Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 52 of 182
Found at i:17684964 original size:14 final size:14
Alignment explanation
Indices: 17684945--17684972 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17684935 CTTAAATTTA
17684945 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
17684959 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
17684973 TTAAAACCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTAAATTTAAAT
Found at i:17694686 original size:17 final size:18
Alignment explanation
Indices: 17694664--17694698 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17694654 ATTTATTGTA
17694664 TATTATTA-ATTTTAAAT
1 TATTATTATATTTTAAAT
17694681 TATTATTATATTTTAAAT
1 TATTATTATATTTTAAAT
17694699 ACGAAATCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATTATATTTTAAAT
Found at i:17698605 original size:18 final size:18
Alignment explanation
Indices: 17698582--17698629 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
17698572 CCAATTTTAC
17698582 ATATTTTAAAAAATAAAA
1 ATATTTTAAAAAATAAAA
* * *
17698600 ATATTTCTTAAAAATTAGA
1 ATATTT-TAAAAAATAAAA
17698619 A-ATTTTAAAAA
1 ATATTTTAAAAA
17698630 TGGTTTAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 5 0.20
18 10 0.40
19 10 0.40
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATTTTAAAAAATAAAA
Found at i:17710204 original size:19 final size:19
Alignment explanation
Indices: 17710180--17710219 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
17710170 CTTAAAACAT
17710180 AAACACTAAATTCTCCAAA
1 AAACACTAAATTCTCCAAA
17710199 AAACACTAAATTCTCCAAA
1 AAACACTAAATTCTCCAAA
17710218 AA
1 AA
17710220 TGTTAGGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (19 bp):
AAACACTAAATTCTCCAAA
Found at i:17710402 original size:24 final size:24
Alignment explanation
Indices: 17710341--17710403 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
17710331 TAGACTAATA
* *
17710341 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
** *
17710365 AGAGTTTATTTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
17710389 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
17710404 GATTATTTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:17712290 original size:24 final size:24
Alignment explanation
Indices: 17712263--17712315 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
17712253 AGTTTGACTC
* * *
17712263 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAATTTAACTG
*
17712287 AAACAATTAAACAGAATTTAACTG
1 AAACAAATAAACAGAATTTAACTG
17712311 AAACA
1 AAACA
17712316 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:17714092 original size:2 final size:2
Alignment explanation
Indices: 17714085--17714110 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17714075 CAGATGATGT
17714085 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
17714111 GTTGTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17718224 original size:12 final size:11
Alignment explanation
Indices: 17718202--17718235 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
17718192 TAGAGAATTC
17718202 AAAACAAAAAAG
1 AAAA-AAAAAAG
17718214 AAAGAAAAAAAG
1 AAA-AAAAAAAG
17718226 AAAAAAAAAA
1 AAAAAAAAAA
17718236 CCTTTGCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.33
12 13 0.62
13 1 0.05
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:17725168 original size:8 final size:8
Alignment explanation
Indices: 17725152--17725180 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
17725142 ATATAAATCT
17725152 CCCCC-CC
1 CCCCCACC
17725159 CCCCCACC
1 CCCCCACC
17725167 CCCCCACC
1 CCCCCACC
17725175 CCCCCA
1 CCCCCA
17725181 AAAAAAAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.10, C:0.90, G:0.00, T:0.00
Consensus pattern (8 bp):
CCCCCACC
Found at i:17729263 original size:13 final size:13
Alignment explanation
Indices: 17729245--17729269 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17729235 TACTTCAATT
17729245 TATAATTTAAAAA
1 TATAATTTAAAAA
17729258 TATAATTTAAAA
1 TATAATTTAAAA
17729270 GTTGAGGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAATTTAAAAA
Found at i:17745366 original size:7 final size:7
Alignment explanation
Indices: 17745354--17745394 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
17745344 AGAGGATTAC
17745354 ATCCAAA
1 ATCCAAA
17745361 ATCCAAA
1 ATCCAAA
17745368 ATCCAAA
1 ATCCAAA
17745375 ATCCAAA
1 ATCCAAA
17745382 ATCCAAA
1 ATCCAAA
17745389 ATCCAA
1 ATCCAA
17745395 GCGTACTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (7 bp):
ATCCAAA
Found at i:17752288 original size:19 final size:19
Alignment explanation
Indices: 17752212--17752288 Score: 50
Period size: 21 Copynumber: 3.8 Consensus size: 19
17752202 ATATACGAAA
* *
17752212 TATATAAATGATT-AAAATT
1 TATA-AAATTATTAAAAAAT
*
17752231 TATAAAAATATTCTAAAAAAT
1 TATAAAATTA-T-TAAAAAAT
*
17752252 ATTTAAAATT-TTAGAAAAAAT
1 -TATAAAATTATT--AAAAAAT
17752273 TATAAAATTATTAAAA
1 TATAAAATTATTAAAA
17752289 GTATATGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
18 4 0.09
19 10 0.22
20 10 0.22
21 14 0.31
22 7 0.16
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (19 bp):
TATAAAATTATTAAAAAAT
Found at i:17752472 original size:19 final size:19
Alignment explanation
Indices: 17752450--17752493 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
17752440 TAGGTTTTAT
* *
17752450 ATTTTTAATATTTTTTAAA
1 ATTTTTAAAATTTTTCAAA
*
17752469 ATTTTTAAAATTTTTCATA
1 ATTTTTAAAATTTTTCAAA
17752488 ATTTTT
1 ATTTTT
17752494 TTAAAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTAAAATTTTTCAAA
Found at i:17752473 original size:8 final size:9
Alignment explanation
Indices: 17752450--17752493 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
17752440 TAGGTTTTAT
17752450 ATTTTTAATA
1 ATTTTTAA-A
*
17752460 TTTTTTAAA
1 ATTTTTAAA
17752469 ATTTTTAAA
1 ATTTTTAAA
*
17752478 ATTTTTCATA
1 ATTTTT-AAA
17752488 ATTTTT
1 ATTTTT
17752494 TTAAAAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 15 0.50
10 15 0.50
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:17752545 original size:10 final size:9
Alignment explanation
Indices: 17752518--17752577 Score: 52
Period size: 10 Copynumber: 6.3 Consensus size: 9
17752508 AATACCTTTC
*
17752518 TATATTTTT
1 TATAATTTT
17752527 ATATAAATTTT
1 -TAT-AATTTT
17752538 TAATAATTTT
1 T-ATAATTTT
17752548 TAT-ATTTT
1 TATAATTTT
17752556 CCTAT-ATTTT
1 --TATAATTTT
17752566 TATAATTTT
1 TATAATTTT
17752575 TAT
1 TAT
17752578 TGATCATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
8 8 0.18
9 10 0.23
10 19 0.43
11 7 0.16
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (9 bp):
TATAATTTT
Found at i:17752553 original size:30 final size:27
Alignment explanation
Indices: 17752518--17752577 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
17752508 AATACCTTTC
*
17752518 TATATTTTTATATAAATTTTTAATAATTTT
1 TATATTTTCATAT--ATTTTT-ATAATTTT
*
17752548 TATATTTTCCTATATTTTTATAATTTT
1 TATATTTTCATATATTTTTATAATTTT
17752575 TAT
1 TAT
17752578 TGATCATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 11 0.39
28 6 0.21
30 11 0.39
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (27 bp):
TATATTTTCATATATTTTTATAATTTT
Found at i:17752673 original size:7 final size:8
Alignment explanation
Indices: 17752656--17752683 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
17752646 ATCTTATAAA
17752656 TTTATTTT
1 TTTATTTT
17752664 TTTATTTT
1 TTTATTTT
17752672 TTTATTTT
1 TTTATTTT
17752680 TTTA
1 TTTA
17752684 AAATTAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTATTTT
Found at i:17753175 original size:19 final size:19
Alignment explanation
Indices: 17753151--17753212 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
17753141 AAAAATTACA
17753151 AAAAAATTAAAATAATTTT
1 AAAAAATTAAAATAATTTT
17753170 AAAAAATTCAAAATAACTTTT
1 AAAAAATT-AAAATAA-TTTT
* *
17753191 -AAAATTTAAAAT-ATTAT
1 AAAAAATTAAAATAATTTT
17753208 AAAAA
1 AAAAA
17753213 TTACAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.08
18 5 0.13
19 13 0.34
20 13 0.34
21 4 0.11
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAAATTAAAATAATTTT
Found at i:17753220 original size:19 final size:18
Alignment explanation
Indices: 17753152--17753226 Score: 57
Period size: 19 Copynumber: 4.1 Consensus size: 18
17753142 AAAATTACAA
*
17753152 AAAAATT-AAAATAATTTT
1 AAAAATTCAAAAT-ATTAT
17753170 AAAAAATTCAAAATAACTT-T
1 -AAAAATTCAAAAT-A-TTAT
* *
17753190 TAAAATTTAAAATATTAT
1 AAAAATTCAAAATATTAT
17753208 AAAAATTACAAAAT-TTAT
1 AAAAATT-CAAAATATTAT
17753226 A
1 A
17753227 TTTTTTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
17 2 0.04
18 13 0.27
19 23 0.48
20 8 0.17
21 2 0.04
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAATTCAAAATATTAT
Found at i:17753249 original size:17 final size:18
Alignment explanation
Indices: 17753198--17753249 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
17753188 TTTAAAATTT
**
17753198 AAAATATTATAAAAATTAC
1 AAAAT-TTATAAATTTTAC
**
17753217 AAAATTTATATTTTTTA-
1 AAAATTTATAAATTTTAC
17753234 AAAATTTATAAATTTT
1 AAAATTTATAAATTTT
17753250 TTTAAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 14 0.52
18 8 0.30
19 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTTATAAATTTTAC
Found at i:17753264 original size:21 final size:20
Alignment explanation
Indices: 17753227--17753266 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
17753217 AAAATTTATA
*
17753227 TTTTTTAAAAATTTATAAAT
1 TTTTTTAAAAATATATAAAT
17753247 TTTTTTAAAGAATATATAAA
1 TTTTTTAAA-AATATATAAA
17753267 AAAAAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTTTAAAAATATATAAAT
Found at i:17761041 original size:31 final size:31
Alignment explanation
Indices: 17760998--17761065 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
17760988 TATTGTTTTG
* *
17760998 GTCACTGTACTATTTGAAAGTTTTCATTTAA
1 GTCACTGAACTATTTAAAAGTTTTCATTTAA
*
17761029 GTCACTGAACTATTTAAAAGTTTTTATTTAA
1 GTCACTGAACTATTTAAAAGTTTTCATTTAA
*
17761060 ATCACT
1 GTCACT
17761066 AGATTGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (31 bp):
GTCACTGAACTATTTAAAAGTTTTCATTTAA
Found at i:17763302 original size:13 final size:13
Alignment explanation
Indices: 17763281--17763329 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
17763271 TTAGCATTGT
*
17763281 TTTTGAAAAGTGC
1 TTTTAAAAAGTGC
* *
17763294 TTTTAAAAAATGA
1 TTTTAAAAAGTGC
*
17763307 TTTTAAAAAGTAC
1 TTTTAAAAAGTGC
*
17763320 TTTTGAAAAG
1 TTTTAAAAAG
