Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 20 of 427
Found at i:5457273 original size:25 final size:23
Alignment explanation
Indices: 5457245--5457302 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
5457235 TTGCAAAGAT
*
5457245 ATTACTTTTTAGTTTTATTTTTTTA
1 ATTA-TTTTT-GTTTTATTTTTTAA
5457270 ATTATTTAGTTGTTTTATTTTTTAA
1 ATTATTT--TTGTTTTATTTTTTAA
5457295 ATTATTTT
1 ATTATTTT
5457303 AGGAATCATC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 24 0.80
26 2 0.07
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (23 bp):
ATTATTTTTGTTTTATTTTTTAA
Found at i:5463564 original size:18 final size:18
Alignment explanation
Indices: 5463543--5463592 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
5463533 AACAGTACTA
5463543 TATACGTAAATAGTGCCG
1 TATACGTAAATAGTGCCG
5463561 TATACGTAAATAGTGCCG
1 TATACGTAAATAGTGCCG
*
5463579 TATACTTAAATAGT
1 TATACGTAAATAGT
5463593 TCCATAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (18 bp):
TATACGTAAATAGTGCCG
Found at i:5466304 original size:18 final size:18
Alignment explanation
Indices: 5466281--5466316 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5466271 AAATTTTGAG
*
5466281 TTAATCAAATTGAGTTAT
1 TTAATCAAATCGAGTTAT
5466299 TTAATCAAATCGAGTTAT
1 TTAATCAAATCGAGTTAT
5466317 ACAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (18 bp):
TTAATCAAATCGAGTTAT
Found at i:5466516 original size:19 final size:19
Alignment explanation
Indices: 5466492--5466532 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5466482 AAAAATTAAA
5466492 AAAAT-AATTTCCAAAATTC
1 AAAATAAATTT-CAAAATTC
*
5466511 AAAATAAATTTTAAAATTC
1 AAAATAAATTTCAAAATTC
5466530 AAA
1 AAA
5466533 TTATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATAAATTTCAAAATTC
Found at i:5466562 original size:19 final size:19
Alignment explanation
Indices: 5466504--5466562 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
5466494 AATAATTTCC
* *
5466504 AAAATTCAAAATAAATTTT-
1 AAAATTC-AAATTATTTTTA
*
5466523 AAAATTCAAATTATTTATA
1 AAAATTCAAATTATTTTTA
*
5466542 AAAATTTC-AATTTTTTTTA
1 AAAA-TTCAAATTATTTTTA
5466561 AA
1 AA
5466563 TTATAAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 8 0.24
19 22 0.67
20 3 0.09
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATTCAAATTATTTTTA
Found at i:5466695 original size:3 final size:3
Alignment explanation
Indices: 5466687--5466735 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
5466677 CATTCTAAAG
5466687 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5466735 T
1 T
5466736 TTTCTTTGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5472380 original size:153 final size:153
Alignment explanation
Indices: 5472083--5472384 Score: 390
Period size: 153 Copynumber: 2.0 Consensus size: 153
5472073 TCTAAGGGAC
* * * * * *
5472083 TGCAATCTTTGTGAAGGAGATATTCCACGTGATATTTCTGGTCTATCCTCTTTGACAGATCTTGA
1 TGCAATCTTGGTGAAGCAGATATTCAAAGTGATATTTCTGGTCTATCCTCTTTGACACATCTTAA
* * * * **
5472148 TCTTAGTGGTAACAATTTCAGCAGCATACCTGCATCTCTTATTGGACTCTCGAAGCTTGGGTTTC
66 TCTTAGTAGTAACAATTTCAGCAGCATACCTGCATCTCTTACTAGACTCTCCAAGCTTCAGTTTC
*
5472213 TTACGTTGTCAAATTGCAACATG
131 TTACATTGTCAAATTGCAACATG
* * ***
5472236 TGCACTCTTGGTGAAGCAGATATTCAAAGTTATATTTCTGGTCTATCCTCTTTGGTTCATCTTAA
1 TGCAATCTTGGTGAAGCAGATATTCAAAGTGATATTTCTGGTCTATCCTCTTTGACACATCTTAA
* * *
5472301 TCTTAGTATTAACAATTTCATCAGCATACCTGCATCTCTTACTAGACTTTCCAAGCTTCAGTTTC
66 TCTTAGTAGTAACAATTTCAGCAGCATACCTGCATCTCTTACTAGACTCTCCAAGCTTCAGTTTC
*
5472366 TTGCATTGGT-AAATTGCAA
131 TTACATT-GTCAAATTGCAA
5472385 GATGCTTAAA
Statistics
Matches: 126, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
153 124 0.98
154 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (153 bp):
TGCAATCTTGGTGAAGCAGATATTCAAAGTGATATTTCTGGTCTATCCTCTTTGACACATCTTAA
TCTTAGTAGTAACAATTTCAGCAGCATACCTGCATCTCTTACTAGACTCTCCAAGCTTCAGTTTC
TTACATTGTCAAATTGCAACATG
Found at i:5480468 original size:6 final size:6
Alignment explanation
Indices: 5480457--5480503 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
5480447 CCAATCTTTC
5480457 TTTTTA TTTTTA TTATTTA TTATTT- TCTTTTA TTTTTA -TTTTA TTTT
1 TTTTTA TTTTTA TT-TTTA TT-TTTA T-TTTTA TTTTTA TTTTTA TTTT
5480504 AGTTAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.14
6 20 0.54
7 12 0.32
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:5480503 original size:16 final size:15
Alignment explanation
Indices: 5480457--5480504 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 15
5480447 CCAATCTTTC
*
5480457 TTTTTATTTTTATTA
1 TTTTTATTTTTTTTA
5480472 TTTATTATTTTCTTTTA
1 TTT-TTATTTT-TTTTA
5480489 TTTTTATTTTATTTTA
1 TTTTTATTTT-TTTTA
5480505 GTTAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 3 0.10
16 19 0.66
17 7 0.24
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTATTTTTTTTA
Found at i:5481682 original size:117 final size:118
Alignment explanation
Indices: 5481462--5481691 Score: 345
Period size: 117 Copynumber: 2.0 Consensus size: 118
5481452 TGTTTTCCAT
* * * *
5481462 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCATGACTGACTGAGTAACCGGGGTAGAGTGCTTGGGTTGTCATT
*
5481527 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCAA
66 CTACTTCGCGTCAAAAGGTTGTGTGACATGACAAGTAAAACTCCGCTAGCCAA
**
5481580 GGTTATGAGTATGGCTCAAATCATGACTGACTGAGTAA-CGGGGTAGAGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCATGACTGACTGAGTAACCGGGGTAGAGTGCTTGGGTTGTCATT
* ****
5481644 CTACTTCGCGTTAAAAGGTTGTGTGACATGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACATGACAAGTAAAACTCCGCTA
5481692 ACCGGAAATA
Statistics
Matches: 100, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
117 67 0.67
118 33 0.33
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCATGACTGACTGAGTAACCGGGGTAGAGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACATGACAAGTAAAACTCCGCTAGCCAA
Found at i:5485102 original size:18 final size:18
Alignment explanation
Indices: 5485079--5485113 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5485069 TAACAGATAT
5485079 ACTTAAAATCTAGTTGGC
1 ACTTAAAATCTAGTTGGC
5485097 ACTTAAAATCTAGTTGG
1 ACTTAAAATCTAGTTGG
5485114 ACTGCCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
ACTTAAAATCTAGTTGGC
Found at i:5492055 original size:13 final size:13
Alignment explanation
Indices: 5492037--5492061 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5492027 GAATATGCAT
5492037 TAGATATAAGTAC
1 TAGATATAAGTAC
5492050 TAGATATAAGTA
1 TAGATATAAGTA
5492062 TTTAATACTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (13 bp):
TAGATATAAGTAC
Found at i:5493478 original size:153 final size:153
Alignment explanation
Indices: 5493192--5493481 Score: 366
Period size: 153 Copynumber: 1.9 Consensus size: 153
5493182 CACGGTCTTT
* * * * *
5493192 GTGAAGGAGATATTCCTAGTGATATTTCTGGTCTATCCTCTTTGAGACGTCTTAATCTTAGCGGT
1 GTGAAGGAGATATTACTAATGATATTTCTGGTCTATCCTCTTTGAAAAGTCTTAATCTTAGAGGT
** * * * * * * *
5493257 AACAATTTCATCAACATGCCTGCCCCTCTTACTCGACTTTACAAGCTTGAATTTCTTATATTGGC
66 AACAATTTCATCAACACACCTGCACCTCTTACTCGACTATACAACCTTCAATTCCTTAGATTAGC
5493322 AAATTGCGGCTTATGCCATTTTG
131 AAATTGCGGCTTATGCCATTTTG
* *
5493345 GTGAAGGAGATATTACTAATGATATTTCTTGTCTATCCTCTTTGAAAAGTCTTGATCTTAGAGAG
1 GTGAAGGAGATATTACTAATGATATTTCTGGTCTATCCTCTTTGAAAAGTCTTAATCTTAGAG-G
* * * * * *
5493410 -AACAATTTCGTCAGCACACCTGCATCTCTTACTCGACTATCCAACCTTCAATTCCTTGGATTAT
65 TAACAATTTCATCAACACACCTGCACCTCTTACTCGACTATACAACCTTCAATTCCTTAGATTAG
5493474 CAAATTGC
130 CAAATTGC
5493482 AGGGAGCTTA
Statistics
Matches: 114, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
153 113 0.99
154 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (153 bp):
GTGAAGGAGATATTACTAATGATATTTCTGGTCTATCCTCTTTGAAAAGTCTTAATCTTAGAGGT
AACAATTTCATCAACACACCTGCACCTCTTACTCGACTATACAACCTTCAATTCCTTAGATTAGC
AAATTGCGGCTTATGCCATTTTG
Found at i:5495306 original size:36 final size:36
Alignment explanation
Indices: 5495259--5495327 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
5495249 GGTCTGACTG
5495259 ATTGGATCGAGAATCGATTAGTATACTAGTCCACTA
1 ATTGGATCGAGAATCGATTAGTATACTAGTCCACTA
5495295 ATTGGATCGAGAATCGATTAGTATACTAGTCCA
1 ATTGGATCGAGAATCGATTAGTATACTAGTCCA
5495328 AACAAAGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (36 bp):
ATTGGATCGAGAATCGATTAGTATACTAGTCCACTA
Found at i:5496297 original size:33 final size:34
Alignment explanation
Indices: 5496222--5496290 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
5496212 TAAATAGGTA
5496222 TAATGACAAAAAATGGTTCTTAATGTTTACAAGG
1 TAATGACAAAAAATGGTTCTTAATGTTTACAAGG
5496256 TAATGACAAAAAATGGTTCTTAATGTTTACAAGG
1 TAATGACAAAAAATGGTTCTTAATGTTTACAAGG
5496290 T
1 T
5496291 TTGACAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (34 bp):
TAATGACAAAAAATGGTTCTTAATGTTTACAAGG
Found at i:5498323 original size:2 final size:2
Alignment explanation
Indices: 5498316--5498372 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
5498306 TTATTTTCAT
*
5498316 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5498358 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
5498373 TCAGTTACAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5499475 original size:16 final size:17
