Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008558.1 Hibiscus syriacus cultivar Beakdansim tig00111463_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: 2950132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:2213407 original size:2 final size:2
Alignment explanation
Indices: 2213400--2213424 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2213390 AAAACTAAAG
2213400 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
2213425 TTTTATAAGC
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:2214990 original size:123 final size:123
Alignment explanation
Indices: 2214845--2215158 Score: 503
Period size: 123 Copynumber: 2.6 Consensus size: 123
2214835 TTTCCTCTGT
* *
2214845 GATA-AGTCGAGAAAAAGATTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCTTTTCAGATG
1 GATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCTTTTCAGATG
* *
2214909 AGTTCTTCTTATTACGAACTCCTTCTGGAAATATTGATGCTGCTTTATCTTCTTCCGC
66 AGTTCTTCTTATTACGAACTCCATCTGGAAATATTGATGCTGCTTTATCTCCTTCCGC
*
2214967 GATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCTTTTTCAGATG
1 GATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCTTTTCAGATG
* *
2215032 AGTTCTTTTTATTACGAACTCCATCTGGAAATATTGATGCTGCTTTATCTCCTTCTGC
66 AGTTCTTCTTATTACGAACTCCATCTGGAAATATTGATGCTGCTTTATCTCCTTCCGC
* *
2215090 TATAGAGTCGAGCAAAAGGTTGAAT-AGTTCTTCAGATTATGAACTTCTTC-T-CTCTTT-AGAT
1 GATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCT-TTTCAGAT
2215151 GAGTTCTT
65 GAGTTCTT
2215159 AGATTATGAA
Statistics
Matches: 180, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
120 13 0.07
121 4 0.02
122 28 0.16
123 135 0.75
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (123 bp):
GATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCTTTTCAGATG
AGTTCTTCTTATTACGAACTCCATCTGGAAATATTGATGCTGCTTTATCTCCTTCCGC
Found at i:2215303 original size:39 final size:39
Alignment explanation
Indices: 2215115--2215295 Score: 234
Period size: 39 Copynumber: 4.8 Consensus size: 39
2215105 AAGGTTGAAT
* *
2215115 AGTTCTTCAGATTATGAACTTCTTC-T-CTCTTTAGATG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
2215152 AGTTCTT-AGATTATGAA--CCTTCTTCCTCTTC--AT-
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* * * *
2215185 AGTTCTTCAGACTATGAACTTCTTCTTCCTTTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
*
2215224 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
*
2215263 AGTTCTTAAGATTATGAACTCCTTCTTCCTCTT
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTT
2215296 AATATGAGAT
Statistics
Matches: 125, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
33 7 0.06
34 15 0.12
35 1 0.01
36 27 0.22
37 7 0.06
38 1 0.01
39 67 0.54
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (39 bp):
AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
Found at i:2215448 original size:73 final size:73
Alignment explanation
Indices: 2215327--2215616 Score: 481
Period size: 73 Copynumber: 4.0 Consensus size: 73
2215317 TATCTAGAGA
** * * *
2215327 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAACTTTATCCAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCTAGCGAG
2215392 AAACAATT
66 AAACAATT
*
2215400 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTATTATTTCAAGTGAAACTTTCTCTAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCTAGCGAG
2215465 AAACAATT
66 AAACAATT
* * *
2215473 TTTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTTAAGTGAAACTTTCTTTAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCTAGCGAG
2215538 AAACAATT
66 AAACAATT
* *
2215546 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACATTCTCTAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCTAGCGAG
2215611 AAACAA
66 AAACAA
2215617 AAACAATCTC
Statistics
Matches: 204, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 204 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCTAGCGAG
AAACAATT
Found at i:2215593 original size:146 final size:140
Alignment explanation
Indices: 2215329--2215785 Score: 644
Period size: 146 Copynumber: 3.3 Consensus size: 140
2215319 TCTAGAGATG
** * *
2215329 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAACTTTATCCAGCGAGAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGAAACTTTCTCTAGCGAGAA
**
2215394 ACAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTATTATTTCAAGTGAAACTTTCTCT
66 ACAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCT
2215459 AGCGAGAAAC
131 AGCGAGAAAC
** *
2215469 AATTTTTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTTAAGTGAAACTTTCTTTAG
1 ------TTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGAAACTTTCTCTAG
*
2215534 CGAGAAACAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACA
60 CGAGAAACAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACT
2215599 TTCTCTAGCGAGAAAC
125 TTCTCTAGCGAGAAAC
*
2215615 -------AAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGGAACTTTCTCTAGCGAGAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGAAACTTTCTCTAGCGAGAA
*
2215673 ACAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCT
66 ACAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCT
***
2215738 AGC-A-AGTG
131 AGCGAGAAAC
* *
2215746 TTTTAAGAAAAACAATCTCAAGTGATATAAATTGCTATTT
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTT
2215786 GAAAACATCT
Statistics
Matches: 283, Mismatches: 21, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
131 1 0.00
132 1 0.00
133 120 0.42
138 31 0.11
146 130 0.46
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (140 bp):
TTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGAAACTTTCTCTAGCGAGAA
ACAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCT
AGCGAGAAAC
Found at i:2215626 original size:60 final size:60
Alignment explanation
Indices: 2215555--2215676 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 60
2215545 TTGTTTTAAG
*
2215555 AAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACATTCTCTAGCGAGAAAC
1 AAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACATTCTCTAGCGAGAAAC
* * *
2215615 AAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGGAACTTTCTCTAGCGAGAAAC
1 AAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACATTCTCTAGCGAGAAAC
2215675 AA
1 AA
2215677 TTTGTTTTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (60 bp):
AAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACATTCTCTAGCGAGAAAC
Found at i:2215635 original size:133 final size:135
Alignment explanation
Indices: 2215482--2215785 Score: 468
Period size: 133 Copynumber: 2.2 Consensus size: 135
2215472 TTTTTTTAAG
* *
2215482 AAAAACAATCTCAAGTGAGATAAATTACTATTTTAAGTGAAACTTTCTTTAGCGAGAAACAATTT
1 AAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCTAGCGAGAAACAATTT
2215547 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACATTCTCTAGC-GAG
66 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACATTCTCTAGCAGAG
2215611 -AAAC
131 TAAAC
* *
2215615 AAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGGAACTTTCTCTAGCGAGAAACAATTT
1 AAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCTAGCGAGAAACAATTT
* * *
2215680 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCTAGCAAGT
66 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACATTCTCTAGC-AGA
* *
2215745 GTTTTAAG
130 G--TAAAC
* *
2215753 AAAAACAATCTCAAGTGATATAAATTGCTATTT
1 AAAAACAATCTCAAGTGAGATAAATTACTATTT
2215786 GAAAACATCT
Statistics
Matches: 155, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
133 120 0.77
135 2 0.01
138 33 0.21
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (135 bp):
AAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCTAGCGAGAAACAATTT
GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACATTCTCTAGCAGAG
TAAAC
Found at i:2216942 original size:53 final size:53
Alignment explanation
Indices: 2216854--2216958 Score: 149
Period size: 53 Copynumber: 2.0 Consensus size: 53
2216844 TAACTGGTTG
* * *
2216854 TAAAACAATTGATAACACAATCATCATTTCTTGTGGTTT-TGCACAGATGTTCA
1 TAAAACAATTGACAACACAATCATCACTTCCTGTGGTTTCTG-ACAGATGTTCA
* *
2216907 TAAAACATTTGACAACACATTCATCACTTCCTGTGGTTTCTGACAGATGTTC
1 TAAAACAATTGACAACACAATCATCACTTCCTGTGGTTTCTGACAGATGTTC
2216959 TCAATAATTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 44 0.96
54 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (53 bp):
TAAAACAATTGACAACACAATCATCACTTCCTGTGGTTTCTGACAGATGTTCA
Found at i:2217431 original size:77 final size:74
Alignment explanation
Indices: 2217334--2217496 Score: 195
Period size: 77 Copynumber: 2.2 Consensus size: 74
2217324 CATGTGAGCT
** * **
2217334 TTCAAAATG-CCCAATTTTTCATACTGATGTGAGCTTTCAAAATGCCCCACATGAATCATTTCT-
1 TTCAAAATGCCCCAAACTTTCATACTAATGTGAGCTTTCAAAACACCCCACAT--ATCATTTCTA
2217397 GTTGAAATAGGC
64 GTTGAAAT-GGC
* *
2217409 GTTCAAAATGCCCCAAACTTTCATACTAATGTGATCTTTCAAAACACCTCACATATCATTTCTAG
1 -TTCAAAATGCCCCAAACTTTCATACTAATGTGAGCTTTCAAAACACCCCACATATCATTTCTAG
2217474 TTGAAATGGC
65 TTGAAATGGC
* *
2217484 TTTAGAATGCCCC
1 TTCAAAATGCCCC
2217497 TTTAGAACAA
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
74 11 0.14
75 12 0.16
76 17 0.22
77 36 0.47
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (74 bp):
TTCAAAATGCCCCAAACTTTCATACTAATGTGAGCTTTCAAAACACCCCACATATCATTTCTAGT
TGAAATGGC
Found at i:2218611 original size:23 final size:23
Alignment explanation
Indices: 2218583--2218636 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
2218573 TGATTCAATT
*
2218583 TCTTTTTT-GTTCTTTCATTTTC
1 TCTTTTTTCATTCTTTCATTTTC
* *
2218605 TCTTTTTTCATTTTTTCATTTTT
1 TCTTTTTTCATTCTTTCATTTTC
2218628 TCTTTTTTC
1 TCTTTTTTC
2218637 TTTTTTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.76
Consensus pattern (23 bp):
TCTTTTTTCATTCTTTCATTTTC
Found at i:2218613 original size:15 final size:14
Alignment explanation
Indices: 2218581--2218684 Score: 109
Period size: 15 Copynumber: 7.1 Consensus size: 14
2218571 CTTGATTCAA
* *
2218581 TTTCTTTTTTGTTC
1 TTTCTTTTTTCTTT
*
2218595 TTTCATTTTCTCTTT
1 TTTC-TTTTTTCTTT
2218610 TTTCATTTTTTCATTT
1 TTTC-TTTTTTC-TTT
2218626 TTTCTTTTTTCTTT
1 TTTCTTTTTTCTTT
*
2218640 TTTCTTTTTTTTTCT
1 TTTCTTTTTTCTT-T
*
2218655 TTTTTTTTTTCTTT
1 TTTCTTTTTTCTTT
*
2218669 TTTTTTTTTTCCTTT
1 TTTCTTTTTT-CTTT
2218684 T
1 T
2218685 CTGATGAATG
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
14 30 0.38
15 42 0.53
16 7 0.09
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (14 bp):
TTTCTTTTTTCTTT
Found at i:2218627 original size:1 final size:1
Alignment explanation
Indices: 2218623--2218678 Score: 67
Period size: 1 Copynumber: 56.0 Consensus size: 1
2218613 CATTTTTTCA
* * * * *
2218623 TTTTTTCTTTTTTCTTTTTTCTTTTTTTTTCTTTTTTTTTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2218679 CCTTTTCTGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:2218641 original size:23 final size:21
Alignment explanation
Indices: 2218581--2218684 Score: 109
