Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 159 of 311
Found at i:54220366 original size:8 final size:8
Alignment explanation
Indices: 54220353--54220457 Score: 57
Period size: 8 Copynumber: 13.9 Consensus size: 8
54220343 TGTCTTTCAA
54220353 AATAAAAT
1 AATAAAAT
54220361 AATAAAAT
1 AATAAAAT
54220369 AATAAAAT
1 AATAAAAT
54220377 --TAAAAT
1 AATAAAAT
*
54220383 GAA-AATAAA
1 -AATAA-AAT
54220392 AAT-AAA-
1 AATAAAAT
54220398 AAT-AAA-
1 AATAAAAT
54220404 AATAAAAAT
1 AAT-AAAAT
*
54220413 AATATAAT
1 AATAAAAT
*
54220421 -ATAATAT
1 AATAAAAT
*
54220428 AATATAAT
1 AATAAAAT
*
54220436 -ATAAAAA
1 AATAAAAT
* *
54220443 AATATAAG
1 AATAAAAT
54220451 AATAAAA
1 AATAAAA
54220458 AGATAAAAGG
Statistics
Matches: 76, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
6 15 0.20
7 12 0.16
8 44 0.58
9 5 0.07
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (8 bp):
AATAAAAT
Found at i:54220382 original size:6 final size:6
Alignment explanation
Indices: 54220351--54220414 Score: 71
Period size: 6 Copynumber: 11.2 Consensus size: 6
54220341 TATGTCTTTC
* * * *
54220351 AAAAT- AAAATA ATAA-A ATAAT- AAAATT AAAATG AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
54220396 AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA A
54220415 TATAATATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
5 14 0.27
6 38 0.73
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:54220429 original size:15 final size:15
Alignment explanation
Indices: 54220354--54220449 Score: 77
Period size: 15 Copynumber: 6.9 Consensus size: 15
54220344 GTCTTTCAAA
54220354 ATAAAATAATA-AA-
1 ATAAAATAATATAAT
*
54220367 ATAATAA-AAT-TAAA
1 ATAA-AATAATATAAT
54220381 ATGAAAATAA-A-AAT
1 AT-AAAATAATATAAT
54220395 A-AAAATAA-A-AAT
1 ATAAAATAATATAAT
54220407 A-AAAATAATATAAT
1 ATAAAATAATATAAT
*
54220421 ATAATATAATATAAT
1 ATAAAATAATATAAT
*
54220436 ATAAAAAAATATAA
1 ATAAAATAATATAA
54220450 GAATAAAAAG
Statistics
Matches: 70, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
12 19 0.27
13 10 0.14
14 13 0.19
15 28 0.40
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (15 bp):
ATAAAATAATATAAT
Found at i:54223994 original size:46 final size:43
Alignment explanation
Indices: 54223851--54223986 Score: 123
Period size: 46 Copynumber: 3.0 Consensus size: 43
54223841 CCAGCCCCTA
*
54223851 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATTT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCA-TT
* * * *
54223898 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATA
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATT
54223944 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT
54223987 CCTAGTGACA
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 29 0.39
47 29 0.39
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATT
Found at i:54233290 original size:13 final size:13
Alignment explanation
Indices: 54233268--54233300 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54233258 AATGGTTTGT
54233268 TTAT-TAAACTAA
1 TTATCTAAACTAA
54233280 TTATCTAAACTAA
1 TTATCTAAACTAA
*
54233293 TTAACTAA
1 TTATCTAA
54233301 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:54241460 original size:146 final size:145
Alignment explanation
Indices: 54241186--54241722 Score: 898
Period size: 146 Copynumber: 3.7 Consensus size: 145
54241176 TGTACAAGAT
* * *
54241186 AAATATATATGAGATATG-TATATGCGGTAAAGCCGAATGGCTAATGTGAAATAAGTATGAGATA
1 AAATATATATGAGAAATGATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATA
* *
54241250 TGTATATGTGGTAAAGCCGAATGGCTACTGTGAAAAATATATGAGATATGTATATGTGGCAAAGC
66 TGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGGTAAAGC
*
54241315 CGAATGGCTACTGTG
131 CGAATGGCTAATGTG
* *
54241330 AAATATATATGAGATATG-TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAAA
1 AAATATATATGAGAAATGATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATA
*
54241394 TGTATATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGAAATGTATATGTGGTAAA
66 TG--TATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGGTAAA
*
54241459 GCTGAATGGCTAATGTG
129 GCCGAATGGCTAATGTG
* *
54241476 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGAT
1 AAATATATATGAGAAATG-ATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
54241541 ATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGGTAAAG
65 ATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGGTAAAG
54241606 CCGAATGGCTAATGTG
130 CCGAATGGCTAATGTG
*
54241622 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
1 AAATATATATGAGAAATG-ATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
*
54241687 ATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAA
65 ATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAA
54241723 CATGTAGGAG
Statistics
Matches: 373, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
144 63 0.17
146 264 0.71
148 46 0.12
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (145 bp):
AAATATATATGAGAAATGATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATA
TGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGGTAAAGC
CGAATGGCTAATGTG
Found at i:54241728 original size:48 final size:48
Alignment explanation
Indices: 54241186--54241734 Score: 846
Period size: 48 Copynumber: 11.3 Consensus size: 48
54241176 TGTACAAGAT
* *
54241186 AAATATATATGAGATATGTATATGCGGTAAAGCCGAATGGCTAATGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
54241234 AAATAAGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* * * *
54241282 AAAAATATATGAGATATGTATATGTGGCAAAGCCGAATGGCTACTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
54241330 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
54241378 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTACTGTG
1 AAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTG
* * *
54241428 AAATATATATGAGAAATGTATATGTGGTAAAGCTGAATGGCTAATGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
54241476 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCAAATGGCTAATGTG
1 AAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTG
*
54241526 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
54241574 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
54241622 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTG
*
54241672 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
54241720 AAACATGTAGGAGAT
1 AAATATGTATGAGAT
54241735 GTGTGTATAT
Statistics
Matches: 464, Mismatches: 31, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
48 326 0.70
50 138 0.30
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (48 bp):
AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
Found at i:54241744 original size:98 final size:96
Alignment explanation
Indices: 54241186--54241734 Score: 846
Period size: 98 Copynumber: 5.7 Consensus size: 96
54241176 TGTACAAGAT
* *
54241186 AAATATATATGAGATATGTATATGCGGTAAAGCCGAATGGCTAATGTGAAATAAGTATGAGATAT
1 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
*
54241251 GTATATGTGGTAAAGCCGAATGGCTACTGTG
66 GTATATGTGGTAAAGCCGAATGGCTAATGTG
* * * *
54241282 AAAAATATATGAGATATGTATATGTGGCAAAGCCGAATGGCTACTGTGAAATATATATGAGATAT
1 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
54241347 GTATATGTGGTAAAGCCGAATGGCTAATGTG
66 GTATATGTGGTAAAGCCGAATGGCTAATGTG
* * * * *
54241378 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGAA
1 AAATATATATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
*
54241443 ATGTATATGTGGTAAAGCTGAATGGCTAATGTG
64 ATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* * *
54241476 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGAT
1 AAATATATATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
*
54241541 ATGTATATGTGGTAAAGCCGAATGGCTACTGTG
64 ATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
54241574 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAAAT
1 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
54241639 GTATATATGTGGTAAAGCCGAATGGCTAATGTG
66 G--TATATGTGGTAAAGCCGAATGGCTAATGTG
* * * *
54241672 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAACATGTAGGAGAT
1 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
54241735 GTGTGTATAT
Statistics
Matches: 420, Mismatches: 29, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
96 150 0.36
98 270 0.64
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (96 bp):
AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
GTATATGTGGTAAAGCCGAATGGCTAATGTG
Found at i:54248512 original size:40 final size:40
Alignment explanation
Indices: 54248467--54248618 Score: 234
Period size: 40 Copynumber: 3.8 Consensus size: 40
54248457 TATAACCACA
* *
54248467 AGCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACT
* *
54248507 CGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATAAAATCACT
*
54248547 AGCATAAATGCCTTCGGGACTTAGCCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATAAAATCACT
*
54248587 AGCATAAATGCCTTCGGGACTTAGCCCGGATA
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATA
54248619 TCATTCAAAT
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 102 0.96
41 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGACTTAGCCCGGATAAAATCACT
Found at i:54250929 original size:40 final size:40
Alignment explanation
Indices: 54250869--54251052 Score: 230
Period size: 40 Copynumber: 4.6 Consensus size: 40
54250859 TATTCGAATG
* *
54250869 ATATCCAGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
54250909 ATATCCGGACTAAGATCCGAAGGCATTTGTCCTAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* *
54250949 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
* *
54250989 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCCAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
54251029 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
54251053 CTTGTGCGAG
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 121 0.96
41 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:54251357 original size:22 final size:22
Alignment explanation
Indices: 54251315--54251358 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54251305 AAAATGTGCA
* *
54251315 TATATGAAGTTATTCATTTAGC
1 TATATGAAGTTATACACTTAGC
54251337 TATATGAATGTTATAC-CTTAGC
1 TATATGAA-GTTATACACTTAGC
54251359 CGAAACTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATATGAAGTTATACACTTAGC
Found at i:54267557 original size:55 final size:53
Alignment explanation
Indices: 54267437--54267625 Score: 202
Period size: 54 Copynumber: 3.5 Consensus size: 53
54267427 AACTTACAAT
* * * *
54267437 TGCCATGTCTTGACATGGTCTTACGTGGTATCCCTGCCTTAT-GAACTCACCAA
1 TGCCATGTCTTGGCATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATCAA
* * *
54267490 TTG-CATGTCTTGGCATGGTCTTAAATGGGACCTTTTCCTTATAGTAACTCATCAA
1 -TGCCATGTCTTGGCATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAA
* * ** *
54267545 TGCCATGTCTTGGCATGGTCTTACATGATTTCCTTGCCCGATAGAACTTATCAA
1 TGCCATGTCTTGGCATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAA
*
