Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 144 of 205
Found at i:43662077 original size:27 final size:27
Alignment explanation
Indices: 43662030--43662093 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
43662020 AAATATTCTC
*
43662030 TAAAATAAT-AAATGTTAATTTATCGA
1 TAAAATAATAAAATATTAATTTATCGA
* * *
43662056 TAAATTAATAAAATATTTATTTATTGA
1 TAAAATAATAAAATATTAATTTATCGA
*
43662083 TAAACTAATAA
1 TAAAATAATAA
43662094 TCTCAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.25
27 24 0.75
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (27 bp):
TAAAATAATAAAATATTAATTTATCGA
Found at i:43666565 original size:25 final size:25
Alignment explanation
Indices: 43666504--43666598 Score: 100
Period size: 26 Copynumber: 3.7 Consensus size: 25
43666494 GCCAACACAC
* * *
43666504 CAGTATCGCAGCAGAGCTGCCAGTAA
1 CAGTAACGCAGCAAAGCTACCAGT-A
*
43666530 TAGTAACGCAGCAAAGCTACCAGTA
1 CAGTAACGCAGCAAAGCTACCAGTA
* *
43666555 CAGTAATGCAGTAAAGCTACCAGTA
1 CAGTAACGCAGCAAAGCTACCAGTA
* *
43666580 TCAGTAACACAACAAAGCT
1 -CAGTAACGCAGCAAAGCT
43666599 GCTAGTAACA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 23 0.40
26 34 0.60
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (25 bp):
CAGTAACGCAGCAAAGCTACCAGTA
Found at i:43667126 original size:27 final size:27
Alignment explanation
Indices: 43666802--43667125 Score: 402
Period size: 27 Copynumber: 12.0 Consensus size: 27
43666792 AGGGGTATAA
* *
43666802 CGGTCATTTTACCCTATAGA-GGTATTT
1 CGGTAATTTTACCC-ATCGAGGGTATTT
* *
43666829 TGGTAACTTTACCCATCGAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
** *
43666856 TAGTAATTTTACCCTTCGAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
* * *
43666883 CAGTTATTTTACCCTTCGAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
* *
43666910 CGGTTATTTTACCTATCGAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
* *
43666937 AGATAATTTTACCCATCGAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
*
43666964 CGATAATTTTACCCATCGAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
*
43666991 CGATAATTTTACCCATCGAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
*
43667018 CGGT-ATCTTTACCCATCGAAGGTATTT
1 CGGTAAT-TTTACCCATCGAGGGTATTT
43667045 CGGT-ATCTTTACCCATCGAGGGTATTT
1 CGGTAAT-TTTACCCATCGAGGGTATTT
*
43667072 CGATAATTTTACCCATCGAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
* * **
43667099 TGGTCATTTTACCCATTAAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
43667126 TAGTCATTTG
Statistics
Matches: 268, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
26 6 0.02
27 260 0.97
28 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (27 bp):
CGGTAATTTTACCCATCGAGGGTATTT
Found at i:43669125 original size:5 final size:5
Alignment explanation
Indices: 43669115--43669151 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
43669105 TTCAAACAAT
*
43669115 AATTA AATTA AATTA AATTA AATTA AATCA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AA
43669152 GTTAGAACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (5 bp):
AATTA
Found at i:43671398 original size:6 final size:6
Alignment explanation
Indices: 43671387--43671431 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
43671377 AAGTTAGTTA
* * *
43671387 TTTATT TTTATT TTTTAT -TTAAT TTTAAT TTTAAT TTTAAT TTTA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTA
43671432 GAAAACTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTAAT
Found at i:43671417 original size:18 final size:17
Alignment explanation
Indices: 43671384--43671431 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
43671374 CAAAAGTTAG
* *
43671384 TTATTTATTTTTATTTT
1 TTATTTAATTTTAATTT
43671401 TTATTTAATTTTAATTT
1 TTATTTAATTTTAATTT
*
43671418 TAATTTTAATTTTA
1 TTA-TTTAATTTTA
43671432 GAAAACTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTAATTTTAATTT
Found at i:43675042 original size:17 final size:17
Alignment explanation
Indices: 43675020--43675053 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
43675010 TCAAAAGTCA
43675020 GTTA-TTTATTTTTAATT
1 GTTATTTTA-TTTTAATT
43675037 GTTATTTTATTTTAATT
1 GTTATTTTATTTTAATT
43675054 TTAGAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
GTTATTTTATTTTAATT
Found at i:43681317 original size:474 final size:474
Alignment explanation
Indices: 43680396--43681317 Score: 1185
Period size: 474 Copynumber: 1.9 Consensus size: 474
43680386 CTTCCAATCG
* * * * * * *
43680396 TAGACACCGACAACCAATTATCACCTTTTTTCCTCGGCCACACTAGTATTAACTACCTCAGCCTT
1 TAGACACCAACAACCAATCATCACCTCTTATCCTCGGCCACACCAGCATCAACTACCTCAGCCTT
* ** *
43680461 CCATTCCTCGTCGCTCTTAAAAGCCCTTCTGTTTCTATTTTTCAACCTATAACATTATGCCTGTA
66 CCATTCCTCGTCGCTCTCAAAAGAACTTCTGTTTCTATTTTTCAACCTATAACATTAAGCCTGTA
* * * * * * * *
43680526 TGTGACTCAACTTCTTGCAGTAGTTAGATGGCTTGTCATGATTCCTCGACTTCGATCTTGACCTA
131 TGTGACCCAACTTATTGCAATAGTTACATGCCTTATCACGATTCCTCGACTTCAATCTTGACCTA
* * * ** *
43680591 GAATTATTCTGATCTGCATCCTTAGACTATTGCTTGCCTCTAGTGACCAAAACTGAGGTTTGACT
196 GAATTATTCTGATCTGAATCCTTAGACTATTGCCTACCTCTAGCAACCAAAACTGAGATTTGACT
* *
43680656 AACAGACTTGCTTCCCAAACCTAACTCATTTATGAGTTTTTCCTAACTCAACAAGTTACCCTTCA
261 AACAGACTTGCTACCCAAACCTAACTCATTTATGAGTTTTTCCTAACTCAACAAGTTACCATTCA
** *
43680721 CATCCTCAAATGAGATTTTATCTCTACCATAAATCAGGGTATCCTTGAAAGTTTTATATGGAGGG
326 CATCCTCAAATGAGATTTTATCTCTACCATAAATCAGGGTATCCTTGAAAGTTTTATATAAAGGA
* * * *
43680786 GACAAAGAGCACAATAATAGCATAGTCTGATCTTCATCATCTATATTGAGCTCGGCATNGAGCGT
391 GACAAAAAGCACAACAATAGCATAGTCTGATCTTCATCATCAATATTGAACTCGGCAT-GAGCGT
43680851 AAGTTTAGAGCTTTCGGTCA
455 AAGTTTAGAGCTTTCGGTCA
43680871 TAGACACCAACAACCAATCATCACC-CTTATCCTCGGCCACACCAGCATCAACTACCTCAGCCTT
1 TAGACACCAACAACCAATCATCACCTCTTATCCTCGGCCACACCAGCATCAACTACCTCAGCCTT
** * * * * *
43680935 CTGTTCCTCGTCGCTCTCAACAA-AATTTCTGTTTTTATTTTTCAACTTATAACATTAAGCTTTT
66 CCATTCCTCGTCGCTCTCAA-AAGAACTTCTGTTTCTATTTTTCAACCTATAACATTAAGCCTGT
* *
43680999 ATGTGACCCAACTTATTGCAATAGTTACATGCCTTATCACGATTCCTCGACTTCAATTTTGATCT
130 ATGTGACCCAACTTATTGCAATAGTTACATGCCTTATCACGATTCCTCGACTTCAATCTTGACCT
* * * * **
43681064 AGATTTGTTCTGA-CTTGAATCCTTAGATTGTTGCCTACCTCTAGCAACTGAAACTGA-ATCTTG
195 AGAATTATTCTGATC-TGAATCCTTAGACTATTGCCTACCTCTAGCAACCAAAACTGAGAT-TTG
* * **
43681127 ACTACCAGACTTGCTACCCAAATCTAACTCA-TTATCGAGTTTTTCCTTGCTCAACAAGTTA-CA
258 ACTAACAGACTTGCTACCCAAACCTAACTCATTTAT-GAGTTTTTCCTAACTCAACAAGTTACCA
* *
43681190 TTCCACATCCTCAAATGAGAGTTTT-TCTCTACCATAAATCAGGGTTTCTTTGAAAGTTTTATAT
322 TT-CACATCCTCAAATGAGA-TTTTATCTCTACCATAAATCAGGGTATCCTTGAAAGTTTTATAT
* * * *
43681254 AAATGAGACAAAAAGCATAACAATGGCATAGTCTGATCTTCATCATCAATGTT-AACATCGGCAT
385 AAAGGAGACAAAAAGCACAACAATAGCATAGTCTGATCTTCATCATCAATATTGAAC-TCGGCAT
43681318 TCTTCAAATC
Statistics
Matches: 381, Mismatches: 59, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
473 11 0.03
474 341 0.90
475 29 0.08
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (474 bp):
TAGACACCAACAACCAATCATCACCTCTTATCCTCGGCCACACCAGCATCAACTACCTCAGCCTT
CCATTCCTCGTCGCTCTCAAAAGAACTTCTGTTTCTATTTTTCAACCTATAACATTAAGCCTGTA
TGTGACCCAACTTATTGCAATAGTTACATGCCTTATCACGATTCCTCGACTTCAATCTTGACCTA
GAATTATTCTGATCTGAATCCTTAGACTATTGCCTACCTCTAGCAACCAAAACTGAGATTTGACT
AACAGACTTGCTACCCAAACCTAACTCATTTATGAGTTTTTCCTAACTCAACAAGTTACCATTCA
CATCCTCAAATGAGATTTTATCTCTACCATAAATCAGGGTATCCTTGAAAGTTTTATATAAAGGA
GACAAAAAGCACAACAATAGCATAGTCTGATCTTCATCATCAATATTGAACTCGGCATGAGCGTA
AGTTTAGAGCTTTCGGTCA
Found at i:43682616 original size:14 final size:14
Alignment explanation
Indices: 43682584--43682617 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
43682574 TTTTAATTTA
*
43682584 AAAAATAAAAATTG
1 AAAAATAAAAAATG
43682598 AAAAATAAAAAAATG
1 AAAAAT-AAAAAATG
43682613 AAAAA
1 AAAAA
43682618 GCTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAAATG
Found at i:43690336 original size:32 final size:29
Alignment explanation
Indices: 43690278--43690337 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
43690268 ATTTTTTATA
* *
43690278 TATATTTTTTATTTTAAAGTGTTTTTTTC
1 TATATTTTTTATTTTAAAATGATTTTTTC
43690307 TATATTTTTTATTATTAAATTATGATTTTTT
1 TATATTTTTTATT-TTAAA--ATGATTTTTT
43690338 ATTTAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 13 0.50
30 5 0.19
32 8 0.31
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (29 bp):
TATATTTTTTATTTTAAAATGATTTTTTC
Found at i:43690349 original size:19 final size:19
Alignment explanation
Indices: 43690313--43690350 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
43690303 TTTCTATATT
43690313 TTTTATTATTAAATTATGA
1 TTTTATTATTAAATTATGA
*
43690332 TTTT-TTATTTAATATATGA
1 TTTTATTATTAAAT-TATGA
43690351 AAAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTATTATTAAATTATGA
Found at i:43690498 original size:22 final size:22
Alignment explanation
Indices: 43690470--43690543 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
43690460 AATTCTTTAA
43690470 AAAAAAATAAATATTTTTAAAT
1 AAAAAAATAAATATTTTTAAAT
43690492 AAAAAAATAAA-A---TTAAAT
1 AAAAAAATAAATATTTTTAAAT
* * *
43690510 GGATAAAAT-AATATTTTAAAAT
1 -AAAAAAATAAATATTTTTAAAT
43690532 AAAAAATATAAA
1 AAAAAA-ATAAA
43690544 AATTGAAAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
18 8 0.20
19 7 0.17
21 5 0.12
22 18 0.45
23 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (22 bp):
AAAAAAATAAATATTTTTAAAT
Found at i:43694214 original size:10 final size:10
Alignment explanation
Indices: 43694184--43694334 Score: 88
Period size: 10 Copynumber: 15.4 Consensus size: 10
43694174 TGGGTGGGGG
*
43694184 GAAGAGAAGGA
1 GAAGA-AAGAA
43694195 GAAGGAAAGAA
1 GAA-GAAAGAA
43694206 GAAGAAAG-A
1 GAAGAAAGAA
43694215 -AAGAAAGAA
1 GAAGAAAGAA
*
43694224 -AAGGAAAGGA
1 GAA-GAAAGAA
*
43694234 GAGGAAAG-A
1 GAAGAAAGAA
43694243 -AAGAAA-AA
1 GAAGAAAGAA
43694251 GAAGGAAAGAA
1 GAA-GAAAGAA
*
43694262 -AAGGAAAGGA
1 GAA-GAAAGAA
*
43694272 GAAGAAAAAA
1 GAAGAAAGAA
*
43694282 AAAGAAAGAA
1 GAAGAAAGAA
**
43694292 GAAGATGGAA
1 GAAGAAAGAA
43694302 GGAAGGAAA-AA
1 -GAA-GAAAGAA
43694313 GAA-AAAGAA
1 GAAGAAAGAA
*
43694322 AAAGAAA-AA
1 GAAGAAAGAA
43694331 GAAG
1 GAAG
43694335 GTCATTTTTG
Statistics
Matches: 111, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
8 16 0.14
9 16 0.14
10 55 0.50
11 20 0.18
12 4 0.04
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.01
Consensus pattern (10 bp):
GAAGAAAGAA
Found at i:43694227 original size:28 final size:28
Alignment explanation
Indices: 43694196--43694328 Score: 121
Period size: 28 Copynumber: 4.8 Consensus size: 28
43694186 AGAGAAGGAG
43694196 AAGGAAAGAAGAAGAAAGAAAGAAAGAA
1 AAGGAAAGAAGAAGAAAGAAAGAAAGAA
* *
43694224 AAGGAAAGGAGAGGAAAGAAAGAAA-AA
1 AAGGAAAGAAGAAGAAAGAAAGAAAGAA
*
43694251 GAAGGAAAGAA-AAGGAAAGGAGAAGAAAAAA
1 -AAGGAAAGAAGAA-GAAA-GA-AAGAAAGAA
* ** * *
43694282 AAAGAAAGAAGAAGATGGAAGGAAGGAA
1 AAGGAAAGAAGAAGAAAGAAAGAAAGAA
*
43694310 AAAGAAA-AAGAA-AAAGAAA
1 AAGGAAAGAAGAAGAAAGAAA
43694329 AAGAAGGTCA
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
26 4 0.05
27 8 0.09
28 49 0.57
29 4 0.05
30 17 0.20
31 4 0.05
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (28 bp):
AAGGAAAGAAGAAGAAAGAAAGAAAGAA
Found at i:43694292 original size:38 final size:38
Alignment explanation
Indices: 43694190--43694292 Score: 145
Period size: 38 Copynumber: 2.7 Consensus size: 38
43694180 GGGGGAAGAG
* *
43694190 AAGGAGAAGGAAAGAAGAAGAAAGAAAGAAAGAAAAGGA
1 AAGGAGAA-GAAAAAAGAAGAAAGAAGGAAAGAAAAGGA
*
43694229 AAGGAGAGGAAAGAAAGAA-AAAGAAGGAAAGAAAAGGA
1 AAGGAGAAGAAA-AAAGAAGAAAGAAGGAAAGAAAAGGA
*
43694267 AAGGAGAAGAAAAAAAAAGAAAGAAG
1 AAGGAGAAGAAAAAAGAAGAAAGAAG
43694293 AAGATGGAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
37 5 0.09
38 40 0.70
39 12 0.21
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (38 bp):
AAGGAGAAGAAAAAAGAAGAAAGAAGGAAAGAAAAGGA
Found at i:43694323 original size:5 final size:6
Alignment explanation
Indices: 43694242--43694333 Score: 58
Period size: 6 Copynumber: 14.0 Consensus size: 6
