Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 158 of 290
Found at i:53897358 original size:43 final size:41
Alignment explanation
Indices: 53897308--53897414 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 41
53897298 CCACATCCTG
*
53897308 GATATGGTCTTACATGTAATCTCGTATCGATGCCAATAGCCCA
1 GATATGGTCTTACA-GTAATCTCATATCGATGCC-ATAGCCCA
* ** *
53897351 GCTATGGTCTTACACAAAGTCTCATATCGATGCCATATCCCA
1 GATATGGTCTTACAGTAA-TCTCATATCGATGCCATAGCCCA
*
53897393 GAGATGGTCTTACACGTAATCT
1 GATATGGTCTTACA-GTAATCT
53897415 TAGTGACCCT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
42 24 0.45
43 29 0.55
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (41 bp):
GATATGGTCTTACAGTAATCTCATATCGATGCCATAGCCCA
Found at i:53897406 original size:42 final size:43
Alignment explanation
Indices: 53897327--53897407 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
53897317 TTACATGTAA
* **
53897327 TCTCGTATCGATGCCAATAGCCCAGCTATGGTCTTACACAAAG
1 TCTCATATCGATGCCAATAGCCCAGAGATGGTCTTACACAAAG
*
53897370 TCTCATATCGATGCC-ATATCCCAGAGATGGTCTTACAC
1 TCTCATATCGATGCCAATAGCCCAGAGATGGTCTTACAC
53897408 GTAATCTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 20 0.59
43 14 0.41
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (43 bp):
TCTCATATCGATGCCAATAGCCCAGAGATGGTCTTACACAAAG
Found at i:53915504 original size:18 final size:18
Alignment explanation
Indices: 53915478--53915512 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53915468 TTGTGCAAAA
*
53915478 ATATGTAAATATATATAC
1 ATATATAAATATATATAC
53915496 ATATATAAATATATATA
1 ATATATAAATATATATA
53915513 TACAGGTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
ATATATAAATATATATAC
Found at i:53919254 original size:38 final size:38
Alignment explanation
Indices: 53919207--53919303 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 38
53919197 GGCTTAAAGA
* * ** *
53919207 CCCGTAGGCTTTGTGCTGGTAAAATATTTGGGTTAAAT
1 CCCGCAGGCTTAGTGCTGGTAAAATATCAGGGATAAAT
* **
53919245 CCCGCAGGCTTCGTGCTGGTATTATATCAGGGATAAAT
1 CCCGCAGGCTTAGTGCTGGTAAAATATCAGGGATAAAT
*
53919283 CCCGCAGGCCTAGTGCTGGTA
1 CCCGCAGGCTTAGTGCTGGTA
53919304 TTATATTCGG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (38 bp):
CCCGCAGGCTTAGTGCTGGTAAAATATCAGGGATAAAT
Found at i:53919360 original size:43 final size:43
Alignment explanation
Indices: 53919307--53919554 Score: 415
Period size: 43 Copynumber: 5.8 Consensus size: 43
53919297 GCTGGTATTA
* * **
53919307 TATTCGGGCCTTTGTGCCTAGCAGGCTTTGTATCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * *
53919350 TATTCAGGCCTTTGTGCCTAGCAGGCTTCGTACCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
53919393 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
53919436 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
53919479 TATTCGGGCCTTCATGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
53919522 TATTCGGGCCTTCATGCCTAGCAGGCTTCGTGC
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
53919555 GCGAAATGTC
Statistics
Matches: 198, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 198 1.00
ACGTcount: A:0.11, C:0.25, G:0.32, T:0.32
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:53930196 original size:40 final size:40
Alignment explanation
Indices: 53930152--53930296 Score: 179
Period size: 40 Copynumber: 3.6 Consensus size: 40
53930142 GCTCCTCGTT
*
53930152 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
53930192 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
53930231 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
53930272 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53930297 CAACATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.37
40 44 0.49
41 11 0.12
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:53931557 original size:55 final size:56
Alignment explanation
Indices: 53931463--53931576 Score: 212
Period size: 55 Copynumber: 2.0 Consensus size: 56
53931453 TTTCTTTAGG
53931463 TCACGGCAATGGGGGGGGGGAACAACTACACACATTTTTTTTTTGTATTCATCATAC
1 TCACGGCAAT-GGGGGGGGGAACAACTACACACATTTTTTTTTTGTATTCATCATAC
53931520 TCACGGCAAT-GGGGGGGGAACAACTACACACATTTTTTTTTTGTATTCATCATAC
1 TCACGGCAATGGGGGGGGGAACAACTACACACATTTTTTTTTTGTATTCATCATAC
53931575 TC
1 TC
53931577 CTTTTCATTA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
55 47 0.82
57 10 0.18
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (56 bp):
TCACGGCAATGGGGGGGGGAACAACTACACACATTTTTTTTTTGTATTCATCATAC
Found at i:53938334 original size:40 final size:39
Alignment explanation
Indices: 53938250--53938434 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
53938240 TTGAATGATG
* * * *
53938250 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
53938290 TCCGGACTAAGATCCGAAGGTATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53938330 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
53938369 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACTA-AA
*
53938410 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
53938435 AACGAGGAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 34 0.28
40 76 0.63
41 11 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53938387 original size:79 final size:81
Alignment explanation
Indices: 53938250--53938432 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
53938240 TTGAATGATG
* * *
53938250 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
53938314 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
53938329 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCTCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATC-CGAAGGCA
*
53938391 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
53938409 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
53938433 TGAACGAGGA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 2 0.02
79 56 0.64
80 30 0.34
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:53938456 original size:79 final size:78
Alignment explanation
Indices: 53938280--53938457 Score: 182
Period size: 79 Copynumber: 2.2 Consensus size: 78
53938270 CTTTGTGCTA
* * * *
53938280 AGTGACCATATCCGGACTAAGATCCGAAGGTATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
1 AGTGACTATATCCGG-TTAAGATCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCG
**
53938345 AAGGCATTGGTGCG
65 AAGGCATTGGAACG
* * * *
53938359 AGTTACTAAATCCGGGTTAAG-TCTCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTC
1 AGTGACTATATCC-GGTTAAGATC-CGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-C
*
53938422 CCGAAGGCATTTGAACG
62 CCGAAGGCATTGGAACG
53938439 AG-GAGCTATATCCGGTTAA
1 AGTGA-CTATATCCGGTTAA
53938458 ATTCCTAAGG
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
78 4 0.05
79 51 0.63
80 26 0.32
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (78 bp):
AGTGACTATATCCGGTTAAGATCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGA
AGGCATTGGAACG
Found at i:53940715 original size:24 final size:23
Alignment explanation
Indices: 53940655--53940995 Score: 177
Period size: 24 Copynumber: 14.2 Consensus size: 23
53940645 CAAGCAAGGA
*
53940655 AATTCGCACCCATAGTGCCATGT-T
1 AATTCGCACACATAGTGCC-T-TAT
**
53940679 AACCCGCACACATAGTGCCTTAGT
1 AATTCGCACACATAGTGCCTTA-T
* * * *
53940703 AATTCACATACATATTGACATTCA-
1 AATTCGCACACATAGTG-CCTT-AT
* *
53940727 AATCCGCACACATAGTGCCATAT
1 AATTCGCACACATAGTGCCTTAT
* * * *
53940750 AAATCCGCACATATAGTGCCATACA
1 -AATTCGCACACATAGTGCCTTA-T
53940775 AATTCGCACACATAGTGCCTTAGT
1 AATTCGCACACATAGTGCCTTA-T
** * * *
53940799 AATTCATATACATATTGACATTCA-
1 AATTCGCACACATAGTG-CCTT-AT
* *
53940823 AATCCGCACACATAGTGCCATAT
1 AATTCGCACACATAGTGCCTTAT
* * * *
53940846 AAATCCGCACATATAGTGCCATACA
1 -AATTCGCACACATAGTGCCTTA-T
53940871 AATTCGCACACATAGTGCCTTAGT
1 AATTCGCACACATAGTGCCTTA-T
** * * *
53940895 AATTCATATACATATTGACATTCA-
1 AATTCGCACACATAGTG-CCTT-AT
* *
53940919 AATCCGCACACATAGTGCCATAT
1 AATTCGCACACATAGTGCCTTAT
* * * *
53940942 AAATCCGCACATATAGTGCCATACA
1 -AATTCGCACACATAGTGCCTTA-T
53940967 AATTCGCACACATAGTGCCTTAGT
1 AATTCGCACACATAGTGCCTTA-T
53940991 AATTC
1 AATTC
53940996 ATATACATAT
Statistics
Matches: 240, Mismatches: 60, Indels: 34
0.72 0.18 0.10
Matches are distributed among these distances:
22 4 0.02
23 7 0.03
24 217 0.90
25 9 0.04
26 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (23 bp):
AATTCGCACACATAGTGCCTTAT
Found at i:53940737 original size:48 final size:48
Alignment explanation
Indices: 53940682--53941033 Score: 392
Period size: 48 Copynumber: 7.3 Consensus size: 48
53940672 CCATGTTAAC
53940682 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCAAAT
1 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCAAAT
* * ** * *
53940730 CCGCACACATAGTGCCATA-TAAATC-CGCACATATAGTGCCATACAAAT
1 CCGCACACATAGTGCCTTAGTAATTCACATACATAT--TGACATTCAAAT
* *
53940778 TCGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAAT
1 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCAAAT
* * ** * *
53940826 CCGCACACATAGTGCCATA-TAAATC-CGCACATATAGTGCCATACAAAT
1 CCGCACACATAGTGCCTTAGTAATTCACATACATAT--TGACATTCAAAT
* *
53940874 TCGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAAT
1 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCAAAT
* * ** * *
53940922 CCGCACACATAGTGCCATA-TAAATC-CGCACATATAGTGCCATACAAAT
1 CCGCACACATAGTGCCTTAGTAATTCACATACATAT--TGACATTCAAAT
* *
53940970 TCGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAAT
1 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCAAAT
