Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008182.1 Hibiscus syriacus cultivar Beakdansim tig00110782_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: 1042344
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:316457 original size:22 final size:22
Alignment explanation
Indices: 316383--316463 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
316373 AGAACCCCAG
*
316383 GGGGGTATCGATTCCCC-T--A
1 GGGGGAATCGATTCCCCTTCAA
*
316402 GTGGGGAATCGGTTCCCCTTCAAA
1 G-GGGGAATCGATTCCCCTTC-AA
* *
316426 AGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
316448 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
316464 TCTGCCCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.02
20 14 0.27
21 1 0.02
22 15 0.29
23 19 0.37
24 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:321225 original size:15 final size:16
Alignment explanation
Indices: 321197--321229 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
321187 AAAATCTTTC
321197 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
321213 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
321228 TT
1 TT
321230 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:322007 original size:16 final size:17
Alignment explanation
Indices: 321979--322010 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
321969 ATCGCCGACA
321979 AAATTTCACTATTCACG
1 AAATTTCACTATTCACG
321996 AAATTT-ACTATTCAC
1 AAATTTCACTATTCAC
322011 ATGAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTTCACTATTCACG
Found at i:323511 original size:27 final size:27
Alignment explanation
Indices: 323453--323514 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
323443 GTCATGTCTG
* * *
323453 ACGTCATTTGTATTTAATGATTCTCCA
1 ACGTCATTTGTATTTAATAATCCTACA
323480 ACGTCATTTGTATTT-ATAATACCTACA
1 ACGTCATTTGTATTTAATAAT-CCTACA
*
323507 TCGTCATT
1 ACGTCATT
323515 CAAACAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (27 bp):
ACGTCATTTGTATTTAATAATCCTACA
Found at i:325254 original size:21 final size:20
Alignment explanation
Indices: 325220--325272 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
325210 GAGTTTATTT
*
325220 TCATTTTTCA-ATTTTGAAATA
1 TCATTTTT-ATATTTT-AAAAA
325241 TCATTTTTATATTTTAAAAA
1 TCATTTTTATATTTTAAAAA
*
325261 TAATTTCTTATA
1 TCATTT-TTATA
325273 ATCCGAAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.55
Consensus pattern (20 bp):
TCATTTTTATATTTTAAAAA
Found at i:325262 original size:22 final size:21
Alignment explanation
Indices: 325220--325259 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
325210 GAGTTTATTT
*
325220 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
325241 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
325260 ATAATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:328223 original size:27 final size:27
Alignment explanation
Indices: 328185--328246 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
328175 AAAGATTTAA
328185 ATAGTGATTCTAAGTAGTGACCATTAT
1 ATAGTGATTCTAAGTAGTGACCATTAT
*
328212 ATAGTGATTCTAAGTAGTGGCCATTAT
1 ATAGTGATTCTAAGTAGTGACCATTAT
328239 ATAGTGAT
1 ATAGTGAT
328247 AATTGCGTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (27 bp):
ATAGTGATTCTAAGTAGTGACCATTAT
Found at i:330831 original size:23 final size:23
Alignment explanation
Indices: 330789--330832 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
330779 CATAATAACA
*
330789 TAATAGGTAGTGCTTATTTAATG
1 TAATAGGTAGTCCTTATTTAATG
330812 TAATAGGTAGTTCCTT-TTTAA
1 TAATAGGTAG-TCCTTATTTAA
330833 GATAGTGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (23 bp):
TAATAGGTAGTCCTTATTTAATG
Found at i:330865 original size:117 final size:115
Alignment explanation
Indices: 330640--330867 Score: 352
Period size: 117 Copynumber: 2.0 Consensus size: 115
330630 ACATAACCAT
330640 TTAATTACTGGAAACATTATCAACCATAATAACATACATGTAGCGCTTATTTAATGTAATAGGTA
1 TTAATTACTGGAAACATTATCAACCATAATAACATACATGTAGCGCTTATTTAATGTAATAGGTA
* *
330705 GATCTTTTTAAGCTGATGGAGCCTTAGAAATCTGACGATAACAAAATAGG
66 GATCTTTTTAAGATGATGGAGCCTTAGAAATCCGACGATAACAAAATAGG
* *
330755 TTAATTACTGGAAACATTATCAAGCATAATAACATA-ATAGGTAGTGCTTATTTAATGTAATAGG
1 TTAATTACTGGAAACATTATCAACCATAATAACATACAT--GTAGCGCTTATTTAATGTAATAGG
* *
330819 TAGTTCCTTTTTAAGAT-AGTGGAGCCTTGGAAATCCGACGATAACAAAA
64 TAGAT-CTTTTTAAGATGA-TGGAGCCTTAGAAATCCGACGATAACAAAA
330868 CCGGTTTATT
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
114 2 0.02
115 35 0.34
116 28 0.27
117 38 0.37
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (115 bp):
TTAATTACTGGAAACATTATCAACCATAATAACATACATGTAGCGCTTATTTAATGTAATAGGTA
GATCTTTTTAAGATGATGGAGCCTTAGAAATCCGACGATAACAAAATAGG
Found at i:332673 original size:18 final size:18
Alignment explanation
Indices: 332650--332704 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
332640 GGTATAAAAC
* **
332650 GACCTTATTTGATCAGAA
1 GACCTTACTTGAGAAGAA
332668 GACCTTACTTGAGAAGAA
1 GACCTTACTTGAGAAGAA
**
332686 GACCTTGGTTGAGAAGAA
1 GACCTTACTTGAGAAGAA
332704 G
1 G
332705 GTTTTGATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (18 bp):
GACCTTACTTGAGAAGAA
Found at i:333506 original size:159 final size:159
Alignment explanation
Indices: 333211--333525 Score: 513
Period size: 159 Copynumber: 2.0 Consensus size: 159
333201 TTCTAATATT
* * * *
333211 GGTATCGATACTTTTTTCCGTGCAAACTGTTGAGAAGCATACTGGAATGAAAATATCAATACCTA
1 GGTATCGATACTTTGTTCAGTGCAAACCGTTGAGAAGCATACTGAAATGAAAATATCAATACCTA
* * * *
333276 CAAATAAAGTATTGATACTTAATGTTTACGCCTTTTATCAATAAACCAATAGACTTTTACCGTTT
66 CAAATAAAGTATCGATACATAATGTTTACGCATTTTATCAATAAACCAATAGACTTTTACCATTT
333341 ACATTGTAAAATTACCTATTACTTTATCG
131 ACATTGTAAAATTACCTATTACTTTATCG
* *
333370 GGTATCGATACTTTGTTCAGTGCAAACCGTTGAGAAGCATACTGAAATGAAAGTATCGATACCTA
1 GGTATCGATACTTTGTTCAGTGCAAACCGTTGAGAAGCATACTGAAATGAAAATATCAATACCTA
**
333435 CAAATAAAGTATCGATACATAATGTTTACGCATTTTATCAATAAACCTGTAGACTTTTACCATTT
66 CAAATAAAGTATCGATACATAATGTTTACGCATTTTATCAATAAACCAATAGACTTTTACCATTT
*
333500 ATATTGTAAAATTACCTATTACTTTA
131 ACATTGTAAAATTACCTATTACTTTA
333526 ACAAGTATAG
Statistics
Matches: 143, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
159 143 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (159 bp):
GGTATCGATACTTTGTTCAGTGCAAACCGTTGAGAAGCATACTGAAATGAAAATATCAATACCTA
CAAATAAAGTATCGATACATAATGTTTACGCATTTTATCAATAAACCAATAGACTTTTACCATTT
ACATTGTAAAATTACCTATTACTTTATCG
Found at i:333539 original size:159 final size:159
Alignment explanation
Indices: 333212--333901 Score: 590
Period size: 180 Copynumber: 4.1 Consensus size: 159
333202 TCTAATATTG
* * * * * *
333212 GTATCGATACTTTTTTCCGTGCAAACTGTTGAGAAGCATACTGGAATGAAAATATCAATACCTAC
1 GTATCGATACTTTATTCAGTGCAAACCGTTGAGAAGCATACTGAAATGAAAGTATCGATACCTAC
* *
333277 AAATAAAGTATTGATACTTAATGTTTACGCCTTTTATCAATAAACCAATAGACTTTTACCGTTTA
66 AAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAATAGACTTTTACCATTTA
* **
333342 CATTGTAAAATTACCTATTACTTTATCGG
131 CATTGTAAAATTACCTATTACTTTAACAA
*
333371 GTATCGATACTTTGTTCAGTGCAAACCGTTGAGAAGCATACTGAAATGAAAGTATCGATACCTAC
1 GTATCGATACTTTATTCAGTGCAAACCGTTGAGAAGCATACTGAAATGAAAGTATCGATACCTAC
* * **
333436 AAATAAAGTATCGATACATAATGTTTACGCATTTTATCAATAAACCTGTAGACTTTTACCATTTA
66 AAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAATAGACTTTTACCATTTA
*
333501 TATTGTAAAATTACCTATTACTTTAACAA
131 CATTGTAAAATTACCTATTACTTTAACAA
* * * * *
333530 GTATAGATACTTCTAATACTGGTATCGATACTTTGTTCTGTGCAAACTGTTGAGAAGCATACT-A
1 GTATCGATACTT-T-ATTC-AGT-GC-AAAC------C-GT------TG---AGAAGCATACTGA
* * *
333594 GAATGAAAGTATCGATACCTATAAATAAAGTATCGATACTTAATGTTTATGCCTTTTATCATTAA
45 -AATGAAAGTATCGATACCTACAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAA
*
333659 ACCAAAAGACTTTTACCATTTACATTGTAAAATTACCTATTACTTTAACAA
109 ACCAATAGACTTTTACCATTTACATTGTAAAATTACCTATTACTTTAACAA
* ** * * * *
333710 GTATTGATACTTATAATATTGGTATCGATACTTTGTTTCGTGCAAACTGTTGAGAAGCATAATGG
1 GTATCGATACTT-T-AT-TCAGT-GC-AAAC-------CGT------TG---AGAAGCATACTGA
* * * *
333775 AATGAAAATATCGATACCTACAAATAAATTATTGATACTTAATGTTTACGCCTTTTATCAATATA
45 AATGAAAGTATCGATACCTACAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAA
** * * ***
333840 CCGGTAGACTTTTACCGTTTACATTGTAAAATTACCTATTAATTTAATGG
110 CCAATAGACTTTTACCATTTACATTGTAAAATTACCTATTACTTTAACAA
333890 GTATCGATACTT
1 GTATCGATACTT
333902 CTAATATTGG
Statistics
Matches: 451, Mismatches: 55, Indels: 29
0.84 0.10 0.05
Matches are distributed among these distances:
159 154 0.34
160 1 0.00
161 2 0.00
162 2 0.00
163 1 0.00
164 3 0.01
170 1 0.00
171 2 0.00
177 2 0.00
179 1 0.00
180 277 0.61
181 5 0.01
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (159 bp):
GTATCGATACTTTATTCAGTGCAAACCGTTGAGAAGCATACTGAAATGAAAGTATCGATACCTAC
AAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAATAGACTTTTACCATTTA
CATTGTAAAATTACCTATTACTTTAACAA
Found at i:333672 original size:180 final size:180
Alignment explanation
Indices: 333370--334102 Score: 1110
Period size: 180 Copynumber: 4.1 Consensus size: 180
333360 TACTTTATCG
* * *
333370 GGTATCGATACTTTGTTCAGTGCAAACCGTTGAGAAGCATACTGAAATGAAAGTATCGATACCTA
1 GGTATCGATACTTTGTTCTGTGCAAACTGTTGAGAAGCATACTGGAATGAAAGTATCGATACCTA
* * *
333435 CAAATAAAGTATCGATACATAATGTTTACGCATTTTATCAATAAACCTGTAGACTTTTACCATTT
66 CAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAGTAGACTTTTACCATTT
* * *
333500 ATATTGTAAAATTACCTATTACTTTAACAAGTATAGATACTTCTAATACT
131 ACATTGTAAAATTACCTATTACTTTAACAAGTATCGATACTTCTAATATT
*
333550 GGTATCGATACTTTGTTCTGTGCAAACTGTTGAGAAGCATACTAGAATGAAAGTATCGATACCTA
1 GGTATCGATACTTTGTTCTGTGCAAACTGTTGAGAAGCATACTGGAATGAAAGTATCGATACCTA
* * * **
333615 TAAATAAAGTATCGATACTTAATGTTTATGCCTTTTATCATTAAACCAAAAGACTTTTACCATTT
66 CAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAGTAGACTTTTACCATTT
* *
333680 ACATTGTAAAATTACCTATTACTTTAACAAGTATTGATACTTATAATATT
131 ACATTGTAAAATTACCTATTACTTTAACAAGTATCGATACTTCTAATATT
* *
333730 GGTATCGATACTTTGTT-TCGTGCAAACTGTTGAGAAGCATAATGGAATGAAAATATCGATACCT
1 GGTATCGATACTTTGTTCT-GTGCAAACTGTTGAGAAGCATACTGGAATGAAAGTATCGATACCT