54267599 TGCCATGCCTTGGCATGGTCTTACATG
1 TGCCATGTCTTGGCATGGTCTTACATG
54267626 ATATCCTTAT
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
52 2 0.02
53 30 0.26
54 40 0.35
55 40 0.35
56 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (53 bp):
TGCCATGTCTTGGCATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAA
Found at i:54267750 original size:24 final size:24
Alignment explanation
Indices: 54267718--54267765 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
54267708 GTGGTCGTAC
54267718 ATGGAGTCCTTAATCAATGCCGAT
1 ATGGAGTCCTTAATCAATGCCGAT
54267742 ATGGAGTCCTTAATCAATGCCGAT
1 ATGGAGTCCTTAATCAATGCCGAT
54267766 GCCATGTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
ATGGAGTCCTTAATCAATGCCGAT
Found at i:54268508 original size:31 final size:30
Alignment explanation
Indices: 54268473--54268531 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
54268463 GTAACTCAAA
*
54268473 CTTTGGCAAAATTGCAATTTTGCCCCTAAAC
1 CTTT-GCAAAATTACAATTTTGCCCCTAAAC
* *
54268504 CTTTGCGAAATTACGATTTTGCCCCTAA
1 CTTTGCAAAATTACAATTTTGCCCCTAA
54268532 GCTCGAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (30 bp):
CTTTGCAAAATTACAATTTTGCCCCTAAAC
Found at i:54269522 original size:40 final size:40
Alignment explanation
Indices: 54269471--54269556 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
54269461 GTTCCAATAT
*
54269471 ATAGCCGAAGCTATCTTGAATCGCACACTAAGTGCCATAC
1 ATAGCCAAAGCTATCTTGAATCGCACACTAAGTGCCATAC
*
54269511 ATAGCCAAAGCTATCTTGAATCGCACACTAAGTGCCTTAC
1 ATAGCCAAAGCTATCTTGAATCGCACACTAAGTGCCATAC
54269551 ATAGCC
1 ATAGCC
54269557 CAATTGTGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (40 bp):
ATAGCCAAAGCTATCTTGAATCGCACACTAAGTGCCATAC
Found at i:54272255 original size:39 final size:39
Alignment explanation
Indices: 54272188--54272410 Score: 340
Period size: 39 Copynumber: 5.7 Consensus size: 39
54272178 ACAAAGCATG
* * *
54272188 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
54272228 CGGGACTTTAACCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
*
54272268 CGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
54272307 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
54272346 CAGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
54272385 CGGGACTTAGCCCGGATATAGCACCA
1 CGGGACTTAGCCCGGATATAACACCA
54272411 TTATAAAGTC
Statistics
Matches: 171, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 151 0.88
40 20 0.12
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:54272524 original size:28 final size:28
Alignment explanation
Indices: 54272483--54272564 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
54272473 ATTTAATCAT
* * *
54272483 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATCTCGCACACTAAGTGCCATTC
* *
54272511 TTAATATCTCGCACATTAAGTGCCATTC
1 TCAATATCTCGCACACTAAGTGCCATTC
* * * *
54272539 TCAATATTTCGTACACTGAGTACCAT
1 TCAATATCTCGCACACTAAGTGCCAT
54272565 ATTTGATTGC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (28 bp):
TCAATATCTCGCACACTAAGTGCCATTC
Found at i:54280806 original size:40 final size:40
Alignment explanation
Indices: 54280759--54280903 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
54280749 CTCGCACAAG
* * * * *
54280759 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
*
54280799 GCCTTCGGGACTTAGCCTGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
54280839 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
54280880 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
54280904 CATTCGAGTA
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.03
40 57 0.63
41 27 0.30
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:54280886 original size:41 final size:39
Alignment explanation
Indices: 54280723--54280903 Score: 168
Period size: 40 Copynumber: 4.5 Consensus size: 39
54280713 AATCAAGCAT
** ** * * *
54280723 CTTCGGGGTTTAGCCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCGGATATAGTCGCTAGCACAAATGC
* * * * *
54280761 CTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTT-AGCCGGATATAGTCGCTAGCACAAATGC
54280801 CTTCGGGACTTAGCCTGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCC-GGATATAGTCGCTAGCACAAATGC
* *
54280841 CTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGC
1 CTTCGGGA-CTTAG-CCGGATATAGTCGC-TAGCACAAATGC
54280882 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAG-CCGGATAT
54280904 CATTCGAGTA
Statistics
Matches: 118, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
38 9 0.08
39 22 0.19
40 55 0.47
41 29 0.25
42 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (39 bp):
CTTCGGGACTTAGCCGGATATAGTCGCTAGCACAAATGC
Found at i:54282134 original size:38 final size:38
Alignment explanation
Indices: 54282092--54282167 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
54282082 CAAGAACTCC
54282092 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
54282130 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
54282168 AAAGGATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:54284434 original size:24 final size:24
Alignment explanation
Indices: 54284405--54284456 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
54284395 CCTTTATACC
* *
54284405 CATATACACGTAAA-CACATCCATA
1 CATATACAC-AAAAGCACATACATA
54284429 CATATACACAAAAGCACATACATA
1 CATATACACAAAAGCACATACATA
54284453 CATA
1 CATA
54284457 CCTTTCACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.50, C:0.27, G:0.04, T:0.19
Consensus pattern (24 bp):
CATATACACAAAAGCACATACATA
Found at i:54286441 original size:24 final size:24
Alignment explanation
Indices: 54286395--54286489 Score: 104
Period size: 24 Copynumber: 4.0 Consensus size: 24
54286385 ACTTTATCAT
*
54286395 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAG-CTCTTTTA
* *
54286420 ATAACTAGGGCAAAAGCTCTTTTA
1 ATAACTGGGGCATAAGCTCTTTTA
* *
54286444 ATAAATGGGGCATAAGC-CCTTTA
1 ATAACTGGGGCATAAGCTCTTTTA
*
54286467 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCTCTTTT
54286490 GCACTTCCTC
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
23 21 0.36
24 29 0.49
25 9 0.15
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCTCTTTTA
Found at i:54286470 original size:23 final size:23
Alignment explanation
Indices: 54286416--54286488 Score: 101
Period size: 23 Copynumber: 3.1 Consensus size: 23
54286406 CCTAGCCTCT
* * *
54286416 TTTAATAACTAGGGCAAAAGCTCT
1 TTTAATAACTGGGGCATAAGC-CC
*
54286440 TTTAATAAATGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54286463 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54286486 TTT
1 TTT
54286489 TGCACTTCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 26 0.59
24 18 0.41
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:54286563 original size:20 final size:20
Alignment explanation
Indices: 54286538--54286604 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
54286528 TTATGAATAC
54286538 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
**
54286558 ATCATGTGCATAGAATACAT
1 ATCATGTGCATATCATACAT
*
54286578 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54286598 ACCATGT
1 ATCATGT
54286605 TTACTAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54294257 original size:31 final size:31
Alignment explanation
Indices: 54294219--54294282 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
54294209 CCCTTTCATA
54294219 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
54294250 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
54294281 TT
1 TT
54294283 ACTGTAACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:54294538 original size:23 final size:24
Alignment explanation
Indices: 54294474--54294566 Score: 113
Period size: 23 Copynumber: 4.0 Consensus size: 24
54294464 GCTTTATCAT
*
54294474 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
54294499 ATAACTGGGACAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
54294523 AT-ACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
54294545 ATAACTGGGGCATAA-CCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54294567 TGCACTTCCT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.15
23 29 0.48
24 10 0.17
25 12 0.20
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:54294645 original size:20 final size:20
Alignment explanation
Indices: 54294608--54294646 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54294598 CCAATGCATT
**
54294608 CATAGCATACATGTCATGTG
1 CATAGCATACATACCATGTG
*
54294628 CATATCATACATACCATGT
1 CATAGCATACATACCATGT
54294647 TTACAAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (20 bp):
CATAGCATACATACCATGTG
Found at i:54302130 original size:30 final size:30
Alignment explanation
Indices: 54302096--54302156 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
54302086 TCCTTAACTC
54302096 AAACTTTTACAAAATTACAATTTTGCCCCT
1 AAACTTTTACAAAATTACAATTTTGCCCCT
* * * *
54302126 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTACAAAATTACAATTTTGCCCCT
54302156 A
1 A
54302157 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTTTTACAAAATTACAATTTTGCCCCT
Found at i:54321310 original size:40 final size:40
Alignment explanation
Indices: 54321255--54321475 Score: 295
Period size: 40 Copynumber: 5.5 Consensus size: 40
54321245 TATTTGAATG
*
54321255 ATATCCGGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
54321295 ATATCCGGGCCAAGTCCCGAAGTCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
54321335 ATATCCGGGCCAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
54321375 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* * * *
54321415 ATATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
54321455 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
54321476 ATACTTGGGT
Statistics
Matches: 166, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 12 0.07
40 152 0.92
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:54321745 original size:22 final size:22
Alignment explanation
Indices: 54321704--54321747 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54321694 GAATGTGCAT
*
54321704 ATATGAAGTTATACATTTAGCC
1 ATATGAAGTTATACACTTAGCC
54321726 ATATGAATGTTATAC-CTTAGCC
1 ATATGAA-GTTATACACTTAGCC
54321748 GAAACTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (22 bp):
ATATGAAGTTATACACTTAGCC
Found at i:54333221 original size:23 final size:23
Alignment explanation
Indices: 54333168--54333239 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
54333158 TGTTTCTCAC
* *
54333168 TTTATATAACTATTATTTTGAAGCTAT
1 TTTATATAA-TATTGTTTT-AA--TAA
*
54333195 TTTATATTATATTGTTTTAATAA
1 TTTATATAATATTGTTTTAATAA
*
54333218 TTTATATAATATTTTTTTAATA
1 TTTATATAATATTGTTTTAATA
54333240 TTTTTGTGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 22 0.55
25 2 0.05
26 8 0.20
27 8 0.20
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTATATAATATTGTTTTAATAA
Found at i:54339428 original size:47 final size:44
Alignment explanation
Indices: 54339367--54339541 Score: 192
Period size: 47 Copynumber: 3.8 Consensus size: 44
