Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 11 of 150
Found at i:3142217 original size:23 final size:22
Alignment explanation
Indices: 3142173--3142230 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
3142163 AAAGGGTATC
* *
3142173 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
3142194 TACAAAATCATATCTTCTACGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
3142217 TGCATATCATATCT
1 TACAAATCATATCT
3142231 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.60
23 9 0.30
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:3142236 original size:19 final size:19
Alignment explanation
Indices: 3142209--3142262 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
3142199 AATCATATCT
*
3142209 TCTACGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
3142228 TCTAAGATTGCATATAATA
1 TCTAAGATTGCATATCATA
3142247 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
3142263 CTTTAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:3146356 original size:21 final size:20
Alignment explanation
Indices: 3146331--3146369 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3146321 GTTCTTGTAT
3146331 TTTTTGAACTTTTGAATTTAA
1 TTTTTGAACTTTT-AATTTAA
**
3146352 TTTTTTTACTTTTAATTT
1 TTTTTGAACTTTTAATTT
3146370 CGAAAATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTTGAACTTTTAATTTAA
Found at i:3147338 original size:3 final size:3
Alignment explanation
Indices: 3147330--3147363 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3147320 TTGCGGCGCT
*
3147330 ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3147364 CACCAGGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3159549 original size:31 final size:31
Alignment explanation
Indices: 3159514--3159576 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
3159504 AGATGCTCAC
3159514 TGAACTATTTAAAAGCTTTCATTTAAGTCAT
1 TGAACTATTTAAAAGCTTTCATTTAAGTCAT
* * *
3159545 TGAACTATTTGAAAGTTTTTATTTAAGTCAT
1 TGAACTATTTAAAAGCTTTCATTTAAGTCAT
3159576 T
1 T
3159577 AGGATGTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (31 bp):
TGAACTATTTAAAAGCTTTCATTTAAGTCAT
Found at i:3175318 original size:19 final size:19
Alignment explanation
Indices: 3175294--3175330 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3175284 ATAATCTTCA
*
3175294 ATGATATGCAATTTTAGAT
1 ATGATATGCAATCTTAGAT
3175313 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
3175331 AGATAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:3176287 original size:24 final size:23
Alignment explanation
Indices: 3176184--3176340 Score: 96
Period size: 24 Copynumber: 6.8 Consensus size: 23
3176174 TATTGTATAT
* * * *
3176184 TATTAGTTTAGATTTATCACGTTT
1 TATTATTTTAAATTTATCATG-TA
*
3176208 TATTATTTGT-AATTTATCA-ATA
1 TATTATTT-TAAATTTATCATGTA
3176230 TCATTATTTTAAA--T-TCATGGTAA
1 T-ATTATTTTAAATTTATCAT-GT-A
*
3176253 CATTATTTTAAATTTATCATGTA
1 TATTATTTTAAATTTATCATGTA
3176276 TATTTATTTTAAAATTTATCAT-TA
1 TA-TTATTTT-AAATTTATCATGTA
* *
3176300 -A-TATTTTAAAGTTATTATGTA
1 TATTATTTTAAATTTATCATGTA
**
3176321 CTATTATTTTGGATTTATCA
1 -TATTATTTTAAATTTATCA
3176341 CATATGATTA
Statistics
Matches: 105, Mismatches: 13, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
20 12 0.11
21 9 0.09
22 15 0.14
23 14 0.13
24 39 0.37
25 16 0.15
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (23 bp):
TATTATTTTAAATTTATCATGTA
Found at i:3176290 original size:25 final size:24
Alignment explanation
Indices: 3176255--3176305 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
3176245 CATGGTAACA
3176255 TTATTTTAAATTTATCATGT-ATAT
1 TTATTTTAAATTTATCAT-TAATAT
3176279 TTATTTTAAAATTTATCATTAATAT
1 TTATTTT-AAATTTATCATTAATAT
3176304 TT
1 TT
3176306 TAAAGTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (24 bp):
TTATTTTAAATTTATCATTAATAT
Found at i:3176480 original size:2 final size:2
Alignment explanation
Indices: 3176473--3176505 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3176463 ATTGTACATT
3176473 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3176506 TATTTAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3183487 original size:24 final size:23
Alignment explanation
Indices: 3183464--3183546 Score: 109
Period size: 22 Copynumber: 3.7 Consensus size: 23
3183454 CAAATCAACA
* * *
3183464 AATGAGGGTTTAGTTCGTTAAAC
1 AATGAGAGCTTAGTACGTTAAAC
3183487 -ATGAGAGCTTAGTACGTTAAAC
1 AATGAGAGCTTAGTACGTTAAAC
*
3183509 -ATGAGAGCTTAGTACGTGAAAC
1 AATGAGAGCTTAGTACGTTAAAC
3183531 -ATGAGAGCTTAGTACG
1 AATGAGAGCTTAGTACG
3183547 GTTTTTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.28
Consensus pattern (23 bp):
AATGAGAGCTTAGTACGTTAAAC
Found at i:3183498 original size:22 final size:22
Alignment explanation
Indices: 3183473--3183546 Score: 130
Period size: 22 Copynumber: 3.4 Consensus size: 22
3183463 AAATGAGGGT
*
3183473 TTAGTTCGTTAAACATGAGAGC
1 TTAGTACGTTAAACATGAGAGC
3183495 TTAGTACGTTAAACATGAGAGC
1 TTAGTACGTTAAACATGAGAGC
*
3183517 TTAGTACGTGAAACATGAGAGC
1 TTAGTACGTTAAACATGAGAGC
3183539 TTAGTACG
1 TTAGTACG
3183547 GTTTTTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (22 bp):
TTAGTACGTTAAACATGAGAGC
Found at i:3196096 original size:59 final size:58
Alignment explanation
Indices: 3196032--3196340 Score: 216
Period size: 59 Copynumber: 5.2 Consensus size: 58
3196022 ATATATGTAA
*
3196032 ATTATATATTTCTATTAAATTATATTTAATAATTATTATTTTAAATTATATTTTATAGT
1 ATTATATATTT-TATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
* ** * * * * *
3196091 ATTATATATTATGATTTTAGTAAATTTATATAAGAA-TA-TTTAATATTAAGAATTTTATTA-A
1 ATTATATATT-TTATTAAATTATATTTA-ATAATAATTATTTTAA-ATT-A-TATTTTA-TAGT
3196152 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
1 ATTATATA-TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
* ** * * * * * * *
3196211 ATTATATATTATGATTTTAGTAAATTCATATAAGAA-TA-TTTAATACTAAGAATTTTATTA-A
1 ATTATATATT-TTATTAAATTATATTTA-ATAATAATTATTTTAA-A-TTA-TATTTTA-TAGT
* * * * *
3196272 ATTATACATTTTAATTAAAATATATTTTATAATAATTATTTCAAATTATATTCTATAGT
1 ATTATATATTTT-ATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
*
3196331 ATCATATATT
1 ATTATATATT
3196341 ATGATTTTAG
Statistics
Matches: 187, Mismatches: 43, Indels: 40
0.69 0.16 0.15
Matches are distributed among these distances:
58 16 0.09
59 67 0.36
60 31 0.17
61 58 0.31
62 15 0.08
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (58 bp):
ATTATATATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
Found at i:3196159 original size:120 final size:119
Alignment explanation
Indices: 3196029--3196436 Score: 654
Period size: 120 Copynumber: 3.4 Consensus size: 119
3196019 GCAATATATG
* *
3196029 TAAATTATATATTTCTATTAAATTATATTTAATAATTATTATTTTAAATTATATTTTATAGTATT
1 TAAATTATATATTT-TATTAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATT
*
3196094 ATATATTATGATTTTAGTAAATTTATATAAGAATATTTAATATTAAGAATTTTAT
65 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTAT
*
3196149 TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATT
1 TAAATTATATA-TTTTATTAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATT
*
3196214 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATACTAAGAATTTTAT
65 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTAT
* * * * *
3196269 TAAATTATACATTTTAATTAAAATATATTTTATAATAATTATTTCAAATTATATTCTATAGTATC
1 TAAATTATATATTTT-ATTAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATT
* *
3196334 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
65 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTAT
* *
3196389 TAAATTATATATCTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 TAAATTATATAT-TTTATTAAAATATATTTAATAATAATTATTTTAAA
3196437 ATATGATTAA
Statistics
Matches: 268, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
119 4 0.01
120 259 0.97
121 5 0.02
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (119 bp):
TAAATTATATATTTTATTAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTA
TATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTAT
Found at i:3196284 original size:17 final size:18
Alignment explanation
Indices: 3196262--3196295 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3196252 AATACTAAGA
*
3196262 ATTTT-ATTAAATTATAC
1 ATTTTAATTAAAATATAC
3196279 ATTTTAATTAAAATATA
1 ATTTTAATTAAAATATA
3196296 TTTTATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTAATTAAAATATAC
Found at i:3196496 original size:6 final size:6
Alignment explanation
Indices: 3196485--3196519 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
3196475 ATTAAAATTT
3196485 AATAAC AATAAC AATAAC AATAAC AATAAC AATAA
1 AATAAC AATAAC AATAAC AATAAC AATAAC AATAA
3196520 TCATTTACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAC
Found at i:3196654 original size:44 final size:45
Alignment explanation
Indices: 3196591--3196686 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 45
3196581 CTATTACACC
* * *
3196591 TCCATTCCATTCAACCAAACACA-AGAA-TACTATTACGTCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAA
* *
3196635 TCCATTACATTCAACCAAACAATTGAATTGCTATTACGCCTCTAA
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAA
3196680 TCCATTA
1 TCCATTA
3196687 TGCCTCTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.31
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAA
Found at i:3196691 original size:16 final size:16
Alignment explanation
Indices: 3196667--3196702 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3196657 TTGAATTGCT
3196667 ATTACGCCTCTAATCC
1 ATTACGCCTCTAATCC
* *
3196683 ATTATGCCTCTATTCC
1 ATTACGCCTCTAATCC
3196699 ATTA
1 ATTA
3196703 GAGCGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTAATCC
Found at i:3206182 original size:13 final size:13
Alignment explanation
Indices: 3206164--3206204 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3206154 GTTTGTAAGA
3206164 AAAAAATAAAAAT
1 AAAAAATAAAAAT
*
3206177 AAAAAATAAAGAT
1 AAAAAATAAAAAT
* *
3206190 AAATAATGAAAAT
1 AAAAAATAAAAAT
3206203 AA
1 AA
3206205 GCAAGAAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:3207086 original size:95 final size:95
Alignment explanation
Indices: 3206967--3207172 Score: 324
Period size: 95 Copynumber: 2.2 Consensus size: 95
3206957 TATTGCGACC
* * *
3206967 TCAGGGAGATAAGATTTAATATGATAAGATTTAATCCAACCCT-CTGTAGCTTAAAAGGTATAGG
1 TCAGGGAGATAAGATTTAATATGATAAGATTTAATCCAA-CCTACTGCAACTTAAAAGGTATAAG
*
3207031 ATTCATCGTTTTAATCCGCTCCACTGCAACT
65 ATTCATCGTTTTAATCAGCTCCACTGCAACT
* * * *
3207062 TCAGGGAGATAAGATTTGATATGATAAGATTTAATCCGACCTACTGCAACTTCAGAGGTATAAGA
1 TCAGGGAGATAAGATTTAATATGATAAGATTTAATCCAACCTACTGCAACTTAAAAGGTATAAGA
3207127 TTCATCGTTTTAATCAGCTCCACTGCAACT
66 TTCATCGTTTTAATCAGCTCCACTGCAACT
3207157 TCAGGGAGATAAGATT
1 TCAGGGAGATAAGATT
3207173 AGCTTCAATC
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 3 0.03
95 99 0.97
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (95 bp):
TCAGGGAGATAAGATTTAATATGATAAGATTTAATCCAACCTACTGCAACTTAAAAGGTATAAGA
TTCATCGTTTTAATCAGCTCCACTGCAACT
Found at i:3207169 original size:44 final size:44
Alignment explanation
Indices: 3207030--3207210 Score: 140
Period size: 44 Copynumber: 4.0 Consensus size: 44
3207020 AAAGGTATAG
*
3207030 GATTCATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAA
1 GATTCATCGTTTTAATCAGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
