Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007967.1 Hibiscus syriacus cultivar Beakdansim tig00110402_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: 2476418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:509868 original size:41 final size:39
Alignment explanation
Indices: 509840--509937 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 39
509830 ATTCGCGTTG
* *
509840 CATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCG--TTTC
* *
509881 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCG--TTTC
509922 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
509938 TTTCCATTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (39 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGTTTC
Found at i:509890 original size:20 final size:20
Alignment explanation
Indices: 509865--509954 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
509855 TAGTTGGAAA
509865 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
509885 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
509906 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
509926 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
509946 TCGCATTGC
1 TCGCGTTGC
509955 TATAGTTGAA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 42 0.74
21 15 0.26
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:509973 original size:30 final size:30
Alignment explanation
Indices: 509939--509998 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
509929 CGTTGCGATT
*
509939 TTCCATTTCGCATTGCTATAGTTGAAAATC
1 TTCCATTTCGCATTGCGATAGTTGAAAATC
*
509969 TTCCATTTCGCGTTGCGATAGTTGAAAATC
1 TTCCATTTCGCATTGCGATAGTTGAAAATC
509999 GCGTTGCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (30 bp):
TTCCATTTCGCATTGCGATAGTTGAAAATC
Found at i:510026 original size:41 final size:40
Alignment explanation
Indices: 509969--510089 Score: 131
Period size: 41 Copynumber: 3.0 Consensus size: 40
509959 GTTGAAAATC
509969 TTCCATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATT
1 TTCCATTTCGC-TTGCGATAGTCT-AAAAT-GTCGTTGCGATT
*
510010 TTCCATTTCGCATTGCGATAGTCTACAATGTCGTTGCGATT
1 TTCCATTTCGC-TTGCGATAGTCTAAAATGTCGTTGCGATT
* **
510051 TTCCAAATTCG-TTGCGATAGTCTACAGTTGTCGTTGCGA
1 TTCC-ATTTCGCTTGCGATAGTCTA-AAATGTCGTTGCGA
510090 AAGTTAAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
40 14 0.20
41 50 0.71
42 6 0.09
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (40 bp):
TTCCATTTCGCTTGCGATAGTCTAAAATGTCGTTGCGATT
Found at i:510064 original size:19 final size:19
Alignment explanation
Indices: 510000--510068 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
509990 TTGAAAATCG
*
510000 CGTTGCGATTTTCC-ATTT
1 CGTTGCGATTTTCCAAATT
** *
510018 CGCATTGCGATAGTCTACAATGT
1 CG--TTGCGATTTTCCA-AAT-T
510041 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
510060 CGTTGCGAT
1 CGTTGCGAT
510069 AGTCTACAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.05
19 10 0.26
20 12 0.31
21 10 0.26
22 2 0.05
23 3 0.08
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:510202 original size:10 final size:11
Alignment explanation
Indices: 510171--510204 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
510161 GACACGTATT
510171 ACCACGACCACG
1 ACCACGACC-CG
510183 ACCACGACCCG
1 ACCACGACCCG
510194 ACC-CGACCCG
1 ACCACGACCCG
510204 A
1 A
510205 GACGAGACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:510721 original size:6 final size:6
Alignment explanation
Indices: 510704--510736 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
510694 TCTCGTCTCG
510704 GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
510737 ATACGTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.18, G:0.48, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:510876 original size:41 final size:41
Alignment explanation
Indices: 510830--511046 Score: 169
Period size: 41 Copynumber: 5.2 Consensus size: 41
510820 CAACGAATTT
510830 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
* ** * * * *
510871 CCGCAAC-ACGATTTTCAACTATCGCAACG-CGATTTTCA-ACTA
1 TCGCAACGA--ATTTGGAA-AATCGCAACGACAACTGT-AGACTA
* * **
510913 TCGCAACACGAA-CTGGAAAATCGCAACG-CGAAATG-A-AAAA
1 TCGC-A-ACGAATTTGGAAAATCGCAACGAC-AACTGTAGACTA
* *
510953 TCGCAACGCGATTTTCTGGAAAATCGCAACGACAATTGTAGACTA
1 TCGCAA--CGA-ATT-TGGAAAATCGCAACGACAACTGTAGACTA
510998 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
511039 TCGCAACG
1 TCGCAACG
511047 CGATTTTCAA
Statistics
Matches: 136, Mismatches: 24, Indels: 32
0.71 0.12 0.17
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 11 0.08
41 52 0.38
42 24 0.18
43 34 0.25
44 4 0.03
45 9 0.07
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:510896 original size:21 final size:21
Alignment explanation
Indices: 510867--510923 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
510857 ACAACTGTAG
*
510867 ACTACCGCAACACGATTTTCA
1 ACTATCGCAACACGATTTTCA
*
510888 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACACGATTTTCA
510909 ACTATCGCAACACGA
1 ACTATCGCAACACGA
510924 ACTGGAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.32, G:0.12, T:0.23
Consensus pattern (21 bp):
ACTATCGCAACACGATTTTCA
Found at i:510979 original size:23 final size:20
Alignment explanation
Indices: 510912--510983 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
510902 ATTTTCAACT
*
510912 ATCGCAACACGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
* *
510932 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAACTGGAAA
*
510952 ATCGCAACGCGATTTTCTGGAAA
1 ATCGCAACGCGA---ACTGGAAA
510975 ATCGCAACG
1 ATCGCAACG
510984 ACAATTGTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
20 29 0.67
23 14 0.33
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAACTGGAAA
Found at i:511003 original size:22 final size:22
Alignment explanation
Indices: 510975--511046 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
510965 TTTCTGGAAA
510975 ATCGCAACGACAATTGTAGACT
1 ATCGCAACGACAATTGTAGACT
* **
510997 ATCGCAACG--AATT-TGGAAA
1 ATCGCAACGACAATTGTAGACT
*
511016 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAATTGTAGACT
511038 ATCGCAACG
1 ATCGCAACG
511047 CGATTTTCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 12 0.30
20 4 0.10
21 3 0.08
22 21 0.52
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAATTGTAGACT
Found at i:511021 original size:19 final size:20
Alignment explanation
Indices: 510969--511025 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
510959 CGCGATTTTC
510969 TGGAAAATCGCAACGACAATTG
1 TGGAAAATCGCAACG--AATTG
* **
510991 TAGACTATCGCAACGAATT-
1 TGGAAAATCGCAACGAATTG
511010 TGGAAAATCGCAACGA
1 TGGAAAATCGCAACGA
511026 CAACTGTAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
22 12 0.41
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
TGGAAAATCGCAACGAATTG
Found at i:511063 original size:84 final size:82
Alignment explanation
Indices: 510830--511068 Score: 272
Period size: 84 Copynumber: 2.9 Consensus size: 82
510820 CAACGAATTT
* *
510830 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTACCGCAACACGATTTTCAACTATCG
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAA-TATCG
* *
510895 CAACGCGATTTTCAACTA
65 CAACGCAATTGTCAACTA
* * **
510913 TCGCAACACGAA-CTGGAAAATCGCAACG-CGAAATG-A-AAAATCGCAACGCGATTTTCTGGAA
1 TCGC-A-ACGAATTTGGAAAATCGCAACGAC-AACTGTAGACTATCGCAACGCGATTTTC---AA
*
510974 AATCGCAACGACAATTGT-AGACTA
60 TATCGCAACG-CAATTGTCA-ACTA
510998 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAATTATCG
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAA-TATCG
511063 CAACGC
65 CAACGC
511069 GAAATGCAAC
Statistics
Matches: 129, Mismatches: 14, Indels: 26
0.76 0.08 0.15
Matches are distributed among these distances:
82 16 0.12
83 14 0.11
84 59 0.46
85 22 0.17
86 18 0.14
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (82 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAATATCGC
AACGCAATTGTCAACTA
Found at i:517542 original size:4 final size:4
Alignment explanation
Indices: 517533--517650 Score: 143
Period size: 4 Copynumber: 30.0 Consensus size: 4
517523 TAACATTCAT
* * **
517533 CATA CATA CATA CATA CATA CATA CAAA CCATA CATA CATT CAT- CAGG
1 CATA CATA CATA CATA CATA CATA CATA -CATA CATA CATA CATA CATA
**
517581 CATA CATA CATA CATA -AT- CAGG CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
517627 CATA CATA CATA CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA
517651 TCATTTCATA
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
3 5 0.05
4 91 0.92
5 3 0.03
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:518265 original size:31 final size:31
Alignment explanation
Indices: 518230--518297 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
518220 TCAAAAATTA
**
518230 TAAGATATAATCACTTT-TGTTTTTATTTAAT
1 TAAGATATAATCA-TTTATAATTTTATTTAAT
* *
518261 TAAGAAATAGTCATTTATAATTTTATTTAAT
1 TAAGATATAATCATTTATAATTTTATTTAAT
518292 TAAGAT
1 TAAGAT
518298 GTGGTCATCC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.50
Consensus pattern (31 bp):
TAAGATATAATCATTTATAATTTTATTTAAT
Found at i:520455 original size:22 final size:22
Alignment explanation
Indices: 520430--520485 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
520420 GGGTATATTA
*
520430 GTCCTTTGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
520452 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
520474 GTCCTTCCGGAC
1 GTCCTTCGGGAC
520486 ATAATGGTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.12, C:0.29, G:0.30, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:522309 original size:14 final size:15
Alignment explanation
Indices: 522290--522319 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
522280 ATTTTGTTCG
522290 ACTCG-TGCTCGTTA
1 ACTCGTTGCTCGTTA
