Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 164 of 199
Found at i:53591750 original size:138 final size:138
Alignment explanation
Indices: 53591506--53591781 Score: 453
Period size: 138 Copynumber: 2.0 Consensus size: 138
53591496 CCCAAATCTA
53591506 GAACCCCAAACCCAAAACTCGAACAACAAACCCGTAACCTCAAACTCTTGAACCATAAATCAAAA
1 GAACCCCAAACCCAAAACTCGAACAACAAACCCGTAACCTCAAACTCTTGAACCATAAATCAAAA
* * * * *
53591571 TCCTAACCCCCAAACTTAAAACACATAACCCCAAACCATTGAACCTTAAGCTTGAACCTCGAATC
66 CCCTAAACCCCAAACTTAAAACACATAACCCCAAACCATTGAACCTTAAACTTGAACCTCAAACC
53591636 CCGAACCC
131 CCGAACCC
* * *
53591644 GAACCCCAAACCCAAAACTCGAACACCAAACCCGTAACCTCGAACTCTTGAATCATAAATCAAAA
1 GAACCCCAAACCCAAAACTCGAACAACAAACCCGTAACCTCAAACTCTTGAACCATAAATCAAAA
* * *
53591709 CCCTAAACCCCAAACTTATAACACATAACCCCAAACTATTGAACCTTAAACTTGAACTTCAAACC
66 CCCTAAACCCCAAACTTAAAACACATAACCCCAAACCATTGAACCTTAAACTTGAACCTCAAACC
53591774 CCGAACCC
131 CCGAACCC
53591782 CAAACCCTAG
Statistics
Matches: 127, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
138 127 1.00
ACGTcount: A:0.42, C:0.36, G:0.06, T:0.16
Consensus pattern (138 bp):
GAACCCCAAACCCAAAACTCGAACAACAAACCCGTAACCTCAAACTCTTGAACCATAAATCAAAA
CCCTAAACCCCAAACTTAAAACACATAACCCCAAACCATTGAACCTTAAACTTGAACCTCAAACC
CCGAACCC
Found at i:53591838 original size:14 final size:13
Alignment explanation
Indices: 53591804--53591854 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
53591794 CCCTAATCTT
53591804 AAACATTGAACCCC
1 AAAC-TTGAACCCC
*
53591818 AAACTTGAACCTC
1 AAACTTGAACCCC
53591831 AAATCTTGAACCCC
1 AAA-CTTGAACCCC
* *
53591845 GAACCTGAAC
1 AAACTTGAAC
53591855 ATTGAACCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 17 0.53
14 15 0.47
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (13 bp):
AAACTTGAACCCC
Found at i:53594872 original size:5 final size:5
Alignment explanation
Indices: 53594857--53594898 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
53594847 ATAATTATTT
* *
53594857 TAATA -AATA TAATA TAATA TAATA TAATA TAACA TAACA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
53594899 GTATTAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (5 bp):
TAATA
Found at i:53595274 original size:30 final size:30
Alignment explanation
Indices: 53595240--53595303 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
53595230 AAAATTACAC
* * *
53595240 TTTAATCTTTTAAAAACAATAAAAATTTAA
1 TTTAATCCTCTAAAAACAATAAAAATATAA
** *
53595270 TTTAATCCTCTAAAAATTATAAAGATATAA
1 TTTAATCCTCTAAAAACAATAAAAATATAA
53595300 TTTA
1 TTTA
53595304 TTAAAATAGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.41
Consensus pattern (30 bp):
TTTAATCCTCTAAAAACAATAAAAATATAA
Found at i:53599692 original size:18 final size:19
Alignment explanation
Indices: 53599662--53599698 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
53599652 CATGAGCATA
53599662 TGTATCATAACA-TTCATT
1 TGTATCATAACATTTCATT
53599680 TGTATACAT-ACATTTCATT
1 TGTAT-CATAACATTTCATT
53599699 CAATGTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (19 bp):
TGTATCATAACATTTCATT
Found at i:53601630 original size:29 final size:28
Alignment explanation
Indices: 53601583--53601643 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
53601573 ATGGCCAACC
* *
53601583 ATGTTGATATTATGTTTTTGTTAAAGTGT
1 ATGTTGATATGATGATTTTGTT-AAGTGT
* *
53601612 ATGTTGTTATGATGATTTTGTTGAGTGT
1 ATGTTGATATGATGATTTTGTTAAGTGT
53601640 ATGT
1 ATGT
53601644 AGCTTGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (28 bp):
ATGTTGATATGATGATTTTGTTAAGTGT
Found at i:53607501 original size:21 final size:21
Alignment explanation
Indices: 53607451--53607501 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
53607441 CCAGTCTATC
*
53607451 CCATCACTCTCTCAGCCTCTT
1 CCATCACTTTCTCAGCCTCTT
53607472 CCATCACTTTCTCAG-CTACTT
1 CCATCACTTTCTCAGCCT-CTT
*
53607493 GCATCACTT
1 CCATCACTT
53607502 CCCACTGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (21 bp):
CCATCACTTTCTCAGCCTCTT
Found at i:53610773 original size:33 final size:33
Alignment explanation
Indices: 53610736--53610804 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
53610726 TTTTTATTCA
*
53610736 TAATAAATATGCTTTTCTTTTATTTAATAATGG
1 TAATAAATATGCTTTTCATTTATTTAATAATGG
53610769 TAATAAATATGCTTTTCATTTATTTAATAATGG
1 TAATAAATATGCTTTTCATTTATTTAATAATGG
53610802 TAA
1 TAA
53610805 AATCGTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (33 bp):
TAATAAATATGCTTTTCATTTATTTAATAATGG
Found at i:53611265 original size:22 final size:24
Alignment explanation
Indices: 53611238--53611301 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
53611228 TTATTTAAAA
53611238 TAAATAAATTAATATTATTAAA-G
1 TAAATAAATTAATATTATTAAATG
53611261 -AAATAAATTAA-ATTACTTAAATG
1 TAAATAAATTAATATTA-TTAAATG
*
53611284 TTAATAAA-TAATATTATT
1 TAAATAAATTAATATTATT
53611302 GAAAATGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 4 0.11
22 16 0.44
23 6 0.17
24 10 0.28
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (24 bp):
TAAATAAATTAATATTATTAAATG
Found at i:53625739 original size:3 final size:3
Alignment explanation
Indices: 53625731--53625760 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
53625721 TTTATCTTAC
*
53625731 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53625761 CTACTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53630322 original size:7 final size:7
Alignment explanation
Indices: 53630297--53630329 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
53630287 AGTGATGTGA
53630297 AAAAATG
1 AAAAATG
53630304 AAAAGATG
1 AAAA-ATG
53630312 -AAAATG
1 AAAAATG
53630318 AAAAATG
1 AAAAATG
53630325 AAAAA
1 AAAAA
53630330 GTAAAAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 18 0.75
8 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:53630336 original size:21 final size:21
Alignment explanation
Indices: 53630297--53630337 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53630287 AGTGATGTGA
*
53630297 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
53630318 AAAAATGAAAA-AGTAAAAAT
1 AAAAATGAAAAGA-TAAAAAT
53630338 AGATAGGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:53631873 original size:133 final size:133
Alignment explanation
Indices: 53631618--53632263 Score: 949
Period size: 133 Copynumber: 4.9 Consensus size: 133
53631608 AGAGAGCAGG
* * *
53631618 TTGAAAATAGTAGATCTTGCCTTCCTACATAGACAGTGGAGCAGATCGAAGATGGCGGA-TTTAC
1 TTGAAGATAGTAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
* * *
53631682 CTCC-CTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAA
66 CTCCTC-GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAA
53631746 TAGA
130 TAGA
** * *
53631750 TTGAAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGATGGCGGATTTTAC
1 TTGAAGATAGTAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
*
53631815 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGGCAGCAGCGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAAT
53631880 AGA
131 AGA
*
53631883 TTGAAGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
1 TTGAAGATAGTAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
* *
53631948 CTCCTTGTGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAGCAGCGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAAT
53632013 AGA
131 AGA
** * * * **
53632016 TTGAAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTAC
1 TTGAAGATAGTAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
* * *
53632081 CT-CTCTGTGGTTACAGTGGAGTACATTGAAGCC-GATAATTTTACTTCTCTGGGCAGCAGTGGA
66 CTCCTC-GTGGTTACAGTGGAGTACATTGAAGCCAG-TAATTCTACTTCCCTGGGCAGCAGCGGA
53632144 ATAGA
129 ATAGA
* * * * * *
53632149 TTAAAGATAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTAC
1 TTGAAGATAGTAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
* *
53632214 CTCATCGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
53632264 AGCAGATCTT
Statistics
Matches: 460, Mismatches: 48, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
132 55 0.12
133 401 0.87
134 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (133 bp):
TTGAAGATAGTAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAAT
AGA
Found at i:53632102 original size:266 final size:266
Alignment explanation
Indices: 53631618--53632263 Score: 1055
Period size: 266 Copynumber: 2.4 Consensus size: 266
53631608 AGAGAGCAGG
* * * *
53631618 TTGAAAATAGTAGATCTTGCCTTCCTACATAGACAGTGGAGCAGATCGAAGATGGCGGA-TTTAC
1 TTGAAGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
* * * *
53631682 CTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAAT
66 CTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAAT
* *
53631747 AGATTGAAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGATGGCGGATTT
131 AGATTGAAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGCAGATTT
53631812 TACCTCCTCGTGGTTACAGTGGAGTACATTGAAGCC-AGTAATTCTACTTCTCTGGGCAGCAGCG
196 TACCTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGA-TAATTCTACTTCTCTGGGCAGCAGCG
53631876 GAATAGA
260 GAATAGA
53631883 TTGAAGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
1 TTGAAGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
*
53631948 CTCCTTGTGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAGCAGCGGAAT
66 CTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAAT
*
53632013 AGATTGAAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTT
131 AGATTGAAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGCAGATTT
* *
53632078 TACCT-CTCTGTGGTTACAGTGGAGTACATTGAAGCCGATAATTTTACTTCTCTGGGCAGCAGTG
196 TACCTCCTC-GTGGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCTCTGGGCAGCAGCG
53632142 GAATAGA
260 GAATAGA
* * * * *
53632149 TTAAAGATAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTAC
1 TTGAAGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
* * *
53632214 CTCATCGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
66 CTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
53632264 AGCAGATCTT
Statistics
Matches: 355, Mismatches: 23, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
265 58 0.16
266 296 0.83
267 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (266 bp):
TTGAAGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
CTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAAT
AGATTGAAGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGCAGATTT
TACCTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCTCTGGGCAGCAGCGG
AATAGA
Found at i:53632342 original size:107 final size:107
Alignment explanation
Indices: 53632156--53632370 Score: 369
Period size: 107 Copynumber: 2.0 Consensus size: 107
53632146 AGATTAAAGA
53632156 TAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTACCTCATCG
1 TAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTACCTCATCG
*
53632221 TGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
66 TGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
* * * *
53632263 TAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCA-GATTTTACCTCCTC
1 TAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGG-AGGATTTTACCTCATC
53632327 GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
65 GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
53632370 T
1 T
53632371 GGGTAGCAGC
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
107 101 0.99
108 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (107 bp):
TAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTACCTCATCG
TGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
