Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_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: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1072403 original size:695 final size:691
Alignment explanation
Indices: 1071249--1073009 Score: 2452
Period size: 696 Copynumber: 2.5 Consensus size: 691
1071239 CTGCCCTTTC
* *
1071249 GGTACTAATTTAATTTTCAGTTGTCTTAAATAAAAAAATTGCAAGTTAAATTTAAAAGTAAAAAT
1 GGTACTAATTTAATTTTCAGTTGTCTTAATTAAGAAAATTGCAAGTTAAATTTAAAAGTAAAAAT
* * *
1071314 TCGATTCAAATTACTTACAGCTAATCGATTTAAAAGAGTACCCCTAAAATATCAAAAAACGTTAG
66 TCGATTCAAATTACTTACCG-TAATCG-TTTAAAAGAGTACCCCTAAAAGATCAAAAAGCGTTAG
**
1071379 ATTTGTAAAATAAAAATACTGAATTAAAAAGAAAAGATAACTATTACATTATGATTCGTTAAAGA
129 ATTTGTAAAATAAAAATACTGAATTAAAAAGAAAAGATAAAGATTACATTATGATTCGTTAAAGA
* *
1071444 TAGATCATACATATCGAAAACATGAAGTAATAG---AAAAAAATAATGTAAAGACAAGGGCCAAT
194 TAGATCATACATATCGAAAACATGAAGTAATAGAAAAAAAAAATAATGTAAAGACAAGAGCCGAT
*
1071506 TAAATTAAGAAT-AAAAATGCAAATTGAGAAATTAAATATAAACAAAGACATAAAAAAATGGGAA
259 TAAATTAAGAATAAAAAATGC-AATTGAGAAATTAAATATAAACAAAGACA-CAAAAAAT-----
*
1071570 AAAAAAAGAAAAATAAAAATAACAGAAATAAAATAAAAAAATACATACCCAAAAAATTATCTAAA
317 -------GAAAAA-AAAAATAACATAAATAAAAT-AAAAAATACATACCCAAAAAATTATCTAAA
*
1071635 TTGAAAAGAGGAAAAAATAAAAAAAATAAAATCAATGAAAATAATATGAAATTGAAACAAAATAA
373 TTGAAAAGAGGAAAAAATAAAAAAAATAAAATCAATGAAAATAATATGAAAATGAAACAAAATAA
* * *
1071700 AAATATAAAACCCTAAAAAATTCTAGTTAATTGATTTAAAGACACAAAAAATTAAGAAT-AAAAA
438 AAATATAAAACCCTAAAAAAATCCAATTAATTGATTTAAAGACACAAAAAATTAAGAATAAAAAA
* *
1071764 ATGCCAATTGAGAAATTAAATGTAAATAAAGACACAAAAAATG-AAAAAAAAATAAAAATAACAG
503 ATGCCAATTGAGAAATTAAATATAAACAAAGACA-AAAAAATGAAAAAAAAAATAAAAATAACAG
*
1071828 AAA-AAAAT-AA-AAAAGACATACCC-AAAAATTATCTAAATTGAAAAGAGG-AAA-AAAAT-AA
567 AAATAAAATAAATAAAAGACATACCCAAAAAAGTATCTAAATTGAAAAGAGGAAAATAAAATCAA
* *
1071886 -AAA-AATGAAATTAATATGAAATTGTAACAAAATAAAAATATAAAACCCTAAAAAAATTT
632 GAAACAATGAAATTAATATGAAAATGAAACAAAATAAAAATATAAAACCC-AAAAAAATTT
* * * * * *
1071945 GGTACTAATTTAATTTCCAATTTTATTAATTAAGAATATTGCAAGATAAATTTAAAAGTAAAAAT
1 GGTACTAATTTAATTTTCAGTTGTCTTAATTAAGAAAATTGCAAGTTAAATTTAAAAGTAAAAAT
1072010 TCGATTCAAATTACTTACCGTTAATCGGTTTAAAAGAGTACCCCTAAAAGATCAAAAAGCGTTAG
66 TCGATTCAAATTACTTACCG-TAATC-GTTTAAAAGAGTACCCCTAAAAGATCAAAAAGCGTTAG
* *
1072075 ATTTGTAAAATAAAAATAC-AAATTAAAAAGAAAAGATAAAGATTACATTATGATTTGTTAAAGA
129 ATTTGTAAAATAAAAATACTGAATTAAAAAGAAAAGATAAAGATTACATTATGATTCGTTAAAGA
1072139 TAGATCATACATATCGAAAACATGAAGTAATAGAAAAAGAAAAATAATGTAAAGACAAGAGCCGA
194 TAGATCATACATATCGAAAACATGAAGTAATAGAAAAA-AAAAATAATGTAAAGACAAGAGCCGA
*
1072204 TTAAATTAAGAATAGAAAAATGTCAACTGAGAAATTAAATATAAACAAAGACACAAAAAATGAAA
258 TTAAATTAAGAATA-AAAAATG-CAATTGAGAAATTAAATATAAACAAAGACACAAAAAATGAAA
*
1072269 TAAAAAAATAACATAAATAAAATAAAAAATTCATACCCAAAAAATTATCTAAATTGAAAAGAGGA
321 -AAAAAAATAACATAAATAAAATAAAAAATACATACCCAAAAAATTATCTAAATTGAAAAGAGGA
*
1072334 AAAAAT-AAAAAAATAAAATCAATGAAATTAATGAAATTAATATGAAAATGAAACAAAATAAATA
385 AAAAATAAAAAAAATAAAATCAATG------A--AAA-TAATATGAAAATGAAACAAAATAAAAA
1072398 TATAAAACCCTAAAAAAATCCAATTAATTGATTTAAAGACACAAAAAATTAAGAATAAAAAAATG
441 TATAAAACCCTAAAAAAATCCAATTAATTGATTTAAAGACACAAAAAATTAAGAATAAAAAAATG
* *
1072463 CTAATTGAGAAATTAAATATAAACAAAGACATAAAAATGAAAAAAAAAATAAAAATAACAGAAAT
506 CCAATTGAGAAATTAAATATAAACAAAGACAAAAAAATGAAAAAAAAAATAAAAATAACAGAAAT
*
1072528 AAAATAAAATAAAATACATACCCAAAAAAGTATCTAAATTGAAAAGAGGATAAAATAAAAAAATA
571 AAAAT-AAATAAAAGACATACCCAAAAAAGTATCTAAATTGAAAAGAGG----------AAAATA
*
1072593 AAATCAATGAAATCAATGAAATTAATATGAAAATGAAACAAAATAAAAATATAAAACCCAAAAAC
625 AAATCAA-GAAA-CAATGAAATTAATATGAAAATGAAACAAAATAAAAATATAAAACCCAAAAAA
1072658 ATTT
688 ATTT
* * *
1072662 GGTCACTAACTTAATTTTCAGTTGTCTTAATTAAGAAAATTACAAGTTAAATTAAAAAGTAAAAA
1 GGT-ACTAATTTAATTTTCAGTTGTCTTAATTAAGAAAATTGCAAGTTAAATTTAAAAGTAAAAA
*
1072727 TTCGATTCAAATTACTTACCG--A---TTTAAAAGAGTACCCCTGAAAGATCAAAAAGCGTTAGA
65 TTCGATTCAAATTACTTACCGTAATCGTTTAAAAGAGTACCCCTAAAAGATCAAAAAGCGTTAGA
*
1072787 TTTGTAAAACTAAAAATACTGAATTAAAAAGAAAAGATAAAGATTACATTATGATTCATTAAAGA
130 TTTGTAAAA-TAAAAATACTGAATTAAAAAGAAAAGATAAAGATTACATTATGATTCGTTAAAGA
* * * *
1072852 CAGATCATACATATCGAAAACATGAAGTAATATAAAAATAAAAACAATGTAAAGACAAGAGTCGA
194 TAGATCATACATATCGAAAACATGAAGTAATAGAAAAA-AAAAATAATGTAAAGACAAGAGCCGA
1072917 TTAAATTAAGAATAAAAAAATGCCAATTGAGAAATTAAATATAAACAAAGACACAAAAAATGAAA
258 TTAAATTAAGAAT-AAAAAATG-CAATTGAGAAATTAAATATAAACAAAGACACAAAAAATGAAA
* *
1072982 AAAATAAAGAAAAATAAA-AAAATAAAAA
321 AAAA-AAA-TAACATAAATAAAATAAAAA
1073010 TAAAAATAAC
Statistics
Matches: 959, Mismatches: 58, Indels: 79
0.88 0.05 0.07
Matches are distributed among these distances:
686 18 0.02
687 47 0.05
688 23 0.02
689 2 0.00
692 1 0.00
694 3 0.00
695 159 0.17
696 195 0.20
697 6 0.01
698 2 0.00
699 39 0.04
700 19 0.02
701 59 0.06
702 1 0.00
711 46 0.05
712 16 0.02
713 181 0.19
714 10 0.01
715 1 0.00
716 3 0.00
717 12 0.01
718 116 0.12
ACGTcount: A:0.58, C:0.09, G:0.10, T:0.23
Consensus pattern (691 bp):
GGTACTAATTTAATTTTCAGTTGTCTTAATTAAGAAAATTGCAAGTTAAATTTAAAAGTAAAAAT
TCGATTCAAATTACTTACCGTAATCGTTTAAAAGAGTACCCCTAAAAGATCAAAAAGCGTTAGAT
TTGTAAAATAAAAATACTGAATTAAAAAGAAAAGATAAAGATTACATTATGATTCGTTAAAGATA
GATCATACATATCGAAAACATGAAGTAATAGAAAAAAAAAATAATGTAAAGACAAGAGCCGATTA
AATTAAGAATAAAAAATGCAATTGAGAAATTAAATATAAACAAAGACACAAAAAATGAAAAAAAA
AATAACATAAATAAAATAAAAAATACATACCCAAAAAATTATCTAAATTGAAAAGAGGAAAAAAT
AAAAAAAATAAAATCAATGAAAATAATATGAAAATGAAACAAAATAAAAATATAAAACCCTAAAA
AAATCCAATTAATTGATTTAAAGACACAAAAAATTAAGAATAAAAAAATGCCAATTGAGAAATTA
AATATAAACAAAGACAAAAAAATGAAAAAAAAAATAAAAATAACAGAAATAAAATAAATAAAAGA
CATACCCAAAAAAGTATCTAAATTGAAAAGAGGAAAATAAAATCAAGAAACAATGAAATTAATAT
GAAAATGAAACAAAATAAAAATATAAAACCCAAAAAAATTT
Found at i:1072628 original size:244 final size:236
Alignment explanation
Indices: 1072206--1072656 Score: 708
Period size: 244 Copynumber: 1.9 Consensus size: 236
1072196 AGAGCCGATT
* *
1072206 AAATTAAGAATAGAAAAATGTCAACTGAGAAATTAAATATAAACAAAGACACAAAAAATGAAATA
1 AAATTAAGAATAAAAAAATGTCAACTGAGAAATTAAATATAAACAAAGACACAAAAAATGAAAAA
* * *
1072271 AAAAAATAACATAAATAAAATAAAAAATTCATACCCAAAAAATTATCTAAATTGAAAAGAGGAAA
66 AAAAAATAACAGAAATAAAATAAAAAATACATACCCAAAAAAGTATCTAAATTGAAAAGAGGAAA
* *
1072336 AAATAAAAAAATAAAATCAATGAAATTAATGAAATTAATATGAAAATGAAACAAAATAAATATAT
131 AAATAAAAAAATAAAATCAATGAAATCAATGAAATTAATATGAAAATGAAACAAAATAAAAATAT
1072401 AAAACCCTAAAAAAATCCAATTAATTGATTTAAAGACACAAA
196 AAAACCC-AAAAAAATCCAATTAATTGATTTAAAGACACAAA
* *
1072443 AAATTAAGAATAAAAAAATG-CTAATTGAGAAATTAAATATAAACAAAGACA-TAAAAATGAAAA
1 AAATTAAGAATAAAAAAATGTC-AACTGAGAAATTAAATATAAACAAAGACACAAAAAATG----
1072506 AAAAAATAAAAATAACAGAAATAAAATAAAATAAAATACATACCCAAAAAAGTATCTAAATTGAA
61 AAAAAA-AAAAATAACAGAAATAAAAT--AA-AAAATACATACCCAAAAAAGTATCTAAATTGAA
*
1072571 AAGAGGATAAAATAAAAAAATAAAATCAATGAAATCAATGAAATTAATATGAAAATGAAACAAAA
122 AAGAGGAAAAAATAAAAAAATAAAATCAATGAAATCAATGAAATTAATATGAAAATGAAACAAAA
1072636 TAAAAATATAAAACCCAAAAA
187 TAAAAATATAAAACCCAAAAA
1072657 CATTTGGTCA
Statistics
Matches: 195, Mismatches: 10, Indels: 12
0.90 0.05 0.06
Matches are distributed among these distances:
236 8 0.04
237 47 0.24
240 5 0.03
241 19 0.10
243 7 0.04
244 109 0.56
ACGTcount: A:0.65, C:0.08, G:0.07, T:0.20
Consensus pattern (236 bp):
AAATTAAGAATAAAAAAATGTCAACTGAGAAATTAAATATAAACAAAGACACAAAAAATGAAAAA
AAAAAATAACAGAAATAAAATAAAAAATACATACCCAAAAAAGTATCTAAATTGAAAAGAGGAAA
AAATAAAAAAATAAAATCAATGAAATCAATGAAATTAATATGAAAATGAAACAAAATAAAAATAT
AAAACCCAAAAAAATCCAATTAATTGATTTAAAGACACAAA
Found at i:1072985 original size:9 final size:8
Alignment explanation
Indices: 1072971--1073036 Score: 55
Period size: 9 Copynumber: 7.6 Consensus size: 8
1072961 ACAAAGACAC
1072971 AAAAAATGA
1 AAAAAAT-A
1072980 AAAAAATAA
1 AAAAAAT-A
1072989 AGAAAAATA
1 A-AAAAATA
1072998 AAAAAATA
1 AAAAAATA
1073006 AAAATAA-A
1 AAAA-AATA
1073014 AATAACAA-A
1 AA-AA-AATA
1073023 AATAAAATA
1 AA-AAAATA
1073032 AAAAA
1 AAAAA
1073037 TGCATACCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
8 19 0.37
9 26 0.51
10 6 0.12
ACGTcount: A:0.83, C:0.02, G:0.03, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:1073000 original size:6 final size:6
Alignment explanation
Indices: 1072981--1073035 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
1072971 AAAAAATGAA
*
1072981 AAAAAT AAAGAA- AAATAA- AAAAAT AAAAAT AAAAAT AACAAAA ATAAAAT
1 AAAAAT AAA-AAT AAA-AAT AAAAAT AAAAAT AAAAAT AA-AAAT A-AAAAT
1073031 AAAAA
1 AAAAA
1073036 ATGCATACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
5 2 0.05
6 29 0.69
7 10 0.24
8 1 0.02
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:1073002 original size:20 final size:19
Alignment explanation
Indices: 1072972--1073028 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1072962 CAAAGACACA
*
1072972 AAAAATGAAAAAAATAAAG
1 AAAAATAAAAAAAATAAAG
* *
1072991 AAAAATAAAAAAATAAAAAT
1 AAAAATAAAAAAA-ATAAAG
*
1073011 AAAAATAACAAAAATAAA
1 AAAAATAAAAAAAATAAA
1073029 ATAAAAAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.12
Consensus pattern (19 bp):
AAAAATAAAAAAAATAAAG
Found at i:1073029 original size:20 final size:19
Alignment explanation
Indices: 1072972--1073035 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 19
1072962 CAAAGACACA
*
1072972 AAAAATGAAAAAAAT-AAAG
1 AAAAAT-AAAAAAATAAAAT
1072991 AAAAATAAAAAAATAAAAAT
1 AAAAATAAAAAAAT-AAAAT
1073011 AAAAATAACAAAAATAAAAT
1 AAAAATAA-AAAAATAAAAT
1073031 AAAAA
1 AAAAA
1073036 ATGCATACCC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 8 0.20
19 6 0.15
20 21 0.51
21 6 0.15
ACGTcount: A:0.83, C:0.02, G:0.03, T:0.12
Consensus pattern (19 bp):
AAAAATAAAAAAATAAAAT
Found at i:1073030 original size:14 final size:13
Alignment explanation
Indices: 1072973--1073036 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 13
1072963 AAAGACACAA
1072973 AAAATGAAAAAAAT
1 AAAAT-AAAAAAAT
1072987 AAAGA-AAAATAAA-
1 AAA-ATAAAA-AAAT
*
1073000 AAAATAAAAATA-
1 AAAATAAAAAAAT
1073012 AAAATAACAAAAAT
1 AAAATAA-AAAAAT
1073026 AAAATAAAAAA
1 AAAATAAAAAA
1073037 TGCATACCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
12 10 0.23
13 19 0.44
14 13 0.30
15 1 0.02
ACGTcount: A:0.83, C:0.02, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:1074530 original size:17 final size:17
Alignment explanation
Indices: 1074467--1074530 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
1074457 ACATATGATA
1074467 AATATATAATATAAATAT
1 AATATAT-ATATAAATAT
* * *
1074485 -ATGTA-ACATACTATAT
1 AATATATATATA-AATAT
* *
1074501 AATATAAAGATAAATAT
1 AATATATATATAAATAT
1074518 AATATATATATAA
1 AATATATATATAA
1074531 TGGTATAATG
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
15 4 0.11
16 4 0.11
17 23 0.66
18 4 0.11
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AATATATATATAAATAT
Found at i:1075509 original size:115 final size:115
