Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 121 of 128
Found at i:40102699 original size:22 final size:21
Alignment explanation
Indices: 40102589--40102734 Score: 80
Period size: 22 Copynumber: 6.8 Consensus size: 21
40102579 CCCTAACCCC
*
40102589 TAAACCATAAATCATAAACCCT
1 TAAACCATAAACCATAAA-CCT
* * * * * *
40102611 TAACCCCTAACCCCTAACCCC
1 TAAACCATAAACCATAAACCT
* ** *
40102632 TAAACCTTAAACCCCAATCCT
1 TAAACCATAAACCATAAACCT
* *
40102653 TAAACCATAAACCATAATCCC
1 TAAACCATAAACCATAAACCT
*
40102674 TAAACCCATAATCCATAAACCT
1 TAAA-CCATAAACCATAAACCT
*
40102696 TAAA--ATAGTAACTCTTAAACCT
1 TAAACCATA--AAC-CATAAACCT
* *
40102718 TAAACCCTAAACTATAA
1 TAAACCATAAACCATAA
40102735 TGATAATTAA
Statistics
Matches: 93, Mismatches: 25, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
19 3 0.03
21 43 0.46
22 45 0.48
24 2 0.02
ACGTcount: A:0.44, C:0.33, G:0.01, T:0.23
Consensus pattern (21 bp):
TAAACCATAAACCATAAACCT
Found at i:40103093 original size:41 final size:41
Alignment explanation
Indices: 40103036--40103234 Score: 308
Period size: 41 Copynumber: 4.9 Consensus size: 41
40103026 AATGTTTTTT
**
40103036 GCGGCGCTTTTTCAAAAACACCGCTAAAGCACCGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCACCGAGCATTA
*
40103077 GCGGCGCTTTTTCAAAAATGCCGCTCAAGCACCGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCACCGAGCATTA
*
40103118 GCGGCGCTTTTTCAAAAATGCCGCTCAAGCACCGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCACCGAGCATTA
* *
40103159 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCCCCTAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCACCGAGCATTA
* * * *
40103200 GTGGCACTTTTTCAAAAACGCCGCTAAAGCCCCGA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCACCGA
40103235 AAGGTCAGAA
Statistics
Matches: 148, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 148 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAATGCCGCTAAAGCACCGAGCATTA
Found at i:40103364 original size:40 final size:40
Alignment explanation
Indices: 40103264--40103373 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 40
40103254 GTTGGGAAAT
* * *
40103264 GCCGCTAATGCT-TATTTTTAGCGGCATGTTCCGAAAAGC
1 GCCGCAAATGCTAGATTTTTAGCGGCATTTTCCGAAAAGC
* *
40103303 GCCGCAAATGCTAGATCTTTAGCGGCGTTTTCC-ATAAAGC
1 GCCGCAAATGCTAGATTTTTAGCGGCATTTTCCGA-AAAGC
* * *
40103343 GCTGCTAATGGTCA-ATTTTTAGCGGCATTTT
1 GCCGCAAATGCT-AGATTTTTAGCGGCATTTT
40103374 TTGTCCAAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
39 12 0.21
40 45 0.78
41 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (40 bp):
GCCGCAAATGCTAGATTTTTAGCGGCATTTTCCGAAAAGC
Found at i:40110101 original size:41 final size:40
Alignment explanation
Indices: 40109995--40110120 Score: 110
Period size: 40 Copynumber: 3.1 Consensus size: 40
40109985 AAAAACATTG
* * ** *
40109995 CAAAATGTAAAGCAATAGCGGCGTTTTTCTCATAAACGCCA
1 CAAAAGGTAAAGCAATAGCGGCGTTTAT-AAAAAAACGCCA
* ** * *
40110036 CAAAAGGT-AAGCAATATCATCGTTTATGAAAAAAATGCCG
1 CAAAAGGTAAAGCAATAGCGGCGTTTAT-AAAAAAACGCCA
* *
40110076 CTAAAGGTAAAGCAATAGCGGCGTTTATAAAAAAACACCA
1 CAAAAGGTAAAGCAATAGCGGCGTTTATAAAAAAACGCCA
*
40110116 TAAAA
1 CAAAA
40110121 TATCCTTTTA
Statistics
Matches: 64, Mismatches: 20, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
40 41 0.64
41 23 0.36
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (40 bp):
CAAAAGGTAAAGCAATAGCGGCGTTTATAAAAAAACGCCA
Found at i:40117722 original size:37 final size:37
Alignment explanation
Indices: 40117681--40117754 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
40117671 AAAGCATTTC
*
40117681 TGGTAATTTTCTCTTCCTCCTCTTCTATTGAGTAATA
1 TGGTAATTTTCTCTTCCTCCTCTTCTATTGAGCAATA
40117718 TGGTAATTTTCTCTTCCTCCTCTTCTATTGAGCAATA
1 TGGTAATTTTCTCTTCCTCCTCTTCTATTGAGCAATA
40117755 AATATCTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.19, C:0.23, G:0.11, T:0.47
Consensus pattern (37 bp):
TGGTAATTTTCTCTTCCTCCTCTTCTATTGAGCAATA
Found at i:40117998 original size:34 final size:34
Alignment explanation
Indices: 40117955--40118025 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
40117945 TTTCCCAAGG
*
40117955 TTTTGGTGCTACGGTTGCTGTCAATGCTAACATT
1 TTTTGGTGCTACGATTGCTGTCAATGCTAACATT
40117989 TTTTGGTGCTACGATTGCTGTCAATGCTAACATT
1 TTTTGGTGCTACGATTGCTGTCAATGCTAACATT
40118023 TTT
1 TTT
40118026 GTGCATTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (34 bp):
TTTTGGTGCTACGATTGCTGTCAATGCTAACATT
Found at i:40118429 original size:11 final size:11
Alignment explanation
Indices: 40118413--40118440 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40118403 GGCAATGGTT
40118413 ACAATGTTTAA
1 ACAATGTTTAA
40118424 ACAATGTTTAA
1 ACAATGTTTAA
40118435 ACAATG
1 ACAATG
40118441 CTTGAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (11 bp):
ACAATGTTTAA
Found at i:40134054 original size:95 final size:95
Alignment explanation
Indices: 40133889--40134071 Score: 215
Period size: 95 Copynumber: 1.9 Consensus size: 95
40133879 CGCAGATAGC
* * * *
40133889 AAATCTTATCTCTCTGAGGTTGCAGTAGAGTAGATTAAAGCTGTAAACCTTGTTTCCCTAAAGTT
1 AAATCTTATCTCTCTGAGGTTGCAGTAGAGCAGATTAAAGATGCAAACCTTATTTCCCTAAAGTT
*
40133954 ACAGTGAAATAGATCCAAGCTACGTGTTAT
66 ACAGTGAAATAGATCAAAGCTACGTGTTAT
* * * * * * *
40133984 AAATCTTATCT-TCTTGAGGTTGCAGTGGAGCAGATTGAGGATGCGAATCTTATTTCCTTGAAGT
1 AAATCTTATCTCTC-TGAGGTTGCAGTAGAGCAGATTAAAGATGCAAACCTTATTTCCCTAAAGT
* * *
40134048 TGCAGTGGAATAGATTAAAGCTAC
65 TACAGTGAAATAGATCAAAGCTAC
40134072 AAGTGAAATC
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
94 2 0.03
95 70 0.97
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (95 bp):
AAATCTTATCTCTCTGAGGTTGCAGTAGAGCAGATTAAAGATGCAAACCTTATTTCCCTAAAGTT
ACAGTGAAATAGATCAAAGCTACGTGTTAT
Found at i:40134895 original size:24 final size:24
Alignment explanation
Indices: 40134847--40134893 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40134837 ACTGGTCATA
*
40134847 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
40134871 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
40134894 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:40135273 original size:27 final size:27
Alignment explanation
Indices: 40135242--40135422 Score: 247
Period size: 27 Copynumber: 6.7 Consensus size: 27
40135232 GCTCAACTTG
*
40135242 CCCCCGAAGGGTAAAATGATCGAAATA
1 CCCCCGAAGGGTAAAATGATCAAAATA
* *
40135269 CCCCCGAAGGGTAAAATGATCGAACTA
1 CCCCCGAAGGGTAAAATGATCAAAATA
* * *
40135296 CCCCCGAAGTGCAAAATGACCAAAATA
1 CCCCCGAAGGGTAAAATGATCAAAATA
40135323 CCCCCGAAGGGTAAAATGATCAAAATA
1 CCCCCGAAGGGTAAAATGATCAAAATA
* * * *
40135350 TCCCCAAATGGTAAAATGACCAAAATA
1 CCCCCGAAGGGTAAAATGATCAAAATA
*
40135377 CCCCCGAAGGGTAAAATGATCGAAATA
1 CCCCCGAAGGGTAAAATGATCAAAATA
40135404 -CCCCGATAGGGTAAAATGA
1 CCCCCGA-AGGGTAAAATGA
40135423 CTGCTATACT
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 6 0.04
27 129 0.96
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.15
Consensus pattern (27 bp):
CCCCCGAAGGGTAAAATGATCAAAATA
Found at i:40135824 original size:30 final size:29
Alignment explanation
Indices: 40135760--40135847 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 29
40135750 GTTGCATTAT
* *
40135760 CACACTGTTATTGTATTA-GGCTAAGGCC-
1 CACACTGTTACTGTA-TAGGGCTAAGCCCA
*
40135788 CACACTGTTACTGTATCGGGCTAAGACCCA
1 CACACTGTTACTGTATAGGGCTAAG-CCCA
*
40135818 CACACTGTTACTGCATAGGGCTCAAGCCCA
1 CACACTGTTACTGTATAGGGCT-AAGCCCA
40135848 GACTGTTACT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.02
28 21 0.41
29 2 0.04
30 24 0.47
31 3 0.06
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (29 bp):
CACACTGTTACTGTATAGGGCTAAGCCCA
Found at i:40135860 original size:28 final size:27
Alignment explanation
Indices: 40135760--40135861 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 27
40135750 GTTGCATTAT
* *
40135760 CACACTGTTATTGTATTA-GGCTAAGGCC
1 CACACTGTTACTGCA-TAGGGCTAA-GCC
* *
40135788 CACACTGTTACTGTATCGGGCTAAGACCC
1 CACACTGTTACTGCATAGGGCTAAG--CC
40135817 ACACACTGTTACTGCATAGGGCTCAAGCC
1 -CACACTGTTACTGCATAGGGCT-AAGCC
*
40135846 CAGACTGTTACTGCAT
1 CACACTGTTACTGCAT
40135862 GTTGTAGGCT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
27 2 0.03
28 35 0.55
29 4 0.06
30 20 0.31
31 3 0.05
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (27 bp):
CACACTGTTACTGCATAGGGCTAAGCC
Found at i:40140117 original size:44 final size:43
Alignment explanation
Indices: 40140026--40140123 Score: 126
Period size: 44 Copynumber: 2.3 Consensus size: 43
40140016 TTTGATATGG
* *
40140026 TCTTTAGCAGCTCTTCTACTAAAAACGCCGCTAAAGAACATGA
1 TCTTTAGCGGCACTTCTACTAAAAACGCCGCTAAAGAACATGA
* * *
40140069 TCTTTAGCGGCACTTCT-CATAGAAAATGCCGCTAAAGATCATGT
1 TCTTTAGCGGCACTTCTAC-TA-AAAACGCCGCTAAAGAACATGA
40140113 TCTTTAGCGGC
1 TCTTTAGCGGC
40140124 GTTTGTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.02
43 17 0.35
44 30 0.62
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (43 bp):
TCTTTAGCGGCACTTCTACTAAAAACGCCGCTAAAGAACATGA
Found at i:40140204 original size:43 final size:41
Alignment explanation
Indices: 40140096--40140204 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 41
40140086 CATAGAAAAT
40140096 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTAAAAAACC
1 GCCGCTAAA-ATCATGTTCTTTAGCGGCGTTTGTAAAAAACC
* * * *
40140138 ACCGCTATAGAAT-ATGATT-TTTAGTGGCGTTTGTAGGAAAAGC
1 GCCGCTA-A-AATCATG-TTCTTTAGCGGCGTTTGTA-AAAAACC
40140181 GCCGCTAAATATCATGTTCTTTAG
1 GCCGCTAAA-ATCATGTTCTTTAG
40140205 ATTTAGCGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
41 1 0.02
42 29 0.53
43 24 0.44
44 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (41 bp):
GCCGCTAAAATCATGTTCTTTAGCGGCGTTTGTAAAAAACC
Found at i:40141110 original size:18 final size:19
Alignment explanation
Indices: 40141068--40141109 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40141058 AAAAATTATA
40141068 TTTTTTAAAATATATAAAT
1 TTTTTTAAAATATATAAAT
**
40141087 GATTTTAAAA-ATAT-AAT
1 TTTTTTAAAATATATAAAT
40141104 TTTTTT
1 TTTTTT
40141110 TCTAGAATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTTTTAAAATATATAAAT
Found at i:40151606 original size:26 final size:26
Alignment explanation
Indices: 40151549--40151612 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 26
40151539 TGTTGAATAC
* * *
40151549 AATTAAAATATGATAACTATTTCAGT
1 AATTAAAATATTACAACTATTTCAAT