Found at i:53632452 original size:240 final size:240
Alignment explanation
Indices: 53632027--53632503 Score: 685
Period size: 240 Copynumber: 2.0 Consensus size: 240
53632017 TGAAGATTTT
* *
53632027 AGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCTCTGTGGT
1 AGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGCAGATTTTACCTCTCTGTGGT
* * *
53632092 TACAGTGGAGTACATTGAAGCCGATAATTTTACTTCTCTGGGCAGCAGTGGAATAGATTAAAGAT
66 TACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAGAT
* * *
53632157 AGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTACCT-CATCG
131 AGCAGATCTTGCATTCCTACATAGACAGCGAAGAAGATCAAAAACGGAGGATTTTACCTCCCT-G
* *
53632221 TGGTTATAGTGGAGTACATTGAAGCC-AGTAATTCTACTTCCCTAGC
195 TGGTTACAGTGGAGTACATTGAAGCCGA-TAACTCTACTTCCCTAGC
* *
53632267 AGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTC-CTCGTGG
1 AGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGCAGATTTTACCTCTCT-GTGG
* *
53632331 TTACAGTGGAGTACATTGAAGCC-AGTAATTCTACTTCCCTGGGTAGCAGCGGAATAGATTGAAG
65 TTACAGTGGAGTACATTGAAGCCGA-TAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAG
*** * * * *
53632395 ATTTTAGATCTTGCCTTCCTACATAGACAGTGAAGAAGATCGAAGACGGTA-GATTTTACCTCCC
129 ATAGCAGATCTTGCATTCCTACATAGACAGCGAAGAAGATCAAAAACGG-AGGATTTTACCTCCC
53632459 TGTGGTTACAGTGGAGTACATTGAAGCCGATAACTCTACTTCCCT
193 TGTGGTTACAGTGGAGTACATTGAAGCCGATAACTCTACTTCCCT
53632504 GGGCAGCAGT
Statistics
Matches: 211, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
239 3 0.01
240 204 0.97
241 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (240 bp):
AGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGCAGATTTTACCTCTCTGTGGT
TACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAAGAT
AGCAGATCTTGCATTCCTACATAGACAGCGAAGAAGATCAAAAACGGAGGATTTTACCTCCCTGT
GGTTACAGTGGAGTACATTGAAGCCGATAACTCTACTTCCCTAGC
Found at i:53632505 original size:133 final size:133
Alignment explanation
Indices: 53632265--53633021 Score: 940
Period size: 133 Copynumber: 5.7 Consensus size: 133
53632255 TACTTCCCTA
* *
53632265 GCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTG
1 GCAGATCTTGCCTTCCTACATAGACAGTGAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTG
* *
53632330 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAATAGATTGAAG
66 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAG
53632395 ATT
131 ATT
** * *
53632398 TTAGATCTTGCCTTCCTACATAGACAGTGAAGAAGATCGAAGACGGTAGATTTTACCTCC-CTGT
1 GCAGATCTTGCCTTCCTACATAGACAGTGAAGAAGATCGAAGATGGCAGATTTTACCTCCTC-GT
* *
53632462 GGTTACAGTGGAGTACATTGAAGCC-GATAACTCTACTTCCCTGGGCAGCAGTGGAATAGATTAA
65 GGTTACAGTGGAGTACATTGAAGCCAG-TAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGA
*
53632526 AGATA
129 AGATT
* * * * *
53632531 GCAGATCTTGCCTTCCTACATAGACAGCGAAGTAGATCAAAAATGGCAGATTTTACCTCATCGTG
1 GCAGATCTTGCCTTCCTACATAGACAGTGAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTG
*
53632596 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAG
66 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAG
*
53632661 ATA
131 ATT
* *
53632664 GCAGATCTTACCTTCCTACATAGACAGTGAAGCAA-ATCGAAGATGGCGGATTTTACCTCCTCGT
1 GCAGATCTTGCCTTCCTACATAGACAGTGAAG-AAGATCGAAGATGGCAGATTTTACCTCCTCGT
* *
53632728 GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCTTGGGCAGCAGTGGAATAGACTGA
65 GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGA
53632792 AGATT
129 AGATT
* * * * * * * * * * *
53632797 TCATATATTGTCTCCCTAAACAGTA-A-TGGAGCAGATCAAAGATGGCAGATTTTACTTCACT-G
1 GCAGATCTTGCCTTCCTACATAG-ACAGTGAAGAAGATCGAAGATGGCAGATTTTACCTC-CTCG
**
53632859 TGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGGCAATAGTGGAATAGATTG
64 TGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGGCAGCAGTGGAATAGATTG
53632924 AAGATT
128 AAGATT
* ** * * * * * * * *
53632930 ACAGATCTTATCTCCCTA-AGCAG-TAGTGGAGTAGATCGAAGATGGCCGATTCTACCTTCCT-A
1 GCAGATCTTGCCTTCCTACA-TAGACAGTGAAGAAGATCGAAGATGGCAGATTTTACC-TCCTCG
*
53632992 AGGTTACAGTGGAGTACATTGAAGCCAGTA
64 TGGTTACAGTGGAGTACATTGAAGCCAGTA
53633022 TTCCTATCTC
Statistics
Matches: 547, Mismatches: 62, Indels: 30
0.86 0.10 0.05
Matches are distributed among these distances:
131 1 0.00
132 71 0.13
133 469 0.86
134 6 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (133 bp):
GCAGATCTTGCCTTCCTACATAGACAGTGAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTG
GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAG
ATT
Found at i:53632575 original size:373 final size:373
Alignment explanation
Indices: 53631890--53632636 Score: 1361
Period size: 373 Copynumber: 2.0 Consensus size: 373
53631880 AGATTGAAGA
* *
53631890 TAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTACCTCCTTG
1 TAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCG
53631955 TGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGA
66 TGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGA
* *
53632020 AGATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCT
131 AGATTTTAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCC
* * *
53632085 CTGTGGTTACAGTGGAGTACATTGAAGCCGATAATTTTACTTCTCTGGGCAGCAGTGGAATAGAT
196 CTGTGGTTACAGTGGAGTACATTGAAGCCGATAACTCTACTTCCCTGGGCAGCAGTGGAATAGAT
53632150 TAAAGATAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGG-AGGATTTTAC
261 TAAAGATAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGCA-GATTTTAC
*
53632214 CTCATCGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
325 CTCATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
53632263 TAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCG
1 TAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCG
* *
53632328 TGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAATAGATTGA
66 TGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGA
*
53632393 AGATTTTAGATCTTGCCTTCCTACATAGACAGTGAAGAAGATCGAAGACGGTAGATTTTACCTCC
131 AGATTTTAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCC
53632458 CTGTGGTTACAGTGGAGTACATTGAAGCCGATAACTCTACTTCCCTGGGCAGCAGTGGAATAGAT
196 CTGTGGTTACAGTGGAGTACATTGAAGCCGATAACTCTACTTCCCTGGGCAGCAGTGGAATAGAT
* *
53632523 TAAAGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGTAGATCAAAAATGGCAGATTTTACC
261 TAAAGATAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGCAGATTTTACC
53632588 TCATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
326 TCATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
53632636 T
1 T
53632637 GGGCAGCAGC
Statistics
Matches: 360, Mismatches: 13, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
373 359 1.00
374 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (373 bp):
TAGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCG
TGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGA
AGATTTTAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCC
CTGTGGTTACAGTGGAGTACATTGAAGCCGATAACTCTACTTCCCTGGGCAGCAGTGGAATAGAT
TAAAGATAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGCAGATTTTACC
TCATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
Found at i:53632717 original size:506 final size:506
Alignment explanation
Indices: 53631761--53632762 Score: 1596
Period size: 506 Copynumber: 2.0 Consensus size: 506
53631751 TGAAGATTTT
* *
53631761 AGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGATGGCGGATTTTACCTCCTCGTGGT
1 AGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTGGT
*
53631826 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGGCAGCAGCGGAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
* * * *
53631891 AGCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCGGATTTTACCTCCTTGT
131 AGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGCAGATTTTACCTCCCTGT
* *
53631956 GGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAA
196 GGTTACAGTGGAGTACATTGAAACCAGTAACTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAA
*** * * * *
53632021 GATTTTAGATCTTGCCTTCCTGCATAGACAGCGAAGAAGATCGAAGACGGTAGATTTTACCTCTC
261 GATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCAAAAACGGCAGATTTTACCTCTC
* * *
53632086 TGTGGTTACAGTGGAGTACATTGAAGCCGATAATTTTACTTCTCTGGGCAGCAGTGGAATAGATT
326 TGTGGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTGGGCAGCAGCGGAATAGATT
* *
53632151 AAAGATAGCAGATCTTGCATTCCTACATAGACAGCGAAGCAGATCAAAAATGGAGGATTTTACCT
391 AAAGATAGCAGATCTTACATTCCTACATAGACAGCGAAGCAAATCAAAAATGGAGGATTTTACCT
*
53632216 CATCGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGC
456 CATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGC
*
53632267 AGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTGGT
1 AGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTGGT
*
53632332 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
*** * *
53632397 TTTAGATCTTGCCTTCCTACATAGACAGTGAAGAAGATCGAAGACGGTAGATTTTACCTCCCTGT
131 AGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGCAGATTTTACCTCCCTGT
* *
53632462 GGTTACAGTGGAGTACATTGAAGCC-GATAACTCTACTTCCCTGGGCAGCAGTGGAATAGATTAA
196 GGTTACAGTGGAGTACATTGAAACCAG-TAACTCTACTTCCCTGGGCAGCAGCGGAATAGATTAA
* *
53632526 AGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGTAGATCAAAAATGGCAGATTTTACCTCA
260 AGATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCAAAAACGGCAGATTTTACCTC-
53632591 TC-GTGGTTACAGTGGAGTACATTGAAGCC-AGTAATTCTACTTCCCTGGGCAGCAGCGGAATAG
324 TCTGTGGTTACAGTGGAGTACATTGAAGCCGA-TAATTCTACTTCCCTGGGCAGCAGCGGAATAG
* * * * * *
53632654 ATTGAAGATAGCAGATCTTACCTTCCTACATAGACAGTGAAGCAAATCGAAGATGGCGGATTTTA
388 ATTAAAGATAGCAGATCTTACATTCCTACATAGACAGCGAAGCAAATCAAAAATGGAGGATTTTA
*
53632719 CCTCCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
453 CCTCATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
53632763 TCTCCTTGGG
Statistics
Matches: 453, Mismatches: 40, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
505 2 0.00
506 449 0.99
507 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (506 bp):
AGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGATGGCAGATTTTACCTCCTCGTGGT
TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
AGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCGAAGACGGCAGATTTTACCTCCCTGT
GGTTACAGTGGAGTACATTGAAACCAGTAACTCTACTTCCCTGGGCAGCAGCGGAATAGATTAAA
GATAGCAGATCTTGCCTTCCTACATAGACAGCGAAGAAGATCAAAAACGGCAGATTTTACCTCTC
TGTGGTTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCTGGGCAGCAGCGGAATAGATT
AAAGATAGCAGATCTTACATTCCTACATAGACAGCGAAGCAAATCAAAAATGGAGGATTTTACCT
CATCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGC
Found at i:53634568 original size:3 final size:3
Alignment explanation
Indices: 53634560--53634589 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
53634550 TTTATCTTAC
*
53634560 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53634590 CTACTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53636192 original size:22 final size:24
Alignment explanation
Indices: 53636165--53636228 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
53636155 TTATTTAAAA
53636165 TAAATAAATTAATATTATTAAA-G
1 TAAATAAATTAATATTATTAAATG
*
53636188 -AAATAAATTAA-AGTACTTAAATG
1 TAAATAAATTAATATTA-TTAAATG
*
53636211 TTAATAAA-TAATATTATT
1 TAAATAAATTAATATTATT
53636229 GAAAATGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
21 3 0.09
22 16 0.47
23 6 0.18
24 9 0.26
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (24 bp):
TAAATAAATTAATATTATTAAATG
Found at i:53638182 original size:30 final size:30
Alignment explanation
Indices: 53638141--53638211 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
53638131 AGCCCTATAT
* * *
53638141 AGTTCCAAGCCTGTTGAAGACAGTAAGCAA
