Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 90 of 356
Found at i:28313010 original size:18 final size:17
Alignment explanation
Indices: 28312972--28313010 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28312962 GGTTTAAAAA
28312972 TTTTAATTAATTAAATTT
1 TTTTAATTAA-TAAATTT
28312990 TTTTAATTAA-AAATTT
1 TTTTAATTAATAAATTT
28313006 ATTTT
1 -TTTT
28313011 CATCCCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATTAATAAATTT
Found at i:28321827 original size:21 final size:20
Alignment explanation
Indices: 28321801--28321851 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
28321791 TTTATTTTTA
28321801 TTAATTTAACCATTTTTAATT
1 TTAATTTAA-CATTTTTAATT
* **
28321822 TTAATTTTAATATTTTTGTTT
1 TTAA-TTTAACATTTTTAATT
28321843 TTAATTTAA
1 TTAATTTAA
28321852 TTGTTACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 16 0.62
22 5 0.19
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (20 bp):
TTAATTTAACATTTTTAATT
Found at i:28328481 original size:26 final size:26
Alignment explanation
Indices: 28328452--28328558 Score: 169
Period size: 26 Copynumber: 4.1 Consensus size: 26
28328442 TGGTACAAAT
**
28328452 TGATAATGGGTTAGAAAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
28328478 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28328504 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28328530 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28328556 TGA
1 TGA
28328559 CGGGCATTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28330209 original size:27 final size:26
Alignment explanation
Indices: 28330179--28330373 Score: 228
Period size: 27 Copynumber: 7.2 Consensus size: 26
28330169 AGGAAGCGTC
*
28330179 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
28330206 CTGGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* * *
28330233 CTAGTGGCTATGCCATGATTATCTGAT
1 CTGGTGGCTCTGCCA-CATTATCTGAT
*
28330260 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
28330287 CTGGTGGTTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
28330314 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
28330341 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
28330368 CTGGTG
1 CTGGTG
28330374 ACTTCGTCAC
Statistics
Matches: 142, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
26 12 0.08
27 126 0.89
28 4 0.03
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:28330264 original size:54 final size:54
Alignment explanation
Indices: 28330179--28330373 Score: 311
Period size: 54 Copynumber: 3.6 Consensus size: 54
28330169 AGGAAGCGTC
* *
28330179 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* *
28330233 CTAGTGGCTATGCCATGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
*
28330287 CTGGTGGTTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* *
28330341 CTGGTGGCTCTGCCAC-AATATCTGTATCTGGTG
1 CTGGTGGCTATGCCACGATTATCTG-ATCTGGTG
28330374 ACTTCGTCAC
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
53 7 0.05
54 123 0.95
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:28338097 original size:48 final size:48
Alignment explanation
Indices: 28338023--28338205 Score: 142
Period size: 48 Copynumber: 3.9 Consensus size: 48
28338013 GGATATATTA
* * * * *
28338023 CCGATACCATATCTCAGGCATGGTCTTGCACTAGCACTCATCTTTGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTTTGTG
* * * *
28338071 CCGATGCCATGTCCCAGACATGGTCTTACATTGGCTA-TCATAGTATG-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGC-ACTCAT-CTTTGTG
* * * * *
28338119 CTGAT-ACATGTCCCAGACAT-GTCTTACACTAGCCCTCGTC-TGGATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTTTG-TG
* * * *
28338165 CCGATGCTATGTCTCAGACATGGTCTTACACTGGCTCTCAT
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCAT
28338206 AATATGGTCG
Statistics
Matches: 103, Mismatches: 25, Indels: 14
0.73 0.18 0.10
Matches are distributed among these distances:
44 1 0.01
46 19 0.18
47 26 0.25
48 53 0.51
49 4 0.04
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.30
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTTTGTG
Found at i:28338206 original size:94 final size:94
Alignment explanation
Indices: 28338069--28338242 Score: 262
Period size: 94 Copynumber: 1.9 Consensus size: 94
28338059 CTCATCTTTG
* *
28338069 TGCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTATCATAGTATGG-CTGATA-CATGTCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAATATGGTC-GA-AGCATGTCC
28338132 CAGACATGTCTTACACTAGCCCTCGTCTGGA
64 CAGACATGTCTTACACTAGCCCTCGTCTGGA
* * * *
28338163 TGCCGATGCTATGTCTCAGACATGGTCTTACACTGGCTCTCATAATATGGTCGAAGCATGTCCTA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAATATGGTCGAAGCATGTCCCA
28338228 GACATGTCTTACACT
66 GACATGTCTTACACT
28338243 GGCGCACAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
93 1 0.01
94 70 0.97
95 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (94 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAATATGGTCGAAGCATGTCCCA
GACATGTCTTACACTAGCCCTCGTCTGGA
Found at i:28338224 original size:47 final size:45
Alignment explanation
Indices: 28338078--28338245 Score: 151
Period size: 47 Copynumber: 3.6 Consensus size: 45
28338068 GTGCCGATGC
* * *
28338078 CATGTCCCAGACATGGTCTTACATTGGCTATCATAGTATGGCTGATA-
1 CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATATGGC-GA-AG
* * * * * *
28338125 CATGTCCCAGACATGTCTTACACTAGCCCTCGT-CTGGATGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATAAT--ATGGCGAAG
*
28338171 CTATGTCTCAGACATGGTCTTACACTGGCTCTCATAATATGGTCGAAG
1 C-ATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATATGG-CGAAG
*
28338219 CATGTCCTAGACATGTCTTACACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
28338246 GCACAAATCA
Statistics
Matches: 97, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
45 1 0.01
46 30 0.31
47 44 0.45
48 21 0.22
49 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCATAATATGGCGAAG
Found at i:28340095 original size:35 final size:35
Alignment explanation
Indices: 28340048--28340118 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
28340038 TATCTATAAC
*
28340048 TGTATCTACATCTGAAATGGGCTCAGG-CTCGAATA
1 TGTATCTACATCTGAAATGGGCCCAGGCCT-GAATA
* * *
28340083 TGTATCTGCATCTTACATGGGCCCAGGCCTGAATA
1 TGTATCTACATCTGAAATGGGCCCAGGCCTGAATA
28340118 T
1 T
28340119 TAATCTATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 29 0.94
36 2 0.06
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (35 bp):
TGTATCTACATCTGAAATGGGCCCAGGCCTGAATA
Found at i:28345519 original size:14 final size:14
Alignment explanation
Indices: 28345500--28345526 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28345490 AAACCAAAAT
28345500 AAAACAAAAATAAA
1 AAAACAAAAATAAA
28345514 AAAACAAAAATAA
1 AAAACAAAAATAA
28345527 TTAGGTCCAA
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:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAACAAAAATAAA
Found at i:28354186 original size:39 final size:38
Alignment explanation
Indices: 28354102--28354452 Score: 436
Period size: 39 Copynumber: 9.0 Consensus size: 38
28354092 CAAATCCAAT
* * * *
28354102 CACCACCACAAAGCATGCGGGACTTTAAGCCCGAATATAA
1 CACCAGCACAAAGCCTTCGGGAC-TT-AGCCCGGATATAA
* * *
28354142 TACCAGCACAAAGCCTACGGGACTTTAGCCCGGATCTAA
1 CACCAGCACAAAGCCTTCGGGAC-TTAGCCCGGATATAA
* *
28354181 CACCAGCACAAATACCTTCGGGGCTTAGCCCGGATATAA
1 CACCAGCACAAA-GCCTTCGGGACTTAGCCCGGATATAA
*
28354220 CACCAGCACGAATGCCTTCGAGG-CTTAGCCCGGATATAA
1 CACCAGCAC-AAAGCCTTCG-GGACTTAGCCCGGATATAA
*
28354259 CACCAGCACAAATGCCTTCGGGGCTTAGCCCGGATATAA
1 CACCAGCACAAA-GCCTTCGGGACTTAGCCCGGATATAA
28354298 CACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACAAA-GCCTTCGGGACTTAGCCCGGATATAA
*
28354337 CACCAGCACGAATGCCTTC-GGACTTAGCCCGGATATAA
1 CACCAGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAA
* **
28354375 CACCAGCACGAATGCCTTTAGGACTTAGCCCGGATATAA
1 CACCAGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAA
* *
28354414 CACCAGCACAAATGCCTTCGAGCCTTAGCCCGGATATAA
1 CACCAGCACAAA-GCCTTCGGGACTTAGCCCGGATATAA
28354453 TTCTCCATTA
Statistics
Matches: 281, Mismatches: 22, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
38 43 0.15
39 202 0.72
40 36 0.13
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.18
Consensus pattern (38 bp):
CACCAGCACAAAGCCTTCGGGACTTAGCCCGGATATAA
Found at i:28354248 original size:78 final size:78
Alignment explanation
Indices: 28354129--28354452 Score: 492
Period size: 78 Copynumber: 4.2 Consensus size: 78
28354119 CGGGACTTTA
* * * * *
28354129 AGCCCGAATATAATACCAGCAC-AAAGCCTACGGGACTTTAGCCCGGATCTAACACCAGCACAAA
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAACACCAGCACAAA
*
28354193 TACCTTCGGGGCTT
65 TGCCTTCGGGGCTT
28354207 AGCCCGGATATAACACCAGCACGAATGCCTTCGAGG-CTTAGCCCGGATATAACACCAGCACAAA
1 AGCCCGGATATAACACCAGCACGAATGCCTTCG-GGACTTAGCCCGGATATAACACCAGCACAAA
28354271 TGCCTTCGGGGCTT
65 TGCCTTCGGGGCTT
* *
28354285 AGCCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAAT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACAAAT
*
28354350 GCCTTC-GGACTT
66 GCCTTCGGGGCTT
**
28354362 AGCCCGGATATAACACCAGCACGAATGCCTTTAGGACTTAGCCCGGATATAACACCAGCACAAAT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACAAAT
* *
28354427 GCCTTCGAGCCTT
66 GCCTTCGGGGCTT
28354440 AGCCCGGATATAA
1 AGCCCGGATATAA
28354453 TTCTCCATTA
Statistics
Matches: 227, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
77 74 0.33
78 142 0.63
79 9 0.04
80 2 0.01
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.18
Consensus pattern (78 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACAAAT
GCCTTCGGGGCTT
Found at i:28354335 original size:117 final size:116
Alignment explanation
Indices: 28354129--28354452 Score: 506
Period size: 117 Copynumber: 2.8 Consensus size: 116
28354119 CGGGACTTTA
* * * *
28354129 AGCCCGAATATAATACCAGCACAAA-GCCTACGGGACTTTAGCCCGGATCTAACACCAGCACAAA
1 AGCCCGGATATAACACCAGCACAAATGCCTTCGGGAC-TTAGCCCGGATATAACACCAGCACAAA
* * *
28354193 TACCTTCGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTTCGAGGCTT
65 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCG-GACTT
*
28354246 AGCCCGGATATAACACCAGCACAAATGCCTTCGGGGCTTAGCCCGGATATAACACCAGCACAAAT
1 AGCCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACAAAT
28354311 GCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGACTT
66 GCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGACTT
* **
