Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 16 of 26
Found at i:2155296 original size:2 final size:2
Alignment explanation
Indices: 2155289--2155321 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2155279 TCTTTCTATT
2155289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2155322 CAATTTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2156039 original size:2 final size:2
Alignment explanation
Indices: 2156032--2156063 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2156022 CGCAAAGAAA
2156032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2156064 TGGATCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2157468 original size:2 final size:2
Alignment explanation
Indices: 2157461--2157486 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2157451 CGAGCATTTG
2157461 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2157487 GACCTCAAAC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2158071 original size:11 final size:11
Alignment explanation
Indices: 2158055--2158079 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2158045 TCTTCTTCCC
2158055 TTTTTTTTTAT
1 TTTTTTTTTAT
2158066 TTTTTTTTTAT
1 TTTTTTTTTAT
2158077 TTT
1 TTT
2158080 CACTTACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTAT
Found at i:2161222 original size:1 final size:1
Alignment explanation
Indices: 2161216--2161240 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2161206 GAATCAACTG
2161216 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2161241 CCCTAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2165816 original size:2 final size:2
Alignment explanation
Indices: 2165809--2165833 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2165799 GAAAGACTTC
2165809 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2165834 GAAAATACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2174427 original size:2 final size:2
Alignment explanation
Indices: 2174420--2174461 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2174410 CCTTAATTCC
2174420 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2174462 ACCTTCACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2175798 original size:16 final size:17
Alignment explanation
Indices: 2175756--2175805 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
2175746 ATTATTCGAA
**
2175756 TTAAATTTTATTTTTAT
1 TTAAATTTTATTAATAT
*
2175773 TTAATTTTTTATTAAT-T
1 TTAA-ATTTTATTAATAT
2175790 TTAAATTTTA-TAATAT
1 TTAAATTTTATTAATAT
2175806 AAATATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 4 0.15
16 6 0.22
17 9 0.33
18 8 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAAATTTTATTAATAT
Found at i:2177176 original size:19 final size:18
Alignment explanation
Indices: 2177134--2177192 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
2177124 ATTAAATAAA
* *
2177134 ATTTTATA-TATTCATAT
1 ATTTTATATTTTTAATAT
2177151 A-TTTATATTTTTAATATT
1 ATTTTATATTTTTAATA-T
*
2177169 ATTTTATATTTTTATTAT
1 ATTTTATATTTTTAATAT
2177187 ATTTTA
1 ATTTTA
2177193 ATAATTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.17
17 7 0.19
18 9 0.25
19 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTATATTTTTAATAT
Found at i:2177441 original size:30 final size:30
Alignment explanation
Indices: 2177400--2177473 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
2177390 GATTTAATAT
2177400 TAAAATTTTAATATTTAATTT-ATAATCAAA
1 TAAAATTTTAATATTTAATTTCA-AATCAAA
* * * *
2177430 TAAATTTTTAATTTTTAATTTCAATTCATA
1 TAAAATTTTAATATTTAATTTCAAATCAAA
2177460 TAAAATTTTAATAT
1 TAAAATTTTAATAT
2177474 AAATTAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
TAAAATTTTAATATTTAATTTCAAATCAAA
Found at i:2177505 original size:16 final size:15
Alignment explanation
Indices: 2177479--2177518 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
2177469 AATATAAATT
*
2177479 AATATATTATTTAAA
1 AATAAATTATTTAAA
2177494 AATAGAATTATTTAAA
1 AATA-AATTATTTAAA
*
2177510 TATAAATTA
1 AATAAATTA
2177519 AAAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
AATAAATTATTTAAA
Found at i:2178579 original size:10 final size:11
Alignment explanation
Indices: 2178549--2178583 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
2178539 ATATTATTTA
2178549 TTTATATAAAT
1 TTTATATAAAT
2178560 TATTATATAAAT
1 T-TTATATAAAT
2178572 TTTA-ATAAAT
1 TTTATATAAAT
2178582 TT
1 TT
2178584 AAATGTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.35
11 4 0.17
12 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTATATAAAT
Found at i:2179578 original size:2 final size:2
Alignment explanation
Indices: 2179573--2179597 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2179563 AAAGATGAAT
2179573 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2179598 TGATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2188554 original size:3 final size:3
Alignment explanation
Indices: 2188548--2188579 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2188538 GTGCATGTTG
2188548 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2188580 TTCACTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2190552 original size:23 final size:23
Alignment explanation
Indices: 2190506--2190552 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2190496 ATTCATATTT
*
2190506 CAGGTATTTATTCATCACAGATG
1 CAGGTATTTATTCATCACAAATG
* * *
2190529 CAGGTGTTTATTTATTACAAATG
1 CAGGTATTTATTCATCACAAATG
2190552 C
1 C
2190553 CTTCTATGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (23 bp):
CAGGTATTTATTCATCACAAATG
Found at i:2195203 original size:11 final size:12
Alignment explanation
Indices: 2195176--2195207 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2195166 AATTTTAATT
2195176 ATAA-AATATAA
1 ATAATAATATAA
2195187 ATAATAATATAA
1 ATAATAATATAA
2195199 A-AATAATAT
1 ATAATAATAT
2195208 TTTAACAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAATAATATAA
Found at i:2195704 original size:15 final size:16
Alignment explanation
Indices: 2195686--2195730 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2195676 TATTGGTATA
2195686 TATAAATTTTAAAAT-
1 TATAAATTTTAAAATC
*
2195701 TATAAATATTTAATATC
1 TATAAAT-TTTAAAATC
*
2195718 TAAAAATTTTAAA
1 TATAAATTTTAAA
2195731 GATCAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 12 0.48
17 6 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAAATTTTAAAATC
Found at i:2197134 original size:14 final size:14
Alignment explanation
Indices: 2197117--2197150 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2197107 TTGCTAATAA
*
2197117 TAAAATTTATTTTT
1 TAAAATTTAATTTT
2197131 TAAAATTTAATTTT
1 TAAAATTTAATTTT
*
2197145 AAAAAT
1 TAAAAT
2197151 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAAATTTAATTTT
Found at i:2203107 original size:2 final size:2
Alignment explanation
Indices: 2203100--2203128 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2203090 TTTGAAATGG