* * * * *
333794 ACAAATAAATTATTGATACTTAATGTTTACGCCTTTTATCAATATACCGGTAGACTTTTACCGTT
65 ACAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAGTAGACTTTTACCATT
* ***
333859 TACATTGTAAAATTACCTATTAATTTAATGGGTATCGATACTTCTAATATT
130 TACATTGTAAAATTACCTATTACTTTAACAAGTATCGATACTTCTAATATT
* * *
333910 GGTATTGATAATTTGTTC-GTGCAAACTTTTGAGAAGCATACTGGAATGAAAGTATCGATACCTA
1 GGTATCGATACTTTGTTCTGTGCAAACTGTTGAGAAGCATACTGGAATGAAAGTATCGATACCTA
* * * *
333974 TAAATAAAGTATCAATACTTAATGTTTACGCCTTTTATCAATAAACTAGTAGACTTTTACCGTTT
66 CAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAGTAGACTTTTACCATTT
**
334039 ACATTGTAAAATTACCTATTACTTTAACGGGTATCGATACTTCTAATATT
131 ACATTGTAAAATTACCTATTACTTTAACAAGTATCGATACTTCTAATATT
334089 GGTATCGATACTTT
1 GGTATCGATACTTT
334103 ATTGAGATCA
Statistics
Matches: 500, Mismatches: 51, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
179 162 0.32
180 338 0.68
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Consensus pattern (180 bp):
GGTATCGATACTTTGTTCTGTGCAAACTGTTGAGAAGCATACTGGAATGAAAGTATCGATACCTA
CAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAGTAGACTTTTACCATTT
ACATTGTAAAATTACCTATTACTTTAACAAGTATCGATACTTCTAATATT
Found at i:333698 original size:339 final size:336
Alignment explanation
Indices: 333078--334080 Score: 1344
Period size: 339 Copynumber: 2.9 Consensus size: 336
333068 TTGTATACAT
* * * *
333078 TGAAAGTATCAATAACTATAAGTAAAGTATTGATACTTAATGTTTACGTCTTTTATCAATAAACC
1 TGAAAGTATCGATACCTACAAATAAAGTATTGATACTTAATGTTTACG-CTTTTATCAATAAACC
* * *
333143 GATAGACTTTTACTGTTTATATTGTAAAATTACTTATTACTTTATCAGGTATCA-ATACTTCTAA
65 G-TAGACTTTTACCGTTTATATTGTAAAATTACCTATTACTTTAACAGGTAT-AGATACTTCTAA
* * *
333207 TATTGGTATCGATACTTTTTTCCGTGCAAACTGTTGAGAAGCATACTGGAATGAAAATATCAATA
128 TATTGGTATCGATACTTTGTT-CGTGCAAACTGTTGAGAAGCATACTGGAATGAAAGTATCGATA
* *
333272 CCTACAAATAAAGTATTGATACTTAATGTTTACGCCTTTTATCAATAAACCAATAGACTTTTACC
192 CCTATAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAATAGACTTTTACC
333337 GTTTACATTGTAAAATTACCTATTACTTTATCGGGTATCGATACTTTG-TTCAGTGCAAACCGTT
257 GTTTACATTGTAAAATTACCTATTACTTTATCGGGTATCGATACTTTGTTTC-GTGCAAACCGTT
*
333401 GAGAAGCATACTGAAA
321 GAGAAGCATAATGAAA
* *
333417 TGAAAGTATCGATACCTACAAATAAAGTATCGATACATAATGTTTACGCATTTTATCAATAAACC
1 TGAAAGTATCGATACCTACAAATAAAGTATTGATACTTAATGTTTACGC-TTTTATCAATAAACC
* *
333482 TGTAGACTTTTACCATTTATATTGTAAAATTACCTATTACTTTAACAAGTATAGATACTTCTAAT
65 -GTAGACTTTTACCGTTTATATTGTAAAATTACCTATTACTTTAACAGGTATAGATACTTCTAAT
* *
333547 ACTGGTATCGATACTTTGTTCTGTGCAAACTGTTGAGAAGCATACTAGAATGAAAGTATCGATAC
129 ATTGGTATCGATACTTTGTTC-GTGCAAACTGTTGAGAAGCATACTGGAATGAAAGTATCGATAC
* * * *
333612 CTATAAATAAAGTATCGATACTTAATGTTTATGCCTTTTATCATTAAACCAAAAGACTTTTACCA
193 CTATAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAATAGACTTTTACCG
*
333677 TTTACATTGTAAAATTACCTATTACTTTAACAAGTATTGATACTTATAATATTGGTATCGATACT
258 TTTACATTGTAAAATTACC---TA--TT-AC---T-TT-AT-C---------GGGTATCGATACT
* *
333742 TTGTTTCGTGCAAACTGTTGAGAAGCATAATGGAA
302 TTGTTTCGTGCAAACCGTTGAGAAGCATAATGAAA
* * *
333777 TGAAAATATCGATACCTACAAATAAATTATTGATACTTAATGTTTACGCCTTTTATCAATATACC
1 TGAAAGTATCGATACCTACAAATAAAGTATTGATACTTAATGTTTACG-CTTTTATCAATAAACC
* * ** *
333842 GGTAGACTTTTACCGTTTACATTGTAAAATTACCTATTAATTTAATGGGTATCGATACTTCTAAT
65 -GTAGACTTTTACCGTTTATATTGTAAAATTACCTATTACTTTAACAGGTATAGATACTTCTAAT
* * *
333907 ATTGGTATTGATAATTTGTTCGTGCAAACTTTTGAGAAGCATACTGGAATGAAAGTATCGATACC
129 ATTGGTATCGATACTTTGTTCGTGCAAACTGTTGAGAAGCATACTGGAATGAAAGTATCGATACC
* * *
333972 TATAAATAAAGTATCAATACTTAATGTTTACGCCTTTTATCAATAAACTAGTAGACTTTTACCGT
194 TATAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAATAGACTTTTACCGT
*
334037 TTACATTGTAAAATTACCTATTACTTTAACGGGTATCGATACTT
259 TTACATTGTAAAATTACCTATTACTTTATCGGGTATCGATACTT
334081 CTAATATTGG
Statistics
Matches: 584, Mismatches: 53, Indels: 55
0.84 0.08 0.08
Matches are distributed among these distances:
338 16 0.03
339 249 0.43
340 1 0.00
342 2 0.00
344 2 0.00
345 2 0.00
347 1 0.00
348 2 0.00
349 4 0.01
350 3 0.01
351 1 0.00
353 2 0.00
354 2 0.00
356 2 0.00
359 118 0.20
360 173 0.30
361 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (336 bp):
TGAAAGTATCGATACCTACAAATAAAGTATTGATACTTAATGTTTACGCTTTTATCAATAAACCG
TAGACTTTTACCGTTTATATTGTAAAATTACCTATTACTTTAACAGGTATAGATACTTCTAATAT
TGGTATCGATACTTTGTTCGTGCAAACTGTTGAGAAGCATACTGGAATGAAAGTATCGATACCTA
TAAATAAAGTATCGATACTTAATGTTTACGCCTTTTATCAATAAACCAATAGACTTTTACCGTTT
ACATTGTAAAATTACCTATTACTTTATCGGGTATCGATACTTTGTTTCGTGCAAACCGTTGAGAA
GCATAATGAAA
Found at i:336308 original size:220 final size:219
Alignment explanation
Indices: 335926--336364 Score: 842
Period size: 220 Copynumber: 2.0 Consensus size: 219
335916 TCACGTTTTG
335926 AAGCACGTGGATTACACATCTATGCCCAAGTCTCTGATTCTAAGTAGGTGGACTAAATAATCTAA
1 AAGCACGTGGATTACACATCTATGCCCAAGTCTCTGATTCTAAGTAGGTGGACTAAATAATCTAA
335991 GGTTTCTGCACCAAGTTTTGTTAACTTCAATGTACCCCAAGAAGTTATACAAATGGCATGGTTCG
66 GGTTTCTGCACCAAGTTTTGTTAACTTCAATGTACCCCAAGAAGTTATACAAATGGCATGGTTCG
*
336056 CTTCTCTATGTGCAACGTCAAGTCGTTTATGCTACATTATGTCAAAGACGGACGTGTCTTTCAAA
131 CTTCTCTATGTGCAACGTCAAGTCGTTTATGCTACATTATGTCAAAGACAGACGTGTCTTTCAAA
336121 ACCGCAAGAGATGAGATTGAAAAGA
196 ACCGCAAGAGATGAGATT-AAAAGA
336146 AAGCACGTGGATTACACATCTATGCCCAAGTCTCTGATTCTAAGTAGGTGGACTAAATAATCTAA
1 AAGCACGTGGATTACACATCTATGCCCAAGTCTCTGATTCTAAGTAGGTGGACTAAATAATCTAA
336211 GGTTTCTGCACCAAGTTTTGTTAACTTCAATGTACCCCAAGAAGTTATACAAATGGCATGGTTCG
66 GGTTTCTGCACCAAGTTTTGTTAACTTCAATGTACCCCAAGAAGTTATACAAATGGCATGGTTCG
* *
336276 CTTCTCTATGTGCAACGTCAAGTCGTTTATGCTACATTGTGTCAAATACAGACGTGTCTTTCAAA
131 CTTCTCTATGTGCAACGTCAAGTCGTTTATGCTACATTATGTCAAAGACAGACGTGTCTTTCAAA
336341 ACCGCAAGAGATGAGATTAAAAGA
196 ACCGCAAGAGATGAGATTAAAAGA
336365 CTAACATTTG
Statistics
Matches: 216, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
219 6 0.03
220 210 0.97
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (219 bp):
AAGCACGTGGATTACACATCTATGCCCAAGTCTCTGATTCTAAGTAGGTGGACTAAATAATCTAA
GGTTTCTGCACCAAGTTTTGTTAACTTCAATGTACCCCAAGAAGTTATACAAATGGCATGGTTCG
CTTCTCTATGTGCAACGTCAAGTCGTTTATGCTACATTATGTCAAAGACAGACGTGTCTTTCAAA
ACCGCAAGAGATGAGATTAAAAGA
Found at i:336758 original size:17 final size:18
Alignment explanation
Indices: 336726--336759 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
336716 TAAATCAAAG
*
336726 GATTAAGGAGTTAGGAGA
1 GATTAAAGAGTTAGGAGA
336744 GATTAAAGA-TTAGGAG
1 GATTAAAGAGTTAGGAG
336760 TTTTTGAATG
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:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (18 bp):
GATTAAAGAGTTAGGAGA
Found at i:337622 original size:28 final size:28
Alignment explanation
Indices: 337586--337650 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
337576 ATAGTTATAA
*
337586 ACATGCATATATTATGGTTATTATAAAC
1 ACATGCATACATTATGGTTATTATAAAC
337614 ACATGCATACATTATGGTTATTATAAAC
1 ACATGCATACATTATGGTTATTATAAAC
337642 ACATGCATA
1 ACATGCATA
337651 AGATATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (28 bp):
ACATGCATACATTATGGTTATTATAAAC
Found at i:338973 original size:18 final size:18
Alignment explanation
Indices: 338950--339000 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
338940 ACTTTGGTAA
* *
338950 TCACATATAACATTTCAT
1 TCACATACAAAATTTCAT
*
338968 TCACATACAAAATTTCAAG
1 TCACATACAAAATTTC-AT
338987 T-ACATACAAAATTT
1 TCACATACAAAATTT
339001 ACAACATCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 27 0.93
19 2 0.07
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (18 bp):
TCACATACAAAATTTCAT
Found at i:340396 original size:21 final size:20
Alignment explanation
Indices: 340354--340396 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
340344 TTCTTTCATT
* *
340354 TCATCCCTTATTTTTCCCCC
1 TCATCCATTATTTTTCCACC
*
340374 TCATCCATTTTTTTTCCAACC
1 TCATCCATTATTTTTCC-ACC
340395 TC
1 TC
340397 TCCCATCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.14, C:0.40, G:0.00, T:0.47
Consensus pattern (20 bp):
TCATCCATTATTTTTCCACC
Found at i:340628 original size:12 final size:12
Alignment explanation
Indices: 340608--340650 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
340598 TCCTACTACC
*
340608 TTCTTTTTTTCA
1 TTCTCTTTTTCA
*
340620 TTCTCTTTTACA
1 TTCTCTTTTTCA
* *
340632 TTCTCTTCTTCC
1 TTCTCTTTTTCA
340644 TTCTCTT
1 TTCTCTT
340651 CCTCCTCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (12 bp):
TTCTCTTTTTCA
Found at i:343160 original size:195 final size:194
Alignment explanation
Indices: 342817--343409 Score: 671
Period size: 195 Copynumber: 3.1 Consensus size: 194
342807 ATATTATAAT
***
342817 GTATCAATACTTTCGAGACGTTTTCCTTTTATCATTTCTTTTCAATTCCTAAAGTACCAATACTA
1 GTATCAATACTTTCGAGACGTTTTCCTTTTATCATTTCTTTTCAATTCCTAAAGTATTGATACTA
* * * * * *
342882 TGGTACATATACTTCAAAAGTGTTGATACTTTCAACAATTCCGGT-AGCACTTGATCGGTTTTGT
66 TGGTACATATACTTCAAAAGTATCGATACTTACAACAATTCAGGTAAG--CTTTACCGGTTTTGT
** *
342946 CAACTTTTACCAAATTTGTCAAATTTTAACCTGTTATATTGTAATGTATCGATACTTGTATGTAA
129 CAACTTTTACCTGATTTGTCAAATTTTAACCTGTTATATTGTAATGTATCGATACATGTATGTAA
343011 G
194 G
*
343012 GTGTCAATACTTTCGAGACGTTTTCCTTTTATCATTTCTTTTCAATTCCTAAAGTATTGATACTA
1 GTATCAATACTTTCGAGACGTTTTCCTTTTATCATTTCTTTTCAATTCCTAAAGTATTGATACTA
* * * *
343077 TGGTACATATACTTCACAAGTATCGATACGTACAACAATTCTGGTATTGCTTTACCGGTTTTGT-
66 TGGTACATATACTTCAAAAGTATCGATACTTACAACAATTCAGGTA-AGCTTTACCGGTTTTGTC
* *
343141 ATACTTTTACCTGATTTGTCAAATTTTAACCTGTTATATTGTCATGTATCGATACATGTGTGTAA
130 A-ACTTTTACCTGATTTGTCAAATTTTAACCTGTTATATTGTAATGTATCGATACATGTATGTAA
343206 G
194 G
* ** * * * * * **
343207 GTATCGATACTTTATAGACATTTT--TATT-GCAATTCTTTTGAATTAATACAA-TATTGATACT
1 GTATCAATACTTTCGAGACGTTTTCCTTTTATCATTTCTTTTCAATTCCTA-AAGTATTGATACT
* * * * *
343268 TTCGTACGTATACTT-ATATAAGTATCGATA-TTATCTACAATTTCAGTTAAGCTTTACCGGTTT
65 ATGGTACATATACTTCA-A-AAGTATCGATACTTA-CAACAA-TTCAGGTAAGCTTTACCGGTTT
* * * * * *
343331 TGTCAAATTTAACTTGATTTGTCAAATTTTAACCTGTTATATTGTAATGTATCAATACACGTATA