28354362 AGCCCGGATATAACACCAGCACGAATGCCTTTAGGACTTAGCCCGGATATAACACCAGCACAAAT
1 AGCCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACAAAT
* *
28354427 GCCTTCGAGCCTTAGCCCGGATATAA
66 GCCTTCGGGACTTAGCCCGGATATAA
28354453 TTCTCCATTA
Statistics
Matches: 192, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
116 89 0.46
117 94 0.49
118 9 0.05
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.18
Consensus pattern (116 bp):
AGCCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACAAAT
GCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGACTT
Found at i:28357984 original size:27 final size:27
Alignment explanation
Indices: 28357951--28358109 Score: 173
Period size: 27 Copynumber: 5.9 Consensus size: 27
28357941 CTGCCAGAAT
* *
28357951 AGATAATGTGACAGAGTCACCAGATAC
1 AGATAATGTGGCAGAGCCACCAGATAC
*
28357978 AAATAATCGTGGCAGAGCCACCAGA-AC
1 AGATAAT-GTGGCAGAGCCACCAGATAC
*
28358005 AGATATATGTGGCAGAGCCGCCAGAT-C
1 AGATA-ATGTGGCAGAGCCACCAGATAC
* *
28358032 AGATAATCATGGCATAGCCACCAGA-AC
1 AGATAAT-GTGGCAGAGCCACCAGATAC
*
28358059 AGATATATATGGCAGAGCCACCAGAT-C
1 AGATA-ATGTGGCAGAGCCACCAGATAC
*
28358086 AGATAATTGTGGCATAGCCACCAG
1 AGATAA-TGTGGCAGAGCCACCAG
28358110 GACGCTTCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
26 3 0.03
27 91 0.81
28 19 0.17
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (27 bp):
AGATAATGTGGCAGAGCCACCAGATAC
Found at i:28358009 original size:54 final size:54
Alignment explanation
Indices: 28357944--28358109 Score: 235
Period size: 54 Copynumber: 3.1 Consensus size: 54
28357934 AGCATGGCTG
* * * * *
28357944 CCAGAATAGATA-ATGTGACAGAGTCACCAGATACAAATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATCGTGGCATAGCCA
* *
28357998 CCAGAACAGATATATGTGGCAGAGCCGCCAGATCAGATAATCATGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGCCA
* *
28358052 CCAGAACAGATATATATGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGCCA
28358106 CCAG
1 CCAG
28358110 GACGCTTCCT
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 83 0.83
55 17 0.17
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGCCA
Found at i:28359736 original size:26 final size:26
Alignment explanation
Indices: 28359700--28359806 Score: 187
Period size: 26 Copynumber: 4.1 Consensus size: 26
28359690 GAAATGCCCG
*
28359700 TCATGGAACATTTACCTAAACCATTA
1 TCATGGAACATTTACCTAACCCATTA
28359726 TCATGGAACATTTACCTAACCCATTA
1 TCATGGAACATTTACCTAACCCATTA
* *
28359752 TCATGGAATATTTACCTAATCCATTA
1 TCATGGAACATTTACCTAACCCATTA
28359778 TCATGGAACATTTACCTAACCCATTA
1 TCATGGAACATTTACCTAACCCATTA
28359804 TCA
1 TCA
28359807 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
TCATGGAACATTTACCTAACCCATTA
Found at i:28364765 original size:28 final size:27
Alignment explanation
Indices: 28364710--28364902 Score: 198
Period size: 27 Copynumber: 7.1 Consensus size: 27
28364700 AGTATGGCTG
* **
28364710 CCAGA-ACAGATAATGTGACAGATTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
28364736 CCAGATACAGATAATCGTGGCAGAGTCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
*
28364764 CCAGATACAGATAATCGTGGCAAAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
* *
28364792 CCAGA-ACAGATATATGTGTCAAAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
* *
28364819 CCAGAT-CAGATAATCATGGCATAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
*
28364846 CCAGA-ACAAATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
*
28364873 CCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGATACAGATAA-TGTGGCAGAGCCA
28364900 CCA
1 CCA
28364903 AGACGCTTCC
Statistics
Matches: 145, Mismatches: 13, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.06
27 92 0.63
28 45 0.31
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:28364845 original size:54 final size:54
Alignment explanation
Indices: 28364734--28364902 Score: 241
Period size: 54 Copynumber: 3.1 Consensus size: 54
28364724 GTGACAGATT
* *
28364734 CACCAGATACAGATA-ATCGTGGCAGAGTCACCAGATACAGATAATCGTGGCAAAGC
1 CACCAGA-ACAGATATAT-GTGGCAGAGCCACCAGAT-CAGATAATCGTGGCATAGC
* * *
28364790 CACCAGAACAGATATATGTGTCAAAGCCACCAGATCAGATAATCATGGCATAGC
1 CACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGC
* *
28364844 CACCAGAACAAATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGC
1 CACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGC
28364898 CACCA
1 CACCA
28364903 AGACGCTTCC
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
54 71 0.70
55 22 0.22
56 9 0.09
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (54 bp):
CACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGC
Found at i:28364899 original size:81 final size:83
Alignment explanation
Indices: 28364710--28364902 Score: 225
Period size: 81 Copynumber: 2.4 Consensus size: 83
28364700 AGTATGGCTG
* * ** * * *
28364710 CCAGAACAGATA-ATGTGACAGATTCACCAGATACAGATAATCGTGGCAGAGTCACCAGATACAG
1 CCAGAACAGATATATGTGGCAAAGCCACCAGATACAGATAATCATGGCAGAGCCACCAGATACAA
28364774 ATAATCGTGGCAAAGCCA
66 ATAATCGTGGCAAAGCCA
* *
28364792 CCAGAACAGATATATGTGTCAAAGCCACCAGAT-CAGATAATCATGGCATAGCCACCAGA-ACAA
1 CCAGAACAGATATATGTGGCAAAGCCACCAGATACAGATAATCATGGCAGAGCCACCAGATACAA
*
28364855 ATATAT-GTGGCAGAGCCA
66 ATA-ATCGTGGCAAAGCCA
* *
28364873 CCAGATCAGATA-ATTGTGGCATAGCCACCA
1 CCAGAACAGATATA-TGTGGCAAAGCCACCA
28364903 AGACGCTTCC
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
80 1 0.01
81 42 0.44
82 37 0.39
83 16 0.17
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (83 bp):
CCAGAACAGATATATGTGGCAAAGCCACCAGATACAGATAATCATGGCAGAGCCACCAGATACAA
ATAATCGTGGCAAAGCCA
Found at i:28366556 original size:26 final size:26
Alignment explanation
Indices: 28366525--28366632 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28366515 TGAAATGCCC
* *
28366525 ATCATGGAACATTTACTTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28366551 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28366577 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
28366603 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28366629 ATCA
1 ATCA
28366633 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28371184 original size:43 final size:43
Alignment explanation
Indices: 28371123--28371207 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
28371113 AAACGAGATT
28371123 GAGGAATAAATTCCTTTGAATTAGCTTCTAGCAAAGCTAAGTC
1 GAGGAATAAATTCCTTTGAATTAGCTTCTAGCAAAGCTAAGTC
28371166 GAGGAATAAATTCCTTTGAATTAGCTTCTAGCAAAGCTAAGT
1 GAGGAATAAATTCCTTTGAATTAGCTTCTAGCAAAGCTAAGT
28371208 ATTTTTCTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (43 bp):
GAGGAATAAATTCCTTTGAATTAGCTTCTAGCAAAGCTAAGTC
Found at i:28374333 original size:48 final size:48
Alignment explanation
Indices: 28374277--28374434 Score: 235
Period size: 48 Copynumber: 3.3 Consensus size: 48
28374267 CACAAAGTAA
* *
28374277 GATGCCAATGCCATATCCCGGATATGGTCTTAAATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
28374325 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
* * * * *
28374373 AATGCCAATGCCATGTCCCAGACATGGTATTACATGGGATCACATAAC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
**
28374421 GATGGAAATGCCAT
1 GATGCCAATGCCAT
28374435 GTCGTAGACA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 100 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
Found at i:28374435 original size:48 final size:48
Alignment explanation
Indices: 28374277--28374456 Score: 234
Period size: 48 Copynumber: 3.8 Consensus size: 48
28374267 CACAAAGTAA
* * *
28374277 GATGCCAATGCCATATCCCGGATATGGTCTTAAATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
*
28374325 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* * * *
28374373 AATGCCAATGCCATGTCCCAGACATGGTATTACATGGGATCACATAAC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
** * ** *
28374421 GATGGAAATGCCATGTCGTAGACATGGTTTTACATG
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATG
28374457 ACGTCACATA
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 119 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:28383422 original size:46 final size:44
Alignment explanation
Indices: 28383302--28383523 Score: 157
Period size: 46 Copynumber: 4.9 Consensus size: 44
28383292 TGGGTTATTG
* * *
28383302 TGAG-CTAGTGTAAGACATGTCTGAGACATGCATAGGCCAT-ATTA
1 TGAGTCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-TGA-GA
* * *
28383346 TGAGAGCTTGTGTAAGACCATGTGTGGGACATGGCATCGGCGCTGAGA
1 TGAG-TCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTGAGA
* **
28383394 TGAGTCTAGTATAAGACATGTCTGGGACATGCATTAGCCTCGAGA
1 TGAGTCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-GAGA
* *
28383439 TGTAAG-CTAGTGTAAGACATGTCTGAGACATTCATCGG-CTACGAGA
1 TG--AGTCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT--GAGA
* * * *
28383485 CGTGTC-AGTGTAAGTCCGTGTCTGGGACATGGCATCGGC
1 TGAGTCTAGTGTAAG-ACATGTCTGGGACAT-GCATCGGC
28383524 AAAGATGTGC
Statistics
Matches: 142, Mismatches: 22, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
44 15 0.11
45 27 0.19
46 62 0.44
47 23 0.16
48 13 0.09
49 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (44 bp):
TGAGTCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTGAGA
Found at i:28385472 original size:46 final size:45
Alignment explanation
Indices: 28385378--28385558 Score: 143
Period size: 46 Copynumber: 3.9 Consensus size: 45
28385368 CACTGACACA
* * * *
28385378 TCTCGCAGC-CGATGCATGTCCCATACATGTCTTACATTGGCTTACG
1 TCTCG-AGCTCGATGCATGTCCCAGACATGTCTTACACTAGCCT-CG
* *
28385424 TCTCGAGCTCAATGCATGTCCCAGACATGTCTTACACTAGCAGTCG
1 TCTCGAGCTCGATGCATGTCCCAGACATGTCTTACACTAGC-CTCG
* * * *
28385470 TCTCGATG-TCGATGCCACGTCCCAAACATGGTCTTACACTGGCTCTCA
1 TCTCGA-GCTCGATG-CATGTCCCAGACAT-GTCTTACACTAGC-CTCG
* * * *
28385518 TATTGTGGC-CGATGCATGTCCTAGACATGTCTTACACTAGC
1 TCTCG-AGCTCGATGCATGTCCCAGACATGTCTTACACTAGC
28385559 TCACACGAGT
Statistics
Matches: 109, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
45 3 0.03
46 58 0.53
47 25 0.23
48 23 0.21
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.29
Consensus pattern (45 bp):
TCTCGAGCTCGATGCATGTCCCAGACATGTCTTACACTAGCCTCG
Found at i:28385504 original size:94 final size:92
Alignment explanation
Indices: 28385387--28385558 Score: 213
Period size: 94 Copynumber: 1.8 Consensus size: 92
28385377 ATCTCGCAGC
* * * * *
28385387 CGATGCATGTCCCATACATGTCTTACATTGGCT-TACGTCTCG-AGCTCAATGCATGTCCCAGAC
1 CGATGCACGTCCCAAACATGTCTTACACTGGCTCT-CATATCGTAGC-CAATGCATGTCCCAGAC