3207074 GATTTGATATGATAAGATTTAATCCGAC-CTACTGCAACTTCAGAGG-TATAA
1 GA-TTCAT-CG-T----TTTAATCAG-CTCCACTGCAACTTCAG-GGAGATAA
3207125 GATTCATCGTTTTAATCAGCTCCACTGCAACTTCAGGGAGATAA
1 GATTCATCGTTTTAATCAGCTCCACTGCAACTTCAGGGAGATAA
* * * *
3207169 GATT-A--GCTTCAATCCA-CTACACTGCAACTTCAGTGAGATAA
1 GATTCATCGTTTTAAT-CAGCTCCACTGCAACTTCAGGGAGATAA
3207210 G
1 G
3207211 GTTTGTTATC
Statistics
Matches: 112, Mismatches: 13, Indels: 27
0.74 0.09 0.18
Matches are distributed among these distances:
41 30 0.27
42 2 0.02
43 4 0.04
44 32 0.29
45 4 0.04
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 4 0.04
51 29 0.26
52 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (44 bp):
GATTCATCGTTTTAATCAGCTCCACTGCAACTTCAGGGAGATAA
Found at i:3207544 original size:87 final size:87
Alignment explanation
Indices: 3207453--3207613 Score: 243
Period size: 87 Copynumber: 1.9 Consensus size: 87
3207443 GCTTCTTCTG
* * *
3207453 TCTGCTCCTCTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACT-CTGCTGCTACTCAG
1 TCTGCTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTACTAC-GCTGCTACTCAG
3207517 GGAGATAAGGCTGGTGCTTTCGA
65 GGAGATAAGGCTGGTGCTTTCGA
* * * *
3207540 TCTGCTCCACTACTACTTAGGGGGATAAGATCTGCAATCTTTAACCTACTACGCTGCTGCTCAGG
1 TCTGCTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTACTACGCTGCTACTCAGG
3207605 GAGATAAGG
66 GAGATAAGG
3207614 TTAGTTTTTG
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
87 65 0.98
88 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (87 bp):
TCTGCTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTACTACGCTGCTACTCAGG
GAGATAAGGCTGGTGCTTTCGA
Found at i:3207721 original size:89 final size:89
Alignment explanation
Indices: 3207623--3207838 Score: 308
Period size: 89 Copynumber: 2.4 Consensus size: 89
3207613 GTTAGTTTTT
* * **
3207623 GATCTGCTTCACTGCCAGTACAAGAAGACAAGATCTGCTACTTTTAGTCTGTTCCGCTACAAACT
1 GATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTACAAACT
*
3207688 CAGGGAGGTCAA-GCTTTTGTCTTC
66 CAGGGAGG-CAAGGCTTGTGTCTTC
* * * * * *
3207712 GATCTGCTTCGCTACCGGTACAGGAAGACAAGATCTACTGCTTTTAGTCTACTCTGCTGCAAACT
1 GATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTACAAACT
3207777 CAGGGAGGCAAGGCTTGTGTCTTC
66 CAGGGAGGCAAGGCTTGTGTCTTC
*
3207801 TATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGC
1 GATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGC
3207839 AATCTTCAAC
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
88 3 0.03
89 108 0.97
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (89 bp):
GATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTACAAACT
CAGGGAGGCAAGGCTTGTGTCTTC
Found at i:3207853 original size:89 final size:88
Alignment explanation
Indices: 3207479--3207854 Score: 263
Period size: 89 Copynumber: 4.3 Consensus size: 88
3207469 TTAGGGAGAT
* ** * * *
3207479 AAGATCTACAATCTTCGACCTACTCTGCTGCTACTCAGGGAGATAAGGCTGGTG-CTTTCGATCT
1 AAGATCTGCAATCTTTAACCTACTCTGCTGCAACTCAGGGAGACAAGGCTTGTGTC-TTCGATCT
* * ** *
3207543 GCTCCACT-AC--TACTTAGGGGGAT
65 GCTTCACTGCCGGTAC--AGGAAGAC
** * *
3207566 AAGATCTGCAATCTTTAACCTACTAC-GCTGCTGCTCAGGGAGATAAGG-TTAGT-T-TTTGATC
1 AAGATCTGCAATCTTTAACCTACT-CTGCTGCAACTCAGGGAGACAAGGCTT-GTGTCTTCGATC
* *
3207627 TGCTTCACTGCCAGTACAAGAAGAC
64 TGCTTCACTGCCGGTACAGGAAGAC
* ** ** * * * *
3207652 AAGATCTGCTA-CTTTTAGTCTGTTCCGCTACAAACTCAGGGAGGTCAA-GCTTTTGTCTTCGAT
1 AAGATCTGCAATC-TTTAACCTACTCTGCTGC-AACTCAGGGA-GACAAGGCTTGTGTCTTCGAT
* *
3207715 CTGCTTCGCTACCGGTACAGGAAGAC
63 CTGCTTCACTGCCGGTACAGGAAGAC
* ** * *
3207741 AAGATCT--ACTGCTTTTAGTCTACTCTGCTGCAAACTCAGGGAGGCAAGGCTTGTGTCTTCTAT
1 AAGATCTGCAAT-C-TTTAACCTACTCTGCTGC-AACTCAGGGAGACAAGGCTTGTGTCTTCGAT
3207804 CTGCTTCACTGCCGGTACAGGAAGAC
63 CTGCTTCACTGCCGGTACAGGAAGAC
*
3207830 AAGATCTGCAATCTTCAACCTACTC
1 AAGATCTGCAATCTTTAACCTACTC
3207855 CATTGTTACT
Statistics
Matches: 228, Mismatches: 43, Indels: 34
0.75 0.14 0.11
Matches are distributed among these distances:
85 16 0.07
86 27 0.12
87 54 0.24
88 14 0.06
89 114 0.50
90 1 0.00
91 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (88 bp):
AAGATCTGCAATCTTTAACCTACTCTGCTGCAACTCAGGGAGACAAGGCTTGTGTCTTCGATCTG
CTTCACTGCCGGTACAGGAAGAC
Found at i:3208262 original size:24 final size:24
Alignment explanation
Indices: 3208211--3208263 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3208201 TTGCCTCTAT
**
3208211 TGTAATCTTCAAAGTTCAATCCGT
1 TGTAATCTTCAAAGTTCAATCCAC
*
3208235 TGTAATCTTCAAGGTT-AAGTCCAC
1 TGTAATCTTCAAAGTTCAA-TCCAC
3208259 TGTAA
1 TGTAA
3208264 CTTTGGGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (24 bp):
TGTAATCTTCAAAGTTCAATCCAC
Found at i:3209217 original size:14 final size:13
Alignment explanation
Indices: 3209190--3209252 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 13
3209180 TCTCCTTTTA
*
3209190 TTTTTTTTCCTTC
1 TTTTTTTTTCTTC
*
3209203 TTTTTCTTTTTTTC
1 TTTTT-TTTTCTTC
*
3209217 TTTATCTTTTCTTC
1 TTT-TTTTTTCTTC
* *
3209231 TTATTATTTCTTC
1 TTTTTTTTTCTTC
3209244 TTTTTTTTT
1 TTTTTTTTT
3209253 TTGAAATATT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
13 20 0.51
14 18 0.46
15 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCTTC
Found at i:3209226 original size:19 final size:18
Alignment explanation
Indices: 3209191--3209229 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3209181 CTCCTTTTAT
*
3209191 TTTTTTTCCTTCTTTTTC
1 TTTTTTTCCTTATTTTTC
*
3209209 TTTTTTTCTTTATCTTTTC
1 TTTTTTTCCTTAT-TTTTC
3209228 TT
1 TT
3209230 CTTATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTCCTTATTTTTC
Found at i:3215959 original size:98 final size:98
Alignment explanation
Indices: 3215767--3215964 Score: 274
Period size: 98 Copynumber: 2.0 Consensus size: 98
3215757 GAGATAAGAC
*
3215767 CTGATGCGATCTACTCTACTGTAACTTTAGAGAGATAAGATCTGTGATTTTAACCCACTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAACCCACTCCACTG
* *
3215832 CAACTCCAGGGAGATAGAATTATCGGCTTCAAT
66 CAACTCCAGAGAGATAGAATTATCAGCTTCAAT
* * *
3215865 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCAT-TTATTTTAATCCACTCCACT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC-TGTGATTTTAACCCACTCCACT
* * * *
3215929 GTAACTTCAGAGAGTTAGGATTA-CTAGCTTCAAT
65 GCAACTCCAGAGAGATAGAATTATC-AGCTTCAAT
3215963 CT
1 CT
3215965 ACTCCGTTAT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
97 1 0.01
98 86 0.98
99 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (98 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAACCCACTCCACTG
CAACTCCAGAGAGATAGAATTATCAGCTTCAAT
Found at i:3216256 original size:131 final size:128
Alignment explanation
Indices: 3216004--3216341 Score: 274
Period size: 131 Copynumber: 2.6 Consensus size: 128
3215994 CTATGGCTTC
*
3216004 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACC
1 AATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTG--A-TCTTCGGTCTACTCCACTGTAACC
* * *
3216069 TCAGGGAGATAAGACCTGATGCGATCTACTCTACTATAACTTCAGAGAGATGAGATCCTTTATTT
63 TCAGGGAGATAAGACCTGATGCAATCTACTCCACTATAACCTCAGAGAGATGAGATCCTTTATTT
3216134 T
128 T
* * * * * *
3216135 AATCTGCTCCACTGTAACTTCAGAGAGATAGGATAGTG-TCTT-GGATCTGCTCCGCTGTAATCT
1 AATCTGCTCCACTGTAACCTCAGAGAGATAAGAT-CTGATCTTCGG-TCTACTCCACTGTAACCT
* * * * * **
3216198 CAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGA-GAAGAT-CTGAA
64 CAGGGAGATAAGA-C-CT-GATGCAATCTACTCCACTATAACCTCAGAGAGATG-AGATCCT-TT
3216261 ATTCTT
124 ATT-TT
** * * * * * ** *
3216267 CGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGA--TGCGATCTACTCTGCTGTAACTTC
1 -AATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGATCTTCGGTCTACTCCACTGTAACCTC
*
3216330 AGAGAGATAAGA
65 AGGGAGATAAGA
3216342 TCCTTTATTT
Statistics
Matches: 164, Mismatches: 32, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
127 2 0.01
128 32 0.20
129 1 0.01
130 5 0.03
131 90 0.55
132 7 0.04
133 27 0.16
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (128 bp):
AATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGATCTTCGGTCTACTCCACTGTAACCTCA
GGGAGATAAGACCTGATGCAATCTACTCCACTATAACCTCAGAGAGATGAGATCCTTTATTTT
Found at i:3216257 original size:218 final size:219
Alignment explanation
Indices: 3215865--3216429 Score: 936
Period size: 218 Copynumber: 2.6 Consensus size: 219
3215855 CGGCTTCAAT
* * *
3215865 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * * * *
3215930 TAACTTCAGAGAGTTAGGATTACTAGCTTCAATCTACTCCGTTATAATCTCAAGGAGATAAGATC
66 TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
*
3215995 TATGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCC
131 TATGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGAGAAGATCTGAAATTCTTCGGTCTACTCC
3216060 ACTGTAACCTCAGGGAGATAAGAC
196 ACTGTAACCTCAGGGAGATAAGAC
* * *
3216084 CTGATGCGATCTACTCTACTATAACTTCAGAGAGATGAGATCCTTTATTTTAATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* **
3216149 TAACTTCAGAGAGATAGGA-TAGT-GTCTTGGATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
66 TAACTTCAGAGAGATAGGATTACTAG-CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
*
3216212 CTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGAGAAGATCTGAAATTCTTCGGTCTACTC
130 CTATGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGAGAAGATCTGAAATTCTTCGGTCTACTC
3216277 CACTGTAACCTCAGGGAGATAAGAC
195 CACTGTAACCTCAGGGAGATAAGAC
*
3216302 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
3216367 TAATTTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
66 TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
3216430 CCTGATACGA
Statistics
Matches: 318, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
217 1 0.00
218 201 0.63
219 115 0.36
220 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (219 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
TATGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGAGAAGATCTGAAATTCTTCGGTCTACTCC
ACTGTAACCTCAGGGAGATAAGAC
Found at i:3216337 original size:41 final size:42
Alignment explanation
Indices: 3215873--3216769 Score: 454
Period size: 44 Copynumber: 20.7 Consensus size: 42
3215863 ATCTGATGTG
* * * * *
3215873 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATC-CTGA-TTCA
* * * * * *
3215917 ATCCACTCCACTGTAACTTCAGAGAGTTAGGATTACTAGCTTCA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGA-TCCT-GATTCA
** * * * *
3215961 ATCTACTCCGTTATAA-TCTCAAGGAGATAAGATCTATGGCTTCA
1 ATCTACTCCACTGTAACT-TCAGGGAGATAAGATC-CT-GATTCA
* * *
3216005 ATCTGCTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCG
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCCTG--A---TTCA
* * * *
3216051 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-CCTGATGCG
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCCTGATTCA
* * * * * *
3216092 ATCTACTCTACTATAACTTCAGAGAGATGAGATCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
* * * ** * **
3216136 ATCTGCTCCACTGTAACTTCAGAGAGATAGGATAGTGTCTTGG
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCCTG-ATTCA
* * *
3216179 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTACTCCACTGTAACT-TCAGGGAGATAAGATC-CT-GATTCA
* * * *
3216223 ATCTGCTCCACTGTAACCTCAGGGAGAGAAGAT-CTGAAATTCTTCG
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCCTG--A---TTCA
* * * *
3216269 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-CCTGATGCG
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCCTGATTCA
** * * *
3216310 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
