Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007845.1 Hibiscus syriacus cultivar Beakdansim tig00110201_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: 2731752
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 11 of 13
Found at i:2211535 original size:16 final size:16
Alignment explanation
Indices: 2211514--2211550 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2211504 TTATTTCACA
*
2211514 TATTTCTATTTTTATT
1 TATTTCCATTTTTATT
*
2211530 TATTTCCATTTTTCTT
1 TATTTCCATTTTTATT
2211546 TATTT
1 TATTT
2211551 AAATATTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTCCATTTTTATT
Found at i:2212334 original size:22 final size:23
Alignment explanation
Indices: 2212286--2212337 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2212276 ATCACCCATT
2212286 TTTTTCAAAATAAAGTTGTAATCG
1 TTTTT-AAAATAAAGTTGTAATCG
*
2212310 TTTTTAAAATAATA-TT-TAATTG
1 TTTTTAAAATAA-AGTTGTAATCG
2212332 TTTTTA
1 TTTTTA
2212338 TAAAAAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 11 0.42
23 9 0.35
24 6 0.23
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (23 bp):
TTTTTAAAATAAAGTTGTAATCG
Found at i:2212336 original size:23 final size:24
Alignment explanation
Indices: 2212285--2212342 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 24
2212275 AATCACCCAT
2212285 TTTTTTCAAAATAAAGTTGTAATCG
1 TTTTTT-AAAATAAAGTTGTAATCG
*
2212310 -TTTTTAAAATAATA-TT-TAATTG
1 TTTTTTAAAATAA-AGTTGTAATCG
2212332 TTTTTATAAAA
1 TTTTT-TAAAA
2212343 AATGGTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 5 0.17
23 13 0.45
24 11 0.38
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (24 bp):
TTTTTTAAAATAAAGTTGTAATCG
Found at i:2213273 original size:29 final size:30
Alignment explanation
Indices: 2213240--2213301 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2213230 TTATTTTACA
2213240 TGTACTAACTTATGT-TTCTCTTTTGTTTG
1 TGTACTAACTTATGTCTTCTCTTTTGTTTG
*
2213269 TGTACTAACTTATTTCTTCTCTTTTGTTTG
1 TGTACTAACTTATGTCTTCTCTTTTGTTTG
2213299 TGT
1 TGT
2213302 CATTTTGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.13, C:0.15, G:0.13, T:0.60
Consensus pattern (30 bp):
TGTACTAACTTATGTCTTCTCTTTTGTTTG
Found at i:2214724 original size:26 final size:25
Alignment explanation
Indices: 2214695--2214772 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
2214685 AATTTTTGAC
2214695 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
2214721 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
* *
2214741 ATTCCCTCTCTTTGAGACCTGGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
2214767 ATTCTT
1 ATTCTT
2214773 TCCACTTTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 13
0.66 0.12 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.13
26 13 0.33
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:2215404 original size:22 final size:22
Alignment explanation
Indices: 2215377--2215484 Score: 94
Period size: 22 Copynumber: 4.7 Consensus size: 22
2215367 AAGATCCAAT
2215377 CAAAAACAAAGAAAAATCAAAG
1 CAAAAACAAAGAAAAATCAAAG
* *
2215399 AGAAAAGAGCAAAGAAAAAAACAAAG
1 -CAAAA-A-CAAAG-AAAAATCAAAG
* * *
2215425 -AGCAGAGAAA-AAAAATCAAAG
1 CA-AAAACAAAGAAAAATCAAAG
2215446 CAAAAACAAAGAAAAATCAAAG
1 CAAAAACAAAGAAAAATCAAAG
*
2215468 CAAAAGTCAAAGAAAAA
1 CAAAA-ACAAAGAAAAA
2215485 AGCAAAGAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
21 15 0.22
22 17 0.25
23 17 0.25
24 3 0.04
25 6 0.09
26 10 0.15
ACGTcount: A:0.71, C:0.11, G:0.14, T:0.04
Consensus pattern (22 bp):
CAAAAACAAAGAAAAATCAAAG
Found at i:2215414 original size:12 final size:11
Alignment explanation
Indices: 2215378--2215493 Score: 69
Period size: 12 Copynumber: 10.2 Consensus size: 11
2215368 AGATCCAATC
2215378 AAAAA-CAAAG
1 AAAAAGCAAAG
*
2215388 AAAAATCAAAGAG
1 AAAAAGC-AA-AG
2215401 AAAAGAGCAAAG
1 AAAA-AGCAAAG
*
2215413 AAAAAAACAAAG
1 -AAAAAGCAAAG
* *
2215425 AGCAGAG-AAA-
1 A-AAAAGCAAAG
*
2215435 AAAAATCAAAG
1 AAAAAGCAAAG
2215446 CAAAAA-CAAAG
1 -AAAAAGCAAAG
*
2215457 AAAAATCAAAG
1 AAAAAGCAAAG
*
2215468 CAAAAGTCAAAG
1 AAAAAG-CAAAG
2215480 AAAAAAGCAAAG
1 -AAAAAGCAAAG
2215492 AA
1 AA
2215494 CAAAAAGAGG
Statistics
Matches: 83, Mismatches: 11, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
9 2 0.02
10 14 0.17
11 21 0.25
12 27 0.33
13 17 0.20
14 2 0.02
ACGTcount: A:0.72, C:0.10, G:0.15, T:0.03
Consensus pattern (11 bp):
AAAAAGCAAAG
Found at i:2215426 original size:19 final size:19
Alignment explanation
Indices: 2215402--2215438 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2215392 ATCAAAGAGA
2215402 AAAGAGCAAAGAAAAAAAC
1 AAAGAGCAAAGAAAAAAAC
*
2215421 AAAGAGCAGAGAAAAAAA
1 AAAGAGCAAAGAAAAAAA
2215439 ATCAAAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.08, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAGAGCAAAGAAAAAAAC
Found at i:2216684 original size:4 final size:4
Alignment explanation
Indices: 2216675--2216740 Score: 73
Period size: 4 Copynumber: 17.0 Consensus size: 4
2216665 AAGAGTATAC
* * * * *
2216675 ACAT ACAT ACAT ACGT ATAT ACAT ACGT ATAT ACAT ACAT ATAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2216723 ACAT ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT
2216741 GATACATAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 2 0.04
4 48 0.96
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (4 bp):
ACAT
Found at i:2216698 original size:12 final size:12
Alignment explanation
Indices: 2216675--2216740 Score: 87
Period size: 12 Copynumber: 5.3 Consensus size: 12
2216665 AAGAGTATAC
*
2216675 ACATACATACAT
1 ACATATATACAT
*
2216687 ACGTATATACAT
1 ACATATATACAT
*
2216699 ACGTATATACAT
1 ACATATATACAT
2216711 ACATATATACAT
1 ACATATATACAT
2216723 ACATACATATACAT
1 ACAT--ATATACAT
2216737 ACAT
1 ACAT
2216741 GATACATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
12 37 0.76
14 12 0.24
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (12 bp):
ACATATATACAT
Found at i:2216698 original size:16 final size:14
Alignment explanation
Indices: 2216671--2216740 Score: 76
Period size: 14 Copynumber: 5.1 Consensus size: 14
2216661 CGAGAAGAGT
*
2216671 ATACACATACATAC
1 ATACATATACATAC
*
2216685 ATACGTAT--ATAC
1 ATACATATACATAC
2216697 ATACGTATATACATAC
1 ATAC--ATATACATAC
2216713 AT--ATATACATAC
1 ATACATATACATAC
2216725 ATACATATACATAC
1 ATACATATACATAC
2216739 AT
1 AT
2216741 GATACATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
12 20 0.43
14 21 0.45
16 6 0.13
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (14 bp):
ATACATATACATAC
Found at i:2217136 original size:36 final size:36
Alignment explanation
Indices: 2217096--2217194 Score: 171
Period size: 36 Copynumber: 2.8 Consensus size: 36
2217086 GATTTTTCTA
2217096 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
*
2217132 AAAACAAATTTTGTCTCGCCTGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
**
2217168 AAAACAAATTTTGTCTCATTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
2217195 TTTTCCCTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
Found at i:2217523 original size:101 final size:98
Alignment explanation
Indices: 2217317--2217550 Score: 251
Period size: 101 Copynumber: 2.3 Consensus size: 98
2217307 TGAGAATTTT
** * *
2217317 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACC
*
2217382 AAAAACAAAATCTCACCTTAGATTGTTGTTTCTTTC
66 AAAAACAAAATCTCACCTTAGA-T-TCGTTTC-TTC
* * *
2217418 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCA-C
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACC
*
2217482 ATTAAACAAAGTTGATCTCA-CTTGAGA-TCGTTTC-TC
66 A-AAAACAAA----ATCTCACCTT-AGATTCGTTTCTTC
* *
2217518 AAAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 -AAAACAAATTTTGTCTCGCTTGAGACATTTTC
2217551 TCTAAAAACA
Statistics
Matches: 114, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
100 4 0.04
101 92 0.81
102 6 0.05
104 3 0.03
105 9 0.08
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (98 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACC
AAAAACAAAATCTCACCTTAGATTCGTTTCTTC
Found at i:2217524 original size:35 final size:33
Alignment explanation
Indices: 2217497--2217614 Score: 137
Period size: 33 Copynumber: 3.4 Consensus size: 33
2217487 ACAAAGTTGA
2217497 TCTCACTTGAGATCGTTTCTCAAAAACAAACTTTG
1 TCTCACTTGAGA-C-TTTCTCAAAAACAAACTTTG
* *
2217532 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGAC--TTTCTC-AAAAACAAACTTTG
* * *
2217568 TCTCATTTGAGACTATATCAAAAACAAACTTTG
1 TCTCACTTGAGACTTTCTCAAAAACAAACTTTG
*
2217601 TCTCATTTGAGACT
1 TCTCACTTGAGACT
2217615 ATATCTTAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
33 27 0.37
34 5 0.07
35 17 0.23
36 24 0.33
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (33 bp):
TCTCACTTGAGACTTTCTCAAAAACAAACTTTG
Found at i:2217602 original size:69 final size:67
Alignment explanation
Indices: 2217497--2217647 Score: 176
Period size: 69 Copynumber: 2.2 Consensus size: 67
2217487 ACAAAGTTGA
* * * *
2217497 TCTCACTTGAGATCGTTTCTCAAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCTAAAAACAA
1 TCTCACTTGAGA-C-TATATCAAAAACAAACTTTGTCTCACTTGAGACAATATCT-T-AAAACAA
*
2217562 ATTTTG
62 ATTTCG
* * * *
2217568 TCTCATTTGAGACTATATCAAAAACAAACTTTGTCTCATTTGAGACTATATCTTAAAGCAAATTT
1 TCTCACTTGAGACTATATCAAAAACAAACTTTGTCTCACTTGAGACAATATCTTAAAACAAATTT
2217633 CG
66 CG
*
2217635 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
2217648 ATCATTTTCT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
67 22 0.32
68 1 0.01
69 34 0.49
70 1 0.01
71 11 0.16
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (67 bp):
TCTCACTTGAGACTATATCAAAAACAAACTTTGTCTCACTTGAGACAATATCTTAAAACAAATTT
CG
Found at i:2217645 original size:34 final size:34
