Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008281.1 Hibiscus syriacus cultivar Beakdansim tig00110943_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: 2054746
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1321211 original size:20 final size:20
Alignment explanation
Indices: 1321148--1321219 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1321138 GAATACGTAC
*
1321148 ATCGCAATGCAAATCTGACT
1 ATCGCAATGCGAATCTGACT
*
1321168 ATCGCAATGCGAATAC-GTA-A
1 ATCGCAATGCGAAT-CTG-ACT
1321188 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
1321208 ATCGCAATGCGA
1 ATCGCAATGCGA
1321220 TTTACATAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
19 2 0.04
20 41 0.91
21 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGACT
Found at i:1321815 original size:20 final size:20
Alignment explanation
Indices: 1321790--1321838 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1321780 CAACGAGTGA
1321790 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1321810 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1321830 ATCGCAACG
1 ATCGCAACG
1321839 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1321905 original size:20 final size:20
Alignment explanation
Indices: 1321880--1321929 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1321870 TGCGATTCTT
1321880 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
1321900 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
1321920 GTGTTGCGAT
1 GCGTTGCGAT
1321930 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:1321935 original size:20 final size:20
Alignment explanation
Indices: 1321897--1321951 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1321887 GATAGTCAAA
* **
1321897 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
1321917 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
1321937 TTCGTGTTGCAATTT
1 TTCGTGTTGCGATTT
1321952 AAAGTTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1321959 original size:20 final size:20
Alignment explanation
Indices: 1321916--1321959 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1321906 CGATAGTCAT
* ** *
1321916 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCAATTTAAAG
1321936 TTTCGTGTTGCAATTTAAAG
1 TTTCGTGTTGCAATTTAAAG
1321956 TTTC
1 TTTC
1321960 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTAAAG
Found at i:1323842 original size:20 final size:20
Alignment explanation
Indices: 1323817--1323920 Score: 130
Period size: 20 Copynumber: 5.5 Consensus size: 20
1323807 AGAATAGTTT
1323817 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1323837 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1323853 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1323871 ACTATCACAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1323891 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1323911 ACTATCGCAA
1 ACTATCGCAA
1323921 CGAAAGAATC
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
14 7 0.10
16 4 0.06
17 4 0.06
18 4 0.06
20 53 0.74
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1323863 original size:34 final size:34
Alignment explanation
Indices: 1323820--1323941 Score: 154
Period size: 34 Copynumber: 3.4 Consensus size: 34
1323810 ATAGTTTACT
*
1323820 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
*
1323854 ATCGCAATGCGAAAATGACTATCACAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
