Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007888.1 Hibiscus syriacus cultivar Beakdansim tig00110270_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: 1558302
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1422446 original size:24 final size:24
Alignment explanation
Indices: 1422412--1422465 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1422402 CTGAAACATC
* * *
1422412 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTCACCAAG
*
1422436 ATCAAAGTCCGGGTATTCACCAAG
1 ATCAAAATCCGGGTATTCACCAAG
1422460 ATCAAA
1 ATCAAA
1422466 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTCACCAAG
Found at i:1423240 original size:70 final size:70
Alignment explanation
Indices: 1423152--1423287 Score: 245
Period size: 70 Copynumber: 1.9 Consensus size: 70
1423142 ATTTGCGAAA
*
1423152 GTATTATCTCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGGCAATAATTTGACCATCGCATTGCG
1 GTATTATCTCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGGCAATAATTTGACCATCGCAATGCG
1423217 ATTCT
66 ATTCT
* *
1423222 GTATTATCTCGTTGCGAAAGTCAGAATCGTGTTGCGAAAGGCAATCATTTGACCATCGCAATGCG
1 GTATTATCTCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGGCAATAATTTGACCATCGCAATGCG
1423287 A
66 A
1423288 AATGCAAATC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (70 bp):
GTATTATCTCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGGCAATAATTTGACCATCGCAATGCG
ATTCT
Found at i:1423580 original size:20 final size:20
Alignment explanation
Indices: 1423555--1423612 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1423545 ATTCATTTGA
1423555 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1423575 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1423595 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1423613 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1423655 original size:14 final size:15
Alignment explanation
Indices: 1423636--1423707 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 15
1423626 GAAAATCGCA
1423636 TTGCGATTTTC-TCG
1 TTGCGATTTTCTTCG
1423650 TTGCGATTTTCATTTCG
1 TTGCGATTTTC--TTCG
*
1423667 CATTGCGATTTTCATTCCCA
1 --TTGCGATTTTC-TT--CG
1423687 TTGCGATTTTC-TCG
1 TTGCGATTTTCTTCG
1423701 TTGCGAT
1 TTGCGAT
1423708 AGCCATTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
14 19 0.40
16 1 0.02
17 3 0.06
18 13 0.27
19 11 0.23
20 1 0.02
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.47
Consensus pattern (15 bp):
TTGCGATTTTCTTCG
Found at i:1423672 original size:19 final size:18
Alignment explanation
Indices: 1423631--1423697 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
1423621 GAAATGAAAA
1423631 TCGCATTGCGATTTTC--
1 TCGCATTGCGATTTTCAT
1423647 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCA-T
1423664 TCGCATTGCGATTTTCAT
1 TCGCATTGCGATTTTCAT
*
1423682 TCCCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1423698 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 16 0.36
19 12 0.27
ACGTcount: A:0.13, C:0.24, G:0.16, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTTCAT
Found at i:1425726 original size:21 final size:19
Alignment explanation
Indices: 1425685--1425730 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
1425675 GAAACTTAAA
1425685 ATCGC-AACGCGAAATGCT
1 ATCGCAAACGCGAAATGCT
1425703 ATCGCAAACGCGGAAATGGCT
1 ATCGCAAACGC-GAAAT-GCT
1425724 ATCGCAA
1 ATCGCAA
1425731 TGCGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.20
19 5 0.20
20 5 0.20
21 10 0.40
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAAACGCGAAATGCT
Found at i:1425756 original size:14 final size:14
Alignment explanation
Indices: 1425737--1425794 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1425727 GCAATGCGAA
1425737 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1425751 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1425767 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1425783 AAAATTGCAACG
1 AAAATCGCAACG
1425795 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1425775 original size:18 final size:18
Alignment explanation
Indices: 1425683--1425780 Score: 73
Period size: 18 Copynumber: 5.6 Consensus size: 18
1425673 ACGAAACTTA
1425683 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
**
1425701 CTATCGCAAACGCGGAAATGG
1 AAATCGC-AACGC-GAAAT-G
** *
1425722 CTATCGCAATGCGAAA--
1 AAATCGCAACGCGAAATG
*
1425738 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
1425752 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
1425770 AAATCGCAACG
1 AAATCGCAACG
1425781 ACAAAATTGC
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
14 13 0.20
16 11 0.17
18 16 0.24
19 9 0.14
20 9 0.14
21 8 0.12
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:1425779 original size:32 final size:30
Alignment explanation
Indices: 1425724--1425799 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 30
1425714 GGAAATGGCT
*
1425724 ATCGCAATGCGAAAAAATCGCAACGACAAA
1 ATCGCAACGCGAAAAAATCGCAACGACAAA
1425754 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAA--AAATCGCAACGACAAA
*
1425786 ATTGCAACGCGAAA
1 ATCGCAACGCGAAA
1425800 CACAAATCGC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 13 0.31
32 29 0.69
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (30 bp):
ATCGCAACGCGAAAAAATCGCAACGACAAA
Found at i:1425828 original size:19 final size:18
Alignment explanation
Indices: 1425806--1425901 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 18
1425796 GAAACACAAA
1425806 TCGCATTGCGATTTTTATT
1 TCGCATTGCGA-TTTTATT
*
1425825 TCGCGTTGCGA-TTT-TT
1 TCGCATTGCGATTTTATT
* *
1425841 TCG--TTCCGATTTCATT
1 TCGCATTGCGATTTTATT
*
1425857 TCGCATTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
1425873 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
1425890 TCGCATTGCGAT
1 TCGCATTGCGAT
1425902 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
14 11 0.18
15 5 0.08
16 14 0.23
17 9 0.15
18 5 0.08
19 17 0.28