53941018 CCGCACACATAGTGCC
1 CCGCACACATAGTGCC
53941034 ATACAAATTC
Statistics
Matches: 245, Mismatches: 47, Indels: 24
0.78 0.15 0.08
Matches are distributed among these distances:
46 19 0.08
47 15 0.06
48 178 0.73
49 15 0.06
50 18 0.07
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.27
Consensus pattern (48 bp):
CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCAAAT
Found at i:53941027 original size:24 final size:24
Alignment explanation
Indices: 53941000--53941065 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 24
53940990 TAATTCATAT
* *
53941000 ACATATTGACATTCAAATCCGCAC
1 ACATAGTGCCATTCAAATCCGCAC
* * * *
53941024 ACATAGTGCCATACAAATTCGTAG
1 ACATAGTGCCATTCAAATCCGCAC
**
53941048 ACATAGTGCTGTTCAAAT
1 ACATAGTGCCATTCAAAT
53941066 TCATAAGACT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (24 bp):
ACATAGTGCCATTCAAATCCGCAC
Found at i:53941067 original size:96 final size:96
Alignment explanation
Indices: 53940683--53941041 Score: 700
Period size: 96 Copynumber: 3.7 Consensus size: 96
53940673 CATGTTAACC
*
53940683 CGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCAAATCCGCACACATAGTGCCAT
1 CGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAATCCGCACACATAGTGCCAT
53940748 ATAAATCCGCACATATAGTGCCATACAAATT
66 ATAAATCCGCACATATAGTGCCATACAAATT
53940779 CGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAATCCGCACACATAGTGCCAT
1 CGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAATCCGCACACATAGTGCCAT
53940844 ATAAATCCGCACATATAGTGCCATACAAATT
66 ATAAATCCGCACATATAGTGCCATACAAATT
53940875 CGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAATCCGCACACATAGTGCCAT
1 CGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAATCCGCACACATAGTGCCAT
53940940 ATAAATCCGCACATATAGTGCCATACAAATT
66 ATAAATCCGCACATATAGTGCCATACAAATT
53940971 CGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAATCCGCACACATAGTGCCAT
1 CGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAATCCGCACACATAGTGCCAT
*
53941036 ACAAAT
66 ATAAAT
53941042 TCGTAGACAT
Statistics
Matches: 261, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 261 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.27
Consensus pattern (96 bp):
CGCACACATAGTGCCTTAGTAATTCATATACATATTGACATTCAAATCCGCACACATAGTGCCAT
ATAAATCCGCACATATAGTGCCATACAAATT
Found at i:53944377 original size:27 final size:27
Alignment explanation
Indices: 53944347--53944402 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
53944337 GAGCATAATC
**
53944347 GTCATTCTACCATACAGGGTTATTACA
1 GTCATTCTACCATACAGGGGCATTACA
* * *
53944374 GTCATTTTGCCCTACAGGGGCATTACA
1 GTCATTCTACCATACAGGGGCATTACA
53944401 GT
1 GT
53944403 TATTTTCAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (27 bp):
GTCATTCTACCATACAGGGGCATTACA
Found at i:53944817 original size:20 final size:19
Alignment explanation
Indices: 53944775--53944817 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
53944765 GGGCCTATTG
* *
53944775 GGCCTATTCAGCCCATTAT
1 GGCCTATTCAGCCCATAAC
*
53944794 GGCCTATTGAGGCCCATAAC
1 GGCCTATTCA-GCCCATAAC
53944814 GGCC
1 GGCC
53944818 CTAGTCCACG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (19 bp):
GGCCTATTCAGCCCATAAC
Found at i:53946737 original size:15 final size:15
Alignment explanation
Indices: 53946717--53946754 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
53946707 CCCATACTCA
53946717 AGGCCCAATACTTCT
1 AGGCCCAATACTTCT
53946732 AGGCCCAATACTTCT
1 AGGCCCAATACTTCT
53946747 AGGCCCAA
1 AGGCCCAA
53946755 ATTCGAGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (15 bp):
AGGCCCAATACTTCT
Found at i:53960302 original size:18 final size:20
Alignment explanation
Indices: 53960272--53960309 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
53960262 CTCATGGGCC
53960272 TGGGCTGCAATGGGC-CGTG
1 TGGGCTGCAATGGGCTCGTG
53960291 TGGGCT-CAATGGGCTCGTG
1 TGGGCTGCAATGGGCTCGTG
53960310 GGCCCGTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.11, C:0.21, G:0.45, T:0.24
Consensus pattern (20 bp):
TGGGCTGCAATGGGCTCGTG
Found at i:53961520 original size:51 final size:50
Alignment explanation
Indices: 53961460--53961597 Score: 168
Period size: 50 Copynumber: 2.7 Consensus size: 50
53961450 ATTGGTCGCA
* * **
53961460 TGTGTAGTACTAAATGCAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAATGCAGGCTACTATGTGTACCAGAT-ACTGAGATCACG
* * * ** *
53961511 TGTGTAGTACTAAATGTAGGCTACTACGTGTATCAGATGGTGAGGTCACG
1 TGTGTAGTACTAAATGCAGGCTACTATGTGTACCAGATACTGAGATCACG
*
53961561 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
1 TGTGTAGTACTAAATGCAGGCTACTATGTGTACCAGA
53961598 GAATTGGTCA
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 40 0.55
51 33 0.45
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
TGTGTAGTACTAAATGCAGGCTACTATGTGTACCAGATACTGAGATCACG
Found at i:53962346 original size:33 final size:34
Alignment explanation
Indices: 53962262--53962354 Score: 106
Period size: 32 Copynumber: 2.9 Consensus size: 34
53962252 TCAAGCCCAT
*
53962262 TGGGCCTAAGCCC--ATTCAGATAACAGTGACAC
1 TGGGCCTAAGCCCTTATTCAGATAACAGTGAAAC
* *
53962294 TGGGCC-AGAGCCCTT-TTCAGATTACA-TTAAAC
1 TGGGCCTA-AGCCCTTATTCAGATAACAGTGAAAC
*
53962326 TGGGCCTTAGCCCTTATTCAGATAACAGT
1 TGGGCCTAAGCCCTTATTCAGATAACAGT
53962355 ATAGCCCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
31 1 0.02
32 28 0.56
33 20 0.40
34 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (34 bp):
TGGGCCTAAGCCCTTATTCAGATAACAGTGAAAC
Found at i:53971655 original size:22 final size:22
Alignment explanation
Indices: 53971627--53971674 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
53971617 GTTGCTGCGA
* *
53971627 TATTTACGGTC-TTTAGTCGTTC
1 TATTTACGG-CGTTGAGCCGTTC
53971649 TATTTACGGCGTTGAGCCGTTC
1 TATTTACGGCGTTGAGCCGTTC
53971671 TATT
1 TATT
53971675 GTCTCAGTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.46
Consensus pattern (22 bp):
TATTTACGGCGTTGAGCCGTTC
Found at i:53971764 original size:15 final size:15
Alignment explanation
Indices: 53971740--53971769 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53971730 TATCCCCACA
53971740 TGGTGAGTTGGTTGG
1 TGGTGAGTTGGTTGG
*
53971755 TGGTGTGTTGGTTGG
1 TGGTGAGTTGGTTGG
53971770 ACTGGGCTAG
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:0.03, C:0.00, G:0.53, T:0.43
Consensus pattern (15 bp):
TGGTGAGTTGGTTGG
Found at i:53971840 original size:27 final size:28
Alignment explanation
Indices: 53971809--53971861 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
53971799 CATCTGATAA
*
53971809 TGATTCTG-TATTGGGCTTAGGCCCACC
1 TGATTCTGTTATTGGGCTAAGGCCCACC
53971836 TGATTCTGTTATTGGGCTAAGGCCCA
1 TGATTCTGTTATTGGGCTAAGGCCCA
53971862 TCTAATACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (28 bp):
TGATTCTGTTATTGGGCTAAGGCCCACC
Found at i:53974892 original size:105 final size:105
Alignment explanation
Indices: 53974710--53974998 Score: 533
Period size: 105 Copynumber: 2.8 Consensus size: 105
53974700 GGATGGTTGA
53974710 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
53974775 TGAGTCCGAGTTCAAATGAGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCAAATGAGAGTTCGTGAGATGTAACTAG
53974815 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
53974880 TGAGTCCGAGTTCAAATGAGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCAAATGAGAGTTCGTGAGATGTAACTAG
* * * *
53974920 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
*
53974985 TGAGTCTGAGTTCA
66 TGAGTCCGAGTTCA
53974999 CTTAGGGGCG
Statistics
Matches: 179, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 179 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (105 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCAAATGAGAGTTCGTGAGATGTAACTAG
Found at i:53977220 original size:15 final size:15
Alignment explanation
Indices: 53977183--53977225 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53977173 TTATGATATG
*
53977183 GTATCTTGGATTTTT
1 GTATCTTGGATTCTT
*
53977198 GTACCTTGGATATCTT
1 GTATCTTGGAT-TCTT
53977214 -TATCTTGGATTC
1 GTATCTTGGATTC
53977226 CTTTATAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 2 0.08
15 19 0.79
16 3 0.12
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (15 bp):
GTATCTTGGATTCTT
Found at i:53977229 original size:15 final size:14
Alignment explanation
Indices: 53977184--53977231 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
53977174 TATGATATGG
*
53977184 TATCTTGGATTTTT
1 TATCTTGGATTCTT
*
53977198 GTACCTTGGATATCTT
1 -TATCTTGGAT-TCTT
53977214 TATCTTGGATTCCTT
1 TATCTTGGATT-CTT
53977229 TAT
1 TAT
53977232 AACACCCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 1 0.04
15 24 0.86
16 3 0.11
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.54
Consensus pattern (14 bp):
TATCTTGGATTCTT
Found at i:53989975 original size:48 final size:48
Alignment explanation
Indices: 53989918--53990050 Score: 194
Period size: 48 Copynumber: 2.8 Consensus size: 48
53989908 TTGGGTTAGG
* *
53989918 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGTATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATA
* *
53989966 TGTGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCAATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATA
** * *
53990014 TGTGATTTCGTGTAAGACCATGTCTAGGACATGGCAT
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCAT
53990051 CGATATGAGA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATA
Found at i:54000288 original size:15 final size:15
