Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009586.1 Hibiscus syriacus cultivar Beakdansim tig00116964_pilon, whole genome shotgun sequence
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: 3773412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 19
Found at i:3094220 original size:23 final size:23
Alignment explanation
Indices: 3094160--3094228 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3094150 CACCACAGCT
* **
3094160 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
*
3094183 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
* *
3094206 CGTAGAATTGTACCGTAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
3094229 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:3094467 original size:26 final size:27
Alignment explanation
Indices: 3094438--3094491 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3094428 CATATTTGTA
* *
3094438 TCAC-AGACATATTATTTTCATACCTT
1 TCACTAGACATATCATTTCCATACCTT
3094464 TCACTAGACATATCATTTCCATACCTT
1 TCACTAGACATATCATTTCCATACCTT
3094491 T
1 T
3094492 ATCACATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.41
Consensus pattern (27 bp):
TCACTAGACATATCATTTCCATACCTT
Found at i:3094539 original size:33 final size:33
Alignment explanation
Indices: 3094501--3094566 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
3094491 TATCACATAA
3094501 CTCATATAACTTTTTCTTGCATATTCATATCAC
1 CTCATATAACTTTTTCTTGCATATTCATATCAC
3094534 CTCATATAACTTTTTCTTGCATATTCATATCAC
1 CTCATATAACTTTTTCTTGCATATTCATATCAC
3094567 ATAATGCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.45
Consensus pattern (33 bp):
CTCATATAACTTTTTCTTGCATATTCATATCAC
Found at i:3094920 original size:63 final size:65
Alignment explanation
Indices: 3094813--3094954 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 65
3094803 AATAGAGGTA
* ** * ** *
3094813 TGCATCGATGCACTACACCATGCATCGATGTATAAATCTTATTCGATGTTTGTA-TTTAATGGGG
1 TGCATCGATGCACTACACCATGCATCGATGCATAAATCGCATTCGATGTTTCTATTTTAAAAGAG
* * *
3094877 TGCATCGATGCACT-C-CTTATGCATCGATGCATCAATGGCATTCGATGTTTCTATTTTAAAAGA
1 TGCATCGATGCACTACAC-CATGCATCGATGCATAAATCGCATTCGATGTTTCTATTTTAAAAGA
3094940 G
65 G
3094941 TGCATCGATGCACT
1 TGCATCGATGCACT
3094955 TCATGTGCAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
62 1 0.02
63 30 0.45
64 35 0.53
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (65 bp):
TGCATCGATGCACTACACCATGCATCGATGCATAAATCGCATTCGATGTTTCTATTTTAAAAGAG
Found at i:3095903 original size:11 final size:11
Alignment explanation
Indices: 3095887--3095917 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
3095877 TATGTAATTT
3095887 TTTTAACTATA
1 TTTTAACTATA
3095898 TTTTAACTATA
1 TTTTAACTATA
3095909 TTTTAACTA
1 TTTTAACTA
3095918 GTCGTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAACTATA
Found at i:3097315 original size:14 final size:15
Alignment explanation
Indices: 3097279--3097319 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
3097269 GATTTTCTGT
3097279 AAAATGAATTACTGG
1 AAAATGAATTACTGG
**
3097294 AATTTGAATTA-TGG
1 AAAATGAATTACTGG
3097308 AAAATGAATTAC
1 AAAATGAATTAC
3097320 ATTTCTGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (15 bp):
AAAATGAATTACTGG
Found at i:3100117 original size:26 final size:25
Alignment explanation
Indices: 3100071--3100119 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3100061 TTGTTTGATT
*
3100071 AAGGATAAAAATTTATTTGTAAAAA
1 AAGGATAAAAATTTATATGTAAAAA
*
3100096 AAGGATAAAAATTTCTCATGTAAA
1 AAGGATAAAAATTTAT-ATGTAAA
3100120 TTATATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (25 bp):
AAGGATAAAAATTTATATGTAAAAA
Found at i:3102248 original size:31 final size:30
Alignment explanation
Indices: 3102202--3102288 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
3102192 TTCGATAATA
*
3102202 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAA-TATTTTATAATATTTTA-ATAAATT
*
3102233 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTTAATAAATT
*
3102264 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATATTTTAA
3102289 ACTTTATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.88
32 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTTAATAAATT
Found at i:3103036 original size:11 final size:10
Alignment explanation
Indices: 3103010--3103093 Score: 50
Period size: 11 Copynumber: 8.3 Consensus size: 10
3103000 CAATAAAATT
*
3103010 TTAAAAATTA
1 TTAAATATTA
*
3103020 TAAAATACTTA
1 TTAAATA-TTA
3103031 TTAAAT-TTA
1 TTAAATATTA
*
3103040 TTAAAAGATTA
1 TT-AAATATTA
3103051 -TAAA-ATTA
1 TTAAATATTA
3103059 TTAAA-ATTTA
1 TTAAATA-TTA
*
3103069 TCTAAATACTA
1 T-TAAATATTA
*
3103080 TAAAATAATTA
1 TTAAAT-ATTA
3103091 TTA
1 TTA
3103094 TTTTATCGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
8 4 0.07
9 13 0.22
10 17 0.29
11 23 0.40
12 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (10 bp):
TTAAATATTA
Found at i:3103045 original size:29 final size:29
Alignment explanation
Indices: 3103010--3103093 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 29
3103000 CAATAAAATT
*
3103010 TTAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAGATTATAAAATA-TTATTAAATTTA
3103040 TTAAAAGATTAT-AAA-ATTATTAAAATTTA
1 TT-AAAGATTATAAAATATTATT-AAATTTA
* *
3103069 TCTAAATACTATAAAATAATTATTA
1 T-TAAAGATTATAAAAT-ATTATTA
3103094 TTTTATCGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
28 5 0.11
29 16 0.36
30 9 0.20
31 9 0.20
32 6 0.13
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (29 bp):
TTAAAGATTATAAAATATTATTAAATTTA
Found at i:3103074 original size:20 final size:19
Alignment explanation
Indices: 3103003--3103074 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
3102993 TTTTCGTCAA
*
3103003 TAAAATTT-TAAAAATTA-
1 TAAAATTTATTAAAATTAT
*
3103020 TAAAATACTTATTAAATTTAT
1 TAAAAT--TTATTAAAATTAT
*
3103041 TAAAAGATTA-TAAAATTAT
1 TAAAA-TTTATTAAAATTAT
3103060 TAAAATTTATCTAAA
1 TAAAATTTAT-TAAA
3103075 TACTATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
17 6 0.14
18 3 0.07
19 15 0.35
20 14 0.33
21 5 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (19 bp):
TAAAATTTATTAAAATTAT
Found at i:3103213 original size:13 final size:13
Alignment explanation
Indices: 3103197--3103230 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3103187 TTAATAGCAA
3103197 AAATGGTTCTTTG
1 AAATGGTTCTTTG
3103210 AAATGGTTCTTTG
1 AAATGGTTCTTTG
*
3103223 AAGTGGTT
1 AAATGGTT
3103231 AGAAAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (13 bp):
AAATGGTTCTTTG
Found at i:3103489 original size:23 final size:22
Alignment explanation
Indices: 3103463--3103507 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
3103453 AATTGATCAG
* *
3103463 TTAATTTTATGTATTATATAATT
1 TTAATTATAGGTATTA-ATAATT
3103486 TTAATTATAGGTATTAATAATT
1 TTAATTATAGGTATTAATAATT
3103508 ACTGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
TTAATTATAGGTATTAATAATT
Found at i:3103787 original size:18 final size:18
Alignment explanation
Indices: 3103764--3103807 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
3103754 TTACGGAATG
3103764 TAAGATTATCGCCGAGAA
1 TAAGATTATCGCCGAGAA
* *
3103782 TAAGATTATCGGCGGGAA
1 TAAGATTATCGCCGAGAA
3103800 TAAGATTA
1 TAAGATTA
3103808 CTGAGAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (18 bp):
TAAGATTATCGCCGAGAA
Found at i:3114518 original size:164 final size:164
Alignment explanation
Indices: 3114237--3114564 Score: 539
Period size: 164 Copynumber: 2.0 Consensus size: 164
3114227 TATGCTACTG
* *
3114237 CAAGCATCTTTCACCATGATCGAATCTACTTAAGCAAAAGAATGACCAAGGGAAAGAAATTAGCT
1 CAAGCATCTTCCACCATGATCGAATCTACTTAAGCAAAAAAATGACCAAGGGAAAGAAATTAGCT
*
3114302 AAAACAGTTTAGGATTAATAAGTTTAGAACATTGGAACAATGAAAATAAATAAAGAAAAAAACTA
66 AAAACAGTTTAGGATTAATAAGTTTAGAACATCGGAACAATGAAAATAAATAAAGAAAAAAACTA
3114367 TTATGCTTGGATTGTAACTCAAGGATAATAACTA
131 TTATGCTTGGATTGTAACTCAAGGATAATAACTA
* * *
3114401 CAAGCATCTTCCACCATGATCGAATCTACTTGAGCAAAAAAATGATCAGGGGAAAGAAATTAGCT
1 CAAGCATCTTCCACCATGATCGAATCTACTTAAGCAAAAAAATGACCAAGGGAAAGAAATTAGCT
* ** *
3114466 AAAACAGTTTATGATTAATAAGTTTAGAACATCGGAACTTTGAAAGTAAATAAAGAAAAAAACTA
66 AAAACAGTTTAGGATTAATAAGTTTAGAACATCGGAACAATGAAAATAAATAAAGAAAAAAACTA
* * *
3114531 TTATGTTTGGCTTGTAATTCAAGGATAATAACTA
131 TTATGCTTGGATTGTAACTCAAGGATAATAACTA
3114565 TTAGCCCCTG
Statistics
Matches: 151, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
164 151 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (164 bp):
CAAGCATCTTCCACCATGATCGAATCTACTTAAGCAAAAAAATGACCAAGGGAAAGAAATTAGCT
AAAACAGTTTAGGATTAATAAGTTTAGAACATCGGAACAATGAAAATAAATAAAGAAAAAAACTA
TTATGCTTGGATTGTAACTCAAGGATAATAACTA
Found at i:3116972 original size:19 final size:20
Alignment explanation
Indices: 3116948--3116998 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3116938 AATGACCAAT
3116948 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
3116967 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
3116987 AAAATCGCAACG
1 AAAATCGCAACG
3116999 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:3116992 original size:20 final size:20
Alignment explanation
Indices: 3116948--3117185 Score: 113
Period size: 20 Copynumber: 11.6 Consensus size: 20
3116938 AATGACCAAT
* *
3116948 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
3116967 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
3116987 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
3117007 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
3117027 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
3117048 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
3117071 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
3117091 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
3117111 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
3117134 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
3117154 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
3117174 AGAATCGCAACG
1 AAAATCGCAACG
3117186 TTGAAAATCG
Statistics
Matches: 168, Mismatches: 39, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
19 17 0.10
20 108 0.64
21 14 0.08
23 29 0.17
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:3117135 original size:63 final size:63
Alignment explanation
Indices: 3117052--3117185 Score: 223
Period size: 63 Copynumber: 2.1 Consensus size: 63
3117042 GCTTCCAAGT
* * *
3117052 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
* *
3117115 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
3117178 TCGCAACG
1 TCGCAACG
3117186 TTGAAAATCG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (63 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:3117299 original size:6 final size:6
Alignment explanation
Indices: 3117288--3117446 Score: 309
Period size: 6 Copynumber: 26.5 Consensus size: 6
3117278 GACACGTATT
3117288 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3117336 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
3117384 AACACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3117432 ACCACG ACCACG ACC
1 ACCACG ACCACG ACC
3117447 CGAGACGAGA
Statistics