43694232 GAGAGGAAAG
* * *
43694242 AAAGAA AAAGAA GGAAAGAA AAGGAA AGGAGAA GAAAAAA AAAGAA AGAAGAA
1 AAAGAA AAAGAA --AAAGAA AAAGAA A-AAGAA -AAAGAA AAAGAA A-AAGAA
** *
43694295 GATGGAA GGAAGGAA AAAGAA AAAGAA AAAGAA AAAGAA
1 -AAAGAA --AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
43694334 GGTCATTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
6 41 0.59
7 14 0.20
8 14 0.20
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:43694893 original size:16 final size:15
Alignment explanation
Indices: 43694867--43694896 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
43694857 ATACTGAAAT
43694867 AATATAAAATAATAA
1 AATATAAAATAATAA
43694882 AATATGAAAATAATA
1 AATAT-AAAATAATA
43694897 TATTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:43695475 original size:316 final size:317
Alignment explanation
Indices: 43694659--43695457 Score: 1323
Period size: 317 Copynumber: 2.5 Consensus size: 317
43694649 AAAATGGTAT
* * * * * * *
43694659 ATTTAAAAAACACACTAAATTAATAAATTTCAACCATAATGTACTAAAATATTGTAAAATAATAA
1 ATTTTAAAAACACACTAAATTAATAAAATTCAAACATAATGCACTGAAATAATGTAAAATTATAA
* *
43694724 AATTATAAATTATGATATTTTTTAAAGTAATAAAAACCGGAGAAAAAAATACGAACAAATGGCCG
66 AATTAGAAATTATGATATTTTTTAAAGTAATAAAAAGCGGAGAAAAAAATACGAACAAA-GGCCG
*
43694789 AAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAA
130 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAA
* *
43694854 AATATACTGAAATAATATAAAATAATAAAATATGAAAATAATATATTTTTATTAAAAGTAATAAA
195 AATATACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTAAAAGTAATAAA
*
43694919 ATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAAGGGTTTTTTTACACTAAATTA
260 ATTCAGGAAAATAATACGAGCAAAGGGCAGGAATAAAGGGTTTTTTTACACTAAATTA
*
43694977 A-TTTAAAAACACACTAAATTAATAAAATTCAAACATAATGCACTGAAATAATATAAAATTATAA
1 ATTTTAAAAACACACTAAATTAATAAAATTCAAACATAATGCACTGAAATAATGTAAAATTATAA
43695041 AATTAGAAATTATGATATTTTTTAAAGTAATAAAAAGCGGAGAAAAAAATACGAACAAAGGCCGA
66 AATTAGAAATTATGATATTTTTTAAAGTAATAAAAAGCGGAGAAAAAAATACGAACAAAGGCCGA
**
43695106 AGTAAGAGTCTTTTACTAAATTTTTTAAAAATTTTGAAATAATTAATACAAATATTTCAAACAAA
131 AGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAA
* * * *
43695171 ATGTACTAAAATGATATAAAATAATAAAATACGAAAATGATATATTTTTATTGAAAGTAATAAAA
196 ATATACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTAAAAGTAATAAAA
43695236 TTCAGGAAAATAATACGAGCAAAGGGCAGGAAT-AAGGGTTTTTTTTACACTAAATTA
261 TTCAGGAAAATAATACGAGCAAAGGGCAGGAATAAAGGG-TTTTTTTACACTAAATTA
*
43695293 ATTTTAAAAACACACTAAATTAATAAAATTCAAACATAATGCACTGAAATAATGTAAAATTAGAA
1 ATTTTAAAAACACACTAAATTAATAAAATTCAAACATAATGCACTGAAATAATGTAAAATTATAA
* * * * *
43695358 AATTAGAAAATATGATATTTTTTAAAGTAATAAAATGAGGAGAAAAAAATACGAAAAAAGGGTCG
66 AATTAGAAATTATGATATTTTTTAAAGTAATAAAAAGCGGAGAAAAAAATACGAACAAA-GGCCG
43695423 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTC
130 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTC
43695458 GGGAAAATAG
Statistics
Matches: 450, Mismatches: 28, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
315 5 0.01
316 178 0.40
317 228 0.51
318 39 0.09
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (317 bp):
ATTTTAAAAACACACTAAATTAATAAAATTCAAACATAATGCACTGAAATAATGTAAAATTATAA
AATTAGAAATTATGATATTTTTTAAAGTAATAAAAAGCGGAGAAAAAAATACGAACAAAGGCCGA
AGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAA
ATATACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTAAAAGTAATAAAA
TTCAGGAAAATAATACGAGCAAAGGGCAGGAATAAAGGGTTTTTTTACACTAAATTA
Found at i:43700831 original size:42 final size:40
Alignment explanation
Indices: 43700703--43700837 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 40
43700693 CCACTAACCC
*
43700703 TAATAACTAACACAATAACAATAATAATAGTTTTATACTCAAAA
1 TAAT-ACTAAC-C-ATAACAATAATAATAGTTTTTTACT-AAAA
**
43700747 TAATACTAA-C-TAACAATAATAATTAGGGTTTTACTAAAAA
1 TAATACTAACCATAACAATAATAA-TAGTTTTTTACT-AAAA
* *
43700787 TAATAACTAACCATAATAATAATACTAGTTTTTTACTAACAA
1 TAAT-ACTAACCATAACAATAATAATAGTTTTTTACTAA-AA
43700829 TAATACTAA
1 TAATACTAA
43700838 GTAACATCTA
Statistics
Matches: 78, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
39 12 0.15
40 17 0.22
41 13 0.17
42 17 0.22
43 15 0.19
44 4 0.05
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.33
Consensus pattern (40 bp):
TAATACTAACCATAACAATAATAATAGTTTTTTACTAAAA
Found at i:43708752 original size:252 final size:251
Alignment explanation
Indices: 43708307--43708809 Score: 979
Period size: 252 Copynumber: 2.0 Consensus size: 251
43708297 ATGGTCGCCG
*
43708307 CCGCTACACCGCCTTTAGCCTACATTTCGCAGCCCCTTGGAAGCCCAACCCTCTTGACCCAGAAA
1 CCGCTACACCGCCTTTAGCCTACATTCCGCAGCCCCTTGGAAGCCCAACCCTCTTGACCCAGAAA
43708372 AGGAGGAGGACTCTCGACCCGCTCTCAAACTCGATGGCAATGACAGAGGAGAGCCCTCCGACGGC
66 AGGAGGAGGACTCTCGACCCGCTCTCAAACTCGATGGCAATGACAGAGGAGAGCCCTCCGACGGC
43708437 GCAGTCACGGGGCGTCTCTGGTGAGCCTTCTCTTCCCTTTTTTTTATTTTACTATTTAGTATGTA
131 GCAGTCACGGGGCGTCTCTGGTGAGCCTTCTCTTCCCTTTTTTTTATTTTACTATTTAGTATGTA
43708502 AAAAATGAAAATAAAATAAAATAGAAAATAGAACAAGAAAGTAAAAGAATCACCTC
196 AAAAATGAAAATAAAATAAAATAGAAAATAGAACAAGAAAGTAAAAGAATCACCTC
*
43708558 NCCGCTACCCCGCCTTTAGCCTACATTCCGCAGCCCCTTGGAAGCCCAACCCTCTTGACCCAGAA
1 -CCGCTACACCGCCTTTAGCCTACATTCCGCAGCCCCTTGGAAGCCCAACCCTCTTGACCCAGAA
43708623 AAGGAGGAGGACTCTCGACCCGCTCTCAAACTCGATGGCAATGACAGAGGAGAGCCCTCCGACGG
65 AAGGAGGAGGACTCTCGACCCGCTCTCAAACTCGATGGCAATGACAGAGGAGAGCCCTCCGACGG
43708688 CGCAGTCACGGGGCGTCTCTGGTGAGCCTTCTCTTCCCTTTTTTTTATTTTACTATTTAGTATGT
130 CGCAGTCACGGGGCGTCTCTGGTGAGCCTTCTCTTCCCTTTTTTTTATTTTACTATTTAGTATGT
43708753 AAAAAATGAAAATAAAATAAAATAGAAAATAGAACAAGAAAGTAAAAGAATCACCTC
195 AAAAAATGAAAATAAAATAAAATAGAAAATAGAACAAGAAAGTAAAAGAATCACCTC
43708810 AAATCTGTTT
Statistics
Matches: 249, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
252 249 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (251 bp):
CCGCTACACCGCCTTTAGCCTACATTCCGCAGCCCCTTGGAAGCCCAACCCTCTTGACCCAGAAA
AGGAGGAGGACTCTCGACCCGCTCTCAAACTCGATGGCAATGACAGAGGAGAGCCCTCCGACGGC
GCAGTCACGGGGCGTCTCTGGTGAGCCTTCTCTTCCCTTTTTTTTATTTTACTATTTAGTATGTA
AAAAATGAAAATAAAATAAAATAGAAAATAGAACAAGAAAGTAAAAGAATCACCTC
Found at i:43709151 original size:12 final size:12
Alignment explanation
Indices: 43709130--43709159 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
43709120 TGTTAGGATT
*
43709130 TTTGGTTATTGG
1 TTTGGGTATTGG
43709142 TTTGGGTATTGG
1 TTTGGGTATTGG
43709154 TTTGGG
1 TTTGGG
43709160 CCTTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.40, T:0.53
Consensus pattern (12 bp):
TTTGGGTATTGG
Found at i:43710144 original size:111 final size:115
Alignment explanation
Indices: 43709937--43710151 Score: 341
Period size: 111 Copynumber: 1.9 Consensus size: 115
43709927 TCATTCATCC
*
43709937 CTACACACCATGTTGTGGATGAACCATTAGTAATTACAGATGAACTGAACTACCAGTAATAAAAG
1 CTACACACCATGTTGTGGATGAACCATTAGTAATTACA-ATGAACTGAACTACCAGTAATAAAAA
*
43710002 TTATGGATGAACCATAAAAATTTATAGATAAAAAGTTTGCAGTTTAATAAT
65 TTATGGATGAACCACAAAAATTTATAGATAAAAAGTTTGCAGTTTAATAAT
*
43710053 CTACACACCATGTTGTGGATGAATCATTAGTAATTAC-A-G-A-TGAACTACCAGTAATAAAAAT
1 CTACACACCATGTTGTGGATGAACCATTAGTAATTACAATGAACTGAACTACCAGTAATAAAAAT
*
43710114 TGTGGATGAACCACAAAAATTT-TCAGATAAAAAGTTTG
66 TATGGATGAACCACAAAAATTTAT-AGATAAAAAGTTTG
43710152 TAGACAAGCT
Statistics
Matches: 94, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
110 1 0.01
111 54 0.57
112 1 0.01
113 1 0.01
114 1 0.01
116 36 0.38
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (115 bp):
CTACACACCATGTTGTGGATGAACCATTAGTAATTACAATGAACTGAACTACCAGTAATAAAAAT
TATGGATGAACCACAAAAATTTATAGATAAAAAGTTTGCAGTTTAATAAT
Found at i:43713550 original size:20 final size:21
Alignment explanation
Indices: 43713525--43713571 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
43713515 ACCAAAAAAT
*
43713525 CTTTTTCATAATTTTTG-AAA
1 CTTTTTCATAATGTTTGTAAA
*
43713545 CTTTTTTATAATGTTTGTAAA
1 CTTTTTCATAATGTTTGTAAA
*
43713566 TTTTTT
1 CTTTTT
43713572 TCTTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (21 bp):
CTTTTTCATAATGTTTGTAAA
Found at i:43713587 original size:16 final size:16
Alignment explanation
Indices: 43713566--43713599 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
43713556 TGTTTGTAAA
43713566 TTTTTTTCT-TTTTATT
1 TTTTTTTCTATTTT-TT
43713582 TTTTTTTCTATTTTTT
1 TTTTTTTCTATTTTTT
43713598 TT
1 TT
43713600 AATTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTCTATTTTTT
Found at i:43715946 original size:67 final size:68
Alignment explanation
Indices: 43715875--43716011 Score: 267
Period size: 67 Copynumber: 2.0 Consensus size: 68
43715865 TTTAGAAAAA
43715875 TTTAACTTTCTTTATATATTTTTTAGATTTTTTTTCCAAATTTTATAATTTTTT-AAAAATATAA
1 TTTAACTTTCTTTATATATTTTTTAGATTTTTTTTCCAAATTTTATAATTTTTTAAAAAATATAA
43715939 ATT
66 ATT
43715942 TTTAACTTTCTTTATATATTTTTTAGATTTTTTTTCCAAATTTTATAATTTTTTAAAAAATATAA
1 TTTAACTTTCTTTATATATTTTTTAGATTTTTTTTCCAAATTTTATAATTTTTTAAAAAATATAA
43716007 ATT
66 ATT
43716010 TT
1 TT
43716012 GAAAATTTTA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 54 0.78
68 15 0.22
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (68 bp):
TTTAACTTTCTTTATATATTTTTTAGATTTTTTTTCCAAATTTTATAATTTTTTAAAAAATATAA
ATT
Found at i:43716023 original size:18 final size:18
Alignment explanation
Indices: 43715979--43716026 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
43715969 TTTTTTTTCC
* *
43715979 AAATTTTATAATTTTTTA
1 AAATTTTATAAATTTTGA
**
43715997 AAA-AATATAAATTTTGA
1 AAATTTTATAAATTTTGA
43716014 AAATTTTATAAAT
1 AAATTTTATAAAT
43716027 ATTTTGAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AAATTTTATAAATTTTGA
Found at i:43716029 original size:68 final size:67
Alignment explanation
Indices: 43715881--43716031 Score: 223
Period size: 67 Copynumber: 2.2 Consensus size: 67
43715871 AAAATTTAAC
* * *
43715881 TTTCTTTATATATTTTTTAGATTTTTTTTCCAAATTTTATAATTTTTTAAAAATATAAATTTTTA
1 TTTCTATAAATATTTTTTAGATTTTTTTTCCAAATTTTATAATTTTTTAAAAATATAAATTTTAA
*
43715946 AC
66 AA
* *
43715948 TTTCTTTATATATTTTTTAGATTTTTTTTCCAAATTTTATAATTTTTTAAAAAATATAAATTTTG
1 TTTCTATAAATATTTTTTAGATTTTTTTTCCAAATTTTATAATTTTTT-AAAAATATAAATTTT-
43716013 AAAA
64 AAAA
43716017 TTT-TATAAATATTTT
1 TTTCTATAAATATTTT
43716032 GAATTTAAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
67 48 0.62
68 25 0.32
69 5 0.06
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (67 bp):
TTTCTATAAATATTTTTTAGATTTTTTTTCCAAATTTTATAATTTTTTAAAAATATAAATTTTAA
AA
Found at i:43716323 original size:16 final size:17
Alignment explanation
Indices: 43716304--43716339 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
43716294 TTAAATTTTA
43716304 AAAATA-AAAAATACAT
1 AAAATATAAAAATACAT
43716320 AAAATATAAAAATACAT
1 AAAATATAAAAATACAT
43716337 AAA
1 AAA
43716340 GATTACAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAATATAAAAATACAT
Found at i:43717341 original size:91 final size:92
Alignment explanation
Indices: 43717173--43717342 Score: 209
Period size: 91 Copynumber: 1.9 Consensus size: 92
43717163 AAAACGCTGG
* * * *
43717173 AAAATTTTAAACCAAAACGCAACGTTTCGTCTTGAGCTATAGCGCCGTCAGCGACGCTTACCCGA
1 AAAATTTTAAACCAAAACGCAACGTTTCGGCTTGACCTATAGAGCCATCAGCGACGCTTACCCGA
*
43717238 AAACGCCACTATATATCAAGCGCCGCA
66 AAACACCACTATATATCAAGCGCCGCA
* * * * **
43717265 AAAATTTT-GACCAAAACGCATCG-TTCTGGCTTGACCTATAGAGGCATTAGCGACGCTTACTTG
1 AAAATTTTAAACCAAAACGCAACGTTTC-GGCTTGACCTATAGAGCCATCAGCGACGCTTACCCG
*
43717328 AAAACACCGCTATAT
65 AAAACACCACTATAT
43717343 CCCTCAATTA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
90 3 0.05
91 54 0.83
92 8 0.12
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (92 bp):
AAAATTTTAAACCAAAACGCAACGTTTCGGCTTGACCTATAGAGCCATCAGCGACGCTTACCCGA
AAACACCACTATATATCAAGCGCCGCA
Found at i:43717364 original size:205 final size:212
Alignment explanation
Indices: 43717129--43717558 Score: 554
Period size: 205 Copynumber: 2.0 Consensus size: 212
43717119 GTAGAAAATG
