Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008979.1 Hibiscus syriacus cultivar Beakdansim tig00112339_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: 1115631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:508094 original size:2 final size:2
Alignment explanation
Indices: 508087--508114 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
508077 TGCATGGCTA
508087 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
508115 TAATGTTTTT
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:511198 original size:11 final size:11
Alignment explanation
Indices: 511182--511207 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
511172 TGAGATAATC
511182 TTTTGAGTATA
1 TTTTGAGTATA
511193 TTTTGAGTATA
1 TTTTGAGTATA
511204 TTTT
1 TTTT
511208 TTAGAGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
TTTTGAGTATA
Found at i:520911 original size:12 final size:13
Alignment explanation
Indices: 520894--520954 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
520884 TGAGTTGATC
520894 GAGTCAACTCG-T
1 GAGTCAACTCGTT
*
520906 GAGTCAACCCGTT
1 GAGTCAACTCGTT
*
520919 GAGTCAACTTG-T
1 GAGTCAACTCGTT
*
520931 GAGTCAACCCGTT
1 GAGTCAACTCGTT
520944 GAGTCAACTCG
1 GAGTCAACTCG
520955 GACAGAGTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
12 20 0.49
13 21 0.51
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (13 bp):
GAGTCAACTCGTT
Found at i:520923 original size:13 final size:12
Alignment explanation
Indices: 520894--520951 Score: 71
Period size: 12 Copynumber: 4.7 Consensus size: 12
520884 TGAGTTGATC
*
520894 GAGTCAACTCGT
1 GAGTCAACCCGT
520906 GAGTCAACCCGTT
1 GAGTCAACCCG-T
**
520919 GAGTCAACTTGT
1 GAGTCAACCCGT
520931 GAGTCAACCCGTT
1 GAGTCAACCCG-T
520944 GAGTCAAC
1 GAGTCAAC
520952 TCGGACAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
12 20 0.51
13 19 0.49
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (12 bp):
GAGTCAACCCGT
Found at i:520932 original size:25 final size:25
Alignment explanation
Indices: 520894--520954 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
520884 TGAGTTGATC
520894 GAGTCAACTCGTGAGTCAACCCGTT
1 GAGTCAACTCGTGAGTCAACCCGTT
*
520919 GAGTCAACTTGTGAGTCAACCCGTT
1 GAGTCAACTCGTGAGTCAACCCGTT
520944 GAGTCAACTCG
1 GAGTCAACTCG
520955 GACAGAGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (25 bp):
GAGTCAACTCGTGAGTCAACCCGTT
Found at i:521034 original size:17 final size:17
Alignment explanation
Indices: 521012--521045 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
521002 CTTTGACCAA
521012 AAAAGTCTAATTTTATG
1 AAAAGTCTAATTTTATG
*
521029 AAAAGTCTTATTTTATG
1 AAAAGTCTAATTTTATG
521046 TTTTGCGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
AAAAGTCTAATTTTATG
Found at i:535704 original size:57 final size:57
Alignment explanation
Indices: 535633--535742 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
535623 AGAATGCAGG
** *
535633 GAGTTAATTGCAGGTTATAGACAACAACTCCCTAAAGAAGGATGATATCATAGCATC
1 GAGTTAATCACAGGTTACAGACAACAACTCCCTAAAGAAGGATGATATCATAGCATC
* *
535690 GAGTTAATCACAGGTTACAGACAACAACTTCCTGAAGAAGGATGATATCATAG
1 GAGTTAATCACAGGTTACAGACAACAACTCCCTAAAGAAGGATGATATCATAG
535743 AATCATGCTC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (57 bp):
GAGTTAATCACAGGTTACAGACAACAACTCCCTAAAGAAGGATGATATCATAGCATC
Found at i:537091 original size:20 final size:20
Alignment explanation
Indices: 537066--537139 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
537056 TTTTCCCAAT
*
537066 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
537086 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
537107 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
537127 TCGCAACGCGAAT
1 TCGCAACGCGAAT
537140 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:537109 original size:21 final size:21
Alignment explanation
Indices: 537083--537158 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
537073 GCGAATAAGT
537083 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
537104 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
537124 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* *
537145 AAATCACAATGCGA
1 AAATCGCAACGCGA
537159 TACTGACTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:537111 original size:41 final size:41
Alignment explanation
Indices: 537066--537158 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
537056 TTTTCCCAAT
537066 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
537107 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
537148 TCACAATGCGA
1 TCGCAATGCGA
537159 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:537176 original size:20 final size:21
Alignment explanation
Indices: 537155--537281 Score: 95
Period size: 20 Copynumber: 6.2 Consensus size: 21
537145 AAATCACAAT
*
537155 GCGATACTGAC-TATCGCAAT
1 GCGATACTGACATATCGCAAC
* *
537175 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC-ATATCGCAAC
* * *
537196 GAGATACTTAC-TTTCGCAAC
1 GCGATACTGACATATCGCAAC
*
537216 GCGATACTGAC-TTTCGCAAC
1 GCGATACTGACATATCGCAAC
* *
537236 GCGATTCTGACGT-TCGCAAC
1 GCGATACTGACATATCGCAAC
* *
537256 GCGATAAT-ACATAATCGCAAT
1 GCGATACTGACAT-ATCGCAAC
537277 GCGAT
1 GCGAT
537282 TTTCAAAGCG
Statistics
Matches: 87, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
19 5 0.06
20 55 0.63
21 25 0.29
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (21 bp):
GCGATACTGACATATCGCAAC
Found at i:537189 original size:41 final size:40
Alignment explanation
Indices: 537144--537281 Score: 127
Period size: 41 Copynumber: 3.4 Consensus size: 40
537134 GCGAATTGGG
* * *
537144 AAAATCACAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACT-TCGCAACGCGATAATAC
* * *
537185 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGAC-TTCGCAACGCGATAAT-AC
** *
537227 --TTTCGCAACGCGATTCTGACGTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGAC-TTCGCAACGCGATAATAC
* *
537266 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
537282 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
39 2 0.03
40 30 0.39
41 42 0.55
42 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (40 bp):
AAAATCGCAACGCGATACTGACTTCGCAACGCGATAATAC
Found at i:537774 original size:20 final size:20
Alignment explanation
Indices: 537735--537793 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
537725 GCGATTCTCT
*
537735 CGTTGCGATAGTCGA-ATTCG
1 CGTTGCGATAGTC-ATTTTCG
537755 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
537775 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
537794 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:539105 original size:18 final size:18
Alignment explanation
Indices: 539084--539128 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
539074 TCCACTTCGG
*
539084 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
539102 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
539120 GAGCCATCA
1 GAGCCATCA
539129 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:539691 original size:15 final size:15
Alignment explanation
Indices: 539671--539700 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
539661 AAATCGCAAT
539671 GCGAAATGAAATCGC
1 GCGAAATGAAATCGC
539686 GCGAAATGAAATCGC
1 GCGAAATGAAATCGC
539701 AAGCGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13
Consensus pattern (15 bp):
GCGAAATGAAATCGC
Found at i:539751 original size:16 final size:14
Alignment explanation
Indices: 539717--539771 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
539707 TTTGTTTTCG
*
539717 CGTTGCGATTTTGT
1 CGTTGCGATTTTTT
539731 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
539747 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
539761 CG-TGCGATTTT
1 CGTTGCGATTTT
539772 CATTTCTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
13 9 0.24
14 16 0.42
16 13 0.34
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:539753 original size:30 final size:30
Alignment explanation
Indices: 539717--539820 Score: 97
Period size: 30 Copynumber: 3.4 Consensus size: 30
539707 TTTGTTTTCG
539717 CGTTGCGATTTTGTCGTTGCGATTTCATTT
1 CGTTGCGATTTTGTCGTTGCGATTTCATTT
*
539747 CGTTGCGATTTTTTCG-TGCGATTTTCATTT
1 CGTTGCGATTTTGTCGTTGCGA-TTTCATTT
* * * *
539777 C-TAGCCATTTCCG-CGTTGCGATAGTCATTT
1 CGTTGCGATTT-TGTCGTTGCGAT-TTCATTT
539807 CGCGTTGCGATTTT
1 --CGTTGCGATTTT
539821 AGTTCGTGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
29 15 0.26
30 35 0.60
32 1 0.02
33 7 0.12
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (30 bp):
CGTTGCGATTTTGTCGTTGCGATTTCATTT
Found at i:541658 original size:14 final size:14
Alignment explanation
Indices: 541639--541674 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
541629 ATTGTTTAAT
541639 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
541653 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
541667 TGATTTGT
1 TGATTTGT
541675 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:541799 original size:14 final size:15
Alignment explanation
Indices: 541780--541855 Score: 50
Period size: 19 Copynumber: 4.7 Consensus size: 15
541770 CGAAATGGCT
541780 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
541794 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
*
541813 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
541831 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
541845 AT-GCAATGCGA
1 ATCGCAA-GCGA
541856 TTTTCATTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
13 4 0.08
14 11 0.22
15 3 0.06
16 7 0.14
17 1 0.02
18 10 0.20
19 15 0.29
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:541847 original size:19 final size:19
Alignment explanation
Indices: 541790--541837 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
541780 ATCGCAACGA
541790 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
541809 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
541828 G-AAATCGCAA
1 GAAAATCGCAA