126 TGTCAACTTTTACCTGATTTGTCAAATTTTAACCTGTTATATTGTAATGTATCGATACATGTATG
*
343396 TGAG
191 TAAG
*
343400 GTATCGATAC
1 GTATCAATAC
343410 CTACTGATAA
Statistics
Matches: 342, Mismatches: 47, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
191 1 0.00
192 39 0.11
193 102 0.30
194 8 0.02
195 191 0.56
197 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (194 bp):
GTATCAATACTTTCGAGACGTTTTCCTTTTATCATTTCTTTTCAATTCCTAAAGTATTGATACTA
TGGTACATATACTTCAAAAGTATCGATACTTACAACAATTCAGGTAAGCTTTACCGGTTTTGTCA
ACTTTTACCTGATTTGTCAAATTTTAACCTGTTATATTGTAATGTATCGATACATGTATGTAAG
Found at i:356363 original size:191 final size:194
Alignment explanation
Indices: 356004--356479 Score: 533
Period size: 191 Copynumber: 2.5 Consensus size: 194
355994 TTATCGGTAG
* *
356004 GTATCGATACTTTACACAAAAGTA-TAATACATTACAATATAACAGGTTAAAATTTGACAAATCA
1 GTATCGATACCTTACACACAAGTATTAATACATTACAATATAACAGGTTAAAATTTGACAAATCA
** *
356068 AATAAAAGTTGACAAAACCGGTAAAGAGCAACCGGAATTGTAGACAGTATCGATACTTATATAAG
66 GGTAAAAGTTGACAAAACCGGTAAAGAGCAACCGGAATTGTAGACAGTATCGATACTTATAGAAG
* * * * * *
356133 TATGCGTACGAAAGTATCGTACTGTATCAATTTAAAAGAATTG-CAATA-AAAACG-C-CAAAAA
131 TATACGTACCAAAGTATCGTACTGTAGCAATTAAAAAGAAATGACAAAAGAAAACGTCTC-AAAA
* * * * *
356194 GTATCGATACCTTACACACATGTATTGATACATGACAATATAACATGTTAAAAATTGACAAATCA
1 GTATCGATACCTTACACACAAGTATTAATACATTACAATATAACAGGTTAAAATTTGACAAATCA
* * * *
356259 GGTAAAAGTAT-ACGAAACCGGTAAA-A-CAATACCGGAATTGTTGA-ACGTATTGATACTTGT-
66 GGTAAAAGT-TGACAAAACCGGTAAAGAGC-A-ACCGGAATTGTAGACA-GTATCGATACTTATA
* * * * *
356319 GAAGTATATGTACCATAGTATCGATACTTTAGGAATTAAAAAGAAATGATAAAAGGAAAACGTCT
127 GAAGTATACGTACCAAAGTATCG-TACTGTAGCAATTAAAAAGAAATGACAAAA-GAAAACGTCT
*
356384 CGAAA
190 CAAAA
* *
356389 GTATCGATACCTTACATACAAGTATCAATACATTACAATATAACAGGTTAAAATTTGACAAATTC
1 GTATCGATACCTTACACACAAGTATTAATACATTACAATATAACAGGTTAAAATTTGACAAA-TC
* *
356454 -GGTAAAAATTGACAAAATCGGTAAAG
65 AGGTAAAAGTTGACAAAACCGGTAAAG
356480 TACTACCGAA
Statistics
Matches: 236, Mismatches: 36, Indels: 22
0.80 0.12 0.07
Matches are distributed among these distances:
189 1 0.00
190 42 0.18
191 100 0.42
192 4 0.02
194 7 0.03
195 79 0.33
196 3 0.01
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (194 bp):
GTATCGATACCTTACACACAAGTATTAATACATTACAATATAACAGGTTAAAATTTGACAAATCA
GGTAAAAGTTGACAAAACCGGTAAAGAGCAACCGGAATTGTAGACAGTATCGATACTTATAGAAG
TATACGTACCAAAGTATCGTACTGTAGCAATTAAAAAGAAATGACAAAAGAAAACGTCTCAAAA
Found at i:356465 original size:19 final size:19
Alignment explanation
Indices: 356437--356478 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
356427 TATAACAGGT
* *
356437 TAAAATTTGACAAATTCGG
1 TAAAAATTGACAAAATCGG
356456 TAAAAATTGACAAAATCGG
1 TAAAAATTGACAAAATCGG
356475 TAAA
1 TAAA
356479 GTACTACCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (19 bp):
TAAAAATTGACAAAATCGG
Found at i:359236 original size:41 final size:41
Alignment explanation
Indices: 359191--359268 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
359181 AATGTTAATC
359191 ACATGTTATTTGAGAATATGTTTAGTTGAAATTAGAATTTA
1 ACATGTTATTTGAGAATATGTTTAGTTGAAATTAGAATTTA
359232 ACATGTTATTTGAGAATATGTTTAGTTGAAATTAGAA
1 ACATGTTATTTGAGAATATGTTTAGTTGAAATTAGAA
359269 AGTAATTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (41 bp):
ACATGTTATTTGAGAATATGTTTAGTTGAAATTAGAATTTA
Found at i:359303 original size:45 final size:45
Alignment explanation
Indices: 359239--359331 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
359229 TTAACATGTT
* *
359239 ATTTGAGAATATGTTTAGTTGAAATTAGAAAGTAATTAGTAACGG
1 ATTTGAGAAAATGTTTAGTTGAAATTAGAAAGTAATCAGTAACGG
359284 ATTTGAGAAAATGTTTAGTTGAAATTAGAAAGTAATCAGTAACGG
1 ATTTGAGAAAATGTTTAGTTGAAATTAGAAAGTAATCAGTAACGG
359329 ATT
1 ATT
359332 AGAATTTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (45 bp):
ATTTGAGAAAATGTTTAGTTGAAATTAGAAAGTAATCAGTAACGG
Found at i:359453 original size:60 final size:61
Alignment explanation
Indices: 359353--359470 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 61
359343 TAAATTATTG
*
359353 ACTTTGGTTATAAATATAAACACTAAACCATTGCACATTATCTCAACTAAAAACTAAACTT
1 ACTTTGATTATAAATATAAACACTAAACCATTGCACATTATCTCAACTAAAAACTAAACTT
* *
359414 ACTTTGATTATAAATAT-AACTCTAAACCATTGCATATTATCTCAACTAAAAACTAAA
1 ACTTTGATTATAAATATAAACACTAAACCATTGCACATTATCTCAACTAAAAACTAAA
359471 GAATGGACGC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 38 0.70
61 16 0.30
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (61 bp):
ACTTTGATTATAAATATAAACACTAAACCATTGCACATTATCTCAACTAAAAACTAAACTT
Found at i:359470 original size:31 final size:31
Alignment explanation
Indices: 359369--359470 Score: 79
Period size: 31 Copynumber: 3.4 Consensus size: 31
359359 GTTATAAATA
* *
359369 TAAACACTAAACCATTGCACATTATCTCAAC
1 TAAAAACTAAACCATTGCATATTATCTCAAC
* * *
359400 TAAAAACTAAA-C-TTAC-T-TTGAT-TATAAA
1 TAAAAACTAAACCATTGCATATT-ATCT-CAAC
**
359428 TATAACTCTAAACCATTGCATATTATCTCAAC
1 TA-AAAACTAAACCATTGCATATTATCTCAAC
359460 TAAAAACTAAA
1 TAAAAACTAAA
359471 GAATGGACGC
Statistics
Matches: 51, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
27 3 0.06
28 6 0.12
29 10 0.20
30 2 0.04
31 20 0.39
32 7 0.14
33 3 0.06
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.30
Consensus pattern (31 bp):
TAAAAACTAAACCATTGCATATTATCTCAAC
Found at i:360347 original size:23 final size:23
Alignment explanation
Indices: 360297--360347 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
360287 CTTCCACAAT
* *
360297 GAATGGTGGAGATTACTTACATC
1 GAATGGTGGAGATTAATTACATA
*
360320 CAATGGTGGAGATTAATTATC-TA
1 GAATGGTGGAGATTAATTA-CATA
360343 GAATG
1 GAATG
360348 CTCCACATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (23 bp):
GAATGGTGGAGATTAATTACATA
Found at i:360553 original size:20 final size:20
Alignment explanation
Indices: 360506--360553 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
360496 CTCCAGAATG
360506 CTCTAGAAAATTCTACAATT
1 CTCTAGAAAATTCTACAATT
* * *
360526 CCCCAGAAAATTCTAGAATT
1 CTCTAGAAAATTCTACAATT
*
360546 TTCTAGAA
1 CTCTAGAA
360554 CCTCTCCAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (20 bp):
CTCTAGAAAATTCTACAATT
Found at i:365212 original size:29 final size:30
Alignment explanation
Indices: 365177--365233 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
365167 TTGAGTCTCT
365177 CGACTATT-AAAAGTTACAAAATAGTCAAC
1 CGACTATTCAAAAGTTACAAAATAGTCAAC
* * *
365206 CGACTATTCATAAGTTCCAAACTAGTCA
1 CGACTATTCAAAAGTTACAAAATAGTCA
365234 TTTTCTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (30 bp):
CGACTATTCAAAAGTTACAAAATAGTCAAC
Found at i:365517 original size:59 final size:60
Alignment explanation
Indices: 365394--365529 Score: 156
Period size: 59 Copynumber: 2.3 Consensus size: 60
365384 ATAATCGGGT
* * ** *
365394 GATCATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAGTAATGCTTTATAATCGGAG
1 GATCATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAGCAATACCCTATAACCGGAG
365454 GATCATTTTGTAACTTTTAATAGTC--GGAGACTCAACATAA-CAATACCCTATAACCAGG-G
1 GATCATTTTGTAACTTTTAATAGTCGAGGA-ACTCAACA-AAGCAATACCCTATAACC-GGAG
365513 GATCATTTGTGT-ACTTT
1 GATCATTT-TGTAACTTT
365530 ACTATAAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
58 3 0.04
59 32 0.48
60 32 0.48
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAGCAATACCCTATAACCGGAG
Found at i:366500 original size:16 final size:15
Alignment explanation
Indices: 366479--366508 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
366469 AATATTAAAA
366479 CTTGAACTCGAAAAGG
1 CTTGAACTC-AAAAGG
366495 CTTGAACTCAAAAG
1 CTTGAACTCAAAAG
366509 CTCAATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (15 bp):
CTTGAACTCAAAAGG
Found at i:368139 original size:5 final size:5
Alignment explanation
Indices: 368129--368153 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
368119 CGCCGTCCGT
368129 CTCGG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG
368154 GTCGTCGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.40, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:368165 original size:6 final size:6
Alignment explanation
Indices: 368153--368190 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
368143 GCTCGGCTCG
* *
368153 GGTCGT CGTCGT CGTCGT GGTCGT GGTCGT GGTCGT GG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GG
368191 AGAACAGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.21, G:0.47, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:372467 original size:21 final size:21
Alignment explanation
Indices: 372443--372485 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
372433 TTCATATTCG
* *
372443 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
372464 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
372485 T
1 T
372486 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:374676 original size:22 final size:22
Alignment explanation
Indices: 374651--374708 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
374641 ATATCAGGAG
* *
374651 TTACAGGAGTTATTTGATTTAA
1 TTACAGGAGTTATATGATATAA
* *
374673 TTACAGGGGTTACATGATATAA
1 TTACAGGAGTTATATGATATAA
* *
374695 TTTCAAGAGTTATA
1 TTACAGGAGTTATA
374709 ACAGCTGAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (22 bp):
TTACAGGAGTTATATGATATAA
Found at i:380016 original size:25 final size:24
Alignment explanation
Indices: 379978--380052 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 24
379968 ACAATGAATT
* *
379978 ATAAATAAAGTAAAAAATGAATGAA
1 ATAAAGAAAATAAAAAAT-AATGAA
*
380003 ATAAAGAAAATAAATAATAATGAA
1 ATAAAGAAAATAAAAAATAATGAA
*
380027 A-AATAGAAAATAAAAATAAAATGAA
1 ATAA-AGAAAATAAAAA-ATAATGAA
380052 A
1 A
380053 AATGAATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 2 0.05
24 18 0.42
25 23 0.53
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (24 bp):
ATAAAGAAAATAAAAAATAATGAA
Found at i:380030 original size:13 final size:13
Alignment explanation
Indices: 380014--380061 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
380004 TAAAGAAAAT
380014 AAATAATAATGAA