Alignment explanation
Indices: 1075354--1075569 Score: 344
Period size: 115 Copynumber: 1.9 Consensus size: 115
1075344 TATGATATTC
1075354 TTCGTTGTGAAGTCGAAATCGTAGGTGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATC
1 TTCGTTGTGAAGTCGAAATCGTAGGTGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATC
* *
1075419 CTTCATTATTAAGTTGAAATCCAATCTTGTAAATTGAATCGCTTTGAGAT
66 CTTCATTATGAAGTTGAAATCCAATCTTGAAAATTGAATCGCTTTGAGAT
* * *
1075469 TTCGTTGTGAAGTGGGAATTGT-GGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATAT
1 TTCGTTGTGAAGTCGAAATCGTAGG-TGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATAT
* * *
1075533 CCTTCGTTGTGAAGTTGAAATTCAATCTTGAAAATTG
65 CCTTCATTATGAAGTTGAAATCCAATCTTGAAAATTG
1075570 TATTGTCTCG
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 2 0.02
115 90 0.98
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.38
Consensus pattern (115 bp):
TTCGTTGTGAAGTCGAAATCGTAGGTGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATC
CTTCATTATGAAGTTGAAATCCAATCTTGAAAATTGAATCGCTTTGAGAT
Found at i:1075814 original size:31 final size:28
Alignment explanation
Indices: 1075722--1075827 Score: 74
Period size: 31 Copynumber: 3.6 Consensus size: 28
1075712 GATCTATAGG
1075722 TGAATCTTCAATCTCTGGTTGTTGGTCCTGA
1 TGAATCTT-AAT-TCTGGTT-TTGGTCCTGA
* * *
1075753 TGACTCTTGATTCTGGAATCTTTGG---AGA
1 TGAATCTTAATTCTGG--T-TTTGGTCCTGA
1075781 TGAATCTTCAATCTCTGGTTTTCGGTCCTGA
1 TGAATCTT-AAT-TCTGGTTTT-GGTCCTGA
*
1075812 TGACTCTTAATTCTGG
1 TGAATCTTAATTCTGG
1075828 AATCTTGAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
27 3 0.05
28 12 0.20
29 12 0.20
30 10 0.17
31 21 0.36
32 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.42
Consensus pattern (28 bp):
TGAATCTTAATTCTGGTTTTGGTCCTGA
Found at i:1075814 original size:59 final size:59
Alignment explanation
Indices: 1075722--1075833 Score: 199
Period size: 59 Copynumber: 1.9 Consensus size: 59
1075712 GATCTATAGG
*
1075722 TGAATCTTCAATCTCTGGTTGTTGGTCCTGATGACTCTTGATTCTGGAATCTTTGGAGA
1 TGAATCTTCAATCTCTGGTTGTTGGTCCTGATGACTCTTAATTCTGGAATCTTTGGAGA
1075781 TGAATCTTCAATCTCTGGTT-TTCGGTCCTGATGACTCTTAATTCTGGAATCTT
1 TGAATCTTCAATCTCTGGTTGTT-GGTCCTGATGACTCTTAATTCTGGAATCTT
1075834 GAATTTTTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
58 2 0.04
59 49 0.96
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (59 bp):
TGAATCTTCAATCTCTGGTTGTTGGTCCTGATGACTCTTAATTCTGGAATCTTTGGAGA
Found at i:1076497 original size:44 final size:44
Alignment explanation
Indices: 1076430--1076514 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
1076420 TGGACCCACC
* * *
1076430 TTTTTTTCAATTTAAGGTTCCCTTTCAGATTTTCACCCTAAACA
1 TTTTTTTCAACTTAAAGTGCCCTTTCAGATTTTCACCCTAAACA
* *
1076474 TTTTTTTCAACTTAAAGTGCCCTTTCAGGTTTTCATCCTAA
1 TTTTTTTCAACTTAAAGTGCCCTTTCAGATTTTCACCCTAA
1076515 GAGAAATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (44 bp):
TTTTTTTCAACTTAAAGTGCCCTTTCAGATTTTCACCCTAAACA
Found at i:1079331 original size:3 final size:3
Alignment explanation
Indices: 1079323--1079362 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1079313 TAATTATTTG
* *
1079323 TAA TAA TAA TAA TAA TAG TAA T-A TAG TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1079363 TATATATGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1079692 original size:36 final size:35
Alignment explanation
Indices: 1079548--1079712 Score: 140
Period size: 36 Copynumber: 4.7 Consensus size: 35
1079538 TTCACTACTT
*
1079548 TTCACTACT-TTTCTGTGAAGGCTTATAATGATTTAC
1 TTCACTACTCTTTC-GTGAAGG-TTAGAATGATTTAC
* * * **
1079584 TTCACTACTCTTTTGTGAAGGCTGGGCTG-TTCTAC
1 TTCACTACTCTTTCGTGAAGGTTAGAATGATT-TAC
* *
1079619 TTCACTACTC-TTCCTGAAGGTCAGAATTGCA-TTAC
1 TTCACTACTCTTTCGTGAAGGTTAGAA-TG-ATTTAC
*
1079654 TTCACTACTCTTTCGTGAAGGTTAAGAATGATTGAC
1 TTCACTACTCTTTCGTGAAGGTT-AGAATGATTTAC
* * *
1079690 TTCAATAATCTTCCGTGAAGGTT
1 TTCACTACTCTTTCGTGAAGGTT
1079713 GGATTACACT
Statistics
Matches: 102, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
34 11 0.11
35 32 0.31
36 52 0.51
37 7 0.07
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (35 bp):
TTCACTACTCTTTCGTGAAGGTTAGAATGATTTAC
Found at i:1079924 original size:20 final size:19
Alignment explanation
Indices: 1079893--1080110 Score: 222
Period size: 20 Copynumber: 10.9 Consensus size: 19
1079883 TTGACAGATG
* *
1079893 ACCCGAAGGATTTACAAATT
1 ACCCG-AGGTTTTACAAATA
* * *
1079913 ACCTAGAGGATTTACAAATG
1 ACC-CGAGGTTTTACAAATA
*
1079933 ACCCGGAGGTTTTACAAATG
1 ACCC-GAGGTTTTACAAATA
*
1079953 ACCCGACGGTTTTACAAATG
1 ACCCGA-GGTTTTACAAATA
1079973 ACCCGAAGGTTTTACAAATA
1 ACCCG-AGGTTTTACAAATA
1079993 ACCCGGAGGTTTTACAAATA
1 ACCC-GAGGTTTTACAAATA
1080013 ACCCGAAGGTTTTACAAATA
1 ACCCG-AGGTTTTACAAATA
1080033 ACCCGGAGGTTTTACAAATA
1 ACCC-GAGGTTTTACAAATA
* * *
1080053 ACCCAAAGATTTTACAAATG
1 ACCC-GAGGTTTTACAAATA
1080073 ACCCGAAGG-TTTACAAATA
1 ACCCG-AGGTTTTACAAATA
* *
1080092 ACCTGGAGGATTTACAAAT
1 ACC-CGAGGTTTTACAAAT
1080111 TTATGGGAAA
Statistics
Matches: 175, Mismatches: 13, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
19 18 0.10
20 153 0.87
21 4 0.02
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (19 bp):
ACCCGAGGTTTTACAAATA
Found at i:1079947 original size:40 final size:39
Alignment explanation
Indices: 1079893--1080110 Score: 258
Period size: 40 Copynumber: 5.5 Consensus size: 39
1079883 TTGACAGATG
* * * * *
1079893 ACCCGAAGGATTTACAAATTACCTAGAGGATTTACAAATG
1 ACCCGAAGGTTTTACAAATAACC-CGAGGTTTTACAAATA
* * *
1079933 ACCCGGAGGTTTTACAAATGACCCGACGGTTTTACAAATG
1 ACCCGAAGGTTTTACAAATAACCCGA-GGTTTTACAAATA
1079973 ACCCGAAGGTTTTACAAATAACCCGGAGGTTTTACAAATA
1 ACCCGAAGGTTTTACAAATAACCC-GAGGTTTTACAAATA
1080013 ACCCGAAGGTTTTACAAATAACCCGGAGGTTTTACAAATA
1 ACCCGAAGGTTTTACAAATAACCC-GAGGTTTTACAAATA
* * *
1080053 ACCCAAAGATTTTACAAATGACCCGAAGG-TTTACAAATA
1 ACCCGAAGGTTTTACAAATAACCCG-AGGTTTTACAAATA
* * *
1080092 ACCTGGAGGATTTACAAAT
1 ACCCGAAGGTTTTACAAAT
1080111 TTATGGGAAA
Statistics
Matches: 159, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 27 0.17
40 130 0.82
41 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (39 bp):
ACCCGAAGGTTTTACAAATAACCCGAGGTTTTACAAATA
Found at i:1079987 original size:60 final size:60
Alignment explanation
Indices: 1079890--1080110 Score: 284
Period size: 60 Copynumber: 3.7 Consensus size: 60
1079880 ACATTGACAG
* * * *
1079890 ATGACCCGAAGGATTTACAAATTA-CCTAGAGGATTTACAAATGACCCGGAGGTTTTACAA
1 ATGACCCGAAGGTTTTACAAATAACCCGA-AGGATTTACAAATAACCCGGAGGTTTTACAA
* * *
1079950 ATGACCCGACGGTTTTACAAATGACCCGAAGGTTTTACAAATAACCCGGAGGTTTTACAA
1 ATGACCCGAAGGTTTTACAAATAACCCGAAGGATTTACAAATAACCCGGAGGTTTTACAA
* * * ** *
1080010 ATAACCCGAAGGTTTTACAAATAACCCGGAGGTTTTACAAATAACCCAAAGATTTTACAA
1 ATGACCCGAAGGTTTTACAAATAACCCGAAGGATTTACAAATAACCCGGAGGTTTTACAA
* *
1080070 ATGACCCGAAGG-TTTACAAATAACCTGGAGGATTTACAAAT
1 ATGACCCGAAGGTTTTACAAATAACCCGAAGGATTTACAAAT
1080111 TTATGGGAAA
Statistics
Matches: 144, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
59 27 0.19
60 114 0.79
61 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (60 bp):
ATGACCCGAAGGTTTTACAAATAACCCGAAGGATTTACAAATAACCCGGAGGTTTTACAA
Found at i:1083132 original size:21 final size:24
Alignment explanation
Indices: 1083072--1083133 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 24
1083062 CTTGATTCAA
*
1083072 TTTCTTTCCCTTTTTTTCATCTATC
1 TTTCTTT-TCTTTTTTTCATCTATC
1083097 TTT-TTCTTC-TTTTTT-AT-TAT-
1 TTTCTT-TTCTTTTTTTCATCTATC
1083117 TTTCTTTTCTTTTTTTC
1 TTTCTTTTCTTTTTTTC
1083134 TGATGGATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
20 6 0.19
21 11 0.34
22 2 0.06
23 6 0.19
24 3 0.09
25 4 0.12
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTCTTTTCTTTTTTTCATCTATC
Found at i:1087660 original size:13 final size:13
Alignment explanation
Indices: 1087642--1087675 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1087632 CCGGCAGTCT
*
1087642 ATCACCGTCGCTG
1 ATCACCGTCGCCG
*
1087655 ATCACCGCCGCCG
1 ATCACCGTCGCCG
1087668 ATCACCGT
1 ATCACCGT
1087676 TTATGGTGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.18, C:0.44, G:0.21, T:0.18
Consensus pattern (13 bp):
ATCACCGTCGCCG
Found at i:1095541 original size:24 final size:24
Alignment explanation
Indices: 1095497--1095542 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1095487 CTGTTCAATT
*
1095497 ATGTATTTATTTATTTATTTATAC
1 ATGTATTTATTTATATATTTATAC
*
1095521 ATGTATTGTATTT-TATCTTTAT
1 ATGTATT-TATTTATATATTTAT
1095543 TTTTTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (24 bp):
ATGTATTTATTTATATATTTATAC
Found at i:1098020 original size:21 final size:19
Alignment explanation
Indices: 1097982--1098027 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1097972 AATTAATCCT
1097982 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
1098002 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
1098023 A-TAAT
1 ACTAAT
1098028 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:1115989 original size:21 final size:21
Alignment explanation
Indices: 1115946--1115996 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1115936 TTGAGAAATT
*
1115946 AAATATAAACAAAGACACAAA
1 AAATAAAAACAAAGACACAAA
1115967 AAATTAAAAACAAAGA-A-AGAA
1 AAA-TAAAAACAAAGACACA-AA
1115988 AAATAAAAA
1 AAATAAAAA
1115997 TAACATACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.76, C:0.08, G:0.06, T:0.10
Consensus pattern (21 bp):
AAATAAAAACAAAGACACAAA
Found at i:1117690 original size:76 final size:77
Alignment explanation
Indices: 1117531--1117739 Score: 291
Period size: 76 Copynumber: 2.8 Consensus size: 77
1117521 AAAGCCAAAA
* * * **
1117531 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
1117595 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
1117608 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
1117673 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * *
1117684 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
1117740 TGTACAACGG
Statistics
Matches: 120, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
74 19 0.16
75 8 0.07
76 54 0.45
77 39 0.32
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:1118448 original size:17 final size:16
Alignment explanation
Indices: 1118422--1118458 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
1118412 CCGATTTCGT
1118422 CAATCGATTAACTCAA
1 CAATCGATTAACTCAA
1118438 CAATACGATTAACTCAA
1 CAAT-CGATTAACTCAA
1118455 CAAT
1 CAAT
1118459 TGGTATCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (16 bp):
CAATCGATTAACTCAA
Found at i:1123571 original size:22 final size:22
Alignment explanation
Indices: 1123506--1123588 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
1123496 TTGGTGCAGA
*
1123506 GGGAATCGA-TCCCCCCTG-A-
1 GGGAACCGATTCCCCCCTGAAG
*
1123525 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-CTGAAG
1123548 GGGAACCGATTCCCCCCT-ACAG
1 GGGAACCGATTCCCCCCTGA-AG
