Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold198
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: 257248
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:863 original size:28 final size:28
Alignment explanation
Indices: 800--922 Score: 185
Period size: 28 Copynumber: 4.4 Consensus size: 28
790 ATATTAAGTC
*
800 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
827 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
855 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
883 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
912 CGCACACTTAG
1 CGCACACTTAG
923 CGCCAATCTC
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.25
28 51 0.57
29 16 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:8124 original size:27 final size:26
Alignment explanation
Indices: 8107--8176 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
8097 ATATTAAGTC
8107 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
8134 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
8162 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
8177 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:8170 original size:28 final size:28
Alignment explanation
Indices: 8107--8201 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
8097 ATATTAAGTC
*
8107 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
8134 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
8162 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
8191 CGCACACTTAG
1 CGCACACTTAG
8202 CGCCAATCTC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.36
28 23 0.38
29 16 0.26
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:26839 original size:22 final size:23
Alignment explanation
Indices: 26814--26862 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
26804 ATCAGCTTCT
26814 TTAATAC-ACCTATTAAGACACA
1 TTAATACGACCTATTAAGACACA
* *
26836 TTAA-ACGACTTATTAGGACACA
1 TTAATACGACCTATTAAGACACA
26858 TTAAT
1 TTAAT
26863 CATACCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (23 bp):
TTAATACGACCTATTAAGACACA
Found at i:30258 original size:25 final size:25
Alignment explanation
Indices: 30230--30306 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
30220 TAATGGCCGA
30230 TGTGATGAATGTGAAAGTGTATATG
1 TGTGATGAATGTGAAAGTGTATATG
* *** ***
30255 TGTGAT-AAGGCCTAA-TGCCGA--
1 TGTGATGAATGTGAAAGTGTATATG
30276 TGTGATGAATGTGAAAGTGTATATG
1 TGTGATGAATGTGAAAGTGTATATG
30301 TGTGAT
1 TGTGAT
30307 AAGGCCTAAT
Statistics
Matches: 34, Mismatches: 14, Indels: 8
0.61 0.25 0.14
Matches are distributed among these distances:
21 6 0.18
22 5 0.15
23 6 0.18
24 5 0.15
25 12 0.35
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (25 bp):
TGTGATGAATGTGAAAGTGTATATG
Found at i:30340 original size:47 final size:47
Alignment explanation
Indices: 30213--30731 Score: 871
Period size: 47 Copynumber: 11.1 Consensus size: 47
30203 GAAATGATAG
* *
30213 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
30260 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
30306 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
30353 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
30400 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
30447 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
30494 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
30541 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
30588 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
30635 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * * *
30681 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
30728 TAAG
1 TAAG
30732 TCCCGAAGGG
Statistics
Matches: 453, Mismatches: 17, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
46 86 0.19
47 367 0.81
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:30906 original size:37 final size:37
Alignment explanation
Indices: 30850--30928 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
30840 CCGAGCTCTA
* * *
30850 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
30887 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
30924 AAGAC
1 AAGAC
30929 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:32833 original size:42 final size:42
Alignment explanation
Indices: 32772--32871 Score: 191
Period size: 42 Copynumber: 2.4 Consensus size: 42
32762 TTGGTTTTCA
32772 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGC-GGCAATAAGTGTTCACGGTTGTGAGATTG
32815 GCACTAAGTGTGCGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGCAATAAGTGTTCACGGTTGTGAGATTG
32857 GCACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
32872 GCTTGAAATG
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 44 0.77
43 13 0.23
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.27
Consensus pattern (42 bp):
GCACTAAGTGTGCGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:32890 original size:29 final size:29
Alignment explanation
Indices: 32855--32928 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
32845 GTTGTGAGAT
* *
32855 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
32884 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
32913 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
32929 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:33362 original size:40 final size:40
Alignment explanation
Indices: 33318--33474 Score: 233
Period size: 40 Copynumber: 3.9 Consensus size: 40
33308 GAGTTACTAA
*
33318 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
33358 ATCCGGGCTAAGTCCCGAAGAGCATTCATACTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * *
33398 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * *
33438 ATCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
33475 CGTGTATTCG
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 105 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:33376 original size:80 final size:80
Alignment explanation
Indices: 33239--33466 Score: 221
Period size: 80 Copynumber: 2.9 Consensus size: 80
33229 TCAAATGATG
** * * *
33239 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAG-GC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGCGA-TATATCCGGGCTAAG-TCCCGAAGAGC
** * *
33300 ATTGGTGCGAGTTACTAAA
63 ATTCATACGAGTGA-TAAA
*
33319 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATATATCCGGGCTAAGTCCCGAAGAGCATT
* **
33384 CATACTAGTGATGTA
66 CATACGAGTGATAAA
* * * * * *
33399 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAAATCCCGAAGAGCAAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATATATCCGGGCTAAGTCCCGAAGAGCATT
33464 CAT
66 CAT
33467 GCTGGTGACG
Statistics
Matches: 124, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
79 1 0.01
80 100 0.81
81 17 0.14
82 6 0.05
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATATATCCGGGCTAAGTCCCGAAGAGCATT
CATACGAGTGATAAA
Found at i:36925 original size:47 final size:47
Alignment explanation
Indices: 36862--37381 Score: 880
Period size: 47 Copynumber: 11.1 Consensus size: 47
36852 GAAATGATAG
* *
36862 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