1 AGTTACAAGCCTGTTGAAGACAGCAAGAAA
53638171 AGTTACAAGCCTGTTGAAGACAGCAAGAAA
1 AGTTACAAGCCTGTTGAAGACAGCAAGAAA
*
53638201 AG-TACGAGCCT
1 AGTTACAAGCCT
53638212 ATCAAAGTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (30 bp):
AGTTACAAGCCTGTTGAAGACAGCAAGAAA
Found at i:53643341 original size:18 final size:19
Alignment explanation
Indices: 53643311--53643348 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53643301 CATGAGCATA
53643311 TGTATCATAACA-TTCATT
1 TGTATCATAACATTTCATT
53643329 TGTATACAT-ACATTTCATT
1 TGTAT-CATAACATTTCATT
53643348 T
1 T
53643349 CAATGTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (19 bp):
TGTATCATAACATTTCATT
Found at i:53645277 original size:29 final size:28
Alignment explanation
Indices: 53645230--53645290 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
53645220 ATGGCCAACC
* *
53645230 ATGTTGATATTATGTTTTTGTTAAAGTGT
1 ATGTTGATATGATGATTTTGTT-AAGTGT
* *
53645259 ATGTTGTTATGATGATTTTGTTGAGTGT
1 ATGTTGATATGATGATTTTGTTAAGTGT
53645287 ATGT
1 ATGT
53645291 AGCTTGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (28 bp):
ATGTTGATATGATGATTTTGTTAAGTGT
Found at i:53651151 original size:21 final size:21
Alignment explanation
Indices: 53651101--53651151 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
53651091 CCAGTCTATC
*
53651101 CCATCACTCTCTCAGCCTCTT
1 CCATCACTTTCTCAGCCTCTT
53651122 CCATCACTTTCTCAG-CTACTT
1 CCATCACTTTCTCAGCCT-CTT
*
53651143 GCATCACTT
1 CCATCACTT
53651152 CCCACTGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (21 bp):
CCATCACTTTCTCAGCCTCTT
Found at i:53654424 original size:33 final size:33
Alignment explanation
Indices: 53654387--53654455 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
53654377 TTTTTATTCA
* *
53654387 TAATAAATATGCTTTTCTTTTATTTAATAATGG
1 TAATAAATATACTTTTCATTTATTTAATAATGG
53654420 TAATAAATATACTTTTCATTTATTTAATAATGG
1 TAATAAATATACTTTTCATTTATTTAATAATGG
53654453 TAA
1 TAA
53654456 AATCGTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (33 bp):
TAATAAATATACTTTTCATTTATTTAATAATGG
Found at i:53654759 original size:23 final size:25
Alignment explanation
Indices: 53654733--53654783 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
53654723 TTTTCACCAC
*
53654733 AAAATCAT-AAA-ATTATTTAATTT
1 AAAATCATAAAATATTATTGAATTT
**
53654756 AAAATTTTAAAATATTATTGAATTT
1 AAAATCATAAAATATTATTGAATTT
53654781 AAA
1 AAA
53654784 TTTTAGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 3 0.13
25 14 0.61
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAATCATAAAATATTATTGAATTT
Found at i:53654915 original size:22 final size:24
Alignment explanation
Indices: 53654888--53654951 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
53654878 TTATTTAAAA
53654888 TAAATAAATTAATATTATTAAA-G
1 TAAATAAATTAATATTATTAAATG
*
53654911 -AAATAAATTAA-AGTACTTAAATG
1 TAAATAAATTAATATTA-TTAAATG
*
53654934 TTAATAAA-TAATATTATT
1 TAAATAAATTAATATTATT
53654952 GAAAATGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
21 3 0.09
22 16 0.47
23 6 0.18
24 9 0.26
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (24 bp):
TAAATAAATTAATATTATTAAATG
Found at i:53660164 original size:23 final size:25
Alignment explanation
Indices: 53660138--53660188 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
53660128 TTTTCACCAC
*
53660138 AAAATCAT-AAA-ATTATTTAATTT
1 AAAATCATAAAATATTATTGAATTT
**
53660161 AAAATTTTAAAATATTATTGAATTT
1 AAAATCATAAAATATTATTGAATTT
53660186 AAA
1 AAA
53660189 TTTTAGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 3 0.13
25 14 0.61
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAATCATAAAATATTATTGAATTT
Found at i:53660335 original size:22 final size:22
Alignment explanation
Indices: 53660294--53660335 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
53660284 TATTTAAAAT
*
53660294 AAATAAATTAATATTATTAAAG
1 AAATAAATTAATAGTATTAAAG
53660316 AAATAAATTAA-AGTACTTAA
1 AAATAAATTAATAGTA-TTAA
53660336 TTGTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AAATAAATTAATAGTATTAAAG
Found at i:53666963 original size:9 final size:9
Alignment explanation
Indices: 53666867--53667056 Score: 59
Period size: 9 Copynumber: 19.8 Consensus size: 9
53666857 ATATTTTCTC
*
53666867 ATAAAAATC
1 ATAAAAATT
*
53666876 ATAAAGATT
1 ATAAAAATT
*
53666885 ATTAAAAAAAT
1 A-T-AAAAATT
*
53666896 AAAAAATATT
1 ATAAAA-ATT
** *
53666906 ATTGAAAGT
1 ATAAAAATT
*
53666915 ATTAAAATT
1 ATAAAAATT
53666924 -TAAAAA-T
1 ATAAAAATT
53666931 ACT-AAAATT
1 A-TAAAAATT
*
53666940 GATATAAACTT
1 -ATA-AAAATT
53666951 ATAAAAATT
1 ATAAAAATT
*
53666960 ATAATAAAAT
1 ATAA-AAATT
53666970 A-ATAAAATT
1 ATA-AAAATT
53666979 AATAAACCATATT
1 -ATAAA--A-ATT
53666992 -TAAAAATCT
1 ATAAAAAT-T
53667001 -TAAAAACTT
1 ATAAAAA-TT
*
53667010 ATCAAAATCATA
1 AT-AAAA--ATT
* *
53667022 AAAAAAATC
1 ATAAAAATT
53667031 ATAAAAACTT
1 ATAAAAA-TT
53667041 ATAAAAATT
1 ATAAAAATT
53667050 ATAAAAA
1 ATAAAAA
53667057 AATTTACTTG
Statistics
Matches: 136, Mismatches: 22, Indels: 46
0.67 0.11 0.23
Matches are distributed among these distances:
7 1 0.01
8 11 0.08
9 64 0.47
10 29 0.21
11 24 0.18
12 3 0.02
13 4 0.03
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:53666966 original size:20 final size:20
Alignment explanation
Indices: 53666934--53667056 Score: 55
Period size: 19 Copynumber: 6.2 Consensus size: 20
53666924 TAAAAATACT
53666934 AAAATTGAT-ATAAACTTATA
1 AAAATT-ATAATAAACTTATA
* *
53666954 AAAATTATAATAAAATAAT-
1 AAAATTATAATAAACTTATA
*
53666973 AAAA-T-TAATAAACCATATTTA
1 AAAATTATAATAAA-C-T-TATA
*
53666994 AAAATCT-TAA-AAACTTATC
1 AAAAT-TATAATAAACTTATA
* * * *
53667013 AAAATCATAAAAAAAATCATA
1 AAAATTAT-AATAAACTTATA
53667034 AAAACTTATAA-AAA-TTATA
1 AAAA-TTATAATAAACTTATA
53667053 AAAA
1 AAAA
53667057 AATTTACTTG
Statistics
Matches: 79, Mismatches: 13, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
17 7 0.09
18 1 0.01
19 23 0.29
20 21 0.27
21 17 0.22
22 6 0.08
23 4 0.05
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.29
Consensus pattern (20 bp):
AAAATTATAATAAACTTATA
Found at i:53666968 original size:31 final size:31
Alignment explanation
Indices: 53666945--53667059 Score: 107
Period size: 31 Copynumber: 3.8 Consensus size: 31
53666935 AAATTGATAT
*
53666945 AAACTTATAAAAATTATAAT-AAAATAAT-A
1 AAACTTATAAAAATTATAATAAAAATCATAA
* * *
53666974 AAA-TTAATAAACCA-TAT-TTAAAAATCTTAA
1 AAACTT-ATAAA-AATTATAATAAAAATCATAA
* * *
53667004 AAACTTATCAAAATCATAAAAAAAATCATAA
1 AAACTTATAAAAATTATAATAAAAATCATAA
53667035 AAACTTATAAAAATTATAA-AAAAAT
1 AAACTTATAAAAATTATAATAAAAAT
53667060 TTACTTGAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
28 3 0.04
29 18 0.27
30 17 0.25
31 29 0.43
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (31 bp):
AAACTTATAAAAATTATAATAAAAATCATAA
Found at i:53666978 original size:19 final size:18
Alignment explanation
Indices: 53666917--53666984 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 18
53666907 TTGAAAGTAT
*
53666917 TAAAATT-TA-AAAATAC
1 TAAAATTATATAAAATAA
* *
53666933 TAAAATTGATATAAACTTA
1 TAAAATT-ATATAAAATAA
53666952 TAAAAATTATAATAAAATAA
1 T-AAAATTAT-ATAAAATAA
53666972 TAAAATTA-ATAAA
1 TAAAATTATATAAA
53666985 CCATATTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
16 7 0.17
17 5 0.12
18 2 0.05
19 14 0.33
20 14 0.33
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (18 bp):
TAAAATTATATAAAATAA
Found at i:53667030 original size:12 final size:12
Alignment explanation
Indices: 53667013--53667037 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53667003 AAAACTTATC
53667013 AAAATCATAAAA
1 AAAATCATAAAA
53667025 AAAATCATAAAA
1 AAAATCATAAAA
53667037 A
1 A
53667038 CTTATAAAAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATCATAAAA
Found at i:53669690 original size:24 final size:24
Alignment explanation
Indices: 53669658--53669713 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
53669648 GAAGACCGTT
* *
53669658 TATATATAT-AATATAGGTAGAATA
1 TATATATATGAA-ATAGGAAAAATA
*
53669682 TATATATATGCAATAGGAAAAATA
1 TATATATATGAAATAGGAAAAATA
53669706 TATATATA
1 TATATATA
53669714 CATAGTACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.36
Consensus pattern (24 bp):
TATATATATGAAATAGGAAAAATA
Found at i:53670649 original size:9 final size:9
Alignment explanation
Indices: 53670628--53670816 Score: 79
Period size: 9 Copynumber: 20.6 Consensus size: 9
53670618 TCAAGTTTTT
53670628 ATTTTT-TA
1 ATTTTTATA
*
53670636 TTTTTTATA
1 ATTTTTATA
53670645 ATTTTTATA
1 ATTTTTATA
**
53670654 AGTTAATATCA
1 A-TTTTTAT-A
*
53670665 ATTTTAATA
1 ATTTTTATA
* *
53670674 TTTTATTATT
1 ATTT-TTATA
*
53670684 ATTATTATGA
1 ATTTTTAT-A
*
53670694 TTTTTTATA
1 ATTTTTATA
53670703 AGTTTTTA-A
1 A-TTTTTATA
53670712 GATTTTTATA
1 -ATTTTTATA
*
53670722 CA-TATT-TA
1 -ATTTTTATA
*
53670730 ATTCTTCATA
1 ATT-TTTATA
*
53670740 ATTTATTA-G
1 ATTT-TTATA
53670749 ATTTTTATA
1 ATTTTTATA
*
53670758 AGTTTATATA
1 A-TTTTTATA
*
53670768 AATTTTA-A
1 ATTTTTATA
53670776 TATTTTTA-A
1 -ATTTTTATA
* *
53670785 GTTTTAATA
1 ATTTTTATA
53670794 ATTTTTAT-
1 ATTTTTATA
53670802 ATTTTTATGA
1 ATTTTTAT-A
53670812 ATTTT
1 ATTTT
53670817 AAATCATTTT
Statistics
Matches: 132, Mismatches: 31, Indels: 34
0.67 0.16 0.17
Matches are distributed among these distances:
7 1 0.01
8 25 0.19
9 55 0.42
10 49 0.37
11 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:53670794 original size:26 final size:25
Alignment explanation
Indices: 53670751--53670808 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 25
53670741 TTTATTAGAT
53670751 TTTTATAAGTTTATATAAATTTTAATA
1 TTTT-TAAGTTTATAT-AATTTTAATA
*
53670778 TTTTTAAGTTT-TAATAATTTTTATA
1 TTTTTAAGTTTAT-ATAATTTTAATA
53670803 TTTTTA
1 TTTTTA
53670809 TGAATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 16 0.55
26 9 0.31
27 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
TTTTTAAGTTTATATAATTTTAATA
Found at i:53672137 original size:41 final size:40
Alignment explanation
Indices: 53672069--53672309 Score: 198
Period size: 41 Copynumber: 5.9 Consensus size: 40
53672059 GAGTTTTTGG
* *
53672069 GGCCCTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCG-TTTTTGAGAAGCGCCGCTAATGCTCT
* *
53672110 GGCCTTTAGCGGCGTTTTTGAGTAAGCGCCGCTAAAAGC-CA
1 GGCCTTTAGCGGCGTTTTTGAG-AAGCGCCGCT-AATGCTCT
* * * * * *
53672151 GAG-CATTAGCGGCACTTCTTAAAAAACGCCGCTAATGCTCT
1 G-GCCTTTAGCGGC-GTTTTTGAGAAGCGCCGCTAATGCTCT
** * *
53672192 ATCCTTTAGCGACGTTTTTGAAGAAGCGCCGGTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTG-AGAAGCGCCGCTAATGCTCT
* * **
53672233 GGCCTTTAGCGGCATTTTTTAAGAAGCGCCGCTAATGCTAA
1 GGCCTTTAGCGGC-GTTTTTGAGAAGCGCCGCTAATGCTCT
*** *
53672274 GATTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGCCTTTAGCGGCGTTTTTG-AGAAGCGCCGCTAAT
53672310 ATATTTTTTA
Statistics
Matches: 155, Mismatches: 36, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
40 20 0.13
41 120 0.77
42 15 0.10
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (40 bp):
GGCCTTTAGCGGCGTTTTTGAGAAGCGCCGCTAATGCTCT
Found at i:53672242 original size:82 final size:81
Alignment explanation
Indices: 53672095--53672309 Score: 229
Period size: 82 Copynumber: 2.6 Consensus size: 81
53672085 TTTTAAGAAG
** *
53672095 CGCCGCTAATGCTCTGGCCTTTAGCGGCGTTTTTG-AGTAAGCGCCGCTAAAAGCCAGAGCATTA
1 CGCCGCTAATGCTCTATCCTTTAGCGGCGTTTTTGAAG-AAGCGCCGCT-AATGCCAGAGCATTA
53672159 GCGGCACTTCTTAAAAAA
64 GCGGCACTTCTTAAAAAA
* * * *
53672177 CGCCGCTAATGCTCTATCCTTTAGCGACGTTTTTGAAGAAGCGCCGGTAATGCTCTG-GCCTTTA
1 CGCCGCTAATGCTCTATCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC-CAGAG-CATTA