* *
1123570 GGGAATCGATACCCCCCTG
1 GGGAACCGATTCCCCCCTG
1123589 GGGTTATGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 8 0.15
20 6 0.11
21 3 0.06
22 20 0.38
23 16 0.30
ACGTcount: A:0.22, C:0.36, G:0.25, T:0.17
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTGAAG
Found at i:1125528 original size:15 final size:15
Alignment explanation
Indices: 1125508--1125549 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
1125498 CATTTTTAAT
*
1125508 ATTTTGGATTGTTTG
1 ATTTTGGATTGTTGG
1125523 ATTTTGTGGATTGTTGG
1 A-TTT-TGGATTGTTGG
1125540 ATTTTGGATT
1 ATTTTGGATT
1125550 TATGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:1125534 original size:17 final size:17
Alignment explanation
Indices: 1125512--1125545 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1125502 TTTAATATTT
*
1125512 TGGATTGTTTGATTTTG
1 TGGATTGTTGGATTTTG
1125529 TGGATTGTTGGATTTTG
1 TGGATTGTTGGATTTTG
1125546 GATTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTG
Found at i:1126243 original size:71 final size:74
Alignment explanation
Indices: 1126124--1126305 Score: 253
Period size: 71 Copynumber: 2.5 Consensus size: 74
1126114 CAAAGCCAAA
* * * *
1126124 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCCATAGGAGGAACCGATTCCCCCTAAA-TG
1 AATTCCAGAATGCTCGGAGGGAACCGATT---CCCCCATAGGAGGAACCGATTCCCCCTAAACAG
1126188 TTTGGCCCCGAG
63 TTTGGCCCCGAG
1126200 -ATTCCAGAATGCTCGGA-GGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
* *
1126263 TGCTCCGAG
66 GGCCCCGAG
*
1126272 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCC
1126306 TTGTACAACG
Statistics
Matches: 96, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
71 30 0.31
72 11 0.11
73 16 0.17
74 25 0.26
75 14 0.15
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
GGCCCCGAG
Found at i:1130949 original size:26 final size:26
Alignment explanation
Indices: 1130897--1130950 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
1130887 CATTGTCCCC
**
1130897 AATGCAATGACAAATTCAACAATAAA
1 AATGCAATGACAAAAACAACAATAAA
* *
1130923 AATGCAATGA-AAAAACAATAATGAA
1 AATGCAATGACAAAAACAACAATAAA
1130948 AAT
1 AAT
1130951 AAAGACAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.19
Consensus pattern (26 bp):
AATGCAATGACAAAAACAACAATAAA
Found at i:1143259 original size:74 final size:72
Alignment explanation
Indices: 1143135--1143277 Score: 223
Period size: 74 Copynumber: 2.0 Consensus size: 72
1143125 TGCTTCATAT
*
1143135 CTAATATGGTACAATGAAATCTTTTATTGTAAATATCATGTTGGATCTCAAAGACACCCTATCAA
1 CTAATATGGTACAATGAAATCTTTTATTGTAAATATCATGTTGGAACTCAAAGACA--CTATCAA
1143200 AAAGTGTAG
64 AAAGTGTAG
* * * *
1143209 CTAATATGGTACAGTTAAATGTTTTATTGTAAATATCATGTTGGAACTCAAAGACACTATTAAAA
1 CTAATATGGTACAATGAAATCTTTTATTGTAAATATCATGTTGGAACTCAAAGACACTATCAAAA
1143274 AGTG
66 AGTG
1143278 CAGTAGTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 12 0.19
74 52 0.81
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (72 bp):
CTAATATGGTACAATGAAATCTTTTATTGTAAATATCATGTTGGAACTCAAAGACACTATCAAAA
AGTGTAG
Found at i:1143996 original size:2 final size:2
Alignment explanation
Indices: 1143989--1144018 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1143979 ATCCTAACCC
1143989 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
1144019 TGACTTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1146888 original size:34 final size:35
Alignment explanation
Indices: 1146845--1146946 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
1146835 TTTCGTCCTA
1146845 TTAGGATTCAAACTCCTAAAAATAGGATAGAA-TT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
1146879 TTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
1146914 TGCTAGGATTCAAACTCTTAAAAATAGGATAGA
1 T--TAGGATTCAAACTCCTAAAAATAGGATAGA
1146947 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
34 31 0.50
35 3 0.05
37 28 0.45
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (35 bp):
TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:1150111 original size:8 final size:8
Alignment explanation
Indices: 1150085--1150154 Score: 58
Period size: 8 Copynumber: 9.0 Consensus size: 8
1150075 CAATCAAGAA
1150085 CAAAAAAG
1 CAAAAAAG
1150093 -AAAAGAAG
1 CAAAA-AAG
1150101 CAAAAAAG
1 CAAAAAAG
1150109 CAAAAAAAG
1 C-AAAAAAG
1150118 CAAAAAA-
1 CAAAAAAG
*
1150125 -AAAAGAG
1 CAAAAAAG
*
1150132 -AAACAAG
1 CAAAAAAG
*
1150139 AAAAAAAG
1 CAAAAAAG
*
1150147 GAAAAAAG
1 CAAAAAAG
1150155 AGCAAAAATC
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
6 5 0.10
7 9 0.17
8 26 0.50
9 12 0.23
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (8 bp):
CAAAAAAG
Found at i:1150113 original size:17 final size:16
Alignment explanation
Indices: 1150080--1150155 Score: 79
Period size: 16 Copynumber: 4.9 Consensus size: 16
1150070 AGATCCAATC
1150080 AAGAA-CAAAAAAGAA
1 AAGAAGCAAAAAAGAA
1150095 AAGAAGCAAAAAAGCAA
1 AAGAAGCAAAAAAG-AA
*
1150112 AAAAAGCAAAAAA-AA
1 AAGAAGCAAAAAAGAA
*
1150127 AAG-AG-AAACAAGAA
1 AAGAAGCAAAAAAGAA
* *
1150141 AAAAAGGAAAAAAGA
1 AAGAAGCAAAAAAGA
1150156 GCAAAAATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
13 5 0.10
14 6 0.12
15 11 0.22
16 15 0.29
17 14 0.27
ACGTcount: A:0.78, C:0.07, G:0.16, T:0.00
Consensus pattern (16 bp):
AAGAAGCAAAAAAGAA
Found at i:1150124 original size:10 final size:9
Alignment explanation
Indices: 1150086--1150162 Score: 61
Period size: 9 Copynumber: 8.4 Consensus size: 9
1150076 AATCAAGAAC
1150086 AAAAAAG-A
1 AAAAAAGCA
*
1150094 AAAGAAGC-
1 AAAAAAGCA
1150102 AAAAAAGCA
1 AAAAAAGCA
1150111 AAAAAAGCA
1 AAAAAAGCA
**
1150120 AAAAAAAAA
1 AAAAAAGCA
1150129 GAGAAACAAG-A
1 -A-AAA-AAGCA
*
1150140 AAAAAAGGA
1 AAAAAAGCA
1150149 AAAAAGAGCA
1 AAAAA-AGCA
1150159 AAAA
1 AAAA
1150163 TCAAAAAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
8 16 0.29
9 25 0.45
10 9 0.16
11 4 0.07
12 2 0.04
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAGCA
Found at i:1150837 original size:22 final size:22
Alignment explanation
Indices: 1150812--1150858 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1150802 CCATCAATCT
* *
1150812 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
*
1150834 TTTGAGTATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
1150856 TTT
1 TTT
1150859 AACCAAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:1151300 original size:18 final size:18
Alignment explanation
Indices: 1151277--1151312 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1151267 TCAACATCAA
* *
1151277 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
1151295 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
1151313 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:1151780 original size:36 final size:35
Alignment explanation
Indices: 1151740--1152073 Score: 227
Period size: 36 Copynumber: 9.5 Consensus size: 35
1151730 ACTCATGATT
* * *
1151740 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAA-ATTTGTCTCTCTTGAGACA
* * * **
1151776 GTTT-TCACTAGAAGAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAATTTGTCTCTCTTGAGACA
* *
1151811 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
* *
1151847 GTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* * * *
1151883 GTTTCCCTTGAAATAAATTTTATCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
* * * * *
1151919 GTTTCCCTTGAAACAAA-----ATAT-TTGA-ATA
1 GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
* *
1151947 TGTTT-TCTTTGAAACAAATTCTGTCTCCCTTGAGACA
1 -GTTTCTC-TTAAAACAAATT-TGTCTCTCTTGAGACA
* * *
1151984 GTTTCTTTTAGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAAC-AA-ATTTGTCTCTCTTGAGACA
* * *
1152021 GTTTCTCTTGAAACAATTTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* *
1152057 GTTTCCCTTGAAACAAA
1 GTTTCTCTTAAAACAAA
1152074 ACCTTTGAAT
Statistics
Matches: 239, Mismatches: 40, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
28 3 0.01
29 18 0.08
30 2 0.01
35 34 0.14
36 146 0.61
37 34 0.14
38 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (35 bp):
GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
Found at i:1151894 original size:72 final size:71
Alignment explanation
Indices: 1151793--1152073 Score: 301
Period size: 72 Copynumber: 4.0 Consensus size: 71
1151783 CTAGAAGAGT
* *
1151793 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
1151858 AACAAA
66 AACAAA
* *
1151864 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
1 TTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1151929 AAACAAA
65 AAACAAA
* * * * * * * *
1151936 -----ATAT-TTGA-ATATGTTTTCTTTGAAACAAATTCTGTCTCCCTTGAGACAGTTT-CTTTT
1 TTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1151993 AGAACTAAGT
65 A-AAC-AA-A
* * *
1152003 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTG
1152067 AAACAAA
65 AAACAAA
1152074 ACCTTTGAAT
Statistics
Matches: 169, Mismatches: 27, Indels: 28
0.75 0.12 0.12
Matches are distributed among these distances:
64 6 0.04
65 41 0.24
66 5 0.03
71 3 0.02
72 73 0.43
73 35 0.21
74 6 0.04
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (71 bp):
TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAA
Found at i:1152033 original size:102 final size:102
Alignment explanation
Indices: 1151848--1152036 Score: 274
Period size: 102 Copynumber: 1.9 Consensus size: 102
1151838 CTTGAGACAG
*
1151848 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTATCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTATCTCTCTT
1151913 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * * *
1151950 TTTCT-TTGAAACAAA-TTCTGTCTCCCTTGAGACAGTTTCTTTTAGAACTAAGTTTTGTCTCTC
1 TTTCTCTTGAAACAAATTTC-GTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTATCTCTC
*
1152013 TTGAGACAGTTTCTCTTGAAACAA
64 TTGAGACAGTTTCCCTTGAAACAA
1152037 TTTTCGTCTA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 3 0.04
101 30 0.39
102 44 0.57
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTATCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:1152065 original size:138 final size:137
Alignment explanation
Indices: 1151812--1152137 Score: 422
Period size: 138 Copynumber: 2.4 Consensus size: 137
1151802 CTTGAGACAG
*
1151812 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* *
1151877 GAGACAGTTTCCCTTGAAATAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTATCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
1151942 GAATATG
131 GAATATA
* * * * * * *
1151949 TTTTCTTTGAAACAAATTCTGTCTCCCTTGAGACAGTTTCT-TTTAGAACTAAGTTTTGTCTCTC
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA-AAC-AAATTTCGTCTATC
* * * *
1152013 TTGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACC
64 TTGAGACAGTTTCCCTTGAAATAAATTTT-ATCTATCTTGAGACAGTTTCCCTTGAAACAAAACA
*
1152077 TTTGAATTTA
128 TTTGAATATA
* * * * *
1152087 TTTCCCCTAAAACAAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1152138 CAGATATCTT
Statistics