54339357 TGTTTGGGCA
54339367 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
*** * *
54339413 TCCGAAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA-
1 TCCG-AACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GGAAG
*
54339461 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-GAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-G
* *
54339505 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54339542 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
42 2 0.02
44 37 0.34
45 1 0.01
46 8 0.07
47 49 0.45
48 8 0.07
49 1 0.01
50 3 0.03
51 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (44 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAG
Found at i:54342480 original size:15 final size:15
Alignment explanation
Indices: 54342460--54342528 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
54342450 GTATCTTGGG
54342460 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
54342475 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
54342490 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
54342505 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
54342520 TTTCTTTAT
1 TTTCTTTAT
54342529 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:54342529 original size:30 final size:30
Alignment explanation
Indices: 54342451--54342538 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
54342441 CATAGTATCG
* * * *
54342451 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
54342481 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
54342511 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
54342539 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:54344973 original size:46 final size:45
Alignment explanation
Indices: 54344919--54345094 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
54344909 TGTTTGGGCA
54344919 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* *** * *
54344965 TCCAAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GGAATG
*
54345012 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * * *
54345058 CCCGAGCTCATTGAGTTGACTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54345095 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 66 0.62
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:54345074 original size:93 final size:93
Alignment explanation
Indices: 54344915--54345086 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
54344905 AGGATGTTTG
* *
54344915 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCAAACTCATTGAG
*
54344980 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGACTCCGAGTTCGAGAGATGTAACTA
* * * *
54345008 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGCCCGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCAAACTCATTGAG
54345073 TTGACTCCGAGTTC
66 TTGACTCCGAGTTC
54345087 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCAAACTCATTGAG
TTGACTCCGAGTTCGAGAGATGTAACTA
Found at i:54345603 original size:13 final size:14
Alignment explanation
Indices: 54345577--54345605 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54345567 ATTATAATCA
54345577 TTTTGTGTATATGG
1 TTTTGTGTATATGG
54345591 TTTTGTG-ATATGG
1 TTTTGTGTATATGG
54345604 TT
1 TT
54345606 ATTGAGTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.59
Consensus pattern (14 bp):
TTTTGTGTATATGG
Found at i:54347590 original size:25 final size:24
Alignment explanation
Indices: 54347544--54347628 Score: 75
Period size: 25 Copynumber: 3.5 Consensus size: 24
54347534 CCTTGAGACC
* **
54347544 TTAAAAATAAAAGAAAGGAAAAGA
1 TTAAAAAAAAAAGAAATTAAAAGA
54347568 TTAAAATAAAAAAGAAATTAAAAGA
1 TTAAAA-AAAAAAGAAATTAAAAGA
* * *
54347593 --GAAAAAAAGAGAAATTAAAAAAA
1 TTAAAAAAAAAAGAAATT-AAAAGA
54347616 TTAAAAAATAAAA
1 TTAAAAAA-AAAA
54347629 ATAAAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
22 11 0.23
23 8 0.17
24 6 0.12
25 20 0.42
26 3 0.06
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (24 bp):
TTAAAAAAAAAAGAAATTAAAAGA
Found at i:54347595 original size:12 final size:12
Alignment explanation
Indices: 54347574--54347612 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
54347564 AAGATTAAAA
*
54347574 TAAAAAAGAAAT
1 TAAAAGAGAAAT
54347586 TAAAAGAGAAA-
1 TAAAAGAGAAAT
54347597 -AAAAGAGAAAT
1 TAAAAGAGAAAT
54347608 TAAAA
1 TAAAA
54347613 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (12 bp):
TAAAAGAGAAAT
Found at i:54347621 original size:22 final size:20
Alignment explanation
Indices: 54347570--54347647 Score: 70
Period size: 22 Copynumber: 3.8 Consensus size: 20
54347560 GGAAAAGATT
54347570 AAAATAAAAAAGAAATTAAA
1 AAAATAAAAAAGAAATTAAA
54347590 AGAGAA-AAAAAGAGAAATTAAA
1 A-A-AATAAAAA-AGAAATTAAA
* *
54347612 AAAATTAAAAAATAAAAATAAA
1 AAAA-TAAAAAA-GAAATTAAA
*
54347634 AAAA-AAGAAAGAAA
1 AAAATAAAAAAGAAA
54347648 AGGAGAGGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
19 3 0.06
20 8 0.17
21 8 0.17
22 29 0.60
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (20 bp):
AAAATAAAAAAGAAATTAAA
Found at i:54348685 original size:16 final size:16
Alignment explanation
Indices: 54348665--54348697 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
54348655 GGAAAAAAGA
54348665 AAAAAGAAAGATCATTT
1 AAAAA-AAAGATCATTT
54348682 AAAAAAAAGATCATTT
1 AAAAAAAAGATCATTT
54348698 TCATTTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24
Consensus pattern (16 bp):
AAAAAAAAGATCATTT
Found at i:54348812 original size:64 final size:64
Alignment explanation
Indices: 54348733--54348968 Score: 330
Period size: 64 Copynumber: 3.7 Consensus size: 64
54348723 ATAACACATT
* * *
54348733 TAGTTAGGTGCATTTGATTCATTTCGATAATAGCATCCTAATTATTTGACATCAGCATTACAGC
1 TAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAGCATCACAGC
** *
54348797 TAGTTAGGAGCATTTGATTCATTTCGATCATAGCGGCCTAATTATTTGACATCAGCATCACATC
1 TAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAGCATCACAGC
* * * * *
54348861 TAGTTAGGAGCATTTGATTAATTTTGATCATAGCATCCTAATTATGTGTCATAAGCATCAC-GTC
1 TAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAGCATCACAG-C
* * *
54348925 TAATTAGGAGTATTTGATTCATTTTGATCATAGCATCCTAATTA
1 TAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTA
54348969 GTTGGCATAA
Statistics
Matches: 154, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
64 154 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.38
Consensus pattern (64 bp):
TAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAGCATCACAGC
Found at i:54354222 original size:135 final size:135
Alignment explanation
Indices: 54353980--54354249 Score: 504
Period size: 135 Copynumber: 2.0 Consensus size: 135
54353970 TAAATGGGCT
*
54353980 ATTTGCACATCTGATCCTTCCCCCATATGTCAATCTTCAATCGGATCCAACCTATGCTACATTTA
1 ATTTGCACATCTGATCCTTCCCCCATATGTCAATCTTCAATCGGATCCAACCTATGCTACACTTA
*
54354045 TTTTTTTATTTCATCTGGGAATTTGTACACTATTGCGATTTGATCCATAGCTAAATTCAGCGTTT
66 TTTTTTTATTTCATCTGGGAATTTGTACACTATTGCGATTTGATCCACAGCTAAATTCAGCGTTT
54354110 TGAAA
131 TGAAA
*
54354115 ATTTGCACGTCTGATCCTTCCCCCATATGTCAATCTTCAATCGGATCCAACCTATGCTACACTTA
1 ATTTGCACATCTGATCCTTCCCCCATATGTCAATCTTCAATCGGATCCAACCTATGCTACACTTA
*
54354180 TTTTTTTATTTCGTCTGGGAATTTGTACACTATTGCGATTTGATCCACAGCTAAATTCAGCGTTT
66 TTTTTTTATTTCATCTGGGAATTTGTACACTATTGCGATTTGATCCACAGCTAAATTCAGCGTTT
54354245 TGAAA
131 TGAAA
54354250 TGAAAATTAT
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
135 131 1.00
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (135 bp):
ATTTGCACATCTGATCCTTCCCCCATATGTCAATCTTCAATCGGATCCAACCTATGCTACACTTA
TTTTTTTATTTCATCTGGGAATTTGTACACTATTGCGATTTGATCCACAGCTAAATTCAGCGTTT
TGAAA
Found at i:54354728 original size:23 final size:24
Alignment explanation
Indices: 54354702--54354747 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
54354692 TTGAAGCTAT
*
54354702 TTTACATTATA-TTGTTTTAATAA
1 TTTACATAATATTTGTTTTAATAA
* *
54354725 TTTATATAATATTTTTTTTAATA
1 TTTACATAATATTTGTTTTAATA
54354748 TTTTTGTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTACATAATATTTGTTTTAATAA
Found at i:54359848 original size:30 final size:31
Alignment explanation
Indices: 54359778--54359860 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 31
54359768 TCAATCTCAA
54359778 CATAT-ACTGGGCCGAAGCCTTTGCATTATT
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
* * *
54359808 CATGTCACTGGGCCAAAGCCTTTTCATTA-T
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
*
54359838 CATATCACTGGGGCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
54359861 ACTGTAAACG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 25 0.54
31 21 0.46
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTGCATTATT
Found at i:54360101 original size:24 final size:25
Alignment explanation
Indices: 54360074--54360151 Score: 86
Period size: 25 Copynumber: 3.1 Consensus size: 25
54360064 GCCTAGCCTC
54360074 TTTTAAT-AACAGGGGCAAAGCCCT
1 TTTTAATAAACAGGGGCAAAGCCCT
* *
54360098 TTTTGATAAACTGGGGCAAAGCCCT
1 TTTTAATAAACAGGGGCAAAGCCCT
*** *
54360123 TTTCGGTAAACTGGGGCAAAAGCCCT
1 TTTTAATAAACAGGGGC-AAAGCCCT
54360149 TTT
1 TTT
54360152 CCACTTCCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.12
25 31 0.65
26 11 0.23
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (25 bp):
TTTTAATAAACAGGGGCAAAGCCCT
Found at i:54360151 original size:26 final size:25
Alignment explanation
Indices: 54360085--54360152 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
54360075 TTTAATAACA
*
54360085 GGGGCAAAGCCCTTTTTGATAAACT
1 GGGGCAAAGCCCTTTTCGATAAACT
*
54360110 GGGGCAAAGCCCTTTTCGGTAAACT
1 GGGGCAAAGCCCTTTTCGATAAACT
54360135 GGGGCAAAAGCCCTTTTC
1 GGGGC-AAAGCCCTTTTC
54360153 CACTTCCTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 28 0.70
26 12 0.30
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (25 bp):
GGGGCAAAGCCCTTTTCGATAAACT
Found at i:54363166 original size:46 final size:46
Alignment explanation
Indices: 54363046--54363171 Score: 216
Period size: 46 Copynumber: 2.7 Consensus size: 46
54363036 AACCCGCCCG
** * *
54363046 TAAGTGAACTCGGACTCAACTCAACGAGCGCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54363092 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54363138 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54363172 TGCCCAAATA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:54369031 original size:29 final size:29
Alignment explanation
Indices: 54368968--54369086 Score: 127
Period size: 29 Copynumber: 4.2 Consensus size: 29
54368958 TACATACATG
* ** *
54368968 CATATGGCCCACTAGAACCAA-TCTTATT
1 CATATGGCCCATTAGGCCCAATTCATATT
* *
54368996 CAAATGGCCCATCT-GGCCCAGTTCATATT
1 CATATGGCCCAT-TAGGCCCAATTCATATT
* *
54369025 CTTATGGCCCATTAGGCCCAATTCACATT
1 CATATGGCCCATTAGGCCCAATTCATATT
*
54369054 CATATGGCCCATTAGGCCCAAATCATATT
1 CATATGGCCCATTAGGCCCAATTCATATT
54369083 -ATAT
1 CATAT
54369087 TCATGCTCAC
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
28 19 0.25
29 56 0.75
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CATATGGCCCATTAGGCCCAATTCATATT