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:1425850 original size:14 final size:14
Alignment explanation
Indices: 1425828--1425885 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1425818 TTTTATTTCG
1425828 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
*
1425842 CGTTCCGATTTCATTT
1 CGTTGCGATTT--TTT
*
1425858 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTTT
1425874 CGTTGCGATTTT
1 CGTTGCGATTTT
1425886 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 9 0.24
18 8 0.22
ACGTcount: A:0.10, C:0.19, G:0.21, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:1425892 original size:33 final size:33
Alignment explanation
Indices: 1425811--1425901 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
1425801 ACAAATCGCA
* * *
1425811 TTGCGATTTTTATTTCGCGTTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1425844 TTCCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1425876 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1425902 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
32 28 0.54
33 24 0.46
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1425920 original size:20 final size:19
Alignment explanation
Indices: 1425886--1425940 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1425876 TTGCGATTTT
*
1425886 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1425905 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1425925 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1425941 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1426438 original size:18 final size:18
Alignment explanation
Indices: 1426412--1426456 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1426402 GTCGATCAGA
*
1426412 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1426430 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1426448 TGATGGCTC
1 TGATGGCTC
1426457 CCGAAGTGGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1427751 original size:20 final size:20
Alignment explanation
Indices: 1427726--1427779 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1427716 AATAGTTTCT
1427726 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
1427746 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
1427766 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
1427780 GTTGCGATTC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1428017 original size:21 final size:21
Alignment explanation
Indices: 1427993--1428032 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1427983 TTAGATAGAT
*
1427993 GGATTTTGCCGGAGATGGGAC
1 GGATTTCGCCGGAGATGGGAC
*
1428014 GGATTTCGTCGGAGATGGG
1 GGATTTCGCCGGAGATGGG
1428033 TGAGAGAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.12, G:0.45, T:0.25
Consensus pattern (21 bp):
GGATTTCGCCGGAGATGGGAC
Found at i:1428309 original size:20 final size:20
Alignment explanation
Indices: 1428215--1428309 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1428205 CTTTATGTAT
*
1428215 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
1428235 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
1428255 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
1428276 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
1428296 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
1428310 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:1428327 original size:21 final size:21
Alignment explanation
Indices: 1428298--1428390 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
1428288 ATAGTCAGTA
1428298 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1428319 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
1428339 TCACATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1428360 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1428380 TCGCATTGCGA
1 TCGCATTGCGA
1428391 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1428328 original size:41 final size:41
Alignment explanation
Indices: 1428237--1428371 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
1428227 AAAGTCAGTA
* * * ** *
1428237 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
* * *
1428277 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
* **
1428319 TCGCGTTGCGAT-TTACTTATTCACATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCACATTGCGATTTTCCCAAT
1428360 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1428372 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
Found at i:1428372 original size:41 final size:41
Alignment explanation
Indices: 1428301--1428390 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
1428291 GTCAGTATCG
1428301 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
*
1428342 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
1428383 CATTGCGA
1 CATTGCGA
1428391 ATTGGGAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (41 bp):
CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
Found at i:1441101 original size:20 final size:21
Alignment explanation
Indices: 1441063--1441101 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1441053 AATGAATGTT
**
1441063 ATGCAGAATGCAATGATGTAA
1 ATGCAGAATGCAAAAATGTAA
1441084 ATGCA-AATGCAAAAATGT
1 ATGCAGAATGCAAAAATGT
1441102 TGATCCCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (21 bp):
ATGCAGAATGCAAAAATGTAA
Found at i:1446660 original size:20 final size:20
Alignment explanation
Indices: 1446631--1446668 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1446621 TAAAGATAAT
1446631 GACAATTT-AAATAAACATG
1 GACAATTTAAAATAAACATG
1446650 GACATATTTAAAATAAACA
1 GACA-ATTTAAAATAAACA
1446669 AATGAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (20 bp):
GACAATTTAAAATAAACATG
Found at i:1451126 original size:32 final size:36
Alignment explanation
Indices: 1451047--1451120 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
1451037 TTGCTATGTA
*
1451047 TATATATTTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATTTTCTTAATATTATATTTTATA-GTTTT
*
1451084 TATATATATTTTCTTAATATTCTATTTT-T-GTTTT