17763330 CTTGAGTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (13 bp):
TTTTAAAAAGTGC
Found at i:17764586 original size:32 final size:30
Alignment explanation
Indices: 17764550--17764621 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 30
17764540 TTCTGCTTTC
** *
17764550 TTCATTTTTTTAAATGTAATTTTTCTATGTTT
1 TTCATTTTTTTAAAACTAA-TTTT-TATATTT
*
17764582 TTCATTTGTTATAAAACTAATTTTTATATTT
1 TTCATTT-TTTTAAAACTAATTTTTATATTT
17764613 TT-ATTTTTT
1 TTCATTTTTT
17764622 CGAGTGAGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 2 0.06
30 4 0.12
31 8 0.24
32 11 0.32
33 9 0.26
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (30 bp):
TTCATTTTTTTAAAACTAATTTTTATATTT
Found at i:17767460 original size:19 final size:20
Alignment explanation
Indices: 17767436--17767480 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
17767426 ATTATATTGT
17767436 TGTTTTAGTATTTTTTT-AC
1 TGTTTTAGTATTTTTTTCAC
17767455 TGTTTTAGTATTTTTTTCAC
1 TGTTTTAGTATTTTTTTCAC
17767475 TGTTTT
1 TGTTTT
17767481 GATGTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.13, C:0.07, G:0.11, T:0.69
Consensus pattern (20 bp):
TGTTTTAGTATTTTTTTCAC
Found at i:17767471 original size:20 final size:19
Alignment explanation
Indices: 17767436--17767480 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
17767426 ATTATATTGT
*
17767436 TGTTTTAGTATTTTTTTAC
1 TGTTTTAGTATTTTTTCAC
17767455 TGTTTTAGTATTTTTTTCAC
1 TGTTTTAGTA-TTTTTTCAC
17767475 TGTTTT
1 TGTTTT
17767481 GATGTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.13, C:0.07, G:0.11, T:0.69
Consensus pattern (19 bp):
TGTTTTAGTATTTTTTCAC
Found at i:17767509 original size:30 final size:31
Alignment explanation
Indices: 17767455--17767521 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
17767445 ATTTTTTTAC
*
17767455 TGTTTTAGTATTTTTTTCACTGTTTTGA-TGT
1 TGTTTTAGTACTTTTTTCACTGTTTT-ACTGT
* *
17767486 TGTTTTAGTGCTTTTTT-ATTGTTTTACTGT
1 TGTTTTAGTACTTTTTTCACTGTTTTACTGT
17767516 TGTTTT
1 TGTTTT
17767522 TGTTGTTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 16 0.50
31 15 0.47
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.67
Consensus pattern (31 bp):
TGTTTTAGTACTTTTTTCACTGTTTTACTGT
Found at i:17767521 original size:19 final size:19
Alignment explanation
Indices: 17767485--17767528 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17767475 TGTTTTGATG
*
17767485 TTGTTTTAGTGCTTTTTTA
1 TTGTTTTACTGCTTTTTTA
* *
17767504 TTGTTTTACTGTTGTTTTTG
1 TTGTTTTACTGCT-TTTTTA
17767524 TTGTT
1 TTGTT
17767529 ATCTTTGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.07, C:0.05, G:0.18, T:0.70
Consensus pattern (19 bp):
TTGTTTTACTGCTTTTTTA
Found at i:17767528 original size:12 final size:12
Alignment explanation
Indices: 17767513--17767591 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 12
17767503 ATTGTTTTAC
17767513 TGTTGTTTTTGT
1 TGTTGTTTTTGT
* *
17767525 TGTTATCTTTGT
1 TGTTGTTTTTGT
*
17767537 TGCTGTTTTTGT
1 TGTTGTTTTTGT
***
17767549 TG--ACATTTG-
1 TGTTGTTTTTGT
*
17767558 TGTTGTTTTTAT
1 TGTTGTTTTTGT
*
17767570 TGTTGTTTTGGT
1 TGTTGTTTTTGT
*
17767582 TGTTATTTTT
1 TGTTGTTTTT
17767592 TTATTTGGAT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
9 2 0.04
10 4 0.08
11 3 0.06
12 39 0.81
ACGTcount: A:0.06, C:0.04, G:0.22, T:0.68
Consensus pattern (12 bp):
TGTTGTTTTTGT
Found at i:17774580 original size:97 final size:97
Alignment explanation
Indices: 17774389--17774584 Score: 290
Period size: 97 Copynumber: 2.0 Consensus size: 97
17774379 TTGAAATGGA
* * *
17774389 AGAGAGTGATGAAGTAAGCTGCTAATAAAGCCTGTGTTCTGACCGCTTGTTTTTCAGCTTTGGGT
1 AGAGAATGATGAAGTAAGCTACTAATAAAGCCTGTGTTCTGAACGCTTGTTTTTCAGCTTTGGGT
17774454 CTAGGGTAAAGTTCTAATTTTTGAATTTTTTT
66 CTAGGGTAAAGTTCTAATTTTTGAATTTTTTT
* * * *
17774486 AGAGAATGATGAAGTAAGCTATTAATAGAA-CTTGTGTTCTGAAGGCTTG-TTTTCAGTTTTGGG
1 AGAGAATGATGAAGTAAGCTACTAATA-AAGCCTGTGTTCTGAACGCTTGTTTTTCAGCTTTGGG
*
17774549 TCTAGGGTAAAGTTCTAATTTTTGGA-TTTTTT
65 TCTAGGGTAAAGTTCTAATTTTTGAATTTTTTT
17774581 AGAG
1 AGAG
17774585 TTTGGGCCTT
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 10 0.11
96 38 0.42
97 40 0.44
98 2 0.02
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (97 bp):
AGAGAATGATGAAGTAAGCTACTAATAAAGCCTGTGTTCTGAACGCTTGTTTTTCAGCTTTGGGT
CTAGGGTAAAGTTCTAATTTTTGAATTTTTTT
Found at i:17779319 original size:41 final size:41
Alignment explanation
Indices: 17779274--17779392 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 41
17779264 TAAAAGATAA
*
17779274 AGCATTAGTGGCACTTATGAAAAAGCGCCGCTAAAAGTCAG
1 AGCATTAGTGGCGCTTATGAAAAAGCGCCGCTAAAAGTCAG
* * * ** *
17779315 AGCATTAATGGCGCTTGTAAAAAAGAACCGCTAAAAGTTAG
1 AGCATTAGTGGCGCTTATGAAAAAGCGCCGCTAAAAGTCAG
* * * *
17779356 AACATTAGCGGCGCTTATG-ACAAGCGTCGCTAAAAGT
1 AGCATTAGTGGCGCTTATGAAAAAGCGCCGCTAAAAGT
17779393 GAGTTTTAAC
Statistics
Matches: 62, Mismatches: 16, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
40 14 0.23
41 48 0.77
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (41 bp):
AGCATTAGTGGCGCTTATGAAAAAGCGCCGCTAAAAGTCAG
Found at i:17781045 original size:20 final size:20
Alignment explanation
Indices: 17781020--17781059 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
17781010 AGCTTTCATG
17781020 GGTTTTCTTTAAAAGGGAAA
1 GGTTTTCTTTAAAAGGGAAA
17781040 GGTTTTCTTTAAAAGGGAAA
1 GGTTTTCTTTAAAAGGGAAA
17781060 AACATTCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (20 bp):
GGTTTTCTTTAAAAGGGAAA
Found at i:17781067 original size:20 final size:20
Alignment explanation
Indices: 17781024--17781067 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
17781014 TTCATGGGTT
****
17781024 TTCTTTAAAAGGGAAAGGTT
1 TTCTTTAAAAGGGAAAAACA
17781044 TTCTTTAAAAGGGAAAAACA
1 TTCTTTAAAAGGGAAAAACA
17781064 TTCT
1 TTCT
17781068 GTCCTTTGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (20 bp):
TTCTTTAAAAGGGAAAAACA
Found at i:17783175 original size:43 final size:42
Alignment explanation
Indices: 17783128--17783267 Score: 147
Period size: 43 Copynumber: 3.3 Consensus size: 42
17783118 TTTGTTAATG
* *
17783128 TTAGCGGCGTTTGTGGGAAAAGCATCGCTAAAAATCATGTTTT
1 TTAGCGGCGTTTGTGGGAAAAGC-TCGCTAAAGACCATGTTTT
* ** * *
17783171 TTAGCGGTGTTTGTGAAAAAAACGTCGTTAAAGACCATGTTTT
1 TTAGCGGCGTTTGTGGGAAAAGC-TCGCTAAAGACCATGTTTT
* * *
17783214 TTAGCGGCTTTTGTGGG-AAAGCGCTGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCTC-GCTAAAGACCATGTTTT
*
17783256 ATAGCGGCGTTT
1 TTAGCGGCGTTT
17783268 TTCCTCAAAA
Statistics
Matches: 78, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
41 1 0.01
42 29 0.37
43 48 0.62
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGGGAAAAGCTCGCTAAAGACCATGTTTT
Found at i:17785070 original size:16 final size:17
Alignment explanation
Indices: 17785045--17785078 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17785035 GGTAAGAAGA
*
17785045 AATTTTATTT-ATTTTT
1 AATTTAATTTAATTTTT
17785061 AATTTAATTTAATTTTT
1 AATTTAATTTAATTTTT
17785078 A
1 A
17785079 CTTAGAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATTTAATTTAATTTTT
Found at i:17789345 original size:17 final size:18
Alignment explanation
Indices: 17789312--17789386 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
17789302 TATTCATTCT
17789312 AAAATTATAAAAATAAAG
1 AAAATTATAAAAATAAAG
*
17789330 AAAATTA-AACAAT-AA-
1 AAAATTATAAAAATAAAG
* **
17789345 AAAATTTTAAAAATTTTA-
1 AAAATTATAAAAA-TAAAG
*
17789363 AAAATTATAAAATTACAAG
1 AAAATTATAAAAATA-AAG
17789382 AAAAT
1 AAAAT
17789387 CACTAAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
15 6 0.14
16 6 0.14
17 7 0.16
18 20 0.45
19 5 0.11
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATTATAAAAATAAAG
Found at i:17789365 original size:8 final size:9
Alignment explanation
Indices: 17789344--17789374 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17789334 TTAAACAATA
17789344 AAAAATTTT
1 AAAAATTTT
17789353 AAAAATTTT
1 AAAAATTTT
*
17789362 AAAAATTAT
1 AAAAATTTT
17789371 AAAA
1 AAAA
17789375 TTACAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAAATTTT
Found at i:17791102 original size:82 final size:82
Alignment explanation
Indices: 17790950--17791217 Score: 306
Period size: 84 Copynumber: 3.2 Consensus size: 82
17790940 CTAAGTGCAT
* * * * *
17790950 ATTCTTCTATTGACTTAGTGAGCAGTACCCTCAAAAGGGTGTTTGCTTAAATAATTTACTAAGTG
1 ATTCTTCTATTGACTTAGCGAGCAATACCCTCAAAA--GTGTGTGCTCAAATAATTTGCTAAGTG
17791015 CCTTAAGAGGCTAGAATCG
64 CCTTAAGAGGCTAGAATCG
* * * *
17791034 ATTCTTCTATTGACTTGGGGAGCAATA-CCTCGAAAAATGTGTGCTCAAATAATTTGCTAAGTGG
1 ATTCTTCTATTGACTTAGCGAGCAATACCCTC-AAAAGTGTGTGCTCAAATAATTTGCTAAGTGC
* * *
17791098 CTTAAGAAGCTAGGATTG
65 CTTAAGAGGCTAGAATCG
* * * *
17791116 ATTCTTATATTGACTTAGCGAGCAATACCCTCAAAGGGTGTGTGCTCAAATTTATTTGTTAAGTG
1 ATTCTTCTATTGACTTAGCGAGCAATACCCTCAAA-AGTGTGTGCTCAAA-TAATTTGCTAAGTG
*
17791181 CCTTAAGAGGCTAGAAGC-
64 CCTTAAGAGGCTAGAATCG
*
17791199 AGTTCTTCTATTGAGTTAG
1 A-TTCTTCTATTGACTTAG
17791218 TGGGCCTAAA
Statistics
Matches: 154, Mismatches: 25, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
82 65 0.42
83 21 0.14
84 68 0.44
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (82 bp):
ATTCTTCTATTGACTTAGCGAGCAATACCCTCAAAAGTGTGTGCTCAAATAATTTGCTAAGTGCC
TTAAGAGGCTAGAATCG
Found at i:17791822 original size:56 final size:56
Alignment explanation
Indices: 17791600--17791807 Score: 285
Period size: 56 Copynumber: 3.7 Consensus size: 56
17791590 TAGTTCGAAC
* * *
17791600 AGGATATTATTATGTGATATTATATTTTAACAATTTAATTCCTAATGTG-ATATTATA
1 AGGATATTATTATGAGATATTATATCTTAACAATTTGATTCCTAATG-GAATATTA-A
* *
17791657 A-GATATTATGATGGGATATTATATCTTAACAATTTGATTCCTAATGGAATATTAA
1 AGGATATTATTATGAGATATTATATCTTAACAATTTGATTCCTAATGGAATATTAA
* * * *
17791712 AGGATATTATTATGAGATATTATCTCTTAACAATCTGATTGCTAATGGAATATTAG
1 AGGATATTATTATGAGATATTATATCTTAACAATTTGATTCCTAATGGAATATTAA
* *
17791768 AGGATATTATTATGAGATATTATCTCTTAGCAATTTGATT
1 AGGATATTATTATGAGATATTATATCTTAACAATTTGATT
17791808 TCTACGTAAC
Statistics
Matches: 137, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
55 3 0.02
56 133 0.97
57 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (56 bp):
AGGATATTATTATGAGATATTATATCTTAACAATTTGATTCCTAATGGAATATTAA
Found at i:17793999 original size:24 final size:24
Alignment explanation
Indices: 17793972--17794017 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
17793962 GTGGAACTAG
17793972 TAGAAAATGAAGATCCAACTCCAA
1 TAGAAAATGAAGATCCAACTCCAA
17793996 TAGAAAATGAAGATCCAACTCC