Alignment explanation
Indices: 5499454--5499491 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
5499444 AACATAAGAA
5499454 TATTATTATTT-AT-TTC
1 TATTATT-TTTAATATTC
5499470 TATTATTTTTAATATTC
1 TATTATTTTTAATATTC
5499487 TATTA
1 TATTA
5499492 CAACTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 9 0.45
17 8 0.40
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTTTTAATATTC
Found at i:5501840 original size:17 final size:17
Alignment explanation
Indices: 5501818--5501858 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
5501808 AACTGTTTAT
5501818 TTTTTTTCTTTCTTTTC
1 TTTTTTTCTTTCTTTTC
*
5501835 TTTTTTTCTTTTTTTTC
1 TTTTTTTCTTTCTTTTC
5501852 TTTTTTT
1 TTTTTTT
5501859 TTCGAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTCTTTCTTTTC
Found at i:5501859 original size:9 final size:9
Alignment explanation
Indices: 5501817--5501859 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
5501807 AAACTGTTTA
5501817 TTTTTTTTC
1 TTTTTTTTC
*
5501826 TTTCTTTTC
1 TTTTTTTTC
5501835 -TTTTTTTC
1 TTTTTTTTC
5501843 TTTTTTTTC
1 TTTTTTTTC
5501852 TTTTTTTT
1 TTTTTTTT
5501860 TCGAATTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 7 0.23
9 24 0.77
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:5509352 original size:63 final size:63
Alignment explanation
Indices: 5509253--5509374 Score: 244
Period size: 63 Copynumber: 1.9 Consensus size: 63
5509243 TTTTCTCTCT
5509253 AATCTGTTATTGTTTTTGACAGTCCTTGTATAAGTTGAAAATAATCAGCTTTAAAGAGTTTTG
1 AATCTGTTATTGTTTTTGACAGTCCTTGTATAAGTTGAAAATAATCAGCTTTAAAGAGTTTTG
5509316 AATCTGTTATTGTTTTTGACAGTCCTTGTATAAGTTGAAAATAATCAGCTTTAAAGAGT
1 AATCTGTTATTGTTTTTGACAGTCCTTGTATAAGTTGAAAATAATCAGCTTTAAAGAGT
5509375 CCCAAAACCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (63 bp):
AATCTGTTATTGTTTTTGACAGTCCTTGTATAAGTTGAAAATAATCAGCTTTAAAGAGTTTTG
Found at i:5515057 original size:11 final size:11
Alignment explanation
Indices: 5515037--5515070 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
5515027 CGCATTTAGT
5515037 TTTATTCTTGA
1 TTTATTCTTGA
*
5515048 TTTGTTCTTGA
1 TTTATTCTTGA
5515059 TTTATTCTTGA
1 TTTATTCTTGA
5515070 T
1 T
5515071 AATTTGACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.65
Consensus pattern (11 bp):
TTTATTCTTGA
Found at i:5518257 original size:21 final size:21
Alignment explanation
Indices: 5518227--5518290 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
5518217 ACAAACTGTT
*
5518227 GATTTTCAAAAGAGAACAGAG
1 GATTTTCAAAAGAAAACAGAG
* *
5518248 GATTTCCAAAAGAAAATAGAG
1 GATTTTCAAAAGAAAACAGAG
*
5518269 GATTTTCAATAGAAAACAGAG
1 GATTTTCAAAAGAAAACAGAG
5518290 G
1 G
5518291 CATCTATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.20
Consensus pattern (21 bp):
GATTTTCAAAAGAAAACAGAG
Found at i:5521974 original size:26 final size:26
Alignment explanation
Indices: 5521938--5522073 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
5521928 CATGATATTC
5521938 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5521964 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5521990 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
5522016 TTATCATGAAACATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5522042 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5522068 TTATCA
1 TTATCA
5522074 ATTTGTATCA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 102 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5525729 original size:3 final size:3
Alignment explanation
Indices: 5525723--5525789 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
5525713 AATAAAGCAC
5525723 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5525771 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
5525790 AAATAAGCTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5527844 original size:14 final size:15
Alignment explanation
Indices: 5527818--5527848 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5527808 TCCAGGTTCA
5527818 TCAACACATTTTTCT
1 TCAACACATTTTTCT
5527833 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
5527847 TC
1 TC
5527849 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:5530557 original size:2 final size:2
Alignment explanation
Indices: 5530550--5530587 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5530540 TTTGTTTCTG
5530550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5530588 GTCTAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5534526 original size:21 final size:21
Alignment explanation
Indices: 5534502--5534541 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5534492 TTCATCTAAC
* *
5534502 TATTCAAATTAATTATATACT
1 TATTCAAAATAATAATATACT
*
5534523 TATTTAAAATAATAATATA
1 TATTCAAAATAATAATATA
5534542 TTTCTATCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTCAAAATAATAATATACT
Found at i:5535552 original size:13 final size:13
Alignment explanation
Indices: 5535534--5535558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5535524 ATTTACAAGA
5535534 TTACATAATCAAT
1 TTACATAATCAAT
5535547 TTACATAATCAA
1 TTACATAATCAA
5535559 ATCTAAACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:5542209 original size:21 final size:21
Alignment explanation
Indices: 5542172--5542218 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5542162 ATTACACATA
* *
5542172 TATATTTTAATGTTATATTTT
1 TATATATTAATGTTATATTAT
5542193 TATATATT-ATGTATATATTAT
1 TATATATTAATGT-TATATTAT
5542214 TATAT
1 TATAT
5542219 CTACTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TATATATTAATGTTATATTAT
Found at i:5542951 original size:21 final size:21
Alignment explanation
Indices: 5542927--5542980 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5542917 ATACTATTAT
* *
5542927 TATATTTATTTTTATTCCTAG
1 TATATTTATTTTTAATACTAG
* *
5542948 TATATTTATTATTAATATTAG
1 TATATTTATTTTTAATACTAG
*
5542969 TATATGTATTTT
1 TATATTTATTTT
5542981 GTTATACGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.61
Consensus pattern (21 bp):
TATATTTATTTTTAATACTAG
Found at i:5545914 original size:15 final size:16
Alignment explanation
Indices: 5545894--5545926 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5545884 ATATATTTTT
5545894 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
5545909 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
5545926 T
1 T
5545927 ATAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:5546006 original size:21 final size:21
Alignment explanation
Indices: 5545973--5546031 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 21
5545963 GTTTTAAGAA
* *
5545973 TTGTTTGAGTATTATTTTTAT
1 TTGTTTTAATATTATTTTTAT
*
5545994 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATA-TTATTTTTAT
*
5546016 GT-TTTTAA-ATATATTT
1 TTGTTTTAATAT-TATTT
5546032 GATTTATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 5 0.16
21 15 0.48
22 10 0.32
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.68
Consensus pattern (21 bp):
TTGTTTTAATATTATTTTTAT
Found at i:5546046 original size:26 final size:24
Alignment explanation
Indices: 5546002--5546051 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
5545992 ATTTGTTTTA
*
5546002 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
5546026 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
5546052 TTTTTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:5547956 original size:28 final size:28
Alignment explanation
Indices: 5547917--5547974 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5547907 TGGTTCTGTG
5547917 ATATAAATCTTGGATATCGAGAGATATT
1 ATATAAATCTTGGATATCGAGAGATATT
*
5547945 ATATAAATCTTGGATATGGAGAGATATT
1 ATATAAATCTTGGATATCGAGAGATATT
5547973 AT
1 AT
5547975 CCGACCTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (28 bp):
ATATAAATCTTGGATATCGAGAGATATT
Found at i:5549187 original size:26 final size:26
Alignment explanation
Indices: 5549150--5549205 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
5549140 TGATACAAAT
*
5549150 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
5549176 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5549202 TGAT
1 TGAT
5549206 GGGAATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5554172 original size:22 final size:23
Alignment explanation
Indices: 5554137--5554181 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
5554127 CAATCTTCAA
* *
5554137 AAACACCTACAAAAGCAC-CTGT
1 AAACACCAACAAAAACACACTGT
*
5554159 AAACACCAAGAAAAACACACTGT
1 AAACACCAACAAAAACACACTGT
5554182 CGAGCCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.51, C:0.29, G:0.09, T:0.11
Consensus pattern (23 bp):
AAACACCAACAAAAACACACTGT
Found at i:5555149 original size:22 final size:21
Alignment explanation
Indices: 5555114--5555189 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
5555104 AAAAGGTATC
* *
5555114 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
5555135 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
5555158 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
5555177 TGC-AATCATATCT
1 TACAAATCATATCT
5555190 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:5555186 original size:18 final size:19
