Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 62 of 195
Found at i:12468951 original size:13 final size:13
Alignment explanation
Indices: 12468928--12468975 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
12468918 AAATTTAGGG
12468928 TTTCA-TTTAAGA
1 TTTCATTTTAAGA
12468940 TTTCATTTTAAGA
1 TTTCATTTTAAGA
* *
12468953 TTTCACTTTAAGG
1 TTTCATTTTAAGA
12468966 TTTCATTTTA
1 TTTCATTTTA
12468976 GGGTTTTGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 5 0.16
13 27 0.84
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTCATTTTAAGA
Found at i:12468980 original size:13 final size:13
Alignment explanation
Indices: 12468921--12468981 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
12468911 TCACATAAAA
*
12468921 TTTAGGGTTTCA-
1 TTTAAGGTTTCAT
*
12468933 TTTAAGATTTCAT
1 TTTAAGGTTTCAT
* *
12468946 TTTAAGATTTCAC
1 TTTAAGGTTTCAT
12468959 TTTAAGGTTTCAT
1 TTTAAGGTTTCAT
*
12468972 TTTAGGGTTT
1 TTTAAGGTTT
12468982 TGGATTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
12 10 0.24
13 32 0.76
ACGTcount: A:0.23, C:0.08, G:0.16, T:0.52
Consensus pattern (13 bp):
TTTAAGGTTTCAT
Found at i:12469211 original size:15 final size:15
Alignment explanation
Indices: 12469127--12469218 Score: 57
Period size: 15 Copynumber: 6.3 Consensus size: 15
12469117 TAAAAAATGA
12469127 ATTTTTATATTTTA-T
1 ATTTTTAT-TTTTATT
* *
12469142 ATTTTTAGTATTATT
1 ATTTTTATTTTTATT
* *
12469157 TTTTTTAATTTTTA-A
1 ATTTTT-ATTTTTATT
* **
12469172 AATTTTA-AATTATT
1 ATTTTTATTTTTATT
* *
12469186 -TATTTACTTTTATT
1 ATTTTTATTTTTATT
12469200 ATTTTTATTTTTATT
1 ATTTTTATTTTTATT
12469215 ATTT
1 ATTT
12469219 AATAATTCTC
Statistics
Matches: 55, Mismatches: 17, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
13 7 0.13
14 10 0.18
15 33 0.60
16 5 0.09
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (15 bp):
ATTTTTATTTTTATT
Found at i:12475112 original size:14 final size:13
Alignment explanation
Indices: 12475095--12475124 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
12475085 AAATAATACT
12475095 AAAAAAATCAAGTA
1 AAAAAAATCAAG-A
12475109 AAAAAAATCAAGA
1 AAAAAAATCAAGA
12475122 AAA
1 AAA
12475125 CTCCCTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (13 bp):
AAAAAAATCAAGA
Found at i:12495859 original size:51 final size:51
Alignment explanation
Indices: 12495803--12495913 Score: 204
Period size: 51 Copynumber: 2.2 Consensus size: 51
12495793 TTGAGATGAG
*
12495803 GGATCGATCGGTTATGGTCTTTGCATTGAGTCGATTGATTGGTTTTGAAAA
1 GGATCGATCGGTTATGGTCTTTGCATTGAGCCGATTGATTGGTTTTGAAAA
*
12495854 GGATCGATCGGTTATGGTCTTTGCATTGAGCCGATTGATTGGTTTTGAAAG
1 GGATCGATCGGTTATGGTCTTTGCATTGAGCCGATTGATTGGTTTTGAAAA
12495905 GGATCGATC
1 GGATCGATC
12495914 AGTTTTGCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.37
Consensus pattern (51 bp):
GGATCGATCGGTTATGGTCTTTGCATTGAGCCGATTGATTGGTTTTGAAAA
Found at i:12495888 original size:27 final size:27
Alignment explanation
Indices: 12495806--12495888 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
12495796 AGATGAGGGA
12495806 TCGATCGGTTATGGTCTTTGCATTGAG
1 TCGATCGGTTATGGTCTTTGCATTGAG
* * * **
12495833 TCGAT-TGAT-TGGT-TTTGAAAAG-G
1 TCGATCGGTTATGGTCTTTGCATTGAG
12495856 ATCGATCGGTTATGGTCTTTGCATTGAG
1 -TCGATCGGTTATGGTCTTTGCATTGAG
*
12495884 CCGAT
1 TCGAT
12495889 TGATTGGTTT
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
23 1 0.03
24 11 0.28
25 6 0.15
26 6 0.15
27 15 0.38
28 1 0.03
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (27 bp):
TCGATCGGTTATGGTCTTTGCATTGAG
Found at i:12503541 original size:123 final size:123
Alignment explanation
Indices: 12503322--12503564 Score: 360
Period size: 123 Copynumber: 2.0 Consensus size: 123
12503312 TAGATTTGTA
* * * * * *
12503322 CCACCTATACCATTTGAGCATAAAGTCATTATAATTGGATTTGTTAATTATTGTTATTTTGTGCA
1 CCACCTATACCATTGGAGCACAAAATCATTACAATTGGATTTGTTAATGATTGTCATTTTGTGCA
* * * *
12503387 AGTATTGCTAATTAGTGTTGATATTTATGTTTATATTATTGATAATGACATTATATTG
66 AGTACTACTAATTAATGTTGATATTTATGTTTACATTATTGATAATGACATTATATTG
* * *
12503445 CCACCTATATCATTGGAGCACAAAATCATTACGATTGGATTTGTTAATGATTGTCATTTTGTGTA
1 CCACCTATACCATTGGAGCACAAAATCATTACAATTGGATTTGTTAATGATTGTCATTTTGTGCA
*
12503510 GGTACTACTAATTAATGTTGATATTTATGTTTACATTATTGATAATGACATTATA
66 AGTACTACTAATTAATGTTGATATTTATGTTTACATTATTGATAATGACATTATA
12503565 CTTATCATTT
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
123 106 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (123 bp):
CCACCTATACCATTGGAGCACAAAATCATTACAATTGGATTTGTTAATGATTGTCATTTTGTGCA
AGTACTACTAATTAATGTTGATATTTATGTTTACATTATTGATAATGACATTATATTG
Found at i:12504635 original size:21 final size:21
Alignment explanation
Indices: 12504586--12504628 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
12504576 AAATTTCATG
* *
12504586 AAATCAATCTTGAAATAAGAA
1 AAATAAATCTTGAAATAACAA
12504607 AAATAAATCTTTGAAATAACAA
1 AAATAAATC-TTGAAATAACAA
12504629 CAAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (21 bp):
AAATAAATCTTGAAATAACAA
Found at i:12508208 original size:12 final size:12
Alignment explanation
Indices: 12508191--12508243 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
12508181 TCACTCTTGT
*
12508191 AACAATAACAAC
1 AACAATAATAAC
12508203 AACAATAATAAC
1 AACAATAATAAC
*
12508215 ATCAATAATAAC
1 AACAATAATAAC
* *
12508227 ATCAATAATATC
1 AACAATAATAAC
12508239 AACAA
1 AACAA
12508244 CATAAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
AACAATAATAAC
Found at i:12508227 original size:21 final size:21
Alignment explanation
Indices: 12508197--12508271 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
12508187 TTGTAACAAT
12508197 AACAACAACAATAATAACATC
1 AACAACAACAATAATAACATC
* * *
12508218 AATAATAAC-ATCAATAATATC
1 AACAACAACAAT-AATAACATC
*
12508239 AACAACATA-AATAATATCATC
1 AACAACA-ACAATAATAACATC
12508260 AACAACAACAAT
1 AACAACAACAAT
12508272 CAACCAATTC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 3 0.07
21 37 0.86
22 3 0.07
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (21 bp):
AACAACAACAATAATAACATC
Found at i:12508236 original size:15 final size:14
Alignment explanation
Indices: 12508194--12508261 Score: 52
Period size: 15 Copynumber: 4.8 Consensus size: 14
12508184 CTCTTGTAAC
*
12508194 AATAACAACAACAAT
1 AATAACATCAA-AAT
12508209 AATAACATC--AAT
1 AATAACATCAAAAT
12508221 AATAACATCAATAAT
1 AATAACATCAA-AAT
*
12508236 -ATCAACAACATAAAT
1 AAT-AACATCA-AAAT
*
12508251 AATATCATCAA
1 AATAACATCAA
12508262 CAACAACAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
12 12 0.28
14 3 0.07
15 25 0.58
16 3 0.07
ACGTcount: A:0.60, C:0.18, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAACATCAAAAT
Found at i:12508251 original size:18 final size:18
Alignment explanation
Indices: 12508224--12508263 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12508214 CATCAATAAT
*
12508224 AACATCAATAATATCAAC
1 AACATAAATAATATCAAC
*
12508242 AACATAAATAATATCATC
1 AACATAAATAATATCAAC
12508260 AACA
1 AACA
12508264 ACAACAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (18 bp):
AACATAAATAATATCAAC
Found at i:12508845 original size:38 final size:38
Alignment explanation
Indices: 12508798--12508872 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
12508788 TAGAAAATGG
*
12508798 ATTTCCATAAGCTTTAA-AAGGCTTTCAAAAATCCATTC
1 ATTTCCATAAGCTTTAATAA-CCTTTCAAAAATCCATTC
*
12508836 ATTTTCATAAGCTTTAATAACCTTTCAAAAATCCATT
1 ATTTCCATAAGCTTTAATAACCTTTCAAAAATCCATT
12508873 TTTGAAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 32 0.94
39 2 0.06
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (38 bp):
ATTTCCATAAGCTTTAATAACCTTTCAAAAATCCATTC
Found at i:12509457 original size:3 final size:3
Alignment explanation
Indices: 12509449--12509481 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12509439 TAACTATCCA
12509449 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12509482 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12509601 original size:2 final size:2
Alignment explanation
Indices: 12509596--12509626 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12509586 ATATATATAA
12509596 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12509627 TTTCAACTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12510353 original size:35 final size:36
Alignment explanation
Indices: 12510297--12510368 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
12510287 AAAATAAAAA
12510297 TAAATAAAAGTTTTTCCATAAAATATTAAATTAATC
1 TAAATAAAAGTTTTTCCATAAAATATTAAATTAATC
*
12510333 TAAATAAAA-TTTTTTCATAAAATATTAAATTAATC
1 TAAATAAAAGTTTTTCCATAAAATATTAAATTAATC
12510368 T
1 T
12510369 TATAATAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 26 0.74
36 9 0.26
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (36 bp):
TAAATAAAAGTTTTTCCATAAAATATTAAATTAATC
Found at i:12511382 original size:125 final size:124
Alignment explanation
Indices: 12511230--12511507 Score: 312
Period size: 125 Copynumber: 2.2 Consensus size: 124
12511220 GTTGAAGTCA
* * * * *
12511230 TTTTTGGCCAGAAAACGCCTTGAATAATCCCTTA-AAAAAATTGAATGAGG-TTATTCAAGGTGT
1 TTTTTGGCCA-AAAACACCTTCAATAATCCCTTACAAAAAATTGAAGGAGGATTATTAAAGGTGG
12511293 TTTATGACAAAAAACG-CTCTCAATAATCCATCAAAAAATTATGGACAGAGAATATTGAAGGTG
65 TTT-TGACAAAAAACGCCT-TCAATAAT-CATCAAAAAATTATGGA-AGAGAATATTGAAGGTG
* ***
12511356 TTTTTGGCCAAAAACATCTTCAATAAT-CCTTACAAAAAATTTTGGGAGGATTATTAAAGGTGGT
1 TTTTTGGCCAAAAACACCTTCAATAATCCCTTACAAAAAATTGAAGGAGGATTATTAAAGGTGGT
* * * * ** * * *
12511420 TTTGTCTAAAAATGCCTTCAATAATCTTCTGAAAATTTTGGAAGGGATTATTGAAGGTG
66 TTTGACAAAAAACGCCTTCAATAATCATCAAAAAATTATGGAAGAGAATATTGAAGGTG
*
12511479 TTTTTGGCAAAAAACACCTTCAATAATCC
1 TTTTTGGCCAAAAACACCTTCAATAATCC
12511508 ACTCAATAAA
Statistics
Matches: 128, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
123 40 0.31
124 19 0.15
125 43 0.34
126 26 0.20
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (124 bp):
TTTTTGGCCAAAAACACCTTCAATAATCCCTTACAAAAAATTGAAGGAGGATTATTAAAGGTGGT
TTTGACAAAAAACGCCTTCAATAATCATCAAAAAATTATGGAAGAGAATATTGAAGGTG
Found at i:12511628 original size:63 final size:62
Alignment explanation
Indices: 12511150--12511631 Score: 340
Period size: 64 Copynumber: 7.7 Consensus size: 62
12511140 TAGGTTTTTC
** * * * * *
12511150 AAGGGATTATTCCAGGTATTTTTGGTCAAAAACACCTTCAATACTCCTCTCGAAACAA--TGGG