36909 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
36956 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
37003 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
37050 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
37097 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
37144 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
37191 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
37238 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
37285 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * * *
37331 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
37378 TAAG
1 TAAG
37382 TCCCGAAGGG
Statistics
Matches: 454, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
46 40 0.09
47 414 0.91
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:37556 original size:37 final size:37
Alignment explanation
Indices: 37500--37578 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
37490 CCGAGCTCTA
* * *
37500 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
37537 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
37574 AAGAC
1 AAGAC
37579 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41184 original size:24 final size:24
Alignment explanation
Indices: 41153--41207 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
41143 CCGTATACAA
41153 TTTTTTTCTTTTCTTTTCGAATT-
1 TTTTTTTCTTTTCTTTTCGAATTC
* *
41176 TTCTTTTTCTTTTTTTTTTGAATTC
1 TT-TTTTTCTTTTCTTTTCGAATTC
41201 TTTTTTT
1 TTTTTTT
41208 ACAAAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 24 0.86
25 2 0.07
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTTTTTCTTTTCTTTTCGAATTC
Found at i:41989 original size:22 final size:23
Alignment explanation
Indices: 41964--42012 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
41954 ATCAGCTTCT
41964 TTAATAC-ACCTATTAAGACACA
1 TTAATACGACCTATTAAGACACA
* *
41986 TTAA-ACGACTTATTAGGACACA
1 TTAATACGACCTATTAAGACACA
42008 TTAAT
1 TTAAT
42013 CATACCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (23 bp):
TTAATACGACCTATTAAGACACA
Found at i:44001 original size:128 final size:127
Alignment explanation
Indices: 43731--44008 Score: 292
Period size: 128 Copynumber: 2.2 Consensus size: 127
43721 AATAGATCAG
* * * *
43731 TGAATATAGCAGATCTGGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
1 TGAA-ATAACAGATCTTGTCTCCCTAAGCAATAGCGGAACAGATCAAAGACGACGAATCTTATCT
* * * * *
43796 TCAAGTTTAAGGAAGCAAATTTAAGCCACAAGTCCTATGTCCCTGATCAGTAGTGGAGTAGGT
65 TCAAGTGTAAGGAAGCAAATTGAAGCCACAAGTCCTATCTCCCTAATCAGTAGTGGAGTAGAT
* * * *
43859 TGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAACAGATCGAAGACGATGAATCTTATCT
1 T-GAAATAACAGATCTTGTCTCCCTAAGCAATAGCGGAACAGATCAAAGACGACGAATCTTATCT
* * * * * *
43924 TCAAGTGTAAGGAAGTAGATTGAAGTCGATAA-TCCTATCTCCCTAAAGT-TGTAGTGGTGTAGA
65 TCAAGTGTAAGGAAGCAAATTGAAG-CCACAAGTCCTATCTCCCT-AA-TCAGTAGTGGAGTAGA
43987 T
127 T
* *
43988 T-AAAGTAATAGATCTTATCTC
1 TGAAA-TAACAGATCTTGTCTC
44009 TCTGATGTTG
Statistics
Matches: 123, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
127 3 0.02
128 98 0.80
129 21 0.17
130 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (127 bp):
TGAAATAACAGATCTTGTCTCCCTAAGCAATAGCGGAACAGATCAAAGACGACGAATCTTATCTT
CAAGTGTAAGGAAGCAAATTGAAGCCACAAGTCCTATCTCCCTAATCAGTAGTGGAGTAGAT
Found at i:44187 original size:44 final size:44
Alignment explanation
Indices: 44041--44378 Score: 190
Period size: 44 Copynumber: 7.7 Consensus size: 44
44031 TCGCATTAGG
* * * * **
44041 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTG-AGTAAGCA-GG
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGT-CG-ATAA
* * * * * *
44085 TCTTATCCCCCTAAAGTTGCAGTGGGGCAGATCGAAGAT-GACAAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAG-TCGA-TAA
* *
44130 TCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGCCGATAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGTCGATAA
* ** * * *
44174 TCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGT-AATAAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGTCGAT-AA
* * ** * * **
44218 TCTTATCTCTCC-GAAATTACAGTAGAGTGGATCGCA-TC-A-GG
1 TCTTATCTC-CCTGAAGTTACAGTGGAGCAGATTGAAGTCGATAA
* *
44259 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGATAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGTCGATAA
* * ** * * *
44303 TCCTATCTCCCTGAGGTTGTAGTGGAGCGGATTAAAGT-AATAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGTCGATA-A
* * *
44347 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGAT
44379 CGCATCAAGT
Statistics
Matches: 225, Mismatches: 56, Indels: 26
0.73 0.18 0.08
Matches are distributed among these distances:
40 2 0.01
41 25 0.11
42 2 0.01
43 9 0.04
44 149 0.66
45 37 0.16
46 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGTCGATAA
Found at i:44301 original size:129 final size:129
Alignment explanation
Indices: 44130--44391 Score: 416
Period size: 129 Copynumber: 2.0 Consensus size: 129
44120 AGATGACAAA
*
44130 TCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTA
** *
44195 GTGGAGCGGATTAAAGTAATAAATCTTATCTCTCCGAAATTACAGTAGAGTGGATCGCATCAGG
66 GTGGAGCGGATTAAAGTAATAAATCTTATCTCTCCGAAATTACAGTAGAGCAGATCGCATCAAG
* * * *
44259 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGATAATCCTATCTCCCTGAGGTTGTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTA
* * * *
44324 GTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAG
66 GTGGAGCGGATTAAAGTAATAAATCTTATCTCTCCGAAATTACAGTAGAGCAGATCGCATCAAG
44388 TCTT
1 TCTT
44392 GCCGACTAGA
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 121 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTA
GTGGAGCGGATTAAAGTAATAAATCTTATCTCTCCGAAATTACAGTAGAGCAGATCGCATCAAG
Found at i:46558 original size:24 final size:25
Alignment explanation
Indices: 46530--46583 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
46520 ACATATATCA
*
46530 ATTTTAAAATTTATTTACAA-ATTTT
1 ATTTTAAAATTTACTTA-AACATTTT
*
46555 -TTTTAGAATTTACTTAAACATTTT
1 ATTTTAAAATTTACTTAAACATTTT
46579 ATTTT
1 ATTTT
46584 TAGTTCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 2 0.08
24 19 0.76
25 4 0.16
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTAAAATTTACTTAAACATTTT
Found at i:48443 original size:21 final size:21
Alignment explanation
Indices: 48417--48479 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
48407 TTGGTATTTG
48417 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
48438 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
48459 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
48480 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:51113 original size:12 final size:11
Alignment explanation
Indices: 51072--51112 Score: 73
Period size: 11 Copynumber: 3.6 Consensus size: 11
51062 GTAGTTTCTC
51072 AAAAAAATTCGA
1 AAAAAAATTC-A
51084 AAAAAAATTCA
1 AAAAAAATTCA
51095 AAAAAAATTCA
1 AAAAAAATTCA
51106 AAAAAAA
1 AAAAAAA
51113 AAATTGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:51177 original size:15 final size:14
Alignment explanation
Indices: 51157--51193 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
