Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008958.1 Hibiscus syriacus cultivar Beakdansim tig00112289_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: 2490255
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2256382 original size:23 final size:23
Alignment explanation
Indices: 2256329--2256415 Score: 72
Period size: 23 Copynumber: 3.9 Consensus size: 23
2256319 GAGTCGATGG
* * *
2256329 TTCTACGAGGTCCTTTGAGAC-A
1 TTCTACGTGGTCTTTTGGGACAA
*
2256351 -TCTATGTGGTCTTTTGGGACAA
1 TTCTACGTGGTCTTTTGGGACAA
*
2256373 TTCTACGTGGT-TCTTTGGGACAT
1 TTCTACGTGGTCT-TTTGGGACAA
** *
2256396 TTCTACACGGTCTTTCGGGA
1 TTCTACGTGGTCTTTTGGGA
2256416 TATTTTATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
21 16 0.31
22 2 0.04
23 33 0.63
24 1 0.02
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (23 bp):
TTCTACGTGGTCTTTTGGGACAA
Found at i:2268262 original size:20 final size:21
Alignment explanation
Indices: 2268237--2268281 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2268227 TTAATAATAA
*
2268237 ATTT-GGAATTATGGTTAAGG
1 ATTTGGGAATTATAGTTAAGG
* *
2268257 ATTTGGGTATTATATTTAAGG
1 ATTTGGGAATTATAGTTAAGG
2268278 ATTT
1 ATTT
2268282 ATATTTAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (21 bp):
ATTTGGGAATTATAGTTAAGG
Found at i:2268285 original size:14 final size:14
Alignment explanation
Indices: 2268266--2268295 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2268256 GATTTGGGTA
*
2268266 TTATATTTAAGGAT
1 TTATATTTAAGAAT
2268280 TTATATTTAAGAAT
1 TTATATTTAAGAAT
2268294 TT
1 TT
2268296 TAGATTTACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (14 bp):
TTATATTTAAGAAT
Found at i:2269566 original size:137 final size:139
Alignment explanation
Indices: 2269345--2269622 Score: 542
Period size: 137 Copynumber: 2.0 Consensus size: 139
2269335 TGATTTAATG
2269345 TACAATATTATCTCATTTATAGATGGACTAGAGACGGGTGAGGATGATCCTCTCCCTAAAAATTT
1 TACAATATTATCTCATTTATAGATGGACTAGAGACGGGTGAGGATGATCCTCTCCCTAAAAATTT
2269410 TAAATTCCTATATATATTAGATTTTGTTTTTTATATTTTCGATTGAAAATCTGATTTTG-CCCCT
66 TAAATTCCTATATATATTAGATTTTGTTTTTTATATTTTCGATTGAAAATCTGATTTTGCCCCCT
2269474 -AAATTTTA
131 AAAATTTTA
2269482 TACAATATTATCTCATTTATAGATGGACTAGAGACGGGTGAGGATGATCCTCTCCCTAAAAATTT
1 TACAATATTATCTCATTTATAGATGGACTAGAGACGGGTGAGGATGATCCTCTCCCTAAAAATTT
2269547 TAAATTCCTATATATATTAGATTTTGTTTTTTATATTTTCGATTGAAAATCTGATTTTGCCCCCT
66 TAAATTCCTATATATATTAGATTTTGTTTTTTATATTTTCGATTGAAAATCTGATTTTGCCCCCT
2269612 AAAATTTTA
131 AAAATTTTA
2269621 TA
1 TA
2269623 AATTCTTTTC
Statistics
Matches: 139, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
137 124 0.89
138 5 0.04
139 10 0.07
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (139 bp):
TACAATATTATCTCATTTATAGATGGACTAGAGACGGGTGAGGATGATCCTCTCCCTAAAAATTT
TAAATTCCTATATATATTAGATTTTGTTTTTTATATTTTCGATTGAAAATCTGATTTTGCCCCCT
AAAATTTTA
Found at i:2277614 original size:2 final size:2
Alignment explanation
Indices: 2277607--2277648 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2277597 TAACGTCTGT
2277607 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
2277649 AAGTCCCATT
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:2278981 original size:23 final size:23
Alignment explanation
Indices: 2278955--2279011 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
2278945 ATCGTTGCAA
*
2278955 AGTAATTTTTTAACA-TTATTTTT
1 AGTAATTTTTT-ACATTTACTTTT
2278978 AGTAGA-TTTTTACATTTACTTTT
1 AGTA-ATTTTTTACATTTACTTTT
*
2279001 AGTATTTTTTT
1 AGTAATTTTTT
2279012 GTAATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 3 0.10
23 25 0.86
24 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.61
Consensus pattern (23 bp):
AGTAATTTTTTACATTTACTTTT
Found at i:2278992 original size:22 final size:24
Alignment explanation
Indices: 2278961--2279004 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2278951 GCAAAGTAAT
*
2278961 TTTTTAACA-TTATTTTTAGTAGA
1 TTTTTAACATTTACTTTTAGTAGA
2278984 TTTTT-ACATTTACTTTTAGTA
1 TTTTTAACATTTACTTTTAGTA
2279005 TTTTTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (24 bp):
TTTTTAACATTTACTTTTAGTAGA
Found at i:2280251 original size:16 final size:16
Alignment explanation
Indices: 2280230--2280261 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2280220 CTTTCAATTT
2280230 ATATTTAGTTATTTTC
1 ATATTTAGTTATTTTC
2280246 ATATTTAGTTATTTTC
1 ATATTTAGTTATTTTC
2280262 TTAATTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
ATATTTAGTTATTTTC
Found at i:2286323 original size:18 final size:18
Alignment explanation
Indices: 2286275--2286323 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
2286265 GATGTAAGCC
*
2286275 AAATTTTGTATGTGAATT
1 AAATTTTGTATGTGAATG
*
2286293 ATAATTTTTTATGTGAATG
1 A-AATTTTGTATGTGAATG
*
2286312 AAATTATGTATG
1 AAATTTTGTATG
2286324 AGATGAGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (18 bp):
AAATTTTGTATGTGAATG
Found at i:2289531 original size:199 final size:200
Alignment explanation
Indices: 2288919--2289829 Score: 1193
Period size: 199 Copynumber: 4.6 Consensus size: 200
2288909 TTCAACATTT
* *
2288919 ATTACTTTAAAGTAATAGGTAAATTTACAATATAAGAGGTAAAAATATACCAGTTTAATGACAAA
1 ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATACCAGTTTAATGACAAA
* * * * * * *
2288984 ATGCGTAAACATAAAGTTTCGATCCTTATTGTATATGTATCCATACTTTTTGT-TCAATATGCTT
66 ATACGTTAACATAAAGTATCGATACTTTTTGTATATGTATCGATACTTTTTGTCT-AGTATGCTT
* * * ** * * * * *
2289048 ACCAAACGATATTTACGCAGAAATTATCGATACACGTA-TAAAACATATCGATTCTTAAAATTTT
130 CCCAAACTAGATGCACGCAGAAAGTATCGATACACATATTAAAA-GTATCGATTCTTAAAACTTC
2289112 GAAACCA
194 GAAACCA
* * * *
2289119 ATTAATTTAAAGAAATAGGTAAATTTACAATGTTAGCAGTAAAAATATACCAGTTTAATGACAAA
1 ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATACCAGTTTAATGACAAA
* * * * *
2289184 ATAC-TTCTACATAAAGTATTGATACTTTTTGTGTTTGTATCGATACTTTTTGTCAAGTATGCTT
66 ATACGTT-AACATAAAGTATCGATACTTTTTGTATATGTATCGATACTTTTTGTCTAGTATGCTT
* * *
2289248 CCCAAACAAGATGCACGCAGAAAGTATCGATACACATATGAAAAGTATCGATTCTTAAAACTGCG
130 CCCAAACTAGATGCACGCAGAAAGTATCGATACACATATTAAAAGTATCGATTCTTAAAACTTCG
*
2289313 AAACCC
195 AAACCA
* *
2289319 ATTAATTTAAAGTAATAGGTAAATTTACAATGTTAGCGGTAAAAATATACCAGTTTAATGACAAA
1 ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATACCAGTTTAATGACAAA
* * * * * *
2289384 TTACTTTAACATAAAATATCGATACTTTTTGTATGTGTATCGACAGTTTTT-TCTAGTATGCTTC
66 ATACGTTAACATAAAGTATCGATACTTTTTGTATATGTATCGATACTTTTTGTCTAGTATGCTTC
*
2289448 CCAAACTAGATGCACGCAGAAAGTATCGATACACATATTAAAAGTATCGATTCTTAAAACTTCAA
131 CCAAACTAGATGCACGCAGAAAGTATCGATACACATATTAAAAGTATCGATTCTTAAAACTTCGA
**
2289513 AACTG
196 AACCA
* * **
2289518 ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAATATATTCTGGTTTAATGACAAA
1 ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATACCAGTTTAATGACAAA
* * * * * * * *
2289583 ATACATTAACATAAAGTTTTGATAGTTTTTGTATGTTTATCGATACGTTTT-TCCAGTATGCTTC
66 ATACGTTAACATAAAGTATCGATACTTTTTGTATATGTATCGATACTTTTTGTCTAGTATGCTTC
* *
2289647 CCAAACTAGATGCACGCAGAAAGTATTGATACACATATCAAAAGTATCGATTCTTAAAACTTCGA
131 CCAAACTAGATGCACGCAGAAAGTATCGATACACATATTAAAAGTATCGATTCTTAAAACTTCGA
2289712 AACCA
196 AACCA
* * * *
2289717 ATTACTTTAAAGTTATAGGTAAATTTATAATGTAAGTGGTAAAAATATATCAGTTTAATGACAAA
1 ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATACCAGTTTAATGACAAA
* *
2289782 ATACGTAAACATAAAGTATCGATACTTTTTGTATATGTGTCGATACTT
66 ATACGTTAACATAAAGTATCGATACTTTTTGTATATGTATCGATACTT
2289830 AAGTATCGAT
Statistics
Matches: 620, Mismatches: 87, Indels: 9
0.87 0.12 0.01
Matches are distributed among these distances:
199 350 0.56
200 264 0.43
201 6 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (200 bp):
ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATACCAGTTTAATGACAAA
ATACGTTAACATAAAGTATCGATACTTTTTGTATATGTATCGATACTTTTTGTCTAGTATGCTTC
CCAAACTAGATGCACGCAGAAAGTATCGATACACATATTAAAAGTATCGATTCTTAAAACTTCGA
AACCA
Found at i:2292821 original size:6 final size:6
Alignment explanation
Indices: 2292810--2292860 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
2292800 TTTATGCAGT
* * * *
2292810 TTTCAA TTTCAA TTTCAA TTTTAA TTTGAG TTTGAA TTTCAA TTTCAA
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
2292858 TTT
1 TTT
2292861 TGGCTCCACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (6 bp):
TTTCAA
Found at i:2293554 original size:21 final size:21
Alignment explanation
Indices: 2293529--2293585 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2293519 GAAATATGAG
2293529 GGGTATCAGTACCTCTTAAGA
1 GGGTATCAGTACCTCTTAAGA
*
2293550 GGGTATCGGTACCTCTTAAGA
1 GGGTATCAGTACCTCTTAAGA
*
2293571 GGGTATCAATACCTC
1 GGGTATCAGTACCTC
2293586 CATATTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (21 bp):
GGGTATCAGTACCTCTTAAGA
Found at i:2295761 original size:351 final size:351
Alignment explanation
Indices: 2295118--2295815 Score: 1288
Period size: 351 Copynumber: 2.0 Consensus size: 351
2295108 CTACTGTGGC