Matches: 151, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 151 1.00
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3118159 original size:6 final size:6
Alignment explanation
Indices: 3118128--3118198 Score: 114
Period size: 6 Copynumber: 12.5 Consensus size: 6
3118118 TCTCGTCTCG
3118128 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3118172 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
3118199 AATACGTGTC
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.31
6 45 0.69
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:3118297 original size:20 final size:20
Alignment explanation
Indices: 3118274--3118576 Score: 160
Period size: 20 Copynumber: 14.8 Consensus size: 20
3118264 TTTTTTTAAC
3118274 ATCGCGTTGCGATTTTCTAA
1 ATCGCGTTGCGATTTTCTAA
* *
3118294 ATCGCGTTGCGATTCTCTCA
1 ATCGCGTTGCGATTTTCTAA
* * * *
3118314 ATTGCATTGCGATTCTATAA
1 ATCGCGTTGCGATTTTCTAA
* * *
3118334 ATCGCATTGCGATTCTCTCA
1 ATCGCGTTGCGATTTTCTAA
* * * *
3118354 GTCGCATTGCGATTCTCTCA
1 ATCGCGTTGCGATTTTCTAA
* *
3118374 GTCGCATTGCGATTTTCTTCTAA
1 ATCGCGTTGCGA--TT-TTCTAA
* * *
3118397 ATCGCGTTGCGACTCTCTCA
1 ATCGCGTTGCGATTTTCTAA
* * *
3118417 ATCGCATTGCGATTCTATAA
1 ATCGCGTTGCGATTTTCTAA
* * * *
3118437 ATCGCATTGCGATTCTATCA
1 ATCGCGTTGCGATTTTCTAA
*
3118457 ATCGCATTGCGATTTTCTTCTAA
1 ATCGCGTTGCGA--TT-TTCTAA
** **
3118480 ATCGCGTTGCGAACTTGGAA
1 ATCGCGTTGCGATTTTCTAA
*
3118500 GCTCGCGTTGCGATTTTCT--
1 -ATCGCGTTGCGATTTTCTAA
* * **
3118519 TTTGACCGTTGCGATTTTCTTT
1 ATCG--CGTTGCGATTTTCTAA
* ***
3118541 TTAATGTTGCGATTTTCTAA
1 ATCGCGTTGCGATTTTCTAA
3118561 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
3118577 ATTGGTCATT
Statistics
Matches: 226, Mismatches: 46, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
18 2 0.01
20 176 0.78
21 14 0.06
22 6 0.03
23 28 0.12
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
ATCGCGTTGCGATTTTCTAA
Found at i:3118335 original size:40 final size:40
Alignment explanation
Indices: 3118274--3118491 Score: 238
Period size: 40 Copynumber: 5.3 Consensus size: 40
3118264 TTTTTTTAAC
* * * * *
3118274 ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCA
1 ATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTAA
* * * *
3118314 ATTGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCA
1 ATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTAA
* *
3118354 GTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAA
1 ATCGCATTGCGATTCTCTCAATCGCATTGCGA--TTC-TCTAA
* * *
3118397 ATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAA
1 ATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTAA
*
3118437 ATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAA
1 ATCGCATTGCGATTCTCTCAATCGCATTGCGA--TTC-TCTAA
*
3118480 ATCGCGTTGCGA
1 ATCGCATTGCGA
3118492 ACTTGGAAGC
Statistics
Matches: 151, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
40 95 0.63
41 3 0.02
42 6 0.04
43 47 0.31
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (40 bp):
ATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTAA
Found at i:3118425 original size:83 final size:83
Alignment explanation
Indices: 3118333--3118491 Score: 273
Period size: 83 Copynumber: 1.9 Consensus size: 83
3118323 CGATTCTATA
* * * * *
3118333 AATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAA
1 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAA
3118398 TCGCGTTGCGACTCTCTC
66 TCGCGTTGCGACTCTCTC
3118416 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAA
1 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAA
3118481 TCGCGTTGCGA
66 TCGCGTTGCGA
3118492 ACTTGGAAGC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (83 bp):
AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAA
TCGCGTTGCGACTCTCTC
Found at i:3118932 original size:22 final size:23
Alignment explanation
Indices: 3118902--3118947 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3118892 AAAATATATT
3118902 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
3118925 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
3118947 T
1 T
3118948 TAAATAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:3118962 original size:32 final size:32
Alignment explanation
Indices: 3118896--3118965 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
3118886 ATATTAAAAA
*
3118896 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAATATAATAT
3118928 TATATTT-TTAATA-TTATAATTAA-ATAATCAAT
1 TATATTTATTAATATTTATAA-TAATATAAT--AT
3118960 TATATT
1 TATATT
3118966 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
30 10 0.29
31 9 0.26
32 15 0.44
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATATAATAT
Found at i:3119155 original size:23 final size:23
Alignment explanation
Indices: 3119129--3119173 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3119119 AATAATATTT
3119129 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
3119152 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
3119174 ATATAACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:3119311 original size:14 final size:14
Alignment explanation
Indices: 3119248--3119317 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
3119238 TACAAATATT
*
3119248 AATAAAATTTTAAA
1 AATAATATTTTAAA
*
3119262 AATAATATTTTAAT
1 AATAATATTTTAAA
** *
3119276 AATAAATAAATT-AT
1 AAT-AATATTTTAAA
**
3119290 TTTAATATTTTAAA
1 AATAATATTTTAAA
3119304 AATAATATTATTAA
1 AATAATATT-TTAA
3119318 GTTTTATAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
13 6 0.14
14 26 0.62
15 10 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATAATATTTTAAA
Found at i:3119312 original size:22 final size:22
Alignment explanation
Indices: 3119254--3119337 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 22
3119244 TATTAATAAA
3119254 ATTTTAAAAATAATATTTTAAT
1 ATTTTAAAAATAATATTTTAAT
* *
3119276 A--ATAAATAA-ATTATTTTAAT
1 ATTTTAAA-AATAATATTTTAAT
3119296 ATTTTAAAAATAATATTATTAAGT
1 ATTTTAAAAATAATATT-TTAA-T
3119320 -TTTATAATAAATAATATT
1 ATTT-TAA-AAATAATATT
3119338 ATTTATTGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
20 15 0.30
21 4 0.08
22 10 0.20
23 7 0.14
24 4 0.08
25 10 0.20
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (22 bp):
ATTTTAAAAATAATATTTTAAT
Found at i:3119331 original size:25 final size:24
Alignment explanation
Indices: 3119268--3119340 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 24
3119258 TAAAAATAAT
3119268 ATTTTAATAATAAATAA-ATTATTTTA
1 ATTTT-ATAATAAATAATATTA--TTA
3119294 ATATTT-TAA-AAATAATATTATTA
1 AT-TTTATAATAAATAATATTATTA
3119317 AGTTTTATAATAAATAATATTATT
1 A-TTTTATAATAAATAATATTATT
3119341 TATTGTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
23 7 0.17
24 10 0.24
25 20 0.48
26 2 0.05
27 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTTTATAATAAATAATATTATTA
Found at i:3120077 original size:188 final size:187
Alignment explanation
Indices: 3119743--3120289 Score: 697
Period size: 188 Copynumber: 2.9 Consensus size: 187
3119733 AACTAATGTT
* * * * * * *
3119743 AAAAACATTTGCGGCCTTTTTTGTCAAAACGCCA-TAAATGTATCG-TTAATTTACGGCGTTTGT
1 AAAAACATTTGCGGCATTTTCTATCAAAACGCCACTAAA-GTCT-GAATCATTTACGGCGTTTGA
* * * * *
3119806 TACTACAACGCCGCTATATGTGCAACCTATTGCGGCGTTTTTGTCAAAACGCTGCTAAAGTACTA
64 TACCAAAACGCCGCTATATGTG-AACCTATTACGGC-TTTTTGTCAAAACACCGCTAAAGTACTA
* * * *
3119871 ATTTATTGCGACGTTTATTAAAAAACACCGATATATGTCTAAAGTAAATGATGTTTAAATA
127 ATTTATTGCGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTAAATGACGTTTAAATA
* * * * * * *
3119932 AAATACATTTGTGGCATTTT-TGTCTAAACGCCTCTAATGTAC-GAATCATTTGCGGCGTTTGAT
1 AAAAACATTTGCGGCATTTTCTATCAAAACGCCACTAAAGT-CTGAATCATTTACGGCGTTTGAT
3119995 ACCAAAACGCCGCTATATGTGAACCATATTACGGCATTTTTGTCAAAACACCGCTAAAGTACTAA
65 ACCAAAACGCCGCTATATGTGAACC-TATTACGGC-TTTTTGTCAAAACACCGCTAAAGTACTAA
* *
3120060 TTTTTTGCGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAATA
128 TTTATTGCGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTAAATGACGTTTAAATA
*
3120120 AAAAACATTTGCGGCGTTTTCTATCAAAACGCCACTAAAGTCTGAATCATTTACGGCGTTTGATA
1 AAAAACATTTGCGGCATTTTCTATCAAAACGCCACTAAAGTCTGAATCATTTACGGCGTTTGATA
* * * * * *
3120185 CCAAAACGCCGCTATATGTTAACCCTATTACGTCGTTTTCTCGAAACACCGCTAAAGTACTAATC
66 CCAAAACGCCGCTATATGTGAA-CCTATTACGGCTTTTTGTCAAAACACCGCTAAAGTACTAATT
*
3120250 TGTTGCGGCGTTTATTAAAAAACGCCGCTATATGTCTAAA
130 TATTGCGGCGTTTATTAAAAAACGCCGCTATATGTCTAAA
3120290 TTTAGTGGCA
Statistics
Matches: 313, Mismatches: 38, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
187 5 0.02
188 220 0.70
189 86 0.27
190 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (187 bp):
AAAAACATTTGCGGCATTTTCTATCAAAACGCCACTAAAGTCTGAATCATTTACGGCGTTTGATA
CCAAAACGCCGCTATATGTGAACCTATTACGGCTTTTTGTCAAAACACCGCTAAAGTACTAATTT
ATTGCGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTAAATGACGTTTAAATA
Found at i:3122797 original size:69 final size:68
Alignment explanation
Indices: 3122700--3122909 Score: 157
Period size: 71 Copynumber: 3.0 Consensus size: 68
3122690 TATAAGTTTT
3122700 AAAACA-TTTTG-AAAA-TTATATAACATATATTTTTGAAATCGTTTTGAAAATATAATGTATAG
1 AAAACATTTTTGAAAAATTTATAT-A-ATATATTTTTGAAATCGTTTTGAAAATATAAT-TATAG
3122762 TTTAAA
63 TTTAAA
* * *
3122768 AAAACATTTTTGAAAAATTTATATAATATATAGTTTTAAAAAT-ATTTTGGAAAACT-TATATAA
1 AAAACATTTTTGAAAAATTTATATAATATAT--TTTT-GAAATCGTTTT-GAAAA-TATA-ATTA
**
3122831 TA-TTTTTA
60 TAGTTTAAA
* * * * * * *
3122839 AAATCATTTTTGAAAACTATATGGT-ATATAGTTTTGAAAACGTTTT-TAAATATAATATATAGT
1 AAAACATTTTTGAAAAATTTAT-ATAATATATTTTTGAAATCGTTTTGAAAATATAAT-TATAGT
3122902 TTAAA
64 TTAAA
3122907 AAA
1 AAA
3122910 TATTTTTTGA
Statistics
Matches: 111, Mismatches: 17, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
66 3 0.03
67 8 0.07
68 16 0.14
69 19 0.17
70 5 0.05
71 42 0.38
72 15 0.14
73 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (68 bp):
AAAACATTTTTGAAAAATTTATATAATATATTTTTGAAATCGTTTTGAAAATATAATTATAGTTT
AAA
Found at i:3122800 original size:39 final size:37
Alignment explanation
Indices: 3122642--3122872 Score: 116
Period size: 37 Copynumber: 6.5 Consensus size: 37
3122632 CGAAAATATA
** *
3122642 TATATAA-ATATAGTTTTTTAAAACGTTTTTG-AAAACT
1 TATATAATATATAG-TTTAAAAAAC-ATTTTGAAAAACT
*
3122679 TATATACAATATATAAGTTT-TAAAACATTTTG-AAAA-T
1 TATAT--AATATAT-AGTTTAAAAAACATTTTGAAAAACT
* * ** * *
3122716 TATATAACATATATTTTTGAAATCGTTTTG--AAA--
1 TATATAATATATAGTTTAAAAAACATTTTGAAAAACT
* *
3122749 -ATATAATGTATAGTTTAAAAAAACATTTTTGAAAAATT
1 TATATAATATATAGTTT-AAAAAACA-TTTTGAAAAACT
* * *
3122787 TATATAATATATAGTTTTAAAAATATTTTGGAAAACT
1 TATATAATATATAGTTTAAAAAACATTTTGAAAAACT
*
3122824 TATATAATAT-T--TTT-AAAATCATTTTTG-AAAAC-
1 TATATAATATATAGTTTAAAAAACA-TTTTGAAAAACT
**
3122856 TATATGGTATATAGTTT
1 TATATAATATATAGTTT
3122873 TGAAAACGTT
Statistics
Matches: 156, Mismatches: 22, Indels: 34
0.74 0.10 0.16
Matches are distributed among these distances:
32 21 0.13
33 15 0.10
34 20 0.13
35 18 0.12
36 4 0.03
37 31 0.20
38 15 0.10
39 23 0.15
40 7 0.04
41 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTAAAAAACATTTTGAAAAACT
Found at i:3122842 original size:32 final size:32