Period size: 22 Copynumber: 4.8 Consensus size: 21
2218571 CTTGATTCAA
* *
2218581 TTTCTTTTTTGTTCTTTCATTT
1 TTTCTTTTTTCTTTTTTC-TTT
*
2218603 TCTCTTTTTTCATTTTTTCATTT
1 TTTCTTTTTTC-TTTTTTC-TTT
2218626 TTTCTTTTTTCTTTTTTCTTT
1 TTTCTTTTTTCTTTTTTCTTT
* *
2218647 TTTTTTCTTTTTTTTTTTCTTT
1 TTTCTT-TTTTCTTTTTTCTTT
* *
2218669 TTTTTTTTTTCCTTTT
1 TTTCTTTTTTCTTTTT
2218685 CTGATGAATG
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
21 16 0.22
22 36 0.50
23 20 0.28
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (21 bp):
TTTCTTTTTTCTTTTTTCTTT
Found at i:2218649 original size:7 final size:7
Alignment explanation
Indices: 2218581--2218684 Score: 109
Period size: 7 Copynumber: 14.1 Consensus size: 7
2218571 CTTGATTCAA
2218581 TTTCTTT
1 TTTCTTT
* *
2218588 TTTGTTC
1 TTTCTTT
2218595 TTTCATTT
1 TTTC-TTT
*
2218603 TCTCTTT
1 TTTCTTT
2218610 TTTCATTT
1 TTTC-TTT
2218618 TTTCATTT
1 TTTC-TTT
2218626 TTTCTTT
1 TTTCTTT
2218633 TTTCTTT
1 TTTCTTT
2218640 TTTCTTT
1 TTTCTTT
*
2218647 TTTTTTCT
1 TTTCTT-T
*
2218655 TTTTTTT
1 TTTCTTT
2218662 TTTCTTT
1 TTTCTTT
*
2218669 TTTTTTT
1 TTTCTTT
2218676 TTTCCTTT
1 TTT-CTTT
2218684 T
1 T
2218685 CTGATGAATG
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
7 52 0.63
8 31 0.37
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (7 bp):
TTTCTTT
Found at i:2218684 original size:10 final size:9
Alignment explanation
Indices: 2218581--2218684 Score: 78
Period size: 9 Copynumber: 12.0 Consensus size: 9
2218571 CTTGATTCAA
2218581 TTTCTTTTT
1 TTTCTTTTT
*
2218590 TGTTCTTTCAT
1 T-TTCTTT-TT
*
2218601 TTTCTCTTT
1 TTTCTTTTT
*
2218610 TTTC-ATTT
1 TTTCTTTTT
*
2218618 TTTC-ATTT
1 TTTCTTTTT
2218626 TTTC--TTT
1 TTTCTTTTT
2218633 TTTCTTTTT
1 TTTCTTTTT
*
2218642 TCT-TTTTT
1 TTTCTTTTT
2218650 TTTCTTTTT
1 TTTCTTTTT
2218659 TTT-TTTCTT
1 TTTCTTT-TT
2218668 TTT-TTTTT
1 TTTCTTTTT
*
2218676 TTTCCTTTT
1 TTTCTTTTT
2218685 CTGATGAATG
Statistics
Matches: 81, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
7 7 0.09
8 30 0.37
9 31 0.38
10 11 0.14
11 2 0.02
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:2221592 original size:6 final size:7
Alignment explanation
Indices: 2221577--2221617 Score: 59
Period size: 6 Copynumber: 6.0 Consensus size: 7
2221567 ATAAAAGTAC
2221577 AAATGCA
1 AAATGCA
2221584 AAATG-A
1 AAATGCA
2221590 AAATGCA
1 AAATGCA
2221597 AAGATGCA
1 AA-ATGCA
2221605 AAATG-A
1 AAATGCA
2221611 AAATGCA
1 AAATGCA
2221618 TGCATGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 12 0.39
7 12 0.39
8 7 0.23
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:2221595 original size:13 final size:14
Alignment explanation
Indices: 2221577--2221617 Score: 59
Period size: 13 Copynumber: 3.0 Consensus size: 14
2221567 ATAAAAGTAC
2221577 AAATGCAAAATG-A
1 AAATGCAAAATGCA
2221590 AAATGCAAAGATGCA
1 AAATGCAAA-ATGCA
2221605 AAATG-AAAATGCA
1 AAATGCAAAATGCA
2221618 TGCATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 14 0.54
14 6 0.23
15 6 0.23
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.15
Consensus pattern (14 bp):
AAATGCAAAATGCA
Found at i:2221754 original size:42 final size:42
Alignment explanation
Indices: 2221693--2221773 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
2221683 TACATCAAAT
*
2221693 AAAACTTTACATATAGGGATAACTTTCATTCCTAACTTCAAC
1 AAAACTTTACATATAGGGATAACTTTCACTCCTAACTTCAAC
*
2221735 AAAACTTTA-ATATAGGGGATAACTTTTACTCCTAACTTC
1 AAAACTTTACATATA-GGGATAACTTTCACTCCTAACTTC
2221774 TCTAAAGCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 5 0.14
42 31 0.86
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.35
Consensus pattern (42 bp):
AAAACTTTACATATAGGGATAACTTTCACTCCTAACTTCAAC
Found at i:2222290 original size:36 final size:36
Alignment explanation
Indices: 2222239--2222310 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2222229 TCTTACCGTT
2222239 GAATACTTTTGGTATCAATCTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATCTAACAGGATCTTTGTG
* *
2222275 GAATACTTTTTGTATCAATCTAACATGATCTTTGTG
1 GAATACTTTTGGTATCAATCTAACAGGATCTTTGTG
2222311 TACATAGCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATCTAACAGGATCTTTGTG
Found at i:2231499 original size:23 final size:23
Alignment explanation
Indices: 2231460--2231539 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 23
2231450 CTTCGGGATA
2231460 ATTT-TATGTGGTC-CTTC-GTGAC
1 ATTTCTATGTGG-CACTTCAGTG-C
*
2231482 ATTTCTATGTGGCACTTCGGTGC
1 ATTTCTATGTGGCACTTCAGTGC
**
2231505 ATATTCTATACGGCACTTCAGTGC
1 AT-TTCTATGTGGCACTTCAGTGC
*
2231529 AATTCTATGTG
1 ATTTCTATGTG
2231540 ACAGTTTTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
22 5 0.10
23 21 0.44
24 22 0.46
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (23 bp):
ATTTCTATGTGGCACTTCAGTGC
Found at i:2232125 original size:16 final size:17
Alignment explanation
Indices: 2232092--2232125 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2232082 AATTTTCAAT
2232092 AAGTTTTCAAAGAGTCA
1 AAGTTTTCAAAGAGTCA
*
2232109 AAGTTTTGAAA-AGTCA
1 AAGTTTTCAAAGAGTCA
2232125 A
1 A
2232126 TGTGACACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (17 bp):
AAGTTTTCAAAGAGTCA
Found at i:2233171 original size:17 final size:18
Alignment explanation
Indices: 2233139--2233172 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2233129 CAAAATAGAT
2233139 TTAATTAGATATATTATC
1 TTAATTAGATATATTATC
*
2233157 TTAATTTGA-ATATTAT
1 TTAATTAGATATATTAT
2233173 ATTTTCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (18 bp):
TTAATTAGATATATTATC
Found at i:2233300 original size:2 final size:2
Alignment explanation
Indices: 2233293--2233319 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2233283 TAATTAAAAT
2233293 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2233320 TTCAACTCAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2233500 original size:92 final size:92
Alignment explanation
Indices: 2233261--2233581 Score: 266
Period size: 92 Copynumber: 3.5 Consensus size: 92
2233251 TCAAATAAAT
* * * * *
2233261 ATATATATTTAATAGAGTTTGATAATT--AA-AATTATAT-ATATATATATATATATATA-T-AT
1 ATATATATTTAATAGAGTTTGATAATTACAATAATTAT-TCCTTTTTA-AAATATATAAACTCAT
* * * * * *
2233320 TTCAACTCAGAATATGTTTTATCATAAAA
64 TTCAAATGAGATTAAGTTTTATTATATAA
* * * * *
2233349 ATATGTATATTTTAATAGAATTTGATACTTAAAATAATTA-TCTCTCTTTGAAATATATAAAC-C
1 ATA--TATA-TTTAATAGAGTTTGATAATTACAATAATTATTC-CTTTTTAAAATATATAAACTC
* *
2233412 TATTTTC-ACTTAGA-TAAGGTTTTATTATATAA
62 -A-TTTCAAATGAGATTAA-GTTTTATTATATAA
* *
2233444 ATATATATTTAATAGAGTTTGATAATTACAATAATGATTCCTTTTTAAAATCTATAAACTCATTT
1 ATATATATTTAATAGAGTTTGATAATTACAATAATTATTCCTTTTTAAAATATATAAACTCATTT
* *
2233509 CAAATGAGATTAAGTTCTATTTTATAA
66 CAAATGAGATTAAGTTTTATTATATAA
* *
2233536 ATATATATTTAATAAAGTTTGATAATGACAATAATTATCTCCTTTT
1 ATATATATTTAATAGAGTTTGATAATTACAATAATTAT-TCCTTTT
2233582 AAATGTATAT
Statistics
Matches: 189, Mismatches: 26, Indels: 31
0.77 0.11 0.13
Matches are distributed among these distances:
88 3 0.02
90 4 0.02
91 22 0.12
92 96 0.51
93 28 0.15
94 10 0.05
95 22 0.12
96 4 0.02
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (92 bp):
ATATATATTTAATAGAGTTTGATAATTACAATAATTATTCCTTTTTAAAATATATAAACTCATTT
CAAATGAGATTAAGTTTTATTATATAA
Found at i:2233585 original size:48 final size:48
Alignment explanation
Indices: 2233441--2233596 Score: 110
Period size: 48 Copynumber: 3.3 Consensus size: 48
2233431 TTTTATTATA
* * *
2233441 TAAATATATATTTAATAGAGTTTGATAATTACAATAATGAT-TCCTTTT
1 TAAATATATATTTAATAAAGTTTGATAATGACAATAATTATCTCC-TTT
* * * * * * * **
2233489 TAAA-ATCTA-TAAACT-CA-TTTCA-AATGAGATTAAGT-TCTATTTT
1 TAAATATATATTTAA-TAAAGTTTGATAATGACAATAATTATCTCCTTT
2233532 ATAAATATATATTTAATAAAGTTTGATAATGACAATAATTATCTCCTTT
1 -TAAATATATATTTAATAAAGTTTGATAATGACAATAATTATCTCCTTT
* *
2233581 TAAATGTATATATAAT
1 TAAATATATATTTAAT
2233597 TATTTATAAA
Statistics
Matches: 77, Mismatches: 22, Indels: 18
0.66 0.19 0.15
Matches are distributed among these distances:
43 4 0.05
44 13 0.17
45 9 0.12
46 8 0.10
47 9 0.12
48 28 0.36
49 6 0.08
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (48 bp):
TAAATATATATTTAATAAAGTTTGATAATGACAATAATTATCTCCTTT
Found at i:2233672 original size:40 final size:39
Alignment explanation
Indices: 2233628--2233754 Score: 105
Period size: 40 Copynumber: 3.2 Consensus size: 39
2233618 CAATAATTTT
2233628 ATTTTAGTTAAAATATTATATGTATCAAATACATATATTA
1 ATTTTAGTTAAAATATTATATGTAT-AAATACATATATTA
* * * *
2233668 ATTTTAACTAAAAATATATATTATTTATAATTACA-ATAATT-
1 ATTTT-AGTTAAAATAT-TA-TATGTATAAATACATAT-ATTA
* * * *
2233709 TTTTTTGTTAAAATATTATATGCATAAAACACATATATTA
1 ATTTTAGTTAAAATATTATATGTAT-AAATACATATATTA
*
2233749 TTTTTA
1 ATTTTA
2233755 ACTAAATATC
Statistics
Matches: 67, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
38 5 0.07
39 10 0.15
40 20 0.30
41 15 0.22
42 11 0.16
43 6 0.09
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (39 bp):
ATTTTAGTTAAAATATTATATGTATAAATACATATATTA
Found at i:2233721 original size:41 final size:40
Alignment explanation
Indices: 2233611--2233729 Score: 100
Period size: 41 Copynumber: 2.9 Consensus size: 40
2233601 TATAAATACA
2233611 ATAATTACAATAATTTTATTTTAGTTAAAATAT-TA-TATGT
1 ATAATTACAATAATTTT-TTTT-GTTAAAATATATATTATGT
* *** * *
2233651 ATCAAATAC-ATATATTAATTTTAACTAAAAATATATATTATTT
1 AT-AATTACAATA-ATT--TTTTTTGTTAAAATATATATTATGT
2233694 ATAATTACAATAATTTTTTTTGTTAAAATATTATAT
1 ATAATTACAATAATTTTTTTTGTTAAAATA-TATAT
2233730 GCATAAAACA
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
40 16 0.27
41 21 0.35
42 12 0.20
43 11 0.18
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (40 bp):
ATAATTACAATAATTTTTTTTGTTAAAATATATATTATGT
Found at i:2245215 original size:2 final size:2
Alignment explanation
Indices: 2245204--2245236 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2245194 AATCAAATCG
2245204 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2245237 GCATAAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2247047 original size:19 final size:20
Alignment explanation
Indices: 2247023--2247067 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2247013 AAAATAATCC
* *
2247023 AATTTC-ACATTCTAACATT
1 AATTTCAACAGTCCAACATT
*
2247042 AATTTCAACAGTCCAATATT
1 AATTTCAACAGTCCAACATT
2247062 AATTTC
1 AATTTC
2247068 CAGCATAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (20 bp):
AATTTCAACAGTCCAACATT
Found at i:2254125 original size:9 final size:9
Alignment explanation
Indices: 2254113--2254159 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
2254103 TTGTAAGAAT
2254113 TAATTATAA
1 TAATTATAA
*
2254122 TAATAATAA
1 TAATTATAA
2254131 TAA-TATAA
1 TAATTATAA
2254139 TATTATTATAA
1 TA--ATTATAA
*
2254150 TATTTATAA
1 TAATTATAA
2254159 T
1 T
2254160 GAATCGGGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
8 6 0.19
9 18 0.56
10 1 0.03
11 7 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TAATTATAA
Found at i:2254369 original size:35 final size:36