2295118 GGTTTGGGACTCATATTGGATGCATATCGCATTGGAATAGAAAATGCGAACAAATTATTGGTAAA
1 GGTTTGGGACTCATATTGGATGCATATCGCATTGGAATAGAAAATGCGAACAAATTATTGGTAAA
*
2295183 CAACTGGTTCAAGTTGATATAATTTATCAAATTAGCATTCTTGGAGGGTAGTAAGATATTTAAAT
66 CAACTGGTTCAAGTTGAAATAATTTATCAAATTAGCATTCTTGGAGGGTAGTAAGATATTTAAAT
*
2295248 TTCATATCAATCATGGCTTGAAGAGAAGGATACGCTCTTCTCGAATTTTATAAGACTCGAAGAGG
131 TTCATATCAATCATGGCTTGAAGAGAAGGATACGCTCTTCCCGAATTTTATAAGACTCGAAGAGG
*
2295313 TTAACAAACCTAGTGTAGAGATTTTCCCGGCGGCCAGGTTCATTAAAACACAAGTTTCGTATTGT
196 TTAACAAACCTAGTGTAGAGATTTTCCCGGCGGCCAGGTTCATTAAAACACAAGTTTCATATTGT
*
2295378 CATATTGGGTTCATTTAGATTTGGATTTCTTGGAGGAATAGGAAGTGTATTTGGAGGACGGTTTG
261 CATATCGGGTTCATTTAGATTTGGATTTCTTGGAGGAATAGGAAGTGTATTTGGAGGACGGTTTG
*
2295443 GAGGTCAGTTTGATCGACTAGATGGT
326 GAAGTCAGTTTGATCGACTAGATGGT
* * *
2295469 GGTTTGGGACTCATTTTGGATGCATATCTCATTGGAATAGAAAATGCGAACAAATTGTTGGTAAA
1 GGTTTGGGACTCATATTGGATGCATATCGCATTGGAATAGAAAATGCGAACAAATTATTGGTAAA
*
2295534 TAACTGGTTCAAGTTGAAATAATTTATCAAATTAGCATTCTTGGAGGGTAGTAAGATATTTAAAT
66 CAACTGGTTCAAGTTGAAATAATTTATCAAATTAGCATTCTTGGAGGGTAGTAAGATATTTAAAT
2295599 TTCATATCAATCATGGCTTGAAGAGAAGGATACGCTCTTCCCGAATTTTATAAGACTCGAAGAGG
131 TTCATATCAATCATGGCTTGAAGAGAAGGATACGCTCTTCCCGAATTTTATAAGACTCGAAGAGG
2295664 TTAACAAACCTAGTGTAGAGATTTTCCCGGCGGCCAGGTTCATTAAAACACAAGTTTCATATTGT
196 TTAACAAACCTAGTGTAGAGATTTTCCCGGCGGCCAGGTTCATTAAAACACAAGTTTCATATTGT
* * *
2295729 CATATCGGGTTCATTTAGATTTGGATTTCTTGGAGTAATAGGAAGTGTATTTGTAGGTCGGTTTG
261 CATATCGGGTTCATTTAGATTTGGATTTCTTGGAGGAATAGGAAGTGTATTTGGAGGACGGTTTG
2295794 GAAGTCAGTTTGATCGACTAGA
326 GAAGTCAGTTTGATCGACTAGA
2295816 CGATGTCCTA
Statistics
Matches: 335, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
351 335 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (351 bp):
GGTTTGGGACTCATATTGGATGCATATCGCATTGGAATAGAAAATGCGAACAAATTATTGGTAAA
CAACTGGTTCAAGTTGAAATAATTTATCAAATTAGCATTCTTGGAGGGTAGTAAGATATTTAAAT
TTCATATCAATCATGGCTTGAAGAGAAGGATACGCTCTTCCCGAATTTTATAAGACTCGAAGAGG
TTAACAAACCTAGTGTAGAGATTTTCCCGGCGGCCAGGTTCATTAAAACACAAGTTTCATATTGT
CATATCGGGTTCATTTAGATTTGGATTTCTTGGAGGAATAGGAAGTGTATTTGGAGGACGGTTTG
GAAGTCAGTTTGATCGACTAGATGGT
Found at i:2298514 original size:21 final size:21
Alignment explanation
Indices: 2298489--2298553 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2298479 AATTTAAAAT
* *
2298489 GTGTATCGATGCACAGCTACA
1 GTGTACCGATGCACTGCTACA
2298510 GTGTACCGATGCACTG-TAACA
1 GTGTACCGATGCACTGCT-ACA
2298531 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
2298552 GT
1 GT
2298554 AATTTCAGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTACA
Found at i:2303597 original size:33 final size:33
Alignment explanation
Indices: 2303555--2303629 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
2303545 CGCTGATATT
2303555 ACATTTACTAAAGGATTAAACCTTTCACTAATC
1 ACATTTACTAAAGGATTAAACCTTTCACTAATC
*
2303588 ACATTTACTAAATGATTAAACCTTTCACTAATC
1 ACATTTACTAAAGGATTAAACCTTTCACTAATC
2303621 ACATTTACT
1 ACATTTACT
2303630 TTTATCCCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (33 bp):
ACATTTACTAAAGGATTAAACCTTTCACTAATC
Found at i:2335074 original size:23 final size:23
Alignment explanation
Indices: 2335048--2335097 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2335038 CTTTTGAGAC
*
2335048 AATTCTACAAGGTCTTTCGGGAT
1 AATTCTACAAGGTCCTTCGGGAT
* * *
2335071 AATTTTACGATGTCCTTCGGGAT
1 AATTCTACAAGGTCCTTCGGGAT
2335094 AATT
1 AATT
2335098 TTATATGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (23 bp):
AATTCTACAAGGTCCTTCGGGAT
Found at i:2335418 original size:24 final size:24
Alignment explanation
Indices: 2335391--2335444 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2335381 CGTTCATTTA
2335391 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
2335415 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
2335439 CGTTCG
1 CGTTCG
2335445 ATTATGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:2335420 original size:14 final size:14
Alignment explanation
Indices: 2335401--2335453 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
2335391 CGTTCGTGAA
2335401 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2335415 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2335429 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
2335439 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
2335453 C
1 C
2335454 ATTTATGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:2335449 original size:24 final size:24
Alignment explanation
Indices: 2335402--2335476 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
2335392 GTTCGTGAAC
* *
2335402 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
2335426 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
* *
2335450 GTTCATTTATGTTCTTTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
2335474 GTT
1 GTT
2335477 TAACCCAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:2336475 original size:10 final size:10
Alignment explanation
Indices: 2336457--2336531 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
2336447 GGGTCTCCAA
*
2336457 CGTTGATGTT
1 CGTTTATGTT
2336467 CGTTTATGTT
1 CGTTTATGTT
2336477 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
2336488 ATGTTCATGTT
1 -CGTTTATGTT
2336499 CGTTTATGTT
1 CGTTTATGTT
2336509 CG----TGTT
1 CGTTTATGTT
2336515 CGTTTATGTT
1 CGTTTATGTT
2336525 CGTTTAT
1 CGTTTAT
2336532 TTATTAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 6 0.12
10 35 0.67
11 7 0.13
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:2336488 original size:16 final size:16
Alignment explanation
Indices: 2336463--2336527 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
2336453 CCAACGTTGA
2336463 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
2336479 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
2336495 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2336511 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2336527 T
1 T
2336528 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2363675 original size:47 final size:49
Alignment explanation
Indices: 2363548--2363677 Score: 144
Period size: 47 Copynumber: 2.7 Consensus size: 49
2363538 ATATAAATTT
* *
2363548 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA--TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
** *
2363594 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* * *
2363644 CTTGCCA-TT-ATTCCGTGAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
2363678 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
46 6 0.08
47 26 0.36
48 21 0.29
49 2 0.03
50 17 0.24
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (49 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
Found at i:2370002 original size:45 final size:48
Alignment explanation
Indices: 2369880--2370007 Score: 140
Period size: 48 Copynumber: 2.8 Consensus size: 48
2369870 ATATAAATTT
* *
2369880 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA-TTTTTACTAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACTAAAATA
* * *
2369926 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTC-AATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTTACTAAAATA
* * *
2369974 CTTGCCA-TT-ATTCCGTGAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
2370008 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
45 22 0.31
46 6 0.09
47 5 0.07
48 31 0.44
49 6 0.09
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (48 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACTAAAATA
Found at i:2374386 original size:111 final size:112
Alignment explanation
Indices: 2374254--2374481 Score: 359
Period size: 112 Copynumber: 2.0 Consensus size: 112
2374244 GTTATGGGTG
* * * * ** *
2374254 CATTTTGACATACTTTGTGTATGATAG-TATCGATCGATTTTGTTTAATGCATAACGGTGCATTT
1 CATTTCGACATACTTCGTGTATGAAAGTTATCGATCAATTTTACTTAATGCATAACGATGCATTT
* * *
2374318 TCGACATAAAAGGTGTCACCCATGGTATTCATAATGAGGTGAATTAC
66 TCGACATAAAAGGTGCCACACATGGTATTCATAATAAGGTGAATTAC
2374365 CATTTCGACATACTTCGTGTATGAAAGTTATCGATCAATTTTACTTAATGCATAACGATGCATTT
1 CATTTCGACATACTTCGTGTATGAAAGTTATCGATCAATTTTACTTAATGCATAACGATGCATTT
2374430 TCGACATAAAAGGTGCCACACATGGTATTCATAATAAGGTGAATTAC
66 TCGACATAAAAGGTGCCACACATGGTATTCATAATAAGGTGAATTAC
2374477 CATTT
1 CATTT
2374482 TGGTACTTCG
Statistics
Matches: 106, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
111 24 0.23
112 82 0.77
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (112 bp):
CATTTCGACATACTTCGTGTATGAAAGTTATCGATCAATTTTACTTAATGCATAACGATGCATTT
TCGACATAAAAGGTGCCACACATGGTATTCATAATAAGGTGAATTAC
Found at i:2375482 original size:16 final size:16
Alignment explanation
Indices: 2375461--2375496 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2375451 ATTCATGCGA
*
2375461 AAATACGATAATGATG
1 AAATACGATAATGACG
2375477 AAATACGATAATGACG
1 AAATACGATAATGACG
2375493 AAAT
1 AAAT