** * * * *
3216354 ATCCGCTCCACTGTAATTTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGA-TCCT-GATTCA
* * * *
3216398 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGA-CCTGATACG
1 ATCTACTCCACTGTAACT-TCAGGGAGATAAGATCCTGATTCA
* * * * *
3216439 ATCTACTCTACTGTAACTTCAGAGAGATAAGATTCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGA-TCCTGA-TTCA
** * * *
3216483 ATCCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTACTCCACTGTAACT-TCAGGGAGATAAGA-TCCT-GATTCA
* * * * * *
3216527 ATCTGCTCCGCTGT-AGTCTCAGGGAGATAAGA-CTTGATACG
1 ATCTACTCCACTGTAACT-TCAGGGAGATAAGATCCTGATTCA
* * * * *
3216568 ATCTACTCTACTGTAACTTCAGAGAGATAATATCCTTAATTTTA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
* *
3216612 ATCCACTCCACTGTAA-TCTCAGGGAGATAAGATCTCTAGCTTCA
1 ATCTACTCCACTGTAACT-TCAGGGAGATAAGATC-CT-GATTCA
* * * *
3216656 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGA-CCGGATACA
1 ATCTACTCCACTGTAACT-TCAGGGAGATAAGATCCTGATTCA
* * * *
3216697 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATC-CTGA-TTCA
*
3216741 ATCCACTCCACTGTAACTTCAGGGAGATA
1 ATCTACTCCACTGTAACTTCAGGGAGATA
3216770 GGATTATCGG
Statistics
Matches: 646, Mismatches: 158, Indels: 98
0.72 0.18 0.11
Matches are distributed among these distances:
41 146 0.23
42 18 0.03
43 49 0.08
44 357 0.55
45 5 0.01
46 71 0.11
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (42 bp):
ATCTACTCCACTGTAACTTCAGGGAGATAAGATCCTGATTCA
Found at i:3216755 original size:85 final size:84
Alignment explanation
Indices: 3216397--3216867 Score: 290
Period size: 85 Copynumber: 5.4 Consensus size: 84
3216387 TACTAGCTTC
* * * * *
3216397 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGA
1 AATCCGCTCCACTGTAATCTCAGGGAGATAATACCGGATACAATCTACTCTACTGTAACTTCAGA
*
3216462 GAGATAAGATTCTTTATTTT
66 GAGATAAGA-TCTTGATTTT
** * * * ** *
3216482 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGT-AGTCT
1 AATCCGCTCCACTGTAATCTCAGGGAGATA--A-TACCGGATACAATCTACTCTACTGTAACT-T
* **
3216546 CAGGGAGATAAGA-CTTGA-TAC
62 CAGAGAGATAAGATCTTGATTTT
* ** * * ** ** * *
3216567 GATCTACTCTACTGTAA-CTTCAGAGAGATAATATCCTTAATTTTAATCCACTCCACTGTAA-TC
1 AATCCGCTCCACTGTAATC-TCAGGGAGATAATA-CC-GGA-TACAATCTACTCTACTGTAACT-
* * *
3216630 TCAGGGAGATAAGATCTCT-AGCTTC
61 TCAGAGAGATAAGATCT-TGA-TTTT
* * *
3216655 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCGGATACAATCTACTCTACTGTAACTTCAGA
1 AATCCGCTCCACTGTAATCTCAGGGAGATAATACCGGATACAATCTACTCTACTGTAACTTCAGA
3216720 GAGATAAGATCTGTGATTTT
66 GAGATAAGATCT-TGATTTT
* * *
3216740 AATCCACTCCACTGTAA-CTTCAGGGAGATAGGATTATCGGCTACAATCTGATGTGATCTACTAT
1 AATCCGCTCCACTGTAATC-TCAGGGAGATA--A-TACCGGATACAATC-----T-A-CT-C--T
* *
3216804 ACTGTAACTTTAGAGAGATAAGATCCTTTATTTT
52 ACTGTAACTTCAGAGAGATAAGAT-CTTGATTTT
3216838 AATCCGCTCCACTGTAATCTCAGGGAGATA
1 AATCCGCTCCACTGTAATCTCAGGGAGATA
3216868 GGATTACTAT
Statistics
Matches: 299, Mismatches: 55, Indels: 51
0.74 0.14 0.13
Matches are distributed among these distances:
82 2 0.01
83 2 0.01
84 2 0.01
85 142 0.47
86 11 0.04
87 7 0.02
88 67 0.22
89 1 0.00
93 1 0.00
94 1 0.00
95 2 0.01
96 1 0.00
98 57 0.19
99 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (84 bp):
AATCCGCTCCACTGTAATCTCAGGGAGATAATACCGGATACAATCTACTCTACTGTAACTTCAGA
GAGATAAGATCTTGATTTT
Found at i:3216789 original size:129 final size:129
Alignment explanation
Indices: 3216274--3216775 Score: 812
Period size: 129 Copynumber: 3.9 Consensus size: 129
3216264 CTTCGGTCTA
* * * *
3216274 CTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
* *
3216339 AGATCCTTTATTTTAATCCGCTCCACTGTAATTTCAGGGAGATAGGATTACTAGCTTCAATCTG
66 AGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
3216403 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
* *
3216468 AGATTCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
66 AGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
* *
3216532 CTCCGCTGTAGTCTCAGGGAGATAAGACTTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
* * *
3216597 ATATCCTTAATTTTAATCCACTCCACTGTAATCTCAGGGAGATAAGATCT-CTAGCTTCAATCTG
66 AGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCAATCTG
* *
3216661 CTCCGCTGTAATCTCAGGGAGATAAGACCGGATACAATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
*
3216726 AGAT-CTGTGATTTTAATCCACTCCACTGTAA-CTTCAGGGAGATAGGATTA
66 AGATCCT-TTATTTTAATCCACTCCACTGTAATC-TCAGGGAGATAGGATTA
3216776 TCGGCTACAA
Statistics
Matches: 349, Mismatches: 20, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
128 4 0.01
129 344 0.99
130 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (129 bp):
CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
AGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
Found at i:3216866 original size:98 final size:98
Alignment explanation
Indices: 3216697--3216873 Score: 286
Period size: 98 Copynumber: 1.8 Consensus size: 98
3216687 ACCGGATACA
*
3216697 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGTAACTTCA
1 ATCTACTATACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGTAACTTCA
3216762 GGGAGATAGGATTATCGGCTACAATCTGATGTG
66 GGGAGATAGGATTATCGGCTACAATCTGATGTG
* * *
3216795 ATCTACTATACTGTAACTTTAGAGAGATAAGATCCT-TTATTTTAATCCGCTCCACTGTAA-TCT
1 ATCTACTATACTGTAACTTCAGAGAGATAAGAT-CTGTGATTTTAATCCACTCCACTGTAACT-T
3216858 CAGGGAGATAGGATTA
64 CAGGGAGATAGGATTA
3216874 CTATATTCAA
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
97 1 0.01
98 70 0.96
99 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (98 bp):
ATCTACTATACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGTAACTTCA
GGGAGATAGGATTATCGGCTACAATCTGATGTG
Found at i:3216867 original size:44 final size:43
Alignment explanation
Indices: 3216818--3216916 Score: 126
Period size: 44 Copynumber: 2.3 Consensus size: 43
3216808 TAACTTTAGA
* *
3216818 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGG
1 GAGATAAGATCCTATA-TTCAATCCGCTCCACTGTAATCTCAGG
* * * *
3216862 GAGATAGGATTACTATATTCAATCTGCTCCGCTGTAATCTCAGG
1 GAGATAAGA-TCCTATATTCAATCCGCTCCACTGTAATCTCAGG
3216906 GAGATAAGATC
1 GAGATAAGATC
3216917 TGAAATTCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
43 1 0.02
44 40 0.87
45 5 0.11
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (43 bp):
GAGATAAGATCCTATATTCAATCCGCTCCACTGTAATCTCAGG
Found at i:3219140 original size:47 final size:50
Alignment explanation
Indices: 3219086--3219184 Score: 141
Period size: 47 Copynumber: 2.0 Consensus size: 50
3219076 TCTTTTTTCA
3219086 TTCTTCTTTCTTTTTCTCATTTTCA-TTTTGA-TCTTGA-TTTTGATTTT
1 TTCTTCTTTCTTTTTCTCATTTTCATTTTTGATTCTTGATTTTTGATTTT
* * * *
3219133 TTCTTCTTTCTTTTTTTTATTTTTATTTTTGATTTTTGATTTTTGATTTT
1 TTCTTCTTTCTTTTTCTCATTTTCATTTTTGATTCTTGATTTTTGATTTT
3219183 TT
1 TT
3219185 TCATTTTCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
47 22 0.49
48 6 0.13
49 5 0.11
50 12 0.27
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (50 bp):
TTCTTCTTTCTTTTTCTCATTTTCATTTTTGATTCTTGATTTTTGATTTT
Found at i:3219191 original size:7 final size:7
Alignment explanation
Indices: 3219145--3219183 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
3219135 CTTCTTTCTT
*
3219145 TTTTTTA
1 TTTTTGA
3219152 TTTTT-A
1 TTTTTGA
3219158 TTTTTGA
1 TTTTTGA
3219165 TTTTTGA
1 TTTTTGA
3219172 TTTTTGA
1 TTTTTGA
3219179 TTTTT
1 TTTTT
3219184 TTCATTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (7 bp):
TTTTTGA
Found at i:3234748 original size:10 final size:11
Alignment explanation
Indices: 3234724--3234748 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3234714 ATTGACTATC
3234724 TTTTCAAACAT
1 TTTTCAAACAT
3234735 TTTTCAAACAT
1 TTTTCAAACAT
3234746 TTT
1 TTT
3234749 GAGGTACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTCAAACAT
Found at i:3245855 original size:20 final size:21
Alignment explanation
Indices: 3245817--3245857 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3245807 CAACCATTTT
*
3245817 CAAAAAAAAAAGAAGAAAGAA
1 CAAAAAAAAAAGAACAAAGAA
*
3245838 CAAAAAAAGAA-AACAAAGAA
1 CAAAAAAAAAAGAACAAAGAA
3245858 AGAGGGTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAAGAACAAAGAA
Found at i:3247313 original size:12 final size:12
Alignment explanation
Indices: 3247298--3247323 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3247288 ATAAATAGTA
3247298 ATAATAATAAAT
1 ATAATAATAAAT
3247310 ATAATAATAAAT
1 ATAATAATAAAT
3247322 AT
1 AT
3247324 GGTACAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:3249115 original size:143 final size:143
Alignment explanation
Indices: 3248857--3249645 Score: 1098
Period size: 143 Copynumber: 5.5 Consensus size: 143
3248847 TGCTTCACTA
* *
3248857 CAACTTTAGGGAGATAAGGCTAGTGGCTTCAATAC-GCTCTACTGCAACTTCAGGAAGATAAGAT
1 CAACTTCAGGGAGATAAGGCTAGTGGCTTCAAT-CTGCTCCACTGCAACTTCAGGAAGATAAGAT
* * * * *
3248921 TCGCCATAATTTGTAGCTTTAATCTATTTCACTACAACGCTAGAGAAATAAGATCCGCTGTCTTC
65 CCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATTCGCTGTCTTC
* *
3248986 AGTTTGCTCCGTTG
130 AGTCTGCTCCGCTG
* **
3249000 CAACTTTAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTCAAAAAGATAAGATC
1 CAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATC
* * *
3249065 CACCATAATTTGTAGCTTTAATCTGTTCTACTGCAACGCTAGAGAAATAAGATTCGTTGTCTTCA
66 CGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATTCGCTGTCTTCA
3249130 GTCTGCTCCGCTG
131 GTCTGCTCCGCTG
* * * * *
3249143 CAACTTTAGGGAGATAAGGCTAGTGGCTTCAATATGTTCCACTGCAACTTTAGGAAGATAAGGTC
1 CAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATC
* * * *
3249208 CGCTATAATTTATAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATTCCCTGTCTTTA
66 CGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATTCGCTGTCTTCA
*
3249273 GTCTGCTCTGCTG
131 GTCTGCTCCGCTG
* * *
3249286 TAACTTCAGGGAGATAAGG-TCGGTGGCTTCAATCTGTTCCACTGCAACTTCAGGAAGATAAGAT
1 CAACTTCAGGGAGATAAGGCT-AGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGAT
* * * *
3249350 CTGCCATAATTTGTAGCTTTAATTTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTC
65 CCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATTCGCTGTCTTC
*
3249415 AGTCTGCTCCGTTG
130 AGTCTGCTCCGCTG
* * * * * *
3249429 TAACTTCAGGGGGATAAGGCTGGTGGCTTCAATCTGCTTCACTGCAACTTTAGGAAGATAATATC
1 CAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATC
* * * * *
3249494 CGCCATAATTTGTAGCTTTAATCTGTTACACTGCAACGCCAGGGAAATAAGATTCGCTATCTTTA
66 CGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATTCGCTGTCTTCA
3249559 GTCTGCTCCGCTG
131 GTCTGCTCCGCTG
* * * *
3249572 CAACTTCAGGGAGATAAGG-TTGATTGCTTCAATTTGTTCCACTGCAACTTCAGGAAGATAAGAT
1 CAACTTCAGGGAGATAAGGCTAG-TGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGAT
3249636 CCGCCATAAT
65 CCGCCATAAT
3249646 GACTTTAATC
Statistics
Matches: 579, Mismatches: 63, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
142 4 0.01
143 574 0.99
144 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (143 bp):
CAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATC
CGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATTCGCTGTCTTCA
GTCTGCTCCGCTG
Found at i:3255183 original size:13 final size:12
Alignment explanation
Indices: 3255161--3255197 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
3255151 ACAATCAAAG
3255161 AAAAAAATAATA
1 AAAAAAATAATA
3255173 AAAATAAATAATA
1 AAAA-AAATAATA
3255186 AAAACAAATAAT
1 AAAA-AAATAAT
3255198 GACGATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAAAAATAATA
