Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007916.1 Hibiscus syriacus cultivar Beakdansim tig00110319_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: 3725575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 16
Found at i:2184609 original size:21 final size:21
Alignment explanation
Indices: 2184583--2184653 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
2184573 GCGAATAAGT
2184583 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
2184604 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
2184624 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
2184645 AAATAGCAA
1 AAATCGCAA
2184654 TACGATACTG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:2184615 original size:41 final size:41
Alignment explanation
Indices: 2184570--2184654 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
2184560 CCCAATTCGT
*
2184570 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGC
1 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATAGC
2184611 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATAGC
1 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATAGC
2184652 AAT
1 AAT
2184655 ACGATACTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.18
Consensus pattern (41 bp):
AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATAGC
Found at i:2185240 original size:19 final size:19
Alignment explanation
Indices: 2185180--2185260 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
2185170 TTCGAGAATG
2185180 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
2185200 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
2185216 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
2185233 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
2185252 AAAATCGCA
1 AAAATCGCA
2185261 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:2185304 original size:20 final size:19
Alignment explanation
Indices: 2185256--2185401 Score: 132
Period size: 19 Copynumber: 8.1 Consensus size: 19
2185246 GAAACCAAAA
*
2185256 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2185275 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2185294 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
2185314 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
2185330 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2185347 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2185361 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2185380 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
2185400 TC
1 TC
2185402 AACCAAAAGA
Statistics
Matches: 104, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.19
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.39
20 35 0.34
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2185337 original size:39 final size:39
Alignment explanation
Indices: 2185261--2185337 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
2185251 CAAAATCGCA
* *
2185261 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTGTCATGTCGCGG
2185300 TTGCGATTTTCATTTCGCGTTGCGATTGTC-TGGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTGTCAT-GTCGCG
2185338 ATAGTCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.09, C:0.21, G:0.26, T:0.44
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTGTCATGTCGCGG
Found at i:2185346 original size:33 final size:33
Alignment explanation
Indices: 2185309--2185393 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
2185299 GTTGCGATTT
* *
2185309 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
2185342 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
2185375 TCATTTCCGCGTTGCGATT
1 TCATTT-CGCGTTGCGATT
2185394 TTCATTTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 36 0.75
34 12 0.25
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:2187324 original size:42 final size:42
Alignment explanation
Indices: 2187264--2187386 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
2187254 GCCCGACTCG
* * *
2187264 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
2187306 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
2187348 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
2187387 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:2187344 original size:21 final size:21
Alignment explanation
Indices: 2187320--2187386 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2187310 TCATTCCTCG
2187320 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2187341 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2187362 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2187383 AGAG
1 AGAG
2187387 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2188739 original size:14 final size:14
Alignment explanation
Indices: 2188720--2188755 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2188710 GATTGTTAAT
2188720 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2188734 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2188748 TGATTTGT
1 TGATTTGT
2188756 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2188901 original size:20 final size:20
Alignment explanation
Indices: 2188862--2188919 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
2188852 AAAAAGTACT
* *
2188862 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATAAAA
2188881 ATCGCAACGCGAAAATAAAA
1 ATCGCAACGCGAAAATAAAA
*
2188901 ATCGCAACGCGAAATTAAA
1 ATCGCAACGCGAAAATAAA
2188920 TTCGCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 10 0.29
20 25 0.71
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAAAA
Found at i:2188974 original size:33 final size:32
Alignment explanation
Indices: 2188924--2189049 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
2188914 ATTAAATTCG
2188924 CGTTGCGA-TTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
2188956 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
2188989 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
2189022 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2189050 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
31 3 0.04
32 8 0.09
33 71 0.84
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2189014 original size:66 final size:65
Alignment explanation
Indices: 2188917--2189048 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 65
2188907 ACGCGAAATT
*
2188917 AAATTCGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
*
2188982 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGA-TTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2189047 G
65 G
2189048 A
1 A
2189049 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 14 0.22
66 50 0.78
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (65 bp):
AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:2191298 original size:12 final size:12
Alignment explanation
Indices: 2191281--2191305 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2191271 TCTTCGGGGA
2191281 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2191293 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2191305 C
1 C
2191306 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2191514 original size:24 final size:24
Alignment explanation
Indices: 2191480--2191533 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2191470 CTGAAACATC
* *
2191480 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
2191504 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
2191528 ATCAAA
1 ATCAAA
2191534 TTTCGAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:2192615 original size:20 final size:20
Alignment explanation
Indices: 2192590--2192647 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2192580 ATTCATTTGA
*
2192590 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATAG
2192610 CTATCGCAACGCGAAAATAG
1 CTATCGCAACGCGAAAATAG
* *
2192630 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
2192648 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATAG
Found at i:2192703 original size:33 final size:33
Alignment explanation
Indices: 2192666--2192780 Score: 128
Period size: 33 Copynumber: 3.5 Consensus size: 33
2192656 GAAATGAAAA
* * *
2192666 TCGCATTGTGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCGCATTGCGATTTTCATT
*
2192699 TCGCATTACGATTTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCGCATTGCGATTTTCATT
* *
2192732 TCGCATTGCGATTTT--CATTTCGCA-TTGCGATTT
1 TCGCATTGCGATTTTCGCATTGCG-ATTTTC-A-TT
2192765 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
2192781 ATTTCGCATT
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
31 9 0.13
32 2 0.03
33 60 0.85
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (33 bp):
TCGCATTGCGATTTTCGCATTGCGATTTTCATT
Found at i:2192710 original size:19 final size:19
