Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 97 of 171
Found at i:31534155 original size:20 final size:20
Alignment explanation
Indices: 31534119--31534156 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31534109 TATATAATTA
**
31534119 ATTTTATATTTTTAATAAAT
1 ATTTTATATTTAAAATAAAT
31534139 ATTTTATATTTAAAATAA
1 ATTTTATATTTAAAATAA
31534157 TGAAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTATATTTAAAATAAAT
Found at i:31535388 original size:28 final size:29
Alignment explanation
Indices: 31535356--31535410 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
31535346 ATTCAAGTTA
31535356 ATTATAAAAT-AAT-TTTTTTAATTTTATG
1 ATTATAAAATAAATATTTTTT-ATTTTATG
*
31535384 ATTATTAAATAAATATTTTTTATTTTA
1 ATTATAAAATAAATATTTTTTATTTTA
31535411 AAAATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 9 0.38
29 9 0.38
30 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
ATTATAAAATAAATATTTTTTATTTTATG
Found at i:31535403 original size:29 final size:28
Alignment explanation
Indices: 31535356--31535410 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
31535346 ATTCAAGTTA
*
31535356 ATTATAAAATAATTTTTTTAATTTTATG
1 ATTATAAAATAATATTTTTAATTTTATG
* *
31535384 ATTATTAAATAAATATTTTTTATTTTA
1 ATTATAAAAT-AATATTTTTAATTTTA
31535411 AAAATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTATAAAATAATATTTTTAATTTTATG
Found at i:31535431 original size:29 final size:28
Alignment explanation
Indices: 31535362--31535431 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
31535352 GTTAATTATA
** *
31535362 AAATAATTTTTTTAATTTTATGATTATT
1 AAATAATTTTTTTAATTTTAAAAATATT
31535390 AAATAAATATTTTTT-ATTTTAAAAATATT
1 AAAT-AAT-TTTTTTAATTTTAAAAATATT
31535419 ATAATAATTTTTT
1 A-AATAATTTTTT
31535432 AAAAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 9 0.25
29 18 0.50
30 9 0.25
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
AAATAATTTTTTTAATTTTAAAAATATT
Found at i:31535660 original size:24 final size:24
Alignment explanation
Indices: 31535626--31535686 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
31535616 TCTATAAACA
* *
31535626 TTTATATATATATATTTTTTATAAAT
1 TTTA-ATATATATGTTTTTGA-AAAT
* *
31535652 TATTAATATTTCTGTTTTTGAAAAT
1 T-TTAATATATATGTTTTTGAAAAT
31535677 TTTAATATAT
1 TTTAATATAT
31535687 TGAATTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 8 0.28
25 5 0.17
26 13 0.45
27 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (24 bp):
TTTAATATATATGTTTTTGAAAAT
Found at i:31538106 original size:91 final size:91
Alignment explanation
Indices: 31537995--31538238 Score: 283
Period size: 91 Copynumber: 2.7 Consensus size: 91
31537985 ATCTACAAAA
* * * * *
31537995 ATGTTTTGTATTCACAACCATTTGGTAGTGTATTAACCTGTAACTATTGGTGGTTCACTCACCCA
1 ATGTTGTGTATTCACAACCATCTGGCAGTGTATTAACCTGCAACTATTGGTGGTTCACCCACCCA
* *
31538060 TTATCTGACAGCTTTTATTTGCAATT
66 TTATCTAACAACTTTTATTTGCAATT
* ** * * ** *
31538086 ATGTTGTGTATTCACAACCATCTAGCAGCATATTAACCTGCAAATTTTGGTGGTTTTCCCACTCA
1 ATGTTGTGTATTCACAACCATCTGGCAGTGTATTAACCTGCAACTATTGGTGGTTCACCCACCCA
*
31538151 TTATCTAACAACTTTTATTTGTAATT
66 TTATCTAACAACTTTTATTTGCAATT
* * * * *
31538177 ATGTTGTGTATTCAAAATCGTCTGACAGTGTATTAACCTGCAAC-ATTTGGTGGTTCATCCAC
1 ATGTTGTGTATTCACAACCATCTGGCAGTGTATTAACCTGCAACTA-TTGGTGGTTCACCCAC
31538239 AACCCAATGT
Statistics
Matches: 124, Mismatches: 28, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
91 124 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (91 bp):
ATGTTGTGTATTCACAACCATCTGGCAGTGTATTAACCTGCAACTATTGGTGGTTCACCCACCCA
TTATCTAACAACTTTTATTTGCAATT
Found at i:31543753 original size:36 final size:36
Alignment explanation
Indices: 31543675--31543753 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
31543665 GTTGAGATAA
* **
31543675 TAAATATGTGGGTATGTTATTCATTCCATGAGGTAG
1 TAAATATGTGGGTATGTTATTCATGCCATGAGACAG
*
31543711 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
1 TAAATATGTGGGTATGTTATTCATGCCATGAGACAG
*
31543747 TGAATAT
1 TAAATAT
31543754 ATTGTGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (36 bp):
TAAATATGTGGGTATGTTATTCATGCCATGAGACAG
Found at i:31544252 original size:10 final size:10
Alignment explanation
Indices: 31544233--31544466 Score: 70
Period size: 10 Copynumber: 21.6 Consensus size: 10
31544223 AAAATATTCT
31544233 TGTGATTAAA
1 TGTGATTAAA
*
31544243 TGTGACTAAA
1 TGTGATTAAA
31544253 TGTGATTAATA
1 TGTGATTAA-A
31544264 TGTGATGTGATAAA
1 TGTGA--T--TAAA
**
31544278 TGCTGAAATATTCA
1 TG-TG--AT-TAAA
*
31544292 TGTGATTGAA
1 TGTGATTAAA
*
31544302 TGTGATCAAA
1 TGTGATTAAA
*
31544312 TGTGACTAAA
1 TGTGATTAAA
*
31544322 TATGATTAATA
1 TGTGATTAA-A
31544333 TGTGATGTGATAAA
1 TGTGA--T--TAAA
*
31544347 TGTTGAAACATT-CA
1 TG-TG----ATTAAA
31544361 TGTGATTAAA
1 TGTGATTAAA
31544371 TGTGATTAAA
1 TGTGATTAAA
*
31544381 TGTGACTAATA
1 TGTGATTAA-A
31544392 TGTGATGTGATAAA
1 TGTGA--T--TAAA
31544406 T-TG-TTGAAA
1 TGTGATT-AAA
*
31544415 --T-ATT-CA
1 TGTGATTAAA
*
31544421 TGTGACT-AA
1 TGTGATTAAA
31544430 TGTGATTAAA
1 TGTGATTAAA
*
31544440 TGTGACTAAA
1 TGTGATTAAA
31544450 TGTGATTAATA
1 TGTGATTAA-A
31544461 TGTGAT
1 TGTGAT
31544467 GTGATAAATG
Statistics
Matches: 170, Mismatches: 23, Indels: 61
0.67 0.09 0.24
Matches are distributed among these distances:
6 1 0.01
8 5 0.03
9 15 0.09
10 81 0.48
11 26 0.15
13 8 0.05
14 16 0.09
15 15 0.09
17 2 0.01
19 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.38
Consensus pattern (10 bp):
TGTGATTAAA
Found at i:31544287 original size:59 final size:59
Alignment explanation
Indices: 31544215--31544555 Score: 360
Period size: 69 Copynumber: 5.5 Consensus size: 59
31544205 AGTCATGCAC
* *
31544215 TAAATGCTAAAATATTCTTGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
1 TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
*
31544274 TAAATGCTGAAATATTCATGTGATTGAATGTGATCAAATGTGACTAAATATGATTAATATGTGAT
1 TAAATGCTGAAATATTCA--TG--TG-A--T--T-AAATGTGACTAAATGTGATTAATATGTGAT
31544339 GTGA
56 GTGA
* * * *
31544343 TAAATGTTGAAACATTCATGTGATTAAATGTGATTAAATGTGACTAATATGTGATGTGA
1 TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
*
31544402 TAAATTGTTGAAATATTCATGTGACTAATGTGATTAAATGTGACTAAATGTGATTAATATGTGAT
1 TAAA-TGCTG-AA-A-T-AT-T--C--ATGTGATTAAATGTGACTAAATGTGATTAATATGTGAT
31544467 GTGA
56 GTGA
* * * * *
31544471 TAAATGCTGAAATATTCATGTGACT-AATGTGATTAAATGTGATTAATATGTGTTATGG
1 TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
* *
31544529 TAAATGCTTAAGTATTCATGTGATTAA
1 TAAATGCTGAAATATTCATGTGATTAA
31544556 TGCGATTAAT
Statistics
Matches: 241, Mismatches: 20, Indels: 42
0.80 0.07 0.14
Matches are distributed among these distances:
58 51 0.21
59 59 0.24
60 6 0.02
61 5 0.02
62 2 0.01
63 3 0.01
64 6 0.02
65 4 0.02
66 2 0.01
67 5 0.02
68 5 0.02
69 93 0.39
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (59 bp):
TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
Found at i:31544313 original size:69 final size:68
Alignment explanation
Indices: 31544233--31544522 Score: 418
Period size: 69 Copynumber: 4.4 Consensus size: 68
31544223 AAAATATTCT
*
31544233 TGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGAT
1 TGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGAC
31544298 TGAA
66 T-AA
* * *
31544302 TGTGATCAAATGTGACTAAATATGATTAATATGTGATGTGATAAATGTTG-AA-A--CAT-T--C
1 TGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGAC
31544360 --A
66 TAA
* * *
31544361 TGTGATTAAATGTGATTAAATGTGACTAATATGTGATGTGATAAATTGTTGAAATATTCATGTGA
1 TGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAA-TGCTGAAATATTCATGTGA
31544426 CTAA
65 CTAA
31544430 TGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGAC
1 TGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGAC
31544495 TAA
66 TAA
*
31544498 TGTGATTAAATGTGATTAATATGTG
1 TGTGATTAAATGTGACTAA-ATGTG
31544523 TTATGGTAAA
Statistics
Matches: 198, Mismatches: 12, Indels: 22
0.85 0.05 0.09
Matches are distributed among these distances:
59 42 0.21
60 5 0.03
61 2 0.01
62 1 0.01
64 4 0.02
65 4 0.02
67 2 0.01
68 42 0.21
69 96 0.48
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.38
Consensus pattern (68 bp):
TGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGAC
TAA
Found at i:31544375 original size:128 final size:127
Alignment explanation
Indices: 31544215--31544557 Score: 508
Period size: 128 Copynumber: 2.7 Consensus size: 127
31544205 AGTCATGCAC
* * * *
31544215 TAAATGCTAAAATATTCTTGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATG
1 TAAATGCTGAAACATTCATGTGATTAAATGTGATTAAATGTGATTAATATGTGATGTGATAAATG
31544280 CTGAAATATTCATGTGATTGAATGTGATCAAATGTGACTAAATATGATTAATATGTGATGTGA
66 CTGAAATATTCATGTGATT-AATGTGATCAAATGTGACTAAATATGATTAATATGTGATGTGA
* *
31544343 TAAATGTTGAAACATTCATGTGATTAAATGTGATTAAATGTGACTAATATGTGATGTGATAAATT
1 TAAATGCTGAAACATTCATGTGATTAAATGTGATTAAATGTGATTAATATGTGATGTGATAAA-T
* * * *
31544408 GTTGAAATATTCATGTGACTAATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
65 GCTGAAATATTCATGTGATTAATGTGATCAAATGTGACTAAATATGATTAATATGTGATGTGA
* * * * *
31544471 TAAATGCTGAAATATTCATGTGACT-AATGTGATTAAATGTGATTAATATGTGTTATGGTAAATG
1 TAAATGCTGAAACATTCATGTGATTAAATGTGATTAAATGTGATTAATATGTGATGTGATAAATG
* *
31544535 CTTAAGTATTCATGTGATTAATG
66 CTGAAATATTCATGTGATTAATG
31544558 CGATTAATGT
Statistics
Matches: 193, Mismatches: 21, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
126 21 0.11
127 33 0.17
128 120 0.62
129 19 0.10
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (127 bp):
TAAATGCTGAAACATTCATGTGATTAAATGTGATTAAATGTGATTAATATGTGATGTGATAAATG
CTGAAATATTCATGTGATTAATGTGATCAAATGTGACTAAATATGATTAATATGTGATGTGA
Found at i:31544508 original size:58 final size:58
Alignment explanation
Indices: 31544429--31544568 Score: 192
Period size: 58 Copynumber: 2.4 Consensus size: 58
31544419 CATGTGACTA
* *
31544429 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
1 ATGTGATT-AATGTGATTAAATGTGATTAATATGTGATATGATAAATGCTGAAATATTC
* * * * *
31544488 ATGTGACTAATGTGATTAAATGTGATTAATATGTGTTATGGTAAATGCTTAAGTATTC
1 ATGTGATTAATGTGATTAAATGTGATTAATATGTGATATGATAAATGCTGAAATATTC
*
31544546 ATGTGATTAATGCGATT-AATGTG
1 ATGTGATTAATGTGATTAAATGTG