2203100 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2203129 GGTCTTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2204319 original size:10 final size:9
Alignment explanation
Indices: 2204300--2204329 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2204290 ATAATTAAAA
2204300 TAAAATTTT
1 TAAAATTTT
2204309 TAAATATTTT
1 TAAA-ATTTT
2204319 TAAAATTTT
1 TAAAATTTT
2204328 TA
1 TA
2204330 TATTAACGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TAAAATTTT
Found at i:2204375 original size:18 final size:18
Alignment explanation
Indices: 2204349--2204383 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2204339 AATATTAATA
* *
2204349 ATATGATATTTTTATTAT
1 ATATCATATTATTATTAT
2204367 ATATCATATTATTATTA
1 ATATCATATTATTATTA
2204384 ATTTTTAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATCATATTATTATTAT
Found at i:2204438 original size:18 final size:16
Alignment explanation
Indices: 2204406--2204436 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2204396 CATTTCAGCA
2204406 ATTTATAAAAAATATT
1 ATTTATAAAAAATATT
2204422 ATTTATAAAAAATAT
1 ATTTATAAAAAATAT
2204437 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTATAAAAAATATT
Found at i:2204443 original size:15 final size:16
Alignment explanation
Indices: 2204409--2204445 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
2204399 TTCAGCAATT
*
2204409 TATAAAAAATATTATT
1 TATAAAAAATATTATA
2204425 TATAAAAAATATATATA
1 TATAAAAAATAT-TATA
2204442 TATA
1 TATA
2204446 TATATGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAAAAAATATTATA
Found at i:2204679 original size:27 final size:27
Alignment explanation
Indices: 2204623--2204680 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
2204613 TTTTTTTTTA
* ** *
2204623 ATTTTTTTCAATATATAAAATGATATT
1 ATTTTTTTCAATAAATAAAAAAATAAT
2204650 ATTTTTTT-AATAAATAAAAAAATAAAT
1 ATTTTTTTCAATAAATAAAAAAAT-AAT
2204677 ATTT
1 ATTT
2204681 ACTAACTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTTTTTTCAATAAATAAAAAAATAAT
Found at i:2205477 original size:17 final size:17
Alignment explanation
Indices: 2205452--2205485 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2205442 ATTTTAAATT
2205452 AAATAAAAAAAACTAAA
1 AAATAAAAAAAACTAAA
* *
2205469 AAATTAAAAAAATTAAA
1 AAATAAAAAAAACTAAA
2205486 TTATAATCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAAAAAAACTAAA
Found at i:2205545 original size:24 final size:26
Alignment explanation
Indices: 2205513--2205562 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2205503 CAAATCTAAT
*
2205513 ATTATATAT-ATATT-ATAATTTTAC
1 ATTATATATAAAATTAATAATTTTAC
2205537 ATTATATATAAAATTAATAATTTTAC
1 ATTATATATAAAATTAATAATTTTAC
2205563 TTGATAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.39
25 4 0.17
26 10 0.43
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTATATATAAAATTAATAATTTTAC
Found at i:2208518 original size:2 final size:2
Alignment explanation
Indices: 2208507--2208537 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2208497 ACTATACATA
2208507 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2208538 TAGACTGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2208875 original size:19 final size:19
Alignment explanation
Indices: 2208829--2208884 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
2208819 AAATATAAAA
* * * *
2208829 ATTAATATAATATCAATTA
1 ATTAAAATAATATTATTTT
2208848 ATT-AAATAATATTATTTT
1 ATTAAAATAATATTATTTT
2208866 ATTAAAATAA-ATTTATTTT
1 ATTAAAATAATA-TTATTTT
2208885 TATTTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAAAATAATATTATTTT
Found at i:2210009 original size:3 final size:3
Alignment explanation
Indices: 2210001--2210029 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2209991 GAAGGTCTAG
2210001 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2210030 GTGAAAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2216790 original size:28 final size:28
Alignment explanation
Indices: 2216750--2216805 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
2216740 GGGTACTGTG
*
2216750 GGAATATAATCCCTAATTTTTAGGGATT
1 GGAAAATAATCCCTAATTTTTAGGGATT
2216778 GGAAAATAATCCCTAATTTTTAGGGATT
1 GGAAAATAATCCCTAATTTTTAGGGATT
2216806 AATCTATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (28 bp):
GGAAAATAATCCCTAATTTTTAGGGATT
Found at i:2223226 original size:17 final size:17
Alignment explanation
Indices: 2223188--2223231 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2223178 TTTATATATT
*
2223188 TATTTAT-TAAAATTTA
1 TATTTATATAAAATTAA
2223204 TATTTATATAAAATTAA
1 TATTTATATAAAATTAA
* *
2223221 TTTTTAAATAA
1 TATTTATATAA
2223232 TTTATTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTATATAAAATTAA
Found at i:2223259 original size:45 final size:44
Alignment explanation
Indices: 2223176--2223265 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 44
2223166 TAAGATGATG
* *
2223176 TTTTTATATATTTATTTATTAAAATTTATATTTATATAAAATTAA
1 TTTTTAAATATTTATTTATTAAAATTTATATATATAT-AAATTAA
**
2223221 TTTTTAAATAATTTA-TTATTACGATATTATATAT-TATAAATTAA
1 TTTTTAAAT-ATTTATTTATTAAAAT-TTATATATATATAAATTAA
2223265 T
1 T
2223266 CATATTGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
44 8 0.21
45 19 0.49
46 12 0.31
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (44 bp):
TTTTTAAATATTTATTTATTAAAATTTATATATATATAAATTAA
Found at i:2224279 original size:2 final size:2
Alignment explanation
Indices: 2224274--2224303 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2224264 TATATGCCAA
2224274 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2224304 TACCTTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2224692 original size:26 final size:26
Alignment explanation
Indices: 2224663--2224715 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2224653 TCATAATATT
*
2224663 TTTTTAATAT-ATATTAATTAATTAAA
1 TTTTTAATATGA-ATTAAATAATTAAA
*
2224689 TTTTTTATATGAATTAAATAATTAAA
1 TTTTTAATATGAATTAAATAATTAAA
2224715 T
1 T
2224716 AATTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTTTAATATGAATTAAATAATTAAA
Found at i:2228180 original size:21 final size:21
Alignment explanation
Indices: 2228140--2228181 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2228130 GTTGCTTTAG
*
2228140 AAAAAAATTTAACAACAAAAT
1 AAAAAAATTTAACAAAAAAAT
2228161 AAAAAAATTTAA-ATAAAAAAT
1 AAAAAAATTTAACA-AAAAAAT
2228182 TTTCTTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAAATTTAACAAAAAAAT
Found at i:2228359 original size:15 final size:15
Alignment explanation
Indices: 2228339--2228385 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
2228329 TAATTGAATT
2228339 AAAATAAATATTTGA
1 AAAATAAATATTTGA
* *
2228354 AGAATAAATATAT-A
1 AAAATAAATATTTGA
*
2228368 AAAATAAATGTTTGA
1 AAAATAAATATTTGA
2228383 AAA
1 AAA
2228386 CTAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.30
Consensus pattern (15 bp):
AAAATAAATATTTGA
Found at i:2228385 original size:14 final size:14
Alignment explanation
Indices: 2228339--2228385 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