Alignment explanation
Indices: 2192685--2192799 Score: 151
Period size: 19 Copynumber: 6.6 Consensus size: 19
2192675 GATTTTCTCG
2192685 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2192704 TTACGA---T--TTTCGCA
1 TTGCGATTTTCATTTCGCA
2192718 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2192737 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2192756 TTGCGA---T--TTTCGCA
1 TTGCGATTTTCATTTCGCA
2192770 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2192789 TTGCGATTTTC
1 TTGCGATTTTC
2192800 TCGTTGCGAT
Statistics
Matches: 84, Mismatches: 2, Indels: 20
0.79 0.02 0.19
Matches are distributed among these distances:
14 25 0.30
16 2 0.02
17 2 0.02
19 55 0.65
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2192746 original size:52 final size:52
Alignment explanation
Indices: 2192685--2192799 Score: 221
Period size: 52 Copynumber: 2.2 Consensus size: 52
2192675 GATTTTCTCG
2192685 TTGCGATTTTCATTTCGCATTACGATTTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTACGATTTTCGCATTGCGATTTTCATTTCGCA
*
2192737 TTGCGATTTTCATTTCGCATTGCGATTTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTACGATTTTCGCATTGCGATTTTCATTTCGCA
2192789 TTGCGATTTTC
1 TTGCGATTTTC
2192800 TCGTTGCGAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTACGATTTTCGCATTGCGATTTTCATTTCGCA
Found at i:2192781 original size:33 final size:33
Alignment explanation
Indices: 2192730--2192828 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
2192720 GCGATTTTCA
2192730 TTTCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TTTCGCATTGCGATTTTCATTTCGCATTGCGAT
2192763 TTTCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TTTCGCATTGCGATTTTCATTTCGCATTGCGAT
* * *** *
2192796 TTTCTCGTTGCGATAGCCATTTCGCGTTGCGAT
1 TTTCGCATTGCGATTTTCATTTCGCATTGCGAT
2192829 AGTTTGTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTCATTTCGCATTGCGAT
Found at i:2192799 original size:14 final size:14
Alignment explanation
Indices: 2192697--2192780 Score: 72
Period size: 14 Copynumber: 6.3 Consensus size: 14
2192687 GCGATTTTCA
*
2192697 TTTCGCATTACGAT
1 TTTCGCATTGCGAT
2192711 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
*
2192725 TTT--CATTTCGCA-
1 TTTCGCATTGCG-AT
* *
2192737 TTGCG-ATTTTC-A-
1 TTTCGCA-TTGCGAT
2192749 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
2192763 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
2192777 TTTC
1 TTTC
2192781 ATTTCGCATT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
12 16 0.28
13 4 0.07
14 38 0.66
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (14 bp):
TTTCGCATTGCGAT
Found at i:2192819 original size:52 final size:52
Alignment explanation
Indices: 2192685--2192828 Score: 188
Period size: 52 Copynumber: 2.8 Consensus size: 52
2192675 GATTTTCTCG
*
2192685 TTGCGATTTTCATTTCGCATTA-CGATTTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA-TAGCCATTTTCGCATTGCGATTTTCATTTCGCA
* *
2192737 TTGCGATTTTCATTTCGCATTGCGATTTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATAGCCATTTTCGCATTGCGATTTTCATTTCGCA
*
2192789 TTGCGATTTTC-TCGTT-GCGATAGCCA-TTTCGCGTTGCGAT
1 TTGCGATTTTCAT--TTCGC-ATAGCCATTTTCGCATTGCGAT
2192829 AGTTTGTTTT
Statistics
Matches: 84, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
51 2 0.02
52 75 0.89
53 7 0.08
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATAGCCATTTTCGCATTGCGATTTTCATTTCGCA
Found at i:2194852 original size:19 final size:20
Alignment explanation
Indices: 2194807--2194857 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2194797 CACGAAACTT
2194807 AAAATCGCAACGCGGAAATG
1 AAAATCGCAACGCGGAAATG
*** *
2194827 GCTATCGCAATGC-GAAATG
1 AAAATCGCAACGCGGAAATG
2194846 AAAATCGCAACG
1 AAAATCGCAACG
2194858 ACAAAATCGC
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAATG
Found at i:2194865 original size:14 final size:14
Alignment explanation
Indices: 2194846--2194903 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2194836 ATGCGAAATG
2194846 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2194860 AAAATCGCAACACGAA
1 AAAATCGC-A-ACGAC
2194876 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2194892 AAAATCGCAACG
1 AAAATCGCAACG
2194904 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 19 0.50
15 1 0.03
16 10 0.26
17 1 0.03
18 7 0.18
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2194888 original size:32 final size:33
Alignment explanation
Indices: 2194830--2194908 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
2194820 GGAAATGGCT
*
2194830 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
2194863 ATCGCAACACGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2194895 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2194909 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 29 0.67
33 14 0.33
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2194937 original size:19 final size:18
Alignment explanation
Indices: 2194915--2194977 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
2194905 GAAACACAAA
2194915 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
2194934 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
2194950 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
2194966 TCGCATTGCGAT
1 TCGCATTGCGAT
2194978 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
16 8 0.22
18 10 0.27
19 10 0.27
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:2194996 original size:20 final size:19
Alignment explanation
Indices: 2194962--2195016 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2194952 GTTGCGATTT
*
2194962 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2194981 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2195001 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
2195017 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:2195515 original size:18 final size:18
Alignment explanation
Indices: 2195489--2195533 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2195479 GTCGATCAGA
*
2195489 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
2195507 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2195525 TGATGGCTC
1 TGATGGCTC
2195534 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:2196876 original size:20 final size:20
Alignment explanation
Indices: 2196851--2196888 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2196841 AATAGTTTCT
2196851 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2196871 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2196889 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2197177 original size:22 final size:22
Alignment explanation
Indices: 2197152--2197195 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2197142 GATTTAGATA
2197152 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2197174 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2197196 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2197408 original size:20 final size:20
Alignment explanation
Indices: 2197383--2197435 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2197373 GATTATGTAT
2197383 TATCGCGTTGCGAAAG-ACAG
1 TATCGCGTTGCGAAAGTA-AG
2197403 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
2197423 TATCTCGTTGCGA
1 TATCGCGTTGCGA
2197436 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:2197454 original size:21 final size:21
Alignment explanation
Indices: 2197421--2197521 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
2197411 TGCGAAAGTA
* * *
2197421 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
2197442 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
2197462 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
2197484 AAT-TCGCGTTGCGATTTAATT-
1 AGTATCGCATTGCGATTT--TTC
2197505 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
2197522 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:2197469 original size:20 final size:20
Alignment explanation
Indices: 2197363--2197477 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
2197353 CGCTTTGAAA
*
2197363 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
2197384 ATCGCGTTGCGAAAGACAGT
1 ATCGCATTGCGATAGTCAGT
* * *
2197404 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
2197424 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
2197445 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2197465 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2197478 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 1 0.01
20 49 0.66
21 24 0.32
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2197496 original size:41 final size:41
Alignment explanation
Indices: 2197405--2197539 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
2197395 AAAGACAGTA
* * * ** *