Alignment explanation
Indices: 2217519--2217647 Score: 136
Period size: 33 Copynumber: 3.8 Consensus size: 34
2217509 TCGTTTCTCA
* * *
2217519 AAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAACAAACTTTGTCTCACTTGAGACTATATCT-T
* * *
2217554 AAAAACAAATTTTGTCTCATTTGAGACTATATC-A
1 -AAAACAAACTTTGTCTCACTTGAGACTATATCTT
*
2217588 AAAACAAACTTTGTCTCATTTGAGACTATATCTT
1 AAAACAAACTTTGTCTCACTTGAGACTATATCTT
* *
2217622 AAAGCAAA-TTTCGTCTCGCTTGAGAC
1 AAAACAAACTTT-GTCTCACTTGAGAC
2217648 ATCATTTTCT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
33 34 0.43
34 19 0.24
36 27 0.34
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (34 bp):
AAAACAAACTTTGTCTCACTTGAGACTATATCTT
Found at i:2217938 original size:29 final size:29
Alignment explanation
Indices: 2217888--2217961 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
2217878 AAGACAATTT
* *
2217888 CTTTTGGA-AAAAATCTTTGAGTTCGTTC
1 CTTTTGAATAAAAATCTTGGAGTTCGTTC
*
2217916 CTTTTGAATAAAAATCTTGGAGTTTGTTC
1 CTTTTGAATAAAAATCTTGGAGTTCGTTC
*
2217945 CTTTGGAATAAAAATCT
1 CTTTTGAATAAAAATCT
2217962 GTGAGTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 7 0.17
29 34 0.83
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (29 bp):
CTTTTGAATAAAAATCTTGGAGTTCGTTC
Found at i:2217970 original size:28 final size:27
Alignment explanation
Indices: 2217896--2217971 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 27
2217886 TTCTTTTGGA
*
2217896 AAAAATCTTTGAGTTCGTTCCTTTTGAAT
1 AAAAATC-TTGAGTT-GTTCCTTTGGAAT
2217925 AAAAATCTTGGAGTTTGTTCCTTTGGAAT
1 AAAAATCTT-GAG-TTGTTCCTTTGGAAT
2217954 AAAAATCTGTGAGTTGTT
1 AAAAATCT-TGAGTTGTT
2217972 TGAGTCTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
28 7 0.16
29 33 0.77
30 3 0.07
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (27 bp):
AAAAATCTTGAGTTGTTCCTTTGGAAT
Found at i:2218060 original size:30 final size:30
Alignment explanation
Indices: 2218026--2218290 Score: 154
Period size: 30 Copynumber: 8.1 Consensus size: 30
2218016 ATTTTGTGAA
2218026 AAAAATCTTTGAGATTGTTTCCTTT-GAAAC
1 AAAAATCTTTGAGATTGTTT-CTTTGGAAAC
*
2218056 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * ** *
2218086 AAAATTTTGTCTCTTTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATC-TTTGAGATTGTTTCTTTGGAAAC
*
2218123 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * * *
2218153 AAAATTTTGTCTCTCTAAAGATAGTTTCTTTTGAAAC
1 AAAA----ATCT-T-T-GAGATTGTTTCTTTGGAAAC
*
2218190 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * *** *
2218220 AAAATTTTGTCTCTCTTAAGATAAATTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATTGTTTCTTTGGAAAC
*
2218257 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
2218287 AAAA
1 AAAA
2218291 TTTTTTCTCT
Statistics
Matches: 176, Mismatches: 37, Indels: 44
0.68 0.14 0.17
Matches are distributed among these distances:
29 4 0.02
30 90 0.51
31 6 0.03
32 1 0.01
33 3 0.02
34 3 0.02
35 1 0.01
36 6 0.03
37 62 0.35
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:2218088 original size:93 final size:97
Alignment explanation
Indices: 2217970--2218156 Score: 242
Period size: 93 Copynumber: 2.0 Consensus size: 97
2217960 CTGTGAGTTG
* *
2217970 TTTGAGTCTATTTACTTTGAAACAAAGTTTTGTCTCTCTTGAGACAA-TT-TTGTG-AA-AAAAA
1 TTTGAGTCTATTTACTTTGAAACAAAATTTTGTCTCTCTTAAGACAATTTCTTGTGAAACAAAAA
2218031 TCTTTGAGATTGTTTCCTTT-GAAACAAAAATC
66 TCTTTGAGATTGTTT-CTTTGGAAACAAAAATC
* * * * *
2218063 TTTGAGTTTGTTT-CTTTGGAAACAAAATTTTGTCTCTTTTAAGATAATTTCTTTTGAAACAAAA
1 TTTGAGTCTATTTACTTT-GAAACAAAATTTTGTCTCTCTTAAGACAATTTCTTGTGAAACAAAA
*
2218127 ATCTTTGAGTTTGTTTCTTTGGAAACAAAA
65 ATCTTTGAGATTGTTTCTTTGGAAACAAAA
2218157 TTTTGTCTCT
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
92 4 0.05
93 36 0.45
94 2 0.03
95 4 0.05
96 6 0.08
97 28 0.35
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (97 bp):
TTTGAGTCTATTTACTTTGAAACAAAATTTTGTCTCTCTTAAGACAATTTCTTGTGAAACAAAAA
TCTTTGAGATTGTTTCTTTGGAAACAAAAATC
Found at i:2218114 original size:37 final size:37
Alignment explanation
Indices: 2218072--2218260 Score: 127
Period size: 37 Copynumber: 5.5 Consensus size: 37
2218062 CTTTGAGTTT
2218072 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
* * * * * *
2218109 ATTTCTTTTGAAACAAAA------ATC-TTTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
* *
2218139 GTTTCTTTGGAAACAAAATTTTGTCTCTCTAAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
* * * * *
2218176 GTTTCTTTTGAAACAAAA------ATC-TTTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
*
2218206 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
** *
2218243 AATTCTTTTGAAACAAAA
1 GTTTCTTTGGAAACAAAA
2218261 ATCTTTGAGT
Statistics
Matches: 108, Mismatches: 30, Indels: 28
0.65 0.18 0.17
Matches are distributed among these distances:
30 43 0.40
31 4 0.04
36 4 0.04
37 57 0.53
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
Found at i:2218127 original size:67 final size:67
Alignment explanation
Indices: 2218043--2218322 Score: 497
Period size: 67 Copynumber: 4.2 Consensus size: 67
2218033 TTTGAGATTG
* *
2218043 TTTCCTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
2218108 AA
66 AA
*
2218110 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTAAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
*
2218175 AG
66 AA
2218177 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
2218242 AA
66 AA
* * *
2218244 ATTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAAAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
2218309 AA
66 AA
2218311 TTTCTTTTGAAA
1 TTTCTTTTGAAA
2218323 AAATCTTTGA
Statistics
Matches: 203, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 203 1.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:2218642 original size:64 final size:63
Alignment explanation
Indices: 2218563--2218687 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 63
2218553 GATGTGATTC
* * *
2218563 ATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTATTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCT-CTAAAGACAACTTCTTTTGAAAAAA
* * **
2218627 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
2218688 TACCAACCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
63 19 0.35
64 35 0.65
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:2218867 original size:15 final size:15
Alignment explanation
Indices: 2218844--2218887 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
2218834 TTTTGAGTCG
*
2218844 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
2218859 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
2218874 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
2218888 AGATCGTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:2219035 original size:64 final size:62
Alignment explanation
Indices: 2218894--2219050 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 62
2218884 AACAAGATCG
* * *
2218894 TCTTTGAGTTTGTTTCTCTGGAAAC--AATGTTTTATCCCTTAAAACAATTTCTTTTGAAAAA
1 TCTTTGAGTTTGTTTCTTTGGAAACAAAAT-TTTTATCCCTCAAAACAATTTCTTTAGAAAAA
* * * * * * * * *
2218955 TCATTGAATCTCTTTCTTTGGAAACAAAATTTTGTGTCTCTCGAGACAGTTTCTTTGAGAAAAA
1 TCTTTGAGTTTGTTTCTTTGGAAACAAAATTTT-TATCCCTCAAAACAATTTCTTT-AGAAAAA
2219019 TCTTTGAGTTTGTTTCTTTGGAAACAAAATTT
1 TCTTTGAGTTTGTTTCTTTGGAAACAAAATTT
2219051 ACCATCTTTG
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
61 20 0.26
62 3 0.04
63 19 0.25
64 34 0.45
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (62 bp):
TCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTATCCCTCAAAACAATTTCTTTAGAAAAA
Found at i:2219602 original size:43 final size:43
Alignment explanation
Indices: 2219451--2219615 Score: 133
Period size: 40 Copynumber: 3.8 Consensus size: 43
2219441 TTATCCCTAG
* *
2219451 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAACCGTGTCA--ACC-AT
** * * * * * **
2219497 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
1 AGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACCAT
* *
2219540 AG---ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACCAT
2219580 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGT
1 AGATAACCAGACC-TCCTCATCACGTAGGAACCGTGT
2219616 TATCACCTTA
Statistics
Matches: 95, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
40 33 0.35
42 1 0.01
43 29 0.31
44 2 0.02
46 29 0.31
47 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (43 bp):
AGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACCAT
Found at i:2219704 original size:130 final size:129
Alignment explanation
Indices: 2219451--2219704 Score: 429
Period size: 130 Copynumber: 2.0 Consensus size: 129
2219441 TTATCCCTAG
*
2219451 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAGAACTCTTCA
* * * *
2219516 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCAGTGTCAACCCCAGACCAGATCTCCTCATCACGTAGGAACCATGTCAACCAT
2219580 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTC
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCC-AGAACTCTTC
*
2219645 ATCACGTATGAGCAGTGTCAACCCTC-GACCAGATTTCCTCATCACGTAGGAACCATGTCA
65 ATCACGTATGAGCAGTGTCAACCC-CAGACCAGATCTCCTCATCACGTAGGAACCATGTCA
2219705 CCCTTAGACG
Statistics
Matches: 117, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
129 53 0.45
130 63 0.54
131 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAGAACTCTTCA
TCACGTATGAGCAGTGTCAACCCCAGACCAGATCTCCTCATCACGTAGGAACCATGTCAACCAT
Found at i:2219907 original size:3 final size:3
Alignment explanation
Indices: 2219899--2219967 Score: 86
Period size: 3 Copynumber: 22.0 Consensus size: 3
2219889 CGGGTCTTTT
2219899 TTA TTA TTA TTTA TATA TATA TCTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