* * * *
53672241 GCGGCATTTTTTAAGAAG
64 GCGGCACTTCTTAAAAAA
** * *
53672259 CGCCGCTAATGCTAAGAT-TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 CGCCGCTAATGCT-CTATCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
53672310 ATATTTTTTA
Statistics
Matches: 112, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
81 5 0.04
82 103 0.92
83 4 0.04
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (81 bp):
CGCCGCTAATGCTCTATCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCCAGAGCATTAGC
GGCACTTCTTAAAAAA
Found at i:53672616 original size:15 final size:16
Alignment explanation
Indices: 53672596--53672629 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
53672586 CAAATATGGT
53672596 GTTTATGGATTT-AGG
1 GTTTATGGATTTAAGG
53672611 GTTTATGGATTTAAGG
1 GTTTATGGATTTAAGG
53672627 GTT
1 GTT
53672630 AGAGGTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (16 bp):
GTTTATGGATTTAAGG
Found at i:53672768 original size:26 final size:27
Alignment explanation
Indices: 53672713--53672770 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
53672703 AATCTGGATT
*
53672713 GGGTTGGGTTTAGGGATTAGGGATTTA
1 GGGTTGGGTTTAGGGATTAAGGATTTA
53672740 GGGTTGGG-TTA-GGATTTAAGG-TTTAA
1 GGGTTGGGTTTAGGGA-TTAAGGATTT-A
53672766 GGGTT
1 GGGTT
53672771 AGGGCTAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.21
26 14 0.50
27 8 0.29
ACGTcount: A:0.19, C:0.00, G:0.43, T:0.38
Consensus pattern (27 bp):
GGGTTGGGTTTAGGGATTAAGGATTTA
Found at i:53673503 original size:19 final size:18
Alignment explanation
Indices: 53673479--53673517 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
53673469 AATTATAAGA
53673479 AAAAATAAAATACAAAAAT
1 AAAAATAAAATA-AAAAAT
**
53673498 AAAAATGGAATAAAAAAT
1 AAAAATAAAATAAAAAAT
53673516 AA
1 AA
53673518 TTCTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAATAAAAAAT
Found at i:53673581 original size:15 final size:14
Alignment explanation
Indices: 53673556--53673594 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
53673546 GGACCAAATT
53673556 ATAAGAAAAAATAAA
1 ATAA-AAAAAATAAA
*
53673571 ATACAAAAAAATGAA
1 ATA-AAAAAAATAAA
53673586 ATAAAAAAA
1 ATAAAAAAA
53673595 TTTCTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 15 0.68
16 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (14 bp):
ATAAAAAAAATAAA
Found at i:53677687 original size:12 final size:12
Alignment explanation
Indices: 53677672--53677705 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53677662 TAACCTACAT
53677672 AACTTACATAGA
1 AACTTACATAGA
*
53677684 AACTTATATAGA
1 AACTTACATAGA
*
53677696 AACTTGCATA
1 AACTTACATA
53677706 ACTTACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (12 bp):
AACTTACATAGA
Found at i:53677772 original size:16 final size:16
Alignment explanation
Indices: 53677751--53677805 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
53677741 AGCGTACTTA
53677751 ACTTACATAATACACC
1 ACTTACATAATACACC
*
53677767 ACTTACATAA-ATA--
1 ACTTACATAATACACC
*
53677780 ACTTGCATAATACACC
1 ACTTACATAATACACC
53677796 ACTTACATAA
1 ACTTACATAA
53677806 ATAACTTGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 9 0.28
14 2 0.06
15 2 0.06
16 19 0.59
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.27
Consensus pattern (16 bp):
ACTTACATAATACACC
Found at i:53677788 original size:13 final size:13
Alignment explanation
Indices: 53677767--53677818 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
53677757 ATAATACACC
53677767 ACTTACATAAATA
1 ACTTACATAAATA
* *
53677780 ACTTGCATAATACA
1 ACTTACATAA-ATA
53677794 CCACTTACATAAATA
1 --ACTTACATAAATA
*
53677809 ACTTGCATAA
1 ACTTACATAA
53677819 TACATAGCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 18 0.58
14 2 0.06
15 2 0.06
16 9 0.29
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.29
Consensus pattern (13 bp):
ACTTACATAAATA
Found at i:53677791 original size:29 final size:29
Alignment explanation
Indices: 53677749--53677822 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
53677739 ATAGCGTACT
*
53677749 TAACTTACATAATACACCACTTACATAAA
1 TAACTTGCATAATACACCACTTACATAAA
53677778 TAACTTGCATAATACACCACTTACATAAA
1 TAACTTGCATAATACACCACTTACATAAA
53677807 TAACTTGCATAATACA
1 TAACTTGCATAATACA
53677823 TAGCCTACGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (29 bp):
TAACTTGCATAATACACCACTTACATAAA
Found at i:53677904 original size:31 final size:31
Alignment explanation
Indices: 53677866--53677956 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
53677856 ACCACTTACG
*
53677866 TAACTTAAATAACTTAAATTTGTCAATCATA
1 TAACTTAAATAACTTAAATTTATCAATCATA
** * *
53677897 TAACTTAAATAACTT-ACGTAAT-AAT-ACA
1 TAACTTAAATAACTTAAATTTATCAATCATA
*
53677925 TAACTTATATAACTTAAATTTATCAATCATA
1 TAACTTAAATAACTTAAATTTATCAATCATA
53677956 T
1 T
53677957 CATAATTTAC
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
28 16 0.34
29 7 0.15
30 6 0.13
31 18 0.38
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.38
Consensus pattern (31 bp):
TAACTTAAATAACTTAAATTTATCAATCATA
Found at i:53678114 original size:9 final size:9
Alignment explanation
Indices: 53678102--53678212 Score: 96
Period size: 9 Copynumber: 13.2 Consensus size: 9
53678092 CAAAATAAAA
53678102 AACTTACAT
1 AACTTACAT
53678111 AACTTACAT
1 AACTTACAT
*
53678120 AA--GACAT
1 AACTTACAT
*
53678127 AAATTACAT
1 AACTTACAT
*
53678136 AAGC-TACTT
1 AA-CTTACAT
53678145 AA--TACAT
1 AACTTACAT
53678152 AACTTACAT
1 AACTTACAT
*
53678161 AACTTAGAT
1 AACTTACAT
53678170 AA--TACAT
1 AACTTACAT
53678177 AACTTACAT
1 AACTTACAT
* *
53678186 AATTTACTT
1 AACTTACAT
53678195 AA--TACAT
1 AACTTACAT
53678202 AACTTACAT
1 AACTTACAT
53678211 AA
1 AA
53678213 ATATCCCTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
7 24 0.29
9 59 0.71
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:53678133 original size:25 final size:25
Alignment explanation
Indices: 53678102--53678212 Score: 152
Period size: 25 Copynumber: 4.4 Consensus size: 25
53678092 CAAAATAAAA
*
53678102 AACTTACATAACTTACATAAGACAT
1 AACTTACATAACTTACATAATACAT
* *
53678127 AAATTACATAAGC-TACTTAATACAT
1 AACTTACATAA-CTTACATAATACAT
*
53678152 AACTTACATAACTTAGATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
53678177 AACTTACATAATTTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
53678202 AACTTACATAA
1 AACTTACATAA
53678213 ATATCCCTTA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
24 1 0.01
25 73 0.97
26 1 0.01
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:53678137 original size:50 final size:51
Alignment explanation
Indices: 53678075--53678188 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 51
53678065 ATCAAATTAA
*
53678075 ATAAGTTACATAATAC-ACAAAATAAAAAACTTACATAACTTACATAAGAC
1 ATAAATTACATAATACTACAAAATAAAAAACTTACATAACTTACATAAGAC
* ** * * * *
53678125 ATAAATTACATAA-GCTACTTAATACATAACTTACATAACTTAGATAATAC
1 ATAAATTACATAATACTACAAAATAAAAAACTTACATAACTTACATAAGAC
*
53678175 ATAACTTACATAAT
1 ATAAATTACATAAT
53678189 TTACTTAATA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
49 1 0.02
50 52 0.98
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.29
Consensus pattern (51 bp):
ATAAATTACATAATACTACAAAATAAAAAACTTACATAACTTACATAAGAC
Found at i:53678188 original size:16 final size:16
Alignment explanation
Indices: 53678106--53678188 Score: 80
Period size: 16 Copynumber: 5.1 Consensus size: 16
53678096 ATAAAAAACT
53678106 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
53678122 GACATAAATTACATAA
1 TACATAACTTACATAA
*
53678138 GCTACTTAA--TACATAA
1 --TACATAACTTACATAA
*
53678154 CTTACATAACTTAGATAA
1 --TACATAACTTACATAA
53678172 TACATAACTTACATAA
1 TACATAACTTACATAA
53678188 T
1 T
53678189 TTACTTAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
16 43 0.80
18 11 0.20
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:53678194 original size:50 final size:50
Alignment explanation
Indices: 53678102--53678212 Score: 177
Period size: 50 Copynumber: 2.2 Consensus size: 50
53678092 CAAAATAAAA
53678102 AACTTACATAACTTACATAAGACATAAATTACATAAGCTACTTAATACAT
1 AACTTACATAACTTACATAAGACATAAATTACATAAGCTACTTAATACAT
* * * **
53678152 AACTTACATAACTTAGATAATACATAACTTACATAATTTACTTAATACAT
1 AACTTACATAACTTACATAAGACATAAATTACATAAGCTACTTAATACAT
53678202 AACTTACATAA
1 AACTTACATAA
53678213 ATATCCCTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (50 bp):
AACTTACATAACTTACATAAGACATAAATTACATAAGCTACTTAATACAT
Found at i:53683831 original size:66 final size:65
Alignment explanation
Indices: 53683724--53683895 Score: 184
Period size: 66 Copynumber: 2.6 Consensus size: 65
53683714 GAGCAAATTA
* * * * * *
53683724 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATTTGAAGAACTTCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
53683788 G
65 G
* * *
53683789 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGTTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
53683854 G
65 G
* * ** *
53683855 CAGCAGCTTAAAGCAGATGCGGCAGTAAGAGAAGCGGAGGT
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGT
53683896 GGCAGCTAGA
Statistics
Matches: 88, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
65 2 0.02
66 82 0.93
67 4 0.05
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.15
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:53683937 original size:21 final size:21
Alignment explanation
Indices: 53683882--53683977 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
53683872 TGCGGCAGTA
* *
53683882 AGAGAAGCGGAGG-TGGCAGCT
1 AGAGAAGCAGAGGCT-GCAGCG
* *
53683903 AGAGAAGTACAGGCTGCAGCG
1 AGAGAAGCAGAGGCTGCAGCG
**
53683924 AGAGAAGCAGAGGCTAAAGCG
1 AGAGAAGCAGAGGCTGCAGCG
*
53683945 AGGGAAGCAGAGGCTGCAGCG
1 AGAGAAGCAGAGGCTGCAGCG
*
53683966 AGGGAAGCAGAG
1 AGAGAAGCAGAG
53683978 CAGCGTCAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 62 0.98
22 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.44, T:0.06
Consensus pattern (21 bp):
AGAGAAGCAGAGGCTGCAGCG
Found at i:53684412 original size:43 final size:43
Alignment explanation
Indices: 53684280--53684489 Score: 233
Period size: 44 Copynumber: 4.8 Consensus size: 43
53684270 ATCTGTCAAA
* * *
53684280 TTTAGTGGCGTTTTTGGTCAAAGTGCCGCTAAAGATAAGGGTC
1 TTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATTAGGTTC
* * ** * * *
53684323 TTTAGCGGCGTTTGTGGAAAAAAGCACCACTAAAGATCATGG-TC
1 TTTAGTGGCGTTTTTGG-TCAAAGCGCCGCTAAAGATTA-GGTTC
* ** *
53684367 TTTAGTGGCATTTTTGGGGAAAGTGCCGCTAAAGATTAGGTTC
1 TTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATTAGGTTC
*
53684410 TTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTAAAGATTAGGTTC
1 TTTAGTGGCGTTTT-TGGTCAAAGCGCCGCTAAAGATTAGGTTC
* *
53684454 TTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGAT
1 TTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGAT
53684490 CAGGGTCTAT
Statistics
Matches: 138, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
42 2 0.01
43 65 0.47
44 69 0.50
45 2 0.01
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (43 bp):
TTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATTAGGTTC
Found at i:53684443 original size:87 final size:87
Alignment explanation
Indices: 53684280--53684497 Score: 260
Period size: 87 Copynumber: 2.5 Consensus size: 87
53684270 ATCTGTCAAA
53684280 TTTAGTGGCGTTTTTGGTCAAAGTGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAA
1 TTTAGTGGCGTTTTTGGTCAAAGTGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAA
53684345 AGCACCACTAAAGATCATGG-TC
66 AGCACCACTAAAGATCA-GGTTC