1 TAGAAAATGAAGATCCAACTCC
17794018 GTGTATGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.22, G:0.13, T:0.17
Consensus pattern (24 bp):
TAGAAAATGAAGATCCAACTCCAA
Found at i:17797535 original size:43 final size:43
Alignment explanation
Indices: 17797474--17797570 Score: 167
Period size: 43 Copynumber: 2.3 Consensus size: 43
17797464 AACTGCACAA
* *
17797474 TTAATAATATGTCACGATATTAACAAGAGTCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGTCAAGTAATATAAT
*
17797517 TTAATAACATGCCACGATATTAACATGAGTCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGTCAAGTAATATAAT
17797560 TTAATAACATG
1 TTAATAACATG
17797571 TCAATGAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (43 bp):
TTAATAACATGCCACGATATTAACAAGAGTCAAGTAATATAAT
Found at i:17798961 original size:5 final size:5
Alignment explanation
Indices: 17798953--17798996 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
17798943 CTTACTAACA
17798953 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAAT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAAT
17798997 AAAAATAACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AAATT
Found at i:17799062 original size:12 final size:12
Alignment explanation
Indices: 17799045--17799084 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
17799035 TTTACTCTAC
17799045 TAAATAAAAAAT
1 TAAATAAAAAAT
*
17799057 TAAATAACAAAT
1 TAAATAAAAAAT
*
17799069 CAAAT-AAAAAT
1 TAAATAAAAAAT
17799080 TAAAT
1 TAAAT
17799085 TAAACAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAATAAAAAAT
Found at i:17799090 original size:25 final size:23
Alignment explanation
Indices: 17799046--17799100 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 23
17799036 TTACTCTACT
*
17799046 AAATAAAAAATTAAATAACAAATC
1 AAAT-AAAAATTAAATAACAAAAC
17799070 AAATAAAAATTAAATTAAACAAAAC
1 AAATAAAAATTAAA-T-AACAAAAC
17799095 AAATAA
1 AAATAA
17799101 CTTAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 10 0.36
24 5 0.18
25 13 0.46
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAAAAATTAAATAACAAAAC
Found at i:17799397 original size:14 final size:14
Alignment explanation
Indices: 17799355--17799397 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
17799345 AAAATAACTT
17799355 TTTC-TTCTTCTTC
1 TTTCTTTCTTCTTC
17799368 TTTCTTTCTT-TCTC
1 TTTCTTTCTTCT-TC
17799382 TTTCTTTCTTCTTC
1 TTTCTTTCTTCTTC
17799396 TT
1 TT
17799398 CTCTCCCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.19
14 21 0.78
15 1 0.04
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTCTTTCTTCTTC
Found at i:17799652 original size:11 final size:12
Alignment explanation
Indices: 17799616--17799656 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
17799606 TTTCAGGTAC
17799616 TTTATCCGTGTAT
1 TTTAT-CGTGTAT
17799629 TTTATCGTGTAT
1 TTTATCGTGTAT
*
17799641 TTTGTC-TGTAT
1 TTTATCGTGTAT
17799652 TTTAT
1 TTTAT
17799657 TCCCCTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 9 0.35
12 12 0.46
13 5 0.19
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.61
Consensus pattern (12 bp):
TTTATCGTGTAT
Found at i:17801930 original size:16 final size:16
Alignment explanation
Indices: 17801893--17801931 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
17801883 GGCGAAATTA
17801893 AATTTTAATTTTTAAT
1 AATTTTAATTTTTAAT
17801909 AA-TTTATATTTTT-AT
1 AATTTTA-ATTTTTAAT
17801924 AATTTTAA
1 AATTTTAA
17801932 AGGATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTTAATTTTTAAT
Found at i:17803352 original size:18 final size:19
Alignment explanation
Indices: 17803324--17803372 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
17803314 GAATCATCTC
*
17803324 TATTATAAAAATATATATA
1 TATTATAAAAAAATATATA
17803343 TATT-TAAAAAAATATAT-
1 TATTATAAAAAAATATATA
17803360 T-TTGATAAAAAAA
1 TATT-ATAAAAAAA
17803373 AAGAATTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 2 0.07
17 1 0.04
18 20 0.74
19 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TATTATAAAAAAATATATA
Found at i:17808927 original size:19 final size:19
Alignment explanation
Indices: 17808892--17808929 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17808882 ATAACATTAT
**
17808892 TAATAAATATTTTTAATAA
1 TAATAAATATTAATAATAA
17808911 TAATAAATATTAATAATAA
1 TAATAAATATTAATAATAA
17808930 ATTTTTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATAAATATTAATAATAA
Found at i:17809161 original size:24 final size:23
Alignment explanation
Indices: 17809131--17809186 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
17809121 TTTTTTTTTA
**
17809131 AAAAAAATTTAAAAATAAAAATG
1 AAAAAAATGGAAAAATAAAAATG
* *
17809154 AAACAAAAGGGAGAAATAAAAATG
1 AAA-AAAATGGAAAAATAAAAATG
17809178 AAAAAAATG
1 AAAAAAATG
17809187 AAAGAACGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.14
Consensus pattern (23 bp):
AAAAAAATGGAAAAATAAAAATG
Found at i:17809192 original size:24 final size:24
Alignment explanation
Indices: 17809143--17809192 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
17809133 AAAAATTTAA
**
17809143 AAATAAAAATGAAACAAAAGGGAG
1 AAATAAAAATGAAACAAAAGAAAG
17809167 AAATAAAAATGAAA-AAAATGAAAG
1 AAATAAAAATGAAACAAAA-GAAAG
17809191 AA
1 AA
17809193 CGAAGGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.72, C:0.02, G:0.16, T:0.10
Consensus pattern (24 bp):
AAATAAAAATGAAACAAAAGAAAG
Found at i:17810026 original size:28 final size:29
Alignment explanation
Indices: 17809979--17810083 Score: 99
Period size: 29 Copynumber: 3.6 Consensus size: 29
17809969 AAAATTTTAG
*
17809979 AAAATTACCATTTTACCCTCGAATCTTTT
1 AAAATTACCATTTTAACCTCGAATCTTTT
* ** *
17810008 AAAATT-CCATTTTAACCTCGATTTCACTG
1 AAAATTACCATTTTAACCTCGA-ATCTTTT
* *
17810037 AAAATTACCATTTT-ACCCCTGAATCTTCT
1 AAAATTACCATTTTAACCTC-GAATCTTTT
17810066 AAAATT-CCATTTTTAACC
1 AAAATTACCA-TTTTAACC
17810084 CCGATTTTAC
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 17 0.28
29 31 0.52
30 12 0.20
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (29 bp):
AAAATTACCATTTTAACCTCGAATCTTTT
Found at i:17810113 original size:59 final size:59
Alignment explanation
Indices: 17809979--17810350 Score: 434
Period size: 59 Copynumber: 6.3 Consensus size: 59
17809969 AAAATTTTAG
* * **
17809979 AAAATTACCATTTTA-CCCTCGAATCTTTTAAAATTCCA-TTTTAACCTCGATTTCACTG
1 AAAATTACCATTTTACCCCT-GAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
*
17810037 AAAATTACCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAACCCCGATTTTACCA
1 AAAATTACCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
17810096 AAAATTACCATTCTACCCCTAAATCTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAA
1 AAAATTACCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACC--A
* * * *
17810157 AAAAATACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCTGATTTCACCG
1 AAAATTACCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* * * * *
17810216 AAAATTACCATTTTACCCCCGAA-CTTTCCAAAATTCCATTGTAAACCCCGATTTCATCA
1 AAAATTACCATTTTACCCCTGAATC-TTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* * * * *
17810275 AAAATCACCATTTTA-CCCTCGAA-CATTCCAAAATTCCA-TTTTAACCCCAATTTTATC-
1 AAAATTACCATTTTACCCCT-GAATC-TTCTAAAATTCCATTTTTAACCCCGATTTCACCA
*
17810332 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
17810351 CGAGTATCCA
Statistics
Matches: 275, Mismatches: 32, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
57 13 0.05
58 54 0.20
59 155 0.56
61 53 0.19
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:17810199 original size:120 final size:115
Alignment explanation
Indices: 17809979--17810350 Score: 430
Period size: 120 Copynumber: 3.2 Consensus size: 115
17809969 AAAATTTTAG
* * *
17809979 AAAATTACCATTTTA-CCCTCGAATCTTTTAAAATTCCA-TTTTAACCTCGATTTCACTGAAAAT
1 AAAATTACCATTTTACCCCT-GAATCTTCTAAAATTCCATTTTTAACCCCGATTTCAC--AAAAA
*
17810042 TACCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAACCCCGATTTTACC
63 TACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTTACC
* * *
17810095 AAAAATTACCATTCTACCCCTAAATCTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAAAA
1 -AAAATTACCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA-C---AAA
* *
17810160 AATACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCTGATTTCACC
61 AATACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTTACC
* * * *
17810215 GAAAATTACCATTTTACCCCCGAA-CTTTCCAAAATTCCATTGTAAACCCCGATTTCATCAAAAA
1 -AAAATTACCATTTTACCCCTGAATC-TTCTAAAATTCCATTTTTAACCCCGATTTCA-CAAAAA
* * * *
17810279 TCACCATTTTACCCTCGAA-CATTCCAAAATTCCA-TTTTAACCCCAATTTTATC
63 T-ACCATTTTACCCCCGAATC-TTCTAAAATTCCATTTTTAACCCCGATTTTACC
*
17810332 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
17810351 CGAGTATCCA
Statistics
Matches: 221, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
116 18 0.08
117 52 0.24
118 47 0.21
119 2 0.01
120 102 0.46
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (115 bp):
AAAATTACCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACAAAAATAC
CATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTTACC
Found at i:17810310 original size:179 final size:176
Alignment explanation
Indices: 17809979--17810327 Score: 488
Period size: 179 Copynumber: 2.0 Consensus size: 176
17809969 AAAATTTTAG
* * * *
17809979 AAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTAACCTCGATTTCACTGAAAATTA
1 AAAAATACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTAACCTCGATTTCACCGAAAATTA
* * * * * *
17810044 CCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTC
66 CCATTTTACCCCCGAATCTTCCAAAATTCCATTGTAAACCCCGATTTCACCAAAAATCACCATTC
* *
17810109 TACCCCTAAATCTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAA
131 TACCCCGAAA-CTTCCAAAATTCCA-TTTTAACCCCAATTTCACCAAA
17810157 AAAAATACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACC-CTGATTTCACCGAAAAT
1 AAAAATACCATTTTACCCCCGAATCTTCTAAAATTCCA-TTTTAACCTC-GATTTCACCGAAAAT
*
17810221 TACCATTTTACCCCCGAA-CTTTCCAAAATTCCATTGTAAACCCCGATTTCATCAAAAATCACCA
64 TACCATTTTACCCCCGAATC-TTCCAAAATTCCATTGTAAACCCCGATTTCACCAAAAATCACCA
*
17810285 TTTTACCCTCG-AACATTCCAAAATTCCATTTTAACCCCAATTT
128 TTCTACCC-CGAAAC-TTCCAAAATTCCATTTTAACCCCAATTT
17810328 TATCAAAATT
Statistics
Matches: 152, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
178 53 0.35
179 98 0.64
180 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (176 bp):
AAAAATACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTAACCTCGATTTCACCGAAAATTA
CCATTTTACCCCCGAATCTTCCAAAATTCCATTGTAAACCCCGATTTCACCAAAAATCACCATTC