1 TATATATATTTTCTTAATATTATATTTTATAGTTTT
1451118 TAT
1 TAT
1451121 TTATTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 8 0.23
36 1 0.03
37 26 0.74
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (36 bp):
TATATATATTTTCTTAATATTATATTTTATAGTTTT
Found at i:1451143 original size:26 final size:24
Alignment explanation
Indices: 1451114--1451167 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1451104 TCTATTTTTG
1451114 TTTTTA-TTTATTTATATATATTATA
1 TTTTTACTTTATTT-TAT-TATTATA
* *
1451139 TTTTTACTTTATTTTATTTTTCTA
1 TTTTTACTTTATTTTATTATTATA
1451163 TTTTT
1 TTTTT
1451168 TTCTTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 10 0.38
25 9 0.35
26 7 0.27
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTTACTTTATTTTATTATTATA
Found at i:1451372 original size:3 final size:3
Alignment explanation
Indices: 1451364--1451389 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1451354 TTCATTTTGT
1451364 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1451390 TTTTACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1451433 original size:26 final size:25
Alignment explanation
Indices: 1451379--1451437 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
1451369 ATTATTATTA
1451379 TTATTATTATTTTTTACATGTTTTG
1 TTATTATTATTTTTTACATGTTTTG
* * *
1451404 TTATTTTTCATTTTTT-CTTGTTTTAT
1 TTATTATT-ATTTTTTACATGTTTT-G
1451430 TTATTATT
1 TTATTATT
1451438 CTCATGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (25 bp):
TTATTATTATTTTTTACATGTTTTG
Found at i:1454211 original size:22 final size:22
Alignment explanation
Indices: 1454183--1454235 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
1454173 GGCTGACCTA
1454183 GAAAAACAACATGAGAGAGATG
1 GAAAAACAACATGAGAGAGATG
1454205 GAAAAACAACATGAGAGAGATG
1 GAAAAACAACATGAGAGAGATG
1454227 GAAAAACAA
1 GAAAAACAA
1454236 TATCCGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.58, C:0.09, G:0.25, T:0.08
Consensus pattern (22 bp):
GAAAAACAACATGAGAGAGATG
Found at i:1454691 original size:18 final size:20
Alignment explanation
Indices: 1454668--1454706 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1454658 ATACTTTGCA
1454668 TTTTATA-TTT-CATGTTTT
1 TTTTATATTTTCCATGTTTT
1454686 TTTTATATTTTCCATGTTTT
1 TTTTATATTTTCCATGTTTT
1454706 T
1 T
1454707 ACATTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTATATTTTCCATGTTTT
Found at i:1460238 original size:23 final size:23
Alignment explanation
Indices: 1460212--1460280 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1460202 CACCACAGCT
*
1460212 CATATAATTGCACCGAAGTGCCA
1 CATAGAATTGCACCGAAGTGCCA
* *
1460235 CATAGAATTGCACCGGAGTGCCG
1 CATAGAATTGCACCGAAGTGCCA
* *
1460258 CGTAGAATTGCACCGTAGTGCCA
1 CATAGAATTGCACCGAAGTGCCA
1460281 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CATAGAATTGCACCGAAGTGCCA
Found at i:1465079 original size:21 final size:21
Alignment explanation
Indices: 1465055--1465099 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1465045 TTTTGTTCGT
* *
1465055 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1465076 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1465097 TTG
1 TTG
1465100 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1470177 original size:17 final size:16
Alignment explanation
Indices: 1470157--1470195 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1470147 AAAAATTTGA
1470157 AAAAAAGAAAAAAGAAC
1 AAAAAAG-AAAAAGAAC
*
1470174 AAAAAAGAGAAAGAAC
1 AAAAAAGAAAAAGAAC
1470190 AAAAAA
1 AAAAAA
1470196 TAAGGTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAGAAC
Found at i:1471310 original size:110 final size:110
Alignment explanation
Indices: 1471112--1471318 Score: 324
Period size: 110 Copynumber: 1.9 Consensus size: 110
1471102 GCTTCCCAGT
* *
1471112 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
*
1471177 CAACGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * * *
1471222 TTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGAACTCGAGACAACACAAGCTTAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * *
1471287 CAGCGAAGGGGCGGCTGACTGTCAATAAACAA
66 CAACGAAGGGGCGACTGACTGTCAACAAACAA
1471319 TTTCCAGAGC
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 87 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.22
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
Found at i:1472847 original size:16 final size:16
Alignment explanation
Indices: 1472826--1472887 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 16
1472816 GCTATGTATA
1472826 TATATTTTCTTAATAT
1 TATATTTTCTTAATAT
1472842 TATATTTATACGTTTATATAT
1 TATATTT-T-C--TTA-ATAT
1472863 ATATATTTTCTTAATAT
1 -TATATTTTCTTAATAT
*
1472880 TCTATTTT
1 TATATTTT
1472888 TGCTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
16 14 0.36
17 5 0.13
18 4 0.10
20 4 0.10
21 5 0.13
22 7 0.18
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (16 bp):
TATATTTTCTTAATAT
Found at i:1472865 original size:20 final size:17
Alignment explanation
Indices: 1472822--1472879 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
1472812 ATTTGCTATG
1472822 TATATATATTTTCTTAA
1 TATATATATTTTCTTAA
1472839 TAT-TATATTTATACGTTTATA
1 TATATATATTT-T-C--TTA-A
1472860 TATATATATTTTCTTAA
1 TATATATATTTTCTTAA
1472877 TAT
1 TAT
1472880 TCTATTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 7 0.20
17 8 0.23
18 4 0.11
20 4 0.11
21 5 0.14
22 7 0.20
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (17 bp):
TATATATATTTTCTTAA
Found at i:1473966 original size:24 final size:24
Alignment explanation
Indices: 1473937--1474066 Score: 172
Period size: 24 Copynumber: 5.5 Consensus size: 24
1473927 AACACAAATG
* * * *
1473937 AACGAACATAAACGAACGGATGTA
1 AACGAACACAAATGAACGAAAGTA
*
1473961 AACGAACAC-AATAAACGAAAGTA
1 AACGAACACAAATGAACGAAAGTA
*
1473984 AACGAACACAATTGAACGAAAGTA
1 AACGAACACAAATGAACGAAAGTA
*
1474008 AACGAACACAATTGAACGAAAGTA
1 AACGAACACAAATGAACGAAAGTA
*
1474032 AACGAACACAAATGAACGAACGTA
1 AACGAACACAAATGAACGAAAGTA
*
1474056 AATGAACACAA
