Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 31
Found at i:4424468 original size:18 final size:18
Alignment explanation
Indices: 4424447--4424491 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4424437 TCCACTTTGG
*
4424447 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
4424465 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
4424483 GAGCCATCA
1 GAGCCATCA
4424492 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:4425027 original size:19 final size:20
Alignment explanation
Indices: 4424973--4425039 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
4424963 TAGTTTACTT
* *
4424973 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
4424993 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
4425013 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
4425032 TCGCAACG
1 TCGCAACG
4425040 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:4425047 original size:14 final size:14
Alignment explanation
Indices: 4425028--4425067 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
4425018 ATGCGAAATG
4425028 AAAATCGCAACGAC
1 AAAATCGCAACGAC
4425042 AAAATCGCAACGAC
1 AAAATCGCAACGAC
4425056 AAAATCGCAACG
1 AAAATCGCAACG
4425068 CGAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.28, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4425109 original size:14 final size:14
Alignment explanation
Indices: 4425084--4425147 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
4425074 GAAAATCGCA
4425084 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
4425097 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
4425111 ATTTAATTTCGCGTTGCG
1 ATTT--TGT--CGTTGCG
4425129 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
4425143 ATTTT
1 ATTTT
4425148 CATTTCGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.14
14 23 0.52
16 4 0.09
18 11 0.25
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.50
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:4425125 original size:32 final size:33
Alignment explanation
Indices: 4425083--4425155 Score: 121
Period size: 32 Copynumber: 2.2 Consensus size: 33
4425073 TGAAAATCGC
*
4425083 AATTTTGCGTTGCGATTTTGTCGTTGCGA-TTT
1 AATTTCGCGTTGCGATTTTGTCGTTGCGATTTT
4425115 AATTTCGCGTTGCGATTTTGTCGTTGCGATTTT
1 AATTTCGCGTTGCGATTTTGTCGTTGCGATTTT
*
4425148 CATTTCGC
1 AATTTCGC
4425156 ATTGTGATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 28 0.74
33 10 0.26
ACGTcount: A:0.12, C:0.16, G:0.23, T:0.48
Consensus pattern (33 bp):
AATTTCGCGTTGCGATTTTGTCGTTGCGATTTT
Found at i:4425190 original size:20 final size:18
Alignment explanation
Indices: 4425104--4425202 Score: 73
Period size: 19 Copynumber: 5.5 Consensus size: 18
4425094 GCGATTTTGT
* *
4425104 CGTTGCGATTTAATTTCG
1 CGTTGCGATATCATTTCG
4425122 CGTTGCG--AT--TTT-G
1 CGTTGCGATATCATTTCG
*
4425135 TCGTTGCGATTTTCATTTCG
1 -CGTTGCGA-TATCATTTCG
* *
4425155 CATTGTGATATCCATTTCCG
1 CGTTGCGATAT-CATTT-CG
4425175 CGTTGCGATAGTCATTTCG
1 CGTTGCGATA-TCATTTCG
4425194 CGTTGCGAT
1 CGTTGCGAT
4425203 TTTAAGTTTC
Statistics
Matches: 64, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
13 1 0.02
14 10 0.16
16 1 0.02
17 1 0.02
18 9 0.14
19 25 0.39
20 16 0.25
21 1 0.02
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.42
Consensus pattern (18 bp):
CGTTGCGATATCATTTCG
Found at i:4427092 original size:14 final size:14
Alignment explanation
Indices: 4427073--4427108 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4427063 ATTGTTTAAT
4427073 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
4427087 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
4427101 TGATTTGT
1 TGATTTGT
4427109 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:4427247 original size:19 final size:19
Alignment explanation
Indices: 4427225--4427292 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
4427215 ATCGCAACGA
4427225 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
4427244 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
4427263 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
4427277 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
4427293 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:4427336 original size:20 final size:20
Alignment explanation
Indices: 4427311--4427368 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
4427301 TCGCATTGCG
*
4427311 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
4427331 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
4427351 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
4427369 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:4428452 original size:24 final size:24
Alignment explanation
Indices: 4428425--4428478 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4428415 GTATTCGAAA
* *
4428425 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
4428449 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
4428473 TTTGAT
1 TTTGAT
4428479 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:4428670 original size:12 final size:12
Alignment explanation
Indices: 4428653--4428677 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4428643 ATATAATCCT
4428653 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4428665 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4428677 G
1 G
4428678 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4430993 original size:19 final size:19
Alignment explanation
Indices: 4430971--4431101 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
4430961 GGAAATTACT
4430971 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4430990 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4431004 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
4431023 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
4431037 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
4431056 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
4431070 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4431089 ATCGCAACGCGAA
1 ATCGCAATGCGAA
4431102 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4431013 original size:33 final size:33
Alignment explanation
Indices: 4430971--4431097 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
4430961 GGAAATTACT
4430971 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
4431004 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
4431036 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
4431070 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
4431098 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 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:4431078 original size:66 final size:66
Alignment explanation
Indices: 4430972--4431104 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
4430962 GAAATTACTA
*
4430972 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
4431037 T
66 T
*
4431038 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
4431103 T
66 T
4431104 T
1 T
4431105 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:4431119 original size:19 final size:19
Alignment explanation
Indices: 4431097--4431159 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
4431087 AAATCGCAAC
*
4431097 GCGAATTTAATTTCGCGTT
1 GCGATTTTAATTTCGCGTT
*
4431116 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AATTTCGCGTT
* *
4431136 GCGATTTTCATTTCGCATT
1 GCGATTTTAATTTCGCGTT
4431155 GCGAT
1 GCGAT
4431160 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 20 0.53
20 18 0.47
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (19 bp):
GCGATTTTAATTTCGCGTT
Found at i:4431132 original size:20 final size:19
Alignment explanation
Indices: 4431106--4431159 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
4431096 CGCGAATTTA
4431106 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
4431125 ATTTTCGCGTTGCGATTTTC
1 A-TTTCGCGTTGCGATTTTC
*
4431145 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
4431160 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:4431285 original size:14 final size:14
Alignment explanation
Indices: 4431266--4431302 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4431256 CATCAATTAA
4431266 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4431280 ACAAATCACCTTTT
1 ACAAATCAACTTTT
4431294 ACAAATCAA
1 ACAAATCAA
4431303 TTAAACAATA
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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:4432685 original size:21 final size:20
Alignment explanation
Indices: 4432661--4432720 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
4432651 TGAATCGGGA
*
4432661 TCTTGAATGGTGGGAGGGACC
1 TCTTGAACGGTGGGAGGG-CC
* * **
4432682 TCTTCAACGATGACAGTGGCC
1 TCTTGAACGGTGGGAG-GGCC
4432703 TCTTGAACGGTGGGAGGG
1 TCTTGAACGGTGGGAGGG
4432721 GACTCTCGAA
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.23
Consensus pattern (20 bp):
TCTTGAACGGTGGGAGGGCC
Found at i:4432726 original size:21 final size:21
Alignment explanation
Indices: 4432657--4432726 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
4432647 CATGTGAATC
*
4432657 GGGA-TCTTGAATGGTGGGA-
1 GGGACTCTTGAACGGTGGGAG
* * **
4432676 GGGACCTCTTCAACGATGACAG
1 GGGA-CTCTTGAACGGTGGGAG
* *
4432698 TGGCCTCTTGAACGGTGGGAG
1 GGGACTCTTGAACGGTGGGAG