Found at i:54380794 original size:43 final size:43
Alignment explanation
Indices: 54380630--54380796 Score: 162
Period size: 43 Copynumber: 3.9 Consensus size: 43
54380620 AGTTCGTACA
* ** * *
54380630 ATGCC-ATGTCCCAGATATGGTCTTACAGGTTATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAATCACATAACG
* * ** *
54380672 ATGCCGATAG-CCCAG-CTATGGTGTTACTTGA-AATCAAATAACG
1 ATGCCAAT-GTCCCAGAC-ATGGTCTTAC-ACATAATCACATAACG
* *
54380715 ATGCCAATGTCCTAGACATGGTCTTACACATAATCACATAATG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAATCACATAACG
*
54380758 ATGCCAATTTCCCAGACATGGTCTTACACATAATCACAT
1 ATGCCAATGTCCCAGACATGGTCTTACACATAATCACAT
54380797 CTCGTTAATC
Statistics
Matches: 102, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
42 7 0.07
43 92 0.90
44 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACATAATCACATAACG
Found at i:54385710 original size:43 final size:43
Alignment explanation
Indices: 54385662--54385765 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 43
54385652 TATCCTAGAT
** * *
54385662 ATGGTCTTACATGTTTTCATATACCGATGCTAACGTCCCAAAC
1 ATGGTCTTACATGTAATCATATAACGATGCCAACGTCCCAAAC
** * * *
54385705 ATGGTCTTACCCGAAATCATATAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCATATAACGATGCCAACGTCCCAAAC
54385748 ATGGTCTTACATGTAATC
1 ATGGTCTTACATGTAATC
54385766 TCATCTTGAT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCATATAACGATGCCAACGTCCCAAAC
Found at i:54390754 original size:27 final size:27
Alignment explanation
Indices: 54390724--54390775 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
54390714 TGTGGGCTAA
* *
54390724 AGCCCATTACA-ATATCATTTGGGTCAC
1 AGCCCATAACAGA-ATCAATTGGGTCAC
54390751 AGCCCATAACAGAATCAATTGGGTC
1 AGCCCATAACAGAATCAATTGGGTC
54390776 TAGCCAGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (27 bp):
AGCCCATAACAGAATCAATTGGGTCAC
Found at i:54391335 original size:27 final size:27
Alignment explanation
Indices: 54391294--54391361 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
54391284 GGGCAAAATA
*
54391294 GTCATTTTACCCTA-CAGGGGTATGTAG
1 GTCATTTTACACTACCA-GGGTATGTAG
* *
54391321 GTCATTTTACACTACCAGGGTATTTTG
1 GTCATTTTACACTACCAGGGTATGTAG
*
54391348 GTAATTTTACACTA
1 GTCATTTTACACTA
54391362 TAAAGGCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 34 0.94
28 2 0.06
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (27 bp):
GTCATTTTACACTACCAGGGTATGTAG
Found at i:54391372 original size:27 final size:27
Alignment explanation
Indices: 54391324--54391385 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
54391314 TATGTAGGTC
* * * * *
54391324 ATTTTACACTACCAGGGTATTTTGGTA
1 ATTTTACACTACAAAGGCATTTCGATA
*
54391351 ATTTTACACTATAAAGGCATTTCGATA
1 ATTTTACACTACAAAGGCATTTCGATA
54391378 ATTTTACA
1 ATTTTACA
54391386 AATTGGGGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (27 bp):
ATTTTACACTACAAAGGCATTTCGATA
Found at i:54391401 original size:54 final size:53
Alignment explanation
Indices: 54391337--54391755 Score: 382
Period size: 53 Copynumber: 7.8 Consensus size: 53
54391327 TTACACTACC
* * * * *
54391337 AGGGTATTTTGGTAATTTTACACTATAAAGGCATTTCGATAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTTACA-AATGAGGGTATTTCGATAATTTTACAAATTG
* * * * * * **
54391391 GGGGTGTTTTGATAATTTTACAAATTGAGGGTGTTTCGGTAATTTTACAAATCA
1 AGGGTATTTCGGTAATTTTACAAA-TGAGGGTATTTCGATAATTTTACAAATTG
* * * * *
54391445 AGGGTGTTTCGATAATTTTACAAATCGAGGGTATTT-TAGTAATTTCAC-AATCG
1 AGGGTATTTCGGTAATTTTACAAAT-GAGGGTATTTCGA-TAATTTTACAAATTG
** *
54391498 AGGGTATTTTAGTAATTTTACAAATGGGGGTATTTCGATAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTTACAAATGAGGGTATTTCGATAATTTTACAAATTG
* * *
54391551 AGGGTGTTTCGGTAATTTCACAAATTACGGGTATTTCGATAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTTACAAATGA-GGGTATTTCGATAATTTTACAAATTG
* *
54391605 AGGGTATTTCGGTAA-TTT-CATAATCGAGGGTATTTTGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACA-AAT-GAGGGTATTTCGATAATTTTACAAATTG
* * ** ***
54391658 AGGGTATTTCAGTAATTTCAC-AATAGAGGGTATTTTAATAATTTTACAAAGCA
1 AGGGTATTTCGGTAATTTTACAAAT-GAGGGTATTTCGATAATTTTACAAATTG
* * *
54391711 AGGGTATTTCGATAATTTTAAAAATTGAGTGTATTTC-AGTAATTT
1 AGGGTATTTCGGTAATTTTACAAA-TGAGGGTATTTCGA-TAATTT
54391756 CTCTTTATTA
Statistics
Matches: 303, Mismatches: 49, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
52 19 0.06
53 142 0.47
54 140 0.46
55 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (53 bp):
AGGGTATTTCGGTAATTTTACAAATGAGGGTATTTCGATAATTTTACAAATTG
Found at i:54391404 original size:27 final size:27
Alignment explanation
Indices: 54391369--54391755 Score: 380
Period size: 27 Copynumber: 14.5 Consensus size: 27
54391359 CTATAAAGGC
*
54391369 ATTTCGATAATTTTACAAATTGGGGGT
1 ATTTCGATAATTTTACAAATTGAGGGT
* *
54391396 GTTTTGATAATTTTACAAATTGAGGGT
1 ATTTCGATAATTTTACAAATTGAGGGT
* * **
54391423 GTTTCGGTAATTTTACAAATCAAGGGT
1 ATTTCGATAATTTTACAAATTGAGGGT
* *
54391450 GTTTCGATAATTTTACAAATCGAGGGT
1 ATTTCGATAATTTTACAAATTGAGGGT
* * *
54391477 ATTT-TAGTAATTTCAC-AATCGAGGGT
1 ATTTCGA-TAATTTTACAAATTGAGGGT
* *
54391503 ATTT-TAGTAATTTTACAAA-TGGGGGT
1 ATTTCGA-TAATTTTACAAATTGAGGGT
54391529 ATTTCGATAATTTTACAAATTGAGGGT
1 ATTTCGATAATTTTACAAATTGAGGGT
* * *
54391556 GTTTCGGTAATTTCACAAATT-ACGGGT
1 ATTTCGATAATTTTACAAATTGA-GGGT
54391583 ATTTCGATAATTTTACAAATTGAGGGT
1 ATTTCGATAATTTTACAAATTGAGGGT
* *
54391610 ATTTCGGTAA-TTT-CATAATCGAGGGT
1 ATTTCGATAATTTTACA-AATTGAGGGT
* *
54391636 ATTTTGATAATTTTACAAATCGAGGGT
1 ATTTCGATAATTTTACAAATTGAGGGT
* *
54391663 ATTTC-AGTAATTTCAC-AATAGAGGGT
1 ATTTCGA-TAATTTTACAAATTGAGGGT
** ***
54391689 ATTTTAATAATTTTACAAAGCAAGGGT
1 ATTTCGATAATTTTACAAATTGAGGGT
* *
54391716 ATTTCGATAATTTTAAAAATTGAGTGT
1 ATTTCGATAATTTTACAAATTGAGGGT
54391743 ATTTC-AGTAATTT
1 ATTTCGA-TAATTT
54391756 CTCTTTATTA
Statistics
Matches: 305, Mismatches: 42, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.01
26 91 0.30
27 209 0.69
28 3 0.01
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
ATTTCGATAATTTTACAAATTGAGGGT
Found at i:54391549 original size:160 final size:160
Alignment explanation
Indices: 54391337--54391755 Score: 497
Period size: 160 Copynumber: 2.6 Consensus size: 160
54391327 TTACACTACC
* * * * * * *
54391337 AGGGTATTTTGGTAATTTTACACTATAAAGGCATTTCGATAATTTTACAAATTGGGGGTGTTTTG
1 AGGGTATTTTAGTAATTTTACA-AATGAGGGTATTTCGATAATTTTACAAATTGAGGGTGTTTCG
* *
54391402 ATAATTTTACAAATTGAGGGTGTTTCGGTAATTTTACAAATCAAGGGTGTTTCGATAATTTTACA
65 ATAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAA-TTT-CA
54391467 -AATCGAGGGTATTTT-AGTAATTTCAC-AATCG
128 TAATCGAGGGTATTTTGA-TAATTTCACAAATCG
* *
54391498 AGGGTATTTTAGTAATTTTACAAATGGGGGTATTTCGATAATTTTACAAATTGAGGGTGTTTCGG
1 AGGGTATTTTAGTAATTTTACAAATGAGGGTATTTCGATAATTTTACAAATTGAGGGTGTTTCGA
* * ** *
54391563 TAATTTCACAAATT-ACGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTCATA
66 TAATTTTACAAATTGA-GGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTCATA
*
54391627 ATCGAGGGTATTTTGATAATTTTACAAATCG
130 ATCGAGGGTATTTTGATAATTTCACAAATCG
* * ** *** *
54391658 AGGGTATTTCAGTAATTTCAC-AATAGAGGGTATTTTAATAATTTTACAAAGCAAGGGTATTTCG
1 AGGGTATTTTAGTAATTTTACAAAT-GAGGGTATTTCGATAATTTTACAAATTGAGGGTGTTTCG
* * *
54391722 ATAATTTTAAAAATTGAGTGTATTTCAGTAATTT
65 ATAATTTTACAAATTGAGGGTATTTCGGTAATTT
54391756 CTCTTTATTA
Statistics
Matches: 220, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
158 2 0.01
159 30 0.14
160 166 0.75
161 22 0.10
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (160 bp):
AGGGTATTTTAGTAATTTTACAAATGAGGGTATTTCGATAATTTTACAAATTGAGGGTGTTTCGA
TAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTCATAA
TCGAGGGTATTTTGATAATTTCACAAATCG
Found at i:54391558 original size:133 final size:133
Alignment explanation
Indices: 54391369--54391756 Score: 530
Period size: 133 Copynumber: 2.9 Consensus size: 133
54391359 CTATAAAGGC
* * *
54391369 ATTTCGATAATTTTACAAATTGGGGGTGTTTTGATAATTTTACAAATTGAGGGTGTTTCGGTAAT
1 ATTTTGATAATTTTACAAA-TGGGGGTATTTCGATAATTTTACAAATTGAGGGTGTTTCGGTAAT
* * *
54391434 TTTACAAATCAAGGGTGTTTCGATAATTTTACAAATCGAGGGTATTTTAGTAATTTCACAATCGA
65 TTTACAAATCAAGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAATCGA
54391499 GGGT
130 GGGT
54391503 ATTTT-AGTAATTTTACAAATGGGGGTATTTCGATAATTTTACAAATTGAGGGTGTTTCGGTAAT
1 ATTTTGA-TAATTTTACAAATGGGGGTATTTCGATAATTTTACAAATTGAGGGTGTTTCGGTAAT
* * * * *
54391567 TTCACAAATTACGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTCATAATCGA
65 TTTACAAATCAAGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAATCGA
54391632 GGGT
130 GGGT
* * * * ***
54391636 ATTTTGATAATTTTACAAATCGAGGGTATTTC-AGTAATTTCAC-AATAGAGGGTATTTTAATAA
1 ATTTTGATAATTTTACAAAT-GGGGGTATTTCGA-TAATTTTACAAATTGAGGGTGTTTCGGTAA
* * *
54391699 TTTTACAAAGCAAGGGTATTTCGATAATTTTAAAAATTGAGTGTATTTCAGTAATTTC
64 TTTTACAAATCAAGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCAGTAATTTC
54391757 TCTTTATTAT
Statistics
Matches: 225, Mismatches: 25, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
133 190 0.84
134 35 0.16
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (133 bp):
ATTTTGATAATTTTACAAATGGGGGTATTTCGATAATTTTACAAATTGAGGGTGTTTCGGTAATT
TTACAAATCAAGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAATCGAG
GGT
Found at i:54392107 original size:28 final size:28
Alignment explanation
Indices: 54392071--54392134 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
54392061 TGGCCCCTTT
* *
54392071 AGGCCCAATCTCGTTCACATGACCCATC
1 AGGCCCAATCACATTCACATGACCCATC
* * *
54392099 AGGCTCAATCACATTCATATGGCCCATC
1 AGGCCCAATCACATTCACATGACCCATC
54392127 AGGCCCAA
1 AGGCCCAA
54392135 CTACTTCTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.36, G:0.16, T:0.20
Consensus pattern (28 bp):
AGGCCCAATCACATTCACATGACCCATC
Found at i:54395073 original size:40 final size:40
Alignment explanation
Indices: 54395043--54395265 Score: 326
Period size: 40 Copynumber: 5.6 Consensus size: 40
54395033 GCTACTTGCT
**
54395043 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAGTTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCA
* * **
54395083 CAAATGCCCTCGGGACTTAGCCCGGATATAAAAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCA
54395123 CAAATGCCTTCGGGACTTAGCCCGGAA-ATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCA
*
54395163 CAAATGCCTTCGGGTCTTAGCCCGGAA-ATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCA
*
54395203 CAAATGCCTTCGGGACTTAGCTCGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGC-CCGAATATAGTAACTCGCA
54395243 CAAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
54395266 CATTATCATC
Statistics
Matches: 166, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 162 0.98
41 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCA
Found at i:54404451 original size:40 final size:40
Alignment explanation
Indices: 54404355--54404536 Score: 167
Period size: 40 Copynumber: 4.6 Consensus size: 40
54404345 ATGCTGTCTG
* * * *
54404355 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-ATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT-T
