Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001700.1 Hibiscus syriacus cultivar Beakdansim tig00003398_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: 2632955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:224412 original size:19 final size:19
Alignment explanation
Indices: 224390--224471 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
224380 GAAACACAAA
224390 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
224409 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
224425 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
224441 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
224460 TCGCATTGCGAT
1 TCGCATTGCGAT
224472 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 9 0.17
16 8 0.15
18 9 0.17
19 28 0.52
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:224490 original size:20 final size:19
Alignment explanation
Indices: 224426--224509 Score: 98
Period size: 19 Copynumber: 4.4 Consensus size: 19
224416 GCGATTTTGT
*
224426 CGTTGCGAT-TTCATTTCG
1 CGTTGCGATAGTCATTTCG
**
224444 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
224463 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
224483 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
224502 TGTTGCGA
1 CGTTGCGA
224510 AAGTAAACTA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
18 9 0.16
19 31 0.54
20 17 0.30
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:225007 original size:18 final size:18
Alignment explanation
Indices: 224981--225025 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
224971 GTCGATCAGA
* *
224981 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
224999 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
225017 TGATGGCTC
1 TGATGGCTC
225026 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:226366 original size:20 final size:20
Alignment explanation
Indices: 226341--226378 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
226331 AATAGTTTCT
226341 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
226361 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
226379 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:226664 original size:22 final size:22
Alignment explanation
Indices: 226639--226682 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
226629 GATTTAGATA
226639 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
226661 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
226683 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:226962 original size:20 final size:20
Alignment explanation
Indices: 226849--226962 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
226839 CGCTTTGAAA
226849 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
226869 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
226889 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
226909 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
226930 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
226950 ATCGCATTGCGAT
1 ATCGCATTGCGAT
226963 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 56 0.73
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:226980 original size:21 final size:21
Alignment explanation
Indices: 226951--227043 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
226941 ATAGTAAGTA
226951 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
226972 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
226992 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
227013 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
227033 TCGCATTGCGA
1 TCGCATTGCGA
227044 ATAAGTAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:226981 original size:41 final size:41
Alignment explanation
Indices: 226890--227024 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
226880 AAAGTCAGTA
* * * ** *
226890 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
226930 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
226972 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
227013 TCGCGTTGCGAT
1 TCGCGTTGCGAT
227025 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:227025 original size:41 final size:41
Alignment explanation
Indices: 226951--227043 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
226941 ATAGTAAGTA
226951 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
226992 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
227033 TCGCATTGCGA
1 TCGCATTGCGA
227044 ATAAGTAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:227713 original size:27 final size:26
Alignment explanation
Indices: 227645--227713 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 26
227635 TAAATTCTTG
*
227645 ATTTTTATAATATT-AAAATTTATTAA
1 ATTTTT-TAATATTAAAAAATTATTAA
* *
227671 ATAGTTTTAATAATTAAAAAAATTATTAT
1 AT-TTTTTAAT-ATT-AAAAAATTATTAA
227700 ATTTTTTAATATTA
1 ATTTTTTAATATTA
227714 TGAGTTCGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
26 7 0.20
27 9 0.26
28 7 0.20
29 12 0.34
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
ATTTTTTAATATTAAAAAATTATTAA
Found at i:251889 original size:12 final size:12
Alignment explanation
Indices: 251872--251906 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
251862 TAGTTGCGAA
251872 AAATTAAAATTT
1 AAATTAAAATTT
*
251884 AAATTAAAAATT
1 AAATTAAAATTT
*
251896 AAATTCAAATT
1 AAATTAAAATT
251907 ACTTACCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:253569 original size:24 final size:25
Alignment explanation
Indices: 253517--253570 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
253507 TCGGCCTACA
* *
253517 AAATAATTGTAATATATAAATTAAT
1 AAATAATAGTAATATATAAATAAAT
253542 -AATAATAGTAATA-ATAAATAAAT
1 AAATAATAGTAATATATAAATAAAT
253565 AAATAA
1 AAATAA
253571 ATAAATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (25 bp):
AAATAATAGTAATATATAAATAAAT
Found at i:253674 original size:2 final size:2
Alignment explanation
Indices: 253665--253706 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
253655 TTTTAAAAAC
*
253665 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
253706 T
1 T
253707 TCATCCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:261617 original size:12 final size:12
Alignment explanation
Indices: 261600--261656 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
261590 CCCTCTTTTG
*
261600 TATCTGTCTGTT
1 TATCTGTCTATT
261612 TATCTGTCTATT
1 TATCTGTCTATT
* * *
261624 TCTCTATCTATC
1 TATCTGTCTATT
*
261636 TATATGTCTATT
1 TATCTGTCTATT
*
261648 TCTCTGTCT
1 TATCTGTCT
261657 GTTTCTATTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.14, C:0.21, G:0.09, T:0.56
Consensus pattern (12 bp):
TATCTGTCTATT
Found at i:263164 original size:59 final size:59
Alignment explanation
Indices: 263096--263212 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 59
263086 AATTAGACTT
* * * *
263096 GATTTAAAAGTTTATGAGTTTGTAATTGTCAAATTTGACCCTAATCATTTTACGTACTC
1 GATTTAAAAGTTTATGAGTTTATAATTGTCAAATTCGACCCGAATCATTATACGTACTC
*
263155 GATTTAAAAGTTTATGAGTTTATAATTGTCAAATTCGACCCGAGTCATTATACGTACT
1 GATTTAAAAGTTTATGAGTTTATAATTGTCAAATTCGACCCGAATCATTATACGTACT
263213 AGTGAACACT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (59 bp):
GATTTAAAAGTTTATGAGTTTATAATTGTCAAATTCGACCCGAATCATTATACGTACTC
Found at i:277292 original size:15 final size:15
Alignment explanation
Indices: 277272--277311 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
277262 AGTTGTATAT
277272 TTCTTCTCCACTCTC
1 TTCTTCTCCACTCTC
*
277287 TTCTTCTCCACTGTC
1 TTCTTCTCCACTCTC
277302 TTCTTCTCCA
1 TTCTTCTCCA
277312 GCAATCTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.07, C:0.42, G:0.03, T:0.47
Consensus pattern (15 bp):
TTCTTCTCCACTCTC
Found at i:277970 original size:31 final size:33
Alignment explanation
Indices: 277934--278002 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 33
277924 ATTCTCTTAA
* *
277934 AAATTTATCGAGGACTAAATTG-AATTTTGATT
1 AAATTTATCGAGGACCAAAGTGAAATTTTGATT
277966 -AA-TT-TCGAGGACCAAAGTGAAATTTTGATT
1 AAATTTATCGAGGACCAAAGTGAAATTTTGATT
277996 AAATTTA
1 AAATTTA
278003 GATACAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
29 13 0.42
30 12 0.39
31 4 0.13
32 2 0.06
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (33 bp):
AAATTTATCGAGGACCAAAGTGAAATTTTGATT
Found at i:279347 original size:44 final size:44
Alignment explanation
Indices: 279297--279560 Score: 357
Period size: 44 Copynumber: 6.0 Consensus size: 44
279287 TTGGAGGAAG
*
279297 TTTCTGATGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCA
1 TTTCTGAAGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCA
*
279341 TTTCTGAAGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCG
1 TTTCTGAAGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCA
* * * *
279385 TTTCTGAAGGCTCCTTTACCATGTGCAAGGGTAAGAACTTACCG
1 TTTCTGAAGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCA
* * * *
279429 TTTCTGAAAGCTCCTTTGCTATGTGCAAGTGTAGGAACTTACCA
1 TTTCTGAAGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCA
* *
279473 TTTCTGAAGGCTCCTCTGCTATGTGCAAGGGTAAGACCTTACCGC
