Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 298 of 318
Found at i:93353290 original size:10 final size:10
Alignment explanation
Indices: 93353212--93353291 Score: 53
Period size: 10 Copynumber: 8.0 Consensus size: 10
93353202 ATATTTAACT
93353212 AAAATAAA-A
1 AAAATAAATA
93353221 TAAAATAAAATA
1 -AAAAT-AAATA
93353233 ATAAAT-AATA
1 A-AAATAAATA
*
93353243 AATAATAAA-G
1 AA-AATAAATA
**
93353253 AAAATAAAGG
1 AAAATAAATA
93353263 AAAAT-AATA
1 AAAATAAATA
93353272 AATAA-AAATA
1 AA-AATAAATA
93353282 AAAATAAATA
1 AAAATAAATA
93353292 TTGGGTTGCC
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
9 13 0.22
10 34 0.59
11 6 0.10
12 5 0.09
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (10 bp):
AAAATAAATA
Found at i:93357056 original size:27 final size:27
Alignment explanation
Indices: 93357026--93357083 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
93357016 AGATAATTAA
93357026 AATAA-AATCCTAAAT-TTGAATAATCCT
1 AATAATAAT-CTAAATATT-AATAATCCT
* *
93357053 AATAATTATCTAAATATTAATTATCCT
1 AATAATAATCTAAATATTAATAATCCT
93357080 AATA
1 AATA
93357084 GAATAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (27 bp):
AATAATAATCTAAATATTAATAATCCT
Found at i:93378200 original size:3 final size:3
Alignment explanation
Indices: 93378192--93378302 Score: 213
Period size: 3 Copynumber: 37.0 Consensus size: 3
93378182 GTAGCAAAAC
93378192 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
93378240 ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
93378288 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
93378303 TATTGTATCA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 106 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:93380278 original size:9 final size:9
Alignment explanation
Indices: 93380263--93380298 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
93380253 AAATACACAA
93380263 AAAGTTTTG
1 AAAGTTTTG
*
93380272 AAGGTTTTG
1 AAAGTTTTG
93380281 AAAGTTTTG
1 AAAGTTTTG
93380290 AAAGTTTTG
1 AAAGTTTTG
93380299 GGAGATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (9 bp):
AAAGTTTTG
Found at i:93386134 original size:42 final size:42
Alignment explanation
Indices: 93386087--93386166 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
93386077 CTTAATAATT
* *
93386087 AGGGGTTAATTCAATTGATAGAGTTTACCCATGTGCTTCAAA
1 AGGGGTTAATTCAATGGATAGAGTTTACCCATGAGCTTCAAA
*
93386129 AGGGGTTAATTCAATGGATAGAGTTTATCCATGAGCTT
1 AGGGGTTAATTCAATGGATAGAGTTTACCCATGAGCTT
93386167 GAAAGCGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (42 bp):
AGGGGTTAATTCAATGGATAGAGTTTACCCATGAGCTTCAAA
Found at i:93387250 original size:90 final size:90
Alignment explanation
Indices: 93387092--93387274 Score: 233
Period size: 90 Copynumber: 2.0 Consensus size: 90
93387082 ATTTTTTATG
* * * *
93387092 AAAAGCAATTAAGCCCCTCCTTTTTTTTTTCACTCAATTAAACATTTGAACTTTCAAAATGCACC
1 AAAAGCAATTAAGCCCCTCCTTTTTCTTTCCACTCAATTAAACACTTGAACTTTCAAAATGAACC
* * *
93387157 AAAAAGGCCCTTAAACTTCTTCAAA
66 AAAAAGACCCTCAAAATTCTTCAAA
**** *
93387182 AAAAGCAATTAAGCCCCTACC-TTTTCTTTCCACTCAATTGGGTACTTGAACTTTCAAAATGAAT
1 AAAAGCAATTAAGCCCCT-CCTTTTTCTTTCCACTCAATTAAACACTTGAACTTTCAAAATGAAC
*
93387246 CAAAAAGACCCTCAAAATTTTTCAAA
65 CAAAAAGACCCTCAAAATTCTTCAAA
93387272 AAA
1 AAA
93387275 GACCCTCAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 77 0.97
91 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (90 bp):
AAAAGCAATTAAGCCCCTCCTTTTTCTTTCCACTCAATTAAACACTTGAACTTTCAAAATGAACC
AAAAAGACCCTCAAAATTCTTCAAA
Found at i:93387263 original size:22 final size:23
Alignment explanation
Indices: 93387235--93387286 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
93387225 ACTTGAACTT
93387235 TCAAAATGAATC-AAAAAGACCC
1 TCAAAATGAATCAAAAAAGACCC
***
93387257 TCAAAATTTTTCAAAAAAGACCC
1 TCAAAATGAATCAAAAAAGACCC
93387280 TCAAAAT
1 TCAAAAT
93387287 TTTTCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.52, C:0.21, G:0.06, T:0.21
Consensus pattern (23 bp):
TCAAAATGAATCAAAAAAGACCC
Found at i:93387289 original size:22 final size:23
Alignment explanation
Indices: 93387247--93387297 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
93387237 AAAATGAATC
93387247 AAAAAGACCCTCAAAATTTTTCA
1 AAAAAGACCCTCAAAATTTTTCA
93387270 AAAAAGACCCTCAAAATTTTTCA
1 AAAAAGACCCTCAAAATTTTTCA
93387293 AAAAA
1 AAAAA
93387298 TCAATAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAAAGACCCTCAAAATTTTTCA
Found at i:93387386 original size:19 final size:19
Alignment explanation
Indices: 93387352--93387411 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
93387342 AATTTTGTAT
93387352 AATTTTCTTATGACTTTATAA
1 AATTTT-TTAT-ACTTTATAA
*
93387373 AATTTTTTATACTTTTTAA
1 AATTTTTTATACTTTATAA
* *
93387392 AATTTCTATATATTTTATAA
1 AATTT-TTTATACTTTATAA
93387412 TTTTTTACGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.38
20 15 0.44
21 6 0.18
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (19 bp):
AATTTTTTATACTTTATAA
Found at i:93387471 original size:10 final size:10
Alignment explanation
Indices: 93387458--93387490 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
93387448 TTTTTTTACA
93387458 TTTTTCTA-T
1 TTTTTCTATT
93387467 TTTTTCTATT
1 TTTTTCTATT
93387477 TTTTTCTAATT
1 TTTTTCT-ATT
93387488 TTT
1 TTT
93387491 AATATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.36
10 8 0.36
11 6 0.27
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTCTATT
Found at i:93396109 original size:13 final size:13
Alignment explanation
Indices: 93396091--93396115 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93396081 CTTTTGGCAA
93396091 TAATATATATTTT
1 TAATATATATTTT
93396104 TAATATATATTT
1 TAATATATATTT
93396116 AATATGTATC
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATATATATTTT
Found at i:93401758 original size:5 final size:5
Alignment explanation
Indices: 93401747--93401781 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
93401737 AAATATGTAT
*
93401747 TTTTCA TTTCA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
93401782 CACATATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 24 0.89
6 3 0.11
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:93401775 original size:15 final size:16
Alignment explanation
Indices: 93401747--93401783 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
93401737 AAATATGTAT
93401747 TTTTCATTTCATTTTA
1 TTTTCATTTCATTTTA
*
93401763 TTTT-ATTTTATTTTA
1 TTTTCATTTCATTTTA
93401778 TTTTCA
1 TTTTCA
93401784 CATATAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTCATTTCATTTTA
Found at i:93405599 original size:3 final size:3
Alignment explanation
Indices: 93405593--93405638 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
93405583 AATATTAATG
93405593 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
93405639 GAATTTAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:93405824 original size:22 final size:21
Alignment explanation
Indices: 93405785--93405829 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
93405775 TTATAAAAAT
*
93405785 TATTTTATATTGATATTTTATA
1 TATTTTATATTGA-AATTTATA
93405807 TATTTTATAATT-AAATTTATA
1 TATTTTAT-ATTGAAATTTATA
93405828 TA
1 TA
93405830 AAAATATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 9 0.43
23 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTTATATTGAAATTTATA
Found at i:93410403 original size:23 final size:21
Alignment explanation
Indices: 93410377--93410424 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
93410367 AAATAAAAAA
93410377 GTTTCAAGAACTAAAATTTATAT
1 GTTT-AAG-ACTAAAATTTATAT
** *
93410400 GTTTTTGTCTAAAATTTATAT
1 GTTTAAGACTAAAATTTATAT
93410421 GTTT
1 GTTT
93410425 TTGCCTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 17 0.77
22 1 0.05
23 4 0.18
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.50
Consensus pattern (21 bp):
GTTTAAGACTAAAATTTATAT
Found at i:93410413 original size:21 final size:21
Alignment explanation
Indices: 93410387--93410427 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