31544569 TTCAAGAATA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
57 6 0.08
58 59 0.82
59 7 0.10
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (58 bp):
ATGTGATTAATGTGATTAAATGTGATTAATATGTGATATGATAAATGCTGAAATATTC
Found at i:31544512 original size:19 final size:21
Alignment explanation
Indices: 31544420--31544465 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
31544410 TGAAATATTC
31544420 ATGTGACT-AATGTGATTAA-
1 ATGTGACTAAATGTGATTAAT
31544439 ATGTGACTAAATGTGATTAAT
1 ATGTGACTAAATGTGATTAAT
31544460 ATGTGA
1 ATGTGA
31544466 TGTGATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 8 0.32
20 11 0.44
21 6 0.24
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (21 bp):
ATGTGACTAAATGTGATTAAT
Found at i:31548227 original size:59 final size:59
Alignment explanation
Indices: 31548135--31548411 Score: 226
Period size: 58 Copynumber: 4.7 Consensus size: 59
31548125 GTTATGAGTC
* * *
31548135 ATGTGTTAAATGCTAAAATATTCATGTGGTTAAATGTGACTAAATATGATTAATATGTG
1 ATGTGATAAATGCTAAAATATTCATGTGATTAAATGTGATTAAATATGATTAATATGTG
* * * *
31548194 ATGTGATAAATGCTGAAATATTCATGTGATTAAATGTGATT-AATA--AGTAATGTGATAAA
1 ATGTGATAAATGCTAAAATATTCATGTGATTAAATGTGATTAAATATGATTAATATG-T--G
* * ** * * * * * *
31548253 ATGTTGATATAT--TCATGTGACTAATGCGATTAAATGTGAGTAAATTTGATCAATATGTG
1 ATG-TGATAAATGCTAAAAT-ATTCATGTGATTAAATGTGATTAAATATGATTAATATGTG
* *
31548312 ATGTGATAAATGCTAAAATATTCATGTGACT-AATGTGATTAAATTTGATTAATATGTG
1 ATGTGATAAATGCTAAAATATTCATGTGATTAAATGTGATTAAATATGATTAATATGTG
* * * * * * *
31548370 TTGTGTTAAATGATTAAGTACTCATGTGATT-AATGCGATTAA
1 ATGTGATAAATGCTAAAATATTCATGTGATTAAATGTGATTAA
31548412 TGTGTAAGAA
Statistics
Matches: 170, Mismatches: 38, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
56 7 0.04
57 1 0.01
58 73 0.43
59 69 0.41
60 13 0.08
61 1 0.01
62 6 0.04
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (59 bp):
ATGTGATAAATGCTAAAATATTCATGTGATTAAATGTGATTAAATATGATTAATATGTG
Found at i:31548284 original size:49 final size:49
Alignment explanation
Indices: 31548168--31548285 Score: 157
Period size: 49 Copynumber: 2.4 Consensus size: 49
31548158 ATGTGGTTAA
* * *
31548168 ATGTGACTAAATATGATTAATATGTGATGTGATAAATGCTGAAATATTC
1 ATGTGACTAAATGTGATTAATAAGTAATGTGATAAATGCTGAAATATTC
* * *
31548217 ATGTGATTAAATGTGATTAATAAGTAATGTGATAAAATGTTGATATATTC
1 ATGTGACTAAATGTGATTAATAAGTAATGTGAT-AAATGCTGAAATATTC
*
31548267 ATGTGACT-AATGCGATTAA
1 ATGTGACTAAATGTGATTAA
31548286 ATGTGAGTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 39 0.65
50 21 0.35
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (49 bp):
ATGTGACTAAATGTGATTAATAAGTAATGTGATAAATGCTGAAATATTC
Found at i:31548291 original size:69 final size:68
Alignment explanation
Indices: 31548217--31548369 Score: 198
Period size: 68 Copynumber: 2.2 Consensus size: 68
31548207 TGAAATATTC
* * * *
31548217 ATGTGATTAAATGTGATTAATAAGTAATGTGATAAAATGTTGATATATTCATGTGACTAATGCGA
1 ATGTGATTAAATGTGATCAATAAGTAATGTGAT-AAATGCTAAAATATTCATGTGACTAATGCGA
31548282 TTAA
65 TTAA
* * * * *
31548286 ATGTGAGTAAATTTGATCAATATGTGATGTGATAAATGCTAAAATATTCATGTGACTAATGTGAT
1 ATGTGATTAAATGTGATCAATAAGTAATGTGATAAATGCTAAAATATTCATGTGACTAATGCGAT
31548351 TAA
66 TAA
*
31548354 ATTTGATTAATATGTG
1 ATGTGATTAA-ATGTG
31548370 TTGTGTTAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
68 39 0.55
69 32 0.45
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.39
Consensus pattern (68 bp):
ATGTGATTAAATGTGATCAATAAGTAATGTGATAAATGCTAAAATATTCATGTGACTAATGCGAT
TAA
Found at i:31563251 original size:18 final size:18
Alignment explanation
Indices: 31563207--31563253 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
31563197 TAACTCTTGT
*
31563207 CCAGTAATGTTCAAACGAG
1 CCAGT-ATGCTCAAACGAG
*
31563226 CTAGTATGCTCAAACGAG
1 CCAGTATGCTCAAACGAG
*
31563244 CCATTATGCT
1 CCAGTATGCT
31563254 ATTCCTTCCG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (18 bp):
CCAGTATGCTCAAACGAG
Found at i:31569727 original size:12 final size:11
Alignment explanation
Indices: 31569712--31569770 Score: 63
Period size: 12 Copynumber: 5.5 Consensus size: 11
31569702 AATATTTTAA
31569712 ATTTTACAAAAT
1 ATTTTA-AAAAT
31569724 ATTTT--AAAT
1 ATTTTAAAAAT
31569733 ATTTTAAAAAAT
1 ATTTT-AAAAAT
31569745 ATTTT--AAAT
1 ATTTTAAAAAT
31569754 ATTTTAAAAAAT
1 ATTTT-AAAAAT
31569766 ATTTT
1 ATTTT
31569771 TTATTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 18 0.44
12 23 0.56
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:31569732 original size:9 final size:9
Alignment explanation
Indices: 31569700--31569761 Score: 63
Period size: 9 Copynumber: 6.4 Consensus size: 9
31569690 AGAATTTTTA
31569700 TAAATATTT
1 TAAATATTT
31569709 TAAAT-TTT
1 TAAATATTT
*
31569717 ACAAAATATTT
1 --TAAATATTT
31569728 TAAATATTT
1 TAAATATTT
31569737 TAAAAAATATTT
1 T---AAATATTT
31569749 TAAATATTT
1 TAAATATTT
31569758 TAAA
1 TAAA
31569762 AAATATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
8 3 0.07
9 26 0.58
10 4 0.09
11 3 0.07
12 9 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (9 bp):
TAAATATTT
Found at i:31569779 original size:21 final size:21
Alignment explanation
Indices: 31569701--31569770 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
31569691 GAATTTTTAT
*
31569701 AAATATTTT-AA-ATTTTACA
1 AAATATTTTAAATATTTTAAA
31569720 AAATATTTTAAATATTTTAAA
1 AAATATTTTAAATATTTTAAA
31569741 AAATATTTTAAATATTTTAAA
1 AAATATTTTAAATATTTTAAA
31569762 AAATATTTT
1 AAATATTTT
31569771 TTATTTTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 9 0.19
20 2 0.04
21 37 0.77
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATATTTTAAATATTTTAAA
Found at i:31570011 original size:19 final size:19
Alignment explanation
Indices: 31569987--31570046 Score: 120
Period size: 19 Copynumber: 3.2 Consensus size: 19
31569977 TAAATTTCAT
31569987 AATTTTAAAAAATATTTTA
1 AATTTTAAAAAATATTTTA
31570006 AATTTTAAAAAATATTTTA
1 AATTTTAAAAAATATTTTA
31570025 AATTTTAAAAAATATTTTA
1 AATTTTAAAAAATATTTTA
31570044 AAT
1 AAT
31570047 ATTTTGATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTTAAAAAATATTTTA
Found at i:31570261 original size:19 final size:20
Alignment explanation
Indices: 31570237--31570275 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31570227 ATAAGTTTCA
*
31570237 AAATTTTT-ATAAATATTTT
1 AAATTTTTAAAAAATATTTT
31570256 AAATTTTTAAAAAATATTTT
1 AAATTTTTAAAAAATATTTT
31570276 GATTTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTTTTAAAAAATATTTT
Found at i:31580180 original size:29 final size:30
Alignment explanation
Indices: 31580123--31580200 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
31580113 GGGCTAAATA
31580123 AGGCCTATAAGTCGATTTTAATAATTAATT
1 AGGCCTATAAGTCGATTTTAATAATTAATT
* * *
31580153 AGGCCTTTAGGTCGTTTTTAA-AATTAATT
1 AGGCCTATAAGTCGATTTTAATAATTAATT
***
31580182 AGGGAAATAAGTCGATTTT
1 AGGCCTATAAGTCGATTTT
31580201 GATGGAAAGC
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 21 0.54
30 18 0.46
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (30 bp):
AGGCCTATAAGTCGATTTTAATAATTAATT
Found at i:31582367 original size:13 final size:13
Alignment explanation
Indices: 31582326--31582367 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
31582316 TGCGCGTATA
*
31582326 TGTATTCTAAATA
1 TGTATTCTAAATT
31582339 TGTGATTTCT-AATT
1 TGT-A-TTCTAAATT
31582353 TGTATTCTAAATT
1 TGTATTCTAAATT
31582366 TG
1 TG
31582368 CGGTTTCCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 4 0.16
13 10 0.40
14 7 0.28
15 4 0.16
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (13 bp):
TGTATTCTAAATT
Found at i:31591502 original size:39 final size:37
Alignment explanation
Indices: 31591459--31591554 Score: 95
Period size: 38 Copynumber: 2.5 Consensus size: 37
31591449 GAGTTACGGT
* *
31591459 GTTTACAGAGTCACCGTTAGTTCA-ACGATGTATTACAGC
1 GTTTACAGTGTCACCGTCAGTT-AGAC-A-GTATTACAGC
* * *
31591498 GTTTATAGTGTCACTGTCAGTTAGTACAGTATTACAGT
1 GTTTACAGTGTCACCGTCAGTTAG-ACAGTATTACAGC
*
31591536 GTTTACAGTGTCACTGTCA
1 GTTTACAGTGTCACCGTCA
31591555 ACTTAATGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
38 28 0.57
39 19 0.39
40 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (37 bp):
GTTTACAGTGTCACCGTCAGTTAGACAGTATTACAGC
Found at i:31594996 original size:21 final size:21
Alignment explanation
Indices: 31594972--31595022 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
31594962 TAGAAGTAGG
31594972 ACTTGTATCGGTAGAA-AAGTC
1 ACTTGTATCGGTAGAACAA-TC
* ** *
31594993 ACTTTTATATGTAGAACTATC
1 ACTTGTATCGGTAGAACAATC
31595014 ACTTGTATC
1 ACTTGTATC
31595023 AGTACAAATC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAATC
Found at i:31595093 original size:155 final size:155
Alignment explanation
Indices: 31594806--31595115 Score: 478
Period size: 155 Copynumber: 2.0 Consensus size: 155
31594796 TTTAACATCC
* * *
31594806 CTAGAGGTAAGACTTGTATCGGTAGAAAAGACACTTGTATTGGTAAAACTGTTACTTGTATCAGT
1 CTAGAAGTAAGACTTGTATCGGTAGAAAAGACACTTGTATTGGTAAAACTATCACTTGTATCAGT
* *
31594871 ACAAATTTGCACTATTCTTGAACTGTTTACTGACTTGAAAACTACCGATACTTATCTAACAGGTA
66 ACAAATCTGCACTATTCTTGAACTGTTTACTGACTTGAAAACTACCGATACTTATCTAACAGATA
* *
31594936 CCGGTAGAAGTCTCTAGAAATGTCT
131 CCGATAGAAGTCTCTAAAAATGTCT
* * * *
31594961 CTAGAAGTAGGACTTGTATCGGTAGAAAAGTCACTTTTATAT-GTAGAACTATCACTTGTATCAG
1 CTAGAAGTAAGACTTGTATCGGTAGAAAAGACACTTGTAT-TGGTAAAACTATCACTTGTATCAG
* *
31595025 TACAAATCTGCACTATTCTTGAACTGTTTACTGACTTGACAACTACCGATACTTATCTAATAGAT
65 TACAAATCTGCACTATTCTTGAACTGTTTACTGACTTGAAAACTACCGATACTTATCTAACAGAT
*
31595090 ACCGATAGAAGTCTTTAAAAATGTCT
130 ACCGATAGAAGTCTCTAAAAATGTCT
31595116 AAAATAACTT
Statistics
Matches: 140, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
155 139 0.99
156 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (155 bp):
CTAGAAGTAAGACTTGTATCGGTAGAAAAGACACTTGTATTGGTAAAACTATCACTTGTATCAGT
ACAAATCTGCACTATTCTTGAACTGTTTACTGACTTGAAAACTACCGATACTTATCTAACAGATA
CCGATAGAAGTCTCTAAAAATGTCT
Found at i:31601356 original size:21 final size:21
Alignment explanation
Indices: 31601330--31601373 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
31601320 ACCGACGCGA
31601330 TGGTTGGGGTACCGCATATGT
1 TGGTTGGGGTACCGCATATGT
31601351 TGGTTGGGGTACCGCATATGT
