Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007749.1 Hibiscus syriacus cultivar Beakdansim tig00110015_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: 1787532
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1441037 original size:45 final size:45
Alignment explanation
Indices: 1440962--1441047 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
1440952 AAACTTAAGT
*
1440962 CGCCCTTTGCGGGTTTTCAATTTGAGCCCTCCTTTGATTTCAAGA
1 CGCCCTTTGCGGGTTTTCAATTTGAACCCTCCTTTGATTTCAAGA
* *
1441007 CGCCCTTTTCGGGTTTTC-ATCTTGAACCCTCCTTTTATTTC
1 CGCCCTTTGCGGGTTTTCAAT-TTGAACCCTCCTTTGATTTC
1441048 TTTTTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 2 0.05
45 35 0.95
ACGTcount: A:0.13, C:0.29, G:0.16, T:0.42
Consensus pattern (45 bp):
CGCCCTTTGCGGGTTTTCAATTTGAACCCTCCTTTGATTTCAAGA
Found at i:1441066 original size:7 final size:7
Alignment explanation
Indices: 1441056--1441277 Score: 245
Period size: 7 Copynumber: 30.7 Consensus size: 7
1441046 TCTTTTTTTT
1441056 TTTTTCA
1 TTTTTCA
1441063 TTTTTCA
1 TTTTTCA
1441070 TTTTTCA
1 TTTTTCA
*
1441077 TTTTTCTC
1 TTTTTC-A
*
1441085 TTTCTTCTC
1 TTT-TTC-A
*
1441094 TTTCTTCTC
1 TTT-TTC-A
*
1441103 TTTCTTCTT
1 TTT-TTC-A
*
1441112 TTTTTCTT
1 TTTTTC-A
*
1441120 TTTTTCT
1 TTTTTCA
*
1441127 TTTTTCT
1 TTTTTCA
1441134 TTTTTCA
1 TTTTTCA
1441141 TTTTTCA
1 TTTTTCA
1441148 TTTTTCA
1 TTTTTCA
1441155 TTTTTTC-
1 -TTTTTCA
1441162 TTTTTCA
1 TTTTTCA
1441169 TTTGTTTCA
1 -TT-TTTCA
1441178 TTTTTCA
1 TTTTTCA
1441185 TTTTTCA
1 TTTTTCA
1441192 TTTTTCA
1 TTTTTCA
*
1441199 GTTTTCA
1 TTTTTCA
1441206 TTTTTCA
1 TTTTTCA
1441213 TTTTTCA
1 TTTTTCA
1441220 TTTTTCA
1 TTTTTCA
1441227 TTTTTCA
1 TTTTTCA
1441234 TTTTTCA
1 TTTTTCA
1441241 TTTTTCA
1 TTTTTCA
1441248 TTTTTCA
1 TTTTTCA
1441255 -TTTTCA
1 TTTTTCA
1441261 -TTTTCA
1 TTTTTCA
1441267 -TTTTCA
1 TTTTTCA
1441273 TTTTT
1 TTTTT
1441278 TCTTTTCTTT
Statistics
Matches: 203, Mismatches: 5, Indels: 14
0.91 0.02 0.06
Matches are distributed among these distances:
6 24 0.12
7 125 0.62
8 24 0.12
9 30 0.15
ACGTcount: A:0.10, C:0.16, G:0.01, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:1441138 original size:9 final size:9
Alignment explanation
Indices: 1441077--1441131 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
1441067 TCATTTTTCA
1441077 TTTTTCTCT
1 TTTTTCTCT
*
1441086 TTCTTCTCT
1 TTTTTCTCT
*
1441095 TTCTTCTCT
1 TTTTTCTCT
*
1441104 TTCTTCT-T
1 TTTTTCTCT
1441112 TTTTTCT-T
1 TTTTTCTCT
1441120 TTTTTCT-T
1 TTTTTCTCT
1441128 TTTT
1 TTTT
1441132 CTTTTTTCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
8 20 0.45
9 24 0.55
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:1441283 original size:7 final size:7
Alignment explanation
Indices: 1441044--1441334 Score: 176
Period size: 7 Copynumber: 39.1 Consensus size: 7
1441034 CCTCCTTTTA
1441044 TTTCTTT
1 TTTCTTT
*
1441051 TTTTTTT
1 TTTCTTT
*
1441058 TTTCATT
1 TTTCTTT
*
1441065 TTTCATT
1 TTTCTTT
1441072 TTTCATTT
1 TTTC-TTT
1441080 TTCTCTTT
1 TT-TCTTT
1441088 CTTCTCTTT
1 -TT-TCTTT
1441097 CTTCTCTTT
1 -TT-TCTTT
*
1441106 CTTCTTTT
1 TTTC-TTT
1441114 TTTCTTTT
1 TTTC-TTT
1441122 TTTCTTT
1 TTTCTTT
1441129 TTTCTTT
1 TTTCTTT
*
1441136 TTTCATT
1 TTTCTTT
*
1441143 TTTCATT
1 TTTCTTT
1441150 TTTCATTT
1 TTTC-TTT
1441158 TTTC-TT
1 TTTCTTT
1441164 TTTCATTT
1 TTTC-TTT
*
1441172 GTTTCATT
1 -TTTCTTT
*
1441180 TTTCATT
1 TTTCTTT
*
1441187 TTTCATT
1 TTTCTTT
**
1441194 TTTCAGT
1 TTTCTTT
*
1441201 TTTCATT
1 TTTCTTT
*
1441208 TTTCATT
1 TTTCTTT
*
1441215 TTTCATT
1 TTTCTTT
*
1441222 TTTCATT
1 TTTCTTT
*
1441229 TTTCATT
1 TTTCTTT
*
1441236 TTTCATT
1 TTTCTTT
*
1441243 TTTCATT
1 TTTCTTT
*
1441250 TTTC-AT
1 TTTCTTT
*
1441256 TTTC-AT
1 TTTCTTT
*
1441262 TTTC-AT
1 TTTCTTT
1441268 TTTCATTT
1 TTTC-TTT
1441276 TTTCTTTTCT
1 TTTC--TT-T
1441286 TTTCTTT
1 TTTCTTT
1441293 TCTTCATTTT
1 T-TTC--TTT
1441303 TTTCTTTT
1 TTTC-TTT
1441311 TTTCTTT
1 TTTCTTT
1441318 TCTTCCTTT
1 T-TT-CTTT
1441327 TTTCTTT
1 TTTCTTT
1441334 T
1 T
1441335 CATTTTTTCA
Statistics
Matches: 253, Mismatches: 14, Indels: 34
0.84 0.05 0.11
Matches are distributed among these distances:
6 23 0.09
7 134 0.53
8 54 0.21
9 33 0.13
10 9 0.04
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.75
Consensus pattern (7 bp):
TTTCTTT
Found at i:1441340 original size:6 final size:5
Alignment explanation
Indices: 1441249--1441340 Score: 59
Period size: 5 Copynumber: 17.8 Consensus size: 5
1441239 CATTTTTCAT
*
1441249 TTTTC ATTTTC ATTTTC ATTTTC -ATT- TTTTC TTTTC TTTTC TTTTC
1 TTTTC -TTTTC -TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
*
1441295 TTCATTT TTTTC -TTT- TTTTC TTTTC TTCCTT- TTTTC TTTTC ATTTT
1 TT--TTC TTTTC TTTTC TTTTC TTTTC TT--TTC TTTTC TTTTC -TTTT
1441341 TTCATCATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
4 12 0.17
5 31 0.43
6 23 0.32
7 6 0.08
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:1441341 original size:30 final size:30
Alignment explanation
Indices: 1441263--1441343 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
1441253 CATTTTCATT
*
1441263 TTCATTTTCATTT-TTTCTTTTCTTTTCTTTTC
1 TTCATTTT--TTTCTTT-TTTTCTTTTCTTTCC
1441295 TTCATTTTTTTCTTTTTTTCTTTTC-TTCC
1 TTCATTTTTTTCTTTTTTTCTTTTCTTTCC
* *
1441324 TT-TTTTCTTTTCATTTTTTC
1 TTCATTT-TTTTCTTTTTTTC
1441344 ATCATTTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 3 0.07
29 17 0.39
30 13 0.30
31 3 0.07
32 8 0.18
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (30 bp):
TTCATTTTTTTCTTTTTTTCTTTTCTTTCC
Found at i:1463298 original size:6 final size:6
Alignment explanation
Indices: 1463287--1463944 Score: 495
Period size: 6 Copynumber: 109.7 Consensus size: 6
1463277 GAAAGAGGTT
* * * *
1463287 AGAAGA AGAAGA AGAAGA AGCAGA AGAAGA AGAAGA ATGAGGA GGAGGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA A-GAAGA AGAAGA
* * * * * *
1463336 GGATG- AGGAGG AGGAGA AGAAGG AGAATG- AGAAGA AGAATG- AGAATG-
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAA-GA AGAAGA AGAA-GA AGAA-GA
* * * *
1463383 AGAATG- AGAAGA AGGATG- AGAAGA AGAAAA AGAAAA AGAA-A GAGGAGA
1 AGAA-GA AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA AGAAGA -AGAAGA
*
1463431 AGAAGA AGAAGA AGAAGA AGAA-A GAGGAGA AGAAGA AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA -AGAAGA AGAAGA AGAAGA AGAAGA
1463479 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * *
1463527 AGAAGA AGAAGA AGAA-A GAGGAGG AGAAGA AGGAGG AGGAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA -AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * *
1463575 AGGAGA ATG-AGA AGAAGG AGAAGA AGGAGA AGGAGA AGAAGA AGAAGA
1 AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * *
1463623 AGAAGA AGAAGG AGAAGG AGAAGA AGAAGA AGGAGA AGAATA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * *
1463671 ATAAGA AAAAGA ATG-AGA AGAAGA AGAAGG AGAAGA AGGAGA AGGAGA
1 AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * * * * * * *
1463719 AGGAGG AGGAGA ATAAGG ATAAGG ATAAGG AGGAGG AGAAGG AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * *
1463767 AGAA-A GAGAAGA AGGATG- AGAAGA AGGAGA AGAAGG AGAAGA AGAAGG
1 AGAAGA -AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * *
1463815 AGAAGG AGAAGA AGGAGA AGGAGA AGAAGA AGGAGA AGAATG- AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAA-GA AGAAGA
* * * *
1463863 AGAAGG AGAAGG AGAAGA ATG-ACA AGAAGA AGAATG- AGAAGGA GGAAGA
1 AGAAGA AGAAGA AGAAGA A-GAAGA AGAAGA AGAA-GA AGAA-GA AGAAGA
* * *
1463912 TGATG- ATAAGA AGAAGA AGAAGA AGAAGA AGAA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAA
1463945 ATCAATGTGG
Statistics
Matches: 545, Mismatches: 78, Indels: 58
0.80 0.11 0.09
Matches are distributed among these distances:
5 20 0.04
6 503 0.92
7 22 0.04
ACGTcount: A:0.57, C:0.00, G:0.39, T:0.03
Consensus pattern (6 bp):
AGAAGA
Found at i:1463311 original size:15 final size:15
Alignment explanation
Indices: 1463287--1463944 Score: 501
Period size: 15 Copynumber: 42.9 Consensus size: 15
1463277 GAAAGAGGTT
*
1463287 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGG
* *
1463302 AGAAGCAGAAGAAGA
1 AGAAGAAGAAGAAGG
*
1463317 AGAAGAATG-AGGAGG
1 AGAAGAA-GAAGAAGG
* * *
1463332 AGGAGGATGAGGAGGAGG
1 A-GAAGA--AGAAGAAGG
* *
1463350 AGAAGAAGGAGAATG
1 AGAAGAAGAAGAAGG
*
1463365 AGAAGAAGAATGAGAATG
1 AGAAGAAG-A--AGAAGG
1463383 AGAATG-AGAAGAAGG
1 AGAA-GAAGAAGAAGG
**
1463398 ATG-AGAAGAAGAAAA
1 A-GAAGAAGAAGAAGG
*
1463413 AGAAAAAGAA-AGAGG
1 AGAAGAAGAAGA-AGG
*
1463428 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGG
1463443 AGAAGAAGAA-AGAGG
1 AGAAGAAGAAGA-AGG
*
1463458 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGG
*
1463473 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGG
*
1463488 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGG
*
1463503 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGG
*
1463518 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGG
1463533 AGAAGAAGAA-AGAGG
1 AGAAGAAGAAGA-AGG
* *
1463548 AGGAGAAGAAGGAGG
1 AGAAGAAGAAGAAGG
*
1463563 AGGAGAAGAAGAAGG
1 AGAAGAAGAAGAAGG
1463578 AGAATG-AGAAGAAGG
1 AGAA-GAAGAAGAAGG
*
1463593 AGAAGAAGGAGAAGG
1 AGAAGAAGAAGAAGG
1463608 AGAAGAAGAAGAAGAAG
1 AGAAGAAGAAGAAG--G
*
1463625 AAGAAGAAGGAGAAGG
1 -AGAAGAAGAAGAAGG
1463641 AGAAGAAGAAGAAGG
1 AGAAGAAGAAGAAGG
* *
1463656 AGAAGAATAAGAAGA
1 AGAAGAAGAAGAAGG
* * *
1463671 ATAAGAAAAAGAATG
1 AGAAGAAGAAGAAGG
1463686 AGAAGAAGAAGAAGG
1 AGAAGAAGAAGAAGG
*
1463701 AGAAGAAGGAGAAGG
1 AGAAGAAGAAGAAGG
*
1463716 AGAAG--G-AGGAGG
1 AGAAGAAGAAGAAGG
* * *
1463728 AGAATAAGGATAAGG
1 AGAAGAAGAAGAAGG
* * * * *
1463743 ATAAGGAGGAGGAGA
1 AGAAGAAGAAGAAGG
* * *
1463758 AGGAGGAGAAGAAAG
1 AGAAGAAGAAGAAGG
* *
1463773 AGAAGAAGGATG-AGA
1 AGAAGAA-GAAGAAGG
*
1463788 AGAAGGAGAAGAAGG
1 AGAAGAAGAAGAAGG
1463803 AGAAGAAGAAGGAGAAGG
1 AGAAGAAG-A--AGAAGG
*
1463821 AGAAGAAGGAGAAGG
1 AGAAGAAGAAGAAGG
* *
1463836 AGAAGAAGAAGGAGA
1 AGAAGAAGAAGAAGG
1463851 AGAATGAGAAGAAGAAGG
1 AG-A--AGAAGAAGAAGG
* *
1463869 AGAAGGAGAAGAATG
1 AGAAGAAGAAGAAGG
* *
1463884 ACAAGAAGAAGAATG
1 AGAAGAAGAAGAAGG
* *
1463899 AGAAGGAGGAAGATGATG
1 AGAA-GAAGAAGA--AGG
* *
1463917 ATAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGG
1463932 AGAAGAAGAAGAA
1 AGAAGAAGAAGAA
1463945 ATCAATGTGG
Statistics
Matches: 526, Mismatches: 80, Indels: 74
0.77 0.12 0.11
Matches are distributed among these distances:
12 9 0.02
13 1 0.00
14 10 0.02
15 403 0.77
16 22 0.04
17 15 0.03
18 65 0.12
19 1 0.00
ACGTcount: A:0.57, C:0.00, G:0.39, T:0.03
Consensus pattern (15 bp):
AGAAGAAGAAGAAGG
Found at i:1464885 original size:47 final size:48
Alignment explanation
Indices: 1464799--1464892 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 48
1464789 TGAATGACAA
*
1464799 TTGACAACTCAAAAAGACATAGGCCCTGGAGCTCGAAAACCGGCAACGG
1 TTGACAACTCAAAAAGACA-AGGCCCCGGAGCTCGAAAACCGGCAACGG