1 TTTCTGAAGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACC-A
* * * * *
279518 TTACTGCAGGCTCCTCTGCTTTGTGCACAGGGTAAGCCCTTAC
1 TTTCTGAAGGCTCCTTTGCTATGTGCA-AGGGTAAGACCTTAC
279561 TGGGTGTACA
Statistics
Matches: 197, Mismatches: 21, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
44 159 0.81
45 24 0.12
46 14 0.07
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (44 bp):
TTTCTGAAGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCA
Found at i:280492 original size:33 final size:33
Alignment explanation
Indices: 280450--280531 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
280440 TTATGAAAAG
* *
280450 GAGAAGAGAAGAGAAGTGATTTATACCGTTTAT
1 GAGAAGAGAAAAGAAGTGATTTATACCGCTTAT
*
280483 GAGAAGAGAAAATAAGTGATTTATACCGCTTAT
1 GAGAAGAGAAAAGAAGTGATTTATACCGCTTAT
280516 GAGAAGAGAAAAGAAG
1 GAGAAGAGAAAAGAAG
280532 AGAGGATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.45, C:0.06, G:0.27, T:0.22
Consensus pattern (33 bp):
GAGAAGAGAAAAGAAGTGATTTATACCGCTTAT
Found at i:280525 original size:38 final size:37
Alignment explanation
Indices: 280437--280530 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 37
280427 TTGTTTCTAT
*
280437 CGCTTATGAAAAGGAGAAGAGAAGAGAAGTGATTTATAC
1 CGCTTATG-AAA-GAGAAGAGAAAAGAAGTGATTTATAC
* *
280476 CG-TT-T--ATGAGAAGAGAAAATAAGTGATTTATAC
1 CGCTTATGAAAGAGAAGAGAAAAGAAGTGATTTATAC
*
280509 CGCTTATGAGAAGAGAAAAGAA
1 CGCTTATGA-AAGAGAAGAGAA
280531 GAGAGGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
33 26 0.58
34 3 0.07
35 1 0.02
37 1 0.02
38 12 0.27
39 2 0.04
ACGTcount: A:0.45, C:0.07, G:0.26, T:0.22
Consensus pattern (37 bp):
CGCTTATGAAAGAGAAGAGAAAAGAAGTGATTTATAC
Found at i:283700 original size:2 final size:2
Alignment explanation
Indices: 283693--283754 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
283683 TCAGTGTCAC
*
283693 AG AG AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
283735 AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG
283755 TGATGATTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:285569 original size:21 final size:22
Alignment explanation
Indices: 285545--285589 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
285535 AAAAATGCTC
285545 ATTAAG-C-TTTTATTTCTTTTA
1 ATTAAGCCTTTTTATTT-TTTTA
285566 ATTAAGTCCTTTTTATTTTTTTA
1 ATTAAG-CCTTTTTATTTTTTTA
285589 A
1 A
285590 AAAAAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.29
23 7 0.33
24 8 0.38
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTAAGCCTTTTTATTTTTTTA
Found at i:286074 original size:24 final size:23
Alignment explanation
Indices: 286039--286089 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
286029 TCGGAAGACA
** *
286039 TTAAAAAAAATAAGTATTTAAAT
1 TTAAAAAAAATAAAAATTAAAAT
*
286062 TTAAAAATTAATAAAAATTAAAAT
1 TTAAAAA-AAATAAAAATTAAAAT
286086 TTAA
1 TTAA
286090 TTGATTGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TTAAAAAAAATAAAAATTAAAAT
Found at i:289284 original size:13 final size:13
Alignment explanation
Indices: 289266--289293 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
289256 ATTTATCATT
289266 TTAAAACACACAC
1 TTAAAACACACAC
289279 TTAAAACACACAC
1 TTAAAACACACAC
289292 TT
1 TT
289294 CTCCCCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (13 bp):
TTAAAACACACAC
Found at i:291075 original size:2 final size:2
Alignment explanation
Indices: 291068--291110 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
291058 TTGAGAAACA
291068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
291110 A
1 A
291111 GTCTTCATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:291634 original size:20 final size:21
Alignment explanation
Indices: 291580--291642 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
291570 GATTCCCCTG
291580 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
291604 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
291624 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
291643 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:300840 original size:11 final size:11
Alignment explanation
Indices: 300824--300857 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
300814 AACACATCCT
300824 TGTAATCCTAC
1 TGTAATCCTAC
300835 TGTAATCCTAC
1 TGTAATCCTAC
300846 TGTAATCCTAC
1 TGTAATCCTAC
300857 T
1 T
300858 ATTCTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.38
Consensus pattern (11 bp):
TGTAATCCTAC
Found at i:302417 original size:21 final size:21
Alignment explanation
Indices: 302364--302417 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
302354 CAACAAAAGG
* * *
302364 GGTATCGGTACCTTTGGGATG
1 GGTATCAGTACTTTTGGGATA
302385 GGTATCAGTACTTTTGGGATA
1 GGTATCAGTACTTTTGGGATA
*
302406 GGTATTAGTACT
1 GGTATCAGTACT
302418 CCTATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.37
Consensus pattern (21 bp):
GGTATCAGTACTTTTGGGATA
Found at i:302856 original size:13 final size:13
Alignment explanation
Indices: 302836--302872 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
302826 TTTGTATTTC
302836 GAAAAATTACTTT
1 GAAAAATTACTTT
*
302849 GCAAAATTACTTT
1 GAAAAATTACTTT
302862 GAAAAATTACT
1 GAAAAATTACT
302873 CCCCCTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (13 bp):
GAAAAATTACTTT
Found at i:311084 original size:98 final size:98
Alignment explanation
Indices: 310861--311076 Score: 335
Period size: 98 Copynumber: 2.2 Consensus size: 98
310851 CTGCACACCT
* * * *
310861 AGTAAATTCCATGATTCCAAAAATCAGGAACAATTCATATTTTTCCAGTGAAAACATGAAACCAA
1 AGTAAATTCCATGATTTCATAAATCATGAACAATTCATATTTTTCCAGTGAAAACAGGAAACCAA
* *
310926 TAACATATTTCATGTAACCATAATTCATAAACC
66 TAACACATTTCAGGTAACCATAATTCATAAACC
* *
310959 AGTATATTCCATGATTTTATAAATCATGAACAATTCATA-TTTTCCAGTGAAAACAGGAAACCAT
1 AGTAAATTCCATGATTTCATAAATCATGAACAATTCATATTTTTCCAGTGAAAACAGGAAACCA-
311023 ATAACACATTTCAGGTAACCATAATTCATAAACC
65 ATAACACATTTCAGGTAACCATAATTCATAAACC
*
311057 AGTAAATTTCATGATTTCAT
1 AGTAAATTCCATGATTTCAT
311077 TATTCATGTA
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 23 0.22
98 83 0.78
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (98 bp):
AGTAAATTCCATGATTTCATAAATCATGAACAATTCATATTTTTCCAGTGAAAACAGGAAACCAA
TAACACATTTCAGGTAACCATAATTCATAAACC
Found at i:311365 original size:20 final size:20
Alignment explanation
Indices: 311340--311378 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
311330 TTTTGAAAGA
*
311340 CATGCATCGATGTACCAATC
1 CATGCATCGATGCACCAATC
311360 CATGCATCGATGCACCAAT
1 CATGCATCGATGCACCAAT
311379 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (20 bp):
CATGCATCGATGCACCAATC
Found at i:311502 original size:65 final size:64
Alignment explanation
Indices: 311428--311550 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 64
311418 CACTCTCCAT
* *
311428 GCATCGATGCACTCAGGGT-TTTATGAAAACATCAAATGCATTTGATGTATCAATGCACAAGCCG
1 GCATCGATGCACTCAGGCTATTT-TG-AAACATCAAATGCATTTGATGCATCAATGCACAAGCCG
311492 A
64 A
* * ** * *
311493 GCATTGATGCACTCATGCTATTTTGAAACATGGAATGCATTTTATGCATCGATGCACA
1 GCATCGATGCACTCAGGCTATTTTGAAACATCAAATGCATTTGATGCATCAATGCACA
311551 CTTAGTGCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
64 28 0.57
65 18 0.37
66 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (64 bp):
GCATCGATGCACTCAGGCTATTTTGAAACATCAAATGCATTTGATGCATCAATGCACAAGCCGA
Found at i:319409 original size:14 final size:15
Alignment explanation
Indices: 319384--319412 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
319374 TTGATTTTGA
319384 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
319399 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
319413 AAACGTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:319737 original size:12 final size:12
Alignment explanation
Indices: 319720--319744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
319710 GGAGAAGTGT
319720 TAAGTGTTAAAG
1 TAAGTGTTAAAG
319732 TAAGTGTTAAAG
1 TAAGTGTTAAAG
319744 T
1 T
319745 GTTTTAAAGG
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:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (12 bp):
TAAGTGTTAAAG
Found at i:319812 original size:13 final size:13
Alignment explanation
Indices: 319782--319821 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
319772 AGGGGAGTAC
319782 TTTCAAAATTAA-
1 TTTCAAAATTAAT
319794 -TTCAAAATTAAT
1 TTTCAAAATTAAT
*
319806 TTTCAAAATTGAT
1 TTTCAAAATTAAT
319819 TTT
1 TTT
319822 TTAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 11 0.44
13 14 0.56
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (13 bp):
TTTCAAAATTAAT
Found at i:320336 original size:64 final size:63
Alignment explanation
Indices: 320172--320336 Score: 204
Period size: 65 Copynumber: 2.6 Consensus size: 63
320162 AATGAATAAA
* * *** * * *
320172 TTGAAACATCGAATGCAATTTATGCACCGATGCACTCTCCATGCATCGATGCACTCAGGGTTT
1 TTGAAACATCGAATGCATTTTATGCATCGATGCACAAGCCAAGCATCGAAGCACTCAGGCTTT
*
320235 TATGAAAACATCGAATGCATTTGATGCATCGATGCACAAGCCAAGCATCGAAGCACTCAGGCTAT
1 T-TG-AAACATCGAATGCATTTTATGCATCGATGCACAAGCCAAGCATCGAAGCACTCAGGCT-T
320300 T
63 T
* *
320301 TTGAAACATCAAATGTATTTTATGCATCGATGCACA
1 TTGAAACATCGAATGCATTTTATGCATCGATGCACA