1 AAGGGATTATTGAAGGTGTTTTTGGTCAAAAACACCTTCAATAATCC-ATC-AAAAAATTTTGG
* * * * * * * *
12511212 AAGGGATTGTTGAA-GTCATTTTTGGCCAGAAAACGCCTTGAATAATCCCTTAAAAAA-ATT-G
1 AAGGGATTATTGAAGGT-GTTTTTGGTCA-AAAACACCTTCAATAATCCATCAAAAAATTTTGG
* * *
12511273 AATGAGG-TTATTCAAGGTGTTTTAT-GACAAAAA-ACGCTCTCAATAATCCATCAAAAAATTAT
1 AA-G-GGATTATTGAAGGTGTTTT-TGGTCAAAAACAC-CT-TCAATAATCCATCAAAAAATTTT
12511335 GG
61 GG
* * * * *
12511337 ACAGAGAATATTGAAGGTGTTTTTGGCCAAAAACATCTTCAATAATCCTTACAAAAAATTTTGG
1 A-AGGGATTATTGAAGGTGTTTTTGGTCAAAAACACCTTCAATAATCCAT-CAAAAAATTTTGG
* * * ** * **
12511401 GA-GGATTATTAAAGGTGGTTTT-GTCTAAAAATGCCTTCAATAAT-CTTCTGAAAATTTTGG
1 AAGGGATTATTGAAGGTGTTTTTGGTC-AAAAACACCTTCAATAATCCATCAAAAAATTTTGG
* **
12511461 AAGGGATTATTGAAGGTGTTTTTGG-CAAAAAACACCTTCAATAATCCACTCAATAAATTTTTAT
1 AAGGGATTATTGAAGGTGTTTTTGGTC-AAAAACACCTTCAATAATCCA-TCAA-AAAATTTTGG
* ** * **
12511525 AAGAGATTATTGAAGGCATTTTTGGTCAAAATCACCTTCAATAATTGATACAAAAAATTTTGG
1 AAGGGATTATTGAAGGTGTTTTTGGTCAAAAACACCTTCAATAATCCAT-CAAAAAATTTTGG
* * * *
12511588 AGGGGATTATTGAAGGTGTTTTTAGTTAGAAACACCTTCAATAA
1 AAGGGATTATTGAAGGTGTTTTTGGTCAAAAACACCTTCAATAA
12511632 CCCCATTCAA
Statistics
Matches: 329, Mismatches: 67, Indels: 47
0.74 0.15 0.11
Matches are distributed among these distances:
60 13 0.04
61 56 0.17
62 87 0.26
63 82 0.25
64 88 0.27
65 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (62 bp):
AAGGGATTATTGAAGGTGTTTTTGGTCAAAAACACCTTCAATAATCCATCAAAAAATTTTGG
Found at i:12511683 original size:127 final size:127
Alignment explanation
Indices: 12511324--12511683 Score: 319
Period size: 127 Copynumber: 2.9 Consensus size: 127
12511314 AATAATCCAT
* * * * * * *
12511324 CAAAAAATTATGGACAGAGAATATTGAAGGTGTTTTTGGCCAAAAACATCTTCAATAATCC-TTA
1 CAAAAAATTTTGGA-AGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTTCAATAATCCACT-
* *** * *** *
12511388 CAA-AAAATTTTGGGAG-GATTATTAAAGGTGGTTTTGTCTAAAAAT-GCCTTCAATAATCT--T
64 CAATAAATTTTTATAAGAGATTATTCAAGGCATTTTTG-CTAAAAATCACCTTCAATAAT-TGAT
12511448 -
127 A
** *
12511448 CTGAAAATTTTGGAAGGGATTATTGAAGGTGTTTTTGGCAAAAAACACCTTCAATAATCCACTCA
1 CAAAAAATTTTGGAAGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTTCAATAATCCACTCA
* * *
12511513 ATAAATTTTTATAAGAGATTATTGAAGGCATTTTTGGTCAAAATCACCTTCAATAATTGATA
66 ATAAATTTTTATAAGAGATTATTCAAGGCATTTTTGCTAAAAATCACCTTCAATAATTGATA
* ** *
12511575 CAAAAAATTTTGGAGGGGATTATTGAAGGTGTTTTTAGTTAGAAACACCTTCAATAA-CC-C-CA
1 CAAAAAATTTTGGAAGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTTCAATAATCCACTCA
* *
12511637 TTCAACA-TTTTGTAAGAGATTATTCAAGGCACTTTTTAGCTAAAAAT
66 AT-AA-ATTTTTATAAGAGATTATTCAAGGCA-TTTTT-GCTAAAAAT
12511684 GCCTTCAGTA
Statistics
Matches: 194, Mismatches: 31, Indels: 19
0.80 0.13 0.08
Matches are distributed among these distances:
123 45 0.23
124 31 0.16
125 52 0.27
126 9 0.05
127 57 0.29
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (127 bp):
CAAAAAATTTTGGAAGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTTCAATAATCCACTCA
ATAAATTTTTATAAGAGATTATTCAAGGCATTTTTGCTAAAAATCACCTTCAATAATTGATA
Found at i:12511707 original size:127 final size:127
Alignment explanation
Indices: 12511312--12511712 Score: 313
Period size: 127 Copynumber: 3.2 Consensus size: 127
12511302 AAAAACGCTC
* * * * * * *
12511312 TCAATAATCCAT-CAAAAAATTATGGACAGAGAATATTGAAGGTGTTTTTGGCCAAAAACATCTT
1 TCAATAATCCATAAAAAAAATTTTGGA-AGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTT
* * *** * *** *
12511376 CAATAATCC-TTACAA-AAAATTTTGGGAG-GATTATTAAAGGTGGTTTTGTCTAAAAAT-GCCT
65 CAATAATCCACT-CAATAAATTTTTATAAGAGATTATTCAAGGCATTTTTG-CTAAAAATCACCT
**** *
12511437 TCAATAAT-C-TTCTGAAAATTTTGGAAGGGATTATTGAAGGTGTTTTTGGCAAAAAACACCTTC
1 TCAATAATCCATAAAAAAAATTTTGGAAGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTTC
* * *
12511500 AATAATCCACTCAATAAATTTTTATAAGAGATTATTGAAGGCATTTTTGGTCAAAATCACCT
66 AATAATCCACTCAATAAATTTTTATAAGAGATTATTCAAGGCATTTTTGCTAAAAATCACCT
** * * ** *
12511562 TCAATAATTGATACAAAAAATTTTGGAGGGGATTATTGAAGGTGTTTTTAGTTAGAAACACCTTC
1 TCAATAATCCATAAAAAAAATTTTGGAAGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTTC
* * *
12511627 AATAA-CC-C-CATTCAACA-TTTTGTAAGAGATTATTCAAGGCACTTTTTAGCTAAAAAT-GCC
66 AATAATCCACTCAAT-AA-ATTTTTATAAGAGATTATTCAAGGCA-TTTTT-GCTAAAAATCACC
12511687 T
127 T
*
12511688 TCAGTAATCCCATAAAAAAACATTT
1 TCAATAAT-CCATAAAAAAA-ATTT
12511713 GGTTTAATTA
Statistics
Matches: 225, Mismatches: 38, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
123 46 0.20
124 31 0.14
125 60 0.27
126 18 0.08
127 66 0.29
128 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (127 bp):
TCAATAATCCATAAAAAAAATTTTGGAAGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTTC
AATAATCCACTCAATAAATTTTTATAAGAGATTATTCAAGGCATTTTTGCTAAAAATCACCT
Found at i:12511714 original size:127 final size:127
Alignment explanation
Indices: 12511312--12511714 Score: 312
Period size: 125 Copynumber: 3.2 Consensus size: 127
12511302 AAAAACGCTC
* * * * *
12511312 TCAATAATCCAT-C-AAAAAATTATGGACAGAGAATATTGAAGGTGTTTTTGGCCAAAAACATCT
1 TCAATAATCCATACAAAAAAATT-TGGA-AGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCT
* * *** * *** *
12511375 TCAATAATCC-TTACAA-AAAATTTTGGGAG-GATTATTAAAGGTGGTTTTGTCTAAAAAT-GCC
64 TCAATAATCCACT-CAATAAATTTTTATAAGAGATTATTCAAGGCATTTTTG-CTAAAAATCACC
12511436 T
127 T
* ** * *
12511437 TCAATAAT-C-TTCTGAAAATTTTGGAAGGGATTATTGAAGGTGTTTTTGGCAAAAAACACCTTC
1 TCAATAATCCATACAAAAAAATTTGGAAGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTTC
* * *
12511500 AATAATCCACTCAATAAATTTTTATAAGAGATTATTGAAGGCATTTTTGGTCAAAATCACCT
66 AATAATCCACTCAATAAATTTTTATAAGAGATTATTCAAGGCATTTTTGCTAAAAATCACCT
** * * ** *
12511562 TCAATAATTGATACAAAAAATTTTGGAGGGGATTATTGAAGGTGTTTTTAGTTAGAAACACCTTC
1 TCAATAATCCATACAAAAAAATTTGGAAGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTTC
* * *
12511627 AATAA-CC-C-CATTCAACA-TTTTGTAAGAGATTATTCAAGGCACTTTTTAGCTAAAAAT-GCC
66 AATAATCCACTCAAT-AA-ATTTTTATAAGAGATTATTCAAGGCA-TTTTT-GCTAAAAATCACC
12511687 T
127 T
*
12511688 TCAGTAATCCCATA-AAAAAACATTTGG
1 TCAATAAT-CCATACAAAAAA-ATTTGG
12511715 TTTAATTATA
Statistics
Matches: 227, Mismatches: 37, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
123 46 0.20
124 25 0.11
125 66 0.29
126 24 0.11
127 66 0.29
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (127 bp):
TCAATAATCCATACAAAAAAATTTGGAAGGGATTATTGAAGGTGTTTTTAGCAAAAAACACCTTC
AATAATCCACTCAATAAATTTTTATAAGAGATTATTCAAGGCATTTTTGCTAAAAATCACCT
Found at i:12511780 original size:35 final size:35
Alignment explanation
Indices: 12511729--12511800 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
12511719 ATTATATATG
*
12511729 TGAAGTTAGTTTTAGGTTTATGCCCAGAAAACATT
1 TGAAGTTAGTTGTAGGTTTATGCCCAGAAAACATT
*
12511764 TGAAGTTAGTTGTAGGTTTATGTCCAGAAAACATT
1 TGAAGTTAGTTGTAGGTTTATGCCCAGAAAACATT
12511799 TG
1 TG
12511801 GTTTATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.38
Consensus pattern (35 bp):
TGAAGTTAGTTGTAGGTTTATGCCCAGAAAACATT
Found at i:12516123 original size:62 final size:62
Alignment explanation
Indices: 12516057--12516290 Score: 233
Period size: 62 Copynumber: 3.8 Consensus size: 62
12516047 TTTTCTTTAA
* ** *
12516057 AAAATTGAATAGGATTATT-ACAGGCGTTTTTAGTAAAAAATGAGTTCAATAATCCCCTCATC
1 AAAATTGAAGAGGATTATTGA-AGGCGTTTTTAGTAAAAAATGCCTTCAATAATCTCCTCATC
* ** * * * * *
12516119 AAAATTTAATGA-GATTATTGAAGATGTTTTTAGTAGACAATGCCTTGAATAATATCCTAAT-
1 AAAATTGAA-GAGGATTATTGAAGGCGTTTTTAGTAAAAAATGCCTTCAATAATCTCCTCATC
* * * *
12516180 AAAAATGAAGGGGATTATTGAAGGCATTTTTAGTAAAAAATGCCTTCAATAATCTCTTCATC
1 AAAATTGAAGAGGATTATTGAAGGCGTTTTTAGTAAAAAATGCCTTCAATAATCTCCTCATC
* * *
12516242 AAAATAT-AAGATGATTATTAAAGGCGTTTTTAGCAAAAAAATGCCTTCA
1 AAAAT-TGAAGAGGATTATTGAAGGCGTTTTTAG-TAAAAAATGCCTTCA
12516291 CTGATTAATT
Statistics
Matches: 136, Mismatches: 30, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
60 1 0.01
61 47 0.35
62 71 0.52
63 17 0.12
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (62 bp):
AAAATTGAAGAGGATTATTGAAGGCGTTTTTAGTAAAAAATGCCTTCAATAATCTCCTCATC
Found at i:12518898 original size:8 final size:8
Alignment explanation
Indices: 12518885--12518973 Score: 69
Period size: 8 Copynumber: 10.8 Consensus size: 8
12518875 GGGCCAAACT
12518885 TTTTATTA
1 TTTTATTA
12518893 TTTTATTA
1 TTTTATTA
12518901 TTTT-TTA
1 TTTTATTA
*
12518908 GCTTT-TTA
1 -TTTTATTA
12518916 TTTT-TGTA
1 TTTTAT-TA
*
12518924 TTATATATA
1 TTTTAT-TA
12518933 TTTTAATATA
1 TTTT-AT-TA
12518943 TTTTTATTA
1 -TTTTATTA
12518952 TTTTA-TA
1 TTTTATTA
12518959 TTTTATTTA
1 TTTTA-TTA
12518968 TTTTAT
1 TTTTAT
12518974 AAAATTTTAG
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
7 14 0.20
8 29 0.42
9 15 0.22
10 7 0.10
11 4 0.06
ACGTcount: A:0.25, C:0.01, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTTATTA
Found at i:12518960 original size:10 final size:11
Alignment explanation
Indices: 12518924--12518959 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
12518914 TATTTTTGTA
12518924 TTATATATATT
1 TTATATATATT
12518935 TTA-ATATATT
1 TTATATATATT
12518945 TT-TAT-TATT
1 TTATATATATT
12518954 TTATAT
1 TTATAT
12518960 TTTATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 6 0.26
10 14 0.61
11 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATATATATT
Found at i:12518980 original size:26 final size:26
Alignment explanation
Indices: 12518929--12518996 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
12518919 TTGTATTATA
**
12518929 TATATTTTAATATATTTTTATTATTT
1 TATATTTTAATATATTTTTAAAATTT
*
12518955 TATATTTT-ATTTATTTTATAAAATTT
1 TATATTTTAATATATTTT-TAAAATTT
* *
12518981 TAGAATTTTTATATAT
1 TA-TATTTTAATATAT
12518997 ACTTTATCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 8 0.24
26 16 0.47
27 5 0.15
28 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (26 bp):
TATATTTTAATATATTTTTAAAATTT
Found at i:12519399 original size:11 final size:10
Alignment explanation
Indices: 12519379--12519421 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 10
12519369 TCCTAAGAAA
12519379 TTTTTTTTTG
1 TTTTTTTTTG
12519389 TTTTGTTTTTG
1 TTTT-TTTTTG
12519400 CTTTTTTTTTCTG
1 --TTTTTTTT-TG
12519413 TTTTTTTTT
1 TTTTTTTTT
12519422 ATAACGACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 4 0.14
13 6 0.21