541838 CGAGAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:541899 original size:20 final size:20
Alignment explanation
Indices: 541874--541911 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
541864 TCGCATTGCG
*
541874 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
541894 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
541912 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:542982 original size:24 final size:24
Alignment explanation
Indices: 542955--543008 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
542945 GTATTCAAAA
* *
542955 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
542979 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
543003 TTTGAT
1 TTTGAT
543009 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:545513 original size:33 final size:33
Alignment explanation
Indices: 545471--545598 Score: 204
Period size: 33 Copynumber: 3.9 Consensus size: 33
545461 GGAAATTACT
545471 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
545504 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
545536 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
545570 ATCGCAATGCGAAATGAAAATCGCAACGA
1 ATCGCAATGCGAAATGAAAATCGCAACGA
545599 ATTTAATTTC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 84 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:545578 original size:66 final size:66
Alignment explanation
Indices: 545472--545597 Score: 243
Period size: 66 Copynumber: 1.9 Consensus size: 66
545462 GAAATTACTA
545472 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
545537 T
66 T
*
545538 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACG
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACG
545598 AATTTAATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
T
Found at i:545797 original size:14 final size:14
Alignment explanation
Indices: 545778--545811 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
545768 CATCAATTAA
545778 ACAAATAAACTTTT
1 ACAAATAAACTTTT
* *
545792 ACAAATGACCTTTT
1 ACAAATAAACTTTT
545806 ACAAAT
1 ACAAAT
545812 CAATTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (14 bp):
ACAAATAAACTTTT
Found at i:547223 original size:21 final size:21
Alignment explanation
Indices: 547157--547223 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
547147 GTGAATCGGG
547157 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * * ** * *
547177 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
547199 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
547220 CTCT
1 CTCT
547224 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:549302 original size:20 final size:19
Alignment explanation
Indices: 549257--549315 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
549247 TCTTTTGGTT
549257 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
549276 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
549297 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
549316 TAGAATCGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:549325 original size:14 final size:14
Alignment explanation
Indices: 549306--549342 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
549296 GGAAATGACT
*
549306 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
549320 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
549334 ATCGCAACG
1 ATCGCAACG
549343 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:549370 original size:47 final size:48
Alignment explanation
Indices: 549282--549375 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 48
549272 ACGAGATAAT
* * *
549282 GAGAATCGCAACGCGGAAATGACTATCGCAACGATAGAATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACGA
*
549330 GAGAATCGCAACGC-GAAATGACTATCGCGACCAGACAATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACG
549376 CGAAATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 28 0.67
48 14 0.33
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (48 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACGA
Found at i:549388 original size:19 final size:19
Alignment explanation
Indices: 549366--549455 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
549356 GCGACCAGAC
*
549366 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
549385 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATAAA
* *
549405 AATTGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
549424 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
*
549443 AATCGCAATGCGA
1 AATCGCAACGCGA
549456 TTTTTGTTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 47 0.73
20 17 0.27
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:549390 original size:33 final size:33
Alignment explanation
Indices: 549319--549394 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
549309 GCAACGATAG
* * *
549319 AATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
549352 TATCGCGACCAGACAATCGCAACGCGAAATGAA
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
549385 AATCGCAACC
1 AATCGCAACC
549395 GCGAAATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACCAGACAATCGCAACGCGAAATGAA
Found at i:549413 original size:39 final size:38
Alignment explanation
Indices: 549366--549455 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
549356 GCGACCAGAC
549366 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
549405 AATTGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
549443 AATCGCAATGCGA
1 AATCGCAACGCGA
549456 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 22 0.46
39 26 0.54
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:549482 original size:17 final size:19
Alignment explanation
Indices: 549451--549493 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 19
549441 AAAATCGCAA
549451 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTGTTTCGCGT
549470 TGCG-TTTTT-TTTCGCGT
1 TGCGATTTTTGTTTCGCGT
549487 TGCGATT
1 TGCGATT
549494 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.52
18 7 0.30
19 4 0.17
ACGTcount: A:0.05, C:0.16, G:0.26, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTGTTTCGCGT
Found at i:550109 original size:20 final size:20
Alignment explanation
Indices: 550084--550137 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
550074 GATTTTGTAT
550084 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
550104 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
550124 TATCGCATTGCGAT
1 TATCGCATTGCGAT
550138 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:550156 original size:61 final size:61
Alignment explanation
Indices: 550044--550158 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
550034 CGCTATGTAA
* * * ** *
550044 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
* *
550105 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
550159 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 43 0.96
62 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
Found at i:555918 original size:24 final size:24
Alignment explanation
Indices: 555884--555956 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
555874 ATTTTCAACT
* * *
555884 TGAATTATGTTCTGATTTCTTATC
1 TGAATTCTGTTCTGATTTCTGATA
* *
555908 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
*
555932 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
555956 T
1 T
555957 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:559234 original size:7 final size:6
Alignment explanation
Indices: 559208--559242 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
559198 TGCTTAATTG
*
559208 AAATAA AAATAA AAGTAA AAATAAA AAATAA AAAT
1 AAATAA AAATAA AAATAA AAAT-AA AAATAA AAAT
559243 GTAACAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:559240 original size:12 final size:13
Alignment explanation
Indices: 559208--559242 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
559198 TGCTTAATTG
559208 AAATAAAAAT-AA
1 AAATAAAAATAAA
*
559220 AAGTAAAAATAAA
1 AAATAAAAATAAA
559233 AAATAAAAAT
1 AAATAAAAAT
559243 GTAACAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:567630 original size:21 final size:20
Alignment explanation
Indices: 567593--567631 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
567583 CATTGCAGGA
**
567593 ATTTATGGCCTTGACAAAAG
1 ATTTATGGCCTCAACAAAAG
567613 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
567632 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:579149 original size:18 final size:18
Alignment explanation
Indices: 579123--579157 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
579113 TCAAAATGAC
*
579123 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
579141 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
579158 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:584546 original size:18 final size:18
Alignment explanation
Indices: 584520--584554 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
584510 TCGAAAGGAC
*
584520 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
584538 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
584555 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:589500 original size:43 final size:42
Alignment explanation
Indices: 589453--589970 Score: 378
Period size: 43 Copynumber: 12.1 Consensus size: 42
589443 AAAATTGATT
*
589453 AAATTAGGGACCAAAATTATAAAAGTAAAAAGTTG-GATTGAAA
1 AAATTAGGGACC-TAATTATAAAAGTAAAAAG-TGAGATTGAAA
* * * *
589496 AAATTAAGGG-CCTCAATTATGAAGGTAAAAAGTGATATTAAAA
1 AAATT-AGGGACCT-AATTATAAAAGTAAAAAGTGAGATTGAAA
* *
589539 AAATTAGGG-CCTTTAATGATAAAAGTAGAAAGTGAGATTGAAA
1 AAATTAGGGACC--TAATTATAAAAGTAAAAAGTGAGATTGAAA
* * * * * * *
589582 ATATTAGGGACATCGATTATAAAAATAAAAATTAAGATTAAAA
1 AAATTAGGGACCT-AATTATAAAAGTAAAAAGTGAGATTGAAA
* * *
589625 AAATTAGGGGATC-AATTCTAAATGTAAAAAGTGAGATT-ACAA
1 AAATTA-GGGACCTAATTATAAAAGTAAAAAGTGAGATTGA-AA
* * * *
589667 AAATTAGGGGA-TTCAATTATAAAGGTAAAAAATGGGATTGAAA
1 AAATTA-GGGACCT-AATTATAAAAGTAAAAAGTGAGATTGAAA