1 TGGTTGGGGTACCGCATATGT
31601372 TG
1 TG
31601374 CGAGTCCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.39, T:0.34
Consensus pattern (21 bp):
TGGTTGGGGTACCGCATATGT
Found at i:31603794 original size:16 final size:18
Alignment explanation
Indices: 31603768--31603800 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31603758 ATTATGAGTA
31603768 ATTTTTATAAT-ATTTTC
1 ATTTTTATAATAATTTTC
31603785 ATTTTT-TAATAATTTT
1 ATTTTTATAATAATTTT
31603801 TATAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTATAATAATTTTC
Found at i:31610153 original size:15 final size:15
Alignment explanation
Indices: 31610133--31610163 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31610123 TGTTTATTTG
31610133 TTATTTAACTTATTA
1 TTATTTAACTTATTA
*
31610148 TTATTTAACTTGTTA
1 TTATTTAACTTATTA
31610163 T
1 T
31610164 AAGACCCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTTAACTTATTA
Found at i:31613771 original size:26 final size:26
Alignment explanation
Indices: 31613730--31613926 Score: 182
Period size: 26 Copynumber: 7.7 Consensus size: 26
31613720 AAAAGTGTGC
31613730 AAGCTGGCGAGCGTAAACACGTAAAT
1 AAGCTGGCGAGCGTAAACACGTAAAT
* * * *
31613756 AAGCTGGCAAGTGTAAACGCATAAAT
1 AAGCTGGCGAGCGTAAACACGTAAAT
*** * ****
31613782 AAGCAAACGAGCATAAA-A-GTGTGC
1 AAGCTGGCGAGCGTAAACACGTAAAT
31613806 AAGCTGGCGAGCGTAAACACGTAAAT
1 AAGCTGGCGAGCGTAAACACGTAAAT
* * * *
31613832 AAGCTGGCAAGTGTAAACGCATAAAT
1 AAGCTGGCGAGCGTAAACACGTAAAT
* * * **
31613858 AAGTTGGTGAGTGTAAATGCGTAAAT
1 AAGCTGGCGAGCGTAAACACGTAAAT
*
31613884 AAGCTGACGAGCGTAAACACGTAAAT
1 AAGCTGGCGAGCGTAAACACGTAAAT
31613910 AAGCTGGCGAGCGTAAA
1 AAGCTGGCGAGCGTAAA
31613927 TGCATAATTG
Statistics
Matches: 129, Mismatches: 40, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
24 14 0.11
25 1 0.01
26 114 0.88
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (26 bp):
AAGCTGGCGAGCGTAAACACGTAAAT
Found at i:31613772 original size:76 final size:76
Alignment explanation
Indices: 31613680--31613860 Score: 344
Period size: 76 Copynumber: 2.4 Consensus size: 76
31613670 GTATTGAAAC
* *
31613680 AAGCTAGCAAGCGTAAACGCATAAATAAGCAAACGAGCATAAAAGTGTGCAAGCTGGCGAGCGTA
1 AAGCTGGCAAGTGTAAACGCATAAATAAGCAAACGAGCATAAAAGTGTGCAAGCTGGCGAGCGTA
31613745 AACACGTAAAT
66 AACACGTAAAT
31613756 AAGCTGGCAAGTGTAAACGCATAAATAAGCAAACGAGCATAAAAGTGTGCAAGCTGGCGAGCGTA
1 AAGCTGGCAAGTGTAAACGCATAAATAAGCAAACGAGCATAAAAGTGTGCAAGCTGGCGAGCGTA
31613821 AACACGTAAAT
66 AACACGTAAAT
31613832 AAGCTGGCAAGTGTAAACGCATAAATAAG
1 AAGCTGGCAAGTGTAAACGCATAAATAAG
31613861 TTGGTGAGTG
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 103 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.15
Consensus pattern (76 bp):
AAGCTGGCAAGTGTAAACGCATAAATAAGCAAACGAGCATAAAAGTGTGCAAGCTGGCGAGCGTA
AACACGTAAAT
Found at i:31620997 original size:50 final size:50
Alignment explanation
Indices: 31620911--31621092 Score: 204
Period size: 50 Copynumber: 3.6 Consensus size: 50
31620901 TGTATTGAAA
* * *
31620911 CAAGTTGGCGAGCGTAAACGCGTAAATAAGCAGACGAGCGTAAACGTGTG
1 CAAGTTGGCGAGCGTAAACACGTAAATAAGCTGACGAGCATAAACGTGTG
* * *
31620961 CAAGCTGGTGAGCGTAAACACATAAATAAGCTGACGAGCATAAACGTGTG
1 CAAGTTGGCGAGCGTAAACACGTAAATAAGCTGACGAGCATAAACGTGTG
* * ***
31621011 CAAGTTGGCAAGCGTAAACACGTAAATAAGCTGGA-AAGCATAAACGCATAAA
1 CAAGTTGGCGAGCGTAAACACGTAAATAAGCT-GACGAGCATAAACG--TGTG
* * *
31621063 TAAGTTGGCGAGTGTAAACGCGTAAATAAG
1 CAAGTTGGCGAGCGTAAACACGTAAATAAG
31621093 TTGGCAAGCG
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
50 82 0.74
51 2 0.02
52 27 0.24
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (50 bp):
CAAGTTGGCGAGCGTAAACACGTAAATAAGCTGACGAGCATAAACGTGTG
Found at i:31620999 original size:26 final size:26
Alignment explanation
Indices: 31620970--31621134 Score: 93
Period size: 26 Copynumber: 6.4 Consensus size: 26
31620960 GCAAGCTGGT
31620970 GAGCGTAAACACATAAATAAGCTGAC
1 GAGCGTAAACACATAAATAAGCTGAC
* * **** * *
31620996 GAGCAT-AA-ACGTGTGCAAGTTGGC
1 GAGCGTAAACACATAAATAAGCTGAC
* *
31621020 AAGCGTAAACACGTAAATAAGCTGGA-
1 GAGCGTAAACACATAAATAAGCT-GAC
* * * * *
31621046 AAGCATAAACGCATAAATAAGTTGGC
1 GAGCGTAAACACATAAATAAGCTGAC
* * * * *
31621072 GAGTGTAAACGCGTAAATAAGTTGGC
1 GAGCGTAAACACATAAATAAGCTGAC
* * *
31621098 AAGCGTAAACACATAAATAAGCTAAT
1 GAGCGTAAACACATAAATAAGCTGAC
31621124 GAGCGTAAACA
1 GAGCGTAAACA
31621135 TGTGCAAGCT
Statistics
Matches: 101, Mismatches: 34, Indels: 8
0.71 0.24 0.06
Matches are distributed among these distances:
24 13 0.13
25 5 0.05
26 82 0.81
27 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (26 bp):
GAGCGTAAACACATAAATAAGCTGAC
Found at i:31621089 original size:52 final size:52
Alignment explanation
Indices: 31621012--31621118 Score: 151
Period size: 52 Copynumber: 2.1 Consensus size: 52
31621002 AAACGTGTGC
*
31621012 AAGTTGGCAAGCGTAAACACGTAAATAAGCTGGAAAGCATAAACGCATAAAT
1 AAGTTGGCAAGCGTAAACACGTAAATAAGCTGGAAAGCATAAACACATAAAT
* * * * * *
31621064 AAGTTGGCGAGTGTAAACGCGTAAATAAGTTGGCAAGCGTAAACACATAAAT
1 AAGTTGGCAAGCGTAAACACGTAAATAAGCTGGAAAGCATAAACACATAAAT
31621116 AAG
1 AAG
31621119 CTAATGAGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (52 bp):
AAGTTGGCAAGCGTAAACACGTAAATAAGCTGGAAAGCATAAACACATAAAT
Found at i:31621132 original size:52 final size:52
Alignment explanation
Indices: 31621021--31621134 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 52
31621011 CAAGTTGGCA
* * **
31621021 AGCGTAAACACGTAAATAAGCTGGAAAGCATAAACGCATAAATAAGTTGGCG
1 AGCGTAAACACGTAAATAAGCTGGAAAGCATAAACACATAAATAAGCTAACG
* * * * * *
31621073 AGTGTAAACGCGTAAATAAGTTGGCAAGCGTAAACACATAAATAAGCTAATG
1 AGCGTAAACACGTAAATAAGCTGGAAAGCATAAACACATAAATAAGCTAACG
31621125 AGCGTAAACA
1 AGCGTAAACA
31621135 TGTGCAAGCT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (52 bp):
AGCGTAAACACGTAAATAAGCTGGAAAGCATAAACACATAAATAAGCTAACG
Found at i:31621133 original size:78 final size:77
Alignment explanation
Indices: 31620969--31621134 Score: 194
Period size: 78 Copynumber: 2.2 Consensus size: 77
31620959 TGCAAGCTGG
* * *
31620969 TGAGCGTAAACACATAAATAAGCTGACGAGCATAAACGTGTGCAAGTTGGCAAGCGTAAACACGT
1 TGAGCGTAAACACATAAATAAGCTGACGAGCATAAACGCGTACAAGTTGGCAAGCGTAAACACAT
31621034 AAATAAGCTGGAA
66 AAATAAGCT-GAA
* * * * ** *
31621047 --AGCATAAACGCATAAATAAGTTGGCGAGTGTAAACGCGTAAATAAGTTGGCAAGCGTAAACAC
1 TGAGCGTAAACACATAAATAAGCTGACGAGCATAAACGCGT--ACAAGTTGGCAAGCGTAAACAC
31621110 ATAAATAAGCT-AA
64 ATAAATAAGCTGAA
31621123 TGAGCGTAAACA
1 TGAGCGTAAACA
31621135 TGTGCAAGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
76 34 0.47
78 38 0.53
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.19
Consensus pattern (77 bp):
TGAGCGTAAACACATAAATAAGCTGACGAGCATAAACGCGTACAAGTTGGCAAGCGTAAACACAT
AAATAAGCTGAA
Found at i:31623188 original size:23 final size:24
Alignment explanation
Indices: 31623149--31623229 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
31623139 ATGTAAGCAC
31623149 TATA-GAAAAGGAAGTGTTATGGT
1 TATACGAAAAGGAAGTGTTATGGT
*
31623172 TATACGAAAAGG-TGTGTT-TGAG-
1 TATACGAAAAGGAAGTGTTATG-GT
* *
31623194 TATCCGAAAAGGAAATGTTATGGT
1 TATACGAAAAGGAAGTGTTATGGT
*
31623218 TATATGAAAAGG
1 TATACGAAAAGG
31623230 TGTTTTTGAG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
22 13 0.28
23 15 0.32
24 19 0.40
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (24 bp):
TATACGAAAAGGAAGTGTTATGGT
Found at i:31623204 original size:22 final size:22
Alignment explanation
Indices: 31623176--31623246 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
31623166 TATGGTTATA
31623176 CGAAAAGGTGTGTTTGAGTATC
1 CGAAAAGGTGTGTTTGAGTATC
** *
31623198 CGAAAAGGAAATGTTATG-GTTATA
1 CGAAAAGG-TGTGTT-TGAG-TATC
* *
31623222 TGAAAAGGTGTTTTTGAGTATC
1 CGAAAAGGTGTGTTTGAGTATC
31623244 CGA
1 CGA
31623247 TGTTATTCTG
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
22 15 0.42
23 9 0.25
24 12 0.33
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.32
Consensus pattern (22 bp):
CGAAAAGGTGTGTTTGAGTATC
Found at i:31623220 original size:46 final size:46
Alignment explanation
Indices: 31623153--31623246 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
31623143 AAGCACTATA
*
31623153 GAAAAGGAAGTGTTATGGTTATACGAAAAGGTGTGTTTGAGTATCC
1 GAAAAGGAAATGTTATGGTTATACGAAAAGGTGTGTTTGAGTATCC
* *
31623199 GAAAAGGAAATGTTATGGTTATATGAAAAGGTGTTTTTGAGTATCC
1 GAAAAGGAAATGTTATGGTTATACGAAAAGGTGTGTTTGAGTATCC
31623245 GA
1 GA
31623247 TGTTATTCTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (46 bp):
GAAAAGGAAATGTTATGGTTATACGAAAAGGTGTGTTTGAGTATCC
Found at i:31638653 original size:21 final size:23
Alignment explanation
Indices: 31638607--31638656 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
31638597 TTTTAAAGAT
* *
31638607 TTATTCTAAAATTCTAAAATAAA
1 TTATTATAAAATTATAAAATAAA
31638630 TTATTATAAAATTAT-AAA-AAA
1 TTATTATAAAATTATAAAATAAA
31638651 TTATTA
1 TTATTA
31638657 AATTATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
TTATTATAAAATTATAAAATAAA
Found at i:31638913 original size:7 final size:7
Alignment explanation
Indices: 31638901--31638933 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
31638891 GCATTCAACA
31638901 TCATTTT
1 TCATTTT
31638908 TCA-TTT
1 TCATTTT
31638914 TCA-TTT
1 TCATTTT
31638920 TCATTTT
1 TCATTTT
31638927 TCATTTT
1 TCATTTT
31638934 AGAGAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
TCATTTT
Found at i:31638916 original size:19 final size:19
Alignment explanation
Indices: 31638894--31638933 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31638884 TATTTTTGCA
31638894 TTCAACATCATTTTTCATT
1 TTCAACATCATTTTTCATT
***
31638913 TTCATTTTCATTTTTCATT
1 TTCAACATCATTTTTCATT
31638932 TT
1 TT
31638934 AGAGAAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCAACATCATTTTTCATT
Found at i:31639038 original size:57 final size:57
Alignment explanation
Indices: 31638906--31639035 Score: 160
Period size: 57 Copynumber: 2.3 Consensus size: 57
31638896 CAACATCATT
*
31638906 TTTCATTT-T-CATTTTCATTTTTCATTTTAGAGAAAGTTGCATTCATTTCCAAATGA
1 TTTCATTTCTCCATTTTCA-TTTTCATTTTAGAGAAAGATGCATTCATTTCCAAATGA
* * *
31638962 TTTCATTTCTTCATTTTCATTTTCATTTTGGAGAAA-AT-CATAATCATTTCCAAATGT