Alignment explanation
Indices: 2254330--2254401 Score: 137
Period size: 35 Copynumber: 2.0 Consensus size: 36
2254320 TGATCTATTC
2254330 TTGCTTCACTACTCTTTTGTGAAGGCTTGA-TTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
2254365 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
2254401 T
1 T
2254402 GACTTAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 30 0.83
36 6 0.17
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.44
Consensus pattern (36 bp):
TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
Found at i:2254530 original size:46 final size:46
Alignment explanation
Indices: 2254411--2254532 Score: 210
Period size: 45 Copynumber: 2.7 Consensus size: 46
2254401 TGACTTAAAC
2254411 AGAATATGTTTCAATACTCTTCCATGGAGATTGGATTGACTTGGAA
1 AGAATATGTTTCAATACTCTTCCATGGAGATTGGATTGACTTGGAA
*
2254457 A-AATCTGTTTCAATACTCTTCCATGGAGATTGGATTGACTTGGAA
1 AGAATATGTTTCAATACTCTTCCATGGAGATTGGATTGACTTGGAA
* *
2254502 AGAATATGTTTCACTACTCTTCCGTGGAGAT
1 AGAATATGTTTCAATACTCTTCCATGGAGAT
2254533 CAAATCTGCA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 44 0.62
46 27 0.38
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (46 bp):
AGAATATGTTTCAATACTCTTCCATGGAGATTGGATTGACTTGGAA
Found at i:2260756 original size:17 final size:17
Alignment explanation
Indices: 2260736--2260771 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2260726 CTTCACTGAC
2260736 TTGCCTTATCAACTGCT
1 TTGCCTTATCAACTGCT
*
2260753 TTGCCTTATCACCTGCT
1 TTGCCTTATCAACTGCT
2260770 TT
1 TT
2260772 CTTTTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.31, G:0.11, T:0.44
Consensus pattern (17 bp):
TTGCCTTATCAACTGCT
Found at i:2266607 original size:18 final size:19
Alignment explanation
Indices: 2266579--2266614 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2266569 TTTTCTATTT
2266579 TTTTGTGGTTTGCTTGCTA
1 TTTTGTGGTTTGCTTGCTA
2266598 TTTT-TGGTTTGCTTGCT
1 TTTTGTGGTTTGCTTGCT
2266615 CCGTTCTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.03, C:0.11, G:0.25, T:0.61
Consensus pattern (19 bp):
TTTTGTGGTTTGCTTGCTA
Found at i:2267188 original size:3 final size:3
Alignment explanation
Indices: 2267180--2267220 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2267170 TTGTAAGAAT
2267180 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2267221 TTATTATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2268630 original size:27 final size:27
Alignment explanation
Indices: 2268583--2268635 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2268573 TAATAATAAC
* * *
2268583 TCATGTCATTTGGTGAGTAGACTTATA
1 TCATGTCACTTGCTGAATAGACTTATA
2268610 TCATGTCACTTGCTGAATAGACTTAT
1 TCATGTCACTTGCTGAATAGACTTAT
2268636 TAACAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (27 bp):
TCATGTCACTTGCTGAATAGACTTATA
Found at i:2274835 original size:9 final size:9
Alignment explanation
Indices: 2274821--2274849 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2274811 GAATAATAGT
2274821 CAATTAATC
1 CAATTAATC
2274830 CAATTAATC
1 CAATTAATC
2274839 CAATTAA-C
1 CAATTAATC
2274847 CAA
1 CAA
2274850 GAGTGGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (9 bp):
CAATTAATC
Found at i:2284214 original size:19 final size:19
Alignment explanation
Indices: 2284192--2284229 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2284182 TGACCCAACC
*
2284192 TATTGACTTTGACCGTTGA
1 TATTGACTTTGACCATTGA
2284211 TATTGACTTTGACCATTGA
1 TATTGACTTTGACCATTGA
2284230 CTTTTTCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (19 bp):
TATTGACTTTGACCATTGA
Found at i:2284595 original size:15 final size:15
Alignment explanation
Indices: 2284575--2284606 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2284565 TATCATAATT
*
2284575 ATTAAATATTTATAA
1 ATTAAATATTTAGAA
2284590 ATTAAATATTTAGAA
1 ATTAAATATTTAGAA
2284605 AT
1 AT
2284607 ATTAATTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
ATTAAATATTTAGAA
Found at i:2291237 original size:7 final size:7
Alignment explanation
Indices: 2291225--2291277 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
2291215 TTTTTAATTC
2291225 ATTATTT
1 ATTATTT
2291232 ATTATTT
1 ATTATTT
2291239 -TTATTT
1 ATTATTT
2291245 ATTATTT
1 ATTATTT
*
2291252 TTTA-TT
1 ATTATTT
*
2291258 -TTA-TA
1 ATTATTT
2291263 ATTATTT
1 ATTATTT
2291270 ATT-TTT
1 ATTATTT
2291276 AT
1 AT
2291278 ACCTTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
5 4 0.10
6 16 0.40
7 20 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTATTT
Found at i:2291239 original size:20 final size:19
Alignment explanation
Indices: 2291225--2291272 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
2291215 TTTTTAATTC
*
2291225 ATTATTTATTATTTTTATTT
1 ATTATTTATTA-TTTTATTA
*
2291245 ATTATTTTTTATTTTA-TA
1 ATTATTTATTATTTTATTA
2291263 ATTATTTATT
1 ATTATTTATT
2291273 TTTATACCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 5 0.20
20 10 0.40
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTATTTATTATTTTATTA
Found at i:2291239 original size:21 final size:19
Alignment explanation
Indices: 2291213--2291277 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 19
2291203 TCTTTATTAC
2291213 TATTTTTAATTCATTATTTAT
1 TATTTTTAATT-ATTATTT-T
*
2291234 TATTTTTATTTATTATTTTT
1 TATTTTTAATTATTA-TTTT
2291254 TATTTTATAATTATTTATTTT
1 TATTTT-TAATTA-TTATTTT
2291275 TAT
1 TAT
2291278 ACCTTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 11 0.28
21 25 0.64
22 3 0.08
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTTAATTATTATTTT
Found at i:2291244 original size:13 final size:13
Alignment explanation
Indices: 2291226--2291277 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
2291216 TTTTAATTCA
2291226 TTATTTATTATTT
1 TTATTTATTATTT
2291239 TTATTTATTATTTT
1 TTATTTATTA-TTT
*
2291253 TTATTTTATAATTAT
1 TTA-TTTATTATT-T
2291268 TTATTT-TTAT
1 TTATTTATTAT
2291278 ACCTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 13 0.38
14 11 0.32
15 10 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTATTTATTATTT
Found at i:2291260 original size:15 final size:15
Alignment explanation
Indices: 2291229--2291274 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
2291219 TAATTCATTA
2291229 TTTATTA-TTTTTA-
1 TTTATTATTTTTTAT
2291242 TTTATTATTTTTTAT
1 TTTATTATTTTTTAT
* *
2291257 TTTATAATTATTTAT
1 TTTATTATTTTTTAT
2291272 TTT
1 TTT
2291275 TATACCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 7 0.24
14 6 0.21
15 16 0.55
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTATTTTTTAT
Found at i:2297866 original size:19 final size:19
Alignment explanation
Indices: 2297844--2297881 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2297834 TCAGTTATTT
2297844 TATTTTAAATAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
2297863 TATTTTAAGTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
2297882 GATATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:2298021 original size:75 final size:75
Alignment explanation
Indices: 2297818--2298032 Score: 254
Period size: 77 Copynumber: 2.8 Consensus size: 75
2297808 TTTAAACATT
* * * * * * *
2297818 ATATTTTATCTTTGTTTCAGTTATTTTATTTTAAATAAGTTTTAGTATTTTAAGTAAGTTTTAGG
1 ATATTTTA-CTTTGTTTTAGGTATTTTAATTTAAAT-AGTTTTAGTATTTTAATTAGGATTTAGA
**
2297883 ATATTATTTTTT
64 ATATTATTTTAA
*
2297895 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGA
1 ATATTTTA-CTTTGTTTTAGGTATTTTAATTTAAATA-GTTTTAGTATTTTAATTAGGATTTAGA
2297960 ATATTATTTTAA
64 ATATTATTTTAA
* *
2297972 ATATTATTA-TTT-TTTTAGGTTTTTTAATTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 ATATT-TTACTTTGTTTTAGGTATTTTAATTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
2298033 AGATGTTTTA
Statistics
Matches: 123, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
74 5 0.04
75 40 0.33
76 4 0.03
77 71 0.58
78 3 0.02
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (75 bp):
ATATTTTACTTTGTTTTAGGTATTTTAATTTAAATAGTTTTAGTATTTTAATTAGGATTTAGAAT
ATTATTTTAA
Found at i:2301048 original size:31 final size:30
Alignment explanation
Indices: 2301013--2301101 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 30
2301003 CTAAGGTGTC
2301013 CCTTGGGTAGGCTCTCAGACCCCAAGGTATT
1 CCTTGGGTAGGCTCT-AGACCCCAAGGTATT
* *
2301044 CCTTGGGTAGTCTCTAAAGCCCCAAGGTATT
1 CCTTGGGTAGGCTCTAGA-CCCCAAGGTATT
* *
2301075 TCTTGGGTAGGCTCTAAGGCCCCAAGG
1 CCTTGGGTAGGCTCT-AGACCCCAAGG
2301102 CATCCCCTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.04
31 47 0.94
32 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.26
Consensus pattern (30 bp):
CCTTGGGTAGGCTCTAGACCCCAAGGTATT
Found at i:2307333 original size:95 final size:94
Alignment explanation
Indices: 2307149--2307406 Score: 378
Period size: 95 Copynumber: 2.7 Consensus size: 94
2307139 TTCAAGTAAT
* *
2307149 AACCAGTAGATTCCATGATCCATAAATCAGGAA-TAATCCTAT-TTTTCCAGTGAAAACATGAAA
1 AACCAGTAGATTCCATGATCCATAAATCAGGAACT-AT--TATATTTTCAAGTGAAAACA-GGAA
*
2307212 TCAGATAACACATTTCAGGTAACATAGTTCATA
62 CCAGATAACACATTTCAGGTAACATAGTTCATA
* *
2307245 AACCAGTAGATTCCATGACCCATCAATCAGGAACTATTATATTTTCAAGTGAAAACAGGAAGCCA
1 AACCAGTAGATTCCATGATCCATAAATCAGGAACTATTATATTTTCAAGTGAAAACAGGAA-CCA
2307310 GATAACACATTTCA-GTAACCATAGTTCATA
65 GATAACACATTTCAGGTAA-CATAGTTCATA
*
2307340 AACCAGTAGATTCCATGATCCATAAATCAGGAACTATTATATTTTCTAGTGAAAACAGGTAACCA
1 AACCAGTAGATTCCATGATCCATAAATCAGGAACTATTATATTTTCAAGTGAAAACAGG-AACCA
2307405 GA
65 GA
2307407 GAATCTAGAT
Statistics
Matches: 149, Mismatches: 8, Indels: 11
0.89 0.05 0.07
Matches are distributed among these distances:
94 10 0.07
95 103 0.69
96 35 0.23
97 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (94 bp):
AACCAGTAGATTCCATGATCCATAAATCAGGAACTATTATATTTTCAAGTGAAAACAGGAACCAG
ATAACACATTTCAGGTAACATAGTTCATA
Found at i:2309664 original size:45 final size:45
Alignment explanation
Indices: 2309615--2309778 Score: 256
Period size: 45 Copynumber: 3.6 Consensus size: 45
2309605 TATTCATTAT
* * *
2309615 TTTCATTTATGGTATCCTTTTATGCCTTTAATGCACCATTATGAA
1 TTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
2309660 TTTCATTTATGGCATCCTATCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
2309705 TTTCATTTATGGAATCCTTTAATGCCTTTAATGCACTGTTATGCA
1 TTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCGTTATGCA
2309750 TTTCATTTATGGTATCCTTTCATGCCTTT
1 TTTCATTTATGGTATCCTTTCATGCCTTT
2309779 TCATATGCAT
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 108 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (45 bp):
TTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:2310280 original size:94 final size:94
Alignment explanation
Indices: 2310099--2310280 Score: 206
Period size: 95 Copynumber: 1.9 Consensus size: 94
2310089 CCTACCATGG
** * * * **
2310099 TATCGATACTTTTATATTATGGTACCGATACCCATTTCAGTATCAATACTATTTCTACATTATTT
1 TATCGATACCGTTATACTAAGGTACCGATACCCATTTCAGTATCAATACCATTTCTACATTATGG
* * *