* * *
40151575 ATTTAAAATATTACAATTATTTTAAT
1 AATTAAAATATTACAACTATTTCAAT
*
40151601 AATTAAATTATT
1 AATTAAAATATT
40151613 TTTCTAATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (26 bp):
AATTAAAATATTACAACTATTTCAAT
Found at i:40165192 original size:2 final size:2
Alignment explanation
Indices: 40165187--40165226 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
40165177 AATTTTGCTG
40165187 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40165227 TATGTGAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40167891 original size:35 final size:34
Alignment explanation
Indices: 40167852--40167917 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
40167842 GAATACATGC
*
40167852 ACATATATATGTTTTTCATAT-TTTTATTATTTTAT
1 ACATATATATGTTTAT-ATATCTTTTA-TATTTTAT
*
40167887 ACATATTTATGTTTATATATCTTTTATATTT
1 ACATATATATGTTTATATATCTTTTATATTT
40167918 GTATCATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 9 0.32
35 19 0.68
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (34 bp):
ACATATATATGTTTATATATCTTTTATATTTTAT
Found at i:40173436 original size:23 final size:23
Alignment explanation
Indices: 40173404--40173515 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
40173394 CTTTTTGAAC
* *
40173404 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
40173427 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
40173450 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
40173473 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
40173496 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
40173516 CCCAAAACTG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:40173480 original size:46 final size:46
Alignment explanation
Indices: 40173404--40173515 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
40173394 CTTTTTGAAC
* *
40173404 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
40173450 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
40173496 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
40173516 CCCAAAACTG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:40181927 original size:208 final size:208
Alignment explanation
Indices: 40181569--40181982 Score: 731
Period size: 208 Copynumber: 2.0 Consensus size: 208
40181559 CCTTGTCTCT
* * *
40181569 CTGAAGTTGTAGTAGAGCAGGTTGAAGTTACAAGTCTTATTTCCCTGAAGATGCAGTGGAGTAGA
1 CTGAAGTTGCAGTAGAGCAGGTCGAAGATACAAGTCTTATTTCCCTGAAGATGCAGTGGAGTAGA
*
40181634 CTAAAAACAACAAGTCATGTCTTCCTAAAGTTGTAGTGGAGCAAACAGTAGATAGCGGTTCTTAC
66 CTAAAAACAACAAGTCATGTCTCCCTAAAGTTGTAGTGGAGCAAACAGTAGATAGCGGTTCTTAC
*
40181699 CATGTCGAATCTTATTTCCCTGAAGTTGCAGCGGATTAGGTTGAAGCATGGAGCAGATCGGCTAC
131 CATGTCGAATCTTATTTCCCTGAAGTTACAGCGGATTAGGTTGAAGCATGGAGCAGATCGGCTAC
*
40181764 GAATCCTATTTCC
196 GAATCATATTTCC
* *
40181777 CTGAAGTTGCAGT-GTAGTAGGTCGAAGATACAAGTGTTATTTCCCTGAAGATGCAGTGGAGTAG
1 CTGAAGTTGCAGTAG-AGCAGGTCGAAGATACAAGTCTTATTTCCCTGAAGATGCAGTGGAGTAG
40181841 ACTAAAAACAACAAGTCATGTCTCCCTAAAGTTGTAGTGGAGCAAACAGTAGATAGCGGTTCTTA
65 ACTAAAAACAACAAGTCATGTCTCCCTAAAGTTGTAGTGGAGCAAACAGTAGATAGCGGTTCTTA
*
40181906 TCATGTCGAATCTTATTTCCCTGAAGTTACAGCGGATTAGGTTGAAGCATGGAGCAGATCGGCTA
130 CCATGTCGAATCTTATTTCCCTGAAGTTACAGCGGATTAGGTTGAAGCATGGAGCAGATCGGCTA
40181971 CGAATCATATTT
195 CGAATCATATTT
40181983 ATTTCCCTGA
Statistics
Matches: 196, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
207 1 0.01
208 195 0.99
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (208 bp):
CTGAAGTTGCAGTAGAGCAGGTCGAAGATACAAGTCTTATTTCCCTGAAGATGCAGTGGAGTAGA
CTAAAAACAACAAGTCATGTCTCCCTAAAGTTGTAGTGGAGCAAACAGTAGATAGCGGTTCTTAC
CATGTCGAATCTTATTTCCCTGAAGTTACAGCGGATTAGGTTGAAGCATGGAGCAGATCGGCTAC
GAATCATATTTCC
Found at i:40186399 original size:12 final size:12
Alignment explanation
Indices: 40186382--40186418 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
40186372 AAAGTGCCGG
40186382 AAATAATAAAAT
1 AAATAATAAAAT
40186394 AAATAATAAAAT
1 AAATAATAAAAT
40186406 AATGATAATAAAA
1 AA--ATAATAAAA
40186419 AATAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.61
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:40186417 original size:21 final size:20
Alignment explanation
Indices: 40186382--40186428 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
40186372 AAAGTGCCGG
*
40186382 AAATAATAAAATAAATAATA
1 AAATAATAAAATAAAAAATA
*
40186402 AAATAATGATAATAAAAAATA
1 AAATAAT-AAAATAAAAAATA
40186423 AAATAA
1 AAATAA
40186429 GTAGGCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAATAATAAAATAAAAAATA
Found at i:40187119 original size:94 final size:95
Alignment explanation
Indices: 40186960--40187224 Score: 352
Period size: 94 Copynumber: 2.8 Consensus size: 95
40186950 TTGCTCTATT
* * * ** *
40186960 GCAACTTTAGAGAGATAAGATTCGCTTTGGTAGATTCTATTTGACCCACTACAACTTTAGAGGTA
1 GCAACTTTAGGGAGATAAGATTCGCTATGGTAGATTCAATCCGACCCACTACAACTTCAGAGGTA
*
40187025 TAGGATTTGTAACTTCAATC-TGCTCCACC
66 TAGGATTTGTAACTTCAATCTTACTCCACC
* * * * *
40187054 GCAACTTTAGGGAGATAACATTTGCTATGGTAGATTCAATCCAACCCACTGCAACTTCAGGGGTA
1 GCAACTTTAGGGAGATAAGATTCGCTATGGTAGATTCAATCCGACCCACTACAACTTCAGAGGTA
* *
40187119 TAGGATTTGTAGCTTCAATCTTACTCCACT
66 TAGGATTTGTAACTTCAATCTTACTCCACC
* * * * *
40187149 GTAACTTTAGGGAGATAAGACTCGCTATGGTAGATTCAATCCGACGCACTACAACTACAAAGGTA
1 GCAACTTTAGGGAGATAAGATTCGCTATGGTAGATTCAATCCGACCCACTACAACTTCAGAGGTA
40187214 TAGGATTTGTA
66 TAGGATTTGTA
40187225 GTTTCACCCA
Statistics
Matches: 146, Mismatches: 24, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
94 73 0.50
95 73 0.50
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (95 bp):
GCAACTTTAGGGAGATAAGATTCGCTATGGTAGATTCAATCCGACCCACTACAACTTCAGAGGTA
TAGGATTTGTAACTTCAATCTTACTCCACC
Found at i:40187186 original size:95 final size:94
Alignment explanation
Indices: 40186960--40187230 Score: 353
Period size: 95 Copynumber: 2.9 Consensus size: 94
40186950 TTGCTCTATT
* * * ** *
40186960 GCAACTTTAGAGAGATAAGATTCGCTTTGGTAGATTCTATTTGACCCACTACAACTTTAGAGGTA
1 GCAACTTTAGGGAGATAAGATTCGCTATGGTAGATTCAATCCGACCCACTACAACTTCAGAGGTA
* *
40187025 TAGGATTTGTAACTTCAATCTGCTCCACC
66 TAGGATTTGTAGCTTCAATCTACTCCACC
* * * * *
40187054 GCAACTTTAGGGAGATAACATTTGCTATGGTAGATTCAATCCAACCCACTGCAACTTCAGGGGTA
1 GCAACTTTAGGGAGATAAGATTCGCTATGGTAGATTCAATCCGACCCACTACAACTTCAGAGGTA
*
40187119 TAGGATTTGTAGCTTCAATCTTACTCCACT
66 TAGGATTTGTAGCTTCAATC-TACTCCACC
* * * * *
40187149 GTAACTTTAGGGAGATAAGACTCGCTATGGTAGATTCAATCCGACGCACTACAACTACAAAGGTA
1 GCAACTTTAGGGAGATAAGATTCGCTATGGTAGATTCAATCCGACCCACTACAACTTCAGAGGTA
*
40187214 TAGGATTTGTAGTTTCA
66 TAGGATTTGTAGCTTCA
40187231 CCCATTTATT
Statistics
Matches: 151, Mismatches: 25, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
94 73 0.48
95 78 0.52
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (94 bp):
GCAACTTTAGGGAGATAAGATTCGCTATGGTAGATTCAATCCGACCCACTACAACTTCAGAGGTA
TAGGATTTGTAGCTTCAATCTACTCCACC
Found at i:40194474 original size:28 final size:28
Alignment explanation
Indices: 40194385--40194633 Score: 156
Period size: 27 Copynumber: 9.1 Consensus size: 28
40194375 TACCCTATAT
* * * *
40194385 GGGTATGTCGGTAA-TTCTACAAATTAA
1 GGGTATTTCGATAATTTTTACAAATTGA
* * *
40194412 GGGTATTTTGATAA-TTTCACAAATTAA
1 GGGTATTTCGATAATTTTTACAAATTGA
* *
40194439 GGGTATTTCGATAATTTTTACATATTGG
1 GGGTATTTCGATAATTTTTACAAATTGA
* * * *
40194467 GGGTATTTTGGTAATTTTGA-AAATTAA
1 GGGTATTTCGATAATTTTTACAAATTGA
* * ** *
40194494 AGGTATTTCAATAATTTTTGTAAATCGA
1 GGGTATTTCGATAATTTTTACAAATTGA
*
40194522 GGGTATTTTGATAATTTTT-CAAATTGA
1 GGGTATTTCGATAATTTTTACAAATTGA
**
40194549 GGGTATTTC-AGTAA-TTTTACAAA-CCA
1 GGGTATTTCGA-TAATTTTTACAAATTGA
* * ** *
40194575 GGGGTTTTTAG-TAATTTTTGTAAATTGG
1 -GGGTATTTCGATAATTTTTACAAATTGA
**
40194603 GGGTATTTC-AGTAATTTTTGTAAATTGA
1 GGGTATTTCGA-TAATTTTTACAAATTGA
40194631 GGG
1 GGG
40194634 ACTTGGCGAC
Statistics
Matches: 170, Mismatches: 42, Indels: 19
0.74 0.18 0.08
Matches are distributed among these distances:
26 9 0.05
27 95 0.56
28 66 0.39
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.43
Consensus pattern (28 bp):
GGGTATTTCGATAATTTTTACAAATTGA
Found at i:40194481 original size:82 final size:82
Alignment explanation
Indices: 40194385--40194571 Score: 207
Period size: 82 Copynumber: 2.3 Consensus size: 82
40194375 TACCCTATAT
* * * ** *
40194385 GGGTATGTCGGTAATTCTACAAATTAAGGGTATTTTGATAA-TTTCACAAATTAAGGGTATTTCG
1 GGGTATTTCGGTAATTTTACAAATTAAAGGTATTTCAATAATTTTCACAAATCAAGGGTATTTCG
* *
40194449 ATAATTTTTACATATTGG
66 ATAATTTTT-CAAATTGA
* *** * *
40194467 GGGTATTTTGGTAATTTTGA-AAATTAAAGGTATTTCAATAATTTTTGTAAATCGAGGGTATTTT
1 GGGTATTTCGGTAATTTT-ACAAATTAAAGGTATTTCAATAATTTTCACAAATCAAGGGTATTTC
40194531 GATAATTTTTCAAATTGA
65 GATAATTTTTCAAATTGA
*
40194549 GGGTATTTCAGTAATTTTACAAA
1 GGGTATTTCGGTAATTTTACAAA
40194572 CCAGGGGTTT
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
81 1 0.01
82 58 0.67
83 27 0.31
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (82 bp):
GGGTATTTCGGTAATTTTACAAATTAAAGGTATTTCAATAATTTTCACAAATCAAGGGTATTTCG
ATAATTTTTCAAATTGA
Found at i:40194482 original size:55 final size:54
Alignment explanation
Indices: 40194402--40194571 Score: 173
Period size: 55 Copynumber: 3.1 Consensus size: 54
40194392 TCGGTAATTC
**
40194402 TACAAATTAAGGGTATTTTGATAATTTCACAAATTAAGGGTATTTCGATAATTTT
1 TACAAATCGAGGGTATTTTGATAATTTCACAAATTAAGGGTATTTC-ATAATTTT
* * * * * *
40194457 TACATATTGGGGGTATTTTGGTAATTTTGA-AAATTAAAGGTATTTCAATAATTTT
1 TACAAATCGAGGGTATTTTGATAA-TTTCACAAATTAAGGGTATTTC-ATAATTTT
** ** *
40194512 TGTAAATCGAGGGTATTTTGATAATTTTTCAAATTGAGGGTATTTCAGTAA-TTT
1 TACAAATCGAGGGTATTTTGATAATTTCACAAATTAAGGGTATTTCA-TAATTTT
40194566 TACAAA
1 TACAAA
40194572 CCAGGGGTTT
Statistics
Matches: 93, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
54 11 0.12
55 78 0.84
56 4 0.04
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (54 bp):
TACAAATCGAGGGTATTTTGATAATTTCACAAATTAAGGGTATTTCATAATTTT
Found at i:40198681 original size:20 final size:21
Alignment explanation
Indices: 40198658--40198699 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
40198648 ACTTTTATTA
*
40198658 GTTTTTGTTTT-TTTTTTTTG
1 GTTTTTGTTTTATTTGTTTTG
40198678 GTTTTTGTTTTATTTGTTTTG
1 GTTTTTGTTTTATTTGTTTTG
40198699 G
1 G
40198700 GGGGAATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.02, C:0.00, G:0.19, T:0.79