***
43717129 CCGCTATATCCCGCAATTAGCGGCGCTTAACTAAAAAACGCTGGAAAATTTTAAACC-AAAACGC
1 CCGCTATATCCCGCAATTAGCGGCGCTTAACTAAAAAACGCCAAAAAATTTTAAACCGAAAA-GC
*
43717193 AACGTTTCGTCTTGAGCTATAGCGCCGTCAGCGACGCTTACCCGAAAA-C-GCCA-CTAT-A-TA
65 AACGTTTCGTCTTGAGCTATAGCGCCGTCAGCGACGCTTACCCGAAAAGCTGCCATATATCATTA
*
43717253 -T-CAAGCGCCGCAAAAATTTTGACCAAAACGCATCG-TTCTGGCTTGACCTATAGAGGCATTAG
130 GTACAAGCGCCGCAAAAATTTTGAACAAAACGCATCGTTTC-GGCTTGACCTATAGAGGCATTAG
43717315 CGACGCTTACTTGAAAACA
194 CGACGCTTACTTGAAAACA
* * * *
43717334 CCGCTATATCCCTCAATTAGTGGTGCTTAACTAAAAAATGCCAAAAAATTTTAAACCGAAAAGCA
1 CCGCTATATCCCGCAATTAGCGGCGCTTAACTAAAAAACGCCAAAAAATTTTAAACCGAAAAGCA
* * * * *
43717399 ACGTTTCGTCTTGAGCTATAGTGTCGTTAGCGGCGCTTACCCGAAAATGCTGCTATATATCAGCT
66 ACGTTTCGTCTTGAGCTATAGCGCCGTCAGCGACGCTTACCCGAAAA-GCTGCCATATATCA---
*
43717464 TTTAGTAGAAGCGCCGCAAAAATTTTGAACAAAACGCATCGTTTCGGCTTGACCTATAGAGGCAT
127 -TTAGTACAAGCGCCGCAAAAATTTTGAACAAAACGCATCGTTTCGGCTTGACCTATAGAGGCAT
* * * *
43717529 TAGTGGCGCTTATTTGAAAACG
191 TAGCGACGCTTACTTGAAAACA
*
43717551 CTGCTATA
1 CCGCTATA
43717559 GAGCAACTTT
Statistics
Matches: 191, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
205 96 0.50
206 4 0.02
207 1 0.01
208 3 0.02
209 3 0.02
210 1 0.01
215 2 0.01
216 1 0.01
217 77 0.40
218 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (212 bp):
CCGCTATATCCCGCAATTAGCGGCGCTTAACTAAAAAACGCCAAAAAATTTTAAACCGAAAAGCA
ACGTTTCGTCTTGAGCTATAGCGCCGTCAGCGACGCTTACCCGAAAAGCTGCCATATATCATTAG
TACAAGCGCCGCAAAAATTTTGAACAAAACGCATCGTTTCGGCTTGACCTATAGAGGCATTAGCG
ACGCTTACTTGAAAACA
Found at i:43718935 original size:46 final size:46
Alignment explanation
Indices: 43718097--43718927 Score: 1653
Period size: 46 Copynumber: 18.1 Consensus size: 46
43718087 ACAAAGATAG
43718097 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718143 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718189 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718235 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718281 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718327 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718373 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718419 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718465 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718511 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718557 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718603 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718649 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718695 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718741 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718787 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718833 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
*
43718879 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
43718925 AAA
1 AAA
43718928 AGAAAATAGA
Statistics
Matches: 784, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 784 1.00
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.35
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
Found at i:43723740 original size:46 final size:46
Alignment explanation
Indices: 43723408--43723732 Score: 641
Period size: 46 Copynumber: 7.1 Consensus size: 46
43723398 ACAAAGATAG
*
43723408 AAACCAAAATATTATCTCTTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
43723454 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
43723500 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
43723546 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
43723592 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
43723638 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
43723684 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
43723730 AAA
1 AAA
43723733 AGAAAATAGA
Statistics
Matches: 278, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 278 1.00
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:43723851 original size:22 final size:21
Alignment explanation
Indices: 43723820--43723862 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
43723810 TGGTGGTTAT
*
43723820 TGTTTGTGGTTTACGAGTTTAA
1 TGTTTATGGTTTA-GAGTTTAA
*
43723842 TGTTTATGGTTTAGGGTTTAA
1 TGTTTATGGTTTAGAGTTTAA
43723863 GATTTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.02, G:0.28, T:0.51
Consensus pattern (21 bp):
TGTTTATGGTTTAGAGTTTAA
Found at i:43724150 original size:15 final size:15
Alignment explanation
Indices: 43724130--43724159 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43724120 GATATTTTAG
*
43724130 AATATAAATGTAAAT
1 AATATAAATATAAAT
43724145 AATATAAATATAAAT
1 AATATAAATATAAAT
43724160 TATTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AATATAAATATAAAT
Found at i:43724407 original size:21 final size:20
Alignment explanation
Indices: 43724367--43724404 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43724357 AATATATTGA
*
43724367 TGTATTTATTTTTTAAAATG
1 TGTAATTATTTTTTAAAATG
43724387 TGTAATTATTTTTTAAAA
1 TGTAATTATTTTTTAAAA
43724405 ATGCATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TGTAATTATTTTTTAAAATG
Found at i:43724938 original size:19 final size:19
Alignment explanation
Indices: 43724916--43724960 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
43724906 CTGTCATCTC
*
43724916 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* *
43724935 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
43724954 CCCCAAA
1 CCCCAAA
43724961 CCCGACGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.42, G:0.02, T:0.22
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:43725326 original size:12 final size:12
Alignment explanation
Indices: 43725309--43725333 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43725299 CGTTGAAATT
43725309 TATATATATGTA
1 TATATATATGTA
43725321 TATATATATGTA
1 TATATATATGTA
43725333 T
1 T
43725334 TAAAACTAAA
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATATATATGTA
Found at i:43726948 original size:43 final size:43
Alignment explanation
Indices: 43726889--43727167 Score: 396
Period size: 43 Copynumber: 6.5 Consensus size: 43
43726879 CGCCAAACGC
* *
43726889 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* * * *
43726932 TAGAGGCGTTTTTGAGATAAGCGCCGCTAAAGAACATGAGCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* *
43726975 TAGCGGTGTTTGTGGGATAAGCGCCGCTAAAGAACATGAGCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* * * *
43727018 TAGCGGTGTTTGTGGAATAAGCGCCACTAAAGAACATGAGCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
**
43727061 TAGCGGCGTTTGTGGGATAAGCGCTACTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* *
43727104 TAGCGGCGTTTGTGGGATAAGCGCCGCTAGATAACATGACCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* *
43727147 TAGCAGCGTTTGTGGAATAAG
1 TAGCGGCGTTTGTGGGATAAG
43727168 TGCCTCAAAA
Statistics
Matches: 216, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 216 1.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
Found at i:43729095 original size:50 final size:51
Alignment explanation
Indices: 43729033--43729170 Score: 197
Period size: 51 Copynumber: 2.7 Consensus size: 51
43729023 TCATGCAATA
* * * *
43729033 CACGTAGAAGCCTTCACATAGTACTACACATGTGATCAA-GCTTTTCGGTT
1 CACGTAGTAGCCTACACATAGTACTACACATGTGACCAAGGCTTTCCGGTT
*
43729083 CACGTAGTAGCCTACACATAGTACTACACACGTGACCAAGGCTTTCCGGTT
1 CACGTAGTAGCCTACACATAGTACTACACATGTGACCAAGGCTTTCCGGTT
* * *
43729134 CACATAGTAGCCTGCACTTAGTACTACACATGTGACC
1 CACGTAGTAGCCTACACATAGTACTACACATGTGACC
43729171 GTTATTTATC
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 35 0.45
51 43 0.55
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (51 bp):
CACGTAGTAGCCTACACATAGTACTACACATGTGACCAAGGCTTTCCGGTT
Found at i:43740350 original size:17 final size:17
Alignment explanation
Indices: 43740325--43740358 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43740315 TTAAAATCAG
*
43740325 ATTGAGAAATTTATTTA
1 ATTGAGAAATTAATTTA
*
43740342 ATTGGGAAATTAATTTA
1 ATTGAGAAATTAATTTA
43740359 TGATGTTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (17 bp):
ATTGAGAAATTAATTTA
Found at i:43741701 original size:43 final size:43
Alignment explanation
Indices: 43741653--43741736 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
43741643 TATCAGCATG
*** *
43741653 ATCTTGCTCAAAGTGATAGTTCCTTTTATCGACGATTAAATTT
1 ATCTTGCTCAAAGTGATAAAACCTTTTATCGACGATCAAATTT
*
43741696 ATCTTGCTCAAAGTGATAAAACTTTTTATCGACGATCAAAT
1 ATCTTGCTCAAAGTGATAAAACCTTTTATCGACGATCAAAT
43741737 AAATTCTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (43 bp):
ATCTTGCTCAAAGTGATAAAACCTTTTATCGACGATCAAATTT
Found at i:43751214 original size:34 final size:35
Alignment explanation
Indices: 43751152--43751247 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 35
43751142 TTATTCAAAT
* * * *
43751152 ACATATGCCAAAAGCATATATTTATACTTATCAAT-T
1 ACATATGCCAAATGCA-ACATATATACTTAT-AATCC
* *
43751188 ACATGTGCCGAATGC-ACATATATACTTATAATCC
1 ACATATGCCAAATGCAACATATATACTTATAATCC
43751222 ACATATGCCAAATGCATACATATATA
1 ACATATGCCAAATGCA-ACATATATA
43751248 TATCCAACAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
33 3 0.06
34 25 0.51
36 21 0.43
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (35 bp):
ACATATGCCAAATGCAACATATATACTTATAATCC
Found at i:43752222 original size:78 final size:78
Alignment explanation
Indices: 43752120--43752553 Score: 773
Period size: 78 Copynumber: 5.6 Consensus size: 78
43752110 CTACTCAACA
* *
43752120 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
43752184 AACATACATACTT
66 AACATACATACTT
*
43752197 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATTCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
43752262 AACATACATACTT
66 AACATACATACTT
*
43752275 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATTCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
43752340 AACATACATACTT
66 AACATACATACTT
*
43752353 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATTCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
43752418 AACATACATACTT
66 AACATACATACTT
*
43752431 TTAACTAAATTCAAGAATTTATTCATGCATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
43752496 AACATACATACTT
66 AACATACATACTT
*
43752509 TTAACTAAATTCAAGAACTTT-TACATGTATATACATATATTATCC
1 TTAACTAAATTCAAGAA-TTTATTCATGTATATACATATA-TATCC
43752554 ACTATTAGTT
Statistics
Matches: 347, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
77 14 0.04
78 325 0.94
79 8 0.02
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (78 bp):
TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTT
Found at i:43755044 original size:22 final size:20
Alignment explanation
Indices: 43755009--43755062 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
43754999 AATTAAGAAT
*
43755009 AAAATAATA-AAAAATCATTTA
1 AAAATAATATTAAAAT-A-TTA
43755030 AAAATAATATTAAAATATTA
1 AAAATAATATTAAAATATTA
43755050 ATAAACTAATATT
1 A-AAA-TAATATT
43755063 TATTGAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.14
21 13 0.45
22 12 0.41
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATAATATTAAAATATTA
Found at i:43759754 original size:19 final size:19
Alignment explanation
Indices: 43759730--43759766 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
43759720 TCTAAAACCA
43759730 AAAAAATTGTTGAAGAAGG
1 AAAAAATTGTTGAAGAAGG
43759749 AAAAAATTGTTGAAGAAG
1 AAAAAATTGTTGAAGAAG
43759767 ACTTTAGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (19 bp):
AAAAAATTGTTGAAGAAGG
Found at i:43761709 original size:40 final size:40
Alignment explanation
Indices: 43761654--43761729 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
43761644 TTAAATTTCT
** *
43761654 TTTTGGATGTGCAATTTAAGCTTGTACTTAAGAGCATCTA
1 TTTTGGATGAACAATTTAAGCTCGTACTTAAGAGCATCTA
* *
43761694 TTTTGGATGAACAATTTAAGCTCGTGCTTAGGAGCA
1 TTTTGGATGAACAATTTAAGCTCGTACTTAAGAGCA
