Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 4 of 172
Found at i:1010968 original size:210 final size:210
Alignment explanation
Indices: 1010583--1010969 Score: 512
Period size: 210 Copynumber: 1.8 Consensus size: 210
1010573 GATATAAAAG
* * *
1010583 ATTGTCCTAATTTAAGTTGGATTCCAGATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATT
1 ATTGTCCTAATTTAAGTTGGATTCCAGACTTGGAAGAATTTTCCTCTCTTCAAAATCTATCAATT
* * * * * * *
1010648 GATAGCTACAAGGAATTGGAAGTTCTTCCTATAACCGGAGGTTGTTCATCTCTTGAAAAGCTTAT
66 AATAGCTACAAGGAATTGAAAGTTCTTCCAATAACAGGAAGATGTTCATCTCTTGAAAAGCTTAA
* * ** *
1010713 TATTTTGGGTTGTGAAAGTTTAAGCAAGATCGAAGACGAATTATTTAGCTCCACTTGTCTGAAAT
131 CATTTTGGGTTGCGAAAAATTAAACAAGATCGAAGACGAATTATTTAGCTCCACTTGTCTGAAAT
1010778 AATTATATCTATGTC
196 AATTATATCTATGTC
*
1010793 ATTGTTCTAATTTAAGTTCGG-TTCCAGACTTGGAAGAATGTTT-CTCTCTT-AAAATTCTATCA
1 ATTGTCCTAATTTAAGTT-GGATTCCAGACTTGGAAGAAT-TTTCCTCTCTTCAAAA-TCTATCA
** *
1010855 ATTAATAGCTGTAAGGAATTGAAAGTTCTTCCAATAATAGGAAGATGTTCATCTCTTGAAAAGCT
63 ATTAATAGCTACAAGGAATTGAAAGTTCTTCCAATAACAGGAAGATGTTCATCTCTTGAAAAGCT
* * *
1010920 TAACATCTTT-GGTTGCGAAAAATTAAACAAGATTGGAGACGGATTATTTA
128 TAACAT-TTTGGGTTGCGAAAAATTAAACAAGATCGAAGACGAATTATTTA
1010970 CCCCCTCTCT
Statistics
Matches: 151, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
209 4 0.03
210 139 0.92
211 8 0.05
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (210 bp):
ATTGTCCTAATTTAAGTTGGATTCCAGACTTGGAAGAATTTTCCTCTCTTCAAAATCTATCAATT
AATAGCTACAAGGAATTGAAAGTTCTTCCAATAACAGGAAGATGTTCATCTCTTGAAAAGCTTAA
CATTTTGGGTTGCGAAAAATTAAACAAGATCGAAGACGAATTATTTAGCTCCACTTGTCTGAAAT
AATTATATCTATGTC
Found at i:1011264 original size:348 final size:348
Alignment explanation
Indices: 1010625--1011269 Score: 841
Period size: 348 Copynumber: 1.9 Consensus size: 348
1010615 GAAGGATTTT
* *
1010625 CCTCTCTTCAAAATCTGTCAATTGATAGCTACAAGGAATTGGAAGTTCTTCCTATAACCGGAGGT
1 CCTCTCTTCAAAACCTGTCAATTGATAGCTACAAGGAATTAGAAGTTCTTCCTATAACCGGAGGT
** * **
1010690 TGTTCATCTCTTGAAAAGCTTATTATTTTGGGTTGTGAAAGTTTAAGCAAGATCGAAGACGAATT
66 TGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGAAGACGAATT
* * * * * * * * * *
1010755 ATTTAGCTCCACTTGTCTGAAATAATTATATCTATGTCATTGTTCTAATTTAAGTTCGGTTCCAG
131 ATCTACCTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTCCAA
** *
1010820 ACTTGGAAGAATGTTTCTCTCTTAAAATTCTATCAATTAATAGCTGTAAGGAATTGAAAGTTCTT
196 ACTTGGAAGAATGTTTCTCTCTTAAAAGCCTATCAATTAATAGCTGCAAGGAATTGAAAGTTCTT
*
1010885 CCAATAATAGGAAGATGTTCATCTCTTGAAAAGCTTAACATCTTTGGTTGCGAAAAATTAAACAA
261 CCAATAATAGGAAGATGTTCATCTATTGAAAAGCTTAACATCTTTGGTTGCGAAAAATTAAACAA
1010950 GATTGGAGACGGATTATTTACCC
326 GATTGGAGACGGATTATTTACCC
* * * * *
1010973 CCTCTCTTCAAAACCTGTCAATTGATAGTTGCAATGAGTTAGAAGTTCTTTCGT-T-ACCTGGAA
1 CCTCTCTTCAAAACCTGTCAATTGATAGCTACAAGGAATTAGAAGTTC-TTCCTATAACC-GG-A
* * * * * *
1011036 GG-TGTTTATCTCTTGAAAAGCTTAGCATTTTTGGTTGCGAAAAATTAAGCAAGATTGGAGATGG
63 GGTTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGAAGACGA
* * *
1011100 ATTATCTACCTGCGCTTGTCTCAAAGAATTAGGTCTATATAATTGTCCTAATTTAAGTTCGATTC
128 ATTATCTACCTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTC
* * * * * *
1011165 CAAATTTGGAAGGAAT-TTTCTCTCTTTAAAGCCTGTCAATTAATAGGTGCAATGAATTGGAAGT
193 CAAACTTGGAA-GAATGTTTCTCTCTTAAAAGCCTATCAATTAATAGCTGCAAGGAATTGAAAGT
1011229 TCTTCCAATAACT-GGAAGATGTTCATCTATTGAAAAGCTTA
257 TCTTCCAATAA-TAGGAAGATGTTCATCTATTGAAAAGCTTA
1011270 GAATTTCCAG
Statistics
Matches: 251, Mismatches: 41, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
347 3 0.01
348 236 0.94
349 12 0.05
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (348 bp):
CCTCTCTTCAAAACCTGTCAATTGATAGCTACAAGGAATTAGAAGTTCTTCCTATAACCGGAGGT
TGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGAAGACGAATT
ATCTACCTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTCCAA
ACTTGGAAGAATGTTTCTCTCTTAAAAGCCTATCAATTAATAGCTGCAAGGAATTGAAAGTTCTT
CCAATAATAGGAAGATGTTCATCTATTGAAAAGCTTAACATCTTTGGTTGCGAAAAATTAAACAA
GATTGGAGACGGATTATTTACCC
Found at i:1011336 original size:210 final size:209
Alignment explanation
Indices: 1010973--1011642 Score: 862
Period size: 210 Copynumber: 3.2 Consensus size: 209
1010963 TTATTTACCC
* * * * * ** * *
1010973 CCTCTCTTCAAAACCTGTCAATTGATAGTTGCAATGAGTTAGAAGTTCTTTCGTTACCTGGAAGG
1 CCTCTCTTCAAAACCTGTCAATTAATAGCTGCAATGAATTGGAAGTTCTTCCAATAACTGGAAGA
* * *** * *
1011038 TGTTTATCTCTTGAAAAGCTTAGCATTTTTGGTTGCGAAAAAT-TAAGCAAGATTGGAGATGGAT
66 TGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTG-TAAAAATATAAGCAAGATCGGAGATGGAT
* * ** *
1011102 TATCTACCTGCGCTTGTCTCAAAGAATTAGGTCTATATAATTGTCCTAATTTAAGTTCGATTCCA
130 TATCTACCTCCACTTGTCTCAAAGAATTA-GTCTATATCTTTGTTCTAATTTAAGTTCGATTCCA
*
1011167 AATTTGGAAGGAATTTT
194 GATTTGGAAGG-ATTTT
* * *
1011184 -CTCTCTTTAAAGCCTGTCAATTAATAGGTGCAATGAATTGGAAGTTCTTCCAATAACTGGAAGA
1 CCTCTCTTCAAAACCTGTCAATTAATAGCTGCAATGAATTGGAAGTTCTTCCAATAACTGGAAGA
*
1011248 TGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGTAAAAATATAAGCAAGATCGGAGATGGATT
66 TGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGTAAAAATATAAGCAAGATCGGAGATGGATT
* * *
1011313 ATCTACCTCCCCTTGTCTCAAAGAATTA-TATATATCTTTGTTCTAATTTAAGTTTGATTCCAGA
131 ATCTACCTCCACTTGTCTCAAAGAATTAGTCTATATCTTTGTTCTAATTTAAGTTCGATTCCAGA
1011377 TTTGGAAGGATTTT
196 TTTGGAAGGATTTT
* * * * **
1011391 CCTCTCTTCAAAATCTGTCAATTAATAGCTACAACGAATTGGAAGTTCTTCCCATAACAAGAAGA
1 CCTCTCTTCAAAACCTGTCAATTAATAGCTGCAATGAATTGGAAGTTCTTCCAATAACTGGAAGA
***
1011456 TGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGTAAAAATATAAGCAAGATCGGAGGCAGATT
66 TGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGTAAAAATATAAGCAAGATCGGAGATGGATT
* *
1011521 ATCTACCTCCACTTATCTTAAAGAATTAGATCTATATCTTTGTTCTAATTTAAG-TCGGATTCCA
131 ATCTACCTCCACTTGTCTCAAAGAATTAG-TCTATATCTTTGTTCTAATTTAAGTTC-GATTCCA
*
1011585 GATTTTGAAGGATTTT
194 GATTTGGAAGGATTTT
* * * *
1011601 CCTTTCTTCAAAATCTGTCAATTGATAGCTGCAAGGAATTGG
1 CCTCTCTTCAAAACCTGTCAATTAATAGCTGCAATGAATTGG
1011643 CGAGTTTTCA
Statistics
Matches: 404, Mismatches: 50, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
207 5 0.01
208 180 0.45
209 7 0.02
210 212 0.52
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (209 bp):
CCTCTCTTCAAAACCTGTCAATTAATAGCTGCAATGAATTGGAAGTTCTTCCAATAACTGGAAGA
TGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGTAAAAATATAAGCAAGATCGGAGATGGATT
ATCTACCTCCACTTGTCTCAAAGAATTAGTCTATATCTTTGTTCTAATTTAAGTTCGATTCCAGA
TTTGGAAGGATTTT
Found at i:1026544 original size:49 final size:49
Alignment explanation
Indices: 1026427--1026524 Score: 141
Period size: 49 Copynumber: 2.1 Consensus size: 49
1026417 TTACCCTTAC
* * *
1026427 TTTTATAAAATTTTATGA----TAATTAATTTCTAATACTTTTTATAAA
1 TTTTATAAAATTTTATGATTTTTAATTAATTTCTAATAATTTATACAAA
1026472 TTTTATAAAATTTTATGATTTTTAATTAATTTCTAATAATTTATACAAA
1 TTTTATAAAATTTTATGATTTTTAATTAATTTCTAATAATTTATACAAA
1026521 TTTT
1 TTTT
1026525 TATGTTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 18 0.39
49 28 0.61
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (49 bp):
TTTTATAAAATTTTATGATTTTTAATTAATTTCTAATAATTTATACAAA
Found at i:1040381 original size:15 final size:13
Alignment explanation
Indices: 1040354--1040394 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 13
1040344 TAAAGGTATG
1040354 ATTGATAAGGTTGA
1 ATTGATAA-GTTGA
1040368 ATTTGATTAAGTTGA
1 A-TTGA-TAAGTTGA
1040383 ATTGATAAGTTG
1 ATTGATAAGTTG
1040395 GATGTCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
14 5 0.20
15 10 0.40
16 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (13 bp):
ATTGATAAGTTGA
Found at i:1042847 original size:22 final size:23
Alignment explanation
Indices: 1042794--1042849 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
1042784 CCCATTTTTA
* * *
1042794 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
1042817 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
1042839 ATTAAAATTAA
1 ATTAAAATTAA
1042850 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:1042862 original size:16 final size:16
Alignment explanation
Indices: 1042825--1042864 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1042815 TTAATAAAAT
* *
1042825 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
1042841 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
1042857 TAAAATTA
1 TAAAATTA
1042865 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:1042943 original size:59 final size:59
Alignment explanation
Indices: 1042875--1043044 Score: 322
Period size: 59 Copynumber: 2.9 Consensus size: 59
1042865 TCAAATTATT
*
1042875 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1042934 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
1042993 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
1043045 ACAAACTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 109 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:1043148 original size:22 final size:24
Alignment explanation
Indices: 1043108--1043151 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1043098 AAATAAACTT