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:12519405 original size:13 final size:12
Alignment explanation
Indices: 12519379--12519421 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
12519369 TCCTAAGAAA
12519379 TTTTTTTT-TGT
1 TTTTTTTTCTGT
*
12519390 TTTGTTTT-TGCT
1 TTTTTTTTCTG-T
12519402 TTTTTTTTCTGT
1 TTTTTTTTCTGT
12519414 TTTTTTTT
1 TTTTTTTT
12519422 ATAACGACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 9 0.32
12 17 0.61
13 2 0.07
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (12 bp):
TTTTTTTTCTGT
Found at i:12519648 original size:29 final size:30
Alignment explanation
Indices: 12519584--12519650 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
12519574 TAAATTGGGT
* *
12519584 TTAAATTCTGGGTGCTAGCTAAACTGGGCA
1 TTAAATTTTGGGTGCTAGCTAAACTAGGCA
*
12519614 TT-AATTTTGGGTGCTAGCTAAGCTAGGC-
1 TTAAATTTTGGGTGCTAGCTAAACTAGGCA
12519642 TTAAATTTT
1 TTAAATTTT
12519651 CATTAAATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 2 0.06
29 29 0.88
30 2 0.06
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (30 bp):
TTAAATTTTGGGTGCTAGCTAAACTAGGCA
Found at i:12519667 original size:33 final size:33
Alignment explanation
Indices: 12519624--12520016 Score: 151
Period size: 33 Copynumber: 11.9 Consensus size: 33
12519614 TTAATTTTGG
*
12519624 GTGCTAGCTAAGCTAGGCTTAAATTTTCATTAA
1 GTGCTAGCTAAACTAGGCTTAAATTTTCATTAA
* * * **
12519657 ATGCTAGCTAAA-TTGAGCTTAAAACTTT-ATTGG
1 GTGCTAGCTAAACTAG-GCTT-AAATTTTCATTAA
* * * *
12519690 GTGCCAGCTAATCTAAGCTTAAATTTTCATTGA
1 GTGCTAGCTAAACTAGGCTTAAATTTTCATTAA
* * * ** * *
12519723 GTACCAACTAAACTAGGCTTAAAACTTCGTTAG
1 GTGCTAGCTAAACTAGGCTTAAATTTTCATTAA
12519756 GTGCTAGCTAAACTAGGCTTAAATCTTTTCA--AGA
1 GTGCTAGCTAAACTAGGCTTAAA--TTTTCATTA-A
** * *
12519790 GTGCTAGCTAAACTAAACTTAAAACTTT-ATTAT
1 GTGCTAGCTAAACTAGGCTT-AAATTTTCATTAA
* * * * *
12519823 GTGCCAACTAGACTGGGCTTAAATTTTCA-TAGG
1 GTGCTAGCTAAACTAGGCTTAAATTTTCATTA-A
* * ** * *
12519856 GTACCAATTAAACTGGGCTAAAATCTTTTCA--AA
1 GTGCTAGCTAAACTAGGCTTAAA--TTTTCATTAA
* * * * ***
12519889 GTGCTAGTTAAAATGGGCTTAAAACTTT-ATGGG
1 GTGCTAGCTAAACTAGGCTT-AAATTTTCATTAA
* * * * * *
12519922 GTGCCAGTTAGACTGGGATTAAATTTTCA-TAG
1 GTGCTAGCTAAACTAGGCTTAAATTTTCATTAA
* ** **
12519954 GTGCTAGCTAAACTTGATTTAAA-TTTCATTGG
1 GTGCTAGCTAAACTAGGCTTAAATTTTCATTAA
* *
12519986 GTGCTAGCTAGACTGGGCTTAAATTTTCATT
1 GTGCTAGCTAAACTAGGCTTAAATTTTCATT
12520017 GAAAGCCAGC
Statistics
Matches: 268, Mismatches: 72, Indels: 40
0.71 0.19 0.11
Matches are distributed among these distances:
31 6 0.02
32 65 0.24
33 155 0.58
34 30 0.11
35 12 0.04
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (33 bp):
GTGCTAGCTAAACTAGGCTTAAATTTTCATTAA
Found at i:12519699 original size:66 final size:65
Alignment explanation
Indices: 12519623--12519852 Score: 214
Period size: 66 Copynumber: 3.5 Consensus size: 65
12519613 ATTAATTTTG
* * *
12519623 GGTGCTAGCTAAGCTAGGCTTAAATTTTCATTAAATGCTAGCTAAATTGAGCTTAAAACTTTATT
1 GGTGCCAGCTAAGCTAGGCTTAAATTTTCATTAAGTGCTAGCTAAACT-AGCTTAAAACTTTATT
*
12519688 G
65 A
* * * * * * **
12519689 GGTGCCAGCTAATCTAAGCTTAAATTTTCATTGAGTACCAACTAAACTAGGCTTAAAACTTCGTT
1 GGTGCCAGCTAAGCTAGGCTTAAATTTTCATTAAGTGCTAGCTAAACTA-GCTTAAAACTTTATT
12519754 A
65 A
* * *
12519755 GGTGCTAGCTAAACTAGGCTTAAATCTTTTCA--AGAGTGCTAGCTAAACTAAACTTAAAACTTT
1 GGTGCCAGCTAAGCTAGGCTTAAA--TTTTCATTA-AGTGCTAGCTAAACT-AGCTTAAAACTTT
12519818 ATTA
62 ATTA
* * *
12519822 TGTGCCAACT-AGACTGGGCTTAAATTTTCAT
1 GGTGCCAGCTAAG-CTAGGCTTAAATTTTCAT
12519853 AGGGTACCAA
Statistics
Matches: 130, Mismatches: 27, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
65 7 0.05
66 74 0.57
67 42 0.32
68 7 0.05
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (65 bp):
GGTGCCAGCTAAGCTAGGCTTAAATTTTCATTAAGTGCTAGCTAAACTAGCTTAAAACTTTATTA
Found at i:12519799 original size:34 final size:32
Alignment explanation
Indices: 12519594--12519816 Score: 118
Period size: 33 Copynumber: 6.9 Consensus size: 32
12519584 TTAAATTCTG
* *
12519594 GGTGCTAGCTAAACTGGGCATT--AA-TT-TTG
1 GGTGCTAGCTAAACTAGGC-TTAAAACTTCTTA
* **
12519623 GGTGCTAGCTAAGCTAGGCTTAAATTTTCATTA
1 GGTGCTAGCTAAACTAGGCTTAAAACTTC-TTA
** * * *
12519656 AATGCTAGCTAAA-TTGAGCTTAAAACTTTATTG
1 GGTGCTAGCTAAACTAG-GCTTAAAAC-TTCTTA
* * * **
12519689 GGTGCCAGCTAATCTAAGCTTAAATTTTCATT-
1 GGTGCTAGCTAAACTAGGCTTAAAACTTC-TTA
* * *
12519721 GAGTACCAACTAAACTAGGCTTAAAACTTCGTTA
1 G-GTGCTAGCTAAACTAGGCTTAAAACTTC-TTA
*
12519755 GGTGCTAGCTAAACTAGGCTTAAATCTT-TTCAA
1 GGTGCTAGCTAAACTAGGCTTAAAACTTCTT--A
**
12519788 GAGTGCTAGCTAAACTAAACTTAAAACTT
1 G-GTGCTAGCTAAACTAGGCTTAAAACTT
12519817 TATTATGTGC
Statistics
Matches: 145, Mismatches: 35, Indels: 23
0.71 0.17 0.11
Matches are distributed among these distances:
28 2 0.01
29 17 0.12
30 1 0.01
31 4 0.03
32 5 0.03
33 88 0.61
34 28 0.19
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (32 bp):
GGTGCTAGCTAAACTAGGCTTAAAACTTCTTA
Found at i:12519860 original size:133 final size:130
Alignment explanation
Indices: 12519623--12519878 Score: 318
Period size: 133 Copynumber: 1.9 Consensus size: 130
12519613 ATTAATTTTG
* * * *
12519623 GGTGCTAGCTAAGCTAGGCTTAAATTTTCATTAAATGCTAGCTAAATTGAGCTTAAAACTTTATT
1 GGTGCTAGCTAAACTAGGCTTAAATTTTCA-TAAATGCTAGCTAAACTAAACTTAAAACTTTATT
* * *
12519688 GGGTGCCAGCTAATCTAAGCTTAAATTTTCATTGAGTACCAACTAAACTAGGCTTAAAACTTCGT
65 AGGTGCCAACTAATCTAAGCTTAAATTTTCATAGAGTACCAACTAAACTAGGC-TAAAACTTCGT
12519753 TA
129 TA
*
12519755 GGTGCTAGCTAAACTAGGCTTAAATCTTTTCA-AGAGTGCTAGCTAAACTAAACTTAAAACTTTA
1 GGTGCTAGCTAAACTAGGCTTAAA--TTTTCATA-AATGCTAGCTAAACTAAACTTAAAACTTTA
* ** * * *
12519819 TTATGTGCCAACTAGA-CTGGGCTTAAATTTTCATAGGGTACCAATTAAACTGGGCTAAAA
63 TTAGGTGCCAACTA-ATCTAAGCTTAAATTTTCATAGAGTACCAACTAAACTAGGCTAAAA
12519879 TCTTTTCAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
132 29 0.27
133 70 0.66
134 7 0.07
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (130 bp):
GGTGCTAGCTAAACTAGGCTTAAATTTTCATAAATGCTAGCTAAACTAAACTTAAAACTTTATTA
GGTGCCAACTAATCTAAGCTTAAATTTTCATAGAGTACCAACTAAACTAGGCTAAAACTTCGTTA
Found at i:12519893 original size:133 final size:131
Alignment explanation
Indices: 12519624--12519916 Score: 308
Period size: 133 Copynumber: 2.2 Consensus size: 131
12519614 TTAATTTTGG
* * * *
12519624 GTGCTAGCTAAGCTAGGCTTAAA-TTTTCATTAAATGCTAGCTAAATTGAGCTTAAAACTTTATT
1 GTGCTAGCTAAACTAGGCTTAAACTTTTCA-TAAATGCTAGCTAAACTAAACTTAAAACTTTATT
* * *
12519688 GGGTGCCAGCTAATCTAAGCTTAAATTTTCATTGAGTACCAACTAAACTAGGCTTAAAACTTCGT
65 AGGTGCCAACTAATCTAAGCTTAAATTTTCATAGAGTACCAACTAAACTAGGCTTAAAACTTC-T
*
12519753 TAG
129 TAA
*
12519756 GTGCTAGCTAAACTAGGCTTAAATCTTTTCA-AGAGTGCTAGCTAAACTAAACTTAAAACTTTAT
1 GTGCTAGCTAAACTAGGCTTAAA-CTTTTCATA-AATGCTAGCTAAACTAAACTTAAAACTTTAT
* ** * * *
12519820 TATGTGCCAACTAGA-CTGGGCTTAAATTTTCATAGGGTACCAATTAAACTGGGC-TAAAATCTT
64 TAGGTGCCAACTA-ATCTAAGCTTAAATTTTCATAGAGTACCAACTAAACTAGGCTTAAAA-CTT
12519883 -TTCAAA
127 CTT--AA
* * *
12519889 GTGCTAGTTAAAATGGGCTTAAAACTTT
1 GTGCTAGCTAAACTAGGCTT-AAACTTT
12519917 ATGGGGTGCC
Statistics
Matches: 135, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
131 2 0.01
132 28 0.21
133 95 0.70
134 10 0.07
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (131 bp):
GTGCTAGCTAAACTAGGCTTAAACTTTTCATAAATGCTAGCTAAACTAAACTTAAAACTTTATTA
GGTGCCAACTAATCTAAGCTTAAATTTTCATAGAGTACCAACTAAACTAGGCTTAAAACTTCTTA
A
Found at i:12519934 original size:99 final size:100
Alignment explanation
Indices: 12519764--12519954 Score: 258
Period size: 99 Copynumber: 1.9 Consensus size: 100
12519754 AGGTGCTAGC
* * * *
12519764 TAAACTAGGCTTAAATCTTTTCAAGAGTGCTAGCTAAACTAAACTTAAAACTTTATTATGTGCCA
1 TAAACTAGGCTAAAATCTTTTCAAGAGTGCTAGCTAAAATAAACTTAAAACTTTATGAGGTGCCA
*
12519829 ACTAGACTGGGCTTAAATTTTCATAGGGTACCAAT
66 ACTAGACTGGGATTAAATTTTCATAGGGTACCAAT
* * *** *
12519864 TAAACTGGGCTAAAATCTTTTCAA-AGTGCTAGTTAAAATGGGCTTAAAACTTTATGGGGTGCCA
1 TAAACTAGGCTAAAATCTTTTCAAGAGTGCTAGCTAAAATAAACTTAAAACTTTATGAGGTGCCA
**
12519928 GTTAGACTGGGATTAAATTTTCATAGG
66 ACTAGACTGGGATTAAATTTTCATAGG
12519955 TGCTAGCTAA
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
99 56 0.72
100 22 0.28
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (100 bp):
TAAACTAGGCTAAAATCTTTTCAAGAGTGCTAGCTAAAATAAACTTAAAACTTTATGAGGTGCCA
ACTAGACTGGGATTAAATTTTCATAGGGTACCAAT
Found at i:12520075 original size:32 final size:32
Alignment explanation
Indices: 12520038--12520131 Score: 93
Period size: 32 Copynumber: 2.9 Consensus size: 32
12520028 AAATTATTGC
*
12520038 GTGCTAGTTAGACTGGGATTAAATTTTCATAG
1 GTGCTAGCTAGACTGGGATTAAATTTTCATAG
* ** *
12520070 GTGCTAGCTA-AATTTGATTTAAA-TTTCATTGG
1 GTGCTAGCTAGACTGGGA-TTAAATTTTCA-TAG
* *
12520102 GTGCCAGCTAGACTGGGCTTAAATTTTCAT
1 GTGCTAGCTAGACTGGGATTAAATTTTCAT
12520132 TGAAAGCCAG
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
31 9 0.19
32 31 0.65
33 8 0.17
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (32 bp):
GTGCTAGCTAGACTGGGATTAAATTTTCATAG
Found at i:12520208 original size:32 final size:32
Alignment explanation
Indices: 12520154--12520265 Score: 93
Period size: 32 Copynumber: 3.5 Consensus size: 32
12520144 AAATTATTGC
* * *
12520154 GTGCTAGTTAGACTGGGA-TTAAATTTTCATAG
1 GTGCTAGCTAAACTAGGACTTAAA-TTTCATAG
* * *
12520186 GTGCTAGCTAAACT-TGATTTAAATTTCATTG
1 GTGCTAGCTAAACTAGGACTTAAATTTCATAG
* * *
12520217 GATGCCAGCTACACTAGGGCTTAAATTTCATTAG
1 G-TGCTAGCTAAACTAGGACTTAAATTTCA-TAG
*
12520251 GTGTTAGCTAAACTA
1 GTGCTAGCTAAACTA
12520266 AGTTTAAAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
31 10 0.16
32 28 0.44
33 22 0.35
34 3 0.05
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (32 bp):
GTGCTAGCTAAACTAGGACTTAAATTTCATAG
Found at i:12520262 original size:116 final size:116
Alignment explanation
Indices: 12519922--12520248 Score: 593
Period size: 116 Copynumber: 2.8 Consensus size: 116
12519912 ACTTTATGGG
*
12519922 GTGCCAGTTAGACTGGGATTAAATTTTCATAGGTGCTAGCTAAACTTGATTTAAATTTCATTGGG
1 GTGCTAGTTAGACTGGGATTAAATTTTCATAGGTGCTAGCTAAACTTGATTTAAATTTCATTGGG
*
12519987 TGCTAGCTAGACTGGGCTTAAATTTTCATTGAAAGCCAGCTAAATTATTGC
66 TGCCAGCTAGACTGGGCTTAAATTTTCATTGAAAGCCAGCTAAATTATTGC
*
12520038 GTGCTAGTTAGACTGGGATTAAATTTTCATAGGTGCTAGCTAAATTTGATTTAAATTTCATTGGG
1 GTGCTAGTTAGACTGGGATTAAATTTTCATAGGTGCTAGCTAAACTTGATTTAAATTTCATTGGG
12520103 TGCCAGCTAGACTGGGCTTAAATTTTCATTGAAAGCCAGCTAAATTATTGC