93410377 GTTTCAAGAA
93410387 CTAAAATTTATATGTTTTTGT
1 CTAAAATTTATATGTTTTTGT
93410408 CTAAAATTTATATGTTTTTG
1 CTAAAATTTATATGTTTTTG
93410428 CCTTTTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (21 bp):
CTAAAATTTATATGTTTTTGT
Found at i:93420171 original size:22 final size:22
Alignment explanation
Indices: 93420141--93420192 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
93420131 AATAATATAG
*
93420141 AAAAGCACTTACAACATGAAAT
1 AAAAACACTTACAACATGAAAT
*
93420163 AAAAACACTTACAACTTGAAAT
1 AAAAACACTTACAACATGAAAT
93420185 AAAAACAC
1 AAAAACAC
93420193 ATCCATATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAAACACTTACAACATGAAAT
Found at i:93429108 original size:93 final size:89
Alignment explanation
Indices: 93429011--93429216 Score: 252
Period size: 93 Copynumber: 2.3 Consensus size: 89
93429001 TTTTTCAAAA
* *
93429011 AAAAAAAGAAGCAATTAAGCCCCTCCTTTT-TTTTATACTCAATTGAGCACTTGAACTTTCAAAA
1 AAAAAAA-AAGCAATTAAGCCCCTACTTTTGTTTT-CACTCAATTGAGCACTTGAACTTTCAAAA
*
93429075 TACATAAAAAAAAATCCCTCAAACTTCTT
64 TACAT-AAAAAAAAT-CCTCAAAATT-TT
* ***
93429104 AAAAAAAAAAGCAATTAAACCCCTACTTTTGTTTTCACTCAATTGAGTGTTTGAACTTTCAAAAT
1 -AAAAAAAAAGCAATTAAGCCCCTACTTTTGTTTTCACTCAATTGAGCACTTGAACTTTCAAAAT
* *
93429169 GCATCAAAAAAATCCTCAAAATTTT
65 ACATAAAAAAAATCCTCAAAATTTT
**
93429194 TCAAAAAAAGCAATTAAGCCCCT
1 AAAAAAAAAGCAATTAAGCCCCT
93429217 GATCTTATTA
Statistics
Matches: 99, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
89 20 0.20
90 2 0.02
91 9 0.09
92 8 0.08
93 49 0.49
94 11 0.11
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (89 bp):
AAAAAAAAAGCAATTAAGCCCCTACTTTTGTTTTCACTCAATTGAGCACTTGAACTTTCAAAATA
CATAAAAAAAATCCTCAAAATTTT
Found at i:93429539 original size:22 final size:24
Alignment explanation
Indices: 93429487--93429539 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 24
93429477 TTATAAAATG
*
93429487 TTTCTTTTGGTACAAAAATTTTTA
1 TTTCTTTTGGTACAAAAATTTATA
** *
93429511 TAACTTTT-TTAC-AAAATTTATA
1 TTTCTTTTGGTACAAAAATTTATA
93429533 TTTCTTT
1 TTTCTTT
93429540 ATATTTTGTA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 14 0.61
23 3 0.13
24 6 0.26
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTCTTTTGGTACAAAAATTTATA
Found at i:93429585 original size:9 final size:9
Alignment explanation
Indices: 93429551--93429637 Score: 57
Period size: 10 Copynumber: 9.0 Consensus size: 9
93429541 TATTTTGTAT
93429551 AATTTTATTA
1 AATTTTA-TA
*
93429561 AGACTTTATAA
1 A-ATTTTAT-A
93429572 AATTTTATA
1 AATTTTATA
*
93429581 AATTTTTTA
1 AATTTTATA
*
93429590 TATTTCTATA
1 AATTT-TATA
*
93429600 TATTTTATA
1 AATTTTATA
*
93429609 AATTTTTATG
1 AA-TTTTATA
**
93429619 TTTTTTATAA
1 AATTTTAT-A
93429629 AATTTTATA
1 AATTTTATA
93429638 GTGTTACAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
9 25 0.42
10 28 0.47
11 7 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (9 bp):
AATTTTATA
Found at i:93429604 original size:19 final size:18
Alignment explanation
Indices: 93429573--93429627 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
93429563 ACTTTATAAA
*
93429573 ATTTTATAAATTTTTTAT
1 ATTTTATATATTTTTTAT
* *
93429591 ATTTCTATATATTTTATAA
1 ATTT-TATATATTTTTTAT
*
93429610 ATTTT-TATGTTTTTTAT
1 ATTTTATATATTTTTTAT
93429627 A
1 A
93429628 AAATTTTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 10 0.33
18 5 0.17
19 15 0.50
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTATATATTTTTTAT
Found at i:93429627 original size:28 final size:29
Alignment explanation
Indices: 93429567--93429637 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 29
93429557 ATTAAGACTT
93429567 TATAAAATTTTATAAATTTTTTATATTTC
1 TATAAAATTTTATAAATTTTTTATATTTC
* * *
93429596 TAT-ATATTTTATAAA-TTTTTATGTTTTT
1 TATAAAATTTTATAAATTTTTTAT-ATTTC
93429624 TATAAAATTTTATA
1 TATAAAATTTTATA
93429638 GTGTTACAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.19
28 17 0.47
29 12 0.33
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (29 bp):
TATAAAATTTTATAAATTTTTTATATTTC
Found at i:93439288 original size:5 final size:5
Alignment explanation
Indices: 93439278--93439309 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
93439268 AATTTGTGGA
93439278 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
93439310 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:93439303 original size:9 final size:9
Alignment explanation
Indices: 93439279--93439309 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
93439269 ATTTGTGGAA
93439279 AAATAAAAT
1 AAATAAAAT
93439288 AAAATAAAAT
1 -AAATAAAAT
93439298 AAATAAAAT
1 AAATAAAAT
93439307 AAA
1 AAA
93439310 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:93441267 original size:21 final size:21
Alignment explanation
Indices: 93441241--93441285 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
93441231 TAAATTGCAA
93441241 TTATCTAAAGGGCCAAAACGG
1 TTATCTAAAGGGCCAAAACGG
*
93441262 TTATCTAAAGGGCCAAAATGG
1 TTATCTAAAGGGCCAAAACGG
93441283 TTA
1 TTA
93441286 ATAAACCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (21 bp):
TTATCTAAAGGGCCAAAACGG
Found at i:93442638 original size:14 final size:13
Alignment explanation
Indices: 93442619--93442655 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
93442609 TTTTAATTTC
93442619 AATTATATTAGGAT
1 AATTAT-TTAGGAT
*
93442633 AATTATTAAGGAT
1 AATTATTTAGGAT
93442646 AATTATTTAG
1 AATTATTTAG
93442656 ATTTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (13 bp):
AATTATTTAGGAT
Found at i:93442685 original size:10 final size:10
Alignment explanation
Indices: 93442670--93442708 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
93442660 AATTTTAGCT
93442670 TTTATCTTTA
1 TTTATCTTTA
*
93442680 TTTATCCTTA
1 TTTATCTTTA
93442690 TTTATCTTTA
1 TTTATCTTTA
*
93442700 ATTATCTTT
1 TTTATCTTT
93442709 TAGAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:93445611 original size:24 final size:24
Alignment explanation
Indices: 93445584--93445646 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
93445574 ATTTCAATTT
93445584 ATCAACCTAAAGTCAATTGTATTA
1 ATCAACCTAAAGTCAATTGTATTA
* *
93445608 ATCAACTTAAAGTCATTTGTATTA
1 ATCAACCTAAAGTCAATTGTATTA
93445632 ATCAACCTAAAGTCA
1 ATCAACCTAAAGTCA
93445647 GCTGTTCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.33
Consensus pattern (24 bp):
ATCAACCTAAAGTCAATTGTATTA
Found at i:93446139 original size:2 final size:2
Alignment explanation
Indices: 93446132--93446157 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
93446122 TTACCGGACA
93446132 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
93446158 TCTTTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93456298 original size:2 final size:2
Alignment explanation
Indices: 93456287--93456320 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
93456277 TTAAGTTAAC
93456287 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93456321 AAGTAAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93456418 original size:17 final size:17
Alignment explanation
Indices: 93456396--93456428 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
93456386 GCAAGGGAGA
93456396 AAAAGAAAGGAAGAAAG
1 AAAAGAAAGGAAGAAAG
93456413 AAAAGAAAGGAAGAAA
1 AAAAGAAAGGAAGAAA
93456429 AGAGAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGGAAGAAAG
Found at i:93481980 original size:28 final size:29
Alignment explanation
Indices: 93481921--93481978 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
93481911 TAATATGATC
*
93481921 AATTAAAATACAATAATCTTAAAAAATATA
1 AATTAAAATA-AATAATCTCAAAAAATATA
93481951 AATTAAAAT-AATAATCTCATAAATAATA
1 AATTAAAATAAATAATCTCA-AAA-AATA
93481979 AAAAATACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 9 0.36
29 3 0.12
30 13 0.52
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (29 bp):
AATTAAAATAAATAATCTCAAAAAATATA
Found at i:93487484 original size:22 final size:22
Alignment explanation
Indices: 93487450--93487492 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