1043108 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
1043132 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
1043152 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:1051903 original size:25 final size:25
Alignment explanation
Indices: 1051841--1051905 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
1051831 GTCATTAGGG
* * *
1051841 TTACCGAT-TTCAGCTCTTATTAGC
1 TTACCGATATTTAGCTCGTATGAGC
*
1051865 TTACCGATACTTAGCTCGTATGAGC
1 TTACCGATATTTAGCTCGTATGAGC
1051890 TTACC-ATTATTTAGCT
1 TTACCGA-TATTTAGCT
1051906 TGGAGGAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 9 0.26
25 25 0.74
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (25 bp):
TTACCGATATTTAGCTCGTATGAGC
Found at i:1054957 original size:18 final size:18
Alignment explanation
Indices: 1054934--1054994 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
1054924 CCATTAACAC
1054934 TCCATTCTAATTAATCAT
1 TCCATTCTAATTAATCAT
* * *
1054952 TCCATTAGTGCCATTAA-CAC
1 TCCATT-CT--AATTAATCAT
1054972 TCCATTCTAATTAATCAT
1 TCCATTCTAATTAATCAT
1054990 TCCAT
1 TCCAT
1054995 AACTAAAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 5 0.15
18 13 0.39
19 2 0.06
20 8 0.24
21 5 0.15
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.39
Consensus pattern (18 bp):
TCCATTCTAATTAATCAT
Found at i:1054961 original size:38 final size:38
Alignment explanation
Indices: 1054918--1054994 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
1054908 ATACATAAAG
1054918 TTAGTGCCATTAACACTCCATTCTAATTAATCATTCCA
1 TTAGTGCCATTAACACTCCATTCTAATTAATCATTCCA
1054956 TTAGTGCCATTAACACTCCATTCTAATTAATCATTCCA
1 TTAGTGCCATTAACACTCCATTCTAATTAATCATTCCA
1054994 T
1 T
1054995 AACTAAAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (38 bp):
TTAGTGCCATTAACACTCCATTCTAATTAATCATTCCA
Found at i:1059661 original size:2 final size:2
Alignment explanation
Indices: 1059649--1059678 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1059639 ATAATTATGG
*
1059649 GA GA AA 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 GA
1059679 CGTGTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1060281 original size:124 final size:124
Alignment explanation
Indices: 1060061--1060305 Score: 454
Period size: 124 Copynumber: 2.0 Consensus size: 124
1060051 ACCACCAATC
*
1060061 CGGTTTAAAAAACATTAAGATTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTTGAA
1 CGGTTTAAAAAACATTAAGACTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTTGAA
* *
1060126 GTGTATAATTCTATGTACCATCAATCAATTTGATTGTTCTCAATCATTAAGGCTTTATA
66 GTGTATAATTCAATGTACCATCAATCAATTTGATTATTCTCAATCATTAAGGCTTTATA
*
1060185 CGGTTTAAAAAACATTGAGACTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTTGAA
1 CGGTTTAAAAAACATTAAGACTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTTGAA
1060250 GTGTATAATTCAATGTACCATCAATCAATTTGATTATTCTCAATCATTAAGGCTTT
66 GTGTATAATTCAATGTACCATCAATCAATTTGATTATTCTCAATCATTAAGGCTTT
1060306 GCTTGATAGA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 117 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (124 bp):
CGGTTTAAAAAACATTAAGACTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTTGAA
GTGTATAATTCAATGTACCATCAATCAATTTGATTATTCTCAATCATTAAGGCTTTATA
Found at i:1067365 original size:21 final size:21
Alignment explanation
Indices: 1067341--1067381 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1067331 GGGGCTATCA
*
1067341 TACACGGGCGTGTGGGATTTC
1 TACACGGGCGTGTGCGATTTC
1067362 TACACGGGCGTGTGCGATTT
1 TACACGGGCGTGTGCGATTT
1067382 GCCAAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.20, G:0.37, T:0.29
Consensus pattern (21 bp):
TACACGGGCGTGTGCGATTTC
Found at i:1069437 original size:46 final size:46
Alignment explanation
Indices: 1069381--1069486 Score: 114
Period size: 45 Copynumber: 2.4 Consensus size: 46
1069371 AAAATGAATA
*
1069381 GAAATAGAGAAATGGAAAAT-ATTCAAAAATGATTATGGTTTTCTCT
1 GAAAT-GAGAAATGGAAAATCATTCAAAAATGAATATGGTTTTCTCT
*** *
1069427 GAAATGGAGAAAT-G-AAATCATTTGTAAATGAATGTGGTTTTCTCT
1 GAAAT-GAGAAATGGAAAATCATTCAAAAATGAATATGGTTTTCTCT
1069472 -AAAT-AGAAATGGAAA
1 GAAATGAGAAATGGAAA
1069487 TGAGAAATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
42 6 0.12
43 1 0.02
44 10 0.20
45 22 0.43
46 12 0.24
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (46 bp):
GAAATGAGAAATGGAAAATCATTCAAAAATGAATATGGTTTTCTCT
Found at i:1074250 original size:22 final size:22
Alignment explanation
Indices: 1074208--1074248 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1074198 TAATAGGTTA
* *
1074208 ATAAGTTAATAGTAAATAAATG
1 ATAAATTAAAAGTAAATAAATG
1074230 ATAAATTAAAAGT-AATAAA
1 ATAAATTAAAAGTAAATAAA
1074249 ATAACACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (22 bp):
ATAAATTAAAAGTAAATAAATG
Found at i:1075102 original size:25 final size:25
Alignment explanation
Indices: 1075062--1075166 Score: 108
Period size: 25 Copynumber: 4.2 Consensus size: 25
1075052 GTCATTAGGG
*
1075062 TTACCGAT-TTCAGCTCTTATGAGC
1 TTACCGATATTCAGCTCATATGAGC
1075086 TTACCGATATTCAGCTCATATGAGC
1 TTACCGATATTCAGCTCATATGAGC
* *
1075111 TTACCGTTATTCAGCTCGA-AGGAGC
1 TTACCGATATTCAGCTC-ATATGAGC
* ** *
1075136 TTACC-ATTATTCAACTCGGAGGAGC
1 TTACCGA-TATTCAGCTCATATGAGC
1075161 TTACCG
1 TTACCG
1075167 TTTACAACTC
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.11
25 61 0.87
26 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (25 bp):
TTACCGATATTCAGCTCATATGAGC
Found at i:1079632 original size:27 final size:27
Alignment explanation
Indices: 1079501--1079648 Score: 134
Period size: 27 Copynumber: 5.5 Consensus size: 27
1079491 ACATATCAAG
** *
1079501 AAAGAATAGCCTTTGTGGTGAACCCTA
1 AAAGAATAGCCTTTGTGGCAAACTCTA
1079528 AAAGAATAGCCTTTGTGGCAAACTCTA
1 AAAGAATAGCCTTTGTGGCAAACTCTA
* * * *
1079555 AAAGAATAGTCTTTGTAGAAAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTA
* * * **
1079582 GAAGAATATCCTTTGTAGTGAACTCTA
1 AAAGAATAGCCTTTGTGGCAAACTCTA
* * * **
1079609 GAAGAATAACCTTTTTGGCAAACTCCG
1 AAAGAATAGCCTTTGTGGCAAACTCTA
*
1079636 AGAGAATAGCCTT
1 AAAGAATAGCCTT
1079649 AATGACAAAT
Statistics
Matches: 98, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 98 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (27 bp):
AAAGAATAGCCTTTGTGGCAAACTCTA
Found at i:1083030 original size:205 final size:205
Alignment explanation
Indices: 1082671--1083086 Score: 769
Period size: 205 Copynumber: 2.0 Consensus size: 205
1082661 TAAAAAGCTG
* * *
1082671 AAAAATATCCATTAAATCTTTAAAAATCTCCAAAATTTCAAATCTTGAAATTTAGGTTTTTATTT
1 AAAAATATCCATTAAATCTTTAAAAATCCCCAAAATTTCAAATCTAGAAATTTAGGTTTTTATTG
*
1082736 ATCAAGATTTAGCAAGAAAACAAGAGAGAGAAAGATCTTACACAAGCTAGATGCTATGGGCGACA
66 ATCAAGATTTAGCAAGAAAACAAGAGAGAAAAAGATCTTACACAAGCTAGATGCTATGGGCGACA
*
1082801 ATGGCACTTCTTGGAAATAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
131 ATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
1082866 TTAATTAGAT
196 TTAATTAGAT
1082876 AAAAATATCCATTAAATCTTTAAAAATCCCCAAAATTTCAAATCTAGAAATTTAGGTTTTTATTG
1 AAAAATATCCATTAAATCTTTAAAAATCCCCAAAATTTCAAATCTAGAAATTTAGGTTTTTATTG
*
1082941 ATCAAGATTTAGCAAGAAAACTAGAGAGAAAAAGATCTTACACAAGCTAGATGCTATGGGCGACA
66 ATCAAGATTTAGCAAGAAAACAAGAGAGAAAAAGATCTTACACAAGCTAGATGCTATGGGCGACA
*
1083006 ATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTTGGGCTGAT
131 ATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
1083071 TTAATTAGAT
196 TTAATTAGAT
1083081 AAAAAT
1 AAAAAT
1083087 GGCAGCAATA
Statistics
Matches: 204, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
205 204 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (205 bp):
AAAAATATCCATTAAATCTTTAAAAATCCCCAAAATTTCAAATCTAGAAATTTAGGTTTTTATTG
ATCAAGATTTAGCAAGAAAACAAGAGAGAAAAAGATCTTACACAAGCTAGATGCTATGGGCGACA
ATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
TTAATTAGAT
Found at i:1096109 original size:18 final size:18
Alignment explanation
Indices: 1096067--1096109 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1096057 TTCTCATTTT
*
1096067 TAGCAACTTCTTCTTCAA
1 TAGCAACTTCCTCTTCAA
* * *
1096085 CAACAACTTCCTCTTCTA
1 TAGCAACTTCCTCTTCAA
1096103 TAGCAAC
1 TAGCAAC
1096110 AATTTTCTTT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.33
Consensus pattern (18 bp):
TAGCAACTTCCTCTTCAA
Found at i:1100225 original size:44 final size:44
Alignment explanation
Indices: 1100161--1100244 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
1100151 GGGACAAGTG
*
1100161 AAAGTTTTTTTCTCCCGATCCTCTGGTGCAATAGCAATTTTATT
1 AAAGTTTTTTTCTCCCGATCCTCTAGTGCAATAGCAATTTTATT
*
1100205 AAAGTTTTTTTCTCCTGATCCTCTAGTGCAATAGCAATTT
1 AAAGTTTTTTTCTCCCGATCCTCTAGTGCAATAGCAATTT
1100245 GATTGTACCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (44 bp):
AAAGTTTTTTTCTCCCGATCCTCTAGTGCAATAGCAATTTTATT
Found at i:1102300 original size:21 final size:21
Alignment explanation
Indices: 1102259--1102300 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1102249 TATCTGAGTG
***
1102259 TGTTGATTGTAATTTTGTTGT
1 TGTTGATTGTAATTCCCTTGT
1102280 TGTTGATTGTAATTCCCTTGT
1 TGTTGATTGTAATTCCCTTGT
