Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold243
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: 1218968
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 59385 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:261583 original size:69 final size:69
Alignment explanation
Indices: 261453--261617 Score: 186
Period size: 69 Copynumber: 2.4 Consensus size: 69
261443 TTTAGGAGTT
* * ** * * ** *
261453 ACAGAATATACCATAAAGGCTTCATAGAATAGGCCACAAAGGCTCTACAGAATATGCCACAAAGT
1 ACAGAATATGCCATAAAGGCTTCACAGAATACACCACAAAGGCTCCACAAAATACACCACAAAGG
261518 CTCC
66 CTCC
* * * *
261522 ACAGAATATGCCATAAATGTTTCACAGAATACACCACAAATGCTCCACAAAATACATCACAAAGG
1 ACAGAATATGCCATAAAGGCTTCACAGAATACACCACAAAGGCTCCACAAAATACACCACAAAGG
*
261587 CTTC
66 CTCC
**
261591 ACAGAATGCGCCATAAAGGCTTCACAG
1 ACAGAATATGCCATAAAGGCTTCACAG
261618 GTAACTTACC
Statistics
Matches: 78, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 78 1.00
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (69 bp):
ACAGAATATGCCATAAAGGCTTCACAGAATACACCACAAAGGCTCCACAAAATACACCACAAAGG
CTCC
Found at i:272760 original size:6 final size:6
Alignment explanation
Indices: 272749--272782 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
272739 AGTTTATTTG
*
272749 TTTTAT TTTTAT TTTTAT GTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
272783 TAAACTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:272791 original size:25 final size:24
Alignment explanation
Indices: 272763--272826 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
272753 ATTTTTATTT
*
272763 TTATGTTTATTTTTATTTTTTAAAC
1 TTAT-TTTATTTTTATCTTTTAAAC
** *
272788 TTATTTGGTTTTTATCTTTTGAAC
1 TTATTTTATTTTTATCTTTTAAAC
272812 TATATTTTTATTTTT
1 T-TA-TTTTATTTTT
272827 TATGGTTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 17 0.55
25 6 0.19
26 8 0.26
ACGTcount: A:0.20, C:0.05, G:0.06, T:0.69
Consensus pattern (24 bp):
TTATTTTATTTTTATCTTTTAAAC
Found at i:272799 original size:24 final size:25
Alignment explanation
Indices: 272772--272818 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
272762 TTTATGTTTA
*
272772 TTTTTATTTTTTAAACT-TATTTGG
1 TTTTTATCTTTTAAACTATATTTGG
*
272796 TTTTTATCTTTTGAACTATATTT
1 TTTTTATCTTTTAAACTATATTT
272819 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.66
Consensus pattern (25 bp):
TTTTTATCTTTTAAACTATATTTGG
Found at i:276182 original size:42 final size:42
Alignment explanation
Indices: 276105--276373 Score: 145
Period size: 42 Copynumber: 6.3 Consensus size: 42
276095 GAGGAGCACA
* * * **
276105 ATCATTTAAGCTCGCATGGGGAGCTTCGCTAATACATAGGTT
1 ATCACTTAAGCTCACATGGGGAGCTTCGCTAATACACAACTT
* * * *
276147 GTCACTTAAGCTCACATGGGGAGCTTGGTTGATACACAACTT
1 ATCACTTAAGCTCACATGGGGAGCTTCGCTAATACACAACTT
** * **
276189 ATCACTTAAGCTCACGA-GGGGAGCTTTACTGATTACACAGTTT
1 ATCACTTAAGCTCAC-ATGGGGAGCTTCGCT-AATACACAACTT
* ** *
276232 ATCACTTAAGTTCAC--GAGGGAGCTTTACTAATTACTCAACTT
1 ATCACTTAAGCTCACATG-GGGAGCTTCGCTAA-TACACAACTT
* ** ** *
276274 ATCATTTAAGCT--CATGAGGGAAGCTTCATTGGTTACACAGCTT
1 ATCACTTAAGCTCACATG-GGG-AGCTTCGCT-AATACACAACTT
* * * * *
276317 ATCACTTAAGTTAACGA-AGGGAGTTTCGCTGATTACACAACTT
1 ATCACTTAAGCTCAC-ATGGGGAGCTTCGCT-AATACACAACTT
*
276360 ATCACTTAAACTCA
1 ATCACTTAAGCTCA
276374 TGAGGATAGT
Statistics
Matches: 175, Mismatches: 41, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
40 1 0.01
41 2 0.01
42 91 0.52
43 76 0.43
44 3 0.02
45 1 0.01
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (42 bp):
ATCACTTAAGCTCACATGGGGAGCTTCGCTAATACACAACTT
Found at i:276240 original size:43 final size:43
Alignment explanation
Indices: 276148--276404 Score: 234
Period size: 43 Copynumber: 6.0 Consensus size: 43
276138 ACATAGGTTG
***
276148 TCACTTAAGCTCAC-ATGGGGAGCTTGGTTGA-TACACAACTTA
1 TCACTTAAGCTCACGA-GGGGAGCTTTACTGATTACACAACTTA
**
276190 TCACTTAAGCTCACGAGGGGAGCTTTACTGATTACACAGTTTA
1 TCACTTAAGCTCACGAGGGGAGCTTTACTGATTACACAACTTA
* * *
276233 TCACTTAAGTTCACGA-GGGAGCTTTACTAATTACTCAACTTA
1 TCACTTAAGCTCACGAGGGGAGCTTTACTGATTACACAACTTA
* * * * * * *
276275 TCATTTAAGCTCATGAGGGAAGCTTCATTGGTTACACAGCTTA
1 TCACTTAAGCTCACGAGGGGAGCTTTACTGATTACACAACTTA
* * * *
276318 TCACTTAAGTTAACGAAGGGAG-TTTCGCTGATTACACAACTTA
1 TCACTTAAGCTCACGAGGGGAGCTTT-ACTGATTACACAACTTA
* * ** * **
276361 TCACTTAAACTCATGAGGATAGTTTTGTTGATTACACAACTTA
1 TCACTTAAGCTCACGAGGGGAGCTTTACTGATTACACAACTTA
276404 T
1 T
276405 AAAACTGTTT
Statistics
Matches: 171, Mismatches: 39, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
42 63 0.37
43 105 0.61
44 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (43 bp):
TCACTTAAGCTCACGAGGGGAGCTTTACTGATTACACAACTTA
Found at i:276284 original size:85 final size:86
Alignment explanation
Indices: 276179--276378 Score: 269
Period size: 85 Copynumber: 2.3 Consensus size: 86
276169 GCTTGGTTGA
* * * *
276179 TACACAACTTATCACTTAAGCTCACGAGGGGAGCTTTACTGATTACACAGTTTATCACTTAAGTT
1 TACACAACTTATCACTTAAGCTCATGAGGGAAGCTTCACTGATTACACAGCTTATCACTTAAGTT
*
276244 CACG-AGGGAGCTTT-ACTAAT
66 AACGAAGGGAG-TTTCACTAAT
* * * *
276264 TACTCAACTTATCATTTAAGCTCATGAGGGAAGCTTCATTGGTTACACAGCTTATCACTTAAGTT
1 TACACAACTTATCACTTAAGCTCATGAGGGAAGCTTCACTGATTACACAGCTTATCACTTAAGTT
* *
276329 AACGAAGGGAGTTTCGCTGAT
66 AACGAAGGGAGTTTCACTAAT
*
276350 TACACAACTTATCACTTAAACTCATGAGG
1 TACACAACTTATCACTTAAGCTCATGAGG
276379 ATAGTTTTGT
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
85 63 0.64
86 36 0.36
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (86 bp):
TACACAACTTATCACTTAAGCTCATGAGGGAAGCTTCACTGATTACACAGCTTATCACTTAAGTT
AACGAAGGGAGTTTCACTAAT
Found at i:282433 original size:15 final size:15
Alignment explanation
Indices: 282413--282443 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
282403 TCGAACCTTA
282413 AAACCTAAAAAATGG
1 AAACCTAAAAAATGG
282428 AAACCTAAAAAATGG
1 AAACCTAAAAAATGG
282443 A
1 A
282444 GTTTTCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (15 bp):
AAACCTAAAAAATGG
Found at i:282995 original size:22 final size:22
Alignment explanation
Indices: 282965--283019 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
282955 TCAAGTCTAT
282965 TTTCT-CTTTCTCTT-ATTTGA
1 TTTCTCCTTTCTCTTCATTTGA
* * *
282985 TTTCTTCCTTTTTCTTCTTTTGT
1 TTTC-TCCTTTCTCTTCATTTGA
283008 TTTCTCCTTTCT
1 TTTCTCCTTTCT
283020 GGTTTCATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.14
21 1 0.04
22 15 0.54
23 8 0.29
ACGTcount: A:0.04, C:0.24, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTCTCCTTTCTCTTCATTTGA
Found at i:283528 original size:49 final size:49
Alignment explanation
Indices: 283386--283531 Score: 195
Period size: 49 Copynumber: 3.0 Consensus size: 49
283376 TCAAGGAAGT
* ** * *
283386 TTTATTGTACTATATTTTTCAAAATAACAACACCATGGTTGTAGACAGC
1 TTTATTGTACTATATTTTTCAGAATAACTGCACCATGGATGTAGGCAGC
* *
283435 TTTATTGTACTATATTTTTCAGAATAA-TAGAACCATGGATGTAGGTAGC
1 TTTATTGTACTATATTTTTCAGAATAACT-GCACCATGGATGTAGGCAGC
* *
283484 TTTATTGTACTATATTTTGCAGAATAACTGCACCGTGGATGTAGGCAG
1 TTTATTGTACTATATTTTTCAGAATAACTGCACCATGGATGTAGGCAG
283532 ACTTATCAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
49 83 0.99
50 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (49 bp):
TTTATTGTACTATATTTTTCAGAATAACTGCACCATGGATGTAGGCAGC
Found at i:283757 original size:24 final size:24
Alignment explanation
Indices: 283730--283822 Score: 125
Period size: 24 Copynumber: 3.9 Consensus size: 24
283720 TTTTTAGAAG
283730 ATTTAGAATTTATTAGTATAATAT
1 ATTTAGAATTTATTAGTATAATAT
*
283754 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGAATTTATTAGTATAATAT
* * *
283778 ATTTAGTACTTATTAGCATAATAT
1 ATTTAGAATTTATTAGTATAATAT
*
283802 ATTTA-ACATTTATTATTATAA
1 ATTTAGA-ATTTATTAGTATAA
283823 AAATATTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (24 bp):
ATTTAGAATTTATTAGTATAATAT
Found at i:283761 original size:14 final size:14
Alignment explanation
Indices: 283742--283785 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
283732 TTAGAATTTA
283742 TTAGTATAATATAT
1 TTAGTATAATATAT
283756 TTAGTAT--T-TA-
1 TTAGTATAATATAT
283766 TTAGTATAATATAT
1 TTAGTATAATATAT
283780 TTAGTA
1 TTAGTA
283786 CTTATTAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
12 2 0.08
13 2 0.08
14 13 0.50
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (14 bp):
TTAGTATAATATAT
Found at i:286117 original size:24 final size:24
Alignment explanation
Indices: 286089--286154 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
286079 TTTCTAGAAA
*
286089 ATTTAGTATTTATTAGTAAAATAT
1 ATTTAGCATTTATTAGTAAAATAT
* * *
286113 ATTTAACATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGTAAAATAT
*
286137 ATTTGGCATTTATTAGTA
1 ATTTAGCATTTATTAGTA
286155 TAAAAATCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTAAAATAT
Found at i:286157 original size:24 final size:24
Alignment explanation
Indices: 286096--286157 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
286086 AAAATTTAGT
*
286096 ATTTATTAGTAAAATATATTTAAC