51147 ATCAAGTTGA
51157 AAAAAAAATTTCGTG
1 AAAAAAAA-TTCGTG
51172 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
51186 AAAAAAAA
1 AAAAAAAA
51194 AAAGAGCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.65, C:0.05, G:0.11, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTCGTG
Found at i:51194 original size:15 final size:16
Alignment explanation
Indices: 51154--51194 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
51144 GATATCAAGT
51154 TGAAAAAAAAATTTCG
1 TGAAAAAAAAATTTCG
51170 TG-AAAAAAAA-TTCG
1 TGAAAAAAAAATTTCG
51184 TGAAAAAAAAA
1 TGAAAAAAAAA
51195 AAGAGCTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.25
15 16 0.67
16 2 0.08
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.20
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:51195 original size:16 final size:16
Alignment explanation
Indices: 51154--51195 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 16
51144 GATATCAAGT
*
51154 TGAAAAAAAAATTTCG
1 TGAAAAAAAAAATTCG
51170 TG--AAAAAAAATTCG
1 TGAAAAAAAAAATTCG
51184 TGAAAAAAAAAA
1 TGAAAAAAAAAA
51196 AGAGCTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 13 0.57
16 10 0.43
ACGTcount: A:0.64, C:0.05, G:0.12, T:0.19
Consensus pattern (16 bp):
TGAAAAAAAAAATTCG
Found at i:54635 original size:19 final size:19
Alignment explanation
Indices: 54613--54650 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
54603 AACTAGCCAA
54613 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
54632 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
54651 TTCTAAGCCA
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:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
GGACAACTCAAGAGTCATT
Found at i:57446 original size:7 final size:6
Alignment explanation
Indices: 57399--57446 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
57389 AAGAGACTGT
* *
57399 AGAAAA AGAAAA AGAACA AGAAAA A-AAGAG AGAAAA AGAAAA ACGAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAA-AA AGAAAA AGAAAA A-GAAA
57447 GATAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 2 0.06
6 27 0.77
7 6 0.17
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:61578 original size:61 final size:61
Alignment explanation
Indices: 61507--61629 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 61
61497 TTAGCAACTT
* * * * * *
61507 ACTTAATTTCACGATCGGGCAATCTAAACGACTCGAATTAACACTAAACTAAGTTCGTATC
1 ACTTAATTTCACGATCAGGCAATCTAAACAACTCAAATAAACACCAAACCAAGTTCGTATC
*
61568 ACTTAATTTCACGATCAGGCAATCTAAACAACTCAAATAAACACCAAACCGAGTTCGTATC
1 ACTTAATTTCACGATCAGGCAATCTAAACAACTCAAATAAACACCAAACCAAGTTCGTATC
61629 A
1 A
61630 TAGCATTTCC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.25
Consensus pattern (61 bp):
ACTTAATTTCACGATCAGGCAATCTAAACAACTCAAATAAACACCAAACCAAGTTCGTATC
Found at i:68916 original size:24 final size:26
Alignment explanation
Indices: 68861--68930 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
68851 AATGAAAAGA
*
68861 AGGATTGAAATTGGCTAAGTGAAATG
1 AGGATGGAAATTGGCTAAGTGAAATG
* *
68887 ATGATGGAAA-TGGCTAGGTG-AATG
1 AGGATGGAAATTGGCTAAGTGAAATG
*
68911 AGGATGGAGATTTGGCTAAG
1 AGGATGGA-AATTGGCTAAG
68931 GTTTTGAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 11 0.31
25 10 0.28
26 15 0.42
ACGTcount: A:0.34, C:0.04, G:0.36, T:0.26
Consensus pattern (26 bp):
AGGATGGAAATTGGCTAAGTGAAATG
Found at i:69410 original size:22 final size:22
Alignment explanation
Indices: 69385--69436 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
69375 TTCTTGTCAA
69385 CTTCCTAGAACGTCCCTTGAAG
1 CTTCCTAGAACGTCCCTTGAAG
* * *
69407 CTTCCTTGAAGGTTCCTTGAAG
1 CTTCCTAGAACGTCCCTTGAAG
69429 CTTCCTAG
1 CTTCCTAG
69437 CATGGGAGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (22 bp):
CTTCCTAGAACGTCCCTTGAAG
Found at i:69415 original size:11 final size:11
Alignment explanation
Indices: 69399--69434 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
69389 CTAGAACGTC
69399 CCTTGAAGCTT
1 CCTTGAAGCTT
*
69410 CCTTGAAGGTT
1 CCTTGAAGCTT
69421 CCTTGAAGCTT
1 CCTTGAAGCTT
69432 CCT
1 CCT
69435 AGCATGGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (11 bp):
CCTTGAAGCTT
Found at i:70167 original size:20 final size:21
Alignment explanation
Indices: 70139--70177 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
70129 CAGAATGAGC
*
70139 AAACGAGCTCA-TTGAGCTGG
1 AAACAAGCTCATTTGAGCTGG
*
70159 AAACAAGCTGATTTGAGCT
1 AAACAAGCTCATTTGAGCT
70178 CAATGAGCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (21 bp):
AAACAAGCTCATTTGAGCTGG
Found at i:71017 original size:27 final size:27
Alignment explanation
Indices: 70981--71057 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
70971 GTGTTTTAAT
*
70981 TTAATGCATGTTTTTAATATGTCCTAG
1 TTAATACATGTTTTTAATATGTCCTAG
* * * *
71008 TTAATACATGTTATTAATTTTTCTTAG
1 TTAATACATGTTTTTAATATGTCCTAG
* **
71035 TCTATTACATAATTTTAATATGT
1 T-TAATACATGTTTTTAATATGT
71058 TTTAGCTCCA
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (27 bp):
TTAATACATGTTTTTAATATGTCCTAG
Found at i:74365 original size:43 final size:42
Alignment explanation
Indices: 74296--74381 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
74286 AAGGCACCTA
** * *
74296 GAAAAGAGAAATCAGTACCTCTTTTAATGCCATCCCTTGCAT
1 GAAAAGAGAAATCAACACCTCATTTAATGCCATCCCATGCAT
*
74338 GAAAAGGAGAAATCAACAGCTCATTTAATGCCATCCCATGCAT
1 GAAAA-GAGAAATCAACACCTCATTTAATGCCATCCCATGCAT
74381 G
1 G
74382 CTTTCTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 5 0.13
43 33 0.87
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.24
Consensus pattern (42 bp):
GAAAAGAGAAATCAACACCTCATTTAATGCCATCCCATGCAT
Found at i:75589 original size:19 final size:18
Alignment explanation
Indices: 75567--75614 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
75557 GTTTAAAACA
*
75567 AAAGAAAATTGAGAAAAAG
1 AAAGAAAATT-AAAAAAAG
*
75586 AAAGGAAAAATAAAAAAAG
1 AAA-GAAAATTAAAAAAAG
75605 AAAGTAAAAT
1 AAAG-AAAAT
75615 AATTGTGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 17 0.71
20 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (18 bp):
AAAGAAAATTAAAAAAAG
Found at i:81056 original size:42 final size:42
Alignment explanation
Indices: 81003--81085 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
80993 AATATGTGTG
*
81003 AAATATTTGAAATTCAAATATTTGAACTCTTGTTCTTATCCA
1 AAATATTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
* **
81045 AAATGTTTGAAATTTGAACATTTGAACTCTTGTTCTTATCC
1 AAATATTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
81086 CGTTGAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (42 bp):
AAATATTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
Found at i:82271 original size:27 final size:27
Alignment explanation
Indices: 82236--82291 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
82226 AAAAATTGTT
*
82236 AAAACTTCTTCTAAAGAAAACTCAAGAG
1 AAAACTTCTTCGAAA-AAAACTCAAGAG
*
82264 AAAA-TTCTTGGAAAAAAACTCAAGAG
1 AAAACTTCTTCGAAAAAAACTCAAGAG
82290 AA
1 AA
82292 TTTGCAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 14 0.54
27 8 0.31
28 4 0.15