2375497 TGATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.22
Consensus pattern (16 bp):
AAATACGATAATGACG
Found at i:2376784 original size:43 final size:43
Alignment explanation
Indices: 2376723--2376808 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
2376713 TAAAGGTTGG
*
2376723 CATTTGTTTCTTTTGTTTTGCCCTTCCATTTCCAAATGATTGT
1 CATTTGTTTCTTGTGTTTTGCCCTTCCATTTCCAAATGATTGT
2376766 CATTTGTTTCTTGTGTTTTGCCCTTCCATTTCCAAATGATTGT
1 CATTTGTTTCTTGTGTTTTGCCCTTCCATTTCCAAATGATTGT
2376809 GTCAAAGAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.14, C:0.21, G:0.13, T:0.52
Consensus pattern (43 bp):
CATTTGTTTCTTGTGTTTTGCCCTTCCATTTCCAAATGATTGT
Found at i:2383564 original size:2 final size:2
Alignment explanation
Indices: 2383557--2383593 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2383547 ATGGCTTATT
2383557 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
2383594 TGATGGTATT
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:2394902 original size:182 final size:181
Alignment explanation
Indices: 2394593--2395425 Score: 1157
Period size: 182 Copynumber: 4.6 Consensus size: 181
2394583 TGTTGGTTTA
* * * *
2394593 TGTCGATACTTTATAAAAATGTATCGATCCACATCAATATAATAGGAAAAAATATGACAAAACCG
1 TGTCGATACTTTAT-AAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * *
2394658 ATCACGAAAAGACAAAACCGGTAAAGCGTTACCGGATATATTGAAAGTGTCGCTACTTTAATATA
65 GTCTCGAAAAGACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
* *
2394723 AGTATCGACACATTGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTATAAAG
130 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* * *
2394775 TGTCGATTCTTTATAAATATGTATCGATCCACAGCGATATAACAGGTAAAAATATAACAAAACCG
1 TGTCGATACTTTATAAA-ATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* *
2394840 GTCTCGAAAAGACAAAATCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATAGTTTAATATA
65 GTCTCGAAAAGACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
* **
2394905 AGTATCGACACTTTGAGAATTTAAAAGAGAAGCAGTTTTAGCTTCTATAAAG
130 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* *
2394957 TGTTGATATTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACC-
1 TGTCGATACTTTATAA-AATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * * * * * * *
2395021 GACATCTAAAGGACATAACCGTTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATAA
65 GTC-TCGAAAAGACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATAT
* *
2395086 AAGTATTGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCACCTATAAAG
129 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* *
2395139 TGTCGATACTTTATAAAAATGTATTGATCCATAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTAT-AAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * * * * * ** * *
2395204 GTATCTAAAGGACAAAACCAGTATAGAGCGACCTAATATATTTAAAGTGTTGATACTTTAATATA
65 GTCTCGAAAAGACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
* *
2395269 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAATTTTAGCGCCTATAAAG
130 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* *
2395321 TATCGATACTTTATAACAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAA-AATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
2395386 GTCTC-AAAATGACAAAACCGGTAAAGCGCTACCGGATATA
65 GTCTCGAAAA-GACAAAACCGGTAAAGCGCTACCGGATATA
2395426 AATAAAAGTA
Statistics
Matches: 579, Mismatches: 65, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
181 10 0.02
182 565 0.98
183 4 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (181 bp):
TGTCGATACTTTATAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGG
TCTCGAAAAGACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAA
GTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
Found at i:2397667 original size:15 final size:15
Alignment explanation
Indices: 2397647--2397679 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2397637 TGGTTGTATT
*
2397647 GGGGGATTACGGTGA
1 GGGGGATGACGGTGA
2397662 GGGGGATGACGGTGA
1 GGGGGATGACGGTGA
2397677 GGG
1 GGG
2397680 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.61, T:0.15
Consensus pattern (15 bp):
GGGGGATGACGGTGA
Found at i:2397880 original size:33 final size:33
Alignment explanation
Indices: 2397843--2397905 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
2397833 AGATGGAGTA
*
2397843 GTGAAAGAAGTTGAGGTGTTGAAGGGTGAAGTG
1 GTGAAAGAAGTGGAGGTGTTGAAGGGTGAAGTG
*
2397876 GTGAAAGAAGTGGAGGTGTTGAGGGGTGAA
1 GTGAAAGAAGTGGAGGTGTTGAAGGGTGAA
2397906 CTTAAGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.22
Consensus pattern (33 bp):
GTGAAAGAAGTGGAGGTGTTGAAGGGTGAAGTG
Found at i:2398125 original size:18 final size:18
Alignment explanation
Indices: 2398088--2398126 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2398078 GAATAAATAT
*
2398088 GAAGAAGAAAAGAGGGAG
1 GAAGAAGAAAAGAGGAAG
*
2398106 GAAGAAGAAAAGATGAAG
1 GAAGAAGAAAAGAGGAAG
2398124 GAA
1 GAA
2398127 ATGAGGAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (18 bp):
GAAGAAGAAAAGAGGAAG
Found at i:2400371 original size:200 final size:199
Alignment explanation
Indices: 2400017--2401183 Score: 1418
Period size: 200 Copynumber: 5.8 Consensus size: 199
2400007 GTAAGCATAT
*
2400017 GTGTCGATACAGTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* ** *
2400082 GGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTAT-ATGAGAATAGGTCTACATAATG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGA-GAGAATAGGTCTACATAATG
** * *
2400146 TATCGACACTTTTTCATTATGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGATGAACG
130 TATCGACACTTTTGAATT-TGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAATGATGCACG
2400211 CATAAA
194 CATAAA
** * * *
2400217 GTGTCGATACATTTATTGAAAGTGTCGATCCCAGAAACATTGAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
2400282 GGTAAATTTACAATGTAACCAGTATAACTAAACCGGTTTTATGAAAGAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* *
2400347 ATCGACACTTTTAGAATTTGTGTCGATACTGTTTT-TCCAGAAGGAATGCCCAAAAAGGGTGCAC
131 ATCGACACTTTT-GAATTTGTGTCGATACT-TTTTGTCCAGAAGGAATGCCC-AAAATGATGCAC
2400411 GCA-ACAA
193 GCATA-AA
* *
2400418 GTGTCGATACATTTATAAACAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAA-AAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * * * *
2400483 AGGTAATTTTTCAATGTAATCGGTATACATATATCGGTTTTATGAGAGAATAGGTCTACA-ATAT
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATA-AT
* * * * * * *
2400547 ATATCGACACTTGTGTAATTTGTGTCGATACGTTTGGTCAAGAAGGAATGTCCAAAAATGGTGCA
129 GTATCGACACTTTTG-AATTTGTGTCGATACTTTTTGTCCAGAAGGAATG-CCCAAAATGATGCA
*
2400612 C-CATTAA
192 CGCATAAA
*
2400619 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATTGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* ** * * * * *
2400684 GGTAATTTTGTAATATAACCAGTATAAATATATCGATTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * * * * *
2400749 A-CTGAGACTTTTTTATTTTGTGTCGATATTTTTTGTCAAGAATGAATGCCCAAAATGATGAACG
131 ATC-GACAC-TTTTGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAATGATGCACG
2400813 CATAAA
194 CATAAA
* * * *
2400819 GTGTCGATATATTTATAAAAAGTGTCGATACCAGAAACATCGAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
2400884 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGATAATAGGTCTACA-ATATG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATA-ATG
* * * *
2400948 TAAT-GACACTTGTGTAATTTGTGTCGATACTTTTTTTCCAGAAGGAATG-CCAAAAGGGTTGCA
130 T-ATCGACACTTTTG-AATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAA-TGATGCA
*
2401011 CGCACAAA
192 CGCATAAA
* * * *
2401019 GTGTCGATACATTTTTAAAAAGTGTCCATCCCAAAAACATTGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
2401084 GGTAAATTTCCAATGTAACCGGTATAAATATACTGGTTTTATGAGAAAATAGGTC-ATCATAAAG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CATAATG
* * * * *
2401148 TATTGACAATTATTAAATTCGTGTTGATACTATTTT
130 TATCGACACTT-TTGAATTTGTGTCGATACT-TTTT
2401184 AAATATCACG
Statistics
Matches: 831, Mismatches: 111, Indels: 49
0.84 0.11 0.05
Matches are distributed among these distances:
199 26 0.03
200 582 0.70
201 78 0.09
202 143 0.17
203 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (199 bp):
GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTTTGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAATGATGCACGCA
TAAA
Found at i:2400798 original size:402 final size:398
Alignment explanation
Indices: 2400017--2401183 Score: 1519
Period size: 402 Copynumber: 2.9 Consensus size: 398
2400007 GTAAGCATAT
*
2400017 GTGTCGATACAGTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
*
2400082 GGTAATTTTGT-AATATAACCGGTATAAATATACCGGTTTTAT-ATGAGAATAGGTCTAC-ATAA
66 GGTAATTTT-TCAATGTAACCGGTATAAATATACCGGTTTTATGA-GAGAATAGGTCTACAAT-A
* * * * *
2400144 TGTATCGACACTT-TTTCATTATGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGATGA
128 TGTATCGACACTTGTGTAATT-TGTGTCGATACTTTTTGTCCAGAAGGAATG-CCAAAATGGTGC
** * *
2400208 ACGCATAAAGTGTCGATACATTTATTGAAAGTGTCGATCCCAGAAACATTGAAACCCATAAATAT