*
2219948 TTA TTA -TA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA
2219968 CATTTTACAT
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.03
3 45 0.75
4 13 0.22
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2222665 original size:23 final size:24
Alignment explanation
Indices: 2222614--2222667 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
2222604 AATCACCCAT
2222614 TTTTTTCAAAATAAAGTTGTAATCG
1 TTTTTT-AAAATAAAGTTGTAATCG
*
2222639 -TTTTTAAAATAATA-TT-TAATTG
1 TTTTTTAAAATAA-AGTTGTAATCG
2222661 TTTTTTA
1 TTTTTTA
2222668 TAAAAAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 5 0.19
23 15 0.58
24 6 0.23
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (24 bp):
TTTTTTAAAATAAAGTTGTAATCG
Found at i:2230321 original size:8 final size:8
Alignment explanation
Indices: 2230308--2230348 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2230298 CTCATTTTCA
2230308 GAGAATTT
1 GAGAATTT
2230316 GAGAATTT
1 GAGAATTT
*
2230324 -AGAGTTT
1 GAGAATTT
*
2230331 GGGAATTT
1 GAGAATTT
2230339 GAGAATTT
1 GAGAATTT
2230347 GA
1 GA
2230349 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:2230628 original size:127 final size:127
Alignment explanation
Indices: 2230359--2230969 Score: 921
Period size: 124 Copynumber: 4.9 Consensus size: 127
2230349 AAGATTGTGA
* * *
2230359 ACTATTCACATGAAGGCACGTTCCCGGGGGGGCGCCTTTCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2230424 CATTGCCCTATTATGT--C-CA-GTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTC
* * *
2230483 ACTATTCAAATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCATAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
* *
2230548 CATTGCCCTATTATGTCACTCA-GTCCCTCGGAAACACTAGATATATTAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGG-GACACTAGATATATCAGTACCTATTATTTC
2230610 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAG-ATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
2230674 CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAG--ATATCATTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
2230734 TC-AGGGACATG-AGGCGCGTT-CC-GGGGCACGCCTTCCATTATTTCGTCAGAG-ATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
2230794 CATTGCCCTAGTATGTCACTCATGTCCCTCGGGACACTAGATATATCA-TACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
* *
2230855 ATTATTCACATGAAGGCGCGTTCCC--GGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
2230918 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTA
2230970 AACCAGGTAA
Statistics
Matches: 445, Mismatches: 29, Indels: 24
0.89 0.06 0.05
Matches are distributed among these distances:
120 76 0.17
121 15 0.03
122 21 0.05
123 41 0.09
124 134 0.30
125 17 0.04
126 43 0.10
127 98 0.22
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (127 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:2231278 original size:33 final size:32
Alignment explanation
Indices: 2231215--2231309 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 32
2231205 AAATTTAATG
*
2231215 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATA-TATAATTTATATTTT-TAT
* *
2231249 TTAAATTT-GAATATATTATTTTTATTTTTAT
1 TTAAATTTCGAATATATAATTTATATTTTTAT
*
2231280 TTAAATTTCGAATAATATAATTTGTATTTT
1 TTAAATTTCGAAT-ATATAATTTATATTTT
2231310 AAAAACATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 10 0.19
32 17 0.31
33 19 0.35
34 8 0.15
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (32 bp):
TTAAATTTCGAATATATAATTTATATTTTTAT
Found at i:2231849 original size:18 final size:18
Alignment explanation
Indices: 2231826--2231863 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2231816 AAAACCCTGC
2231826 GGGCTAGGCATGTAACCT
1 GGGCTAGGCATGTAACCT
2231844 GGGCTAGGCATGTAACCT
1 GGGCTAGGCATGTAACCT
2231862 GG
1 GG
2231864 CGGGCTAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.37, T:0.21
Consensus pattern (18 bp):
GGGCTAGGCATGTAACCT
Found at i:2231870 original size:21 final size:20
Alignment explanation
Indices: 2231821--2231908 Score: 108
Period size: 21 Copynumber: 4.3 Consensus size: 20
2231811 GGTATAAAAC
*
2231821 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
*
2231841 CCT--GGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
2231859 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
2231880 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
2231901 CCCTGCGG
1 -CCTGCGG
2231909 AGATGGCATA
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
18 18 0.29
20 3 0.05
21 38 0.61
22 3 0.05
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:2233691 original size:33 final size:32
Alignment explanation
Indices: 2233652--2233734 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
2233642 AATTCTAAAT
**
2233652 AAATAATAATTATATAAATATTATTTTTAAAAA
1 AAATAATAATTATATAAATA-TATTAATAAAAA
* * *
2233685 AAATAATATTTACATAAATATATTAATATAAA
1 AAATAATAATTATATAAATATATTAATAAAAA
* *
2233717 AAATAATAACTATTTAAA
1 AAATAATAATTATATAAA
2233735 AAATACTAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 23 0.56
33 18 0.44
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATAATAATTATATAAATATATTAATAAAAA
Found at i:2233723 original size:32 final size:33
Alignment explanation
Indices: 2233647--2233725 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
2233637 TTAATAATTC
* **
2233647 TAAATAAATAATAATTATATAAATATTATTTTTA
1 TAAA-AAATAATAATTACATAAATATTATTAATA
* *
2233681 AAAAAAATAATATTTACATAAATA-TATTAATA
1 TAAAAAATAATAATTACATAAATATTATTAATA
2233713 TAAAAAATAATAA
1 TAAAAAATAATAA
2233726 CTATTTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 17 0.45
33 18 0.47
34 3 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAAATAATAATTACATAAATATTATTAATA
Found at i:2233736 original size:18 final size:17
Alignment explanation
Indices: 2233631--2233739 Score: 61
Period size: 16 Copynumber: 6.5 Consensus size: 17
2233621 TATAATTAGC
*
2233631 AAAAAATTAATAAT-TCT
1 AAAAAA-TAATAATATTT
*
2233648 AAATAAATAATAAT-TAT
1 AAA-AAATAATAATATTT
* * *
2233665 -ATAAAT-ATTATTTTT
1 AAAAAATAATAATATTT
2233680 AAAAAA-AATAATATTT
1 AAAAAATAATAATATTT
*
2233696 ACATAAATATATTAATA--T
1 A-A-AAA-ATAATAATATTT
2233714 AAAAAATAATAACTATTT
1 AAAAAATAATAA-TATTT
2233732 AAAAAATA
1 AAAAAATA
2233740 CTAACATAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 21
0.71 0.09 0.21
Matches are distributed among these distances:
14 4 0.06
15 12 0.17
16 18 0.25
17 14 0.19
18 17 0.24
19 1 0.01
20 6 0.08
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAAATAATAATATTT
Found at i:2233749 original size:33 final size:34
Alignment explanation
Indices: 2233679--2233750 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 34
2233669 ATATTATTTT
* *
2233679 TAAAAAAAATAATATTTACATAAATATATTAATA
1 TAAAAAAAATAATATTTACATAAATATACTAACA
2233713 TAAAAAATAATAACTATTTA-A-AAA-ATACTAACA
1 TAAAAAA-AATAA-TATTTACATAAATATACTAACA
2233746 TAAAA
1 TAAAA
2233751 TTAAATTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 12 0.35
34 10 0.29
35 6 0.18
36 6 0.18
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (34 bp):
TAAAAAAAATAATATTTACATAAATATACTAACA
Found at i:2235166 original size:25 final size:23
Alignment explanation
Indices: 2235121--2235204 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 23
2235111 TTACAAATAT
2235121 TAAATATAATAAATAAATTATTTATCA
1 TAAATAT--TAAAT-AATTATTTAT-A
*
2235148 TAAATATTTAATATATTATTT-TA
1 TAAATATTAAATA-ATTATTTATA
2235171 -AAATATTAAATAATTTATTTATTA
1 TAAATATTAAATAA-TTATTTA-TA
2235195 TTAAATATTA
1 -TAAATATTA
2235205 TTTTTATAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
21 1 0.02
22 17 0.35
23 1 0.02
24 4 0.08
25 11 0.22
26 8 0.16
27 7 0.14
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAATATTAAATAATTATTTATA
Found at i:2235341 original size:11 final size:12
Alignment explanation
Indices: 2235325--2235393 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 12
2235315 AAATAATTAG
2235325 TATATT-TTAAA
1 TATATTATTAAA
2235336 TATATTTATTAAA
1 TATA-TTATTAAA
2235349 -ATATTATTAAA
1 TATATTATTAAA
*
2235360 TATA-TAATAATA
1 TATATTATTAA-A
2235372 TTATTCATTATTAAA
1 -TA-T-ATTATTAAA
2235387 TATATTA
1 TATATTA
2235394 ATTTTTTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
11 17 0.35
12 13 0.27
13 8 0.17
14 3 0.06
15 2 0.04
16 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATTATTAAA
Found at i:2235479 original size:55 final size:55
Alignment explanation
Indices: 2235366--2235489 Score: 146
Period size: 55 Copynumber: 2.2 Consensus size: 55
2235356 TAAATATATA
2235366 ATAATATTATTCATTATTAAATATATTAATTTTTTATTATATATATTAAAATAAAAT
1 ATAATA-TATT-ATTATTAAATATATTAATTTTTTATTATATATATTAAAATAAAAT
* * *
2235423 ATAATATCTTATTATTATAATATAATTGATTATTTTA-TATA-ATATTAAAA-ATAAT
1 ATAATATATTATTATTA-AATAT-ATTAATT-TTTTATTATATATATTAAAATAAAAT
*
2235478 ATTATATATTAT
1 ATAATATATTAT
2235490 AAATATTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
55 21 0.36
56 17 0.29
57 16 0.27
58 5 0.08
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (55 bp):
ATAATATATTATTATTAAATATATTAATTTTTTATTATATATATTAAAATAAAAT
Found at i:2235513 original size:29 final size:29
Alignment explanation
Indices: 2235400--2235513 Score: 80
Period size: 29 Copynumber: 4.0 Consensus size: 29
2235390 ATTAATTTTT
*
2235400 TATTATAT-ATATTAAAATAAAATATAATA
1 TATTATATAATATTAAAA-ATAATATAATA
* * * *
2235429 TCTTAT-TATTA-T-AATATAAT-TGATTA
1 TATTATATAATATTAAAAATAATAT-AATA
* *
2235455 TTTTATATAATATTAAAAATAATATTATA
1 TATTATATAATATTAAAAATAATATAATA
2235484 TATTATA-AATATTTAATAAATAA-ATAATA
1 TATTATATAATA-TTAA-AAATAATATAATA
2235513 T
1 T
2235514 TTTGATGAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