4432719 GGGACTCT
1 GGGACTCT
4432727 CGAAGAATGA
Statistics
Matches: 35, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 4 0.11
21 29 0.83
22 2 0.06
ACGTcount: A:0.20, C:0.19, G:0.39, T:0.23
Consensus pattern (21 bp):
GGGACTCTTGAACGGTGGGAG
Found at i:4432745 original size:42 final size:42
Alignment explanation
Indices: 4432661--4432753 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
4432651 TGAATCGGGA
* *
4432661 TCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGCC
1 TCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGCC
*
4432703 TCTTGAACGGTGGGAGGGGA-CTC-TCGAA-GAATGATAGGGGCC
1 TCTTGAACGGTGGGA-GGGACCTCTTC-AACG-ATGACAGGGGCC
*
4432745 TCTTCAACG
1 TCTTGAACG
4432754 ATAGGAGTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
41 3 0.07
42 37 0.84
43 4 0.09
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (42 bp):
TCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGCC
Found at i:4434848 original size:19 final size:19
Alignment explanation
Indices: 4434784--4434946 Score: 174
Period size: 19 Copynumber: 8.7 Consensus size: 19
4434774 TCTTTTGGTT
*
4434784 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
4434803 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
4434823 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
** *
4434843 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
4434861 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4434876 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
4434896 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4434915 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
4434934 GAAATAAAAATCG
1 GAAATGAAAATCG
4434947 AAATGCGATT
Statistics
Matches: 125, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.08
15 2 0.02
18 2 0.02
19 61 0.49
20 48 0.38
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:4434908 original size:39 final size:38
Alignment explanation
Indices: 4434784--4434946 Score: 165
Period size: 39 Copynumber: 4.3 Consensus size: 38
4434774 TCTTTTGGTT
* * *
4434784 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATAAAAATCGCAACGCGA-AATGAAAATCGCAACGC
* ** ** *
4434823 GGAAATGACTATCGCAACGCGAAATGACTATCGCGAC-C
1 -GAAATAAAAATCGCAACGCGAAATGAAAATCGCAACGC
* *
4434861 ---A-GACAATCGCAACGCGAAATGAAAATCGCAACCGC
1 GAAATAAAAATCGCAACGCGAAATGAAAATCGCAA-CGC
4434896 GAAATAAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATAAAAATCGCAACGCGAAATGAAAATCGCAACGC
4434934 GAAATAAAAATCG
1 GAAATAAAAATCG
4434947 AAATGCGATT
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
33 26 0.25
34 2 0.02
35 1 0.01
38 18 0.17
39 40 0.38
40 18 0.17
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (38 bp):
GAAATAAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:4434972 original size:19 final size:19
Alignment explanation
Indices: 4434950--4434990 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
4434940 AAAATCGAAA
*
4434950 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
4434969 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
4434988 TGC
1 TGC
4434991 AATTATCTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.17, G:0.24, T:0.54
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:4435571 original size:20 final size:20
Alignment explanation
Indices: 4435546--4435598 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
4435536 GCGCTATGTA
4435546 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
4435566 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
4435586 TATCTCGTTGCGA
1 AATCGCGTTGCGA
4435599 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:4435635 original size:20 final size:20
Alignment explanation
Indices: 4435607--4435660 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
4435597 GATTTTGTAT
4435607 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
4435627 TATCACATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
4435647 TATCGCATTGCGAT
1 TATCGCATTGCGAT
4435661 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:4435679 original size:61 final size:61
Alignment explanation
Indices: 4435547--4435681 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
4435537 CGCTATGTAA
* * * * * * ** *
4435547 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
4435608 ATCGCATTGCGATAGTAAGTATCACATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
4435670 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
4435682 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:4445262 original size:15 final size:14
Alignment explanation
Indices: 4445244--4445279 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
4445234 TTATAAATTT
4445244 AATTATTATTCTTAA
1 AATTATTATT-TTAA
4445259 AATTATTATTTTAA
1 AATTATTATTTTAA
*
4445273 ATTTATT
1 AATTATT
4445280 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTATTATTTTAA
Found at i:4446085 original size:21 final size:20
Alignment explanation
Indices: 4446061--4446102 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4446051 TGTTAAGTTC
* *
4446061 TCAAATCAATTTAAATTCAAA
1 TCAAATAAACTTAAATT-AAA
4446082 TCAAATAAACTTAAATTAAA
1 TCAAATAAACTTAAATTAAA
4446102 T
1 T
4446103 ATTAACTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (20 bp):
TCAAATAAACTTAAATTAAA
Found at i:4446983 original size:16 final size:17
Alignment explanation
Indices: 4446953--4446985 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4446943 AAATCGATTC
*
4446953 AAAAAATGGATAACCGA
1 AAAAAATCGATAACCGA
4446970 AAAAAATCGA-AACCGA
1 AAAAAATCGATAACCGA
4446986 TTTGTGTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.15, G:0.15, T:0.09
Consensus pattern (17 bp):
AAAAAATCGATAACCGA
Found at i:4449251 original size:19 final size:19
Alignment explanation
Indices: 4449227--4449263 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4449217 ATGACCAACA
*
4449227 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
4449246 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
4449264 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:4449312 original size:20 final size:20
Alignment explanation
Indices: 4449289--4449378 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
4449279 GTTTCCAGAT
*
4449289 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
4449309 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
*
4449329 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
* *
4449350 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTATGACTA
4449370 TCGCAACGC
1 TCGCAACGC
4449379 TGAATTTCAA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.02
20 35 0.65
21 16 0.30
22 2 0.04
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:4450224 original size:24 final size:24
Alignment explanation
Indices: 4450197--4450250 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
4450187 GTATTCGAAA
4450197 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
4450221 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
4450245 TTTGAT
1 TTTGAT
4450251 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:4450469 original size:14 final size:14
Alignment explanation
Indices: 4450450--4450476 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4450440 GAAGACGAAA
4450450 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
4450464 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
4450477 TGCCACGGGA
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:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:4452731 original size:20 final size:20
Alignment explanation
Indices: 4452706--4452836 Score: 148
Period size: 20 Copynumber: 6.8 Consensus size: 20
4452696 TTACACATTC
* *
4452706 ATTTGAATATCGGAACGCGA
1 ATTTGACTATCGCAACGCGA
*
4452726 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
4452746 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
4452765 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
4452780 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
4452800 ATTTGATTATCGCAATGGGA
1 ATTTGACTATCGCAACGCGA
4452820 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
4452837 AGAAAATCGC
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
14 10 0.11
15 3 0.03
19 3 0.03
20 77 0.83
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:4452781 original size:34 final size:34
Alignment explanation
Indices: 4452734--4452871 Score: 134
Period size: 34 Copynumber: 3.9 Consensus size: 34
4452724 GAATTTGACT
*
4452734 ATCGCAACACGAATTTGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* *
4452768 ATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATT
1 ATCGCAACGCGAATTTGACTATCGCAACG-CAA----A-A
* *
4452808 ATCGCAATGGGAATTTGACTATCGCAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCA-AAA
* * *
4452842 ATCGCAAAGCGTATTAGACTATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCGCAACGC
4452872 TTGCGATTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
34 53 0.62
35 3 0.03
38 1 0.01
39 2 0.02
40 27 0.31
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:4452827 original size:74 final size:74
Alignment explanation
Indices: 4452706--4452871 Score: 226
Period size: 74 Copynumber: 2.2 Consensus size: 74
4452696 TTACACATTC
* *