1 ATTTATTAGTATAATATATTTAAC
* **
286120 ATTTATTAGCATAATATATTTGGC
1 ATTTATTAGTATAATATATTTAAC
286144 ATTTATTAGTATAA
1 ATTTATTAGTATAA
286158 AAATCTTTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTAAC
Found at i:287296 original size:100 final size:100
Alignment explanation
Indices: 287123--287321 Score: 380
Period size: 100 Copynumber: 2.0 Consensus size: 100
287113 TAAAAATCAT
287123 ATTAGTTGCATATGCACCTTTAACTTGAGGAAATGTCAAAATATTTTTTTATGCCTACTAAGATG
1 ATTAGTTGCATATGCACCTTTAACTTGAGGAAATGTCAAAATATTTTTTTATGCCTACTAAGATG
287188 ATGAATGTGTGGAAATGTGTGTTATTGAAACCCAC
66 ATGAATGTGTGGAAATGTGTGTTATTGAAACCCAC
*
287223 ATTAGTTGCATATTCACCTTTAACTTGAGGAAATGTCAAAATATTTTTTTATGCCTACTAAGATG
1 ATTAGTTGCATATGCACCTTTAACTTGAGGAAATGTCAAAATATTTTTTTATGCCTACTAAGATG
*
287288 ATGAATGTGTGGAAGTGTGTGTTATTGAAACCCA
66 ATGAATGTGTGGAAATGTGTGTTATTGAAACCCA
287322 TATGTTGATT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (100 bp):
ATTAGTTGCATATGCACCTTTAACTTGAGGAAATGTCAAAATATTTTTTTATGCCTACTAAGATG
ATGAATGTGTGGAAATGTGTGTTATTGAAACCCAC
Found at i:290025 original size:20 final size:21
Alignment explanation
Indices: 290002--290049 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
289992 AAATAATTTT
*
290002 AATAATTTTTA-ATTTTTAAA
1 AATAATTTTTATATATTTAAA
*
290022 AATAAATTTTATATATTTAAA
1 AATAATTTTTATATATTTAAA
290043 AA-AATTT
1 AATAATTT
290050 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATTTTTATATATTTAAA
Found at i:295460 original size:18 final size:18
Alignment explanation
Indices: 295437--295471 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
295427 ATAAGTTTTA
295437 AAAGTAAAAACGAAAAAT
1 AAAGTAAAAACGAAAAAT
*
295455 AAAGTAAAATCGAAAAA
1 AAAGTAAAAACGAAAAA
295472 AGAGAGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.06, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAGTAAAAACGAAAAAT
Found at i:295557 original size:13 final size:13
Alignment explanation
Indices: 295539--295563 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
295529 TACAATATTC
295539 ATTTTCATTTTAT
1 ATTTTCATTTTAT
295552 ATTTTCATTTTA
1 ATTTTCATTTTA
295564 AATTATGCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTCATTTTAT
Found at i:296191 original size:21 final size:21
Alignment explanation
Indices: 296167--296213 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
296157 AAGAATATGG
* *
296167 TCGTGTGGCTACTTCACACGC
1 TCGTGTGACTACCTCACACGC
296188 TCGTGTGACTACCTCACACGC
1 TCGTGTGACTACCTCACACGC
*
296209 CCGTG
1 TCGTG
296214 GACGCTGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.36, G:0.23, T:0.26
Consensus pattern (21 bp):
TCGTGTGACTACCTCACACGC
Found at i:301355 original size:4 final size:4
Alignment explanation
Indices: 301346--301402 Score: 105
Period size: 4 Copynumber: 14.2 Consensus size: 4
301336 CTCAAAGTAA
*
301346 ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
301394 ACAT ACAT A
1 ACAT ACAT A
301403 TATGCTCAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:305557 original size:27 final size:27
Alignment explanation
Indices: 305526--305612 Score: 122
Period size: 27 Copynumber: 3.2 Consensus size: 27
305516 GCCTCCACAG
*
305526 GCTTTTCTTTCATATTATGCCACAAAA
1 GCTTTTCTTTCATATTACGCCACAAAA
* *
305553 GCTTTTCTTTTATATTACGTCAC-AAA
1 GCTTTTCTTTCATATTACGCCACAAAA
*
305579 GACTTTTCTTTCATATTACGCCACAAAG
1 G-CTTTTCTTTCATATTACGCCACAAAA
305607 GCTTTT
1 GCTTTT
305613 ACTTCCTGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.08
27 45 0.87
28 3 0.06
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (27 bp):
GCTTTTCTTTCATATTACGCCACAAAA
Found at i:307771 original size:21 final size:19
Alignment explanation
Indices: 307729--307775 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
307719 CAATGTTGGA
* *
307729 ACATCCAATTGATGTTGCG
1 ACATCCAATTAATGTCGCG
307748 ACATCCAATTCAAGTGTCGCG
1 ACATCCAATT-AA-TGTCGCG
307769 ACATCCA
1 ACATCCA
307776 TGGTAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.42
20 1 0.04
21 13 0.54
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (19 bp):
ACATCCAATTAATGTCGCG
Found at i:314891 original size:23 final size:23
Alignment explanation
Indices: 314855--314899 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
314845 CTCTGAATAA
314855 TAAAATTGTTAATAAA-AAAACC
1 TAAAATTGTTAATAAACAAAACC
*
314877 TAAAATATTTTAATAAACAAAAC
1 TAAAAT-TGTTAATAAACAAAAC
314900 TAAGTTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 9 0.45
24 5 0.25
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAAATTGTTAATAAACAAAACC
Found at i:318288 original size:9 final size:9
Alignment explanation
Indices: 318271--318307 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
318261 TGAGTTTTCG
318271 AATTCGAAT
1 AATTCGAAT
*
318280 AACTCGAAT
1 AATTCGAAT
*
318289 AATTAGAAT
1 AATTCGAAT
318298 AATTCGAAT
1 AATTCGAAT
318307 A
1 A
318308 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:318576 original size:30 final size:29
Alignment explanation
Indices: 318520--318576 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
318510 AACCTTTTAT
* *
318520 TTTTTCCCAAAATTTTTACTCCCTTCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCAC
* *
318549 TTTTCCCCTAAAACTTTTATTCTCTTCC
1 TTTTCCCC-AAAACTTTTACTCCCTTCC
318577 CATTCCACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCAC
Found at i:319805 original size:23 final size:22
Alignment explanation
Indices: 319755--319805 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
319745 ATAAATAATA
* *
319755 AATATGTATATACAAAATATGT
1 AATATATATATACAAAATATGG
*
319777 ACATATATATATATAAAATTATGG
1 A-ATATATATATACAAAA-TATGG
319801 AATAT
1 AATAT
319806 GAAAATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 18 0.75
24 5 0.21
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
AATATATATATACAAAATATGG
Found at i:321431 original size:46 final size:46
Alignment explanation
Indices: 321349--322216 Score: 1246
Period size: 46 Copynumber: 18.9 Consensus size: 46
321339 AAGACTAGTT
* *
321349 TCTTCGATGTACTCCGCTTCCAAA-ACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* *
321394 TCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
321440 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGACAAGATCTGCCA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * * *
321486 TCTTTC-ATCTGCT-CGACTGTC-AGTACAGGAAGGCAAGA-CTAG-TT
1 TC-TTCGATCTACTCCG-CTGCCAAATACAGGAAGACAAGATCT-GCTA
321530 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
321576 TCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGACCTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
321622 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
321668 TCTTCGATCTTCTCCGCTGCTAAATACATGAAGACAAGATCTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
321714 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* *
321760 TCTTCGATCTACTCTGCTGCCAAATACAGGAAGACAAGATCTGATA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* *
321806 TCTTCGATCTACTCTGCTGCCAAATACAGGAAGACAAGATCTGATA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
321852 TCTTCGATCTACTCTGCTGCCAAATACAGGAAGACAAGATCTGTTG
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * *
321898 CCTTCAATCTCCTCCGCTGCCAAATACAGAAAGACAAGATCTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * *
321944 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGATAAGATCTGTTG
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * * *
321990 CCTTCAATCTTCTCCGCTGCCAAATACAGAAAGACAAGATTTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
*
322036 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * *
322082 TCTTCGATCT-CTTCTGCTACCAAATATAGGAAGACAAGATCTGCTG
1 TCTTCGATCTAC-TCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
*
322128 TCTTCGATCTACTCTGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
*
322174 TCTTCGATCTACTCCACTGCCAAATACAGGAAGACAAGATCTG
1 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTG
322217 TTGCTTCTAG
Statistics
Matches: 742, Mismatches: 70, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
43 3 0.00
44 14 0.02
45 56 0.08
46 665 0.90
47 4 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (46 bp):
TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
Found at i:323661 original size:8 final size:8
Alignment explanation
Indices: 323639--323698 Score: 74
Period size: 8 Copynumber: 7.9 Consensus size: 8
323629 CCTCTCCTTT
323639 TTCTTTTC
1 TTCTTTTC
323647 -T-TTTTC
1 TTCTTTTC
323653 TTCTTTTC
1 TTCTTTTC
323661 TT-TTTTC
1 TTCTTTTC
*
323668 TTCTTTTT
1 TTCTTTTC
323676 TTCTTTT-
1 TTCTTTTC
323683 TTCCTTTTC
1 TT-CTTTTC
323692 TTCTTTT
1 TTCTTTT
323699 TGTTTCTTCT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
6 5 0.11
7 11 0.24
8 28 0.61
9 2 0.04
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTCTTTTC
Found at i:323676 original size:26 final size:25
Alignment explanation
Indices: 323636--323717 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 25
323626 TGGCCTCTCC