2310164 AATTCATGTTATCGATACCTTTCTCTCAA
66 AATCCATGGTATCAATACCTTTCTCTCAA
* * *
2310193 TATCGATACCGTTATACTAAGGTACCGATACTCCCTTTCAGTATCGATACCATTT-TGACATTCT
1 TATCGATACCGTTATACTAAGGTACCGATAC-CCATTTCAGTATCAATACCATTTCT-ACATTAT
*
2310257 GGAATCCATGGTATTAATA-CTTTC
64 GGAATCCATGGTATCAATACCTTTC
2310281 CTTTTAGTAT
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
94 33 0.46
95 39 0.54
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.40
Consensus pattern (94 bp):
TATCGATACCGTTATACTAAGGTACCGATACCCATTTCAGTATCAATACCATTTCTACATTATGG
AATCCATGGTATCAATACCTTTCTCTCAA
Found at i:2314807 original size:12 final size:13
Alignment explanation
Indices: 2314790--2314819 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2314780 TACATATATA
2314790 AATATTT-TTTTT
1 AATATTTGTTTTT
2314802 AATATTTGTTTTT
1 AATATTTGTTTTT
2314815 AATAT
1 AATAT
2314820 CGAAGAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (13 bp):
AATATTTGTTTTT
Found at i:2315484 original size:15 final size:16
Alignment explanation
Indices: 2315466--2315504 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2315456 TTCTTTTCAA
*
2315466 ATTTTTATTATTA-TT
1 ATTTTTATTAATATTT
2315481 ATTTTTA-TAATATTT
1 ATTTTTATTAATATTT
2315496 ATTTTTATT
1 ATTTTTATT
2315505 TGCAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 16 0.76
16 1 0.05
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTATTAATATTT
Found at i:2326098 original size:7 final size:7
Alignment explanation
Indices: 2326086--2326161 Score: 66
Period size: 7 Copynumber: 10.6 Consensus size: 7
2326076 ATTATGCTTG
2326086 AAGAAAA
1 AAGAAAA
2326093 AAGAAAA
1 AAGAAAA
*
2326100 GAAAAAGAA
1 -AAGAA-AA
2326109 AAGAAAGAA
1 AAG-AA-AA
2326118 AAGAAAA
1 AAGAAAA
2326125 AAG-AAA
1 AAGAAAA
*
2326131 AGGAAAA
1 AAGAAAA
2326138 AA-AAAA
1 AAGAAAA
*
2326144 TAGAAAA
1 AAGAAAA
*
2326151 TAGAAAA
1 AAGAAAA
2326158 AAGA
1 AAGA
2326162 GAAGAAAAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
6 10 0.17
7 30 0.52
8 8 0.14
9 10 0.17
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (7 bp):
AAGAAAA
Found at i:2326101 original size:5 final size:5
Alignment explanation
Indices: 2326091--2326173 Score: 66
Period size: 5 Copynumber: 16.6 Consensus size: 5
2326081 GCTTGAAGAA
2326091 AAAAG AAAAG AAAAAG AAAAG -AAAG AAAAG AAAAAAG AAAAGG AAAA-
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG --AAAAG AAAA-G AAAAG
* * * *
2326138 AAAA- AATAG AAAAT AGAA- AAAAG AGAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
2326174 GGGGGTCAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
4 14 0.22
5 35 0.55
6 10 0.16
7 5 0.08
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:2326118 original size:27 final size:27
Alignment explanation
Indices: 2326086--2326173 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 27
2326076 ATTATGCTTG
2326086 AAGAAAA-AAGAAAAGAAAAAGAAAAGA
1 AAGAAAAGAA-AAAAGAAAAAGAAAAGA
*
2326113 AAGAAAAGAAAAAAGAAAAGGAAAA-A
1 AAGAAAAGAAAAAAGAAAAAGAAAAGA
* *
2326139 AA-AAATAGAAAATAGAAAAAAGAGAAGAA
1 AAGAAA-AGAAAAAAG-AAAAAGAAAAG-A
2326168 AAGAAA
1 AAGAAA
2326174 GGGGGTCAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
25 3 0.06
26 11 0.22
27 29 0.57
28 2 0.04
29 3 0.06
30 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (27 bp):
AAGAAAAGAAAAAAGAAAAAGAAAAGA
Found at i:2326137 original size:33 final size:32
Alignment explanation
Indices: 2326086--2326173 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
2326076 ATTATGCTTG
2326086 AAGAAAAAAGAAAAGAAAAAGAAAAGAAAG-AA
1 AAGAAAAAAGAAAAGAAAAAGAAAA-AAAGAAA
*
2326118 AAGAAAAAAGAAAAGGAAAAA-AAAAATAGAAA
1 AAGAAAAAAGAAAA-GAAAAAGAAAAAAAGAAA
*
2326150 ATAGAAAAAAGAGAAG-AAAAGAAA
1 A-AGAAAAAAGAAAAGAAAAAGAAA
2326174 GGGGGTCAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
31 7 0.14
32 25 0.50
33 18 0.36
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (32 bp):
AAGAAAAAAGAAAAGAAAAAGAAAAAAAGAAA
Found at i:2327669 original size:83 final size:82
Alignment explanation
Indices: 2327294--2327803 Score: 817
Period size: 82 Copynumber: 6.2 Consensus size: 82
2327284 AAACATTAAA
*
2327294 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
*
2327359 AGAACATTCATTGAATT
66 AGAACAATCATTGAATT
*
2327376 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
**
2327441 AGAACAATCATTGAAAA
66 AGAACAATCATTGAATT
*
2327458 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
*
2327523 AGAACATTCATTGAATT
66 AGAACAATCATTGAATT
2327540 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
*
2327605 AGAACCAAGCATTGAATT
66 AGAA-CAATCATTGAATT
* * * *
2327623 TGGAAGATGAATTTGCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTATA-
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAG
* *
2327687 TAGAACCAAGCATTGAATT
65 CAGAA-CAATCATTGAATT
* *
2327706 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGA
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG-
*
2327770 TAGAACAATCATTGAATT
65 CAGAACAATCATTGAATT
2327788 TGGAAGATGAATTTGC
1 TGGAAGATGAATTTGC
2327804 TCATAGTAAA
Statistics
Matches: 405, Mismatches: 19, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
81 1 0.00
82 255 0.63
83 147 0.36
84 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (82 bp):
TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
AGAACAATCATTGAATT
Found at i:2328541 original size:113 final size:113
Alignment explanation
Indices: 2328360--2328983 Score: 991
Period size: 113 Copynumber: 5.5 Consensus size: 113
2328350 ATTACCAGAT
*
2328360 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * *
2328425 CAACCTTTTACCTGAATCCATCATTTGGTGAATCATCTTTTCCAGAGA
66 CAACCTTTTACTTGAATCCATCATTTGATGGATCAACTTTTCCAGAGA
2328473 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* *
2328538 CAACCTTTTACTTGAATCCGTCATTTGATGGATCAGCTTTTCCAGAGA
66 CAACCTTTTACTTGAATCCATCATTTGATGGATCAACTTTTCCAGAGA
*
2328586 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* ** * * * *
2328651 CAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGA
66 CAACCTTTTACTTGAATCCATCATTTGATGGATCAACTTTTCCAGAGA
* *
2328699 AGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * *
2328764 CAACCTTTTACCTGAATCCATCATTTGGTGAATCATCTTTTCCAGAGA
66 CAACCTTTTACTTGAATCCATCATTTGATGGATCAACTTTTCCAGAGA
2328812 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * *
2328877 CAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTA
66 CAACCTTTTACTTGAATCCATCATTTGATGGATCAACTTTTCCAGAG-A
2328925 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAGTTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGAGAAGAA
2328984 CTCATCAAGA
Statistics
Matches: 469, Mismatches: 40, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
112 3 0.01
113 466 0.99
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTACTTGAATCCATCATTTGATGGATCAACTTTTCCAGAGA
Found at i:2328956 original size:339 final size:339
Alignment explanation
Indices: 2328336--2328985 Score: 1171
Period size: 339 Copynumber: 1.9 Consensus size: 339
2328326 TCAAATCCAC
* *
2328336 TTGATGGATCATTCATTACCAGATAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATACATTACCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
2328401 AATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGAATCATCTTTT
66 AATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGAATCATCTTTT
2328466 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
131 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* * * *
2328531 ATTTGTTCAACCTTTTACTTGAATCCGTCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAA
196 ATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAA
2328596 TGAGAAGAACTCATCTGAAGAAGGAAGA-AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTT
261 TGAGAAGAACTCATCTGAAGAAGGAAGAGA-AAGTTCATAATGAGAAGAACTTGTTCAACTTTTT
2328660 GTTTAAATTCATCAT
325 GTTTAAATTCATCAT
*
2328675 TTGATGGATCA-ACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCATACATTACCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
2328739 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGAATCATCTTT
65 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGAATCATCTTT
2328804 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
130 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
* *
2328869 AATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCAT
195 AATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAACATTGCCAGAG-AAAGTTCAT
2328933 AATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGAAGAACT
259 AATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGAAGAACT
2328986 CATCAAGAGC
Statistics
Matches: 299, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
338 12 0.04
339 286 0.96
340 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (339 bp):
TTGATGGATCATACATTACCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGAATCATCTTTT
CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
ATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAA
TGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
TTTAAATTCATCAT
Found at i:2329241 original size:3 final size:3
Alignment explanation
Indices: 2329235--2329323 Score: 133
Period size: 3 Copynumber: 29.7 Consensus size: 3
2329225 TTTTTATCCA
* ** *
2329235 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2329283 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2329324 ATTTATATTA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2329253 original size:12 final size:12
Alignment explanation
Indices: 2329238--2329334 Score: 110
Period size: 12 Copynumber: 8.0 Consensus size: 12
2329228 TTATCCATAT
2329238 TATTATTATTAA
1 TATTATTATTAA
*
2329250 TATTATTATTATCCT
1 TATTATTATTA---A
2329265 TATTATTATTAA
1 TATTATTATTAA
2329277 TATTATTATT-A
1 TATTATTATTAA
*
2329288 TCATTATTATTAT
1 T-ATTATTATTAA
*
2329301 TATTATTATTAT
1 TATTATTATTAA
2329313 TATTATTATTAA
1 TATTATTATTAA
2329325 T-TTA-TATTAA
1 TATTATTATTAA
2329335 ATATATTAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
10 6 0.08
11 5 0.07
12 53 0.70
13 1 0.01
15 11 0.14
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:2330812 original size:12 final size:13
Alignment explanation
Indices: 2330797--2330826 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2330787 ACATATAATA
2330797 AATATTT-TTTTT
1 AATATTTGTTTTT
2330809 AATATTTGTTTTT
1 AATATTTGTTTTT
2330822 AATAT
1 AATAT
2330827 CGAAGAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (13 bp):
AATATTTGTTTTT
Found at i:2332917 original size:9 final size:9
Alignment explanation
Indices: 2332903--2332966 Score: 62
Period size: 9 Copynumber: 7.4 Consensus size: 9
2332893 ATTTTTTCAA
2332903 AAAAAAACC
1 AAAAAAACC
2332912 AAAAAAA-C
1 AAAAAAACC
2332920 AAAAAAA--
1 AAAAAAACC
* **
2332927 AAAAGAGGC
1 AAAAAAACC
2332936 AAAAAAACC
1 AAAAAAACC
*
2332945 AAAAAAAAC
1 AAAAAAACC
*
2332954 AAAAAAGCC
1 AAAAAAACC
2332963 AAAA
1 AAAA