522304 ACTCGTTGCTCGTTA
1 ACTCGTTGCTCGTTA
522319 A
1 A
522320 GCTCATCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (15 bp):
ACTCGTTGCTCGTTA
Found at i:529247 original size:65 final size:65
Alignment explanation
Indices: 529151--529272 Score: 210
Period size: 65 Copynumber: 1.9 Consensus size: 65
529141 ATTCATTATA
529151 TTCCAAACTCATCATTTTCTGTTAAAAAATTGAAGGTCGAT-TGATATGGATGTTAACTCATTTT
1 TTCCAAACTCATCATTTTCTGTTAAAAAATTGAAGGTCG-TCTGATATGGATGTTAACTCATTTT
529215 G
65 G
* *
529216 TTCCAAACTCGTCATTTTCTGTTAAAAAATTGGAGGTCGTCTGATATGGATGTTAAC
1 TTCCAAACTCATCATTTTCTGTTAAAAAATTGAAGGTCGTCTGATATGGATGTTAAC
529273 ATAATGATTG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
64 1 0.02
65 53 0.98
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (65 bp):
TTCCAAACTCATCATTTTCTGTTAAAAAATTGAAGGTCGTCTGATATGGATGTTAACTCATTTTG
Found at i:532378 original size:23 final size:23
Alignment explanation
Indices: 532352--532395 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
532342 TTGGGTCGGT
* *
532352 ACAATTAAAATTTTAGGATAGAC
1 ACAAATAAAATTTCAGGATAGAC
532375 ACAAATAAAATTTCAGGATAG
1 ACAAATAAAATTTCAGGATAG
532396 GCGCGATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (23 bp):
ACAAATAAAATTTCAGGATAGAC
Found at i:537868 original size:47 final size:47
Alignment explanation
Indices: 537777--537868 Score: 105
Period size: 47 Copynumber: 2.0 Consensus size: 47
537767 ATACCCAAAT
* * *
537777 CGACCCGACTTATTATAGATCCAAATAAAACCAAATCCGGAATGACC
1 CGACCCGACTTACTATAGATCCAAATAAAACCAAAACCGAAATGACC
* * * *
537824 CGACCCGACTTACTATAGA-CTCGAATAAAGCTAAAACTGAAATGA
1 CGACCCGACTTACTATAGATC-CAAATAAAACCAAAACCGAAATGA
537869 ATCGAACCCA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
46 1 0.03
47 36 0.97
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (47 bp):
CGACCCGACTTACTATAGATCCAAATAAAACCAAAACCGAAATGACC
Found at i:538400 original size:59 final size:59
Alignment explanation
Indices: 538316--538461 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 59
538306 ATTATGATTC
* * ** *
538316 TCATTCTAAATTAATCCCTAAACTTTT-AACA-TTCTAATTTCATCCTTAAACTATGATCA
1 TCATTCTAAATTAGTCCC-AAACTTTTGAACATTTC-AATTCCATCCCCAAACTATGACCA
* * * *
538375 TCGTTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTCCTTCCCCAAACTATGGCCT
1 TCATTCTAAATTAGTCC-CAAACTTTTGAACATTTCAATTCCATCCCCAAACTATGACCA
538435 TCATTCTAAATTAGTTCCCAAACTTTT
1 TCATTCTAAATTAG-TCCCAAACTTTT
538462 TAAATATTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
59 23 0.32
60 44 0.60
61 6 0.08
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.40
Consensus pattern (59 bp):
TCATTCTAAATTAGTCCCAAACTTTTGAACATTTCAATTCCATCCCCAAACTATGACCA
Found at i:538769 original size:4 final size:4
Alignment explanation
Indices: 538760--538826 Score: 116
Period size: 4 Copynumber: 16.8 Consensus size: 4
538750 CTACTTGCTT
* *
538760 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
538808 ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATA
538827 TTTAATATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:538845 original size:12 final size:12
Alignment explanation
Indices: 538830--538854 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
538820 ATACATATTT
538830 AATATTATAAAA
1 AATATTATAAAA
538842 AATATTATAAAA
1 AATATTATAAAA
538854 A
1 A
538855 GCGAACGATA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATTATAAAA
Found at i:539758 original size:104 final size:102
Alignment explanation
Indices: 539553--539802 Score: 311
Period size: 104 Copynumber: 2.4 Consensus size: 102
539543 TAGGGTTCAT
* * * * * * *
539553 TGGATAGTGGATAAGCTCAATTATGTATGCATGTATGGATAGTGGATAAGCTCAATTATGTATGC
1 TGGATAGTGGATAAGCTCAAGTATGTGTTCATGGAAGG--A-TGGATAAGCTCAATTATGCATAC
* * *
539618 ATGTATGGATAGTGGATAAGCTAAATTATGTCTGCATGTA
63 ATGCATGGATAGTGGATAAGCTAAAGTATGTCTGCATGCA
*
539658 TGGATAGTGGATAAGCTCAAGTATGCGTTCATGGAAGGATGGATAAGCTCAATTGTATGCATACA
1 TGGATAGTGGATAAGCTCAAGTATGTGTTCATGGAAGGATGGATAAGCTCAA-T-TATGCATACA
* * *
539723 TGCATGGGTAGTGGATAAGCTCAAGTATGTGTGCATGCA
64 TGCATGGATAGTGGATAAGCTAAAGTATGTCTGCATGCA
* *
539762 CGGATAGTGGATAAACTCAAGTATGTGTTCATGGAAGGATG
1 TGGATAGTGGATAAGCTCAAGTATGTGTTCATGGAAGGATG
539803 ATCGGTAAGC
Statistics
Matches: 126, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
102 13 0.10
103 2 0.02
104 79 0.63
105 32 0.25
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.30
Consensus pattern (102 bp):
TGGATAGTGGATAAGCTCAAGTATGTGTTCATGGAAGGATGGATAAGCTCAATTATGCATACATG
CATGGATAGTGGATAAGCTAAAGTATGTCTGCATGCA
Found at i:539788 original size:35 final size:35
Alignment explanation
Indices: 539553--539981 Score: 276
Period size: 35 Copynumber: 12.4 Consensus size: 35
539543 TAGGGTTCAT
* * *
539553 TGGATAGTGGATAAGCTCAATTATGTATGCATGTA
1 TGGATAGTGGATAAGCTCAAGTATGTGTGCATGCA
* * *
539588 TGGATAGTGGATAAGCTCAATTATGTATGCATGTA
1 TGGATAGTGGATAAGCTCAAGTATGTGTGCATGCA
* * * *
539623 TGGATAGTGGATAAGCTAAATTATGTCTGCATGTA
1 TGGATAGTGGATAAGCTCAAGTATGTGTGCATGCA
* * *
539658 TGGATAGTGGATAAGCTCAAGTATGCGTTCATGGA
1 TGGATAGTGGATAAGCTCAAGTATGTGTGCATGCA
* ** *
539693 AGG--A-TGGATAAGCTCAATTGTATGCATACATGCA
1 TGGATAGTGGATAAGCTCAA--GTATGTGTGCATGCA
*
539727 TGGGTAGTGGATAAGCTCAAGTATGTGTGCATGCA
1 TGGATAGTGGATAAGCTCAAGTATGTGTGCATGCA
* * * *
539762 CGGATAGTGGATAAACTCAAGTATGTGTTCATGGA
1 TGGATAGTGGATAAGCTCAAGTATGTGTGCATGCA
* * * * * *
539797 AGGAT-GATCGG-TAAGCTTAAATATTTATGCATACA
1 TGGATAG-T-GGATAAGCTCAAGTATGTGTGCATGCA
* ** *
539832 T-GA-ATTGG-T-AGCAGTGGA-TATGTATGCATGCA
1 TGGATAGTGGATAAGC--TCAAGTATGTGTGCATGCA
* *
539864 TGGGA-AGTGGATAAACTCAATTA-GTGTGCATGCA
1 T-GGATAGTGGATAAGCTCAAGTATGTGTGCATGCA
* * * * *
539898 CGGATAGTGGATAAACTCAAGTATTTGTTCACGC-
1 TGGATAGTGGATAAGCTCAAGTATGTGTGCATGCA
* * *
539932 TAGTG-TAATGGATAAGCGCAATTATGTGTGCATGCA
1 T-G-GATAGTGGATAAGCTCAAGTATGTGTGCATGCA
539968 -GGTTATAGTGGATA
1 TGG--ATAGTGGATA
539982 TGAATGCATA
Statistics
Matches: 316, Mismatches: 55, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
31 3 0.01
32 29 0.09
33 8 0.03
34 53 0.17
35 196 0.62
36 14 0.04
37 13 0.04
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (35 bp):
TGGATAGTGGATAAGCTCAAGTATGTGTGCATGCA
Found at i:541139 original size:60 final size:56
Alignment explanation
Indices: 541053--541165 Score: 172
Period size: 60 Copynumber: 1.9 Consensus size: 56
541043 AAAGATAAAA
*
541053 ATATCTTGAACTCAAGGCAGTGAGTCATAAAGATAAAAATATCTTGATCTCTAAGGTTG
1 ATATCTTGAACTCAAGGCAGTGAGTCATAAAG--AAAAATATCTTGAACTC-AAGGTTG
*
541112 ATATCTTGAACTCTAAGGCATTGAGTCATAAAGAAAAATATCTTGAACTCAAGG
1 ATATCTTGAACTC-AAGGCAGTGAGTCATAAAGAAAAATATCTTGAACTCAAGG
541166 CATTGAGTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
57 4 0.08
58 16 0.31
59 13 0.25
60 18 0.35
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (56 bp):
ATATCTTGAACTCAAGGCAGTGAGTCATAAAGAAAAATATCTTGAACTCAAGGTTG
Found at i:541186 original size:37 final size:36
Alignment explanation
Indices: 541112--541215 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
541102 TCTAAGGTTG
541112 ATATCTTGAACTCTAAGGCATTGAGTCATAAAGAAAA
1 ATATCTTGAACTC-AAGGCATTGAGTCATAAAGAAAA
*
541149 ATATCTTGAACTCAAGGCATTGAGTCATAAGATAAAA
1 ATATCTTGAACTCAAGGCATTGAGTCATAA-AGAAAA
541186 ATATCTTGAA-TCAAGGCATTGAGTCA-AAAG
1 ATATCTTGAACTCAAGGCATTGAGTCATAAAG
541216 CCCAATCCTC
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 1 0.02
35 2 0.03
36 33 0.52
37 28 0.44
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (36 bp):
ATATCTTGAACTCAAGGCATTGAGTCATAAAGAAAA
Found at i:541489 original size:7 final size:7
Alignment explanation
Indices: 541477--541502 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
541467 AAATAATAAA
541477 AAAATCT
1 AAAATCT
541484 AAAATCT
1 AAAATCT
541491 AAAATCT
1 AAAATCT
541498 AAAAT
1 AAAAT
541503 ATAAGATATT
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:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATCT
Found at i:545120 original size:223 final size:226
Alignment explanation
Indices: 544802--545253 Score: 851
Period size: 224 Copynumber: 2.0 Consensus size: 226
544792 GAGTACCTCG
544802 AAAATAATATATTAAAATTTTATTTGTTTAAAATTAAATTATTAATATATTAACATTTATGTGTT
1 AAAATAATATATTAAAATTTTATTTGTTTAAAATTAAATTATTAATATATTAACATTTATGTGTT
544867 GAATTTTTATAAAAAAATACAGTAAGACTTTTATGT-TTTAAGGTTCTAGTTCGAGTTTGAGGGT
66 GAATTTTTATAAAAAAATACAGTAAGACTTTTATGTATTTAAGGTTCTAGTTCGAGTTTGAGGGT
544931 TCAATCTAGTTAAGTTTAATATTTTTTTTTTATTTC-AGCTTTTTCAAACTTCTCACGAGCTTCA
131 TCAATCTAGTTAAGTTTAATATTTTTTTTTTATTTCGAGCTTTTTCAAACTTCTCACGAGCTTCA
544995 ATTCCGGATTTCGAGTTCGAGTCGAGCTTAA
196 ATTCCGGATTTCGAGTTCGAGTCGAGCTTAA
545026 AAAATAATATATTAAAATTTTATTTGTTTAAAA-TAAATTATTAATAATATT-A-ATTTATGTGT
1 AAAATAATATATTAAAATTTTATTTGTTTAAAATTAAATTATTAAT-ATATTAACATTTATGTGT
545088 TGAATTTTTTATAAAAAAATACAGTAAGACTTTTATGTATTTAAGGTTCTAGTTCGAGTTTGAGG
65 TGAA-TTTTTATAAAAAAATACAGTAAGACTTTTATGTATTTAAGGTTCTAGTTCGAGTTTGAGG
545153 GTTCAATCTAGTTAAGTTTAATATTTTTTTTTTATTTCGAGCTTTTTCAAACTTCTCACGAGCTT
129 GTTCAATCTAGTTAAGTTTAATATTTTTTTTTTATTTCGAGCTTTTTCAAACTTCTCACGAGCTT
545218 CAATTCCGGATTTCGAGTTCGAGTCGAGCTTAA
194 CAATTCCGGATTTCGAGTTCGAGTCGAGCTTAA
545251 AAA
1 AAA
545254 TTTTAAGCTC
Statistics
Matches: 224, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
222 14 0.06
223 46 0.21
224 102 0.46
225 62 0.28
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (226 bp):
AAAATAATATATTAAAATTTTATTTGTTTAAAATTAAATTATTAATATATTAACATTTATGTGTT
GAATTTTTATAAAAAAATACAGTAAGACTTTTATGTATTTAAGGTTCTAGTTCGAGTTTGAGGGT
TCAATCTAGTTAAGTTTAATATTTTTTTTTTATTTCGAGCTTTTTCAAACTTCTCACGAGCTTCA
ATTCCGGATTTCGAGTTCGAGTCGAGCTTAA
Found at i:546722 original size:33 final size:34
Alignment explanation
Indices: 546658--546951 Score: 141
Period size: 33 Copynumber: 8.7 Consensus size: 34
546648 TAGGGTTCCT