93487440 CATCCAAACA
*
93487450 ATAACAATTAAAT-AGTAGTAAT
1 ATAACAATAAAATGA-TAGTAAT
*
93487472 ATAATAATAAAATGATAGTAA
1 ATAACAATAAAATGATAGTAA
93487493 AATAGCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACAATAAAATGATAGTAAT
Found at i:93494982 original size:28 final size:29
Alignment explanation
Indices: 93494921--93494989 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
93494911 TCCGGGCCGG
* *
93494921 ATGGGCCATATAAATGTGATTTGGGCCTA
1 ATGGGCCATATGAATGAGATTTGGGCCTA
93494950 ATGGGCCATATGAATGAGA-TTGGGCCTA
1 ATGGGCCATATGAATGAGATTTGGGCCTA
*
93494978 GTGGGCCATATG
1 ATGGGCCATATG
93494990 CATGTAAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 20 0.54
29 17 0.46
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (29 bp):
ATGGGCCATATGAATGAGATTTGGGCCTA
Found at i:93500463 original size:44 final size:47
Alignment explanation
Indices: 93500353--93500521 Score: 134
Period size: 44 Copynumber: 3.6 Consensus size: 47
93500343 AGGATATATT
* * *
93500353 GCCGATGCCATGTCTCAGACATGGTCTTACACTAGCT--CTCATATACGCG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTAACTC-TGT-CGAG
* * *
93500402 TTCTGATGCATGTCCCAGACATGTCTTACACTAGCATAACT-T-T-TA-
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGC-TAACTCTGTCGAG
* ** * *
93500447 GCCGATGCGTGTCCCAGACACATCTTACACTGGCTATCTCTGTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTAACTCTGTCGAG
*
93500494 GCCGATGCATGTCCCAAACATGTCTTAC
1 GCCGATGCATGTCCCAGACATGTCTTAC
93500522 TCTGGCACTC
Statistics
Matches: 95, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
43 4 0.04
44 29 0.31
45 1 0.01
46 1 0.01
47 24 0.25
48 14 0.15
49 15 0.16
50 5 0.05
51 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTAACTCTGTCGAG
Found at i:93500520 original size:47 final size:44
Alignment explanation
Indices: 93500406--93500621 Score: 157
Period size: 47 Copynumber: 4.7 Consensus size: 44
93500396 TACGCGTTCT
* * * *
93500406 GATGCATGTCCCAGACATGTCTTACACTAGCATAACT-TTTAGCC
1 GATGCATGTCCCAAACATGTCTTACACTGGC-TATCTCTGTAGCC
* * **
93500450 GATGCGTGTCCCAGACACATCTTACACTGGCTATCTCTGTCGAGGCC
1 GATGCATGTCCCAAACATGTCTTACACTGGCTATCTCTGT--A-GCC
*
93500497 GATGCATGTCCCAAACATGTCTTACTCTGGCACTCATCTCTGTA-CC
1 GATGCATGTCCCAAACATGTCTTACACTGG--CT-ATCTCTGTAGCC
* * * *
93500543 GATGCCATGTCCCAAACATGGTCTTACGCTGGCTCTCATAATGTGGCC
1 GATG-CATGTCCCAAACAT-GTCTTACACTGGCTATC-T-CTGTAGCC
* * ** *
93500591 AAAGCATGTCTTAGACATGTCTTACACTGGC
1 GATGCATGTCCCAAACATGTCTTACACTGGC
93500622 GCACAAATCA
Statistics
Matches: 139, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
43 4 0.03
44 29 0.21
45 2 0.01
46 22 0.16
47 56 0.40
48 16 0.12
49 2 0.01
50 8 0.06
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (44 bp):
GATGCATGTCCCAAACATGTCTTACACTGGCTATCTCTGTAGCC
Found at i:93501001 original size:30 final size:30
Alignment explanation
Indices: 93500961--93501017 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
93500951 AATTTACATC
* *
93500961 TTTGGTAAAATGACCATTTTGCCCCTAGAT
1 TTTGGCAAAATGACCATTTTACCCCTAGAT
93500991 TTTGGCAAAATGACCATTTTACCCCTA
1 TTTGGCAAAATGACCATTTTACCCCTA
93501018 TGCCTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (30 bp):
TTTGGCAAAATGACCATTTTACCCCTAGAT
Found at i:93504342 original size:43 final size:40
Alignment explanation
Indices: 93504249--93504363 Score: 155
Period size: 43 Copynumber: 2.9 Consensus size: 40
93504239 TTTATTGGAA
*
93504249 AAAAACGCCGCTAAAGGTCAAGGCTTTTA---GCGGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGGTGGG
93504286 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCG---GTGGG
* *
93504329 TAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
93504364 CTTTTTTTAC
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
37 28 0.41
40 3 0.04
43 38 0.55
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (40 bp):
AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGGTGGG
Found at i:93504505 original size:31 final size:31
Alignment explanation
Indices: 93504438--93504503 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
93504428 CTTCCTGCAT
*
93504438 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAATACAACAAATATAACA
* * * *
93504469 TAAAATGCAGCCAAA-ACAGCAAATTTAACA
1 TAAAATCCAACCAAATACAACAAATATAACA
93504499 TAAAA
1 TAAAA
93504504 ATACAACTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (31 bp):
TAAAATCCAACCAAATACAACAAATATAACA
Found at i:93504784 original size:21 final size:21
Alignment explanation
Indices: 93504760--93504805 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
93504750 GCTCGTGCCT
*
93504760 CTGCCTCTCTCGCTGCAGCCG
1 CTGCCTCCCTCGCTGCAGCCG
* * *
93504781 CTGCCTCCCTCTCTGCTGCCT
1 CTGCCTCCCTCGCTGCAGCCG
93504802 CTGC
1 CTGC
93504806 TCTAAGTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.50, G:0.20, T:0.28
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCAGCCG
Found at i:93508097 original size:9 final size:9
Alignment explanation
Indices: 93508062--93508150 Score: 108
Period size: 9 Copynumber: 10.0 Consensus size: 9
93508052 ATTATATTGG
93508062 ATAAGTTAT
1 ATAAGTTAT
*
93508071 AT-ATTTAT
1 ATAAGTTAT
* *
93508079 CTAAGCTAT
1 ATAAGTTAT
93508088 ATAAGTTAT
1 ATAAGTTAT
93508097 ATAAGTTAT
1 ATAAGTTAT
* *
93508106 GTATGTTAT
1 ATAAGTTAT
93508115 ATAAGTTAT
1 ATAAGTTAT
*
93508124 GTAAGTTAT
1 ATAAGTTAT
*
93508133 ATATGTTAT
1 ATAAGTTAT
93508142 ATAAGTTAT
1 ATAAGTTAT
93508151 GTAAATTATG
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
8 6 0.09
9 59 0.91
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.47
Consensus pattern (9 bp):
ATAAGTTAT
Found at i:93508115 original size:27 final size:27
Alignment explanation
Indices: 93508062--93508160 Score: 119
Period size: 27 Copynumber: 3.7 Consensus size: 27
93508052 ATTATATTGG
* * * *
93508062 ATAAGTTATAT-ATTTATCTAAGCTAT
1 ATAAGTTATATAAGTTATGTATGTTAT
93508088 ATAAGTTATATAAGTTATGTATGTTAT
1 ATAAGTTATATAAGTTATGTATGTTAT
* *
93508115 ATAAGTTATGTAAGTTATATATGTTAT
1 ATAAGTTATATAAGTTATGTATGTTAT
* *
93508142 ATAAGTTATGTAAATTATG
1 ATAAGTTATATAAGTTATG
93508161 ATATCAAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 11 0.17
27 53 0.83
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.46
Consensus pattern (27 bp):
ATAAGTTATATAAGTTATGTATGTTAT
Found at i:93508283 original size:15 final size:15
Alignment explanation
Indices: 93508263--93508318 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
93508253 AAGTAGCGGG
93508263 ATTAAATAATATTTA
1 ATTAAATAATATTTA
93508278 ATTAAATAATATTT-
1 ATTAAATAATATTTA
93508292 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
93508307 ATTAAATAATAT
1 ATTAAATAATAT
93508319 ACATGTCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:93508558 original size:24 final size:24
Alignment explanation
Indices: 93508495--93508561 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
93508485 ACTTAAATGG
93508495 TAAAACGGACGATAA-ATTTGTAA
1 TAAAACGGACGATAATATTTGTAA
*
93508518 TAAAACGGA-GAATAATATTTGTGA
1 TAAAACGGACG-ATAATATTTGTAA
*
93508542 TAAAACGGACGAGAATATTT
1 TAAAACGGACGATAATATTT
93508562 CAATAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 1 0.03
23 13 0.33
24 24 0.62
25 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.27
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTAA
Found at i:93508874 original size:21 final size:21
Alignment explanation
Indices: 93508849--93508890 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
93508839 TAAAGAAATT
*
93508849 TAAAAA-TATTAAATATTAAAA
1 TAAAAATTATT-AATATAAAAA
93508870 TAAAAATTATTAATATAAAAA
1 TAAAAATTATTAATATAAAAA
93508891 AATAGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAATTATTAATATAAAAA
Found at i:93512636 original size:14 final size:15
Alignment explanation
Indices: 93512612--93512641 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
93512602 CACAAACTTC
93512612 AGAATTTATGTATTT
1 AGAATTTATGTATTT
93512627 AGAA-TTATGTATTT
1 AGAATTTATGTATTT
93512641 A
1 A