2228329 TAATTGAATT
2228339 AAAATAAATATTTG
1 AAAATAAATATTTG
* *
2228353 AAGAATAAATATATA
1 AA-AATAAATATTTG
*
2228368 AAAATAAATGTTTG
1 AAAATAAATATTTG
2228382 AAAA
1 AAAA
2228386 CTAATTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.30
Consensus pattern (14 bp):
AAAATAAATATTTG
Found at i:2228847 original size:3 final size:3
Alignment explanation
Indices: 2228841--2228870 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2228831 GACGCCGACG
*
2228841 ATC ATC ATC ATC ACC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2228871 CATCCAATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:2229418 original size:2 final size:2
Alignment explanation
Indices: 2229411--2229443 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2229401 ATACCTATGT
2229411 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2229444 TATCTGACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2230418 original size:46 final size:46
Alignment explanation
Indices: 2230362--2230454 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
2230352 GTTTTAGTTT
* *
2230362 GCACACGAGGCAGATACAAGTTTCAGCTTGACGACTTTTGGATTTA
1 GCACACGAGGCAGATACAAGTTTCAGCTTAACGACTTCTGGATTTA
* *
2230408 GCACATGAGGCAGATACAAGTTTCAGCTTAATGACTTCTGGATTTA
1 GCACACGAGGCAGATACAAGTTTCAGCTTAACGACTTCTGGATTTA
2230454 G
1 G
2230455 TTTTGGTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (46 bp):
GCACACGAGGCAGATACAAGTTTCAGCTTAACGACTTCTGGATTTA
Found at i:2231080 original size:36 final size:36
Alignment explanation
Indices: 2230964--2231081 Score: 109
Period size: 36 Copynumber: 3.3 Consensus size: 36
2230954 TGAATTTAAA
* * *
2230964 TTATTAAATTTAATAAT-TTAATAATTTATATATTT
1 TTATTAATTTTAATACTGTTAATTATTTATATATTT
* * *
2230999 TTA-TATATTTTAATTAC-GTTAACGTA-ATATAAATTT
1 TTATTA-ATTTTAA-TACTGTTAA-TTATTTATATATTT
* *
2231035 ATATAAATTTTAATACTGTTAATTATTTATATATTT
1 TTATTAATTTTAATACTGTTAATTATTTATATATTT
2231071 TTATTAATTTT
1 TTATTAATTTT
2231082 TTATATTATG
Statistics
Matches: 63, Mismatches: 13, Indels: 13
0.71 0.15 0.15
Matches are distributed among these distances:
34 2 0.03
35 14 0.22
36 45 0.71
37 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (36 bp):
TTATTAATTTTAATACTGTTAATTATTTATATATTT
Found at i:2235356 original size:47 final size:47
Alignment explanation
Indices: 2235303--2235402 Score: 148
Period size: 47 Copynumber: 2.1 Consensus size: 47
2235293 GTGCATCTAA
* *
2235303 TTGTTTAAATGCATGTCAAGAAGCATGA-GTGGTATTTTCTTCTTCTT
1 TTGTTTAAATGCATGTCAAGAAGAAT-ACATGGTATTTTCTTCTTCTT
**
2235350 TTGTTTAAATGCATGTCAAGTGGAATACATGGTATTTTCTTCTTCTT
1 TTGTTTAAATGCATGTCAAGAAGAATACATGGTATTTTCTTCTTCTT
2235397 TTGTTT
1 TTGTTT
2235403 GAATTTCATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 1 0.02
47 47 0.98
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (47 bp):
TTGTTTAAATGCATGTCAAGAAGAATACATGGTATTTTCTTCTTCTT
Found at i:2236433 original size:6 final size:6
Alignment explanation
Indices: 2236414--2236459 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
2236404 TTTTGTAATT
** **
2236414 AAGTGA AAACGA AAGTGA AAACGA AAGTGA AAGTGA AAGTGA AAGT
1 AAGTGA AAGTGA AAGTGA AAGTGA AAGTGA AAGTGA AAGTGA AAGT
2236460 ATCACAATGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.54, C:0.04, G:0.28, T:0.13
Consensus pattern (6 bp):
AAGTGA
Found at i:2236459 original size:12 final size:12
Alignment explanation
Indices: 2236414--2236457 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
2236404 TTTTGTAATT
2236414 AAGTGAAAACGA
1 AAGTGAAAACGA
2236426 AAGTGAAAACGA
1 AAGTGAAAACGA
**
2236438 AAGTGAAAGTGA
1 AAGTGAAAACGA
2236450 AAGTGAAA
1 AAGTGAAA
2236458 GTATCACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.57, C:0.05, G:0.27, T:0.11
Consensus pattern (12 bp):
AAGTGAAAACGA
Found at i:2237016 original size:2 final size:2
Alignment explanation
Indices: 2237009--2237039 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2236999 TGATAAAATT
2237009 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2237040 TAGCATTCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2237248 original size:19 final size:20
Alignment explanation
Indices: 2237221--2237260 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2237211 TTTATATTTT
*
2237221 TTTACATATCATA-ATTATA
1 TTTAAATATCATATATTATA
*
2237240 TTTAAATATTATATATTATA
1 TTTAAATATCATATATTATA
2237260 T
1 T
2237261 AAATTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAATATCATATATTATA
Found at i:2237292 original size:32 final size:32
Alignment explanation
Indices: 2237244--2237317 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 32
2237234 ATTATATTTA
2237244 AATATTATATATTATATAAATTTTGATACATTAAT
1 AATATT-T-TATTATATAAATTTTGATACATT-AT
* *
2237279 AAT-TTTTATTATATTAATTTTGATATATTAT
1 AATATTTTATTATATAAATTTTGATACATTAT
2237310 AATATTTT
1 AATATTTT
2237318 TGTTGTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 5 0.14
32 25 0.69
33 1 0.03
34 2 0.06
35 3 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (32 bp):
AATATTTTATTATATAAATTTTGATACATTAT
Found at i:2237294 original size:18 final size:18
Alignment explanation
Indices: 2237250--2237317 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 18
2237240 TTTAAATATT
2237250 ATATATTATATAAATTTTG
1 ATATATTA-ATAAATTTTG
* *
2237269 ATACATTAAT-AATTTTT
1 ATATATTAATAAATTTTG
*
2237286 AT-TA-T-ATTAATTTTG
1 ATATATTAATAAATTTTG
2237301 ATATATT-ATAATATTTT
1 ATATATTAATAA-ATTTT
2237318 TGTTGTGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
14 2 0.05
15 9 0.22
16 3 0.08
17 12 0.30
18 7 0.17
19 7 0.17
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (18 bp):
ATATATTAATAAATTTTG
Found at i:2238989 original size:80 final size:80
Alignment explanation
Indices: 2238833--2238981 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
2238823 AAGTCACATT
* * *
2238833 ATTATTTAAACAGATTTTGTATAAAATTGTTAATAATTTTTATTGTTTCTTCTAATTTCAAATGT
1 ATTATTTAAACAGATTTTGTATAAAATTGTTAATAATTTTTAATATTTCTTCTAATTTCAAATGA
2238898 TTAAAAATAAAAATG
66 TTAAAAATAAAAATG
* * *
2238913 ATTATTTAAATAGATTTCT-T-TAAATATTGTTAATGATTTTTAATATTTAC-TCTCATTTCAAA
1 ATTATTTAAACAGATTT-TGTATAAA-ATTGTTAATAATTTTTAATATTT-CTTCTAATTTCAAA
2238975 TGATTAA
63 TGATTAA
2238982 GGATAAAAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
79 4 0.07
80 54 0.90
81 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (80 bp):
ATTATTTAAACAGATTTTGTATAAAATTGTTAATAATTTTTAATATTTCTTCTAATTTCAAATGA
TTAAAAATAAAAATG
Found at i:2244871 original size:16 final size:18
Alignment explanation
Indices: 2244838--2244871 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2244828 CTTTAGTTCC
2244838 TTCAACCAAAGTAGCATA
1 TTCAACCAAAGTAGCATA
2244856 TTCAA-CAAAG-AGCATA
1 TTCAACCAAAGTAGCATA
2244872 CCATCCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (18 bp):
TTCAACCAAAGTAGCATA
Found at i:2245067 original size:20 final size:22
Alignment explanation
Indices: 2245031--2245073 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2245021 TATTAAAATT
