Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 132 of 182
Found at i:40734203 original size:82 final size:81
Alignment explanation
Indices: 40734063--40734218 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
40734053 AAATTGTACA
* * * *
40734063 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
40734128 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
40734144 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
40734207 TGTGCGAGTTGA
63 TGTGCGAATTGA
40734219 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:40737565 original size:45 final size:46
Alignment explanation
Indices: 40737499--40737622 Score: 135
Period size: 45 Copynumber: 2.7 Consensus size: 46
40737489 TTAAGTATGC
* * * * *
40737499 CATAGTGTCTTTTAGCCATGGTCTTATTTATTTCCGA-CATATTGA
1 CATAGTGTCTTTCAACTATGGTCTTATTTATTTCCGATAATAGTGA
* * *
40737544 CATAGTGTCTTTCAACTATGGTCTTATTTGTTT-CTATAATAGTGC
1 CATAGTGTCTTTCAACTATGGTCTTATTTATTTCCGATAATAGTGA
* * *
40737589 CATAGTGTCTTTCAACTATGTTCTAATTCATTTC
1 CATAGTGTCTTTCAACTATGGTCTTATTTATTTC
40737623 TGGTATAATT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 2 0.03
45 63 0.97
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (46 bp):
CATAGTGTCTTTCAACTATGGTCTTATTTATTTCCGATAATAGTGA
Found at i:40740393 original size:40 final size:40
Alignment explanation
Indices: 40740241--40740386 Score: 172
Period size: 40 Copynumber: 3.6 Consensus size: 40
40740231 TTGAATGATG
* * * * *
40740241 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
40740281 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40740321 TCCGGACTAAGTTCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
40740362 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGACTAAGTCCCGAAGGCATTTG
40740387 AACGAGTAGC
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
39 1 0.01
40 83 0.88
41 10 0.11
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40740393 original size:80 final size:79
Alignment explanation
Indices: 40740245--40740419 Score: 185
Period size: 80 Copynumber: 2.2 Consensus size: 79
40740235 ATGATGTCCG
* * **
40740245 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGC
1 GGCTAAGTTCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAAC
40740310 GAGTTA-CTAAATCC
66 GAG-TAGCTAAATCC
* * * * *
40740324 GGACTAAGTTCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCATTTG
1 GG-CTAAGTTCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCATTTG
*
40740387 AACGAGTAGCTATATCC
63 AACGAGTAGCTAAATCC
* *
40740404 GGTTAAATTCCGAAGG
1 GGCTAAGTTCCGAAGG
40740420 TACGTGATTT
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
79 17 0.21
80 56 0.70
81 7 0.09
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
GGCTAAGTTCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAAC
GAGTAGCTAAATCC
Found at i:40744197 original size:20 final size:21
Alignment explanation
Indices: 40744158--40744197 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40744148 CCCTGCAGTA
* *
40744158 CAAAAATTTTGTAATTTTTCC
1 CAAAAATTCTGTAATGTTTCC
40744179 CAAAAATTCTGT-ATGTTTC
1 CAAAAATTCTGTAATGTTTC
40744198 TAATTTAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (21 bp):
CAAAAATTCTGTAATGTTTCC
Found at i:40745446 original size:106 final size:106
Alignment explanation
Indices: 40745273--40745465 Score: 307
Period size: 106 Copynumber: 1.8 Consensus size: 106
40745263 TGCACAAGAT
* * *
40745273 GAAGTTTCTGCTCCAGATATTATTACTGGGACTTTTTCTATCTTTGACACTAATGCTACTGCTTT
1 GAAGCTTCTGCTCCAGATATTATTACTAGGACTTTTTCTATCTTTGACACTAATGCTACTACTTT
*
40745338 GATTGATTCGGGATCAA-CCTATCTAGATTCGTGCACGATAG
66 GATTGATCCGGGAT-AAGCCTATCTAGATTCGTGCACGATAG
* * *
40745379 GAAGCTTCTGCTCCAGATGTTATTACTAGTACTTTTTCTATCTTTGACACTAATGTTACTACTTT
1 GAAGCTTCTGCTCCAGATATTATTACTAGGACTTTTTCTATCTTTGACACTAATGCTACTACTTT
40745444 GATTGATCCGGGATAAGCCTAT
66 GATTGATCCGGGATAAGCCTAT
40745466 TCGTATGTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
105 2 0.03
106 77 0.97
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (106 bp):
GAAGCTTCTGCTCCAGATATTATTACTAGGACTTTTTCTATCTTTGACACTAATGCTACTACTTT
GATTGATCCGGGATAAGCCTATCTAGATTCGTGCACGATAG
Found at i:40751566 original size:21 final size:22
Alignment explanation
Indices: 40751540--40751587 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
40751530 ATTAAATTGG
*
40751540 ATTAAAATAAATTGGATTAT-A
1 ATTAAAATAAATTAGATTATGA
* *
40751561 ATTAAAATTAATTATATTATGA
1 ATTAAAATAAATTAGATTATGA
40751583 ATTAA
1 ATTAA
40751588 TATTCATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (22 bp):
ATTAAAATAAATTAGATTATGA
Found at i:40752090 original size:12 final size:13
Alignment explanation
Indices: 40752063--40752094 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40752053 TCATCTATCA
40752063 TTCCCTTTTCCAT
1 TTCCCTTTTCCAT
40752076 TTCCCTTTTCC-T
1 TTCCCTTTTCCAT
40752088 TTCCCTT
1 TTCCCTT
40752095 GCATAGCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.56
Consensus pattern (13 bp):
TTCCCTTTTCCAT
Found at i:40753201 original size:14 final size:15
Alignment explanation
Indices: 40753184--40753243 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 15
40753174 CAGTTTAGTT
40753184 TTTATTT-TTATTTA
1 TTTATTTATTATTTA
40753198 TTTAATTT-TTAACTTTA
1 TTT-ATTTATT-A-TTTA
* *
40753215 CTAATTTATTATTTA
1 TTTATTTATTATTTA
40753230 -TTATTTATTATTTA
1 TTTATTTATTATTTA
40753244 GGTGTTCTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 16 0.41
15 10 0.26
16 6 0.15
17 7 0.18
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATTTATTATTTA
Found at i:40753201 original size:21 final size:20
Alignment explanation
Indices: 40753177--40753244 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
40753167 ATTTTTACAG
40753177 TTTAGTTTTTATTTTTATTTA
1 TTTAGTTTTTATTTTTA-TTA
* ** *
40753198 TTTAATTTTTAACTTTACTAA
1 TTTAGTTTTTATTTTTA-TTA
40753219 TTTA-TTATTTATTATTTATTA
1 TTTAGTT-TTTATT-TTTATTA
40753240 TTTAG
1 TTTAG
40753245 GTGTTCTATG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
20 2 0.06
21 30 0.83
22 4 0.11
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTAGTTTTTATTTTTATTA
Found at i:40753228 original size:7 final size:7
Alignment explanation
Indices: 40753218--40753243 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40753208 AACTTTACTA
40753218 ATTTATT
1 ATTTATT
40753225 ATTTATT
1 ATTTATT
40753232 ATTTATT
1 ATTTATT
40753239 ATTTA
1 ATTTA
40753244 GGTGTTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTTATT
Found at i:40756127 original size:41 final size:40
Alignment explanation
Indices: 40756048--40756156 Score: 119
Period size: 41 Copynumber: 2.6 Consensus size: 40
40756038 ACTTGCTTTT
* * * * * *
40756048 AGCCTGCTAGACTTATAGTCCGAATAATTTCACTGGCATTA
1 AGCCTGCTAGAC-AATAGTCTGAATTATATCACCGGCATCA
40756089 AGCCTGCTAGACAATGAGTCTGAATTATATCACCGGCATCA
1 AGCCTGCTAGACAAT-AGTCTGAATTATATCACCGGCATCA
* *
40756130 AGCCTCCTGGACAATAAGTCTGAATTA
1 AGCCTGCTAGACAAT-AGTCTGAATTA
40756157 CATTCGATCA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 2 0.03
41 56 0.97
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (40 bp):
AGCCTGCTAGACAATAGTCTGAATTATATCACCGGCATCA
Found at i:40757834 original size:13 final size:13
Alignment explanation
Indices: 40757816--40757840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40757806 TCAAACGATT
40757816 AAATTTTCACACG
1 AAATTTTCACACG
40757829 AAATTTTCACAC
1 AAATTTTCACAC
40757841 ATATAACCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:40758078 original size:21 final size:22
Alignment explanation
Indices: 40758052--40758092 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40758042 CCTTTTTTTT
*
40758052 AAGGAAT-ATTAAATAAAAGGA
1 AAGGAATCATAAAATAAAAGGA
40758073 AAGGAATCATAAAATAAAAG
1 AAGGAATCATAAAATAAAAG
40758093 CCTAGGGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.63, C:0.02, G:0.17, T:0.17
Consensus pattern (22 bp):
AAGGAATCATAAAATAAAAGGA
Found at i:40770071 original size:15 final size:14
Alignment explanation
Indices: 40770050--40770085 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
40770040 ATAATCCTTA
*
40770050 ATAATTATCTTAAT
1 ATAATTATCCTAAT
40770064 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
40770079 ATAATTA
1 ATAATTA
40770086 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:40772028 original size:13 final size:13
Alignment explanation
Indices: 40772009--40772062 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
40771999 AAATAAGTAG
40772009 TAAATAATAA-AA
1 TAAATAATAATAA
*
40772021 TAAAATAA-AGTAA
1 T-AAATAATAATAA
40772034 TAAATAATAATAA
1 TAAATAATAATAA
*
40772047 TAACTAA-AATAA
1 TAAATAATAATAA
40772059 -AAAT
1 TAAAT
40772063 TGGGTTGCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 3 0.09
12 13 0.37
13 19 0.54
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (13 bp):
TAAATAATAATAA
Found at i:40772036 original size:18 final size:17
Alignment explanation
Indices: 40772009--40772060 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
40771999 AAATAAGTAG
40772009 TAAATAATAAAATAAAA
1 TAAATAATAAAATAAAA
40772026 TAAAGTAAT-AAATAATAA
1 TAAA-TAATAAAATAA-AA
40772044 T-AATAACTAAAATAAAA
1 TAAATAA-TAAAATAAAA
40772061 ATTGGGTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.10
17 15 0.48
18 13 0.42
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
TAAATAATAAAATAAAA
Found at i:40772054 original size:25 final size:25
Alignment explanation
Indices: 40771999--40772049 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
40771989 ATTAATATCC
*
40771999 AAAT-AAGTAGTAAATAATAAAATA
1 AAATAAAGTAATAAATAATAAAATA
40772023 AAATAAAGTAATAAATAATAATAATA
1 AAATAAAGTAATAAATAATAA-AATA
40772049 A
1 A
40772050 CTAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 4 0.17
25 15 0.62
26 5 0.21
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (25 bp):
AAATAAAGTAATAAATAATAAAATA
Found at i:40779833 original size:40 final size:40
Alignment explanation
Indices: 40779784--40779964 Score: 179
Period size: 40 Copynumber: 4.5 Consensus size: 40
40779774 GAGCTCGAAT
* *
40779784 GAGCAATACCTACTGAATCTACT-AATACATATGCGATTTC
1 GAGCCATACCTACTGAATCTACTGAA-ACGTATGCGATTTC
**
40779824 GAGTGATACCTACTGAATCTACTGAAACGTATGC-ACTTTC
1 GAGCCATACCTACTGAATCTACTGAAACGTATGCGA-TTTC
* * * *
40779864 GAGCCATACCTATTGAATGTACTGAAACGTATGTGCTTTC
1 GAGCCATACCTACTGAATCTACTGAAACGTATGCGATTTC
* * * * *
40779904 GAGCCATACCTATTGAATTTATTGAAATGTATGCGCTCTT-
1 GAGCCATACCTACTGAATCTACTGAAACGTATGCGAT-TTC
* *
40779944 AAGTCATACCTACTGAATCTA
1 GAGCCATACCTACTGAATCTA
40779965 TTTAAAAGAA
Statistics
Matches: 120, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 115 0.96
41 4 0.03
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (40 bp):
GAGCCATACCTACTGAATCTACTGAAACGTATGCGATTTC
Found at i:40779881 original size:80 final size:80
Alignment explanation
Indices: 40779783--40779964 Score: 197
Period size: 80 Copynumber: 2.3 Consensus size: 80
40779773 GGAGCTCGAA
* **
40779783 TGAGCAATACCTACTGAATCTACT-AATACATATGCGATTTCGAGTGATACCTACTGAATCTACT