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.20
Consensus pattern (27 bp):
AAAACTTCTTCGAAAAAAACTCAAGAG
Found at i:85846 original size:22 final size:22
Alignment explanation
Indices: 85818--85861 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
85808 TTTTGAACCA
85818 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
* *
85840 TTACCATTTCTTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
85862 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.36, G:0.02, T:0.36
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:90610 original size:12 final size:12
Alignment explanation
Indices: 90593--90617 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90583 AAAATCTAAT
90593 TTCAATGTGTAA
1 TTCAATGTGTAA
90605 TTCAATGTGTAA
1 TTCAATGTGTAA
90617 T
1 T
90618 GTGTATAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:94065 original size:23 final size:22
Alignment explanation
Indices: 94013--94065 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
94003 TCCACGTCTT
*
94013 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
94035 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
94058 TTTCTTTT
1 TTTCTTTT
94066 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:96421 original size:4 final size:4
Alignment explanation
Indices: 96412--96443 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
96402 TTAAACTAAG
96412 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
96444 ACTTTACAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:97065 original size:10 final size:11
Alignment explanation
Indices: 97039--97081 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
97029 AGTAGTTTCT
**
97039 TCAAAAAAATT
1 TCAAAAAAAAA
97050 TC-AAAAAAAA
1 TCAAAAAAAAA
97060 T-AAAAAAAAA
1 TCAAAAAAAAA
97070 TCAAAAAAAAA
1 TCAAAAAAAAA
97081 T
1 T
97082 TTGGTTTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 16 0.57
11 12 0.43
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (11 bp):
TCAAAAAAAAA
Found at i:97066 original size:11 final size:10
Alignment explanation
Indices: 97052--97081 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
97042 AAAAAATTTC
97052 AAAAAAAATA
1 AAAAAAAATA
97062 AAAAAAAATCA
1 AAAAAAAAT-A
97073 AAAAAAAAT
1 AAAAAAAAT
97082 TTGGTTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:97141 original size:14 final size:15
Alignment explanation
Indices: 97120--97159 Score: 73
Period size: 14 Copynumber: 2.7 Consensus size: 15
97110 GATATCAAGT
97120 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
97135 T-AAAAAAAAATTCG
1 TGAAAAAAAAATTCG
97149 TGAAAAAAAAA
1 TGAAAAAAAAA
97160 ATTTTTCGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:97158 original size:19 final size:19
Alignment explanation
Indices: 97136--97177 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
97126 AAAAATTCGT
97136 AAAAAAAAATTCGTGAAAA
1 AAAAAAAAATTCGTGAAAA
***
97155 AAAAAATTTTTCGTGAAAA
1 AAAAAAAAATTCGTGAAAA
97174 AAAA
1 AAAA
97178 GAAGAAGCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (19 bp):
AAAAAAAAATTCGTGAAAA
Found at i:97160 original size:16 final size:16
Alignment explanation
Indices: 97122--97177 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 16
97112 TATCAAGTTG
97122 AAAAAAAAATTCGT--
1 AAAAAAAAATTCGTGA
97136 AAAAAAAAATTCGTGA
1 AAAAAAAAATTCGTGA
97152 AAAAAAAAATTTTTCGTGA
1 AAAAAAAAA---TTCGTGA
97171 AAAAAAA
1 AAAAAAA
97178 GAAGAAGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.38
16 9 0.24
19 14 0.38
ACGTcount: A:0.64, C:0.05, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAAAAAAATTCGTGA
Found at i:98809 original size:17 final size:18
Alignment explanation
Indices: 98770--98811 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
98760 AAGAAGAAAA
98770 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
98787 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
98804 TCAAAAGA
1 ACAAAAGA
98812 AAAAGAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:104324 original size:18 final size:17
Alignment explanation
Indices: 104301--104339 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
104291 CTCTTTTTGC
104301 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
104319 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
104337 TCT
1 TCT
104340 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:121443 original size:11 final size:10
Alignment explanation
Indices: 121418--121478 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
121408 ACCAATAAAA
121418 TAAA-TGAGC
1 TAAATTGAGC
*
121427 TGAATTGTAGC
1 TAAATTG-AGC
121438 TAAATTGAGC
1 TAAATTGAGC
**
121448 TCGATTGAGC
1 TAAATTGAGC
121458 TGAAA-TGAGC
1 T-AAATTGAGC
*
121468 TCAATTGAGC
1 TAAATTGAGC
121478 T
1 T
121479 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:121479 original size:20 final size:20
Alignment explanation
Indices: 121419--121479 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
121409 CCAATAAAAT
*
121419 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
121439 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
121460 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
121480 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:123563 original size:18 final size:18
Alignment explanation
Indices: 123542--123576 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
123532 TTTTTCTTTT
123542 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
123560 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
123577 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:123573 original size:6 final size:6
Alignment explanation
Indices: 123564--123668 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
123554 TCAATCTCAA
* * * ** **
123564 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
123616 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
123662 TTTCTT T
1 TTTCTT T
123669 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:123635 original size:18 final size:18
Alignment explanation
Indices: 123614--123698 Score: 77
Period size: 18 Copynumber: 4.8 Consensus size: 18
123604 CACTATTTTG
*
123614 ATTTCTTTTTCTTTTGCA
1 ATTTCTTTTTCTTTTTCA
*
123632 ATTTCTTTTTCTTTTTCG
1 ATTTCTTTTTCTTTTTCA
* *
123650 TTTTCTTTTT-GTTTTC-
1 ATTTCTTTTTCTTTTTCA
**
123666 -TTTCAATTTCTTTTTCA
1 ATTTCTTTTTCTTTTTCA
*
123683 ATCTCTTTCTTCTTTT
1 ATTTCTTT-TTCTTTT
123699 CTCACTCAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
15 7 0.13
16 5 0.09
17 5 0.09
18 29 0.55
19 7 0.13
ACGTcount: A:0.08, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
ATTTCTTTTTCTTTTTCA
Found at i:123681 original size:6 final size:6
Alignment explanation
Indices: 123615--123668 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
123605 ACTATTTTGA
* ** * *
123615 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
123662 TTTCTT T
1 TTTCTT T
123669 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:123884 original size:20 final size:20
Alignment explanation
Indices: 123861--123914 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
123851 AGTTTTTCCC
*