Alignment explanation
Indices: 3122793--3122860 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
3122783 AATTTATATA
3122793 ATATATAGTTTTAAAAAT-ATTTTGGAAAACTT
1 ATATATAGTTTTAAAAATCATTTTGGAAAAC-T
* *
3122825 ATATAATA-TTTTTAAAATCATTTTTGAAAACT
1 ATAT-ATAGTTTTAAAAATCATTTTGGAAAACT
3122857 ATAT
1 ATAT
3122861 GGTATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (32 bp):
ATATATAGTTTTAAAAATCATTTTGGAAAACT
Found at i:3122986 original size:19 final size:20
Alignment explanation
Indices: 3122957--3123005 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
3122947 TTATTATTAG
*
3122957 TATTTTTATTTTTATT-ATT
1 TATTTTCATTTTTATTCATT
*
3122976 TCTTTTCA-TTTTATTCATT
1 TATTTTCATTTTTATTCATT
*
3122995 TAATTTCATTT
1 TATTTTCATTT
3123006 ATTCTGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 7 0.29
19 15 0.62
20 2 0.08
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTTCATTTTTATTCATT
Found at i:3128861 original size:94 final size:94
Alignment explanation
Indices: 3128740--3129673 Score: 1697
Period size: 94 Copynumber: 9.9 Consensus size: 94
3128730 ATATCGTGCC
* * *
3128740 ACTCGAGACAACACAAGTTCAACTTCACGACGGAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
3128805 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
3128834 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
3128899 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
3128928 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
3128993 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
3129022 ACTCCAGAAAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
3129087 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
3129116 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
3129181 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
3129210 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
3129275 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
3129304 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* **
3129369 AATTTCAACTTCACAACGAAGGATATCAG
66 AATTTCAACTTCGCAACGAAGGATATTGG
3129398 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
3129463 AATTTCAACTTCACAACGAAGGATATCGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
3129492 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
3129557 AATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
3129586 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC-
** * *
3129651 CGGTTTCAACTTCACGACGAAGG
65 CAATTTCAACTTCGCAACGAAGG
3129674 GAATCGTACC
Statistics
Matches: 821, Mismatches: 18, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
94 801 0.98
95 20 0.02
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (94 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAACTTCGCAACGAAGGATATTGG
Found at i:3129819 original size:80 final size:80
Alignment explanation
Indices: 3129686--3129963 Score: 394
Period size: 80 Copynumber: 3.4 Consensus size: 80
3129676 ATCGTACCGA
3129686 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
3129751 GAGAAGGGCTATCTG
66 GAGAAGGGCTATCTG
* * *
3129766 CCAAAGACCTACGAGTTCGACTCCGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
3129831 GAGAAGGGCTATCTG
66 GAGAAGGGCTATCTG
* ** * * *
3129846 CCAAAGACCTTCGAGTTCGATTATACTCAGCTTCGAAGACACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGT
*
3129911 CGAGAAGGGTTATCTG
65 CGAGAAGGGCTATCTG
* * *
3129927 TCAACCGAAGACCTTCGAGTTCGATTACACTCAGCTC
1 ----CCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
3129964 AGAGGCAAAC
Statistics
Matches: 178, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
80 103 0.58
81 44 0.25
84 2 0.01
85 29 0.16
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
GAGAAGGGCTATCTG
Found at i:3130711 original size:39 final size:38
Alignment explanation
Indices: 3130600--3130712 Score: 104
Period size: 39 Copynumber: 2.9 Consensus size: 38
3130590 TATAGTATAA
** *
3130600 TTTTTTAAAGTGTTTTTGAAAAATATA-AC-ATATAGT
1 TTTTTTAAAACGTTTTTGAAAATTATATACAATATAGT
*** ** *
3130636 TTTCAAAAAACGGTTTCCGAAAATATATATATAATATAGT
1 TTTTTTAAAAC-GTTTTTGAAAAT-TATATACAATATAGT
3130676 TTTTTTAAAACGTTTTTGAAAACTTATATACAATATA
1 TTTTTTAAAACGTTTTTGAAAA-TTATATACAATATA
3130713 TAAGTTTTAA
Statistics
Matches: 57, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
36 6 0.11
37 9 0.16
38 4 0.07
39 22 0.39
40 16 0.28
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (38 bp):
TTTTTTAAAACGTTTTTGAAAATTATATACAATATAGT
Found at i:3130810 original size:21 final size:23
Alignment explanation
Indices: 3130770--3130812 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
3130760 TTAAAAAAAC
3130770 ATTTTTGAAAAATTTATATAATAT
1 ATTTTTGAAAAA-TTATATAATAT
3130794 ATTTTT-AAAAA-TATATAAT
1 ATTTTTGAAAAATTATATAAT
3130813 TTTTTAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTTTGAAAAATTATATAATAT
Found at i:3130817 original size:19 final size:20
Alignment explanation
Indices: 3130770--3130821 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 20
3130760 TTAAAAAAAC
3130770 ATTTTTGAAAAATTTATATAATAT
1 ATTTTT-AAAAA--TATATAA-AT
3130794 ATTTTTAAAAATATAT-AAT
1 ATTTTTAAAAATATATAAAT
3130813 -TTTTTAAAA
1 ATTTTTAAAA
3130822 CTTATATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.32
19 2 0.07
20 1 0.04
21 5 0.18
23 5 0.18
24 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTTTTAAAAATATATAAAT
Found at i:3130925 original size:16 final size:18
Alignment explanation
Indices: 3130893--3130925 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3130883 TTTTTTGAGA
3130893 TATATATATTATATAGTC
1 TATATATATTATATAGTC
3130911 TATAT-TATTAT-TAGT
1 TATATATATTATATAGT
3130926 ATTTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (18 bp):
TATATATATTATATAGTC
Found at i:3130960 original size:9 final size:9
Alignment explanation
Indices: 3130934--3130986 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
3130924 GTATTTTTAT
3130934 TTTTATT-A
1 TTTTATTCA
*
3130942 TTTCTTTTCA
1 TTT-TATTCA
3130952 TTTTATTCA
1 TTTTATTCA
3130961 TTTTATTCA
1 TTTTATTCA
*
3130970 TTTAATTTCA
1 TTTTA-TTCA
3130980 -TTTATTC
1 TTTTATTC
3130987 TGTTTTGTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
8 6 0.16
9 24 0.63
10 8 0.21
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTATTCA
Found at i:3130964 original size:27 final size:27
Alignment explanation
Indices: 3130934--3130986 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3130924 GTATTTTTAT
**
3130934 TTTTATT-ATTTCTTTTCATTTTATTCA
1 TTTTATTCATTTAATTTCA-TTTATTCA
3130961 TTTTATTCATTTAATTTCATTTATTC
1 TTTTATTCATTTAATTTCATTTATTC
3130987 TGTTTTGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTATTCATTTAATTTCATTTATTCA
Found at i:3132333 original size:5 final size:5
Alignment explanation
Indices: 3132318--3132347 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
3132308 TTTATCCCGT
3132318 TTTTCA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTT
3132348 TGATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:3133112 original size:31 final size:30
Alignment explanation
Indices: 3133063--3133121 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
3133053 TGATTTATAA
*
3133063 TTTAATTTAATTTAATAATAAATAAATAAAT
1 TTTAATTAAATTTAATAATAAA-AAATAAAT
*
3133094 TTTAATTAAATATT-ATAATATAAAATAA
1 TTTAATTAAAT-TTAATAATAAAAAATAA
3133122 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.24
31 17 0.68
32 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TTTAATTAAATTTAATAATAAAAAATAAAT
Found at i:3133139 original size:38 final size:39
Alignment explanation
Indices: 3133070--3133143 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
3133060 TAATTTAATT
* *
3133070 TAATTTAATAATAAATAAATAAATTTTAATTAAATATTA
1 TAATATAATAATAAATAAATAAATTTAAATTAAATATTA
*
3133109 TAATATAA-AATAATTAAA-AATATTTAAATTAAATA
1 TAATATAATAATAAATAAATAA-ATTTAAATTAAATA
3133144 AAACAATAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 2 0.06
38 22 0.71
39 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (39 bp):
TAATATAATAATAAATAAATAAATTTAAATTAAATATTA
Found at i:3139503 original size:56 final size:57
Alignment explanation
Indices: 3139432--3139611 Score: 167
Period size: 56 Copynumber: 3.3 Consensus size: 57
3139422 TCTTATTTTC
* ** * *
3139432 TAGATATATTTGATTTCGGGATTCT-TAGTTTTATGCTTCTTAATAGCAATAACTGA
1 TAGATATATTCGATTTCGGGAGCCTCTAGTTTTATGCTTATTAATAGCAACAACTGA
* * * * *
3139488 TAGATATACTCGATTT-TGGAGCCTCTATTTTTATGCTTATTAATGGCAACAATTGA
1 TAGATATATTCGATTTCGGGAGCCTCTAGTTTTATGCTTATTAATAGCAACAACTGA
* * * *
3139544 TAGATATATTCGATTTCAGG-G-CTCCTATTTTTATACTTATTAAT---AACAACTAA
1 TAGATATATTCGATTTCGGGAGCCT-CTAGTTTTATGCTTATTAATAGCAACAACTGA
*
3139597 TAGATATATTTGATT
1 TAGATATATTCGATT
3139612 CGGAACTCCT
Statistics
Matches: 105, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
53 21 0.20
55 7 0.07
56 75 0.71
57 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (57 bp):
TAGATATATTCGATTTCGGGAGCCTCTAGTTTTATGCTTATTAATAGCAACAACTGA
Found at i:3149521 original size:21 final size:21
Alignment explanation
Indices: 3149478--3149530 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
3149468 TTAATTTTTA
*
3149478 AATATTTAAATATACTATTTT
1 AATATTTAAATATACTATATT
*
3149499 AATATTTTAATATA-TATCATT
1 AATATTTAAATATACTAT-ATT
*
3149520 AAATAATTAAA
1 -AATATTTAAA
3149531 GATAAAACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 15 0.58
22 8 0.31
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATTTAAATATACTATATT
Found at i:3153331 original size:29 final size:29
Alignment explanation
Indices: 3153289--3153363 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
3153279 AACCCAACCA
**
3153289 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
3153318 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
3153347 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
3153364 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:3153369 original size:29 final size:29
Alignment explanation
Indices: 3153290--3153377 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
3153280 ACCCAACCAT
* * ****
3153290 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
3153319 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
3153348 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
3153377 A
1 A
3153378 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:3153629 original size:29 final size:29
Alignment explanation
Indices: 3153594--3153680 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
3153584 GTTGGCTGGT
*
3153594 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
3153623 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
3153652 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
3153681 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:3158136 original size:214 final size:214
Alignment explanation
Indices: 3157757--3158188 Score: 812
Period size: 214 Copynumber: 2.0 Consensus size: 214
3157747 TAAGGATAGC
3157757 GTTTGACTCCCTACTTTTTGGTAATCCAACGAAAAAACAGAGGGAGTTTGACTGCACCGGTGTGG
1 GTTTGACTCCCTACTTTTTGGTAATCCAACGAAAAAACAGAGGGAGTTTGACTGCACCGGTGTGG