Found at i:3255422 original size:16 final size:17
Alignment explanation
Indices: 3255384--3255422 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3255374 AATAAGATAC
*
3255384 ATAAATAAATAGTAATA
1 ATAAATAAATAGCAATA
3255401 AT-AATAAATA-CAATA
1 ATAAATAAATAGCAATA
3255416 ATAAATA
1 ATAAATA
3255423 TGGTACAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 6 0.30
16 12 0.60
17 2 0.10
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
ATAAATAAATAGCAATA
Found at i:3257211 original size:2 final size:2
Alignment explanation
Indices: 3257204--3257233 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3257194 GATTGTTTTC
3257204 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
3257234 TTGGGCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3257840 original size:8 final size:8
Alignment explanation
Indices: 3257823--3257864 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
3257813 TTTACCCCAA
3257823 AAAAAAAG
1 AAAAAAAG
*
3257831 AAAGAAAG
1 AAAAAAAG
3257839 AAAGAAAA-
1 AAA-AAAAG
*
3257847 AGAAAAAG
1 AAAAAAAG
3257855 AAAAAAAG
1 AAAAAAAG
3257863 AA
1 AA
3257865 CTTAATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 4 0.14
8 21 0.75
9 3 0.11
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:3261163 original size:32 final size:33
Alignment explanation
Indices: 3261093--3261163 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 33
3261083 ATAATAACAA
* * *
3261093 CAAAATAGTAACAATATAATAGTAAACTAGCAG
1 CAAAATAGCAACAAAATAATAGCAAACTAGCAG
* *
3261126 C-AAATAGCAACAAAATAGTAGCAAAC-AGTAG
1 CAAAATAGCAACAAAATAATAGCAAACTAGCAG
3261157 CAAAATA
1 CAAAATA
3261164 ACATTGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 5 0.16
32 26 0.81
33 1 0.03
ACGTcount: A:0.56, C:0.14, G:0.13, T:0.17
Consensus pattern (33 bp):
CAAAATAGCAACAAAATAATAGCAAACTAGCAG
Found at i:3262821 original size:31 final size:31
Alignment explanation
Indices: 3262783--3262849 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
3262773 AATGTGTTTG
3262783 TTTCAATATCTAAAATTGAAATAAGACATAT
1 TTTCAATATCTAAAATTGAAATAAGACATAT
*
3262814 TTTCAATATCTAAAATTGAAATAAGATATAT
1 TTTCAATATCTAAAATTGAAATAAGACATAT
3262845 TTTCA
1 TTTCA
3262850 GGTGCGAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (31 bp):
TTTCAATATCTAAAATTGAAATAAGACATAT
Found at i:3268946 original size:29 final size:29
Alignment explanation
Indices: 3268923--3268979 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3268913 TATTATTGTT
*
3268923 ATTATTTTATTATATTAT-AAATTAAATTG
1 ATTATATTATTATATTATGAAATT-AATTG
*
3268952 ATTATATTATTATATTATGAAATAAATT
1 ATTATATTATTATATTATGAAATTAATT
3268980 AAGAAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (29 bp):
ATTATATTATTATATTATGAAATTAATTG
Found at i:3269078 original size:31 final size:32
Alignment explanation
Indices: 3269038--3269107 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
3269028 AAATGAGTAC
3269038 ATTTGTATTATATA-TA-TAATTAGTAAAAATAT
1 ATTT-TATTATATATTATTAATTAGT-AAAATAT
*
3269070 ATTTTATTATTTATTATTAATTAGTAAAATAT
1 ATTTTATTATATATTATTAATTAGTAAAATAT
3269102 -TTTTAT
1 ATTTTAT
3269108 ATGATAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
31 14 0.40
32 13 0.37
33 8 0.23
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (32 bp):
ATTTTATTATATATTATTAATTAGTAAAATAT
Found at i:3269092 original size:33 final size:33
Alignment explanation
Indices: 3269045--3269107 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
3269035 TACATTTGTA
3269045 TTATATATATAATTAGTAAAAATATATTTTATTAT
1 TTATATATATAATTAGT-AAAATAT-TTTTATTAT
3269080 TTAT-TAT-TAATTAGTAAAATATTTTTAT
1 TTATATATATAATTAGTAAAATATTTTTAT
3269108 ATGATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.21
32 7 0.25
33 8 0.29
34 3 0.11
35 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (33 bp):
TTATATATATAATTAGTAAAATATTTTTATTAT
Found at i:3269234 original size:3 final size:3
Alignment explanation
Indices: 3269228--3269283 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
3269218 AATAATAATA
* *
3269228 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT -TA ATT GA-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
3269272 ATT A-T ATT ATT A
1 ATT ATT ATT ATT A
3269284 GATTAATGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 40 0.89
4 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3270436 original size:38 final size:39
Alignment explanation
Indices: 3270333--3270442 Score: 125
Period size: 38 Copynumber: 2.8 Consensus size: 39
3270323 CGACCTCAAG
*
3270333 TCGATGAGACACTGGGTGTCACTATTTTACTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCA--ACTTTACTTCGGATAGAT
* * * *
3270374 TCGATGAGATACTGGGTATC-ACTTTACTTCGGCTAGGT
1 TCGATGAGACACTGGGTGTCAACTTTACTTCGGATAGAT
* *
3270412 T-GATGGGACACTGGGTGTCAACTTTGCTTCG
1 TCGATGAGACACTGGGTGTCAACTTTACTTCG
3270443 AACTATCCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
37 15 0.25
38 26 0.44
41 18 0.31
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAACTTTACTTCGGATAGAT
Found at i:3279366 original size:2 final size:2
Alignment explanation
Indices: 3279359--3279392 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3279349 GCCTACATGC
3279359 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
3279393 TTGGGGTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3280223 original size:28 final size:29
Alignment explanation
Indices: 3280168--3280232 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 29
3280158 AAAAAATAAA
* *
3280168 CAAAATATTATAACTTTTTTTTTATTTAC
1 CAAAATATTATAACATTTTTTTAATTTAC
3280197 CAAAATATTATAA-ATTTTTTTAATTTAC
1 CAAAATATTATAACATTTTTTTAATTTAC
3280225 CAAAATAT
1 CAAAATAT
3280233 ACCAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (29 bp):
CAAAATATTATAACATTTTTTTAATTTAC
Found at i:3280514 original size:18 final size:18
Alignment explanation
Indices: 3280493--3280545 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
3280483 AGTAATAACT
*
3280493 CTATTTTAATTTAATAAA
1 CTATTCTAATTTAATAAA
*
3280511 CTATTCTCATTTAATAAA
1 CTATTCTAATTTAATAAA
3280529 C---TCTAATTTAATAAA
1 CTATTCTAATTTAATAAA
3280544 CT
1 CT
3280546 CTATTTTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 14 0.45
18 17 0.55
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (18 bp):
CTATTCTAATTTAATAAA
Found at i:3280539 original size:15 final size:15
Alignment explanation
Indices: 3280499--3280548 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
3280489 AACTCTATTT
3280499 TAATTTAATAAACTATTC
1 TAATTTAATAAAC---TC
*
3280517 TCATTTAATAAACTC
1 TAATTTAATAAACTC
3280532 TAATTTAATAAACTC
1 TAATTTAATAAACTC
3280547 TA
1 TA
3280549 TTTTGGTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 18 0.60
18 12 0.40
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTTAATAAACTC
Found at i:3280642 original size:23 final size:23
Alignment explanation
Indices: 3280572--3280647 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
3280562 ATGAGAATAG
3280572 TTTATTAAATTAAAATAGAGTTA
1 TTTATTAAATTAAAATAGAGTTA
* * ** * *
3280595 TTAAGT-AATT-TGATGAGAATAA
1 TTTATTAAATTAAAAT-AGAGTTA
3280617 TTTATTAAATTAAAATAGAGTTA
1 TTTATTAAATTAAAATAGAGTTA
*
3280640 TTTCTTAA
1 TTTATTAA
3280648 TTAGAATTCT
Statistics
Matches: 37, Mismatches: 13, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
21 2 0.05
22 13 0.35
23 20 0.54
24 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.43
Consensus pattern (23 bp):
TTTATTAAATTAAAATAGAGTTA
Found at i:3281317 original size:27 final size:28
Alignment explanation
Indices: 3281287--3281353 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
3281277 TTTTTTTGGT
*
3281287 ATATTTTGGTTAAT-AAAAAAATTTATA
1 ATATTTTGGTTAATAAAAAAAAGTTATA
* *
3281314 ATATTTTGATAAATAAAAAAAAGTTATA
1 ATATTTTGGTTAATAAAAAAAAGTTATA
3281342 ATATTTTGGTTA
1 ATATTTTGGTTA
3281354 TTTTTTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (28 bp):
ATATTTTGGTTAATAAAAAAAAGTTATA
Found at i:3288024 original size:46 final size:46
Alignment explanation
Indices: 3287971--3288061 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
3287961 TTCTTACATG
3287971 CAGAGACTTTTTTGCCTAAAATTATACCCTCAATCATTTAACATCA
1 CAGAGACTTTTTTGCCTAAAATTATACCCTCAATCATTTAACATCA
* *
3288017 CAGAGACTTTTTTGGCTAAATTTATACCCTCAATCATTTAACATC
1 CAGAGACTTTTTTGCCTAAAATTATACCCTCAATCATTTAACATC
3288062 TCCTTTTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (46 bp):
CAGAGACTTTTTTGCCTAAAATTATACCCTCAATCATTTAACATCA
Found at i:3288573 original size:2 final size:2
Alignment explanation
Indices: 3288566--3288610 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3288556 ATTCAATACA
3288566 AT AT 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 AT AT
3288608 AT A
1 AT A
3288611 AAGTTCAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3294407 original size:19 final size:19
Alignment explanation
Indices: 3294383--3294420 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3294373 ACAATAGAAA
3294383 TGGATAAAATTTTTAACAG
1 TGGATAAAATTTTTAACAG
3294402 TGGATAAAATTTTTAACAG
1 TGGATAAAATTTTTAACAG
3294421 AGGACTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (19 bp):
TGGATAAAATTTTTAACAG
Found at i:3300058 original size:21 final size:20
Alignment explanation
Indices: 3300034--3300074 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3300024 CACCAGTTAA
3300034 AATTAATTAGCCAATACTTGC
1 AATTAATTA-CCAATACTTGC
* *
3300055 AATTTATTACTAATACTTGC
1 AATTAATTACCAATACTTGC
3300075 TGATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (20 bp):
AATTAATTACCAATACTTGC
Found at i:3304472 original size:16 final size:16
Alignment explanation
Indices: 3304442--3304475 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3304432 TTTTTTCAAA
3304442 TTTATTAAAATATTAT
1 TTTATTAAAATATTAT
3304458 TTTA-TAAAATAATTAT
1 TTTATTAAAAT-ATTAT
3304474 TT
1 TT
3304476 CCATCCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATTAAAATATTAT
Found at i:3305446 original size:20 final size:19
Alignment explanation
Indices: 3305403--3305448 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3305393 TGCACAAAAA
*
3305403 TAAAAAATGTTAACTTATG
1 TAAAAAATGTTAAATTATG
* *
3305422 GAAAAAATGATTAAATTTTG
1 TAAAAAATG-TTAAATTATG
3305442 TAAAAAA
1 TAAAAAA
3305449 AATGTTTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (19 bp):
TAAAAAATGTTAAATTATG
Found at i:3306976 original size:43 final size:43
Alignment explanation
Indices: 3306901--3307128 Score: 298
Period size: 43 Copynumber: 5.3 Consensus size: 43
3306891 ACGTCGCTAA
* *
3306901 CTTTTGCGGCGCTTACAGAAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGC-TA-AGGAAAAAAACGCCGCTAAAGATCATGTT
*
3306946 CTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAGATCATGAT
1 CTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAGATCATGTT
* *
3306989 CTTTAGCGGCGCTTACG-AAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAGATCATGTT
* * *
3307031 CTTTAGTGGCGCT-TGGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAGATCATGTT
* * * *
3307073 CTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAAAATAATGTT
1 CTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAGATCATGTT
* *
3307116 CTATAGTGGCGCT
1 CTTTAGCGGCGCT
3307129 TTGTCAAAAA
Statistics
Matches: 164, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.01
42 73 0.45