1 TGAGCCATACCTACTGAATCTACTGAA-ACATATGCGATTTCGAGCCATACCTACTGAATCTACT
40779847 GAAACGTATGCACT-T
65 GAAACGTATGCACTCT
* * * * * * * *
40779862 TCGAGCCATACCTATTGAATGTACTGAAACGTATGTGCTTTCGAGCCATACCTATTGAATTTATT
1 T-GAGCCATACCTACTGAATCTACTGAAACATATGCGATTTCGAGCCATACCTACTGAATCTACT
* *
40779927 GAAATGTATGCGCTCT
65 GAAACGTATGCACTCT
* *
40779943 TAAGTCATACCTACTGAATCTA
1 TGAGCCATACCTACTGAATCTA
40779965 TTTAAAAGAA
Statistics
Matches: 83, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
79 1 0.01
80 78 0.94
81 4 0.05
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (80 bp):
TGAGCCATACCTACTGAATCTACTGAAACATATGCGATTTCGAGCCATACCTACTGAATCTACTG
AAACGTATGCACTCT
Found at i:40780020 original size:36 final size:36
Alignment explanation
Indices: 40779979--40780050 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
40779969 AAAGAATGCT
* *
40779979 CTATCAAGTAAAACAATCTACTAATATACTGAATAA
1 CTATCAAGGAAAACAATCCACTAATATACTGAATAA
****
40780015 CTATCAAGGAATGTTATCCACTAATATACTGAATAA
1 CTATCAAGGAAAACAATCCACTAATATACTGAATAA
40780051 GCTCAGTCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (36 bp):
CTATCAAGGAAAACAATCCACTAATATACTGAATAA
Found at i:40781488 original size:25 final size:25
Alignment explanation
Indices: 40781449--40781521 Score: 96
Period size: 25 Copynumber: 2.9 Consensus size: 25
40781439 TGCAGACACA
*
40781449 CCAGCTCATGAGAGCTTACCGA-TT
1 CCAGCTCGTGAGAGCTTACCGATTT
40781473 CTCAGCTCGT-ATGAGCTTACCGATTT
1 C-CAGCTCGTGA-GAGCTTACCGATTT
*
40781499 CCAGCTCGTGAGAGCATACCGAT
1 CCAGCTCGTGAGAGCTTACCGAT
40781522 CCATAGCTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 2 0.05
25 37 0.86
26 4 0.09
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (25 bp):
CCAGCTCGTGAGAGCTTACCGATTT
Found at i:40781529 original size:25 final size:24
Alignment explanation
Indices: 40781451--40781530 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
40781441 CAGACACACC
* *
40781451 AGCTCATGAGAGCTTACCGATTCT
1 AGCTCGTGAGAGCTTACCGATCCT
40781475 CAGCTCGT-ATGAGCTTACCGATTTCC-
1 -AGCTCGTGA-GAGCTTACCGA--TCCT
*
40781501 AGCTCGTGAGAGCATACCGATCCAT
1 AGCTCGTGAGAGCTTACCGATCC-T
40781526 AGCTC
1 AGCTC
40781531 ACATGAGCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
23 3 0.07
24 1 0.02
25 39 0.85
26 1 0.02
27 2 0.04
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (24 bp):
AGCTCGTGAGAGCTTACCGATCCT
Found at i:40791115 original size:61 final size:61
Alignment explanation
Indices: 40791017--40791146 Score: 206
Period size: 61 Copynumber: 2.1 Consensus size: 61
40791007 CATGGTCCAT
*
40791017 GCACACGGGCATGTAAGGTCGTACATGGGCGTATAGGTTAACCACACGACCTTTTTTGGAG
1 GCACACGGGCATGTAAGGTCGTACATGGGCGTATAGGTTAACCACACGACCTTGTTTGGAG
* * * * *
40791078 TCACACGTGCATGTGAGGTCGTACATGGGTGTGTAGGTTAACCACACGACCTTGTTTGGAG
1 GCACACGGGCATGTAAGGTCGTACATGGGCGTATAGGTTAACCACACGACCTTGTTTGGAG
40791139 GCACACGG
1 GCACACGG
40791147 ACTGGACTCT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.25
Consensus pattern (61 bp):
GCACACGGGCATGTAAGGTCGTACATGGGCGTATAGGTTAACCACACGACCTTGTTTGGAG
Found at i:40801532 original size:50 final size:50
Alignment explanation
Indices: 40801452--40801597 Score: 195
Period size: 50 Copynumber: 2.9 Consensus size: 50
40801442 GATAATAACA
* * * **
40801452 TGCCAAAGCCATGTCCCAGATATAGCCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
* * *
40801502 TGGCC-ATGTCATGTCCCAGATATGGTCTTACAGGGGACCTCTCATCTCGG
1 T-GCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
*
40801552 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATA
40801598 ATCTCAATGA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 3 0.04
50 76 0.93
51 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
Found at i:40809727 original size:14 final size:14
Alignment explanation
Indices: 40809708--40809734 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40809698 CCAACCCCAA
40809708 TACAGATATAGATG
1 TACAGATATAGATG
40809722 TACAGATATAGAT
1 TACAGATATAGAT
40809735 ATAAGCATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (14 bp):
TACAGATATAGATG
Found at i:40810741 original size:12 final size:11
Alignment explanation
Indices: 40810724--40810754 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
40810714 GTGAAGAAAG
40810724 GAAAAGAAAAA
1 GAAAAGAAAAA
40810735 GACAAAGAAAAA
1 GA-AAAGAAAAA
40810747 GAAAAGAA
1 GAAAAGAA
40810755 GAACGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:40812186 original size:41 final size:40
Alignment explanation
Indices: 40812139--40812216 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 40
40812129 ATTATTATCA
*
40812139 TATTTAA-AATAAAATTATATTTATATATTTAAAATTATATT
1 TATTTAATAA-AAAATTAGATTTAT-TATTTAAAATTATATT
* * *
40812180 TATTTAATAAAAACTTAGATTTATTTTTTAAATTTAT
1 TATTTAATAAAAAATTAGATTTATTATTTAAAATTAT
40812217 CCAATTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 11 0.34
41 19 0.59
42 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (40 bp):
TATTTAATAAAAAATTAGATTTATTATTTAAAATTATATT
Found at i:40812192 original size:20 final size:20
Alignment explanation
Indices: 40812139--40812205 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
40812129 ATTATTATCA
*
40812139 TATTTAAAATAAAATTATATT
1 TATTTAATA-AAAATTATATT
* * *
40812160 TATATATTTAAAATTATATT
1 TATTTAATAAAAATTATATT
*
40812180 TATTTAATAAAAACTTAGATT
1 TATTTAATAAAAA-TTATATT
40812201 TATTT
1 TATTT
40812206 TTTAAATTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (20 bp):
TATTTAATAAAAATTATATT
Found at i:40820721 original size:18 final size:17
Alignment explanation
Indices: 40820695--40820728 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40820685 ATTATTGCTC
40820695 TTATGTGTATTGTATTGT
1 TTATGTGTATT-TATTGT
*
40820713 TTATTTGTATTTATTG
1 TTATGTGTATTTATTG
40820729 ATTCTTTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (17 bp):
TTATGTGTATTTATTGT
Found at i:40820736 original size:17 final size:18
Alignment explanation
Indices: 40820695--40820737 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
40820685 ATTATTGCTC
* *
40820695 TTATGTGTATTGTATTGT
1 TTATTTGTATTGTATTGA
40820713 TTATTTGTATT-TATTGA
1 TTATTTGTATTGTATTGA
*
40820730 TTCTTTGT
1 TTATTTGT
40820738 CGCTCATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.16, C:0.02, G:0.16, T:0.65
Consensus pattern (18 bp):
TTATTTGTATTGTATTGA
Found at i:40824884 original size:6 final size:6
Alignment explanation
Indices: 40824875--40824926 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
40824865 AACAAAATAG
* * * *
40824875 AAGAAA AAGAAA AATCAAA AACAAA AACAAA AAAAAA GAAGAAA AAGAAA
1 AAGAAA AAGAAA AA-GAAA AAGAAA AAGAAA AAGAAA -AAGAAA AAGAAA
40824925 AA
1 AA
40824927 TCAAAATCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
6 31 0.76
7 10 0.24
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:40824910 original size:29 final size:29
Alignment explanation
Indices: 40824850--40824914 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
40824840 TCCAATCCCC
* *
40824850 AAAAA-AAAAATCAAAAACAAAATAGAAG
1 AAAAAGAAAAATCAAAAACAAAATAAAAA
40824878 AAAAAGAAAAATCAAAAACAAAA-ACAAAA
1 AAAAAGAAAAATCAAAAACAAAATA-AAAA
40824907 AAAAAGAA
1 AAAAAGAA
40824915 GAAAAAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.82, C:0.08, G:0.06, T:0.05
Consensus pattern (29 bp):
AAAAAGAAAAATCAAAAACAAAATAAAAA
Found at i:40824915 original size:38 final size:42
Alignment explanation
Indices: 40824849--40824958 Score: 135
Period size: 38 Copynumber: 2.8 Consensus size: 42
40824839 ATCCAATCCC
40824849 CAAAAA-AAAAATCAAAAACAAAATAGAAGAAAAAGAAAAAT
1 CAAAAACAAAAATCAAAAACAAAATAGAAGAAAAAGAAAAAT
40824890 CAAAAACAAAAA-C-AAAA-AAAA-AGAAGAAAAAGAAAAAT
1 CAAAAACAAAAATCAAAAACAAAATAGAAGAAAAAGAAAAAT
* * **
40824928 CAAAATC-AAAGTCAAAATGAAAAT-GAAGAAA
1 CAAAAACAAAAATCAAAAACAAAATAGAAGAAA
40824959 GAGAGAATAA
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
37 3 0.05
38 24 0.39
39 7 0.11
40 15 0.25
41 7 0.11
42 5 0.08
ACGTcount: A:0.75, C:0.08, G:0.09, T:0.07
Consensus pattern (42 bp):
CAAAAACAAAAATCAAAAACAAAATAGAAGAAAAAGAAAAAT
Found at i:40825837 original size:7 final size:7
Alignment explanation
Indices: 40825827--40825871 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
40825817 GAAAAAAATG
40825827 ATGAAAA
1 ATGAAAA
40825834 ATG-AAA
1 ATGAAAA
40825840 ATGAAAA
1 ATGAAAA
40825847 ATGAAAAA
1 ATG-AAAA
40825855 ATGAAAA
1 ATGAAAA
40825862 A-GTAAAA
1 ATG-AAAA
40825869 ATG
1 ATG
40825872 GAGAGGCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.21
7 19 0.56
8 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
ATGAAAA
Found at i:40825843 original size:13 final size:13
Alignment explanation
Indices: 40825827--40825853 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40825817 GAAAAAAATG
40825827 ATGAAAAATGAAA
1 ATGAAAAATGAAA
40825840 ATGAAAAATGAAA
1 ATGAAAAATGAAA
40825853 A
1 A
40825854 AATGAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:40825856 original size:8 final size:8
Alignment explanation
Indices: 40825812--40825862 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
40825802 ACTTTGAGTC
40825812 AAAATGAAA
1 AAAATG-AA
40825821 AAAATGATGA
1 AAAATGA--A
40825831 AAAATG--
1 AAAATGAA
40825837 AAAATG-A
1 AAAATGAA
40825844 AAAATGAA
1 AAAATGAA
40825852 AAAATGAA
1 AAAATGAA
40825860 AAA
1 AAA
40825863 GTAAAAATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
6 6 0.16
7 6 0.16
8 13 0.34
9 6 0.16
10 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (8 bp):
AAAATGAA
Found at i:40825857 original size:15 final size:14
Alignment explanation
Indices: 40825827--40825871 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
40825817 GAAAAAAATG
40825827 ATGAAAAATG-AAA
1 ATGAAAAATGAAAA
40825840 ATGAAAAATGAAAAA
1 ATGAAAAATG-AAAA
40825855 ATGAAAAA-GTAAAA
1 ATGAAAAATG-AAAA
40825869 ATG
1 ATG
40825872 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 10 0.34
14 8 0.28
15 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (14 bp):
ATGAAAAATGAAAA
Found at i:40827188 original size:44 final size:43
Alignment explanation
Indices: 40827073--40827596 Score: 252
Period size: 44 Copynumber: 11.9 Consensus size: 43
40827063 TAAGTTTTTC
*
40827073 AAGCAAGTCTTATCCCCCCTGAGGTTGCAGTGGGGCAGATCGGAG
1 AAGCAAGTCTTAT--CCCCTGAGGTTGCAGTGGAGCAGATCGGAG
* * *
40827118 AAGACAAGTCTTATCTCCCTAAGGTTGTAGTGGAGCAGA-CTGAG
1 AAG-CAAGTCTTATC-CCCTGAGGTTGCAGTGGAGCAGATCGGAG
* **
40827162 TAAGCAGGTCTTATCCCCTTGAGGTTGCAGTGG-GCCAGATCAAAG
1 -AAGCAAGTCTTATCCCC-TGAGGTTGCAGTGGAG-CAGATCGGAG
* * * * *
40827207 ATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAACAGATTGAAG
1 A-AGCAAGTCTTATC-CCCTGAGGTTGCAGTGGAGCAGATCGGAG
** * * * * * * * *
40827252 CTG-ATAATCCTATCTCCCTGAAGCTGTACTGGAGCGGAT--TA-
1 AAGCA-AGTCTTATC-CCCTGAGGTTGCAGTGGAGCAGATCGGAG
* * * *
40827293 AAGTAATAGATCTTATCTCTCTGAAGTTGCAGT--AG-AG-T-GGAC
1 AAG-CA-AG-TCTTATC-CCCTGAGGTTGCAGTGGAGCAGATCGGAG
* * * *
40827335 TA-CATTAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGA-CTGAG
1 AAGCA--A-GTCTTATC-CCCTGAGGTTGCAGTGGAGCAGATCGGAG
* * *
40827380 AAGACAAGTTTTATCTCCCTGAGGTTGCCGTGGAGCAGA-CTGAG