28385450 ATGTCTTACACTAGCAGTCGTCTCGATGT
64 ATGTCTTACACTAGCAGTCGTCTCGATGT
* * * *
28385479 CGATGCCACGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTGGCCGATGCATGTCCTAGAC
1 CGATG-CACGTCCCAAACAT-GTCTTACACTGGCTCTCATATCGTAGCCAATGCATGTCCCAGAC
28385544 ATGTCTTACACTAGC
64 ATGTCTTACACTAGC
28385559 TCACACGAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
92 5 0.07
93 12 0.18
94 47 0.70
95 3 0.04
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (92 bp):
CGATGCACGTCCCAAACATGTCTTACACTGGCTCTCATATCGTAGCCAATGCATGTCCCAGACAT
GTCTTACACTAGCAGTCGTCTCGATGT
Found at i:28387816 original size:17 final size:18
Alignment explanation
Indices: 28387789--28387822 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28387779 CACACAATAA
*
28387789 ACCCAAAATAATCCCAAC
1 ACCCAAAATAAGCCCAAC
28387807 ACCC-AAATAAGCCCAA
1 ACCCAAAATAAGCCCAA
28387823 GAGGAGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.38, G:0.03, T:0.09
Consensus pattern (18 bp):
ACCCAAAATAAGCCCAAC
Found at i:28389719 original size:28 final size:29
Alignment explanation
Indices: 28389688--28389746 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
28389678 AAAGTGATTT
*
28389688 TTGACAAAAATGTAAAT-TAGGGATTAAA
1 TTGACAAAAATGTAAATAGAGGGATTAAA
* *
28389716 TTGAGAAAAATGTAAATAGAGGGGTTAAA
1 TTGACAAAAATGTAAATAGAGGGATTAAA
28389745 TT
1 TT
28389747 ATGAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (29 bp):
TTGACAAAAATGTAAATAGAGGGATTAAA
Found at i:28390363 original size:43 final size:43
Alignment explanation
Indices: 28390284--28390365 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
28390274 ATTGTGTTTA
* * *
28390284 CGTGTAAGACCATGTCTGCGACATTGGTATCGTTATATGATTT
1 CGTGTAAGACCACGTCTGCGACATTGGCATCATTATATGATTT
* **
28390327 CGTGTAAGACCACGTCTGGGATGTTGGCATCATTATATG
1 CGTGTAAGACCACGTCTGCGACATTGGCATCATTATATG
28390366 TTAACATGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGCGACATTGGCATCATTATATGATTT
Found at i:28398510 original size:5 final size:4
Alignment explanation
Indices: 28398483--28398523 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
28398473 TTGCTTGTAC
28398483 ATAA ATAA ATAA ATAA ATAAA ATGAA AT-- ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA AT-AA AT-AA ATAA ATAA ATAA ATAA A
28398524 GGCTCAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
2 2 0.06
4 23 0.70
5 8 0.24
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:28422752 original size:13 final size:13
Alignment explanation
Indices: 28422734--28422759 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28422724 ATATTTTTAT
28422734 CCCATGCTTAGCA
1 CCCATGCTTAGCA
28422747 CCCATGCTTAGCA
1 CCCATGCTTAGCA
28422760 TATTTTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (13 bp):
CCCATGCTTAGCA
Found at i:28426751 original size:47 final size:48
Alignment explanation
Indices: 28426678--28426860 Score: 164
Period size: 47 Copynumber: 3.9 Consensus size: 48
28426668 AAGGTAAGGT
*
28426678 GCCGATGCCATGTCCTAGACACGGTCTTACATTGGCTCAT-ATCTCAA
1 GCCGATGCCATGTCCTAGACATGGTCTTACATTGGCTCATCATCTCAA
* * * * *
28426725 GTCGATGCCATGT-CTCAGACATGGTCTTATACTGACT-ATCATCTCGTA
1 GCCGATGCCATGTCCT-AGACATGGTCTTACATTGGCTCATCATCTC-AA
* * * * * * * *
28426773 GCCGATG-CATATCCCAGACAT-TTCTCACAGTAGC-CCTCGTCTCAA
1 GCCGATGCCATGTCCTAGACATGGTCTTACATTGGCTCATCATCTCAA
28426818 TGCCGATGCCATGTCCTAGACATGGTCTTACATTGGCTC-TCAT
1 -GCCGATGCCATGTCCTAGACATGGTCTTACATTGGCTCATCAT
28426861 AATGTGGCCG
Statistics
Matches: 102, Mismatches: 25, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
45 1 0.01
46 24 0.24
47 56 0.55
48 20 0.20
49 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (48 bp):
GCCGATGCCATGTCCTAGACATGGTCTTACATTGGCTCATCATCTCAA
Found at i:28453245 original size:21 final size:22
Alignment explanation
Indices: 28453219--28453259 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28453209 CACTTGACAC
28453219 AGGGGCA-CACGCCCGTGTGGG
1 AGGGGCACCACGCCCGTGTGGG
*
28453240 AGGGGCACCACGTCCGTGTG
1 AGGGGCACCACGCCCGTGTG
28453260 AGCATTCCAA
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:0.15, C:0.29, G:0.44, T:0.12
Consensus pattern (22 bp):
AGGGGCACCACGCCCGTGTGGG
Found at i:28454778 original size:19 final size:19
Alignment explanation
Indices: 28454762--28454799 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28454752 GGGTAAGCAT
28454762 TTACATGCTTAGTAAGCTC
1 TTACATGCTTAGTAAGCTC
28454781 TTACATGCTTAGTAAGCTC
1 TTACATGCTTAGTAAGCTC
28454800 AAATAGCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (19 bp):
TTACATGCTTAGTAAGCTC
Found at i:28457399 original size:47 final size:47
Alignment explanation
Indices: 28457308--28457577 Score: 205
Period size: 47 Copynumber: 5.8 Consensus size: 47
28457298 AGGGTAAGGT
* * * *
28457308 GCCGATGTCATGTCCTAGACACGGTCTTACACTGGCTCAT-ATCTCAAA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAGCT-ATCATCTCGAA
* * * *
28457356 TCC-ATGCCATGTCCCAGACATGGTCTTATACTAACTATCATCTCGTA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAA
* * * *
28457403 GCCAATGCATGTCCCAGACAT-GTTTTACACTGGCT-TACATCTCGAG
1 GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTAT-CATCTCGAA
* ** *
28457449 GCCGATGAATGTCCCAGACAT-GTCTTACACTAGCCCTCGTCTC-AA
1 GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAA
* * * * **
28457494 TGCCGATGCCATGTACCAGACATGGTCTTACACTGGCTTTCATAAT-GTG
1 -GCCGATG-CATGTCCCAGACATGGTCTTACACTAGCTATCAT-CTCGAA
* *
28457543 GCCGATACATGTCCCAGACAT-ATCTTACACTAGCT
1 GCCGATGCATGTCCCAGACATGGTCTTACACTAGCT
28457578 CACACATGAA
Statistics
Matches: 177, Mismatches: 36, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
45 2 0.01
46 73 0.41
47 75 0.42
48 26 0.15
49 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAA
Found at i:28457462 original size:46 final size:45
Alignment explanation
Indices: 28457364--28457573 Score: 165
Period size: 46 Copynumber: 4.5 Consensus size: 45
28457354 AATCCATGCC
* ** * *
28457364 ATGTCCCAGACATGGTCTTATACTAACTATCATCTCGTA-GCCAATGC
1 ATGTCCCAGACAT-GTCTTACACTGGCT-TCATCTCG-AGGCCGATGA
*
28457411 ATGTCCCAGACATGTTTTACACTGGCTTACATCTCGAGGCCGATGA
1 ATGTCCCAGACATGTCTTACACTGGCTT-CATCTCGAGGCCGATGA
* * * * * *
28457457 ATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGATGCC
1 ATGTCCCAGACATGTCTTACACT-GGCTTCATCTCGAGGCCGATG-A
* * *
28457504 ATGTACCAGACATGGTCTTACACTGGCTTTCATAAT-GTGGCCGAT-A
1 ATGTCCCAGACAT-GTCTTACACTGGC-TTCAT-CTCGAGGCCGATGA
*
28457550 CATGTCCCAGACATATCTTACACT
1 -ATGTCCCAGACATGTCTTACACT
28457574 AGCTCACACA
Statistics
Matches: 131, Mismatches: 24, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
45 2 0.02
46 67 0.51
47 42 0.32
48 19 0.15
49 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (45 bp):
ATGTCCCAGACATGTCTTACACTGGCTTCATCTCGAGGCCGATGA
Found at i:28462100 original size:3 final size:3
Alignment explanation
Indices: 28462092--28462148 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
28462082 TTTTAAAGCA
28462092 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28462140 TAT TAT TAT
1 TAT TAT TAT
28462149 AGGGAGTGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28462496 original size:3 final size:3
Alignment explanation
Indices: 28462488--28462521 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
28462478 TGGATTTCTC
*
28462488 CCT CCT CCT CCT CCT CCT TCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT C
28462522 ATTATTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CCT
Found at i:28463045 original size:7 final size:8
Alignment explanation
Indices: 28463023--28463047 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28463013 TGATTTGAAT
28463023 TATAAAAA
1 TATAAAAA
28463031 TATAAAAA
1 TATAAAAA
28463039 TATAAAAA
1 TATAAAAA
28463047 T
1 T
28463048 GAAAAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
TATAAAAA
Found at i:28468287 original size:30 final size:30
Alignment explanation
Indices: 28468253--28468322 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
28468243 ACTGATTCCC
28468253 AGAGGCAACACCTTGCGGAGCTGATGAGCG
1 AGAGGCAACACCTTGCGGAGCTGATGAGCG
28468283 AGAGGCAACACCTTGCGGAGCTGATGAGCG
1 AGAGGCAACACCTTGCGGAGCTGATGAGCG
28468313 AGAGGCAACA
1 AGAGGCAACA
28468323 AATAGACTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.36, T:0.11
Consensus pattern (30 bp):
AGAGGCAACACCTTGCGGAGCTGATGAGCG
Found at i:28473381 original size:22 final size:21
Alignment explanation
Indices: 28473356--28473399 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
28473346 TTAAATATAT
*
28473356 ATAGAAAAAGTAAAAAGTAAAA
1 ATAGAAAAAG-AAAAAGAAAAA
28473378 ATAGAAAAAGAAAAAGAAAAA
1 ATAGAAAAAGAAAAAGAAAAA
28473399 A
1 A
28473400 GTAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (21 bp):
ATAGAAAAAGAAAAAGAAAAA
Found at i:28473864 original size:18 final size:18
Alignment explanation
Indices: 28473841--28473876 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28473831 TACCAACAAC
28473841 ATTTAGACTGATGACATG
1 ATTTAGACTGATGACATG
28473859 ATTTAGACTGATGACATG
1 ATTTAGACTGATGACATG
28473877 TGAGGTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (18 bp):
ATTTAGACTGATGACATG
Found at i:28475558 original size:20 final size:20
Alignment explanation
Indices: 28475535--28475577 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
28475525 TAAATTGATG
28475535 CTCAAATTAAACAATTGTAT
1 CTCAAATTAAACAATTGTAT
28475555 CTCAAATTAAACAATTGTAT
1 CTCAAATTAAACAATTGTAT
28475575 CTC
1 CTC
28475578 TTGGTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.35
Consensus pattern (20 bp):
CTCAAATTAAACAATTGTAT
Found at i:28481092 original size:25 final size:25
Alignment explanation
Indices: 28481044--28481092 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
28481034 CCAAAATTCT
*
28481044 AAGGAAAATATTTTTTTGAACAATCC
1 AAGGAAAATATTTTATTG-ACAATCC
28481070 AAGGAAAATATTTTAATTG-CAAT
1 AAGGAAAATATTTT-ATTGACAAT
28481093 AGGATGGGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 14 0.67
27 3 0.14
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (25 bp):
AAGGAAAATATTTTATTGACAATCC
Found at i:28491533 original size:21 final size:21
Alignment explanation
Indices: 28491507--28491548 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28491497 TGCTTGAGTA
*
28491507 TTTAAATGTTTAATGATAGAT
1 TTTAAAGGTTTAATGATAGAT
28491528 TTTAAAGGTTTAATGATAGAT
1 TTTAAAGGTTTAATGATAGAT
28491549 ATACAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (21 bp):
