Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold112
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: 1714866
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 134939 characters in sequence are not A, C, G, or T
File 10 of 11
Found at i:1405198 original size:38 final size:35
Alignment explanation
Indices: 1405156--1405239 Score: 89
Period size: 37 Copynumber: 2.3 Consensus size: 35
1405146 ATAAATATTA
* **
1405156 AAAAAATATTTCAAGTTATTTATATTTTAAAATTTAAT
1 AAAAAATATTTCAAATTA-TTATAGATTAAAATTT--T
*
1405194 AAAAAAT-TTATTAAATTATTATAGATTAAAATTTT
1 AAAAAATATT-TCAAATTATTATAGATTAAAATTTT
1405229 AAAAAATATTT
1 AAAAAATATTT
1405240 GTATTAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
35 9 0.22
36 2 0.05
37 16 0.40
38 13 0.32
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (35 bp):
AAAAAATATTTCAAATTATTATAGATTAAAATTTT
Found at i:1412684 original size:6 final size:6
Alignment explanation
Indices: 1412658--1412732 Score: 52
Period size: 6 Copynumber: 12.7 Consensus size: 6
1412648 TAAAATATGA
*
1412658 TATATT TA-ATA TATA-T TATATT TATATT TATAATTT TGATAATT TA-A-T
1 TATATT TATATT TATATT TATATT TATATT TAT-A-TT T-AT-ATT TATATT
* *
1412706 AAAATT TATA-T TATATT TATATT TATA
1 TATATT TATATT TATATT TATATT TATA
1412733 CGATTGACAT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
4 2 0.04
5 15 0.27
6 27 0.48
7 2 0.04
8 6 0.11
9 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (6 bp):
TATATT
Found at i:1414254 original size:2 final size:2
Alignment explanation
Indices: 1414247--1414283 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1414237 GCCTCACAGT
1414247 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1414284 GACATTTGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1422507 original size:12 final size:12
Alignment explanation
Indices: 1422490--1422518 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1422480 TGACATATTA
1422490 CTTTTATAAACT
1 CTTTTATAAACT
1422502 CTTTTATAAACT
1 CTTTTATAAACT
1422514 CTTTT
1 CTTTT
1422519 TTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (12 bp):
CTTTTATAAACT
Found at i:1424471 original size:20 final size:20
Alignment explanation
Indices: 1424435--1424489 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1424425 AAATATATTT
1424435 ATAATTT-AA-TT-TAAATA
1 ATAATTTAAATTTATAAATA
* **
1424452 ATATTTTTTATTTATAAATA
1 ATAATTTAAATTTATAAATA
1424472 ATAATTTAAATTTATAAA
1 ATAATTTAAATTTATAAA
1424490 AATTTTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 6 0.20
18 1 0.03
19 2 0.07
20 21 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATTTAAATTTATAAATA
Found at i:1427382 original size:20 final size:21
Alignment explanation
Indices: 1427339--1427383 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
1427329 TGTTAACATT
**
1427339 AAATAACTTTTTAAATTTTTA
1 AAATAACTTTTTAAATTTAAA
*
1427360 AAATAA-TTTTTGAATTTAAA
1 AAATAACTTTTTAAATTTAAA
1427380 AAAT
1 AAAT
1427384 TTACAAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATAACTTTTTAAATTTAAA
Found at i:1427512 original size:21 final size:20
Alignment explanation
Indices: 1427475--1427513 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1427465 TGCCTGAACG
*
1427475 TATTTTAATTATGTTTTTAT
1 TATTTTAATTATATTTTTAT
*
1427495 TATTCTTAATTTTATTTTT
1 TATT-TTAATTATATTTTT
1427514 TAGGATACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (20 bp):
TATTTTAATTATATTTTTAT
Found at i:1428131 original size:43 final size:43
Alignment explanation
Indices: 1428070--1428155 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
1428060 CACTCGAATT
1428070 CCTTCACTGGCTTTTAAGTCATGAAAACTTTGAATTGAGACAA
1 CCTTCACTGGCTTTTAAGTCATGAAAACTTTGAATTGAGACAA
* *
1428113 CCTTCACTGGTTTTTAAGTCATGAAAACTTTGAATTGGGACAA
1 CCTTCACTGGCTTTTAAGTCATGAAAACTTTGAATTGAGACAA
1428156 GTATGAAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (43 bp):
CCTTCACTGGCTTTTAAGTCATGAAAACTTTGAATTGAGACAA
Found at i:1437920 original size:174 final size:171
Alignment explanation
Indices: 1437486--1438044 Score: 941
Period size: 171 Copynumber: 3.3 Consensus size: 171
1437476 TTTTAGAGAT
* * * *
1437486 GATGAAGGTGCTAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAATGATGATGAGAAAA
* * *
1437551 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAAAAAGGA
*
1437616 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* * *
1437657 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACATAAAAATGATGATGAGAAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAATGATGATGAGAAAA
1437722 GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAAAAAGGA
1437787 TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
1437828 GATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAATGATGATGAGA
1 GAT-G--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAATGATGATGAGA
1437893 AAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAAAAA
63 AAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAAAAA
1437958 GGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTT-AA
128 GGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
*
1438001 -A-G-A--TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1438045 GGTGAAGGTG
Statistics
Matches: 371, Mismatches: 14, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
165 40 0.11
167 1 0.00
170 1 0.00
171 164 0.44
172 2 0.01
173 2 0.01
174 161 0.43
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.25
Consensus pattern (171 bp):
GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAATGATGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAAAAAGGA
TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:1438076 original size:49 final size:49
Alignment explanation
Indices: 1437964--1438145 Score: 241
Period size: 49 Copynumber: 3.8 Consensus size: 49
1437954 AAAAGGATGT
* * *
1437964 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA---G-A--TGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
*
1438007 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
**
1438056 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
* *
1438105 CAATATGGTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-AAGG
1438146 GTTGCCACCG
Statistics
Matches: 123, Mismatches: 9, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
43 36 0.29
46 1 0.01
47 1 0.01
49 83 0.67
50 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
Found at i:1438106 original size:98 final size:93
Alignment explanation
Indices: 1437900--1438145 Score: 253
Period size: 98 Copynumber: 2.5 Consensus size: 93
1437890 AGAAAAGTGA
* * * * * * *
1437900 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTA-AAGCTGAGAAAAAGGATGT
1 TAAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAG--GTG---AAGG-TGC
*
1437964 CAATGTGCTGATTCAAGGCCAGCTACATTGAACT
60 CAATATGCTGATTCAAGGCCAGCTACATTGAACT
*
1437998 TAAAGATGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTA-AAGGTGAAGGTGCCAATAT
1 TAAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAGGTGAAGGTGCCAATAT
* *
1438062 GCTGATTCAAGGCCAGCTATATTGGACT