**
1323892 CTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
1323928 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1323942 TGAAAATCGC
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
34 39 0.51
36 4 0.05
37 5 0.07
38 4 0.05
40 24 0.32
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:1324026 original size:87 final size:87
Alignment explanation
Indices: 1323935--1324100 Score: 260
Period size: 87 Copynumber: 1.9 Consensus size: 87
1323925 AGAATCGCAA
1323935 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
*
1324000 TTTCGCGTTGCGATTTTGATAT
66 TTTCGCATTGCGATTTTGATAT
** ** ** *
1324022 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTTAAATTCGCATTGCGATAGTCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1324087 TTTCGCATTGCGAT
66 TTTCGCATTGCGAT
1324101 AGTCATTTTC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (87 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGATAT
Found at i:1324106 original size:20 final size:20
Alignment explanation
Indices: 1323967--1324120 Score: 93
Period size: 20 Copynumber: 8.3 Consensus size: 20
1323957 GATTCTCTCG
**
1323967 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1323987 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
1324007 TTGC----G--ATTTT-GATA
1 TTGCGATAGTCATTTTCG-CA
**
1324021 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1324040 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
* **
1324054 TTGCGATAGTTAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1324074 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
1324094 TTGCGATAGTCATTTTCACG
1 TTGCGATAGTCATTTTCGCA
1324114 TTGCGAT
1 TTGCGAT
1324121 TTTAAGTTTC
Statistics
Matches: 104, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
13 1 0.01
14 16 0.15
16 6 0.06
17 2 0.02
18 3 0.03
19 11 0.11
20 65 0.62
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1326081 original size:14 final size:14
Alignment explanation
Indices: 1326062--1326097 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1326052 ATTGTTTAAT
1326062 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1326076 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1326090 TGATTTGT
1 TGATTTGT
1326098 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:1326287 original size:34 final size:33
Alignment explanation
Indices: 1326199--1326294 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
1326189 AAAACAGACT
* **
1326199 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
1326233 ATCGCAATGCGAAATGAAAATCGTAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1326266 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
1326295 CGAAGCTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1326329 original size:20 final size:19
Alignment explanation
Indices: 1326303--1326503 Score: 116
Period size: 20 Copynumber: 10.8 Consensus size: 19
1326293 CGCGAAGCTA
*
1326303 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATATTC
*
1326322 ATTTTCGCATTGCG--ATTC
1 A-TTTCGCGTTGCGATATTC
* *
1326340 A---CTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATATTC
* * *
1326356 AATTCGCATTGCGATTTTC
1 ATTTCGCGTTGCGATATTC
*
1326375 ATTTCGCATTGCG--ATTC
1 ATTTCGCGTTGCGATATTC
* *
1326392 ---TCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATATTC
*
1326408 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGATATTC
*
1326428 AATTTCGCGTTGCGATAGTC
1 -ATTTCGCGTTGCGATATTC
* * * *
1326448 AATTACGCATTTCGATAGTC
1 -ATTTCGCGTTGCGATATTC
* *
1326468 ATTTCCGTGTTGCGATAGTC
1 ATTT-CGCGTTGCGATATTC
1326488 ATATTCGCGTTGCGAT
1 AT-TTCGCGTTGCGAT
1326504 TTCTGCGTTG
Statistics
Matches: 146, Mismatches: 21, Indels: 29
0.74 0.11 0.15
Matches are distributed among these distances:
14 15 0.10
16 7 0.05
17 3 0.02
18 4 0.03
19 30 0.21
20 81 0.55
21 6 0.04
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40
Consensus pattern (19 bp):
ATTTCGCGTTGCGATATTC
Found at i:1326464 original size:40 final size:40
Alignment explanation
Indices: 1326395--1326503 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 40
1326385 GCGATTCTCT
* * *
1326395 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAATTT-CG
1 CGTTGCGATAGTCAATTACGCATTGCGATAGTC-ATTTCCG
*
1326435 CGTTGCGATAGTCAATTACGCATTTCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTACGCATTGCGATAGTCATTTCCG
* *
1326475 TGTTGCGATAGTCATATT-CGCGTTGCGAT
1 CGTTGCGATAGTCA-ATTACGCATTGCGAT
1326504 TTCTGCGTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
39 4 0.07
40 53 0.88
41 3 0.05
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCAATTACGCATTGCGATAGTCATTTCCG
Found at i:1329958 original size:20 final size:20
Alignment explanation
Indices: 1329840--1329992 Score: 132
Period size: 20 Copynumber: 7.7 Consensus size: 20
1329830 CGATAGTCAG
*
1329840 AATCTCGTTGCGATTTACAG-
1 AATCGCGTTGCGATTTAC-GT
* * *
1329860 ATTTGCATTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
* * * * *
1329880 ATTCGCATTGCAATAGT-CAT
1 AATCGCGTTGCGAT-TTACGT
* *
1329900 ATTCGCATTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
* * *
1329920 ATTCACGTTGCGGTTTACGT
1 AATCGCGTTGCGATTTACGT
1329940 AATCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
1329960 AATCGCGTT-CTGATTTACGT
1 AATCGCGTTGC-GATTTACGT
1329980 AATCGCGTTGCGA
1 AATCGCGTTGCGA
1329993 ATTAGGGAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
19 3 0.03
20 106 0.95
21 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
AATCGCGTTGCGATTTACGT
Found at i:1334450 original size:14 final size:14
Alignment explanation
Indices: 1334431--1334466 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1334421 CAATGGAGCG
1334431 GCCCAAATCAGTTA
1 GCCCAAATCAGTTA
*
1334445 GCCCAAATCAGTTG
1 GCCCAAATCAGTTA
1334459 GCCCAAAT
1 GCCCAAAT
1334467 GAAGGCTGAG
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:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (14 bp):
GCCCAAATCAGTTA
Found at i:1337363 original size:140 final size:140
Alignment explanation
Indices: 1337111--1337387 Score: 446
Period size: 140 Copynumber: 2.0 Consensus size: 140
1337101 TCACGAAACA
* * *
1337111 CCCCGCTGATCGAGCTAAAATCAGCGGTGGTGGAGACTACTCCATTAGAGTTAAGGCATATCCAA
1 CCCCGCCGATCGAGCTAAAACCAACGGTGGTGGAGACTACTCCATTAGAGTTAAGGCATATCCAA
* * * *
1337176 TTAGGTGAGAGACGTTGCCATTGAATCATCTCCATCACAAGTTGACGAGTAGAGGACTTGTGGGT
66 TGACGAGAGAGACGTTGCCATTGAATCATCTCCATCACAAGTTGACGAGTAGAGGACTTATGGGT
1337241 GATAGAAGAG
131 GATAGAAGAG
* *
1337251 CCCCGCCGATCGAGCTAAAACCAATGGTGGTGGAGACTACTCCATTAGAGTTGAGGCATATCCAA
1 CCCCGCCGATCGAGCTAAAACCAACGGTGGTGGAGACTACTCCATTAGAGTTAAGGCATATCCAA
* * *
1337316 TGACGAGAGGGAGGTTGCCATTGAATCGTCTCCATCACAAGTTGACGAGTAGAGGACTTATGGGT
66 TGACGAGAGAGACGTTGCCATTGAATCATCTCCATCACAAGTTGACGAGTAGAGGACTTATGGGT
