Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 32
Found at i:2210490 original size:3 final size:3
Alignment explanation
Indices: 2210383--2210479 Score: 87
Period size: 3 Copynumber: 33.7 Consensus size: 3
2210373 TTCATTTGAA
* *
2210383 TAT TAT T-T ATAT T-T TAT TAA TAT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
2210427 CAT TAT TAT TAT AAT TAT TAT AAT AAT AAT TAT TAT TA- TAT T-T T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2210472 TAT TAT TA
1 TAT TAT TA
2210480 AATAATTATT
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
2 9 0.11
3 69 0.87
4 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2211864 original size:3 final size:3
Alignment explanation
Indices: 2211850--2211915 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
2211840 TATTTAATTC
*
2211850 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2211897 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
2211916 AAATATATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2212781 original size:2 final size:2
Alignment explanation
Indices: 2212770--2212800 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2212760 TATTTTCATA
2212770 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
2212801 TATTGTTATT
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:2214657 original size:196 final size:197
Alignment explanation
Indices: 2214322--2214709 Score: 769
Period size: 196 Copynumber: 2.0 Consensus size: 197
2214312 CGACGATATC
2214322 GTTTGGCGTGCCCCGTGGCAAATTCAAAGGGAGTTCTTTTACAAATATGGTGACTACAACTAGGT
1 GTTTGGCGTGCCCCGTGGCAAATTCAAAGGGAGTTCTTTTACAAATATGGTGACTACAACTAGGT
2214387 GATGTTACTTGGTTTGTGGGGAGGAATCGGATATGCACCACTTCTGGTTATAAGACAGTACGAGG
66 GATGTTACTTGGTTTGTGGGGAGGAATCGGATATGCACCACTTCTGGTTATAAGACAGTACGAGG
2214452 GTCGTCAATTTGTTCCTGTTACTGCTGGATTACATTCATCTGAGTTCGCTTTTCATAGCAAACAA
131 GTCGTCAATTTGTTCCTGTTACTGCTGGATTACATTCATCTGAGTTCGCTTTTCATAGCAAACAA
2214517 AA
196 AA
2214519 GTTTGGCGTGCCCCGTGGC-AATTCAAAGGGAGTTCTTTTACAAATATGGTGACTACAACTAGGT
1 GTTTGGCGTGCCCCGTGGCAAATTCAAAGGGAGTTCTTTTACAAATATGGTGACTACAACTAGGT
2214583 GATGTTACTTGGTTTGTGGGGAGGAATCGGATATGCACCACTTCTGGTTATAAGACAGTACGAGG
66 GATGTTACTTGGTTTGTGGGGAGGAATCGGATATGCACCACTTCTGGTTATAAGACAGTACGAGG
2214648 GTCGTCAATTTGTTCCTGTTACTGCTGGATTACATTCATCTGAGTTCGCTTTTCATAGCAAA
131 GTCGTCAATTTGTTCCTGTTACTGCTGGATTACATTCATCTGAGTTCGCTTTTCATAGCAAA
2214710 AATTACAAAA
Statistics
Matches: 191, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
196 172 0.90
197 19 0.10
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (197 bp):
GTTTGGCGTGCCCCGTGGCAAATTCAAAGGGAGTTCTTTTACAAATATGGTGACTACAACTAGGT
GATGTTACTTGGTTTGTGGGGAGGAATCGGATATGCACCACTTCTGGTTATAAGACAGTACGAGG
GTCGTCAATTTGTTCCTGTTACTGCTGGATTACATTCATCTGAGTTCGCTTTTCATAGCAAACAA
AA
Found at i:2225385 original size:13 final size:13
Alignment explanation
Indices: 2225369--2225394 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2225359 AACTTATCTG
2225369 AAGATTATTTTAA
1 AAGATTATTTTAA
2225382 AAGATTATTTTAA
1 AAGATTATTTTAA
2225395 GTATTTGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
AAGATTATTTTAA
Found at i:2229711 original size:14 final size:14
Alignment explanation
Indices: 2229692--2229719 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2229682 AAGTGAAAAA
2229692 ATAGTTATATAATT
1 ATAGTTATATAATT
2229706 ATAGTTATATAATT
1 ATAGTTATATAATT
2229720 TTGTTATGAT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:2230663 original size:21 final size:21
Alignment explanation
Indices: 2230608--2230665 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
2230598 ACTTAATGCT
2230608 TAGTTTAGATACTAAAAATGA
1 TAGTTTAGATACTAAAAATGA
* ** * *
2230629 -AATAAAAAGGACTAAAAATGA
1 TAGTTTAGA-TACTAAAAATGA
2230650 TAGTTTAGATACTAAA
1 TAGTTTAGATACTAAA
2230666 CCCGTTAAGT
Statistics
Matches: 25, Mismatches: 10, Indels: 4
0.64 0.26 0.10
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (21 bp):
TAGTTTAGATACTAAAAATGA
Found at i:2234051 original size:31 final size:31
Alignment explanation
Indices: 2234016--2234084 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
2234006 GAGCTACTCA
* *
2234016 CGAGCTTCAGTTCAAGA-TTTCGAGTTCGAGT
1 CGAGCTCCAGTTCAAAATTTTCGAG-TCGAGT
* *
2234047 CGAGCTCCATTTCAAAATTTTTGAGTCGAGT
1 CGAGCTCCAGTTCAAAATTTTCGAGTCGAGT
2234078 CGAGCTC
1 CGAGCTC
2234085 AGCAATACTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 27 0.82
32 6 0.18
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (31 bp):
CGAGCTCCAGTTCAAAATTTTCGAGTCGAGT
Found at i:2235114 original size:34 final size:34
Alignment explanation
Indices: 2235071--2235140 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
2235061 GTTTAATTAT
2235071 TTTATCTTACTAATATGA-TGCTAACAAAGTCATG
1 TTTATCTTACTAATATGATTG-TAACAAAGTCATG
*
2235105 TTTATCTTACTAATATGATTGTAACACAGTCATG
1 TTTATCTTACTAATATGATTGTAACAAAGTCATG
2235139 TT
1 TT
2235141 GTTCCAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 32 0.94
35 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (34 bp):
TTTATCTTACTAATATGATTGTAACAAAGTCATG
Found at i:2236190 original size:3 final size:3
Alignment explanation
Indices: 2236182--2236210 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2236172 TAATGGATCT
2236182 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2236211 TATGATATAA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2237027 original size:2 final size:2
Alignment explanation
Indices: 2237020--2237087 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
2237010 TTCCCCAACA
*
2237020 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2237062 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
2237088 TAATTTCTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2239820 original size:2 final size:2
Alignment explanation
Indices: 2239809--2239860 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
2239799 TTATCCCATA
2239809 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2239849 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2239861 TAAATGTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2242534 original size:33 final size:34
Alignment explanation
Indices: 2242497--2242564 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 34
2242487 CATAATTTAC
*
2242497 AACTTCGATGACATTGTTAATTGGTTTTCA-TTA
1 AACTTCGATGACATTGCTAATTGGTTTTCACTTA
*
2242530 AACTTCGATGATATTGCTAATTGGTTTTCACTTA
1 AACTTCGATGACATTGCTAATTGGTTTTCACTTA
2242564 A
1 A
2242565 TCTTTATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (34 bp):
AACTTCGATGACATTGCTAATTGGTTTTCACTTA
Found at i:2244459 original size:11 final size:11
Alignment explanation
Indices: 2244443--2244505 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
2244433 GTATTATAGA
2244443 ATTTTTAATAT
1 ATTTTTAATAT
2244454 ATTTTTAA-A-
1 ATTTTTAATAT
2244463 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
2244474 ATCAATAGTGT
1 ATTTTTAATAT
2244485 ATTTTTAATAT
1 ATTTTTAATAT
2244496 ATTTTTAATA
1 ATTTTTAATA
2244506 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:2244987 original size:37 final size:35
Alignment explanation
Indices: 2244898--2245001 Score: 100
Period size: 37 Copynumber: 2.8 Consensus size: 35
2244888 CTTTTCGTTC
* *
2244898 TACTACGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTA-GATTTAAACT-CTTAAAATAGGATAGAATTT
* * *
2244935 TGCTAGGTTTCAAACTCTTTAAAATAGGATAGAGTTT
1 TACTAGATTT-AAACTC-TTAAAATAGGATAGAATTT
*
2244972 TACTATGATTTAAACTCCTAAAGATAGGAT
1 TACTA-GATTTAAACTCTTAAA-ATAGGAT
2245002 CCACAAGCAT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
36 8 0.15
37 43 0.78
38 4 0.07
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (35 bp):
TACTAGATTTAAACTCTTAAAATAGGATAGAATTT
Found at i:2245446 original size:21 final size:21
Alignment explanation
Indices: 2245420--2245462 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2245410 TATATGTATA
2245420 TATTTAATTAT-ATTTTATTTT
1 TATTT-ATTATAATTTTATTTT
*
2245441 TATTTATTATAATTTTTTTTT
1 TATTTATTATAATTTTATTTT
2245462 T
1 T
2245463 TTTCTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TATTTATTATAATTTTATTTT
Found at i:2245464 original size:24 final size:25
Alignment explanation
Indices: 2245428--2245487 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
2245418 TATATTTAAT
2245428 TATA-TTTTATTTTTATTTATTATA
1 TATATTTTTATTTTTATTTATTATA
* * * *
2245452 -ATTTTTTTTTTTTTCTTTTTTATA
1 TATATTTTTATTTTTATTTATTATA
2245476 TATATTTTTATT
1 TATATTTTTATT
2245488 AATATATATG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 2 0.07
24 17 0.61
25 9 0.32
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (25 bp):
TATATTTTTATTTTTATTTATTATA
Found at i:2245510 original size:18 final size:15
Alignment explanation
Indices: 2245467--2245569 Score: 63
Period size: 16 Copynumber: 6.6 Consensus size: 15
2245457 TTTTTTTTTC
2245467 TTTT-TTATATATAT
1 TTTTATTATATATAT
2245481 TTTTATTAATATATAT
1 TTTTATT-ATATATAT
2245497 GTAATTTA-T-TATAT-T
1 -T--TTTATTATATATAT
*
2245512 TTTTATT-TATATTTT
1 TTTTATTATATA-TAT
2245527 ATTTTATTATATATAT
1 -TTTTATTATATATAT
*
2245543 TTTATATTTTATAGATAT
1 TTT-TA--TTATATATAT
*
2245561 ATTTATTAT
1 TTTTATTAT
2245570 TTATTTATAC
Statistics
Matches: 73, Mismatches: 3, Indels: 25
0.72 0.03 0.25
Matches are distributed among these distances:
12 4 0.05
13 5 0.07
14 6 0.08
15 11 0.15
16 24 0.33
17 7 0.10
18 12 0.16
19 4 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTTATTATATATAT
Found at i:2245510 original size:32 final size:29
Alignment explanation
Indices: 2245397--2245575 Score: 91
Period size: 31 Copynumber: 6.0 Consensus size: 29
2245387 TTAACCGTTA
*
2245397 TTATTTATA-TGT-ATATATGTATATATTT
1 TTATTTATATTGTAATTTAT-TATATATTT
* * *
2245425 AATTATATTTTATTTTTATTTATTATA-ATTT
1 --TTAT-TTATATTGTAATTTATTATATATTT
* * * **
2245456 TT-TTTTTTTTCTTTTTTA-TATATATTT
1 TTATTTATATTGTAATTTATTATATATTT
2245483 TTATTAATATATATGTAATTTATTATAT-TTT
1 TTATT--TATAT-TGTAATTTATTATATATTT
* *
2245514 TTATTTATATTTTATTTTATTATATATATT
1 TTATTTATATTGTAATTTATTATATAT-TT
* * *
2245544 TTATATTTTATAGATATATTTATTATTTATTT
1 TTAT-TTATATTG-TA-ATTTATTATATATTT
2245576 ATACTATTTA
Statistics
Matches: 117, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
26 4 0.03
27 18 0.15
28 16 0.14
29 8 0.07
30 13 0.11
31 27 0.23
32 15 0.13
33 16 0.14
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.68
Consensus pattern (29 bp):
TTATTTATATTGTAATTTATTATATATTT
Found at i:2245530 original size:48 final size:46
Alignment explanation
Indices: 2245422--2245543 Score: 128
Period size: 48 Copynumber: 2.7 Consensus size: 46
2245412 TATGTATATA
* * * *
2245422 TTTAATTATATTTTATTTTTATT-TAT-TA-TAATTTTTTTTTTTT
1 TTTATTTATATTTTATTTTTATTATATATATTAATTTATTATATTT
* *
2245465 TCTTTTTTATA-TATATTTTTATTAATATATATGTAATTTATTATATTT
1 T-TTATTTATATTTTATTTTTATT-ATATATAT-TAATTTATTATATTT
2245513 TTTATTTATATTTTA-TTTTATTATATATATT
1 TTTATTTATATTTTATTTTTATTATATATATT
2245544 TTATATTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
43 12 0.19
44 7 0.11
45 4 0.06
46 10 0.16
47 15 0.23
48 16 0.25
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (46 bp):
TTTATTTATATTTTATTTTTATTATATATATTAATTTATTATATTT
Found at i:2245760 original size:18 final size:19
Alignment explanation
Indices: 2245726--2245761 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2245716 CCAATATTTT
2245726 ATTTATTATTATTGGTTTC
1 ATTTATTATTATTGGTTTC
*
2245745 ATTTATT-TTCTTGGTTT
1 ATTTATTATTATTGGTTT
2245762 ACTCTTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.67
Consensus pattern (19 bp):
ATTTATTATTATTGGTTTC
Found at i:2250334 original size:15 final size:15
Alignment explanation
Indices: 2250310--2250356 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2250300 AGATCCAATC
*
2250310 AAGAACAAAAAAGAA
1 AAGAAAAAAAAAGAA
*
2250325 AAGAAGAAAAAAGCAA
1 AAGAAAAAAAAAG-AA
2250341 AA-AAAAAACAAAGAA
1 AAGAAAAAA-AAAGAA
2250356 A
1 A
2250357 CAAGAGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 20 0.71
16 8 0.29
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAGAA
Found at i:2250342 original size:8 final size:7
Alignment explanation
Indices: 2250316--2250390 Score: 53
Period size: 8 Copynumber: 9.7 Consensus size: 7
2250306 AATCAAGAAC
2250316 AAAAAAG
1 AAAAAAG
2250323 AAAAGAAG
1 AAAA-AAG
2250331 AAAAAAG
1 AAAAAAG
*
2250338 CAAAAAAA
1 -AAAAAAG
2250346 AAACAAAG
1 AAA-AAAG
2250354 AAACAAGAG
1 AAA-AA-AG
*
2250363 AAACAAG
1 AAAAAAG
2250370 AACAAAA-
1 AA-AAAAG
2250377 ATCAAAAAG
1 A--AAAAAG
2250386 AAAAA
1 AAAAA
2250391 GGGACAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
7 19 0.34
8 30 0.54
9 7 0.12
ACGTcount: A:0.79, C:0.08, G:0.12, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:2251199 original size:22 final size:22
Alignment explanation
Indices: 2251166--2251286 Score: 206
Period size: 22 Copynumber: 5.5 Consensus size: 22
2251156 GCTACCCCAT
*
2251166 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
2251188 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
2251210 CAAACCTTTAAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
2251232 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
2251254 CAAACCTTTGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGC
2251276 CAAACCTTTGA
1 CAAACCTTTGA
2251287 CCAAACATAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 93 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:2252281 original size:106 final size:106
Alignment explanation
Indices: 2252091--2253784 Score: 2524
Period size: 106 Copynumber: 16.0 Consensus size: 106
2252081 ATATCGTGCC
* * * * * * *
2252091 ACTCAAGACAACACAAGTTCAACATCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
2252156 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2252197 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
2252262 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
2252303 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
2252368 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2252409 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
2252474 AATTTTAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2252515 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2252580 AATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2252621 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2252686 AATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2252727 ATTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2252792 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2252833 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2252898 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
2252939 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
2253004 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2253045 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
2253110 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2253151 ACTCAAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
2253216 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2253257 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2253322 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2253363 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2253428 AATTTCAGAGCCAATTTCAACTTCACGACGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2253469 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
2253534 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * * * * * *
2253575 AC-CCAAGACAACATAAGCTCAACTTCATGACGAAGGGGCGGCTGATTGTCAA-CAA-AA-TAT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT-TC
* * * *
2253635 -C-A-TTCAGAGTCAATTTCGACTTCACAGCGAAGGACATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * * * * *
2253675 ACTTGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAATAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAACTTCC
** * * *
2253739 CGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
2253781 ACTC
1 ACTC
2253785 AGAACAATGC
Statistics
Matches: 1441, Mismatches: 136, Indels: 22
0.90 0.09 0.01
Matches are distributed among these distances:
99 1 0.00
100 73 0.05
101 3 0.00
102 4 0.00
103 2 0.00
104 4 0.00
105 3 0.00
106 1351 0.94
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2254561 original size:37 final size:37
Alignment explanation
Indices: 2254509--2254612 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
2254499 CTTTTCATCC
*
2254509 TACTAGGATTCAAACTCGTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
2254546 TGCTAGGATTCAAACTCCTTAAAATAGGATAGAGTTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
2254583 TACTATGATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
2254613 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:2255284 original size:17 final size:17
Alignment explanation
Indices: 2255264--2255301 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2255254 TTTTTTCATT
*
2255264 TATTTATTA-TTTATTA
1 TATTTAATATTTTATTA
2255280 CTATTTAATATTTTATTA
1 -TATTTAATATTTTATTA
2255298 TATT
1 TATT
2255302 ATACATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTAATATTTTATTA
Found at i:2255337 original size:41 final size:42
Alignment explanation
Indices: 2255290--2255377 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 42
2255280 CTATTTAATA
*
2255290 TTTTATTATATTATACATAC-ATTT-TATATTTTTATATATAT
1 TTTTATTATATTATACATACTATTTATATATTTTCAT-TATAT
* ** *
2255331 TTTTATTATTTTATTTATACTATTTATTTATTTTCATTATAT
1 TTTTATTATATTATACATACTATTTATATATTTTCATTATAT
2255373 TTTTA
1 TTTTA
2255378 GTTTCTTTGC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
41 17 0.43
42 14 0.35
43 9 0.22
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (42 bp):
TTTTATTATATTATACATACTATTTATATATTTTCATTATAT
Found at i:2255361 original size:22 final size:20
Alignment explanation
Indices: 2255262--2255377 Score: 64
Period size: 21 Copynumber: 5.8 Consensus size: 20
2255252 ATTTTTTTCA
*
2255262 TTTATTTAT-TATTTATTACT
1 TTTATATATATATTTATTA-T
*
2255282 ATT-TA-ATAT-TTTATTAT
1 TTTATATATATATTTATTAT
* * *
2255299 ATTATACATACATTT-TATATT
1 TTTATATATATATTTAT-TA-T
*
2255320 TTTATATATATTTTTATTAT
1 TTTATATATATATTTATTAT
*
2255340 TTTATTTATACTATTTATTTAT
1 TTTATATATA-TATTTA-TTAT
*
2255362 TTTCAT-TATATTTTTA
1 TTT-ATATATATATTTA
2255378 GTTTCTTTGC
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
17 4 0.05
18 11 0.14
19 6 0.08
20 17 0.22
21 24 0.32
22 12 0.16
23 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATATATATATTTATTAT
Found at i:2259732 original size:106 final size:106
Alignment explanation
Indices: 2259542--2260854 Score: 2105
Period size: 106 Copynumber: 12.4 Consensus size: 106
2259532 ATATCGTGCC
* * * * * * *
2259542 ACTCAAGACAACACAAGTTCAACATCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
2259607 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2259648 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