3157822 CACCGATTGATCGGTTGGCCTCGTGAATATAAGAATATATACATACACACCCTTGACATTTGAAA
66 CACCGATTGATCGGTTGGCCTCGTGAATATAAGAATATATACATACACACCCTTGACATTTGAAA
3157887 ATTAAATGTTTCAACCGGTGTTTTTTGTTTTTTTTTCTTGAGATGTAAGTAGAAACGATTAATTC
131 ATTAAATGTTTCAACCGGTGTTTTTTG-TTTTTTTTCTTGAGATGTAAGTAGAAACGATTAATTC
3157952 AACTGG-AAACGATACGAGG
195 AACTGGAAAACGATACGAGG
3157971 GTTTGACTCCCTACTTTTTGGTAATCCAACGAAAAAACAGAGGGAGTTTGACTGCACCGGTGTGG
1 GTTTGACTCCCTACTTTTTGGTAATCCAACGAAAAAACAGAGGGAGTTTGACTGCACCGGTGTGG
3158036 CACCGATTGATCGGTTGGCCTCGTGAATATAAGAATATATACATACACACCCTTGACATTTGAAA
66 CACCGATTGATCGGTTGGCCTCGTGAATATAAGAATATATACATACACACCCTTGACATTTGAAA
3158101 ATTAAATATGTTTCAACCGGTGTTTTTTGTTTTTTTTTTCTTGAGATGTAAGTAGAAACGATTAA
131 ATT-AA-ATGTTTCAACCGGTGTTTTTTG--TTTTTTTTCTTGAGATGTAAGTAGAAACGATTAA
3158166 TTCAACTGGAAAACGATACGAGG
192 TTCAACTGGAAAACGATACGAGG
3158189 AGATCTTTGA
Statistics
Matches: 214, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
214 133 0.62
215 2 0.01
216 22 0.10
217 44 0.21
218 13 0.06
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (214 bp):
GTTTGACTCCCTACTTTTTGGTAATCCAACGAAAAAACAGAGGGAGTTTGACTGCACCGGTGTGG
CACCGATTGATCGGTTGGCCTCGTGAATATAAGAATATATACATACACACCCTTGACATTTGAAA
ATTAAATGTTTCAACCGGTGTTTTTTGTTTTTTTTCTTGAGATGTAAGTAGAAACGATTAATTCA
ACTGGAAAACGATACGAGG
Found at i:3159305 original size:2 final size:2
Alignment explanation
Indices: 3159298--3159335 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3159288 ATAAATAATC
3159298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3159336 TTTCTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3162646 original size:28 final size:28
Alignment explanation
Indices: 3162598--3162654 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
3162588 CCATTGTTGC
**
3162598 TTTCAAGCACTTGCTCAACGACATAATA
1 TTTCAAGCACTAACTCAACGACATAATA
*
3162626 TTTCAAGCACTAACTCGACGACATAATA
1 TTTCAAGCACTAACTCAACGACATAATA
3162654 T
1 T
3162655 AAACAGAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (28 bp):
TTTCAAGCACTAACTCAACGACATAATA
Found at i:3164138 original size:25 final size:26
Alignment explanation
Indices: 3164108--3164167 Score: 97
Period size: 25 Copynumber: 2.4 Consensus size: 26
3164098 AAAAAATAGT
3164108 TTTTGAAAACA-TATATAATATAAAG
1 TTTTGAAAACAGTATATAATATAAAG
*
3164133 TTTTGAAAA-AGTATATAATATATAG
1 TTTTGAAAACAGTATATAATATAAAG
3164158 TTTTGAAAAC
1 TTTTGAAAAC
3164168 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 1 0.03
25 31 0.97
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (26 bp):
TTTTGAAAACAGTATATAATATAAAG
Found at i:3164299 original size:15 final size:15
Alignment explanation
Indices: 3164274--3164317 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
3164264 AATATATAAA
3164274 ATATA-TTATATATT
1 ATATAGTTATATATT
3164288 ATATAGTTATATATT
1 ATATAGTTATATATT
3164303 ATAT-GTTCATATATT
1 ATATAGTT-ATATATT
3164318 TTCATTACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.29
15 20 0.71
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (15 bp):
ATATAGTTATATATT
Found at i:3164347 original size:15 final size:15
Alignment explanation
Indices: 3164280--3164380 Score: 66
Period size: 15 Copynumber: 6.5 Consensus size: 15
3164270 TAAAATATAT
*
3164280 TATATATTATATAGT-
1 TATATATTATAT-TTA
3164295 TATATATTATATGTTCA
1 TATATATTATAT-TT-A
* *
3164312 TATATTTTCATTACCTTA
1 TATATATT-A-TA-TTTA
3164330 TATATATTATATTTA
1 TATATATTATATTTA
3164345 TAT-TATTTATATTT-
1 TATATA-TTATATTTA
* *
3164359 T-TTTATTATATATA
1 TATATATTATATTTA
3164373 TATATATT
1 TATATATT
3164381 TTTTATTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
13 8 0.12
14 6 0.09
15 32 0.46
16 2 0.03
17 8 0.12
18 9 0.13
19 4 0.06
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (15 bp):
TATATATTATATTTA
Found at i:3164377 original size:30 final size:28
Alignment explanation
Indices: 3164334--3164392 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 28
3164324 ACCTTATATA
3164334 TATTATATTTATAT-TATTTATATTTTTT
1 TATTATATTTATATAT-TTTATATTTTTT
*
3164362 TATTATATATATATATATTTTTTATTTTTT
1 TATTATAT-T-TATATATTTTATATTTTTT
3164392 T
1 T
3164393 TCCAGGTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 8 0.30
29 1 0.04
30 17 0.63
31 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (28 bp):
TATTATATTTATATATTTTATATTTTTT
Found at i:3164378 original size:23 final size:22
Alignment explanation
Indices: 3164342--3164384 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3164332 TATATTATAT
*
3164342 TTATATTATTTATATTTTTTTA
1 TTATATTATATATATTTTTTTA
3164364 TTATATATATATATATTTTTT
1 TTATAT-TATATATATTTTTT
3164385 ATTTTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATATTATATATATTTTTTTA
Found at i:3164379 original size:32 final size:33
Alignment explanation
Indices: 3164327--3164393 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
3164317 TTTCATTACC
*
3164327 TTATATATATTATATTTATATTATTTATATTTTT
1 TTATATATATTATATATATATTATTTAT-TTTTT
*
3164361 TTAT-TATA-TATATATATATTTTTTATTTTTT
1 TTATATATATTATATATATATTATTTATTTTTT
3164392 TT
1 TT
3164394 CCAGGTCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 7 0.23
32 16 0.52
33 4 0.13
34 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (33 bp):
TTATATATATTATATATATATTATTTATTTTTT
Found at i:3165497 original size:18 final size:19
Alignment explanation
Indices: 3165474--3165511 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3165464 CTTTGGATTC
3165474 TTTTATTTA-TTTAATATT
1 TTTTATTTACTTTAATATT
*
3165492 TTTTATTTACTTTATTATT
1 TTTTATTTACTTTAATATT
3165511 T
1 T
3165512 GACTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATTTACTTTAATATT
Found at i:3167356 original size:28 final size:27
Alignment explanation
Indices: 3167325--3167408 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 27
3167315 TCTTCGATTG
3167325 TTTTTATTTTTTATTCTATTCTTATTTA
1 TTTTTATTTTTTATTCT-TTCTTATTTA
* *
3167353 -TTTTATTTTTTCATTCTTTGATTAATTCTT
1 TTTTTATTTTTT-ATTCTTT-CTT-ATT-TA
*
3167383 TTTTTATTTTTTATTTTTTCTTATTT
1 TTTTTATTTTTTATTCTTTCTTATTT
3167409 TCAATTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
27 14 0.30
28 10 0.21
29 5 0.11
30 7 0.15
31 11 0.23
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.76
Consensus pattern (27 bp):
TTTTTATTTTTTATTCTTTCTTATTTA
Found at i:3167476 original size:23 final size:25
Alignment explanation
Indices: 3167424--3167480 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 25
3167414 TTTTTTAATG
*
3167424 TTTTATTTAATTTTTCTTTTCTTTGA
1 TTTT-TTTAATTTTTCTTCTCTTTGA
3167450 TTTTTTTAATTTTT-TTCTC-TTGA
1 TTTTTTTAATTTTTCTTCTCTTTGA
3167473 TTTTTTTA
1 TTTTTTTA
3167481 TTTGATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 12 0.40
24 4 0.13
25 10 0.33
26 4 0.13
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTTTTTAATTTTTCTTCTCTTTGA
Found at i:3171688 original size:168 final size:168
Alignment explanation
Indices: 3171410--3172536 Score: 1298
Period size: 168 Copynumber: 6.7 Consensus size: 168
3171400 AAACTATTGG
* * * * *
3171410 CAGCATAACTCAAGGCTAGAATGATTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAA
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
* * * *
3171475 CACCAAGGCACATAAATTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAAACCTT
66 CTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
* *
3171540 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
131 CGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTA
**
3171578 CAGCATAACTCACA-GCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCA
1 CAGCATAACTCA-AGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCA
* * *
3171642 ACTCCAAGGCACACCATTTGCAACATAGCTCAAGGAAAGAAGGGCTATTTGCCAACAAAAGACCT
65 GCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCT
* * * *
3171707 TCAAGTTCGACTACGCTCAGCTCAAAGGCATATCATTTG
130 TCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTA
* * *
3171746 CAGCATAACTCAAGGCTAGAAGGGTTA--T-CCAACCAAAGACCTTTGAGTTCTACTACGCTCAG
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
* *
3171808 CTCCAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
66 CTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
* * * * *
3171873 TGAGTTCGACTACGCTCAGCTCAAAGGCATATTATTTG
131 CGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTA
* * * *
3171911 TAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAAACAAAGACCTTCGAGCTCGACTACACTCAG
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
* * * * * *
3171976 CTCCAAGGAACATCATTTGCATCATAGCTCAAGACAATAAGAGTTATTTGCCAACAAAAGACCTT
66 CTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
* * * *
3172041 CGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTA
131 CGAGTTCGACTACACTCAGC-TCAAAGGCACATCATTTA
* * * * * *
3172080 CATCATAACTCAAGGCTAGAAGGGTTACCTGTCAA-CAAAGACCTTTGAGTTCGATTACACTCAT
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
* * * * ** * * *
3172144 CTCAAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAGGGCTATATGCCAACTAAAGACCTT
66 CTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
* * ** *
3172209 CGAGTTCGATTACATTCAGCTCAAATACGCATCATTTA
131 CGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTA
* * ** * * *
3172247 TAGCATAACTCAAGGCTAGAAGGGTCATCTTTCAA-CAAAGACCTTCAAGTTTGATTACACTCAG
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
* * * * * * * * **
3172311 CTCAAAGGCGCATCCTTTACAACATAACTCAAGGCTAGAAGGGTTATCTATCAAC-AAAGACCTT
66 CTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
* *
3172375 CGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTG
131 CGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTA
* * * * * * * *
3172413 CAGCATAGCTTAAGG-TGAGAATGGTTATCTGTCAACAAAATACCTTTGAGTTCGATTACACTCA
1 CAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCA
* * * * * *
3172477 GCTCAAAGGCACATCATTTACAACATAGCTTAAGGCAAGAAGGGTTATCTGTCAACAAAA
65 GCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAA
3172537 TTGTTGAGTT
Statistics
Matches: 832, Mismatches: 118, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
165 153 0.18
166 70 0.08
167 185 0.22
168 379 0.46
169 45 0.05
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (168 bp):
CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
CTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
CGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTA
Found at i:3172061 original size:333 final size:335
Alignment explanation
Indices: 3171409--3172536 Score: 1372
Period size: 333 Copynumber: 3.4 Consensus size: 335
3171399 GAAACTATTG
* * * *
3171409 GCAGCATAACTCAAGGCTAGAATGATTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTA-CTGCCAACAAAAGACCTTTGAGTTCGACTACACTCA
* * * * * * * *
3171474 ACACCAAGGCACATAAATTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAAACCT
65 GCTCAAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCT
* *
3171539 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCACA-GCTAGAAGGGT
130 TCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTATAGCATAACTCA-AGGCTAGAAGGGT
* * ** * *
3171603 TATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAACTCCAAGGCACACCATTTGCAACAT