1 AACGAACACAA
1474067 TAAATGAACA
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
23 19 0.20
24 76 0.80
ACGTcount: A:0.55, C:0.18, G:0.16, T:0.11
Consensus pattern (24 bp):
AACGAACACAAATGAACGAAAGTA
Found at i:1475516 original size:29 final size:29
Alignment explanation
Indices: 1475482--1475540 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1475472 CCTAAATTAA
1475482 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
1475511 TTTGATGTCGTTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1475540 T
1 T
1475541 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1480522 original size:29 final size:29
Alignment explanation
Indices: 1480488--1480546 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1480478 CCTAAATTAA
*
1480488 TTTGATGTCATTGCTTACATGAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
1480517 TTTGATGTCATTGCTTACATCTATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1480546 T
1 T
1480547 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1487850 original size:30 final size:26
Alignment explanation
Indices: 1487783--1487839 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
1487773 TTCATTTACA
*
1487783 TTCGTGAATGTTTGGTAATATGCTCG
1 TTCGTGTATGTTTGGTAATATGCTCG
* *
1487809 TTCGTGTATGTTTGGTAATATGTTTG
1 TTCGTGTATGTTTGGTAATATGCTCG
1487835 TTCGT
1 TTCGT
1487840 TCGTGTATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.16, C:0.09, G:0.26, T:0.49
Consensus pattern (26 bp):
TTCGTGTATGTTTGGTAATATGCTCG
Found at i:1510734 original size:15 final size:15
Alignment explanation
Indices: 1510705--1510750 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
1510695 AAATAAAAAT
1510705 AATTAAAATAA--TA
1 AATTAAAATAATTTA
1510718 AATTAAAATAATTTA
1 AATTAAAATAATTTA
*
1510733 AATTAAAATAATTAA
1 AATTAAAATAATTTA
1510748 AAT
1 AAT
1510751 AAGAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 11 0.37
15 19 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATTAAAATAATTTA
Found at i:1510757 original size:15 final size:14
Alignment explanation
Indices: 1510691--1510758 Score: 65
Period size: 15 Copynumber: 5.1 Consensus size: 14
1510681 ATCTAGAATG
1510691 ATTAAAATAAAAATA
1 ATTAAAAT-AAAATA
*
1510706 ATTAAAATAATA-A
1 ATTAAAATAAAATA
1510719 ATTAAAAT--AAT-
1 ATTAAAATAAAATA
*
1510730 -TTAAATTAAAATA
1 ATTAAAATAAAATA
1510743 ATTAAAATAAGAATA
1 ATTAAAATAA-AATA
1510758 A
1 A
1510759 AAAGATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 6 0.14
11 1 0.02
12 3 0.07
13 9 0.21
14 11 0.26
15 13 0.30
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (14 bp):
ATTAAAATAAAATA
Found at i:1516288 original size:18 final size:18
Alignment explanation
Indices: 1516258--1516294 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1516248 TTGTAAACCC
1516258 TCTAAACTATTAAAATAAA
1 TCTAAACTATTAAAA-AAA
1516277 TCTAAA-TATTAAAAAAA
1 TCTAAACTATTAAAAAAA
1516294 T
1 T
1516295 AAAGCATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 8 0.44
19 6 0.33
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (18 bp):
TCTAAACTATTAAAAAAA
Found at i:1518003 original size:41 final size:42
Alignment explanation
Indices: 1517958--1518044 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
1517948 ATAATAAAAT
* *
1517958 AATATATTATCGAT-GAATTTTATATAAATAATTTTTATTTA
1 AATATATTATAGATGGAATTTTATATAAATAATTTTTATATA
*
1517999 AATATATTATAGATGGATTTTTATATAAATAATTTTTATATA
1 AATATATTATAGATGGAATTTTATATAAATAATTTTTATATA
1518041 AATA
1 AATA
1518045 ATTTTTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 13 0.31
42 29 0.69
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (42 bp):
AATATATTATAGATGGAATTTTATATAAATAATTTTTATATA
Found at i:1518058 original size:14 final size:15
Alignment explanation
Indices: 1517975--1518061 Score: 85
Period size: 15 Copynumber: 6.1 Consensus size: 15
1517965 TATCGATGAA
1517975 TTTTATATAAATAAT
1 TTTTATATAAATAAT
*
1517990 TTTTATTTAAAT-A-
1 TTTTATATAAATAAT
* * *
1518003 -TAT-TATAGATGGAT
1 TTTTATATAAAT-AAT
1518017 TTTTATATAAATAAT
1 TTTTATATAAATAAT
1518032 TTTTATATAAATAAT
1 TTTTATATAAATAAT
*
1518047 TTTTAT-TTAATAAT
1 TTTTATATAAATAAT
1518061 T
1 T
1518062 AGAACAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
11 5 0.08
12 2 0.03
13 1 0.02
14 9 0.15
15 36 0.61
16 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTTATATAAATAAT
Found at i:1518802 original size:21 final size:20
Alignment explanation
Indices: 1518716--1518873 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1518706 AAATGACCAA
**
1518716 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1518735 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1518755 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1518775 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1518796 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1518817 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1518837 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1518858 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1518874 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1518864 original size:20 final size:20
Alignment explanation
Indices: 1518840--1519189 Score: 414
Period size: 20 Copynumber: 17.5 Consensus size: 20
1518830 CGATTTTCCA
* ** *
1518840 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
1518860 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
1518880 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* *
1518900 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
1518920 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
1518940 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
1518960 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
*
1518980 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
1519000 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
1519020 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
1519040 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