* ** * * * ***
53684367 TTTAGTGGCATTTTTGGGGAAAGTGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGG-TCG
1 TTTAGTGGCGTTTTTGGTCAAAGTGCCGCTAAAGATAAGGGTCTTTAGCGGCG-TTTGTGGAAAA
* * *
53684431 AAGCGCCGCTAAAGATTAGGTTC
65 AAGCACCACTAAAGATCAGGTTC
* * * *
53684454 TTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCT
1 TTTAGTGGCGTTTTTGGTCAAAGTGCCGCTAAAGATAAGGGTCT
53684498 ATTTCGGCAT
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
86 2 0.02
87 100 0.92
88 7 0.06
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (87 bp):
TTTAGTGGCGTTTTTGGTCAAAGTGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAA
AGCACCACTAAAGATCAGGTTC
Found at i:53684445 original size:44 final size:44
Alignment explanation
Indices: 53684280--53684489 Score: 232
Period size: 43 Copynumber: 4.8 Consensus size: 44
53684270 ATCTGTCAAA
* * *
53684280 TTTAGTGGCGTTTT-TGGTCAAAGTGCCGCTAAAGATAAGGGTC
1 TTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTAAAGATTAGGTTC
* ** * * *
53684323 TTTAGCGGCG-TTTGTGGAAAAAAGCACCACTAAAGATCATGG-TC
1 TTTAGTGGCGTTTTGTGG-TCAAAGCGCCGCTAAAGATTA-GGTTC
* ** *
53684367 TTTAGTGGCATTTT-TGGGGAAAGTGCCGCTAAAGATTAGGTTC
1 TTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTAAAGATTAGGTTC
*
53684410 TTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTAAAGATTAGGTTC
1 TTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTAAAGATTAGGTTC
*
53684454 TTTAGTGGCG-TTTGTGGTCAAAGCGCCGCTATAGAT
1 TTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTAAAGAT
53684490 CAGGGTCTAT
Statistics
Matches: 139, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
42 5 0.04
43 66 0.47
44 63 0.45
45 5 0.04
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (44 bp):
TTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTAAAGATTAGGTTC
Found at i:53689051 original size:16 final size:17
Alignment explanation
Indices: 53689030--53689061 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
53689020 CGTTCTATAC
53689030 TAAAACAAAT-TACCGG
1 TAAAACAAATATACCGG
53689046 TAAAACAAATATACCG
1 TAAAACAAATATACCG
53689062 TTGAAGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (17 bp):
TAAAACAAATATACCGG
Found at i:53689320 original size:21 final size:21
Alignment explanation
Indices: 53689294--53689335 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53689284 ACCGGAGGAA
53689294 AGGAAAGA-AGAGAGGGCGAAG
1 AGGAAAGAGAGA-AGGGCGAAG
*
53689315 AGGAAAGAGAGAATGGCGAAG
1 AGGAAAGAGAGAAGGGCGAAG
53689336 GTGAGGAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.48, C:0.05, G:0.45, T:0.02
Consensus pattern (21 bp):
AGGAAAGAGAGAAGGGCGAAG
Found at i:53690248 original size:6 final size:6
Alignment explanation
Indices: 53690220--53690259 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
53690210 TTCATCCAAC
*
53690220 TTAAAT TT-AAT TTAAAT AATAAAT TTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAA
53690260 TTATAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 20 0.67
7 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:53690266 original size:12 final size:13
Alignment explanation
Indices: 53690220--53690266 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 13
53690210 TTCATCCAAC
53690220 TTAAATT-T-AAT
1 TTAAATTATAAAT
*
53690231 TTAAATAATAAAT
1 TTAAATTATAAAT
53690244 TTAAATT-TAAAT
1 TTAAATTATAAAT
53690256 TT-AATTATAAA
1 TTAAATTATAAA
53690267 ATATATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 10 0.32
12 12 0.39
13 9 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTAAATTATAAAT
Found at i:53694521 original size:41 final size:41
Alignment explanation
Indices: 53694431--53694615 Score: 108
Period size: 41 Copynumber: 4.5 Consensus size: 41
53694421 ACGGCCTACC
* *
53694431 ACACGGTCTACCACATAGGCTACCACATGTTCGTGTGACCA
1 ACACGGTCTACCACATAGGCTACCACATGCTCGTGTAACCA
* *
53694472 ACACGGTCTACCACAT-GGCTTACCATATGGCT-GTGTAACCG
1 ACACGGTCTACCACATAGGC-TACCACAT-GCTCGTGTAACCA
* ** * ** * ** * *
53694513 ACATGGTCTATAACACAACCTACCACATGGTTATGTGACCC
1 ACACGGTCTACCACATAGGCTACCACATGCTCGTGTAACCA
*** * * *
53694554 ACACGGTCTGTTACAT-GGCCTACCACACGATCGTGTAACCC
1 ACACGGTCTACCACATAGG-CTACCACATGCTCGTGTAACCA
* *
53694595 ACATGGTCTGCCACAT-GGCTA
1 ACACGGTCTACCACATAGGCTA
53694616 GTTACACGAC
Statistics
Matches: 110, Mismatches: 29, Indels: 11
0.73 0.19 0.07
Matches are distributed among these distances:
40 8 0.07
41 99 0.90
42 3 0.03
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.23
Consensus pattern (41 bp):
ACACGGTCTACCACATAGGCTACCACATGCTCGTGTAACCA
Found at i:53695267 original size:37 final size:38
Alignment explanation
Indices: 53695201--53695272 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
53695191 TCAGCCCAAA
*
53695201 GTTCATAGAAAACAACAGAAAGAAGGAAGATTGTGAAG
1 GTTCATAGAAAACAACAGAAAGAAGGAAGAATGTGAAG
*
53695239 GTTCATAGGAAACAA-AGAAAGATA-GAAGAATGTG
1 GTTCATAGAAAACAACAGAAAGA-AGGAAGAATGTG
53695273 GAAAAAGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.50, C:0.07, G:0.26, T:0.17
Consensus pattern (38 bp):
GTTCATAGAAAACAACAGAAAGAAGGAAGAATGTGAAG
Found at i:53706965 original size:41 final size:41
Alignment explanation
Indices: 53706920--53707164 Score: 190
Period size: 41 Copynumber: 6.0 Consensus size: 41
53706910 TGCCATACGC
* * *
53706920 CCTACCACACGGTCATGTGACCCACACGATCTACCACATAG
1 CCTACCACACGGTCCTGTGACCCACACGATCTGCCACATGG
* * * * * * *
53706961 CCTACCACATGTTCGTGTGACACACACGGTCTGCTAAATGG
1 CCTACCACACGGTCCTGTGACCCACACGATCTGCCACATGG
* * * * * * ***
53707002 CTTACTATATGGTCCTGTGACCGACAC-ATTCTACCACACCA
1 CCTACCACACGGTCCTGTGACCCACACGA-TCTGCCACATGG
* *
53707043 CCTACCACACGGTCGTGTGACCCACACGA-CTGCCGCATGG
1 CCTACCACACGGTCCTGTGACCCACACGATCTGCCACATGG
* *
53707083 CCTACCACACGG-CCTGTGACGCACACGATCTGTCACATGG
1 CCTACCACACGGTCCTGTGACCCACACGATCTGCCACATGG
* * * * * * *
53707123 CCTACCACATGATCGTGTAACCCACATGGTCTGCCACTTGG
1 CCTACCACACGGTCCTGTGACCCACACGATCTGCCACATGG
53707164 C
1 C
53707165 TAGTTACACG
Statistics
Matches: 153, Mismatches: 47, Indels: 8
0.74 0.23 0.04
Matches are distributed among these distances:
39 14 0.09
40 37 0.24
41 101 0.66
42 1 0.01
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (41 bp):
CCTACCACACGGTCCTGTGACCCACACGATCTGCCACATGG
Found at i:53717627 original size:41 final size:41
Alignment explanation
Indices: 53717459--53717705 Score: 203
Period size: 41 Copynumber: 6.1 Consensus size: 41
53717449 TTTGCCATAC
*
53717459 GGCCTACCACACGGTCATGTGACCCACACGATCT--CACAT
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGCCACAT
* * * * * * *
53717498 AGCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAAT
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGCCACAT
* * * * * * * *
53717539 GGCTTACTATATGGTCCTGTGACCGACAC-ATTCTACCACAC
1 GGCCTACCACACGGTCGTGTGACCCACACGA-TCTGCCACAT
** * *
53717580 CACCTACCACACGGTCGTGTGACCCACACGACCTGCCGCAT
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGCCACAT
* * * *
53717621 GGCCTACCACACGGCCCTGTGACGCACACGATCTGTCACAT
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGCCACAT
* * * * *
53717662 GGCCTACCACATGATCGTGTAACCCACATGGTCTGCCACAT
1 GGCCTACCACACGGTCGTGTGACCCACACGATCTGCCACAT
53717703 GGC
1 GGC
53717706 TAGTTACACG
Statistics
Matches: 154, Mismatches: 50, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
39 28 0.18
41 125 0.81
42 1 0.01
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (41 bp):
GGCCTACCACACGGTCGTGTGACCCACACGATCTGCCACAT
Found at i:53717698 original size:82 final size:80
Alignment explanation
Indices: 53717459--53717705 Score: 230
Period size: 82 Copynumber: 3.0 Consensus size: 80
53717449 TTTGCCATAC
* * *
53717459 GGCCTACCACACGGTCATGTGACCCACACGATC-TCACATAGCCTACCACATGTTCGTGTGACAC
1 GGCCTACCACACGGTCCTGTGA-CCACACGATCTTCACATAGCCTACCACATGATCGTGTGACCC
* *
53717523 ACACGGTCTGCTAAAT
65 ACACGGTCTGCCACAT
* * * * * * * *
53717539 GGCTTACTATATGGTCCTGTGACCGACAC-ATTCTACCACACCA-CCTACCACACGGTCGTGTGA
1 GGCCTACCACACGGTCCTGTGACC-ACACGA-TCT-TCACA-TAGCCTACCACATGATCGTGTGA
** *
53717602 CCCACACGACCTGCCGCAT
62 CCCACACGGTCTGCCACAT
* * *
53717621 GGCCTACCACACGGCCCTGTGACGCACACGATCTGTCACATGGCCTACCACATGATCGTGTAACC
1 GGCCTACCACACGGTCCTGTGAC-CACACGATCT-TCACATAGCCTACCACATGATCGTGTGACC
*
53717686 CACATGGTCTGCCACAT
64 CACACGGTCTGCCACAT
53717703 GGC
1 GGC
53717706 TAGTTACACG
Statistics
Matches: 128, Mismatches: 31, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
79 3 0.02
80 23 0.18
82 99 0.77
83 3 0.02
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (80 bp):
GGCCTACCACACGGTCCTGTGACCACACGATCTTCACATAGCCTACCACATGATCGTGTGACCCA
CACGGTCTGCCACAT
Found at i:53720507 original size:7 final size:7
Alignment explanation
Indices: 53720495--53720519 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53720485 TTACCCTATT
53720495 AAATTCA
1 AAATTCA
53720502 AAATTCA
1 AAATTCA
53720509 AAATTCA
1 AAATTCA
53720516 AAAT
1 AAAT
53720520 ATACTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTCA
Found at i:53729452 original size:41 final size:41
Alignment explanation
Indices: 53729406--53729654 Score: 176
Period size: 41 Copynumber: 6.1 Consensus size: 41
53729396 TTTGCCATAG
* *
53729406 GGCCTACCACACGGTCATGTGACCCACACGATCTATCACAT
1 GGCCTACCACACGGTCCTGTGACCCACACGATCTACCACAT
* * * * * * * * *
53729447 AGCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAAT
1 GGCCTACCACACGGTCCTGTGACCCACACGATCTACCACAT
* * * * * *
53729488 GGCTTACTATATGGTCCTGTGACCGACAC-ATTCTACCACAC
1 GGCCTACCACACGGTCCTGTGACCCACACGA-TCTACCACAT
** * * * *
53729529 CACCTACCACACGGTCGTGTGACCCACACGACCTGCCGCAT
1 GGCCTACCACACGGTCCTGTGACCCACACGATCTACCACAT
* * **
53729570 GGCCTACCACACGGCCCTGTGACGCACACGATCTGTCACAT
1 GGCCTACCACACGGTCCTGTGACCCACACGATCTACCACAT
* * * * * * *
53729611 GGCCTACCACATGATCGTGTAACCCACATGGTCTGCCACAT
1 GGCCTACCACACGGTCCTGTGACCCACACGATCTACCACAT
53729652 GGC
1 GGC
53729655 TAGTTACACG
Statistics
Matches: 154, Mismatches: 52, Indels: 4
0.73 0.25 0.02
Matches are distributed among these distances:
41 153 0.99
42 1 0.01
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (41 bp):
GGCCTACCACACGGTCCTGTGACCCACACGATCTACCACAT
Found at i:53729647 original size:82 final size:81
Alignment explanation
Indices: 53729406--53729654 Score: 250
Period size: 82 Copynumber: 3.0 Consensus size: 81
53729396 TTTGCCATAG
* * *
53729406 GGCCTACCACACGGTCATGTGACCCACACGATCTATCACATAGCCTACCACATGTTCGTGTGACA
1 GGCCTACCACACGGTCCTGTGA-CCACACGATCTATCACATAGCCTACCACATGATCGTGTGACC
* *
53729471 CACACGGTCTGCTAAAT
65 CACACGGTCTGCCACAT
* * * * * * * *
53729488 GGCTTACTATATGGTCCTGTGACCGACAC-ATTCTACCACACCA-CCTACCACACGGTCGTGTGA
1 GGCCTACCACACGGTCCTGTGACC-ACACGA-TCTATCACA-TAGCCTACCACATGATCGTGTGA
** *
53729551 CCCACACGACCTGCCGCAT
63 CCCACACGGTCTGCCACAT
* * * *
53729570 GGCCTACCACACGGCCCTGTGACGCACACGATCTGTCACATGGCCTACCACATGATCGTGTAACC
1 GGCCTACCACACGGTCCTGTGAC-CACACGATCTATCACATAGCCTACCACATGATCGTGTGACC
*
53729635 CACATGGTCTGCCACAT
65 CACACGGTCTGCCACAT
53729652 GGC
1 GGC
53729655 TAGTTACACG
Statistics
Matches: 130, Mismatches: 31, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
81 3 0.02
82 124 0.95
83 3 0.02
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (81 bp):
GGCCTACCACACGGTCCTGTGACCACACGATCTATCACATAGCCTACCACATGATCGTGTGACCC
ACACGGTCTGCCACAT
Found at i:53729650 original size:123 final size:122
Alignment explanation
Indices: 53729408--53729639 Score: 261
Period size: 123 Copynumber: 1.9 Consensus size: 122
53729398 TGCCATAGGG
* * * ** *
53729408 CCTACCACACGGTCATGTGACCCACACGATCTATCACATAGCCTACCACATGTTCGTGTGACACA