194 TATCTTCCAAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACAT
* * * *
3171668 AGCTCAAGGA-AAGAAGGGCTATTTGCCAACAAAAGACCTTCAAGTTCGACTACGCTCAGCTCAA
259 AGCTCAA-GACAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAA
3171732 AGGCATATCATTT
323 AGGCATATCATTT
* * *
3171745 GCAGCATAACTCAAGGCTAGAAGGGTTA-T-CCAACCAAAGACCTTTGAGTTCTACTACGCTCAG
1 GCAGCATAACTCAAGGCTAGAAGGGTTACTGCCAACAAAAGACCTTTGAGTTCGACTACACTCAG
*
3171808 CTCCAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
66 CTCAAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
* * * *
3171873 TGAGTTCGACTACGCTCAGCTCAAAGGCATATTATTTGTAGCATAACTCAAGGCTAGAAGGGTTA
131 CGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTA
* * *
3171938 TCTTCCAAACAAAGACCTTCGAGCTCGACTACACTCAGCTCCAAGGAACATCATTTGCATCATAG
196 TCTTCCAAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAG
* * * *
3172003 CTCAAGACAATAAGAGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGG
261 CTCAAGACAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAG
3172068 GCATATCATTT
325 GCATATCATTT
* * * *
3172079 ACATCATAACTCAAGGCTAGAAGGGTTACCTGTCAAC-AAAGACCTTTGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTA-CTGCCAACAAAAGACCTTTGAGTTCGACTACACTCA
* * * * ** * * *
3172143 TCTCAAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAGGGCTATATGCCAACTAAAGACCT
65 GCTCAAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCT
* ** ** * *
3172208 TCGAGTTCGATTACATTCAGCTCAAATACGCATCATTTATAGCATAACTCAAGGCTAGAAGGGTC
130 TCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTT
* * * * * * * *
3172273 ATCTTTC-AACAAAGACCTTCAAGTTTGATTACACTCAGCTCAAAGGCGCATCCTTTACAACATA
195 ATCTTCCAAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATA
* * * * **
3172337 ACTCAAGGCTAGAAGGGTTATCTATCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAG
260 GCTCAAGACAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAG
*
3172401 GCACATCATTT
325 GCATATCATTT
* * * * * *
3172412 GCAGCATAGCTTAAGG-TGAGAATGGTTATCTGTCAACAAAATACCTTTGAGTTCGATTACACTC
1 GCAGCATAACTCAAGGCT-AGAAGGGTTA-CTGCCAACAAAAGACCTTTGAGTTCGACTACACTC
* * * * *
3172476 AGCTCAAAGGCACATCATTTACAACATAGCTTAAGGCAAGAAGGGTTATCTGTCAACAAAA
64 AGCTCAAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAA
3172537 TTGTTGAGTT
Statistics
Matches: 682, Mismatches: 102, Indels: 18
0.85 0.13 0.02
Matches are distributed among these distances:
332 4 0.01
333 294 0.43
334 146 0.21
335 68 0.10
336 166 0.24
337 4 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (335 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTACTGCCAACAAAAGACCTTTGAGTTCGACTACACTCAG
CTCAAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
CGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTA
TCTTCCAAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAG
CTCAAGACAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
CATATCATTT
Found at i:3172537 original size:84 final size:84
Alignment explanation
Indices: 3171409--3172536 Score: 1176
Period size: 84 Copynumber: 13.5 Consensus size: 84
3171399 GAAACTATTG
* * *
3171409 GCAGCATAACTCAAGGCTAGAATGATTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
* * * * *
3171474 ACACCAAGGCACATAAATT
66 GCTCAAAGGCACATCATTT
* * * * * * *
3171493 GCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAAACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
*
3171558 GCTCCAAGGCACATCATTT
66 GCTCAAAGGCACATCATTT
* * **
3171577 ACAGCATAACTCACA-GCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTC
1 GCAGCATAACTCA-AGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTC
* * *
3171641 AACTCCAAGGCACACCATTT
65 AGCTCAAAGGCACATCATTT
* * ** * * * *
3171661 GCAACATAGCTCAAGGAAAGAAGGGCTATTTGCCAACAAAAGACCTTCAAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
*
3171726 GCTCAAAGGCATATCATTT
66 GCTCAAAGGCACATCATTT
* * * *
3171745 GCAGCATAACTCAAGGCTAGAAGGGTTA--T-CCAACCAAAGACCTTTGAGTTCTACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
*
3171807 GCTCCAAGGCACATCATTT
66 GCTCAAAGGCACATCATTT
* * * * * * *
3171826 ACAACATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
* *
3171891 GCTCAAAGGCATATTATTT
66 GCTCAAAGGCACATCATTT
* * *
3171910 GTAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAA-ACAAAGACCTTCGAGCTCGACTACACTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACA-AAAGACCTTCGAGTTCGACTACACTC
* *
3171974 AGCTCCAAGGAACATCATTT
65 AGCTCAAAGGCACATCATTT
* * * * * * * *
3171994 GCATCATAGCTCAAGACAATAAGAGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
* * *
3172059 GCTTCGAGGGCATATCATTT
66 GC-TCAAAGGCACATCATTT
* * * * * *
3172079 ACATCATAACTCAAGGCTAGAAGGGTTACCTGTCAAC-AAAGACCTTTGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
*
3172143 TCTCAAAGGCACATCATTT
66 GCTCAAAGGCACATCATTT
* ** * * * * * *
3172162 GCAGCATAACTTAAATCGAGAAGGGCTATATGCCAACTAAAGACCTTCGAGTTCGATTACATTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
** *
3172227 GCTCAAATACGCATCATTT
66 GCTCAAAGGCACATCATTT
** * ** * * *
3172246 ATAGCATAACTCAAGGCTAGAAGGGTCATCTTTCAAC-AAAGACCTTCAAGTTTGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
* *
3172310 GCTCAAAGGCGCATCCTTT
66 GCTCAAAGGCACATCATTT
* * ** *
3172329 ACAACATAACTCAAGGCTAGAAGGGTTATCTATCAAC-AAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
3172393 GCTCAAAGGCACATCATTT
66 GCTCAAAGGCACATCATTT
* * * * * * *
3172412 GCAGCATAGCTTAAGG-TGAGAATGGTTATCTGTCAACAAAATACCTTTGAGTTCGATTACACTC
1 GCAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTC
3172476 AGCTCAAAGGCACATCATTT
65 AGCTCAAAGGCACATCATTT
* * * * * *
3172496 ACAACATAGCTTAAGGCAAGAAGGGTTATCTGTCAACAAAA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAA
3172537 TTGTTGAGTT
Statistics
Matches: 879, Mismatches: 153, Indels: 24
0.83 0.14 0.02
Matches are distributed among these distances:
81 70 0.08
82 2 0.00
83 188 0.21
84 576 0.66
85 43 0.05
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (84 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCA
GCTCAAAGGCACATCATTT
Found at i:3172985 original size:2 final size:2
Alignment explanation
Indices: 3172978--3173021 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
3172968 CAAAGTTAAT
3172978 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3173019 TA T
1 TA T
3173022 TATCATTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3174126 original size:4 final size:4
Alignment explanation
Indices: 3174119--3174254 Score: 59
Period size: 4 Copynumber: 33.2 Consensus size: 4
3174109 TATTCTATTC
* * * * *
3174119 TTAT TTATT TTAT TTTT TTCT TTCT TTGAT TAAT TCTTT TTAT TT-T TT-T
1 TTAT TTA-T TTAT TTAT TTAT TTAT TT-AT TTAT T-TAT TTAT TTAT TTAT
* * *
3174168 CTTAT TT-T TTAAT TTAT TTAA TTAT TTAT TTAT TT-T TCTCT TGAT TTAAT
1 -TTAT TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TT-AT
* *
3174218 TTA- TTAT TTAAT TTATT TTAT TTA- ATAT TCAT TTAT T
1 TTAT TTAT TT-AT TTA-T TTAT TTAT TTAT TTAT TTAT T
3174255 ATTATTATTA
Statistics
Matches: 102, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
3 14 0.14
4 62 0.61
5 26 0.25
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:3175797 original size:44 final size:44
Alignment explanation
Indices: 3175734--3175830 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
3175724 TTATTTAAAA
*
3175734 TAAAT-ATTTCTAAAATTAATATCTATAATAAAAAATAACATTT
1 TAAATAATATCTAAAATTAATATCTATAATAAAAAATAACATTT
* * * * * **
3175777 TAAGTAATATCTAATATTAATATTTTTGATAAAAAATAATTTTT
1 TAAATAATATCTAAAATTAATATCTATAATAAAAAATAACATTT
3175821 TAAATAATAT
1 TAAATAATAT
3175831 TCTATCAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 4 0.09
44 40 0.91
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (44 bp):
TAAATAATATCTAAAATTAATATCTATAATAAAAAATAACATTT
Found at i:3179570 original size:3 final size:3
Alignment explanation
Indices: 3179510--3179551 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3179500 ACCAAAATTT
3179510 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3179552 TACGCGGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3186709 original size:34 final size:37
Alignment explanation
Indices: 3186665--3186766 Score: 149
Period size: 34 Copynumber: 2.8 Consensus size: 37
3186655 TTTCGTCATA
3186665 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
*
3186700 -TAGGATTCAAACTCCTAAAAATAGGACA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
*
3186735 GCTAGGATTCAAACTCCTAAAAATATGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
3186767 GTTCTACTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.47
35 3 0.05
37 26 0.44
38 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:3187495 original size:16 final size:16
Alignment explanation
Indices: 3187474--3187508 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3187464 ATGTATTTAT
3187474 TTATTATATTACATTA
1 TTATTATATTACATTA
* *
3187490 TTATTATTTTACTTTA
1 TTATTATATTACATTA
3187506 TTA
1 TTA
3187509 AATTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTATATTACATTA
Found at i:3187515 original size:21 final size:22
Alignment explanation
Indices: 3187489--3187539 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3187479 ATATTACATT
*
3187489 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
3187510 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
3187532 TTTATTAT
1 ATTATTAT
3187540 ATATATATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:3190868 original size:22 final size:22
Alignment explanation
Indices: 3190844--3190905 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
3190834 ACAAAAGGGC
3190844 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
3190867 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
3190888 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
3190906 TAAAAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:3190896 original size:20 final size:20
Alignment explanation
Indices: 3190844--3190913 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
3190834 ACAAAAGGGC
*
3190844 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
3190867 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
3190888 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
3190908 AAAAAG
1 AAAAAG
3190914 GGAACAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 18 0.43
21 7 0.17
22 6 0.14
23 10 0.24
24 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:3192634 original size:36 final size:36
Alignment explanation
Indices: 3192526--3192649 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
3192516 ATTGAAAACA
* * *
3192526 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
3192562 TTTCCCTTGGAACTAAGTTTT-GTCTCTCTTAAGACAG
1 TTTCCCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
* *
3192599 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
3192635 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
3192650 AACCTTTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:3192743 original size:67 final size:68
Alignment explanation
Indices: 3192625--3192781 Score: 205
Period size: 68 Copynumber: 2.4 Consensus size: 68