2197405 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
2197445 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
2197487 TCGCGTTGCGAT-TTAATTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
2197528 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2197540 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:2197510 original size:20 final size:20
Alignment explanation
Indices: 2197485--2197551 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
2197475 GATTTTCCCA
*
2197485 ATTCGCGTTGCGATTTAATT
1 ATTCGCGTTGCGATTTACTT
* * **
2197505 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
2197526 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
2197546 ATTCGC
1 ATTCGC
2197552 ATTGTGAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 22 0.59
21 15 0.41
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:2197531 original size:21 final size:21
Alignment explanation
Indices: 2197466--2197541 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2197456 ATAGTCAGTA
2197466 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* ****
2197487 TCGCGTTGCGA-TTTAATTAT
1 TCGCATTGCGATTTTCCCAAT
2197507 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
2197528 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
2197542 ACTTATTCGC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:2197540 original size:41 final size:41
Alignment explanation
Indices: 2197466--2197555 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
2197456 ATAGTCAGTA
2197466 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTAATTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTAATTAT
*
2197507 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTAATTAT
2197548 TCGCATTG
1 TCGCATTG
2197556 TGAATTGGGA
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:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTAATTAT
Found at i:2204146 original size:31 final size:32
Alignment explanation
Indices: 2204100--2204165 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
2204090 ACGTCATTAT
* * *
2204100 TTTTAATGATGTGACATATATCAT-TCATCAC
1 TTTTAATGAAGTGACACATATCATGACATCAC
* *
2204131 TTTTGATGAAGTGACACATGTCATGACATCAC
1 TTTTAATGAAGTGACACATATCATGACATCAC
2204163 TTT
1 TTT
2204166 GGCTGACTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 20 0.69
32 9 0.31
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (32 bp):
TTTTAATGAAGTGACACATATCATGACATCAC
Found at i:2211825 original size:49 final size:49
Alignment explanation
Indices: 2211715--2211816 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
2211705 TTAATGACGA
2211715 TTGACAAACAAAACCAAAACGGAACGTTAGATATGATTTAAAAAATAGT
1 TTGACAAACAAAACCAAAACGGAACGTTAGATATGATTTAAAAAATAGT
2211764 TTGACAAACAAAACCAAAACGGAACGTTAGATATGATTTAAAAAATAGT
1 TTGACAAACAAAACCAAAACGGAACGTTAGATATGATTTAAAAAATAGT
2211813 TTGA
1 TTGA
2211817 TGACCAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.24
Consensus pattern (49 bp):
TTGACAAACAAAACCAAAACGGAACGTTAGATATGATTTAAAAAATAGT
Found at i:2212087 original size:60 final size:58
Alignment explanation
Indices: 2211992--2212153 Score: 157
Period size: 60 Copynumber: 2.7 Consensus size: 58
2211982 AATCATCCCC
* ** * *
2211992 GGTGTTGCTTTATTGAGTCAC-CAACTATTCGAAGTTATAATACGGCCCCCCGACTATAA
1 GGTGTTGCTTTATTGAGTCTCTC-ACTATTAAAAGTTACAAAACGGCCCCCCGACTAT-A
* * * * *
2212051 GGTGTTGCTTTGTTAAGTCTCTCGACTATTAAAAGTTACAAAATGGTCCCTCGACTATA
1 GGTGTTGCTTTATTGAGTCTCTC-ACTATTAAAAGTTACAAAACGGCCCCCCGACTATA
*
2212110 GGTTGTTGTTTTATTGAGATCTCAT-ACTATTAAAAGTTACAAAA
1 GG-TGTTGCTTTATTGAG-TCTC-TCACTATTAAAAGTTACAAAA
2212154 TGGTTACATG
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
59 21 0.25
60 59 0.69
61 4 0.05
62 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (58 bp):
GGTGTTGCTTTATTGAGTCTCTCACTATTAAAAGTTACAAAACGGCCCCCCGACTATA
Found at i:2212579 original size:35 final size:35
Alignment explanation
Indices: 2212533--2212600 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
2212523 TAGTCAAATG
*
2212533 ACTCAACAAAACAATGTCCTACATGTGGGAAACGA
1 ACTCAACAAAACAATATCCTACATGTGGGAAACGA
2212568 ACTCAACAAAACAATATCCTACATGTGGGAAAC
1 ACTCAACAAAACAATATCCTACATGTGGGAAAC
2212601 ATTTGTGTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (35 bp):
ACTCAACAAAACAATATCCTACATGTGGGAAACGA
Found at i:2212688 original size:16 final size:16
Alignment explanation
Indices: 2212667--2212706 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2212657 ACCAGATCCG
*
2212667 ATCCAAAAAATTGGAT
1 ATCCAAAAAATTAGAT
*
2212683 ATCCAAAATATTAGAT
1 ATCCAAAAAATTAGAT
*
2212699 ATCTAAAA
1 ATCCAAAA
2212707 TAGCGATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (16 bp):
ATCCAAAAAATTAGAT
Found at i:2213732 original size:7 final size:7
Alignment explanation
Indices: 2213720--2213764 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
2213710 ATTGAGTGAT
2213720 ATGCAGA
1 ATGCAGA
2213727 ATGCAGA
1 ATGCAGA
2213734 ATGCAGA
1 ATGCAGA
2213741 ATGCAGA
1 ATGCAGA
2213748 ATGCAGA
1 ATGCAGA
2213755 ATGCAGA
1 ATGCAGA
2213762 ATG
1 ATG
2213765 TTTTAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.29, T:0.16
Consensus pattern (7 bp):
ATGCAGA
Found at i:2214420 original size:60 final size:59
Alignment explanation
Indices: 2214322--2214489 Score: 185
Period size: 60 Copynumber: 2.8 Consensus size: 59
2214312 CCATCATTTT
* * *
2214322 AAATTGGTCCCTAAACTTTTAAATATTATAATTACATCCCTAAACTATGAC-TATCCTTCA
1 AAATTGGTCCCTAAACTTTTGAATATTATAATTTCAT-CCTAAACTATGACAT-TCATTCA
* * * * * * *
2214382 AAATTAGTCCTTAGACTTTTGAACATTTTAATTTCATCCTCAAACAATGACATTCATTCT
1 AAATTGGTCCCTAAACTTTTGAATATTATAATTTCATCCT-AAACTATGACATTCATTCA
**
2214442 AAATTGGTCCCTAAACTTTTTGAATATTCCAATTTCATCCTAAACTAT
1 AAATTGGTCCCTAAAC-TTTTGAATATTATAATTTCATCCTAAACTAT
2214490 ATGTATATAC
Statistics
Matches: 88, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
59 3 0.03
60 63 0.72
61 22 0.25
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.39
Consensus pattern (59 bp):
AAATTGGTCCCTAAACTTTTGAATATTATAATTTCATCCTAAACTATGACATTCATTCA
Found at i:2214947 original size:21 final size:25
Alignment explanation
Indices: 2214899--2214950 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 25
2214889 TAAAAACGTT
*
2214899 ATAAATAAAGAAGAAGAGATATTAA
1 ATAAATAAAGAAGAAGAGAAATTAA
2214924 ATAAA-AAAGAA-AA-AGAAATTAA
1 ATAAATAAAGAAGAAGAGAAATTAA
2214946 TATAA
1 -ATAA
2214951 TAATAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 8 0.32
23 6 0.24
24 6 0.24
25 5 0.20
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (25 bp):
ATAAATAAAGAAGAAGAGAAATTAA
Found at i:2215035 original size:19 final size:19
Alignment explanation
Indices: 2215003--2215042 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2214993 ATTAAAGAGG
*
2215003 AAAAGAAAAGAAAAT-TAA
1 AAAAAAAAAGAAAATATAA
2215021 AAAAAAAAAGAAAAATATAA
1 AAAAAAAAAG-AAAATATAA
2215041 AA
1 AA
2215043 TAATAATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 5 0.26
20 5 0.26
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAAAAAAGAAAATATAA
Found at i:2215167 original size:24 final size:24
Alignment explanation
Indices: 2215139--2215188 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2215129 ATAGGAATAG
*
2215139 AAATAAAATCA-AATCAAATAAAAA
1 AAATAAAATCATAA-AAAATAAAAA
*
2215163 AAATAAAATTATAAAAAATAAAAA
1 AAATAAAATCATAAAAAATAAAAA
2215187 AA
1 AA
2215189 GGTTAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (24 bp):
AAATAAAATCATAAAAAATAAAAA
Found at i:2216602 original size:39 final size:38
Alignment explanation
Indices: 2216477--2216609 Score: 118
Period size: 38 Copynumber: 3.6 Consensus size: 38
2216467 TTTAAAAACG
* * *
2216477 TTTTCAAAACTATATATTATAT-AGTTTT-CAAAAAT-A
1 TTTTTAAAA-TATATATTATATAAATTTTCCAAAAATGT
* **
2216513 ATTTT-AAA-A-ATATTATATAAGCTTTCC-AAAATGT
1 TTTTTAAAATATATATTATATAAATTTTCCAAAAATGT
2216547 TTTTTAAAATTATATATTATATAAATTTTCCAAAAATGTT
1 TTTTTAAAA-TATATATTATATAAATTTTCCAAAAATG-T
2216587 TTTTTAAAAACTATATATTATAT
1 TTTTT-AAAA-TATATATTATAT
2216610 TTTCAAAATG
Statistics
Matches: 79, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
32 9 0.11
33 11 0.14
34 5 0.06
35 6 0.08
36 3 0.04
37 1 0.01
38 16 0.20
39 6 0.08
40 6 0.08
41 16 0.20
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTTTAAAATATATATTATATAAATTTTCCAAAAATGT
Found at i:2216602 original size:72 final size:71
Alignment explanation
Indices: 2216454--2216658 Score: 195
Period size: 70 Copynumber: 2.9 Consensus size: 71
2216444 ATATTTTTAA
* * * * **
2216454 ACTATATATTATATTT-AAAAACGTTTTCAAAACTATATATTATATAGTTTTCAAAAAT-AATTT
1 ACTATATA-TAGATTTCCAAAATGTTTTCAAAACTATATATTATATAATTTTCAAAAATGTTTTT
2216517 TAAAAAT
65 TAAAAAT
* * * *
2216524 ATTATATA-AGCTTTCCAAAATGTTTTTTAAAATTATATATTATATAAATTTTCCAAAAATGTTT