323636 TTTTTCTTTTCTTTTTCTTCTTTTCT
1 TTTTTCTTTT-TTTTTCTTCTTTTCT
323662 TTTTTCTTCTTTTTTTCTT-TTTTCCT
1 TTTTTCTT-TTTTTTTCTTCTTTT-CT
*
323688 TTTCTTCTTTTTGTTTCTTCTTTT-T
1 TTT-TTCTTTTTTTTTCTTCTTTTCT
323713 TTTTT
1 TTTTT
323718 GAATATTCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
24 2 0.04
25 8 0.16
26 30 0.59
27 11 0.22
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (25 bp):
TTTTTCTTTTTTTTTCTTCTTTTCT
Found at i:323706 original size:34 final size:33
Alignment explanation
Indices: 323639--323718 Score: 53
Period size: 34 Copynumber: 2.4 Consensus size: 33
323629 CCTCTCCTTT
323639 TTCTTTTCTTTTT-CTTCTT-TTCTT-TTTTCTTC
1 TTCTTTTCTTTTTGCTTCTTCTT-TTCTTTT-TTC
* *
323671 TTTTTTTCTTTTTTCCTT-TTCTTCTT-TTTGTTTC
1 TTCTTTTC-TTTTTGCTTCTTCTT-TTCTTT-TTTC
*
323705 TTCTTTTTTTTTTG
1 TTCTTTTCTTTTTG
323719 AATATTCTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 7 0.17
33 12 0.30
34 20 0.50
35 1 0.03
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (33 bp):
TTCTTTTCTTTTTGCTTCTTCTTTTCTTTTTTC
Found at i:323713 original size:15 final size:14
Alignment explanation
Indices: 323639--323717 Score: 78
Period size: 13 Copynumber: 5.9 Consensus size: 14
323629 CCTCTCCTTT
*
323639 TTCTTTTCTTTTTC
1 TTCTTTTTTTTTTC
323653 TTCTTTTCTTTTTTC
1 TTCTTTT-TTTTTTC
323668 TTC---TTTTTTTC
1 TTCTTTTTTTTTTC
**
323679 TT-TTTTCCTTTTC
1 TTCTTTTTTTTTTC
*
323692 TTC-TTTTTGTTTC
1 TTCTTTTTTTTTTC
323705 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
323718 GAATATTCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
11 9 0.17
12 1 0.02
13 18 0.35
14 15 0.29
15 9 0.17
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (14 bp):
TTCTTTTTTTTTTC
Found at i:323716 original size:39 final size:39
Alignment explanation
Indices: 323642--323714 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 39
323632 CTCCTTTTTC
*
323642 TTTTCTTTTTCTTCTTTTCTTTTTTCTTCTTTTTTTCTT
1 TTTTCCTTTTCTTCTTTTCTTTTTTCTTCTTTTTTTCTT
*
323681 TTTTCCTTTTCTTC-TTT-TTGTTTCTTCTTTTTTT
1 TTTTCCTTTTCTTCTTTTCTTTTTTCTTCTTTTTTT
323715 TTTGAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 16 0.50
38 3 0.09
39 13 0.41
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (39 bp):
TTTTCCTTTTCTTCTTTTCTTTTTTCTTCTTTTTTTCTT
Found at i:329786 original size:22 final size:23
Alignment explanation
Indices: 329729--329787 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
329719 TCACATTCTC
* *
329729 AATTCTCTCTCAAATCCCTTTTA
1 AATTCTCTCTCAATTCCCTCTTA
329752 AATT-TCTCTCAATTCCCTCTT-
1 AATTCTCTCTCAATTCCCTCTTA
*
329773 AATTCTCACTCAATT
1 AATTCTCTCTCAATT
329788 TTTATTTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.12
22 24 0.75
23 4 0.12
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTCTCTCTCAATTCCCTCTTA
Found at i:339206 original size:22 final size:22
Alignment explanation
Indices: 339160--339206 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
339150 TTTATAACTC
*
339160 AAAA-AATTATAAAAAGTTTCT
1 AAAAGAATTATAAAAAATTTCT
339181 -AAAGAATATATAAAAAATTT-T
1 AAAAGAAT-TATAAAAAATTTCT
339202 AAAAG
1 AAAAG
339207 TAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 3 0.14
21 4 0.18
22 15 0.68
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (22 bp):
AAAAGAATTATAAAAAATTTCT
Found at i:341693 original size:20 final size:21
Alignment explanation
Indices: 341658--341696 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
341648 GACGGAATTG
*
341658 ATTTTCCGGAAAATCATTTCT
1 ATTTTCCAGAAAATCATTTCT
341679 ATTTTCCAG-AAATCATTT
1 ATTTTCCAGAAAATCATTT
341697 TACGGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.44
Consensus pattern (21 bp):
ATTTTCCAGAAAATCATTTCT
Found at i:347509 original size:9 final size:9
Alignment explanation
Indices: 347495--347525 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
347485 GGTCAAGTAA
347495 AATTAAATT
1 AATTAAATT
347504 AATTAAATT
1 AATTAAATT
347513 AATTAAAATT
1 AATT-AAATT
347523 AAT
1 AAT
347526 ATGATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:352928 original size:17 final size:19
Alignment explanation
Indices: 352896--352936 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
352886 TTTGAACTAA
352896 GTTTTAGGCTTTGGTTTT-
1 GTTTTAGGCTTTGGTTTTG
*
352914 GTTTTGGGC-TTGGTTTTG
1 GTTTTAGGCTTTGGTTTTG
352932 GTTTT
1 GTTTT
352937 TGTTTTTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.02, C:0.05, G:0.32, T:0.61
Consensus pattern (19 bp):
GTTTTAGGCTTTGGTTTTG
Found at i:354443 original size:16 final size:16
Alignment explanation
Indices: 354422--354455 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
354412 GAGTAGCACG
**
354422 TTCTTTTTTTTCTTTT
1 TTCTTTTTCCTCTTTT
354438 TTCTTTTTCCTCTTTT
1 TTCTTTTTCCTCTTTT
354454 TT
1 TT
354456 TTCTCTCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTCTTTTTCCTCTTTT
Found at i:355201 original size:21 final size:22
Alignment explanation
Indices: 355175--355228 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
355165 GTCCCTAGCT
*
355175 CACACGGGTGTGTGCCTCA-GC
1 CACACGGGCGTGTGCCTCATGC
** *
355196 CACACGACCGTGTGCCTCATTC
1 CACACGGGCGTGTGCCTCATGC
355218 CACACGGGCGT
1 CACACGGGCGT
355229 ATTGACCCCC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.17, C:0.37, G:0.28, T:0.19
Consensus pattern (22 bp):
CACACGGGCGTGTGCCTCATGC
Found at i:358763 original size:64 final size:64
Alignment explanation
Indices: 358675--358798 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 64
358665 GCATCTCGAT
* * * * *
358675 CGGTATTTGTCCTACATATGTTGCGGATATA-CTGTAGCTCTTTGTGAGCGTCCTGTTATATGAC
1 CGGTATTTGTCCTACATATATTGCGGACATATC-GCAGCTCTTTATGAGCGTCCTGATATATGAC
*
358739 CGGTA-TTGATCCTGCATATATTGCGGACATATCGCAGCTCTTTATGAGCGTCCTGATATA
1 CGGTATTTG-TCCTACATATATTGCGGACATATCGCAGCTCTTTATGAGCGTCCTGATATA
358799 GGCTCTTTGT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 3 0.06
64 48 0.92
65 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (64 bp):
CGGTATTTGTCCTACATATATTGCGGACATATCGCAGCTCTTTATGAGCGTCCTGATATATGAC
Found at i:358829 original size:25 final size:25
Alignment explanation
Indices: 358776--358830 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
358766 CATATCGCAG
*
358776 CTCTTTATGAGCGTCCTGATATAGG
1 CTCTTTATGAGCGTCCTGATATAGA
*
358801 CTCTTTGTGAGC-TGCCTGATAATA-A
1 CTCTTTATGAGCGT-CCTGAT-ATAGA
358826 CTCTT
1 CTCTT
358831 CGGAGTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 22 0.85
26 3 0.12
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (25 bp):
CTCTTTATGAGCGTCCTGATATAGA
Found at i:362562 original size:3 final size:3
Alignment explanation
Indices: 362554--362587 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
362544 AGGTGTTAAA
362554 ATT ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
362588 TCCTTTCGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:369263 original size:23 final size:22
Alignment explanation
Indices: 369237--369297 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
369227 GGCTCTATTA
369237 AGCTAAAATGGTAAGCAC-TGACG
1 AGCTAAAA-GGTAAGCACAT-ACG
* *
369260 AGCTGAACA-GTAAGCTCATACG
1 AGCT-AAAAGGTAAGCACATACG
369282 AGCTAAAACGGTAAGC
1 AGCTAAAA-GGTAAGC
369298 TTCAACGTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 3 0.10
22 14 0.45
23 11 0.35
24 3 0.10
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (22 bp):
AGCTAAAAGGTAAGCACATACG
Found at i:369298 original size:23 final size:23
Alignment explanation
Indices: 369237--369359 Score: 81
Period size: 23 Copynumber: 5.2 Consensus size: 23
369227 GGCTCTATTA
* *
369237 AGCTAAAATGGTAAGCAC-TGACG
1 AGCTAAAACGGTAAGCTCAT-ACG
* *
369260 AGCT-GAACAGTAAGCTCATACG
1 AGCTAAAACGGTAAGCTCATACG
369282 AGCTAAAACGGTAAGCTTCA-ACG
1 AGCTAAAACGGTAAGC-TCATACG
* * * *
369305 TGCTGAAAACAGTAAGCTCTTACA
1 AGCT-AAAACGGTAAGCTCATACG
* *
369329 AGCTGATATATCGGTAAGCTCATATG
1 AGCT-A-A-AACGGTAAGCTCATACG
369355 AGCTA
1 AGCTA
369360 TGGTGAGTTC
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
22 16 0.21
23 22 0.29
24 21 0.27
25 2 0.03
26 16 0.21
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (23 bp):
AGCTAAAACGGTAAGCTCATACG
Found at i:369333 original size:24 final size:24
Alignment explanation
Indices: 369247--369334 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
369237 AGCTAAAATG
* *
369247 GTAAGCACTGACGAGCTG--AACA
1 GTAAGCTCTTACGAGCTGAAAACA
* *
369269 GTAAGCTCATACGAGCT-AAAACG
1 GTAAGCTCTTACGAGCTGAAAACA
* *
369292 GTAAGCT-TCAACGTGCTGAAAACA
1 GTAAGCTCT-TACGAGCTGAAAACA
*
369316 GTAAGCTCTTACAAGCTGA
1 GTAAGCTCTTACGAGCTGA
369335 TATATCGGTA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
22 14 0.28
23 16 0.32
24 19 0.38
25 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (24 bp):
GTAAGCTCTTACGAGCTGAAAACA
Found at i:382979 original size:35 final size:35
Alignment explanation
Indices: 382937--383006 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
382927 TTTTTATATT
*
382937 CTTTAAATGTTTGTGTAAGTTATGATAATCATTAA
1 CTTTAAATGTTTATGTAAGTTATGATAATCATTAA