1102301 CTGGGATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.57
Consensus pattern (21 bp):
TGTTGATTGTAATTCCCTTGT
Found at i:1103412 original size:23 final size:23
Alignment explanation
Indices: 1103383--1103429 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1103373 GGAGTATGGT
1103383 TCCATTGTTCCCTGGTATACCCA
1 TCCATTGTTCCCTGGTATACCCA
1103406 TCCATTGTTCCCTGGTATACCCA
1 TCCATTGTTCCCTGGTATACCCA
1103429 T
1 T
1103430 ATTTCTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.34, G:0.13, T:0.36
Consensus pattern (23 bp):
TCCATTGTTCCCTGGTATACCCA
Found at i:1105938 original size:13 final size:13
Alignment explanation
Indices: 1105912--1105952 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1105902 AAATGTCTCC
*
1105912 TTTCATATATCCA
1 TTTCATATAACCA
1105925 TTTCCATA-AACCA
1 TTT-CATATAACCA
1105938 TTTCATATAACCA
1 TTTCATATAACCA
1105951 TT
1 TT
1105953 CTAATTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 4 0.16
13 17 0.68
14 4 0.16
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTCATATAACCA
Found at i:1106040 original size:25 final size:25
Alignment explanation
Indices: 1106012--1106081 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 25
1106002 TATGTGGAAC
* *
1106012 AATGCTCACACAAGCTGTAACTGTA
1 AATGCTCACACAAGCTGTAAATGGA
* *
1106037 AATGCTCACGCAAGCTGTGAAATGGG
1 AATGCTCACACAAGCTGT-AAATGGA
**
1106063 CCTGCTCACACAAGCTGTA
1 AATGCTCACACAAGCTGTA
1106082 GGTCGGGATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
25 18 0.49
26 19 0.51
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (25 bp):
AATGCTCACACAAGCTGTAAATGGA
Found at i:1110391 original size:6 final size:6
Alignment explanation
Indices: 1110380--1110418 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1110370 AATACATATG
1110380 TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA TGG
1 TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA TGG
1110419 AGAGAGGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.15, G:0.51, T:0.18
Consensus pattern (6 bp):
TGGGCA
Found at i:1111582 original size:16 final size:16
Alignment explanation
Indices: 1111561--1111591 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1111551 GCTCCCTTCG
1111561 GTGTTTTAAAGGATAT
1 GTGTTTTAAAGGATAT
1111577 GTGTTTTAAAGGATA
1 GTGTTTTAAAGGATA
1111592 CTATGGCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (16 bp):
GTGTTTTAAAGGATAT
Found at i:1113015 original size:273 final size:273
Alignment explanation
Indices: 1112520--1113208 Score: 1112
Period size: 273 Copynumber: 2.5 Consensus size: 273
1112510 TTCTGTAGGA
* *
1112520 CTTCA-TTCATTTAATTTTTTTACACGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTC
1 CTTCACTT-ATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTC
*
1112584 CCATGAGAG-AAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCAATAAGAAATTTCCTAA
65 CCATGAGAGAAAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCATTAAGAAATTTCCTAA
* *
1112648 AAAGCTATCAATGACTGTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTGTCTCTGTGGTCT
130 AAAGCTATCAATGACTGTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTATCTATGTGGTCT
*
1112713 CTATTATGATGACTGGAAAACAAACTCCTCTATCATTATATGCTTTTGCATACATGTTCACATTT
195 CTATTATGATGACTGGAAAACAAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTT
1112778 TATTTTCCAAGTGG
260 TATTTTCCAAGTGG
*
1112792 CTTCACTTTTTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCC
1 CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCC
1112857 CATGAGAGAAAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCATTAAGAAATTTCCTAAA
66 CATGAGAGAAAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCATTAAGAAATTTCCTAAA
* *
1112922 AAGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTGAAGGAAATGCATTATCTATGTGGTCTC
131 AAGCTATCAATGACTGTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTATCTATGTGGTCTC
*
1112987 TATTATGATGACTGGAAAACGAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTTT
196 TATTATGATGACTGGAAAACAAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTTT
1113052 ATTTTCCAAGTGG
261 ATTTTCCAAGTGG
1113065 CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCA
1 CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTC-
* * * * *** *
1113130 CTCCTAAAAGAAGTAATTTATGTTGTATTGATTGATGTTACAGTTCTTCTGGTTCATTAAGAAAT
65 C-CATGAGAGAA-AAAAAAATGTTGTATTGATTGATG-T----TTCTTTTGGTTCATTAAGAAAT
*
1113195 TTCCTAGAAAGCTA
123 TTCCTAAAAAGCTA
1113209 CAGACTCGAT
Statistics
Matches: 387, Mismatches: 20, Indels: 11
0.93 0.05 0.03
Matches are distributed among these distances:
272 67 0.17
273 257 0.66
274 1 0.00
275 7 0.02
276 20 0.05
277 1 0.00
281 34 0.09
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (273 bp):
CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCC
CATGAGAGAAAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCATTAAGAAATTTCCTAAA
AAGCTATCAATGACTGTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTATCTATGTGGTCTC
TATTATGATGACTGGAAAACAAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTTT
ATTTTCCAAGTGG
Found at i:1116970 original size:22 final size:22
Alignment explanation
Indices: 1116942--1116987 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1116932 TTGATGTGGT
1116942 ATTAAATTATTGGAAAAGAATA
1 ATTAAATTATTGGAAAAGAATA
**
1116964 ATTAAATTATTGGAATGGAATA
1 ATTAAATTATTGGAAAAGAATA
1116986 AT
1 AT
1116988 ATTCATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (22 bp):
ATTAAATTATTGGAAAAGAATA
Found at i:1118600 original size:12 final size:12
Alignment explanation
Indices: 1118585--1118610 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1118575 TAAACTAACC
1118585 TCAAATTCCTGG
1 TCAAATTCCTGG
1118597 TCAAATTCCTGG
1 TCAAATTCCTGG
1118609 TC
1 TC
1118611 CAGATGCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (12 bp):
TCAAATTCCTGG
Found at i:1123352 original size:4 final size:4
Alignment explanation
Indices: 1123343--1123368 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1123333 CCCTGTTTAA
1123343 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1123369 CAAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1126228 original size:22 final size:22
Alignment explanation
Indices: 1126203--1126247 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1126193 TTTAATAAAG
1126203 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
1126225 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
1126247 A
1 A
1126248 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:1130729 original size:22 final size:22
Alignment explanation
Indices: 1130704--1130753 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1130694 TTTAATAAAG
1130704 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
1130726 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
*
1130748 ACAATA
1 AAAATA
1130754 AGTGAAACGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:1142291 original size:29 final size:29
Alignment explanation
Indices: 1142222--1142292 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1142212 TTACAATTCA
* * *
1142222 GACTTATTTGATTCATTTTAATAATATAGG
1 GACTGATTTGA-TCATTTTAATAATAGAAG
* *
1142252 GACTGAATTGATCATTTTAATAATAGAAT
1 GACTGATTTGATCATTTTAATAATAGAAG
1142281 GACT-AGTTTGAT
1 GACTGA-TTTGAT
1142293 ACAGTCCCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.03
29 24 0.71
30 9 0.26
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (29 bp):
GACTGATTTGATCATTTTAATAATAGAAG
Found at i:1142505 original size:12 final size:12
Alignment explanation
Indices: 1142488--1142517 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1142478 TTTTAATCAT
1142488 CACATGGCAACC
1 CACATGGCAACC
*
1142500 CACATGGCAATC
1 CACATGGCAACC
1142512 CACATG
1 CACATG
1142518 TATTTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.37, G:0.17, T:0.13
Consensus pattern (12 bp):
CACATGGCAACC
Found at i:1142624 original size:20 final size:21
Alignment explanation
Indices: 1142571--1142630 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
1142561 ACAAATAATT
*
1142571 TTAAAAAGATTAAAACAAAAATA
1 TTAAAAAG-TTCAAA-AAAAATA
*
1142594 TTTAAAA-TTCAAAAAAAATA
1 TTAAAAAGTTCAAAAAAAATA
*
1142614 -TAAAAAGTTCATAAAAA
1 TTAAAAAGTTCAAAAAAA
1142631 TTCAAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 5 0.16
20 16 0.50
21 5 0.16
23 6 0.19
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (21 bp):
TTAAAAAGTTCAAAAAAAATA
Found at i:1156817 original size:10 final size:10
Alignment explanation
Indices: 1156796--1156825 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1156786 AATAAATAAG
1156796 ATTTAA-ATA
1 ATTTAATATA
1156805 ATTTAATATA
1 ATTTAATATA
1156815 ATTTAATATA
1 ATTTAATATA
1156825 A
1 A
1156826 AATATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTTAATATA
Found at i:1165831 original size:27 final size:27
Alignment explanation
Indices: 1165801--1165864 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
1165791 TCTAAAGTTT
1165801 TACATTTTTTCCTATAATTACTTCTTA
1 TACATTTTTTCCTATAATTACTTCTTA
*
1165828 TACATTTTTTCCTATAGTTACTTCTTA