320337 CTTAGTGCAC
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 32 0.37
65 51 0.59
66 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (63 bp):
TTGAAACATCGAATGCATTTTATGCATCGATGCACAAGCCAAGCATCGAAGCACTCAGGCTTT
Found at i:325183 original size:10 final size:10
Alignment explanation
Indices: 325168--325210 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
325158 CATTTAATAA
325168 ATAAACGAAC
1 ATAAACGAAC
325178 ATAAACGAAC
1 ATAAACGAAC
325188 ----ACGAAC
1 ATAAACGAAC
325194 ATAAACGAAC
1 ATAAACGAAC
325204 ATAAACG
1 ATAAACG
325211 TTGGAGACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.21
10 23 0.79
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:325193 original size:16 final size:16
Alignment explanation
Indices: 325172--325204 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
325162 TAATAAATAA
325172 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
325188 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
325204 A
1 A
325205 TAAACGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:326325 original size:24 final size:24
Alignment explanation
Indices: 326284--326329 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
326274 AGATTGGGTT
*
326284 AAACATAAATGAACGAACATAAAC
1 AAACATAAACGAACGAACATAAAC
* *
326308 AAACATAACCGAATGAACATAA
1 AAACATAAACGAACGAACATAA
326330 CCGAATGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.17, G:0.09, T:0.13
Consensus pattern (24 bp):
AAACATAAACGAACGAACATAAAC
Found at i:326328 original size:14 final size:14
Alignment explanation
Indices: 326309--326336 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
326299 AACATAAACA
326309 AACATAACCGAATG
1 AACATAACCGAATG
326323 AACATAACCGAATG
1 AACATAACCGAATG
326337 TTCACGAACG
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:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
AACATAACCGAATG
Found at i:326815 original size:17 final size:18
Alignment explanation
Indices: 326795--326837 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
326785 TTATATTCGA
*
326795 ATAATTT-AATCGAATAT
1 ATAATTTGAATCAAATAT
326812 ATAATTTTGAATCAAATAT
1 ATAA-TTTGAATCAAATAT
*
326831 AAAATTT
1 ATAATTT
326838 TAAAATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
19 12 0.55
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (18 bp):
ATAATTTGAATCAAATAT
Found at i:326829 original size:19 final size:19
Alignment explanation
Indices: 326802--326838 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
326792 CGAATAATTT
* *
326802 AATCGAATATATAATTTTG
1 AATCAAATATAAAATTTTG
326821 AATCAAATATAAAATTTT
1 AATCAAATATAAAATTTT
326839 AAAATTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
AATCAAATATAAAATTTTG
Found at i:326973 original size:8 final size:8
Alignment explanation
Indices: 326962--326988 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
326952 GTTTATTTGT
326962 AATATCAA
1 AATATCAA
326970 AATATCAA
1 AATATCAA
326978 AATATCAA
1 AATATCAA
326986 AAT
1 AAT
326989 GTTTTCTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (8 bp):
AATATCAA
Found at i:327040 original size:97 final size:97
Alignment explanation
Indices: 326874--327055 Score: 355
Period size: 97 Copynumber: 1.9 Consensus size: 97
326864 CACTTTTGTT
*
326874 ATATCAAAATATCAAAATGTTTTCTCCACACGTGGTCCATCAACTTTTTCGCCATCAATCTAATT
1 ATATCAAAATATCAAAATGTTTTCTCCACACGTGGTCCATCAACTTTTGCGCCATCAATCTAATT
326939 TGTGGGTTCTTCGGTTTATTTGTAATATCAAA
66 TGTGGGTTCTTCGGTTTATTTGTAATATCAAA
326971 ATATCAAAATATCAAAATGTTTTCTCCACACGTGGTCCATCAACTTTTGCGCCATCAATCTAATT
1 ATATCAAAATATCAAAATGTTTTCTCCACACGTGGTCCATCAACTTTTGCGCCATCAATCTAATT
327036 TGTGGGTTCTTCGGTTTATT
66 TGTGGGTTCTTCGGTTTATT
327056 AAACTTGAAG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (97 bp):
ATATCAAAATATCAAAATGTTTTCTCCACACGTGGTCCATCAACTTTTGCGCCATCAATCTAATT
TGTGGGTTCTTCGGTTTATTTGTAATATCAAA
Found at i:327802 original size:3 final size:3
Alignment explanation
Indices: 327794--327835 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
327784 TTTAACTTGC
327794 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
327836 GACTCATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:329613 original size:8 final size:7
Alignment explanation
Indices: 329599--329643 Score: 51
Period size: 6 Copynumber: 6.7 Consensus size: 7
329589 TTTACCAATC
329599 TTATTTA
1 TTATTTA
329606 TATATTTA
1 T-TATTTA
329614 TTA-TTA
1 TTATTTA
*
329620 TTA-TCA
1 TTATTTA
329626 TTATTTA
1 TTATTTA
329633 TTA-TTA
1 TTATTTA
329639 TTATT
1 TTATT
329644 GTTATTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 17 0.52
7 9 0.27
8 7 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTTA
Found at i:329619 original size:3 final size:3
Alignment explanation
Indices: 329611--329659 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
329601 ATTTATATAT
* * *
329611 TTA TTA TTA TTA TCA TTA TTTA TTA TTA TTA TTG TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
329657 TTA
1 TTA
329660 AATATTACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:331252 original size:116 final size:113
Alignment explanation
Indices: 331126--331354 Score: 259
Period size: 115 Copynumber: 2.0 Consensus size: 113
331116 TTAACTTATT
* * *
331126 TTAATCTGTTTTAATACTTATTTA-TTTTTAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGG
1 TTAATCTGTTTT-A-A-TTATTTATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAG
* *
331188 ATGTCCATTTTCTAATATTTTTAAATAAATAATATCCTATTTTATAAATTATATA
63 AAGTCC-TTTTCTAATATTTCTAAATAAATAATAT-CTA-TTTATAAA-TATATA
* * ** *
331243 TTAAT-TGTTTTAATTATTTATTTTTTAATATCGAGGAAAAGAGCTGTCTTAAGGCACCTAGAAG
1 TTAATCTGTTTTAATTATTTATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAG
* *
331307 TCCTTTTCTGATATTTCTAAATAAATAATATTTATTTATAAATATATA
66 TCCTTTTCTAATATTTCTAAATAAATAATATCTATTTATAAATATATA
331355 AACTAATATA
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
112 6 0.06
113 15 0.15
114 13 0.13
115 29 0.30
116 29 0.30
117 5 0.05
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (113 bp):
TTAATCTGTTTTAATTATTTATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAG
TCCTTTTCTAATATTTCTAAATAAATAATATCTATTTATAAATATATA
Found at i:339418 original size:114 final size:115
Alignment explanation
Indices: 338962--339722 Score: 1065
Period size: 114 Copynumber: 6.8 Consensus size: 115
338952 TAGTAGAAGA
*
338962 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAA-CCCAAAAA
1 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAAA
* ** *
339026 CCAATCATTGGATTTAAAAGATCCATGTGCTCATAGTAG----AA-GA--
66 CCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGG
* * *
339069 CCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCCCAAAAA
1 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAAA
* *
339134 CCAATCATTGGATTTGAAAGATGCATGTGCTCATAGTAG----AA-GA--
66 CCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGG
*
339177 CCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAAA
1 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAAA
*
339242 CCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGG
66 CCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGG
*
339292 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCC-AAAA
1 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAAA
* *
339356 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGG
66 CCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGG
* *
339406 CCCAATAGCATCTTCTTGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCC-AAAA
1 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAAA
* * * *
339470 TCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTACAAATAAAGAGA
66 CCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGG
* * *
339520 CCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAA
1 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAAA
* * *
339585 -CAATCATTAGATTTGAAAGATGAATTTTCTCATGGTAGAAATAAGGAGG
66 CCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGG
* * * * * *
339634 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGATAGGAACCAC-AGAA
1 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAAA
* * *
339698 CTAATCATTGGAATTAAAAGATGAA
66 CCAATCATTGGATTTGAAAGATGAA
339723 CTGCATGATC
Statistics
Matches: 603, Mismatches: 41, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
107 54 0.09
108 146 0.24
112 2 0.00
113 5 0.01
114 334 0.55
115 62 0.10
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (115 bp):
CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAAA
CCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGG
Found at i:342734 original size:113 final size:113
Alignment explanation
Indices: 342536--343045 Score: 948
Period size: 113 Copynumber: 4.5 Consensus size: 113
342526 TAGCAAAGAT
342536 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
342601 AGAAGGAAGAAGAAATTCATAATGAGAAAAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAAAATTTGTTCAACCTTTTGC
* *
342649 TCAAATCTATCATTTGATGGATCAGCTTTTACAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