93512642 TATAAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
AGAATTTATGTATTT
Found at i:93515746 original size:28 final size:28
Alignment explanation
Indices: 93515676--93515768 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 28
93515666 TCTTGTGGGG
93515676 GGGTTTAGGGTTT-TGGAGTTTATAGA-TTA
1 GGGTTTAGGGTTTAT-GA-TTTA-AGATTTA
* * * *
93515705 GTGTTTATGTTTTATGATTTAAAATTTA
1 GGGTTTAGGGTTTATGATTTAAGATTTA
93515733 GGGTTTAGGGTTTAATG-TTTAAGATTTAA
1 GGGTTTAGGGTTT-ATGATTTAAGATTT-A
93515762 GGGTTTA
1 GGGTTTA
93515769 CAGAAAGCCA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.04
28 26 0.50
29 23 0.44
30 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (28 bp):
GGGTTTAGGGTTTATGATTTAAGATTTA
Found at i:93516114 original size:41 final size:41
Alignment explanation
Indices: 93516058--93516315 Score: 222
Period size: 41 Copynumber: 6.6 Consensus size: 41
93516048 AACTTTTTGC
*
93516058 GGCG-TTTGGACTAAAAACGCCGCTATTAATCAGTTTTTAGT
1 GGCGTTTTGGA-TAAAAACGCCGCTATTGATCAGTTTTTAGT
* * *
93516099 GGCGTTTTGGATAAAAACGCCACAATTGATCAGTTTTTTGT
1 GGCGTTTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* *
93516140 GGCGTTTGGGACAAAAACGCCGC-----A--A---TTTAGT
1 GGCGTTTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
** * *
93516171 GGCGTTTGAGATTAAAACGCCGCTATTGATCAGCTTTTAGT
1 GGCGTTTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
*
93516212 GGCGTTTT-GATAAAAACGCCGCTATTGACCAGTTTTTAGT
1 GGCGTTTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * * * *
93516252 GGCGTTTTTGG-CAAAAACGCCACTATAGTTTAGCTTTTAGT
1 GGCG-TTTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* *
93516293 GGCG-TTTCGA-ACAAACGCCGCTA
1 GGCGTTTTGGATAAAAACGCCGCTA
93516316 ATGTATATTA
Statistics
Matches: 178, Mismatches: 25, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
31 25 0.14
34 1 0.01
36 2 0.01
38 1 0.01
39 15 0.08
40 33 0.19
41 94 0.53
42 7 0.04
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (41 bp):
GGCGTTTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
Found at i:93516188 original size:72 final size:71
Alignment explanation
Indices: 93516093--93516233 Score: 194
Period size: 72 Copynumber: 2.0 Consensus size: 71
93516083 TTAATCAGTT
* *
93516093 TTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGTTTTTTGTGGCGTTTGGGACAAAAAC
1 TTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGCTTTTAGTGGCGTTT-GGACAAAAAC
93516158 GCCGCAA
65 GCCGCAA
* * * * *
93516165 TTTAGTGGCG-TTTGAGATTAAAACGCCGCTATTGATCAGCTTTTAGTGGCGTTTTGATAAAAAC
1 TTTAGTGGCGTTTTG-GATAAAAACGCCACAATTGATCAGCTTTTAGTGGCGTTTGGACAAAAAC
93516229 GCCGC
65 GCCGC
93516234 TATTGACCAG
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
71 17 0.28
72 44 0.72
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (71 bp):
TTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGCTTTTAGTGGCGTTTGGACAAAAACG
CCGCAA
Found at i:93521860 original size:27 final size:28
Alignment explanation
Indices: 93521830--93521894 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 28
93521820 AAATAAACTA
93521830 TTTTTATAAATTTTATAA-AA-TATTATT
1 TTTTTATAAA-TTTATAATAATTATTATT
* *
93521857 TTTTTAATTAATTTATAATAATTTTTATT
1 TTTTT-ATAAATTTATAATAATTATTATT
93521886 TTTTTATAA
1 TTTTTATAA
93521895 TTTCAGATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 12 0.38
28 9 0.28
29 11 0.34
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTTATAAATTTATAATAATTATTATT
Found at i:93521861 original size:28 final size:28
Alignment explanation
Indices: 93521830--93521894 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
93521820 AAATAAACTA
93521830 TTTTTATAAATTTTATAA-AATATTAT-TT
1 TTTTTATAAA-TTTATAATAAT-TTATATT
* * *
93521858 TTTTAATTAATTTATAATAATTTTTATT
1 TTTTTATAAATTTATAATAATTTATATT
93521886 TTTTTATAA
1 TTTTTATAA
93521895 TTTCAGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTTATAAATTTATAATAATTTATATT
Found at i:93523311 original size:2 final size:2
Alignment explanation
Indices: 93523304--93523339 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
93523294 GTAAGATTTG
*
93523304 TA TA TA TA TC 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
93523340 AAGCTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93539465 original size:21 final size:19
Alignment explanation
Indices: 93539425--93539467 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
93539415 TTATAATTAA
*
93539425 TTAAAATATTTTTCTTTTT
1 TTAAAATATTTTACTTTTT
* *
93539444 TTAAAATATATTTAGTTATT
1 TTAAAATAT-TTTACTTTTT
93539464 TTAA
1 TTAA
93539468 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTAAAATATTTTACTTTTT
Found at i:93543296 original size:24 final size:24
Alignment explanation
Indices: 93543264--93543322 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
93543254 TTCTTTCCAC
93543264 ATTCAACATTTGTAATATATAGAT
1 ATTCAACATTTGTAATATATAGAT
93543288 ATTCAACATTTGTAATATATAGAT
1 ATTCAACATTTGTAATATATAGAT
93543312 ATTCAACATTT
1 ATTCAACATTT
93543323 TTCTCATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (24 bp):
ATTCAACATTTGTAATATATAGAT
Found at i:93546105 original size:2 final size:2
Alignment explanation
Indices: 93546098--93546122 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
93546088 ACATGCGCAC
93546098 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
93546123 ATTTGTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:93550054 original size:6 final size:6
Alignment explanation
Indices: 93550045--93550072 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
93550035 GATAAGTTCG
93550045 GGGAGA GGGAGA GGGAGA GGGAGA GGGA
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGA
93550073 CCACAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:93555889 original size:19 final size:18
Alignment explanation
Indices: 93555851--93555888 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
93555841 CCCTAATGCA
*
93555851 TTATCTGTCTTGTTACTT
1 TTATCTGTCTTGCTACTT
93555869 TTATCTGTACTTGCTA-TT
1 TTATCTGT-CTTGCTACTT
93555887 TT
1 TT
93555889 TTTTTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.61
Consensus pattern (18 bp):
TTATCTGTCTTGCTACTT
Found at i:93569974 original size:19 final size:20
Alignment explanation
Indices: 93569938--93569979 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
93569928 GTCTTTTCGC
* *
93569938 GAAATTTAATACACATG-AT
1 GAAATGTAATACAAATGAAT
*
93569957 GAAATGTAATGCAAATGAAT
1 GAAATGTAATACAAATGAAT
93569977 GAA
1 GAA
93569980 TGCAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (20 bp):
GAAATGTAATACAAATGAAT
Found at i:93575928 original size:26 final size:26
Alignment explanation
Indices: 93575889--93575992 Score: 147
Period size: 26 Copynumber: 4.0 Consensus size: 26
93575879 TGGTACAAAT
* *
93575889 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATGGATTAGGTAAATATTCCA
93575915 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATATTCCA
*
93575941 TGATAAT-GAGTTAGGTAAATGTTCCA
1 TGATAATGGA-TTAGGTAAATATTCCA
* *
93575967 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATATTCCA
93575993 AGATGGGAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
25 2 0.03
26 69 0.96
27 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.37
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATATTCCA
Found at i:93575954 original size:52 final size:52
Alignment explanation
Indices: 93575889--93575992 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
93575879 TGGTACAAAT
* *
93575889 TGATAATGGGTTAGGTAAATATTTCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGAGTTAGGTAAATATTCCATGATAATGGATTAGGTAAATATTCCA
* * *
93575941 TGATAATGAGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGAGTTAGGTAAATATTCCATGATAATGGATTAGGTAAATATTCCA
93575993 AGATGGGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.37
Consensus pattern (52 bp):
TGATAATGAGTTAGGTAAATATTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:93583008 original size:26 final size:26
Alignment explanation