1337381 GATAGAA
131 GATAGAA
1337388 AATCCATAGA
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (140 bp):
CCCCGCCGATCGAGCTAAAACCAACGGTGGTGGAGACTACTCCATTAGAGTTAAGGCATATCCAA
TGACGAGAGAGACGTTGCCATTGAATCATCTCCATCACAAGTTGACGAGTAGAGGACTTATGGGT
GATAGAAGAG
Found at i:1338635 original size:12 final size:12
Alignment explanation
Indices: 1338615--1338645 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1338605 TATTTGATAA
*
1338615 CATACCACATTT
1 CATATCACATTT
1338627 CATATCACATTT
1 CATATCACATTT
1338639 CATATCA
1 CATATCA
1338646 ATCATGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (12 bp):
CATATCACATTT
Found at i:1340033 original size:21 final size:21
Alignment explanation
Indices: 1340007--1340062 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
1339997 TTTTCCATAA
*
1340007 AAAGGATTGATCTCTTAGGGG
1 AAAGGATTGATCCCTTAGGGG
*
1340028 AAAGGATTTATCCCTTAGGGG
1 AAAGGATTGATCCCTTAGGGG
*
1340049 AAAGGATCGATCCC
1 AAAGGATTGATCCC
1340063 CTTGGCCAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (21 bp):
AAAGGATTGATCCCTTAGGGG
Found at i:1341177 original size:10 final size:10
Alignment explanation
Indices: 1341162--1341187 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1341152 AGCTCTCCTC
1341162 CAGCTAAGTT
1 CAGCTAAGTT
1341172 CAGCTAAGTT
1 CAGCTAAGTT
1341182 CAGCTA
1 CAGCTA
1341188 CATGCTAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (10 bp):
CAGCTAAGTT
Found at i:1342135 original size:15 final size:15
Alignment explanation
Indices: 1342102--1342140 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1342092 TGTTTATTAT
*
1342102 TTTATTCATCTTTCA
1 TTTATTTATCTTTCA
**
1342117 TTTATTTATCTTTTG
1 TTTATTTATCTTTCA
1342132 TTTATTTAT
1 TTTATTTAT
1342141 TCTAATCGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTATTTATCTTTCA
Found at i:1342527 original size:13 final size:12
Alignment explanation
Indices: 1342511--1342559 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
1342501 AAAAAAACAC
1342511 AAAAAAGGCAAAA
1 AAAAAAGGC-AAA
1342524 AAAAAAGGC-AA
1 AAAAAAGGCAAA
*
1342535 AAAAAAGGCACA
1 AAAAAAGGCAAA
*
1342547 AAAAAAGCCAAA
1 AAAAAAGGCAAA
1342559 A
1 A
1342560 TTTCAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.34
12 12 0.38
13 9 0.28
ACGTcount: A:0.73, C:0.12, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGGCAAA
Found at i:1342527 original size:24 final size:24
Alignment explanation
Indices: 1342495--1342552 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1342485 TGTAAAAAAT
*
1342495 AAAACAAAAAAAACACAAAAAAGGC
1 AAAA-AAAAAAAACAAAAAAAAGGC
**
1342520 AAAAAAAAAAGGCAAAAAAAAGGC
1 AAAAAAAAAAAACAAAAAAAAGGC
*
1342544 ACAAAAAAA
1 AAAAAAAAA
1342553 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAAACAAAAAAAAGGC
Found at i:1345147 original size:9 final size:9
Alignment explanation
Indices: 1345133--1345168 Score: 72
Period size: 9 Copynumber: 4.0 Consensus size: 9
1345123 TCATAACTCG
1345133 GATATTTCT
1 GATATTTCT
1345142 GATATTTCT
1 GATATTTCT
1345151 GATATTTCT
1 GATATTTCT
1345160 GATATTTCT
1 GATATTTCT
1345169 ACCCATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:1348401 original size:200 final size:202
Alignment explanation
Indices: 1348058--1348461 Score: 794
Period size: 200 Copynumber: 2.0 Consensus size: 202
1348048 ATTCATTGCC
1348058 ACATGTTGTATGATGTATGATTTAAATTTGTATGTTTCTGCTTAGTGCACATGATTTAGGGTTTG