25 1 0.02
26 12 0.18
27 6 0.09
28 7 0.11
29 32 0.49
30 7 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
TATTATATAATATTAAAAATAATATAATA
Found at i:2235734 original size:41 final size:42
Alignment explanation
Indices: 2235689--2235799 Score: 170
Period size: 42 Copynumber: 2.7 Consensus size: 42
2235679 AATTACATTC
* *
2235689 CGAAAAACCAATTACGTGAAACAAACACGG-AAAATATTTTT
1 CGAAAAACGAATTACGTGAAACAAACACGGAAAAACATTTTT
* *
2235730 CGAAAAACGAATTACATGAAATAAACACGGAAAAACATTTTT
1 CGAAAAACGAATTACGTGAAACAAACACGGAAAAACATTTTT
*
2235772 CAAAAAACGAATTACGTGAAACAAACAC
1 CGAAAAACGAATTACGTGAAACAAACAC
2235800 ACCCTAAGAG
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 27 0.44
42 35 0.56
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (42 bp):
CGAAAAACGAATTACGTGAAACAAACACGGAAAAACATTTTT
Found at i:2235826 original size:15 final size:16
Alignment explanation
Indices: 2235806--2235837 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2235796 ACACACCCTA
2235806 AGAGAAAAGAAA-ATT
1 AGAGAAAAGAAATATT
2235821 AGAGAAAAGAAATATT
1 AGAGAAAAGAAATATT
2235837 A
1 A
2235838 TTCTCGTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.16
Consensus pattern (16 bp):
AGAGAAAAGAAATATT
Found at i:2242607 original size:57 final size:57
Alignment explanation
Indices: 2242539--2242656 Score: 229
Period size: 57 Copynumber: 2.1 Consensus size: 57
2242529 AGCCCTAAAT
2242539 GGTA-AGTAGTAAATTAGAAAATTTAGAATAGGAATAAATGTAAACAGAGGAAACAG
1 GGTAGAGTAGTAAATTAGAAAATTTAGAATAGGAATAAATGTAAACAGAGGAAACAG
2242595 GGTAGAGTAGTAAATTAGAAAATTTAGAATAGGAATAAATGTAAACAGAGGAAACAG
1 GGTAGAGTAGTAAATTAGAAAATTTAGAATAGGAATAAATGTAAACAGAGGAAACAG
2242652 GGTAG
1 GGTAG
2242657 TAAAGTATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 4 0.07
57 57 0.93
ACGTcount: A:0.50, C:0.03, G:0.25, T:0.21
Consensus pattern (57 bp):
GGTAGAGTAGTAAATTAGAAAATTTAGAATAGGAATAAATGTAAACAGAGGAAACAG
Found at i:2244565 original size:30 final size:30
Alignment explanation
Indices: 2244531--2244604 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
2244521 TCACCTCCCC
2244531 CCTCCAGTTTACTCGCCTCCACCACCACCA
1 CCTCCAGTTTACTCGCCTCCACCACCACCA
*
2244561 CCTCCAGTTTACTCGCCTCCACCACCACCT
1 CCTCCAGTTTACTCGCCTCCACCACCACCA
* *
2244591 CCACCTGTTTACTC
1 CCTCCAGTTTACTC
2244605 TCCACCGCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.18, C:0.51, G:0.07, T:0.24
Consensus pattern (30 bp):
CCTCCAGTTTACTCGCCTCCACCACCACCA
Found at i:2244619 original size:30 final size:27
Alignment explanation
Indices: 2244531--2244619 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 27
2244521 TCACCTCCCC
2244531 CCTCCAGTTTACTCGCCTCCACCACCACCA
1 CCTCCAGTTTACT---CTCCACCACCACCA
* *
2244561 CCTCCAGTTTACTCGCCTCCACCACCA
1 CCTCCAGTTTACTCTCCACCACCACCA
* *
2244588 CCTCCACCTGTTTACTCTCCACCGCCTCCA
1 CCTCCA---GTTTACTCTCCACCACCACCA
2244618 CC
1 CC
2244620 ACACCCTCCC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
27 18 0.36
30 32 0.64
ACGTcount: A:0.17, C:0.54, G:0.07, T:0.22
Consensus pattern (27 bp):
CCTCCAGTTTACTCTCCACCACCACCA
Found at i:2244628 original size:21 final size:20
Alignment explanation
Indices: 2244604--2244692 Score: 92
Period size: 21 Copynumber: 4.3 Consensus size: 20
2244594 CCTGTTTACT
2244604 CTCCACCGCCTCCACCACACC
1 CTCCACCGCCTCCACCAC-CC
*
2244625 CTCCCCCGCCT-CACCACCAC
1 CTCCACCGCCTCCACCACC-C
* * *
2244645 CTCCACCTCCGCCACCATCAC
1 CTCCACCGCCTCCACCA-CCC
2244666 CTCCACCGCC-CTCACCACCC
1 CTCCACCGCCTC-CACCACCC
2244686 CTCCACC
1 CTCCACC
2244693 TGTTACTCTC
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.02
20 25 0.44
21 30 0.53
22 1 0.02
ACGTcount: A:0.17, C:0.67, G:0.04, T:0.11
Consensus pattern (20 bp):
CTCCACCGCCTCCACCACCC
Found at i:2244654 original size:104 final size:106
Alignment explanation
Indices: 2244458--2244766 Score: 339
Period size: 104 Copynumber: 3.0 Consensus size: 106
2244448 CACATTCTCG
2244458 CTCCAGTTTACTCGCCTCCACCACCACCTCCACCTGTTTACTCTCCACCGCCCTCCACCACCATC
1 CTCCAGTTTACTCGCCTCCACCACCACCTCCACCTGTTTACTCTCCACCG-CCTCCACCACCATC
** *
2244523 ACCTCCCC-CCT--CCAGTTTA-CT-CGCCTCCACCACCACCAC
65 ACCTCCCCGCCTCACCA--CCACCTCCACCTCCACCACCACCAC
2244562 CTCCAGTTTACTCGCCTCCACCACCACCTCCACCTGTTTACTCTCCACCGCCTCCACCA-CA-C-
1 CTCCAGTTTACTCGCCTCCACCACCACCTCCACCTGTTTACTCTCCACCGCCTCCACCACCATCA
* *
2244624 CCTCCCCCGCCTCACCACCACCTCCACCTCCGCCACCATCAC
66 CCT-CCCCGCCTCACCACCACCTCCACCTCCACCACCACCAC
* *
2244666 CTCC-----AC-CGCC-CTCACCACC-CCTCCACCTG-TTACTCTCCACCACCTCCGCCACCATC
1 CTCCAGTTTACTCGCCTC-CACCACCACCTCCACCTGTTTACTCTCCACCGCCTCCACCACCATC
* * *
2244722 ACCTCCCCGCCCTCACCGCCACCCCCGACCT-CACCTCCACCAC
65 ACCTCCCCG-CCTCACCACCACCTCC-ACCTCCACCACCACCAC
2244765 CT
1 CT
2244767 TCACCCCCAC
Statistics
Matches: 181, Mismatches: 12, Indels: 29
0.82 0.05 0.13
Matches are distributed among these distances:
96 20 0.11
97 13 0.07
98 17 0.09
99 30 0.17
100 7 0.04
101 5 0.03
102 6 0.03
103 11 0.06
104 72 0.40
ACGTcount: A:0.17, C:0.59, G:0.06, T:0.18
Consensus pattern (106 bp):
CTCCAGTTTACTCGCCTCCACCACCACCTCCACCTGTTTACTCTCCACCGCCTCCACCACCATCA
CCTCCCCGCCTCACCACCACCTCCACCTCCACCACCACCAC
Found at i:2244693 original size:41 final size:41
Alignment explanation
Indices: 2244604--2244693 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
2244594 CCTGTTTACT
* * *
2244604 CTCCACCGCCTCCACCACACCCTCCCCCGCCTCACCACCAC
1 CTCCACCTCCGCCACCACACCCTCCACCGCCTCACCACCAC
2244645 CTCCACCTCCGCCACCATCA-CCTCCACCGCCCTCACCACC-C
1 CTCCACCTCCGCCACCA-CACCCTCCACCG-CCTCACCACCAC
2244686 CTCCACCT
1 CTCCACCT
2244694 GTTACTCTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
41 32 0.73
42 12 0.27
ACGTcount: A:0.17, C:0.67, G:0.04, T:0.12
Consensus pattern (41 bp):
CTCCACCTCCGCCACCACACCCTCCACCGCCTCACCACCAC
Found at i:2244753 original size:18 final size:18
Alignment explanation
Indices: 2244726--2244762 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2244716 ACCATCACCT
*
2244726 CCCCGCCCTCACCGCCAC
1 CCCCGACCTCACCGCCAC
*
2244744 CCCCGACCTCACCTCCAC
1 CCCCGACCTCACCGCCAC
2244762 C
1 C
2244763 ACCTTCACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.70, G:0.08, T:0.08
Consensus pattern (18 bp):
CCCCGACCTCACCGCCAC
Found at i:2245022 original size:27 final size:24
Alignment explanation
Indices: 2244968--2245027 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
2244958 ATCGCCGCCG
2244968 CCACCACCACCTGTGGTTCACTCC
1 CCACCACCACCTGTGGTTCACTCC
2244992 CCACCACCACCTGTGGTTCACTCC
1 CCACCACCACCTGTGGTTCACTCC
2245016 CCACCACCACCT
1 CCACCACCACCT
2245028 TCACCTCCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.18, C:0.53, G:0.10, T:0.18
Consensus pattern (24 bp):
CCACCACCACCTGTGGTTCACTCC
Found at i:2256320 original size:3 final size:3
Alignment explanation
Indices: 2256312--2256424 Score: 147
Period size: 3 Copynumber: 37.7 Consensus size: 3
2256302 TTTTTATCCA
* ** *
2256312 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2256360 TAT TAT CAT TAT TAT TAT TAA TAT TAT TAT TAT CCA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
2256405 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
2256425 ATTTATATTA
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
2 1 0.01
3 92 0.98
4 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2256344 original size:27 final size:27
Alignment explanation
Indices: 2256314--2256419 Score: 185
Period size: 27 Copynumber: 3.9 Consensus size: 27
2256304 TTTATCCATA
2256314 TTATTATTATTAATATTATTATTATCC
1 TTATTATTATTAATATTATTATTATCC
*
2256341 TTATTATTATTAATATTATTATTATCA
1 TTATTATTATTAATATTATTATTATCC
2256368 TTATTATTATTAATATTATTATTATCC
1 TTATTATTATTAATATTATTATTATCC
* *
2256395 ATATTATTATTATTATTATTATTAT
1 TTATTATTATTAATATTATTATTAT
2256420 TATTAATTTA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATTATTATTAATATTATTATTATCC
Found at i:2256963 original size:18 final size:19
Alignment explanation
Indices: 2256940--2256978 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2256930 AAAACCAGAG
*
2256940 ACAGAGACA-GAAAAAAAA
1 ACAGAGAAAGGAAAAAAAA
2256958 ACAGAGAAAGGAAAAAAAA
1 ACAGAGAAAGGAAAAAAAA
2256977 AC
1 AC
2256979 TATACCAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.72, C:0.10, G:0.18, T:0.00
Consensus pattern (19 bp):
ACAGAGAAAGGAAAAAAAA
Found at i:2257787 original size:21 final size:20
Alignment explanation
Indices: 2257761--2257829 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
2257751 ATGCTTGAAG
2257761 AAAAAGAAAAGAAAGAAAAGA
1 AAAAAGAAAAGAAAGAAAA-A
*
2257782 AAAAAGAAAAGAAA-AATAA
1 AAAAAGAAAAGAAAGAAAAA
* *
2257801 AAAAATAAAA-AAGAGAAGAA
1 AAAAAGAAAAGAA-AGAAAAA
2257821 AAAAAGAAA
1 AAAAAGAAA
2257830 GGGGGTCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 2 0.05
19 11 0.26
20 15 0.36
21 14 0.33
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (20 bp):
AAAAAGAAAAGAAAGAAAAA
Found at i:2257794 original size:26 final size:25
Alignment explanation
Indices: 2257762--2257829 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 25
2257752 TGCTTGAAGA
2257762 AAAAGAAAAGAAAGAAAAGAAAAAAG
1 AAAAGAAAA-AAAGAAAAGAAAAAAG
* *
2257788 AAAAGAAAAATAAAAAAATAAAAAAG
1 AAAAGAAAAA-AAGAAAAGAAAAAAG
*
2257814 AGAAGAAAAAAAGAAA
1 AAAAGAAAAAAAGAAA
2257830 GGGGGTCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 6 0.16
26 31 0.84
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (25 bp):
AAAAGAAAAAAAGAAAAGAAAAAAG
Found at i:2258163 original size:16 final size:16
Alignment explanation
Indices: 2258144--2258180 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2258134 CAATTATATC
2258144 TATTTCAAATTCAATT
1 TATTTCAAATTCAATT
* *
2258160 TATTTGAGATTCAATT
1 TATTTCAAATTCAATT