Alignment explanation
Indices: 5555150--5555204 Score: 103
Period size: 18 Copynumber: 2.9 Consensus size: 19
5555140 AATCATATCT
5555150 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5555169 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
5555187 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
5555205 TGAAGATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5555677 original size:44 final size:45
Alignment explanation
Indices: 5555561--5555754 Score: 264
Period size: 45 Copynumber: 4.3 Consensus size: 45
5555551 TGATATCTAC
* *
5555561 TATCTTTGATCTGCTCCCCATCTAATATAGAGACGCCAAATCTGT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* * *
5555606 TATCTTCGATCTGCTCCCTGTCTAATACAGAGACGCCAAATCTGC
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* * *
5555651 T-TCTTTAATCTGCACCCCGTCTAATACAGAGATGCCAAATCTGT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* * *
5555695 TATCTCTGATTTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* *
5555740 CATCTTGGATCTGCT
1 TATCTTTGATCTGCT
5555755 TCAATGTAAA
Statistics
Matches: 129, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
44 38 0.29
45 91 0.71
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (45 bp):
TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
Found at i:5555688 original size:89 final size:89
Alignment explanation
Indices: 5555563--5555738 Score: 264
Period size: 89 Copynumber: 2.0 Consensus size: 89
5555553 ATATCTACTA
* * * *
5555563 TCTTTGATCTGCTCCCCATCTAATATAGAGACGCCAAATCTGTTATCT-TCGATCTGCTCCCTGT
1 TCTTTAATCTGCACCCCATCTAATACAGAGACGCCAAATCTGTTATCTCT-GATCTGCTCCCCGT
5555627 CTAATACAGAGACGCCAAATCTGCT
65 CTAATACAGAGACGCCAAATCTGCT
* * *
5555652 TCTTTAATCTGCACCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCTGATTTGCTCCCCGTC
1 TCTTTAATCTGCACCCCATCTAATACAGAGACGCCAAATCTGTTATCTCTGATCTGCTCCCCGTC
*
5555717 TAATACAGAGATGCCAAATCTG
66 TAATACAGAGACGCCAAATCTG
5555739 TCATCTTGGA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
89 77 0.99
90 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (89 bp):
TCTTTAATCTGCACCCCATCTAATACAGAGACGCCAAATCTGTTATCTCTGATCTGCTCCCCGTC
TAATACAGAGACGCCAAATCTGCT
Found at i:5555897 original size:78 final size:78
Alignment explanation
Indices: 5555768--5556062 Score: 418
Period size: 78 Copynumber: 3.8 Consensus size: 78
5555758 ATGTAAACAC
* * *
5555768 ATGAAGGT-CAGATATGCTATGTCTTTGATCTGCTC-CTTGTCTAATACAGAGATGCCAAATCAT
1 ATGAAGGTCCA-ATCTGCTATGTCTTCGATCTGCTCTC-CGTCTAATACAGAGATGCCAAATCAT
5555831 CTTGGATCTGCTTCA
64 CTTGGATCTGCTTCA
* *
5555846 ATGAAGGTCCAATCTGTTATGCCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCCAATCTGCTATGTCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATCT
*
5555911 TGGATCTGCTTTA
66 TGGATCTGCTTCA
* * *
5555924 ATGAAGGTCAAATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCCAATCTGCTATGTCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATCT
5555989 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* **
5556002 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCT-TCCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCCA-ATCTGCTATGTCTTCGATCTGCTCT-CCGTCTAATACAGAGATGCCAAATC
5556063 TGTTTCTTCA
Statistics
Matches: 195, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
77 1 0.01
78 191 0.98
79 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCCAATCTGCTATGTCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:5556272 original size:78 final size:78
Alignment explanation
Indices: 5556144--5556427 Score: 426
Period size: 78 Copynumber: 3.6 Consensus size: 78
5556134 TGAAAGCCAA
* * *
5556144 ATCTGCTATGTCTTCGATTTGCTCCCCGTCTAATATAGAGATGCCAAATCATCTTGGATCTGCTT
1 ATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
5556209 CAATGAAGGTCCA-
66 CAATGAAGGT-CAG
**
5556222 ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
1 ATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
5556287 CAATGAAGGTCAG
66 CAATGAAGGTCAG
* * *
5556300 ATCTATTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGTTT
1 ATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
*
5556365 CAATGAAAGTCAG
66 CAATGAAGGTCAG
* * * **
5556378 ATCTACTATGTCTTCGATCTACTCTCCGTCGAATATGGAGATGCCAAATC
1 ATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
5556428 TATTTCTTCG
Statistics
Matches: 191, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
77 2 0.01
78 189 0.99
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (78 bp):
ATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
CAATGAAGGTCAG
Found at i:5556409 original size:365 final size:364
Alignment explanation
Indices: 5555720--5556573 Score: 1345
Period size: 365 Copynumber: 2.3 Consensus size: 364
5555710 CCCCGTCTAA
* * * * * * *
5555720 TACAGAGATGCCAAATCTGTCATCTTGGATCTGCTTCAATGTAAACACATGAAGGTCAGATATGC
1 TACAGAGATGCCAAA----TCATCTTAGATCTGCTTCAGTGTAAACACGTGAAAGCCAAATCTGC
*
5555785 TATGTCTTTGATCTGCTCCTTGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGA
62 TATGTCTTCGATCTGCTCCTTGTCTAATA-AGAGATGCCAAATCATCTTGGATCTGCTTCAATGA
*
5555850 AGGTCCAATCTGTTATGCCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATCTTGGA
126 AGGTCCAATCTGTTATGCCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGA
* *
5555915 TCTGCTTTAATGAAGGTCAAATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCC
191 TCTGCTTCAATGAAGGTCAAATCTACTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCC
* * *
5555980 AAATCATCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTTCCCGTCGA
256 AAATCATCTTGGATCTGCTTCAATGAAAGTCAGATCTACTATGTCTTCGATCTACTTCCCGTCGA
*
5556045 ATATGGAGATGCCAAATCTGTTTCTTCAATTTGTTCTCTGACAG
321 ATATGGAGATGCCAAATCTATTTCTTCAATTTGTTCTCTGACAG
* * *
5556089 TACATATATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTATG
1 TACAGAGATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACGTGAAAGCCAAATCTGCTATG
* **
5556154 TCTTCGATTTGCTCCCCGTCTAATATAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
66 TCTTCGATCTGCTCCTTGTCTAATA-AGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
*
5556219 CCAATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTG
130 CCAATCTGTTATGCCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTG
* *
5556284 CTTCAATGAAGGTCAGATCTATTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAAT
195 CTTCAATGAAGGTCAAATCTACTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAAT
*
5556349 CATCTTGGATCTGTTTCAATGAAAGTCAGATCTACTATGTCTTCGATCTAC-TCTCCGTCGAATA
260 CATCTTGGATCTGCTTCAATGAAAGTCAGATCTACTATGTCTTCGATCTACTTC-CCGTCGAATA
*
5556413 TGGAGATGCCAAATCTATTTCTTCGATTTGTTCTCTGACAG
324 TGGAGATGCCAAATCTATTTCTTCAATTTGTTCTCTGACAG
* *
5556454 TACAGAGATTCCAAATCATCTTAGATCTGCTTCAGTGTAAACATGTGAAAGCCAAATCTGCTATG
1 TACAGAGATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACGTGAAAGCCAAATCTGCTATG
*
5556519 TCTTCGATCTGCTCCTTGTC-AACGTAAG-GATGCCAAATCATCTTGGATCTACTTC
66 TCTTCGATCTGCTCCTTGTCTAA--TAAGAGATGCCAAATCATCTTGGATCTGCTTC
5556574 GATGTGAAAA
Statistics
Matches: 446, Mismatches: 36, Indels: 11
0.90 0.07 0.02
Matches are distributed among these distances:
364 30 0.07
365 401 0.90
366 2 0.00
369 13 0.03
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (364 bp):
TACAGAGATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACGTGAAAGCCAAATCTGCTATG
TCTTCGATCTGCTCCTTGTCTAATAAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTC
CAATCTGTTATGCCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGC
TTCAATGAAGGTCAAATCTACTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
ATCTTGGATCTGCTTCAATGAAAGTCAGATCTACTATGTCTTCGATCTACTTCCCGTCGAATATG
GAGATGCCAAATCTATTTCTTCAATTTGTTCTCTGACAG
Found at i:5556521 original size:287 final size:284
Alignment explanation
Indices: 5555854--5556573 Score: 716
Period size: 287 Copynumber: 2.5 Consensus size: 284
5555844 CAATGAAGGT
* * * * * * *
5555854 CCAATCTGTTATGCCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTG
1 CCAAACTGCTATGTCTTCGATTTGCTCCCCGACTAATACAGAGATGCCAAATCATCTTAGATCTG
* * *
5555919 CTTTAATGAA-GGTCAAATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAA
66 CTTCAATGAAGGGCCAAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAA
* *
5555983 TCATCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTTCCCGTCGAATA
131 TCATCTTGGATCTGCTTCAATGAAGGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCGAATA
** * * * * *
5556048 TGGAGATGCCAAATCTGTTTCTTCAATTTGTTCTCTGACAGTACATATATGCCAAATCATCTTAG
196 CAGAGATGCCAAATC--TATCTTCAATCTGTTCTCTGAAAGTACAGATATGACAAATCATCTTAG
*
5556113 ATCTGCTTCAGCGTAAACACGTGAAAG
259 ATCTACTTCA-CGTAAACACGTGAAAG
* * *
5556140 CCAAATCTGCTATGTCTTCGATTTGCTCCCCGTCTAATATAGAGATGCCAAATCATCTTGGATCT
1 CCAAA-CTGCTATGTCTTCGATTTGCTCCCCGACTAATACAGAGATGCCAAATCATCTTAGATCT
* *
5556205 GCTTCAATGAAGGTCC-AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
65 GCTTCAATGAAGGGCCAAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * *
5556269 ATCATCTTGGATCTGCTTCAATGAAGGTCAGATCTATTGTGTCTTCGATCTGCTCCCCGTCTAAT
130 ATCATCTTGGATCTGCTTCAATGAAGGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCGAAT
** * * * *
5556334 ACAGAGATGCCAAATC-ATCTTGGATCTGTT-TCAATGAAAGT-CAGATCT-AC-TAT-GTCTTC