1519060 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
1519080 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
1519100 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
1519120 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
1519140 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
1519160 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
1519180 AAATCACAAC
1 AAATCGCAAC
1519190 ACTGAAATTT
Statistics
Matches: 292, Mismatches: 36, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
20 291 1.00
21 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:1518889 original size:40 final size:40
Alignment explanation
Indices: 1518840--1519189 Score: 465
Period size: 40 Copynumber: 8.8 Consensus size: 40
1518830 CGATTTTCCA
* * * ** *
1518840 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATC-CGT
* * * *
1518880 AAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGAT-AATCCGT
* * * *
1518920 ATATCGCAACGCGTATCCGTAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAA--CGATAATCCGT
* * * *
1518960 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1519000 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1519040 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1519080 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1519120 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
*
1519160 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCTGTAAATCGCAAC
1519190 ACTGAAATTT
Statistics
Matches: 291, Mismatches: 13, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
38 2 0.01
39 1 0.00
40 284 0.98
41 1 0.00
42 3 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
Found at i:1519916 original size:24 final size:24
Alignment explanation
Indices: 1519872--1519918 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1519862 AAATTTGGTC
*
1519872 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCAGACTTTGATA
*
1519896 TTGGTCAATA-CACAGATTTTGAT
1 TTGGTCAATATC-CAGACTTTGAT
1519919 GATGTTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCAGACTTTGATA
Found at i:1522401 original size:33 final size:34
Alignment explanation
Indices: 1522350--1522514 Score: 183
Period size: 33 Copynumber: 4.7 Consensus size: 34
1522340 CGGAAATTAC
* *
1522350 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
1522383 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
1522417 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
1522455 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
1522488 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
1522515 CGAGAGAATC
Statistics
Matches: 113, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 50 0.44
34 16 0.14
35 1 0.01
36 2 0.02
37 1 0.01
38 26 0.23
39 16 0.14
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:1522433 original size:19 final size:19
Alignment explanation
Indices: 1522364--1522543 Score: 210
Period size: 19 Copynumber: 10.2 Consensus size: 19
1522354 GCAACGAGAG
1522364 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1522383 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1522397 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1522417 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1522436 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1522455 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1522469 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1522488 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1522507 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1522521 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1522540 AATC
1 AATC
1522544 ACATTGCGAT
Statistics
Matches: 138, Mismatches: 7, Indels: 32
0.78 0.04 0.18
Matches are distributed among these distances:
14 32 0.23
15 2 0.01
16 5 0.04
17 5 0.04
18 2 0.01
19 76 0.55
20 16 0.12
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1522491 original size:52 final size:52
Alignment explanation
Indices: 1522350--1522552 Score: 272
Period size: 52 Copynumber: 3.9 Consensus size: 52
1522340 CGGAAATTAC
*
1522350 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1522397 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1522455 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * *
1522507 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCACATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1522553 TTCTCCCGTT
Statistics
Matches: 139, Mismatches: 6, Indels: 17
0.86 0.04 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 84 0.60
53 29 0.21
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1522601 original size:19 final size:19
Alignment explanation
Indices: 1522561--1522657 Score: 134
Period size: 18 Copynumber: 5.4 Consensus size: 19
1522551 GATTCTCCCG
1522561 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1522581 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1522600 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1522614 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1522633 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1522651 TTGCGAT
1 TTGCGAT
1522658 AGTCAATTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
18 18 0.26
19 16 0.23
20 15 0.22
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1522603 original size:53 final size:51
Alignment explanation
Indices: 1522545--1522657 Score: 199
Period size: 53 Copynumber: 2.2 Consensus size: 51
1522535 ATTAAAATCA
1522545 CATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1 CATTGCGATTCTCCCGTTGCGATTTTCATTT-CGCATTGCGA-TTTCATTTCG
*
1522598 CATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCG
1 CATTGCGATTCTCCCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCG
1522649 CATTGCGAT
1 CATTGCGAT
1522658 AGTCAATTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
51 19 0.32
52 10 0.17
53 30 0.51
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (51 bp):
CATTGCGATTCTCCCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCG
Found at i:1522783 original size:14 final size:14
Alignment explanation
Indices: 1522764--1522800 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1522754 CATCAATTAC
1522764 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1522778 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1522792 ACAAATCAA
1 ACAAATCAA
1522801 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1524800 original size:14 final size:14
Alignment explanation
Indices: 1524781--1524837 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1524771 GCGAAATGAA
*
1524781 AATCGCAACGACAG
1 AATCGCAACGAAAG
1524795 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1524812 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1524828 AATCGCAACG
1 AATCGCAACG
1524838 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1524808 original size:33 final size:33
Alignment explanation
Indices: 1524762--1524854 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1524752 GCGAAACCAA
*
1524762 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1524795 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1524828 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1524855 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1524819 original size:19 final size:19
Alignment explanation
Indices: 1524725--1524859 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1524715 TAGTTTACTT
* *
1524725 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1524745 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1524764 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1524783 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1524797 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1524816 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1524830 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1524849 TCGCAATGCGA
1 TCGCAACGCGA
1524860 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1524877 original size:19 final size:19
Alignment explanation
Indices: 1524855--1524983 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1524845 AAAATCGCAA
1524855 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1524874 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1524888 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1524907 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1524921 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1524940 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1524959 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1524979 TGCGA
1 TGCGA
1524984 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1524897 original size:33 final size:33
Alignment explanation
Indices: 1524855--1524946 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1524845 AAAATCGCAA
1524855 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1524888 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1524921 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1524947 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1525147 original size:93 final size:93
Alignment explanation
Indices: 1525031--1525499 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
1525021 ATGGATTGCA
1525031 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1525095 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1525123 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1525188 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1525216 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1525281 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1525309 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1525374 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1525402 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1525467 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1525495 TTACT
1 TTACT
1525500 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 371 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1527224 original size:14 final size:14
Alignment explanation
Indices: 1527202--1527299 Score: 61
Period size: 14 Copynumber: 6.3 Consensus size: 14
1527192 TGGTTGAAAT
1527202 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
1527216 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
*
1527234 TGAAAATCGCAACTA
1 -GAAAATCGCAACGA
*
1527249 GATAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
1527267 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
1527282 GAGAATCGCAACGC
1 GAAAATCGCAACGA
1527296 GAAA
1 GAAA
1527300 TGAAAATCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
14 35 0.54
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.31
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1527237 original size:33 final size:33
Alignment explanation
Indices: 1527197--1527311 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1527187 TCTTTTGGTT
1527197 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1527230 GAAATGAAAATCGCAACTAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1527263 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1527296 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1527312 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1527243 original size:19 final size:19
Alignment explanation
Indices: 1527219--1527316 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1527209 GCAACGAGAG
1527219 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
1527238 AATCGCAA--C--TA-GAT
1 AATCGCAACGCGAAATGAA
1527252 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1527271 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1527285 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1527304 AATCGCAATGCGA
1 AATCGCAACGCGA
1527317 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1527347 original size:14 final size:14
Alignment explanation
Indices: 1527328--1527384 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1527318 TTTGGTTTCG