382972 CTTTAAATGTTTATGTAAGTTATGATAATCATTAA
1 CTTTAAATGTTTATGTAAGTTATGATAATCATTAA
383007 ATTTTATTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.46
Consensus pattern (35 bp):
CTTTAAATGTTTATGTAAGTTATGATAATCATTAA
Found at i:383687 original size:25 final size:24
Alignment explanation
Indices: 383647--383696 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
383637 AATGTTTGAT
*
383647 AAATTTAAATATCAAATTAGAAAAA
1 AAATTTAAATACCAAATTA-AAAAA
*
383672 AAATTTAAGTACCAAATTAAAAAA
1 AAATTTAAATACCAAATTAAAAAA
383696 A
1 A
383697 TATAATATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (24 bp):
AAATTTAAATACCAAATTAAAAAA
Found at i:384820 original size:13 final size:13
Alignment explanation
Indices: 384799--384828 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
384789 TATTTTAATT
*
384799 ATTTTCTAATAAA
1 ATTTCCTAATAAA
384812 ATTTCCTAATAAA
1 ATTTCCTAATAAA
384825 ATTT
1 ATTT
384829 TTGCCTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTCCTAATAAA
Found at i:385577 original size:78 final size:78
Alignment explanation
Indices: 385484--385655 Score: 213
Period size: 78 Copynumber: 2.2 Consensus size: 78
385474 GTGATTTCAC
* * * *
385484 AGAGGGGGAACTGATTTAGGGAAAAGGAATT-GGGGAAAAATGAAAGAGGTCTCGGAAAGAAACT
1 AGAGGGGGAACTGATTTAGGG-AAAGAAATTAGGGAAAAAAAGAAAGAGGTCTCGGAAAAAAACT
* * *
385548 TAGGGATTTCGGGG
65 TAAGGACTTCGAGG
* * * *
385562 AGAGGGGGAATTGATTTAGGGAAAGAAATTAGGGAAAAAAAGAAAGGGGTCTGGGAAAAAAATTT
1 AGAGGGGGAACTGATTTAGGGAAAGAAATTAGGGAAAAAAAGAAAGAGGTCTCGGAAAAAAACTT
385627 AAGGACTTCGAGG
66 AAGGACTTCGAGG
*
385640 AGA-GGGGAACTAATTT
1 AGAGGGGGAACTGATTT
385656 GGGTTTCGGG
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
77 19 0.24
78 61 0.76
ACGTcount: A:0.40, C:0.05, G:0.36, T:0.19
Consensus pattern (78 bp):
AGAGGGGGAACTGATTTAGGGAAAGAAATTAGGGAAAAAAAGAAAGAGGTCTCGGAAAAAAACTT
AAGGACTTCGAGG
Found at i:393844 original size:37 final size:37
Alignment explanation
Indices: 393803--393877 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
393793 CTGTTATAAG
*
393803 ATTAAGTAAAAATTGGCTAGCATGATTTATGGTTAAA
1 ATTAAGTAAAAACTGGCTAGCATGATTTATGGTTAAA
393840 ATTAAGTAAAAACTGGCTAGCATGATTTATGGTTAAA
1 ATTAAGTAAAAACTGGCTAGCATGATTTATGGTTAAA
393877 A
1 A
393878 ATGGTGAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (37 bp):
ATTAAGTAAAAACTGGCTAGCATGATTTATGGTTAAA
Found at i:396839 original size:22 final size:20
Alignment explanation
Indices: 396811--396859 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
396801 GATCCAAGTT
396811 CTGATACATAAAAGACTATGTA
1 CTGATACAT-AAAGAC-ATGTA
* *
396833 CTGATACATATAGGCATGTA
1 CTGATACATAAAGACATGTA
396853 CTGATAC
1 CTGATAC
396860 CTTGGATCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.48
21 4 0.16
22 9 0.36
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (20 bp):
CTGATACATAAAGACATGTA
Found at i:403986 original size:9 final size:9
Alignment explanation
Indices: 403972--403997 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
403962 TTATTTATTC
403972 AATTAATTA
1 AATTAATTA
403981 AATTAATTA
1 AATTAATTA
403990 AATTAATT
1 AATTAATT
403998 TCTCAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AATTAATTA
Found at i:405847 original size:24 final size:22
Alignment explanation
Indices: 405796--405847 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
405786 TGGCCCTTCC
* *
405796 CTTC-TTTTCTGTCAAAAGCTG
1 CTTCTTTTTCTATCAAAAACTG
*
405817 CTCCTTTTTCTATCCAAAAACTG
1 CTTCTTTTTCTAT-CAAAAACTG
405840 ACTTCTTT
1 -CTTCTTT
405848 ACTAGAGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 7 0.29
23 8 0.33
24 6 0.25
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.44
Consensus pattern (22 bp):
CTTCTTTTTCTATCAAAAACTG
Found at i:425072 original size:27 final size:27
Alignment explanation
Indices: 425042--425123 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
425032 CTCGTCGAAG
*
425042 TATCTCGTGTTTAATGTCCCATCAGAC
1 TATCTCGTGTTTAAAGTCCCATCAGAC
** * *
425069 TATCTTATGTTTAACA-T-CTAGTCATAC
1 TATCTCGTGTTTAA-AGTCCCA-TCAGAC
* *
425096 AATCTCGTGTTTAAAGTCCCATTAGAC
1 TATCTCGTGTTTAAAGTCCCATCAGAC
425123 T
1 T
425124 TCTTTGATGC
Statistics
Matches: 39, Mismatches: 12, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
26 3 0.08
27 34 0.87
28 2 0.05
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (27 bp):
TATCTCGTGTTTAAAGTCCCATCAGAC
Found at i:430149 original size:63 final size:63
Alignment explanation
Indices: 429968--430151 Score: 194
Period size: 63 Copynumber: 2.9 Consensus size: 63
429958 TACCCTTGGA
** * * *
429968 GAAGGTGTTGATGCAATGAATAATTGTGTATGTTGTGGTGCTTGTGTAAAATAAACTGCTGCT
1 GAAGGTGTTGATGCAGGGAATGATTGTGTATGTTGTGGTGCTTGTGTAAAATAAATTGCAGCT
* * * **
430031 GAATGTGTTGATGCAGGGAATGATTGTGCATGCTGCAGTG-TTAGTGTAAAATAAATTAG-AGCT
1 GAAGGTGTTGATGCAGGGAATGATTGTGTATGTTGTGGTGCTT-GTGTAAAATAAATT-GCAGCT
* * * *
430094 GAAGGTTTTGATTC-GAGGAATGATTGTGTGTGTTGTGGTGCTTGTGTCAAATAAATTG
1 GAAGGTGTTGATGCAG-GGAATGATTGTGTATGTTGTGGTGCTTGTGTAAAATAAATTG
430152 GTTTAGAACC
Statistics
Matches: 98, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
62 4 0.04
63 91 0.93
64 3 0.03
ACGTcount: A:0.27, C:0.07, G:0.30, T:0.36
Consensus pattern (63 bp):
GAAGGTGTTGATGCAGGGAATGATTGTGTATGTTGTGGTGCTTGTGTAAAATAAATTGCAGCT
Found at i:436770 original size:12 final size:11
Alignment explanation
Indices: 436752--436786 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
436742 ACTGAATTTT
436752 TAATTTTTTAA
1 TAATTTTTTAA
*
436763 TAAATTTTTAA
1 TAATTTTTTAA
436774 TAATTTATTTAA
1 TAATTT-TTTAA
436786 T
1 T
436787 CCAACCGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TAATTTTTTAA
Found at i:440301 original size:119 final size:115
Alignment explanation
Indices: 440089--440545 Score: 429
Period size: 119 Copynumber: 3.9 Consensus size: 115
440079 ATGACATAAT
* * * * * * *
440089 TCTTGGTCTCAGAGACACATCTCAAACAATGCTACCTTATCTCAAAATCATAAATTTCAAATCTT
1 TCTTGGTCTAAGAGACAGA-C-CAAACATTGGTACCTTATGTCAAAATCATAAAATTCAAATATT
* * * * * *
440154 TACACTTTGAAGTAATAATAAAAGGAATTTGTCATTGTACAGACACATATATG
64 TACATTTTAAAGTAACAATAAATGGAATTTGTCATAGTACACACACA-ATATG
* *
440207 TCCTTGGTCTAAGAGACACGGACCAAACATTGGTACTTTATGTCAAAATGATAAAATTCAAATAT
1 T-CTTGGTCTAAGAGACA--GACCAAACATTGGTACCTTATGTCAAAATCATAAAATTCAAATAT
* * * *
440272 TTACATTTTAAAGCAACAATAAATGGAATTTGCCATAGAACACACAAGCGAATCTG
63 TTACATTTTAAAGTAACAATAAATGGAATTTGTCATAGTACACAC-A-C-AATATG
* * * * *
440328 TCTTTGTCTCAGAGACAGATCAAACCTTGGTACCTTATGTCAAAAATCATGAAATTCAAATATTT
1 TCTTGGTCTAAGAGACAGACCAAACATTGGTACCTTATGTC-AAAATCATAAAATTCAAATATTT
* * * * *
440393 ACATTTTAAAGTAACAATAAATGGAATTAGTCATACTACACAGACACACACG
65 ACATTTTAAAGTAACAATAAATGGAATTTGTCATAGTACACACACA-ATATG
* * * * *
440445 TCTTGGTCTAACAGAGAGATCAAATATTGGCT-CCTT-TG--AAAAT-AAAAAATTTCAAATATT
1 TCTTGGTCTAAGAGACAGACCAAACATTGG-TACCTTATGTCAAAATCATAAAA-TTCAAATATT
* * *
440505 TACATCTTAAAGTGACAATAAATGGAATTTGTCATGGTACA
64 TACATTTTAAAGTAACAATAAATGGAATTTGTCATAGTACA
440546 TGGACATGTG
Statistics
Matches: 281, Mismatches: 48, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
112 4 0.01
113 51 0.18
116 3 0.01
117 31 0.11
118 24 0.09
119 144 0.51
120 16 0.06
121 7 0.02
122 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (115 bp):
TCTTGGTCTAAGAGACAGACCAAACATTGGTACCTTATGTCAAAATCATAAAATTCAAATATTTA
CATTTTAAAGTAACAATAAATGGAATTTGTCATAGTACACACACAATATG
Found at i:440686 original size:1 final size:1
Alignment explanation
Indices: 440680--440725 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
440670 ACAGAAAACC
* * **
440680 AAAAAAAAAAAAAAAAAAAAAAAAAACAAACAAGGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
440726 TGCAACAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.91, C:0.04, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:440709 original size:27 final size:27
Alignment explanation
Indices: 440674--440725 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
440664 AATTGAACAG
*
440674 AAAACCAAAAAAAAAAAAAAAAAAAAA
1 AAAAACAAAAAAAAAAAAAAAAAAAAA
* **
440701 AAAAACAAACAAGGAAAAAAAAAAA
1 AAAAACAAAAAAAAAAAAAAAAAAA
440726 TGCAACAAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (27 bp):
AAAAACAAAAAAAAAAAAAAAAAAAAA
Found at i:440732 original size:21 final size:22
Alignment explanation
Indices: 440693--440738 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
440683 AAAAAAAAAA
440693 AAAAAAAAAAAAACAAACAAGG
1 AAAAAAAAAAAAACAAACAAGG
**
440715 AAAAAAAAAAATGC-AACAAGG
1 AAAAAAAAAAAAACAAACAAGG
440736 AAA
1 AAA
440739 CAAATACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.78, C:0.09, G:0.11, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAAAACAAACAAGG
Found at i:448672 original size:118 final size:118
Alignment explanation
Indices: 448524--448967 Score: 856
Period size: 118 Copynumber: 3.8 Consensus size: 118
448514 AAACTAAACC
448524 TTTGACTGAAAATAGGAGCCATACTTAACAGAAACAATTTTAAACGAAAAATACAACCTAAAACC