2259713 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
2259754 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
2259819 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2259860 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
2259925 AATTTTAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2259966 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2260031 AATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2260072 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2260137 AATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2260178 ATTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
2260243 AATTTCAGAGCCAA-TTC-ACTTCACAGCG-AGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2260281 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2260346 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
2260387 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
2260452 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2260493 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
2260558 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2260599 ACTCAAGGCAACGCAAGTTCAACTTCACGGACGAA-GGA-CGCTGGTTGTCAATAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCAC-GACGAAGGGACCGCTGGTTGTCAATAAACAACTTCC
*
2260662 CAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2260704 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2260769 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2260810 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGG
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
2260855 ACGCAAGTTC
Statistics
Matches: 1117, Mismatches: 84, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
103 82 0.07
104 18 0.02
105 106 0.09
106 906 0.81
107 5 0.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2260869 original size:35 final size:35
Alignment explanation
Indices: 2260823--2260889 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
2260813 CCAGACAACA
*
2260823 CAAGTTCAACTTCACGACGAAGGGACCACTGGACG
1 CAAGTTCAACTTCACGACGAAGGAACCACTGGACG
*
2260858 CAAGTTCAACTTCACGACGAAGGAACCGCTGG
1 CAAGTTCAACTTCACGACGAAGGAACCACTGG
2260890 TTGTCAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.15
Consensus pattern (35 bp):
CAAGTTCAACTTCACGACGAAGGAACCACTGGACG
Found at i:2260912 original size:247 final size:235
Alignment explanation
Indices: 2260609--2261090 Score: 635
Period size: 247 Copynumber: 2.0 Consensus size: 235
2260599 ACTCAAGGCA
2260609 ACGCAAGTTCAACTTCACGGACGAAGGACGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGC
1 ACGCAAGTTCAACTTCACGGACGAAGGACGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGC
* * *
2260674 CAATTTCAACTTCACAATGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAA
66 CAATTTCAACTTCACAACGAAGGATATTGGAC-CCAAGACAACACAAGCTCAACTTCACGACGAA
* * *
2260738 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGG
130 GGGACCGCTGATTGTCAA-AAA-AA--TATC-A-TTCAGAGCCAATTTCAACTT--C-ACGAAGG
* *
2260803 ATATTAGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGG
186 ACATTAGACT--AGACAACACAAGTTCAACTTCACAACGAAGGGACCACTGG
2260855 ACGCAAGTTCAACTTCAC-GACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGA
1 ACGCAAGTTCAACTTCACGGACGAAGG-A-CGCTGGTTGTCAATAAACAACTTCCCAATTTCAGA
* * * * *
2260919 GCCAATTTCAACTTCTCAGCGAAGGATCTTGGACCCAAGACAACATAAGCTCAACTTCATGACGA
64 GCCAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACGACGA
* * * * * *
2260984 AGGGGCGGCTGATTGTCAACAAAATATCATTCAGAGTCAATTTCGACTTCACGAAGGACATTGGA
129 AGGGACCGCTGATTGTCAAAAAAATATCATTCAGAGCCAATTTCAACTTCACGAAGGACATTAGA
* *
2261049 CTTGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGG
194 CTAGACAACACAAGTTCAACTTCACAACGAAGGGACCACTGG
2261091 TTGTCAACAA
Statistics
Matches: 212, Mismatches: 21, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
236 37 0.17
238 15 0.07
239 1 0.00
241 17 0.08
242 1 0.00
243 3 0.01
245 10 0.05
246 23 0.11
247 105 0.50
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (235 bp):
ACGCAAGTTCAACTTCACGGACGAAGGACGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGC
CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACGACGAAG
GGACCGCTGATTGTCAAAAAAATATCATTCAGAGCCAATTTCAACTTCACGAAGGACATTAGACT
AGACAACACAAGTTCAACTTCACAACGAAGGGACCACTGG
Found at i:2260973 original size:141 final size:141
Alignment explanation
Indices: 2260714--2260987 Score: 442
Period size: 141 Copynumber: 1.9 Consensus size: 141
2260704 ACTCCAGACA
* * *
2260714 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTTAGAG
1 ACGCAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
*
2260779 CCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACACAAGTTCAACTTCACGACGAA
66 CCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACACAAGCTCAACTTCACGACGAA
2260844 GGGACCACTGG
131 GGGACCACTGG
2260855 ACGCAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
1 ACGCAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
* * * * * *
2260920 CCAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACATAAGCTCAACTTCATGACGA
66 CCAATTTCAACTTCACAACGAAGGATATTAGACTCC-AGACAACACAAGCTCAACTTCACGACGA
2260984 AGGG
130 AGGG
2260988 GCGGCTGATT
Statistics
Matches: 122, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
140 2 0.02
141 120 0.98
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (141 bp):
ACGCAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
CCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACACAAGCTCAACTTCACGACGAA
GGGACCACTGG
Found at i:2261902 original size:37 final size:37
Alignment explanation
Indices: 2261850--2261953 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
2261840 CTTTTCATCC
*
2261850 TACTAGGATTCAAACTCGTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
2261887 TGCTAGGATTCAAACTCCTTAAAATAGGATAGAGTTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
2261924 TACTATGATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
2261954 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:2262670 original size:24 final size:22
Alignment explanation
Indices: 2262640--2262695 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
2262630 CTATTTAATA
2262640 TTTTATTATATTATACATACATT
1 TTTTATTAT-TTATACATACATT
* *
2262663 TTTATATT-TTTATATATATATT
1 TTT-TATTATTTATACATACATT
2262685 TTTTATTATTT
1 TTTTATTATTT
2262696 TATTTATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 17 0.59
23 4 0.14
24 4 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATTATTTATACATACATT
Found at i:2262675 original size:22 final size:21
Alignment explanation
Indices: 2262640--2262718 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 21
2262630 CTATTTAATA
2262640 TTTTATTATATTATACATACATT
1 TTTTATT-T-TTATACATACATT
* *
2262663 TTTATATTTTTATATATATATT
1 TTT-TATTTTTATACATACATT
**
2262685 TTTTATTATTTTATTTATACTATT
1 TTTTA-T-TTTTATACATAC-ATT
2262709 TATTTATTTT
1 T-TTTATTTT
2262719 CATTATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.04
22 15 0.32
23 17 0.36
24 9 0.19
25 4 0.09
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTTTTATACATACATT
Found at i:2262691 original size:21 final size:21
Alignment explanation
Indices: 2262661--2262730 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 21
2262651 TATACATACA
2262661 TTTTTATATTTTTATATATATAT
1 TTTTTATA-TTTTAT-TATATAT
2262684 TTTTTATTATTTTATTTATACTAT
1 TTTTTA-TATTTTA-TTATA-TAT
*
2262708 TTATTTAT-TTTCATTATAT-T
1 TT-TTTATATTTTATTATATAT
2262728 TTT
1 TTT
2262731 AGTTTCTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 1 0.02
22 5 0.12
23 19 0.45
24 9 0.21
25 4 0.10
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATATTTTATTATATAT
Found at i:2262726 original size:45 final size:44
Alignment explanation
Indices: 2262640--2262730 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 44
2262630 CTATTTAATA
*
2262640 TTTTATTATATTATACATACATTTTTATATTTTTATATATATATT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATAT-TT
* **
2262685 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATATTT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATTT
2262729 TT
1 TT
2262731 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
44 4 0.10
45 22 0.55
46 12 0.30
47 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (44 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATTT
Found at i:2262727 original size:28 final size:27
Alignment explanation
Indices: 2262671--2262728 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
2262661 TTTTTATATT
* *
2262671 TTTATATATATATTTTTTATTATTTTA
1 TTTATATATATATTTTTTATCATTATA
*
2262698 TTTATACTATTTATTTATTT-TCATTATA
1 TTTATA-TATATATTT-TTTATCATTATA
2262726 TTT
1 TTT
2262729 TTAGTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTATATATATATTTTTTATCATTATA
Found at i:2262957 original size:19 final size:19
Alignment explanation
Indices: 2262917--2262956 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2262907 GTTTTGTTAC
*
2262917 TTTCTTTTAATATTATTAT
1 TTTCTTTTAATAATATTAT
*
2262936 TTTCTTTTAA-AATCTTAT
1 TTTCTTTTAATAATATTAT
2262954 TTT
1 TTT
2262957 TAAGGGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTTTTAATAATATTAT
Found at i:2270813 original size:59 final size:60
Alignment explanation
Indices: 2270744--2270862 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 60
2270734 ATAAATGAAC
2270744 AAAACTCTTCCATTCCACTGTTGCCCTCAAAAATAAAAGAGACACAATACACA-TCTCAT
1 AAAACTCTTCCATTCCACTGTTGCCCTCAAAAATAAAAGAGACACAATACACATTCTCAT