Matches: 160, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
136 3 0.02
137 48 0.30
138 107 0.67
139 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTATCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:1152959 original size:105 final size:105
Alignment explanation
Indices: 1152780--1153611 Score: 1296
Period size: 105 Copynumber: 8.0 Consensus size: 105
1152770 GCACTCGAGG
* * * *
1152780 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGTTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
1152845 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
1152886 CAACGCAATTTCAACTTCACGATGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
1152951 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
1152991 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1153056 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
1153096 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1153161 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
1153201 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1153266 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * *
1153306 CAATGCAAGTTCAACTTCACGACGAAGGGACCGTTGCTTGTCAACAACAACTTCCCAATCTAAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1153371 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
1153411 TAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
1153471 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * * ** *
1153511 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
1153576 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1153612 TGGAACAATG
Statistics
Matches: 675, Mismatches: 45, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
100 81 0.12
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 507 0.75
106 74 0.11
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:1154203 original size:34 final size:36
Alignment explanation
Indices: 1154159--1154260 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
1154149 TTTCGTCCTA
1154159 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
1154194 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
1154229 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1154261 GTTATACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:1154878 original size:48 final size:48
Alignment explanation
Indices: 1154787--1154879 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
1154777 ATAGCAATAT
* **
1154787 TTATATAACAGTAGCGGTGCGCTCAATACCGTTATTGCCTAATCGGGA
1 TTATATAACAGTAGCAGTGCGCTCAATACCGTTATTGAATAATCGGGA
* *
1154835 TTATATAACAGTAGTAGTGCGTTCAATACCGTTATTGAATAATCG
1 TTATATAACAGTAGCAGTGCGCTCAATACCGTTATTGAATAATCG
1154880 CAATATCCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (48 bp):
TTATATAACAGTAGCAGTGCGCTCAATACCGTTATTGAATAATCGGGA
Found at i:1156102 original size:14 final size:15
Alignment explanation
Indices: 1156077--1156105 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1156067 TAAACTACTA
1156077 AATTGTTAAATTATT
1 AATTGTTAAATTATT
1156092 AATTG-TAAATTATT
1 AATTGTTAAATTATT
1156106 TTTATGTAGA
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (15 bp):
AATTGTTAAATTATT
Found at i:1157613 original size:24 final size:24
Alignment explanation
Indices: 1157565--1157623 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
1157555 AACAACCCTT
*
1157565 AAAGATAATT-CCTAATAAATGCA
1 AAAGATAATTCCCTAATAAATACA
1157588 AAAGATAATTCCCTAA-AAATTACA
1 AAAGATAATTCCCTAATAAA-TACA
1157612 AAAGATAATTCC
1 AAAGATAATTCC
1157624 TTTAATTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (24 bp):
AAAGATAATTCCCTAATAAATACA
Found at i:1170433 original size:15 final size:17
Alignment explanation
Indices: 1170403--1170434 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1170393 CCTGTATGAA
1170403 ATTAAGACTCTTTTTTC
1 ATTAAGACTCTTTTTTC
1170420 ATTAAGA-T-TTTTTTC
1 ATTAAGACTCTTTTTTC
1170435 TACTTTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (17 bp):
ATTAAGACTCTTTTTTC
Found at i:1171574 original size:16 final size:17
Alignment explanation
Indices: 1171553--1171584 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1171543 CTTATCTATC
1171553 TAAATGTCAT-GAAAAG
1 TAAATGTCATGGAAAAG
1171569 TAAATGTCATGGAAAA
1 TAAATGTCATGGAAAA
1171585 CTTGAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (17 bp):
TAAATGTCATGGAAAAG
Found at i:1173627 original size:22 final size:22
Alignment explanation
Indices: 1173602--1173644 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1173592 GAAAGTCAAC
1173602 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1173624 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
1173645 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1173665 original size:19 final size:19
Alignment explanation
Indices: 1173643--1173748 Score: 101
Period size: 19 Copynumber: 5.5 Consensus size: 19
1173633 TCGGGTCGGG
1173643 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
1173662 TCAGACCGGTTAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
1173681 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
* *
1173700 TCAAACCGGTTCGAACCGGT
1 TCAGACCGG-TCAAACCGGT
* *
1173720 TGAAACCGGTCAAACCGG-
1 TCAGACCGGTCAAACCGGT
1173738 TCAGAACCGGT
1 TCAG-ACCGGT
1173749 TGAAAACCGG
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
18 3 0.04
19 54 0.74
20 16 0.22
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1173671 original size:10 final size:10
Alignment explanation
Indices: 1173647--1173769 Score: 132
Period size: 10 Copynumber: 12.7 Consensus size: 10
1173637 GTCGGGTCAG
1173647 ACCGG-TCAA
1 ACCGGTTCAA
*
1173656 ACCGGTTCAG
1 ACCGGTTCAA
1173666 ACCGGTT-AA
1 ACCGGTTCAA
*
1173675 ACCGGTTCGA
1 ACCGGTTCAA
*
1173685 ACCGGTTGAA
1 ACCGGTTCAA
1173695 ACCGG-TCAA
1 ACCGGTTCAA
*
1173704 ACCGGTTCGA
1 ACCGGTTCAA
*
1173714 ACCGGTTGAA
1 ACCGGTTCAA
1173724 ACCGG-TCAA
1 ACCGGTTCAA
1173733 ACCGG-TCAGA
1 ACCGGTTCA-A
*
1173743 ACCGGTTGAAA
1 ACCGGTT-CAA
1173754 ACCGGTT-AA
1 ACCGGTTCAA
1173763 ACCGGTT
1 ACCGGTT
1173770 TCCAGCAGCC
Statistics
Matches: 97, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
9 41 0.42
10 46 0.47
11 9 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:1173689 original size:29 final size:29
Alignment explanation
Indices: 1173654--1173738 Score: 54
Period size: 29 Copynumber: 2.9 Consensus size: 29
1173644 CAGACCGGTC
* *
1173654 AAACCGGTTCAGACCGGT-TAAACCGGTTCG
1 AAACCGG-TCAAACCGGTCCAAACCGGTT-G
*
1173684 -AACCGGTTGAAACCGGT-CAAACCGGTTCG
1 AAACCGG-TCAAACCGGTCCAAACCGGTT-G
*
1173713 -AACCGGTTGAAACCGGT-CAAACCGGT
1 AAACCGG-TCAAACCGGTCCAAACCGGT
1173739 CAGAACCGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (29 bp):
AAACCGGTCAAACCGGTCCAAACCGGTTG
Found at i:1173744 original size:29 final size:28
Alignment explanation
Indices: 1173666--1173769 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 28
1173656 ACCGGTTCAG
* *
1173666 ACCGGTTAAACCGGTTCG-AACCGGTTGAA
1 ACCGGTCAAACCGGTTAGAAACCGG-T-AA
*
1173695 ACCGGTCAAACCGGTTCG-AACCGGTTGAA
1 ACCGGTCAAACCGGTTAGAAACCGG-T-AA
*
1173724 ACCGGTCAAACCGGTCAG-AACCGGTTGAAA
1 ACCGGTCAAACCGGTTAGAAACCGG-T--AA
*
1173754 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
1173770 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
29 52 0.76
30 16 0.24
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (28 bp):
ACCGGTCAAACCGGTTAGAAACCGGTAA
Found at i:1180967 original size:22 final size:22
Alignment explanation
Indices: 1180939--1180981 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1180929 AACGGTCAAC
1180939 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1180961 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
1180982 AAAAGTCGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1180971 original size:17 final size:17
Alignment explanation
Indices: 1180951--1181001 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
1180941 TCAACGGTCG
*
1180951 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAA
1180968 GGTCGGGTCGGGTCAAA
1 GGTCGGGTCGGGTCAAA
*
1180985 AGTCGGGTCGGGTCAAA
1 GGTCGGGTCGGGTCAAA
1181002 CCGGTTAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAA
Found at i:1181025 original size:10 final size:10
Alignment explanation
Indices: 1180997--1181085 Score: 87
Period size: 10 Copynumber: 9.1 Consensus size: 10
1180987 TCGGGTCGGG
1180997 TCAAACCGGT
1 TCAAACCGGT
1181007 T-AAACCGGT
1 TCAAACCGGT
*
1181016 TCAGACCGG-
1 TCAAACCGGT
*
1181025 TCAAACTGGT
1 TCAAACCGGT
*
1181035 TCGAACCGGT
1 TCAAACCGGT
*
1181045 TGAAACCGG-
1 TCAAACCGGT
1181054 TCAGAACCGGT
1 TCA-AACCGGT
*
1181065 TGAAAACCGGT
1 T-CAAACCGGT
1181076 T-AAACCGGT
1 TCAAACCGGT
1181085 T
1 T
1181086 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
9 27 0.42
10 28 0.43
11 9 0.14
12 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1184170 original size:15 final size:15
Alignment explanation
Indices: 1184150--1184181 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1184140 TCATTGAATT
1184150 AAGTAAAAATGACGC
1 AAGTAAAAATGACGC
1184165 AAGTAAAAATGACGC
1 AAGTAAAAATGACGC
1184180 AA
1 AA
1184182 TTCATGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.12
Consensus pattern (15 bp):
AAGTAAAAATGACGC
Found at i:1185642 original size:20 final size:21
Alignment explanation
Indices: 1185606--1185644 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1185596 ATAATTCACA
1185606 TGAATGTACCACAACTTAACT
1 TGAATGTACCACAACTTAACT
*
1185627 TGAATGTA-CTCAACTTAA
1 TGAATGTACCACAACTTAA
1185645 TGACATGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (21 bp):
TGAATGTACCACAACTTAACT
Found at i:1192252 original size:22 final size:22
Alignment explanation
Indices: 1192225--1192268 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1192215 TTCTATTCAG
1192225 CATCAA-CTCCATCAACATCTTC
1 CATCAAGCT-CATCAACATCTTC
*
1192247 CATCAAGGTCATCAACATCTTC
1 CATCAAGCTCATCAACATCTTC
1192269 ATAATTCTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.27
Consensus pattern (22 bp):
CATCAAGCTCATCAACATCTTC
Found at i:1197966 original size:60 final size:60
Alignment explanation
Indices: 1197852--1197968 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
1197842 CCCTAAATAG
* * * * *
1197852 GCATTCATAAGGATTTACCCTAGACCACTGAGATCCAGGAATCCATTATAGAAGATACAA
1 GCATCCATAAGAACTTACCCTAGACCACTAAGATCCAGGAATCCAATATAGAAGATACAA
* * * * *
1197912 GCATCCATAAGAACTTACCGTAGACCACTAAGATCTAGGAGTCTAATATGGAAGATA
1 GCATCCATAAGAACTTACCCTAGACCACTAAGATCCAGGAATCCAATATAGAAGATA
1197969 AGAACATGAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (60 bp):
GCATCCATAAGAACTTACCCTAGACCACTAAGATCCAGGAATCCAATATAGAAGATACAA
Found at i:1204235 original size:49 final size:49
Alignment explanation
Indices: 1204144--1204242 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 49
1204134 ATCTGCTCTA
* * *