1 TTTGACTGAAAATAGGAGCCATACTTAACAGAAACAATTTTAAACGAAAAATACAACCTAAAACC
448589 TTGCAACGCTCTCTAATCTAATTTTAAACAATTTTAAAAGATTATTTCTCAAA
66 TTGCAACGCTCTCTAATCTAATTTTAAACAATTTTAAAAGATTATTTCTCAAA
448642 TTTGACTGAAAATAGGAGCCATACTTAACAGAAACAATTTTAAACGAAAAATACAACCTAAAACC
1 TTTGACTGAAAATAGGAGCCATACTTAACAGAAACAATTTTAAACGAAAAATACAACCTAAAACC
448707 TTGCAACGCTCTCTAATCTAATTTTAAACAATTTTAAAAGATTATTTCTCAAA
66 TTGCAACGCTCTCTAATCTAATTTTAAACAATTTTAAAAGATTATTTCTCAAA
448760 TTTGACTGAAAATAGGAGCCATACTTAACAGAAACAATTTTTTAAACG--AAATACAACCTAAAA
1 TTTGACTGAAAATAGGAGCCATACTTAACAGAAACAA--TTTTAAACGAAAAATACAACCTAAAA
448823 CCTTGCAACGCTCTCTAATCTAATTTTAAACAATTTTAAAAGATTATTTCTCAAA
64 CCTTGCAACGCTCTCTAATCTAATTTTAAACAATTTTAAAAGATTATTTCTCAAA
448878 TTTGACTGAAAATAGGAGCCATACTTAACAGAAACAATTTTAAACGAAAAATACAACCTAAAACC
1 TTTGACTGAAAATAGGAGCCATACTTAACAGAAACAATTTTAAACGAAAAATACAACCTAAAACC
448943 TTGCAACGCTCTCTAATCTAATTTT
66 TTGCAACGCTCTCTAATCTAATTTT
448968 TGCATGAGGT
Statistics
Matches: 322, Mismatches: 0, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
116 9 0.03
118 304 0.94
120 9 0.03
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (118 bp):
TTTGACTGAAAATAGGAGCCATACTTAACAGAAACAATTTTAAACGAAAAATACAACCTAAAACC
TTGCAACGCTCTCTAATCTAATTTTAAACAATTTTAAAAGATTATTTCTCAAA
Found at i:449874 original size:47 final size:46
Alignment explanation
Indices: 449805--449893 Score: 151
Period size: 47 Copynumber: 1.9 Consensus size: 46
449795 TGTTGCTAGG
449805 AATGAAGTGGTCGGTGTTTGGATAGGAGGAAAGTGAAAGAAAACTAT
1 AATGAAGTGGTCGGTGTTTGGATAGGA-GAAAGTGAAAGAAAACTAT
* *
449852 AATGAAGTGGTGGGTGTTTGGATGGGAGAAAGTGAAAGAAAA
1 AATGAAGTGGTCGGTGTTTGGATAGGAGAAAGTGAAAGAAAA
449894 TGGTGCGACG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 15 0.38
47 25 0.62
ACGTcount: A:0.38, C:0.02, G:0.37, T:0.22
Consensus pattern (46 bp):
AATGAAGTGGTCGGTGTTTGGATAGGAGAAAGTGAAAGAAAACTAT
Found at i:450483 original size:6 final size:7
Alignment explanation
Indices: 450465--450489 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
450455 TAAGATGTAG
450465 TAAAAAA
1 TAAAAAA
450472 TAAAAAA
1 TAAAAAA
450479 TAAAAAA
1 TAAAAAA
450486 TAAA
1 TAAA
450490 TTATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:453925 original size:24 final size:24
Alignment explanation
Indices: 453898--453949 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
453888 CTAGTAGGTC
* *
453898 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
453922 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
453946 AAAT
1 AAAT
453950 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:460062 original size:19 final size:19
Alignment explanation
Indices: 460038--460085 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
460028 TTGTTTAAGT
* *
460038 TTAATATATTTTAATTTTA
1 TTAATATATTTCAATATTA
460057 TTAATACTATTTCAATATTA
1 TTAATA-TATTTCAATATTA
460077 -TAATATATT
1 TTAATATATT
460086 ATTATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 11 0.42
20 11 0.42
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATATATTTCAATATTA
Found at i:460198 original size:32 final size:31
Alignment explanation
Indices: 460143--460221 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
460133 TTGTTCAAAA
* *
460143 TTTATTATATATCTTTATTTAAATTTCCACAT-T
1 TTTA-TATATAT-TTTATGTAAA-TTCAACATGT
*
460176 TTTATATATATTTTCATGTAAATTCAATATGT
1 TTTATATATATTTT-ATGTAAATTCAACATGT
*
460208 TTTATATACATTTT
1 TTTATATATATTTT
460222 TTTAATATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 9 0.22
32 27 0.68
33 4 0.10
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.57
Consensus pattern (31 bp):
TTTATATATATTTTATGTAAATTCAACATGT
Found at i:466498 original size:142 final size:142
Alignment explanation
Indices: 466242--466603 Score: 589
Period size: 142 Copynumber: 2.5 Consensus size: 142
466232 AAGGAAGCAA
* * *
466242 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGAAACAGATTGAAGCTAGTAATCCTATC
1 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATC
* * ***
466307 TCCCTGAGATTACAGTGGAGTTGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGT
66 TCCCTAAGATTACAGTAGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGT
*
466372 AGATCGCATCAG
131 AGATCACATCAG
* *
466384 ATTGAAGCCAGAAATCTTATCTCCCTGAAATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATC
1 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATC
*
466449 TCCCTAAGATTACAGTAGAACGGATTAAAATAAAGGGTCTTATCTCTCTGAAGTTACAGTAGAGT
66 TCCCTAAGATTACAGTAGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGT
466514 AGATCACATCAG
131 AGATCACATCAG
* * *
466526 ATTAAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATT
1 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATC
466591 TCCCTAAGATTAC
66 TCCCTAAGATTAC
466604 GGTGGAATAG
Statistics
Matches: 203, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 203 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (142 bp):
ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATC
TCCCTAAGATTACAGTAGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGT
AGATCACATCAG
Found at i:466913 original size:50 final size:50
Alignment explanation
Indices: 466859--467341 Score: 393
Period size: 50 Copynumber: 9.7 Consensus size: 50
466849 ATAGTGGAGC
*
466859 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACGTTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACGTTGCAGTTAAAA
* * * * * ** **
466909 AGATTAAAGCCACAGCGGTGAATCCTACTTCCCTGGAAG-TGCAGTGGAGT
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCC-CGACGTTGCAGTTAAAA
* *
466959 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACGTTGCAGTTAAAA
* ** * * * * ** *
467009 AGATTAAAGCCAGAGT-GGCAAATCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACA-TCGGTGAATCTTGCTTCCCCGACGTTGCAGTTAAAA
* *
467059 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGATAAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACGTTGCAGTTAAAA
* * * * * * * * ** **
467109 AGATTAAAGCCACAACGGTGAATCCTACTGCCCTGGCGATGCCGTGGAGT
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACGTTGCAGTTAAAA
* * *
467159 AGATTAAAGCCATATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACGTTGCAGTTAAAA
* * * * * *
467209 AGATTAAAGCCACAGT-GGCGAATCTTAC-CCCCCAAGCGATGCA-TGGAAACA
1 AGATTAAAGCCACA-TCGGTGAATCTTGCTTCCCCGA-CGTTGCAGT-TAAA-A
* * *
467260 A-ATTAAAGCCACAACGGTGAATCTTGTTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACGTTGCAGTTAAAA
* * * * *
467309 AGATTAAAGCTACAACAGCGAATCTTACTTCCC
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCC
467342 AGGCGGTGTA
Statistics
Matches: 324, Mismatches: 97, Indels: 24
0.73 0.22 0.05
Matches are distributed among these distances:
49 11 0.03
50 300 0.93
51 13 0.04
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACGTTGCAGTTAAAA
Found at i:467360 original size:100 final size:100
Alignment explanation
Indices: 466641--467368 Score: 789
Period size: 100 Copynumber: 7.3 Consensus size: 100
466631 CTTACTCTTT
* * * * *
466641 CAGGCAGTGCAGTGGAGCAGATTAAAACCACATCGGTGAATCTCGCTT-CCCGGCATTACAGTTA
1 CAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTA
* * * *
466705 AAAAGATTAAAGCTATAGCAGCGAATCTTACTTCT
66 AAAAGATTAAAGCCACAGCGGCGAATCTTACTTCC
* * * * * ** * *
466740 CTGGCGGT-TACGTGGAATAGATTAAAACCACAACGGCAAATCTCACTTCCCCGACAATAGCAGT
1 CAGGCGGTGCA-GTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGAC-ATTGCAGT
* * * *
466804 TAAAAAGGTTAAAGCCACAACGGCAAATCCTACTTCTC
64 TAAAAAGATTAAAGCCACAGCGGCGAATCTTACTTC-C
* ** * *
466842 TA-GCGGTATAGTGGAGCAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACGTTGCAGTTA
1 CAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTA
* *
466906 AAAAGATTAAAGCCACAGCGGTGAATCCTACTTCC
66 AAAAGATTAAAGCCACAGCGGCGAATCTTACTTCC
* ** **
466941 CTGGAAGTGCAGTGGAGTAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTA
1 CAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTA
* * *
467006 AAAAGATTAAAGCCAGAGTGGCAAATCTTACTTCC
66 AAAAGATTAAAGCCACAGCGGCGAATCTTACTTCC
* * *
467041 CTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGATA
1 CAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTA
* * * *
467106 AAAAGATTAAAGCCACAACGGTGAATCCTACTGCC
66 AAAAGATTAAAGCCACAGCGGCGAATCTTACTTCC
* * * ** * * *
467141 CTGGCGATGCCGTGGAGTAGATTAAAGCCATATCAGTGAATCTTGCTTCCCCGACATTGCAGTTA
1 CAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTA
* **
467206 AAAAGATTAAAGCCACAGTGGCGAATCTTACCCCC
66 AAAAGATTAAAGCCACAGCGGCGAATCTTACTTCC
* * * * * *
467241 CAAGCGATGCA-TGGAAACAAATTAAAGCCACAACGGTGAATCTTGTTTCCCCGACATTGCAGTT
1 CAGGCGGTGCAGTGG-AACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTT
* * *
467305 AAAAAGATTAAAGCTACAACAGCGAATCTTACTTCC
65 AAAAAGATTAAAGCCACAGCGGCGAATCTTACTTCC
* * *
467341 CAGGCGGTGTAGTGGAACAAATTGAAGC
1 CAGGCGGTGCAGTGGAACAGATTAAAGC
467369 TACAATAGCG
Statistics
Matches: 527, Mismatches: 94, Indels: 15
0.83 0.15 0.02
Matches are distributed among these distances:
98 1 0.00
99 41 0.08
100 403 0.76