Alignment explanation
Indices: 54000265--54000299 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
54000255 CGTTTAAGGG
54000265 CACACGGCCAAGGCA
1 CACACGGCCAAGGCA
*
54000280 CACATGGCCAAGGCA
1 CACACGGCCAAGGCA
54000295 CACAC
1 CACAC
54000300 CCGTGGCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.40, G:0.23, T:0.03
Consensus pattern (15 bp):
CACACGGCCAAGGCA
Found at i:54014439 original size:40 final size:40
Alignment explanation
Indices: 54014380--54014560 Score: 249
Period size: 40 Copynumber: 4.5 Consensus size: 40
54014370 TATTCGGATG
**
54014380 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
* *
54014420 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
** *
54014460 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
* *
54014500 ATAACCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACT
*
54014540 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
54014561 ATACTTGGGT
Statistics
Matches: 125, Mismatches: 15, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
39 13 0.10
40 110 0.88
41 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
Found at i:54021228 original size:20 final size:21
Alignment explanation
Indices: 54021203--54021244 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54021193 TTCTGAACTG
* *
54021203 TATGATGAT-AGCGTATGAAA
1 TATGATAATGAGCATATGAAA
54021223 TATGATAATGAGCATATGAAA
1 TATGATAATGAGCATATGAAA
54021244 T
1 T
54021245 GTATAATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (21 bp):
TATGATAATGAGCATATGAAA
Found at i:54023728 original size:18 final size:18
Alignment explanation
Indices: 54023679--54023715 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
54023669 CTAGGCCCAT
54023679 TACAATAACAGTAAACAG
1 TACAATAACAGTAAACAG
54023697 TACAATAACAGTAAACAG
1 TACAATAACAGTAAACAG
54023715 T
1 T
54023716 GCAGTAGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (18 bp):
TACAATAACAGTAAACAG
Found at i:54024059 original size:27 final size:27
Alignment explanation
Indices: 54024020--54024148 Score: 116
Period size: 27 Copynumber: 4.8 Consensus size: 27
54024010 CATCACGTAG
* *
54024020 GGGCAAAACAGTCATCTTACCTCCTAA
1 GGGCAAAACAGTCATCTTACCACATAA
** *
54024047 GGGCAAATTAGTCATTTTACCACATAA
1 GGGCAAAACAGTCATCTTACCACATAA
* * *
54024074 GGGCAAAACCGTCATTTTACCACATGA
1 GGGCAAAACAGTCATCTTACCACATAA
* * *
54024101 GGGCAAAATAGTTAGT-TTATCACATAA
1 GGGCAAAACAGTCA-TCTTACCACATAA
* * *
54024128 GGGAAAAATAGTCATTTTACC
1 GGGCAAAACAGTCATCTTACC
54024149 TTATAGAGGG
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.01
27 81 0.98
28 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (27 bp):
GGGCAAAACAGTCATCTTACCACATAA
Found at i:54024104 original size:54 final size:54
Alignment explanation
Indices: 54024020--54024176 Score: 170
Period size: 54 Copynumber: 2.9 Consensus size: 54
54024010 CATCACGTAG
* * *
54024020 GGGCAAAACAGTCATCTTACCTCCTAAGGGCAAATTAGTCATTTTACCACATAA
1 GGGCAAAACAGTCATTTTACCTCATGAGGGCAAATTAGTCATTTTACCACATAA
* * * * * *
54024074 GGGCAAAACCGTCATTTTACCACATGAGGGCAAAATAGTTAGTTTATCACATAA
1 GGGCAAAACAGTCATTTTACCTCATGAGGGCAAATTAGTCATTTTACCACATAA
* * * * **
54024128 GGGAAAAATAGTCATTTTACCTTATAGAGGGTATTTTAGTCATTTTACC
1 GGGCAAAACAGTCATTTTACCTCAT-GAGGGCAAATTAGTCATTTTACC
54024177 TCTGGGGGTA
Statistics
Matches: 81, Mismatches: 21, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
54 65 0.80
55 16 0.20
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (54 bp):
GGGCAAAACAGTCATTTTACCTCATGAGGGCAAATTAGTCATTTTACCACATAA
Found at i:54024254 original size:26 final size:27
Alignment explanation
Indices: 54024137--54024253 Score: 148
Period size: 27 Copynumber: 4.3 Consensus size: 27
54024127 AGGGAAAAAT
* *
54024137 AGTCATTTTACCTTATAGAGGGTATTTT
1 AGTCATTTTACCTTAT-GGGGGTATTTC
*
54024165 AGTCATTTTACC-TCTGGGGGTATTT-
1 AGTCATTTTACCTTATGGGGGTATTTC
*
54024190 AGGTCATTTTACCCTATGGGGGTATTTC
1 A-GTCATTTTACCTTATGGGGGTATTTC
* *
54024218 GGTCATTTTTCCTTATGGGGGTATTTC
1 AGTCATTTTACCTTATGGGGGTATTTC
54024245 AGTCATTTT
1 AGTCATTTT
54024254 CAGGTAAATA
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.01
26 20 0.25
27 46 0.58
28 12 0.15
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (27 bp):
AGTCATTTTACCTTATGGGGGTATTTC
Found at i:54045221 original size:42 final size:42
Alignment explanation
Indices: 54045129--54045278 Score: 180
Period size: 43 Copynumber: 3.6 Consensus size: 42
54045119 TAAGACTACA
*
54045129 TGTAAGACAATATCTGGGATATGGCATCG-TATGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCG
* *
54045170 TGTAAGACCATATCTGGGATATGGCGTAGATATG-GTATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAG-ATTTCG
* * * *
54045212 TGTAAGACCATAACTAGGCCAT-TGGCATCGATATGAGATTACA
1 TGTAAGACCATATCT-GG-GATATGGCATCGATATGAGATTTCG
*
54045255 TGTATGACCATATCTGGGATATGG
1 TGTAAGACCATATCTGGGATATGG
54045279 TATTGGTATG
Statistics
Matches: 91, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
41 29 0.32
42 29 0.32
43 30 0.33
44 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCG
Found at i:54049823 original size:43 final size:43
Alignment explanation
Indices: 54049757--54049851 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
54049747 CTTAGGCTTG
* * * * *
54049757 AGCCCGATATCATTTCACTGGCATTATAGCCTGCTAGGCTCAA
1 AGCCCGATATCATCTCACCGGCATTATAGCCTACGAGGCCCAA
* *
54049800 AGCCCGATATTATCTCACCGGCATTATAGCCTACGAGGCCCGA
1 AGCCCGATATCATCTCACCGGCATTATAGCCTACGAGGCCCAA
54049843 AGCCCGATA
1 AGCCCGATA
54049852 ATATTATTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (43 bp):
AGCCCGATATCATCTCACCGGCATTATAGCCTACGAGGCCCAA
Found at i:54050789 original size:70 final size:70
Alignment explanation
Indices: 54050669--54050800 Score: 210
Period size: 70 Copynumber: 1.9 Consensus size: 70
54050659 TAGCACATAA
* * * * *
54050669 CACCATGATTTTGTCCTAATTTGGACAGCCAATAATTTACAGTATTACAGCAGCATATTAATCAG
1 CACCATAAATTTGTCCTAATTTGGACAGCCAATAATTTACAATATCACAGCAGCAAATTAATCAG
54050734 CTAAG
66 CTAAG
*
54050739 CACCATAAATTTGTCCTAATTTGGACAGCCACTAATTTACAATATCACAGCAGCAAATTAAT
1 CACCATAAATTTGTCCTAATTTGGACAGCCAATAATTTACAATATCACAGCAGCAAATTAAT
54050801 TAGTAATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (70 bp):
CACCATAAATTTGTCCTAATTTGGACAGCCAATAATTTACAATATCACAGCAGCAAATTAATCAG
CTAAG
Found at i:54055402 original size:28 final size:29
Alignment explanation
Indices: 54055370--54055431 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
54055360 TACATACGTG
* *
54055370 CATATGGCCCACTAGGCTC-AATCTCATT
1 CATATGGCCCACTAGGCCCAAATCACATT
*
54055398 CATATGGCCCATTAGGCCCAAATCACATT
1 CATATGGCCCACTAGGCCCAAATCACATT
54055427 CATAT
1 CATAT
54055432 ACATGCTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (29 bp):
CATATGGCCCACTAGGCCCAAATCACATT
Found at i:54066616 original size:42 final size:41
Alignment explanation
Indices: 54066528--54066680 Score: 173
Period size: 42 Copynumber: 3.7 Consensus size: 41
54066518 TAAGACTACG
* * *
54066528 TGTAAGACCATATCTGGGATATGGCATCGTATGAGATTTCG
1 TGTAAGACCATATCTGGGATATAGCATCATATGAGATTTCA
* *
54066569 TGTAAGACCATATCTGGGATATCGCGTCAATATGAGATTTCA
1 TGTAAGACCATATCTGGGATATAGCATC-ATATGAGATTTCA
* * *
54066611 TGTAAGACCATAACTAGGCCAT-TAGCATCGATATGAGATTACA
1 TGTAAGACCATATCT-GG-GATATAGCATC-ATATGAGATTTCA
* *
54066654 TGTAAGACCATATTTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATAGCAT
54066681 TGGTATGGTA
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
41 28 0.30
42 32 0.34
43 32 0.34
44 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (41 bp):
TGTAAGACCATATCTGGGATATAGCATCATATGAGATTTCA
Found at i:54066656 original size:43 final size:42
Alignment explanation
Indices: 54066528--54066665 Score: 154
Period size: 43 Copynumber: 3.3 Consensus size: 42
54066518 TAAGACTACG
* * * *
54066528 TGTAAGACCATATCTGGGATATGGCATCG-TATGAGATTTCG
1 TGTAAGACCATAACTGGCATATAGCATCGATATGAGATTTCA
* * * * *
54066569 TGTAAGACCATATCTGGGATATCGCGTCAATATGAGATTTCA
1 TGTAAGACCATAACTGGCATATAGCATCGATATGAGATTTCA
*
54066611 TGTAAGACCATAACTAGGCCAT-TAGCATCGATATGAGATTACA
1 TGTAAGACCATAACT-GG-CATATAGCATCGATATGAGATTTCA
54066654 TGTAAGACCATA
1 TGTAAGACCATA
54066666 TTTGGGATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
41 26 0.31
42 25 0.30
43 31 0.37
44 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATAACTGGCATATAGCATCGATATGAGATTTCA
Found at i:54069290 original size:29 final size:29
Alignment explanation
Indices: 54069248--54069354 Score: 128
Period size: 29 Copynumber: 3.7 Consensus size: 29
54069238 GTATATGAAT
*
54069248 GTGATTTGGGCCTAATGGGCCATAGGAAA
1 GTGATTTGGGCCTAATGGGCCATAAGAAA
*
54069277 GTGATTTGGGCCTAATGGGCCATAAGAAT
1 GTGATTTGGGCCTAATGGGCCATAAGAAA
* * *
54069306 GTGATTTAGGCCTAGTGGGCCATATG-AA
1 GTGATTTGGGCCTAATGGGCCATAAGAAA
* *
54069334 -TGATATTGAGCCTAGTGGGCC
1 GTGAT-TTGGGCCTAATGGGCC
54069355 TAGTGGGCGA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
27 4 0.06
28 15 0.22
29 50 0.72
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (29 bp):
GTGATTTGGGCCTAATGGGCCATAAGAAA
Found at i:54069311 original size:58 final size:57
Alignment explanation
Indices: 54069244--54069354 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 57
54069234 GCATGTATAT
* *
54069244 GAATGTGATTTGGGCCTAATGGGCCATAGGAAAGTGAT-TTGGGCCTAATGGGCCATAA
1 GAATGTGATTTAGGCCTAATGGGCCATAGG-AA-TGATATTGAGCCTAATGGGCCATAA
* * *
54069302 GAATGTGATTTAGGCCTAGTGGGCCATATGAATGATATTGAGCCTAGTGGGCC