66 GCTGATTCAAGGCCAGCTACATTGAACT
* *
1438090 TAAAAATGAAGGTGCCAATATGGTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
1 T--AAA-G-A--TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAGG
1438146 GTTGCCACCG
Statistics
Matches: 127, Mismatches: 14, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
92 34 0.27
93 4 0.03
94 3 0.02
95 1 0.01
96 3 0.02
98 78 0.61
99 4 0.03
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (93 bp):
TAAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAGGTGAAGGTGCCAATAT
GCTGATTCAAGGCCAGCTACATTGAACT
Found at i:1438271 original size:30 final size:29
Alignment explanation
Indices: 1438161--1438612 Score: 336
Period size: 30 Copynumber: 15.5 Consensus size: 29
1438151 CACCGACTTG
* * *
1438161 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAA-GATGCCACTGACT
1438191 TGTGGGC-TTTG--AAGATTGCCACTGACT
1 TGTGGGCTTTTGAAAAGA-TGCCACTGACT
* *
1438218 TGTGGGCTTTT-AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
*
1438246 TGTGGGCTTTTGAACAATATGCCACTGACT
1 TGTGGGCTTTTGAA-AAGATGCCACTGACT
* * *
1438276 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGCTTTTGAA-AAGATGCCACTGACT
* *
1438306 TGTGGGCTTTT-AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
*
1438334 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTTG-AAAAGATGCCACTGACT
* * *
1438364 TGTGGGCTTTT-AAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* *
1438392 TGTGGGC---TGAAAAGAGTGCTA-TAGAGT
1 TGTGGGCTTTTGAAAAGA-TGCCACT-GACT
* ** * *
1438419 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT----TTG-AAAAGA-TGCCACTGACT
* * * *
1438454 TGTGGACTTTGGAAAAGATGCCGCCGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
** * *
1438483 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAA-GATGCCACTGACT
* *
1438513 TGTGGGC-TTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* * *
1438540 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTTTG-AAAAGATGCCACTGACT
*
1438570 TGTGGGC-TTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTTG-AAAAGATGCCACTGACT
*
1438599 TGTGGACTTTTGAA
1 TGTGGGCTTTTGAA
1438613 GGGTGATGAA
Statistics
Matches: 341, Mismatches: 56, Indels: 51
0.76 0.12 0.11
Matches are distributed among these distances:
25 1 0.00
26 6 0.02
27 49 0.14
28 74 0.22
29 61 0.18
30 126 0.37
31 1 0.00
34 1 0.00
35 22 0.06
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAAGATGCCACTGACT
Found at i:1438325 original size:88 final size:86
Alignment explanation
Indices: 1438145--1438399 Score: 363
Period size: 88 Copynumber: 2.9 Consensus size: 86
1438135 GGCTTAGAAG
* * ** * **
1438145 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGATT
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAA-TATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
1438208 GCCACTGACTTGTGGGCTTTTAAA
63 GCCACTAACTTGTGGGCTTTTAAA
1438232 GGTTGCCACTGACTTGTGGGCTTTTGAACAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAA-AATATGCCACTGACTTGTGGGCTTTTGAA-AGGGTG
1438297 CCACTAACTTGTGGGCTTTTAAA
64 CCACTAACTTGTGGGCTTTTAAA
1438320 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTT-AAAGGGTGC
1 GGTTGCCACTGACTTGTGGGCTTTTG-AAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGC
1438384 CACTAACTTGTGGGCT
65 CACTAACTTGTGGGCT
1438400 GAAAAGAGTG
Statistics
Matches: 155, Mismatches: 8, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
85 30 0.19
86 30 0.19
87 15 0.10
88 78 0.50
89 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (86 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGCC
ACTAACTTGTGGGCTTTTAAA
Found at i:1438327 original size:58 final size:58
Alignment explanation
Indices: 1438145--1438399 Score: 311
Period size: 58 Copynumber: 4.4 Consensus size: 58
1438135 GGCTTAGAAG
* * * *
1438145 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTGAA
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAA
* *
1438204 GATTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTGAACA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTT-AA-A
* * *
1438262 -ATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTTAAA
1 GGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAA
***
1438320 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAA
* *
1438378 GGGTGCCACTAACTTGTGGGCT
1 GGTTGCCACTGACTTGTGGGCT
1438400 GAAAAGAGTG
Statistics
Matches: 172, Mismatches: 17, Indels: 15
0.84 0.08 0.07
Matches are distributed among these distances:
55 22 0.13
56 3 0.02
57 13 0.08
58 95 0.55
59 14 0.08
60 25 0.15
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (58 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAA
Found at i:1438485 original size:29 final size:29
Alignment explanation
Indices: 1438436--1438608 Score: 161
Period size: 29 Copynumber: 5.9 Consensus size: 29
1438426 TTACAAAAGA
* * *
1438436 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* * *
1438466 AAAAGATGCCGCCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
1438495 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
1438524 -AAGGTTGCCACTGACTTGTGGGCTTTCGA
1 AAAAGATGCCACTGACTTGTGGGCTTT-GG
* * *
1438553 AAAAAATGCCACCGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
1438582 AAAAAATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
1438609 TGAAGGGTGA
Statistics
Matches: 119, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
27 21 0.18
28 2 0.02
29 50 0.42
30 46 0.39
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:1440055 original size:1 final size:1
Alignment explanation
Indices: 1440051--1440152 Score: 69
Period size: 1 Copynumber: 102.0 Consensus size: 1
1440041 CCGGACCCCC
* * * * * * ** *
1440051 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTCCTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** **
1440116 TTTGGTTTTTCATTTTTTTCGTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1440153 GGAGGACGCC
Statistics
Matches: 77, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:1440089 original size:34 final size:32
Alignment explanation
Indices: 1440051--1440153 Score: 107
Period size: 34 Copynumber: 3.0 Consensus size: 32
1440041 CCGGACCCCC
* *
1440051 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTG
1 TTTTTT-TTTTT-TTTGTTTTTTTTTTTTTTTTG
1440085 TTTTTTTTTTCCTTTTGTTTTTTTTTTTTTTTTTGG
1 TTTTTTTTTT--TTTTG-TTTTTTTTTTTTTTTT-G
* *
1440121 TTTTTCATTTTTTTCGTTTTTTTTTTTTTTTTG
1 TTTTT-TTTTTTTTTGTTTTTTTTTTTTTTTTG
1440154 GAGGACGCCG
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
33 5 0.08
34 26 0.43
35 19 0.32
36 6 0.10
37 4 0.07
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.84
Consensus pattern (32 bp):
TTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTG
Found at i:1449858 original size:10 final size:10
Alignment explanation
Indices: 1449843--1449869 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1449833 ATGTATCAAG
1449843 CAAAAACAAA
1 CAAAAACAAA
1449853 CAAAAACAAA
1 CAAAAACAAA
1449863 CAAAAAC
1 CAAAAAC
1449870 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:1454291 original size:19 final size:20
Alignment explanation