2270803 AAAACTCTTCCATTCCACTGTTGCCCTCAAAAATAAAAGAGACACAATACACATTCTCAT
1 AAAACTCTTCCATTCCACTGTTGCCCTCAAAAATAAAAGAGACACAATACACATTCTCAT
2270863 TGACGAACAA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 53 0.90
60 6 0.10
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (60 bp):
AAAACTCTTCCATTCCACTGTTGCCCTCAAAAATAAAAGAGACACAATACACATTCTCAT
Found at i:2272870 original size:76 final size:76
Alignment explanation
Indices: 2272742--2272907 Score: 244
Period size: 76 Copynumber: 2.2 Consensus size: 76
2272732 TTAAACTCAA
* *
2272742 ATTTAGGATAATATTTTAAACATTATATTTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
2272807 ATTTTAATTAAG
65 ATTTTAATTAAG
* * * *
2272819 TTTTAGGATATTATTTT-TATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
*
2272883 TTTTAATTAGG
66 TTTTAATTAAG
*
2272894 ATTTAGAATATTAT
1 ATTTAGGATATTAT
2272908 ATTATTTTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 30 0.38
76 35 0.44
77 15 0.19
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (76 bp):
ATTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
TTTTAATTAAG
Found at i:2272893 original size:19 final size:19
Alignment explanation
Indices: 2272865--2272927 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
2272855 TGTATTTTAG
*
2272865 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
2272884 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
2272903 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
2272924 TTTA
1 TTTA
2272928 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:2273582 original size:21 final size:22
Alignment explanation
Indices: 2273557--2273597 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2273547 CTTTAATTTG
2273557 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
2273578 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
2273598 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:2279309 original size:20 final size:20
Alignment explanation
Indices: 2279277--2279323 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
2279267 CATTTCGTTA
2279277 TATTTTTGTTTTTATTTTTTT
1 TATTTTTGTTTTTA-TTTTTT
2279298 TATTTTTG-TTTTATTTTTT
1 TATTTTTGTTTTTATTTTTT
2279317 TATTTTT
1 TATTTTT
2279324 TTAACGAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 13 0.50
20 5 0.19
21 8 0.31
ACGTcount: A:0.11, C:0.00, G:0.04, T:0.85
Consensus pattern (20 bp):
TATTTTTGTTTTTATTTTTT
Found at i:2279324 original size:21 final size:22
Alignment explanation
Indices: 2279274--2279325 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
2279264 ACACATTTCG
2279274 TTATATTTTTGTTTTTATTTTT
1 TTATATTTTTGTTTTTATTTTT
2279296 TT-TATTTTTG-TTTTATTTTT
1 TTATATTTTTGTTTTTATTTTT
*
2279316 TTATTTTTTT
1 TTATATTTTT
2279326 AACGAACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 14 0.50
22 2 0.07
ACGTcount: A:0.12, C:0.00, G:0.04, T:0.85
Consensus pattern (22 bp):
TTATATTTTTGTTTTTATTTTT
Found at i:2279326 original size:8 final size:9
Alignment explanation
Indices: 2279285--2279325 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
2279275 TATATTTTTG
2279285 TTTTTATTT
1 TTTTTATTT
2279294 TTTTTATTT
1 TTTTTATTT
2279303 TTGTTT-TATT
1 TT-TTTAT-TT
2279313 TTTTTATTT
1 TTTTTATTT
2279322 TTTT
1 TTTT
2279326 AACGAACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.10, C:0.00, G:0.02, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:2279535 original size:30 final size:30
Alignment explanation
Indices: 2279499--2279568 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
2279489 ATTTGGTTCG
*
2279499 AACAATGCAGAAAAATACACAGCATATTCA
1 AACAATGCAGAAAAATACACAGCAGATTCA
2279529 AACAATGCAGAAAAATACACAGCAGATTCA
1 AACAATGCAGAAAAATACACAGCAGATTCA
2279559 AACAATGCAG
1 AACAATGCAG
2279569 TGCAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.53, C:0.20, G:0.13, T:0.14
Consensus pattern (30 bp):
AACAATGCAGAAAAATACACAGCAGATTCA
Found at i:2280940 original size:87 final size:87
Alignment explanation
Indices: 2280843--2281017 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
2280833 AAATTGAAGA
2280843 TGACAACTTATGATTTTGATATGTTAATTGAAGAATGCTTGAGGACAAACATTGAATAAGTGAGG
1 TGACAACTTATGATTTTGATATGTTAATTGAAGAATGCTTGAGGACAAACATTGAATAAGTGAGG
2280908 GGGAATTTGATAAGTGCTTAAT
66 GGGAATTTGATAAGTGCTTAAT
2280930 TGACAACTTATGATTTTGATATGTTAATTGAAGAATGCTTGAGGACAAACATTGAATAAGTGAGG
1 TGACAACTTATGATTTTGATATGTTAATTGAAGAATGCTTGAGGACAAACATTGAATAAGTGAGG
2280995 GGGAATTTGATAAGTGCTTAAT
66 GGGAATTTGATAAGTGCTTAAT
2281017 T
1 T
2281018 TAATTAATAT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (87 bp):
TGACAACTTATGATTTTGATATGTTAATTGAAGAATGCTTGAGGACAAACATTGAATAAGTGAGG
GGGAATTTGATAAGTGCTTAAT
Found at i:2281282 original size:76 final size:75
Alignment explanation
Indices: 2281202--2281349 Score: 217
Period size: 76 Copynumber: 2.0 Consensus size: 75
2281192 TAAACTCAAA
* *
2281202 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTACCTTTGTATTTTAGTTTAAATAGG-TTTTAATA
2281266 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * *
2281278 TTTAGGATATTATTTTTATATTTTATCTTTACCTTTGTATTTTAGTTTAAATAGGTTTTAATATT
1 TTTAGGATAATATTTTAACATTATATCTTTACCTTTGTATTTTAGTTTAAATAGGTTTTAATATT
2281343 TTAATTA
66 TTAATTA
2281350 GGATTTAGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 23 0.35
76 42 0.65
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.57
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTACCTTTGTATTTTAGTTTAAATAGGTTTTAATATT
TTAATTAAGT
Found at i:2282038 original size:23 final size:23
Alignment explanation
Indices: 2282012--2282061 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2282002 CTTTAATTTG
* *
2282012 TTTATTTAATTATTATTTTTTCT
1 TTTATTTAATTATAATTTTTTAT
2282035 TTTATTTAATTATAATTTTTTAT
1 TTTATTTAATTATAATTTTTTAT
2282058 TTTA
1 TTTA
2282062 ACCACAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTATTTAATTATAATTTTTTAT
Found at i:2286062 original size:37 final size:37
Alignment explanation
Indices: 2286004--2286122 Score: 156
Period size: 37 Copynumber: 3.3 Consensus size: 37
2285994 TCCTATTATC
* *
2286004 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
2286040 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
* * *
2286076 A-TTTTCAAAAAAACAGTTACCAAACTTTGAAAATC-
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
2286111 ATTTTTTCAAAG
1 A-TTTTTCAAAG
2286123 TTGTCAAACT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
35 27 0.37
36 18 0.25
37 28 0.38
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.33
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
Found at i:2286090 original size:35 final size:36
Alignment explanation
Indices: 2286004--2286121 Score: 152
Period size: 35 Copynumber: 3.3 Consensus size: 36
2285994 TCCTATTATC
* *
2286004 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAAAAACATTTACCAAACTTTG-AAAACT
*
2286040 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAAAAACATTTACCAAACTTTGAAAACT
*
2286076 A-TTTTCAAAAAAACAGTTACCAAACTTTGAAAA-T
1 ATTTTTCAAAAAAACATTTACCAAACTTTGAAAACT
2286110 CATTTTTTCAAA
1 -A-TTTTTCAAA
2286122 GTTGTCAAAC
Statistics
Matches: 74, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
34 1 0.01
35 31 0.42
36 14 0.19
37 28 0.38
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (36 bp):
ATTTTTCAAAAAAACATTTACCAAACTTTGAAAACT
Found at i:2290685 original size:36 final size:36
Alignment explanation
Indices: 2290615--2290734 Score: 154
Period size: 37 Copynumber: 3.3 Consensus size: 36
2290605 TCTCGTTATC
* *
2290615 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAAAAACATTTACCAAACTTTG-AAAACT
*
2290651 ATTTTTCAAATAAACATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAAAAACATTTACCAAACTTTGAAAACT
*
2290687 A-TTTTCAAAAAAAAACATTTACCAAACTTTGAAAATT
1 ATTTTTC--AAAAAAACATTTACCAAACTTTGAAAACT
2290724 ATTTTTTCAAA
1 A-TTTTTCAAA
2290735 GTTGGTTGCC
Statistics
Matches: 75, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
35 5 0.07
36 14 0.19
37 51 0.68
39 5 0.07
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.35
Consensus pattern (36 bp):
ATTTTTCAAAAAAACATTTACCAAACTTTGAAAACT
Found at i:2291391 original size:20 final size:20
Alignment explanation
Indices: 2291366--2291466 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
2291356 AATTGGGAAA
2291366 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
2291386 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2291406 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
2291427 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
2291447 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
2291467 TTTGCAACGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 51 0.75
21 13 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2291410 original size:61 final size:61
Alignment explanation
Indices: 2291363--2291479 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
2291353 GCGAATTGGG
* * * * *
2291363 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
2291424 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTTGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
2291480 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:2291467 original size:20 final size:20
Alignment explanation
Indices: 2291428--2291480 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2291418 TAATACAAAA
* *
2291428 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
2291448 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
2291468 TTGCAACGCGATT