1 GAATGTGATTTAGGCCTAATGGGCCATAGGAATGATATTGAGCCTAATGGGCC
54069355 TAGTGGGCGA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
56 4 0.09
57 16 0.34
58 27 0.57
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.27
Consensus pattern (57 bp):
GAATGTGATTTAGGCCTAATGGGCCATAGGAATGATATTGAGCCTAATGGGCCATAA
Found at i:54075873 original size:81 final size:81
Alignment explanation
Indices: 54075738--54075900 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
54075728 TTTCGTACTA
54075738 CCCAGATGCACAAATAACCGACTGTTATGAGCTTCACTCAAAATCATCTGAATTAACTCTAGATT
1 CCCAGATGCACAAATAACCGACTGTTATGAGCTTCACTCAAAATCATCTGAATTAACTCTAGATT
54075803 TCTCAGGACACAAATT
66 TCTCAGGACACAAATT
* *
54075819 CCCAGATGCACAAATAACCGACTGTTATGAGCTTCACTCAAAATCATTTGAATTAACTCTGGATT
1 CCCAGATGCACAAATAACCGACTGTTATGAGCTTCACTCAAAATCATCTGAATTAACTCTAGATT
54075884 TCTCAGGACACAAATT
66 TCTCAGGACACAAATT
54075900 C
1 C
54075901 TATCTCAAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.28
Consensus pattern (81 bp):
CCCAGATGCACAAATAACCGACTGTTATGAGCTTCACTCAAAATCATCTGAATTAACTCTAGATT
TCTCAGGACACAAATT
Found at i:54080411 original size:27 final size:27
Alignment explanation
Indices: 54080352--54080411 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
54080342 GGAAGTACCG
54080352 TATTAGTGGCTTTGCACGTAATTACTGC
1 TATTAGTGGCTTTGCACGT-ATTACTGC
*
54080380 T-TTAGTGGCTTTGCCACGT-TTACTGT
1 TATTAGTGGCTTTG-CACGTATTACTGC
54080406 TATTAG
1 TATTAG
54080412 CAGTTCTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.24
27 16 0.55
28 6 0.21
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (27 bp):
TATTAGTGGCTTTGCACGTATTACTGC
Found at i:54089172 original size:54 final size:54
Alignment explanation
Indices: 54089109--54089216 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
54089099 ATTAGAGAAT
*
54089109 CAAGCATGATAAGTTGATTTTTAAGAATTTAAAATCTTAGGTTGTTTCCCCAAA
1 CAAGCATGATAAGTTGATTTTTAAGAATTTAAAATCTTAAGTTGTTTCCCCAAA
54089163 CAAGCATGATAAGTTGATTTTTAAGAATTTAAAATCTTAAGTTGTTTCCCCAAA
1 CAAGCATGATAAGTTGATTTTTAAGAATTTAAAATCTTAAGTTGTTTCCCCAAA
54089217 GTTTAGGTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (54 bp):
CAAGCATGATAAGTTGATTTTTAAGAATTTAAAATCTTAAGTTGTTTCCCCAAA
Found at i:54091205 original size:214 final size:214
Alignment explanation
Indices: 54090836--54091224 Score: 742
Period size: 214 Copynumber: 1.8 Consensus size: 214
54090826 TTAGTTATGA
* * *
54090836 ATGAAACCTAAGACGAATCTTGTTATTATTTTCTGAATTGTATGATAAATATTTAACTTGTTCTT
1 ATGAAACCTAAGACGAATCTTGCTATTATTTTCTAAATTGTACGATAAATATTTAACTTGTTCTT
54090901 AATTATGCGTTCTTAATTCTTGTTTTGATATCCTAGGATACTGATCTTATTCAGAGGAGGAATAG
66 AATTATGCGTTCTTAATTCTTGTTTTGATATCCTAGGATACTGATCTTATTCAGAGGAGGAATAG
54090966 ACCCTGTCTAAGAGTACATTTATCATAATTAAGCGGAGTTGATTGATTTAGTTATGAACTAAATC
131 ACCCTGTCTAAGAGTACATTTATCATAATTAAGCGGAGTTGATTGATTTAGTTATGAACTAAATC
54091031 CCCTAAATACCTAAGGGGG
196 CCCTAAATACCTAAGGGGG
*
54091050 ATGAAACCTAAGATGAATCTTGCTATTATTTTCTAAATTGTACGATAAATATTTAACTTGTTCTT
1 ATGAAACCTAAGACGAATCTTGCTATTATTTTCTAAATTGTACGATAAATATTTAACTTGTTCTT
54091115 AATTATGCGTTCTTAATTCTTGTTTTGATATCCTAGGATACTGATCTTATTCAGAGGAGGAATAG
66 AATTATGCGTTCTTAATTCTTGTTTTGATATCCTAGGATACTGATCTTATTCAGAGGAGGAATAG
54091180 ACCCTGTCTAAGAGTACATTTATCATAATTAAGCGGAGTTGATTG
131 ACCCTGTCTAAGAGTACATTTATCATAATTAAGCGGAGTTGATTG
54091225 TGCGCCTAGA
Statistics
Matches: 171, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
214 171 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (214 bp):
ATGAAACCTAAGACGAATCTTGCTATTATTTTCTAAATTGTACGATAAATATTTAACTTGTTCTT
AATTATGCGTTCTTAATTCTTGTTTTGATATCCTAGGATACTGATCTTATTCAGAGGAGGAATAG
ACCCTGTCTAAGAGTACATTTATCATAATTAAGCGGAGTTGATTGATTTAGTTATGAACTAAATC
CCCTAAATACCTAAGGGGG
Found at i:54092971 original size:27 final size:27
Alignment explanation
Indices: 54092941--54092994 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
54092931 TCATACAACC
* *
54092941 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
54092968 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
54092995 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:54094010 original size:11 final size:12
Alignment explanation
Indices: 54093982--54094014 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
54093972 GCCCAAACGT
54093982 CGAAATTTTCGAA
1 CGAAATTTTC-AA
54093995 CGAAATTTTC-A
1 CGAAATTTTCAA
54094006 CGAAATTTT
1 CGAAATTTT
54094015 TCCATGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:54095449 original size:15 final size:15
Alignment explanation
Indices: 54095429--54095472 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
54095419 GAGGCCTAGA
54095429 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
54095444 ATAAAGAAATCCATG
1 ATAAAGAAATCCAAG
*
54095459 ATAAGGAAATCCAA
1 ATAAAGAAATCCAA
54095473 ATTACAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:54095969 original size:42 final size:42
Alignment explanation
Indices: 54095817--54095993 Score: 174
Period size: 43 Copynumber: 4.1 Consensus size: 42
54095807 AAACGTCGCA
* * * * * * **
54095817 AAAGAACATGACCTTTAGCGGCACTTTTCCCAGAAACGCTGCT
1 AAAG-ACATGATCTTTAGCGACGCTTTCCCCAAAAATGCCACT
* * * * * *
54095860 AAAGAACATGACCTTTAGCGGCGCTTTCCCTAGAAACGCCGCT
1 AAAG-ACATGATCTTTAGCGACGCTTTCCCCAAAAATGCCACT
*
54095903 AAAGAACATGATCTTTAGCAACGCTTTCCCCAAAAATGCCACT
1 AAAG-ACATGATCTTTAGCGACGCTTTCCCCAAAAATGCCACT
* *
54095946 ATAGACATGATCTTTAGCGACGCTTTCCCCAAGAATGCCACT
1 AAAGACATGATCTTTAGCGACGCTTTCCCCAAAAATGCCACT
54095988 AAAGAC
1 AAAGAC
54095994 CATATCAAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 41 0.34
43 78 0.66
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (42 bp):
AAAGACATGATCTTTAGCGACGCTTTCCCCAAAAATGCCACT
Found at i:54100712 original size:29 final size:29
Alignment explanation
Indices: 54100677--54100752 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
54100667 GGACCTAAAA
*
54100677 GGCCATATGAATGTGATTTAGGCCTAATG
1 GGCCATATGAATGTGATTCAGGCCTAATG
* *
54100706 GGCCATAT-ACAGGTGATTCGGGCCTAATG
1 GGCCATATGA-ATGTGATTCAGGCCTAATG
*
54100735 GGCCATATGAATATGATT
1 GGCCATATGAATGTGATT
54100753 AGCTTAATGG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 38 0.95
30 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (29 bp):
GGCCATATGAATGTGATTCAGGCCTAATG
Found at i:54103880 original size:40 final size:41
Alignment explanation
Indices: 54103687--54103910 Score: 193
Period size: 41 Copynumber: 5.5 Consensus size: 41
54103677 AAAAAAGGCA
* * *
54103687 TTTATGGGAAAAACGCCGCTATTGCTTTACCTTTAGCGGCG
1 TTTATGAGAAAAACGCCACTATTGCTTTACCTTTTGCGGCG
** * * *
54103728 CTTT-T-TTATAAACGCCGCTATTGCTTTACCTTTTGTGGCG
1 -TTTATGAGAAAAACGCCACTATTGCTTTACCTTTTGCGGCG
* ** * *
54103768 TTTATGAGACAAACATCACTATTGCTTTACCTTTTGCAGCC
1 TTTATGAGAAAAACGCCACTATTGCTTTACCTTTTGCGGCG
* **
54103809 TTTATGAGAAAAACGCCAATATTGCAGTACCTTTTGCGGCG
1 TTTATGAGAAAAACGCCACTATTGCTTTACCTTTTGCGGCG
* * * * *
54103850 TTTAT-ATAAAAACGCTATTAATGCTTTACCTTTTGCGACG
1 TTTATGAGAAAAACGCCACTATTGCTTTACCTTTTGCGGCG
* ***
54103890 TTTTTGATCCAAACGCCACTA
1 TTTATGAGAAAAACGCCACTA
54103911 AAAACGCCGC
Statistics
Matches: 145, Mismatches: 34, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
39 3 0.02
40 63 0.43
41 76 0.52
42 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (41 bp):
TTTATGAGAAAAACGCCACTATTGCTTTACCTTTTGCGGCG
Found at i:54103910 original size:122 final size:122
Alignment explanation
Indices: 54103687--54103910 Score: 261
Period size: 122 Copynumber: 1.8 Consensus size: 122
54103677 AAAAAAGGCA
* ** ** * * * *
54103687 TTTATGGGAAAAACGCCGCTATTGCTTTACCTTTAGCGGCGCTTTTTTATAAACGCCGCTATTGC
1 TTTATGAGAAAAACGCCAATATTGCAGTACCTTTAGCGGCGCTTTTATAAAAACGCCACTAATGC
* * *
54103752 TTTACCTTTTGTGGCGTTTATGAGACAAACATCACTATTGCTTTACCTTTTGCAGCC
66 TTTACCTTTTGCGACGTTTATGAGACAAACACCACTATTGCTTTACCTTTTGCAGCC
* * *
54103809 TTTATGAGAAAAACGCCAATATTGCAGTACCTTTTGCGGCG-TTTATATAAAAACGCTATTAATG
1 TTTATGAGAAAAACGCCAATATTGCAGTACCTTTAGCGGCGCTTT-TATAAAAACGCCACTAATG
* ** *
54103873 CTTTACCTTTTGCGACGTTTTTGATCCAAACGCCACTA
65 CTTTACCTTTTGCGACGTTTATGAGACAAACACCACTA
54103911 AAAACGCCGC
Statistics
Matches: 82, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
121 3 0.04
122 79 0.96
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (122 bp):
TTTATGAGAAAAACGCCAATATTGCAGTACCTTTAGCGGCGCTTTTATAAAAACGCCACTAATGC
TTTACCTTTTGCGACGTTTATGAGACAAACACCACTATTGCTTTACCTTTTGCAGCC
Found at i:54104484 original size:40 final size:41
Alignment explanation
Indices: 54104296--54104495 Score: 206
Period size: 41 Copynumber: 4.9 Consensus size: 41
54104286 ATTTAAGGCA
* *
54104296 TTTATGGGAAAAACGCCGCTATTGCTTTACCTTTAGCGGCG
1 TTTATGAGAAAAACGCCGCTATTGCTTTACCTTTTGCGGCG
*** * * * *
54104337 TTT-TTTTATAAATGCTGCTATTGCTTTACCTTTTGTGGCG
1 TTTATGAGAAAAACGCCGCTATTGCTTTACCTTTTGCGGCG
* * * * *
54104377 TTTATGAGACAAACGTCACTATTGCTTTACCTTTTGCAGCC
1 TTTATGAGAAAAACGCCGCTATTGCTTTACCTTTTGCGGCG
* *
54104418 TTTATGAGAAAAACGCCACTGTTGCTTTACCTTTTGCGGCG
1 TTTATGAGAAAAACGCCGCTATTGCTTTACCTTTTGCGGCG
* * * *
54104459 TTTAT-ATAAAAACGCCGTTAATGCTTTACCATTTGCG
1 TTTATGAGAAAAACGCCGCTATTGCTTTACCTTTTGCG
54104496 ACGCTTTTGA
Statistics
Matches: 128, Mismatches: 30, Indels: 3
0.80 0.19 0.02
Matches are distributed among these distances:
40 58 0.45
41 70 0.55
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (41 bp):
TTTATGAGAAAAACGCCGCTATTGCTTTACCTTTTGCGGCG
Found at i:54104513 original size:122 final size:122