4452706 ATTTGAATATCGGAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGCA-AAAAT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACG-AGAAAAT
*
4452770 CGCAACGCGA
65 CGCAAAGCGA
* * ***
4452780 ATTTGACTATCGCAACGTGAATTTGATTATCGCAATGGGAATTTGACTATCGCAACGAGAAAATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGAGAAAATC
*
4452845 GCAAAGCGT
66 GCAAAGCGA
*
4452854 ATTAGACTATCGCAACGC
1 ATTTGACTATCGCAACGC
4452872 TTGCGATTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
73 1 0.01
74 79 0.99
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (74 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGAGAAAATC
GCAAAGCGA
Found at i:4452897 original size:20 final size:20
Alignment explanation
Indices: 4452872--4452937 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
4452862 ATCGCAACGC
* **
4452872 TTGCGATTTTGGCTTTTTCA
1 TTGCGATTTTGACTTTCGCA
4452892 TTGCGATTTTGACTTTCGCA
1 TTGCGATTTTGACTTTCGCA
* * *
4452912 TTGCGATTTTGAGTTTAGCG
1 TTGCGATTTTGACTTTCGCA
4452932 TTGCGA
1 TTGCGA
4452938 AAGTGTACCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.14, C:0.15, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGCGATTTTGACTTTCGCA
Found at i:4453053 original size:36 final size:36
Alignment explanation
Indices: 4453005--4453123 Score: 125
Period size: 36 Copynumber: 3.6 Consensus size: 36
4452995 TCAACTTTTA
4453005 TATTT-CA-ATCAATTAAATAAGCACAAATAAGAAT
1 TATTTACACATCAATTAAATAAGCACAAATAAGAAT
* *
4453039 TATTTACACATCAA-T---TAA--ACAAAT--CAAC
1 TATTTACACATCAATTAAATAAGCACAAATAAGAAT
* *
4453067 T-TTTACAAATCAATTAAACAAGCACAAATAAGAAT
1 TATTTACACATCAATTAAATAAGCACAAATAAGAAT
4453102 TATTTACACATCAATTAAATAA
1 TATTTACACATCAATTAAATAA
4453124 ATCAACTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
27 11 0.17
28 4 0.06
30 6 0.09
31 2 0.03
32 3 0.05
33 6 0.09
34 5 0.08
35 6 0.09
36 23 0.35
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.29
Consensus pattern (36 bp):
TATTTACACATCAATTAAATAAGCACAAATAAGAAT
Found at i:4453095 original size:63 final size:63
Alignment explanation
Indices: 4453011--4453142 Score: 246
Period size: 63 Copynumber: 2.1 Consensus size: 63
4453001 TTTATATTTC
*
4453011 AATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACA
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACA
*
4453074 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAATAAATCAACTTTTACA
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACA
4453137 AATCAA
1 AATCAA
4453143 CTTTTACAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.28
Consensus pattern (63 bp):
AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACA
Found at i:4453141 original size:14 final size:14
Alignment explanation
Indices: 4453122--4453153 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4453112 TCAATTAAAT
4453122 AAATCAACTTTTAC
1 AAATCAACTTTTAC
4453136 AAATCAACTTTTAC
1 AAATCAACTTTTAC
4453150 AAAT
1 AAAT
4453154 TAATTAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:4454565 original size:21 final size:21
Alignment explanation
Indices: 4454532--4454649 Score: 71
Period size: 21 Copynumber: 5.6 Consensus size: 21
4454522 ATGAATCGGG
*
4454532 CTCTTGAATGATGGGAGGGAC
1 CTCTTGAACGATGGGAGGGAC
* ** *
4454553 CTCTTCAACGATGATAGGGGC
1 CTCTTGAACGATGGGAGGGAC
4454574 CTCTTGAAC-AGTGGGAGGGGA-
1 CTCTTGAACGA-TGGGA-GGGAC
** ** *
4454595 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGGGAGGGAC
* *
4454616 CTCTTGAATGATAGGAGAGG-C
1 CTCTTGAACGATGGGAG-GGAC
*
4454637 CTCTTGAATGATG
1 CTCTTGAACGATG
4454650 ACAGGTGAGT
Statistics
Matches: 72, Mismatches: 20, Indels: 10
0.71 0.20 0.10
Matches are distributed among these distances:
20 4 0.06
21 62 0.86
22 6 0.08
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGAC
Found at i:4454641 original size:42 final size:41
Alignment explanation
Indices: 4454532--4454650 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 41
4454522 ATGAATCGGG
*
4454532 CTCTTGAATGATGGGAGGGACCTCTTCAACGATGATAGGGGC
1 CTCTTGAATGATGGGAGGG-CCTCTTGAACGATGATAGGGGC
* * **
4454574 CTCTTGAA-CAGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGA-TGGGA-GGGCCTCTTGAACGATGATAGGGGC
* *
4454616 CTCTTGAATGATAGGAGAGGCCTCTTGAATGATGA
1 CTCTTGAATGATGGGAG-GGCCTCTTGAACGATGA
4454651 CAGGTGAGTC
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.03
42 57 0.90
43 4 0.06
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGATGGGAGGGCCTCTTGAACGATGATAGGGGC
Found at i:4455302 original size:19 final size:20
Alignment explanation
Indices: 4455259--4455311 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
4455249 CAAAACTAAA
*
4455259 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
*
4455279 TTCGCATTGCGATTTTTA-T
1 TTCGCATTGCGATTTTCATT
4455298 TTCGCATTGCGATT
1 TTCGCATTGCGATT
4455312 ATCCCGTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.49
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:4455345 original size:20 final size:20
Alignment explanation
Indices: 4455320--4455364 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4455310 TTATCCCGTT
4455320 GCGATAATCAAATTCGCGTA
1 GCGATAATCAAATTCGCGTA
* ** *
4455340 GCGATAGTCATTTTCGCGTT
1 GCGATAATCAAATTCGCGTA
4455360 GCGAT
1 GCGAT
4455365 TTTTAAGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (20 bp):
GCGATAATCAAATTCGCGTA
Found at i:4457403 original size:20 final size:20
Alignment explanation
Indices: 4457283--4457419 Score: 90
Period size: 20 Copynumber: 7.2 Consensus size: 20
4457273 GAAACTTAAA
**
4457283 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
4457303 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * **
4457323 ATCGCAACGCTAATTTGACT
1 ATCGCAACACGAAAATGACT
*
4457343 ATCGC-A-ACG-AGAT-A--
1 ATCGCAACACGAAAATGACT
* * **
4457357 ATCACAACGCG-AAATGAAA
1 ATCGCAACACGAAAATGACT
*
4457376 ATCACAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
4457396 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
4457416 ATCG
1 ATCG
4457420 TTGCGATTTT
Statistics
Matches: 91, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
14 4 0.04
15 1 0.01
16 6 0.07
17 3 0.03
18 1 0.01
19 11 0.12
20 65 0.71
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:4457442 original size:19 final size:20
Alignment explanation
Indices: 4457418--4457455 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
4457408 ATTTGACTAT
4457418 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCAGTTTCG
4457437 CGTTGCGATTTTCAGTTTC
1 CGTTGCGATTTTCAGTTTC
4457456 AAATAGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (20 bp):
CGTTGCGATTTTCAGTTTCG
Found at i:4457842 original size:22 final size:21
Alignment explanation
Indices: 4457787--4457850 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
4457777 TCTGAGAGAT
*
4457787 GGAGATA-GATGGATTTCGCC
1 GGAGATAGGATGGATTTCGTC
4457807 GGAGATAGGATGGATTTCGTC
1 GGAGATAGGATGGATTTCGTC
* *
4457828 GGAGATGGGGATGGATGTCGTC
1 GGAGAT-AGGATGGATTTCGTC
4457850 G
1 G
4457851 TAGAGAGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 7 0.18
21 18 0.46
22 14 0.36
ACGTcount: A:0.22, C:0.11, G:0.42, T:0.25
Consensus pattern (21 bp):
GGAGATAGGATGGATTTCGTC
Found at i:4457864 original size:25 final size:22
Alignment explanation
Indices: 4457787--4457867 Score: 78
Period size: 21 Copynumber: 3.7 Consensus size: 22
4457777 TCTGAGAGAT
* *
4457787 GGAGAT-A-GATGGATTTCGCC
1 GGAGATGAGGATGGATGTCGTC
*
4457807 GGAGAT-AGGATGGATTTCGTC
1 GGAGATGAGGATGGATGTCGTC
*
4457828 GGAGATGGGGATGGATGTCGTC
1 GGAGATGAGGATGGATGTCGTC
4457850 GTAGAGAGTGAGGATGGA
1 G--GAGA-TGAGGATGGA
4457868 GATGAGACTG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
20 7 0.13
21 18 0.35
22 14 0.27
24 4 0.08
25 9 0.17
ACGTcount: A:0.25, C:0.09, G:0.43, T:0.23
Consensus pattern (22 bp):
GGAGATGAGGATGGATGTCGTC
Found at i:4458042 original size:20 final size:20
Alignment explanation
Indices: 4458017--4458058 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4458007 TTATTGCAAC
4458017 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
4458037 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
4458057 GC
1 GC
4458059 AATTTACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:4458160 original size:20 final size:19
Alignment explanation
Indices: 4458137--4458182 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4458127 GGAAACTGAT
*
4458137 TTGCGATACAGGAGATCGCG
1 TTGCGATACA-GAGATCGCA
**
4458157 TTGCGATTTAGAGATCGCA
1 TTGCGATACAGAGATCGCA
4458176 TTGCGAT
1 TTGCGAT
4458183 TTTCTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (19 bp):
TTGCGATACAGAGATCGCA
Found at i:4458172 original size:19 final size:19
Alignment explanation
Indices: 4458148--4458184 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4458138 TGCGATACAG
*
4458148 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
4458167 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
4458185 TCTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:4458638 original size:86 final size:89
Alignment explanation
Indices: 4458420--4458627 Score: 271
Period size: 86 Copynumber: 2.4 Consensus size: 89
4458410 AAGTGGCTTA
* * * * *
4458420 ATATATCAAACATATAGTATTTAATAAATATATGTATCACATTGGTTAAAAAGAAAAGACATGTA
1 ATATATCAAATATATAATATTTGATAAATATATGTATCAAATTGGTTAAAAAGAAAAGACA-GCA
*
4458485 CTATATTTATAAAATTAAAAAATTT
65 CTATATTTATAAAAGTAAAAAATTT