1464848 TTGACAACTCAAAAAGAC-AGGCCCCGGAGCTCGAAAACCGGCAAC
1 TTGACAACTCAAAAAGACAAGGCCCCGGAGCTCGAAAACCGGCAAC
1464893 AGCGAGATCG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 26 0.59
49 18 0.41
ACGTcount: A:0.37, C:0.29, G:0.23, T:0.11
Consensus pattern (48 bp):
TTGACAACTCAAAAAGACAAGGCCCCGGAGCTCGAAAACCGGCAACGG
Found at i:1471276 original size:12 final size:11
Alignment explanation
Indices: 1471259--1471297 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1471249 TTGCATTAAA
1471259 TTTTTTTTATT
1 TTTTTTTTATT
*
1471270 TTCTTTTATATT
1 TT-TTTTTTATT
*
1471282 TTTTTTTCATT
1 TTTTTTTTATT
1471293 TTTTT
1 TTTTT
1471298 GATTAATCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:1472019 original size:32 final size:32
Alignment explanation
Indices: 1471977--1472067 Score: 119
Period size: 35 Copynumber: 2.8 Consensus size: 32
1471967 ACAAATCGTC
* *
1471977 AGTCACACAATGTAACTAGAGGAGTATTTCCT
1 AGTCAAACAATGTAGCTAGAGGAGTATTTCCT
1472009 AGTCAAACAATGTAGCTAGAGGAGGAGTATTTCCT
1 AGTCAAACAATGTAGCT--A-GAGGAGTATTTCCT
* *
1472044 AGTCAAGCAATGGAGCTAGAGGAG
1 AGTCAAACAATGTAGCTAGAGGAG
1472068 GAGCATTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
32 21 0.40
33 1 0.02
34 1 0.02
35 29 0.56
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.23
Consensus pattern (32 bp):
AGTCAAACAATGTAGCTAGAGGAGTATTTCCT
Found at i:1472041 original size:35 final size:35
Alignment explanation
Indices: 1471995--1472077 Score: 139
Period size: 35 Copynumber: 2.4 Consensus size: 35
1471985 AATGTAACTA
*
1471995 GAGGAGTATTTCCTAGTCAAACAATGTAGCTAGAG
1 GAGGAGTATTTCCTAGTCAAACAATGGAGCTAGAG
*
1472030 GAGGAGTATTTCCTAGTCAAGCAATGGAGCTAGAG
1 GAGGAGTATTTCCTAGTCAAACAATGGAGCTAGAG
*
1472065 GAGGAGCATTTCC
1 GAGGAGTATTTCC
1472078 AAAACACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (35 bp):
GAGGAGTATTTCCTAGTCAAACAATGGAGCTAGAG
Found at i:1473760 original size:32 final size:32
Alignment explanation
Indices: 1473706--1473791 Score: 118
Period size: 32 Copynumber: 2.6 Consensus size: 32
1473696 TTTTCACCCT
* *
1473706 AAACCCGAACCTGACCCGAATATCACACTTAAA
1 AAACCCG-ACCCGACCCAAATATCACACTTAAA
1473739 AAACCCGACCCGACCCAAATATCACACTTAAA
1 AAACCCGACCCGACCCAAATATCACACTTAAA
**
1473771 AAAATCGACCCGAACCCAAAT
1 AAACCCGACCCG-ACCCAAAT
1473792 TTTTTTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 33 0.69
33 15 0.31
ACGTcount: A:0.44, C:0.35, G:0.08, T:0.13
Consensus pattern (32 bp):
AAACCCGACCCGACCCAAATATCACACTTAAA
Found at i:1474375 original size:23 final size:23
Alignment explanation
Indices: 1474348--1474393 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1474338 TCAACCTTTT
*
1474348 TTATTTAATTTTTTTATAAAAAA
1 TTATTCAATTTTTTTATAAAAAA
1474371 TTATTCAATTTTTTTATAAAAAA
1 TTATTCAATTTTTTTATAAAAAA
1474394 ACTTCAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTATTCAATTTTTTTATAAAAAA
Found at i:1474406 original size:23 final size:22
Alignment explanation
Indices: 1474357--1474406 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1474347 TTTATTTAAT
*
1474357 TTTTTTATAAAAAATTATTCAAT
1 TTTTTTATAAAAAA-TATTCAAA
1474380 TTTTTTATAAAAAA-ACTTCAACA
1 TTTTTTATAAAAAATA-TTCAA-A
1474403 TTTT
1 TTTT
1474407 AACTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.04
22 5 0.21
23 18 0.75
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTTTATAAAAAATATTCAAA
Found at i:1477370 original size:2 final size:2
Alignment explanation
Indices: 1477363--1477389 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1477353 TTTTGTAAGC
1477363 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1477390 AACACAGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1480320 original size:31 final size:31
Alignment explanation
Indices: 1480282--1480359 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
1480272 CACTTACATC
*
1480282 AGGGACTATATTGCAAATGAACTAAATGTTG
1 AGGGACTATATTGCAAATGAACTAAATATTG
* *
1480313 -GGAGACTATATTGTAAATGGACTAAATATTG
1 AGG-GACTATATTGCAAATGAACTAAATATTG
*
1480344 AGGGACTGTATTGCAA
1 AGGGACTATATTGCAA
1480360 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 2 0.05
31 36 0.90
32 2 0.05
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.29
Consensus pattern (31 bp):
AGGGACTATATTGCAAATGAACTAAATATTG
Found at i:1482693 original size:31 final size:31
Alignment explanation
Indices: 1482641--1482715 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1482631 TTATGTCAGT
* * *
1482641 GACCATATTGCAAACGGACTAAATGTTGGGG
1 GACCATATTGCAAACAGACTAAATATTAGGG
* *
1482672 GACCATATTGCAAATATACTAAATATTAGGG
1 GACCATATTGCAAACAGACTAAATATTAGGG
**
1482703 GACTGTATTGCAA
1 GACCATATTGCAA
1482716 GTTTTAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (31 bp):
GACCATATTGCAAACAGACTAAATATTAGGG
Found at i:1482842 original size:17 final size:17
Alignment explanation
Indices: 1482817--1482891 Score: 64
Period size: 17 Copynumber: 4.5 Consensus size: 17
1482807 TTAAAATGTA
*
1482817 TAATAATTTTTTAAAAT
1 TAATAATTTATTAAAAT
* *
1482834 TAATCATTTATTAAATT
1 TAATAATTTATTAAAAT
*
1482851 TAAT--TTTAATAAAAT
1 TAATAATTTATTAAAAT
** *
1482866 TATATTTTTTATTAAAAA
1 TA-ATAATTTATTAAAAT
1482884 TAATAATT
1 TAATAATT
1482892 AATTTAAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
15 11 0.24
16 2 0.04
17 22 0.48
18 11 0.24
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATAATTTATTAAAAT
Found at i:1483626 original size:19 final size:19
Alignment explanation
Indices: 1483594--1483641 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
1483584 ATCCTAATCA
*
1483594 AATTAAATTATTAAATTTAT
1 AATT-AATTATTTAATTTAT
*
1483614 -TTTAATTATTTAATTTAT
1 AATTAATTATTTAATTTAT
1483632 AATTAATTAT
1 AATTAATTAT
1483642 AATTTTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTAATTATTTAATTTAT
Found at i:1492846 original size:623 final size:621
Alignment explanation
Indices: 1491619--1492866 Score: 2113
Period size: 623 Copynumber: 2.0 Consensus size: 621
1491609 GCTAGCGAGC
* *
1491619 TAAAATGGTTCGTGGTGGCCAAGGAGACCTCCGGTGGCGCTTCGAAGGCTCTTTCTCACTTCCTT
1 TAAAATGGTTCGTGGTGGCCAAGGAGACCTCCGGTGGCGCGTCGAAGGCTCTTTCTCACTTCCCT
*
1491684 TTACTATTATTTTATTTATTTTATTTGTGGGTTGTTGGAACGAATATTTTATGGATTTTTCTATG
66 TTACTATTATTTTATTTATTTTATTTGTGGGTTGTTGGAACAAATATTTTATGGATTTTTCTATG
1491749 GATATTTCGAACCCCACCATGAACTAACTTATTTGGTGGTGGTTGGTGTAATGGATGTTTTAACT
131 GATATTTCGAACCCCACCATGAACTAACTTATTTGGTGGTGGTTGGTGTAATGGATGTTTTAACT
*
1491814 TTATTTTAATGGTATATTTAAGTTTATTTTGGTTCTTTATTTTCTTTGCTTATGAATGCTTCACC
196 TTATTTTAATGGTATATTTAAGTTTATTTTGGTTCTTTATTTGCTTTGCTTATGAATGCTTCACC
* * *
1491879 ATCTAGGCTTGTAAGAGGCATGAAAATGTCCATTTCTTAGATGAAGGTTAGGTGTTCGGAAGAAT
261 ATCTAGGCTTGTAAGAGGCATGAAAATGTCCATTTCTTAGATAAAGGTTAAGTGTTCGAAAGAAT
* * * *
1491944 CCTAAGCTAAATATACTTGTAAGTATTCGGAAGAAATGCAAGATAATATCCTCATAAGCAATGGG
326 CCTAAGCTAAAAATACTTGTAAGTATTCGGAAGAAACGCAAGACAAGATCCTCATAAGCAATGGG
* *
1492009 TTATAGTATTTTCAAGGGGCTTTGAACTGGCCTAGGAATATTATAACCTAATCCCTTAGATCTCG
391 TTATAGTATTTTCAAGGGGCTTTGAACCGACCTAGGAATATTATAACCTAATCCCTTAGATCTCG
* * * * * *
1492074 GAAGAGACTAGGATAGAGTTTCAATGGCTAAAATGGGTGTCTTTATCAATATGGTATAATGTCCA
456 AAAGAGACTAGGATAGAGTTTCAACGACTAAAATGGGTGTATTTATCAATAGGGTAGAATGTCCA
*
1492139 ACATCGTTGAGTGAGAGCAGATGCCTTGGCATCCTATTCTGTTAGGTTCCTATGAGAACATTTTA
521 ACATCGTTGAGTGAGAGCAGATGCCTTGGCATACTATTCTGTTAGGTTCCTATGAGAACATTTTA
*
1492204 GGAAAGCCCTGTTGAGTAAGTAAAGACCAGATAGCT
586 GGAAAGCCCTGTCGAGTAAGTAAAGACCAGATAGCT
* *
1492240 TAAAGTGGTTCGTGGTGGCCGAGGAGACCTCCGGTGGCGCACGTCGAAGGCTCTTTCTCACTTCC
1 TAAAATGGTTCGTGGTGGCCAAGGAGACCTCCGGTGGCG--CGTCGAAGGCTCTTTCTCACTTCC
* * *
1492305 CTTTGCTGTTATTTTATTTATTTTATTTGTGGGTTGTTGGAACAAATATTTTGTGGATTTTTCTA
64 CTTTACTATTATTTTATTTATTTTATTTGTGGGTTGTTGGAACAAATATTTTATGGATTTTTCTA
* *
1492370 TGGATATTTCGAACCCCACCATGAACTAATTTATTTGGTGGTGGTTGGTTTAATGGATGTTTTAA
129 TGGATATTTCGAACCCCACCATGAACTAACTTATTTGGTGGTGGTTGGTGTAATGGATGTTTTAA
1492435 CTTTATTTTAATGGTATATTTAAGTTTATTTTGGTTCTTTATTTGCTTTGCTTATGAATGCTTCA
194 CTTTATTTTAATGGTATATTTAAGTTTATTTTGGTTCTTTATTTGCTTTGCTTATGAATGCTTCA
1492500 CCATCTAGGCTTGTAAGAGGCATGAAAATGTCCATTTCTTAGATAAAGGTTAAGTGTTCGAAAGA
259 CCATCTAGGCTTGTAAGAGGCATGAAAATGTCCATTTCTTAGATAAAGGTTAAGTGTTCGAAAGA
* *
1492565 ATCCTAAGCTAAAAATACTTGTAAGTATTCGGAAGAAACGCAGGACAAGATCCTCATAAGTAATG
324 ATCCTAAGCTAAAAATACTTGTAAGTATTCGGAAGAAACGCAAGACAAGATCCTCATAAGCAATG
*
1492630 GGTTATAGTATTTTCAAGGGTCTTTGAACCGACCTAGGAATATTATAACCTAATCCCTTAGATCT
389 GGTTATAGTATTTTCAAGGGGCTTTGAACCGACCTAGGAATATTATAACCTAATCCCTTAGATCT
* **
1492695 CGAAAGAGACTAGGATAG-GATTTTAACGACTAAAAAT-GGTGTATTTATCAATAGGGTAGGCTG
454 CGAAAGAGACTAGGATAGAG-TTTCAACGACT-AAAATGGGTGTATTTATCAATAGGGTAGAATG
* *
1492758 TCCAACATCGTTGAGTGAGAGCAGATGTCTTGGCATACTATTCTGTTAGGTTCCTGTGAGAACAT
517 TCCAACATCGTTGAGTGAGAGCAGATGCCTTGGCATACTATTCTGTTAGGTTCCTATGAGAACAT
*
1492823 TTTAGGAAAGCCCTGTCGAGTAAGTAAAGACCAGATATCT
582 TTTAGGAAAGCCCTGTCGAGTAAGTAAAGACCAGATAGCT
1492863 TAAA
1 TAAA
1492867 TCTGCCTGAG
Statistics
Matches: 586, Mismatches: 37, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
621 37 0.06
622 1 0.00
623 543 0.93
624 5 0.01
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.36
Consensus pattern (621 bp):
TAAAATGGTTCGTGGTGGCCAAGGAGACCTCCGGTGGCGCGTCGAAGGCTCTTTCTCACTTCCCT
TTACTATTATTTTATTTATTTTATTTGTGGGTTGTTGGAACAAATATTTTATGGATTTTTCTATG
GATATTTCGAACCCCACCATGAACTAACTTATTTGGTGGTGGTTGGTGTAATGGATGTTTTAACT
TTATTTTAATGGTATATTTAAGTTTATTTTGGTTCTTTATTTGCTTTGCTTATGAATGCTTCACC
ATCTAGGCTTGTAAGAGGCATGAAAATGTCCATTTCTTAGATAAAGGTTAAGTGTTCGAAAGAAT
CCTAAGCTAAAAATACTTGTAAGTATTCGGAAGAAACGCAAGACAAGATCCTCATAAGCAATGGG
TTATAGTATTTTCAAGGGGCTTTGAACCGACCTAGGAATATTATAACCTAATCCCTTAGATCTCG
AAAGAGACTAGGATAGAGTTTCAACGACTAAAATGGGTGTATTTATCAATAGGGTAGAATGTCCA
ACATCGTTGAGTGAGAGCAGATGCCTTGGCATACTATTCTGTTAGGTTCCTATGAGAACATTTTA
GGAAAGCCCTGTCGAGTAAGTAAAGACCAGATAGCT
Found at i:1493589 original size:21 final size:21
Alignment explanation
Indices: 1493563--1493639 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
1493553 TATAGAATTA
1493563 TCCCGAATGACCACATATATG
1 TCCCGAATGACCACATATATG
* * *
1493584 TCCCGAATGACCTCGTAGAATTG
1 TCCCGAATGACCACATA-TA-TG
*
1493607 TTCCGAATGACCACATATATG
1 TCCCGAATGACCACATATATG
* *
1493628 TCTCGAAGGACC
1 TCCCGAATGACC
1493640 TCGTAGAACC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 26 0.59
22 2 0.05
23 16 0.36
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (21 bp):
TCCCGAATGACCACATATATG
Found at i:1493618 original size:44 final size:44
Alignment explanation
Indices: 1493555--1493647 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
1493545 GAGTTCCATA
*
1493555 TAGAATTATCCCGAATGACCACATATATGTCCCGAATGACCTCG
1 TAGAATTATCCCGAATGACCACATATATGTCCCGAAGGACCTCG
* * *
1493599 TAGAATTGTTCCGAATGACCACATATATGTCTCGAAGGACCTCG
1 TAGAATTATCCCGAATGACCACATATATGTCCCGAAGGACCTCG
1493643 TAGAA
