Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008676.1 Hibiscus syriacus cultivar Beakdansim tig00111693_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: 957917
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 4
Found at i:207117 original size:106 final size:106
Alignment explanation
Indices: 206746--207419 Score: 1073
Period size: 106 Copynumber: 6.4 Consensus size: 106
206736 AGGATTTACC
206746 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
206811 ACGAAGGGACCACTGGTTGTCAACAAAC-ATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
206851 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
206916 ACGAAGGGACCGCTGGTTGTCAACAAA-TATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
*
206956 CAGAGCCAATTTCAACTTCACAACGGAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
207021 ACGAAGGGACCGCTGGTTGTCAATAAGCAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
* *
207062 CAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
207127 ACGAAGGGACTGCTGGTTGTCAGTAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
*
207168 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
207233 ACGAAGGGACCGCTGGTTGTCAATAAGCAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
* * *
207274 CGGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
207339 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
* * *** *
207380 CAGAACCAATTTCAACTCCACGGTGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
207420 GGAACAATAC
Statistics
Matches: 533, Mismatches: 34, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
105 192 0.36
106 341 0.64
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
Found at i:209156 original size:15 final size:16
Alignment explanation
Indices: 209131--209168 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
209121 TAGTATGTAT
*
209131 ATATTTATTTTAT-TA
1 ATATTTTTTTTATCTA
*
209146 TTATTTTTTTTATCTA
1 ATATTTTTTTTATCTA
209162 ATATTTT
1 ATATTTT
209169 ATATGTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
ATATTTTTTTTATCTA
Found at i:209184 original size:16 final size:16
Alignment explanation
Indices: 209124--209186 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
209114 ATTTAGTTAG
*
209124 TATGTATATATTTATTT
1 TATGTATATATTT-TTA
*
209141 TAT-TAT-TATTTTTTT
1 TATGTATATA-TTTTTA
*
209156 TATCTA-ATA-TTTTA
1 TATGTATATATTTTTA
209170 TATGTATATATTTTTA
1 TATGTATATATTTTTA
209186 T
1 T
209187 TATTTTTACT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
14 9 0.23
15 11 0.28
16 16 0.41
17 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.67
Consensus pattern (16 bp):
TATGTATATATTTTTA
Found at i:209187 original size:40 final size:41
Alignment explanation
Indices: 209128--209222 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 41
209118 AGTTAGTATG
* *
209128 TATATATTTAT-TTTATTATTATTTTT-TTTATCTA-ATATTT
1 TATATATATATATTT-TTATTATTTTTATTTAT-TACATATTA
*
209168 TATATGTATATATTTTTATTATTTTTACTTTATTACATATTA
1 TATATATATATATTTTTATTATTTTTA-TTTATTACATATTA
209210 TATATATATATAT
1 TATATATATATAT
209223 ATATATATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
40 20 0.43
41 5 0.11
42 22 0.47
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (41 bp):
TATATATATATATTTTTATTATTTTTATTTATTACATATTA
Found at i:209215 original size:2 final size:2
Alignment explanation
Indices: 209204--209234 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
209194 ACTTTATTAC
209204 AT AT -T 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
209235 TCTACACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:220124 original size:15 final size:16
Alignment explanation
Indices: 220104--220133 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
220094 CGTCGGAAGA
220104 GGGCTTCTGG-ATTTG
1 GGGCTTCTGGTATTTG
220119 GGGCTTCTGGTATTT
1 GGGCTTCTGGTATTT
220134 CTCCTCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.13, G:0.37, T:0.43
Consensus pattern (16 bp):
GGGCTTCTGGTATTTG
Found at i:220794 original size:24 final size:24
Alignment explanation
Indices: 220760--220808 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
220750 TCTCGCTAGC
220760 CACTTCCTATTGTTAATCCACCTT
1 CACTTCCTATTGTTAATCCACCTT
*
220784 CACTTCTTATTGTTAATCCACCTT
1 CACTTCCTATTGTTAATCCACCTT
220808 C
1 C
220809 TATCCACTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTTCCTATTGTTAATCCACCTT
Found at i:223342 original size:37 final size:37
Alignment explanation
Indices: 223266--223342 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
223256 TTTTTATTTT
*
223266 TTTAATTTTGTAAACAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAACAAAATTATATAAATATTATCAA
* * * *
223303 TTTAATTTTTTTAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAACAAAATTATATAAATATTAT-CAA
223340 TTT
1 TTT
223343 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 13 0.38
37 21 0.62
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAACAAAATTATATAAATATTATCAA
Found at i:223564 original size:20 final size:20
Alignment explanation
Indices: 223492--223558 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
223482 TATTCTCTGG
*
223492 TAATCTTTTATTCTCACTGG
1 TAATCTTTTATTCTCACTGA
223512 TAATCTTTTATTCTCACTGA
1 TAATCTTTTATTCTCACTGA
223532 TAATCTTTTATTCTCACTGA
1 TAATCTTTTATTCTCACTGA
223552 TAATCTT
1 TAATCTT
223559 ACATTCCGTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.51
Consensus pattern (20 bp):
TAATCTTTTATTCTCACTGA
Found at i:223611 original size:47 final size:47
Alignment explanation
Indices: 223542--223635 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
223532 TAATCTTTTA
*
223542 TTCTCACTGATAATCTTACATTCCGTGAACCAAACTCACCCCTAAAT
1 TTCTCACTGATAATCTTACATTCCGTGAACCAAAATCACCCCTAAAT
223589 TTCTCACTGATAATCTTACATTCCGTGAACCAAAATCACCCCTAAAT
1 TTCTCACTGATAATCTTACATTCCGTGAACCAAAATCACCCCTAAAT
223636 ATATGTTCTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.30
Consensus pattern (47 bp):
TTCTCACTGATAATCTTACATTCCGTGAACCAAAATCACCCCTAAAT
Found at i:249015 original size:68 final size:68
Alignment explanation
Indices: 248906--249042 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
248896 GAGCTATTTT
248906 ATGGATTGCCAAATAAAGGCCTGAAACCAACAGTTGTAACTTATTCTATAATGATCCAGTTTCTG
1 ATGGATTGCCAAATAAAGGCCTGAAACCAACAGTTGTAACTTATTCTATAATGATCCAGTTTCTG
248971 TGC
66 TGC
248974 ATGGATTGCCAAATAAAGGCCTGAAACCAACAGTTGTAACTTATTCTATAATGATCCAGTTTCTG
1 ATGGATTGCCAAATAAAGGCCTGAAACCAACAGTTGTAACTTATTCTATAATGATCCAGTTTCTG
249039 TGC
66 TGC
249042 A
1 A
249043 AGGAAGGGCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (68 bp):
ATGGATTGCCAAATAAAGGCCTGAAACCAACAGTTGTAACTTATTCTATAATGATCCAGTTTCTG
TGC
Found at i:250427 original size:2 final size:2
Alignment explanation
Indices: 250416--250469 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
250406 TAGAATTCTT
250416 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
250457 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
250470 TGCCGAAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:250981 original size:2 final size:2
Alignment explanation
Indices: 250974--251018 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
250964 TAAGCTGATA
250974 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
251016 AT A
1 AT A
251019 AAACCAAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:253873 original size:7 final size:7
Alignment explanation
Indices: 253861--253886 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
253851 CTTCAAATGA
253861 TGACGGG
1 TGACGGG
253868 TGACGGG
1 TGACGGG
253875 TGACGGG
1 TGACGGG
253882 TGACG
1 TGACG
253887 ATTGGTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.54, T:0.15
Consensus pattern (7 bp):
TGACGGG
Found at i:256596 original size:34 final size:34
Alignment explanation
Indices: 256550--256619 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
256540 ATTTTTTAAA
*
256550 AAATGTTTGCATTTACTTTCAAAAGTCATGCATT
1 AAATGTTAGCATTTACTTTCAAAAGTCATGCATT
*
256584 AAATGTTAGCATTTACTTTCAAAAGTCGTGCATT
1 AAATGTTAGCATTTACTTTCAAAAGTCATGCATT
256618 AA
1 AA
256620 GAACTGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (34 bp):
AAATGTTAGCATTTACTTTCAAAAGTCATGCATT
Found at i:259989 original size:41 final size:41
Alignment explanation
Indices: 259944--260026 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
259934 CCGGTGAAAG
*
259944 GGTCCGATCACAATCCGTGCACGTACATCCCTGGAAGAGAA
1 GGTCCGATCACAATCCGTGCACGAACATCCCTGGAAGAGAA
* *
259985 GGTCCGGTCACAATTCGTGCACGAACATCCCTGGAAGAGAA
1 GGTCCGATCACAATCCGTGCACGAACATCCCTGGAAGAGAA