3192615 TTTCGTCTAT
* **
3192625 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTT-TT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
3192686 CTCC
66 -TCC
* * *
3192690 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
3192755 TCC
66 TCC
* *
3192758 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
3192782 ACAGATATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.35
68 30 0.38
69 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
TCC
Found at i:3193615 original size:105 final size:105
Alignment explanation
Indices: 3193386--3194046 Score: 972
Period size: 105 Copynumber: 6.3 Consensus size: 105
3193376 GCCATCCGCG
* * * * * *
3193386 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
3193451 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
*
3193495 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3193560 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
3193600 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3193665 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
3193705 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3193770 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
3193810 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
3193875 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
3193910 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** * *
3193975 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGTCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
3194016 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
3194047 TGGAACAATG
Statistics
Matches: 515, Mismatches: 31, Indels: 15
0.92 0.06 0.03
Matches are distributed among these distances:
100 83 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 310 0.60
106 84 0.16
107 3 0.01
109 22 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:3194638 original size:34 final size:37
Alignment explanation
Indices: 3194594--3194695 Score: 158
Period size: 34 Copynumber: 2.8 Consensus size: 37
3194584 TTTCGTCCTA
3194594 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
3194629 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
*
3194664 GCTAGGATTCAAACTCCTAAAAATATGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
3194696 GTTCTACTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.48
35 3 0.05
37 27 0.44
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:3194679 original size:37 final size:35
Alignment explanation
Indices: 3194594--3194729 Score: 159
Period size: 37 Copynumber: 3.8 Consensus size: 35
3194584 TTTCGTCCTA
3194594 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
3194629 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
* *
3194664 GCTAGGATTCAAACTCCTAAAAATATGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
3194701 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
3194730 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 3 0.03
36 2 0.02
37 51 0.59
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:3195297 original size:14 final size:12
Alignment explanation
Indices: 3195269--3195301 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3195259 TCATTATATG
3195269 TATATTTTTTAT
1 TATATTTTTTAT
3195281 TATATTTTTTAT
1 TATATTTTTTAT
*
3195293 TTTATTTTT
1 TATATTTTT
3195302 ACTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TATATTTTTTAT
Found at i:3197659 original size:27 final size:27
Alignment explanation
Indices: 3197629--3197682 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3197619 GTACCCAAAG
3197629 TCAACCTTAATATTTAGTTCAAAAACA
1 TCAACCTTAATATTTAGTTCAAAAACA
3197656 TCAACCTTAATATTTAGTTCAAAAACA
1 TCAACCTTAATATTTAGTTCAAAAACA
3197683 AGTTAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (27 bp):
TCAACCTTAATATTTAGTTCAAAAACA
Found at i:3201491 original size:52 final size:52
Alignment explanation
Indices: 3201413--3201517 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
3201403 CAATCACTTT
3201413 GCAATTTTCCTTTTACGTTTCTTATTGTTTTTATTCAACTATCATTGAAGCC
1 GCAATTTTCCTTTTACGTTTCTTATTGTTTTTATTCAACTATCATTGAAGCC
3201465 GCAATTTTCCTTTTACGTTTCTTATTGTTTTTATTCAACTATCATTGAAGCC
1 GCAATTTTCCTTTTACGTTTCTTATTGTTTTTATTCAACTATCATTGAAGCC
3201517 G
1 G
3201518 TTGTCTATCG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (52 bp):
GCAATTTTCCTTTTACGTTTCTTATTGTTTTTATTCAACTATCATTGAAGCC
Found at i:3205603 original size:6 final size:6
Alignment explanation
Indices: 3205592--3205684 Score: 186
Period size: 6 Copynumber: 15.5 Consensus size: 6
3205582 AAATACATTG
3205592 AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT
1 AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT
3205640 AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAA
1 AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAA
3205685 AGTACGAACA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
AAATGT
Found at i:3207823 original size:32 final size:32
Alignment explanation
Indices: 3207729--3207828 Score: 107
Period size: 31 Copynumber: 3.2 Consensus size: 32
3207719 GCAACTGTCC
* *
3207729 AGGTAA-ATTGTCCATATGTTCCTTAGAACAT
1 AGGTAATAATGTCCATATGTTCCGTAGAACAT
* *
3207760 AGGT-ATAATGTCCATATGTCCCG-AAAGACAT
1 AGGTAATAATGTCCATATGTTCCGTAGA-ACAT
* * *
3207791 AAGTAATTATGTCCATATGTTTCGTAGAACAT
1 AGGTAATAATGTCCATATGTTCCGTAGAACAT
3207823 AGGTAA
1 AGGTAA
3207829 ACCCTCGACT
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
30 3 0.05
31 25 0.45
32 25 0.45
33 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (32 bp):
AGGTAATAATGTCCATATGTTCCGTAGAACAT
Found at i:3210881 original size:21 final size:21
Alignment explanation
Indices: 3210839--3210881 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3210829 TTTCTAGGCT
* *
3210839 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
3210860 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
3210881 A
1 A
3210882 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3211641 original size:103 final size:103
Alignment explanation
Indices: 3211416--3211633 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
3211406 GTAGAGGGTC
*
3211416 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
3211481 TTGATCCTTGATATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGATATATGTATATGATTCTTAAGGAATGA
3211519 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
3211584 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGATATATGTATATGATTCTTAAGGAATGA
3211622 TATGTGGTCCTT
1 TATGTGGTCCTT
3211634 ATGGACATTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGATATATGTATATGATTCTTAAGGAATGA
Found at i:3211683 original size:23 final size:23
Alignment explanation
Indices: 3211650--3211712 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
3211640 ATTATTATAT
3211650 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
3211673 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
3211696 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
3211713 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3217673 original size:21 final size:21
Alignment explanation
Indices: 3217631--3217673 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3217621 TTTCTAGGCT
* *
3217631 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
3217652 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
3217673 A
1 A
3217674 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3218441 original size:103 final size:103
Alignment explanation
Indices: 3218216--3218433 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
3218206 GTAGAGGGTC
* *
3218216 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTAGTGAGACACATAC
3218281 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
3218319 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTAGTGAGACACATAC
3218384 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
3218422 TATGTGGTCCTT
1 TATGTGGTCCTT
3218434 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.39
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTAGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:3218508 original size:23 final size:23
Alignment explanation
Indices: 3218449--3218512 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
3218439 CATTATTATA
3218449 TGGCAC-TACGGTGCAATTCTACG
1 TGGCACTTA-GGTGCAATTCTACG
* *
3218472 CGGCACTCCA-GTGCAATTCTACG
1 TGGCACT-TAGGTGCAATTCTACG
3218495 TGGCACTTAGGTGCAATT
1 TGGCACTTAGGTGCAATT
3218513 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
25 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:3231866 original size:15 final size:14
Alignment explanation
Indices: 3231841--3231870 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3231831 ATGCGGACTT
3231841 TTTAACCCGCACCG
1 TTTAACCCGCACCG
3231855 TTTAAGCCCGCACCG
1 TTTAA-CCCGCACCG
3231870 T
1 T
3231871 CAAAACCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.40, G:0.17, T:0.23
Consensus pattern (14 bp):
TTTAACCCGCACCG
Found at i:3232288 original size:16 final size:16
Alignment explanation
Indices: 3232261--3232305 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
3232251 CAACTCTACT
3232261 TTATTCATAATATTTAA
1 TTATTCATAATA-TTAA
3232278 TTATT-ATAATATTAA
1 TTATTCATAATATTAA
*
3232293 TTTTTCAATAATA
1 TTATTC-ATAATA
3232306 AAATAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 11 0.44
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTCATAATATTAA
Found at i:3233864 original size:13 final size:13
Alignment explanation
Indices: 3233848--3233877 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3233838 CTTAATTGCG
3233848 AAAATTAAAATTT
1 AAAATTAAAATTT
*
3233861 AAAATTGAAATTT
1 AAAATTAAAATTT
3233874 AAAA
1 AAAA
3233878 AATCGGTTTG
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:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:3234036 original size:28 final size:27
Alignment explanation
Indices: 3233998--3234067 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 27
3233988 ACTGAAGGAA
*
3233998 AAATAATAATAAAAATATGTATAA-CAAAT
1 AAATAA-AATAAAAA-AT-TAAAATCAAAT
*
3234027 AAATAAAATAATAAAATTAAAATTAAAT
1 AAATAAAATAA-AAAATTAAAATCAAAT
3234055 AAATAAAACTAAA
1 AAATAAAA-TAAA
3234068 GAAGTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 4 0.11
28 20 0.56
29 12 0.33
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (27 bp):
AAATAAAATAAAAAATTAAAATCAAAT
Found at i:3234059 original size:20 final size:19
Alignment explanation
Indices: 3234027--3234067 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3234017 TATAACAAAT
*
3234027 AAATAAAATAATAAAATTA
1 AAATAAAATAATAAAACTA
*
3234046 AAATTAAATAAATAAAACTA
1 AAATAAAAT-AATAAAACTA
3234066 AA
1 AA
3234068 GAAGTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAAATAATAAAACTA
Found at i:3235314 original size:15 final size:15
Alignment explanation
Indices: 3235294--3235352 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 15
3235284 AAATTAGATT
* *
3235294 AATAAAATGAAATGA
1 AATAAAATAAAATAA
3235309 AATAAAATAAAATAA
1 AATAAAATAAAATAA
3235324 AATAAATATTAATAATAA
1 AATAAA-A-TAA-AATAA