342714 AGAAGGAATAAGAAATTCATAATGAGAAAATTTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAAAATTTGTTCAACCTTTTGC
342762 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
342827 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAAAATTTGTTCAACCTTTTGC
342875 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
342940 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAAAATTTGTTCAACCTTTTGC
* *
342988 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
343046 TGTTCAACTT
Statistics
Matches: 386, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 386 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAAAATTTGTTCAACCTTTTGC
Found at i:343103 original size:73 final size:73
Alignment explanation
Indices: 342950--343118 Score: 196
Period size: 73 Copynumber: 2.3 Consensus size: 73
342940 AGAAGGAAGA
* * * * *
342950 AGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCATC
1 AGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGAACAGC
** *
343014 TTTTCCAG
66 AGTACCAG
* * * *
343022 AGAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGAACAGC
1 AGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGAACAGC
343087 AGTACCAG
66 AGTACCAG
** *
343095 TTAGAGTTCATAATGAGAAGAACT
1 AGAAAGTTCATAATGAGAAGAACT
343119 CATCTAAAGA
Statistics
Matches: 81, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
72 5 0.06
73 76 0.94
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (73 bp):
AGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGAACAGC
AGTACCAG
Found at i:343105 original size:186 final size:185
Alignment explanation
Indices: 342837--343197 Score: 497
Period size: 186 Copynumber: 1.9 Consensus size: 185
342827 AGAAGGAAGA
* * * * *
342837 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCT
1 AGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGAACAGCA
* * *
342902 TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
66 GTACCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGA
* * **
342967 AGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCATCTTTTCCAG
131 AGAACTTGTTCAAACTTTTGCTCAAATCCATCATTCAATGGATCATCTTTTCCAG
* * * *
343022 AGAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGAACAGC
1 AGAAA-TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGAACAGC
** * *
343087 AGTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAG
65 AGTACCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAG
* ** *
343152 AAGAACTTGTTCAAATTTTTGCTTGAATTCATCATTCAATGGATCA
130 AAGAACTTGTTCAAACTTTTGCTCAAATCCATCATTCAATGGATCA
343198 GCATTACCAG
Statistics
Matches: 151, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
185 5 0.03
186 146 0.97
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (185 bp):
AGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGAACAGCA
GTACCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGA
AGAACTTGTTCAAACTTTTGCTCAAATCCATCATTCAATGGATCATCTTTTCCAG
Found at i:343146 original size:113 final size:113
Alignment explanation
Indices: 343025--343383 Score: 479
Period size: 113 Copynumber: 3.2 Consensus size: 113
343015 TTTCCAGAGA
* * * *
343025 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGAACAGCAGT
1 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGATGGATCAGCATT
343090 ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAG
66 ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAG
* * *
343138 AAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGCTTGAATTCATCATTCAATGGATCAGCATT
1 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGATGGATCAGCATT
* * *
343203 ACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAG
66 ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAG
* * * * * *
343251 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATT
1 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGATGGATCAGCATT
* * * * **
343316 GCCAGGTAGAGTTCATAATGAGCAGAACTCGTC-ATCTGAA-GAAGAAG
66 ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTA-AAGAAGGAAGAAG
* *
343363 AAGTTCACAATGAAAAGAACT
1 AAGTTCATAATGAGAAGAACT
343384 CATCTGAAGA
Statistics
Matches: 214, Mismatches: 31, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
112 25 0.12
113 189 0.88
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGATGGATCAGCATT
ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAG
Found at i:343154 original size:299 final size:299
Alignment explanation
Indices: 342724--343344 Score: 834
Period size: 299 Copynumber: 2.1 Consensus size: 299
342714 AGAAGGAATA
* * * *
342724 AGAAA-TTCATAATGAGAA-AATTTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAG
1 AGAAAGTTCATAATGAGAAGAA-CTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGAACAG
** * *
342787 CTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
65 CAGTACCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGA
* * ** * *
342852 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTT
130 GAAGAACTTGTTCAAACTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGAAAAAGTT
*
342917 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC
195 CATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC
* * *
342982 TTTTGCTCAAATCCATCATTTGATGGATCATCTTTTCCAG
260 TTTTGCTCAAATCCATCATTTGATGGATCAACATTGCCAG
* * * *
343022 AGAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGAACAGC
1 AGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGAACAGC
** * *
343087 AGTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAG
66 AGTACCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAG
* ** * ****
343152 AAGAACTTGTTCAAATTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTC
131 AAGAACTTGTTCAAACTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGAAAAAGTTC
*
343217 ATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCT
196 ATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCT
* * * *
343282 TTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAG
261 TTTGCTCAAATCCATCATTTGATGGATCAACATTGCCAG
* *
343321 -GTAGAGTTCATAATGAGCAGAACT
1 AG-AAAGTTCATAATGAGAAGAACT
343345 CGTCATCTGA
Statistics
Matches: 279, Mismatches: 41, Indels: 5
0.86 0.13 0.02
Matches are distributed among these distances:
298 6 0.02
299 271 0.97
300 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (299 bp):
AGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGAACAGC
AGTACCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAG
AAGAACTTGTTCAAACTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGAAAAAGTTC
ATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCT
TTTGCTCAAATCCATCATTTGATGGATCAACATTGCCAG
Found at i:343394 original size:36 final size:36
Alignment explanation
Indices: 343347--343416 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
343337 GCAGAACTCG
343347 TCATCTGAAGAAGAAGAAGTTCACAATGAAAAGAAC
1 TCATCTGAAGAAGAAGAAGTTCACAATGAAAAGAAC
*
343383 TCATCTGAAGAAGAAGAAGTTCACAATGAGAAGA
1 TCATCTGAAGAAGAAGAAGTTCACAATGAAAAGA
343417 GCTTGTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (36 bp):
TCATCTGAAGAAGAAGAAGTTCACAATGAAAAGAAC
Found at i:343416 original size:17 final size:17
Alignment explanation
Indices: 343358--343416 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
343348 CATCTGAAGA
343358 AGAAGAAGTTCACAATG
1 AGAAGAAGTTCACAATG
* *
343375 AAAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
343393 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
343411 AGAAGA
1 AGAAGA
343417 GCTTGTTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 3 0.09
17 15 0.47
18 2 0.06
19 9 0.28
20 3 0.09
ACGTcount: A:0.51, C:0.12, G:0.22, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:343672 original size:3 final size:3
Alignment explanation
Indices: 343664--343709 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
343654 ATTTATATAT
* * *
343664 TTA TTA TTA TTA TCA TTA TTTA TTA TTA TTG TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
343710 AATATTACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:343715 original size:25 final size:25
Alignment explanation
Indices: 343664--343716 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
343654 ATTTATATAT
* *
343664 TTATTATTATTATCATTATTTATTA
1 TTATTATTATTATCATTATTAAATA
*
343689 TTATTGTTATTAAT-ATTATTAAATA
1 TTATTATTATT-ATCATTATTAAATA
343714 TTA
1 TTA
343717 CAAAGCCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTATTATTATTATCATTATTAAATA
Found at i:345327 original size:20 final size:19
Alignment explanation
Indices: 345302--345343 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
345292 CTATTTTATA
345302 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
345322 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
345341 AAT
1 AAT
345344 ATCGAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:345400 original size:120 final size:117
Alignment explanation
Indices: 345198--345430 Score: 281
Period size: 120 Copynumber: 2.0 Consensus size: 117
345188 TATTTTAATC
* * * *
345198 TTGTTTTAATATTTATTTATTTTTAATATTAAGAAAGGGCAGTCTTAAAACAACGGGATGTCCAT
1 TTGTTTTAATATTTATTTATTTTTAATATGAAGAAAGAGCAGTCTTAAAACAACGAGAAGTCCAT
*