TACCCCGAAACTTCCAAAATTCCATTTTAACCCCAATTTCACCAAA
Found at i:17814264 original size:31 final size:31
Alignment explanation
Indices: 17814229--17814288 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
17814219 AACACGTATA
17814229 CATAGATTTCACCTC-TATTACTTGAAATACG
1 CATAGATTTCA-CTCATATTACTTGAAATACG
* *
17814260 CATAGATTTTACTCATATTGCTTGAAATA
1 CATAGATTTCACTCATATTACTTGAAATA
17814289 TAATATATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (31 bp):
CATAGATTTCACTCATATTACTTGAAATACG
Found at i:17815638 original size:14 final size:14
Alignment explanation
Indices: 17815619--17815649 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17815609 AGAATAGATT
17815619 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
17815633 TTTAATTAATTAAA
1 TTTAATTAAATAAA
17815647 TTT
1 TTT
17815650 TTTAAACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:17821985 original size:41 final size:43
Alignment explanation
Indices: 17821928--17822009 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 43
17821918 TAAAAAGATA
17821928 GGTGTTTTGACCATTTCAGTCA-TTT-TTTAGGACATTTTGGG
1 GGTGTTTTGACCATTTCAGTCATTTTCTTTAGGACATTTTGGG
17821969 GGTGTTTTGACCATTTCAGTCATTTTCTTTAGGACATTTTG
1 GGTGTTTTGACCATTTCAGTCATTTTCTTTAGGACATTTTG
17822010 AGGAATTCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 22 0.56
42 3 0.08
43 14 0.36
ACGTcount: A:0.17, C:0.13, G:0.22, T:0.48
Consensus pattern (43 bp):
GGTGTTTTGACCATTTCAGTCATTTTCTTTAGGACATTTTGGG
Found at i:17822434 original size:16 final size:16
Alignment explanation
Indices: 17822413--17822443 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17822403 CATGTTCGAG
17822413 CACATAAATTTGAAAT
1 CACATAAATTTGAAAT
*
17822429 CACATATATTTGAAA
1 CACATAAATTTGAAA
17822444 ATTTTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (16 bp):
CACATAAATTTGAAAT
Found at i:17823656 original size:50 final size:50
Alignment explanation
Indices: 17823602--17823728 Score: 157
Period size: 50 Copynumber: 2.5 Consensus size: 50
17823592 GGACAATGAA
* * *
17823602 GATATTTTTTCTGGCTCGTAAAAGCGGTATTCTGCCTGGCTCGTAAGAGC
1 GATATTTTTTCTGGCTCGTAAGAGCGGTATTCTACCTGGCTCATAAGAGC
* * **
17823652 GATATTCTGTCTGGCTCGTAAGAGCGGTATTCTATTTGGCTCATAAGAGC
1 GATATTTTTTCTGGCTCGTAAGAGCGGTATTCTACCTGGCTCATAAGAGC
*
17823702 GATACTTTATTT-GGGCTCGTAAGAGCG
1 GATA-TTT-TTTCTGGCTCGTAAGAGCG
17823729 ATACTCTATC
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 47 0.72
51 16 0.25
52 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (50 bp):
GATATTTTTTCTGGCTCGTAAGAGCGGTATTCTACCTGGCTCATAAGAGC
Found at i:17823712 original size:25 final size:25
Alignment explanation
Indices: 17823613--17823753 Score: 140
Period size: 25 Copynumber: 5.6 Consensus size: 25
17823603 ATATTTTTTC
* * ***
17823613 TGGCTCGTAAAAGCGGTATTCTGCC
1 TGGCTCGTAAGAGCGATATTCTATT
* *
17823638 TGGCTCGTAAGAGCGATATTCTGTC
1 TGGCTCGTAAGAGCGATATTCTATT
*
17823663 TGGCTCGTAAGAGCGGTATTCTATT
1 TGGCTCGTAAGAGCGATATTCTATT
*
17823688 TGGCTCATAAGAGCGATACTT-TATT
1 TGGCTCGTAAGAGCGATA-TTCTATT
*
17823713 TGGGCTCGTAAGAGCGATACTCTATCT
1 T-GGCTCGTAAGAGCGATATTCTAT-T
* *
17823740 GGGCTTGTAAGAGC
1 TGGCTCGTAAGAGC
17823754 TAAACTTTGT
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
25 66 0.66
26 33 0.33
27 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (25 bp):
TGGCTCGTAAGAGCGATATTCTATT
Found at i:17823725 original size:26 final size:26
Alignment explanation
Indices: 17823639--17823770 Score: 128
Period size: 26 Copynumber: 5.2 Consensus size: 26
17823629 TATTCTGCCT
* *
17823639 GGCTCGTAAGAGCGATA-TTCTGTCT-
1 GGCTCGTAAGAGCGATACTT-TATTTG
*
17823664 GGCTCGTAAGAGCGGTA-TTCTATTT-
1 GGCTCGTAAGAGCGATACTT-TATTTG
*
17823689 GGCTCATAAGAGCGATACTTTATTTG
1 GGCTCGTAAGAGCGATACTTTATTTG
* *
17823715 GGCTCGTAAGAGCGATACTCTATCTG
1 GGCTCGTAAGAGCGATACTTTATTTG
* * * *
17823741 GGCTTGTAAGAGCTAAACTTTGTTTG
1 GGCTCGTAAGAGCGATACTTTATTTG
17823767 GGCT
1 GGCT
17823771 TGTTTGAGCT
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
25 42 0.46
26 49 0.54
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.33
Consensus pattern (26 bp):
GGCTCGTAAGAGCGATACTTTATTTG
Found at i:17824320 original size:43 final size:43
Alignment explanation
Indices: 17824252--17824650 Score: 489
Period size: 43 Copynumber: 9.3 Consensus size: 43
17824242 TTATGTGGAA
* * * *
17824252 AAACGCAGCTAAAGAAAATAGTCTTTAACGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
17824295 AAACGCCGGTAAAGAACATGATCTTTAGCGGCG-TTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTT-CCCAC
* * * * *
17824338 AAACGTCGCTAAAGAACATGGTTTTTAGCGACGCTTTCCCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
17824381 AAACGTCGCTAAAGAACATGGTCTTTAGCGGTGC-TTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * *
17824423 AAATGCCGCTAAAAAACATGGTCTTTAGCGGCACTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * *
17824466 AAACGCCACTAAAGAACATGGTCTTTAGCGACGCTTTTCACAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
17824509 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCTAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCC-AC
* * *
17824552 AAACGTCGCTAAAGAACACGGTCTTTAGCGGCTCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * * *
17824595 AAATGTCTCTAAAGAACATGGTGTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
17824638 AAACGCCGCTAAA
1 AAACGCCGCTAAA
17824651 TTAACAGATT
Statistics
Matches: 301, Mismatches: 50, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
42 44 0.15
43 248 0.82
44 9 0.03
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Found at i:17824558 original size:171 final size:172
Alignment explanation
Indices: 17824259--17824650 Score: 540
Period size: 171 Copynumber: 2.3 Consensus size: 172
17824249 GAAAAACGCA
* * *
17824259 GCTAAAGAAA-ATAGTCTTTAACGGCGCTTTTCCCACAAACGCCGGTAAAGAACATGATCTTTAG
1 GCTAAA-AAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGATCTTTAG
* * ** * *
17824323 CGGCGTTTTCCCCACAAACGTCGCTAAAGAACATGGTTTTTAGCGACGCTTTCCCCATAAACGTC
65 CGACGTTTTCCACACAAACACCGCTAAAGAACATGGTCTTTAGCGACGCTTTCCCCAAAAACGTC
*
17824388 GCTAAAGAACATGGTCTTTAGCGG-TGC-TTTCCCACAAATGCC
130 GCTAAAGAACACGGTCTTTAGCGGCT-CTTTTCCCACAAATGCC
* * * *
17824430 GCTAAAAAACATGGTCTTTAGCGGCACTTTCCCCACAAACGCCACTAAAGAACATGGTCTTTAGC
1 GCTAAAAAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGATCTTTAGC
* *
17824495 GACGCTTTT-CACACAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCTAAAAACGTC
66 GACG-TTTTCCACACAAACACCGCTAAAGAACATGGTCTTTAGCGACGCTTTCCCCAAAAACGTC
*
17824559 GCTAAAGAACACGGTCTTTAGCGGCTCTTTTCCCACAAATGTC
130 GCTAAAGAACACGGTCTTTAGCGGCTCTTTTCCCACAAATGCC
* * * *
17824602 TCTAAAGAACATGGTGTTTAGCAGCGCTTTTCCCACAAACGCCGCTAAA
1 GCTAAAAAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
17824651 TTAACAGATT
Statistics
Matches: 193, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
170 3 0.02
171 129 0.67
172 61 0.32
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (172 bp):
GCTAAAAAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGATCTTTAGC
GACGTTTTCCACACAAACACCGCTAAAGAACATGGTCTTTAGCGACGCTTTCCCCAAAAACGTCG
CTAAAGAACACGGTCTTTAGCGGCTCTTTTCCCACAAATGCC
Found at i:17824985 original size:66 final size:65
Alignment explanation
Indices: 17824902--17825039 Score: 179
Period size: 66 Copynumber: 2.1 Consensus size: 65
17824892 TCATATTTTG
* * *
17824902 AAGTTGTAGCTGCAGTTCGTCATACTTTCTTGTTG-CCTCTGCTTCTCTCACTGCTGCCTCCGCT
1 AAGTTGTAGCTGAAGTTCATCATACTTTC-T-TTGACCTCTGCTTCTCTCACTGCAGCCTCCGCT
17824966 TT
64 TT
* * *
17824968 AAGTTGTAGCTGAAGTTCATTATATTTTCTTTGAACCTCTGCTTCTCTCACTGCAGCCTCCTCTT
1 AAGTTGTAGCTGAAGTTCATCATACTTTCTTTG-ACCTCTGCTTCTCTCACTGCAGCCTCCGCTT
17825033 T
65 T
*
17825034 ATGTTG
1 AAGTTG
17825040 AGCAATTTGC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
64 3 0.05
65 1 0.02
66 59 0.94
ACGTcount: A:0.14, C:0.27, G:0.17, T:0.42
Consensus pattern (65 bp):
AAGTTGTAGCTGAAGTTCATCATACTTTCTTTGACCTCTGCTTCTCTCACTGCAGCCTCCGCTTT
Found at i:17829822 original size:21 final size:19
Alignment explanation
Indices: 17829770--17829822 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 19
17829760 ATGGGATCGG
17829770 GAAATGACAAATATTTATAA
1 GAAATGA-AAATATTTATAA
*
17829790 GATATAGTAAAATATTTATAAAA
1 GAAAT-G-AAAATATTTAT--AA
17829813 GAAATGAAAA
1 GAAATGAAAA
17829823 CTCATGACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
20 4 0.15
21 15 0.56
22 2 0.07
23 6 0.22
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.28
Consensus pattern (19 bp):
GAAATGAAAATATTTATAA
Found at i:17831455 original size:41 final size:41
Alignment explanation
Indices: 17831410--17831741 Score: 382
Period size: 41 Copynumber: 8.1 Consensus size: 41
17831400 TTAAATAAAA
*
17831410 TAGCGGCGTTTATGAGAAAGCGCCGCTAATGCTCTGATCTT
1 TAGCGGCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTT
* * *
17831451 TAGCGACGTTTATGAGAAAGCGTCACTAATGCTCTGACCTT
1 TAGCGGCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTT
* * *
17831492 TAGCGGCGTTTGA-GGGAAAGCGTCGCTAATGCTCTGACATT
1 TAGCGGCGTTT-ATGAGAAAGCGCCGCTAATGCTCTGACCTT
* * * *
17831533 TAGCGACATTTGA-GGGAAAGCGCCGTTAATGCTCTGACCTT
1 TAGCGGCGTTT-ATGAGAAAGCGCCGCTAATGCTCTGACCTT
* * *
17831574 TAGCAGCGTTTATGAGAAAGTGCCGCTAATACTCTGACCTT
1 TAGCGGCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTT
* * * *
17831615 TAGCAGCGTTTATGAGAATGCGCTGCTAATGCTCTGATCTT
1 TAGCGGCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTT
** *
17831656 TAGCGATGTTTATGAGAAAGCGCTGCTAATGCTCTGACCTT
1 TAGCGGCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTT
*** * *
17831697 TAGCGGCGTTT-TCCCATAAGCGTCGCTAATGCTCTGACTTT
1 TAGCGGCGTTTATGAGA-AAGCGCCGCTAATGCTCTGACCTT
17831738 TAGC
1 TAGC
17831742 TGTGTTTTTT
Statistics
Matches: 250, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
40 3 0.01
41 246 0.98
42 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (41 bp):
TAGCGGCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTT
Found at i:17831913 original size:28 final size:28
Alignment explanation
Indices: 17831881--17831937 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
17831871 TGCTGTAGTG
*
17831881 AAGCATGCCTAGTGTTATAAGTTGGTTT
1 AAGCATGCCTAGTGTTATAAGTTAGTTT
17831909 AAGCATGCCTAGTGTTATAAGTTAGTTT
1 AAGCATGCCTAGTGTTATAAGTTAGTTT
17831937 A
1 A
17831938 TGTGTTTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (28 bp):
AAGCATGCCTAGTGTTATAAGTTAGTTT
Found at i:17833515 original size:24 final size:25
Alignment explanation