1 ACATGTTGTATGATGTATGATTTAAATTTGTATGTTTCTGCTTAGTGCACATGATTTAGGGTTTG
1348123 GTTCTGTCTAACAAGATCGAAATCTAATGTATGCTTAGGTAGCCGAGTATTTCTTCGTGATAGGG
66 GTTCTGTCTAACAAGATCGAAATCTAATGTATGCTTAGGTAGCCGAGTATTTCTTCGTGATAGGG
1348188 TATGGGGTGTTACAG-CCCATTA-GTCGTTTCCAACTTTTCCATAGCAGCGCACTGAAGAGAAGG
131 TATGGGGTGTTACAGCCCCATTATGTCGTTTCCAACTTTTCCATAGCAGCGCACTGAAGAGAAGG
1348251 TTCCAAT
196 TTCCAAT
1348258 ACATGTTGTATGATGTATGATTTAAATTTGTATGTTTCTGCTTAGTGCACATGATTTAGGGTTTG
1 ACATGTTGTATGATGTATGATTTAAATTTGTATGTTTCTGCTTAGTGCACATGATTTAGGGTTTG
1348323 GTTCTGTCTAACAAGATCGAAATCTAATGTATGCTTAGGTAGCCGAGTATTTCTTCGTGATAGGG
66 GTTCTGTCTAACAAGATCGAAATCTAATGTATGCTTAGGTAGCCGAGTATTTCTTCGTGATAGGG
1348388 TATGGGGTGTTACAGCCCCATTATGTCGTTTCCAACTTTTCCATAGCAGCGCACTGAAGAGAAGG
131 TATGGGGTGTTACAGCCCCATTATGTCGTTTCCAACTTTTCCATAGCAGCGCACTGAAGAGAAGG
1348453 TTCCAAT
196 TTCCAAT
1348460 AC
1 AC
1348462 GTCCTTCATT
Statistics
Matches: 202, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
200 145 0.72
201 7 0.03
202 50 0.25
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (202 bp):
ACATGTTGTATGATGTATGATTTAAATTTGTATGTTTCTGCTTAGTGCACATGATTTAGGGTTTG
GTTCTGTCTAACAAGATCGAAATCTAATGTATGCTTAGGTAGCCGAGTATTTCTTCGTGATAGGG
TATGGGGTGTTACAGCCCCATTATGTCGTTTCCAACTTTTCCATAGCAGCGCACTGAAGAGAAGG
TTCCAAT
Found at i:1356074 original size:2 final size:2
Alignment explanation
Indices: 1356067--1356106 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1356057 TATATCCTTT
1356067 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
1356107 CAAAATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1356509 original size:21 final size:19
Alignment explanation
Indices: 1356483--1356526 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
1356473 GAAAGGTGTT
*
1356483 AATACCCTTGAGTATAGTATC
1 AATACCCATG-GTA-AGTATC
1356504 AATA-CCATGGTAAGTATC
1 AATACCCATGGTAAGTATC
1356522 AATAC
1 AATAC
1356527 TAAGGGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.48
19 3 0.14
20 4 0.19
21 4 0.19
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (19 bp):
AATACCCATGGTAAGTATC
Found at i:1357338 original size:16 final size:17
Alignment explanation
Indices: 1357317--1357349 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1357307 ACATAAGGAT
*
1357317 GAATCCATCTC-TAAAA
1 GAATCCAGCTCATAAAA
1357333 GAATCCAGCTCATAAAA
1 GAATCCAGCTCATAAAA
1357350 ATATTGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.21
Consensus pattern (17 bp):
GAATCCAGCTCATAAAA
Found at i:1357844 original size:12 final size:13
Alignment explanation
Indices: 1357816--1357848 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1357806 CAATCTACTC
1357816 CAACATCAGCGTA
1 CAACATCAGCGTA
*
1357829 CAACATCGGC-TA
1 CAACATCAGCGTA
1357841 CAACATCA
1 CAACATCA
1357849 ACAATGTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.39, C:0.33, G:0.12, T:0.15
Consensus pattern (13 bp):
CAACATCAGCGTA
Found at i:1398922 original size:55 final size:55
Alignment explanation
Indices: 1398862--1399076 Score: 286
Period size: 55 Copynumber: 3.9 Consensus size: 55
1398852 CTATACGGTA
* ** * * * *
1398862 ATTCATCAACTCATGCTGAATTCTATGGTTTTGTACACATAGTGCTTGTACAATT
1 ATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACATAGTGCATGTACGACT
* * *
1398917 ATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACATATTGCCTGCACGACT
1 ATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACATAGTGCATGTACGACT
* * * * *
1398972 ATTCATCAACTCATGAGGAATTCTGTGGTTTTTCACACATAGTTCATGTACGGCT
1 ATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACATAGTGCATGTACGACT
*
1399027 ATTCATCAACTCATGATGAATTCCGTGGTTATGCACACATAGTGCATGTA
1 ATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACATAGTGCATGTA
1399077 GTACACTTAG
Statistics
Matches: 138, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 138 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACATAGTGCATGTACGACT
Found at i:1398982 original size:110 final size:110
Alignment explanation
Indices: 1398862--1399067 Score: 315
Period size: 110 Copynumber: 1.9 Consensus size: 110
1398852 CTATACGGTA
** * *
1398862 ATTCATCAACTCATGCTGAATTCTATGGTTTTGT-ACACATAGTGCTTGTACAATTATTCATCAA
1 ATTCATCAACTCATGAGGAATTCTATGGTTTT-TCACACATAGTGCATGTACAACTATTCATCAA
*
1398926 CTCATGATGAATTCCGTGGTTTTGCACACATATTGCCTGCACGACT
65 CTCATGATGAATTCCGTGGTTATGCACACATATTGCCTGCACGACT
* * **
1398972 ATTCATCAACTCATGAGGAATTCTGTGGTTTTTCACACATAGTTCATGTACGGCTATTCATCAAC
1 ATTCATCAACTCATGAGGAATTCTATGGTTTTTCACACATAGTGCATGTACAACTATTCATCAAC
1399037 TCATGATGAATTCCGTGGTTATGCACACATA
66 TCATGATGAATTCCGTGGTTATGCACACATA
1399068 GTGCATGTAG
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
109 1 0.01
110 85 0.99
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (110 bp):
ATTCATCAACTCATGAGGAATTCTATGGTTTTTCACACATAGTGCATGTACAACTATTCATCAAC
TCATGATGAATTCCGTGGTTATGCACACATATTGCCTGCACGACT
Found at i:1399423 original size:20 final size:20
Alignment explanation
Indices: 1399395--1399434 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1399385 ATTTCTGGCT
*
1399395 CCATAGTATTGATACTACTA
1 CCATAGTATCGATACTACTA
*
1399415 CCATGGTATCGATACTACTA
1 CCATAGTATCGATACTACTA
1399435 TACTATAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (20 bp):
CCATAGTATCGATACTACTA
Found at i:1399520 original size:20 final size:20
Alignment explanation
Indices: 1399495--1399544 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1399485 GTTTCGAAAT
1399495 GGTATCGATACCTT-CCCTTC
1 GGTATCGATA-CTTCCCCTTC
*
1399515 GGTATCGATATTTCCCCTTC
1 GGTATCGATACTTCCCCTTC
*
1399535 GATATCGATA
1 GGTATCGATA
1399545 TTGATTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (20 bp):
GGTATCGATACTTCCCCTTC
Found at i:1399545 original size:20 final size:20
Alignment explanation
Indices: 1399509--1399546 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1399499 TCGATACCTT
*
1399509 CCCTTCGGTATCGATATTTC
1 CCCTTCGATATCGATATTTC
1399529 CCCTTCGATATCGATATT
1 CCCTTCGATATCGATATT
1399547 GATTCAATCA
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:0.18, C:0.29, G:0.13, T:0.39
Consensus pattern (20 bp):
CCCTTCGATATCGATATTTC
Found at i:1407530 original size:13 final size:13
Alignment explanation
Indices: 1407512--1407536 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1407502 GTAAGAAAAA
1407512 GAAAAGGAGAAAT
1 GAAAAGGAGAAAT
1407525 GAAAAGGAGAAA
1 GAAAAGGAGAAA
1407537 GAGAAAATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (13 bp):
GAAAAGGAGAAAT
Found at i:1407554 original size:25 final size:26
Alignment explanation
Indices: 1407507--1407579 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
1407497 TTGTTGTAAG
* **
1407507 AAAAAGAAAAGGAGAAATGAAAAG-GA
1 AAAAAGAAAAGCA-AAAAAAAAAGAGA
* *
1407533 GAAAGAGAAAATCAAAAAAAAAAGAGA
