Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 56 of 74
Found at i:11190423 original size:14 final size:13
Alignment explanation
Indices: 11190406--11190491 Score: 59
Period size: 14 Copynumber: 6.4 Consensus size: 13
11190396 TTTTTTTTCA
*
11190406 TTTTCTTTTTATT
1 TTTTTTTTTTATT
11190419 TTTTTATTTTTATT
1 TTTTT-TTTTTATT
*
11190433 TTATTTTATTTATT
1 TT-TTTTTTTTATT
*
11190447 TTACTTATATTTTA-T
1 TT--TT-TTTTTTATT
* *
11190462 TTTCTATTTT-TT
1 TTTTTTTTTTATT
*
11190474 TCTTTTTTTTATT
1 TTTTTTTTTTATT
11190487 TTTTT
1 TTTTT
11190492 AAAAAAAGAG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
12 14 0.25
13 11 0.19
14 19 0.33
15 8 0.14
16 5 0.09
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTTATT
Found at i:11190428 original size:25 final size:23
Alignment explanation
Indices: 11190395--11190490 Score: 77
Period size: 25 Copynumber: 3.9 Consensus size: 23
11190385 TGATTACAGG
*
11190395 TTTTTT-TTTCATTTTCTTTTTAT
1 TTTTTTATTTTATTTT-TTTTTAT
*
11190418 TTTTTTATTTTTATTTTATTTTAT
1 TTTTTTA-TTTTATTTTTTTTTAT
*
11190442 TTATTTTACTTATATTTTATTTTCTAT
1 TT-TTTTA-TTTTATTTT-TTTT-TAT
* *
11190469 TTTTTTCTTTTTTTTATTTTTT
1 TTTTTTATTTTATTT-TTTTTT
11190491 TAAAAAAAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
23 6 0.10
24 9 0.15
25 31 0.53
26 8 0.14
27 5 0.08
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTATTTTATTTTTTTTTAT
Found at i:11190491 original size:20 final size:20
Alignment explanation
Indices: 11190396--11190491 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
11190386 GATTACAGGT
*
11190396 TTTTTTTTCATTTTCTTTTTA
1 TTTTTTTT-ATTTTTTTTTTA
*
11190417 -TTTTTTTATTTTTATTTTA
1 TTTTTTTTATTTTTTTTTTA
* ** *
11190436 TTTTATTTATTTTACTTATA
1 TTTTTTTTATTTTTTTTTTA
* * *
11190456 TTTTATTTT-CTATTTTTTTC
1 TTTT-TTTTATTTTTTTTTTA
11190476 TTTTTTTTATTTTTTT
1 TTTTTTTTATTTTTTT
11190492 AAAAAAAGAG
Statistics
Matches: 57, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
19 14 0.25
20 40 0.70
21 3 0.05
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTTATTTTTTTTTTA
Found at i:11199816 original size:11 final size:11
Alignment explanation
Indices: 11199800--11199833 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11199790 TTTGTGTTAT
11199800 TTGTTTAGATC
1 TTGTTTAGATC
*
11199811 TTGTTTAAATC
1 TTGTTTAGATC
*
11199822 TCGTTTAGATC
1 TTGTTTAGATC
11199833 T
1 T
11199834 ATCATATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.53
Consensus pattern (11 bp):
TTGTTTAGATC
Found at i:11203074 original size:10 final size:11
Alignment explanation
Indices: 11203053--11203096 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
11203043 GAAACTACTT
11203053 AAAATTTAAAA
1 AAAATTTAAAA
11203064 AAAATTTAAAA
1 AAAATTTAAAA
**
11203075 ATATTTTTTAAAA
1 A-A-AATTTAAAA
11203088 AAAATTTAA
1 AAAATTTAA
11203097 TATAATTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 17 0.63
12 2 0.07
13 8 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:11205323 original size:22 final size:21
Alignment explanation
Indices: 11205293--11205335 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
11205283 TATTTAAAGA
11205293 AAATAGATAGAAATTAAA-AAAT
1 AAATAGATA-AAA-TAAATAAAT
*
11205315 AAATTGATAAAATAAATAAAT
1 AAATAGATAAAATAAATAAAT
11205336 GAGAACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (21 bp):
AAATAGATAAAATAAATAAAT
Found at i:11206451 original size:234 final size:235
Alignment explanation
Indices: 11205847--11207081 Score: 925
Period size: 234 Copynumber: 5.3 Consensus size: 235
11205837 TAAGAAGTGT
* * * * **
11205847 TATGACAATTCTAAACATAATGGAATGTAAGAACAACTGTAAAAATATATTATTGTAACATAAAT
1 TATGACAATTTTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAACATAAAT
* ** * * * * * *
11205912 AATTATGTT-AGCAATTTAAAATTTTAACTAATTATTATTTTTTAAATACATAAGGAATATAACT
66 AATTATATTGA-CAACATAAAATTTTAATTAATTATTATTTTATAAATATATAAGAAAAATAGCT
* * ** * * * *
11205976 AAAAATTGAAAAATAAATAAGTAACGTAAAAAAATGA-AAAAAAAGTAAAATTA-ATATAATTTG
130 AAAAATTAAAAAACAAATTGGTAACGTAAACAAGTGAGAAAAAACGTAAAATTAGA-ATCATTTG
* * * * * *
11206039 ATGTAAAATGAGTAAAAAATGTCATAATATATTAATAAAAAGC
194 ATATAAAATAAGTAAAAAGTATCGTAATATACTAA-AAAAAGC
* * * * * * * * *
11206082 AATGACAATTTTAAACATAATTAAAGGTAAGAGCAATCATAAAAAAAAATTATTATAACATAAAT
1 TATGACAATTTTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAACATAAAT
* ** * * * *
11206147 TATTACGTTGTCAACGTAAAATTTTAATCATTTA-T-TTTTATAAATATATAAGAAAAATAGCTA
66 AATTATATTGACAACATAAAATTTTAATTAATTATTATTTTATAAATATATAAGAAAAATAGCTA
* *
11206210 AAAATTAAAAAACAAATTGGTAACGTGAACAAGTGAGAAGAAACGTAAAATTAGAATCATTTGAT
131 AAAATTAAAAAACAAATTGGTAACGTAAACAAGTGAGAAAAAACGTAAAATTAGAATCATTTGAT
** * * *
11206275 ATAAAATAAGTATGAACTATCGTAATATGCT-AAAAAAGT
196 ATAAAATAAGTAAAAAGTATCGTAATATACTAAAAAAAGC
* ** * * * *
11206314 TATGACAATTCTAAATGTAATTAAAATTAAAAATAACCATAATAATATATTATTGTAACATAAAT
1 TATGACAATTTTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAACATAAAT
* * * *
11206379 AATTATATTGGCAACATAAAATTTTAATTAATTATTATTTTATACATATCTAAGAAAAATAGTTA
66 AATTATATTGACAACATAAAATTTTAATTAATTATTATTTTATAAATATATAAGAAAAATAGCTA
* * * * * * * * * *
11206444 GAAATTAAAAAATAAATTGGTAGCATAAATAAGTGAGAACAAATGT-AAATTTGTACCATTT-AG
131 AAAATTAAAAAACAAATTGGTAACGTAAACAAGTGAGAAAAAACGTAAAATTAGAATCATTTGA-
** * * ** *
11206507 GGTAAAATAAATAAAAAGTATTGTAATATGTTAAAAAAGAGT
195 TATAAAATAAGTAAAAAGTATCGTAATATACTAAAAAA-AGC
* * * *
11206549 TATGACAATTGTAAACATAATGAAAAGTAAAAACAACTATAAAAAAATGTTATTGTAA-AGGT-A
1 TATGACAATTTTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAACA--TAA
* * *
11206612 ATAATTATATTGACAACATAAAATTTTAATTATTTATTATTCTTGTAAATATA-AA-AAAATTAG
64 ATAATTATATTGACAACATAAAATTTTAATTAATTATTATT-TTATAAATATATAAGAAAAATAG
* * * *
11206675 CT-AAAATTAAAAAACAAATTGATAATC-TAAATAAGTGA-AAAATAACATAAAATTAGTATCAT
128 CTAAAAATTAAAAAACAAATTGGTAA-CGTAAACAAGTGAGAAAA-AACGTAAAATTAGAATCAT
* * * * * * * *
11206737 TTGAAATAAAATAGGTTAGAAGTGTTGTAACACACTAAAAAAAAGC
191 TTGATATAAAATAAGTAAAAAGTATCGTAATATACT-AAAAAAAGC
** * * * * * **
11206783 TACAACAATTTTAAATATGATGAAAAGTAAAAATAACAATAAAAATATATTATTATAATGTAAAT
1 TATGACAATTTTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAACATAAAT
* * * * * *
11206848 AATTATGA-TGATAATATAAAATTTTAATTAATTATTGTTGTTGTATATATATAAGGAAAATAGC
66 AATTAT-ATTGACAACATAAAATTTTAATTAATTATTATT-TTATAAATATATAAGAAAAATAGC
* * * * * *
11206912 TAGAAA-T--AAAA-AAATTGATAATGTAAACAAGTGAGAAGAAATGTAAAATTA-ATACCATTT
129 TAAAAATTAAAAAACAAATTGGTAACGTAAACAAGTGAGAAAAAACGTAAAATTAGA-ATCATTT
* * * * * *
11206972 -AGTGTAAAATGAA-TAAGAAGTGTTGTAACATACTAAAAAAAAGT
193 GA-TATAAAAT-AAGTAAAAAGTATCGTAATATACT-AAAAAAAGC
* ** * * * * * *
11207016 TATGATAATTTTAAATGTAATG-AATGATAAGAACAACCATAAAAAGATTTTATTATAATATAAA
1 TATGACAATTTTAAACATAATGAAAAG-TAAAAACAACCATAAAAATATATTATTGTAACATAAA
11207080 TA
65 TA
11207082 TTTAAGTAAA
Statistics
Matches: 801, Mismatches: 171, Indels: 58
0.78 0.17 0.06
Matches are distributed among these distances:
232 92 0.11
233 244 0.30
234 262 0.33
235 182 0.23
236 18 0.02
237 3 0.00
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (235 bp):
TATGACAATTTTAAACATAATGAAAAGTAAAAACAACCATAAAAATATATTATTGTAACATAAAT
AATTATATTGACAACATAAAATTTTAATTAATTATTATTTTATAAATATATAAGAAAAATAGCTA
AAAATTAAAAAACAAATTGGTAACGTAAACAAGTGAGAAAAAACGTAAAATTAGAATCATTTGAT
ATAAAATAAGTAAAAAGTATCGTAATATACTAAAAAAAGC
Found at i:11206846 original size:21 final size:20
Alignment explanation
Indices: 11206821--11206868 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
11206811 AAAAATAACA
* *
11206821 ATAAAAATATATTATTATAAT
1 ATAAAAAT-TATGATGATAAT
*
11206842 GTAAATAATTATGATGATAAT
1 ATAAA-AATTATGATGATAAT
11206863 ATAAAA
1 ATAAAA
11206869 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.82
22 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (20 bp):
ATAAAAATTATGATGATAAT
Found at i:11207060 original size:233 final size:234
Alignment explanation
Indices: 11205364--11205847 Score: 309
Period size: 231 Copynumber: 2.0 Consensus size: 234
11205354 AGTATCATTT
* * * * * * *
11205364 AGAAGTATTGTAACATATTAAGAAAGAGTTATGACAATTTTAAGCGTAATGAAAA--AATAAACA
1 AGAAGTGTTGTAATATACTAAAAAAAAGTTATGACAATTTTAAACATAATGAAAAGTAA-AAACA
** * * * * * * *
11205427 ACCATAGGAAGATATTATTGTAAAATAAATAATTATGTTGACAACTTTAAATTTTAATTAATTTT
65 ACCATAAAAATATATTATTATAACATAAATAATTATGATGACAACATAAAATTTTAATTAATTAT
* * * **
11205492 TGTTCTTGTAAGTATATAAGAAAAATAGCTAAAAA--AAAAACAAATTGATAATATAAACAAGTG
130 TATT-TTATAAATATATAAGAAAAATAGCTAAAAATTAAAAACAAATTGATAACGTAAACAAGTG
* * * * * *
11205555 AG---AAATGTAAAATTAGTATCATTTGGTATGAAATGGATA
194 AGAAAAAACGTAAAATTAATATCATTTGATGTAAAAT-AATA
* * * * * * ** * *
11205594 AGAAGTGTTGTAAAATGCTAAGAAAGAGTTATGATAATTCTAAATGTAATGGAAAGTAAGAACAA
1 AGAAGTGTTGTAATATACTAAAAAAAAGTTATGACAATTTTAAACATAATGAAAAGTAAAAACAA
* * ** *
11205659 TCATAAAAATATATTATTATAATATAAATAATTATGATGACAATGTAAAATTTTAATCAATTATT
66 CCATAAAAATATATTATTATAACATAAATAATTATGATGACAACATAAAATTTTAATTAATTATT
* * * *
11205724 ATTTTTATATATATATATATATATAAGAAATATAGCTAAAACTTAAAAAATAAATT-AGTAATGT
131 A----T-T-T-TATA-A-ATATATAAGAAAAATAGCTAAAAATT-AAAAACAAATTGA-TAACGT
* * * * * *
11205788 AAACAAGTGAGAAGAAACATAAAATTAGTATTATTTGACGTAAAATGGATA
185 AAACAAGTGAGAAAAAACGTAAAATTAATATCATTTGATGTAAAAT-AATA
11205839 AGAAGTGTT
1 AGAAGTGTT
11205848 ATGACAATTC
Statistics
Matches: 200, Mismatches: 37, Indels: 19
0.78 0.14 0.07
Matches are distributed among these distances:
230 46 0.23
231 58 0.29
232 2 0.01
235 1 0.00
236 2 0.01
237 3 0.01
238 1 0.00
239 21 0.10
241 1 0.00
242 26 0.13
245 39 0.19
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (234 bp):
AGAAGTGTTGTAATATACTAAAAAAAAGTTATGACAATTTTAAACATAATGAAAAGTAAAAACAA
CCATAAAAATATATTATTATAACATAAATAATTATGATGACAACATAAAATTTTAATTAATTATT
ATTTTATAAATATATAAGAAAAATAGCTAAAAATTAAAAACAAATTGATAACGTAAACAAGTGAG