1 ACTATATATAGATTTCCAAAATG-TTTTCAAAACTATATATTATAT-AATTTT-CAAAAATGTTT
*
2216588 TTTTAAAA-
63 TTTAAAAAT
* * * *
2216596 ACTATATATTATATTTTCAAAATGCTTTCAAAACTATATACTATATAATTTTC-AAAATGTTTT
1 ACTATATA-TAGATTTCCAAAATGTTTTCAAAACTATATATTATATAATTTTCAAAAATGTTTT
2216659 AAAACTTATA
Statistics
Matches: 109, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
68 4 0.04
69 5 0.05
70 37 0.34
71 6 0.06
72 20 0.18
73 26 0.24
74 11 0.10
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (71 bp):
ACTATATATAGATTTCCAAAATGTTTTCAAAACTATATATTATATAATTTTCAAAAATGTTTTTT
AAAAAT
Found at i:2216615 original size:108 final size:107
Alignment explanation
Indices: 2216470--2216727 Score: 260
Period size: 108 Copynumber: 2.4 Consensus size: 107
2216460 TATTATATTT
* *
2216470 AAAAACG-TTTTCAAAACTATATATTATATAGTTTTCAAAAATAATTTTAAAA-ATAT-TATATA
1 AAAAACGTTTTTAAAAACTATATA-T-TATA-TTTTCAAAAATAATTTCAAAACATATATATATA
**
2216532 AGCTTTCCAAAATGTTTTTTAAAA-TTATATA-T-TATATAAATTTTCC
63 A--TTTCCAAAATG--TTTTAAAACTTATATATTGTATATAAATTTTAA
* **
2216578 AAAAATGTTTTTTTAAAAACTATATATTATATTTTC-AAAATGCTTTCAAAACTATATACTATAT
1 AAAAACG--TTTTTAAAAACTATATATTATATTTTCAAAAATAATTTCAAAAC-ATATA-TATAT
* *
2216642 AATTTTCAAAATGTTTTAAAACTTATATATTGTATATAAGTTTTAA
62 AATTTCCAAAATGTTTTAAAACTTATATATTGTATATAAATTTTAA
* *
2216688 AAAAACGTTTTAAAAAACTATATAATATATATTTCAAAAA
1 AAAAACGTTTTTAAAAACTATATATTATAT-TTTCAAAAA
2216728 ATATTTTTTG
Statistics
Matches: 126, Mismatches: 12, Indels: 22
0.79 0.08 0.14
Matches are distributed among these distances:
107 20 0.16
108 39 0.31
109 23 0.18
110 22 0.17
111 22 0.17
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (107 bp):
AAAAACGTTTTTAAAAACTATATATTATATTTTCAAAAATAATTTCAAAACATATATATATAATT
TCCAAAATGTTTTAAAACTTATATATTGTATATAAATTTTAA
Found at i:2216680 original size:37 final size:34
Alignment explanation
Indices: 2216447--2216671 Score: 166
Period size: 34 Copynumber: 6.6 Consensus size: 34
2216437 AAAAAATATA
* *
2216447 TTTTT-AAACTATATAT-TAT-A-TTTAAAAACG
1 TTTTTAAAACTATATATATATAATTTTCAAAATG
* * *
2216477 TTTTCAAAACTATATATTATATAGTTTTCAAAAATA
1 TTTTTAAAACTATATA-TATATAATTTTC-AAAATG
* *
2216513 ATTTTAAAA--ATAT-TATATAAGCTTTCCAAAATG
1 TTTTTAAAACTATATATATATAA--TTTTCAAAATG
*
2216546 TTTTTTAAAATTATATATTATATAAATTTTCCAAAAATG
1 -TTTTTAAAACTATATA-TATAT-AATTTT-C-AAAATG
2216585 TTTTTTTAAAAACTATATAT-TAT-ATTTTCAAAATG
1 --TTTTT-AAAACTATATATATATAATTTTCAAAATG
* *
2216620 CTTTCAAAACTATATACTATATAATTTTCAAAATG
1 TTTTTAAAACTATATA-TATATAATTTTCAAAATG
2216655 -TTTTAAAACT-TATATAT
1 TTTTTAAAACTATATATAT
2216672 TGTATATAAG
Statistics
Matches: 158, Mismatches: 16, Indels: 40
0.74 0.07 0.19
Matches are distributed among these distances:
30 4 0.03
31 10 0.06
32 21 0.13
33 16 0.10
34 28 0.18
35 21 0.13
36 16 0.10
37 8 0.05
38 6 0.04
39 11 0.07
40 7 0.04
41 10 0.06
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (34 bp):
TTTTTAAAACTATATATATATAATTTTCAAAATG
Found at i:2216717 original size:39 final size:37
Alignment explanation
Indices: 2216540--2216788 Score: 139
Period size: 35 Copynumber: 6.8 Consensus size: 37
2216530 TAAGCTTTCC
* * * **
2216540 AAAATGTTTTTTAAAATTATATATTATATAAATTTTCCA
1 AAAATG-TTTTAAAAACTATATACTATAT-AATTTTAAA
*
2216579 AAAATGTTTTTTTAAAAACTATATA-T-TAT-ATTTT--C
1 AAAATG---TTTTAAAAACTATATACTATATAATTTTAAA
* * *
2216614 AAAATGCTTTCAAAACTATATACTATATAATTTT--C
1 AAAATGTTTTAAAAACTATATACTATATAATTTTAAA
*
2216649 AAAATGTTTT-AAAACTTATATATTGTATATAAGTTTTAAA
1 AAAATGTTTTAAAAAC-TATATA--CTATATAA-TTTTAAA
* * *
2216689 AAAACGTTTTAAAAAACTATATAATATAT-ATTTCAAA
1 AAAATGTTTT-AAAAACTATATACTATATAATTTTAAA
*
2216726 AAATATTTTTTGAAAAACTATATACTATAT--TTTTCAAA
1 AAA-ATGTTTT-AAAAACTATATACTATATAATTTT-AAA
* *
2216764 AACAT-TTTCAAAAA-T-TATACTATAT
1 AAAATGTTTTAAAAACTATATACTATAT
2216789 TACTATAATA
Statistics
Matches: 177, Mismatches: 18, Indels: 36
0.77 0.08 0.16
Matches are distributed among these distances:
32 14 0.08
33 11 0.06
34 9 0.05
35 32 0.18
36 3 0.02
37 26 0.15
38 32 0.18
39 14 0.08
40 10 0.06
41 21 0.12
42 5 0.03
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATACTATATAATTTTAAA
Found at i:2219062 original size:20 final size:21
Alignment explanation
Indices: 2219023--2219063 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2219013 ATTTAAATGT
2219023 ATTTTTAAAATTGCAGATTAA
1 ATTTTTAAAATTGCAGATTAA
*
2219044 ATTTTTAAAATTTCA-ATTAA
1 ATTTTTAAAATTGCAGATTAA
2219064 TAATATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (21 bp):
ATTTTTAAAATTGCAGATTAA
Found at i:2220328 original size:33 final size:34
Alignment explanation
Indices: 2220291--2220356 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
2220281 TTTACAACTC
* *
2220291 CCTAG-TTTTTCACGGGATAAACTATAACCTTTT
1 CCTAGCTTTTACACGGGATAAACTAGAACCTTTT
* * *
2220324 CCTAGCTTTTACATGGGCTAAGCTAGAACCTTT
1 CCTAGCTTTTACACGGGATAAACTAGAACCTTT
2220357 CCCCTTTACA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 5 0.19
34 22 0.81
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (34 bp):
CCTAGCTTTTACACGGGATAAACTAGAACCTTTT
Found at i:2222585 original size:21 final size:21
Alignment explanation
Indices: 2222559--2222628 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
2222549 CATATTCGCA
2222559 TTGCGATAGTCCAAGTTTGCG
1 TTGCGATAGTCCAAGTTTGCG
* *
2222580 TTGCGATTTATTCCAA-ATT-CG
1 TTGCGA--TAGTCCAAGTTTGCG
* *
2222601 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTTGCG
2222622 TTGCGAT
1 TTGCGAT
2222629 TTATTCCAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 6 0.15
20 1 0.03
21 23 0.59
22 2 0.05
23 7 0.18
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTTGCG
Found at i:2222610 original size:42 final size:42
Alignment explanation
Indices: 2222559--2222642 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
2222549 CATATTCGCA
*
2222559 TTGCGATAGTCCAAGTTTGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
2222601 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
2222643 CAACGACTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:2223413 original size:42 final size:42
Alignment explanation
Indices: 2223354--2223513 Score: 293
Period size: 42 Copynumber: 3.8 Consensus size: 42
2223344 TGCGATTTTG
2223354 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2223396 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
2223438 GACTATGGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2223480 GACTATCGCAACGAATTTGGAATAAATCGCAACG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACG
2223514 AATTTGGAAT
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 113 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:2223488 original size:63 final size:64
Alignment explanation
Indices: 2223421--2223622 Score: 202
Period size: 63 Copynumber: 3.2 Consensus size: 64
2223411 TTTGGAATAA
* * *
2223421 ATCGCAACGCGAACTTCGACT-ATGGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGAATAATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
* * *
2223484 ATCGCAA--CGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGAAT-AATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
* * * * * *
2223547 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGCTAACTTGGA
1 ATCGCAACGCGAACTTCGAAT-AATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCGA
2223608 CT
63 CT
*
2223610 ATCGCAATGCGAA
1 ATCGCAACGCGAA
2223623 TATGTAAATC
Statistics
Matches: 122, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
61 9 0.07
63 100 0.82
65 13 0.11
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (64 bp):
ATCGCAACGCGAACTTCGAATAATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:2223614 original size:105 final size:104
Alignment explanation
Indices: 2223379--2223616 Score: 379
Period size: 105 Copynumber: 2.3 Consensus size: 104
2223369 TTTGGAATAA
*
2223379 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
1 ATCGCAACGC-AACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
* *
2223444 GGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
65 CGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
* *
2223484 ATCGCAACG-AATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
1 ATCGCAACGCAACTTGGACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
*
2223548 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
64 TCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
2223589 ATCGCAACGCTAACTTGGACTATCGCAA
1 ATCGCAACGC-AACTTGGACTATCGCAA
2223617 TGCGAATATG
Statistics
Matches: 121, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
103 7 0.06
105 106 0.88
107 8 0.07
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (104 bp):
ATCGCAACGCAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
GCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:2223622 original size:42 final size:41
Alignment explanation
Indices: 2223351--2223616 Score: 247
Period size: 42 Copynumber: 6.3 Consensus size: 41
2223341 CATTGCGATT
*
2223351 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* *
2223393 TTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* *
2223435 TTCGACTATGGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* *
2223477 TTGGACTATCGCAACGAATTTGGAATAAATCGCAA--CGAAT
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* * * *
2223517 TTGGAATAAATCGCAACGCGAACTTCGACT-ATCGCAA--CGAAT
1 TTGGACT--ATCGCAA--CGAACTTGGAATAATCGCAACGCGAAC
* * * *
2223559 TTGGAATAAATCGCAACGCGAACTTCGACT-ATCGCAACGCTAAC
1 TTGGACT--ATCGCAA--CGAACTTGGAATAATCGCAACGCGAAC
2223603 TTGGACTATCGCAA
1 TTGGACTATCGCAA
2223617 TGCGAATATG
Statistics
Matches: 204, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
40 10 0.05
42 176 0.86
44 18 0.09
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (41 bp):
TTGGACTATCGCAACGAACTTGGAATAATCGCAACGCGAAC
Found at i:2227317 original size:21 final size:22
Alignment explanation
Indices: 2227273--2227318 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2227263 GATTTCCGGG
* *
2227273 CAAGGGGAATCGGTAACCCATT
1 CAAGGGGAACCGATAACCCATT
*
2227295 CAAGGGGAACCGAT-ACCCCTT
1 CAAGGGGAACCGATAACCCATT
2227316 CAA
1 CAA
2227319 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (22 bp):
CAAGGGGAACCGATAACCCATT
Found at i:2228690 original size:14 final size:14
Alignment explanation
Indices: 2228671--2228697 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2228661 ATGAAAGAAG
2228671 ATGTGATACGTGAT
1 ATGTGATACGTGAT
2228685 ATGTGATACGTGA
1 ATGTGATACGTGA
2228698 ATTACAATTT
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:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (14 bp):
ATGTGATACGTGAT
Found at i:2229092 original size:23 final size:23
Alignment explanation
Indices: 2229065--2229109 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2229055 ATTTTTATAT
*
2229065 GGCACTAT-GGTGCAATTCTACGC
1 GGCACT-TCGGTGCAATTATACGC
2229088 GGCACTTCGGTGCAATTATACG
1 GGCACTTCGGTGCAATTATACG
2229110 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGC
Found at i:2230462 original size:34 final size:32
Alignment explanation
Indices: 2230395--2230464 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2230385 ACCTTACAAC
* * *
2230395 TCCCTAGTTTTTCCGGGCTAAACTATAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
2230427 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
2230461 TCCC
1 TCCC
2230465 CTTTACAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:2230773 original size:21 final size:21
Alignment explanation
Indices: 2230747--2230788 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2230737 CCAGAATGGG
*
2230747 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2230768 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2230789 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:2231012 original size:29 final size:31
Alignment explanation
Indices: 2230980--2231039 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
2230970 AAATTTTGAA
*
2230980 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
2231009 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
2231040 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:2233709 original size:20 final size:19
Alignment explanation
Indices: 2233673--2233715 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2233663 GGTATTTTTG
2233673 AAAATTTATTTAAAAAATAA
1 AAAATTTATTTAAAAAA-AA
**
2233693 AAAATTTA-TTAGGAAAAA
1 AAAATTTATTTAAAAAAAA
2233711 AAAAT
1 AAAAT
2233716 CAAACAGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAATTTATTTAAAAAAAA
Found at i:2236427 original size:57 final size:57
Alignment explanation
Indices: 2236339--2236447 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
2236329 GAATAATAGA
* *
2236339 ACTGTTCTTAAAGCTGCTTAGGATGCAAACATCCTTCTACATTAGTTTTCTGGTAGC
1 ACTGTTCTTAAAGCTGCATAGGATGCAAACATCCTTCTACACTAGTTTTCTGGTAGC
* *
2236396 ACTGTTCTTAAAGCTGCATAGGATGCAAACATCCTTCTGCGCTAGTTTTCTG
1 ACTGTTCTTAAAGCTGCATAGGATGCAAACATCCTTCTACACTAGTTTTCTG
2236448 TTCTAATATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (57 bp):
ACTGTTCTTAAAGCTGCATAGGATGCAAACATCCTTCTACACTAGTTTTCTGGTAGC
Found at i:2239818 original size:6 final size:6
Alignment explanation
Indices: 2239807--2239840 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
2239797 GACCGTTTTG
2239807 TTGTTT TTGTTTGT TTGTTT TTGTTT TTGTTT TT
1 TTGTTT TTG-TT-T TTGTTT TTGTTT TTGTTT TT
2239841 ATTTGATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 18 0.69
7 4 0.15
8 4 0.15
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (6 bp):
TTGTTT
Found at i:2239818 original size:14 final size:15
Alignment explanation
Indices: 2239801--2239838 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2239791 ATTTGTGACC
2239801 GTTTTG-TTGTTTTT
1 GTTTTGTTTGTTTTT
2239815 G-TTTGTTTGTTTTT
1 GTTTTGTTTGTTTTT
2239829 GTTTTTGTTT
1 G-TTTTGTTT
2239839 TTATTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.19
14 10 0.48
16 7 0.33
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (15 bp):
GTTTTGTTTGTTTTT
Found at i:2239822 original size:10 final size:10
Alignment explanation
Indices: 2239802--2239856 Score: 53
Period size: 10 Copynumber: 5.4 Consensus size: 10
2239792 TTTGTGACCG
2239802 TTTTG-TTGT
1 TTTTGTTTGT
2239811 TTTTGTTTGT
1 TTTTGTTTGT
2239821 TTGTT-TTTGT
1 TT-TTGTTTGT
2239831 TTTTGTTT-T
1 TTTTGTTTGT
2239840 TATTTGATTTGAT
1 T-TTTG-TTTG-T
2239853 TTTT
1 TTTT
2239857 CCTTTTTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.23
10 20 0.51
11 5 0.13
12 3 0.08
13 2 0.05
ACGTcount: A:0.05, C:0.00, G:0.16, T:0.78
Consensus pattern (10 bp):
TTTTGTTTGT
Found at i:2239867 original size:6 final size:6
Alignment explanation
Indices: 2239852--2239881 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
2239842 TTTGATTTGA
2239852 TTTTTCC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTT-C TTTTTC TTTTTC TTTTTC TTTTT
2239882 TCTCTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:2239882 original size:13 final size:13
Alignment explanation
Indices: 2239852--2239889 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
2239842 TTTGATTTGA
*
2239852 TTTTTCCTTTTTC
1 TTTTTTCTTTTTC
2239865 -TTTTTCTTTTTC
1 TTTTTTCTTTTTC
2239877 TTTTTTCTCTTTT
1 TTTTTTCT-TTTT
2239890 TAACAGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 7 0.32
14 4 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:2246742 original size:31 final size:34
Alignment explanation
Indices: 2246701--2246764 Score: 98
Period size: 31 Copynumber: 2.0 Consensus size: 34
2246691 GATTTTGTTC
2246701 TTCATCTTCTATGATTAATTATA-TTT-TATCTA
1 TTCATCTTCTATGATTAATTATACTTTGTATCTA
*
2246733 TTCAT-TTCTATGATTATTTATACTTTGTATCT
1 TTCATCTTCTATGATTAATTATACTTTGTATCT
2246765 TTTAAGTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 16 0.55
32 8 0.28
33 5 0.17
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.58
Consensus pattern (34 bp):
TTCATCTTCTATGATTAATTATACTTTGTATCTA
Found at i:2251374 original size:23 final size:23
Alignment explanation
Indices: 2251348--2251422 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
2251338 TGTTCATTCG
*
2251348 TTTAACGTTTACGAACATGTTCA
1 TTTAACGTTTACAAACATGTTCA
** * * *
2251371 TTTAATATTCATAAACATATTCA
1 TTTAACGTTTACAAACATGTTCA
*
2251394 TTTAACGTTTGCAAACATGTTCA
1 TTTAACGTTTACAAACATGTTCA
2251417 TTTAAC
1 TTTAAC
2251423 ATTATAAAAA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (23 bp):
TTTAACGTTTACAAACATGTTCA
Found at i:2251411 original size:46 final size:45
Alignment explanation
Indices: 2251343--2251430 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 45
2251333 GTTTGTGTTC
* * *
2251343 ATTCGTTTAACGTTTACGAACATGTTCATTTAATATTCATAAACAT
1 ATTCATTTAACGTTTACAAACATGTTCATTTAACATT-ATAAACAT
*
2251389 ATTCATTTAACGTTTGCAAACATGTTCATTTAACATTATAAA
1 ATTCATTTAACGTTTACAAACATGTTCATTTAACATTATAAA
2251431 AAATATTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 5 0.13
46 33 0.87
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (45 bp):
ATTCATTTAACGTTTACAAACATGTTCATTTAACATTATAAACAT
Found at i:2252693 original size:2 final size:2
Alignment explanation
Indices: 2252686--2252743 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2252676 CTTACGAGCT
2252686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2252728 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
2252744 AGCTCATGGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2259922 original size:15 final size:16
Alignment explanation