345263 TTTCTAATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATATTAA
66 TTTCTAATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATATATTAA
* * ** * *
345315 TTGTTTTAATTATTTATTTATTTTTTAATATCGAGGAAAAGAGCTGTCTTAAGGCACCTAGAAGT
1 TTGTTTTAA-TATTTATTTA-TTTTTAATAT-GAAG-AAAGAGCAGTCTTAAAACAACGAGAAGT
* **
345380 CC-TTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATA
62 CCATTTTCTAATATTTCTAAATAAATAAATATCCTATTTATAAATATATATA
345431 AACTAATATA
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
117 9 0.09
118 10 0.10
119 19 0.20
120 37 0.38
121 22 0.23
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.45
Consensus pattern (117 bp):
TTGTTTTAATATTTATTTATTTTTAATATGAAGAAAGAGCAGTCTTAAAACAACGAGAAGTCCAT
TTTCTAATATTTCTAAATAAATAAATATCCTATTTATAAATATATATATTAA
Found at i:354382 original size:20 final size:22
Alignment explanation
Indices: 354329--354385 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
354319 TACATAGGCA
354329 GTGTACCGATACACCAATTAAGG
1 GTGTACCGATAC-CCAATTAAGG
* *
354352 GATGTATCGATACCCTA-T-AGG
1 G-TGTACCGATACCCAATTAAGG
354373 GTGTACCGATACC
1 GTGTACCGATACC
354386 TTTTCAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 11 0.37
21 4 0.13
22 1 0.03
23 4 0.13
24 10 0.33
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (22 bp):
GTGTACCGATACCCAATTAAGG
Found at i:354837 original size:24 final size:24
Alignment explanation
Indices: 354793--354852 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
354783 AGCATGTGAA
* *
354793 ATAAGTAAAGTG-ATCATATGTGT
1 ATAAGTGAAGTGAATCAAATGTGT
* *
354816 ATAAGTGAAGTGAATGAAATGTTT
1 ATAAGTGAAGTGAATCAAATGTGT
* *
354840 ATATGAGAAGTGA
1 ATAAGTGAAGTGA
354853 TAAGTTAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (24 bp):
ATAAGTGAAGTGAATCAAATGTGT
Found at i:354984 original size:18 final size:18
Alignment explanation
Indices: 354958--355041 Score: 71
Period size: 18 Copynumber: 4.7 Consensus size: 18
354948 TTAAAATTGG
* *
354958 TCCTACGGGACACAGTGA
1 TCCTTCGGGACAAAGTGA
* *
354976 TCCTTCGGGATAAAGTGG
1 TCCTTCGGGACAAAGTGA
* * *
354994 TCCTACAGGACATAGTGA
1 TCCTTCGGGACAAAGTGA
* * *
355012 T-CGTCGGGATAAAGTGG
1 TCCTTCGGGACAAAGTGA
355029 TCCTTCGGGACAA
1 TCCTTCGGGACAA
355042 GGGTTAAGTT
Statistics
Matches: 48, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
17 11 0.23
18 37 0.77
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (18 bp):
TCCTTCGGGACAAAGTGA
Found at i:355026 original size:35 final size:36
Alignment explanation
Indices: 354955--355032 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
354945 GGGTTAAAAT
* *
354955 TGGTCCTACGGGACACAGTGATCCTTCGGGATAAAG
1 TGGTCCTACAGGACACAGTGATCCGTCGGGATAAAG
*
354991 TGGTCCTACAGGACATAGTGAT-CGTCGGGATAAAG
1 TGGTCCTACAGGACACAGTGATCCGTCGGGATAAAG
355026 TGGTCCT
1 TGGTCCT
355033 TCGGGACAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 19 0.49
36 20 0.51
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (36 bp):
TGGTCCTACAGGACACAGTGATCCGTCGGGATAAAG
Found at i:355040 original size:35 final size:36
Alignment explanation
Indices: 354955--355040 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 36
354945 GGGTTAAAAT
*
354955 TGGTCCTACGGGACACAGTGATCCTTCGGGATAAAG
1 TGGTCCTACGGGACACAGTGATCCGTCGGGATAAAG
* *
354991 TGGTCCTACAGGACATAGTGAT-CGTCGGGATAAAG
1 TGGTCCTACGGGACACAGTGATCCGTCGGGATAAAG
*
355026 TGGTCCTTCGGGACA
1 TGGTCCTACGGGACA
355041 AGGGTTAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 25 0.56
36 20 0.44
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.23
Consensus pattern (36 bp):
TGGTCCTACGGGACACAGTGATCCGTCGGGATAAAG
Found at i:361482 original size:13 final size:13
Alignment explanation
Indices: 361464--361489 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
361454 TAGTATTTTA
361464 TTATTTATTTGTT
1 TTATTTATTTGTT
361477 TTATTTATTTGTT
1 TTATTTATTTGTT
361490 ATATATGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TTATTTATTTGTT
Found at i:361485 original size:25 final size:28
Alignment explanation
Indices: 361420--361486 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
361410 AGTATTGTTA
*
361420 GTTTT-TTTATTTTATTTTTGTATATAT
1 GTTTTATTTATTTTATTATTGTATATAT
*
361447 GTGTTATTAGTATTTTATTATT-TAT-T-T
1 GTTTTATT--TATTTTATTATTGTATATAT
361474 GTTTTATTTATTT
1 GTTTTATTTATTT
361487 GTTATATATG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
25 5 0.15
27 12 0.35
28 3 0.09
29 3 0.09
30 11 0.32
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (28 bp):
GTTTTATTTATTTTATTATTGTATATAT
Found at i:361490 original size:38 final size:36
Alignment explanation
Indices: 361417--361491 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 36
361407 GATAGTATTG
361417 TTAGTTTTTTTATTTTATTTTTGTATATATGTGTTA
1 TTAGTTTTTTTATTTTATTTTTGTATATATGTGTTA
* * *
361453 TTAGTATTTTATTA-TTTATTTGTTTTATTTATTTGTTA
1 TTAGT-TTTT-TTATTTTATTT-TTGTATATATGTGTTA
361491 T
1 T
361492 ATATGTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 5 0.15
37 11 0.33
38 17 0.52
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (36 bp):
TTAGTTTTTTTATTTTATTTTTGTATATATGTGTTA
Found at i:361693 original size:18 final size:18
Alignment explanation
Indices: 361649--361694 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
361639 GATTTTTTCG
361649 TATTTTATTTATTTACCT
1 TATTTTATTTATTTACCT
*
361667 T-TGTTTATTTATTTATCT
1 TAT-TTTATTTATTTACCT
*
361685 TATTCTATTT
1 TATTTTATTT
361695 TGTCTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (18 bp):
TATTTTATTTATTTACCT
Found at i:372257 original size:60 final size:59
Alignment explanation
Indices: 372143--372256 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
372133 AGTACTTCGC
* * *
372143 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTAAAAAAAGGAAAAAACAAAAAAATCGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAA-GAAAAAACAAAAAAATCGT
* * * *
372203 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAA-AAAAGAGAAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAGAAAAAACAAAAAAA
372257 ACAAGAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 12 0.26
60 35 0.74
ACGTcount: A:0.52, C:0.13, G:0.22, T:0.13
Consensus pattern (59 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAGAAAAAACAAAAAAATCGT
Found at i:372280 original size:12 final size:12
Alignment explanation
Indices: 372236--372272 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
372226 GCCCTAAATT
*
372236 GAAAAAAAAAAGA
1 GAAAAAAAACA-A
372249 GAAAAAAAACAA
1 GAAAAAAAACAA
372261 GAAAAAAAACAA
1 GAAAAAAAACAA
372273 AAAGAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (12 bp):
GAAAAAAAACAA
Found at i:373506 original size:99 final size:99
Alignment explanation
Indices: 373365--373612 Score: 397
Period size: 99 Copynumber: 2.5 Consensus size: 99
373355 ATCGGGCGCA
* * *
373365 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCCGCTGACTGTCAACTTTCCAATTTCAGAG
1 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACTTCCCAATTCCAGAG
*
373430 CCAATTTCAACTTCACAGCAAAGGATATTGGACT
66 CCAATTTCAACTTCACAACAAAGGATATTGGACT
373464 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACTTCCCAATTCCAGAG
1 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACTTCCCAATTCCAGAG
* * *
373529 CTAATTTCAACTTCACAACGAAGGATGTTGGACT
66 CCAATTTCAACTTCACAACAAAGGATATTGGACT
* * * *
373563 CAAGACAGCACAAGCTCAACTTCACGGTGAAGGGGTGGCTGATTGTCAAC
1 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAAC
373613 AAACAATTTC
Statistics
Matches: 138, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 138 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (99 bp):
CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACTTCCCAATTCCAGAG
CCAATTTCAACTTCACAACAAAGGATATTGGACT
Found at i:375715 original size:41 final size:43
Alignment explanation
Indices: 375637--375718 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
375627 TTAAAATATT
*
375637 TATATATATTTGATAGTATTGTTAGTTTTTTATTTTATTTTTG
1 TATATATATTTGATAGTATTGTTAGTTATTTATTTTATTTTTG
375680 TATATATATGTT-ATTAGTATT-TTA-TTATTTA-TTTATTTT
1 TATATATAT-TTGA-TAGTATTGTTAGTTATTTATTTTATTTT
375719 ATTTATTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
41 8 0.22
42 6 0.17
43 13 0.36
44 9 0.25
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (43 bp):
TATATATATTTGATAGTATTGTTAGTTATTTATTTTATTTTTG
Found at i:380438 original size:23 final size:22
Alignment explanation
Indices: 380408--380488 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
380398 ACACTACCTA
380408 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCA-CCCTTGAAT
* * *
380431 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
380452 GTACATCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
*
380475 GTGCATTGATGCAC
1 GTGCATCGATGCAC
380489 TCTGTTGTGC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.36
23 30 0.64
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:382910 original size:65 final size:65
Alignment explanation
Indices: 382790--382934 Score: 159
Period size: 65 Copynumber: 2.2 Consensus size: 65
382780 TTTCGAATGC
* * * * * * *
382790 AATTTATGCACTGATGCACA-GCCATGCATCGATACACTCTGGATTTTATTAAAACATCGAATTG