2245031 TTTATAAATTAATTATA-AAAA
1 TTTATAAATTAATTATACAAAA
2245052 TTTATAAATT-ATTATACAAAA
1 TTTATAAATTAATTATACAAAA
2245073 T
1 T
2245074 AATATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTATAAATTAATTATACAAAA
Found at i:2246327 original size:17 final size:18
Alignment explanation
Indices: 2246287--2246328 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
2246277 AGTGTGAATA
2246287 TTAAATAAAAATATATAT
1 TTAAATAAAAATATATAT
*
2246305 TT-AATATAAAT-TATAT
1 TTAAATAAAAATATATAT
2246321 TTAAATAA
1 TTAAATAA
2246329 TTATATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 7 0.33
17 12 0.57
18 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATAAAAATATATAT
Found at i:2246332 original size:14 final size:14
Alignment explanation
Indices: 2246300--2246355 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
2246290 AATAAAAATA
2246300 TATATTTAATATAAAT
1 TATATTTAA-AT-AAT
2246316 TATATTTAAATAAT
1 TATATTTAAATAAT
*
2246330 TATATCTT-TAT-AT
1 TATAT-TTAAATAAT
2246343 TCATATTTAAATA
1 T-ATATTTAAATA
2246356 TACATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 5 0.15
14 16 0.47
15 4 0.12
16 9 0.26
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATTTAAATAAT
Found at i:2246357 original size:16 final size:15
Alignment explanation
Indices: 2246300--2246357 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
2246290 AATAAAAATA
*
2246300 TATATTTAATATAAAT
1 TATATTTAA-ATATAT
2246316 TATATTTAAATA-AT
1 TATATTTAAATATAT
2246330 TATATCTT---TATAT
1 TATAT-TTAAATATAT
2246343 TCATATTTAAATATA
1 T-ATATTTAAATATA
2246358 CATAAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
12 2 0.06
13 5 0.14
14 11 0.31
15 5 0.14
16 13 0.36
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATTTAAATATAT
Found at i:2248472 original size:30 final size:30
Alignment explanation
Indices: 2248438--2248497 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2248428 GAAACTCCCA
2248438 AGTGATATATGTTGCTTTGGATTAGAATTG
1 AGTGATATATGTTGCTTTGGATTAGAATTG
*
2248468 AGTGATGTATGTTGCTTTGGATTAGAATTG
1 AGTGATATATGTTGCTTTGGATTAGAATTG
2248498 TAAGTATCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.28, T:0.43
Consensus pattern (30 bp):
AGTGATATATGTTGCTTTGGATTAGAATTG
Found at i:2250099 original size:2 final size:2
Alignment explanation
Indices: 2250092--2250224 Score: 101
Period size: 2 Copynumber: 66.5 Consensus size: 2
2250082 TTTGGTAAAT
* * *
2250092 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA GCA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
** * * * *
2250135 GG TA -A T- TA TA TA TG TT TA -A AA GTG TGA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA
* * * *
2250176 TG TG TA TA TA TA TA TA TG TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2250218 TA TA TA T
1 TA TA TA T
2250225 TGCACAGATA
Statistics
Matches: 105, Mismatches: 20, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
1 3 0.03
2 100 0.95
3 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2252308 original size:16 final size:17
Alignment explanation
Indices: 2252287--2252325 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2252277 ACTATTCTTT
*
2252287 ACAAAAAT-AAAATAAA
1 ACAAAAATCAAAAGAAA
2252303 ACAAAAATCAAAAGAAA
1 ACAAAAATCAAAAGAAA
*
2252320 AGAAAA
1 ACAAAA
2252326 TATTAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.79, C:0.08, G:0.05, T:0.08
Consensus pattern (17 bp):
ACAAAAATCAAAAGAAA
Found at i:2257014 original size:2 final size:2
Alignment explanation
Indices: 2257007--2257046 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2256997 AATTAGGTGC
*
2257007 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2257047 GATTGTTGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2266073 original size:2 final size:2
Alignment explanation
Indices: 2266066--2266107 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2266056 GAACTTTTTC
2266066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2266107 A
1 A
2266108 ACGAAATTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2268252 original size:4 final size:4
Alignment explanation
Indices: 2268243--2268272 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2268233 AACATGTAGC
2268243 AATT AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
2268273 ATGGTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:2268578 original size:62 final size:62
Alignment explanation
Indices: 2268504--2268636 Score: 167
Period size: 62 Copynumber: 2.1 Consensus size: 62
2268494 TACGATAAAT
* * ** * *
2268504 TTTAATTGACTTAAACATCATATTATTATTCGAATAATCATTTTTGACGCTCTTTAAACATA
1 TTTAATTTACTTAAACATCATACTACGATTCGAATAATCATTTTCGACACTCTTTAAACATA
* * * *
2268566 TTTAATTTACTTAAATATCATACTGCGATTCGAATAATCATTTTCGATACTCTTTAAACATG
1 TTTAATTTACTTAAACATCATACTACGATTCGAATAATCATTTTCGACACTCTTTAAACATA
*
2268628 TTTAGTTTA
1 TTTAATTTA
2268637 TATATATATA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (62 bp):
TTTAATTTACTTAAACATCATACTACGATTCGAATAATCATTTTCGACACTCTTTAAACATA
Found at i:2268869 original size:33 final size:35
Alignment explanation
Indices: 2268822--2268886 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
2268812 TTAGGTGTGA
2268822 GTTTAATCTAATTTTAT-GTTTATTT-TTTTAATTT
1 GTTTAATCTAATTTT-TGGTTTATTTATTTTAATTT
*
2268856 GTTTAAT-TAATTTTTGGTTTCTTTATTTTAA
1 GTTTAATCTAATTTTTGGTTTATTTATTTTAA
2268887 ATATAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 1 0.04
33 14 0.50
34 13 0.46
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.66
Consensus pattern (35 bp):
GTTTAATCTAATTTTTGGTTTATTTATTTTAATTT
Found at i:2269056 original size:13 final size:13
Alignment explanation
Indices: 2269038--2269062 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2269028 AAAAGAAAGA
2269038 CAACTTGAAGTGG
1 CAACTTGAAGTGG
2269051 CAACTTGAAGTG
1 CAACTTGAAGTG
2269063 TACCATTGTA
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:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (13 bp):
CAACTTGAAGTGG
Found at i:2269839 original size:50 final size:50
Alignment explanation
Indices: 2269780--2270039 Score: 358
Period size: 50 Copynumber: 5.2 Consensus size: 50
2269770 AGTTGCTCAA
* * *
2269780 AGTCAACAATTACGGCCACATCTCTCTATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* * * *
2269830 AGTCAACAATTACGACCACTTCTTTTTATTGTCAAAGGTTGATGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* * * *
2269880 AGTCAACAATTATGACCACCCCTCTCTATTGTCAAAGGTTTGTGAAAAAT
1 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* * *
2269930 AGTTAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTAGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* * **
2269980 AGTCAACAATTACGATCATCTCTCTCTATTGTCAAAAATTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
2270030 AGTCAACAAT
1 AGTCAACAAT
2270040 GGCAACACTT
Statistics
Matches: 183, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 183 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:2274478 original size:50 final size:50