** *
54404395 CCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAATT
1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAATT
* * *
54404435 CCGGGTTAAGTCCCGAA-GCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAATT
* ** *
54404474 CCGAGTTAAGTCCCGAAGGCATTCATGCGAGTT-TTAAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AATT
54404514 CCGGGTTAAGTCCCGAAGGCATT
1 CCGGGTTAAGTCCCGAAGGCATT
54404537 GAATGAGTTA
Statistics
Matches: 117, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 36 0.31
40 71 0.61
41 10 0.09
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAATT
Found at i:54404473 original size:39 final size:38
Alignment explanation
Indices: 54404415--54404536 Score: 136
Period size: 39 Copynumber: 3.1 Consensus size: 38
54404405 ATCCGAAGGT
54404415 ATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGC
1 ATTTGTGCGAG-TATTAATTCCGGGTTAAGTCCCGAAGC
* * *
54404454 CTTTGTGCGAGATACTAATTCCGAGTTAAGTCCCGAAGGC
1 ATTTGTGCGAG-TATTAATTCCGGGTTAAGTCCCGAA-GC
** * *
54404494 ATTCATGCGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGC
1 ATTTGTGCGAGTATT-AATTCCGGGTTAAGTCCCGAA-GC
54404534 ATT
1 ATT
54404537 GAATGAGTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 35 0.50
40 35 0.50
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (38 bp):
ATTTGTGCGAGTATTAATTCCGGGTTAAGTCCCGAAGC
Found at i:54404557 original size:39 final size:40
Alignment explanation
Indices: 54404434--54404583 Score: 116
Period size: 39 Copynumber: 3.8 Consensus size: 40
54404424 AGTTATTAAT
* * * *
54404434 TCCGGGTTAAGTCCCGAAGCCTTTG--TGCGAGATACT-AAT
1 TCCGGGTTAAGTCCCGAAGGCATTGAAT-CGAG-TTCTAAAA
* * *
54404473 TCCGAGTTAAGTCCCGAAGGCATT-CATGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAAT-CGAGTTCTAAAA
*
54404513 TCCGGGTTAAGTCCCGAAGGCATTGAAT-GAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAATCGAGTT-CTAAAA
* *
54404553 -CCGGGCTATGTCCCGAAGGCACTTGAA-CGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAATCGAG
54404584 GAGCTAAATC
Statistics
Matches: 92, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
39 47 0.51
40 43 0.47
41 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAATCGAGTTCTAAAA
Found at i:54408632 original size:40 final size:40
Alignment explanation
Indices: 54408559--54408691 Score: 103
Period size: 40 Copynumber: 3.3 Consensus size: 40
54408549 CGGGCTAAGG
*
54408559 TCCCGAAGGC-TTTGTGCTA-AGTGACT-ATATCCGGACTAAAA
1 TCCCGAAGGCATTTGTGCGAGA-T-ACTAAT-TCCGG-CTAAAA
* * * * * *
54408600 T-CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAG
1 TCCCGAAGGCATTTGTGCGAGATACTAATTCCGGCTAAAA
* * * *
54408639 TCCCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAG
1 TCCCGAAGGCATTTGTGCGAGATACTAATTCCGGCTAAAA
54408679 TCCCGAAGGCATT
1 TCCCGAAGGCATT
54408692 CTGCGAGTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
39 4 0.05
40 60 0.79
41 12 0.16
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (40 bp):
TCCCGAAGGCATTTGTGCGAGATACTAATTCCGGCTAAAA
Found at i:54408711 original size:39 final size:38
Alignment explanation
Indices: 54408614--54408730 Score: 153
Period size: 39 Copynumber: 3.0 Consensus size: 38
54408604 AAGGTATTTG
* *
54408614 TGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTG
1 TGCGAGTT-TTAATTCCGGGTTAAGTCCCGAAGG-CATTC
**
54408654 TGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTC
1 TGCGAG-TTTTAATTCCGGGTTAAGTCCCGAAGGCATTC
*
54408693 TGCGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATT
1 TGCGAGTTTT-AATTCCGGGTTAAGTCCCGAAGGCATT
54408731 GAATGAGTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.03
39 35 0.51
40 30 0.44
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (38 bp):
TGCGAGTTTTAATTCCGGGTTAAGTCCCGAAGGCATTC
Found at i:54408739 original size:39 final size:40
Alignment explanation
Indices: 54408628--54408777 Score: 144
Period size: 39 Copynumber: 3.8 Consensus size: 40
54408618 AGTTATTAAT
* ** * *
54408628 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACT-AAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAAAA
*** *
54408668 TCCGGGTTAAGTCCCGAAGGCATTCTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAAA
* *
54408707 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAAA
* *
54408747 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
54408778 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 60 0.65
40 32 0.34
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAAA
Found at i:54411065 original size:27 final size:28
Alignment explanation
Indices: 54410981--54411078 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
54410971 CATGAGATTG
* * *
54410981 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
54411010 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
54411038 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
54411065 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
54411079 GACTTAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.38
28 21 0.33
29 19 0.30
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:54411092 original size:29 final size:27
Alignment explanation
Indices: 54411009--54411093 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 27
54410999 TAAATTGTTC
* *
54411009 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
54411037 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
54411064 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
54411093 A
1 A
54411094 TTTTTGAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.45
28 22 0.43
29 6 0.12
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:54419052 original size:27 final size:28
Alignment explanation
Indices: 54418965--54419065 Score: 134
Period size: 27 Copynumber: 3.6 Consensus size: 28
54418955 TGATCATGAG
* * *
54418965 ATAGCACTAAGTGTGCGGGTTTAAATTGT
1 ATAGCACTAAGTGTGCGAGTTT-GATTAT
54418994 -TCAGCACTAAGTGTGCGAGTTTGATTAT
1 AT-AGCACTAAGTGTGCGAGTTTGATTAT
54419022 ATAGCACTAAGTGTGCGAG-TTGATTAT
1 ATAGCACTAAGTGTGCGAGTTTGATTAT
*
54419049 ATAGCACTGAGTGTGCG
1 ATAGCACTAAGTGTGCG
54419066 GACTTAATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
27 24 0.36
28 22 0.33
29 20 0.30
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
ATAGCACTAAGTGTGCGAGTTTGATTAT
Found at i:54419076 original size:27 final size:27
Alignment explanation
Indices: 54418996--54419078 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
54418986 TAAATTGTTC
* *
54418996 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
54419024 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
54419051 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
54419078 A
1 A
54419079 TATTTTTGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:54419079 original size:29 final size:27
Alignment explanation
Indices: 54418965--54419080 Score: 99
Period size: 28 Copynumber: 4.1 Consensus size: 27
54418955 TGATCATGAG
** *
54418965 ATAGCACTAAGTGTGCGGGTTTAAATTGT
1 ATAGCACTAAGTGTGC-GACTT-AATTAT
* *
54418994 -TCAGCACTAAGTGTGCGAGTTTGATTAT
1 AT-AGCACTAAGTGTGCGA-CTTAATTAT
* *
54419022 ATAGCACTAAGTGTGCGAGTTGATTAT
1 ATAGCACTAAGTGTGCGACTTAATTAT
*
54419049 ATAGCACTGAGTGTGCGGACTTAATATAT
1 ATAGCACTAAGTGTGC-GACTTAAT-TAT
54419078 ATA
1 ATA
54419081 TTTTTGAATC
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
27 23 0.31
28 28 0.37
29 24 0.32
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (27 bp):
ATAGCACTAAGTGTGCGACTTAATTAT
Found at i:54425260 original size:24 final size:25
Alignment explanation
Indices: 54425182--54425253 Score: 108
Period size: 25 Copynumber: 2.8 Consensus size: 25
54425172 GAGGAAGTGC
* *
54425182 AAAAGGGCTTTTTGCCCCAGTTTACCG
1 AAAAGGGC--TTTGCCCCAGTTTATCA
54425209 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
54425234 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54425254 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 35 0.81
27 8 0.19
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:54425266 original size:24 final size:24
Alignment explanation
Indices: 54425192--54425280 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 24
54425182 AAAAGGGCTT
*
54425192 TTTGCCCCAGTTTACCGAAAAG-GGC
1 TTTGCCCCAG-TTATC-AAAAGAGGC
54425217 TTTGCCCCAGTTTATCAAAA-AGGGC
1 TTTGCCCCAG-TTATCAAAAGA-GGC
*
54425242 TTTGCCCCAGTTATTAAAAGAGGC
1 TTTGCCCCAGTTATCAAAAGAGGC
**
54425266 TAGGCCTCCAGTTAT
1 TTTGCC-CCAGTTAT
54425281 ATGATAAAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
24 19 0.34
25 37 0.66
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (24 bp):
TTTGCCCCAGTTATCAAAAGAGGC
Found at i:54425510 original size:30 final size:30
Alignment explanation
Indices: 54425474--54425556 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
54425464 CATTTACAGT
54425474 AAAGGCTTCAGCCCAGTGATATGATAATGA
1 AAAGGCTTCAGCCCAGTGATATGATAATGA
* * * *
54425504 AAAGGCTTCGGCCCAGTGACATCAATAATGC
1 AAAGGCTTCAGCCCAGTGATAT-GATAATGA
54425535 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTCAGCCCAGTGATATG
54425557 TTGAGATTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 23 0.51
31 22 0.49
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (30 bp):
AAAGGCTTCAGCCCAGTGATATGATAATGA
Found at i:54425539 original size:31 final size:30
Alignment explanation
Indices: 54425474--54425551 Score: 111
Period size: 31 Copynumber: 2.6 Consensus size: 30
54425464 CATTTACAGT
* *
54425474 AAAGGCTTCAGCCCAGTGATATGATAATGA
1 AAAGGCTTCAGCCCAGTGACATAATAATGA
* *
54425504 AAAGGCTTCGGCCCAGTGACATCAATAATGC
1 AAAGGCTTCAGCCCAGTGACAT-AATAATGA
54425535 AAAGGCTTCAGCCCAGT
1 AAAGGCTTCAGCCCAGT
54425552 ATATGTTGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 20 0.48
31 22 0.52
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (30 bp):
AAAGGCTTCAGCCCAGTGACATAATAATGA
Found at i:54433156 original size:25 final size:25
Alignment explanation
Indices: 54433111--54433178 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
54433101 GAGGAAGTGC
*
54433111 AAAAGGGCTTTTGCCCCAGTTTATCG
1 AAAAGGGC-TTTGCCCCAGTTTATCA
*
54433137 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
54433162 AAAAGGGCTTTGCCCCA
1 AAAAGGGCTTTGCCCCA
54433179 ATTATTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 31 0.79
26 8 0.21
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:54433436 original size:30 final size:31
Alignment explanation
Indices: 54433402--54433484 Score: 125
Period size: 30 Copynumber: 2.7 Consensus size: 31
54433392 CGTTTACAGT
54433402 AAAGGCTTCGGCCCAGTGATATG-ATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* * *
54433432 AAAGGCTTCGGCCTAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
54433463 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
54433485 TTGAGATTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 25 0.53
31 22 0.47
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:54433467 original size:31 final size:30
Alignment explanation