66 TGCCAGCTAGACTGGGCTTAAATTTTCATTGAAAGCCAGCTAAATTATTGC
*
12520154 GTGCTAGTTAGACTGGGATTAAATTTTCATAGGTGCTAGCTAAACTTGATTTAAATTTCATTGGA
1 GTGCTAGTTAGACTGGGATTAAATTTTCATAGGTGCTAGCTAAACTTGATTTAAATTTCATTGGG
*
12520219 TGCCAGCTACACTAGGGCTTAAA-TTTCATT
66 TGCCAGCTAGACT-GGGCTTAAATTTTCATT
12520249 AGGTGTTAGC
Statistics
Matches: 204, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
116 195 0.96
117 9 0.04
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.36
Consensus pattern (116 bp):
GTGCTAGTTAGACTGGGATTAAATTTTCATAGGTGCTAGCTAAACTTGATTTAAATTTCATTGGG
TGCCAGCTAGACTGGGCTTAAATTTTCATTGAAAGCCAGCTAAATTATTGC
Found at i:12520276 original size:33 final size:32
Alignment explanation
Indices: 12520172--12520310 Score: 97
Period size: 33 Copynumber: 4.2 Consensus size: 32
12520162 TAGACTGGGA
*
12520172 TTAAATTTTCA-TAGGTGCTAGCTAAACT-TGAT
1 TTAAA-TTTCATTAGGTGCTAGCTAAACTAAG-T
* * * *
12520204 TTAAATTTCATT-GGATGCCAGCTACACTAGGGC
1 TTAAATTTCATTAGG-TGCTAGCTAAACTA-AGT
*
12520237 TTAAATTTCATTAGGTGTTAGCTAAACTAAGT
1 TTAAATTTCATTAGGTGCTAGCTAAACTAAGT
* * * *
12520269 TTAAAATTTTTCATT-GGTACCAGCTAAATTAGGT
1 TT-AAA--TTTCATTAGGTGCTAGCTAAACTAAGT
12520303 TTAAATTT
1 TTAAATTT
12520311 TTGTTGGGTC
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
31 10 0.12
32 20 0.24
33 29 0.34
34 19 0.22
35 7 0.08
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (32 bp):
TTAAATTTCATTAGGTGCTAGCTAAACTAAGT
Found at i:12520470 original size:32 final size:31
Alignment explanation
Indices: 12520357--12520475 Score: 98
Period size: 32 Copynumber: 3.7 Consensus size: 31
12520347 TGGGTGTCAT
* *
12520357 CTAAACTAGGCTTAAAACTTCTCA-AGAGTGCCAG
1 CTAAACTAAGCTT-AAA-TT-TCACAG-GTGCCAA
*
12520391 CTAAACTGAA-CTTATATTTTCACAGGTGCCAA
1 CTAAACT-AAGCTTA-AATTTCACAGGTGCCAA
* *
12520423 TTAAACTAAGTTTAAATTTCACTAGGTGCCAA
1 CTAAACTAAGCTTAAATTTCAC-AGGTGCCAA
* *
12520455 CTAGACTAGGCTTAAATTTCA
1 CTAAACTAAGCTTAAATTTCA
12520476 ATTAGACTAG
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
31 9 0.13
32 44 0.63
33 5 0.07
34 11 0.16
35 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (31 bp):
CTAAACTAAGCTTAAATTTCACAGGTGCCAA
Found at i:12520479 original size:54 final size:54
Alignment explanation
Indices: 12520420--12520527 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
12520410 TCACAGGTGC
* *
12520420 CAATTAAACTAAGTTTAAATTTCACTAGGTGCCAACTAGACTAGGCTTAAATTT
1 CAATTAAACTAAGCTTAAATTTCACTAGGTGCCAACTAGACTAAGCTTAAATTT
* * ** * * *
12520474 CAATTAGACTAGGCTTAAATTTCGTTTGGTGCCAGCTAGACTAAGTTTAAATTT
1 CAATTAAACTAAGCTTAAATTTCACTAGGTGCCAACTAGACTAAGCTTAAATTT
12520528 TCATTAAGGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (54 bp):
CAATTAAACTAAGCTTAAATTTCACTAGGTGCCAACTAGACTAAGCTTAAATTT
Found at i:12521060 original size:8 final size:8
Alignment explanation
Indices: 12521047--12521080 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
12521037 GACACATTCA
12521047 TTATTTTT
1 TTATTTTT
12521055 TTA-TTTT
1 TTATTTTT
12521062 TTATTTTT
1 TTATTTTT
*
12521070 TTCTTTTT
1 TTATTTTT
12521078 TTA
1 TTA
12521081 CATCATACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (8 bp):
TTATTTTT
Found at i:12521067 original size:15 final size:15
Alignment explanation
Indices: 12521047--12521078 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12521037 GACACATTCA
12521047 TTATTTTTTTATTTT
1 TTATTTTTTTATTTT
*
12521062 TTATTTTTTTCTTTT
1 TTATTTTTTTATTTT
12521077 TT
1 TT
12521079 TACATCATAC
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:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (15 bp):
TTATTTTTTTATTTT
Found at i:12521405 original size:10 final size:11
Alignment explanation
Indices: 12521385--12521416 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
12521375 GTATATTCCC
12521385 TTTCATTTTTT
1 TTTCATTTTTT
*
12521396 TTTCTTTTTTT
1 TTTCATTTTTT
12521407 TTTCATTTTT
1 TTTCATTTTT
12521417 CTTCATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCATTTTTT
Found at i:12521428 original size:22 final size:22
Alignment explanation
Indices: 12521385--12521428 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12521375 GTATATTCCC
* *
12521385 TTTCATTTTTTTTTCTTTTTTT
1 TTTCATTTTTTCTTCTTATTTT
12521407 TTTCA-TTTTTCTTCATTATTTT
1 TTTCATTTTTTCTTC-TTATTTT
12521429 ATTTTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTCATTTTTTCTTCTTATTTT
Found at i:12525847 original size:14 final size:14
Alignment explanation
Indices: 12525828--12525854 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12525818 GGACTCCTCT
12525828 TTTTTCTCTTTTTC
1 TTTTTCTCTTTTTC
12525842 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
12525855 GATCTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTCTTTTTC
Found at i:12525854 original size:23 final size:22
Alignment explanation
Indices: 12525824--12525868 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
12525814 ATTTGGACTC
**
12525824 CTCTTTTTTCTCTTTTTCTTTTT
1 CTCTTTTTGATCTTTTT-TTTTT
12525847 CTCTTTTTGATCTTTTTTTTTT
1 CTCTTTTTGATCTTTTTTTTTT
12525869 AATCCTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (22 bp):
CTCTTTTTGATCTTTTTTTTTT
Found at i:12528052 original size:51 final size:50
Alignment explanation
Indices: 12527965--12528087 Score: 124
Period size: 50 Copynumber: 2.4 Consensus size: 50
12527955 TTTGTAATTT
* * * ***
12527965 TTTCAAAAAATTAATTTTTTAATATTTATTTAGAACAAG-TTTGTTTTGCATAA
1 TTTCTAAAAATTAA-TTTTT-ACATCTATTTAGAACAAGCTCACTTTT--ATAA
*
12528018 TTTCTAGAAAA-TAATTTTTACATCTATTTGGAACAAGCTCACTTTTATAA
1 TTTCTA-AAAATTAATTTTTACATCTATTTAGAACAAGCTCACTTTTATAA
12528068 TTTCTAAAAATTAATTTTTA
1 TTTCTAAAAATTAATTTTTA
12528088 TGTTTTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
49 4 0.07
50 19 0.32
51 15 0.25
52 10 0.17
53 8 0.13
54 4 0.07
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (50 bp):
TTTCTAAAAATTAATTTTTACATCTATTTAGAACAAGCTCACTTTTATAA
Found at i:12530118 original size:17 final size:17
Alignment explanation
Indices: 12530080--12530116 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12530070 TATTGTTCTA
12530080 TTTT-TTTTTTTGGTTT
1 TTTTATTTTTTTGGTTT
12530096 TTTTATTTTTTTGTGTTT
1 TTTTATTTTTTTG-GTTT
12530114 TTT
1 TTT
12530117 ATATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 8 0.42
18 7 0.37
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (17 bp):
TTTTATTTTTTTGGTTT
Found at i:12530184 original size:35 final size:32
Alignment explanation
Indices: 12530126--12530208 Score: 87
Period size: 35 Copynumber: 2.5 Consensus size: 32
12530116 TATATATATT
* * *
12530126 TTTTAATATTTAATATTTTATTTAT-TTTATAAA
1 TTTTAA-ATTTTATATATAATTTATCTTT-TAAA
12530159 TTTTTAGAATTTTTATATATAATTTATCTTTTAAA
1 -TTTTA-AA-TTTTATATATAATTTATCTTTTAAA
12530194 TTTTAAATTTTATAT
1 TTTTAAATTTTATAT
12530209 TTTCCTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
32 8 0.19
33 2 0.05
34 11 0.26
35 19 0.44
36 3 0.07
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (32 bp):
TTTTAAATTTTATATATAATTTATCTTTTAAA
Found at i:12532741 original size:17 final size:18
Alignment explanation
Indices: 12532719--12532759 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12532709 CGATGTGTTA
12532719 TTTTTTTC-TCTTCT-TC
1 TTTTTTTCATCTTCTCTC
*
12532735 TTTTTTTCATTTTCTCTC
1 TTTTTTTCATCTTCTCTC
12532753 TTTTTTT
1 TTTTTTT
12532760 TTGACCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTCATCTTCTCTC
Found at i:12532769 original size:22 final size:22
Alignment explanation
Indices: 12532722--12532761 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
12532712 TGTGTTATTT
12532722 TTTTCTCTTCTTCTTTTTTTCA
1 TTTTCTCTTCTTCTTTTTTTCA
12532744 TTTTCTC-TCTT-TTTTTTT
1 TTTTCTCTTCTTCTTTTTTT
12532762 GACCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTCTCTTCTTCTTTTTTTCA
Found at i:12535749 original size:83 final size:83
Alignment explanation
Indices: 12535637--12535891 Score: 293
Period size: 84 Copynumber: 3.0 Consensus size: 83
12535627 AGGGGAAAAC
* * *
12535637 TTATTTTTCAATTTTTCATAGCTTCAACAAAGATTATGTTTTTTAGATAAAAATGTAGTTTTTGT
1 TTATTTTTTAAATTTTCATAGTTTCAACAAAGATTATGTTTTTTAGATAAAAATGTAGTTTTTGT
*
12535702 TGATATATTATAAGAAAT
66 TGATATATTATGAGAAAT
* * * *
12535720 TT-TTTTTATTAATTTTCATA-TTGTTAACAAAGATTATGTTTTTTGGGTAAAAAATGTAGTTTT
1 TTATTTTT-TAAATTTTCATAGTT-TCAACAAAGATTATGTTTTTTAGAT-AAAAATGTAGTTTT
12535783 TGTT-AGTATATTATGAGAAAAT
63 TGTTGA-TATATTATGAG-AAAT
* * * ** *
12535805 TTATTTTTTAAATTTTCATAGTTTCAACAAAAAATTATATTTTATCTA-AAAAAGGTAGTTTTTG
1 TTATTTTTTAAATTTTCATAGTTTCAAC-AAAGATTATGTTTTTTAGATAAAAATGTAGTTTTTG
*
12535869 TTGATATATTATGAGTAAT
65 TTGATATATTATGAGAAAT
12535888 TTAT
1 TTAT
12535892 CTAAAAGGGA
Statistics
Matches: 145, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
82 6 0.04
83 41 0.28
84 56 0.39
85 22 0.15
86 20 0.14
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.49
Consensus pattern (83 bp):
TTATTTTTTAAATTTTCATAGTTTCAACAAAGATTATGTTTTTTAGATAAAAATGTAGTTTTTGT
TGATATATTATGAGAAAT
Found at i:12540458 original size:12 final size:12
Alignment explanation
Indices: 12540441--12540467 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12540431 GGAAACAAAG
12540441 AAATAGAATAAA
1 AAATAGAATAAA
12540453 AAATAGAATAAA
1 AAATAGAATAAA
12540465 AAA
1 AAA
12540468 CTTCAGACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (12 bp):
AAATAGAATAAA
Found at i:12541651 original size:55 final size:55
Alignment explanation
Indices: 12541567--12541673 Score: 187
Period size: 55 Copynumber: 1.9 Consensus size: 55
12541557 CAAGAGTTAT
*
12541567 CAAAAGATCTAATTGCCTATATTAAATATTGTAAAGGTTGAATTTTTATGCCTAG
1 CAAAAGATCTAATGGCCTATATTAAATATTGTAAAGGTTGAATTTTTATGCCTAG
* *
12541622 CAAAAGATGTAATGGCCTATATTAAATATTGTAAATGTTGAATTTTTATGCC
1 CAAAAGATCTAATGGCCTATATTAAATATTGTAAAGGTTGAATTTTTATGCC
12541674 CCTCAAACCC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (55 bp):
CAAAAGATCTAATGGCCTATATTAAATATTGTAAAGGTTGAATTTTTATGCCTAG
Found at i:12542051 original size:145 final size:144
Alignment explanation
Indices: 12541771--12542188 Score: 447
Period size: 145 Copynumber: 2.9 Consensus size: 144
12541761 CATTTTTTGC
* * * * * * * * *
12541771 ATTTTAAAGCACTAAAAATCATTAAATATTATGAAATTAAAATATGAAAGGTTTTATGAAAATTC
1 ATTTTAATGCACCAAAAATTATGAAATATTATAAAATTAAGATATAAAAAGTTTCAT-AAAATTC