Indices: 1454248--1454318 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
1454238 AATGATCATC
*
1454248 TAATATGATTACATTCAACA
1 TAATATAATTACATTCAACA
1454268 TAATATAATTACATTCAA-A
1 TAATATAATTACATTCAACA
*
1454287 TAATATAATTACATTCAACC
1 TAATATAATTACATTCAACA
*
1454307 TAATATGATTAC
1 TAATATAATTAC
1454319 TTTTGATGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 19 0.40
20 28 0.60
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (20 bp):
TAATATAATTACATTCAACA
Found at i:1454359 original size:20 final size:20
Alignment explanation
Indices: 1454334--1454374 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1454324 ATGGCATTCA
*
1454334 AACAATATGATCATTCAAAC
1 AACAATATAATCATTCAAAC
*
1454354 AACAATATAATTATTCAAAC
1 AACAATATAATCATTCAAAC
1454374 A
1 A
1454375 TTTAAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (20 bp):
AACAATATAATCATTCAAAC
Found at i:1457531 original size:13 final size:13
Alignment explanation
Indices: 1457513--1457543 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1457503 TCTTTTTAAA
*
1457513 AATATTTATTTTT
1 AATATTTATATTT
1457526 AATATTTATATTT
1 AATATTTATATTT
1457539 AATAT
1 AATAT
1457544 ATTTAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1457600 original size:16 final size:17
Alignment explanation
Indices: 1457579--1457612 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1457569 ATTTTTTTAA
1457579 AAAAATT-TAAATATAT
1 AAAAATTATAAATATAT
1457595 AAAAATTACTAAATATAT
1 AAAAATTA-TAAATATAT
1457613 TTATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAATTATAAATATAT
Found at i:1458610 original size:11 final size:11
Alignment explanation
Indices: 1458594--1458754 Score: 52
Period size: 11 Copynumber: 16.0 Consensus size: 11
1458584 AAAAATAATT
1458594 ATATAAATATA
1 ATATAAATATA
1458605 ATATAAATA-A
1 ATATAAATATA
*
1458615 A-ATAAATAAA
1 ATATAAATATA
*
1458625 ATGT-AATATA
1 ATATAAATATA
* *
1458635 GTATTAATAT-
1 ATATAAATATA
1458645 ATATTAAA-AT-
1 ATA-TAAATATA
*
1458655 TTATAAA-AT-
1 ATATAAATATA
*
1458664 ATA-AATTACTA
1 ATATAAATA-TA
* *
1458675 ATAT-ATTAAA
1 ATATAAATATA
*
1458685 AT-TATATA-A
1 ATATAAATATA
1458694 ATATAAA-ATA
1 ATATAAATATA
* * *
1458704 TTTTAAATTTA
1 ATATAAATATA
1458715 AT-T--ATATA
1 ATATAAATATA
1458723 ATAATAAA-AT-
1 AT-ATAAATATA
1458733 ATATAAATATA
1 ATATAAATATA
*
1458744 ATGTAAATATA
1 ATATAAATATA
1458755 TAAAATTTTT
Statistics
Matches: 113, Mismatches: 19, Indels: 36
0.67 0.11 0.21
Matches are distributed among these distances:
8 8 0.07
9 26 0.23
10 38 0.34
11 40 0.35
12 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (11 bp):
ATATAAATATA
Found at i:1458688 original size:17 final size:16
Alignment explanation
Indices: 1458643--1458690 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
1458633 TAGTATTAAT
1458643 ATATATTAAAATTTATA
1 ATATATTAAAA-TTATA
*
1458660 AAATA-T-AAATTACTA
1 ATATATTAAAATTA-TA
1458675 ATATATTAAAATTATA
1 ATATATTAAAATTATA
1458691 TAAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
16 4 0.15
17 10 0.38
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATTAAAATTATA
Found at i:1458720 original size:30 final size:30
Alignment explanation
Indices: 1458684--1458766 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
1458674 AATATATTAA
*
1458684 AATTATATAAATATAAAATATTTTAAATTT
1 AATTATATAAATATAAAATATTTTAAATAT
*
1458714 AATTATAT-AATAATAAAATA-TATAAATAT
1 AATTATATAAAT-ATAAAATATTTTAAATAT
*
1458743 AATGTA-A-ATATATAAAAT-TTTTAA
1 AAT-TATATAAATATAAAATATTTTAA
1458767 TCTATCAACT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
28 11 0.24
29 16 0.36
30 18 0.40
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (30 bp):
AATTATATAAATATAAAATATTTTAAATAT
Found at i:1458744 original size:15 final size:15
Alignment explanation
Indices: 1458649--1458744 Score: 65
Period size: 15 Copynumber: 6.2 Consensus size: 15
1458639 TAATATATAT
*
1458649 TAAAATTTATAAA-A
1 TAAAATATATAAATA
1458663 TATAAAT-TACTAATATA
1 TA-AAATATA-TAA-ATA
1458680 TTAAAATTATATAAATA
1 -TAAAA-TATATAAATA
*
1458697 TAAAATATTTTAAAT-
1 TAAAATA-TATAAATA
* *
1458712 TTAATTATAT-AATAA
1 TAAAATATATAAAT-A
1458727 TAAAATATATAAATA
1 TAAAATATATAAATA
1458742 TAA
1 TAA
1458745 TGTAAATATA
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
13 3 0.05
14 6 0.09
15 26 0.40
16 15 0.23
17 7 0.11
18 6 0.09
19 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAATATATAAATA
Found at i:1463216 original size:13 final size:15
Alignment explanation
Indices: 1463187--1463221 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1463177 TGTTAATTTC
1463187 ATACAACTGCAACAT
1 ATACAACTGCAACAT
*
1463202 ATACAACTGCAATAT
1 ATACAACTGCAACAT
1463217 ATACA
1 ATACA
1463222 TTAAATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.23
Consensus pattern (15 bp):
ATACAACTGCAACAT
Found at i:1466904 original size:15 final size:15
Alignment explanation
Indices: 1466875--1466919 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1466865 TAATTAATTA
1466875 ATTA-TATTA-TTTT
1 ATTATTATTATTTTT
*
1466888 ATTATTTTTATTTTT
1 ATTATTATTATTTTT
1466903 ATTATTATTATTTTT
1 ATTATTATTATTTTT
1466918 AT
1 AT
1466920 GAAAAGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 4 0.14
14 4 0.14
15 20 0.71
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTATTATTATTTTT
Found at i:1469437 original size:3 final size:3
Alignment explanation
Indices: 1469424--1469466 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1469414 CATAAAATAA
* * *
1469424 TAT TAT AAT TAT TAT TAT T-T TAT TTT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1469467 ACCGTTATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1473411 original size:28 final size:28
Alignment explanation
Indices: 1473380--1473435 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1473370 TGGTCTTCGC
1473380 CCCTAACA-GTGACGACTGGGTCCTTGGA
1 CCCTAACATG-GACGACTGGGTCCTTGGA
**
1473408 CCCTGGCATGGACGACTGGGTCCTTGGA
1 CCCTAACATGGACGACTGGGTCCTTGGA
1473436 GTGGTGCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.18, C:0.29, G:0.32, T:0.21
Consensus pattern (28 bp):
CCCTAACATGGACGACTGGGTCCTTGGA
Found at i:1473846 original size:2 final size:2
Alignment explanation
Indices: 1473839--1473883 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1473829 AGCCCTCTCC
*
1473839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1473881 AT A
1 AT A
1473884 CACCAAGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1474657 original size:2 final size:2
Alignment explanation
Indices: 1474650--1474674 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1474640 AACTCTCAGT
1474650 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1474675 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1476317 original size:2 final size:2
Alignment explanation
Indices: 1476312--1476338 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1476302 ACTTATGTAC
1476312 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1476339 CATTGCTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:1476658 original size:8 final size:8
Alignment explanation