Indices: 93582979--93583079 Score: 166
Period size: 26 Copynumber: 3.9 Consensus size: 26
93582969 TGGTACAAAT
93582979 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
93583005 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
93583031 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
93583057 TGATAATGGTTTAGGTAAATGTT
1 TGATAATGGGTTAGGTAAATGTT
93583080 TCAGATGGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 68 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:93595145 original size:26 final size:26
Alignment explanation
Indices: 93595115--93595165 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
93595105 GTTTTAGAGC
* *
93595115 TAATTTGGTAATATTTTTTATTTAAT
1 TAATTTGGCAATACTTTTTATTTAAT
* *
93595141 TAATTTTGCAATGCTTTTTATTTAA
1 TAATTTGGCAATACTTTTTATTTAA
93595166 AAATGTGAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.59
Consensus pattern (26 bp):
TAATTTGGCAATACTTTTTATTTAAT
Found at i:93595252 original size:22 final size:19
Alignment explanation
Indices: 93595224--93595266 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 19
93595214 ATATTTATTT
93595224 TAAATATGATATTATAAAGTAA
1 TAAATATG-TATT-TAAA-TAA
93595246 TAAATATGTATTTAAATAA
1 TAAATATGTATTTAAATAA
93595265 TA
1 TA
93595267 TTTAAATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 4 0.19
22 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (19 bp):
TAAATATGTATTTAAATAA
Found at i:93595379 original size:24 final size:22
Alignment explanation
Indices: 93595334--93595390 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
93595324 ACTTATTGTT
*
93595334 AATA-TTTTAATATTAATTTTA
1 AATATTTTTAATATTAATATTA
93595355 AATATTTTTAAGTAATTAATATTA
1 AATATTTTTAA-T-ATTAATATTA
*
93595379 ATTATTTATTAA
1 AATATTT-TTAA
93595391 ATTTAATTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 4 0.13
22 6 0.20
23 1 0.03
24 15 0.50
25 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
AATATTTTTAATATTAATATTA
Found at i:93595442 original size:86 final size:81
Alignment explanation
Indices: 93595334--93595526 Score: 259
Period size: 79 Copynumber: 2.3 Consensus size: 81
93595324 ACTTATTGTT
* * *
93595334 AATATTTTAATATTAAT-TTTAAATATTTTTAAGTAATTA-ATATTAATTATTTATTAAATTTAA
1 AATATTTAAATA-TAATAATTAAATATTTTT--GTAATTAGATATTAATTATTCATTAAATTTAA
93595397 TTAGAATATATAAACTATATTTA
63 -T---ATATATAAACTATATTTA
*
93595420 AATATTTAAATATAATAATTAAATA--TTTGTAATTAGATATTGATTATTCATTAAATTTAATAT
1 AATATTTAAATATAATAATTAAATATTTTTGTAATTAGATATTAATTATTCATTAAATTTAATAT
93595483 ATATAAACTATATTTA
66 ATATAAACTATATTTA
93595499 AATATTTAAATATAATAATTAAATATTT
1 AATATTTAAATATAATAATTAAATATTT
93595527 ATAATTAAAT
Statistics
Matches: 99, Mismatches: 4, Indels: 13
0.85 0.03 0.11
Matches are distributed among these distances:
79 43 0.43
81 1 0.01
82 8 0.08
83 22 0.22
84 3 0.03
85 4 0.04
86 18 0.18
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.49
Consensus pattern (81 bp):
AATATTTAAATATAATAATTAAATATTTTTGTAATTAGATATTAATTATTCATTAAATTTAATAT
ATATAAACTATATTTA
Found at i:93595498 original size:79 final size:80
Alignment explanation
Indices: 93595366--93595539 Score: 271
Period size: 79 Copynumber: 2.1 Consensus size: 80
93595356 ATATTTTTAA
*
93595366 GTAATTAATATTAATTATTTATTAAATTTAATTAGAATATATAAACTATATTTAAATATTTAAAT
1 GTAATTAATATTAATTATTCATTAAATTTAATT--AATATATAAACTATATTTAAATATTTAAAT
93595431 ATAATAATTAAATATTT
64 ATAATAATTAAATATTT
*
93595448 GTAATTAGATATTGATTATTCATTAAATTTAA-T-ATATATAAACTATATTTAAATATTTAAATA
1 GTAATTA-ATATTAATTATTCATTAAATTTAATTAATATATAAACTATATTTAAATATTTAAATA
93595511 TAATAATTAAATATTT
65 TAATAATTAAATATTT
*
93595527 ATAATTAAATATT
1 GTAATT-AATATT
93595540 TGGAAGAAGA
Statistics
Matches: 87, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
79 56 0.64
80 1 0.01
82 8 0.09
83 22 0.25
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (80 bp):
GTAATTAATATTAATTATTCATTAAATTTAATTAATATATAAACTATATTTAAATATTTAAATAT
AATAATTAAATATTT
Found at i:93595511 original size:27 final size:27
Alignment explanation
Indices: 93595401--93595512 Score: 69
Period size: 21 Copynumber: 4.2 Consensus size: 27
93595391 ATTTAATTAG
93595401 AATATATAAACTATATTTAAATATTT-
1 AATATATAAACTATATTTAAATATTTA
*
93595427 AA-ATAT-AA-TA-A-TTAAATATTTGT
1 AATATATAAACTATATTTAAATATTT-A
* * * *
93595450 AAT-TAGATATTGATTATTCATTAA-ATTTA
1 AATATATAAACT-A-TATT--TAAATATTTA
93595479 ATATATATAAACTATATTTAAATATTTA
1 A-ATATATAAACTATATTTAAATATTTA
93595507 AATATA
1 AATATA
93595513 ATAATTAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 27
0.65 0.08 0.27
Matches are distributed among these distances:
21 10 0.16
22 1 0.02
23 6 0.09
24 3 0.05
25 5 0.08
26 3 0.05
27 8 0.12
28 7 0.11
29 6 0.09
30 7 0.11
31 8 0.12
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (27 bp):
AATATATAAACTATATTTAAATATTTA
Found at i:93595532 original size:14 final size:14
Alignment explanation
Indices: 93595504--93595540 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
93595494 ATTTAAATAT
*
93595504 TTAAATA-TAATAA
1 TTAAATATTTATAA
93595517 TTAAATATTTATAA
1 TTAAATATTTATAA
93595531 TTAAATATTT
1 TTAAATATTT
93595541 GGAAGAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAAATATTTATAA
Found at i:93596401 original size:19 final size:19
Alignment explanation
Indices: 93596377--93596414 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
93596367 CAACAGGACC
93596377 GAAAGCACCCAAAATCAAA
1 GAAAGCACCCAAAATCAAA
93596396 GAAAGCACCCAAAATCAAA
1 GAAAGCACCCAAAATCAAA
93596415 CCTAATACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.26, G:0.11, T:0.05
Consensus pattern (19 bp):
GAAAGCACCCAAAATCAAA
Found at i:93597647 original size:50 final size:50
Alignment explanation
Indices: 93597572--93597793 Score: 356
Period size: 50 Copynumber: 4.4 Consensus size: 50
93597562 GCAACAAGTG
93597572 ATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAACAAGTGAAACTA
1 ATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAACAAGTGAAACTA
93597622 ATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAACAAGTGAAACTA
1 ATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAACAAGTGAAACTA
* *
93597672 ATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAACAAGTGAAAGTG
1 ATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAACAAGTGAAACTA
* * * *
93597722 ATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGACAAATGACAAGTGA
1 ATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAACAAGTGA-AACT-A
*
93597774 A-AAGTGGTAGCTTCGGCTAC
1 ATAAGTGATAGCTTCGGCTAC
93597794 CTGATCAGTG
Statistics
Matches: 163, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
50 140 0.86
51 22 0.13
52 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (50 bp):
ATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAACAAGTGAAACTA
Found at i:93597807 original size:31 final size:31
Alignment explanation
Indices: 93597769--93597886 Score: 200
Period size: 31 Copynumber: 3.8 Consensus size: 31
93597759 ACAAATGACA
93597769 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
93597800 AGTGAAAAGTGGTAGCTTTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
93597831 AATGAAAAATGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
93597862 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
93597887 AAGTGACAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 80 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:93597965 original size:47 final size:48
Alignment explanation
Indices: 93597905--93598027 Score: 142
Period size: 47 Copynumber: 2.6 Consensus size: 48
93597895 AGTGATTTCC
* * * **
93597905 ATGTAAAATCATATCTGGGATATGGCATCAGA-GTGATAAGTGCATTTG
1 ATGTAAGACCATATCTGGGATATGGCATC-GATCTGATAAGTGCATAAG
* *
93597953 -TGTAAGACCATATCTGGGATATGGCATCGATCTGATATGTGTATAAG
1 ATGTAAGACCATATCTGGGATATGGCATCGATCTGATAAGTGCATAAG
* *
93598000 ATGTAAGACCATAGCTGGGCTATGGCAT
1 ATGTAAGACCATATCTGGGATATGGCAT
93598028 TTTAGTAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 2 0.03
47 37 0.58