* * * *
12541836 -GAGCTCGAGAAGACTAAATTATGAAAATACCCTTATA-AGGGTATTTTAGTAATTTCT-CACTT
65 TGAGCTCGAAAAGGCTAAATTATGAAAATACCCCTATATA-GGTATTTTGGTAATTT-TAC-CTT
*
12541898 T-CTGGGGTACTGCTATG
127 TCCTAGGGTACTGCTATG
*
12541915 ATTTTAGATGCACCAAAAATTATGAAATATTATAAAATTAAGATCTAAAAAGTTTCATAAAATTC
1 ATTTTA-ATGCACCAAAAATTATGAAATATTATAAAATTAAGATATAAAAAGTTTCATAAAATTC
*
12541980 TGAGCTCGAAAAGGCTAAATTATGAAAATACCCCTAGATAGGTATTTTGGTAATTTTACCTTTCC
65 TGAGCTCGAAAAGGCTAAATTATGAAAATACCCCTATATAGGTATTTTGGTAATTTTACCTTTCC
* *
12542045 TAGGGTATTGCTGTG
130 TAGGGTACTGCTATG
* * * *
12542060 ATTTTAAATACAGCAAAAATTATGAAATATTATAAAATTAAGATTTAAAAAGTTTCACAAAATT-
1 ATTTT-AATGCACCAAAAATTATGAAATATTATAAAATTAAGATATAAAAAGTTTCATAAAATTC
* * ** *
12542124 TGAGGTC-AAGAAGG-TCAATTTACAAAAATACCCCT-TATAAGCGTATTTTGATAATTTTACCT
65 TGAGCTCGAA-AAGGCT-AAATTATGAAAATACCCCTATAT-AG-GTATTTTGGTAATTTTACCT
12542186 TTC
126 TTC
12542189 TCGAGGCACG
Statistics
Matches: 236, Mismatches: 28, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
143 5 0.02
144 46 0.19
145 183 0.78
146 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (144 bp):
ATTTTAATGCACCAAAAATTATGAAATATTATAAAATTAAGATATAAAAAGTTTCATAAAATTCT
GAGCTCGAAAAGGCTAAATTATGAAAATACCCCTATATAGGTATTTTGGTAATTTTACCTTTCCT
AGGGTACTGCTATG
Found at i:12543487 original size:13 final size:13
Alignment explanation
Indices: 12543470--12543549 Score: 60
Period size: 14 Copynumber: 6.3 Consensus size: 13
12543460 TGGGCCAAAT
*
12543470 TTTTTATTGTTTTA
1 TTTTTATT-ATTTA
12543484 TTTTTATTATTTA
1 TTTTTATTATTTA
12543497 -TTTT-TT-TTTA
1 TTTTTATTATTTA
* *
12543507 TTTTTATGTTTTTT
1 TTTTTAT-TATTTA
*
12543521 TTTTTAATATTTA
1 TTTTTATTATTTA
* *
12543534 ATATT-TTATTTA
1 TTTTTATTATTTA
12543546 TTTT
1 TTTT
12543550 ATCAATTTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
10 4 0.08
11 6 0.12
12 13 0.25
13 12 0.23
14 17 0.33
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTTATTATTTA
Found at i:12543490 original size:6 final size:6
Alignment explanation
Indices: 12543479--12543523 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
12543469 TTTTTTATTG
12543479 TTTTAT TTTTAT TATTTA- TTTT-T TTTTAT TTTTAT GTTTT-T TTTT
1 TTTTAT TTTTAT T-TTTAT TTTTAT TTTTAT TTTTAT -TTTTAT TTTT
12543524 TTAATATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 11 0.31
6 16 0.46
7 8 0.23
ACGTcount: A:0.13, C:0.00, G:0.02, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:12543497 original size:21 final size:20
Alignment explanation
Indices: 12543472--12543544 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 20
12543462 GGCCAAATTT
12543472 TTTATTGTTTTATTTTTATTA
1 TTTATT-TTTTATTTTTATTA
12543493 TTTA--TTTT-TTTTTATT-
1 TTTATTTTTTATTTTTATTA
* *
12543509 TTTATGTTTTTTTTTTTAATA
1 TTTAT-TTTTTATTTTTATTA
*
12543530 TTTAATATTTTATTT
1 TTT-ATTTTTTATTT
12543545 ATTTTATCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
16 4 0.09
17 8 0.19
18 4 0.09
19 4 0.09
20 7 0.16
21 14 0.33
22 2 0.05
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTATTTTTTATTTTTATTA
Found at i:12543503 original size:16 final size:17
Alignment explanation
Indices: 12543470--12543525 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 17
12543460 TGGGCCAAAT
12543470 TTTTTATTGTTTTATTTTTA
1 TTTTTATTG--TT-TTTTTA
12543490 TTATTTATT-TTTTTTTA
1 TT-TTTATTGTTTTTTTA
12543507 TTTTTA-TGTTTTTTT-
1 TTTTTATTGTTTTTTTA
12543522 TTTT
1 TTTT
12543526 AATATTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.15
16 11 0.32
17 8 0.24
18 2 0.06
20 2 0.06
21 6 0.18
ACGTcount: A:0.12, C:0.00, G:0.04, T:0.84
Consensus pattern (17 bp):
TTTTTATTGTTTTTTTA
Found at i:12543504 original size:17 final size:16
Alignment explanation
Indices: 12543479--12543522 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
12543469 TTTTTTATTG
12543479 TTTTATTTTTATTATTTA
1 TTTT-TTTTTATT-TTTA
12543497 TTTTTTTTTATTTTTA
1 TTTTTTTTTATTTTTA
12543513 TGTTTTTTTT
1 T-TTTTTTTT
12543523 TTTAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 16 0.64
18 4 0.16
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTATTTTTA
Found at i:12543509 original size:23 final size:22
Alignment explanation
Indices: 12543479--12543549 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
12543469 TTTTTTATTG
12543479 TTTTATTTTTATTATTTATTTTT
1 TTTTATTTTTA-TATTTATTTTT
*
12543502 TTTTATTTTTATGTTT-TTTTT
1 TTTTATTTTTATATTTATTTTT
* * *
12543523 TTTAATATTTAATATTTTATTTAT
1 TTTTAT-TTTTATA-TTTATTTTT
12543547 TTT
1 TTT
12543550 ATCAATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.25
22 9 0.22
23 14 0.35
24 7 0.17
ACGTcount: A:0.20, C:0.00, G:0.01, T:0.79
Consensus pattern (22 bp):
TTTTATTTTTATATTTATTTTT
Found at i:12543525 original size:37 final size:39
Alignment explanation
Indices: 12543470--12543549 Score: 103
Period size: 37 Copynumber: 2.1 Consensus size: 39
12543460 TGGGCCAAAT
* *
12543470 TTTTTATTGTTTTATTTTTATTATTT-AT-TTTTTTTTA
1 TTTTTATTGTTTTATTTTTAATATTTAATATTTTATTTA
*
12543507 TTTTTA-TGTTTTTTTTTTTAATATTTAATATTTTATTTA
1 TTTTTATTG-TTTTATTTTTAATATTTAATATTTTATTTA
12543546 TTTT
1 TTTT
12543550 ATCAATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 2 0.05
37 21 0.57
38 2 0.05
39 12 0.32
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.79
Consensus pattern (39 bp):
TTTTTATTGTTTTATTTTTAATATTTAATATTTTATTTA
Found at i:12547524 original size:15 final size:16
Alignment explanation
Indices: 12547506--12547535 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12547496 AAAATACCTT
12547506 GAAAAAAAA-AGAAAG
1 GAAAAAAAAGAGAAAG
12547521 GAAAAAAAAGAGAAA
1 GAAAAAAAAGAGAAA
12547536 AAAAGTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAGAGAAAG
Found at i:12547558 original size:9 final size:10
Alignment explanation
Indices: 12547523--12547559 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
12547513 AAAGAAAGGA
*
12547523 AAAAAAAGAG
1 AAAAAAAGTG
12547533 AAAAAAAGTG
1 AAAAAAAGTG
12547543 AAAAAAA-TG
1 AAAAAAAGTG
12547552 AAAAAAAG
1 AAAAAAAG
12547560 ACAAAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (10 bp):
AAAAAAAGTG
Found at i:12548777 original size:3 final size:3
Alignment explanation
Indices: 12548769--12548822 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
12548759 TAAAGATGAA
12548769 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AATT AAT AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA-T
*
12548815 AAA AAT AA
1 AAT AAT AA
12548823 AAAATCTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 38 0.83
4 6 0.13
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12548798 original size:20 final size:21
Alignment explanation
Indices: 12548773--12548812 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
12548763 GATGAAAATA
12548773 ATAATAATAATAA-TAATAAT
1 ATAATAATAATAATTAATAAT
12548793 ATAATAATAATAATTAATAA
1 ATAATAATAATAATTAATAA
12548813 GTAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATAATAATAATTAATAAT
Found at i:12548821 original size:20 final size:18
Alignment explanation
Indices: 12548769--12548850 Score: 68
Period size: 17 Copynumber: 4.7 Consensus size: 18
12548759 TAAAGATGAA
*
12548769 AATAATAATAATAATAAT
1 AATAATAATAAAAATAAT
*
12548787 AATAAT-ATAATAATAAT
1 AATAATAATAAAAATAAT
12548804 AATTAATAAGTAAAAATAA-
1 AA-TAATAA-TAAAAATAAT
*
12548823 AA-AAT-CTAAAAATAA-
1 AATAATAATAAAAATAAT
12548838 AATGAA-AATAAAA
1 AAT-AATAATAAAA
12548851 TAGAAAAAGT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
15 11 0.20
17 23 0.42
18 10 0.18
19 3 0.05
20 8 0.15
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (18 bp):
AATAATAATAAAAATAAT
Found at i:12548839 original size:5 final size:5
Alignment explanation
Indices: 12548831--12548879 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
12548821 AAAAAATCTA
* *
12548831 AAAAT AAAAT GAAAAT AAAAT AGAA- AAAGT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
12548880 ACCAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 2 0.05
5 31 0.82
6 5 0.13
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:12548857 original size:24 final size:23
Alignment explanation
Indices: 12548830--12548880 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
12548820 TAAAAAATCT
12548830 AAAAA-TAAAATGAAAATAAAATA
1 AAAAAGTAAAAT-AAAATAAAATA
12548853 GAAAAAGTAAAATAAAATAAAATA
1 -AAAAAGTAAAATAAAATAAAATA
12548877 AAAA
1 AAAA
12548881 CCAAAAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 4 0.15
24 16 0.62
25 6 0.23
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (23 bp):
AAAAAGTAAAATAAAATAAAATA
Found at i:12548879 original size:46 final size:47
Alignment explanation
Indices: 12548767--12548880 Score: 110
Period size: 46 Copynumber: 2.4 Consensus size: 47
12548757 ATTAAAGATG
* * * *
12548767 AAAATAATAATAATAATAATAATAATATAATAATAATAATTAATAAGTA
1 AAAATAA-AATAA-AATAAAAATAAAATAATAATAATAATGAAAAAGTA
**
12548816 AAAATAAAA-AATCTAAAAATAAAATGAA-AATAA-AATAGAAAAAGT-
1 AAAATAAAATAAAATAAAAATAAAAT-AATAATAATAAT-GAAAAAGTA
12548861 AAAATAAAATAAAATAAAAA
1 AAAATAAAATAAAATAAAAA
12548881 CCAAAAATAG
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
45 12 0.22
46 29 0.54
47 4 0.07
48 2 0.04
49 7 0.13
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.24
Consensus pattern (47 bp):
AAAATAAAATAAAATAAAAATAAAATAATAATAATAATGAAAAAGTA
Found at i:12549931 original size:86 final size:86
Alignment explanation
Indices: 12549778--12550034 Score: 248
Period size: 86 Copynumber: 3.0 Consensus size: 86
12549768 ATGAATGAAG
* * * * ** * * *
12549778 AAATAAGCTCCTCTAAACAGAGGCTAAACAACCTTAAAATAGGAAAT-GGGTCCCTTTATTTAAA
1 AAATAAGCTCCTCTACATAAAGGCTAAACAACTTTAAAATAGGAAATAGACT-CCTCTAATTAGA
** *
12549842 GGCTAAATGACTTTAAAGTAAC
65 GGCTAAACAACTTTAAAATAAC
* *
12549864 AAAT-GGACTCCTCTATATAAAGGCTAAACAACTTTAAAATAGGAAATAGACTCCTCTAATTAGA
1 AAATAAG-CTCCTCTACATAAAGGCTAAACAACTTTAAAATAGGAAATAGACTCCTCTAATTAGA
* **
12549928 GGCTAAACAATTTTAAAATATG
65 GGCTAAACAACTTTAAAATAAC
* * ** * * * *
12549950 AAATAAGCTCTTCTACATAGAGGCTAAACAACTTTAAAATAAAAAATATATTCTTCTAAATAGAG
1 AAATAAGCTCCTCTACATAAAGGCTAAACAACTTTAAAATAGGAAATAGACTCCTCTAATTAGAG
*
12550015 GCTAAACAAATTTAAAATAA
66 GCTAAACAACTTTAAAATAA
12550035 GTGATTCGGA
Statistics
Matches: 140, Mismatches: 28, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