1 CCTACCACACGGTCATGTGACCCACACGACCTACCACATAGCCTACCACACGGCCCTGTGACACA
* * * * * *
53729473 CACGGTCTGCTAAATGGCTTACTATATGGTCCTGTGACCGACACATTCTACCACACCA
66 CACGATCTGCTAAATGGCCTACCACATGATCCTGTAACC-ACACATTCTACCACACCA
* * * * *
53729531 CCTACCACACGGTCGTGTGACCCACACGACCTGCCGCATGGCCTACCACACGGCCCTGTGACGCA
1 CCTACCACACGGTCATGTGACCCACACGACCTACCACATAGCCTACCACACGGCCCTGTGACACA
* *
53729596 CACGATCTG-TCACATGGCCTACCACATGATCGTGTAACC-CACAT
66 CACGATCTGCT-AAATGGCCTACCACATGATCCTGTAACCACACAT
53729640 GGTCTGCCAC
Statistics
Matches: 89, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
121 5 0.06
122 1 0.01
123 83 0.93
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (122 bp):
CCTACCACACGGTCATGTGACCCACACGACCTACCACATAGCCTACCACACGGCCCTGTGACACA
CACGATCTGCTAAATGGCCTACCACATGATCCTGTAACCACACATTCTACCACACCA
Found at i:53740115 original size:41 final size:40
Alignment explanation
Indices: 53740070--53740243 Score: 136
Period size: 41 Copynumber: 4.3 Consensus size: 40
53740060 TTGCCATAGG
* *
53740070 GCCTACCACACGGTCATGTGACCCACACGATCTATCACATA
1 GCCTACCACACGGTCGTGTGACCCACACGATCT-GCACATA
* * * * * *
53740111 GCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAATG
1 GCCTACCACACGGTCGTGTGACCCACACGATCTGC-ACATA
* * * * * * * * *
53740152 GCTTACTATATGGTCCTGTGACCGACACGTTCTACACACCA
1 GCCTACCACACGGTCGTGTGACCCACACGATCTGCACA-TA
* *
53740193 -CCTACCACACGGTCGTGTGACCCACACGA-CTGCGCATG
1 GCCTACCACACGGTCGTGTGACCCACACGATCTGCACATA
53740231 GCCTACCACACGG
1 GCCTACCACACGG
53740244 CCATCTGTCA
Statistics
Matches: 99, Mismatches: 31, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
39 17 0.17
40 25 0.25
41 57 0.58
ACGTcount: A:0.25, C:0.35, G:0.20, T:0.21
Consensus pattern (40 bp):
GCCTACCACACGGTCGTGTGACCCACACGATCTGCACATA
Found at i:53749868 original size:41 final size:41
Alignment explanation
Indices: 53749800--53750047 Score: 212
Period size: 41 Copynumber: 6.1 Consensus size: 41
53749790 TTTGCCATAC
* * *
53749800 GGCCTACCACA-GGTCATGTGACCCACACGATCTACCACAT
1 GGCCTACCACATGGTCGTGTGACGCACACGATCTGCCACAT
* * * * * *
53749840 AGCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAAT
1 GGCCTACCACATGGTCGTGTGACGCACACGATCTGCCACAT
* * * * * * *
53749881 GGCTTACTATATGGTCCTGTGAC-CGACACGTTCTACCACAC
1 GGCCTACCACATGGTCGTGTGACGC-ACACGATCTGCCACAT
** * *
53749922 CACCTACCACACGGTCGTGTGACGCACACGATCTGCCGCAT
1 GGCCTACCACATGGTCGTGTGACGCACACGATCTGCCACAT
* * * *
53749963 GGCCTACCACACGGCCATGTGACGCACACGATCTGTCACAT
1 GGCCTACCACATGGTCGTGTGACGCACACGATCTGCCACAT
* * * * *
53750004 GGCCTACCACATGATCGTGTAACCCACATGGTCTGCCACAT
1 GGCCTACCACATGGTCGTGTGACGCACACGATCTGCCACAT
53750045 GGC
1 GGC
53750048 TAGTTACACG
Statistics
Matches: 160, Mismatches: 45, Indels: 5
0.76 0.21 0.02
Matches are distributed among these distances:
40 11 0.07
41 148 0.93
42 1 0.01
ACGTcount: A:0.24, C:0.35, G:0.21, T:0.21
Consensus pattern (41 bp):
GGCCTACCACATGGTCGTGTGACGCACACGATCTGCCACAT
Found at i:53750043 original size:123 final size:122
Alignment explanation
Indices: 53749802--53750043 Score: 261
Period size: 123 Copynumber: 2.0 Consensus size: 122
53749792 TGCCATACGG
* ** *
53749802 CCTACCACAGGTCATGTGACCCACACGATCTACCACATAGCCTACCACATGTTCGTGTGACACAC
1 CCTACCACAGGTCATGTGACCCACACGATCTACCACATAGCCTACCACACGGCCATGTGACACAC
* * * * * * * *
53749867 ACGGTCTGCTAAATGGCTTACTATATGGTCCTGTGACCGACACGTTCTACCACACCA
66 ACGATCTGCTAAATGGCCTACCACATGATCCTGTAACCCACACGGTCTACCACACCA
* * * * * *
53749924 CCTACCACACGGTCGTGTGACGCACACGATCTGCCGCATGGCCTACCACACGGCCATGTGACGCA
1 CCTACCACA-GGTCATGTGACCCACACGATCTACCACATAGCCTACCACACGGCCATGTGACACA
* * * *
53749989 CACGATCTG-TCACATGGCCTACCACATGATCGTGTAACCCACATGGTCTGCCACA
65 CACGATCTGCT-AAATGGCCTACCACATGATCCTGTAACCCACACGGTCTACCACA
53750044 TGGCTAGTTA
Statistics
Matches: 96, Mismatches: 22, Indels: 3
0.79 0.18 0.02
Matches are distributed among these distances:
122 10 0.10
123 86 0.90
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (122 bp):
CCTACCACAGGTCATGTGACCCACACGATCTACCACATAGCCTACCACACGGCCATGTGACACAC
ACGATCTGCTAAATGGCCTACCACATGATCCTGTAACCCACACGGTCTACCACACCA
Found at i:53752919 original size:42 final size:38
Alignment explanation
Indices: 53752825--53752996 Score: 148
Period size: 42 Copynumber: 4.6 Consensus size: 38
53752815 ATTCCCCCAA
*
53752825 GGGGTTGCTAAGTGCTGATTCC-CCG-A-TTCATT--G
1 GGGGTTGCTAAGTGCTGATTCCACCGTATTTAATTAAG
* *
53752858 GTGGTTGCTAAGTGTTGATTCCACCGTATCTTGAATATAAAG
1 GGGGTTGCTAAGTGCTGATTCCACCGTAT-TT-AAT-T-AAG
*
53752900 GGGGTTGCTAAGTGCTGATTCC-CCG-A-TTCATT--G
1 GGGGTTGCTAAGTGCTGATTCCACCGTATTTAATTAAG
* *
53752933 GTGGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAG
1 GGGGTTGCTAAGTGCTGATTCCACCGTA-TTT-AAT-T-AAG
53752975 GGGGTTGCTAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATTCC
53752997 CCCAAGGGGT
Statistics
Matches: 110, Mismatches: 11, Indels: 27
0.74 0.07 0.18
Matches are distributed among these distances:
33 41 0.37
34 6 0.05
35 2 0.02
36 1 0.01
37 6 0.05
38 6 0.05
39 2 0.02
40 1 0.01
41 3 0.03
42 42 0.38
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (38 bp):
GGGGTTGCTAAGTGCTGATTCCACCGTATTTAATTAAG
Found at i:53752957 original size:75 final size:75
Alignment explanation
Indices: 53752825--53752998 Score: 294
Period size: 75 Copynumber: 2.3 Consensus size: 75
53752815 ATTCCCCCAA
* *
53752825 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
*
53752890 GAATATAAAG
66 AAATATAAAG
*
53752900 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
* *
53752965 AAATGTGAAG
66 AAATATAAAG
53752975 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
53752999 CAAGGGGTTG
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 93 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (75 bp):
GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
AAATATAAAG
Found at i:53753006 original size:102 final size:103
Alignment explanation
Indices: 53752900--53753101 Score: 334
Period size: 102 Copynumber: 2.0 Consensus size: 103
53752890 GAATATAAAG
* * *
53752900 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTAT-TT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCACCATATCTT
*
53752964 TAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
* *
53753002 GGGGTTGCTATGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCACCATATCTT
*
53753067 TGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
53753102 AAATCACTGG
Statistics
Matches: 92, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 57 0.62
103 35 0.38
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (103 bp):
GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCACCATATCTT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:53760414 original size:41 final size:41
Alignment explanation
Indices: 53760368--53760616 Score: 187
Period size: 41 Copynumber: 6.1 Consensus size: 41
53760358 TTTGCCATAC
* *
53760368 GGCCTACCACACGGTCATGTGACCCACACGATCTACCACAT
1 GGCCTACCACACGGTCATGTGACACACACGATCTGCCACAT
* * * * * * *
53760409 AGCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAAT
1 GGCCTACCACACGGTCATGTGACACACACGATCTGCCACAT
* * * * * * *
53760450 GGCTTACTATATGGTCCTGTGAC-CGACAC-ATTCTACCACAC
1 GGCCTACCACACGGTCATGTGACAC-ACACGA-TCTGCCACAT
** * * *
53760491 CACCTACCATACGGTCGTGTGACACACACGATCTGCCGCAT
1 GGCCTACCACACGGTCATGTGACACACACGATCTGCCACAT
* * *
53760532 GGCCTACCACACGGCCATGTGACGCACACGATCTGTCACAT
1 GGCCTACCACACGGTCATGTGACACACACGATCTGCCACAT
* * * * * * *
53760573 GGCCTACCACATGATCGTGTAACCCACATGGTCTGCCACAT
1 GGCCTACCACACGGTCATGTGACACACACGATCTGCCACAT
53760614 GGC
1 GGC
53760617 TAGTTACACG
Statistics
Matches: 158, Mismatches: 46, Indels: 8
0.75 0.22 0.04
Matches are distributed among these distances:
40 1 0.01
41 155 0.98
42 2 0.01
ACGTcount: A:0.25, C:0.35, G:0.20, T:0.21
Consensus pattern (41 bp):
GGCCTACCACACGGTCATGTGACACACACGATCTGCCACAT
Found at i:53760612 original size:123 final size:122
Alignment explanation
Indices: 53760370--53760601 Score: 261
Period size: 123 Copynumber: 1.9 Consensus size: 122
53760360 TGCCATACGG
* * ** *
53760370 CCTACCACACGGTCATGTGACCCACACGATCTACCACATAGCCTACCACATGTTCGTGTGACACA
1 CCTACCACACGGTCATGTGACACACACGATCTACCACATAGCCTACCACACGGCCATGTGACACA
* * * * * *
53760435 CACGGTCTGCTAAATGGCTTACTATATGGTCCTGTGACCGACACATTCTACCACACCA
66 CACGATCTGCTAAATGGCCTACCACATGATCCTGTAACC-ACACATTCTACCACACCA
* * * * * *
53760493 CCTACCATACGGTCGTGTGACACACACGATCTGCCGCATGGCCTACCACACGGCCATGTGACGCA
1 CCTACCACACGGTCATGTGACACACACGATCTACCACATAGCCTACCACACGGCCATGTGACACA
* *
53760558 CACGATCTG-TCACATGGCCTACCACATGATCGTGTAACC-CACAT
66 CACGATCTGCT-AAATGGCCTACCACATGATCCTGTAACCACACAT
53760602 GGTCTGCCAC
Statistics
Matches: 89, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
121 5 0.06
122 1 0.01
123 83 0.93
ACGTcount: A:0.26, C:0.35, G:0.18, T:0.21
Consensus pattern (122 bp):
CCTACCACACGGTCATGTGACACACACGATCTACCACATAGCCTACCACACGGCCATGTGACACA
CACGATCTGCTAAATGGCCTACCACATGATCCTGTAACCACACATTCTACCACACCA
Found at i:53763483 original size:42 final size:38
Alignment explanation
Indices: 53763389--53763560 Score: 148
Period size: 42 Copynumber: 4.6 Consensus size: 38
53763379 ATTCCCCCAA
*
53763389 GGGGTTGCTAAGTGCTGATTCC-CCG-A-TTCATT--G
1 GGGGTTGCTAAGTGCTGATTCCACCGTATTTAATTAAG
* *
53763422 GTGGTTGCTAAGTGTTGATTCCACCGTATCTTGAATATAAAG
1 GGGGTTGCTAAGTGCTGATTCCACCGTAT-TT-AAT-T-AAG
*
53763464 GGGGTTGCTAAGTGCTGATTCC-CCG-A-TTCATT--G
1 GGGGTTGCTAAGTGCTGATTCCACCGTATTTAATTAAG
* *
53763497 GTGGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAG
1 GGGGTTGCTAAGTGCTGATTCCACCGTA-TTT-AAT-T-AAG
53763539 GGGGTTGCTAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATTCC
53763561 CCAAGGGGTT
Statistics
Matches: 110, Mismatches: 11, Indels: 27
0.74 0.07 0.18
Matches are distributed among these distances:
33 41 0.37
34 6 0.05
35 2 0.02
36 1 0.01
37 6 0.05
38 6 0.05
39 2 0.02
40 1 0.01
41 3 0.03
42 42 0.38
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (38 bp):
GGGGTTGCTAAGTGCTGATTCCACCGTATTTAATTAAG
Found at i:53763521 original size:75 final size:75
Alignment explanation
Indices: 53763389--53763562 Score: 294
Period size: 75 Copynumber: 2.3 Consensus size: 75
53763379 ATTCCCCCAA
* *
53763389 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
*
53763454 GAATATAAAG
66 AAATATAAAG
*
53763464 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
* *
53763529 AAATGTGAAG
66 AAATATAAAG
53763539 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
53763563 AAGGGGTTGC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 93 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (75 bp):
GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
AAATATAAAG
Found at i:53763644 original size:101 final size:101
Alignment explanation
Indices: 53763464--53763665 Score: 325
Period size: 101 Copynumber: 2.0 Consensus size: 101
53763454 GAATATAAAG
* * *
53763464 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCACCATATTTT
*
53763529 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCAA
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAA
* *
53763565 GGGGTTGCTATGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCACCATAT-TT
*
53763629 TGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAA
65 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAA
53763666 ATCACTGGTG
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
100 37 0.40
101 56 0.60
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (101 bp):
GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCACCATATTTT
AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:53763659 original size:176 final size:177
Alignment explanation
Indices: 53763345--53763698 Score: 572
Period size: 176 Copynumber: 2.0 Consensus size: 177
53763335 ATAAGCCGAA
53763345 GTATTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTC
1 GTATTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTC
* * * *
53763410 CCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATCTTGAATATAAAGGGGGTTGCTAA
66 CCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATCTTGAATATAAAGGGGGTTGCTAA
* * *
53763475 GTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTG-ATCCCACC
131 GTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTGAAT-CCACC
*
53763522 GTATTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATT-CCCCAAGGGGTTGCTATGTGCTGATT-
1 GTATTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTC
*
53763585 CCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATCTTTGAATGTGAAA-GGGGTTGCT
66 CCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATC-TTGAATAT-AAAGGGGGTTGCT
53763649 AAGTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTGAATCCACC
129 AAGTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTGAATCCACC
53763698 G
1 G
53763699 ATAACGGTTA
Statistics
Matches: 165, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
175 38 0.23
176 85 0.52
177 42 0.25
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.32
Consensus pattern (177 bp):
GTATTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTC
CCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATCTTGAATATAAAGGGGGTTGCTAA
GTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTGAATCCACC
Found at i:53772566 original size:7 final size:7
Alignment explanation
Indices: 53772554--53772578 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53772544 TTACCCTATT
53772554 AAATTCA
1 AAATTCA
53772561 AAATTCA
1 AAATTCA
53772568 AAATTCA
1 AAATTCA
53772575 AAAT
1 AAAT
53772579 ATACTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTCA
Found at i:53781511 original size:41 final size:41
Alignment explanation
Indices: 53781465--53781713 Score: 212
Period size: 41 Copynumber: 6.1 Consensus size: 41
53781455 TTTGCCATAC
* *
53781465 GGCCTACCACACGGTCATGTGACCCACACGATCTACCACAT
1 GGCCTACCACACGGTCCTGTGACCCACACGATCTGCCACAT
* * * * * * * *
53781506 AGCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAAT
1 GGCCTACCACACGGTCCTGTGACCCACACGATCTGCCACAT
* * * * * * *
53781547 GGCTTACTATATGGTCCTGTGACCGACAC-ATTCTACCACAC
1 GGCCTACCACACGGTCCTGTGACCCACACGA-TCTGCCACAT
** * *
53781588 CACCTACCACACGGTCGTGTGACCCACACGATCTGCCGCAT
1 GGCCTACCACACGGTCCTGTGACCCACACGATCTGCCACAT
* * *
53781629 GGCCTACCACACGGCCCTGTGACGCACACGATCTGTCACAT
1 GGCCTACCACACGGTCCTGTGACCCACACGATCTGCCACAT
* * * * * *
53781670 GGCCTACCACATGATCGTGTAACCCACATGGTCTGCCACAT
1 GGCCTACCACACGGTCCTGTGACCCACACGATCTGCCACAT
53781711 GGC
1 GGC
53781714 TAGTTACACG
Statistics
Matches: 157, Mismatches: 49, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
41 156 0.99
42 1 0.01
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (41 bp):
GGCCTACCACACGGTCCTGTGACCCACACGATCTGCCACAT
Found at i:53781709 original size:123 final size:122
Alignment explanation
Indices: 53781467--53781698 Score: 279
Period size: 123 Copynumber: 1.9 Consensus size: 122
53781457 TGCCATACGG
* ** *
53781467 CCTACCACACGGTCATGTGACCCACACGATCTACCACATAGCCTACCACATGTTCGTGTGACACA
1 CCTACCACACGGTCATGTGACCCACACGATCTACCACATAGCCTACCACACGGCCCTGTGACACA
* * * * * *
53781532 CACGGTCTGCTAAATGGCTTACTATATGGTCCTGTGACCGACACATTCTACCACACCA
66 CACGATCTGCTAAATGGCCTACCACATGATCCTGTAACC-ACACATTCTACCACACCA
* * * * *
53781590 CCTACCACACGGTCGTGTGACCCACACGATCTGCCGCATGGCCTACCACACGGCCCTGTGACGCA
1 CCTACCACACGGTCATGTGACCCACACGATCTACCACATAGCCTACCACACGGCCCTGTGACACA
* *
53781655 CACGATCTG-TCACATGGCCTACCACATGATCGTGTAACC-CACAT
66 CACGATCTGCT-AAATGGCCTACCACATGATCCTGTAACCACACAT
53781699 GGTCTGCCAC
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
121 5 0.05
122 1 0.01
123 85 0.93
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (122 bp):
CCTACCACACGGTCATGTGACCCACACGATCTACCACATAGCCTACCACACGGCCCTGTGACACA
CACGATCTGCTAAATGGCCTACCACATGATCCTGTAACCACACATTCTACCACACCA
Found at i:53784577 original size:75 final size:74
Alignment explanation
Indices: 53784484--53784659 Score: 262
Period size: 75 Copynumber: 2.4 Consensus size: 74
53784474 TGATTCCCCC
* *
53784484 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAATGTTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAATGCTGATCCCACCGTATC
* *
53784549 TTGAATATA
66 TTAAAGATA
*
53784558 AAGGGAGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTAT
1 AAGGG-GTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAATGCTGATCCCACCGTAT
* *
53784623 TTTAAAGGTGA
65 CTTAAAGAT-A
*
53784634 AGGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
53784660 CAAGGGGTTG
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
74 5 0.05
75 82 0.89
76 5 0.05
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (74 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAATGCTGATCCCACCGTATC
TTAAAGATA
Found at i:53792092 original size:82 final size:80
Alignment explanation
Indices: 53791944--53792092 Score: 217
Period size: 82 Copynumber: 1.8 Consensus size: 80
53791934 ACGGCCTACC
* * *
53791944 ATATGGTCATGTGACCCACACGATCTACCACAACCTACCACATGTTCGTGTGACACACACGGTCT
1 ATATGGTCATGTGACCCACACGATCTACCACAACCTACCACACGGTCGTGTGACACACACGATCT
53792009 GCTAAATGGCTTACT
66 GCTAAATGGCTTACT
* * * *
53792024 ATATGGTCCTGTGACCGACACGTTCTACCACACCACCTACCACACGGTCGTGTGACCCACACGAT
1 ATATGGTCATGTGACCCACACGATCTACCACA--ACCTACCACACGGTCGTGTGACACACACGAT
53792089 CTGC
64 CTGC
53792093 CGCATGGCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 29 0.48
82 31 0.52
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.23
Consensus pattern (80 bp):
ATATGGTCATGTGACCCACACGATCTACCACAACCTACCACACGGTCGTGTGACACACACGATCT
GCTAAATGGCTTACT
Found at i:53792110 original size:41 final size:41
Alignment explanation
Indices: 53791936--53792108 Score: 143
Period size: 41 Copynumber: 4.3 Consensus size: 41
53791926 TTTGCCATAC
* *
53791936 GGCCTACCATATGGTCATGTGACCCACACGATCTACCACA-
1 GGCCTACCACATGGTCGTGTGACCCACACGATCTACCACAT
* * * * * * *
53791976 -ACCTACCACATGTTCGTGTGACACACACGGTCTGCTAAAT
1 GGCCTACCACATGGTCGTGTGACCCACACGATCTACCACAT
* * * * * * *
53792016 GGCTTACTATATGGTCCTGTGACCGACACGTTCTACCACAC
1 GGCCTACCACATGGTCGTGTGACCCACACGATCTACCACAT
** * * *
53792057 CACCTACCACACGGTCGTGTGACCCACACGATCTGCCGCAT
1 GGCCTACCACATGGTCGTGTGACCCACACGATCTACCACAT
53792098 GGCCTACCACA
1 GGCCTACCACA
53792109 CGATCTGTCA
Statistics
Matches: 95, Mismatches: 36, Indels: 3
0.71 0.27 0.02
Matches are distributed among these distances:
39 30 0.32
41 65 0.68
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.21
Consensus pattern (41 bp):
GGCCTACCACATGGTCGTGTGACCCACACGATCTACCACAT
Found at i:53792112 original size:24 final size:24
Alignment explanation
Indices: 53792080--53792137 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
53792070 GTCGTGTGAC
*
53792080 CCACACGATCTGCCGCATGGCCTA
1 CCACACGATCTGCCACATGGCCTA
*
53792104 CCACACGATCTGTCACATGGCCTA
1 CCACACGATCTGCCACATGGCCTA
*
53792128 CCACATGATC
1 CCACACGATC
53792138 GTCTAACCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.40, G:0.17, T:0.19
Consensus pattern (24 bp):
CCACACGATCTGCCACATGGCCTA
Found at i:53802534 original size:41 final size:41
Alignment explanation
Indices: 53802489--53802664 Score: 156
Period size: 41 Copynumber: 4.3 Consensus size: 41
53802479 TTGCCATACG
*
53802489 GCCTACCACACGGTCATGTGACCCACACGATCTACCACATA
1 GCCTACCACACGGTCGTGTGACCCACACGATCTACCACATA
* * * * * * * *
53802530 GCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAATG
1 GCCTACCACACGGTCGTGTGACCCACACGATCTACCACATA
* * * * * * * *
53802571 GCTTACTATATGGTCCTGTGACCGACACGTTCTACCACACCA
1 GCCTACCACACGGTCGTGTGACCCACACGATCTACCACA-TA
* * *
53802613 -CCTACCACACGGTCGTGTGACCCACACGATCTGCCGCATG
1 GCCTACCACACGGTCGTGTGACCCACACGATCTACCACATA
53802653 GCCTACCACACG
1 GCCTACCACACG
53802665 ATCTGTCACA
Statistics
Matches: 100, Mismatches: 33, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.20
Consensus pattern (41 bp):
GCCTACCACACGGTCGTGTGACCCACACGATCTACCACATA
Found at i:53802666 original size:24 final size:24
Alignment explanation
Indices: 53802634--53802691 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
53802624 GTCGTGTGAC
*
53802634 CCACACGATCTGCCGCATGGCCTA
1 CCACACGATCTGCCACATGGCCTA
*
53802658 CCACACGATCTGTCACATGGCCTA
1 CCACACGATCTGCCACATGGCCTA
*
53802682 CCACATGATC
1 CCACACGATC
53802692 GTGAAACCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.40, G:0.17, T:0.19
Consensus pattern (24 bp):
CCACACGATCTGCCACATGGCCTA
Found at i:53805271 original size:17 final size:18
Alignment explanation
Indices: 53805232--53805271 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
53805222 ATCTATAAGA
53805232 AAAATATTAAATTTAATT
1 AAAATATTAAATTTAATT
*
53805250 -TAATATTAAATTT-ATT
1 AAAATATTAAATTTAATT
53805266 AAAATA
1 AAAATA
53805272 ATATTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATATTAAATTTAATT
Found at i:53810678 original size:19 final size:19
Alignment explanation
Indices: 53810654--53810691 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
53810644 AATCTGAAGA
53810654 ACAATCCTAAGGTGCTCGT
1 ACAATCCTAAGGTGCTCGT
53810673 ACAATCCTAAGGTGCTCGT
1 ACAATCCTAAGGTGCTCGT
53810692 CATGCTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
ACAATCCTAAGGTGCTCGT
Found at i:53819664 original size:17 final size:17
Alignment explanation
Indices: 53819633--53819682 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
53819623 CATGTGGTTT
53819633 GCCCGTGTGGGCCCACAC
1 GCCCGTGT-GGCCCACAC
53819651 GCCCGTGTGGCCCACAC
1 GCCCGTGTGGCCCACAC
53819668 GCCCGTGTGGCCCAC
1 GCCCGTGTGGCCCAC
53819683 TCAGCCTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 24 0.75
18 8 0.25
ACGTcount: A:0.10, C:0.46, G:0.32, T:0.12
Consensus pattern (17 bp):
GCCCGTGTGGCCCACAC
Found at i:53822468 original size:15 final size:15
Alignment explanation
Indices: 53822450--53822481 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
53822440 TTCTGCTCTA
53822450 TTCTATTTTGTTTTG
1 TTCTATTTTGTTTTG
53822465 TTCTATTTTGTTTTG
1 TTCTATTTTGTTTTG
53822480 TT
1 TT
53822482 TTGTTGAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.75
Consensus pattern (15 bp):
TTCTATTTTGTTTTG
Found at i:53822482 original size:20 final size:20
Alignment explanation
Indices: 53822432--53822486 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
53822422 CATACATTTG
* *
53822432 CTATTTTGTTCTGCTCTATT
1 CTATTTTGTTTTGTTCTATT
53822452 CTATTTTGTTTTGTTCTATT
1 CTATTTTGTTTTGTTCTATT
* *
53822472 TTGTTTTGTTTTGTT
1 CTATTTTGTTTTGTT
53822487 GAACTACCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.07, C:0.11, G:0.13, T:0.69
Consensus pattern (20 bp):
CTATTTTGTTTTGTTCTATT
Found at i:53822693 original size:15 final size:14
Alignment explanation
Indices: 53822673--53822726 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
53822663 ATTAACACAC
53822673 TAGCCTAAACCCAA
1 TAGCCTAAACCCAA
*
53822687 TTAGCCTAAGCCCAA
1 -TAGCCTAAACCCAA
* *
53822702 TA-CCTTAGCCCAA
1 TAGCCTAAACCCAA
53822715 CTAGCCTAAACC
1 -TAGCCTAAACC
53822727 AGAAATCAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 10 0.30
14 4 0.12
15 19 0.58
ACGTcount: A:0.35, C:0.37, G:0.09, T:0.19