43761730 ATGTGACAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (40 bp):
TTTTGGATGAACAATTTAAGCTCGTACTTAAGAGCATCTA
Found at i:43771246 original size:51 final size:51
Alignment explanation
Indices: 43771160--43771266 Score: 178
Period size: 51 Copynumber: 2.1 Consensus size: 51
43771150 AAATTCATTT
* *
43771160 TAATTACCCGATTTTACATATTTTACTTACCCATTAAACTTGAAATAGCTA
1 TAATTACCCAATTTTACATATTTTAATTACCCATTAAACTTGAAATAGCTA
*
43771211 TAATTACCCAATTTTACATATTTTAATTACTCATTAAACTTGAAATAGCTA
1 TAATTACCCAATTTTACATATTTTAATTACCCATTAAACTTGAAATAGCTA
*
43771262 CAATT
1 TAATT
43771267 CATTACCATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (51 bp):
TAATTACCCAATTTTACATATTTTAATTACCCATTAAACTTGAAATAGCTA
Found at i:43771527 original size:40 final size:40
Alignment explanation
Indices: 43771481--43771591 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 40
43771471 CGTTTGGACA
* *
43771481 AAAAACGCCACTAAAAATCAAGCATTAGTGGCAC-TTTTAC
1 AAAAACGCCACTAAAAATCAAGCATTAGCGGCACATATT-C
* * * *
43771521 AAAAACGCCACTAAATATCGAGCATTAGCGGCGCATATTG
1 AAAAACGCCACTAAAAATCAAGCATTAGCGGCACATATTC
**
43771561 AAAAACGCCGTTAAAAAT-AAGCATTAGCGGC
1 AAAAACGCCACTAAAAATCAAGCATTAGCGGC
43771592 GTTTTCCAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 12 0.20
40 45 0.75
41 3 0.05
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (40 bp):
AAAAACGCCACTAAAAATCAAGCATTAGCGGCACATATTC
Found at i:43771709 original size:41 final size:41
Alignment explanation
Indices: 43771663--43771779 Score: 164
Period size: 41 Copynumber: 2.9 Consensus size: 41
43771653 ATTTAGCGAC
*
43771663 GCTTTTAGCAGCGTTTTTTCAAAAGCGCCGCTAATGCTCGG
1 GCTTTTAGCGGCGTTTTTTCAAAAGCGCCGCTAATGCTCGG
* *
43771704 TCTTTTAGCGGCATTTTTTCAAAAGCGCCGCTAATGCTCGG
1 GCTTTTAGCGGCGTTTTTTCAAAAGCGCCGCTAATGCTCGG
* * *
43771745 GCCTTTAGTGGCG-TTTTTGAAAATGCGCCGCTAAT
1 GCTTTTAGCGGCGTTTTTTCAAAA-GCGCCGCTAAT
43771780 AATAAAATCT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 9 0.13
41 58 0.87
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (41 bp):
GCTTTTAGCGGCGTTTTTTCAAAAGCGCCGCTAATGCTCGG
Found at i:43772879 original size:7 final size:7
Alignment explanation
Indices: 43772869--43772924 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
43772859 TTTTGAGTTC
43772869 AGGGTTT
1 AGGGTTT
43772876 AGGGTTT
1 AGGGTTT
43772883 A-GGTTT
1 AGGGTTT
*
43772889 AGGGCTT
1 AGGGTTT
* *
43772896 GGGGATT
1 AGGGTTT
*
43772903 GGGGTTT
1 AGGGTTT
*
43772910 AAGGTTT
1 AGGGTTT
*
43772917 AGAGTTT
1 AGGGTTT
43772924 A
1 A
43772925 CATTTTAGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 6 0.15
7 34 0.85
ACGTcount: A:0.18, C:0.02, G:0.41, T:0.39
Consensus pattern (7 bp):
AGGGTTT
Found at i:43777585 original size:20 final size:21
Alignment explanation
Indices: 43777558--43777604 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
43777548 ATGCTCAAAA
43777558 GTTTTTTTTCTAAGGCTCATT
1 GTTTTTTTTCTAAGGCTCATT
43777579 GTTTTTTTTCTAAGGCTCATT
1 GTTTTTTTTCTAAGGCTCATT
43777600 GTTTT
1 GTTTT
43777605 GTGGGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.60
Consensus pattern (21 bp):
GTTTTTTTTCTAAGGCTCATT
Found at i:43777663 original size:43 final size:43
Alignment explanation
Indices: 43777602--43777692 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
43777592 GGCTCATTGT
43777602 TTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTATTTAGCGGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTATTTAGCGGCG
*
43777645 TTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTATTTAGCGGCG
43777688 TTTGT
1 TTTGT
43777693 TTCTAAAAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (43 bp):
TTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTATTTAGCGGCG
Found at i:43786033 original size:16 final size:16
Alignment explanation
Indices: 43786014--43786059 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
43786004 TGAAAATAAA
43786014 AAAAAATTAAAATTAT
1 AAAAAATTAAAATTAT
43786030 AAAAAA-TAGAAATTAT
1 AAAAAATTA-AAATTAT
43786046 AAAAAATATAAAAT
1 AAAAAAT-TAAAAT
43786060 ATTACAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.07
16 19 0.70
17 4 0.15
18 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAAAATTAAAATTAT
Found at i:43786325 original size:42 final size:42
Alignment explanation
Indices: 43786261--43786627 Score: 430
Period size: 42 Copynumber: 8.8 Consensus size: 42
43786251 GTTTTCAAAT
* *
43786261 AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGGA
43786303 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGG-
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGGA
* *
43786344 AAAAATGCCGCTAAAGAACATGTTCTTTAGCGGTGCTTAGGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGGA
* *
43786386 AAAAATGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGGA
43786428 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-GA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGGA
* *
43786469 ACAAAATGCCGCT--A-AACATGTTCTTTAGCGGCGCTTAGAA
1 A-AAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGGA
* * * *
43786509 AAGAAACGTCGCTAAAGAAAATGTTCTTTAGCGGCACTTTA-AA
1 AA-AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TTAGGA
* * * **
43786552 AAGAAATGCTGCTAAAG-ACAATGTTCTTTTAGCGGCGTTTATTA
1 AA-AAACGCCGCTAAAGAAC-ATGTTC-TTTAGCGGCGCTTAGGA
** *
43786596 TTAAGCGCCGCTAAAG---ATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
43786628 TTTTTGTAAA
Statistics
Matches: 288, Mismatches: 26, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
39 34 0.12
40 17 0.06
41 41 0.14
42 129 0.45
43 54 0.19
44 13 0.05
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGGA
Found at i:43786406 original size:83 final size:83
Alignment explanation
Indices: 43786261--43786627 Score: 453
Period size: 83 Copynumber: 4.4 Consensus size: 83
43786251 GTTTTCAAAT
* * *
43786261 AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-GAAAAAATGCCGCTAAAGAACATGT
*
43786326 TCTTTAGCGGCGCTTAG-G
65 TCTTTAGCGGCGCTTAGAA
* *
43786344 AAAAATGCCGCTAAAGAACATGTTCTTTAGCGGTGCTTAGGAAAAAATGCCGCTAAAGAACATGT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-GAAAAAATGCCGCTAAAGAACATGT
43786409 TCTTTAGCGGCGCTTAGAA
65 TCTTTAGCGGCGCTTAGAA
43786428 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAACAAAATGCCGCT--A-AACATGT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA-AAAATGCCGCTAAAGAACATGT
43786490 TCTTTAGCGGCGCTTAGAA
65 TCTTTAGCGGCGCTTAGAA
* * * * *
43786509 AAGAAACGTCGCTAAAGAAAATGTTCTTTAGCGGCACTTTAAAAAGAAATGCTGCTAAAG-ACAA
1 AA-AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TTAGAAA-AAATGCCGCTAAAGAAC-A
* **
43786573 TGTTCTTTTAGCGGCGTTTATTA
62 TGTTC-TTTAGCGGCGCTTAGAA
** *
43786596 TTAAGCGCCGCTAAAG---ATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
43786628 TTTTTGTAAA
Statistics
Matches: 253, Mismatches: 21, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
81 28 0.11
82 33 0.13
83 109 0.43
84 48 0.19
85 3 0.01
86 18 0.07
87 14 0.06
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (83 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAATGCCGCTAAAGAACATGTT
CTTTAGCGGCGCTTAGAA
Found at i:43786419 original size:125 final size:124
Alignment explanation
Indices: 43786266--43786627 Score: 462
Period size: 125 Copynumber: 2.9 Consensus size: 124
43786256 CAAATAAAAG
* *
43786266 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTT
* * *
43786331 AGCGGCGCTTAGGA-AAAATGCCGCTAAAGAACATGTTCTTTAGCGGTGCTTAGGAAA-AAA
66 AGCGGCGCTTAGAACAAAATGCCGCT--A-AACATGTTCTTTAGCGGCGCTTAGAAAAGAAA
*
43786391 TGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTT
43786456 AGCGGCGCTTAGAACAAAATGCCGCTAAACATGTTCTTTAGCGGCGCTTAGAAAAGAAA
66 AGCGGCGCTTAGAACAAAATGCCGCTAAACATGTTCTTTAGCGGCGCTTAGAAAAGAAA
* * * * *
43786515 CGTCGCTAAAGAAAATGTTCTTTAGCGGCACTTTA-AAAAGAAATGCTGCTAAAG-ACAATGTTC
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TTAGAAAA-AAACGCCGCTAAAGAAC-ATGTTC
* ** ** ** *
43786578 TTTTAGCGGCGTTTATTATTAAGCGCCGCTAAAGATGTTCTTTAGCGGCG
63 -TTTAGCGGCGCTTAGAACAAAATGCCGCTAAACATGTTCTTTAGCGGCG
43786628 TTTTTGTAAA
Statistics
Matches: 211, Mismatches: 20, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
123 26 0.12
124 37 0.18
125 96 0.45
126 52 0.25
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (124 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTT
AGCGGCGCTTAGAACAAAATGCCGCTAAACATGTTCTTTAGCGGCGCTTAGAAAAGAAA
Found at i:43786975 original size:21 final size:22
Alignment explanation
Indices: 43786949--43787000 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
43786939 TTTGGCCTGC
43786949 TCTGCTTCTCTT-GTTGCAGCT
1 TCTGCTTCTCTTCGTTGCAGCT
43786970 TCTGCTTCT-TTCGTTGCAGCT
1 TCTGCTTCTCTTCGTTGCAGCT
43786991 TCTGCTTCTC
1 TCTGCTTCTC
43787001 GCGCTGTCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.04, C:0.31, G:0.17, T:0.48
Consensus pattern (22 bp):
TCTGCTTCTCTTCGTTGCAGCT
Found at i:43792575 original size:9 final size:9
Alignment explanation
Indices: 43792563--43792745 Score: 123
Period size: 9 Copynumber: 21.1 Consensus size: 9
43792553 TGTACATCTA
43792563 TAAGTTATG
1 TAAGTTATG
43792572 TAAGTTATG
1 TAAGTTATG
*
43792581 T-A-TTAAG
1 TAAGTTATG
* *
43792588 TAAGCTATT
1 TAAGTTATG
*
43792597 TAAGTTGTG
1 TAAGTTATG
43792606 T-AG-TATG
1 TAAGTTATG
43792613 TAAGTTATG
1 TAAGTTATG
* *
43792622 TAAGTTTTC
1 TAAGTTATG
* *
43792631 AAAGTAATG
1 TAAGTTATG
*
43792640 TATGTTATG
1 TAAGTTATG
43792649 TAAG-T-TG
1 TAAGTTATG
43792656 TAAGTTAT-
1 TAAGTTATG
*
43792664 TATGTATTATG
1 TAAG--TTATG
*
43792675 TAGGTTATG
1 TAAGTTATG
43792684 TAAGTTATG
1 TAAGTTATG
*
43792693 TAAGTTTTG
1 TAAGTTATG
*
43792702 T-A-TTATT
1 TAAGTTATG
*
43792709 TAAGTTGTG
1 TAAGTTATG
43792718 TAAGTTATG
1 TAAGTTATG
* * *
43792727 GATGCTATG
1 TAAGTTATG
*
43792736 TAAGTAATG
1 TAAGTTATG
43792745 T
1 T
43792746 GTATTATCTA
Statistics
Matches: 129, Mismatches: 34, Indels: 22
0.70 0.18 0.12
Matches are distributed among these distances:
7 19 0.15
8 13 0.10
9 90 0.70
10 4 0.03
11 3 0.02
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:43792600 original size:25 final size:25
Alignment explanation
Indices: 43792563--43792726 Score: 92
Period size: 25 Copynumber: 6.7 Consensus size: 25
43792553 TGTACATCTA
*
43792563 TAAGTTATGTAAGTTATGTATTAAG
1 TAAGTTATGTAAGTTATGTAGTAAG
* * * *
43792588 TAAGCTATTTAAGTTGTGTAGTATG
1 TAAGTTATGTAAGTTATGTAGTAAG
* **
43792613 TAAGTTATGTAAGTTTTCAAAGTAATG
1 TAAGTTATGTAAGTTAT-GTAGTAA-G
*
43792640 TATGTTATGTAAG---T-T-GTAAG
1 TAAGTTATGTAAGTTATGTAGTAAG
* *
43792660 TTA-TTATGT-A-TTATGTAGGTTATG
1 TAAGTTATGTAAGTTATGTA-G-TAAG
* * **
43792684 TAAGTTATGTAAGTTTTGTATTATT
1 TAAGTTATGTAAGTTATGTAGTAAG
*
43792709 TAAGTTGTGTAAGTTATG
1 TAAGTTATGTAAGTTATG
43792727 GATGCTATGT
Statistics
Matches: 105, Mismatches: 22, Indels: 24
0.70 0.15 0.16
Matches are distributed among these distances:
18 1 0.01
19 6 0.06
20 3 0.03
21 5 0.05
23 1 0.01
24 6 0.06
25 59 0.56
26 5 0.05
27 19 0.18
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.47
Consensus pattern (25 bp):
TAAGTTATGTAAGTTATGTAGTAAG
Found at i:43792712 original size:16 final size:16
Alignment explanation
Indices: 43792666--43792719 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
43792656 TAAGTTATTA
* *
43792666 TGTATTATGTAGGTTA
1 TGTATTATGTAAGTTG
*
43792682 TGTAAGTTATGTAAGTTT
1 TGT-A-TTATGTAAGTTG
*
43792700 TGTATTATTTAAGTTG
1 TGTATTATGTAAGTTG
43792716 TGTA
1 TGTA
43792720 AGTTATGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 17 0.53
17 2 0.06
18 13 0.41
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (16 bp):
TGTATTATGTAAGTTG
Found at i:43792853 original size:16 final size:16
Alignment explanation
Indices: 43792811--43792853 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
43792801 TTTGAGAATT
* *
43792811 TTATATAAGTCATGTA
1 TTATGTAAGTTATGTA
43792827 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
43792843 TTATGTAAGTT
1 TTATGTAAGTT