123861 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* **
123881 AGCTTAATTTAGCTCATTTG
1 AGCTCAATTTAGCTCACATG
123901 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
123915 TACTTTAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:123905 original size:30 final size:30
Alignment explanation
Indices: 123861--123934 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
123851 AGTTTTTCCC
123861 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTC-ATTTGAGCTCA-ATTGAGCTTAATTT
* *
123891 AGCTCATTTGAGCTCAATTTAGCTTACTTT
1 AGCTCATTTGAGCTCAATTGAGCTTAATTT
*
123921 AGCTCGTTTGAGCT
1 AGCTCATTTGAGCT
123935 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 5 0.13
30 34 0.87
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (30 bp):
AGCTCATTTGAGCTCAATTGAGCTTAATTT
Found at i:123924 original size:20 final size:20
Alignment explanation
Indices: 123861--123925 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
123851 AGTTTTTCCC
* * *
123861 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACTTT
*
123881 AGCTTAATTTAGCTCA-TTT
1 AGCTCAATTTAGCTCACTTT
*
123900 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTCACTTT
123921 AGCTC
1 AGCTC
123926 GTTTGAGCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.89
21 3 0.08
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACTTT
Found at i:127792 original size:11 final size:10
Alignment explanation
Indices: 127767--127827 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
127757 ACCAATAAAA
127767 TAAA-TGAGC
1 TAAATTGAGC
*
127776 TGAATTGTAGC
1 TAAATTG-AGC
127787 TAAATTGAGC
1 TAAATTGAGC
**
127797 TTGATTGAGC
1 TAAATTGAGC
127807 TGAAA-TGAGC
1 T-AAATTGAGC
*
127817 TCAATTGAGC
1 TAAATTGAGC
127827 T
1 T
127828 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:127828 original size:20 final size:20
Alignment explanation
Indices: 127768--127828 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
127758 CCAATAAAAT
*
127768 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
**
127788 AAATTGAGCTTGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
127809 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
127829 GTCGGAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:129992 original size:18 final size:19
Alignment explanation
Indices: 129971--130007 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
129961 AAAGGAAGAC
129971 AGAAAAAGA-AATCAAAAA
1 AGAAAAAGAGAATCAAAAA
*
129989 AGAAAAAGAGAATGAAAAA
1 AGAAAAAGAGAATCAAAAA
130008 GAGTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (19 bp):
AGAAAAAGAGAATCAAAAA
Found at i:133483 original size:12 final size:12
Alignment explanation
Indices: 133463--133498 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
133453 TAGTAGTTTC
*
133463 TTCAAAAAAAAT
1 TTCAAAAAAAAA
*
133475 TTGAAAAAAAAA
1 TTCAAAAAAAAA
133487 TTCAAAAAAAAA
1 TTCAAAAAAAAA
133499 ATTTGGTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:133484 original size:13 final size:13
Alignment explanation
Indices: 133466--133503 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
133456 TAGTTTCTTC
133466 AAAAAAAATTTGA
1 AAAAAAAATTTGA
**
133479 AAAAAAAATTCAA
1 AAAAAAAATTTGA
133492 AAAAAAAATTTG
1 AAAAAAAATTTG
133504 GTTTCCATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:133559 original size:15 final size:15
Alignment explanation
Indices: 133539--133577 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
133529 GATATCAAGT
133539 TGAAAAAAAAATTCA-
1 TGAAAAAAAAATT-AG
*
133554 TGAAAAATAAATTAG
1 TGAAAAAAAAATTAG
133569 TGAAAAAAA
1 TGAAAAAAA
133578 GAAGAAGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.67, C:0.03, G:0.10, T:0.21
Consensus pattern (15 bp):
TGAAAAAAAAATTAG
Found at i:138922 original size:48 final size:48
Alignment explanation
Indices: 138867--138972 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
138857 TTGTCTTTTC
*
138867 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
138915 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
138963 TTTCTTTTTC
1 TTTCTTTTTC
138973 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:138969 original size:18 final size:17
Alignment explanation
Indices: 138948--139032 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
138938 TTTTCACATC
138948 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTC-ATTT
* *
138966 CTTTTTCCATGACACTCGTTT
1 CTTTTT-CA--A-TCTCATTT
* *
138987 CTTTTACACTCTCATTT
1 CTTTTTCAATCTCATTT
*
139004 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCA-TTT
139023 CTTTTTCAAT
1 CTTTTTCAAT
139033 TTCTTGTTCC
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
17 10 0.19
18 20 0.38
19 8 0.15
20 2 0.04
21 9 0.17
22 3 0.06
ACGTcount: A:0.18, C:0.28, G:0.02, T:0.52
Consensus pattern (17 bp):
CTTTTTCAATCTCATTT
Found at i:141032 original size:4 final size:4
Alignment explanation
Indices: 141023--141050 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
141013 TTAAACTAAG
141023 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
141051 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:142880 original size:21 final size:21
Alignment explanation
Indices: 142854--142916 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
142844 TTGGTATTTG
142854 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
142875 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
142896 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
142917 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:147662 original size:21 final size:21
Alignment explanation
Indices: 147636--147697 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
147626 TGGTATTTGG
147636 GAATTGGTACGAAATGGTATA
1 GAATTGGTACGAAATGGTATA
* *
147657 GAATTGGTATGAAATGGTATG
1 GAATTGGTACGAAATGGTATA
* *
147678 GTATTTGGTACGAATTGGTA
1 G-AATTGGTACGAAATGGTA
147698 ATGGTTCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (21 bp):
GAATTGGTACGAAATGGTATA
Found at i:151370 original size:21 final size:23
Alignment explanation
Indices: 151325--151371 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
151315 TCACCTGCAA
* *
151325 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
151348 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
151369 TAA
1 TAA
151372 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:156727 original size:18 final size:16
Alignment explanation
Indices: 156704--156746 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
156694 TAGCTTCTTC
156704 TTTTTTTCACGAAAATTT
1 TTTTTTTCACG--AATTT
156722 TTTTTTTCACGAATTT
1 TTTTTTTCACGAATTT
156738 TTTTTTTCA
1 TTTTTTTCA
156747 ACTTGATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 14 0.56
18 11 0.44
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.63
Consensus pattern (16 bp):
TTTTTTTCACGAATTT
Found at i:156805 original size:11 final size:11
Alignment explanation
Indices: 156789--156844 Score: 62
Period size: 11 Copynumber: 5.0 Consensus size: 11
156779 AACCAAATTT
156789 TTTTTTTTGAA
1 TTTTTTTTGAA
156800 TTTTTTTTTTTG-A
1 ---TTTTTTTTGAA
*
156813 -TTTTTTTGAT
1 TTTTTTTTGAA