Alignment explanation
Indices: 2274417--2274526 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
2274407 AGTTGCTTAA
* * * *
2274417 AGTCAATAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGATGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAAGTTGATGAAAAAT
* ** *
2274467 AGTCAACAATTATGGTTACCTCTCTCGATTGTTAAAAGTTGATGAAAAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAAGTTGATGAAAAAT
*
2274517 AATCAACAAT
1 AGTCAACAAT
2274527 GATAACACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAAGTTGATGAAAAAT
Found at i:2275427 original size:18 final size:19
Alignment explanation
Indices: 2275398--2275433 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2275388 TTTAGAATTC
2275398 ATGTATTTATATTATATTT
1 ATGTATTTATATTATATTT
2275417 ATGTA-TTATATTATATT
1 ATGTATTTATATTATATT
2275434 ATAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
ATGTATTTATATTATATTT
Found at i:2275443 original size:18 final size:18
Alignment explanation
Indices: 2275403--2275544 Score: 64
Period size: 18 Copynumber: 8.4 Consensus size: 18
2275393 AATTCATGTA
2275403 TTTATATTATATT-T-AT
1 TTTATATTATATTATAAT
2275419 GTATTATATTATATTATAAT
1 -T-TTATATTATATTATAAT
*
2275439 TTTATA-TA-A-AAT-AT
1 TTTATATTATATTATAAT
2275453 TTTAATATT-TA-TATAAAT
1 TTT-ATATTATATTAT-AAT
*
2275471 TTTGATA-TAT-TAATAA-
1 TTT-ATATTATATTATAAT
2275487 TTTATATTATA-TA-AAT
1 TTTATATTATATTATAAT
* *
2275503 TTTAAAATAT-TTATATAT
1 TTTATATTATATTATA-AT
*
2275521 TTT-T-TTCATATCATAAT
1 TTTATATT-ATATTATAAT
2275538 TTTATAT
1 TTTATAT
2275545 ATAAAATTAT
Statistics
Matches: 95, Mismatches: 10, Indels: 38
0.66 0.07 0.27
Matches are distributed among these distances:
14 5 0.05
15 10 0.11
16 23 0.24
17 14 0.15
18 38 0.40
19 3 0.03
20 2 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (18 bp):
TTTATATTATATTATAAT
Found at i:2275452 original size:20 final size:21
Alignment explanation
Indices: 2275429--2275469 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2275419 GTATTATATT
2275429 ATATTATAAT-TTTATATAAA
1 ATATTATAATATTTATATAAA
*
2275449 ATATTTTAATATTTATATAAA
1 ATATTATAATATTTATATAAA
2275470 TTTTGATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTATAATATTTATATAAA
Found at i:2275513 original size:32 final size:31
Alignment explanation
Indices: 2275422--2275546 Score: 101
Period size: 32 Copynumber: 3.8 Consensus size: 31
2275412 TATTTATGTA
* *
2275422 TTATATTATATTATAATTTTATATA-AAATATT
1 TTATATTATA-TA-AATTTTATATATTAATAAT
2275454 TTAATATTTATATAAATTTTGATATATTAATAAT
1 TT-ATA-TTATATAAATTTT-ATATATTAATAAT
* *
2275488 TTATATTATATAAATTTTAAAATATTTATATAT
1 TTATATTATATAAATTTT-ATATATTAATA-AT
*
2275521 TT-TTTTCATATCATAATTTTATATAT
1 TTATATT-ATAT-A-AATTTTATATAT
2275547 AAAATTATGA
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
32 33 0.42
33 21 0.27
34 18 0.23
35 6 0.08
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.56
Consensus pattern (31 bp):
TTATATTATATAAATTTTATATATTAATAAT
Found at i:2276838 original size:2 final size:2
Alignment explanation
Indices: 2276831--2276867 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2276821 ATGTATTTCT
2276831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2276868 TTTATAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2278564 original size:2 final size:2
Alignment explanation
Indices: 2278557--2278593 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2278547 AAATCTTTTC
2278557 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2278594 AACATGTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2281535 original size:2 final size:2
Alignment explanation
Indices: 2281528--2281559 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2281518 GTATCTCTAA
2281528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2281560 CTTTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2282637 original size:27 final size:27
Alignment explanation
Indices: 2282607--2282696 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 27
2282597 AACATAACTA
2282607 TATATATATATATATATATATAATATT
1 TATATATATATATATATATATAATATT
* * *
2282634 TATATATTTGATCATATATTTAAAATATT
1 TATATATAT-AT-ATATATATATAATATT
2282663 T-TATAT-T-TA-ATATAT-TAATAATT
1 TATATATATATATATATATATAAT-ATT
2282686 TATAT-TATATA
1 TATATATATATA
2282697 AATTTTAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
22 3 0.06
23 10 0.19
24 5 0.10
25 3 0.06
27 9 0.17
28 7 0.13
29 15 0.29
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
TATATATATATATATATATATAATATT
Found at i:2282641 original size:8 final size:8
Alignment explanation
Indices: 2282605--2282690 Score: 52
Period size: 8 Copynumber: 10.4 Consensus size: 8
2282595 CAAACATAAC
*
2282605 TATATATA
1 TATATTTA
*
2282613 TATATATA
1 TATATTTA
*
2282621 TATATATA
1 TATATTTA
2282629 -ATATTTA
1 TATATTTA
2282636 TATATTTGATCA
1 TATA-TT--T-A
2282648 TATATTTAA
1 TATATTT-A
*
2282657 AATATTT-
1 TATATTTA
2282664 TATATTTAA
1 TATATTT-A
*
2282673 TATATTAA
1 TATATTTA
2282681 TA-ATTTA
1 TATATTTA
2282688 TAT
1 TAT
2282691 TATATAAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
7 18 0.28
8 22 0.34
9 16 0.25
11 3 0.05
12 5 0.08
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (8 bp):
TATATTTA
Found at i:2282652 original size:2 final size:2
Alignment explanation
Indices: 2282605--2282640 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2282595 CAAACATAAC
*
2282605 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2282641 TTGATCATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2283589 original size:31 final size:31
Alignment explanation
Indices: 2283554--2283612 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2283544 TAATTGTTTC
2283554 AAAAATTAATATTATTAT-TTAA-AATAATATT
1 AAAAATT--TATTATTATATTAATAATAATATT
*
2283585 AAAAATTTATTTTTATATTAATAATAAT
1 AAAAATTTATTATTATATTAATAATAAT
2283613 TAAATCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 8 0.32
30 4 0.16
31 13 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
AAAAATTTATTATTATATTAATAATAATATT
Found at i:2284600 original size:10 final size:10
Alignment explanation
Indices: 2284579--2284612 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
2284569 GACAAAAAGT
2284579 TATATA-ATA
1 TATATACATA
2284588 TATATACATA
1 TATATACATA
2284598 TATATACATA
1 TATATACATA
2284608 TATAT
1 TATAT
2284613 GTATACATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATACATA
Found at i:2285621 original size:22 final size:22
Alignment explanation
Indices: 2285578--2285622 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2285568 AAATAAATTA
* **
2285578 AAAAAATTTATTTATTCGATAT
1 AAAAAATTTAATTATTAAATAT
*
2285600 AAAAATTTTAATTATTAAATAT
1 AAAAAATTTAATTATTAAATAT
2285622 A
1 A
2285623 TATAATAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAAAATTTAATTATTAAATAT
Found at i:2298952 original size:28 final size:28
Alignment explanation