260026 G
1 G
260027 CCGGCGTCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (41 bp):
GGTCCGATCACAATCCGTGCACGAACATCCCTGGAAGAGAA
Found at i:283015 original size:3 final size:3
Alignment explanation
Indices: 283007--283063 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
282997 TCTCTACTTG
* * *
283007 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT GAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
283055 AAT AAT AAT
1 AAT AAT AAT
283064 CCATCTTCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:298130 original size:10 final size:10
Alignment explanation
Indices: 298101--298142 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
298091 AATACTAATA
*
298101 TAAATTATTAT
1 TAAAATATT-T
*
298112 TATAATATTT
1 TAAAATATTT
298122 TAAAATATTT
1 TAAAATATTT
298132 TAAAATATTT
1 TAAAATATTT
298142 T
1 T
298143 TATGATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 21 0.75
11 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TAAAATATTT
Found at i:301115 original size:14 final size:14
Alignment explanation
Indices: 301096--301126 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
301086 ACATAAAACT
301096 TAACCACACTCTAA
1 TAACCACACTCTAA
301110 TAACCACACTCTAA
1 TAACCACACTCTAA
301124 TAA
1 TAA
301127 GCACTAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (14 bp):
TAACCACACTCTAA
Found at i:309480 original size:14 final size:14
Alignment explanation
Indices: 309461--309494 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
309451 GGCTATCAGT
309461 ACTGTATGGCTGTG
1 ACTGTATGGCTGTG
309475 ACTGTATGGCTGTG
1 ACTGTATGGCTGTG
309489 ACTGTA
1 ACTGTA
309495 AGTCTTGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.32, T:0.35
Consensus pattern (14 bp):
ACTGTATGGCTGTG
Found at i:309645 original size:33 final size:33
Alignment explanation
Indices: 309603--309671 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
309593 AAAGAATGGC
309603 TGCATTTAGGAAGAACTATAAGCTGGCATTTCA
1 TGCATTTAGGAAGAACTATAAGCTGGCATTTCA
309636 TGCATTTAGGAAGAACTATAAGCTGGCATTTCA
1 TGCATTTAGGAAGAACTATAAGCTGGCATTTCA
309669 TGC
1 TGC
309672 TCTTGGAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (33 bp):
TGCATTTAGGAAGAACTATAAGCTGGCATTTCA
Found at i:310749 original size:23 final size:23
Alignment explanation
Indices: 310722--310795 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
310712 AACATGAAAA
310722 ATAAAGATATAGTAAAACATATC
1 ATAAAGATATAGTAAAACATATC
310745 ATAAAGATATAGTAAAACATGA-C
1 ATAAAGATATAGTAAAACAT-ATC
* * * *
310768 ATAAAGACAAAGGAAAACATATT
1 ATAAAGATATAGTAAAACATATC
310791 ATAAA
1 ATAAA
310796 ATCAAAGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 43 0.96
24 1 0.02
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.22
Consensus pattern (23 bp):
ATAAAGATATAGTAAAACATATC
Found at i:314610 original size:75 final size:72
Alignment explanation
Indices: 314518--314668 Score: 230
Period size: 75 Copynumber: 2.1 Consensus size: 72
314508 TTTTATTTCG
* * *
314518 GGTCGGATCGGGTCGGATGAAACCTTAATTTTGTCGGGTCGGGTCACGAGTGGATGACCCTTTTT
1 GGTCGGATCGGGTCGGATGAAACCTTAATTTTGTCGGATCGGATCACGAATGGATGA-CCTTTTT
314583 CTCGGGTCC
65 -TCGGGTCC
*
314592 GGTCGGGATCGGGTCGGATGAAACTTTAATTTTGTCGGATCGGATCACGAATGGATGACCTTTTT
1 GGTC-GGATCGGGTCGGATGAAACCTTAATTTTGTCGGATCGGATCACGAATGGATGACCTTTTT
*
314657 TCGGGTCG
65 TCGGGTCC
314665 GGTC
1 GGTC
314669 AGATGGCCCA
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
73 11 0.15
74 11 0.15
75 49 0.69
ACGTcount: A:0.17, C:0.19, G:0.34, T:0.30
Consensus pattern (72 bp):
GGTCGGATCGGGTCGGATGAAACCTTAATTTTGTCGGATCGGATCACGAATGGATGACCTTTTTT
CGGGTCC
Found at i:333533 original size:2 final size:2
Alignment explanation
Indices: 333526--333560 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
333516 AACATCTTAA
*
333526 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
333561 AAATTAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:335692 original size:49 final size:49
Alignment explanation
Indices: 335543--335692 Score: 109
Period size: 49 Copynumber: 3.1 Consensus size: 49
335533 ATTGTCAAAC
335543 TCTACTATTCTTTCCAAGATGATGGCTACCTTTATCTCGTAATGGAATA
1 TCTACTATTCTTTCCAAGATGATGGCTACCTTTATCTCGTAATGGAATA
** ** * ** * *
335592 TCTAC----CTGGCGGAGAT-AT-GATGACCTTACTTAT-GAGTATTGTCAA-A
1 TCTACTATTCTTTCCAAGATGATGGCT-ACC-T--TTATCTCGTAATG-GAATA
335638 CTCTACTATTCTTTCCAAGATGATGGCTACCTTTATCTCGTAATGGAATA
1 -TCTACTATTCTTTCCAAGATGATGGCTACCTTTATCTCGTAATGGAATA
335688 TCTAC
1 TCTAC
335693 CTGGCGGAGA
Statistics
Matches: 69, Mismatches: 18, Indels: 28
0.60 0.16 0.24
Matches are distributed among these distances:
43 2 0.03
44 5 0.07
45 8 0.12
46 6 0.09
47 11 0.16
49 16 0.23
50 6 0.09
51 8 0.12
52 5 0.07
53 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.37
Consensus pattern (49 bp):
TCTACTATTCTTTCCAAGATGATGGCTACCTTTATCTCGTAATGGAATA
Found at i:335695 original size:96 final size:96
Alignment explanation
Indices: 335531--335723 Score: 386
Period size: 96 Copynumber: 2.0 Consensus size: 96
335521 GACAGCAATT
335531 GTATTGTCAAACTCTACTATTCTTTCCAAGATGATGGCTACCTTTATCTCGTAATGGAATATCTA
1 GTATTGTCAAACTCTACTATTCTTTCCAAGATGATGGCTACCTTTATCTCGTAATGGAATATCTA
335596 CCTGGCGGAGATATGATGACCTTACTTATGA
66 CCTGGCGGAGATATGATGACCTTACTTATGA
335627 GTATTGTCAAACTCTACTATTCTTTCCAAGATGATGGCTACCTTTATCTCGTAATGGAATATCTA
1 GTATTGTCAAACTCTACTATTCTTTCCAAGATGATGGCTACCTTTATCTCGTAATGGAATATCTA
335692 CCTGGCGGAGATATGATGACCTTACTTATGA
66 CCTGGCGGAGATATGATGACCTTACTTATGA
335723 G
1 G
335724 AAAGGATATC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (96 bp):
GTATTGTCAAACTCTACTATTCTTTCCAAGATGATGGCTACCTTTATCTCGTAATGGAATATCTA
CCTGGCGGAGATATGATGACCTTACTTATGA
Found at i:338611 original size:3 final size:3
Alignment explanation
Indices: 338603--338633 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
338593 TGCTTAAGCA
338603 TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
338634 AAGCTGGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:342338 original size:18 final size:17
Alignment explanation
Indices: 342317--342350 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
342307 ATAAAAGTTG
342317 GTTTGCAAATGCATTTTA
1 GTTTGCAAATGC-TTTTA
*
342335 GTTTGCAGATGCTTTT
1 GTTTGCAAATGCTTTT
342351 CGTCATTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (17 bp):
GTTTGCAAATGCTTTTA
Found at i:344154 original size:3 final size:3
Alignment explanation
Indices: 344146--344177 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
344136 ATTGTCATCT
344146 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
344178 TTCATTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:352546 original size:17 final size:18
Alignment explanation
Indices: 352521--352556 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
352511 GGCTTACGGA
*
352521 GATCTTCAT-TGTCCTGG
1 GATCATCATATGTCCTGG
352538 GATCATCATATGTCCTGG
1 GATCATCATATGTCCTGG
352556 G
1 G
352557 CATGTGGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (18 bp):
GATCATCATATGTCCTGG
Found at i:370973 original size:21 final size:21
Alignment explanation
Indices: 370947--370991 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
370937 GATTTCTGGG
* *
370947 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
370968 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
370989 CAA
1 CAA
370992 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:372523 original size:13 final size:13
Alignment explanation
Indices: 372505--372567 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
372495 TCTACGGGCA
372505 CTACGGTGCAATT
1 CTACGGTGCAATT
372518 CTACGG-GC-A--
1 CTACGGTGCAATT
372527 CTACGGTGCAATT
1 CTACGGTGCAATT
372540 CTACGG-GC-A--
1 CTACGGTGCAATT
*
372549 CTTCGGTGCAATT
1 CTACGGTGCAATT
372562 CTACGG
1 CTACGG
372568 GGCACTTCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 11 0.28
10 4 0.10
11 4 0.10
12 4 0.10
13 17 0.43
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:372589 original size:23 final size:22
Alignment explanation
Indices: 372492--372581 Score: 153
Period size: 22 Copynumber: 4.0 Consensus size: 22
372482 TTATGGACAT
372492 AATTCTACGGGCACTACGGTGC
1 AATTCTACGGGCACTACGGTGC
372514 AATTCTACGGGCACTACGGTGC
1 AATTCTACGGGCACTACGGTGC
*
372536 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTACGGTGC
*
372558 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTACGGTGC
372581 A
1 A
372582 TTTATACGAG
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
22 51 0.77
23 15 0.23
ACGTcount: A:0.21, C:0.27, G:0.28, T:0.24