1 AAATAATAATGAA
*
380027 AAATAGAAAAT-AA
1 AAATA-ATAATGAA
380040 AAATAA-AATGAA
1 AAATAATAATGAA
380052 AAATGAATAA
1 AAAT-AATAA
380062 AATAGATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 3 0.10
12 7 0.23
13 14 0.47
14 6 0.20
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (13 bp):
AAATAATAATGAA
Found at i:380034 original size:24 final size:24
Alignment explanation
Indices: 379990--380055 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 24
379980 AAATAAAGTA
*
379990 AAAAATGAATGAAATAA-AGAAAAT
1 AAAAATAAATGAAA-AATAGAAAAT
380014 AAATAAT-AATGAAAAATAGAAAAT
1 AAA-AATAAATGAAAAATAGAAAAT
380038 AAAAATAAAATGAAAAAT
1 AAAAAT-AAATGAAAAAT
380056 GAATAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.13
24 20 0.53
25 13 0.34
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (24 bp):
AAAAATAAATGAAAAATAGAAAAT
Found at i:380243 original size:3 final size:3
Alignment explanation
Indices: 380235--380274 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
380225 AAGATAGGAA
* *
380235 AAT AAT AAT AAT AAT AAT AAT AAT AGT GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
380275 GAAAGAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:380347 original size:18 final size:18
Alignment explanation
Indices: 380326--380368 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
380316 ATAGTAACGT
380326 ATAAATAAAATAAAATAA
1 ATAAATAAAATAAAATAA
380344 AT-AATAAAAATAAAATAA
1 ATAAAT-AAAATAAAATAA
*
380362 ACAAATA
1 ATAAATA
380369 TATATATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.14
18 16 0.73
19 3 0.14
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (18 bp):
ATAAATAAAATAAAATAA
Found at i:381965 original size:36 final size:36
Alignment explanation
Indices: 381907--381995 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
381897 GATTGGTGAT
* * *
381907 TCAAGAG-GA-AAACTTCGTTTCAAGGGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
381941 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
* * *
381977 TAAAAAGAGACGAAATTTG
1 TCAAGAGAGACAAAATTTG
381996 CTCAAAAGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 7 0.15
35 2 0.04
36 38 0.81
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (36 bp):
TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
Found at i:382018 original size:86 final size:86
Alignment explanation
Indices: 381923--382081 Score: 255
Period size: 86 Copynumber: 1.8 Consensus size: 86
381913 GGAAAACTTC
* *
381923 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTAAAAAGAGAC
1 GTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAACTGTCTAAAAAGAGAC
381988 GAAATTTGCTCAAAAGATTTT
66 GAAATTTGCTCAAAAGATTTT
* * * **
382009 GTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAATTGTCTCAAGGGAGAC
1 GTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAACTGTCTAAAAAGAGAC
382074 GAAATTTG
66 GAAATTTG
382082 ATTCAAGGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (86 bp):
GTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAACTGTCTAAAAAGAGAC
GAAATTTGCTCAAAAGATTTT
Found at i:382048 original size:36 final size:36
Alignment explanation
Indices: 382006--382371 Score: 216
Period size: 36 Copynumber: 10.5 Consensus size: 36
381996 CTCAAAAGAT
* *
382006 TTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
382042 TTTGTTTTAAAAGAAATTGTCTCAAGGGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
382078 TTTGATTCAAG-GAAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAA
382107 TTTGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAA
* * * * *
382143 TTTAGTTCCGAA-AGAAACTATATCAAGGGAGACGAAA
1 TTT-GTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
382180 GTTGTTTTAAG-GAAAATAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGAGAAACT-G-TCTCAAGAGAGACAAAA
* *
382209 TTTGTTTCAATG-GAGACTGTCTCAAAAGAGACAAAA
1 TTTGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAA
* * *
382245 TTTGTTTTAAGAGAAAGTGTCTCAAGAAAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
382281 TTTGTTTTAAGAGAAACTGTCTCTAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
** *
382317 CTTTGTTTTGAGAGAATCTGTCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
**
382354 CTTTGTTTTGAGAGAAAC
1 -TTTGTTTCAAGAGAAAC
382372 AATCTCAAAG
Statistics
Matches: 257, Mismatches: 46, Indels: 53
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.01
29 32 0.12
30 7 0.03
31 2 0.01
32 4 0.02
33 4 0.02
35 11 0.04
36 115 0.45
37 77 0.30
38 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:382105 original size:101 final size:101
Alignment explanation
Indices: 382000--382284 Score: 381
Period size: 102 Copynumber: 2.8 Consensus size: 101
381990 AATTTGCTCA
* *
382000 AAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAATTGTCTC
1 AAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTC
382065 AAGGGAGACGAAATTTGATTCAAGGAAAACAGATTC
66 AAGGGAGACGAAATTTGATTCAAGGAAAACAGATTC
* *** * *
382101 AAAGATTTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATTTAGTTCCGAAAGAAACTATAT
1 AAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT-GTTTTAAAAGAAACTGTCT
* * * *
382166 CAAGGGAGACGAAAGTTGTTTTAAGGAAAATAGATTC
65 CAAGGGAGACGAAATTTGATTCAAGGAAAACAGATTC
* * * * *
382203 AAAGATTTTGTTTCAATGGAGACTGTCTCAAAAGAGACAAAATTTGTTTTAAGAGAAAGTGTCTC
1 AAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTC
** *
382268 AAGAAAGACAAAATTTG
66 AAGGGAGACGAAATTTG
382285 TTTTAAGAGA
Statistics
Matches: 156, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
101 69 0.44
102 87 0.56
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (101 bp):
AAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTC
AAGGGAGACGAAATTTGATTCAAGGAAAACAGATTC
Found at i:382350 original size:73 final size:73
Alignment explanation
Indices: 382224--382380 Score: 217
Period size: 73 Copynumber: 2.2 Consensus size: 73
382214 TTCAATGGAG
*
382224 ACTGTCTCAAAAGAGACAAAATTTGTTTTAAGAGAAAGTGTCTCAAGAAAGACAAAA-TTTGTTT
1 ACTGTCTCAAAAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAAAGACAAAACTTTGTTT
382288 TAAGAGAA
66 TAAGAGAA
* * * * *
382296 ACTGTCTCTAGAGAGACAAAACTTTGTTTTGAGAGAATCTGTCTCAAGAGAGACAAAACTTTGTT
1 ACTGTCTCAAAAGAGACAAAA-TTTGTTTTAAGAGAAACTGTCTCAAGAAAGACAAAACTTTGTT
*
382361 TTGAGAGAA
65 TTAAGAGAA
**
382370 ACAATCTCAAA
1 ACTGTCTCAAA
382381 GGTGATCGAT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
72 19 0.26
73 32 0.44
74 21 0.29
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (73 bp):
ACTGTCTCAAAAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAAAGACAAAACTTTGTTT
TAAGAGAA
Found at i:383464 original size:21 final size:21
Alignment explanation
Indices: 383438--383483 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
383428 ATTCTGTTTA
*
383438 GTTCTCTGAAATCTTCCATTT
1 GTTCTCTAAAATCTTCCATTT
383459 GTTCTCTAAAATCTTCCATTT
1 GTTCTCTAAAATCTTCCATTT
383480 GTTC
1 GTTC
383484 AAGTTTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.48
Consensus pattern (21 bp):
GTTCTCTAAAATCTTCCATTT
Found at i:383871 original size:95 final size:94
Alignment explanation
Indices: 383704--383901 Score: 265
Period size: 95 Copynumber: 2.1 Consensus size: 94
383694 GGACATCTCA
* ** *
383704 ATATATAAAT-ACCTTTATCAGGTTAGCTGGATCTTATCCATAAAGCCGGGGAGTTTAACCAATT
1 ATATAT-AATCACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCCGGGGAGTTTAACCAATT
* * **
383768 GCCTTAGAGGGATAGCTTAAGCTTTATTGT
65 GCCTTAGAGGGACAACCCAAGCTTTATTGT
* *
383798 ATAGTATAATCACCTTTATCAGGCTAGCTAAATATTATCCATAAAGTCGGGGTGTTTAACCAATT
1 ATA-TATAATCACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCCGGGGAGTTTAACCAATT
383863 G-CTCTAGAGGGACAACCCAAGCTTTATTGT
65 GCCT-TAGAGGGACAACCCAAGCTTTATTGT
383893 ATATATAAT
1 ATATATAAT
383902 ATTATAATGT
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
94 14 0.15
95 77 0.85
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (94 bp):
ATATATAATCACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCCGGGGAGTTTAACCAATTG
CCTTAGAGGGACAACCCAAGCTTTATTGT
Found at i:399617 original size:27 final size:25
Alignment explanation
Indices: 399586--399646 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
399576 GATGTGTTAG
*
399586 ATAAAAAAACAATGAATGATAAATAAA
1 ATAAAAAAACAATGAA--ATAAAGAAA
* **
399613 GTAAAAAATGAATGAAATAAAGAAA
1 ATAAAAAAACAATGAAATAAAGAAA
399638 ATAAAAAAA
1 ATAAAAAAA
399647 AAAAAAAGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
25 15 0.54
27 13 0.46
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.16
Consensus pattern (25 bp):
ATAAAAAAACAATGAAATAAAGAAA
Found at i:399643 original size:23 final size:22
Alignment explanation
Indices: 399586--399694 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 22
399576 GATGTGTTAG
*
399586 ATAAA-AAAACAATGAATGATAA
1 ATAAAGAAAAAAATGAATGA-AA
*
399608 ATAAAGTAAAAAATGAATG-AA
1 ATAAAGAAAAAAATGAATGAAA
*
399629 ATAAAGAAAATAAA--AA-AAAA
1 ATAAAGAAAA-AAATGAATGAAA
* **
399649 AAAAAGTGAAAAATGAAT-AAA
1 ATAAAGAAAAAAATGAATGAAA
* *
399670 ATAGATAAAACAAATGAAATGAAA
1 ATAAAGAAAA-AAATG-AATGAAA
399694 A
1 A
399695 AGAGGTAATA
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.05
20 11 0.17
21 21 0.32
22 13 0.20
23 14 0.21
24 4 0.06
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.16
Consensus pattern (22 bp):
ATAAAGAAAAAAATGAATGAAA
Found at i:399913 original size:5 final size:5
Alignment explanation
Indices: 399903--399936 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
399893 AGTAACGTAT
399903 AAATA AAATA AAATAA ATAATA AAATA AAATA AA
1 AAATA AAATA AAAT-A A-AATA AAATA AAATA AA
399937 CAAATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 20 0.74
6 4 0.15
7 3 0.11
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:399926 original size:17 final size:17
Alignment explanation
Indices: 399904--399936 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
399894 GTAACGTATA
399904 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
399921 AATAAAATAAAATAAA
1 AATAAAATAAAATAAA