* *
546658 TGGATAGTGGATAAGCTCAATTATGTGTGCATGCC
1 TGGATAGT-GATAAGCTCAATTATGTATGCATGCA
* *
546693 TGGATAGT-ATAAGCTTAATTGTGTATGCATGCA
1 TGGATAGTGATAAGCTCAATTATGTATGCATGCA
* * * * *
546726 TGGATAGTGGATAAACTCAAGTATGTGTTCATGGA
1 TGGATAGT-GATAAGCTCAATTATGTATGCATGCA
* * *
546761 -GGCA-AATGGATAAGCTCAATATGTGTGTGCATGCA
1 TGG-ATAGT-GATAAGCTCAAT-TATGTATGCATGCA
* * * *
546796 TGGATAGTGGATATG-T-ACTGCAT-AATGCATGCA
1 TGGATAGT-GATAAGCTCAAT-TATGTATGCATGCA
* * * * *
546829 TGTAGAGTGGATAAGCTC-GTTATGCATGCATGGATA
1 TGGATAGT-GATAAGCTCAATTATGTATGCAT-G-CA
* *
546865 CTGGATACTGGATACGCTC-A--AT-TATGCATGCA
1 -TGGATAGT-GATAAGCTCAATTATGTATGCATGCA
546897 TGGATAGTGGATAAGCTC-A--AT-TATGCATGCA
1 TGGATAGT-GATAAGCTCAATTATGTATGCATGCA
*
546928 TGGATAGTGGATAAGCTCGATTAT
1 TGGATAGT-GATAAGCTCAATTAT
546952 TCTCATCCAA
Statistics
Matches: 203, Mismatches: 41, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
31 47 0.23
32 2 0.01
33 52 0.26
34 34 0.17
35 43 0.21
36 11 0.05
37 14 0.07
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.31
Consensus pattern (34 bp):
TGGATAGTGATAAGCTCAATTATGTATGCATGCA
Found at i:546807 original size:70 final size:68
Alignment explanation
Indices: 546658--546808 Score: 187
Period size: 68 Copynumber: 2.2 Consensus size: 68
546648 TAGGGTTCCT
* * * * * *
546658 TGGATAGTGGATAAGCTCAATTATGTGTGCATGCCTGGATAGTATAAGCTTAATTGTGTATGCAT
1 TGGATAGTGGATAAACTCAAGTATGTGTGCATGCCAGGAAAGGATAAGCTCAATTGTGTATGCAT
546723 GCA
66 GCA
* * *
546726 TGGATAGTGGATAAACTCAAGTATGTGTTCATG-GAGGCAAATGGATAAGCTCAATATGTGTGTG
1 TGGATAGTGGATAAACTCAAGTATGTGTGCATGCCAGG-AAA-GGATAAGCTCAAT-TGTGTATG
546790 CATGCA
63 CATGCA
546796 TGGATAGTGGATA
1 TGGATAGTGGATA
546809 TGTACTGCAT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
67 2 0.03
68 32 0.45
69 11 0.15
70 26 0.37
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (68 bp):
TGGATAGTGGATAAACTCAAGTATGTGTGCATGCCAGGAAAGGATAAGCTCAATTGTGTATGCAT
GCA
Found at i:546908 original size:31 final size:31
Alignment explanation
Indices: 546658--546951 Score: 173
Period size: 31 Copynumber: 8.8 Consensus size: 31
546648 TAGGGTTCCT
*
546658 TGGATAGTGGATAAGCTCAATTATGTGTGCATGCC
1 TGGATAGTGGATAAGCTCAATTA----TGCATGCA
*
546693 TGGATAGT--ATAAGCTTAATTGTGTATGCATGCA
1 TGGATAGTGGATAAGCTCAA---T-TATGCATGCA
* * ** *
546726 TGGATAGTGGATAAACTCAAGTATGTGTTCA
1 TGGATAGTGGATAAGCTCAATTATGCATGCA
* * *
546757 TGGAGGCAAATGGATAAGCTCAATATGTGTGTGCATGCA
1 TGGA---TAGTGGATAAGCTC-A-A--T-TATGCATGCA
* *
546796 TGGATAGTGGATATGTACTGC-ATAATGCATGCA
1 TGGATAGTGGATAAG--CT-CAATTATGCATGCA
* * *
546829 TGTAGAGTGGATAAGCTC-GTTATGCATGCA
1 TGGATAGTGGATAAGCTCAATTATGCATGCA
*
546859 TGGATACTGGATACTGGATACGCTCAATTATGCATGCA
1 TGGATA---G----TGGATAAGCTCAATTATGCATGCA
546897 TGGATAGTGGATAAGCTCAATTATGCATGCA
1 TGGATAGTGGATAAGCTCAATTATGCATGCA
*
546928 TGGATAGTGGATAAGCTCGATTAT
1 TGGATAGTGGATAAGCTCAATTAT
546952 TCTCATCCAA
Statistics
Matches: 202, Mismatches: 32, Indels: 54
0.70 0.11 0.19
Matches are distributed among these distances:
30 15 0.07
31 59 0.29
33 45 0.22
34 12 0.06
35 18 0.09
36 11 0.05
37 12 0.06
38 19 0.09
39 11 0.05
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.31
Consensus pattern (31 bp):
TGGATAGTGGATAAGCTCAATTATGCATGCA
Found at i:554763 original size:10 final size:10
Alignment explanation
Indices: 554736--554768 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
554726 ACACCTTAAA
554736 ATATATAATT
1 ATATATAATT
554746 ATAT-TAATT
1 ATATATAATT
*
554755 ATATATAATA
1 ATATATAATT
554765 ATAT
1 ATAT
554769 TTTTAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATATATAATT
Found at i:567782 original size:52 final size:52
Alignment explanation
Indices: 567720--567825 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
567710 TTCGGTTCGG
567720 GTGGACCGAGACCCGACCCGACCGTTGCCCTTCCTTATAAACATCTAAAAAT
1 GTGGACCGAGACCCGACCCGACCGTTGCCCTTCCTTATAAACATCTAAAAAT
*
567772 GTGGACCGAGACCCGACTCGACCGTTGCCCTTCCTTATAAACATCTAAAAAT
1 GTGGACCGAGACCCGACCCGACCGTTGCCCTTCCTTATAAACATCTAAAAAT
567824 GT
1 GT
567826 AAAGGAAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (52 bp):
GTGGACCGAGACCCGACCCGACCGTTGCCCTTCCTTATAAACATCTAAAAAT
Found at i:572659 original size:22 final size:21
Alignment explanation
Indices: 572633--572694 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
572623 AGACAAGCTG
*
572633 TTAATATCAGGAGTTATTTGAT
1 TTAAT-TCAGGAGTTATATGAT
* *
572655 TTAATTCCAGGGGTTACATGAT
1 TTAATT-CAGGAGTTATATGAT
*
572677 ATAATTTCAGGAGTTATA
1 TTAA-TTCAGGAGTTATA
572695 ACAGCTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.91
23 2 0.06
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (21 bp):
TTAATTCAGGAGTTATATGAT
Found at i:572773 original size:81 final size:81
Alignment explanation
Indices: 572638--572799 Score: 297
Period size: 81 Copynumber: 2.0 Consensus size: 81
572628 AGCTGTTAAT
* *
572638 ATCAGGAGTTATTTGATTTAATTCCAGGGGTTACATGATATAATTTCAGGAGTTATAACAGCTGA
1 ATCAGGAGTTATTTAATTTAATTCCAGGGGTTACATGAAATAATTTCAGGAGTTATAACAGCTGA
572703 ATAATGATGCAATGAA
66 ATAATGATGCAATGAA
*
572719 ATCAGGAGTTATTTAATTTAATTTCAGGGGTTACATGAAATAATTTCAGGAGTTATAACAGCTGA
1 ATCAGGAGTTATTTAATTTAATTCCAGGGGTTACATGAAATAATTTCAGGAGTTATAACAGCTGA
572784 ATAATGATGCAATGAA
66 ATAATGATGCAATGAA
572800 CTTGGACTAT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.33
Consensus pattern (81 bp):
ATCAGGAGTTATTTAATTTAATTCCAGGGGTTACATGAAATAATTTCAGGAGTTATAACAGCTGA
ATAATGATGCAATGAA
Found at i:575441 original size:11 final size:11
Alignment explanation
Indices: 575425--575466 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
575415 GAGTTTGAGT
575425 TCGAGCTTCAA
1 TCGAGCTTCAA
575436 TCGAGC-TCAA
1 TCGAGCTTCAA
575446 GTCTCGAGCTTCAA
1 ---TCGAGCTTCAA
575460 TCGAGCT
1 TCGAGCT
575467 CCTGAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 4 0.15
11 13 0.48
13 6 0.22
14 4 0.15
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (11 bp):
TCGAGCTTCAA
Found at i:579755 original size:23 final size:23
Alignment explanation
Indices: 579729--579776 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
579719 ATAAAGTACA
*
579729 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
579752 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
579775 AT
1 AT
579777 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:580229 original size:23 final size:23
Alignment explanation
Indices: 580203--580265 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
580193 ATATAACCAC
580203 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
580226 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
580249 TACCTATTACATCATAT
1 TACCTATTACATTATAT
580266 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:580584 original size:425 final size:429
Alignment explanation
Indices: 579843--580884 Score: 1946
Period size: 425 Copynumber: 2.5 Consensus size: 429
579833 TATTACATTA
579843 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
579908 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
579973 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTAT-AAATATTATTTAGAATTTTTAATTTA
580038 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
195 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
*
580103 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
260 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTT
580168 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
325 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
580233 TACATTATATAAGCGCTACCTATTACATCATATGTTTACC
390 TACATTATATAAGCGCTACCTATTACATCATATGTTTACC
580273 TATTATATTGAAAGTGTCCATAC-TTTTAT-AAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
580336 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
580401 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAA-A-TATTTAGAATTTTTAATTTAA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAATATTATTTAGAATTTTTAATTTAA
580464 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
196 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
* *
580529 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACATTGGAAAAAGTATAGACACTTT
261 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTT
580594 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
326 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
*
580659 ACATTATATAAGCGCTACCTATTACATCATTTGTTTACC
391 ACATTATATAAGCGCTACCTATTACATCATATGTTTACC
*
580698 TATTATATTGAAAGTGTTCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
580763 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
580827 ATTTGCACAAAAAATTATTTGATT-TTT--TA---TA-AAATATTATTTAGAATTTTTAATTTAA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAATATTATTTAGAATTTTTAATTTAA
580885 CAACATTAAC
Statistics
Matches: 603, Mismatches: 5, Indels: 17
0.96 0.01 0.03
Matches are distributed among these distances:
419 3 0.00
420 3 0.00
421 21 0.03
423 2 0.00
425 276 0.46
426 84 0.14
427 48 0.08
428 137 0.23
429 6 0.01
430 23 0.04
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (429 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAATATTATTTAGAATTTTTAATTTAA
TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTT
TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
ACATTATATAAGCGCTACCTATTACATCATATGTTTACC
Found at i:580654 original size:23 final size:23
Alignment explanation
Indices: 580628--580685 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
580618 ATATAACCAC
580628 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
580651 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
580674 TACCTATTACAT
1 TACCTATTACAT
580686 CATTTGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:580865 original size:22 final size:23
Alignment explanation