1 TAGAA
1493648 CCCTTGACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (44 bp):
TAGAATTATCCCGAATGACCACATATATGTCCCGAAGGACCTCG
Found at i:1496717 original size:21 final size:21
Alignment explanation
Indices: 1496678--1496717 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1496668 AACAAAAAAG
*
1496678 AAGAATGATAGAAATAAGGCA
1 AAGAATGATAGAAAAAAGGCA
1496699 AAGAATGAT-GAAGAAAAGG
1 AAGAATGATAGAA-AAAAGG
1496718 AAGAGGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.57, C:0.03, G:0.28, T:0.12
Consensus pattern (21 bp):
AAGAATGATAGAAAAAAGGCA
Found at i:1498886 original size:20 final size:20
Alignment explanation
Indices: 1498861--1498898 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1498851 CATATATTAA
1498861 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
1498881 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
1498899 TCAAGGGGAA
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:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:1502986 original size:65 final size:63
Alignment explanation
Indices: 1502891--1503032 Score: 180
Period size: 65 Copynumber: 2.2 Consensus size: 63
1502881 CACATTGAAT
* *
1502891 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGAAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAATGAAATTGGTGCATCGATGCAT-AGGTA
* * * *
1502954 GTGCATCGATGCATCCCTTTAAA-AATGAAAACATCAAATGTAATTTGTGTATCGATGCATGGGT
1 GTGCATCGATGCA-CCCTTTAAAGAA-G-AAACATCAAATGAAATTGGTGCATCGATGCATAGGT
1503018 A
63 A
1503019 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1503033 ATGTTAAAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
63 15 0.22
64 12 0.17
65 42 0.61
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAATGAAATTGGTGCATCGATGCATAGGTA
Found at i:1506123 original size:103 final size:103
Alignment explanation
Indices: 1505939--1506153 Score: 385
Period size: 103 Copynumber: 2.1 Consensus size: 103
1505929 GTCGAGGGTC
1505939 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1506004 GTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 GTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
1506042 TATGTGGTCCTTCGGGACATATATGTATTGTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1506107 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 GTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1506145 TATGTGGTC
1 TATGTGGTC
1506154 TTTATAGACA
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
GTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1506536 original size:2 final size:2
Alignment explanation
Indices: 1506524--1506555 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1506514 TGATAATGAC
*
1506524 AT AT AT GT 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
1506556 TTGTTACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1510783 original size:21 final size:21
Alignment explanation
Indices: 1510741--1510783 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1510731 TTTCTGGGCT
* *
1510741 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1510762 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1510783 A
1 A
1510784 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1511803 original size:104 final size:104
Alignment explanation
Indices: 1511623--1511824 Score: 368
Period size: 104 Copynumber: 1.9 Consensus size: 104
1511613 GTGGTCATTC
* * *
1511623 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCA
1 GGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
1511688 TATGTATATGATTCTTAAGGAATGATATGTGGTTTCTTT
66 TATGTATATGATTCTTAAGGAATGATATGTGGTTTCTTT
*
1511727 GGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGTA
1 GGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
1511792 TATGTATATGATTCTTAAGGAATGATATGTGGT
66 TATGTATATGATTCTTAAGGAATGATATGTGGT
1511825 CCTTATGGAC
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 94 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (104 bp):
GGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
TATGTATATGATTCTTAAGGAATGATATGTGGTTTCTTT
Found at i:1511884 original size:23 final size:23
Alignment explanation
Indices: 1511858--1511910 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1511848 ACTACAGTGT
*
1511858 AATTCTACGTGGCACTCCGGTGC
1 AATTATACGTGGCACTCCGGTGC
* *
1511881 AATTATATGTGGCACTTCGGTGC
1 AATTATACGTGGCACTCCGGTGC
1511904 AATTATA
1 AATTATA
1511911 TGAGCTGTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
AATTATACGTGGCACTCCGGTGC
Found at i:1511911 original size:23 final size:23
Alignment explanation
Indices: 1511866--1511912 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1511856 GTAATTCTAC
1511866 GTGGCACTCCGGTGCAATTATAT
1 GTGGCACTCCGGTGCAATTATAT
*
1511889 GTGGCACTTCGGTGCAATTATAT
1 GTGGCACTCCGGTGCAATTATAT
1511912 G
1 G
1511913 AGCTGTGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (23 bp):
GTGGCACTCCGGTGCAATTATAT
Found at i:1518713 original size:21 final size:21
Alignment explanation
Indices: 1518687--1518726 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1518677 CCCCCTTTGA
*
1518687 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1518708 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1518727 TGAGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1522594 original size:11 final size:11
Alignment explanation
Indices: 1522578--1522602 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1522568 CTCAGACTCA
1522578 GATCCAGGTCG
1 GATCCAGGTCG
1522589 GATCCAGGTCG
1 GATCCAGGTCG
1522600 GAT
1 GAT
1522603 TCGGGTTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.24, G:0.36, T:0.20
Consensus pattern (11 bp):
GATCCAGGTCG
Found at i:1550860 original size:2 final size:2
Alignment explanation
Indices: 1550853--1550877 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1550843 TTTTCGAAAT
1550853 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1550878 TAAGTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1557705 original size:14 final size:14
Alignment explanation
Indices: 1557678--1557717 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1557668 ACACATATAC
*
1557678 TTATTAAATTCACA
1 TTATTAAGTTCACA
1557692 TTCA-TAAGTTCACA
1 TT-ATTAAGTTCACA
1557706 TTATTAAGTTCA
1 TTATTAAGTTCA
1557718 TTAGTCCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (14 bp):
TTATTAAGTTCACA
Found at i:1557820 original size:23 final size:23
Alignment explanation
Indices: 1557794--1557862 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
1557784 TACCACAGCT
*
1557794 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1557817 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1557840 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1557863 TATAATAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1564710 original size:23 final size:23
Alignment explanation
Indices: 1564679--1564747 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1564669 CACCATAGCT
* *
1564679 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1564702 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1564725 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1564748 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1565001 original size:30 final size:30
Alignment explanation
Indices: 1564957--1565026 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
1564947 ACATAATTTG
* *
1564957 TATCACGTAAACATATTATTTTCATACCTT
1 TATCACATAAACATATCATTTTCATACCTT
*
1564987 TATCACATAGACATATCATTTTCATACCTT
1 TATCACATAAACATATCATTTTCATACCTT
1565017 TATCACATAA
1 TATCACATAA
1565027 CTCTCATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (30 bp):
TATCACATAAACATATCATTTTCATACCTT
Found at i:1582364 original size:18 final size:18
Alignment explanation
Indices: 1582338--1582374 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1582328 AAACAAGTTT
* *
1582338 AAATTATATATTATTTAA
1 AAATAATATATAATTTAA
1582356 AAATAATATATAATTTAA
1 AAATAATATATAATTTAA
1582374 A
1 A
1582375 CTTATTTAAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAATATATAATTTAA
Found at i:1584550 original size:7 final size:7
Alignment explanation
Indices: 1584532--1584599 Score: 63
Period size: 7 Copynumber: 10.0 Consensus size: 7
1584522 ACACTCGAAA
1584532 AAAAAAGG
1 AAAAAA-G
1584540 AAAAGAA-
1 AAAA-AAG
1584547 AAAAAAG
1 AAAAAAG
*
1584554 AATAAAG
1 AAAAAAG
*
1584561 AATAAAG
1 AAAAAAG
*
1584568 -AAGAAG
1 AAAAAAG
1584574 -AAAAAG
1 AAAAAAG
1584580 AAAAAAG
1 AAAAAAG
1584587 -AAAAAG
1 AAAAAAG
1584593 AAAAAAG
1 AAAAAAG
1584600 GATAGATAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
6 17 0.33
7 29 0.56
8 4 0.08
9 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:1584550 original size:13 final size:13
Alignment explanation
Indices: 1584529--1584599 Score: 74
Period size: 13 Copynumber: 5.5 Consensus size: 13
1584519 ACCACACTCG
*
1584529 AAAAA-AAAAGGA
1 AAAAAGAAAAAGA
*
1584541 AAAGAAAAAAAAGA
1 AAA-AAGAAAAAGA
*
1584555 ATAAAGAATAAAG-
1 AAAAAGAA-AAAGA
*
1584568 AAGAAGAAAAAGA
1 AAAAAGAAAAAGA
1584581 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
1584594 AAAAAG
1 AAAAAG
1584600 GATAGATAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
12 7 0.14
13 30 0.61
14 12 0.24
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:1584616 original size:6 final size:6
Alignment explanation
Indices: 1584529--1584597 Score: 65
Period size: 6 Copynumber: 11.7 Consensus size: 6
1584519 ACCACACTCG
* *
1584529 AAAA-A AAAAGG AAAAG- -AAA-A AAAAGA ATAAAGA ATAAAGA AGAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A-AAAGA A-AAAGA AAAAGA
1584575 AAAAGAA AAAAGA AAAAGA AAAA
1 AAAAG-A AAAAGA AAAAGA AAAA
1584598 AGGATAGATA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
4 3 0.05
5 7 0.13
6 26 0.47
7 19 0.35
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:1585824 original size:232 final size:233
Alignment explanation
Indices: 1585415--1586493 Score: 1614
Period size: 232 Copynumber: 4.7 Consensus size: 233
1585405 GTAAAAAAAT
* * *
1585415 AAAATGAGAAATGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCT
1 AAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCT
*
1585480 TACCTAGTAAACTATTTCC-AAA-TT-TAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
66 TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * * * *
1585542 TGCTTAAATTCGTCGGGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCAATCCA
131 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCAGGCCATCCA
1585607 TAAGTCCTTCGGGCAGGATGTTTTCACATGTCTCTCGA
196 TAAGTCCTTCGGGCAGGATGTTTTCACATGTCTCTCGA
*
1585645 AAAATGAGAAAGGTTTCTTATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCT
1 AAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCT
*
1585710 TACCTAGT-AACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGA
66 TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * * ** *
1585774 TCCTTAAATCTTTCGAGTCATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTTCAAGCCATCCA
131 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCAGGCCATCCA
1585839 TAAGTCCTTCGGGCAGGATGTTTTCACATGTCTCTCGA
196 TAAGTCCTTCGGGCAGGATGTTTTCACATGTCTCTCGA
* * *
1585877 AAAATTAGAAATGTTTCTCATTTAAATCTGAAATTTGAAAATTTTG-AAAGTAAGAAAGGTTTCT
1 AAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCT
* *
1585941 TACCCAGTAAACTATTTCCAAAATTTATAAGTCCTTAGGGCCATCAGTAAGTCTTTCGAAGCATG
66 TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCG-AGCATG
* * **
1586006 ATGCTTAAATCCTTCGGGTAATCTGTAAGTTTTTCAAGCAAGATGATAAGTCCTTTGGGCCATCC
130 ATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCAGGCCATCC
* * ** *
1586071 ATAAGACCTTCGGGCAAGATGTTTTCACATGAGTATCGA
195 ATAAGTCCTTCGGGCAGGATGTTTTCACATGTCTCTCGA
* * * * * *
1586110 AAAATGAGAAAAGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTATGAAAGTTTTCC
1 AAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCT
1586175 TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
66 TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * * *
1586240 TACTTAAATCCTTCGGGTCATTTGTAAGTATTTCAAGCAAGATGATAAGTCCTTC-GAGCCATGC
131 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCAG-GCCATCC
* *
1586304 AAAAGTCCTTCGAGCAGGATGTTTTCACATGTCTCTCGA
195 ATAAGTCCTTCGGGCAGGATGTTTTCACATGTCTCTCGA
* * *
1586343 AAAATGAGAAAGATTTCTCATTTAAATCTGAAATTTGAAA-TTTTGAAAAGTAAGCAAGGCTTCT
1 AAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCT
* * ** * *
1586407 TATCTATTAAACTATTTCCAAAATTTATAAGTCCTTCAAGCCATCAATAAGTTTTTCGAGCATGA
66 TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
*
1586472 TGCTTAAATCATTCGGGTCATC
131 TGCTTAAATCCTTCGGGTCATC
1586494 CATAAGACCT
Statistics
Matches: 764, Mismatches: 78, Indels: 12
0.89 0.09 0.01
Matches are distributed among these distances:
229 10 0.01
230 72 0.09
231 27 0.04
232 317 0.41
233 267 0.35
234 71 0.09
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (233 bp):
AAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCT
TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCAGGCCATCCA
TAAGTCCTTCGGGCAGGATGTTTTCACATGTCTCTCGA
Found at i:1586420 original size:466 final size:464
Alignment explanation
Indices: 1585415--1586489 Score: 1640
Period size: 466 Copynumber: 2.3 Consensus size: 464
1585405 GTAAAAAAAT
* *
1585415 AAAATGAGAAATGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCT
1 AAAATGAGAAATGTTTCTCATTTAAATCTGAAATTTGAAA-TTTTGAAAAGTAAGAAAGGTTTCT
* *
1585480 TACCTAGTAAACTATTTCC-AAA-TT-TAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
65 TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGA
* * * *
1585542 TGCTTAAATTCGTCGGGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCAATCCA
130 TGCTTAAATCCTTCGGGTAATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCAGGCAATCCA
* * * * * *
1585607 TAAGTCCTTCGGGCAGGATGTTTTCACATGTCTCTCGAAAAATGAGAAAGGTTTCTTATTTAAAT
195 TAAGACCTTCGGGCAAGATGTTTTCACATGACTATCGAAAAATGAGAAAAGTTTCTCATTTAAAT
* * *
1585672 CTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAACTATTTCCAAAATTTAT
260 ATGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCCTACCTAGTAACTATTTCCAAAATTTAT
* *
1585737 AAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATCCTTAAATCTTTCGAGTCATCTGTAAG
325 AAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATACTTAAATCCTTCGAGTCATCTGTAAG
* ** * *
1585802 TCTTTTGAGCAAGATGATAAGTCCTTCAAGCCATCCATAAGTCCTTCGGGCAGGATGTTTTCACA
390 TATTTCAAGCAAGATGATAAGTCCTTCAAGCCATCCAAAAGTCCTTCGAGCAGGATGTTTTCACA
1585867 TGTCTCTCGA
455 TGTCTCTCGA
*
1585877 AAAATTAGAAATGTTTCTCATTTAAATCTGAAATTTGAAAATTTTG-AAAGTAAGAAAGGTTTCT
1 AAAATGAGAAATGTTTCTCATTTAAATCTGAAATTTG-AAATTTTGAAAAGTAAGAAAGGTTTCT
*
1585941 TACCCAGTAAACTATTTCCAAAATTTATAAGTCCTTAGGGCCATCAGTAAGTCTTTCGAAGCATG
65 TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTAGGGCCATCAGTAAGTCTTTCG-AGCATG
* ** *
1586006 ATGCTTAAATCCTTCGGGTAATCTGTAAGTTTTTCAAGCAAGATGATAAGTCCTTTGGGCCATCC
129 ATGCTTAAATCCTTCGGGTAATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCAGGCAATCC
*
1586071 ATAAGACCTTCGGGCAAGATGTTTTCACATGAGTATCGAAAAATGAGAAAAGTTTCTCATTTAAA
194 ATAAGACCTTCGGGCAAGATGTTTTCACATGACTATCGAAAAATGAGAAAAGTTTCTCATTTAAA
* *
1586136 TATGAAAATTGAAATTTTTGAAAAGTATGAAAGTTTTCCTACCTAGTAAACTATTTCCAAAATTT
259 TATGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCCTACCTAGT-AACTATTTCCAAAATTT
* * *
1586201 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCGGGTCATTTGTA
323 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATACTTAAATCCTTCGAGTCATCTGTA
* *
1586266 AGTATTTCAAGCAAGATGATAAGTCCTTCGAGCCATGCAAAAGTCCTTCGAGCAGGATGTTTTCA
388 AGTATTTCAAGCAAGATGATAAGTCCTTCAAGCCATCCAAAAGTCCTTCGAGCAGGATGTTTTCA
1586331 CATGTCTCTCGA
453 CATGTCTCTCGA
* *
1586343 AAAATGAGAAA-GATTTCTCATTTAAATCTGAAATTTGAAATTTTGAAAAGTAAGCAAGGCTTCT
1 AAAATGAGAAATG-TTTCTCATTTAAATCTGAAATTTGAAATTTTGAAAAGTAAGAAAGGTTTCT
* * * * *
1586407 TATCTATTAAACTATTTCCAAAATTTATAAGTCCTTCA-AGCCATCAATAAGTTTTTCGAGCATG
65 TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTT-AGGGCCATCAGTAAGTCTTTCGAGCATG
*
1586471 ATGCTTAAATCATTCGGGT
129 ATGCTTAAATCCTTCGGGT
1586490 CATCCATAAG
Statistics
Matches: 556, Mismatches: 48, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
461 36 0.06
462 42 0.08
463 5 0.01
464 29 0.05
465 196 0.35
466 247 0.44
467 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (464 bp):
AAAATGAGAAATGTTTCTCATTTAAATCTGAAATTTGAAATTTTGAAAAGTAAGAAAGGTTTCTT
ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGAT
GCTTAAATCCTTCGGGTAATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCAGGCAATCCAT
AAGACCTTCGGGCAAGATGTTTTCACATGACTATCGAAAAATGAGAAAAGTTTCTCATTTAAATA
TGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCCTACCTAGTAACTATTTCCAAAATTTATA
AGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATACTTAAATCCTTCGAGTCATCTGTAAGT
ATTTCAAGCAAGATGATAAGTCCTTCAAGCCATCCAAAAGTCCTTCGAGCAGGATGTTTTCACAT
GTCTCTCGA
Found at i:1586651 original size:20 final size:19
Alignment explanation
Indices: 1586626--1586693 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 19
1586616 CCAAAATATA
1586626 TAAGTCCTTCGGGCCATCAG
1 TAAGTCCTTCGGG-CATCAG
* * *
1586646 TAAGTCTTTCGAGCATGATG
1 TAAGTCCTTCGGGCATCA-G
*
1586666 CTTAAATCCTTCGGGTCATCAG
1 --TAAGTCCTTCGGG-CATCAG
1586688 TAAGTC
1 TAAGTC
1586694 TTTCAAGAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 4 0.11
20 17 0.47
22 11 0.31
23 4 0.11
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (19 bp):
TAAGTCCTTCGGGCATCAG
Found at i:1586658 original size:192 final size:191
Alignment explanation
Indices: 1586310--1586685 Score: 572
Period size: 192 Copynumber: 2.0 Consensus size: 191
1586300 ATGCAAAAGT
* * * *
1586310 CCTTCGAGCAGGATGTTTTCACATGTCTCTCGAAAAATGAGAAAGATTTCTCATTTAAATCTGAA
1 CCTTCGAGCAGGATGTTTCCACATATCTATCGAAAAATGAGAAAGATTTCTCATTTAAATCTAAA
* * * * *
1586375 ATTTGAAATTTTGAAAAGTAAGCAAGGCTTCTTATCTATTAAACTATTTCCAAAATTTATAAGTC
66 ATTTGAAATTTTGAAAAGTAAGAAAGACTTCTTACCTAGTAAACTATTTCCAAAATATATAAGTC
*
1586440 CTTCAAGCCATCAATAAGTTTTTCGAGCATGATGCTTAAATCATTCGGGTCATCCATAAGA
131 CTTCAAGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCCATAAGA
* * * *
1586501 CCTTCGGGCTGGATGTTTCCACATATCTATCGAAATATGAGAAAGGTTTCTCATTTAAATCTAAA
1 CCTTCGAGCAGGATGTTTCCACATATCTATCGAAAAATGAGAAAGATTTCTCATTTAAATCTAAA
*
1586566 ATTTGAAATTTTTGAAAAGTAAGAAAGATTTCTTACCTAGTAAACTATTTCCAAAATATATAAGT
66 ATTTGAAA-TTTTGAAAAGTAAGAAAGACTTCTTACCTAGTAAACTATTTCCAAAATATATAAGT
** * *
1586631 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATC
130 CCTTCAAGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATC
1586686 AGTAAGTCTT
Statistics
Matches: 165, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
191 65 0.39
192 100 0.61
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (191 bp):
CCTTCGAGCAGGATGTTTCCACATATCTATCGAAAAATGAGAAAGATTTCTCATTTAAATCTAAA
ATTTGAAATTTTGAAAAGTAAGAAAGACTTCTTACCTAGTAAACTATTTCCAAAATATATAAGTC
CTTCAAGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCCATAAGA
Found at i:1587501 original size:23 final size:23
Alignment explanation
Indices: 1587467--1587535 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1587457 CACCATAGCT
*
1587467 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1587490 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1587513 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1587536 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1588979 original size:21 final size:21
Alignment explanation
Indices: 1588955--1588998 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1588945 TTTTGTTCGT
* *
1588955 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1588976 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1588997 TT
1 TT
1588999 ACCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1589878 original size:20 final size:20
Alignment explanation
Indices: 1589853--1589908 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
1589843 TCCAAATTTG
* *
1589853 GTAAGTCCTTCGGGCCATAA
1 GTAAGTCCTTCGGGCAAGAA
* *
1589873 GTAAGTCTTTCGAGCAAGAA
1 GTAAGTCCTTCGGGCAAGAA
1589893 GATTAAGTCCTTCGGG
1 G--TAAGTCCTTCGGG
1589909 TCATCTATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 17 0.61
22 11 0.39
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (20 bp):
GTAAGTCCTTCGGGCAAGAA
Found at i:1589901 original size:42 final size:41
Alignment explanation
Indices: 1589854--1589949 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
1589844 CCAAATTTGG
* * *
1589854 TAAGTCCTTCGGGCCAT-AAGTAAGTCTTTCGAGCAAGAAGA
1 TAAGTCCTTCGGGCCATCAA-TAAGCCTCTCGAACAAGAAGA
* * *
1589895 TTAAGTCCTTCGGGTCATCTATAAGCCTCTCGAACAAGATGA
1 -TAAGTCCTTCGGGCCATCAATAAGCCTCTCGAACAAGAAGA
1589937 TAAGTCCTTCGGG
1 TAAGTCCTTCGGG
1589950 TAGGATGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 13 0.28
42 33 0.70
43 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (41 bp):
TAAGTCCTTCGGGCCATCAATAAGCCTCTCGAACAAGAAGA
Found at i:1590515 original size:134 final size:133
Alignment explanation
Indices: 1590276--1590624 Score: 477
Period size: 134 Copynumber: 2.6 Consensus size: 133
1590266 GCGAATCAAA
* * * *
1590276 CTCGATTCAATCTTCCCTGAGTGATAGTGTAATTGATCAACTACCCATATCTGATATTCCCTCCA
1 CTCGATTCAATCTTCCCTGAGTGATAGT-TAAATGATCAACTCCCCATATCTGATTTTCCCTCAA
* * *
1590341 GAAGAAGCGGAACAG-ATCCATCTCTATCAAGATTTGATATTCCCTGAGTGATAGTGGAACAAGT
65 GAAGAAGCGGAACAGAAACCATCTCTATCAAGATTTGATATTCCCTGAGTGACAGTGAAACAAGT
1590405 CTAC
130 CTAC
*
1590409 CTCGATTCAATCTTCCCTGAGTGATAGTTAAATGAATCAACTCCCCCATATCTAATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTGATAGTTAAATG-ATCAACT-CCCCATATCTGATTTTCCCTCA
* *
1590474 AGAAGAAGCGTAACAGAAACC-TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGAAACAAG
64 AGAAGAAGCGGAACAGAAACCATCTCTATCAAGATTTGATATTCCCTGAGTGACAGTGAAACAAG
*
1590538 TCTAT
129 TCTAC
* * *** * *
1590543 CTCGATTCAATCTTCCTTGAGTGACAGTGGGATGGATCAACGTCCCCAGATTTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTGATAGTTAAAT-GATCAAC-TCCCCATATCTGATTTTCCCTCA
1590608 AGAAGAAGCGGAACAGA
64 AGAAGAAGCGGAACAGA
1590625 TCCCTCATCA
Statistics
Matches: 191, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
132 5 0.03
133 35 0.18
134 146 0.76
135 5 0.03
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (133 bp):
CTCGATTCAATCTTCCCTGAGTGATAGTTAAATGATCAACTCCCCATATCTGATTTTCCCTCAAG
AAGAAGCGGAACAGAAACCATCTCTATCAAGATTTGATATTCCCTGAGTGACAGTGAAACAAGTC
TAC
Found at i:1601998 original size:30 final size:30
Alignment explanation
Indices: 1601975--1602032 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1601965 CTCTTTCTCT
*
1601975 TTCCCGTTCCATATCTCGCTCTCTATCCCG
1 TTCCCGTTCCATATCTCGATCTCTATCCCG
* *
1602005 TTCCCGTTCCCTTTCTCGATCTCTATCC
1 TTCCCGTTCCATATCTCGATCTCTATCC
1602033 TTCTTTCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.09, C:0.43, G:0.09, T:0.40
Consensus pattern (30 bp):
TTCCCGTTCCATATCTCGATCTCTATCCCG
Found at i:1604151 original size:3 final size:3
Alignment explanation
Indices: 1604143--1604180 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1604133 TGTATTAAAT
* *
1604143 AAC AAC AAC AAC AAT AAC AAC AAC AAT AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1604181 AACCCTATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.05
Consensus pattern (3 bp):
AAC
Found at i:1604163 original size:12 final size:12
Alignment explanation
Indices: 1604146--1604180 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
1604136 ATTAAATAAC
1604146 AACAACAACAAT
1 AACAACAACAAT
1604158 AACAACAACAAT
1 AACAACAACAAT
1604170 AACAACAACAA
1 AACAACAACAA
1604181 AACCCTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.69, C:0.26, G:0.00, T:0.06
Consensus pattern (12 bp):
AACAACAACAAT
Found at i:1610868 original size:20 final size:20
Alignment explanation
Indices: 1610836--1610885 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
1610826 TATTCTATCT
*
1610836 AATTTAAATAAAATTTATTG
1 AATTTAAATAAAATCTATTG
1610856 AATTT-AATAAAAATCTATT-
1 AATTTAAAT-AAAATCTATTG
1610875 AA--TAAATAAAA
1 AATTTAAATAAAA
1610886 CAATTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 5 0.19
18 3 0.11
19 5 0.19
20 14 0.52
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTTAAATAAAATCTATTG
Found at i:1611538 original size:16 final size:16
Alignment explanation
Indices: 1611517--1611552 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1611507 CTCCTAAGAT
1611517 TTTTAAATTTTTTATA
1 TTTTAAATTTTTTATA
*
1611533 TTTTAACTTTTTTATA
1 TTTTAAATTTTTTATA
1611549 TTTT
1 TTTT
1611553 TATTAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAAATTTTTTATA
Found at i:1625514 original size:3 final size:3
Alignment explanation
Indices: 1625506--1625549 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
1625496 ATGGAACATA
1625506 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
1625550 GAAAAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 32 0.84
4 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1632340 original size:2 final size:2
Alignment explanation
Indices: 1632333--1632372 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1632323 ATAAAAATTG
1632333 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
1632373 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1634502 original size:12 final size:12
Alignment explanation
Indices: 1634485--1634521 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1634475 AATATAAAAA
1634485 ATATGAAAAATT
1 ATATGAAAAATT
1634497 ATATGAAAAATT
1 ATATGAAAAATT
1634509 ATATGAAAAATT
1 ATATGAAAAATT
1634521 A
1 A
1634522 AAATTTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATATGAAAAATT
Found at i:1639260 original size:208 final size:208
Alignment explanation
Indices: 1638902--1639318 Score: 834
Period size: 208 Copynumber: 2.0 Consensus size: 208
1638892 CCCTGATGGT
1638902 TACACCCCTCTATTTTTCAAGAAATCTTGGTCTATGGTTGGTGAAGATGTTATTAATGCTGTCAA
1 TACACCCCTCTATTTTTCAAGAAATCTTGGTCTATGGTTGGTGAAGATGTTATTAATGCTGTCAA
1638967 ATATTTCTTCCAAGAGTCTCTTATTATTCCAGCTTTCAACTCTACCGTAATATCCTTAATTCCAA
66 ATATTTCTTCCAAGAGTCTCTTATTATTCCAGCTTTCAACTCTACCGTAATATCCTTAATTCCAA
1639032 AAATTCAAAACCCAAGCAAAGTCAAGGATTATAGGCCTATTTCTTGTTGTTCTGTGGTGTACAAA
131 AAATTCAAAACCCAAGCAAAGTCAAGGATTATAGGCCTATTTCTTGTTGTTCTGTGGTGTACAAA
1639097 TCTATCACAAAAA
196 TCTATCACAAAAA
1639110 TACACCCCTCTATTTTTCAAGAAATCTTGGTCTATGGTTGGTGAAGATGTTATTAATGCTGTCAA
1 TACACCCCTCTATTTTTCAAGAAATCTTGGTCTATGGTTGGTGAAGATGTTATTAATGCTGTCAA
1639175 ATATTTCTTCCAAGAGTCTCTTATTATTCCAGCTTTCAACTCTACCGTAATATCCTTAATTCCAA
66 ATATTTCTTCCAAGAGTCTCTTATTATTCCAGCTTTCAACTCTACCGTAATATCCTTAATTCCAA
1639240 AAATTCAAAACCCAAGCAAAGTCAAGGATTATAGGCCTATTTCTTGTTGTTCTGTGGTGTACAAA
131 AAATTCAAAACCCAAGCAAAGTCAAGGATTATAGGCCTATTTCTTGTTGTTCTGTGGTGTACAAA
1639305 TCTATCACAAAAA
196 TCTATCACAAAAA
1639318 T
1 T
1639319 TCTTGTCAAA
Statistics
Matches: 209, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
208 209 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (208 bp):
TACACCCCTCTATTTTTCAAGAAATCTTGGTCTATGGTTGGTGAAGATGTTATTAATGCTGTCAA
ATATTTCTTCCAAGAGTCTCTTATTATTCCAGCTTTCAACTCTACCGTAATATCCTTAATTCCAA
AAATTCAAAACCCAAGCAAAGTCAAGGATTATAGGCCTATTTCTTGTTGTTCTGTGGTGTACAAA
TCTATCACAAAAA
Found at i:1641112 original size:32 final size:31
Alignment explanation
Indices: 1641059--1641118 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
1641049 TTAAAAAATA
*
1641059 TAAATTAAATTTATTTTTATTTTGTTTTACAT
1 TAAAATAAATTTATTTTTATTTT-TTTTACAT
1641091 TAAAATAAATTT-TTTTATATTTTTTTTA
1 TAAAATAAATTTATTTT-TATTTTTTTTA
1641119 TTTTAATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (31 bp):
TAAAATAAATTTATTTTTATTTTTTTTACAT
Found at i:1641361 original size:22 final size:22
Alignment explanation
Indices: 1641336--1641379 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1641326 AGTGATCAAT
1641336 GTCGATCAAACTGAAAATAAAA
1 GTCGATCAAACTGAAAATAAAA
*
1641358 GTCGATCAAATTGAAAATAAAA
1 GTCGATCAAACTGAAAATAAAA
1641380 AATAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (22 bp):
GTCGATCAAACTGAAAATAAAA
Found at i:1643326 original size:28 final size:31
Alignment explanation
Indices: 1643293--1643359 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
1643283 TTATTATTAT
1643293 TATTATTTTTAATT-TAAA-TTTATAATGAA
1 TATTATTTTTAATTATAAATTTTATAATGAA
* *
1643322 T-TTA-TATTAATTATAAATTTTTATAATGCA
1 TATTATTTTTAATTATAAA-TTTTATAATGAA
1643352 TATTATTT
1 TATTATTT
1643360 AAGAAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.23
28 7 0.23
29 1 0.03
30 11 0.37
31 3 0.10
32 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (31 bp):
TATTATTTTTAATTATAAATTTTATAATGAA
Found at i:1644119 original size:21 final size:21
Alignment explanation
Indices: 1644053--1644119 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1644043 ATCTCCGCAT
*
1644053 GGTTACATTCCTATCCCT-CAG
1 GGTTACATTCCTA-GCCTGCAG
* *
1644074 GGTTACATTCATAGCCCGCTA-
1 GGTTACATTCCTAGCCTGC-AG
*
1644095 GGTTACATGCCTAGCCTGCAG
1 GGTTACATTCCTAGCCTGCAG
1644116 GGTT
1 GGTT
1644120 TTATGACACC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.08
21 33 0.89
22 1 0.03
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.30
Consensus pattern (21 bp):
GGTTACATTCCTAGCCTGCAG
Found at i:1644671 original size:34 final size:34
Alignment explanation
Indices: 1644623--1644695 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
1644613 TTACATGTTT
*
1644623 TTAATATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* *
1644657 TTAAAATACAAATTATGGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1644691 TTAAA
1 TTAAA
1644696 TTCAACTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:1644822 original size:14 final size:14
Alignment explanation
Indices: 1644803--1644833 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1644793 TTTTATCCTT
1644803 AACATATACATTAA
1 AACATATACATTAA
1644817 AACATATACATTAA
1 AACATATACATTAA
1644831 AAC
1 AAC
1644834 CAACTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:1644947 original size:23 final size:22
Alignment explanation
Indices: 1644918--1645008 Score: 66
Period size: 23 Copynumber: 4.3 Consensus size: 22
1644908 TTATCACTTC
1644918 ACATTTATTCAATTTATCCATA
1 ACATTTATTCAATTTATCCATA
* * *
1644940 ACATTTTATCCAATATATTCA-A
1 ACA-TTTATTCAATTTATCCATA
* *
1644962 ACA---A-TCAATTGATCACTTA
1 ACATTTATTCAATTTATC-CATA
*
1644981 ACATTTATTCAATTTATTCATA
1 ACATTTATTCAATTTATCCATA
*
1645003 ATATTT
1 ACATTT
1645009 TATCTAATTT
Statistics
Matches: 50, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
17 6 0.12
18 2 0.04
19 4 0.08
22 16 0.32
23 22 0.44
ACGTcount: A:0.38, C:0.16, G:0.01, T:0.44
Consensus pattern (22 bp):
ACATTTATTCAATTTATCCATA
Found at i:1644978 original size:63 final size:63
Alignment explanation
Indices: 1644902--1645026 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 63
1644892 CAATGTCACG
*
1644902 ATCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAAACA
1 ATCAACTTATCACTTAACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAAACA
* * * *
1644965 ATCAA-TTGATCACTTAACATTTATTCAATTTATTCATAATATTTTATCTAATTTATTCAAAC
1 ATCAACTT-ATCACTTAACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAAAC
1645027 TTCACATAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 2 0.04
63 54 0.96
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.43
Consensus pattern (63 bp):
ATCAACTTATCACTTAACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAAACA
Found at i:1645918 original size:138 final size:138
Alignment explanation
Indices: 1645158--1646489 Score: 2123
Period size: 139 Copynumber: 9.6 Consensus size: 138
1645148 CCATCCATCT
* * *
1645158 ATAGTTCCCCGGGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTCTAACAAAATAAT
1 ATAGTGCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
1645223 TGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTTCCAAGTCCCCTCAGAAATAATAGGTAC
66 TGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
*
1645288 TGACATAA
131 TGACATGA
* *
1645296 ATAGTGCCCCGGGGGACATGAGTGACATAATAGGACAATTATAACATATTCTCTGACAAAATAAT
1 ATAGTGCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1645361 TGAA-G-GCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
66 TGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
1645424 TGACATGA
131 TGACATGA
* *
1645432 ATAGTGCCCCGGGGGATATGAGTGACATAATAGGGCAATTATAACATATTCTCTGACAAAATAAT
1 ATAGTGCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1645497 TGAA-G-GCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
66 TGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