1 TACATTTTTTCCTATAATTACTTCTTA
1165855 TACATTTTTT
1 TACATTTTTT
1165865 TTACAAAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.02, T:0.58
Consensus pattern (27 bp):
TACATTTTTTCCTATAATTACTTCTTA
Found at i:1165879 original size:154 final size:154
Alignment explanation
Indices: 1165715--1166022 Score: 607
Period size: 154 Copynumber: 2.0 Consensus size: 154
1165705 TAATTTTGAA
*
1165715 AAAGAATATAATATAAAATATTTCAATTGGATTCAATATTTTGGGCCTTCAAACCCAAGTCACCT
1 AAAGAATATAATATAAAATATTTCAATTGAATTCAATATTTTGGGCCTTCAAACCCAAGTCACCT
1165780 CATATTTCTTTTCTAAAGTTTTACATTTTTTCCTATAATTACTTCTTATACATTTTTTCCTATAG
66 CATATTTCTTTTCTAAAGTTTTACATTTTTTCCTATAATTACTTCTTATACATTTTTTCCTATAG
1165845 TTACTTCTTATACATTTTTTTTAC
131 TTACTTCTTATACATTTTTTTTAC
1165869 AAAGAATATAATATAAAATATTTCAATTGAATTCAATATTTTGGGCCTTCAAACCCAAGTCACCT
1 AAAGAATATAATATAAAATATTTCAATTGAATTCAATATTTTGGGCCTTCAAACCCAAGTCACCT
1165934 CATATTTCTTTTCTAAAGTTTTACATTTTTTCCTATAATTACTTCTTATACATTTTTTCCTATAG
66 CATATTTCTTTTCTAAAGTTTTACATTTTTTCCTATAATTACTTCTTATACATTTTTTCCTATAG
1165999 TTACTTCTTATACATTTTTTTTAC
131 TTACTTCTTATACATTTTTTTTAC
1166023 TTTCAACACT
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 153 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (154 bp):
AAAGAATATAATATAAAATATTTCAATTGAATTCAATATTTTGGGCCTTCAAACCCAAGTCACCT
CATATTTCTTTTCTAAAGTTTTACATTTTTTCCTATAATTACTTCTTATACATTTTTTCCTATAG
TTACTTCTTATACATTTTTTTTAC
Found at i:1165985 original size:27 final size:27
Alignment explanation
Indices: 1165955--1166018 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
1165945 TCTAAAGTTT
1165955 TACATTTTTTCCTATAATTACTTCTTA
1 TACATTTTTTCCTATAATTACTTCTTA
*
1165982 TACATTTTTTCCTATAGTTACTTCTTA
1 TACATTTTTTCCTATAATTACTTCTTA
1166009 TACATTTTTT
1 TACATTTTTT
1166019 TTACTTTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.02, T:0.58
Consensus pattern (27 bp):
TACATTTTTTCCTATAATTACTTCTTA
Found at i:1167944 original size:19 final size:20
Alignment explanation
Indices: 1167916--1167955 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1167906 AACAACTTCC
1167916 ATAAAATGATTT-CTAAAAA
1 ATAAAATGATTTCCTAAAAA
*
1167935 ATAAATTGATTTCCTAAAAA
1 ATAAAATGATTTCCTAAAAA
1167955 A
1 A
1167956 GGTAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAAAATGATTTCCTAAAAA
Found at i:1168159 original size:17 final size:18
Alignment explanation
Indices: 1168126--1168165 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1168116 AAAATTTATT
1168126 TTATAATAAGATAATATC
1 TTATAATAAGATAATATC
*
1168144 TTATAATAA-TTAATATC
1 TTATAATAAGATAATATC
1168161 TTATA
1 TTATA
1168166 TAAACTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (18 bp):
TTATAATAAGATAATATC
Found at i:1176742 original size:37 final size:37
Alignment explanation
Indices: 1176691--1176785 Score: 104
Period size: 37 Copynumber: 2.5 Consensus size: 37
1176681 ATTCCAAAAA
*
1176691 TAATATTATTTTAATAGT-TTACTATTAAATTAA-ATT
1 TAATATTATCTTAATAGTATT-CTATTAAATTAATATT
* *
1176727 TAATACTTATCTTAATAGTATTTTATTAATTTAATATT
1 TAATA-TTATCTTAATAGTATTCTATTAAATTAATATT
*
1176765 AAAGTGATTATCTTAATAGTA
1 TAA-T-ATTATCTTAATAGTA
1176786 AATTTAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
36 5 0.10
37 22 0.44
38 7 0.14
39 15 0.30
40 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (37 bp):
TAATATTATCTTAATAGTATTCTATTAAATTAATATT
Found at i:1176836 original size:69 final size:68
Alignment explanation
Indices: 1176716--1176843 Score: 193
Period size: 69 Copynumber: 1.9 Consensus size: 68
1176706 AGTTTACTAT
* * *
1176716 TAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAA
1 TAAATTAAATATAATACTTATCTTAATAATATTATATTAATTTAATATTAAAGTGATTATCTTAA
1176781 TAG
66 TAG
* * *
1176784 TAAATTTAATATAATATTTATCTTTATAAATATTATATTAATTTAATATTAAAGTGATTA
1 TAAATTAAATATAATACTTATCTTAAT-AATATTATATTAATTTAATATTAAAGTGATTA
1176844 AGTTTAATCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
68 23 0.43
69 30 0.57
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (68 bp):
TAAATTAAATATAATACTTATCTTAATAATATTATATTAATTTAATATTAAAGTGATTATCTTAA
TAG
Found at i:1184557 original size:33 final size:33
Alignment explanation
Indices: 1184515--1184583 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
1184505 AGTATTGTTC
1184515 AAGATTTTAGATATCGACATTGTTGAATAGTTT
1 AAGATTTTAGATATCGACATTGTTGAATAGTTT
* *
1184548 AAGATTTTAGATGTTGACATTGTTGAATAGTTT
1 AAGATTTTAGATATCGACATTGTTGAATAGTTT
1184581 AAG
1 AAG
1184584 TATTAGGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.42
Consensus pattern (33 bp):
AAGATTTTAGATATCGACATTGTTGAATAGTTT
Found at i:1185529 original size:16 final size:18
Alignment explanation
Indices: 1185508--1185545 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1185498 GATTGATATT
1185508 GAAATG-ACA-AAGATGA
1 GAAATGAACATAAGATGA
*
1185524 GAAATGAATATAAGATGA
1 GAAATGAACATAAGATGA
1185542 GAAA
1 GAAA
1185546 ATATTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
18 11 0.58
ACGTcount: A:0.58, C:0.03, G:0.24, T:0.16
Consensus pattern (18 bp):
GAAATGAACATAAGATGA
Found at i:1185551 original size:43 final size:43
Alignment explanation
Indices: 1185503--1185588 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
1185493 TATGTGATTG
*
1185503 ATATTGAAATGACAAAGATGAG-AAATGAATATAAGATGAGAAA
1 ATATTGAAATGACAAAGAT-AGTAAATGAATATAAAATGAGAAA
* *
1185546 ATATTGAAATGGCAAAGATAGTAATTGAATATAAAATGAGAAA
1 ATATTGAAATGACAAAGATAGTAAATGAATATAAAATGAGAAA
1185589 TAAAATATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 2 0.05
43 37 0.95
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.23
Consensus pattern (43 bp):
ATATTGAAATGACAAAGATAGTAAATGAATATAAAATGAGAAA
Found at i:1185601 original size:19 final size:20
Alignment explanation
Indices: 1185573--1185620 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1185563 ATAGTAATTG
*
1185573 AATATAAAATGA-GAAATAA
1 AATATGAAATGATGAAATAA
1185592 AATATGAAATGATGAAATAA
1 AATATGAAATGATGAAATAA
*
1185612 GATATGAAA
1 AATATGAAA
1185621 CTTGAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
AATATGAAATGATGAAATAA
Found at i:1189725 original size:12 final size:12
Alignment explanation
Indices: 1189707--1189738 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1189697 ATGCTCCGTA
1189707 TCATCCTCCTCT
1 TCATCCTCCTCT
*
1189719 TCCTCCTCCTCT
1 TCATCCTCCTCT
1189731 TCATCCTC
1 TCATCCTC
1189739 ATTATCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.53, G:0.00, T:0.41
Consensus pattern (12 bp):
TCATCCTCCTCT
Found at i:1191627 original size:22 final size:20
Alignment explanation
Indices: 1191585--1191627 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
1191575 ATCTTGCTGG
**
1191585 AAATTGTTGGTTGAGTTATT
1 AAATTGTTGGTTGAGAAATT
1191605 AAATTGTATGGTATGAGAAATT
1 AAATTGT-TGGT-TGAGAAATT
1191627 A
1 A
1191628 TTACTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (20 bp):
AAATTGTTGGTTGAGAAATT
Found at i:1197468 original size:18 final size:17
Alignment explanation
Indices: 1197435--1197473 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1197425 TTTTATAAAT
1197435 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
1197453 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
1197470 TGTG
1 TGTG
1197474 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:1197608 original size:8 final size:8
Alignment explanation
Indices: 1197595--1197620 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1197585 TAGAGACCAA
1197595 TGTTACAG
1 TGTTACAG
1197603 TGTTACAG
1 TGTTACAG
1197611 TGTTACAG
1 TGTTACAG
1197619 TG
1 TG
1197621 AGTCCCGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (8 bp):
TGTTACAG
Found at i:1197737 original size:23 final size:23
Alignment explanation
Indices: 1197707--1197759 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1197697 AGTGTTATTG
1197707 ATCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
*
1197730 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
1197753 ATCAGTG
1 ATCAGTG
1197760 TGGCACTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:1202577 original size:2 final size:2
Alignment explanation
Indices: 1202570--1202626 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1202560 AGCTTCGTGT
1202570 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1202612 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
1202627 TTTATATATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1202940 original size:10 final size:10
Alignment explanation
Indices: 1202925--1202961 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1202915 GTAACCATCA
*
1202925 TCTCTCTCTC
1 TCTCTCTGTC
1202935 TCTCTCTGTC
1 TCTCTCTGTC
1202945 TCTCTCTGTC
1 TCTCTCTGTC
*
1202955 TGTCTCT
1 TCTCTCT
1202962 ACAGCTGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.00, C:0.41, G:0.08, T:0.51
Consensus pattern (10 bp):
TCTCTCTGTC
Found at i:1202948 original size:14 final size:14
Alignment explanation
Indices: 1202929--1202961 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1202919 CCATCATCTC
1202929 TCTCTCTCTCTCTG
1 TCTCTCTCTCTCTG