* *
4458510 ATATATTAAATATATAA-AGTTTGATAAATATATGCATCAAATTGGTTAAAAAG-AAA-ACA-CA
1 ATATATCAAATATATAATA-TTTGATAAATATATGTATCAAATTGGTTAAAAAGAAAAGACAGCA
* *
4458571 CTATATTTATAAAAGTGATAAATTT
65 CTATATTTATAAAAGTAAAAAATTT
*
4458596 ATATATCATATATATAATATTTGATAAATATA
1 ATATATCAAATATATAATATTTGATAAATATA
4458628 AATAACAAAT
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
86 51 0.49
87 1 0.01
88 3 0.03
89 4 0.04
90 45 0.43
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.37
Consensus pattern (89 bp):
ATATATCAAATATATAATATTTGATAAATATATGTATCAAATTGGTTAAAAAGAAAAGACAGCAC
TATATTTATAAAAGTAAAAAATTT
Found at i:4459296 original size:31 final size:31
Alignment explanation
Indices: 4459258--4459344 Score: 156
Period size: 31 Copynumber: 2.8 Consensus size: 31
4459248 CGAGTATTGC
*
4459258 TGAGCTCGACTCGACTCGAAAACTTTGAAAT
1 TGAGCTCGACTCGACTCGAAAACTCTGAAAT
4459289 TGAGCTCGACTCGACTCGAAAACTCTGAAAT
1 TGAGCTCGACTCGACTCGAAAACTCTGAAAT
*
4459320 TGAGCTCGACTCGACTCAAAAACTC
1 TGAGCTCGACTCGACTCGAAAACTC
4459345 GCGAGCTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (31 bp):
TGAGCTCGACTCGACTCGAAAACTCTGAAAT
Found at i:4460694 original size:20 final size:20
Alignment explanation
Indices: 4460671--4460823 Score: 155
Period size: 20 Copynumber: 7.6 Consensus size: 20
4460661 ACACATAAGT
*
4460671 CAAATTTGCAACGCGATTTC
1 CAAATTCGCAACGCGATTTC
* *
4460691 CAAATTTGCAATGCGATTTC
1 CAAATTCGCAACGCGATTTC
* **
4460711 CAAATTTGCATTGCGATTTC
1 CAAATTCGCAACGCGATTTC
* *
4460731 CAAATTCGCAACGTGATTTA
1 CAAATTCGCAACGCGATTTC
*
4460751 CAAATTCGCAACACTGAATTT-
1 CAAATTCGCAACGC-G-ATTTC
*
4460772 CAAATTCGCAACTCGATTTC
1 CAAATTCGCAACGCGATTTC
* * *
4460792 TAAATTCGCAACTCGATTTT
1 CAAATTCGCAACGCGATTTC
*
4460812 CGAATTCGCAAC
1 CAAATTCGCAAC
4460824 ACGAATTTTA
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
19 4 0.03
20 94 0.81
21 14 0.12
22 4 0.03
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:4460797 original size:61 final size:60
Alignment explanation
Indices: 4460671--4460843 Score: 172
Period size: 61 Copynumber: 2.9 Consensus size: 60
4460661 ACACATAAGT
* * * * ** * *
4460671 CAAATTTGCAACGCGATTTCCAAATTTGCAATGCG-ATTTCCAAATTTGC-ATTGCGATTTC
1 CAAATTCGCAACTCGATTTACAAATTCGCAACACGAATTT-CAAATTCGCAACT-CGATTTC
4460731 CAAATTCGCAACGT-GATTTACAAATTCGCAACACTGAATTTCAAATTCGCAACTCGATTTC
1 CAAATTCGCAAC-TCGATTTACAAATTCGCAACAC-GAATTTCAAATTCGCAACTCGATTTC
* * * * *
4460792 TAAATTCGCAACTCGATTTTCGAATTCGCAACACGAATTTTAATTTCGCAAC
1 CAAATTCGCAACTCGATTTACAAATTCGCAACACGAATTTCAAATTCGCAAC
4460844 AGGTTTTATT
Statistics
Matches: 95, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
60 44 0.46
61 45 0.47
62 6 0.06
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (60 bp):
CAAATTCGCAACTCGATTTACAAATTCGCAACACGAATTTCAAATTCGCAACTCGATTTC
Found at i:4460839 original size:20 final size:19
Alignment explanation
Indices: 4460732--4460844 Score: 100
Period size: 20 Copynumber: 5.6 Consensus size: 19
4460722 TGCGATTTCC
** *
4460732 AAATTCGCAACGTGATTTAC
1 AAATTCGCAACACGATTT-T
*
4460752 AAATTCGCAACACTGAATTTC
1 AAATTCGCAACAC-G-ATTTT
*
4460773 AAATTCGCAACTCGATTTCT
1 AAATTCGCAACACGATTT-T
*
4460793 AAATTCGCAACTCGATTTT
1 AAATTCGCAACACGATTTT
*
4460812 CGAATTCGCAACACGAATTTT
1 -AAATTCGCAACACG-ATTTT
*
4460833 AATTTCGCAACA
1 AAATTCGCAACA
4460845 GGTTTTATTT
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
19 5 0.06
20 52 0.65
21 19 0.24
22 4 0.05
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.31
Consensus pattern (19 bp):
AAATTCGCAACACGATTTT
Found at i:4460840 original size:40 final size:41
Alignment explanation
Indices: 4460726--4460844 Score: 127
Period size: 41 Copynumber: 2.9 Consensus size: 41
4460716 TTGCATTGCG
**
4460726 ATTTCCAAATTCGCAACGTGATTTAC-AAATTCGCAACACTGA
1 ATTT-CAAATTCGCAACACGATTT-CTAAATTCGCAACACTGA
* *
4460768 ATTTCAAATTCGCAACTCGATTTCTAAATTCGCAACTC-GA
1 ATTTCAAATTCGCAACACGATTTCTAAATTCGCAACACTGA
* * *
4460808 TTTTCGAATTCGCAACACGAATTT-TAATTTCGCAACA
1 ATTTCAAATTCGCAACACG-ATTTCTAAATTCGCAACA
4460845 GGTTTTATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
40 30 0.45
41 33 0.49
42 4 0.06
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (41 bp):
ATTTCAAATTCGCAACACGATTTCTAAATTCGCAACACTGA
Found at i:4461019 original size:14 final size:15
Alignment explanation
Indices: 4461000--4461037 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
4460990 TCCCCATCTC
4461000 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
4461014 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
4461030 TAATTTTT
1 TAATTTTT
4461038 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:4461801 original size:24 final size:24
Alignment explanation
Indices: 4461772--4461827 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
4461762 GTGAGTACTA
**
4461772 GTCAATATTCAAAATTTGATCTTG
1 GTCAATACCCAAAATTTGATCTTG
* *
4461796 GTCAATACCCAGACTTTGATCTTG
1 GTCAATACCCAAAATTTGATCTTG
4461820 GTCAATAC
1 GTCAATAC
4461828 TCGGATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (24 bp):
GTCAATACCCAAAATTTGATCTTG
Found at i:4464646 original size:25 final size:25
Alignment explanation
Indices: 4464601--4464650 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4464591 AAATCAATTA
*
4464601 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
* *
4464626 AACATTGTTATGTGTATATTATTTG
1 AACATTGTTATGGGTACATTATTTG
4464651 GAAAATAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.48
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:4465057 original size:18 final size:18
Alignment explanation
Indices: 4465036--4465072 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4465026 GTAATTGTAG
4465036 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
4465054 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
4465072 T
1 T
4465073 ATAAATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:4465079 original size:24 final size:24
Alignment explanation
Indices: 4465034--4465080 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4465024 ATGTAATTGT
* *
4465034 AGTTTGAATTTAAATTTCAATTTG
1 AGTTTGAATTTAAATATAAATTTG
*
4465058 AGTTTGAATTTCAATATAAATTT
1 AGTTTGAATTTAAATATAAATTT
4465081 CAGCTCCACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (24 bp):
AGTTTGAATTTAAATATAAATTTG
Found at i:4466984 original size:22 final size:22
Alignment explanation
Indices: 4466951--4467000 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
4466941 TTTAAATATG
* *
4466951 AAAAATCTAATAATAATAA-AA
1 AAAAATCAAATAAAAATAATAA
4466972 AAAAATCAAAATAAAAATAATTAA
1 AAAAATC-AAATAAAAATAA-TAA
4466996 AAAAA
1 AAAAA
4467001 CTAACCCTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 10 0.42
24 7 0.29
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAAATCAAATAAAAATAATAA
Found at i:4467256 original size:19 final size:20
Alignment explanation
Indices: 4467234--4467272 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4467224 AATATTGTGT
4467234 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
4467253 TTCGCGTTGCGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
4467273 GCGCTTTGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:4467283 original size:19 final size:20
Alignment explanation
Indices: 4467242--4467284 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4467232 GTTTCGAATT
*
4467242 CGAAAATAAAATTCGCGTTG
1 CGAAAATAAAATGCGCGTTG
*
4467262 CGAAAATAAAA-GCGCTTTG
1 CGAAAATAAAATGCGCGTTG
4467281 CGAA
1 CGAA
4467285 TTTGACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (20 bp):
CGAAAATAAAATGCGCGTTG
Found at i:4467318 original size:20 final size:20
Alignment explanation
Indices: 4467295--4467346 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
4467285 TTTGACTTTT
4467295 GCGTTGCGAATTACAGATTC
1 GCGTTGCGAATTACAGATTC
* *
4467315 GCGTTGCGATTTACATATTC
1 GCGTTGCGAATTACAGATTC
4467335 GCGTTGCGAATT
1 GCGTTGCGAATT
4467347 TGGAAACTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
GCGTTGCGAATTACAGATTC
Found at i:4469468 original size:2 final size:2
Alignment explanation
Indices: 4469461--4469499 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4469451 TCCAAAGAAG
4469461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4469500 GAAAATAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4472479 original size:68 final size:70
Alignment explanation
Indices: 4472363--4472507 Score: 167
Period size: 68 Copynumber: 2.1 Consensus size: 70
4472353 TCGAATTAAG
* * *
4472363 ATAAAAAATATGTAAATATGATAATAATAAACAAAAAAATAATAATAATAATAATAAA-AT-AAG
1 ATAAAAAATATGTAAACATGATAAAAATAAACAAAAAAATAATAATAATAAAAATAAAGATAAAG
*
4472426 TAGAA
66 TAAAA
4472431 ATAAAAAA-ATG-ATAACATGAGTAAAAATATAACAAAACAAA-AA-AATAATAAAAATAAAGAT
1 ATAAAAAATATGTA-AACATGA-TAAAAATA-AACAAAA-AAATAATAATAATAAAAATAAAGAT
4472492 AAAAGTAAAA
62 -AAAGTAAAA
4472502 ATAAAA
1 ATAAAA
4472508 CAAAAAATGA
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
66 1 0.02
67 9 0.14
68 29 0.44
69 11 0.17
70 3 0.05
71 13 0.20
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (70 bp):
ATAAAAAATATGTAAACATGATAAAAATAAACAAAAAAATAATAATAATAAAAATAAAGATAAAG
TAAAA
Found at i:4472499 original size:45 final size:45
Alignment explanation
Indices: 4472450--4472547 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