48 25 0.39
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (48 bp):
ATGTAAGACCATATCTGGGATATGGCATCGATCTGATAAGTGCATAAG
Found at i:93599769 original size:20 final size:22
Alignment explanation
Indices: 93599729--93599770 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
93599719 ATTGTTAATA
*
93599729 TAATAAATATATTTTATTATTT
1 TAATAAATATATTTTAATATTT
93599751 TAATAAAT-TA-TTTAATATTT
1 TAATAAATATATTTTAATATTT
93599771 CAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAATAAATATATTTTAATATTT
Found at i:93600788 original size:21 final size:20
Alignment explanation
Indices: 93600762--93600800 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
93600752 ATTAACAATA
93600762 AAATAATAATATATAATATCC
1 AAATAATAATA-ATAATATCC
93600783 AAATAATAATAATAATAT
1 AAATAATAATAATAATAT
93600801 AGTAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAATAATAATAATATCC
Found at i:93600807 original size:20 final size:21
Alignment explanation
Indices: 93600762--93600815 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
93600752 ATTAACAATA
*
93600762 AAATAATAATATATAATATCC
1 AAATAATAATATATAATATAC
*
93600783 AAATAATAATA-ATAATATAG
1 AAATAATAATATATAATATAC
* *
93600803 TAATAATATTATA
1 AAATAATAATATA
93600816 ACGAAATGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATAATAATATATAATATAC
Found at i:93604200 original size:18 final size:19
Alignment explanation
Indices: 93604174--93604217 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
93604164 TTGCTCTTTA
93604174 TTTTCTGCTTCTT-TTTGT
1 TTTTCTGCTTCTTGTTTGT
* *
93604192 TTTTTTGCTTGTTGTTTGT
1 TTTTCTGCTTCTTGTTTGT
*
93604211 TTGTCTG
1 TTTTCTG
93604218 TTGCTTGCGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.00, C:0.11, G:0.18, T:0.70
Consensus pattern (19 bp):
TTTTCTGCTTCTTGTTTGT
Found at i:93613874 original size:94 final size:93
Alignment explanation
Indices: 93613776--93613945 Score: 277
Period size: 94 Copynumber: 1.8 Consensus size: 93
93613766 TTTTTTGCTT
* * ** *
93613776 TTTCAATTATAATGGCAAAATTTTAGTTTTGATCCCTCTTTTAAACTCAAATTTAAGATTTAATC
1 TTTCAATTATAATGGCAAAAATTCAGTTTTGATCCCTCTAGTAAACT-AAATTTAAGATTTAATA
93613841 TTTATATTTTTACACCCTTTTGTTTGTCA
65 TTTATATTTTTACACCCTTTTGTTTGTCA
*
93613870 TTTCAATTATAATGGTAAAAATTCAGTTTTGATCCCTCTAGTAAACTAAATTTAAGATTTAATAT
1 TTTCAATTATAATGGCAAAAATTCAGTTTTGATCCCTCTAGTAAACTAAATTTAAGATTTAATAT
93613935 TTATATTTTTA
66 TTATATTTTTA
93613946 TTTGACATAA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 28 0.40
94 42 0.60
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (93 bp):
TTTCAATTATAATGGCAAAAATTCAGTTTTGATCCCTCTAGTAAACTAAATTTAAGATTTAATAT
TTATATTTTTACACCCTTTTGTTTGTCA
Found at i:93620292 original size:48 final size:48
Alignment explanation
Indices: 93620238--93620336 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
93620228 ATTGTTATCA
93620238 TCTCTATCTCAGTTAGCTCGGGTAATTTTTCCATAAAGACCTGTTTTT
1 TCTCTATCTCAGTTAGCTCGGGTAATTTTTCCATAAAGACCTGTTTTT
*
93620286 TCTCTATCTCAGTTAGCTCGGGTAATTTTTCCATAAATACCTGTTTTT
1 TCTCTATCTCAGTTAGCTCGGGTAATTTTTCCATAAAGACCTGTTTTT
93620334 TCT
1 TCT
93620337 TTTTCCTACC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.45
Consensus pattern (48 bp):
TCTCTATCTCAGTTAGCTCGGGTAATTTTTCCATAAAGACCTGTTTTT
Found at i:93635484 original size:56 final size:55
Alignment explanation
Indices: 93635424--93635573 Score: 167
Period size: 56 Copynumber: 2.7 Consensus size: 55
93635414 ATGTAGAAAT
* * *
93635424 ATGAAACATTTAAAAATGATTAAAGTTTTCTCCAAAATGAAAATGAAAATAGAGAA
1 ATGAAACATTTAGAAATGAATAAGGTTTTCTCCAAAATGAAAATGAAAAT-GAGAA
* * ** * *
93635480 ATGAAATCATTTAGAAGTTAATGTGGTTTTCTCTAAAATGGAAATGAAAATGAGAA
1 ATGAAA-CATTTAGAAATGAATAAGGTTTTCTCCAAAATGAAAATGAAAATGAGAA
* *
93635536 ATGAATTCATTTAGAAATGAATAAGGATTTCT-CAAAAT
1 ATGAA-ACATTTAGAAATGAATAAGGTTTTCTCCAAAAT
93635574 TGATCGTAAG
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
55 5 0.07
56 36 0.47
57 35 0.46
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (55 bp):
ATGAAACATTTAGAAATGAATAAGGTTTTCTCCAAAATGAAAATGAAAATGAGAA
Found at i:93643456 original size:24 final size:24
Alignment explanation
Indices: 93643428--93643479 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
93643418 TTAGTAGGTC
* *
93643428 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
93643452 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
93643476 AAAT
1 AAAT
93643480 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:93644933 original size:8 final size:8
Alignment explanation
Indices: 93644920--93644959 Score: 80
Period size: 8 Copynumber: 5.0 Consensus size: 8
93644910 ATATATAATA
93644920 GATGAATT
1 GATGAATT
93644928 GATGAATT
1 GATGAATT
93644936 GATGAATT
1 GATGAATT
93644944 GATGAATT
1 GATGAATT
93644952 GATGAATT
1 GATGAATT
93644960 TGAAATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (8 bp):
GATGAATT
Found at i:93645346 original size:30 final size:29
Alignment explanation
Indices: 93645311--93645373 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
93645301 TTATATATGT
93645311 AATAGATTT-GAA-AACATAAATATGTATATA
1 AATAGATTTAGAAGAA-AT-AATATGTATA-A
*
93645341 AATAGATTTAGAAGAAATTATATGTATAA
1 AATAGATTTAGAAGAAATAATATGTATAA
93645370 AATA
1 AATA
93645374 ACATAGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 18 0.60
31 5 0.17
32 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (29 bp):
AATAGATTTAGAAGAAATAATATGTATAA
Found at i:93645596 original size:2 final size:2
Alignment explanation
Indices: 93645589--93645614 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
93645579 TATCATGAAT
93645589 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
93645615 ATAATGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93647160 original size:18 final size:18
Alignment explanation
Indices: 93647137--93647171 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
93647127 GCAGGCCCGA
93647137 CCCTAGAGTAGTTTGGGG
1 CCCTAGAGTAGTTTGGGG
93647155 CCCTAGAGTAGTTTGGG
1 CCCTAGAGTAGTTTGGG
93647172 AGTACAGCTG
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:0.17, C:0.17, G:0.37, T:0.29
Consensus pattern (18 bp):
CCCTAGAGTAGTTTGGGG
Found at i:93653576 original size:21 final size:21
Alignment explanation
Indices: 93653541--93653592 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
93653531 AAAGATAAAG
*
93653541 ATAAAATTAAACCCT-AAAAC
1 ATAAAATAAAACCCTCAAAAC
*
93653561 CTAAAATAAGAACCCTCAAAAC
1 ATAAAATAA-AACCCTCAAAAC
93653583 ATAAACATAA
1 ATAAA-ATAA
93653593 TATTCTCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 6 0.23
22 9 0.35
23 4 0.15
ACGTcount: A:0.60, C:0.21, G:0.02, T:0.17
Consensus pattern (21 bp):
ATAAAATAAAACCCTCAAAAC
Found at i:93656436 original size:4 final size:4
Alignment explanation
Indices: 93656411--93656460 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
93656401 GAATATGTAT
* * * * *
93656411 GTGC GTGG GTGC GTGG GTGC GTGC GTGG GTAC ATGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
93656459 GT
1 GT
93656461 ACATGCGCGC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.04, C:0.18, G:0.52, T:0.26
Consensus pattern (4 bp):
GTGC
Found at i:93656436 original size:20 final size:20
Alignment explanation
Indices: 93656411--93656467 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
93656401 GAATATGTAT
* * *
93656411 GTGCGTGGGTGCGTGGGTGC
1 GTGCGTGGGTACATGCGTGC
93656431 GTGCGTGGGTACATGCGTGC
1 GTGCGTGGGTACATGCGTGC
*
93656451 GTGCGTGCGTACATGCG
1 GTGCGTGGGTACATGCG
93656468 CGCGCGCGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.07, C:0.19, G:0.49, T:0.25
Consensus pattern (20 bp):
GTGCGTGGGTACATGCGTGC
Found at i:93656486 original size:2 final size:2
Alignment explanation
Indices: 93656481--93656563 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
93656471 GCGCGCGCAC
93656481 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
93656523 GT GT GT GT GT GT GT GT GT GT GT AT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