Consensus pattern (22 bp):
AATTCTACGGGCACTACGGTGC
Found at i:373941 original size:26 final size:24
Alignment explanation
Indices: 373912--373981 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 24
373902 TAACCTACCA
373912 TATTTATTTCATTTTTTAACATCATT
1 TATTTATTTC-TTTTTTAACATCA-T
*
373938 TATTTCCTTT-TTTTATTAACATCAT
1 TATTT-ATTTCTTTT-TTAACATCAT
*
373963 CATTTATTTCCCTTTTTTA
1 TATTTATTT--CTTTTTTA
373982 TTGCATATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
24 3 0.08
25 9 0.25
26 17 0.47
27 7 0.19
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTATTTCTTTTTTAACATCAT
Found at i:375209 original size:17 final size:18
Alignment explanation
Indices: 375176--375209 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
375166 ATTTAAATTG
375176 CGGTTGCAGTCGCATTTT
1 CGGTTGCAGTCGCATTTT
*
375194 CGGTTGC-GTTGCATTT
1 CGGTTGCAGTCGCATTT
375210 ATCGCGATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.09, C:0.21, G:0.29, T:0.41
Consensus pattern (18 bp):
CGGTTGCAGTCGCATTTT
Found at i:386348 original size:6 final size:6
Alignment explanation
Indices: 386337--386368 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
386327 AGACACGTAT
386337 GACCAC GACCAC GACCAC GACCAC GACCAC GA
1 GACCAC GACCAC GACCAC GACCAC GACCAC GA
386369 GACGAGACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.47, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:386797 original size:21 final size:21
Alignment explanation
Indices: 386773--386926 Score: 134
Period size: 21 Copynumber: 7.5 Consensus size: 21
386763 GTTTTAAGGT
*
386773 GCAACGCGATTTTCAACTATC
1 GCAACGCGAATTTCAACTATC
* ** *
386794 GCAACGCGAAATGGAA-AATC
1 GCAACGCGAATTTCAACTATC
386814 GCAACGCGAATTTCAACTATC
1 GCAACGCGAATTTCAACTATC
* ** *
386835 GCAACGCGAAATGGAA-AATC
1 GCAACGCGAATTTCAACTATC
*
386855 GCAACGCGATTTTCAACTATC
1 GCAACGCGAATTTCAACTATC
* ** * *
386876 GCAACGCGAAATGGAA-AAAC
1 GCAACGCGAATTTCAACTATC
*
386896 GCAACGCGATTTTCAACTATC
1 GCAACGCGAATTTCAACTATC
*
386917 GCAATGCGAA
1 GCAACGCGAA
386927 ATGCAACGTG
Statistics
Matches: 98, Mismatches: 32, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
20 45 0.46
21 53 0.54
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (21 bp):
GCAACGCGAATTTCAACTATC
Found at i:386816 original size:20 final size:20
Alignment explanation
Indices: 386791--386904 Score: 120
Period size: 20 Copynumber: 5.6 Consensus size: 20
386781 ATTTTCAACT
386791 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** *
386811 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAAATGGAA-A
386832 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
386852 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
386873 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
386893 AACGCAACGCGA
1 ATCGCAACGCGA
386905 TTTTCAACTA
Statistics
Matches: 73, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
20 42 0.58
21 31 0.42
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:386830 original size:41 final size:41
Alignment explanation
Indices: 386773--386929 Score: 287
Period size: 41 Copynumber: 3.8 Consensus size: 41
386763 GTTTTAAGGT
386773 GCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
1 GCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
*
386814 GCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATC
1 GCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
*
386855 GCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAAAC
1 GCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
*
386896 GCAACGCGATTTTCAACTATCGCAATGCGAAATG
1 GCAACGCGATTTTCAACTATCGCAACGCGAAATG
386930 CAACGTGAAT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
GCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
Found at i:387412 original size:15 final size:14
Alignment explanation
Indices: 387384--387410 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
387374 GTTTTTTAAT
387384 TTTTTTAAAATTTA
1 TTTTTTAAAATTTA
387398 TTTTTTAAAATTT
1 TTTTTTAAAATTT
387411 TAAAATTTTA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTAAAATTTA
Found at i:394389 original size:20 final size:20
Alignment explanation
Indices: 394366--394403 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
394356 TCAGTCAACT
* *
394366 ATCACTTTAATTTTGTTTTG
1 ATCACTCTAACTTTGTTTTG
394386 ATCACTCTAACTTTGTTT
1 ATCACTCTAACTTTGTTT
394404 CTTCAAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (20 bp):
ATCACTCTAACTTTGTTTTG
Found at i:404837 original size:2 final size:2
Alignment explanation
Indices: 404827--404860 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
404817 ATAGTTAAAT
*
404827 TA TA T- TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
404861 GTCATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:404961 original size:14 final size:14
Alignment explanation
Indices: 404944--404970 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
404934 AAAACAATGG
404944 GAGAGAGAAAAGTA
1 GAGAGAGAAAAGTA
404958 GAGAGAGAAAAGT
1 GAGAGAGAAAAGT
404971 TAAAAGGGAA
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:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (14 bp):
GAGAGAGAAAAGTA
Found at i:405170 original size:17 final size:19
Alignment explanation
Indices: 405148--405182 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
405138 GCTTTTGTTC
405148 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
405165 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
405183 GAGATGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:411621 original size:6 final size:6
Alignment explanation
Indices: 411610--411637 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
411600 AAATAACTCC
411610 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
411638 TATGTCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:413478 original size:22 final size:22
Alignment explanation
Indices: 413438--413480 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
413428 TGTTCCACTC
*
413438 TCCTATTCCCTCTATCTTTCCA
1 TCCTATTCCCTCTACCTTTCCA
* *
413460 TCCTATTTCCTCTCCCTTTCC
1 TCCTATTCCCTCTACCTTTCC
413481 CTTAATTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.44, G:0.00, T:0.47
Consensus pattern (22 bp):
TCCTATTCCCTCTACCTTTCCA
Found at i:436466 original size:40 final size:40
Alignment explanation
Indices: 436401--436480 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
436391 AAAAGTGTGA
* *
436401 AATAAAATAACAATTATCATATATTAAGTAAAATTAATCT
1 AATAAAATAACAATGACCATATATTAAGTAAAATTAATCT
* *
436441 AATAAAATAACAATGGCCATCTATTAAGTAAAATTAATCT
1 AATAAAATAACAATGACCATATATTAAGTAAAATTAATCT
436481 GATTCCTAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (40 bp):
AATAAAATAACAATGACCATATATTAAGTAAAATTAATCT
Found at i:437419 original size:20 final size:18
Alignment explanation
Indices: 437394--437440 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
437384 TTTGGTTCAC
437394 GGAATATAAGATTACCAGTG
1 GGAATATAAGATTACCA--G
* *
437414 GGAATAAAAGATTATCAG
1 GGAATATAAGATTACCAG
437432 GGAATATAA
1 GGAATATAA
437441 TTACTTAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
20 15 0.62
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.23
Consensus pattern (18 bp):
GGAATATAAGATTACCAG
Found at i:455436 original size:21 final size:20
Alignment explanation
Indices: 455407--455446 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
455397 ATAACCAAAA
455407 TGATCATTTAATATAATTTAG
1 TGATCATTT-ATATAATTTAG
* *
455428 TGATTATTTGTATAATTTA
1 TGATCATTTATATAATTTA
455447 CACTAAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (20 bp):
TGATCATTTATATAATTTAG
Found at i:456420 original size:22 final size:22
Alignment explanation
Indices: 456394--456439 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
456384 CAATTTTTAC
456394 TAAGGGCCTCTTTATAAGAATT
1 TAAGGGCCTCTTTATAAGAATT
* *
456416 TAAGGGTCTCTTTTTAAGAATT
1 TAAGGGCCTCTTTATAAGAATT
456438 TA
1 TA
456440 CACAGAGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (22 bp):
TAAGGGCCTCTTTATAAGAATT
Found at i:459958 original size:14 final size:14
Alignment explanation
Indices: 459939--459977 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
459929 CAAAAATAAA
* *
459939 AATAAAATAAAGTT
1 AATAAAATAAAATG
459953 AATAAAATAAAATG
1 AATAAAATAAAATG
459967 AAT-AAATAAAA
1 AATAAAATAAAA
459978 AAATAATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (14 bp):
AATAAAATAAAATG
Found at i:460080 original size:36 final size:36
Alignment explanation
Indices: 459996--460381 Score: 333