Indices: 580835--580878 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
580825 TCATTTGCAC
*
580835 AAAAAATTATTT-GATTTTTTAT
1 AAAAAATTATTTAGAATTTTTAT
*
580857 AAAATATTATTTAGAATTTTTA
1 AAAAAATTATTTAGAATTTTTA
580879 ATTTAACAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
AAAAAATTATTTAGAATTTTTAT
Found at i:581158 original size:39 final size:39
Alignment explanation
Indices: 581104--581189 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
581094 CAAGTTGTAG
*
581104 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
581143 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
581182 ATTTTGAT
1 ATTTTGAT
581190 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:581471 original size:18 final size:18
Alignment explanation
Indices: 581448--581484 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
581438 CGAAATATAT
581448 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
581466 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
581484 A
1 A
581485 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:581944 original size:23 final size:23
Alignment explanation
Indices: 581918--581980 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
581908 ATATAACCAC
581918 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
581941 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
581964 TACCTATTACATCATAT
1 TACCTATTACATTATAT
581981 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:582379 original size:25 final size:25
Alignment explanation
Indices: 582322--582387 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
582312 CACTCAAAAG
*
582322 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
582347 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
582372 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
582388 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:585372 original size:182 final size:182
Alignment explanation
Indices: 584851--585340 Score: 851
Period size: 182 Copynumber: 2.7 Consensus size: 182
584841 TTAAAATTAC
*
584851 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
584916 ATTATAAAGTGTCGATATAGGTT-TAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCACATAAAACCGGTATATTTATACCGGTT
* *
584980 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTAC-AAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* *
585033 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACAT-AAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
585097 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCACATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCACATAAAACCGGTATATTTATACCGGTT
585162 ATATTACAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
585214 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
* *
585278 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCACATAAAACCGGTATATTTATACCG
585341 ATAGCATTGC
Statistics
Matches: 293, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
181 122 0.42
182 171 0.58
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (182 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCACATAAAACCGGTATATTTATACCGGTT
ATATTACAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:586842 original size:3 final size:3
Alignment explanation
Indices: 586834--586908 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
586824 ACTTGTTTGG
* * * ** * *
586834 ATC ATC ATC TTC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
586882 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
586909 GTCAGCTTCA
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:586851 original size:12 final size:12
Alignment explanation
Indices: 586838--586920 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
586828 GTTTGGATCA
*
586838 TCATCTTCATCA
1 TCATCTTCATCG
* * *
586850 TCATCATCGTCA
1 TCATCTTCATCG
586862 TCATCTTCATCG
1 TCATCTTCATCG
* *
586874 CCAGCTTCATCG
1 TCATCTTCATCG
*
586886 TCATCATCATCG
1 TCATCTTCATCG
586898 TCATCTTCATCG
1 TCATCTTCATCG
*
586910 TCAGCTTCATC
1 TCATCTTCATC
586921 TTCTGCGACC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:586882 original size:36 final size:36
Alignment explanation
Indices: 586842--586920 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
586832 GGATCATCAT
*
586842 CTTCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
586878 CTTCATCGTCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
586914 CTTCATC
1 CTTCATC
586921 TTCTGCGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.20, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
CTTCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:586921 original size:18 final size:18
Alignment explanation
Indices: 586862--586923 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
586852 ATCATCGTCA
*
586862 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* * * *
586880 TCATCGTCATCATCATCG
1 TCATCTTCATCGTCAGCT
586898 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
586916 TCATCTTC
1 TCATCTTC
586924 TGCGACCGCT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.18, C:0.35, G:0.10, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:586923 original size:6 final size:6
Alignment explanation
Indices: 586838--586923 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
586828 GTTTGGATCA
* * * * * * * *
586838 TCATCT TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
586886 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
586924 TGCGACCGCT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:588740 original size:148 final size:148
Alignment explanation
Indices: 588472--588774 Score: 554
Period size: 148 Copynumber: 2.0 Consensus size: 148
588462 TTGAAAAATT
588472 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGAC
1 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGAC
* *
588537 ACTTTATGGGTACACCATGTTTTCCATTCATTCTGGGAAAAAAATATCGACACAAACTATATTAG
66 ACTTTATGAGTACACCATGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAG
588602 TGTCGACACATTATTTAG
131 TGTCGACACATTATTTAG
588620 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT-TAATGGATCGA
1 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT-ATGGATCGA
* *
588684 CACTTTATGAGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTA
65 CACTTTATGAGTACACCATGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTA
588749 GTGTCGACACATTATTTAG
130 GTGTCGACACATTATTTAG
588768 ACATATT
1 ACATATT
588775 CTCTCATAAA
Statistics
Matches: 150, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
147 1 0.01
148 149 0.99
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (148 bp):
ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGAC
ACTTTATGAGTACACCATGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAG
TGTCGACACATTATTTAG
Found at i:588871 original size:199 final size:199
Alignment explanation
Indices: 588620--589498 Score: 1556
Period size: 199 Copynumber: 4.4 Consensus size: 199
588610 CATTATTTAG
588620 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT-TAATGGATCGA
1 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT-ATGGATCGA
*
588684 CACTTTATGAGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTA
65 CACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTA
588749 GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGATTAGATTGAA
130 GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGATTAGATTGAA
588814 AAATT
195 AAATT
588819 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGAC
1 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGAC
*
588884 ACTTTAT-GGTGCACCATGTTTTCCATTCATTCTGG-AAAAAAATATCGACACAAACTATATTAG
66 ACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAG
* * *
588947 TGTCGACACATTATTTATACATATTATCTCATAAAAACCGGTATAATTGTACCGGTTAGATTGAA
131 TGTCGACACATTATTTAGACATATTCTCTCAT-AAAACCGGTATAATTGTACCGATTAGATTGAA
589012 AAATT
195 AAATT
589017 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGAC
1 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGAC
589082 ACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAG
66 ACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAG
*
589147 TGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATAATTGTACC-AGTTAGATTGAA
131 TGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGA-TTAGATTGAA
589211 AAATT
195 AAATT
589216 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGAC
1 ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGAC
*
589281 ACTTTATGGGTGCACCCTATTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAG
66 ACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAG
* * *
589346 TGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGACTTGTACCGGTTAGATTGAAA
131 TGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGATTAGATTGAAA
589411 AATT
196 AATT
* * *
589415 ACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATTGACAC--TTT-TATATGGATCGA
1 ACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGA
589477 CACTTTATGGGTGCACCCTGTT
65 CACTTTATGGGTGCACCCTGTT
589499 GGCCATATTG
Statistics
Matches: 656, Mismatches: 17, Indels: 16
0.95 0.02 0.02
Matches are distributed among these distances:
197 91 0.14
198 137 0.21
199 347 0.53
200 81 0.12
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (199 bp):
ACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGAC
ACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAG
TGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGATTAGATTGAAA
AATT
Found at i:589649 original size:19 final size:19
Alignment explanation
Indices: 589617--589664 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
589607 TTATATTCAC
589617 ATACAAAA-TATAAATCGT
1 ATACAAAATTATAAATCGT
*
589635 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
589654 ATACAAAATTA
1 ATACAAAATTA