Indices: 17833482--17833528 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
17833472 TTTCAGTTAA
*
17833482 TAAAATTTTCT-TTGAGTTTTTTCT
1 TAAAAATTTCTCTTGAGTTTTTTCT
17833506 TAAAAATTTCTCTTGAGTTTTTT
1 TAAAAATTTCTCTTGAGTTTTTT
17833529 TTTTGAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (25 bp):
TAAAAATTTCTCTTGAGTTTTTTCT
Found at i:17835027 original size:21 final size:21
Alignment explanation
Indices: 17835011--17835059 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
17835001 TTTCACTATT
*
17835011 GTTTTTCCTCACCTCACCATC
1 GTTTTCCCTCACCTCACCATC
*
17835032 GTTTTCCCTTACCTCACCATC
1 GTTTTCCCTCACCTCACCATC
*
17835053 ATTTTCC
1 GTTTTCC
17835060 TTTTTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.14, C:0.41, G:0.04, T:0.41
Consensus pattern (21 bp):
GTTTTCCCTCACCTCACCATC
Found at i:17836056 original size:23 final size:22
Alignment explanation
Indices: 17836026--17836075 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
17836016 TTAAATATCG
17836026 TATCTAAAAAAAACCATCCATC
1 TATCTAAAAAAAACCATCCATC
*
17836048 ATATCTAAATAAAACCATCCATC
1 -TATCTAAAAAAAACCATCCATC
17836071 TATCT
1 TATCT
17836076 CCATGGCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (22 bp):
TATCTAAAAAAAACCATCCATC
Found at i:17836643 original size:14 final size:14
Alignment explanation
Indices: 17836624--17836692 Score: 68
Period size: 14 Copynumber: 4.8 Consensus size: 14
17836614 AATAAACATA
17836624 ACATACATAATTAT
1 ACATACATAATTAT
*
17836638 ACATACATAA-TAC
1 ACATACATAATTAT
* **
17836651 ATATAACAGTAAACAT
1 ACAT-ACA-TAATTAT
17836667 AACATACATAATTAT
1 -ACATACATAATTAT
17836682 ACATACATAAT
1 ACATACATAAT
17836693 ACATATAACA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
13 5 0.11
14 24 0.55
15 8 0.18
16 4 0.09
17 3 0.07
ACGTcount: A:0.54, C:0.16, G:0.01, T:0.29
Consensus pattern (14 bp):
ACATACATAATTAT
Found at i:17836664 original size:44 final size:44
Alignment explanation
Indices: 17836607--17836821 Score: 219
Period size: 44 Copynumber: 4.9 Consensus size: 44
17836597 AGACATACAA
*
17836607 ACATAACAATAAACATAACATACATAATTATACATACATAATAC
1 ACATAACAGTAAACATAACATACATAATTATACATACATAATAC
*
17836651 ATATAACAGTAAACATAACATACATAATTATACATACATAATAC
1 ACATAACAGTAAACATAACATACATAATTATACATACATAATAC
* * *
17836695 ATATAACAGTACACATTACATACATAA-TATACATAACATACATAC
1 ACATAACAGTAAACATAACATACATAATTATACAT-ACATA-ATAC
* *
17836740 AAATATAC---AAACATAACAGTAAACATAA-CATACATA-ATAATAC
1 ACATA-ACAGTAAACATAACA-T--ACATAATTATACATACATAATAC
* * * * *
17836783 ATA-CACAATATACATAACATACATAATTATACATGCATA
1 ACATAACAGTAAACATAACATACATAATTATACATACATA
17836822 CACAAACAGT
Statistics
Matches: 147, Mismatches: 13, Indels: 23
0.80 0.07 0.13
Matches are distributed among these distances:
41 8 0.05
42 6 0.04
43 25 0.17
44 85 0.58
45 9 0.06
46 14 0.10
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.26
Consensus pattern (44 bp):
ACATAACAGTAAACATAACATACATAATTATACATACATAATAC
Found at i:17836717 original size:23 final size:22
Alignment explanation
Indices: 17836618--17836807 Score: 157
Period size: 23 Copynumber: 8.5 Consensus size: 22
17836608 CATAACAATA
17836618 AACATAACATACATAATTATACAT
1 AACAT-ACATACATAA-TATACAT
17836642 -ACATA-ATACAT-ATA-ACAGT
1 AACATACATACATAATATACA-T
17836661 AAACATAACATACATAATTATACAT
1 -AACAT-ACATACATAA-TATACAT
17836686 -ACATA-ATACAT-ATA-ACAGT
1 AACATACATACATAATATACA-T
17836705 ACACATTACATACATAATATACAT
1 A-ACA-TACATACATAATATACAT
17836729 AACATACATACA-AATATACA-
1 AACATACATACATAATATACAT
*
17836749 AACATAACAGTAAACATAACATACAT
1 AACAT-ACA-T--ACATAATATACAT
* *
17836775 AATAATACATACACAATATACAT
1 AA-CATACATACATAATATACAT
17836798 AACATACATA
1 AACATACATA
17836808 ATTATACATG
Statistics
Matches: 139, Mismatches: 5, Indels: 46
0.73 0.03 0.24
Matches are distributed among these distances:
18 6 0.04
19 6 0.04
20 7 0.05
21 30 0.22
22 21 0.15
23 36 0.26
24 9 0.06
25 14 0.10
26 8 0.06
27 2 0.01
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (22 bp):
AACATACATACATAATATACAT
Found at i:17836724 original size:26 final size:23
Alignment explanation
Indices: 17836594--17836807 Score: 106
Period size: 23 Copynumber: 9.4 Consensus size: 23
17836584 CAAATTAATA
* *
17836594 AACAGACATACA-AACATAACAAT
1 AACATACATACATAATATAAC-AT
17836617 AAACATAACATACATAAT-TATACAT
1 -AACAT-ACATACATAATATA-ACAT
17836642 -ACATA-ATAC---ATATAACAGT
1 AACATACATACATAATATAACA-T
17836661 AAACATAACATACATAAT-TATACAT
1 -AACAT-ACATACATAATATA-ACAT
17836686 -ACATA-ATAC---ATATAACAGT
1 AACATACATACATAATATAACA-T
17836705 ACACATTACATACATAATAT-ACAT
1 A-ACA-TACATACATAATATAACAT
17836729 AACATACATACA-AATAT-ACA-
1 AACATACATACATAATATAACAT
*
17836749 AACATAACAGTAAACATAACAT-ACAT
1 AACAT-ACA-T--ACATAATATAACAT
* *
17836775 AATAATACATACACAATAT-ACAT
1 AA-CATACATACATAATATAACAT
17836798 AACATACATA
1 AACATACATA
17836808 ATTATACATG
Statistics
Matches: 154, Mismatches: 7, Indels: 60
0.70 0.03 0.27
Matches are distributed among these distances:
18 10 0.06
19 6 0.04
20 5 0.03
21 26 0.17
22 21 0.14
23 32 0.21
24 9 0.06
25 25 0.16
26 18 0.12
27 2 0.01
ACGTcount: A:0.56, C:0.18, G:0.02, T:0.24
Consensus pattern (23 bp):
AACATACATACATAATATAACAT
Found at i:17836770 original size:99 final size:96
Alignment explanation
Indices: 17836619--17836805 Score: 259
Period size: 99 Copynumber: 1.9 Consensus size: 96
17836609 ATAACAATAA
* * * *
17836619 ACATAACATACATAATTATACATACATAATACATATAACAGTAAACATAACATACATAATTATAC
1 ACATAACATACATAATCATACATACAAAATACACATAACAGTAAACATAACATACATAATAATAC
* *
17836684 ATACATAATACATATAACAGTACACATTACAT
66 ATACACAATACACATAACA-TACACATTACAT
*
17836716 ACATAATATACATAA-CATACATACAAATATACAAACATAACAGTAAACATAACATACATAATAA
1 ACATAACATACATAATCATACATACAAA-ATAC--ACATAACAGTAAACATAACATACATAATAA
*
17836780 TACATACACAATATACATAACATACA
63 TACATACACAATACACATAACATACA
17836806 TAATTATACA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
96 10 0.13
97 18 0.23
98 4 0.05
99 47 0.59
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (96 bp):
ACATAACATACATAATCATACATACAAAATACACATAACAGTAAACATAACATACATAATAATAC
ATACACAATACACATAACATACACATTACAT
Found at i:17836800 original size:32 final size:32
Alignment explanation
Indices: 17836669--17836816 Score: 122
Period size: 32 Copynumber: 4.5 Consensus size: 32
17836659 GTAAACATAA
* * * *
17836669 CATACATAATTATACATACATAATACATATAA
1 CATACATAATAATACATACACAATATACATAA
* *
17836701 CAGTACA-CAT--TACATACATAATATACATAA
1 CA-TACATAATAATACATACACAATATACATAA
* * * *
17836731 CATACATACAAATATACAAACATAACAGTAAACATAA
1 CATACATA-ATA-ATACATAC---ACAATATACATAA
17836768 CATACATAATAATACATACACAATATACATAA
1 CATACATAATAATACATACACAATATACATAA
*
17836800 CATACATAATTATACAT
1 CATACATAATAATACAT
17836817 GCATACACAA
Statistics
Matches: 93, Mismatches: 14, Indels: 18
0.74 0.11 0.14
Matches are distributed among these distances:
29 4 0.04
30 20 0.22
31 1 0.01
32 31 0.33
33 4 0.04
34 6 0.06
35 7 0.08
36 2 0.02
37 18 0.19
ACGTcount: A:0.54, C:0.18, G:0.01, T:0.26
Consensus pattern (32 bp):
CATACATAATAATACATACACAATATACATAA
Found at i:17836821 original size:18 final size:18
Alignment explanation
Indices: 17836707--17836826 Score: 92
Period size: 18 Copynumber: 6.8 Consensus size: 18
17836697 ATAACAGTAC
* *
17836707 ACATTACATACATAATAT
1 ACATAACATACACAATAT
17836725 ACATAACATACATACAAATAT
1 ACATAACATAC--AC-AATAT
* *
17836746 ACA-AACATA-ACAGTAA
1 ACATAACATACACAATAT
*
17836762 ACATAACATACA-TA-AT
1 ACATAACATACACAATAT
17836778 A-AT-ACATACACAATAT
1 ACATAACATACACAATAT
*
17836794 ACATAACATACATAATTAT
1 ACATAACATACACAA-TAT
*
17836813 ACAT-GCATACACAA
1 ACATAACATACACAA
17836827 ACAGTAGAGA
Statistics
Matches: 81, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
14 7 0.09
15 3 0.04
16 11 0.14
17 10 0.12
18 28 0.35
19 7 0.09
20 7 0.09
21 8 0.10
ACGTcount: A:0.55, C:0.19, G:0.02, T:0.24
Consensus pattern (18 bp):
ACATAACATACACAATAT
Found at i:17836967 original size:30 final size:30
Alignment explanation
Indices: 17836931--17836994 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
17836921 CAACAAAAAC
*
17836931 AAAAAATAAAAGTTAGATATAATACGAATT
1 AAAAAATAAAAGTTAGATATAATACGAAAT
* *
17836961 AAAAAATAAAAGTTATATATAATATGAAAT
1 AAAAAATAAAAGTTAGATATAATACGAAAT
17836991 AAAA
1 AAAA
17836995 CAATCAACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.27
Consensus pattern (30 bp):
AAAAAATAAAAGTTAGATATAATACGAAAT
Found at i:17838101 original size:20 final size:20
Alignment explanation
Indices: 17838051--17838112 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
17838041 GCGCTGGATT
* *
17838051 ATTTTTGTATATTAATATTA
1 ATTTTTGTTTAATAATATTA
* *
17838071 TAATATT-TTTAATAATATTA
1 -ATTTTTGTTTAATAATATTA
17838091 ATTTTTGTTTAA-AATTATTA
1 ATTTTTGTTTAATAA-TATTA
17838111 AT
1 AT
17838113 GAGTTGATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 6 0.18
20 23 0.70
21 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTTTGTTTAATAATATTA
Found at i:17841663 original size:22 final size:21
Alignment explanation
Indices: 17841633--17841683 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
17841623 TTATTTTAAA
*
17841633 TTTATTATATTTTTAAAAAATAT
1 TTTA-TATATATTT-AAAAATAT
*
17841656 TTTATATATATTTATAAATAT
1 TTTATATATATTTAAAAATAT
17841677 TTT-TATA
1 TTTATATA
17841684 AATATCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 10 0.38
22 8 0.31
23 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATATATATTTAAAAATAT
Found at i:17841676 original size:12 final size:12
Alignment explanation
Indices: 17841638--17841688 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
17841628 TTAAATTTAT
*
17841638 TATATTTTTAAAA
1 TATATTTAT-AAA
* *
17841651 AATATTT-TATA
1 TATATTTATAAA
17841662 TATATTTATAAA
1 TATATTTATAAA
*
17841674 TATTTTTATAAA
1 TATATTTATAAA
17841686 TAT
1 TAT
17841689 CAAATATGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 8 0.25
12 18 0.56
13 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATTTATAAA
Found at i:17842707 original size:22 final size:22
Alignment explanation
Indices: 17842660--17842707 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
17842650 TGATCTAAGG
* *
17842660 AAAAATAAAAGAAACTGAATTA
1 AAAAATAAAAGAAAATGAACTA
17842682 AAAAATAAAAGAAAATAGAACTA
1 AAAAATAAAAGAAAAT-GAACTA
17842705 AAA
1 AAA
17842708 GAAGTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATGAACTA
Found at i:17843546 original size:19 final size:19
Alignment explanation