Indices: 2298917--2298987 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
2298907 AGTACTAAAG
* *
2298917 AATTTAAATTTAATTTATTTAATAATT-A
1 AATTTAAATTTAATTAAATTAA-AATTAA
**
2298945 AATTTAAAAATAATTAAATTAAAATTAA
1 AATTTAAATTTAATTAAATTAAAATTAA
2298973 AATTTTTAAATTTAA
1 AA--TTTAAATTTAA
2298988 ACTCAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 4 0.12
28 21 0.62
30 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTTAAATTTAATTAAATTAAAATTAA
Found at i:2298956 original size:16 final size:15
Alignment explanation
Indices: 2298937--2298968 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
2298927 TAATTTATTT
2298937 AATAATTAAATTTAAA
1 AATAATTAAA-TTAAA
2298953 AATAATTAAATTAAA
1 AATAATTAAATTAAA
2298968 A
1 A
2298969 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAATTAAATTAAA
Found at i:2299185 original size:22 final size:21
Alignment explanation
Indices: 2299167--2299208 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2299157 TCTTTTATTT
*
2299167 TATTTATTATTAATATTTAAAA
1 TATTTA-TATTAATATTTATAA
*
2299189 TATTTATATTTATATTTATA
1 TATTTATATTAATATTTATA
2299209 TAAAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTATATTAATATTTATAA
Found at i:2299212 original size:25 final size:26
Alignment explanation
Indices: 2299162--2299214 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 26
2299152 TTTGATCTTT
*
2299162 TATTTTATTTATTATTAATATTTAAAA
1 TATTTTATTTATTATT-ATATATAAAA
2299189 TATTTATATTTA-TATT-TATATAAAA
1 TATTT-TATTTATTATTATATATAAAA
2299214 T
1 T
2299215 TTAATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 9 0.38
27 9 0.38
28 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTTTATTTATTATTATATATAAAA
Found at i:2299217 original size:32 final size:34
Alignment explanation
Indices: 2299162--2299236 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 34
2299152 TTTGATCTTT
* *
2299162 TATTT-TATTTATTATTAATATTTAAAATATTTA
1 TATTTATATTTATTATTAAAATTTAAAATATTAA
*
2299195 TATTTATATTTA-TA-TAAAATTTAATATATTAA
1 TATTTATATTTATTATTAAAATTTAAAATATTAA
*
2299227 TAATTATATT
1 TATTTATATT
2299237 ATTTTTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 24 0.65
33 7 0.19
34 6 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
TATTTATATTTATTATTAAAATTTAAAATATTAA
Found at i:2299251 original size:24 final size:25
Alignment explanation
Indices: 2299218--2299268 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
2299208 ATAAAATTTA
2299218 ATATATTAATAATTAT-ATTATTTTT
1 ATATATTAAT-ATTATAATTATTTTT
*
2299243 ATATA-TAATATTTTAATTATTTTT
1 ATATATTAATATTATAATTATTTTT
2299267 AT
1 AT
2299269 CGTATGTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.62
25 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATATATTAATATTATAATTATTTTT
Found at i:2299884 original size:18 final size:19
Alignment explanation
Indices: 2299853--2299902 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
2299843 TAACACATAA
2299853 TATATTTT-TATTAT-TTT
1 TATATTTTATATTATATTT
2299870 TATATTTTATATTATATTT
1 TATATTTTATATTATATTT
*
2299889 TA-ATTTTATTTTAT
1 TATATTTTATATTAT
2299903 CATATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 8 0.27
18 17 0.57
19 5 0.17
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATATTTTATATTATATTT
Found at i:2299900 original size:11 final size:12
Alignment explanation
Indices: 2299869--2299902 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2299859 TTTATTATTT
2299869 TTATATTTTATA
1 TTATATTTTATA
2299881 TTATATTTTA-A
1 TTATATTTTATA
*
2299892 TTTTATTTTAT
1 TTATATTTTAT
2299903 CATATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:2300734 original size:37 final size:37
Alignment explanation
Indices: 2300684--2300758 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2300674 CCCTTTGTAT
*
2300684 ATGACATTTGCCAAAAGAATGATAATAATTTATACAA
1 ATGACATCTGCCAAAAGAATGATAATAATTTATACAA
2300721 ATGACATCTGCCAAAAGAATGATAATAATTTATACAA
1 ATGACATCTGCCAAAAGAATGATAATAATTTATACAA
2300758 A
1 A
2300759 ATATTTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.28
Consensus pattern (37 bp):
ATGACATCTGCCAAAAGAATGATAATAATTTATACAA
Found at i:2301452 original size:4 final size:4
Alignment explanation
Indices: 2301413--2301447 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2301403 ATATATATAT
2301413 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
2301448 TATATTATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:2306591 original size:3 final size:3
Alignment explanation
Indices: 2306577--2306615 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2306567 AGTTTTAAAA
*
2306577 TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2306616 CATCATCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2309704 original size:28 final size:30
Alignment explanation
Indices: 2309673--2309739 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
2309663 CTTTTTTTAG
** *
2309673 ATTTAATATTTTGTTA-ATAAA-AAAATTT
1 ATTTAATATTTAATTATATAAATAAAATTA
2309701 ATTTAA-ATTTAATTATATAAATAAAATTA
1 ATTTAATATTTAATTATATAAATAAAATTA
2309730 ATATTAATAT
1 AT-TTAATAT
2309740 AAAATTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 7 0.22
28 11 0.34
29 8 0.25
30 4 0.12
31 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
ATTTAATATTTAATTATATAAATAAAATTA
Found at i:2319364 original size:245 final size:242
Alignment explanation
Indices: 2318937--2319424 Score: 789
Period size: 245 Copynumber: 2.0 Consensus size: 242
2318927 GAATAATATT
* * *
2318937 ACATGCAAGAATTAAGCACTAAAACATTTTCTGTGCTATTGCATGTCCTTTTCTTTTTTCTGTAC
1 ACATGCAAGAATTAAGAACAAAAACACTTTCTGTGCTATTGCATGTCCTTTTCTTTTTTCTGTAC
* *
2319002 AGACTGATATTGGATGTCTAGGCATCTTACGGAAATAGGAAAGAAAACTTTCAGTTTAATACCCT
66 AGACTGATATTGGATGTCTAGGCATCTTACGGAAATAGGAAAGAAAACTTTCAGCTGAATACCCT
*
2319067 ATCAAGTATCATGAGCCAATTGGTAAATTAGGCTAACATAACAGAATGCAGATAACAACATAGTC
131 ATCAAGTATCATGAGCCAATTAGTAAATTAGGCTAACATAACAGAATGCAGATAACAACATAGTC
* * *
2319132 ACTCTTAGATCACATAGGAACTAAACATTGTATCCATAGAGTAACCA
196 ACGCTTAGATCACATAGGAACTAAACATTGCACCCATAGAGTAACCA
2319179 ACATGCAAGAATTAAGAACAAAAACACTTTCTGTGCTATTGCATGTCTTTCTTTTCTTTTTTCTG
1 ACATGCAAGAATTAAGAACAAAAACACTTTCTGTGCTATTGCATGTC---CTTTTCTTTTTTCTG
* * *
2319244 TACAGACTGCTATTGGATGTCTAGGCATCTTATGGAAATAGGAAAGATAACTTTCAGCTGAATAC
63 TACAGACTGATATTGGATGTCTAGGCATCTTACGGAAATAGGAAAGAAAACTTTCAGCTGAATAC
**
2319309 CCTATCAAGTATCATGAGCCAATTAGTAAATTAAGG-TCCCATAACAGAATGCAGATAACAACAT
128 CCTATCAAGTATCATGAGCCAATTAGTAAATT-AGGCTAACATAACAGAATGCAGATAACAACAT
* *
2319373 AGTCGCGCTTAGATCAGATAGGAACTAAACATTGCACCCATAGAGTAACCA
192 AGTCACGCTTAGATCACATAGGAACTAAACATTGCACCCATAGAGTAACCA
2319424 A
1 A
2319425 GGATGACTTC
Statistics
Matches: 226, Mismatches: 16, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
242 44 0.19
245 179 0.79
246 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (242 bp):
ACATGCAAGAATTAAGAACAAAAACACTTTCTGTGCTATTGCATGTCCTTTTCTTTTTTCTGTAC
AGACTGATATTGGATGTCTAGGCATCTTACGGAAATAGGAAAGAAAACTTTCAGCTGAATACCCT