589665 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:591574 original size:21 final size:21
Alignment explanation
Indices: 591549--591613 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
591539 CCCCTTATGC
* *
591549 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
591570 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
591591 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
591612 CT
1 CT
591614 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:593969 original size:20 final size:20
Alignment explanation
Indices: 593939--593984 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
593929 TCCGATAACG
593939 TTTTA-CGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
593957 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
593978 TTTTACC
1 TTTTACC
593985 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 17 0.68
21 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:594049 original size:178 final size:180
Alignment explanation
Indices: 593821--594196 Score: 501
Period size: 180 Copynumber: 2.1 Consensus size: 180
593811 CGGTTTGTTG
* * * *
593821 TGGATCGATA-TTTTTTTAAAGCATCGACACATTATAGGCGCTATAACTGCTTCTCTTTTAAATT
1 TGGATCGATACATTTTTAAAAGCATCGACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATT
* * * *
593885 CACAAAGTGTCGATCCTTATA-T-AAGTATCGACACTTTTAATATATCCGATAACGTTTTA-CGG
66 CACAAAGTGTCGATCCTTATATTAAAGTACCGACACTTTAAATATAT-CGATAACGCTTGACCGG
* * *
593947 TTTTATCATTT-TGTTACCGGTTTTATCATATTTTTACCTGGTATATCGTTT
130 TTTTATCATTTCT-ATACCGGTTTTATCATAGTTTTACATGGTATATCGTTT
* * **
593998 TGGATCGATACATTTTTAAAAGTATCGACACTTTATAGGATTTAAAACTGCTTCTCTTTTAAATT
1 TGGATCGATACATTTTTAAAAGCATCGACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATT
* * * *
594063 CACGAAGTGTCGATCCTTATATTAAAGTACCGACACTTTAAATGTATCGGTAGCGCTTGACCGGT
66 CACAAAGTGTCGATCCTTATATTAAAGTACCGACACTTTAAATATATCGATAACGCTTGACCGGT
* *
594128 TTTATCATTTCTATACCGGTTTTGTCATAGTTTTACATGTTATATCGTTT
131 TTTATCATTTCTATACCGGTTTTATCATAGTTTTACATGGTATATCGTTT
*
594178 TGGATCGACACATTTTTAA
1 TGGATCGATACATTTTTAA
594197 TTTGGATCGA
Statistics
Matches: 172, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
177 10 0.06
178 66 0.38
179 10 0.06
180 85 0.49
181 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (180 bp):
TGGATCGATACATTTTTAAAAGCATCGACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATT
CACAAAGTGTCGATCCTTATATTAAAGTACCGACACTTTAAATATATCGATAACGCTTGACCGGT
TTTATCATTTCTATACCGGTTTTATCATAGTTTTACATGGTATATCGTTT
Found at i:594659 original size:225 final size:216
Alignment explanation
Indices: 594260--594723 Score: 688
Period size: 225 Copynumber: 2.1 Consensus size: 216
594250 GACCTACTTT
*
594260 TAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA
1 TAAGTATGGACACTTTTAT-AAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCAA
594325 TTTATTTAATAGGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAAAT
65 TTTATTTAATAGGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAAA-
*
594390 TTATTTGATTGTTTTGATATTTTATAAAATATTATTAGAATTTAAATTTAACAATATTAACCAAA
129 TAATTTGATTGTTTTGATATTTTATAAAATATTA-T-G--TTTAAATTTAACAATATTAACCAAA
* *
594455 TATAATAATAAATATGTTTTCAACAGTGAAA
190 GAT-A-AAT-AATATATTTTC-ACAGTGAAA
594486 TAAGTATGGACACTTTTATAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCAAT
1 TAAGTATGGACACTTTTATAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCAAT
* *
594551 TTTTTTAATA-GTGTTCATGTTTTCCA-CTACAATA-TAATTTAATAATTTCATTTACACAAAA-
66 TTATTTAATAGGT-TTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAAAT
*
594612 AATTT-ATTGTTTTGATATTTTATAAAATTATT-TAGATTTTAAATTTAACAATATTAACTAAAG
130 AATTTGATTGTTTTGATATTTTATAAAA-TATTAT-G--TTTAAATTTAACAATATTAACCAAAG
594675 ATAAATAATATATTTTCACAGTGAAA
191 ATAAATAATATATTTTCACAGTGAAA
594701 TAAGTATGGACACTTTTATAAAA
1 TAAGTATGGACACTTTTATAAAA
594724 AGGATAAATA
Statistics
Matches: 228, Mismatches: 8, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
215 32 0.14
216 10 0.04
217 3 0.01
218 1 0.00
219 30 0.13
220 22 0.10
221 8 0.04
223 26 0.11
224 10 0.04
225 67 0.29
226 19 0.08
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (216 bp):
TAAGTATGGACACTTTTATAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCAAT
TTATTTAATAGGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAAATA
ATTTGATTGTTTTGATATTTTATAAAATATTATGTTTAAATTTAACAATATTAACCAAAGATAAA
TAATATATTTTCACAGTGAAA
Found at i:598256 original size:2 final size:2
Alignment explanation
Indices: 598249--598283 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
598239 AACAAAATAC
598249 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
598284 TGTTGTGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:606217 original size:19 final size:20
Alignment explanation
Indices: 606193--606241 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
606183 CCATAGTACG
606193 TTTTTTC-CATCGTCAACAA
1 TTTTTTCTCATCGTCAACAA
*
606212 TTTTTTCTTTGATCGTCAACAA
1 TTTTTTC--TCATCGTCAACAA
606234 TTTTTTCT
1 TTTTTTCT
606242 TTGTTCTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
22 18 0.69
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.53
Consensus pattern (20 bp):
TTTTTTCTCATCGTCAACAA
Found at i:606229 original size:22 final size:22
Alignment explanation
Indices: 606201--606244 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
606191 CGTTTTTTCC
606201 ATCGTCAACAATTTTTTCTTTG
1 ATCGTCAACAATTTTTTCTTTG
606223 ATCGTCAACAATTTTTTCTTTG
1 ATCGTCAACAATTTTTTCTTTG
606245 TTCTACATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (22 bp):
ATCGTCAACAATTTTTTCTTTG
Found at i:608505 original size:24 final size:24
Alignment explanation
Indices: 608478--608526 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
608468 TTTTGGACCA
*
608478 TTTTAAAAACTAAACTTTCAATTT
1 TTTTAAAAACTAAACTTTAAATTT
* * *
608502 TTTTCAAAATTGAACTTTAAATTT
1 TTTTAAAAACTAAACTTTAAATTT
608526 T
1 T
608527 GAACGGGTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTTAAAAACTAAACTTTAAATTT
Found at i:609441 original size:21 final size:21
Alignment explanation
Indices: 609380--609441 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
609370 AGACTCATCT
*
609380 ATATATTATTTTT-TAAATTAA
1 ATATA-TATTTTTATAAATAAA
*
609401 ATATATATTTTTATTGAATAAA
1 ATATATATTTTTA-TAAATAAA
609423 AGTA-ATATTTTTATAAATA
1 A-TATATATTTTTATAAATA
609442 TATTATTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 7 0.20
21 10 0.29
22 16 0.46
23 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
ATATATATTTTTATAAATAAA
Found at i:611939 original size:33 final size:33
Alignment explanation
Indices: 611902--611969 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
611892 ACAAGTAAGC
611902 CTATGTATACCATAACTTCTTCGTAATTTAATA
1 CTATGTATACCATAACTTCTTCGTAATTTAATA
*
611935 CTATGTATACCATATCTTCTTCGTAATTTAATA
1 CTATGTATACCATAACTTCTTCGTAATTTAATA
611968 CT
1 CT
611970 TGAAATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (33 bp):
CTATGTATACCATAACTTCTTCGTAATTTAATA
Found at i:614780 original size:59 final size:60
Alignment explanation
Indices: 614717--614832 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
614707 AATAGTCCCT
* * * *
614717 TGACTATAGGATGTTGTTTTATTAAGTCA-TTGACTATTAAAAGTTATAAAATGGTCCTC
1 TGACTATAGAAAGTTATTTTATTAAGTCATTTGACTATTAAAAGTTACAAAATGGTCCTC
* *
614776 TGACTATAGAAAGTTATTTTGTTGAGTCATTTGACTATTAAAAGTTACAAAATGGTC
1 TGACTATAGAAAGTTATTTTATTAAGTCATTTGACTATTAAAAGTTACAAAATGGTC
614833 ATCGAATATT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
59 24 0.48
60 26 0.52
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (60 bp):
TGACTATAGAAAGTTATTTTATTAAGTCATTTGACTATTAAAAGTTACAAAATGGTCCTC
Found at i:617045 original size:16 final size:15
Alignment explanation
Indices: 617021--617056 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
617011 ATTATATAAA
*
617021 ATATAATGAATTATTT
1 ATATTATGAATTA-TT
617037 ATATTATGAATTATT
1 ATATTATGAATTATT
617052 ATATT
1 ATATT
617057 TTGTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
ATATTATGAATTATT
Found at i:618722 original size:5 final size:5
Alignment explanation
Indices: 618712--618739 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
618702 AAAGCGTATC
618712 ATTTA ATTTA ATTTA ATTTA ATTTA ATT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATT
618740 AATCTCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTTA
Found at i:621678 original size:23 final size:23
Alignment explanation
Indices: 621648--621691 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
621638 TCCAAAGGGA
621648 CGATAAAAGGCTTTTGCTGTTGG
1 CGATAAAAGGCTTTTGCTGTTGG
621671 CGATAAAAGGCTTTTGCTGTT
1 CGATAAAAGGCTTTTGCTGTT
621692 ATTTGATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (23 bp):
CGATAAAAGGCTTTTGCTGTTGG
Found at i:636561 original size:60 final size:60
Alignment explanation
Indices: 636437--636561 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 60
636427 CGGATGATTA
* * * * * * *
636437 ATTTTGTAACTTTTAATAGTCGATGGACTTAACAAAACAACGTCTTATAGTCAGAAGACT
1 ATTTTATAAATTTTAATAGTCGAAGAACTCAACAAAACAACGACTTATAGTCAGAAGACC
* * * *
636497 ATTTTATAAATTTTAATAGTCGAAGAACTCAATAAAATAATGACTTATAGTC-GGAGAACC
1 ATTTTATAAATTTTAATAGTCGAAGAACTCAACAAAACAACGACTTATAGTCAGAAG-ACC
636557 ATTTT
1 ATTTT
636562 TTTTATTTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
59 3 0.06
60 50 0.94
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (60 bp):
ATTTTATAAATTTTAATAGTCGAAGAACTCAACAAAACAACGACTTATAGTCAGAAGACC
Found at i:636934 original size:32 final size:31
Alignment explanation
Indices: 636855--636953 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 31
636845 GTTTAATTTC
*
636855 TTTTATTTAATTAACATCATTCAATAAAATAA
1 TTTTATTTAATTAATATCATT-AATAAAATAA
636887 TTTTATTTAATTAATATCATATAATAAAATAA