43 77 0.47
44 2 0.01
45 11 0.07
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:3307021 original size:85 final size:84
Alignment explanation
Indices: 3306901--3307172 Score: 332
Period size: 85 Copynumber: 3.2 Consensus size: 84
3306891 ACGTCGCTAA
* *
3306901 CTTTTGCGGCGCTTACAGAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAA
1 CTTTAGCGGCGCTTAC-G--AAAAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCT-AGGAAA
3306966 AAAACGCCGCTAAAGATCATGAT
62 AAAACGCCGCTAAAGATCATGAT
* *
3306989 CTTTAGCGGCGCTTACGAAAAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTTGGGAAAAAA
1 CTTTAGCGGCGCTTACGAAAAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTAGGAAAAAAA
*
3307054 CGCCGCTAAAGATCATGTT
66 CGCCGCTAAAGATCATGAT
* * * * ** **
3307073 CTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAAAATAATGTTCTATAGTGGCGCTTTGTCAAAA
1 CTTTAGCGGCGCTTACGAA-AAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTAGGAAAAAA
*
3307138 ACGCCGCTAACAG-T-AGTGCT
65 ACGCCGCTAA-AGATCA-TGAT
*
3307158 CTTTAGCAGCGCTTA
1 CTTTAGCGGCGCTTA
3307173 TTTCACAAAC
Statistics
Matches: 167, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
84 45 0.27
85 104 0.62
86 2 0.01
87 1 0.01
88 15 0.09
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (84 bp):
CTTTAGCGGCGCTTACGAAAAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTAGGAAAAAAA
CGCCGCTAAAGATCATGAT
Found at i:3307023 original size:42 final size:43
Alignment explanation
Indices: 3306901--3307172 Score: 320
Period size: 42 Copynumber: 6.3 Consensus size: 43
3306891 ACGTCGCTAA
* *
3306901 CTTTTGCGGCGCTTACAGAAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGGAAAAAAACGCCGCTAAAGATCATGTT
* *
3306946 CTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAGATCATGAT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
*
3306989 CTTTAGCGGCGCTTACG-AAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
* *
3307031 CTTTAGTGGCGCTT-GGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
* * *
3307073 CTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAAAATAATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
* * * ** *
3307116 CTATAGTGGCGCTT-TGTCAAAAACGCCGCTAACAG-T-AGTGCT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAA-AGATCA-TGTT
*
3307158 CTTTAGCAGCGCTTA
1 CTTTAGCGGCGCTTA
3307173 TTTCACAAAC
Statistics
Matches: 197, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.01
42 104 0.53
43 79 0.40
45 12 0.06
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:3307161 original size:127 final size:127
Alignment explanation
Indices: 3306921--3307163 Score: 348
Period size: 127 Copynumber: 1.9 Consensus size: 127
3306911 GCTTACAGAA
* *
3306921 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAGATCAT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAAATAAT
* *
3306986 GATCTTTAGCGGCGCTTACGAAAAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTTGGG
66 GATCTATAGCGGCGCTTACGAAAAAACGCCGCTAAAGATCATGCTCTTTAGTGGCGCTTGGG
* *
3307048 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAAAATAAT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAAATAAT
* * * *
3307113 GTTCTATAGTGGCGCTT-TGTCAAAAACGCCGCTAACAG-T-AGTGCTCTTTAG
66 GATCTATAGCGGCGCTTACG-AAAAAACGCCGCTAA-AGATCA-TGCTCTTTAG
3307164 CAGCGCTTAT
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
126 2 0.02
127 99 0.96
128 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (127 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAAAAAACGCCGCTAAAAATAAT
GATCTATAGCGGCGCTTACGAAAAAACGCCGCTAAAGATCATGCTCTTTAGTGGCGCTTGGG
Found at i:3307633 original size:12 final size:12
Alignment explanation
Indices: 3307618--3307647 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3307608 CTGCTTCTAC
3307618 CGCTGTTTCTCT
1 CGCTGTTTCTCT
*
3307630 CGCTGCTTCTCT
1 CGCTGTTTCTCT
3307642 CGCTGT
1 CGCTGT
3307648 AACCTCTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.37, G:0.20, T:0.43
Consensus pattern (12 bp):
CGCTGTTTCTCT
Found at i:3313312 original size:25 final size:25
Alignment explanation
Indices: 3313234--3313641 Score: 129
Period size: 25 Copynumber: 16.3 Consensus size: 25
3313224 ACGGGTAAGT
*
3313234 TATGTATTATGTAAGCTATGTAAGT
1 TATGTATTATGTAAGTTATGTAAGT
*
3313259 TGTGTATTATGTAAGTTAT-T-A-T
1 TATGTATTATGTAAGTTATGTAAGT
*
3313281 TATGTAAGTTATGTAAGTAATGT-A-T
1 TATGT-A-TTATGTAAGTTATGTAAGT
* * *
3313306 TATGTAAGTTGTGT-A-TAATGTTAGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
**
3313331 TATCAAAGTTATGT-A-TTATGTAAGT
1 TAT-GTA-TTATGTAAGTTATGTAAGT
* *
3313356 TATTTAAGTTATGTAAGTTGTGT-A-T
1 TATGT-A-TTATGTAAGTTATGTAAGT
* * *
3313381 TATGTAAGTTATGTAGGCTATGTATGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
** *
3313408 TAAATAAGTAATGT-A-TTATGTAAGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
* * * **
3313433 TGTGTA-TA-ATCAGCTTCATCAAAGT
1 TATGTATTATGTAAG-TT-ATGTAAGT
* * **
3313458 TAGGTATTATGTAAGTTATTTGTGT
1 TATGTATTATGTAAGTTATGTAAGT
*
3313483 TATGTAAGTTGTGT-A-TTATGTAAGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
* * *
3313508 TATGTAGGCTATGTATGTTAAGTAAGT
1 TATGTA--TTATGTAAGTTATGTAAGT
* *
3313535 AATGTATTATGTAAGTTGTGT-A-T
1 TATGTATTATGTAAGTTATGTAAGT
* **
3313558 AATGTTAGTTATCAAAGTTATGT--GT
1 TATG-TA-TTATGTAAGTTATGTAAGT
*
3313583 TATGTAAGTTATTTAAGTTATGTAAGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
* * *
3313610 TGTGTATTATGTAAGTTATGTAGGC
1 TATGTATTATGTAAGTTATGTAAGT
3313635 TATGTAT
1 TATGTAT
3313642 GTTAAGTAAG
Statistics
Matches: 291, Mismatches: 64, Indels: 56
0.71 0.16 0.14
Matches are distributed among these distances:
21 1 0.00
22 7 0.02
23 13 0.04
24 23 0.08
25 193 0.66
26 9 0.03
27 45 0.15
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (25 bp):
TATGTATTATGTAAGTTATGTAAGT
Found at i:3313320 original size:16 final size:16
Alignment explanation
Indices: 3313250--3313749 Score: 158
Period size: 16 Copynumber: 29.9 Consensus size: 16
3313240 TTATGTAAGC
*
3313250 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
3313266 TATGTAAGTTAT-TAT
1 TATGTAAGTTATGTAT
3313281 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
*
3313299 AATGT-A-TTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
3313315 TGTGT-A-TAATGTTAGT
1 TATGTAAGTTATG-TA-T
**
3313331 TATCAAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
3313347 TATGTAAGTTATTTAAGT
1 TATGTAAGTTATGT-A-T
*
3313365 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
*
3313381 TATGTAAGTTATGTAGGC
1 TATGTAAGTTATGTA--T
*
3313399 TATGTATGTTA---A-
1 TATGTAAGTTATGTAT
*
3313411 -A--TAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
3313424 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* *
3313440 AATCAGCTTCATCAAAGTTAGGTAT
1 --T-A---T-GT--AAGTTATGTAT
*
3313465 TATGTAAGTTATTTGTGT
1 TATGTAAGTTA--TGTAT
*
3313483 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
*
3313499 TATGTAAGTTATGTAGGC
1 TATGTAAGTTATGTA--T
* *
3313517 TATGTATGTTAAGTAAGT
1 TATGTAAGTTATGT-A-T
*
3313535 AATGT-A-TTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
3313551 TGTGT-A-TAATGTTAGT
1 TATGTAAGTTATG-TA-T
** *
3313567 TATCAAAGTTATGTGT
1 TATGTAAGTTATGTAT
*
3313583 TATGTAAGTTATTTAAGT
1 TATGTAAGTTATGT-A-T
*
3313601 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
*
3313617 TATGTAAGTTATGTAGGC
1 TATGTAAGTTATGTA--T
* *
3313635 TATGTATGTTAAGTAAGT
1 TATGTAAGTTATGT-A-T
*
3313653 AATGT-A-TTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
3313669 TGTGT-A-TAATGTTAGT
1 TATGTAAGTTATG-TA-T
**
3313685 TATCAAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
3313701 TATGTAAGTTATTTAAGT
1 TATGTAAGTTATGT-A-T
*
3313719 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
3313735 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
3313750 GGCTATGTAT
Statistics
Matches: 368, Mismatches: 72, Indels: 88
0.70 0.14 0.17
Matches are distributed among these distances:
9 5 0.01
11 1 0.00
12 1 0.00
14 1 0.00
15 16 0.04
16 194 0.53
17 18 0.05
18 115 0.31
19 4 0.01
22 2 0.01
23 2 0.01
25 9 0.02
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:3313403 original size:34 final size:34
Alignment explanation
Indices: 3313250--3313645 Score: 132
Period size: 34 Copynumber: 11.9 Consensus size: 34
3313240 TTATGTAAGC
* *
3313250 TATGTAAGTTGTGT-A-TTATGTAAGTTAT-TAT
1 TATGTAAGTTATGTAAGCTATGTAAGTTATGTAT
3313281 TATGTAAGTTATGTAAG-TAATGT-A-TTATGTAAGT
1 TATGTAAGTTATGTAAGCT-ATGTAAGTTATGT-A-T
* * * * **
3313315 TGTGT-A-TAATGTTAGTTATCAAAGTTATGTAT
1 TATGTAAGTTATGTAAGCTATGTAAGTTATGTAT
* * *
3313347 TATGTAAGTTATTTAAGTTATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAAGCTATGTAAGTTATGTAT
* * **
3313381 TATGTAAGTTATGTAGGCTATGTATGTTAAATAAGT
1 TATGTAAGTTATGTAAGCTATGTAAGTTATGT-A-T
* * * * *
3313417 AATGT-A-TTATGTAAGTTGTGTATAATCA-GCT-T
1 TATGTAAGTTATGTAAGCTATGTA-AGTTATG-TAT
* ** * * *
3313449 CATCAAAGTTAGGT-A-TTATGTAAGTTATTTGTGT
1 TATGTAAGTTATGTAAGCTATGTAAGTTA--TGTAT
* * *
3313483 TATGTAAGTTGTGT-A-TTATGTAAGTTATGTAGGC
1 TATGTAAGTTATGTAAGCTATGTAAGTTATGTA--T
* *
3313517 TATGTATGTTAAGTAAG-TAATGT-A-TTATGTAAGT
1 TATGTAAGTTATGTAAGCT-ATGTAAGTTATGT-A-T
* * * * ** *
3313551 TGTGT-A-TAATGTTAGTTATCAAAGTTATGTGT
1 TATGTAAGTTATGTAAGCTATGTAAGTTATGTAT
* * *
3313583 TATGTAAGTTATTTAAGTTATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAAGCTATGTAAGTTATGTAT
* *
3313617 TATGTAAGTTATGTAGGCTATGTATGTTA
1 TATGTAAGTTATGTAAGCTATGTAAGTTA
3313646 AGTAAGTAAT
Statistics
Matches: 266, Mismatches: 67, Indels: 61
0.68 0.17 0.15
Matches are distributed among these distances:
31 20 0.08
32 43 0.16
33 16 0.06
34 169 0.64
35 9 0.03
36 9 0.03
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (34 bp):
TATGTAAGTTATGTAAGCTATGTAAGTTATGTAT
Found at i:3313436 original size:118 final size:118
Alignment explanation
Indices: 3313233--3313759 Score: 888
Period size: 118 Copynumber: 4.5 Consensus size: 118
3313223 CACGGGTAAG
* * * * *
3313233 TTATGT-A-TTATGTAAGCTATGTAAGTTGTGTATTATGTAAGTTAT-TA--TTATGTAAGTTAT
1 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATGTTAA
3313293 GTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
66 GTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
3313346 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATGTTAA
1 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATGTTAA
* * *
3313411 ATAAGTAATGTATTATGTAAGTTGTGTATAA--TCAGCTTCATCAAAGTTAGGTA
66 GTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAG-TT-ATCAAAGTTATGTA
**
3313464 TTATGTAAGTTATTTGTGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATGTTAA
1 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATGTTAA
*
3313529 GTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTG
66 GTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
3313582 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATGTTAA
1 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATGTTAA
3313647 GTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
66 GTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
3313700 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTAT
1 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTAT
3313760 TATGTAAGTT
Statistics
Matches: 388, Mismatches: 17, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
113 6 0.02
114 1 0.00
115 36 0.09
116 5 0.01
117 2 0.01
118 333 0.86