Indices: 1476613--1476680 Score: 82
Period size: 8 Copynumber: 8.5 Consensus size: 8
1476603 AAAGGATATG
*
1476613 ATATATAT
1 ATATTTAT
*
1476621 ATATATAT
1 ATATTTAT
1476629 ATATTTAT
1 ATATTTAT
*
1476637 TTATTTAT
1 ATATTTAT
1476645 ATATTTAT
1 ATATTTAT
* *
1476653 ACATTTCT
1 ATATTTAT
*
1476661 ATATTTCT
1 ATATTTAT
1476669 ATATTTAT
1 ATATTTAT
1476677 ATAT
1 ATAT
1476681 GGATAATAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 53 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (8 bp):
ATATTTAT
Found at i:1478761 original size:28 final size:27
Alignment explanation
Indices: 1478742--1478798 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
1478732 TTGAATTGTT
*
1478742 ATTTAATAATAAAAATATTTTTAATTAA
1 ATTTAATAATAAAAATA-TTTGAATTAA
* * *
1478770 ATTTAATTATAAAAATATATAAATTAA
1 ATTTAATAATAAAAATATTTGAATTAA
1478797 AT
1 AT
1478799 ATAAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATTTAATAATAAAAATATTTGAATTAA
Found at i:1480012 original size:3 final size:3
Alignment explanation
Indices: 1480004--1480042 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1479994 ACGCATACAT
1480004 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
1480043 TCATTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1480440 original size:19 final size:17
Alignment explanation
Indices: 1480390--1480426 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1480380 ATACTAATAA
1480390 TATAAAAGAAAATTACT
1 TATAAAAGAAAATTACT
*
1480407 TATAAAAGAACATTACT
1 TATAAAAGAAAATTACT
1480424 TAT
1 TAT
1480427 GGTGAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (17 bp):
TATAAAAGAAAATTACT
Found at i:1491188 original size:2 final size:2
Alignment explanation
Indices: 1491183--1491217 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1491173 TCTTTCAGCT
1491183 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1491218 TATGCCAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1499251 original size:21 final size:22
Alignment explanation
Indices: 1499225--1499268 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1499215 CATTTGTAAA
*
1499225 TTATAATAAAGTAT-CAATTTT
1 TTATAAAAAAGTATACAATTTT
*
1499246 TTATAAAAAAGTATACACTTTT
1 TTATAAAAAAGTATACAATTTT
1499268 T
1 T
1499269 CACTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (22 bp):
TTATAAAAAAGTATACAATTTT
Found at i:1502439 original size:2 final size:2
Alignment explanation
Indices: 1502426--1502460 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1502416 ATGGTGGGTC
*
1502426 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1502461 TTTTAATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1504546 original size:15 final size:16
Alignment explanation
Indices: 1504519--1504552 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1504509 TATGATTATA
*
1504519 TATATATATATAAATT
1 TATATATATATAAAAT
1504535 TATATA-ATATAAAAT
1 TATATATATATAAAAT
1504550 TAT
1 TAT
1504553 TAACATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATATATAAAAT
Found at i:1504614 original size:22 final size:22
Alignment explanation
Indices: 1504569--1504624 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
1504559 ATTAAAATTT
***
1504569 AAATAATTATATAATATTTTAA
1 AAATAATTATATAATATGAAAA
*
1504591 AAATAATTATATTATATGAAAA
1 AAATAATTATATAATATGAAAA
*
1504613 AATATAAATATA
1 AA-ATAATTATA
1504625 ACATAATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATAATTATATAATATGAAAA
Found at i:1505430 original size:3 final size:3
Alignment explanation
Indices: 1505422--1505467 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1505412 TCTATGTCAT
1505422 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1505468 ATTTATTTAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1506969 original size:14 final size:16
Alignment explanation
Indices: 1506950--1506982 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1506940 AATAATATAT
1506950 AATATTAAA-ATG-TA
1 AATATTAAAGATGTTA
1506964 AATATTAAAGATGTTA
1 AATATTAAAGATGTTA
1506980 AAT
1 AAT
1506983 TATTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 3 0.18
16 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (16 bp):
AATATTAAAGATGTTA
Found at i:1507760 original size:2 final size:2
Alignment explanation
Indices: 1507753--1507780 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1507743 AAGAAGTTTA
1507753 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
1507781 TATCACAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1508659 original size:15 final size:17
Alignment explanation
Indices: 1508628--1508659 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1508618 AAATTTTTAT
1508628 TATTTTATAATTAAAAA
1 TATTTTATAATTAAAAA
1508645 TATTTTA-AA-TAAAAA
1 TATTTTATAATTAAAAA
1508660 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTTATAATTAAAAA
Found at i:1508668 original size:7 final size:7
Alignment explanation
Indices: 1508651--1508685 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
1508641 AAAATATTTT
1508651 AAATAAAA
1 AAAT-AAA
1508659 AAATAAA
1 AAATAAA
1508666 AAATAAA
1 AAATAAA
*
1508673 AGATAAA
1 AAATAAA
1508680 AAATAA
1 AAATAA
1508686 TAATATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (7 bp):
AAATAAA
Found at i:1508693 original size:15 final size:15
Alignment explanation
Indices: 1508651--1508707 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
1508641 AAAATATTTT
*
1508651 AAATAAAAAAATAAA
1 AAATAAAAATATAAA
*
1508666 AAAT-AAAAGATAAA
1 AAATAAAAATATAAA
* *
1508680 AAATAATAATATAAT
1 AAATAAAAATATAAA
*
1508695 TAATAAAAATATA
1 AAATAAAAATATA
1508708 TTTATCTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 13 0.37
15 22 0.63
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
AAATAAAAATATAAA
Found at i:1509246 original size:3 final size:3
Alignment explanation
Indices: 1509238--1509278 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1509228 AATCGACGCC
*
1509238 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAC GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1509279 CGAGGACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.02, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1513501 original size:2 final size:2
Alignment explanation
Indices: 1513494--1513527 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1513484 TGGAATCTTG
1513494 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
1513528 CAATCACCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1516147 original size:2 final size:2
Alignment explanation
Indices: 1516140--1516164 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1516130 TGCTATAGAT
1516140 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1516165 TAATTATACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1516513 original size:20 final size:19
Alignment explanation
Indices: 1516472--1516518 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
1516462 TAAGATTAGT
*
1516472 TAATATTTTTTTTTGGAAG
1 TAATATTTTTTTTTGAAAG
1516491 TAATATTATTTTTTT-AAATG
1 TAATATT-TTTTTTTGAAA-G
1516511 TAATATTT
1 TAATATTT