1 AAG-CAAGTCTTATC-CCCTGAGGTTGCAGTGGAGCAGATCGGAG
* * *
40827424 TAAGCAGGTCTTATCCCCCTGAGGTTGTAGTGGGGCAGATCGGAG
1 -AAGCAAGTCTTAT-CCCCTGAGGTTGCAGTGGAGCAGATCGGAG
* *
40827469 AAGACAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGA-CTGAG
1 AAG-CAAGTCTTATC-CCCTGAGGTTGCAGTGGAGCAGATCGGAG
* * * * * * *
40827513 TAAGCAGGTCTTATCCCCTAAAGTTGTAGTGG-GACCGATCGAAT
1 -AAGCAAGTCTTATCCCCTGAGGTTGCAGTGGAG-CAGATCGGAG
* *
40827557 ATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGAT
1 A-AGCAAGTCTTATC-CCCTGAGGTTGCAGTGGAGCAGAT
40827597 TGAAGCCGAT
Statistics
Matches: 370, Mismatches: 74, Indels: 70
0.72 0.14 0.14
Matches are distributed among these distances:
40 2 0.01
41 25 0.07
42 6 0.02
43 27 0.07
44 171 0.46
45 123 0.33
46 14 0.04
47 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (43 bp):
AAGCAAGTCTTATCCCCTGAGGTTGCAGTGGAGCAGATCGGAG
Found at i:40827225 original size:89 final size:87
Alignment explanation
Indices: 40827073--40827595 Score: 423
Period size: 89 Copynumber: 5.9 Consensus size: 87
40827063 TAAGTTTTTC
* * *
40827073 AAGCAAGTCTTATCCCCCCTGAGGTTGCAGTGGGGCAGATCGGAGAAGACAAGTCTTATCTCCCT
1 AAGCAGGTCTTAT--CCCCTGAGGTTGCAGT-GGGCAGATCGAAGAAGACAAATCTTATCTCCCT
* *
40827138 AAGGTTGTAGTGGAGCAGACTGAGT
63 GAGGTTGCAGTGGAGCAGACTGAGT
* * *
40827163 AAGCAGGTCTTATCCCCTTGAGGTTGCAGTGGGCCAGATCAAAGATGGCAAATCTTATCTCCCTG
1 AAGCAGGTCTTATCCCC-TGAGGTTGCAGTGGG-CAGATCGAAGAAGACAAATCTTATCTCCCTG
* *
40827228 AGGTTGCAGTGGAACAGATTGAAGCT
64 AGGTTGCAGTGGAGCAGACTG-AG-T
* * * * * * * * * ** * * * *
40827254 GA-TA-ATCCTATCTCCCTGAAGCTGTACTGGAGCGGATTAAAGTA-ATAGATCTTATCTCTCTG
1 AAGCAGGTCTTATC-CCCTGAGGTTGCAGTGG-GCAGATCGAAGAAGACAAATCTTATCTCCCTG
* * **
40827316 AAGTTGCAGTAGAGTGGACT-A--
64 AGGTTGCAGTGGAGCAGACTGAGT
* ** * * * *
40827337 CATTAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGA-CTG-AGAAGACAAGTTTTATCTCCCT
1 AAGCAGGTCTTATC-CCCTGAGGTTGCAGTGG-GCAGATC-GAAGAAGACAAATCTTATCTCCCT
*
40827400 GAGGTTGCCGTGGAGCAGACTGAGT
63 GAGGTTGCAGTGGAGCAGACTGAGT
* * *
40827425 AAGCAGGTCTTATCCCCCTGAGGTTGTAGTGGGGCAGATCGGAGAAGACAAGTCTTATCTCCCTG
1 AAGCAGGTCTTAT-CCCCTGAGGTTGCAGT-GGGCAGATCGAAGAAGACAAATCTTATCTCCCTG
*
40827490 AGGTTACAGTGGAGCAGACTGAGT
64 AGGTTGCAGTGGAGCAGACTGAGT
* * * * * * *
40827514 AAGCAGGTCTTATCCCCTAAAGTTGTAGTGGGACCGATCGAATATGGCAAATCTTATCTCCCTGA
1 AAGCAGGTCTTATCCCCTGAGGTTGCAGTGGG-CAGATCGAAGAAGACAAATCTTATCTCCCTGA
40827579 GGTTGCAGTGGAGCAGA
65 GGTTGCAGTGGAGCAGA
40827596 TTGAAGCCGA
Statistics
Matches: 342, Mismatches: 73, Indels: 38
0.75 0.16 0.08
Matches are distributed among these distances:
83 1 0.00
84 5 0.01
85 51 0.15
86 2 0.01
87 3 0.01
88 119 0.35
89 140 0.41
90 19 0.06
91 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (87 bp):
AAGCAGGTCTTATCCCCTGAGGTTGCAGTGGGCAGATCGAAGAAGACAAATCTTATCTCCCTGAG
GTTGCAGTGGAGCAGACTGAGT
Found at i:40827581 original size:133 final size:133
Alignment explanation
Indices: 40827076--40827596 Score: 382
Period size: 133 Copynumber: 3.9 Consensus size: 133
40827066 GTTTTTCAAG
* * * * *
40827076 CAAGTCTTATCCCCCCTGAGGTTGCAGTGGGGCAGATCGGAGAAGACAAGTCTTATCTCCCTAAG
1 CAAGTCTTAT-CTCCCTGAGGTTACAGTGGAGCAGA-CTGAGAAGACAAGTCTTATCTCCCTAAA
* * ** * **
40827141 GTTGTAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCTTGAGGTTGCAGTGG-GCCAGATCAA
64 GTTGCAGTGGAGCAGACTGAATAAGCAAATCTTATCCCCCTGAGGTTGCAGTGGAG-CAGATCGG
* *
40827205 AGATGG
128 AGAAGA
* * * * ** * * *
40827211 CAAATCTTATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGCTGATAA-TCCTATCTCCCTGAAG
1 CAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACTG-AGAAGACAAGTCTTATCTCCCTAAAG
* * * * * * * * * * *
40827275 CTGTACTGGAGCGGATTAAAGTAA-TAGATCTTATCTCTCTGAAGTTGCAGT--AG-AG-T-GGA
65 TTGCAGTGGAGCAGACTGAA-TAAGCAAATCTTATCCCCCTGAGGTTGCAGTGGAGCAGATCGGA
** *
40827334 CTACA
129 GAAGA
* * * * * *
40827339 TTAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAGAAGACAAGTTTTATCTCCCTGAGG
1 -CAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACTGAGAAGACAAGTCTTATCTCCCTAAAG
* * ** * *
40827404 TTGCCGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTGTAGTGGGGCAGATCGGAG
65 TTGCAGTGGAGCAGACTGAATAAGCAAATCTTATCCCCCTGAGGTTGCAGTGGAGCAGATCGGAG
40827469 AAGA
130 AAGA
*
40827473 CAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACTGAGTAAG-CAGGTCTTATC-CCCTAAAG
1 CAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACTGAG-AAGACAAGTCTTATCTCCCTAAAG
* * * *
40827536 TTGTAGTGG-GACCGA-TCGAATATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGAT
65 TTGCAGTGGAG-CAGACT-GAATA-AGCAAATCTTATCCCCCTGAGGTTGCAGTGGAGCAGAT
40827597 TGAAGCCGAT
Statistics
Matches: 292, Mismatches: 79, Indels: 32
0.72 0.20 0.08
Matches are distributed among these distances:
128 10 0.03
129 78 0.27
130 2 0.01
131 3 0.01
132 23 0.08
133 128 0.44
134 39 0.13
135 9 0.03
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (133 bp):
CAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACTGAGAAGACAAGTCTTATCTCCCTAAAGT
TGCAGTGGAGCAGACTGAATAAGCAAATCTTATCCCCCTGAGGTTGCAGTGGAGCAGATCGGAGA
AGA
Found at i:40827586 original size:262 final size:264
Alignment explanation
Indices: 40827079--40828209 Score: 612
Period size: 262 Copynumber: 4.3 Consensus size: 264
40827069 TTTCAAGCAA
* *
40827079 GTCTTATCCCCCCTGAGGTTGCAGTGGGGCAGATCGGAGAAGACAAGTCTTATCTCCCTAAGGTT
1 GTCTTATCCCCCCTGAGGTTACAGTGGAGCAGATCGGAGAAGACAAGTCTTATCTCCCTAAGGTT
* * *
40827144 GTAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCTTGAGGTTGCAGTGGGCCAGATCAAAGAT
66 GCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTGCAGTGGGCCAGATCAAAGAA
* * * * * *
40827209 GGCAAATCTTATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGCTGATAATCCTATCTCCCTGAA
131 GACAAATCTTATCTCCCTGAGGTTACAGTGGAACAGACTGAAGCTAACAATCCTATCTCCCTAAA
* * * *
40827274 GCTGTACTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGACTACA
196 GCTGTACTGGAGCCGATCAAAGTAATAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGGACTACA
40827339 TTAG
261 TTAG
* * * * *
40827343 GTCTTAT-CTCCCTGAGGTTACAGTGGAGTAGA-CTGAGAAGACAAGTTTTATCTCCCTGAGGTT
1 GTCTTATCCCCCCTGAGGTTACAGTGGAGCAGATCGGAGAAGACAAGTCTTATCTCCCTAAGGTT
* * * **
40827406 GCCGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTGTAGTGGGGCAGATCGGAGAA
66 GCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTGCAGTGGGCCAGATCAAAGAA
* * * *
40827471 GACAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACTG-AG-TAAGCAGGTCTTATC-CCCTA
131 GACAAATCTTATCTCCCTGAGGTTACAGTGGAACAGACTGAAGCTAA-CA-ATCCTATCTCCCTA
* * * *
40827533 AAGTTGTAGTGG-GACCGATCGAA-T-ATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAG
194 AAGCTGTACTGGAG-CCGATCAAAGTAAT---AAATCTTATCTCCCTGAAGTTGCAGT--AG-AG
* ***
40827595 ATTGAAGCCGA-TA-
252 -TGGACTAC-ATTAG
* * * * ** ** * * * **
40827608 ATCCTAT-CTCCCTGAAGTTGTAGTGGAGTGGGT--TA-AAGTA-ATAGATCATATCTCTTTGAA
1 GTCTTATCCCCCCTGAGGTTACAGTGGAGCAGATCGGAGAAG-ACA-AG-TCTTATCTCCCT-AA
** ** * * ** * * * *
40827668 -GTTGCAGTATAGTGGA-TCA--CATTAGGTCTTATCCCCCTAAAGTTTCAGTGGGACC-GATCG
62 GGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTGCAGTGGG-CCAGATCA
* * * * * ** *
40827728 AAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCC
126 AAGAAGACAAATCTTATCTCCCTGAGGTTACAGTGGAACAGACTGAAGCTAACAATCCTATCTCC
* * ** * * * * * *
40827793 CTAAAGTTGTAGTGGAGTGGGTTAAAGTACTAGATCTTATCTCTCTGAAGTTGCAGTGGGACCGA
191 CTAAAGCTGTACTGGAGCCGATCAAAGTAATAAATCTTATCTCCCTGAAGTTGCAGT-AGA--G-
* * * *
40827858 TCGA--AGATGGCAA
252 TGGACTACAT--TAG
* * * * * ** * * *
40827871 ATCTTAT-CTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAA-TCCTATCTACCTGAA-GT
1 GTCTTATCCCCCCTGAGGTTACAGTGGAGCAGATCGGAGAAGACAAGTCTTATCTCCCT-AAGGT
* * ** ** * * * * * * *
40827933 TGTAGTTGAGTGGGTTAAAGTAA-CAGATATTATCTCTCTGAAGTTGCAGTGGGACC-GATCGAA
65 TGCAGTGGAGCAGACT-GAGTAAGCAGGTCTTATCCCCCTGAGGTTGCAGTGGG-CCAGATCAAA
* * ** * * ** *
40827996 GATGGCAAATCTTATCTCCCTGAGGTTGTAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCT
128 GAAGACAAATCTTATCTCCCTGAGGTTACAGTGGAACAGACTGAAGCTAACAATCCTATCTCCCT
* * ** * * * *
40828061 AAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGA-T
193 AAAGCTGTACTGGAGCCGATCAAAGTAATAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGGACT
*
40828125 CGCATTAG
258 -ACATTAG
* * * * * * * *
40828133 GTGTTAT-CCCCCTGAAGTTGCAGTGG-GACCGATCGAAGATGGCAAATCTTATCTCCCTAAGGT
1 GTCTTATCCCCCCTGAGGTTACAGTGGAG-CAGATCGGAGAAGACAAGTCTTATCTCCCTAAGGT
40828196 TGCAGTGGAGCAGA
65 TGCAGTGGAGCAGA
40828210 TTGAAGCCTA
Statistics
Matches: 685, Mismatches: 140, Indels: 85
0.75 0.15 0.09
Matches are distributed among these distances:
259 3 0.00
260 5 0.01
261 26 0.04
262 293 0.43
263 122 0.18
264 21 0.03
265 53 0.08
266 160 0.23
267 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (264 bp):
GTCTTATCCCCCCTGAGGTTACAGTGGAGCAGATCGGAGAAGACAAGTCTTATCTCCCTAAGGTT
GCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTGCAGTGGGCCAGATCAAAGAA
GACAAATCTTATCTCCCTGAGGTTACAGTGGAACAGACTGAAGCTAACAATCCTATCTCCCTAAA
GCTGTACTGGAGCCGATCAAAGTAATAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGGACTACA
TTAG
Found at i:40827741 original size:174 final size:174
Alignment explanation
Indices: 40827167--40827849 Score: 705
Period size: 174 Copynumber: 3.9 Consensus size: 174
40827157 CTGAGTAAGC
* * * * *
40827167 AGGTCTTATCCCCTTGAGGTTGCAGTGGG-CCAGATCAAAGATGGCAAATCTTATCTCCCTGAGG
1 AGGTCTTATCCCCCTAAAGTTTCAGTGGGACC-GATCGAAGATGGCAAATCTTATCTCCCTGAGG
* * * * * *
40827231 TTGCAGTGGAACAGATTGAAGCTGATAATCCTATCTCCCTGAAGCTGTACTGGAGCGGATTAAAG
65 TTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGGTTAAAG
40827296 TAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGA-CTACATT
130 TAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATC-ACATT
* * * * * * * *
40827341 AGGTCTTATCTCCCTGAGGTTACAGTGGAGTA--GA-CTG-AGAAGACAAGTTTTATCTCCCTGA
1 AGGTCTTATCCCCCTAAAGTTTCAGTGG-G-ACCGATC-GAAGATGGCAAATCTTATCTCCCTGA
* * ** * * *
40827402 GGTTGCCGTGGAGCAGACTGAGTAAG-C-A-GGTCTTATCCCCCTGAGGTTGTAGTGGGGCAGAT
63 GGTTGCAGTGGAGCAGA-T-TG-AAGCCGATAATCCTATCTCCCTGAAGTTGTAGT--GG-AG-T
* * * * * ** * * **
40827464 CGG--AGAAG-ACA-AG-TCTTATCTCCCTGAGGTTACAGTGGAGCAGACTGAGTAAGC
121 GGGTTA-AAGTA-ATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGA-TCA--CATT
*
40827518 AGGTCTTAT-CCCCTAAAGTTGT-AGTGGGACCGATCGAATATGGCAAATCTTATCTCCCTGAGG
1 AGGTCTTATCCCCCTAAAGTT-TCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGG
40827581 TTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGGTTAAAG
65 TTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGGTTAAAG
* * *
40827646 TAATAGATCATATCTCTTTGAAGTTGCAGTATAGTGGATCACATT
130 TAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCACATT
40827691 AGGTCTTATCCCCCTAAAGTTTCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGT
1 AGGTCTTATCCCCCTAAAGTTTCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGT
*
40827756 TGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGT
66 TGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGGTTAAAGT
*
40827821 ACTAGATCTTATCTCTCTGAAGTTGCAGT
131 AATAGATCTTATCTCTCTGAAGTTGCAGT