* * *
589710 AAGTTAGAGG-TCTCAATTATAAAAGTAAAAAGTGAGATTAAAA
1 AAATTAG-GGACCT-AATTATAAAAGTAAAAAGTGAGATTGAAA
* * *
589753 AAATTAGGGGCTTCAATTAT-AAAGCTAAAAAGCGAGATTGAAAA
1 AAATTAGGGACCT-AATTATAAAAG-TAAAAAGTGAGATTG-AAA
* * *
589797 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAA
1 AAATTAGGGACCT-AATTATAAAAGTAAAAAGTGAGATTGAAA
* * * *
589840 AAATTAGGG-CTTTAACTATAAAGGTAAAAAAGTGATATTGAAAAA
1 AAATTAGGGAC-CTAATTATAAAAGT-AAAAAGTGAGATTG--AAA
* *
589885 AAATTAAGGG-TCTCAATTAT---AGTAAAAAGTGGGATTGAAA
1 AAATT-AGGGACCT-AATTATAAAAGTAAAAAGTGAGATTGAAA
* * *
589925 AAGTTAGGGGCCTTAATTATAAATGTAAAAAGTGAGATTGAAA
1 AAATTAGGGACC-TAATTATAAAAGTAAAAAGTGAGATTGAAA
589968 AAA
1 AAA
589971 AACTAAGAAC
Statistics
Matches: 382, Mismatches: 64, Indels: 58
0.76 0.13 0.12
Matches are distributed among these distances:
39 4 0.01
40 14 0.04
41 2 0.01
42 72 0.19
43 223 0.58
44 46 0.12
45 12 0.03
46 9 0.02
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.25
Consensus pattern (42 bp):
AAATTAGGGACCTAATTATAAAAGTAAAAAGTGAGATTGAAA
Found at i:589561 original size:86 final size:86
Alignment explanation
Indices: 589453--589971 Score: 511
Period size: 86 Copynumber: 6.0 Consensus size: 86
589443 AAAATTGATT
** * *
589453 AAATTAGGGACCAAAATTATAAAAGTAAAAAGTTG-GATTGAAAAAATTAAGGGCCTCAATTATG
1 AAATTAGGG-CCTCAATTATAAAAGTAAAAAG-TGAGATTGAAAAAATTAAGGGCTTCAATTATA
*
589517 AAGGTAAAAAGTGATATT-AAAA
64 AAGGTAAAAAGTGAGATTGAAAA
* * * * * *
589539 AAATTAGGGCCTTTAATGATAAAAGTAGAAAGTGAGATTGAAAATATT-AGGGACATCGATTATA
1 AAATTAGGGCC-TCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAAGGG-CTTCAATTATA
** * *
589603 AAAATAAAAATTAAGATT-AAAA
64 AAGGTAAAAAGTGAGATTGAAAA
** * * * *
589625 AAATTAGGGGATCAATTCTAAATGTAAAAAGTGAGATT-ACAAAAATTAGGGGATTCAATTATAA
1 AAATTAGGGCCTCAATTATAAAAGTAAAAAGTGAGATTGA-AAAAATTAAGGGCTTCAATTATAA
* *
589689 AGGTAAAAAATGGGATTG-AAA
65 AGGTAAAAAGTGAGATTGAAAA
* * * *
589710 AAGTTAGAGGTCTCAATTATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGGGCTTCAATTATAA
1 AAATTAG-GGCCTCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAAGGGCTTCAATTATAA
* *
589775 AGCTAAAAAGCGAGATTGAAAA
65 AGGTAAAAAGTGAGATTGAAAA
* * * *
589797 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATT-AGGGCTTTAACTATAA
1 AAATTA-GGGCCTCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAAGGGCTTCAATTATAA
*
589861 AGGTAAAAAAGTGATATTGAAAAA
65 AGGT-AAAAAGTGAGATTG-AAAA
* * * *
589885 AAATTAAGGGTCTCAATTAT---AGTAAAAAGTGGGATTGAAAAAGTTAGGGGCCTT-AATTATA
1 AAATT-AGGGCCTCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAAGGG-CTTCAATTATA
*
589946 AATGTAAAAAGTGAGATTGAAAA
64 AAGGTAAAAAGTGAGATTGAAAA
589969 AAA
1 AAA
589972 ACTAAGAACC
Statistics
Matches: 360, Mismatches: 58, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
84 8 0.02
85 100 0.28
86 167 0.46
87 62 0.17
88 22 0.06
89 1 0.00
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (86 bp):
AAATTAGGGCCTCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAAGGGCTTCAATTATAAA
GGTAAAAAGTGAGATTGAAAA
Found at i:589969 original size:128 final size:126
Alignment explanation
Indices: 589467--589970 Score: 518
Period size: 128 Copynumber: 3.9 Consensus size: 126
589457 TAGGGACCAA
* *
589467 AATTATAAAAGTAAAAAGTTG-GATTGAAAAAATTAAGGGCCTCAATTATGAAGGTAAAAAGTGA
1 AATTATAAAAGTAAAAAG-TGAGATTAAAAAAATT-AGGGGCTCAATTAT-AAGGTAAAAAGTGA
* * * * * * *
589531 TATTAAAAAAATTA-GGGCCTTTAATGATAAAAGTAGAAAGTGAGATTGAAAATATTAGGGACAT
63 GATTGAAAAAATTAGGGGCC-TTAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGG-CTT
589595 C
126 C
* * * * * * *
589596 GATTATAAAAATAAAAATTAAGATTAAAAAAATTAGGGGATCAATTCTAAATGTAAAAAGTGAGA
1 AATTATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGGGCTCAATTAT-AAGGTAAAAAGTGAGA
* * * *
589661 TT-ACAAAAATTAGGGG-ATTCAATTATAAAGGTAAAAAATGGGATTGAAAAAGTTAGAGG-TCT
65 TTGA-AAAAATTAGGGGCCTT-AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAG-GGCT-T
589723 C
126 C
* *
589724 AATTATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGGGCTTCAATTATAAAGCTAAAAAGCGAG
1 AATTATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGGGC-TCAATTAT-AAGGTAAAAAGTGAG
* * *
589789 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGCTTT
64 ATTG-AAAAAATTAGGGGCCTTAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGCTTC
* * * *
589853 AACTATAAAGGTAAAAAAGTGATATTGAAAAAAAATTAAGGGTCTCAATTAT-A-GTAAAAAGTG
1 AATTATAAAAGT-AAAAAGTGAGATT--AAAAAAATT-AGGGGCTCAATTATAAGGTAAAAAGTG
* * *
589916 GGATTGAAAAAGTTAGGGGCCTTAATTATAAATGTAAAAAGTGAGATTGAAAAAA
62 AGATTGAAAAAATTAGGGGCCTTAATTATAAAGGTAAAAAGTGAGATTGAAAAAA
589971 AACTAAGAAC
Statistics
Matches: 313, Mismatches: 47, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
127 3 0.01
128 147 0.47
129 81 0.26
130 58 0.19
131 2 0.01
132 17 0.05
133 5 0.02
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.26
Consensus pattern (126 bp):
AATTATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGGGCTCAATTATAAGGTAAAAAGTGAGAT
TGAAAAAATTAGGGGCCTTAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGCTTC
Found at i:590016 original size:215 final size:214
Alignment explanation
Indices: 589467--590054 Score: 543
Period size: 215 Copynumber: 2.7 Consensus size: 214
589457 TAGGGACCAA
* * * * * *
589467 AATTATAAAAGTAAAAAGTTGGATTGAAAAAATTA-AGGGCCTCAATTATGAAGGTAAAAAGTGA
1 AATTAT-AAGGTAAAAAATGGGATTGAAAAAGTTAGA-GGCCTCAATTATAAAAGTAAAAAGTGA
* * ** * * * * *
589531 TATTAAAAAAA-TTAGGGCCTTTAATGATAAAAG-TAGAAAGTGAGATTG-AAAATATTAGGGAC
64 GATTAAAAAAACTAAGAACC-TCAATTAT-AAAGCTAAAAAGAGAGATTGAAAAAAATTAGGGAC
* * * * * * *
589593 ATCGATTATAAAAATAAAAATTAAGATTAAAAAAATTAGGGGATCAATTCTAAATGTAAAAAGTG
127 CTCAATTATAAAAATAAAAAGTAAGATTAAAAAAATTAGGGCATCAACTATAAAGGTAAAAAGTG
* *
589658 AGATTACAAAAATTAGGGGATTC
192 AGATTAAAAAAATTAAGGGATTC
*
589681 AATTATAAAGGTAAAAAATGGGATTGAAAAAGTTAGAGGTCTCAATTATAAAAGTAAAAAGTGAG
1 AATTAT-AAGGTAAAAAATGGGATTGAAAAAGTTAGAGGCCTCAATTATAAAAGTAAAAAGTGAG
* * ** * * *
589746 ATTAAAAAAATTAGGGGCTTCAATTATAAAGCTAAAAAGCGAGATTGAAAAAAATTAGGGGCCTC
65 ATTAAAAAAACTAAGAACCTCAATTATAAAGCTAAAAAGAGAGATTGAAAAAAATTAGGGACCTC
** * * * *
589811 AATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGCTTTAACTATAAAGGTAAAAAAGTGAT
130 AATTATAAAAATAAAAAGTAAGATTAAAAAAATTAGGGCATCAACTATAAAGGT-AAAAAGTGAG
589876 ATTGAAAAAAAATTAAGGG-TCTC
194 ATT--AAAAAAATTAAGGGAT-TC
* * * *
589899 AATTAT-A-GTAAAAAGTGGGATTGAAAAAGTTAGGGGCCTTAATTATAAATGTAAAAAGTGAGA
1 AATTATAAGGTAAAAAATGGGATTGAAAAAGTTAGAGGCCTCAATTATAAAAGTAAAAAGTGAGA
* * *
589962 TTGAAAAAAAACTAAGAACCTCAATTAT-AAGAC-AAAATGTAG-GATT-ACAAAAATTAGTGAC
66 TT--AAAAAAACTAAGAACCTCAATTATAAAG-CTAAAAAG-AGAGATTGAAAAAAATTAGGGAC
*
590023 CTCAATTATATAAAAATAAAAA-TAAAATTAAA
127 CTCAA-T-TATAAAAATAAAAAGTAAGATTAAA
590055 GGTCTCAATT
Statistics
Matches: 309, Mismatches: 51, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
213 4 0.01
214 84 0.27
215 133 0.43
216 34 0.11
217 34 0.11
218 20 0.06
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (214 bp):
AATTATAAGGTAAAAAATGGGATTGAAAAAGTTAGAGGCCTCAATTATAAAAGTAAAAAGTGAGA
TTAAAAAAACTAAGAACCTCAATTATAAAGCTAAAAAGAGAGATTGAAAAAAATTAGGGACCTCA
ATTATAAAAATAAAAAGTAAGATTAAAAAAATTAGGGCATCAACTATAAAGGTAAAAAGTGAGAT
TAAAAAAATTAAGGGATTC
Found at i:601007 original size:42 final size:42
Alignment explanation
Indices: 600960--601074 Score: 158
Period size: 42 Copynumber: 2.7 Consensus size: 42
600950 TTCCTCGAAA
* * *
600960 TCCCGTGTTTGTTTCATGTAATTCGTTTTTCGGAAAATATTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATATTT
* *
601002 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCATAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATATTT
* * *
601044 TCTCATATTTGTTTCACGTAATTCGTTTTCC
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCC
601075 GAATGTAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATATTT
Found at i:601308 original size:22 final size:23
Alignment explanation
Indices: 601261--601352 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 23
601251 TAATTATTAA
* *
601261 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
601282 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
*
601305 -ATATTTTTAATATTATATAAAATAATT
1 AATATTTATAATA--ATAT--AAT-ATT
601332 AATTATATTATAATAATATAA
1 AA-TAT-TTATAATAATATAA
601353 GATATTATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
21 11 0.19
22 15 0.26
23 4 0.07
24 4 0.07
26 5 0.09
27 3 0.05
28 5 0.09
29 3 0.05
30 7 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:601317 original size:31 final size:30
Alignment explanation
Indices: 601272--601439 Score: 107
Period size: 29 Copynumber: 5.8 Consensus size: 30
601262 ATATTTAAAA
601272 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTT-TT-ATATTTATAATAATATAATAT
*
601304 TATATTTTTA-ATATTAT-ATAAAAT-A-AT
1 TATATTTTTATAT-TTATAATAATATAATAT
601331 TA-A---TTATA-TTATAATAATATAAGATAT
1 TATATTTTTATATTTATAATAATAT-A-ATAT
*
601358 TATATTTTTAT-TTTAATAAT-ATATAATAA
1 TATATTTTTATATTT-ATAATAATATAATAT
*
601387 TGT-TTTTTATATATT-TAATAATGAATAATA-
1 TATATTTTTATAT-TTATAATAAT--ATAATAT
*
601417 T-TATTTATATATTTA-AATAATAT
1 TATATTTTTATATTTATAATAATAT
601440 TTTAGTAAAG
Statistics
Matches: 111, Mismatches: 5, Indels: 45
0.69 0.03 0.28
Matches are distributed among these distances:
22 4 0.04
23 9 0.08
24 1 0.01
26 2 0.02
27 10 0.09
28 13 0.12
29 25 0.23
30 17 0.15
31 18 0.16
32 12 0.11
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
TATATTTTTATATTTATAATAATATAATAT
Found at i:601348 original size:18 final size:19
Alignment explanation
Indices: 601316--601361 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
601306 TATTTTTAAT
*
601316 ATTATA-TAAAATAAT-TA
1 ATTATATTATAATAATATA
601333 ATTATATTATAATAATATA
1 ATTATATTATAATAATATA
*
601352 A-GATATTATA
1 ATTATATTATA
601362 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 16 0.64
19 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTATATTATAATAATATA
Found at i:601384 original size:54 final size:51
Alignment explanation
Indices: 601265--601384 Score: 140
Period size: 52 Copynumber: 2.3 Consensus size: 51
601255 TATTAAAATA
*
601265 TTTAA-AATATATTTATTAATATTTATAATAATATAATATTATATTTTTAAT
1 TTTAATAATATA-TAATTAATATTTATAATAATATAATATTATATTTTTAAT
*
601316 ATTATATAA-A-ATAATTAATTATATTATAATAATATAAGATATTATATTTTT-AT
1 TTTA-ATAATATATAATTAA-TAT-TTATAATAATAT-A-ATATTATATTTTTAAT
601369 TTTAATAATATATAAT
1 TTTAATAATATATAAT
601385 AATGTTTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
50 6 0.10
51 7 0.12
52 18 0.31
53 9 0.16
54 18 0.31
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (51 bp):
TTTAATAATATATAATTAATATTTATAATAATATAATATTATATTTTTAAT
Found at i:601392 original size:21 final size:21
Alignment explanation
Indices: 601368--601409 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
601358 TATATTTTTA
601368 TTTTA-ATAATATATAATAATG
1 TTTTATAT-ATATATAATAATG
* *
601389 TTTTTTATATATTTAATAATG
1 TTTTATATATATATAATAATG
601410 AATAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTATATATATATAATAATG
Found at i:601397 original size:54 final size:52
Alignment explanation
Indices: 601246--601367 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 52
601236 TTTTCATCAA
* * * *
601246 AATATTA-ATTATTAA-AATATTTAAAATATATTTATTAATATTTATAATAATAT
1 AATATTATATTTTTAATATTATATAAAATA-ATTAATT-AT-TTTATAATAATAT
*
601299 AATATTATATTTTTAATATTATATAAAATAATTAATTATATTATAATAATAT
1 AATATTATATTTTTAATATTATATAAAATAATTAATTATTTTATAATAATAT
601351 AAGATATTATATTTTTA
1 -A-ATATTATATTTTTA
601368 TTTTAATAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
52 12 0.20
53 10 0.17
54 27 0.45
55 11 0.18
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (52 bp):
AATATTATATTTTTAATATTATATAAAATAATTAATTATTTTATAATAATAT
Found at i:601405 original size:28 final size:28
Alignment explanation
Indices: 601374--601437 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
601364 TTTATTTTAA
* *
601374 TAATATAT-AATAATGTTTTTTATATATT
1 TAATA-ATGAATAATATTATTTATATATT
601402 TAATAATGAATAATATTATTTATATATT
1 TAATAATGAATAATATTATTTATATATT
601430 TAAATAAT
1 T-AATAAT
601438 ATTTTAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 2 0.06
28 24 0.75
29 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
TAATAATGAATAATATTATTTATATATT
Found at i:601591 original size:48 final size:47
Alignment explanation
Indices: 601539--601645 Score: 108
Period size: 48 Copynumber: 2.2 Consensus size: 47
601529 CCAATATTAA
*
601539 TATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA-AT
1 TATTTTTATT-ATAAAATAATAAAAATAA-ATTTAATAATAAATAATAT
* * * * *
601587 TATTTTAATATTTTAAAATAATAATATTAAATTTTATGATAAATAATAT
1 TATTTT--TATTATAAAATAATAAAAATAAATTTAATAATAAATAATAT
601636 TATTTATTAT
1 TATTT-TTAT
601646 ATTTAATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
48 23 0.47
49 21 0.43
50 5 0.10
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (47 bp):
TATTTTTATTATAAAATAATAAAAATAAATTTAATAATAAATAATAT
Found at i:601780 original size:29 final size:30
Alignment explanation
Indices: 601747--601803 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
601737 TTCCATAAAT
601747 GTAATTCATTTTCCAG-AATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCTA
601776 GTAATTCATTTTCCAGTAATTCAAATTC
1 GTAATTCATTTTCCAGTAATTCAAATTC
601804 CAGTTCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCTA
Found at i:601783 original size:15 final size:15
Alignment explanation
Indices: 601747--601823 Score: 72
Period size: 15 Copynumber: 5.4 Consensus size: 15
601737 TTCCATAAAT
**
601747 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
601762 G-AATTCAAATTCTA
1 GTAATTCAAATTCCA
**
601776 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
601791 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
*
601806 G---TTCAAATTTCA
1 GTAATTCAAATTCCA
601818 GTAATT
1 GTAATT
601824 TATTTTCCGG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
12 11 0.22
14 11 0.22
15 27 0.55
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:601822 original size:42 final size:43
Alignment explanation
Indices: 601747--601831 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 43
601737 TTCCATAAAT
**
601747 GTAATTCATTTTCCAGAATTCAAATTCTAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAG-ATTCAAATTCTAGTAATTCATTTTCCA
*
601791 GTAATTCAAATTCCAG-TTCAAATT-TCAGTAATTTATTTTCC
1 GTAATTCAAATTCCAGATTCAAATTCT-AGTAATTCATTTTCC
601832 GGAAAACCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 1 0.03
42 22 0.59
44 14 0.38
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.44
Consensus pattern (43 bp):
GTAATTCAAATTCCAGATTCAAATTCTAGTAATTCATTTTCCA
Found at i:604427 original size:16 final size:16
Alignment explanation
Indices: 604390--604421 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
604380 ATATTTGCAA
*
604390 AAAATATTATATAAGT
1 AAAATATTATATAAAT
604406 AAAATATTATATAAAT
1 AAAATATTATATAAAT
604422 TCAATACTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAATATTATATAAAT
Found at i:605308 original size:15 final size:17
Alignment explanation
Indices: 605271--605311 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
605261 ATATTTATTT
*
605271 ATTAATTTTTAAAATAA
1 ATTATTTTTTAAAATAA
*
605288 ATTATTTTTTAACA-AA
1 ATTATTTTTTAAAATAA
605304 A-TATTTTT
1 ATTATTTTT
605312 AGACATACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 3 0.14
17 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATTTTTTAAAATAA
Found at i:615821 original size:128 final size:128
Alignment explanation
Indices: 615588--616042 Score: 806
Period size: 128 Copynumber: 3.6 Consensus size: 128
615578 GGGATTCTGA
*
615588 TGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA-G-GCGCCCCTGGGAACG
1 TGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACG
* *
615651 CGCCTTCAAGTCTCCTAAGAAATAATAGGTACTGATATGAATAGTGTCCCCGAGGGACATGAG
66 CGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGTGTCCCCGAGGGACATGAG
*
615714 TGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCACGCCCCCGGGAACG
1 TGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACG
* *
615779 CGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAATAGTATCCCCGAGGGACATGAG
66 CGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGTGTCCCCGAGGGACATGAG
*
615842 TGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCGCCCCCGGGAACG
1 TGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACG
* *
615907 CGCCTTCAAGTCCCCTGAGAAATAATAGGTACTTATATGAATAGTGTCTCCGAGGGACATGAG
66 CGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGTGTCCCCGAGGGACATGAG
*
615970 TGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCTGGAACG
1 TGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACG
616035 CGCCTTCA
66 CGCCTTCA
616043 TGTGAATAGT
Statistics
Matches: 313, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
126 47 0.15
127 1 0.00
128 265 0.85
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (128 bp):
TGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACG
CGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGTGTCCCCGAGGGACATGAG
Found at i:616135 original size:8 final size:8
Alignment explanation
Indices: 616122--616162 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
616112 TCACAAGCTT
616122 TCAAATTC
1 TCAAATTC
616130 TCAAATTC
1 TCAAATTC
*
616138 TCAAACTC
1 TCAAATTC
616146 T-AAATTC
1 TCAAATTC
616153 TCAAATTC
1 TCAAATTC
616161 TC
1 TC
616163 TGAAAATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (8 bp):
TCAAATTC
Found at i:616152 original size:15 final size:16
Alignment explanation
Indices: 616122--616162 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
616112 TCACAAGCTT
*
616122 TCAAATTCTCAAATTC
1 TCAAACTCTCAAATTC
616138 TCAAACTCT-AAATTC
1 TCAAACTCTCAAATTC
*
616153 TCAAATTCTC
1 TCAAACTCTC
616163 TGAAAATGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (16 bp):
TCAAACTCTCAAATTC
Found at i:623552 original size:19 final size:19
Alignment explanation
Indices: 623528--623564 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
623518 TAAAATTAGT
* *
623528 TAATAATAGTATTCAATAA
1 TAATAATAATATTAAATAA
623547 TAATAATAATATTAAATA
1 TAATAATAATATTAAATA
623565 TGATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
TAATAATAATATTAAATAA
Found at i:623786 original size:41 final size:41
Alignment explanation
Indices: 623741--623836 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
623731 CGTTGATCCA
* *
623741 TTCCACTATCACTCCATGAAGATTGATTCGAGTCAGACTTG
1 TTCCACTATCACTCCAGGAAGATTGATTCGAGGCAGACTTG
* * *
623782 TTCCACTGTCACTCCAGGAAGATTTATTTGAGGCAGACTTG
1 TTCCACTATCACTCCAGGAAGATTGATTCGAGGCAGACTTG
623823 TTCCACTATCACTC
1 TTCCACTATCACTC
623837 AGGGAATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (41 bp):
TTCCACTATCACTCCAGGAAGATTGATTCGAGGCAGACTTG
Found at i:624027 original size:132 final size:133
Alignment explanation
Indices: 623811--624050 Score: 351
Period size: 132 Copynumber: 1.8 Consensus size: 133
623801 AGATTTATTT
* * *
623811 GAGGCAGACTTGTTCCACTATCACTCAGGGAATATTAAATCTTGAAAGAGAGTGATATGTTTCGC
1 GAGGCAGACTTGTTCCACTATCACTCAGGGAATATTAAATCTTCAAAGAGAGGGATATATTTCGC
*
623876 TTCTTCTGGAGGGAATATCATATCA-AGGGGA-GTTGATACATTTTTTTCACTCAGGGAAGATTG
66 TTCTTCTGAAGGGAATATCATAT-ATAGGGGAGGTTGATACATTTTTTTCACTCAGGGAAGATTG
623939 AATC
130 AATC
* * * * *
623943 GAGGTAGACTTGTTCTACTGTGACTTAGGGAATATTAAATCTTCAAAGAGAGGGATATATTAT-G
1 GAGGCAGACTTGTTCCACTATCACTCAGGGAATATTAAATCTTCAAAGAGAGGGATATATT-TCG
*
624007 CTTCTTCTGAAGGGAATATCATATATAGGGGAGGTTGATCCATT
65 CTTCTTCTGAAGGGAATATCATATATAGGGGAGGTTGATACATT
624051 CCACTGTCAC
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
131 1 0.01
132 83 0.87
133 11 0.12
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (133 bp):
GAGGCAGACTTGTTCCACTATCACTCAGGGAATATTAAATCTTCAAAGAGAGGGATATATTTCGC
TTCTTCTGAAGGGAATATCATATATAGGGGAGGTTGATACATTTTTTTCACTCAGGGAAGATTGA
ATC