*
1645560 TGATATGA
131 TGACATGA
*
1645568 ATAGTGCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTGCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* ** * *
1645633 TGAAGGCTCGCCCCCGGGAACATGCTTTCACCACTTTGCCAAGTCCTCTCAGAAATAATAGATAC
66 TGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
*
1645698 TGACATAA
131 TGACATGA
1645706 ATAGTGCCACCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAA
1 ATAGTGCC-CCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAA
* * * *
1645771 TTGAAGGCGCGCCCTCGGGAATGCGCTTTCACCACTTTGCCAAGTCCCCTAAGAAATAATATGTA
65 TTGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTA
1645836 CTGACATGA
130 CTGACATGA
*
1645845 ATAGTGCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTGCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
1645910 TGAAGGCGCGTCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTTAGAAATTATAGGTAC
66 TGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
*
1645975 TGACATAA
131 TGACATGA
*
1645983 ATAGTGCCCCGGAGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTGCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * * *
1646048 TGAAGGCGCTCCCCCCCCCGAGAACGCGCTTTCACCACTTTGCCAAGTCCTCTAAAAAATAATAG
66 TGAAGGCG----CGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAG
* *
1646113 GTATTGATATGA
127 GTACTGACATGA
* ** * *
1646125 ATAGTGCCCCCGAGGGACATGAGTGACATAATAGGATAATGATAATATATTCTCTGATAAAATAA
1 ATAGTG-CCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAA
* *
1646190 TTGAAGGCGCGCCCCCGGGAACGCGTTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGCA
65 TTGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTA
1646255 CTGACATGA
130 CTGACATGA
* * *
1646264 ATAGTGCCCCCGGGTGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGATAAAATAA
1 ATAGTG-CCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAA
* * *
1646329 TCGAAGGTGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCATAAATAATAGGTA
65 TTGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTA
1646394 CTGACATGA
130 CTGACATGA
* *
1646403 ATAGTACCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGACAAAATAA
1 ATAGT-GCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAA
1646468 TTGAAGGCGCGCCCCCGGGAAC
65 TTGAAGGCGCGCCCCCGGGAAC
1646490 ACGCCTTTAC
Statistics
Matches: 1102, Mismatches: 83, Indels: 17
0.92 0.07 0.01
Matches are distributed among these distances:
136 263 0.24
137 2 0.00
138 324 0.29
139 391 0.35
142 61 0.06
143 61 0.06
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (138 bp):
ATAGTGCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
TGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
TGACATGA
Found at i:1650419 original size:21 final size:20
Alignment explanation
Indices: 1650337--1650439 Score: 55
Period size: 21 Copynumber: 5.0 Consensus size: 20
1650327 CGCAAATCAG
1650337 TTTCCAAAATCGCAACGCGAT
1 TTTCC-AAATCGCAACGCGAT
* *
1650358 TCTT-GACAATCGCAATGCGAT
1 T-TTCCA-AATCGCAACGCGAT
** * **
1650379 AGTACAAATTCGCATTGCGAT
1 TTTCCAAA-TCGCAACGCGAT
*
1650400 TTTCCATAATCGCAACGCGAA
1 TTTCCA-AATCGCAACGCGAT
* **
1650421 TATGAAAATCGCAACGCGA
1 TTTCCAAATCGCAACGCGA
1650440 ACACATAAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 11
0.70 0.17 0.12
Matches are distributed among these distances:
20 17 0.27
21 41 0.66
22 4 0.06
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
TTTCCAAATCGCAACGCGAT
Found at i:1650432 original size:20 final size:20
Alignment explanation
Indices: 1650407--1650619 Score: 286
Period size: 20 Copynumber: 10.6 Consensus size: 20
1650397 GATTTTCCAT
* ** *
1650407 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1650427 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1650447 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1650467 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1650487 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1650507 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1650527 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1650547 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1650567 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
1650588 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1650608 AATCGCAACGCG
1 AATCGCAACGCG
1650620 ATTTTTAAAG
Statistics
Matches: 171, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 151 0.88
21 19 0.11
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1651038 original size:33 final size:33
Alignment explanation
Indices: 1650999--1651069 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1650989 TTCACTTAGA
1650999 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1651032 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1651065 TTTCA
1 TTTCA
1651070 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1651216 original size:21 final size:20
Alignment explanation
Indices: 1651149--1651254 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
1651139 TGCAGAAGAG
*
1651149 TCGCAACGAGATAATGAAAA
1 TCGCAACGAGAAAATGAAAA
* **
1651169 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
1651189 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
1651211 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
1651225 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
1651244 TCGCAACGAGA
1 TCGCAACGAGA
1651255 GAATCGCAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 18 0.26
21 15 0.22
22 10 0.14
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1651228 original size:14 final size:14
Alignment explanation
Indices: 1651209--1651265 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1651199 GAAAAATGAA
1651209 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1651223 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1651242 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1651256 AATCGCAACG
1 AATCGCAACG
1651266 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1651240 original size:33 final size:33
Alignment explanation
Indices: 1651202--1651281 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1651192 GCAACGAGAA
1651202 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1651235 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
1651268 AAACCAAAATCGCA
1 AAATGAAAATCGCA
1651282 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1651318 original size:14 final size:14
Alignment explanation
Indices: 1651299--1651355 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1651289 TTTCATTTCG
1651299 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1651313 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
1651332 CGTTGCGTTTCTCT
1 CGTTGCGATTCTCT
1651346 CGTTGCGATT
1 CGTTGCGATT
1651356 TTCATTTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1651324 original size:33 final size:33
Alignment explanation
Indices: 1651282--1651362 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
1651272 CAAAATCGCA
1651282 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1651315 TTGCGATTTTCATTTCGCGTTGCGTTTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1651348 TTGCGATTTTCATTT
1 TTGCGATTTTCATTT
1651363 ATCTCGTTGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.09, C:0.22, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1651369 original size:21 final size:21
Alignment explanation
Indices: 1651343--1651403 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1651333 GTTGCGTTTC
1651343 TCTCGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTA
*** *
1651364 TCTCGTTGCGACAGTCA-TTC
1 TCTCGTTGCGATTTTCATTTA
*
1651384 TCTCATTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
1651404 CAACCAAAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.48
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTA
Found at i:1651401 original size:20 final size:20
Alignment explanation
Indices: 1651306--1651402 Score: 82
Period size: 20 Copynumber: 5.2 Consensus size: 20
1651296 TCGCGTTGCG
1651306 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1651326 ATT-TCGCGTTGCG----T-
1 ATTCTCTCGTTGCGATTTTC
1651340 -TTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* ***
1651359 ATTTATCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
*
1651380 ATTCTCTCATTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1651400 ATT
1 ATT
1651403 TCAACCAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
13 2 0.03
14 9 0.16
15 1 0.02
18 1 0.02
19 9 0.16
20 20 0.34
21 16 0.28
ACGTcount: A:0.12, C:0.24, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1653346 original size:92 final size:93
Alignment explanation
Indices: 1653089--1653403 Score: 605
Period size: 93 Copynumber: 3.4 Consensus size: 93
1653079 TAGATTGCTT
*
1653089 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1653154 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1653182 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1653247 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1653275 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1653339 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1653367 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1653404 AATACCCTGA
Statistics
Matches: 218, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 91 0.42
93 127 0.58
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1653538 original size:14 final size:14
Alignment explanation
Indices: 1653519--1653575 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1653509 CGAAACTTAA
1653519 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1653533 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1653552 AATCGCAACGACAG
1 AATCGCAACGAGAG
1653566 AATCGCAACG
1 AATCGCAACG
1653576 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1653617 original size:38 final size:33
Alignment explanation
Indices: 1653501--1653629 Score: 141
Period size: 33 Copynumber: 3.7 Consensus size: 33
1653491 TAGTTTACTT
* * * *
1653501 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAAAA
** *
1653535 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1653568 TCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAATCGCAA--CG--A-CAAAA
1653606 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
1653630 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
33 40 0.48
34 12 0.14
35 2 0.02
37 1 0.01
38 28 0.34
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAAAA
Found at i:1653635 original size:19 final size:19
Alignment explanation
Indices: 1653533--1653629 Score: 132
Period size: 19 Copynumber: 5.4 Consensus size: 19
1653523 GCAACGAGAG
**
1653533 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
*
1653552 AATCGCAA--CG--A-CAG
1 AATCGCAACGCGAAACCAA