1527328 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1527342 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1527361 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1527375 CGTTGCGATT
1 CGTTGCGATT
1527385 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1527360 original size:33 final size:33
Alignment explanation
Indices: 1527312--1527392 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1527302 AAAATCGCAA
**
1527312 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1527345 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1527378 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1527393 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1527395 original size:21 final size:21
Alignment explanation
Indices: 1527369--1527444 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1527359 CGCGTTGCGA
1527369 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1527390 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1527410 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1527431 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1527445 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1527425 original size:41 final size:41
Alignment explanation
Indices: 1527368--1527445 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1527358 TCGCGTTGCG
*
1527368 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1527409 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1527446 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1527570 original size:33 final size:33
Alignment explanation
Indices: 1527524--1527594 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1527514 AATACTAACT
*
1527524 TGAAAATCACAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCACAACGACAGAATAGCAACGCGAAA
* * *
1527557 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCACAACGACAGAATAGCAACGCGAAA
1527590 TGAAA
1 TGAAA
1527595 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCACAACGACAGAATAGCAACGCGAAA
Found at i:1527828 original size:22 final size:22
Alignment explanation
Indices: 1527776--1527830 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1527766 TGGTTGTGAG
**
1527776 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1527798 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1527820 GGATTTCTTCG
1 GGATTTCTTCG
1527831 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1528002 original size:20 final size:20
Alignment explanation
Indices: 1527977--1528130 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
1527967 CTTTAAATAT
*
1527977 CGCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1527997 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1528019 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1528038 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1528058 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1528078 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1528098 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1528118 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1528131 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 93 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1528104 original size:40 final size:40
Alignment explanation
Indices: 1527976--1528130 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
1527966 GCTTTAAATA
* *
1527976 TCGCGTTACGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
1528017 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
1528057 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
1528097 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
1528131 TGGAAAATCG
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
40 66 0.69
41 29 0.31
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:1528147 original size:21 final size:21
Alignment explanation
Indices: 1528117--1528199 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1528107 ATTTTCATAT
*
1528117 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1528138 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1528159 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1528180 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1528200 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1528190 original size:42 final size:43
Alignment explanation
Indices: 1528097--1528195 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1528087 ATTTATGTGT
* *
1528097 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1528138 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1528180 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1528196 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1531066 original size:18 final size:17
Alignment explanation
Indices: 1531026--1531073 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1531016 ACTTGAATAT
*
1531026 AAAACAAAATTGAAAAA
1 AAAACAAAATTCAAAAA
*
1531043 AGAAACAAAATATCATAAA
1 A-AAACAAAAT-TCAAAAA
1531062 AAAACTAAAATT
1 AAAAC-AAAATT
1531074 ACACATGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 14 0.54
19 11 0.42
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.17
Consensus pattern (17 bp):
AAAACAAAATTCAAAAA
Found at i:1531158 original size:16 final size:17
Alignment explanation
Indices: 1531128--1531160 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1531118 AAGAGAATTT
1531128 GAATACAAAAAATAAAA
1 GAATACAAAAAATAAAA
*
1531145 GAAT-CAAAATATAAAA
1 GAATACAAAAAATAAAA
1531161 TCACAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (17 bp):
GAATACAAAAAATAAAA
Found at i:1536738 original size:8 final size:10
Alignment explanation
Indices: 1536722--1536753 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
1536712 CAACACAATA
1536722 TAAATATATG
1 TAAATATATG
1536732 TAAATATATG
1 TAAATATATG
1536742 TAAATATATG
1 TAAATATATG
1536752 TA
1 TA
1536754 TGCTAGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (10 bp):