1 AATTTGTGCACCGATGTACATGTCATGCATCGATACACCCTGGATTTTATTAAAACATCGAAGTA
* * * * *
382854 ATTTTGTGCATCGATGTACATGTCATGCATCGATGCACCCTGGCTATTT-TTGAAACATCGAAGT
1 AATTTGTGCACCGATGTACATGTCATGCATCGATACACCCTGGAT-TTTATTAAAACATCGAAGT
382918 A
65 A
382919 AATTTGTGCACCGATG
1 AATTTGTGCACCGATG
382935 CACACCCTAG
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
64 15 0.23
65 47 0.72
66 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (65 bp):
AATTTGTGCACCGATGTACATGTCATGCATCGATACACCCTGGATTTTATTAAAACATCGAAGTA
Found at i:386659 original size:17 final size:17
Alignment explanation
Indices: 386637--386690 Score: 90
Period size: 17 Copynumber: 3.2 Consensus size: 17
386627 CGATTTTGAG
*
386637 CTCGATTCAAACTCGAA
1 CTCGATTCAAGCTCGAA
386654 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
*
386671 CTCAATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
386688 CTC
1 CTC
386691 AAACTCGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.24
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:389578 original size:7 final size:6
Alignment explanation
Indices: 389564--389625 Score: 52
Period size: 7 Copynumber: 9.2 Consensus size: 6
389554 TTTGAATTGA
*
389564 AGGTTT AGCGTTT AGTGTTT AGGTTT AGGATTT AAGATTT AGAGTTT ATGGTTT
1 AGGTTT AG-GTTT AG-GTTT AGGTTT AGG-TTT -AGGTTT AG-GTTT A-GGTTT
389618 AGGGTTT A
1 A-GGTTT A
389626 TTACAAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
6 11 0.23
7 33 0.70
8 3 0.06
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.47
Consensus pattern (6 bp):
AGGTTT
Found at i:390618 original size:18 final size:18
Alignment explanation
Indices: 390585--390694 Score: 114
Period size: 18 Copynumber: 6.1 Consensus size: 18
390575 TCGAGGGTTA
* *
390585 AAAGTAGTCCTACGGGAC
1 AAAGTGGTCCTTCGGGAC
* * *
390603 ATAGTGATCCTTCGGGAT
1 AAAGTGGTCCTTCGGGAC
*
390621 AAAGTGGTCCTAT-GGGTC
1 AAAGTGGTCCT-TCGGGAC
* * *
390639 ATAGTGATCCTTCGGGAT
1 AAAGTGGTCCTTCGGGAC
*
390657 AAAGTGGTCCTTCGGGAT
1 AAAGTGGTCCTTCGGGAC
390675 AAAGTGGTCCTTCGGGAC
1 AAAGTGGTCCTTCGGGAC
390693 AA
1 AA
390695 GTGTTAAGTG
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
17 1 0.01
18 72 0.97
19 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (18 bp):
AAAGTGGTCCTTCGGGAC
Found at i:390632 original size:36 final size:36
Alignment explanation
Indices: 390585--390691 Score: 151
Period size: 36 Copynumber: 3.0 Consensus size: 36
390575 TCGAGGGTTA
*
390585 AAAGTAGTCCTACGGGACATAGTGATCCTTCGGGAT
1 AAAGTGGTCCTACGGGACATAGTGATCCTTCGGGAT
* *
390621 AAAGTGGTCCTATGGGTCATAGTGATCCTTCGGGAT
1 AAAGTGGTCCTACGGGACATAGTGATCCTTCGGGAT
* * * *
390657 AAAGTGGTCCTTCGGGATAAAGTGGTCCTTCGGGA
1 AAAGTGGTCCTACGGGACATAGTGATCCTTCGGGA
390692 CAAGTGTTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (36 bp):
AAAGTGGTCCTACGGGACATAGTGATCCTTCGGGAT
Found at i:395278 original size:21 final size:21
Alignment explanation
Indices: 395252--395293 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
395242 ATTTGAATAT
*
395252 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
395273 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
395294 CCATTCTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:395354 original size:21 final size:21
Alignment explanation
Indices: 395321--395360 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
395311 TTTTTGTAGA
*
395321 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
395343 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
395361 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:395614 original size:34 final size:32
Alignment explanation
Indices: 395575--395644 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
395565 TATTGTAAAG
* *
395575 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
395609 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
395641 GGGA
1 GGGA
395645 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:396920 original size:10 final size:12
Alignment explanation
Indices: 396897--396955 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
396887 TCCGGATAAG
396897 ATATTTAAATAT
1 ATATTTAAATAT
396909 ATATTTAAATATT
1 ATATTTAAATA-T
* *
396922 ACAATTAAAT-T
1 ATATTTAAATAT
*
396933 ATATTGATAAT-T
1 ATATTTA-AATAT
396945 ATGATTTAAAT
1 AT-ATTTAAAT
396956 TAATTAATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 5 0.13
12 20 0.53
13 13 0.34
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (12 bp):
ATATTTAAATAT
Found at i:396961 original size:16 final size:16
Alignment explanation
Indices: 396940--396973 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
396930 ATTATATTGA
396940 TAATT-ATGATTTAAAT
1 TAATTAATGA-TTAAAT
396956 TAATTAATGATTAAAT
1 TAATTAATGATTAAAT
396972 TA
1 TA
396974 GATATCGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATTAATGATTAAAT
Found at i:406142 original size:21 final size:21
Alignment explanation
Indices: 406116--406155 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
406106 CATAACCCCA
*
406116 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
406137 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
406156 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:406190 original size:20 final size:21
Alignment explanation
Indices: 406136--406198 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
406126 GATTCCCCTG
406136 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
406160 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
406180 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
406199 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:410037 original size:22 final size:21
Alignment explanation
Indices: 409995--410034 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
409985 GAGTTTGTTT
*
409995 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
410016 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
410035 ACAATTTCTC
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:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:412526 original size:14 final size:14
Alignment explanation
Indices: 412509--412541 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
412499 ATTTCTATGT
*
412509 AGGGAATTATTTGC
1 AGGGAATTATTTAC
412523 AGGGAATTATTTAC
1 AGGGAATTATTTAC
412537 AGGGA
1 AGGGA
412542 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:419906 original size:61 final size:61
Alignment explanation
Indices: 419802--419917 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
419792 ATTGGATGAA
* * *
419802 TTTGGGGATGAAATTGGATGATTCAAAAGTTTGGAGACCAATTTAGAATGAGAGTTATACT
1 TTTGAGGATGAAATTGAATGATTCAAAAGTTTGAAGACCAATTTAGAATGAGAGTTATACT
**
419863 TTTGAGGATGAAATTAGAATG-TTCAAAAG-TTGAAGGATTAATTTAGAATGAGAGT
1 TTTGAGGATGAAATT-GAATGATTCAAAAGTTTGAA-GACCAATTTAGAATGAGAGT
419918 CAAAGTTTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 4 0.08
61 40 0.83
62 4 0.08
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (61 bp):
TTTGAGGATGAAATTGAATGATTCAAAAGTTTGAAGACCAATTTAGAATGAGAGTTATACT
Found at i:420549 original size:11 final size:11
Alignment explanation
Indices: 420533--420563 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
420523 GCTCCCCGGC
420533 TTCCTGCTTGT
1 TTCCTGCTTGT
420544 TTCCTGCTTGT
1 TTCCTGCTTGT
420555 TTCCTGCTT
1 TTCCTGCTT
420564 CTATATAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.29, G:0.16, T:0.55
Consensus pattern (11 bp):
TTCCTGCTTGT
Found at i:421616 original size:17 final size:18
Alignment explanation
Indices: 421590--421624 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
421580 GAAAAATATA
421590 TTTTTATAAA-ATTTAAT
1 TTTTTATAAATATTTAAT
*
421607 TTTTTTTAAATATTTAAT
1 TTTTTATAAATATTTAAT
421625 ATATGTGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTATAAATATTTAAT
Found at i:421944 original size:21 final size:20
Alignment explanation
Indices: 421914--421952 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
421904 TATATTTTAA
*
421914 TAATATTTTAGATTTATTAT
1 TAATATTTTAGAATTATTAT
421934 TAATAATTTTAGAATTATT
1 TAAT-ATTTTAGAATTATT
421953 TTATCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TAATATTTTAGAATTATTAT
Found at i:422051 original size:10 final size:11
Alignment explanation
Indices: 422033--422062 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
422023 ATAATTATTT
422033 TAAATTTTTAA
1 TAAATTTTTAA
422044 TAAATTTTTAA
1 TAAATTTTTAA
*
422055 CAAATTTT
1 TAAATTTT
422063 ACTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TAAATTTTTAA
Found at i:422308 original size:2 final size:2
Alignment explanation
Indices: 422301--422336 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
422291 ATTAGCTTTC
422301 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
422337 GGGTTGGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:427246 original size:2 final size:2
Alignment explanation
Indices: 427239--427291 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
427229 AAATCTATTA
427239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
427281 AT AT AT AT AT A
1 AT AT AT AT AT A