1 TTTCATTTCTCCATTTTCATTTTCATTTTAGAGAAAGATGCAT--TCATTTCCAAATGA
31639019 TTTCTATTTCTCCATTT
1 TTTC-ATTTCTCCATTT
31639036 CATCATTTCT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
55 3 0.05
56 9 0.14
57 34 0.52
58 19 0.29
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (57 bp):
TTTCATTTCTCCATTTTCATTTTCATTTTAGAGAAAGATGCATTCATTTCCAAATGA
Found at i:31649869 original size:22 final size:22
Alignment explanation
Indices: 31649841--31649892 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
31649831 GGTCTTTCAA
31649841 TCCGTCGTGGCCTCGCCATCGC
1 TCCGTCGTGGCCTCGCCATCGC
31649863 TCCGTCGTGGCCTCGCCATCGC
1 TCCGTCGTGGCCTCGCCATCGC
31649885 TCCGTCGT
1 TCCGTCGT
31649893 CTCCGGTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.04, C:0.44, G:0.27, T:0.25
Consensus pattern (22 bp):
TCCGTCGTGGCCTCGCCATCGC
Found at i:31653062 original size:93 final size:93
Alignment explanation
Indices: 31652903--31653089 Score: 356
Period size: 93 Copynumber: 2.0 Consensus size: 93
31652893 GGTAAGTCCC
*
31652903 AATGAATTAAATGTAATTGGAGCACCTCGATTATCTATATATTATATAAAACCAGCTCCTACGGG
1 AATGAATTAAATGTAATTGGAGCACCTCGATTATCTATAAATTATATAAAACCAGCTCCTACGGG
*
31652968 AGCCTTTAGGAGTTGATAGGGGTATTTT
66 AGCCTTTAGGAGTTGATAGAGGTATTTT
31652996 AATGAATTAAATGTAATTGGAGCACCTCGATTATCTATAAATTATATAAAACCAGCTCCTACGGG
1 AATGAATTAAATGTAATTGGAGCACCTCGATTATCTATAAATTATATAAAACCAGCTCCTACGGG
31653061 AGCCTTTAGGAGTTGATAGAGGTATTTT
66 AGCCTTTAGGAGTTGATAGAGGTATTTT
31653089 A
1 A
31653090 GGTAGTATAA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.33
Consensus pattern (93 bp):
AATGAATTAAATGTAATTGGAGCACCTCGATTATCTATAAATTATATAAAACCAGCTCCTACGGG
AGCCTTTAGGAGTTGATAGAGGTATTTT
Found at i:31654404 original size:20 final size:20
Alignment explanation
Indices: 31654379--31654417 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31654369 TGCAAACACC
*
31654379 GTCTCAAATACATCGTAAAT
1 GTCTCAAATACATCATAAAT
31654399 GTCTCAAATACATCATAAA
1 GTCTCAAATACATCATAAA
31654418 ATGCTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.28
Consensus pattern (20 bp):
GTCTCAAATACATCATAAAT
Found at i:31655289 original size:41 final size:41
Alignment explanation
Indices: 31655233--31655310 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
31655223 TTTTGTCTCG
31655233 AAAAAATTGTCTGTACTTATTATATCCGGGTTTTAAACTCA
1 AAAAAATTGTCTGTACTTATTATATCCGGGTTTTAAACTCA
31655274 AAAAAATTGTCTGTACTTATTATATCCGGGTTTTAAA
1 AAAAAATTGTCTGTACTTATTATATCCGGGTTTTAAA
31655311 TGGTTTTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (41 bp):
AAAAAATTGTCTGTACTTATTATATCCGGGTTTTAAACTCA
Found at i:31656223 original size:16 final size:18
Alignment explanation
Indices: 31656202--31656242 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
31656192 ATATATTAGA
31656202 TTAAATATAA-AAAAT-G
1 TTAAATATAATAAAATAG
*
31656218 TTAAATTTAATAAAATAG
1 TTAAATATAATAAAATAG
31656236 -TAAATAT
1 TTAAATAT
31656243 TATTTATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 9 0.43
17 11 0.52
18 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
TTAAATATAATAAAATAG
Found at i:31661582 original size:45 final size:45
Alignment explanation
Indices: 31661518--31661616 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 45
31661508 TTATTGCATC
* * *
31661518 GGCTCGTAAGAGCGATATACTATACTAGGAGCGATATACTGAATT
1 GGCTCGTAAAAGCGATATACTATACTAGGAGAGATATACTGAACT
* *
31661563 GGCTCGTAAAAGCGATATACTATACTGGGAGAGATATATTGAACT
1 GGCTCGTAAAAGCGATATACTATACTAGGAGAGATATACTGAACT
31661608 GGCTCGTAA
1 GGCTCGTAA
31661617 GAGAGATACT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (45 bp):
GGCTCGTAAAAGCGATATACTATACTAGGAGAGATATACTGAACT
Found at i:31661627 original size:19 final size:19
Alignment explanation
Indices: 31661605--31661677 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
31661595 GATATATTGA
*
31661605 ACTGGCTCGTAAGAGAGAT
1 ACTGGCTCGTAAGAGCGAT
* *
31661624 ACTGGTTCATAAGAGCGAT
1 ACTGGCTCGTAAGAGCGAT
* * *
31661643 ATTGGTTCGTAAGGGCGAT
1 ACTGGCTCGTAAGAGCGAT
31661662 ACTGGCTCGTAAGAGC
1 ACTGGCTCGTAAGAGC
31661678 AATATACTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (19 bp):
ACTGGCTCGTAAGAGCGAT
Found at i:31661708 original size:26 final size:26
Alignment explanation
Indices: 31661661--31661755 Score: 104
Period size: 26 Copynumber: 3.7 Consensus size: 26
31661651 GTAAGGGCGA
*
31661661 TACTGGCTCGTAAGAGCAATATACTG
1 TACTGGCTCGTAAGAGCGATATACTG
* *
31661687 TATTGGCTCGT-AGAAGCGATATATTG
1 TACTGGCTCGTAAG-AGCGATATACTG
* *
31661713 TACTGGCTCGTAAGAGCGATTTATTG
1 TACTGGCTCGTAAGAGCGATATACTG
*
31661739 -ACTAGGCTCGTATGAGC
1 TACT-GGCTCGTAAGAGC
31661756 TAAATTTACT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
25 5 0.08
26 53 0.88
27 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (26 bp):
TACTGGCTCGTAAGAGCGATATACTG
Found at i:31671237 original size:21 final size:21
Alignment explanation
Indices: 31671211--31671310 Score: 93
Period size: 21 Copynumber: 4.8 Consensus size: 21
31671201 ATTATATTAT
31671211 TGTTTTGGTGCTT-TTTTTTAC
1 TGTTTTGGTG-TTATTTTTTAC
31671232 TGTTTTGGTTGTTATTTTTTAC
1 TGTTTTGG-TGTTATTTTTTAC
* *
31671254 T-TTTTTGTGTTATTTTTTAT
1 TGTTTTGGTGTTATTTTTTAC
*
31671274 TATTTT-G-G-TACTTTTTTAC
1 TGTTTTGGTGTTA-TTTTTTAC
*
31671293 TGTTTTGGTTGTTGTTTT
1 TGTTTTGG-TGTTATTTT
31671311 CGTGTTGTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.03
19 13 0.20
20 15 0.23
21 19 0.29
22 16 0.24
23 1 0.02
ACGTcount: A:0.08, C:0.05, G:0.17, T:0.70
Consensus pattern (21 bp):
TGTTTTGGTGTTATTTTTTAC
Found at i:31671257 original size:20 final size:20
Alignment explanation
Indices: 31671224--31671310 Score: 56
Period size: 20 Copynumber: 4.2 Consensus size: 20
31671214 TTTGGTGCTT
31671224 TTTTTTACTGTTTTGGTTGTTA
1 TTTTTTAC-GTTTT-GTTGTTA
*
31671246 TTTTTTAC-TTTTTTGTGTTA
1 TTTTTTACGTTTTGT-TGTTA
*
31671266 TTTTTTA--TTATT-TTGGTA
1 TTTTTTACGTT-TTGTTGTTA
*
31671284 CTTTTTTACTGTTTTGGTTGTTG
1 -TTTTTTAC-GTTTT-GTTGTTA
31671307 TTTT
1 TTTT
31671311 CGTGTTGTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
18 4 0.08
19 11 0.21
20 18 0.34
21 2 0.04
22 14 0.26
23 4 0.08
ACGTcount: A:0.09, C:0.05, G:0.15, T:0.71
Consensus pattern (20 bp):
TTTTTTACGTTTTGTTGTTA
Found at i:31671310 original size:12 final size:12
Alignment explanation
Indices: 31671293--31671392 Score: 67
Period size: 12 Copynumber: 8.1 Consensus size: 12
31671283 ACTTTTTTAC
*
31671293 TGTTTTGGTTGT
1 TGTTTTTGTTGT
*
31671305 TGTTTTCG-TGT
1 TGTTTTTGTTGT
*
31671316 TGTTTTTGCTGT
1 TGTTTTTGTTGT
* *
31671328 TATTTTTGTTGC
1 TGTTTTTGTTGT
*
31671340 TGTTTTTGTTGA
1 TGTTTTTGTTGT
* * *
31671352 TATTTTCTTTTGC
1 TGTTTT-TGTTGT
31671365 TGCTATTTTGGTTGT
1 TG-T-TTTT-GTTGT
*
31671380 TATTTTTGTTGT
1 TGTTTTTGTTGT
31671392 T
1 T
31671393 TGGATTTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
11 10 0.14
12 40 0.58
13 9 0.13
14 3 0.04
15 7 0.10
ACGTcount: A:0.05, C:0.06, G:0.22, T:0.67
Consensus pattern (12 bp):
TGTTTTTGTTGT
Found at i:31671373 original size:28 final size:28
Alignment explanation
Indices: 31671331--31671385 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
31671321 TTGCTGTTAT
* * *
31671331 TTTTGTTGCTGTTTTTGTTGATATTTTC
1 TTTTGCTGCTATTTTGGTTGATATTTTC
*
31671359 TTTTGCTGCTATTTTGGTTGTTATTTT
1 TTTTGCTGCTATTTTGGTTGATATTTT
31671386 TGTTGTTTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.67
Consensus pattern (28 bp):
TTTTGCTGCTATTTTGGTTGATATTTTC
Found at i:31671932 original size:16 final size:17
Alignment explanation
Indices: 31671901--31671933 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31671891 TATCTTCAAT
31671901 ATTATATTAAAAATATA
1 ATTATATTAAAAATATA
*
31671918 ATTAT-TTATAAATATA
1 ATTATATTAAAAATATA
31671934 CTGGATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTATATTAAAAATATA
Found at i:31673366 original size:11 final size:11
Alignment explanation
Indices: 31673350--31673380 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
31673340 TTACTACCAT
31673350 TTCTTTCTTTC
1 TTCTTTCTTTC
*
31673361 TTCTTTCTTTG
1 TTCTTTCTTTC
31673372 TTCTTTCTT
1 TTCTTTCTT
31673381 CTATTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (11 bp):
TTCTTTCTTTC
Found at i:31674684 original size:22 final size:22
Alignment explanation
Indices: 31674659--31674700 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31674649 AGGATTTTGA
31674659 ATCTATATCTGATATACTCTAC
1 ATCTATATCTGATATACTCTAC
* *
31674681 ATCTGTATCTGATATGCTCT
1 ATCTATATCTGATATACTCT
31674701 CTGTACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (22 bp):
ATCTATATCTGATATACTCTAC
Found at i:31674778 original size:40 final size:40
Alignment explanation
Indices: 31674675--31674780 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 40
31674665 ATCTGATATA
* * * *
31674675 CTCTACATCTGTATCTGATATGCTCTCTGTACTTTTTATG
1 CTCTGCATCTATATCTGATATGCTCTCTATACTTGTTATG
* * *
31674715 CTATGCATCTATGA-CTAATATGCTCAT-TATACTTGTTGTG
1 CTCTGCATCTAT-ATCTGATATGCTC-TCTATACTTGTTATG
*
31674755 CTCTGCATCTATATCTGAGATGCTCT
1 CTCTGCATCTATATCTGATATGCTCT
31674781 GTTTTTTATT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
39 2 0.04
40 49 0.92
41 2 0.04
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (40 bp):
CTCTGCATCTATATCTGATATGCTCTCTATACTTGTTATG
Found at i:31686652 original size:21 final size:21
Alignment explanation
Indices: 31686628--31686681 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
31686618 TGAGACAATA
31686628 CTACCAATACAAGT-ATGACTT
1 CTACCAATACAAGTCATG-CTT
*
31686649 CTACCGAA-ACATGTCATGCTT
1 CTACC-AATACAAGTCATGCTT
*
31686670 CTACCGATACAA
1 CTACCAATACAA
31686682 AAAAACTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.04
21 21 0.78
22 5 0.19
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (21 bp):
CTACCAATACAAGTCATGCTT
Found at i:31701696 original size:39 final size:41
Alignment explanation
Indices: 31701638--31701719 Score: 114
Period size: 39 Copynumber: 2.0 Consensus size: 41
31701628 ATCAGACCCC
31701638 TTTAATTATTTTTCCTTTCA-TTTTCCTTAAAAAT-ATTCT
1 TTTAATTATTTTTCCTTTCATTTTTCCTTAAAAATGATTCT
** *
31701677 TTTAATTATTTTTTTTTTCATTTTTTCTTTAAAAATGATTCT
1 TTTAATTATTTTTCCTTTCA-TTTTTCCTTAAAAATGATTCT
31701719 T
1 T