TTTAAAGGTTTAATGATAGAT
Found at i:28492063 original size:34 final size:34
Alignment explanation
Indices: 28492020--28492091 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
28492010 TATGAATGCC
28492020 TTGATGATATGTTGTATTCGTTACCGAGCCTCGT
1 TTGATGATATGTTGTATTCGTTACCGAGCCTCGT
28492054 TTGATGATATGTTGTATTCGTTACCGAGCCTCGT
1 TTGATGATATGTTGTATTCGTTACCGAGCCTCGT
28492088 TTGA
1 TTGA
28492092 ACTATGTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (34 bp):
TTGATGATATGTTGTATTCGTTACCGAGCCTCGT
Found at i:28492212 original size:23 final size:22
Alignment explanation
Indices: 28492176--28492264 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 22
28492166 AGACTCACCA
*
28492176 CAGCTCGTAAGAGCTTACTGTTT
1 CAGCTCAT-AGAGCTTACTGTTT
* *
28492199 CAGCTCATTGGAGCTTACCGATTT
1 CAGCTCA-TAGAGCTTACTG-TTT
* *
28492223 -AGCTTGATAGAGCTTACTATTTT
1 CAGC-TCATAGAGCTTACT-GTTT
28492246 CAGCTCAATAGAGCTTACT
1 CAGCTC-ATAGAGCTTACT
28492265 ATTTATCAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
23 31 0.60
24 21 0.40
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (22 bp):
CAGCTCATAGAGCTTACTGTTT
Found at i:28492256 original size:24 final size:24
Alignment explanation
Indices: 28492185--28492277 Score: 93
Period size: 24 Copynumber: 3.9 Consensus size: 24
28492175 ACAGCTCGTA
* *
28492185 AGAGCTTACT-GTTTCAGCTCATT
1 AGAGCTTACTATTTTCAGCTCAAT
* * **
28492208 GGAGCTTACCGA-TTT-AGCTTGAT
1 AGAGCTTA-CTATTTTCAGCTCAAT
28492231 AGAGCTTACTATTTTCAGCTCAAT
1 AGAGCTTACTATTTTCAGCTCAAT
28492255 AGAGCTTACTATTTATCAGCTCA
1 AGAGCTTACTATTT-TCAGCTCA
28492278 GGAGGAGCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
22 2 0.04
23 22 0.39
24 24 0.43
25 8 0.14
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (24 bp):
AGAGCTTACTATTTTCAGCTCAAT
Found at i:28494164 original size:37 final size:37
Alignment explanation
Indices: 28494106--28494213 Score: 189
Period size: 37 Copynumber: 2.9 Consensus size: 37
28494096 GCTCAGACGA
* *
28494106 AATCTCCACACGAAGTTATCGGGTCTTACCCGGACAG
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAG
*
28494143 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAG
28494180 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
28494214 ATATATTTCC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAG
Found at i:28494481 original size:47 final size:47
Alignment explanation
Indices: 28494423--28494609 Score: 293
Period size: 47 Copynumber: 4.0 Consensus size: 47
28494413 ATTTCGCATA
* * * *
28494423 GGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATT
1 GGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATT
* *
28494470 GACCATTCGGCCTTATCACACATATGGATGCTCACATTCATCACATT
1 GGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATT
*
28494517 GGCCATTCGGCCTTATCACACATATACATGCTCACATTCATCACATT
1 GGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATT
* *
28494564 GGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACAT
1 GGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACAT
28494610 AAAATCCTAA
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 128 1.00
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (47 bp):
GGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATT
Found at i:28498236 original size:40 final size:40
Alignment explanation
Indices: 28498172--28498756 Score: 938
Period size: 40 Copynumber: 14.6 Consensus size: 40
28498162 CCAGCATGAT
* * * *
28498172 TGCTCTTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTC-TTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * * *
28498213 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28498253 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28498293 TGCTCTTCGGGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28498333 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28498373 TGCTCTTCGGGACTTAGCCCGGTTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28498413 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28498453 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28498493 TGCTCTTTGGGACTTAGCCCGGTTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28498533 TGCTCTTCGGGACTTAGCCTGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
28498573 TGCTCTTCGAGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28498613 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28498653 TGCTCTTC-GGACTTAGCCCGGTTACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28498692 TGCTCTTCGGGACTTAGCCTGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28498732 TGCTCTTTGGGACTTAGCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATA
28498757 TATATATAAC
Statistics
Matches: 502, Mismatches: 41, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
39 37 0.07
40 460 0.92
41 5 0.01
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:28500087 original size:37 final size:37
Alignment explanation
Indices: 28500023--28500131 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
28500013 AGCTCAGACG
* *
28500023 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
28500060 AAATCTCCACACGTAGTCATCGAGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
28500097 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
28500132 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:28500427 original size:25 final size:25
Alignment explanation
Indices: 28500399--28500476 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 25
28500389 ATTCGGCCTT
28500399 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
*
28500424 AT--CACAT-TGGCCAT--TCAGCCTT-
1 ATCACACATAT-G-CATGCTCA-CATTC
28500446 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
28500471 ATCACA
1 ATCACA
28500477 TTGGCCATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
22 6 0.14
23 12 0.29
24 12 0.29
25 12 0.29
ACGTcount: A:0.31, C:0.32, G:0.09, T:0.28
Consensus pattern (25 bp):
ATCACACATATGCATGCTCACATTC
Found at i:28500445 original size:93 final size:94
Alignment explanation
Indices: 28500335--28500624 Score: 444
Period size: 93 Copynumber: 3.1 Consensus size: 94
28500325 ACATATTTCG
* * * * *
28500335 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATA-TGACCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTT
28500399 ATCACACATATGCATGCTCACATTCATCA
66 ATCACACATATGCATGCTCACATTCATCA
* *
28500428 CATTGGCCATTCAGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTC-ACCTT
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTT
* * * *
28500492 ATCACATATATGAATGTTCATATTCATCA
66 ATCACACATATGCATGCTCACATTCATCA
*
28500521 TATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTT
28500586 ATCA-ACATATGCATGCTCACA-TCATCA
66 ATCACACATATGCATGCTCACATTCATCA
28500613 CATTGGCCATTC
1 CATTGGCCATTC
28500625 TATAATATAT
Statistics
Matches: 176, Mismatches: 19, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
92 17 0.10
93 143 0.81
94 16 0.09
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (94 bp):
CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTT
ATCACACATATGCATGCTCACATTCATCA
Found at i:28500451 original size:22 final size:21
Alignment explanation
Indices: 28500424--28500498 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 21
28500414 GCTCACATTC
28500424 ATCACATTGGCCATTCAGCCTT
1 ATCACATTGGCCATTCA-CCTT
*
28500446 ATCACACATAT-G-CATGCTCACATT
1 AT--CACAT-TGGCCAT--TCACCTT
28500470 CATCACATTGGCCATTCACCTT
1 -ATCACATTGGCCATTCACCTT
28500492 ATCACAT
1 ATCACAT
28500499 ATATGAATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 17
0.69 0.03 0.27
Matches are distributed among these distances:
21 7 0.16
22 9 0.21
23 9 0.21
24 12 0.28
25 6 0.14
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.31
Consensus pattern (21 bp):
ATCACATTGGCCATTCACCTT
Found at i:28500451 original size:47 final size:47
Alignment explanation
Indices: 28500335--28500624 Score: 444
Period size: 47 Copynumber: 6.3 Consensus size: 47
28500325 ACATATTTCG
* * *
28500335 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
* *
28500382 TA-TGACCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
*
28500428 CATTGGCCATTCAGCCTTATCACACATATGCATGCTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
* * * * *
28500475 CATTGGCCATTC-ACCTTATCACATATATGAATGTTCATATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
*
28500521 TATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
28500568 CATTGGCCATTCGGCCTTATCA-ACATATGCATGCTCACA-TCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
28500613 CATTGGCCATTC
1 CATTGGCCATTC
28500625 TATAATATAT
Statistics
Matches: 221, Mismatches: 20, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
45 18 0.08
46 98 0.44
47 105 0.48
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
Found at i:28504230 original size:38 final size:39
Alignment explanation
Indices: 28504114--28504568 Score: 586
Period size: 39 Copynumber: 11.9 Consensus size: 39
28504104 CCAGCATGAT
* * * *
28504114 TGCTCTTTCCGGACCTAGCCCGAATA-AACACCAGCACGAA
1 TGCTC-TT-CGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28504154 TGCTCTTCGG--TTAAGCACGGATTATATCACTAGCACGAA
1 TGCTCTTCGGACTT-AGCCCGGA-TACATCACTAGCACGAA
* *
28504193 AGCTCTTCGAACTTAGCCC-GATACATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
28504231 TGCTCTTCGGAC-TA-CCCGGATACATCACT---ACG-A
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28504264 TGCTCTTCGGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
28504303 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
*
28504342 TGCTTCTTCGGACTTAGCCCCGGTTACATCACTAGCACGAA
1 TGC-TCTTCGGACTTAG-CCCGGATACATCACTAGCACGAA
*
28504383 TGCTCTTCGGACTTA-CCCGGATACATCACTAGCAATGAA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGC-ACGAA
*
28504422 TGCTCTTCTGGACTTAGCCC-GTTACATCACTAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
28504461 TGCTCTTCGGACTTAG-CCGGATACATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
28504499 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCAC-AA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
28504538 TGCTCTTC-GACTTAGCCC-G-TACAT-ACTAGCA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCA
28504569 TCGGGAAATA
Statistics
Matches: 375, Mismatches: 20, Indels: 46
0.85 0.05 0.10
Matches are distributed among these distances:
33 13 0.03
34 12 0.03
35 20 0.05
36 5 0.01
37 31 0.08
38 84 0.22
39 107 0.29