Period size: 36 Copynumber: 10.6 Consensus size: 36
459986 CTAATGATAT
* * *
459996 AAACTATATA--ATATATATTTCAAAAATATTTT-T
1 AAACTATATATTATATATATTTTAAAAATGTTTTAA
*
460029 AAACTATATATTATATATATTTTAAAAATGTTTTCA
1 AAACTATATATTATATATATTTTAAAAATGTTTTAA
*** *
460065 ACGTTATATATTATATAGT-TTTCAAAAATGTTTT-A
1 AAACTATATATTATATA-TATTTTAAAAATGTTTTAA
* * *
460100 AAACTATATATTATATATGTTCTCAAAAAATGTTTTTA
1 AAACTATATATTATATATATT-T-TAAAAATGTTTTAA
*
460138 AAACTATAT-TATATATATATTTTCAAAATGTTTTAA
1 AAACTATATAT-TATATATATTTTAAAAATGTTTTAA
*
460174 AAACTATATATATATATATATGTTTTCAAAATGTTTTAA
1 AAACTATATAT-TATATATA--TTTTAAAAATGTTTTAA
* *
460213 AAACCATATA-T-TATATATTTTCAAAATGTTTTTAA
1 AAACTATATATTATATATATTTTAAAAATG-TTTTAA
*
460248 AAACTATATATT-T-TATAGTTTTCAAAATGTTTTTAA
1 AAACTATATATTATATATA-TTTTAAAAATG-TTTTAA
* * *
460284 AAACTATATAATATATACATTTTCAAAAAAGTGTTTTCA
1 AAACTATATATTATATATATTTT--AAAAA-TGTTTTAA
* * ** **
460323 AAGCTATATATATTATATATATTTCAAAAATCATTTGC
1 AAAC--TATATATTATATATATTTTAAAAATGTTTTAA
460361 AAACTATATATATATATATAT
1 AAACTATATAT-TATATATAT
460382 AATAAAAAAA
Statistics
Matches: 300, Mismatches: 30, Indels: 42
0.81 0.08 0.11
Matches are distributed among these distances:
33 10 0.03
34 12 0.04
35 56 0.19
36 93 0.31
37 39 0.13
38 29 0.10
39 43 0.14
40 2 0.01
41 16 0.05
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
AAACTATATATTATATATATTTTAAAAATGTTTTAA
Found at i:460153 original size:73 final size:71
Alignment explanation
Indices: 459996--460379 Score: 329
Period size: 73 Copynumber: 5.3 Consensus size: 71
459986 CTAATGATAT
* * * * *
459996 AAACTATATAATATATA-TTTCAAAAATATTTT-TAAACTATATATTATATATATTTTAAAAATG
1 AAACTATATTATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATATGTTTCAAAAATG
*
460059 TTTTCA
66 TTTTTA
***
460065 ACGTTATA-TATTATATAGTTTTCAAAAATGTTTT-AAAACTATATATTATATATGTTCTCAAAA
1 AAACTATATTA-TATATA-TTTTCAAAAATGTTTTAAAAACTATATATTATATATGTT-TC-AAA
460128 AATGTTTTTA
62 AATGTTTTTA
460138 AAACTATATTATATATATATTTTC-AAAATGTTTTAAAAACTATATATATATATATATGTTTTC-
1 AAACTATA-T-TATATATATTTTCAAAAATGTTTTAAAAAC--TATATAT-TATATATG-TTTCA
*
460201 AAAATGTTTTAA
60 AAAATGTTTTTA
* *
460213 AAACCATA-TATTATATATTTTC-AAAATGTTTTTAAAAACTATATATTTTATA-GTTTTC-AAA
1 AAACTATATTA-TATATATTTTCAAAAATG-TTTTAAAAACTATATATTATATATG-TTTCAAAA
460274 ATGTTTTTAA
63 ATGTTTTT-A
* * * *
460284 AAACTATATAATATATACATTTTCAAAAAAGTGTTTTCAAAGCTATATATATTATATATATTTCA
1 AAACTATAT--TATATATATTTTC-AAAAA-TGTTTTAAAAAC--TATATATTATATATGTTTCA
** **
460349 AAAATCATTTGC
60 AAAATGTTTTTA
460361 AAACTATATATATATATAT
1 AAACTATAT-TATATATAT
460380 ATAATAAAAA
Statistics
Matches: 262, Mismatches: 27, Indels: 45
0.78 0.08 0.13
Matches are distributed among these distances:
68 1 0.00
69 11 0.04
70 16 0.06
71 47 0.18
72 10 0.04
73 54 0.21
74 22 0.08
75 36 0.14
76 20 0.08
77 35 0.13
78 10 0.04
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (71 bp):
AAACTATATTATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATATGTTTCAAAAATG
TTTTTA
Found at i:461643 original size:3 final size:3
Alignment explanation
Indices: 461635--461689 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
461625 TAATCAAGAA
461635 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
461683 AAT AAT A
1 AAT AAT A
461690 GAATGAAGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:465499 original size:40 final size:40
Alignment explanation
Indices: 465453--465536 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
465443 TTTGTGATTT
* *
465453 TAAATTTTTAATATAATTTTTTAAGTTTGTATTCCTAACA
1 TAAATTTGTAATATAAATTTTTAAGTTTGTATTCCTAACA
* * *
465493 TAAATTTGTAATATAAATTTTTAGGTTTGTATTTCTAACG
1 TAAATTTGTAATATAAATTTTTAAGTTTGTATTCCTAACA
465533 TAAA
1 TAAA
465537 ATCATGTCGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (40 bp):
TAAATTTGTAATATAAATTTTTAAGTTTGTATTCCTAACA
Found at i:467859 original size:73 final size:74
Alignment explanation
Indices: 467740--467888 Score: 257
Period size: 73 Copynumber: 2.0 Consensus size: 74
467730 GCTACATCTG
*
467740 AATTAAGATGTTTAATTTGTTTATTATGTTATGTATGAATAATTAAATATATATA-ATATATAGT
1 AATTAAGATGTTTAATTTGTTTATTATATTATGTATGAATAATTAAATATATATAGA-ATATAGT
*
467804 AGATGT-TAA
65 AGAAGTATAA
467813 AATTAAGATGTTTAATTTGTTTATTATATTATGTATGAATAATTAAATATATATAGAATATAGTA
1 AATTAAGATGTTTAATTTGTTTATTATATTATGTATGAATAATTAAATATATATAGAATATAGTA
467878 GAAGTATAA
66 GAAGTATAA
467887 AA
1 AA
467889 GATATTGCTT
Statistics
Matches: 72, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
73 66 0.92
74 6 0.08
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (74 bp):
AATTAAGATGTTTAATTTGTTTATTATATTATGTATGAATAATTAAATATATATAGAATATAGTA
GAAGTATAA
Found at i:471465 original size:37 final size:37
Alignment explanation
Indices: 471392--471466 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
471382 TTTATAAAAT
*
471392 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
471429 ATTTATATAATATTT-TTTACAAAATTTAAAAT-ATAAA
1 ATTTATAT-AT-TTTCTTTAAAAAAATTAAAATCATAAA
471466 A
1 A
471467 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 16 0.48
39 3 0.09
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:474067 original size:29 final size:29
Alignment explanation
Indices: 474026--474091 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
474016 GAAGCAAACG
* *
474026 CGCTGAATGCTGAACGCTTCAACATTTAA
1 CGCTGAATACTGAACGATTCAACATTTAA
474055 CGCTGAATACTGAACGATTCAACATTTAA
1 CGCTGAATACTGAACGATTCAACATTTAA
474084 CGCTGAAT
1 CGCTGAAT
474092 GATTTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (29 bp):
CGCTGAATACTGAACGATTCAACATTTAA
Found at i:490587 original size:20 final size:19
Alignment explanation
Indices: 490559--490604 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
490549 AAATTAATGG
490559 GTCAAAGTC-AGATTTAACA
1 GTCAAAGTCAAGA-TTAACA
490578 GTCAATAGTCAAGATTAACA
1 GTCAA-AGTCAAGATTAACA
*
490598 ATCAAAG
1 GTCAAAG
490605 GTCTATGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (19 bp):
GTCAAAGTCAAGATTAACA
Found at i:491454 original size:3 final size:3
Alignment explanation
Indices: 491448--491483 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
491438 AGAAGAGATT
*
491448 TTC TTC TTC GTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
491484 ATAAAACTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:505699 original size:136 final size:137
Alignment explanation
Indices: 505475--505728 Score: 345
Period size: 136 Copynumber: 1.9 Consensus size: 137
505465 CATGTGTTCT
* * * * *
505475 TTTGTGTAATGATTGAGCTTTAACACAAGCTTTACGAGGGCATTTGATAGTTCTTCTAATCTTCA
1 TTTGTGTAATGATTGAGATTGAACACAAGCTTTACGAGGGCATATGATAGTTATTCTAATCATCA
*
505540 TGCTCCCAAATATTATATTAATAAGC-AGAGGACTATCTGTTTTGGGTCTTTCAGTCAATTCAAT
66 TGCTCCCAAATATTATATAAATAAGCAAGAGGACTATCTGTTTTGGGTCTTTCAGTCAATTCAAT
505604 ATGTTGA
131 ATGTTGA
*
505611 TTTGTGTAATGATTGA-ATTGATACACAAGCTTTACTAGGGCATATGATA-TTAATTCTAATCAT
1 TTTGTGTAATGATTGAGATTGA-ACACAAGCTTTACGAGGGCATATGATAGTT-ATTCTAATCAT
* * * *
505674 CATGCT-TCAAATCTTATACTAAATAAGCAAAGGGGGCTATCTGTTTTGGGTCTTT
64 CATGCTCCCAAATATTATA-TAAATAAGC-AAGAGGACTATCTGTTTTGGGTCTTT
505729 GTGTTACAAT
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
135 15 0.15
136 64 0.63
138 23 0.23
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (137 bp):
TTTGTGTAATGATTGAGATTGAACACAAGCTTTACGAGGGCATATGATAGTTATTCTAATCATCA
TGCTCCCAAATATTATATAAATAAGCAAGAGGACTATCTGTTTTGGGTCTTTCAGTCAATTCAAT
ATGTTGA
Found at i:514629 original size:10 final size:10
Alignment explanation
Indices: 514614--514639 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
514604 ATGTGTCACT
514614 CCAAGATACC
1 CCAAGATACC
514624 CCAAGATACC
1 CCAAGATACC
514634 CCAAGA
1 CCAAGA
514640 AGTCTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.38, G:0.12, T:0.08
Consensus pattern (10 bp):
CCAAGATACC
Found at i:515272 original size:16 final size:16
Alignment explanation
Indices: 515253--515283 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
515243 CAAAAGAGAG
515253 AGTAAAGAAAACATTA
1 AGTAAAGAAAACATTA
515269 AGTAAAGAAAACATT
1 AGTAAAGAAAACATT
515284 GTGTTTAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (16 bp):
AGTAAAGAAAACATTA
Found at i:529682 original size:3 final size:3
Alignment explanation
Indices: 529674--529698 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
529664 GTAATTAAGA
529674 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
529699 GCCTACTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:532176 original size:31 final size:31
Alignment explanation