4472440 TGATAACATG
* * *
4472450 AGTAAAAATATAACAAAACAA-AAA-AATAATAAAAATAAAGATAAA
1 AGTAAAAATAAAACAAAA-AAGAAACAAGAATAAAAACAAAGA-AAA
4472495 AGTAAAAATAAAACAAAAAATGAAACAAGAATAAAAACAAAGAAAA
1 AGTAAAAATAAAACAAAAAA-GAAACAAGAATAAAAACAAAGAAAA
4472541 A-TAAAAA
1 AGTAAAAA
4472548 AAGTACATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 2 0.04
45 23 0.49
46 7 0.15
47 15 0.32
ACGTcount: A:0.77, C:0.05, G:0.06, T:0.12
Consensus pattern (45 bp):
AGTAAAAATAAAACAAAAAAGAAACAAGAATAAAAACAAAGAAAA
Found at i:4472502 original size:7 final size:6
Alignment explanation
Indices: 4472464--4472805 Score: 82
Period size: 6 Copynumber: 54.7 Consensus size: 6
4472454 AAAATATAAC
* * * *
4472464 AAAACA AAAA-A ATAATA AAAATA AAGATA AAAGTA AAAATA AAACA-A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA-ATA
* * * * * *
4472511 AAAAT- GAAACA AGAATA AAAACA AAGAA-A AATAA-A AAAAGTA CATATA
1 AAAATA AAAATA AAAATA AAAATA AA-AATA AA-AATA AAAA-TA AAAATA
* * * * *
4472559 TAAATA AGTTGAATA AAAA-G AAAATA ATAATA GGAATAATA ATAATA
1 AAAATA A---AAATA AAAATA AAAATA AAAATA --AA-AATA AAAATA
* * * * *
4472606 ATATTA ATAATA AAAATA AAAATA AATATA TAAAAT- AAGATA TAAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA -AAAATA AAAATA -AAAATA
* * *
4472655 AAAATA AAACA-A ACAAATAA AAAATA ATAATAA AATAATA ATAATA AAATGATT
1 AAAATA AAA-ATA A-AAAT-A AAAATA AAAAT-A AA-AATA AAAATA AAA--ATA
* * * *
4472709 AGAAT- AAAATA AAAATA ATAAA-A AATATATA ATAACGTA TAAA-C AAAATA
1 AAAATA AAAATA AAAATA A-AAATA AA-A-ATA A-AA-ATA AAAATA AAAATA
*
4472759 TAAAA-A ATAATA AGAAAT- AAAATA AAAAT- AAAATGA ATAAATA AAAA
1 -AAAATA AAAATA A-AAATA AAAATA AAAATA AAAAT-A A-AAATA AAAA
4472806 ATAATAAAAA
Statistics
Matches: 248, Mismatches: 49, Indels: 78
0.66 0.13 0.21
Matches are distributed among these distances:
5 38 0.15
6 138 0.56
7 43 0.17
8 19 0.08
9 10 0.04
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:4472547 original size:74 final size:74
Alignment explanation
Indices: 4472391--4472549 Score: 173
Period size: 74 Copynumber: 2.1 Consensus size: 74
4472381 TGATAATAAT
* ** * *
4472391 AAACAAAAAAATAATAATAATAATAATAAAATAAGTAGAAATAAAAAAATGATAACATGAGTAAA
1 AAACAAAAAAATAATAAAAATAATAATAAAATAAAAAGAAATAAAAAAATGATAACAAGAATAAA
* *
4472456 AATATAACA
66 AACATAAAA
*
4472465 AAACAAAAAAATAATAAAAATAA-AGATAAAAGTAAAAATAAA-ACAAAAAATGA-AACAAGAAT
1 AAACAAAAAAATAATAAAAATAATA-ATAAAA-TAAAAAGAAATA-AAAAAATGATAACAAGAAT
4472527 AAAAACA-AAGAA
63 AAAAACATAA-AA
*
4472539 AAATAAAAAAA
1 AAACAAAAAAA
4472550 GTACATATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
73 3 0.04
74 53 0.74
75 16 0.22
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.15
Consensus pattern (74 bp):
AAACAAAAAAATAATAAAAATAATAATAAAATAAAAAGAAATAAAAAAATGATAACAAGAATAAA
AACATAAAA
Found at i:4472589 original size:3 final size:3
Alignment explanation
Indices: 4472581--4472743 Score: 89
Period size: 3 Copynumber: 56.7 Consensus size: 3
4472571 ATAAAAAGAA
** * * *
4472581 AAT AAT AAT AGG AAT AAT AAT AAT AAT ATT AAT AAT AAA AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
4472629 AAAT ATAT AA- AAT AAG ATAT AA- AAT AAA AAT AA- AAC AA- ACA- AAT
1 -AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * *
4472673 AA- AA- AAT AAT AAT AA- AAT AAT AAT AAT AA- AAT GAT TAG AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
4472716 AAT AAA AAT AAT AA- AA- AAT ATAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AA
4472744 CGTATAAACA
Statistics
Matches: 125, Mismatches: 21, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
2 22 0.18
3 92 0.74
4 11 0.09
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:4472656 original size:31 final size:30
Alignment explanation
Indices: 4472618--4472790 Score: 90
Period size: 31 Copynumber: 5.5 Consensus size: 30
4472608 ATTAATAATA
4472618 AAAATAAAAATAAATATATAAAATAAGATAT
1 AAAATAAAAATAAATATATAAAATAAGA-AT
* * *
4472649 AAAATAAAAATAAA-ACAAACAAATAAAAAAT
1 AAAATAAAAATAAATATATA-AAAT-AAGAAT
4472680 AATAAT-AAAAT-AATAATAATAAAATGATTAGAAT
1 AA-AATAAAAATAAAT-AT-ATAAAAT-A--AGAAT
*
4472714 AAAATAAAAAT-AATA-A-AAAATATATAAT
1 AAAATAAAAATAAATATATAAAATA-AGAAT
* * *
4472742 AACGTATAAACAA-AATATAAAAAATAATAAGAAAT
1 AA--AATAAA-AATAA-ATATATAA-AATAAG-AAT
4472777 AAAATAAAAATAAA
1 AAAATAAAAATAAA
4472791 ATGAATAAAT
Statistics
Matches: 112, Mismatches: 11, Indels: 37
0.70 0.07 0.23
Matches are distributed among these distances:
28 7 0.06
29 1 0.01
30 15 0.13
31 31 0.28
32 18 0.16
33 14 0.12
34 17 0.15
35 9 0.08
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (30 bp):
AAAATAAAAATAAATATATAAAATAAGAAT
Found at i:4472806 original size:20 final size:21
Alignment explanation
Indices: 4472596--4472812 Score: 100
Period size: 20 Copynumber: 10.4 Consensus size: 21
4472586 TAATAGGAAT
* * *
4472596 AATAATAATAATATTAATAATA
1 AATAATAAGAA-ATAAATAAAA
* *
4472618 AA-AATAA-AAATAAATATAT
1 AATAATAAGAAATAAATAAAA
*
4472637 AA-AATAAGATATAAA-ATAAA
1 AATAATAAGAAATAAATA-AAA
* *
4472657 AATAA-AACAAACAAATAAAA
1 AATAATAAGAAATAAATAAAA
*
4472677 AATAATAATAAAATAATAATAATAA
1 AATAATAA-GAAAT-A-AATAA-AA
* *
4472702 AATGATTAG-AATAAA-ATAAA
1 AATAATAAGAAATAAATA-AAA
* *
4472722 AATAATAAAAAATATATAATAA
1 AATAATAAGAAATAAATAA-AA
**
4472744 CGT-ATAA-ACAA-AATATAAAA
1 AATAATAAGA-AATAA-ATAAAA
4472764 AATAATAAGAAATAAA-ATAAA
1 AATAATAAGAAATAAATA-AAA
4472785 AATAA-AATG-AATAAATAAAA
1 AATAATAA-GAAATAAATAAAA
4472805 AATAATAA
1 AATAATAA
4472813 AAAGGAATAA
Statistics
Matches: 149, Mismatches: 24, Indels: 45
0.68 0.11 0.21
Matches are distributed among these distances:
19 14 0.09
20 57 0.38
21 48 0.32
22 13 0.09
23 4 0.03
24 5 0.03
25 8 0.05
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.24
Consensus pattern (21 bp):
AATAATAAGAAATAAATAAAA
Found at i:4472813 original size:14 final size:14
Alignment explanation
Indices: 4472611--4472826 Score: 88
Period size: 13 Copynumber: 15.6 Consensus size: 14
4472601 TAATAATATT
*
4472611 AATAATAAA-AATA
1 AATAATAAATAAAA
* *
4472624 AA-AATAAATATAT
1 AATAATAAATAAAA
*
4472637 AA-AATAAGATATAA
1 AATAATAA-ATAAAA
4472651 AATAA-AAATAAAA
1 AATAATAAATAAAA
* *
4472664 CA-AACAAATAAAA
1 AATAATAAATAAAA
4472677 AATAAT-AAT--AA
1 AATAATAAATAAAA
4472688 AATAAT-AATAATAA
1 AATAATAAATAA-AA
*
4472702 AATGATTAGAATAAAA
1 AAT-AATA-AATAAAA
*
4472718 TAAAAAT-AATAAAA
1 -AATAATAAATAAAA
4472732 AAT-ATATAATAACGTATA
1 AATAATA-AATAA---A-A
*
4472750 AACAA-AATATAAAA
1 AATAATAA-ATAAAA
4472764 AATAATAAGA-AATAA
1 AATAATAA-ATAA-AA
4472779 AATAA-AAAT--AA
1 AATAATAAATAAAA
4472790 AATGAATAAATAAAA
1 AAT-AATAAATAAAA
**
4472805 AATAATAAA-AAGG
1 AATAATAAATAAAA
4472818 AATAATAAA
1 AATAATAAA
4472827 AGGATTAAAT
Statistics
Matches: 159, Mismatches: 17, Indels: 54
0.69 0.07 0.23
Matches are distributed among these distances:
11 16 0.10
12 12 0.08
13 46 0.29
14 43 0.27
15 20 0.13
16 4 0.03
17 9 0.06
18 8 0.05
19 1 0.01
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (14 bp):
AATAATAAATAAAA
Found at i:4472824 original size:23 final size:24
Alignment explanation
Indices: 4472773--4472827 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
4472763 AAATAATAAG
*
4472773 AAATAAAATAAAAATAAAATGAAT
1 AAATAAAATAAAAATAAAAGGAAT
*
4472797 AAATAAAA-AATAATAAAAAGGAAT
1 AAATAAAATAAAAAT-AAAAGGAAT
4472821 -AATAAAA
1 AAATAAAA
4472828 GGATTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (24 bp):
AAATAAAATAAAAATAAAAGGAAT
Found at i:4473506 original size:23 final size:22
Alignment explanation
Indices: 4473465--4473507 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
4473455 TATCAATTTT
**
4473465 TTCTTGTATTTCGTGCGTAATA
1 TTCTTGTATTTCGAACGTAATA
4473487 TTCTCTGTATTTCGAACGTAA
1 TTCT-TGTATTTCGAACGTAA
4473508 ATGTTACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (22 bp):
TTCTTGTATTTCGAACGTAATA
Found at i:4474549 original size:85 final size:84
Alignment explanation
Indices: 4474353--4474585 Score: 304
Period size: 85 Copynumber: 2.7 Consensus size: 84
4474343 ACGTTGCATC
* * * * * * *
4474353 GAGCTGAATGAAACCGAACTCGAATGTATTTGTTGATAGATAACCCTTCTCGCCTTGATTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGATGACAGATAA-CCTTCTCGCCTTGAGTTATGT
4474418 TGTAAATTTGATGTGCCTTT
65 TGTAAATTTGATGTGCCTTT
* ** * * * *
4474438 GATCTGTGTGTAGTCGAGCTCAAAGGTCTTTGCTGACAGATAACTCTTCTCGCCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGATGACAGATAAC-CTTCTCGCCTTGAGTTATGT
4474503 TGTAAATTTGATGTGCCTTT
65 TGTAAATTTGATGTGCCTTT
*
4474523 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGATGACATATAACCTTTCTCGCCTTGAGTTAT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGATGACAGATAACC-TTCTCGCCTTGAGTTAT
4474586 ACTGCATTGG
Statistics
Matches: 125, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
84 2 0.02
85 123 0.98
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (84 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGATGACAGATAACCTTCTCGCCTTGAGTTATGTT
GTAAATTTGATGTGCCTTT
Found at i:4474861 original size:65 final size:61
Alignment explanation
Indices: 4474727--4474887 Score: 198
Period size: 65 Copynumber: 2.6 Consensus size: 61
4474717 GAGCTTTTAA
* * * * *
4474727 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAA-GGATTGTTTTACCAAATTTGTTTTGAG