Found at i:624225 original size:228 final size:226
Alignment explanation
Indices: 623823--624296 Score: 727
Period size: 228 Copynumber: 2.1 Consensus size: 226
623813 GGCAGACTTG
*
623823 TTCCACTATCACTCAGGGAATATTAAATCTTGAAAGAGAGTGATATGTTTCGCTTCTTCTGGAGG
1 TTCCACTATCACTCAGGGAATATTAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTGGAGG
* * *
623888 GAATATCATATCAAGGGGAGTTGATACATTTTTTTCACTCAGGGAAGATTGAATCGAGGTAGACT
66 GAATATAAGATCAAGGGGAGTTGATACATTTTTTTCACTCAGGGAAGATTGAATCGAGGCAGACT
* * * *
623953 TGTTCTACTGTGACTTAGGGAATATTAAATCTTCAAAGAGAGGGATATATTATGCTTCTTCTGAA
131 TGTTCCACCGTGACTCAGGGAATATCAAATCTTCAAAGAGAGGGATATATTATGCTTCTTCTGAA
*
624018 GGGAATATCATATATAGGGGAGGTTGATCCA
196 GGGAATATCATATATAGGGGAGATTGATCCA
* *
624049 TTCCACTGTCACTCAGGGAATATTATATCTTGAAAGAGAGGGATATG-TTCTGCTTCTTCTGGAG
1 TTCCACTATCACTCAGGGAATATTAAATCTTGAAAGAGAGGGATATGTTTC-GCTTCTTCTGGAG
* * * *
624113 GGAATATAAGATC-TGATGGAGTTTATCCATTCTATTTTCACTCAGGGAAGATTGAATCGAGGCA
65 GGAATATAAGATCAAG-GGGAGTTGATACATT-T-TTTTCACTCAGGGAAGATTGAATCGAGGCA
* *
624177 GACTTGTTCCACCGTGACTCAGGGAATATCAAATCTTCAAAGAGAGGGATATGTTTTGCTTCTTC
127 GACTTGTTCCACCGTGACTCAGGGAATATCAAATCTTCAAAGAGAGGGATATATTATGCTTCTTC
* *
624242 TGGAGGGAATATCATATCTAGGGGAGATTGATCCA
192 TGAAGGGAATATCATATATAGGGGAGATTGATCCA
624277 TTCCACTATCACTCAGGGAA
1 TTCCACTATCACTCAGGGAA
624297 GATTGAATAA
Statistics
Matches: 224, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
225 4 0.02
226 80 0.36
227 1 0.00
228 139 0.62
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (226 bp):
TTCCACTATCACTCAGGGAATATTAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTGGAGG
GAATATAAGATCAAGGGGAGTTGATACATTTTTTTCACTCAGGGAAGATTGAATCGAGGCAGACT
TGTTCCACCGTGACTCAGGGAATATCAAATCTTCAAAGAGAGGGATATATTATGCTTCTTCTGAA
GGGAATATCATATATAGGGGAGATTGATCCA
Found at i:624978 original size:134 final size:134
Alignment explanation
Indices: 624049--624974 Score: 1126
Period size: 134 Copynumber: 6.9 Consensus size: 134
624039 GGTTGATCCA
* * *
624049 TTCCACTGTCACTCAGGGAATATTATATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGGAGG
1 TTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGGAGG
* * * * * *
624114 GAATATAAGATCTGATGGA-GTTTATCCATTCTATTTTCACTCAGGGAAGATTGAATCGAGGCAG
66 GAATATCAGATCTG-GGGACGTTGATTCATTCCATTGTCACTCAGGGAAGATTGAATCGAGGCAG
624178 ACTTG
130 ACTTG
* * * *
624183 TTCCACCGTGACTCAGGGAATATCAAATCTTCAAAGAGAGGGATATGTTTTGCTTCTTCTGGAGG
1 TTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGGAGG
* * * * * *
624248 GAATATCATATCTAGGGGA-GATTGATCCATTCCACTATCACTCAGGGAAGATTGAAT-AAGGGA
66 GAATATCAGATCT-GGGGACG-TTGATTCATTCCATTGTCACTCAGGGAAGATTGAATCGA-GGC
624311 AGACTTG
128 AGACTTG
* ** * * *
624318 TTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGATATAGATTTATTCCGCTTCTTCTGGAGG
1 TTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGGAGG
* * *** * * *
624383 GAATATCATATATGGGGACGTTGATTCATTCTGCTATCACTTAGGGAAGATTGAATCGAGCCAGA
66 GAATATCAGATCTGGGGACGTTGATTCATTCCATTGTCACTCAGGGAAGATTGAATCGAGGCAGA
624448 CTTG
131 CTTG
* * * * * *
624452 TTCCAGTGTTACTGAGGGAATATCAAATCTTGAAAGAGATGGATTTGTTCCGCTTCTTCTAGAGG
1 TTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGGAGG
* * * * * * * *
624517 GAATATAAGATATGGGGACGTCGATTCATTTTC-TTGTCACTCATGGAAAATTGAATCAAGCCAG
66 GAATATCAGATCTGGGGACGTTGATTCA-TTCCATTGTCACTCAGGGAAGATTGAATCGAGGCAG
624581 ACTTG
130 ACTTG
* * * * * * *
624586 CTCCACTGTTACTCAGGGAATATAAAATCTTGAAAAAGAGGGATTTGTT-TATCTTTTTCTGAAG
1 TTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCT-GCTTCTTCTGGAG
* * *
624650 GGAATATCAGATATGGGGACATTGATTCATTCCGTTGTCACTCAGGGAAGATTGAATCGAGGCAG
65 GGAATATCAGATCTGGGGACGTTGATTCATTCCATTGTCACTCAGGGAAGATTGAATCGAGGCAG
624715 ACTTG
130 ACTTG
* *
624720 TTCCACTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTATGCTTCTTCTGGAGG
1 TTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGGAGG
* * * * * *
624785 GAATATCATATCTGGGGACATTGATTCATTCCGTTGTCACTCAGGGAAGATTAAATTGAGGTAGA
66 GAATATCAGATCTGGGGACGTTGATTCATTCCATTGTCACTCAGGGAAGATTGAATCGAGGCAGA
624850 CTTG
131 CTTG
* *
624854 TTCCACTGTTACTCAGAGAATATCAAATCTTGAAAGAGAGGGATATGTTCTTCTTCTTCTGGAGG
1 TTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGGAGG
* *
624919 GAATATCAGATCTGGATGA-GTTGATTCATTCCACTGTCACTCAGGGAAGATTGAAT
66 GAATATCAGATCTGG-GGACGTTGATTCATTCCATTGTCACTCAGGGAAGATTGAAT
624975 TGAGTTCGAC
Statistics
Matches: 690, Mismatches: 92, Indels: 20
0.86 0.11 0.02
Matches are distributed among these distances:
133 3 0.00
134 571 0.83
135 116 0.17
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (134 bp):
TTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGGAGG
GAATATCAGATCTGGGGACGTTGATTCATTCCATTGTCACTCAGGGAAGATTGAATCGAGGCAGA
CTTG
Found at i:626585 original size:2 final size:2
Alignment explanation
Indices: 626578--626648 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
626568 GGCTTTATTG
626578 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
626620 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
626649 ATCGCCTTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:632453 original size:12 final size:12
Alignment explanation
Indices: 632436--632466 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
632426 GATCTCTGGT
632436 TGGTGGCAACAA
1 TGGTGGCAACAA
632448 TGGTGGCAACAA
1 TGGTGGCAACAA
632460 TGGTGGC
1 TGGTGGC
632467 TACCGGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.39, T:0.19
Consensus pattern (12 bp):
TGGTGGCAACAA
Found at i:633741 original size:133 final size:133
Alignment explanation
Indices: 633490--633748 Score: 348
Period size: 133 Copynumber: 1.9 Consensus size: 133
633480 ATAAATAAAC
* *
633490 ATTTATTTGTTCTTTAATATGAACATGTAAAAATATGAAATTCAATGTCATCTTATTATTTTGTT
1 ATTTATTTGTCCTTTAATATGAACATGTAAAAATATGAAAATCAATGTCATC-T-TTATTTTGTT
* * * *
633555 TATTTGGGCAAATTTCCAATTATTTTTTGTAGTTGAGGAATAATGAGAACAAAAATGAAAATGGG
64 TATTTGGGAAAATTTCCAATTATTTTCTATAGTTGAGGAATAATGAGAACAAAAAAGAAAATGGG
633620 GTAAT
129 GTAAT
633625 ATTTATTTGTCCTTTAATATGAACATGTAAAAAAATAT-AAAATCAAATG-CTATC-TTATTTTG
1 ATTTATTTGTCCTTTAATATGAACATGT--AAAAATATGAAAATC-AATGTC-ATCTTTATTTTG
* *
633687 TTTATTT-GGAAAAGTTTTC-ATTATTTTCTATAGTTGAGGAATAATGGGAACAAAAAAGAAAA
62 TTTATTTGGGAAAA-TTTCCAATTATTTTCTATAGTTGAGGAATAATGAGAACAAAAAAGAAAA
633749 ATTAGGTCCA
Statistics
Matches: 111, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
133 44 0.40
134 19 0.17
135 27 0.24
136 6 0.05
137 15 0.14
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (133 bp):
ATTTATTTGTCCTTTAATATGAACATGTAAAAATATGAAAATCAATGTCATCTTTATTTTGTTTA
TTTGGGAAAATTTCCAATTATTTTCTATAGTTGAGGAATAATGAGAACAAAAAAGAAAATGGGGT
AAT
Found at i:636838 original size:27 final size:27
Alignment explanation
Indices: 636808--636864 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
636798 AGAAACCATA
636808 TAATTTGTATAATCAATGTCTATAAGT
1 TAATTTGTATAATCAATGTCTATAAGT
636835 TAATTTGTATAATCAATGTCTATAAGT
1 TAATTTGTATAATCAATGTCTATAAGT
636862 TAA
1 TAA
636865 CTATAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.44
Consensus pattern (27 bp):
TAATTTGTATAATCAATGTCTATAAGT
Found at i:636873 original size:27 final size:27
Alignment explanation
Indices: 636816--636874 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
636806 TATAATTTGT
* *
636816 ATAATCAATGTCTATAAGTTAATTTGT
1 ATAATCAATGTCTATAAGTTAATATGA
636843 ATAATCAATGTCTATAAGTTAACTAT-A
1 ATAATCAATGTCTATAAGTTAA-TATGA
636870 ATAAT
1 ATAAT
636875 AATAAGGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (27 bp):
ATAATCAATGTCTATAAGTTAATATGA
Found at i:639243 original size:21 final size:21
Alignment explanation
Indices: 639200--639264 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
639190 AATATATAAA
*
639200 TCGCATTGCGATTTTCC-AAT
1 TCGCGTTGCGATTTTCCAAAT
639220 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
*
639241 TCGCGTTGCAATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
639262 TCG
1 TCG
639265 GAACGTGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:639308 original size:20 final size:19
Alignment explanation
Indices: 639279--639321 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
639269 GTGAATCTGT
*
639279 AAATCACAACACATAAGTC
1 AAATCACAACACAGAAGTC
639298 AAATGCACAACACAGAAGTC
1 AAAT-CACAACACAGAAGTC
639318 AAAT
1 AAAT
639322 TCGCAACACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.53, C:0.23, G:0.09, T:0.14
Consensus pattern (19 bp):
AAATCACAACACAGAAGTC
Found at i:639328 original size:20 final size:19
Alignment explanation
Indices: 639293--639407 Score: 90
Period size: 20 Copynumber: 5.8 Consensus size: 19
639283 CACAACACAT
* *
639293 AAGTCAAATGCACAACACAG
1 AAGTCAAATTCGCAACAC-G
639313 AAGTCAAATTCGCAACACTG
1 AAGTCAAATTCGCAACAC-G
* *
639333 AATTTCAAATTCGCAACGCG
1 AA-GTCAAATTCGCAACACG
* *
639353 ATAGTC-AATTTGCAATACG
1 A-AGTCAAATTCGCAACACG
*
639372 ATAATCAAATTCGCAA-AGCG
1 A-AGTCAAATTCGCAACA-CG
639392 AAAGTCAAATTCGCAA
1 -AAGTCAAATTCGCAA
639408 AGCGCGTTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
19 16 0.21
20 46 0.59
21 16 0.21
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.21
Consensus pattern (19 bp):
AAGTCAAATTCGCAACACG
Found at i:639588 original size:22 final size:22
Alignment explanation
Indices: 639563--639613 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
639553 CTACGGTGAC
639563 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
639585 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
639607 ATCCGTC
1 ATCCGTC
639614 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:640022 original size:14 final size:14
Alignment explanation
Indices: 640005--640036 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
639995 GCGATTTTAG
640005 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
*
640019 TTTCTCGTTGCGAT
1 TTTCGCGTTGCGAT
640033 TTTC
1 TTTC
640037 ATTTTCGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:640062 original size:20 final size:20