427292 GATTTTATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:427633 original size:3 final size:3
Alignment explanation
Indices: 427625--427728 Score: 99
Period size: 3 Copynumber: 35.3 Consensus size: 3
427615 TATAAGACTA
*
427625 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
427672 -AT ATT AAA AAT -TT GACT AAGT AAT AAT GAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
*
427717 ATT AAT AA- AAT A
1 AAT AAT AAT AAT A
427729 TATTGAAAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
2 7 0.09
3 71 0.87
4 4 0.05
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:427739 original size:25 final size:25
Alignment explanation
Indices: 427711--427766 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
427701 TAATAATAAT
*
427711 AATAATA-TTAATAAAATATATTGAA
1 AATAATACATAATAAAATATATT-AA
* *
427736 AATAA-ACATATTAAAATATATTTA
1 AATAATACATAATAAAATATATTAA
427760 AATAATA
1 AATAATA
427767 ACTAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
AATAATACATAATAAAATATATTAA
Found at i:429114 original size:3 final size:3
Alignment explanation
Indices: 429106--429202 Score: 137
Period size: 3 Copynumber: 33.3 Consensus size: 3
429096 CTGTAATGTA
* * *
429106 AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT ATT AAT ATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
429154 -AT AAT TAT AA- AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
429199 AAT A
1 AAT A
429203 TAAAAGTAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
2 6 0.07
3 77 0.93
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:429965 original size:112 final size:112
Alignment explanation
Indices: 429560--429997 Score: 423
Period size: 112 Copynumber: 3.8 Consensus size: 112
429550 GAATTAAGGC
* *
429560 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* *** * *** * * *
429625 GAACACTTCTGGAAATATTGATGCTGATCTATCTCCTTCTGCGATAGAGTTATGC-A
66 G-A-AC-TCT--AACTAGAAATGCTGATCCA--T-CGAAT--GATAAAGTAAAGCAA
*
429681 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
* * ** *
429746 TGAACTCTAACTGGCAATGCTGATCCATCGGGTGATAAATTAAAGCAA
65 TGAACTCTAACTAGAAATGCTGATCCATCGAATGATAAAGTAAAGCAA
* * *
429794 AAGGTTGAACAAGTTCGTCTCATTATGAACTTCTTCTTCCTCTGT-AGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCT-TCAGATGAGTTCTTCTCATTA
* ** * * ** *
429858 TGAACTTTCTCTAGAAATGTTGATCCATCGAATGATGAAGTCGA-TAA
65 TGAACTCTAACTAGAAATGCTGATCCATCGAATGATAAAGTAAAGCAA
* * *
429905 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTTTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATTA
* *
429970 TGAACTCTAACTGGCAATGCTGATCCAT
65 TGAACTCTAACTAGAAATGCTGATCCAT
429998 TGAGTAATGG
Statistics
Matches: 267, Mismatches: 45, Indels: 19
0.81 0.14 0.06
Matches are distributed among these distances:
111 39 0.15
112 105 0.39
113 38 0.14
114 2 0.01
115 1 0.00
117 13 0.05
119 3 0.01
120 2 0.01
121 36 0.13
122 28 0.10
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTAACTAGAAATGCTGATCCATCGAATGATAAAGTAAAGCAA
Found at i:430377 original size:22 final size:22
Alignment explanation
Indices: 430322--430378 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
430312 AATAAAGCTT
* *
430322 TCATCGTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
430344 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
430366 TCATCTTTGAAGA
1 TCATCTTTGAAGA
430379 ATGTAGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:430839 original size:54 final size:54
Alignment explanation
Indices: 430749--430991 Score: 306
Period size: 54 Copynumber: 4.5 Consensus size: 54
430739 TTACTGGTTC
* * *
430749 GTAAAACATTTGACAACACATTCATCATCTCATGTGGTTTCTACTCAGATACTA
1 GTAAAACATTTGACAACACATTCATCCTCTCATGTGGTTTCTACCCAGATGCTA
* * * * *
430803 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCCCAGATGTTT
1 GTAAAACATTTGACAACACATTCATCCTCTCATGTGGTTTCTACCCAGATGCTA
* * * *
430857 GTAAAACATTTGACAACATATTCATCATCTCATATGGTTTCTACTCAGATGCTA
1 GTAAAACATTTGACAACACATTCATCCTCTCATGTGGTTTCTACCCAGATGCTA
* * * * *
430911 GTAAAACATTTGTCAACACATTCATCCTTTCCTGTGGTTTCTACCCAGATGTTT
1 GTAAAACATTTGACAACACATTCATCCTCTCATGTGGTTTCTACCCAGATGCTA
* * *
430965 GTAAAATATTTGACAATACATTTATCC
1 GTAAAACATTTGACAACACATTCATCC
430992 AGTTGTGGCT
Statistics
Matches: 159, Mismatches: 30, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 159 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCCTCTCATGTGGTTTCTACCCAGATGCTA
Found at i:430884 original size:108 final size:108
Alignment explanation
Indices: 430749--430986 Score: 413
Period size: 108 Copynumber: 2.2 Consensus size: 108
430739 TTACTGGTTC
*
430749 GTAAAACATTTGACAACACATTCATCATCTCATGTGGTTTCTACTCAGATACTAGTAAAACATTT
1 GTAAAACATTTGACAACACATTCATCATCTCATATGGTTTCTACTCAGATACTAGTAAAACATTT
*
430814 GACAACACATTCATCCTTTCCTGTGGTTTCTGCCCAGATGTTT
66 GACAACACATTCATCCTTTCCTGTGGTTTCTACCCAGATGTTT
* *
430857 GTAAAACATTTGACAACATATTCATCATCTCATATGGTTTCTACTCAGATGCTAGTAAAACATTT
1 GTAAAACATTTGACAACACATTCATCATCTCATATGGTTTCTACTCAGATACTAGTAAAACATTT
*
430922 GTCAACACATTCATCCTTTCCTGTGGTTTCTACCCAGATGTTT
66 GACAACACATTCATCCTTTCCTGTGGTTTCTACCCAGATGTTT
* *
430965 GTAAAATATTTGACAATACATT
1 GTAAAACATTTGACAACACATT
430987 TATCCAGTTG
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 122 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (108 bp):
GTAAAACATTTGACAACACATTCATCATCTCATATGGTTTCTACTCAGATACTAGTAAAACATTT
GACAACACATTCATCCTTTCCTGTGGTTTCTACCCAGATGTTT
Found at i:432021 original size:75 final size:75
Alignment explanation
Indices: 431888--432043 Score: 222
Period size: 75 Copynumber: 2.1 Consensus size: 75
431878 GATATGGATC
* * *
431888 TTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAAAATACATTAACATTCTTGATTCTGATT
1 TTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATTATGATT
431953 GAAAGGGGCT
66 GAAAGGGGCT
* * *** *
431963 TTCAGCATGCCTCAGCATTGGCTAATACAAACGTTCAAAATGTGTCAATATTCCTGATTATGATT
1 TTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATTATGATT
*
432028 GAAATGGGCT
66 GAAAGGGGCT
432038 TTCAGC
1 TTCAGC
432044 GTGCTCCATC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATTATGATT
GAAAGGGGCT
Found at i:438145 original size:16 final size:16
Alignment explanation
Indices: 438124--438154 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
438114 TTGAAATCCT
438124 TATTTTAATGAATGAA
1 TATTTTAATGAATGAA
*
438140 TATTTTAATGTATGA
1 TATTTTAATGAATGA
438155 TGACATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (16 bp):
TATTTTAATGAATGAA
Found at i:438268 original size:14 final size:14
Alignment explanation
Indices: 438244--438284 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
438234 AAACAAACAT
*
438244 AAAAATACAAATGC
1 AAAAATGCAAATGC
*
438258 AAAGATGCAAATGC
1 AAAAATGCAAATGC
*
438272 AAAAATGTAAATG
1 AAAAATGCAAATG
438285 TAAATTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.59, C:0.10, G:0.15, T:0.17
Consensus pattern (14 bp):
AAAAATGCAAATGC
Found at i:439980 original size:23 final size:23
Alignment explanation
Indices: 439931--439980 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
439921 ACAAACAAAT
*
439931 AAAATAATAAAAAGAAATATATG
1 AAAATAATAAAAAGAAATATATA
*
439954 AAAATAATAAAAAGGAAT-TAATA
1 AAAATAATAAAAAGAAATAT-ATA
439977 AAAA
1 AAAA
439981 AGAATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (23 bp):
AAAATAATAAAAAGAAATATATA
Found at i:446321 original size:20 final size:21
Alignment explanation
Indices: 446284--446322 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
446274 TATTTAAAAA
446284 TAAATAAATATTATTATTTTT
1 TAAATAAATATTATTATTTTT
446305 TAAA-AAATA-TATATATTT
1 TAAATAAATATTAT-TATTT
446323 ATATGACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAATAAATATTATTATTTTT
Found at i:447695 original size:23 final size:23
Alignment explanation
Indices: 447662--447723 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
447652 CTCGTATAAA
*
447662 TGCACCAAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
* **
447685 TGCACTGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
447708 TGCACCGAAGTGCCAT
1 TGCACCGAAGTGCCAT
447724 ATAAAATGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:448973 original size:112 final size:111
Alignment explanation
Indices: 448836--449286 Score: 490
Period size: 112 Copynumber: 3.9 Consensus size: 111
448826 GTAATCTATC
* **
448836 AAAAAGTTGAACTAGTTCTTCTCATTATGAACTTCTTCTTTATCTTCAGATGAGTTCTTCTCATT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* * * * * *
448901 ATGAACTCCTTCTAGTAATGTTAATCCATCGGGTAATGGATTTGCGT
66 ATGAACT-CTTCTGGAAATGTTGATCCATCGTGTAATGGATTAGAGT
448948 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* * * * * *
449013 ATGAACTCTACCTGGCAATGTTGATCCATTGTGTGATGGATTCGAGC
66 ATGAACTCT-TCTGGAAATGTTGATCCATCGTGTAATGGATTAGAGT
* ** * *
449060 AAAAGGTTGATGATGTTCTTCTCATTTTGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* * ** **
449125 ATGAACT-TCTCTGGAAATGTTGATGCCGATCTATCTCCTTCTATGATAGAGT
66 ATGAACTCT-TCTGGAAATGTTGAT-CC-ATC-GTGT-AATGGAT--TAGAGT
449177 CATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTC
1 -A---AAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTC
* * * *