Consensus pattern (21 bp):
GTTTTTGTTTTATTTGTTTTG
Found at i:40198683 original size:15 final size:15
Alignment explanation
Indices: 40198661--40198697 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
40198651 TTTATTAGTT
40198661 TTTGTTTTT-TTTT-
1 TTTGTTTTTGTTTTA
40198674 TTTGGTTTTTGTTTTA
1 TTT-GTTTTTGTTTTA
40198690 TTTGTTTT
1 TTTGTTTT
40198698 GGGGGGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.14
14 6 0.29
15 9 0.43
16 3 0.14
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.84
Consensus pattern (15 bp):
TTTGTTTTTGTTTTA
Found at i:40198826 original size:3 final size:3
Alignment explanation
Indices: 40198818--40198845 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40198808 TTAATATCAA
40198818 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40198846 TGGTATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40201369 original size:26 final size:26
Alignment explanation
Indices: 40201323--40201386 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
40201313 TGTTGATTAC
* * *
40201323 AATTAAAATATGATAACTATTTCAGT
1 AATTAAAATATTACAACTATTTCAAT
* *
40201349 AATTAAAATATTACAATTATTTTAAT
1 AATTAAAATATTACAACTATTTCAAT
*
40201375 AATTAAATTATT
1 AATTAAAATATT
40201387 TTTCTAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (26 bp):
AATTAAAATATTACAACTATTTCAAT
Found at i:40205280 original size:31 final size:31
Alignment explanation
Indices: 40205242--40205300 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
40205232 AATTGGGCTT
*
40205242 TTACAATTATAATCTACTTTGAATATTTATC
1 TTACAATTATAATCTACCTTGAATATTTATC
40205273 TTACAATTATAATCTACCTTGAATATTT
1 TTACAATTATAATCTACCTTGAATATTT
40205301 CTTATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (31 bp):
TTACAATTATAATCTACCTTGAATATTTATC
Found at i:40205312 original size:3 final size:3
Alignment explanation
Indices: 40205304--40205339 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
40205294 AATATTTCTT
40205304 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40205340 TGGTATCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40205313 original size:29 final size:31
Alignment explanation
Indices: 40205242--40205314 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
40205232 AATTGGGCTT
* *
40205242 TTACAATTATAATCTACTTTGAATATTTATC
1 TTACAATAATAATCTACCTTGAATATTTATC
*
40205273 TTACAATTATAATCTACCTTGAATA-TT-TC
1 TTACAATAATAATCTACCTTGAATATTTATC
*
40205302 TTATAATAATAAT
1 TTACAATAATAAT
40205315 AATAATAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 13 0.33
30 2 0.05
31 24 0.62
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (31 bp):
TTACAATAATAATCTACCTTGAATATTTATC
Found at i:40206535 original size:3 final size:3
Alignment explanation
Indices: 40206527--40206554 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40206517 TTAATATCAA
40206527 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40206555 TGGTATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40209339 original size:11 final size:11
Alignment explanation
Indices: 40209318--40209352 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40209308 TATAACAGTA
40209318 AATAAATAAAT
1 AATAAATAAAT
* *
40209329 AGTACATAAAT
1 AATAAATAAAT
40209340 AATAAATAAAT
1 AATAAATAAAT
40209351 AA
1 AA
40209353 ATGATGAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:40209565 original size:54 final size:52
Alignment explanation
Indices: 40209490--40209591 Score: 118
Period size: 54 Copynumber: 1.9 Consensus size: 52
40209480 AAAATAATAT
* *
40209490 ATAAAAAATTTTAAAAGATATTATA-TACAAGATATTTTAAAACAAATAATGTAA
1 ATAAAAAATTTCAAAAGATATTA-AGTA-AA-ACATTTTAAAACAAATAATGTAA
* *
40209544 ATAAAAAATTTCAGTAA-ATATTAAGTAAAACATTTTAAAATAAATAAT
1 ATAAAAAATTTCA-AAAGATATTAAGTAAAACATTTTAAAACAAATAAT
40209592 ATGTTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
52 17 0.40
53 3 0.07
54 20 0.48
55 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (52 bp):
ATAAAAAATTTCAAAAGATATTAAGTAAAACATTTTAAAACAAATAATGTAA
Found at i:40210848 original size:30 final size:30
Alignment explanation
Indices: 40210800--40210856 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
40210790 GGCTGTTGGG
40210800 TTTGGATTTAGTTATGTTTGGGTTTTAATT
1 TTTGGATTTAGTTATGTTTGGGTTTTAATT
* * *
40210830 TTTGTATTTGGTTTTGTTTGGGTTTTA
1 TTTGGATTTAGTTATGTTTGGGTTTTA
40210857 TTGGACCTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.63
Consensus pattern (30 bp):
TTTGGATTTAGTTATGTTTGGGTTTTAATT
Found at i:40211091 original size:44 final size:44
Alignment explanation
Indices: 40211033--40211287 Score: 178
Period size: 44 Copynumber: 5.8 Consensus size: 44
40211023 CGTCTTGTTG
** * *
40211033 CTTCAATCCACTCCACTGTAACTTCAGAGAGATACGACTTGTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAT
* * * *
40211077 CTTCAATCTGCTCCACTGCAATTTCAGGGAGATATGA-TTCGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTT-GTAT
* * ** * * **
40211121 CTTTAACCTATTCCACTGCAACTTTAGGGAGATAAGGTTTG-AT
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAT
* * ** * * *
40211164 -GT-GATCTGCTCTTCTGCAACTTCAAAGAGATAAGATTTACTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTT-GTAT
* * * **
40211207 CTTCAGTCTGC-CTCACTGCAACTTCAGGGAGATAAGACTAGTGG
1 CTTCAATCTGCTC-CACTGCAACTTCAGAGAGATAAGACTTGTAT
* *
40211251 CTTCAATATGCTCCACTGCAACTTCAGAAAGATAAGA
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGA
40211288 TTCGCAATAA
Statistics
Matches: 159, Mismatches: 44, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
41 26 0.16
42 1 0.01
43 5 0.03
44 98 0.62
45 29 0.18
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAT
Found at i:40211416 original size:44 final size:44
Alignment explanation
Indices: 40211304--40211715 Score: 169
Period size: 44 Copynumber: 8.8 Consensus size: 44
40211294 ATAATTTGTA
* * * * ** *
40211304 GCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTCGCTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCT-GGTG
* * * ** * *
40211349 TCTTCAGTCTACTCTGCTACAACTTTAGGGAGATAAGGCTGGTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTG
* * *
40211393 GCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGACATAATTTGTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG----G-C-----TGGTG
* ** ** * * ** *
40211447 GCTTTAATCTATTCCACTGCAACGCCAGGAAAATAAGATTCGCTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCT-GGTG
* * * *
40211492 TCTTCAGTCTGCTCCACTACAACTTTAGGGAGATAAGGCTGGTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTG
* * * *
40211536 GCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCACCATAAATTGTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG-----GC-----TGGTG
* * ** * * ** **
40211590 GCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCACTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCT-GGTG
* * *
40211635 TCTTCAGTCTGCT-CAGCTGCAACTTCAGGGGGATAAGGCTGGTG
1 GCTTCAATCTGCTCCA-CTGCAACTTCAGGGAGATAAGGCTGGTG
40211679 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
40211716 ATCTGCCATA
Statistics
Matches: 258, Mismatches: 85, Indels: 49
0.66 0.22 0.12
Matches are distributed among these distances:
44 104 0.40
45 84 0.33
48 1 0.00
49 2 0.01
54 67 0.26
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (44 bp):
GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTG
Found at i:40211426 original size:143 final size:143
Alignment explanation
Indices: 40211206--40211870 Score: 958
Period size: 143 Copynumber: 4.7 Consensus size: 143
40211196 AGATTTACTA
* * * * *
40211206 TCTTCAGTCTGC-CTCACTGCAACTTCAGGGAGATAAGACTAGTGGCTTCAATATGCTCCACTGC
1 TCTTCAGTCTGCTCT-GCTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGC
* * * *
40211270 AACTTCAGAAAGATAAGATTCGCAATAATTTGTAGCTTTAATCTGTTCCACTGCAACGTCAGGGA
65 AACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGGGA
40211335 AATAAGATTCGCTG
130 AATAAGATTCGCTG
* *
40211349 TCTTCAGTCTACTCTGCTACAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCA
1 TCTTCAGTCTGCTCTGCTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCA
* *
40211414 ACTTCAGGAAGATAAGA-TCTGACATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGGAA
66 ACTTCAGGAAGATAAGATTC-GCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGGGA
40211478 AATAAGATTCGCTG
130 AATAAGATTCGCTG
** *
40211492 TCTTCAGTCTGCTCCACTACAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCA
1 TCTTCAGTCTGCTCTGCTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCA
* * * * *
40211557 ACTTCAGGAAGATAAGATCCACCATAAATTGTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAA
66 ACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGGGAA
*
40211622 ATAAGATTCACTG
131 ATAAGATTCGCTG
* * *
40211635 TCTTCAGTCTGCTCAGCTGCAACTTCAGGGGGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCA
1 TCTTCAGTCTGCTCTGCTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCA
* * *
40211700 ACTTCAGGGAGATAAGA-TCTGCCATAATTTGTAGCTTTAATCTATTCCACTACAACGCCGGGGA
66 ACTTCAGGAAGATAAGATTC-GCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGGGA
*
40211764 AATAAGATTCGTTG
130 AATAAGATTCGCTG
* * ** * *
40211778 TTTTCAGTCTGCTCTGCTGCAACTTCAGAAAGATAAGGCTGGTGGCTTTAATCTGCTCCGCTGCA
1 TCTTCAGTCTGCTCTGCTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCA
*
40211843 ACTTCAGGAAGAGAAGATTCGCCATAAT
66 ACTTCAGGAAGATAAGATTCGCCATAAT
40211871 GACTTCAATC
Statistics
Matches: 469, Mismatches: 48, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
142 3 0.01
143 461 0.98
144 5 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (143 bp):
TCTTCAGTCTGCTCTGCTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCA
ACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGGGAA
ATAAGATTCGCTG
Found at i:40218199 original size:8 final size:8
Alignment explanation
Indices: 40218186--40218224 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
40218176 ACCAAATAAG
40218186 AAAAAATA
1 AAAAAATA
40218194 AAAAAATA
1 AAAAAATA
**
40218202 ACCAAATCA
1 AAAAAAT-A
40218211 AAAAAATA
1 AAAAAATA
40218219 AAAAAA
1 AAAAAA
40218225 ATAACCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:40218227 original size:9 final size:9
Alignment explanation
Indices: 40218179--40218228 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
40218169 GAATAATACC
40218179 AAATAAGAAA
1 AAATAA-AAA