Consensus pattern (14 bp):
TAGCCTAAACCCAA
Found at i:53823807 original size:3 final size:3
Alignment explanation
Indices: 53823799--53823881 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
53823789 ACTGAACATT
53823799 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53823847 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
53823882 TCTGTACTTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53824054 original size:16 final size:16
Alignment explanation
Indices: 53824033--53824063 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53824023 TGATGTGATA
53824033 TATTATTATTTTAAAT
1 TATTATTATTTTAAAT
*
53824049 TATTATTTTTTTAAA
1 TATTATTATTTTAAA
53824064 ATTTATCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATTATTTTAAAT
Found at i:53826318 original size:8 final size:8
Alignment explanation
Indices: 53826307--53826333 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
53826297 TAATAAAAAC
53826307 ATTTTTAT
1 ATTTTTAT
53826315 ATTTTTAT
1 ATTTTTAT
53826323 ATTTTTAT
1 ATTTTTAT
53826331 ATT
1 ATT
53826334 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTAT
Found at i:53826705 original size:21 final size:20
Alignment explanation
Indices: 53826674--53826712 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
53826664 TTTTTAATAA
53826674 TTTTAAATTTTTAAAATTAT
1 TTTTAAATTTTTAAAATTAT
53826694 TTTTATAATTTTTAAAATT
1 TTTTA-AATTTTTAAAATT
53826713 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAAATTTTTAAAATTAT
Found at i:53829658 original size:20 final size:20
Alignment explanation
Indices: 53829577--53829669 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
53829567 GTATATCAAT
*
53829577 ATTTACCAAGATTTTTAAAG
1 ATTTACCAAAATTTTTAAAG
*
53829597 TTTTACCAAAATTTTT-AAG
1 ATTTACCAAAATTTTTAAAG
** ** *** **
53829616 GCTTACCACGATACCTATGG
1 ATTTACCAAAATTTTTAAAG
53829636 ATTTACCAAAATTTTTAAAG
1 ATTTACCAAAATTTTTAAAG
*
53829656 ATTTATCAAAATTT
1 ATTTACCAAAATTT
53829670 ATAAGATTAT
Statistics
Matches: 51, Mismatches: 21, Indels: 2
0.69 0.28 0.03
Matches are distributed among these distances:
19 12 0.24
20 39 0.76
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
ATTTACCAAAATTTTTAAAG
Found at i:53829677 original size:19 final size:20
Alignment explanation
Indices: 53829635--53829677 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
53829625 GATACCTATG
*
53829635 GATTTACCAAAATTTTTAAA
1 GATTTACCAAAATTTATAAA
*
53829655 GATTTATCAAAATTTAT-AA
1 GATTTACCAAAATTTATAAA
53829674 GATT
1 GATT
53829678 ATACGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (20 bp):
GATTTACCAAAATTTATAAA
Found at i:53829764 original size:20 final size:20
Alignment explanation
Indices: 53829741--53829788 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
53829731 CGTTACCAAA
53829741 ATTTCTAAG-G-TTATACTAAT
1 ATTTCTAAGTGTTTATA--AAT
*
53829761 ATTTTTAAGTGTTTATAAAT
1 ATTTCTAAGTGTTTATAAAT
53829781 ATTTCTAA
1 ATTTCTAA
53829789 AGTTTTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 18 0.75
21 1 0.04
22 5 0.21
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.50
Consensus pattern (20 bp):
ATTTCTAAGTGTTTATAAAT
Found at i:53829795 original size:20 final size:21
Alignment explanation
Indices: 53829758--53829830 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 21
53829748 AGGTTATACT
*
53829758 AATATTT-TTAAGTGTTTATA-
1 AATATTTCTAAAGTGTTTA-AC
53829778 AATATTTCTAAAGT-TTTAAC
1 AATATTTCTAAAGTGTTTAAC
* * *
53829798 AATATTCCTAAAG-GTTCACC
1 AATATTTCTAAAGTGTTTAAC
*
53829818 ATTATTTCTAAAG
1 AATATTTCTAAAG
53829831 ATTTTCCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 38 0.86
21 5 0.11
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (21 bp):
AATATTTCTAAAGTGTTTAAC
Found at i:53830066 original size:20 final size:20
Alignment explanation
Indices: 53829977--53830071 Score: 54
Period size: 20 Copynumber: 4.8 Consensus size: 20
53829967 GGATATTTAA
* *
53829977 CTTTAAAAATTTGGGTAAAT
1 CTTTAGAAATTTTGGTAAAT
* *
53829997 CCTTATG-CATTTTGGTATAA-
1 CTTTA-GAAATTTTGGTA-AAT
*
53830017 CCTTAGAAAATTTT-GTAAAT
1 CTTTAG-AAATTTTGGTAAAT
* *
53830037 -TCTCGTAAATTTTGGTAAAT
1 CTTTAG-AAATTTTGGTAAAT
*
53830057 CTTTAGAAATATTGG
1 CTTTAGAAATTTTGG
53830072 AAAACCTTGG
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
19 12 0.21
20 34 0.61
21 10 0.18
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (20 bp):
CTTTAGAAATTTTGGTAAAT
Found at i:53830185 original size:20 final size:20
Alignment explanation
Indices: 53830116--53830258 Score: 92
Period size: 20 Copynumber: 7.0 Consensus size: 20
53830106 TGTCTCAATG
*
53830116 AAATCTTTAGAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* * * **
53830136 AAAAACCCTTAGATATATTAAT
1 --AAATCCTTAGAAATTTTGGT
53830158 AAATCCTTAGAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* * *
53830178 ATAA-CCTTAAAAATTCTAGT
1 A-AATCCTTAGAAATTTTGGT
* *
53830198 AAATCCTTACATATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* *
53830218 ATAA-CCTTATAAATTTCGGT
1 A-AATCCTTAGAAATTTTGGT
* * *
53830238 AATTTCTTAAAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
53830258 A
1 A
53830259 TGCCAAAATA
Statistics
Matches: 92, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.03
20 71 0.77
21 4 0.04
22 14 0.15
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (20 bp):
AAATCCTTAGAAATTTTGGT
Found at i:53830201 original size:40 final size:39
Alignment explanation
Indices: 53830116--53830259 Score: 135
Period size: 40 Copynumber: 3.6 Consensus size: 39
53830106 TGTCTCAATG
* * * * *
53830116 AAATCTTTAGAAATTTTGGTAAAAACCCTTAGATATATTAAT
1 AAATCCTTAGAAATTTTGGT-ATAA-CCTTAAAAAT-TTAGT
53830158 AAATCCTTAGAAATTTTGGTATAACCTTAAAAATTCTAGT
1 AAATCCTTAGAAATTTTGGTATAACCTTAAAAATT-TAGT
* * * *
53830198 AAATCCTTACATATTTTGGTATAACCTTATAAATTTCGGT
1 AAATCCTTAGAAATTTTGGTATAACCTTAAAAATTT-AGT
* * *
53830238 AATTTCTTAAAAATTTTGGTAT
1 AAATCCTTAGAAATTTTGGTAT
53830260 GCCAAAATAT
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 63 0.72
41 3 0.03
42 19 0.22
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (39 bp):
AAATCCTTAGAAATTTTGGTATAACCTTAAAAATTTAGT
Found at i:53830367 original size:20 final size:20
Alignment explanation
Indices: 53830323--53830373 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
53830313 TGGGTAAATT
* *
53830323 CTTAGAAATTTGGGTAAAGC
1 CTTAGAAATTTGGCTAAACC
* *
53830343 TTTAGAAATTTTGCTAAACC
1 CTTAGAAATTTGGCTAAACC
*
53830363 CTTAGATATTT
1 CTTAGAAATTT
53830374 CATTATAAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (20 bp):
CTTAGAAATTTGGCTAAACC
Found at i:53832970 original size:32 final size:32
Alignment explanation
Indices: 53832934--53832997 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
53832924 TTGGTAAATG
*
53832934 ATACCAGTGTTTGCTAATATGAAACTGATTAT
1 ATACCAGCGTTTGCTAATATGAAACTGATTAT
53832966 ATACCAGCGTTTGCTAATATGAAACTGATTAT
1 ATACCAGCGTTTGCTAATATGAAACTGATTAT
53832998 CTTCAGCTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
ATACCAGCGTTTGCTAATATGAAACTGATTAT
Found at i:53838905 original size:23 final size:23
Alignment explanation
Indices: 53838874--53838931 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
53838864 ATAACACTTC
*
53838874 AAAA-ATTTTATTTTCATTTATT
1 AAAATATTTTATTTGCATTTATT
*
53838896 AAAATATTTT-GTTGCATTTATT
1 AAAATATTTTATTTGCATTTATT
*
53838918 AAAACTATATTATT
1 AAAA-TATTTTATT
53838932 ACGTATGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 18 0.62
23 10 0.34
24 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (23 bp):
AAAATATTTTATTTGCATTTATT
Found at i:53839556 original size:42 final size:42
Alignment explanation
Indices: 53839489--53839631 Score: 157
Period size: 42 Copynumber: 3.4 Consensus size: 42
53839479 TAAAAATATC
* *
53839489 AAGGAAGCAACATGGAAAAGCAACATCCATG-TCTAGACAAAA
1 AAGGAAGCAACTTGGAAAAGCAACATCCAAGTTC-AGACAAAA
* *
53839531 AATGAAGCAACTTGGGAAAA-TAACATCCAAGTTCAGACAAAA
1 AAGGAAGCAACTT-GGAAAAGCAACATCCAAGTTCAGACAAAA
* ** *
53839573 AAGGAAGCAACTT-AAGAAAGCAACATTTAGGTTCAGACAAAA
1 AAGGAAGCAACTTGGA-AAAGCAACATCCAAGTTCAGACAAAA
*
53839615 AAGGAAGCAACGTGGAA
1 AAGGAAGCAACTTGGAA
53839632 GCAACCATGT
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
40 1 0.01
41 3 0.04
42 71 0.85
43 9 0.11
ACGTcount: A:0.50, C:0.16, G:0.20, T:0.14
Consensus pattern (42 bp):
AAGGAAGCAACTTGGAAAAGCAACATCCAAGTTCAGACAAAA
Found at i:53843687 original size:19 final size:20
Alignment explanation
Indices: 53843665--53843707 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
53843655 TTTTTAATTT
*
53843665 TTAAAAAATTTTAAATAT-A
1 TTAAAAAATGTTAAATATAA
*
53843684 TTAAAAAATGTTAAGTATAA
1 TTAAAAAATGTTAAATATAA
53843704 TTAA
1 TTAA
53843708 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
TTAAAAAATGTTAAATATAA
Found at i:53843772 original size:35 final size:35
Alignment explanation
Indices: 53843694--53843805 Score: 127
Period size: 35 Copynumber: 3.1 Consensus size: 35
53843684 TTAAAAAATG
53843694 TTAAGTATAATTAATTTTAAAATTTTAATATATA-T
1 TTAA-TATAATTAATTTTAAAATTTTAATATATATT
*
53843729 ATATATATAATTAATTTTAAAATTTTAATATATATT
1 TTA-ATATAATTAATTTTAAAATTTTAATATATATT
* * *
53843765 TTAATATATTTAAAATTTTTAATATACTTAATATATATT
1 TTAATATAATT--AA-TTTTAAAAT-TTTAATATATATT
53843804 TT
1 TT
53843806 TAAGGGTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
35 38 0.58
36 4 0.06
37 2 0.03
38 8 0.12
39 14 0.21
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (35 bp):
TTAATATAATTAATTTTAAAATTTTAATATATATT
Found at i:53843800 original size:29 final size:29
Alignment explanation
Indices: 53843744--53843804 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
53843734 TATAATTAAT
* *
53843744 TTTAAAATTTTAATATATATTTTAATATA
1 TTTAAAATTTTAATATATACTTAAATATA
*
53843773 TTTAAAATTTTTA-ATATACTTAATATATA
1 TTTAAAATTTTAATATATACTTAA-ATATA
53843802 TTT
1 TTT
53843805 TTAAGGGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTAAAATTTTAATATATACTTAAATATA
Found at i:53843860 original size:31 final size:29
Alignment explanation
Indices: 53843825--53843894 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
53843815 ACTACCAAAA
* *
53843825 TAGTCACTTTTGTTTGACTCAGGTTACATTT
1 TAGTCACTTATGTTTGA--AAGGTTACATTT
* *
53843856 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAAGGTTACATTT
53843885 TAGTCACTTA
1 TAGTCACTTA
53843895 CGTTATCGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAAGGTTACATTT
Found at i:53844648 original size:18 final size:19
Alignment explanation
Indices: 53844627--53844663 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
53844617 AAAAAAAACT
53844627 TAAAAAAAT-TTAAATATA
1 TAAAAAAATATTAAATATA
*
53844645 TAAAAAAATATTAAGTATA
1 TAAAAAAATATTAAATATA
53844664 ACCAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAAAATATTAAATATA
Found at i:53844699 original size:17 final size:17
Alignment explanation
Indices: 53844671--53844776 Score: 108
Period size: 17 Copynumber: 5.9 Consensus size: 17
53844661 ATAACCAATT
53844671 TTAAAA-TTTTAATATA
1 TTAAAATTTTTAATATA
53844687 TTAAAATTTTTAATATA
1 TTAAAATTTTTAATATA
53844704 TTCAATATATTTTTTAAATATA
1 TT-AA-A-A-TTTTT-AATATA
* *
53844726 TTGAAATTTTAAATATA
1 TTAAAATTTTTAATATA
53844743 TTAAAA-TTTTAATATA
1 TTAAAATTTTTAATATA
53844759 TTTAATATATTTTTAATA
1 -TTAA-A-ATTTTTAATA
53844777 GGTAAAGAGA
Statistics
Matches: 76, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
16 15 0.20
17 27 0.36
18 7 0.09
19 3 0.04
20 10 0.13
21 6 0.08
22 8 0.11
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
TTAAAATTTTTAATATA
Done.