40827850 GGGACCGATC
Statistics
Matches: 410, Mismatches: 67, Indels: 64
0.76 0.12 0.12
Matches are distributed among these distances:
173 68 0.17
174 206 0.50
175 20 0.05
176 49 0.12
177 67 0.16
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (174 bp):
AGGTCTTATCCCCCTAAAGTTTCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGT
TGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGGTTAAAGT
AATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCACATT
Found at i:40827791 original size:44 final size:44
Alignment explanation
Indices: 40827737--40828289 Score: 242
Period size: 44 Copynumber: 12.6 Consensus size: 44
40827727 GAAGATGGCA
*
40827737 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGAT
* * * ** * * *
40827781 AATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAG--TACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGA-T
* * * **
40827824 AGATCTTATCTCTCTGAAGTTGCAGTGG-GACCGATCGAAGATGGCA-
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAG-CCG-AT
*
40827870 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGAT
* * * * ** * * ** *
40827914 AATCCTATCTACCTGAAGTTGTAGTTGAGTGGGTTAAAG-TAAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGAT
* * * * **
40827957 AGATATTATCTCTCTGAAGTTGCAGTGG-GACCGATCGAAGATGGCA-
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAG-CCG-AT
* *
40828003 AATCTTATCTCCCTGAGGTTGTAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGAT
* * * ** * * **
40828047 AATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAG-TAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGAT
* * *
40828090 AGATCTTATCTCTCTGAAGTTGCAGT--AG-AG--TGGA-TCGCATT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCG-A-T
* * * * * **
40828131 AGGTGTTATCCCCCTGAAGTTGCAGTGG-GACCGATCGAAGATGGCA-
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAG-CCG-AT
*
40828177 AATCTTATCTCCCT-AAGGTTGCAGTGGAGCAGATTGAAGCCTAT
1 AATCTTATCTCCCTGAA-GTTGCAGTGGAGCAGATTGAAGCCGAT
* * * ** * * **
40828221 AATCCTATCTCCTTGAAGTTGTAGTGGAGTGGGTTAAAG-TAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGAT
*
40828264 AGATCTTATCTCTCTGAAGTTGCAGT
1 A-ATCTTATCTCCCTGAAGTTGCAGT
40828290 AGAGTGGATC
Statistics
Matches: 371, Mismatches: 105, Indels: 66
0.68 0.19 0.12
Matches are distributed among these distances:
39 2 0.01
40 1 0.00
41 24 0.06
42 4 0.01
43 15 0.04
44 219 0.59
45 92 0.25
46 8 0.02
47 1 0.00
48 5 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGAT
Found at i:40828126 original size:133 final size:133
Alignment explanation
Indices: 40827185--40828115 Score: 747
Period size: 133 Copynumber: 7.1 Consensus size: 133
40827175 TCCCCTTGAG
* *
40827185 GTTGCAGTGGG-CCAGATCAAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAACAGATTG
1 GTTGCAGTGGGACC-GATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTG
* * * * * *
40827249 AAGCTGATAATCCTATCTCCCTGAAGCTGTACTGGAGCGGATTAAAGTAATAGATCTTATCTCTC
65 AAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATCTCTC
40827314 TGAA
130 TGAA
* * * * ** * * *
40827318 GTTGCAGT-AGA--G-TGGACTACAT--TAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACT
1 GTTGCAGTGGGACCGATCGA--AGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATT
** * ** * * ** ** ** * * * *
40827377 G-AGAAGACAAGTTTTATCTCCCTGAGGTTGCCGTGGAGCAGACT-GAGTAAGCAGGTCTTATCC
64 GAAGCCGATAA-TCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAA-TAGATCTTATCT
* *
40827440 CCCTGAG
127 CTCTGAA
* * * * * * * * *
40827447 GTTGTAGTGGGGCAGATCGGAGAAGACAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACTGA
1 GTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGA-T-T
** * ** * ** *
40827512 GTAAG-C-A-GGTCTTATC-CCCTAAAGTTGTAGTGG-GACCGATCGAA-T-ATGGCAAATCTTA
64 G-AAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAG-TGGGTTAAAGTAAT---AGATCTTA
* *
40827570 TCTCCCTGAG
124 TCTCTCTGAA
* * ** * * * ** *
40827580 GTTGCAGT-GGAGCAGATTGAAG-CCG-ATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGGTT
1 GTTGCAGTGGGA-CCGATCGAAGATGGCA-AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATT
* ** * ** * * ** * * * * *
40827642 AAAG-TAATAGATCATATCTCTTTGAAGTTGCAGTATAGTGGATCACA-T--TAGGTCTTATCCC
64 GAAGCCGATA-ATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATCTC
* *
40827703 CCTAAA
128 TCTGAA
*
40827709 GTTTCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGA
1 GTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGA
*
40827774 AGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTACTAGATCTTATCTCTCT
66 AGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATCTCTCT
40827839 GAA
131 GAA
40827842 GTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGA
1 GTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGA
* * * * *
40827907 AGCCGATAATCCTATCTACCTGAAGTTGTAGTTGAGTGGGTTAAAGTAACAGATATTATCTCTCT
66 AGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATCTCTCT
40827972 GAA
131 GAA
*
40827975 GTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGTAGTGGAGCAGATTGA
1 GTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGA
40828040 AGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATCTCTCT
66 AGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATCTCTCT
40828105 GAA
131 GAA
40828108 GTTGCAGT
1 GTTGCAGT
40828116 AGAGTGGATC
Statistics
Matches: 630, Mismatches: 134, Indels: 68
0.76 0.16 0.08
Matches are distributed among these distances:
128 11 0.02
129 109 0.17
130 66 0.10
131 14 0.02
132 53 0.08
133 372 0.59
134 1 0.00
135 2 0.00
137 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (133 bp):
GTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGA
AGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATCTCTCT
GAA
Found at i:40828168 original size:174 final size:174
Alignment explanation
Indices: 40827970--40828498 Score: 644
Period size: 174 Copynumber: 3.1 Consensus size: 174
40827960 TATTATCTCT
* *
40827970 CTGAAGTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGTAGTGGAGCAG
1 CTGAAGTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTAAGGTTGCAGTGGAGCAG
40828035 ATTGAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATC
66 ATTGAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATC
* *
40828100 TCTCTGAAGTTGCAGTAGAGTGGATCGCATTAGGTGTTATCCCC
131 TCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCCCC
40828144 CTGAAGTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTAAGGTTGCAGTGGAGCAG
1 CTGAAGTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTAAGGTTGCAGTGGAGCAG
* * *
40828209 ATTGAAGCCTATAATCCTATCTCCTTGAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATC
66 ATTGAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATC
*
40828274 TCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCC
131 TCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCCCC
* * * * ** * *
40828318 CTGAGGTTGCAG-CGGAGCAGACCG-AGAAAGCAAGTCTTATCCCCCTGAA-GTTGCAGT-GAGG
1 CTGAAGTTGCAGTGGGA-CCGATCGAAGATGGCAAATCTTATCTCCCT-AAGGTTGCAGTGGA-G
* * ** * * * * * * **
40828379 TAGACTGAAGATGCTGAATCCTATCTCCCTGAAGATGCAATGGA----G-CAAAACAATAGATCT
63 CAGATTGAAGCCGAT-AATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCT
** * * * *
40828439 TATCTCTCTGAAGTTGTGGCAGAGTAGATCACATCAGGTCTTATCTCC
127 TATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCCCC
*
40828487 CTGAGGTTGCAG
1 CTGAAGTTGCAG
40828499 AGGGGCAGAC
Statistics
Matches: 317, Mismatches: 34, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
169 67 0.21
170 1 0.00
172 2 0.01
173 39 0.12
174 208 0.66
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (174 bp):
CTGAAGTTGCAGTGGGACCGATCGAAGATGGCAAATCTTATCTCCCTAAGGTTGCAGTGGAGCAG
ATTGAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGGTTAAAGTAATAGATCTTATC
TCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCCCC
Found at i:40830074 original size:3 final size:3
Alignment explanation
Indices: 40830066--40830098 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
40830056 ATTTTTAACT
*
40830066 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40830099 AGGTTTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:40830829 original size:18 final size:17
Alignment explanation
Indices: 40830803--40830836 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40830793 ATTATTGCTC
40830803 TTATGTGTATTGTATTGT
1 TTATGTGTATT-TATTGT
*
40830821 TTATTTGTATTTATTG
1 TTATGTGTATTTATTG
40830837 ATTCTTTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (17 bp):
TTATGTGTATTTATTGT
Found at i:40830844 original size:17 final size:18
Alignment explanation
Indices: 40830803--40830845 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
40830793 ATTATTGCTC
* *
40830803 TTATGTGTATTGTATTGT
1 TTATTTGTATTGTATTGA
40830821 TTATTTGTATT-TATTGA
1 TTATTTGTATTGTATTGA
*
40830838 TTCTTTGT
1 TTATTTGT
40830846 CGCTCATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.16, C:0.02, G:0.16, T:0.65
Consensus pattern (18 bp):
TTATTTGTATTGTATTGA
Found at i:40838960 original size:41 final size:41
Alignment explanation
Indices: 40838851--40838963 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 41
40838841 GCTTATTAAA
* *
40838851 ATACACCAGCATGAAGCCTTG-TAGGCACAAAGCCAGATATG
1 ATACACCGGCATGAAG-CTTGCTAGGCATAAAGCCAGATATG
* * * *
40838892 ATACATCGGCACGAAGCCTGCTAGGCATAAAGCCTGATATTG
1 ATACACCGGCATGAAGCTTGCTAGGCATAAAGCCAGATA-TG
40838934 -TACACCGGCATGAAGCTTGCTAGGCATAAA
1 ATACACCGGCATGAAGCTTGCTAGGCATAAA
40838964 CCTCTATCTA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
40 3 0.05
41 56 0.92
42 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (41 bp):
ATACACCGGCATGAAGCTTGCTAGGCATAAAGCCAGATATG
Found at i:40843055 original size:41 final size:41
Alignment explanation
Indices: 40842934--40843071 Score: 150
Period size: 41 Copynumber: 3.4 Consensus size: 41
40842924 AATACACCAA
* * * *
40842934 CATGAAGCCTTCTTGGCACAAAGCCAGATATGATTCACCGG
1 CATGAAGCCTGCTAGGCATAAAGCCAAATATGATTCACCGG
* * * * *
40842975 CACGAACCCTGCTAGGCATAAAGCCTAATATGGTACACCGG
1 CATGAAGCCTGCTAGGCATAAAGCCAAATATGATTCACCGG
* **
40843016 CATGAAGCCTGCTAGGCATAAATCCAAATACAATTCACCGG
1 CATGAAGCCTGCTAGGCATAAAGCCAAATATGATTCACCGG
* *
40843057 CATAAAGCCTTCTAG
1 CATGAAGCCTGCTAG
40843072 CCACAGAGCC
Statistics
Matches: 78, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (41 bp):
CATGAAGCCTGCTAGGCATAAAGCCAAATATGATTCACCGG
Found at i:40844191 original size:33 final size:34
Alignment explanation
Indices: 40844154--40844225 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
40844144 GCCCTTTTTT
40844154 TAAAAAAAATCAAACA-ATAAAATTTTTAAACGA
1 TAAAAAAAATCAAACATATAAAATTTTTAAACGA
* * *
40844187 T--AAAAATTCACACATTTTAAAATTTTTAAACGA
1 TAAAAAAAATCAAACA-TATAAAATTTTTAAACGA
40844220 TAAAAA
1 TAAAAA
40844226 TTCACATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
31 11 0.34
33 18 0.56
35 3 0.09
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (34 bp):
TAAAAAAAATCAAACATATAAAATTTTTAAACGA
Found at i:40848362 original size:106 final size:104
Alignment explanation
Indices: 40848243--40848449 Score: 285