2258176 TATTT
1 TATTT
2258181 TTGGAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (16 bp):
TATTTCAAATTCAATT
Found at i:2258192 original size:19 final size:18
Alignment explanation
Indices: 2258150--2258198 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
2258140 TATCTATTTC
2258150 AAATTCAATTTA--TTTG
1 AAATTCAATTTATTTTTG
*
2258166 AGATTCAATTTATTTTTGG
1 AAATTCAATTTATTTTT-G
2258185 AAATTCAATTTATT
1 AAATTCAATTTATT
2258199 CTTTTCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
18 3 0.11
19 14 0.50
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (18 bp):
AAATTCAATTTATTTTTG
Found at i:2259826 original size:21 final size:21
Alignment explanation
Indices: 2259801--2259840 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2259791 CTTGTTGAAT
2259801 TTTTAACAGAA-ATTTCAAAGA
1 TTTTAACA-AAGATTTCAAAGA
*
2259822 TTTTAGCAAAGATTTCAAA
1 TTTTAACAAAGATTTCAAA
2259841 TCCACTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (21 bp):
TTTTAACAAAGATTTCAAAGA
Found at i:2260059 original size:113 final size:113
Alignment explanation
Indices: 2259846--2260496 Score: 1074
Period size: 113 Copynumber: 5.8 Consensus size: 113
2259836 TCAAATCCAC
*
2259846 TTGATGGATCATACGTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AG
1 TTGATGGATCA-ACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
2259910 AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
65 -AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
*
2259960 TTGATGAATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
2260025 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
2260073 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
2260138 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
* *** *
2260186 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
2260251 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
* *** *
2260299 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
2260364 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
2260412 TTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AG
1 TTGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
2260475 AAAGTTCATAATGAGAAGAACT
65 -AAGTTCATAATGAGAAGAACT
2260497 CATCAAGAGC
Statistics
Matches: 513, Mismatches: 21, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
112 3 0.01
113 498 0.97
114 12 0.02
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (113 bp):
TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
Found at i:2260757 original size:3 final size:3
Alignment explanation
Indices: 2260744--2260853 Score: 132
Period size: 3 Copynumber: 36.7 Consensus size: 3
2260734 TTTTTATCCA
* * ** *
2260744 TAT TTT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2260792 TAT TAT CAT TAT TAT TAT TAA TAT TAT TAT TAT CCA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
2260837 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
2260854 ATTTATATTA
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
2 1 0.01
3 87 0.98
4 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2260762 original size:9 final size:9
Alignment explanation
Indices: 2260750--2260873 Score: 94
Period size: 9 Copynumber: 14.0 Consensus size: 9
2260740 TCCATATTTT
2260750 TATTATTAA
1 TATTATTAA
*
2260759 TATTATTAT
1 TATTATTAA
** *
2260768 TATCCTTAT
1 TATTATTAA
2260777 TATTATTAA
1 TATTATTAA
*
2260786 TATTATTAT
1 TATTATTAA
* *
2260795 TATCATTAT
1 TATTATTAA
2260804 TATTATTAA
1 TATTATTAA
2260813 TATTA-T--
1 TATTATTAA
**
2260819 TATTATCCA
1 TATTATTAA
*
2260828 TATTATTAT
1 TATTATTAA
*
2260837 TATTATTAT
1 TATTATTAA
2260846 TATTATTAA
1 TATTATTAA
*
2260855 TTTATATTAA
1 TAT-TATTAA
2260865 -ATATATTAA
1 TAT-TATTAA
2260874 ATACATAATA
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
6 5 0.05
8 1 0.01
9 82 0.87
10 6 0.06
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATTAA
Found at i:2260779 original size:27 final size:27
Alignment explanation
Indices: 2260749--2260851 Score: 179
Period size: 27 Copynumber: 3.8 Consensus size: 27
2260739 ATCCATATTT
2260749 TTATTATTAATATTATTATTATCCTTA
1 TTATTATTAATATTATTATTATCCTTA
*
2260776 TTATTATTAATATTATTATTATCATTA
1 TTATTATTAATATTATTATTATCCTTA
*
2260803 TTATTATTAATATTATTATTATCCATA
1 TTATTATTAATATTATTATTATCCTTA
*
2260830 TTATTATTATTATTATTATTAT
1 TTATTATTAATATTATTATTAT
2260852 TAATTTATAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATTATTAATATTATTATTATCCTTA
Found at i:2261390 original size:18 final size:18
Alignment explanation
Indices: 2261367--2261404 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2261357 AAAACCAGAG
*
2261367 ACAGAGACAGAAAAAAAA
1 ACAGAGAAAGAAAAAAAA
*
2261385 ACAGAGAAAGGAAAAAAA
1 ACAGAGAAAGAAAAAAAA
2261403 AC
1 AC
2261405 TATACCAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.11, G:0.18, T:0.00
Consensus pattern (18 bp):
ACAGAGAAAGAAAAAAAA
Found at i:2273703 original size:9 final size:9
Alignment explanation
Indices: 2273689--2273757 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
2273679 GCTTGAAGAA
2273689 AAAGAAAAG
1 AAAGAAAAG
2273698 AAAGAAAAG
1 AAAGAAAAG
2273707 -AA-AAAAG
1 AAAGAAAAG
*
2273714 AAAAGAAAAAT
1 -AAAG-AAAAG
* *
2273725 AAAAAAAAT
1 AAAGAAAAG
2273734 AAA-AAAAG
1 AAAGAAAAG
2273742 AGAAGAAAA-
1 A-AAGAAAAG
2273751 AAAGAAA
1 AAAGAAA
2273758 GGGGGTCAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
7 5 0.10
8 13 0.25
9 22 0.43
10 7 0.14
11 4 0.08
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:2273713 original size:21 final size:21
Alignment explanation
Indices: 2273687--2273757 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
2273677 ATGCTTGAAG
2273687 AAAAAGAAAAGAAAGAAAAGA
1 AAAAAGAAAAGAAAGAAAAGA
2273708 AAAAAGAAAAGAAA-AATAA-A
1 AAAAAGAAAAGAAAGAA-AAGA
* *
2273728 AAAAATAAAA-AAAGAGAAGAA
1 AAAAAGAAAAGAAAGAAAAG-A
2273749 AAAAAGAAA
1 AAAAAGAAA
2273758 GGGGGTCAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
19 5 0.12
20 13 0.30
21 25 0.58
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (21 bp):
AAAAAGAAAAGAAAGAAAAGA
Found at i:2274091 original size:16 final size:16
Alignment explanation
Indices: 2274072--2274108 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2274062 CAATTATATC
2274072 TATTTCAAATTCAATT
1 TATTTCAAATTCAATT
* *
2274088 TATTTGAGATTCAATT
1 TATTTCAAATTCAATT
2274104 TATTT
1 TATTT
2274109 TTGGAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (16 bp):
TATTTCAAATTCAATT
Found at i:2274120 original size:19 final size:18
Alignment explanation
Indices: 2274078--2274126 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
2274068 TATCTATTTC
2274078 AAATTCAATTTA--TTTG
1 AAATTCAATTTATTTTTG
*
2274094 AGATTCAATTTATTTTTGG
1 AAATTCAATTTATTTTT-G
2274113 AAATTCAATTTATT
1 AAATTCAATTTATT
2274127 CTTTTCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
18 3 0.11
19 14 0.50
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (18 bp):
AAATTCAATTTATTTTTG
Found at i:2275754 original size:21 final size:21
Alignment explanation
Indices: 2275729--2275768 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2275719 CTTGTTGAAT
2275729 TTTTAACAGAA-ATTTCAAAGA
1 TTTTAACA-AAGATTTCAAAGA
*
2275750 TTTTAGCAAAGATTTCAAA
1 TTTTAACAAAGATTTCAAA
2275769 TCCACTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (21 bp):
TTTTAACAAAGATTTCAAAGA
Found at i:2275987 original size:113 final size:113
Alignment explanation
Indices: 2275774--2276424 Score: 1074
Period size: 113 Copynumber: 5.8 Consensus size: 113
2275764 TCAAATCCAC
*
2275774 TTGATGGATCATACGTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AG
1 TTGATGGATCA-ACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
2275838 AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
65 -AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
*
2275888 TTGATGAATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
2275953 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
2276001 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
2276066 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
* *** *
2276114 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
2276179 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
* *** *
2276227 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
2276292 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
2276340 TTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AG
1 TTGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
2276403 AAAGTTCATAATGAGAAGAACT
65 -AAGTTCATAATGAGAAGAACT
2276425 CATCAAGAGC
Statistics
Matches: 513, Mismatches: 21, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
112 3 0.01
113 498 0.97
114 12 0.02
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (113 bp):
TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
Found at i:2276680 original size:3 final size:3
Alignment explanation
Indices: 2276672--2276767 Score: 106
Period size: 3 Copynumber: 31.7 Consensus size: 3
2276662 TTTTTATCCA
** *
2276672 TAT TAT TAT TA- TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2276719 CAT TAT TAT TAT TAAT TAT TAT TAT CCA- TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT -TAT TAT TAT TAT TA-T TAT TAT
2276766 TA
1 TA
2276768 ATTTATATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.04
3 68 0.87
4 7 0.09
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2276776 original size:13 final size:13
Alignment explanation
Indices: 2276671--2276777 Score: 93
Period size: 12 Copynumber: 8.5 Consensus size: 13
2276661 TTTTTTATCC
2276671 ATATTATTATTAT
1 ATATTATTATTAT
**
2276684 ATTATTATTATCCT
1 A-TATTATTATTAT
2276698 -TATTATTATTA-
