Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 185 of 204
Found at i:54711490 original size:13 final size:13
Alignment explanation
Indices: 54711456--54711492 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
54711446 GCTTCCTTAA
54711456 TATTTGA-TTTAT
1 TATTTGATTTTAT
54711468 TATTTGATTTTAGT
1 TATTTGATTTTA-T
54711482 TATTT-ATTTTA
1 TATTTGATTTTA
54711493 ATTGTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 10 0.43
14 6 0.26
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
TATTTGATTTTAT
Found at i:54718030 original size:25 final size:25
Alignment explanation
Indices: 54718010--54718122 Score: 163
Period size: 25 Copynumber: 4.5 Consensus size: 25
54718000 GCGTGCTTTT
*
54718010 TGATTATTAGCACATCAGTGCTCTC
1 TGATTATTAGCACATCAGTGCTATC
*
54718035 TGATTATTAGCACGTCAGTGCTATC
1 TGATTATTAGCACATCAGTGCTATC
* *
54718060 TGATTATTACCGCATCAGTGCTATC
1 TGATTATTAGCACATCAGTGCTATC
* *
54718085 TGATTATTAGCGCATCAGTGCTCTC
1 TGATTATTAGCACATCAGTGCTATC
*
54718110 TGATTACTAGCAC
1 TGATTATTAGCAC
54718123 GCTCTTTGAT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 79 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (25 bp):
TGATTATTAGCACATCAGTGCTATC
Found at i:54718132 original size:19 final size:19
Alignment explanation
Indices: 54718104--54718141 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54718094 GCGCATCAGT
54718104 GCTCTCTGATTACTAGCAC
1 GCTCTCTGATTACTAGCAC
* *
54718123 GCTCTTTGATTATTAGCAC
1 GCTCTCTGATTACTAGCAC
54718142 AGTAGTGCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (19 bp):
GCTCTCTGATTACTAGCAC
Found at i:54718161 original size:22 final size:22
Alignment explanation
Indices: 54718135--54718203 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
54718125 TCTTTGATTA
* * *
54718135 TTAGCACAGTAGTGCTCTCTAT
1 TTAGCACATTTGTGCTCTCTGT
54718157 TTAGCACATTTGTGCTCTCTGT
1 TTAGCACATTTGTGCTCTCTGT
* *
54718179 ATAGCACTTTTGTGCTCTCTGT
1 TTAGCACATTTGTGCTCTCTGT
54718201 TTA
1 TTA
54718204 ATAGTGCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (22 bp):
TTAGCACATTTGTGCTCTCTGT
Found at i:54721019 original size:24 final size:25
Alignment explanation
Indices: 54720961--54721019 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
54720951 ATAAATATTA
54720961 ATTTATA-ATATTTTGATTTATTTT
1 ATTTATATATATTTTGATTTATTTT
54720985 -TTTA-ATGATATTTT-A-TTATTTT
1 ATTTATAT-ATATTTTGATTTATTTT
54721007 ATTTAGTATATAT
1 ATTTA-TATATAT
54721020 ATATGGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.27
23 9 0.30
24 11 0.37
25 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (25 bp):
ATTTATATATATTTTGATTTATTTT
Found at i:54721394 original size:28 final size:22
Alignment explanation
Indices: 54721337--54721382 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
54721327 TCTGCCAGCC
54721337 TCCCTCGCGCATGCGCACGCCA
1 TCCCTCGCGCATGCGCACGCCA
54721359 TCCCTCGCGCATGCGCACGCCA
1 TCCCTCGCGCATGCGCACGCCA
54721381 TC
1 TC
54721383 ACCGCCGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.50, G:0.22, T:0.15
Consensus pattern (22 bp):
TCCCTCGCGCATGCGCACGCCA
Found at i:54729234 original size:22 final size:23
Alignment explanation
Indices: 54729207--54729273 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
54729197 TAAATTGTGT
* *
54729207 ATAAATAATATTAAAT-TTACATA
1 ATAAAT-ATATAAAATAATACATA
54729230 A-AAATATATAAAATAATACATA
1 ATAAATATATAAAATAATACATA
54729252 ATAAAT-T-TGAAGAATAATACAT
1 ATAAATATAT-AA-AATAATACAT
54729274 GAAACTTAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 9 0.24
22 14 0.37
23 15 0.39
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (23 bp):
ATAAATATATAAAATAATACATA
Found at i:54729329 original size:23 final size:22
Alignment explanation
Indices: 54729303--54729360 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
54729293 AAAAGAAACC
*
54729303 TTTAAAAATAATAATACAATAGA
1 TTTAAAAATAATAA-ACAATAAA
*
54729326 TTTAAACAAT-ATCAACAATAAA
1 TTTAAA-AATAATAAACAATAAA
*
54729348 TTT-ATAATAATAA
1 TTTAAAAATAATAA
54729361 GTTTAATTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 3 0.10
21 4 0.14
22 10 0.34
23 9 0.31
24 3 0.10
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
TTTAAAAATAATAAACAATAAA
Found at i:54741346 original size:26 final size:26
Alignment explanation
Indices: 54741309--54741360 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
54741299 GAATCAGCAA
*
54741309 ACACACACATATCTGCACATATAGAC
1 ACACACACATATCTGCACAGATAGAC
*
54741335 ACACACATATATCTGCACAGATAGAC
1 ACACACACATATCTGCACAGATAGAC
54741361 TACTAGGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (26 bp):
ACACACACATATCTGCACAGATAGAC
Found at i:54745930 original size:14 final size:14
Alignment explanation
Indices: 54745878--54745930 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
54745868 GAGTTTTGAC
54745878 TTTAGGATTTAGGG
1 TTTAGGATTTAGGG
* *
54745892 TTTGGGATTTGGGG
1 TTTAGGATTTAGGG
*
54745906 TTTA-AAGTTTAGGG
1 TTTAGGA-TTTAGGG
*
54745920 TTTATGATTTA
1 TTTAGGATTTA
54745931 ATGTTAAGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 1 0.03
14 29 0.94
15 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (14 bp):
TTTAGGATTTAGGG
Found at i:54745999 original size:14 final size:13
Alignment explanation
Indices: 54745980--54746032 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
54745970 AGTTTACTAT
54745980 TTTAGGGTTTGATG
1 TTTAGGGTTT-ATG
*
54745994 TTTAGGGTTTAAGG
1 TTTAGGGTTT-ATG
54746008 TTTAGGGTTTATG
1 TTTAGGGTTTATG
*
54746021 ATTTAAGGTTTA
1 -TTTAGGGTTTA
54746033 CAATGCATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 2 0.06
14 32 0.94
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (13 bp):
TTTAGGGTTTATG
Found at i:54746017 original size:21 final size:21
Alignment explanation
Indices: 54745993--54746032 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54745983 AGGGTTTGAT
*
54745993 GTTTAGGGTTTAAGGTTTAGG
1 GTTTAGGATTTAAGGTTTAGG
*
54746014 GTTTATGATTTAAGGTTTA
1 GTTTAGGATTTAAGGTTTA
54746033 CAATGCATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
GTTTAGGATTTAAGGTTTAGG
Found at i:54748675 original size:13 final size:14
Alignment explanation
Indices: 54748659--54748699 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
54748649 TTTACAGACA
54748659 CAGATA-ACAGAAT
1 CAGATATACAGAAT
*
54748672 CAGATATGCAGAA-
1 CAGATATACAGAAT
54748685 CAGATATACAGAAT
1 CAGATATACAGAAT
54748699 C
1 C
54748700 CTACCCCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (14 bp):
CAGATATACAGAAT
Found at i:54752516 original size:14 final size:14
Alignment explanation
Indices: 54752482--54752520 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54752472 TTATTGTCCT
54752482 TATTATTA-TATAA
1 TATTATTATTATAA
* *
54752495 TATCATTATTATAG
1 TATTATTATTATAA
54752509 TATTATTATTAT
1 TATTATTATTAT
54752521 TATAACCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TATTATTATTATAA
Found at i:54752881 original size:12 final size:12
Alignment explanation
Indices: 54752860--54752893 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54752850 TTTTACATAC
*
54752860 ATATATATATAT
1 ATATACATATAT
54752872 ATATACATATAT
1 ATATACATATAT
*
54752884 ACATACATAT
1 ATATACATAT
54752894 TGTCGAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATACATATAT
Found at i:54757263 original size:50 final size:50
Alignment explanation
Indices: 54757206--54757514 Score: 194
Period size: 50 Copynumber: 6.2 Consensus size: 50
54757196 GACCTGCCCT
* * *
54757206 CTTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCGTAG
1 CTTCAATCTTTTTAACTGCAATGTCAGGGAAATAAGATTCACCGTCGTAG
* ** * **** * ** * *
54757256 CTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATTTGCCGTTGTGG
1 CTTCAATCTTTTTAACTGCAATGTCAGGGAAATAAGATTCACCGTCGTAG
* * * * **
54757306 CTTCAATATTTTTAATTGCAATGTC-GAGAAAGTAAGATTCGCTAAT-GTAG
1 CTTCAATCTTTTTAACTGCAATGTCAGGGAAA-TAAGATTCAC-CGTCGTAG
* **
54757356 CTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAG
1 CTTCAATCTTTTTAACTGCAATGTCAGGGAAATAAGATTCACCGTCGTAG
* ** * ** * * *
54757406 CTTCAATCTATTCCACTGCACA-G-CTAGGGAAGTAAGATTCGTCTTTGTGG
1 CTTCAATCTTTTTAACTGCA-ATGTC-AGGGAAATAAGATTCACCGTCGTAG
* * * * * *
54757456 CTTTAATCTTTTTAATTGCAATGTCGGGGAAATAAGATCCACTGTCGTGG
1 CTTCAATCTTTTTAACTGCAATGTCAGGGAAATAAGATTCACCGTCGTAG
54757506 CTTCAATCT
1 CTTCAATCT
54757515 ATTCCACTAC
Statistics
Matches: 190, Mismatches: 61, Indels: 16
0.71 0.23 0.06
Matches are distributed among these distances:
49 7 0.04
50 176 0.93
51 7 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (50 bp):
CTTCAATCTTTTTAACTGCAATGTCAGGGAAATAAGATTCACCGTCGTAG
Found at i:54757384 original size:100 final size:100
Alignment explanation
Indices: 54757280--54757564 Score: 254
Period size: 100 Copynumber: 2.9 Consensus size: 100
54757270 ACTACACCAC
** * * * * *
54757280 CAGGGAAGTAAGATTTGCCGTTGTGGCTTCAATATTTTTAATTGCA-ATGTCGA-GAAAGTAAGA
1 CAGGGAAGTAAGATTCACCGTCGTAGCTTCAATATATTCAACTGCACA-G-CGAGGAAAGTAAGA
54757343 TTCG-CTAATGTAGCTTCAATCTTTTTAATTGCAATGT
64 TTCGTCT-ATGTAGCTTCAATCTTTTTAATTGCAATGT
* * * * *
54757380 CAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCACTGCACAGCTAGGGAAGTAAGATT
1 CAGGGAAGTAAGATTCACCGTCGTAGCTTCAATATATTCAACTGCACAGCGAGGAAAGTAAGATT
* * *
54757445 CGTCTTTGTGGCTTTAATCTTTTTAATTGCAATGT
66 CGTCTATGTAGCTTCAATCTTTTTAATTGCAATGT
* * * * * * * * * * *
54757480 CGGGGAAATAAGATCCACTGTCGTGGCTTCAATCTATTCCACTACACGGCCAGGGAAGTAAGATT
1 CAGGGAAGTAAGATTCACCGTCGTAGCTTCAATATATTCAACTGCACAGCGAGGAAAGTAAGATT
* *
54757545 CG-CTATTGTGGCTTAAATCT
66 CGTCTA-TGTAGCTTCAATCT
54757565 ATTCCACTGT
Statistics
Matches: 155, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
99 4 0.03
100 148 0.95
101 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (100 bp):
CAGGGAAGTAAGATTCACCGTCGTAGCTTCAATATATTCAACTGCACAGCGAGGAAAGTAAGATT
CGTCTATGTAGCTTCAATCTTTTTAATTGCAATGT
Found at i:54757493 original size:150 final size:150
Alignment explanation
Indices: 54757206--54757481 Score: 428
Period size: 150 Copynumber: 1.8 Consensus size: 150
54757196 GACCTGCCCT
* *
54757206 CTTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTGTTTAACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAGCTTCAATCTATTCCA
*
54757271 CTACACCACCAGGGAAGTAAGATTTGCCGTTGTGGCTTCAATATTTTTAATTGCAATGTCGAGAA
66 CTACACCACCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATATTTTTAATTGCAATGTCGAGAA
54757336 AGTAAGATTCGCTAATGTAG
131 AGTAAGATTCGCTAATGTAG
* * *
54757356 CTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCA
1 CTTCAATCTGTTTAACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAGCTTCAATCTATTCCA
* * * * * *
54757421 CTGCA-CAGCTAGGGAAGTAAGATTCGTCTTTGTGGCTTTAATCTTTTTAATTGCAATGTCG
66 CTACACCA-CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATATTTTTAATTGCAATGTCG
54757482 GGGAAATAAG
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
149 2 0.02
150 111 0.98
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (150 bp):
CTTCAATCTGTTTAACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAGCTTCAATCTATTCCA
CTACACCACCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATATTTTTAATTGCAATGTCGAGAA
AGTAAGATTCGCTAATGTAG
Found at i:54757534 original size:150 final size:150
Alignment explanation
Indices: 54757232--54757573 Score: 375
Period size: 150 Copynumber: 2.3 Consensus size: 150
54757222 TGCAATGTCG
* * * *
54757232 GGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATTTG
1 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCACTGCACCACCAGGGAAGTAAGATTCG
* *
54757297 CCGTTGTGGCTTCAATATTTTTAATTGCAATGTCGAGAAAGTAAGATTCGCTAATGTAGCTTCAA
66 CCGTTGTGGCTTCAATATTTTTAATTGCAATGTCGAGAAAGTAAGATCCACTAATGTAGCTTCAA
* * * * * *
54757362 TCTTTTTAATTGCAATGTCA
131 TCTATTCAACTACAAGGCCA
*
54757382 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCACTGCA-CAGCTAGGGAAGTAAGATTC
1 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCACTGCACCA-CCAGGGAAGTAAGATTC
* * * * * * *
54757446 GTCTTTGTGGCTTTAATCTTTTTAATTGCAATGTCGGGGAAA-TAAGATCCACT-GTCGTGGCTT
65 GCCGTTGTGGCTTCAATATTTTTAATTGCAATGTC-GAGAAAGTAAGATCCACTAAT-GTAGCTT
* *
54757509 CAATCTATTCCACTACACGGCCA
128 CAATCTATTCAACTACAAGGCCA
* * ** * * *
54757532 GGGAAGTAAGATTCGCTATTGTGGCTTAAATCTATTCCACTG
1 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCACTG
54757574 TAATGCCAAA
Statistics
Matches: 160, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
149 3 0.02
150 152 0.95
151 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (150 bp):
GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCACTGCACCACCAGGGAAGTAAGATTCG
CCGTTGTGGCTTCAATATTTTTAATTGCAATGTCGAGAAAGTAAGATCCACTAATGTAGCTTCAA
TCTATTCAACTACAAGGCCA
Found at i:54757599 original size:100 final size:100
Alignment explanation
Indices: 54757389--54757613 Score: 245
Period size: 100 Copynumber: 2.2 Consensus size: 100
54757379 TCAGGGAAGC
* * *
54757389 AAGATTCACCGTCGTAGCTTCAATCTATTCCACTGCACAGCTAGGGAAGTAAGATTCGTCTTTGT
1 AAGATTCACTGTCGTAGCTTCAATCTATTCCACTACACAGCCAGGGAAGTAAGATTCGTCTTTGT
* * * * * ***
54757454 GGCTTTAATCTTTTTAATTGCAATGTCGGGGAAAT
66 GGCTTAAATCTATTCAACTGCAATGCCAAAGAAAT
* * *
54757489 AAGATCCACTGTCGTGGCTTCAATCTATTCCACTACACGGCCAGGGAAGTAAGATTCG-CTATTG
1 AAGATTCACTGTCGTAGCTTCAATCTATTCCACTACACAGCCAGGGAAGTAAGATTCGTCT-TTG
* * *
54757553 TGGCTTAAATCTATTCCACTGTAATGCCAAAGAGAT
65 TGGCTTAAATCTATTCAACTGCAATGCCAAAGAAAT
* * *
54757589 AGGATTCACTGCCCATAGCTTCAAT
1 AAGATTCACTG-TCGTAGCTTCAAT
54757614 TCGCTCCACT
Statistics
Matches: 101, Mismatches: 22, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
99 2 0.02
100 89 0.88
101 10 0.10
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (100 bp):
AAGATTCACTGTCGTAGCTTCAATCTATTCCACTACACAGCCAGGGAAGTAAGATTCGTCTTTGT
GGCTTAAATCTATTCAACTGCAATGCCAAAGAAAT
Found at i:54757731 original size:50 final size:50
Alignment explanation
Indices: 54757642--54757759 Score: 128
Period size: 50 Copynumber: 2.4 Consensus size: 50
54757632 TCCAAGCCTT
* *
54757642 AACGCCAAGGAGATAAGATTCGCCATCATAGCTTCAATCTTCTCCGCTAC
1 AACGCCAAGGAAATAAGATTCGCCATCATAGCTTCAATCTTCTCCACTAC
* * ** * * * * *
54757692 AACGCCAGGGAAATAAGATTCGCCGTTGTGGCTTTAATCTTTTCCATTGC
1 AACGCCAAGGAAATAAGATTCGCCATCATAGCTTCAATCTTCTCCACTAC
*
54757742 AACGCCAAGGCAATAAGA
1 AACGCCAAGGAAATAAGA
54757760 CTAGTGTCTT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (50 bp):
AACGCCAAGGAAATAAGATTCGCCATCATAGCTTCAATCTTCTCCACTAC
Found at i:54757920 original size:88 final size:88
Alignment explanation
Indices: 54757766--54757938 Score: 258
Period size: 88 Copynumber: 2.0 Consensus size: 88
54757756 AAGACTAGTG
* * * * *
54757766 TCTTCGATCTGCTTCACTGCCAATACAAGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCACTACCAATACAAAAAGGCAAAATCTACTATTTTCAACCTACTCCACTGC
54757831 TGCTCAGGGAGACAAGGCTGGTA
66 TGCTCAGGGAGACAAGGCTGGTA
* * *
54757854 TCTTCGATCTACTTCGCTACCAATACAAAAAGAG-AAAATCTACTATTTTCAACCTACTTCATTG
1 TCTTCGATCTACTTCACTACCAATACAAAAAG-GCAAAATCTACTATTTTCAACCTACTCCACTG
54757918 CTGCTCAGGGAGACAAGGCTG
65 CTGCTCAGGGAGACAAGGCTG
54757939 AAGTTTCACC
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
88 75 0.99
89 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (88 bp):
TCTTCGATCTACTTCACTACCAATACAAAAAGGCAAAATCTACTATTTTCAACCTACTCCACTGC
TGCTCAGGGAGACAAGGCTGGTA
Found at i:54764010 original size:5 final size:5
Alignment explanation
Indices: 54764002--54764026 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54763992 CCAATAAACT
54764002 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
54764027 GAAACATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:54764046 original size:15 final size:15
Alignment explanation
Indices: 54763997--54764046 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
54763987 ACAATCCAAT
54763997 AAACTATAAAATAAAA
1 AAAC-ATAAAATAAAA
*
54764013 TAAA-ATAAAATAAAG
1 -AAACATAAAATAAAA
*
54764028 AAACATAAAGTAAAA
1 AAACATAAAATAAAA
54764043 AAAC
1 AAAC
54764047 GTGTCAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 3 0.10
15 23 0.79
17 3 0.10
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.16
Consensus pattern (15 bp):
AAACATAAAATAAAA
Found at i:54764351 original size:5 final size:5
Alignment explanation
Indices: 54764341--54764375 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
54764331 ATATATTTAC
54764341 AAAAT AAAAT AAAAT AAAAT AAATAT ATAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT A-AAAT AAA
54764376 CTACAAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 20 0.71
6 6 0.21
7 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:54764437 original size:18 final size:18
Alignment explanation
Indices: 54764416--54764451 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54764406 GTATGTATAT
* *
54764416 AAATGTATATATAAAATG
1 AAATATATATAAAAAATG
54764434 AAATATATATAAAAAATG
1 AAATATATATAAAAAATG
54764452 TAAGTACATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATATATATAAAAAATG
Found at i:54764543 original size:18 final size:18
Alignment explanation
Indices: 54764520--54764555 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54764510 AAATGCATGG
54764520 TTATAATAATAATAATTT
1 TTATAATAATAATAATTT
54764538 TTATAATAATAATAATTT
1 TTATAATAATAATAATTT
54764556 AAAACAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATAATAATAATAATTT
Found at i:54764580 original size:22 final size:22
Alignment explanation
Indices: 54764540--54764581 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54764530 AATAATTTTT
*
54764540 ATAATAATAATAATTTAAAACA
1 ATAATAATAATAATGTAAAACA
*
54764562 ATAATAATAATAGTGTAAAA
1 ATAATAATAATAATGTAAAA
54764582 ATAAAAGAAG
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:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (22 bp):
ATAATAATAATAATGTAAAACA
Found at i:54769464 original size:21 final size:20
Alignment explanation
Indices: 54769413--54769464 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
54769403 GATATGTTAA
*
54769413 AAAAGTAAAGAAAATAATATT
1 AAAAGT-AATAAAATAATATT
* *
54769434 AATAATTAATAAAGTAATACTT
1 AA-AAGTAATAAAATAATA-TT
54769456 AAAAGTAAT
1 AAAAGTAAT
54769465 TGAAAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAAGTAATAAAATAATATT
Found at i:54771011 original size:2 final size:2
Alignment explanation
Indices: 54771004--54771049 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
54770994 CTAATCTCCT
54771004 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54771046 TA TA
1 TA TA
54771050 GGAATATACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54771179 original size:24 final size:24
Alignment explanation
Indices: 54771134--54771179 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
54771124 TTGTGTTCTT
* * *
54771134 CACATTATTAATACTATTTTATAA
1 CACATTATTAACACAATATTATAA
*
54771158 CACATTATTAGCACAATATTAT
1 CACATTATTAACACAATATTAT
54771180 TCAAGAGTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (24 bp):
CACATTATTAACACAATATTATAA
Found at i:54773875 original size:2 final size:2
Alignment explanation
Indices: 54773868--54773898 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54773858 ATGTTTGTTC
54773868 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54773899 TAAATTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54775647 original size:3 final size:3
Alignment explanation
Indices: 54775639--54775689 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
54775629 TAAATAAGTA
* *
54775639 AAT AAT AAT AAT AAT AACGT AAT -AT AAT AGT AAT AAT AAT ATT AA-
1 AAT AAT AAT AAT AAT AA--T AAT AAT AAT AAT AAT AAT AAT AAT AAT
54775684 AAT AAT
1 AAT AAT
54775690 TAATTTAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
5 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54775672 original size:22 final size:20
Alignment explanation
Indices: 54775631--54775677 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
54775621 AAATGACATA
54775631 AATAAGTAAATAATAATAAT
1 AATAAGTAAATAATAATAAT
*
54775651 AATAACGTAATATAATAGTAAT
1 AATAA-GTAA-ATAATAATAAT
54775673 AATAA
1 AATAA
54775678 TATTAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.21
21 4 0.17
22 15 0.62
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (20 bp):
AATAAGTAAATAATAATAAT
Found at i:54775689 original size:28 final size:27
Alignment explanation
Indices: 54775641--54775693 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
54775631 AATAAGTAAA
**
54775641 TAATAATAATAATAACGTAATATAATAG
1 TAATAATAATAATAAAATAAT-TAATAG
*
54775669 TAATAATAATATTAAAATAATTAAT
1 TAATAATAATAATAAAATAATTAAT
54775694 TTAATGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (27 bp):
TAATAATAATAATAAAATAATTAATAG
Found at i:54777144 original size:40 final size:41
Alignment explanation
Indices: 54777095--54777636 Score: 548
Period size: 40 Copynumber: 12.9 Consensus size: 41
54777085 TTTTTTTTCG
*
54777095 TCTGTTCCACTACTGCTTAGGGAGATAAGA-CTGGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGATGTGA
* *
54777135 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGG---ATGT-GA
* *
54777179 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGG---ATGT-GA
*
54777223 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGATGTGA
* * *
54777263 TTTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGG---ATGT-GA
*
54777307 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGATGTGA
* **
54777347 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC--TGG--ATGTGA
* *
54777392 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CTTGATGTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGATGTGA
* ** *
54777432 TCTGCTCCACTACTGCTTAGTGAGATAAGATCTAGTTTCTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-G--GATGT-GA
* *
54777476 TCTGCTCCACTACTACTTAGGGAGATAAGA-CTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGATGTGA
* *
54777516 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC--TGG---ATGT-GA
* *