156823 TTTTTTTTGAA
1 TTTTTTTTGAA
156834 TTTTTTTTGAA
1 TTTTTTTTGAA
156845 GAAACTACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 8 0.21
11 20 0.53
13 1 0.03
14 9 0.24
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:156825 original size:20 final size:21
Alignment explanation
Indices: 156802--156840 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
156792 TTTTTGAATT
156802 TTTTTTTTTG-ATTTTTTTGA
1 TTTTTTTTTGAATTTTTTTGA
156822 TTTTTTTTTGAATTTTTTT
1 TTTTTTTTTGAATTTTTTT
156841 TGAAGAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (21 bp):
TTTTTTTTTGAATTTTTTTGA
Found at i:156839 original size:9 final size:9
Alignment explanation
Indices: 156804--156828 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
156794 TTTGAATTTT
156804 TTTTTTTGA
1 TTTTTTTGA
156813 TTTTTTTGA
1 TTTTTTTGA
156822 TTTTTTT
1 TTTTTTT
156829 TTGAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:156841 original size:14 final size:14
Alignment explanation
Indices: 156784--156819 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
156774 ATGGAAACCA
156784 AATTTTTTTTTTTG
1 AATTTTTTTTTTTG
156798 AATTTTTTTTTTTG
1 AATTTTTTTTTTTG
156812 -ATTTTTTT
1 AATTTTTTT
156820 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (14 bp):
AATTTTTTTTTTTG
Found at i:157880 original size:21 final size:23
Alignment explanation
Indices: 157835--157881 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
157825 TCACGTGCAA
* *
157835 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
157858 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
157879 TAA
1 TAA
157882 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:160369 original size:33 final size:34
Alignment explanation
Indices: 160332--160403 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
160322 GAGTTAGTTC
*
160332 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGCTAGTA
* *
160365 ATTAATTTTAGTTCAGCTTAAATAAGTGCTAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGCTAGTA
160399 ATTAA
1 ATTAA
160404 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGCTAGTA
Found at i:160799 original size:20 final size:20
Alignment explanation
Indices: 160776--160829 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
160766 AGTTTTTCCC
*
160776 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
160796 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
160816 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
160830 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:160811 original size:30 final size:30
Alignment explanation
Indices: 160776--160849 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
160766 AGTTTTTCCC
160776 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
160806 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
160836 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
160850 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:160839 original size:20 final size:20
Alignment explanation
Indices: 160776--160840 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
160766 AGTTTTTCCC
* * * *
160776 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
160796 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
160815 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
160836 AGCTC
1 AGCTC
160841 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:162468 original size:10 final size:10
Alignment explanation
Indices: 162453--162485 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
162443 AAAAGAGAAG
162453 AAATTCAAAA
1 AAATTCAAAA
162463 AAATTCAAAA
1 AAATTCAAAA
*
162473 AAATTGAAAA
1 AAATTCAAAA
162483 AAA
1 AAA
162486 AGGAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:163574 original size:6 final size:6
Alignment explanation
Indices: 163556--163662 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
163546 AAATAAATTG
* * ** *
163556 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
163603 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTG-A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
163653 AAAGAA AAAG
1 AAAGAA AAAG
163663 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 9
0.69 0.23 0.08
Matches are distributed among these distances:
5 4 0.05
6 62 0.85
7 3 0.04
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:163586 original size:18 final size:18
Alignment explanation
Indices: 163560--163618 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
163550 AAATTGAAAG
* *
163560 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* *
163578 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
163596 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
163614 AAAAG
1 AAAAG
163619 TGAGAGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:163714 original size:33 final size:33
Alignment explanation
Indices: 163677--163739 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
163667 AAAAGAAATT
163677 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
163710 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
163740 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:168891 original size:11 final size:10
Alignment explanation
Indices: 168877--168906 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
168867 AAAAAACTCG
168877 AAAAAAAATT
1 AAAAAAAATT
168887 AAAAAAAATT
1 AAAAAAAATT
168897 AAAAAAAATT
1 AAAAAAAATT
168907 TTGGTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:168968 original size:14 final size:14
Alignment explanation
Indices: 168944--168996 Score: 90
Period size: 14 Copynumber: 3.9 Consensus size: 14
168934 GGATATCAAG
168944 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
*
168957 TTTTGAAAAAAAAA
1 TTGTGAAAAAAAAA
168971 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
168985 TTGTGAAAAAAA
1 TTGTGAAAAAAA
168997 GAGAGAGCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
13 4 0.11
14 33 0.89
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:173096 original size:11 final size:12
Alignment explanation
Indices: 173075--173120 Score: 60
Period size: 11 Copynumber: 4.0 Consensus size: 12
173065 ATAGTAGTTT
173075 CTCGAAAAAAAA
1 CTCGAAAAAAAA
173087 CTCGAAAAAAAA
1 CTCGAAAAAAAA
*
173099 TTC-AAAAAAAA
1 CTCGAAAAAAAA
*
173110 ATC-AAAAAAAA
1 CTCGAAAAAAAA
173121 AAAAATTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 18 0.56
12 14 0.44
ACGTcount: A:0.72, C:0.13, G:0.04, T:0.11
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:173189 original size:14 final size:14
Alignment explanation
Indices: 173164--173217 Score: 90
Period size: 14 Copynumber: 3.8 Consensus size: 14
173154 GGATATCAAG
173164 TTGTGAAAAAAAAAA
1 TTGTG-AAAAAAAAA
*
173179 TTTTGAAAAAAAAA
1 TTGTGAAAAAAAAA
173193 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
173207 TTGTGAAAAAA
1 TTGTGAAAAAA
173218 GAGAGAGCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
14 33 0.89
15 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:177753 original size:12 final size:12
Alignment explanation
Indices: 177683--177754 Score: 63