1 TCGCAACGCGATT
2291481 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:2292076 original size:19 final size:19
Alignment explanation
Indices: 2292054--2292251 Score: 147
Period size: 19 Copynumber: 11.1 Consensus size: 19
2292044 GAAACCAAAA
2292054 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
2292073 TCGCGTTACGA--TTC-TC
1 TCGCATTGCGATTTTCATT
2292089 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2292106 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2292125 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2292144 TCGCATTGCGATTCTC--T
1 TCGCATTGCGATTTTCATT
**
2292161 T-G--TTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
* *
2292177 TCGCGTTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
**
2292193 TCG--TTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
*
2292210 TCCGCATTGCGATTCTCATT
1 T-CGCATTGCGATTTTCATT
* *
2292230 ATCTCGTTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
2292250 TC
1 TC
2292252 AACCAAAAGA
Statistics
Matches: 143, Mismatches: 19, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
14 20 0.14
16 16 0.11
17 14 0.10
18 2 0.01
19 63 0.44
20 27 0.19
21 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2292101 original size:33 final size:33
Alignment explanation
Indices: 2292059--2292226 Score: 201
Period size: 33 Copynumber: 4.9 Consensus size: 33
2292049 CAAAATCGCA
* *
2292059 TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2292092 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC---TCTCG
*
2292130 TTGCGATTTTCATTTCGCATTGCGATTCTCTTG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
** *
2292163 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
**
2292196 TTGCGATAGTCATTTCCGCATTGCGATTCTC
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC
2292227 ATTATCTCGT
Statistics
Matches: 119, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
33 70 0.59
34 14 0.12
35 3 0.03
36 3 0.03
38 29 0.24
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:2292156 original size:71 final size:66
Alignment explanation
Indices: 2292054--2292226 Score: 202
Period size: 71 Copynumber: 2.5 Consensus size: 66
2292044 GAAACCAAAA
* * * **
2292054 TCGCATTGCGATTTTCATTTCGCGTTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCGCATTGCGA--
2292119 TTC
64 TTC
* *
2292122 ATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTTGTTGCGATAGTCATTTCGCGTTGCG
1 ---TCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCGCATTGCG
2292187 ATTC
63 ATTC
* **
2292191 TCTCGTTGCGATAGTCATTTCCGCATTGCGATTCTC
1 TCGCGTTGCGATTTTCATTT-CGCATTGCGATTCTC
2292227 ATTATCTCGT
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
66 17 0.19
67 15 0.16
69 3 0.03
71 56 0.62
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (66 bp):
TCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCGCATTGCGATT
C
Found at i:2294395 original size:42 final size:42
Alignment explanation
Indices: 2294324--2294521 Score: 175
Period size: 42 Copynumber: 4.7 Consensus size: 42
2294314 GCCTGTAATC
* * * * * *
2294324 CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATT
* *
2294366 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATC
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATT
* ** * * * * * *
2294408 CCTCAAGAGTCTACTTCTATCGTTGAAGATGCCCCTATCATT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATT
*
2294450 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCA-T
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATT
* * *
2294491 CGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
2294522 CCCGATTCAC
Statistics
Matches: 122, Mismatches: 32, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
41 4 0.03
42 116 0.95
43 2 0.02
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATT
Found at i:2294479 original size:21 final size:21
Alignment explanation
Indices: 2294455--2294521 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2294445 TCATTCCTCG
2294455 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2294476 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2294497 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2294518 AGAG
1 AGAG
2294522 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2294500 original size:84 final size:84
Alignment explanation
Indices: 2294316--2294491 Score: 316
Period size: 84 Copynumber: 2.1 Consensus size: 84
2294306 CCCGACTCGC
*
2294316 CTGTAATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
2294381 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * *
2294400 CTGTCATCCCTCAAGAGTCTACTTCTATCGTTGAAGATGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
2294465 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
2294484 CTGTCATC
1 CTGTCATC
2294492 GTTGAAGAGG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:2295814 original size:19 final size:19
Alignment explanation
Indices: 2295790--2295846 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
2295780 GTAGAAAGCG
2295790 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2295809 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2295823 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2295842 TTGCG
1 TTGCG
2295847 TAACTGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 6 0.19
16 7 0.23
17 7 0.23
19 11 0.35
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2298041 original size:3 final size:3
Alignment explanation
Indices: 2298033--2298068 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
2298023 TCGGGGACTT
* *
2298033 TTC TTC TTC TTT TTC TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2298069 AGGATTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:2298053 original size:15 final size:15
Alignment explanation
Indices: 2298033--2298068 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
2298023 TCGGGGACTT
2298033 TTCTTCTTCTTTTTC
1 TTCTTCTTCTTTTTC
2298048 TTCTTCTTCTTTTTC
1 TTCTTCTTCTTTTTC
2298063 TTCTTC
1 TTCTTC
2298069 AGGATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
TTCTTCTTCTTTTTC
Found at i:2298277 original size:24 final size:24
Alignment explanation
Indices: 2298243--2298296 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2298233 CTGAAACATC
*
2298243 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
2298267 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2298291 ATCAAA
1 ATCAAA
2298297 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2299102 original size:20 final size:21
Alignment explanation
Indices: 2299077--2299125 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2299067 TCCTAATTCA
*
2299077 CAATGCGAA-TAAGTAAATCG
1 CAATGCGAATTAAGAAAATCG
**
2299097 CAATGCGAATTTGGAAAATCG
1 CAATGCGAATTAAGAAAATCG
2299118 CAATGCGA
1 CAATGCGA
2299126 TACTGACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
CAATGCGAATTAAGAAAATCG
Found at i:2299199 original size:20 final size:20
Alignment explanation
Indices: 2299110--2299201 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
2299100 TGCGAATTTG
* *
2299110 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
2299130 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
2299150 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
2299171 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
2299191 GAAAATCGCAA
1 GAAAATCGCAA
2299202 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:2299509 original size:20 final size:20
Alignment explanation
Indices: 2299417--2299501 Score: 93
Period size: 20 Copynumber: 4.2 Consensus size: 20
2299407 CGGGGAAATT
2299417 GCAACGCGAAAAATGGCTATC
1 GCAACGCG-AAAATGGCTATC
2299438 GCAACGCGAAAATGGCTATC
1 GCAACGCGAAAATGGCTATC
** ***
2299458 GCAATTCG-AAATGAAAAATC
1 GCAACGCGAAAATG-GCTATC
2299478 GCAACGCG-AAATGGCTATC
1 GCAACGCGAAAATGGCTATC
2299497 GCAAC
1 GCAAC
2299502 TAGAAAATCG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
19 13 0.25
20 32 0.60
21 8 0.15
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
GCAACGCGAAAATGGCTATC
Found at i:2299550 original size:19 final size:18
Alignment explanation
Indices: 2299528--2299595 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
2299518 GAAATAAAAA
2299528 TTGCATTGCGATTTTC--
1 TTGCATTGCGATTTTCAT
*
2299544 -T-CGTTGCGATTTTCAT
1 TTGCATTGCGATTTTCAT
2299560 TTCGCATTGCGATTTTCAT
1 TT-GCATTGCGATTTTCAT
2299579 TTCGCATTGCGATTTTC
1 TT-GCATTGCGATTTTC
2299596 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
17 1 0.02
19 31 0.69
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (18 bp):
TTGCATTGCGATTTTCAT
Found at i:2299552 original size:14 final size:16
Alignment explanation
Indices: 2299532--2299605 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
2299522 TAAAAATTGC
2299532 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
2299547 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
2299564 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
2299583 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
2299599 -TTGCGAT
1 ATTGCGAT
2299606 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:2299750 original size:14 final size:14
Alignment explanation
Indices: 2299731--2299767 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2299721 CATCAATTAA
2299731 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2299745 ACAAATCATCTTTT
1 ACAAATCAACATTT
2299759 ACAAATCAA
1 ACAAATCAA
2299768 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2301639 original size:20 final size:19