31701720 GTCACCATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 18 0.49
41 13 0.35
42 6 0.16
ACGTcount: A:0.24, C:0.11, G:0.01, T:0.63
Consensus pattern (41 bp):
TTTAATTATTTTTCCTTTCATTTTTCCTTAAAAATGATTCT
Found at i:31701993 original size:18 final size:18
Alignment explanation
Indices: 31701970--31702010 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
31701960 TAAGAAACAG
31701970 AGAACCCAACACATTCAA
1 AGAACCCAACACATTCAA
*
31701988 AGAACCCAGCACATTCAA
1 AGAACCCAACACATTCAA
31702006 AGAAC
1 AGAAC
31702011 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.32, G:0.10, T:0.10
Consensus pattern (18 bp):
AGAACCCAACACATTCAA
Found at i:31705675 original size:16 final size:17
Alignment explanation
Indices: 31705654--31705687 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31705644 TCATATTTTT
*
31705654 TATTTAAA-AATAGAAA
1 TATTTAAATAATAAAAA
31705670 TATTTAAATAATAAAAA
1 TATTTAAATAATAAAAA
31705687 T
1 T
31705688 TGAACTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TATTTAAATAATAAAAA
Found at i:31713997 original size:16 final size:16
Alignment explanation
Indices: 31713971--31714017 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
31713961 CATTAGAATT
*
31713971 GAATAATGTTGTAATG
1 GAATAAAGTTGTAATG
*
31713987 GAATATAGTTGTAATG
1 GAATAAAGTTGTAATG
31714003 GAATAAAGTTGTAAT
1 GAATAAAGTTGTAAT
31714018 CAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.36
Consensus pattern (16 bp):
GAATAAAGTTGTAATG
Found at i:31714347 original size:15 final size:15
Alignment explanation
Indices: 31714299--31714359 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
31714289 AAATCATATT
31714299 AAATATTTTATTTTA
1 AAATATTTTATTTTA
**
31714314 AATTATATTTTGA-AATA
1 AA--ATATTTT-ATTTTA
31714331 AAATATTTTATTTTA
1 AAATATTTTATTTTA
* *
31714346 AAATGTTTCATTTT
1 AAATATTTTATTTT
31714360 TATATTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
14 1 0.03
15 23 0.64
17 11 0.31
18 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (15 bp):
AAATATTTTATTTTA
Found at i:31716816 original size:30 final size:30
Alignment explanation
Indices: 31716780--31716840 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
31716770 TTTGGTTTAA
*
31716780 ATGTTTTTGGTAAATTTTAATGTTACTTGC
1 ATGTTTTTGGCAAATTTTAATGTTACTTGC
31716810 ATGTTTTTGGCAAATTTTAATGTTACTTGC
1 ATGTTTTTGGCAAATTTTAATGTTACTTGC
31716840 A
1 A
31716841 AATGTTGGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (30 bp):
ATGTTTTTGGCAAATTTTAATGTTACTTGC
Found at i:31719674 original size:22 final size:22
Alignment explanation
Indices: 31719646--31719715 Score: 140
Period size: 22 Copynumber: 3.2 Consensus size: 22
31719636 GGGCCTTTAC
31719646 TTTAGCAATTACGAATGATAAT
1 TTTAGCAATTACGAATGATAAT
31719668 TTTAGCAATTACGAATGATAAT
1 TTTAGCAATTACGAATGATAAT
31719690 TTTAGCAATTACGAATGATAAT
1 TTTAGCAATTACGAATGATAAT
31719712 TTTA
1 TTTA
31719716 CATCCAAGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (22 bp):
TTTAGCAATTACGAATGATAAT
Found at i:31720307 original size:20 final size:20
Alignment explanation
Indices: 31720282--31720323 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31720272 ATCTATGATC
31720282 ATCTTCGTGGTAATGAAACG
1 ATCTTCGTGGTAATGAAACG
31720302 ATCTTCGTGGTAATGAAACG
1 ATCTTCGTGGTAATGAAACG
31720322 AT
1 AT
31720324 AATCGCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (20 bp):
ATCTTCGTGGTAATGAAACG
Found at i:31722586 original size:34 final size:34
Alignment explanation
Indices: 31722543--31722612 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
31722533 CACAATGAAC
31722543 AAAGATGAAGTTCAAAAGATGGAACAAATAGGCA
1 AAAGATGAAGTTCAAAAGATGGAACAAATAGGCA
*
31722577 AAAGATGAAGTTCAAAAGATGGAACAAATGGGCA
1 AAAGATGAAGTTCAAAAGATGGAACAAATAGGCA
31722611 AA
1 AA
31722613 CGTGCTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.53, C:0.09, G:0.24, T:0.14
Consensus pattern (34 bp):
AAAGATGAAGTTCAAAAGATGGAACAAATAGGCA
Found at i:31749464 original size:51 final size:51
Alignment explanation
Indices: 31749397--31749588 Score: 276
Period size: 51 Copynumber: 3.8 Consensus size: 51
31749387 TCATATAGGA
* ** * * * * *
31749397 ATTCATATACTCACGATGACACAAAGTTATCGGACCCTTAATCCATCATGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
*
31749448 ATTCATTTACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
*
31749499 ATTCATTTACTCACGATGATACTTAGTCATCGGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
* *
31749550 ATTCATTTACTCACGATGACACTTAGTCATTGAACCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTT
31749589 TTGTTTATAG
Statistics
Matches: 127, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 127 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
Found at i:31754549 original size:3 final size:3
Alignment explanation
Indices: 31754541--31754588 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
31754531 AAAATTCCAA
* *
31754541 AAT AAT AAT ATT AAT AAT AAT AA- AAA AAT AAT AAAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT
31754587 AA
1 AA
31754589 ACCAAAATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.79
4 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:31754578 original size:7 final size:7
Alignment explanation
Indices: 31754540--31754589 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
31754530 TAAAATTCCA
31754540 AAATAAT
1 AAATAAT
31754547 AATATTAAT
1 AA-A-TAAT
31754556 -AATAAT
1 AAATAAT
31754562 -AA-AA-
1 AAATAAT
31754566 AAATAAT
1 AAATAAT
31754573 AAATAAT
1 AAATAAT
31754580 AAATAAT
1 AAATAAT
31754587 AAA
1 AAA
31754590 CCAAAATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
5 4 0.11
6 8 0.21
7 20 0.53
8 2 0.05
9 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:31755647 original size:7 final size:7
Alignment explanation
Indices: 31755635--31755673 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
31755625 TTCAAAAAAA
31755635 GTCAACG
1 GTCAACG
31755642 GTCAACG
1 GTCAACG
31755649 GTCAAAC-
1 GTC-AACG
*
31755656 GTCAAAG
1 GTCAACG
31755663 GTCAACG
1 GTCAACG
31755670 GTCA
1 GTCA
31755674 GTCAACGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 2 0.07
7 23 0.82
8 3 0.11
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:31758993 original size:51 final size:51
Alignment explanation
Indices: 31758817--31759053 Score: 280
Period size: 51 Copynumber: 4.6 Consensus size: 51
31758807 TTTCATTTAA
* * ** * *
31758817 TACTCACGATGTCA-TATAGTTATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
** * * * *
31758870 TACTCACGATGACACAAAGTTATCGGACCCTTAATCCATCATGGATTCA-T
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
31758920 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
31758971 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * *
31759022 TACTCACAATAACACTTAGTCATCAGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
31759054 TTGTTTATAG
Statistics
Matches: 162, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 42 0.26
51 86 0.53
52 9 0.06
53 25 0.15
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:31758996 original size:101 final size:103
Alignment explanation
Indices: 31758817--31759053 Score: 282
Period size: 101 Copynumber: 2.3 Consensus size: 103
31758807 TTTCATTTAA
* * ** *
31758817 TACTCACGATGTCA-TATAGTTATCGGACCTCTTGTTCCATATAGGAATTCATATACTCACGATG
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGGAATTCATATACTCACGATG
* * *
31758881 ACACAAAGTTATCGGACCCTTAATCCATCATGGATTCA-T
64 ACACAAAGTCATCGGACCCTTAATCCATAAAGGATTCATT
* *
31758920 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG-ATTCATTTACTCACGATGAC
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGAATTCATATACTCACGATGAC
** * *
31758984 ACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
66 ACAAAGTCATCGGACCCTTAATCCATAAAGGATTCATT
* * *
31759022 TACTCACAATAACACTTAGTCATCAGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
31759054 TTGTTTATAG
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
101 48 0.42
102 40 0.35
103 26 0.23
104 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (103 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGAATTCATATACTCACGATGAC
ACAAAGTCATCGGACCCTTAATCCATAAAGGATTCATT
Found at i:31762029 original size:101 final size:101
Alignment explanation
Indices: 31761914--31762106 Score: 341
Period size: 101 Copynumber: 1.9 Consensus size: 101
31761904 AAAGAATATG
* *
31761914 TATCGATTTTAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACCATACCAAGTATGTTAGG
1 TATCGATTTTAAATAGAATATTCAATTACTTAGGTTCAAAGAAAAACCATACCAAGTACGTTAGG
* *
31761979 GCACAATTTCTCGAGTTCCCTAAAATATTGAACATT
66 ACACAATTTCTCAAGTTCCCTAAAATATTGAACATT
*
31762015 TATCGATTTTAAATAGAATATTCAATTACTTAGGTTCAAAGAAAAACCATACCTAGTACGTTAGG
1 TATCGATTTTAAATAGAATATTCAATTACTTAGGTTCAAAGAAAAACCATACCAAGTACGTTAGG
31762080 ACACAATTTCTCAAGTTCCCTAAAATA
66 ACACAATTTCTCAAGTTCCCTAAAATA
31762107 GAAGAACATT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 87 1.00
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (101 bp):
TATCGATTTTAAATAGAATATTCAATTACTTAGGTTCAAAGAAAAACCATACCAAGTACGTTAGG
ACACAATTTCTCAAGTTCCCTAAAATATTGAACATT
Found at i:31763500 original size:13 final size:13
Alignment explanation
Indices: 31763477--31763510 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
31763467 ATCATGCTAT
31763477 TTTGTTCTTTTCTG
1 TTTG-TCTTTTCTG
*
31763491 TTTGTCTTTTGTG
1 TTTGTCTTTTCTG
31763504 TTTGTCT
1 TTTGTCT
31763511 GTTTTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.00, C:0.12, G:0.18, T:0.71
Consensus pattern (13 bp):
TTTGTCTTTTCTG
Found at i:31763933 original size:15 final size:15
Alignment explanation
Indices: 31763913--31763964 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
31763903 ACCTCAAAAA
31763913 TCAAAATAAAAACCC
1 TCAAAATAAAAACCC
*
31763928 TCAAAAACCTCAAAA--C
1 TC-AAAA--TAAAAACCC
31763944 TCAAAATAAAAACCC
1 TCAAAATAAAAACCC
31763959 TCAAAA
1 TCAAAA
31763965 CATAAACACA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 5 0.17
15 13 0.43
16 7 0.23
18 5 0.17
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (15 bp):
TCAAAATAAAAACCC
Found at i:31763938 original size:31 final size:31
Alignment explanation