Indices: 532140--532198 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
532130 AACTTAAAAG
* *
532140 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
532171 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
532199 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:532249 original size:22 final size:22
Alignment explanation
Indices: 532223--532265 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
532213 TAATAAATTA
532223 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
532245 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
532266 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:532271 original size:18 final size:18
Alignment explanation
Indices: 532250--532306 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
532240 CATATTTTAA
532250 AATAAATCAATCCATACT
1 AATAAATCAATCCATACT
* * *
532268 AATAAAT-TAT--TTA-A
1 AATAAATCAATCCATACT
532282 AATAAATCAATCCATACT
1 AATAAATCAATCCATACT
532300 AATAAAT
1 AATAAAT
532307 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 7 0.24
15 4 0.14
17 4 0.14
18 14 0.48
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATCAATCCATACT
Found at i:532274 original size:22 final size:22
Alignment explanation
Indices: 532225--532273 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
532215 ATAAATTATT
**
532225 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
532247 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
532270 TAAA
1 TAAA
532274 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:532283 original size:32 final size:32
Alignment explanation
Indices: 532245--532458 Score: 196
Period size: 32 Copynumber: 6.3 Consensus size: 32
532235 CAATCCATAT
532245 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
532277 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
532309 TTTAAAATAAATCAATCTATATTTTAAAATAAATTAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAATT-A
* ** * ** * * *
532346 TCCATACTGATAAAT-TATTTAAAATAAATCAATCCATA
1 T--TTA-AAATAAATCAATCCATACT-AATAAAT---TA
532384 TTTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
*
532417 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
532449 TTTAAAATAA
1 TTTAAAATAA
532459 TTTATTTTAA
Statistics
Matches: 149, Mismatches: 20, Indels: 26
0.76 0.10 0.13
Matches are distributed among these distances:
32 93 0.62
33 2 0.01
34 1 0.01
36 27 0.18
37 10 0.07
38 1 0.01
39 9 0.06
40 6 0.04
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:532311 original size:86 final size:85
Alignment explanation
Indices: 532212--532458 Score: 318
Period size: 86 Copynumber: 2.9 Consensus size: 85
532202 TACAACTACA
*
532212 ATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
1 ATAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATTA
532277 TTTAAAATAAATCAATCCAT
66 TTTAAAATAAATCAATCCAT
* * *
532297 ACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATTAATCCATACTGATAAATT
1 A-TAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATT
532362 ATTTAAAATAAATCAATCCAT
65 ATTTAAAATAAATCAATCCAT
** * ** * ** * *
532383 ATTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATTCATACTAATAAA
1 ATAATAAATTATTTAAAATAAAT-C-AATCAATAT-TTTAAAATAAATCAATCCATACTAATAAA
532446 TTATTTAAAATAA
63 TTATTTAAAATAA
532459 TTTATTTTAA
Statistics
Matches: 142, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
84 5 0.04
85 11 0.08
86 126 0.89
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (85 bp):
ATAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATTA
TTTAAAATAAATCAATCCAT
Found at i:532335 original size:54 final size:54
Alignment explanation
Indices: 532277--532437 Score: 286
Period size: 54 Copynumber: 3.0 Consensus size: 54
532267 TAATAAATTA
*
532277 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
532331 TTTAAAATAAATTAATCCATACTGATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
532385 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
532438 CTAATAAATT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 101 1.00
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.37
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:532388 original size:22 final size:22
Alignment explanation
Indices: 532363--532405 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
532353 TGATAAATTA
532363 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
532385 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
532406 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:532414 original size:22 final size:22
Alignment explanation
Indices: 532365--532413 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
532355 ATAAATTATT
**
532365 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
532387 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
532410 TAAA
1 TAAA
532414 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:532443 original size:18 final size:18
Alignment explanation
Indices: 532390--532446 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
532380 CATATTTTAA
*
532390 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
* *
532408 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
532422 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
532440 AATAAAT
1 AATAAAT
532447 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 7 0.23
15 5 0.17
17 4 0.13
18 14 0.47
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:532469 original size:15 final size:15
Alignment explanation
Indices: 532408--532557 Score: 133
Period size: 15 Copynumber: 9.5 Consensus size: 15
532398 AATCCATACT
532408 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
* * *
532422 AATAAATCAATTCATACT
1 AATAAAT-TATT-TTA-A
532440 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
*
532454 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
532469 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
532491 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
532506 AATAAATTATTTTAT
1 AATAAATTATTTTAA
532521 AATAAATTATTTTAA
1 AATAAATTATTTTAA
532536 AATAAATTATTTTAA
1 AATAAATTATTTTAA
532551 AATAAAT
1 AATAAAT
532558 AACCTTATTA
Statistics
Matches: 110, Mismatches: 14, Indels: 23
0.75 0.10 0.16
Matches are distributed among these distances:
14 15 0.14
15 67 0.61
16 2 0.02
17 4 0.04
18 9 0.08
19 2 0.02
20 1 0.01
22 10 0.09
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:537849 original size:2 final size:2
Alignment explanation
Indices: 537842--537869 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
537832 TCCCTTTTTC
537842 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
537870 GGTAAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:550465 original size:42 final size:42
Alignment explanation
Indices: 550418--550500 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
550408 TATGACTGAA
* *
550418 AATGAAATCTTT-AGTATAAATCAATGCAGTTTAGGAGGAAAC
1 AATGAAATATTTAAG-ATAAATCAATGCAATTTAGGAGGAAAC
* * *
550460 AATGAAATATTTAAGATAAGTTAATGCAATTTATGAGGAAA
1 AATGAAATATTTAAGATAAATCAATGCAATTTAGGAGGAAA
550501 TACATTGGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (42 bp):
AATGAAATATTTAAGATAAATCAATGCAATTTAGGAGGAAAC
Found at i:555561 original size:21 final size:21
Alignment explanation
Indices: 555535--555584 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
555525 AACCATTCTC
555535 CGACCGAACTAAATAGGTGGT
1 CGACCGAACTAAATAGGTGGT
*
555556 CGACCGAACTAATTAGGTGGT
1 CGACCGAACTAAATAGGTGGT
555577 CGACCGAA
1 CGACCGAA
555585 TTAACCGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (21 bp):
CGACCGAACTAAATAGGTGGT
Found at i:557391 original size:38 final size:37
Alignment explanation
Indices: 557336--557418 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 37
557326 TTTTACCCTA
*
557336 AACCCGAACTCGACCCGAATATCACACTTAAAAAACCTC
1 AACCCG-ACTCCACCCGAATATCACACTTAAAAAACC-C
*
557375 GACCCGACTCCACCCGAATATCACACTTAAAAAACCC
1 AACCCGACTCCACCCGAATATCACACTTAAAAAACCC
557412 AACCCGA
1 AACCCGA
557419 ATATATGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
37 7 0.17
38 29 0.71
39 5 0.12
ACGTcount: A:0.40, C:0.39, G:0.08, T:0.13
Consensus pattern (37 bp):
AACCCGACTCCACCCGAATATCACACTTAAAAAACCC
Found at i:557865 original size:20 final size:20
Alignment explanation
Indices: 557840--557884 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
557830 TTGGATTCCA
* *
557840 ATTCCCTCTAATTTCAAGTG
1 ATTCCCTCCAATTTCAAGGG
557860 ATTCCCTCCAATTTCAAGGG
1 ATTCCCTCCAATTTCAAGGG
557880 ATTCC
1 ATTCC
557885 AACCAACCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.36