54777562 TCTGCTCCACTACTGCTTAGGGAGATAATA-CTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGATGTGA
54777602 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGG
54777637 GGTTTCTTTC
Statistics
Matches: 426, Mismatches: 44, Indels: 63
0.80 0.08 0.12
Matches are distributed among these distances:
39 4 0.01
40 186 0.44
41 14 0.03
42 2 0.00
43 14 0.03
44 138 0.32
45 36 0.08
46 31 0.07
47 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (41 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGATGTGA
Found at i:54777188 original size:84 final size:82
Alignment explanation
Indices: 54777095--54777658 Score: 758
Period size: 84 Copynumber: 6.6 Consensus size: 82
54777085 TTTTTTTTCG
* * *
54777095 TCTGTTCCACTACTGCTTAGGGAGATAAGA-CTGG-ATGT-GATCTGCTCCACTACTGCTTAGGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTCTTTCG-TCTGCTCCACTACTGCTTAGGG
** *
54777157 AGATAAGATCTGGTTTCTTTCG-
65 AGATAAGA-C---TTGATGT-GA
54777179 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGG--TCTTTCGTCTGCTCCACTACTGCTTAGG
54777244 GAGATAAGACTTGATGTGA
64 GAGATAAGACTTGATGTGA
*
54777263 TTTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGG--TCTTTCGTCTGCTCCACTACTGCTTAGG
54777328 GAGATAAGACTTGATGTGA
64 GAGATAAGACTTGATGTGA
* *
54777347 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTTCTGCTCCACTACTGCTTAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC--TGG-TCTTTCGTCTGCTCCACTACTGCTTAG
*
54777412 GGAGATAAGACTTGATGTTA
63 GGAGATAAGACTTGATGTGA
* * *
54777432 TCTGCTCCACTACTGCTTAGTGAGATAAGATCTAGTTTCTTTCGTCTGCTCCACTACTACTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-G-GTCTTTCGTCTGCTCCACTACTGCTTAGG
54777497 GAGATAAGACTTGATGTGA
64 GAGATAAGACTTGATGTGA
*
54777516 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTTTTCGTCTGCTCCACTACTGCTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC--TGG--TCTTTCGTCTGCTCCACTACTGCTTA
*
54777581 GGGAGATAATACTTGATGTGA
62 GGGAGATAAGACTTGATGTGA
54777602 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGGGTTTCTTTCGTCTGCTCCACT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT--GG--TCTTTCGTCTGCTCCACT
54777659 NNNNNNNNNN
Statistics
Matches: 441, Mismatches: 23, Indels: 30
0.89 0.05 0.06
Matches are distributed among these distances:
83 2 0.00
84 223 0.51
85 81 0.18
86 101 0.23
87 1 0.00
88 32 0.07
89 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (82 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTCTTTCGTCTGCTCCACTACTGCTTAGGGA
GATAAGACTTGATGTGA
Found at i:54777459 original size:169 final size:169
Alignment explanation
Indices: 54777095--54777658 Score: 854
Period size: 169 Copynumber: 3.3 Consensus size: 169
54777085 TTTTTTTTCG
* * *
54777095 TCTGTTCCACTACTGCTTAGGGAGATAAGA-CTGG---ATGT-GATCTGCTCCACTACTGCTTAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCG-TCTGCTCCACTACTGCTTAG
** * *
54777155 GGAGATAAGATCTGGTTTCTTTCG-TCTGCTCCACTACTGCTTAGGGAGATAAGATCTG-GTTTC
65 GGAGATAAGA-C---TTGATGT-GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTC
54777218 TTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
125 TTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
*
54777263 TTTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
* *
54777328 GAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTT
66 GAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTTTCGT
*
54777393 CTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTTA
131 CTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
* * *
54777432 TCTGCTCCACTACTGCTTAGTGAGATAAGATCTAGTTTCTTTCGTCTGCTCCACTACTACTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
*
54777497 GAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTTTTCG
66 GAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGG-TTCTTTCG
*
54777562 TCTGCTCCACTACTGCTTAGGGAGATAATACTTGATGTGA
130 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
54777602 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGGGTTTCTTTCGTCTGCTCCACT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT--GGTTTCTTTCGTCTGCTCCACT
54777659 NNNNNNNNNN
Statistics
Matches: 364, Mismatches: 22, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
167 1 0.00
168 66 0.18
169 167 0.46
170 75 0.21
171 1 0.00
172 53 0.15
173 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (169 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
GAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTTTCGT
CTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
Found at i:54777996 original size:40 final size:40
Alignment explanation
Indices: 54777759--54777992 Score: 292
Period size: 40 Copynumber: 5.8 Consensus size: 40
54777749 NNNNNNNNNN
*
54777759 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
* ** *
54777799 TCTGCTCCACTACTGCTTAGTGAGATAAGATCTAGTTTCTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGT-GA
*
54777843 TCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
*
54777883 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
* ** * *
54777923 TCTGCTTCACTACTATTTAGTGAGATAAGA-TCTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACT-TGATGTGA
54777963 TCTGCTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
54777993 TCTGTAATCT
Statistics
Matches: 165, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.01
40 129 0.78
41 1 0.01
43 1 0.01
44 32 0.19
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
Found at i:54778016 original size:124 final size:121
Alignment explanation
Indices: 54777763--54778033 Score: 321
Period size: 124 Copynumber: 2.2 Consensus size: 121
54777753 NNNNNNTCTG
* * *
54777763 CTCCACTACTGCTTAGGGAGATAAGACTTGATGTTATCTGCTCCACTACTGCTTAGTGAGATAAG
1 CTCCACTACTGCTTAGGGAGATAAGACTTAATGTGATCTGCTCCACTACTACTTAGTGAGATAAG
* * * * *
54777828 ATCTAGTTTCTTTCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGTGATCTG
66 ATCTAG--T-ATGCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGTAATCTA
* *
54777887 CTCCACTACTGCTTAGGGAGATAAGACTTAATGTGATCTGCTTCACTACTATTTAGTGAGATAAG
1 CTCCACTACTGCTTAGGGAGATAAGACTTAATGTGATCTGCTCCACTACTACTTAGTGAGATAAG
* *
54777952 ATCT-G-ATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTA
66 ATCTAGTATGCG-TCTGCTCCACTACTACTTAGGGAGATAAGA-CT-TAAT-GT-AATCTA
* * *
54778011 TTCCACTACTGCCTAGAGAGATA
1 CTCCACTACTGCTTAGGGAGATA
54778034 GAACTACGGG
Statistics
Matches: 127, Mismatches: 15, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
119 3 0.02
120 29 0.23
121 2 0.02
122 3 0.02
123 2 0.02
124 88 0.69
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (121 bp):
CTCCACTACTGCTTAGGGAGATAAGACTTAATGTGATCTGCTCCACTACTACTTAGTGAGATAAG
ATCTAGTATGCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGTAATCTA
Found at i:54778130 original size:132 final size:132
Alignment explanation
Indices: 54777964--54778281 Score: 546
Period size: 132 Copynumber: 2.4 Consensus size: 132
54777954 CTGATGCGAT
*
54777964 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCCTAGAG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCCCAGAG
* *
54778029 AGATAGAACTACGGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCTATCTTCG
66 AGATAGAACTACGGGCTTCAATGTACTCCACTATAATCTCAGGGAGGTAAAATCCGCCATCTTCG
54778094 AC
131 AC
* * * *
54778096 CTGCTCCACTACTGCTTAGGGAGATAAGACCTGTAATCTTCAATCTATTCCATTGCTGCCCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCCCAGAG
*
54778161 AGATAGAACTACTGGCTTCAATGTACTCCACTATAATCTCAGGGAGGTAAAATCCGCCATCTTCG
66 AGATAGAACTACGGGCTTCAATGTACTCCACTATAATCTCAGGGAGGTAAAATCCGCCATCTTCG
54778226 AC
131 AC
* *
54778228 CTGCTCCACTATTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCACT
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACT
54778282 GCCAAATACA
Statistics
Matches: 174, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 174 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (132 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCCCAGAG
AGATAGAACTACGGGCTTCAATGTACTCCACTATAATCTCAGGGAGGTAAAATCCGCCATCTTCG
AC
Found at i:54778280 original size:44 final size:44
Alignment explanation
Indices: 54777962--54778281 Score: 168
Period size: 44 Copynumber: 7.3 Consensus size: 44
54777952 ATCTGATGCG
* *
54777962 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCA
* * * * *****
54778006 ATCTATTCCACTACTGCCTAGAGAGATAGAA-CTACGGGCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCA
* * * * * *
54778049 ATGTACTCCACTGTAAT-CTCAGGGAGGTAAAATCCGCT-ATCTTCG
1 ATCTACTCCAC--TACTGCTTAGGGAGATAAAATCTG-TAATCTTCA
* * * *
54778094 ACCTGCTCCACTACTGCTTAGGGAGATAAGACCTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCA
* * * ** * *
54778138 ATCTATTCCATTGCTGCCCAGGGAGATAGAACTACTG---GCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATA-AAAT-CTGTAATCTTCA
* * * * * ** *
54778181 ATGTACTCCACTA-TAATCTCAGGGAGGTAAAATCCGCCATCTTCG
1 ATCTACTCCACTACT--GCTTAGGGAGATAAAATCTGTAATCTTCA
* * *
54778226 ACCTGCTCCACTATTGCTTAGGGAGATAAAATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCA
*
54778270 ATCTATTCCACT
1 ATCTACTCCACT
54778282 GCCAAATACA
Statistics
Matches: 192, Mismatches: 70, Indels: 28
0.66 0.24 0.10
Matches are distributed among these distances:
42 3 0.02
43 37 0.19
44 117 0.61
45 31 0.16
46 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCA
Found at i:54778561 original size:95 final size:94
Alignment explanation
Indices: 54778396--54778681 Score: 439
Period size: 95 Copynumber: 3.0 Consensus size: 94
54778386 AAGATCTACA
* * * *
54778396 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATGGAGTTATTGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
*
54778461 TAGTCATAGGGAGGTAAAATCTGCCGTCTTTG
64 TAGTCA-AGGGAGGTAAAATCTGCCATCTTTG
* * *
54778493 ATCTTCAATCTATTCCACAGCCAACCAAGGAGATAGAATTATCAGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
*
54778558 GTCACAGGGAGGTAAAATCTGTCATCTTTG
66 GTCA-AGGGAGGTAAAATCTGCCATCTTTG
54778588 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
*
54778653 GTC-AGGGAGGTAAAATCCGCCATCTTTG
66 GTCAAGGGAGGTAAAATCTGCCATCTTTG
54778681 A
1 A
54778682 CCTGCTTCGC
Statistics
Matches: 174, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
93 24 0.14
95 127 0.73
96 2 0.01
97 21 0.12
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (94 bp):
ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
GTCAAGGGAGGTAAAATCTGCCATCTTTG
Found at i:54779725 original size:15 final size:16
Alignment explanation
Indices: 54779701--54779742 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
54779691 CCTTTTTCTT
54779701 TTTCTTTTTCATTTTG
1 TTTCTTTTTCATTTTG
*
54779717 TTT-TTTTTCGTTTTG
1 TTTCTTTTTCATTTTG
54779732 TTTCTTTTTCA
1 TTTCTTTTTCA
54779743 AGTGAAGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (16 bp):
TTTCTTTTTCATTTTG
Found at i:54781497 original size:62 final size:62
Alignment explanation
Indices: 54781400--54781516 Score: 180
Period size: 62 Copynumber: 1.9 Consensus size: 62
54781390 CTCGATGTAC
* *