40 73 0.19
41 30 0.08
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (39 bp):
TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:28505784 original size:36 final size:36
Alignment explanation
Indices: 28505737--28505843 Score: 171
Period size: 36 Copynumber: 3.0 Consensus size: 36
28505727 AGCTCAGACG
* *
28505737 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGAC
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAC
*
28505773 AAATCTCCACACGTAGTCATC-GGTCTTACCCAGAC
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAC
28505808 ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 A-AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
28505844 ATATATTTCC
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 14 0.22
36 39 0.60
37 12 0.18
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (36 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAC
Found at i:28506234 original size:47 final size:47
Alignment explanation
Indices: 28506071--28506348 Score: 351
Period size: 47 Copynumber: 6.3 Consensus size: 47
28506061 TATCACATAT
28506071 ACATTCATCATCAATT-GCCATTCGGCCTTATCACACATA-GCAT--TC
1 ACATTCATCA-C-ATTGGCCATTCGGCCTTATCACACATATGCATGCTC
28506116 ACATTCATCA-A-T-GCCATTC--CC-TA-CACA-ATATGCA---T-
1 ACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGCTC
* *
28506151 -CATTC-TCACATTGGCCATTC-GCCTTATCACATATATGCATGTTC
1 ACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGCTC
* *
28506195 ATATTCATCATATTGGCCATTCGGCCTTATCACACATATGCATGCTC
1 ACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGCTC
28506242 ACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGCTC
1 ACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGCTC
* *
28506289 ACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTC
1 ACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGCTC
28506336 ACATTCATCACAT
1 ACATTCATCACAT
28506349 AAAATCCTAA
Statistics
Matches: 210, Mismatches: 8, Indels: 28
0.85 0.03 0.11
Matches are distributed among these distances:
33 3 0.01
34 6 0.03
35 1 0.00
36 11 0.05
37 9 0.04
38 4 0.02
39 6 0.03
40 7 0.03
41 8 0.04
42 1 0.00
43 1 0.00
45 14 0.07
46 14 0.07
47 125 0.60
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
ACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGCTC
Found at i:28506252 original size:25 final size:25
Alignment explanation
Indices: 28506223--28506300 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 25
28506213 ATTCGGCCTT
28506223 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
* *
28506248 AT--CACAT-TGGCCAT--TCGGCCTT-
1 ATCACACATAT-G-CATGCTC-ACATTC
28506270 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
28506295 ATCACA
1 ATCACA
28506301 TTGGCCATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 5 0.12
23 12 0.30
24 12 0.30
25 11 0.28
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.28
Consensus pattern (25 bp):
ATCACACATATGCATGCTCACATTC
Found at i:28506275 original size:22 final size:22
Alignment explanation
Indices: 28506248--28506323 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
28506238 GCTCACATTC
28506248 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
28506270 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCCTT
28506294 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
28506317 ATCACAT
1 ATCACAT
28506324 ATATGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 12 0.29
25 5 0.12
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:28509892 original size:39 final size:39
Alignment explanation
Indices: 28509861--28510160 Score: 353
Period size: 39 Copynumber: 7.8 Consensus size: 39
28509851 CCAACATGAT
* *
28509861 TGCTCTTCGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATATATCACCAGCACGAA
** *
28509900 TGCTCTTCGGGTTTAG-CCGGATATATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATATATCACCAGCACGAA
* *
28509938 TGCTCTTCGGAACTTAGCCCGGATACATCA-CTGCACGAA
1 TGCTCTTCGG-ACTTAGCCCGGATATATCACCAGCACGAA
*
28509977 TGCTC-TCAGGACTTAGCCCGGATATATCACTAGCACG-A
1 TGCTCTTC-GGACTTAGCCCGGATATATCACCAGCACGAA
* *
28510015 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATATATCACCAGCACGAA
** * * *
28510055 AACTCCTC-GACTTA-CCCAGATATATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATATATCACCAGCACGAA
* * *
28510092 TGCTCCTCGAACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATATATCACCAGCACGAA
28510131 TGCTC-TCGGGACTTAGCCCGGATATATCAC
1 TGCTCTTC-GGACTTAGCCCGGATATATCAC
28510161 ATATCGACTA
Statistics
Matches: 230, Mismatches: 22, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
37 28 0.12
38 69 0.30
39 115 0.50
40 18 0.08
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (39 bp):
TGCTCTTCGGACTTAGCCCGGATATATCACCAGCACGAA
Found at i:28509974 original size:77 final size:78
Alignment explanation
Indices: 28509861--28510160 Score: 407
Period size: 77 Copynumber: 3.9 Consensus size: 78
28509851 CCAACATGAT
* * * * **
28509861 TGCTCTTCGG-ACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGTTTAG-CCGGATAT
1 TGCTCCTCGGAACTTAGCCCGGATATATCACTAGCACGAATGCTC-TCGGACTTAGCCCGGATAT
28509924 ATCACTAGCACGAA
65 ATCACTAGCACGAA
* *
28509938 TGCTCTTCGGAACTTAGCCCGGATACATCACT-GCACGAATGCTCTCAGGACTTAGCCCGGATAT
1 TGCTCCTCGGAACTTAGCCCGGATATATCACTAGCACGAATGCTCTC-GGACTTAGCCCGGATAT
28510002 ATCACTAGCACG-A
65 ATCACTAGCACGAA
* ** *
28510015 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAAAACTCCTC-GACTTA-CCCAGATAT
1 TGCTCCTCGGAACTTAGCCCGGATATATCACTAGCACGAATGCT-CTCGGACTTAGCCCGGATAT
28510078 ATCACTAGCACGAA
65 ATCACTAGCACGAA
28510092 TGCTCCTC-GAACTTAGCCCGGATATATCACTAGCACGAATGCTCTCGGGACTTAGCCCGGATAT
1 TGCTCCTCGGAACTTAGCCCGGATATATCACTAGCACGAATGCTCTC-GGACTTAGCCCGGATAT
28510156 ATCAC
65 ATCAC
28510161 ATATCGACTA
Statistics
Matches: 198, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
75 3 0.02
76 54 0.27
77 79 0.40
78 59 0.30
79 3 0.02
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (78 bp):
TGCTCCTCGGAACTTAGCCCGGATATATCACTAGCACGAATGCTCTCGGACTTAGCCCGGATATA
TCACTAGCACGAA
Found at i:28510106 original size:115 final size:118
Alignment explanation
Indices: 28509874--28510160 Score: 410
Period size: 115 Copynumber: 2.5 Consensus size: 118
28509864 TCTTCGGACC
* * * *
28509874 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGG-TTTAG-CCGGATATATCACTAGCACGA
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGA
** * * *
28509937 ATGCTCTTCGGAACTTAGCCCGGATACATCACTGCACGAATGCTCTCAGGACT
66 AAACTCCTCGGAACTTAGCCCAGATACATCACTGCACGAATGCTCTCAGAACT
28509990 TAGCCCGGATATATCACTAGCACG-ATGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGA
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGA
*
28510054 AAACTCCTC-G-ACTTA-CCCAGATATATCACTAGCACGAATGCTCCTC-GAACT
66 AAACTCCTCGGAACTTAGCCCAGATACATCACT-GCACGAATGCT-CTCAGAACT
28510105 TAGCCCGGATATATCACTAGCACGAATGCT-CTCGGGACTTAGCCCGGATATATCAC
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATATCAC
28510161 ATATCGACTA
Statistics
Matches: 156, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
114 13 0.08
115 81 0.52
116 35 0.22
117 27 0.17
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (118 bp):
TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGA
AAACTCCTCGGAACTTAGCCCAGATACATCACTGCACGAATGCTCTCAGAACT
Found at i:28510182 original size:46 final size:42
Alignment explanation
Indices: 28510115--28510201 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 42
28510105 TAGCCCGGAT
28510115 ATATCACTAGCACGAATGCTCTCGGGACTTAGCCCGGATATATCAC
1 ATATCACTAGCACGAATGCTCTC--GAC-TAG-CCGGATATATCAC
28510161 ATATCGACTAGC-CGAATGCTCTCGACTAGCCGGATATATCA
1 ATATC-ACTAGCACGAATGCTCTCGACTAGCCGGATATATCA
28510202 TAATTCTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
42 12 0.30
43 3 0.08
44 3 0.08
46 16 0.40
47 6 0.15
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (42 bp):
ATATCACTAGCACGAATGCTCTCGACTAGCCGGATATATCAC
Found at i:28511504 original size:36 final size:37
Alignment explanation
Indices: 28511400--28511505 Score: 171
Period size: 37 Copynumber: 2.9 Consensus size: 37
28511390 GCTCAGACGA
* *
28511400 AATCT-CACACGAAGTTATCGGGTCTTACCCGGACAG
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAG
*
28511436 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAG
28511473 AATCTCCACACGTAGTCATC-GGTCTTACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
28511506 ATATATTTCC
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 18 0.27
37 48 0.73
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAG
Found at i:28511824 original size:47 final size:47
Alignment explanation
Indices: 28511714--28511898 Score: 291
Period size: 47 Copynumber: 4.0 Consensus size: 47
28511704 ATTTCGCATA
* * * *
28511714 GCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATT-
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
*
28511760 GCCATTCGGCCTTATCACACATATGGATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
*
28511807 GCCATTCGGCCTTATCACACATATACATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
* *
28511854 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACAT
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACAT
28511899 AAAATCCTAA
Statistics
Matches: 128, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 41 0.32
47 87 0.68
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
Found at i:28515513 original size:40 final size:40
Alignment explanation
Indices: 28515449--28516029 Score: 911
Period size: 40 Copynumber: 14.6 Consensus size: 40
28515439 CCAGCATGAT
* * * *
28515449 TGCTCTTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTC-TTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * * *
28515490 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28515530 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28515570 TGCTCTTC-GGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28515609 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28515649 TGCTCTTCGGGACTTAGCCCGGTTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28515689 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28515729 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28515769 TGCTCTTTGGGACTTAGCCCGGTTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28515809 TGCTCTTCGGGACTTAGCCTGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