Alignment explanation
Indices: 640019--640062 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
640009 GCGTTGCGAT
* * * *
640019 TTTCTCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
640039 TTTCGCGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
640059 TTTC
1 TTTC
640063 AGAAACTACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:641782 original size:42 final size:42
Alignment explanation
Indices: 641735--641849 Score: 128
Period size: 42 Copynumber: 2.7 Consensus size: 42
641725 CACCTGTCAT
* * *
641735 CGTTCAAGAGGCACC-TCCTATCATTCAAGAGGCTCCTCTCAC
1 CGTTCAAGAGGC-CCTTCCCACCATTCAAGAGGCCCCTCTCAC
* *
641777 CGTTCAAGAGGCCCTTCCCACCATTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCTTCCCACCATTCAAGAGGCCCCTCTCAC
*
641819 CGTTCAATG-GGTCCC-TCCCACCATTTAAGAG
1 CGTTCAA-GAGG-CCCTTCCCACCATTCAAGAG
641850 CTCGATTCAC
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
41 2 0.03
42 58 0.91
43 4 0.06
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CGTTCAAGAGGCCCTTCCCACCATTCAAGAGGCCCCTCTCAC
Found at i:641824 original size:21 final size:21
Alignment explanation
Indices: 641731--641825 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
641721 GATTCACCTG
*
641731 TCATCGTTCAAGAGGCACCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
641752 -CTATCATTCAAGAGGCTCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
641773 TCACCGTTCAAGAGGCCCTTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
641794 CCACCATTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
641815 TCATCGTTCAA
1 TCATCGTTCAA
641826 TGGGTCCCTC
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 1 0.02
21 57 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:643249 original size:69 final size:76
Alignment explanation
Indices: 643176--643349 Score: 206
Period size: 79 Copynumber: 2.4 Consensus size: 76
643166 CTGGGGTACC
*
643176 TTTTTGCTTGTTTAATTGAATTT-T-A-CA-TTG-AAA-GTTGATTTGTTTAA-TTGATG-AGGA
1 TTTTTTCTTGTTTAATTGAATTTGTAATCAGTTGTAAATGTTGATTTGTTTAATTTGATGTA-GA
643233 AATAAGAATTAT
65 AATAAGAATTAT
*
643245 TTTTTTCTTGTTTAATTG-ATTTGTAAAAGTTGAGTTGTAAATGTTGATTTGTTTAATTTGATGT
1 TTTTTTCTTGTTTAATTGAATTTGT--AA--TCAGTTGTAAATGTTGATTTGTTTAATTTGATGT
*
643309 ATAAATAAGAATTAT
62 AGAAATAAGAATTAT
643324 TTTTTTCTTGTTTAATTG-ATTTGTAA
1 TTTTTTCTTGTTTAATTGAATTTGTAA
643350 AAGTTGATTT
Statistics
Matches: 90, Mismatches: 3, Indels: 16
0.83 0.03 0.15
Matches are distributed among these distances:
68 4 0.04
69 18 0.20
72 1 0.01
75 1 0.01
76 3 0.03
77 5 0.06
78 14 0.16
79 43 0.48
80 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.52
Consensus pattern (76 bp):
TTTTTTCTTGTTTAATTGAATTTGTAATCAGTTGTAAATGTTGATTTGTTTAATTTGATGTAGAA
ATAAGAATTAT
Found at i:643282 original size:14 final size:14
Alignment explanation
Indices: 643260--643296 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
643250 TCTTGTTTAA
643260 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
643274 TTGAGTTGTAAATG
1 TTGATTTGTAAAAG
643288 TTGATTTGT
1 TTGATTTGT
643297 TTAATTTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:643339 original size:79 final size:78
Alignment explanation
Indices: 643209--643361 Score: 263
Period size: 79 Copynumber: 1.9 Consensus size: 78
643199 TACATTGAAA
643209 GTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTCTTGTTTAATTGATTTGTAAAAG
1 GTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTCTTGTTTAATTGATTTGTAAAAG
643274 TTGAGTTGTAAAT
66 TTGAGTTGTAAAT
*
643287 GTTGATTTGTTTAATTTGATGTA-TAAATAAGAATTATTTTTTTCTTGTTTAATTGATTTGTAAA
1 GTTGATTTGTTTAA-TTGATG-AGGAAATAAGAATTATTTTTTTCTTGTTTAATTGATTTGTAAA
*
643351 AGTTGATTTGT
64 AGTTGAGTTGT
643362 TGTTTTAAAT
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
78 14 0.20
79 56 0.79
80 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.18, T:0.52
Consensus pattern (78 bp):
GTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTCTTGTTTAATTGATTTGTAAAAG
TTGAGTTGTAAAT
Found at i:646168 original size:12 final size:12
Alignment explanation
Indices: 646151--646178 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
646141 GGTTGTGAGT
646151 TTTGAGATTGTG
1 TTTGAGATTGTG
646163 TTTGAGATTGTG
1 TTTGAGATTGTG
646175 TTTG
1 TTTG
646179 TGGTGAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.32, T:0.54
Consensus pattern (12 bp):
TTTGAGATTGTG
Found at i:648825 original size:21 final size:21
Alignment explanation
Indices: 648796--648868 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
648786 TGGGCCTGTA
* *
648796 ATATGTAATAATATTATTAAT
1 ATATATAATAATATTAATAAT
*
648817 ATATATAATAATAATAAATAAT
1 ATATATAATAAT-ATTAATAAT
*
648839 A-ATATAATAATAATAATAAT
1 ATATATAATAATATTAATAAT
648859 AATAATATAA
1 -AT-ATATAA
648869 ATATATTCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 7 0.16
21 22 0.51
22 8 0.19
23 6 0.14
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (21 bp):
ATATATAATAATATTAATAAT
Found at i:648827 original size:3 final size:3
Alignment explanation
Indices: 648801--648865 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
648791 CTGTAATATG
* *
648801 TAA TAA TAT TAT TAA T-A TATA TAA TAA TAA TAAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TAA TAA
648846 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
648866 TAAATATATT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 4 0.07
3 46 0.82
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:649440 original size:113 final size:112
Alignment explanation
Indices: 649202--649988 Score: 969
Period size: 113 Copynumber: 6.9 Consensus size: 112
649192 ATTATACAAG
* *
649202 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTGCTTCTTCAGATGAGTTCTTCTTATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * ** * *
649267 GAACTTTCTCTAGAAAAATTGATGTTGATCTATCTCCTTCTGTGAT-AGATTCATGCAAA
66 GAAC-TTCTCT-G--GAA---ATGTTGATCCA--T-C--GAGTGATGA-ATTGAAGCAAA
649326 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
* *
649391 GAACTTCTCTGGAAAATGCTGATCCATCGAGTGATGAATTGAAGAAAA
66 GAACTTCTCTGG-AAATGTTGATCCATCGAGTGATGAATTGAAGCAAA
* * *
649439 AGGCTGAACAAGCTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
*
649504 GAACTTTCTCTGGAAAATGCTGATCCATCGAGTGATGAATTGAAGCAAA
66 GAAC-TTCTCTGG-AAATGTTGATCCATCGAGTGATGAATTGAAGCAAA
649553 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTCC-TCTTCAGATGAGTTCTTCTCATTA
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
649617 TGAACTTTCTCTGGAAATATTGATCCATCAAGTGATGGATTTG-AGCAAA
65 TGAAC-TTCTCTGGAAATGTTGATCCATCGAGTGAT-GAATTGAAGCAAA
* *
649666 AGGTTGAACAAGCTCTTCTCATTATGAACTTCCTCTTCCTTATTCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * * *
649731 GAAC-ACTTCTGGAAATGTTGATCCAT--TGTTATGGATTTGAA-CAAA
66 GAACTTC-TCTGGAAATGTTGATCCATCGAGTGAT-GAATTGAAGCAAA
** * * *
649776 AGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTTTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * * * * *
649841 GAACTTCTCTGGAAACGTTGATTCTTCGAATGATGAATTCAAACAAA
66 GAACTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTGAAGCAAA
** *
649888 AGGTTCGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG-TCATTCTCATT
1 AGGTT-GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-TTCTCATT
*
649952 ATGAACTTCTCTGGAAATGTTGATCCATCGAATGATG
64 ATGAACTTCTCTGGAAATGTTGATCCATCGAGTGATG
649989 GATTCGAATC
Statistics
Matches: 601, Mismatches: 48, Indels: 39
0.87 0.07 0.06
Matches are distributed among these distances:
110 93 0.15
111 9 0.01
112 36 0.06
113 253 0.42
114 120 0.20
115 4 0.01
116 1 0.00
118 9 0.01
121 2 0.00
122 1 0.00
123 6 0.01
124 67 0.11
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (112 bp):
AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTGAAGCAAA
Found at i:649612 original size:227 final size:225
Alignment explanation
Indices: 649202--649988 Score: 959
Period size: 227 Copynumber: 3.4 Consensus size: 225
649192 ATTATACAAG
* *
649202 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTGCTTCTTCAGATGAGTTCTTCTTATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * ** * *
649267 GAACTTTCTCTAGAAAAATTGATGTTGATCTATCTCCTTCTGTGAT-AGATTCATGCAAAAGGTT
66 GAACTTTCTCT-G--GAA---ATGTTGATCCA--T-C--GAGTGATGA-ATTGAAGCAAAAGGTT
649331 GAACAAGCTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
119 GAACAAGCTCTTCTCATTATGAACTTCTTCTTTCC-TCTTCAGATGAGTTCTTCTCATTATGAAC
649395 TTCTCTGGAAAATGCTGATCCATCGAGTGATGAATTGAAGAAAA
183 TTCTCTGGAAAATG-TGATCCATCGAGTGATGAATTGAAGAAAA
* * *
649439 AGGCTGAACAAGCTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
*
649504 GAACTTTCTCTGGAAAATGCTGATCCATCGAGTGATGAATTGAAGCAAAAGGTTGAACAAGCTCT
66 GAACTTTCTCTGG-AAATGTTGATCCATCGAGTGATGAATTGAAGCAAAAGGTTGAACAAGCTCT
649569 TCTCATTATGAACTTCTTCTTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
130 TCTCATTATGAACTTCTTCTTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
* * *
649634 TAT-TGATCCATCAAGTGATGGATTTG-AGCAAA
194 -ATGTGATCCATCGAGTGAT-GAATTGAAGAAAA
* *
649666 AGGTTGAACAAGCTCTTCTCATTATGAACTTCCTCTTCCTTATTCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
** * * * **
649731 GAACACT-TCTGGAAATGTTGATCCAT--TGTTATGGATTTGAA-CAAAAGGTTGAACAAATTCT
66 GAACTTTCTCTGGAAATGTTGATCCATCGAGTGAT-GAATTGAAGCAAAAGGTTGAACAAGCTCT
* * *
649792 TCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTTTCATTATGAACTTCTCTGG-AAA
130 TCTCATTATGAACTTCTTCTTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAA
* * * * *
649856 CGTTGATTCTTCGAATGATGAATTCAA-ACAAA
195 TG-TGATCCATCGAGTGATGAATTGAAGA-AAA
** *
649888 AGGTTCGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG-TCATTCTCATT
1 AGGTT-GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-TTCTCATT
*
649952 ATGAAC-TTCTCTGGAAATGTTGATCCATCGAATGATG
64 ATGAACTTTCTCTGGAAATGTTGATCCATCGAGTGATG
649989 GATTCGAATC
Statistics
Matches: 487, Mismatches: 47, Indels: 45
0.84 0.08 0.08
Matches are distributed among these distances:
220 1 0.00
221 6 0.01