191 ACGCATAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATTGAAACCCATAATTAT
* * *
2400273 AATGTAATAGGTAAATTTACAATGTAACCAGTATAACTAAACCGGTTTTATGAAAGAATAGGTCT
256 AATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATA-CGGTTTTATGAGAGAATAGGTCT
*
2400338 ACATAATGTATCGACACTTTTAGAATTTGTGTCGATACTGTTTTTCCAGAAGGAATGCCCAAAAA
320 ACATAATGTATCGACACTTTTAGAATTTGTGTCGATACTGTTTTTCAAGAAGGAATGCCC-AAAA
* *
2400403 GGGTGCACGCA-ACAA
384 GGATGAACGCATA-AA
* *
2400418 GTGTCGATACATTTATAAACAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAA-AAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * * *
2400483 AGGTAATTTTTCAATGTAATCGGTATACATATATCGGTTTTATGAGAGAATAGGTCTACAATATA
65 AGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAATATG
* * *
2400548 TATCGACACTTGTGTAATTTGTGTCGATACGTTTGGTCAAGAAGGAATGTCCAAAAATGGTGCAC
130 TATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATG-CC-AAAATGGTGCAC
*
2400613 -CATTAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATTGAAACCCATAATTATAA
193 GCATAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATTGAAACCCATAATTATAA
* ** * * *
2400677 TGTAATAGGTAATTTTGTAATATAACCAGTATAAATATATCGATTTTATGTGAGAATAGGTCTAC
258 TGTAATAGGTAAATTTACAATGTAACCAGTATAAATATA-CGGTTTTATGAGAGAATAGGTCTAC
* ** * * * *
2400742 ATAATGTA-CTGAGACTTTTTTATTTTGTGTCGATA-TTTTTTGTCAAGAATGAATGCCCAAAAT
322 ATAATGTATC-GACACTTTTAGAATTTGTGTCGATACTGTTTT-TCAAGAAGGAATGCCCAAAAG
2400805 GATGAACGCATAAA
385 GATGAACGCATAAA
* * * *
2400819 GTGTCGATATATTTATAAAAAGTGTCGATACCAGAAACATCGAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
2400884 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGATAATAGGTCTACAATATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAATATGT
* *
2400949 AAT-GACACTTGTGTAATTTGTGTCGATACTTTTTTTCCAGAAGGAATGCCAAAAGGGTTGCACG
131 -ATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAATGG-TGCACG
* * * *
2401013 CACAAAGTGTCGATACATTTTTAAAAAGTGTCCATCCCAAAAACATTGAAACCGATAATTATAAT
194 CATAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATTGAAACCCATAATTATAAT
* * *
2401078 GTAATAGGTAAATTTCCAATGTAACCGGTATAAATATACTGGTTTTATGAGAAAATAGGTC-ATC
259 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATAC-GGTTTTATGAGAGAATAGGTCTA-C
* * * * * *
2401142 ATAAAGTATTGACAATTATTA-AATTCGTGTTGATACTATTTT
322 ATAATGTATCGACACTT-TTAGAATTTGTGTCGATACTGTTTT
2401184 AAATATCACG
Statistics
Matches: 666, Mismatches: 83, Indels: 34
0.85 0.11 0.04
Matches are distributed among these distances:
398 6 0.01
399 9 0.01
400 274 0.41
401 66 0.10
402 293 0.44
403 18 0.03
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (398 bp):
GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAATATGT
ATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAATGGTGCACGCA
TAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATTGAAACCCATAATTATAATGT
AATAGGTAAATTTACAATGTAACCAGTATAAATATACGGTTTTATGAGAGAATAGGTCTACATAA
TGTATCGACACTTTTAGAATTTGTGTCGATACTGTTTTTCAAGAAGGAATGCCCAAAAGGATGAA
CGCATAAA
Found at i:2402485 original size:21 final size:21
Alignment explanation
Indices: 2402461--2402506 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
2402451 TATTTCATCA
2402461 TTGCGCGATGAAGTCTCCATG
1 TTGCGCGATGAAGTCTCCATG
2402482 TTGCGCGATGAAGTCTCCATG
1 TTGCGCGATGAAGTCTCCATG
2402503 TTGC
1 TTGC
2402507 ATGATGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGCGCGATGAAGTCTCCATG
Found at i:2402512 original size:21 final size:21
Alignment explanation
Indices: 2402461--2402514 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2402451 TATTTCATCA
*
2402461 TTGCGCGATGAAGTCTCCATG
1 TTGCACGATGAAGTCTCCATG
*
2402482 TTGCGCGATGAAGTCTCCATG
1 TTGCACGATGAAGTCTCCATG
*
2402503 TTGCATGATGAA
1 TTGCACGATGAA
2402515 TTACGTCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGCACGATGAAGTCTCCATG
Found at i:2402653 original size:3 final size:3
Alignment explanation
Indices: 2402628--2402677 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
2402618 CAAGAGGTCA
* * * * *
2402628 ATG AAG ATG ACG ATG AAG ATG ATG ATG ATA ATG ATG ATG ATT ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
2402676 AT
1 AT
2402678 TCAAATAAGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.40, C:0.02, G:0.28, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:2404413 original size:21 final size:21
Alignment explanation
Indices: 2404389--2404429 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
2404379 ACCCATAAAG
2404389 TGTCGATACTTTTTAAAAAAA
1 TGTCGATACTTTTTAAAAAAA
2404410 TGTCGATACTTTTTAAAAAA
1 TGTCGATACTTTTTAAAAAA
2404430 GAATCAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (21 bp):
TGTCGATACTTTTTAAAAAAA
Found at i:2404588 original size:222 final size:222
Alignment explanation
Indices: 2404188--2404629 Score: 559
Period size: 222 Copynumber: 2.0 Consensus size: 222
2404178 TCCCATAAAG
* * * * *
2404188 TGTCGATACAGTTTTAAAAAGTATCGATCCCAGAAACATCGAAATCCATAAATATAATGTAATAG
1 TGTCGATACAGTTTTAAAAAGAATCAATCCCAAAAACATCAAAACCCATAAATATAATGTAATAG
* * * * *
2404253 GTAAATTTACATTGTAACCAGTATAACTAAACTGGTTTTATGAGAGAATAGGTCTACATAAGGTA
66 GTAAATTTACAATATAACCAGTATAAATAAACCGATTTTATGAGAGAATAGGTCTACATAAGGTA
*
2404318 TCGACACTTCTGGAATTTGTGTCGATACTGTTTGTCCAGAAGGAATGCCCAAAAAGGGTGCA-CC
131 TCAACACTTCTGGAATTTGTGTCGATACTGTTTGTCCAGAAGGAATGCCC-AAAAGGGTG-AGCC
*
2404382 CATAAAGTGTCGATAC-TTTTTAAAAAAA
194 CATAAAGTGTCGATACATTTATAAAAAAA
* *
2404410 TGTCGATAC-TTTTTAAAAAAGAATCAATCCCAAAAACATCAAAACCCATAATTATAATGTAATA
1 TGTCGATACAGTTTT-AAAAAGAATCAATCCCAAAAACATCAAAACCCATAAATATAATGTAATA
* ** * * * * * *
2404474 GGTAATTTTGTAATATAATCGGTATAAATATACCGATTTTATGTGAGAATAGGTTTACATAATGT
65 GGTAAATTTACAATATAACCAGTATAAATAAACCGATTTTATGAGAGAATAGGTCTACATAAGGT
* * * * * *
2404539 GTCAACACTT-TTGAATGTTGTGTCGATACTTTTTGTCTAGAATGAATGCCCAAAAGGGTGAGCG
130 ATCAACACTTCTGGAAT-TTGTGTCGATACTGTTTGTCCAGAAGGAATGCCCAAAAGGGTGAGCC
2404603 CATAAAGTGTCGATACATTTATAAAAA
194 CATAAAGTGTCGATACATTTATAAAAA
2404630 GTATCGATCC
Statistics
Matches: 187, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
220 1 0.01
221 35 0.19
222 151 0.81
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (222 bp):
TGTCGATACAGTTTTAAAAAGAATCAATCCCAAAAACATCAAAACCCATAAATATAATGTAATAG
GTAAATTTACAATATAACCAGTATAAATAAACCGATTTTATGAGAGAATAGGTCTACATAAGGTA
TCAACACTTCTGGAATTTGTGTCGATACTGTTTGTCCAGAAGGAATGCCCAAAAGGGTGAGCCCA
TAAAGTGTCGATACATTTATAAAAAAA
Found at i:2405032 original size:200 final size:199
Alignment explanation
Indices: 2404410--2405362 Score: 1153
Period size: 200 Copynumber: 4.8 Consensus size: 199
2404400 TTTAAAAAAA
* * *
2404410 TGTCGATAC-TTTTTAAAAAAGAATCAATCCCAAAAACATCAAAACCCATAATTATAATGTAATA
1 TGTCGATACATTTTT-AAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
* ** * * * * *
2404474 GGTAATTTTGTAATATAATCGGTATAAATATACCGATTTTATGTGAGAATAGGTTTACATAATGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTGTACATAATGT
* * * *
2404539 GTCAACACTTTTGAATGTTGTGTCGATACTTTTTGTCTAGAATGAATGCCCAAAAGGGTGAGCGC
130 ATCGACACTTTTGAATGTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCCAAAAGGGTGAACGC
2404604 ATAAAG
194 ATAAAG
* *
2404610 TGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
1 TGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAG
* * * * ****
2404675 TTAAATTTACAATGTAATCGGTATAAATAAACCAGTTTT-T-TGAAAA-AAAAATACATAATGTA
66 GTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTGTACATAATGTA
* * * *** *
2404737 TCGACACTTGTGGAAT-TTGTGTCGATACTTTTGGTCCATAAGGAAAATCCAAAA---AG-AC-C
131 TCGACACTT-TTGAATGTTGTGTCGATACTTTT-GTCCAGAATGAATGCCCAAAAGGGTGAACGC
2404796 ATAAAG
194 ATAAAG
* * * *
2404802 TGTCGATACATTTTTAAATAGTATCGATCCCTAAAACATAAAAACTC-ATAAATATAATGTAATA
1 TGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCAAAAC-CGATAATTATAATGTAATA
* ** * * *
2404866 GGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTCAAAATAGGTCTACATAATGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTGTACATAATGT
* * *
2404931 GTCGACACTTTTGAATGATGTGTCGATACGTTTTGTCCAGAATGAATGCCCAAAAGGGTGAACGA
130 ATCGACACTTTTGAATGTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCCAAAAGGGTGAACGC
2404996 ATAAAG
194 ATAAAG
* * **
2405002 TGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATTGAAACCGATAATTATAATGTAATAG
1 TGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAG
* * *
2405067 GTAAATTTACAATGTAACTGGTATAAATATACCGGTTTTATGTTAAAATAGGTGAACATAATGTA
66 GTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTGTACATAATGTA
* * * * *
2405132 TCGACACGTTTAAGAT-TTATGTCGATACCTTTTGTCCAAAATGAATG-CCAAAAGGGTTGCACG
131 TCGACACTTTTGA-ATGTTGTGTCGATA-CTTTTGTCCAGAATGAATGCCCAAAAGGG-TGAACG
2405195 CATAAAG
193 CATAAAG
2405202 TGTCGATACATTTTTTAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
1 TGTCGATACA-TTTTTAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
* * *
2405267 GGTAAATTTACAATGTAACCGGTATAAATGTACCGGTTTTATGAGAAAATAGGTGAACATAATGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTGTACATAATGT
2405332 ATCGACACGTTTT-AGAT-TTGTGTCGATACTT
130 ATCGACAC-TTTTGA-ATGTTGTGTCGATACTT
2405363 GTAAATAACA
Statistics
Matches: 642, Mismatches: 91, Indels: 40
0.83 0.12 0.05
Matches are distributed among these distances:
192 95 0.15
193 3 0.00
194 11 0.02
195 47 0.07
196 8 0.01
197 46 0.07
198 11 0.02
199 13 0.02
200 265 0.41
201 140 0.22
202 3 0.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (199 bp):
TGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTGTACATAATGTA
TCGACACTTTTGAATGTTGTGTCGATACTTTTGTCCAGAATGAATGCCCAAAAGGGTGAACGCAT
AAAG
Found at i:2407664 original size:15 final size:15
Alignment explanation
Indices: 2407644--2407673 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2407634 TGTAAATTAT
2407644 AATCGAAACCAATAA
1 AATCGAAACCAATAA
*
2407659 AATCGAAACCGATAA
1 AATCGAAACCAATAA
2407674 TTATAATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.13
Consensus pattern (15 bp):
AATCGAAACCAATAA
Found at i:2408091 original size:197 final size:196
Alignment explanation
Indices: 2407652--2408138 Score: 626
Period size: 197 Copynumber: 2.5 Consensus size: 196
2407642 ATAATCGAAA
* * *
2407652 CCAATAAAATCGAAACCGATAATTATAATGTAATATGTAAATTTACAATGTAACCGGTATAAATA
1 CCAAAAAAATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGT-ACCGATATAAATA
* * *
2407717 TACCGGTTTTATGAGAAAATAGGTCATCATAAAGTATCGACACTTATTAAATTTGTGTTGATACA
65 TACCGGTTTTATGAAAAAATAGGTCATAATAAAGTATCGACACTTATTAAATTTGTGTCGATACA
* *
2407782 TTTTTTCCATAATGAATGCCAAACGGGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATC
130 TTGTTTCCAGAATGAATGCCAAACGGGTGCACACATAAAGTGTCGATACATTTA-TAAAAGTATC
2407847 GAT
194 GAT
* * * *
2407850 CCCAAAAACATCGAAACCGATAATTACAATGTGATAGGTAAATTTACAATGTACCCGATAGAAAT
1 -CCAAAAAAATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTA-CCGATATAAAT
* *
2407915 ATACCGGTTTTAT-AAAAAATAGGTC-TAAATAATGTATCGACACTCT-TTAAGTTTGTGTCGAT
64 ATACCGGTTTTATGAAAAAATAGGTCAT-AATAAAGTATCGACACT-TATTAAATTTGTGTCGAT
* * ** *
2407977 AC-TTGTTTCCAGAATGAATGCCCAACGATGTGCATGCATAAAGTGTCGATACATTTA-AAATTG
127 ACATTGTTTCCAGAATGAATGCCAAACG-GGTGCACACATAAAGTGTCGATACATTTATAAA-AG
2408040 TATCGAT
190 TATCGAT
* *
2408047 CCAAAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATGTTACCAATATAAAT
1 CCAAAAAA-ATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG-TACCGATATAAAT
* *
2408112 ATACCGG-TTTACTTATAAAATAGGTCA
64 ATACCGGTTTTA-TGAAAAAATAGGTCA
2408139 ATATAAGCGC
Statistics
Matches: 252, Mismatches: 26, Indels: 20
0.85 0.09 0.07
Matches are distributed among these distances:
196 14 0.06
197 87 0.35
198 82 0.33
199 69 0.27
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (196 bp):
CCAAAAAAATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACCGATATAAATAT
ACCGGTTTTATGAAAAAATAGGTCATAATAAAGTATCGACACTTATTAAATTTGTGTCGATACAT
TGTTTCCAGAATGAATGCCAAACGGGTGCACACATAAAGTGTCGATACATTTATAAAAGTATCGA
T
Found at i:2408237 original size:87 final size:86
Alignment explanation
Indices: 2408139--2408305 Score: 289
Period size: 87 Copynumber: 1.9 Consensus size: 86
2408129 AAATAGGTCA
2408139 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
2408204 CCGGTTAAATGCATATTTTATT
66 CCGGTTAAATG-ATATTTTATT
* * *
2408226 ATATAATCGCTATCTATTACATTATATAAGCGCTATCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
2408291 TCGGTTAAATGATAT
66 CCGGTTAAATGATAT
2408306 AACATAATCA
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 4 0.05
87 72 0.95
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (86 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGATATTTTATT
Found at i:2408273 original size:23 final size:23
Alignment explanation
Indices: 2408223--2408267 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2408213 TGCATATTTT
* *
2408223 ATTATATAATCGCTATCTATTAC
1 ATTATATAAGCGCTATCTAATAC
2408246 ATTATATAAGCGCTATCTAATA
1 ATTATATAAGCGCTATCTAATA
2408268 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.40
Consensus pattern (23 bp):
ATTATATAAGCGCTATCTAATAC
Found at i:2411295 original size:45 final size:43
Alignment explanation
Indices: 2411206--2411307 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 43
2411196 GCCCCCTTCA
* * **
2411206 TCCAGCAGCTTCCAGCACTGCAGCAGTCCCTCCACGTTACCGT
1 TCCAGCAGCTTCCAGCAATGCAACAACCCCTCCACGTTACCGT
*
2411249 TCCAGCAGCTTCCAGCAAATGACAACAACCCCTCCACGTTTCCGT
1 TCCAGCAGCTTCCAGC-AATG-CAACAACCCCTCCACGTTACCGT
*
2411294 TCCAGCAACTTCCA
1 TCCAGCAGCTTCCA
2411308 CTAAACCAGC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
43 16 0.31
44 3 0.06
45 32 0.63
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.21
Consensus pattern (43 bp):
TCCAGCAGCTTCCAGCAATGCAACAACCCCTCCACGTTACCGT
Found at i:2412328 original size:21 final size:20
Alignment explanation
Indices: 2412287--2412328 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
2412277 CAGATTATGC
*
2412287 AGGGGGTACAGATTCTCCCT
1 AGGGGGTACAGATTCCCCCT
2412307 AGGGGGTATC-GATTCCCTCCT
1 AGGGGGTA-CAGATTCCC-CCT
2412328 A
1 A
2412329 AAGAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCT
Found at i:2413189 original size:24 final size:24
Alignment explanation
Indices: 2413119--2413189 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
2413109 TAATCTTATA
* *
2413119 TGGCACTACAGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
2413142 TGGCACTTCGGTGCAAATGCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
2413166 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
2413190 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 12 0.30
24 28 0.70
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:2413996 original size:11 final size:11
Alignment explanation
Indices: 2413971--2414047 Score: 82
Period size: 11 Copynumber: 7.0 Consensus size: 11
2413961 TTCCCTATTT
* *
2413971 TACTATAGCAA
1 TACTATAGTAG
*
2413982 TACTGTAGTAG
1 TACTATAGTAG
* *
2413993 TACTATAGCAA
1 TACTATAGTAG
*
2414004 TACTGTAGTAG
1 TACTATAGTAG
* *
2414015 TACTATAGCAA
1 TACTATAGTAG
2414026 TACTATAGTAG
1 TACTATAGTAG
2414037 TACTATAGTAG
1 TACTATAGTAG
2414048 GGTATTTTAC
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 52 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (11 bp):
TACTATAGTAG
Found at i:2413999 original size:22 final size:22
Alignment explanation
Indices: 2413971--2414044 Score: 139
Period size: 22 Copynumber: 3.4 Consensus size: 22
2413961 TTCCCTATTT
2413971 TACTATAGCAATACTGTAGTAG
1 TACTATAGCAATACTGTAGTAG
2413993 TACTATAGCAATACTGTAGTAG
1 TACTATAGCAATACTGTAGTAG
*
2414015 TACTATAGCAATACTATAGTAG
1 TACTATAGCAATACTGTAGTAG
2414037 TACTATAG
1 TACTATAG
2414045 TAGGGTATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (22 bp):
TACTATAGCAATACTGTAGTAG
Found at i:2418464 original size:19 final size:19
Alignment explanation
Indices: 2418440--2418477 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2418430 AGATTATGCA
2418440 GGGGGTA-CAGATTCCCCCT
1 GGGGGTATC-GATTCCCCCT
2418459 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
2418478 TAAAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.13, C:0.32, G:0.32, T:0.24
Consensus pattern (19 bp):
GGGGGTATCGATTCCCCCT
Found at i:2421190 original size:88 final size:89
Alignment explanation
Indices: 2421083--2421275 Score: 275
Period size: 88 Copynumber: 2.2 Consensus size: 89
2421073 ATTTATTCTG
* * * * *
2421083 TTATTAT--TTTATTTTTAAATATGATTCTATAGTTTTAATTTCTTTTATTTTGGTGATTGTTTA
1 TTATTATCCTTTATTTTTAAATACGATGCTATAATTTTAATTTCTTTTATTTTAGTCATTGTTTA
* *
2421146 ATTATAATTTTA-TTTTACTTTTA
66 ATTACAACTTTATTTTTACTTTTA
*
2421169 TTATTGTCCTTTATTTTTAAATACGATGCTATAATTTTAATTTCTTTTATTTTAGTCATTGTTTA
1 TTATTATCCTTTATTTTTAAATACGATGCTATAATTTTAATTTCTTTTATTTTAGTCATTGTTTA
* *
2421234 ATTGCAACTTTATTTTTATTTTTA
66 ATTACAACTTTATTTTTACTTTTA
2421258 TTATTATCCTTTATTTTT
1 TTATTATCCTTTATTTTT
2421276 TGATATGTTT
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
86 6 0.06
88 60 0.65
89 27 0.29
ACGTcount: A:0.24, C:0.07, G:0.06, T:0.63
Consensus pattern (89 bp):
TTATTATCCTTTATTTTTAAATACGATGCTATAATTTTAATTTCTTTTATTTTAGTCATTGTTTA
ATTACAACTTTATTTTTACTTTTA
Found at i:2421468 original size:2 final size:2
Alignment explanation
Indices: 2421461--2421507 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2421451 TACTTAAAAG
2421461 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
2421503 TA TA T
1 TA TA T
2421508 TCAAATTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2425324 original size:18 final size:18
Alignment explanation
Indices: 2425297--2425383 Score: 93
Period size: 19 Copynumber: 4.4 Consensus size: 18
2425287 CATTCATCAG
*
2425297 AAAAGAAAAAAAGAGATGA
1 AAAAGAAAAAAA-AGAAGA
2425316 AAAAGAAAAAAAAGAAGA
1 AAAAGAAAAAAAAGAAGA
*
2425334 AAAAGAAGAAAAAAAAAGTA
1 AAAAGAA-AAAAAAGAAG-A
2425354 AAAAGAGAAAAGGAAAGAAGAA
1 AAAAGA-AAAA--AAAGAAG-A
2425376 AAAAGAAA
1 AAAAGAAA
2425384 TTGAATCAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
18 12 0.20