Indices: 2259902--2259940 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2259892 TTTGTAAGAA
2259902 ACAATTTTAATATTAT
1 ACAATTTTAATATTAT
* *
2259918 A-AATTTTGATATTTT
1 ACAATTTTAATATTAT
2259933 ACAATTTT
1 ACAATTTT
2259941 GTTTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (16 bp):
ACAATTTTAATATTAT
Found at i:2270025 original size:20 final size:20
Alignment explanation
Indices: 2270000--2270047 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
2269990 CAAAAATCAT
2270000 TTTGATCACTGATGTTTCAA
1 TTTGATCACTGATGTTTCAA
2270020 TTTGATCACTGATGTTTCAA
1 TTTGATCACTGATGTTTCAA
2270040 TTTGATCA
1 TTTGATCA
2270048 ATCAAACCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (20 bp):
TTTGATCACTGATGTTTCAA
Found at i:2270398 original size:2 final size:2
Alignment explanation
Indices: 2270391--2270444 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2270381 ATAAGAAATG
2270391 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
2270433 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2270445 TTGCTTTTGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2276125 original size:14 final size:13
Alignment explanation
Indices: 2276092--2276134 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2276082 TATTAAATAA
*
2276092 TTTAAAAATA-AT
1 TTTAAAAATACTT
*
2276104 TCTAAAAATCACTT
1 TTTAAAAAT-ACTT
2276118 TTTAAAAATACTT
1 TTTAAAAATACTT
2276131 TTTA
1 TTTA
2276135 TCACTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 8 0.31
13 9 0.35
14 9 0.35
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTAAAAATACTT
Found at i:2276638 original size:15 final size:16
Alignment explanation
Indices: 2276618--2276656 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2276608 ACAATATTTT
2276618 TAATCT-TGAATTCGA
1 TAATCTGTGAATTCGA
*
2276633 TAATCTGTTAATTCGA
1 TAATCTGTGAATTCGA
*
2276649 TCATCTGT
1 TAATCTGT
2276657 TAAGAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (16 bp):
TAATCTGTGAATTCGA
Found at i:2276647 original size:16 final size:16
Alignment explanation
Indices: 2276626--2276659 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2276616 TTTAATCTTG
2276626 AATTCGATAATCTGTT
1 AATTCGATAATCTGTT
*
2276642 AATTCGATCATCTGTT
1 AATTCGATAATCTGTT
2276658 AA
1 AA
2276660 GAAAAACGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (16 bp):
AATTCGATAATCTGTT
Found at i:2286736 original size:13 final size:13
Alignment explanation
Indices: 2286718--2286743 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2286708 TATACTCCCT
2286718 CAAAATATCATTC
1 CAAAATATCATTC
2286731 CAAAATATCATTC
1 CAAAATATCATTC
2286744 AAATGCACGC
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:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
CAAAATATCATTC
Found at i:2290999 original size:44 final size:44
Alignment explanation
Indices: 2290936--2291019 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
2290926 TTTTAAGCGG
* *
2290936 CGTTTTTCGGATACAAACGCCGTAACAA-GTCTAGTATATAGCTA
1 CGTTTTTCAGATACAAACGCCGCAA-AAGGTCTAGTATATAGCTA
*
2290980 CGTTTTT-AGATACAAAACGCCGCAAAAGGTCTGGTATATA
1 CGTTTTTCAGATAC-AAACGCCGCAAAAGGTCTAGTATATA
2291020 ATGGCGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 7 0.20
44 28 0.80
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (44 bp):
CGTTTTTCAGATACAAACGCCGCAAAAGGTCTAGTATATAGCTA
Found at i:2294320 original size:19 final size:17
Alignment explanation
Indices: 2294296--2294331 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
2294286 TTTTTTAAAG
2294296 TATTAAATAATTTATTTAT
1 TATTAAAT-ATTT-TTTAT
2294315 TATTAAATATTTTTTAT
1 TATTAAATATTTTTTAT
2294332 AATTTATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTAAATATTTTTTAT
Found at i:2294415 original size:26 final size:27
Alignment explanation
Indices: 2294342--2294415 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 27
2294332 AATTTATCAA
*
2294342 TAAAAATATTAATTAGTATATATTATTT
1 TAAAAATATTATTTAGTAT-TATTATTT
**
2294370 TAAAGTTA-TAGTGTTA-TATTA-TATTT
1 TAAAAATATTA-T-TTAGTATTATTATTT
2294396 TAAAAATATTATTTAGTATT
1 TAAAAATATTATTTAGTATT
2294416 TTAAATATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
25 3 0.08
26 16 0.43
27 6 0.16
28 9 0.24
29 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (27 bp):
TAAAAATATTATTTAGTATTATTATTT
Found at i:2294485 original size:24 final size:23
Alignment explanation
Indices: 2294454--2294498 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2294444 ATTATAGATA
2294454 TATTATAATATAATATTATTCAT
1 TATTATAATATAATATTATTCAT
*
2294477 TATTAATAATTTAATATTATTC
1 TATT-ATAATATAATATTATTC
2294499 TATGAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTATAATATAATATTATTCAT
Found at i:2294508 original size:27 final size:24
Alignment explanation
Indices: 2294458--2294514 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 24
2294448 TAGATATATT
*
2294458 ATAATATAATATTATTCATTATTA
1 ATAATATAATATTATTCATAATTA
*
2294482 ATAATTTAATATTATTCTATGAAATTA
1 ATAATATAATATTATTC-AT--AATTA
2294509 ATAATA
1 ATAATA
2294515 ATATAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 16 0.59
25 2 0.07
27 9 0.33
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
ATAATATAATATTATTCATAATTA
Found at i:2294534 original size:27 final size:27
Alignment explanation
Indices: 2294458--2294534 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
2294448 TAGATATATT
* * *
2294458 ATAATATAATATTATTCATTATTAATA
1 ATAATATAATTTTATTAATAATTAATA
* * *
2294485 ATTTAATATTATTCTA-TGA-AATTAATA
1 A--TAATATAATTTTATTAATAATTAATA
2294512 ATAATATAATTTTATTAATAATT
1 ATAATATAATTTTATTAATAATT
2294535 TATTATATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
25 11 0.29
26 2 0.05
27 13 0.34
28 2 0.05
29 10 0.26
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (27 bp):
ATAATATAATTTTATTAATAATTAATA
Found at i:2294579 original size:59 final size:59
Alignment explanation
Indices: 2294507--2294665 Score: 160
Period size: 59 Copynumber: 2.7 Consensus size: 59
2294497 TCTATGAAAT
* * *
2294507 TAATAATAATATAATTTTATTAATAATTTATTATATTATTAAATAAAA-AATATAATATC
1 TAATATTAATATAATTTTATTAATAATTTATTATAATATTAAA-AAAATAATATAATATA
* * * * * * * *
2294566 TTATATTATTATAATATAATTGATTATTTATTATAATATTAAAAAAATATTATATTATA
1 TAATATTAATATAATTTTATTAATAATTTATTATAATATTAAAAAAATAATATAATATA
* *
2294625 TAATATTAATATATATTTT-TAAATAATTTATAATTAATATT
1 TAATATTAATATA-ATTTTATTAATAATTTATTA-TAATATT
2294666 TTAATTAAAG
Statistics
Matches: 78, Mismatches: 19, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
58 4 0.05
59 64 0.82
60 10 0.13
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (59 bp):
TAATATTAATATAATTTTATTAATAATTTATTATAATATTAAAAAAATAATATAATATA
Found at i:2301868 original size:23 final size:23
Alignment explanation
Indices: 2301842--2301890 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2301832 TAGTTTATCC
2301842 AAGTGAAAAACTAGGGAGTTGTA
1 AAGTGAAAAACTAGGGAGTTGTA
2301865 AAGTGAAAAACTAGGGAGTTGTA
1 AAGTGAAAAACTAGGGAGTTGTA
2301888 AAG
1 AAG
2301891 GTTATCTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.31, T:0.20
Consensus pattern (23 bp):
AAGTGAAAAACTAGGGAGTTGTA
Found at i:2313024 original size:21 final size:22
Alignment explanation
Indices: 2312982--2313024 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
2312972 ATAATTTTTA
* *
2312982 TTCTCTAAATTTTTATTATAAT
1 TTCTCTAAATTTTGATCATAAT
*
2313004 TTCT-TAAATTTTGATCCTAAT
1 TTCTCTAAATTTTGATCATAAT
2313025 ATAAAATCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.56
Consensus pattern (22 bp):
TTCTCTAAATTTTGATCATAAT
Found at i:2321307 original size:20 final size:20
Alignment explanation
Indices: 2321284--2321322 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2321274 TCTATATGTA
2321284 TTTTT-TATTAAAATTTTAT
1 TTTTTCTATTAAAATTTTAT
* *
2321303 TTTTTCTCTTGAAATTTTAT
1 TTTTTCTATTAAAATTTTAT
2321323 AAATTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTTCTATTAAAATTTTAT
Found at i:2330871 original size:25 final size:25
Alignment explanation
Indices: 2330837--2330885 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
2330827 CAACGTGAAG
2330837 TCCAAAGTATAACTAGAAAATAAAT
1 TCCAAAGTATAACTAGAAAATAAAT
2330862 TCCAAAGTATAACTAGAAAATAAA
1 TCCAAAGTATAACTAGAAAATAAA
2330886 CTCACCTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.22
Consensus pattern (25 bp):
TCCAAAGTATAACTAGAAAATAAAT
Found at i:2334521 original size:2 final size:2
Alignment explanation
Indices: 2334514--2334544 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2334504 GAAAGCAAAT
2334514 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2334545 TTTTTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2338941 original size:37 final size:36
Alignment explanation
Indices: 2338898--2339014 Score: 166