Alignment explanation
Indices: 2301616--2301683 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
2301606 GAAACTTAAA
2301616 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
2301636 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
2301656 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
2301675 ATCGCAACG
1 ATCGCAACG
2301684 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2301691 original size:14 final size:14
Alignment explanation
Indices: 2301672--2301762 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
2301662 ATGCGAAATG
2301672 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2301686 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
2301705 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2301719 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
2301735 ATGAAATCGCAATGAC
1 A--AAATCGCAACGAC
*
2301751 AAAATCGTAACG
1 AAAATCGCAACG
2301763 CGAAACACAA
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
14 29 0.48
15 1 0.02
16 9 0.15
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2301752 original size:32 final size:33
Alignment explanation
Indices: 2301656--2301767 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
2301646 GGAAATGGCT
2301656 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2301689 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2301722 ATCGCAATGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
2301754 ATCGTAACGCGAAA
1 ATCGCAATGCGAAA
2301768 CACAAATCGC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 27 0.36
33 49 0.64
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2301775 original size:65 final size:66
Alignment explanation
Indices: 2301656--2301778 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 66
2301646 GGAAATGGCT
* *
2301656 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
2301721 A
66 A
* *
2301722 ATCGCAATGCGAAATG-AAATCGCAATGACAAAATCGTAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
2301779 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.02
65 35 0.67
66 16 0.31
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:2301809 original size:18 final size:18
Alignment explanation
Indices: 2301774--2301891 Score: 154
Period size: 18 Copynumber: 6.7 Consensus size: 18
2301764 GAAACACAAA
*
2301774 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
2301793 TCGCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
2301811 TCGCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
2301829 TCGCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
* *
2301847 TCGCATTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
2301863 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
*
2301880 TCGCATTGCGAT
1 TCGCGTTGCGAT
2301892 AGCCATTTCC
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
14 7 0.08
15 3 0.03
16 2 0.02
17 2 0.02
18 57 0.65
19 17 0.19
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:2301830 original size:36 final size:36
Alignment explanation
Indices: 2301774--2301891 Score: 172
Period size: 36 Copynumber: 3.3 Consensus size: 36
2301764 GAAACACAAA
2301774 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
1 TCGCATTGCGA-TTTCATTTCGCGTTGCGATTTCATT
*
2301811 TCGCGTTGCGATTTCATTTCGCGTTGCGATTTCATT
1 TCGCATTGCGATTTCATTTCGCGTTGCGATTTCATT
*
2301847 TCGCATTGCGATTT--TGT--CGTTGCGATTTTCATT
1 TCGCATTGCGATTTCATTTCGCGTTGCGA-TTTCATT
2301880 TCGCATTGCGAT
1 TCGCATTGCGAT
2301892 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
32 8 0.10
33 19 0.25
34 2 0.03
36 38 0.49
37 10 0.13
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (36 bp):
TCGCATTGCGATTTCATTTCGCGTTGCGATTTCATT
Found at i:2301928 original size:20 final size:20
Alignment explanation
Indices: 2301876--2301919 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2301866 TTGCGATTTT
2301876 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
2301895 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
2301915 CATTT
1 CATTT
2301920 TCGTGTTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:2302435 original size:17 final size:18
Alignment explanation
Indices: 2302410--2302453 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2302400 GTCGATCAGA
*
2302410 TGATGGCTCT-GGTGAGG
1 TGATGGCTCTGGGCGAGG
*
2302427 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2302445 TGATGGCTC
1 TGATGGCTC
2302454 CGAATGGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.14, C:0.16, G:0.43, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:2303792 original size:20 final size:20
Alignment explanation
Indices: 2303744--2303802 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2303734 AATAGTTTCT
** *
2303744 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
2303764 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
2303784 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
2303803 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:2304084 original size:22 final size:22
Alignment explanation
Indices: 2304058--2304101 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2304048 GATGGAGATA
2304058 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
2304080 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
2304102 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:2304375 original size:20 final size:20
Alignment explanation
Indices: 2304269--2304403 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
2304259 CGCTTTGAAA
*
2304269 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
2304290 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
2304310 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
2304330 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
2304351 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
2304371 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2304391 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2304404 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2304375 original size:61 final size:61
Alignment explanation
Indices: 2304269--2304406 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
2304259 CGCTTTGAAA
* * * *
2304269 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
2304330 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
2304391 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
2304407 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:2304422 original size:61 final size:61
Alignment explanation
Indices: 2304269--2304424 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
2304259 CGCTTTGAAA
* ** * * * *
2304269 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
2304330 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
2304391 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
2304425 CTACTTTTTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:2310700 original size:179 final size:181
Alignment explanation
Indices: 2310400--2310759 Score: 706
Period size: 179 Copynumber: 2.0 Consensus size: 181
2310390 TCCTTCAAAC
2310400 CATCAATCCAACTGTATCCAACTCCATCACTGAACTGCTCTTTCTGCCTGTATAAAATGTGCTGA
1 CATCAATCCAACTGTATCCAACTCCATCACTGAACTGCTCTTTCTGCCTGTATAAAATGTGCTGA
2310465 AACAGAGGGAATAAGAAGTTTCAATCTTCCAGGAAGTTTTTCATAACAAATCATAGTGAAACATA
66 AACAGAGGGAATAAGAAGTTTCAATCTTCCAGGAAGTTTTTCATAACAAATCATAGTGAAACATA
2310530 AATACAGAG-AGAAAGATAATCAAAGAAACAAGGACCAGAT-AAATGATGG
131 AATACAGAGAAGAAAGATAATCAAAGAAACAAGGACCAGATAAAATGATGG
2310579 CATCAATCCAACTGTATCCAACTCCATCACTGAACTGCTCTTTCTGCCTGTATAAAATGTGCTGA
1 CATCAATCCAACTGTATCCAACTCCATCACTGAACTGCTCTTTCTGCCTGTATAAAATGTGCTGA
2310644 AACAGAGGGAATAAGAAGTTTCAATCTTCCAGGAAGTTTTTCATAACAAATCATAGTGAAACATA
66 AACAGAGGGAATAAGAAGTTTCAATCTTCCAGGAAGTTTTTCATAACAAATCATAGTGAAACATA
2310709 AATACAGAGAAGAAAGATAATCAAAGAAACAAGGACCAGATAAAATGATGG
131 AATACAGAGAAGAAAGATAATCAAAGAAACAAGGACCAGATAAAATGATGG
2310760 TGCCCCAATA
Statistics
Matches: 179, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
179 139 0.78
180 31 0.17
181 9 0.05
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (181 bp):
CATCAATCCAACTGTATCCAACTCCATCACTGAACTGCTCTTTCTGCCTGTATAAAATGTGCTGA
AACAGAGGGAATAAGAAGTTTCAATCTTCCAGGAAGTTTTTCATAACAAATCATAGTGAAACATA
AATACAGAGAAGAAAGATAATCAAAGAAACAAGGACCAGATAAAATGATGG
Found at i:2316618 original size:2 final size:2
Alignment explanation
Indices: 2316611--2316650 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2316601 AATATAATGT
2316611 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
2316651 CTCACACATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2323297 original size:35 final size:37
Alignment explanation
Indices: 2323226--2323298 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
2323216 GTTAGAAAAT
* *
2323226 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
2323263 ATTTATATATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
2323298 A
1 A
2323299 AAGGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 6 0.18
36 14 0.42
37 13 0.39
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:2323846 original size:225 final size:224
Alignment explanation
Indices: 2323415--2323854 Score: 798
Period size: 226 Copynumber: 2.0 Consensus size: 224
2323405 TAATTTAACC
2323415 TAGAATTTTTATTATTCAATGACAGAAAAATGATATTTTAAAAAAAAATTAAGGACATTTTAGTC
1 TAGAATTTTTATTATTCAATGACAGAAAAATGATATTTTAAAAAAAAATTAAGGACATTTTAGTC
2323480 CAAAATGCCGGTAATCGAACAATACCTAAAGGAAATGGAGGTAATGACATTCCCGTAATATACTC