1 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATGGATAGTTTCACCAAATTGGCTTTGAG
* * * *
4474787 CTAGATATCCTTCGTCATGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTGGCTTTGAG
1 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAA--TGGA-T-AGTTTCACCAAATTGGCTTTGAG
4474852 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATGG
1 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATGG
4474888 GCACGATATC
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
60 29 0.35
63 4 0.05
64 1 0.01
65 49 0.59
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (61 bp):
TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATGGATAGTTTCACCAAATTGGCTTTGAG
Found at i:4474905 original size:37 final size:37
Alignment explanation
Indices: 4474855--4474955 Score: 184
Period size: 37 Copynumber: 2.7 Consensus size: 37
4474845 CTTTGAGTTG
4474855 GATATCCTTCGTCGTGAAGTTGAAATCCAATGGGCAC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATGGGCAC
*
4474892 GATATCCTTCGTCGTGAAGTTGAAATCCAATGGGCAT
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATGGGCAC
*
4474929 GATATCCTTTGTCGTGAAGTTGAAATC
1 GATATCCTTCGTCGTGAAGTTGAAATC
4474956 ATGGATGGCT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (37 bp):
GATATCCTTCGTCGTGAAGTTGAAATCCAATGGGCAC
Found at i:4475142 original size:124 final size:124
Alignment explanation
Indices: 4474922--4475269 Score: 552
Period size: 124 Copynumber: 2.8 Consensus size: 124
4474912 TGAAATCCAA
* * * *
4474922 TGGGCATGATATCCTTTGTCGTGAAGTTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCT
*
4474987 TTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAATCTAGAGATGGATGATGCTTG
66 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGATGCTTG
* *
4475046 TGGGCACGATATCCTTCGCCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCT
* *
4475111 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGCTTCTTG
66 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGATGCTTG
** * * *
4475170 TGGGCACGATATTGTTCATCATGAAGTTGAAATCGTGGATGGCTCCTTCGTAGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCT
* *
4475235 TTGAATTGGATATACTTCGTCGTGAAGTTGAAATC
66 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATC
4475270 AAAGTATTGT
Statistics
Matches: 206, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 206 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (124 bp):
TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCT
TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGATGCTTG
Found at i:4475372 original size:65 final size:64
Alignment explanation
Indices: 4475231--4475407 Score: 229
Period size: 65 Copynumber: 2.8 Consensus size: 64
4475221 AGTGAAGTTG
* * *
4475231 AGCTTTGAATTGGATATACTTCGTCGTGAAGTTGAAAT-CAA----AGTATTGTTTCACCAAATT
1 AGCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAGTA-AGTTTCACCAAATT
* *
4475291 GGTTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATT
1 AGCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATC-TGAGTAAGTTTCACCAAATT
* *
4475356 AGCTTTGAGTTTGATATCCTTCGTCGTGATGTTGAAATCCAATCTCGAGTAA
1 AGCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT-GAGTAA
4475408 ATTGTATCAC
Statistics
Matches: 101, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
60 34 0.34
61 3 0.03
64 1 0.01
65 59 0.58
66 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (64 bp):
AGCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAGTAAGTTTCACCAAATT
Found at i:4475497 original size:64 final size:64
Alignment explanation
Indices: 4475421--4475715 Score: 446
Period size: 64 Copynumber: 4.6 Consensus size: 64
4475411 GTATCACTTC
* * *
4475421 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGATTATGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
4475485 GAGTCCAATATCCTTCACAGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * * *
4475549 GAGTCCAATACCCTTCGCTGTGAAATTGAAATTGACTCTGAATGAAACTGGAAATTTTTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * * * *
4475613 GAGTCTAATAACCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAATTGGAAAGTTGTTTGCT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
4475677 GAGTCCAATATCATTCGCTGTGAATTTGAAATTGACTCT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
4475716 AAAAGATGCA
Statistics
Matches: 207, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 207 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:4476731 original size:85 final size:90
Alignment explanation
Indices: 4476609--4477031 Score: 392
Period size: 99 Copynumber: 4.5 Consensus size: 90
4476599 GGCTAGCTGA
*
4476609 ATCCATAAAGTCGGGGCGTTTAA-TCAATTGCCCTAGAGGGACAA-CTTTA-T-T-A-TTATAAT
1 ATCCATAAAGTCGGGGCGTTTAACT-AATTGCTCTAGAGGGACAAGCTTTATTATAATTTATAAT
* *
4476668 CACCTTTATCAGGCTAGCTGAATCTT
65 CACCTTTATCAAGCTAGCTGAAGCTT
* *
4476694 ATCCATAAAGTCGGGACGTTTAACTAATTTCTCTAGAGGGACGGTTCAAGCTTTATTGTATAGAT
1 ATCCATAAAGTCGGGGCGTTTAACTAATTGCTCTAGAGGGA-----CAAGCTTTA-T-TATA-A-
4476759 TTTATAATCACCTTTATCAAGCTAGCTGAAGCTT
57 TTTATAATCACCTTTATCAAGCTAGCTGAAGCTT
* *
4476793 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACTGTTCAAGTTTTATTGTATAGAT
1 ATCCATAAAGTCGGGGCGTTTAACTAATTGCTCTAGAGGGA-----CAAGCTTTA-T-TATA-AT
*
4476858 ATTATAATCACCTTTATCAGGCTAGCTGAAGCTT
58 -TTATAATCACCTTTATCAAGCTAGCTGAAGCTT
* * * * *
4476892 ATCCATAAAGCCAGGGCGTTTAACCAACTGCTCTAGAGGGACGGTTCAAGCTTGATTGTATAGAT
1 ATCCATAAAGTCGGGGCGTTTAACTAATTGCTCTAGAGGGA-----CAAGCTTTA-T-TATA-AT
* *
4476957 ATTATAATCACCTTTATCAGGCTAGCTGAAACTT
58 -TTATAATCACCTTTATCAAGCTAGCTGAAGCTT
* *
4476991 ATCCATAAAG-CTGGGCGTTTAACCAATTGCTCTAGAGGGAC
1 ATCCATAAAGTCGGGGCGTTTAACTAATTGCTCTAGAGGGAC
4477032 GGCTCAAGCT
Statistics
Matches: 302, Mismatches: 20, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
85 36 0.12
86 1 0.00
90 3 0.01
91 5 0.02
93 1 0.00
94 1 0.00
95 1 0.00
97 1 0.00
98 29 0.10
99 224 0.74
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (90 bp):
ATCCATAAAGTCGGGGCGTTTAACTAATTGCTCTAGAGGGACAAGCTTTATTATAATTTATAATC
ACCTTTATCAAGCTAGCTGAAGCTT
Found at i:4476788 original size:99 final size:99
Alignment explanation
Indices: 4476659--4477056 Score: 638
Period size: 99 Copynumber: 4.0 Consensus size: 99
4476649 ACAACTTTAT
* *
4476659 TATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTC-GGGACGTTTAACTAATT
1 TATTATAATCACCTTTATCAGGCTAGCTGAAGCTTATCCATAAAGTCAGGG-CGTTTAACCAATT
*
4476723 TCTCTAGAGGGACGGTTCAAGCTTTATTGTATAGA
65 GCTCTAGAGGGACGGTTCAAGCTTTATTGTATAGA
* * *
4476758 TTTTATAATCACCTTTATCAAGCTAGCTGAAGCTTATCCATAAAGTCGGGGCGTTTAACCAATTG
1 TATTATAATCACCTTTATCAGGCTAGCTGAAGCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
* *
4476823 CTCTAGAGGGACTGTTCAAGTTTTATTGTATAGA
66 CTCTAGAGGGACGGTTCAAGCTTTATTGTATAGA
* *
4476857 TATTATAATCACCTTTATCAGGCTAGCTGAAGCTTATCCATAAAGCCAGGGCGTTTAACCAACTG
1 TATTATAATCACCTTTATCAGGCTAGCTGAAGCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
*
4476922 CTCTAGAGGGACGGTTCAAGCTTGATTGTATAGA
66 CTCTAGAGGGACGGTTCAAGCTTTATTGTATAGA
* *
4476956 TATTATAATCACCTTTATCAGGCTAGCTGAAACTTATCCATAAAG-CTGGGCGTTTAACCAATTG
1 TATTATAATCACCTTTATCAGGCTAGCTGAAGCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
* *
4477020 CTCTAGAGGGACGGCTCAAGCTTTATTGTATATA
66 CTCTAGAGGGACGGTTCAAGCTTTATTGTATAGA
4477054 TAT
1 TAT
4477057 AATATTATAA
Statistics
Matches: 277, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
98 51 0.18
99 223 0.81
100 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (99 bp):
TATTATAATCACCTTTATCAGGCTAGCTGAAGCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
CTCTAGAGGGACGGTTCAAGCTTTATTGTATAGA
Found at i:4481281 original size:15 final size:16
Alignment explanation
Indices: 4481219--4481288 Score: 72
Period size: 15 Copynumber: 4.2 Consensus size: 16
4481209 ACGTATAAAC
4481219 AAAATATAAAAAATAAT
1 AAAATA-AAAAAATAAT
4481236 AAGAAATAAAATAAA-AAT
1 -A-AAATAAAA-AAATAAT
* *
4481254 AAAATGAACAAATAA-
1 AAAATAAAAAAATAAT
4481269 AAAATAAAAAAATAAT
1 AAAATAAAAAAATAAT
4481285 AAAA
1 AAAA
4481289 GGATTAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
15 16 0.36
16 12 0.27
17 1 0.02
18 7 0.16
19 8 0.18
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAAATAAT
Found at i:4481288 original size:11 final size:12
Alignment explanation
Indices: 4481213--4481287 Score: 68
Period size: 11 Copynumber: 6.4 Consensus size: 12
4481203 ATAATAACGT
*
4481213 ATAAACAAAAT-
1 ATAAATAAAATA
*
4481224 ATAAAAAATAATA
1 ATAAATAA-AATA
*
4481237 AGAAATAAAATA
1 ATAAATAAAATA
4481249 A-AAATAAAATGA
1 ATAAATAAAAT-A
*
4481261 ACAAATAAAA-A
1 ATAAATAAAATA
4481272 ATAAA-AAAATA
1 ATAAATAAAATA
4481283 ATAAA
1 ATAAA
4481288 AGGATTAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
10 4 0.07
11 27 0.49
12 10 0.18
13 14 0.25
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (12 bp):
ATAAATAAAATA
Found at i:4485541 original size:59 final size:59
Alignment explanation
Indices: 4485402--4485569 Score: 216
Period size: 60 Copynumber: 2.8 Consensus size: 59
4485392 GCCCTTATTT
4485402 TAAATTGGTCCCTAAACTTTTAAATA-TTCAAATTTCATCCCCAAACTATGACTATCATCC
1 TAAATTGGTCCCTAAACTTTTAAATATTTC-AATTTCAT-CCCAAACTATGACTATCATCC
* * * *
4485462 TAAATTAGT-CCTCAAACTTTTAAACATTTCAATTTCATCCCAAACTATGGC-ATTCATTC
1 TAAATTGGTCCCT-AAACTTTTAAATATTTCAATTTCATCCCAAACTATGACTA-TCATCC
* *
4485521 TTAATTGGTCCCTAAACTTTTTAAATATTCCAATTTCATCCCAAACTAT