101 80 0.15
102 2 0.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (100 bp):
CAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTA
AAAAGATTAAAGCCACAGCGGCGAATCTTACTTCC
Found at i:468517 original size:18 final size:18
Alignment explanation
Indices: 468482--468524 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
468472 AAAATAAAGG
* **
468482 AAGAAATAAATTTTTTTT
1 AAGAAAAAAATTGGTTTT
468500 AAGAAAAAAATTGGTTTT
1 AAGAAAAAAATTGGTTTT
468518 ATAGAAA
1 A-AGAAA
468525 CCCTAAACGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (18 bp):
AAGAAAAAAATTGGTTTT
Found at i:469074 original size:19 final size:19
Alignment explanation
Indices: 469050--469097 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
469040 TTGTTTAAGT
* *
469050 TTAATATATTTTAATTTTA
1 TTAATATATTTCAATATTA
469069 TTAATACTATTTCAATATTA
1 TTAATA-TATTTCAATATTA
469089 -TAATATATT
1 TTAATATATT
469098 ATTATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 11 0.42
20 11 0.42
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATATATTTCAATATTA
Found at i:469210 original size:32 final size:31
Alignment explanation
Indices: 469155--469233 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
469145 TTGTTCAAAA
* *
469155 TTTATTATATATCTTTATTTAAATTTCCACAT-T
1 TTTA-TATATAT-TTTATGTAAA-TTCAACATGT
*
469188 TTTATATATATTTTCATGTAAATTCAATATGT
1 TTTATATATATTTT-ATGTAAATTCAACATGT
*
469220 TTTATATACATTTT
1 TTTATATATATTTT
469234 TTATATTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 9 0.22
32 27 0.68
33 4 0.10
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.57
Consensus pattern (31 bp):
TTTATATATATTTTATGTAAATTCAACATGT
Found at i:469455 original size:29 final size:30
Alignment explanation
Indices: 469423--469502 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 30
469413 ATTTTATCTC
469423 TTTCAAA-TATTTTAACATTTTTTAATTTA
1 TTTCAAATTATTTTAACATTTTTTAATTTA
* * *
469452 TTTCAAATTATTTCAATA-TTGTTAATTTA
1 TTTCAAATTATTTTAACATTTTTTAATTTA
469481 TTT-AAATTTATTTTAACATTTT
1 TTTCAAA-TTATTTTAACATTTT
469503 AATTCATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 3 0.07
29 29 0.69
30 10 0.24
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTCAAATTATTTTAACATTTTTTAATTTA
Found at i:472194 original size:38 final size:38
Alignment explanation
Indices: 472136--472212 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
472126 GCTTGGTGGG
* *
472136 GGAGCGTTGGAGTGATTTTAGGAGGAAAATATGGGATT
1 GGAGCGTTGGAGTGACTTTAGGAGGAAAATATAGGATT
*
472174 GGAGTGTTGGAGTGACTTTAGGAGGAAAATATAGGATT
1 GGAGCGTTGGAGTGACTTTAGGAGGAAAATATAGGATT
472212 G
1 G
472213 TAGAGTTATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.30, C:0.03, G:0.39, T:0.29
Consensus pattern (38 bp):
GGAGCGTTGGAGTGACTTTAGGAGGAAAATATAGGATT
Found at i:475539 original size:111 final size:112
Alignment explanation
Indices: 475409--475633 Score: 425
Period size: 112 Copynumber: 2.0 Consensus size: 112
475399 ATATAAGAGA
475409 ATCTTTGACTTTTAGTATAGTATGCCTATATATAATATTAATTA-TTTTTCACTAATTGTACATA
1 ATCTTTGACTTTTAGTATAGTATGCCTATATATAATATTAATTATTTTTTCACTAATTGTACATA
* *
475473 TACTTTTAATAGGGTTGTCTACTTGAGTAGTTGTCACTAAATTATTT
66 TACTTTTAATAAGGTTGTCTACTTAAGTAGTTGTCACTAAATTATTT
475520 ATCTTTGACTTTTAGTATAGTATGCCTATATATAATATTAATTATTTTTTCACTAATTGTACATA
1 ATCTTTGACTTTTAGTATAGTATGCCTATATATAATATTAATTATTTTTTCACTAATTGTACATA
475585 TACTTTTAATAAGGTTGTCTACTTAAGTAGTTGTCACTAAATTATTT
66 TACTTTTAATAAGGTTGTCTACTTAAGTAGTTGTCACTAAATTATTT
475632 AT
1 AT
475634 ATTTTAGCCT
Statistics
Matches: 111, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
111 44 0.40
112 67 0.60
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (112 bp):
ATCTTTGACTTTTAGTATAGTATGCCTATATATAATATTAATTATTTTTTCACTAATTGTACATA
TACTTTTAATAAGGTTGTCTACTTAAGTAGTTGTCACTAAATTATTT
Found at i:488351 original size:29 final size:29
Alignment explanation
Indices: 488309--488367 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
488299 TTGATTGTCT
488309 TAATATTTATTATGTAGGATTTTTAATTA
1 TAATATTTATTATGTAGGATTTTTAATTA
488338 TAATATTTATTATGTAGGATTTTTAATTA
1 TAATATTTATTATGTAGGATTTTTAATTA
488367 T
1 T
488368 GTTTCTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (29 bp):
TAATATTTATTATGTAGGATTTTTAATTA
Found at i:488368 original size:17 final size:17
Alignment explanation
Indices: 488317--488369 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
488307 CTTAATATTT
488317 ATTATGTAGGATTTTTA
1 ATTATGTAGGATTTTTA
*
488334 ATTA--TA--ATATTT-
1 ATTATGTAGGATTTTTA
488346 ATTATGTAGGATTTTTA
1 ATTATGTAGGATTTTTA
488363 ATTATGT
1 ATTATGT
488370 TTCTTTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 4 0.14
13 5 0.17
14 2 0.07
15 2 0.07
16 5 0.17
17 11 0.38
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (17 bp):
ATTATGTAGGATTTTTA
Found at i:493010 original size:20 final size:22
Alignment explanation
Indices: 492970--493010 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
492960 TTTCTTTACT
*
492970 TTTAGTTGATATTCTATTATTA
1 TTTAGTTGATATTCTAATATTA
492992 TTTAGTTG-T-TTCTAATATT
1 TTTAGTTGATATTCTAATATT
493011 TTATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (22 bp):
TTTAGTTGATATTCTAATATTA
Found at i:519135 original size:13 final size:13
Alignment explanation
Indices: 519117--519143 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
519107 AAGGGAAGGG
519117 ATCCACTTGCACA
1 ATCCACTTGCACA
519130 ATCCACTTGCACA
1 ATCCACTTGCACA
519143 A
1 A
519144 GTATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.37, G:0.07, T:0.22
Consensus pattern (13 bp):
ATCCACTTGCACA
Found at i:519723 original size:44 final size:44
Alignment explanation
Indices: 519635--519725 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
519625 ATAAATGTAA
* * * * * *
519635 ATTATAATTATAATTATTTTAAATGTGTAATTTTCACAATTTCT
1 ATTATAATTATAATTATTTGAAATGTATAATTATAAAAAATTCT
519679 ATTA-AATTATAATTATTGTGAAATGTATAATTATAAAAAATTCT
1 ATTATAATTATAATTATT-TGAAATGTATAATTATAAAAAATTCT
519723 ATT
1 ATT
519726 TTATTCCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
43 13 0.32
44 27 0.68
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (44 bp):
ATTATAATTATAATTATTTGAAATGTATAATTATAAAAAATTCT
Found at i:525807 original size:13 final size:13
Alignment explanation
Indices: 525789--525817 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
525779 TTACTTAACT
525789 TAAAAATATTAAG
1 TAAAAATATTAAG
525802 TAAAAATATTAAG
1 TAAAAATATTAAG
525815 TAA
1 TAA
525818 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (13 bp):
TAAAAATATTAAG
Found at i:525967 original size:26 final size:26
Alignment explanation
Indices: 525938--525987 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
525928 TAGTGATTGG
525938 TTTGACCAACTAATTCTAATAACTAA
1 TTTGACCAACTAATTCTAATAACTAA
** * *
525964 TTTGATTAACTGATTCTATTAACT
1 TTTGACCAACTAATTCTAATAACT
525988 GTTTATTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (26 bp):
TTTGACCAACTAATTCTAATAACTAA
Found at i:525988 original size:13 final size:13
Alignment explanation
Indices: 525945--525987 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
525935 TGGTTTGACC
*
525945 AACTAATTCTAAT
1 AACTAATTCTATT
525958 AACTAATT-TGATT
1 AACTAATTCT-ATT
*
525971 AACTGATTCTATT
1 AACTAATTCTATT
525984 AACT
1 AACT
525988 GTTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (13 bp):
AACTAATTCTATT
Found at i:529246 original size:21 final size:20
Alignment explanation
Indices: 529222--529275 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
529212 CCATTGTTTC
*
529222 CAATCTCACCGCTACAGTATT
1 CAATCTCACCGCTACAGTA-A
529243 CAATCTCACCGCTACAGTAA
1 CAATCTCACCGCTACAGTAA
529263 CTAATCTCACCGC
1 C-AATCTCACCGC
529276 CACCGTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.30, C:0.37, G:0.09, T:0.24
Consensus pattern (20 bp):
CAATCTCACCGCTACAGTAA
Found at i:529795 original size:25 final size:24
Alignment explanation
Indices: 529767--529814 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
529757 GCTATGATAT
* *
529767 TAAATATATTTTATTTTAGTTAAAG
1 TAAATA-ATTTAAATTTAGTTAAAG
*
529792 TAAATAGTTTAAATTTAGTTAAA
1 TAAATAATTTAAATTTAGTTAAA
529815 CCTTTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (24 bp):
TAAATAATTTAAATTTAGTTAAAG
Found at i:530041 original size:21 final size:20
Alignment explanation
Indices: 530003--530041 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
529993 TATTATATTA
530003 TAAAAATCAATTATATATGT
1 TAAAAATCAATTATATATGT
530023 TAAATAAT-AATTAATATAT
1 TAAA-AATCAATT-ATATAT
530042 ACTTATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
TAAAAATCAATTATATATGT
Found at i:537759 original size:26 final size:25
Alignment explanation
Indices: 537712--537761 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
537702 CTCAAAAAAG
*
537712 AAAAAAAACTCCATCATAAATCTAC
1 AAAAAAAACTCCACCATAAATCTAC
* *
537737 AAAAACAAACTCCACCGTGAATCTA
1 AAAAA-AAACTCCACCATAAATCTA
537762 TTTAAATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.52, C:0.26, G:0.04, T:0.18