399937 CAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAAAATAAAATAAAT
Found at i:401767 original size:103 final size:98
Alignment explanation
Indices: 401582--401783 Score: 332
Period size: 103 Copynumber: 2.0 Consensus size: 98
401572 ATATGGTTTG
*
401582 ATTTTTCAGTGTAGTAAAATTCTAATTAATAATTTAGTATTTTTTATTATAAAATTAACAGATTA
1 ATTTTTCAGTGTAGTAAAATACTAATTAATAATTTAGTATTTTTTATTATAAAATTAACAGATTA
401647 ATAATTTATCATCTTTTCTATTATCTATGAGTA
66 ATAATTTATCATCTTTTCTATTATCTATGAGTA
* *
401680 ATTTTTTAGTGTAGTAAAATACTAATTAATAATTTAGTATTTTTATTTTTATTATAAAATTAATA
1 ATTTTTCAGTGTAGTAAAATACTAATTAATAATTTAGTA----T-TTTTTATTATAAAATTAACA
401745 GATTAATAATTTATCATCTTTTCTATTATCTATGAGTA
61 GATTAATAATTTATCATCTTTTCTATTATCTATGAGTA
401783 A
1 A
401784 ATTAGTATTT
Statistics
Matches: 96, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
98 37 0.39
102 1 0.01
103 58 0.60
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (98 bp):
ATTTTTCAGTGTAGTAAAATACTAATTAATAATTTAGTATTTTTTATTATAAAATTAACAGATTA
ATAATTTATCATCTTTTCTATTATCTATGAGTA
Found at i:408945 original size:104 final size:104
Alignment explanation
Indices: 408761--408970 Score: 384
Period size: 104 Copynumber: 2.0 Consensus size: 104
408751 TTTTCAAAAG
* *
408761 TGGCTGCCAAGTAAGCCTGATTAGCAAGGAAACAACGTGTAATATTCTTGCTCACGTGGGCTCAA
1 TGGCTGCCAAGTAAACCTGATTAGCAAGGAAACAACGTGTAATATTCTTGCTCACGTGAGCTCAA
*
408826 AACCGGAAATGTCAAAAGCAGAGGAAGACAAATGCCACT
66 AACCGGAAATATCAAAAGCAGAGGAAGACAAATGCCACT
*
408865 TGGCTGCTAAGTAAACCTGATTAGCAAGGAAACAACGTGTAATATTCTTGCTCACGTGAGCTCAA
1 TGGCTGCCAAGTAAACCTGATTAGCAAGGAAACAACGTGTAATATTCTTGCTCACGTGAGCTCAA
408930 AACCGGAAATATCAAAAGCAGAGGAAGACAAATGCCACT
66 AACCGGAAATATCAAAAGCAGAGGAAGACAAATGCCACT
408969 TG
1 TG
408971 ATGACTTCAA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (104 bp):
TGGCTGCCAAGTAAACCTGATTAGCAAGGAAACAACGTGTAATATTCTTGCTCACGTGAGCTCAA
AACCGGAAATATCAAAAGCAGAGGAAGACAAATGCCACT
Found at i:409117 original size:38 final size:39
Alignment explanation
Indices: 409075--409214 Score: 131
Period size: 45 Copynumber: 3.5 Consensus size: 39
409065 GAGTTTAAGG
* *
409075 ATTACGATCGAAAAAATTATAAAGAATATAACATTTT-T
1 ATTACAATCGAAAATATTATAAAGAATATAACATTTTGT
* * *
409113 ATTACAATCGAAAATATTTTGAAGAA-ATTAATATTTTTTATTGGT
1 ATTACAATCGAAAATATTATAAAGAATA-TAACA----TT-TT-GT
* *
409158 ATTACAATCGAAAATATTATAAAAAATATAACATTTTCT
1 ATTACAATCGAAAATATTATAAAGAATATAACATTTTGT
*
409197 ATTACACTCGAAAATATT
1 ATTACAATCGAAAATATT
409215 TTGAAGAAAG
Statistics
Matches: 82, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
37 1 0.01
38 26 0.32
39 18 0.22
40 2 0.02
41 2 0.02
42 2 0.02
43 2 0.02
45 28 0.34
46 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (39 bp):
ATTACAATCGAAAATATTATAAAGAATATAACATTTTGT
Found at i:409162 original size:83 final size:84
Alignment explanation
Indices: 409075--409239 Score: 260
Period size: 84 Copynumber: 2.0 Consensus size: 84
409065 GAGTTTAAGG
* *
409075 ATTACGATCGAAAAAATTATAAAGAATATAACATTTT-TATTACAATCGAAAATATTTTGAAGAA
1 ATTACAATCGAAAAAATTATAAAAAATATAACATTTTCTATTACAATCGAAAATATTTTGAAGAA
*
409139 ATTAATATTTTTTATTGGT
66 AGTAATATTTTTTATTGGT
* *
409158 ATTACAATCGAAAATATTATAAAAAATATAACATTTTCTATTACACTCGAAAATATTTTGAAGAA
1 ATTACAATCGAAAAAATTATAAAAAATATAACATTTTCTATTACAATCGAAAATATTTTGAAGAA
* *
409223 AGTGATGTTTTTTATTG
66 AGTAATATTTTTTATTG
409240 TAACATGTCC
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
83 34 0.46
84 40 0.54
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (84 bp):
ATTACAATCGAAAAAATTATAAAAAATATAACATTTTCTATTACAATCGAAAATATTTTGAAGAA
AGTAATATTTTTTATTGGT
Found at i:409583 original size:4 final size:4
Alignment explanation
Indices: 409574--409598 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
409564 CATTCTTTAG
409574 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
409599 TAGTACGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:416531 original size:319 final size:319
Alignment explanation
Indices: 415952--416596 Score: 1227
Period size: 319 Copynumber: 2.0 Consensus size: 319
415942 AGAGGGTGGG
415952 ATGATATCAAGAAAGGCCACGATAGCCCTATCACCGGAAACCAGTAGCTTTTTGTTTGCCTTTGA
1 ATGATATCAAGAAAGGCCACGATAGCCCTATCACCGGAAACCAGTAGCTTTTTGTTTGCCTTTGA
416017 GATTGCAGGTTCTGAAGGCAGTTCAGTTTCGAACAAATTAGGATTCATATATGTATTTGGTCGAT
66 GATTGCAGGTTCTGAAGGCAGTTCAGTTTCGAACAAATTAGGATTCATATATGTATTTGGTCGAT
*
416082 ATGGTATACTGGAATATGAATAAGGGTGGCTGCATAGCAGCAATGAAGCTGGAGGTGTGAGCAGG
131 ATGGTATACTGGAATATGAATAAGGGTGGCTGCATAGCAGCAATAAAGCTGGAGGTGTGAGCAGG
*
416147 CCGTTTCTGAGATGGTGGCCGTAGGGCGAACTAAAAAAATTAGTCCCTTGATCTAGGATTTAAAT
196 CCGTTTCTGAGATGGTGGCCGTAGGGCGAACTAAAAAAATTAGTCCCTTGATCAAGGATTTAAAT
416212 TACAATTTGCATTTGTGTCTTCGACCTCGTTGTGTTTATCACTATTGCGGACATAACTA
261 TACAATTTGCATTTGTGTCTTCGACCTCGTTGTGTTTATCACTATTGCGGACATAACTA
*
416271 ATGATATCAAGAAAGGCCGCGATAGCCCTATCACCGGAAACCAGTAGCTTTTTGTTTGCCTTTGA
1 ATGATATCAAGAAAGGCCACGATAGCCCTATCACCGGAAACCAGTAGCTTTTTGTTTGCCTTTGA
416336 GATTGCAGGTTCTGAAGGCAGTTCAGTTTCGAACAAATTAGGATTCATATATGTATTTGGTCGAT
66 GATTGCAGGTTCTGAAGGCAGTTCAGTTTCGAACAAATTAGGATTCATATATGTATTTGGTCGAT
416401 ATGGTATACTGGAATATGAATAAGGGTGGCTGCATAGCAGCAATAAAGCTGGAGGTGTGAGCAGG
131 ATGGTATACTGGAATATGAATAAGGGTGGCTGCATAGCAGCAATAAAGCTGGAGGTGTGAGCAGG
*
416466 CCGTTTCTGAGATGGTGGCCGTAGGGCGAACTAAAAAAATTAGTCCCTTGGTCAAGGATTTAAAT
196 CCGTTTCTGAGATGGTGGCCGTAGGGCGAACTAAAAAAATTAGTCCCTTGATCAAGGATTTAAAT
* * *
416531 TACAGTTTGCATTTGTGTTTTCGACCTCGTTGTGTTTATCGCTATTGCGGACATAACTA
261 TACAATTTGCATTTGTGTCTTCGACCTCGTTGTGTTTATCACTATTGCGGACATAACTA
416590 ATGATAT
1 ATGATAT
416597 TACGATCACT
Statistics
Matches: 319, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
319 319 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (319 bp):
ATGATATCAAGAAAGGCCACGATAGCCCTATCACCGGAAACCAGTAGCTTTTTGTTTGCCTTTGA
GATTGCAGGTTCTGAAGGCAGTTCAGTTTCGAACAAATTAGGATTCATATATGTATTTGGTCGAT
ATGGTATACTGGAATATGAATAAGGGTGGCTGCATAGCAGCAATAAAGCTGGAGGTGTGAGCAGG
CCGTTTCTGAGATGGTGGCCGTAGGGCGAACTAAAAAAATTAGTCCCTTGATCAAGGATTTAAAT
TACAATTTGCATTTGTGTCTTCGACCTCGTTGTGTTTATCACTATTGCGGACATAACTA
Found at i:421153 original size:30 final size:31
Alignment explanation
Indices: 421088--421154 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
421078 TTATAATACA
*
421088 GTCCCCCAACATTTAGTCCGTTTGCAATATG
1 GTCCCCCAACATTTAGTCCGTTTGAAATATG
* *
421119 GTCCCCCAACATTTAGT-CTTTTGAAATGTG
1 GTCCCCCAACATTTAGTCCGTTTGAAATATG
421149 GTCCCC
1 GTCCCC
421155 GATATAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCCGTTTGAAATATG
Found at i:424678 original size:29 final size:29
Alignment explanation
Indices: 424602--424687 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 29
424592 TTGAAAGTAT
424602 ATCCTTAATAACAAATATTAAAAAATTAG
1 ATCCTTAATAACAAATATTAAAAAATTAG
* * * * *
424631 A-CCTATGATAATAAGTATTAGAAAATTTG
1 ATCCT-TAATAACAAATATTAAAAAATTAG
* *
424660 ATCCTTAAAAACAAATATTAAAATATTA
1 ATCCTTAATAACAAATATTAAAAAATTA
424688 ACAAGAATTT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
28 3 0.07
29 37 0.86
30 3 0.07
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (29 bp):
ATCCTTAATAACAAATATTAAAAAATTAG
Found at i:424727 original size:20 final size:19
Alignment explanation
Indices: 424670--424728 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
424660 ATCCTTAAAA
*
424670 ACAAATATTAAAATATTA-
1 ACAAATATTAAAAAATTAT
* *
424688 ACAAGA-ATTTAGAAATTTAT
1 ACAA-ATA-TTAAAAAATTAT
424708 ACAAATATTAAAAAAATTAT
1 ACAAATATT-AAAAAATTAT
424728 A
1 A
424729 AGAGTAGACC
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 5 0.16
19 12 0.39
20 14 0.45
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (19 bp):
ACAAATATTAAAAAATTAT
Found at i:424782 original size:32 final size:32
Alignment explanation
Indices: 424741--424803 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
424731 AGTAGACCTC
424741 TAATAATAAATATTAGA-ACAAAATTAAACCCA
1 TAATAATAAATATTAGAGA-AAAATTAAACCCA
*
424773 TAATAATAAATATTAGAGAAAAGTTAAACCC
1 TAATAATAAATATTAGAGAAAAATTAAACCC
424804 TTAACCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.25
Consensus pattern (32 bp):
TAATAATAAATATTAGAGAAAAATTAAACCCA
Found at i:424819 original size:32 final size:32
Alignment explanation
Indices: 424745--424819 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
424735 GACCTCTAAT
*
424745 AATAAATATTAGAACAAAATTAAACCCATAAT
1 AATAAATATTAGAACAAAATTAAACCCATAAC
* *
424777 AATAAATATTAGAGA-AAAGTTAAACCCTTAAC
1 AATAAATATTAGA-ACAAAATTAAACCCATAAC
* *
424809 CATAAGTATTA
1 AATAAATATTA
424820 AAAATAATCG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 36 0.97
33 1 0.03
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.27
Consensus pattern (32 bp):
AATAAATATTAGAACAAAATTAAACCCATAAC
Found at i:425190 original size:21 final size:21
Alignment explanation
Indices: 425163--425211 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
425153 CCGGTCATCC
425163 AATTTTTTAAACCCCAGACCG
1 AATTTTTTAAACCCCAGACCG
*
425184 GA-TTTTTAAACCCCAGACCG
1 AATTTTTTAAACCCCAGACCG
425204 AATTTTTT
1 AATTTTTT
425212 TCGGATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (21 bp):
AATTTTTTAAACCCCAGACCG
Found at i:438179 original size:25 final size:25
Alignment explanation
Indices: 438151--438199 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
438141 CGACATTGAG
**
438151 GTAGTGTTTGTTTTTACTGTGTAAA
1 GTAGTGTTAATTTTTACTGTGTAAA
*
438176 GTAGTGTTAATTTTTATTGTGTAA
1 GTAGTGTTAATTTTTACTGTGTAA
438200 GGTATGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.53
Consensus pattern (25 bp):
GTAGTGTTAATTTTTACTGTGTAAA
Found at i:438368 original size:17 final size:18
Alignment explanation
Indices: 438346--438394 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
438336 CAAAGAAGTT
438346 TTATATTTAATTTT-ATA
1 TTATATTTAATTTTCATA
*
438363 TTATATTTGATTTTCATA
1 TTATATTTAATTTTCATA
438381 TTA-ATATTAATTTT
1 TTATAT-TTAATTTT
438395 TAAATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATATTTAATTTTCATA
Found at i:438430 original size:42 final size:43