222 32 0.07
223 147 0.30
224 8 0.02
225 16 0.03
226 5 0.01
227 163 0.33
228 21 0.04
229 3 0.01
230 1 0.00
232 9 0.02
235 2 0.00
236 1 0.00
237 72 0.15
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (225 bp):
AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTGAAGCAAAAGGTTGAACAAGCTCTT
CTCATTATGAACTTCTTCTTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAT
GTGATCCATCGAGTGATGAATTGAAGAAAA
Found at i:651116 original size:18 final size:19
Alignment explanation
Indices: 651093--651164 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
651083 CAAAATAAAG
651093 ATAAATTGAATTTC-AAAA
1 ATAAATTGAATTTCAAAAA
* *
651111 ATAAATTAAATCTCAAAAA
1 ATAAATTGAATTTCAAAAA
651130 ATAAATTGAATTT-AGAGAAA
1 ATAAATTGAATTTCA-A-AAA
651150 ATAAACTTAGAATTT
1 ATAAA-TT-GAATTT
651165 ATTAATAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 13 0.29
19 16 0.36
20 8 0.18
21 2 0.04
22 6 0.13
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.32
Consensus pattern (19 bp):
ATAAATTGAATTTCAAAAA
Found at i:651131 original size:19 final size:18
Alignment explanation
Indices: 651093--651136 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
651083 CAAAATAAAG
* *
651093 ATAAATTGAATTTCAAAA
1 ATAAATTAAATCTCAAAA
651111 ATAAATTAAATCTCAAAAA
1 ATAAATTAAATCTC-AAAA
651130 ATAAATT
1 ATAAATT
651137 GAATTTAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAAATTAAATCTCAAAA
Found at i:651527 original size:18 final size:19
Alignment explanation
Indices: 651491--651535 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
651481 CTCTTTTTTA
651491 TTTTT-TCTTTTTCAACATT
1 TTTTTCTCTTTTTC-ACATT
651510 TTTTTCTCTTTTTC-CATT
1 TTTTTCTCTTTTTCACATT
651528 TTCTTTCT
1 TT-TTTCT
651536 TCATTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.25
19 10 0.42
20 8 0.33
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTCTCTTTTTCACATT
Found at i:658756 original size:15 final size:15
Alignment explanation
Indices: 658733--658764 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
658723 TGCAATGAAT
658733 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
658748 AATGCATGTATGCAA
1 AATGAATGTATGCAA
658763 AA
1 AA
658765 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:659567 original size:15 final size:15
Alignment explanation
Indices: 659547--659583 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
659537 ACATGATATT
659547 TTTCTCACCTTCAAA
1 TTTCTCACCTTCAAA
659562 TTTCTCACCTTCAAA
1 TTTCTCACCTTCAAA
659577 TTTCTCA
1 TTTCTCA
659584 AGTATGTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTCTCACCTTCAAA
Found at i:663140 original size:13 final size:13
Alignment explanation
Indices: 663122--663146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
663112 TAAATTAAAA
663122 TTATATCAAATTC
1 TTATATCAAATTC
663135 TTATATCAAATT
1 TTATATCAAATT
663147 AAAAGAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATATCAAATTC
Found at i:664303 original size:3 final size:3
Alignment explanation
Indices: 664297--664357 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
664287 TAATATTTAT
664297 TAA TAA TAA -AA TAA TAA TAA TATA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
664341 TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA T-AA TAA TA
664358 TTCAAATGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.11
3 42 0.79
4 5 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:664311 original size:21 final size:21
Alignment explanation
Indices: 664285--664358 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
664275 TGTAATATGT
*
664285 AATAATATTTATTAATAATAA
1 AATAATATATATTAATAATAA
*
664306 AATAATAATAATATATAATAATAT
1 AATAAT-AT-ATAT-TAATAATAA
*
664330 AATAATA-ATAATAATAATATA
1 AATAATATATATTAATAATA-A
664351 AATAATAT
1 AATAATAT
664359 TCAAATGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
20 8 0.18
21 16 0.36
22 2 0.05
23 4 0.09
24 14 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAATATATATTAATAATAA
Found at i:664311 original size:24 final size:24
Alignment explanation
Indices: 664284--664357 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
664274 CTGTAATATG
*
664284 TAATAAT-ATTTATTAATAATAAAA
1 TAATAATAATATA-TAATAATAAAA
*
664308 TAATAATAATATATAATAATATAA
1 TAATAATAATATATAATAATAAAA
664332 TAATAATAATA-ATAAT-AT-AAA
1 TAATAATAATATATAATAATAAAA
664353 TAATA
1 TAATA
664358 TTCAAATGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.15
22 2 0.04
23 5 0.11
24 28 0.61
25 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TAATAATAATATATAATAATAAAA
Found at i:664314 original size:27 final size:27
Alignment explanation
Indices: 664284--664358 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
664274 CTGTAATATG
* *
664284 TAATAATATTTATTAATAATAA-AATAA
1 TAATAATATATAATAAT-ATAATAATAA
664311 TAATAATATATAATAATATAATAATAA
1 TAATAATATATAATAATATAATAATAA
664338 TAATAATAATATAAATAATAT
1 TAATAAT-ATAT-AATAATAT
664359 TCAAATGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.09
27 27 0.63
28 4 0.09
29 8 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TAATAATATATAATAATATAATAATAA
Found at i:664358 original size:9 final size:10
Alignment explanation
Indices: 664277--664358 Score: 93
Period size: 10 Copynumber: 8.6 Consensus size: 10
664267 TTTGGGCCTG
*
664277 TAATATGTAA
1 TAATATATAA
* *
664287 TAATATTTAT
1 TAATATATAA
664297 TAATA-ATAA
1 TAATATATAA
664306 -AATA-ATAA
1 TAATATATAA
664314 TAATATATAA
1 TAATATATAA
664324 TAATATAATAA
1 TAATAT-ATAA
664335 TAATA-ATAA
1 TAATATATAA
664344 TAATATA-AA
1 TAATATATAA
664353 TAATAT
1 TAATAT
664359 TCAAATGAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
8 8 0.12
9 23 0.36
10 24 0.38
11 9 0.14
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (10 bp):
TAATATATAA
Found at i:664612 original size:20 final size:20
Alignment explanation
Indices: 664579--664758 Score: 165
Period size: 20 Copynumber: 9.1 Consensus size: 20
664569 TTGAGAAATT
* *
664579 AAATTCGTGTTGCGAATTCG
1 AAATTCGAGTTGCGAATTTG
*
664599 AAAATCGAGTTGCGAATTTG
1 AAATTCGAGTTGCGAATTTG
664619 AAATTC-AGTTGCGAATTTG
1 AAATTCGAGTTGCGAATTTG
664638 AAATTC-AGTTGCGAATTTG
1 AAATTCGAGTTGCGAATTTG
*
664657 AAATTCAGTGTTGCGAATTTG
1 AAATTC-GAGTTGCGAATTTG
* *
664678 -ACTATCGCGTTGCGAATTTG
1 AAAT-TCGAGTTGCGAATTTG
* *
664698 -ACTTCTGTGTTGCGAATTTG
1 AAATTC-GAGTTGCGAATTTG
* *
664718 -ACTATCGCGTTGCGAATTTG
1 AAAT-TCGAGTTGCGAATTTG
* *
664738 -ACTTCTGTGTTGCGAATTTG
1 AAATTC-GAGTTGCGAATTTG
664758 A
1 A
664759 GTTTTGTGTT
Statistics
Matches: 143, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
19 42 0.29
20 85 0.59
21 16 0.11
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (20 bp):
AAATTCGAGTTGCGAATTTG
Found at i:664628 original size:19 final size:19
Alignment explanation
Indices: 664587--664678 Score: 139
Period size: 19 Copynumber: 4.7 Consensus size: 19
664577 TTAAATTCGT
* *
664587 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTC-A
664607 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
664626 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
664645 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
664664 GTGTTGCGAATTTGA
1 --GTTGCGAATTTGA
664679 CTATCGCGTT
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
19 39 0.57
20 16 0.24
21 13 0.19
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:664708 original size:40 final size:40
Alignment explanation
Indices: 664585--664912 Score: 246
Period size: 40 Copynumber: 8.2 Consensus size: 40
664575 AATTAAATTC
* ** * *
664585 GTGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTC-
1 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTG-ACTTCT
* * * * *
664625 -AGTTGCGAATTTGA-AATTC-AGTTGCGAATTTGAAATTCA
1 GTGTTGCGAATTTGACTA-TCGCGTTGCGAATTTG-ACTTCT
664664 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
1 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
664704 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
1 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
* * * *
664744 GTGTTGCGAATTTGAGTTTTGTGTTGCG-ATTT-ACAAATTC-
1 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGAC---TTCT
** * * * *
664784 GCATTGCG-ATTT-ACAAATTTGCATTGCGATTTATAGA-TT-T
1 GTGTTGCGAATTTGAC-TA-TCGCGTTGCGAATT-T-GACTTCT
* * * * * *
664824 GCGTTGTGAATTTGACTTTTGTGTTGCGAATTTGACTTCA
1 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
664864 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
1 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
*
664904 GTTTTGCGA
1 GTGTTGCGA
664913 TTTATAGATT
Statistics
Matches: 235, Mismatches: 34, Indels: 38
0.77 0.11 0.12
Matches are distributed among these distances:
38 26 0.11
39 25 0.11
40 158 0.67
41 22 0.09
42 3 0.01
44 1 0.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (40 bp):
GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
Found at i:664730 original size:60 final size:60
Alignment explanation
Indices: 664585--664899 Score: 190
Period size: 60 Copynumber: 5.3 Consensus size: 60
664575 AATTAAATTC
* * * * * *
664585 GTGTTGCGAATTCGAAAATCGAGTTGCGAATTTGA-AATTC-AGTTGCGAATTTGAAATTC-
1 GTGTTGCGAATTTGACAATCGCGTTGCGAATTTGACTA-TCGCGTTGCGAATTTG-ACTTCT
* *
664644 -AGTTGCGAATTTGA-AATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
1 GTGTTGCGAATTTGACAA-TC-GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
* * * *
664704 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT-TCTGTGTTGCGAATTTGAGTTTT
1 GTGTTGCGAATTTGACAATCGCGTTGCGAATTTGACTATC-GCGTTGCGAATTTGACTTCT
* * * * *
664764 GTGTTGCG-ATTT-ACAAATTCGCATTGCG-ATTT-ACAAATTTGCATTGCGATTTATAGA-TT-
1 GTGTTGCGAATTTGAC-AA-TCGCGTTGCGAATTTGAC-TA-TCGCGTTGCGAATT-T-GACTTC
664823 T
60 T
* * ** * * *
664824 GCGTTGTGAATTTGACTTTTGTGTTGCGAATTTGACT-TCAGTGTTGCGAATTTGACTATC-
1 GTGTTGCGAATTTGACAATCGCGTTGCGAATTTGACTATC-GCGTTGCGAATTTGACT-TCT
*
664884 GCGTTGCGAATTTGAC
1 GTGTTGCGAATTTGAC
664900 TTCTGTTTTG
Statistics