19 21 0.36
20 10 0.17
21 3 0.05
22 13 0.22
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAAAGAAGA
Found at i:2425333 original size:12 final size:12
Alignment explanation
Indices: 2425318--2425379 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
2425308 AGAGATGAAA
2425318 AAGAAAAAAAAG
1 AAGAAAAAAAAG
*
2425330 AAGAAAAAGAAG
1 AAGAAAAAAAAG
* *
2425342 AAAAAAAAAGTAAA
1 AAGAAAAAA--AAG
2425356 AAGAGAAAAGGAAAG
1 AAGA-AAAA--AAAG
2425371 AAGAAAAAA
1 AAGAAAAAA
2425380 GAAATTGAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
12 19 0.49
14 9 0.23
15 10 0.26
17 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (12 bp):
AAGAAAAAAAAG
Found at i:2425379 original size:29 final size:29
Alignment explanation
Indices: 2425297--2425380 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
2425287 CATTCATCAG
*
2425297 AAAAGAA-AAAAAGAGATGAAAAAGAAA--A
1 AAAAGAAGAAAAAGA-A-GAAAAAAAAAGTA
2425325 AAAAGAAGAAAAAGAAGAAAAAAAAAGTA
1 AAAAGAAGAAAAAGAAGAAAAAAAAAGTA
* *
2425354 AAAAG-AGAAAAGGAAAGAAGAAAAAAG
1 AAAAGAAGAAAAAG-AAGAAAAAAAAAG
2425381 AAATTGAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 9 0.18
28 15 0.31
29 25 0.51
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (29 bp):
AAAAGAAGAAAAAGAAGAAAAAAAAAGTA
Found at i:2427752 original size:22 final size:22
Alignment explanation
Indices: 2427688--2427766 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
2427678 ACATCTACAT
2427688 TCTTCAAAGATGATAGATTCAT-
1 TCTTCAAAGATGATAGATTC-TC
2427710 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
2427732 TCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
2427754 TTTTTAAAGATGA
1 TCTTCAAAGATGA
2427767 AATATTTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
21 1 0.02
22 52 0.98
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:2428574 original size:73 final size:73
Alignment explanation
Indices: 2428455--2428640 Score: 336
Period size: 73 Copynumber: 2.5 Consensus size: 73
2428445 GGATGTTTTC
**
2428455 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTGGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCAATGGAGAAAGT
2428520 TTCACTCG
66 TTCACTCG
2428528 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCAATGGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCAATGGAGAAAGT
2428593 TTCACTCG
66 TTCACTCG
**
2428601 AAATAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
2428641 TATTTCCAGA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 109 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (73 bp):
AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCAATGGAGAAAGT
TTCACTCG
Found at i:2428618 original size:37 final size:37
Alignment explanation
Indices: 2428510--2428618 Score: 96
Period size: 36 Copynumber: 3.0 Consensus size: 37
2428500 TGTTTCTCGC
** *
2428510 TGGAGAAAGTTTCACTCGAAATAGCAATTTATCTCAC
1 TGGAGAAAGTTTCACTCGAAATAAAAATTTATCTCAA
* ** ** * * *
2428547 TTGAGATTGTTTTTCT-TAAA-ACAAATTGTTTCTCAA
1 TGGAGAAAGTTTCACTCGAAATAAAAATT-TATCTCAA
2428583 TGGAGAAAGTTTCACTCGAAATAAAAATTTATCTCA
1 TGGAGAAAGTTTCACTCGAAATAAAAATTTATCTCA
2428619 CTTGAGATTG
Statistics
Matches: 51, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
35 5 0.10
36 20 0.39
37 20 0.39
38 6 0.12
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (37 bp):
TGGAGAAAGTTTCACTCGAAATAAAAATTTATCTCAA
Found at i:2428708 original size:39 final size:39
Alignment explanation
Indices: 2428654--2428868 Score: 299
Period size: 39 Copynumber: 5.5 Consensus size: 39
2428644 TTCCAGATAG
*
2428654 AGTTCATAATCTGAAGAACTCATATGAAGAGGAAGAATG-
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAA-GA
* *
2428693 AGTTCATAATTTGAAGAACTCATCTGAAGATGAAGAAGA
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGA
* *
2428732 AGTTCATAATCTGAAGAACTTATCTGAAGAGGAAGAAGG
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGA
* *
2428771 AGTTCATAATCTGAAGAACTCGTCTAAAGAGGAAGAAGA
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGA
* *
2428810 AGTTCATAGTCTGAAGAACTCACCTTG-AGAGGAAGAAGA
1 AGTTCATAATCTGAAGAACTCATC-TGAAGAGGAAGAAGA
* *
2428849 AATTCATAATATGAAGAACT
1 AGTTCATAATCTGAAGAACT
2428869 TATTCAACCT
Statistics
Matches: 156, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
38 1 0.01
39 154 0.99
40 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (39 bp):
AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGA
Found at i:2429212 original size:35 final size:35
Alignment explanation
Indices: 2429154--2429305 Score: 236
Period size: 35 Copynumber: 4.4 Consensus size: 35
2429144 TTTTAGCTGT
* *
2429154 AGTAG-CCCTTCCATCCAGCAGCTTCCAACACTGC
1 AGTAGCCCCCTCCATCCAGCAGCTTCCAGCACTGC
* * * *
2429188 AGTAGCCCCCTCTATCCAGTAGCTTCTAGCACTAC
1 AGTAGCCCCCTCCATCCAGCAGCTTCCAGCACTGC
2429223 AGTAGCCCCCTCCATCCAGCAGCTTCCAGCACTGC
1 AGTAGCCCCCTCCATCCAGCAGCTTCCAGCACTGC
2429258 AGTAGCCCCCTCCATCCAGCAGCTTCCAGCACTGC
1 AGTAGCCCCCTCCATCCAGCAGCTTCCAGCACTGC
2429293 AGTAG-CCCCTCCA
1 AGTAGCCCCCTCCA
2429306 CGTTACAGTT
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
34 13 0.12
35 94 0.88
ACGTcount: A:0.22, C:0.43, G:0.16, T:0.20
Consensus pattern (35 bp):
AGTAGCCCCCTCCATCCAGCAGCTTCCAGCACTGC
Found at i:2429358 original size:45 final size:45
Alignment explanation
Indices: 2429272--2429423 Score: 191
Period size: 45 Copynumber: 3.4 Consensus size: 45
2429262 GCCCCCTCCA
* * * *
2429272 TCCAGCAGCTTCCAG-CACTG-CAGTAGCCCCTCCACGTTACAGT
1 TCCAGCAGCTTCCAGTAAATGACAGCAACCCCTCCACGTTACAGT
*
2429315 TCCAGCAGCTTCCAGTAAATGACAGCAACCCCTCCATGTTACAGT
1 TCCAGCAGCTTCCAGTAAATGACAGCAACCCCTCCACGTTACAGT
* * *
2429360 TCCAGCAGCTTCCAGTAAATGACAGCAACCCCTCCACATTCCCGT
1 TCCAGCAGCTTCCAGTAAATGACAGCAACCCCTCCACGTTACAGT
* * *
2429405 TTCAGTAGCTTCCACTAAA
1 TCCAGCAGCTTCCAGTAAA
2429424 CCAGTTGTCC
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 15 0.16
44 3 0.03
45 77 0.81
ACGTcount: A:0.26, C:0.36, G:0.15, T:0.22
Consensus pattern (45 bp):
TCCAGCAGCTTCCAGTAAATGACAGCAACCCCTCCACGTTACAGT
Found at i:2429639 original size:13 final size:13
Alignment explanation
Indices: 2429611--2429654 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 13
2429601 TTCTTTTCCA
*
2429611 TTTTGTTTTTC-G
1 TTTTATTTTTCAG
2429623 -TTTATTTTTCAG
1 TTTTATTTTTCAG
2429635 TTTTATTTTTCA-
1 TTTTATTTTTCAG
2429647 TTTT-TTTT
1 TTTTATTTT
2429655 CTCTTCGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 13 0.45
12 5 0.17
13 11 0.38
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.77
Consensus pattern (13 bp):
TTTTATTTTTCAG
Found at i:2430486 original size:88 final size:88
Alignment explanation
Indices: 2430387--2430578 Score: 325
Period size: 88 Copynumber: 2.2 Consensus size: 88
2430377 TTAATTAATT
* *
2430387 TTATTAT--TTTATTTTTAAATATGATGCTATAGTTTTAATTTGTTTTATTTTGGTCATTGTTTA
1 TTATTATCCTTTATTTTTAAATATGATGCTATAATTTTAATTTCTTTTATTTTGGTCATTGTTTA
2430450 ATTGCAATTTTATTTTATTTTTA
66 ATTGCAATTTTATTTTATTTTTA
* *
2430473 TTATTGTCCTTTATTTTTAAATATGATGTTATAATTTTAATTTCTTTTATTTTGGTCATTGTTTA
1 TTATTATCCTTTATTTTTAAATATGATGCTATAATTTTAATTTCTTTTATTTTGGTCATTGTTTA
2430538 ATTGCAATTTTATTTTATTTTTA
66 ATTGCAATTTTATTTTATTTTTA
*
2430561 TTATTATTCTTTATTTTT
1 TTATTATCCTTTATTTTT
2430579 TTGATATGTT
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
86 6 0.06
88 92 0.94
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (88 bp):
TTATTATCCTTTATTTTTAAATATGATGCTATAATTTTAATTTCTTTTATTTTGGTCATTGTTTA
ATTGCAATTTTATTTTATTTTTA
Found at i:2430758 original size:2 final size:2
Alignment explanation
Indices: 2430751--2430786 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2430741 ATATCCTACT
2430751 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
2430787 ATTTTATTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2431650 original size:17 final size:18
Alignment explanation
Indices: 2431628--2431661 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2431618 TCATGAAAAT
2431628 TTTAAAT-TTATTTATAA
1 TTTAAATATTATTTATAA
*
2431645 TTTAAATATTTTTTATA
1 TTTAAATATTATTTATA
2431662 TTTTCTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAATATTATTTATAA
Found at i:2433838 original size:24 final size:24
Alignment explanation
Indices: 2433788--2433838 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2433778 TTACTTTTTA
* **
2433788 ATTTTAATTTTATTGTTTATTTAT
1 ATTTTAATTTTAATGTTTAAATAT
2433812 ATTTTAATTTTAAATGTTTAAAT-T
1 ATTTTAATTTT-AATGTTTAAATAT
2433836 ATT
1 ATT
2433839 ATTTTCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
ATTTTAATTTTAATGTTTAAATAT
Found at i:2434702 original size:14 final size:15
Alignment explanation
Indices: 2434642--2434702 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 15
2434632 TTTCTTTCAA
2434642 ATTTTTTATTACTTATT
1 ATTTTTTATTA-TT-TT
2434659 ATTTTTATATTATTTT
1 ATTTTT-TATTATTTT
** *
2434675 A-TTAATATTTTTTT
1 ATTTTTTATTATTTT
2434689 ATTTTTT-TTATTTT
1 ATTTTTTATTATTTT