Alignment explanation
Indices: 54104296--54104519 Score: 279
Period size: 122 Copynumber: 1.8 Consensus size: 122
54104286 ATTTAAGGCA
* * * * * * * *
54104296 TTTATGGGAAAAACGCCGCTATTGCTTTACCTTTAGCGGCGTTTTTTTATAAATGCTGCTATTGC
1 TTTATGAGAAAAACGCCACTATTGCTTTACCTTTAGCGGCGTTTATATAAAAACGCCGCTAATGC
* * * *
54104361 TTTACCTTTTGTGGCGTTTATGAGACAAACGTCACTATTGCTTTACCTTTTGCAGCC
66 TTTACCATTTGCGACGTTTATGAGACAAACGCCACTATTGCTTTACCTTTTGCAGCC
* * *
54104418 TTTATGAGAAAAACGCCACTGTTGCTTTACCTTTTGCGGCGTTTATATAAAAACGCCGTTAATGC
1 TTTATGAGAAAAACGCCACTATTGCTTTACCTTTAGCGGCGTTTATATAAAAACGCCGCTAATGC
**
54104483 TTTACCATTTGCGACGCTTT-TGATCCAAACGCCACTA
66 TTTACCATTTGCGACG-TTTATGAGACAAACGCCACTA
54104520 AAAACGCCGC
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
122 81 0.96
123 3 0.04
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (122 bp):
TTTATGAGAAAAACGCCACTATTGCTTTACCTTTAGCGGCGTTTATATAAAAACGCCGCTAATGC
TTTACCATTTGCGACGTTTATGAGACAAACGCCACTATTGCTTTACCTTTTGCAGCC
Found at i:54108619 original size:28 final size:28
Alignment explanation
Indices: 54108588--54108642 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
54108578 AATCTTATTC
*
54108588 ATATGGCCCATC-GGCCCCAATCACATTT
1 ATATGGCCCACCAGG-CCCAATCACATTT
*
54108616 ATATGGCCCACCAGGCCTAATCACATT
1 ATATGGCCCACCAGGCCCAATCACATT
54108643 CATAGTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.24
Consensus pattern (28 bp):
ATATGGCCCACCAGGCCCAATCACATTT
Found at i:54108884 original size:16 final size:16
Alignment explanation
Indices: 54108863--54108895 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54108853 CCAAACTTTT
*
54108863 GACTTTTTGGCATTTC
1 GACTTTTCGGCATTTC
54108879 GACTTTTCGGCATTTC
1 GACTTTTCGGCATTTC
54108895 G
1 G
54108896 GGATTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (16 bp):
GACTTTTCGGCATTTC
Found at i:54114884 original size:46 final size:46
Alignment explanation
Indices: 54114834--54115009 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54114824 TGGTTGAGCA
54114834 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54114880 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
54114925 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54114973 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54115010 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54114990 original size:93 final size:93
Alignment explanation
Indices: 54114831--54115001 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
54114821 GGATGGTTGA
* * *
54114831 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAACTCGTTGAGT
54114896 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
54114924 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAACTCGTTGAGT
54114989 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54115002 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54117954 original size:15 final size:15
Alignment explanation
Indices: 54117934--54118002 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
54117924 GTATCTTGGG
54117934 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
54117949 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
54117964 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
54117979 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
54117994 TTTCTTTAT
1 TTTCTTTAT
54118003 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:54118003 original size:30 final size:30
Alignment explanation
Indices: 54117925--54118012 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
54117915 CATAGTATCG
* * * *
54117925 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
54117955 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
54117985 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
54118013 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:54120454 original size:46 final size:45
Alignment explanation
Indices: 54120404--54120579 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
54120394 TGGTTGAGCA
54120404 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
54120450 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
54120497 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
54120543 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54120580 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:54120560 original size:93 final size:93
Alignment explanation
Indices: 54120401--54120571 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
54120391 GGATGGTTGA
* *
54120401 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54120466 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
54120494 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54120559 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54120572 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:54125414 original size:13 final size:13
Alignment explanation
Indices: 54125392--54125428 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
54125382 AGGTAGGCAG
*
54125392 CACGGGCGTGTGC
1 CACGGACGTGTGC
54125405 CACGGACGTGTGC
1 CACGGACGTGTGC
54125418 CACGGACGTGT
1 CACGGACGTGT
54125429 TGATAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.30, G:0.41, T:0.16
Consensus pattern (13 bp):
CACGGACGTGTGC
Found at i:54127602 original size:28 final size:28
Alignment explanation
Indices: 54127557--54127631 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
54127547 TGGCCCATTT
*
54127557 AGGCCCAATCTCATTCATATGGCCTAT-
1 AGGCCCAATCACATTCATATGGCCTATC
* *
54127584 TGGCCCCAATCACAATCATATGGCCTATC
1 AGG-CCCAATCACATTCATATGGCCTATC
54127613 AGGCCCAATCACATTCATA
1 AGGCCCAATCACATTCATA
54127632 GTCATGCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 2 0.05
28 37 0.90
29 2 0.05
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.25
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCTATC
Found at i:54127868 original size:16 final size:16
Alignment explanation
Indices: 54127847--54127880 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
54127837 CCAAACTTTC
*
54127847 GGCTTTTTGGCATTTT
1 GGCTTTTTGACATTTT
54127863 GGCTTTTTGACATTTT
1 GGCTTTTTGACATTTT
54127879 GG
1 GG
54127881 GATTTGCCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.12, G:0.26, T:0.53
Consensus pattern (16 bp):
GGCTTTTTGACATTTT
Found at i:54129807 original size:27 final size:27
Alignment explanation
Indices: 54129767--54129820 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
54129757 TTATACAACC
* *
54129767 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
54129794 CATGTAACAATAATTTTCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
54129821 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.41
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:54139182 original size:40 final size:40
Alignment explanation
Indices: 54139093--54139356 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
54139083 TTGAATGATG
* *
54139093 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
54139132 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
54139172 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54139211 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54139251 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54139291 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54139332 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54139357 AACGAGGAGC
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
39 53 0.26
40 143 0.69
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54139374 original size:120 final size:118
Alignment explanation
Indices: 54139093--54139389 Score: 338
Period size: 119 Copynumber: 2.5 Consensus size: 118
54139083 TTGAATGATG
* *
54139093 TCCGGGCTAAGTCCCGAAGGC-TTGTG--CTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
1 TCCGGGCTAAGTCCCGAAGGCATT-TGAAC-GAGTGACTAA-ATCCGG-TTAA-ATCCCGAAGGC
* *
54139153 ATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
61 ATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
* ** * *
54139211 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTT
* *
54139276 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
65 GTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAATTACTA-AA
* * *
54139332 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
54139390 TACGTGATTT
Statistics
Matches: 153, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
118 23 0.15
119 64 0.42
120 64 0.42
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTG
TGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
Found at i:54159028 original size:16 final size:18
Alignment explanation
Indices: 54158997--54159029 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
54158987 AACTCGTCAC
54158997 ACTATCTATCATTTTGGT
1 ACTATCTATCATTTTGGT
54159015 ACTA-CTAT-ATTTTGG
1 ACTATCTATCATTTTGG
54159030 AGCTAGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (18 bp):
ACTATCTATCATTTTGGT
Found at i:54163094 original size:42 final size:43
Alignment explanation
Indices: 54162980--54163094 Score: 119
Period size: 42 Copynumber: 2.7 Consensus size: 43
54162970 CGGAGATATC
* * * *
54162980 GTGTAAGACCGTGTCCGGGACACAGGCCTCGATTTGAGATTTAT
1 GTGTAAGACCATGTCAGGGACACAGGCATCGATCT-AGATTTAT
*
54163024 GTGTAAGACCATGTCTGGGACATC-GGCATCGTATCT-GATTT-T
1 GTGTAAGACCATGTCAGGGACA-CAGGCATCG-ATCTAGATTTAT
* *
54163066 GTGTAAGACCCTGTCAGGGACAGAGGCAT
1 GTGTAAGACCATGTCAGGGACACAGGCAT