40218189 AAAT-AAAA
1 AAATAAAAA
**
40218197 AAAT-AACC
1 AAATAAAAA
*
40218205 AAATCAAAA
1 AAATAAAAA
40218214 AAATAAAAA
1 AAATAAAAA
40218223 AAATAA
1 AAATAA
40218229 CCAAATCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
8 13 0.38
9 17 0.50
10 4 0.12
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.12
Consensus pattern (9 bp):
AAATAAAAA
Found at i:40218235 original size:26 final size:25
Alignment explanation
Indices: 40218176--40218237 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 25
40218166 AATGAATAAT
*
40218176 ACCAAATAAGAAAAAATAAAAAAATA
1 ACCAAATCA-AAAAAATAAAAAAATA
40218202 ACCAAATCAAAAAAATAAAAAAAATA
1 ACCAAATCAAAAAAAT-AAAAAAATA
40218228 ACCAAATCAA
1 ACCAAATCAA
40218238 TCAAAATCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 7 0.21
26 27 0.79
ACGTcount: A:0.74, C:0.13, G:0.02, T:0.11
Consensus pattern (25 bp):
ACCAAATCAAAAAAATAAAAAAATA
Found at i:40221565 original size:113 final size:111
Alignment explanation
Indices: 40221294--40221622 Score: 360
Period size: 113 Copynumber: 2.9 Consensus size: 111
40221284 AAAATAAGCA
* * * * *
40221294 TTAGCGGCGTTTTCGAGAAAGCACCGCAAAACACCTAATCCCAACGACGCCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTAGACAAAGCGCCACAAAA-ACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* *
40221359 CGGGGAATTAGCGGCGTTTTTTT-TGAAGCGACGCTAATACCCAGGAC
65 CGGGGATTTAGCGGCGTTTTTTTGT-AAGCGCCGCTAATACCCAGGAC
* * * * *
40221406 TTAGCGGAGTTTTCAG-CAAAGCGCCACAAAAAAAACTGAGCCCAACGATGTCGTTTTC-GAGCT
1 TTAGCGGCGTTTT-AGACAAAGCGCCAC--AAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
** * * *
40221469 TTCGGGGATTTAGCGGCGTTTTTCAAGTAAGCGCCGCTAATATCTAGGGC
63 TTCGGGGATTTAGCGGCGTTTTT-TTGTAAGCGCCGCTAATACCCAGGAC
* *
40221519 TTTAGCGGCGTTTTAGATAAAGCGCCACAAATAACCTAAGCACAACGACGCCGTTTTCTGAGCTT
1 -TTAGCGGCGTTTTAGACAAAGCGCCACAAA-AACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
40221584 TC-AGGATTTAGTGGCGTTTTTTTGTAAAGCGCCGCTAAT
64 TCGGGGATTTAGCGGCGTTTTTTTGT-AAGCGCCGCTAAT
40221623 GCTCAGTAAT
Statistics
Matches: 179, Mismatches: 28, Indels: 19
0.79 0.12 0.08
Matches are distributed among these distances:
112 52 0.29
113 92 0.51
114 35 0.20
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (111 bp):
TTAGCGGCGTTTTAGACAAAGCGCCACAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTC
GGGGATTTAGCGGCGTTTTTTTGTAAGCGCCGCTAATACCCAGGAC
Found at i:40223683 original size:445 final size:445
Alignment explanation
Indices: 40222854--40223760 Score: 1697
Period size: 445 Copynumber: 2.0 Consensus size: 445
40222844 TATTTTTATA
* *
40222854 AAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTGGCGTTTCCAATTAAACGCCGCAAAAAG
1 AAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTGGCATTTCCAATTAAACACCGCAAAAAG
40222919 TTTGACATTACCGGCGTTTTTATAAAAAGCGCCACAAATATTTATTGCATTTACCGATACGTCGT
66 TTTGACATTACCGGCGTTTTTATAAAAAGCGCCACAAATATTTATTGCATTTACCGATACGTCGT
*
40222984 CGTTTCGACTGAGGGGATAAATTTATCTTGTGGCGTTTTTCCTTAAAGCGCCGTAAAGATATGAA
131 CGTTTCGACTGAGGGGATAAATTTATCTTGTGGCATTTTTCCTTAAAGCGCCGTAAAGATATGAA
40223049 GTACTCTGCGAAAACGACGCTGTTTTAGTTGAAGGATAGAATCTTTTAGTGGCGTTTTATTAAAA
196 GTACTCTGCGAAAACGACGCTGTTTTAGTTGAAGGATAGAATCTTTTAGTGGCGTTTTATTAAAA
* *
40223114 ACGCCGCAAATATGTATAAAATTTTGTGAAAACAACGCTGGTTCGATAATATATTGATTGTGGCG
261 ACGCCGCAAATATGTATAAAATTTTGTGAAAACAACGCCGATTCGATAATATATTGATTGTGGCG
*
40223179 TGTTTGGGAAAACGCCAGGTTTTCTTGTATTTTTATAAAACGGCGCCGTTTCCATTAATGACTTG
326 TGTTTGGGAAAACACCAGGTTTTCTTGTATTTTTATAAAACGGCGCCGTTTCCATTAATGACTTG
* *
40223244 AAATTTTAGTGGCGTTTTTAACTAAAACGCCGCAACTCTGACTTAAAATTACTTT
391 AAATTTTAGTGGCGTTTTTAACTAAAACGCCACAACTCTGACTTAAAATTACGTT
* *
40223299 AAACGGCGCCATTTCTTTCTGTACTTGAAATTTTAGTGGCATTTCCAATTAAACACCGTAAAAAG
1 AAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTGGCATTTCCAATTAAACACCGCAAAAAG
40223364 TTTGACATTACCGGCGTTTTTATAAAAAGCGCCACAAATATTTATTGCATTTACCGATACGTCGT
66 TTTGACATTACCGGCGTTTTTATAAAAAGCGCCACAAATATTTATTGCATTTACCGATACGTCGT
40223429 CGTTTCGACTGAGGGGATAAATTTATCTTGTGGCATTTTTCCTTAAAGCGCCGTAAAGATATGAA
131 CGTTTCGACTGAGGGGATAAATTTATCTTGTGGCATTTTTCCTTAAAGCGCCGTAAAGATATGAA
*
40223494 GTACTCTGCGAAAACGACGCTGTTTTAGTTGAAGGATGGAATCTTTTAGTGGCGTTTTATTAAAA
196 GTACTCTGCGAAAACGACGCTGTTTTAGTTGAAGGATAGAATCTTTTAGTGGCGTTTTATTAAAA
* *
40223559 ACGTCGCAAATATGTATAAAATTTTGTGAAAACGACGCCGATTCGATAATATATTGATTGTGGCG
261 ACGCCGCAAATATGTATAAAATTTTGTGAAAACAACGCCGATTCGATAATATATTGATTGTGGCG
40223624 TGTTTGGGAAAACACCAGGTTTTCTTGTATTTTTATAAAACGGCGCCGTTTCCATTAATGACTTG
326 TGTTTGGGAAAACACCAGGTTTTCTTGTATTTTTATAAAACGGCGCCGTTTCCATTAATGACTTG
40223689 AAATTTTAGTGGCGTTTTTAACTAAAACGCCACAACTCTGACTTAAAATTACGTT
391 AAATTTTAGTGGCGTTTTTAACTAAAACGCCACAACTCTGACTTAAAATTACGTT
40223744 AAACGGCGCCGTTTCTT
1 AAACGGCGCCGTTTCTT
40223761 AGGAGGACAT
Statistics
Matches: 448, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
445 448 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (445 bp):
AAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTGGCATTTCCAATTAAACACCGCAAAAAG
TTTGACATTACCGGCGTTTTTATAAAAAGCGCCACAAATATTTATTGCATTTACCGATACGTCGT
CGTTTCGACTGAGGGGATAAATTTATCTTGTGGCATTTTTCCTTAAAGCGCCGTAAAGATATGAA
GTACTCTGCGAAAACGACGCTGTTTTAGTTGAAGGATAGAATCTTTTAGTGGCGTTTTATTAAAA
ACGCCGCAAATATGTATAAAATTTTGTGAAAACAACGCCGATTCGATAATATATTGATTGTGGCG
TGTTTGGGAAAACACCAGGTTTTCTTGTATTTTTATAAAACGGCGCCGTTTCCATTAATGACTTG
AAATTTTAGTGGCGTTTTTAACTAAAACGCCACAACTCTGACTTAAAATTACGTT
Found at i:40225407 original size:28 final size:27
Alignment explanation
Indices: 40225375--40225432 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
40225365 TTACGTAAAG
* *
40225375 TAAATTAAATAATTTACATAAACTTGCA
1 TAAATTAAATAACTTACA-AAACTTACA
40225403 TAAATTAAATAACTTACAAAACTTACA
1 TAAATTAAATAACTTACAAAACTTACA
40225430 TAA
1 TAA
40225433 CCTACATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAATTAAATAACTTACAAAACTTACA
Found at i:40225432 original size:18 final size:18
Alignment explanation
Indices: 40225383--40225444 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
40225373 AGTAAATTAA
* *
40225383 ATAATTTACATAAACTTGC
1 ATAAATTACAT-AACTTAC
*
40225402 ATAAATTAAATAACTTAC
1 ATAAATTACATAACTTAC
*
40225420 A-AAACTTACATAACCTAC
1 ATAAA-TTACATAACTTAC
40225438 ATAAATT
1 ATAAATT
40225445 NNNNNNNNNN
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 3 0.08
18 21 0.58
19 12 0.33
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAAATTACATAACTTAC
Found at i:40225438 original size:9 final size:9
Alignment explanation
Indices: 40225383--40225441 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
40225373 AGTAAATTAA
*
40225383 ATAATTTAC
1 ATAACTTAC
*
40225392 ATAAACTTGC
1 AT-AACTTAC
* *
40225402 ATAAATTAA
1 ATAACTTAC
40225411 ATAACTTAC
1 ATAACTTAC
*
40225420 AAAACTTAC
1 ATAACTTAC
*
40225429 ATAACCTAC
1 ATAACTTAC
40225438 ATAA
1 ATAA
40225442 ATTNNNNNNN
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
9 32 0.82
10 7 0.18
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:40225441 original size:27 final size:28
Alignment explanation
Indices: 40225375--40225441 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
40225365 TTACGTAAAG
* * *
40225375 TAAATTAAATAATTTACATAAACTTGCA
1 TAAACTAAATAACTTACATAAACTTACA
*
40225403 TAAATTAAATAACTTACA-AAACTTACA
1 TAAACTAAATAACTTACATAAACTTACA
* *
40225430 TAACCTACATAA
1 TAAACTAAATAA
40225442 ATTNNNNNNN
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 17 0.50
28 17 0.50
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.31
Consensus pattern (28 bp):
TAAACTAAATAACTTACATAAACTTACA
Found at i:40232678 original size:21 final size:21
Alignment explanation
Indices: 40232664--40232721 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
40232654 GCAGAGGCGA
*
40232664 CAGCGCGAGAAGCAGAAGCTG
1 CAGCGAGAGAAGCAGAAGCTG
40232685 CAGCGAGAGAAGCAGAAGCTG
1 CAGCGAGAGAAGCAGAAGCTG
*
40232706 CAGCAAGAGAAGCAGA
1 CAGCGAGAGAAGCAGA
40232722 GCAGGCCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.40, C:0.21, G:0.36, T:0.03
Consensus pattern (21 bp):
CAGCGAGAGAAGCAGAAGCTG
Found at i:40233143 original size:42 final size:43
Alignment explanation
Indices: 40233042--40233160 Score: 168
Period size: 42 Copynumber: 2.8 Consensus size: 43
40233032 TTTTGTATAA
* *
40233042 AAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTTTTT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGAGGCG-TTTTTCTTCT
* * * *
40233086 AAGCGCCACTGAAGAACATGATCTTTAGCGGC-TTTTTCTTCT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTCTTCT
40233128 AAGCGCCGCTAAAGAACATGGTCTTTAGAGGCG
1 AAGCGCCGCTAAAGAACATGGTCTTTAGAGGCG
40233161 NNNNNNNNNN
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 36 0.56
44 28 0.44
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTCTTCT
Found at i:40233391 original size:22 final size:22
Alignment explanation
Indices: 40233360--40233403 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40233350 TAGTGGCGTT
* * *
40233360 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCACTAAAGACCTA
40233382 AAAAAACGCCACTAAAGACCTA
1 AAAAAACGCCACTAAAGACCTA
40233404 TTTTGGTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCACTAAAGACCTA
Found at i:40235119 original size:22 final size:21
Alignment explanation
Indices: 40235097--40235136 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40235087 ACCTTTTTTA
40235097 AAGGTAAAAGCCAAAACTATT
1 AAGGTAAAAGCCAAAACTATT
* * *
40235118 AAGTTATAAGGCAAAACTA
1 AAGGTAAAAGCCAAAACTA
40235137 CGTTATATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.20
Consensus pattern (21 bp):
AAGGTAAAAGCCAAAACTATT
Found at i:40237990 original size:12 final size:12
Alignment explanation
Indices: 40237973--40237998 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40237963 CTTCATCATA
40237973 AATCGAAATTAT
1 AATCGAAATTAT
40237985 AATCGAAATTAT
1 AATCGAAATTAT
40237997 AA
1 AA
40237999 ATATTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (12 bp):
AATCGAAATTAT
Found at i:40238599 original size:41 final size:41
Alignment explanation
Indices: 40238542--40238880 Score: 572
Period size: 41 Copynumber: 8.3 Consensus size: 41
40238532 TAATTTCTAA
40238542 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
1 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