195 ACAGAGATGCCAAATCTATCTTCAATCTGTTCTC--TGAAAGTACAGATATGACAAATCATCTTA
* * * *
5556393 GATCTACTCTC-CGTCGAATATG-GAGATG
258 GATCTACT-TCACGT-AAACACGTGA-AAG
* * * * * *
5556421 CCAAA-T-CTATTTCTTCGATTTGTTCTCTGAC-AGTACAGAGATTCCAAATCATCTTAGATCTG
1 CCAAACTGCTATGTCTTCGATTTGCTCCCCGACTAATACAGAGATGCCAAATCATCTTAGATCTG
* **
5556483 CTTCAGTGTAAACATGTGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTGTC-AACGTA-A
66 CTTCAATG---A-A-G-G---GCCAAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAA--TACA
*
5556546 G-GATGCCAAATCATCTTGGATCTACTTC
120 GAGATGCCAAATCATCTTGGATCTGCTTC
5556574 GATGTGAAAA
Statistics
Matches: 366, Mismatches: 49, Indels: 38
0.81 0.11 0.08
Matches are distributed among these distances:
277 34 0.09
278 20 0.05
279 1 0.00
280 6 0.02
281 23 0.06
282 5 0.01
283 4 0.01
284 15 0.04
285 6 0.02
286 34 0.09
287 214 0.58
288 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (284 bp):
CCAAACTGCTATGTCTTCGATTTGCTCCCCGACTAATACAGAGATGCCAAATCATCTTAGATCTG
CTTCAATGAAGGGCCAAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAA
TCATCTTGGATCTGCTTCAATGAAGGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCGAATA
CAGAGATGCCAAATCTATCTTCAATCTGTTCTCTGAAAGTACAGATATGACAAATCATCTTAGAT
CTACTTCACGTAAACACGTGAAAG
Found at i:5560347 original size:70 final size:70
Alignment explanation
Indices: 5560256--5560844 Score: 962
Period size: 70 Copynumber: 8.2 Consensus size: 70
5560246 CAAGTGACAG
*
5560256 AAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
5560321 GTTTC
66 GTTTC
*
5560326 AAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
5560391 GTTTC
66 GTTTC
* *
5560396 AAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
5560461 GTTTC
66 GTTTC
*
5560466 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AA-TTTC
5560531 AATTTATGTTTC
59 AATTTATGTTTC
*
5560543 AAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
5560608 GTTTC
66 GTTTC
*
5560613 AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
5560678 GTTTC
66 GTTTC
*
5560683 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AA-TTTC
5560748 AATTTATGTTTC
59 AATTTATGTTTC
*
5560760 AAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
5560825 GTTTC
66 GTTTC
5560830 AAAAATCAACTCATA
1 -AAAATCAACTCATA
5560845 GGTGAGTTGA
Statistics
Matches: 490, Mismatches: 14, Indels: 29
0.92 0.03 0.05
Matches are distributed among these distances:
70 334 0.68
71 18 0.04
72 2 0.00
75 2 0.00
76 4 0.01
77 130 0.27
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
GTTTC
Found at i:5560542 original size:77 final size:77
Alignment explanation
Indices: 5560450--5560822 Score: 603
Period size: 77 Copynumber: 5.0 Consensus size: 77
5560440 GTTGAGGTAA
*
5560450 TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGA
1 TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGA
5560515 GGTAATTTCAAT
66 GGTAATTTCAAT
*
5560527 TTTCAATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGA
1 TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGA
5560592 GG-----T-AA-
66 GGTAATTTCAAT
*
5560597 TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGA
1 TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGA
5560662 GG-----T-AA-
66 GGTAATTTCAAT
*
5560667 TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGA
1 TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGA
5560732 GGTAATTTCAAT
66 GGTAATTTCAAT
*
5560744 TTTCAATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGA
1 TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGA
5560809 GGTAATTTCAAT
66 GGTAATTTCAAT
5560821 TT
1 TT
5560823 ATGTTTCAAA
Statistics
Matches: 281, Mismatches: 8, Indels: 14
0.93 0.03 0.05
Matches are distributed among these distances:
70 133 0.47
71 2 0.01
72 1 0.00
75 1 0.00
76 2 0.01
77 142 0.51
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (77 bp):
TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGA
GGTAATTTCAAT
Found at i:5560621 original size:147 final size:140
Alignment explanation
Indices: 5560256--5560844 Score: 962
Period size: 147 Copynumber: 4.1 Consensus size: 140
5560246 CAAGTGACAG
*
5560256 AAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
*
5560321 GTTTCAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
66 GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
5560386 TTTATGTTTC
131 TTTATGTTTC
* *
5560396 AAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
*
5560461 GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAA
66 GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AA
5560526 TTTTCAATTTATGTTTC
125 -TTTCAATTTATGTTTC
*
5560543 AAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
*
5560608 GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGGTAATTTCAA
66 GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
5560673 TTTATGTTTC
131 TTTATGTTTC
*
5560683 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AA-TTTC
*
5560748 AATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
59 AATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
5560813 ATTTCAATTTATGTTTC
124 ATTTCAATTTATGTTTC
5560830 AAAAATCAACTCATA
1 -AAAATCAACTCATA
5560845 GGTGAGTTGA
Statistics
Matches: 420, Mismatches: 14, Indels: 22
0.92 0.03 0.05
Matches are distributed among these distances:
140 181 0.43
141 2 0.00
142 1 0.00
145 2 0.00
146 4 0.01
147 216 0.51
148 14 0.03
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (140 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
TTTATGTTTC
Found at i:5560624 original size:217 final size:217
Alignment explanation
Indices: 5560256--5560844 Score: 1075
Period size: 217 Copynumber: 2.7 Consensus size: 217
5560246 CAAGTGACAG
* *
5560256 AAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AA-TTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
**
5560314 AATTTATGTTTCAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
66 AATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
5560379 ATTTCAATTTATGTTTCAAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAAGACACGTTG
131 ATTTCAATTTATGTTTCAAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAAGACACGTTG
5560444 AGGTAATTTCAATTTATGTTTC
196 AGGTAATTTCAATTTATGTTTC
5560466 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
5560531 AATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
66 AATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
*
5560596 ATTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTG
131 ATTTCAATTTATGTTTCAAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAAGACACGTTG
5560661 AGGTAATTTCAATTTATGTTTC
196 AGGTAATTTCAATTTATGTTTC
5560683 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
5560748 AATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
66 AATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
5560813 ATTTCAATTTATGTTTCAAAAATCAACTCATA
131 ATTTCAATTTATGTTTC-AAAATCAACTCATA
5560845 GGTGAGTTGA
Statistics
Matches: 366, Mismatches: 5, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
210 49 0.13
215 1 0.00
216 2 0.01
217 300 0.82
218 14 0.04
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (217 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
AATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
ATTTCAATTTATGTTTCAAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAAGACACGTTG
AGGTAATTTCAATTTATGTTTC
Found at i:5560898 original size:147 final size:142
Alignment explanation
Indices: 5560276--5560945 Score: 668
Period size: 147 Copynumber: 4.7 Consensus size: 142
5560266 CACATTGCGA
* *
5560276 GAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AATTT-CAATTTATGTTTCAAAATCAA
1 GAGGTGAGTTGAGCCTCAAAACACGCTGAGGTAATTTCAATTTCCAATTTATGTTTCAAAATCAA
*
5560334 CTCATATTACGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAA
66 CTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAA
5560399 ATCAACTCATATT
131 ATCAACTCA-ATT
* * *
5560412 ACGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGG-----T-AATTT-CAATTTATGTTTCAAAA
1 ----GAGGTGAGTTGAGCCTCAAAACACGCTGAGGTAATTTCAATTTCCAATTTATGTTTCAAAA
*
5560470 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTCAATT
62 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AA-TTTCAATT
*
5560535 TATGTTTCAAAATCAACTCATATGGCGA
120 TATGTTTCAAAATCAACTCA-AT----T
* *
5560563 GAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AATTT-CAATTTATGTTTCAAAATCAA
1 GAGGTGAGTTGAGCCTCAAAACACGCTGAGGTAATTTCAATTTCCAATTTATGTTTCAAAATCAA
*
5560621 CTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAA
66 CTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAA
5560686 ATCAACTCATATT
131 ATCAACTCA-ATT
* *
5560699 GCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTCAATTTATGTTTCAAAA
1 ----GAGGTGAGTTGAGCCTCAAAACACGCTGAGGTAATTTCAATTTCCAATTTATGTTTCAAAA
*
5560764 TCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTT
62 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTT
5560829 CAAAAATCAACTC-A-T
127 C-AAAATCAACTCAATT
**** * * * *
5560844 -AGGTGAGTTGAGCCTCGGGGCATGCTGAGGTATTTTCAGTCTCTACTTTCCAATTCCTGTTTTT