43792854 TAATAAGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:43792986 original size:34 final size:34
Alignment explanation
Indices: 43792942--43793065 Score: 133
Period size: 34 Copynumber: 3.5 Consensus size: 34
43792932 GTAAGTAATG
* *
43792942 TAAGTCATGTAAAATGTACTTAATAATATATATT
1 TAAGTAATGTAAAATATACTTAATAATATATATT
* *
43792976 TAAGTAATGTAAGATATAAATTTTAA-AATAATATATT
1 TAAGTAATGTAA-A-ATATA-CTTAATAAT-ATATATT
*
43793013 AATAAGTCATGTAAAATATACTTAATAATATATATT
1 --TAAGTAATGTAAAATATACTTAATAATATATATT
*
43793049 TAAGTAATGTAAGATAT
1 TAAGTAATGTAAAATAT
43793066 CAATTTTAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
34 26 0.35
35 1 0.01
36 17 0.23
37 18 0.24
38 1 0.01
39 11 0.15
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.40
Consensus pattern (34 bp):
TAAGTAATGTAAAATATACTTAATAATATATATT
Found at i:43793019 original size:39 final size:39
Alignment explanation
Indices: 43792963--43793095 Score: 127
Period size: 39 Copynumber: 3.5 Consensus size: 39
43792953 AAATGTACTT
*
43792963 AATAATATA-TATTTAAGTAATGTAAGATATAAATTTTAA
1 AATAATATATTA-ATAAGTAATGTAAGATATAAATTTTAA
* * *
43793002 AATAATATATTAATAAGTCATGTAA-A-ATATA-CTTAA
1 AATAATATATTAATAAGTAATGTAAGATATAAATTTTAA
*
43793038 TAAT-ATATATT--TAAGTAATGTAAGATATCAATTTTAA
1 -AATAATATATTAATAAGTAATGTAAGATATAAATTTTAA
43793075 AATATATATTCATTAATAAGT
1 AATA-ATA-T-ATTAATAAGT
43793096 TAAATGAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 19
0.74 0.08 0.19
Matches are distributed among these distances:
34 11 0.15
35 1 0.01
36 17 0.23
37 11 0.15
38 4 0.05
39 21 0.28
40 5 0.07
42 5 0.07
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.41
Consensus pattern (39 bp):
AATAATATATTAATAAGTAATGTAAGATATAAATTTTAA
Found at i:43793025 original size:73 final size:76
Alignment explanation
Indices: 43792942--43793095 Score: 269
Period size: 73 Copynumber: 2.1 Consensus size: 76
43792932 GTAAGTAATG
*
43792942 TAAGTCATGTAAAATGTACTTAATAATATATATTTAAGTAATGTAAGATATAAATTTTAAAATA-
1 TAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATAAATTTTAAAATAT
43793006 ATA-T-ATTAA
66 ATATTCATTAA
*
43793015 TAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTTAAAATAT
1 TAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATAAATTTTAAAATAT
43793080 ATATTCATTAA
66 ATATTCATTAA
43793091 TAAGT
1 TAAGT
43793096 TAAATGAAAT
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
73 62 0.82
74 3 0.04
75 1 0.01
76 10 0.13
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (76 bp):
TAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATAAATTTTAAAATAT
ATATTCATTAA
Found at i:43793080 original size:34 final size:33
Alignment explanation
Indices: 43792969--43793081 Score: 109
Period size: 34 Copynumber: 3.2 Consensus size: 33
43792959 ACTTAATAAT
43792969 ATATATTTAAGTAATGTAAGATATAAATTTTAAAATA
1 ATATATTTAAGTAATGTAAGATAT-AATTTT--AA-A
* * * * *
43793006 ATATATTAATAAGTCATGTAAAATATACTTAATAAT
1 ATATATT--TAAGTAATGTAAGATATAATT-TTAAA
43793042 ATATATTTAAGTAATGTAAGATATCAATTTTAAA
1 ATATATTTAAGTAATGTAAGATAT-AATTTTAAA
43793076 ATATAT
1 ATATAT
43793082 ATTCATTAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
34 24 0.39
35 3 0.05
36 7 0.11
37 9 0.15
38 3 0.05
39 16 0.26
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.41
Consensus pattern (33 bp):
ATATATTTAAGTAATGTAAGATATAATTTTAAA
Found at i:43793116 original size:73 final size:72
Alignment explanation
Indices: 43792966--43793118 Score: 193
Period size: 73 Copynumber: 2.1 Consensus size: 72
43792956 TGTACTTAAT
**
43792966 AATATATATTTAAGTAATGTAAGATATAAATTTTAAAATAATATATTAATAAGTCATGTAAAATA
1 AATATATATTTAAGTAATGTAAGATATAAATTTTAAAATAATATATTAATAAGTCAAATAAAATA
* *
43793031 TACTTAAT
66 TA-GTAAA
* * *
43793039 AATATATATTTAAGTAATGTAAGATATCAATTTTAAAATATATATTCATTAATAAGTTAAATGAA
1 AATATATATTTAAGTAATGTAAGATATAAATTTTAAAATA-ATA-T-ATTAATAAGTCAAATAAA
43793104 AT-T-GTAAA
63 ATATAGTAAA
43793112 AATATAT
1 AATATAT
43793119 TTAAAAAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
73 49 0.70
74 3 0.04
75 2 0.03
76 16 0.23
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (72 bp):
AATATATATTTAAGTAATGTAAGATATAAATTTTAAAATAATATATTAATAAGTCAAATAAAATA
TAGTAAA
Found at i:43793291 original size:67 final size:67
Alignment explanation
Indices: 43793219--43793357 Score: 253
Period size: 67 Copynumber: 2.1 Consensus size: 67
43793209 TTTGTTGAGA
*
43793219 ATTCATTATATAATGAATTTATTAAACATTCAATCAATTA-ACTAACCAAAATTGATAATTCATT
1 ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACA-TAACCAAAATTGATAATTCATT
43793283 GAC
65 GAC
43793286 ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
1 ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
43793351 AC
66 AC
43793353 ATTCA
1 ATTCA
43793358 ATCAATTAAT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 69 0.99
68 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (67 bp):
ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
AC
Found at i:43793438 original size:16 final size:16
Alignment explanation
Indices: 43793417--43793452 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
43793407 ATTAATTGAA
*
43793417 ATAAAATTGTAAATCG
1 ATAAAATTGCAAATCG
43793433 ATAAAATTGCAAATCG
1 ATAAAATTGCAAATCG
43793449 ATAA
1 ATAA
43793453 TTATAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAAAATTGCAAATCG
Found at i:43796070 original size:21 final size:21
Alignment explanation
Indices: 43796046--43796121 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
43796036 TATAATTTCT
*
43796046 AATCCTTAAACCTCAAAAACC-
1 AATCCCTAAACC-CAAAAACCA
*
43796067 AATCCCTAAACCCTAAAACCA
1 AATCCCTAAACCCAAAAACCA
* **
43796088 AATCCCTAAATCCTAAACCCCA
1 AATCCCTAAA-CCCAAAAACCA
43796110 AA-CCCTAAACCC
1 AATCCCTAAACCC
43796122 TAAACCCTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 9 0.20
21 28 0.61
22 9 0.20
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (21 bp):
AATCCCTAAACCCAAAAACCA
Found at i:43796082 original size:7 final size:7
Alignment explanation
Indices: 43796070--43796134 Score: 87
Period size: 7 Copynumber: 9.3 Consensus size: 7
43796060 AAAAACCAAT
43796070 CCCTAAA
1 CCCTAAA
43796077 CCCTAAA
1 CCCTAAA
*
43796084 ACC-AAA
1 CCCTAAA
43796090 TCCCTAAA
1 -CCCTAAA
*
43796098 TCCTAAA
1 CCCTAAA
*
43796105 CCCCAAA
1 CCCTAAA
43796112 CCCTAAA
1 CCCTAAA
43796119 CCCTAAA
1 CCCTAAA
43796126 CCCTAAA
1 CCCTAAA
43796133 CC
1 CC
43796135 ACAAAACCCC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
6 3 0.06
7 44 0.88
8 3 0.06
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (7 bp):
CCCTAAA
Found at i:43796116 original size:14 final size:14
Alignment explanation
Indices: 43796065--43796139 Score: 71
Period size: 14 Copynumber: 5.4 Consensus size: 14
43796055 ACCTCAAAAA
*
43796065 CCAATCCCTAAACC
1 CCAAACCCTAAACC
* *
43796079 CTAAAACC-AAATCC
1 CCAAACCCTAAA-CC
* *
43796093 CTAAATCCTAAACC
1 CCAAACCCTAAACC
43796107 CCAAACCCTAAACC
1 CCAAACCCTAAACC
*
43796121 CTAAACCCTAAACC
1 CCAAACCCTAAACC
*
43796135 ACAAA
1 CCAAA
43796140 ACCCCGAGCA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
13 3 0.06
14 44 0.88
15 3 0.06
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.13
Consensus pattern (14 bp):
CCAAACCCTAAACC
Found at i:43796123 original size:21 final size:21
Alignment explanation
Indices: 43796065--43796143 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 21
43796055 ACCTCAAAAA
* *
43796065 CCAATCCCTAAACCCTAAA-A
1 CCAAACCCTAAACCCTAAACC
*
43796085 CCAAATCCCTAAATCCTAAACC
1 CCAAA-CCCTAAACCCTAAACC
43796107 CCAAACCCTAAACCCTAAACC
1 CCAAACCCTAAACCCTAAACC
* *
43796128 CTAAACCACAAAACCC
1 CCAAACC-CTAAACCC
43796144 CGAGCAGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.08
21 34 0.68
22 12 0.24
ACGTcount: A:0.44, C:0.43, G:0.00, T:0.13
Consensus pattern (21 bp):
CCAAACCCTAAACCCTAAACC
Found at i:43796944 original size:21 final size:19
Alignment explanation
Indices: 43796914--43796952 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 19
43796904 GTATCTTTTA
43796914 TAATTATATATAAAATTATT
1 TAATTATATAT-AAATTATT
43796934 TAATATATATATAAATTAT
1 TAAT-TATATATAAATTAT
43796953 AAATCAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATTATATATAAATTATT
Found at i:43797081 original size:18 final size:18
Alignment explanation
Indices: 43797058--43797093 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
43797048 ATTGAATTTT
43797058 AATT-AATATAAATAAACA
1 AATTAAATATAAA-AAACA
43797076 AATTAAATATAAAAAACA
1 AATTAAATATAAAAAACA
43797094 TATAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AATTAAATATAAAAAACA
Found at i:43797101 original size:18 final size:19
Alignment explanation
Indices: 43797062--43797102 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
43797052 AATTTTAATT
*
43797062 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
43797081 AATATAAA-AAACATATAA
1 AATATAAATAAACAAATAA
43797099 AATA
1 AATA
43797103 ATTTTGTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:43797692 original size:228 final size:228
Alignment explanation
Indices: 43797203--43797719 Score: 756
Period size: 228 Copynumber: 2.3 Consensus size: 228
43797193 CCGCTAATAC
* * * *
43797203 TATACTTCAGCGGCGTTTTTAACCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGATTTTAATCAAACGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
43797268 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGATATACTTTAGCGGCGT
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGATATACTTTAGCGGCGT
*
43797333 TTTTAATCAAGCGCCACTAATTCTAATACTCCTAATGACCAAAACTCTGCGTTTTGGTTAAGATG
131 TTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTGCGTTTTGGTTAAGATG
* * *
43797398 ATTTGCGGCGCATCCGACAAACGCCACTGATGA
196 ATTTGAGGCGCATCCCACAAACGCCACTGATAA
* * *
43797431 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAATGACCAAAACTCTG
1 TATACTTTAGCGGCGATTTTAATCAAACGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
*
43797496 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAATGCCGCTGATGATATACTTTAGCGGCGT
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGATATACTTTAGCGGCGT
43797561 TTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTGCGTTTTGGTTAAGAT-
131 TTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTGCGTTTTGGTTAAGATG
* **
43797625 ATTTGGAGGCGCTTCCCACCAAACGCTGCT-ATAA
196 ATTT-GAGGCGCATCCCA-CAAACGCCACTGATAA
* ** * * * *
43797659 CTATCCTTTA-CTGGC-ATTTTCCTTAAACGCCACTAATTATAATA-TACATCAAGACCAAAAC
1 -TATACTTTAGC-GGCGATTTTAATCAAACGCCACTAATTCTAATACT-CCTAAAGACCAAAAC
43797720 GGAGCGTTTT
Statistics
Matches: 263, Mismatches: 21, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
227 5 0.02
228 238 0.90
229 20 0.08
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (228 bp):
TATACTTTAGCGGCGATTTTAATCAAACGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGATATACTTTAGCGGCGT
TTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTGCGTTTTGGTTAAGATG
ATTTGAGGCGCATCCCACAAACGCCACTGATAA
Found at i:43797702 original size:114 final size:114
Alignment explanation
Indices: 43797203--43797629 Score: 793
Period size: 114 Copynumber: 3.8 Consensus size: 114
43797193 CCGCTAATAC
* *
43797203 TATACTTCAGCGGCGTTTTTAACCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
43797268 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
*
43797317 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAATGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
*
43797382 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCACTGATGA
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
*
43797431 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAATGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
*
43797496 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAATGCCGCTGATGA
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
43797545 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
43797610 CGTTTTGGTTAAGAT-ATTTG
66 CGTTTTGGTTAAGATGATTTG