40238583 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
1 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
40238624 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
1 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
40238665 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTA-CTGGCGTTT
1 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGC-GGCGTTT
* * * *
40238706 TTGAAGCAGCGCTGCTAATGCTCAGGGCTTTAGCGGCATTT
1 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
* *
40238747 TTGAAGAACCGCCGCTAATGCTCGGGGCTTTAGCGACGTTT
1 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
* *
40238788 TTGAAGAAGCGCCGCTAATGGTCGGGGCTTTAGTGGCGTTT
1 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
*
40238829 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCATTT
1 TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
*
40238870 TTTAAGAAGCG
1 TTGAAGAAGCG
40238881 TCACTTTTAG
Statistics
Matches: 278, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
40 1 0.00
41 276 0.99
42 1 0.00
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28
Consensus pattern (41 bp):
TTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTT
Found at i:40239081 original size:21 final size:21
Alignment explanation
Indices: 40239041--40239117 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
40239031 GATTTATCAC
* *
40239041 TATAGTTTAAGGTTTTTGGTT
1 TATAGTTTAAGGTATATGGTT
* * *
40239062 TTTGGTTTAGGGTATATGGTT
1 TATAGTTTAAGGTATATGGTT
* *
40239083 TATAGTTTAAGGTATAGGGGT
1 TATAGTTTAAGGTATATGGTT
*
40239104 TACTATTTTAAGGT
1 TA-TAGTTTAAGGT
40239118 TTTTACTGAT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
21 34 0.77
22 10 0.23
ACGTcount: A:0.22, C:0.01, G:0.27, T:0.49
Consensus pattern (21 bp):
TATAGTTTAAGGTATATGGTT
Found at i:40240611 original size:10 final size:10
Alignment explanation
Indices: 40240596--40240632 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
40240586 TCTTCTCTGA
40240596 TTCATTGTAC
1 TTCATTGTAC
40240606 TTCATTGTAC
1 TTCATTGTAC
40240616 TTCATTGTAC
1 TTCATTGTAC
40240626 TTCATTG
1 TTCATTG
40240633 AACTGTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (10 bp):
TTCATTGTAC
Found at i:40241564 original size:18 final size:18
Alignment explanation
Indices: 40241541--40241590 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
40241531 AAAGCACCGC
40241541 TAAAGGTCAGGGTCCTGT
1 TAAAGGTCAGGGTCCTGT
40241559 TAAAGGTCAGGGTCCTGT
1 TAAAGGTCAGGGTCCTGT
*
40241577 TAAAGGTCATGGTC
1 TAAAGGTCAGGGTC
40241591 TATAGTGGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (18 bp):
TAAAGGTCAGGGTCCTGT
Found at i:40241664 original size:42 final size:42
Alignment explanation
Indices: 40241371--40241688 Score: 219
Period size: 43 Copynumber: 7.6 Consensus size: 42
40241361 TATATATTTT
* * * * *
40241371 TAAAGGTTAT-GTTTTTAGCGGTGTTTTTGCAATAAGCACCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGAA-AAGCGCCGC
* * *
40241413 TAAAGGTTTAT--TCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
1 TAAAGG-TCATGGTCTTTAGCGGCGTTTTTG-GAAAAGCGCCGC
* * *
40241455 TAAAGGTCATGTTCTTTAGCGGCCTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTT-TTGGAAAAGCGCCGC
* * *
40241498 TAAAGGTCAGGGTCTTTAGCGGCGTTTGTGGGAAAAGCACCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTT-TTGGAAAAGCGCCGC
* ** ** * *
40241541 TAAAGGTCAGGGTCCTGTTA-AAG-G--TCAGG----GTC-CTGT
1 TAAAGGTCATGGT-CT-TTAGCGGCGTTTTTGGAAAAG-CGCCGC
* * *
40241577 TAAAGGTCATGGTCTATAGTGGCGTTTGTTGGAGAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTT-TTGGAAAAGCGCCGC
**
40241620 TAAAGGTTGTGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGC
**
40241662 TAAAGGTCATGACCTTTAGCGGCGTTT
1 TAAAGGTCATGGTCTTTAGCGGCGTTT
40241689 ATTTCTAGAA
Statistics
Matches: 221, Mismatches: 37, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
34 2 0.01
35 3 0.01
36 16 0.07
37 1 0.00
38 1 0.00
39 2 0.01
40 2 0.01
41 4 0.02
42 73 0.33
43 110 0.50
44 4 0.02
45 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (42 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGC
Found at i:40243151 original size:16 final size:17
Alignment explanation
Indices: 40243121--40243152 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40243111 CCTACATAAG
40243121 TATAAATACAATAATAT
1 TATAAATACAATAATAT
40243138 TATAAATA-AATAATA
1 TATAAATACAATAATA
40243153 AAGGAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TATAAATACAATAATAT
Found at i:40249485 original size:20 final size:20
Alignment explanation
Indices: 40249462--40249499 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40249452 TGGTAATGAT
40249462 AGTACAAT-ATTAATAATATA
1 AGTACAATGA-TAATAATATA
*
40249482 AGTATAATGATAATAATA
1 AGTACAATGATAATAATA
40249500 ATAATATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (20 bp):
AGTACAATGATAATAATATA
Found at i:40249538 original size:18 final size:18
Alignment explanation
Indices: 40249517--40249561 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
40249507 TGATCAATGC
*
40249517 TAATAATCATAACAATA-T
1 TAATAATAAT-ACAATATT
*
40249535 TAATCATAATACAATATT
1 TAATAATAATACAATATT
40249553 TAATAATAA
1 TAATAATAA
40249562 AATAAACATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAATAATACAATATT
Found at i:40249540 original size:15 final size:16
Alignment explanation
Indices: 40249520--40249565 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
40249510 TCAATGCTAA
40249520 TAATCATAACAATA-T
1 TAATCATAACAATATT
40249535 TAATCATAATACAATATT
1 TAATCAT-A-ACAATATT
*
40249553 TAATAATAA-AATA
1 TAATCATAACAATA
40249566 AACATGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 11 0.41
16 2 0.07
17 7 0.26
18 7 0.26
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATCATAACAATATT
Found at i:40251066 original size:15 final size:15
Alignment explanation
Indices: 40251048--40251132 Score: 62
Period size: 15 Copynumber: 5.3 Consensus size: 15
40251038 TATTATTGAA
40251048 TCCTATAAATATGAT
1 TCCTATAAATATGAT
* * *
40251063 TCCTTTTATACTATTGAA
1 TCC-TATA-AATA-TGAT
40251081 TCCTATAAATATGAT
1 TCCTATAAATATGAT
* * *
40251096 TCCTTTTATATTATTGAA
1 TCC-TATA-AATA-TGAT
40251114 TCCTATAAATATGAT
1 TCCTATAAATATGAT
40251129 TCCT
1 TCCT
40251133 CGTTTTTTAC
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
15 16 0.31
16 12 0.23
17 12 0.23
18 12 0.23
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (15 bp):
TCCTATAAATATGAT
Found at i:40251078 original size:33 final size:33
Alignment explanation
Indices: 40251034--40251132 Score: 189
Period size: 33 Copynumber: 3.0 Consensus size: 33
40251024 TTTTGTACTA
40251034 TTTATATTATTGAATCCTATAAATATGATTCCT
1 TTTATATTATTGAATCCTATAAATATGATTCCT
*
40251067 TTTATACTATTGAATCCTATAAATATGATTCCT
1 TTTATATTATTGAATCCTATAAATATGATTCCT
40251100 TTTATATTATTGAATCCTATAAATATGATTCCT
1 TTTATATTATTGAATCCTATAAATATGATTCCT
40251133 CGTTTTTTAC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.47
Consensus pattern (33 bp):
TTTATATTATTGAATCCTATAAATATGATTCCT
Found at i:40251084 original size:18 final size:18
Alignment explanation
Indices: 40251034--40251117 Score: 63
Period size: 18 Copynumber: 5.0 Consensus size: 18
40251024 TTTTGTACTA
*
40251034 TTTATATTATTGAATCC-
1 TTTATAATATTGAATCCT
* *
40251051 TATA-AATA-TGATTCCT
1 TTTATAATATTGAATCCT
*
40251067 TTTATACTATTGAATCC-
1 TTTATAATATTGAATCCT
* *
40251084 TATA-AATA-TGATTCCT
1 TTTATAATATTGAATCCT
*
40251100 TTTATATTATTGAATCCT
1 TTTATAATATTGAATCCT
40251118 ATAAATATGA
Statistics
Matches: 49, Mismatches: 12, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
15 12 0.24
16 12 0.24
17 12 0.24
18 13 0.27
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (18 bp):
TTTATAATATTGAATCCT
Found at i:40255254 original size:63 final size:63
Alignment explanation
Indices: 40255155--40255348 Score: 212
Period size: 63 Copynumber: 3.1 Consensus size: 63
40255145 ACCCATCACT
* * *
40255155 CGGCCTAGACACACGCATGTGTCCCTGGCCCGTGTGACCCTAAATCCAAAATAATGAGTTACA
1 CGGCCTAGACACACACATGTGTCCCTAGCCCGTGTGACCCTAAATCCAAAACAATGAGTTACA
* * *
40255218 CGGCCTGGACACACACCTGTGTCCCTAGCCCGTGTGACCCTAAATCCAAAACAGTGAGTTACA
1 CGGCCTAGACACACACATGTGTCCCTAGCCCGTGTGACCCTAAATCCAAAACAATGAGTTACA
* * * * * * * * * *
40255281 CGGCCTAAAAACACGC-TCGTGTCCCTA-CTTCATGTGATCTTAAATCCAAAACAGTAAGTTATA
1 CGGCCTAGACACACACAT-GTGTCCCTAGC-CCGTGTGACCCTAAATCCAAAACAATGAGTTACA
40255344 CGGCC
1 CGGCC
40255349 GTGTGGCTCA
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
62 2 0.02
63 111 0.98
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (63 bp):
CGGCCTAGACACACACATGTGTCCCTAGCCCGTGTGACCCTAAATCCAAAACAATGAGTTACA
Found at i:40258864 original size:19 final size:19
Alignment explanation
Indices: 40258831--40258883 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
40258821 AACAAATAAT
40258831 TTAAAAATGAT-AAAATTCA
1 TTAAAAAT-ATAAAAATTCA
40258850 TTAAAAATATAAAAAGTTCA
1 TTAAAAATATAAAAA-TTCA
*
40258870 -T-AAAATTTAAAAAT
1 TTAAAAATATAAAAAT
40258884 AGCATAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 1 0.03
18 13 0.42
19 13 0.42
20 4 0.13
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (19 bp):
TTAAAAATATAAAAATTCA
Found at i:40258874 original size:18 final size:18
Alignment explanation
Indices: 40258853--40258896 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
40258843 AAATTCATTA
*
40258853 AAAATATAAAAAGT-TCAT
1 AAAATATAAAAA-TAGCAT
*
40258871 AAAATTTAAAAATAGCAT
1 AAAATATAAAAATAGCAT
40258889 AAAATATA
1 AAAATATA
40258897 TTATGATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAATATAAAAATAGCAT
Found at i:40259534 original size:23 final size:24
Alignment explanation
Indices: 40259490--40259535 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
40259480 ATAAATATAT
* **
40259490 TTTTTATTTTAAAATACTTTTTTA
1 TTTTTATTTAAAAATAAATTTTTA
40259514 TTTTT-TTTAAAAATAAATTTTT
1 TTTTTATTTAAAAATAAATTTTT
40259536 GGTGTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTTATTTAAAAATAAATTTTTA
Found at i:40260162 original size:15 final size:15
Alignment explanation
Indices: 40260139--40260168 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40260129 AGACAAAAAA
*
40260139 ATATTATTTTCTCTT
1 ATATAATTTTCTCTT
40260154 ATATAATTTTCTCTT
1 ATATAATTTTCTCTT
40260169 TTTCTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATAATTTTCTCTT
Found at i:40266997 original size:19 final size:19
Alignment explanation
Indices: 40266962--40267013 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
40266952 CTCTTTTTTT
*
40266962 GCATT-CATTTCATTCATCC
1 GCATTACATTTCA-TCATAC
*
40266981 GCATTACATTTCATCATAT
1 GCATTACATTTCATCATAC
*
40267000 GCATTAAATTTCAT
1 GCATTACATTTCAT
40267014 AAAACGACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (19 bp):
GCATTACATTTCATCATAC
Found at i:40274674 original size:44 final size:44
Alignment explanation
Indices: 40274598--40274976 Score: 307
Period size: 44 Copynumber: 8.5 Consensus size: 44
40274588 GTGGCGAATA
* ** * * *
40274598 TTATCTCCCTAAAGTTAAAGTGGAGCATATTGAAGTTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGCTACAAATC
* * *
40274642 TTATTTCACTGAAGTTGCAGTGGAGAAGATTGAAGTTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGCTACAAATC
* * * * *
40274686 TTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGATACGAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGCTACAAATC
*
40274730 TTATCTCCCTGAAGTTGCAGTGGA-ACAGATTAAAGCTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGA-AGATTGAAGCTACAAATC
* * * * *
40274774 TAATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGCGACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGCTACAAATC
* * * * * * *
40274818 CTATAC-CTCTAAAGTTACAGTGG-GTCAGATTAAATCAAGTCACAAATC
1 TTAT-CTCCCTGAAGTTGCAGTGGAG-AAGATTGAAGC---T-ACAAATC
* *
40274866 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGCTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGCTACAAATC
* * * * * * * *
40274910 TTATTTCCTTAAAGTTGAAGTGGAGTAGATTGAACCAACAAATT
1 TTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGCTACAAATC
* *
40274954 TTATAC-CTCTAAAGTTGCAGTGG
1 TTAT-CTCCCTGAAGTTGCAGTGG
40274977 GTTAAAATGA
Statistics
Matches: 270, Mismatches: 54, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
43 1 0.00
44 233 0.86
45 2 0.01
47 1 0.00
48 32 0.12
49 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGCTACAAATC
Found at i:40274789 original size:132 final size:135
Alignment explanation
Indices: 40274598--40274978 Score: 394
Period size: 136 Copynumber: 2.8 Consensus size: 135
40274588 GTGGCGAATA
* ** * * * *
40274598 TTATCTCCCTAAAGTTAAAGTGGAGCATATTGAAGTTACAAATCTTATTTCACTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATTTCCCTAAAGTTGCAGT
** * * * * * *
40274663 GGAGAAGATTGAAGTTACAAATCTTAT-CTCCCTGAGGTTGCAGTGGAGT-AGATTGAA-GA-T-
66 GGAGAAGATTGAAGCGACAAATCCTATAC-CCCTAAAGTTACAGTGG-GTCAGATTAAACAAGTC
* *
40274723 ACGAGTC
129 ACAAATC
* * * *
40274730 TTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATCTAATCTCCCTAAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATTTCCCTAAAGTTGCAGT
* * *
40274795 GGAGCAGGTTGAAGCGACAAATCCTATACCTCTAAAGTTACAGTGGGTCAGATTAAATCAAGTCA
66 GGAGAAGATTGAAGCGACAAATCCTATACCCCTAAAGTTACAGTGGGTCAGATTAAA-CAAGTCA
40274860 CAAATC
130 CAAATC
* * *
40274866 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGCTACAAATCTTATTTCCTTAAAGTTGAAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATTTCCCTAAAGTTGCAGT
* * * ** * *
40274931 GGAGTAGATTGAACCAACAAATTTTATACCTCTAAAGTTGCAGTGGGT
66 GGAGAAGATTGAAGCGACAAATCCTATACCCCTAAAGTTACAGTGGGT
40274979 TAAAATGAAG
Statistics
Matches: 205, Mismatches: 38, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
131 2 0.01
132 96 0.47
133 1 0.00
134 1 0.00
135 1 0.00
136 104 0.51
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (135 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATTTCCCTAAAGTTGCAGT
GGAGAAGATTGAAGCGACAAATCCTATACCCCTAAAGTTACAGTGGGTCAGATTAAACAAGTCAC
AAATC
Found at i:40281618 original size:28 final size:28
Alignment explanation
Indices: 40281575--40281639 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
40281565 CCCTCAAACA
*
40281575 TTCATTCTTTCCTCCTAAATACTCCATAC
1 TTCATTCTTTCCTCCTAAATACTCAAT-C
* *
40281604 -TCATTCTTTCTTCCTAAATTCTCAATC
1 TTCATTCTTTCCTCCTAAATACTCAATC
40281631 TTCATTCTT
1 TTCATTCTT
40281640 CAATCCCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.48
Consensus pattern (28 bp):
TTCATTCTTTCCTCCTAAATACTCAATC
Found at i:40281692 original size:7 final size:7
Alignment explanation
Indices: 40281647--40281715 Score: 52
Period size: 7 Copynumber: 10.0 Consensus size: 7
40281637 CTTCAATCCC
*
40281647 CAATTTC
1 CAATTTT
40281654 CAA-TTT
1 CAATTTT
*
40281660 AAATTTT
1 CAATTTT
*
40281667 CAATCTT
1 CAATTTT
40281674 CAAATTTT
1 C-AATTTT
40281682 -AATTTT
1 CAATTTT
40281688 CAATTTT
1 CAATTTT
*
40281695 AAATTTT
1 CAATTTT
* **
40281702 TAATCCT
1 CAATTTT
40281709 CAATTTT
1 CAATTTT
40281716 TTTAATTCTT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
6 10 0.21
7 32 0.68
8 5 0.11
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.52
Consensus pattern (7 bp):
CAATTTT
Found at i:40281702 original size:21 final size:20
Alignment explanation
Indices: 40281655--40281715 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
40281645 CCCAATTTCC
* *
40281655 AATTTAAATTTTCAATCTTCA
1 AATTTTAATTTTCAAT-TTTA
40281676 AATTTTAATTTTCAATTTTA
1 AATTTTAATTTTCAATTTTA
**
40281696 AATTTTTAATCCTCAATTTT
1 AA-TTTTAATTTTCAATTTT
40281716 TTTAATTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.14
21 30 0.86
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTTTAATTTTCAATTTTA
Found at i:40287050 original size:20 final size:20
Alignment explanation
Indices: 40286992--40287043 Score: 74
Period size: 17 Copynumber: 2.8 Consensus size: 20
40286982 AGCAATGAAT
40286992 CTGTTCATCAAGAGATACAA
1 CTGTTCATCAAGAGATACAA
*
40287012 TTGTTCA--AA-AGATACAA
1 CTGTTCATCAAGAGATACAA
40287029 CTGTTCATCAAGAGA
1 CTGTTCATCAAGAGA
40287044 AAGAACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 2 0.07
20 9 0.33
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (20 bp):
CTGTTCATCAAGAGATACAA
Found at i:40294765 original size:32 final size:31
Alignment explanation
Indices: 40294725--40294901 Score: 97
Period size: 32 Copynumber: 5.9 Consensus size: 31
40294715 TAGTATTTCA
40294725 TTAATTTAATATTAAAGTGATTATCTTAATAT
1 TTAATTTAATATTAAA-TGATTATCTTAATAT
* *
40294757 TTAATTTAAT-TT-AATGTTTATCTTATAGAT
1 TTAATTTAATATTAAATGATTATCTTA-ATAT
** * * **
40294787 AAATATTCTATTAATTTAAT-AAGAT-TTAATAT
1 TTA-ATT-TAAT-ATTAAATGATTATCTTAATAT
* * * * *
40294819 TAAATTTAATCTT-GAT-A-AATATT-ATA-
1 TTAATTTAATATTAAATGATTATCTTAATAT
40294845 TTAATTTAATATTAAAGTGATTATCTTAATAT
1 TTAATTTAATATTAAA-TGATTATCTTAATAT
*
40294877 TTAATTTAAT-TT-AATGTTTATCTTA
1 TTAATTTAATATTAAATGATTATCTTA
40294902 TAGATAAATA
Statistics
Matches: 112, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
26 11 0.10
27 6 0.05
28 6 0.05
29 23 0.21
30 15 0.13
31 13 0.12
32 28 0.25
33 3 0.03
34 4 0.04
35 3 0.03
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.51
Consensus pattern (31 bp):
TTAATTTAATATTAAATGATTATCTTAATAT
Found at i:40294849 original size:120 final size:120
Alignment explanation
Indices: 40294724--40294987 Score: 528
Period size: 120 Copynumber: 2.2 Consensus size: 120
40294714 ATAGTATTTC
40294724 ATTAATTTAATATTAAAGTGATTATCTTAATATTTAATTTAATTTAATGTTTATCTTATAGATAA
1 ATTAATTTAATATTAAAGTGATTATCTTAATATTTAATTTAATTTAATGTTTATCTTATAGATAA
40294789 ATATTCTATTAATTTAATAAGATTTAATATTAAATTTAATCTTGATAAATATTAT
66 ATATTCTATTAATTTAATAAGATTTAATATTAAATTTAATCTTGATAAATATTAT
40294844 ATTAATTTAATATTAAAGTGATTATCTTAATATTTAATTTAATTTAATGTTTATCTTATAGATAA
1 ATTAATTTAATATTAAAGTGATTATCTTAATATTTAATTTAATTTAATGTTTATCTTATAGATAA
40294909 ATATTCTATTAATTTAATAAGATTTAATATTAAATTTAATCTTGATAAATATTAT
66 ATATTCTATTAATTTAATAAGATTTAATATTAAATTTAATCTTGATAAATATTAT
40294964 ATTAATTTAATATTAAAGTGATTA
1 ATTAATTTAATATTAAAGTGATTA
40294988 AGTTTAAACA
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 144 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
ATTAATTTAATATTAAAGTGATTATCTTAATATTTAATTTAATTTAATGTTTATCTTATAGATAA
ATATTCTATTAATTTAATAAGATTTAATATTAAATTTAATCTTGATAAATATTAT
Found at i:40299341 original size:14 final size:15
Alignment explanation
Indices: 40299308--40299344 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
40299298 TGAATTTGAT
40299308 TGTTTGAAATTTTCG
1 TGTTTGAAATTTTCG
40299323 TGTTT-AAATTTT-G
1 TGTTTGAAATTTTCG
40299336 TCGTTTGAA
1 T-GTTTGAA
40299345 TGACCGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.10
14 11 0.55
15 7 0.35
ACGTcount: A:0.22, C:0.05, G:0.19, T:0.54
Consensus pattern (15 bp):
TGTTTGAAATTTTCG
Found at i:40305932 original size:38 final size:38
Alignment explanation
Indices: 40305866--40305938 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
40305856 CATATCTGAC
*
40305866 TCCATTGTTGGAGATTGTCCAGAAGGTTTTCATCTAAA
1 TCCATTGTTGGAGATTGTCCAGAAGGTTTTAATCTAAA
40305904 TCCATTGTTGGAGATTG-CTCA-AAGGGTTTTAATCT
1 TCCATTGTTGGAGATTGTC-CAGAA-GGTTTTAATCT
40305939 TCCAATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 3 0.09
38 29 0.91
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (38 bp):
TCCATTGTTGGAGATTGTCCAGAAGGTTTTAATCTAAA
Found at i:40306748 original size:30 final size:32
Alignment explanation
Indices: 40306706--40306769 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 32
40306696 CATTAAAAAA
**
40306706 ATTAAGAAAATTAACATCACAAAC-AAAATCC
1 ATTAAGAAAATTAACAGAACAAACAAAAATCC
40306737 ATTAA-AAAATTAACAGAACAAACAAAAATCC
1 ATTAAGAAAATTAACAGAACAAACAAAAATCC
40306768 AT
1 AT
40306770 CAATCTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.61, C:0.17, G:0.03, T:0.19
Consensus pattern (32 bp):
ATTAAGAAAATTAACAGAACAAACAAAAATCC
Found at i:40308951 original size:21 final size:21
Alignment explanation
Indices: 40308927--40309015 Score: 115
Period size: 21 Copynumber: 4.0 Consensus size: 21
40308917 CCCACAACCT
40308927 CCACCCCCACAACCTCCACCC
1 CCACCCCCACAACCTCCACCC
40308948 CCACCCCCACAACCTCCACCTCC
1 CCACCCCCACAACCTCCA-C-CC
40308971 ACCACCACCTTCACAACCTCCACCC
1 -CCACC-CC--CACAACCTCCACCC
*
40308996 TCACCCCCACAACCTCCACC
1 CCACCCCCACAACCTCCACC
40309016 TCCAGCTCCA
Statistics
Matches: 61, Mismatches: 1, Indels: 12
0.82 0.01 0.16
Matches are distributed among these distances:
21 31 0.51
22 1 0.02
23 4 0.07
24 9 0.15
25 4 0.07
26 1 0.02
27 11 0.18
ACGTcount: A:0.25, C:0.66, G:0.00, T:0.09
Consensus pattern (21 bp):
CCACCCCCACAACCTCCACCC
Found at i:40308967 original size:15 final size:15
Alignment explanation