2332967 TTTCAAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
7 5 0.11
8 8 0.18
9 32 0.71
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (9 bp):
AAAAAAACC
Found at i:2333265 original size:13 final size:13
Alignment explanation
Indices: 2333233--2333270 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2333223 AAATTTTGGA
2333233 GATCAAGAAAAAC
1 GATCAAGAAAAAC
* *
2333246 -TTCAAGAAAAGC
1 GATCAAGAAAAAC
2333258 GATCAAGAAAAAC
1 GATCAAGAAAAAC
2333271 AGATTGTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.11
Consensus pattern (13 bp):
GATCAAGAAAAAC
Found at i:2334033 original size:39 final size:39
Alignment explanation
Indices: 2333989--2334067 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
2333979 CAACTGGATC
2333989 TACCAAACCAGAATCCAAGACCAAACAATATTGAACTTT
1 TACCAAACCAGAATCCAAGACCAAACAATATTGAACTTT
*
2334028 TACCAAACCAGAATCCAAGACCAAATAATATTGAACTTT
1 TACCAAACCAGAATCCAAGACCAAACAATATTGAACTTT
2334067 T
1 T
2334068 GGTACCCAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.23
Consensus pattern (39 bp):
TACCAAACCAGAATCCAAGACCAAACAATATTGAACTTT
Found at i:2339900 original size:45 final size:45
Alignment explanation
Indices: 2339849--2339967 Score: 202
Period size: 45 Copynumber: 2.6 Consensus size: 45
2339839 TATTCATTAT
* * *
2339849 TTTCATTTATGACATTCTTTCATGCCTTTCATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
*
2339894 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
2339939 TTTCATTTATGGCATCCTTTCATGCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTT
2339968 TAATATGCAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.46
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:2340507 original size:19 final size:18
Alignment explanation
Indices: 2340491--2340541 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
2340481 AAAATCAAGC
2340491 AAGAAACTTTGAATCAAA
1 AAGAAACTTTGAATCAAA
2340509 AGAGAAACTTTGAATCAAA
1 A-AGAAACTTTGAATCAAA
*
2340528 TGAGAAACTTTGAA
1 -AAGAAACTTTGAA
2340542 AATCATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 29 0.97
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.24
Consensus pattern (18 bp):
AAGAAACTTTGAATCAAA
Found at i:2340807 original size:19 final size:19
Alignment explanation
Indices: 2340780--2340817 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2340770 TTTTGGAAAG
*
2340780 TCAAGTAAGAAACTTTGAA
1 TCAAATAAGAAACTTTGAA
2340799 TCAAATAAGAAACTTTGAA
1 TCAAATAAGAAACTTTGAA
2340818 AATCGTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (19 bp):
TCAAATAAGAAACTTTGAA
Found at i:2341001 original size:270 final size:273
Alignment explanation
Indices: 2340511--2341011 Score: 650
Period size: 270 Copynumber: 1.8 Consensus size: 273
2340501 GAATCAAAAG
* *
2340511 AGAAACTTTGAATCAAATGAGAAACTTTGAAAATCATTTTCTTATTTTCACAAATATCATACAAA
1 AGAAACTTTGAATCAAATAAGAAACTTTGAAAATC--TGTC-TATTTTCACAAATATCATACAAA
* * * * * *
2340576 AACACCATGCCCGAAGGCCTTATAGATGGCCTCGGGGACTTATCATCATGCTCTGAAGACTCATA
63 AACACCATACCCGAAGGCCTTATAAATGGCCTAGAGGACTTATCATCATGCTCGGAAGACTCACA
* * * * * * *
2340641 GATGACCTGGAGGATTTAACCATCATGCTCAGAATACATACTGATGGCACAGAGGACTTACTCAT
128 GATGACCCGGAGAATTTAACCATCATCCTCAGAAGACATACTGATGCCACAAAGGACTTAATCAT
**
2340706 TTTGGAAATATTATACTACGTAAGAAACATTGAAAACCACTTTATTACTTTTCAAATATTTAATT
193 AATGGAAATATTATACTACGTAAGAAACATTGAAAACCACTTTATTACTTTTCAAATATTTAATT
2340771 TTTGGAAAGTCAAGTA
258 TTTGGAAAGTCAAGTA
* *
2340787 AGAAACTTTGAATCAAATAAGAAACTTTGAAAATC-GTC-ATTTTCATAAATATCATACAACAA-
1 AGAAACTTTGAATCAAATAAGAAACTTTGAAAATCTGTCTATTTTCACAAATATCATACAAAAAC
* * * *
2340849 ATCATACCC-AGGTGTCTTATAAATGGCCTAGAGGACTTATCATCTTGCTCGGAAGACTCACAGA
66 ACCATACCCGAAG-GCCTTATAAATGGCCTAGAGGACTTATCATCATGCTCGGAAGACTCACAGA
* * * * *
2340913 TGACCCGGAGAATTTAATCATCATCCTCGGAAGACTTATTGATGCCCCAAAGGACTTAATCATAA
130 TGACCCGGAGAATTTAACCATCATCCTCAGAAGACATACTGATGCCACAAAGGACTTAATCATAA
* * * *
2340978 TGTAAATATTCTACTAGGTAAGAAACTTTGAAAA
195 TGGAAATATTATACTACGTAAGAAACATTGAAAA
2341012 TTGCTTTCTT
Statistics
Matches: 192, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
269 2 0.01
270 132 0.69
271 22 0.11
273 2 0.01
276 34 0.18
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (273 bp):
AGAAACTTTGAATCAAATAAGAAACTTTGAAAATCTGTCTATTTTCACAAATATCATACAAAAAC
ACCATACCCGAAGGCCTTATAAATGGCCTAGAGGACTTATCATCATGCTCGGAAGACTCACAGAT
GACCCGGAGAATTTAACCATCATCCTCAGAAGACATACTGATGCCACAAAGGACTTAATCATAAT
GGAAATATTATACTACGTAAGAAACATTGAAAACCACTTTATTACTTTTCAAATATTTAATTTTT
GGAAAGTCAAGTA
Found at i:2346576 original size:3 final size:3
Alignment explanation
Indices: 2346556--2346635 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
2346546 TGTGTGGCTC
* *
2346556 TTA TTT TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2346604 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2346636 GCTTTGTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2354028 original size:2 final size:2
Alignment explanation
Indices: 2354021--2354050 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2354011 AAATGATGAA
2354021 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
2354051 TTAGAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2354316 original size:28 final size:28
Alignment explanation
Indices: 2354262--2354334 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
2354252 TACCACTTTT
*
2354262 TTCTTTTAAAAT--GATTTTTCTTAAAA
1 TTCTTTTAAAATACGTTTTTTCTTAAAA
2354288 TTCTTTTAAAATACGTTTTTTCTTAAAA
1 TTCTTTTAAAATACGTTTTTTCTTAAAA
2354316 TTCTTTTAAAATACGTTTT
1 TTCTTTTAAAATACGTTTT
2354335 CTTAAGTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 12 0.27
28 32 0.73
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.55
Consensus pattern (28 bp):
TTCTTTTAAAATACGTTTTTTCTTAAAA
Found at i:2367567 original size:2 final size:2
Alignment explanation
Indices: 2367560--2367584 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2367550 TTCATTTTCG
2367560 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 A
2367585 GGAAAAATAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2368522 original size:126 final size:130
Alignment explanation
Indices: 2368194--2368627 Score: 425
Period size: 134 Copynumber: 3.3 Consensus size: 130
2368184 CAAATTAATC
* * * * *
2368194 GATTTGCTTCACTGCTCTTCAAGGAAGATCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTTT
1 GATTTGCTTCGCTGCTCTTC-AGGAAGACCGAATCTGAAAGAAGAAGAATCTGCTCCAATACTCT
*
2368259 TTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCATTTCTCTTCAGGGAATATTGAATCA
65 TTAGGGGAGATCAGACTCGAGAAAACTTT-ATCCA--TCA-TTCTCTTCAGGGAAGATTGAATCA
*
2368324 AACGT
126 AACAT
* * * * * * * * *
2368329 GATTTACTTCGCTGTTGTTCAGGAATACTGAATCTGAAAGAAGAAAAATATGTTCCACA-ACTGT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCGAATCTGAAAGAAGAAGAATCTGCTCCA-ATACTCT
* *
2368393 TTAGGGGAAATCAGACTCGAGAAAACTTT-T-CA-C-TTCTCTTCAGGGAAGATTGAATCGAACA
65 TTAGGGGAGATCAGACTCGAGAAAACTTTATCCATCATTCTCTTCAGGGAAGATTGAATCAAACA
2368454 T
130 T
*
2368455 GATTTGC-TCGCTGCTCTTCAGGAAGACCGAATCTGAAAAAAAGAAGAATCTGCTCCAATACTCT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCGAATCTG-AAAGAAGAAGAATCTGCTCCAATACTCT
* * * * * *
2368519 TTAGGGGAGACCAGACTCAAGAAATCTTTGACCCACTTCATTGTTCTTCAGGGAATATTGAATCA
65 TTAGGGGAGATCAGACTCGAGAAAACTTT-ATCCA--TCATT-CTCTTCAGGGAAGATTGAATCA
2368584 AA-AGT
126 AACA-T
* ** * *
2368589 GATTTGTTTCATTTG-TCTTCAAGAAGACCAAATCTGAAA
1 GATTTGCTTC-GCTGCTCTTCAGGAAGACCGAATCTGAAA
2368628 ATCTAACATC
Statistics
Matches: 245, Mismatches: 40, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
125 25 0.10
126 78 0.32
128 1 0.00
129 2 0.01
131 2 0.01
132 2 0.01
133 3 0.01
134 93 0.38
135 37 0.15
136 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (130 bp):
GATTTGCTTCGCTGCTCTTCAGGAAGACCGAATCTGAAAGAAGAAGAATCTGCTCCAATACTCTT
TAGGGGAGATCAGACTCGAGAAAACTTTATCCATCATTCTCTTCAGGGAAGATTGAATCAAACAT
Found at i:2369390 original size:45 final size:45
Alignment explanation
Indices: 2369302--2369390 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
2369292 GAATGAAATC
* * ** *
2369302 ACTAAAATATTGACTCTTCTTCGCGAGAAAGTCAAGAAGGACAAT
1 ACTAAAATAATGACTCCTCTTAACGAGAAAGTAAAGAAGGACAAT
*
2369347 ACTAAAATAATGACTCCTCTTAATGAGAAAGTAAAGGAA-GACAA
1 ACTAAAATAATGACTCCTCTTAACGAGAAAGTAAA-GAAGGACAA
2369391 CACCGAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
45 34 0.92
46 3 0.08
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (45 bp):
ACTAAAATAATGACTCCTCTTAACGAGAAAGTAAAGAAGGACAAT
Found at i:2369493 original size:38 final size:38
Alignment explanation
Indices: 2369396--2370111 Score: 547
Period size: 38 Copynumber: 18.0 Consensus size: 38
2369386 GACAACACCG
* * * *
2369396 AAAGATTGAATCCTCTTCGCGAGAAAGTCAAGAATAACAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-AC
*
2369436 TGAAAGATTGAC-TCATCTTCACGAGGAAATCAAGAATAAC
1 --AAAGATTGACTTC-TCTTCACGAGGAAGTCAAGAATAAC
* *
2369476 AAAGATTGACTACTCTTCACGAGGAAGTCCAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
2369514 AAAGATTGACTTCTCTTCACGAGGAAGTCGAGAATAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
2369552 AAAGATTGACTTCACTTTACGAGGAAGTCCAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
2369590 ATTGGGAGAATGAC-TCATCTTCACGAGGAATTCAAGAATAA-
1 A----AAGATTGACTTC-TCTTCACGAGGAAGTCAAGAATAAC
* * * *
2369631 AAAGATTAACTCCTCTTCACGAGAAAGTCAAGAACAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
2369669 AAAGATCGACTTCTCTTCACGAGGAAGTCCAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
2369707 AAAGATTTACTTCTCTTCATGATGAAGTCCAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** * *
2369745 ACTAGGAGATTGACTCCTCTTCGTGAGGGAGTCAGGAATAAC
1 A--A--AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * ** *
2369787 AAAGATTGATTTCTCTTTATAAGAAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** * * *
2369825 AAAGACCGACTTTTGTTCACGAGGAAGTCGAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
2369863 AAAGATTGATTTCTCTTCATGAGGAAGTCAAGAATGACAATAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT----A-AC
* * * * * *
2369906 TGAGAGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACATAC
1 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT---A-AC
* * * * * *
2369950 TGAGAGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATAC
1 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT----A-AC
* *
2369995 TGAAAGATTAACTTCTCTTCACGAGAAAGTCAAGAATAAC
1 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
2370035 AAAGATTGACTCCTCTTCACGAGGGAGTCAAGAATAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
2370073 AAGGATTGACTTCTCTTCATGAGGAAGTTAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
2370111 A
1 A
2370112 TTGGAATATT
Statistics
Matches: 554, Mismatches: 99, Indels: 46
0.79 0.14 0.07
Matches are distributed among these distances:
37 27 0.05
38 321 0.58
39 1 0.00
40 6 0.01
41 6 0.01
42 86 0.16
43 2 0.00
44 41 0.07
45 64 0.12