119 2 0.01
120 3 0.01
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (118 bp):
TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATGTTAA
GTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
Found at i:3313687 original size:25 final size:24
Alignment explanation
Indices: 3313534--3313786 Score: 115
Period size: 25 Copynumber: 10.7 Consensus size: 24
3313524 GTTAAGTAAG
*
3313534 TAATG-TATTATGTAAGTTGTGTA
1 TAATGTTATTATGTAAGTTATGTA
** *
3313557 TAATGTTAGTTATCAAAGTTATGTG
1 TAATGTTA-TTATGTAAGTTATGTA
* * *
3313582 TTATGTAAGTTATTTAAGTTATGTA
1 TAATGTTA-TTATGTAAGTTATGTA
*
3313607 -AGTTGTGTATTATGTAAGTTATG--
1 TA-ATGT-TATTATGTAAGTTATGTA
* * *
3313630 T-AGGCTATGTATGTTAAG-TAAG--
1 TAATGTTAT-TATG-TAAGTTATGTA
*
3313652 TAATG-TATTATGTAAGTTGTGTA
1 TAATGTTATTATGTAAGTTATGTA
**
3313675 TAATGTTAGTTATCAAAGTTATGTA
1 TAATGTTA-TTATGTAAGTTATGTA
* * *
3313700 TTATGTAAGTTATTTAAGTTATGTA
1 TAATGTTA-TTATGTAAGTTATGTA
*
3313725 -AGTTGTGTATTATGTAAGTTATGTA
1 TA-ATGT-TATTATGTAAGTTATGTA
3313750 GGCT-ATG-TATTATGTAAGTTA--T-
1 ---TAATGTTATTATGTAAGTTATGTA
3313772 T-ATGTTATTATGTAA
1 TAATGTTATTATGTAA
3313787 TAAGTTTATA
Statistics
Matches: 178, Mismatches: 32, Indels: 43
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.02
20 14 0.08
21 9 0.05
22 12 0.07
23 17 0.10
24 4 0.02
25 114 0.64
26 2 0.01
27 2 0.01
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.47
Consensus pattern (24 bp):
TAATGTTATTATGTAAGTTATGTA
Found at i:3313757 original size:34 final size:34
Alignment explanation
Indices: 3313454--3313765 Score: 132
Period size: 34 Copynumber: 9.3 Consensus size: 34
3313444 AGCTTCATCA
* * ** *
3313454 AAGTTAGGTATTATGTAAGTTATTTGTGTTATGT
1 AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
* *
3313488 AAGTTGTGTATTATGTAAGTTATGTAGGCTATGT
1 AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
* * * * *
3313522 ATGTTAAGTAAGTAATGT-A-TTATGTAAGTTGTGT
1 AAGTTATGT-A-TTATGTAAGTTATGTAAGCTATGT
* ** *
3313556 -A-TAATGTTAGTTATCAAAGTTATGT--GTTATGT
1 AAGTTATG-TA-TTATGTAAGTTATGTAAGCTATGT
* * *
3313588 AAGTTATTTAAGTTATGTAAGTTGTGT-A-TTATGT
1 AAGTTATGT-A-TTATGTAAGTTATGTAAGCTATGT
* * *
3313622 AAGTTATGTAGGCTATGTATGTTAAGTAAG-TAATGT
1 AAGTTATGTA--TTATGTAAGTTATGTAAGCT-ATGT
* * * * **
3313658 -A-TTATGTAAGTTGTGT-A-TAATGTTAGTTATCA
1 AAGTTATGT-A-TTATGTAAGTTATGTAAGCTATGT
* *
3313690 AAGTTATGTATTATGTAAGTTATTTAAGTTATGT
1 AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
* *
3313724 AAGTTGTGTATTATGTAAGTTATGTAGGCTATGT
1 AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
3313758 -A-TTATGTA
1 AAGTTATGTA
3313766 AGTTATTATG
Statistics
Matches: 210, Mismatches: 49, Indels: 40
0.70 0.16 0.13
Matches are distributed among these distances:
32 33 0.16
33 10 0.05
34 152 0.72
35 6 0.03
36 9 0.04
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (34 bp):
AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
Found at i:3319360 original size:18 final size:18
Alignment explanation
Indices: 3319320--3319361 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3319310 CACAGGACAC
* *
3319320 AAGAAAACAACAATCAAA
1 AAGAAAAAAACAATAAAA
3319338 AAGAAAAAAACAA-AAAA
1 AAGAAAAAAACAATAAAA
3319355 AGAGAAA
1 A-AGAAA
3319362 GTGGTTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.79, C:0.10, G:0.10, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAACAATAAAA
Found at i:3319436 original size:68 final size:68
Alignment explanation
Indices: 3319357--3319494 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
3319347 ACAAAAAAAG
3319357 AGAAAGTGGTTAAGACAAGAAAGCACCGCAAGAACACCCAGAAAAGCACCCGGAGAAAGAGGGAA
1 AGAAAGTGGTTAAGACAAGAAAGCACCGCAAGAACACCCAGAAAAGCACCCGGAGAAAGAGGGAA
3319422 ATC
66 ATC
3319425 AGAAAGTGGTTAAGACAAGAAAGCACCGCAAGAACACCCAGAAAAGCACCCGGAGAAAGAGGGAA
1 AGAAAGTGGTTAAGACAAGAAAGCACCGCAAGAACACCCAGAAAAGCACCCGGAGAAAGAGGGAA
3319490 ATC
66 ATC
3319493 AG
1 AG
3319495 GTCCGAGTAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.47, C:0.20, G:0.27, T:0.06
Consensus pattern (68 bp):
AGAAAGTGGTTAAGACAAGAAAGCACCGCAAGAACACCCAGAAAAGCACCCGGAGAAAGAGGGAA
ATC
Found at i:3319808 original size:18 final size:18
Alignment explanation
Indices: 3319785--3319873 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
3319775 NNNNNNNNNT
3319785 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
3319803 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
**
3319825 TTTTTGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
3319842 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
3319860 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
3319874 GTAATATATA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 13 0.21
18 30 0.49
19 3 0.05
20 3 0.05
21 4 0.07
22 8 0.13
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:3319863 original size:35 final size:37
Alignment explanation
Indices: 3319784--3319873 Score: 121
Period size: 39 Copynumber: 2.4 Consensus size: 37
3319774 NNNNNNNNNN
3319784 TTTTAAGTAATGTAATATATTTAAGTAATGTAAGTTATAAA
1 TTTT-AGTAA-GTAATATATTTAAGTAATGTAAG-TAT-AA
*
3319825 TTTTTGTAAGTAATATATTTAAGTAATGTAA-TAT-A
1 TTTTAGTAAGTAATATATTTAAGTAATGTAAGTATAA
3319860 TTTTAGTAAGTAAT
1 TTTTAGTAAGTAAT
3319874 GTAATATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
35 14 0.30
37 3 0.06
39 22 0.47
40 4 0.09
41 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (37 bp):
TTTTAGTAAGTAATATATTTAAGTAATGTAAGTATAA
Found at i:3319941 original size:13 final size:13
Alignment explanation
Indices: 3319896--3319986 Score: 62
Period size: 13 Copynumber: 6.8 Consensus size: 13
3319886 TTAATCTTAG
*
3319896 TAAGTCATGTATT
1 TAAGTAATGTATT
* *
3319909 TAAGTAAAT-TCTAG
1 TAAGT-AATGTAT-T
3319923 TAAGTAATGTATT
1 TAAGTAATGTATT
*
3319936 TAAGTAATATATT
1 TAAGTAATGTATT
3319949 TAAGTAAAT-T-TT
1 TAAGT-AATGTATT
* *
3319961 AGTAATTAATATATT
1 --TAAGTAATGTATT
3319976 TAAGTAATGTA
1 TAAGTAATGTA
3319987 AGTTATAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
12 2 0.03
13 40 0.66
14 17 0.28
15 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (13 bp):
TAAGTAATGTATT
Found at i:3319949 original size:40 final size:40
Alignment explanation
Indices: 3319896--3319983 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
3319886 TTAATCTTAG
* * *
3319896 TAAGTCATGTATTTAAGTAAATTCTAGTAAGTAATGTATT
1 TAAGTAATATATTTAAGTAAATTCTAGTAAGTAATATATT
* *
3319936 TAAGTAATATATTTAAGTAAATTTTAGTAATTAATATATT
1 TAAGTAATATATTTAAGTAAATTCTAGTAAGTAATATATT
3319976 TAAGTAAT
1 TAAGTAAT
3319984 GTAAGTTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (40 bp):
TAAGTAATATATTTAAGTAAATTCTAGTAAGTAATATATT
Found at i:3320049 original size:11 final size:11
Alignment explanation
Indices: 3320018--3320050 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
3320008 ATATATTAAT
3320018 AATTCATTGAC
1 AATTCATTGAC
3320029 -ATTCATTGAC
1 AATTCATTGAC
*
3320039 AATTCACTGAC
1 AATTCATTGAC
3320050 A
1 A
3320051 GTCAATCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (11 bp):
AATTCATTGAC
Found at i:3323193 original size:2 final size:2
Alignment explanation
Indices: 3323188--3323222 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3323178 TCTCTCTCTT
*
3323188 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3323223 CTAATTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3323645 original size:8 final size:7
Alignment explanation
Indices: 3323624--3323769 Score: 55
Period size: 7 Copynumber: 20.0 Consensus size: 7
3323614 TACCCTTGAC
3323624 ACCCTAA
1 ACCCTAA
3323631 ACCCTAA
1 ACCCTAA
3323638 ATCCCTAA
1 A-CCCTAA
*
3323646 CCCCT-A
1 ACCCTAA
3323652 ACCCTTAA
1 ACCC-TAA
*
3323660 ATCTCCTAG
1 A-C-CCTAA
*
3323669 CCCCTAA
1 ACCCTAA
*
3323676 ATTCCTAA
1 A-CCCTAA
*
3323684 CCCCTAA
1 ACCCTAA
*
3323691 CCCCTAA
1 ACCCTAA
*
3323698 ATTCCT-A
1 A-CCCTAA
3323705 ACCCTTAA
1 ACCC-TAA
*
3323713 CCCCTAA
1 ACCCTAA
*
3323720 CCCCTAA
1 ACCCTAA
*
3323727 ATCTCTAA
1 A-CCCTAA
* *
3323735 TCCTTAA
1 ACCCTAA
*
3323742 CCCCTAA
1 ACCCTAA
*
3323749 ACCTTATA
1 ACCCTA-A
*
3323757 TCCC-AA
1 ACCCTAA
3323763 ACCCTAA
1 ACCCTAA
3323770 TAGAGTACAT
Statistics
Matches: 102, Mismatches: 25, Indels: 24
0.68 0.17 0.16
Matches are distributed among these distances:
6 10 0.10
7 58 0.57
8 29 0.28
9 3 0.03
10 2 0.02
ACGTcount: A:0.33, C:0.42, G:0.01, T:0.24
Consensus pattern (7 bp):
ACCCTAA
Found at i:3323652 original size:22 final size:22
Alignment explanation
Indices: 3323625--3323749 Score: 96
Period size: 22 Copynumber: 5.6 Consensus size: 22
3323615 ACCCTTGACA
3323625 CCCTAAACCCTAAATCCCTAAC
1 CCCTAAACCCTAAATCCCTAAC
*
3323647 CCCT-AACCCTTAAATCTCCTAGC
1 CCCTAAACCC-TAAATC-CCTAAC
* *
3323670 CCCTAAATTCCT-AACCCCTAAC
1 CCCTAAA-CCCTAAATCCCTAAC
*
3323692 CCCTAAATTCCT-AA-CCCTTAAC
1 CCCTAAA-CCCTAAATCCC-TAAC
* * *
3323714 CCCTAACCCCTAAATCTCTAAT
1 CCCTAAACCCTAAATCCCTAAC
* *
3323736 CCTTAACCCCTAAA
1 CCCTAAACCCTAAA
3323750 CCTTATATCC
Statistics
Matches: 87, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
21 11 0.13
22 57 0.66
23 14 0.16
24 3 0.03
25 2 0.02
ACGTcount: A:0.32, C:0.43, G:0.01, T:0.24
Consensus pattern (22 bp):
CCCTAAACCCTAAATCCCTAAC
Found at i:3323676 original size:16 final size:15
Alignment explanation
Indices: 3323648--3323690 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
3323638 ATCCCTAACC
*
3323648 CCTAACCCTTAAATCT
1 CCTAACCCCTAAAT-T
*
3323664 CCTAGCCCCTAAATT
1 CCTAACCCCTAAATT
3323679 CCTAACCCCTAA
1 CCTAACCCCTAA
3323691 CCCCTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.30, C:0.42, G:0.02, T:0.26
Consensus pattern (15 bp):
CCTAACCCCTAAATT
Found at i:3323713 original size:29 final size:29
Alignment explanation
Indices: 3323681--3323748 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 29
3323671 CCTAAATTCC
3323681 TAACCCCTAACCCCTAAAT-TCCTAACCCT
1 TAACCCCTAACCCCTAAATCT-CTAACCCT
*
3323710 TAACCCCTAACCCCTAAATCTCTAATCCT
1 TAACCCCTAACCCCTAAATCTCTAACCCT
3323739 TAACCCCTAA
1 TAACCCCTAA
3323749 ACCTTATATC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
29 36 0.97
30 1 0.03
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.25
Consensus pattern (29 bp):
TAACCCCTAACCCCTAAATCTCTAACCCT
Found at i:3323765 original size:22 final size:21
Alignment explanation
Indices: 3323701--3323766 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
3323691 CCCCTAAATT
* *
3323701 CCTAACCCTTAACCCCTAACC
1 CCTAAACCTTAATCCCTAACC
* *
3323722 CCTAAATCTCTAATCCTTAACC
1 CCTAAACCT-TAATCCCTAACC
*
3323744 CCTAAACCTTATATCCCAAACC
1 CCTAAACCTTA-ATCCCTAACC
3323766 C
1 C
3323767 TAATAGAGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 9 0.25
22 27 0.75
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (21 bp):
CCTAAACCTTAATCCCTAACC
Found at i:3325633 original size:41 final size:40
Alignment explanation
Indices: 3325588--3325724 Score: 166
Period size: 41 Copynumber: 3.4 Consensus size: 40
3325578 GCGCTTCGGC
* *
3325588 AAAAACGCCGCTAAAGCTAAATGCATTAGTGGCGCTTAGAT
1 AAAAACGCCGCTAAAGCTAGA-GCATTAGCGGCGCTTAGAT
* * * *
3325629 AAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCACTCAGAT
1 AAAAACGCCGCTAAA-GCTAGAGCATTAGCGGCGCTTAGAT
** *
3325670 AAAAACGCCGCTAAATATCCGAGCATTAGCGGCGCTTAGAT
1 AAAAACGCCGCTAAAGCT-AGAGCATTAGCGGCGCTTAGAT
3325711 AAAAACGCCGCTAA
1 AAAAACGCCGCTAA
3325725 TTCCTATTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