1204144 TAATGAAAGTTAAATGCATAATGGTGCATTTTTGACAGAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTTCGACAAAAAGGTGCCAC
* * *
1204193 TAATGCAAGTTAAATGCATAACGGTGTA-TTTCGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTTCGACA-AAAAGGTGCCAC
1204242 T
1 T
1204243 CATAGTTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 6 0.14
49 37 0.86
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (49 bp):
TAATGAAAGTTAAATGCATAACGGTGCATTTTCGACAAAAAGGTGCCAC
Found at i:1205958 original size:16 final size:18
Alignment explanation
Indices: 1205937--1205970 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1205927 TTTTTGGTAT
1205937 TTTCAA-GAA-TTTAGGA
1 TTTCAAGGAACTTTAGGA
1205953 TTTCAAGGAACTTTAGGA
1 TTTCAAGGAACTTTAGGA
1205971 ATTTTGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (18 bp):
TTTCAAGGAACTTTAGGA
Found at i:1209997 original size:60 final size:59
Alignment explanation
Indices: 1209945--1210057 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
1209935 GATACAGACA
*
1209945 TCCAT-AAGAACTTACCCTAGACCACTAAGATCTTGGAGTCCAATATGGAAGATACATGC
1 TCCATAAAG-ACTTAACCTAGACCACTAAGATCTTGGAGTCCAATATGGAAGATACATGC
** * * * *
1210004 TCCATAAAGACTTAATGTAGGCCATTAAGATATAGGAGTCCAATATGGAAGATA
1 TCCATAAAGACTTAACCTAGACCACTAAGATCTTGGAGTCCAATATGGAAGATA
1210058 AGAACATGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 43 0.93
60 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (59 bp):
TCCATAAAGACTTAACCTAGACCACTAAGATCTTGGAGTCCAATATGGAAGATACATGC
Found at i:1210904 original size:8 final size:8
Alignment explanation
Indices: 1210891--1210917 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1210881 GCTAATTATT
1210891 AAGAATGG
1 AAGAATGG
1210899 AAGAATGG
1 AAGAATGG
1210907 AAGAATGG
1 AAGAATGG
1210915 AAG
1 AAG
1210918 GGCAATTTAG
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:0.52, C:0.00, G:0.37, T:0.11
Consensus pattern (8 bp):
AAGAATGG
Found at i:1212547 original size:54 final size:54
Alignment explanation
Indices: 1212438--1212555 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 54
1212428 AACAGTGCAT
* *
1212438 TTTCGGCACTAAATGTGCAACCCATGGTATTCATAATGTGTTTATGAATGACCA
1 TTTCGGCACTAAATGTACAACCCATGGAATTCATAATGTGTTTATGAATGACCA
* * * * *
1212492 TTTCGACACTATATGTACAATCCATGGAATTCATAAT-TAGTTTTTGAAAT-TCCA
1 TTTCGGCACTAAATGTACAACCCATGGAATTCATAATGT-GTTTATG-AATGACCA
1212546 TTTCGGCACT
1 TTTCGGCACT
1212556 TCGGTGCAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 1 0.02
54 50 0.93
55 3 0.06
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (54 bp):
TTTCGGCACTAAATGTACAACCCATGGAATTCATAATGTGTTTATGAATGACCA
Found at i:1231535 original size:9 final size:9
Alignment explanation
Indices: 1231523--1231551 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1231513 GTTTTTTACC
1231523 ATTTTATTT
1 ATTTTATTT
1231532 ATTTTATTT
1 ATTTTATTT
1231541 ATTTT-TTT
1 ATTTTATTT
1231549 ATT
1 ATT
1231552 AATATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
ATTTTATTT
Found at i:1240197 original size:3 final size:3
Alignment explanation
Indices: 1240189--1240262 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
1240179 GTAACCGATT
1240189 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1240237 CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CT
1240263 TCTTCTTCTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:1243454 original size:17 final size:17
Alignment explanation
Indices: 1243402--1243454 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 17
1243392 GATGAATTCT
*
1243402 AAATGTTTACAGTTATC
1 AAATGATTACAGTTATC
* *
1243419 ATATGATTTTCAGTTATC
1 AAATGA-TTACAGTTATC
*
1243437 AAATGATTACAATTATC
1 AAATGATTACAGTTATC
1243454 A
1 A
1243455 GATATTTATG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (17 bp):
AAATGATTACAGTTATC
Found at i:1249697 original size:118 final size:118
Alignment explanation
Indices: 1249532--1250008 Score: 648
Period size: 118 Copynumber: 4.0 Consensus size: 118
1249522 GAAGAAGAGT
* * ** *
1249532 GATTCTAATATATTGTGGTGTTACCTGAAGGTACACTAGTATATATATTATGATCTGATTGCACT
1 GATTCTGATATATTGTGGTG-TACCGGTGGGTGCACTAGTATATATATTATGATCTGATTGCACT
* * * * *
1249597 TTTTGTGAACATTATGGTTCTAATATGATAGCACTGTGTGTGCTTATATGTTCC
65 TTGTGTGCACATTACGATTCTGATATGATAGCACTGTGTGTGCTTATATGTTCC
* * ** * * * *
1249651 AATTCTGATATACTGTGGTGTACAAGTGGGTCCCCTAGTATATATATTAAGATATGATTGCACTT
1 GATTCTGATATATTGTGGTGTACCGGTGGGTGCACTAGTATATATATTATGATCTGATTGCACTT
*
1249716 TGTGTGCACATTACGATTCTGATATGATAGCACTGTGTGTGCTTATATGTTAC
66 TGTGTGCACATTACGATTCTGATATGATAGCACTGTGTGTGCTTATATGTTCC
* * **
1249769 GATTCTGATATATTGTGGTGTACCGGTGGGTGCACTAGTATATATATTCTGATTTGATTGCGTTT
1 GATTCTGATATATTGTGGTGTACCGGTGGGTGCACTAGTATATATATTATGATCTGATTGCACTT
* * * *
1249834 TGTGTGCACATTACGATTCTGATATAACAACACTGTGTGTGCTTATATGTTCT
66 TGTGTGCACATTACGATTCTGATATGATAGCACTGTGTGTGCTTATATGTTCC
*
1249887 GATTCTGATATATTGTGGTGTACCGGTGGGTGCACTAGTATATATATTCTGATCTGATTGCACTT
1 GATTCTGATATATTGTGGTGTACCGGTGGGTGCACTAGTATATATATTATGATCTGATTGCACTT
* * * * *
1249952 TGTGTGCACATTACGATTCTGACATGATAGCACTATGTGTGTTTATATATTCT
66 TGTGTGCACATTACGATTCTGATATGATAGCACTGTGTGTGCTTATATGTTCC
1250005 GATT
1 GATT
1250009 ATGACGATAA
Statistics
Matches: 315, Mismatches: 43, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
118 298 0.95
119 17 0.05
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (118 bp):
GATTCTGATATATTGTGGTGTACCGGTGGGTGCACTAGTATATATATTATGATCTGATTGCACTT
TGTGTGCACATTACGATTCTGATATGATAGCACTGTGTGTGCTTATATGTTCC
Found at i:1251653 original size:15 final size:17
Alignment explanation
Indices: 1251633--1251665 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1251623 TATGATTTTC
1251633 TTAAATT-CAAG-TAGA
1 TTAAATTGCAAGATAGA
1251648 TTAAATTGCAAGATAGA
1 TTAAATTGCAAGATAGA
1251665 T
1 T
1251666 AGAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (17 bp):
TTAAATTGCAAGATAGA
Found at i:1251729 original size:19 final size:19
Alignment explanation
Indices: 1251705--1251746 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1251695 ATACTATTTT
1251705 TTTTGTAATTTTTATGATA
1 TTTTGTAATTTTTATGATA
*
1251724 TTTTGTAATTTTTCTGATA
1 TTTTGTAATTTTTATGATA
1251743 TTTT
1 TTTT
1251747 TTTAAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (19 bp):
TTTTGTAATTTTTATGATA
Found at i:1251768 original size:15 final size:17
Alignment explanation
Indices: 1251748--1251780 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1251738 TGATATTTTT
1251748 TTAAATT-CAAG-TAGA
1 TTAAATTACAAGATAGA
1251763 TTAAATTACAAGATAGA
1 TTAAATTACAAGATAGA
1251780 T
1 T
1251781 AAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (17 bp):
TTAAATTACAAGATAGA
Found at i:1251838 original size:9 final size:10
Alignment explanation
Indices: 1251819--1251853 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
1251809 CATACTAATT
1251819 TTTTTCGTAA
1 TTTTTCGTAA
1251829 TTTTTC-TAA
1 TTTTTCGTAA
1251838 TTTTTCGTAA
1 TTTTTCGTAA
1251848 TTTTTC
1 TTTTTC
1251854 TGATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (10 bp):
TTTTTCGTAA
Found at i:1251843 original size:19 final size:19
Alignment explanation
Indices: 1251819--1251861 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1251809 CATACTAATT
1251819 TTTTTCGTAATTTTTCTAA
1 TTTTTCGTAATTTTTCTAA
*
1251838 TTTTTCGTAATTTTTCTGA
1 TTTTTCGTAATTTTTCTAA
1251857 TTTTT
1 TTTTT
1251862 TTTAAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTTCGTAATTTTTCTAA
Found at i:1251859 original size:9 final size:9
Alignment explanation
Indices: 1251819--1251861 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
1251809 CATACTAATT
1251819 TTTTTCGTAA
1 TTTTTC-TAA
1251829 TTTTTCTAA
1 TTTTTCTAA
1251838 TTTTTCGTAA
1 TTTTTC-TAA
*
1251848 TTTTTCTGA
1 TTTTTCTAA
1251857 TTTTT
1 TTTTT
1251862 TTTAAATTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
9 16 0.52
10 15 0.48
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.67
Consensus pattern (9 bp):
TTTTTCTAA
Found at i:1251954 original size:95 final size:94
Alignment explanation
Indices: 1251834--1252033 Score: 355
Period size: 95 Copynumber: 2.1 Consensus size: 94
1251824 CGTAATTTTT
* *
1251834 CTAATTTTTCGTAATTTTTCTGATTTTTTTTAAATTCAAGTAGATTAAATTGTAAGATAGATAAA
1 CTAATTTTTTGTAATTTTTCTGATTTTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAA
1251899 AATACATTGAAATTAGATAAATAAACATA
66 AATACATTGAAATTAGATAAATAAACATA
* *
1251928 CTACTCTTTTTGTAATTTTTTTGATTTTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAA
1 CTAAT-TTTTTGTAATTTTTCTGATTTTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAA
1251993 AAATACATTGAAATTAGATAAATAAACATA
65 AAATACATTGAAATTAGATAAATAAACATA
1252023 CTAATTTTTTG
1 CTAATTTTTTG
1252034 AAACATAAGA
Statistics
Matches: 100, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
94 10 0.10
95 90 0.90
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.43
Consensus pattern (94 bp):
CTAATTTTTTGTAATTTTTCTGATTTTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAA
AATACATTGAAATTAGATAAATAAACATA
Found at i:1251957 original size:115 final size:114
Alignment explanation
Indices: 1251597--1251957 Score: 555
Period size: 115 Copynumber: 3.1 Consensus size: 114
1251587 GCTACGCTAC
* *
1251597 AATTTTTTTG-TTGTTGTTGTAATTTTTATGA-TTTTCTTAAATTCAAGTAGATTAAATTGCAAG
1 AATTTTTTTGATT-TT-TTGTAATTTTTCTGATTTTTTTTAAATTCAAGTAGATTAAATTGCAAG
* *
1251660 ATAGATAGAAATACATTGAAATTAGATAAATAAACATACTATTTTTTTTGT
64 ATAGATAAAAATACATTGAAATTAGATAAATAAACATACTAATTTTTTTGT
* * *
1251711 AATTTTTATGATATTTTGTAATTTTTCTGATATTTTTTTAAATTCAAGTAGATTAAATTACAAGA
1 AATTTTTTTGATTTTTTGTAATTTTTCTGAT-TTTTTTTAAATTCAAGTAGATTAAATTGCAAGA
1251776 TAGATAAAAATACATTGAAATTAGATAAATAAACATACTAATTTTTTTCGT
65 TAGATAAAAATACATTGAAATTAGATAAATAAACATACTAATTTTTTT-GT
* * * *
1251827 AATTTTTCTAATTTTTCGTAATTTTTCTGATTTTTTTTAAATTCAAGTAGATTAAATTGTAAGAT
1 AATTTTTTTGATTTTTTGTAATTTTTCTGATTTTTTTTAAATTCAAGTAGATTAAATTGCAAGAT
* *
1251892 AGATAAAAATACATTGAAATTAGATAAATAAACATACTACTCTTTTTGT
66 AGATAAAAATACATTGAAATTAGATAAATAAACATACTAATTTTTTTGT
1251941 AATTTTTTTGATTTTTT
1 AATTTTTTTGATTTTTT
1251958 TTAAATTCAA
Statistics
Matches: 225, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
113 14 0.06
114 27 0.12
115 155 0.69
116 29 0.13
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (114 bp):
AATTTTTTTGATTTTTTGTAATTTTTCTGATTTTTTTTAAATTCAAGTAGATTAAATTGCAAGAT
AGATAAAAATACATTGAAATTAGATAAATAAACATACTAATTTTTTTGT
Found at i:1251978 original size:15 final size:17
Alignment explanation
Indices: 1251958--1251990 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1251948 TTGATTTTTT
1251958 TTAAATT-CAAG-TAGA
1 TTAAATTGCAAGATAGA
1251973 TTAAATTGCAAGATAGA
1 TTAAATTGCAAGATAGA
1251990 T
1 T
1251991 AAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (17 bp):
TTAAATTGCAAGATAGA
Found at i:1254103 original size:2 final size:2
Alignment explanation
Indices: 1254091--1254143 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