Period size: 12 Copynumber: 5.7 Consensus size: 12
177673 GACGAGAAGA
*
177683 GAAAAATGAAAGT
1 GAAAAA-GAAATT
*
177696 GAAAAAGAGATT
1 GAAAAAGAAATT
177708 GAAAAAGAAATT
1 GAAAAAGAAATT
**
177720 GCAAAAGAAGAAAAA
1 G--AAA-AAGAAATT
*
177735 GAGAAAGAAATT
1 GAAAAAGAAATT
177747 GAAAAAGA
1 GAAAAAGA
177755 GAGTGAGATT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
12 29 0.62
13 8 0.17
14 3 0.06
15 7 0.15
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.11
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:182656 original size:30 final size:30
Alignment explanation
Indices: 182620--182716 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
182610 AGCTCACTCC
182620 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
182650 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
182680 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
182710 TAGCTCA
1 TAGCTCA
182717 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:189294 original size:23 final size:22
Alignment explanation
Indices: 189242--189294 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
189232 TCCACGTCTT
*
189242 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
189264 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
189287 TTTCTTTT
1 TTTCTTTT
189295 TCATCTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:193248 original size:21 final size:23
Alignment explanation
Indices: 193203--193249 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
193193 TCACCTGCAA
* *
193203 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
193226 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
193247 TAA
1 TAA
193250 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:197768 original size:18 final size:18
Alignment explanation
Indices: 197722--197768 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
197712 AAAGAGAGAC
197722 GAGAGAAGAAATCGAAAAA
1 GAGAGAA-AAATCGAAAAA
* *
197741 GAAACG-AAAATTGAAAAA
1 GAGA-GAAAAATCGAAAAA
197759 GAGAGAAAAA
1 GAGAGAAAAA
197769 GATTGGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
17 1 0.04
18 17 0.74
19 4 0.17
20 1 0.04
ACGTcount: A:0.66, C:0.04, G:0.23, T:0.06
Consensus pattern (18 bp):
GAGAGAAAAATCGAAAAA
Found at i:206148 original size:30 final size:30
Alignment explanation
Indices: 206112--206209 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
206102 AAGCCACTCC
206112 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
206142 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
206172 CAGCTCAACTTTAGCTCACGAGCTAAAACTT
1 TAGCTCAACTTTAGCTCACGAGCT-AAACCT
206203 TAGCTCA
1 TAGCTCA
206210 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
29 1 0.02
30 41 0.80
31 9 0.18
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:218238 original size:9 final size:10
Alignment explanation
Indices: 218202--218244 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
218192 TAGTTAGTTC
*
218202 TTCAAAAAAT
1 TTCAAAAAAA
218212 TTCAAAAAAAA
1 TTC-AAAAAAA
218223 TTCAAAAAAA
1 TTCAAAAAAA
**
218233 TGAAAAAAAA
1 TTCAAAAAAA
218243 TT
1 TT
218245 TGGTTTCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (10 bp):
TTCAAAAAAA
Found at i:218302 original size:15 final size:15
Alignment explanation
Indices: 218282--218334 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
218272 GATATCAAGT
218282 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
218297 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
*
218312 TG-AAAAAAATTTCG
1 TGAAAAAAAAATTCG
218326 TGAAAAAAA
1 TGAAAAAAA
218335 GAAGAAGAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 13 0.36
15 23 0.64
ACGTcount: A:0.60, C:0.06, G:0.13, T:0.21
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:218304 original size:14 final size:14
Alignment explanation
Indices: 218285--218334 Score: 82
Period size: 14 Copynumber: 3.5 Consensus size: 14
218275 ATCAAGTTGA
218285 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
218299 AAAAAAAAATTCGTG
1 -AAAAAAAATTCGTG
*
218314 AAAAAAATTTCGTG
1 AAAAAAAATTCGTG
218328 AAAAAAA
1 AAAAAAA
218335 GAAGAAGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 20 0.59
15 14 0.41
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.20
Consensus pattern (14 bp):
AAAAAAAATTCGTG
Found at i:222618 original size:17 final size:18
Alignment explanation
Indices: 222596--222632 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
222586 TGGAATAAAC
222596 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
222613 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
222631 TT
1 TT
222633 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:223584 original size:4 final size:4
Alignment explanation
Indices: 223575--223605 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
223565 TTTAATGATT
223575 TTTA TTTA TTTA TTT- TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
223606 CTTAGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:223593 original size:15 final size:15
Alignment explanation
Indices: 223573--223604 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
223563 AGTTTAATGA
223573 TTTTTATTTATTTAT
1 TTTTTATTTATTTAT
223588 TTTTTATTTATTTAT
1 TTTTTATTTATTTAT
223603 TT
1 TT
223605 ACTTAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTATTTATTTAT
Found at i:224408 original size:12 final size:12
Alignment explanation
Indices: 224391--224425 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
224381 AGGAAATTTG
224391 AAAAAAAAATTC
1 AAAAAAAAATTC
224403 AAAAAAAAATTC
1 AAAAAAAAATTC
224415 AAAAAAAAATT
1 AAAAAAAAATT
224426 TTTTGAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:229288 original size:11 final size:11
Alignment explanation
Indices: 229268--229304 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
229258 TTTTATATAC
*
229268 TTTGATTTTTT
1 TTTGAATTTTT
229279 TTTGAATTTTTT
1 TTTGAA-TTTTT
229291 TTTGAATTTTT
1 TTTGAATTTTT
229302 TTT
1 TTT
229305 TCAAATTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (11 bp):
TTTGAATTTTT
Found at i:229312 original size:13 final size:12
Alignment explanation
Indices: 229268--229305 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
229258 TTTTATATAC
229268 TTTG-ATTTTTT
1 TTTGAATTTTTT
229279 TTTGAATTTTTT
1 TTTGAATTTTTT
229291 TTTGAATTTTTT
1 TTTGAATTTTTT
229303 TTT
1 TTT
229306 CAAATTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (12 bp):
TTTGAATTTTTT
Found at i:231318 original size:18 final size:18
Alignment explanation
Indices: 231262--231321 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
231252 AGTGCGAGCG
231262 AGAAAAAGAAATCAAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
231283 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
231301 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
231319 AGA
1 AGA
231322 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:233147 original size:17 final size:18
Alignment explanation
Indices: 233125--233161 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
233115 TGGAATAAAC
233125 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