ATCAAGTATCATGAGCCAATTAGTAAATTAGGCTAACATAACAGAATGCAGATAACAACATAGTC
ACGCTTAGATCACATAGGAACTAAACATTGCACCCATAGAGTAACCA
Found at i:2321679 original size:34 final size:32
Alignment explanation
Indices: 2321601--2321689 Score: 81
Period size: 34 Copynumber: 2.7 Consensus size: 32
2321591 TTTTATATTT
*
2321601 ATATAAATTTTAAATTATATATTCATATTACATC
1 ATAT-AATTTT-AATTATATATTCATATTAAATC
* * *
2321635 ATAAATATTTTAATTATTTTATTTATATTATAATC
1 ATATA-ATTTTAATTA-TATATTCATATTA-AATC
*
2321670 ATATAATTTTATTTA-ATATT
1 ATATAATTTTAATTATATATT
2321690 ATCATATCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
32 4 0.09
33 6 0.13
34 28 0.62
35 7 0.16
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (32 bp):
ATATAATTTTAATTATATATTCATATTAAATC
Found at i:2322486 original size:20 final size:19
Alignment explanation
Indices: 2322444--2322506 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
2322434 CCAAACGTTT
*
2322444 ATATTCAACA-TACATTATA
1 ATATTCAACATTATATT-TA
2322463 ATATTCAACATTTATATTTA
1 ATATTCAACA-TTATATTTA
2322483 ATATAT-AACATCTATATTTA
1 ATAT-TCAACAT-TATATTTA
2322503 ATAT
1 ATAT
2322507 ATATTCGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 11 0.28
20 22 0.56
21 6 0.15
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTCAACATTATATTTA
Found at i:2322507 original size:20 final size:20
Alignment explanation
Indices: 2322469--2322509 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2322459 TATAATATTC
*
2322469 AACATTTATATTTAATATAT
1 AACATCTATATTTAATATAT
2322489 AACATCTATATTTAATATAT
1 AACATCTATATTTAATATAT
2322509 A
1 A
2322510 TTCGAATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (20 bp):
AACATCTATATTTAATATAT
Found at i:2322877 original size:36 final size:36
Alignment explanation
Indices: 2322821--2322894 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
2322811 AGGACTGCAA
* ** *
2322821 AACTAAATAATCCCATCATCAAACGTTGGCTGCCAG
1 AACTAAATAATCCCAACATCAAACACTGGCTACCAG
* *
2322857 AACTCAATAATCTCAACATCAAACACTGGCTACCAG
1 AACTAAATAATCCCAACATCAAACACTGGCTACCAG
2322893 AA
1 AA
2322895 AAAGGAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (36 bp):
AACTAAATAATCCCAACATCAAACACTGGCTACCAG
Found at i:2325870 original size:240 final size:229
Alignment explanation
Indices: 2325449--2325872 Score: 555
Period size: 240 Copynumber: 1.8 Consensus size: 229
2325439 ATAAAAGGTA
* * * **
2325449 AAAATCTCACAAAAGGGGCTTATCACGATCAATCAATTAACAAAATAAAAATAAAATTCAAAAGT
1 AAAATCTCACAAAAGGGGCTTAACACGATCAATCAATTAACAAAATAAAAAAAAAATACAAAAAC
* * * * **
2325514 AATCATGCTAAATATATAAAGAAAATAAAATTATGCAATCCAAAGGGTAAAAGGAAAAAAAATTA
66 AAACATGCTAAATACAGAAAGAAAATAAAATTATACAATCCAAAACGTAAAAGGAAAAAAAATTA
* *
2325579 GCCACAGATTTCAACCATCCAAACACAATAACCCAGAATTCCAAACAGAATAAAACCCCCAGAAA
131 CCCACAGATTTCAAACATCCAAACACAATAACCCAGAATTCCAAACAGAATAAAACCCCCAGAAA
2325644 GAAAATCCAGAAAAAAACAAAAACTCACATAAAG
196 GAAAATCCAGAAAAAAACAAAAACTCACATAAAG
*
2325678 AAAATCTCACAAAAGGGGCTTAACACGATTAATCAATTAACAAAAATAAACAAAAAAAATACAAA
1 AAAATCTCACAAAAGGGGCTTAACACGATCAATCAATTAAC-AAAAT-AA-AAAAAAAATACAAA
*
2325743 AACAAACATGCTAAATACAGAAAGAAAATAAAATTTATACAATCCAAACACTTAAAAAAAAGAAG
63 AACAAACATGCTAAATACAGAAAGAAAATAAAA-TTATACAATCCAAA-ACGT----AAAAG--G
* * *
2325808 AAAAAAAATTTACCCA-AGATTTCAAACA-CTTAACCACAGTAACCCAGAATTCCAAACAGAATA
120 AAAAAAAA-TTACCCACAGATTTCAAACATC-CAAACACAATAACCCAGAATTCCAAACAGAATA
2325871 AA
183 AA
2325873 TCCCAAAACC
Statistics
Matches: 164, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
229 39 0.24
230 5 0.03
231 2 0.01
232 40 0.24
233 13 0.08
234 1 0.01
238 5 0.03
239 1 0.01
240 52 0.32
241 6 0.04
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.17
Consensus pattern (229 bp):
AAAATCTCACAAAAGGGGCTTAACACGATCAATCAATTAACAAAATAAAAAAAAAATACAAAAAC
AAACATGCTAAATACAGAAAGAAAATAAAATTATACAATCCAAAACGTAAAAGGAAAAAAAATTA
CCCACAGATTTCAAACATCCAAACACAATAACCCAGAATTCCAAACAGAATAAAACCCCCAGAAA
GAAAATCCAGAAAAAAACAAAAACTCACATAAAG
Found at i:2326456 original size:18 final size:19
Alignment explanation
Indices: 2326422--2326457 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2326412 TTATTTTTGG
*
2326422 AAAAATAAATGTTATAAAT
1 AAAAATAAATGTGATAAAT
2326441 AAAAATAAA-GTGATAAA
1 AAAAATAAATGTGATAAA
2326458 AAATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (19 bp):
AAAAATAAATGTGATAAAT
Found at i:2327218 original size:19 final size:19
Alignment explanation
Indices: 2327172--2327218 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
2327162 ATTTTATGTT
2327172 TATTTAATATTAAAATCATA
1 TATTTAATATTAAAAT-ATA
2327192 TATTTAATATTTAAAAT-TA
1 TATTTAATA-TTAAAATATA
*
2327211 TTTTTAAT
1 TATTTAAT
2327219 TAAATTGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 9 0.36
21 7 0.28
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTAATATTAAAATATA
Found at i:2327467 original size:21 final size:21
Alignment explanation
Indices: 2327409--2327473 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 21
2327399 AAATAAATTT
* *
2327409 TTTTAATTATAAAATT-TATA
1 TTTTAATAATATAATTATATA
2327429 TTTTAATAATATAATTATATA
1 TTTTAATAATATAATTATATA
*
2327450 TTTT-ATAATAATAGTTATA-A
1 TTTTAATAAT-ATAATTATATA
2327470 TTTT
1 TTTT
2327474 GTTTTATTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
20 24 0.60
21 16 0.40
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTAATAATATAATTATATA
Found at i:2327876 original size:3 final size:3
Alignment explanation
Indices: 2327868--2327906 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2327858 TAAGGTTGAC
2327868 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2327907 GTGTTAGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2329364 original size:18 final size:19
Alignment explanation
Indices: 2329334--2329369 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2329324 TTTATGTTAA
2329334 TATTTATAATAATAATTTT
1 TATTTATAATAATAATTTT
2329353 TATTTA-AATAATAATTT
1 TATTTATAATAATAATTT
2329370 AAATTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTATAATAATAATTTT
Found at i:2329941 original size:18 final size:19
Alignment explanation
Indices: 2329912--2329949 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2329902 TTTATATAAT
*
2329912 ATTTTAAATAATTTAATTA
1 ATTTTAAATAATTGAATTA
2329931 ATTTT-AATAATTGAATTA
1 ATTTTAAATAATTGAATTA
2329949 A
1 A
2329950 ATTAACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
ATTTTAAATAATTGAATTA
Found at i:2329959 original size:18 final size:18
Alignment explanation
Indices: 2329918--2329959 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2329908 TAATATTTTA
* *
2329918 AATAATTTAATTAATTTT
1 AATAATTGAATTAATATT
2329936 AATAATTGAATTAA-ATT
1 AATAATTGAATTAATATT
2329953 AACTAAT
1 AA-TAAT
2329960 AATATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
AATAATTGAATTAATATT
Found at i:2330046 original size:29 final size:27
Alignment explanation
Indices: 2329972--2330060 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 27
2329962 TATAAAATTT
* * *