54781400 TTTTGGATTTTAAGAAATTTATTATATGCAATGAAACGTAATGTTGATGCATGAATGCGTAT
1 TTTTGGATTTTAAGAAATTTATTATATGCAATGAAACGTAATGTTAATGAATGAATGCGTAT
* * * *
54781462 TTTTGGATTTTAGGAAATTTATTGTATGTAATGAAATGTAATGTTAATGAATGAA
1 TTTTGGATTTTAAGAAATTTATTATATGCAATGAAACGTAATGTTAATGAATGAA
54781517 AAGATACGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (62 bp):
TTTTGGATTTTAAGAAATTTATTATATGCAATGAAACGTAATGTTAATGAATGAATGCGTAT
Found at i:54784112 original size:3 final size:3
Alignment explanation
Indices: 54784104--54784160 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
54784094 TAAATAAGTA
*
54784104 AAT AAT AAT AAT AAT AAT AAT AACGT AAT -AT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT AAT AAT AAT AAT AAT
*
54784150 ATT AA- AAT AAT
1 AAT AAT AAT AAT
54784161 TAATTTAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
5 3 0.07
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54784160 original size:28 final size:28
Alignment explanation
Indices: 54784105--54784195 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
54784095 AAATAAGTAA
**
54784105 ATAATAATAATAATAATAATAACGTAAT
1 ATAATAATAATAATAATAATAAAATAAT
* *
54784133 ATAATAGTAATAATAATATTAAAATAAT
1 ATAATAATAATAATAATAATAAAATAAT
* *
54784161 -TAATTTAATGATAA-AATAACTGAAATAAT
1 ATAA--TAATAATAATAATAA-TAAAATAAT
54784190 A-AATAA
1 ATAATAA
54784196 AGGATTAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
27 6 0.12
28 28 0.55
29 17 0.33
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (28 bp):
ATAATAATAATAATAATAATAAAATAAT
Found at i:54784846 original size:7 final size:8
Alignment explanation
Indices: 54784801--54784848 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
54784791 CAAAAGAAAG
54784801 GAAAAAAA
1 GAAAAAAA
*
54784809 GAATAAAA
1 GAAAAAAA
* *
54784817 CAAACAAA
1 GAAAAAAA
*
54784825 TAAATAAAA
1 GAAA-AAAA
54784834 GAAAAAAA
1 GAAAAAAA
54784842 GAAAAAA
1 GAAAAAA
54784849 CGAAGAGGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
8 26 0.81
9 6 0.19
ACGTcount: A:0.81, C:0.04, G:0.08, T:0.06
Consensus pattern (8 bp):
GAAAAAAA
Found at i:54786035 original size:13 final size:13
Alignment explanation
Indices: 54786017--54786043 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54786007 CTAATATGCC
54786017 TATATTTTTCTAA
1 TATATTTTTCTAA
54786030 TATATTTTTCTAA
1 TATATTTTTCTAA
54786043 T
1 T
54786044 TTCATAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTTTTCTAA
Found at i:54791760 original size:9 final size:9
Alignment explanation
Indices: 54791748--54791774 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
54791738 TAAAATTCAA
54791748 AAAATTATT
1 AAAATTATT
54791757 AAAATTATT
1 AAAATTATT
54791766 AAAATTATT
1 AAAATTATT
54791775 TTAAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTATT
Found at i:54797055 original size:35 final size:35
Alignment explanation
Indices: 54797009--54797085 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
54796999 GCACAATAAT
* *
54797009 AATTTTTGAAAACACGGAAAATTT-TAAAATATGAG
1 AATTTTTGAAAACAAGG-AAATTTATAAAACATGAG
*
54797044 AATTTTTGAAAACAAGGAAATTTATGAAACATGAG
1 AATTTTTGAAAACAAGGAAATTTATAAAACATGAG
54797079 AATTTTT
1 AATTTTT
54797086 TTTTTGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 6 0.16
35 32 0.84
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (35 bp):
AATTTTTGAAAACAAGGAAATTTATAAAACATGAG
Found at i:54797065 original size:18 final size:18
Alignment explanation
Indices: 54797009--54797072 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
54796999 GCACAATAAT
*
54797009 AATTTTTGAAAACACGGA
1 AATTTTTGAAAACAAGGA
* * *
54797027 AAATTTT-AAAA-TATGA
1 AATTTTTGAAAACAAGGA
54797043 GAATTTTTGAAAACAAGGA
1 -AATTTTTGAAAACAAGGA
*
54797062 AATTTATGAAA
1 AATTTTTGAAA
54797073 CATGAGAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
16 2 0.06
17 10 0.29
18 20 0.57
19 3 0.09
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (18 bp):
AATTTTTGAAAACAAGGA
Found at i:54797082 original size:17 final size:18
Alignment explanation
Indices: 54797034--54797083 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
54797024 GGAAAATTTT
* *
54797034 AAAATATGAGAATTTTTG
1 AAAACATGAGAATTTATG
*
54797052 AAAACAAG-GAAATTTATG
1 AAAACATGAG-AATTTATG
54797070 -AAACATGAGAATTT
1 AAAACATGAGAATTT
54797084 TTTTTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.50, C:0.04, G:0.16, T:0.30
Consensus pattern (18 bp):
AAAACATGAGAATTTATG
Found at i:54797121 original size:58 final size:58
Alignment explanation
Indices: 54797044--54797181 Score: 215
Period size: 58 Copynumber: 2.4 Consensus size: 58
54797034 AAAATATGAG
* *
54797044 AATTTTTGAAAACAAGGAAATTTATGAAACATGAGAATTTTTTTTTTGAAAACACAAA
1 AATTTTTGAAAACACGGAAATTTATGAAACACGAGAATTTTTTTTTTGAAAACACAAA
* *
54797102 AATTGTTGAAAACACGGAAATTTATGAAACACGAGAATTTTTTTTTTGAAAACACGAA
1 AATTTTTGAAAACACGGAAATTTATGAAACACGAGAATTTTTTTTTTGAAAACACAAA
* *
54797160 AATTTTTCAAAA-ACGGGAATTT
1 AATTTTTGAAAACACGGAAATTT
54797182 TTTGAAAACA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
57 9 0.12
58 64 0.88
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (58 bp):
AATTTTTGAAAACACGGAAATTTATGAAACACGAGAATTTTTTTTTTGAAAACACAAA
Found at i:54797129 original size:18 final size:18
Alignment explanation
Indices: 54797089--54797140 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
54797079 AATTTTTTTT
*
54797089 TTGAAAACACAAAAATTG
1 TTGAAAACACGAAAATTG
*
54797107 TTGAAAACACGGAAATT-
1 TTGAAAACACGAAAATTG
*
54797124 TATG-AAACACGAGAATT
1 T-TGAAAACACGAAAATT
54797141 TTTTTTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (18 bp):
TTGAAAACACGAAAATTG
Found at i:54797151 original size:40 final size:40
Alignment explanation
Indices: 54797107--54797184 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
54797097 ACAAAAATTG
* * *
54797107 TTGAAAACACGGAAATTTATGAAACACGAGAATTTTTTTT
1 TTGAAAACACGAAAATTTATCAAAAACGAGAATTTTTTTT
* *
54797147 TTGAAAACACGAAAATTTTTCAAAAACGGGAATTTTTT
1 TTGAAAACACGAAAATTTATCAAAAACGAGAATTTTTT
54797185 GAAAACATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (40 bp):
TTGAAAACACGAAAATTTATCAAAAACGAGAATTTTTTTT
Found at i:54797207 original size:27 final size:27
Alignment explanation
Indices: 54797168--54797248 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
54797158 AAAATTTTTC
* *
54797168 AAAA-ACGGGAATTTTTTGAAAACATG
1 AAAACACGAGAATTTTTTGAAAACACG
* *
54797194 ATAACATGAGAATTTTTTGAAAACACG
1 AAAACACGAGAATTTTTTGAAAACACG
*
54797221 AAAACACGA-AAGTTTTTG-AAACACG
1 AAAACACGAGAATTTTTTGAAAACACG
54797246 AAA
1 AAA
54797249 TTTTTTATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
25 10 0.21
26 11 0.23
27 26 0.55
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (27 bp):
AAAACACGAGAATTTTTTGAAAACACG
Found at i:54797254 original size:17 final size:17
Alignment explanation
Indices: 54797222--54797253 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54797212 GAAAACACGA
54797222 AAACACGAAAGTTTTTG
1 AAACACGAAAGTTTTTG
54797239 AAACACGAAA-TTTTT
1 AAACACGAAAGTTTTT
54797254 TATTTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (17 bp):
AAACACGAAAGTTTTTG
Found at i:54798043 original size:23 final size:24
Alignment explanation
Indices: 54798011--54798074 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
54798001 ATTTAATTAT
* * *
54798011 TTTTTATTTTTTTCTCTTTTTTC-
1 TTTTTCTTTTTTTCTTTTTTTCCT
*
54798034 TTTTTCTTTTCTTCTTTTTTTCCT
1 TTTTTCTTTTTTTCTTTTTTTCCT
*
54798058 TTTTTCTTTCTTTCTTT
1 TTTTTCTTTTTTTCTTT
54798075 CTTCTTTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTTCTTTTTTTCTTTTTTTCCT
Found at i:54798051 original size:19 final size:19
Alignment explanation
Indices: 54798012--54798124 Score: 57
Period size: 17 Copynumber: 6.1 Consensus size: 19
54798002 TTTAATTATT
* *
54798012 TTTTATTTTT-TTCTCTT-
1 TTTTCTTTTTCTTTTCTTC
54798029 TTTTCTTTTTCTTTTCTTC
1 TTTTCTTTTTCTTTTCTTC
*
54798048 -TTT-TTTTCCTTTT-TTC
1 TTTTCTTTTTCTTTTCTTC
54798064 -TTTC--TTTC-TTTCTTC
1 TTTTCTTTTTCTTTTCTTC
54798079 -TTTCTTTCCTTCCTTCTTCTTC
1 TTTTCTTT--TT-CTT-TTCTTC
*
54798101 TTCTTCTTCCTTCTTCTTCTTC
1 TT-TTCTT-TTTCTT-TTCTTC
54798123 TT
1 TT
54798125 CAAAACCAAG
Statistics
Matches: 77, Mismatches: 5, Indels: 23
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.04
15 10 0.13
16 6 0.08
17 19 0.25
18 9 0.12
19 2 0.03
20 1 0.01
21 1 0.01
22 18 0.23
23 3 0.04
24 5 0.06
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTCTTTTTCTTTTCTTC
Found at i:54798055 original size:31 final size:30
Alignment explanation
Indices: 54798017--54798109 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 30
54798007 TTATTTTTTA
54798017 TTTTTTTCTCTTTTTTCTTTTTCTTTTCTTC
1 TTTTTTTC-CTTTTTTCTTTTTCTTTTCTTC
54798048 TTTTTTTCCTTTTTTCTTTCTT-TCTTTCTTC
1 TTTTTTTCCTTTTTTCTTT-TTCT-TTTCTTC
* ** *
54798079 TTTCTTTCCTTCCTTCTTCTTCTTCTTCTTC
1 TTTTTTTCCTTTTTTCTTTTTCTT-TTCTTC
54798110 CTTCTTCTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
30 15 0.28
31 39 0.72
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (30 bp):
TTTTTTTCCTTTTTTCTTTTTCTTTTCTTC
Found at i:54798069 original size:4 final size:4
Alignment explanation
Indices: 54798025--54798096 Score: 57
Period size: 4 Copynumber: 19.0 Consensus size: 4
54798015 TATTTTTTTC
*
54798025 TCTT T-TT TC-T T-TT TCTT T-TCT TCTT TTTT TCCTT T-TT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCT-T TCTT TCTT T-CTT TCTT TCTT TCTT
* *
54798070 TCTT TC-T TCTT TCTT TCCT TCCT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
54798097 CTTCTTCTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
3 14 0.25
4 38 0.68
5 4 0.07
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:54798070 original size:11 final size:11
Alignment explanation
Indices: 54798025--54798085 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
54798015 TATTTTTTTC
54798025 TCTTTTTTCTT
1 TCTTTTTTCTT
54798036 T-TTCTTTTC-T
1 TCTT-TTTTCTT
54798046 TCTTTTTTTCCTT
1 TC-TTTTTT-CTT
54798059 T-TTTCTTTCTT
1 TCTTT-TTTCTT
*
54798070 TCTTTCTTCTT
1 TCTTTTTTCTT
54798081 TCTTT
1 TCTTT
54798086 CCTTCCTTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
10 4 0.10
11 27 0.64
12 9 0.21
13 2 0.05
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:54798097 original size:3 final size:3
Alignment explanation
Indices: 54798073--54798125 Score: 63
Period size: 3 Copynumber: 17.0 Consensus size: 3
54798063 CTTTCTTTCT
*
54798073 TTC TTC TTTC TT- TCC TTCC TTC TTC TTC TTC TTC TTCC TTC TTC TTC
1 TTC TTC -TTC TTC TTC TT-C TTC TTC TTC TTC TTC TT-C TTC TTC TTC
54798120 TTC TTC
1 TTC TTC
54798126 AAAACCAAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 1 0.02
3 34 0.77
4 9 0.20
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:54798116 original size:16 final size:16
Alignment explanation
Indices: 54798073--54798125 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
54798063 CTTTCTTTCT
* *
54798073 TTCTTCTTTCTT-TCC
1 TTCTTCCTTCTTCTTC
54798088 TTCCTT-CTTCTTCTTC