1 TAAATTGGTCCCTAAAC-TTTTAAATATTTCAATTTCATCCCAAACTAT
4485570 ATATATATAC
Statistics
Matches: 95, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
58 1 0.01
59 31 0.33
60 60 0.63
61 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.38
Consensus pattern (59 bp):
TAAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCCCAAACTATGACTATCATCC
Found at i:4485812 original size:60 final size:60
Alignment explanation
Indices: 4485691--4485867 Score: 182
Period size: 60 Copynumber: 3.0 Consensus size: 60
4485681 TTTGCATGAA
* * * * * * **
4485691 TTTGGAGATGAAGTTGAAATATTTAAAAGTTTAAGGACCAATCTAGAAAGAAGGTCGTAG
1 TTTGGGGATGAAATTGAAATCTTTAAAAGTTTAAGGACCAATTTAGAATGAAAGTTATAG
* *
4485751 TTTATGGGG-T-AAATT-ATAAT-TTTCAAATGTTTAAGGACTAATTTAGAATGAAAGTTATAG
1 -TT-TGGGGATGAAATTGA-AATCTTT-AAAAGTTTAAGGACCAATTTAGAATGAAAGTTATAG
* *
4485811 TTTGGGGATGGAATTGAAATCTTTAAAAGTTTAAGGACCAATTTAAAATGAAAGTTA
1 TTTGGGGATGAAATTGAAATCTTTAAAAGTTTAAGGACCAATTTAGAATGAAAGTTA
4485868 GGTGGTGTTT
Statistics
Matches: 96, Mismatches: 13, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
58 5 0.05
59 7 0.07
60 73 0.76
61 7 0.07
62 4 0.04
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (60 bp):
TTTGGGGATGAAATTGAAATCTTTAAAAGTTTAAGGACCAATTTAGAATGAAAGTTATAG
Found at i:4486086 original size:31 final size:31
Alignment explanation
Indices: 4486051--4486110 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4486041 AATTTAAAAG
* * *
4486051 AGTTTTGCAATACTGAGATTTCAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
4486082 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
4486111 CATACAACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:4486595 original size:19 final size:19
Alignment explanation
Indices: 4486554--4486602 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
4486544 ATGACCAACA
* * *
4486554 AATTCACAACGTGATCTCG
1 AATTCACAACGCGAACTCC
*
4486573 AATTCGCAACGCGAACTCC
1 AATTCACAACGCGAACTCC
4486592 AATTTCACAAC
1 AA-TTCACAAC
4486603 TCAGTTTCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.22
Consensus pattern (19 bp):
AATTCACAACGCGAACTCC
Found at i:4486636 original size:21 final size:21
Alignment explanation
Indices: 4486573--4486700 Score: 77
Period size: 20 Copynumber: 6.3 Consensus size: 21
4486563 CGTGATCTCG
*
4486573 AATTCGCAACGCGAA-CTCCA
1 AATTCGCAACGCGAATATCCA
* * * * *
4486593 ATTTCACAACTC-AGTTTCCA
1 AATTCGCAACGCGAATATCCA
**
4486613 AATTCGCAACGCGAATATGTA
1 AATTCGCAACGCGAATATCCA
** * *
4486634 AA-TCGCATTGCGATTTTCCA
1 AATTCGCAACGCGAATATCCA
*
4486654 AATTCGCAACGCG-ATTTCCA
1 AATTCGCAACGCGAATATCCA
* *
4486674 AATTCGCAACACTGAAT-TTCA
1 AATTCGCAACGC-GAATATCCA
4486695 AATTCG
1 AATTCG
4486701 TAACTCGATT
Statistics
Matches: 80, Mismatches: 23, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 53 0.66
21 24 0.30
22 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (21 bp):
AATTCGCAACGCGAATATCCA
Found at i:4486697 original size:41 final size:40
Alignment explanation
Indices: 4486652--4486765 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
4486642 TGCGATTTTC
* *
4486652 CAAATTCGCAACGCGATTTCCAAATTCGCAACACTGAATTT
1 CAAATTCGCAACTCGATTTCCGAATTCGCAACAC-GAATTT
* * * *
4486693 CAAATTCGTAACTCGATTTCTGAATTTGCAACGCGAATTT
1 CAAATTCGCAACTCGATTTCCGAATTCGCAACACGAATTT
**** *
4486733 TGTTTTCGCAACTCGATTTTCGAATTCGCAACA
1 CAAATTCGCAACTCGATTTCCGAATTCGCAACA
4486766 GGTTTTAGTT
Statistics
Matches: 58, Mismatches: 15, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
40 30 0.52
41 28 0.48
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (40 bp):
CAAATTCGCAACTCGATTTCCGAATTCGCAACACGAATTT
Found at i:4486760 original size:20 final size:20
Alignment explanation
Indices: 4486611--4486764 Score: 91
Period size: 20 Copynumber: 7.6 Consensus size: 20
4486601 ACTCAGTTTC
*
4486611 CAAATTCGCAACGCGAATATGT
1 CAAATTCGCAACGCG-AT-TTT
**
4486633 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGATTTT
*
4486651 CCAAATTCGCAACGCGATTTC
1 -CAAATTCGCAACGCGATTTT
* *
4486672 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACGC-GATTTT
* *
4486693 CAAATTCGTAACTCGA-TTT
1 CAAATTCGCAACGCGATTTT
* *
4486712 CTGAATTTGCAACGCGAATTTT
1 C-AAATTCGCAACGCG-ATTTT
*** *
4486734 -GTTTTCGCAACTCGATTTT
1 CAAATTCGCAACGCGATTTT
*
4486753 CGAATTCGCAAC
1 CAAATTCGCAAC
4486765 AGGTTTTAGT
Statistics
Matches: 103, Mismatches: 21, Indels: 18
0.73 0.15 0.13
Matches are distributed among these distances:
18 2 0.02
19 11 0.11
20 55 0.53
21 32 0.31
22 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTT
Found at i:4490384 original size:14 final size:14
Alignment explanation
Indices: 4490365--4490398 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4490355 CATCAATTAA
4490365 ACAAATCAACATTT
1 ACAAATCAACATTT
*
4490379 ACAAATCAACTTTT
1 ACAAATCAACATTT
4490393 ACAAAT
1 ACAAAT
4490399 TAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:4490393 original size:78 final size:77
Alignment explanation
Indices: 4490301--4490477 Score: 284
Period size: 78 Copynumber: 2.3 Consensus size: 77
4490291 ATTTAAAACA
4490301 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
4490366 CAAATCAACATTT
66 CAAATCAAC-TTT
* *** * *
4490379 ACAAATCAACTTTTACAAATTAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
4490444 CAAATCAACTTT
66 CAAATCAACTTT
4490456 ACAAATCAAC-TTTACAAATCAA
1 ACAAATCAACTTTTACAAATCAA
4490478 CTTTTACAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
76 11 0.12
77 13 0.14
78 68 0.74
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (77 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
CAAATCAACTTT
Found at i:4490485 original size:14 final size:13
Alignment explanation
Indices: 4490443--4490488 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
4490433 CATCAATTAA
4490443 ACAAATCAACTTT
1 ACAAATCAACTTT
4490456 ACAAATCAACTTT
1 ACAAATCAACTTT
4490469 ACAAATCAACTTTT
1 ACAAATCAAC-TTT
4490483 ACAAAT
1 ACAAAT
4490489 ACATCAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 23 0.72
14 9 0.28
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
ACAAATCAACTTT
Found at i:4491856 original size:42 final size:42
Alignment explanation
Indices: 4491810--4491889 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
4491800 TTGGGAGGGA
* *
4491810 CCTCTTAAACGATAACAGGGGCCTCTTGAAGGATGATATGGG
1 CCTCTTAAACGATAACAGAGGCCTCTTGAACGATGATATGGG
* * **
4491852 CCTCTTGAATGATAGGAGAGGCCTCTTGAACGATGATA
1 CCTCTTAAACGATAACAGAGGCCTCTTGAACGATGATA
4491890 GGTGAATCGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (42 bp):
CCTCTTAAACGATAACAGAGGCCTCTTGAACGATGATATGGG
Found at i:4494384 original size:20 final size:21
Alignment explanation
Indices: 4494359--4494416 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
4494349 TCTAAGAGAT
4494359 GGAGAT-AGACGGATTTTGCC
1 GGAGATGAGACGGATTTTGCC
* *
4494379 GGAGATGGGGACGGATTTTGTC
1 GGAGAT-GAGACGGATTTTGCC
*
4494401 GGAGATGGGGACGGAT
1 GGAGAT-GAGACGGAT
4494417 GTCGCCGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.18
22 28 0.82
ACGTcount: A:0.22, C:0.10, G:0.45, T:0.22
Consensus pattern (21 bp):
GGAGATGAGACGGATTTTGCC
Found at i:4494393 original size:22 final size:22
Alignment explanation
Indices: 4494366--4494416 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
4494356 GATGGAGATA
4494366 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTTGCCGGAGATGGG
*
4494388 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTTGCCGGAGATGGG
4494410 GACGGAT
1 GACGGAT
4494417 GTCGCCGTAG
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:0.12, G:0.45, T:0.24
Consensus pattern (22 bp):
GACGGATTTTGCCGGAGATGGG
Found at i:4494947 original size:21 final size:23
Alignment explanation
Indices: 4494909--4494960 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
4494899 ATAATATATA
4494909 AAATAATTTATATGATATAAAATT
1 AAATAATTTATA-GATATAAAATT
*
4494933 AAAT-ATTTATA-ATATAATATT
1 AAATAATTTATAGATATAAAATT
4494954 AAA-AATT
1 AAATAATT
4494961 AATATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 15 0.58
23 7 0.27
24 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AAATAATTTATAGATATAAAATT
Found at i:4494953 original size:14 final size:13
Alignment explanation
Indices: 4494929--4495031 Score: 63
Period size: 14 Copynumber: 7.9 Consensus size: 13
4494919 TATGATATAA
4494929 AATTAAATATTTAT
1 AATT-AATATTTAT
* *
4494943 AATATAATATTAAA
1 AAT-TAATATTTAT
4494957 AATTAATA-TT-T
1 AATTAATATTTAT
*
4494968 AATT--TATTTAAA
1 AATTAATATTT-AT
*
4494980 AATTAATA-TTAA
1 AATTAATATTTAT
*
4494992 AATTAATATCTAT
1 AATTAATATTTAT
* *
4495005 AATATAATATTAAAA
1 AAT-TAATATT-TAT
4495020 AATTAATATTTA
1 AATTAATATTTA
4495032 ATTTATTTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
9 2 0.03
10 2 0.03
11 4 0.06
12 15 0.22
13 13 0.19
14 28 0.41
15 5 0.07
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTAATATTTAT
Found at i:4494964 original size:27 final size:24
Alignment explanation
Indices: 4494927--4494998 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 24
4494917 TATATGATAT
4494927 AAAATTAAATATTTATAATATAATATTA
1 AAAATT-AATATTT-TAAT-TAAT-TTA
*
4494955 AAAATTAATA-TTTAATTTATTTA
1 AAAATTAATATTTTAATTAATTTA
**
4494978 AAAATTAATATTAAAATTAAT
1 AAAATTAATATTTTAATTAAT