28515849 TGCTCTTCGAGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28515889 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28515929 TGCTCTTCGGGACTTAG-CCGG-TACATCACTAGCATG-A
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28515966 TGCTCTTC-GGACTTAGCCTGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28516005 TGCTCTTTGGGACTTAGCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATA
28516030 TATATATAAC
Statistics
Matches: 496, Mismatches: 39, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
36 8 0.02
37 12 0.02
38 28 0.06
39 48 0.10
40 395 0.80
41 5 0.01
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:28517372 original size:37 final size:37
Alignment explanation
Indices: 28517308--28517416 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
28517298 AGCTCAGACG
* *
28517308 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
28517345 AAATCTCCACACGTAGTCATCGAGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
28517382 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
28517417 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:28517684 original size:47 final size:47
Alignment explanation
Indices: 28517622--28517952 Score: 520
Period size: 47 Copynumber: 7.1 Consensus size: 47
28517612 ACATATTTCG
* * *
28517622 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
* *
28517669 TATTGACCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
*
28517716 CATTGGCCATTCAGCCTTATCACACATATGCATGCTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
** * * * *
28517763 CATTGGCCATTCAACCTTATCACATATATGAATGTTCATATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
*
28517810 TATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
28517857 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
* *
28517904 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA-TCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
28517950 CAT
1 CAT
28517953 AAATCCTAAA
Statistics
Matches: 261, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
46 9 0.03
47 252 0.97
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
Found at i:28517716 original size:25 final size:25
Alignment explanation
Indices: 28517687--28517764 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 25
28517677 ATTCGGCCTT
28517687 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
*
28517712 AT--CACAT-TGGCCAT--TCAGCCTT-
1 ATCACACATAT-G-CATGCTCA-CATTC
28517734 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
28517759 ATCACA
1 ATCACA
28517765 TTGGCCATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
22 6 0.14
23 12 0.29
24 12 0.29
25 12 0.29
ACGTcount: A:0.31, C:0.32, G:0.09, T:0.28
Consensus pattern (25 bp):
ATCACACATATGCATGCTCACATTC
Found at i:28517739 original size:22 final size:21
Alignment explanation
Indices: 28517712--28517787 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 21
28517702 GCTCACATTC
28517712 ATCACATTGGCCATTCAGCCTT
1 ATCACATTGGCCATTCA-CCTT
*
28517734 ATCACACATAT-G-CATGCTCACATT
1 AT--CACAT-TGGCCAT--TCACCTT
28517758 CATCACATTGGCCATTCAACCTT
1 -ATCACATTGGCCATTC-ACCTT
28517781 ATCACAT
1 ATCACAT
28517788 ATATGAATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
22 12 0.28
23 13 0.30
24 12 0.28
25 6 0.14
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.30
Consensus pattern (21 bp):
ATCACATTGGCCATTCACCTT
Found at i:28517791 original size:141 final size:141
Alignment explanation
Indices: 28517622--28517949 Score: 595
Period size: 141 Copynumber: 2.3 Consensus size: 141
28517612 ACATATTTCG
28517622 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGACCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGACCATTCGGCCTT
28517687 ATCACACATATGCATGCTCACATTCATCACATTGGCCATTCAGCCTTATCACACATATGCATGCT
66 ATCACACATATGCATGCTCACATTCATCACATTGGCCATTCAGCCTTATCACACATATGCATGCT
28517752 CACATTCATCA
131 CACATTCATCA
** * *
28517763 CATTGGCCATTCAACCTTATCACATATATGAATGTTCATATTCATCATATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGACCATTCGGCCTT
*
28517828 ATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGCT
66 ATCACACATATGCATGCTCACATTCATCACATTGGCCATTCAGCCTTATCACACATATGCATGCT
28517893 CACATTCATCA
131 CACATTCATCA
*
28517904 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA-TCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCA
28517950 CATAAATCCT
Statistics
Matches: 178, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
140 6 0.03
141 172 0.97
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.33
Consensus pattern (141 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGACCATTCGGCCTT
ATCACACATATGCATGCTCACATTCATCACATTGGCCATTCAGCCTTATCACACATATGCATGCT
CACATTCATCA
Found at i:28517857 original size:25 final size:25
Alignment explanation
Indices: 28517828--28517905 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 25
28517818 ATTCGGCCTT
28517828 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
* *
28517853 AT--CACAT-TGGCCAT--TCGGCCTT-
1 ATCACACATAT-G-CATGCTC-ACATTC
28517875 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
28517900 ATCACA
1 ATCACA
28517906 TTGGCCATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 5 0.12
23 12 0.30
24 12 0.30
25 11 0.28
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.28
Consensus pattern (25 bp):
ATCACACATATGCATGCTCACATTC
Found at i:28517880 original size:22 final size:22
Alignment explanation
Indices: 28517853--28517928 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
28517843 GCTCACATTC
28517853 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
28517875 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCCTT
28517899 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
28517922 ATCACAT
1 ATCACAT
28517929 ATATGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 12 0.29
25 5 0.12
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:28520918 original size:69 final size:70
Alignment explanation
Indices: 28520803--28520936 Score: 225
Period size: 69 Copynumber: 1.9 Consensus size: 70
28520793 TAGTTTATTA
* * * *
28520803 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTG
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
28520868 CTTAG
66 CTTAG
28520873 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
28520937 TTATGTGCTA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
69 37 0.62
70 23 0.38
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
CTTAG
Found at i:28522063 original size:45 final size:45
Alignment explanation
Indices: 28521996--28522214 Score: 304
Period size: 45 Copynumber: 4.9 Consensus size: 45
28521986 TGTTGATTTG
*
28521996 ATTATTCGGGCCTTTGAACCTAGCAGGCTATAATGCCGGTGAGAT
1 ATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
*
28522041 ATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAG
1 ATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
* *
28522086 ATTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGTCGGTGAGAT
1 ATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
* *
28522131 ACTATTCGGG-CTTTCGAGCCTAGCAAGCTATAATGCCGGTGA-A-
1 ATTATTCGGGCCTTT-GAGCCTAGCAGGCTATAATGCCGGTGAGAT
* * *
28522174 ATGATATCGGGCC-TCGAGCCTAGCAGGCGA-AATGCCGGTGA
1 ATTAT-TCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
28522215 ATGAATTCGG
Statistics
Matches: 157, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
42 11 0.07
43 16 0.10
44 11 0.07
45 119 0.76
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (45 bp):
ATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
Found at i:28526649 original size:16 final size:17
Alignment explanation
Indices: 28526610--28526650 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
28526600 AAACTTCAGG
*
28526610 TTAATAAT-ATGTTATA
1 TTAATAATAATGTAATA
*
28526626 TTATTAATAATGTAAT-
1 TTAATAATAATGTAATA
28526642 TTAATAATA
1 TTAATAATA
28526651 TAAAAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
TTAATAATAATGTAATA
Found at i:28527616 original size:55 final size:55
Alignment explanation
Indices: 28527556--28527667 Score: 127
Period size: 55 Copynumber: 2.0 Consensus size: 55
28527546 AAACTAAATC
* *
28527556 TTAAAAAAATTCAATAATTTTTAAATAATTTAATTATTT-TTTTTAAAATTGAAAA
1 TTAAAAAAATTCAATAATTTTAAAATAATTGAATTATTTATTTTTAAAATT-AAAA
*** * * * *
28527611 TTAAAACTTTTCAGTACTTTTAAAATAATTGGATTATTTATTTTTAATATTAAAA
1 TTAAAAAAATTCAATAATTTTAAAATAATTGAATTATTTATTTTTAAAATTAAAA
28527666 TT
1 TT
28527668 TATAAATTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
55 37 0.79
56 10 0.21
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (55 bp):
TTAAAAAAATTCAATAATTTTAAAATAATTGAATTATTTATTTTTAAAATTAAAA
Found at i:28530407 original size:193 final size:193
Alignment explanation
Indices: 28530070--28530453 Score: 623
Period size: 193 Copynumber: 2.0 Consensus size: 193
28530060 AAACTTTGCA
*
28530070 TAAGCGTATTGTTAATCTTTTTGCTCAGCTTTGGATAGAGTTTCGGTTGTAGATGGATTTTGAGT
1 TAAGCGTATTGTTAATCTTTTTGCTCAGCTTTGGATAGAGTTTCGGTTGTAGATGGATTCTGAGT
* * *
28530135 AGTGGGTGGTTGAGGATGAGTGATTAGTAATCAAAATTAGTTTTTATCTTTTGTTTAAAAAAAAT
66 AATGGATGGTTGAGGATGAGTGATTAGTAATCAAAATTAGTTTTTATCTTTTATTTAAAAAAAAT
* *
28530200 CCTAATTCTCTCTCT-TACAGAAATTCTGCT-CAGAATTTTTGACGTGCTTTCTTTTCCTCTGCT
131 CCTAATTCTCTCTCTCAACAGAAATTCTACTACA-AA-TTTTGACGTGCTTTCTTTTCCTCTGCT
28530263 TAAGCGTATTGTTAATCTTTTTGCTCAGCTTTGGATAGAGTTTCGGTTGCTA-ATGGATTCTGAG
1 TAAGCGTATTGTTAATCTTTTTGCTCAGCTTTGGATAGAGTTTCGGTTG-TAGATGGATTCTGAG
28530327 TAATGGATGGTTGAGGATGAGTGATTAGTAATCAAAATTAGTTTTTATCTTTTATTTCAAAAAAA
65 TAATGGATGGTTGAGGATGAGTGATTAGTAATCAAAATTAGTTTTTATCTTTTATTT--AAAAAA
* *
28530392 AATCCTGATTCTCTCTC-CAACCGAAATTCTACTACAAATTTTGACGTGCTTTCTTTTCCTCT
128 AATCCTAATTCTCTCTCTCAACAGAAATTCTACTACAAATTTTGACGTGCTTTCTTTTCCTCT
28530454 ACCATCTTTC
Statistics
Matches: 178, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
193 114 0.64
194 26 0.15
195 36 0.20
196 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (193 bp):
TAAGCGTATTGTTAATCTTTTTGCTCAGCTTTGGATAGAGTTTCGGTTGTAGATGGATTCTGAGT
AATGGATGGTTGAGGATGAGTGATTAGTAATCAAAATTAGTTTTTATCTTTTATTTAAAAAAAAT
CCTAATTCTCTCTCTCAACAGAAATTCTACTACAAATTTTGACGTGCTTTCTTTTCCTCTGCT
Found at i:28532394 original size:40 final size:40
Alignment explanation
Indices: 28532350--28532425 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
28532340 TTGTGCCTCA
* *
28532350 TATAGTCGAAGCTATTCT-AATTTGCACACTAAGTGCTATT