*
1202943 TCTCTCTCTGTCTG
1 TCTCTCTCTCTCTG
1202957 TCTCT
1 TCTCT
1202962 ACAGCTGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.39, G:0.09, T:0.52
Consensus pattern (14 bp):
TCTCTCTCTCTCTG
Found at i:1212331 original size:27 final size:27
Alignment explanation
Indices: 1212301--1212355 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1212291 GAGGATAATG
1212301 TAAGGATATTAGGGATTGAATCAAAGT
1 TAAGGATATTAGGGATTGAATCAAAGT
1212328 TAAGGATATTAGGGATTGAATCAAAGT
1 TAAGGATATTAGGGATTGAATCAAAGT
1212355 T
1 T
1212356 CTTTTTTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (27 bp):
TAAGGATATTAGGGATTGAATCAAAGT
Found at i:1212805 original size:20 final size:21
Alignment explanation
Indices: 1212782--1212826 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1212772 GTTTAAAAAA
*
1212782 ATAAAA-AAATATTAAATTTT
1 ATAAAAGAAATAATAAATTTT
* *
1212802 ATAAAAGGAATAATAATTTTT
1 ATAAAAGAAATAATAAATTTT
1212823 ATAA
1 ATAA
1212827 TATTTATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
ATAAAAGAAATAATAAATTTT
Found at i:1213135 original size:10 final size:10
Alignment explanation
Indices: 1213120--1213167 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
1213110 TATTTTATTA
1213120 TTTTTATAAC
1 TTTTTATAAC
1213130 TTTTTA-ATAC
1 TTTTTATA-AC
*
1213140 TTTTAATAAC
1 TTTTTATAAC
*
1213150 TTTTTATAAA
1 TTTTTATAAC
1213160 TTTTTATA
1 TTTTTATA
1213168 TACAACTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 1 0.03
10 31 0.94
11 1 0.03
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTTATAAC
Found at i:1213182 original size:34 final size:35
Alignment explanation
Indices: 1213138--1213204 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
1213128 ACTTTTTAAT
* *
1213138 ACTTTTAATAACTTTTTATA-AATTTTTATATACA
1 ACTTTCAATAAATTTTTATATAATTTTTATATACA
* *
1213172 ACTTTCAATAAATTTTTTTATAGTTTTTATATA
1 ACTTTCAATAAATTTTTATATAATTTTTATATA
1213205 TTTTTGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 17 0.61
35 11 0.39
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.55
Consensus pattern (35 bp):
ACTTTCAATAAATTTTTATATAATTTTTATATACA
Found at i:1213209 original size:10 final size:10
Alignment explanation
Indices: 1213104--1213169 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 10
1213094 AATTTTCTTA
1213104 TATATATATTT
1 TATATAT-TTT
1213115 TAT-TATTTT
1 TATATATTTT
1213124 TATA-ACTTTT
1 TATATA-TTTT
*
1213134 TA-ATACTTT
1 TATATATTTT
1213143 TA-ATAACTTTT
1 TATAT-A-TTTT
*
1213154 TATAAATTTT
1 TATATATTTT
1213164 TATATA
1 TATATA
1213170 CAACTTTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
9 15 0.33
10 20 0.44
11 9 0.20
12 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.61
Consensus pattern (10 bp):
TATATATTTT
Found at i:1213279 original size:10 final size:10
Alignment explanation
Indices: 1213236--1213326 Score: 82
Period size: 10 Copynumber: 9.3 Consensus size: 10
1213226 TCTAAATTTA
*
1213236 TTTATAGTAT
1 TTTATAATAT
1213246 TTATATAATAT
1 TT-TATAATAT
*
1213257 TTTCAT-ATTT
1 TTT-ATAATAT
*
1213267 TTTATAACAT
1 TTTATAATAT
1213277 TTTATAATA-
1 TTTATAATAT
*
1213286 TTTAAAATAT
1 TTTATAATAT
*
1213296 CTTATAATAT
1 TTTATAATAT
*
1213306 TGTATAAT-T
1 TTTATAATAT
1213315 TTTATAA-AT
1 TTTATAATAT
1213324 TTT
1 TTT
1213327 CTTTGTAATG
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
9 21 0.32
10 33 0.51
11 11 0.17
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (10 bp):
TTTATAATAT
Found at i:1213319 original size:19 final size:19
Alignment explanation
Indices: 1213236--1213325 Score: 67
Period size: 19 Copynumber: 4.6 Consensus size: 19
1213226 TCTAAATTTA
*
1213236 TTTATAGTATTTATATAATAT
1 TTTATAATATTTA-A-AATAT
* * * *
1213257 TTTCATATTTTTTATAACAT
1 TTT-ATAATATTTAAAATAT
1213277 TTTATAATATTTAAAATAT
1 TTTATAATATTTAAAATAT
* *
1213296 CTTATAATATTGTATAAT-T
1 TTTATAATATT-TAAAATAT
1213315 TTTATAA-ATTT
1 TTTATAATATTT
1213326 TCTTTGTAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
17 1 0.02
18 3 0.05
19 29 0.52
20 12 0.21
21 3 0.05
22 8 0.14
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTATAATATTTAAAATAT
Found at i:1213755 original size:38 final size:38
Alignment explanation
Indices: 1213712--1213784 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
1213702 CTTTAAAATC
* *
1213712 AAACCTTGAAAAGGTAAATAGATATTTAT-TTAAAGCAT
1 AAACCTTAAAAAAGTAAATAGATATTT-TCTTAAAGCAT
**
1213750 AAACCTTAAAAAAGTAGGTAGATATTTTCTTAAAG
1 AAACCTTAAAAAAGTAAATAGATATTTTCTTAAAG
1213785 TATGAGAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 1 0.03
38 29 0.97
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.32
Consensus pattern (38 bp):
AAACCTTAAAAAAGTAAATAGATATTTTCTTAAAGCAT
Found at i:1223847 original size:4 final size:4
Alignment explanation
Indices: 1223829--1223863 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1223819 TGAAAAAGGT
*
1223829 TAAA GAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1223864 ATAGTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:1225002 original size:33 final size:33
Alignment explanation
Indices: 1224960--1225025 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1224950 TATAGGATTT
*
1224960 GTTGCTTCAATCTACTCTACTGCAATTTCAGGG
1 GTTGCTTCAATCTACTCTACTGCAACTTCAGGG
*
1224993 GTTGCTTCAATCTACTCTACTTCAACTTCAGGG
1 GTTGCTTCAATCTACTCTACTGCAACTTCAGGG
1225026 AGATTAGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (33 bp):
GTTGCTTCAATCTACTCTACTGCAACTTCAGGG
Found at i:1225050 original size:44 final size:44
Alignment explanation
Indices: 1224996--1225131 Score: 141
Period size: 44 Copynumber: 3.1 Consensus size: 44
1224986 TTCAGGGGTT
* *
1224996 GCTTCAATCTACTCTACTTCAACTTCAGGGAGATTAGACTCGTA
1 GCTTTAATCTACTCTACTTCAACTTCAGGGAGATAAGACTCGTA
* * * * *
1225040 GCTTTAATCTACTCCACTGCAACTTTAGGAAGATGAGACTCGTA
1 GCTTTAATCTACTCTACTTCAACTTCAGGGAGATAAGACTCGTA
* * * *
1225084 TCTTTAATCTACT-T-CATTGCAACTTCAAGGAGATAAGATTTGTA
1 GCTTTAATCTACTCTAC-TT-CAACTTCAGGGAGATAAGACTCGTA
1225128 GCTT
1 GCTT
1225132 GTAGTTTTAA
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 72 0.97
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (44 bp):
GCTTTAATCTACTCTACTTCAACTTCAGGGAGATAAGACTCGTA
Found at i:1225366 original size:44 final size:45
Alignment explanation
Indices: 1225273--1225538 Score: 254
Period size: 44 Copynumber: 6.0 Consensus size: 45
1225263 AAGATTTGTA
* * ** * *
1225273 ATTTGTAACTTTAATCTGTTCCATTGTAACTTTCAGGGAAATAAG
1 ATTTGTAGCTTTAATATACTCCATTGCAACTTTCAGGGAGATAAG
* * *
1225318 ATTTGTAGTTTTAATATGCTCCATTGCAA-TTTCAAGGAGATAAG
1 ATTTGTAGCTTTAATATACTCCATTGCAACTTTCAGGGAGATAAG
* * * * * *
1225362 ATTTGTGGCTTTAATATGCTCCACTGCAAC-TTCAAGGAGACAAT
1 ATTTGTAGCTTTAATATACTCCATTGCAACTTTCAGGGAGATAAG
* ** * * * *
1225406 ATTTGTATCTCCAATATACTCTACTGTAACTTT-AGGGAAATAAG
1 ATTTGTAGCTTTAATATACTCCATTGCAACTTTCAGGGAGATAAG
* * *
1225450 ATTTGTAACTTCAATCTACTCCATTGCAACTTT-AGGGAGATAAG
1 ATTTGTAGCTTTAATATACTCCATTGCAACTTTCAGGGAGATAAG
* *
1225494 ATTTGTGGCTTTAATCTACTCCATTGCAAC-TTCAGGGAGATAAG
1 ATTTGTAGCTTTAATATACTCCATTGCAACTTTCAGGGAGATAAG
1225538 A
1 A
1225539 CTCATCACGA
Statistics
Matches: 185, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
43 2 0.01
44 157 0.85
45 26 0.14
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (45 bp):
ATTTGTAGCTTTAATATACTCCATTGCAACTTTCAGGGAGATAAG
Found at i:1233556 original size:19 final size:20
Alignment explanation
Indices: 1233534--1233578 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1233524 TTATGAAGCT
1233534 TAATGCAGATG-ATGAAATG
1 TAATGCAGATGAATGAAATG
* *
1233553 TAATGCTGATGAATGACATG
1 TAATGCAGATGAATGAAATG
1233573 -AATGCA
1 TAATGCA
1233579 AATAGAGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (20 bp):
TAATGCAGATGAATGAAATG
Found at i:1235445 original size:42 final size:43
Alignment explanation
Indices: 1235345--1235447 Score: 122
Period size: 42 Copynumber: 2.4 Consensus size: 43
1235335 GTCCACGTCT
* *
1235345 CAGAC-GAGCTCTTACATGTAATCAAATATCGATGCCACTGTCC
1 CAGACAGAG-TCTTACACGTAATCAAATATCGATGCCAATGTCC
* * *
1235388 GAGACAGAGTTTTACACGTAATCATATA-CGATGCCAATGTCC
1 CAGACAGAGTCTTACACGTAATCAAATATCGATGCCAATGTCC
1235430 CAGACATG-GTCTTACACG
1 CAGACA-GAGTCTTACACG
1235448 AGGTCTTACA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
42 27 0.53
43 21 0.41
44 3 0.06
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
CAGACAGAGTCTTACACGTAATCAAATATCGATGCCAATGTCC
Found at i:1240481 original size:18 final size:17
Alignment explanation
Indices: 1240459--1240504 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1240449 ATAAATAAAT
*
1240459 AAATAAAAATGATAATA
1 AAATAAAAATGACAATA
*
1240476 ATAATAACAATGACAATA
1 A-AATAAAAATGACAATA
*
1240494 AAATATAAATG
1 AAATAAAAATG
1240505 TATATAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (17 bp):
AAATAAAAATGACAATA
Found at i:1240588 original size:12 final size:12
Alignment explanation
Indices: 1240557--1240597 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1240547 AAGGTTAAAG
*
1240557 AAATAATAAA-G
1 AAATAATAAATA
1240568 AAATAAATAAATA