449242 TCATTATGAACTTCCTCTGGAAATGTTGGTCCATCGAGTGATGGA
61 TCATTATGAAC-TCTTCTGGAAATGTTGATCCATCGTGTAATGGA
449287 AATTTCTGTT
Statistics
Matches: 281, Mismatches: 44, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
111 16 0.06
112 165 0.59
113 2 0.01
114 2 0.01
115 3 0.01
117 4 0.01
118 1 0.00
119 2 0.01
120 1 0.00
121 6 0.02
122 64 0.23
123 15 0.05
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (111 bp):
AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTTCTGGAAATGTTGATCCATCGTGTAATGGATTAGAGT
Found at i:449388 original size:37 final size:37
Alignment explanation
Indices: 449339--449443 Score: 124
Period size: 36 Copynumber: 2.9 Consensus size: 37
449329 TGCTTTAAGA
*
449339 AAAACAATCTCAAGTGAGATAAATTGTTGTTTCGAGTG
1 AAAACAATCTCAAGTGAGATAAATTGTTGTTTCAAG-G
** * * * *
449377 -AAACTGTCTCAAGCGAGACAAATT-TTCTTTTAAGG
1 AAAACAATCTCAAGTGAGATAAATTGTTGTTTCAAGG
449412 AAAACAATCTCAAGTGAGATAAATTGTTGTTT
1 AAAACAATCTCAAGTGAGATAAATTGTTGTTT
449444 GAAAACATCC
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
35 1 0.02
36 27 0.51
37 25 0.47
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (37 bp):
AAAACAATCTCAAGTGAGATAAATTGTTGTTTCAAGG
Found at i:449409 original size:73 final size:73
Alignment explanation
Indices: 449293--449443 Score: 232
Period size: 73 Copynumber: 2.1 Consensus size: 73
449283 TGGAAATTTC
* **
449293 TGTTTCTAGTGAAACTGCCTCAAGCGAGATGAATCTTGCTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGCCTCAAGCGAGACAAATCTTGCTTTAAGAAAAACAATCTCAAGTGAGA
449358 TAAATTGT
66 TAAATTGT
* * *
449366 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAAT-TTTCTTTTAAGGAAAACAATCTCAAGTGAG
1 TGTTTCGAGTGAAACTGCCTCAAGCGAGACAAATCTTGC-TTTAAGAAAAACAATCTCAAGTGAG
449430 ATAAATTGT
65 ATAAATTGT
449439 TGTTT
1 TGTTT
449444 GAAAACATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
72 3 0.04
73 68 0.96
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (73 bp):
TGTTTCGAGTGAAACTGCCTCAAGCGAGACAAATCTTGCTTTAAGAAAAACAATCTCAAGTGAGA
TAAATTGT
Found at i:450629 original size:54 final size:53
Alignment explanation
Indices: 450517--450668 Score: 191
Period size: 54 Copynumber: 2.9 Consensus size: 53
450507 TCATTGGTTC
** * * * *
450517 GTAAAACATTTGACAACACATTCATCCAGT-TGTGGCTTATGCACAGATGTTT
1 GTAAAACATTTGACAACACATTCATCCTTTCTGTGGCTTCTACACAAATATTT
450569 GTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTACACAAATATTT
1 GTAAAACATTTGACAACACATTCATCCTTTC-TGTGGCTTCTACACAAATATTT
* * *
450623 GTAAAACATTTGACAA-ATATTCATCCTTTTCTGTGGTTTCTTCACA
1 GTAAAACATTTGACAACACATTCATCC-TTTCTGTGGCTTCTACACA
450669 GATTTCTGCT
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
52 28 0.32
53 22 0.25
54 38 0.43
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (53 bp):
GTAAAACATTTGACAACACATTCATCCTTTCTGTGGCTTCTACACAAATATTT
Found at i:451667 original size:30 final size:30
Alignment explanation
Indices: 451631--451695 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
451621 TTAATCCATG
*
451631 AAGTTAGTAGTTTACAACTTTTTCATTATT
1 AAGTTAGTAGTTTACAACTTTTTCATTATA
451661 AAGTTAGTAGTTTACAACTTTTTCATTATA
1 AAGTTAGTAGTTTACAACTTTTTCATTATA
451691 AAGTT
1 AAGTT
451696 TGCCCTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (30 bp):
AAGTTAGTAGTTTACAACTTTTTCATTATA
Found at i:468825 original size:41 final size:40
Alignment explanation
Indices: 468771--468848 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 40
468761 GATGAAAAAA
468771 ATGAAAAAAGAAAAAGAAAAAAAGAG-AAAATAAAAAATG
1 ATGAAAAAAGAAAAAGAAAAAAAGAGCAAAATAAAAAATG
*
468810 ATGAAGAAAATGAAAAAGAAAAAAAGAGCAAAATGAAAA
1 ATGAA-AAAA-GAAAAAGAAAAAAAGAGCAAAATAAAAA
468849 GGAAAAAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 5 0.14
40 4 0.11
41 17 0.49
42 9 0.26
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (40 bp):
ATGAAAAAAGAAAAAGAAAAAAAGAGCAAAATAAAAAATG
Found at i:468846 original size:23 final size:23
Alignment explanation
Indices: 468816--468859 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
468806 AATGATGAAG
468816 AAAATGAAAAAGAAAAAAAGAGC
1 AAAATGAAAAAGAAAAAAAGAGC
*
468839 AAAATGAAAAGGAAAAAAAGA
1 AAAATGAAAAAGAAAAAAAGA
468860 AAAGGAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (23 bp):
AAAATGAAAAAGAAAAAAAGAGC
Found at i:468855 original size:48 final size:48
Alignment explanation
Indices: 468754--468855 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
468744 TTCGCTTAAA
* *
468754 GAAAAATGATGAAAAAAATGAAAAAAGAAAAAGAAAAAAAGAGAAAAT
1 GAAAAATGATGAAAAAAATGAAAAAAAAAAAAGAAAAAAAGAGAAAAG
* * ** *
468802 AAAAAATGATGAAGAAAATGAAAAAGAAAAAAAGAGCAAAA-TGAAAAG
1 GAAAAATGATGAAAAAAATGAAAAA-AAAAAAAGAAAAAAAGAGAAAAG
468850 GAAAAA
1 GAAAAA
468856 AAGAAAAGGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
48 33 0.73
49 12 0.27
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.08
Consensus pattern (48 bp):
GAAAAATGATGAAAAAAATGAAAAAAAAAAAAGAAAAAAAGAGAAAAG
Found at i:468879 original size:71 final size:71
Alignment explanation
Indices: 468768--468938 Score: 195
Period size: 70 Copynumber: 2.3 Consensus size: 71
468758 AATGATGAAA
*
468768 AAAATGAAAAAAGAAAAAGAAAAAAAGAGAAAATAAAAAAT-GATGAAGAAAATGAAAAAGAAAA
1 AAAATGAAAAAAGAAAAAGAAAAAAAGAGAAAATAAAAAATGGAAGAA-AAAATGAAAAAGAAAA
468832 AAAGAGC
65 AAAGAGC
* * *
468839 AAAATG-AAAAGGAAAAA-AAGAAAAGGAGAAAATAGGAAAATGGAAGAAAAAATGAAAAAGAAA
1 AAAATGAAAAAAGAAAAAGAA-AAAAAGAGAAAATA-AAAAATGGAAGAAAAAATGAAAAAG--A
*
468902 AACGAAAAGAGA
62 AA--AAAAGAGC
*
468914 AAAATGAAAAATGAAAAATGAAAAA
1 AAAATGAAAAAAGAAAAA-GAAAAA
468939 TGAAAAATGA
Statistics
Matches: 84, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
69 2 0.02
70 23 0.27
71 23 0.27
72 5 0.06
73 3 0.04
75 13 0.15
76 10 0.12
77 3 0.04
78 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (71 bp):
AAAATGAAAAAAGAAAAAGAAAAAAAGAGAAAATAAAAAATGGAAGAAAAAATGAAAAAGAAAAA
AAGAGC
Found at i:468960 original size:14 final size:14
Alignment explanation
Indices: 468831--468966 Score: 118
Period size: 14 Copynumber: 9.4 Consensus size: 14
468821 GAAAAAGAAA
*
468831 AAAAGAGCAAAATG
1 AAAAGAGAAAAATG
*
468845 AAAAG-GAAAAAAAG
1 AAAAGAG-AAAAATG
*
468859 AAAAGGAGAAAATAGG
1 AAAA-GAGAAAA-ATG
468875 AAAATGGAAGAAAAAATG
1 AAAA--G-AG-AAAAATG
*
468893 AAAA-AGAAAAACG
1 AAAAGAGAAAAATG
468906 AAAAGAGAAAAATG
1 AAAAGAGAAAAATG
468920 AAAA-ATGAAAAATG
1 AAAAGA-GAAAAATG
468934 AAAA-ATGAAAAATG
1 AAAAGA-GAAAAATG
*
468948 AAAAGAGAAAAATA
1 AAAAGAGAAAAATG
468962 AAAAG
1 AAAAG
468967 GGGGTTCAAG
Statistics
Matches: 105, Mismatches: 7, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
13 12 0.11
14 66 0.63
15 6 0.06
16 7 0.07
17 2 0.02
18 8 0.08
19 4 0.04
ACGTcount: A:0.71, C:0.01, G:0.20, T:0.07
Consensus pattern (14 bp):
AAAAGAGAAAAATG
Found at i:468965 original size:7 final size:7
Alignment explanation
Indices: 468767--468965 Score: 107
Period size: 7 Copynumber: 28.7 Consensus size: 7
468757 AAATGATGAA
468767 AAAAATG
1 AAAAATG
*
468774 AAAAAAG
1 AAAAATG
468781 AAAAA-G
1 AAAAATG
*
468787 AAAAAAAG
1 -AAAAATG
*
468795 AGAAAATA
1 A-AAAATG
468803 AAAAATG
1 AAAAATG
**
468810 ATGAA-G
1 AAAAATG
468816 -AAAATG
1 AAAAATG
468822 AAAAA-G
1 AAAAATG
*
468828 AAAAAAAG
1 -AAAAATG
468836 AGCAAAATG
1 A--AAAATG
*
468845 -AAAAGG
1 AAAAATG
*
468851 AAAAA-A
1 AAAAATG
*
468857 AGAAAAGG
1 A-AAAATG
468865 AGAAAATAG
1 A-AAAAT-G
*
468874 GAAAATG
1 AAAAATG
* *
468881 GAAGA--
1 AAAAATG
468886 AAAAATG
1 AAAAATG
468893 AAAAA-G
1 AAAAATG
*
468899 AAAAACG
1 AAAAATG
468906 AAAAGA-G
1 AAAA-ATG
468913 AAAAATG
1 AAAAATG
468920 AAAAATG
1 AAAAATG
468927 AAAAATG
1 AAAAATG
468934 AAAAATG
1 AAAAATG
468941 AAAAATG
1 AAAAATG
468948 AAAAGA-G
1 AAAA-ATG
468955 AAAAAT-
1 AAAAATG
468961 AAAAA
1 AAAAA
468966 GGGGGTTCAA
Statistics
Matches: 155, Mismatches: 17, Indels: 41
0.73 0.08 0.19
Matches are distributed among these distances:
5 5 0.03
6 23 0.15
7 101 0.65
8 20 0.13
9 6 0.04
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.08
Consensus pattern (7 bp):
AAAAATG
Found at i:470429 original size:55 final size:55
Alignment explanation
Indices: 470298--470606 Score: 342
Period size: 55 Copynumber: 5.7 Consensus size: 55
470288 TTTATGAAGA
* *
470298 TCGAGTTCTATACTCTCTGATGGAATGGAGAGCGGACCCGTTTGTTGAAGA----
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * * *
470349 TCGAGTTCTATACTCTCTGATGGAATAGAGGGCAGACCCGTTTGTTGAAGAGTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* *
470404 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGTGGACCCATTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * *
470459 TCGAGTTCTACACTCTCTGAAGGAATAGAGAGCGGACACGTTTATTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * * *** * * * *
470514 TCGAG-TCTTATACTCCCTGAACGAATAGGGAGAACACACATTTGCTGAAGATTAT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * *
470569 TCGAG-TCTTATACTCCCTGAAGGAATAGGGAGTGGACC
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACC
470607 AGTCATTCGA
Statistics
Matches: 223, Mismatches: 30, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
51 48 0.22
54 2 0.01
55 173 0.78
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
Done.