1 TATAGCCGAAGCTATTCTGAA-ATGCACACTAAGTGCTATT
*
28532390 TATAGCCGAAGCTATTTTGAAATGCACACTAAGTGC
1 TATAGCCGAAGCTATTCTGAAATGCACACTAAGTGC
28532426 CAAACGTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 30 0.94
41 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (40 bp):
TATAGCCGAAGCTATTCTGAAATGCACACTAAGTGCTATT
Found at i:28553606 original size:24 final size:25
Alignment explanation
Indices: 28553574--28553625 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
28553564 AGTTTATAAA
*
28553574 TTAGTTTTTTG-AAGTCTTT-TTTAT
1 TTAGGTTTTTGTAA-TCTTTATTTAT
*
28553598 TTAGGTTTTTGTTATCTTTATTTAT
1 TTAGGTTTTTGTAATCTTTATTTAT
28553623 TTA
1 TTA
28553626 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.17, C:0.04, G:0.12, T:0.67
Consensus pattern (25 bp):
TTAGGTTTTTGTAATCTTTATTTAT
Found at i:28554081 original size:10 final size:10
Alignment explanation
Indices: 28554062--28554095 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
28554052 ATGTGATGCC
*
28554062 AAATGGATAG
1 AAATGAATAG
28554072 AAATGAATAG
1 AAATGAATAG
*
28554082 AAATAAATAG
1 AAATGAATAG
28554092 AAAT
1 AAAT
28554096 AATGAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.21
Consensus pattern (10 bp):
AAATGAATAG
Found at i:28554096 original size:10 final size:10
Alignment explanation
Indices: 28554068--28554097 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28554058 TGCCAAATGG
*
28554068 ATAGAAATGA
1 ATAGAAATAA
28554078 ATAGAAATAA
1 ATAGAAATAA
28554088 ATAGAAATAA
1 ATAGAAATAA
28554098 TGAAGTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (10 bp):
ATAGAAATAA
Found at i:28554218 original size:14 final size:13
Alignment explanation
Indices: 28554196--28554248 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
28554186 GAATTATTAT
*
28554196 TTAACTAATTATAA
1 TTAAATAATTA-AA
28554210 TTAAATAATTAAA
1 TTAAATAATTAAA
* *
28554223 ATAAAAAATTAAA
1 TTAAATAATTAAA
28554236 TTAAATTAATTAA
1 TTAAA-TAATTAA
28554249 TCATTATGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
13 17 0.52
14 16 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAATAATTAAA
Found at i:28555912 original size:21 final size:21
Alignment explanation
Indices: 28555868--28555909 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
28555858 TTAAGATTAA
* *
28555868 TAATTTAATATTCATTAATTT
1 TAATTTAATATTAATAAATTT
28555889 TAATTTAAT-TTAATAAATTT
1 TAATTTAATATTAATAAATTT
28555909 T
1 T
28555910 TAAAATAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATTTAATATTAATAAATTT
Found at i:28556669 original size:9 final size:8
Alignment explanation
Indices: 28556634--28556691 Score: 64
Period size: 9 Copynumber: 7.0 Consensus size: 8
28556624 TAAAAACTAT
28556634 TTTTAAAA
1 TTTTAAAA
28556642 TTTTAAAA
1 TTTTAAAA
*
28556650 TCATTAAAA
1 T-TTTAAAA
28556659 TTATTAAAA
1 TT-TTAAAA
28556668 TTTATAAAA
1 TTT-TAAAA
*
28556677 TTAT-AAA
1 TTTTAAAA
28556684 TTTTAAAA
1 TTTTAAAA
28556692 AATAATTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.14
8 14 0.33
9 22 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (8 bp):
TTTTAAAA
Found at i:28556688 original size:17 final size:18
Alignment explanation
Indices: 28556632--28556701 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 18
28556622 TATAAAAACT
*
28556632 ATTTTTAAAATT-TTAAA
1 ATTTATAAAATTATTAAA
*
28556649 A-TCATTAAAATTATTAAA
1 ATTTA-TAAAATTATTAAA
28556667 ATTTATAAAATTA-TAAA
1 ATTTATAAAATTATTAAA
* * *
28556684 TTTTAAAAAATAATTAAA
1 ATTTATAAAATTATTAAA
28556702 TATTAATATC
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
16 1 0.02
17 22 0.51
18 18 0.42
19 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTATAAAATTATTAAA
Found at i:28556826 original size:16 final size:18
Alignment explanation
Indices: 28556789--28556831 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
28556779 ATTTGACAAA
*
28556789 AAATATAAATTAAAAGATT
1 AAATA-AAATGAAAAGATT
28556808 AAA-AAAATGAAAA-ATT
1 AAATAAAATGAAAAGATT
28556824 AAATAAAA
1 AAATAAAA
28556832 AATTATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 12 0.55
18 1 0.05
19 3 0.14
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAATGAAAAGATT
Found at i:28559850 original size:18 final size:18
Alignment explanation
Indices: 28559829--28559863 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28559819 AAAATAAAAA
28559829 AAAATAAAAAAAGTAATT
1 AAAATAAAAAAAGTAATT
* *
28559847 AAAATAATAATAGTAAT
1 AAAATAAAAAAAGTAAT
28559864 CATTTAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAATAAAAAAAGTAATT
Found at i:28567208 original size:43 final size:42
Alignment explanation
Indices: 28567089--28567246 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 42
28567079 AAGCTCGTAA
* ***
28567089 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACAAAATCAAATA-CG
* * **
28567132 ATGCC-ACTATCCCAAACAAGGTCTTACACAAAATCAAATACG
1 ATGCCAAC-GTCCCAGACGTGGTCTTACACAAAATCAAATACG
*
28567174 ATGCCAACGTCCCAGACGTGGTCCTACACAAAAATCATAAGT-CG
1 ATGCCAACGTCCCAGACGTGGTCTTACAC-AAAATCA-AA-TACG
* *
28567218 ATGCCAACGTACCAGATGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
28567247 GACTACACAT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 24 0.26
43 39 0.41
44 30 0.32
45 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACAAAATCAAATACG
Found at i:28569475 original size:11 final size:11
Alignment explanation
Indices: 28569459--28569484 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28569449 CCTAGCCCTA
28569459 TTTTTTTATGT
1 TTTTTTTATGT
28569470 TTTTTTTATGT
1 TTTTTTTATGT
28569481 TTTT
1 TTTT
28569485 GAGATCCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTTATGT
Found at i:28571950 original size:23 final size:23
Alignment explanation
Indices: 28571920--28571965 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28571910 AGGGGTGTTA
28571920 CATGTTAAAGATTTTAGATTTTT
1 CATGTTAAAGATTTTAGATTTTT
28571943 CATGTTAAAGATTTTAGATTTTT
1 CATGTTAAAGATTTTAGATTTTT
28571966 TCATTAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.52
Consensus pattern (23 bp):
CATGTTAAAGATTTTAGATTTTT
Found at i:28573200 original size:21 final size:21
Alignment explanation
Indices: 28573169--28573242 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
28573159 TGTGTCTAAT
28573169 TTTGAAATATTGATGTATACCA
1 TTTG-AATATTGATGTATACCA
* **
28573191 TTTGAATATTGTAT-CA-AGAA
1 TTTGAATATTG-ATGTATACCA
*
28573211 TGAT-AATATTGATGTATACCA
1 T-TTGAATATTGATGTATACCA
28573232 TTTGAATATTG
1 TTTGAATATTG
28573243 TATCAAGAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
19 2 0.05
20 12 0.31
21 19 0.49
22 6 0.15
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (21 bp):
TTTGAATATTGATGTATACCA
Found at i:28573231 original size:41 final size:41
Alignment explanation
Indices: 28573174--28573255 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
28573164 CTAATTTTGA
28573174 AATATTGATGTATACCATTTGAATATTGTATCAAGAATGAT
1 AATATTGATGTATACCATTTGAATATTGTATCAAGAATGAT
28573215 AATATTGATGTATACCATTTGAATATTGTATCAAGAATGAT
1 AATATTGATGTATACCATTTGAATATTGTATCAAGAATGAT
28573256 TTTTTAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (41 bp):
AATATTGATGTATACCATTTGAATATTGTATCAAGAATGAT
Found at i:28573554 original size:13 final size:13
Alignment explanation
Indices: 28573528--28573571 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
28573518 ATTATGTGTT
28573528 AAATGTGTAAATG
1 AAATGTGTAAATG
28573541 AAATG-GTAAGATG
1 AAATGTGTAA-ATG
*
28573554 AAATGTTTAAATG
1 AAATGTGTAAATG
28573567 AAATG
1 AAATG
28573572 GCTATACGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 4 0.14
13 21 0.75
14 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.30
Consensus pattern (13 bp):
AAATGTGTAAATG
Found at i:28573641 original size:13 final size:13
Alignment explanation
Indices: 28573538--28573632 Score: 52
Period size: 13 Copynumber: 7.4 Consensus size: 13
28573528 AAATGTGTAA
* *
28573538 ATGAAATGGTAAG
1 ATGAAATGGTTAT
* *
28573551 ATGAAATGTTTAA
1 ATGAAATGGTTAT
*
28573564 ATGAAATGGCTAT
1 ATGAAATGGTTAT
* *
28573577 ACGAACATGCTTAT
1 ATGAA-ATGGTTAT
***
28573591 ATGAAA-AAATAT
1 ATGAAATGGTTAT
*
28573603 AT-ATAT-GTATAT
1 ATGAAATGGT-TAT
28573615 ATGAAATGGTTAT
1 ATGAAATGGTTAT
28573628 ATGAA
1 ATGAA
28573633 GTGTTTATAC
Statistics
Matches: 60, Mismatches: 17, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
11 2 0.03
12 10 0.17
13 36 0.60
14 12 0.20
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (13 bp):
ATGAAATGGTTAT
Found at i:28577158 original size:48 final size:47
Alignment explanation
Indices: 28577066--28577184 Score: 152
Period size: 48 Copynumber: 2.6 Consensus size: 47
28577056 TAGTGTAGGA
* * * *
28577066 CATGTCTGAGACAT-GCATCGGC-TGTGAGATGTGTCAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCACGTGAGAGGTGTCAGTATAAGAC
*
28577111 CATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTCAGTATAAGAC
1 CATGTCTGGGACATGGCATCGGCACGT-GAGAGGTGTCAGTATAAGAC
* *
28577159 CATGTCTAGGACATGGCCTCGGCACG
1 CATGTCTGGGACATGGCATCGGCACG
28577185 AAAATGTGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
45 13 0.20
46 8 0.12
47 2 0.03
48 41 0.64
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (47 bp):
CATGTCTGGGACATGGCATCGGCACGTGAGAGGTGTCAGTATAAGAC
Found at i:28577221 original size:50 final size:48
Alignment explanation
Indices: 28577100--28577320 Score: 150
Period size: 48 Copynumber: 4.6 Consensus size: 48
28577090 TGAGATGTGT
* *
28577100 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAAAGGTGG
* * * *
28577148 CAGTATAAGACCATGTCTAGGACATGGCCTCGGCACG-A-AAATGTGAAAG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAAAGGTG---G
* * * *** * *
28577197 CTAGTGTAAGACCATGTCTGGGACATGGCGTTGGC-CTTGATTTTGATAGT
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGT-ATAAAGGT-GG
* * * *
28577247 CAGTGTAAGACCACGTTTGGGACATGGCATC-G-AC-T-TCATGGATGAG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAAAGG-TG-G
28577293 CCAGTGTAAGACCATGTCTGGGACATGG
1 -CAGTGTAAGACCATGTCTGGGACATGG
28577321 TGTCGGTATT
Statistics
Matches: 134, Mismatches: 27, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
45 4 0.03
46 6 0.04
47 27 0.20
48 36 0.27
49 28 0.21
50 30 0.22
51 1 0.01
52 1 0.01
53 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAAAGGTGG
Found at i:28578103 original size:20 final size:21
Alignment explanation
Indices: 28578064--28578103 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28578054 GTTACAATGA