1516519 GATGTTTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (19 bp):
TAATATTTTTTTTTGAAAG
Found at i:1517605 original size:20 final size:21
Alignment explanation
Indices: 1517539--1517601 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 21
1517529 TATATTTTAA
*
1517539 AAATATTTTTATATTTAAAATAT
1 AAATATTTATATA-TTAAAAT-T
**
1517562 TTATATTTATATATTAAAATT
1 AAATATTTATATATTAAAATT
1517583 AAATATTTA-ATA-TAAAATT
1 AAATATTTATATATTAAAATT
1517602 TAAAAAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 7 0.20
20 3 0.09
21 8 0.23
22 7 0.20
23 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATATTTATATATTAAAATT
Found at i:1533766 original size:20 final size:19
Alignment explanation
Indices: 1533741--1533789 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1533731 AGTATTTAAA
*
1533741 AATTTATTTAAATTTTAATT
1 AATTTATTTAAA-TTAAATT
* *
1533761 ATTTTAATTTGAATTAAATT
1 AATTT-ATTTAAATTAAATT
1533781 AATTTATTT
1 AATTTATTT
1533790 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
AATTTATTTAAATTAAATT
Found at i:1535868 original size:2 final size:2
Alignment explanation
Indices: 1535855--1535893 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1535845 CGGAATTTCT
*
1535855 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1535894 GTATATAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:1536572 original size:2 final size:2
Alignment explanation
Indices: 1536565--1536596 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1536555 CTTATTCTTC
1536565 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
1536597 TTCTTTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1542128 original size:16 final size:16
Alignment explanation
Indices: 1542085--1542128 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1542075 AAATTTAAAA
*
1542085 TAAATATTTT-ATTTT
1 TAAAAATTTTAATTTT
*
1542100 AAAACAATTTTAATTTT
1 TAAA-AATTTTAATTTT
1542117 TAAAAATTTTAA
1 TAAAAATTTTAA
1542129 AATATTAACG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAAAATTTTAATTTT
Found at i:1542407 original size:22 final size:24
Alignment explanation
Indices: 1542357--1542410 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
1542347 TAACTTTTTT
*
1542357 AAAAATATAAATAATTAAATATAT
1 AAAAATATAAATAATTAAATATAC
*
1542381 AAAAATA-AAATAATT-AATGTAC
1 AAAAATATAAATAATTAAATATAC
*
1542403 GAAAATAT
1 AAAAATAT
1542411 CGATCATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 11 0.42
23 8 0.31
24 7 0.27
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAAATATAAATAATTAAATATAC
Found at i:1543443 original size:18 final size:19
Alignment explanation
Indices: 1543402--1543443 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1543392 ATAAATAGAT
* * *
1543402 TTTTTTTTGTGTTTATTTA
1 TTTTTTTTGAGTTCATTCA
1543421 TTTTTTTTGAGTTCATTCA
1 TTTTTTTTGAGTTCATTCA
1543440 TTTT
1 TTTT
1543444 AGTTGGTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTTTTTTGAGTTCATTCA
Found at i:1546459 original size:22 final size:22
Alignment explanation
Indices: 1546440--1546492 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1546430 AAAGTATGTA
*
1546440 ATAATATAAACATAATTATGAT
1 ATAAAATAAACATAATTATGAT
* * *
1546462 ATAAAATTAACATAAATATAAT
1 ATAAAATAAACATAATTATGAT
1546484 AT-AAATAAA
1 ATAAAATAAA
1546493 TAAATTACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (22 bp):
ATAAAATAAACATAATTATGAT
Found at i:1547154 original size:2 final size:2
Alignment explanation
Indices: 1547142--1547183 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1547132 TATAAAAAGG
1547142 AT AT A- 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
1547183 A
1 A
1547184 GAAAGGGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1547396 original size:16 final size:16
Alignment explanation
Indices: 1547375--1547427 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
1547365 ATTCAAGTTA
1547375 TTTAAATTTTGATCAT
1 TTTAAATTTTGATCAT
1547391 TTTAAATTTATG-TCAT
1 TTTAAATTT-TGATCAT
*
1547407 TTT-AATTTTAGATTAT
1 TTTAAATTTT-GATCAT
1547423 TTTAA
1 TTTAA
1547428 GTTTGAGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.03
15 6 0.19
16 22 0.69
17 3 0.09
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTAAATTTTGATCAT
Found at i:1547396 original size:31 final size:32
Alignment explanation
Indices: 1547361--1547427 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
1547351 TTGTGTTACC
*
1547361 TTAAATTCAAGTTATTTAAATTTT-GATCATT
1 TTAAATTCAAGTCATTTAAATTTTAGATCATT
* * * *
1547392 TTAAATTTATGTCATTTTAATTTTAGATTATT
1 TTAAATTCAAGTCATTTAAATTTTAGATCATT
1547424 TTAA
1 TTAA
1547428 GTTTGAGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (32 bp):
TTAAATTCAAGTCATTTAAATTTTAGATCATT
Found at i:1547441 original size:32 final size:30
Alignment explanation
Indices: 1547361--1547441 Score: 81
Period size: 32 Copynumber: 2.6 Consensus size: 30
1547351 TTGTGTTACC
* *
1547361 TTAAATTCAAGTTATTTAAATTTTGATCATT
1 TTAAATT-TAGTTATTTTAATTTTGATCATT
* *
1547392 TTAAATTTATGTCATTTTAATTTTAGATTATT
1 TTAAATTTA-GTTATTTTAATTTT-GATCATT
*
1547424 TTAAGTTTGAGTTATTTT
1 TTAAATTT-AGTTATTTT
1547442 TGTTTCGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 19 0.46
32 20 0.49
33 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.57
Consensus pattern (30 bp):
TTAAATTTAGTTATTTTAATTTTGATCATT
Found at i:1547785 original size:19 final size:18
Alignment explanation
Indices: 1547749--1547788 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1547739 TATTGAAATA
1547749 TAAAATATAAAAATATTT
1 TAAAATATAAAAATATTT
1547767 TAAATATATATAAAA-ATTT
1 TAAA-ATATA-AAAATATTT
1547786 TAA
1 TAA
1547789 TTTTTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATATAAAAATATTT
Found at i:1548490 original size:32 final size:32
Alignment explanation
Indices: 1548422--1548495 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1548412 GGTTCAGATT
*
1548422 ATTTTAAATTCGGATCACTTCGGATTCAAGTT
1 ATTTTAAATTCGGATCACTTCGGATTCAAGTC
* * **
1548454 ATTTTGAATTCGGATCACTT-TGAGTTTGAGTC
1 ATTTTAAATTCGGATCACTTCGGA-TTCAAGTC
1548486 ATTTTAAATT
1 ATTTTAAATT
1548496 TAAATTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 2 0.06
32 33 0.94
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (32 bp):
ATTTTAAATTCGGATCACTTCGGATTCAAGTC
Found at i:1548507 original size:16 final size:16
Alignment explanation
Indices: 1548486--1548522 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1548476 AGTTTGAGTC
1548486 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
*
1548502 ATTTTAGATTTAAATT
1 ATTTTAAATTTAAATT
1548518 ATTTT
1 ATTTT
1548523 CAGGCTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:1549442 original size:3 final size:3
Alignment explanation
Indices: 1549434--1549464 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1549424 TGCAGTTCCA
1549434 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1549465 CTCCTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:1550732 original size:2 final size:2
Alignment explanation
Indices: 1550688--1550723 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1550678 GACGAGAGTT
*