Indices: 54433402--54433479 Score: 120
Period size: 31 Copynumber: 2.6 Consensus size: 30
54433392 CGTTTACAGT
*
54433402 AAAGGCTTCGGCCCAGTGATATGATAATGA
1 AAAGGCTTCGGCCCAGTGACATGATAATGA
* *
54433432 AAAGGCTTCGGCCTAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGACATG-ATAATGA
54433463 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
54433480 ATATGTTGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 21 0.49
31 22 0.51
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTGACATGATAATGA
Found at i:54436022 original size:29 final size:29
Alignment explanation
Indices: 54435986--54436087 Score: 125
Period size: 29 Copynumber: 3.6 Consensus size: 29
54435976 ATAGGGTGAC
*
54435986 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
54436015 TGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* * *
54436044 TGGGCCTAATGAGCCATATGAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
54436072 TGTGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
54436088 GATACAGGTA
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 14 0.23
29 48 0.77
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:54436093 original size:57 final size:58
Alignment explanation
Indices: 54435986--54436096 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 58
54435976 ATAGGGTGAC
* * *
54435986 TGGGCCTAACGGGCCATATAAATGTGATTTGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAACGAGCCATATAAATATGATTTGGGCCTAATGGGCCAGATACAGGTGATT
* * * *
54436044 TGGGCCTAATGAGCCATATGAATATGA-TTGTGCTTAATGGGCCAGATACAGGT
1 TGGGCCTAACGAGCCATATAAATATGATTTGGGCCTAATGGGCCAGATACAGGT
54436097 ATGCGAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 23 0.50
58 23 0.50
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (58 bp):
TGGGCCTAACGAGCCATATAAATATGATTTGGGCCTAATGGGCCAGATACAGGTGATT
Found at i:54443994 original size:15 final size:16
Alignment explanation
Indices: 54443952--54444000 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
54443942 TGTGGCTCAA
54443952 CCGTGTGTGACACAAGG
1 CCGTGTGTGACAC-AGG
*
54443969 CCTTG-GT-ACACA-G
1 CCGTGTGTGACACAGG
54443982 CCGTGTGTGACACAAGG
1 CCGTGTGTGACAC-AGG
54443999 CC
1 CC
54444001 CCCTGAAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 5 0.19
14 3 0.12
15 8 0.31
16 3 0.12
17 7 0.27
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.18
Consensus pattern (16 bp):
CCGTGTGTGACACAGG
Found at i:54447315 original size:8 final size:8
Alignment explanation
Indices: 54447297--54447326 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
54447287 AAGAAAATTA
54447297 TGTGTATTT
1 TGTG-ATTT
54447306 TGTGATTT
1 TGTGATTT
54447314 TGTGATTT
1 TGTGATTT
54447322 TGTGA
1 TGTGA
54447327 ATTAGGAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (8 bp):
TGTGATTT
Found at i:54457948 original size:57 final size:57
Alignment explanation
Indices: 54457879--54457987 Score: 209
Period size: 57 Copynumber: 1.9 Consensus size: 57
54457869 TAGCTACCAT
54457879 AGTTTGACATTACAAGTACATTAAAACAAACCATTACTAGCCATTCCAATGGTAATC
1 AGTTTGACATTACAAGTACATTAAAACAAACCATTACTAGCCATTCCAATGGTAATC
*
54457936 AGTTTGACATTACAAGTACATTAAAACAAGCCATTACTAGCCATTCCAATGG
1 AGTTTGACATTACAAGTACATTAAAACAAACCATTACTAGCCATTCCAATGG
54457988 CTAGATTACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (57 bp):
AGTTTGACATTACAAGTACATTAAAACAAACCATTACTAGCCATTCCAATGGTAATC
Found at i:54460770 original size:27 final size:27
Alignment explanation
Indices: 54460731--54460784 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
54460721 CTCATATCTA
* *
54460731 TAGGCTAGTATTACTTAAATACCCTTG
1 TAGGCTAGAATTACTGAAATACCCTTG
*
54460758 TAGGGTAGAATTACTGAAATACCCTTG
1 TAGGCTAGAATTACTGAAATACCCTTG
54460785 GTTTACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (27 bp):
TAGGCTAGAATTACTGAAATACCCTTG
Found at i:54460796 original size:27 final size:27
Alignment explanation
Indices: 54460766--54461160 Score: 223
Period size: 27 Copynumber: 14.7 Consensus size: 27
54460756 TGTAGGGTAG
* * *
54460766 AATTACTGAAATACCCTTGGTTTACAA
1 AATTACTAAAATACCCTTGATTTGCAA
* *
54460793 AATTACT-GAATACCCTTG-GTT-CAA
1 AATTACTAAAATACCCTTGATTTGCAA
* * *
54460817 AATTACCAAAATACCCTCGATTAGCAA
1 AATTACTAAAATACCCTTGATTTGCAA
* * *
54460844 AATTACAAAAATACCCCT-AGTTTGTAA
1 AATTACTAAAATACCCTTGA-TTTGCAA
* * * *
54460871 AATTACCAAAATACCCATGGTTTGTAA
1 AATTACTAAAATACCCTTGATTTGCAA
* * * *
54460898 AATTACCAAAATACCCCTAATTTGTGAA
1 AATTACTAAAATACCCTTGATTTG-CAA
* * * ** *
54460926 AA-TA-TCGAAATATCATTGACCTGTAA
1 AATTACT-AAAATACCCTTGATTTGCAA
* * * *
54460952 AATTACTGAAATACCCTTAACTTGTAA
1 AATTACTAAAATACCCTTGATTTGCAA
* ** * *
54460979 AATTGCCGAAATACCCTCGATTTGTAA
1 AATTACTAAAATACCCTTGATTTGCAA
* * *
54461006 AATGACCAAAATACCCTTGATTTGGAA
1 AATTACTAAAATACCCTTGATTTGCAA
*
54461033 AATTACTAAAATACCCTTGATTTGGAA
1 AATTACTAAAATACCCTTGATTTGCAA
* * * *
54461060 AATTGC-AGAAATACCCCTAATTTACAA
1 AATTACTA-AAATACCCTTGATTTGCAA
* *
54461087 AATTACAAAAATACCCTTAACTTT-CAGA
1 AATTACTAAAATACCCTTGA-TTTGCA-A
* * *
54461115 AATTAC-ATAAATACCATTGGTTTGAAA
1 AATTACTA-AAATACCCTTGATTTGCAA
* *
54461142 AATTATTGAAATACCCTTG
1 AATTACTAAAATACCCTTG
54461161 GTTAGTAGAT
Statistics
Matches: 294, Mismatches: 58, Indels: 32
0.77 0.15 0.08
Matches are distributed among these distances:
24 9 0.03
25 11 0.04
26 17 0.06
27 231 0.79
28 26 0.09
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (27 bp):
AATTACTAAAATACCCTTGATTTGCAA
Found at i:54460811 original size:26 final size:25
Alignment explanation
Indices: 54460766--54460833 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 25
54460756 TGTAGGGTAG
54460766 AATTACTGAAATACCCTTGGTTTACAA
1 AATTACTGAAATACCCTTGG-TT-CAA
54460793 AATTACTG-AATACCCTTGGTTCAA
1 AATTACTGAAATACCCTTGGTTCAA
**
54460817 AATTACCAAAATACCCT
1 AATTACTGAAATACCCT
54460834 CGATTAGCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 9 0.24
25 10 0.26
26 11 0.29
27 8 0.21
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (25 bp):
AATTACTGAAATACCCTTGGTTCAA
Found at i:54460884 original size:54 final size:54
Alignment explanation
Indices: 54460815--54461103 Score: 267
Period size: 54 Copynumber: 5.4 Consensus size: 54
54460805 CCCTTGGTTC
* * *
54460815 AAAATTACCAAAATACCCTCGATTAGCAAAATTACAAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTCGATTTGTAAAATTACAAAAATACCCCTAATTTGT
* *
54460869 AAAATTACCAAAATACCCAT-GGTTTGTAAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCC-TCGATTTGTAAAATTACAAAAATACCCCTAATTTGT
* * * * * ** ** * *
54460923 GAAAA-TATCGAAATATCATTGACCTGTAAAATTACTGAAATACCCTTAACTTGT
1 -AAAATTACCAAAATACCCTCGATTTGTAAAATTACAAAAATACCCCTAATTTGT
* * * * * * *
54460977 AAAATTGCCGAAATACCCTCGATTTGTAAAATGACCAAAATACCCTTGATTTGG
1 AAAATTACCAAAATACCCTCGATTTGTAAAATTACAAAAATACCCCTAATTTGT
* * * * * **
54461031 AAAATTACTAAAATACCCTTGATTTGGAAAATTGCAGAAATACCCCTAATTTAC
1 AAAATTACCAAAATACCCTCGATTTGTAAAATTACAAAAATACCCCTAATTTGT
*
54461085 AAAATTACAAAAATACCCT
1 AAAATTACCAAAATACCCT
54461104 TAACTTTCAG
Statistics
Matches: 188, Mismatches: 43, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
53 5 0.03
54 178 0.95
55 5 0.03
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (54 bp):
AAAATTACCAAAATACCCTCGATTTGTAAAATTACAAAAATACCCCTAATTTGT
Found at i:54461460 original size:36 final size:39
Alignment explanation
Indices: 54461413--54461500 Score: 128
Period size: 41 Copynumber: 2.3 Consensus size: 39
54461403 GATTATACCA
54461413 TGGATCCACCGATT-GA-AG-ATGGTTGCTTGACGACCG
1 TGGATCCACCGATTAGATAGCATGGTTGCTTGACGACCG
*
54461449 TGGATCCACCGATTAAGGATCGCATGGTTGCTTGACGACCG
1 TGGATCCACCGATT-A-GATAGCATGGTTGCTTGACGACCG
54461490 TGGATCCACCG
1 TGGATCCACCG
54461501 GTGGCTTTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
36 14 0.30
39 2 0.04
40 1 0.02
41 29 0.63
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.24
Consensus pattern (39 bp):
TGGATCCACCGATTAGATAGCATGGTTGCTTGACGACCG
Found at i:54461926 original size:22 final size:22
Alignment explanation
Indices: 54461901--54461961 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
54461891 CTGGCAGTGT
*
54461901 TGTTGTGATGTTTACGGCTATG
1 TGTTGTCATGTTTACGGCTATG
*
54461923 TGTTGTCCTGTTTACGGCTATG
1 TGTTGTCATGTTTACGGCTATG
* *
54461945 TGTTGTCTTGTCTACGG
1 TGTTGTCATGTTTACGG
54461962 TTTTGAGCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.10, C:0.15, G:0.30, T:0.46
Consensus pattern (22 bp):
TGTTGTCATGTTTACGGCTATG
Found at i:54464678 original size:27 final size:27
Alignment explanation
Indices: 54464648--54464724 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 27
54464638 CCCATATATG
*
54464648 TAGGCTAGTATTACTGAAATACCCCTA
1 TAGGCTAGAATTACTGAAATACCCCTA
* *
54464675 TAGGGTAGAATTACTGAAATGCCCCTA
1 TAGGCTAGAATTACTGAAATACCCCTA
** * *
54464702 TAGGGGAGAATTATTAAAATACC
1 TAGGCTAGAATTACTGAAATACC
54464725 TTTGGTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (27 bp):
TAGGCTAGAATTACTGAAATACCCCTA
Found at i:54464755 original size:26 final size:27
Alignment explanation
Indices: 54464717--54465083 Score: 122
Period size: 27 Copynumber: 13.6 Consensus size: 27
54464707 GAGAATTATT
*
54464717 AAAATACCTTTGGTTTAAAAAATT-CC
1 AAAATACCCTTGGTTTAAAAAATTACC
* *
54464743 TAAATACCCTTGGTTTACAAAATTACC
1 AAAATACCCTTGGTTTAAAAAATTACC
* * *
54464770 AAAATACCC-TCGATTAGAAAAATTACA
1 AAAATACCCTTGGTTTA-AAAAATTACC
* **
54464797 AAAATA-TCTCTGGTTTTTAAAATTACC
1 AAAATACCCT-TGGTTTAAAAAATTACC
* * **
54464824 AAAATACCCCTGATTTGTGAAAA-TA-C
1 AAAATACCCTTGGTTT-AAAAAATTACC
* *** ** *
54464850 AGAAATACCCTCGACCTGCAAAATTACT
1 A-AAATACCCTTGGTTTAAAAAATTACC
* ** ** *
54464878 GAAATACCC-TGAACTTGCAAAATTATC
1 AAAATACCCTTG-GTTTAAAAAATTACC
* * ** **
54464905 GAAATACCTTTAATTTGTAAAATTACC
1 AAAATACCCTTGGTTTAAAAAATTACC
* * ** *
54464932 AAAATACCCCTGATTTGGAAAATTATC
1 AAAATACCCTTGGTTTAAAAAATTACC
* * **
54464959 AAAATACCTTTGATTTGGAAAATTA-C
1 AAAATACCCTTGGTTTAAAAAATTACC
* * *
54464985 AGAAATACCCTTGATTTACAAAATTA-T
1 A-AAATACCCTTGGTTTAAAAAATTACC
* * *
54465012 AGAAATACCCTTAGATTTCAAAAATTA-T
1 A-AAATACCCTT-GGTTTAAAAAATTACC
* * **
54465040 AGAAATACCATTAGTTTTCAAAATTACC
1 A-AAATACCCTTGGTTTAAAAAATTACC
*
54465068 GAAATACCCTTGGTTT
1 AAAATACCCTTGGTTT
54465084 GTAGATTTAC
Statistics
Matches: 269, Mismatches: 58, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
26 36 0.13
27 198 0.74
28 35 0.13
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.31
Consensus pattern (27 bp):
AAAATACCCTTGGTTTAAAAAATTACC
Found at i:54464967 original size:54 final size:54
Alignment explanation
Indices: 54464761--54465038 Score: 219
Period size: 54 Copynumber: 5.1 Consensus size: 54
54464751 CTTGGTTTAC
* * * * * *
54464761 AAAATTACCAAAATA-CCCTCGATTAGAAAAATTA-CAAAAATATCTCTGGTTTTT
1 AAAATTACCAAAATACCCCT-GATTTGCAAAATTATC-AAAATACCTTTGATTTGT
* * * ** *
54464815 AAAATTACCAAAATACCCCTGATTTGTGAAAA-TA-CAGAAATACCCTCGACCTGC
1 AAAATTACCAAAATACCCCTGATTTG-CAAAATTATCA-AAATACCTTTGATTTGT
** * * *
54464869 AAAATTACTGAAATA-CCCTGAACTTGCAAAATTATCGAAATACCTTTAATTTGT