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:2369859 original size:156 final size:157
Alignment explanation
Indices: 2369396--2370111 Score: 628
Period size: 156 Copynumber: 4.5 Consensus size: 157
2369386 GACAACACCG
* * ** * *
2369396 AAAGATTGAATCCTCTTCGCGAGAAAGTCAAGAATAACACT-GAAAGATTGACTCATCTTCACGA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTAGAGAGATTGACTCATCTTCACGA
* * *
2369460 GGAAATCAAGAATAACAAAGATTGACTACTCTTCACGAGGAAGTCCAGAATAACAAAGATTGACT
66 GGAAATCAAGAATAACAAAGATTGACTACTCTTCACGAGAAAGTCAAGAATAACAAAGATCGACT
*
2369525 TCTCTTCACGAGGAAGTCGAGAATAAT
131 TCTCTTCACGAGGAAGTCGAGAATAAC
* * * * * * *
2369552 AAAGATTGACTTCACTTTACGAGGAAGTCCAGAATAACA-TTGGGAGAATGACTCATCTTCACGA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTAGAGAGATTGACTCATCTTCACGA
* * * *
2369616 GGAATTCAAGAATAA-AAAGATTAACTCCTCTTCACGAGAAAGTCAAGAACAACAAAGATCGACT
66 GGAAATCAAGAATAACAAAGATTGACTACTCTTCACGAGAAAGTCAAGAATAACAAAGATCGACT
*
2369680 TCTCTTCACGAGGAAGTCCAGAATAAC
131 TCTCTTCACGAGGAAGTCGAGAATAAC
* * * * **
2369707 AAAGATTTACTTCTCTTCATGATGAAGTCCAGAATAACACTAG-GAGATTGACTCCTCTTCGTGA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTAGAGAGATTGACTCATCTTCACGA
* * * * * * ** *
2369771 GGGAGTCAGGAATAACAAAGATTGATTTCTCTTTATAAGAAAGTCAAGAATAACAAAGACCGACT
66 GGAAATCAAGAATAACAAAGATTGACTACTCTTCACGAGAAAGTCAAGAATAACAAAGATCGACT
* *
2369836 TTTGTTCACGAGGAAGTCGAGAATAAC
131 TCTCTTCACGAGGAAGTCGAGAATAAC
* * * *
2369863 AAAGATTGATTTCTCTTCATGAGGAAGTCAAGAATGACAATACTGAGAGATTGACTTC-TCTTAA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTA--GAGAGATTGAC-TCATCTTCA
* * * * * * * * *
2369927 TGA-GAAAGTGAAAAATGACATACTGAGAGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACA
63 CGAGGAAA-TCAAGAAT---A-AC--AAAGATTGACTACTCTTCACGAGAAAGTCAAGAAT----
** * *
2369991 ATACTGAAAGATTAACTTCTCTTCACGAGAAAGTCAAGAATAAC
117 A-AC--AAAGATCGACTTCTCTTCACGAGGAAGTCGAGAATAAC
* * * *
2370035 AAAGATTGACTCCTCTTCACGAGGGAGTCAAGAAT-A-A-TA-AG-GATTGACTTC-TCTTCATG
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTAGAGAGATTGAC-TCATCTTCACG
* *
2370094 AGGAAGTTAAGAATAACA
65 AGGAAATCAAGAATAACA
2370112 TTGGAATATT
Statistics
Matches: 461, Mismatches: 77, Indels: 41
0.80 0.13 0.07
Matches are distributed among these distances:
155 132 0.29
156 169 0.37
158 3 0.01
159 22 0.05
160 2 0.00
161 2 0.00
162 2 0.00
163 2 0.00
165 53 0.11
166 5 0.01
169 3 0.01
170 3 0.01
171 1 0.00
172 62 0.13
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (157 bp):
AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTAGAGAGATTGACTCATCTTCACGA
GGAAATCAAGAATAACAAAGATTGACTACTCTTCACGAGAAAGTCAAGAATAACAAAGATCGACT
TCTCTTCACGAGGAAGTCGAGAATAAC
Found at i:2369964 original size:44 final size:45
Alignment explanation
Indices: 2369865--2370024 Score: 232
Period size: 45 Copynumber: 3.6 Consensus size: 45
2369855 AGAATAACAA
* * * * *
2369865 AGATTGATTTCTCTTCATGAGGAAGTCAAGAATGACAATACTGAG
1 AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATACTGAG
2369910 AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGAC-ATACTGAG
1 AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATACTGAG
*
2369954 AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATACTGAA
1 AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATACTGAG
* * *
2369999 AGATTAACTTCTCTTCACGAGAAAGT
1 AGATTGACTTCTCTTAATGAGAAAGT
2370025 CAAGAATAAC
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
44 44 0.42
45 61 0.58
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (45 bp):
AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATACTGAG
Found at i:2370895 original size:43 final size:43
Alignment explanation
Indices: 2370819--2370950 Score: 151
Period size: 43 Copynumber: 3.0 Consensus size: 43
2370809 TATTCCTGGA
* *
2370819 TGATATGAGCCTTCAAAAATGTCTCAACATTTATTATTTCTTGC
1 TGATATGAGCCTTC-AAAATGCCCCAACATTTATTATTTCTTGC
* * *
2370863 TGATATGGGCCTTCAAAATGCCCCAACATTTATTATTTCTAGA
1 TGATATGAGCCTTCAAAATGCCCCAACATTTATTATTTCTTGC
* *
2370906 TGATACAT-A-CCTTCAAAAGTTCCCCAACATTTATCATTTCTTGC
1 TGAT--ATGAGCCTTCAAAA-TGCCCCAACATTTATTATTTCTTGC
2370950 T
1 T
2370951 CCAGAACTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 38 0.51
44 35 0.47
45 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (43 bp):
TGATATGAGCCTTCAAAATGCCCCAACATTTATTATTTCTTGC
Found at i:2381114 original size:22 final size:21
Alignment explanation
Indices: 2381075--2381131 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
2381065 AATGCATGAG
**
2381075 TTATATAAAAATATATTTTA-
1 TTATATAATTATATATTTTAT
2381095 -T-TATAATTATAT-TTTTAT
1 TTATATAATTATATATTTTAT
*
2381113 TTATATATTTATATATTTT
1 TTATATAATTATATATTTT
2381132 TATTATAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 5 0.17
18 9 0.30
19 2 0.07
20 10 0.33
21 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATATAATTATATATTTTAT
Found at i:2382486 original size:21 final size:21
Alignment explanation
Indices: 2382438--2382487 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2382428 CATCAGATTC
*
2382438 AGTTCGAGTTCGGATCGTGTTA
1 AGTTC-AGTTCGGATCGTGCTA
*
2382460 ATTTCAGTTCGGATCGATGCT-
1 AGTTCAGTTCGGATCG-TGCTA
2382481 AGTTCAG
1 AGTTCAG
2382488 GTCAAAACGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (21 bp):
AGTTCAGTTCGGATCGTGCTA
Found at i:2383449 original size:22 final size:21
Alignment explanation
Indices: 2383423--2383481 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
2383413 TATATATATA
2383423 TATAAAATATAAATATACAAAC
1 TATAAAATATAAATATA-AAAC
* * *
2383445 TATAAACTAT--ATATATAAG
1 TATAAAATATAAATATAAAAC
2383464 TATAAAATATATAATATA
1 TATAAAATATA-AATATA
2383482 TAAGCATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 11 0.37
20 5 0.17
22 14 0.47
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
TATAAAATATAAATATAAAAC
Found at i:2383482 original size:7 final size:7
Alignment explanation
Indices: 2383413--2383484 Score: 51
Period size: 7 Copynumber: 10.0 Consensus size: 7
2383403 ATGATGTATG
2383413 TATATATA
1 TATATA-A
2383421 TATATAA
1 TATATAA
*
2383428 AATATAA
1 TATATAA
2383435 -ATATACA
1 TATATA-A
*
2383442 AACTATAA
1 TA-TATAA
2383450 -ACTAT-A
1 TA-TATAA
2383456 TATATAA
1 TATATAA
*
2383463 GTATAAAA
1 -TATATAA
2383471 TATATAA
1 TATATAA
2383478 TATATAA
1 TATATAA
2383485 GCATAAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
6 9 0.16
7 28 0.51
8 14 0.25
9 4 0.07
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (7 bp):
TATATAA
Found at i:2386471 original size:7 final size:7
Alignment explanation
Indices: 2386463--2386495 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2386453 TAAATAAAAT
*
2386463 ATATTAT
1 ATATTAA
2386470 ATATTAA
1 ATATTAA
2386477 ATATTAA
1 ATATTAA
2386484 ATATTAA
1 ATATTAA
2386491 ATATT
1 ATATT
2386496 TATTACCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
ATATTAA
Found at i:2389020 original size:3 final size:3
Alignment explanation
Indices: 2389012--2389085 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
2389002 AGTTGATGGT
2389012 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2389060 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2389086 TTTTTAAGAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2389741 original size:66 final size:66
Alignment explanation
Indices: 2389633--2389827 Score: 273
Period size: 66 Copynumber: 3.0 Consensus size: 66
2389623 TTAGGGATAA
*
2389633 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGATGG
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATGG
2389698 G
66 G
* * * *
2389699 TGTTTGAAGAGAAATTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAAGAATCTCAAAGGTTG
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATGG
2389764 G
66 G
* * * * * ** *
2389765 TGTTTCACGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGATAAACAAACTCAAAGAT
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAT
2389828 TATAAATTTT
Statistics
Matches: 113, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 113 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (66 bp):
TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATGG
G
Found at i:2395965 original size:3 final size:3
Alignment explanation
Indices: 2395957--2396015 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
2395947 ATGTAATAGT
2395957 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2396005 TAA TAA TAA TA
1 TAA TAA TAA TA
2396016 TATTTTTAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2396148 original size:21 final size:20
Alignment explanation
Indices: 2396109--2396148 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2396099 TGATACCCAA
* *
2396109 TTCATCCAGTATTGATACTG
1 TTCATCCAATATAGATACTG
2396129 TTCATCCCAATATAGATACT
1 TTCAT-CCAATATAGATACT
2396149 CAAACCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (20 bp):
TTCATCCAATATAGATACTG
Found at i:2404646 original size:42 final size:41
Alignment explanation
Indices: 2404444--2404663 Score: 174
Period size: 41 Copynumber: 5.5 Consensus size: 41
2404434 AAACACAAAT
* *
2404444 GCCACTACA-TACGAGTATATAGCG--GTATTTGTATAAAAAC
1 GCCACTAAAGTACGAGTCTATAGCGACGT-TTT-TATAAAAAC
* * * * * *
2404484 ACCACTAAAGTACTATTCTATAGCGGCGTTTATATAAAAAT
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTTTATAAAAAC
* * *
2404525 GCCACTAAAGTACGAGTATATAAC-ATCG--TTTAT-----T
1 GCCACTAAAGTACGAGTCTATAGCGA-CGTTTTTATAAAAAC
*
2404559 GCCACTAAAGTACGAGTCTATAGCGACGTTTTTATAAAAAT
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTTTATAAAAAC
* ** *
2404600 GCCACTAAAATACGAGTCTATAGTTACTTTTTTTATAAAAAC
1 GCCACTAAAGTACGAGTCTATAGCGAC-GTTTTTATAAAAAC
*
2404642 GCCACTAAAGTATGAGTCTATA
1 GCCACTAAAGTACGAGTCTATA
2404664 ACGGTAAAGG
Statistics
Matches: 144, Mismatches: 23, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
34 25 0.17
35 1 0.01
36 5 0.03
39 4 0.03
40 7 0.05
41 66 0.46
42 34 0.24
43 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (41 bp):
GCCACTAAAGTACGAGTCTATAGCGACGTTTTTATAAAAAC
Found at i:2404783 original size:82 final size:83
Alignment explanation
Indices: 2404685--2404900 Score: 265
Period size: 82 Copynumber: 2.6 Consensus size: 83
2404675 ACCGAAGCAA
* ** *
2404685 ATAGATGAACCCTATTATGGCATTTGTATAAAAACTCTGCTAAAGTACTACTATGTTGCGGCGTT
1 ATAGATGAACCCTATTACGGCATTTGTATAAAAACTCTGCTAAAGTACTACTATGTAACAGCGTT
2404750 TGTTG-AAAAACACCACT
66 TGTTGAAAAAACACCACT
* * * * *
2404767 ATAGATGAACCCTATTACGGTATTTTTATATAAACGCTGCTAAAGTACTACTCTGTAACAGCGTT
1 ATAGATGAACCCTATTACGGCATTTGTATAAAAACTCTGCTAAAGTACTACTATGTAACAGCGTT
*
2404832 TGTTGAAAAAATACCACT
66 TGTTGAAAAAACACCACT
* * * * * **
2404850 ATGGATGAA-CCTATTGCAGCGTTTGTATAAAAATTCCACTAAAGTACTACT
1 ATAGATGAACCCTATTACGGCATTTGTATAAAAACTCTGCTAAAGTACTACT
2404901 CTATCGTGGC
Statistics
Matches: 112, Mismatches: 21, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
82 93 0.83
83 19 0.17
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (83 bp):
