATATTATTA
Found at i:12516601 original size:59 final size:62
Alignment explanation
Indices: 12516426--12516594 Score: 202
Period size: 59 Copynumber: 2.7 Consensus size: 62
12516416 ATACTATTTT
* ** * * *
12516426 TTAATATTATATATTATGATTTTTATT-CATTCATATTTTAATAATAATTATATTAAGAATGTTA
1 TTAA-ATTATATATTATTATCATTATTAAATT-ATA-TTTAATAATAATTATATTAAGAATATAA
* *
12516490 TTAAATTATATATTATTATCTTTATTAAATTATATTTAATAATAATTATATTAA-AGTATAA
1 TTAAATTATATATTATTATCATTATTAAATTATATTTAATAATAATTATATTAAGAATATAA
*
12516551 TTAAATTATTTATTATT-T-ATTATTAAATTATATTTAATAATAAT
1 TTAAATTATATATTATTATCATTATTAAATTATATTTAATAATAAT
12516595 CCTATTATAA
Statistics
Matches: 96, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
59 25 0.26
60 1 0.01
61 20 0.21
62 20 0.21
63 23 0.24
64 7 0.07
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (62 bp):
TTAAATTATATATTATTATCATTATTAAATTATATTTAATAATAATTATATTAAGAATATAA
Found at i:12516751 original size:44 final size:46
Alignment explanation
Indices: 12516697--12516790 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 46
12516687 ATTACAATAT
* * *
12516697 CATTCTATTCAATCAAACA-CAAGAA-TACT-ATTACAGTTCTATTC
1 CATTCCATTCAACCAAACAGC-AGAATTACTGATTACAGCTCTATTC
*
12516741 CATTCCATTCAACCAAACAGCTGAATTACTGATTACAGCTCTATTC
1 CATTCCATTCAACCAAACAGCAGAATTACTGATTACAGCTCTATTC
12516787 CATT
1 CATT
12516791 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 20 0.47
45 5 0.12
46 18 0.42
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.33
Consensus pattern (46 bp):
CATTCCATTCAACCAAACAGCAGAATTACTGATTACAGCTCTATTC
Found at i:12516793 original size:16 final size:16
Alignment explanation
Indices: 12516772--12516826 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
12516762 TGAATTACTG
12516772 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
12516788 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
12516804 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
12516820 ATTACAG
1 ATTACAG
12516827 TGAACCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:12523771 original size:14 final size:15
Alignment explanation
Indices: 12523749--12523782 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12523739 AATTGTTTAA
*
12523749 TATTTTTTTATAATT
1 TATTTTTTAATAATT
*
12523764 TATTTTTTAATATTT
1 TATTTTTTAATAATT
12523779 TATT
1 TATT
12523783 ATATACTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTTTAATAATT
Found at i:12526771 original size:40 final size:40
Alignment explanation
Indices: 12526725--12526811 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
12526715 AATTCATTAC
* * *
12526725 TTCAGTAATTTCACAGTTCAATGCAGTACACATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
* *
12526765 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
12526805 TTCAGTA
1 TTCAGTA
12526812 TTCCATAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:12526790 original size:21 final size:21
Alignment explanation
Indices: 12526725--12526792 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
12526715 AATTCATTAC
* *
12526725 TTCAGTAATTTCACAGTTCAA
1 TTCAGTAACTTCACAATTCAA
* * *
12526746 TGCAGTACACATAACAA-T--A
1 TTCAGTA-ACTTCACAATTCAA
12526765 TTCAGTAACTTCACAATTCAA
1 TTCAGTAACTTCACAATTCAA
12526786 TTCAGTA
1 TTCAGTA
12526793 CTCAAAACAA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 7 0.20
19 8 0.23
21 15 0.43
22 5 0.14
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (21 bp):
TTCAGTAACTTCACAATTCAA
Done.