28578064 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
28578085 CCACACGGGCGTG-TGCCCT
1 CCACACGGGCGTGTTGCCCT
28578104 GTTTCAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.10, C:0.40, G:0.30, T:0.20
Consensus pattern (21 bp):
CCACACGGGCGTGTTGCCCTT
Found at i:28581230 original size:16 final size:16
Alignment explanation
Indices: 28581209--28581242 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28581199 TAGAGTTTTC
*
28581209 TTTATGTTTTTTTATT
1 TTTATGTTTTGTTATT
28581225 TTTATGTTTTGTTATT
1 TTTATGTTTTGTTATT
28581241 TT
1 TT
28581243 CATACTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (16 bp):
TTTATGTTTTGTTATT
Found at i:28585530 original size:11 final size:11
Alignment explanation
Indices: 28585514--28585539 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28585504 CTGAATTAAT
28585514 CCTCACTTTTC
1 CCTCACTTTTC
28585525 CCTCACTTTTC
1 CCTCACTTTTC
28585536 CCTC
1 CCTC
28585540 CATTTTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.50, G:0.00, T:0.42
Consensus pattern (11 bp):
CCTCACTTTTC
Found at i:28585548 original size:12 final size:12
Alignment explanation
Indices: 28585517--28585553 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
28585507 AATTAATCCT
28585517 CACTTTTCCCT-
1 CACTTTTCCCTC
28585528 CACTTTTCCCTC
1 CACTTTTCCCTC
*
28585540 CA-TTTTTCCTC
1 CACTTTTCCCTC
28585551 CAC
1 CAC
28585554 ACAACTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 21 0.91
12 2 0.09
ACGTcount: A:0.11, C:0.46, G:0.00, T:0.43
Consensus pattern (12 bp):
CACTTTTCCCTC
Found at i:28587211 original size:5 final size:6
Alignment explanation
Indices: 28587196--28587234 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
28587186 TCTTATTATC
* *
28587196 TTTTTA TTTTTA TTTTTA TTTTTC TTTTTC TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
28587235 CCATTTCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:28587240 original size:24 final size:24
Alignment explanation
Indices: 28587194--28587240 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
28587184 AATCTTATTA
**
28587194 TCTTTTTATTTTTATTTTTATTTT
1 TCTTTTTATTTTTATTTCCATTTT
*
28587218 TCTTTTTCTTTTTATTTCCATTT
1 TCTTTTTATTTTTATTTCCATTT
28587241 CAATTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (24 bp):
TCTTTTTATTTTTATTTCCATTTT
Found at i:28593640 original size:45 final size:45
Alignment explanation
Indices: 28593580--28593694 Score: 135
Period size: 48 Copynumber: 2.5 Consensus size: 45
28593570 CAAGAGCTAA
* * *
28593580 TGTAAGA-CATGTCTGGGACATGCATCAGCTGCG-AGATGTGTCAT
1 TGTAAGACCATGTCTGGGACATGCATCAGC-ACGTAGAGGTGTCAG
*
28593624 TGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTCAG
1 TGTAAGACCATGTCTGGGACAT-GCATCAGCACG--TAGAGGTGTCAG
*
28593672 TATAAGACCATGTCTGGGACATG
1 TGTAAGACCATGTCTGGGACATG
28593695 GCCTCGGTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
44 7 0.11
45 16 0.26
46 7 0.11
47 1 0.02
48 30 0.49
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (45 bp):
TGTAAGACCATGTCTGGGACATGCATCAGCACGTAGAGGTGTCAG
Found at i:28594667 original size:41 final size:41
Alignment explanation
Indices: 28594580--28594669 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
28594570 TGTGTCTAGG
*
28594580 CCGTGTGCGACACACGGTCAGCCCCATGGGTGTGTTCTCGA
1 CCGTGTGTGACACACGGTCAGCCCCATGGGTGTGTTCTCGA
*
28594621 CCGTGTGTGACACACGGTCAGCCCCATGGGTGTGTTCTCGG
1 CCGTGTGTGACACACGGTCAGCCCCATGGGTGTGTTCTCGA
*
28594662 TCGTGTGT
1 CCGTGTGT
28594670 CCGCTATACG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.12, C:0.29, G:0.33, T:0.26
Consensus pattern (41 bp):
CCGTGTGTGACACACGGTCAGCCCCATGGGTGTGTTCTCGA
Found at i:28602428 original size:58 final size:60
Alignment explanation
Indices: 28602347--28602547 Score: 156
Period size: 69 Copynumber: 3.2 Consensus size: 60
28602337 ATCACTTTAA
* **
28602347 TATTAAATTAATATAATACTTA-T-CAAGATAAATATTAGGTTGAATTTAATATTAAATC
1 TATTAAATTAATAAAATACTTACTACAAGATAAATATTAAATTGAATTTAATATTAAATC
** * *
28602405 TATTAAATTAATAAAATTTTTATCTACAAGATAAATATTAAATTTAATTTAATATTAAGATAA
1 TATTAAATTAATAAAATACTTA-CTACAAGATAAATATTAAATTGAATTTAATATTAA-AT-C
** * ** *
28602468 TCACTTTAATATTAAATTAACAA-AAATACTATTAAGATAGGTATTAAATTAAATTTAATATTAA
1 T-A--TTAA-ATT-AA-TAA-AATACTTACTA-CAAGATAAATATTAAATTGAATTTAATATTAA
28602532 ATC
58 ATC
*
28602535 TATTAAAATAATA
1 TATTAAATTAATA
28602548 TTATTTTTGG
Statistics
Matches: 114, Mismatches: 16, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
58 19 0.17
60 1 0.01
61 31 0.27
62 4 0.04
63 3 0.03
64 5 0.04
66 5 0.04
67 4 0.04
68 7 0.06
69 33 0.29
70 2 0.02
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (60 bp):
TATTAAATTAATAAAATACTTACTACAAGATAAATATTAAATTGAATTTAATATTAAATC
Found at i:28617921 original size:21 final size:22
Alignment explanation
Indices: 28617897--28617952 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
28617887 AGCTAGAGAA
* *
28617897 TGAAATGAAATTAGATTG-AAT
1 TGAAATGAAATAAGAATGAAAT
28617918 TGAAATGAAATAAGAATGACAAT
1 TGAAATGAAATAAGAATGA-AAT
*
28617941 TGATATGAAATA
1 TGAAATGAAATA
28617953 GTACAGAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 16 0.53
23 14 0.47
ACGTcount: A:0.52, C:0.02, G:0.18, T:0.29
Consensus pattern (22 bp):
TGAAATGAAATAAGAATGAAAT
Found at i:28621256 original size:14 final size:14
Alignment explanation
Indices: 28621230--28621263 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
28621220 TGACAGAATC
28621230 AAGAAAGGAAGAGG
1 AAGAAAGGAAGAGG
28621244 AAAGAAA-GAAGAGG
1 -AAGAAAGGAAGAGG
28621258 AAGAAA
1 AAGAAA
28621264 AACATCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 7 0.37
15 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
AAGAAAGGAAGAGG
Found at i:28624774 original size:27 final size:27
Alignment explanation
Indices: 28624677--28624781 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
28624667 AGGAAGTGTC
*
28624677 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
28624704 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
28624731 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
28624758 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
28624782 GCAGCCTCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 9 0.13
27 61 0.86
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:28626412 original size:9 final size:9
Alignment explanation
Indices: 28626385--28626430 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
28626375 ACCTATAAAC
*
28626385 AAACATATT
1 AAACACATT
*
28626394 AAAACTCATT
1 -AAACACATT
28626404 AAACACATT
1 AAACACATT
28626413 AAACACATTT
1 AAACACA-TT
28626423 AAACACAT
1 AAACACAT
28626431 ATTATACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 16 0.50
10 16 0.50
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (9 bp):
AAACACATT
Found at i:28626545 original size:54 final size:54
Alignment explanation
Indices: 28626483--28626611 Score: 186
Period size: 54 Copynumber: 2.4 Consensus size: 54
28626473 CAACAATAAA
* * ** * ** *
28626483 TTATTCCAGTAACTAAATTAGGTAAGATGAACTTAATTAACTAAGGTGAGTAAT
1 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGACGAGGAAT
28626537 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGACGAGGAAT
1 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGACGAGGAAT
28626591 TTATTCCAGCAACTTAATTAA
1 TTATTCCAGCAACTTAATTAA
28626612 TTAAACTAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (54 bp):
TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGACGAGGAAT
Found at i:28627491 original size:16 final size:16
Alignment explanation
Indices: 28627470--28627501 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28627460 TTTCCAGAAT
28627470 CAATAACACAATTCAC
1 CAATAACACAATTCAC
28627486 CAATAACACAATTCAC
1 CAATAACACAATTCAC
28627502 AAGCTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (16 bp):
CAATAACACAATTCAC
Found at i:28635925 original size:23 final size:26
Alignment explanation
Indices: 28635874--28635931 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 26
28635864 TATTATAAAA
28635874 ATATTAT-TTAATTAAAACATTATAG
1 ATATTATATTAATTAAAACATTATAG
28635899 --ATTATATTAATT-AAA-ATTA-AG
1 ATATTATATTAATTAAAACATTATAG
28635920 ATATTATATTAA
1 ATATTATATTAA
28635932 AGGAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 2 0.07
22 4 0.13
23 18 0.60
24 6 0.20
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (26 bp):
ATATTATATTAATTAAAACATTATAG
Found at i:28636093 original size:18 final size:19
Alignment explanation
Indices: 28636059--28636094 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28636049 TATTATTTAT
28636059 TATAATTATTAAATTAAAA
1 TATAATTATTAAATTAAAA
*
28636078 TATATTTATT-AATTAAA
1 TATAATTATTAAATTAAA
28636095 TAACTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATAATTATTAAATTAAAA
Found at i:28636254 original size:27 final size:27
Alignment explanation
Indices: 28636211--28636269 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
28636201 TTTATACTTG
28636211 TTATTAAATAGATATTTATTATT-ATTA
1 TTATTAAATAGATATTTA-TATTAATTA
*
28636238 TTATTAAAT-TATAATTTATATTAATTA
1 TTATTAAATAGAT-ATTTATATTAATTA
28636265 -TATTA
1 TTATTA
28636270 TGAGATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TTATTAAATAGATATTTATATTAATTA
Found at i:28637309 original size:6 final size:6
Alignment explanation
Indices: 28637294--28637324 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
28637284 ATTGAGTTGT
28637294 AATT-A AATTGA AATTGA AATTGA AATTGA AA
1 AATTGA AATTGA AATTGA AATTGA AATTGA AA
28637325 AGTAATATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (6 bp):
AATTGA
Found at i:28643291 original size:15 final size:15
Alignment explanation
Indices: 28643271--28643324 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
28643261 ATACTACAAA
28643271 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
28643286 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
28643303 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
28643320 ATATT
1 ATATT
28643325 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:28644726 original size:3 final size:3
Alignment explanation
Indices: 28644718--28644748 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
28644708 TAATATCAGA
28644718 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28644749 TTCATACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Done.