Indices: 17843522--17843564 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17843512 AAATATAAAT
17843522 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
17843541 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
17843560 TAAAT
1 TAAAT
17843565 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:17844346 original size:104 final size:104
Alignment explanation
Indices: 17844134--17844346 Score: 263
Period size: 104 Copynumber: 2.1 Consensus size: 104
17844124 TTTATTTTGT
* *
17844134 GAATTTTTTCCTTTTTTTTTCTTTAAGAATACATTGGACCTTTTGACGCGAAATGAAATGACACC
1 GAATTTTTTCCTTTTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAAC
* **
17844199 CAAGCACTCCATCCCGGTTACTCAGCCCAACATGCTCTC
66 CAAGCACTCCACCCCGGTTACTCAGCCCAACACACTCTC
* * * *
17844238 -AATTTTTTTCTTCTCTCTTTTT-TTT-AGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGAC
1 GAATTTTTTCCTT-T-T-TTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGAC
* * *
17844300 AACCAAGCACTCCACCCCGGTTACTCAGTCTAACACATTC-C
63 AACCAAGCACTCCACCCCGGTTACTCAGCCCAACACACTCTC
17844341 GAATTT
1 GAATTT
17844347 ATTTATTATT
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
103 12 0.13
104 72 0.77
105 4 0.04
106 5 0.05
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (104 bp):
GAATTTTTTCCTTTTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAAC
CAAGCACTCCACCCCGGTTACTCAGCCCAACACACTCTC
Found at i:17845023 original size:4 final size:4
Alignment explanation
Indices: 17845014--17845067 Score: 53
Period size: 4 Copynumber: 13.8 Consensus size: 4
17845004 TCCTGGACAA
17845014 AAAT AAAT AAAT AAAT AAAT AAAAT AAGAT AGAA- AAAT -AA- AAAT AAA-
1 AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT
17845061 AAAT AAA
1 AAAT AAA
17845068 AATAATTGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
3 9 0.21
4 25 0.58
5 8 0.19
6 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:17845069 original size:13 final size:13
Alignment explanation
Indices: 17845012--17845072 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
17845002 TTTCCTGGAC
17845012 AAAAATAAATAAAT
1 AAAAATAAA-AAAT
*
17845026 AAATAA-ATAAAAT
1 AAA-AATAAAAAAT
*
17845039 -AAGATAGAAAAAT
1 AAAAATA-AAAAAT
17845052 AAAAATAAAAAAT
1 AAAAATAAAAAAT
17845065 AAAAATAA
1 AAAAATAA
17845073 TTGGGTTGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
11 1 0.03
12 3 0.08
13 23 0.59
14 10 0.26
15 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:17849142 original size:21 final size:21
Alignment explanation
Indices: 17849112--17849161 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
17849102 TAGATGCCTC
*
17849112 AGTTTTCTTTTGAAAATCCAT
1 AGTTTGCTTTTGAAAATCCAT
* *
17849133 AGTTTGCTTTTGGAAATCTAT
1 AGTTTGCTTTTGAAAATCCAT
*
17849154 AGATTGCT
1 AGTTTGCT
17849162 GCTGAAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (21 bp):
AGTTTGCTTTTGAAAATCCAT
Found at i:17850747 original size:22 final size:22
Alignment explanation
Indices: 17850700--17850747 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
17850690 TGATCTAAGG
* *
17850700 AAAAATAAAAGAAACTGAATTA
1 AAAAATAAAAGAAAATGAACTA
17850722 AAAAATAAAAGAAAATAGAACTA
1 AAAAATAAAAGAAAAT-GAACTA
17850745 AAA
1 AAA
17850748 GAAGTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATGAACTA
Found at i:17851583 original size:19 final size:19
Alignment explanation
Indices: 17851559--17851601 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17851549 AAATATAAAT
17851559 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
17851578 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
17851597 TAAAT
1 TAAAT
17851602 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:17854958 original size:32 final size:32
Alignment explanation
Indices: 17854919--17854979 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
17854909 GCAAAAGAAA
17854919 TTCTTAGTGAGATAGGAAATTAGAAACTCGTC
1 TTCTTAGTGAGATAGGAAATTAGAAACTCGTC
17854951 TTCTTAGTGAGATAGGAAATTAGAAACTC
1 TTCTTAGTGAGATAGGAAATTAGAAACTC
17854980 ATCTAGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (32 bp):
TTCTTAGTGAGATAGGAAATTAGAAACTCGTC
Found at i:17860605 original size:24 final size:24
Alignment explanation
Indices: 17860536--17860605 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
17860526 AATAATTAAC
17860536 AAATACTATATAATTTAGTTGAAAT
1 AAATACTATATAATTTAGTT-AAAT
* * *
17860561 TAGTA-TAAATAATTTA--T-AAT
1 AAATACTATATAATTTAGTTAAAT
*
17860581 AAATACTATGTAATTTAGTTAAAT
1 AAATACTATATAATTTAGTTAAAT
17860605 A
1 A
17860606 TTTAGTAAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 9
0.68 0.14 0.18
Matches are distributed among these distances:
20 6 0.18
21 9 0.26
22 1 0.03
23 1 0.03
24 14 0.41
25 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (24 bp):
AAATACTATATAATTTAGTTAAAT
Found at i:17870836 original size:28 final size:28
Alignment explanation
Indices: 17870776--17870862 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
17870766 GGACATTTTT
*
17870776 TATTTGAAATTAATTAAGTTTATGAA--TG
1 TATTTGAAATTAATTATGTTTA--AATTTG
*
17870804 AATTTGAAATTAATTATGTTTAAATTTG
1 TATTTGAAATTAATTATGTTTAAATTTG
* * **
17870832 TATTT--AATTAATAATTTTTATGTTTG
1 TATTTGAAATTAATTATGTTTAAATTTG
17870858 TATTT
1 TATTT
17870863 TGGTTTAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
26 24 0.48
28 26 0.52
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (28 bp):
TATTTGAAATTAATTATGTTTAAATTTG
Found at i:17870851 original size:26 final size:26
Alignment explanation
Indices: 17870811--17870862 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
17870801 ATGAATTTGA
*
17870811 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
17870837 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
17870863 TGGTTTAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:17871101 original size:15 final size:15
Alignment explanation
Indices: 17871076--17871122 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
17871066 GAGTTTAAAA
*
17871076 TTTAGGGTTTAAGGT
1 TTTAGGATTTAAGGT
* *
17871091 TTTATGATTTAAGAT
1 TTTAGGATTTAAGGT
*
17871106 TTTAGGGTTTAAGGT
1 TTTAGGATTTAAGGT
17871121 TT
1 TT
17871123 AATTTATGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (15 bp):
TTTAGGATTTAAGGT
Found at i:17872432 original size:41 final size:41
Alignment explanation
Indices: 17872324--17872625 Score: 290
Period size: 41 Copynumber: 7.3 Consensus size: 41
17872314 AATGTAAAGC
** * * * *
17872324 ATTAGCGGCGC-TTAACAAAAGCGTCGCTAAAGGTCTGGTC
1 ATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCAGGTA
* **
17872364 ATTAACGGCGCTATAACCACAAGCGCCGCTAAAGGTCAGGTA
1 ATTAGCGGCGCT-TTCCCACAAGCGCCGCTAAAGGTCAGGTA
** **
17872406 ATTAGCAACGCTTTATCACAAGCGCCGCTAAAGGTCAGGTA
1 ATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCAGGTA
*
17872447 ATTAGCGGCGCTTTCTCA-AATGCGCCGCTAAAGGT-AGGGTA
1 ATTAGCGGCGCTTTCCCACAA-GCGCCGCTAAAGGTCA-GGTA
* *
17872488 ATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCAGGTC
1 ATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCAGGTA
17872529 ATTAGCGGCGCTTTCCCTA-AAGCGCCGCTAAAGGT-AGGATCA
1 ATTAGCGGCGCTTTCCC-ACAAGCGCCGCTAAAGGTCAGG-T-A
* **** * * * *
17872571 TTTAGCGGCGCTTTCATTTAAGCGCCACTAAAGTTCGGGTC
1 ATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCAGGTA
17872612 ATTAGCGGCGCTTT
1 ATTAGCGGCGCTTT
17872626 TATAATAAGC
Statistics
Matches: 222, Mismatches: 29, Indels: 21
0.82 0.11 0.08
Matches are distributed among these distances:
40 16 0.07
41 140 0.63
42 64 0.29
43 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCAGGTA
Found at i:17872612 original size:83 final size:82
Alignment explanation
Indices: 17872263--17872625 Score: 335
Period size: 82 Copynumber: 4.4 Consensus size: 82
17872253 TTTGGAAATA
* * * * ** * * * **
17872263 AAGCGCCGCAAAAGGTAAAG-CATTAGCGGCGCTTTTCTTAATGCGCCGCAAAATGTA-AAGCAT
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAAATGCGCCGCTAAAGGTAGGATAAT
* **
17872326 TAGCGGCGC-TTAACAA
66 TAGCGGCGCTTTCACTC
* * * **
17872342 AAGCGTCGCTAAAGGTCTGGTCATTAACGGCGCTATAACCACAA-GCGCCGCTAAAGGTCAGG-T
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCT-TTCCCA-AATGCGCCGCTAAAGGT-AGGAT
** *
17872405 AATTAGCAACGCTTT-ATCAC
63 AATTAGCGGCGCTTTCA-CTC
* * *
17872425 AAGCGCCGCTAAAGGTCAGGTAATTAGCGGCGCTTTCTCAAATGCGCCGCTAAAGGTAGGGTAAT
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAAATGCGCCGCTAAAGGTAGGATAAT
*
17872490 TAGCGGCGCTTTCCCTC
66 TAGCGGCGCTTTCACTC
17872507 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCTAAA-GCGCCGCTAAAGGTAGGATCA
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCC-AAATGCGCCGCTAAAGGTAGGAT-A
* * *
17872571 TTTAGCGGCGCTTTCATTT
64 ATTAGCGGCGCTTTCACTC
* * *
17872590 AAGCGCCACTAAAGTTCGGGTCATTAGCGGCGCTTT
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTT
17872626 TATAATAAGC
Statistics
Matches: 233, Mismatches: 39, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
79 15 0.06
80 12 0.05
81 19 0.08
82 101 0.43
83 86 0.37
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.23
Consensus pattern (82 bp):
AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAAATGCGCCGCTAAAGGTAGGATAAT
TAGCGGCGCTTTCACTC
Found at i:17875002 original size:49 final size:49
Alignment explanation
Indices: 17874959--17875670 Score: 585
Period size: 49 Copynumber: 14.2 Consensus size: 49
17874949 AAGTATCCTT
17874959 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * *
17875008 GTATATTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAA
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * * * *
17875056 GTATATTAATTTAAAAGATATAATTATTTAATTGTATTAAACTAAATAA
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * * ** * *
17875105 TTATATTAAATTATTTAATCATG-TTTAATTATGTATTTA-ATTATAAACACTATCGA
1 TTATATTAAGTTA---AA--A-GATTTAATTATTTAATTATATTA-AAGTA-AAT-AA
* ** *
17875161 TTA-ATTAAATATTTAAG-TTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
1 TTATATTAAGT-TAAAAGATT--TA-A-TT-ATT---TAATTATATTAAAGTAAATAA
*
17875217 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAACTAA
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
*
17875266 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * **
17875315 GTATATTAAATT-AATTATTTAATTATTTAATTATATTAAAGTAAATAA
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * * * *
17875363 GTATATTAATTTAAAAGATATAATTATTTAATTGTATTAAACTAAATAA
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * * * * *
17875412 TTATATTAAATTATTTAATCATG-TTTAATTATGTATTTAATTATAAACACTACCGATTAA