2329972 TTAAAA-TCTTTAATCCATT-ATTTTA
1 TTAAAATTTTTTAATCAATTAATTTAA
2329997 TTAAAATTTTTTAA-CTAATTAATTTAA
1 TTAAAATTTTTTAATC-AATTAATTTAA
*
2330024 TTAAATTTTATTTTAATCAATTAATTTAA
1 TTAAA-ATT-TTTTAATCAATTAATTTAA
2330053 TTAAAATT
1 TTAAAATT
2330061 AAATAATCGT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
25 7 0.13
26 9 0.17
27 10 0.19
28 4 0.08
29 22 0.42
30 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAAAATTTTTTAATCAATTAATTTAA
Found at i:2331149 original size:21 final size:22
Alignment explanation
Indices: 2331114--2331168 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
2331104 AATTATAATA
*
2331114 ATTATTGAAAATTAA-AATATT
1 ATTATTTAAAATTAATAATATT
* *
2331135 TTTATTTAAATTTAATAATATT
1 ATTATTTAAAATTAATAATATT
2331157 ATTATTTAAAAT
1 ATTATTTAAAAT
2331169 ATTAATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTATTTAAAATTAATAATATT
Found at i:2331161 original size:22 final size:22
Alignment explanation
Indices: 2331099--2331166 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
2331089 AATTTAAATT
* * *
2331099 AATTTAATTATAATAATTATTGA
1 AATTTAATAAT-ATTATTATTTA
* *
2331122 AAATTAA-AATATTTTTATTTA
1 AATTTAATAATATTATTATTTA
2331143 AATTTAATAATATTATTATTTA
1 AATTTAATAATATTATTATTTA
2331165 AA
1 AA
2331167 ATATTAATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 14 0.38
22 17 0.46
23 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (22 bp):
AATTTAATAATATTATTATTTA
Found at i:2331564 original size:15 final size:15
Alignment explanation
Indices: 2331546--2331588 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
2331536 ACATATTTTT
2331546 AATTTTTATATATTA
1 AATTTTTATATATTA
*
2331561 AATTTTTTTAAATATTA
1 AA--TTTTTATATATTA
*
2331578 TATTTTTATAT
1 AATTTTTATAT
2331589 TAATATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 10 0.43
17 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTTTATATATTA
Found at i:2331568 original size:17 final size:17
Alignment explanation
Indices: 2331548--2331584 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2331538 ATATTTTTAA
*
2331548 TTTTTATATATTAAATT
1 TTTTTAAATATTAAATT
*
2331565 TTTTTAAATATTATATT
1 TTTTTAAATATTAAATT
2331582 TTT
1 TTT
2331585 ATATTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTAAATATTAAATT
Found at i:2331652 original size:30 final size:30
Alignment explanation
Indices: 2331596--2331653 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
2331586 TATTAATATT
*
2331596 TAAATATATATTAAAAATAAATATCAAATA
1 TAAATATATATTAAAAATAAAAATCAAATA
2331626 TAAATAT-T-TTAAAAATTAAAAAATCAAA
1 TAAATATATATTAAAAA-T-AAAAATCAAA
2331654 ACAGTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 7 0.28
29 2 0.08
30 16 0.64
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (30 bp):
TAAATATATATTAAAAATAAAAATCAAATA
Found at i:2331829 original size:3 final size:3
Alignment explanation
Indices: 2331821--2331861 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
2331811 TTGGTGCCAA
*
2331821 AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2331862 AGGGCTAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2332062 original size:2 final size:2
Alignment explanation
Indices: 2332055--2332083 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2332045 TCCTATACGC
2332055 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2332084 GACACACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2332360 original size:2 final size:2
Alignment explanation
Indices: 2332353--2332377 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2332343 ACTACCAATG
2332353 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2332378 TAAAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2333272 original size:22 final size:22
Alignment explanation
Indices: 2333223--2333291 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
2333213 TTTAATTTTT
* * * *
2333223 TTAAAAATCATTATATAAAATA
1 TTAAAATTTATTATATTAATTA
2333245 -TAAAATATT-TTA-ATTAATATA
1 TTAAAAT-TTATTATATTAAT-TA
2333266 TTAAAATTTATTATATTAATTA
1 TTAAAATTTATTATATTAATTA
2333288 TTAA
1 TTAA
2333292 TATAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
20 4 0.11
21 12 0.32
22 16 0.42
23 6 0.16
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAATTTATTATATTAATTA
Found at i:2333318 original size:21 final size:21
Alignment explanation
Indices: 2333292--2333342 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
2333282 TAATTATTAA
2333292 TATAAATAAAATTTTTAA-AAT
1 TATAAA-AAAATTTTTAATAAT
*
2333313 TATAAAATAATTTTTAATAAT
1 TATAAAAAAATTTTTAATAAT
*
2333334 TTTAAAAAA
1 TATAAAAAA
2333343 TTATAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAAAAAAATTTTTAATAAT
Found at i:2334550 original size:3 final size:3
Alignment explanation
Indices: 2334542--2334568 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2334532 GTTAAAAATG
2334542 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2334569 AAAATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2346437 original size:2 final size:2
Alignment explanation
Indices: 2346430--2346464 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2346420 AAACCTAGGT
2346430 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2346465 TTTAACATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2349488 original size:22 final size:20
Alignment explanation
Indices: 2349443--2349482 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2349433 CACAGCACTC
*
2349443 ACATTCATAAATTACATATA
1 ACATTTATAAATTACATATA
2349463 ACATTTATATAATGTACATA
1 ACATTTATA-AAT-TACATA
2349483 AGACATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (20 bp):
ACATTTATAAATTACATATA
Found at i:2349826 original size:45 final size:45
Alignment explanation
Indices: 2349733--2349826 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
2349723 CCTTGAGTAA
* *
2349733 CAAAAGGGTTAACTTTGCTTCCCTACCCAAACTGTCATATGTTGG
1 CAAAAGGGTTAACTTTGCTTCCCTACCCAAACTCTCATATGATGG
*
2349778 CAAAAGGGTTAACTTTGCTTCCCTACCCAAACTCTCTTATGCAT-G
1 CAAAAGGGTTAACTTTGCTTCCCTACCCAAACTCTCATATG-ATGG
2349823 CAAA
1 CAAA
2349827 GAATTGGAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (45 bp):
CAAAAGGGTTAACTTTGCTTCCCTACCCAAACTCTCATATGATGG
Found at i:2350603 original size:17 final size:17
Alignment explanation
Indices: 2350581--2350616 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2350571 AGCCACTTAG
*
2350581 TAAAGTATAAATCCTAT
1 TAAAGTACAAATCCTAT
2350598 TAAAGTACAAATCCTAT
1 TAAAGTACAAATCCTAT
2350615 TA
1 TA
2350617 TGATTGCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (17 bp):
TAAAGTACAAATCCTAT
Found at i:2351920 original size:17 final size:17
Alignment explanation
Indices: 2351898--2351936 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2351888 GAATTAGTAT
*
2351898 AATTTTTAATT-TTATTA
1 AATTTTT-ATTATTAATA
2351915 AATTTTTATTATTAATA
1 AATTTTTATTATTAATA
2351932 AATTT
1 AATTT
2351937 ATTTATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTTATTATTAATA
Done.