Indices: 31763902--31763964 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
31763892 AGATGAATAT
31763902 AACCTCAAAAATCAAAATAAAAACCCTCAAA
1 AACCTCAAAAATCAAAATAAAAACCCTCAAA
*
31763933 AACCTCAAAACTCAAAATAAAAACCCTCAAA
1 AACCTCAAAAATCAAAATAAAAACCCTCAAA
31763964 A
1 A
31763965 CATAAACACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (31 bp):
AACCTCAAAAATCAAAATAAAAACCCTCAAA
Found at i:31769875 original size:27 final size:27
Alignment explanation
Indices: 31769828--31769891 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
31769818 AAATATTCTC
*
31769828 TAAATTAAT-AAATGTTAATTTATCAA
1 TAAATTAATAAAATATTAATTTATCAA
* *
31769854 TAAATTAATAAAATATTCATTTATCGA
1 TAAATTAATAAAATATTAATTTATCAA
*
31769881 TAAACTAATAA
1 TAAATTAATAA
31769892 TCTAGCGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (27 bp):
TAAATTAATAAAATATTAATTTATCAA
Found at i:31774580 original size:28 final size:28
Alignment explanation
Indices: 31774542--31774596 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
31774532 AAATGAGCAT
* *
31774542 CATGACCTTTGGGTTAATAGGGAGTAAG
1 CATGACCTTTGGGTCAACAGGGAGTAAG
*
31774570 CATGACTTTTGGGTCAACAGGGAGTAA
1 CATGACCTTTGGGTCAACAGGGAGTAA
31774597 ATCAGATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACAGGGAGTAAG
Found at i:31782394 original size:17 final size:17
Alignment explanation
Indices: 31782372--31782413 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
31782362 CTCCCTTGAC
31782372 CTTTAACCTTCCATATT
1 CTTTAACCTTCCATATT
*
31782389 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
31782406 CTTGTAAC
1 CTT-TAAC
31782414 TACTTTTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.24, C:0.26, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:31787767 original size:17 final size:17
Alignment explanation
Indices: 31787747--31787788 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
31787737 CTCCCTTGAC
31787747 CTTTAACCTTCCATATT
1 CTTTAACCTTCCATATT
*
31787764 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
31787781 CTTGTAAC
1 CTT-TAAC
31787789 TACTTTTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.24, C:0.26, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:31788777 original size:74 final size:74
Alignment explanation
Indices: 31788696--31788838 Score: 218
Period size: 74 Copynumber: 1.9 Consensus size: 74
31788686 TATTATATTG
**
31788696 AAATGACAAACATAAGAAATAAGAAGAATATAAAATTCTGTTTCTAAT-GTACATT-AAATTCTT
1 AAATGACAAACATAAGAAATAAGAAGAATATAAAATTCCATTTCTAATAG-ACATTAAAATT-TT
31788759 AAAGTACATCA
64 AAAGTACATCA
* *
31788770 AAATGACAAACATAATAAATAAGAAGAATATACAATTCCATTTCTAATAGACATTAAAATTTTAA
1 AAATGACAAACATAAGAAATAAGAAGAATATAAAATTCCATTTCTAATAGACATTAAAATTTTAA
31788835 AGTA
66 AGTA
31788839 TATTAAATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
74 57 0.90
75 6 0.10
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.29
Consensus pattern (74 bp):
AAATGACAAACATAAGAAATAAGAAGAATATAAAATTCCATTTCTAATAGACATTAAAATTTTAA
AGTACATCA
Found at i:31790580 original size:41 final size:41
Alignment explanation
Indices: 31790523--31790618 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
31790513 TAATTTTATT
*
31790523 TTAACAAGAATTCTAGTCGCCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
31790564 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
31790605 TTGACAAGAATTCT
1 TTAACAAGAATTCT
31790619 CTACGAACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.35, C:0.29, G:0.07, T:0.28
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:31790630 original size:17 final size:17
Alignment explanation
Indices: 31790608--31790646 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
31790598 CTCCACCTTG
* *
31790608 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
31790625 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
31790642 ACAAG
1 ACAAG
31790647 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:31793697 original size:15 final size:15
Alignment explanation
Indices: 31793661--31793693 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
31793651 TTGTAGCACT
31793661 CTTTCTTAATGTGTC
1 CTTTCTTAATGTGTC
31793676 CTTTCTTAATGTG-C
1 CTTTCTTAATGTGTC
31793690 CTTT
1 CTTT
31793694 TCTTCTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.12, C:0.21, G:0.12, T:0.55
Consensus pattern (15 bp):
CTTTCTTAATGTGTC
Found at i:31801734 original size:47 final size:47
Alignment explanation
Indices: 31801676--31801775 Score: 175
Period size: 47 Copynumber: 2.1 Consensus size: 47
31801666 TCCAATTAAG
31801676 TTAG-GAAAAGGGAGATTTGTTGGGTGCAACCCTTCGTAATTGAGAA
1 TTAGAGAAAAGGGAGATTTGTTGGGTGCAACCCTTCGTAATTGAGAA
* *
31801722 TTAGAGAAAAGGGATATTTGTTGGGTGCAATCCTTCGTAATTGAGAA
1 TTAGAGAAAAGGGAGATTTGTTGGGTGCAACCCTTCGTAATTGAGAA
31801769 TTAGAGA
1 TTAGAGA
31801776 GATGAACCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 4 0.08
47 47 0.92
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
TTAGAGAAAAGGGAGATTTGTTGGGTGCAACCCTTCGTAATTGAGAA
Found at i:31802069 original size:24 final size:25
Alignment explanation
Indices: 31802042--31802088 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
31802032 ATAGAGAGAG
31802042 AGCCATCATTATGTGAGA-ATTGTA
1 AGCCATCATTATGTGAGATATTGTA
* *
31802066 AGCCATTATTGTGTGAGATATTG
1 AGCCATCATTATGTGAGATATTG
31802089 AATGTAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (25 bp):
AGCCATCATTATGTGAGATATTGTA
Found at i:31802522 original size:5 final size:5
Alignment explanation
Indices: 31802497--31802547 Score: 61
Period size: 5 Copynumber: 10.4 Consensus size: 5
31802487 GCAATATTAT
* *
31802497 TAATA -AAT- TAATA TAATTA TAATA TAATA TAATA CAATA CAATA TAATA
1 TAATA TAATA TAATA TAA-TA TAATA TAATA TAATA TAATA TAATA TAATA
31802546 TA
1 TA
31802548 TTCAACTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 6 0.15
5 30 0.73
6 5 0.12
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (5 bp):
TAATA
Found at i:31803327 original size:22 final size:22
Alignment explanation
Indices: 31803302--31803369 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
31803292 AAACATTTAA
31803302 TACAATTAATTAAATTTAAAAT
1 TACAATTAATTAAATTTAAAAT
*
31803324 TACAATGTAATTATA-TTAATATAT
1 TACAAT-TAATTAAATTTAA-A-AT
**
31803348 TA-AAAAAATTAAATTTAAAAT
1 TACAATTAATTAAATTTAAAAT
31803369 T
1 T
31803370 TTATAAATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
21 3 0.08
22 17 0.45
23 14 0.37
24 4 0.11
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (22 bp):
TACAATTAATTAAATTTAAAAT
Found at i:31813216 original size:17 final size:17
Alignment explanation
Indices: 31813194--31813317 Score: 51
Period size: 17 Copynumber: 7.2 Consensus size: 17
31813184 AACCACTGTA
31813194 TATGCGAGCCTATATGT
1 TATGCGAGCCTATATGT
* * * *
31813211 TATGCGATCC-CTAGGAA
1 TATGCGAGCCTATATG-T
*
31813228 CATGCGA-CCTTATATGT
1 TATGCGAGCC-TATATGT
* *
31813245 TATGCGAACCT-TAGGT
1 TATGCGAGCCTATATGT
31813261 GTATGC-AGGCCTATATGAT
1 -TATGCGA-GCCTATATG-T
* * *
31813280 TATGCGAACC-CTAGGT
1 TATGCGAGCCTATATGT
* *
31813296 ACATGCGAGCCTAAATGT
1 -TATGCGAGCCTATATGT
31813314 TATG
1 TATG
31813318 TGAAACTATG
Statistics
Matches: 75, Mismatches: 21, Indels: 22
0.64 0.18 0.19
Matches are distributed among these distances:
16 11 0.15
17 44 0.59
18 18 0.24
19 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (17 bp):
TATGCGAGCCTATATGT
Found at i:31813242 original size:34 final size:34
Alignment explanation
Indices: 31813195--31813317 Score: 151
Period size: 34 Copynumber: 3.6 Consensus size: 34
31813185 ACCACTGTAT
* *
31813195 ATGCGAGCCTATATGTTATGCGATCCCTAGGAAC
1 ATGCGAGCCTATATGTTATGCGAACCCTAGGTAC
* **
31813229 ATGCGA-CCTTATATGTTATGCGAACCTTAGGTGT
1 ATGCGAGCC-TATATGTTATGCGAACCCTAGGTAC
31813263 ATGC-AGGCCTATATGATTATGCGAACCCTAGGTAC
1 ATGCGA-GCCTATATG-TTATGCGAACCCTAGGTAC
*
31813298 ATGCGAGCCTAAATGTTATG
1 ATGCGAGCCTATATGTTATG
31813318 TGAAACTATG
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
33 3 0.04
34 41 0.55
35 30 0.40
36 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (34 bp):
ATGCGAGCCTATATGTTATGCGAACCCTAGGTAC
Found at i:31813522 original size:43 final size:43
Alignment explanation
Indices: 31813464--31813592 Score: 170
Period size: 43 Copynumber: 3.0 Consensus size: 43
31813454 CATATAATGC
* * *
31813464 AAGACCATGGTCTTTAGCGGCGCTTTTCCCATAAACGCCGCTA
1 AAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
* * *
31813507 AAGATCATGTTCTTTAGCGGCGCTTTCCCCACAAACGCCGCTA
1 AAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
* * *
31813550 AAGAACATGATCTTTAGCGACGCTTTT-CCACAAATGCCACTA
1 AAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
31813592 A
1 A
31813593 CATTTAACTA
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
42 14 0.18
43 62 0.82
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (43 bp):
AAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
Found at i:31820384 original size:42 final size:42
Alignment explanation
Indices: 31820315--31820536 Score: 209
Period size: 41 Copynumber: 5.3 Consensus size: 42
31820305 TTTAAATAAA
* *
31820315 TTAGCGGCGCTTATTAGAAAAGTGCCGCTAATGACCTGACCT
1 TTAGCGGCGCTTATTAGAAAAGCGCCGCTAATGACCCGACCT
* *
31820357 TTAGCGGCGCTTTTTATATAAA-CGCCGCTAATGACCCGACCT
1 TTAGCGGCGCTTATTAGA-AAAGCGCCGCTAATGACCCGACCT
* ** * **
31820399 TTAGTGGCGCTT-GCAGGAAAGAACCGCTAATGACCCGACCT
1 TTAGCGGCGCTTATTAGAAAAGCGCCGCTAATGACCCGACCT
* ** * *
31820440 TTCGCGGCGCTTA-CGGGAAAGCGCCGCTAATGACTCGACCT
1 TTAGCGGCGCTTATTAGAAAAGCGCCGCTAATGACCCGACCT
* * * * *
31820481 TTAGTGGCACTT-GTGGGAAAGCGCCGCTAATGACCCGACCTT
1 TTAGCGGCGCTTATTAGAAAAGCGCCGCTAATGACCCGACC-T
*
31820523 TTAGCGGTGCTTAT
1 TTAGCGGCGCTTAT
31820537 GACCCGACCT
Statistics
Matches: 148, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
40 3 0.02
41 87 0.59
42 55 0.37
43 3 0.02
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.25
Consensus pattern (42 bp):
TTAGCGGCGCTTATTAGAAAAGCGCCGCTAATGACCCGACCT
Found at i:31820437 original size:41 final size:41
Alignment explanation
Indices: 31820333--31820523 Score: 211
Period size: 41 Copynumber: 4.6 Consensus size: 41
31820323 GCTTATTAGA
* * * *****
31820333 AAAGTGCCGCTAATGACCTGACCTTTAGCGGCGCTTTTTAT