1 AAAATTACCAAAATACCCCTG-ATTTGCAAAATTATCAAAATACCTTTGATTTGT
* *
54464923 AAAATTACCAAAATACCCCTGATTTGGAAAATTATCAAAATACCTTTGATTTGG
1 AAAATTACCAAAATACCCCTGATTTGCAAAATTATCAAAATACCTTTGATTTGT
* * * **
54464977 AAAATTA-CAGAAATACCCTTGATTTACAAAATTAT-AGAAATACCCTTAGATTTCA
1 AAAATTACCA-AAATACCCCTGATTTGCAAAATTATCA-AAATA-CCTTTGATTTGT
54465032 AAAATTA
1 AAAATTA
54465039 TAGAAATACC
Statistics
Matches: 179, Mismatches: 35, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
53 13 0.07
54 136 0.76
55 30 0.17
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (54 bp):
AAAATTACCAAAATACCCCTGATTTGCAAAATTATCAAAATACCTTTGATTTGT
Found at i:54465048 original size:55 final size:56
Alignment explanation
Indices: 54464815--54465078 Score: 201
Period size: 54 Copynumber: 4.9 Consensus size: 56
54464805 TCTGGTTTTT
* * * * ** *
54464815 AAAATTACCA-AAATACCCCTGATTTGTGAAAA-TACAGAAATACCC-TCGACCTGC
1 AAAATTACCAGAAATACCCTTGATTTG-CAAAATTATAGAAATACCCTTAGATTTGA
* * * * *
54464869 AAAATTA-CTGAAATACCC-TGAACTTGCAAAATTATCGAAATACCTTTA-ATTTGT
1 AAAATTACCAGAAATACCCTTG-ATTTGCAAAATTATAGAAATACCCTTAGATTTGA
* * * *
54464923 AAAATTACCA-AAATACCCCTGATTTGGAAAATTATCA-AAATA-CCTTTGATTTGG
1 AAAATTACCAGAAATACCCTTGATTTGCAAAATTAT-AGAAATACCCTTAGATTTGA
* *
54464977 AAAATTA-CAGAAATACCCTTGATTTACAAAATTATAGAAATACCCTTAGATTTCA
1 AAAATTACCAGAAATACCCTTGATTTGCAAAATTATAGAAATACCCTTAGATTTGA
* * * **
54465032 AAAATTA-TAGAAATACCATT-AGTTTTCAAAATTACCGAAATACCCTT
1 AAAATTACCAGAAATACCCTTGA-TTTGCAAAATTATAGAAATACCCTT
54465079 GGTTTGTAGA
Statistics
Matches: 170, Mismatches: 28, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
53 13 0.08
54 104 0.61
55 53 0.31
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (56 bp):
AAAATTACCAGAAATACCCTTGATTTGCAAAATTATAGAAATACCCTTAGATTTGA
Found at i:54465404 original size:41 final size:41
Alignment explanation
Indices: 54465344--54465466 Score: 201
Period size: 41 Copynumber: 3.0 Consensus size: 41
54465334 AGAGGAAGAA
*
54465344 ATTGAGGATCGCATAGTTGCTTGACGACCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
*
54465385 ATTGAGGATCGCATGGTTGCTTGACGATCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
* * *
54465426 ATTAAGGATTGCATGGTTGCTTGATGACCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
54465467 GTGGCTTTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
Found at i:54465633 original size:22 final size:22
Alignment explanation
Indices: 54465608--54465672 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
54465598 GCCAATTATT
*
54465608 CTACTTATGGCTTTGTGCCAAC
1 CTACTTATGGCTATGTGCCAAC
* * *
54465630 CTACATATGGCTCTGTACCAAC
1 CTACTTATGGCTATGTGCCAAC
54465652 CTTA-TTATGGCTATGTGCCAA
1 C-TACTTATGGCTATGTGCCAA
54465673 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 34 0.94
23 2 0.06
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (22 bp):
CTACTTATGGCTATGTGCCAAC
Found at i:54465679 original size:22 final size:22
Alignment explanation
Indices: 54465612--54465679 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
54465602 ATTATTCTAC
*
54465612 TTATGGCTTTGTGCC-AACCTA
1 TTATGGCTATGTGCCAAACCTA
* * *
54465633 CATATGGCTCTGTACC-AACCTTA
1 -TTATGGCTATGTGCCAAACC-TA
*
54465656 TTATGGCTATGTGCCAAACGTA
1 TTATGGCTATGTGCCAAACCTA
54465678 TT
1 TT
54465680 TGCCTAAAGC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 32 0.86
23 5 0.14
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (22 bp):
TTATGGCTATGTGCCAAACCTA
Found at i:54469833 original size:27 final size:27
Alignment explanation
Indices: 54469803--54469980 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54469793 ATATTGAGTC
* * * *
54469803 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54469830 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54469857 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54469885 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54469912 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54469939 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54469966 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54469981 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54469942 original size:82 final size:81
Alignment explanation
Indices: 54469824--54469979 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54469814 TGCTATATAA
* *
54469824 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54469889 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54469906 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54469970 CACTTAGTGC
65 CACTTAGTGC
54469980 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54477989 original size:26 final size:26
Alignment explanation
Indices: 54477960--54478042 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
54477950 ATGAGTCCGC
*
54477960 CACATCAGTGCTATATAATCAACTCG
1 CACATCAGTGCTACATAATCAACTCG
* * *
54477986 CACACTTAGTGCTACGTAATCAAATCG
1 CACA-TCAGTGCTACATAATCAACTCG
*
54478013 CACA-CTAGTGCTACATAGTCAACTCG
1 CACATC-AGTGCTACATAATCAACTCG
54478039 CACA
1 CACA
54478043 CTTAGTGCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
26 25 0.53
27 22 0.47
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (26 bp):
CACATCAGTGCTACATAATCAACTCG
Found at i:54478005 original size:27 final size:27
Alignment explanation
Indices: 54477966--54478110 Score: 150
Period size: 27 Copynumber: 5.4 Consensus size: 27
54477956 CCGCCACATC
*
54477966 AGTGCTATATAATCAACTCGCACACTT
1 AGTGCTACATAATCAACTCGCACACTT
* *
54477993 AGTGCTACGTAATCAAATCGCACAC-T
1 AGTGCTACATAATCAACTCGCACACTT
*
54478019 AGTGCTACATAGTCAACTCGCACACTT
1 AGTGCTACATAATCAACTCGCACACTT
** ** *
54478046 AGTGCCGCATGGTCAATTCGCACACTT
1 AGTGCTACATAATCAACTCGCACACTT
* **
54478073 AGTGC-ATCATATTCATTTCGCACACTT
1 AGTGCTA-CATAATCAACTCGCACACTT
*
54478100 AGTGCAACATA
1 AGTGCTACATA
54478111 GGACAAATGC
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
26 23 0.23
27 77 0.76
28 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
AGTGCTACATAATCAACTCGCACACTT
Found at i:54478046 original size:53 final size:54
Alignment explanation
Indices: 54477966--54478110 Score: 159
Period size: 53 Copynumber: 2.7 Consensus size: 54
54477956 CCGCCACATC
* * *
54477966 AGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACAC-T
1 AGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTT
* * ** *
54478019 AGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTT
1 AGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTT
* ** *
54478073 AGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATA
1 AGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATA
54478111 GGACAAATGC
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
53 45 0.59
54 31 0.41
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (54 bp):
AGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTT
Found at i:54479828 original size:41 final size:41
Alignment explanation
Indices: 54479781--54479952 Score: 269
Period size: 41 Copynumber: 4.3 Consensus size: 41
54479771 AATGCTTTGA
* **
54479781 GACTTAGCCCAGAATATAGTAGTTCGCACAAATGCCTTCGG
1 GACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGG
* *
54479822 GACTTAGCCTGGATTATAGTAACTCGCACAAATGCCTTCGG
1 GACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGG
*
54479863 GACTTAGCCCGGAAAATAGTAACTCGCACAAATGCCTTCGG
1 GACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGG
54479904 GACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTT-GG
1 GACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGG
54479943 GACTTA-CCCG
1 GACTTAGCCCG
54479953 TTATCATCCG
Statistics
Matches: 122, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
38 4 0.03
39 8 0.07
40 22 0.18
41 88 0.72
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (41 bp):
GACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGG
Found at i:54488684 original size:27 final size:27
Alignment explanation
Indices: 54488649--54488891 Score: 265
Period size: 27 Copynumber: 9.0 Consensus size: 27
54488639 ATAAATACCT
* *
54488649 CACATAGGGGCAAAACAGTCAATTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
** * **
54488676 CATGTAGGGGCATTTA-AGTCATTTTAC
1 CACATAAGGGCA-AAACAGTCATTTTAC
*
54488703 CACGTAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
54488730 CTCATAAGGGCAAAACAATCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
*
54488757 CACATAAGGGGAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
54488784 CACATAAGGGCAAAATAATCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
54488811 CATATAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
54488838 CACATAAGGGCAAATAATAGTTATTTTAC
1 CACATAAGGGC-AA-AACAGTCATTTTAC
* * *
54488867 CACAAAAGGG-TAAATAGTCATTTTA
1 CACATAAGGGCAAAACAGTCATTTTA
54488892 TTAATTTGGG
Statistics
Matches: 187, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.07
27 149 0.80
28 3 0.02
29 22 0.12
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:54489711 original size:23 final size:24
Alignment explanation
Indices: 54489665--54489712 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
54489655 AAGAAAGAGT
54489665 ATAGGGAGTCCAAAAATTTAGCAA
1 ATAGGGAGTCCAAAAATTTAGCAA
*
54489689 ATAGGGAGTCC-AAAATTTGGCAA
1 ATAGGGAGTCCAAAAATTTAGCAA
54489712 A
1 A
54489713 ACAAAGAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (24 bp):
ATAGGGAGTCCAAAAATTTAGCAA
Found at i:54490999 original size:43 final size:43
Alignment explanation
Indices: 54490894--54491001 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 43
54490884 TAGCCCATCT
* * *
54490894 ATGGTCTTACTCGA-AATCAAATAATGAGGCCAATGTCCTAGAC
1 ATGGTCTTACAC-ATAATCACATAATGAGGCCAATGTCCCAGAC
* *
54490937 ATGGTCTTACACATAATCACATAATGATGCCAATGTCCCAGCC
1 ATGGTCTTACACATAATCACATAATGAGGCCAATGTCCCAGAC
*
54490980 ATGGTCTTACATATAATCACAT
1 ATGGTCTTACACATAATCACAT
54491002 CTCGTTAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.02
43 57 0.98
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACATAATCACATAATGAGGCCAATGTCCCAGAC
Found at i:54496730 original size:21 final size:20
Alignment explanation
Indices: 54496706--54496744 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
54496696 GCAGAGTATT
*
54496706 GTACTGAAAATTTTAGAATTG
1 GTACAGAAAATTTT-GAATTG
*
54496727 GTACAGAAGATTTTGAAT
1 GTACAGAAAATTTTGAAT
54496745 GAAGCTCAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (20 bp):
GTACAGAAAATTTTGAATTG
Found at i:54503889 original size:48 final size:48
Alignment explanation
Indices: 54503812--54504191 Score: 379
Period size: 48 Copynumber: 7.8 Consensus size: 48
54503802 AGTGTTTTGT
* *
54503812 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGATATGA
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGATATGA
* * * * * *
54503860 GAGCTAGTGTAAGACCATATCTGGGACATGGCATCAGCCTCGATATGT
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGATATGA
* * * *
54503908 GATCCAGTGTAAGACCATGTTTAGAACATGGCATCGGCATTGATATGA
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGATATGA
* * * * *