1 ATATTATTATTAT
*
2276709 ATATTATTATCAT
1 ATATTATTATTAT
2276722 -TATTATTA-T-T
1 ATATTATTATTAT
2276732 A-ATTATTATTAT
1 ATATTATTATTAT
2276744 CCATATTATTATTAT
1 --ATATTATTATTAT
*
2276759 TTATTATTAATT-T
1 ATATTATT-ATTAT
2276772 ATATTA
1 ATATTA
2276778 AATATATTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
10 8 0.11
11 1 0.01
12 28 0.37
13 14 0.18
14 14 0.18
15 11 0.14
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTATTATTAT
Found at i:2277304 original size:18 final size:18
Alignment explanation
Indices: 2277281--2277318 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2277271 AAAACCAGAG
*
2277281 ACAGAGACAGAAAAAAAA
1 ACAGAGAAAGAAAAAAAA
*
2277299 ACAGAGAAAGGAAAAAAA
1 ACAGAGAAAGAAAAAAAA
2277317 AC
1 AC
2277319 TATACCAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.11, G:0.18, T:0.00
Consensus pattern (18 bp):
ACAGAGAAAGAAAAAAAA
Found at i:2285391 original size:13 final size:13
Alignment explanation
Indices: 2285373--2285399 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2285363 TGTTACCACG
2285373 GATTTCTGCACTA
1 GATTTCTGCACTA
2285386 GATTTCTGCACTA
1 GATTTCTGCACTA
2285399 G
1 G
2285400 TGCAGACCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (13 bp):
GATTTCTGCACTA
Found at i:2293143 original size:27 final size:27
Alignment explanation
Indices: 2293112--2293179 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
2293102 TCTATTTACA
*
2293112 AAATCATATCTCTATAGGAATTATAAC
1 AAATCATATCTCTATAGGAATGATAAC
*
2293139 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGATAAC
2293166 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
2293180 ATTCCTACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 9 0.23
27 30 0.77
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGATAAC
Found at i:2294355 original size:18 final size:18
Alignment explanation
Indices: 2294332--2294372 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2294322 TCCTTCAACA
2294332 GACTTTAAGCCAGGTGGC
1 GACTTTAAGCCAGGTGGC
2294350 GACTTTAAGCCAGGTGGC
1 GACTTTAAGCCAGGTGGC
*
2294368 AACTT
1 GACTT
2294373 CATATAGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (18 bp):
GACTTTAAGCCAGGTGGC
Found at i:2294618 original size:17 final size:17
Alignment explanation
Indices: 2294596--2294636 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
2294586 TGAGTTATAC
2294596 TTTACAGTAAAGATCCA
1 TTTACAGTAAAGATCCA
2294613 TTTACAGTAAAGATCCA
1 TTTACAGTAAAGATCCA
2294630 TTTACAG
1 TTTACAG
2294637 CTAACAACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (17 bp):
TTTACAGTAAAGATCCA
Found at i:2296970 original size:25 final size:26
Alignment explanation
Indices: 2296908--2296975 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
2296898 TCTATTTACA
**
2296908 AAATCAAATCTCTATAGGAATGGTAAC
1 AAATC-AATCTCTATAGGAATGACAAC
*
2296935 AAATCATATCTATATAGGAATGACAAC
1 AAATCA-ATCTCTATAGGAATGACAAC
2296962 AAATC-ATCTCTATA
1 AAATCAATCTCTATA
2296976 ATTCCTACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 8 0.22
26 1 0.03
27 27 0.75
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (26 bp):
AAATCAATCTCTATAGGAATGACAAC
Found at i:2303821 original size:17 final size:19
Alignment explanation
Indices: 2303799--2303836 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2303789 TACATCTATT
*
2303799 ATAAATG-ATT-TAATTTA
1 ATAAATGCATTATAATATA
2303816 ATAAATGCATTATAATATA
1 ATAAATGCATTATAATATA
2303835 AT
1 AT
2303837 CATAAATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (19 bp):
ATAAATGCATTATAATATA
Found at i:2304053 original size:21 final size:21
Alignment explanation
Indices: 2304029--2304083 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2304019 TGGTTCACTA
*
2304029 GTTCAATCAGATTCAACTACG
1 GTTCAATCGGATTCAACTACG
* *
2304050 GTTCAACCGGATTCAACTGCG
1 GTTCAATCGGATTCAACTACG
2304071 GTTCAATCGGATT
1 GTTCAATCGGATT
2304084 TTATATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (21 bp):
GTTCAATCGGATTCAACTACG
Found at i:2311870 original size:31 final size:31
Alignment explanation
Indices: 2311834--2311893 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2311824 AACTTAAAAG
* *
2311834 AGTTTTGCAATACTGATATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2311865 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
2311894 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2312375 original size:36 final size:40
Alignment explanation
Indices: 2312330--2312405 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 40
2312320 ACAAATCCAA
*
2312330 AAAACTTAATAT-T-TAAT-TTAT-TTAAAAAATTAATATT
1 AAAACTTAATATCTATAATATAATATTAAAAAA-TAATATT
2312367 AAAA-TTAATATCTATAATATAATATTAAAAAATAATATT
1 AAAACTTAATATCTATAATATAATATTAAAAAATAATATT
2312406 TAATTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
36 7 0.21
37 5 0.15
38 4 0.12
39 10 0.29
40 8 0.24
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (40 bp):
AAAACTTAATATCTATAATATAATATTAAAAAATAATATT
Found at i:2312383 original size:74 final size:62
Alignment explanation
Indices: 2312322--2312455 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
2312312 TAAAAATAAC
2312322 AAATCCAAAAAACTTAATATTTAATTTATTTAAAAAATTAATATTAAAATTAATATCTATAATAT
1 AAAT-CAAAAAA--TAATATTTAATTTATTTAAAAAA-TAATATTAAAATTAATATCTATAATAT
2312387 A
62 A
* * *
2312388 ATATTAAAAAATAATATTTAATTTATTTAAAAAATAATATTAAAATTAAAATCAAATATAATATA
1 AAATCAAAAAATAATATTTAATTTATTTAAAAAATAATATTAAAATTAATATC---TATAATATA
2312453 AAA
1 AAA
2312456 CCTCTTTGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
62 18 0.30
63 23 0.38
65 17 0.28
66 3 0.05
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (62 bp):
AAATCAAAAAATAATATTTAATTTATTTAAAAAATAATATTAAAATTAATATCTATAATATA
Found at i:2312409 original size:63 final size:59
Alignment explanation
Indices: 2312336--2312455 Score: 195
Period size: 63 Copynumber: 2.0 Consensus size: 59
2312326 CCAAAAAACT
*
2312336 TAATATTTAATTTATTTAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAAA
1 TAATATTTAATTTATTTAAAAAA-TAATATTAAAATTAAAATC-A-AATATAATA-TAAAAAA
2312399 TAATATTTAATTTATTTAAAAAATAATATTAAAATTAAAATCAAATATAATATAAAA
1 TAATATTTAATTTATTTAAAAAATAATATTAAAATTAAAATCAAATATAATATAAAA
2312456 CCTCTTTGAA
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
59 5 0.09
60 9 0.16
61 1 0.02
62 18 0.32
63 23 0.41
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (59 bp):
TAATATTTAATTTATTTAAAAAATAATATTAAAATTAAAATCAAATATAATATAAAAAA
Found at i:2313843 original size:31 final size:31
Alignment explanation
Indices: 2313807--2313867 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2313797 AAACTTAAAA
* *
2313807 TAGTTTTGCAATACTGATATTTAAATAATTT
1 TAGTTTTACAATACTGAAATTTAAATAATTT
2313838 TAGTTTTACAATACTGAAATTTAAATAATT
1 TAGTTTTACAATACTGAAATTTAAATAATT
2313868 CATACAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (31 bp):
TAGTTTTACAATACTGAAATTTAAATAATTT
Found at i:2314344 original size:14 final size:13
Alignment explanation
Indices: 2314325--2314380 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
2314315 TTTAATTTAT
2314325 TTAAAAAAGTAATA
1 TTAAAAAA-TAATA
*
2314339 TT-AAAATTAATA
1 TTAAAAAATAATA
* *
2314351 TATATAATATAATA
1 T-TAAAAAATAATA
2314365 TTAAAAAAATAATA
1 TT-AAAAAATAATA
2314379 TT
1 TT
2314381 TAATTTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
12 6 0.18
13 6 0.18
14 21 0.64
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
TTAAAAAATAATA
Found at i:2314379 original size:26 final size:25
Alignment explanation
Indices: 2314334--2314412 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 25
2314324 TTTAAAAAAG
*
2314334 TAATATTAAAATTAAT-ATATATAAT
1 TAATATTAAAA-AAATAATATATAAT
*
2314359 ATAATATTAAAAAAATAATATTTAAT
1 -TAATATTAAAAAAATAATATATAAT
* * *
2314385 TTAT-TTAAAAAATTAATATGAAAAT
1 TAATATTAAAAAAATAATAT-ATAAT
2314410 TAA
1 TAA
2314413 AATCAAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
24 14 0.32
25 11 0.25
26 19 0.43
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (25 bp):
TAATATTAAAAAAATAATATATAAT
Found at i:2314379 original size:64 final size:61
Alignment explanation
Indices: 2314310--2314431 Score: 183
Period size: 64 Copynumber: 2.0 Consensus size: 61
2314300 CCAAAAAACT
*
2314310 TAATATTTAATTTATTTAAAAAAGTAATATTAAAATTAATATAT-ATAATATAATATTAAAAAAA
1 TAATATTTAATTTATTTAAAAAAGTAATATGAAAATTAA-A-ATCA-AATATAATA-TAAAAAAA
*
2314374 TAATATTTAATTTATTTAAAAAATTAATATGAAAATTAAAATCAAATATAATATAAAA
1 TAATATTTAATTTATTTAAAAAAGTAATATGAAAATTAAAATCAAATATAATATAAAA
2314432 CCTCTTTGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
61 5 0.09
62 11 0.20
63 2 0.04
64 37 0.67
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (61 bp):
TAATATTTAATTTATTTAAAAAAGTAATATGAAAATTAAAATCAAATATAATATAAAAAAA
Found at i:2315828 original size:31 final size:31
Alignment explanation
Indices: 2315792--2315851 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2315782 AACTTAAAAG
* *
2315792 AGTTTTGCAATACTGATATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2315823 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
2315852 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2316329 original size:14 final size:14
Alignment explanation
Indices: 2316310--2316392 Score: 56
Period size: 13 Copynumber: 6.4 Consensus size: 14
2316300 TTTAATTTAT
2316310 TTAAAAAATTAATA
1 TTAAAAAATTAATA
2316324 TT--AAAATTAATA
1 TTAAAAAATTAATA
* *
2316336 TCTATAATA-TAATA
1 T-TAAAAAATTAATA
*
2316350 TTAAAAAA-TAAAA
1 TTAAAAAATTAATA
* *
2316363 TT---TAATTTAT-
1 TTAAAAAATTAATA
2316373 TTAAAAAATTAATA
1 TTAAAAAATTAATA
2316387 TTAAAA
1 TTAAAA
2316393 TTAAAATCAA
Statistics