Indices: 40308913--40308951 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
40308903 TACCCTCAAT
40308913 CACCCCCACAACCTC
1 CACCCCCACAACCTC
40308928 CACCCCCACAACCTC
1 CACCCCCACAACCTC
40308943 CACCCCCAC
1 CACCCCCAC
40308952 CCCCACAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.69, G:0.00, T:0.05
Consensus pattern (15 bp):
CACCCCCACAACCTC
Found at i:40308968 original size:27 final size:27
Alignment explanation
Indices: 40308938--40309005 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
40308928 CACCCCCACA
40308938 ACCTCCACCCCCACCCCCACAACCTCC
1 ACCTCCACCCCCACCCCCACAACCTCC
* **
40308965 ACCTCCACCACCACCTTCACAACCTCC
1 ACCTCCACCCCCACCCCCACAACCTCC
40308992 ACC-CTCACCCCCAC
1 ACCTC-CACCCCCAC
40309006 AACCTCCACC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.24, C:0.66, G:0.00, T:0.10
Consensus pattern (27 bp):
ACCTCCACCCCCACCCCCACAACCTCC
Found at i:40311402 original size:21 final size:21
Alignment explanation
Indices: 40311378--40311429 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
40311368 CCCACAACCT
40311378 CCACCCCCACAACCTCCACCC
1 CCACCCCCACAACCTCCACCC
*
40311399 CCACCCCCACAACCTCCACCT
1 CCACCCCCACAACCTCCACCC
*
40311420 CCACCTCCAC
1 CCACCCCCAC
40311430 CTCCAGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.69, G:0.00, T:0.08
Consensus pattern (21 bp):
CCACCCCCACAACCTCCACCC
Found at i:40311418 original size:15 final size:15
Alignment explanation
Indices: 40311364--40311402 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
40311354 TACCCTCAAT
40311364 CACCCCCACAACCTC
1 CACCCCCACAACCTC
40311379 CACCCCCACAACCTC
1 CACCCCCACAACCTC
40311394 CACCCCCAC
1 CACCCCCAC
40311403 CCCCACAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.69, G:0.00, T:0.05
Consensus pattern (15 bp):
CACCCCCACAACCTC
Found at i:40311419 original size:6 final size:6
Alignment explanation
Indices: 40311410--40311434 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40311400 CACCCCCACA
40311410 ACCTCC ACCTCC ACCTCC ACCTCC A
1 ACCTCC ACCTCC ACCTCC ACCTCC A
40311435 GAACTTCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.64, G:0.00, T:0.16
Consensus pattern (6 bp):
ACCTCC
Found at i:40312496 original size:50 final size:50
Alignment explanation
Indices: 40312442--40312559 Score: 157
Period size: 50 Copynumber: 2.4 Consensus size: 50
40312432 TATATAATGG
* * * * *
40312442 GAAGCTCATGTGAGCTG-TATATCAGAAAGCTCTTGTGAGCCAAATATCGA
1 GAAGCTCAAGAGAGCTGTTA-ATCAGAAAGATCGTGAGAGCCAAATATCGA
* *
40312492 GAAGCTCAAGAGAGCTGTTAATCTGAAAGATCGTGAGAGCCAAGTATCGA
1 GAAGCTCAAGAGAGCTGTTAATCAGAAAGATCGTGAGAGCCAAATATCGA
40312542 GAAGCTCAAGAGAGCTGT
1 GAAGCTCAAGAGAGCTGT
40312560 GGTGTGTTCG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 58 0.97
51 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (50 bp):
GAAGCTCAAGAGAGCTGTTAATCAGAAAGATCGTGAGAGCCAAATATCGA
Found at i:40312506 original size:25 final size:25
Alignment explanation
Indices: 40312478--40312556 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
40312468 AAGCTCTTGT
40312478 GAGCCAAATATCGAGAAGCTCAAGA
1 GAGCCAAATATCGAGAAGCTCAAGA
*** * **
40312503 GAG-CTGTTAATCTGA-AAGATCGTGA
1 GAGCCAAAT-ATC-GAGAAGCTCAAGA
*
40312528 GAGCCAAGTATCGAGAAGCTCAAGA
1 GAGCCAAATATCGAGAAGCTCAAGA
40312553 GAGC
1 GAGC
40312557 TGTGGTGTGT
Statistics
Matches: 38, Mismatches: 12, Indels: 8
0.66 0.21 0.14
Matches are distributed among these distances:
24 4 0.11
25 30 0.79
26 4 0.11
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.16
Consensus pattern (25 bp):
GAGCCAAATATCGAGAAGCTCAAGA
Found at i:40317108 original size:46 final size:46
Alignment explanation
Indices: 40317038--40317323 Score: 404
Period size: 46 Copynumber: 6.3 Consensus size: 46
40317028 TATGTGTGTA
*
40317038 AAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAT
1 AAAGTGATAAGTGGAAGCATTAGCTACACTTATCTGATCAAGTGAT
* *
40317084 AATGTGATAAGTGGAAGCATTAGCTATACTTATCTGATCAAGTGAT
1 AAAGTGATAAGTGGAAGCATTAGCTACACTTATCTGATCAAGTGAT
*
40317130 AAAGTGATAAGT-GATAGCATTAGCTATACTTATCTGATCAAGTGAT
1 AAAGTGATAAGTGGA-AGCATTAGCTACACTTATCTGATCAAGTGAT
*
40317176 AAAGTGATAAGT-GATAGCATTAGCTATACTTATCTGATCAAGTGAT
1 AAAGTGATAAGTGGA-AGCATTAGCTACACTTATCTGATCAAGTGAT
* *
40317222 AAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGGAAGCATTAGCTACACTTATCTGATCAAGTGAT
* * *
40317268 AAAGTGATAAGTTGTAG--TCTAGCTACACTTATCTGATC-AGGGA-
1 AAAGTGATAAGTGGAAGCAT-TAGCTACACTTATCTGATCAAGTGAT
*
40317311 CAAGTGATAAGTG
1 AAAGTGATAAGTG
40317324 ATCATAAGTA
Statistics
Matches: 226, Mismatches: 11, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
43 11 0.05
44 5 0.02
45 21 0.09
46 188 0.83
47 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (46 bp):
AAAGTGATAAGTGGAAGCATTAGCTACACTTATCTGATCAAGTGAT
Found at i:40323749 original size:43 final size:43
Alignment explanation
Indices: 40323688--40323844 Score: 260
Period size: 43 Copynumber: 3.7 Consensus size: 43
40323678 TGGTATACCA
40323688 AAAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCT
1 AAAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCT
*
40323731 AAAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCTGCT
1 AAAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCT
* *
40323774 AAAGACCATGACCTTTAGCGGCGCTTTTCCCATAAACGCCACT
1 AAAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCT
** *
40323817 AAAGAATATGACCTTTAGCGACGCTTTT
1 AAAGACCATGACCTTTAGCGGCGCTTTT
40323845 TGTTAAAAAT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 107 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (43 bp):
AAAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCT
Found at i:40323905 original size:86 final size:86
Alignment explanation
Indices: 40323688--40323910 Score: 252
Period size: 86 Copynumber: 2.6 Consensus size: 86
40323678 TGGTATACCA
* * ** *
40323688 AAAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGC
1 AAAGACCATAACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGAATATGACCTTTAGCGAC
* *
40323753 GCTTTTCCCACAAACGCTGCT
66 GCTTTTCCCAAAAACGCCGCT
* * *
40323774 AAAGACCATGACCTTTAGCGGCGCTTTTCCCATAAACGCCACTAAAGAATATGACCTTTAGCGAC
1 AAAGACCATAACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGAATATGACCTTTAGCGAC
*** *
40323839 GCTTTTTGTTAAAAATGCCGCT
66 GC-TTTTCCCAAAAACGCCGCT
* * * * *
40323861 ATAGATCA-AACCTTTAGCGGCGCTTCTCACAAAAACGCTGCTAAA-AATAT
1 AAAGACCATAACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGAATAT
40323911 AACTTTTAAA
Statistics
Matches: 117, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
85 5 0.04
86 93 0.79
87 19 0.16
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (86 bp):
AAAGACCATAACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGAATATGACCTTTAGCGAC
GCTTTTCCCAAAAACGCCGCT
Found at i:40323932 original size:15 final size:16
Alignment explanation
Indices: 40323914--40323947 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40323904 AAAATATAAC
40323914 TTTTAAACAAATT-TA
1 TTTTAAACAAATTATA
*
40323929 TTTTAATCAAATTATA
1 TTTTAAACAAATTATA
40323945 TTT
1 TTT
40323948 ATTTTTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAACAAATTATA
Found at i:40325171 original size:24 final size:24
Alignment explanation
Indices: 40325142--40325195 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
40325132 CTGATGAAAG
* *
40325142 ATGAACTGTTAAATACATGCAGAA
1 ATGAACTGTTAAACACATACAGAA
* *
40325166 ATGAACCGTTCAACACATACAGAA
1 ATGAACTGTTAAACACATACAGAA
40325190 A-GAACT
1 ATGAACT
40325196 TACTTTTCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (24 bp):
ATGAACTGTTAAACACATACAGAA
Found at i:40328175 original size:41 final size:41
Alignment explanation
Indices: 40328116--40328277 Score: 193
Period size: 41 Copynumber: 4.0 Consensus size: 41
40328106 TAAAATATTT
*
40328116 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCCAACA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGACCCCAACA
*
40328157 TTAGCGGCGC-TTTATCAAAAACGCCGCTAAAGACACCAGA-A
1 TTAGCGGCGCTTTTA-CAAAAACGCCGCTAAAGACCCCA-ACA
* * * * * *
40328198 TTAGCGGCGATTTTCCAAAGACGTCGCTAAAAACCCCAGCA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGACCCCAACA
* * *
40328239 TTAGCGGCGCTTTTACGAAAACACCGCTAAAGCCCCCAA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGACCCCAA
40328278 AGGTAAGAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
40 3 0.03
41 92 0.93
42 4 0.04
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGACCCCAACA
Found at i:40328260 original size:82 final size:82
Alignment explanation
Indices: 40328116--40328270 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 82
40328106 TAAAATATTT
* * * *
40328116 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCCAACATTAGCGGCGCTTTATCAAAAACGC
1 TTAGCGGCGATTTTCCAAAAACGCCGCTAAAAACCCCAACATTAGCGGCGCTTTATCAAAAACAC
40328181 CGCTAAAGACACCAGAA
66 CGCTAAAGACACCAGAA
* * * *
40328198 TTAGCGGCGATTTTCCAAAGACGTCGCTAAAAACCCCAGCATTAGCGGCGCTTT-TACGAAAACA
1 TTAGCGGCGATTTTCCAAAAACGCCGCTAAAAACCCCAACATTAGCGGCGCTTTAT-CAAAAACA
40328262 CCGCTAAAG
65 CCGCTAAAG
40328271 CCCCCAAAGG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 1 0.02
82 63 0.98
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (82 bp):
TTAGCGGCGATTTTCCAAAAACGCCGCTAAAAACCCCAACATTAGCGGCGCTTTATCAAAAACAC
CGCTAAAGACACCAGAA
Found at i:40328364 original size:40 final size:39
Alignment explanation
Indices: 40328308--40328443 Score: 125
Period size: 39 Copynumber: 3.4 Consensus size: 39
40328298 TGGGCTTTGG
* *
40328308 TTTTTTGCGGCGTTTTTAAAAAAAAAGCCGCTAATGCTC-A
1 TTTTTAGCGGCATTTTT--AAAAAAAGCCGCTAATGCTCGA
* *
40328348 TTTTTAGCGGCATTTTTTGAAAAACGCCGCTAATGCTCGA
1 TTTTTAGCGGCA-TTTTTAAAAAAAGCCGCTAATGCTCGA
* * **
40328388 TCTTTAG-GGCGATTTTCTTAAAGCA-CCGCTAATGCTCGA
1 TTTTTAGCGGC-ATTTT-TAAAAAAAGCCGCTAATGCTCGA
*
40328427 TTTTTACCGGCATTTTT
1 TTTTTAGCGGCATTTTT
40328444 TATCCAAACG
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
38 1 0.01
39 49 0.61
40 25 0.31
41 5 0.06
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCATTTTTAAAAAAAGCCGCTAATGCTCGA
Found at i:40328371 original size:39 final size:39
Alignment explanation
Indices: 40328328--40328445 Score: 143
Period size: 39 Copynumber: 3.0 Consensus size: 39
40328318 CGTTTTTAAA
40328328 AAAAAAGCCGCTAATGCTC-ATTTTTAGCGGCATTTTTT