43797630 GAGGCGCTTC
Statistics
Matches: 306, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
113 5 0.02
114 301 0.98
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (114 bp):
TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
Found at i:43797827 original size:116 final size:113
Alignment explanation
Indices: 43797686--43797955 Score: 278
Period size: 114 Copynumber: 2.4 Consensus size: 113
43797676 TTTCCTTAAA
** * *
43797686 CGCCACTAATTATAATATACATCAAGACCAAAACGGAGCGTTTTGATTAGGATATC-TTGCGGCG
1 CGCCACTAATTGCAATATACATCAAGACCAAAACGCAGCGTTTTGATTA--ACATCGTTGCGGCG
* ** * * *
43797750 TTTAATGC-TATGCGCCGCTAATACAATACATTAGCGGCGTTTTATTTATAAG
64 CTT--CCCATAAGCGCCGCTAATACAATACATTACCGGCGTTTT-TTCATAAG
* * *
43797802 CGCCACTAATTGCAATATACATCAAGACC-AAACTCTGCGTTTTGGTTAACATCGTTTGCGGCGC
1 CGCCACTAATTGCAATATACATCAAGACCAAAACGCAGCGTTTTGATTAACATCG-TTGCGGCGC
* * *
43797866 TTCCCATAAGCGCCGCTAATACTATACATTACCGGTGTTTTTTCGTAAG
65 TTCCCATAAGCGCCGCTAATACAATACATTACCGGCGTTTTTTCATAAG
* * *
43797915 CGCCAC-AAATGCCAATATACATCAAGACCAGAACGCTGCGT
1 CGCCACTAATTG-CAATATACATCAAGACCAAAACGCAGCGT
43797956 GTTGGTCTTG
Statistics
Matches: 130, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
112 4 0.03
113 34 0.26
114 40 0.31
115 25 0.19
116 27 0.21
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (113 bp):
CGCCACTAATTGCAATATACATCAAGACCAAAACGCAGCGTTTTGATTAACATCGTTGCGGCGCT
TCCCATAAGCGCCGCTAATACAATACATTACCGGCGTTTTTTCATAAG
Found at i:43815182 original size:5 final size:5
Alignment explanation
Indices: 43815167--43815199 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
43815157 AGTTGATATA
43815167 TTATCT TTATT TTATT TTATT TTATT TTATT TT
1 TTAT-T TTATT TTATT TTATT TTATT TTATT TT
43815200 CTCAAAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:43819847 original size:27 final size:27
Alignment explanation
Indices: 43819815--43819869 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
43819805 GTACAATATA
* *
43819815 TGTGGCAAAGCCACCAGTAATAGTAAT
1 TGTGGCAAAGCCACCAGAAACAGTAAT
43819842 TGTGGCAAAGCCACCAGAAACAGTAAT
1 TGTGGCAAAGCCACCAGAAACAGTAAT
43819869 T
1 T
43819870 CTTCCATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (27 bp):
TGTGGCAAAGCCACCAGAAACAGTAAT
Found at i:43820036 original size:27 final size:27
Alignment explanation
Indices: 43819997--43820116 Score: 127
Period size: 27 Copynumber: 4.5 Consensus size: 27
43819987 ACCCTAACGG
*
43819997 GGGTATTAT-GGTAATTTTACCCATCGA
1 GGGTATT-TCGGTAATTTTACCCATTGA
* *
43820024 GGGTGTTTCGGTAATTTTA-CCATTAA
1 GGGTATTTCGGTAATTTTACCCATTGA
* ** *
43820050 AGGTATTTCGAAAATTTTACCCATTGG
1 GGGTATTTCGGTAATTTTACCCATTGA
* * *
43820077 GGGTATTTCAGTAAGTTTACCTATTGA
1 GGGTATTTCGGTAATTTTACCCATTGA
43820104 GGGTATTTCGGTA
1 GGGTATTTCGGTA
43820117 TAGTTAACAA
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
26 21 0.28
27 53 0.72
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCCATTGA
Found at i:43820066 original size:53 final size:54
Alignment explanation
Indices: 43820009--43820113 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 54
43819999 GTATTATGGT
* * *
43820009 AATTTTACCCATCGAGGGTGTTTCGGTAATTTTACC-ATTAAAGGTATTTCGAA
1 AATTTTACCCATCGAGGGTATTTCAGTAAGTTTACCTATTAAAGGTATTTCGAA
* * * *
43820062 AATTTTACCCATTGGGGGTATTTCAGTAAGTTTACCTATTGAGGGTATTTCG
1 AATTTTACCCATCGAGGGTATTTCAGTAAGTTTACCTATTAAAGGTATTTCG
43820114 GTATAGTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
53 31 0.70
54 13 0.30
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (54 bp):
AATTTTACCCATCGAGGGTATTTCAGTAAGTTTACCTATTAAAGGTATTTCGAA
Found at i:43835153 original size:38 final size:39
Alignment explanation
Indices: 43835020--43835153 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
43835010 CGTTTGGACA
* *
43835020 AAAAACGCCACTAAAAATTGAA-CATTAGCGGCGCCTT-T-A
1 AAAAACGCCGCTAAAAA-T-AAGCATTAGCGGCG-CTTATCC
* * **
43835059 AAAAATGTCGCTAAAGGTAGAGCATTAGCGGCGCTTATCC
1 AAAAACGCCGCTAAAAATA-AGCATTAGCGGCGCTTATCC
* *
43835099 AAAAACGCCGCTAAAAATAAGCATTAGCGGCG-TTTTCT
1 AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTATCC
43835137 AAAAAGCGCCGC-AAAAA
1 AAAAA-CGCCGCTAAAAA
43835154 GTCTAAGCCA
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
37 1 0.01
38 19 0.24
39 43 0.55
40 15 0.19
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTATCC
Found at i:43835250 original size:41 final size:40
Alignment explanation
Indices: 43835193--43835469 Score: 304
Period size: 41 Copynumber: 6.8 Consensus size: 40
43835183 TTTTTGGGGG
43835193 CTTTAGCGGCGTTTTTGAATAAACGCCGCTAATGCTCTGGC
1 CTTTAGCGGCGTTTTTGAA-AAACGCCGCTAATGCTCTGGC
* *
43835234 CTTTAGCGGCGTTTTTGAGTAAGCGCCGCTAATGCTCTGGC
1 CTTTAGCGGCGTTTTTGA-AAAACGCCGCTAATGCTCTGGC
* * *
43835275 CTTTAGCGGCGTTTATTCAAAAGCGCCGCTAATGCTCTGTC
1 CTTTAGCGGCGTTT-TTGAAAAACGCCGCTAATGCTCTGGC
* **
43835316 TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTATC
1 CTTTAGCGGCGTTTTTGAAAAA-CGCCGCTAATGCTCTGGC
* * * **
43835357 TTTTAGCGGCGTTTTTGAAGAACTGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAC-GCCGCTAATGCTCTGGC
* * * * *
43835398 CTTTAGCGGCATTTTT-AAAGAAGCGTCGGTATTGCTGTGGC
1 CTTTAGCGGCGTTTTTGAAA-AA-CGCCGCTAATGCTCTGGC
*
43835439 CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTA
1 CTTTAGCGGCGTTTTTGAAAAA-CGCCGCTA
43835470 GTAATAATAA
Statistics
Matches: 202, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
40 9 0.04
41 186 0.92
42 7 0.03
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.32
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTGAAAAACGCCGCTAATGCTCTGGC
Found at i:43835422 original size:123 final size:123
Alignment explanation
Indices: 43835193--43835469 Score: 355
Period size: 123 Copynumber: 2.3 Consensus size: 123
43835183 TTTTTGGGGG
*
43835193 CTTTAGCGGCGTTTTTGAATAAA-CGCCGCTAATGCTCTGGCCTTTAGCGGCGTTTTTGAGTAAG
1 CTTTAGCGGCGTTTTTGAA-AAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTGAGTAAG
* * * * *
43835257 CGCCGCTAATGCTCTGGCCTTTAGCGGCGTTTATTCAAAAGCGCCGCTAATGCTCTGTC
65 CGCCGCTAATGCTCAGACCTTTAGCGGCATTTATTAAAAAGCGCCGCTAATGCTCTGGC
* * *
43835316 TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTATCTTTTAGCGGCGTTTTTGAAG-AA-
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTG-AGTAAG
* * * * *
43835379 CTGCCGCTAATGCTCAGATCTTTAGCGGCATTT-TTAAAGAAGCGTCGGTATTGCTGTGGC
65 C-GCCGCTAATGCTCAGACCTTTAGCGGCATTTATTAAA-AAGCGCCGCTAATGCTCTGGC
*
43835439 CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTA
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTA
43835470 GTAATAATAA
Statistics
Matches: 134, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
122 8 0.06
123 124 0.93
124 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.32
Consensus pattern (123 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTGAGTAAGC
GCCGCTAATGCTCAGACCTTTAGCGGCATTTATTAAAAAGCGCCGCTAATGCTCTGGC
Found at i:43836403 original size:14 final size:15
Alignment explanation
Indices: 43836366--43836408 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
43836356 GGGGATTATA
43836366 TATGGATTT-AGGGAT
1 TATGGATTTAAGGG-T
43836381 TATGG-TTTAAGGGT
1 TATGGATTTAAGGGT
43836395 TA-GGATTTAAGGGT
1 TATGGATTTAAGGGT
43836409 CGGGTTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.08
14 15 0.58
15 9 0.35
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.40
Consensus pattern (15 bp):
TATGGATTTAAGGGT
Found at i:43837485 original size:7 final size:7
Alignment explanation
Indices: 43837473--43837591 Score: 67
Period size: 7 Copynumber: 15.9 Consensus size: 7
43837463 GATATAAGGT
43837473 TTAGGGG
1 TTAGGGG
43837480 TTAGGGG
1 TTAGGGG
*
43837487 TTAGGGAT
1 TTAGGG-G
43837495 TTAGGGG
1 TTAGGGG
* **
43837502 CTATGAGAT
1 TTA-G-GGG
43837511 TTAGGGG
1 TTAGGGG
43837518 TTAGGGG
1 TTAGGGG
**
43837525 TTATGGAT
1 TTA-GGGG
*
43837533 TTAGGGAT
1 TTAGGG-G
43837541 TTAGGGG
1 TTAGGGG
* *
43837548 CTAGGAGA
1 TTAGG-GG
43837556 TCTAGGGG
1 T-TAGGGG
43837564 TTAGGGG
1 TTAGGGG
*
43837571 TTAGGGAT
1 TTAGGG-G
*
43837579 TTAGGGT
1 TTAGGGG
43837586 TTAGGG
1 TTAGGG
43837592 TGTCAATTAA
Statistics
Matches: 87, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
7 51 0.59
8 29 0.33
9 7 0.08
ACGTcount: A:0.20, C:0.03, G:0.45, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:43837523 original size:23 final size:23
Alignment explanation
Indices: 43837495--43837591 Score: 108
Period size: 23 Copynumber: 4.3 Consensus size: 23
43837485 GGTTAGGGAT
43837495 TTAGGGGCTATGAGATTTAGGGG
1 TTAGGGGCTATGAGATTTAGGGG
* *
43837518 TTAGGGGTTATG-GATTTAGGGAT
1 TTAGGGGCTATGAGATTTAGGG-G
* *
43837541 TTAGGGGCTAGGAGATCTAGGGG
1 TTAGGGGCTATGAGATTTAGGGG
* * *
43837564 TTAGGGGTTA-GGGATTTAGGGT
1 TTAGGGGCTATGAGATTTAGGGG
43837586 TTAGGG
1 TTAGGG
43837592 TGTCAATTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
22 24 0.39
23 30 0.48
24 8 0.13
ACGTcount: A:0.21, C:0.03, G:0.44, T:0.32
Consensus pattern (23 bp):
TTAGGGGCTATGAGATTTAGGGG
Found at i:43837542 original size:46 final size:45
Alignment explanation
Indices: 43837473--43837591 Score: 177
Period size: 46 Copynumber: 2.6 Consensus size: 45
43837463 GATATAAGGT
** * *
43837473 TTAGGGGTTAGGGGTTAGGGATTTAGGGGCTATGAGATTTAGGGG
1 TTAGGGGTTAGGATTTAGGGATTTAGGGGCTAGGAGATCTAGGGG
43837518 TTAGGGGTTATGGATTTAGGGATTTAGGGGCTAGGAGATCTAGGGG
1 TTAGGGGTTA-GGATTTAGGGATTTAGGGGCTAGGAGATCTAGGGG
43837564 TTAGGGGTTAGGGATTTAGGG-TTTAGGG
1 TTAGGGGTTA-GGATTTAGGGATTTAGGG
43837592 TGTCAATTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
45 17 0.25
46 51 0.75
ACGTcount: A:0.20, C:0.03, G:0.45, T:0.32
Consensus pattern (45 bp):
TTAGGGGTTAGGATTTAGGGATTTAGGGGCTAGGAGATCTAGGGG
Found at i:43837592 original size:7 final size:7
Alignment explanation
Indices: 43837452--43837592 Score: 59
Period size: 7 Copynumber: 19.0 Consensus size: 7
43837442 TATATGATTA
43837452 TTAGGGT
1 TTAGGGT
43837459 TT-GGGAT
1 TTAGGG-T
* *
43837466 ATAAGGT
1 TTAGGGT
*
43837473 TTAGGGG
1 TTAGGGT
*
43837480 TTAGGGG
1 TTAGGGT
43837487 TTAGGGAT
1 TTAGGG-T
*
43837495 TTAGGGG
1 TTAGGGT
* *
43837502 CTATGAGAT
1 TTA-G-GGT
*
43837511 TTAGGGG
1 TTAGGGT
*
43837518 TTAGGGG
1 TTAGGGT
*
43837525 TTATGGAT
1 TTA-GGGT
43837533 TTAGGGAT
1 TTAGGG-T
*
43837541 TTAGGGG
1 TTAGGGT
*
43837548 CTAGGAGAT
1 TTAGG-G-T
* *
43837557 CTAGGGG
1 TTAGGGT
*
43837564 TTAGGGG
1 TTAGGGT
43837571 TTAGGGAT
1 TTAGGG-T
43837579 TTAGGGT
1 TTAGGGT
43837586 TTAGGGT
1 TTAGGGT
43837593 GTCAATTAAT
Statistics
Matches: 102, Mismatches: 22, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
6 3 0.03
7 61 0.60
8 30 0.29
9 8 0.08
ACGTcount: A:0.21, C:0.02, G:0.44, T:0.33
Consensus pattern (7 bp):
TTAGGGT
Found at i:43841018 original size:29 final size:30
Alignment explanation
Indices: 43840977--43841036 Score: 68
Period size: 33 Copynumber: 1.9 Consensus size: 30
43840967 GATTAGTTTA
*
43840977 TTCGGTTTAATG-TGAATAAATTATCGATT
1 TTCGATTTAATGATGAATAAATTATCGATT
*
43841006 TTCGATTTTATGTCAATGAATAAATTATCGA
1 TTCGATTTAATG---ATGAATAAATTATCGA
43841037 CGTTATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 10 0.40
33 15 0.60
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (30 bp):
TTCGATTTAATGATGAATAAATTATCGATT
Found at i:43841138 original size:11 final size:11
Alignment explanation
Indices: 43841118--43841150 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
43841108 ATTGATTGAC
*
43841118 TGTCAGTGAAT
1 TGTCAATGAAT
43841129 TGTCAATGAA-
1 TGTCAATGAAT
43841139 TGTCAATGAAT
1 TGTCAATGAAT
43841150 T
1 T
43841151 ATTAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (11 bp):
TGTCAATGAAT
Found at i:43841231 original size:13 final size:13
Alignment explanation
Indices: 43841185--43841276 Score: 73
Period size: 13 Copynumber: 6.9 Consensus size: 13
43841175 TATAACTTAC
43841185 ATTACTTAAATAT
1 ATTACTTAAATAT
* *
43841198 ATTAATTACTAAAAT
1 ATTACTTA--AATAT
43841213 -TTACTTAAATAT
1 ATTACTTAAATAT
*
43841225 ATTACTTAAATAC