1 TTTTATTTAATTAATATCAT-TAATAAAATAA
* * *
636919 TTTTATATAAATAATACCATTTAATTAGAAATAA
1 TTTTATTTAATTAATATCA-TTAA-TA-AAATAA
636953 T
1 T
636954 ACGTGTAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
32 48 0.81
33 4 0.07
34 7 0.12
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.44
Consensus pattern (31 bp):
TTTTATTTAATTAATATCATTAATAAAATAA
Found at i:638675 original size:23 final size:23
Alignment explanation
Indices: 638649--638696 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
638639 ATTTAAACAT
638649 TTTAAATATTATA-TAAAAATATA
1 TTTAAAT-TTATATTAAAAATATA
* *
638672 TTTAAATTTTTATTAAAATTATA
1 TTTAAATTTATATTAAAAATATA
638695 TT
1 TT
638697 AATTGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAATTTATATTAAAAATATA
Found at i:639073 original size:152 final size:152
Alignment explanation
Indices: 638794--639084 Score: 467
Period size: 152 Copynumber: 1.9 Consensus size: 152
638784 AATAGTATAA
638794 ATATTAGGGTAAACTATGCATTTAGTACCTAAACTATAAGTTTTGGTATATTTCAGTATCTAAAC
1 ATATTAGGGTAAACTATGCATTTAGTACCTAAACTATAAGTTTTGGTATATTTCAGTATCTAAAC
* * * *
638859 TTTCAATTTTTTCAGAACCATACCTAATGTTTAGTTTTCATTTTCATTTCAATATCCCGCCATTA
66 TTTCAATTTTTTCAGAACCAGACCGAACGTTTAGTTTTCATTTTCATTTCAATATCACGCCATTA
638924 AAAACTTAAGCTATCAGTTTTG
131 AAAACTTAAGCTATCAGTTTTG
* * * * *
638946 ATATTTGGGTAAACTATGCATTTAGTACCTAAGCTATCAGTTTTGGTATATTTTAGTATTTAAAC
1 ATATTAGGGTAAACTATGCATTTAGTACCTAAACTATAAGTTTTGGTATATTTCAGTATCTAAAC
* *
639011 TTTCATTTTTTTCAGAACCACGA-CGAACGTTTAGTTTTCATTTTCATTTCAATATCATGCCATT
66 TTTCAATTTTTTCAGAACCA-GACCGAACGTTTAGTTTTCATTTTCATTTCAATATCACGCCATT
639075 AAAAACTTAA
130 AAAAACTTAA
639085 TGCGTTTATG
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
152 126 0.99
153 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (152 bp):
ATATTAGGGTAAACTATGCATTTAGTACCTAAACTATAAGTTTTGGTATATTTCAGTATCTAAAC
TTTCAATTTTTTCAGAACCAGACCGAACGTTTAGTTTTCATTTTCATTTCAATATCACGCCATTA
AAAACTTAAGCTATCAGTTTTG
Found at i:642947 original size:40 final size:39
Alignment explanation
Indices: 642903--642979 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 39
642893 AAAATTTAAG
642903 TTAAATTATA-TT-TAAATTATTAATTAATTATTACATAAAA
1 TTAAATTA-ACTTATAAA-TATTAATTAATT-TTACATAAAA
* *
642943 TTAAATTAACTTATAAATATTTATTAATTTTATATAA
1 TTAAATTAACTTATAAATATTAATTAATTTTACATAA
642980 TCTAATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
39 8 0.24
40 21 0.64
41 4 0.12
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (39 bp):
TTAAATTAACTTATAAATATTAATTAATTTTACATAAAA
Found at i:644927 original size:2 final size:2
Alignment explanation
Indices: 644920--644948 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
644910 TTTCTTTTTA
644920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
644949 ATTTTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:647665 original size:2 final size:2
Alignment explanation
Indices: 647658--647740 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
647648 AAATTACGAT
647658 TA TA TA 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
647700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
647741 TATTTTTAAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:649095 original size:2 final size:2
Alignment explanation
Indices: 649090--649116 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
649080 ATACTACATC
649090 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
649117 AGATTCCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:661474 original size:15 final size:15
Alignment explanation
Indices: 661454--661538 Score: 107
Period size: 15 Copynumber: 5.7 Consensus size: 15
661444 ATTTTATTAG
*
661454 TATGTGAATATGTTA
1 TATGTGAATATGTTC
661469 TATGTGAATATGTTC
1 TATGTGAATATGTTC
* *
661484 TACGTGAAAATGTTC
1 TATGTGAATATGTTC
*
661499 TATGTGAATATGTTT
1 TATGTGAATATGTTC
* * *
661514 TTTGTGAATGTGTTT
1 TATGTGAATATGTTC
661529 TATGTGAATA
1 TATGTGAATA
661539 AATGATACTT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 60 1.00
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (15 bp):
TATGTGAATATGTTC
Found at i:661699 original size:23 final size:23
Alignment explanation
Indices: 661673--661717 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
661663 AATCTATGTG
* * *
661673 GCACTTTGGTGCATATTCTACGT
1 GCACTTCGATGCAAATTCTACGT
661696 GCACTTCGATGCAAATTCTACG
1 GCACTTCGATGCAAATTCTACG
661718 CGGCAGTTTT
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:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (23 bp):
GCACTTCGATGCAAATTCTACGT
Found at i:669528 original size:166 final size:166
Alignment explanation
Indices: 669254--669586 Score: 666
Period size: 166 Copynumber: 2.0 Consensus size: 166
669244 TACCCAATAA
669254 GCAGGATTTCGGGTATCGGGACTTCAAATAACATGTTCGAAATGCCGACTACGGTTCCATCAATG
1 GCAGGATTTCGGGTATCGGGACTTCAAATAACATGTTCGAAATGCCGACTACGGTTCCATCAATG
669319 TTGGACTGCATCCCCATGGAGAATTCTTCGACGTTTTGTGGGTCGGTGAGCGAAACGACGTCGTC
66 TTGGACTGCATCCCCATGGAGAATTCTTCGACGTTTTGTGGGTCGGTGAGCGAAACGACGTCGTC
669384 TCGGTTGGACCAGGAGCAACACTATCAGGTCTCAAG
131 TCGGTTGGACCAGGAGCAACACTATCAGGTCTCAAG
669420 GCAGGATTTCGGGTATCGGGACTTCAAATAACATGTTCGAAATGCCGACTACGGTTCCATCAATG
1 GCAGGATTTCGGGTATCGGGACTTCAAATAACATGTTCGAAATGCCGACTACGGTTCCATCAATG
669485 TTGGACTGCATCCCCATGGAGAATTCTTCGACGTTTTGTGGGTCGGTGAGCGAAACGACGTCGTC
66 TTGGACTGCATCCCCATGGAGAATTCTTCGACGTTTTGTGGGTCGGTGAGCGAAACGACGTCGTC
669550 TCGGTTGGACCAGGAGCAACACTATCAGGTCTCAAG
131 TCGGTTGGACCAGGAGCAACACTATCAGGTCTCAAG
669586 G
1 G
669587 GCACCATTAT
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 167 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (166 bp):
GCAGGATTTCGGGTATCGGGACTTCAAATAACATGTTCGAAATGCCGACTACGGTTCCATCAATG
TTGGACTGCATCCCCATGGAGAATTCTTCGACGTTTTGTGGGTCGGTGAGCGAAACGACGTCGTC
TCGGTTGGACCAGGAGCAACACTATCAGGTCTCAAG
Found at i:673183 original size:13 final size:13
Alignment explanation
Indices: 673165--673192 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
673155 TTTACAACAG
673165 GCTGTTTCTGCTA
1 GCTGTTTCTGCTA
673178 GCTGTTTCTGCTA
1 GCTGTTTCTGCTA
673191 GC
1 GC
673193 AAGTATAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.25, G:0.25, T:0.43
Consensus pattern (13 bp):
GCTGTTTCTGCTA
Found at i:675812 original size:120 final size:121
Alignment explanation
Indices: 675608--675833 Score: 382
Period size: 120 Copynumber: 1.9 Consensus size: 121
675598 TAAAAAATAT
*
675608 ACTATTGGTAATCTTACATTACCGGGAATAAGATTCCCGGGCTAACCAAACGAGGGAATGTGGAT
1 ACTATTGGTAATCTTACATTACCGGGAATAAGATTCCCGGGCTAACCAAACGAGGGAATGTGAAT
*
675673 TTCATTCCCATGGGAATCCAATATTCTCCCATCCAAACACCGCCTAAAAAATACAC
66 TTCATTCCCATGGGAATCCAACATTCTCCCATCCAAACACCGCCTAAAAAATACAC
* * * *
675729 ACTATTGGTAATCTTACATTATCGGGAATAATA-TCCTGGGCTAACCAAACGGGGGAATGTGAAT
1 ACTATTGGTAATCTTACATTACCGGGAATAAGATTCCCGGGCTAACCAAACGAGGGAATGTGAAT
*
675793 TTCATTCCCATGGGAATCCAACATTCTCCTATCCAAACACC
66 TTCATTCCCATGGGAATCCAACATTCTCCCATCCAAACACC
675834 CCCTTATGGT
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
120 67 0.68
121 31 0.32
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (121 bp):
ACTATTGGTAATCTTACATTACCGGGAATAAGATTCCCGGGCTAACCAAACGAGGGAATGTGAAT
TTCATTCCCATGGGAATCCAACATTCTCCCATCCAAACACCGCCTAAAAAATACAC
Found at i:676251 original size:60 final size:59
Alignment explanation
Indices: 676106--676252 Score: 179
Period size: 60 Copynumber: 2.4 Consensus size: 59
676096 TTTTTTTAGT
* * *
676106 AAAG-TACACAAATGGTCCTCTGATTATAGGATATTATTTTATTAAGTCTCTCAACTATTA
1 AAAGTTACA-AAATGGTCC-CTGATTATAGAATATTACTTTATTAAGTCCCTCAACTATTA
* ** * *
676166 AAAGTTATAAAATAATTCTTCGATTATAGAATATTACTTTATTAAGTCCCTCAACTATTA
1 AAAGTTACAAAATGGTCCCT-GATTATAGAATATTACTTTATTAAGTCCCTCAACTATTA
676226 AAAGTTACAAAATGGTCACCTGATTAT
1 AAAGTTACAAAATGGTC-CCTGATTAT
676253 TTATTATGTT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 1 0.01
60 65 0.92
61 5 0.07
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCCCTGATTATAGAATATTACTTTATTAAGTCCCTCAACTATTA
Found at i:677117 original size:30 final size:30
Alignment explanation
Indices: 677075--677143 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
677065 GAAAGGAAAT
*
677075 TATATAACGTTAGTGATGATTTTATTAAAA
1 TATATAACGTTAGTGATGATTTTACTAAAA
* *
677105 TGTATAATGTTAGTGATGATTTTACTAAAA
1 TATATAACGTTAGTGATGATTTTACTAAAA
677135 TATATAACG
1 TATATAACG
677144 GTATTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.42
Consensus pattern (30 bp):
TATATAACGTTAGTGATGATTTTACTAAAA
Found at i:679740 original size:12 final size:12
Alignment explanation
Indices: 679695--679742 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
679685 AAGAATATAT
679695 TTATATTATAAA
1 TTATATTATAAA
*
679707 -TATATT-TTAA
1 TTATATTATAAA
*
679717 TTGATGTTATAAA
1 TT-ATATTATAAA
679730 TTATATTATAAA
1 TTATATTATAAA
679742 T
1 T
679743 GTTTATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
10 3 0.10
11 7 0.24
12 14 0.48
13 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (12 bp):
TTATATTATAAA
Found at i:679792 original size:18 final size:18
Alignment explanation
Indices: 679769--679804 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
679759 ATTATTTATG
*
679769 TATTAATTAGTATATTTT
1 TATTAATTAGTACATTTT
679787 TATTAATTAGTACATTTT
1 TATTAATTAGTACATTTT
679805 AATTGATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (18 bp):
TATTAATTAGTACATTTT
Found at i:680014 original size:15 final size:15
Alignment explanation
Indices: 679978--680028 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
679968 TAAACATATA
679978 ATATTTGTCATA-TT
1 ATATTTGTCATATTT
* *
679992 ATTTTTTGTCACATTT
1 A-TATTTGTCATATTT
680008 ATATTTGATCATATTGT
1 ATATTTG-TCATATT-T
680025 ATAT
1 ATAT
680029 ATGTTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 1 0.03