1 GAGGTGAGTTGAGCCTCAAAACACGCTGAGGTAATTTCA------A-TTTCCAATT--TATGTTT
*
5560908 CAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCT
57 C-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5560946 GTTAATTTCT
Statistics
Matches: 474, Mismatches: 23, Indels: 56
0.86 0.04 0.10
Matches are distributed among these distances:
140 190 0.40
141 2 0.00
142 1 0.00
145 3 0.01
146 9 0.02
147 218 0.46
148 11 0.02
149 6 0.01
150 34 0.07
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (142 bp):
GAGGTGAGTTGAGCCTCAAAACACGCTGAGGTAATTTCAATTTCCAATTTATGTTTCAAAATCAA
CTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAA
ATCAACTCAATT
Found at i:5560987 original size:54 final size:52
Alignment explanation
Indices: 5560895--5561049 Score: 194
Period size: 54 Copynumber: 3.0 Consensus size: 52
5560885 TCTACTTTCC
* *
5560895 AATTCCTGTTTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTGTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC--TT
* *
5560949 AATTTCTGTCTTTCAAAAAGCAACTCATATTGCGAGAGGTGAGTTGTA-CC-T
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG-AGCCTT
**
5561000 --TTT-TGTTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
5561049 A
1 A
5561050 GGTCATATGT
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
47 1 0.01
48 38 0.43
49 4 0.04
51 1 0.01
54 44 0.49
55 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (52 bp):
AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
Found at i:5561800 original size:35 final size:35
Alignment explanation
Indices: 5561754--5561859 Score: 194
Period size: 35 Copynumber: 3.0 Consensus size: 35
5561744 CACTTGCCTC
5561754 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
5561789 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
* *
5561824 CTCCCACTCTCCCATGCTGTCTGCCGCCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
5561859 T
1 T
5561860 CACACACCCC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.16, C:0.49, G:0.12, T:0.23
Consensus pattern (35 bp):
TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
Found at i:5562280 original size:15 final size:15
Alignment explanation
Indices: 5562262--5562346 Score: 63
Period size: 13 Copynumber: 5.7 Consensus size: 15
5562252 AAAGAGGGGA
5562262 AGCAAAAAAAAATCC
1 AGCAAAAAAAAATCC
*
5562277 AGC--AAAAAATTCC
1 AGCAAAAAAAAATCC
5562290 AGCACCAAAAAAAATTTCC
1 AGCA--AAAAAAAA--TCC
**
5562309 AG-AAAAAAATTTCC
1 AGCAAAAAAAAATCC
*
5562323 AGCAAAAAAAAAACC
1 AGCAAAAAAAAATCC
5562338 A--AAAAAAAA
1 AGCAAAAAAAA
5562347 CAATAGAACG
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
13 20 0.36
14 5 0.09
15 13 0.23
16 6 0.11
17 6 0.11
18 1 0.02
19 5 0.09
ACGTcount: A:0.65, C:0.19, G:0.06, T:0.11
Consensus pattern (15 bp):
AGCAAAAAAAAATCC
Found at i:5562283 original size:14 final size:14
Alignment explanation
Indices: 5562266--5562333 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 14
5562256 AGGGGAAGCA
5562266 AAAAAAAATCCAGC
1 AAAAAAAATCCAGC
*
5562280 -AAAAAATTCCAGCACC
1 AAAAAAAATCCAG---C
5562296 AAAAAAAATTTCCAG-
1 AAAAAAAA--TCCAGC
*
5562311 AAAAAAATTTCCAGC
1 AAAAAAA-ATCCAGC
5562326 AAAAAAAA
1 AAAAAAAA
5562334 AACCAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 16
0.68 0.06 0.26
Matches are distributed among these distances:
13 11 0.26
14 5 0.12
15 14 0.33
16 1 0.02
17 6 0.14
19 5 0.12
ACGTcount: A:0.62, C:0.19, G:0.06, T:0.13
Consensus pattern (14 bp):
AAAAAAAATCCAGC
Found at i:5562310 original size:32 final size:31
Alignment explanation
Indices: 5562264--5562346 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
5562254 AGAGGGGAAG
*
5562264 CAAAAAAAAATCCAGCAAAAAA-TTCCAGCA
1 CAAAAAAAAATCCAGAAAAAAATTTCCAGCA
*
5562294 CCAAAAAAAATTTCCAGAAAAAAATTTCCAGCA
1 -CAAAAAAAA-ATCCAGAAAAAAATTTCCAGCA
*
5562327 -AAAAAAAAA-CCAAAAAAAAA
1 CAAAAAAAAATCCAGAAAAAAA
5562347 CAATAGAACG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 10 0.22
31 17 0.37
32 11 0.24
33 8 0.17
ACGTcount: A:0.65, C:0.19, G:0.05, T:0.11
Consensus pattern (31 bp):
CAAAAAAAAATCCAGAAAAAAATTTCCAGCA
Found at i:5563179 original size:22 final size:21
Alignment explanation
Indices: 5563149--5563198 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
5563139 ATTTCTAATA
5563149 TGTATATATATATATATTATG
1 TGTATATATATATATATTATG
5563170 TGTATTATATATATATATTATG
1 TGTA-TATATATATATATTATG
*
5563192 TATATAT
1 TGTATAT
5563199 GCCATTAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (21 bp):
TGTATATATATATATATTATG
Found at i:5566003 original size:26 final size:26
Alignment explanation
Indices: 5565967--5566075 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5565957 CATGAAATTC
5565967 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5565993 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
5566019 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
5566045 TTATCATG-AACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5566070 TTATCA
1 TTATCA
5566076 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 21 0.27
26 57 0.73
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5571705 original size:26 final size:26
Alignment explanation
Indices: 5571669--5571777 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5571659 CATGAAATTC
5571669 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5571695 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
5571721 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
5571747 TTATCATG-AACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5571772 TTATCA
1 TTATCA
5571778 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 21 0.27
26 57 0.73
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5572887 original size:12 final size:12
Alignment explanation
Indices: 5572870--5572896 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5572860 TTTTGTTTGC
5572870 TTACAAACTATA
1 TTACAAACTATA
5572882 TTACAAACTATA
1 TTACAAACTATA
5572894 TTA
1 TTA
5572897 AAATGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (12 bp):
TTACAAACTATA
Found at i:5574178 original size:13 final size:13
Alignment explanation
Indices: 5574139--5574178 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5574129 AGTTTAGCAA
5574139 TACTTTTGAAAAG
1 TACTTTTGAAAAG
* *
5574152 TACTATGGAAAAG
1 TACTTTTGAAAAG
*
5574165 TACTTTTGAGAAG
1 TACTTTTGAAAAG
5574178 T
1 T
5574179 GTTTTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:5576034 original size:26 final size:26
Alignment explanation
Indices: 5575998--5576107 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5575988 TGATACAAAT
5575998 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5576024 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5576050 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5576076 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5576102 TGATAA
1 TGATAA
5576108 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5577619 original size:26 final size:26
Alignment explanation
Indices: 5577590--5577642 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5577580 TTTACAGTTT
5577590 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
5577616 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
5577642 T
1 T
5577643 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:5581871 original size:26 final size:26
Alignment explanation
Indices: 5581835--5581944 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
5581825 TGATACAAAT
5581835 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
5581861 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5581887 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5581913 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
5581939 TGATAA
1 TGATAA
5581945 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:5583482 original size:25 final size:25
Alignment explanation
Indices: 5583434--5583482 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5583424 ACAGTTTTAC
5583434 CCCTAGGAGATAAATTACCGAAATA
1 CCCTAGGAGATAAATTACCGAAATA
* *
5583459 CCCTAGG-GTTAAATTGACCTAAAT
1 CCCTAGGAGATAAATT-ACCGAAAT
5583483 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGAGATAAATTACCGAAATA
Found at i:5584847 original size:3 final size:3
Alignment explanation
Indices: 5584839--5584904 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
5584829 GAATAAGATA
5584839 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5584887 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
5584905 GATGAGATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5599059 original size:17 final size:16
Alignment explanation
Indices: 5599037--5599080 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
5599027 CTTTGAGCCC
5599037 TTTATTTTACTATTATA
1 TTTATTTTA-TATTATA
* *
5599054 TTTATTTTTATTTTATT
1 TTTA-TTTTATATTATA
5599071 TTTATTTTAT
1 TTTATTTTAT
5599081 TTTGCCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 13 0.54
18 5 0.21
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTATTTTATATTATA
Found at i:5599068 original size:11 final size:11
Alignment explanation
Indices: 5599037--5599083 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