AAAAAACGTAAAATTAATATCATTTGATGTAAAATAATA
Found at i:11207060 original size:467 final size:466
Alignment explanation
Indices: 11205851--11207069 Score: 1086
Period size: 467 Copynumber: 2.6 Consensus size: 466
11205841 AAGTGTTATG
* * * * * ** *
11205851 ACAATTCTAAACATAATGGAATGTAAGAACAACTGTAAAAATATATTATTGTAACATAAATAATT
1 ACAATTCTAAATATAATGAAAAGTAAAAATAACAATAAAAATATATTATTATAACATAAATAATT
* ** * * * * * * * *
11205916 ATGTT-AGCAATTTAAAATTTTAACTAATTATTATTTTTTAAATACATAAGGAATATAACTAAAA
66 ATATTGA-CAACATAAAATTTTAATTAATTATTATTTTATACATATATAAGAAAAATAGCTAGAA
* * * * * * ** *
11205980 ATTGAAAAATAAA-TAAGTAACGTAAAAAAATGA-AAAAAAAGTAAAATTAATATAATTT-GATG
130 ATT-AAAAATAAATTGA-TAACATAAACAAGTGAGAACAAATGT-AAATTAATACCATTTAG-GG
* * * * ** * * * ** * *
11206042 TAAAATGAGTAAAAAATGTCATAATATATTAATAAAAAGCAATGACAATTTTAAACATAATTAAA
191 TAAAATAAATAAAAAGTATTGTAACATACTAAAAAAAAGTTATGACAATTGTAAACATAATGAAA
* * * * ** * * ** * *
11206107 GGTAAGAGCAATCATAAAAAAAAATTATTATAACA--TAAATTATTACGTTGTCAACGTAAAATT
256 AGTAAAAACAACCATAAAAAAATGTTATTGTAA-AGGT-AATAATTATATTGACAACATAAAATT
*
11206170 TTAATCATTTATTTTTATAAATATATAAGAAAAATAGCTAAAAATTAAAAAACAAATTGGTAACG
319 TTAATCATTTATTTTTATAAATATATAAGAAAAATAGCTAAAAATTAAAAAACAAATTGATAACG
* * * *
11206235 TGAACAAGTGAGAAGAAACGTAAAATTAGAATCATTTGATATAAAATAAGTATGAACTATCGTAA
384 TAAACAAGTGAGAAAAAACATAAAATTAGAATCATTTGAAATAAAATAAGTATGAACTATCGTAA
* ** * **
11206300 TATGCTAAAAAAGTTATG
449 CACACTAAAAAAGCTACA
* * * * * *
11206318 ACAATTCTAAATGTAATTAAAATTAAAAATAACCATAATAATATATTATTGTAACATAAATAATT
1 ACAATTCTAAATATAATGAAAAGTAAAAATAACAATAAAAATATATTATTATAACATAAATAATT
* * *
11206383 ATATTGGCAACATAAAATTTTAATTAATTATTATTTTATACATATCTAAGAAAAATAGTTAGAAA
66 ATATTGACAACATAAAATTTTAATTAATTATTATTTTATACATATATAAGAAAAATAGCTAGAAA
* * * **
11206448 TTAAAAAATAAATTGGTAGCATAAATAAGTGAGAACAAATGTAAATTTGTACCATTTAGGGTAAA
131 TT-AAAAATAAATTGATAACATAAACAAGTGAGAACAAATGTAAATTAATACCATTTAGGGTAAA
* ** *
11206513 ATAAATAAAAAGTATTGTAATATGTTAAAAAAGAGTTATGACAATTGTAAACATAATGAAAAGTA
195 ATAAATAAAAAGTATTGTAACATACTAAAAAAAAGTTATGACAATTGTAAACATAATGAAAAGTA
* *
11206578 AAAACAACTATAAAAAAATGTTATTGTAAAGGTAATAATTATATTGACAACATAAAATTTTAATT
260 AAAACAACCATAAAAAAATGTTATTGTAAAGGTAATAATTATATTGACAACATAAAATTTTAATC
* *
11206643 ATTTATTATTCTTGTAAATATA-AA-AAAATTAGCT-AAAATTAAAAAACAAATTGATAATC-TA
325 ATTTA-T-TT-TTATAAATATATAAGAAAAATAGCTAAAAATTAAAAAACAAATTGATAA-CGTA
* * * * * *
11206704 AATAAGTGA-AAAATAACATAAAATTAGTATCATTTGAAATAAAATAGGT-TAGAAGTGTTGTAA
386 AACAAGTGAGAAAA-AACATAAAATTAGAATCATTTGAAATAAAATAAGTAT-GAACTATCGTAA
11206767 CACACTAAAAAAAAGCTACA
449 CACACT--AAAAAAGCTACA
* * **
11206787 ACAATTTTAAATATGATGAAAAGTAAAAATAACAATAAAAATATATTATTATAATGTAAATAATT
1 ACAATTCTAAATATAATGAAAAGTAAAAATAACAATAAAAATATATTATTATAACATAAATAATT
* * * * * *
11206852 ATGA-TGATAATATAAAATTTTAATTAATTATTGTTGTTGTATATATATAAGGAAAATAGCTAGA
66 AT-ATTGACAACATAAAATTTTAATTAATTATTATT-TTATACATATATAAGAAAAATAGCTAGA
** * *
11206916 AA-T-AAAA-AAATTGATAATGTAAACAAGTGAGAAGAAATGTAAAATTAATACCATTTAGTGTA
129 AATTAAAAATAAATTGATAACATAAACAAGTGAGAACAAATGT-AAATTAATACCATTTAGGGTA
* * * * * ** *
11206978 AAATGAATAAGAAGTGTTGTAACATACTAAAAAAAAGTTATGATAATTTTAAATGTAATG-AATG
193 AAATAAATAAAAAGTATTGTAACATACTAAAAAAAAGTTATGACAATTGTAAACATAATGAAAAG
* * *
11207042 ATAAGAACAACCATAAAAAGATTTTATT
258 -TAAAAACAACCATAAAAAAATGTTATT
11207070 ATAATATAAA
Statistics
Matches: 605, Mismatches: 129, Indels: 36
0.79 0.17 0.05
Matches are distributed among these distances:
466 35 0.06
467 415 0.69
468 21 0.03
469 98 0.16
470 36 0.06
ACGTcount: A:0.52, C:0.06, G:0.11, T:0.32
Consensus pattern (466 bp):
ACAATTCTAAATATAATGAAAAGTAAAAATAACAATAAAAATATATTATTATAACATAAATAATT
ATATTGACAACATAAAATTTTAATTAATTATTATTTTATACATATATAAGAAAAATAGCTAGAAA
TTAAAAATAAATTGATAACATAAACAAGTGAGAACAAATGTAAATTAATACCATTTAGGGTAAAA
TAAATAAAAAGTATTGTAACATACTAAAAAAAAGTTATGACAATTGTAAACATAATGAAAAGTAA
AAACAACCATAAAAAAATGTTATTGTAAAGGTAATAATTATATTGACAACATAAAATTTTAATCA
TTTATTTTTATAAATATATAAGAAAAATAGCTAAAAATTAAAAAACAAATTGATAACGTAAACAA
GTGAGAAAAAACATAAAATTAGAATCATTTGAAATAAAATAAGTATGAACTATCGTAACACACTA
AAAAAGCTACA
Found at i:11207826 original size:2 final size:2
Alignment explanation
Indices: 11207819--11207843 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11207809 AATTTCTAGG
11207819 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
11207844 TTTAAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11208825 original size:16 final size:16
Alignment explanation
Indices: 11208804--11208845 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
11208794 CATGGATAGG
11208804 AAGAAAAAAAA-TAAAA
1 AAGAAAAAAAACT-AAA
*
11208820 AAGAAAAAAAACTGAA
1 AAGAAAAAAAACTAAA
11208836 AAGAAAAAAA
1 AAGAAAAAAA
11208846 TCAATCCGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.05
Consensus pattern (16 bp):
AAGAAAAAAAACTAAA
Found at i:11213363 original size:3 final size:3
Alignment explanation
Indices: 11213355--11213389 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
11213345 TAGACATTGG
11213355 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11213390 TGTCAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11215523 original size:3 final size:3
Alignment explanation
Indices: 11215517--11215548 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
11215507 CAACATTTTT
*
11215517 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11215549 TTCCTTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11216610 original size:10 final size:11
Alignment explanation
Indices: 11216571--11216608 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
11216561 TTTGTTGTTT
11216571 TATAATAATAA
1 TATAATAATAA
11216582 T-TAATAATAA
1 TATAATAATAA
11216592 -ATAATAA-AA
1 TATAATAATAA
11216601 TATAATAA
1 TATAATAA
11216609 AAGTTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 2 0.08
10 22 0.88
11 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TATAATAATAA
Found at i:11220407 original size:17 final size:17
Alignment explanation
Indices: 11220351--11220407 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
11220341 ATTTATCTGC
11220351 TTTTATTTAT-TATTATTA
1 TTTTATTTATCTA--ATTA
* * *
11220369 TTATTATTTACCTATTTC
1 TT-TTATTTATCTAATTA
11220387 TTTTATTTATCTAATTA
1 TTTTATTTATCTAATTA
11220404 TTTT
1 TTTT
11220408 TTGTTATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 16 0.52
18 6 0.19
19 7 0.23
20 2 0.06
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATTTATCTAATTA
Found at i:11220427 original size:22 final size:21
Alignment explanation
Indices: 11220381--11220428 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
11220371 ATTATTTACC
*
11220381 TATTTCTTTTATTTATCTAAT
1 TATTTCTTTTATATATCTAAT
*
11220402 TATTTTTTGTTATATAT-TAAT
1 TATTTCTT-TTATATATCTAAT
11220423 ATATTT
1 -TATTT
11220429 ATCTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTTCTTTTATATATCTAAT
Found at i:11220719 original size:22 final size:22
Alignment explanation
Indices: 11220692--11220736 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11220682 GCAGTATAAG
*
11220692 ATTTTTAGAAGTT-TTTTTTTGA
1 ATTTTT-GAAGTTCTTTTTCTGA
*
11220714 ATTTTTGGAGTTCTTTTTCTGA
1 ATTTTTGAAGTTCTTTTTCTGA
11220736 A
1 A
11220737 AAATTTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.60
Consensus pattern (22 bp):
ATTTTTGAAGTTCTTTTTCTGA
Found at i:11221196 original size:9 final size:9
Alignment explanation
Indices: 11221184--11221233 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
11221174 TGGTATTTTC
11221184 TTATTTATT
1 TTATTTATT
11221193 TTATTT-TAT
1 TTATTTAT-T
11221202 TTATTTATT
1 TTATTTATT
11221211 TTACTTGT-TT
1 TTA-TT-TATT
*
11221221 TTTTTTATT
1 TTATTTATT
11221230 TTAT
1 TTAT
11221234 CAAAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
8 2 0.06
9 24 0.71
10 7 0.21
11 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (9 bp):
TTATTTATT
Found at i:11222957 original size:37 final size:38
Alignment explanation
Indices: 11222870--11222957 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 38
11222860 TAAACTATCA
* * *
11222870 AATATATAAATTATTTCAAAACAAATATAAATCTTAAT
1 AATATATAAATTACTTCAAAACAAAGATAAATATTAAT
** * *
11222908 AATATATAAATTACTTCAAAA-TGAGATAACTATTAGT
1 AATATATAAATTACTTCAAAACAAAGATAAATATTAAT
11222945 AATATATAAATTA
1 AATATATAAATTA
11222958 TAATATCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 23 0.53
38 20 0.47
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.36
Consensus pattern (38 bp):
AATATATAAATTACTTCAAAACAAAGATAAATATTAAT
Found at i:11223358 original size:59 final size:59
Alignment explanation
Indices: 11223288--11223435 Score: 174
Period size: 59 Copynumber: 2.5 Consensus size: 59
11223278 AACAAATATA
* *
11223288 TAACCAAAACCCAAACAAATTTCAACAAATATAA-AACCAATAAAAACTCAATAAATTGG
1 TAACCAAAACCCAAACAAATTTCAACAAATA-AATAACCAACAAAAACTCAACAAATTGG
* * * * ** * *
11223347 TAACTAAAACCCAAATAAATTTTAAAAAATAAATAATTAACAAAAACTTAACACATTGG
1 TAACCAAAACCCAAACAAATTTCAACAAATAAATAACCAACAAAAACTCAACAAATTGG
11223406 TAACCAAAA-CCAATACAAATTTCAACAAAT
1 TAACCAAAACCCAA-ACAAATTTCAACAAAT
11223436 TTATAACAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
58 6 0.08
59 67 0.92
ACGTcount: A:0.57, C:0.18, G:0.03, T:0.22
Consensus pattern (59 bp):
TAACCAAAACCCAAACAAATTTCAACAAATAAATAACCAACAAAAACTCAACAAATTGG
Found at i:11223606 original size:14 final size:15
Alignment explanation
Indices: 11223587--11223619 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11223577 TGCAAGGTGG
*
11223587 AGGGGA-AAAAGGGA
1 AGGGGAGAAAAGGAA
11223601 AGGGGAGAAAAGGAA
1 AGGGGAGAAAAGGAA
11223616 AGGG
1 AGGG
11223620 AATTAGGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (15 bp):
AGGGGAGAAAAGGAA
Found at i:11229313 original size:38 final size:36
Alignment explanation
Indices: 11229262--11229335 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