85 1 0.01
86 136 0.97
87 3 0.02
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (86 bp):
AAATAAGCTCCTCTACATAAAGGCTAAACAACTTTAAAATAGGAAATAGACTCCTCTAATTAGAG
GCTAAACAACTTTAAAATAAC
Found at i:12550034 original size:43 final size:42
Alignment explanation
Indices: 12549775--12550035 Score: 209
Period size: 43 Copynumber: 6.1 Consensus size: 42
12549765 TAAATGAATG
* * *
12549775 AAGAAATAAGCTCCTCTAAACAGAGGCTAAACAACCTTAAAAT
1 AAGAAATAA-CTCTTCTAAATAGAGGCTAAACAACTTTAAAAT
* ** * ** * ** *
12549818 AGGAAATGGGTCCCTT-TATTTAAAGGCTAAATGACTTTAAAGT
1 AAGAAAT--AACTCTTCTAAATAGAGGCTAAACAACTTTAAAAT
* * * * *
12549861 AACAAATGGACTCCTCTATATAAAGGCTAAACAACTTTAAAAT
1 AAGAAAT-AACTCTTCTAAATAGAGGCTAAACAACTTTAAAAT
* * * *
12549904 AGGAAATAGACTCCTCTAATTAGAGGCTAAACAATTTTAAAAT
1 AAGAAATA-ACTCTTCTAAATAGAGGCTAAACAACTTTAAAAT
* *
12549947 ATGAAATAAGCTCTTCTACATAGAGGCTAAACAACTTTAAAAT
1 AAGAAATAA-CTCTTCTAAATAGAGGCTAAACAACTTTAAAAT
* * *
12549990 AAAAAATATATTCTTCTAAATAGAGGCTAAACAAATTTAAAAT
1 AAGAAATA-ACTCTTCTAAATAGAGGCTAAACAACTTTAAAAT
12550033 AAG
1 AAG
12550036 TGATTCGGAT
Statistics
Matches: 172, Mismatches: 40, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
42 6 0.03
43 162 0.94
44 4 0.02
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (42 bp):
AAGAAATAACTCTTCTAAATAGAGGCTAAACAACTTTAAAAT
Found at i:12550310 original size:65 final size:64
Alignment explanation
Indices: 12550232--12550519 Score: 324
Period size: 64 Copynumber: 4.5 Consensus size: 64
12550222 ATCTGAATTA
* * * * *
12550232 AACCAAGATCGAAGATGAGTAATCAAGATTGAATTGCAGGTCAAAAAAATAGATGTTTTGGATTG
1 AACCAAGATTGAAGATGAGTAACCAAGATTGAACTGCAGGT-AAAAAAATAAATGATTTGGATTG
* * * * * * * *
12550297 AACCAAGATCGAAGATGAGTGACCGAGATTGAACTACAAGTTAAAAAATAAATGATATGGACTG
1 AACCAAGATTGAAGATGAGTAACCAAGATTGAACTGCAGGTAAAAAAATAAATGATTTGGATTG
* * *
12550361 AACCAAGATTGAAGTTGAGTAACCAAGATTGAACTGCAGGTCAAAAAAATAAATGATCTAGATTG
1 AACCAAGATTGAAGATGAGTAACCAAGATTGAACTGCAGGT-AAAAAAATAAATGATTTGGATTG
* * * * * * **
12550426 AAACAAGATTAAAGATGAATGATCGAGATTGAACTGCAGGTTGAAAAATAAATGATTTGGATTG
1 AACCAAGATTGAAGATGAGTAACCAAGATTGAACTGCAGGTAAAAAAATAAATGATTTGGATTG
* *
12550490 AACCAAGATTGAAGATAAGTAACCAGGATT
1 AACCAAGATTGAAGATGAGTAACCAAGATT
12550520 AAACCATGGT
Statistics
Matches: 182, Mismatches: 40, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
64 94 0.52
65 88 0.48
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (64 bp):
AACCAAGATTGAAGATGAGTAACCAAGATTGAACTGCAGGTAAAAAAATAAATGATTTGGATTG
Found at i:12550380 original size:64 final size:64
Alignment explanation
Indices: 12550232--12550505 Score: 314
Period size: 65 Copynumber: 4.2 Consensus size: 64
12550222 ATCTGAATTA
* * * * * * * *
12550232 AACCAAGATCGAAGATGAGTAATCAAGATTGAATTGCAGGTCAAAAAAATAGATGTTTTGGATTG
1 AACCAAGATTGAAGATGAGTGACCGAGATTGAACTGCAGGT-TAAAAAATAAATGATTTGGATTG
* * * * *
12550297 AACCAAGATCGAAGATGAGTGACCGAGATTGAACTACAAGTTAAAAAATAAATGATATGGACTG
1 AACCAAGATTGAAGATGAGTGACCGAGATTGAACTGCAGGTTAAAAAATAAATGATTTGGATTG
* * * * * *
12550361 AACCAAGATTGAAGTTGAGTAACCAAGATTGAACTGCAGGTCAAAAAAATAAATGATCTAGATTG
1 AACCAAGATTGAAGATGAGTGACCGAGATTGAACTGCAGGT-TAAAAAATAAATGATTTGGATTG
* * * * *
12550426 AAACAAGATTAAAGATGAATGATCGAGATTGAACTGCAGGTTGAAAAATAAATGATTTGGATTG
1 AACCAAGATTGAAGATGAGTGACCGAGATTGAACTGCAGGTTAAAAAATAAATGATTTGGATTG
12550490 AACCAAGATTGAAGAT
1 AACCAAGATTGAAGAT
12550506 AAGTAACCAG
Statistics
Matches: 174, Mismatches: 34, Indels: 3
0.82 0.16 0.01
Matches are distributed among these distances:
64 86 0.49
65 88 0.51
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (64 bp):
AACCAAGATTGAAGATGAGTGACCGAGATTGAACTGCAGGTTAAAAAATAAATGATTTGGATTG
Found at i:12550401 original size:129 final size:129
Alignment explanation
Indices: 12550232--12550519 Score: 396
Period size: 129 Copynumber: 2.2 Consensus size: 129
12550222 ATCTGAATTA
* * * * * * *
12550232 AACCAAGATCGAAGATGAGTAATCAAGATTGAATTGCAGGTCAAAAAAATAGATGTTTTGGATTG
1 AACCAAGATTGAAGATGAGTAACCAAGATTGAACTGCAGGTCAAAAAAATAAATGATCTAGATTG
* * *
12550297 AACCAAGATCGAAGATGAGTGACCGAGATTGAACTACAAGTTAAAAAATAAATGATATGGACTG
66 AAACAAGATCAAAGATGAATGACCGAGATTGAACTACAAGTTAAAAAATAAATGATATGGACTG
*
12550361 AACCAAGATTGAAGTTGAGTAACCAAGATTGAACTGCAGGTCAAAAAAATAAATGATCTAGATTG
1 AACCAAGATTGAAGATGAGTAACCAAGATTGAACTGCAGGTCAAAAAAATAAATGATCTAGATTG
* * * * * * *
12550426 AAACAAGATTAAAGATGAATGATCGAGATTGAACTGCAGGTTGAAAAATAAATGATTTGGATTG
66 AAACAAGATCAAAGATGAATGACCGAGATTGAACTACAAGTTAAAAAATAAATGATATGGACTG
* *
12550490 AACCAAGATTGAAGATAAGTAACCAGGATT
1 AACCAAGATTGAAGATGAGTAACCAAGATT
12550520 AAACCATGGT
Statistics
Matches: 138, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
129 138 1.00
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (129 bp):
AACCAAGATTGAAGATGAGTAACCAAGATTGAACTGCAGGTCAAAAAAATAAATGATCTAGATTG
AAACAAGATCAAAGATGAATGACCGAGATTGAACTACAAGTTAAAAAATAAATGATATGGACTG
Found at i:12550744 original size:17 final size:17
Alignment explanation
Indices: 12550695--12550841 Score: 96
Period size: 17 Copynumber: 8.6 Consensus size: 17
12550685 GATTCATAAA
* *
12550695 GTTTACAAGAATTTCAG
1 GTTTGCAAGAATTTTAG
* * *
12550712 TTTTCACAAGAGTTTTAG
1 GTTT-GCAAGAATTTTAG
*
12550730 GTTTGTAAGAATTTTAG
1 GTTTGCAAGAATTTTAG
* * *
12550747 GTTGGCAAGAGTTTCAG
1 GTTTGCAAGAATTTTAG
* *
12550764 GTTTGCAAGATTTTTAA
1 GTTTGCAAGAATTTTAG
*
12550781 GTTTGCAAGAATTTAAG
1 GTTTGCAAGAATTTTAG
* * * *
12550798 GTTCGTAAGAACTTCAG
1 GTTTGCAAGAATTTTAG
* * * *
12550815 ATTTACAAGAACTTTGG
1 GTTTGCAAGAATTTTAG
*
12550832 GTTTGTAAGA
1 GTTTGCAAGA
12550842 GTTTCTATTT
Statistics
Matches: 98, Mismatches: 31, Indels: 2
0.75 0.24 0.02
Matches are distributed among these distances:
17 84 0.86
18 14 0.14
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (17 bp):
GTTTGCAAGAATTTTAG
Found at i:12550759 original size:34 final size:34
Alignment explanation
Indices: 12550718--12550808 Score: 110
Period size: 34 Copynumber: 2.7 Consensus size: 34
12550708 TCAGTTTTCA
* *
12550718 CAAGAGTTTTAGGTTTGTAAGAATTTTAGGTTGG
1 CAAGAGTTTAAGGTTTGTAAGAATTTTAAGTTGG
* * * *
12550752 CAAGAGTTTCAGGTTTGCAAGATTTTTAAGTTTG
1 CAAGAGTTTAAGGTTTGTAAGAATTTTAAGTTGG
* *
12550786 CAAGAATTTAAGGTTCGTAAGAA
1 CAAGAGTTTAAGGTTTGTAAGAA
12550809 CTTCAGATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.37
Consensus pattern (34 bp):
CAAGAGTTTAAGGTTTGTAAGAATTTTAAGTTGG
Found at i:12550785 original size:51 final size:52
Alignment explanation
Indices: 12550700--12550824 Score: 137
Period size: 51 Copynumber: 2.4 Consensus size: 52
12550690 ATAAAGTTTA
* * * *
12550700 CAAGAATTTCAGTTTTCACAAGAGTTTTAGGTTTGTAAGAATTTTAGGTTGG
1 CAAGAATTTCAGGTTTCACAAGAGTTTTAAGTTTGCAAGAATTTAAGGTTGG
* * * *
12550752 CAAGAGTTTCAGGTTT-GCAAGATTTTTAAGTTTGCAAGAATTTAAGGTTCG
1 CAAGAATTTCAGGTTTCACAAGAGTTTTAAGTTTGCAAGAATTTAAGGTTGG
* * *
12550803 TAAGAACTTCAGATTT-ACAAGA
1 CAAGAATTTCAGGTTTCACAAGA
12550825 ACTTTGGGTT
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
51 46 0.77
52 14 0.23
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (52 bp):
CAAGAATTTCAGGTTTCACAAGAGTTTTAAGTTTGCAAGAATTTAAGGTTGG
Found at i:12551278 original size:23 final size:24
Alignment explanation
Indices: 12551241--12551291 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
12551231 TTTCACATCT
12551241 AAAATTTTAAAGATTCATATTCAA
1 AAAATTTTAAAGATTCATATTCAA
* *
12551265 AAAATTTT-AGGATTCATATTCGA
1 AAAATTTTAAAGATTCATATTCAA
12551288 AAAA
1 AAAA
12551292 CTCCTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (24 bp):
AAAATTTTAAAGATTCATATTCAA
Found at i:12552600 original size:16 final size:16
Alignment explanation
Indices: 12552581--12552611 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12552571 TTTTTTCCTT
12552581 TTTATTTTTATTTTTC
1 TTTATTTTTATTTTTC
*
12552597 TTTATTTTTCTTTTT
1 TTTATTTTTATTTTT
12552612 TTTTGTCCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTATTTTTATTTTTC
Found at i:12553749 original size:45 final size:46
Alignment explanation
Indices: 12553693--12553784 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 46
12553683 GTGATGCTAC
*
12553693 TCATAGCTGGGCAATGAGGCTAGTAAAGGAC-TTGTGCAATATTAT
1 TCATAGCTGGGCAATGAGGCTAGTAAAAGACTTTGTGCAATATTAT
* *
12553738 TCATAGTTGGGCAATGAGGCTGGTAAAAGACTTTGTGCAATATTAT
1 TCATAGCTGGGCAATGAGGCTAGTAAAAGACTTTGTGCAATATTAT
12553784 T
1 T
12553785 GGCTATCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
45 28 0.65
46 15 0.35
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (46 bp):
TCATAGCTGGGCAATGAGGCTAGTAAAAGACTTTGTGCAATATTAT
Found at i:12555189 original size:21 final size:21
Alignment explanation
Indices: 12555164--12555222 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
12555154 AGTAAACATG
12555164 ATATATACAAAGAACAATATA
1 ATATATACAAAGAACAATATA
* *
12555185 GTATATACAAAGAATAATATA
1 ATATATACAAAGAACAATATA
* *
12555206 ATACATACAAAAAACAA
1 ATATATACAAAGAACAA
12555223 CTTAAAAGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.63, C:0.10, G:0.05, T:0.22
Consensus pattern (21 bp):
ATATATACAAAGAACAATATA
Found at i:12556657 original size:19 final size:19
Alignment explanation
Indices: 12556616--12556659 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12556606 AGTAATGAGT
* *
12556616 AAAATAATAATTAAAGATG
1 AAAATAATAATAAAAGATA
12556635 AAAATAATAATAATAAG-TA
1 AAAATAATAATAA-AAGATA
12556654 AAAATA
1 AAAATA
12556660 TAAAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (19 bp):
AAAATAATAATAAAAGATA
Found at i:12556682 original size:24 final size:24
Alignment explanation
Indices: 12556635--12556706 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 24
12556625 ATTAAAGATG
*
12556635 AAAATAATAATAATAAGTAAAAATA-TA
1 AAAATAA-AATAA-AA-T-AAAATAGCA
*
12556662 AAAATCAAATGAAAATAAAATAGCA
1 AAAATAAAAT-AAAATAAAATAGCA
*
12556687 AAACTAAAATAAAATAAAAT
1 AAAATAAAATAAAATAAAAT
12556707 CAAAATAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 16 0.41
25 10 0.26
26 5 0.13
27 8 0.21
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (24 bp):
AAAATAAAATAAAATAAAATAGCA
Found at i:12556696 original size:30 final size:29
Alignment explanation
Indices: 12556662--12556718 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
12556652 TAAAAATATA
*
12556662 AAAATCAAATGAAAAT-AAAATAGCAAAACT