1550688 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1550724 CGCGTGTGTA
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:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1555420 original size:5 final size:5
Alignment explanation
Indices: 1555410--1555443 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1555400 TAAATAATAT
* *
1555410 ATTAG ATTAG ATTAG ATGAG ATTAG ATTGG ATTA
1 ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTA
1555444 TATATTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (5 bp):
ATTAG
Found at i:1557207 original size:2 final size:2
Alignment explanation
Indices: 1557200--1557231 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1557190 AGCAAGAATG
1557200 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
1557232 GTGCTAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1559818 original size:2 final size:2
Alignment explanation
Indices: 1559811--1559840 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1559801 AGTAGGAGTT
*
1559811 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1559841 ATCTTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1564089 original size:28 final size:28
Alignment explanation
Indices: 1564047--1564116 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 28
1564037 ATTATTTTGA
* *
1564047 AAAAAAAATTATTATCATTTTTTT-AATTT
1 AAAAATAATT-TTAT-ATTTTTTTAAAATT
1564076 AAAAATAATTTTATATTTTTTTAAAATT
1 AAAAATAATTTTATATTTTTTTAAAATT
1564104 AAAAATATATTTT
1 AAAAATA-ATTTT
1564117 TTAAATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 8 0.22
28 15 0.41
29 14 0.38
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
AAAAATAATTTTATATTTTTTTAAAATT
Found at i:1564143 original size:29 final size:29
Alignment explanation
Indices: 1564111--1564170 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1564101 ATTAAAAATA
1564111 TATTTTTTAA-ATTTAA-TATAAAATATATT
1 TATTTTTTAATA-TTAATTATAAAATA-ATT
*
1564140 TATTTTTTAATATTAATTATAAATTAATT
1 TATTTTTTAATATTAATTATAAAATAATT
1564169 TA
1 TA
1564171 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TATTTTTTAATATTAATTATAAAATAATT
Found at i:1564148 original size:23 final size:23
Alignment explanation
Indices: 1564105--1564152 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
1564095 TTTAAAATTA
1564105 AAAATATATTTTTTAAATTTAATAT
1 AAAATATATTTTTT--ATTTAATAT
1564130 AAAATATATTTATTT-TTTAATAT
1 AAAATATATTT-TTTATTTAATAT
1564153 TAATTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.36
25 11 0.50
26 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AAAATATATTTTTTATTTAATAT
Found at i:1564600 original size:11 final size:13
Alignment explanation
Indices: 1564574--1564605 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1564564 ATCATATTTT
1564574 AATATTTAAAATA
1 AATATTTAAAATA
1564587 AAT-TTTAAAA-A
1 AATATTTAAAATA
1564598 AATATTTA
1 AATATTTA
1564606 TTTAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 11 0.61
13 3 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATTTAAAATA
Found at i:1564698 original size:29 final size:28
Alignment explanation
Indices: 1564644--1564698 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1564634 ATTATTAACT
*
1564644 AAATTTTAAAAATAAATAAATATTTTTC
1 AAATGTTAAAAATAAATAAATATTTTTC
*
1564672 AAATGTTAAAATATAAATATAT-TTTTT
1 AAATGTTAAAA-ATAAATAAATATTTTT
1564699 ATAAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
AAATGTTAAAAATAAATAAATATTTTTC
Found at i:1564738 original size:3 final size:3
Alignment explanation
Indices: 1564730--1564757 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1564720 TTTTTGACCA
1564730 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1564758 GTTGTTGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1566966 original size:19 final size:19
Alignment explanation
Indices: 1566942--1566979 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1566932 CCACATATCC
1566942 TTCATTTCTATGATTGATT
1 TTCATTTCTATGATTGATT
1566961 TTCATTTCTATGATTGATT
1 TTCATTTCTATGATTGATT
1566980 GTTGTAATAT
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:0.21, C:0.11, G:0.11, T:0.58
Consensus pattern (19 bp):
TTCATTTCTATGATTGATT
Found at i:1568664 original size:2 final size:2
Alignment explanation
Indices: 1568659--1568692 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1568649 AACTCTCTTA
1568659 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
1568693 CAATGAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1572628 original size:7 final size:7
Alignment explanation
Indices: 1572612--1572666 Score: 103
Period size: 7 Copynumber: 8.0 Consensus size: 7
1572602 TGTGGGGCTT
1572612 TGGC-AA
1 TGGCAAA
1572618 TGGCAAA
1 TGGCAAA
1572625 TGGCAAA
1 TGGCAAA
1572632 TGGCAAA
1 TGGCAAA
1572639 TGGCAAA
1 TGGCAAA
1572646 TGGCAAA
1 TGGCAAA
1572653 TGGCAAA
1 TGGCAAA
1572660 TGGCAAA
1 TGGCAAA
1572667 GGCGGGCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 4 0.08
7 44 0.92
ACGTcount: A:0.42, C:0.15, G:0.29, T:0.15
Consensus pattern (7 bp):
TGGCAAA
Found at i:1573165 original size:2 final size:2
Alignment explanation
Indices: 1573158--1573190 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1573148 CGTTTCACTG
1573158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1573191 CTAAATTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1573479 original size:23 final size:23
Alignment explanation
Indices: 1573453--1573496 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1573443 TTACTTTACT
1573453 TTTAAGATGTAAAATTTAATAAA
1 TTTAAGATGTAAAATTTAATAAA
* *
1573476 TTTAAGATTTAAATTTTAATA
1 TTTAAGATGTAAAATTTAATA
1573497 TTTTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (23 bp):
TTTAAGATGTAAAATTTAATAAA
Found at i:1573502 original size:23 final size:23
Alignment explanation
Indices: 1573452--1573503 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1573442 GTTACTTTAC
1573452 TTTTAAGATGTAAAATTTAATAA
1 TTTTAAGATGTAAAATTTAATAA
* * * *
1573475 ATTTAAGATTTAAATTTTAATAT
1 TTTTAAGATGTAAAATTTAATAA
1573498 TTTTAA
1 TTTTAA
1573504 TTATTTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTTAAGATGTAAAATTTAATAA
Found at i:1574220 original size:2 final size:2
Alignment explanation
Indices: 1574213--1574237 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1574203 TCATGCACCA
1574213 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
1574238 CACACACACA
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:1578594 original size:2 final size:2
Alignment explanation
Indices: 1578587--1578618 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1578577 ACCACGTACA
*
1578587 TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1578619 AGAAAAAAGT
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:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1584919 original size:3 final size:3
Alignment explanation
Indices: 1584913--1584939 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1584903 ATAATAATCA
1584913 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1584940 AACTTATGGG