11229252 ATTCGAATAT
11229262 TTTTTTTAAATATATAAACATATATTATACTACATA
1 TTTTTTTAAATATATAAACATATATTATACTACATA
* * *
11229298 TTTTTTTAAATATATAAACATGTATTCTACTATATA
1 TTTTTTTAAATATATAAACATATATTATACTACATA
11229334 TT
1 TT
11229336 ATACTATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (36 bp):
TTTTTTTAAATATATAAACATATATTATACTACATA
Found at i:11241214 original size:32 final size:29
Alignment explanation
Indices: 11241173--11241237 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 29
11241163 TTAAAATTTT
11241173 TTAATATAATA-TCTAAAATATTAATTTATTAA
1 TTAATATAATACT-TAAAATA-TAA--TATTAA
11241205 TTAATATAATACTTAAAATATAATATTAA
1 TTAATATAATACTTAAAATATAATATTAA
11241234 TTAA
1 TTAA
11241238 CATATTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 10 0.31
31 3 0.09
32 18 0.56
33 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAATATAATACTTAAAATATAATATTAA
Found at i:11241226 original size:14 final size:13
Alignment explanation
Indices: 11241175--11241233 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 13
11241165 AAAATTTTTT
11241175 AATATAATATCTAA
1 AATATAATAT-TAA
11241189 AATATTAATTTATTAA
1 AATA-TAA--TATTAA
11241205 TTAATATAATACTTAA
1 --AATATAATA-TTAA
11241221 AATATAATATTAA
1 AATATAATATTAA
11241234 TTAACATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 4 0.10
14 13 0.33
15 5 0.13
16 7 0.18
17 6 0.15
18 4 0.10
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
AATATAATATTAA
Found at i:11244411 original size:19 final size:19
Alignment explanation
Indices: 11244387--11244424 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
11244377 ATCACTCGTG
11244387 AATTAA-AATTATTTTATTT
1 AATTAATAATTA-TTTATTT
*
11244406 AATTAATGATTATTTATTT
1 AATTAATAATTATTTATTT
11244425 TAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
AATTAATAATTATTTATTT
Found at i:11246246 original size:2 final size:2
Alignment explanation
Indices: 11246239--11246264 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11246229 TTTGGTTCAA
11246239 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11246265 TTACGAACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11247790 original size:26 final size:27
Alignment explanation
Indices: 11247744--11247795 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
11247734 TTAATTTTTA
11247744 TAAAATTTATATTCTATTTTT-TTATT
1 TAAAATTTATATTCTATTTTTGTTATT
11247770 TAAAATTT-TAATT-TATATTTTGTTAT
1 TAAAATTTAT-ATTCTAT-TTTTGTTAT
11247796 AATTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
25 4 0.17
26 15 0.65
27 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (27 bp):
TAAAATTTATATTCTATTTTTGTTATT
Found at i:11251294 original size:62 final size:62
Alignment explanation
Indices: 11251197--11251331 Score: 207
Period size: 62 Copynumber: 2.2 Consensus size: 62
11251187 ATACATACAC
*
11251197 GCATTTGACAGTCGAGACAAGTGATACATCCTTTGCATTTGACTTCTATTACAAAAAGACAA
1 GCATTTGACAGTAGAGACAAGTGATACATCCTTTGCATTTGACTTCTATTACAAAAAGACAA
* * * * * *
11251259 GCATTTGACAGTAGAGACAAGTGATGCATCTTTTGCGTTTGACTTCTATTGCAAAAATACAC
1 GCATTTGACAGTAGAGACAAGTGATACATCCTTTGCATTTGACTTCTATTACAAAAAGACAA
11251321 GCATTTGACAG
1 GCATTTGACAG
11251332 ACTTTTGATT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (62 bp):
GCATTTGACAGTAGAGACAAGTGATACATCCTTTGCATTTGACTTCTATTACAAAAAGACAA
Found at i:11252378 original size:24 final size:24
Alignment explanation
Indices: 11252323--11252378 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
11252313 TAAAAATTAA
11252323 AATA-TTAATATTAAAAATTTTTT
1 AATATTTAATATTAAAAATTTTTT
* *
11252346 AATACTTTAATTTTAAATATTTTTAT
1 AATA-TTTAATATTAAAAATTTTT-T
11252372 AAT-TTTA
1 AATATTTA
11252379 CTCAAGTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 4 0.14
25 16 0.57
26 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
AATATTTAATATTAAAAATTTTTT
Found at i:11257576 original size:63 final size:64
Alignment explanation
Indices: 11257456--11257593 Score: 197
Period size: 63 Copynumber: 2.2 Consensus size: 64
11257446 ATACATACAC
**
11257456 GCATTTGACAGTCCGAGACAAGTGAATACATCCTTTGCATTTGACTTCTATTACAAAAAGACAA
1 GCATTTGACAGTAAGAGACAAGTGAATACATCCTTTGCATTTGACTTCTATTACAAAAAGACAA
* * * * * *
11257520 GCATTTGACAGTAAGAGACAAGTG-ATGCATCTTTTGCGTTTGACTTCTATTGCAAAAATACAC
1 GCATTTGACAGTAAGAGACAAGTGAATACATCCTTTGCATTTGACTTCTATTACAAAAAGACAA
11257583 GCATTTGACAG
1 GCATTTGACAG
11257594 ACTTTTGATT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
63 44 0.67
64 22 0.33
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (64 bp):
GCATTTGACAGTAAGAGACAAGTGAATACATCCTTTGCATTTGACTTCTATTACAAAAAGACAA
Found at i:11258616 original size:23 final size:25
Alignment explanation
Indices: 11258590--11258641 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
11258580 AAAAAATTAA
11258590 AATA-TTAATATTAAAAATTTTT-T
1 AATACTTAATATTAAAAATTTTTAT
* *
11258613 AATACTTTAATTTTAAATATTTTTAT
1 AATAC-TTAATATTAAAAATTTTTAT
11258639 AAT
1 AAT
11258642 TTTACTCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
25 16 0.67
26 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
AATACTTAATATTAAAAATTTTTAT
Found at i:11268213 original size:2 final size:2
Alignment explanation
Indices: 11268206--11268274 Score: 52
Period size: 2 Copynumber: 34.0 Consensus size: 2
11268196 TTCAATCTTA
* * * *
11268206 AT AT AT AT AT AT AT AT AT AT AT AT -T AC AA ACT CAT A- AT AA AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT
*
11268248 AA AT CAT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT
11268275 TTTTGCATAC
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
1 2 0.04
2 49 0.89
3 3 0.05
4 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:11268999 original size:22 final size:22
Alignment explanation
Indices: 11268972--11269016 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
11268962 GTGAATCAAT
11268972 GAATGAAAGTGGAAGAAATGAA
1 GAATGAAAGTGGAAGAAATGAA
11268994 GAATGAAAGTGGAAGAAATGAA
1 GAATGAAAGTGGAAGAAATGAA
11269016 G
1 G
11269017 TTTAACTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (22 bp):
GAATGAAAGTGGAAGAAATGAA
Found at i:11269791 original size:20 final size:21
Alignment explanation
Indices: 11269766--11269820 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
11269756 AATAACAAAA
*
11269766 AATTAACACAATAAAAAT-AT
1 AATTAACAAAATAAAAATAAT
* *
11269786 AATTAAAAAAATAATAATAAT
1 AATTAACAAAATAAAAATAAT
11269807 AATATAACTAAAAT
1 AAT-TAAC-AAAAT
11269821 TCATGTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 15 0.54
21 5 0.18
22 3 0.11
23 5 0.18
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.27
Consensus pattern (21 bp):
AATTAACAAAATAAAAATAAT
Found at i:11274389 original size:14 final size:14
Alignment explanation
Indices: 11274348--11274388 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
11274338 ATATTATACG
11274348 AAATACAAAAAAAT
1 AAATACAAAAAAAT
11274362 AAATACTAAAAAAAT
1 AAATAC-AAAAAAAT
11274377 -AATACAAAAAAA
1 AAATACAAAAAAA
11274389 AAGAAGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.27
14 11 0.42
15 8 0.31
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (14 bp):
AAATACAAAAAAAT
Found at i:11274426 original size:14 final size:14
Alignment explanation
Indices: 11274352--11274428 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
11274342 TATACGAAAT
* *
11274352 ACAAAAAAATAAAT
1 ACAAAAAAAAAAAA
* * *
11274366 ACTAAAAAAATAAT
1 ACAAAAAAAAAAAA
11274380 ACAAAAAAAAAGAAGA
1 ACAAAAAAAAA-AA-A
11274396 ACAGTAGAAAAACAAAAA
1 ACA--A-AAAAA-AAAAA
11274414 ACAAAAAAAAAAAA
1 ACAAAAAAAAAAAA
11274428 A
1 A
11274429 TCGAGGATGG
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 26 0.51
15 7 0.14
16 4 0.08
18 5 0.10
19 7 0.14
20 2 0.04
ACGTcount: A:0.79, C:0.08, G:0.05, T:0.08
Consensus pattern (14 bp):
ACAAAAAAAAAAAA
Found at i:11274695 original size:14 final size:14
Alignment explanation
Indices: 11274676--11274702 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11274666 TCTGTCAAAA
11274676 ATAAAAAAAAAACT
1 ATAAAAAAAAAACT
11274690 ATAAAAAAAAAAC
1 ATAAAAAAAAAAC
11274703 AGAAACCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.11
Consensus pattern (14 bp):
ATAAAAAAAAAACT
Found at i:11274708 original size:20 final size:20
Alignment explanation
Indices: 11274672--11274713 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
11274662 AGATTCTGTC
*
11274672 AAAAATAAAAAAAAAACTAT
1 AAAAATAAAAAAAAAACCAT
*
11274692 AAAAA-AAAAACAGAAACCAT
1 AAAAATAAAAA-AAAAACCAT
11274712 AA
1 AA
11274714 TCCTCGCCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.79, C:0.10, G:0.02, T:0.10
Consensus pattern (20 bp):
AAAAATAAAAAAAAAACCAT
Found at i:11275690 original size:22 final size:21
Alignment explanation
Indices: 11275665--11275706 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11275655 CATAAAAAAA
11275665 TAAATATAAAAAATTTTTAAAT
1 TAAAT-TAAAAAATTTTTAAAT
**
11275687 TAAATTTTAAAATTTTTAAA
1 TAAATTAAAAAATTTTTAAA
11275707 ATCGAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATTAAAAAATTTTTAAAT
Found at i:11275867 original size:30 final size:29
Alignment explanation
Indices: 11275827--11275894 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
11275817 GTGTTCTAAA
*
11275827 CCCT-AAAATCAAAACCTTCTAAATCCAAC
1 CCCTAAAAATCAAAACCTT-TAAATCAAAC
* *
11275856 CCCTAAAAATCAAAATCTTTAACTCAAAC
1 CCCTAAAAATCAAAACCTTTAAATCAAAC
*
11275885 CCTTAAAAAT
1 CCCTAAAAAT
11275895 TTCAAACCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (29 bp):
CCCTAAAAATCAAAACCTTTAAATCAAAC
Found at i:11275901 original size:17 final size:15
Alignment explanation
Indices: 11275879--11275946 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
11275869 AATCTTTAAC
*
11275879 TCAAACCCTTAAAAATT
1 TCAAACCCCT-AAAA-T
11275896 TCAAACCCCTAAAAT
1 TCAAACCCCTAAAAT