1 TTATATTAAGTTA---AA--A-GATTTAATTATTTAATT-A-TATTAA-AGTA---AATAA
* *
17875472 TTAAATATTTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAACTAA
1 TT--ATA-TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * ** *
17875524 TTATATCAAGTTGAAAGATTTAATTATTTAATTATATTAAAGTATCCT-T
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTA-AATAA
*
17875573 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTTAATAA
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* *
17875622 --GTA-T-A-TT--AA-A-TTAATTATTTAATTATATTAAGGTAAATAA
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
17875662 TTATATTAA
1 TTATATTAA
17875671 ATTATTTAAT
Statistics
Matches: 545, Mismatches: 73, Indels: 95
0.76 0.10 0.13
Matches are distributed among these distances:
40 28 0.05
41 1 0.00
42 4 0.01
43 1 0.00
44 3 0.01
45 1 0.00
46 1 0.00
47 2 0.00
48 92 0.17
49 250 0.46
50 8 0.01
51 1 0.00
52 14 0.03
53 8 0.01
54 32 0.06
55 17 0.03
56 23 0.04
57 15 0.03
58 22 0.04
59 4 0.01
60 8 0.01
62 3 0.01
63 7 0.01
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (49 bp):
TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
Found at i:17875123 original size:18 final size:18
Alignment explanation
Indices: 17874980--17875692 Score: 143
Period size: 18 Copynumber: 41.3 Consensus size: 18
17874970 TAAAAGATTT
17874980 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* ** *
17874998 AAGTAAATAAGTATATTA
1 AATTATTTAATTATATTA
17875016 AATTA---AA-TAT-TT-
1 AATTATTTAATTATATTA
17875028 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* ** *
17875046 AAGTAAATAAGTATATT-
1 AATTATTTAATTATATTA
* **
17875063 AA-T-TTAAAAGATA-T-
1 AATTATTTAATTATATTA
*
17875077 AATTATTTAATTGTATTA
1 AATTATTTAATTATATTA
* **
17875095 AACTAAATAATTATATTA
1 AATTATTTAATTATATTA
* *
17875113 AATTATTTAATCATGTTTA
1 AATTATTTAATTAT-ATTA
17875132 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* **
17875151 ACACTA-TCGATTA-ATTA
1 A-ATTATTTAATTATATTA
* *
17875168 AA-TATTTAAGTTAAAAGATTT
1 AATTATTTAA-TT---ATATTA
17875189 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
17875207 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* * *
17875225 AGTTA---AA--AGATTT
1 AATTATTTAATTATATTA
17875238 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
17875256 AAGTAACTAATTATATTA
1 AATTATTTAATTATATTA
* *
17875274 AATTA---AA--AGATTT
1 AATTATTTAATTATATTA
17875287 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* ** *
17875305 AAGTAAATAAGTATATT-
1 AATTATTTAATTATATTA
17875322 AA--A-TTAATTAT-TT-
1 AATTATTTAATTATATTA
17875335 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* ** *
17875353 AAGTAAATAAGTATATT-
1 AATTATTTAATTATATTA
* **
17875370 AA-T-TTAAAAGATA-T-
1 AATTATTTAATTATATTA
*
17875384 AATTATTTAATTGTATTA
1 AATTATTTAATTATATTA
* **
17875402 AACTAAATAATTATATTA
1 AATTATTTAATTATATTA
* *
17875420 AATTATTTAATCATGTTTA
1 AATTATTTAATTAT-ATTA
17875439 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* ***
17875458 ACACTA-CCGATTA-ATTA
1 A-ATTATTTAATTATATTA
* *
17875475 AA-TATTTAAGTTAAAAAATTT
1 AATTATTTAA-TT---ATATTA
17875496 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* ** *
17875514 AAGTAACTAATTATATCA
1 AATTATTTAATTATATTA
* *
17875532 AGTTGA---AA-GAT-TT-
1 AATT-ATTTAATTATATTA
17875545 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
*
17875563 AAGTATCCTT--TTATATTA
1 AATTAT--TTAATTATATTA
* * *
17875581 AGTTA---AA--AGATTT
1 AATTATTTAATTATATTA
17875594 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* *
17875612 AAGTTA-ATAAGTATATTAAA
1 AA-TTATTTAATTATATT--A
17875632 TTAATTATTTAATTATATTA
1 --AATTATTTAATTATATTA
** **
17875652 AGGTAAATAATTATATTA
1 AATTATTTAATTATATTA
*
17875670 AATTATTTAATTATATTT
1 AATTATTTAATTATATTA
17875688 AATTA
1 AATTA
17875693 ACTATTTAAC
Statistics
Matches: 490, Mismatches: 128, Indels: 154
0.63 0.17 0.20
Matches are distributed among these distances:
12 6 0.01
13 34 0.07
14 16 0.03
15 32 0.07
16 49 0.10
17 26 0.05
18 239 0.49
19 16 0.03
20 6 0.01
21 21 0.04
22 45 0.09
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
AATTATTTAATTATATTA
Found at i:17875201 original size:161 final size:160
Alignment explanation
Indices: 17875024--17875564 Score: 743
Period size: 161 Copynumber: 3.5 Consensus size: 160
17875014 TAAATTAAAT
*
17875024 ATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAATT
1 ATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATATAATTATTTAATT
*
17875089 GTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACA
66 ATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACA
*
17875154 CTATCGATTAATTAAATATTTAAGTTAAAAG
131 CTA-CGATTAATTAAATATTTAAGTTAAAAA
* *
17875185 ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATT
1 ATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATATAATTATTTAATT
* * * * *
17875250 ATATTAAAGTAACTAATTATATTAAATTA---AA--A-GATTTAATTATTTAATT-A-TATTAA-
66 ATATTAAACTAAATAATTATATTAAATTATTTAATCATG-TTTAATTATGTATTTAATTATAAAC
* * * * **
17875306 AGTA--AATAAGT--ATA-TTAAATT-AATT
130 ACTACGATTAATTAAATATTTAAGTTAAAAA
*
17875331 ATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAATT
1 ATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATATAATTATTTAATT
*
17875396 GTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACA
66 ATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACA
17875461 CTACCGATTAATTAAATATTTAAGTTAAAAA
131 CTA-CGATTAATTAAATATTTAAGTTAAAAA
* * * * *
17875492 ATTTAATTATTTAATTATATTAAAGTAACTAATTATATCAAGTTGAAAGATTTAATTATTTAATT
1 ATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATATAATTATTTAATT
17875557 ATATTAAA
66 ATATTAAA
17875565 GTATCCTTTT
Statistics
Matches: 326, Mismatches: 37, Indels: 34
0.82 0.09 0.09
Matches are distributed among these distances:
146 90 0.28
147 6 0.02
148 3 0.01
149 2 0.01
150 5 0.02
151 14 0.04
152 2 0.01
153 8 0.02
154 8 0.02
155 2 0.01
156 14 0.04
157 5 0.02
158 2 0.01
159 3 0.01
160 6 0.02
161 156 0.48
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (160 bp):
ATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATATAATTATTTAATT
ATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACA
CTACGATTAATTAAATATTTAAGTTAAAAA
Found at i:17875247 original size:8 final size:8
Alignment explanation
Indices: 17875234--17875353 Score: 52
Period size: 8 Copynumber: 14.8 Consensus size: 8
17875224 AAGTTAAAAG
17875234 ATTTAATT
1 ATTTAATT
17875242 ATTTAATT
1 ATTTAATT
*
17875250 ATATTAAAGT
1 AT-TT-AATT
**
17875260 AACTAATT
1 ATTTAATT
17875268 ATATTAA--
1 AT-TTAATT
* **
17875275 ATTAAAAG
1 ATTTAATT
17875283 ATTTAATT
1 ATTTAATT
17875291 ATTTAATT
1 ATTTAATT
*
17875299 ATATTAAAGT
1 AT-TT-AATT
** *
17875309 AAATAAGT
1 ATTTAATT
17875317 ATATTAA--
1 AT-TTAATT
17875324 A-TTAATT
1 ATTTAATT
17875331 ATTTAATT
1 ATTTAATT
17875339 ATTTAATT
1 ATTTAATT
17875347 ATATTAA
1 AT-TTAA
17875354 AGTAAATAAG
Statistics
Matches: 85, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
5 4 0.05
6 3 0.04
7 4 0.05
8 50 0.59
9 16 0.19
10 8 0.09
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (8 bp):
ATTTAATT
Found at i:17875513 original size:307 final size:307
Alignment explanation
Indices: 17874949--17875652 Score: 1275
Period size: 307 Copynumber: 2.3 Consensus size: 307
17874939 AAACTTAAAT
* *
17874949 AAGTATCCTTTTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATAT
1 AAGTATACTATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATAT
*
17875014 TAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAA
66 TAAATTAATTATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAA
17875079 TTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTA
131 TTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTA
* *
17875144 ATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAA
196 ATTATAAACACTACCGATTAATTAAATATTTAAGTTAAAAAATTTAATTATTTAATTATATTAAA
*
17875209 GTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTA
261 GTAAATAATTATATCAAGTTAAAAGATTTAATTATTTAATTATATTA
*
17875256 AAGTA-ACTAATTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATA
1 AAGTATACT-ATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATA
17875320 TTAAATTAATTATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATA
65 TTAAATTAATTATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATA
17875385 ATTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTT
130 ATTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTT
17875450 AATTATAAACACTACCGATTAATTAAATATTTAAGTTAAAAAATTTAATTATTTAATTATATTAA
195 AATTATAAACACTACCGATTAATTAAATATTTAAGTTAAAAAATTTAATTATTTAATTATATTAA
* *
17875515 AGTAACTAATTATATCAAGTTGAAAGATTTAATTATTTAATTATATTA
260 AGTAAATAATTATATCAAGTTAAAAGATTTAATTATTTAATTATATTA
* * *
17875563 AAGTATCCTTTTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTTAATAAGTATAT
1 AAGTATACTATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATAT
17875628 TAAATTAATTATTTAATTATATTAA
66 TAAATTAATTATTTAATTAT-TTAA
17875653 GGTAAATAAT
Statistics
Matches: 381, Mismatches: 13, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
306 2 0.01
307 373 0.98
308 6 0.02
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (307 bp):
AAGTATACTATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATAT
TAAATTAATTATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAA
TTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTA
ATTATAAACACTACCGATTAATTAAATATTTAAGTTAAAAAATTTAATTATTTAATTATATTAAA
GTAAATAATTATATCAAGTTAAAAGATTTAATTATTTAATTATATTA
Found at i:17875636 original size:40 final size:40
Alignment explanation
Indices: 17875592--17875674 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
17875582 GTTAAAAGAT
*
17875592 TTAATTATTTAATTATATTAAAGTTAATAAGTATATTAAA
1 TTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAA
* *
17875632 TTAATTATTTAATTATATTAAGGTAAATAATTATATTAAA
1 TTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAA
17875672 TTA
1 TTA
17875675 TTTAATTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (40 bp):
TTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAA
Found at i:17875665 original size:210 final size:209
Alignment explanation
Indices: 17875271--17875666 Score: 510
Period size: 210 Copynumber: 1.9 Consensus size: 209
17875261 ACTAATTATA
* * **
17875271 TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAATTAATTATTTA
1 TTAAATTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAAGTATATCAAATTAAAGATTTA
* *