5599027 CTTTGAGCCC
*
5599037 TTTATTTTACT
1 TTTATTTTATT
*
5599048 ATTATATTTATT
1 TTTAT-TTTATT
5599060 TTTATTTTATT
1 TTTATTTTATT
5599071 TTTATTTTATT
1 TTTATTTTATT
5599082 TT
1 TT
5599084 GCCTTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 23 0.72
12 9 0.28
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:5600097 original size:2 final size:2
Alignment explanation
Indices: 5600090--5600121 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5600080 TTATTCTTAA
*
5600090 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5600122 TCATTCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5604702 original size:43 final size:43
Alignment explanation
Indices: 5604654--5604740 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
5604644 CCTTCCTCAA
*
5604654 TGGTATTCTTGAAAAAGAGATTTATGTTGAACAACCTTAGGGT
1 TGGTATTCTTGAAAAAGAGATTTATGTTGAACAACCTAAGGGT
*
5604697 TGGTATTCTTGAAGAAGAGATTTATGTTGAACAACCTAAGGGT
1 TGGTATTCTTGAAAAAGAGATTTATGTTGAACAACCTAAGGGT
5604740 T
1 T
5604741 TTAAAGTGGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.34
Consensus pattern (43 bp):
TGGTATTCTTGAAAAAGAGATTTATGTTGAACAACCTAAGGGT
Found at i:5608637 original size:17 final size:17
Alignment explanation
Indices: 5608615--5608652 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
5608605 CACTTTGTTA
5608615 ATTAAGCAAGACTTGTC
1 ATTAAGCAAGACTTGTC
5608632 ATTAAGCAAGACTTGTC
1 ATTAAGCAAGACTTGTC
5608649 ATTA
1 ATTA
5608653 TTCATAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (17 bp):
ATTAAGCAAGACTTGTC
Found at i:5611097 original size:61 final size:61
Alignment explanation
Indices: 5610965--5611086 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
5610955 GTTAATAGAA
5610965 TCTGATTTTTATTTTTACCACATATGTATACACATTAAATCCTTATTTCTATGAATATTTT
1 TCTGATTTTTATTTTTACCACATATGTATACACATTAAATCCTTATTTCTATGAATATTTT
*
5611026 TCTGATTTTTATTTTTACCACATATGTATATACATTAAATCCTTATTTCTATGAATATTTT
1 TCTGATTTTTATTTTTACCACATATGTATACACATTAAATCCTTATTTCTATGAATATTTT
5611087 ATTATCTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.52
Consensus pattern (61 bp):
TCTGATTTTTATTTTTACCACATATGTATACACATTAAATCCTTATTTCTATGAATATTTT
Found at i:5613380 original size:27 final size:27
Alignment explanation
Indices: 5613344--5613398 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
5613334 TACCTAAAGA
5613344 GATGAGATTCTTCTTCAAACCAAGCAT
1 GATGAGATTCTTCTTCAAACCAAGCAT
* *
5613371 GATGAGATTCTTCTTCAAATCAGGCAT
1 GATGAGATTCTTCTTCAAACCAAGCAT
5613398 G
1 G
5613399 TGTCTAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (27 bp):
GATGAGATTCTTCTTCAAACCAAGCAT
Found at i:5617951 original size:14 final size:14
Alignment explanation
Indices: 5617920--5617950 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5617910 GTTAAAATTG
5617920 TTTTAGGATCTTAA
1 TTTTAGGATCTTAA
5617934 TTTTAGGAT-TTAA
1 TTTTAGGATCTTAA
5617947 TTTT
1 TTTT
5617951 TCTATTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (14 bp):
TTTTAGGATCTTAA
Found at i:5621610 original size:21 final size:21
Alignment explanation
Indices: 5621584--5621624 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5621574 ATCTGCTCAA
* *
5621584 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5621605 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5621625 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5628752 original size:153 final size:153
Alignment explanation
Indices: 5628459--5628760 Score: 394
Period size: 153 Copynumber: 2.0 Consensus size: 153
5628449 ACTAAGGGAC
* * * *
5628459 TGCAATCTTGGTGAAGGAGATATCCATAGTGCTATTTCTTGTCTATCCTCTTTGACAAACCTTGA
1 TGCAATATTGGTGAAGGAGATATCCATAGTGATATTTCTGGTCTATCCTCATTGACAAACCTTGA
* * **
5628524 TCTTAGCGGTAACAATTTCAACAGCATACCAGCGTCTCTTACTCGACTCTCCAAGCTTGAATTTC
66 TCTTAGCGGTAACAATTTCAACAGCATACCAGCGTCTCTTACTCGACTCTCCAAGCCTCAAAATC
*
5628589 TTATATTGTCAAATTGCAGCCTG
131 TTATAGTGTCAAATTGCAGCCTG
* **
5628612 TGCAATATTGGTGAAGGAGATATTCC-TAGTGATATTTCTGGTCTATCCTCATTGAGAATTCTTG
1 TGCAATATTGGTGAAGGAGATA-TCCATAGTGATATTTCTGGTCTATCCTCATTGACAAACCTTG
* * * * * *
5628676 ATCTTAGTGGTAACAATTTCACCAGCATAGCTGCGTCTCTTACTCGTCTTTCC-AGTCCTCAAAA
65 ATCTTAGCGGTAACAATTTCAACAGCATACCAGCGTCTCTTACTCGACTCTCCAAG-CCTCAAAA
5628740 TCTTGA-AGTGTCAAATTGCAG
129 TCTT-ATAGTGTCAAATTGCAG
5628761 TGAGCTTGAA
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
152 2 0.02
153 122 0.95
154 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (153 bp):
TGCAATATTGGTGAAGGAGATATCCATAGTGATATTTCTGGTCTATCCTCATTGACAAACCTTGA
TCTTAGCGGTAACAATTTCAACAGCATACCAGCGTCTCTTACTCGACTCTCCAAGCCTCAAAATC
TTATAGTGTCAAATTGCAGCCTG
Found at i:5630631 original size:22 final size:22
Alignment explanation
Indices: 5630606--5630650 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5630596 AACTACTTCT
5630606 TGTTTAGAATAAATTAGAGTTC
1 TGTTTAGAATAAATTAGAGTTC
5630628 TGTTTAGAATAAATTAGAGTTC
1 TGTTTAGAATAAATTAGAGTTC
5630650 T
1 T
5630651 AGTATACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (22 bp):
TGTTTAGAATAAATTAGAGTTC
Found at i:5636266 original size:30 final size:30
Alignment explanation
Indices: 5636232--5636292 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
5636222 TTCCCGAGCC
5636232 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
5636262 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
5636292 T
1 T
5636293 GAATTAAGGA
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:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:5637078 original size:68 final size:65
Alignment explanation
Indices: 5636991--5637213 Score: 172
Period size: 67 Copynumber: 3.4 Consensus size: 65
5636981 ATGGTGCTGA
* *
5636991 GTGTACATCATGT-GTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATA
1 GTGTACACCATGTAG-ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATA
*
5637055 CTA-T
61 CCAGT
** * *
5637059 GTGTACACCATGTAGACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGG
1 GTGTACACCATGTAGACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-G
5637124 T
65 T
* * * * * * * *
5637125 GAAGGACACCATGTAGACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTGGTACTA
1 G-TGTACACCATGTAGACAAGAGAGCTACGACATATA-TGTAGCTAGGTCGCATGCGTGATAC-C
5637188 AGT
63 AGT
5637191 GT-T-CACCATGT-GTACAAGAGAGC
1 GTGTACACCATGTAG-ACAAGAGAGC
5637214 CGAACTATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 19
0.78 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 18 0.14
64 24 0.18
65 3 0.02
66 25 0.19
67 32 0.24
68 27 0.21
69 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (65 bp):
GTGTACACCATGTAGACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGT
Found at i:5638303 original size:2 final size:2
Alignment explanation
Indices: 5638296--5638341 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5638286 GTATCATGAC
5638296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5638338 AT AT
1 AT AT
5638342 GTATGACTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5649678 original size:15 final size:17
Alignment explanation
Indices: 5649658--5649694 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
5649648 TATAGTGAAA
5649658 AAAATTGGAA-GGAT-G
1 AAAATTGGAAGGGATAG
*
5649673 AAAATTTGAAGGGATAG
1 AAAATTGGAAGGGATAG
5649690 AAAAT
1 AAAAT
5649695 ATATTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 4 0.21
17 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (17 bp):
AAAATTGGAAGGGATAG
Found at i:5657985 original size:17 final size:16
Alignment explanation
Indices: 5657963--5658016 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 16
5657953 AATTACTCCC
5657963 TTAATTTTATTTATATT
1 TTAATTTTATTT-TATT
5657980 TTAATTTTCTATTTTATT
1 TTAA-TTT-TATTTTATT
5657998 TTCAATTTT-TTTGTATT
1 TT-AATTTTATTT-TATT
5658015 TT
1 TT
5658017 TTTGTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.09
17 11 0.33
18 12 0.36
19 7 0.21
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (16 bp):
TTAATTTTATTTTATT
Found at i:5657998 original size:12 final size:12
Alignment explanation
Indices: 5657966--5658043 Score: 52
Period size: 12 Copynumber: 6.2 Consensus size: 12
5657956 TACTCCCTTA
*
5657966 ATTTTA-TTTAT
1 ATTTTATTTTCT
5657977 ATTTTAATTTTCT
1 ATTTT-ATTTTCT
*
5657990 ATTTTATTTTCA
1 ATTTTATTTTCT
* *
5658002 ATTTTTTTGTATTT
1 ATTTTATT-T-TCT
*
5658016 TTTTGTATTTT-T
1 ATTT-TATTTTCT
5658028 ATTATTATTTTCT
1 ATT-TTATTTTCT
5658041 ATT
1 ATT
5658044 ATTGTCATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
11 5 0.10
12 23 0.44
13 16 0.31
14 5 0.10
15 3 0.06
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.73
Consensus pattern (12 bp):
ATTTTATTTTCT
Found at i:5658004 original size:19 final size:19
Alignment explanation
Indices: 5657970--5658006 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5657960 CCCTTAATTT
5657970 TATTTATATTTTAATTTTC
1 TATTTATATTTTAATTTTC
5657989 TATTT-TATTTTCAATTTT
1 TATTTATATTTT-AATTTT
5658007 TTTGTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTATATTTTAATTTTC
Found at i:5658016 original size:9 final size:10
Alignment explanation