11275911 TCAAA-CCC-AAAAT
1 TCAAACCCCTAAAAT
* *
11275924 CCAAAATCCCTAAAAT
1 TC-AAACCCCTAAAAT
*
11275940 CCAAACC
1 TCAAACC
11275947 TTAAACAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
13 6 0.13
14 6 0.13
15 13 0.29
16 11 0.24
17 9 0.20
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (15 bp):
TCAAACCCCTAAAAT
Found at i:11276253 original size:14 final size:14
Alignment explanation
Indices: 11276218--11276257 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
11276208 TAATTCGCAT
*
11276218 TAATAATAAGATTA
1 TAATAATAAAATTA
*
11276232 -ATTAATAAAATTA
1 TAATAATAAAATTA
11276245 TAATAATAAAATT
1 TAATAATAAAATT
11276258 GGGATCTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TAATAATAAAATTA
Found at i:11280040 original size:254 final size:254
Alignment explanation
Indices: 11279558--11280047 Score: 759
Period size: 255 Copynumber: 1.9 Consensus size: 254
11279548 CCAAGTCTCT
* *
11279558 AACCTTTCTCTTGAACTGATCTTCATCTAAACAATTTCCATTCTTAACTTTCTGCTCAAACTCAT
1 AACCTTTCTCCTGAACTGATCTTCATCTAAACAATTTCCATTCTTAACTTTCTGCTCAAACTCAG
* * * * *
11279623 TTGCTCACTCATTCCAAAAACCTTTTCCCCTGCTTCCCACCTTGCTGCTTTTGCCTTTTTCTAAG
66 TTGCTCACTCATTCCAAAAACCCTTTCCCCTACTTCCCACATTGCTGCTTTTGCCTTTTTCCAAC
* * * * *
11279688 CTGGTTTTAGTCCCCTTGTTTTGTTTTTCCCCTTTGTTTTTCTCTGGTTTCCTCATTCATAGCTA
131 CTAGTTGTAGTCCCCTTGTTCTGTTTTTCCCCTTTGTTTATCTCTGGTTCCCTCATTCATAGCTA
* *
11279753 CTGGATATGAAGAAGAGTCTGTCCAAGCCATTTCTTGTCTTCTCTATACCCAAAGCTTC
196 CTGGATAGGAAGAAGAGTCTGTCCAAACCATTTCTTGTCTTCTCTATACCCAAAGCTTC
*
11279812 AACCTTTCTCCTGAACTGATCTTTC-TCTAAAACAATTTCCTTTCTTAACTTTCTGCTCAAACTC
1 AACCTTTCTCCTGAACTGATC-TTCATCT-AAACAATTTCCATTCTTAACTTTCTGCTCAAACTC
* *
11279876 AGTTGCTCATTCATTCGAAAAACCCTTTCCCCTACTTCCCACATTGCTGCTTTTGCCTTTTTCCA
64 AGTTGCTCACTCATTCCAAAAACCCTTTCCCCTACTTCCCACATTGCTGCTTTTGCCTTTTTCCA
*
11279941 ACCTAGTTGTAGTCCCCTTGTTCTG-TTTTCCTCTTTGTTTATCTCTGGTTCCCTCATTCATAGC
129 ACCTAGTTGTAGTCCCCTTGTTCTGTTTTTCCCCTTTGTTTATCTCTGGTTCCCTCATTCATAGC
* * *
11280005 TGCTGGATCGGAAGACGAGTCTGTCCAAACCATTTCTTGTCTT
194 TACTGGATAGGAAGAAGAGTCTGTCCAAACCATTTCTTGTCTT
11280048 TACCCATAAC
Statistics
Matches: 213, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
254 97 0.46
255 116 0.54
ACGTcount: A:0.19, C:0.29, G:0.11, T:0.41
Consensus pattern (254 bp):
AACCTTTCTCCTGAACTGATCTTCATCTAAACAATTTCCATTCTTAACTTTCTGCTCAAACTCAG
TTGCTCACTCATTCCAAAAACCCTTTCCCCTACTTCCCACATTGCTGCTTTTGCCTTTTTCCAAC
CTAGTTGTAGTCCCCTTGTTCTGTTTTTCCCCTTTGTTTATCTCTGGTTCCCTCATTCATAGCTA
CTGGATAGGAAGAAGAGTCTGTCCAAACCATTTCTTGTCTTCTCTATACCCAAAGCTTC
Found at i:11287036 original size:9 final size:9
Alignment explanation
Indices: 11287024--11287062 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
11287014 TTTTTTTTTG
11287024 TTTTGAAAA
1 TTTTGAAAA
11287033 TTTTG-AAA
1 TTTTGAAAA
* *
11287041 TTTTCAATA
1 TTTTGAAAA
11287050 TTTTGAAAA
1 TTTTGAAAA
11287059 TTTT
1 TTTT
11287063 CAATAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.54
Consensus pattern (9 bp):
TTTTGAAAA
Found at i:11287036 original size:26 final size:26
Alignment explanation
Indices: 11287000--11287066 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
11286990 AAATAAATCA
*** *
11287000 TTGAAAATTTTCAATTTTTTTTTGTT
1 TTGAAAATTTTCAATTTTTCAATATT
* *
11287026 TTGAAAATTTTGAAATTTTCAATATT
1 TTGAAAATTTTCAATTTTTCAATATT
11287052 TTGAAAATTTTCAAT
1 TTGAAAATTTTCAAT
11287067 AAATTATCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.55
Consensus pattern (26 bp):
TTGAAAATTTTCAATTTTTCAATATT
Found at i:11287044 original size:17 final size:18
Alignment explanation
Indices: 11287024--11287065 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
11287014 TTTTTTTTTG
*
11287024 TTTTGAAAATTTTG-AAA
1 TTTTCAAAATTTTGAAAA
*
11287041 TTTTCAATATTTTGAAAA
1 TTTTCAAAATTTTGAAAA
11287059 TTTTCAA
1 TTTTCAA
11287066 TAAATTATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (18 bp):
TTTTCAAAATTTTGAAAA
Found at i:11287061 original size:18 final size:17
Alignment explanation
Indices: 11287032--11287067 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
11287022 TGTTTTGAAA
11287032 ATTTTGAAATTTTCAAT
1 ATTTTGAAATTTTCAAT
11287049 ATTTTGAAAATTTTCAAT
1 ATTTTG-AAATTTTCAAT
11287067 A
1 A
11287068 AATTATCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTTGAAATTTTCAAT
Found at i:11302999 original size:25 final size:25
Alignment explanation
Indices: 11302956--11303016 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
11302946 TGTAATTTGT
*
11302956 TAATAAAATATAGTATTTGCAT-ATA
1 TAATTAAATATAGTATTTG-ATGATA
* *
11302981 TAATTTAATATAG-ATTTTGATGGTA
1 TAATTAAATATAGTA-TTTGATGATA
11303006 TAATTAAATAT
1 TAATTAAATAT
11303017 TTTTATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 3 0.10
25 27 0.90
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (25 bp):
TAATTAAATATAGTATTTGATGATA
Found at i:11308522 original size:15 final size:14
Alignment explanation
Indices: 11308482--11308524 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
11308472 ATAAGTTCTT
11308482 TTTTATTTTTTTAAA
1 TTTTA-TTTTTTAAA
**
11308497 TTTTGGTTTTTAAA
1 TTTTATTTTTTAAA
11308511 TTTTATTCTTTTAA
1 TTTTATT-TTTTAA
11308525 TTAAGTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (14 bp):
TTTTATTTTTTAAA
Found at i:11311092 original size:3 final size:3
Alignment explanation
Indices: 11311084--11311110 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11311074 CACCATTTTG
11311084 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
11311111 ATTTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11311137 original size:17 final size:16
Alignment explanation
Indices: 11311112--11311155 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
11311102 TATTATTATA
11311112 TTTTTTCTTTTTTCTT
1 TTTTTTCTTTTTTCTT
*
11311128 TTTCTTTCTTTCTTCTT
1 TTT-TTTCTTTTTTCTT
11311145 TTTTTT-TTTTT
1 TTTTTTCTTTTT
11311156 CAGTTTAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 6 0.24
17 15 0.60
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTCTTTTTTCTT
Found at i:11311155 original size:7 final size:7
Alignment explanation
Indices: 11311112--11311152 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
11311102 TATTATTATA
11311112 TTTTTTC
1 TTTTTTC
11311119 TTTTTTC
1 TTTTTTC
11311126 -TTTTTC
1 TTTTTTC
11311132 TTTCTTTC
1 TTT-TTTC
11311140 TTCTTTT-
1 TT-TTTTC
11311147 TTTTTT
1 TTTTTT
11311153 TTTCAGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 10 0.32
7 11 0.35
8 9 0.29
9 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:11312313 original size:20 final size:21
Alignment explanation
Indices: 11312271--11312313 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
11312261 AAAAGGTTGT
*
11312271 AATTAAATAAAAACAATACAA
1 AATTAAATAAAAACAATAAAA
11312292 AATT-AATAAAAA-ATATAAAA
1 AATTAAATAAAAACA-ATAAAA
11312312 AA
1 AA
11312314 AATTATCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 15 0.75
21 4 0.20
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (21 bp):
AATTAAATAAAAACAATAAAA
Found at i:11314561 original size:24 final size:25
Alignment explanation
Indices: 11314513--11314573 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 25
11314503 TGTCCTATTT
* *
11314513 TTTTTTA-ATA-TCTAAAATTTTTA
1 TTTTTTATATATTTTAAAATTTATA
11314536 TTTTTTATATATTTTAAAA-TTATA
1 TTTTTTATATATTTTAAAATTTATA
*
11314560 --TTATATATATTTTA
1 TTTTTTATATATTTTA
11314574 TTTTTTAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 13 0.39
23 7 0.21
24 7 0.21
25 6 0.18
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTTTATATATTTTAAAATTTATA
Found at i:11315440 original size:13 final size:13
Alignment explanation
Indices: 11315422--11315446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11315412 AAAAGCTATC
11315422 AAGTAATAATATT
1 AAGTAATAATATT
11315435 AAGTAATAATAT
1 AAGTAATAATAT
11315447 AAAATATTAT
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAGTAATAATATT
Found at i:11315454 original size:20 final size:20
Alignment explanation
Indices: 11315429--11315486 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
11315419 ATCAAGTAAT
*
11315429 AATATTAAGTAATAATATAA
1 AATATTAAGCAATAATATAA
* *
11315449 AATATTATGCAATGATATAA
1 AATATTAAGCAATAATATAA
* *
11315469 AATATCAACCAATAATAT
1 AATATTAAGCAATAATAT
11315487 CATGCAAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (20 bp):
AATATTAAGCAATAATATAA
Found at i:11315509 original size:19 final size:19
Alignment explanation
Indices: 11315485--11315548 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
11315475 AACCAATAAT
11315485 ATCATGCAAATAATAATTA
1 ATCATGCAAATAATAATTA
* *
11315504 ATCATGGAAATAA-AATCAA
1 ATCATGCAAATAATAAT-TA
* *
11315523 AACATGCAAAAAATAATTA
1 ATCATGCAAATAATAATTA
11315542 ATCATGC
1 ATCATGC
11315549 CGTTGAATAG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
18 3 0.08
19 30 0.83
20 3 0.08
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (19 bp):
ATCATGCAAATAATAATTA
Found at i:11315607 original size:24 final size:24
Alignment explanation
Indices: 11315554--11315681 Score: 96
Period size: 24 Copynumber: 5.2 Consensus size: 24
11315544 CATGCCGTTG
* * *
11315554 AATAGATTAATAACCATGTAAATA
1 AATATATTAATAATCATGCAAATA
*
11315578 AATATATTAATAATCATGCAACTA
1 AATATATTAATAATCATGCAAATA
* * * * *
11315602 ATTATATTAATCATTATACAATTA
1 AATATATTAATAATCATGCAAATA
* **
11315626 ATTAATGATT-ATGCAATCAAACAAATA
1 AAT-AT-ATTAAT--AATCATGCAAATA
*
11315653 AATATATTAATAATCATGTAAATA
1 AATATATTAATAATCATGCAAATA
11315677 AATAT
1 AATAT
11315682 TAATCGTGCA
Statistics
Matches: 82, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
24 57 0.70
25 7 0.09
26 7 0.09
27 11 0.13
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.35
Consensus pattern (24 bp):
AATATATTAATAATCATGCAAATA
Found at i:11315631 original size:19 final size:20