17875336 ATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAATTGTATT
66 ATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATATAATTATTTAATTATATT
* * * * * **
17875401 AAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTACC
131 AAACTAAATAAGTATATTAAATTAATTAATAATGTATAATTAGGTAAATAATTATAAACACTACC
17875466 GATTAATTAAATAT
196 GATTAATTAAATAT
* * * *
17875480 TTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAACTAATTATATCAAGTTGAAAGATTT
1 TTAAATTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAAGTATATCAAATT-AAAGATTT
** ** *
17875545 AATTATTTAATTATATTAAAGTATCCT-TTTATATTAAGTTAAAAGATTTAATTATTTAATTATA
65 AATTATTTAATTATATTAAAGTA-AATAAGTATATTAAGTTAAAAGATATAATTATTTAATTATA
* * *
17875609 TTAAAGTTAATAAGTATATTAAATTAATTATTTAAT-TAT-ATTAAGGTAAATAATTATA
129 TTAAACTAAATAAGTATATTAAATTAATTA-ATAATGTATAATT-AGGTAAATAATTATA
17875667 TTAAATTATT
Statistics
Matches: 158, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
209 53 0.34
210 101 0.64
211 4 0.03
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (209 bp):
TTAAATTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAAGTATATCAAATTAAAGATTTA
ATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATATAATTATTTAATTATATT
AAACTAAATAAGTATATTAAATTAATTAATAATGTATAATTAGGTAAATAATTATAAACACTACC
GATTAATTAAATAT
Found at i:17875681 original size:36 final size:38
Alignment explanation
Indices: 17875593--17875686 Score: 129
Period size: 40 Copynumber: 2.5 Consensus size: 38
17875583 TTAAAAGATT
*
17875593 TAATTATTTAATTATATTAAAGTTAATAAGTATATTAAA
1 TAATTATTTAATTATATTAAAGTAAATAAGTATATT-AA
* *
17875632 TTAATTATTTAATTATATTAAGGTAAATAATTATATT-A
1 -TAATTATTTAATTATATTAAAGTAAATAAGTATATTAA
17875670 -AATTATTTAATTATATT
1 TAATTATTTAATTATATT
17875687 TAATTAACTA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 17 0.33
38 1 0.02
40 33 0.65
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (38 bp):
TAATTATTTAATTATATTAAAGTAAATAAGTATATTAA
Found at i:17875707 original size:36 final size:36
Alignment explanation
Indices: 17875594--17875707 Score: 108
Period size: 36 Copynumber: 3.1 Consensus size: 36
17875584 TAAAAGATTT
*
17875594 AATTATTTAATTATATTAAAGTTAATAAGTATATTAAATT-
1 AATTATTTAATTATATTTAAGTT-A-AA-TAT-TT-AATTA
* *
17875634 AATTATTTAATTATA-TTAAGGTAAATAATTATATTA
1 AATTATTTAATTATATTTAAGTTAAATATTTA-ATTA
*
17875670 AATTATTTAATTATATTTAA-TTAACTATTTAACTTA
1 AATTATTTAATTATATTTAAGTTAAATATTTAA-TTA
17875706 AA
1 AA
17875708 ATGTGGTCGT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
34 1 0.02
35 6 0.09
36 30 0.47
37 6 0.09
38 1 0.02
39 5 0.08
40 15 0.23
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (36 bp):
AATTATTTAATTATATTTAAGTTAAATATTTAATTA
Found at i:17875757 original size:8 final size:8
Alignment explanation
Indices: 17875721--17875814 Score: 65
Period size: 8 Copynumber: 11.8 Consensus size: 8
17875711 TGGTCGTAAA
17875721 TAATTATAT
1 TAATTAT-T
17875730 ATAATTATT
1 -TAATTATT
17875739 TAAGCTTATT
1 TAA--TTATT
17875749 TAATTATT
1 TAATTATT
17875757 TAATTGA--
1 TAATT-ATT
**
17875764 -AAAGATT
1 TAATTATT
17875771 TAATTATT
1 TAATTATT
17875779 TAATTATAT
1 TAATTAT-T
17875788 TAA--A-T
1 TAATTATT
*
17875793 TAAATATT
1 TAATTATT
17875801 TAATTATT
1 TAATTATT
17875809 TAATTA
1 TAATTA
17875815 ATAAAAACAG
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
5 5 0.07
6 2 0.03
7 2 0.03
8 39 0.57
9 6 0.09
10 15 0.22
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (8 bp):
TAATTATT
Found at i:17875780 original size:30 final size:30
Alignment explanation
Indices: 17875744--17875814 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
17875734 TTATTTAAGC
17875744 TTATTTAATTAT-TT-AATTGAAAAGATTTAA
1 TTATTTAATTATATTAAATT--AAAGATTTAA
*
17875774 TTATTTAATTATATTAAATTAAATATTTAA
1 TTATTTAATTATATTAAATTAAAGATTTAA
17875804 TTATTTAATTA
1 TTATTTAATTA
17875815 ATAAAAACAG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
30 32 0.84
31 2 0.05
32 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TTATTTAATTATATTAAATTAAAGATTTAA
Found at i:17881438 original size:66 final size:66
Alignment explanation
Indices: 17881332--17881488 Score: 226
Period size: 66 Copynumber: 2.4 Consensus size: 66
17881322 CAAATTGCTC
*
17881332 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
17881396 AA
65 AA
* * *
17881398 AACTTAAAGAGGAGGTTGCAATGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
17881463 C
66 A
* * *
17881464 AACTTAAAGTGGAGGCAGCAGCGAG
1 AACTTAAAGAGGAGGCTGCAACGAG
17881489 GCAAGCCGAG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 1 0.01
66 79 0.99
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.15
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:17881504 original size:21 final size:21
Alignment explanation
Indices: 17881475--17881515 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17881465 ACTTAAAGTG
*
17881475 GAGGCAGCAGCGAGGCAAGCC
1 GAGGCAGCAGCAAGGCAAGCC
*
17881496 GAGGTAGCAGCAAGGCAAGC
1 GAGGCAGCAGCAAGGCAAGC
17881516 GAAGGAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.41, T:0.02
Consensus pattern (21 bp):
GAGGCAGCAGCAAGGCAAGCC
Found at i:17881525 original size:21 final size:21
Alignment explanation
Indices: 17881475--17881526 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
17881465 ACTTAAAGTG
* *
17881475 GAGGCAGCAGCGAGGCAAGCC
1 GAGGAAGCAGCAAGGCAAGCC
*
17881496 GAGGTAGCAGCAAGGCAAG-C
1 GAGGAAGCAGCAAGGCAAGCC
17881516 GAAGGAAGCAG
1 G-AGGAAGCAG
17881527 AGGCTACAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.35, C:0.21, G:0.42, T:0.02
Consensus pattern (21 bp):
GAGGAAGCAGCAAGGCAAGCC
Found at i:17881877 original size:43 final size:43
Alignment explanation
Indices: 17881812--17882122 Score: 451
Period size: 43 Copynumber: 7.2 Consensus size: 43
17881802 CTGTTATATT
* * *
17881812 AGCGGCGCTTTTGGATAAAGCGCTGCTAAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
* *
17881855 AGCAGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
* * * * *
17881898 AGCGACGCTTGTGGAGAAAGCGCCGCTGAAGAACATAGCATTC
1 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
*
17881941 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGGCTTC
1 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
*
17881984 AGCGGCGCTTGTGGAAAAAGCACCGCTAAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
*
17882027 AGCGGAGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
* * * ** *
17882070 AGCGGCGCTTATGGGAAAAGCGCCGCTAAAGACCATGTTCTTT
1 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
17882113 AGCGGCGCTT
1 AGCGGCGCTT
17882123 TTTGGCATAA
Statistics
Matches: 242, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 242 1.00
ACGTcount: A:0.28, C:0.24, G:0.30, T:0.18
Consensus pattern (43 bp):
AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
Found at i:17883591 original size:3 final size:3
Alignment explanation
Indices: 17883583--17883620 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
17883573 TAGATATTTG
17883583 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
17883621 GTTTAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17884032 original size:21 final size:21
Alignment explanation
Indices: 17884007--17884046 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17883997 TACTTACTAC
17884007 TACTAACAAAATAAAATTACT
1 TACTAACAAAATAAAATTACT
*
17884028 TACTAACAAAATTAAATTA
1 TACTAACAAAATAAAATTA
17884047 AAAATAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
TACTAACAAAATAAAATTACT
Found at i:17884116 original size:11 final size:12
Alignment explanation
Indices: 17884095--17884137 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
17884085 TTACTCAACT
17884095 AAATAAAAAATC
1 AAATAAAAAATC
* *
17884107 AAATAAAAATTA
1 AAATAAAAAATC
*
17884119 AAATAAACAAAAC
1 AAATAAA-AAATC
17884132 AAATAA
1 AAATAA
17884138 CTTAAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATAAAAAATC
Found at i:17884189 original size:24 final size:24
Alignment explanation
Indices: 17884160--17884249 Score: 114
Period size: 24 Copynumber: 3.9 Consensus size: 24
17884150 ATTACTAAAC
17884160 AAAATATAACTTTAAATTACCAAT
1 AAAATATAACTTTAAATTACCAAT
17884184 AAAATATAACTTTAAATTACC--T
1 AAAATATAACTTTAAATTACCAAT
**** *
17884206 TTCTTTTAA-TTTAAATTACCAAT
1 AAAATATAACTTTAAATTACCAAT
17884229 AAAATATAACTTTAAATTACC
1 AAAATATAACTTTAAATTACC
17884250 TTTCTTTTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 11 0.21
22 5 0.09
23 5 0.09
24 32 0.60
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATATAACTTTAAATTACCAAT
Found at i:17884221 original size:45 final size:45
Alignment explanation
Indices: 17884170--17884259 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
17884160 AAAATATAAC
17884170 TTTAAATTACCAATAAAATATAACTTTAAATTACCTTTCTTTTAA
1 TTTAAATTACCAATAAAATATAACTTTAAATTACCTTTCTTTTAA
17884215 TTTAAATTACCAATAAAATATAACTTTAAATTACCTTTCTTTTAA
1 TTTAAATTACCAATAAAATATAACTTTAAATTACCTTTCTTTTAA
17884260 CCTTTTTATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (45 bp):
TTTAAATTACCAATAAAATATAACTTTAAATTACCTTTCTTTTAA
Found at i:17887374 original size:20 final size:22
Alignment explanation
Indices: 17887340--17887379 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
17887330 ACTTAATCCC
*
17887340 TCTACTTTTTGAATT-TATAAA
1 TCTACTTTTTAAATTATATAAA
17887361 TCTA-TTTTTAAATTATATA
1 TCTACTTTTTAAATTATATA
17887380 TAACCACGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (22 bp):
TCTACTTTTTAAATTATATAAA
Found at i:17889428 original size:19 final size:19
Alignment explanation
Indices: 17889404--17889441 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17889394 TAATAGGGTC
17889404 ATTCTTAGTGAAAAGTGCA
1 ATTCTTAGTGAAAAGTGCA
17889423 ATTCTTAGTGAAAAGTGCA
1 ATTCTTAGTGAAAAGTGCA
17889442 TATTGGATGA
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:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
ATTCTTAGTGAAAAGTGCA
Found at i:17891127 original size:6 final size:6
Alignment explanation
Indices: 17891116--17891218 Score: 124
Period size: 6 Copynumber: 17.3 Consensus size: 6
17891106 AATTGATTTT
17891116 ATTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
17891164 CTTTAA ATTTAA ATTTAA ATTT-A CTTTAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
17891211 ATTAAA AT
1 ATTTAA AT
17891219 ACTAAACATT
Statistics
Matches: 85, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
4 2 0.02
5 10 0.12
6 65 0.76
7 2 0.02
8 6 0.07
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Done.