93656564 ATGGCAATGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.01, C:0.00, G:0.49, T:0.49
Consensus pattern (2 bp):
GT
Found at i:93663269 original size:18 final size:18
Alignment explanation
Indices: 93663246--93663281 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
93663236 TAATAGAGTG
93663246 AGTAAAATGAAATCAACT
1 AGTAAAATGAAATCAACT
93663264 AGTAAAATGAAATCAACT
1 AGTAAAATGAAATCAACT
93663282 CTTAATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (18 bp):
AGTAAAATGAAATCAACT
Found at i:93672988 original size:25 final size:25
Alignment explanation
Indices: 93672941--93672988 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
93672931 TCTGAGCTAA
*
93672941 TCAGGAAACTCATAAGAGTTTTTAC
1 TCAGGAAACTCATAAGAGCTTTTAC
*
93672966 TCAGGAAGCTCAT-AGAGCCTTTT
1 TCAGGAAACTCATAAGAG-CTTTT
93672989 TGATATCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (25 bp):
TCAGGAAACTCATAAGAGCTTTTAC
Found at i:93677496 original size:29 final size:29
Alignment explanation
Indices: 93677454--93677510 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
93677444 GAAGTCGAAT
93677454 TTATAATGAAATTGGATTATTAGATACCC
1 TTATAATGAAATTGGATTATTAGATACCC
*
93677483 TTATAATGAAATTGGATTATTGGATACC
1 TTATAATGAAATTGGATTATTAGATACC
93677511 TTAGTGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (29 bp):
TTATAATGAAATTGGATTATTAGATACCC
Found at i:93678259 original size:21 final size:21
Alignment explanation
Indices: 93678233--93678272 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
93678223 TTCGGGTGGA
93678233 TCAACTCTTACGAGCTTCTGT
1 TCAACTCTTACGAGCTTCTGT
*
93678254 TCAACTCTTATGAGCTTCT
1 TCAACTCTTACGAGCTTCT
93678273 ATTGGCGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (21 bp):
TCAACTCTTACGAGCTTCTGT
Found at i:93681506 original size:22 final size:22
Alignment explanation
Indices: 93681481--93681546 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
93681471 AAAGCACATG
93681481 GGCGTGTGCATTGTCTCCACAC
1 GGCGTGTGCATTGTCTCCACAC
* ** *
93681503 GGCGTGTCCCAAAG-C-CCAC-G
1 GGCGTGT-GCATTGTCTCCACAC
93681523 GGCGTGTGCATTGTCTCCACAC
1 GGCGTGTGCATTGTCTCCACAC
93681545 GG
1 GG
93681547 GCATGTGAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
19 3 0.09
20 8 0.25
21 8 0.25
22 10 0.31
23 3 0.09
ACGTcount: A:0.15, C:0.33, G:0.30, T:0.21
Consensus pattern (22 bp):
GGCGTGTGCATTGTCTCCACAC
Found at i:93681517 original size:42 final size:42
Alignment explanation
Indices: 93681464--93681546 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
93681454 GGACACGGGT
* *
93681464 GTGTCCTAAAGCACATGGGCGTGTGCATTGTCTCCACACGGC
1 GTGTCCCAAAGCACACGGGCGTGTGCATTGTCTCCACACGGC
*
93681506 GTGTCCCAAAGCCCACGGGCGTGTGCATTGTCTCCACACGG
1 GTGTCCCAAAGCACACGGGCGTGTGCATTGTCTCCACACGG
93681547 GCATGTGAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.18, C:0.31, G:0.29, T:0.22
Consensus pattern (42 bp):
GTGTCCCAAAGCACACGGGCGTGTGCATTGTCTCCACACGGC
Found at i:93684357 original size:46 final size:46
Alignment explanation
Indices: 93684290--93684380 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
93684280 AAATTGTCAC
* * *
93684290 CCACGCTCATACAAGGATTCAAACACAAGACCTCTAGCAAGCTAAT
1 CCACGCTCATACAAAGATTCAAACAAAAGACCTCCAGCAAGCTAAT
*
93684336 CCACGCTCATACAAAGATTCAAACAAAAGACCTCCAGGAAGCTAA
1 CCACGCTCATACAAAGATTCAAACAAAAGACCTCCAGCAAGCTAA
93684381 CTCCTTACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.42, C:0.30, G:0.13, T:0.15
Consensus pattern (46 bp):
CCACGCTCATACAAAGATTCAAACAAAAGACCTCCAGCAAGCTAAT
Found at i:93688974 original size:29 final size:29
Alignment explanation
Indices: 93688940--93689042 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
93688930 TAATCAGCCG
** *
93688940 CGCACACTTAGTGCCATATACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAGCT
93688969 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
93688998 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
*
93689027 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
93689043 ATCTCTCAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 3 0.04
29 66 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAGCT
Found at i:93693693 original size:27 final size:25
Alignment explanation
Indices: 93693630--93693693 Score: 58
Period size: 27 Copynumber: 2.4 Consensus size: 25
93693620 ACACCCCTCT
**
93693630 TCCCTT-TTTCTTTTCCTTCCCCTT
1 TCCCTTCTTTCTTTTCCTTCCCCCA
*
93693654 TCTCTTTCTTTTCTTTTCTTCTTCCCCCA
1 TC-CCTTC-TTTCTTTTC--CTTCCCCCA
93693683 TCCCTTCTTTC
1 TCCCTTCTTTC
93693694 CCCCTCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
24 2 0.06
25 3 0.10
27 13 0.42
28 4 0.13
29 9 0.29
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.58
Consensus pattern (25 bp):
TCCCTTCTTTCTTTTCCTTCCCCCA
Found at i:93693741 original size:26 final size:25
Alignment explanation
Indices: 93693687--93693746 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
93693677 CCCCCATCCC
* *
93693687 TTCTTTCCCCCTCTTTTCCTTTCTT
1 TTCTTTCCCCCTCTTTTCCCTTCTA
*
93693712 TTCTTTTCCCCTCTTCTTCCCCTT-TA
1 TTCTTTCCCCCTCTT-TT-CCCTTCTA
93693738 TTCTTTCCC
1 TTCTTTCCC
93693747 TCCGAACACC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 14 0.48
26 11 0.38
27 4 0.14
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.57
Consensus pattern (25 bp):
TTCTTTCCCCCTCTTTTCCCTTCTA
Found at i:93695619 original size:6 final size:6
Alignment explanation
Indices: 93695604--93695657 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
93695594 ATTGAGTCCA
*
93695604 TTTATT TTTATG TTTATT TTTATT TTTATT TTTATT TTTA-T TTTA-T
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
93695650 TTTATT TT
1 TTTATT TT
93695658 CCTTTTTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
5 10 0.22
6 35 0.78
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:93698937 original size:18 final size:19
Alignment explanation
Indices: 93698911--93698955 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
93698901 TACTTATACT
*
93698911 TTAAGTATAATATATT-TA
1 TTAATTATAATATATTATA
93698929 TTAATTATAATATATTATA
1 TTAATTATAATATATTATA
93698948 TTAATTAT
1 TTAATTAT
93698956 TAATTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTAATTATAATATATTATA
Found at i:93705831 original size:5 final size:5
Alignment explanation
Indices: 93705821--93705848 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
93705811 TTGTGTGTTC
93705821 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
93705849 CATAAGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:93709729 original size:43 final size:43
Alignment explanation
Indices: 93709681--93710050 Score: 562
Period size: 43 Copynumber: 8.6 Consensus size: 43
93709671 CCGGCATTAC
*
93709681 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
93709724 GCCTGCTAGGCACAAAGGCCTGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * * *
93709767 GCCTACTAGGTACG-AGGGCCGAAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCG-AATACACATCACCGGCACGAA
* * *
93709810 GCCTGCTAGGCACGATGGCTCGAATATACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
93709853 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTACAAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * *
93709896 GCCTGCTAGGCACGAAGGCTCGAATATACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
93709939 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
93709982 GCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
93710025 GCCTGATAGGCACGAAGGCCTGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
93710051 TAATACCAGC
Statistics
Matches: 293, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
42 5 0.02
43 284 0.97
44 4 0.01
ACGTcount: A:0.31, C:0.31, G:0.25, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:93710090 original size:38 final size:38
Alignment explanation
Indices: 93710048--93710188 Score: 192
Period size: 38 Copynumber: 3.7 Consensus size: 38
93710038 GAAGGCCTGA
* * * * *
93710048 ATATAATACCAGCACTAGGCCTGCGGGATTTATCCCTG