1254081 ACTTATATGT
1254091 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1254132 TA TG TA TA TA TA
1 TA TA TA TA TA TA
1254144 CATTTTGCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1258412 original size:21 final size:20
Alignment explanation
Indices: 1258386--1258426 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1258376 ACTTTGATGA
*
1258386 GGAAGATAAAGCCAAAAATAT
1 GGAAGA-AAAGACAAAAATAT
*
1258407 GGAAGAAAAGATAAAAATAT
1 GGAAGAAAAGACAAAAATAT
1258427 TAGAAGATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.61, C:0.05, G:0.20, T:0.15
Consensus pattern (20 bp):
GGAAGAAAAGACAAAAATAT
Found at i:1266013 original size:105 final size:105
Alignment explanation
Indices: 1265831--1266570 Score: 1257
Period size: 105 Copynumber: 7.0 Consensus size: 105
1265821 TTTTACCCAA
* *
1265831 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACG
1 AGCCAATTTCTACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1265896 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGTTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
1265936 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCTACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1266001 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
1266041 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCTACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
**
1266106 AAGGGACCGCTGGTTGTCAATGAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* ** *
1266146 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAATACAAGTTCAACTTCACGAAG
1 AGCCAATTTCTACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1266211 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
1266251 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCTACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1266316 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* * * *
1266356 AACCAATTTCTGCTTCACAACAAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACG
1 AGCCAATTTCTACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1266421 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTTAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* *
1266461 AGCCAATTT-TAACTTCACAACGAAGGATGTTGGACTCCAGACAAAGCAAGTTCAAACTTCACGA
1 AGCCAATTTCT-ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC-AACTTCACGA
* *
1266525 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAG
64 CGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAG
1266568 AGC
1 AGC
1266571 TCGTTTTCAA
Statistics
Matches: 599, Mismatches: 33, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
104 1 0.00
105 544 0.91
106 37 0.06
107 17 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
AGCCAATTTCTACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
Found at i:1268048 original size:12 final size:13
Alignment explanation
Indices: 1268033--1268072 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
1268023 ATTATTTCAC
1268033 TTATATGT-TATA
1 TTATATGTATATA
*
1268045 TTATATATATATA
1 TTATATGTATATA
1268058 TATATATGTATATA
1 T-TATATGTATATA
1268072 T
1 T
1268073 ACATTTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 7 0.29
13 5 0.21
14 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (13 bp):
TTATATGTATATA
Found at i:1268053 original size:2 final size:2
Alignment explanation
Indices: 1268041--1268073 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1268031 ACTTATATGT
*
1268041 TA TA T- TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1268074 CATTTTGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1268073 original size:12 final size:12
Alignment explanation
Indices: 1268034--1268073 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1268024 TTATTTCACT
1268034 TATATGTTATATTA
1 TATATG-TATA-TA
*
1268048 TATATATATATA
1 TATATGTATATA
1268060 TATATGTATATA
1 TATATGTATATA
1268072 TA
1 TA
1268074 CATTTTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 15 0.62
13 4 0.17
14 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (12 bp):
TATATGTATATA
Found at i:1269906 original size:304 final size:300
Alignment explanation
Indices: 1269351--1270168 Score: 1357
Period size: 304 Copynumber: 2.7 Consensus size: 300
1269341 AAAGAGTCAA
* * *
1269351 TTCTTAATCAATGGGTAGAATTGTTTTCTCATGGATTGTGTTTTCTTGTAAGCACAATTCACATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
* *
1269416 GATTGTGAATGAACGGTTGAGATTGAAAGATTCCTTTCTTTATCAATGGGTAGAATTGTTTTCAC
66 GATTGTGAATGAACGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGGTAGAATTGTTTTCAC
* * *
1269481 ATGGATTGTGTTTTCTTGCAAGCACAATTCACATGGATTATGAATGAACGGCTAAGATCGAAAGA
131 ATGGATTGTGTTTTCTTGCAAGCATAATTCACATGGATTGTGAATGAACGGCTGAGATCGAAAGA
1269546 TTCATTTCTTTATCAATGGGTAGAATTATTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTC
196 TTCATTTCTTTATCAATGGGTAGAATTATTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTC
** *
1269611 ACATGGAATATGAATGAAAGAAAGGTTGGGATCAAAAGATTCCT
261 ACATGG-AT-TG--TGAAAGAAAGACTGAGATCAAAAGATTCCT
* * *
1269655 TTCTTTATCAATGGGTAAAATTGTTTTCACATGGATTGTGTTTTATTGCAAGAACAATTCACATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
* *
1269720 AATTGTGAATGAACGGCTGAGATCGAAATATTCCTTTCTTTATCAATGGGTAGAATTGTTTTCAC
66 GATTGTGAATGAACGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGGTAGAATTGTTTTCAC
* *
1269785 ATGGATTGTGTTTTCTTGCAAGCATAATTCTCATGGATTGTGAATGAACGGCTGGGATCGAAAGA
131 ATGGATTGTGTTTTCTTGCAAGCATAATTCACATGGATTGTGAATGAACGGCTGAGATCGAAAGA
*
1269850 TTCATTTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTC
196 TTCATTTCTTTATCAATGGGTAGAATTATTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTC
* *
1269915 ACATGGATTGTGAATGAACGACTGAGATCAAAAGATTCCT
261 ACATGGATTGTGAAAGAAAGACTGAGATCAAAAGATTCCT
* *
1269955 TTCTTTATCAATGGGTAGAATTGTTTTCAAATGGAATGTGTTTTCTTGCAAGCACAATTCACATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
* *
1270020 GATTGTGAATAAACGGCTGGGATCGAAAGATTCCTTTCTTTATCAATGGGTAGAATTGTTTTCAC
66 GATTGTGAATGAACGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGGTAGAATTGTTTTCAC
*
1270085 ATGGATTGTGTTTTCTTGCAAGCATAATTCACATGGATTGTGAATGAATGGCTGAGATCGAAAGA
131 ATGGATTGTGTTTTCTTGCAAGCATAATTCACATGGATTGTGAATGAACGGCTGAGATCGAAAGA
*
1270150 TTCCTTTCTTTATCAATGG
196 TTCATTTCTTTATCAATGG
1270169 TTGTAATCCA
Statistics
Matches: 480, Mismatches: 34, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
300 226 0.47
302 2 0.00
303 2 0.00
304 250 0.52
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (300 bp):
TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
GATTGTGAATGAACGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGGTAGAATTGTTTTCAC
ATGGATTGTGTTTTCTTGCAAGCATAATTCACATGGATTGTGAATGAACGGCTGAGATCGAAAGA
TTCATTTCTTTATCAATGGGTAGAATTATTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTC
ACATGGATTGTGAAAGAAAGACTGAGATCAAAAGATTCCT
Found at i:1270194 original size:100 final size:100
Alignment explanation
Indices: 1269351--1270168 Score: 1321
Period size: 100 Copynumber: 8.1 Consensus size: 100
1269341 AAAGAGTCAA
* * *
1269351 TTCTTAATCAATGGGTAGAATTGTTTTCTCATGGATTGTGTTTTCTTGTAAGCACAATTCACATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
* *
1269416 GATTGTGAATGAACGGTTGAGATTGAAAGATTCCT
66 GATTGTGAATGAACGGCTGAGATCGAAAGATTCCT
1269451 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
* * *
1269516 GATTATGAATGAACGGCTAAGATCGAAAGATTCAT
66 GATTGTGAATGAACGGCTGAGATCGAAAGATTCCT
*
1269551 TTCTTTATCAATGGGTAGAATTATTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
* * * * *
1269616 GAATATGAATGAAAGAAAGGTTGGGATCAAAAGATTCCT
66 G-AT-TG--TGAATGAACGGCTGAGATCGAAAGATTCCT
* * *
1269655 TTCTTTATCAATGGGTAAAATTGTTTTCACATGGATTGTGTTTTATTGCAAGAACAATTCACATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
* *
1269720 AATTGTGAATGAACGGCTGAGATCGAAATATTCCT
66 GATTGTGAATGAACGGCTGAGATCGAAAGATTCCT
* *
1269755 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCATAATTCTCATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
* *
1269820 GATTGTGAATGAACGGCTGGGATCGAAAGATTCAT
66 GATTGTGAATGAACGGCTGAGATCGAAAGATTCCT
1269855 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
* *
1269920 GATTGTGAATGAACGACTGAGATCAAAAGATTCCT
66 GATTGTGAATGAACGGCTGAGATCGAAAGATTCCT
* *
1269955 TTCTTTATCAATGGGTAGAATTGTTTTCAAATGGAATGTGTTTTCTTGCAAGCACAATTCACATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
* *
1270020 GATTGTGAATAAACGGCTGGGATCGAAAGATTCCT
66 GATTGTGAATGAACGGCTGAGATCGAAAGATTCCT
*
1270055 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCATAATTCACATG
1 TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
*
1270120 GATTGTGAATGAATGGCTGAGATCGAAAGATTCCT
66 GATTGTGAATGAACGGCTGAGATCGAAAGATTCCT
1270155 TTCTTTATCAATGG
1 TTCTTTATCAATGG
1270169 TTGTAATCCA
Statistics
Matches: 659, Mismatches: 55, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
100 568 0.86
101 2 0.00
102 3 0.00
103 2 0.00
104 84 0.13
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (100 bp):
TTCTTTATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCACAATTCACATG
GATTGTGAATGAACGGCTGAGATCGAAAGATTCCT
Found at i:1270219 original size:68 final size:68
Alignment explanation
Indices: 1270110--1270534 Score: 751
Period size: 68 Copynumber: 6.2 Consensus size: 68
1270100 TTGCAAGCAT
1270110 AATTCACATGGATTGTGAATGAATGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGTTGTAA
1 AATTCACATGGATTGTGAATGAATGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGTTGTAA
1270175 TCC
66 TCC
* * *
1270178 AATTCACATGGATTGTGAATGAACGGTTGAGATCGAAAGATTACTTTCTTTATCAATGGTTGTAA
1 AATTCACATGGATTGTGAATGAATGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGTTGTAA
1270243 TCC
66 TCC
* * * *
1270246 AATTCACATGGATTGTGAATGAATGGTTGAGATCGAAAGGTTTCTTTCTTTATCAATGGATGTAA
1 AATTCACATGGATTGTGAATGAATGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGTTGTAA
1270311 TCC
66 TCC
* *
1270314 AATTCACATGGATTGTGAATGAATAGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGCTGTAA
1 AATTCACATGGATTGTGAATGAATGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGTTGTAA
1270379 TCC
66 TCC
* *
1270382 AATTCACATGGATTGTGAATGAATGGATGAGATCGAAAGATTCTTTTCTTTATCAATGGTTGTAA
1 AATTCACATGGATTGTGAATGAATGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGTTGTAA
1270447 TCC
66 TCC
1270450 AATTCACATGGATTGTGAATGAATGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGTTGTAA
1 AATTCACATGGATTGTGAATGAATGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGTTGTAA
1270515 TCC
66 TCC
1270518 AATTCACATGGATTGTG
1 AATTCACATGGATTGTG
1270535 TTTTCTAAAA
Statistics
Matches: 339, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 339 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (68 bp):
AATTCACATGGATTGTGAATGAATGGCTGAGATCGAAAGATTCCTTTCTTTATCAATGGTTGTAA
TCC
Found at i:1270271 original size:35 final size:35
Alignment explanation