1 TT-CTTCCTTCTTCTTC
54798104 TTCTTCCTTCTTCTTC
1 TTCTTCCTTCTTCTTC
54798120 TTCTTC
1 TTCTTC
54798126 AAAACCAAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 10 0.30
16 23 0.70
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TTCTTCCTTCTTCTTC
Found at i:54798125 original size:19 final size:19
Alignment explanation
Indices: 54798073--54798125 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
54798063 CTTTCTTTCT
*
54798073 TTCTTCTTTCTT-TCCTTCC
1 TTCTTC-TTCTTCTTCTTCC
54798092 TTCTTCTTCTTCTTCTTCC
1 TTCTTCTTCTTCTTCTTCC
54798111 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTTC
54798126 AAAACCAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 5 0.16
19 27 0.84
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (19 bp):
TTCTTCTTCTTCTTCTTCC
Found at i:54798521 original size:30 final size:29
Alignment explanation
Indices: 54798429--54798521 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 29
54798419 TACTGGAAGC
*
54798429 AAAACTTTTGGGG-CTTAAATGTAATTTTGA
1 AAAAATTTTGGGGTC-TAAATGTAA-TTTGA
* * * *
54798459 GACAATTTTGGGGTCAAAATATAA-TTGCA
1 AAAAATTTTGGGGTCTAAATGTAATTTG-A
54798488 AAAAATTTTTGGGGTCTAAATGTAATTTGA
1 AAAAA-TTTTGGGGTCTAAATGTAATTTGA
54798518 AAAA
1 AAAA
54798522 GGTAAGGGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
28 3 0.06
29 4 0.08
30 39 0.78
31 4 0.08
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (29 bp):
AAAAATTTTGGGGTCTAAATGTAATTTGA
Found at i:54798597 original size:30 final size:30
Alignment explanation
Indices: 54798445--54798604 Score: 119
Period size: 30 Copynumber: 5.4 Consensus size: 30
54798435 TTTGGGGCTT
* * *
54798445 AAATGTAATTTTGAGACAA-TTTTGGGGTCA
1 AAATGTAATTTT-AAAAAAGTTTAGGGGTCA
* ** * * *
54798475 AAATATAATTGCAAAAAATTTTTGGGGTCT
1 AAATGTAATTTTAAAAAAGTTTAGGGGTCA
* * * * *
54798505 AAATGTAA-TTTGAAAAAGGTAAGGGTTTA
1 AAATGTAATTTTAAAAAAGTTTAGGGGTCA
* * * *
54798534 AAATATAATTTTAAAAAAGTTTAAGGATTA
1 AAATGTAATTTTAAAAAAGTTTAGGGGTCA
*
54798564 AAATGTAATTTTAAAAAAGTTCAGGGGTCA
1 AAATGTAATTTTAAAAAAGTTTAGGGGTCA
54798594 AAATG-AATTTT
1 AAATGTAATTTT
54798605 TTTATAAAAC
Statistics
Matches: 100, Mismatches: 28, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
29 28 0.28
30 72 0.72
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.35
Consensus pattern (30 bp):
AAATGTAATTTTAAAAAAGTTTAGGGGTCA
Found at i:54804663 original size:2 final size:2
Alignment explanation
Indices: 54804656--54804681 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54804646 CTAGACATTT
54804656 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
54804682 AATTATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54810958 original size:21 final size:21
Alignment explanation
Indices: 54810934--54810978 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
54810924 GTCCCAGTTG
*
54810934 GCATTGTAGGCATTTTTTTGA
1 GCATTCTAGGCATTTTTTTGA
*
54810955 GCATTCTAGGCATTTTTTTTA
1 GCATTCTAGGCATTTTTTTGA
54810976 GCA
1 GCA
54810979 CTAAACACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (21 bp):
GCATTCTAGGCATTTTTTTGA
Found at i:54811477 original size:24 final size:24
Alignment explanation
Indices: 54811445--54811490 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
54811435 GAATCAGCAA
*
54811445 ACACACACATATCTGCACATATTG
1 ACACACACATATATGCACATATTG
54811469 ACACACACATATATGCACATAT
1 ACACACACATATATGCACATAT
54811491 AGACTACTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (24 bp):
ACACACACATATATGCACATATTG
Found at i:54811781 original size:39 final size:39
Alignment explanation
Indices: 54811738--54811820 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
54811728 AAATTCTACT
*
54811738 GAAATTTAATTATGTGTCAAGCTTAATAATTGCAATTTA
1 GAAATTTAATTATGTGTCAAGCTTAAGAATTGCAATTTA
*
54811777 GAAATTTGATTATGTGTCAAGCTTAAGAATTGCAATTTA
1 GAAATTTAATTATGTGTCAAGCTTAAGAATTGCAATTTA
54811816 GAAAT
1 GAAAT
54811821 GTTATCAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (39 bp):
GAAATTTAATTATGTGTCAAGCTTAAGAATTGCAATTTA
Found at i:54822587 original size:20 final size:20
Alignment explanation
Indices: 54822551--54822588 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54822541 AAAATATTTC
54822551 AAAAAAAAGAAAGAAGAAGG
1 AAAAAAAAGAAAGAAGAAGG
54822571 AAAAGAAAAGAAA-AAGAA
1 AAAA-AAAAGAAAGAAGAA
54822589 AAATGAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAAGAAGAAGG
Found at i:54822597 original size:17 final size:16
Alignment explanation
Indices: 54822554--54822597 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
54822544 ATATTTCAAA
*
54822554 AAAAAGAAAGAAGAAG
1 AAAAAGAAAGAAAAAG
*
54822570 GAAAAGAAAAGAAAAAG
1 AAAAAG-AAAGAAAAAG
54822587 AAAAATGAAAG
1 AAAAA-GAAAG
54822598 GCCAAGGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 5 0.22
17 17 0.74
18 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:54824048 original size:51 final size:51
Alignment explanation
Indices: 54823972--54824070 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
54823962 GAGCGGACTG
*
54823972 AAGGTAGCGAATCTTATTTCCCTGGCTTTGCAGTGGAACAGATTAAAGCTA
1 AAGGTAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTA
* * *
54824023 AAGGTAGTGAATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAG
1 AAGGTAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAG
54824071 TTGAAGTGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (51 bp):
AAGGTAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTA
Found at i:54824164 original size:123 final size:123
Alignment explanation
Indices: 54823969--54824322 Score: 566
Period size: 123 Copynumber: 2.9 Consensus size: 123
54823959 GTGGAGCGGA
** * * *
54823969 CTGAAGGTAGCGAATCTTATTTCCCTGGCTTTGCAGTGGAACAGATTAAAGCTAAAGGTAGTGAA
1 CTGAAGGCGGCGAATCCTATCTCCTTGGCTTTGCAGTGGAACAGATTAAAGCTAAAGGTAGTGAA
*
54824034 TCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGTTGAAGTGGAGCGGATTAAAG
66 TCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAG
* *
54824092 CTGAAGGGGGCGAATCCTATCTCCTTGGCTTTGTAGTGGAACAGATTAAAGCTAAAGGTAG-GAA
1 CTGAAGGCGGCGAATCCTATCTCCTTGGCTTTGCAGTGGAACAGATTAAAGCTAAAGGTAGTG-A
*
54824156 ATCTTGTTTCCCTAGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAG
65 ATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAG
* *
54824215 CTGAAGGCGGCGAATCCTATCTCCTTGGCGTTACAGTGGAACAGATTAAAGCTAAAGGTAGTGAA
1 CTGAAGGCGGCGAATCCTATCTCCTTGGCTTTGCAGTGGAACAGATTAAAGCTAAAGGTAGTGAA
* * *
54824280 TCTTGTTTCCCTGGCATTGCAGCGGAGTATATTAAAGCTGAAG
66 TCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTGAAG
54824323 GCAACGAATT
Statistics
Matches: 213, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
122 1 0.00
123 211 0.99
124 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (123 bp):
CTGAAGGCGGCGAATCCTATCTCCTTGGCTTTGCAGTGGAACAGATTAAAGCTAAAGGTAGTGAA
TCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAG
Found at i:54824203 original size:21 final size:21
Alignment explanation
Indices: 54824177--54824220 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
54824167 CTAGCATTGC
*
54824177 AGTGGAATAGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
* *
54824198 AGTGGAGCGGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
54824219 AG
1 AG
54824221 GCGGCGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.20
Consensus pattern (21 bp):
AGTGGAACAGATTAAAGCTGA
Found at i:54826304 original size:18 final size:18
Alignment explanation
Indices: 54826266--54826310 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
54826256 TTTAATGGTG
* *
54826266 TTATCATTATTTTTACCA
1 TTATTATTATTTTTAACA
*
54826284 TTATTATTATTTTTAATA
1 TTATTATTATTTTTAACA
*
54826302 TTACTATTA
1 TTATTATTA
54826311 CTATTATTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATTATTTTTAACA
Found at i:54826457 original size:2 final size:2
Alignment explanation
Indices: 54826450--54826554 Score: 58
Period size: 2 Copynumber: 54.5 Consensus size: 2
54826440 TGTACACGTG
*
54826450 TA TA TA TA TA TA T- TT TA TA TA -A CT- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
** ** * * * * *
54826490 TA TA CG TA CC CA TA TA TA TA TA TA TT TA TA T- TT TA TC TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
54826531 TA TC TA CA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
54826555 TTTCATGAAT
Statistics
Matches: 77, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
1 5 0.06
2 72 0.94
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54826548 original size:35 final size:38
Alignment explanation
Indices: 54826503--54826603 Score: 120
Period size: 39 Copynumber: 2.7 Consensus size: 38
54826493 ACGTACCCAT
*
54826503 ATATATATATATTTATATTTTAT-CTACATAT-C-TAC
1 ATATATATATATTTATATTTTATAATACATATACATAC
54826538 ATATATATATA-TTATATTTTCATGAATACATATACATAC
1 ATATATATATATTTATATTTT-AT-AATACATATACATAC
* *
54826577 TTATATATATTTTTTATATTTTATAAT
1 ATATATATA-TATTTATATTTTATAAT
54826604 TTTTATATAC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
34 9 0.16
35 13 0.23
37 7 0.12
38 1 0.02
39 14 0.25
40 3 0.05
41 9 0.16
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (38 bp):
ATATATATATATTTATATTTTATAATACATATACATAC
Found at i:54846636 original size:14 final size:16
Alignment explanation
Indices: 54846600--54846637 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
54846590 ACACATTTTA
54846600 TATATATATAAATTAT
1 TATATATATAAATTAT
*
54846616 TAAATAT-TAAATT-T
1 TATATATATAAATTAT
54846630 TATATATA
1 TATATATA
54846638 AAAAAAATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 7 0.37
15 6 0.32
16 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATATATAAATTAT
Found at i:54849348 original size:31 final size:32
Alignment explanation
Indices: 54849282--54849350 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
54849272 TTTAAGTCAT
* * *
54849282 TATATATACGTACATGTGTTTTTTATAATACA
1 TATATACACGTACATATGTTTTCTATAATACA
*
54849314 TATATACACGTACATAT-TTTTCTATAATATA
1 TATATACACGTACATATGTTTTCTATAATACA
54849345 TATATA
1 TATATA
54849351 TACTCATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 18 0.55
32 15 0.45
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (32 bp):
TATATACACGTACATATGTTTTCTATAATACA
Found at i:54852901 original size:24 final size:24
Alignment explanation
Indices: 54852880--54852934 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
54852870 ATAGAAAAAC
54852880 AAAAAAAGCAAAAACAAAAAAATA
1 AAAAAAAGCAAAAACAAAAAAATA
* *
54852904 AAAAAATGCGAAAAC-AAAAAATA
1 AAAAAAAGCAAAAACAAAAAAATA
54852927 AAACAAAA
1 AAA-AAAA
54852935 AAACCTCTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.80, C:0.09, G:0.05, T:0.05
Consensus pattern (24 bp):
AAAAAAAGCAAAAACAAAAAAATA
Found at i:54852907 original size:15 final size:15
Alignment explanation
Indices: 54852864--54852908 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
54852854 TAGTGGAGGT
54852864 AAAAAAATAGAAAAAC
1 AAAAAAATA-AAAAAC
**
54852880 AAAAAAAGCAAAAAC
1 AAAAAAATAAAAAAC