Alignment explanation
Indices: 438373--438510 Score: 118
Period size: 42 Copynumber: 3.0 Consensus size: 43
438363 TTATATTTGA
*
438373 TTTTCATATTAATATTAATTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTAATATTAATTTTTAAATAAATTAAATATTAATT
* * * * *
438416 TTTTAATATT-ATATT-ATATATATATTAATTTTAATATTAATT
1 TTTTAATATTAATATTAATTTTTA-AATAAATTAAATATTAATT
*
438458 TTTTAAATAAATTAAATATTAATTTTTAATATTATATTATATATATTAATT
1 TTTT-AAT--ATT-AATATTAATTTTTAA-A-TAAATTA-A-ATATTAATT
438509 TT
1 TT
438511 ATATTATATA
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
41 5 0.07
42 25 0.35
43 12 0.17
45 3 0.04
47 6 0.08
48 5 0.07
49 4 0.06
50 1 0.01
51 11 0.15
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.57
Consensus pattern (43 bp):
TTTTAATATTAATATTAATTTTTAAATAAATTAAATATTAATT
Found at i:438477 original size:24 final size:27
Alignment explanation
Indices: 438419--438526 Score: 91
Period size: 28 Copynumber: 4.0 Consensus size: 27
438409 ATTAATTTTT
* * *
438419 TAATATTATATTATATATATATT-AATTT
1 TAATATTA-ATTTTTTA-ATATTAAATTA
438447 TAATATTAATTTTTTAA-A-TAAATTA
1 TAATATTAATTTTTTAATATTAAATTA
*
438472 -AATATTAA-TTTTTAATATTATATTA
1 TAATATTAATTTTTTAATATTAAATTA
* *
438497 TATATATTAATTTTATATTATATAAATTA
1 TA-ATATTAATTTTTTAATAT-TAAATTA
438526 T
1 T
438527 TTTATATATT
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
23 7 0.11
24 10 0.15
25 11 0.17
26 2 0.03
27 13 0.20
28 16 0.24
29 7 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TAATATTAATTTTTTAATATTAAATTA
Found at i:438486 original size:65 final size:65
Alignment explanation
Indices: 438351--438516 Score: 241
Period size: 66 Copynumber: 2.6 Consensus size: 65
438341 AAGTTTTATA
* * * * *
438351 TTTAATTTTATATTATATTTGATTTTCATATTAATATTAATTTTTAAATAAATTAAATATTAATT
1 TTTAATATTATATTATATAT-ATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATT
438416 T
65 T
438417 TTTAATATTATATTATATATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAA-T
1 TTTAATATTATATTATATATATATTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTAATT
438481 T
65 T
438482 TTTAATATTATA-T-TATATATATTAATTTT-ATATTA
1 TTTAATATTATATTATATATATATTAATTTTAATATTA
438517 TATAAATTAT
Statistics
Matches: 94, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
62 6 0.06
63 16 0.17
64 1 0.01
65 30 0.32
66 41 0.44
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (65 bp):
TTTAATATTATATTATATATATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTT
Found at i:438496 original size:25 final size:25
Alignment explanation
Indices: 438448--438523 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 25
438438 TATTAATTTT
*
438448 AATATTAATTTTTTAA-A-TAAATTA
1 AATATTAA-TTTTTAATATTATATTA
438472 AATATTAATTTTTAATATTATATTA
1 AATATTAATTTTTAATATTATATTA
438497 TATATATTAA-TTTT-ATATTATA-TA
1 -A-ATATTAATTTTTAATATTATATTA
438521 AAT
1 AAT
438524 TATTTTATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
22 2 0.04
23 8 0.17
24 11 0.23
25 14 0.30
26 5 0.11
27 7 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AATATTAATTTTTAATATTATATTA
Found at i:438506 original size:20 final size:20
Alignment explanation
Indices: 438418--438525 Score: 69
Period size: 20 Copynumber: 5.2 Consensus size: 20
438408 TATTAATTTT
438418 TTAATATTATATTATATATATA
1 TTAATATTATA-T-TATATATA
* * *
438440 TTAATTTTAATATTA-ATTTT
1 TTAATATT-ATATTATATATA
*
438460 TTAAATAAATTAAATATTA-AT-TT
1 TT-AAT--ATT--ATATTATATATA
438483 TTAATATTATATTATATATA
1 TTAATATTATATTATATATA
* *
438503 TTAATTTTATATTATATAAA
1 TTAATATTATATTATATATA
438523 TTA
1 TTA
438526 TTTTATATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.08
19 2 0.03
20 30 0.42
21 5 0.07
22 11 0.15
23 9 0.12
24 9 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATATTATATTATATATA
Found at i:438520 original size:27 final size:23
Alignment explanation
Indices: 438448--438542 Score: 67
Period size: 24 Copynumber: 4.1 Consensus size: 23
438438 TATTAATTTT
* *
438448 AATATTAATTTTTTAAATAAATTA
1 AATATTAA-TTTTTATATATATTA
438472 AATATTAATTTTTAATATTATATTA
1 AATATTAATTTTT-ATA-TATATTA
438497 TATATATTAA-TTTTATAT-TA-TA
1 -A-ATATTAATTTTTATATATATTA
438519 TAA-ATT-A-TTTTATATATTATTA
1 -AATATTAATTTTTATATA-TATTA
438541 AA
1 AA
438543 ATTTTATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 17
0.77 0.02 0.21
Matches are distributed among these distances:
19 9 0.15
20 3 0.05
21 5 0.08
22 6 0.10
23 7 0.11
24 11 0.18
25 9 0.15
26 5 0.08
27 7 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATATTAATTTTTATATATATTA
Found at i:438542 original size:20 final size:21
Alignment explanation
Indices: 438490--438567 Score: 85
Period size: 20 Copynumber: 4.0 Consensus size: 21
438480 TTTTTAATAT
* *
438490 TATATTATATATATTAATTT-
1 TATATTATATAAATTATTTTA
438510 TATATTATATAAATTATTTTA
1 TATATTATATAAATTATTTTA
438531 TATATTAT-TAAA--ATTTTA
1 TATATTATATAAATTATTTTA
* *
438549 TAT-TTATTTTAATTATTTT
1 TATATTATATAAATTATTTT
438568 GATTTAAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
17 4 0.08
18 12 0.24
20 27 0.53
21 8 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTATATAAATTATTTTA
Found at i:438548 original size:63 final size:61
Alignment explanation
Indices: 438381--438516 Score: 166
Period size: 65 Copynumber: 2.1 Consensus size: 61
438371 GATTTTCATA
* **
438381 TTAATATTAATTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATATATATATTAATT
1 TTAATATTAATTTTTTAATAAATT-AATA-TAAAATTTTAATATTATA-T-TATATATATTAATT
* *
438446 TTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTAATATTATATTATATATATTAATT
1 TTAATATTAATTTTTT-AATAAATT-AATATAAAATTTTAATATTATATTATATATATTAATT
438509 TT-ATATTA
1 TTAATATTA
438517 TATAAATTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
62 6 0.09
63 16 0.24
64 1 0.01
65 31 0.46
66 13 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (61 bp):
TTAATATTAATTTTTTAATAAATTAATATAAAATTTTAATATTATATTATATATATTAATT
Found at i:438741 original size:8 final size:8
Alignment explanation
Indices: 438728--438752 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
438718 TAAATTATAT
438728 TTTTAAAA
1 TTTTAAAA
438736 TTTTAAAA
1 TTTTAAAA
438744 TTTTAAAA
1 TTTTAAAA
438752 T
1 T
438753 ATAATCACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:438912 original size:17 final size:19
Alignment explanation
Indices: 438890--438927 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
438880 ATAATTGCAT
438890 ATTTAAAAA-ATCAT-ATA
1 ATTTAAAAATATCATAATA
438907 ATTTAAAAATATCATAATA
1 ATTTAAAAATATCATAATA
438926 AT
1 AT
438928 ACATGTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 5 0.26
19 5 0.26
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTTAAAAATATCATAATA
Found at i:439046 original size:31 final size:31
Alignment explanation
Indices: 439009--439068 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
438999 TAGTTGTATG
* * *
439009 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAATATTGCAAAACTAA
439040 AATTATTTAAATCTCAATATTGCAAAACT
1 AATTATTTAAATCTCAATATTGCAAAACT
439069 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGCAAAACTAA
Found at i:439503 original size:21 final size:21
Alignment explanation
Indices: 439479--439533 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
439469 TATATATTTT
*
439479 AAATATTATATTGTAAAT-TGA
1 AAATATTATATT-TAAATATAA
439500 AAATA-TAGTATTTAAATATAA
1 AAATATTA-TATTTAAATATAA
439521 AAATATTAT-TTTA
1 AAATATTATATTTA
439534 TTCAAAAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 11 0.37
21 17 0.57
22 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
AAATATTATATTTAAATATAA
Found at i:440582 original size:6 final size:6
Alignment explanation
Indices: 440571--440597 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
440561 GACACGTATT
440571 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
440598 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:441101 original size:5 final size:5
Alignment explanation
Indices: 441091--441139 Score: 71
Period size: 5 Copynumber: 9.6 Consensus size: 5
441081 TCCGTCTGTC
* *
441091 TCGGG TCGGG TCGGG TCGGG TCGTG TCGGG TCGTG TCGGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG
441140 TGGTTGTGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
5 34 0.87
6 5 0.13
ACGTcount: A:0.00, C:0.20, G:0.53, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:441761 original size:26 final size:24
Alignment explanation
Indices: 441699--441761 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
441689 CATTTTAATC
441699 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
441723 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
441746 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
441762 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:441763 original size:22 final size:23
Alignment explanation
Indices: 441733--441779 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
441723 AAAATATATT
441733 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
441756 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
441778 TA
1 TA
441780 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:441793 original size:32 final size:32
Alignment explanation
Indices: 441727--441815 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
441717 ATATTTAAAA
* *
441727 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
441759 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
* *
441791 TATATTATAATAATATTTTTAATAA
1 TATATT-TATTAATATTTATAATAA
441816 TTATTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
30 13 0.27
31 6 0.12
32 15 0.31
33 1 0.02
34 5 0.10
35 8 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:449228 original size:26 final size:25
Alignment explanation
Indices: 449192--449246 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
449182 TCAATAAATT
449192 ACTTTAAAAT-ATTTTATAAAAAAAA
1 ACTTTAAAATAATTTT-TAAAAAAAA
* *
449217 ACTTATAAAATAATTTTTAGAAAATA
1 ACTT-TAAAATAATTTTTAAAAAAAA
449243 ACTT
1 ACTT