1 AAAT-AATAAATA
1240581 AAATAATAAATA
1 AAATAATAAATA
1240593 AAATA
1 AAATA
1240598 GTTTGTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 4 0.15
12 19 0.70
13 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
AAATAATAAATA
Found at i:1246128 original size:25 final size:25
Alignment explanation
Indices: 1246091--1246222 Score: 185
Period size: 25 Copynumber: 5.3 Consensus size: 25
1246081 CGGACACACC
* *
1246091 ACAGCTCGTATGAGCTTCTCGTTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
1246116 ACAGCTCGCATGAGCTTCCCGTTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
* *
1246141 ATAGCTCGCATGAGCTTCTCGTTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
1246166 ACAGCT-GCATGAGCTTCCCGTTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
***
1246190 TTGGCTCGCATGAGCTTCCCGTTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
*
1246215 TCAGCTCG
1 ACAGCTCG
1246223 GAGGAGTTTC
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
24 20 0.21
25 75 0.79
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (25 bp):
ACAGCTCGCATGAGCTTCCCGTTAT
Found at i:1246197 original size:49 final size:50
Alignment explanation
Indices: 1246093--1246222 Score: 208
Period size: 49 Copynumber: 2.6 Consensus size: 50
1246083 GACACACCAC
*
1246093 AGCTCGTATGAGCTTCTCGTTATACAGCTCGCATGAGCTTCCCGTTATAT
1 AGCTCGCATGAGCTTCTCGTTATACAGCTCGCATGAGCTTCCCGTTATAT
*
1246143 AGCTCGCATGAGCTTCTCGTTATACAGCT-GCATGAGCTTCCCGTTATTT
1 AGCTCGCATGAGCTTCTCGTTATACAGCTCGCATGAGCTTCCCGTTATAT
* * *
1246192 GGCTCGCATGAGCTTCCCGTTATTCAGCTCG
1 AGCTCGCATGAGCTTCTCGTTATACAGCTCG
1246223 GAGGAGTTTC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
49 45 0.61
50 29 0.39
ACGTcount: A:0.18, C:0.28, G:0.22, T:0.33
Consensus pattern (50 bp):
AGCTCGCATGAGCTTCTCGTTATACAGCTCGCATGAGCTTCCCGTTATAT
Found at i:1253307 original size:25 final size:25
Alignment explanation
Indices: 1253209--1253303 Score: 109
Period size: 25 Copynumber: 3.8 Consensus size: 25
1253199 ACATCACAGT
* * *
1253209 TCGCATGAGCTTCTCGTTATACAAC
1 TCGCATGAGCTTCCCGTTATATAGC
* * *
1253234 TCACATGAGTTTTCCGTTATATAGC
1 TCGCATGAGCTTCCCGTTATATAGC
* * *
1253259 TCGTATGAGCTTCCCATTATTTAGC
1 TCGCATGAGCTTCCCGTTATATAGC
1253284 TCGCATGAGCTTCCCGTTAT
1 TCGCATGAGCTTCCCGTTAT
1253304 TTAGTTCAGA
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (25 bp):
TCGCATGAGCTTCCCGTTATATAGC
Found at i:1253318 original size:25 final size:25
Alignment explanation
Indices: 1253250--1253322 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
1253240 GAGTTTTCCG
* * *
1253250 TTATATAGCTCGTATGAGCTTCCCA
1 TTATTTAGCTCGCAGGAGCTTCCCA
* *
1253275 TTATTTAGCTCGCATGAGCTTCCCG
1 TTATTTAGCTCGCAGGAGCTTCCCA
*
1253300 TTATTTAGTTCAG-AGGAGCTTCC
1 TTATTTAGCTC-GCAGGAGCTTCC
1253323 TGTTTACAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 41 0.98
26 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (25 bp):
TTATTTAGCTCGCAGGAGCTTCCCA
Found at i:1255750 original size:136 final size:136
Alignment explanation
Indices: 1255506--1255769 Score: 429
Period size: 136 Copynumber: 1.9 Consensus size: 136
1255496 AAAATTCCCC
* * * *
1255506 TTACTTATAACTTTTAAAAGAATAGTGATATAAACGCTTAGCAAATACATTCAAATAGTTATTTG
1 TTACTCATAACTTTCAAAAGAATAGTGATATAAACGCTTAGCAAATACATTCAAATACTCATTTG
1255571 AAAGACTAGTATTCAAGATTGAATACGTAGAATATGAGAAAGTATGTAATGTTTTCATGAGGGGG
66 AAAGACTAGTATTCAAGATTGAATACGTAGAATATGAGAAAGTATGTAATGTTTTCATGAGGGGG
1255636 AACCCT
131 AACCCT
* * * *
1255642 TTACTCATGACTTTCAAAAGAATGGTGATATAAATGCTTAGCAAATACATTTAAATACTCATTTG
1 TTACTCATAACTTTCAAAAGAATAGTGATATAAACGCTTAGCAAATACATTCAAATACTCATTTG
* * *
1255707 AAAGATTAGTATTCAAGATTGAATACGTAGAATATGAGGAAGTATGTGATGTTTTCATGAGGG
66 AAAGACTAGTATTCAAGATTGAATACGTAGAATATGAGAAAGTATGTAATGTTTTCATGAGGG
1255770 AGAGTAAATA
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
136 117 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (136 bp):
TTACTCATAACTTTCAAAAGAATAGTGATATAAACGCTTAGCAAATACATTCAAATACTCATTTG
AAAGACTAGTATTCAAGATTGAATACGTAGAATATGAGAAAGTATGTAATGTTTTCATGAGGGGG
AACCCT
Found at i:1256452 original size:25 final size:25
Alignment explanation
Indices: 1256424--1256473 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1256414 ATATAGTTTT
1256424 TATATTAT-TTATAAATGTTATAATA
1 TATATTATATTAT-AATGTTATAATA
1256449 TATATTATATTATAATGTTATAATA
1 TATATTATATTATAATGTTATAATA
1256474 AAACAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
TATATTATATTATAATGTTATAATA
Found at i:1256537 original size:5 final size:5
Alignment explanation
Indices: 1256527--1256552 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1256517 AACTGAAACT
1256527 AAAGA AAAGA AAAGA AAAGA AAAGA A
1 AAAGA AAAGA AAAGA AAAGA AAAGA A
1256553 GAAAAACCTA
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:1257448 original size:43 final size:43
Alignment explanation
Indices: 1257361--1257489 Score: 129
Period size: 43 Copynumber: 3.0 Consensus size: 43
1257351 CATAGGATTC
* * *
1257361 CGATATGTGTTTTCGTGTAAGACCACATCTGGGATGTTGGCAT
1 CGATATGTGTTTACGTGTAAGACCACATCTGGGAAGTTGACAT
*
1257404 CGACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGACAT
1 CGA-TATGTGTTTACGTGTAAGACCAC-ATCTGGGA-AGTTGACAT
* * * * *
1257447 CGATATGTGATTACATGTAAGACCACGTCCGGGACGTTGACAT
1 CGATATGTGTTTACGTGTAAGACCACATCTGGGAAGTTGACAT
1257490 TGTACAAGCC
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.04
43 66 0.92
44 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
CGATATGTGTTTACGTGTAAGACCACATCTGGGAAGTTGACAT
Found at i:1259731 original size:16 final size:16
Alignment explanation
Indices: 1259700--1259746 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1259690 TGCTTTCTCT
*
1259700 TTTGTTCTCCTATTTTC
1 TTTGTTCT-TTATTTTC
1259717 TTTGTTCTTTATTTTC
1 TTTGTTCTTTATTTTC
* *
1259733 TATCTT-TTTATTTT
1 TTTGTTCTTTATTTT
1259747 ATAACAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 8 0.30
16 11 0.41
17 8 0.30
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (16 bp):
TTTGTTCTTTATTTTC
Found at i:1269818 original size:34 final size:35
Alignment explanation
Indices: 1269774--1269840 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1269764 TGGTAAAATG
* *
1269774 TTTTCCGTAAAATGATTT-TTGGAAAATGTTTTGT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTGT
*
1269808 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
1269841 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTGT
Found at i:1269899 original size:32 final size:32
Alignment explanation
Indices: 1269821--1269905 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 32
1269811 TCTGTAAAAT
* * *
1269821 GATTTACTGGAAAATATTTTCTGGTGTTTGGTA
1 GATTT-CTTGAAAATATTTTCTGCTGTTTGGCA
* * *
1269854 AATCTGTAT-AAAATATTTTCTGCTGTTTGGCA
1 GATTTCT-TGAAAATATTTTCTGCTGTTTGGCA
1269886 GATTTCTTGAAAATATTTTC
1 GATTTCTTGAAAATATTTTC
1269906 CGAAAAAGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
31 1 0.02
32 37 0.90
33 3 0.07
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (32 bp):
GATTTCTTGAAAATATTTTCTGCTGTTTGGCA
Found at i:1271219 original size:35 final size:36
Alignment explanation
Indices: 1271173--1271241 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
1271163 TGTCAATCAT
1271173 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
1271208 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1271242 TCTAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:1271239 original size:27 final size:28
Alignment explanation
Indices: 1271209--1271278 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
1271199 AATAATAAAT
*
1271209 TCAATATCCAACAAGCTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
1271236 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
1271264 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
1271279 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:1275384 original size:28 final size:27
Alignment explanation
Indices: 1275352--1275419 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
1275342 AAGCTTTGAG
1275352 GAATGGAAAATGTCTACTGCTTAGA-AGA
1 GAATGGAAAATGTCT-CTGCTTAGAGA-A
1275380 GAATGGAAAATG--TCTGCTTAGAGAA
1 GAATGGAAAATGTCTCTGCTTAGAGAA
1275405 GAATGGAAAATGTCT
1 GAATGGAAAATGTCT
1275420 TACCAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
25 22 0.59
26 2 0.05
27 1 0.03
28 12 0.32
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.25
Consensus pattern (27 bp):
GAATGGAAAATGTCTCTGCTTAGAGAA
Found at i:1281125 original size:2 final size:2
Alignment explanation
Indices: 1281118--1281146 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1281108 AGCAGAATTT
1281118 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 T
1281147 GGAATTGTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1284557 original size:40 final size:40
Alignment explanation
Indices: 1284508--1284671 Score: 197
Period size: 40 Copynumber: 4.1 Consensus size: 40
1284498 AGTGTTATCA
* *
1284508 ATCCGACTAGTGATGGACACACATTTGATATTGTAGGTTT
1 ATCCAACTAGTGATGGGCACACATTTGATATTGTAGGTTT
* *