54852895 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
54852909 ATGCGAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.84, C:0.07, G:0.04, T:0.04
Consensus pattern (15 bp):
AAAAAAATAAAAAAC
Found at i:54853405 original size:12 final size:13
Alignment explanation
Indices: 54853373--54853423 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
54853363 CTTCACTTGA
*
54853373 AAAAGAAACGAAAC
1 AAAA-AAACAAAAC
54853387 AAAAAAACAAAAC
1 AAAAAAACAAAAC
*
54853400 AAAAAAGA-AAAAG
1 AAAAAA-ACAAAAC
*
54853413 AAAAAGACAAA
1 AAAAAAACAAA
54853424 GAAAAAGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 1 0.03
13 26 0.81
14 5 0.16
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:54853410 original size:6 final size:6
Alignment explanation
Indices: 54853371--54853430 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
54853361 TACTTCACTT
* *
54853371 GAAAAA G-AAAC GAAACAA -AAAAA CAAAACA -AAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAA-AA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
*
54853418 GACAAA GAAAAA G
1 GAAAAA GAAAAA G
54853431 GAGAGGCTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
5 7 0.16
6 36 0.80
7 2 0.04
ACGTcount: A:0.78, C:0.08, G:0.13, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:54853965 original size:108 final size:108
Alignment explanation
Indices: 54853772--54853967 Score: 277
Period size: 108 Copynumber: 1.8 Consensus size: 108
54853762 TTTGTATTCT
* * *
54853772 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAATAAATTTCCATCTT
1 AGCAAAATTTGATATCTTGATTAATTTATTCATTTAGAGCTTTGCTCTCAAAAAATTTCCATCTT
54853837 ATCAATTGTGATAATATTTTTCATCTTATTCATCTCGTATATC
66 ATCAATTGTGATAATATTTTTCATCTTATTCATCTCGTATATC
* ** *
54853880 AGCAAAATTTGATATCTTGATTGATTTATTTGTTTAGAGCTTTGCTCTCAACAAAATTT-CATTT
1 AGCAAAATTTGATATCTTGATTAATTTATTCATTTAGAGCTTTGCTCTCAA-AAAATTTCCATCT
* * * *
54853944 TGTCCATTTTGATAATCTTTTTCA
65 TATCAATTGTGATAATATTTTTCA
54853968 AGCATTTTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
108 70 0.92
109 6 0.08
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (108 bp):
AGCAAAATTTGATATCTTGATTAATTTATTCATTTAGAGCTTTGCTCTCAAAAAATTTCCATCTT
ATCAATTGTGATAATATTTTTCATCTTATTCATCTCGTATATC
Found at i:54854527 original size:44 final size:45
Alignment explanation
Indices: 54854447--54854893 Score: 398
Period size: 44 Copynumber: 10.2 Consensus size: 45
54854437 TTATTAAAGT
* * * *
54854447 AGATCTTGTCTTCATGTATTGG-CGTAAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGC
* * * *
54854491 AGGTCATGCCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGC
* * * *
54854534 AGATCTTGTCTT-CTCGTGTTGGCAGTGAAGTAGATTGAAGATAGC
1 AGATCTTGTCTTCCT-ATATTGGTAGTGAAGTAGATCGAAGATAGC
* *
54854579 AGGTCTTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGC
* * * *
54854622 AGATCTTGTCTT-CTCGTGTTGGCAGTGAAGTAGATTGAAGATAGC
1 AGATCTTGTCTTCCT-ATATTGGTAGTGAAGTAGATCGAAGATAGC
* * *
54854667 AGGTCTTGTCTTCCTATATTGGTAG-GAAGTGGATCAAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGC
* * * *
54854710 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGC
* * ** * *
54854755 AAATCTTGTCTTCATGCATTGG-CGTGAAGTAGATCGAAAAT-GC
1 AGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGC
* * * *
54854798 AGATCTTGTCTTCCCATATTGGTGGCGGAGTAGATC-AA-ATATGC
1 AGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATA-GC
* * * * * * *
54854842 AGATCTTGTCTTCCCATACTGGTGGCGAAGTGGATCGAAGAAAAC
1 AGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGC
54854887 AGATCTT
1 AGATCTT
54854894 ATCTCTCTGA
Statistics
Matches: 323, Mismatches: 64, Indels: 31
0.77 0.15 0.07
Matches are distributed among these distances:
42 6 0.02
43 82 0.25
44 160 0.50
45 69 0.21
46 6 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (45 bp):
AGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGC
Found at i:54854595 original size:88 final size:88
Alignment explanation
Indices: 54854447--54854882 Score: 504
Period size: 88 Copynumber: 5.0 Consensus size: 88
54854437 TTATTAAAGT
* * * *
54854447 AGATCTTGTCTTCAT-GTATTGGC-GTAAAGTAGATCGAAGATAGCAGGTCATGCCTTCCTATAT
1 AGATCTTGTCTTC-TCGTATTGGCAGTGAAGTAGATTGAAGATAGCAGGTCTTGTCTTCCTATAT
54854510 TGGTAGGAAGTGGATCGAAGATGC
65 TGGTAGGAAGTGGATCGAAGATGC
*
54854534 AGATCTTGTCTTCTCGTGTTGGCAGTGAAGTAGATTGAAGATAGCAGGTCTTGTCTTCCTATATT
1 AGATCTTGTCTTCTCGTATTGGCAGTGAAGTAGATTGAAGATAGCAGGTCTTGTCTTCCTATATT
54854599 GGTAGGAAGTGGATCGAAGATGC
66 GGTAGGAAGTGGATCGAAGATGC
*
54854622 AGATCTTGTCTTCTCGTGTTGGCAGTGAAGTAGATTGAAGATAGCAGGTCTTGTCTTCCTATATT
1 AGATCTTGTCTTCTCGTATTGGCAGTGAAGTAGATTGAAGATAGCAGGTCTTGTCTTCCTATATT
*
54854687 GGTAGGAAGTGGATCAAAGATGC
66 GGTAGGAAGTGGATCGAAGATGC
* * * ** * * ** * **
54854710 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAAATCTTGTCTTCATGCATT
1 AGATCTTGTCTTCTCGTATTGGCAGTGAAGTAGATTGAAGATAGCAGGTCTTGTCTTCCTATATT
* * *
54854775 GG-CGTGAAGTAGATCGAAAATGC
66 GGTAG-GAAGTGGATCGAAGATGC
* * ** * * * * * *
54854798 AGATCTTGTCTTCCCATATTGGTGGCGGAGTAGA-TCAA-ATATGCAGATCTTGTCTTCCCATAC
1 AGATCTTGTCTTCTCGTATTGGCAGTGAAGTAGATTGAAGATA-GCAGGTCTTGTCTTCCTATAT
*
54854861 TGGTGGCGAAGTGGATCGAAGA
65 TGGTAG-GAAGTGGATCGAAGA
54854883 AAACAGATCT
Statistics
Matches: 305, Mismatches: 39, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
86 3 0.01
87 41 0.13
88 261 0.86
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (88 bp):
AGATCTTGTCTTCTCGTATTGGCAGTGAAGTAGATTGAAGATAGCAGGTCTTGTCTTCCTATATT
GGTAGGAAGTGGATCGAAGATGC
Found at i:54855119 original size:100 final size:100
Alignment explanation
Indices: 54854942--54855206 Score: 359
Period size: 100 Copynumber: 2.6 Consensus size: 100
54854932 CTTATCTCTC
* * *
54854942 TGGCGATGCAGTGAAGCAGATTAAAACTACAACGGCGAATCTTGTTTCCCCGACATTGCAATTAA
1 TGGCGATGCAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAA
* *
54855007 AAAGATTAAAGCCGTAACGGCAAATCTTACTTCCA
66 AAAGATTAAAGCCGCAACGACAAATCTTACTTCCA
* * *
54855042 TGGCGATGCAGTGGAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCCGACATTGCAATTTA
1 TGGCGATGCAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAA
* * *
54855107 AAAGATTGAAGCCGCAACGACGAATCTTACTTCCT
66 AAAGATTAAAGCCGCAACGACAAATCTTACTTCCA
* * ** * * * *
54855142 TGGTGGTGCAGCAGAACTGATTAAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAA
1 TGGCGATGCAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAA
54855207 TCAAACTAAA
Statistics
Matches: 143, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 143 1.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.25
Consensus pattern (100 bp):
TGGCGATGCAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAA
AAAGATTAAAGCCGCAACGACAAATCTTACTTCCA
Found at i:54855132 original size:50 final size:50
Alignment explanation
Indices: 54854971--54855140 Score: 144
Period size: 50 Copynumber: 3.4 Consensus size: 50
54854961 ATTAAAACTA
**
54854971 CAACGGCGAATCTTGTTTCCCCGACATTGCAATTAAAAAGATTAAAGCCG
1 CAACGGCGAATCTTACTTCCCCGACATTGCAATTAAAAAGATTAAAGCCG
* * ** * * ** ** **
54855021 TAACGGCAAATCTTACTTCCATGGCGA-TGCAGTGGAGCAGATTAAAGCTA
1 CAACGGCGAATCTTACTTCCCCGAC-ATTGCAATTAAAAAGATTAAAGCCG
* * * * *
54855071 CGACGGTGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAAGCCG
1 CAACGGCGAATCTTACTTCCCCGACATTGCAATTAAAAAGATTAAAGCCG
*
54855121 CAACGACGAATCTTACTTCC
1 CAACGGCGAATCTTACTTCC
54855141 TTGGTGGTGC
Statistics
Matches: 84, Mismatches: 34, Indels: 4
0.69 0.28 0.03
Matches are distributed among these distances:
49 1 0.01
50 82 0.98
51 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (50 bp):
CAACGGCGAATCTTACTTCCCCGACATTGCAATTAAAAAGATTAAAGCCG
Found at i:54855468 original size:127 final size:127
Alignment explanation
Indices: 54855221--54855507 Score: 483
Period size: 127 Copynumber: 2.3 Consensus size: 127
54855211 ACTAAAAATA
*
54855221 ACAGATCTTATCTCCCTAAGCAGTAG-GGA-TCAGATCGCATCAAGTCTTATCTCCCTAAGCAGT
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGTCAGATCGCATCAAATCTTATCTCCCTAAGCAGT
*
54855284 AGTGGAGCAGATAAAAAAACCAATCCTATCTCCCTGAAGTTACAGTGGAACGGATTAAAACC
66 AGTGGAGCAGAGAAAAAAACCAATCCTATCTCCCTGAAGTTACAGTGGAACGGATTAAAACC
*
54855346 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGT-AGATTGCATCAAATCTTATCTCCCTAAGCAGT
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGTCAGATCGCATCAAATCTTATCTCCCTAAGCAGT
* * *
54855410 AGTGGAGTAGACGAAAAAAACCAATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAACC
66 AGTGGAGCAGA-GAAAAAAACCAATCCTATCTCCCTGAAGTTACAGTGGAACGGATTAAAACC
54855473 ACAGATCTTATCTCCCTAAGCAGTAGTGGAG-CAGA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGTCAGA
54855508 CGAAAAAAAC
Statistics
Matches: 152, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
125 26 0.17
126 43 0.28
127 83 0.55
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (127 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGTCAGATCGCATCAAATCTTATCTCCCTAAGCAGT
AGTGGAGCAGAGAAAAAAACCAATCCTATCTCCCTGAAGTTACAGTGGAACGGATTAAAACC
Found at i:54855489 original size:87 final size:87
Alignment explanation
Indices: 54855390--54855678 Score: 390
Period size: 87 Copynumber: 3.4 Consensus size: 87
54855380 ATTGCATCAA
* *
54855390 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAAAAACCAATCCTATCTCCTTGAAGTTACA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGTTACA
54855455 GTGGAGCGGATTAAAACCACAG
66 GTGGAGCGGATTAAAACCACAG
*
54855477 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGTTGCA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGTTACA
*
54855542 GTGGAGTGGATTAAAACCACAG
66 GTGGAGCGGATTAAAACCACAG
* * ** * *
54855564 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGAC-AGAACCA-CAGATCTTATCTCCCT-AAG-CAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCA-ATCCTATCTCCCTGAAGTTA-
* * * *
54855625 TAGTGGAGCAGA-CAGAACCACAG
64 CAGTGGAGCGGATTAAAACCACAG
*
54855648 ATCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
54855679 TCACCTCAAG
Statistics
Matches: 182, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
84 38 0.21
85 14 0.08
86 16 0.09
87 114 0.63
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (87 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGTTACA
GTGGAGCGGATTAAAACCACAG
Found at i:54855674 original size:214 final size:210
Alignment explanation
Indices: 54855261--54855787 Score: 699
Period size: 214 Copynumber: 2.5 Consensus size: 210
54855251 CAGATCGCAT
* *
54855261 CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAAAAACCAATCCTATCTCCCTGAAGTTA
1 CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAAAACCAATCCTATCTCCCTGAAGTTG
* * * ** * *
54855326 CAGTGGAACGGATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGCATCAAA
66 CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGACAGAACCAAA
* *
54855391 TCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAAAAACCAATCCTATCTCCTTGAAGTTACAG
131 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGTTACAG
*
54855456 TGGAGCGGATTAAAACCA
196 TGGAGCAGA-T--AACCA