Alignment explanation
Indices: 11315601--11315642 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
11315591 TCATGCAACT
11315601 AATTATATTAATCATTATAC
1 AATTATATTAATCATTATAC
* *
11315621 AATTA-ATTAATGATTATGC
1 AATTATATTAATCATTATAC
11315640 AAT
1 AAT
11315643 CAAACAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (20 bp):
AATTATATTAATCATTATAC
Found at i:11315895 original size:7 final size:7
Alignment explanation
Indices: 11315860--11315926 Score: 59
Period size: 7 Copynumber: 9.6 Consensus size: 7
11315850 AAAAAGTAAA
11315860 AAAAAAT
1 AAAAAAT
*
11315867 AAACAAAGA
1 AAA-AAA-T
11315876 AAAAAATT
1 AAAAAA-T
*
11315884 TAAAAAT
1 AAAAAAT
11315891 AAAAAAT
1 AAAAAAT
11315898 AAAAAAT
1 AAAAAAT
11315905 --AAAAT
1 AAAAAAT
*
11315910 -CAAAAT
1 AAAAAAT
11315916 AAAAAAT
1 AAAAAAT
11315923 AAAA
1 AAAA
11315927 TGAAAAATAG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 5 0.10
6 5 0.10
7 26 0.52
8 11 0.22
9 3 0.06
ACGTcount: A:0.81, C:0.03, G:0.01, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:11315914 original size:18 final size:18
Alignment explanation
Indices: 11315893--11315932 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
11315883 TTAAAAATAA
11315893 AAAATAAAAAATAAAATC
1 AAAATAAAAAATAAAATC
*
11315911 AAAATAAAAAATAAAATG
1 AAAATAAAAAATAAAATC
11315929 AAAA
1 AAAA
11315933 ATAGAAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAATAAAAAATAAAATC
Found at i:11316085 original size:2 final size:2
Alignment explanation
Indices: 11316078--11316132 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
11316068 ATAAGCATTT
11316078 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
11316120 TC TT TC TT TC TC T
1 TC TC TC TC TC TC T
11316133 AGGTTTGATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:11316977 original size:12 final size:12
Alignment explanation
Indices: 11316960--11316986 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11316950 TTAAACAAAA
11316960 AAAATCTAAATT
1 AAAATCTAAATT
11316972 AAAATCTAAATT
1 AAAATCTAAATT
11316984 AAA
1 AAA
11316987 TCAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATCTAAATT
Found at i:11316992 original size:17 final size:18
Alignment explanation
Indices: 11316961--11316994 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11316951 TAAACAAAAA
*
11316961 AAATCTAAATTAAAATCT
1 AAATCTAAATCAAAATCT
11316979 AAAT-TAAATCAAAATC
1 AAATCTAAATCAAAATC
11316995 AACACCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATCTAAATCAAAATCT
Found at i:11320540 original size:12 final size:12
Alignment explanation
Indices: 11320523--11320548 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11320513 ACCATAAGTG
11320523 ATGAGTCACTAT
1 ATGAGTCACTAT
11320535 ATGAGTCACTAT
1 ATGAGTCACTAT
11320547 AT
1 AT
11320549 CATAATGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGAGTCACTAT
Found at i:11320553 original size:34 final size:35
Alignment explanation
Indices: 11320488--11320553 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
11320478 GTTTTTTAGT
*
11320488 ATGAGTCATAGTGATGAGTCACCGTACCATAAGTG
1 ATGAGTCATAGTGATGAGTCACCATACCATAAGTG
* *
11320523 ATGAGTCACTA-T-ATGAGTCACTATATCATAA
1 ATGAGTCA-TAGTGATGAGTCACCATACCATAA
11320554 TGAACCTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 16 0.59
35 9 0.33
36 2 0.07
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (35 bp):
ATGAGTCATAGTGATGAGTCACCATACCATAAGTG
Found at i:11320604 original size:21 final size:21
Alignment explanation
Indices: 11320561--11320616 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
11320551 TAATGAACCT
* *
11320561 TTGTACCATAAGTCATGAGTCA
1 TTGTACC-TTAGTCATGACTCA
*
11320583 TTGTACCTTAGTTATGACTCA
1 TTGTACCTTAGTCATGACTCA
11320604 TTGT-CCTTTAGTC
1 TTGTACC-TTAGTC
11320617 TTATCCTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (21 bp):
TTGTACCTTAGTCATGACTCA
Found at i:11325778 original size:15 final size:14
Alignment explanation
Indices: 11325757--11325784 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11325747 ATATTAAATA
11325757 AAATTTTTAATATT
1 AAATTTTTAATATT
11325771 AAATTTTTAATATT
1 AAATTTTTAATATT
11325785 TATATGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AAATTTTTAATATT
Found at i:11329658 original size:15 final size:15
Alignment explanation
Indices: 11329638--11329670 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11329628 TGACCGTAGC
11329638 TAACGATTTGAATGA
1 TAACGATTTGAATGA
*
11329653 TAACGATTTGATTGA
1 TAACGATTTGAATGA
11329668 TAA
1 TAA
11329671 TGATGATTTA
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:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (15 bp):
TAACGATTTGAATGA
Found at i:11329686 original size:16 final size:16
Alignment explanation
Indices: 11329665--11329696 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11329655 ACGATTTGAT
11329665 TGATAATGATGATTTA
1 TGATAATGATGATTTA
*
11329681 TGATAATGGTGATTTA
1 TGATAATGATGATTTA
11329697 CGATGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (16 bp):
TGATAATGATGATTTA
Found at i:11331608 original size:28 final size:29
Alignment explanation
Indices: 11331568--11331650 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 29
11331558 TTTTGGTTAA
11331568 AAATGATTGTTTGAAATCTTACAAGTG-C
1 AAATGATTGTTTGAAATCTTACAAGTGAC
*
11331596 AAATGATTGTTTG-AATTTTACAAG-GAC
1 AAATGATTGTTTGAAATCTTACAAGTGAC
* * *
11331623 AAAAGATTGGTCGAAATCTTACAAGTGA
1 AAATGATTGTTTGAAATCTTACAAGTGA
11331651 TGATTTTGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.02
27 21 0.45
28 23 0.49
29 2 0.04
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (29 bp):
AAATGATTGTTTGAAATCTTACAAGTGAC
Found at i:11334346 original size:15 final size:15
Alignment explanation
Indices: 11334326--11334358 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11334316 TGACCGTAGC
11334326 TAACGATTTGAATGA
1 TAACGATTTGAATGA
*
11334341 TAACGATTTGATTGA
1 TAACGATTTGAATGA
11334356 TAA
1 TAA
11334359 TGATGATTTA
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:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (15 bp):
TAACGATTTGAATGA
Found at i:11334374 original size:16 final size:16
Alignment explanation
Indices: 11334353--11334384 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11334343 ACGATTTGAT
11334353 TGATAATGATGATTTA
1 TGATAATGATGATTTA
*
11334369 TGATAATGGTGATTTA
1 TGATAATGATGATTTA
11334385 CGATGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (16 bp):
TGATAATGATGATTTA
Found at i:11342141 original size:16 final size:16
Alignment explanation
Indices: 11342122--11342183 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
11342112 TTTATTTGTG
*
11342122 TGATTTATTATTTATA
1 TGATTTATTAATTATA
*
11342138 TGATTATTAATATAATTACA
1 TGA-T-TT-AT-TAATTATA
11342158 TGATTTATTAATTATA
1 TGATTTATTAATTATA
*
11342174 TGATTAATTA
1 TGATTTATTA
11342184 TATATTTGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 19 0.50
17 3 0.08
18 4 0.11
19 3 0.08
20 9 0.24
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (16 bp):
TGATTTATTAATTATA
Found at i:11342145 original size:12 final size:12
Alignment explanation
Indices: 11342128--11342186 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
11342118 TGTGTGATTT
*
11342128 ATTATTTATATG
1 ATTAATTATATG
*
11342140 ATT-ATTAATATA
1 ATTAATT-ATATG
* *
11342152 ATTACATGAT-TT
1 ATTA-ATTATATG
11342164 ATTAATTATATG
1 ATTAATTATATG
11342176 ATTAATTATAT
1 ATTAATTATAT
11342187 ATTTGCATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
11 6 0.16
12 27 0.73
13 2 0.05
14 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (12 bp):
ATTAATTATATG
Found at i:11342162 original size:20 final size:20
Alignment explanation
Indices: 11342137--11342335 Score: 145
Period size: 20 Copynumber: 10.4 Consensus size: 20
11342127 TATTATTTAT
* *
11342137 ATGATTATTAATATAATTAC
1 ATGATTATTAATATATTTGC
11342157 ATGATTTATTAAT-TA--T--
1 ATGA-TTATTAATATATTTGC
11342173 ATGATTAATT-ATATATTTGC
1 ATGATT-ATTAATATATTTGC
* *
11342193 ATGATTATTTAT-TAATTGC
1 ATGATTATTAATATATTTGC
* **
11342212 ATGATTAATAATATATTTAT
1 ATGATTATTAATATATTTGC
* *
11342232 ATGATTATTTAT-TAATTGC
1 ATGATTATTAATATATTTGC
* * *
11342251 AAGATTAATACTATATTTGC
1 ATGATTATTAATATATTTGC
*
11342271 ATGATTATTGAT-TATTTGC
1 ATGATTATTAATATATTTGC
* *
11342290 TTGATTTTTAATATATTTGC
1 ATGATTATTAATATATTTGC
11342310 ATG---ATTAA-ATATTTGC
1 ATGATTATTAATATATTTGC
11342326 ATGATATATT
1 ATGAT-TATT
11342336 TACATGTTTT
Statistics
Matches: 139, Mismatches: 25, Indels: 30
0.72 0.13 0.15
Matches are distributed among these distances:
15 4 0.03
16 20 0.14
17 4 0.03
18 2 0.01
19 47 0.34
20 54 0.39
21 8 0.06
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (20 bp):
ATGATTATTAATATATTTGC
Found at i:11342164 original size:36 final size:36
Alignment explanation
Indices: 11342122--11342245 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 36
11342112 TTTATTTGTG
*
11342122 TGATTTATTATTTATATGATT-ATTAATATAATTACA
1 TGATTTATTAATTATATGATTAATT-ATATAATTACA
* *
11342158 TGATTTATTAATTATATGATTAATTATATATTTGCA
1 TGATTTATTAATTATATGATTAATTATATAATTACA
** * * *
11342194 TGATTATTTATTAATTGCATGATTAATAATATATTTATA
1 TG---ATTTATTAATTATATGATTAATTATATAATTACA
*
11342233 TGA-TTATTTATTA
1 TGATTTATTAATTA
11342246 ATTGCAAGAT
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
35 8 0.11
36 32 0.43
37 3 0.04
39 31 0.42
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (36 bp):
TGATTTATTAATTATATGATTAATTATATAATTACA
Found at i:11342216 original size:39 final size:39
Alignment explanation
Indices: 11342160--11342316 Score: 192
Period size: 39 Copynumber: 4.0 Consensus size: 39
11342150 TAATTACATG
**
11342160 ATTTATTAATTATATGATTAATTATATATTTGCATGATT
1 ATTTATTAATTGCATGATTAATTATATATTTGCATGATT
* **