Matches: 52, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
10 4 0.08
11 2 0.04
12 11 0.21
13 18 0.35
14 14 0.27
15 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAAAAATTAATA
Found at i:2316331 original size:12 final size:12
Alignment explanation
Indices: 2316314--2316396 Score: 62
Period size: 12 Copynumber: 6.7 Consensus size: 12
2316304 ATTTATTTAA
2316314 AAAATTAATATT
1 AAAATTAATATT
2316326 AAAATTAATATCT
1 AAAATTAATAT-T
*
2316339 ATAATATAATATT
1 AAAAT-TAATATT
* *
2316352 AAAAAATAAAATT
1 -AAAATTAATATT
* *
2316365 -TAATTTAT-TT
1 AAAATTAATATT
2316375 AAAAAATTAATATT
1 --AAAATTAATATT
2316389 AAAATTAA
1 AAAATTAA
2316397 AATCAAATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
10 2 0.04
11 4 0.07
12 19 0.35
13 18 0.33
14 11 0.20
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:2316372 original size:63 final size:60
Alignment explanation
Indices: 2316299--2316415 Score: 198
Period size: 63 Copynumber: 1.9 Consensus size: 60
2316289 AAAACTTAAT
*
2316299 ATTTAATTTATTTAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAAATAAA
1 ATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATC-A-AATATAATA-TAAAAAATAAA
2316362 ATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCAAATATAATATAAAA
1 ATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCAAATATAATATAAAA
2316416 CCTCTTTGAA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
60 5 0.09
61 9 0.17
62 1 0.02
63 38 0.72
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (60 bp):
ATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCAAATATAATATAAAAAATAAA
Found at i:2316398 original size:20 final size:20
Alignment explanation
Indices: 2316310--2316398 Score: 65
Period size: 20 Copynumber: 4.3 Consensus size: 20
2316300 TTTAATTTAT
2316310 TTAAAAAATTAATATTAAAA
1 TTAAAAAATTAATATTAAAA
* ** *
2316330 TTAATATCTATAATA-TAATA
1 TTAAAAAAT-TAATATTAAAA
* *
2316350 TTAAAAAA-TAAAATTTAATTTAT
1 TTAAAAAATTAATA-TTAA---AA
2316373 TTAAAAAATTAATATTAAAA
1 TTAAAAAATTAATATTAAAA
2316393 TTAAAA
1 TTAAAA
2316399 TCAAATATAA
Statistics
Matches: 50, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
18 4 0.08
20 25 0.50
21 5 0.10
23 12 0.24
24 4 0.08
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAAAAATTAATATTAAAA
Found at i:2322883 original size:3 final size:3
Alignment explanation
Indices: 2322875--2322899 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2322865 CCAATGTAAA
2322875 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
2322900 GGGTAAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2331340 original size:2 final size:2
Alignment explanation
Indices: 2331335--2331376 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2331325 GTGTGTGCGT
*
2331335 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2331377 TCCTTCTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2338907 original size:110 final size:110
Alignment explanation
Indices: 2338762--2338994 Score: 387
Period size: 110 Copynumber: 2.1 Consensus size: 110
2338752 CTTATATGAC
2338762 AGTATCGATACTTGTACATTTACGCCTATTTTCATTATATCGATAAAAACGTTTACCGTGTACAT
1 AGTATCGATACTTGTACATTTACGCCTATTTTCATTATATCGATAAAAACGTTTACCGTGTACAT
*
2338827 TGTTAATTTACATATTACTTTAAAGTAATAGGTTTCGAAATTTTA
66 TGTTAATTTACATATTACTTTAAAGTAATAGGTTTCGAAATTATA
* * * *
2338872 AGTATCGATACTTAG-ACATTTATGCCTATTTTCATTATATCGGTAGAAATGTTTACCGTGTACA
1 AGTATCGATACTT-GTACATTTACGCCTATTTTCATTATATCGATAAAAACGTTTACCGTGTACA
* *
2338936 TTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTTGAAATTATA
65 TTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCGAAATTATA
2338982 AGTATCGATACTT
1 AGTATCGATACTT
2338995 TGTATATGAG
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
110 114 0.99
111 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (110 bp):
AGTATCGATACTTGTACATTTACGCCTATTTTCATTATATCGATAAAAACGTTTACCGTGTACAT
TGTTAATTTACATATTACTTTAAAGTAATAGGTTTCGAAATTATA
Found at i:2339308 original size:178 final size:177
Alignment explanation
Indices: 2339004--2339348 Score: 462
Period size: 178 Copynumber: 1.9 Consensus size: 177
2338994 TTGTATATGA
* *
2339004 GTATCGATACTTGGACATTTACGCCTATTTTCATTCCGGTAGAAACGTTTACCATGTACATTGTT
1 GTATCGATACTTGGACATTTACACCTATTATCATTCCGGTAG-AACGTTTACCATGTACATTGTT
* * * * *
2339069 AATTTACCTATTACTTTAAAGTATTAGGTTTTAAATTATAAATATCGATACTTTATATATGTGTA
65 AATTAACATATTACTTTAAAGTAATAGGTTTGAAATTACAAATATCGATACTTTATATATGTGTA
* *
2339134 TTAATACATTTTGCGTGCAAATTGTTTGAGAAGCATATTAGAATAAAG
130 TCAATACATTTTGCATGCAAATTGTTTGAGAAGCATATTAGAATAAAG
* * * * * *
2339182 GTATTGATACTTGG-TATTTACACCTATTATCAATATACCGGTAG-ACTTTTACCGTTTACTTTG
1 GTATCGATACTTGGACATTTACACCTATTATC-AT-T-CCGGTAGAACGTTTACCATGTACATTG
*
2339245 TTAATTAACATATTACTTTAAAGTAATAGGTTTCGAAATT-CAAGTATCGATACTTTATATATGT
63 TTAATTAACATATTACTTTAAAGTAATAGGTTT-GAAATTACAAATATCGATACTTTATATATGT
* *
2339309 GTATCGATACGTTTTGCATGCAAATTGTTTGAGAAGCATA
127 GTATCAATACATTTTGCATGCAAATTGTTTGAGAAGCATA
2339349 CTGAAATAAA
Statistics
Matches: 145, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
177 14 0.10
178 118 0.81
179 6 0.04
180 7 0.05
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.41
Consensus pattern (177 bp):
GTATCGATACTTGGACATTTACACCTATTATCATTCCGGTAGAACGTTTACCATGTACATTGTTA
ATTAACATATTACTTTAAAGTAATAGGTTTGAAATTACAAATATCGATACTTTATATATGTGTAT
CAATACATTTTGCATGCAAATTGTTTGAGAAGCATATTAGAATAAAG
Found at i:2339783 original size:49 final size:49
Alignment explanation
Indices: 2339728--2339843 Score: 187
Period size: 49 Copynumber: 2.4 Consensus size: 49
2339718 CATTATTTAC
* * * *
2339728 TAACTTTGGTAATTACATATATAATTTCATTCACATACAAAATTTGTTG
1 TAACTTTGGTAATCACATACATAACTTCATTCACATACAAAATTTGTTA
*
2339777 TAACTTTGGTAATCACGTACATAACTTCATTCACATACAAAATTTGTTA
1 TAACTTTGGTAATCACATACATAACTTCATTCACATACAAAATTTGTTA
2339826 TAACTTTGGTAATCACAT
1 TAACTTTGGTAATCACAT
2339844 TTCATTCCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (49 bp):
TAACTTTGGTAATCACATACATAACTTCATTCACATACAAAATTTGTTA
Found at i:2339864 original size:17 final size:18
Alignment explanation
Indices: 2339842--2339880 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2339832 TGGTAATCAC
2339842 ATTTCATTC-CATACAAA
1 ATTTCATTCACATACAAA
2339859 ATTTCATTCACATACAAA
1 ATTTCATTCACATACAAA
2339877 ATTT
1 ATTT
2339881 ACAAGCTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTCATTCACATACAAA
Found at i:2340225 original size:22 final size:21
Alignment explanation
Indices: 2340196--2340242 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 21
2340186 TGTGTTAAAA
2340196 AAATTGAATACCACAAATGTC
1 AAATTGAATACCACAAATGTC
2340217 AAATATGAATACCACAAATGTC
1 AAAT-TGAATACCACAAATGTC
2340239 AAAT
1 AAAT
2340243 GTCTCAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (21 bp):
AAATTGAATACCACAAATGTC
Found at i:2342270 original size:13 final size:13
Alignment explanation
Indices: 2342252--2342297 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
2342242 CAAATTTCAA
2342252 CATGTTATATTGT
1 CATGTTATATTGT
*
2342265 CATGTTATATTAAT
1 CATGTTATATT-GT
*
2342279 ATATGTTATATTGT
1 -CATGTTATATTGT
2342293 CATGT
1 CATGT
2342298 ATCGATACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 15 0.56
14 2 0.07
15 10 0.37
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (13 bp):
CATGTTATATTGT
Found at i:2346814 original size:16 final size:16
Alignment explanation
Indices: 2346793--2346824 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2346783 AATAAATAAG
2346793 CGAACATAAACGAACA
1 CGAACATAAACGAACA
2346809 CGAACATAAACGAACA
1 CGAACATAAACGAACA
2346825 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:2346918 original size:16 final size:16
Alignment explanation
Indices: 2346894--2346953 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
2346884 TAATAAATAA
2346894 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2346910 ACAAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2346926 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
2346942 ACGAACATAAAC
1 ACGAACATAAAC
2346954 ATTGGAGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.58, C:0.23, G:0.10, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2348212 original size:27 final size:29
Alignment explanation
Indices: 2348146--2348212 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 29
2348136 GAAGGGAAAG
*
2348146 AGATGAAGCTCTGTCGAATCGTTGCAGTTGA
1 AGATGAAGCTCCGTCGAATCGTTGCA--TGA
2348177 AGACTTGAAGCTCCGTCGAATCGTTGCA-GA
1 AGA--TGAAGCTCCGTCGAATCGTTGCATGA
2348207 A-ATGAA
1 AGATGAA
2348213 AATTGTGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 4 0.12
29 1 0.03
30 3 0.09
31 3 0.09
33 22 0.67
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (29 bp):
AGATGAAGCTCCGTCGAATCGTTGCATGA
Found at i:2348498 original size:24 final size:24
Alignment explanation
Indices: 2348437--2348498 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
2348427 TATTAGGTTA
*
2348437 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* * *
2348461 AATATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
2348485 AACATAACCGAACG
1 AACATAACTGAACG
2348499 TTCACGAACG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.15
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:2349112 original size:127 final size:126
Alignment explanation
Indices: 2348881--2349163 Score: 530
Period size: 127 Copynumber: 2.2 Consensus size: 126
2348871 CTTTTCTATG
2348881 TTTAGTTCTTGAAAATATTCCAATTTAGTTATAAATTTCATTTCTTCGTTTTATAAAATTTATAA
1 TTTAGTTCTTGAAAATATTCCAATTTAGTTATAAATTTCATTTCTTCGTTTTATAAAATTTATAA
2348946 AATATTCCAATTTCATTTCTTCGTGTTATAAATTCCTTTTTTCTATAAATTTCATTTATATA