Indices: 1270164--1270274 Score: 90
Period size: 35 Copynumber: 3.2 Consensus size: 35
1270154 TTTCTTTATC
1270164 AATGGTTGTAATCCAATTCACATGGATTGTGAATG
1 AATGGTTGTAATCCAATTCACATGGATTGTGAATG
* * * ** *
1270199 AACGGTTG-AGATCGAAAGATT-AC-T---TTCTTTATC
1 AATGGTTGTA-ATC--CA-ATTCACATGGATTGTGAATG
1270232 AATGGTTGTAATCCAATTCACATGGATTGTGAATG
1 AATGGTTGTAATCCAATTCACATGGATTGTGAATG
1270267 AATGGTTG
1 AATGGTTG
1270275 AGATCGAAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 20
0.63 0.14 0.23
Matches are distributed among these distances:
30 3 0.06
31 3 0.06
32 1 0.02
33 15 0.28
34 2 0.04
35 23 0.43
36 1 0.02
37 3 0.06
38 3 0.06
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (35 bp):
AATGGTTGTAATCCAATTCACATGGATTGTGAATG
Found at i:1272898 original size:24 final size:24
Alignment explanation
Indices: 1272866--1272912 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1272856 GACGGCGCTT
* *
1272866 GTAATCCATCTGTCGGAGACGCGA
1 GTAACCCATCAGTCGGAGACGCGA
1272890 GTAACCCATCAGTCGGAGACGCG
1 GTAACCCATCAGTCGGAGACGCG
1272913 TGTGAAGCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.17
Consensus pattern (24 bp):
GTAACCCATCAGTCGGAGACGCGA
Found at i:1275230 original size:20 final size:20
Alignment explanation
Indices: 1275206--1275399 Score: 97
Period size: 20 Copynumber: 9.5 Consensus size: 20
1275196 CAAAGTTTCC
1275206 AAATTCGCAACACGAATTTG
1 AAATTCGCAACACGAATTTG
* * *
1275226 GAATTCGCAACACAAAAGTT-
1 AAATTCGCAACAC-GAATTTG
*
1275246 AAATTCGCAACTCGAATTTG
1 AAATTCGCAACACGAATTTG
*
1275266 ACAATTTCGCAACTCGAATTTG
1 A-AA-TTCGCAACACGAATTTG
* * *
1275288 ACAATTTTGCAACACGGATTTC
1 A-AA-TTCGCAACACGAATTTG
*** *
1275310 TTTTTCGCAACAC-AATTTTT
1 AAATTCGCAACACGAA-TTTG
* * *
1275330 AAATTCGCAACGCAAATTTT
1 AAATTCGCAACACGAATTTG
** ** *
1275350 ATTTTCGCAACTTGATTTTCG
1 AAATTCGCAACACGAATTT-G
* *
1275371 -AATTCGCTACACGAATTTT
1 AAATTCGCAACACGAATTTG
*
1275390 AATTTCGCAA
1 AAATTCGCAA
1275400 AACAACTTTT
Statistics
Matches: 129, Mismatches: 37, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
19 5 0.04
20 81 0.63
21 8 0.06
22 35 0.27
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
AAATTCGCAACACGAATTTG
Found at i:1275308 original size:22 final size:22
Alignment explanation
Indices: 1275249--1275300 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1275239 AAAAGTTAAA
1275249 TTCGCAACTCGAATTTGACAAT
1 TTCGCAACTCGAATTTGACAAT
1275271 TTCGCAACTCGAATTTGACAAT
1 TTCGCAACTCGAATTTGACAAT
*
1275293 TTTGCAAC
1 TTCGCAAC
1275301 ACGGATTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (22 bp):
TTCGCAACTCGAATTTGACAAT
Found at i:1275355 original size:40 final size:40
Alignment explanation
Indices: 1275311--1275426 Score: 115
Period size: 40 Copynumber: 2.9 Consensus size: 40
1275301 ACGGATTTCT
*
1275311 TTTTCGCAACACAATTTTTAAATTCGCAACGCAAATTTTA
1 TTTTCGCAACACAATTTTTAAATTCGCAACACAAATTTTA
*** ** * *
1275351 TTTTCGCAACTTGATTTTCGAATTCGCTACACGAATTTTA
1 TTTTCGCAACACAATTTTTAAATTCGCAACACAAATTTTA
* * * **
1275391 ATTTCGCAAAACAACTTTTATTTTCGCAACACAAAT
1 TTTTCGCAACACAATTTTTAAATTCGCAACACAAAT
1275427 GTTTTGGGTA
Statistics
Matches: 56, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.38
Consensus pattern (40 bp):
TTTTCGCAACACAATTTTTAAATTCGCAACACAAATTTTA
Found at i:1275409 original size:20 final size:20
Alignment explanation
Indices: 1275386--1275424 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1275376 GCTACACGAA
1275386 TTTTAATTTCGCAAAACAAC
1 TTTTAATTTCGCAAAACAAC
* *
1275406 TTTTATTTTCGCAACACAA
1 TTTTAATTTCGCAAAACAA
1275425 ATGTTTTGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (20 bp):
TTTTAATTTCGCAAAACAAC
Found at i:1276782 original size:20 final size:21
Alignment explanation
Indices: 1276759--1276833 Score: 59
Period size: 20 Copynumber: 3.7 Consensus size: 21
1276749 AAAAGTTGTT
1276759 TTGCGAAATT-AAAATTCATG
1 TTGCGAAATTCAAAATTCATG
* *
1276779 TTGCG-AATTCAAAAATCGA-A
1 TTGCGAAATTCAAAATTC-ATG
* * *
1276799 TTGCAAAAAT-AAAATTCGTG
1 TTGCGAAATTCAAAATTCATG
*
1276819 TTGCGAAATTGAAAA
1 TTGCGAAATTCAAAA
1276834 GCGCTTTGCG
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
19 4 0.10
20 29 0.71
21 8 0.20
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (21 bp):
TTGCGAAATTCAAAATTCATG
Found at i:1276943 original size:21 final size:21
Alignment explanation
Indices: 1276914--1276971 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1276904 CGAATTTGTC
*
1276914 TTCTGTGTTGCTAATTCCAAA
1 TTCTGTGTTGCAAATTCCAAA
*
1276935 TTCTATGTTGCAAATTCCAAA
1 TTCTGTGTTGCAAATTCCAAA
*
1276956 TTATGTGTTGCAAATT
1 TTCTGTGTTGCAAATT
1276972 TGGAAACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (21 bp):
TTCTGTGTTGCAAATTCCAAA
Found at i:1282362 original size:21 final size:21
Alignment explanation
Indices: 1282336--1282375 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1282326 CTGGAATCTC
*
1282336 GGTCTCGATATCAAACCCTTT
1 GGTCTCAATATCAAACCCTTT
1282357 GGTCTCAATATCAAACCCT
1 GGTCTCAATATCAAACCCT
1282376 CAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (21 bp):
GGTCTCAATATCAAACCCTTT
Found at i:1284231 original size:25 final size:25
Alignment explanation
Indices: 1284203--1284257 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1284193 TACAAAATCA
1284203 AAAACCAAAAATGAATAAATTGAA-T
1 AAAACCAAAAATGAA-AAATTGAATT
** *
1284228 AAAATTAAGAATGAAAAATTGAATT
1 AAAACCAAAAATGAAAAATTGAATT
1284253 AAAAC
1 AAAAC
1284258 GAATCAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.64, C:0.05, G:0.09, T:0.22
Consensus pattern (25 bp):
AAAACCAAAAATGAAAAATTGAATT
Found at i:1285740 original size:21 final size:21
Alignment explanation
Indices: 1285714--1285765 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1285704 GACTTTCGAA
1285714 TTTCTCCTGGGAAGTAACCAG
1 TTTCTCCTGGGAAGTAACCAG
*
1285735 TTTCTCCTGGGAATTAACCAG
1 TTTCTCCTGGGAAGTAACCAG
1285756 TTTCTCCTGG
1 TTTCTCCTGG
1285766 AAAATCACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (21 bp):
TTTCTCCTGGGAAGTAACCAG
Found at i:1285775 original size:21 final size:21
Alignment explanation
Indices: 1285714--1285775 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
1285704 GACTTTCGAA
*
1285714 TTTCTCCTGGGAAGTAACCAG
1 TTTCTCCTGGGAAATAACCAG
*
1285735 TTTCTCCTGGGAATTAACCAG
1 TTTCTCCTGGGAAATAACCAG
* *
1285756 TTTCTCCTGGAAAATCACCA
1 TTTCTCCTGGGAAATAACCA
1285776 ACTTTTCCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (21 bp):
TTTCTCCTGGGAAATAACCAG
Found at i:1287227 original size:20 final size:20
Alignment explanation
Indices: 1287204--1287241 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1287194 AGTAAAATAA
1287204 AATA-AAAATAAGTAAATAGG
1 AATATAAAA-AAGTAAATAGG
*
1287224 AATATTAAAAAGTAAATA
1 AATATAAAAAAGTAAATA
1287242 AGATTAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (20 bp):
AATATAAAAAAGTAAATAGG
Found at i:1289496 original size:2 final size:2
Alignment explanation
Indices: 1289489--1289534 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1289479 AATAGAAGTA
1289489 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
1289531 AT AT
1 AT AT
1289535 GTTTATAAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1290225 original size:23 final size:23
Alignment explanation
Indices: 1290192--1290259 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
1290182 CATCTTATAT
1290192 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* * *
1290215 GGCACTTCGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
* * *
1290238 GGCACTCCAGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
1290260 AGCTGTAGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:1295122 original size:22 final size:21
Alignment explanation
Indices: 1295094--1295135 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
1295084 AAAAAATATA
1295094 GTTTTTTAAATAATAATTTTAC
1 GTTTTTTAAATAA-AATTTTAC
1295116 GTTTTTTAAATAAAATTTTA
1 GTTTTTTAAATAAAATTTTA
1295136 TAAGCATGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (21 bp):
GTTTTTTAAATAAAATTTTAC
Found at i:1300600 original size:86 final size:86
Alignment explanation
Indices: 1300493--1300668 Score: 237
Period size: 86 Copynumber: 2.0 Consensus size: 86
1300483 AGTATGATCG
* * * *
1300493 AAAAAATTAGGGATCTCAATTATAA-AGGTAAAAAGTGATATTAAAAAAATAGGGACATCAATTT
1 AAAAAATTAGGGATCTAAATTATAAGA-GTAAAAAATGAGATTAAAAAAATAGGGACATCAATTA
1300557 TAAAGGTAAAAAGTGAGATTGA
65 TAAAGGTAAAAAGTGAGATTGA
* * * * ** *
1300579 AAAAAATTAGGGGTCTAAATTATATGAGTAAAAAATGGGATTGAAAATTTAGGGACCTCAATTAT
1 AAAAAATTAGGGATCTAAATTATAAGAGTAAAAAATGAGATTAAAAAAATAGGGACATCAATTAT
1300644 AAAGGTAAAAAGTGAGATTGA
66 AAAGGTAAAAAGTGAGATTGA
1300665 AAAA
1 AAAA
1300669 GGCAGGAGCT
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 77 0.99
87 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.26
Consensus pattern (86 bp):
AAAAAATTAGGGATCTAAATTATAAGAGTAAAAAATGAGATTAAAAAAATAGGGACATCAATTAT
AAAGGTAAAAAGTGAGATTGA
Found at i:1300689 original size:128 final size:129
Alignment explanation
Indices: 1300492--1300826 Score: 326
Period size: 128 Copynumber: 2.6 Consensus size: 129
1300482 AAGTATGATC
* * *
1300492 GAAAAAATTAGGGATCTCAATTATAAAGGTAAAAAGTGATATT-AAAAAAATAGGGACATCAATT
1 GAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAACAGGGACATCAATT
* * *
1300556 TTAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGGTC-TAAATTAT-ATG-AGTAAAAAATGGG
66 ATAAAGATAAAAAGTGAGATTG-AAAAAATTA--GGTCATAAATTATAATGTA-AAAAAAATGGG
1300618 ATT
127 ATT
* ** *
1300621 G-AAAATTTAGGGACCTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAGGCA-GGAGC-TTAAT
1 GAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAACAGGGA-CATCAAT
* * * * *
1300683 TATAAAGATACAAGGTGGGATTGAAAAACTTAGGTCATCAATTATAAATGTAAAAAAAATGGGAT
65 TATAAAGATAAAAAGTGAGATTGAAAAAATTAGGTCATAAATTAT-AATGTAAAAAAAATGGGAT
1300748 T
129 T
* * * * * * ** *
1300749 GAAAAACTTA-GGTCATCAATTATAAATGTAAAAAAATGGGATTGAAAAAATTAGGGACCTCAAT
1 GAAAAAATTAGGGACCTCAATTATAAAGGT-AAAAAGTGAGATTGAAAAAAACAGGGACATCAAT
*
1300813 TATAAGGATAAAAA
65 TATAAAGATAAAAA
1300827 ACTAAAATTA
Statistics
Matches: 168, Mismatches: 28, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
125 4 0.02
126 7 0.04
127 8 0.05
128 96 0.57
129 35 0.21
130 18 0.11
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (129 bp):
GAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAACAGGGACATCAATT
ATAAAGATAAAAAGTGAGATTGAAAAAATTAGGTCATAAATTATAATGTAAAAAAAATGGGATT
Found at i:1300726 original size:84 final size:86
Alignment explanation
Indices: 1300542--1300826 Score: 228
Period size: 86 Copynumber: 3.3 Consensus size: 86
1300532 ATTAAAAAAA
* ** * *
1300542 TAGGGACATCAATTTTAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGGTCTAAATTATATGAG
1 TAGGGACATCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAAGCAGGAGTCTAAATTATAAGAG
*
1300607 TAAAAAATGGGATTGAAAATT
66 TAAAAAATGGGATTGAAAACT
* * *