Period size: 35 Copynumber: 3.2 Consensus size: 36
2338888 TGGCAACCAA
2338898 CTTTGAACAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAA-AATTGGTTTTCAAAGTTTGGTAAATGTTT
2338935 CTTTGAAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
* * *
2338970 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATTGGTTTTCAAAGTTTGGTAAATGTTT
*
2339007 -GTTGAAAA
1 CTTTGAAAA
2339015 ATGATAATGG
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
35 35 0.47
36 9 0.12
37 30 0.41
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2343510 original size:35 final size:36
Alignment explanation
Indices: 2343460--2343581 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
2343450 TGGCAACCAA
*
2343460 CTTTGAAAATTTGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAA-ATGATTTTCAAAGTTTGGTAAATGTTT
2343497 CTTTG-AAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
2343532 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
2343569 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
2343582 AATGGGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 33 0.42
36 17 0.22
37 28 0.36
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:2351312 original size:10 final size:10
Alignment explanation
Indices: 2351297--2351331 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
2351287 GTAGTTTACC
2351297 ATTATTTTTT
1 ATTATTTTTT
2351307 ATTATTTTTT
1 ATTATTTTTT
*
2351317 -TTAGTTTTT
1 ATTATTTTTT
2351326 ATTATT
1 ATTATT
2351332 AAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (10 bp):
ATTATTTTTT
Found at i:2351374 original size:18 final size:20
Alignment explanation
Indices: 2351346--2351397 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
2351336 TAAAAAATGC
*
2351346 ATTAATTTAATTTAAA-ATT
1 ATTAATATAATTTAAAGATT
2351365 -TTAATATAA-TTAAATGATT
1 ATTAATATAATTTAAA-GATT
*
2351384 ATTGATATAATTTA
1 ATTAATATAATTTA
2351398 TATTGTGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 5 0.19
18 8 0.30
19 3 0.11
20 8 0.30
21 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
ATTAATATAATTTAAAGATT
Found at i:2355316 original size:60 final size:60
Alignment explanation
Indices: 2355248--2355396 Score: 162
Period size: 60 Copynumber: 2.5 Consensus size: 60
2355238 AAATTGACCT
* * *
2355248 CTAAACTTTTAAATGTTTCAATTTCATCT-TTAAACTATGA-TTATCA-TTCTAAATTAGTCC
1 CTAAACTTTT-AATATTTCAATTTCATCTCTTAAACTATGACTTAT-ATTTCAAAATGA-TCC
* *
2355308 TTAAACTTTTAATCATTCCAATTTCAT-TCTTAAACTATGACTTATATTTCAAAATGATCC
1 CTAAACTTTTAAT-ATTTCAATTTCATCTCTTAAACTATGACTTATATTTCAAAATGATCC
*
2355368 CTAAATTTTTTCAATATTTCAATTTCATC
1 CTAAA-CTTTT-AATATTTCAATTTCATC
2355397 CTAAATTATG
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
59 4 0.05
60 39 0.53
61 28 0.38
62 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (60 bp):
CTAAACTTTTAATATTTCAATTTCATCTCTTAAACTATGACTTATATTTCAAAATGATCC
Found at i:2355645 original size:61 final size:59
Alignment explanation
Indices: 2355580--2355708 Score: 134
Period size: 59 Copynumber: 2.2 Consensus size: 59
2355570 AGAAAGTGGG
* * * *
2355580 TCATAGTTTAGGGATGAAAATTAGAATGTTCAAAAGTTCAAGGA-CTAATTTAGAATGAGAA
1 TCATAGTTTAGGAATG-AAATT-GAATATTCAAAAGTTCAAGAATC-AATTTAAAATGAGAA
* * * * *
2355641 TCATAGTCTAGGAATGTAATTGAATATTCCAAAGTTTAAGAATCAATTTAAAATGAGAG
1 TCATAGTTTAGGAATGAAATTGAATATTCAAAAGTTCAAGAATCAATTTAAAATGAGAA
*
2355700 TTATAGTTT
1 TCATAGTTT
2355709 GAGAACATAT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
59 37 0.66
60 5 0.09
61 14 0.25
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (59 bp):
TCATAGTTTAGGAATGAAATTGAATATTCAAAAGTTCAAGAATCAATTTAAAATGAGAA
Found at i:2363624 original size:17 final size:17
Alignment explanation
Indices: 2363568--2363622 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
2363558 AAAATTTAAA
2363568 TAAACTAAATCTATATT
1 TAAACTAAATCTATATT
2363585 TAAACTAAATCTATATT
1 TAAACTAAATCTATATT
* *
2363602 TAAATTAAATTTATATT
1 TAAACTAAATCTATATT
2363619 TAAA
1 TAAA
2363623 TTGATTGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAACTAAATCTATATT
Found at i:2374658 original size:30 final size:30
Alignment explanation
Indices: 2374623--2374706 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
2374613 ACCATTGGCC
*
2374623 TAAAATAATATTAGAATTTATTAAAATATTA
1 TAAAATAATATTA-AATTTATCAAAATATTA
* * *
2374654 -AAAATAATTATTAATTTTATCGAATTATTA
1 TAAAATAA-TATTAAATTTATCAAAATATTA
* *
2374684 TAAAATAATGTTTCAATTTATCA
1 TAAAATAAT-ATTAAATTTATCA
2374707 TTATTTTATA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
30 21 0.50
31 21 0.50
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (30 bp):
TAAAATAATATTAAATTTATCAAAATATTA
Found at i:2374689 original size:31 final size:32
Alignment explanation
Indices: 2374623--2374692 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
2374613 ACCATTGGCC
*
2374623 TAAAATAA-TATTAGAATTTATTAAAATATTA
1 TAAAATAATTATTAGAATTTATCAAAATATTA
* * *
2374654 -AAAATAATTATTA-ATTTTATCGAATTATTA
1 TAAAATAATTATTAGAATTTATCAAAATATTA
2374684 TAAAATAAT
1 TAAAATAAT
2374693 GTTTCAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (32 bp):
TAAAATAATTATTAGAATTTATCAAAATATTA
Found at i:2383347 original size:59 final size:60
Alignment explanation
Indices: 2383237--2383349 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 60
2383227 GAGCCTCTAC
* * * * *
2383237 TTTAAATTAATTCTTAAACTTTTGAATATTTTAATTTCATCCTTGAACTATGACTCTTAT
1 TTTAAATTAATCCTTAAACTTTTAAACATTCTAATTTCATCCCTGAACTATGACTCTTAT
*
2383297 TTTAAATTAGTCCTTAAA-TTTTAAACATTCTAATTTCATCCCT-AACCTATGAC
1 TTTAAATTAATCCTTAAACTTTTAAACATTCTAATTTCATCCCTGAA-CTATGAC
2383350 CCTCTTTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 2 0.04
59 28 0.61
60 16 0.35
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (60 bp):
TTTAAATTAATCCTTAAACTTTTAAACATTCTAATTTCATCCCTGAACTATGACTCTTAT
Found at i:2388068 original size:24 final size:20
Alignment explanation
Indices: 2388017--2388054 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2388007 TTCCCATTGA
*
2388017 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
2388037 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
2388055 TTAACAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2389681 original size:28 final size:31
Alignment explanation
Indices: 2389618--2389681 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 31
2389608 GAGAGTTTAT
*
2389618 TTTAT-ATTTTAGAATTTTTTTGAATAATAA
1 TTTATAATTTTAGAATTTTTTTAAATAATAA
*
2389648 -TAATAATTTTA-AA-TTTTTTAAATAA-AA
1 TTTATAATTTTAGAATTTTTTTAAATAATAA
2389675 TTTATAA
1 TTTATAA
2389682 ATAAATATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
27 2 0.07
28 16 0.55
29 5 0.17
30 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTATAATTTTAGAATTTTTTTAAATAATAA
Found at i:2389810 original size:11 final size:11
Alignment explanation
Indices: 2389796--2389863 Score: 64
Period size: 11 Copynumber: 5.8 Consensus size: 11
2389786 CCTAACAAGG
2389796 CCCAACCAAAA
1 CCCAACCAAAA
2389807 CCCAACCTAAAA
1 CCCAACC-AAAA
**
2389819 CCCAAATAAAA
1 CCCAACCAAAA
*
2389830 CCTAACCAAAA
1 CCCAACCAAAA
*
2389841 CTCAACCTAAATA
1 CCCAACC-AAA-A
2389854 CCCAAACCAA
1 CCC-AACCAA
2389864 GACCTGACCC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
11 24 0.53
12 12 0.27
13 5 0.11
14 4 0.09
ACGTcount: A:0.53, C:0.38, G:0.00, T:0.09
Consensus pattern (11 bp):
CCCAACCAAAA
Found at i:2389851 original size:23 final size:24
Alignment explanation
Indices: 2389796--2389858 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
2389786 CCTAACAAGG
2389796 CCCAACC-AAAACCCAACCTAAAA
1 CCCAACCTAAAACCCAACCTAAAA
* *
2389819 CCCAA-ATAAAACCTAACC-AAAA
1 CCCAACCTAAAACCCAACCTAAAA
*
2389841 CTCAACCTAAATACCCAA
1 CCCAACCTAAA-ACCCAA
2389859 ACCAAGACCT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 8 0.25
23 19 0.59
24 5 0.16
ACGTcount: A:0.52, C:0.38, G:0.00, T:0.10
Consensus pattern (24 bp):
CCCAACCTAAAACCCAACCTAAAA
Found at i:2390882 original size:34 final size:34
Alignment explanation
Indices: 2390839--2390911 Score: 130
Period size: 34 Copynumber: 2.2 Consensus size: 34
2390829 TTTCCCCTTA
*
2390839 TATTT-TATGTTATATATTTTTTGGTTAATTCAC
1 TATTTATATGTTATATATTTTTTGCTTAATTCAC
2390872 TATTTATATGTTATATATTTTTTGCTTAATTCAC
1 TATTTATATGTTATATATTTTTTGCTTAATTCAC
2390906 TATTTA
1 TATTTA
2390912 GTCCCTCTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 5 0.13
34 33 0.87
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (34 bp):
TATTTATATGTTATATATTTTTTGCTTAATTCAC
Found at i:2396945 original size:23 final size:23
Alignment explanation
Indices: 2396910--2396982 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2396900 ATACTTTACA
*
2396910 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2396933 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2396956 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2396979 ATAT