Period size: 106 Copynumber: 2.0 Consensus size: 104
40848233 CGAACACCTA
* * *
40848243 TTGGTATGTAAAAGTTTGTTGAAATAGTTAATAATATCTTATATTTA-TAACGATCTCATTAATA
1 TTGGTATATAAAAGTTTGTTGAAATAGTTAATAATATCTTACA-TAAGTAACGATCTCATTAATA
40848307 ATAAATTTGTAACATTTTTT-ATAAAATATTG-GGGTAGGGGTG
65 AT--ATTT-TAA-ATTTTTTAATAAAATATTGAGGGTAGGGGTG
* *
40848349 TTGGTATATAAAAGTTTGTTGAAATAGTTAATAATATCTTCCATAAGTAATGATCTCATTAATAA
1 TTGGTATATAAAAGTTTGTTGAAATAGTTAATAATATCTTACATAAGTAACGATCTCATTAATAA
* *
40848414 TATTTTTAATTTTTTAATACAATATTGAGGGTAGGG
66 TATTTTAAATTTTTTAATAAAATATTGAGGGTAGGG
40848450 ATGGAGTAAC
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
102 7 0.08
103 12 0.13
104 12 0.13
105 2 0.02
106 58 0.64
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (104 bp):
TTGGTATATAAAAGTTTGTTGAAATAGTTAATAATATCTTACATAAGTAACGATCTCATTAATAA
TATTTTAAATTTTTTAATAAAATATTGAGGGTAGGGGTG
Found at i:40865656 original size:12 final size:12
Alignment explanation
Indices: 40865639--40865675 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
40865629 TGTGTCATGG
40865639 AAAAATGAATGA
1 AAAAATGAATGA
40865651 AAAAATGAATGA
1 AAAAATGAATGA
40865663 AAAAATGAA-GA
1 AAAAATGAATGA
40865674 AA
1 AA
40865676 TATTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (12 bp):
AAAAATGAATGA
Found at i:40866196 original size:14 final size:16
Alignment explanation
Indices: 40866177--40866214 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
40866167 ATTTCTAATA
40866177 TTTAAAATTA-AT-TT
1 TTTAAAATTATATATT
40866191 TTTAAAA-TATATATT
1 TTTAAAATTATATATT
40866206 TTTAAAATT
1 TTTAAAATT
40866215 TTCTAGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 9 0.43
15 9 0.43
16 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAAAATTATATATT
Found at i:40873352 original size:27 final size:27
Alignment explanation
Indices: 40873322--40873386 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
40873312 TTGAAAATCT
*
40873322 TGATGTAAAATTTAAAGCTCTCTAAAA
1 TGATGTAAAATTTAAAGCTCTATAAAA
* **
40873349 TGATGTAAAATTTGAAGCTCTATAATC
1 TGATGTAAAATTTAAAGCTCTATAAAA
40873376 TGATGTAAAAT
1 TGATGTAAAAT
40873387 GTGTCAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (27 bp):
TGATGTAAAATTTAAAGCTCTATAAAA
Found at i:40883925 original size:16 final size:16
Alignment explanation
Indices: 40883904--40883972 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
40883894 TTTGGTTCGC
40883904 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40883920 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40883936 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
40883953 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40883969 TGTA
1 TGTA
40883973 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40883950 original size:33 final size:32
Alignment explanation
Indices: 40883904--40883972 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
40883894 TTTGGTTCGC
40883904 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
40883936 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
40883969 TGTA
1 TGTA
40883973 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:40884037 original size:44 final size:45
Alignment explanation
Indices: 40883953--40884043 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
40883943 GGATTAGAGG
* * *
40883953 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
40883998 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
40884042 TG
1 TG
40884044 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:40884225 original size:16 final size:16
Alignment explanation
Indices: 40884188--40884242 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
40884178 TTAATCATAT
*
40884188 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
40884204 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
40884219 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
40884237 -TAAAAT
1 TTAAAAT
40884243 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:40884235 original size:18 final size:18
Alignment explanation
Indices: 40884194--40884242 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
40884184 ATATTTAAAC
40884194 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
40884212 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
40884228 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
40884243 TCTTAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:40884301 original size:61 final size:61
Alignment explanation
Indices: 40884223--40884422 Score: 189
Period size: 61 Copynumber: 3.3 Consensus size: 61
40884213 TTTTAATTAA
*
40884223 AATATATAAT-TTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATACT-ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * *
40884284 AATATATGATACTATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAATACTATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
* *
40884343 AATATATAAT-TTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATACT-ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
*
40884404 AATATATTATACTATAAAA
1 AATATATAATACTATAAAA
40884423 GATAATTTTA
Statistics
Matches: 105, Mismatches: 23, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.29
60 23 0.22
61 45 0.43
62 4 0.04
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (61 bp):
AATATATAATACTATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:40884356 original size:14 final size:15
Alignment explanation
Indices: 40884307--40884358 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40884297 ATAAAATATA
40884307 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
40884322 TATTAAATATATTAT
1 AATTAAATATATTAT
40884337 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40884350 AATTTAATA
1 AATTAAATA
40884359 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40884404 original size:120 final size:121
Alignment explanation
Indices: 40884191--40884483 Score: 500
Period size: 120 Copynumber: 2.4 Consensus size: 121
40884181 ATCATATTTA
40884191 AACATAATTATAATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATAATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
40884256 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA-ATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATATT
* * *
40884311 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATAATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
40884376 TATTCTTATATGAATTTACTCAAATCATAATATATTATACTATAAAAGATAATTTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATATT
* *
40884432 AA-ATAATTAAAATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATAATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
40884484 TAAAATAATT
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
120 158 0.98
121 4 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (121 bp):
AACATAATTATAATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATATT
Found at i:40884467 original size:16 final size:17
Alignment explanation
Indices: 40884442--40884482 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
40884432 AAATAATTAA
40884442 AATT-AAATATAT-TTT
1 AATTAAAATATATATTT
40884457 AATTAAAATATATGATTT
1 AATTAAAATATAT-ATTT
40884475 AA-TAAAAT
1 AATTAAAAT
40884483 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 6 0.26
18 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTAAAATATATATTT
Found at i:40894692 original size:14 final size:14
Alignment explanation
Indices: 40894673--40894699 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40894663 TTTATTTTTT
40894673 CCTTAGTTTTTAAC
1 CCTTAGTTTTTAAC
40894687 CCTTAGTTTTTAA
1 CCTTAGTTTTTAA
40894700 TCATCTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
CCTTAGTTTTTAAC
Found at i:40895208 original size:48 final size:48
Alignment explanation
Indices: 40895156--40895313 Score: 235
Period size: 48 Copynumber: 3.3 Consensus size: 48
40895146 AAGAGTTATC
* * *
40895156 ACTTACTTATTTCAATACATAACATATATCACATACAAAGTCATTTTA
1 ACTTACTCATTTCAATACATAACATATATCACATACAGAGTCATATTA
* * *
40895204 ACTTACTCATTTCAATACATAACAAATATCACATGCAGGGTCATATTA
1 ACTTACTCATTTCAATACATAACATATATCACATACAGAGTCATATTA
* *
40895252 ACTTACTCATTTCAATACGTAACATATATCACATAGAGAGTCATATTA
1 ACTTACTCATTTCAATACATAACATATATCACATACAGAGTCATATTA
*
40895300 ACTTACTCTTTTCA
1 ACTTACTCATTTCA
40895314 TATCCTTCCC
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 98 1.00
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (48 bp):
ACTTACTCATTTCAATACATAACATATATCACATACAGAGTCATATTA
Found at i:40900915 original size:13 final size:13
Alignment explanation
Indices: 40900897--40900921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40900887 TAATGGTATA
40900897 TTGAATCCATGAC
1 TTGAATCCATGAC
40900910 TTGAATCCATGA
1 TTGAATCCATGA
40900922 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:40901501 original size:27 final size:26
Alignment explanation
Indices: 40901470--40901647 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
40901460 TAAATTGTAC
40901470 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
40901497 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
40901523 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
40901551 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
40901579 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
40901606 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
40901633 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40901648 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 103 0.80
28 25 0.19
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:40901586 original size:82 final size:81
Alignment explanation
Indices: 40901471--40901626 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
40901461 AAATTGTACA
* *
40901471 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40901535 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
40901552 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
40901617 TGCGAGTTGA
65 TGCGAATTGA
40901627 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40901638 original size:82 final size:81
Alignment explanation
Indices: 40901467--40901647 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
40901457 GATTAAATTG
* *
40901467 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40901532 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
40901548 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40901612 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40901630 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40901648 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40901658 original size:27 final size:27
Alignment explanation
Indices: 40901552--40901658 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
40901542 TGACCATGCG
* * * *
40901552 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
40901580 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
40901607 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
40901634 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