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:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1596283 original size:2 final size:2
Alignment explanation
Indices: 1596259--1596309 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
1596249 CTTTCAACTC
* *
1596259 AT AT AT AA AT AT AA AT AT A- 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
1596300 AT AT AT AT AT
1 AT AT AT AT AT
1596310 CCCAGCCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1596740 original size:6 final size:6
Alignment explanation
Indices: 1596729--1596757 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1596719 ATCAATGACC
1596729 CCAGTT CCAGTT CCAGTT CCAGTT CCAGT
1 CCAGTT CCAGTT CCAGTT CCAGTT CCAGT
1596758 CCAACAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.31
Consensus pattern (6 bp):
CCAGTT
Found at i:1596936 original size:2 final size:2
Alignment explanation
Indices: 1596929--1596964 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1596919 TTGAAAGAAA
1596929 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1596965 GGCTTAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1599139 original size:2 final size:2
Alignment explanation
Indices: 1599132--1599160 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1599122 ATTGTTGAAT
1599132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1599161 CTCAAACCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1604086 original size:14 final size:15
Alignment explanation
Indices: 1604062--1604094 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1604052 AATCCCCTAC
1604062 TTTGAGCTTAATCTA
1 TTTGAGCTTAATCTA
*
1604077 TTTG-GCTTAATTTA
1 TTTGAGCTTAATCTA
1604091 TTTG
1 TTTG
1604095 TCCCATCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.55
Consensus pattern (15 bp):
TTTGAGCTTAATCTA
Found at i:1604556 original size:2 final size:2
Alignment explanation
Indices: 1604549--1604584 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1604539 AGAGTGAACT
1604549 TA TA TA TA TA 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
1604585 GCATCAGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1605271 original size:3 final size:3
Alignment explanation
Indices: 1605263--1605296 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1605253 AATTTATAAC
*
1605263 ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1605297 GGTTTTCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1605364 original size:15 final size:16
Alignment explanation
Indices: 1605338--1605369 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1605328 CTAAAAAGAA
1605338 TTTAATTTAATTTATT
1 TTTAATTTAATTTATT
1605354 TTTAA-TTAATTTATT
1 TTTAATTTAATTTATT
1605369 T
1 T
1605370 AATGTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTAATTTAATTTATT
Found at i:1605364 original size:20 final size:20
Alignment explanation
Indices: 1605339--1605380 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1605329 TAAAAAGAAT
*
1605339 TTAATTTAATTT-ATTTTTAA
1 TTAATTT-ATTTAATGTTTAA
1605359 TTAATTTATTTAATGTTTAA
1 TTAATTTATTTAATGTTTAA
1605379 TT
1 TT
1605381 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTAATTTATTTAATGTTTAA
Found at i:1605858 original size:22 final size:20
Alignment explanation
Indices: 1605833--1605872 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
1605823 AATAAAAAAT
1605833 TATTTTTATATTAATATTTATA
1 TATTTTTA-ATTAA-ATTTATA
1605855 TATTTTTAATTAAATTTA
1 TATTTTTAATTAAATTTA
1605873 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTAATTAAATTTATA
Found at i:1605883 original size:34 final size:35
Alignment explanation
Indices: 1605845--1605930 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
1605835 TTTTTATATT
* *
1605845 AATATTTATATATT-TTTAATTA-AATTTAAATAAA
1 AATATTTATA-ATTATTAAATAATAATTTAAATAAA
*
1605879 AATATTTTTAATTATTAAATAATAATTTAAATAAA
1 AATATTTATAATTATTAAATAATAATTTAAATAAA
*
1605914 ATTAATTTA-AATTATTA
1 AAT-ATTTATAATTATTA
1605931 TAAATTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 3 0.07
34 15 0.34
35 22 0.50
36 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
AATATTTATAATTATTAAATAATAATTTAAATAAA
Found at i:1608025 original size:45 final size:45
Alignment explanation
Indices: 1607961--1608049 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
1607951 CGTAGGAGAC
*
1607961 TTCTTAAGTTGTTTAATCCCCAGCAGTTCCACCTTCTGGTTTTAT
1 TTCTTAAGTTGTTTAATCCCCAGCAGCTCCACCTTCTGGTTTTAT
*
1608006 TTCTTAAGTTGTTTAATCCCCAGCAGCTCCACCTTCTGTTTTTA
1 TTCTTAAGTTGTTTAATCCCCAGCAGCTCCACCTTCTGGTTTTA
1608050 GATCCTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.18, C:0.26, G:0.12, T:0.44
Consensus pattern (45 bp):
TTCTTAAGTTGTTTAATCCCCAGCAGCTCCACCTTCTGGTTTTAT
Found at i:1630288 original size:2 final size:2
Alignment explanation
Indices: 1630281--1630307 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1630271 TCTAGTACAA
1630281 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 A
1630308 CCCGGCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1632584 original size:64 final size:64
Alignment explanation
Indices: 1632515--1632642 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
1632505 GAACAATAAG
1632515 CTTGTATGAAGATACAAGATGTACAGACATCATTACTAGTTGTTCTCACAAAAAATCTATTCCT
1 CTTGTATGAAGATACAAGATGTACAGACATCATTACTAGTTGTTCTCACAAAAAATCTATTCCT
*
1632579 CTTGTATGAAGATACAAGATGTACAGACATCGTTACTAGTTGTTCTCACAAAAAATCTATTCCT
1 CTTGTATGAAGATACAAGATGTACAGACATCATTACTAGTTGTTCTCACAAAAAATCTATTCCT
1632643 AGCACATAAC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (64 bp):
CTTGTATGAAGATACAAGATGTACAGACATCATTACTAGTTGTTCTCACAAAAAATCTATTCCT
Found at i:1634433 original size:15 final size:15
Alignment explanation
Indices: 1634413--1634449 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1634403 GTCTCAAGGA
*
1634413 ATGAGATTAATTGAG
1 ATGAGATGAATTGAG
*
1634428 ATGAGATGAGTTGAG
1 ATGAGATGAATTGAG
1634443 ATGAGAT
1 ATGAGAT
1634450 CTGGTTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (15 bp):
ATGAGATGAATTGAG
Found at i:1634528 original size:7 final size:7
Alignment explanation
Indices: 1634516--1634545 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1634506 GCCCCGTCGG
1634516 GGGGCCT
1 GGGGCCT
1634523 GGGGCCT
1 GGGGCCT
1634530 GGGGCCT
1 GGGGCCT
1634537 GGGG-CT
1 GGGGCCT
1634543 GGG
1 GGG
1634546 CTAGGTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.00, C:0.23, G:0.63, T:0.13
Consensus pattern (7 bp):
GGGGCCT
Found at i:1635837 original size:2 final size:2
Alignment explanation
Indices: 1635830--1635874 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1635820 TCACCCTCTT
*
1635830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1635872 TA T
1 TA T
1635875 CCCTTTAACG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 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):
TA
Found at i:1639224 original size:23 final size:23
Alignment explanation
Indices: 1639198--1639255 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1639188 ACTACATGAG
1639198 ATAAAAA-ATAAATAAAATATAAC
1 ATAAAAATATAAA-AAAATATAAC
*
1639221 ATAAAAATATAAAATAATATAA-