Indices: 5658002--5658027 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5657992 TTTATTTTCA
5658002 ATTTTTTTGT
1 ATTTTTTTGT
5658012 ATTTTTTTGT
1 ATTTTTTTGT
5658022 ATTTTT
1 ATTTTT
5658028 ATTATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.81
Consensus pattern (10 bp):
ATTTTTTTGT
Found at i:5658032 original size:3 final size:3
Alignment explanation
Indices: 5658021--5658184 Score: 138
Period size: 3 Copynumber: 54.3 Consensus size: 3
5658011 TATTTTTTTG
* * * * *
5658021 TAT TTT TAT TAT TAT TTT CTAT TAT TGT CAT TAT TAG TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
5658066 TAT TAT TCT TAAT GTAT TAT TAT TAT TAT TAT TAT TAC TAT TAC TAT
1 TAT TAT TAT T-AT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * ** *
5658113 T-T TCGT TGT TGG TAT T-T GTAT CAT TAT TAT TAT TA- TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
5658157 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5658185 GTTGTTGTTG
Statistics
Matches: 132, Mismatches: 20, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
2 7 0.05
3 116 0.88
4 8 0.06
5 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:5665943 original size:12 final size:12
Alignment explanation
Indices: 5665926--5665951 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5665916 TGAATGCGAT
5665926 GAGATGTCTTTC
1 GAGATGTCTTTC
5665938 GAGATGTCTTTC
1 GAGATGTCTTTC
5665950 GA
1 GA
5665952 AGGCACACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.38
Consensus pattern (12 bp):
GAGATGTCTTTC
Found at i:5668509 original size:25 final size:25
Alignment explanation
Indices: 5668475--5668525 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
5668465 CTCATTCGAG
*
5668475 AATTTATGGAAATTAATCACAATAA
1 AATTTATGGAAATTAAGCACAATAA
5668500 AATTTATGGAAATTAAGCACAATAA
1 AATTTATGGAAATTAAGCACAATAA
5668525 A
1 A
5668526 CAGATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (25 bp):
AATTTATGGAAATTAAGCACAATAA
Found at i:5670073 original size:37 final size:37
Alignment explanation
Indices: 5670023--5670096 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
5670013 CAATTAATCC
5670023 ATTTAAAAAATAACGCAGACCAAGAGCTAAAAACTAT
1 ATTTAAAAAATAACGCAGACCAAGAGCTAAAAACTAT
5670060 ATTTAAAAAATAACGCAGACCAAGAGCTAAAAACTAT
1 ATTTAAAAAATAACGCAGACCAAGAGCTAAAAACTAT
5670097 GTGACACGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (37 bp):
ATTTAAAAAATAACGCAGACCAAGAGCTAAAAACTAT
Found at i:5671871 original size:28 final size:28
Alignment explanation
Indices: 5671777--5671868 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
5671767 TATGTTTTAA
* * *
5671777 TTATAAAATTTTGAAACTTCTATAAGATT
1 TTATAAAATTTT-AAATTTTTATATGATT
*
5671806 TTATAAGAATTTAAAATTTTTAT-T--TT
1 TTATAA-AATTTTAAATTTTTATATGATT
*
5671832 TTAGTTAGATATTTTAAATTTTTATATGATT
1 TTA--TA-AAATTTTAAATTTTTATATGATT
5671863 TTATAA
1 TTATAA
5671869 TATGCATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
26 5 0.10
28 17 0.34
29 18 0.36
30 5 0.10
31 5 0.10
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (28 bp):
TTATAAAATTTTAAATTTTTATATGATT
Found at i:5672702 original size:27 final size:27
Alignment explanation
Indices: 5672666--5672719 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5672656 CCCCACCTGA
5672666 AACAAAACTCAAATTAGCCTAACTATG
1 AACAAAACTCAAATTAGCCTAACTATG
5672693 AACAAAACTCAAATTAGCCTAACTATG
1 AACAAAACTCAAATTAGCCTAACTATG
5672720 TATAGTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (27 bp):
AACAAAACTCAAATTAGCCTAACTATG
Found at i:5674051 original size:19 final size:19
Alignment explanation
Indices: 5674015--5674052 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5674005 TGGGAAGCCA
**
5674015 TATGTTAAAAATCCTATAT
1 TATGTTAAAAATAATATAT
5674034 TATGTTAAAAATAATATAT
1 TATGTTAAAAATAATATAT
5674053 AACTATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
TATGTTAAAAATAATATAT
Found at i:5683742 original size:23 final size:21
Alignment explanation
Indices: 5683716--5683839 Score: 90
Period size: 23 Copynumber: 5.5 Consensus size: 21
5683706 ATACGTACAT
5683716 ATATATATATAATGATATTAGAA
1 ATATATA-ATAATGATATTA-AA
*
5683739 ATATACAATATAT-AGTATTAGAA
1 ATATATAATA-ATGA-TATTA-AA
*
5683762 ATATATACGTAA-GATAGTATAAA
1 ATATATA-ATAATGATA-T-TAAA
*
5683785 AAATATAACTAATGATATTAAA
1 ATATATAA-TAATGATATTAAA
*
5683807 ATATATACATAATAATATATAAA
1 ATATATA-ATAATGATAT-TAAA
*
5683830 AAATATAATA
1 ATATATAATA
5683840 TTAAAAAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
22 27 0.33
23 48 0.58
24 8 0.10
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (21 bp):
ATATATAATAATGATATTAAA
Found at i:5683851 original size:16 final size:16
Alignment explanation
Indices: 5683818--5683847 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5683808 TATATACATA
5683818 ATAATATATAAAAAAT
1 ATAATATATAAAAAAT
5683834 ATAATAT-TAAAAAA
1 ATAATATATAAAAAA
5683848 ATATGTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATATATAAAAAAT
Found at i:5684414 original size:21 final size:21
Alignment explanation
Indices: 5684362--5684436 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
5684352 ATACTAATGC
5684362 TAATAAATAATAAATATAATAA
1 TAAT-AATAATAAATATAATAA
*
5684384 TAATAGTAATAAATATAATAGTA
1 TAATAATAATAAATATAATA--A
*
5684407 TACATAATATTAAA-ATTAA-AA
1 TA-ATAATAATAAATA-TAATAA
5684428 TAA-AATAAT
1 TAATAATAAT
5684437 GAGAAAAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.11
20 1 0.02
21 18 0.40
22 4 0.09
23 5 0.11
24 12 0.27
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (21 bp):
TAATAATAATAAATATAATAA
Found at i:5685065 original size:23 final size:25
Alignment explanation
Indices: 5685027--5685074 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
5685017 GTATTTATTA
*
5685027 TTTTTTTGTATTTTTAATATATAAT
1 TTTTTTTGTATTTATAATATATAAT
5685052 TTTTTTTGTATTTATAATATATA
1 TTTTTTTGTATTTATAATATATA
5685075 TAAGTTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTTTTGTATTTATAATATATAAT
Found at i:5688502 original size:25 final size:23
Alignment explanation
Indices: 5688441--5688505 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
5688431 TCTCATTTTT
*
5688441 TATTTGTTTTT-CATTTT-AA--
1 TATTTGTTTTTATATTTTAAATG
*
5688460 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
5688483 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
5688506 GTTTTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.30
20 4 0.11
21 2 0.05
23 6 0.16
24 3 0.08
25 11 0.30
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.65
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:5696681 original size:16 final size:16
Alignment explanation
Indices: 5696656--5696686 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5696646 CACCACTTGG
*
5696656 ATTGTTTGCCATTAAA
1 ATTGTCTGCCATTAAA
5696672 ATTGTCTGCCATTAA
1 ATTGTCTGCCATTAA
5696687 TCATAATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (16 bp):
ATTGTCTGCCATTAAA
Found at i:5698633 original size:21 final size:21
Alignment explanation
Indices: 5698604--5698644 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5698594 ATCTGCTCAA
*
5698604 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
*
5698625 ACTCTACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
5698645 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:5699897 original size:30 final size:30
Alignment explanation
Indices: 5699861--5699920 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
5699851 AAACAACTCC
5699861 TCCATTTAGTTCTACTAAATCAGAAAACCA
1 TCCATTTAGTTCTACTAAATCAGAAAACCA
5699891 TCCATTTAGTTCTACTAAATCAGAAAACCA
1 TCCATTTAGTTCTACTAAATCAGAAAACCA
5699921 CTCCCGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (30 bp):
TCCATTTAGTTCTACTAAATCAGAAAACCA
Found at i:5701500 original size:16 final size:16
Alignment explanation
Indices: 5701475--5701505 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5701465 CACCACTTGG
*
5701475 ATTGTTTGCCATTAAA
1 ATTGTCTGCCATTAAA
5701491 ATTGTCTGCCATTAA
1 ATTGTCTGCCATTAA
5701506 TCATAATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (16 bp):
ATTGTCTGCCATTAAA
Found at i:5704241 original size:2 final size:2
Alignment explanation
Indices: 5704234--5704276 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5704224 TTAATTGGTA
5704234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5704276 A
1 A
5704277 AAAGAATGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5710975 original size:21 final size:21
Alignment explanation
Indices: 5710942--5710981 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5710932 TTATGCCATA
5710942 TCAGCATTCTCATCCTGAATT
1 TCAGCATTCTCATCCTGAATT
* * *
5710963 TCAGTATTTTCATCTTGAA
1 TCAGCATTCTCATCCTGAA
5710982 AAAAATCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (21 bp):
TCAGCATTCTCATCCTGAATT
Found at i:5714279 original size:25 final size:25
Alignment explanation
Indices: 5714230--5714303 Score: 105
Period size: 25 Copynumber: 2.9 Consensus size: 25
5714220 CTCACTTCTC
5714230 GCTAAGCTTGCAGCTTACACATTTT
1 GCTAAGCTTGCAGCTTACACATTTT
5714255 GCTAAGCTTGCAGCTTACACATTTTT
1 GCTAAGCTTGCAGCTTACACA-TTTT
* *
5714281 GTTGAA-CTTGCAGCTTGCACATT
1 GCT-AAGCTTGCAGCTTACACATT