11342199 ATTTATTAATTGCATGATTAATAATATATTTATATGATT
1 ATTTATTAATTGCATGATTAATTATATATTTGCATGATT
*
11342238 ATTTATTAATTGCAAGATTAA-TACTATATTTGCATGATT
1 ATTTATTAATTGCATGATTAATTA-TATATTTGCATGATT
* * * *
11342277 ATTGATTATTTGCTTGATT-TTTAATATATTTGCATGATT
1 ATTTATTAATTGCATGATTAATT-ATATATTTGCATGATT
11342316 A
1 A
11342317 AATATTTGCA
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 99 0.98
40 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.10, T:0.52
Consensus pattern (39 bp):
ATTTATTAATTGCATGATTAATTATATATTTGCATGATT
Found at i:11342271 original size:78 final size:78
Alignment explanation
Indices: 11342137--11342316 Score: 215
Period size: 78 Copynumber: 2.3 Consensus size: 78
11342127 TATTATTTAT
* * * *
11342137 ATGATTATTAATATAATTACATG---ATTTATTAATTATATGATTAATTATATATTTGCATGATT
1 ATGATTAATAATATATTTACATGATTATTTATTAATTACAAGATTAATTATATATTTGCATGATT
*
11342199 ATTTATTAATTGC
66 ATTGATTAATTGC
* *
11342212 ATGATTAATAATATATTTATATGATTATTTATTAATTGCAAGATTAA-TACTATATTTGCATGAT
1 ATGATTAATAATATATTTACATGATTATTTATTAATTACAAGATTAATTA-TATATTTGCATGAT
*
11342276 TATTGATTATTTGC
65 TATTGATTAATTGC
* ** *
11342290 TTGATTTTTAATATATTTGCATGATTA
1 ATGATTAATAATATATTTACATGATTA
11342317 AATATTTGCA
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
75 20 0.23
77 2 0.02
78 66 0.75
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (78 bp):
ATGATTAATAATATATTTACATGATTATTTATTAATTACAAGATTAATTATATATTTGCATGATT
ATTGATTAATTGC
Found at i:11343697 original size:10 final size:10
Alignment explanation
Indices: 11343682--11343707 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11343672 AAAATTATTC
11343682 TTTTAATAAA
1 TTTTAATAAA
11343692 TTTTAATAAA
1 TTTTAATAAA
11343702 TTTTAA
1 TTTTAA
11343708 GATTTCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:11345584 original size:10 final size:11
Alignment explanation
Indices: 11345559--11345586 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
11345549 AAGTTGCCAT
11345559 TTTTTTATTGA
1 TTTTTTATTGA
11345570 TTTTTTATTGA
1 TTTTTTATTGA
11345581 TTTTTT
1 TTTTTT
11345587 GTCTCAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTATTGA
Found at i:11346384 original size:12 final size:13
Alignment explanation
Indices: 11346359--11346435 Score: 71
Period size: 12 Copynumber: 6.4 Consensus size: 13
11346349 CTTATATATA
11346359 AATTATT-T-TTT
1 AATTATTATATTT
11346370 AATTATT-TATTT
1 AATTATTATATTT
11346382 AATT-TTATATTT
1 AATTATTATATTT
*
11346394 ATTTATATATATTT
1 AATTAT-TATATTT
11346408 -A-TA-TATATTT
1 AATTATTATATTT
11346418 AATT-TTATATTT
1 AATTATTATATTT
11346430 ATATTA
1 A-ATTA
11346436 AAAAATAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
10 7 0.13
11 11 0.20
12 26 0.47
13 4 0.07
14 7 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
AATTATTATATTT
Found at i:11346395 original size:20 final size:20
Alignment explanation
Indices: 11346372--11346431 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
11346362 TATTTTTTAA
11346372 TTATTTATTTAATTTTATAT
1 TTATTTATTTAATTTTATAT
*
11346392 TTATTTATAT-ATATTTATA-
1 TTATTTATTTAAT-TTTATAT
11346411 -TA--TATTTAATTTTATAT
1 TTATTTATTTAATTTTATAT
11346428 TTAT
1 TTAT
11346432 ATTAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
16 10 0.30
17 2 0.06
18 4 0.12
19 2 0.06
20 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATTTAATTTTATAT
Found at i:11346398 original size:10 final size:10
Alignment explanation
Indices: 11346372--11346434 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
11346362 TATTTTTTAA
11346372 TTATTTAT-T
1 TTATTTATAT
*
11346381 TAATTTTATAT
1 TTA-TTTATAT
11346392 TTATTTATAT
1 TTATTTATAT
*
11346402 ATATTTATAT
1 TTATTTATAT
* *
11346412 ATATTTAATTT
1 TTATTT-ATAT
11346423 TATATTTATAT
1 T-TATTTATAT
11346434 T
1 T
11346435 AAAAAATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
9 2 0.05
10 27 0.61
11 10 0.23
12 5 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATTTATAT
Found at i:11347390 original size:62 final size:62
Alignment explanation
Indices: 11347291--11347429 Score: 197
Period size: 62 Copynumber: 2.2 Consensus size: 62
11347281 TTGCATAAAT
* * * *
11347291 ACACGCATTTGACAGTAAAGACAAGTGATGCATCTTTTCCACTTGACTTCTATTCCAAAGAG
1 ACACGCATTTGACAGTAAAGACAAGTGATGCAGCTTTTCCACTTGACTTCTATTACAAAAAC
* * * **
11347353 ACACGCAATTGACAGTAGAGACAAGTGATGCAGCTTTTGCGTTTGACTTCTATTACAAAAAC
1 ACACGCATTTGACAGTAAAGACAAGTGATGCAGCTTTTCCACTTGACTTCTATTACAAAAAC
11347415 ACACGCATTTGACAG
1 ACACGCATTTGACAG
11347430 ACTTTTGATA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (62 bp):
ACACGCATTTGACAGTAAAGACAAGTGATGCAGCTTTTCCACTTGACTTCTATTACAAAAAC
Found at i:11348507 original size:194 final size:196
Alignment explanation
Indices: 11348168--11348543 Score: 702
Period size: 194 Copynumber: 1.9 Consensus size: 196
11348158 TTATTCATTA
*
11348168 AAAAAAAGAATTATTCTTGAGAAAAATAAATCAAAACCTTTTTATTGAAATAATTCTTAAAATGT
1 AAAAAAAGAATTATTCTCGAGAAAAATAAATCAAAACCTTTTTATTGAAATAATTCTTAAAATGT
*
11348233 TCTAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTACT
66 TCCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTACT
11348298 CGGAATACTTTTAGAATCTCATCTTTGG-AGGCTCGAATTTATTTTTCGTAAAAAAATATCATGT
131 CGGAATACTTTTAGAATCTCATCTTTGGAAGGCTCGAATTTATTTTTCGTAAAAAAATATCATGT
11348362 T
196 T
* *
11348363 AAAAAAA-ATTTATTCTCGAGAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAATGT
1 AAAAAAAGAATTATTCTCGAGAAAAATAAATCAAAACCTTTTTATTGAAATAATTCTTAAAATGT
11348427 TCCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTACT
66 TCCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTACT
11348492 CGGAATACTTTTAGAATCTCATCTTTGGAAGGCTCGAATTTATTTTTCGTAA
131 CGGAATACTTTTAGAATCTCATCTTTGGAAGGCTCGAATTTATTTTTCGTAA
11348544 GAAATTATGT
Statistics
Matches: 176, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
194 146 0.83
195 30 0.17
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (196 bp):
AAAAAAAGAATTATTCTCGAGAAAAATAAATCAAAACCTTTTTATTGAAATAATTCTTAAAATGT
TCCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTACT
CGGAATACTTTTAGAATCTCATCTTTGGAAGGCTCGAATTTATTTTTCGTAAAAAAATATCATGT
T
Found at i:11348835 original size:18 final size:17
Alignment explanation
Indices: 11348812--11348858 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
11348802 TATTCTCATT
11348812 TTTATTATTTATTTTTAA
1 TTTATTATTTATTTTT-A
**
11348830 TTTATTAACCTATTTTTA
1 TTTATT-ATTTATTTTTA
11348848 TTTATTATTTA
1 TTTATTATTTA
11348859 AAAAAAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 3 0.12
18 13 0.54
19 8 0.33
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTATTTATTTTTA
Found at i:11349054 original size:208 final size:207
Alignment explanation
Indices: 11348655--11349062 Score: 486
Period size: 208 Copynumber: 2.0 Consensus size: 207
11348645 AATTTTGAAG
* * * * *
11348655 AAAAAGAAATTTAATTATATTGAAGATTTTCTATAAATATTCCAATACGCTGGTAATATTTTACA
1 AAAAAGAAATTTAATTATATTGAAAATTTTCTATAAATACTCAAATACACTGGTAATATTTTAAA
* * * * * *
11348720 AAAAATCTTCTCACCTAGAGATTTCTTAAAGCATCTCTACTCGGAATACTTTTAGAATCCCATCA
66 AAAAATCTTATCACCTAAAGATTTCGTAAAGCATCACTACTCGAAATACCTTTAGAATCCCATCA
* * * * *
11348785 TTGGATTAAATTTCTTTTATTCTCATTTTTATTATTTATTTTTAATTTATTAACCTATTTTTAT-
131 TTGGATAAAATTTCATTTATCCTCATTTTTATTATTTAGTATTAATTTATTAACCTATTTTTATA
11348849 TTATTATTTAAA
196 TTATTATTTAAA
* * * *
11348861 AAAAAGAAAATCTTTATTGTATTGAAAATTTTTTATAAATACTCAAATACACTGGTAGTATTTTA
1 AAAAAG-AAAT-TTAATTATATTGAAAATTTTCTATAAATACTCAAATACACTGGTAATATTTTA
* *
11348926 AAAAAAATCTTATCACCTAAAGATTTCGT-AGGCATCACTACTCGAAATACCTTT-GAATCTCAT
64 AAAAAAATCTTATCACCTAAAGATTTCGTAAAGCATCACTACTCGAAATACCTTTAGAATCCCAT
* **
11348989 CGTTGGATAAAAATTTCATTT-TCCTACATTTTTTATTACTTTAGTATT-A-TTATTAAGTTTAT
129 CATTGGAT-AAAATTTCATTTATCCT-CA-TTTTTATTA-TTTAGTATTAATTTATTAA-CCTAT
11349051 TTTTATATTATT
189 TTTTATATTATT
11349063 GTTTTTTAAA
Statistics
Matches: 169, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
206 24 0.14
207 44 0.26
208 89 0.53
209 12 0.07
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (207 bp):
AAAAAGAAATTTAATTATATTGAAAATTTTCTATAAATACTCAAATACACTGGTAATATTTTAAA
AAAAATCTTATCACCTAAAGATTTCGTAAAGCATCACTACTCGAAATACCTTTAGAATCCCATCA
TTGGATAAAATTTCATTTATCCTCATTTTTATTATTTAGTATTAATTTATTAACCTATTTTTATA
TTATTATTTAAA
Found at i:11349188 original size:14 final size:14
Alignment explanation
Indices: 11349162--11349201 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
11349152 AATATGCATA
11349162 AATAT-TAATAAAAT
1 AATATATAA-AAAAT
11349176 AATATATAAAAAAT
1 AATATATAAAAAAT
11349190 AA-ATA-AAAAAAT
1 AATATATAAAAAAT
11349202 TTTTTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.28
13 3 0.12
14 12 0.48
15 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AATATATAAAAAAT
Found at i:11349254 original size:13 final size:13
Alignment explanation
Indices: 11349236--11349267 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
11349226 TCAACGTACT
*
11349236 GTTCGGTTCGGCG
1 GTTCGGTCCGGCG
11349249 GTTCGGTCCGGCG
1 GTTCGGTCCGGCG
11349262 GTTCGG
1 GTTCGG
11349268 CTTGGTCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.25, G:0.47, T:0.28
Consensus pattern (13 bp):
GTTCGGTCCGGCG
Found at i:11350270 original size:20 final size:19
Alignment explanation
Indices: 11350245--11350307 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
11350235 TTTTTTTTTG
11350245 TATTTTTATTATGTATTTCA
1 TATTTTT-TTATGTATTTCA
* *
11350265 TA-TTTTTT-TGTAGTTCG
1 TATTTTTTTATGTATTTCA
11350282 TATTTTTTTATTGTATTTCA
1 TATTTTTTTA-TGTATTTCA
11350302 TATTTT
1 TATTTT
11350308 ATACTTATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 9 0.25
18 8 0.22
19 4 0.11
20 15 0.42
ACGTcount: A:0.19, C:0.05, G:0.08, T:0.68
Consensus pattern (19 bp):
TATTTTTTTATGTATTTCA
Found at i:11350307 original size:17 final size:17
Alignment explanation