Consensus pattern (20 bp):
ATTCCCTCCAATTTCAAGGG
Found at i:557890 original size:20 final size:20
Alignment explanation
Indices: 557849--557890 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
557839 AATTCCCTCT
* **
557849 AATTTCAAGTGATTCCCTCC
1 AATTTCAAGGGATTCCAACC
557869 AATTTCAAGGGATTCCAACC
1 AATTTCAAGGGATTCCAACC
557889 AA
1 AA
557891 CCAAACGCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (20 bp):
AATTTCAAGGGATTCCAACC
Found at i:576892 original size:2 final size:2
Alignment explanation
Indices: 576885--576914 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
576875 CCTAAAGAAG
576885 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
576915 TCTGGTTTCA
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:580390 original size:14 final size:14
Alignment explanation
Indices: 580371--580417 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
580361 ATCAAAATAT
580371 TATTTATTTATTAA
1 TATTTATTTATTAA
* *
580385 TATTTATAATAATAA
1 TATTTAT-TTATTAA
580400 TATTATATTT-TTAA
1 TATT-TATTTATTAA
580414 TATT
1 TATT
580418 ATATAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 14 0.52
15 10 0.37
16 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTTATTTATTAA
Found at i:580402 original size:32 final size:31
Alignment explanation
Indices: 580366--580499 Score: 96
Period size: 27 Copynumber: 4.7 Consensus size: 31
580356 TTTTCATCAA
*
580366 AATATTATT-TATTTATTAATATT-TAT-AAT
1 AATAATATTATATTT-TTAATATTATATAAAT
580395 AATAATATTATATTTTTAATATTATATAAAT
1 AATAATATTATATTTTTAATATTATATAAAT
* *
580426 AATCA-ATTATA-TTATAATA--ATATAAGAT
1 AATAATATTATATTTTTAATATTATATAA-AT
* *
580454 -AT-ATATTTTA-TTTTAATA--ATATATAT
1 AATAATATTATATTTTTAATATTATATAAAT
* *
580480 AA-AATTTTATATATTTAATA
1 AATAATATTATATTTTTAATA
580500 ATGAATAATA
Statistics
Matches: 88, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
26 3 0.03
27 32 0.36
28 9 0.10
29 23 0.26
30 14 0.16
31 7 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
AATAATATTATATTTTTAATATTATATAAAT
Found at i:580428 original size:14 final size:15
Alignment explanation
Indices: 580382--580448 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 15
580372 ATTTATTTAT
580382 TAATATT-TATAATAA
1 TAATATTATAT-ATAA
**
580397 TAATATTATAT-TTT
1 TAATATTATATATAA
580411 TAATATTATATA-AA
1 TAATATTATATATAA
580425 TAATCAATTATATTATAA
1 TAAT--ATTATA-TATAA
580443 TAATAT
1 TAATAT
580449 AAGATATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
14 16 0.38
15 7 0.17
16 11 0.26
17 2 0.05
18 6 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATATTATATATAA
Found at i:580498 original size:25 final size:25
Alignment explanation
Indices: 580379--580528 Score: 87
Period size: 27 Copynumber: 5.8 Consensus size: 25
580369 ATTATTTATT
*
580379 TATTA-ATA-TTT-ATAATA-ATAA
1 TATTATATATTTTAATAATATAAAA
*
580400 TATTATAT-TTTTAATATTATATAAA
1 TATTATATATTTTAATAATATA-AAA
* * *
580425 TAATCAATTATATTATAATAATATAAGA
1 T-AT-TA-TATATTTTAATAATATAAAA
*
580453 TATATATTTTATTTTAATAATATATATAA
1 TAT-TA-TATATTTTAATAATATA-A-AA
* * *
580482 AATTTTATATATTTAATAATGA-ATAA
1 TATTATATAT-TTTAATAAT-ATAAAA
580508 TATTATATATTTTAATAATAT
1 TATTATATATTTTAATAATAT
580529 TTAATAAAGA
Statistics
Matches: 98, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
21 5 0.05
22 5 0.05
23 5 0.05
24 2 0.02
25 12 0.12
26 12 0.12
27 24 0.24
28 18 0.18
29 15 0.15
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (25 bp):
TATTATATATTTTAATAATATAAAA
Found at i:580533 original size:25 final size:25
Alignment explanation
Indices: 580462--580534 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 25
580452 ATATATATTT
* *
580462 TATTTTAATAATATATATAAAATTTTA
1 TATTTTAATAATAT-T-TAATATTATA
*
580489 TATATTTAATAATGA-ATAATATTATA
1 TAT-TTTAATAAT-ATTTAATATTATA
580515 TATTTTAATAATATTTAATA
1 TATTTTAATAATATTTAATA
580535 AAGATATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 1 0.03
25 14 0.36
26 11 0.28
27 3 0.08
28 9 0.23
29 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
TATTTTAATAATATTTAATATTATA
Found at i:580556 original size:23 final size:23
Alignment explanation
Indices: 580530--580574 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
580520 TAATAATATT
580530 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
580553 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
580575 ATATACTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:580965 original size:15 final size:15
Alignment explanation
Indices: 580924--580959 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
580914 CATTTTCCAG
580924 AATTCAAATTCCAAT
1 AATTCAAATTCCAAT
580939 AATTCAAATTCCAAT
1 AATTCAAATTCCAAT
580954 AATTCA
1 AATTCA
580960 TTTTCCGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTCAAATTCCAAT
Found at i:584557 original size:27 final size:27
Alignment explanation
Indices: 584509--584561 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
584499 TTACCAGACC
* *
584509 AAATAAAATTATTGTAAAGCATACTAA
1 AAATAAAATCATTGGAAAGCATACTAA
* *
584536 AAATAAAATCCTTGGAAGGCATACTA
1 AAATAAAATCATTGGAAAGCATACTA
584562 TAAGAACAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (27 bp):
AAATAAAATCATTGGAAAGCATACTAA
Found at i:588015 original size:6 final size:6
Alignment explanation
Indices: 588004--588073 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
587994 TAGCATGGAA
* * * * *
588004 GATGAG GATGAG GATGAA AATGAG GATGAT GATGAT GATGAT GATGAT
1 GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT
* *
588052 GATGGT GATGAT GATGAA GATG
1 GATGAT GATGAT GATGAT GATG
588074 GAGATATTGG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.26
Consensus pattern (6 bp):
GATGAT
Found at i:592223 original size:18 final size:18
Alignment explanation
Indices: 592196--592234 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
592186 AATTAAATTG
592196 TGAGGGTTTTTTTTATTA
1 TGAGGGTTTTTTTTATTA
*
592214 TGAGGTTTTTTTTTATTA
1 TGAGGGTTTTTTTTATTA
592232 TGA
1 TGA
592235 ATGAGTACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.62
Consensus pattern (18 bp):
TGAGGGTTTTTTTTATTA
Found at i:593225 original size:26 final size:28
Alignment explanation
Indices: 593202--593258 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
593192 TTATGCTCGT
*
593202 GAGTTTTCGAGTCGAGTCGAGCTCCATTTCA
1 GAGTTTTCGAGTCGAGTCGAGCT-CA-GT-A
593233 GAGTTTTCGAGTCGAGTCGAGCTCAG
1 GAGTTTTCGAGTCGAGTCGAGCTCAG
593259 CAATACCCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (28 bp):
GAGTTTTCGAGTCGAGTCGAGCTCAGTA
Found at i:627730 original size:26 final size:26
Alignment explanation
Indices: 627701--627750 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
627691 TATATTGTTA
627701 CTTTT-CTAAAAGATTTATAAATTCGT
1 CTTTTACTAAAA-ATTTATAAATTCGT
* *
627727 CTTTTATTAAAATTTTATAAATTC
1 CTTTTACTAAAAATTTATAAATTC
627751 ATGTACTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.50
Consensus pattern (26 bp):
CTTTTACTAAAAATTTATAAATTCGT
Found at i:631871 original size:19 final size:19
Alignment explanation
Indices: 631847--631895 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
631837 ACCAACAAAT
631847 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAATAAAAA
631866 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAATAAAAA
631885 TCGCAACGCGA
1 TCGCAACGCGA
631896 TCCCCAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATAAAAA
Found at i:632080 original size:20 final size:20
Alignment explanation
Indices: 631986--632354 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
631976 GATTTTCCAT
* ** *
631986 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
632006 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
632026 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
632046 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
632066 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
632086 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
632106 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
632126 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
632146 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
632166 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
632186 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
632206 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
632226 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
632246 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
632266 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