449247 GAAATACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 17 0.65
27 5 0.19
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (25 bp):
ACTTTAAAATAATTTTTAAAAAAAA
Found at i:450869 original size:22 final size:22
Alignment explanation
Indices: 450836--450877 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
450826 TTAACTTATA
450836 AAACGTTAAATTATAAATTAGC
1 AAACGTTAAATTATAAATTAGC
450858 AAACG-TATAATTATAAATTA
1 AAACGTTA-AATTATAAATTA
450878 ATTAAGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (22 bp):
AAACGTTAAATTATAAATTAGC
Found at i:454003 original size:21 final size:21
Alignment explanation
Indices: 453986--454081 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
453976 CGCGTTGCAT
453986 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
*
454007 ATCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
* ** * ** *
454028 ATCGCGTTGTAAT-TTTCCAT
1 TTCGCGTTGCGATAGTTGAAA
454048 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
*
454069 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
454082 TTTCCATTTT
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 13 0.22
21 46 0.78
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTTGAAA
Found at i:454056 original size:41 final size:41
Alignment explanation
Indices: 454008--454104 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
453998 TAGTTGAAAA
*
454008 TCGCGTTGCGATAGTTGAAAATCGCGTTGTAATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
* * *
454049 TCGCGTTGCGATAGTTGAAATTCGTGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
*
454090 TTGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
454105 CTACAGTTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
Found at i:454234 original size:6 final size:6
Alignment explanation
Indices: 454223--454263 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
454213 GACACGTATT
* *
454223 ACCACG ACCACG ACCACG A-GACG A-GACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
454264 GACGAGACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.37, C:0.41, G:0.22, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:454251 original size:22 final size:22
Alignment explanation
Indices: 454226--454272 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
454216 ACGTATTACC
454226 ACGACCACGACCACGAGACGAG
1 ACGACCACGACCACGAGACGAG
454248 ACGACCACGACCACGAGACGAG
1 ACGACCACGACCACGAGACGAG
454270 ACG
1 ACG
454273 GACGGCGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.36, G:0.28, T:0.00
Consensus pattern (22 bp):
ACGACCACGACCACGAGACGAG
Found at i:454255 original size:28 final size:26
Alignment explanation
Indices: 454223--454276 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
454213 GACACGTATT
454223 ACCACGACCACGACCACGAGACGAGACG
1 ACCACGACCACGA-CACGAGACG-GACG
*
454251 ACCACGACCACGAGACGAGACGGACG
1 ACCACGACCACGACACGAGACGGACG
454277 GCGGTGGCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 8 0.32
28 13 0.52
ACGTcount: A:0.35, C:0.37, G:0.28, T:0.00
Consensus pattern (26 bp):
ACCACGACCACGACACGAGACGGACG
Found at i:454899 original size:22 final size:21
Alignment explanation
Indices: 454874--454945 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
454864 AATTTGGAAA
454874 ATCGCAACGATAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
* * **
454896 ATCGCAACG-AA-TTTGGAAA
1 ATCGCAACGAAACTGTAGACT
*
454915 ATCGCAACGACAACTGCAGACT
1 ATCGCAACGA-AACTGTAGACT
454937 ATCGCAACG
1 ATCGCAACG
454946 CGAAATGGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (21 bp):
ATCGCAACGAAACTGTAGACT
Found at i:454910 original size:41 final size:41
Alignment explanation
Indices: 454859--454945 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
454849 CTTTTTTTTT
* * *
454859 CAACTAATTTGGAAAATCGCAACGATAACTGTAGACTATCG
1 CAACGAATTTGGAAAATCGCAACGACAACTGCAGACTATCG
454900 CAACGAATTTGGAAAATCGCAACGACAACTGCAGACTATCG
1 CAACGAATTTGGAAAATCGCAACGACAACTGCAGACTATCG
454941 CAACG
1 CAACG
454946 CGAAATGGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
CAACGAATTTGGAAAATCGCAACGACAACTGCAGACTATCG
Found at i:454920 original size:19 final size:19
Alignment explanation
Indices: 454859--454924 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
454849 CTTTTTTTTT
*
454859 CAACTAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
454878 CAACGATAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
454900 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
454919 CAACGA
1 CAACGA
454925 CAACTGCAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 18 0.51
20 2 0.06
21 2 0.06
22 13 0.37
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:454966 original size:20 final size:20
Alignment explanation
Indices: 454941--454988 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
454931 CAGACTATCG
454941 CAACGCGAAATGGAAAATCA
1 CAACGCGAAATGGAAAATCA
*
454961 CAACGCGAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCA
454981 CAACGCGA
1 CAACGCGA
454989 TTTTCAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.08
Consensus pattern (20 bp):
CAACGCGAAATGGAAAATCA
Found at i:463654 original size:19 final size:22
Alignment explanation
Indices: 463628--463674 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
463618 AAAGACCCCT
*
463628 TTTTTTTC-TCTTCATCGGTTC
1 TTTTTCTCTTCTTCATCGGTTC
463649 TTTTTCTCTTCTTCATCGGTTC
1 TTTTTCTCTTCTTCATCGGTTC
463671 TTTT
1 TTTT
463675 AGGTGAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.04, C:0.23, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTTTCTCTTCTTCATCGGTTC
Found at i:463772 original size:18 final size:18
Alignment explanation
Indices: 463749--463786 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
463739 GTTTCATGGC
463749 TTGTTGGATGTTT-GGGTT
1 TTGTTGGA-GTTTCGGGTT
*
463767 TTGTTGTAGTTTCGGGTT
1 TTGTTGGAGTTTCGGGTT
463785 TT
1 TT
463787 TTTGTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.05, C:0.03, G:0.34, T:0.58
Consensus pattern (18 bp):
TTGTTGGAGTTTCGGGTT
Found at i:463791 original size:18 final size:17
Alignment explanation
Indices: 463758--463791 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
463748 CTTGTTGGAT
463758 GTTTGGGTTTTGTTGTA
1 GTTTGGGTTTTGTTGTA
*
463775 GTTTCGGGTTTTTTTGT
1 GTTT-GGGTTTTGTTGT
463792 TTAAAGATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.03, C:0.03, G:0.32, T:0.62
Consensus pattern (17 bp):
GTTTGGGTTTTGTTGTA
Found at i:471516 original size:23 final size:22
Alignment explanation
Indices: 471490--471545 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
471480 GTACTAAACG
471490 TATAATTTTAAATTAATTAAAAA
1 TATAATTTTAAATTAATT-AAAA
* * *
471513 TATAAATGTAATTTAATTAAAA
1 TATAATTTTAAATTAATTAAAA
471535 TATAATATTTA
1 TATAAT-TTTA
471546 TAAAACATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATAATTTTAAATTAATTAAAA
Found at i:471718 original size:19 final size:19
Alignment explanation
Indices: 471694--471736 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
471684 ATCGTAGTCG
471694 TCACCACCGGTATCATCTT
1 TCACCACCGGTATCATCTT
471713 TCACCACCGGTATCATCTT
1 TCACCACCGGTATCATCTT
471732 TCACC
1 TCACC
471737 GCCGACGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.21, C:0.40, G:0.09, T:0.30
Consensus pattern (19 bp):
TCACCACCGGTATCATCTT
Found at i:476314 original size:20 final size:20
Alignment explanation
Indices: 476255--476314 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
476245 ATATGAAATT
* *
476255 TGTCCCGAAAGACCTATGAA
1 TGTCCCGAAGGACCTATGTA
* * *
476275 TATCCCGAAGGATCTCTGTA
1 TGTCCCGAAGGACCTATGTA
*
476295 TGTCCAGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
476315 ACTTTCCATA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATGTA
Found at i:481533 original size:28 final size:29
Alignment explanation
Indices: 481480--481558 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
481470 TCGAACTAAC
*
481480 TTACTAAC-TTTTATTTATTCACTTTATTATTA
1 TTACTAACATTTTATTT-TT---TTTACTATTA
* *
481512 -TACTAACTTTTTATTTTTTTTACTGTTA
1 TTACTAACATTTTATTTTTTTTACTATTA
481540 TTACTAACATTTTATTTTT
1 TTACTAACATTTTATTTTT
481559 ACTGTACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.19
29 17 0.40
31 9 0.21
32 8 0.19
ACGTcount: A:0.25, C:0.11, G:0.01, T:0.62
Consensus pattern (29 bp):
TTACTAACATTTTATTTTTTTTACTATTA
Found at i:493798 original size:21 final size:21
Alignment explanation
Indices: 493721--493800 Score: 56
Period size: 22 Copynumber: 3.9 Consensus size: 21
493711 TATTTGGCAG
* *
493721 AGGGAATCGATA-CCCC-ATA
1 AGGGAACCGATACCCCCTTTA
* *
493740 AGGGAACCGATTCTCCCTTTGA
1 AGGGAACCGATACCCCCTTT-A
* * *
493762 TGGGAACCAATTCCCCCTTTA
1 AGGGAACCGATACCCCCTTTA
* *
493783 GGGGAATCGATACCCCCT
1 AGGGAACCGATACCCCCT
493801 GAGTTTTGGT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.21
20 3 0.06
21 16 0.34
22 18 0.38
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAACCGATACCCCCTTTA
Found at i:501031 original size:13 final size:13
Alignment explanation
Indices: 501015--501039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
501005 TTTTAAAAAA
501015 AACAAAAAAAAGG
1 AACAAAAAAAAGG
501028 AACAAAAAAAAG
1 AACAAAAAAAAG
501040 CCAAAATTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (13 bp):
AACAAAAAAAAGG
Found at i:506733 original size:192 final size:196
Alignment explanation
Indices: 506397--506776 Score: 511
Period size: 192 Copynumber: 2.0 Consensus size: 196
506387 TGTTGTCTCC
* * * * * * *
506397 AAGTCATCTTCTGATCGACCTGGTTTCTTCAAAATGAAGGAGCAACGTCATTTTTTACCTGAAAA
1 AAGTCATCTCCTGATCGACCCGATTTCCTCAAAACGAAGGAGCAACATCATTTTTTACATGAAAA
* * * * * *
506462 CGACCAGATCTCTTCAACATGGATGAACATTGTCGTCTTCAACATCAAATTGTGTCCAGGTCGAC
66 CGACCAGATCTCTTCAACATGGATGAACAGTGTCATCTTCAACATCAAACTATCTCCAGATCGAC
* *
506527 CTGATCTCCTCAACACGAAGGAGCAGTGTCATCCGCAGACAATCAGACTTCCTCAACGTGAAGGA
131 CCGATCTCCTCAACACGAAGGAGCAGCGTCATCCGCAGACAATCAGACTTCCTCAACGTGAAGGA
506592 A
196 A
*
506593 AAGTCATCTCCTGATTGACCCGATTTCCTCAAAACGAA-G-G-AACATCATCTTTTTACATG-AA