Consensus pattern (25 bp):
AAAAAAAACTCCACCATAAATCTAC
Found at i:546157 original size:44 final size:46
Alignment explanation
Indices: 546075--546162 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 46
546065 GATGTAATGA
* * * *
546075 AATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGGAATAG
1 AATAGAGACGTAATAGGTAATTCTTGTGCTTAGTTGAATGGAATAG
546121 AATAGAGACGTAATA-GT-ATTCTTGTGCTTAGTTGAATGGAAT
1 AATAGAGACGTAATAGGTAATTCTTGTGCTTAGTTGAATGGAAT
546163 GGATGTGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 22 0.58
45 2 0.05
46 14 0.37
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (46 bp):
AATAGAGACGTAATAGGTAATTCTTGTGCTTAGTTGAATGGAATAG
Found at i:546343 original size:18 final size:17
Alignment explanation
Indices: 546322--546356 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
546312 TTATTATTAA
*
546322 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
546340 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
546357 TCTTAATANN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:547947 original size:48 final size:49
Alignment explanation
Indices: 547876--547977 Score: 145
Period size: 48 Copynumber: 2.1 Consensus size: 49
547866 AAAAAAAAAC
* *
547876 AAATTAAATTTAAGTTTAATATCATGAATCAAAAG-TGAACACTTTATA
1 AAATTAAATTTAAGTTAAATATCATGAATCAAAAGCTGAACACTATATA
*
547924 AAATTATAA-TTAAGTTAAATATCATGAATCAAAAGCTTAACACTATATA
1 AAATTA-AATTTAAGTTAAATATCATGAATCAAAAGCTGAACACTATATA
*
547973 TAATT
1 AAATT
547978 TCATAACACA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
48 31 0.65
49 17 0.35
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (49 bp):
AAATTAAATTTAAGTTAAATATCATGAATCAAAAGCTGAACACTATATA
Found at i:551659 original size:20 final size:20
Alignment explanation
Indices: 551629--551674 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
551619 TCTGAATCAC
*
551629 TACCAAACGAACCAACCAAA
1 TACCCAACGAACCAACCAAA
*
551649 TGCCCAACGAACCAACCAAA
1 TACCCAACGAACCAACCAAA
551669 TACCCA
1 TACCCA
551675 GTAACCAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.39, G:0.07, T:0.07
Consensus pattern (20 bp):
TACCCAACGAACCAACCAAA
Found at i:557329 original size:16 final size:15
Alignment explanation
Indices: 557292--557339 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
557282 TGAAATTTAA
557292 AAATAAAGAATAAAT
1 AAATAAAGAATAAAT
** *
557307 ATTTAAAGTAATAACT
1 AAATAAAG-AATAAAT
557323 AAATAAAGAA-AAAT
1 AAATAAAGAATAAAT
557337 AAA
1 AAA
557340 CTAGGTGGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 6 0.23
15 8 0.31
16 12 0.46
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (15 bp):
AAATAAAGAATAAAT
Found at i:561518 original size:24 final size:22
Alignment explanation
Indices: 561487--561536 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
561477 CCTAAAAATG
*
561487 AAAATAAACATAC-AAAACAATAT
1 AAAATAAA-AAACTAAAAC-ATAT
561510 AAAAGTAAAAAACTAAAACATAT
1 AAAA-TAAAAAACTAAAACATAT
561533 AAAA
1 AAAA
561537 ATATGTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.72, C:0.10, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAATAAAAAACTAAAACATAT
Found at i:563639 original size:22 final size:22
Alignment explanation
Indices: 563614--563688 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
563604 TGTTGAAGAA
563614 ATCGCGATATCCTCATTTAGAT
1 ATCGCGATATCCTCATTTAGAT
* * * *
563636 ATCGCGATTTCACT-GTATAAGAA
1 ATCGCGATATC-CTCAT-TTAGAT
* *
563659 ATTGCGATATCCTCCTTTAGAT
1 ATCGCGATATCCTCATTTAGAT
563681 ATCGCGAT
1 ATCGCGAT
563689 TTCATTGTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
22 24 0.60
23 16 0.40
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCGCGATATCCTCATTTAGAT
Found at i:563660 original size:45 final size:45
Alignment explanation
Indices: 563609--563700 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
563599 GAATATGTTG
563609 AAGAAATCGCGATATCCTCATTTAGATATCGCGATTTCACTGTAT
1 AAGAAATCGCGATATCCTCATTTAGATATCGCGATTTCACTGTAT
* * *
563654 AAGAAATTGCGATATCCTCCTTTAGATATCGCGATTTCATTGTAT
1 AAGAAATCGCGATATCCTCATTTAGATATCGCGATTTCACTGTAT
563699 AA
1 AA
563701 CTCCCCAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (45 bp):
AAGAAATCGCGATATCCTCATTTAGATATCGCGATTTCACTGTAT
Found at i:578891 original size:17 final size:17
Alignment explanation
Indices: 578869--578903 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
578859 CTAATATGTG
578869 TAAGATTCAAAAGACCT
1 TAAGATTCAAAAGACCT
578886 TAAGATTCAAAAGACCT
1 TAAGATTCAAAAGACCT
578903 T
1 T
578904 CCTTCTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (17 bp):
TAAGATTCAAAAGACCT
Found at i:579115 original size:13 final size:14
Alignment explanation
Indices: 579088--579120 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
579078 AATTTTAATT
579088 TTAATTTTTATACA
1 TTAATTTTTATACA
579102 TTAATTTTTA-ACA
1 TTAATTTTTATACA
*
579115 TAAATT
1 TTAATT
579121 GGTCCCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAATTTTTATACA
Found at i:580420 original size:23 final size:21
Alignment explanation
Indices: 580386--580427 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
580376 TTTTATTCAA
580386 AAAACTATAATAACAAATTATGC
1 AAAACTATAAT-AC-AATTATGC
580409 AAAA-TATAAATACAATTAT
1 AAAACTAT-AATACAATTAT
580428 CGACATGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAACTATAATACAATTATGC
Found at i:589887 original size:25 final size:25
Alignment explanation
Indices: 589841--589923 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
589831 ACGCAATTCA
* * *
589841 AACAGAACAGAACCGAATAGAGTAG
1 AACAGAACAGGACGGAACAGAGTAG
* *
589866 AACAGAACAGGATGGAACAGAGCAG
1 AACAGAACAGGACGGAACAGAGTAG
* * * *
589891 AACAAAACAAGAGGGAACAGAATAG
1 AACAGAACAGGACGGAACAGAGTAG
*
589916 AACGGAAC
1 AACAGAAC
589924 GGAGCAGACC
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.53, C:0.16, G:0.27, T:0.05
Consensus pattern (25 bp):
AACAGAACAGGACGGAACAGAGTAG
Found at i:590462 original size:43 final size:43
Alignment explanation
Indices: 590408--590687 Score: 268
Period size: 43 Copynumber: 6.6 Consensus size: 43
590398 TTTGGAAAAG
* *
590408 CGCCGCTAAAGACCATGACATTTAGCGACGCTTCTCCTACAAA
1 CGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTCCTACAAA
* * *
590451 CGCCGCAAAAGACGC-TGACCTTTAGCGGCGCTTCTCCCATAAA
1 CGCCGCTAAAGAC-CATGACCTTTAGCGGCGCTTCTCCTACAAA
** * * * *
590494 CATCGCGATAGACCCTGACCTTTAGCGGCGCTT-TTCTCACAAA
1 CGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTCCT-ACAAA
* * *
590537 CACCGCTAAAGACCACGACCTTTAGCGGCGCTTCTCCCACAAA
1 CGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTCCTACAAA
**
590580 CGCCGCTAAAGACCACT-ACCTTTAGCGGCGCTT-TTATCACAAA
1 CGCCGCTAAAGACCA-TGACCTTTAGCGGCGCTTCTCCT-ACAAA
* * * *
590623 CGCCGCTAAAGAACA-AACCTTTAGCGGCGCTTCTAGC-AAAAA
1 CGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCT-CCTACAAA
* *
590665 CGCCGCTAAA-AACATAACCTTTA
1 CGCCGCTAAAGACCATGACCTTTA
590688 AAAAAATTAT
Statistics
Matches: 199, Mismatches: 28, Indels: 21
0.80 0.11 0.08
Matches are distributed among these distances:
41 4 0.02
42 42 0.21
43 150 0.75
44 3 0.02
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.20
Consensus pattern (43 bp):
CGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTCCTACAAA
Found at i:590536 original size:86 final size:85
Alignment explanation
Indices: 590410--590656 Score: 300
Period size: 86 Copynumber: 2.9 Consensus size: 85
590400 TGGAAAAGCG
* * * * * * *
590410 CCGCTAAAGACCATGACATTTAGCGACGCTTCTC-CTACAAACGCCGCAAAAGACGCTGACCTTT
1 CCGCGAAAGACCCTGACCTTTAGCGGCGCTTTTCTC-ACAAACGCCGCTAAAGAC-CAGACCTTT
*
590474 AGCGGCGCTTCTCCCATAAACA
64 AGCGGCGCTTCTCCCACAAACA
* * *
590496 TCGCGATAGACCCTGACCTTTAGCGGCGCTTTTCTCACAAACACCGCTAAAGACCACGACCTTTA
1 CCGCGAAAGACCCTGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCA-GACCTTTA
*
590561 GCGGCGCTTCTCCCACAAACG
65 GCGGCGCTTCTCCCACAAACA
* * * *
590582 CCGCTAAAGACCACT-ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACAAACCTTTA
1 CCGCGAAAGACC-CTGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAGACCTTTA
590646 GCGGCGCTTCT
65 GCGGCGCTTCT
590657 AGCAAAAACG
Statistics
Matches: 139, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
85 19 0.14
86 117 0.84
87 3 0.02
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.21
Consensus pattern (85 bp):
CCGCGAAAGACCCTGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAGACCTTTAG
CGGCGCTTCTCCCACAAACA
Found at i:592544 original size:31 final size:31
Alignment explanation
Indices: 592506--592567 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
592496 GAATAAAAGC
*
592506 ACCTGGGTTAAAAACAAACACAGACGAGACT
1 ACCTGGGTTAAAAACAAACACAAACGAGACT
592537 ACCTGGGTTAAAAACAAACACAAACGAGACT
1 ACCTGGGTTAAAAACAAACACAAACGAGACT
592568 CTATCACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.13
Consensus pattern (31 bp):
ACCTGGGTTAAAAACAAACACAAACGAGACT
Found at i:594596 original size:15 final size:15
Alignment explanation