632286 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
632306 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
632326 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
632346 AATCACAAC
1 AATCGCAAC
632355 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:633076 original size:24 final size:24
Alignment explanation
Indices: 633037--633083 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
633027 AAATTTGGTC
633037 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
633061 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
633084 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:633275 original size:12 final size:12
Alignment explanation
Indices: 633258--633282 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
633248 ATATAATCCT
633258 GAAGAAGAAAAA
1 GAAGAAGAAAAA
633270 GAAGAAGAAAAA
1 GAAGAAGAAAAA
633282 G
1 G
633283 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:635588 original size:19 final size:19
Alignment explanation
Indices: 635566--635872 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
635556 CGGAAAATAC
*
635566 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
635585 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
635599 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
635619 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
635633 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
635652 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
635671 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
635685 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
635704 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
635723 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
635737 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
635756 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
635775 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
635794 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
635813 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
635827 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
635846 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
635865 AATCGCAA
1 AATCGCAA
635873 CGAGATAATC
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 16 0.06
17 14 0.06
18 3 0.01
19 156 0.62
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:635681 original size:52 final size:52
Alignment explanation
Indices: 635594--635872 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
635584 AAATCCCAAC
635594 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
635647 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
635699 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
635751 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
635808 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
635860 ATGAAAATCGCAA
1 ATGAAAATCGCAA
635873 CGAGATAATC
Statistics
Matches: 216, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 164 0.76
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.12
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:635717 original size:71 final size:71
Alignment explanation
Indices: 635633--635872 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
635623 GCAACGAGAG
*
635633 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
635698 AATGAA
66 AATGAA
* *
635704 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
635764 TGCGAAATGAA
61 TGCGAAATGAA
635775 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
635840 AATGAA
66 AATGAA
635846 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
635873 CGAGATAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
71 121 0.79
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:635818 original size:142 final size:138
Alignment explanation
Indices: 635566--635910 Score: 518
Period size: 142 Copynumber: 2.5 Consensus size: 138
635556 CGGAAAATAC
* * *
635566 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAAATCGCAATGC-GAAATTAAAATCGCAATGCG
* *
635629 -AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
63 AAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
635693 TGCGAAATGAA
128 TGCGAAATGAA
635704 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTAAAATCGCAATGCG-
635769 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 AA-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
635834 ATGCGAAATGAA
127 ATGCGAAATGAA
*
635846 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTA-AAATCGCAATGCG
635910 A
63 A
635911 TTTTCATTTC
Statistics
Matches: 191, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 16 0.08
138 37 0.19
139 2 0.01
141 2 0.01
142 129 0.68
143 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (138 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAG
AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC
GAAATGAA
Found at i:635873 original size:52 final size:55
Alignment explanation
Indices: 635566--635894 Score: 332
Period size: 52 Copynumber: 6.3 Consensus size: 55
635556 CGGAAAATAC
* *
635566 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-A
*
635619 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
635671 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
* *
635723 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
635775 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
635827 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
635879 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
635895 TATAAACGCA
Statistics
Matches: 257, Mismatches: 6, Indels: 27
0.89 0.02 0.09
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 181 0.70
53 24 0.09
54 7 0.03
55 6 0.02
57 26 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:636010 original size:19 final size:19
Alignment explanation
Indices: 635901--636002 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
635891 AAATTATAAA
635901 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
635920 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
635940 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
635956 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
635973 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
635992 CGCATTGCGAT
1 CGCATTGCGAT
636003 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:636128 original size:14 final size:14
Alignment explanation
Indices: 636109--636145 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
636099 CATCAATTAC
636109 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
636123 ACAAATCATCTTTT
1 ACAAATCAACTTTT
636137 ACAAATCAA
1 ACAAATCAA
636146 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:638120 original size:14 final size:14
Alignment explanation
Indices: 638101--638157 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
638091 GCGAAATGAA
*
638101 AATCGCAACGACAG
1 AATCGCAACGAAAG
638115 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
638132 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
638148 AATCGCAACG
1 AATCGCAACG
638158 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:638128 original size:33 final size:33
Alignment explanation
Indices: 638082--638174 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
638072 GCGAAACCAA
*
638082 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
638115 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
638148 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
638175 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:638139 original size:19 final size:19
Alignment explanation
Indices: 638045--638179 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
638035 TAGTTTACTT
* *
638045 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
638065 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
638084 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
638103 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
638117 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
638136 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
638150 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
638169 TCGCAATGCGA
1 TCGCAACGCGA
638180 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:638217 original size:33 final size:33
Alignment explanation
Indices: 638175--638299 Score: 234
Period size: 33 Copynumber: 3.8 Consensus size: 33
638165 AAAATCGCAA
638175 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
638208 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