54503956 GAGCTGGTGTAAAACCATGTCTGGGGCATGGCATCGGCCTTGATATGTA
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGATATG-A
* * *
54504005 -AGCTAGTGTAAGACCGTGTTTGAGTCATGGCATCGGCATTGATATGA
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGATATGA
* * * *
54504052 GAGCTAGTGTGAGACCATGTTTGGGTCATGGCATCGACACCAAT-ATATGA
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCG---GCATTGATATGA
* * * *
54504102 GAGAC-AGTGTATGACCATGTTTGGAACATGGCATCGACATGGATATATGA
1 GAG-CTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTG--ATATGA
** * * *
54504152 GAGCCCGTGTATGACCATGTCTGGGACATGGCATTGGCAT
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCAT
54504192 CTCACCCTTT
Statistics
Matches: 271, Mismatches: 51, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
47 3 0.01
48 187 0.69
49 2 0.01
50 75 0.28
51 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (48 bp):
GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGATATGA
Found at i:54503973 original size:96 final size:96
Alignment explanation
Indices: 54503809--54504185 Score: 459
Period size: 96 Copynumber: 3.9 Consensus size: 96
54503799 ACTAGTGTTT
54503809 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGATATGAGAGCTAGTGTAAGA
1 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGATATGAGAGCTAGTGTAAGA
* *
54503874 CCATATCTGGGACATGGCATCAGCCTCGATA
66 CCATGTCTGGGACATGGCATCAGCCTAGATA
* * * *
54503905 TGTGATCCAGTGTAAGACCATGTTTAGAACATGGCATCGGCATTGATATGAGAGCTGGTGTAAAA
1 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGATATGAGAGCTAGTGTAAGA
* * *
54503970 CCATGTCTGGGGCATGGCATCGGCCTTGATA
66 CCATGTCTGGGACATGGCATCAGCCTAGATA
* * * * *
54504001 TGTAAGCTAGTGTAAGACCGTGTTT-GAGTCATGGCATCGGCATTGATATGAGAGCTAGTGTGAG
1 TGTGAGCCAGTGTAAGACCATGTTTGGA-ACATGGCATCGGCATTGATATGAGAGCTAGTGTAAG
* * * * *
54504065 ACCATGTTTGGGTCATGGCATCGACACCAATATA
65 ACCATGTCTGGGACATGGCATC-A-GCCTAGATA
* * * * * ** *
54504099 TGAGAGACAGTGTATGACCATGTTTGGAACATGGCATCGACATGGATATATGAGAGCCCGTGTAT
1 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTG--ATATGAGAGCTAGTGTAA
54504164 GACCATGTCTGGGACATGGCAT
64 GACCATGTCTGGGACATGGCAT
54504186 TGGCATCTCA
Statistics
Matches: 237, Mismatches: 38, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
95 2 0.01
96 161 0.68
98 38 0.16
99 2 0.01
100 34 0.14
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (96 bp):
TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGATATGAGAGCTAGTGTAAGA
CCATGTCTGGGACATGGCATCAGCCTAGATA
Found at i:54504118 original size:50 final size:49
Alignment explanation
Indices: 54504046--54504185 Score: 174
Period size: 50 Copynumber: 2.8 Consensus size: 49
54504036 ATCGGCATTG
*
54504046 ATATGAGAGCTAGTGTGA-GACCATGTTTGGGTCATGGCATCGACACCAAT
1 ATATGAGAGC-AGTGT-ATGACCATGTTTGGGACATGGCATCGACACCAAT
* ***
54504096 ATATGAGAGACAGTGTATGACCATGTTTGGAACATGGCATCGACATGGAT
1 ATATGAGAG-CAGTGTATGACCATGTTTGGGACATGGCATCGACACCAAT
* *
54504146 ATATGAGAGCCCGTGTATGACCATGTCTGGGACATGGCAT
1 ATATGAGAG-CAGTGTATGACCATGTTTGGGACATGGCAT
54504186 TGGCATCTCA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.01
50 77 0.97
51 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (49 bp):
ATATGAGAGCAGTGTATGACCATGTTTGGGACATGGCATCGACACCAAT
Found at i:54506413 original size:27 final size:26
Alignment explanation
Indices: 54506382--54506476 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 26
54506372 TTAGTTTACC
**
54506382 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCCAAATACCCTCGA-TTGTA
* *
54506409 AAATTA-CCAAAGTACCCCCGATTTATA
1 AAATTACCCAAA-TACCCTCGA-TTGTA
* *
54506436 AAATTACCCAAATATCCTCGATAAGTA
1 AAATTACCCAAATACCCTCGAT-TGTA
*
54506463 AAATTACCGAAATA
1 AAATTACCCAAATA
54506477 AGATAGAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
26 4 0.07
27 46 0.84
28 5 0.09
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.26
Consensus pattern (26 bp):
AAATTACCCAAATACCCTCGATTGTA
Found at i:54506513 original size:27 final size:27
Alignment explanation
Indices: 54506483--54506652 Score: 207
Period size: 27 Copynumber: 6.3 Consensus size: 27
54506473 AATAAGATAG
54506483 AATTACCATTTTACCCTCGATTTACAA
1 AATTACCATTTTACCCTCGATTTACAA
* * * *
54506510 AATTATCGTTTTACCCTCGATTTATAG
1 AATTACCATTTTACCCTCGATTTACAA
54506537 AATTACCATTTTACCCTCGATTTACAA
1 AATTACCATTTTACCCTCGATTTACAA
* *
54506564 AATTACCGTTTTACCCTCGATTTACAT
1 AATTACCATTTTACCCTCGATTTACAA
* * *
54506591 AATTATCGTTTTACCCTCAATTTACAA
1 AATTACCATTTTACCCTCGATTTACAA
* ** *
54506618 AATTACTGA-AATACCCTTGATTTACAA
1 AATTAC-CATTTTACCCTCGATTTACAA
54506645 AATTACCA
1 AATTACCA
54506653 AAATACCTTC
Statistics
Matches: 121, Mismatches: 21, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
26 1 0.01
27 120 0.99
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (27 bp):
AATTACCATTTTACCCTCGATTTACAA
Found at i:54506537 original size:54 final size:54
Alignment explanation
Indices: 54506479--54506623 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
54506469 CCGAAATAAG
*
54506479 ATAGAATTACCATTTTACCCTCGATTTACAAAATTATCGTTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTT
54506533 ATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTT
* * * * *
54506587 ACATAATTATCGTTTTACCCTCAATTTACAAAATTAC
1 ATAGAATTACCATTTTACCCTCGATTTACAAAATTAC
54506624 TGAAATACCC
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 85 1.00
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (54 bp):
ATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTT
Found at i:54506577 original size:81 final size:81
Alignment explanation
Indices: 54506483--54506652 Score: 243
Period size: 81 Copynumber: 2.1 Consensus size: 81
54506473 AATAAGATAG
* * * *
54506483 AATTACCATTTTACCCTCGATTTACAAAATTATCGTTTTACCCTCGATTTATAGAATTAC-CATT
1 AATTACCATTTTACCCTCGATTTACAAAATTATCGTTTTACCCTCAATTTACAAAATTACTCA-A
*
54506547 TTACCCTCGATTTACAA
65 ATACCCTCGATTTACAA
* * *
54506564 AATTACCGTTTTACCCTCGATTTACATAATTATCGTTTTACCCTCAATTTACAAAATTACTGAAA
1 AATTACCATTTTACCCTCGATTTACAAAATTATCGTTTTACCCTCAATTTACAAAATTACTCAAA
*
54506629 TACCCTTGATTTACAA
66 TACCCTCGATTTACAA
54506645 AATTACCA
1 AATTACCA
54506653 AAATACCTTC
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 77 0.99
82 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (81 bp):
AATTACCATTTTACCCTCGATTTACAAAATTATCGTTTTACCCTCAATTTACAAAATTACTCAAA
TACCCTCGATTTACAA
Found at i:54506656 original size:27 final size:27
Alignment explanation
Indices: 54506610--54506706 Score: 97
Period size: 27 Copynumber: 3.6 Consensus size: 27
54506600 TTTACCCTCA
**
54506610 ATTTACAAAATTACTGAAATACCCTTG
1 ATTTACAAAATTACCAAAATACCCTTG
54506637 ATTTACAAAATTACCAAAATA-CCTTCG
1 ATTTACAAAATTACCAAAATACCCTT-G
** * *
54506664 ATCAATAAAATTACCAAAATACCCCTG
1 ATTTACAAAATTACCAAAATACCCTTG
* **
54506691 GTTTGTAAAATTACCA
1 ATTTACAAAATTACCA
54506707 TTTTGCCCCT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
26 4 0.07
27 51 0.88
28 3 0.05
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (27 bp):
ATTTACAAAATTACCAAAATACCCTTG
Found at i:54506676 original size:81 final size:81
Alignment explanation
Indices: 54506494--54506676 Score: 188
Period size: 81 Copynumber: 2.3 Consensus size: 81
54506484 ATTACCATTT
** * * * **
54506494 TACCCTCGATTTACAAAATTATCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATT
1 TACCCTCGATCAACAAAATTATCGTTTTACCCTCAATTTACAAAATTACCATAATACCCTCGATT
****
54506559 TACAAAATTACCGTTT
66 TACAAAATTACCAAAA
** * * *
54506575 TACCCTCGATTTACATAATTATCGTTTTACCCTCAATTTACAAAATTACTGA-AATACCCTTGAT
1 TACCCTCGATCAACAAAATTATCGTTTTACCCTCAATTTACAAAATTAC-CATAATACCCTCGAT
54506639 TTACAAAATTACCAAAA
65 TTACAAAATTACCAAAA
* *
54506656 TACCTTCGATCAATAAAATTA
1 TACCCTCGATCAACAAAATTA
54506677 CCAAAATACC
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
81 83 0.99
82 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (81 bp):
TACCCTCGATCAACAAAATTATCGTTTTACCCTCAATTTACAAAATTACCATAATACCCTCGATT
TACAAAATTACCAAAA
Found at i:54507135 original size:31 final size:31
Alignment explanation
Indices: 54507100--54507178 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
54507090 TTGCATTCAC
* *
54507100 ATTCTGATTTTGATTCTGTTACCTGATACTA
1 ATTCTGATTCTGATTCTGTCACCTGATACTA
** *
54507131 ATTCTGATTCTGATTCTGTCACCTGATTTTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTA
54507162 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
54507179 AGTTCTGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTA
Found at i:54507142 original size:6 final size:6
Alignment explanation
Indices: 54507100--54507187 Score: 65
Period size: 6 Copynumber: 14.3 Consensus size: 6
54507090 TTGCATTCAC
* * *
54507100 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTA ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
54507149 -TCACCTG ATTTTG ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
54507188 AATGTTTCTT
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 4 0.06
6 51 0.80
7 7 0.11
8 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:54520388 original size:40 final size:40
Alignment explanation
Indices: 54520294--54520388 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
54520284 GACTATGTTC
*
54520294 GGCACTAAGTATGC-AATTTAAATAGCTTCGGCTATAAAT
1 GGCACTAAGTATGCGAATTGAAATAGCTTCGGCTATAAAT
* ** * * *
54520333 AGCACTAAGCGTGCGAGTTGGAATAGCTTTGGCTATATAA-
1 GGCACTAAGTATGCGAATTGAAATAGCTTCGGCTATA-AAT
54520373 GGCACTAAGTATGCGA
1 GGCACTAAGTATGCGA
54520389 TTCTGAGATA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
39 11 0.25
40 31 0.70
41 2 0.05
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (40 bp):
GGCACTAAGTATGCGAATTGAAATAGCTTCGGCTATAAAT
Found at i:54526653 original size:19 final size:19
Alignment explanation
Indices: 54526624--54526667 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54526614 CAACAGACAT
**
54526624 AAAACTCTTGACATGGCATG
1 AAAA-TCTTGACATGAAATG
*
54526644 AAAATCTTGAGATGAAATG
1 AAAATCTTGACATGAAATG
54526663 AAAAT
1 AAAAT
54526668 GACTTGAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.25
Consensus pattern (19 bp):
AAAATCTTGACATGAAATG
Found at i:54530178 original size:40 final size:40
Alignment explanation
Indices: 54530096--54530313 Score: 223
Period size: 40 Copynumber: 5.5 Consensus size: 40
54530086 ACCCAAGTAT
** * *
54530096 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
54530134 CTTCGGGTCTTAGCCCAGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
54530174 CTTCGGGACTTAGCCCGGATATAGTCGCTAGC-CAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
54530213 CTT-GGGT-TTTGGCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
54530251 CTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCAC-TAGCACAAATGC
*
54530292 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
54530314 CATTCGAATA
Statistics
Matches: 146, Mismatches: 27, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
37 19 0.13
38 24 0.16
39 26 0.18
40 48 0.33
41 29 0.20
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Done.