1 AAGTCATCTCCTGATCGACCCGATTTCCTCAAAACGAAGGAGCAACATCAT-TTTTTACATGAAA
* * *
506654 ATGACTAGATCTCTTCAACACT-GATGAACAGTGTCATCTT-AACATCAAACTATCTCCAGATTG
65 ACGACCAGATCTCTTCAACA-TGGATGAACAGTGTCATCTTCAACATCAAACTATCTCCAGATCG
* *
506717 ACCCGATCTCCTCAACACGAAGGAGCAGCGTCATCCTCATACAATCAGACTTCCTCAACG
129 ACCCGATCTCCTCAACACGAAGGAGCAGCGTCATCCGCAGACAATCAGACTTCCTCAACG
506777 CGAAAGAACC
Statistics
Matches: 161, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
192 74 0.46
193 43 0.27
194 11 0.07
195 1 0.01
196 32 0.20
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (196 bp):
AAGTCATCTCCTGATCGACCCGATTTCCTCAAAACGAAGGAGCAACATCATTTTTTACATGAAAA
CGACCAGATCTCTTCAACATGGATGAACAGTGTCATCTTCAACATCAAACTATCTCCAGATCGAC
CCGATCTCCTCAACACGAAGGAGCAGCGTCATCCGCAGACAATCAGACTTCCTCAACGTGAAGGA
A
Found at i:508360 original size:25 final size:25
Alignment explanation
Indices: 508309--508360 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 25
508299 CGCTTTATTA
508309 TTATACTAACTTTTATTTTTTTACTG
1 TTATACTAACTTTTA-TTTTTTACTG
508335 TTATACTAACATTTTA-TTTTTACTG
1 TTATACTAAC-TTTTATTTTTTACTG
508360 T
1 T
508361 ACAAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.40
26 10 0.40
27 5 0.20
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.60
Consensus pattern (25 bp):
TTATACTAACTTTTATTTTTTACTG
Found at i:514844 original size:12 final size:12
Alignment explanation
Indices: 514827--514851 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
514817 ATCAGTTTAG
514827 GACTGAAATGGT
1 GACTGAAATGGT
514839 GACTGAAATGGT
1 GACTGAAATGGT
514851 G
1 G
514852 CATGCCGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.36, T:0.24
Consensus pattern (12 bp):
GACTGAAATGGT
Found at i:516538 original size:88 final size:87
Alignment explanation
Indices: 516390--516597 Score: 310
Period size: 89 Copynumber: 2.4 Consensus size: 87
516380 TTGCCCTAAA
* * * *
516390 ATCTAAAATGAAACGTTGGGGACCAAAATGCTCCAAAAAAGAATAAGGGTTAAAGTGACTATTTA
1 ATCTAAAATGAGACGTTGGGG-CCAAAATGCTCAAAAAAAGAATAAAGGTTAAAGCGACTATTTA
*
516455 GTCAAACTTTA-GGACCTTTTTG
65 ATCAAACTTTAGGGACCTTTTTG
* *
516477 ATCTAAAATTAGACGTTGGGGCCAAAGTGCTCAAAAAAAAAGAATAAAGGTTAAAGCGACTATTT
1 ATCTAAAATGAGACGTTGGGGCCAAAATGCTC--AAAAAAAGAATAAAGGTTAAAGCGACTATTT
516542 AATCAAACTTTAGGGACCTTTTTG
64 AATCAAACTTTAGGGACCTTTTTG
*
516566 ACCTAAAATGAGACGTTGGGGCCAAAATGCTC
1 ATCTAAAATGAGACGTTGGGGCCAAAATGCTC
516598 CGAAAGTGAT
Statistics
Matches: 108, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
86 10 0.09
87 19 0.18
88 39 0.36
89 40 0.37
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (87 bp):
ATCTAAAATGAGACGTTGGGGCCAAAATGCTCAAAAAAAGAATAAAGGTTAAAGCGACTATTTAA
TCAAACTTTAGGGACCTTTTTG
Found at i:519279 original size:18 final size:18
Alignment explanation
Indices: 519256--519306 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
519246 AATACATAAA
519256 AAAAATTTTAAAAAAAAT
1 AAAAATTTTAAAAAAAAT
*
519274 AAAAA-TTTAAAAATACAT
1 AAAAATTTTAAAAA-AAAT
* *
519292 AAAACTTCTAAAAAA
1 AAAAATTTTAAAAAA
519307 TTTAAAAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.29
18 13 0.46
19 7 0.25
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATTTTAAAAAAAAT
Found at i:520289 original size:21 final size:20
Alignment explanation
Indices: 520263--520360 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
520253 ATCAGTTTCC
520263 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
520284 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
520303 ACAAATTCGCATTGCGATTTTCT
1 A-AAA-TCGCAACGCGATTTT-G
* *
520326 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
520346 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
520361 ACACATAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 19 0.31
21 38 0.61
22 3 0.05
23 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:520389 original size:20 final size:20
Alignment explanation
Indices: 520327--520556 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
520317 CGATTTTCTA
* ** *
520327 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
520347 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
520367 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
520387 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
520407 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
520427 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
520447 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
520467 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
520487 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
520507 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
520527 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
520547 AAATCACAAC
1 AAATCGCAAC
520557 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:521277 original size:24 final size:23
Alignment explanation
Indices: 521238--521283 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
521228 AAATTTGGTC
521238 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
521262 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
521284 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:521475 original size:12 final size:12
Alignment explanation
Indices: 521458--521482 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
521448 ATATAATCCT
521458 GAAGAAGAAAAA
1 GAAGAAGAAAAA
521470 GAAGAAGAAAAA
1 GAAGAAGAAAAA
521482 G
1 G
521483 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:523859 original size:33 final size:33
Alignment explanation
Indices: 523755--523862 Score: 173
Period size: 33 Copynumber: 3.2 Consensus size: 33
523745 CGGAAATTAC
523755 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
523788 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
523822 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
523855 AATCGCAA
1 AATCGCAA
523863 TGCGAAATGA
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.01
33 37 0.54
34 29 0.43
35 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:523860 original size:19 final size:19
Alignment explanation
Indices: 523769--523881 Score: 129
Period size: 19 Copynumber: 6.4 Consensus size: 19
523759 GCAACGAGAG
523769 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
523788 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
523802 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
523822 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
523836 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
523855 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
523874 AATCGCAA
1 AATCGCAA
523882 CGAGAGAATT
Statistics
Matches: 79, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
14 22 0.28
15 1 0.01
16 3 0.04
17 2 0.03
18 2 0.03
19 36 0.46
20 13 0.16
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:523882 original size:52 final size:53
Alignment explanation
Indices: 523797--523903 Score: 198
Period size: 52 Copynumber: 2.0 Consensus size: 53
523787 AAATCCCAAC
523797 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
523850 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATTGCAATGCGAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
523902 AT
1 AT
523904 TATAAACGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 37 0.70
53 16 0.30
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:524022 original size:52 final size:53
Alignment explanation
Indices: 523910--524025 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
523900 AAATTATAAA
523910 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
523963 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
524015 CGCATTGCGAT
1 CGCATTGCGAT
524026 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:524033 original size:19 final size:19
Alignment explanation
Indices: 523928--524025 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
523918 GATTCTCTCG
523928 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
523948 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
523967 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
523981 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
524000 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
524019 TTGCGAT
1 TTGCGAT
524026 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:524151 original size:14 final size:14
Alignment explanation
Indices: 524132--524168 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
524122 CATCAATTAC
524132 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
524146 ACAAATCATCTTTT
1 ACAAATCAACTTTT
524160 ACAAATCAA
1 ACAAATCAA
524169 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:526125 original size:18 final size:19
Alignment explanation
Indices: 526085--526217 Score: 83
Period size: 18 Copynumber: 7.6 Consensus size: 19
526075 TAGTTTACTT
* *
526085 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TCAAAA
*
526105 TCGCAACGCGAAA-CCAAA
1 TCGCAACGCGAAATCAAAA
*
526123 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
526142 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
* *
526156 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
526175 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAATCAAAA
*
526189 TCGCAACGCGAAAT-GAAA
1 TCGCAACGCGAAATCAAAA
*
526207 TCGCAATGCGA
1 TCGCAACGCGA
526218 TTTTGGTTTC
Statistics
Matches: 90, Mismatches: 13, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
14 18 0.20
15 1 0.01
16 6 0.07
17 6 0.07
18 29 0.32
19 18 0.20
20 12 0.13
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:526159 original size:14 final size:14
Alignment explanation
Indices: 526140--526196 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
526130 GCGAAATGAA
*
526140 AATCGCAACGACAG
1 AATCGCAACGAAAG
526154 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
526171 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
526187 AATCGCAACG
1 AATCGCAACG
526197 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Done.