54855474 C-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGT
1 CAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGAC-AAAAAAACCAATCCTATCTCCCTGAAGT
*
54855538 TGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGACAGAACCA
64 TGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGACAGAACCA
* ** *
54855603 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAC-AGAACCA-CAGATCTTATCTCCCT-AAG-
129 -A-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCA-ATCCTATCTCCCTGAAGT
* * *
54855664 TAGTAGTGGAGCAGATCACCT
191 TA-CAGTGGAGCAGATAACCA
* *
54855685 CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGGCAGAAAAAA--AATCCTATCTCCTTGAAGTT
1 CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACA-AAAAAACCAATCCTATCTCCCTGAAGTT
* *
54855748 GTAGTGGAGCGGATTAAAAACACAGATCTTATCTCTCTAA
65 GCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAA
54855788 AGTTGCAGTA
Statistics
Matches: 281, Mismatches: 25, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
209 56 0.20
210 1 0.00
211 40 0.14
212 4 0.01
213 34 0.12
214 99 0.35
215 16 0.06
216 31 0.11
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (210 bp):
CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAAAACCAATCCTATCTCCCTGAAGTTG
CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGACAGAACCAAA
TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGTTACAG
TGGAGCAGATAACCA
Found at i:54855715 original size:40 final size:41
Alignment explanation
Indices: 54855221--54855717 Score: 327
Period size: 42 Copynumber: 11.8 Consensus size: 41
54855211 ACTAAAAATA
* ** *
54855221 ACAGATCTTATCTCCCTAAGCAGTAG-GGATCAGATCGCATC
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAACC
* **
54855262 A-AG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAAAA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAACC
* * * * * *
54855302 ACCA-ATCCTATCTCCCTGAAGTTA-CAGTGGAACGGATTAAAACC
1 A-CAGATCTTATCTCCCT-AAG-CAGTAGTGGAGCAGA--CAAACC
* ***
54855346 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAG--ATTGC
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAACC
* * **
54855385 ATCAAATCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAAAA
1 A-CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAC--AAACC
* * * * * *
54855429 ACCA-ATCCTATCTCCTTGAAGTTA-CAGTGGAGCGGATTAAAACC
1 A-CAGATCTTATCTCCCT-AAG-CAGTAGTGGAGCAGA--CAAACC
**
54855473 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAC--AAACC
* ** * ** *
54855516 ACCA-ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACC
1 A-CAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGA--CAAACC
*
54855560 ACAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGACAGAACC
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACA-AACC
54855602 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACC
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACA-AACC
*
54855644 ACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATC--ACC
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAACC
*
54855684 TCA-AGTCTTATCTCCCTAAGCAGTAGTGGAGCAG
1 ACAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAG
54855718 GCAGAAAAAA
Statistics
Matches: 360, Mismatches: 66, Indels: 61
0.74 0.14 0.13
Matches are distributed among these distances:
39 25 0.07
40 77 0.21
41 2 0.01
42 93 0.26
43 82 0.23
44 80 0.22
45 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (41 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAACC
Found at i:54855752 original size:82 final size:82
Alignment explanation
Indices: 54855568--54855757 Score: 224
Period size: 82 Copynumber: 2.3 Consensus size: 82
54855558 CCACAGATCT
* * *
54855568 TATCTCTCTAAGCAGTAGTGGAGCAGA-CAGAAC-CACAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGTAGTAGTGGAGCAGATC--ACCTCA-AG-TCTTATCTCCCTAAGCAGTAGTGG
* * * *
54855631 AGCAGACAGAACCACAGATCT
62 AGCAGACAGAACAAAAAATCC
54855652 TATCTCCCTAAGTAGTAGTGGAGCAGATCACCTCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
1 TATCTCCCTAAGTAGTAGTGGAGCAGATCACCTCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
*
54855717 GGCAGAA-AAAAAATCC
66 GACAGAACAAAAAATCC
* *
54855733 TATCTCCTTGAAGTTGTAGTGGAGC
1 TATCTCCCT-AAGTAGTAGTGGAGC
54855758 GGATTAAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
81 13 0.14
82 48 0.52
83 4 0.04
84 27 0.29
85 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (82 bp):
TATCTCCCTAAGTAGTAGTGGAGCAGATCACCTCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
GACAGAACAAAAAATCC
Found at i:54855754 original size:124 final size:126
Alignment explanation
Indices: 54855481--54855820 Score: 330
Period size: 124 Copynumber: 2.7 Consensus size: 126
54855471 CCACAGATCT
* * * *
54855481 TATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAAAAACCA-ATCCTATCTCCCTGAAGTTGCAGT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATC-AAAAACA-CAGATCTTATCTCCCTAAAGTAGCAGT
* ** * * * * * * *
54855544 GGAGTGGATTAAAACCACAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGACAGAACCACAGATC
64 AGAGCAGA-TCACATCA-AG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACAAAAAATC
*
54855609 T
126 C
* * * *
54855610 TATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAACCACAGATCTTATCTCCCT-AAGTAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAACACAGATCTTATCTCCCTAAAGTAGCAGTAG
* *
54855673 AGCAGATCACCTCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGGCAGAA-AAAAAATCC
66 AGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACAAAAAATCC
* ** * * * *
54855733 TATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAAACACAGATCTTATCTCTCTAAAGTTGCAGTA
1 TATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAAACACAGATCTTATCTCCCTAAAGTAGCAGTA
*
54855798 GAGCAGATCACATCCAGTCTTAT
65 GAGCAGATCACATCAAGTCTTAT
54855821 TTCTCTGAAG
Statistics
Matches: 176, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
123 13 0.07
124 48 0.27
125 22 0.12
126 33 0.19
127 16 0.09
128 16 0.09
129 28 0.16
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (126 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAACACAGATCTTATCTCCCTAAAGTAGCAGTAG
AGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACAAAAAATCC
Found at i:54856183 original size:23 final size:22
Alignment explanation
Indices: 54856152--54856195 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
54856142 AGCCCAGATT
54856152 CCTAACCCAAATCAAAACTAAAC
1 CCTAACCCAAAT-AAAACTAAAC
* *
54856175 CCTAGCCCAACTAAAACTAAA
1 CCTAACCCAAATAAAACTAAA
54856196 AATTATCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.50, C:0.34, G:0.02, T:0.14
Consensus pattern (22 bp):
CCTAACCCAAATAAAACTAAAC
Found at i:54862580 original size:11 final size:11
Alignment explanation
Indices: 54862566--54862610 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
54862556 TCAATTATTT
54862566 TCTCAATTTCC
1 TCTCAATTTCC
*
54862577 TCTCAATTTGC
1 TCTCAATTTCC
*
54862588 TCTCAATTTAC
1 TCTCAATTTCC
*
54862599 ACTCAATTTCC
1 TCTCAATTTCC
54862610 T
1 T
54862611 TCCAAATTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.22, C:0.31, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:54863846 original size:7 final size:7
Alignment explanation
Indices: 54863834--54863859 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54863824 TAGTCGATTG
54863834 GTATTTA
1 GTATTTA
54863841 GTATTTA
1 GTATTTA
54863848 GTATTTA
1 GTATTTA
54863855 GTATT
1 GTATT
54863860 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:54864528 original size:18 final size:18
Alignment explanation
Indices: 54864505--54864547 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54864495 TGTCAGGTGC
* *
54864505 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
54864523 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
54864541 GTTTCCT
1 GTATCCT
54864548 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:54864828 original size:21 final size:21
Alignment explanation
Indices: 54864803--54864849 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
54864793 AGATGCCCTA
* * *
54864803 CCGGAGGAATCAGAATCCCCG
1 CCGGAGCAATCACAACCCCCG
*
54864824 TCGGAGCAATCACAACCCCCG
1 CCGGAGCAATCACAACCCCCG
54864845 CCGGA
1 CCGGA
54864850 AGCTGGACGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.38, G:0.26, T:0.09
Consensus pattern (21 bp):
CCGGAGCAATCACAACCCCCG
Found at i:54865062 original size:7 final size:7
Alignment explanation
Indices: 54865042--54865079 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
54865032 ATTTATTAAA
54865042 AATTTAT
1 AATTTAT
54865049 AAATTTAT
1 -AATTTAT
54865057 AATTTAT
1 AATTTAT
54865064 AA-TTA-
1 AATTTAT
54865069 AATTTAT
1 AATTTAT
54865076 AATT
1 AATT
54865080 AAATTGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.07
6 6 0.21
7 13 0.46
8 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTAT
Found at i:54865074 original size:12 final size:12
Alignment explanation
Indices: 54865041--54865084 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 12
54865031 AATTTATTAA
54865041 AAATTTATAAATTT
1 AAATTTAT-AA-TT
54865055 ATAATTTATAATT
1 A-AATTTATAATT
54865068 AAATTTATAATT
1 AAATTTATAATT
54865080 AAATT
1 AAATT
54865085 GACAAACCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 16 0.55
13 3 0.10
14 3 0.10
15 7 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATTTATAATT
Found at i:54865112 original size:6 final size:6
Alignment explanation
Indices: 54865101--54865126 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
54865091 CCCTAACAAA
54865101 AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AA
54865127 AAACCATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:54865149 original size:22 final size:21
Alignment explanation
Indices: 54865107--54865180 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
54865097 CAAAAACCCT
* *
54865107 AACCCTAACCC-TAACCCTAAA
1 AACCCAAACCCTTAA-CTTAAA
*
54865128 AACCATAAACCCTTAACTTAAA
1 AACC-CAAACCCTTAACTTAAA
* *
54865150 AACCCCAACCCTTAATTTAAA
1 AACCCAAACCCTTAACTTAAA
*
54865171 AACCCTAACC
1 AACCCAAACC
54865181 TAATTTATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 27 0.61
22 14 0.32
23 3 0.07
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCAAACCCTTAACTTAAA
Found at i:54865193 original size:21 final size:21
Alignment explanation
Indices: 54865135--54865187 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
54865125 AAAAACCATA
*
54865135 AACCCTTAACTTAAAAACCCC
1 AACCCTTAATTTAAAAACCCC
*
54865156 AACCCTTAATTTAAAAACCCT
1 AACCCTTAATTTAAAAACCCC
54865177 AA-CC-TAATTTA
1 AACCCTTAATTTA
54865188 TTAAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 7 0.23
20 2 0.07
21 21 0.70
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.26
Consensus pattern (21 bp):
AACCCTTAATTTAAAAACCCC
Found at i:54865223 original size:12 final size:12
Alignment explanation
Indices: 54865206--54865235 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54865196 TTATAAATTA