Indices: 11350256--11350309 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
11350246 ATTTTTATTA
*
11350256 TGTATTTCATATTTTTT
1 TGTATTTCATATTTTAT
* *
11350273 TGTAGTTCGTATTTTTTTAT
1 TGTATTTC--A-TATTTTAT
11350293 TGTATTTCATATTTTAT
1 TGTATTTCATATTTTAT
11350310 ACTTATACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 14 0.48
18 1 0.03
19 1 0.03
20 13 0.45
ACGTcount: A:0.19, C:0.06, G:0.09, T:0.67
Consensus pattern (17 bp):
TGTATTTCATATTTTAT
Found at i:11350568 original size:49 final size:49
Alignment explanation
Indices: 11350504--11350617 Score: 185
Period size: 49 Copynumber: 2.3 Consensus size: 49
11350494 TTAAAATCTG
*
11350504 AAAGAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGGA
1 AAAG-GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGGA
* *
11350554 AAAGGCTTCTCTCAGCAGAGGCTCGACAACTTTAAAATCTCATCTTGGA
1 AAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGGA
11350603 AAA-GCTCCTCTCAGC
1 AAAGGCTCCTCTCAGC
11350618 TGTAGACACC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 11 0.18
49 45 0.75
50 4 0.07
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (49 bp):
AAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGGA
Found at i:11351490 original size:20 final size:20
Alignment explanation
Indices: 11351447--11351491 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11351437 CCGACCAACT
*
11351447 TCCGGCGAAAAAACCCAGAT
1 TCCGGCGAAAAAACCCAGAA
***
11351467 TCCGGCGAAAATTTCCAGAA
1 TCCGGCGAAAAAACCCAGAA
11351487 TCCGG
1 TCCGG
11351492 TGAATCTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (20 bp):
TCCGGCGAAAAAACCCAGAA
Found at i:11351854 original size:20 final size:20
Alignment explanation
Indices: 11351828--11351866 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
11351818 CAGGTTTTTT
*
11351828 TTTTTTTTTTTTCTCTTTGAA
1 TTTTTTTTTATT-TCTTTGAA
11351849 TTTTTTTTTATTTCTTTG
1 TTTTTTTTTATTTCTTTG
11351867 TTTATTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTATTTCTTTGAA
Found at i:11351874 original size:28 final size:27
Alignment explanation
Indices: 11351822--11351874 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
11351812 CCGCTTCAGG
* *
11351822 TTTTTTTTTTTTTTTTTTCTCTTTGAA
1 TTTTTTTTTTTTTTTGTTCTATTTGAA
11351849 TTTTTTTTTATTTCTTTGTT-TATTTG
1 TTTTTTTTT-TTT-TTTGTTCTATTTG
11351875 TTTATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 9 0.41
28 8 0.36
29 5 0.23
ACGTcount: A:0.08, C:0.06, G:0.06, T:0.81
Consensus pattern (27 bp):
TTTTTTTTTTTTTTTGTTCTATTTGAA
Found at i:11352224 original size:60 final size:59
Alignment explanation
Indices: 11351943--11352298 Score: 440
Period size: 60 Copynumber: 5.9 Consensus size: 59
11351933 TCTTTAAATA
* * *
11351943 AAAATAAAAAATTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
1 AAAAT-AAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---G
*
11352006 AAAAAATAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-
1 AAAATA-AAATTT-CAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
* * *
11352066 AGAAAT-AAATTTC--CAAAAATATTTTT-GAGGAAGAGTTGAAAGTATCAATTTTCC-TC
1 A-AAATAAAATTTCAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTG
11352122 AGAAAT-AAATTTCAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
1 A-AAATAAAATTTCAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
* *
11352182 AAAATCAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCG
1 AAAAT-AAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
* *
11352242 AAAATCGAAATTTCAAAAAATAA-ATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAT-AAAATTTCAAAAAA-AATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
11352299 CCACACACAA
Statistics
Matches: 268, Mismatches: 12, Indels: 29
0.87 0.04 0.09
Matches are distributed among these distances:
55 2 0.01
56 50 0.19
58 5 0.02
59 43 0.16
60 94 0.35
61 19 0.07
62 1 0.00
63 9 0.03
64 45 0.17
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (59 bp):
AAAATAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
Found at i:11356233 original size:33 final size:34
Alignment explanation
Indices: 11356161--11356234 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
11356151 TCAATAATAG
*
11356161 ATGAAAATGAAAAAAAGATGAAAAAAAAGTAAAA
1 ATGAAAAAGAAAAAAAGATGAAAAAAAAGTAAAA
* *
11356195 A-GAAAAAGAAAAAAA-A-GGAAAAAATGTAGAAA
1 ATGAAAAAGAAAAAAAGATGAAAAAAAAGTA-AAA
11356227 ATGAAAAA
1 ATGAAAAA
11356235 AGAGATTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 10 0.29
32 5 0.14
33 19 0.54
34 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (34 bp):
ATGAAAAAGAAAAAAAGATGAAAAAAAAGTAAAA
Found at i:11356235 original size:34 final size:33
Alignment explanation
Indices: 11356171--11356237 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 33
11356161 ATGAAAATGA
11356171 AAAAAAGATGAAAAAAAAGTAAAAAG-AAAAAG
1 AAAAAAGATGAAAAAAAAGTAAAAAGAAAAAAG
* * *
11356203 AAAAAA-AAGGAAAAAATGTAGAAAATGAAAAAAG
1 AAAAAAGATGAAAAAAAAGTA-AAAA-GAAAAAAG
11356237 A
1 A
11356238 GATTCAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 11 0.38
32 10 0.34
33 1 0.03
34 7 0.24
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (33 bp):
AAAAAAGATGAAAAAAAAGTAAAAAGAAAAAAG
Found at i:11357539 original size:41 final size:41
Alignment explanation
Indices: 11357455--11357909 Score: 616
Period size: 41 Copynumber: 11.1 Consensus size: 41
11357445 ATGATTGTTA
* * * *
11357455 AGGAGTAATTTACTTTCCAAAGTC-TGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
*
11357495 AGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
11357536 AGGAGCAATTTACTTTTCAAAGTCCGT--TGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGT-CGTGGTGCCTCTGTTGAG
*
11357576 AGGAGCAATTTACTTTTCAAAGTCGTGTTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
* * *
11357617 AGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
* * *
11357658 AGGAGCAATTTACTTTTCAAAGTCATGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
* *
11357699 AGGAGCAATTTACTTTCCAACGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
* *
11357740 AGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
* *
11357781 AGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTGAG
* *
11357823 AGGAGCAATTTACTTTCCAAAGTCCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGT-CGTGGTGCCTCTGTTGAG
* * * *
11357863 AGGAGCAATTTAC-TTTCAAAGGTCGTTGAGTCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAA-GTCGTGGTGCCTCTGTTGAG
11357904 AGGAGC
1 AGGAGC
11357910 TTCGGCAAAA
Statistics
Matches: 379, Mismatches: 27, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
39 12 0.03
40 86 0.23
41 239 0.63
42 42 0.11
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
Found at i:11357922 original size:1 final size:1
Alignment explanation
Indices: 11357916--11358019 Score: 64
Period size: 1 Copynumber: 104.0 Consensus size: 1
11357906 GAGCTTCGGC
* * ** ** ** **
11357916 AAAAAAAAAAAACAAAAAAACAAAAAAAATTAAAAAAAATCAAAAAAAATCAAAAAAATCAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * ** *
11357981 AATAAAAACAAAAATAAAAAAAAATCAAAAAATAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11358020 TGTTGAGTTG
Statistics
Matches: 77, Mismatches: 26, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.09
Consensus pattern (1 bp):
A
Found at i:11357953 original size:30 final size:31
Alignment explanation
Indices: 11357916--11358018 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
11357906 GAGCTTCGGC
11357916 AAAAAAA-AAAAACAAAAAAACAAAAAAAATT
1 AAAAAAATAAAAACAAAAAAACAAAAAAAA-T
** *
11357947 AAAAAAA-ATCAA-AAAAAATC-AAAAAAAT
1 AAAAAAATAAAAACAAAAAAACAAAAAAAAT
*
11357975 CAAAAAAATAAAAACAAAAATA-AAAAAAAAT
1 -AAAAAAATAAAAACAAAAAAACAAAAAAAAT
*
11358006 CAAAAAATAAAAA
1 AAAAAAATAAAAA
11358019 ATGTTGAGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
28 1 0.02
29 14 0.23
30 22 0.37
31 23 0.38
ACGTcount: A:0.84, C:0.07, G:0.00, T:0.09
Consensus pattern (31 bp):
AAAAAAATAAAAACAAAAAAACAAAAAAAAT
Found at i:11358010 original size:9 final size:9
Alignment explanation
Indices: 11357920--11358012 Score: 83
Period size: 9 Copynumber: 10.7 Consensus size: 9
11357910 TTCGGCAAAA
*
11357920 AAAAAAAAC
1 AAAAAAATC
11357929 AAAAAAA-C
1 AAAAAAATC
*
11357937 AAAAAAAATTA
1 -AAAAAAA-TC
11357948 AAAAAAATC
1 AAAAAAATC
11357957 AAAAAAAATC
1 -AAAAAAATC
11357967 AAAAAAATC
1 AAAAAAATC
11357976 AAAAAAAT-
1 AAAAAAATC
11357984 --AAAAA-C
1 AAAAAAATC
11357990 AAAAATAA--
1 AAAAA-AATC
11357998 AAAAAAATC
1 AAAAAAATC
11358007 AAAAAA
1 AAAAAA
11358013 TAAAAAATGT
Statistics
Matches: 72, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
6 5 0.07
7 2 0.03
8 9 0.12
9 40 0.56
10 16 0.22
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAAATC
Found at i:11358019 original size:9 final size:9
Alignment explanation
Indices: 11357918--11358019 Score: 89
Period size: 10 Copynumber: 10.7 Consensus size: 9
11357908 GCTTCGGCAA
*
11357918 AAAAAAAAA
1 AAAAAAAAT
*
11357927 ACAAAAAAAC
1 A-AAAAAAAT
11357937 AAAAAAAATT
1 AAAAAAAA-T
11357947 AAAAAAAAT
1 AAAAAAAAT
11357956 CAAAAAAAAT
1 -AAAAAAAAT
*
11357966 CAAAAAAAT
1 AAAAAAAAT
*
11357975 CAAAAAAATAA
1 -AAAAAAA-AT
11357986 AAACAAAAAT
1 AAA-AAAAAT
11357996 AAAAAAAA-
1 AAAAAAAAT
*
11358004 ATCAAAAAAT
1 A-AAAAAAAT
11358014 AAAAAA
1 AAAAAA
11358020 TGTTGAGTTG
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.01
9 32 0.42
10 39 0.51
11 5 0.06
ACGTcount: A:0.84, C:0.07, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:11359353 original size:1 final size:1
Alignment explanation
Indices: 11359311--11359336 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
11359301 CCGCTCCAGG
11359311 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
11359337 CTCTTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11359368 original size:12 final size:12
Alignment explanation