54163095 TGATACTGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
42 26 0.43
43 5 0.08
44 26 0.43
45 4 0.07
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (43 bp):
GTGTAAGACCATGTCAGGGACACAGGCATCGATCTAGATTTAT
Found at i:54163222 original size:15 final size:16
Alignment explanation
Indices: 54163195--54163224 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54163185 AGAGTACGAG
54163195 ATATGAGAATGTATAT
1 ATATGAGAATGTATAT
54163211 ATATGA-AATGTATA
1 ATATGAGAATGTATA
54163225 ATCTTTACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.37
Consensus pattern (16 bp):
ATATGAGAATGTATAT
Found at i:54164501 original size:9 final size:9
Alignment explanation
Indices: 54164487--54164516 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
54164477 AATTCATCAA
54164487 TTAAACAAC
1 TTAAACAAC
54164496 TTAAACAAC
1 TTAAACAAC
54164505 TTAAACAAC
1 TTAAACAAC
54164514 TTA
1 TTA
54164517 TTACCAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (9 bp):
TTAAACAAC
Found at i:54165788 original size:49 final size:48
Alignment explanation
Indices: 54165706--54165937 Score: 266
Period size: 49 Copynumber: 4.7 Consensus size: 48
54165696 AAGCTATCTG
* *
54165706 GTACGCATAGTAGCCTGCACTTAGTACTGCACATGCGACCAATTATCCA
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTAT-CA
* * *** *
54165755 GTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCGTCT
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCA
* * * *
54165804 GATACACATAGTAGCCTGCACTTAGTACCACACACGTGATCGAAGTTATCA
1 G-TACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCA
*
54165855 GGTACCCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTA
1 -GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATC-A
* *
54165905 GTACACGTAGTAGCCTACACTTAGTACTACACA
1 GTACACATAGTAGCCTGCACTTAGTACTACACA
54165938 CGTGACCTCA
Statistics
Matches: 153, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
49 73 0.48
50 43 0.28
51 36 0.24
52 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (48 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCA
Found at i:54165879 original size:101 final size:98
Alignment explanation
Indices: 54165701--54165944 Score: 294
Period size: 100 Copynumber: 2.5 Consensus size: 98
54165691 AGCCGAAGCT
* * * * * *
54165701 ATCTGGTACGCATAGTAGCCTGCACTTAGTACTGCACATGCGACCAATTATCCAGTACACGTAGT
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACATAGT
*
54165766 AGCCTGCACTTAGTACTACACATGTGACCTAACC
66 AGCCTGCACTTAGTACTACACATGCGACC-AACC
* * * *
54165800 GTCTGATACACATAGTAGCCTGCACTTAGTACCACACACGTGATCGAAGTTAT-CAGGTACCCAT
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCA-GTACACAT
**
54165864 AGTAGCCTGCACTTAGTACTACACATGCGACCAATT
63 AGTAGCCTGCACTTAGTACTACACATGCGACCAACC
* *
54165900 ATCT-AGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACC
1 ATCTGA-TACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
54165945 TCACAATAGC
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
99 38 0.31
100 44 0.36
101 41 0.33
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (98 bp):
ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACATAGT
AGCCTGCACTTAGTACTACACATGCGACCAACC
Found at i:54168738 original size:15 final size:15
Alignment explanation
Indices: 54168708--54168757 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
54168698 AACAGAGAAG
*
54168708 CCAAGAATAAAAAAAT
1 CCAAG-ATAAAGAAAT
54168724 CCAAGATAAAGAAAT
1 CCAAGATAAAGAAAT
*
54168739 CCATGATACAAG-AAT
1 CCAAGATA-AAGAAAT
54168754 CCAA
1 CCAA
54168758 TTTACAGCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 22 0.73
16 8 0.27
ACGTcount: A:0.58, C:0.18, G:0.10, T:0.14
Consensus pattern (15 bp):
CCAAGATAAAGAAAT
Found at i:54172275 original size:30 final size:30
Alignment explanation
Indices: 54172241--54172300 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
54172231 CCTTTAATAC
* *
54172241 GAACTTTGGCAAAATTACCCTTTTTCCCCT
1 GAACTTTGGCAAAATTACACTTTTGCCCCT
* *
54172271 GAACTTTTGCATAATTACACTTTTGCCCCT
1 GAACTTTGGCAAAATTACACTTTTGCCCCT
54172301 TGGCTCGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.38
Consensus pattern (30 bp):
GAACTTTGGCAAAATTACACTTTTGCCCCT
Found at i:54174081 original size:40 final size:39
Alignment explanation
Indices: 54174003--54174226 Score: 258
Period size: 40 Copynumber: 5.5 Consensus size: 39
54173993 ACCCAAGTAT
*
54174003 CTTCGGGATTTAG-CCGGATATAG-CAACTCA-CACAAATGC
1 CTTC-GGACTTAGCCCGGATATAGTC-ACT-AGCACAAATGC
* **
54174042 CTTCGCGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCG-GACTTAGCCCGGATATAGTCACTAGCACAAATGC
54174082 CTTCAGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTC-GGACTTAGCCCGGATATAGTCACTAGCACAAATGC
54174122 CTTCGGGACTTAGCCCGGATATAG-CAACTACTTGCACAAATGC
1 CTTC-GGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
54174165 CTTCAGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTC-GGACTTAGCCCGGATATAGTCACTAGCACAAATGC
54174205 CTTCGGGACTTAGCCCGGATAT
1 CTTC-GGACTTAGCCCGGATAT
54174227 CATCCGAATA
Statistics
Matches: 163, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.01
39 11 0.07
40 113 0.69
41 2 0.01
43 36 0.22
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
CTTCGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:54174189 original size:83 final size:80
Alignment explanation
Indices: 54174003--54174226 Score: 294
Period size: 83 Copynumber: 2.8 Consensus size: 80
54173993 ACCCAAGTAT
* * * *
54174003 CTTCGGGATTTAG-CCGGATATAG-CAACTCA-CACAAATGCCTTCGCGTCTTAGCCCGGATATA
1 CTTCAGGACTTAGCCCGGATATAGTC-ACT-AGCACAAATGCCTTCGGGACTTAGCCCGGATATA
**
54174065 GTCACTAGCATGAATGC
64 GTCACTAGCACAAATGC
54174082 CTTCAGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG-
1 CTTCAGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
54174146 CAACTACTTGCACAAATGC
66 C-ACTA---GCACAAATGC
* *
54174165 CTTCAGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCAGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
54174227 CATCCGAATA
Statistics
Matches: 130, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
79 13 0.10
80 48 0.37
81 1 0.01
83 68 0.52
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
CTTCAGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:54175798 original size:38 final size:38
Alignment explanation
Indices: 54175756--54175831 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
54175746 TTCATCCTTT
54175756 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
54175794 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
54175832 GGAGTTCTTG
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:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:54177113 original size:40 final size:40
Alignment explanation
Indices: 54177019--54177163 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
54177009 TACTCGAATG
*
54177019 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
54177060 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
54177100 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
54177140 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
54177164 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:54177231 original size:61 final size:61
Alignment explanation
Indices: 54177136--54177256 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 61
54177126 TTATGCTAGT
54177136 GACCATATCCGGGTTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCCGGCTAAACCCCA
1 GACCATATCCGGGTTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCCGGCTAAACCCCA
*
54177197 GACCATATCCGGGTTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCTGGCTAAACCCC
1 GACCATATCCGGGTTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCCGGCTAAACCCC
54177257 GAAGATGCTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.24, C:0.27, G:0.26, T:0.22
Consensus pattern (61 bp):
GACCATATCCGGGTTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCCGGCTAAACCCCA
Found at i:54192532 original size:11 final size:11
Alignment explanation
Indices: 54192516--54192547 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
54192506 GTTTTGTCCC
54192516 TTTTTGGCTCA
1 TTTTTGGCTCA
*
54192527 TTTTTGGCTCG
1 TTTTTGGCTCA
54192538 TTTTTGGCTC
1 TTTTTGGCTC
54192548 CTGGTGCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.03, C:0.19, G:0.22, T:0.56
Consensus pattern (11 bp):
TTTTTGGCTCA
Found at i:54199763 original size:33 final size:32
Alignment explanation
Indices: 54199724--54199788 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
54199714 ACTTCGATTT
*
54199724 TGGTTCCCAATAGAGAAAGTAAACTTTCCCTA
1 TGGTTCCCAATAGAGAAAGTAAACATTCCCTA
*
54199756 NTGGTTCCCAATAGAGAAGGTAAACATTCCCTA
1 -TGGTTCCCAATAGAGAAAGTAAACATTCCCTA
54199789 CTGGAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (32 bp):
TGGTTCCCAATAGAGAAAGTAAACATTCCCTA
Found at i:54201377 original size:25 final size:26
Alignment explanation
Indices: 54201347--54201401 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
54201337 AGACAAAATA
* *
54201347 TAATCCTAACTTCTTAACTTAAG-TC
1 TAATCCAAACTTCTAAACTTAAGTTC
*
54201372 TAATCCAAATTTCTAAACTTAAGTTC
1 TAATCCAAACTTCTAAACTTAAGTTC
54201398 TAAT
1 TAAT
54201402 TTTGGTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (26 bp):
TAATCCAAACTTCTAAACTTAAGTTC
Found at i:54201602 original size:14 final size:14
Alignment explanation
Indices: 54201583--54201610 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54201573 CATTTAGCCA