Matches: 201, Mismatches: 32, Indels: 45
0.72 0.12 0.16
Matches are distributed among these distances:
57 2 0.01
58 20 0.10
59 34 0.17
60 111 0.55
61 27 0.13
62 7 0.03
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.40
Consensus pattern (60 bp):
GTGTTGCGAATTTGACAATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT
Found at i:664766 original size:20 final size:20
Alignment explanation
Indices: 664645--664912 Score: 198
Period size: 20 Copynumber: 13.3 Consensus size: 20
664635 TTGAAATTCA
* *
664645 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTCTGT
*
664666 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
664686 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
664706 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
664726 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
* *
664746 GTTGCGAATTTGAGTTTTGT
1 GTTGCGAATTTGACTTCTGT
*
664766 GTTGCG-ATTT-ACAAATTC-GC
1 GTTGCGAATTTGAC---TTCTGT
* *
664786 ATTGCG-ATTT-ACAAATT-TGC
1 GTTGCGAATTTGAC---TTCTGT
* * *
664806 ATTGCGATTTATAGA-TT-TGC
1 GTTGCGAATT-T-GACTTCTGT
* *
664826 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
*
664846 GTTGCGAATTTGACTTCAGT
1 GTTGCGAATTTGACTTCTGT
*
664866 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
664886 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
664906 TTTGCGA
1 GTTGCGA
664913 TTTATAGATT
Statistics
Matches: 209, Mismatches: 22, Indels: 33
0.79 0.08 0.12
Matches are distributed among these distances:
18 3 0.01
19 13 0.06
20 169 0.81
21 22 0.11
22 1 0.00
24 1 0.00
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:664838 original size:140 final size:140
Alignment explanation
Indices: 664684--664948 Score: 390
Period size: 140 Copynumber: 1.9 Consensus size: 140
664674 TTTGACTATC
*
664684 GCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTATC-GCGTTGCGAATTTGACT-TCTGTG
1 GCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACT-TCAGCGTTGCGAATTTGACTATC-GCG
* * *
664747 TTGCGAATTTGAGTTTTGTGTTGCGATTTACAAATTCGCATTGCGATTTACAAATTTGCATTGCG
64 TTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCATTGCGATTTACAAATTCGCATTGCG
664812 ATTTATAGATTT
129 ATTTATAGATTT
* * *
664824 GCGTTGTGAATTTGACTTTTGTGTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTATCGCGTT
1 GCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTCAGCGTTGCGAATTTGACTATCGCGTT
* * * * *
664889 GCGAATTTGACTTCTGTTTTGCGATTTATAGATTCGCGTTGCGATTTACAGATTCGCATT
66 GCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCATTGCGATTTACAAATTCGCATT
664949 ACAAATTTGG
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
139 2 0.02
140 107 0.96
141 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (140 bp):
GCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTCAGCGTTGCGAATTTGACTATCGCGTT
GCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCATTGCGATTTACAAATTCGCATTGCGAT
TTATAGATTT
Found at i:664930 original size:20 final size:20
Alignment explanation
Indices: 664907--664945 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
664897 GACTTCTGTT
*
664907 TTGCGATTTATAGATTCGCG
1 TTGCGATTTACAGATTCGCG
664927 TTGCGATTTACAGATTCGC
1 TTGCGATTTACAGATTCGC
664946 ATTACAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACAGATTCGCG
Found at i:664966 original size:21 final size:21
Alignment explanation
Indices: 664949--664989 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
664939 GATTCGCATT
664949 ACAAATTTGGAAAATCGCAAC
1 ACAAATTTGGAAAATCGCAAC
*
664970 ACGAATTTGGAAAATCGCAA
1 ACAAATTTGGAAAATCGCAA
664990 TGCTATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (21 bp):
ACAAATTTGGAAAATCGCAAC
Found at i:665594 original size:15 final size:15
Alignment explanation
Indices: 665574--665605 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
665564 TTATGTTTCA
*
665574 TTGAATATTTTAAAT
1 TTGAATATATTAAAT
665589 TTGAATATATTAAAT
1 TTGAATATATTAAAT
665604 TT
1 TT
665606 TTATCAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TTGAATATATTAAAT
Found at i:671090 original size:21 final size:21
Alignment explanation
Indices: 671064--671127 Score: 103
Period size: 21 Copynumber: 3.0 Consensus size: 21
671054 CCGTTAGACA
671064 GGGGGGAAT-TAGTACCCCCTG
1 GGGGGGAATCT-GTACCCCCTG
*
671085 GGGGGGAATCTGTTCCCCCTG
1 GGGGGGAATCTGTACCCCCTG
671106 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
671127 G
1 G
671128 CAATTTGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.14, C:0.27, G:0.39, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:672475 original size:21 final size:21
Alignment explanation
Indices: 672431--672499 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
672421 TTGCAGCCTT
* *
672431 GATGCATGGATGCATGAC-AG
1 GATGCATCGATGCATGGCAAG
672451 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
672472 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
672493 GATGCAT
1 GATGCAT
672500 TAAGAAATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.17, G:0.33, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:673662 original size:19 final size:20
Alignment explanation
Indices: 673619--673666 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
673609 TCTAAATCCT
*
673619 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
673639 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
673658 TTTTCAAAA
1 TTTTCAAAA
673667 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:674980 original size:21 final size:21
Alignment explanation
Indices: 674933--675008 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
674923 TTGCAGCCTT
* *
674933 GATGCATGGATGCATGAC-AG
1 GATGCATCGATGCATGGCAAG
674953 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
*
674974 TATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
674995 GATGCATCGATGCA
1 GATGCATCGATGCA
675009 CTAATTGCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 16 0.31
21 35 0.69
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.21
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:675222 original size:30 final size:30
Alignment explanation
Indices: 675188--675247 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
675178 AACTTTGAAT
675188 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
675218 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
675248 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:675973 original size:14 final size:14
Alignment explanation
Indices: 675954--675980 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
675944 TTATTGAACT
675954 AAATGATTTATTTA
1 AAATGATTTATTTA
675968 AAATGATTTATTT
1 AAATGATTTATTT
675981 TTCTTTTGTT
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
AAATGATTTATTTA
Found at i:676113 original size:19 final size:20
Alignment explanation
Indices: 676070--676117 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
676060 TCTAAATCCT
*
676070 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
676090 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
676109 TTTTCAAAA
1 TTTTCAAAA
676118 GAAAATCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:677037 original size:35 final size:32
Alignment explanation
Indices: 676974--677045 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 32
676964 ACCTTACAAC
* *
676974 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACC-TT
*
677007 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
677041 TCCCT
1 TCCCT
677046 TTACAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 12 0.35
35 15 0.44
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:677416 original size:20 final size:20
Alignment explanation
Indices: 677391--677454 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
677381 CCGTTAGACA
*
677391 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
**
677411 GGGGGGGAATCTGTTTCCCCT
1 -GGGGGGAATCTGTACCCCCT
677432 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
677452 GGG
1 GGG
677455 CAATCTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.12, C:0.27, G:0.41, T:0.20
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:677417 original size:21 final size:21
Alignment explanation
Indices: 677391--677454 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
677381 CCGTTAGACA
*
677391 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
**
677412 GGGGGGAATCTGTTTCCCCT-
1 GGGGGGAATCTGTACCCCCTG
677432 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
677453 GG
1 GG
677455 CAATCTGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 18 0.49
21 19 0.51
ACGTcount: A:0.12, C:0.27, G:0.41, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:681650 original size:22 final size:21
Alignment explanation
Indices: 681625--681680 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 21
681615 TAATTAAATA
681625 TTATATATTTATATGTTAGTTT
1 TTATATATTTATAT-TTAGTTT
*
681647 TTATATTATGTTATATTTATTTT
1 TTATA-TAT-TTATATTTAGTTT
*
681670 TTAAATATTTA
1 TTATATATTTA
681681 GTTTTTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.10
22 8 0.27
23 13 0.43
24 6 0.20
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTATATATTTATATTTAGTTT
Found at i:681664 original size:52 final size:52
Alignment explanation
Indices: 681535--681678 Score: 134
Period size: 52 Copynumber: 2.7 Consensus size: 52
681525 AAGACATCAC
* * ** *
681535 TAGTTTTTATATTATGTTTTTATGTTTTTAATTGAATGCTATATTTTTTATATT
1 TAGTTTTTATATTATG-TTATAT-TTTTTAATTAAATATTATATTATTTATATT
* *
681589 TAGTTTTTATGGTTA--ATATTATTTTTTAATTAAATATTATA-TATTTATATGT
1 TAGTTTTTAT-ATTATGTTA-TATTTTTTAATTAAATATTATATTATTTATAT-T
*
681641 TAGTTTTTATATTATGTTATATTTATTT-TTTAAATATT
1 TAGTTTTTATATTATGTTATATTT-TTTAATTAAATATT
681679 TAGTTTTTGT
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
51 11 0.15
52 42 0.57
53 8 0.11
54 10 0.14
55 3 0.04
ACGTcount: A:0.28, C:0.01, G:0.08, T:0.63
Consensus pattern (52 bp):
TAGTTTTTATATTATGTTATATTTTTTAATTAAATATTATATTATTTATATT
Done.