1 AAAAAAGCCGCTAATGCTCGATTTTTAGCGGCATTTTTT
* *
40328366 GAAAAACGCCGCTAATGCTCGATCTTTAG-GGCGATTTTCTT
1 -AAAAAAGCCGCTAATGCTCGATTTTTAGCGGC-ATTTT-TT
** *
40328407 AAAGCA-CCGCTAATGCTCGATTTTTACCGGCATTTTTT
1 AAAAAAGCCGCTAATGCTCGATTTTTAGCGGCATTTTTT
40328445 A
1 A
40328446 TCCAAACGCC
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
38 3 0.04
39 45 0.66
40 18 0.26
41 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (39 bp):
AAAAAAGCCGCTAATGCTCGATTTTTAGCGGCATTTTTT
Found at i:40330105 original size:13 final size:13
Alignment explanation
Indices: 40330087--40330112 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40330077 CATGGTCATA
40330087 ATTATAATAATTT
1 ATTATAATAATTT
40330100 ATTATAATAATTT
1 ATTATAATAATTT
40330113 TAGTAAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATAATAATTT
Found at i:40339335 original size:63 final size:64
Alignment explanation
Indices: 40339259--40339387 Score: 242
Period size: 63 Copynumber: 2.0 Consensus size: 64
40339249 AAGTTTAATA
40339259 AATTCTAAATTTGTTTGTGAATTGATGCACTTGTGACATTCATGGTGTGACTTAACTAAATCCT
1 AATTCTAAATTTGTTTGTGAATTGATGCACTTGTGACATTCATGGTGTGACTTAACTAAATCCT
*
40339323 AATT-TAAATTTGTTTGTGAATTGATGCACTTGTGACGTTCATGGTGTGACTTAACTAAATCCT
1 AATTCTAAATTTGTTTGTGAATTGATGCACTTGTGACATTCATGGTGTGACTTAACTAAATCCT
40339386 AA
1 AA
40339388 GTTAGTCACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 60 0.94
64 4 0.06
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (64 bp):
AATTCTAAATTTGTTTGTGAATTGATGCACTTGTGACATTCATGGTGTGACTTAACTAAATCCT
Found at i:40340258 original size:19 final size:19
Alignment explanation
Indices: 40340234--40340271 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40340224 GTAATTAAAC
*
40340234 TTGAAAATTGAATCAGAGA
1 TTGAAAATTGAACCAGAGA
40340253 TTGAAAATTGAACCAGAGA
1 TTGAAAATTGAACCAGAGA
40340272 ACCAAAACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (19 bp):
TTGAAAATTGAACCAGAGA
Found at i:40343496 original size:18 final size:19
Alignment explanation
Indices: 40343473--40343511 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
40343463 GCGAAGGGTG
40343473 TTACT-ATTTAGTCTCTTC
1 TTACTAATTTAGTCTCTTC
40343491 TTACTACAATTTAGTCTCTTC
1 TTACT--AATTTAGTCTCTTC
40343512 ATTCAAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
21 13 0.72
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (19 bp):
TTACTAATTTAGTCTCTTC
Found at i:40346624 original size:23 final size:23
Alignment explanation
Indices: 40346598--40346658 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
40346588 TATATTAAAA
* *
40346598 ATAATTTTTTGAATATATGTTTT
1 ATAATTTTTTGAATAAATATTTT
40346621 ATAATTTTTTAGAA-AAATATTTT
1 ATAATTTTTT-GAATAAATATTTT
*
40346644 ATAAATATTTTGAAT
1 AT-AATTTTTTGAAT
40346659 TTTACAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (23 bp):
ATAATTTTTTGAATAAATATTTT
Found at i:40346836 original size:23 final size:24
Alignment explanation
Indices: 40346790--40346838 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
40346780 CAAACTCAAA
* *
40346790 AAAAAAACCGAATTACTTTGATTC
1 AAAAAAACCGAATAACTTTAATTC
*
40346814 AAAAGAACCGAATAAC-TTAATTC
1 AAAAAAACCGAATAACTTTAATTC
40346837 AA
1 AA
40346839 TTAACTCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.24
Consensus pattern (24 bp):
AAAAAAACCGAATAACTTTAATTC
Found at i:40347099 original size:19 final size:18
Alignment explanation
Indices: 40347077--40347110 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40347067 CACAGTTATT
40347077 TTTTTTA-AATATCAAAC
1 TTTTTTATAATATCAAAC
40347094 TTTTTTATAATATCAAA
1 TTTTTTATAATATCAAA
40347111 TAACAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTTATAATATCAAAC
Found at i:40357000 original size:16 final size:16
Alignment explanation
Indices: 40356979--40357014 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
40356969 GATTTGCTAT
40356979 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40356995 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40357011 TACA
1 TACA
40357015 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40364688 original size:27 final size:27
Alignment explanation
Indices: 40364650--40364709 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
40364640 CAGCAAAACG
40364650 CGTCCCTGGGGGCGCGCTTTGCTAACA
1 CGTCCCTGGGGGCGCGCTTTGCTAACA
40364677 CGTCCCTGGGGGCGCGCTTTGCTAACA
1 CGTCCCTGGGGGCGCGCTTTGCTAACA
40364704 CGTCCC
1 CGTCCC
40364710 CTGATATCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.10, C:0.37, G:0.32, T:0.22
Consensus pattern (27 bp):
CGTCCCTGGGGGCGCGCTTTGCTAACA
Found at i:40374626 original size:89 final size:89
Alignment explanation
Indices: 40374470--40374740 Score: 533
Period size: 89 Copynumber: 3.0 Consensus size: 89
40374460 AACTGAAGCA
*
40374470 AAAGCTGTGTATTTTTGAACAAAAGTGGGAAACGAACTAAAATAATTTCCCCTCAACTATACAGA
1 AAAGATGTGTATTTTTGAACAAAAGTGGGAAACGAACTAAAATAATTTCCCCTCAACTATACAGA
40374535 AGGAATATTTAGCAAATAATCTAT
66 AGGAATATTTAGCAAATAATCTAT
40374559 AAAGATGTGTATTTTTGAACAAAAGTGGGAAACGAACTAAAATAATTTCCCCTCAACTATACAGA
1 AAAGATGTGTATTTTTGAACAAAAGTGGGAAACGAACTAAAATAATTTCCCCTCAACTATACAGA
40374624 AGGAATATTTAGCAAATAATCTAT
66 AGGAATATTTAGCAAATAATCTAT
40374648 AAAGATGTGTATTTTTGAACAAAAGTGGGAAACGAACTAAAATAATTTCCCCTCAACTATACAGA
1 AAAGATGTGTATTTTTGAACAAAAGTGGGAAACGAACTAAAATAATTTCCCCTCAACTATACAGA
40374713 AGGAATATTTAGCAAATAATCTAT
66 AGGAATATTTAGCAAATAATCTAT
40374737 AAAG
1 AAAG
40374741 CCTTGATTTC
Statistics
Matches: 181, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 181 1.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (89 bp):
AAAGATGTGTATTTTTGAACAAAAGTGGGAAACGAACTAAAATAATTTCCCCTCAACTATACAGA
AGGAATATTTAGCAAATAATCTAT
Found at i:40375609 original size:2 final size:2
Alignment explanation
Indices: 40375602--40375642 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
40375592 CAAACAGAAA
40375602 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
40375643 CTTACTGGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40377711 original size:61 final size:58
Alignment explanation
Indices: 40377610--40377722 Score: 156
Period size: 61 Copynumber: 1.9 Consensus size: 58
40377600 ACTTTAATAC
* *
40377610 TAAATTAATATAATACTTATTAAGATAAATAATTGATTAAATTTAATATTAAATCTGT
1 TAAATTAATAGAATACTTATTAAGATAAATAATTAATTAAATTTAATATTAAATCTGT
*
40377668 TAAATTAATAGAATATTTATCTACAAGATAAAT-ATTAAATTAAATTTAATATTAA
1 TAAATTAATAGAATACTTAT-T--AAGATAAATAATT-AATTAAATTTAATATTAA
40377723 TATAATCACT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 18 0.38
59 1 0.02
60 3 0.06
61 26 0.54
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (58 bp):
TAAATTAATAGAATACTTATTAAGATAAATAATTAATTAAATTTAATATTAAATCTGT
Found at i:40377748 original size:20 final size:18
Alignment explanation
Indices: 40377698--40377749 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
40377688 CTACAAGATA
40377698 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
40377715 AATATT-AATATAATCACTTT
1 AATATTAAAT-TAAT-A-TTT
40377735 AATATTAAATTAATA
1 AATATTAAATTAATA
40377750 AAATATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.10
17 9 0.30
19 2 0.07
20 13 0.43
21 3 0.10
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:40377822 original size:68 final size:68
Alignment explanation
Indices: 40377667--40377812 Score: 168
Period size: 70 Copynumber: 2.1 Consensus size: 68
40377657 ATTAAATCTG
* *
40377667 TTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATTAATATAATCAC
1 TTAAATTAATAAAATATTT-T-T--AAGATAAATATTAAATTAAATTTAATATTAATATAATCAA
**
40377732 TTTAATA
62 AATAATA
* *
40377739 TTAAATTAATAAAATATTTTTAAGATAAGTATTAAATTAAATATTAAATATTAA-ATATATGAAA
1 TTAAATTAATAAAATATTTTTAAGATAAATATTAAATTAAAT-TT-AATATTAATATA-ATCAAA
40377803 ATAATA
63 ATAATA
40377809 TTAA
1 TTAA
40377813 TTTTGAAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
68 20 0.31
69 5 0.08
70 21 0.32
71 1 0.02
72 18 0.28
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (68 bp):
TTAAATTAATAAAATATTTTTAAGATAAATATTAAATTAAATTTAATATTAATATAATCAAAATA
ATA
Found at i:40378902 original size:9 final size:9
Alignment explanation
Indices: 40378884--40378941 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
40378874 TTTGGTTAAA
40378884 AATTAACCG
1 AATTAACCG
*
40378893 AATTACCCG
1 AATTAACCG
40378902 AATTAACCG
1 AATTAACCG
* *
40378911 GATTACCCG
1 AATTAACCG
*
40378920 AATTATCCG
1 AATTAACCG
40378929 AATTAACCG
1 AATTAACCG
40378938 AATT
1 AATT
40378942 GAATTNNNNN
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:40378907 original size:18 final size:18
Alignment explanation
Indices: 40378884--40378941 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
40378874 TTTGGTTAAA
40378884 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
40378902 AATTAACCGGATTACCCG
1 AATTAACCGAATTACCCG
* *
40378920 AATTATCCGAATTAACCG
1 AATTAACCGAATTACCCG
40378938 AATT
1 AATT
40378942 GAATTNNNNN
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:40387902 original size:20 final size:18
Alignment explanation
Indices: 40387852--40387903 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
40387842 CTACAAGATA
40387852 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
40387869 AATATT-AATATAATCACTTT
1 AATATTAAAT-TAAT-A-TTT
40387889 AATATTAAATTAATA
1 AATATTAAATTAATA
40387904 AAATATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.10
17 9 0.30
19 2 0.07
20 13 0.43
21 3 0.10
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:40387976 original size:68 final size:68
Alignment explanation
Indices: 40387819--40387966 Score: 172
Period size: 70 Copynumber: 2.1 Consensus size: 68
40387809 TATTAAATCT
*
40387819 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATTAATATAATC
1 TATTAAATTAATAAAATATTT-T-T--AAGATAAATATTAAATTAAATTTAATATTAATATAATC
***
40387884 ACTTTAA
62 AAAATAA
* *
40387891 TATTAAATTAATAAAATATTTTTAAGATAAGTATTAAATTAAATATTAAATATTAA-ATATATGA
1 TATTAAATTAATAAAATATTTTTAAGATAAATATTAAATTAAAT-TT-AATATTAATATA-ATCA
40387955 AAATAA
63 AAATAA
40387961 TATTAA
1 TATTAA
40387967 TTTTGAAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
68 20 0.30
69 5 0.07
70 21 0.31
71 1 0.01
72 20 0.30
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (68 bp):
TATTAAATTAATAAAATATTTTTAAGATAAATATTAAATTAAATTTAATATTAATATAATCAAAA
TAA
Done.