66 CAAAATGCCGGTAATCGAACAATACCTAAAGGAAATGGAGGTAATGACATTCCCGTAATATACTC
*
2323545 CAAAAAATATACTATTGGTAATAAAATATTACCGGGAATGAGATTCTCTGCCAACCAAACATGGG
131 CAAAAAATATACTATTGGTAATAAAATATTACCGGGAATGAGATTCCCTGCCAACCAAACATGGG
2323610 AATGTGAATTCCATTCCCATTAACCTTCG
196 AATGTGAATTCCATTCCCATTAACCTTCG
2323639 TAGAATTTTTATTATTCAATGACAGAAAAATGATATTTTTGAAAAAAAAAATTAA-GACATTTTA
1 TAGAATTTTTATTATTCAATGACAGAAAAATGATA-TTTT--AAAAAAAAATTAAGGACATTTTA
2323703 GTCCAAAATGCCGGTAATCGAACAATACCT-AAGGAAA-GAGAGGTAATGACATTCCCGGTAATA
63 GTCCAAAATGCCGGTAATCGAACAATACCTAAAGGAAATG-GAGGTAATGACATTCCC-GTAATA
2323766 TACTCCAAAAAATATACTATTGGTAATAAAATATTACC-GGAATGAGATTCCCTGCCAACCAAAC
126 TACTCCAAAAAATATACTATTGGTAATAAAATATTACCGGGAATGAGATTCCCTGCCAACCAAAC
2323830 ATGGGAATGTGAATTCCATTCCCAT
191 ATGGGAATGTGAATTCCATTCCCAT
2323855 GGGAATCTAC
Statistics
Matches: 210, Mismatches: 1, Indels: 9
0.95 0.00 0.04
Matches are distributed among these distances:
224 36 0.17
225 78 0.37
226 83 0.40
227 13 0.06
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (224 bp):
TAGAATTTTTATTATTCAATGACAGAAAAATGATATTTTAAAAAAAAATTAAGGACATTTTAGTC
CAAAATGCCGGTAATCGAACAATACCTAAAGGAAATGGAGGTAATGACATTCCCGTAATATACTC
CAAAAAATATACTATTGGTAATAAAATATTACCGGGAATGAGATTCCCTGCCAACCAAACATGGG
AATGTGAATTCCATTCCCATTAACCTTCG
Found at i:2323892 original size:16 final size:16
Alignment explanation
Indices: 2323871--2323903 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2323861 CTACATTCCT
2323871 TGATCCAAACACCCCC
1 TGATCCAAACACCCCC
2323887 TGATCCAAACACCCCC
1 TGATCCAAACACCCCC
2323903 T
1 T
2323904 AAGTGTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.48, G:0.06, T:0.15
Consensus pattern (16 bp):
TGATCCAAACACCCCC
Found at i:2333450 original size:14 final size:14
Alignment explanation
Indices: 2333410--2333479 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 14
2333400 TTCGGTAATC
* *
2333410 CGTTCGTTTATGAT
1 CGTTCATTTATGTT
2333424 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
2333438 TGTTCATTTATG-T
1 CGTTCATTTATGTT
* *
2333451 C---CGTGTATGTT
1 CGTTCATTTATGTT
*
2333462 CATTCATTTATGTT
1 CGTTCATTTATGTT
2333476 CGTT
1 CGTT
2333480 TATGTTCATT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
10 6 0.14
11 2 0.05
13 1 0.02
14 34 0.79
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.54
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:2333467 original size:24 final size:24
Alignment explanation
Indices: 2333440--2333489 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2333430 TTTATGTTTG
2333440 TTCATTTATGTCCGTGTATGTTCA
1 TTCATTTATGTCCGTGTATGTTCA
* *
2333464 TTCATTTATGTTCGTTTATGTTCA
1 TTCATTTATGTCCGTGTATGTTCA
2333488 TT
1 TT
2333490 TATATTCAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.56
Consensus pattern (24 bp):
TTCATTTATGTCCGTGTATGTTCA
Found at i:2333483 original size:10 final size:10
Alignment explanation
Indices: 2333464--2333497 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2333454 TGTATGTTCA
2333464 TTCATTTATG
1 TTCATTTATG
*
2333474 TTCGTTTATG
1 TTCATTTATG
*
2333484 TTCATTTATA
1 TTCATTTATG
2333494 TTCA
1 TTCA
2333498 GCTCAATCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:2334377 original size:24 final size:23
Alignment explanation
Indices: 2334350--2334395 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
2334340 TGTGTAAAAT
* *
2334350 CGTTTACCGTTGACCTTTGACCGC
1 CGTTGACCATTGA-CTTTGACCGC
*
2334374 CGTTGACTATTGACTTTGACCG
1 CGTTGACCATTGACTTTGACCG
2334396 AAAAAGTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (23 bp):
CGTTGACCATTGACTTTGACCGC
Found at i:2336826 original size:57 final size:57
Alignment explanation
Indices: 2336729--2336843 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
2336719 GTTGGAGGAA
* *
2336729 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGTCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTCAGAGCCTTACTGTTCGTGACGGGGTT
* * * *
2336786 GAATACTTGTAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTCGTGGCGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTCAGAGCCTTACTGTTCGTGACGGGGTT
2336843 G
1 G
2336844 TATGGTTATG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.12, C:0.19, G:0.33, T:0.36
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTCGGCTTTGTGCTCAGAGCCTTACTGTTCGTGACGGGGTT
Found at i:2337705 original size:83 final size:83
Alignment explanation
Indices: 2337562--2337730 Score: 284
Period size: 83 Copynumber: 2.0 Consensus size: 83
2337552 TTAAAGAAAA
* * *
2337562 TATAAACCATATCTATTTAAAACCCAAATAATTTTAACTATGAAGTTGTAGGTTACATTAATGAA
1 TATAAACCATACCTATTTAAAACCCAAATAATTTTAACTATGAAGATGTAAGTTACATTAATGAA
2337627 TAATGAATTTTATGTGAT
66 TAATGAATTTTATGTGAT
* *
2337645 TATAAACCATACCTATTTAAAACTCAAATAATTTTAACTATGAAGATGTAAGTTATATTAATGAA
1 TATAAACCATACCTATTTAAAACCCAAATAATTTTAACTATGAAGATGTAAGTTACATTAATGAA
*
2337710 TAATGAATTTTATGTGGT
66 TAATGAATTTTATGTGAT
2337728 TAT
1 TAT
2337731 TGTTGTTGTT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (83 bp):
TATAAACCATACCTATTTAAAACCCAAATAATTTTAACTATGAAGATGTAAGTTACATTAATGAA
TAATGAATTTTATGTGAT
Found at i:2339322 original size:27 final size:27
Alignment explanation
Indices: 2339284--2339351 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
2339274 TGGAATGTGT
2339284 CTCCGAAGATCACACTCAATAGACCTG
1 CTCCGAAGATCACACTCAATAGACCTG
2339311 CTCCGAAGATCACACTCAATAGACCTG
1 CTCCGAAGATCACACTCAATAGACCTG
2339338 CTCCGAAGATCACA
1 CTCCGAAGATCACA
2339352 TTTCTTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.18
Consensus pattern (27 bp):
CTCCGAAGATCACACTCAATAGACCTG
Found at i:2342635 original size:30 final size:30
Alignment explanation
Indices: 2342601--2342671 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
2342591 GAGCAATTTC
* * *
2342601 TTTTGGTTGCAAATATTCGCTGTTTGTACT
1 TTTTGGTTGCAAATATTCACGGTTTCTACT
*
2342631 TTTTGGTTTGCAAATTTTCACGGTTTCTACT
1 TTTTGG-TTGCAAATATTCACGGTTTCTACT
*
2342662 TCTTGGTTGC
1 TTTTGGTTGC
2342672 TGTAACGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.14, C:0.15, G:0.20, T:0.51
Consensus pattern (30 bp):
TTTTGGTTGCAAATATTCACGGTTTCTACT
Found at i:2344719 original size:2 final size:2
Alignment explanation
Indices: 2344712--2344764 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2344702 TGTTTCTGTT
2344712 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2344754 TC TC TC TC TC T
1 TC TC TC TC TC T
2344765 TGCATAGGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2346994 original size:23 final size:23
Alignment explanation
Indices: 2346954--2347004 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
2346944 CAATTTTTTG
*
2346954 AAAAACAATTATATATT-ATTTA
1 AAAAACAATTATACATTAATTTA
* *
2346976 AAAAACGATTATGACATTAATTTG
1 AAAAACAATTAT-ACATTAATTTA
2347000 AAAAA
1 AAAAA
2347005 TTGGCGGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 4 0.17
24 9 0.38
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (23 bp):
AAAAACAATTATACATTAATTTA
Found at i:2347924 original size:30 final size:30
Alignment explanation
Indices: 2347890--2348081 Score: 203
Period size: 30 Copynumber: 6.4 Consensus size: 30
2347880 TCATATTCGA
* *
2347890 TTAAAAGACCAAAATAGAAAAAACAGAAAC
1 TTAAAGGACTAAAATAGAAAAAACAGAAAC
* *
2347920 TTAAAGGACTAAAATA-ACAAAAATAGAAAT
1 TTAAAGGACTAAAATAGA-AAAAACAGAAAC
*
2347950 TTAAAGGACTAAAATAGAAAAAAATAGAAA-
1 TTAAAGGACTAAAATAG-AAAAAACAGAAAC
* * * *
2347980 TTCAGAGGATTAAAATAG-CAAAATAGAAAC
1 TT-AAAGGACTAAAATAGAAAAAACAGAAAC
* * *
2348010 TTAAGGGACTAAAATAGCAAAAACAAAAAC
1 TTAAAGGACTAAAATAGAAAAAACAGAAAC
* *
2348040 TTAAAGGACTAAAATAGAAAAAACATAAAT
1 TTAAAGGACTAAAATAGAAAAAACAGAAAC
2348070 TTAAA-GACTAAA
1 TTAAAGGACTAAA
2348082 CCACAAATTT
Statistics
Matches: 139, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
29 30 0.22
30 84 0.60
31 24 0.17
32 1 0.01
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.17
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGAAAAAACAGAAAC
Found at i:2348100 original size:90 final size:89
Alignment explanation
Indices: 2347909--2348081 Score: 224
Period size: 90 Copynumber: 1.9 Consensus size: 89
2347899 CAAAATAGAA
* * *
2347909 AAAACAGAAACTTAAAGGACTAAAATAACAAAAATAGAAATTTAAAGGACTAAAATAGAAAAAAA
1 AAAACAGAAACTTAAAGGACTAAAATAACAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAAA
* * *
2347974 TAGAAATTCAGAGGATTAAAATAGC
66 TA-AAATTCAGAAGACTAAAACAGC
* * *
2347999 AAAATAGAAACTTAAGGGACTAAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAAC
1 AAAACAGAAACTTAAAGGACTAAAATAACAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAA-
*
2348064 AT-AAATTTA-AAGACTAAA
65 ATAAAATTCAGAAGACTAAA
2348082 CCACAAATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
88 7 0.10
89 6 0.08
90 58 0.79
91 2 0.03
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.17
Consensus pattern (89 bp):
AAAACAGAAACTTAAAGGACTAAAATAACAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAAA
TAAAATTCAGAAGACTAAAACAGC
Found at i:2349587 original size:12 final size:12
Alignment explanation
Indices: 2349554--2349588 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
2349544 ATTTAGTTAT
*
2349554 TAATAATAAAAG
1 TAATAATAATAG
2349566 TAATAATAATAG
1 TAATAATAATAG
2349578 TAATAATAATA
1 TAATAATAATA
2349589 ATTTTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (12 bp):
TAATAATAATAG
Found at i:2352893 original size:29 final size:30
Alignment explanation
Indices: 2352823--2352882 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2352813 CAATTTAAGG