1 ATAT
2396983 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2397377 original size:23 final size:23
Alignment explanation
Indices: 2397351--2397413 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2397341 ATATAACCAC
2397351 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2397374 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2397397 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2397414 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2397788 original size:427 final size:429
Alignment explanation
Indices: 2396744--2398037 Score: 2370
Period size: 431 Copynumber: 3.0 Consensus size: 429
2396734 ATGTTTATTG
2396744 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
*
2396809 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCTACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
* * *
2396874 TATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
*
2396939 ACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
*
2397004 TGTCAATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
261 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TT
*
2397069 TTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
325 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
2397134 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
390 TTATTTGATTGTTTTGATATTTTATAAAAT-ATATTTAGAA
* *
2397175 TTTTTAATTTAATAATAATATATATAGTAACATAAAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
2397240 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
2397305 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
2397370 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
*
2397435 TGCCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
261 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
2397500 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
326 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
2397565 TATTTGATTGTTTTGATATTTTATAAAATATATTTAGAA
391 TATTTGATTGTTTTGATATTTTATAAAATATATTTAGAA
*
2397604 TTTTTAATTTAATAAT-A-ATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
* *
2397667 AAATTAATATCTTAAAACTTACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
2397732 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
2397797 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
2397862 TGTCCATACTTTTTAT-AAAAGGATCGATACTTC-TTTAAAGTTATGTAATTTATGTTTCAATTT
261 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
*
2397925 TTTTAATAGTG-TTCATGTTTTCCACCTACAATA-TAATTTAATAATTTCATTTACACAAAAAAT
326 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
2397988 TATTTGATTGTTTTGATATTTTATAAAATA-ATATTAGAA
391 TATTTGATTGTTTTGATATTTTATAAAATATAT-TTAGAA
*
2398027 -TTTAAATTTAA
1 TTTTTAATTTAA
2398038 CAACATTAAC
Statistics
Matches: 844, Mismatches: 18, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
422 12 0.01
423 65 0.08
424 22 0.03
425 41 0.05
426 17 0.02
427 251 0.30
428 1 0.00
429 26 0.03
430 96 0.11
431 313 0.37
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (429 bp):
TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
TATTTGATTGTTTTGATATTTTATAAAATATATTTAGAA
Found at i:2397804 original size:23 final size:23
Alignment explanation
Indices: 2397778--2397840 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2397768 ATATAACCAC
2397778 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2397801 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2397824 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2397841 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2398206 original size:25 final size:25
Alignment explanation
Indices: 2398178--2398242 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
2398168 GCTCAAAAGA
*
2398178 TGTATATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
2398203 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
2398228 TGTACATACCTAAAT
1 TGTACATACCTAAAT
2398243 TTAATGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:2400789 original size:177 final size:177
Alignment explanation
Indices: 2400491--2401145 Score: 1060
Period size: 177 Copynumber: 3.7 Consensus size: 177
2400481 CTTAAATTAC
* * *
2400491 CGACACTTTTT-A-AATGGTATCGACACATTTTTCTTTCAATATGGACATAAAGTACCAACACAA
1 CGACACTTTTTGACAAT-GTATCGACACA-TTTTCTTCCAATCTGGACATAAAGTACCGA-ACAA
*
2400554 TATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAATCGGTATATTTATACCGGT
63 TATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGT
*
2400619 TATA-CA-AAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
128 TATATTACAAA--ATCTATTACATTATAAAT-TGGGTTCCGATGTGTAAATGT
2400670 CGACACTTTTT-A-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCG-ACAAT
1 CGACACTTTTTGACAAT-GTATCGACACA-TTTTCTTCCAATCTGGACATAAAGTACCGAACAAT
* *
2400732 ATTAGAAACTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATATCGGTT
64 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
*
2400797 ATATTACAAAAT-TATTACATTATAATTATGGGTT-CGATGTGTAAATGT
129 ATATTACAAAATCTATTACATTATAAAT-TGGGTTCCGATGTGTAAATGT
2400845 CGACACTTTTTGACAATGTATCGACACATTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
1 CGACACTTTTTGACAATGTATCGACACATTTTCTTCCAATCTGGACATAAAGTACCGA-ACAATA
2400910 TTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
65 TTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
2400975 TATTACAAAATCTATTACATTAT-AATTGGGTTCCGATGTGTAAATGT
130 TATTACAAAATCTATTACATTATAAATTGGGTTCCGATGTGTAAATGT
2401022 CGACACTTTTTGACAATGTATCGACACATTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
1 CGACACTTTTTGACAATGTATCGACACATTTTCTTCCAATCTGGACATAAAGTACCGA-ACAATA
*
2401087 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATAC
65 TTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATAC
2401146 GATAGCATTG
Statistics
Matches: 455, Mismatches: 13, Indels: 18
0.94 0.03 0.04
Matches are distributed among these distances:
175 54 0.12
176 38 0.08
177 294 0.65
178 12 0.03
179 57 0.13
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (177 bp):
CGACACTTTTTGACAATGTATCGACACATTTTCTTCCAATCTGGACATAAAGTACCGAACAATAT
TAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTAT
ATTACAAAATCTATTACATTATAAATTGGGTTCCGATGTGTAAATGT
Found at i:2403140 original size:12 final size:12
Alignment explanation
Indices: 2403123--2403211 Score: 79
Period size: 12 Copynumber: 7.2 Consensus size: 12
2403113 ACTTGTTTGG
2403123 ATCATCATCTTC
1 ATCATCATCTTC
2403135 ATCATCATCATCATC
1 ATCATCATC-T--TC
*
2403150 GTCATCATCTTC
1 ATCATCATCTTC
* *
2403162 ATCGTCAGCTTC
1 ATCATCATCTTC
*
2403174 ATCATCATCGTC
1 ATCATCATCTTC
* *
2403186 ATCTTCATCGTC
1 ATCATCATCTTC
* *
2403198 AGCTTCATCTTC
1 ATCATCATCTTC
2403210 AT
1 AT
2403212 GACCGCTTGG
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
12 51 0.81
13 1 0.02
14 1 0.02
15 10 0.16
ACGTcount: A:0.22, C:0.33, G:0.07, T:0.38
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:2403142 original size:6 final size:6
Alignment explanation
Indices: 2403123--2403194 Score: 72
Period size: 6 Copynumber: 12.0 Consensus size: 6
2403113 ACTTGTTTGG
* * * * *
2403123 ATCATC ATCTTC ATCATC ATCATC ATCGTC ATCATC TTCATC GTCAGC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * *
2403171 TTCATC ATCATC GTCATC TTCATC
1 ATCATC ATCATC ATCATC ATCATC
2403195 GTCAGCTTCA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.38
Consensus pattern (6 bp):
ATCATC
Found at i:2403146 original size:18 final size:18
Alignment explanation
Indices: 2403123--2403211 Score: 88
Period size: 18 Copynumber: 4.8 Consensus size: 18
2403113 ACTTGTTTGG
2403123 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
*
2403141 ATCATCATCGTCATCATCTTC
1 ATCATCATC-T--TCATCATC
* *
2403162 ATCGTCAGCTTCATCATC
1 ATCATCATCTTCATCATC
* *
2403180 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
2403198 AGCTTCATCTTCAT
1 ATCATCATCTTCAT
2403212 GACCGCTTGG
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
18 44 0.73
19 1 0.02
20 1 0.02
21 14 0.23
ACGTcount: A:0.22, C:0.33, G:0.07, T:0.38
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:2403209 original size:6 final size:6
Alignment explanation
Indices: 2403127--2403211 Score: 71
Period size: 6 Copynumber: 13.7 Consensus size: 6
2403117 GTTTGGATCA
* * * * *
2403127 TCATCT TCATCA TCATCA TCATCGT CATCATCT TCATCG TCAGCT TCATCA
1 TCATCT TCATCT TCATCT TCATC-T --TCATCT TCATCT TCATCT TCATCT
* * *
2403178 TCATCG TCATCT TCATCG TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
2403212 GACCGCTTGG
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
6 57 0.90
8 1 0.02
9 5 0.08
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (6 bp):
TCATCT
Done.