638241 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
638274 TGCGATTTTGGTTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
638300 TTGGTTTCGC
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
33 89 0.98
34 2 0.02
ACGTcount: A:0.06, C:0.18, G:0.30, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:638243 original size:14 final size:14
Alignment explanation
Indices: 638224--638280 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
638214 TTTGGTTTCG
638224 CGTTGCGATTCTGT
1 CGTTGCGATTCTGT
*
638238 CGTTGCGATTTTGGTTT
1 CGTTGCGATTCT-G--T
638255 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTGT
638271 CGTTGCGATT
1 CGTTGCGATT
638281 TTGGTTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTGT
Found at i:638261 original size:52 final size:50
Alignment explanation
Indices: 638205--638336 Score: 149
Period size: 52 Copynumber: 2.5 Consensus size: 50
638195 GCGATCTTGT
* *
638205 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCGTGTTGCGATTC-G-CGTTGCGATTTTGGTTTCG
* * * *
638257 CGTTGCGATTCTGTCGTTGCGATTTTG-GTTTCGCGTTGCGATTTTGGTTTCG
1 CGTTGCGATT-T-TAGTTTCG-TGTTGCGATTCGCGTTGCGATTTTGGTTTCG
638309 CGTTGCGATTTTAAGTTTCGTGTTGCGA
1 CGTTGCGATTTT-AGTTTCGTGTTGCGA
638337 AAGTAAACTA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
50 5 0.08
51 7 0.11
52 39 0.59
53 2 0.03
54 10 0.15
55 3 0.05
ACGTcount: A:0.08, C:0.17, G:0.30, T:0.45
Consensus pattern (50 bp):
CGTTGCGATTTTAGTTTCGTGTTGCGATTCGCGTTGCGATTTTGGTTTCG
Found at i:638328 original size:20 final size:19
Alignment explanation
Indices: 638175--638336 Score: 165
Period size: 19 Copynumber: 9.3 Consensus size: 19
638165 AAAATCGCAA
638175 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
638194 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
638208 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
638227 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
638241 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
638260 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
638274 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
638293 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
638312 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
638332 TGCGA
1 TGCGA
638337 AAGTAAACTA
Statistics
Matches: 119, Mismatches: 8, Indels: 31
0.75 0.05 0.20
Matches are distributed among these distances:
14 33 0.28
15 3 0.03
16 3 0.03
17 3 0.03
18 3 0.03
19 61 0.51
20 13 0.11
ACGTcount: A:0.07, C:0.17, G:0.30, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:638539 original size:93 final size:93
Alignment explanation
Indices: 638380--639037 Score: 1293
Period size: 93 Copynumber: 7.1 Consensus size: 93
638370 TTGAATGGAT
638380 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638445 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
638473 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638538 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
638566 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638630 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
638658 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638723 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
638751 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638816 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
638844 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638908 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
638936 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
639001 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
639029 AAATTTACT
1 AAATTTACT
639038 AAGCAATCTA
Statistics
Matches: 562, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.33
93 378 0.67
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:638693 original size:185 final size:186
Alignment explanation
Indices: 638380--639037 Score: 1293
Period size: 185 Copynumber: 3.5 Consensus size: 186
638370 TTGAATGGAT
638380 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638445 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
638510 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
638566 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638630 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
638695 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
638751 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638816 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
638881 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
638936 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
639001 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
639038 AAGCAATCTA
Statistics
Matches: 470, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 339 0.72
186 131 0.28
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:638877 original size:278 final size:278
Alignment explanation
Indices: 638380--639037 Score: 1307
Period size: 278 Copynumber: 2.4 Consensus size: 278
638370 TTGAATGGAT
638380 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638445 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
638510 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
638575 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
638640 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
638658 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
638723 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
638788 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
638853 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
638918 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
638936 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
639001 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
639038 AAGCAATCTA
Statistics
Matches: 379, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 379 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (278 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
AATTGGCAGCAACCGAAC
Found at i:640760 original size:14 final size:14
Alignment explanation
Indices: 640741--640830 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
640731 TTGAAATGAA
640741 AATCGCAACGAGAG
1 AATCGCAACGAGAG
640755 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
640772 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
640788 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
640807 AATCGCAACGAGAG
1 AATCGCAACGAGAG
640821 AATCGCAACG
1 AATCGCAACG
640831 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:640778 original size:33 final size:33
Alignment explanation
Indices: 640733--640847 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
640723 TCTTTTGGTT
640733 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
640766 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
640799 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
640832 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
640848 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:640779 original size:19 final size:18
Alignment explanation
Indices: 640740--640852 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
640730 GTTGAAATGA
640740 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
640755 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
640772 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
640788 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
640805 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
640821 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
640838 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
640853 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:640883 original size:14 final size:14
Alignment explanation
Indices: 640864--640918 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
640854 TTTGGTTTCG
640864 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
640878 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
640897 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
640911 CGTTGCGA
1 CGTTGCGA
640919 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:640896 original size:33 final size:33
Alignment explanation
Indices: 640848--640918 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
640838 AAAATCGCAA
**
640848 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
640881 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
640914 TGCGA
1 TGCGA
640919 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Done.