233142 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
233160 TT
1 TT
233162 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:236478 original size:12 final size:12
Alignment explanation
Indices: 236461--236505 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
236451 TGAGGAAAAA
236461 GAAAAAGAGAAT
1 GAAAAAGAGAAT
236473 GAAAAAGAGAA-
1 GAAAAAGAGAAT
236484 -AAAAAGAGAAT
1 GAAAAAGAGAAT
236495 GAAAAAGAGAA
1 GAAAAAGAGAA
236506 AAAAGAGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.32
12 21 0.68
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.04
Consensus pattern (12 bp):
GAAAAAGAGAAT
Found at i:236490 original size:22 final size:21
Alignment explanation
Indices: 236462--236513 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 21
236452 GAGGAAAAAG
236462 AAAAAGAGAATGAAAAAGAGAA
1 AAAAAGAGAATGAAAAAGAG-A
236484 AAAAAGAGAATGAAAAAGAGA
1 AAAAAGAGAATGAAAAAGAGA
236505 AAAAAGAGA
1 AAAAAGAGA
236514 TTGAGAGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (21 bp):
AAAAAGAGAATGAAAAAGAGA
Found at i:242776 original size:9 final size:9
Alignment explanation
Indices: 242762--242787 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
242752 AGATTTCAAG
242762 AATCAAGAA
1 AATCAAGAA
242771 AATCAAGAA
1 AATCAAGAA
242780 AATCAAGA
1 AATCAAGA
242788 TTTCAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (9 bp):
AATCAAGAA
Found at i:244665 original size:219 final size:219
Alignment explanation
Indices: 244286--244729 Score: 658
Period size: 219 Copynumber: 2.0 Consensus size: 219
244276 GAAACACTTA
* * *
244286 ATGTCCCTCATTCGGTTGGAAGAAGACTCGGTCACCTTGCCTTTGTTGGTGTCGCCCAAAGGCTT
1 ATGTCCCTCATTCGATTGGAAGAAGACTCGATCACCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
* * *
244351 GCTTGTTTTGGACAGCACTATTTGCTTCTTGGCACGGATTAGTGGATTGTTTTTACTCGTGCTTT
66 GCTTGTTTTGGACAGCACTATTTGCTCCTTGGCACAGATCAGTGGATTGTTTTTACTCGTGCTTT
*
244416 GGCCCCATTTTGTTGTGCCTACAGTGGTATAACCTCGAACGGCACCTTTTCGCTTGAGCTT-CTT
131 GGCCCCATTTTGTTGTGCCTACAGTGGTATAACCTCGAACAGCACCTTTTCGCTTGAG-TTGCTT
244480 TTCCACCTTGATGGT-CATGTACACC
195 TTCCACCTTGAT-GTCCATGTACACC
* * **
244505 ATGTCCCTCGTTCGATTGGAAGAAGACTCTATTGCCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
1 ATGTCCCTCATTCGATTGGAAGAAGACTCGATCACCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
* * * * *
244570 GTTTGTTTTGGACGGCACTATTTGCTCCTTGGCACAGATCGGTGGATTGTTTTTAGTTGTGCTTT
66 GCTTGTTTTGGACAGCACTATTTGCTCCTTGGCACAGATCAGTGGATTGTTTTTACTCGTGCTTT
* * * **
244635 GGCTCCATTTTGTTGTGCCTGCGGTGGTATAACCTCGAACAGTGCCTTTTCGCTTGAGTTGCTTT
131 GGCCCCATTTTGTTGTGCCTACAGTGGTATAACCTCGAACAGCACCTTTTCGCTTGAGTTGCTTT
*
244700 TCCACCTTGATGTCCATGTGCACC
196 TCCACCTTGATGTCCATGTACACC
244724 ATGTCC
1 ATGTCC
244730 ATGATTTCAA
Statistics
Matches: 201, Mismatches: 22, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
218 4 0.02
219 197 0.98
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (219 bp):
ATGTCCCTCATTCGATTGGAAGAAGACTCGATCACCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
GCTTGTTTTGGACAGCACTATTTGCTCCTTGGCACAGATCAGTGGATTGTTTTTACTCGTGCTTT
GGCCCCATTTTGTTGTGCCTACAGTGGTATAACCTCGAACAGCACCTTTTCGCTTGAGTTGCTTT
TCCACCTTGATGTCCATGTACACC
Found at i:251928 original size:20 final size:19
Alignment explanation
Indices: 251905--251969 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
251895 AAGCTCAAAC
251905 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
251925 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
251945 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
251965 GAGCT
1 GAGCT
251970 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:253784 original size:33 final size:33
Alignment explanation
Indices: 253746--253808 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
253736 GATTACTCAC
253746 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
253779 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
253809 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:253835 original size:21 final size:21
Alignment explanation
Indices: 253806--253861 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
253796 CAAGCTCTCT
*
253806 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
253827 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
253848 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
253862 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:253854 original size:14 final size:14
Alignment explanation
Indices: 253805--253861 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
253795 TCAAGCTCTC
253805 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
253818 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
253832 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
253846 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
253860 TT
1 TT
253862 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:253921 original size:18 final size:18
Alignment explanation
Indices: 253823--253926 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
253813 TCTTTTTTCG
253823 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
253842 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
253862 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
253880 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
253898 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
253916 CTTTTTGTTTT
1 CTTTTTCTTTT
253927 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:253943 original size:6 final size:6
Alignment explanation
Indices: 253823--253930 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
253813 TCTTTTTTCG
* * * **
253823 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
253874 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
253922 -GTTTT CTTT
1 CTTTTT CTTT
253931 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:254974 original size:14 final size:14
Alignment explanation
Indices: 254957--254989 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
254947 TTTTGCTCAC
*
254957 TTTTTTTTT-CTTT
1 TTTTTTTTTAATTT
254970 TTTTTTTTTAATTT
1 TTTTTTTTTAATTT
254984 TTTTTT
1 TTTTTT
254990 GAATTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.06, C:0.03, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTTTTAATTT
Found at i:254984 original size:12 final size:12
Alignment explanation
Indices: 254969--255003 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
254959 TTTTTTTCTT
254969 TTTTTTTTTTAA
1 TTTTTTTTTTAA
*
254981 TTTTTTTTTGAA
1 TTTTTTTTTTAA
254993 TTTTTCTTTTT
1 TTTTT-TTTTT
255004 TTTAACTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:256621 original size:20 final size:19
Alignment explanation
Indices: 256598--256662 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
256588 AAGCTCAAAC
256598 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
256618 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
256638 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
256658 GAGCT
1 GAGCT
256663 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Done.