15 14 0.48
16 9 0.31
17 5 0.17
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (15 bp):
ATATTTGTCATATTT
Found at i:680469 original size:22 final size:22
Alignment explanation
Indices: 680444--680486 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
680434 ATCAAAATGT
*
680444 CTCTTATTTGTTATCATGATGG
1 CTCTTATTTGTTATCACGATGG
680466 CTCTTATTTGTTATCACGATG
1 CTCTTATTTGTTATCACGATG
680487 ATCTTCCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (22 bp):
CTCTTATTTGTTATCACGATGG
Found at i:681141 original size:3 final size:3
Alignment explanation
Indices: 681133--681197 Score: 121
Period size: 3 Copynumber: 21.3 Consensus size: 3
681123 ATTGCAGTAA
681133 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC
681179 TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC T
681198 CACCCATTAC
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:682163 original size:3 final size:3
Alignment explanation
Indices: 682155--682255 Score: 202
Period size: 3 Copynumber: 33.7 Consensus size: 3
682145 TAATTTATAT
682155 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
682203 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
682251 AGG AG
1 AGG AG
682256 AACGATTTGT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:682309 original size:30 final size:30
Alignment explanation
Indices: 682274--682338 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
682264 GTTAACGTCA
* * *
682274 AGTGACTATTTTATAACTAACGATAACGTT
1 AGTGACCATTTTATAACAAACGATAACATT
* * *
682304 AGTGACCATTTTGTAAGAAATGATAACATT
1 AGTGACCATTTTATAACAAACGATAACATT
682334 AGTGA
1 AGTGA
682339 TTAATTTGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (30 bp):
AGTGACCATTTTATAACAAACGATAACATT
Found at i:684183 original size:40 final size:40
Alignment explanation
Indices: 684136--684241 Score: 135
Period size: 40 Copynumber: 2.6 Consensus size: 40
684126 TGTTCAGGGG
684136 TAAATCAGTGTTTTTTCAGGCTTTTCATCGTATGCTTAGT
1 TAAATCAGTGTTTTTTCAGGCTTTTCATCGTATGCTTAGT
** ** *
684176 TAAATCAGTGTCTTGATC--TTTATTTCTTCGTATGCTTAGT
1 TAAATCAGTGT-TTTTTCAGGCT-TTTCATCGTATGCTTAGT
684216 TAAATCAGTGTTTTTTCAGGCTTTTC
1 TAAATCAGTGTTTTTTCAGGCTTTTC
684242 CATGGAATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
39 5 0.09
40 43 0.81
41 5 0.09
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (40 bp):
TAAATCAGTGTTTTTTCAGGCTTTTCATCGTATGCTTAGT
Found at i:686504 original size:19 final size:19
Alignment explanation
Indices: 686479--686522 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
686469 AAATTTATTA
686479 TTTTATAATTTAATTC-TT
1 TTTTATAATTTAATTCATT
* *
686497 TATTTATATTTTATTTCATT
1 T-TTTATAATTTAATTCATT
686517 TTTTAT
1 TTTTAT
686523 TATAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 3 0.14
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATAATTTAATTCATT
Found at i:686512 original size:23 final size:23
Alignment explanation
Indices: 686486--686535 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
686476 TTATTTTATA
686486 ATTTAATTCTTTATT-TATATTTT
1 ATTTAATTCTTTATTATA-ATTTT
* *
686509 ATTTCATTTTTTATTATAATTTT
1 ATTTAATTCTTTATTATAATTTT
686532 ATTT
1 ATTT
686536 TTGTAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTAATTCTTTATTATAATTTT
Found at i:688867 original size:27 final size:26
Alignment explanation
Indices: 688819--688869 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
688809 TAGAGGTGCA
688819 TAAAAAATTCGAATATTCGATTTGCG
1 TAAAAAATTCGAATATTCGATTTGCG
*
688845 TAAAAAATATCTGAA-ATTGGATTTG
1 TAAAAAAT-TC-GAATATTCGATTTG
688870 GGAAAAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (26 bp):
TAAAAAATTCGAATATTCGATTTGCG
Found at i:688875 original size:26 final size:26
Alignment explanation
Indices: 688820--688876 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
688810 AGAGGTGCAT
*
688820 AAAAAATTCGAATATTCGATTTGCGT
1 AAAAAATTCGAATATTCGATTTGCGG
*
688846 AAAAAATATCTGAA-ATTGGATTTG-GG
1 AAAAAAT-TC-GAATATTCGATTTGCGG
688872 AAAAA
1 AAAAA
688877 TCGTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 13 0.48
27 11 0.41
28 3 0.11
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.30
Consensus pattern (26 bp):
AAAAAATTCGAATATTCGATTTGCGG
Found at i:688876 original size:27 final size:26
Alignment explanation
Indices: 688820--688876 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
688810 AGAGGTGCAT
*
688820 AAAAAATTCGAATATTCGATTTGCGT
1 AAAAAATTCGAATATTCGATTTGCGA
* *
688846 AAAAAATATCTGAA-ATTGGATTTGGGA
1 AAAAAAT-TC-GAATATTCGATTTGCGA
688873 AAAA
1 AAAA
688877 TCGTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 7 0.27
27 16 0.62
28 3 0.12
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.30
Consensus pattern (26 bp):
AAAAAATTCGAATATTCGATTTGCGA
Found at i:689697 original size:35 final size:35
Alignment explanation
Indices: 689648--689718 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
689638 GTTAAAAATT
* *
689648 ATATTAATATACTAAATTAAAAGCATGGTCCATAA
1 ATATTAATAAACTAAATTAAAAGCAGGGTCCATAA
*
689683 ATATTAATAAACTAAATTAGAAGCAGGGTCCATAA
1 ATATTAATAAACTAAATTAAAAGCAGGGTCCATAA
689718 A
1 A
689719 CTTATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAAAAGCAGGGTCCATAA
Found at i:695395 original size:3 final size:3
Alignment explanation
Indices: 695387--695419 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
695377 TAGAAACTCA
*
695387 ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
695420 CTGAAATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:703257 original size:60 final size:60
Alignment explanation
Indices: 703189--703303 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
703179 AAAATGGTCC
** * *
703189 CCGACTATAGGGTATTATTTTATTTAGTCCATCAACTATTAAAAGATATAAAATAATCAT
1 CCGACTATAGAATATTATTTTATTAAATCCATCAACTATTAAAAGATATAAAATAATCAT
* * * * *
703249 CCGACTATAGAATGTTATTTTATTAAATTCTTCGACTATTAAAAGTTATAAAATA
1 CCGACTATAGAATATTATTTTATTAAATCCATCAACTATTAAAAGATATAAAATA
703304 GTCACCCAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (60 bp):
CCGACTATAGAATATTATTTTATTAAATCCATCAACTATTAAAAGATATAAAATAATCAT
Found at i:707410 original size:28 final size:29
Alignment explanation
Indices: 707346--707410 Score: 66
Period size: 28 Copynumber: 2.3 Consensus size: 29
707336 TTAAAATATT
*
707346 ATATTT-AAAAAATCATAATTTCTCTAAA
1 ATATTTAAAAAAATCATAATTTCTCAAAA
**
707374 AT-TACAAAAAAATCCA-AATTTCT-AAAA
1 ATATTTAAAAAAAT-CATAATTTCTCAAAA
707401 ATATTTAAAA
1 ATATTTAAAA
707411 TCATCCCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
27 6 0.21
28 21 0.72
29 2 0.07
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (29 bp):
ATATTTAAAAAAATCATAATTTCTCAAAA
Found at i:713216 original size:60 final size:60
Alignment explanation
Indices: 713121--713419 Score: 402
Period size: 60 Copynumber: 5.0 Consensus size: 60
713111 AAACCCCAGA
* * * *
713121 ACAGGCATCTATAAGGACTTTCCCTAGACCACTAAGATCTAGGAGTCCATTATGGAAGAT
1 ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
* *
713181 AAAGGCATCCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
1 ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
* * * *
713241 ACATG-ATCCATAAGGACTTACCGTAGATCATTAAGATCTAAGAGTCCAATATGGAAGAT
1 ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
* * * * *
713300 GCAGACATCCATAAGGACTTACTGTAAACCACTAAGATCTAGGAGTCTAATATGGAAGAT
1 ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
** * * * *
713360 ACATACATCCATAAGGACTTACCGTAAACCACTAAGATATAGGAGTCTAATATGAAAGAT
1 ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
713420 CAGAACATAC
Statistics
Matches: 214, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
59 52 0.24
60 162 0.76
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (60 bp):
ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
Found at i:713342 original size:119 final size:119
Alignment explanation
Indices: 713126--713423 Score: 409
Period size: 119 Copynumber: 2.5 Consensus size: 119
713116 CCAGAACAGG
* * * * * *
713126 CATCTATAAGGACTTTCCCTAGACCACTAAGATCTAGGAGTCCATTATGGAAGATAAAGGCATCC
1 CATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT-CAGACATCC
*
713191 ATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGATACAT-
65 ATAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCCAATATGGAAGATACATA
* * * *
713245 GATCCATAAGGACTTACCGTAGATCATTAAGATCTAAGAGTCCAATATGGAAGATGCAGACATCC
1 CATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT-CAGACATCC
** *
713310 ATAAGGACTTACTGTAAACCACTAAGATCTAGGAGTCTAATATGGAAGATACATA
65 ATAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCCAATATGGAAGATACATA
* * * *
713365 CATCCATAAGGACTTACCGTAAACCACTAAGATATAGGAGTCTAATATGAAAGATCAGA
1 CATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGATCAGA
713424 ACATACATGA
Statistics
Matches: 155, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
119 108 0.70
120 47 0.30
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.23
Consensus pattern (119 bp):
CATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGATCAGACATCCA
TAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCCAATATGGAAGATACATA
Found at i:714680 original size:16 final size:17
Alignment explanation
Indices: 714659--714691 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
714649 AGGTGTCACG
714659 TTGACT-TTTCAAAACT
1 TTGACTCTTTCAAAACT
*
714675 TTGACTCTTTTAAAACT
1 TTGACTCTTTCAAAACT
714692 CATTGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (17 bp):
TTGACTCTTTCAAAACT
Found at i:715320 original size:24 final size:25
Alignment explanation
Indices: 715288--715361 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
715278 TGCCACATAT
* * * *
715288 ATTTATCCCGAAGGACCGTGTA-TA
1 ATTTGTCCCGAAAGACCGCGTAGAA
*
715312 ATTTGTCCCGAAAGACCACGTAGAA
1 ATTTGTCCCGAAAGACCGCGTAGAA
*
715337 ATTTGTCCCGAATGACCGCGTAGAA