1284548 ATCCAACTAGTGCTGGGCACACATTTGATATTGTTGGTTT
1 ATCCAACTAGTGATGGGCACACATTTGATATTGTAGGTTT
* *
1284588 ATCCGACTAG-CACTGGGCACACATTTGATATTGTTA-GTTT
1 ATCCAACTAGTGA-TGGGCACACATTTGATATTG-TAGGTTT
* ** * *
1284628 ATCTAACTAGTTCTAGGCACACATTTGATATTGTCGGTTT
1 ATCCAACTAGTGATGGGCACACATTTGATATTGTAGGTTT
1284668 ATCC
1 ATCC
1284672 GGCTAGCGCT
Statistics
Matches: 105, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 103 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (40 bp):
ATCCAACTAGTGATGGGCACACATTTGATATTGTAGGTTT
Found at i:1284609 original size:80 final size:80
Alignment explanation
Indices: 1284508--1284688 Score: 258
Period size: 80 Copynumber: 2.3 Consensus size: 80
1284498 AGTGTTATCA
* * *
1284508 ATCCGACTAGTGA-TGGACACACATTTGATATTG-TAGGTTTATCCAACTAGTGCTGGGCACACA
1 ATCCGACTAG-CACTGGGCACACATTTGATATTGTTA-GTTTATCCAACTAGTGCTAGGCACACA
*
1284571 TTTGATATTGTTGGTTT
64 TTTGATATTGTCGGTTT
* *
1284588 ATCCGACTAGCACTGGGCACACATTTGATATTGTTAGTTTATCTAACTAGTTCTAGGCACACATT
1 ATCCGACTAGCACTGGGCACACATTTGATATTGTTAGTTTATCCAACTAGTGCTAGGCACACATT
1284653 TGATATTGTCGGTTT
66 TGATATTGTCGGTTT
* *
1284668 ATCCGGCTAGCGCTGGGCACA
1 ATCCGACTAGCACTGGGCACA
1284689 AAAAATTATC
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 1 0.01
80 88 0.97
81 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (80 bp):
ATCCGACTAGCACTGGGCACACATTTGATATTGTTAGTTTATCCAACTAGTGCTAGGCACACATT
TGATATTGTCGGTTT
Found at i:1284687 original size:40 final size:40
Alignment explanation
Indices: 1284525--1284688 Score: 220
Period size: 40 Copynumber: 4.1 Consensus size: 40
1284515 TAGTGATGGA
* *
1284525 CACACATTTGATATTGTAGGTTTATCCAACTAGTGCTGGG
1 CACACATTTGATATTGTTGGTTTATCCAACTAGCGCTGGG
* *
1284565 CACACATTTGATATTGTTGGTTTATCCGACTAGCACTGGG
1 CACACATTTGATATTGTTGGTTTATCCAACTAGCGCTGGG
* * ** *
1284605 CACACATTTGATATTGTTAGTTTATCTAACTAGTTCTAGG
1 CACACATTTGATATTGTTGGTTTATCCAACTAGCGCTGGG
* **
1284645 CACACATTTGATATTGTCGGTTTATCCGGCTAGCGCTGGG
1 CACACATTTGATATTGTTGGTTTATCCAACTAGCGCTGGG
1284685 CACA
1 CACA
1284689 AAAAATTATC
Statistics
Matches: 106, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 106 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (40 bp):
CACACATTTGATATTGTTGGTTTATCCAACTAGCGCTGGG
Found at i:1291507 original size:21 final size:20
Alignment explanation
Indices: 1291481--1291519 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1291471 AATAAATACC
*
1291481 AAAAATTTATTTTAAAAATT
1 AAAAAATTATTTTAAAAATT
1291501 AAAAAATTATTTTAAAAAT
1 AAAAAATTATTTTAAAAAT
1291520 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAAATTATTTTAAAAATT
Found at i:1291539 original size:39 final size:39
Alignment explanation
Indices: 1291494--1291597 Score: 156
Period size: 39 Copynumber: 2.6 Consensus size: 39
1291484 AATTTATTTT
1291494 AAAAATTAAAAAATTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAATTATTTTAAAAATATTTTAAAATTAA
1291533 AAAAATT-AAAAATGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAT-TATTTTAAAAATATTTTAAAATTAA
* *
1291572 AAAATTTTAAAAAAAGTATTTTAAAA
1 AAAA-ATT-AAAAAATTATTTTAAAA
1291598 TTAAAAAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
38 6 0.10
39 36 0.61
40 2 0.03
41 10 0.17
42 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (39 bp):
AAAAATTAAAAAATTATTTTAAAAATATTTTAAAATTAA
Found at i:1291556 original size:20 final size:19
Alignment explanation
Indices: 1291481--1291558 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 19
1291471 AATAAATACC
1291481 AAAAATTTATTTTAAAAATT
1 AAAAA-TTATTTTAAAAATT
1291501 AAAAAATTATTTTAAAAATATTT
1 -AAAAATTATTTT-AAAA-A-TT
* *
1291524 TAAAATTA---AAAAAATT
1 AAAAATTATTTTAAAAATT
1291540 AAAAATGTATTTTAAAAAT
1 AAAAAT-TATTTTAAAAAT
1291559 ATTTTAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
16 7 0.15
17 3 0.07
18 4 0.09
20 13 0.28
21 9 0.20
22 8 0.17
23 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (19 bp):
AAAAATTATTTTAAAAATT
Found at i:1291570 original size:30 final size:29
Alignment explanation
Indices: 1291534--1291605 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 29
1291524 TAAAATTAAA
1291534 AAAATTAAAAATGTATTTT-AAAAA-TATTTT
1 AAAATTAAAAA---ATTTTAAAAAAGTATTTT
1291564 AAAATTAAAAAATTTTAAAAAAAGTATTTT
1 AAAATTAAAAAATTTT-AAAAAAGTATTTT
1291594 AAAATTAAAAAA
1 AAAATTAAAAAA
1291606 ATAAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
27 5 0.13
29 5 0.13
30 29 0.74
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTAAAAAATTTTAAAAAAGTATTTT
Found at i:1291614 original size:30 final size:29
Alignment explanation
Indices: 1291553--1291618 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 29
1291543 AATGTATTTT
* *
1291553 AAAAATATTTTAAAATTAAAAAATTTTAAA
1 AAAAATATTTTAAAATTAAAAAA-ATAAAA
*
1291583 AAAAGTATTTTAAAATTAAAAAAATAAAA
1 AAAAATATTTTAAAATTAAAAAAATAAAA
1291612 AAAAATA
1 AAAAATA
1291619 AAAATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 10 0.31
30 22 0.69
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAAATATTTTAAAATTAAAAAAATAAAA
Found at i:1297530 original size:21 final size:21
Alignment explanation
Indices: 1297491--1297530 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1297481 AAATTTAAGA
*
1297491 GTTTAGAATCTTAGGTTTTGG
1 GTTTAGAATCTTAGATTTTGG
1297512 GTTTAGAAT-TTAGAATTTT
1 GTTTAGAATCTTAG-ATTTT
1297531 AGCATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.50
Consensus pattern (21 bp):
GTTTAGAATCTTAGATTTTGG
Found at i:1297572 original size:21 final size:21
Alignment explanation
Indices: 1297534--1297573 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1297524 GAATTTTAGC
* *
1297534 ATTTATTTATGATGAATTATT
1 ATTTAATTATGATCAATTATT
*
1297555 ATTTAATTATGTTCAATTA
1 ATTTAATTATGATCAATTA
1297574 AAATGATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTTAATTATGATCAATTATT
Found at i:1299266 original size:22 final size:22
Alignment explanation
Indices: 1299241--1299289 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1299231 AATAAATACC
*
1299241 AAAAATTTATTTTAAAAATTAAA
1 AAAAATGTATTTT-AAAATTAAA
*
1299264 AAAAAAGTATTTTAAAATTAAA
1 AAAAATGTATTTTAAAATTAAA
1299286 AAAA
1 AAAA
1299290 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAATGTATTTTAAAATTAAA
Found at i:1304038 original size:9 final size:9
Alignment explanation
Indices: 1304024--1304053 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1304014 GTTAAACGAA
1304024 TCGAGTTAT
1 TCGAGTTAT
*
1304033 TCGAGTTAA
1 TCGAGTTAT
1304042 TCGAGTTAT
1 TCGAGTTAT
1304051 TCG
1 TCG
1304054 GATCAACTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:1304126 original size:9 final size:9
Alignment explanation
Indices: 1304107--1304143 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1304097 TGAGTTTTCG
*
1304107 AATTTGAAT
1 AATTCGAAT
*
1304116 AACTCGAAT
1 AATTCGAAT
1304125 AATTCGAAT
1 AATTCGAAT
1304134 AATTCGAAT
1 AATTCGAAT
1304143 A
1 A
1304144 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1307247 original size:4 final size:4
Alignment explanation
Indices: 1307238--1307267 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1307228 CCTCTCTTTC
1307238 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC
1307268 AATTCATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (4 bp):
TCTA
Found at i:1310910 original size:29 final size:30
Alignment explanation
Indices: 1310872--1310933 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1310862 ATTTTTTATG
*
1310872 CTTTCTTTTTTGAT-AAAAAACTTTTGATA
1 CTTTCGTTTTTGATGAAAAAACTTTTGATA
* *
1310901 CTTTCGTTTTTGATGAATAAGCTTTTGATA
1 CTTTCGTTTTTGATGAAAAAACTTTTGATA
1310931 CTT
1 CTT
1310934 GTTATAACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (30 bp):
CTTTCGTTTTTGATGAAAAAACTTTTGATA
Found at i:1316076 original size:58 final size:58
Alignment explanation
Indices: 1316008--1316121 Score: 219
Period size: 58 Copynumber: 2.0 Consensus size: 58
1315998 TATGTTACAC
*
1316008 TATGAACGTCACAAGTGAATAAATCCATGCACGAATTCAGGATCTATTCTACTTGGAT
1 TATGAACGTCACAAGTGAATAAATCCATGCACAAATTCAGGATCTATTCTACTTGGAT
1316066 TATGAACGTCACAAGTGAATAAATCCATGCACAAATTCAGGATCTATTCTACTTGG
1 TATGAACGTCACAAGTGAATAAATCCATGCACAAATTCAGGATCTATTCTACTTGG
1316122 GTTCTGCCCG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (58 bp):
TATGAACGTCACAAGTGAATAAATCCATGCACAAATTCAGGATCTATTCTACTTGGAT
Found at i:1333828 original size:27 final size:27
Alignment explanation
Indices: 1333731--1333890 Score: 151
Period size: 27 Copynumber: 5.9 Consensus size: 27
1333721 CAGAAAATGG
* *
1333731 AAGCCTTTGTGGAAATATATGAAA-TA
1 AAGCCTTTGTGGAAATTTATGAAACGA
*
1333757 GAAGCCTTTGTGGAAATCTATGAAACGA
1 -AAGCCTTTGTGGAAATTTATGAAACGA
1333785 AAGCCTTTGTGGAAATTTATGAAACGA
1 AAGCCTTTGTGGAAATTTATGAAACGA
* * * * *
1333812 AAGCCTTTGTGGCAATTGATGAGATGG
1 AAGCCTTTGTGGAAATTTATGAAACGA
* * ** * *
1333839 AAGCTTTTGCGGTGATTTAAGGAAAAGA
1 AAGCCTTTGTGGAAATTT-ATGAAACGA
* *
1333867 AAGCCTTTGTGGAAAATGATGAAA
1 AAGCCTTTGTGGAAATTTATGAAA
1333891 GGAACGTCTT
Statistics
Matches: 107, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
27 89 0.83
28 18 0.17