2434703 TATTCAGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
14 15 0.42
15 5 0.14
16 3 0.08
17 8 0.22
18 5 0.14
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:2440021 original size:14 final size:14
Alignment explanation
Indices: 2439967--2440026 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
2439957 AAATCCAGCA
2439967 AAGAAAAAAA-AAG
1 AAGAAAAAAAGAAG
* *
2439980 ATGAAAAAGGAAAAATG
1 AAGAAAAA--AAGAA-G
*
2439997 AGGAAAAAAAGAAG
1 AAGAAAAAAAGAAG
*
2440011 AAGAAAAAAAGGAG
1 AAGAAAAAAAGAAG
2440025 AA
1 AA
2440027 ATTGAATCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 7 0.18
14 15 0.39
15 6 0.16
16 2 0.05
17 8 0.21
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAAGAAG
Found at i:2444786 original size:22 final size:22
Alignment explanation
Indices: 2444760--2444836 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
2444750 ATCTACACTC
2444760 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
2444782 TTCAAAGATGATAGGTTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
2444804 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2444826 TTCAAAGATGA
1 TTCAAAGATGA
2444837 AAGCCTTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2445666 original size:166 final size:167
Alignment explanation
Indices: 2445360--2445686 Score: 541
Period size: 166 Copynumber: 2.0 Consensus size: 167
2445350 AAAATTAGTA
2445360 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAAACAGAATGAGAAAAC
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-AAAAAAACAGAATGAGAAAAC
* ** *
2445425 GATTTTCATAGTTTCTCATTTTATCTTTTCTGAAATGAAATTGTTGAAAAGTAAGAAAATGATTT
65 GATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTT
* *
2445490 TCTTAGTTTTTTTACTTAGTAAACTATTTCCAACAGCC
130 CCTTAGTTTTTTTACTTAATAAACTATTTCCAACAGCC
** *
2445528 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAAA-ATAATGAGAAAACG
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAACAGAATGAGAAAACG
2445591 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAATGATTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAATGATTT
2445656 CCTTAGTTTTTTTACTTAATAAACTATTTCC
130 CCTTAGTTTTTTTACTTAATAAACTATTTCC
2445687 CACATCTGTA
Statistics
Matches: 149, Mismatches: 9, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
165 40 0.27
166 66 0.44
168 43 0.29
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (167 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAACAGAATGAGAAAACG
ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTC
CTTAGTTTTTTTACTTAATAAACTATTTCCAACAGCC
Found at i:2446362 original size:76 final size:76
Alignment explanation
Indices: 2445689--2446361 Score: 1206
Period size: 76 Copynumber: 8.9 Consensus size: 76
2445679 CTATTTCCCA
*
2445689 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2445754 AGCCTTAGGGT
66 AGCCTTAGGGT
2445765 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2445830 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2445841 CATCTGTAAGTCCTGCAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2445906 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2445917 CATCTGTAAGTCCTGCAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2445982 AGCCTTAGGGT
66 AGCCTTAGGGT
2445993 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2446058 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2446069 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAGGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2446134 ATCCTTAGGGT
66 AGCCTTAGGGT
* *
2446145 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2446209 AGCCTTCA-GGT
66 AGCCTT-AGGGT
* *
2446220 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2446285 AACCTTAGGGT
66 AGCCTTAGGGT
* *
2446296 CATCTGTAAGTCCTACAGTGCATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2446361 A
66 A
2446362 AAAAAACCTT
Statistics
Matches: 578, Mismatches: 16, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
75 71 0.12
76 507 0.88
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:2446554 original size:16 final size:16
Alignment explanation
Indices: 2446535--2446602 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 16
2446525 TTCATAATAA
2446535 TAATAATAAT-TATTAT
1 TAAT-ATAATATATTAT
2446551 TAATATAATATATTAT
1 TAATATAATATATTAT
*
2446567 TATTATATATATATATAT
1 TAATATA-ATATAT-TAT
2446585 ATATATATATATATATTA
1 -TA-ATATA-ATATATTA
2446603 CAAATTACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.11
16 16 0.36
17 6 0.13
18 3 0.07
19 4 0.09
20 11 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATAATATATTAT
Found at i:2446554 original size:19 final size:19
Alignment explanation
Indices: 2446532--2446584 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
2446522 TTTTTCATAA
2446532 TAATAATAATA-ATTATTAT
1 TAAT-ATAATATATTATTAT
2446551 TAATATAATATATTATTAT
1 TAATATAATATATTATTAT
2446570 TATATATATATATAT
1 TA-ATATA-ATATAT
2446585 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.19
19 14 0.45
20 5 0.16
21 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATAATATATTATTAT
Found at i:2446575 original size:2 final size:2
Alignment explanation
Indices: 2446553--2446600 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
2446543 ATTATTATTA
2446553 AT AT A- AT AT AT -T AT -T AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2446591 AT AT AT AT AT
1 AT AT AT AT AT
2446601 TACAAATTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2447832 original size:29 final size:30
Alignment explanation
Indices: 2447797--2447864 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
2447787 TTAGTCACCA
2447797 ATTTTAATTATAAGTTTTATTACTT-TTTAT
1 ATTTTAATTATAA-TTTTATTACTTATTTAT
* **
2447827 A-TTTAATTTTAATTTTATTGTTTATTTAT
1 ATTTTAATTATAATTTTATTACTTATTTAT
2447856 ATTTTAATT
1 ATTTTAATT
2447865 TTATGTGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.27
29 16 0.48
30 8 0.24
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.66
Consensus pattern (30 bp):
ATTTTAATTATAATTTTATTACTTATTTAT
Found at i:2447861 original size:24 final size:24
Alignment explanation
Indices: 2447826--2447875 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
2447816 TTACTTTTTA
2447826 TATTTAATTTTAATTTTAT-TGTT
1 TATTTAATTTTAATTTTATGTGTT
2447849 TATTTATATTTTAATTTTATGTGTT
1 TATTTA-ATTTTAATTTTATGTGTT
2447874 TA
1 TA
2447876 AATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 6 0.24
24 13 0.52
25 6 0.24
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (24 bp):
TATTTAATTTTAATTTTATGTGTT
Found at i:2447882 original size:24 final size:24
Alignment explanation
Indices: 2447832--2447882 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2447822 TTTATATTTA
**
2447832 ATTTTAATTTTATTGTTTATTTAT
1 ATTTTAATTTTATTGTTTAAATAT
2447856 ATTTTAATTTTATGTGTTTAAAT-T
1 ATTTTAATTTTAT-TGTTTAAATAT
2447880 ATT
1 ATT
2447883 ATTTTCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (24 bp):
ATTTTAATTTTATTGTTTAAATAT
Found at i:2449357 original size:2 final size:2
Alignment explanation
Indices: 2449350--2449382 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2449340 ATCAAGTTAT
2449350 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
2449383 CAAACTGAAA
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:2453235 original size:16 final size:16
Alignment explanation
Indices: 2453214--2453245 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2453204 TGAAGGTTTG
2453214 AAATCAACCACAATCA
1 AAATCAACCACAATCA
2453230 AAATCAACCACAATCA
1 AAATCAACCACAATCA
2453246 CACCATATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.12
Consensus pattern (16 bp):
AAATCAACCACAATCA
Found at i:2455816 original size:82 final size:82
Alignment explanation
Indices: 2455684--2456040 Score: 534
Period size: 82 Copynumber: 4.4 Consensus size: 82
2455674 CCAAATAATG
* * *
2455684 GTGGTGTATTATCATCTTTTGCAACTTTTCAGAGGTCATTTAATGCATAATTTAAACAACTTTTC
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACTTTTC
*
2455749 AGAAAACGAGTGAAATA
66 AGAAAACGGGTGAAATA
*
2455766 GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAAATTTTC
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACTTTTC
* *
2455831 ATAAAATGGGTGAAATA
66 AGAAAACGGGTGAAATA
** * * *
2455848 GTGGTGCATTATCATCTTCTATAACTTTTCAGAGATCATTCAATGTATAATTTAAATAACTTTTC
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACTTTTC
*
2455913 AGAAAACGGCTGAAATA
66 AGAAAACGGGTGAAATA
* * * * * *
2455930 ATGGTGCATTATCACCGTCTGCAACTTTTCAGAGGTCATTTAATGCATACTTTAAACAACTTTTT
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACTTTTC
2455995 AGAAAACGGGTGAAATA
66 AGAAAACGGGTGAAATA
*
2456012 ATGGTGCATTATCATCTTCTGCAACTTTT
1 GTGGTGCATTATCATCTTCTGCAACTTTT
2456041 TAGTTATTTA
Statistics
Matches: 245, Mismatches: 30, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 245 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (82 bp):
GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACTTTTC
AGAAAACGGGTGAAATA
Found at i:2459200 original size:13 final size:13
Alignment explanation
Indices: 2459182--2459211 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2459172 AATCCCTACA
2459182 ATCCCCCAATCCT
1 ATCCCCCAATCCT
2459195 ATCCCCCAATCCT
1 ATCCCCCAATCCT
2459208 ATCC
1 ATCC
2459212 TTAACCCGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.53, G:0.00, T:0.23
Consensus pattern (13 bp):
ATCCCCCAATCCT
Found at i:2460358 original size:24 final size:24
Alignment explanation
Indices: 2460331--2460386 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
2460321 CTATTATTTC
2460331 GCTTCAATTGAGCT-AAATTTTTAG
1 GCTTCAATTGAGCTCAAA-TTTTAG
2460355 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
2460379 GCTTCAAT
1 GCTTCAAT
2460387 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:2461517 original size:21 final size:20
Alignment explanation
Indices: 2461487--2461539 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
2461477 TTATAAATGC
* *
2461487 AAAAAATAAAATATTTAAAT
1 AAAAAATAAAAAAATTAAAT
2461507 AAAATAATAAAAAAATTAAAT
1 AAAA-AATAAAAAAATTAAAT
*
2461528 AATTAAATAAAA
1 AA-AAAATAAAA
2461540 TACTAACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 23 0.82
22 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATAAAAAAATTAAAT
Found at i:2461527 original size:29 final size:29
Alignment explanation
Indices: 2461487--2461560 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
2461477 TTATAAATGC
*
2461487 AAAAAATAAAATATTTAAATAAAATAATA
1 AAAAAATTAAATATTTAAATAAAATAATA
* *
2461516 AAAAAATTAAATAATTAAATAAAATACTA
1 AAAAAATTAAATATTTAAATAAAATAATA
2461545 ACAAAATATTAAATAT
1 A-AAAA-ATTAAATAT
2461561 AACAAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 27 0.69
30 4 0.10
31 8 0.21
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAAAATTAAATATTTAAATAAAATAATA
Found at i:2461565 original size:17 final size:18
Alignment explanation
Indices: 2461537--2461570 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2461527 TAATTAAATA
2461537 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
2461555 AAATA-TAACAAAATAT
1 AAATACTAACAAAATAT
2461571 ACCTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:2462091 original size:19 final size:19
Alignment explanation
Indices: 2462067--2462105 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2462057 TCTTATGCGG
2462067 TGCATGTACCGCACCTTTC
1 TGCATGTACCGCACCTTTC
2462086 TGCATGTACCGCACCTTTC
1 TGCATGTACCGCACCTTTC
2462105 T
1 T
2462106 ACAAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.36, G:0.15, T:0.33
Consensus pattern (19 bp):
TGCATGTACCGCACCTTTC
Found at i:2467323 original size:2 final size:2
Alignment explanation
Indices: 2467318--2467344 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2467308 TATATATATA
2467318 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
2467345 CTTTGCATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2479639 original size:27 final size:27
Alignment explanation
Indices: 2479601--2479654 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2479591 AGTGGGGTTC
2479601 ACAGCAGCTGCACCTACCGCAACTGTT
1 ACAGCAGCTGCACCTACCGCAACTGTT
* * *
2479628 ACAGCAGTTGCACCTGCCGCGACTGTT
1 ACAGCAGCTGCACCTACCGCAACTGTT
2479655 GCAACTAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.20
Consensus pattern (27 bp):
ACAGCAGCTGCACCTACCGCAACTGTT
Found at i:2480904 original size:2 final size:2
Alignment explanation
Indices: 2480897--2480925 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2480887 TCTGTAATGC
2480897 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
2480926 AAGGGAAGAT
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:2482276 original size:25 final size:25
Alignment explanation
Indices: 2482248--2482298 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2482238 AATACAACAC
* * *
2482248 CTGCAAACAGGATTATAAGATCAAT
1 CTGCAAACAAGAATATAAGAACAAT
2482273 CTGCAAACAAGAATATAAGAACAAT
1 CTGCAAACAAGAATATAAGAACAAT
2482298 C
1 C
2482299 AAGTAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.20
Consensus pattern (25 bp):
CTGCAAACAAGAATATAAGAACAAT
Found at i:2483125 original size:76 final size:77
Alignment explanation
Indices: 2482993--2483149 Score: 298
Period size: 76 Copynumber: 2.1 Consensus size: 77
2482983 GATAGTAGAT
*
2482993 ACTTAGATTTTCAACAATTTACAAGGCCAATAAACATCATTGTACTCTGCATCTAGATAAAAGCT
1 ACTTAGATTTTCAACAATTTACAAGGCCAATAAACATCATTGTACTCTGCAGCTAGATAAAAGCT
2483058 CAAGGAAATGCA
66 CAAGGAAATGCA
2483070 ACTT-GATTTTCAACAATTTACAAGGCCAATAAACATCATTGTACTCTGCAGCTAGATAAAAGCT
1 ACTTAGATTTTCAACAATTTACAAGGCCAATAAACATCATTGTACTCTGCAGCTAGATAAAAGCT
2483134 CAAGGAAATGCA
66 CAAGGAAATGCA
2483146 ACTT
1 ACTT
2483150 CTCTATACCA
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
76 75 0.95
77 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (77 bp):
ACTTAGATTTTCAACAATTTACAAGGCCAATAAACATCATTGTACTCTGCAGCTAGATAAAAGCT
CAAGGAAATGCA
Found at i:2483405 original size:14 final size:14
Alignment explanation
Indices: 2483353--2483446 Score: 59
Period size: 14 Copynumber: 6.7 Consensus size: 14
2483343 TAAGTTATAG
* *
2483353 TTTATGGTTTAAGA
1 TTTAGGGTTTAGGA
* *
2483367 TTTATGGTTTA-CA
1 TTTAGGGTTTAGGA
*
2483380 TGTTACGGGTTTATGA
1 T-TTA-GGGTTTAGGA
*
2483396 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGA
*
2483410 TTATA--GTTTAGGG
1 TT-TAGGGTTTAGGA
**
2483423 TTTAGGGTTTATAA
1 TTTAGGGTTTAGGA
2483437 TTTAGGGTTT
1 TTTAGGGTTT
2483447 TAAGTTAGGG
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
12 2 0.03
13 12 0.18
14 39 0.59
15 11 0.17
16 2 0.03
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTAGGA
Found at i:2483406 original size:7 final size:7
Alignment explanation
Indices: 2483386--2483433 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
2483376 TACATGTTAC
2483386 GGGTTTA
1 GGGTTTA
* *
2483393 TGATTTA
1 GGGTTTA
2483400 GGGTTTA
1 GGGTTTA
2483407 GGGTTATA
1 GGGTT-TA
2483415 --GTTTA
1 GGGTTTA
2483420 GGGTTTA
1 GGGTTTA
2483427 GGGTTTA
1 GGGTTTA
2483434 TAATTTAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 2 0.06
6 3 0.09
7 27 0.79
8 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
GGGTTTA
Found at i:2483419 original size:20 final size:21
Alignment explanation
Indices: 2483386--2483446 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 21
2483376 TACATGTTAC
*
2483386 GGGTTTATGATTTAGGGTTTA
1 GGGTTTATAATTTAGGGTTTA
*
2483407 GGG-TTATAGTTTAGGGTTTA
1 GGGTTTATAATTTAGGGTTTA
2483427 GGGTTTATAATTTAGGGTTT
1 GGGTTTATAATTTAGGGTTT
2483447 TAAGTTAGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.48
Consensus pattern (21 bp):
GGGTTTATAATTTAGGGTTTA
Found at i:2483456 original size:13 final size:14
Alignment explanation
Indices: 2483424--2483457 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2483414 AGTTTAGGGT
*
2483424 TTAGGGTTTATAAT
1 TTAGGGTTTATAAG
2483438 TTAGGGTTT-TAAG
1 TTAGGGTTTATAAG
2483451 TTAGGGT
1 TTAGGGT
2483458 AGGGTAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (14 bp):
TTAGGGTTTATAAG
Found at i:2484140 original size:184 final size:183
Alignment explanation
Indices: 2483825--2484180 Score: 475
Period size: 184 Copynumber: 1.9 Consensus size: 183
2483815 ACATTTTTAC
* *
2483825 ACCTACTGCCTTACAAAAGAATGTGCTTAAACGCACCAGACATAAGCCTCTCTCTAAAGGGTTAA
1 ACCTACTGCCTTACAAAAGAATGTGCTTAAACGAACCAGACATAAGCCTCTCTCTAAACGGTTAA
* * * * *
2483890 AGCCCTGGTCTGGCCTTGAGGTGCAACCTCTAAGTGCACGCCTTAAAAACATTGTTCAACATTAG
66 AGCCCTAGTCTGGCCTTGAGCTGAAACCTCTAAGTGCACGCATTAAAAACATTGCTCAACATTAG
* **
2483955 TCTTTATGGGCATTGGAA-CAAACATCTATATATCATGCTAGTGGTAACGTTAA
131 TCTTTATGGGAATTAAAACCAAA-ATCTATATATCATGCTAGTGGTAACGTTAA
* * *
2484008 ACCTACT-CCTTACAAAAGAATGTGCTTAAATGGAAACCCGACATAAGCCT-TGTTCTAAACGGT
1 ACCTACTGCCTTACAAAAGAATGTGCTTAAA-CG-AACCAGACATAAGCCTCT-CTCTAAACGGT
* * * * *
2484071 TAATGCCCTAGTCTGGTCTTGAGCTGAAACCTCTAAGTGCATGCATTGAAAACATTGCTGAACAT
63 TAAAGCCCTAGTCTGGCCTTGAGCTGAAACCTCTAAGTGCACGCATTAAAAACATTGCTCAACAT
* *
2484136 TAGTCTTTCTGGGAATTAAAACCAAAATTTATATATCATGCTAGT
128 TAGTCTTTATGGGAATTAAAACCAAAATCTATATATCATGCTAGT
2484181 ATTAAGTAAA
Statistics
Matches: 149, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
182 23 0.15
183 9 0.06
184 113 0.76
185 4 0.03
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (183 bp):
ACCTACTGCCTTACAAAAGAATGTGCTTAAACGAACCAGACATAAGCCTCTCTCTAAACGGTTAA
AGCCCTAGTCTGGCCTTGAGCTGAAACCTCTAAGTGCACGCATTAAAAACATTGCTCAACATTAG
TCTTTATGGGAATTAAAACCAAAATCTATATATCATGCTAGTGGTAACGTTAA
Found at i:2486149 original size:16 final size:16
Alignment explanation
Indices: 2486128--2486164 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
2486118 TACTATCATT
2486128 GTTACTGCTTTTACAA
1 GTTACTGCTTTTACAA
2486144 GTTACTGCTTTTACAA
1 GTTACTGCTTTTACAA
2486160 GTTAC
1 GTTAC
2486165 GAGATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (16 bp):
GTTACTGCTTTTACAA
Done.