1 ATAAAAATATAAAAAAATATAAC
1639243 A-AAATAATATAAA
1 ATAAA-AATATAAA
1639256 TATGAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 3 0.09
22 9 0.28
23 15 0.47
24 5 0.16
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (23 bp):
ATAAAAATATAAAAAAATATAAC
Found at i:1639257 original size:18 final size:18
Alignment explanation
Indices: 1639207--1639342 Score: 57
Period size: 18 Copynumber: 7.2 Consensus size: 18
1639197 GATAAAAAAT
* *
1639207 AAATAAAATATAACATAAA
1 AAATAATATA-AATATAAA
*
1639226 AATATAAAAT-AATATAAA
1 AA-ATAATATAAATATAAA
1639244 AAATAATATAAATATGAATA
1 AAATAATATAAATAT-AA-A
* *
1639264 TTAAT-ATATAAATATATTA
1 -AAATAATATAAATATA-AA
*
1639283 AAAT-TTATATAATATAAA
1 AAATAATATA-AATATAAA
*
1639301 AGAGATCAATATTAAT-TAAAA
1 A-A-AT-AATATAAATAT-AAA
*
1639322 AAATAA-ATCAAAAATAAA
1 AAATAATAT-AAATATAAA
1639340 AAA
1 AAA
1639343 ATCATCTATG
Statistics
Matches: 92, Mismatches: 11, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
17 8 0.09
18 33 0.36
19 16 0.17
20 22 0.24
21 10 0.11
22 3 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATAATATAAATATAAA
Found at i:1639263 original size:6 final size:6
Alignment explanation
Indices: 1639205--1639279 Score: 59
Period size: 6 Copynumber: 12.5 Consensus size: 6
1639195 GAGATAAAAA
* *
1639205 ATAAAT A-AAAT ATAACAT AAAAAT ATAAA- AT-AAT ATAAA- AAATAAT
1 ATAAAT ATAAAT ATAA-AT ATAAAT ATAAAT ATAAAT ATAAAT ATA-AAT
*
1639251 ATAAAT ATGAAT ATTAATAT ATAAAT ATA
1 ATAAAT ATAAAT A-TAA-AT ATAAAT ATA
1639280 TTAAAATTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
4 2 0.04
5 11 0.20
6 27 0.49
7 12 0.22
8 3 0.05
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (6 bp):
ATAAAT
Found at i:1640151 original size:2 final size:2
Alignment explanation
Indices: 1640144--1640170 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1640134 CCTTTTACAT
1640144 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1640171 TAATTAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1640203 original size:4 final size:4
Alignment explanation
Indices: 1640183--1640228 Score: 67
Period size: 4 Copynumber: 11.5 Consensus size: 4
1640173 ATTAATAGGA
*
1640183 AAGG -AGG AAGA AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAAGG AA
1 AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAGG -AAGG AA
1640229 CAGTATGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 3 0.08
4 31 0.82
5 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (4 bp):
AAGG
Found at i:1640796 original size:5 final size:5
Alignment explanation
Indices: 1640786--1640828 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
1640776 AAATAGTGAG
*
1640786 TAGGC TAGGC TAGGC TAGGC TAGGC TAGGC TAGGC TAGAC TAG
1 TAGGC TAGGC TAGGC TAGGC TAGGC TAGGC TAGGC TAGGC TAG
1640829 TCTTTTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (5 bp):
TAGGC
Found at i:1641055 original size:2 final size:2
Alignment explanation
Indices: 1641048--1641091 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1641038 ACCTTACCCC
*
1641048 AT AT AT AT CT 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
1641090 AT
1 AT
1641092 TCACATCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1644833 original size:2 final size:2
Alignment explanation
Indices: 1644826--1644860 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1644816 TTTTGTTTAT
1644826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1644861 GGACTATGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1645679 original size:2 final size:2
Alignment explanation
Indices: 1645672--1645705 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1645662 CATGCATAAG
1645672 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1645706 TTGGTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1647419 original size:37 final size:37
Alignment explanation
Indices: 1647369--1647446 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
1647359 AACAAAACTA
1647369 ATTTGACTTAATAATTAAAACTTTTAAACTAACCCTT
1 ATTTGACTTAATAATTAAAACTTTTAAACTAACCCTT
1647406 ATTTGACTTAATAATTAAAACTTTTAAACTAACCCTT
1 ATTTGACTTAATAATTAAAACTTTTAAACTAACCCTT
1647443 ATTT
1 ATTT
1647447 ACATGTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (37 bp):
ATTTGACTTAATAATTAAAACTTTTAAACTAACCCTT
Found at i:1647483 original size:22 final size:20
Alignment explanation
Indices: 1647453--1647505 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
1647443 ATTTACATGT
1647453 AAAT-ATTATTAAATAATTATC
1 AAATAATTATTAAAT--TTATC
*
1647474 AAATAATTATTTAATTTATC
1 AAATAATTATTAAATTTATC
1647494 ATACATAATTAT
1 A-A-ATAATTAT
1647506 CTAGTCCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 6 0.21
21 5 0.18
22 17 0.61
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAATTATTAAATTTATC
Found at i:1648849 original size:24 final size:24
Alignment explanation
Indices: 1648771--1648849 Score: 58
Period size: 26 Copynumber: 3.2 Consensus size: 24
1648761 AGTCCTCATT
*
1648771 ATATTAATCTATTTTGAAATTAATAA
1 ATATTAATTTA-TTT-AAATTAATAA
*
1648797 A-ATT--TTCTATTTAAA-TATTAA
1 ATATTAATT-TATTTAAATTAATAA
1648818 ATTTTATTAATTTATTTAAATTAATAA
1 A---TATTAATTTATTTAAATTAATAA
1648845 ATATT
1 ATATT
1648850 TTAAAATAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 4 0.10
24 6 0.14
25 6 0.14
26 9 0.21
27 8 0.19
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (24 bp):
ATATTAATTTATTTAAATTAATAA
Found at i:1648853 original size:26 final size:26
Alignment explanation
Indices: 1648804--1648853 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1648794 TAAAATTTTC
* *
1648804 TATTTAAATATTAAATTTTATTAATT
1 TATTTAAATAATAAATATTATTAATT
1648830 TATTTAAATTAATAAATATT-TTAA
1 TATTTAAA-TAATAAATATTATTAA
1648854 AATAGTGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TATTTAAATAATAAATATTATTAATT
Found at i:1649196 original size:25 final size:26
Alignment explanation
Indices: 1649151--1649201 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
1649141 TAAAAAATAA
1649151 AAATAATGATATATAACATAA-AAAT
1 AAATAATGATATATAACATAATAAAT
1649176 AAATAATTGATGATAT-A-ATAATAAAT
1 AAATAA-TGAT-ATATAACATAATAAAT
1649202 GTTGGAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
25 10 0.43
26 9 0.39
27 4 0.17
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (26 bp):
AAATAATGATATATAACATAATAAAT
Found at i:1649519 original size:2 final size:2
Alignment explanation
Indices: 1649514--1649547 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1649504 AATTAGTGTG
* *
1649514 TA TA TA TA TA CA TT 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
1649548 GAAACAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1651004 original size:29 final size:29
Alignment explanation
Indices: 1650962--1651017 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1650952 ATCCTTACTG
1650962 TTACTGTTAAGTGAAGATCTTGGTTATGC
1 TTACTGTTAAGTGAAGATCTTGGTTATGC
1650991 TTACTGTTAAGTGAAGATCTTGGTTAT
1 TTACTGTTAAGTGAAGATCTTGGTTAT
1651018 CTCACTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (29 bp):
TTACTGTTAAGTGAAGATCTTGGTTATGC
Done.