1 ATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGG
*
93710086 ATATAATACCAGCACGAAGCCTACAGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGG
* *
93710124 ATACAATACCAACACGAAGCCTGCAGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGG
**
93710162 ATATTTTACCAGCACGAAGCCTGCAGG
1 ATATAATACCAGCACGAAGCCTGCAGG
93710189 TCTTTAAGCC
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 90 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGG
Found at i:93710153 original size:76 final size:78
Alignment explanation
Indices: 93710052--93710206 Score: 197
Period size: 76 Copynumber: 2.0 Consensus size: 78
93710042 GCCTGAATAT
* * * * * *
93710052 AATACCAGCACTAGGCCTGCGGGATTTATCCCTGATATAATACCAGCACGAAGCCTACAGG-ATT
1 AATACCAACACGAAGCCTGCAGGATTTAACCCGGATATAATACCAGCACGAAGCCTACAGGTATT
*
93710116 TAA-CCCGGATAC
66 TAAGCCCAGATAC
** * *
93710128 AATACCAACACGAAGCCTGCAGGATTTAACCCGGATATTTTACCAGCACGAAGCCTGCAGGTCTT
1 AATACCAACACGAAGCCTGCAGGATTTAACCCGGATATAATACCAGCACGAAGCCTACAGGTATT
93710193 TAAGCCCAGATAC
66 TAAGCCCAGATAC
93710206 A
1 A
93710207 CATCAAATAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
76 52 0.79
77 5 0.08
78 9 0.14
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (78 bp):
AATACCAACACGAAGCCTGCAGGATTTAACCCGGATATAATACCAGCACGAAGCCTACAGGTATT
TAAGCCCAGATAC
Found at i:93711170 original size:2 final size:2
Alignment explanation
Indices: 93711163--93711200 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
93711153 CACTTTCAAA
93711163 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
93711201 TCAACTTTCA
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:93715773 original size:14 final size:14
Alignment explanation
Indices: 93715754--93715780 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
93715744 AGAAAATTGT
93715754 AGGAAGGGAAGAAA
1 AGGAAGGGAAGAAA
93715768 AGGAAGGGAAGAA
1 AGGAAGGGAAGAA
93715781 TGACATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (14 bp):
AGGAAGGGAAGAAA
Found at i:93719719 original size:26 final size:26
Alignment explanation
Indices: 93719683--93719732 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
93719673 TGAAGGTGAT
93719683 CGTCTAAACCATTCTATTAAAACTGA
1 CGTCTAAACCATTCTATTAAAACTGA
93719709 CGTCTAAACCATTCTATTAAAACT
1 CGTCTAAACCATTCTATTAAAACT
93719733 AACCACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
CGTCTAAACCATTCTATTAAAACTGA
Found at i:93730622 original size:38 final size:38
Alignment explanation
Indices: 93730559--93730678 Score: 136
Period size: 38 Copynumber: 3.1 Consensus size: 38
93730549 ATTTGATGTG
* * *
93730559 TATCCAGGCTTAAAGACCCGTAGGCTATATGCTGGAATTA
1 TATCCAGG-TTAAA-TCCCGCAGGCTATGTGCTGGAATTA
*
93730599 TATCCGGGTTAAATCCCGCAGGCT-TCGTGCTGGAATTA
1 TATCCAGGTTAAATCCCGCAGGCTAT-GTGCTGGAATTA
* *
93730637 TGTCCAGGTTAAATCCCGCAGGCCTA-GTGCTGGTATTA
1 TATCCAGGTTAAATCCCGCAGG-CTATGTGCTGGAATTA
93730675 TATC
1 TATC
93730679 TGAGCTTAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
37 1 0.01
38 54 0.78
39 7 0.10
40 7 0.10
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (38 bp):
TATCCAGGTTAAATCCCGCAGGCTATGTGCTGGAATTA
Found at i:93736292 original size:29 final size:29
Alignment explanation
Indices: 93736259--93736314 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
93736249 CTTCAAAAAT
93736259 AAATAAAAGA-AAAAATAG-AATTAAAATGG
1 AAATAAAA-ATAAAAATAGTAA-TAAAATGG
93736288 AAATAAAAATAAAAATAGTAATAAAAT
1 AAATAAAAATAAAAATAGTAATAAAAT
93736315 AAAGGGACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 1 0.04
29 22 0.88
30 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (29 bp):
AAATAAAAATAAAAATAGTAATAAAATGG
Found at i:93736435 original size:21 final size:21
Alignment explanation
Indices: 93736405--93736445 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
93736395 CTGTAAAGTC
*
93736405 GCATCGATACTATCGAACCTT
1 GCATCAATACTATCGAACCTT
* *
93736426 GCATCAATACTGTTGAACCT
1 GCATCAATACTATCGAACCT
93736446 CCAAGCACAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (21 bp):
GCATCAATACTATCGAACCTT
Found at i:93740223 original size:6 final size:6
Alignment explanation
Indices: 93740209--93740247 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
93740199 CACTGCAACG
* * *
93740209 GTAATA GTAACA GTAACA GTAACA ATCACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GTA
93740248 CACAAAGTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (6 bp):
GTAACA
Found at i:93741138 original size:13 final size:13
Alignment explanation
Indices: 93741120--93741151 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
93741110 GGGATTAAAT
93741120 TGACTTACCAAAG
1 TGACTTACCAAAG
93741133 TGACTTACCAAAG
1 TGACTTACCAAAG
93741146 TGACTT
1 TGACTT
93741152 TAAACCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (13 bp):
TGACTTACCAAAG
Found at i:93745711 original size:35 final size:35
Alignment explanation
Indices: 93745643--93745769 Score: 193
Period size: 35 Copynumber: 3.6 Consensus size: 35
93745633 AGTACATTGA
*
93745643 TAATCCAACCGAAACACACCAGATGCTCATAAGAGC
1 TAATCCATCCGAAACACACCA-ATGCTCATAAGAGC
* *
93745679 TAATCCATCCGGAACACACCAATGCTTATAAGAGC
1 TAATCCATCCGAAACACACCAATGCTCATAAGAGC
*
93745714 TAATCCATCCGGAACACACCAATGCTCATAAGAGC
1 TAATCCATCCGAAACACACCAATGCTCATAAGAGC
*
93745749 T-ATCCATCCAAAACACACCAA
1 TAATCCATCCGAAACACACCAA
93745770 AACAAAGAGG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
34 18 0.21
35 48 0.56
36 19 0.22
ACGTcount: A:0.40, C:0.31, G:0.12, T:0.17
Consensus pattern (35 bp):
TAATCCATCCGAAACACACCAATGCTCATAAGAGC
Found at i:93750693 original size:23 final size:22
Alignment explanation
Indices: 93750667--93750710 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
93750657 TTTTGTGTGG
* *
93750667 AATTCAATTTTCTTTTTGAAAAT
1 AATT-AATTTTCTATTTAAAAAT
*
93750690 AATTTATTTTCTATTTAAAAA
1 AATTAATTTTCTATTTAAAAA
93750711 ATAGATGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTAATTTTCTATTTAAAAAT
Found at i:93754909 original size:28 final size:28
Alignment explanation
Indices: 93754872--93754925 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
93754862 AAAAGACTCA
93754872 AAAGCACAAGCTAAACTAAGCCATTCTC
1 AAAGCACAAGCTAAACTAAGCCATTCTC
93754900 AAAGCACAAGCTAAACTAAGCCATTC
1 AAAGCACAAGCTAAACTAAGCCATTC
93754926 AACACCCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.17
Consensus pattern (28 bp):
AAAGCACAAGCTAAACTAAGCCATTCTC
Found at i:93762644 original size:6 final size:7
Alignment explanation
Indices: 93762629--93762653 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
93762619 TGCATAATTC
93762629 AAAATAA
1 AAAATAA
93762636 AAAATAA
1 AAAATAA
93762643 AAAATAA
1 AAAATAA
93762650 AAAA
1 AAAA
93762654 GGGGAGCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:93763071 original size:3 final size:3
Alignment explanation
Indices: 93763063--93763089 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
93763053 TCATCTTCCA
93763063 ACT ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT
93763090 TCCGTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ACT
Found at i:93771959 original size:18 final size:18
Alignment explanation
Indices: 93771936--93771979 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
93771926 ATAATGTTAT
*
93771936 ATAATATTAATTTAATTA
1 ATAATATTAAGTTAATTA
*
93771954 ATAATATTAAGTTATTTA
1 ATAATATTAAGTTAATTA
*
93771972 ATTATATT
1 ATAATATT
93771980 GGATGATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATAATATTAAGTTAATTA
Found at i:93778866 original size:25 final size:24
Alignment explanation
Indices: 93778830--93778880 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
93778820 CACACAAGTC
93778830 TTTTCCCTATTTCTCTC-TTCTTT
1 TTTTCCCTATTTCTCTCTTTCTTT
* *
93778853 TTTTCTCCTTATTTTTTTCTTTCTTT
1 TTTTC-CC-TATTTCTCTCTTTCTTT
93778879 TT
1 TT
93778881 CACGGCTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.22
24 2 0.09
25 8 0.35
26 8 0.35
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTCCCTATTTCTCTCTTTCTTT
Done.