40901659 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:40909979 original size:27 final size:27
Alignment explanation
Indices: 40909948--40910125 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40909938 TAAATTGTAC
40909948 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40909975 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40910001 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40910029 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40910057 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40910084 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40910111 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40910126 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40910062 original size:82 final size:81
Alignment explanation
Indices: 40909949--40910104 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40909939 AAATTGTACA
* *
40909949 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40910013 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40910030 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
40910095 TGCGAGTTGA
65 TGCGAATTGA
40910105 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40910116 original size:82 final size:81
Alignment explanation
Indices: 40909945--40910125 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
40909935 GATTAAATTG
* *
40909945 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40910010 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40910026 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40910090 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40910108 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40910126 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40921565 original size:43 final size:44
Alignment explanation
Indices: 40921517--40921691 Score: 255
Period size: 44 Copynumber: 4.0 Consensus size: 44
40921507 ACAAACAACC
* *
40921517 CAACAACCCATGTTTATCTTCTCCTCTTTTT-AAATTCTTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTGAAATTCTTTTTT
**
40921560 CAACAACCCAAGAAGATCTTCTCCTCTTTTTGAAATTCTTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTGAAATTCTTTTTT
* * *
40921604 CAACAACCTAAGATTATCTTTTCCTCTTTTTGAAATTATTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTGAAATTCTTTTTT
* *
40921648 CAACAATCCAATATTATCTTCTCCTCTTTTT-AAATTCTTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTGAAATTCTTTTTT
40921691 C
1 C
40921692 TAGTATAAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
43 39 0.33
44 78 0.67
ACGTcount: A:0.25, C:0.23, G:0.03, T:0.48
Consensus pattern (44 bp):
CAACAACCCAAGATTATCTTCTCCTCTTTTTGAAATTCTTTTTT
Found at i:40928191 original size:50 final size:50
Alignment explanation
Indices: 40928066--40928350 Score: 426
Period size: 50 Copynumber: 5.6 Consensus size: 50
40928056 ATTTAGGTAA
* * *
40928066 AGAGATCCCATGTAAGACCTTGTCTGGGACATGGCGTTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATG
*
40928122 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
40928172 AGAGGTCCAATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
40928222 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
40928272 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
40928322 AGAGGTCCCATGTAAGACCATGTCTGGGA
1 AGAGGTCCCATGTAAGACCATGTCTGGGA
40928351 TATAGCATTA
Statistics
Matches: 215, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
50 172 0.80
53 3 0.01
55 1 0.00
56 39 0.18
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:40935040 original size:50 final size:50
Alignment explanation
Indices: 40934941--40935226 Score: 304
Period size: 50 Copynumber: 5.6 Consensus size: 50
40934931 AAAGAGATCT
*
40934941 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCA---AG---ATGAGAGGTCC
* * *
40934997 CATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATGAGGGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTCC
** *
40935047 CAT-TGAAGACCATGTCTGGGACATGGTGTTGGCAACAAGATGAGAGGTCC
1 CATGT-AAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTCC
* * *
40935097 CATGTAAGACCATGTCTAGGACATGACGTTGGCACCAAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTCC
** * * * ** *
40935147 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTCC
* * * *
40935197 CTTGTAAGACCATATCTTGGATATGGCATT
1 CATGTAAGACCATGTCTGGGACATGGCATT
40935227 AGCAGTACAA
Statistics
Matches: 197, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.01
50 159 0.81
51 1 0.01
53 2 0.01
56 34 0.17
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTCC
Found at i:40936966 original size:39 final size:39
Alignment explanation
Indices: 40936923--40937021 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 39
40936913 ATGATTTTGA
* *
40936923 GTATTGAGATGTATGCTTAAATGTTACGAGATTATATGT
1 GTATTGAGATATATGCTTAAACGTTACGAGATTATATGT
* * * *
40936962 GTATTGTGATATATGCTTGAACGTTAGGTGATTATATGT
1 GTATTGAGATATATGCTTAAACGTTACGAGATTATATGT
*
40937001 GTAAT-AGGATATATGCTTAAA
1 GTATTGA-GATATATGCTTAAA
40937022 ATTGAGTATG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.40
Consensus pattern (39 bp):
GTATTGAGATATATGCTTAAACGTTACGAGATTATATGT
Found at i:40938611 original size:31 final size:30
Alignment explanation
Indices: 40938518--40938762 Score: 89
Period size: 31 Copynumber: 7.8 Consensus size: 30
40938508 TAAACGAATC
* * * *
40938518 CAATTCAGCAATGAATATCAATATACCAAA-
1 CAATTCGGCAATGTATAACCATATA-CAAAT
* **
40938548 CAATTCGGCAATGTATAACCATACACGTAT
1 CAATTCGGCAATGTATAACCATATACAAAT
* *
40938578 CAAGTTCGGTAATGTATAATCATATACAAAT
1 CAA-TTCGGCAATGTATAACCATATACAAAT
* ** * *
40938609 CAAATTCGGCTTCCTATATTCCTATATTCATAAACAATT
1 C-AATTCGG----C-A-A-T-GTATAACCATATACAAAT
* * * * *
40938648 AAATTTTGACAATATATAACCATGTACAAAT
1 CAA-TTCGGCAATGTATAACCATATACAAAT
* ** * *
40938679 TAATTCCAACAATGTACAACCATATACGAAT
1 CAATT-CGGCAATGTATAACCATATACAAAT
* ** *
40938710 CAATTCAGCAACCTATATCCATATACCAAA-
1 CAATTCGGCAATGTATAACCATATA-CAAAT
*
40938740 CAATTCGACAATGTATAACCATA
1 CAATTCGGCAATGTATAACCATA
40938763 CATGAATCAA
Statistics
Matches: 156, Mismatches: 45, Indels: 28
0.68 0.20 0.12
Matches are distributed among these distances:
29 2 0.01
30 58 0.37
31 68 0.44
32 3 0.02
33 1 0.01
34 1 0.01
35 1 0.01
36 1 0.01
37 1 0.01
38 3 0.02
39 17 0.11
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (30 bp):
CAATTCGGCAATGTATAACCATATACAAAT
Found at i:40938762 original size:30 final size:30
Alignment explanation
Indices: 40938655--40938762 Score: 85
Period size: 30 Copynumber: 3.6 Consensus size: 30
40938645 ATTAAATTTT
* * *
40938655 GACAATATATAACCATGTA-CAAATTAATTCC
1 GACAATGTATAACCATATACCAAA-CAATT-C
* * * *
40938686 AACAATGTACAACCATATACGAATCAATTC
1 GACAATGTATAACCATATACCAAACAATTC
** *
40938716 -AGCAACCTATATCCATATACCAAACAATTC
1 GA-CAATGTATAACCATATACCAAACAATTC
40938746 GACAATGTATAACCATA
1 GACAATGTATAACCATA
40938763 CATGAATCAA
Statistics
Matches: 58, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
29 1 0.02
30 35 0.60
31 20 0.34
32 2 0.03
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.25
Consensus pattern (30 bp):
GACAATGTATAACCATATACCAAACAATTC
Found at i:40959341 original size:23 final size:23
Alignment explanation
Indices: 40959315--40959363 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
40959305 AGAAAAACTA
* * *
40959315 TAATATCCCGAAAATTACTACTG
1 TAATACCCCAAAAATTACTACAG
40959338 TAATACCCCAAAAATTACTACAG
1 TAATACCCCAAAAATTACTACAG
40959361 TAA
1 TAA
40959364 GAAAGTAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (23 bp):
TAATACCCCAAAAATTACTACAG
Found at i:40973586 original size:20 final size:20
Alignment explanation
Indices: 40973557--40973610 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40973547 GTGTTAGATG
* *
40973557 ATTTTAACTTGATTGAAATC
1 ATTTTAACTTGATTAAAATA
* *
40973577 ATTTTTACTTGGTTAAAATA
1 ATTTTAACTTGATTAAAATA
*
40973597 ATTTTCACTTGATT
1 ATTTTAACTTGATT
40973611 TTAAAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
ATTTTAACTTGATTAAAATA
Found at i:40982431 original size:20 final size:19
Alignment explanation
Indices: 40982390--40982431 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
40982380 CCTTTCAACT
*
40982390 TTTCTTACTTTCATTTGCA
1 TTTCTTACTTTCATTTGAA
40982409 TTTCATTACTTTCCATTT-AA
1 TTTC-TTACTTT-CATTTGAA
40982429 TTT
1 TTT
40982432 ACTTTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.19, C:0.19, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTCTTACTTTCATTTGAA
Found at i:40983108 original size:25 final size:25
Alignment explanation
Indices: 40983074--40983168 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
40983064 TTATACATGT
* *
40983074 ATGCTCACACGAGCTGTGAATCAAA
1 ATGCTCACACGAGCTATGAATCAGA
*
40983099 ATGCTCACACAAGCTATGAATCAGA
1 ATGCTCACACGAGCTATGAATCAGA
*
40983124 ATGCTCACACGAGCTGTGAATCAGA
1 ATGCTCACACGAGCTATGAATCAGA
40983149 ATGCTCACACGAGCTATGAA
1 ATGCTCACACGAGCTATGAA
40983169 AATGGGTCTG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (25 bp):
ATGCTCACACGAGCTATGAATCAGA
Found at i:40983152 original size:50 final size:50
Alignment explanation
Indices: 40983074--40983168 Score: 172
Period size: 50 Copynumber: 1.9 Consensus size: 50
40983064 TTATACATGT
40983074 ATGCTCACACGAGCTGTGAATCAAAATGCTCACACAAGCTATGAATCAGA
1 ATGCTCACACGAGCTGTGAATCAAAATGCTCACACAAGCTATGAATCAGA
* *
40983124 ATGCTCACACGAGCTGTGAATCAGAATGCTCACACGAGCTATGAA
1 ATGCTCACACGAGCTGTGAATCAAAATGCTCACACAAGCTATGAA
40983169 AATGGGTCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (50 bp):
ATGCTCACACGAGCTGTGAATCAAAATGCTCACACAAGCTATGAATCAGA
Found at i:40988255 original size:16 final size:16
Alignment explanation
Indices: 40988221--40988256 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40988211 CCAGAAAAGT
*
40988221 AAAGAAATTTTATGAA
1 AAAGAAATTTTACGAA
*
40988237 AAAGAAATTTTACGGA
1 AAAGAAATTTTACGAA
40988253 AAAG
1 AAAG
40988257 TGGTCACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.17, T:0.25
Consensus pattern (16 bp):
AAAGAAATTTTACGAA
Found at i:40989682 original size:40 final size:40
Alignment explanation
Indices: 40989633--40989844 Score: 293
Period size: 40 Copynumber: 5.3 Consensus size: 40
40989623 TCTTCGGAAT
* ** *
40989633 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* *
40989672 TTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
*
40989712 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
*
40989752 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * * *
40989792 TTAGCCCGGATAAAATC-ACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGATATAA-CAACTCGCACAAATGCCTTCGGGTC
40989832 TTAGCCCGGATAT
1 TTAGCCCGGATAT
40989845 CATTCAAATG
Statistics
Matches: 157, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 3 0.02
40 153 0.97
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
Found at i:40992482 original size:21 final size:20
Alignment explanation
Indices: 40992444--40992506 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
40992434 ATTCAATTTC
40992444 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATAATATCATT
40992461 TCAATACCACAATAAT-TCATT
1 TCAAT-CCA-AATAATATCATT
*
40992482 T-AATTCAAATAATATCATT
1 TCAATCCAAATAATATCATT
40992501 TGCAAT
1 T-CAAT
40992507 TTCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATAATATCATT
Found at i:40999756 original size:20 final size:20
Alignment explanation
Indices: 40999733--40999835 Score: 59
Period size: 21 Copynumber: 4.8 Consensus size: 20
40999723 AGATATAAAC
40999733 TTATAAAAATAAAAAATATA
1 TTATAAAAATAAAAAATATA
*
40999753 TTATAAAAAACTAAAAAA-ATC
1 TTAT-AAAAA-TAAAAAATATA
* *
40999774 TAATAAATTATAGAAAAATATAA
1 TTATAAA-AATA-AAAAATAT-A
*
40999797 TTTTTTATAAAATATAAAAAT-T-
1 --TTATA-AAAATA-AAAAATATA
*
40999819 TTATAAAAATATAAAAT
1 TTATAAAAATAAAAAAT
40999836 TAATAAATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
18 5 0.08
19 6 0.09
20 13 0.20
21 16 0.25
22 9 0.14
24 1 0.02
25 12 0.19
26 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (20 bp):
TTATAAAAATAAAAAATATA
Found at i:40999827 original size:19 final size:19
Alignment explanation
Indices: 40999767--40999834 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 19
40999757 AAAAAACTAA
* * *
40999767 AAAAATCTAATAAATTATAG
1 AAAAATATAA-AAATTTTAT
**
40999787 AAAAATAT-AATTTTTTAT
1 AAAAATATAAAAATTTTAT
40999805 -AAAATATAAAAATTTTAT
1 AAAAATATAAAAATTTTAT
40999823 AAAAATATAAAA
1 AAAAATATAAAA
40999835 TTAATAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 7 0.18
18 13 0.33
19 12 0.31
20 7 0.18
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (19 bp):
AAAAATATAAAAATTTTAT
Found at i:41000362 original size:9 final size:9
Alignment explanation
Indices: 41000344--41000591 Score: 58
Period size: 10 Copynumber: 25.4 Consensus size: 9
41000334 CCAGTTCAAG
41000344 TTTTTATAA
1 TTTTTATAA
41000353 TTTTTTTAATAA
1 --TTTTT-ATAA
41000365 TTTTTATAAA
1 TTTTTAT-AA
* *
41000375 TTTTAATAT
1 TTTTTATAA
41000384 TTTTTAATAA
1 TTTTT-ATAA
*
41000394 TTTGTTTTACAA
1 --T-TTTTATAA
*
41000406 TTTTTATTATC
1 TTTTTA-TA-A
*
41000417 TTTTTAAGAA
1 TTTTT-ATAA
* * *
41000427 TTCTAATAC
1 TTTTTATAA
41000436 TTTATT-TAA
1 TTT-TTATAA
*
41000445 ATTTTA-AA
1 TTTTTATAA
41000453 TATTTTAATAA
1 T-TTTT-ATAA
*
41000464 GTTTTATTAA
1 TTTTTA-TAA
* *
41000474 -TGTTATATT
1 TTTTTATA-A
41000483 TTTTTATAA
1 TTTTTATAA
41000492 TTTATTAT-A
1 TTT-TTATAA
41000501 TTTTGT-TAGA
1 TTTT-TATA-A
*
41000511 TTTTTTTATA
1 TTTTTATA-A
41000521 TTTTTATAA
1 TTTTTATAA
*
41000530 TATTTATAAA
1 TTTTTAT-AA
* *
41000540 ATTTGATAA
1 TTTTTATAA
41000549 TTATTTTATAA
1 -T-TTTTATAA
*
41000560 -TTTTATAG
1 TTTTTATAA
*
41000568 TTTTAATAA
1 TTTTTATAA
*
41000577 GTTTATATCAA
1 -TTTTTAT-AA
41000588 TTTT
1 TTTT
41000592 AATATTGTTA
Statistics
Matches: 172, Mismatches: 37, Indels: 57
0.65 0.14 0.21
Matches are distributed among these distances:
8 15 0.09
9 53 0.31
10 69 0.40
11 22 0.13
12 9 0.05
13 4 0.02
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:41000368 original size:10 final size:10
Alignment explanation
Indices: 41000355--41000396 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
41000345 TTTTATAATT
41000355 TTTTTAATAA
1 TTTTTAATAA
41000365 TTTTT-ATAA
1 TTTTTAATAA
* *
41000374 ATTTTAATAT
1 TTTTTAATAA
41000384 TTTTTAATAA
1 TTTTTAATAA
41000394 TTT
1 TTT
41000397 GTTTTACAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:41000501 original size:20 final size:20
Alignment explanation
Indices: 41000476--41000525 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
41000466 TTTATTAATG
*
41000476 TTATATTTTTTTATAATTTA
1 TTATATTTTTTTAGAATTTA
* * *
41000496 TTATATTTTGTTAGATTTTT
1 TTATATTTTTTTAGAATTTA
41000516 TTATATTTTT
1 TTATATTTTT
41000526 ATAATATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (20 bp):
TTATATTTTTTTAGAATTTA
Found at i:41000561 original size:19 final size:18
Alignment explanation
Indices: 41000514--41000562 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
41000504 TGTTAGATTT
* *
41000514 TTTTATATTTTTATAATA
1 TTTTATAATTTGATAATA
*
41000532 TTTATAAAATTTGATAATTA
1 TTT-TATAATTTGATAA-TA
41000552 TTTTATAATTT
1 TTTTATAATTT
41000563 TATAGTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 3 0.12
19 17 0.68
20 5 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTATAATTTGATAATA
Found at i:41001328 original size:12 final size:12
Alignment explanation
Indices: 41001311--41001364 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
41001301 AACTAATCCT
41001311 CTCTCAAATTTC
1 CTCTCAAATTTC
*
41001323 CTCTC-AATTTG
1 CTCTCAAATTTC
41001334 CTCTCAAA-TTC
1 CTCTCAAATTTC
41001345 CT-TCAATATTT-
1 CTCTCAA-ATTTC
41001356 CTCTCAAAT
1 CTCTCAAAT
41001365 CCATATTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 4 0.11
11 19 0.53
12 13 0.36
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:41001337 original size:23 final size:23
Alignment explanation
Indices: 41001311--41001364 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
41001301 AACTAATCCT
41001311 CTCTCAAATTTCCTCTCAAT-TTG
1 CTCTCAAATTTCCT-TCAATATTG
*
41001334 CTCTCAAA-TTCCTTCAATATTT
1 CTCTCAAATTTCCTTCAATATTG
41001356 CTCTCAAAT
1 CTCTCAAAT
41001365 CCATATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 15 0.54
23 8 0.29
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.43
Consensus pattern (23 bp):
CTCTCAAATTTCCTTCAATATTG
Found at i:41001389 original size:51 final size:50
Alignment explanation
Indices: 41001326--41001423 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 50
41001316 AAATTTCCTC
41001326 TCAATTTGCTCTCAAATTCCTTC-AATATTTCTCTCAAATCCATATTTACTT
1 TCAATTTGCTCTCAAATT-CTTCTAA-ATTTCTCTCAAATCCATATTTACTT
* * * *
41001377 TCAATTTTCTCTCAAGTTCTTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAAATTCTTC-TAAATTTCTCTCAAATCCATATTT
41001424 TTAAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 4 0.10
51 35 0.85
52 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.02, T:0.48
Consensus pattern (50 bp):
TCAATTTGCTCTCAAATTCTTCTAAATTTCTCTCAAATCCATATTTACTT
Found at i:41003270 original size:18 final size:18
Alignment explanation
Indices: 41003243--41003282 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41003233 CAAGTGCGTT
*
41003243 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
*
41003261 TCCTAACCCTTATGTGTA
1 TCCTAACCCTTATATGTA
41003279 TCCT
1 TCCT
41003283 TTTCTGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:41008088 original size:18 final size:18
Alignment explanation
Indices: 41008061--41008100 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41008051 CAAGTGCGTT
*
41008061 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
*
41008079 TCCTAACCCTTATGTGTA
1 TCCTAACCCTTATATGTA
41008097 TCCT
1 TCCT
41008101 TTTCTGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:41008380 original size:21 final size:21
Alignment explanation
Indices: 41008355--41008404 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
41008345 CAGATGCCGT
*
41008355 ACCGGAAGAACCAGAATCC-CC
1 ACCGGAAGAACAAGAA-CCGCC
* *
41008376 GCCGGAGGAACAAGAACCGCC
1 ACCGGAAGAACAAGAACCGCC
41008397 ACCGGAAG
1 ACCGGAAG
41008405 CTAGACAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.36, C:0.34, G:0.28, T:0.02
Consensus pattern (21 bp):
ACCGGAAGAACAAGAACCGCC
Found at i:41008560 original size:44 final size:46
Alignment explanation
Indices: 41008510--41008605 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
41008500 TTTGTACAAA
* * *
41008510 TATTTTGA-ATGTTTTGATATTATTTTATGTAGTAAAATAGAAATT
1 TATTTTGAGATATTTTGATATTATTTAATGTAATAAAATAGAAATT
* *
41008555 T-TTTTGAGTTATTTTGATATTATTTAATGTAATAAAATAGAAGTT
1 TATTTTGAGATATTTTGATATTATTTAATGTAATAAAATAGAAATT
41008600 TATTTT
1 TATTTT
41008606 ATATAATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
44 6 0.14
45 34 0.77
46 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (46 bp):
TATTTTGAGATATTTTGATATTATTTAATGTAATAAAATAGAAATT
Found at i:41008602 original size:25 final size:25
Alignment explanation
Indices: 41008574--41008621 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
41008564 TATTTTGATA
*
41008574 TTATTTAATGTAATAAAATAGAAGT
1 TTATTTAATATAATAAAATAGAAGT
*
41008599 TTATTTTATATAATAAAATAGAA
1 TTATTTAATATAATAAAATAGAA
41008622 AATTTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (25 bp):
TTATTTAATATAATAAAATAGAAGT
Found at i:41008616 original size:70 final size:70
Alignment explanation
Indices: 41008529--41008659 Score: 217
Period size: 70 Copynumber: 1.9 Consensus size: 70
41008519 TGTTTTGATA
* * *
41008529 TTATTTTATGTAGTAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTAATGTAATAAAATA
1 TTATTTTATATAATAAAATAGAAAATTTTTTGAGTTATTTTGATATTATTTAATGTAATAAAATA
41008594 GAAGT
66 GAAGT
**
41008599 TTATTTTATATAATAAAATAGAAAATTTTTTGAGTTATTTTGATATTATTTGGTGTAATAA
1 TTATTTTATATAATAAAATAGAAAATTTTTTGAGTTATTTTGATATTATTTAATGTAATAA
41008660 CATGAGCGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (70 bp):
TTATTTTATATAATAAAATAGAAAATTTTTTGAGTTATTTTGATATTATTTAATGTAATAAAATA
GAAGT
Found at i:41008720 original size:60 final size:60
Alignment explanation
Indices: 41008634--41008771 Score: 258
Period size: 60 Copynumber: 2.3 Consensus size: 60
41008624 TTTTTTGAGT
*
41008634 TATTTTGATATTATTTGGTGTAATAACATGAGCGTAATTAATTTGTACAAATATTTTGAA
1 TATTTTGATATTATTTGATGTAATAACATGAGCGTAATTAATTTGTACAAATATTTTGAA
*
41008694 TATTTTGATATTATTTGATGTAATAACATGAGCTTAATTAATTTGTACAAATATTTTGAA
1 TATTTTGATATTATTTGATGTAATAACATGAGCGTAATTAATTTGTACAAATATTTTGAA
41008754 TATTTTGATATTATTTGA
1 TATTTTGATATTATTTGA
41008772 GAATTCTATT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 76 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (60 bp):
TATTTTGATATTATTTGATGTAATAACATGAGCGTAATTAATTTGTACAAATATTTTGAA
Found at i:41011849 original size:125 final size:125
Alignment explanation
Indices: 41011590--41011887 Score: 438
Period size: 125 Copynumber: 2.4 Consensus size: 125
41011580 CCAAACATGC
* *
41011590 TACTATAGCAAAAGCGCGTCCACGTGGGCGCGGTTTCACAAATTCTTCTCATAAAGCATCCTGGT
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGT
* ** *
41011655 AGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTTTAGGACA
66 AGAAGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAAGACA
* *
41011715 TACTGTAGCAAAAGCGCGTCCACGTGGGCACGATTTAACAAATTCTTCTCATAAAGCATCCTGGT
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGT
*
41011780 AGAAGCG-ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACCA
66 AGAAGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTT-TTCCAAGA-CA
* * * * *
41011841 -ACTTTAGCAAAATCGCGTCCAGGAGGGCGTGATTTCACAAATTCTTC
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTC
41011888 GCGTCCATGT
Statistics
Matches: 155, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
124 40 0.26
125 113 0.73
126 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (125 bp):
TACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGT
AGAAGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAAGACA
Found at i:41017186 original size:80 final size:80
Alignment explanation
Indices: 41017053--41017211 Score: 300