ATAGATGAACCCTATTACGGCATTTGTATAAAAACTCTGCTAAAGTACTACTATGTAACAGCGTT
TGTTGAAAAAACACCACT
Found at i:2405593 original size:41 final size:42
Alignment explanation
Indices: 2405533--2405642 Score: 109
Period size: 41 Copynumber: 2.6 Consensus size: 42
2405523 TGCAAAAACT
* *
2405533 TCATGCTCGAAGGTA-TTATAGATGGCCCAAATGACTTA-TCA
1 TCATGCTCGAAAG-ACTTATAGATGGCCCAAAGGACTTACTCA
* * * * *
2405574 TCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTACTCA
1 TCATGCTCGAAAGACTTATAGATGGCCCAAAGGACTTACTCA
*
2405616 TCATGCTTGAAAGACTTACT-GATGGCC
1 TCATGCTCGAAAGACTTA-TAGATGGCC
2405643 TGAAGGACCT
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
41 30 0.55
42 24 0.44
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (42 bp):
TCATGCTCGAAAGACTTATAGATGGCCCAAAGGACTTACTCA
Found at i:2408235 original size:100 final size:100
Alignment explanation
Indices: 2408062--2408264 Score: 370
Period size: 100 Copynumber: 2.0 Consensus size: 100
2408052 ACAAAGCCCG
* **
2408062 ACTATGGAGGGTACCAAGGATGGTCGAGTGTGGATGGTAGAAAAAGTGAGTTGTTGCAGTCACTT
1 ACTATGGAGGGTACCAAGGATGGTCGAGTGAGGACAGTAGAAAAAGTGAGTTGTTGCAGTCACTT
*
2408127 ACTCCAAGCCTCCTCTCAATGTATATTCTCCTCTC
66 ACTCCAAGCCTCCTCTCAAGGTATATTCTCCTCTC
2408162 ACTATGGAGGGTACCAAGGATGGTCGAGTGAGGACAGTAGAAAAAGTGAGTTGTTGCAGTCACTT
1 ACTATGGAGGGTACCAAGGATGGTCGAGTGAGGACAGTAGAAAAAGTGAGTTGTTGCAGTCACTT
2408227 ACTCCAAGCCTCCTCTCAAGGTATATTCTCCTCTC
66 ACTCCAAGCCTCCTCTCAAGGTATATTCTCCTCTC
2408262 ACT
1 ACT
2408265 TTATGAAGAG
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 99 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (100 bp):
ACTATGGAGGGTACCAAGGATGGTCGAGTGAGGACAGTAGAAAAAGTGAGTTGTTGCAGTCACTT
ACTCCAAGCCTCCTCTCAAGGTATATTCTCCTCTC
Found at i:2409064 original size:14 final size:15
Alignment explanation
Indices: 2409041--2409073 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2409031 ATTATCGTGA
2409041 CATCATTCCTTACAT
1 CATCATTCCTTACAT
2409056 CATCA-TCCTTACAT
1 CATCATTCCTTACAT
2409070 CATC
1 CATC
2409074 CATGAACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.36
Consensus pattern (15 bp):
CATCATTCCTTACAT
Found at i:2421352 original size:43 final size:43
Alignment explanation
Indices: 2421305--2421391 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
2421295 GGAAAAATAA
** *
2421305 AATAAATAAGTAAGAAAAAAATAGTAAAGTAATA-AT-TATATAT
1 AATAAATAAAAAAG-AAAAAATA-TAAAATAATATATATATATAT
*
2421348 AATAATTAAAAAAGAAAAAATATAAAATAATATATATATATAT
1 AATAAATAAAAAAGAAAAAATATAAAATAATATATATATATAT
2421391 A
1 A
2421392 TATATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 9 0.24
42 10 0.26
43 19 0.50
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (43 bp):
AATAAATAAAAAAGAAAAAATATAAAATAATATATATATATAT
Found at i:2421382 original size:2 final size:2
Alignment explanation
Indices: 2421377--2421432 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2421367 ATATAAAATA
2421377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2421419 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
2421433 CAAAGTATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2421896 original size:18 final size:17
Alignment explanation
Indices: 2421873--2421923 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
2421863 AAATATATAT
2421873 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
2421891 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
2421908 ATATATAATAAATAAA
1 ATA-ATAAT-AATAAA
2421924 GGGACTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 7 0.24
18 16 0.55
19 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:2421899 original size:45 final size:43
Alignment explanation
Indices: 2421819--2421918 Score: 100
Period size: 45 Copynumber: 2.3 Consensus size: 43
2421809 AGATAATTAC
* * *
2421819 AATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAA-G
1 AATATATATATAATAATAATAGACTAATAAGTAAAA-A-TAAATG
2421863 AAATATATATATAATAATAATA-ACATGAATAA-TAAAAATAAATG
1 -AATATATATATAATAATAATAGAC-T-AATAAGTAAAAATAAATG
2421907 AATATATA-ATAA
1 AATATATATATAA
2421919 ATAAAGGGAC
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
42 4 0.08
43 12 0.24
44 4 0.08
45 25 0.51
46 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (43 bp):
AATATATATATAATAATAATAGACTAATAAGTAAAAATAAATG
Found at i:2422313 original size:37 final size:37
Alignment explanation
Indices: 2422263--2422367 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
2422253 GTGCTTGTGG
* * * *
2422263 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
2422300 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
2422337 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
2422368 GACAAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:2423222 original size:105 final size:105
Alignment explanation
Indices: 2422909--2423538 Score: 887
Period size: 105 Copynumber: 6.0 Consensus size: 105
2422899 GCATCATTCC
* * ** * *
2422909 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGATA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
2422973 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2423015 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * *
2423075 CAGCGGTCCCTTTGTCGTGGAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2423115 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * * *
2423180 CAGCGGTCCCTTCATTGTGAAGTTGAACTTGCATTGTTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2423220 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
2423285 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
2423325 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAAATTGAGAAGTTGTTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
2423390 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2423430 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
2423494 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2423535 GAGT
1 GAGT
2423539 TTCACGATAT
Statistics
Matches: 476, Mismatches: 41, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
100 80 0.17
101 1 0.00
102 7 0.01
104 17 0.04
105 335 0.70
106 36 0.08
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2423785 original size:36 final size:36
Alignment explanation
Indices: 2423738--2423813 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
2423728 TGTTTGGAGA
* * *
2423738 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
2423774 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
2423810 GAAA
1 GAAA
2423814 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:2423934 original size:106 final size:105
Alignment explanation
Indices: 2423713--2424032 Score: 497
Period size: 106 Copynumber: 3.1 Consensus size: 105
2423703 TTCGTTAAAT
* ** *
2423713 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
2423775 AAACTATCTCA-AGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
* * *
2423814 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGCAGACAAAATTTTCTGTTTCGAGGA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
2423879 AAACTATCTCAAGAGAGAGAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTC-AGAGAGAGAAAAAATTCATTTCAAGGGAAA
2423920 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
2423985 AAACTATCTCAG-GAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
2424024 TGTTTTCAA
1 TGTTTTCAA
2424033 GAGAAACTGT
Statistics
Matches: 199, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
101 44 0.22
103 3 0.02
104 52 0.26
105 3 0.02
106 97 0.49
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (105 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:2423989 original size:39 final size:39
Alignment explanation
Indices: 2423935--2424009 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
2423925 TCAATGTTTA
* *
2423935 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
* *
2423974 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
2424010 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:2424208 original size:36 final size:36
Alignment explanation
Indices: 2424168--2424277 Score: 89
Period size: 36 Copynumber: 3.1 Consensus size: 36
2424158 CAAGCGAGAC
2424168 AAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAAT
1 AAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAAT
* ** * * ** * *
2424204 AAATCTTCTTTCGAGAAAAATAGTCTCAAGTGACAC
1 AAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAAT
* *
2424240 AAAGT-ATGTTTTAAGAAAAACAAAT-TTGAGTGAGAT
1 AAA-TCTTGTTTTAAGAAAAAC-AATCTTGAGTGAAAT
2424276 AA
1 AA
2424278 TCATCTGCAT
Statistics
Matches: 53, Mismatches: 19, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
36 50 0.94
37 3 0.06
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (36 bp):
AAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAAT
Found at i:2424250 original size:72 final size:75
Alignment explanation
Indices: 2424116--2424277 Score: 190
Period size: 72 Copynumber: 2.2 Consensus size: 75
2424106 AAAAAATAGC
* * * * *
2424116 CTTGAGTAAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAATCTTGTTTTA
1 CTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGACACAAATCATGTTTTA
2424181 AGAAAAAC-AAT
64 AGAAAAACAAAT
* *
2424192 CTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAATAGTCTCAAGTGACACAAAGT-ATGTTTTAA
1 CTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGACACAAA-TCATGTTTTAA
2424254 GAAAAACAAAT
65 GAAAAACAAAT
*
2424265 -TTGAGTGAGATAA
1 CTTGAGTGAAATAA
2424278 TCATCTGCAT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
72 46 0.61
73 15 0.20
75 4 0.05
76 11 0.14
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (75 bp):
CTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGACACAAATCATGTTTTAAG
AAAAACAAAT
Found at i:2425707 original size:183 final size:183
Alignment explanation
Indices: 2425399--2425935 Score: 932
Period size: 183 Copynumber: 2.9 Consensus size: 183
2425389 ATCAGGATTA
*
2425399 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * **
2425464 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCTGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
* * *
2425528 TTCCACTATAACCAATTGCCTTAGTGGAATAGCTCAACTTTAGAGGGATAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * * *
2425582 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGAAAAAAGTAGTGGAGAAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
2425647 GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGACAGGGCTTTCGAGTT
66 GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
2425712 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
2425765 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
2425830 GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTTGAGTT
66 GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
2425895 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
2425936 CGGATTTAAT
Statistics
Matches: 334, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