*
2352823 CAAAATGGTTTTTGGACTTGAATTGAGTTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
2352854 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2352883 TTCAATGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:2352988 original size:21 final size:20
Alignment explanation
Indices: 2352962--2353060 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
2352952 AGGGTGTCAA
2352962 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
2352983 AGTGCATCCATGCATCACTGC
1 AGTGCATCCATGCA-CCCTGC
2353004 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
2353025 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
2353046 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
2353061 TCAAACACGG
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.04
20 14 0.21
21 35 0.51
22 13 0.19
23 3 0.04
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:2353106 original size:20 final size:21
Alignment explanation
Indices: 2353081--2353175 Score: 95
Period size: 21 Copynumber: 4.6 Consensus size: 21
2353071 AATGCACTTA
*
2353081 GTGCATCGATGCATC-CTTCT
1 GTGCATCGATGCATCACTGCT
** *
2353101 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATCACTGCT
* * **
2353122 ATGTATCGATGCATCAAGGCT
1 GTGCATCGATGCATCACTGCT
2353143 GTGCATCGATGCATC-CTGCT
1 GTGCATCGATGCATCACTGCT
*
2353163 GTGCATCCATGCA
1 GTGCATCGATGCA
2353176 CGAAGGCTGT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
20 30 0.48
21 32 0.52
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.29
Consensus pattern (21 bp):
GTGCATCGATGCATCACTGCT
Found at i:2353327 original size:20 final size:22
Alignment explanation
Indices: 2353289--2353328 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2353279 TTTTAGTAGA
2353289 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
2353311 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
2353329 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:2354234 original size:15 final size:15
Alignment explanation
Indices: 2354214--2354246 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2354204 GATAACTCCG
2354214 TAAAAAGGCTATATT
1 TAAAAAGGCTATATT
2354229 TAAAAAGGCTATATT
1 TAAAAAGGCTATATT
2354244 TAA
1 TAA
2354247 GGCCTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (15 bp):
TAAAAAGGCTATATT
Found at i:2355129 original size:32 final size:32
Alignment explanation
Indices: 2354997--2355146 Score: 192
Period size: 33 Copynumber: 4.6 Consensus size: 32
2354987 AAAAAAAGGG
* * *
2354997 TTCGGGTCGGGCCGGATTTTTTTAAGTTTGATA
1 TTCGGGTCGGGTCGG-GTTTTTTAAGTGTGATA
*
2355030 TTCGGGTCGGGTCGAGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCG-GGTTTTTTAAGTGTGATA
*
2355063 TTCGGGTCAGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGG-TTTTTTAAGTGTGATA
* * *
2355096 TTCGGGTCGGGTTGGGTTTTTTAAATGTAATA
1 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
*
2355128 TTTGGGTCGGGTCGGGTTT
1 TTCGGGTCGGGTCGGGTTT
2355147 AGGGTGGTCG
Statistics
Matches: 105, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
32 32 0.30
33 72 0.69
34 1 0.01
ACGTcount: A:0.14, C:0.09, G:0.34, T:0.43
Consensus pattern (32 bp):
TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
Found at i:2355157 original size:20 final size:21
Alignment explanation
Indices: 2355132--2355172 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2355122 GTAATATTTG
2355132 GGTC-GGGTCGGGTTTAGGGT
1 GGTCGGGGTCGGGTTTAGGGT
*
2355152 GGTCGGGGTCTGGTTTAGGGT
1 GGTCGGGGTCGGGTTTAGGGT
2355173 TAAAAATACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.05, C:0.10, G:0.54, T:0.32
Consensus pattern (21 bp):
GGTCGGGGTCGGGTTTAGGGT
Found at i:2367230 original size:17 final size:17
Alignment explanation
Indices: 2367208--2367258 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
2367198 GTGTATAAAT
2367208 TAATCAACTCCACAAAA
1 TAATCAACTCCACAAAA
2367225 TAATCAACTCCACAAAA
1 TAATCAACTCCACAAAA
*
2367242 TAATTAACTCCACAAAA
1 TAATCAACTCCACAAAA
2367259 GTGATCAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (17 bp):
TAATCAACTCCACAAAA
Found at i:2368489 original size:13 final size:14
Alignment explanation
Indices: 2368459--2368492 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2368449 ATAATAAAAG
2368459 AATCATTTATTTTA
1 AATCATTTATTTTA
*
2368473 AATCATTT-TTTTC
1 AATCATTTATTTTA
2368486 AATCATT
1 AATCATT
2368493 CACCCCTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (14 bp):
AATCATTTATTTTA
Found at i:2373099 original size:18 final size:19
Alignment explanation
Indices: 2373064--2373100 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2373054 CACGGAATGT
2373064 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2373084 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2373101 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2373282 original size:37 final size:36
Alignment explanation
Indices: 2373248--2373316 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
2373238 TACAAATTGT
2373248 AAAATATTTATAT-ATTTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTAAAAAATTAAATTC
* *
2373284 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTAAAAAATTAAA
2373317 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 25 0.83
37 5 0.17
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTAAAAAATTAAATTC
Found at i:2373796 original size:3 final size:3
Alignment explanation
Indices: 2373790--2373821 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2373780 TCAACCCTCC
2373790 TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2373822 CGTGCAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:2376700 original size:161 final size:163
Alignment explanation
Indices: 2376429--2376749 Score: 619
Period size: 161 Copynumber: 2.0 Consensus size: 163
2376419 GTAAATAGAA
2376429 ACAAGAAAAATAGAATATTCTGCTAGTGTCCCAGCGGTTATAAAACGCTTAAGGTTTACAATGTT
1 ACAAGAAAAATAGAATATTCTGCTAGTGTCCCAGCGGTTATAAAACGCTTAAGGTTTACAATGTT
*
2376494 TTATGCACACATTTGATGTGGTGGTTTGACATCTAAGCTTGCCCTTTTATCAGATTGAATGCGA-
66 TTATGCACACATTTGATGTGGTGGTTTGACATCTAAGCTTGCCCTTTTATCAGATTGAATGAGAT
2376558 TTGTACATAAGTTGAAAAACATGTTAATCTCTT
131 TTGTACATAAGTTGAAAAACATGTTAATCTCTT
2376591 ACAAG-AAAATAGAATATTCTGCTAGTGTCCCAGCGGTTATAAAACGCTTAAGGTTTACAATGTT
1 ACAAGAAAAATAGAATATTCTGCTAGTGTCCCAGCGGTTATAAAACGCTTAAGGTTTACAATGTT
2376655 TTATGCACACATTTGATGTGGTGGTTTGACATCTAAGCTTGCCCTTTTATCAGATTGAATGAGAT
66 TTATGCACACATTTGATGTGGTGGTTTGACATCTAAGCTTGCCCTTTTATCAGATTGAATGAGAT
2376720 TTGTACATAAGTTGAAAAACATGTTAATCT
131 TTGTACATAAGTTGAAAAACATGTTAATCT
2376750 TCTTCTGGTT
Statistics
Matches: 157, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
161 122 0.78
162 35 0.22
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (163 bp):
ACAAGAAAAATAGAATATTCTGCTAGTGTCCCAGCGGTTATAAAACGCTTAAGGTTTACAATGTT
TTATGCACACATTTGATGTGGTGGTTTGACATCTAAGCTTGCCCTTTTATCAGATTGAATGAGAT
TTGTACATAAGTTGAAAAACATGTTAATCTCTT
Found at i:2382653 original size:15 final size:15
Alignment explanation
Indices: 2382633--2382663 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2382623 CGGCATTAAT
2382633 AGCATGTGATCGATA
1 AGCATGTGATCGATA
2382648 AGCATGTGATCGATA
1 AGCATGTGATCGATA
2382663 A
1 A
2382664 AGGGGTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (15 bp):
AGCATGTGATCGATA
Found at i:2383791 original size:223 final size:222
Alignment explanation
Indices: 2383484--2383935 Score: 838
Period size: 223 Copynumber: 2.0 Consensus size: 222
2383474 TCCAAATCAA
2383484 AACT-ACCAGATTGCTATCAAGATATCAAATACATGAAAACTAAGGTTAAGCAAATTAAACGTGC
1 AACTGACCAGATTGCTATCAAGATATCAAATACATGAAAACTAAGGTTAAGCAAATTAAACGTGC
2383548 AAGGTACATATTTTCTCTTCTTTCCAGTAATGGGAAACAAAAT-A-AAATTCCTCAAAGGGAAAA
66 AAGGTACATATTTTCTCTTCTTTCCAGTAATGGGAAACAAAATAATAAATTCCTCAAAGGGAAAA
2383611 ACAAACGACTTTGTCAAATAAACGACCATCATCTATCTAAAACATCAAACATTTAAACCAGCTAT
131 ACAAACGACTTTGTCAAATAAACGACCATCATCTATCTAAAACATCAAACATTTAAACCAGCTAT
2383676 TAGCCTTATTTTTTTTTTTTTGTTTGAAAG
196 TAGCCTTA---TTTTTTTTTTGTTTGAAAG
*
2383706 AACTGACCAGATTGCTATCAAGATATCAAATACATGAACACTAAGGTTAAGCAAATTAAACGTGC
1 AACTGACCAGATTGCTATCAAGATATCAAATACATGAAAACTAAGGTTAAGCAAATTAAACGTGC
2383771 AAGGTACATATTTTCTCTTCTTTCCAGTAATGGGAAACAAAATAAATAAATTCCTCAAAGGGAAA
66 AAGGTACATATTTTCTCTTCTTTCCAGTAATGGGAAACAAAAT-AATAAATTCCTCAAAGGGAAA
2383836 AACAAACGACTTTGTCAAATAAACGACCATCATCTATCTAAAACATCAAACATTTAAACCAGCTA
130 AACAAACGACTTTGTCAAATAAACGACCATCATCTATCTAAAACATCAAACATTTAAACCAGCTA
2383901 TTAGCCTTATTTTTTTTTTGTTTGAAAG
195 TTAGCCTTATTTTTTTTTTGTTTGAAAG
2383929 AACTGAC
1 AACTGAC
2383936 TATTAGTTGT
Statistics
Matches: 225, Mismatches: 1, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
222 4 0.02
223 128 0.57
225 1 0.00
226 92 0.41
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (222 bp):
AACTGACCAGATTGCTATCAAGATATCAAATACATGAAAACTAAGGTTAAGCAAATTAAACGTGC
AAGGTACATATTTTCTCTTCTTTCCAGTAATGGGAAACAAAATAATAAATTCCTCAAAGGGAAAA
ACAAACGACTTTGTCAAATAAACGACCATCATCTATCTAAAACATCAAACATTTAAACCAGCTAT
TAGCCTTATTTTTTTTTTGTTTGAAAG
Found at i:2384683 original size:27 final size:27
Alignment explanation
Indices: 2384645--2384698 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2384635 GTTAAAAAAG
2384645 TTATGAATAGACAACACCTTATAATAA
1 TTATGAATAGACAACACCTTATAATAA
*
2384672 TTATGAATAGACAACACCTTGTAATAA
1 TTATGAATAGACAACACCTTATAATAA
2384699 CTATACGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (27 bp):
TTATGAATAGACAACACCTTATAATAA
Done.