4494999 ATCTATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 13 0.33
24 10 0.26
25 4 0.10
26 2 0.05
27 4 0.10
28 6 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAATTAATATTTTAATTAATTTA
Found at i:4495015 original size:62 final size:63
Alignment explanation
Indices: 4494926--4495084 Score: 247
Period size: 63 Copynumber: 2.6 Consensus size: 63
4494916 TTATATGATA
*
4494926 TAAAATTAAATATTTATAATATAATATTAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
4494989 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
4495053 TAAAATTAAAATC-A-AATATAATA-T-AAAATTAA
1 TAAAATTAATATCTATAATATAATATTAAAAATTAA
4495085 GTATAAAACC
Statistics
Matches: 92, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
59 8 0.09
61 1 0.01
62 28 0.30
63 31 0.34
64 24 0.26
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:4495027 original size:40 final size:36
Alignment explanation
Indices: 4494947--4495029 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 36
4494937 ATTTATAATA
*
4494947 TAATATTAAAAATTAATATTTAATTTATTTAAAAAT
1 TAATATTAAAAATTAATATTTAATTTATTAAAAAAT
4494983 TAATATT-AAAATTAATATCTATAATATAATATTAAAAAAT
1 TAATATTAAAAATTAATAT-T-TAAT-T--TATTAAAAAAT
4495023 TAATATT
1 TAATATT
4495030 TAATTTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
35 11 0.27
36 8 0.20
37 4 0.10
38 1 0.02
40 17 0.41
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (36 bp):
TAATATTAAAAATTAATATTTAATTTATTAAAAAAT
Found at i:4495033 original size:26 final size:26
Alignment explanation
Indices: 4494980--4495061 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 26
4494970 TTTATTTAAA
4494980 AATTAATATT--AAAATTAATATCTAT
1 AATTAATATTAAAAAATTAATAT-TAT
4495005 AATATAATATTAAAAAATTAATATT-T
1 AAT-TAATATTAAAAAATTAATATTAT
* *
4495031 AATTTAT-TTAAAAAATTAATATTAA
1 AATTAATATTAAAAAATTAATATTAT
4495056 AATTAA
1 AATTAA
4495062 AATCAAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
24 16 0.32
25 11 0.22
26 11 0.22
27 1 0.02
28 11 0.22
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTAATATTAAAAAATTAATATTAT
Found at i:4495089 original size:12 final size:11
Alignment explanation
Indices: 4494923--4495092 Score: 62
Period size: 12 Copynumber: 14.7 Consensus size: 11
4494913 AATTTATATG
4494923 ATATAAAATTAA
1 ATATAAAATT-A
*
4494935 ATATTTATAATATA
1 ATA--TAAAAT-TA
4494949 ATATTAAAAATTA
1 ATA-T-AAAATTA
** *
4494962 ATATTTAATTT
1 ATATAAAATTA
*
4494973 ATTTAAAAATTA
1 ATAT-AAAATTA
4494985 ATATTAAAATTA
1 ATA-TAAAATTA
**
4494997 ATAT-CTA-TA
1 ATATAAAATTA
*
4495006 ATATAATATT-
1 ATATAAAATTA
4495016 A-A-AAAATTA
1 ATATAAAATTA
* *
4495025 ATATTTAATTTA
1 ATA-TAAAATTA
* *
4495037 TTTAAAAAATTA
1 -ATATAAAATTA
4495049 ATATTAAAATTA
1 ATA-TAAAATTA
* *
4495061 AAATCAAATATA
1 ATATAAAAT-TA
4495073 ATATAAAATTA
1 ATATAAAATTA
4495084 AGTATAAAA
1 A-TATAAAA
4495093 CCTCTTTGAA
Statistics
Matches: 116, Mismatches: 26, Indels: 32
0.67 0.15 0.18
Matches are distributed among these distances:
8 5 0.04
9 8 0.07
10 5 0.04
11 19 0.16
12 55 0.47
13 10 0.09
14 13 0.11
15 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
ATATAAAATTA
Found at i:4500157 original size:13 final size:13
Alignment explanation
Indices: 4500139--4500164 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4500129 CGTGGCTAGG
4500139 AGAAGAATGCAAC
1 AGAAGAATGCAAC
4500152 AGAAGAATGCAAC
1 AGAAGAATGCAAC
4500165 TCTAAATACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (13 bp):
AGAAGAATGCAAC
Found at i:4500814 original size:20 final size:20
Alignment explanation
Indices: 4500781--4500818 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4500771 TAATATGTTT
4500781 TTAAAATAATATTGACACCC
1 TTAAAATAATATTGACACCC
4500801 TTAAATATAA-ATTGACAC
1 TTAAA-ATAATATTGACAC
4500819 TTATTATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (20 bp):
TTAAAATAATATTGACACCC
Found at i:4502399 original size:33 final size:33
Alignment explanation
Indices: 4502362--4502428 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
4502352 GTTTGAAGAG
4502362 TATAATGATAATTCCATAAGAAAGATTTTTATT
1 TATAATGATAATTCCATAAGAAAGATTTTTATT
* *
4502395 TATAATGGTAATTCCATAAGAAATATTTTTATT
1 TATAATGATAATTCCATAAGAAAGATTTTTATT
4502428 T
1 T
4502429 CTCCTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (33 bp):
TATAATGATAATTCCATAAGAAAGATTTTTATT
Found at i:4503016 original size:21 final size:21
Alignment explanation
Indices: 4502974--4503016 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4502964 TTTCTGGGCT
* * *
4502974 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
4502995 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
4503016 A
1 A
4503017 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:4504645 original size:23 final size:23
Alignment explanation
Indices: 4504609--4504676 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
4504599 AACCTTATAT
*
4504609 GGCACTTCGATGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * **
4504632 GGCACTACGGTGCAATTCTACAT
1 GGCACTTCGGTGCATTTCTACGC
*
4504655 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
4504677 AGCTATGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:4508371 original size:21 final size:21
Alignment explanation
Indices: 4508329--4508371 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4508319 TTTCTGGGCT
* * *
4508329 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
4508350 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
4508371 A
1 A
4508372 ACGAACCATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:4509950 original size:23 final size:23
Alignment explanation
Indices: 4509915--4509981 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
4509905 ACCTTATATG
4509915 GCACTTCGGTGCATTTCTACGCA
1 GCACTTCGGTGCATTTCTACGCA
* * * **
4509938 GCACTACGATGCAATTCTACGTG
1 GCACTTCGGTGCATTTCTACGCA
*
4509961 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTTCTACG
4509982 AGCTCTGGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCA
Found at i:4510305 original size:8 final size:8
Alignment explanation
Indices: 4510279--4510314 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
4510269 TGAACAAGAA
4510279 ATAAGAG-
1 ATAAGAGT
4510286 ATAAGAAGT
1 ATAAG-AGT
4510295 ATAAGAGT
1 ATAAGAGT
4510303 ATAAGAGT
1 ATAAGAGT
4510311 ATAA
1 ATAA
4510315 TAAAAACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 5 0.19
8 17 0.63
9 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (8 bp):
ATAAGAGT
Found at i:4511610 original size:29 final size:30
Alignment explanation
Indices: 4511557--4511631 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
4511547 TATTTAATTT
*
4511557 TTTAAAAAATAAAAATATTTTAAATTTAAA
1 TTTAAAAAATAAAAATATTTCAAATTTAAA
*
4511587 TTTAAAATATAAAAATA-TTCAAATTTAAA
1 TTTAAAAAATAAAAATATTTCAAATTTAAA
*
4511616 --AAAAAAACTAAAAATA
1 TTTAAAAAA-TAAAAATA
4511632 GCCAACAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 5 0.12
28 8 0.20
29 11 0.28
30 16 0.40
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (30 bp):
TTTAAAAAATAAAAATATTTCAAATTTAAA
Found at i:4521238 original size:91 final size:89
Alignment explanation
Indices: 4521105--4521285 Score: 299
Period size: 91 Copynumber: 2.0 Consensus size: 89
4521095 TCAAATGTAC
* *
4521105 AATATAAAAAATAATAATAAATATTACGAATGATAACTAATATCAATATTGATGTCGTCATCGAT
1 AATATAAAAAATAATAATAAATATTACGAATGATAACCAATATCAATATTGATGTCGTCACCGAT
*
4521170 CAATTAAGATAAAGAATAAGACAA
66 CAATTAAGATAAAGAAGAAGACAA
**
4521194 AATATAAAAAATATAATAATAAATATTACGAATGATAACCAATATCAATATTGATGTCGTTGCCG
1 AATAT-AAAAA-ATAATAATAAATATTACGAATGATAACCAATATCAATATTGATGTCGTCACCG
4521259 ATCAATTAAGATAAAGAAGAAGACAA
64 ATCAATTAAGATAAAGAAGAAGACAA
4521285 A
1 A
4521286 CGACGCAATC
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
89 5 0.06
90 5 0.06
91 75 0.88
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.27
Consensus pattern (89 bp):
AATATAAAAAATAATAATAAATATTACGAATGATAACCAATATCAATATTGATGTCGTCACCGAT
CAATTAAGATAAAGAAGAAGACAA
Found at i:4521454 original size:2 final size:2
Alignment explanation
Indices: 4521442--4521493 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
4521432 TCTGACTTAA
*
4521442 AT AT CT 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
4521484 AT AT AT AT AT
1 AT AT AT AT AT
4521494 TACTCGAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4522107 original size:20 final size:20
Alignment explanation
Indices: 4522082--4522130 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
4522072 TAGTTTACTC
4522082 TTTTATTTTTATTAATCTCT
1 TTTTATTTTTATTAATCTCT
* *
4522102 TTTTATTATTATTAATTTCT
1 TTTTATTTTTATTAATCTCT
4522122 TTCTTATTT
1 TT-TTATTT
4522131 AATCTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATTTTTATTAATCTCT
Found at i:4525342 original size:41 final size:41
Alignment explanation
Indices: 4525285--4525369 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
4525275 ACAGTAAAAA
4525285 TCCCATCCCCAGTTCCTTTCCAAATCAATCGATCAGAAAGT
1 TCCCATCCCCAGTTCCTTTCCAAATCAATCGATCAGAAAGT
4525326 TCCCATCCCCAGTTCCTTTCCAAATCAATCGATCAGAAAGT
1 TCCCATCCCCAGTTCCTTTCCAAATCAATCGATCAGAAAGT
4525367 TCC
1 TCC
4525370 GATGATAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.28, C:0.35, G:0.09, T:0.27
Consensus pattern (41 bp):
TCCCATCCCCAGTTCCTTTCCAAATCAATCGATCAGAAAGT
Done.