1653566 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1653585 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1653604 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1653623 AATCGCA
1 AATCGCA
1653630 TTGCGATTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 55 0.79
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1653647 original size:19 final size:19
Alignment explanation
Indices: 1653625--1653797 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
1653615 GAAACCAAAA
*
1653625 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1653644 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1653658 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1653677 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
1653693 T--CGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1653710 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1653729 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1653748 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1653767 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1653787 TCGTGTTGCGA
1 TCGCGTTGCGA
1653798 AAGTAAACTA
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
14 16 0.13
16 8 0.06
17 8 0.06
19 80 0.65
20 12 0.10
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1653755 original size:38 final size:38
Alignment explanation
Indices: 1653625--1653797 Score: 159
Period size: 33 Copynumber: 4.8 Consensus size: 38
1653615 GAAACCAAAA
*
1653625 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
1653660 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* * **
1653693 T--CGTTGCAATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
1653729 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
1653767 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
1653798 AAGTAAACTA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 51 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 43 0.38
39 11 0.10
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:1655738 original size:14 final size:14
Alignment explanation
Indices: 1655719--1655754 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1655709 ATTGTTTAAT
1655719 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1655733 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1655747 TGATTTGT
1 TGATTTGT
1655755 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1655877 original size:19 final size:19
Alignment explanation
Indices: 1655861--1655958 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1655851 AAAAATGACT
1655861 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1655880 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1655899 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1655918 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1655932 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1655952 ATCGCAA
1 ATCGCAA
1655959 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 3 0.04
19 46 0.65
20 10 0.14
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1655952 original size:34 final size:33
Alignment explanation
Indices: 1655861--1655977 Score: 171
Period size: 34 Copynumber: 3.4 Consensus size: 33
1655851 AAAAATGACT
*
1655861 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGA
1655899 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1655932 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1655966 ATCGCAATGCGA
1 ATCGCAATGCGA
1655978 TTTTCATTTC
Statistics
Matches: 77, Mismatches: 1, Indels: 7
0.91 0.01 0.08
Matches are distributed among these distances:
33 15 0.19
34 34 0.44
36 2 0.03
38 26 0.34
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1656036 original size:53 final size:53
Alignment explanation
Indices: 1655973--1656162 Score: 264
Period size: 53 Copynumber: 3.6 Consensus size: 53
1655963 AGAATCGCAA
1655973 TGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1656026 TGCGATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* * * * *
1656078 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATTTTCATTTCCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
1656131 TGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TGCGATTTTCATTTCCGCATTGCGATTTTCAT
1656163 GTTGGGATTT
Statistics
Matches: 127, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
51 3 0.02
52 34 0.27
53 76 0.60
54 5 0.04
55 9 0.07
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1656212 original size:33 final size:33
Alignment explanation
Indices: 1655991--1656204 Score: 136
Period size: 34 Copynumber: 6.2 Consensus size: 33
1655981 TCATTTCGCA
1655991 TTGCGATTTTCATTTCCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCAT-G
*
1656025 TTGCGATTTTCATTTCGCATTGCGATTTTCAT-
1 TTGCGATTTTCATTTCGCATTGCGATTCTCATG
* * * *
1656057 TT-CGCA-TTGCGATTCTCTCGTTGCGATTTTCAT-
1 TTGCG-ATTTTC-ATT-TCGCATTGCGATTCTCATG
* * * * *
1656090 TTCCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 TTGCG-ATTTTC-ATT-TCGCATTGCGATTCTCA--T-G
*
1656128 CATTGCGATTTTCATTTCCGCATTGCGATTTTCATG
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTCATG
*
1656164 TTGGGATTTTCATTTCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCAT-G
1656197 TTGCGATT
1 TTGCGATT
1656205 GTAATTTCCG
Statistics
Matches: 155, Mismatches: 11, Indels: 29
0.79 0.06 0.15
Matches are distributed among these distances:
31 5 0.03
32 7 0.05
33 54 0.35
34 60 0.39
36 2 0.01
37 1 0.01
38 1 0.01
39 18 0.12
40 7 0.05
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCATG
Found at i:1656212 original size:86 final size:86
Alignment explanation
Indices: 1655991--1656204 Score: 378
Period size: 86 Copynumber: 2.5 Consensus size: 86
1655981 TCATTTCGCA
1655991 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1656056 TTTCGCATTGCGATTCTCTCG
66 TTTCGCATTGCGATTCTCTCG
1656077 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
*
1656142 TTTCCGCATTGCGATTTTCAT-G
66 TTT-CGCATTGCGATTCTC-TCG
*
1656164 TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1656205 GTAATTTCCG
Statistics
Matches: 124, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
86 94 0.76
87 29 0.23
88 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (86 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
TTTCGCATTGCGATTCTCTCG
Found at i:1656219 original size:53 final size:53
Alignment explanation
Indices: 1656077--1656223 Score: 149
Period size: 53 Copynumber: 2.8 Consensus size: 53
1656067 GATTCTCTCG
* *
1656077 TTGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT-GTTGCGATTTTCATTTCGCA
* * * *
1656130 TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTCCATGTTGCGATTTTCATTTCGCA
* * *
1656183 TTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGTGTTGCGAT
1 TTGCGATT-T-TCAGTTCCGCATTGCAATTTCCATGTTGCGAT
1656224 AGTCAAATGC
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
53 71 0.88
54 8 0.10
55 2 0.02
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCAGTTCCGCATTGCAATTTCCATGTTGCGATTTTCATTTCGCA
Found at i:1658491 original size:12 final size:12
Alignment explanation
Indices: 1658474--1658498 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1658464 TTCTTCGGGA
1658474 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1658486 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1658498 C
1 C
1658499 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1658707 original size:24 final size:24
Alignment explanation
Indices: 1658673--1658719 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1658663 CTGAAACATC
1658673 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1658697 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1658720 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1659440 original size:20 final size:20
Alignment explanation
Indices: 1659412--1659617 Score: 199
Period size: 20 Copynumber: 10.4 Consensus size: 20
1659402 AAATTTCAGT
* * * *
1659412 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1659432 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1659452 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1659472 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1659492 GTTGCGA-TT--GGATACGC
1 GTTGCGATTTACGGATACGC
*
1659509 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1659529 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1659549 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1659569 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1659589 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
1659609 GTTGCGATT
1 GTTGCGATT
1659618 CTTGAAAATC
Statistics
Matches: 158, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
16 2 0.01
17 11 0.07
18 1 0.01
19 3 0.02
20 138 0.87
21 3 0.02
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1660560 original size:22 final size:22
Alignment explanation
Indices: 1660530--1660581 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1660520 CGGAACTTAT
*
1660530 ATTAGAAATTTAAAAGTAT-GAA
1 ATTATAAATTT-AAAGTATGGAA
*
1660552 ATTATAAATTTAAAGTTTGGAA
1 ATTATAAATTTAAAGTATGGAA
1660574 ATTATAAA
1 ATTATAAA
1660582 ATTTTAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.37
Consensus pattern (22 bp):
ATTATAAATTTAAAGTATGGAA
Found at i:1662724 original size:70 final size:71
Alignment explanation
Indices: 1662601--1662735 Score: 191
Period size: 70 Copynumber: 1.9 Consensus size: 71
1662591 ATAGTACTCG
* * * **
1662601 ACTTGTGCTCGTTAAAATTTTTTTATGTTCGACTCGACTCATTGCTCGTTAAGCTCGTTAAAATT
1 ACTTGTGCTCGTTAAAA-TTTTTGATGTTCAACTCGACTAATTGCTCGTTAAGCTCACTAAAATT
1662666 GTGTTCA
65 GTGTTCA
* *
1662673 ACTTGTGCTCGTTAAAA-TTTTGATGTTCAATTCGACTAATTGTTCGTTAAGCTCACTAAAATT
1 ACTTGTGCTCGTTAAAATTTTTGATGTTCAACTCGACTAATTGCTCGTTAAGCTCACTAAAATT
1662736 TTTTATCTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 39 0.70
72 17 0.30
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (71 bp):
ACTTGTGCTCGTTAAAATTTTTGATGTTCAACTCGACTAATTGCTCGTTAAGCTCACTAAAATTG
TGTTCA
Found at i:1662825 original size:18 final size:18
Alignment explanation
Indices: 1662804--1662898 Score: 50
Period size: 18 Copynumber: 5.0 Consensus size: 18
1662794 TGGGGTTTTT
1662804 ATTAAAATAATATTATTA
1 ATTAAAATAATATTATTA
* *
1662822 ATTAATAATATTTTATTATTT
1 ATTAA-AATA--ATATTATTA
1662843 ATTAAAA-AATAATATATTA
1 ATTAAAATAAT-AT-TATTA
* ** *
1662862 GTTAACTTATTATTTATTA
1 ATTAAAATAATA-TTATTA
*
1662881 A-TAAATTAATAATTATTA
1 ATTAAAATAAT-ATTATTA
1662899 TTTAGATTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
17 1 0.02
18 20 0.34
19 20 0.34
20 5 0.09
21 12 0.21
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
ATTAAAATAATATTATTA
Found at i:1663568 original size:31 final size:31
Alignment explanation
Indices: 1663530--1663628 Score: 114
Period size: 31 Copynumber: 3.2 Consensus size: 31
1663520 CGATAAGAAT
*