Period size: 80 Copynumber: 2.0 Consensus size: 80
41017043 ACCAATTTAA
41017053 ACATCACTCCTATTTCAACGTTTATCGAATATAATCAGGCATATAACCAATTATACACAATTCAT
1 ACATCACTCCTATTTCAACGTTTATCGAATATAATCAGGCATATAACCAATTATACACAATTCAT
41017118 TCATATACTTTGTTT
66 TCATATACTTTGTTT
* *
41017133 ACATCACTCCTATTTCAACGTTTATTGAATATAATTAGGCATATAACCAATTATACACAATTCAT
1 ACATCACTCCTATTTCAACGTTTATCGAATATAATCAGGCATATAACCAATTATACACAATTCAT
41017198 TCATATACTTTGTT
66 TCATATACTTTGTT
41017212 GTCCTCCTCC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.38
Consensus pattern (80 bp):
ACATCACTCCTATTTCAACGTTTATCGAATATAATCAGGCATATAACCAATTATACACAATTCAT
TCATATACTTTGTTT
Found at i:41018223 original size:51 final size:50
Alignment explanation
Indices: 41018165--41018349 Score: 212
Period size: 51 Copynumber: 3.7 Consensus size: 50
41018155 ACGGTTCACA
* *
41018165 TAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCATCCGATACACG
* * * *
41018216 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-ATCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATATC-ATCCGATACACG
* * * *
41018267 TAGTAGCCTGCACATGGTACTACACATGCGACC-TATCATTCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATATCA-TCCGATACACG
* *
41018317 TAGTAACCTACACATAGTACTACACACGTGACC
1 TAGTAGCCTGCACATAGTACTACACACGTGACC
41018350 TAGCAACTTC
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
49 1 0.01
50 41 0.37
51 67 0.60
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATATCATCCGATACACG
Found at i:41018342 original size:101 final size:101
Alignment explanation
Indices: 41018163--41018347 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
41018153 ACACGGTTCA
* * * *
41018163 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TATCATCCGATACACGTAGTAACCTACA
41018228 CATAGTACTACACACGTGATCGAATCTATCCGGTACG
65 CATAGTACTACACACGTGATCGAATCTATCCGGTACG
* *
41018265 CATAGTAGCCTGCACATGGTACTACACATGCGACC-TATCATTCTGATACACGTAGTAACCTACA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATATCA-TCCGATACACGTAGTAACCTACA
41018329 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
41018348 CCTAGCAACT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 33 0.43
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATATCATCCGATACACGTAGTAACCTACAC
ATAGTACTACACACGTGATCGAATCTATCCGGTACG
Found at i:41019991 original size:3 final size:3
Alignment explanation
Indices: 41019983--41020041 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
41019973 TAGTTGATGT
41019983 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
41020031 TTA TTA TTA TT
1 TTA TTA TTA TT
41020042 CACTATTCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41025428 original size:16 final size:16
Alignment explanation
Indices: 41025407--41025437 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41025397 AACAACTACA
*
41025407 AATTGATCCAAATACG
1 AATTGATACAAATACG
41025423 AATTGATACAAATAC
1 AATTGATACAAATAC
41025438 AAATGAAACA
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:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (16 bp):
AATTGATACAAATACG
Found at i:41028453 original size:21 final size:21
Alignment explanation
Indices: 41028423--41028479 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
41028413 GTGGATAAAA
* *
41028423 TCTTATGAGCTTTTGTTCAGC
1 TCTTACGAGCTTCTGTTCAGC
41028444 TCTTACGAGCTTCTGTTCAGC
1 TCTTACGAGCTTCTGTTCAGC
*
41028465 T-TT-CAAGCTTCTGTT
1 TCTTACGAGCTTCTGTT
41028480 ACGTATTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 11 0.33
20 2 0.06
21 20 0.61
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (21 bp):
TCTTACGAGCTTCTGTTCAGC
Found at i:41028747 original size:18 final size:19
Alignment explanation
Indices: 41028724--41028761 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41028714 GATTTATCAT
41028724 TAAAC-TCATCGAA-CTTAC
1 TAAACTTCAT-GAAGCTTAC
41028742 TAAACTTCATGAAGCTTAC
1 TAAACTTCATGAAGCTTAC
41028761 T
1 T
41028762 TGTGTTTTTT
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:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (19 bp):
TAAACTTCATGAAGCTTAC
Found at i:41042910 original size:67 final size:68
Alignment explanation
Indices: 41042824--41043269 Score: 441
Period size: 67 Copynumber: 6.7 Consensus size: 68
41042814 ATCCCGACAA
* * * * * *
41042824 ACTCTATATGCTGTCATAGTCGAGCTGTGGTCTTACACATCATACCCCATGTTTAATGTCCTAGG
1 ACTCTCTATGTTGCCATAGTCGAGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTAGG
*
41042889 -AA
66 CAG
* * * * *
41042891 ACTCTCTATGTTGCCATAGTCAAGCTATGGTCTTACACAATATACCATATGTTTAATAT-CTTGG
1 ACTCTCTATGTTGCCATAGTCGAGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTAGG
*
41042955 CGG
66 CAG
* * * * *
41042958 ACTCTTTATGTTGTCATAG-CGAACTATGTTTTTACACATTATACC-CTATGTTTAATGTCCTAG
1 ACTCTCTATGTTGCCATAGTCGAGCTATGGTCTTACACATTATACCAC-ATGTTTAATGTCCTAG
41043021 TG--G
65 -GCAG
* * * *
41043024 ACTTTTTATGTTACCATAGTCGCGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTAGT
1 ACTCTCTATGTTGCCATAGTCGAGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTAG-
41043089 G-A-
65 GCAG
*
41043091 ACTCTCTATGTTGCCATAGTCG-GCTATAGTCTTACACATTATA-CACTATGTTTAATGTCCT-G
1 ACTCTCTATGTTGCCATAGTCGAGCTATGGTCTTACACATTATACCAC-ATGTTTAATGTCCTAG
41043153 GCAG
65 GCAG
* * * *
41043157 ACTCTCTATGTTTCCATAGAT-GAGCTATGGTCTTACACATAATACCACATGTTTAACGTCAT-G
1 ACTCTCTATGTTGCCATAG-TCGAGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTAG
**
41043220 GTGG
65 GCAG
** * * **
41043224 ACTCTCTATGTTATCATAGTCGAGTTATGATCTTACATGTTATACC
1 ACTCTCTATGTTGCCATAGTCGAGCTATGGTCTTACACATTATACC
41043270 CCATTATAGC
Statistics
Matches: 317, Mismatches: 48, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
64 1 0.00
65 5 0.02
66 106 0.33
67 200 0.63
68 5 0.02
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (68 bp):
ACTCTCTATGTTGCCATAGTCGAGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTAGG
CAG
Found at i:41043044 original size:133 final size:132
Alignment explanation
Indices: 41042824--41043270 Score: 499
Period size: 133 Copynumber: 3.3 Consensus size: 132
41042814 ATCCCGACAA
* * * * *
41042824 ACTCTATATGCTGTCATAGTCGAGCTGTGGTCTTACACATCATACCCCATGTTTAATGTCCTAGG
1 ACTCTCTATGTTGTCATAGTCGAGCTAT-GTCTTACACATTATACCCTATGTTTAATGTCCTAGG
* * * * * *
41042889 AAACTCTCTATGTTGCCATAGTCAAGCTATGGTCTTACACAATATACCATATGTTTAATATCTTG
65 -GACTCTCTATGTTACCATAGTCGAGCTATGGTCTTACACAATATACCACATGTTTAATGTCATG
*
41042954 GCGG
129 GTGG
* * *
41042958 ACTCTTTATGTTGTCATAG-CGAACTATGTTTTTACACATTATACCCTATGTTTAATGTCCTAGT
1 ACTCTCTATGTTGTCATAGTCGAGCTATG-TCTTACACATTATACCCTATGTTTAATGTCCTAG-
* * * * * *
41043022 GGACTTTTTATGTTACCATAGTCGCGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTA
64 GGACTCTCTATGTTACCATAGTCGAGCTATGGTCTTACACAATATACCACATGTTTAATGTCATG
*
41043087 GTGA
129 GTGG
* *
41043091 ACTCTCTATGTTGCCATAGTCG-GCTATAGTCTTACACATTATACACTATGTTTAATGTCCT-GG
1 ACTCTCTATGTTGTCATAGTCGAGCTAT-GTCTTACACATTATACCCTATGTTTAATGTCCTAGG
* *
41043154 CAGACTCTCTATGTTTCCATAGAT-GAGCTATGGTCTTACAC-ATAATACCACATGTTTAACGTC
65 --GACTCTCTATGTTACCATAG-TCGAGCTATGGTCTTACACAAT-ATACCACATGTTTAATGTC
41043217 ATGGTGG
126 ATGGTGG
* * **
41043224 ACTCTCTATGTTATCATAGTCGAGTTATGATCTTACATGTTATACCC
1 ACTCTCTATGTTGTCATAGTCGAGCTATG-TCTTACACATTATACCC
41043271 CATTATAGCC
Statistics
Matches: 263, Mismatches: 40, Indels: 20
0.81 0.12 0.06
Matches are distributed among these distances:
131 1 0.00
132 3 0.01
133 219 0.83
134 40 0.15
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (132 bp):
ACTCTCTATGTTGTCATAGTCGAGCTATGTCTTACACATTATACCCTATGTTTAATGTCCTAGGG
ACTCTCTATGTTACCATAGTCGAGCTATGGTCTTACACAATATACCACATGTTTAATGTCATGGT
GG
Found at i:41043195 original size:200 final size:200
Alignment explanation
Indices: 41042838--41043269 Score: 550
Period size: 200 Copynumber: 2.2 Consensus size: 200
41042828 TATATGCTGT
* * *
41042838 CATAGTCGAGCTGTGGTCTTACACATCATACCCCATGTTTAATGTCCTAGGAAACTCTCTATGTT
1 CATAGTCGAGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTAGGAAACTCTCTATGTT
* * * *
41042903 GCCATAGTCAAGCTATGGTCTTACACAATATACCATATGTTTAATATCTTGGCGGACTCTTTATG
66 GCCATAGTCAAGCTATAGTCTTACACAATATACCATATGTTTAATATCCTGGCAGACTCTCTATG
* * * * * * *
41042968 TTGTCATAGCGAACTATGTTTTTACACATTATACC-CTATGTTTAATGTCCTAGTGGACTTTTTA
131 TTGTCATAGCGAACTATGGTCTTACACATAATACCAC-ATGTTTAACGTCATAGTGGACTCTCTA
41043032 TGTTAC
195 TGTTAC
*
41043038 CATAGTCGCGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTAGTG-AACTCTCTATGT
1 CATAGTCGAGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTAG-GAAACTCTCTATGT
* * *
41043102 TGCCATAGTC-GGCTATAGTCTTACACATTATA-CACTATGTTTAATGTCCTGGCAGACTCTCTA
65 TGCCATAGTCAAGCTATAGTCTTACACAATATACCA-TATGTTTAATATCCTGGCAGACTCTCTA
* * *
41043165 TGTT-TCCATAGATGAGCTATGGTCTTACACATAATACCACATGTTTAACGTCATGGTGGACTCT
129 TGTTGT-CATAG-CGAACTATGGTCTTACACATAATACCACATGTTTAACGTCATAGTGGACTCT
*
41043229 CTATGTTAT
192 CTATGTTAC
* * **
41043238 CATAGTCGAGTTATGATCTTACATGTTATACC
1 CATAGTCGAGCTATGGTCTTACACATTATACC
41043270 CCATTATAGC
Statistics
Matches: 200, Mismatches: 27, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
198 3 0.01
199 52 0.26
200 143 0.71
201 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (200 bp):
CATAGTCGAGCTATGGTCTTACACATTATACCACATGTTTAATGTCCTAGGAAACTCTCTATGTT
GCCATAGTCAAGCTATAGTCTTACACAATATACCATATGTTTAATATCCTGGCAGACTCTCTATG
TTGTCATAGCGAACTATGGTCTTACACATAATACCACATGTTTAACGTCATAGTGGACTCTCTAT
GTTAC
Found at i:41047496 original size:24 final size:24
Alignment explanation
Indices: 41047465--41047510 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
41047455 TCATTTAACT
*
41047465 TAATTGAACATGTTCATGAACATA
1 TAATTGAACATGTTCACGAACATA
41047489 TAATTGAACATGTTCACGAACA
1 TAATTGAACATGTTCACGAACA
41047511 ATGTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
TAATTGAACATGTTCACGAACATA
Found at i:41047707 original size:12 final size:12
Alignment explanation
Indices: 41047680--41047712 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
41047670 ATCATGAATA
*
41047680 AATAAATGAGTC
1 AATAAACGAGTC
41047692 -ATAAACGAGTC
1 AATAAACGAGTC
41047703 AATAAACGAG
1 AATAAACGAG
41047713 CTTATAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:41047719 original size:12 final size:12
Alignment explanation
Indices: 41047704--41047751 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
41047694 AAACGAGTCA
41047704 ATAAACGAGCTT
1 ATAAACGAGCTT
* **
41047716 ATAAACAAGCCA
1 ATAAACGAGCTT
*
41047728 ATAAATGAGCTT
1 ATAAACGAGCTT
*
41047740 TTAAACGAGCTT
1 ATAAACGAGCTT
41047752 GTTCGTGAAC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.25
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:41047721 original size:24 final size:24
Alignment explanation
Indices: 41047692--41047749 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
41047682 TAAATGAGTC
*
41047692 ATAAACGAGTCAATAAACGAGCTT
1 ATAAACGAGCCAATAAACGAGCTT
* *
41047716 ATAAACAAGCCAATAAATGAGCTT
1 ATAAACGAGCCAATAAACGAGCTT
*
41047740 TTAAACGAGC
1 ATAAACGAGC
41047750 TTGTTCGTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (24 bp):
ATAAACGAGCCAATAAACGAGCTT
Done.