54865206 TAAATTTATAAT
1 TAAATTTATAAT
54865218 TAAATTTATAAT
1 TAAATTTATAAT
*
54865230 TTAATT
1 TAAATT
54865236 GACAAACCCT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TAAATTTATAAT
Found at i:54865263 original size:18 final size:18
Alignment explanation
Indices: 54865240--54865278 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
54865230 TTAATTGACA
54865240 AACCCTAACAAAAACCCT
1 AACCCTAACAAAAACCCT
**
54865258 AACCCTAACCCAAACCCT
1 AACCCTAACAAAAACCCT
54865276 AAC
1 AAC
54865279 AAAACCCCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.44, G:0.00, T:0.10
Consensus pattern (18 bp):
AACCCTAACAAAAACCCT
Found at i:54865577 original size:21 final size:21
Alignment explanation
Indices: 54865534--54865578 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
54865524 TTTTCTCTAA
*
54865534 AACCCTAAAACCCTAAACCCT
1 AACCCTAAAACCCTAAAACCT
*
54865555 AACCCTGAAAACCC-AAAAGCT
1 AACCCT-AAAACCCTAAAACCT
54865576 AAC
1 AAC
54865579 ATGGGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.47, C:0.38, G:0.04, T:0.11
Consensus pattern (21 bp):
AACCCTAAAACCCTAAAACCT
Found at i:54866034 original size:12 final size:12
Alignment explanation
Indices: 54866017--54866041 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54866007 TAGATGAAGA
54866017 TAAATTTTATAC
1 TAAATTTTATAC
54866029 TAAATTTTATAC
1 TAAATTTTATAC
54866041 T
1 T
54866042 TAGAGATGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATTTTATAC
Found at i:54879770 original size:26 final size:26
Alignment explanation
Indices: 54879740--54879790 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
54879730 TAATATATAA
54879740 CACACACATATCTGCACATATAGACG
1 CACACACATATCTGCACATATAGACG
*
54879766 CACACATATATCTGCACATATAGAC
1 CACACACATATCTGCACATATAGAC
54879791 TACAAGGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (26 bp):
CACACACATATCTGCACATATAGACG
Found at i:54880910 original size:20 final size:20
Alignment explanation
Indices: 54880887--54880934 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
54880877 AATATTTAGA
* *
54880887 AAAATAATTTATAAAATATT
1 AAAATAAATAATAAAATATT
*
54880907 AAAATAAATAATCAAATATT
1 AAAATAAATAATAAAATATT
54880927 AAAA-AAAT
1 AAAATAAAT
54880935 GAAATGCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATAAATAATAAAATATT
Found at i:54882529 original size:44 final size:44
Alignment explanation
Indices: 54882481--54882681 Score: 118
Period size: 44 Copynumber: 4.3 Consensus size: 44
54882471 CCAATGTAAT
* * * *
54882481 TTCAGGGAGA-AGAGACTTGTAGCTTCGATCTGCTTCGCTGCAAC
1 TTCAGGGAGATA-AGACTAGTAGCTTCAATCTGCTCCACTGCAAC
* *
54882525 TTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAAC
1 TTCAGGGAGATAAGACTAGTAGCTTCAATCTGCTCCACTGCAAC
* * * * *
54882569 TTTAGGAAGATAAGATTTGCCATAATTTGTAGCTTTAATTTGTTCCACTGCAAC
1 TTCAGGGAGATAAGA-----C-T-A---GTAGCTTCAATCTGCTCCACTGCAAC
** * * * *
54882623 GCCAGGGAAATAAGATTTGCT-GTCTTCAATCTGCTCCACTGTAAC
1 TTCAGGGAGATAAGACTAG-TAG-CTTCAATCTGCTCCACTGCAAC
54882668 TTCAGGGAGATAAG
1 TTCAGGGAGATAAG
54882682 GTTTGATATG
Statistics
Matches: 117, Mismatches: 27, Indels: 25
0.69 0.16 0.15
Matches are distributed among these distances:
44 50 0.43
45 31 0.26
48 1 0.01
49 1 0.01
50 1 0.01
51 1 0.01
54 32 0.27
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (44 bp):
TTCAGGGAGATAAGACTAGTAGCTTCAATCTGCTCCACTGCAAC
Found at i:54882912 original size:235 final size:233
Alignment explanation
Indices: 54882543--54882996 Score: 746
Period size: 235 Copynumber: 1.9 Consensus size: 233
54882533 GATAAGGCTA
* * *
54882543 GTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATTTGCCATAATTTGTAGCTTTAAT
1 GTGGCTTCAATCTGCTCCACCGCAACTTTAAGAAGATAAGATCTGCCATAATTTGTAGCTTTAAT
* * * *
54882608 TTGTTCCACTGCAACGCCAGGGAAATAAGATTTGCTGTCTTCAATCTGCTCCACTGTAACTTCAG
66 CTATTCCACTGCAACACCAGGGAAATAAGATTTGCTGTCTTCAATCTGCTCCACTGCAACTTCAG
* *
54882673 GGAGATAAGGTTTGATATGATCTGCTCTACTGCAATTTCAAATAGATAAGATCTACAATTTATAG
131 GGAGATAAGGCTTGATATGATCTGCTCTACTGCAACTTCAAATAGATAAGATCTACAATTTATAG
54882738 CTTCAATCTGTTCCACTGTAACTTTAGAGAAATAATACTG
196 CTTCAATC--TTCCACTGTAACTTTAGAGAAATAATACTG
* *
54882778 GTGGCTTCAATTTGCTCCACCGCAACTTTAAGAAGATAAGATCTGTCATAATTTGTAGCTTTAAT
1 GTGGCTTCAATCTGCTCCACCGCAACTTTAAGAAGATAAGATCTGCCATAATTTGTAGCTTTAAT
** ** *
54882843 CTATTCCACTGCAACATTAGGGAAATAAGATTTGCTGTCTTCAATCTGCTCCGTTGCAACTTTAG
66 CTATTCCACTGCAACACCAGGGAAATAAGATTTGCTGTCTTCAATCTGCTCCACTGCAACTTCAG
54882908 GGAGATAAGGCTTGATATGATCTGCTCTACTGCAACTTCAAATAGATAAGATCTACAATTTATAG
131 GGAGATAAGGCTTGATATGATCTGCTCTACTGCAACTTCAAATAGATAAGATCTACAATTTATAG
54882973 CTTCAATCTTCCACTGTAACTTTA
196 CTTCAATCTTCCACTGTAACTTTA
54882997 AGGAAAATAA
Statistics
Matches: 203, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
233 16 0.08
235 187 0.92
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (233 bp):
GTGGCTTCAATCTGCTCCACCGCAACTTTAAGAAGATAAGATCTGCCATAATTTGTAGCTTTAAT
CTATTCCACTGCAACACCAGGGAAATAAGATTTGCTGTCTTCAATCTGCTCCACTGCAACTTCAG
GGAGATAAGGCTTGATATGATCTGCTCTACTGCAACTTCAAATAGATAAGATCTACAATTTATAG
CTTCAATCTTCCACTGTAACTTTAGAGAAATAATACTG
Found at i:54883052 original size:235 final size:234
Alignment explanation
Indices: 54882534--54883052 Score: 702
Period size: 235 Copynumber: 2.2 Consensus size: 234
54882524 CTTCAGGGAG
* * * * * * *
54882534 ATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATTTGCCATAATTTGT
1 ATAAGACTACTGGCTTCAATCTACTCCACCGCAACTTAAAGAAGATAAGATCTGCCATAATTTGT
* * *
54882599 AGCTTTAATTTGTTCCACTGCAACGCCAGGGAAATAAGATTTGCTGTCTTCAATCTGCTCCACTG
66 AGCTTTAATCTATTCCACTGCAACACCAGGGAAATAAGATTTGCTGTCTTCAATCTGCTCCACTG
* * *
54882664 TAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAATTTCAAATAGATAAGATCTAC
131 CAACTTCAGGGAGATAAGGCTTGATATGATCTGCTCTACTGCAACTTCAAATAGATAAGATCTAC
54882729 AATTTATAGCTTCAATCTGTTCCACTGTAACTTTAGAGAA
196 AATTTATAGCTTCAATC-GTTCCACTGTAACTTTAGAGAA
* ** * * * *
54882769 ATAATACTGGTGGCTTCAATTTGCTCCACCGCAACTTTAAGAAGATAAGATCTGTCATAATTTGT
1 ATAAGACTACTGGCTTCAATCTACTCCACCGCAACTTAAAGAAGATAAGATCTGCCATAATTTGT
** **
54882834 AGCTTTAATCTATTCCACTGCAACATTAGGGAAATAAGATTTGCTGTCTTCAATCTGCTCCGTTG
66 AGCTTTAATCTATTCCACTGCAACACCAGGGAAATAAGATTTGCTGTCTTCAATCTGCTCCACTG
*
54882899 CAACTTTAGGGAGATAAGGCTTGATATGATCTGCTCTACTGCAACTTCAAATAGATAAGATCTAC
131 CAACTTCAGGGAGATAAGGCTTGATATGATCTGCTCTACTGCAACTTCAAATAGATAAGATCTAC
54882964 AATTTATAGCTTCAATC-TTCCACTGTAACTTTA-AGGAAA
196 AATTTATAGCTTCAATCGTTCCACTGTAACTTTAGA-G-AA
* * * * *
54883003 ATAAGATTCACTGTCTTCAGTCTACTCCACTGCATCTTCAAAG-AGATAAG
1 ATAAGACT-ACTGGCTTCAATCTACTCCACCGCAACTT-AAAGAAGATAAG
54883053 GCTGGTGGCT
Statistics
Matches: 250, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
232 1 0.00
233 17 0.07
234 8 0.03
235 221 0.88
236 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (234 bp):
ATAAGACTACTGGCTTCAATCTACTCCACCGCAACTTAAAGAAGATAAGATCTGCCATAATTTGT
AGCTTTAATCTATTCCACTGCAACACCAGGGAAATAAGATTTGCTGTCTTCAATCTGCTCCACTG
CAACTTCAGGGAGATAAGGCTTGATATGATCTGCTCTACTGCAACTTCAAATAGATAAGATCTAC
AATTTATAGCTTCAATCGTTCCACTGTAACTTTAGAGAA
Found at i:54883185 original size:143 final size:140
Alignment explanation
Indices: 54882757--54883241 Score: 455
Period size: 143 Copynumber: 3.4 Consensus size: 140
54882747 GTTCCACTGT
* * ** * * *
54882757 AACTTTAGAGAAATAATACTGGTGGCTTCAATTTGCTCCACCGCAACTTTAAGAAGATAAGATCT
1 AACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAA-AAGATAAGATCT
* * * *
54882822 GTCATAATTTGTAGCTTTAATCTATTCCACTGCAACATTAGGGAAATAAGATTTGCTGTCTTCAA
65 G-CATAATTTGTAGCTTTAAT-TATTCCACTTCAATATAAGGGAAATAAGATTTGCTGTCTTCAG
* *
54882887 TCTGCTCCGTTGC
128 TCTACTCCGCTGC
* * * * *
54882900 AACTTTAGGGAGATAAGGCT--T-GATAT-GATCTGCTCTACTGCAACTTCAAATAGATAAGATC
1 AACTTCAGAGAGATAAGGCTGGTGGCT-TCAATCTGCTCCACTGCAACTTCAAA-AGATAAGATC
* * * * * * **
54882961 T--ACAATTTATAGCTTCAA-TCTTCCACTGT-AACTTTAAGGAAAATAAGATTCACTGTCTTCA
64 TGCATAATTTGTAGCTTTAATTATTCCACT-TCAA-TATAAGGGAAATAAGATTTGCTGTCTTCA
*
54883022 GTCTACTCCACTGC
127 GTCTACTCCGCTGC
* *
54883036 ATCTTCAAAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGAAAGATAAGATCT
1 AACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCA-AAAGATAAGATCT
* *** * *
54883101 GCCATAATTTGTAGCTTTAATTTGTTCCACTTCAATGCCAGGGAAATAAGATTTGTTGTCTTTAG
65 G-CATAATTTGTAGCTTTAA-TTATTCCACTTCAATATAAGGGAAATAAGATTTGCTGTCTTCAG
* *
54883166 TCTTCTCCGCTGT
128 TCTACTCCGCTGC
* * *
54883179 AACTTCAGAGAGATAAGGCTGGTGGTTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGAT
1 AACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCA-AAAGATAAGAT
54883242 TCACCATAAT
Statistics
Matches: 275, Mismatches: 52, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
135 10 0.04
136 49 0.18
137 14 0.05
138 2 0.01
139 34 0.12
140 33 0.12
141 2 0.01
142 14 0.05
143 107 0.39
144 10 0.04
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (140 bp):
AACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAAAGATAAGATCTG
CATAATTTGTAGCTTTAATTATTCCACTTCAATATAAGGGAAATAAGATTTGCTGTCTTCAGTCT
ACTCCGCTGC
Found at i:54884543 original size:18 final size:18
Alignment explanation
Indices: 54884504--54884572 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
54884494 AGGTTTTTAT
54884504 TTTTTGTTCTTTGTT-TTGA
1 TTTTTGTTCTTT-TTATT-A
54884523 TTTTTGTTCTTTTTATTA
1 TTTTTGTTCTTTTTATTA
* *
54884541 TTTTT-TTGTTTTTTATCTT
1 TTTTTGTT-CTTTTTAT-TA
54884560 TTTTTGTT-TTTTT
1 TTTTTGTTCTTTTT
54884573 TGTTTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
17 2 0.05
18 20 0.45
19 20 0.45
20 2 0.05
ACGTcount: A:0.06, C:0.04, G:0.09, T:0.81
Consensus pattern (18 bp):
TTTTTGTTCTTTTTATTA
Found at i:54884545 original size:19 final size:19
Alignment explanation
Indices: 54884500--54884582 Score: 70
Period size: 19 Copynumber: 4.5 Consensus size: 19
54884490 GTAGAGGTTT
54884500 TTATTTTTTGTTCTTTGTT-
1 TTATTTTTTGTTCTTT-TTA
54884519 TTGA-TTTTTGTTCTTTTTA
1 TT-ATTTTTTGTTCTTTTTA
54884538 TTATTTTTT-TGT-TTTTTA
1 TTATTTTTTGT-TCTTTTTA
* *
54884556 TCT-TTTTTTGTTTTTTTTG
1 T-TATTTTTTGTTCTTTTTA
54884575 TT-TTTTTT
1 TTATTTTTT
54884583 CCTCTACTGC
Statistics
Matches: 56, Mismatches: 1, Indels: 15
0.78 0.01 0.21
Matches are distributed among these distances:
18 25 0.45
19 30 0.54
20 1 0.02
ACGTcount: A:0.06, C:0.04, G:0.08, T:0.82
Consensus pattern (19 bp):
TTATTTTTTGTTCTTTTTA
Found at i:54884546 original size:26 final size:25
Alignment explanation
Indices: 54884497--54884580 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 25
54884487 CCAGTAGAGG
*
54884497 TTTTTAT-TTTTTGTTCTTTGTTTTGAT
1 TTTTTATCTTTTT-TTATTT-TTTTG-T
54884524 TTTTGT-TCTTTTTATTATTTTTTTGT
1 TTTT-TATCTTTTT-TTATTTTTTTGT
*
54884550 TTTTTATCTTTTTTTGTTTTTTTTGT
1 TTTTTATCTTTTTTT-ATTTTTTTGT
54884576 TTTTT
1 TTTTT
54884581 TTCCTCTACT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
25 3 0.06
26 26 0.52
27 10 0.20
28 11 0.22
ACGTcount: A:0.06, C:0.04, G:0.08, T:0.82
Consensus pattern (25 bp):
TTTTTATCTTTTTTTATTTTTTTGT
Done.