1663530 AAATTTAAGTGTTAGATTAATATTTTATTTA
1 AAATTTAAGTGTTAAATTAATATTTTATTTA
* *
1663561 AAATTTAAAG-ATTAAATTAATATTTTATATA
1 AAATTT-AAGTGTTAAATTAATATTTTATTTA
* *
1663592 AAA-TTCA-TGATCAAATTAATATTTTATTTA
1 AAATTTAAGTG-TTAAATTAATATTTTATTTA
1663622 AAATTTA
1 AAATTTA
1663629 GTAATCGAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 1 0.02
30 23 0.41
31 29 0.52
32 3 0.05
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (31 bp):
AAATTTAAGTGTTAAATTAATATTTTATTTA
Found at i:1663610 original size:30 final size:30
Alignment explanation
Indices: 1663545--1663626 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
1663535 TAAGTGTTAG
*
1663545 ATTAATATTTTATTTAAAATTTAAAGATTAA
1 ATTAATATTTTATTTAAAA-TTAAAGATCAA
* * *
1663576 ATTAATATTTTATATAAAATTCATGATCAA
1 ATTAATATTTTATTTAAAATTAAAGATCAA
1663606 ATTAATATTTTATTTAAAATT
1 ATTAATATTTTATTTAAAATT
1663627 TAGTAATCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 28 0.61
31 18 0.39
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
ATTAATATTTTATTTAAAATTAAAGATCAA
Found at i:1664743 original size:90 final size:90
Alignment explanation
Indices: 1664583--1664763 Score: 335
Period size: 90 Copynumber: 2.0 Consensus size: 90
1664573 GTTCCAGTTT
1664583 AGTGCCTAATATTTCATTCCGTTACTTAAAATGAGTCCAACCGTAACGAACGGTTAAATTTAATC
1 AGTGCCTAATATTTCATTCCGTTACTTAAAATGAGTCCAACCGTAACGAACGGTTAAATTTAATC
*
1664648 TTTAACCCATTAAAAATACCACATG
66 GTTAACCCATTAAAAATACCACATG
* *
1664673 AGTGTCTAATGTTTCATTCCGTTACTTAAAATGAGTCCAACCGTAACGAACGGTTAAATTTAATC
1 AGTGCCTAATATTTCATTCCGTTACTTAAAATGAGTCCAACCGTAACGAACGGTTAAATTTAATC
1664738 GTTAACCCATTAAAAATACCACATG
66 GTTAACCCATTAAAAATACCACATG
1664763 A
1 A
1664764 CATATTTTTT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (90 bp):
AGTGCCTAATATTTCATTCCGTTACTTAAAATGAGTCCAACCGTAACGAACGGTTAAATTTAATC
GTTAACCCATTAAAAATACCACATG
Found at i:1665853 original size:18 final size:19
Alignment explanation
Indices: 1665818--1665854 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1665808 CACGGAATGT
1665818 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
1665838 AAGATTACCA-GAGAATA
1 AAGATTACCAGGAGAATA
1665855 GAATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:1681258 original size:22 final size:21
Alignment explanation
Indices: 1681223--1681264 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1681213 TATCTTCGTG
1681223 TATATATTTAAAAATAATATTA
1 TATATATTTAAAAAT-ATATTA
* *
1681245 TATATCTTTCAAAATATATT
1 TATATATTTAAAAATATATT
1681265 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATATTTAAAAATATATTA
Found at i:1681314 original size:27 final size:27
Alignment explanation
Indices: 1681256--1681357 Score: 89
Period size: 27 Copynumber: 3.6 Consensus size: 27
1681246 ATATCTTTCA
*
1681256 AAATATATTTTATTTTTATTTTAAATTATT
1 AAATATATTTTATTATTATTTT-AA-T-TT
**
1681286 AAATATATTTTATTATTAACTTAATTT
1 AAATATATTTTATTATTATTTTAATTT
* *
1681313 AAA-AGTGTTTTATTATTTTTTTAATTT
1 AAATA-TATTTTATTATTATTTTAATTT
* *
1681340 AAAAATATATATATTATT
1 AAATATAT-TTTATTATT
1681358 CTTATCTTAG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
26 1 0.02
27 28 0.47
28 10 0.17
29 2 0.03
30 19 0.32
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (27 bp):
AAATATATTTTATTATTATTTTAATTT
Found at i:1687809 original size:16 final size:17
Alignment explanation
Indices: 1687769--1687812 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1687759 GATGATTAGA
1687769 TAAATAAAATAATATAT
1 TAAATAAAATAATATAT
**
1687786 TTTA-AAAATAATA-AT
1 TAAATAAAATAATATAT
1687801 TAAATAAAATAA
1 TAAATAAAATAA
1687813 AATAAGTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 4 0.18
16 16 0.73
17 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAATAAAATAATATAT
Found at i:1691908 original size:37 final size:37
Alignment explanation
Indices: 1691855--1691943 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
1691845 TTTTGTTCGG
* * * *
1691855 GTCGGGTAGGGATTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCAGATCGA
*
1691892 GTCGGGTCGGGTTTTTTAAGTGTGATATTCAGATCGG
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCAGATCGA
1691929 GTCGGGTTCGGGTTT
1 GTCGGG-TCGGGTTT
1691944 AGGTGAAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 38 0.83
38 8 0.17
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.37
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTAAGTGTGATATTCAGATCGA
Found at i:1692520 original size:17 final size:18
Alignment explanation
Indices: 1692498--1692542 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1692488 AATTGGATTG
1692498 GATTCCAATTTC-TGACA
1 GATTCCAATTTCATGACA
*
1692515 GATTCCAA-TTCATTTACA
1 GATTCCAATTTCA-TGACA
1692533 GATTCCAATT
1 GATTCCAATT
1692543 CCCTCAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 12 0.50
19 1 0.04
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (18 bp):
GATTCCAATTTCATGACA
Found at i:1693629 original size:11 final size:12
Alignment explanation
Indices: 1693600--1693627 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1693590 GCTCTCAGCC
1693600 AAAAATATTAAT
1 AAAAATATTAAT
1693612 AAAAATATTAAT
1 AAAAATATTAAT
1693624 AAAA
1 AAAA
1693628 TAAATCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATATTAAT
Found at i:1693684 original size:21 final size:24
Alignment explanation
Indices: 1693653--1693697 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
1693643 TAAAATGAAT
1693653 AATTAGAAAATTATA-TT-AATTA
1 AATTAGAAAATTATACTTCAATTA
1693675 AATTA-AAAATTATACTTCAATTA
1 AATTAGAAAATTATACTTCAATTA
1693698 TTAAAGGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 7 0.33
23 5 0.24
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTAGAAAATTATACTTCAATTA
Found at i:1693700 original size:21 final size:20
Alignment explanation
Indices: 1693652--1693702 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 20
1693642 TTAAAATGAA
1693652 TAATTAGAAAATTATATTAAT
1 TAATTA-AAAATTATATTAAT
1693673 TAAATTAAAAATTATACTTCAAT
1 T-AATTAAAAATTATA-TT-AAT
1693696 T-ATTAAA
1 TAATTAAA
1693703 GGGTCAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 16 0.59
22 7 0.26
23 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (20 bp):
TAATTAAAAATTATATTAAT
Found at i:1695674 original size:20 final size:20
Alignment explanation
Indices: 1695649--1695777 Score: 100
Period size: 20 Copynumber: 6.3 Consensus size: 20
1695639 TTTTCCCAAT
*
1695649 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
1695669 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAG-AAAA
*
1695690 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
1695710 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
* **
1695731 TCGCAATGCG-ATACTGACTA
1 TCGCAATGCGAATA-AGAAAA
1695751 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCG--AATAAGAAAA
1695772 TCGCAA
1 TCGCAA
1695778 CGAGATACTT
Statistics
Matches: 83, Mismatches: 20, Indels: 11
0.73 0.18 0.10
Matches are distributed among these distances:
19 1 0.01
20 41 0.49
21 38 0.46
23 3 0.04
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1695692 original size:21 final size:20
Alignment explanation
Indices: 1695666--1695741 Score: 89
Period size: 21 Copynumber: 3.7 Consensus size: 20
1695656 GCGAATAAGT
1695666 AAATCGCAACGCGAATTGGAA
1 AAATCGCAACGCGAATTGG-A
* ** *
1695687 AAATCGCAATGCGAATAAGT
1 AAATCGCAACGCGAATTGGA
1695707 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATT-GGA
*
1695728 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1695742 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (20 bp):
AAATCGCAACGCGAATTGGA
Found at i:1695694 original size:41 final size:41
Alignment explanation
Indices: 1695649--1695741 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1695639 TTTTCCCAAT
1695649 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
*
1695690 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
1695731 TCGCAATGCGA
1 TCGCAATGCGA
1695742 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
Found at i:1695754 original size:41 final size:41
Alignment explanation
Indices: 1695668--1695801 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
1695658 GAATAAGTAA
* *
1695668 ATCGCAACGCGAATTGGAAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGAAAAATCGCAATGCG-ATACTG-ACT
*
1695709 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTGACT
* * * * * *
1695750 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGAAAAATCGCAATGCGATACTGACT
1695791 -TCGCAACGCGA
1 ATCGCAACGCGA
1695802 TACTGACTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
40 14 0.18
41 63 0.80
42 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTGACT
Found at i:1695796 original size:19 final size:20
Alignment explanation
Indices: 1695772--1695823 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1695762 TAATAAAAAA
* *
1695772 TCGCAACGAGATACTTAC-T
1 TCGCAACGCGATACTGACTT
1695791 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
1695811 TCGCAACGCGATA
1 TCGCAACGCGATA
1695824 ATACATAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:1695815 original size:20 final size:20
Alignment explanation
Indices: 1695730--1695823 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1695720 AATTGGGAAA
*
1695730 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1695750 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1695771 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
1695791 -TCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1695810 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1695824 ATACATAATC
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
19 17 0.28
20 29 0.48
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1696039 original size:22 final size:22
Alignment explanation
Indices: 1696011--1696054 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1696001 CACTCTCTCA
1696011 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1696033 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1696055 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1696327 original size:20 final size:20
Alignment explanation
Indices: 1696298--1696341 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1696288 GCGATTTTAG
1696298 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
1696318 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
1696338 TTTC
1 TTTC
1696342 AGAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:1697682 original size:18 final size:18
Alignment explanation
Indices: 1697661--1697705 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1697651 TCCACTTCGG
*
1697661 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1697679 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1697697 GAGCCATCA
1 GAGCCATCA
1697706 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Done.