TAAATATATG
Found at i:1538177 original size:21 final size:19
Alignment explanation
Indices: 1538145--1538202 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
1538135 AAACAACAAT
1538145 AAAAATAATGAAGAAAAATAC
1 AAAAA-AATGAAGAAAAA-AC
*
1538166 AAAGAAAATGAA-AAAAAAG
1 AAA-AAAATGAAGAAAAAAC
*
1538185 AAAAAAAAGAAGAAAAAA
1 AAAAAAATGAAGAAAAAA
1538203 AATACAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 7 0.21
19 10 0.30
20 5 0.15
21 9 0.27
22 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAAAAATGAAGAAAAAAC
Found at i:1538314 original size:10 final size:10
Alignment explanation
Indices: 1538299--1538323 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1538289 TAATAGCAAA
1538299 AATAAATAGT
1 AATAAATAGT
1538309 AATAAATAGT
1 AATAAATAGT
1538319 AATAA
1 AATAA
1538324 TTCTAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (10 bp):
AATAAATAGT
Found at i:1538345 original size:2 final size:2
Alignment explanation
Indices: 1538338--1538394 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1538328 AGTTATATGA
1538338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1538380 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1538395 AAAAAATAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1538443 original size:24 final size:25
Alignment explanation
Indices: 1538410--1538463 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
1538400 ATAACTTATA
* *
1538410 AATAAGGTATAAAAATAATAGTAAT
1 AATAAGGTATAAAAATAAAAATAAT
*
1538435 AATAA-GTATTAAAATAAAAATAAT
1 AATAAGGTATAAAAATAAAAATAAT
1538459 AATAA
1 AATAA
1538464 TAGTAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (25 bp):
AATAAGGTATAAAAATAAAAATAAT
Found at i:1539929 original size:106 final size:106
Alignment explanation
Indices: 1539744--1539960 Score: 283
Period size: 106 Copynumber: 2.0 Consensus size: 106
1539734 TGTATTGCTC
* * * *
1539744 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTAGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGTCGTGAAGTTAAAATTGACTATGAAACTAGGAAATTGTTTGTTGACA
** *
1539809 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * *
1539850 CGAGTCTAATATCCTTCG-CTGTGAAGTTAAAATTGACTATGAAATTGGGAAGTTGTTTGTTGAC
1 CGAGTCCAATATCCTCCGTC-GTGAAGTTAAAATTGACTATGAAACTAGGAAATTGTTTGTTGAC
* *
1539914 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
65 AACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
*
1539956 TGAGT
1 CGAGT
1539961 GTTGAGCCTG
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 1 0.01
106 94 0.99
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTCCGTCGTGAAGTTAAAATTGACTATGAAACTAGGAAATTGTTTGTTGACA
ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
Found at i:1540161 original size:106 final size:99
Alignment explanation
Indices: 1540024--1540265 Score: 286
Period size: 99 Copynumber: 2.4 Consensus size: 99
1540014 TGTATTGCTC
* *
1540024 TGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTTTGGAACTGACAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC--T----CTGA-AAATTGTTTGTTGACA
* *
1540089 GTCAGCCGCCCCTTCACCGTGAAGTTGAGCTTGTGTTGTCT
59 ATCAGCCGCCCCTTCACCGTGAAGTTGAACTTGTGTTGTCT
* * * *
1540130 TGAGTCTAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAAAGTTGTTTGTTGACAATCAGCC
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAATTGTTTGTTGACAATCAGCC
* * *
1540195 GTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
66 GCCCCTTCACCGTGAAGTTGAACTTGTGTTGTCT
* ** *
1540229 CGAGTCCAATATAATTCGCTGTGAAGTTGAAATTGGC
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
1540266 ACGATATCCT
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
99 81 0.69
100 4 0.03
104 1 0.01
106 32 0.27
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (99 bp):
TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAATTGTTTGTTGACAATCAGCC
GCCCCTTCACCGTGAAGTTGAACTTGTGTTGTCT
Found at i:1540731 original size:14 final size:14
Alignment explanation
Indices: 1540712--1540738 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1540702 CGATTGCATG
1540712 TCTGGAATCTTGAC
1 TCTGGAATCTTGAC
1540726 TCTGGAATCTTGA
1 TCTGGAATCTTGA
1540739 AATTCTGATC
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:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (14 bp):
TCTGGAATCTTGAC
Found at i:1546828 original size:22 final size:22
Alignment explanation
Indices: 1546803--1546847 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1546793 TGAGCTGGAC
1546803 TAATGTCCTGAATTCAGAGCAT
1 TAATGTCCTGAATTCAGAGCAT
1546825 TAATGTCCTGAATTCAGAGCAT
1 TAATGTCCTGAATTCAGAGCAT
1546847 T
1 T
1546848 CTTCGTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (22 bp):
TAATGTCCTGAATTCAGAGCAT
Found at i:1547242 original size:21 final size:22
Alignment explanation
Indices: 1547216--1547257 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1547206 ATACAAATAG
1547216 GGAATCG-GTACCCTGCTACAA
1 GGAATCGAGTACCCTGCTACAA
* *
1547237 GGAATCGATTCCCCTGCTACA
1 GGAATCGAGTACCCTGCTACA
1547258 GTACTGCCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.21
Consensus pattern (22 bp):
GGAATCGAGTACCCTGCTACAA
Found at i:1550745 original size:27 final size:27
Alignment explanation
Indices: 1550713--1550766 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1550703 TGCTGGGATG
1550713 GGGCTGGGTGTTTCTTCGACAGGGACA
1 GGGCTGGGTGTTTCTTCGACAGGGACA
*
1550740 GGGCTGGGTGTTTCTTCGACATGGACA
1 GGGCTGGGTGTTTCTTCGACAGGGACA
1550767 ATGGGCGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.19, G:0.39, T:0.28
Consensus pattern (27 bp):
GGGCTGGGTGTTTCTTCGACAGGGACA
Found at i:1552045 original size:19 final size:19
Alignment explanation
Indices: 1552023--1552065 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1552013 GAGAAAAGGT
1552023 AAAAGTTAAAATGAAAGAG
1 AAAAGTTAAAATGAAAGAG
* * *
1552042 AAAAATTAATATGAAAGAT
1 AAAAGTTAAAATGAAAGAG
1552061 AAAAG
1 AAAAG
1552066 AAAAAGTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (19 bp):
AAAAGTTAAAATGAAAGAG
Done.