1 AAAATAAAAT-AAAATCAAAATAG-AAAACT
12556692 AAAATAAAATAAAATCAAAATAGAAAA
1 AAAATAAAATAAAATCAAAATAGAAAA
12556719 TAGGATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (29 bp):
AAAATAAAATAAAATCAAAATAGAAAACT
Found at i:12561367 original size:11 final size:11
Alignment explanation
Indices: 12561351--12561379 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
12561341 AAAAATGTTT
12561351 TTTCATTTTTA
1 TTTCATTTTTA
12561362 TTTCA-TTTTA
1 TTTCATTTTTA
12561372 TTTCATTT
1 TTTCATTT
12561380 CATTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTCATTTTTA
Found at i:12562293 original size:26 final size:26
Alignment explanation
Indices: 12562264--12562314 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
12562254 AAATGAGAAG
*
12562264 AAAAAAAAGAGAAAAAGAGAAAAAAT
1 AAAAAAAAGAAAAAAAGAGAAAAAAT
*
12562290 AAAAAAAAGAAAAAAAGTGAAAAAA
1 AAAAAAAAGAAAAAAAGAGAAAAAA
12562315 GATGAATCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (26 bp):
AAAAAAAAGAAAAAAAGAGAAAAAAT
Found at i:12562320 original size:10 final size:9
Alignment explanation
Indices: 12562261--12562316 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
12562251 AAAAAATGAG
*
12562261 AAGAAAAAA
1 AAGAGAAAA
12562270 AAGAG-AAA
1 AAGAGAAAA
12562278 AAGAGAAAA
1 AAGAGAAAA
* *
12562287 AATAAAAAA
1 AAGAGAAAA
12562296 AAGA-AAAA
1 AAGAGAAAA
*
12562304 AAGTGAAAA
1 AAGAGAAAA
12562313 AAGA
1 AAGA
12562317 TGAATCGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 15 0.38
9 24 0.62
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (9 bp):
AAGAGAAAA
Found at i:12565461 original size:10 final size:10
Alignment explanation
Indices: 12565435--12565464 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
12565425 AAAAAGGATC
12565435 AAAAAAA-AA
1 AAAAAAAGAA
12565444 AAAAAAAGAA
1 AAAAAAAGAA
12565454 AAAAAAAGAA
1 AAAAAAAGAA
12565464 A
1 A
12565465 GAGAGAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.35
10 13 0.65
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:12565529 original size:12 final size:12
Alignment explanation
Indices: 12565514--12565538 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12565504 AGGAGAAAAG
12565514 AAAGAAGAAGAA
1 AAAGAAGAAGAA
12565526 AAAGAAGAAGAA
1 AAAGAAGAAGAA
12565538 A
1 A
12565539 TGAAGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAGAA
Found at i:12565587 original size:20 final size:21
Alignment explanation
Indices: 12565562--12565602 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12565552 GGTTCAGCTA
*
12565562 GGAGAA-AAGAAAAAAGAAAG
1 GGAGAAGAAGAAAAAAAAAAG
12565582 GGAGAAGAAGAAAAAAAAAAG
1 GGAGAAGAAGAAAAAAAAAAG
12565603 ATTAGGGGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (21 bp):
GGAGAAGAAGAAAAAAAAAAG
Found at i:12568316 original size:131 final size:129
Alignment explanation
Indices: 12568170--12568588 Score: 413
Period size: 131 Copynumber: 3.2 Consensus size: 129
12568160 AGCTTGATTA
* *
12568170 ATTTGTAATGATTTTTCAATGTCGTTACTTGAGTCTTTTTAAATATTTTATATAATGACAAAAAA
1 ATTTGCAATGATTTTTCAATGTCATTACTT-AGT-TTTTTAAATATTTTATATAATGACAAAAAA
* * *
12568235 AAGTTATTACAAAAAAATTTATCATATTTATAACAATAATAAAAAT-TTGTTGTGAAAACTTTTT
64 AAGTTATTACAAAAAATTTTATCATATTTGTAACAATAA-AAAAATATTGTTGTGAAAACTTATT
12568299 TT
128 TT
* * * *
12568301 ATTTGCAATGATTTTTCAAAGTAATTGCTTAAGTTATTTTTAAATATTTTATATAATGATAAAAA
1 ATTTGCAATGATTTTTCAATGTCATTACTT-AG-T-TTTTTAAATATTTTATATAATGACAAAAA
* * * * * * * *
12568366 AAA-TTATTGCAAAAAATTTTCTAATATTTGTAACAACAACAAAATGTTATTGTGAAAACTTGTT
63 AAAGTTATTACAAAAAATTTTATCATATTTGTAACAATAAAAAAATATTGTTGTGAAAACTTATT
12568430 TT
128 TT
* ** *
12568432 ATTTGTAACCA-TTTTCAATGTCATTAAGTTA-TTTTTT-AATATTTTA-A-AGATCGAC-AAAA
1 ATTTGCAATGATTTTTCAATGTCATT-ACTTAGTTTTTTAAATATTTTATATA-AT-GACAAAAA
** * ** * ** *
12568491 ATTGTTGTTATGAAAACTTTTATCATATTTGTAACAATAAAAACTTATTGTTGTGTAAACTTATT
63 AAAGTTATTACAAAAAATTTTATCATATTTGTAACAATAAAAAAATATTGTTGTGAAAACTTATT
12568556 TT
128 TT
* *
12568558 ATTTGCAATAATTTTTCAATGTCGTTACTTA
1 ATTTGCAATGATTTTTCAATGTCATTACTTA
12568589 AAAATTTTTT
Statistics
Matches: 234, Mismatches: 47, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
124 1 0.00
125 8 0.03
126 71 0.30
127 18 0.08
128 1 0.00
130 18 0.08
131 85 0.36
132 32 0.14
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (129 bp):
ATTTGCAATGATTTTTCAATGTCATTACTTAGTTTTTTAAATATTTTATATAATGACAAAAAAAA
GTTATTACAAAAAATTTTATCATATTTGTAACAATAAAAAAATATTGTTGTGAAAACTTATTTT
Found at i:12568615 original size:14 final size:15
Alignment explanation
Indices: 12568596--12568649 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 15
12568586 TTAAAAATTT
12568596 TTTAAT-ATTTTATG
1 TTTAATAATTTTATG
*
12568610 TTTAATTAATATT-T-
1 TTTAA-TAATTTTATG
12568624 TTTAAT-ATTTTATG
1 TTTAATAATTTTATG
12568638 TTTAATAATTTT
1 TTTAATAATTTT
12568650 TCATGATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
12 4 0.12
13 2 0.06
14 16 0.48
15 7 0.21
16 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (15 bp):
TTTAATAATTTTATG
Found at i:12568623 original size:28 final size:28
Alignment explanation
Indices: 12568592--12568688 Score: 107
Period size: 28 Copynumber: 3.6 Consensus size: 28
12568582 TTACTTAAAA
12568592 ATTTTTTAATATTTTATGTTTAATTAAT
1 ATTTTTTAATATTTTATGTTTAATTAAT
12568620 ATTTTTTAATATTTTATGTTTAA-T-A-
1 ATTTTTTAATATTTTATGTTTAATTAAT
* *
12568645 A-TTTTTCATGATTGT-TGTTTAATTAAT
1 ATTTTTTAAT-ATTTTATGTTTAATTAAT
*
12568672 -TTTTTTAGTATTCTTAT
1 ATTTTTTAATATT-TTAT
12568689 ATATGGATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
24 14 0.25
25 6 0.11
26 5 0.09
27 8 0.14
28 24 0.42
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (28 bp):
ATTTTTTAATATTTTATGTTTAATTAAT
Found at i:12576216 original size:3 final size:3
Alignment explanation
Indices: 12576210--12576243 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12576200 GATGATGAAG
12576210 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12576244 GAGATATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12577976 original size:20 final size:18
Alignment explanation
Indices: 12577948--12578004 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
12577938 AAATACATAA
12577948 TTAGTTTTAGGGTTTGAAGG
1 TTAGTTTTAGGGTTTG--GG
* *
12577968 TTGGTTTTAAGGTTTGGG
1 TTAGTTTTAGGGTTTGGG
*
12577986 TTAG-TTTAGGGTTTAGG
1 TTAGTTTTAGGGTTTGGG
12578003 TT
1 TT
12578005 TTTGGATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
17 13 0.41
18 5 0.16
20 14 0.44
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (18 bp):
TTAGTTTTAGGGTTTGGG
Found at i:12578024 original size:27 final size:27
Alignment explanation
Indices: 12577991--12578056 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
12577981 TTGGGTTAGT
**
12577991 TTAGGGTTTAGG-TTTTTGGATTATGG
1 TTAGGGTTTAGGATTTAAGGATTATGG
*
12578017 CTTAGGGTTTAGGATTTAAGGTTTATGG
1 -TTAGGGTTTAGGATTTAAGGATTATGG
*
12578045 TTAAGGTTTAGG
1 TTAGGGTTTAGG
12578057 GTTTGAGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.20, C:0.02, G:0.33, T:0.45
Consensus pattern (27 bp):
TTAGGGTTTAGGATTTAAGGATTATGG
Found at i:12578056 original size:34 final size:35
Alignment explanation
Indices: 12577989--12578068 Score: 94
Period size: 34 Copynumber: 2.3 Consensus size: 35
12577979 GTTTGGGTTA
* * *
12577989 GTTTAGGGTTT-AGGTTTTTGGATTATGGCTTAGG
1 GTTTAGGATTTAAGGTTTATGGATTAAGGCTTAGG
*
12578023 GTTTAGGATTTAAGGTTTATGG-TTAAGGTTTAGG
1 GTTTAGGATTTAAGGTTTATGGATTAAGGCTTAGG
12578057 GTTT-GAGATTTA
1 GTTTAG-GATTTA
12578069 GGGTATAGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
33 1 0.03
34 30 0.75
35 9 0.22
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (35 bp):
GTTTAGGATTTAAGGTTTATGGATTAAGGCTTAGG
Found at i:12578068 original size:27 final size:28
Alignment explanation
Indices: 12577995--12578068 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 28
12577985 GTTAGTTTAG
* *
12577995 GGTTTAGGTTTTTG-GA-TTATGGCTTAG
1 GGTTTAGG-ATTTGAGATTTATGGCTTAA
* *
12578022 GGTTTAGGATTTAAGGTTTATGG-TTAA
1 GGTTTAGGATTTGAGATTTATGGCTTAA
*
12578049 GGTTTAGGGTTTGAGATTTA
1 GGTTTAGGATTTGAGATTTA
12578069 GGGTATAGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 3 0.08
27 29 0.76
28 6 0.16
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.46
Consensus pattern (28 bp):
GGTTTAGGATTTGAGATTTATGGCTTAA
Found at i:12579914 original size:20 final size:20
Alignment explanation
Indices: 12579889--12579927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12579879 AATTTTGATT
* *
12579889 TTGTTTGACTAAGTTTAACA
1 TTGTTTGACCAAATTTAACA
12579909 TTGTTTGACCAAATTTAAC
1 TTGTTTGACCAAATTTAAC
12579928 CAGATTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
TTGTTTGACCAAATTTAACA
Found at i:12580279 original size:23 final size:23
Alignment explanation
Indices: 12580253--12580303 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
12580243 GCTTTTAGCT
* *
12580253 TTTTTCTATCTTTTTTTTTTTAG
1 TTTTTCTATATTTTTGTTTTTAG
* * *
12580276 TTTTTGTTTATTTTTGTTTTTGG
1 TTTTTCTATATTTTTGTTTTTAG
12580299 TTTTT
1 TTTTT
12580304 AATTTGTGGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.06, C:0.04, G:0.10, T:0.80
Consensus pattern (23 bp):
TTTTTCTATATTTTTGTTTTTAG
Found at i:12580600 original size:35 final size:36
Alignment explanation
Indices: 12580532--12580602 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
12580522 TCTTGGAAAT
** *
12580532 CATTCAAAAATTTAAAATTTTGCTTAGATGTCTTGG
1 CATTCAAAAATTTAAAATTTTGCCCAGAAGTCTTGG
*
12580568 CATTC-AAAATTTAAAGTTTTGCCCAGAAGTCTTGG
1 CATTCAAAAATTTAAAATTTTGCCCAGAAGTCTTGG
12580603 AAATCATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 26 0.84
36 5 0.16
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (36 bp):
CATTCAAAAATTTAAAATTTTGCCCAGAAGTCTTGG
Found at i:12580731 original size:40 final size:39
Alignment explanation
Indices: 12580675--12580836 Score: 130
Period size: 40 Copynumber: 4.1 Consensus size: 39
12580665 GAGGTTTTTA
* * *
12580675 AAATCATTCAAGAATTTAAGATTTTGCTTTAAGATCTTAG
1 AAATCATTCAAAAATTTAAGATTTTGC-TAAAGGTCTTAG
* *
12580715 AAATCATTCAAAAATTTAAGGTTTTTCCTAAAGGTCTTAG
1 AAATCATTCAAAAATTTAA-GATTTTGCTAAAGGTCTTAG
* * ** * * *
12580755 AATTCTTTTGAAAATTTAA-AGTTTGCCCAGAGGTCTTAG
1 AAATCATTCAAAAATTTAAGATTTTG-CTAAAGGTCTTAG
* * * *
12580794 AAATCATTTAATAATTTAAGATTTTGTCCAAAAGTCTT-G