5714304 GGAAAGCTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 23 0.51
26 20 0.44
27 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (25 bp):
GCTAAGCTTGCAGCTTACACATTTT
Found at i:5714290 original size:26 final size:26
Alignment explanation
Indices: 5714230--5714303 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
5714220 CTCACTTCTC
5714230 GCTAAGCTTGCAGCTTACACA-TTTT
1 GCTAAGCTTGCAGCTTACACATTTTT
5714255 GCTAAGCTTGCAGCTTACACATTTTT
1 GCTAAGCTTGCAGCTTACACATTTTT
* *
5714281 GTTGAA-CTTGCAGCTTGCACATT
1 GCT-AAGCTTGCAGCTTACACATT
5714304 GGAAAGCTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 21 0.47
26 22 0.49
27 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (26 bp):
GCTAAGCTTGCAGCTTACACATTTTT
Found at i:5721736 original size:27 final size:27
Alignment explanation
Indices: 5721671--5721767 Score: 99
Period size: 27 Copynumber: 3.5 Consensus size: 27
5721661 GAATATCCAA
*
5721671 CCCAAACACACCCAGAATAATATAAATCCT
1 CCCAAACACA-CCAGTATAATAT--ATCCT
*
5721701 -CCATAACACACCAGTATAATATAGCCT
1 CCCA-AACACACCAGTATAATATATCCT
*
5721728 CCCAAACACACCGGTAT-ATCATATCCT
1 CCCAAACACACCAGTATAAT-ATATCCT
*
5721755 CCCAAATACACCA
1 CCCAAACACACCA
5721768 ATAAGGCATT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
26 2 0.03
27 33 0.57
28 3 0.05
29 14 0.24
30 6 0.10
ACGTcount: A:0.41, C:0.35, G:0.05, T:0.19
Consensus pattern (27 bp):
CCCAAACACACCAGTATAATATATCCT
Found at i:5721738 original size:29 final size:29
Alignment explanation
Indices: 5721671--5721739 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
5721661 GAATATCCAA
*
5721671 CCCAAACACACCCAGAATAATATAAATCCT
1 CCCAAACACACCCAGAATAATAT-AAGCCT
*
5721701 -CCATAACACA-CCAGTATAATAT-AGCCT
1 CCCA-AACACACCCAGAATAATATAAGCCT
5721728 CCCAAACACACC
1 CCCAAACACACC
5721740 GGTATATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 10 0.29
28 4 0.12
29 14 0.41
30 6 0.18
ACGTcount: A:0.43, C:0.36, G:0.04, T:0.16
Consensus pattern (29 bp):
CCCAAACACACCCAGAATAATATAAGCCT
Found at i:5722291 original size:18 final size:17
Alignment explanation
Indices: 5722268--5722301 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5722258 AATTTTTATT
*
5722268 CAATTTATTCCTTAATTC
1 CAATTTAATCC-TAATTC
5722286 CAATTTAATCCTAATT
1 CAATTTAATCCTAATT
5722302 AACTCTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (17 bp):
CAATTTAATCCTAATTC
Found at i:5722789 original size:26 final size:26
Alignment explanation
Indices: 5722756--5722865 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
5722746 TGATACAAAT
5722756 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
5722782 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5722808 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5722834 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5722860 TGATAA
1 TGATAA
5722866 GAATTACATG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5726919 original size:26 final size:26
Alignment explanation
Indices: 5726883--5726949 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
5726873 TTATATCTTC
*
5726883 AAATAATAATAATTAAATACACTAAT-
1 AAATAAAAATAATTAAATA-ACTAATG
* * * *
5726909 TAATAAAAATAAATATATAATTAATG
1 AAATAAAAATAATTAAATAACTAATG
5726935 AAATAAAAATAATTA
1 AAATAAAAATAATTA
5726950 GAAGTATGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
25 5 0.15
26 28 0.85
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (26 bp):
AAATAAAAATAATTAAATAACTAATG
Found at i:5733720 original size:17 final size:17
Alignment explanation
Indices: 5733694--5733726 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5733684 TGTACATTTA
5733694 TATTAA-TTTTATTTTT
1 TATTAATTTTTATTTTT
5733710 TATTAAATTTTTATTTT
1 TATT-AATTTTTATTTT
5733727 CATTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 2 0.13
18 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTAATTTTTATTTTT
Found at i:5740645 original size:2 final size:2
Alignment explanation
Indices: 5740638--5740683 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5740628 AAGTACGCTA
5740638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5740680 AT AT
1 AT AT
5740684 TAAATTAGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5741347 original size:19 final size:19
Alignment explanation
Indices: 5741325--5741362 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5741315 TAATAATAAC
5741325 TATAAATATATA-TATAAGA
1 TATAAATATA-AGTATAAGA
*
5741344 TATATATATAAGTATAAGA
1 TATAAATATAAGTATAAGA
5741363 ATTAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
TATAAATATAAGTATAAGA
Found at i:5743901 original size:25 final size:25
Alignment explanation
Indices: 5743854--5743902 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5743844 CTACATACAT
* *
5743854 ATATACATATAAATATATTAAATAC
1 ATATACATATAAATACATGAAATAC
**
5743879 ATATACATATATGTACATGAAATA
1 ATATACATATAAATACATGAAATA
5743903 TATACGCTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATACATATAAATACATGAAATAC
Found at i:5745597 original size:9 final size:9
Alignment explanation
Indices: 5745554--5745606 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
5745544 TGGGGAATTT
*
5745554 TGGGTTTAC
1 TGGGTTTAG
5745563 TGGGTATTTAG
1 TGGG--TTTAG
* * *
5745574 TTGGTCTAT
1 TGGGTTTAG
5745583 TGGGTTTAG
1 TGGGTTTAG
5745592 TGGGTTTAG
1 TGGGTTTAG
5745601 TGGGTT
1 TGGGTT
5745607 GGGGTAGATT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
9 28 0.80
11 7 0.20
ACGTcount: A:0.11, C:0.04, G:0.38, T:0.47
Consensus pattern (9 bp):
TGGGTTTAG
Found at i:5746016 original size:26 final size:26
Alignment explanation
Indices: 5745987--5746045 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
5745977 TTTGCATTAC
*
5745987 ATAA-AATAATATACATTTTTAAATAA
1 ATAATAAT-ATATACATCTTTAAATAA
* *
5746013 ATAATCATATATATATCTTTAAAT-A
1 ATAATAATATATACATCTTTAAATAA
5746038 ATAATAAT
1 ATAATAAT
5746046 TAAATACACT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 8 0.29
26 18 0.64
27 2 0.07
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (26 bp):
ATAATAATATATACATCTTTAAATAA
Found at i:5746064 original size:20 final size:20
Alignment explanation
Indices: 5746036--5746098 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
5746026 TATCTTTAAA
5746036 TAATAATAATTAAATACACTAAT
1 TAATAA-AA-TAAATACA-TAAT
*
5746059 TAATAAAATAAATATATAAT
1 TAATAAAATAAATACATAAT
*
5746079 TAATGAAATAAA-A-ATAAT
1 TAATAAAATAAATACATAAT
5746097 TA
1 TA
5746099 GAAGTATGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
18 7 0.18
19 1 0.03
20 15 0.39
21 7 0.18
22 2 0.05
23 6 0.16
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (20 bp):
TAATAAAATAAATACATAAT
Found at i:5754234 original size:32 final size:32
Alignment explanation
Indices: 5754189--5754254 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
5754179 GCAATTTTCC
*
5754189 TCTGACTTGATTAGAATGATATTATCAAATGT
1 TCTGACTTGATTAGAATGAAATTATCAAATGT
* *
5754221 TCTGACTTTATTAGAATGAAATTATGAAATGT
1 TCTGACTTGATTAGAATGAAATTATCAAATGT
5754253 TC
1 TC
5754255 ACCTCTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (32 bp):
TCTGACTTGATTAGAATGAAATTATCAAATGT
Found at i:5754688 original size:26 final size:26
Alignment explanation
Indices: 5754651--5754708 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
5754641 TGATACAAAT
5754651 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5754677 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
5754703 TGATAA
1 TGATAA
5754709 GAATTTCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:5756360 original size:27 final size:27
Alignment explanation
Indices: 5756319--5756431 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
5756309 GAGGAAGCAT
*
5756319 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5756346 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5756373 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
5756401 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
5756427 TCTGG
1 TCTGG
5756432 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:5756424 original size:54 final size:54
Alignment explanation
Indices: 5756318--5756431 Score: 167
Period size: 54 Copynumber: 2.1 Consensus size: 54
5756308 GGAGGAAGCA
*
5756318 TTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTG
1 TTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTG
* * * *
5756372 TTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTG
1 TTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCTG
5756426 TTCTGG
1 TTCTGG
5756432 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.37
Consensus pattern (54 bp):
TTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTG
Found at i:5760057 original size:22 final size:21
Alignment explanation
Indices: 5760018--5760067 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5760008 ACATTACATA
*
5760018 AAATAATATACATTTTTAAAT
1 AAATAATATACATCTTTAAAT
*
5760039 AAATAATCATATATCTTTAAAT
1 AAATAAT-ATACATCTTTAAAT
5760061 -AATAATA
1 AAATAATA
5760068 ATTAAATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.50
22 12 0.46
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATAATATACATCTTTAAAT
Done.