1 ATTACTTAAATAT
* *
43841238 ATTACTT-ACTAGA
1 ATTACTTAAATA-T
43841251 ATTGGA-TTAAATAT
1 ATT--ACTTAAATAT
43841265 ATTACTTAAATA
1 ATTACTTAAATA
43841277 CATGACTTAC
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
12 8 0.13
13 35 0.56
14 11 0.18
15 8 0.13
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (13 bp):
ATTACTTAAATAT
Found at i:43841247 original size:40 final size:39
Alignment explanation
Indices: 43841168--43841423 Score: 206
Period size: 40 Copynumber: 6.5 Consensus size: 39
43841158 TATATATTTT
* * * *
43841168 TAAAATTTA-TAACTTACATTACTTAAATATATTAATTAC
1 TAAAATTTATTAA-ATATATTACTTAAATACATTACTTAC
43841207 TAAAATTTACTTAAATATATTACTTAAATACATTACTTAC
1 TAAAATTTA-TTAAATATATTACTTAAATACATTACTTAC
* * *
43841247 TAGAATTGGATTAAATATATTACTTAAATACATGACTTAC
1 TAAAATT-TATTAAATATATTACTTAAATACATTACTTAC
**
43841287 TAAAA-TTA--AAGTATATATTACATTACTTACATTACTTAC
1 TAAAATTTATTAA--ATATATTAC-TTAAATACATTACTTAC
* * *
43841326 TAAAA--TA-T-ATTACATTACTTAAATATATTACTTAC
1 TAAAATTTATTAAATATATTACTTAAATACATTACTTAC
* * * *
43841361 AAAAATTTA-TAACTTACATTACTTAAATATATTACATTAC
1 TAAAATTTATTAA-ATATATTACTTAAATACATTAC-TTAC
*
43841401 TTAAAATTTATATATATATATTA
1 -TAAAATTTAT-TAAATATATTA
43841424 AAAATTTATA
Statistics
Matches: 180, Mismatches: 22, Indels: 27
0.79 0.10 0.12
Matches are distributed among these distances:
35 18 0.10
36 9 0.05
37 3 0.02
38 14 0.08
39 51 0.28
40 65 0.36
41 12 0.07
42 6 0.03
43 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (39 bp):
TAAAATTTATTAAATATATTACTTAAATACATTACTTAC
Found at i:43841341 original size:22 final size:21
Alignment explanation
Indices: 43841313--43841403 Score: 72
Period size: 22 Copynumber: 4.6 Consensus size: 21
43841303 ATTACATTAC
43841313 TTACATTACTTACTAAAATATA
1 TTACATTACTTA-TAAAATATA
43841335 TTACATTAC-T-T-AAATATA
1 TTACATTACTTATAAAATATA
*
43841353 TTAC-TTAC--A-AAAATTTA
1 TTACATTACTTATAAAATATA
* *
43841370 TAAC-TTACATTACTTAAATATA
1 TTACATTAC-TTA-TAAAATATA
43841392 TTACATTACTTA
1 TTACATTACTTA
43841404 AAATTTATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
17 17 0.30
18 11 0.20
19 1 0.02
20 1 0.02
21 1 0.02
22 21 0.38
23 4 0.07
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (21 bp):
TTACATTACTTATAAAATATA
Found at i:43841343 original size:18 final size:18
Alignment explanation
Indices: 43841317--43841407 Score: 96
Period size: 18 Copynumber: 4.9 Consensus size: 18
43841307 CATTACTTAC
43841317 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
*
43841334 ATTACATTACTTAAATAT
1 ATTACATTACTAAAATAT
*
43841352 ATTAC-TTACAAAAATTTAT
1 ATTACATTACTAAAA--TAT
*
43841371 AACTTACATTACTTAAATAT
1 -A-TTACATTACTAAAATAT
43841391 ATTACATTACTTAAAAT
1 ATTACATTAC-TAAAAT
43841408 TTATATATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
17 12 0.20
18 25 0.41
19 9 0.15
20 4 0.07
21 4 0.07
22 7 0.11
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:43841366 original size:17 final size:17
Alignment explanation
Indices: 43841317--43841378 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
43841307 CATTACTTAC
*
43841317 ATTACTTACTAAAATAT
1 ATTACTTACAAAAATAT
**
43841334 ATTACATTACTTAAATAT
1 ATTAC-TTACAAAAATAT
*
43841352 ATTACTTACAAAAATTT
1 ATTACTTACAAAAATAT
*
43841369 ATAACTTACA
1 ATTACTTACA
43841379 TTACTTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
17 23 0.59
18 16 0.41
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTACTTACAAAAATAT
Found at i:43841545 original size:27 final size:27
Alignment explanation
Indices: 43841512--43841563 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
43841502 TTGTAAATGC
43841512 TATTTTTAAATATTAAAACCTATATGT
1 TATTTTTAAATATTAAAACCTATATGT
43841539 TATTTTTAAATATTAAAACCTATAT
1 TATTTTTAAATATTAAAACCTATAT
43841564 TTCTAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (27 bp):
TATTTTTAAATATTAAAACCTATATGT
Found at i:43841663 original size:121 final size:121
Alignment explanation
Indices: 43841535--43841805 Score: 499
Period size: 121 Copynumber: 2.2 Consensus size: 121
43841525 TAAAACCTAT
43841535 ATGTTATTTTTAAATATTAAAACCTATATTTCTAATATATCACCCCATATATGGTATGGATATAT
1 ATGTTATTTTTAAATATTAAAACCTATATTTCTAATATATCACCCCATATATGGTATGGATATAT
*
43841600 AACCTATATTTCAATTTTATT-GTCAATAAATTTTATAATTTTAAAAATAATTGTAA
66 AACCTATATTTCAATTTTATTAG-AAATAAATTTTATAATTTTAAAAATAATTGTAA
*
43841656 ATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCACCCCATATATGGTATGGATATAT
1 ATGTTATTTTTAAATATTAAAACCTATATTTCTAATATATCACCCCATATATGGTATGGATATAT
43841721 AACCTATATTTCAATTTTATTAGAAATAAATTTTATAATTTTAAAAATAATTGTAA
66 AACCTATATTTCAATTTTATTAGAAATAAATTTTATAATTTTAAAAATAATTGTAA
*
43841777 ATGCTATTTTTAAATATTAAAACCTATAT
1 ATGTTATTTTTAAATATTAAAACCTATAT
43841806 GTTATTTTTA
Statistics
Matches: 146, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
121 145 0.99
122 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.45
Consensus pattern (121 bp):
ATGTTATTTTTAAATATTAAAACCTATATTTCTAATATATCACCCCATATATGGTATGGATATAT
AACCTATATTTCAATTTTATTAGAAATAAATTTTATAATTTTAAAAATAATTGTAA
Found at i:43841721 original size:148 final size:145
Alignment explanation
Indices: 43841433--43841695 Score: 458
Period size: 148 Copynumber: 1.8 Consensus size: 145
43841423 AAAAATTTAT
43841433 ATATATGGTATGGATATATAACCTATATTTCAATTTTATTGTCAATAAATTTTATAATTTTAAAA
1 ATATATGGTATGGATATATAACCTATATTTCAATTTTATTGTCAATAAATTTTATAATTTTAAAA
43841498 ATAATTGTAAATGCTATTTTTAAATATTAAAACCTATATGTTATTTTTAAATATTAAAACCTATA
66 ATAATTGTAAATGCTATTTTTAAATATTAAAACC-ATA--TTATTTTTAAATATTAAAACCTATA
*
43841563 TTTCTAATATATCACCCC
128 TTTCGAATATATCACCCC
43841581 ATATATGGTATGGATATATAACCTATATTTCAATTTTATTGTCAATAAATTTTATAATTTTAAAA
1 ATATATGGTATGGATATATAACCTATATTTCAATTTTATTGTCAATAAATTTTATAATTTTAAAA
*
43841646 ATAATTGTAAATGTTATTTTTAAATATTAAAACC-TA-TATTTTTAATATAT
66 ATAATTGTAAATGCTATTTTTAAATATTAAAACCATATTATTTTTAA-ATAT
43841696 CACCCCATAT
Statistics
Matches: 113, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
143 9 0.08
144 4 0.04
146 2 0.02
148 98 0.87
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (145 bp):
ATATATGGTATGGATATATAACCTATATTTCAATTTTATTGTCAATAAATTTTATAATTTTAAAA
ATAATTGTAAATGCTATTTTTAAATATTAAAACCATATTATTTTTAAATATTAAAACCTATATTT
CGAATATATCACCCC
Found at i:43841814 original size:27 final size:27
Alignment explanation
Indices: 43841781--43841832 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
43841771 TTGTAAATGC
43841781 TATTTTTAAATATTAAAACCTATATGT
1 TATTTTTAAATATTAAAACCTATATGT
43841808 TATTTTTAAATATTAAAACCTATAT
1 TATTTTTAAATATTAAAACCTATAT
43841833 TTCTAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (27 bp):
TATTTTTAAATATTAAAACCTATATGT
Found at i:43841918 original size:25 final size:25
Alignment explanation
Indices: 43841889--43842179 Score: 143
Period size: 25 Copynumber: 11.5 Consensus size: 25
43841879 TCAATTTTTA
*
43841889 ATAACTTACATAATACACAACTTAC
1 ATAACTTACATAATACATAACTTAC
* *
43841914 ATAACTTAAATAGAAACGCATAA--TAC
1 ATAACTTACATA-ATA--CATAACTTAC
** *
43841940 ATAACTTTGATAACTAACATTA--TAC
1 ATAACTTACATAA-T-ACATAACTTAC
* *
43841965 ACAACTTACATAATACATTACTTAC
1 ATAACTTACATAATACATAACTTAC
* * *
43841990 TTAACATACATAGCCTACATAACTTAC
1 ATAACTTACATA--ATACATAACTTAC
* ** *
43842017 ATAATTTACATGTTACATAACTTAA
1 ATAACTTACATAATACATAACTTAC
**
43842042 ATAACTTACATAATACATAACTTTG
1 ATAACTTACATAATACATAACTTAC
* * *
43842067 ATAACTAACATTATACACAACTTAC
1 ATAACTTACATAATACATAACTTAC
* * *
43842092 ATAA--TACATTACTTACTTAACATAC
1 ATAACTTACA-TA-ATACATAACTTAC
* * *
43842117 ATAGCCTACATAACTTACATAATTTAC
1 ATAACTTACATAA--TACATAACTTAC
* *
43842144 AT--GTTACATAACTTAAATAACTTAC
1 ATAACTTACATAA--TACATAACTTAC
43842169 ATAA--TACATAA
1 ATAACTTACATAA
43842180 CTTTGACAAC
Statistics
Matches: 203, Mismatches: 46, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
23 9 0.04
24 2 0.01
25 136 0.67
26 17 0.08
27 35 0.17
28 4 0.02
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (25 bp):
ATAACTTACATAATACATAACTTAC
Found at i:43842180 original size:25 final size:25
Alignment explanation
Indices: 43841995--43842297 Score: 126
Period size: 25 Copynumber: 12.0 Consensus size: 25
43841985 CTTACTTAAC
* *
43841995 ATACATAGCCTACATAACTTACATA
1 ATACATAACTTACATAACTTACATA
* *
43842020 ATTTACAT--GTTACATAACTTAAATA
1 A--TACATAACTTACATAACTTACATA
**
43842045 ACTTACATAA--TACATAACTTTGATA
1 A--TACATAACTTACATAACTTACATA
* *
43842070 ACTAACATTA--TACACAACTTACATA
1 A-T-ACATAACTTACATAACTTACATA
* * *
43842095 ATACATTACTTACTTAACATACATA
1 ATACATAACTTACATAACTTACATA
* * *
43842120 GCCTACATAACTTACATAATTTACATG
1 --ATACATAACTTACATAACTTACATA
* *
43842147 TTACATAACTTAAATAACTTACATA
1 ATACATAACTTACATAACTTACATA
** * * *
43842172 ATACATAACTTTGACAACTAACATT
1 ATACATAACTTACATAACTTACATA
*
43842197 ATACACAACTTACATAA--TACATTA
1 ATACATAACTTACATAACTTACA-TA
* * * * *
43842221 CTTACTTAACATACATAGCCTACATA
1 -ATACATAACTTACATAACTTACATA
* *
43842247 ACTTACATAATTTACAT--GTTACATA
1 A--TACATAACTTACATAACTTACATA
*
43842272 ACTTAAATAACTTACATAA--TACATA
1 A--TACATAACTTACATAACTTACATA
43842297 A
1 A
43842298 CTTTGACAAC
Statistics
Matches: 212, Mismatches: 49, Indels: 34
0.72 0.17 0.12
Matches are distributed among these distances:
23 9 0.04
24 3 0.01
25 159 0.75
26 2 0.01
27 39 0.18
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (25 bp):
ATACATAACTTACATAACTTACATA
Found at i:43842211 original size:93 final size:91
Alignment explanation
Indices: 43842030--43842275 Score: 210
Period size: 93 Copynumber: 2.7 Consensus size: 91
43842020 ATTTACATGT
* * ** * * *
43842030 TACATAACTTAAATAACTTACATAATACATAACTTTGATAACTAACATTATACACAAC-TTACAT
1 TACATAACTTACATAACTTACATGATACATAACTTAAATAACTTACATAATACATAACTTTACAT
** *
43842094 AATACATTACTTACTTAACATACATAGCC
66 AATACATTAC-TACACAACATACATA--A
* *
43842123 TACATAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGACA
1 TACATAACTTACATAACTTACATGATACATAACTTAAATAACTTACATAATACATAACTTT-ACA
* *
43842188 -ACTAACATTA-TACACAACTTACATAA
65 TAAT-ACATTACTACACAACATACATAA
* * * * * * **
43842214 TACATTACTTACTTAACATACATAGCCTACATAACTTACATAATTTACATGTTACATAACTT
1 TACATAACTTACATAACTTACAT-G-ATACATAACTTAAATAACTTACATAATACATAACTT
43842276 AAATAACTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
91 19 0.15
92 1 0.01
93 92 0.74
94 4 0.03
95 9 0.07
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (91 bp):
TACATAACTTACATAACTTACATGATACATAACTTAAATAACTTACATAATACATAACTTTACAT
AATACATTACTACACAACATACATAA
Found at i:43842308 original size:25 final size:25
Alignment explanation
Indices: 43842266--43842326 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
43842256 ATTTACATGT
* *
43842266 TACATAACTTAAATAACTTACATAA
1 TACATAACTTAAACAACTAACATAA
** *
43842291 TACATAACTTTGACAACTAACATTA
1 TACATAACTTAAACAACTAACATAA
*
43842316 TACACAACTTA
1 TACATAACTTA
43842327 CATAATACAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.31
Consensus pattern (25 bp):
TACATAACTTAAACAACTAACATAA
Found at i:43842371 original size:118 final size:118
Alignment explanation
Indices: 43841889--43842348 Score: 812
Period size: 118 Copynumber: 3.9 Consensus size: 118
43841879 TCAATTTTTA
** ** **** *
43841889 ATAACTTACATAATACACAACTTACATAACTTAAATAGAAACGCATAATACATAACTTTGATAAC
1 ATAACTTACATAATTTACATGTTACATAACTTAAATA-ACTTACATAATACATAACTTTGACAAC
43841954 TAACATTATACACAACTTACATAATACATTACTTACTTAACATACATAGCCTAC
65 TAACATTATACACAACTTACATAATACATTACTTACTTAACATACATAGCCTAC
*
43842008 ATAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGATAACT
1 ATAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGACAACT
43842073 AACATTATACACAACTTACATAATACATTACTTACTTAACATACATAGCCTAC
66 AACATTATACACAACTTACATAATACATTACTTACTTAACATACATAGCCTAC
43842126 ATAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGACAACT
1 ATAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGACAACT
43842191 AACATTATACACAACTTACATAATACATTACTTACTTAACATACATAGCCTAC
66 AACATTATACACAACTTACATAATACATTACTTACTTAACATACATAGCCTAC