1 AAATCATTCAAAAATTTAAGATTTTG-CTAAAGGTCTTAG
12580833 AAAT
1 AAAT
12580837 TCTTTTTAAA
Statistics
Matches: 97, Mismatches: 22, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
38 3 0.03
39 31 0.32
40 57 0.59
41 6 0.06
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (39 bp):
AAATCATTCAAAAATTTAAGATTTTGCTAAAGGTCTTAG
Found at i:12580810 original size:39 final size:39
Alignment explanation
Indices: 12580709--12580853 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 39
12580699 TGCTTTAAGA
* * * *
12580709 TCTTAGAAATCATTCAAAAATTTAAGGTTTTTCCTAAAGG
1 TCTTAGAAATCATT-TAAAATTTAAAGTTTTGCCCAAAGG
* * *
12580749 TCTTAGAATTCTTTTGAAAATTTAAAG-TTTGCCCAGAGG
1 TCTTAGAAATCATTT-AAAATTTAAAGTTTTGCCCAAAGG
* *
12580788 TCTTAGAAATCATTTAATAATTT-AAGATTTTGTCCAAAAG
1 TCTTAGAAATCATTTAA-AATTTAAAG-TTTTGCCCAAAGG
*
12580828 TCTT-GAAATTCTTTTTAAAATTTAAA
1 TCTTAGAAA-TC-ATTTAAAATTTAAA
12580854 AATTTGATTC
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
38 5 0.06
39 31 0.36
40 42 0.49
41 7 0.08
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (39 bp):
TCTTAGAAATCATTTAAAATTTAAAGTTTTGCCCAAAGG
Found at i:12580850 original size:40 final size:40
Alignment explanation
Indices: 12580725--12580875 Score: 125
Period size: 40 Copynumber: 3.8 Consensus size: 40
12580715 AAATCATTCA
* *
12580725 AAAATTTAAGGTTTT-TCCTAAAGGTCTT-AGAATTCTTTTG
1 AAAATTTAAGATTTTGTCC-AAAGGTCTTGA-AATTCTTTTT
* * * *
12580765 AAAATTTAA-AGTTTGCCCAGAGGTCTTAGAAA-TC-ATTT
1 AAAATTTAAGATTTTGTCCAAAGGTCTT-GAAATTCTTTTT
*
12580803 AATAATTTAAGATTTTGTCCAAAAGTCTTGAAATTCTTTTT
1 AA-AATTTAAGATTTTGTCCAAAGGTCTTGAAATTCTTTTT
* * *
12580844 AAAATTTAAAAATTTGATTC-AAGGTCTTGAAA
1 AAAATTTAAGATTTTG-TCCAAAGGTCTTGAAA
12580876 GTTTTGTACT
Statistics
Matches: 88, Mismatches: 15, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
38 4 0.05
39 24 0.27
40 52 0.59
41 8 0.09
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (40 bp):
AAAATTTAAGATTTTGTCCAAAGGTCTTGAAATTCTTTTT
Found at i:12581526 original size:23 final size:23
Alignment explanation
Indices: 12581500--12581545 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12581490 AGGGTTTTGA
12581500 TTTTCCTTTCACTTTT-AACATGC
1 TTTT-CTTTCACTTTTCAACATGC
**
12581523 TTTTCTTTTTCTTTTCAACATGC
1 TTTTCTTTCACTTTTCAACATGC
12581546 AATATGCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.15, C:0.24, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTCTTTCACTTTTCAACATGC
Found at i:12582672 original size:5 final size:5
Alignment explanation
Indices: 12582662--12582749 Score: 51
Period size: 5 Copynumber: 17.4 Consensus size: 5
12582652 ATTTCTTCCT
* *
12582662 TTTTC TTTTC TTTTC TTTT- TTCT- TTTTC TTTT- TTTT- TTGTTC TTTCCAC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTT--TC
* *
12582711 TTTTT TTTTC TTTTC TCCTTT- ATTTC TTTTCC TTTTC TT
1 TTTTC TTTTC TTTTC T--TTTC TTTTC TTTT-C TTTTC TT
12582750 ACTTTCTTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
4 15 0.23
5 37 0.56
6 7 0.11
7 7 0.11
ACGTcount: A:0.02, C:0.19, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:12582683 original size:17 final size:17
Alignment explanation
Indices: 12582661--12582762 Score: 68
Period size: 19 Copynumber: 5.8 Consensus size: 17
12582651 CATTTCTTCC
12582661 TTTTTCTTTTCTTTTCT
1 TTTTTCTTTTCTTTTCT
*
12582678 TTTTTCTTTTTCTTTTTTT
1 TTTTTC-TTTTC-TTTTCT
* *
12582697 TTTGTTCTTTCCACTTT-T
1 TTT-TTCTTTTC-TTTTCT
*
12582715 TTTTTCTTTTC--TCCT
1 TTTTTCTTTTCTTTTCT
12582730 TTATTTCTTTTCCTTTTCT
1 TT-TTTCTTTT-CTTTTCT
*
12582749 TACTTTC-TTTCTTT
1 T-TTTTCTTTTCTTT
12582763 CACCATTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
14 1 0.01
15 3 0.04
16 8 0.12
17 18 0.26
18 12 0.18
19 23 0.34
20 3 0.04
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTCT
Found at i:12582707 original size:18 final size:18
Alignment explanation
Indices: 12582661--12582699 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
12582651 CATTTCTTCC
12582661 TTTTTC-TTTTCTTTTCT
1 TTTTTCTTTTTCTTTTCT
12582678 TTTTTCTTTTTCTTTT-T
1 TTTTTCTTTTTCTTTTCT
12582695 TTTTT
1 TTTTT
12582700 GTTCTTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTTCT
Found at i:12582731 original size:18 final size:17
Alignment explanation
Indices: 12582661--12582731 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 17
12582651 CATTTCTTCC
*
12582661 TTTTTC-TTTTCTTTTCT
1 TTTTTCTTTTTCCTTT-T
*
12582678 TTTTTCTTTTTCTTTTT
1 TTTTTCTTTTTCCTTTT
*
12582695 TTTTTGTTCTTTCCACTTTT
1 TTTTTCTT-TTT-C-CTTTT
12582715 TTTTTCTTTTCTCCTTT
1 TTTTTCTTTT-TCCTTT
12582732 ATTTCTTTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
17 14 0.30
18 16 0.35
19 4 0.09
20 12 0.26
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTCCTTTT
Found at i:12582740 original size:22 final size:23
Alignment explanation
Indices: 12582715--12582762 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12582705 TTCCACTTTT
* *
12582715 TTTTTCTTTTC-TCCTTTATTTC
1 TTTTCCTTTTCTTACTTTATTTC
*
12582737 TTTTCCTTTTCTTACTTTCTTTC
1 TTTTCCTTTTCTTACTTTATTTC
12582760 TTT
1 TTT
12582763 CACCATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTCCTTTTCTTACTTTATTTC
Found at i:12582759 original size:23 final size:22
Alignment explanation
Indices: 12582710--12582762 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
12582700 GTTCTTTCCA
* * *
12582710 CTTTTTTTTTCTTTTCTCCTTT
1 CTTTCTTTTCCTTTTCTACTTT
*
12582732 ATTTCTTTTCCTTTTCTTACTTT
1 CTTTCTTTTCCTTTTC-TACTTT
12582755 CTTTCTTT
1 CTTTCTTT
12582763 CACCATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.74
Consensus pattern (22 bp):
CTTTCTTTTCCTTTTCTACTTT
Found at i:12583944 original size:19 final size:20
Alignment explanation
Indices: 12583916--12583962 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
12583906 CAAAAAAAAA
*
12583916 TTTCTCTTTTCTATTTTT-T
1 TTTCTTTTTTCTATTTTTGT
*
12583935 TTTCTTTTTTCTCTTTTTGT
1 TTTCTTTTTTCTATTTTTGT
*
12583955 TTTGTTTT
1 TTTCTTTT
12583963 CAAGACACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (20 bp):
TTTCTTTTTTCTATTTTTGT
Found at i:12586494 original size:167 final size:167
Alignment explanation
Indices: 12586214--12586545 Score: 513
Period size: 167 Copynumber: 2.0 Consensus size: 167
12586204 TAAGATAGAG
*
12586214 ATTTTATTTTAGGGGTTTTAGACAAAAAAGTTTATATTATTACCATTATTGAATGAATGCCACAA
1 ATTTTATTTCAGGGGTTTTAGACAAAAAAGTTTATATTATTACCATTATTGAATGAATGCCACAA
*
12586279 AATAATTTCTAACTTATATGACATACAAAACATGTCTATGAATGTATGAATATGATAATGGTGTA
66 AATAATTTCTAACTTATATGACACACAAAACATGTCTATGAATGTATGAATATGATAATGGTGTA
**
12586344 AAAGATATTGTGAAATGCAAAGATGAATAAGACAAAT
131 AAAGATATCATGAAATGCAAAGATGAATAAGACAAAT
* * *
12586381 ATTTTATTTCAGGGAG-TTTAGACCAAAAAGTTTATGTTATTACCCTTATTGAATGAATGCCACA
1 ATTTTATTTCAGGG-GTTTTAGACAAAAAAGTTTATATTATTACCATTATTGAATGAATGCCACA
* * * * * *
12586445 AAATAATTTCTAACTTATGTGACACATAGAGCATGTTTATGAGTGTATGAATATGATAATGGTGT
65 AAATAATTTCTAACTTATATGACACACAAAACATGTCTATGAATGTATGAATATGATAATGGTGT
**
12586510 AAAAGATATCATGAAATGCAAAGATGCTTAAGACAA
130 AAAAGATATCATGAAATGCAAAGATGAATAAGACAA
12586546 TGGATTTTCA
Statistics
Matches: 149, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
167 148 0.99
168 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (167 bp):
ATTTTATTTCAGGGGTTTTAGACAAAAAAGTTTATATTATTACCATTATTGAATGAATGCCACAA
AATAATTTCTAACTTATATGACACACAAAACATGTCTATGAATGTATGAATATGATAATGGTGTA
AAAGATATCATGAAATGCAAAGATGAATAAGACAAAT
Found at i:12586692 original size:23 final size:22
Alignment explanation
Indices: 12586645--12586685 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
12586635 GTGATAAGGT
* *
12586645 ATGTTTATATAGAATGTGATGC
1 ATGTTTATATAAAATGTAATGC
12586667 ATGTTT-TATAAAATGTAAT
1 ATGTTTATATAAAATGTAAT
12586686 AGTCATGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (22 bp):
ATGTTTATATAAAATGTAATGC
Found at i:12587059 original size:30 final size:30
Alignment explanation
Indices: 12587023--12587082 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
12587013 TATTACCCTT
*
12587023 ATTGAATGAATGTCGCAAAATAATTTCTAA
1 ATTGAATGAATGCCGCAAAATAATTTCTAA
12587053 ATTGAATGAATGCCGCAAAATAATTTCTAA
1 ATTGAATGAATGCCGCAAAATAATTTCTAA
12587083 CTTATATGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (30 bp):
ATTGAATGAATGCCGCAAAATAATTTCTAA
Found at i:12587606 original size:26 final size:26
Alignment explanation
Indices: 12587577--12587627 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
12587567 CATGAGAAGA
*
12587577 AATACATATACTATCTATCAAGATGG
1 AATACATATAATATCTATCAAGATGG
*
12587603 AATACATGTAATATCTATCAAGATG
1 AATACATATAATATCTATCAAGATG
12587628 TGCATGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (26 bp):
AATACATATAATATCTATCAAGATGG
Found at i:12587655 original size:37 final size:37
Alignment explanation
Indices: 12587614--12587811 Score: 145
Period size: 37 Copynumber: 5.4 Consensus size: 37
12587604 ATACATGTAA
* * ** **
12587614 TATCTATCAAGATGTGCATGAAATGGAATGCACTTTT
1 TATCTATTAAGATGTGCATGAAATGAAATGCAAGTAC
12587651 TATCTATTAAGATGTGCATGAAATGAAATGCAAGTAC
1 TATCTATTAAGATGTGCATGAAATGAAATGCAAGTAC
* * *
12587688 TATCTATTAAGATATGCATGAAA-G-AGTGTACATGTAC
1 TATCTATTAAGATGTGCATGAAATGAAATG--CAAGTAC
* ** *
12587725 TTATCTTATTAAGATGTGCATGAGAT-AAGGGCATGTAC
1 -TATC-TATTAAGATGTGCATGAAATGAAATGCAAGTAC
** * * * *
12587763 TATCTATTGGGA--TGCTTGAGATGGAATGCATGTAC
1 TATCTATTAAGATGTGCATGAAATGAAATGCAAGTAC
*
12587798 TATCTATTGAGATG
1 TATCTATTAAGATG
12587812 CATGAGATGA
Statistics
Matches: 133, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
34 9 0.07
35 23 0.17
36 7 0.05
37 63 0.47
38 11 0.08
39 17 0.13
40 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (37 bp):
TATCTATTAAGATGTGCATGAAATGAAATGCAAGTAC
Found at i:12588815 original size:25 final size:25
Alignment explanation
Indices: 12588786--12588850 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
12588776 AAAGAACAAC
12588786 AATATAAAAT-AAATGACATAATTAA
1 AATAT-AAATGAAATGACATAATTAA
** *
12588811 AATATTTATGAAATGATATAATTAA
1 AATATAAATGAAATGACATAATTAA
**
12588836 AATATGCATGAAATG
1 AATATAAATGAAATG
12588851 CAAAAAAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 2 0.06
25 32 0.94
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.32
Consensus pattern (25 bp):
AATATAAATGAAATGACATAATTAA
Done.