41 77 0.95
42 4 0.05
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGCTAGAGCATTAGCGGCGCTTAGAT
Found at i:3325784 original size:40 final size:39
Alignment explanation
Indices: 3325716--3325808 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 39
3325706 TAGATAAAAA
* **
3325716 CGCCGCTAATTC-CTATTTTTAGCGGCGCTTGGTGG-AAAT
1 CGCCGCTAATGCTCTACCTTTAGCGGCGCTT--TGGCAAAT
*
3325755 CGCCGCTGATGCTCTACCTTTAGCGGCGCTTTGGCTAAAT
1 CGCCGCTAATGCTCTACCTTTAGCGGCGCTTTGGC-AAAT
3325795 CGCCGCTAATGCTC
1 CGCCGCTAATGCTC
3325809 GATTTTTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 3 0.07
39 10 0.22
40 33 0.72
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.30
Consensus pattern (39 bp):
CGCCGCTAATGCTCTACCTTTAGCGGCGCTTTGGCAAAT
Found at i:3326090 original size:22 final size:23
Alignment explanation
Indices: 3326062--3326104 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3326052 GGTATTTTAA
3326062 ATATAAATACTTATTT-TATTTT
1 ATATAAATACTTATTTATATTTT
*
3326084 ATATAAATATTTATTTATATT
1 ATATAAATACTTATTTATATT
3326105 CATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATAAATACTTATTTATATTTT
Found at i:3326109 original size:22 final size:22
Alignment explanation
Indices: 3326062--3326109 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3326052 GGTATTTTAA
*
3326062 ATATAAATACTTATTTTATTTT
1 ATATAAATACTTATTTTATTTC
*
3326084 ATATAAATATTTA-TTTATATTC
1 ATATAAATACTTATTTTAT-TTC
3326106 ATAT
1 ATAT
3326110 TTTTTGACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATAAATACTTATTTTATTTC
Found at i:3327429 original size:9 final size:9
Alignment explanation
Indices: 3327415--3327587 Score: 61
Period size: 10 Copynumber: 18.0 Consensus size: 9
3327405 AAAAATTAGA
3327415 ATAAAAATT
1 ATAAAAATT
3327424 ATAAAAA--
1 ATAAAAATT
3327431 ATAAAATTATT
1 ATAAAA--ATT
*
3327442 AATATTAAATTT
1 -ATA--AAAATT
*
3327454 ATATAAACTT
1 ATA-AAAATT
*
3327464 CTAAAAATT
1 ATAAAAATT
3327473 ATAAAAAATAT
1 AT-AAAAAT-T
3327484 ATAAAAA-T
1 ATAAAAATT
*
3327492 A-ATAAATT
1 ATAAAAATT
3327500 ATAATAAAATT
1 AT-A-AAAATT
3327511 AT--AAATT
1 ATAAAAATT
*
3327518 ATAATAAAATA
1 AT-A-AAAATT
3327529 ATAAAATATTTT
1 ATAAAA-A--TT
*
3327541 TTAAAAATAT
1 ATAAAAAT-T
* *
3327551 TTAAAATTTT
1 ATAAAA-ATT
3327561 ATAAAAATT
1 ATAAAAATT
* *
3327570 TTAAAAATC
1 ATAAAAATT
3327579 ATAAAAATT
1 ATAAAAATT
3327588 TGAATTGGAC
Statistics
Matches: 125, Mismatches: 17, Indels: 44
0.67 0.09 0.24
Matches are distributed among these distances:
7 17 0.14
8 4 0.03
9 34 0.27
10 35 0.28
11 21 0.17
12 11 0.09
14 3 0.02
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (9 bp):
ATAAAAATT
Found at i:3327508 original size:18 final size:18
Alignment explanation
Indices: 3327487--3327533 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
3327477 AAAATATATA
3327487 AAAATAATAAATTATAAT
1 AAAATAATAAATTATAAT
*
3327505 AAAATTATAAATTATAAT
1 AAAATAATAAATTATAAT
3327523 AAAATAATAAA
1 AAAATAATAAA
3327534 ATATTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATAATAAATTATAAT
Found at i:3327527 original size:11 final size:11
Alignment explanation
Indices: 3327467--3327514 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 11
3327457 TAAACTTCTA
3327467 AAAATTATAA-
1 AAAATTATAAT
3327477 AAAA-TAT-AT
1 AAAATTATAAT
3327486 AAAA--ATAAT
1 AAAATTATAAT
3327495 -AAATTATAAT
1 AAAATTATAAT
3327505 AAAATTATAA
1 AAAATTATAA
3327515 ATTATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.18
9 9 0.27
10 9 0.27
11 9 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTATAAT
Found at i:3327555 original size:10 final size:9
Alignment explanation
Indices: 3327539--3327588 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
3327529 ATAAAATATT
3327539 TTTTAAAAA
1 TTTTAAAAA
*
3327548 TATTTAAAAT
1 T-TTTAAAAA
3327558 TTTATAAAAA
1 TTT-TAAAAA
3327568 TTTTAAAAA
1 TTTTAAAAA
**
3327577 TCATAAAAA
1 TTTTAAAAA
3327586 TTT
1 TTT
3327589 GAATTGGACC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:3331653 original size:108 final size:108
Alignment explanation
Indices: 3331509--3331914 Score: 469
Period size: 108 Copynumber: 3.8 Consensus size: 108
3331499 TTCAAATGAA
* * * * * *
3331509 AATGCCGCACAGAGCAACACC-AGCAACAAAGAAAATGCGGGTCAGGACGAGAAGAATGCCACTC
1 AATGCCACTCAGAGCAACACCGAG-AACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTC
* * *
3331573 AGAGTAACACTGACAACAATGAAAATGTGGGTCAGAATGAGAAC
65 AGAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAAC
** * * * *
3331617 AATGCTGCTCAGAGCAACACTGAGAACAATGAAAATGCGGGTCAGAATGAGAGCAATGCTGCTCA
1 AATGCCACTCAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCA
* * * *
3331682 GAGCAACACCGAGAACAATGAAAATGCGAGTCAGAACGAGAGC
66 GAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAAC
* * * * *
3331725 AATGCAACTCAGAGCAACACCGAGAACAATGAGAATGCGGATCAGAACGAGCACAATGCTGCTCC
1 AATGCCACTCAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACT-C
* * *
3331790 A-AGTAACACTGAGAACAATGAGAATGCGGGTCAGAACGAGAAC
65 AGAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAAC
* * * *
3331833 AATGCCACTCCA-AGTAACACCGACAACAATGAGAATGCAGGTCAGAACGAGAACAATG-TGACT
1 AATGCCACT-CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCT-ACT
3331896 CAGAGCAACACTGACAACA
64 CAGAGCAACACTGACAACA
3331915 GCAACAGCAA
Statistics
Matches: 254, Mismatches: 39, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
107 3 0.01
108 245 0.96
109 6 0.02
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (108 bp):
AATGCCACTCAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCA
GAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAAC
Found at i:3331707 original size:162 final size:162
Alignment explanation
Indices: 3331509--3331914 Score: 514
Period size: 162 Copynumber: 2.5 Consensus size: 162
3331499 TTCAAATGAA
* * * *
3331509 AATGCCGCACAGAGCAACACC-AGCAACAAAGAAAATGCGGGTCAGGACGAGAAGAATGCCACTC
1 AATGCCGCTCAGAGCAACACCGAG-AACAATGAAAATGCGGGTCAGAACGAGAAGAATGCAACTC
* * * *
3331573 AGAGTAACACTGACAACAATGAAAATGTGGGTCAGAATGAGAACAATGCTGCT-CAGAGCAACAC
65 AGAGCAACACTGACAACAATGAAAATGCGGATCAGAACGAGAACAATGCTGCTCCA-AGCAACAC
* *
3331637 TGAGAACAATGAAAATGCGGGTCAGAATGAGAGC
129 TGAGAACAATGAAAATGCGGGTCAGAACGAGAAC
* *
3331671 AATGCTGCTCAGAGCAACACCGAGAACAATGAAAATGCGAGTCAGAACGAG-AGCAATGCAACTC
1 AATGCCGCTCAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAAG-AATGCAACTC
* * * * *
3331735 AGAGCAACACCGAGAACAATGAGAATGCGGATCAGAACGAGCACAATGCTGCTCCAAGTAACACT
65 AGAGCAACACTGACAACAATGAAAATGCGGATCAGAACGAGAACAATGCTGCTCCAAGCAACACT
*
3331800 GAGAACAATGAGAATGCGGGTCAGAACGAGAAC
130 GAGAACAATGAAAATGCGGGTCAGAACGAGAAC
* * * * * * **
3331833 AATGCCACTCCA-AGTAACACCGACAACAATGAGAATGCAGGTCAGAACGAGAACAATGTGACTC
1 AATGCCGCT-CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAAGAATGCAACTC
3331897 AGAGCAACACTGACAACA
65 AGAGCAACACTGACAACA
3331915 GCAACAGCAA
Statistics
Matches: 209, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
161 2 0.01
162 200 0.96
163 7 0.03
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (162 bp):
AATGCCGCTCAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAAGAATGCAACTCA
GAGCAACACTGACAACAATGAAAATGCGGATCAGAACGAGAACAATGCTGCTCCAAGCAACACTG
AGAACAATGAAAATGCGGGTCAGAACGAGAAC
Found at i:3331721 original size:27 final size:27
Alignment explanation
Indices: 3331691--3331890 Score: 94
Period size: 27 Copynumber: 7.4 Consensus size: 27
3331681 AGAGCAACAC
*
3331691 CGAGAACAATGAAAATGCGAGTCAGAA
1 CGAGAACAATGAGAATGCGAGTCAGAA
* *
3331718 CGAGAGCAATGCA-ACT-CAGAG-CA-ACA
1 CGAGAACAATG-AGAATGC-GAGTCAGA-A
3331744 CCGAGAACAATGAGAATGCG-GATCAGAA
1 -CGAGAACAATGAGAATGCGAG-TCAGAA
* * * * *
3331772 CGAGCACAATGCTG-CTCCAAGT-A-ACA
1 CGAGAACAATG-AGAATGCGAGTCAGA-A
*
3331798 CTGAGAACAATGAGAATGCGGGTCAGAA
1 C-GAGAACAATGAGAATGCGAGTCAGAA
** * * * * * *
3331826 CGAGAACAATGCCACTCCAAGTAACAC
1 CGAGAACAATGAGAATGCGAGTCAGAA
*
3331853 CGACAACAATGAGAATGC-AGGTCAGAA
1 CGAGAACAATGAGAATGCGA-GTCAGAA
3331880 CGAGAACAATG
1 CGAGAACAATG
3331891 TGACTCAGAG
Statistics
Matches: 123, Mismatches: 33, Indels: 34
0.65 0.17 0.18
Matches are distributed among these distances:
25 2 0.02
26 11 0.09
27 98 0.80
28 10 0.08
29 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (27 bp):
CGAGAACAATGAGAATGCGAGTCAGAA
Found at i:3331912 original size:54 final size:54
Alignment explanation
Indices: 3331518--3331914 Score: 410
Period size: 54 Copynumber: 7.4 Consensus size: 54
3331508 AAATGCCGCA
* * * * **
3331518 CAGAGCAACAC-CAGCAACAAAGAAAATGCGGGTCAGGACGAGAAGAATGCCACT
1 CAGAGCAACACTGA-CAACAATGAAAATGCGGGTCAGAACGAGAACAATGTGACT
* * *
3331572 CAGAGTAACACTGACAACAATGAAAATGTGGGTCAGAATGAGAACAATGCTG-CT
1 CAGAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAACAATG-TGACT
* * *
3331626 CAGAGCAACACTGAGAACAATGAAAATGCGGGTCAGAATGAGAGCAATGCTG-CT
1 CAGAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAACAATG-TGACT
* * * * **
3331680 CAGAGCAACACCGAGAACAATGAAAATGCGAGTCAGAACGAGAGCAATGCAACT
1 CAGAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAACAATGTGACT
* * * * *
3331734 CAGAGCAACACCGAGAACAATGAGAATGCGGATCAGAACGAGCACAATGCTG-CT
1 CAGAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAACAATG-TGACT
* * * **
3331788 CCA-AGTAACACTGAGAACAATGAGAATGCGGGTCAGAACGAGAACAATGCCACT
1 -CAGAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAACAATGTGACT
* * * *
3331842 CCA-AGTAACACCGACAACAATGAGAATGCAGGTCAGAACGAGAACAATGTGACT
1 -CAGAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAACAATGTGACT
3331896 CAGAGCAACACTGACAACA
1 CAGAGCAACACTGACAACA
3331915 GCAACAGCAA
Statistics
Matches: 298, Mismatches: 38, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
53 2 0.01
54 293 0.98
55 3 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (54 bp):
CAGAGCAACACTGACAACAATGAAAATGCGGGTCAGAACGAGAACAATGTGACT
Found at i:3331987 original size:51 final size:51
Alignment explanation
Indices: 3331932--3332030 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 51
3331922 CAACAACAAC
3331932 AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGC-TGCTCAGAGCAGT
1 AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCAT-CTCAGAGCAGT
* ** *
3331983 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGC
1 AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCATCTCAGAGC
3332031 TTCACCGACA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (51 bp):
AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCATCTCAGAGCAGT
Found at i:3332082 original size:63 final size:63
Alignment explanation
Indices: 3331983--3332177 Score: 318
Period size: 63 Copynumber: 3.1 Consensus size: 63
3331973 TCAGAGCAGT
3331983 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
* *
3332046 AACAACAATGAAAATACAAGTCAGGATGAGAACAATGCATCTCAAAGCTTCACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
* * * * *
3332109 AACAACAATGAAAATGCAAGTCAGAACGAAAACAATGCTTCTCAGAGCTACACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
*
3332172 ACCAAC
1 AACAAC
3332178 GAGAGCAACG
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 122 1.00
ACGTcount: A:0.44, C:0.28, G:0.15, T:0.13
Consensus pattern (63 bp):
AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
Found at i:3333900 original size:31 final size:31
Alignment explanation
Indices: 3333843--3333903 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3333833 CCTGAATTTA