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (27 bp):
AAGCCTTTGTGGAAATTTATGAAACGA
Found at i:1334026 original size:27 final size:26
Alignment explanation
Indices: 1333942--1334017 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
1333932 CATTTATTTG
* *
1333942 AAGGGATAATATGTTTGTCAGAATCTA
1 AAGGGATAATATGTATGGC-GAATCTA
* *
1333969 AAGGGATATTATGTATGGTGAATTCTA
1 AAGGGATAATATGTATGGCGAA-TCTA
* *
1333996 AATGGATAATATGTCTGGCGAA
1 AAGGGATAATATGTATGGCGAA
1334018 CTCTGAATGA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 3 0.08
27 37 0.93
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.33
Consensus pattern (26 bp):
AAGGGATAATATGTATGGCGAATCTA
Found at i:1336784 original size:40 final size:40
Alignment explanation
Indices: 1336740--1336861 Score: 128
Period size: 40 Copynumber: 3.1 Consensus size: 40
1336730 GCATCCAGCG
1336740 CTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACA
1 CTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACA
* * * * **
1336780 CTAGTTAGATAAA-C-AAGCA-ATC-AGT-TGCGCCCAATG
1 CTAGTCAGATAAACCGATG-ATATCAAATGTGTGCCCAACA
* *
1336816 CTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCA
1 CTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACA
1336856 CTAGTC
1 CTAGTC
1336862 GAATAAATCG
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
36 19 0.31
37 4 0.06
38 10 0.16
39 4 0.06
40 25 0.40
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (40 bp):
CTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACA
Found at i:1336862 original size:40 final size:38
Alignment explanation
Indices: 1336734--1336908 Score: 117
Period size: 36 Copynumber: 4.6 Consensus size: 38
1336724 TGTTTTGCAT
* * *
1336734 CCAGCGCTAGTCAGATAAACCGATGATATCAAATGTGTGC
1 CCAGCACTAGTCGGATAAACCGATGA-ATC-AATGTGCGC
* ** * *
1336774 CCAACACTAGTTAGATAAA-C-AAGCAATCAGT-TGCGC
1 CCAGCACTAGTCGGATAAACCGATG-AATCAATGTGCGC
*** *
1336810 CCAATGCTAGTCGGATAAACCGATGATATCAAATGTGTGC
1 CCAGCACTAGTCGGATAAACCGATGA-ATC-AATGTGCGC
* * * *
1336850 CCAGCACTAGTCGAATAAATCGAT-AAT-GATTTGCGC
1 CCAGCACTAGTCGGATAAACCGATGAATCAATGTGCGC
*
1336886 CCAGCACTAGCCGGATAAACCGA
1 CCAGCACTAGTCGGATAAACCGA
1336909 CAAATACATA
Statistics
Matches: 105, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
36 45 0.43
37 4 0.04
38 12 0.11
39 5 0.05
40 39 0.37
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (38 bp):
CCAGCACTAGTCGGATAAACCGATGAATCAATGTGCGC
Found at i:1336884 original size:76 final size:76
Alignment explanation
Indices: 1336656--1336908 Score: 268
Period size: 76 Copynumber: 3.4 Consensus size: 76
1336646 GTAACAAAGT
* * * * *
1336656 TTTGCGCCCAGCCCTAGTCGGATAAACCAATG--AT---AGGTGTGCCCTGCACTAGTCGAATAG
1 TTTGCGCCCAGCGCTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCACTAGTCGAATAA
*
1336716 ATCAACAATGT
66 ATCAACAATGA
** * * *
1336727 TTTGCATCCAGCGCTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACACTAGT-TAGATA
1 TTTGCGCCCAGCGCTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCACTAGTCGA-ATA
*
1336791 AA-CAAGCAATCA
65 AATCAA-CAATGA
* **
1336803 GTTGCGCCCAATGCTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCACTAGTCGAATAA
1 TTTGCGCCCAGCGCTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCACTAGTCGAATAA
* *
1336868 ATCGATAATGA
66 ATCAACAATGA
* *
1336879 TTTGCGCCCAGCACTAGCCGGATAAACCGA
1 TTTGCGCCCAGCGCTAGTCGGATAAACCGA
1336909 CAAATACATA
Statistics
Matches: 145, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
71 27 0.19
73 2 0.01
75 4 0.03
76 109 0.75
77 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (76 bp):
TTTGCGCCCAGCGCTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCACTAGTCGAATAA
ATCAACAATGA
Found at i:1338034 original size:67 final size:67
Alignment explanation
Indices: 1337955--1338093 Score: 278
Period size: 67 Copynumber: 2.1 Consensus size: 67
1337945 TTTATCTTTC
1337955 CTTAACTATTTGACAACTTTAACTAATAGAACTTATTTTTGAAGCTTTTATAATTTAATCCTTTT
1 CTTAACTATTTGACAACTTTAACTAATAGAACTTATTTTTGAAGCTTTTATAATTTAATCCTTTT
1338020 TA
66 TA
1338022 CTTAACTATTTGACAACTTTAACTAATAGAACTTATTTTTGAAGCTTTTATAATTTAATCCTTTT
1 CTTAACTATTTGACAACTTTAACTAATAGAACTTATTTTTGAAGCTTTTATAATTTAATCCTTTT
1338087 TA
66 TA
1338089 CTTAA
1 CTTAA
1338094 TTAACTATTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 72 1.00
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (67 bp):
CTTAACTATTTGACAACTTTAACTAATAGAACTTATTTTTGAAGCTTTTATAATTTAATCCTTTT
TA
Found at i:1347019 original size:15 final size:15
Alignment explanation
Indices: 1346999--1347074 Score: 134
Period size: 15 Copynumber: 5.1 Consensus size: 15
1346989 AAAGTTAAAA
1346999 CATGACCAAAATAAG
1 CATGACCAAAATAAG
*
1347014 CATGACCAAAATAAA
1 CATGACCAAAATAAG
1347029 CATGACCAAAATAAG
1 CATGACCAAAATAAG
*
1347044 CATGACCAAAATAAA
1 CATGACCAAAATAAG
1347059 CATGACCAAAATAAG
1 CATGACCAAAATAAG
1347074 C
1 C
1347075 TTGAAAATCC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.55, C:0.21, G:0.11, T:0.13
Consensus pattern (15 bp):
CATGACCAAAATAAG
Found at i:1347032 original size:30 final size:30
Alignment explanation
Indices: 1346996--1347074 Score: 158
Period size: 30 Copynumber: 2.6 Consensus size: 30
1346986 GACAAAGTTA
1346996 AAACATGACCAAAATAAGCATGACCAAAAT
1 AAACATGACCAAAATAAGCATGACCAAAAT
1347026 AAACATGACCAAAATAAGCATGACCAAAAT
1 AAACATGACCAAAATAAGCATGACCAAAAT
1347056 AAACATGACCAAAATAAGC
1 AAACATGACCAAAATAAGC
1347075 TTGAAAATCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.13
Consensus pattern (30 bp):
AAACATGACCAAAATAAGCATGACCAAAAT
Found at i:1355551 original size:24 final size:24
Alignment explanation
Indices: 1355513--1355571 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1355503 GTTGTCTAAG
1355513 GGGAAGCTCAT-AAGAGCCAATAAC
1 GGGAAGCTC-TGAAGAGCCAATAAC
* *
1355537 GGGTAGCTCTGAAGAGCCATTAAC
1 GGGAAGCTCTGAAGAGCCAATAAC
1355561 GGGAAGCTCTG
1 GGGAAGCTCTG
1355572 GATAGCTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.17
Consensus pattern (24 bp):
GGGAAGCTCTGAAGAGCCAATAAC
Found at i:1355670 original size:26 final size:26
Alignment explanation
Indices: 1355606--1355664 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
1355596 AGCGATCCAT
* *
1355606 ATCGGGAAGCTCACAAAGAGCCTTTA
1 ATCGGGAAGCTTACAAAGAGCCTATA
1355632 ATCGGGAAGCTTACAAAGAGCCATATA
1 ATCGGGAAGCTTACAAAGAGCC-TATA
1355659 A-CGGGA
1 ATCGGGA
1355665 CACTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.17
Consensus pattern (26 bp):
ATCGGGAAGCTTACAAAGAGCCTATA
Found at i:1356689 original size:14 final size:16
Alignment explanation
Indices: 1356659--1356691 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1356649 TTTTCTTTAT
1356659 TTTATTATTTATCATC
1 TTTATTATTTATCATC
1356675 TTTATT-TTT-TCATC
1 TTTATTATTTATCATC
1356689 TTT
1 TTT
1356692 CCAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTATTTATCATC
Found at i:1362013 original size:27 final size:26
Alignment explanation
Indices: 1361967--1362022 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
1361957 AACTGAGTTC
* *
1361967 TATTTTTATTTAATATATAATTACTTT
1 TATTTTTATTTAATAAATAAATA-TTT
1361994 TATTTTTATTATAA-AAATAAATATTT
1 TATTTTTATT-TAATAAATAAATATTT
1362020 TAT
1 TAT
1362023 ACTGAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 17 0.65
28 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TATTTTTATTTAATAAATAAATATTT
Found at i:1362969 original size:2 final size:2
Alignment explanation
Indices: 1362962--1362996 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1362952 GAATTTACAA
1362962 AG AG AG AG AG 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 AG AG AG AG AG A
1362997 ACAATGCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1367753 original size:30 final size:30
Alignment explanation
Indices: 1367702--1367790 Score: 91
Period size: 25 Copynumber: 3.1 Consensus size: 30
1367692 ATTTCTTATG
*
1367702 CCAATATCTCGATA-CTCATATCTTTGACTTT
1 CCAATAT-TTGATACCT-ATATCTTTGACTTT
1367733 CCAATATTTGATACCTATATCTTTGAC-TT
1 CCAATATTTGATACCTATATCTTTGACTTT
**
1367762 ----TATTTGATACCCGTATCTTTGACTTT
1 CCAATATTTGATACCTATATCTTTGACTTT
1367788 CCA
1 CCA
1367791 TAAATATGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
25 21 0.42
26 2 0.04
29 2 0.04
30 16 0.32
31 9 0.18
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCTATATCTTTGACTTT
Found at i:1368398 original size:11 final size:11
Alignment explanation
Indices: 1368382--1368414 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
1368372 CGCTGTCGAA
1368382 AAAAAAAAAAT
1 AAAAAAAAAAT
1368393 AAAAAAAAAAT
1 AAAAAAAAAAT
1368404 AAAAAAGAAAA
1 AAAAAA-AAAA
1368415 GAGGACGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:1369642 original size:6 final size:6
Alignment explanation
Indices: 1369625--1369672 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
1369615 AGAGAATCCA
* * * *
1369625 ACCATC ATCATC ACCATC ACCACC ACCATC ATCATC ACCATC ATCATC
1 ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC
1369673 CTCTCACTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (6 bp):
ACCATC
Done.