Indices: 594576--594604 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
594566 ATAATTTAAA
594576 CTATCTCCTAAACCT
1 CTATCTCCTAAACCT
594591 CTATCTCCTAAACC
1 CTATCTCCTAAACC
594605 CTAAATCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.41, G:0.00, T:0.31
Consensus pattern (15 bp):
CTATCTCCTAAACCT
Found at i:594745 original size:28 final size:28
Alignment explanation
Indices: 594709--594775 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
594699 AATTAATCTA
* * * * *
594709 AACCTTAAATCACTAACTCTTAACCCCT
1 AACCCTAAACCACAAACCCTTAACCACT
* *
594737 AACCCTAAACCCCAAACCCTTAACTACT
1 AACCCTAAACCACAAACCCTTAACCACT
594765 AACCCTAAACC
1 AACCCTAAACC
594776 TTATTTAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.39, C:0.40, G:0.00, T:0.21
Consensus pattern (28 bp):
AACCCTAAACCACAAACCCTTAACCACT
Found at i:594747 original size:14 final size:14
Alignment explanation
Indices: 594730--594775 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
594720 ACTAACTCTT
594730 AACCCCTAACCCTA
1 AACCCCTAACCCTA
* *
594744 AACCCCAAACCCTT
1 AACCCCTAACCCTA
**
594758 AACTACTAACCCTA
1 AACCCCTAACCCTA
594772 AACC
1 AACC
594776 TTATTTAATA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.39, C:0.46, G:0.00, T:0.15
Consensus pattern (14 bp):
AACCCCTAACCCTA
Found at i:594810 original size:105 final size:101
Alignment explanation
Indices: 594670--594859 Score: 265
Period size: 105 Copynumber: 1.8 Consensus size: 101
594660 TATATAAGAA
* *
594670 CTTAATTAATATATAAATTAAAAAATACTAATTAATCTAAACCTTAAA-TCACTAACTCTTAACC
1 CTTAATTAATATATAAATTAAAAAATACTAATTAATCTAAACCCTAAAGT--CTAACTC-AAACC
594734 CCTAACCCTAAACCCCAAACCCTTAACTACTAACCCTAAAC
63 CCTAACCCT-AA-CCCAAACCCTTAACTACTAACCCTAAAC
* * * *
594775 CTTATTTAATATGTAAATTTAAAAATACTAATTAATCTAAACCCTAAAGTCTAACTCAAATCCCT
1 CTTAATTAATATATAAATTAAAAAATACTAATTAATCTAAACCCTAAAGTCTAACTCAAACCCCT
*
594840 AACCCTAACCCTAACCCTTA
66 AACCCTAACCCAAACCCTTA
594860 GCCCCTAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
101 11 0.14
102 2 0.03
103 12 0.16
104 7 0.09
105 44 0.57
106 1 0.01
ACGTcount: A:0.43, C:0.26, G:0.01, T:0.29
Consensus pattern (101 bp):
CTTAATTAATATATAAATTAAAAAATACTAATTAATCTAAACCCTAAAGTCTAACTCAAACCCCT
AACCCTAACCCAAACCCTTAACTACTAACCCTAAAC
Found at i:595363 original size:41 final size:41
Alignment explanation
Indices: 595304--595411 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
595294 AATGTTTTTT
*
595304 CGGCGC-TTTCCAAAAACGCCGCTAAAGCCTT-AAGCATTAG
1 CGGCGCTTTTTCAAAAACGCCGCTAAAG-CTTCAAGCATTAG
*
595344 CGGCGCTTTTTCAAAAACGCCGCTAAAGCTTCGAGCATTAG
1 CGGCGCTTTTTCAAAAACGCCGCTAAAGCTTCAAGCATTAG
*
595385 CGGCGCTTTCTCAAAAACGCCGCTAAA
1 CGGCGCTTTTTCAAAAACGCCGCTAAA
595412 AGCCCCGAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
40 9 0.14
41 54 0.86
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (41 bp):
CGGCGCTTTTTCAAAAACGCCGCTAAAGCTTCAAGCATTAG
Found at i:620720 original size:9 final size:9
Alignment explanation
Indices: 620706--620736 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
620696 GTTAAACGAA
620706 TCGAGTTAT
1 TCGAGTTAT
*
620715 TCGAGTTAA
1 TCGAGTTAT
620724 TCGAGTTAT
1 TCGAGTTAT
620733 TCGA
1 TCGA
620737 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:620806 original size:9 final size:9
Alignment explanation
Indices: 620789--620825 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
620779 TGAGTTTTCG
620789 AATTCGAAT
1 AATTCGAAT
*
620798 AACTCGAAT
1 AATTCGAAT
620807 AATTCGAAT
1 AATTCGAAT
620816 AATTCGAAT
1 AATTCGAAT
620825 A
1 A
620826 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:622301 original size:5 final size:5
Alignment explanation
Indices: 622291--622316 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
622281 CTCGAAAATT
622291 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
622317 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:626693 original size:101 final size:102
Alignment explanation
Indices: 626557--626760 Score: 401
Period size: 101 Copynumber: 2.0 Consensus size: 102
626547 ACATAAATTT
626557 TGATTTGATACAATTATATATATAAAATTTTGATTATGGTTCAAAATTATATAAAAAAAAATAAT
1 TGATTTGATACAATTATATATATAAAATTTTGATTATGGTTCAAAATTATATAAAAAAAAATAAT
626622 TTTGATTCAATTATAAACATTTAAAGAAACAAATACA
66 TTTGATTCAATTATAAACATTTAAAGAAACAAATACA
626659 TGATTTGATAC-ATTATATATATAAAATTTTGATTATGGTTCAAAATTATATAAAAAAAAATAAT
1 TGATTTGATACAATTATATATATAAAATTTTGATTATGGTTCAAAATTATATAAAAAAAAATAAT
626723 TTTGATTCAATTATAAACATTTAAAGAAACAAATACA
66 TTTGATTCAATTATAAACATTTAAAGAAACAAATACA
626760 T
1 T
626761 CATATAATTA
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 91 0.89
102 11 0.11
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.38
Consensus pattern (102 bp):
TGATTTGATACAATTATATATATAAAATTTTGATTATGGTTCAAAATTATATAAAAAAAAATAAT
TTTGATTCAATTATAAACATTTAAAGAAACAAATACA
Found at i:627044 original size:3 final size:3
Alignment explanation
Indices: 627038--627080 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
627028 TTCTTCTTCT
627038 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 T
627081 CTTTTGGGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:627277 original size:11 final size:11
Alignment explanation
Indices: 627261--627285 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
627251 AATTATAGAA
627261 ATTTTAAAAAT
1 ATTTTAAAAAT
627272 ATTTTAAAAAT
1 ATTTTAAAAAT
627283 ATT
1 ATT
627286 AAAATCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:627793 original size:20 final size:20
Alignment explanation
Indices: 627764--627807 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
627754 GTTGATGAGA
*
627764 AAAATGT-AAATATAAATTAT
1 AAAATGTAAAACATAAA-TAT
*
627784 AAAATTTAAAACATAAATAT
1 AAAATGTAAAACATAAATAT
627804 AAAA
1 AAAA
627808 ATATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAATGTAAAACATAAATAT
Found at i:630722 original size:3 final size:3
Alignment explanation
Indices: 630714--631524 Score: 1622
Period size: 3 Copynumber: 270.3 Consensus size: 3
630704 NNNNNNNNNN
630714 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
630762 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
630810 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
630858 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
630906 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
630954 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631002 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631050 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631098 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631146 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631194 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631242 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631290 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631338 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631386 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631434 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
631482 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 T
631525 CTTTTGGGTA
Statistics
Matches: 808, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 808 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:631721 original size:11 final size:11
Alignment explanation
Indices: 631705--631729 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
631695 AATTATAGAA
631705 ATTTTAAAAAT
1 ATTTTAAAAAT
631716 ATTTTAAAAAT
1 ATTTTAAAAAT
631727 ATT
1 ATT
631730 AAAATCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:632237 original size:20 final size:20
Alignment explanation
Indices: 632208--632251 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
632198 GTTGATGAGA
*
632208 AAAATGT-AAATATAAATTAT
1 AAAATGTAAAACATAAA-TAT
*
632228 AAAATTTAAAACATAAATAT
1 AAAATGTAAAACATAAATAT
632248 AAAA
1 AAAA
632252 ATATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAATGTAAAACATAAATAT
Found at i:633042 original size:3 final size:3
Alignment explanation
Indices: 633036--633078 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
633026 TTCTTCTTCT
633036 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 T
633079 CTTTTGGGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:633275 original size:11 final size:11
Alignment explanation
Indices: 633259--633283 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
633249 AATTATAGAA
633259 ATTTTAAAAAT
1 ATTTTAAAAAT
633270 ATTTTAAAAAT
1 ATTTTAAAAAT
633281 ATT
1 ATT
633284 AAAATCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:633791 original size:20 final size:20
Alignment explanation
Indices: 633762--633805 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
633752 GTTGATGAGA
*
633762 AAAATGT-AAATATAAATTAT
1 AAAATGTAAAACATAAA-TAT
*
633782 AAAATTTAAAACATAAATAT
1 AAAATGTAAAACATAAATAT
633802 AAAA
1 AAAA
633806 ATATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAATGTAAAACATAAATAT
Done.