1300628 TAGGGACCTCAATTATAAAGGTAAAAAGTGAGATTG-AAAAAGGCAGGAG-CTTAATTATAA-AG
1 TAGGGACATCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAAGCAGGAGTCTAAATTATAAGAG
* **
1300690 ATACAAGGTGGGATTGAAAAACT
66 -TAAAAAATGGGATTG-AAAACT
* * * * *** *
1300713 TA-GGTCATCAATTATAAATGTAAAAAAAATGGGATTG-AAAAACTTA-G-GTCATCAATTATAA
1 TAGGGACATCAATTATAAAGGT--AAAAAGTGAGATTGAAAAAAAGCAGGAGTC-TAAATTATAA
*
1300774 -ATGTAAAAAAATGGGATTGAAAAAAT
63 GA-GT-AAAAAATGGGATTG-AAAACT
*
1300800 TAGGGACCTCAATTAT-AAGGATAAAAA
1 TAGGGACATCAATTATAAAGG-TAAAAA
1300827 ACTAAAATTA
Statistics
Matches: 161, Mismatches: 28, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
83 2 0.01
84 38 0.24
85 18 0.11
86 68 0.42
87 23 0.14
88 12 0.07
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (86 bp):
TAGGGACATCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAAGCAGGAGTCTAAATTATAAGAG
TAAAAAATGGGATTGAAAACT
Found at i:1300761 original size:44 final size:43
Alignment explanation
Indices: 1300698--1300817 Score: 195
Period size: 44 Copynumber: 2.7 Consensus size: 43
1300688 AGATACAAGG
1300698 TGGGATTGAAAAACTTAGGTCATCAATTATAAATGTAAAAAAAA
1 TGGGATTGAAAAACTTAGGTCATCAATTATAAATGT-AAAAAAA
1300742 TGGGATTGAAAAACTTAGGTCATCAATTATAAATGTAAAAAAA
1 TGGGATTGAAAAACTTAGGTCATCAATTATAAATGTAAAAAAA
* * *
1300785 TGGGATTGAAAAAATTAGGGACCTCAATTATAA
1 TGGGATTGAAAAACTTA-GGTCATCAATTATAA
1300818 GGATAAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
43 23 0.32
44 49 0.68
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (43 bp):
TGGGATTGAAAAACTTAGGTCATCAATTATAAATGTAAAAAAA
Found at i:1300827 original size:44 final size:43
Alignment explanation
Indices: 1300492--1300826 Score: 279
Period size: 42 Copynumber: 7.8 Consensus size: 43
1300482 AAGTATGATC
* **
1300492 GAAAAAATTAGGGATCTCAATTATAAAGGTAAAAAGTGATATT
1 GAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGGGATT
* * * *
1300535 -AAAAAAATAGGGACATCAATTTTAAAGGTAAAAAGTGAGATT
1 GAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGGGATT
** * * *
1300577 GAAAAAAATTAGGGGTCTAAATTAT-ATGAGTAAAAAATGGGATT
1 G-AAAAAATTAGGGACCTCAATTATAAAG-GTAAAAAGTGGGATT
* *
1300621 G-AAAATTTAGGGACCTCAATTATAAAGGTAAAAAGTGAGATT
1 GAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGGGATT
*** * * * * *
1300663 GAAAAAGGCA-GGAGCTTAATTATAAAGATACAAGGTGGGATT
1 GAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGGGATT
* * * * *
1300705 GAAAAACTTA-GGTCATCAATTATAAATGTAAAAAAAATGGGATT
1 GAAAAAATTAGGGACCTCAATTATAAAGGT--AAAAAGTGGGATT
* * * * *
1300749 GAAAAACTTA-GGTCATCAATTATAAATGTAAAAAAATGGGATT
1 GAAAAAATTAGGGACCTCAATTATAAAGGT-AAAAAGTGGGATT
1300792 GAAAAAATTAGGGACCTCAATTAT-AAGGATAAAAA
1 GAAAAAATTAGGGACCTCAATTATAAAGG-TAAAAA
1300827 ACTAAAATTA
Statistics
Matches: 237, Mismatches: 46, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
42 115 0.49
43 40 0.17
44 82 0.35
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (43 bp):
GAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGGGATT
Found at i:1301528 original size:26 final size:26
Alignment explanation
Indices: 1301498--1301564 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
1301488 TGTTTAGCTG
1301498 AGTAGTCGGCTACCCCGAACTAGCCA
1 AGTAGTCGGCTACCCCGAACTAGCCA
*
1301524 AGTAGTCGGCTACCCCGAACTAGCTA
1 AGTAGTCGGCTACCCCGAACTAGCCA
*
1301550 AGCAGTCGGCTACCC
1 AGTAGTCGGCTACCC
1301565 TGTTGCCTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.25, C:0.34, G:0.24, T:0.16
Consensus pattern (26 bp):
AGTAGTCGGCTACCCCGAACTAGCCA
Found at i:1305216 original size:21 final size:19
Alignment explanation
Indices: 1305182--1305221 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1305172 CTCACGTCTA
1305182 ACAACCTTCTCTTTTTCTTC
1 ACAACCTTCTC-TTTTCTTC
*
1305202 ACAACTCTTGTCTTTTCTTC
1 ACAAC-CTTCTCTTTTCTTC
1305222 TCTTCTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.15, C:0.33, G:0.03, T:0.50
Consensus pattern (19 bp):
ACAACCTTCTCTTTTCTTC
Found at i:1309320 original size:144 final size:144
Alignment explanation
Indices: 1309060--1309492 Score: 784
Period size: 144 Copynumber: 3.0 Consensus size: 144
1309050 GGTTATGAAG
1309060 AATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGTCGTTTATTTGGAT
1 AATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGTCGTTTATTTGGAT
*
1309125 TGATAAGTGTCAAGCAAATTAAAGATGCAGACAAATAAAATATGCCAAGATTCTATGATTTTAAT
66 TGATAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAAGATTCTATGATTTTAAT
1309190 GGTAACTTTGGAAT
131 GGTAACTTTGGAAT
*
1309204 AATTTCTCATTGATTTCCTTATCGATTACCTAGCTATGGAGAAAAGATGTGTCGTTTATTTGGAT
1 AATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGTCGTTTATTTGGAT
*
1309269 TGATAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAAGATTCTATGATTTTAAA
66 TGATAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAAGATTCTATGATTTTAAT
* *
1309334 GGT---TGT-GAAG
131 GGTAACTTTGGAAT
1309344 AATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGTCGTTTATTTGGAT
1 AATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGTCGTTTATTTGGAT
*
1309409 TGACAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAAGATTCTATGATTTTAAT
66 TGATAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAAGATTCTATGATTTTAAT
1309474 GGTAACTTTGGAAT
131 GGTAACTTTGGAAT
1309488 AATTT
1 AATTT
1309493 TCCATAAATT
Statistics
Matches: 275, Mismatches: 10, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
140 133 0.48
141 2 0.01
143 2 0.01
144 138 0.50
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (144 bp):
AATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGTCGTTTATTTGGAT
TGATAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAAGATTCTATGATTTTAAT
GGTAACTTTGGAAT
Found at i:1309439 original size:140 final size:140
Alignment explanation
Indices: 1309047--1309472 Score: 753
Period size: 140 Copynumber: 3.0 Consensus size: 140
1309037 GGTTGTTATC
1309047 AAAGGTTATGAAGAATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGT
1 AAAGGTTATGAAGAATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGT
*
1309112 CGTTTATTTGGATTGATAAGTGTCAAGCAAATTAAAGATGCAGACAAATAAAATATGCCAAGATT
66 CGTTTATTTGGATTGATAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAAGATT
1309177 CTATGATTTT
131 CTATGATTTT
* * * *
1309187 AATGGTAACTTTGGAATAATTTCTCATTGATTTCCTTATCGATTACCTAGCTATGGAGAAAAGAT
1 AAAGGT---TAT-GAAGAATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGAT
1309252 GTGTCGTTTATTTGGATTGATAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAA
62 GTGTCGTTTATTTGGATTGATAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAA
1309317 GATTCTATGATTTT
127 GATTCTATGATTTT
*
1309331 AAAGGTTGTGAAGAATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGT
1 AAAGGTTATGAAGAATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGT
*
1309396 CGTTTATTTGGATTGACAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAAGATT
66 CGTTTATTTGGATTGATAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAAGATT
1309461 CTATGATTTT
131 CTATGATTTT
1309471 AA
1 AA
1309473 TGGTAACTTT
Statistics
Matches: 272, Mismatches: 10, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
140 135 0.50
141 2 0.01
143 2 0.01
144 133 0.49
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.35
Consensus pattern (140 bp):
AAAGGTTATGAAGAATTTCTCATTGATTTCCTTATCGATTACCTAGTTATGGAGAAAAGATGTGT
CGTTTATTTGGATTGATAAGTGTCAAGCAAATTAAAGATGCAGAAAAATAAAATATGCCAAGATT
CTATGATTTT
Found at i:1310963 original size:21 final size:20
Alignment explanation
Indices: 1310912--1310963 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
1310902 TTTTCCCAAT
*
1310912 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
1310932 TCGAAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1310953 TCGCAATGCGA
1 TCGCAATGCGA
1310964 TACTGACTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1310977 original size:20 final size:20
Alignment explanation
Indices: 1310952--1311066 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1310942 AATTGGGAAA
*
1310952 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1310972 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
1310992 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1311013 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1311033 TTCGCAACGTGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1311053 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1311067 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1311014 original size:61 final size:61
Alignment explanation
Indices: 1310949--1311086 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
1310939 GCGAATTGGG
* * *
1310949 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * * *
1311010 AAAATCGCAACGAGATACTGACTTTCGCAACGTGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
1311071 ATAATCGTAATGCGAT
1 AAAATCGCAATGCGAT
1311087 TTTCAAAGCG
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1311281 original size:22 final size:22
Alignment explanation
Indices: 1311254--1311297 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1311244 CACTCTCTCA
*
1311254 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCAGACGAAATCCGTC
*
1311276 CCCATCTCAGGCGAAATCCGTC
1 CCCATCTCAGACGAAATCCGTC
1311298 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCAGACGAAATCCGTC
Found at i:1311614 original size:20 final size:20
Alignment explanation
Indices: 1311560--1311618 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1311550 GCGATTCTCT
**
1311560 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1311580 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1311600 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1311619 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1311809 original size:25 final size:24
Alignment explanation
Indices: 1311755--1311809 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1311745 TGTTTATTAT
* *
1311755 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1311779 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1311805 TGTTT
1 TGTTT
1311810 ATTTTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1312959 original size:18 final size:18
Alignment explanation
Indices: 1312938--1312982 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1312928 TCCACTTCGG
1312938 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1312956 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1312974 GAGCCATCA
1 GAGCCATCA
1312983 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1313489 original size:20 final size:20
Alignment explanation
Indices: 1313464--1313509 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1313454 TAGTTTACTT
1313464 TCGCAACAC-GAAAATGACTA
1 TCGCAACACAG-AAATGACTA
* *
1313484 TCGCAACGCAGAAATGGCTA
1 TCGCAACACAGAAATGACTA
1313504 TCGCAA
1 TCGCAA
1313510 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAATGACTA
Done.