54201583 AACCAAACTGGCCC
1 AACCAAACTGGCCC
54201597 AACCAAACTGGCCC
1 AACCAAACTGGCCC
54201611 GGTGATTGGA
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:0.36, C:0.43, G:0.14, T:0.07
Consensus pattern (14 bp):
AACCAAACTGGCCC
Found at i:54202950 original size:22 final size:22
Alignment explanation
Indices: 54202902--54202947 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
54202892 TTTGTATGAC
*
54202902 ATTATAAGCATCATAATAATCT
1 ATTATAAGAATCATAATAATCT
54202924 ATTATAAGAAT-ATATATAAT-T
1 ATTATAAGAATCATA-ATAATCT
54202945 ATT
1 ATT
54202948 TATTTGTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
ATTATAAGAATCATAATAATCT
Found at i:54206088 original size:10 final size:10
Alignment explanation
Indices: 54206073--54206106 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
54206063 AATTTTAGCT
54206073 TTTATCTTTA
1 TTTATCTTTA
*
54206083 TTTATCCTTA
1 TTTATCTTTA
54206093 TTTATCTTTA
1 TTTATCTTTA
54206103 TTTA
1 TTTA
54206107 ATTGAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:54213550 original size:5 final size:5
Alignment explanation
Indices: 54213542--54213569 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
54213532 TCAATCCAAT
54213542 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
54213570 CATCATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:54214815 original size:13 final size:13
Alignment explanation
Indices: 54214797--54214821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54214787 TCTGCAGGGA
54214797 CACGCCCGTGTGC
1 CACGCCCGTGTGC
54214810 CACGCCCGTGTG
1 CACGCCCGTGTG
54214822 TGATTACTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.44, G:0.32, T:0.16
Consensus pattern (13 bp):
CACGCCCGTGTGC
Found at i:54216771 original size:5 final size:6
Alignment explanation
Indices: 54216755--54216779 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54216745 TTAAATCTGC
54216755 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
54216780 TAGTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:54223060 original size:5 final size:6
Alignment explanation
Indices: 54223047--54223093 Score: 76
Period size: 6 Copynumber: 7.5 Consensus size: 6
54223037 ATAATTTAAT
54223047 AAATAA AAATAA AAATCTAA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA AAA
54223094 ATATATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 33 0.85
8 6 0.15
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:54223076 original size:26 final size:25
Alignment explanation
Indices: 54223047--54223096 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
54223037 ATAATTTAAT
*
54223047 AAATAAAAATAAAAATCTAAAAATAA
1 AAATAAAAATAAAAAT-AAAAAATAA
54223073 AAATAAAAATAAAAATAAAAAATA
1 AAATAAAAATAAAAATAAAAAATA
54223097 TATAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (25 bp):
AAATAAAAATAAAAATAAAAAATAA
Found at i:54223132 original size:9 final size:9
Alignment explanation
Indices: 54223120--54223162 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
54223110 AAATAATTTA
54223120 GTTAATTCG
1 GTTAATTCG
54223129 GTTAATTCG
1 GTTAATTCG
54223138 GTTAATTCG
1 GTTAATTCG
*
54223147 ATTAATTCG
1 GTTAATTCG
54223156 GTTAATT
1 GTTAATT
54223163 TTATACTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.47
Consensus pattern (9 bp):
GTTAATTCG
Found at i:54227991 original size:12 final size:12
Alignment explanation
Indices: 54227974--54227999 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54227964 TAGAGTGGCT
54227974 TAATGAGCCATG
1 TAATGAGCCATG
54227986 TAATGAGCCATG
1 TAATGAGCCATG
54227998 TA
1 TA
54228000 CATAGGTTAA
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:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (12 bp):
TAATGAGCCATG
Found at i:54229552 original size:63 final size:63
Alignment explanation
Indices: 54229485--54229615 Score: 154
Period size: 63 Copynumber: 2.1 Consensus size: 63
54229475 CAATGTTTGG
* * * *
54229485 CATTAAGGACCATATGGGCCAAGGAAACGGGCGTGTGTCCAGGCCGTATGACTCACTACTTGC
1 CATTAAGGACCACATGGACCAAGGAAACAGACGTGTGTCCAGGCCGTATGACTCACTACTTGC
* * * * * * **
54229548 CATTAAGGACCACATGGACCAGGGACATAGATGTGTGTCCAGGCTGTGTGACTCACTGTTTGC
1 CATTAAGGACCACATGGACCAAGGAAACAGACGTGTGTCCAGGCCGTATGACTCACTACTTGC
54229611 CATTA
1 CATTA
54229616 CATGAGCCAG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (63 bp):
CATTAAGGACCACATGGACCAAGGAAACAGACGTGTGTCCAGGCCGTATGACTCACTACTTGC
Found at i:54232708 original size:21 final size:21
Alignment explanation
Indices: 54232671--54232717 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
54232661 AAGCCAGTTA
54232671 TAAAA-GTCCATAAACAGTCCT
1 TAAAATGTCCATAAACAG-CCT
*
54232692 TAAAATGTCCAT-TACAGCCT
1 TAAAATGTCCATAAACAGCCT
*
54232712 AAAAAT
1 TAAAAT
54232718 ATCAAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.35
21 9 0.39
22 6 0.26
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.26
Consensus pattern (21 bp):
TAAAATGTCCATAAACAGCCT
Found at i:54234796 original size:43 final size:43
Alignment explanation
Indices: 54234670--54234831 Score: 168
Period size: 43 Copynumber: 3.8 Consensus size: 43
54234660 TAATATCTGT
* *
54234670 TTTCGTGTAAGACCACGTCTGGGACGTTGGAATCGA-ATTATGA
1 TTTCATGTAAGACCACGTCTGGGACGTTGGCATCGATATT-TGA
* * * * *
54234713 TTTACATGTAAGACCATGTTTGGGACATTGGTATTG-TATTTGA
1 TTT-CATGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGA
* **
54234756 TTTCGTGTAAGACCTTGTCTGGGACAG-TGGCATCGATATTTGA
1 TTTCATGTAAGACCACGTCTGGGAC-GTTGGCATCGATATTTGA
* *
54234799 TTACATGTAGGACCACGTCTGGGACGTTGGCAT
1 TTTCATGTAAGACCACGTCTGGGACGTTGGCAT
54234832 TGTACGAGCT
Statistics
Matches: 97, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
42 26 0.27
43 42 0.43
44 29 0.30
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.34
Consensus pattern (43 bp):
TTTCATGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGA
Found at i:54250886 original size:68 final size:68
Alignment explanation
Indices: 54250720--54250908 Score: 236
Period size: 68 Copynumber: 2.8 Consensus size: 68
54250710 GTAATATGAC
* * * * *
54250720 ATGCTTATAATAAATCAATACGGTAGCAATTAACATGCTTGTAGCAAATCAAT-AGGTAGCAATC
1 ATGCTTATAATAGATCAATACGGTAGCAATTAATATGCTTATAACAAATCAATAAGCTAGCAATC
54250784 AAT
66 AAT
* * * * * * *
54250787 ATACTTATAACAGATCAATACAGTAGCAATTAATATGCTTCTAACATATCAATAAGCTAGTAATT
1 ATGCTTATAATAGATCAATACGGTAGCAATTAATATGCTTATAACAAATCAATAAGCTAGCAATC
*
54250852 TAT
66 AAT
* *
54250855 ATGCTTAAAATAGATCAATATGGTAGCAATTAATATGCTTATAACAAATCAATA
1 ATGCTTATAATAGATCAATACGGTAGCAATTAATATGCTTATAACAAATCAATA
54250909 TATTAGCAAA
Statistics
Matches: 102, Mismatches: 19, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
67 45 0.44
68 57 0.56
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (68 bp):
ATGCTTATAATAGATCAATACGGTAGCAATTAATATGCTTATAACAAATCAATAAGCTAGCAATC
AAT
Found at i:54250909 original size:34 final size:34
Alignment explanation
Indices: 54250720--54250908 Score: 209
Period size: 34 Copynumber: 5.6 Consensus size: 34
54250710 GTAATATGAC
* *
54250720 ATGCTTATAATAAATCAATACGGTAGCAATTAAC
1 ATGCTTATAACAAATCAATACGGTAGCAATTAAT
* * *
54250754 ATGCTTGTAGCAAATCAATA-GGTAGCAATCAAT
1 ATGCTTATAACAAATCAATACGGTAGCAATTAAT
* * *
54250787 ATACTTATAACAGATCAATACAGTAGCAATTAAT
1 ATGCTTATAACAAATCAATACGGTAGCAATTAAT
* * * * * *
54250821 ATGCTTCTAACATATCAATAAGCTAGTAATTTAT
1 ATGCTTATAACAAATCAATACGGTAGCAATTAAT
* * * *
54250855 ATGCTTAAAATAGATCAATATGGTAGCAATTAAT
1 ATGCTTATAACAAATCAATACGGTAGCAATTAAT
54250889 ATGCTTATAACAAATCAATA
1 ATGCTTATAACAAATCAATA
54250909 TATTAGCAAA
Statistics
Matches: 124, Mismatches: 30, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
33 27 0.22
34 97 0.78
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (34 bp):
ATGCTTATAACAAATCAATACGGTAGCAATTAAT
Found at i:54251827 original size:21 final size:21
Alignment explanation
Indices: 54251802--54251851 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 21
54251792 GTTTTAATCC
54251802 AATAAAGTAAAAATAAAAAAT
1 AATAAAGTAAAAATAAAAAAT
* *
54251823 AAT-AAG-AAAGATGAAAAAT
1 AATAAAGTAAAAATAAAAAAT
*
54251842 -ATAATGTAAA
1 AATAAAGTAAA
54251852 GAAGAGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 6 0.25
21 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (21 bp):
AATAAAGTAAAAATAAAAAAT
Found at i:54253657 original size:47 final size:46
Alignment explanation
Indices: 54253588--54253678 Score: 155
Period size: 47 Copynumber: 2.0 Consensus size: 46
54253578 CTCATAAAGC
* *
54253588 AAAGTGATTATATTGGTTAAATATCAAATCAAATCAAAATTAAAACA
1 AAAGTGATTATATTAGTCAAATATCAAATCAAATCAAAA-TAAAACA
54253635 AAAGTGATTATATTAGTCAAATATCAAATCAAATCAAAATAAAA
1 AAAGTGATTATATTAGTCAAATATCAAATCAAATCAAAATAAAA
54253679 TAATAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
46 5 0.12
47 37 0.88
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.29
Consensus pattern (46 bp):
AAAGTGATTATATTAGTCAAATATCAAATCAAATCAAAATAAAACA
Found at i:54254268 original size:5 final size:5
Alignment explanation
Indices: 54254258--54254284 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
54254248 TTAAGGGTGT
54254258 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
54254285 AAGTTGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:54255368 original size:30 final size:29
Alignment explanation
Indices: 54255279--54255369 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 29
54255269 ACACATCAAT
*
54255279 AATTCTTTGTATTTTCATAAATTTT-AAATTT