1 AAAGCGCCGCTAATGACCCGACCTTTAGTGGCGCTTGCGGG
* *
31820374 ATAAACGCCGCTAATGACCCGACCTTTAGTGGCGCTTGCAGG
1 A-AAGCGCCGCTAATGACCCGACCTTTAGTGGCGCTTGCGGG
** * * *
31820416 AAAGAACCGCTAATGACCCGACCTTTCGCGGCGCTTACGGG
1 AAAGCGCCGCTAATGACCCGACCTTTAGTGGCGCTTGCGGG
* * *
31820457 AAAGCGCCGCTAATGACTCGACCTTTAGTGGCACTTGTGGG
1 AAAGCGCCGCTAATGACCCGACCTTTAGTGGCGCTTGCGGG
31820498 AAAGCGCCGCTAATGACCCGACCTTT
1 AAAGCGCCGCTAATGACCCGACCTTT
31820524 TAGCGGTGCT
Statistics
Matches: 124, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
41 92 0.74
42 32 0.26
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (41 bp):
AAAGCGCCGCTAATGACCCGACCTTTAGTGGCGCTTGCGGG
Found at i:31820439 original size:83 final size:82
Alignment explanation
Indices: 31820339--31820535 Score: 241
Period size: 82 Copynumber: 2.4 Consensus size: 82
31820329 TAGAAAAGTG
* *** *
31820339 CCGCTAATGACCTGACCTTTAGCGGCGCTTTTTATATAAACGCCGCTAATGACCCGACCTTTAGT
1 CCGCTAATGACCCGACCTTTAGCGGCGCTTACGAGA-AAACGCCGCTAATGACCCGACCTTTAGT
*
31820404 GGCGCTTGCAGGAAAGAA
65 GGCACTTGCAGGAAAGAA
* * * *
31820422 CCGCTAATGACCCGACCTTTCGCGGCGCTTACGGGAAAGCGCCGCTAATGACTCGACCTTTAGTG
1 CCGCTAATGACCCGACCTTTAGCGGCGCTTACGAGAAAACGCCGCTAATGACCCGACCTTTAGTG
** **
31820487 GCACTTGTGGGAAAGCG
66 GCACTTGCAGGAAAGAA
*
31820504 CCGCTAATGACCCGACCTTTTAGCGGTGCTTA
1 CCGCTAATGACCCGACC-TTTAGCGGCGCTTA
31820536 TGACCCGACC
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
82 56 0.58
83 41 0.42
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.24
Consensus pattern (82 bp):
CCGCTAATGACCCGACCTTTAGCGGCGCTTACGAGAAAACGCCGCTAATGACCCGACCTTTAGTG
GCACTTGCAGGAAAGAA
Found at i:31820558 original size:24 final size:25
Alignment explanation
Indices: 31820505--31820558 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
31820495 GGGAAAGCGC
* *
31820505 CGCTAATGACCCGACCTTTTAGCGG
1 CGCTTATGACCCGACCTTTTAGCAG
*
31820530 TGCTTATGACCCGACC-TTTAGCAG
1 CGCTTATGACCCGACCTTTTAGCAG
31820554 CGCTT
1 CGCTT
31820559 GTGGAAAAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.19, C:0.31, G:0.22, T:0.28
Consensus pattern (25 bp):
CGCTTATGACCCGACCTTTTAGCAG
Found at i:31820575 original size:66 final size:65
Alignment explanation
Indices: 31820459--31820599 Score: 192
Period size: 66 Copynumber: 2.2 Consensus size: 65
31820449 CTTACGGGAA
* * * ** * *
31820459 AGCGCCGCTAATGACTCGACCTTTAGTGGCACTTGTGGGAAAGCGCCGCTAATGACCCGACCTTT
1 AGCGGCGCTTATGACCCGACCTTTAGCAGCACTTGTGGAAAAGCACCGCTAATGACCCGACC-TT
31820524 T
65 T
* *
31820525 AGCGGTGCTTATGACCCGACCTTTAGCAGCGCTTGTGGAAAAGCACCGCTAATGACCCGACCTTT
1 AGCGGCGCTTATGACCCGACCTTTAGCAGCACTTGTGGAAAAGCACCGCTAATGACCCGACCTTT
31820590 AGCGGCGCTT
1 AGCGGCGCTT
31820600 TGGGTAAAGC
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
65 12 0.18
66 53 0.82
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.23
Consensus pattern (65 bp):
AGCGGCGCTTATGACCCGACCTTTAGCAGCACTTGTGGAAAAGCACCGCTAATGACCCGACCTTT
Found at i:31820617 original size:107 final size:106
Alignment explanation
Indices: 31820428--31820634 Score: 299
Period size: 107 Copynumber: 1.9 Consensus size: 106
31820418 AGAACCGCTA
* * * * * *
31820428 ATGACCCGACCTTTCGCGGCGCTTACGGGAAAGCGCCGCTAATGACTCGACCTTTAGTGGCACTT
1 ATGACCCGACCTTTAGCAGCGCTTACGGAAAAGCACCGCTAATGACCCGACCTTTAGCGGCACTT
31820493 GTGGGAAAGCGCCGCTAATGACCCGACCTTTTAGCGGTGCTT
66 GTGGGAAAGCGCCGCTAATGACCCGACC-TTTAGCGGTGCTT
** *
31820535 ATGACCCGACCTTTAGCAGCGCTTGTGGAAAAGCACCGCTAATGACCCGACCTTTAGCGGCGCTT
1 ATGACCCGACCTTTAGCAGCGCTTACGGAAAAGCACCGCTAATGACCCGACCTTTAGCGGCACTT
*
31820600 -TGGGTAAAGCGCTGCTAATGACCCGACCTTTAGCG
66 GTGGG-AAAGCGCCGCTAATGACCCGACCTTTAGCG
31820635 ACGCTTGGGG
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
106 11 0.12
107 78 0.88
ACGTcount: A:0.21, C:0.29, G:0.27, T:0.23
Consensus pattern (106 bp):
ATGACCCGACCTTTAGCAGCGCTTACGGAAAAGCACCGCTAATGACCCGACCTTTAGCGGCACTT
GTGGGAAAGCGCCGCTAATGACCCGACCTTTAGCGGTGCTT
Found at i:31820656 original size:148 final size:147
Alignment explanation
Indices: 31820382--31820681 Score: 424
Period size: 148 Copynumber: 2.0 Consensus size: 147
31820372 ATATAAACGC
* ** *
31820382 CGCTAATGACCCGACCTTTAGTGGCGCTTGCAGGAAAGAACCGCTAATGACCCGACCTTTCGCGG
1 CGCTTATGACCCGACCTTTAGCAGCGCTTGCAGGAAAGAACCGCTAATGACCCGACCTTTAGCGG
* * * * *
31820447 CGCTTACGGGAAAGCGCCGCTAATGACTCGACCTTTAGTGGCACTTGTGGGAAAGCGCCGCTAAT
66 CGCTTACGGGAAAGCGCCGCTAATGACCCGACCTTTAGCGACACTTGGGGGAAAGCACCGCTAAT
31820512 GACCCGACCTTTTAGCGG
131 GACCCGACC-TTTAGCGG
* * *
31820530 TGCTTATGACCCGACCTTTAGCAGCGCTTG-TGGAAAAGCACCGCTAATGACCCGACCTTTAGCG
1 CGCTTATGACCCGACCTTTAGCAGCGCTTGCAGG-AAAGAACCGCTAATGACCCGACCTTTAGCG
* * *
31820594 GCGCTT-TGGGTAAAGCGCTGCTAATGACCCGACCTTTAGCGACGCTTGGGGGAAAGCACCGCTA
65 GCGCTTACGGG-AAAGCGCCGCTAATGACCCGACCTTTAGCGACACTTGGGGGAAAGCACCGCTA
31820658 ATGACCCGACCTTTAGCGG
129 ATGACCCGACCTTTAGCGG
31820677 CGCTT
1 CGCTT
31820682 GGGAGAAAGC
Statistics
Matches: 134, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
147 17 0.13
148 117 0.87
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22
Consensus pattern (147 bp):
CGCTTATGACCCGACCTTTAGCAGCGCTTGCAGGAAAGAACCGCTAATGACCCGACCTTTAGCGG
CGCTTACGGGAAAGCGCCGCTAATGACCCGACCTTTAGCGACACTTGGGGGAAAGCACCGCTAAT
GACCCGACCTTTAGCGG
Found at i:31820672 original size:82 final size:82
Alignment explanation
Indices: 31820535--31820782 Score: 360
Period size: 82 Copynumber: 3.0 Consensus size: 82
31820525 AGCGGTGCTT
* *
31820535 ATGACCCGACCTTTAGC-AGCGCTTGTGGAAAAGCACCGCTAATGACCCGACCTTTAGCGGCGCT
1 ATGACCCGACCTTTAGCGA-CGCTTGGGGGAAAGCACCGCTAATGACCCGACCTTTAGCGGCGCT
* *
31820599 TTGGGTAAAGCGCTGCTA
65 TTGGGAAAAGCGCCGCTA
31820617 ATGACCCGACCTTTAGCGACGCTTGGGGGAAAGCACCGCTAATGACCCGACCTTTAGCGGCGC-T
1 ATGACCCGACCTTTAGCGACGCTTGGGGGAAAGCACCGCTAATGACCCGACCTTTAGCGGCGCTT
31820681 TGGGAGAAAGCGCCGCTA
66 TGGGA-AAAGCGCCGCTA
* *** *
31820699 ATGACCCGACCTTTAGCGGCGCTTGGGGGAAAGCACCGCTAATG-CTTTACCTTTTGCGGCGCAT
1 ATGACCCGACCTTTAGCGACGCTTGGGGGAAAGCACCGCTAATGACCCGACCTTTAGCGGCGC-T
31820763 TT-GGAAAAGCGCCGCTA
65 TTGGGAAAAGCGCCGCTA
31820780 ATG
1 ATG
31820783 CTTTACCTTT
Statistics
Matches: 153, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
81 34 0.22
82 116 0.76
83 3 0.02
ACGTcount: A:0.23, C:0.28, G:0.29, T:0.21
Consensus pattern (82 bp):
ATGACCCGACCTTTAGCGACGCTTGGGGGAAAGCACCGCTAATGACCCGACCTTTAGCGGCGCTT
TGGGAAAAGCGCCGCTA
Found at i:31820701 original size:189 final size:187
Alignment explanation
Indices: 31820381--31820722 Score: 508
Period size: 189 Copynumber: 1.8 Consensus size: 187
31820371 TATATAAACG
* *
31820381 CCGCTAATGACCCGACCTTTAGTGGCGCTTGCAGGAAAGAACCGCTAATGACCCGACCTTTCGCG
1 CCGCTAATGACCCGACCTTTAGCGGCGCTTG-AGGAAAGAACCGCTAATGACCCGACCTTTAGCG
* * * *
31820446 GCGCTTACGGGAAAGCGCCGCTAATGACTCGACCTTTAGTGGCACTTGTGGGAAAGCGCCGCTAA
65 ACGCTTACGGGAAAGCACCGCTAATGACCCGACCTTTAGCGGCACTTGTGGGAAAGCGCCGCTAA
*
31820511 TGACCCGACCTTTTAGCGGTGCTTATGACCCGACCTTTAGCAGCGCTTGTGGAAAAGCA
130 TGACCCGACC-TTTAGCGGCGCTTATGACCCGACCTTTAGCAGCGCTTGTGGAAAAGCA
** *
31820570 CCGCTAATGACCCGACCTTTAGCGGCGCTTTG-GGTAAAGCGCTGCTAATGACCCGACCTTTAGC
1 CCGCTAATGACCCGACCTTTAGCGGCGC-TTGAGG-AAAGAACCGCTAATGACCCGACCTTTAGC
** *
31820634 GACGCTTGGGGGAAAGCACCGCTAATGACCCGACCTTTAGCGGCGCTTG-GGAGAAAGCGCCGCT
64 GACGCTTACGGGAAAGCACCGCTAATGACCCGACCTTTAGCGGCACTTGTGG-GAAAGCGCCGCT
31820698 AATGACCCGACCTTTAGCGGCGCTT
128 AATGACCCGACCTTTAGCGGCGCTT
31820723 GGGGGAAAGC
Statistics
Matches: 137, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
188 16 0.12
189 118 0.86
190 3 0.02
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.21
Consensus pattern (187 bp):
CCGCTAATGACCCGACCTTTAGCGGCGCTTGAGGAAAGAACCGCTAATGACCCGACCTTTAGCGA
CGCTTACGGGAAAGCACCGCTAATGACCCGACCTTTAGCGGCACTTGTGGGAAAGCGCCGCTAAT
GACCCGACCTTTAGCGGCGCTTATGACCCGACCTTTAGCAGCGCTTGTGGAAAAGCA
Found at i:31820772 original size:40 final size:40
Alignment explanation
Indices: 31820535--31820782 Score: 309
Period size: 41 Copynumber: 6.1 Consensus size: 40
31820525 AGCGGTGCTT
*
31820535 ATGACCCGACCTTTAGCAGCGCTTGTGGAAAAGCACCGCTA
1 ATGACCCGACCTTTAGCGGCGCTTG-GGAAAAGCACCGCTA
* * *
31820576 ATGACCCGACCTTTAGCGGCGCTTTGGGTAAAGCGCTGCTA
1 ATGACCCGACCTTTAGCGGCGC-TTGGGAAAAGCACCGCTA
* *
31820617 ATGACCCGACCTTTAGCGACGCTTGGGGGAAAGCACCGCTA
1 ATGACCCGACCTTTAGCGGCGCTT-GGGAAAAGCACCGCTA
*
31820658 ATGACCCGACCTTTAGCGGCGCTTGGGAGAAAGCGCCGCTA
1 ATGACCCGACCTTTAGCGGCGCTTGGGA-AAAGCACCGCTA
*
31820699 ATGACCCGACCTTTAGCGGCGCTTGGGGGAAAGCACCGCTA
1 ATGACCCGACCTTTAGCGGCGCTT-GGGAAAAGCACCGCTA
*** * * *
31820740 ATG-CTTTACCTTTTGCGGCGCATTTGGAAAAGCGCCGCTA
1 ATGACCCGACCTTTAGCGGCGC-TTGGGAAAAGCACCGCTA
31820780 ATG
1 ATG
31820783 CTTTACCTTT
Statistics
Matches: 182, Mismatches: 20, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
40 35 0.19
41 141 0.77
42 6 0.03
ACGTcount: A:0.23, C:0.28, G:0.29, T:0.21
Consensus pattern (40 bp):
ATGACCCGACCTTTAGCGGCGCTTGGGAAAAGCACCGCTA
Found at i:31822884 original size:127 final size:126
Alignment explanation
Indices: 31822734--31822984 Score: 330
Period size: 127 Copynumber: 2.0 Consensus size: 126
31822724 ATTTTTGCCC
* *
31822734 AAAAAACTTTACTTTCACACAAACCCTCAAAAAAATTTT-CCTTTTATTTTCTCCTCAAAACTTT
1 AAAAAACTTTACTTTCACACAAACCC-C-AAAAAATTTTCCCTTTTACTTTCTCCTCAAAAATTT
* * * *
31822798 TACTTCCCCTCAAAACCCTAGAACTTTTTTTC-TTTATTTTTTTCCCAAAACTTTTACTTCCCGT
64 TACTTCCCC-CAAAACCCCA-AACTTTTTTCCTTTTACTTTCTTCCCAAAACTTTTACTTCCCGT
* **
31822862 AAAAAA-TTTAC-TTCACCCCAAACCCCCGAAAATTTTCCCCTTTTACTTTCTCCTCAAAAATTT
1 AAAAAACTTTACTTTCA-CACAAACCCCAAAAAATTTT-CCCTTTTACTTTCTCCTCAAAAATTT
*
31822925 TACTTCCCCCAAATCCCCAAACTTTTTTCCTTTTACTTTCTTCCCAAAACTTTTACTTCC
64 TACTTCCCCCAAAACCCCAAACTTTTTTCCTTTTACTTTCTTCCCAAAACTTTTACTTCC
31822985 TCCAAACCCT
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
125 18 0.17
126 40 0.37
127 45 0.41
128 6 0.06
ACGTcount: A:0.29, C:0.31, G:0.01, T:0.39
Consensus pattern (126 bp):
AAAAAACTTTACTTTCACACAAACCCCAAAAAATTTTCCCTTTTACTTTCTCCTCAAAAATTTTA
CTTCCCCCAAAACCCCAAACTTTTTTCCTTTTACTTTCTTCCCAAAACTTTTACTTCCCGT
Found at i:31822959 original size:53 final size:53
Alignment explanation
Indices: 31822862--31823044 Score: 185