* *
3333843 GCAATTAGGTCCACTTTGGTACTTGAACTTG
1 GCAACTAGATCCACTTTGGTACTTGAACTTG
*
3333874 GCAACTAGATCCATTTTGGT-CTTTGAACTT
1 GCAACTAGATCCACTTTGGTAC-TTGAACTT
3333904 AGATCCTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (31 bp):
GCAACTAGATCCACTTTGGTACTTGAACTTG
Found at i:3338161 original size:2 final size:2
Alignment explanation
Indices: 3338154--3338180 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3338144 TCATCTGCAA
3338154 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3338181 ATTCGTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3340156 original size:23 final size:23
Alignment explanation
Indices: 3340127--3340180 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
3340117 ATTTGATTTT
3340127 TAATTTTT-GAATTATTTAGTGA
1 TAATTTTTAGAATTATTTAGTGA
3340149 TAATTTTTAGAATTATTTAGTGA
1 TAATTTTTAGAATTATTTAGTGA
*
3340172 TAATATTTA
1 TAATTTTTA
3340181 CAAAAATTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 8 0.27
23 22 0.73
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (23 bp):
TAATTTTTAGAATTATTTAGTGA
Found at i:3343996 original size:5 final size:5
Alignment explanation
Indices: 3343976--3344009 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
3343966 GGCAACCCAC
* *
3343976 ATTTA TTTTT ATTTA ATTTA ATTTA ATTTA ATTT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTT
3344010 TGAATTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (5 bp):
ATTTA
Found at i:3348194 original size:13 final size:13
Alignment explanation
Indices: 3348176--3348220 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
3348166 ATTTTTGAAT
3348176 TATTTAGCGATAA
1 TATTTAGCGATAA
*
3348189 TATTTAGTGATAA
1 TATTTAGCGATAA
3348202 TATTTAG-GA-AA
1 TATTTAGCGATAA
*
3348213 AATTTAGC
1 TATTTAGC
3348221 TAAATTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 19 0.66
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (13 bp):
TATTTAGCGATAA
Found at i:3351166 original size:11 final size:11
Alignment explanation
Indices: 3351150--3351176 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3351140 ATTTTTTTAA
3351150 TTTTAAAATAC
1 TTTTAAAATAC
3351161 TTTTAAAATAC
1 TTTTAAAATAC
3351172 TTTTA
1 TTTTA
3351177 TTAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:3351188 original size:40 final size:39
Alignment explanation
Indices: 3351134--3351273 Score: 169
Period size: 41 Copynumber: 3.6 Consensus size: 39
3351124 ATTTTTATTA
* *
3351134 TTTTTT-ATTTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATAC
* *
3351172 TTTTATTAAATTTTTTAAATTTTAAATTTTTTTTAAAAATAC
1 TTTT-TTAAATTTTTT-AATTTTAAAATATTTTT-AAAATAC
* *
3351214 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAA
1 TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATAC
*
3351253 TTTTTTTAA-TTTTT-ATTTTAA
1 TTTTTTAAATTTTTTAATTTTAA
3351274 TTTTTAAAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
37 7 0.08
38 9 0.10
39 15 0.17
40 22 0.25
41 24 0.27
42 11 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:3351193 original size:41 final size:39
Alignment explanation
Indices: 3351134--3351284 Score: 178
Period size: 40 Copynumber: 3.7 Consensus size: 39
3351124 ATTTTTATTA
*
3351134 TTTTTT-ATTTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
* * *
3351172 TTTTATTAAATTTTTTAAATTTTAAATTTTTTTTAAAAATAC
1 TTTT-TT-AATTTTTTTAATTTTAAAATATTTTT-AAAATAC
*
3351214 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAAT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAAT-AC
3351254 TTTTTTAATTTTTATTTTAATTTTTAAAATA
1 TTTTTTAA--TTT-TTTTAA-TTTTAAAATA
3351285 AATTTTGGTA
Statistics
Matches: 96, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
38 4 0.04
39 7 0.07
40 32 0.33
41 23 0.24
42 14 0.15
43 6 0.06
44 10 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:3357191 original size:21 final size:22
Alignment explanation
Indices: 3357163--3357209 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
3357153 AAAAATAAAA
3357163 AATATATATAATAATTTTAT-ATT
1 AATATATAT-AT-ATTTTATAATT
3357186 AATATATATATATTTTATAATT
1 AATATATATATATTTTATAATT
3357208 AA
1 AA
3357210 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.30
22 7 0.30
23 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATATATATATTTTATAATT
Found at i:3365362 original size:16 final size:15
Alignment explanation
Indices: 3365335--3365366 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3365325 TCCAAACGTT
3365335 TTCTTTTTTGATTTC
1 TTCTTTTTTGATTTC
3365350 TTCTTTCTTTGATTTC
1 TTCTTT-TTTGATTTC
3365366 T
1 T
3365367 GTTTGCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.72
Consensus pattern (15 bp):
TTCTTTTTTGATTTC
Found at i:3365826 original size:17 final size:17
Alignment explanation
Indices: 3365804--3365843 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
3365794 TGTGGTTGGT
3365804 CGTGTGTGAGACATGGC
1 CGTGTGTGAGACATGGC
3365821 CGTGTGTGAGACATGGC
1 CGTGTGTGAGACATGGC
3365838 CGTGTG
1 CGTGTG
3365844 ACTGTCGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.15, C:0.17, G:0.42, T:0.25
Consensus pattern (17 bp):
CGTGTGTGAGACATGGC
Found at i:3373101 original size:44 final size:43
Alignment explanation
Indices: 3373003--3373129 Score: 161
Period size: 44 Copynumber: 2.9 Consensus size: 43
3372993 ATTTCGTACA
* * *
3373003 ATGCCAACGTCCCAGACGTGGTCTTATATGTAATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
3373046 ATGCCACTGTCCCAGACAG-GGTCTTACACGTAAGTCACA-AGTCG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGTAA-TCACATA-TCG
3373090 ATGCCAATGTCCCAGACGTGGTCTTACACGATAA-CACATA
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-TAATCACATA
3373130 ACGGAATCCT
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
43 33 0.45
44 37 0.51
45 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:3376411 original size:113 final size:113
Alignment explanation
Indices: 3376293--3376534 Score: 294
Period size: 113 Copynumber: 2.1 Consensus size: 113
3376283 CAGATTCAAA
* *
3376293 GACATTAGTGGCGCTTTA-AAGAAAACGCCGCAAAAGA-GAAACATTAGCGGCGCTTTCTACAAA
1 GACATTAGTGGCG-TTTATAAGAAAACGCCGCAAAAGATCAAACATTAGCGGCGCGTTC-ACAAA
* **
3376356 AGCGCCGCAAAAGTGATTAACAGACGACG-C-CGTATTGATTTACGTTTGAT
64 AGCGACGCAAAACAGATTAACAGACGACGACTCGT-TTGATTTA-GTTTGAT
* *** *
3376406 GACATTAGTGGCGTTTATAAGCAAACGCCGCAAAAGATCATGTATTCGCGGCGCGTTCACAAAAG
1 GACATTAGTGGCGTTTATAAGAAAACGCCGCAAAAGATCAAACATTAGCGGCGCGTTCACAAAAG
* * * *
3376471 CGACGCAGACCAGATTAACATACGACGACTTGTTTGATTTAGTTTGAT
66 CGACGCAAAACAGATTAACAGACGACGACTCGTTTGATTTAGTTTGAT
3376519 GACATTAGTGGCGTTT
1 GACATTAGTGGCGTTT
3376535 TCGTGAAGCG
Statistics
Matches: 111, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
112 4 0.04
113 82 0.74
114 23 0.21
115 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (113 bp):
GACATTAGTGGCGTTTATAAGAAAACGCCGCAAAAGATCAAACATTAGCGGCGCGTTCACAAAAG
CGACGCAAAACAGATTAACAGACGACGACTCGTTTGATTTAGTTTGAT
Found at i:3377374 original size:14 final size:14
Alignment explanation
Indices: 3377352--3377383 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3377342 TTATATATGT
*
3377352 TTTATGATTTAGGG
1 TTTAAGATTTAGGG
3377366 TTTAAGATTTAGGG
1 TTTAAGATTTAGGG
3377380 TTTA
1 TTTA
3377384 TATGTTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (14 bp):
TTTAAGATTTAGGG
Found at i:3377711 original size:21 final size:21
Alignment explanation
Indices: 3377681--3377743 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
3377671 TCTAGGTCAA
*
3377681 TTTATGGTTAAGGGTTAAGGG
1 TTTAGGGTTAAGGGTTAAGGG
* *
3377702 TTTAGTGTTAAGGGTTAATGG
1 TTTAGGGTTAAGGGTTAAGGG
*
3377723 TTTAGGGTTTAAGGTTTAAGG
1 TTTAGGG-TTAAGGGTTAAGG
3377744 AATAGAGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 24 0.69
22 11 0.31
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (21 bp):
TTTAGGGTTAAGGGTTAAGGG
Found at i:3377769 original size:7 final size:7
Alignment explanation
Indices: 3377681--3377793 Score: 66
Period size: 7 Copynumber: 16.1 Consensus size: 7
3377671 TCTAGGTCAA
*
3377681 TTTATGG
1 TTTAGGG
*
3377688 TTAAGGG
1 TTTAGGG
*
3377695 TTAAGGG
1 TTTAGGG
*
3377702 TTTAGTG
1 TTTAGGG
*
3377709 TTAAGGG
1 TTTAGGG
* *
3377716 TTAATGG
1 TTTAGGG
3377723 TTTAGGG
1 TTTAGGG
*
3377730 TTTAAGG
1 TTTAGGG
*
3377737 TTTAAGG
1 TTTAGGG
** *
3377744 AATAGAG
1 TTTAGGG
*
3377751 TTTACGG
1 TTTAGGG
3377758 TTTAGGG
1 TTTAGGG
3377765 TTTAGGG
1 TTTAGGG
**
3377772 GATAGGG
1 TTTAGGG
*
3377779 GTT-GTGG
1 TTTAG-GG
3377786 TTTAGGG
1 TTTAGGG
3377793 T
1 T
3377794 CTAGTTTATT
Statistics
Matches: 81, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
6 1 0.01
7 79 0.98
8 1 0.01
ACGTcount: A:0.22, C:0.01, G:0.38, T:0.39
Consensus pattern (7 bp):
TTTAGGG
Found at i:3378505 original size:251 final size:251
Alignment explanation
Indices: 3378100--3378587 Score: 696
Period size: 251 Copynumber: 1.9 Consensus size: 251
3378090 TCCGTTTGGC
* * * * *
3378100 TACAGGAATTTGAATTTTAGTGGCGTTTTTCATAAAAACGCGACTGAAGGTATGCTATAGTGGCG
1 TACAGGAATTTGAATTTTAGTGGCGTTTTTCATAAAAAAGCCACAGAAGGTATACTATAGTGGCA
* * * *
3378165 TTTTATATTGAAACTCCACAAATCCATAAATGTTTGTTTGTACGAAAACGGCGTTGTTTTCTTAA
66 TTTTATATAGAAACGCCACAAATCCATAAATGTTTGTTTGAACGAAAACGGCGTCGTTTTCTTAA
* * *
3378230 ATGATTTGAACTCCTTACTGGCGTTTTTATTTAAAACGCCGCAAACTGTGATCTTTAGCAGCGTT
131 ATGATTTGAACTCCTTACTGGCGTTTGTATTTAAAACGCCGC-AACTGTAAGCTTTAGCAGCGTT
* * *
3378295 CGGTATGGAAACGCCACAAATGTGTATTACAAAATGTTCAGAATGTCACTGTTTCGT
195 CAGTATGAAAACGCCACAAATGTGTATTACAAAATATTCAGAATGTCACTGTTTCGT
*
3378352 TACATGAATTTGAATTTTAGTGGCGTTTTT-ATGAAAAAAGCCACAGAAGGTATAC-AGTAGTGG
1 TACAGGAATTTGAATTTTAGTGGCGTTTTTCAT-AAAAAAGCCACAGAAGGTATACTA-TAGTGG
*
3378415 CATTTT-TATAGAAACGCCACAAATCCATATATGTTT-TTGTGAACGAAAACGGCGTCGTTTTCT
64 CATTTTATATAGAAACGCCACAAATCCATAAATGTTTGTT-TGAACGAAAACGGCGTCGTTTTCT
* * * * *
3378478 TAAATGATTTGAACTCGTTAGTGGCGTTTGTATTTAAAACGCTGCAACTGTAAGCTTTAGCGGTG
128 TAAATGATTTGAACTCCTTACTGGCGTTTGTATTTAAAACGCCGCAACTGTAAGCTTTAGCAGCG
* *
3378543 TTTAGTATGAAAACGCCGCAAATGTGTATTACAAAATATTCAGAA
193 TTCAGTATGAAAACGCCACAAATGTGTATTACAAAATATTCAGAA
3378588 CGGCGTCGTT
Statistics
Matches: 209, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
250 58 0.28
251 93 0.44
252 58 0.28
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (251 bp):
TACAGGAATTTGAATTTTAGTGGCGTTTTTCATAAAAAAGCCACAGAAGGTATACTATAGTGGCA
TTTTATATAGAAACGCCACAAATCCATAAATGTTTGTTTGAACGAAAACGGCGTCGTTTTCTTAA
ATGATTTGAACTCCTTACTGGCGTTTGTATTTAAAACGCCGCAACTGTAAGCTTTAGCAGCGTTC
AGTATGAAAACGCCACAAATGTGTATTACAAAATATTCAGAATGTCACTGTTTCGT
Found at i:3380613 original size:18 final size:18
Alignment explanation
Indices: 3380590--3380630 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
3380580 AATTTTTAAG
3380590 TTATATAACTTACATAAA
1 TTATATAACTTACATAAA
*
3380608 TTATATAACTTACATAAC
1 TTATATAACTTACATAAA
3380626 TTATA
1 TTATA
3380631 AATATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (18 bp):
TTATATAACTTACATAAA
Found at i:3380615 original size:9 final size:9
Alignment explanation
Indices: 3380590--3380630 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
3380580 AATTTTTAAG
3380590 TTATATAAC
1 TTATATAAC
* *
3380599 TTACATAAA
1 TTATATAAC
3380608 TTATATAAC
1 TTATATAAC
*
3380617 TTACATAAC
1 TTATATAAC
3380626 TTATA
1 TTATA
3380631 AATATTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (9 bp):
TTATATAAC
Done.