183 333 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:2430918 original size:24 final size:25
Alignment explanation
Indices: 2430868--2430919 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
2430858 GTTTTTTTTA
*
2430868 AAAAAAATAATATAATAATAATGAAT
1 AAAAAAATAAAATAATAATAA-GAAT
2430894 AAAAAAATGAAAATAATAA-AA-AAT
1 AAAAAAAT-AAAATAATAATAAGAAT
2430918 AA
1 AA
2430920 TATAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.21
26 10 0.42
27 9 0.38
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (25 bp):
AAAAAAATAAAATAATAATAAGAAT
Found at i:2431145 original size:18 final size:17
Alignment explanation
Indices: 2431124--2431174 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
2431114 ATATATATAT
2431124 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
2431142 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
2431159 ATATATAATAAATAAA
1 ATA-ATAAT-AATAAA
2431175 GGGACTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 7 0.24
18 16 0.55
19 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:2431148 original size:21 final size:20
Alignment explanation
Indices: 2431120--2431174 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
2431110 AAATATATAT
2431120 ATATATAATAATAATAACATGA
1 ATATATAATAA-AATAA-ATGA
2431142 ATA-AT-A-AAAATAAATGA
1 ATATATAATAAAATAAATGA
2431159 ATATATAAT-AAATAAA
1 ATATATAATAAAATAAA
2431175 GGGACTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.23
18 7 0.23
19 10 0.33
20 1 0.03
21 2 0.07
22 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
ATATATAATAAAATAAATGA
Found at i:2434149 original size:11 final size:11
Alignment explanation
Indices: 2434133--2434173 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2434123 TTACTGTTGA
2434133 TTTTTTTTTAT
1 TTTTTTTTTAT
2434144 TTTTTTTTTA-
1 TTTTTTTTTAT
*
2434154 -TTTCTTTTAT
1 TTTTTTTTTAT
*
2434164 TTTTATTTTA
1 TTTTTTTTTA
2434174 GTCTTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 8 0.31
11 18 0.69
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTAT
Found at i:2434151 original size:15 final size:15
Alignment explanation
Indices: 2434133--2434171 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2434123 TTACTGTTGA
2434133 TTTTTT-TTTATTTT
1 TTTTTTATTTATTTT
*
2434147 TTTTTTATTTCTTTT
1 TTTTTTATTTATTTT
*
2434162 ATTTTTATTT
1 TTTTTTATTT
2434172 TAGTCTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTATTTATTTT
Found at i:2434180 original size:18 final size:19
Alignment explanation
Indices: 2434138--2434197 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
2434128 GTTGATTTTT
* *
2434138 TTTTATTTTTTTTTTATTTC
1 TTTTATTTTTATTTTA-GTC
2434158 TTTTATTTTTATTTTAGTC
1 TTTTATTTTTATTTTAGTC
* *
2434177 -TTTATATTTAATTTAGT-
1 TTTTATTTTTATTTTAGTC
2434194 TTTT
1 TTTT
2434198 TTGTTTGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 18 0.51
19 2 0.06
20 15 0.43
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTTATTTTTATTTTAGTC
Found at i:2434184 original size:20 final size:20
Alignment explanation
Indices: 2434138--2434185 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2434128 GTTGATTTTT
* *
2434138 TTTTATTTTTTTTTTATTTC
1 TTTTATTTTTATTTTATGTC
2434158 TTTTATTTTTATTTTA-GTC
1 TTTTATTTTTATTTTATGTC
2434177 TTTATATTT
1 TTT-TATTT
2434186 AATTTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTATTTTTATTTTATGTC
Found at i:2436249 original size:25 final size:26
Alignment explanation
Indices: 2436212--2436263 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
2436202 ATGATAAAGA
* *
2436212 TAAAAGAGTTTTACTA-CTTTTTTAT
1 TAAAAGAGATTTACTACCTCTTTTAT
*
2436237 TAAAAGAGATTTATTACCTCTTTTAT
1 TAAAAGAGATTTACTACCTCTTTTAT
2436263 T
1 T
2436264 CCAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.50
Consensus pattern (26 bp):
TAAAAGAGATTTACTACCTCTTTTAT
Found at i:2436296 original size:491 final size:491
Alignment explanation
Indices: 2435374--2436323 Score: 1758
Period size: 491 Copynumber: 1.9 Consensus size: 491
2435364 TGTATAAAAG
*
2435374 TGTTATATTTTCTACCCTTTTCCCATATTTATTGCTAGATTTAGGCTCAGTTTAGTTGCATTATT
1 TGTTATATTTTCTACCCTTTTCCCATATTTATTGCTAGATTTAGGCTCAATTTAGTTGCATTATT
*
2435439 AGTCATTCATGCATGATTTCATAGTTTACTTCAACGTTAAGTTTGGTATTACATTTTGGTTGGTT
66 AGTCATTCATGCATGATTTCATAATTTACTTCAACGTTAAGTTTGGTATTACATTTTGGTTGGTT
*
2435504 TTTGTTGAAAAGATAATGTTAGTGTGTATTAATTTGTGTAGATTAGGAATTTCCCTAGCAAGCAG
131 TTTGTTGAAAAGATAATGCTAGTGTGTATTAATTTGTGTAGATTAGGAATTTCCCTAGCAAGCAG
*
2435569 AAAATTACGTGCCATTTGAAGCTGACTTTTGAAGAGGTCTACCTAATTCAAGATAATCACGGCAC
196 AAAATTACGTGCCATTTGAAGCTGACTTTTGAAGAGGTCTACCTAATTCAAGATAATCACAGCAC
* *
2435634 AAGGGGATAAGCCCTAGAAAAGTGGATATTCATGCAGAATTTAAGGAAGAAAAGAGGTCTTATTT
261 AAGGGGATAAGCCCTAGAAAAGTGGATATTCATGCAGAATTTAAAGAAGAAAAGAAGTCTTATTT
* * *
2435699 TCGAGGAATTTGATGATAAAGATAAAAGAGTTTTACTTCTTTTTTATTAAAAGATATTTATTACC
326 TCAAGGAATTTGATGATAAAGATAAAAGAGTTTTACTACTTTTTTATTAAAAGAGATTTATTACC
2435764 TCTTTTATTCCAATTAAAACTCTTCTTCATCAATAACCAAAGTTAACCTAATCATCCTCTATAAA
391 TCTTTTATTCCAATTAAAACTCTTCTTCATCAATAACCAAAGTTAACCTAATCATCCTCTATAAA
2435829 TAAGAAGGAGGCACAATAAGAAAAATGGATTATTAA
456 TAAGAAGGAGGCACAATAAGAAAAATGGATTATTAA
2435865 TGTTATATTTTCTACCCTTTTCCCATATTTATTGCTAGATTTAGGCTCAATTTAGTTGCATTATT
1 TGTTATATTTTCTACCCTTTTCCCATATTTATTGCTAGATTTAGGCTCAATTTAGTTGCATTATT
* *
2435930 AGTCATTCATGCCTGATTTCATAATTTACTTCACCGTTAAGTTTGAG-ATTACATTTTGGTTGGT
66 AGTCATTCATGCATGATTTCATAATTTACTTCAACGTTAAGTTTG-GTATTACATTTTGGTTGGT
* *
2435994 TTTTGTTGAAAAGATACTGCTAGTGTGTGTTAATTTGTGTAGATTAGGAATTTCCCTAGCAAGCA
130 TTTTGTTGAAAAGATAATGCTAGTGTGTATTAATTTGTGTAGATTAGGAATTTCCCTAGCAAGCA
2436059 GAAAATTACGTGCCATTTGAAGCTGACTTTTGAAGAGGTCTACCTAATTCAAGATAATCACAGCA
195 GAAAATTACGTGCCATTTGAAGCTGACTTTTGAAGAGGTCTACCTAATTCAAGATAATCACAGCA
2436124 CAAGGGGATAAGCCCTAGAAAAGTGGATATTCATGCAGAATTTAAAGAAGAAAAGAAGTCTTATT
260 CAAGGGGATAAGCCCTAGAAAAGTGGATATTCATGCAGAATTTAAAGAAGAAAAGAAGTCTTATT
*
2436189 TTCAAGGGATTTGATGATAAAGATAAAAGAGTTTTACTACTTTTTTATTAAAAGAGATTTATTAC
325 TTCAAGGAATTTGATGATAAAGATAAAAGAGTTTTACTACTTTTTTATTAAAAGAGATTTATTAC
2436254 CTCTTTTATTCCAATTAAAACTCTTCTTCATCAATAACCAAAGTTAACCTAATCATCCTCTATAA
390 CTCTTTTATTCCAATTAAAACTCTTCTTCATCAATAACCAAAGTTAACCTAATCATCCTCTATAA
2436319 ATAAG
455 ATAAG
2436324 GAGGCGCAAC
Statistics
Matches: 444, Mismatches: 14, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
491 443 1.00
492 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (491 bp):
TGTTATATTTTCTACCCTTTTCCCATATTTATTGCTAGATTTAGGCTCAATTTAGTTGCATTATT
AGTCATTCATGCATGATTTCATAATTTACTTCAACGTTAAGTTTGGTATTACATTTTGGTTGGTT
TTTGTTGAAAAGATAATGCTAGTGTGTATTAATTTGTGTAGATTAGGAATTTCCCTAGCAAGCAG
AAAATTACGTGCCATTTGAAGCTGACTTTTGAAGAGGTCTACCTAATTCAAGATAATCACAGCAC
AAGGGGATAAGCCCTAGAAAAGTGGATATTCATGCAGAATTTAAAGAAGAAAAGAAGTCTTATTT
TCAAGGAATTTGATGATAAAGATAAAAGAGTTTTACTACTTTTTTATTAAAAGAGATTTATTACC
TCTTTTATTCCAATTAAAACTCTTCTTCATCAATAACCAAAGTTAACCTAATCATCCTCTATAAA
TAAGAAGGAGGCACAATAAGAAAAATGGATTATTAA
Found at i:2440849 original size:21 final size:23
Alignment explanation
Indices: 2440798--2440849 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
2440788 AGAGTGAATA
2440798 AAGCTAAAAAAGGATAATAAAATG
1 AAGC-AAAAAAGGATAATAAAATG
* *
2440822 AA-AAAAAAAGTA-AATAAAAT-
1 AAGCAAAAAAGGATAATAAAATG
2440842 AAGCAAAA
1 AAGCAAAA
2440850 TGAAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 2 0.08
21 12 0.50
22 8 0.33
24 2 0.08
ACGTcount: A:0.71, C:0.04, G:0.12, T:0.13
Consensus pattern (23 bp):
AAGCAAAAAAGGATAATAAAATG
Found at i:2440891 original size:10 final size:9
Alignment explanation
Indices: 2440851--2440967 Score: 55
Period size: 9 Copynumber: 12.8 Consensus size: 9
2440841 TAAGCAAAAT
2440851 GAAAATAAA
1 GAAAATAAA
*
2440860 GAAACAGAAA
1 GAAA-ATAAA
* *
2440870 CAAAATAGA
1 GAAAATAAA
2440879 -AAAATAAA
1 GAAAATAAA
2440887 GAAAATAAA
1 GAAAATAAA
* *
2440896 -TAAACAAA
1 GAAAATAAA
2440904 GTAAAAT-AA
1 G-AAAATAAA
2440913 -AAAATAAA
1 GAAAATAAA
* *
2440921 AATAAAGACAA
1 GA-AAATA-AA
2440932 GAGAAATAAA
1 GA-AAATAAA
2440942 TG-AAATAAA
1 -GAAAATAAA
* *
2440951 TAAAATATA
1 GAAAATAAA
2440960 GACAAATA
1 GA-AAATA
2440968 TAGTAAAAGT
Statistics
Matches: 81, Mismatches: 16, Indels: 21
0.69 0.14 0.18
Matches are distributed among these distances:
7 5 0.06
8 15 0.19
9 32 0.40
10 21 0.26
11 8 0.10
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.14
Consensus pattern (9 bp):
GAAAATAAA
Found at i:2440891 original size:17 final size:17
Alignment explanation
Indices: 2440871--2440920 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
2440861 AAACAGAAAC
2440871 AAAATAGAAAAATAAAG-
1 AAAATA-AAAAATAAAGT
*
2440888 AAAATAAATAAACAAAGT
1 AAAATAAA-AAATAAAGT
2440906 AAAATAAAAAATAAA
1 AAAATAAAAAATAAA
2440921 AATAAAGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 2 0.07
17 19 0.66
18 8 0.28
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAATAAAAAATAAAGT
Found at i:2440898 original size:13 final size:13
Alignment explanation
Indices: 2440880--2440954 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 13
2440870 CAAAATAGAA
2440880 AAATAAAGAAAAT
1 AAATAAAGAAAAT
* *
2440893 AAATAAACAAAGT
1 AAATAAAGAAAAT
*
2440906 AAAATAAA-AAATAA
1 -AAATAAAGAAA-AT
*
2440920 AAATAAAGACAAGAG
1 AAATAAAGA-AA-AT
2440935 AAATAAATG-AAAT
1 AAATAAA-GAAAAT
2440948 AAATAAA
1 AAATAAA
2440955 ATATAGACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 29 0.58
14 10 0.20
15 10 0.20
16 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.15
Consensus pattern (13 bp):
AAATAAAGAAAAT
Found at i:2441108 original size:38 final size:38
Alignment explanation
Indices: 2441030--2441128 Score: 91
Period size: 38 Copynumber: 2.7 Consensus size: 38
2441020 TAGTATATGT
* * * ***
2441030 AAAAAATAAAAAAATATCATGTATATATATAAAGGTAA
1 AAAAAATAAAAAAATATAATATATATATAAAAAACCAA
2441068 AAAAAATAAAAAAATATAATATA-ATAGTAAAAAACC--
1 AAAAAATAAAAAAATATAATATATATA-TAAAAAACCAA
*
2441104 -AAAAATAGAAAAATAT-ATATATATA
1 AAAAAATAAAAAAATATAATATATATA
2441129 CAATTATAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
34 5 0.10
35 18 0.35
37 3 0.06
38 26 0.50
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (38 bp):
AAAAAATAAAAAAATATAATATATATATAAAAAACCAA
Found at i:2443353 original size:43 final size:42
Alignment explanation
Indices: 2443251--2443370 Score: 161
Period size: 43 Copynumber: 2.9 Consensus size: 42
2443241 TATAAAGTTA
*
2443251 CACGATATCCTTCATCGTGAAGTTAAAATCGTGGA-TGTGGG
1 CACGATATCCTTCATCGTGGAGTTAAAATCGTGGATTGTGGG
* * * *
2443292 CACGATATCCTTCGTCGTGGAGTTGAAATCATGGATTTTTGGG
1 CACGATATCCTTCATCGTGGAGTTAAAATCGTGGA-TTGTGGG
* *
2443335 TACGATATCCTTCATCGTGGACTTAAAATCGTGGAT
1 CACGATATCCTTCATCGTGGAGTTAAAATCGTGGAT
2443371 GGCTCATTCG
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 31 0.46
42 1 0.01
43 35 0.52
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
CACGATATCCTTCATCGTGGAGTTAAAATCGTGGATTGTGGG
Done.