66 AATATTCCAATTTCATTTCTTCGTGTTATAAATTCCTTTTTT-TATAAATTTCATTTATATA
*
2349008 TTTAGTTCTTGAAAATAATCCAATTTAGTTATAAATTTCATTTCTTCGTTTTATAAAATTTATAA
1 TTTAGTTCTTGAAAATATTCCAATTTAGTTATAAATTTCATTTCTTCGTTTTATAAAATTTATAA
* *
2349073 AATATTCCAATTTCATTTCTTCGTGTTATAAATTTCTTTTTTTATAAATTTCATTTCTATA
66 AATATTCCAATTTCATTTCTTCGTGTTATAAATTCCTTTTTTTATAAATTTCATTTATATA
2349134 TTTAGTTCTTGAAAATATTCCAATTTAGTT
1 TTTAGTTCTTGAAAATATTCCAATTTAGTT
2349164 CGTCGATTTA
Statistics
Matches: 152, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
126 47 0.31
127 105 0.69
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.52
Consensus pattern (126 bp):
TTTAGTTCTTGAAAATATTCCAATTTAGTTATAAATTTCATTTCTTCGTTTTATAAAATTTATAA
AATATTCCAATTTCATTTCTTCGTGTTATAAATTCCTTTTTTTATAAATTTCATTTATATA
Found at i:2354192 original size:292 final size:290
Alignment explanation
Indices: 2353654--2354235 Score: 1114
Period size: 292 Copynumber: 2.0 Consensus size: 290
2353644 ACTGTGTTGT
2353654 ACAGTTTATAGATAAGGATCAAAAGTTATCTAATAGTGTGATTAAGGGGCTGTTAAAATACTGGC
1 ACAGTTTATAGATAAGGATCAAAAGTTATCTAATAGTGTGATTAAGGGGCTGTTAAAATACTGGC
2353719 CAATTACAAACAGCCAGAAGGAGTTGATGTTTATGAGTGTTAGAAGAGATTTTGGAGAGACTAAC
66 CAATTACAAACAGCCAGAAGGAGTTGATGTTTATGAGTGTTAGAAGAGATTTTGGAGAGACTAAC
2353784 ATGGTTGAGTTCCAAAGATCATGGTTCCAGTGTTTCGGCGAATTGCATGCTGCTTAAACAGCTCC
131 ATGGTTGAGTTCCAAAGATCATGGTTCCAGTGTTTCGGCGAATTGCATGCTGCTTAAACAGCTCC
2353849 CATTACCAGGTAAATTTTCCTCATTTAATCACTATGCGAAAATGTTTACCTTAAACGATATCAGG
196 CATTACCAGGTAAATTTTCCTCATTTAATCACTATGCGAAAATGTTTACCTTAAACGATATCAGG
2353914 ATTGC-TTT-TTTTTGGTTGATCAAGAACC
261 ATTGCTTTTGTTTTTGGTTGATCAAGAACC
2353942 ACAGTTTATAGATAAGGATCAAAAGTTATCTAATAGTGTGATTAAGGGGCTGTTAAAATACTGGC
1 ACAGTTTATAGATAAGGATCAAAAGTTATCTAATAGTGTGATTAAGGGGCTGTTAAAATACTGGC
2354007 CAATTACAAACAGCCAGAAGGAGTTGATGTTTATGAGTGAGTTAGAAGAGATTTTGGAGATGACT
66 CAATTACAAACAGCCAGAAGGAGTTGATGTTTATGAGT--GTTAGAAGAGATTTTGGAGA-GACT
2354072 AACATGGTTGAGTTCCAAAAGATCATGGTTCCAGTGTTTCGGCGAATTGCATGCTGCTTAAACAG
128 AACATGGTTGAGTTCC-AAAGATCATGGTTCCAGTGTTTCGGCGAATTGCATGCTGCTTAAACAG
2354137 CTCCCATTACCAGGTAAATTTTCCTCATTTAATCACTATGCGAAAATGTTTACCTTAAACGATAT
192 CTCCCATTACCAGGTAAATTTTCCTCATTTAATCACTATGCGAAAATGTTTACCTTAAACGATAT
2354202 CAGGATTGCTTTTGTTTTTGGTTGATCAAGAACC
257 CAGGATTGCTTTTGTTTTTGGTTGATCAAGAACC
2354236 TCATATCAAG
Statistics
Matches: 288, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
288 103 0.36
290 20 0.07
291 20 0.07
292 122 0.42
293 3 0.01
294 20 0.07
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (290 bp):
ACAGTTTATAGATAAGGATCAAAAGTTATCTAATAGTGTGATTAAGGGGCTGTTAAAATACTGGC
CAATTACAAACAGCCAGAAGGAGTTGATGTTTATGAGTGTTAGAAGAGATTTTGGAGAGACTAAC
ATGGTTGAGTTCCAAAGATCATGGTTCCAGTGTTTCGGCGAATTGCATGCTGCTTAAACAGCTCC
CATTACCAGGTAAATTTTCCTCATTTAATCACTATGCGAAAATGTTTACCTTAAACGATATCAGG
ATTGCTTTTGTTTTTGGTTGATCAAGAACC
Found at i:2356229 original size:116 final size:116
Alignment explanation
Indices: 2356073--2356307 Score: 445
Period size: 116 Copynumber: 2.0 Consensus size: 116
2356063 CAAGTTCATC
2356073 CTACTTGCTGCAGAAACACACCATAGACCTCAGTGATGTTCTGTACGATTTGATGTAGTGAGGGC
1 CTACTTGCTGCAGAAACACACCATAGACCTCAGTGATGTTCTGTACGATTTGATGTAGTGAGGGC
2356138 GGGAAGC-TATTTGCCTATTGGTATCCGCTCACCACCTAAGTCAGCAAAGT
66 GGGAAGCATATTTGCCTATTGGTATCCGCTCACCACCTAAGTCAGCAAAGT
2356188 CTACTTGCTGCAGAAACATCACCATAGACCTCAGTGATGTTCTGTACGATTTGATGTAGTGAGGG
1 CTACTTGCTGCAGAAACA-CACCATAGACCTCAGTGATGTTCTGTACGATTTGATGTAGTGAGGG
2356253 CGGGAAGCTATATTTGCCTATTGGTATCCGCTCACCACCTAAGTCAGCAAAGT
65 CGGGAAGC-ATATTTGCCTATTGGTATCCGCTCACCACCTAAGTCAGCAAAGT
2356306 CT
1 CT
2356308 GATAACTTCA
Statistics
Matches: 117, Mismatches: 0, Indels: 3
0.98 0.00 0.03
Matches are distributed among these distances:
115 18 0.15
116 54 0.46
118 45 0.38
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (116 bp):
CTACTTGCTGCAGAAACACACCATAGACCTCAGTGATGTTCTGTACGATTTGATGTAGTGAGGGC
GGGAAGCATATTTGCCTATTGGTATCCGCTCACCACCTAAGTCAGCAAAGT
Found at i:2357701 original size:69 final size:69
Alignment explanation
Indices: 2357589--2357726 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
2357579 ACTTTGGACG
*
2357589 ACATTTAGATATTCCAAAGGTTCACCCTTTATAGAAGGCTTAGAGATCCCATCAGTCTCATTGTC
1 ACATTTAGATATTCCAAAGGTTCACCCCTTATAGAAGGCTTAGAGATCCCATCAGTCTCATTGTC
2357654 GACT
66 GACT
* *
2357658 ACATTTAGATATTCCAAAGGTTCACCCCTTATAGCAGGGTTAGAGATCCCATCAGTCTCATTGTC
1 ACATTTAGATATTCCAAAGGTTCACCCCTTATAGAAGGCTTAGAGATCCCATCAGTCTCATTGTC
2357723 GACT
66 GACT
2357727 CCAAATTGTA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (69 bp):
ACATTTAGATATTCCAAAGGTTCACCCCTTATAGAAGGCTTAGAGATCCCATCAGTCTCATTGTC
GACT
Found at i:2358422 original size:9 final size:9
Alignment explanation
Indices: 2358408--2358432 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2358398 CTCAACATAT
2358408 CATATCCAA
1 CATATCCAA
2358417 CATATCCAA
1 CATATCCAA
2358426 CATATCC
1 CATATCC
2358433 TACGGTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (9 bp):
CATATCCAA
Found at i:2364224 original size:2 final size:2
Alignment explanation
Indices: 2364217--2364253 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2364207 AAAATATCAT
2364217 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2364254 TGAGGGTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2366093 original size:5 final size:5
Alignment explanation
Indices: 2366085--2366269 Score: 356
Period size: 5 Copynumber: 37.4 Consensus size: 5
2366075 TTGGTACAAC
2366085 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2366135 ATTAT ATTAT A-TAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2366184 ATT-T ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2366233 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
2366270 GCTCAAGTGT
Statistics
Matches: 178, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
4 8 0.04
5 170 0.96
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:2367688 original size:29 final size:30
Alignment explanation
Indices: 2367629--2367689 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
2367619 AATTTTAAAT
** *
2367629 AACGAAATGAAACATTATGCATCAAATTGA
1 AACGAAATGAAACATTAAACATCAAACTGA
2367659 AACGAAAT-AAACATTAAACA-CTAAACTGA
1 AACGAAATGAAACATTAAACATC-AAACTGA
2367688 AA
1 AA
2367690 AAACATGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 18 0.67
30 8 0.30
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.20
Consensus pattern (30 bp):
AACGAAATGAAACATTAAACATCAAACTGA
Found at i:2368110 original size:60 final size:60
Alignment explanation
Indices: 2368008--2368122 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
2367998 TAGATGGTCC
* *
2368008 TCGACTATAGGGTGATGCTTTGTTGAGTCCAACGACTGTTAAAAGTTACAAAATGATCAT
1 TCGACCATAGGGTGATGCTTTGTTGAGTCCAACGACTATTAAAAGTTACAAAATGATCAT
* * * *
2368068 TCGACCATAGGGTGTTGCTTTGTTGAG-CACTATGATTATTAAAAGTTACAAAATG
1 TCGACCATAGGGTGATGCTTTGTTGAGTC-CAACGACTATTAAAAGTTACAAAATG
2368123 GTCACCTAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (60 bp):
TCGACCATAGGGTGATGCTTTGTTGAGTCCAACGACTATTAAAAGTTACAAAATGATCAT
Found at i:2368607 original size:20 final size:20
Alignment explanation
Indices: 2368584--2368628 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2368574 GTTTCCAGAT
2368584 TCGCAACGCGATTCTAACTA
1 TCGCAACGCGATTCTAACTA
** * *
2368604 TCGCATTGCGATTTTGACTA
1 TCGCAACGCGATTCTAACTA
2368624 TCGCA
1 TCGCA
2368629 TTGCGATTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (20 bp):
TCGCAACGCGATTCTAACTA
Found at i:2368629 original size:20 final size:20
Alignment explanation
Indices: 2368600--2368637 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2368590 CGCGATTCTA
2368600 ACTATCGCATTGCGATTTTG
1 ACTATCGCATTGCGATTTTG
2368620 ACTATCGCATTGCGATTT
1 ACTATCGCATTGCGATTT
2368638 CCCAAATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (20 bp):
ACTATCGCATTGCGATTTTG
Found at i:2368653 original size:21 final size:21
Alignment explanation
Indices: 2368624--2368668 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2368614 ATTTTGACTA
2368624 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
2368645 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
2368666 TCG
1 TCG
2368669 TAATGCGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:2368715 original size:41 final size:40
Alignment explanation
Indices: 2368670--2368774 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 40
2368660 CCTAATTCGT
* **
2368670 AATGCGAAAATGTAAATCGCAACGCGAATTTGGAAAATCGC
1 AATGCGAATATGTAAATCGCAACGCGAA-TACGAAAATCGC
* * * *
2368711 AATGCGATTACGTAAATCGCAATGCGAATACGTAAATCGC
1 AATGCGAATATGTAAATCGCAACGCGAATACGAAAATCGC
* * *
2368751 AATGTGAATCTGTGAATCGCAACG
1 AATGCGAATATGTAAATCGCAACG
2368775 AGATTCTGAC
Statistics
Matches: 51, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
40 27 0.53
41 24 0.47
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (40 bp):
AATGCGAATATGTAAATCGCAACGCGAATACGAAAATCGC
Found at i:2368759 original size:20 final size:20
Alignment explanation
Indices: 2368670--2368772 Score: 100
Period size: 20 Copynumber: 5.1 Consensus size: 20
2368660 CCTAATTCGT
* *
2368670 AATGCGAAAATGTAAATCGC
1 AATGCGAATACGTAAATCGC
* ** *
2368690 AACGCGAATTTGGAAAATCGC
1 AATGCGAA-TACGTAAATCGC
*
2368711 AATGCGATTACGTAAATCGC
1 AATGCGAATACGTAAATCGC
2368731 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* *
2368751 AATGTGAAT-CTGTGAATCGC
1 AATGCGAATAC-GTAAATCGC
2368771 AA
1 AA
2368773 CGAGATTCTG
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
19 1 0.01
20 53 0.78
21 14 0.21
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.22
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Done.