3235342 TAATAATAATA
1 -AATAA-AATA
3235353 TAGATTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
15 19 0.51
16 1 0.03
17 3 0.08
18 7 0.19
19 6 0.16
20 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATAAAATAAAATAA
Found at i:3235556 original size:34 final size:33
Alignment explanation
Indices: 3235377--3235610 Score: 136
Period size: 35 Copynumber: 6.7 Consensus size: 33
3235367 TATGTTTCAA
* * * *
3235377 AAAATATTTTTTAAACTATATATT-TTA-TTTA
1 AAAATGTTTTTAAAACTATATATTATAATTTTC
* * *
3235408 AAAATGTTTTCAAAACTATATATTACATAGTTTC
1 AAAATGTTTTTAAAACTATATATTATA-ATTTTC
* * * *
3235442 AAAAACGATTTTAAAAATGT-TA-TATAAGTTTTCC
1 -AAAATGTTTTTAAAACTATATATTATAA-TTTT-C
* **
3235476 AAAATGTTTTTTTAAACTATATATTATATAAAATTTAAAAA
1 AAAATG-TTTTTAAAACTATATA-T-TAT--AATTT---TC
3235517 AAAATGTTTTTTAAAAACTATATATTAT-ATTTTC
1 AAAATG-TTTTT-AAAACTATATATTATAATTTTC
* *
3235551 AAAATGATTTCAAAACTATATACTATATAATTTTC
1 AAAATGTTTTTAAAACTATATA-T-TATAATTTTC
3235586 AAAATGTTTTTAAAACTTATATATT
1 AAAATGTTTTTAAAAC-TATATATT
3235611 GTACATAAGT
Statistics
Matches: 155, Mismatches: 27, Indels: 39
0.70 0.12 0.18
Matches are distributed among these distances:
31 21 0.14
32 12 0.08
33 16 0.10
34 25 0.16
35 37 0.24
36 6 0.04
37 4 0.03
38 3 0.02
39 3 0.02
40 5 0.03
41 13 0.08
42 10 0.06
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (33 bp):
AAAATGTTTTTAAAACTATATATTATAATTTTC
Found at i:3236654 original size:165 final size:164
Alignment explanation
Indices: 3236378--3237251 Score: 1180
Period size: 165 Copynumber: 5.3 Consensus size: 164
3236368 AGGTTTTCGG
* * **
3236378 TTGGCAGATAGTCCTTCTCAACTTAAGCTATATTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * ** * * * *
3236443 CAAACTCGAAGGTTTTTTAGTAACAGATAACCCTTTTAGTCTTGAGTTATGCTGTAAATGATATG
66 CGAACTCGAAGG-TCTTTGGTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGTA
*
3236508 CCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
130 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
* ** *
3236543 TTGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATACGCCTTGTAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * *
3236608 CAAACTCGAAGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTA
66 CGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGTA
*
3236673 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
130 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
* * * *
3236708 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAACGATGCGCCTTGGAGCTAAACGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
3236773 CGAACTCAAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTAC
66 CGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGTAC
* *
3236838 CCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCT
131 CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
* * *
3236872 TTGGTAGATAGCCCTTCTCGACTTAAGGTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * *
3236937 CGAACTCGAAGGTATTTGGTTGGCAGATAACCTTTCTCGACTT-AGGTTATGCTGTAAATGATGT
66 CGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGACTTGA-GTTATGCTGTAAATGATGT
3237001 ACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
129 ACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
* *
3237037 TTGGCAGATATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTACCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * *
3237102 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT-AGGTTATGCTGCAAATGATAT
66 CGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGACTTGA-GTTATGCTGTAAATGATGT
* * * * * *
3237166 -GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
129 ACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
* * * *
3237201 TGGTGGCAGATAGCCCTTCTGGCCTTGAGCTATGGTGCAAATGATGT-CCTT
1 T--TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
3237252 TTTAAAAAAA
Statistics
Matches: 641, Mismatches: 63, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
164 189 0.29
165 413 0.64
166 39 0.06
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (164 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGTAC
CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
Found at i:3236897 original size:329 final size:328
Alignment explanation
Indices: 3236378--3237245 Score: 1184
Period size: 329 Copynumber: 2.6 Consensus size: 328
3236368 AGGTTTTCGG
* * **
3236378 TTGGCAGATAGTCCTTCTCAACTTAAGCTATATTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * ** * *
3236443 CAAACTCGAAGGTTTTTTAGTAACAGATAACCCTTTTAGTCTTGAGTTATGCTGTAAATGATATG
66 CGAACTCGAAGG-TCTTTGGTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATAT-
* *
3236508 CCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCTTTCTCGACTTAAGCTA
129 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
* * *
3236573 TGCTGCAAATGATACGCCTTGTAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG-TGACATATA
194 TGCTGCAAATGATACGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGT-ATTTGGTTGACAGATA
*
3236637 ACCCTTCTAGCCTT-GAGTTATGCTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCG
258 ACCCTTCTAGACTTAG-GTTATGCTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCG
*
3236701 GGGGTCT
322 AGGGTCT
* * * *
3236708 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAACGATGCGCCTTGGAGCTAAACGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * *
3236773 CGAACTCAAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTAC
66 CGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATAT-C
* * * *
3236838 CCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGGTAT
130 CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
* ** * *
3236903 GTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGGCAGATAAC
195 GCTGCAAATGATACGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTATTTGGTTGACAGATAAC
* *
3236968 CTTTCTCGACTTAGGTTATGCTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGG
260 CCTTCTAGACTTAGGTTATGCTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGG
3237033 GTCT
325 GTCT
* *
3237037 TTGGCAGATATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTACCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
3237102 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT-AGGTTATGCTGCAAATGATAT
66 CGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGACTTGA-GTTATGCTGTAAATGATAT
* * * * * * * * *
3237166 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGATAGCCCTTCTGGCCTTGAGC
129 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTT--TGGCAGATAGCCCTTCTCGACTTAAGC
*
3237231 TATGGTGCAAATGAT
192 TATGCTGCAAATGAT
3237246 GTCCTTTTTA
Statistics
Matches: 471, Mismatches: 61, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
328 5 0.01
329 324 0.69
330 106 0.23
331 36 0.08
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (328 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATATCC
CTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
CTGCAAATGATACGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTATTTGGTTGACAGATAACC
CTTCTAGACTTAGGTTATGCTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGG
TCT
Found at i:3242181 original size:13 final size:13
Alignment explanation
Indices: 3242165--3242196 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3242155 CTTAATTGCG
3242165 AAAATTAAAATTT
1 AAAATTAAAATTT
*
3242178 AAAATTGAAATTT
1 AAAATTAAAATTT
3242191 AAAATT
1 AAAATT
3242197 TCGGTTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:3242378 original size:20 final size:19
Alignment explanation
Indices: 3242346--3242386 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3242336 TATACCAAAG
*
3242346 AAATAAAATAATAAAATTA
1 AAATAAAATAATAAAACTA
*
3242365 AAATTAAATAAATAAAACTA
1 AAATAAAAT-AATAAAACTA
3242385 AA
1 AA
3242387 GAAGTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAAATAATAAAACTA
Found at i:3242490 original size:19 final size:21
Alignment explanation
Indices: 3242435--3242495 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 21
3242425 CAATACGAGG
*
3242435 TAAAAAAAATACTAATAATAA
1 TAAAAAAAATAATAATAATAA
* * *
3242456 TAAAAAAGCATGATAATAAAAAA
1 TAAAAAA-AATAATAAT-AATAA
3242479 TAAAAAAAATAA-AATAA
1 TAAAAAAAATAATAATAA
3242496 GAATTTAGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.06
21 10 0.31
22 9 0.28
23 11 0.34
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAAAAAAATAATAATAATAA
Found at i:3243636 original size:15 final size:15
Alignment explanation
Indices: 3243616--3243665 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3243606 AAATTAGATT
* *
3243616 AATAAAATGAAATGA
1 AATAAAATAAAATAA
3243631 AATAAAATAAAATAA
1 AATAAAATAAAATAA
3243646 AAT-AAATAATAATAA
1 AATAAAATAA-AATAA
3243661 TAATA
1 -AATA
3243666 TAGATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 6 0.20
15 21 0.70
16 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (15 bp):
AATAAAATAAAATAA
Found at i:3243818 original size:38 final size:38
Alignment explanation
Indices: 3243732--3243945 Score: 143
Period size: 35 Copynumber: 5.9 Consensus size: 38
3243722 AACGTTTTCA
*
3243732 AAACTATATATTATAT-AGTTTTCAAAAATG--ATTTT
1 AAACTATATATTATATAAGTTTTCAAAAATGTTTTTTT
* *
3243767 AAA--A-ATGTTATATAAGTTTTCCAAAATGTTTTTTT
1 AAACTATATATTATATAAGTTTTCAAAAATGTTTTTTT
* * *
3243802 AAACTATATATTATATAAATTTTTAAAAAATGTTTTTTAA
1 AAACTATATATTATAT-AAGTTTTCAAAAATGTTTTTT-T
* * **
3243842 AAACTATATA-T-TAT-A-TTTTC-AGAATG-ATTTCA
1 AAACTATATATTATATAAGTTTTCAAAAATGTTTTTTT
* * *
3243874 AAATTATATACTATATAA-TTTTC-AAAATG-TTTTTA
1 AAACTATATATTATATAAGTTTTCAAAAATGTTTTTTT
* *
3243909 AAACTTATATATTGTACATAAGTTTTCAAAAACGTTT
1 AAAC-TATATA-T-TATATAAGTTTTCAAAAATGTTT
3243946 CAAAAAATTA
Statistics
Matches: 142, Mismatches: 20, Indels: 28
0.75 0.11 0.15
Matches are distributed among these distances:
32 18 0.13
33 18 0.13
34 8 0.06
35 32 0.23
36 7 0.05
37 1 0.01
38 17 0.12
39 24 0.17
40 15 0.11
41 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.46
Consensus pattern (38 bp):
AAACTATATATTATATAAGTTTTCAAAAATGTTTTTTT
Found at i:3250286 original size:17 final size:17
Alignment explanation
Indices: 3250264--3250296 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3250254 TATCATTGAA
3250264 ATCCCTAATCCCCTTCG
1 ATCCCTAATCCCCTTCG
*
3250281 ATCCCTAATTCCCTTC
1 ATCCCTAATCCCCTTC
3250297 TCTCTTTCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.45, G:0.03, T:0.33
Consensus pattern (17 bp):
ATCCCTAATCCCCTTCG
Found at i:3270615 original size:18 final size:18
Alignment explanation
Indices: 3270592--3270632 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3270582 AGAGAGAGAG
**
3270592 AGAAAAAACAAAACTAAA
1 AGAAAAAACAAAAAAAAA
*
3270610 AGAAAAAAGAAAAAAAAA
1 AGAAAAAACAAAAAAAAA
3270628 AGAAA
1 AGAAA
3270633 GGACCTGCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.83, C:0.05, G:0.10, T:0.02
Consensus pattern (18 bp):
AGAAAAAACAAAAAAAAA
Found at i:3276710 original size:58 final size:58
Alignment explanation
Indices: 3276642--3276759 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
3276632 TAAACAAACC
3276642 ATATATGATAAAATATAAACTAGCATCAAGGTGGATTTAAAATTATATATATATATAT