1 -AAAAAGAAAAGCAAAAAAAAAAGAGA
*
1407560 AAAAAGAAAAGGAAAAAAAA
1 AAAAAGAAAAGCAAAAAAAA
1407580 TGAAAGGAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
26 25 0.68
27 12 0.32
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.03
Consensus pattern (26 bp):
AAAAAGAAAAGCAAAAAAAAAAGAGA
Found at i:1407590 original size:27 final size:27
Alignment explanation
Indices: 1407506--1407591 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
1407496 ATTGTTGTAA
*
1407506 GAAAAAGAAAAGG---AGAAATGAAAAG
1 GAAAAAGAAAAGGAAAAAAAATG-AAAG
**
1407531 GAGAAAGAGAAAATCAAAAAAAA--AAGAG
1 GA-AAA-AGAAAAGGAAAAAAAATGAA-AG
*
1407559 AAAAAAGAAAAGGAAAAAAAATGAAAG
1 GAAAAAGAAAAGGAAAAAAAATGAAAG
1407586 GAAAAA
1 GAAAAA
1407592 AAAGAAAGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
25 2 0.04
26 17 0.37
27 18 0.39
28 5 0.11
30 4 0.09
ACGTcount: A:0.73, C:0.01, G:0.22, T:0.03
Consensus pattern (27 bp):
GAAAAAGAAAAGGAAAAAAAATGAAAG
Found at i:1407599 original size:14 final size:14
Alignment explanation
Indices: 1407546--1407599 Score: 67
Period size: 15 Copynumber: 3.9 Consensus size: 14
1407536 AGAGAAAATC
1407546 AAAAAAA-AAA-GA
1 AAAAAAAGAAAGGA
*
1407558 GAAAAAAGAAAAGGA
1 AAAAAAAG-AAAGGA
1407573 AAAAAAATGAAAGGA
1 AAAAAAA-GAAAGGA
1407588 AAAAAAAGAAAG
1 AAAAAAAGAAAG
1407600 AATAAGAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
12 6 0.17
14 8 0.22
15 21 0.58
16 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAGGA
Found at i:1410017 original size:31 final size:31
Alignment explanation
Indices: 1409955--1410047 Score: 100
Period size: 31 Copynumber: 3.0 Consensus size: 31
1409945 GTCAATAAAG
*
1409955 TTTAAAAAATTATAAAA-TACTTATTAAATTT
1 TTTAAAAAATTATAAAATTA-TTATTATATTT
* *
1409986 TTTAAAAGATTATAAAATTATTAATATATTT
1 TTTAAAAAATTATAAAATTATTATTATATTT
* *
1410017 TATCT-AAATACTATAAAATTATTATTATATT
1 T-T-TAAAAAATTATAAAATTATTATTATATT
1410048 ATCGAACTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
31 26 0.49
32 26 0.49
33 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (31 bp):
TTTAAAAAATTATAAAATTATTATTATATTT
Found at i:1410205 original size:13 final size:13
Alignment explanation
Indices: 1410187--1410238 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
1410177 CTCATAAATC
1410187 TATGACGCGCATT
1 TATGACGCGCATT
**
1410200 TATGACAAGCATT
1 TATGACGCGCATT
*
1410213 TATGACGTGCATT
1 TATGACGCGCATT
*
1410226 TATGACGCTCATT
1 TATGACGCGCATT
1410239 GCGCATCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:1410398 original size:2 final size:2
Alignment explanation
Indices: 1410391--1410417 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1410381 TTTCGTAAAT
1410391 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1410418 TGTAGATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1413435 original size:110 final size:108
Alignment explanation
Indices: 1413014--1413444 Score: 477
Period size: 107 Copynumber: 4.0 Consensus size: 108
1413004 TGGCGGGTAT
* * *
1413014 GCTCCCTATTCTTTCATG-GAGTATAAGACTCGAACAATCTTCAGTAAACGTGTCTGCTCCCTAT
1 GCTCCCTATTCCTTCA-GAGAGTATAAGACTCGAAC-ATCTTCA-TAAACGGGTCCGCTCCCTAT
* * * *
1413078 TCATTCAGGGAGTATA-AGACTCAAACAATCTTCA-ACAAACGTGTCT
63 TCCTTCAGAGAGTATAGA-ACTCAAACAATCTTCATA-AAACGGGTCC
* * * * *
1413124 GCTCCCTATTCGTTTA-AGGAGTATAAGACTCGATC-T-TTAATAAACGTGTCCGCTCCCTATTC
1 GCTCCCTATTCCTTCAGA-GAGTATAAGACTCGAACATCTTCATAAACGGGTCCGCTCCCTATTC