43842244 ATAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGACAACT
1 ATAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGACAACT
*
43842309 AACATTATACACAACTTACATAATACATTACTTACATAAC
66 AACATTATACACAACTTACATAATACATTACTTACTTAAC
43842349 TTAAAGCATA
Statistics
Matches: 331, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
118 298 0.90
119 33 0.10
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (118 bp):
ATAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGACAACT
AACATTATACACAACTTACATAATACATTACTTACTTAACATACATAGCCTAC
Found at i:43847899 original size:66 final size:65
Alignment explanation
Indices: 43847792--43847962 Score: 218
Period size: 66 Copynumber: 2.6 Consensus size: 65
43847782 GAGCAAGTTA
* * *
43847792 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAACAGCGAGAGAAGCTGAGGTTCAATAAAAG-TATGAAGAACTCCA
43847856 G
65 G
* *
43847857 CTACAACTGAAAGCAGATGCAACAGCGAGAGAAGCTGAGGTTCAATGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAACAGCGAGAGAAGCTGAGGTTCAATAAAAGTATGAAGAACTCCA
43847922 G
65 G
* ** * *
43847923 CAGCAGCTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAACAGCGAGAGAAGCTGAGG
43847963 CGGTAGCAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 2 0.02
66 86 0.93
67 4 0.04
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAACAGCGAGAGAAGCTGAGGTTCAATAAAAGTATGAAGAACTCCAG
Found at i:43848045 original size:21 final size:21
Alignment explanation
Indices: 43847933--43848045 Score: 91
Period size: 21 Copynumber: 5.4 Consensus size: 21
43847923 CAGCAGCTTA
* * * *
43847933 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
* * * *
43847954 AAGCAGAGGCGGTAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
* *
43847975 AAGTACAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* ** *
43847996 AAGCAGAAGCTAAAGTGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
43848017 AAACAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
43848038 AAGCAGAG
1 AAGCAGAG
43848046 CAGCGTTAAA
Statistics
Matches: 72, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.37, C:0.16, G:0.41, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:43848505 original size:43 final size:43
Alignment explanation
Indices: 43848416--43848803 Score: 214
Period size: 43 Copynumber: 9.0 Consensus size: 43
43848406 GTTTGTAGGG
* * * *
43848416 TAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAACGCCAC
1 TAAAGATCAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCGC
* * *
43848459 TAAAGATCATGGTCTTTAGCGGCGTTTGTGGGGAAAGCACCGC
1 TAAAGATCAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCGC
* * * * * *
43848502 TAAAGATTAGGTTCTTTAGTGGTGTTTGTGGTCG-AAGCGCCGT
1 TAAAGATCAGGGTCTTTAGCGGCGTTTGTGG-AGAAAGCGCCGC
* * * *
43848545 TATAGATCAGGGTCTATT-GCGGCATTTGAGGGGAAAGCGCCGC
1 TAAAGATCAGGGTCT-TTAGCGGCGTTTGTGGAGAAAGCGCCGC
* * * * * * ** *
43848588 TAAAGATTAGGTTCTTTCGTGGCATTTCTGGTCAAAGTGCCGC
1 TAAAGATCAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCGC
* * * * * *
43848631 TATAGATCAGGGTCTATT-GCGGCGTTTGAGAAAAAAACACCGC
1 TAAAGATCAGGGTCT-TTAGCGGCGTTTGTGGAGAAAGCGCCGC
* ** * * * ** *
43848674 TAAAGACCCTGATCTTTAGCGGCGCTTCTCCCA-AAAACGCCGC
1 TAAAGATCAGGGTCTTTAGCGGCGTTTGT-GGAGAAAGCGCCGC
* * ** *
43848717 TAAAGATCAGGGTCTTTAGCAGCG-CT-TCCACTAAAGCGCCGC
1 TAAAGATCAGGGTCTTTAGCGGCGTTTGTGGA-GAAAGCGCCGC
* *** *
43848759 TAAAGGTCTTAGTCTTTAGCGGCGTTTGTGCTAG-AAGCGCCGC
1 TAAAGATCAGGGTCTTTAGCGGCGTTTGTG-GAGAAAGCGCCGC
43848802 TA
1 TA
43848804 TAGACCAACA
Statistics
Matches: 260, Mismatches: 73, Indels: 24
0.73 0.20 0.07
Matches are distributed among these distances:
40 3 0.01
41 1 0.00
42 34 0.13
43 214 0.82
44 7 0.03
45 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (43 bp):
TAAAGATCAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCGC
Found at i:43848567 original size:86 final size:86
Alignment explanation
Indices: 43848416--43848679 Score: 287
Period size: 86 Copynumber: 3.1 Consensus size: 86
43848406 GTTTGTAGGG
* * * * * ** * * * *
43848416 TAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAACGCCACTAAAGATCATGGTCT-TTAGCG
1 TAAAGATTAGGTTCTTTAGTGGCATTTCTGGTCAAAGCGCCGCTATAGATCAGGGTCTATT-GCG
*
43848480 GCGTTTGTGGGGAAAGCACCGC
65 GCGTTTGAGGGGAAAGCACCGC
** * * *
43848502 TAAAGATTAGGTTCTTTAGTGGTGTTTGTGGTCGAAGCGCCGTTATAGATCAGGGTCTATTGCGG
1 TAAAGATTAGGTTCTTTAGTGGCATTTCTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTGCGG
* *
43848567 CATTTGAGGGGAAAGCGCCGC
66 CGTTTGAGGGGAAAGCACCGC
* *
43848588 TAAAGATTAGGTTCTTTCGTGGCATTTCTGGTCAAAGTGCCGCTATAGATCAGGGTCTATTGCGG
1 TAAAGATTAGGTTCTTTAGTGGCATTTCTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTGCGG
*** *
43848653 CGTTTGAGAAAAAAACACCGC
66 CGTTTGAGGGGAAAGCACCGC
43848674 TAAAGA
1 TAAAGA
43848680 CCCTGATCTT
Statistics
Matches: 149, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
86 147 0.99
87 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (86 bp):
TAAAGATTAGGTTCTTTAGTGGCATTTCTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTGCGG
CGTTTGAGGGGAAAGCACCGC
Found at i:43848950 original size:22 final size:22
Alignment explanation
Indices: 43848922--43848965 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43848912 CTGCGACACT
*
43848922 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
43848944 AAAAAGCGCCGCTAAAAGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
43848966 TTTTGGTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.27, G:0.20, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:43850490 original size:15 final size:15
Alignment explanation
Indices: 43850446--43850497 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
43850436 TAATGAGTAC
43850446 TCGTGGTACGTGAGG
1 TCGTGGTACGTGAGG
* *
43850461 TCATGGTA-TTCGAGG
1 TCGTGGTACGT-GAGG
43850476 TCGTGGTACGTGAGG
1 TCGTGGTACGTGAGG
*
43850491 GCGTGGT
1 TCGTGGT
43850498 GGACATCATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (15 bp):
TCGTGGTACGTGAGG
Found at i:43853627 original size:29 final size:29
Alignment explanation
Indices: 43853594--43853762 Score: 221
Period size: 29 Copynumber: 5.8 Consensus size: 29
43853584 AATGGTTAGA
* *
43853594 ACCATCCCTTTTCATATTTGATGGTCATC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* *
43853623 ACCATCCCTTGTCATATTCGATGGTTGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* * ***
43853652 ACCAACCCTTTTCATATTCAATGGTCAAA
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* *
43853681 ACTATCCCTTTTCATATTCGATGGCCGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
43853710 ACCATCCCTTTTCATATTCGATGGTCGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* *
43853739 ACCATCTCTTTTCATATTCAATGG
1 ACCATCCCTTTTCATATTCGATGG
43853763 GCATCGATAC
Statistics
Matches: 118, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 118 1.00
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTCGATGGTCGTC
Found at i:43853729 original size:87 final size:87
Alignment explanation
Indices: 43853583--43853762 Score: 270
Period size: 87 Copynumber: 2.1 Consensus size: 87
43853573 GTGTGCTAAG
* * * *
43853583 CAATGGTTAGAACCATCCCTTTTCATATTTGATGGTCATCACCATCCCTTGTCATATTCGATGGT
1 CAATGGTCAAAACCATCCCTTTTCATATTCGATGGCCATCACCATCCCTTGTCATATTCGATGGT
*
43853648 TGTCACCAACCCTTTTCATATT
66 CGTCACCAACCCTTTTCATATT
* * *
43853670 CAATGGTCAAAACTATCCCTTTTCATATTCGATGGCCGTCACCATCCCTTTTCATATTCGATGGT
1 CAATGGTCAAAACCATCCCTTTTCATATTCGATGGCCATCACCATCCCTTGTCATATTCGATGGT
* *
43853735 CGTCACCATCTCTTTTCATATT
66 CGTCACCAACCCTTTTCATATT
43853757 CAATGG
1 CAATGG
43853763 GCATCGATAC
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (87 bp):
CAATGGTCAAAACCATCCCTTTTCATATTCGATGGCCATCACCATCCCTTGTCATATTCGATGGT
CGTCACCAACCCTTTTCATATT
Found at i:43855633 original size:43 final size:43
Alignment explanation
Indices: 43855579--43855808 Score: 280
Period size: 43 Copynumber: 5.3 Consensus size: 43
43855569 AAGCGCCAGA
* ** *
43855579 AAAAACACCGCTAAAGACCAATCCCTTTAGCGGCACTTTTCCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* *
43855622 AAAAACGCCGCTAAAAACCAAGACCTTTAGCGGCACTTTTCCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * * *
43855665 ACAAACGCCGCTAAAGACCAAGAACTTTAACAGCGCTTTTCCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * * *
43855708 GAAAACGCCGCTAAAGACCAGGACCTTTAACAGCGCTTTTCCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * * *
43855751 ACAAACGCCACTGAAGACCAAGAACTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* *
43855794 ACAAACGTCGCTAAA
1 AAAAACGCCGCTAAA
43855809 AACATGACTT
Statistics
Matches: 162, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 162 1.00
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.19
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
Found at i:43855693 original size:86 final size:86
Alignment explanation
Indices: 43855581--43855811 Score: 309
Period size: 86 Copynumber: 2.7 Consensus size: 86
43855571 GCGCCAGAAA
* *** *
43855581 AAACACCGCTAAAGACCAATCCCTTTAGCGGCACTTTTCCCAAAAACGCCGCTAAAAACCAAGAC
1 AAACGCCGCTAAAGACCAAGAACTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAAACCAAGAC
* *
43855646 CTTTAGCGGCACTTTTCCCAC
66 CTTTAACAGCACTTTTCCCAC
* * * * *
43855667 AAACGCCGCTAAAGACCAAGAACTTTAACAGCGCTTTTCCCGAAAACGCCGCTAAAGACCAGGAC
1 AAACGCCGCTAAAGACCAAGAACTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAAACCAAGAC
*
43855732 CTTTAACAGCGCTTTTCCCAC
66 CTTTAACAGCACTTTTCCCAC
* * * *
43855753 AAACGCCACTGAAGACCAAGAACTTTAGCGGCGCTTTTCCCACAAACGTCGCTAAAAAC
1 AAACGCCGCTAAAGACCAAGAACTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAAAC
43855812 ATGACTTAAA
Statistics
Matches: 124, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 124 1.00
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.19
Consensus pattern (86 bp):
AAACGCCGCTAAAGACCAAGAACTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAAACCAAGAC
CTTTAACAGCACTTTTCCCAC
Found at i:43856032 original size:18 final size:18
Alignment explanation
Indices: 43856009--43856067 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
43855999 TTAAAACAAG
43856009 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
43856027 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
43856044 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
43856062 TTACAT
1 TTACAT
43856068 AAGTTCTGTT
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
16 4 0.14
17 7 0.25
18 13 0.46
19 4 0.14
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:43860154 original size:16 final size:16
Alignment explanation
Indices: 43860133--43860164 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43860123 AAACAAAGGG
43860133 TTTGAGATGCCTAAAC
1 TTTGAGATGCCTAAAC
43860149 TTTGAGATGCCTAAAC
1 TTTGAGATGCCTAAAC
43860165 AAAGGGTTAT
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:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (16 bp):
TTTGAGATGCCTAAAC
Found at i:43860446 original size:21 final size:21
Alignment explanation
Indices: 43860420--43860465 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
43860410 TCTTGGATGT
43860420 GGGAAA-TTAGGGATTTTAGGG
1 GGGAAAGTTAGGGA-TTTAGGG
* *
43860441 GGGAAAGTTGGGGATTTCGGG
1 GGGAAAGTTAGGGATTTAGGG
43860462 GGGA
1 GGGA
43860466 GGGGGGAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.24, C:0.02, G:0.50, T:0.24
Consensus pattern (21 bp):
GGGAAAGTTAGGGATTTAGGG
Found at i:43861053 original size:33 final size:33
Alignment explanation
Indices: 43861011--43861081 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
43861001 ATCTAAATCA
* *
43861011 TAAACCCTAACCCGACCCTAAATCCCTAATCCC
1 TAAACCCTAACCCGACCCCAAATCCCTAACCCC
* * *
43861044 TAAACCCTAACTCGACCCCGAATGCCTAACCCC
1 TAAACCCTAACCCGACCCCAAATCCCTAACCCC
43861077 TAAAC
1 TAAAC
43861082 ATTATTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.44, G:0.06, T:0.17
Consensus pattern (33 bp):
TAAACCCTAACCCGACCCCAAATCCCTAACCCC
Done.