1 ATATATGATAAAATATAAACTAGCATCAAGGTGGATTTAAAATTATATATATATATAT
3276700 ATATATGATAAAATATAAACTAGCATCAAGGTGGATTTAAAATTATATATATATATAT
1 ATATATGATAAAATATAAACTAGCATCAAGGTGGATTTAAAATTATATATATATATAT
3276758 AT
1 AT
3276760 GGTATTTTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.36
Consensus pattern (58 bp):
ATATATGATAAAATATAAACTAGCATCAAGGTGGATTTAAAATTATATATATATATAT
Found at i:3278644 original size:23 final size:23
Alignment explanation
Indices: 3278611--3278654 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3278601 GAGTCGAGGG
3278611 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGGGACAAT
*
3278634 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
3278655 TATATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAT
Found at i:3280283 original size:3 final size:3
Alignment explanation
Indices: 3280270--3280308 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
3280260 TCTTTCTTAC
*
3280270 TAT TTT TAT TAT TAT TAT TAT TAT ATAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TA
3280309 AATAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3280300 original size:16 final size:15
Alignment explanation
Indices: 3280270--3280308 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
3280260 TCTTTCTTAC
*
3280270 TATTTTTATTATTAT
1 TATTATTATTATTAT
3280285 TATTATTATATATTAT
1 TATTATTAT-TATTAT
3280301 TATTATTA
1 TATTATTA
3280309 AATAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTATTATTATTAT
Found at i:3281871 original size:24 final size:24
Alignment explanation
Indices: 3281847--3281892 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3281837 TTTAAAATTA
*
3281847 AATATTAT-AAAAAATTATTATTT
1 AATATTATGAAAAAAATATTATTT
*
3281870 AATTTTATGAAAAAAATATTATT
1 AATATTATGAAAAAAATATTATT
3281893 ATTATCAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AATATTATGAAAAAAATATTATTT
Found at i:3289112 original size:93 final size:93
Alignment explanation
Indices: 3288927--3289114 Score: 263
Period size: 93 Copynumber: 2.0 Consensus size: 93
3288917 AGAAGACCCA
* * * * *
3288927 ATAGTATCTCCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTCCTGAAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAAACCACAAAACCAA
*
3288992 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCATTGAATTTGAAAGATGAATGTGCTC
*
3289020 ATAGCATCTCCTGAAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATG-AACTC-CAAAATCA
1 ATAGCATCTCCTGAAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAAAC-CACAAAACCA
* *
3289083 ATCATTGGATTTGAAAGATGAATTTTGCTC
65 ATCATTGAATTTGAAAGATGAA-TGTGCTC
3289113 AT
1 AT
3289115 GGTAGAAATA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
92 29 0.35
93 55 0.65
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (93 bp):
ATAGCATCTCCTGAAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAAACCACAAAACCAA
TCATTGAATTTGAAAGATGAATGTGCTC
Found at i:3290900 original size:158 final size:158
Alignment explanation
Indices: 3290612--3290928 Score: 609
Period size: 158 Copynumber: 2.0 Consensus size: 158
3290602 GCTTCGTTCA
3290612 TCAGGCAATTACATTATGATCATGATGTTGAATAAATGTTTACTCAGCAAGTATGTTTTTCAAAT
1 TCAGGCAATTACATTATGATCATGATGTTGAATAAATGTTTACTCAGCAAGTATGTTTTTCAAAT
3290677 ACCTAATCTTCTAAACCGTATGTCACATGACAGTGTGTCTTTGATAAACTACATTACGGTTGCAT
66 ACCTAATCTTCTAAACCGTATGTCACATGACAGTGTGTCTTTGATAAACTACATTACGGTTGCAT
3290742 GAATAAAGATGATCCCCAGGTAGACTAC
131 GAATAAAGATGATCCCCAGGTAGACTAC
3290770 TCAGGCAATTACATTATGATCATGATGTTGAATAAATGTTTACTCAGCAAGTATG-TTTTCAAAT
1 TCAGGCAATTACATTATGATCATGATGTTGAATAAATGTTTACTCAGCAAGTATGTTTTTCAAAT
*
3290834 ACCTAATCTTCTTAACCGTATGTCACATGACAGTGTGTTCTTTGATAAACTACATTACGGTTGCA
66 ACCTAATCTTCTAAACCGTATGTCACATGACAGTGTG-TCTTTGATAAACTACATTACGGTTGCA
3290899 TGAATAAAGATGATCCCCAGGTAGACTAC
130 TGAATAAAGATGATCCCCAGGTAGACTAC
3290928 T
1 T
3290929 TGATCCAGGG
Statistics
Matches: 157, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
157 45 0.29
158 112 0.71
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (158 bp):
TCAGGCAATTACATTATGATCATGATGTTGAATAAATGTTTACTCAGCAAGTATGTTTTTCAAAT
ACCTAATCTTCTAAACCGTATGTCACATGACAGTGTGTCTTTGATAAACTACATTACGGTTGCAT
GAATAAAGATGATCCCCAGGTAGACTAC
Found at i:3292004 original size:22 final size:22
Alignment explanation
Indices: 3291975--3292029 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
3291965 ATCTACACTC
*
3291975 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
3291997 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
3292019 TTCAAAGATGA
1 TTCAAAGATGA
3292030 AAGCTTTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:3292862 original size:165 final size:166
Alignment explanation
Indices: 3292545--3292867 Score: 488
Period size: 165 Copynumber: 2.0 Consensus size: 166
3292535 AAAATGAGCA
3292545 TTATCTTTAGATTAGGTCATGTTACCCAATCAACATGCTATTTCAAAACACAGAATGAGAAAACG
1 TTATCTTTAGATTAGGTCATGTTACCCAATCAACATGCTATTTCAAAACACAGAATGAGAAAACG
* * ** *
3292610 ATTTTCATAATTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTT
66 ATTTCCATAATTTCTCAATCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATTTT
* *
3292675 CTTAGTTTTTTACTTAGTAAACTATTTCTAACAGCC
131 CATAGTTTCTTACTTAGTAAACTATTTCTAACAGCC
* ** *
3292711 TTATCTTTAGATTAGGTCATGTTACCCAATCAACATGTTATTTTGAAA-A-ATAATGAGAAAACG
1 TTATCTTTAGATTAGGTCATGTTACCCAATCAACATGCTATTTCAAAACACAGAATGAGAAAACG
* * *
3292774 ATTTCCATAGTTTCTCAATCAATCTTTTCTAAAAATGAAATTGTTGACAAGTAAGAAAATAATTT
66 ATTTCCATAATTTCTCAATCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACAATTT
*
3292839 TCATAGTTTCTTATTTAGTAAACTATTTC
130 TCATAGTTTCTTACTTAGTAAACTATTTC
3292868 CCTTATCTGT
Statistics
Matches: 141, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
164 38 0.27
165 58 0.41
166 45 0.32
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (166 bp):
TTATCTTTAGATTAGGTCATGTTACCCAATCAACATGCTATTTCAAAACACAGAATGAGAAAACG
ATTTCCATAATTTCTCAATCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATTTT
CATAGTTTCTTACTTAGTAAACTATTTCTAACAGCC
Found at i:3292998 original size:76 final size:76
Alignment explanation
Indices: 3292872--3293555 Score: 1248
Period size: 76 Copynumber: 9.0 Consensus size: 76
3292862 TATTTCCCTT
3292872 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
*
3292937 ACCTTCGAGTC
66 ACCTTCGGGTC
*
3292948 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
3293013 ACCTTCGGGTC
66 ACCTTCGGGTC
3293024 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
3293089 ACCTTCGGGTC
66 ACCTTCGGGTC
* *
3293100 ATCTGTAAGTCCTTCATTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
*
3293165 GCCTTCGGGTC
66 ACCTTCGGGTC
3293176 ATCTGTAAGCCCTTCAGTGCATGATGTTTCC--AAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
3293239 ACCTTCGGGTC
66 ACCTTCGGGTC
*
3293250 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
*
3293315 GCCTTCGGGTC
66 ACCTTCGGGTC
3293326 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
3293391 ACCTTCGGGTC
66 ACCTTCGGGTC
3293402 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
*
3293467 GCCTTCGGGTC
66 ACCTTCGGGTC
*
3293478 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-AA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
*
3293542 ACCCTCAGGGTC
66 ACCTTC-GGGTC
3293554 AT
1 AT
3293556 TCATAAGACC
Statistics
Matches: 588, Mismatches: 17, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
74 72 0.12
75 6 0.01
76 510 0.87
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (76 bp):
ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
ACCTTCGGGTC
Found at i:3293425 original size:302 final size:303
Alignment explanation
Indices: 3292872--3293555 Score: 1273
Period size: 302 Copynumber: 2.3 Consensus size: 303
3292862 TATTTCCCTT
3292872 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
*
3292937 ACCTTCGAGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTG
65 ACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTG
3293002 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
130 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
* *
3293067 GGAACTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCATTGCATGATGTTTCCA
195 GGAACTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCA
3293132 AAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTC
260 AAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTC
3293176 ATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAGCCTTCGGGAACTTTTTGATGTTTTCAAAA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAA
3293240 CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGA
66 CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGA
*
3293305 TGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
131 TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
3293370 GAACTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAA
196 GAACTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAA
3293435 AAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTC
261 AAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTC
*
3293478 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-AA
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAACTTTTTGATGTTTTCAAA
*
3293542 ACCCTCAGGGTCAT
65 ACCTTC-GGGTCAT
3293556 TCATAAGACC
Statistics
Matches: 371, Mismatches: 6, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
302 298 0.80
303 7 0.02
304 66 0.18
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (303 bp):
ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAA
CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGA
TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
GAACTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAA
AAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTC
Found at i:3296206 original size:2 final size:2
Alignment explanation
Indices: 3296199--3296291 Score: 163
Period size: 2 Copynumber: 47.5 Consensus size: 2
3296189 ACTGGAAGGA
*
3296199 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3296241 AT AT AT AT AT A- AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3296281 AT AT AT AT AT A
1 AT AT AT AT AT A
3296292 GTTTGATAAA
Statistics
Matches: 87, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 85 0.98
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3299702 original size:21 final size:21
Alignment explanation
Indices: 3299676--3299716 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3299666 GAAATTTTAG
*
3299676 TGCATCGATGCATTGTAGCAA
1 TGCATCGATGCACTGTAGCAA
3299697 TGCATCGATGCACTGTAGCA
1 TGCATCGATGCACTGTAGCA
3299717 TTGTTCATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCACTGTAGCAA
Found at i:3303279 original size:33 final size:31
Alignment explanation
Indices: 3303252--3303310 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
3303242 TTAATAAAAC
3303252 TAGCA-TAATTATACATTTGGTCCTTAAT-A
1 TAGCAGTAATTATACATTTGGTCCTTAATAA
* *
3303281 TTGGAGTAATTATACATTTGGTCCTTAATA
1 TAGCAGTAATTATACATTTGGTCCTTAATA
3303311 TTTACATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (31 bp):
TAGCAGTAATTATACATTTGGTCCTTAATAA
Done.