Period size: 53 Copynumber: 3.4 Consensus size: 53
31822852 TACTTCCCGT
* **
31822862 AAAAAATTTACTTCACCCCAAACCCCCGAAAA-TTTTCCCCTTTTACTTTCTCCTC
1 AAAAATTTTACTTC-CCCCAAA-CCCC-AAAACTTTTTTCCTTTTACTTTCTCCTC
31822917 AAAAATTTTACTTCCCCCAAATCCCC-AAACTTTTTTCCTTTTACTTTCTTCC-C
1 AAAAATTTTACTTCCCCCAAA-CCCCAAAACTTTTTTCCTTTTACTTTC-TCCTC
* * * ** *
31822970 AAAACTTTTACTTCCTCCAAACCCTCAAAACTTTTTTCTTTTTGGTTTCCCCT-
1 AAAAATTTTACTTCCCCCAAACCC-CAAAACTTTTTTCCTTTTACTTTCTCCTC
* *
31823023 AAAACTGTTACTTCCCCCAAAC
1 AAAAATTTTACTTCCCCCAAAC
31823045 TCTAAAAACT
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
52 6 0.05
53 59 0.53
54 33 0.30
55 13 0.12
ACGTcount: A:0.27, C:0.34, G:0.02, T:0.37
Consensus pattern (53 bp):
AAAAATTTTACTTCCCCCAAACCCCAAAACTTTTTTCCTTTTACTTTCTCCTC
Found at i:31823053 original size:53 final size:53
Alignment explanation
Indices: 31822902--31823066 Score: 165
Period size: 53 Copynumber: 3.1 Consensus size: 53
31822892 AATTTTCCCC
* * * * * *
31822902 TTTTACTTTCTCCTCAAAAATTTTACTTCCCCCAAA-TCCCCAAACTTTTTTCC
1 TTTTGCTTTCTCC-CAAAACTGTTACTTCCCCCAAACTCTCAAAACTTTTTTCT
* * * *
31822955 TTTTACTTTCTTCCCAAAACTTTTACTTCCTCCAAACCCTCAAAACTTTTTTCT
1 TTTTGCTTTC-TCCCAAAACTGTTACTTCCCCCAAACTCTCAAAACTTTTTTCT
* *
31823009 TTTTGGTTTC-CCCTAAAACTGTTACTTCCCCCAAACTCTAAAAACTTATTTT-T
1 TTTTGCTTTCTCCC-AAAACTGTTACTTCCCCCAAACTCTCAAAACTT-TTTTCT
31823062 TTTTG
1 TTTTG
31823067 AATTTACATC
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
52 3 0.03
53 65 0.68
54 28 0.29
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (53 bp):
TTTTGCTTTCTCCCAAAACTGTTACTTCCCCCAAACTCTCAAAACTTTTTTCT
Found at i:31827851 original size:261 final size:263
Alignment explanation
Indices: 31827356--31828006 Score: 670
Period size: 262 Copynumber: 2.5 Consensus size: 263
31827346 CTAGCCTGAA
*
31827356 ATTTATATTGTGTTGTTAATTTGCACTACTATTAAAATAAATGTGACATCC---AT---GATTGC
1 ATTTATATTGTGTTGTTAATTTGCACTAATATTAAAATAAATGTGACATCCATAATAAAGATTGC
* * * *
31827415 TACTATTATCGTCTAATATGTCATCAGTTTAACAGTTTGTAATTTGAATAAATGGAATCGTTTGT
66 TACTACTATCGTCTAATGTGTCATCAGTTTGACAGTTTGTAATTTGAATAAATGGTATCGTTTGT
** *
31827480 CAATTTAGTTTTTTTTTAATAATTTCATTATAAATTTTAAAAATATCTGTTTTTTTTACACAATA
131 CAATTTAG---TTTTTT-ATAATTTCATTATAAATTTTAAAAATATCTGCCTTTTTAACACAATA
* * * * * * * *
31827545 TTTATAATTACTCATAACCCACCCCTTCTTAACTTATACATAGGAGGATAATGCGCTTTAAAAAT
192 CTTAGAACTACCCATAACCCACCCC-TC-TAACTCATAAATAGGAGAATAATGCGCTTCAAAAAT
31827610 TTATA-T-T
255 TTATATTGT
*
31827617 ATTTATATTGTGTTGTTAATTTGCACTAGTATTAAAATAAATGTGACATCCATTAATAAAGATTG
1 ATTTATATTGTGTTGTTAATTTGCACTAATATTAAAATAAATGTGACATCCA-TAATAAAGATTG
* * **
31827682 CTACTACTATCGTATAATGTGTTATCAGTTTGACAGTTTGTAATTTGAATAAATGGTATTTTTTG
65 CTACTACTATCGTCTAATGTGTCATCAGTTTGACAGTTTGTAATTTGAATAAATGGTATCGTTTG
* * * *
31827747 TAAGCAATTTAG-TTTTT-TAA-TTCTTTATAAATTTTGATAATATTTGCCCTTTTTAACACAAT
130 T---CAATTTAGTTTTTTATAATTTCATTATAAATTTTAAAAATATCTG-CCTTTTTAACACAAT
* * ** * **
31827809 GCTTGGAACTACCCATAACCCTTCCC-C-AACTCATAAATAGGAGAATAATTCGCTTCAGCAATT
191 ACTTAGAACTACCCATAACCCACCCCTCTAACTCATAAATAGGAGAATAATGCGCTTCAAAAATT
31827872 TATATTGT
256 TATATTGT
*** * **
31827880 ATTGT-TAATT-TG-AACTAGTATTATA-TAATATTAAAATAAATGTGACATCCACTAATAAAGA
1 ATT-TAT-ATTGTGTTGTTAAT-TTGCACTAATATTAAAATAAATGTGACATCCA-TAATAAAGA
* * * *
31827941 TTGCTACTACTATCGTCTAATGTGTGATCAGTTTGACAATTTGTAGTTTGAAAAAATGGTATCGT
62 TTGCTACTACTATCGTCTAATGTGTCATCAGTTTGACAGTTTGTAATTTGAATAAATGGTATCGT
31828006 T
127 T
31828007 CATGAGCAAC
Statistics
Matches: 328, Mismatches: 46, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
261 83 0.25
262 97 0.30
263 11 0.03
264 26 0.08
265 35 0.11
267 5 0.02
268 63 0.19
271 8 0.02
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (263 bp):
ATTTATATTGTGTTGTTAATTTGCACTAATATTAAAATAAATGTGACATCCATAATAAAGATTGC
TACTACTATCGTCTAATGTGTCATCAGTTTGACAGTTTGTAATTTGAATAAATGGTATCGTTTGT
CAATTTAGTTTTTTATAATTTCATTATAAATTTTAAAAATATCTGCCTTTTTAACACAATACTTA
GAACTACCCATAACCCACCCCTCTAACTCATAAATAGGAGAATAATGCGCTTCAAAAATTTATAT
TGT
Found at i:31833703 original size:19 final size:19
Alignment explanation
Indices: 31833681--31833717 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
31833671 TTTTTTGGTT
31833681 TTTTTGGACTGGACTCTAA
1 TTTTTGGACTGGACTCTAA
**
31833700 TTTTTGGTTTGGACTCTA
1 TTTTTGGACTGGACTCTA
31833718 GAATTTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.49
Consensus pattern (19 bp):
TTTTTGGACTGGACTCTAA
Found at i:31833991 original size:33 final size:34
Alignment explanation
Indices: 31833952--31834026 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
31833942 TTATAACTCT
* *
31833952 TATTTAAATTGGGTTTTAAAATCGTTAATTTAA-
1 TATTTAAATTGAGTTTTAAAATAGTTAATTTAAC
*
31833985 TATTTAAATTGATTTTTAAAATAGTTAATTTAAC
1 TATTTAAATTGAGTTTTAAAATAGTTAATTTAAC
31834019 TA-TTAAAT
1 TATTTAAAT
31834027 GATATCTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 36 0.95
34 2 0.05
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (34 bp):
TATTTAAATTGAGTTTTAAAATAGTTAATTTAAC
Found at i:31834037 original size:33 final size:33
Alignment explanation
Indices: 31833952--31834037 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 33
31833942 TTATAACTCT
* *
31833952 TATTTAAATTGGGTT-TTAAAATCGTTAATTTAA
1 TATTTAAATT-GATTCTTAAAATAGTTAATTTAA
*
31833985 TATTTAAATTGATTTTTAAAATAGTTAATTTAA
1 TATTTAAATTGATTCTTAAAATAGTTAATTTAA
31834018 CTA-TTAAA-TGATATCTTAAA
1 -TATTTAAATTGAT-TCTTAAA
31834038 TCCTATTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 7 0.15
33 38 0.81
34 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (33 bp):
TATTTAAATTGATTCTTAAAATAGTTAATTTAA
Found at i:31841591 original size:28 final size:28
Alignment explanation
Indices: 31841551--31841604 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
31841541 GGTAACAGGC
* *
31841551 ATGATCTTTGGGTTAACAGGGAGTAAGA
1 ATGACCTTTGGGTTAACAAGGAGTAAGA
31841579 ATGACCTTTGGGTTAACAAGGAGTAA
1 ATGACCTTTGGGTTAACAAGGAGTAA
31841605 ATCAGATACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (28 bp):
ATGACCTTTGGGTTAACAAGGAGTAAGA
Found at i:31845776 original size:59 final size:59
Alignment explanation
Indices: 31845713--31845837 Score: 232
Period size: 59 Copynumber: 2.1 Consensus size: 59
31845703 TTTTTCACAC
*
31845713 TTTTTCTTACTCTTGCCTTTTTGTGTTTTTAATCATTTTCTTTTTGTTCTTTTCACTTG
1 TTTTTCTTACTCTTGCCTTTTTGTGTTTTTAATCATTTACTTTTTGTTCTTTTCACTTG
*
31845772 TTTTTCTTACTCTTGCCTTTTTGTGTTTTTACTCATTTACTTTTTGTTCTTTTCACTTG
1 TTTTTCTTACTCTTGCCTTTTTGTGTTTTTAATCATTTACTTTTTGTTCTTTTCACTTG
31845831 TTTTTCT
1 TTTTTCT
31845838 CTTCTTTGGC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.08, C:0.18, G:0.08, T:0.66
Consensus pattern (59 bp):
TTTTTCTTACTCTTGCCTTTTTGTGTTTTTAATCATTTACTTTTTGTTCTTTTCACTTG
Found at i:31845833 original size:34 final size:33
Alignment explanation
Indices: 31845736--31845835 Score: 81
Period size: 34 Copynumber: 3.2 Consensus size: 33
31845726 TGCCTTTTTG
*
31845736 TGTTTTTAATCATTTTCTTTTTGTTCTTTTCACT
1 TGTTTTT-ATCATTTACTTTTTGTTCTTTTCACT
* * **
31845770 TG-TTTT-TC--TTAC-TCTTG-CCTTTT--TG
1 TGTTTTTATCATTTACTTTTTGTTCTTTTCACT
31845795 TGTTTTTACTCATTTACTTTTTGTTCTTTTCACT
1 TGTTTTTA-TCATTTACTTTTTGTTCTTTTCACT
31845829 TGTTTTT
1 TGTTTTT
31845836 CTCTTCTTTG
Statistics
Matches: 48, Mismatches: 9, Indels: 18
0.64 0.12 0.24
Matches are distributed among these distances:
25 2 0.04
26 4 0.08
27 5 0.10
28 6 0.12
29 3 0.06
30 4 0.08
31 6 0.12
32 5 0.10
33 4 0.08
34 9 0.19
ACGTcount: A:0.09, C:0.16, G:0.08, T:0.67
Consensus pattern (33 bp):
TGTTTTTATCATTTACTTTTTGTTCTTTTCACT
Found at i:31854530 original size:25 final size:27
Alignment explanation
Indices: 31854491--31854543 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
31854481 TAGTATTTTG
*
31854491 TTTAATAGAAGCAAA-AAA-ATAAGTA
1 TTTAATAGAAACAAATAAATATAAGTA
*
31854516 TTTAATTGAAACAAATAAATATAAGTA
1 TTTAATAGAAACAAATAAATATAAGTA
31854543 T
1 T
31854544 CACATTGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.54
26 3 0.12
27 8 0.33
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (27 bp):
TTTAATAGAAACAAATAAATATAAGTA
Found at i:31856913 original size:17 final size:17
Alignment explanation
Indices: 31856881--31856919 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
31856871 TATTATTTTA
*
31856881 TATTTATTTTATTATTT
1 TATTTATTTTAGTATTT
*
31856898 TATTTATTTTGGTATTT
1 TATTTATTTTAGTATTT
*
31856915 AATTT
1 TATTT
31856920 TCATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
TATTTATTTTAGTATTT
Found at i:31856975 original size:24 final size:23
Alignment explanation
Indices: 31856923--31856975 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
31856913 TTAATTTTCA
*
31856923 TTTATTTATTGTTTTTATGATGT
1 TTTATTTATTGTTTTTATGATAT
*
31856946 TCTTATTTATTTGTTTGTTAT-TTAT
1 T-TTATTTA-TTGTTT-TTATGATAT
31856971 TTTAT
1 TTTAT
31856976 GCCATTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.04
24 11 0.44
25 9 0.36
26 4 0.16
ACGTcount: A:0.17, C:0.02, G:0.09, T:0.72
Consensus pattern (23 bp):
TTTATTTATTGTTTTTATGATAT
Found at i:31857986 original size:31 final size:31
Alignment explanation
Indices: 31857951--31858024 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
31857941 AGTGCCTACG
31857951 TGGAAGCGCTTTTGCCAAACAAGCGCACACA
1 TGGAAGCGCTTTTGCCAAACAAGCGCACACA
* * * *
31857982 TGGAAGCGTTTTTTCCAAATAAGTGCACACA
1 TGGAAGCGCTTTTGCCAAACAAGCGCACACA
31858013 TGGAAGC-CTTTT
1 TGGAAGCGCTTTT
31858025 TGGTCGTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (31 bp):
TGGAAGCGCTTTTGCCAAACAAGCGCACACA
Found at i:31858309 original size:28 final size:26
Alignment explanation
Indices: 31858231--31858310 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 26
31858221 TAATAAAATC
31858231 TTTTATTTTTTAATAATATTTAATT-A
1 TTTTATTTTTT-ATAATATTTAATTAA
* * *
31858257 TTTTA-TTTTTAT-TTGTATAATTTAA
1 TTTTATTTTTTATAATATTTAA-TTAA
31858282 TTATTATTTTTTCATAATATTTAATTAA
1 TT-TTATTTTTT-ATAATATTTAATTAA
31858310 T
1 T
31858311 CCGTATCGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
23 5 0.12
24 4 0.10
25 8 0.19
26 8 0.19
27 5 0.12
28 7 0.17
29 5 0.12
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTTATTTTTTATAATATTTAATTAA
Done.