1 ATTTGTCCCGAAAGACCGCGTAGAA
715362 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 18 0.43
25 24 0.57
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (25 bp):
ATTTGTCCCGAAAGACCGCGTAGAA
Found at i:715513 original size:15 final size:15
Alignment explanation
Indices: 715493--715552 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
715483 ACATAGGGTA
*
715493 TTTCACGTAGAACAT
1 TTTCACATAGAACAT
* *
715508 TTTCACTTAGCACAT
1 TTTCACATAGAACAT
*
715523 TTTCACATAAAACAT
1 TTTCACATAGAACAT
* *
715538 TTTCATATAAAACAT
1 TTTCACATAGAACAT
715553 AATCACATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (15 bp):
TTTCACATAGAACAT
Found at i:720496 original size:11 final size:11
Alignment explanation
Indices: 720480--720515 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
720470 CGTATTTTGC
*
720480 TTGTTTATGTT
1 TTGTTTTTGTT
720491 TTGTTTTTGTTT
1 TTGTTTTTG-TT
720503 TTGTTTTTGTT
1 TTGTTTTTGTT
720514 TT
1 TT
720516 TTTCACAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.81
Consensus pattern (11 bp):
TTGTTTTTGTT
Found at i:720498 original size:6 final size:6
Alignment explanation
Indices: 720480--720516 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
720470 CGTATTTTGC
*
720480 TTGTTT ATG-TT TTGTTT TTGTTT TTGTTT TTGTTT TT
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TT
720517 TTCACAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.03, C:0.00, G:0.16, T:0.81
Consensus pattern (6 bp):
TTGTTT
Found at i:723967 original size:17 final size:18
Alignment explanation
Indices: 723947--723991 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
723937 AAATAGAGTA
723947 ATTAAAATATATAA-ATT
1 ATTAAAATATATAATATT
*
723964 ATTATAATATTATAATATT
1 ATTAAAATA-TATAATATT
723983 -TT-AAATATA
1 ATTAAAATATA
723992 ATGTCATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 2 0.08
17 12 0.50
18 7 0.29
19 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAAAATATATAATATT
Found at i:732170 original size:23 final size:23
Alignment explanation
Indices: 732126--732170 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
732116 TGCTTTCATA
* *
732126 GCACACTTTTTCTCTTCCTTTTG
1 GCACACTTTTTATCTTCATTTTG
* *
732149 GCACGCTTTTTATTTTCATTTT
1 GCACACTTTTTATCTTCATTTT
732171 CGATCATTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.24, G:0.09, T:0.56
Consensus pattern (23 bp):
GCACACTTTTTATCTTCATTTTG
Found at i:736216 original size:2 final size:2
Alignment explanation
Indices: 736209--736246 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
736199 CAGTAATTAA
736209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
736247 GTAAAAGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:736554 original size:21 final size:21
Alignment explanation
Indices: 736530--736571 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
736520 AAATGCAAAT
736530 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
736551 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
736572 CCACGACCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:737134 original size:6 final size:6
Alignment explanation
Indices: 737125--737149 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
737115 GTCGTGGTCG
737125 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
737150 ACGTGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:737254 original size:19 final size:19
Alignment explanation
Indices: 737230--737495 Score: 187
Period size: 19 Copynumber: 13.3 Consensus size: 19
737220 TTAACTATCA
737230 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
737249 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
737268 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
737287 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
*
737309 CAACGCGAA-ATGGAAAATCG
1 CAA--CGAATTTGGAAAATCG
* ** *
737329 CAACGCGATTTTCAACTATCG
1 CAACG-AATTTGGAA-AATCG
*
737350 CAACGCGAA-ATGGAAAATCG
1 CAA--CGAATTTGGAAAATCG
* ** *
737370 CAACGCGATTTTCAACTATCG
1 CAACG-AATTTGGAA-AATCG
*
737391 CAACGCGAA-ATGGAAAATCG
1 CAA--CGAATTTGGAAAATCG
* * **
737411 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
737433 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
737452 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
*
737471 CAACTAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
737490 CAACGA
1 CAACGA
737496 CAACTGTAGA
Statistics
Matches: 190, Mismatches: 38, Indels: 38
0.71 0.14 0.14
Matches are distributed among these distances:
18 6 0.03
19 95 0.50
20 34 0.18
21 22 0.12
22 27 0.14
23 4 0.02
24 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:737327 original size:61 final size:61
Alignment explanation
Indices: 737245--737474 Score: 215
Period size: 61 Copynumber: 3.8 Consensus size: 61
737235 AATTTGGAAA
737245 ATCGCAA--CGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
1 ATCGCAACGCGAA-TTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
* * ** * * **
737305 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGCGAATTGGAAAATCGCAACG-AATTTGGAA-AATCGCAACGAC-AACTGTAGACT
* ** * *
737366 ATCGCAACGCGATTTTCAACTATCGCAACGCGAA-ATGGAAAATCGCAACGACAACTGTAGACT
1 ATCGCAACGCGAATTGGAA-AATCGCAA--CGAATTTGGAAAATCGCAACGACAACTGTAGACT
737429 ATCGCAA--CGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAAC
1 ATCGCAACGCGAA-TTGGAAAATCGCAACGAATTTGGAAAATCGCAAC
737475 TAATTTGGAA
Statistics
Matches: 131, Mismatches: 26, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
59 4 0.03
60 21 0.16
61 55 0.42
62 26 0.20
63 23 0.18
64 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (61 bp):
ATCGCAACGCGAATTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
Found at i:737347 original size:41 final size:41
Alignment explanation
Indices: 737302--737580 Score: 331
Period size: 41 Copynumber: 6.9 Consensus size: 41
737292 ACAACTGTAG
737302 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
737343 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* * *
737384 ACTATCGCAACGCGAAATGGAAAATCGCAACGACAACTGT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG-CGATTTTCA
* * **
737425 GACTATCGCAA--CGAATTTGGAAAATCGCAACG-AATTTGGA
1 -ACTATCGCAACGCGAA-ATGGAAAATCGCAACGCGATTTTCA
* * * * * *
737465 A-AATCGCAA--CTAATTTGGAAAATCGCAACGACAACTGT-A
1 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATTTTCA
737504 GACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
737546 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
737581 ATTTGCGATA
Statistics
Matches: 209, Mismatches: 18, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
38 27 0.13
39 5 0.02
40 9 0.04
41 135 0.65
42 30 0.14
43 3 0.01
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:737351 original size:21 final size:21
Alignment explanation
Indices: 737325--737398 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
737315 GAAATGGAAA
737325 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
737346 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
737366 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
737387 ATCGCAACGCGA
1 ATCGCAACGCGA
737399 AATGGAAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:737511 original size:162 final size:163
Alignment explanation
Indices: 737264--737577 Score: 474
Period size: 162 Copynumber: 1.9 Consensus size: 163
737254 AATTTGGAAA
**
737264 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGAATTTGGAAAATCGCAACGA-AACTGTAGAAAATCGCAAC-CGAAATGGAAAATCG
* * *
737329 CAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAA
64 CAACGCAACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAA
737394 CGCGAAATGGAAAATCGCAACGACAACTGTAGACT
129 CGCGAAATGGAAAATCGCAACGACAACTGTAGACT
* * * *
737429 ATCGCAACGAATTTGGAAAATCGCAACG-AA-TTTGGAAAATCGCAA-CTAATTTGGAAAATCGC
1 ATCGCAACGAATTTGGAAAATCGCAACGAAACTGTAGAAAATCGCAACCGAA-ATGGAAAATCGC
737491 AACGACAACTGT-AGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
65 AACG-CAACTGTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
737555 ACGCGAAATGGAAAATCGCAACG
128 ACGCGAAATGGAAAATCGCAACG
737578 CGAATTTGCG
Statistics
Matches: 137, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
160 3 0.02
161 16 0.12
162 88 0.64
163 2 0.01
165 28 0.20
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (163 bp):
ATCGCAACGAATTTGGAAAATCGCAACGAAACTGTAGAAAATCGCAACCGAAATGGAAAATCGCA
ACGCAACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACG
CGAAATGGAAAATCGCAACGACAACTGTAGACT
Found at i:738014 original size:39 final size:39
Alignment explanation
Indices: 737971--738082 Score: 109
Period size: 39 Copynumber: 2.9 Consensus size: 39
737961 ATGAATACTT
*
737971 CACGACTGCATGACGTATTCAGGCCAATGAAGAAGACCC
1 CACGACTGCATGACGTCTTCAGGCCAATGAAGAAGACCC
* * * * * * *
738010 CACGACTGTATGGCATCTTCAGACAAATGGAGAAGACCT
1 CACGACTGCATGACGTCTTCAGGCCAATGAAGAAGACCC
* * **
738049 CAAGAGTGCACAACGTCTTCAGGCCAAT-AAGAAG
1 CACGACTGCATGACGTCTTCAGGCCAATGAAGAAG
738083 TCATAGTTCG
Statistics
Matches: 55, Mismatches: 18, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
38 5 0.09
39 50 0.91
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (39 bp):
CACGACTGCATGACGTCTTCAGGCCAATGAAGAAGACCC
Found at i:742517 original size:24 final size:25
Alignment explanation
Indices: 742473--742538 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 25
742463 ACATTTATTT
*
742473 TTATATAATAATATTACATATTTAA
1 TTATATAATAATATTACATATTAAA
*
742498 TTAT-TAATAAT-TTCATATATTAAA
1 TTATATAATAATATT-ACATATTAAA
* *
742522 TTAAACTAATAAAATTA
1 TTATA-TAATAATATTA
742539 AAAAATCACC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
23 2 0.06
24 18 0.55
25 4 0.12
26 7 0.21
27 2 0.06
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (25 bp):
TTATATAATAATATTACATATTAAA
Done.