1 AATTCTTT-TATTTT--TAAATTTTAAAATTC
* *
54255310 AA-TCTCTTTATTTTT-ATTTTTAGGAATTC
1 AATTCT-TTTATTTTTAAATTTTA-AAATTC
54255339 AATTCTTTTACTTTTTAAATTTTAAAATTC
1 AATTCTTTTA-TTTTTAAATTTTAAAATTC
54255369 A
1 A
54255370 GTTCCAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
27 5 0.10
28 1 0.02
29 10 0.20
30 23 0.47
31 10 0.20
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (29 bp):
AATTCTTTTATTTTTAAATTTTAAAATTC
Found at i:54259597 original size:18 final size:18
Alignment explanation
Indices: 54259574--54259609 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54259564 TCCTTAACCT
*
54259574 CTTTTGGTTCAGCAGTAG
1 CTTTTGGTGCAGCAGTAG
54259592 CTTTTGGTGCAGCAGTAG
1 CTTTTGGTGCAGCAGTAG
54259610 ACTTGCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.36
Consensus pattern (18 bp):
CTTTTGGTGCAGCAGTAG
Found at i:54263600 original size:6 final size:6
Alignment explanation
Indices: 54263589--54263628 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
54263579 GAAAAAAGAA
*
54263589 AAAAAT AGAAAT AGCAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT A--AAAAT AAAAAT AAAAAT AAAAAT AA
54263629 TAAAAGTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 25 0.83
8 5 0.17
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:54263643 original size:19 final size:17
Alignment explanation
Indices: 54263609--54263675 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
54263599 ATAGCAAAAT
54263609 AAAAATAAAA-ATA-AA
1 AAAAATAAAATATATAA
* *
54263624 AATAATAAAAGTGTATAA
1 AAAAATAAAA-TATATAA
*
54263642 AAAATTAAAATATATAA
1 AAAAATAAAATATATAA
*
54263659 AAAATTTAAAA-ATATAA
1 AAAA-ATAAAATATATAA
54263676 GTATAAGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 9 0.21
17 18 0.42
18 16 0.37
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAAATAAAATATATAA
Found at i:54267668 original size:17 final size:17
Alignment explanation
Indices: 54267646--54267680 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54267636 CTAATTAAAA
*
54267646 ATATTAGGGCAAAAATT
1 ATATTAAGGCAAAAATT
*
54267663 ATATTAAGGCAAGAATT
1 ATATTAAGGCAAAAATT
54267680 A
1 A
54267681 AGAACACATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.29
Consensus pattern (17 bp):
ATATTAAGGCAAAAATT
Found at i:54272496 original size:16 final size:16
Alignment explanation
Indices: 54272475--54272505 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54272465 TTCACTATTA
*
54272475 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
54272491 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
54272506 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:54275252 original size:4 final size:4
Alignment explanation
Indices: 54275243--54275278 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
54275233 GATTTATGCA
54275243 TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
54275279 AAGTCAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:54276855 original size:37 final size:37
Alignment explanation
Indices: 54276809--54276920 Score: 105
Period size: 37 Copynumber: 3.2 Consensus size: 37
54276799 AAAAATAAAA
*
54276809 TTATTTTAATAGTTTAATATTAAATTCAATTTAATAT
1 TTATCTTAATAGTTTAATATTAAATTCAATTTAATAT
*
54276846 TTATCTTAATAG--T-AT-TT-TATT-AATTTAATA-
1 TTATCTTAATAGTTTAATATTAAATTCAATTTAATAT
***
54276876 TTAAAATAATTA-TATTAATATTAAATTCAATTTAATAT
1 TTATCTTAA-TAGT-TTAATATTAAATTCAATTTAATAT
54276914 TTATCTT
1 TTATCTT
54276921 GTAAATAAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
30 6 0.11
31 11 0.19
32 3 0.05
33 3 0.05
34 4 0.07
35 3 0.05
36 3 0.05
37 20 0.35
38 4 0.07
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (37 bp):
TTATCTTAATAGTTTAATATTAAATTCAATTTAATAT
Found at i:54279243 original size:45 final size:43
Alignment explanation
Indices: 54279194--54279398 Score: 209
Period size: 45 Copynumber: 4.6 Consensus size: 43
54279184 CCGAAGTGAG
**
54279194 GCCATAGTATCTTTCAACTATGGTCTTATTTGTATTGGTTTTAAT
1 GCCATAGTATCTTTCAACTATGGTCTTATTCAT-TTGG-TTTAAT
* * *
54279239 GCCATAGTATCTTTCAATTATGGTCTTATACATTTCCGGTATAAT
1 GCCATAGTATCTTTCAACTATGGTCTTATTCATTT--GGTTTAAT
*
54279284 GTCATAGTATCTTTCAACTATGG-CTTTATTCATTCTGGTTTAAT
1 GCCATAGTATCTTTCAACTATGGTC-TTATTCATT-TGGTTTAAT
* *
54279328 GTCATAGTATCTTTCAACTATGGTCTT-TCTCATTTCGGGTATAAT
1 GCCATAGTATCTTTCAACTATGGTCTTAT-TCATTT--GGTTTAAT
* *
54279373 GTCATGGTATCTTTCAACCT-TGGTCT
1 GCCATAGTATCTTTCAA-CTATGGTCT
54279399 ATCTCGTTTC
Statistics
Matches: 140, Mismatches: 11, Indels: 18
0.83 0.07 0.11
Matches are distributed among these distances:
43 2 0.01
44 40 0.29
45 93 0.66
46 5 0.04
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.45
Consensus pattern (43 bp):
GCCATAGTATCTTTCAACTATGGTCTTATTCATTTGGTTTAAT
Found at i:54279369 original size:89 final size:90
Alignment explanation
Indices: 54279196--54279398 Score: 272
Period size: 89 Copynumber: 2.3 Consensus size: 90
54279186 GAAGTGAGGC
** *
54279196 CATAGTATCTTTCAACTATGGTCTTATTTGTATTGGTTTTAATGCCATAGTATCTTTCAATTATG
1 CATAGTATCTTTCAACTATGGTCTTATTCATATTGGTTTTAATGCCATAGTATCTTTCAACTATG
54279261 GTCTTATACATTTCCGGTATAATGT
66 GTCTTATACATTTCCGGTATAATGT
*
54279286 CATAGTATCTTTCAACTATGG-CTTTATTCAT-TCTGG-TTTAATGTCATAGTATCTTTCAACTA
1 CATAGTATCTTTCAACTATGGTC-TTATTCATAT-TGGTTTTAATGCCATAGTATCTTTCAACTA
* *
54279348 TGGTCTT-TCTCATTTCGGGTATAATGT
64 TGGTCTTAT-ACATTTCCGGTATAATGT
*
54279375 CATGGTATCTTTCAACCT-TGGTCT
1 CATAGTATCTTTCAA-CTATGGTCT
54279399 ATCTCGTTTC
Statistics
Matches: 101, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
88 1 0.01
89 67 0.66
90 33 0.33
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.46
Consensus pattern (90 bp):
CATAGTATCTTTCAACTATGGTCTTATTCATATTGGTTTTAATGCCATAGTATCTTTCAACTATG
GTCTTATACATTTCCGGTATAATGT
Found at i:54281448 original size:22 final size:22
Alignment explanation
Indices: 54281423--54281464 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54281413 TTTTGCTTTG
*
54281423 TTTATTTTATTTTAACTTAACT
1 TTTATTTTAATTTAACTTAACT
*
54281445 TTTATTTTAATTTAATTTAA
1 TTTATTTTAATTTAACTTAA
54281465 TTTAAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATTTTAATTTAACTTAACT
Found at i:54281449 original size:17 final size:17
Alignment explanation
Indices: 54281427--54281459 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54281417 GCTTTGTTTA
54281427 TTTTATTTTAACTTAAC
1 TTTTATTTTAACTTAAC
*
54281444 TTTTATTTTAATTTAA
1 TTTTATTTTAACTTAA
54281460 TTTAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATTTTAACTTAAC
Found at i:54284663 original size:22 final size:21
Alignment explanation
Indices: 54284633--54284679 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
54284623 TACAAATTAA
54284633 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
54284655 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
54284676 ATCT
1 ATCT
54284680 AAGATTGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:54284685 original size:19 final size:19
Alignment explanation
Indices: 54284650--54284728 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
54284640 AGATTACAAG
54284650 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
54284671 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
54284688 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
54284707 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
54284726 ATC
1 ATC
54284729 CTTAAAGATT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
20 1 0.02
21 8 0.14
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:54284705 original size:36 final size:38
Alignment explanation
Indices: 54284650--54284722 Score: 132
Period size: 36 Copynumber: 2.0 Consensus size: 38
54284640 AGATTACAAG
54284650 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGT
1 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGT
54284688 ATCATATC-T-AAGATTGCATATCATATCTAAGATTG
1 ATCATATCTTCAAGATTGCATATCATATCTAAGATTG
54284723 CATATCCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 26 0.74
37 1 0.03
38 8 0.23
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (38 bp):
ATCATATCTTCAAGATTGCATATCATATCTAAGATTGT
Found at i:54284737 original size:36 final size:35
Alignment explanation
Indices: 54284651--54284738 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 35
54284641 GATTACAAGA
54284651 TCATATCTTCAAGATTGCATATCATATCTAAGATTG
1 TCATATCTT-AAGATTGCATATCATATCTAAGATTG
54284687 TATCATATC-TAAGATTGCATATCATATCTAAGATTG
1 --TCATATCTTAAGATTGCATATCATATCTAAGATTG
54284723 -CATATCCTTAAAGATT
1 TCATAT-CTT-AAGATT
54284739 ATATTTCCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
33 5 0.11
34 1 0.02
35 1 0.02
36 32 0.68
37 1 0.02
38 7 0.15
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (35 bp):
TCATATCTTAAGATTGCATATCATATCTAAGATTG
Found at i:54285534 original size:44 final size:44
Alignment explanation
Indices: 54285469--54285570 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 44
54285459 ATCTGCTCCA
* * *
54285469 CTACTGCTTA-GGGAGATAAGATCCACAATTTTGACTTGTTACC
1 CTACTGCTTAGGGGAGATAAGATCCACAAATTTAACCTGTTACC
* **
54285512 CTACTGTTTAGGGGAGATAAGATCTGCAAATTTAACCTGTTACC
1 CTACTGCTTAGGGGAGATAAGATCCACAAATTTAACCTGTTACC
54285556 CTACTGCTTAGGGGA
1 CTACTGCTTAGGGGA
54285571 TTAAGGCACT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 9 0.18
44 42 0.82
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (44 bp):
CTACTGCTTAGGGGAGATAAGATCCACAAATTTAACCTGTTACC
Done.