Indices: 11359351--11359393 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
11359341 TTGAATTTTT
*
11359351 TTTATTTCTTTG
1 TTTATTTCTTTA
*
11359363 TTTATTTGTTTA
1 TTTATTTCTTTA
*
11359375 TTTTATTTTTTTA
1 -TTTATTTCTTTA
11359388 TTTATT
1 TTTATT
11359394 AGATTAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (12 bp):
TTTATTTCTTTA
Found at i:11359404 original size:25 final size:25
Alignment explanation
Indices: 11359351--11359405 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
11359341 TTGAATTTTT
* * * *
11359351 TTTATTTCTTTGTTTATTTGTTTAT
1 TTTATTTCTTTATTTATTAGATTAG
*
11359376 TTTATTTTTTTATTTATTAGATTAG
1 TTTATTTCTTTATTTATTAGATTAG
11359401 TTTAT
1 TTTAT
11359406 GTAATATTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (25 bp):
TTTATTTCTTTATTTATTAGATTAG
Found at i:11359715 original size:60 final size:59
Alignment explanation
Indices: 11359437--11359789 Score: 402
Period size: 60 Copynumber: 5.9 Consensus size: 59
11359427 TTCTTTAAAT
* * *
11359437 AAAATAAAAAATTCCAAAAAAATATTTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAA
1 AAAAT-AAAATTTCAAAAAAAATA-TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT--G
*
11359500 AAAAAATAAATTTCCAAAAAAAATA-TTTTAGGG-AAAGTTGAAAGTATCAA-TTTCCTT-
1 AAAATA-AAATTT-CAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
*** * * *
11359557 AGAAAT-AAATTTC-CCTAAAATA-TTTTGGGGAAGAGTTGAAAGTATCAATTTTCC-TC
1 A-AAATAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
11359613 AGAAAT-AAATTTCAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
1 A-AAATAAAATTTCAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
* *
11359673 AAAATCAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCG
1 AAAAT-AAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
* *
11359733 AAAATCGAAATTTCAAAAAATAA-ATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAT-AAAATTTCAAAAAA-AATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
11359790 CCACACAAAA
Statistics
Matches: 259, Mismatches: 18, Indels: 29
0.85 0.06 0.09
Matches are distributed among these distances:
54 13 0.05
55 18 0.07
56 24 0.09
57 4 0.02
58 6 0.02
59 34 0.13
60 99 0.38
61 33 0.13
62 9 0.03
63 9 0.03
64 10 0.04
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (59 bp):
AAAATAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
Found at i:11360371 original size:48 final size:47
Alignment explanation
Indices: 11360268--11360577 Score: 418
Period size: 47 Copynumber: 6.6 Consensus size: 47
11360258 CGTTATGACA
** *
11360268 TCAGCAGAGGCTCAATGACTTTAAAATTTTCTT-GAAAAGGCTCCTC
1 TCAGCAGAGGCTCAACAACTTTAAAATTCTCTTGGAAAAGGCTCCTC
11360314 TCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGGAAAA-GCTCCTC
1 TCAGCAGAGGCTCAACAACTTTAAAAT-TC-TCTTGGAAAAGGCTCCTC
* *
11360362 TCAGTAGAGGCTCAA-AGACTTTAAAATTCTCTT-AAAAAGGCTCCTC
1 TCAGCAGAGGCTCAACA-ACTTTAAAATTCTCTTGGAAAAGGCTCCTC
* *
11360408 TCAGTAGAGGCTCAACAACTTTAAAAATTCTCTT-GAAAAAGCTCCTC
1 TCAGCAGAGGCTCAACAACTTT-AAAATTCTCTTGGAAAAGGCTCCTC
11360455 TCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGGAAAA-GCTCCTC
1 TCAGCAGAGGCTCAACAACTTTAAAAT-TC-TCTTGGAAAAGGCTCCTC
* *
11360503 TCAGCAGAGGCTCAACGATTTTAAAATTCTCTT-GAAAGAGGCTCCTC
1 TCAGCAGAGGCTCAACAACTTTAAAATTCTCTTGGAAA-AGGCTCCTC
*
11360550 TCAGTAGAGGCTCAACAACTTTAAAATT
1 TCAGCAGAGGCTCAACAACTTTAAAATT
11360578 TTATCTTGTT
Statistics
Matches: 239, Mismatches: 13, Indels: 23
0.87 0.05 0.08
Matches are distributed among these distances:
45 8 0.03
46 66 0.28
47 84 0.35
48 71 0.30
49 10 0.04
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (47 bp):
TCAGCAGAGGCTCAACAACTTTAAAATTCTCTTGGAAAAGGCTCCTC
Found at i:11360576 original size:141 final size:140
Alignment explanation
Indices: 11360268--11360577 Score: 521
Period size: 141 Copynumber: 2.2 Consensus size: 140
11360258 CGTTATGACA
* ** * *
11360268 TCAGCAGAGGCTCAATGACTTTAAAATTTTCTTGAAAAGGCTCCTCTCAGCAGAGGCTCAACAAC
1 TCAGTAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAAC
*
11360333 TTTAAAATCTCATCTTGGAAAAGCTCCTCTCAGTAGAGGCTCAAAGACTTTAAAATTCTCTTAAA
66 TTTAAAATCTCATCTTGGAAAAGCTCCTCTCAGCAGAGGCTCAAAGACTTTAAAATTCTCTTAAA
11360398 AAGGCTCCTC
131 AAGGCTCCTC
11360408 TCAGTAGAGGCTCAACAACTTTAAAAATTCTCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAA
1 TCAGTAGAGGCTCAACAACTTT-AAAATTCTCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAA
* *
11360473 CTTTAAAATCTCATCTTGGAAAAGCTCCTCTCAGCAGAGGCTCAACGATTTTAAAATTCTCTTGA
65 CTTTAAAATCTCATCTTGGAAAAGCTCCTCTCAGCAGAGGCTCAAAGACTTTAAAATTCTCTT-A
*
11360538 AAGAGGCTCCTC
129 AAAAGGCTCCTC
11360550 TCAGTAGAGGCTCAACAACTTTAAAATT
1 TCAGTAGAGGCTCAACAACTTTAAAATT
11360578 TTATCTTGTT
Statistics
Matches: 159, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
140 19 0.12
141 106 0.67
142 34 0.21
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (140 bp):
TCAGTAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAAC
TTTAAAATCTCATCTTGGAAAAGCTCCTCTCAGCAGAGGCTCAAAGACTTTAAAATTCTCTTAAA
AAGGCTCCTC
Found at i:11370980 original size:13 final size:13
Alignment explanation
Indices: 11370961--11370995 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11370951 CGGTCAACGT
*
11370961 ACGGTTCGGTTCG
1 ACGGTTCGGTCCG
*
11370974 GCGGTTCGGTCCG
1 ACGGTTCGGTCCG
11370987 ACGGTTCGG
1 ACGGTTCGG
11370996 CTTGGTCTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.26, G:0.43, T:0.26
Consensus pattern (13 bp):
ACGGTTCGGTCCG
Found at i:11372008 original size:20 final size:20
Alignment explanation
Indices: 11371984--11372027 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
11371974 TATGTATTTC
*
11371984 ATTTTTTT-TTGTAATTCGT
1 ATTTTTTTATTGTAATTCAT
*
11372003 ATTTTTTTATTGTATTTCAT
1 ATTTTTTTATTGTAATTCAT
11372023 ATTTT
1 ATTTT
11372028 ATACTTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (20 bp):
ATTTTTTTATTGTAATTCAT
Found at i:11372391 original size:14 final size:14
Alignment explanation
Indices: 11372354--11372382 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11372344 TTTGTTTCGC
11372354 AAAAAATTATTTTT
1 AAAAAATTATTTTT
11372368 AAAAAATTATTTTT
1 AAAAAATTATTTTT
11372382 A
1 A
11372383 TAATTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAAAATTATTTTT
Found at i:11373204 original size:21 final size:21
Alignment explanation
Indices: 11373180--11373243 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
11373170 AGATACTTTC
11373180 AATATAAAATATAAATATTTT
1 AATATAAAATATAAATATTTT
*
11373201 -A-AT--AGTATAAATATTTT
1 AATATAAAATATAAATATTTT
* *
11373218 AATA-ATAAATATTATTATTTT
1 AATATA-AAATATAAATATTTT
11373239 AATAT
1 AATAT
11373244 TAATAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
17 13 0.39
18 1 0.03
19 3 0.09
20 1 0.03
21 15 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AATATAAAATATAAATATTTT
Found at i:11373211 original size:17 final size:16
Alignment explanation
Indices: 11373188--11373230 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 16
11373178 TCAATATAAA
11373188 ATATAAATATTTTAAT
1 ATATAAATATTTTAAT
11373204 AGTATAAATATTTTAAT
1 A-TATAAATATTTTAAT
11373221 A-ATAAATATT
1 ATATAAATATT
11373231 ATTATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.35
16 1 0.04
17 16 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATAAATATTTTAAT
Found at i:11373424 original size:26 final size:25
Alignment explanation
Indices: 11373395--11373454 Score: 86
Period size: 26 Copynumber: 2.4 Consensus size: 25
11373385 TATTAATAAT
11373395 TTTAATAATAAATAATTTCA-AGATAC
1 TTTAATAATAAATAATTT-ATA-ATAC
*
11373421 TTTAATAATAAATAATTTATAATAT
1 TTTAATAATAAATAATTTATAATAC
11373446 TTTAATAAT
1 TTTAATAAT
11373455 TATATTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 13 0.41
26 19 0.59
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTAATAATAAATAATTTATAATAC
Found at i:11375061 original size:22 final size:22
Alignment explanation
Indices: 11375020--11375063 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11375010 TAGATCTTTT
*
11375020 TATAAAAAAACTCATGCTTTCA
1 TATAAAAAAACTCATACTTTCA
* *
11375042 TATAAAAAAATTGATACTTTCA
1 TATAAAAAAACTCATACTTTCA
11375064 ACTTTTTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (22 bp):
TATAAAAAAACTCATACTTTCA
Found at i:11375193 original size:28 final size:26
Alignment explanation
Indices: 11375107--11375194 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 26
11375097 TATTTTTAAG
*
11375107 AAAAAATTGTACTTTCAATTTTTCCTC
1 AAAAAATTGTACTTTTAATTTTT-CTC
* * * *
11375134 AAAAATATTTTA-TTTTATTTTATTTTTA
1 AAAAA-ATTGTACTTTTA-ATT-TTTCTC
11375162 AAAAAATTGATACTTTTAACTTTTTCTC
1 AAAAAATTG-TACTTTTAA-TTTTTCTC
11375190 AAAAA
1 AAAAA
11375195 TATATTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
27 12 0.26
28 24 0.52
29 10 0.22
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (26 bp):
AAAAAATTGTACTTTTAATTTTTCTC
Found at i:11375222 original size:56 final size:55
Alignment explanation
Indices: 11375044--11375222 Score: 161
Period size: 57 Copynumber: 3.1 Consensus size: 55
11375034 TGCTTTCATA
** *
11375044 TAAAAAAATTGATACTTTCAACTTTTT-CTTTAAAATATTTT-TCTTGATAATTTTATTTT
1 TAAAAAAATTG-TACTTTCAA-TTTTTCCTCAAAAATATTTTAT-TT--T-ATTTTATTGT
*
11375103 TAAGAAAAAATTGTACTTTCAATTTTTCCTCAAAAATATTTTATTTTATTTTATTTT
1 T-A-AAAAAATTGTACTTTCAATTTTTCCTCAAAAATATTTTATTTTATTTTATTGT
*
11375160 TAAAAAAATTGATACTTTTAACTTTTT-CTCAAAAATATATTT-TTTTAATTTT-TATGT
1 TAAAAAAATTG-TACTTTCAA-TTTTTCCTCAAAAATAT-TTTATTTT-ATTTTAT-TGT
11375217 TAAAAA
1 TAAAAA
11375223 GATTATTAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 20
0.82 0.03 0.15
Matches are distributed among these distances:
55 9 0.08
56 25 0.23
57 32 0.30
58 1 0.01
59 6 0.06
60 24 0.22
61 10 0.09
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (55 bp):
TAAAAAAATTGTACTTTCAATTTTTCCTCAAAAATATTTTATTTTATTTTATTGT
Done.