* * *
1413186 CTTCAGAGAGTATAGGACTCAAACAATCTTCAAAAAACAGGTCC
65 CTTCAGAGAGTATAGAACTCAAACAATCTTCATAAAACGGGTCC
* * * *
1413230 GCGCTCT-TATCCTTCAGAGAGTAT-AGAACTCAAACATCTTCATAAAC-GGTCCGCTCTCTATT
1 GCTCCCTAT-TCCTTCAGAGAGTATAAG-ACTCGAACATCTTCATAAACGGGTCCGCTCCCTATT
*
1413292 CCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
64 CCTTCAGAGAGTATAGAACTCAAACAATCTTCATAAAACGGGTCC
* * *
1413337 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCATAAAATGGGTCCGCTCTCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAAC-ATCTTCAT-AAACGGGTCCGCTCCCTAT
*
1413401 TCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
63 TCCTTCAGAGAGTATAGAACTCAAACAATCTTCATAAAACGGGT
1413445 TTGCTTCACT
Statistics
Matches: 281, Mismatches: 27, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
105 3 0.01
106 78 0.28
107 91 0.32
108 18 0.06
109 3 0.01
110 88 0.31
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (108 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTCATAAACGGGTCCGCTCCCTATTCC
TTCAGAGAGTATAGAACTCAAACAATCTTCATAAAACGGGTCC
Found at i:1413439 original size:55 final size:55
Alignment explanation
Indices: 1413014--1413444 Score: 469
Period size: 55 Copynumber: 8.0 Consensus size: 55
1413004 TGGCGGGTAT
* * *
1413014 GCTCCCTATTCTTTCATG-GAGTATA-AGACTCGAACAATCTTCAGT-AAACGTGTCT
1 GCTCCCTATTCCTTCA-GAGAGTATAGA-ACTCGAACAATCTTCA-TAAAACGGGTCC
* * * * *
1413069 GCTCCCTATTCATTCAGGGAGTATA-AGACTCAAACAATCTTCA-ACAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATA-AAACGGGTCC
* * * * *
1413124 GCTCCCTATTCGTTTA-AGGAGTATA-AGACTCGATC--T-TTAAT-AAACGTGTCC
1 GCTCCCTATTCCTTCAGA-GAGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCC
* * * *
1413175 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAAAAAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
* * *
1413230 GCGCTCT-TATCCTTCAGAGAGTATAGAACTCAAAC-ATCTTCAT-AAAC-GGTCC
1 GCTCCCTAT-TCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
*
1413282 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
* *
1413337 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
*
1413392 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
1413445 TTGCTTCACT
Statistics
Matches: 334, Mismatches: 26, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
51 36 0.11
52 40 0.12
53 15 0.04
54 16 0.05
55 227 0.68
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
Found at i:1413498 original size:37 final size:37
Alignment explanation
Indices: 1413444--1413526 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 37
1413434 ATAAAACGGG
*
1413444 TTTGCTTCACTATTCTTCCGTGAAGGCTTATAGA-TGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTA-AGATTGA
1413481 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
*
1413518 TTTGTTTCA
1 TTTGCTTCA
1413527 AAGATCCAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 3 0.07
37 40 0.93
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.42
Consensus pattern (37 bp):
TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
Found at i:1414832 original size:8 final size:8
Alignment explanation
Indices: 1414804--1414916 Score: 58
Period size: 8 Copynumber: 13.9 Consensus size: 8
1414794 TTCTCTTTTT
1414804 TTTTCTTCA
1 TTTT-TTCA
1414813 TTTTTCTC-
1 TTTTT-TCA
1414821 TTTTTTCA
1 TTTTTTCA
*
1414829 -TTTTCCA
1 TTTTTTCA
1414836 TTTTTTC-
1 TTTTTTCA
**
1414843 TTTTTTTT
1 TTTTTTCA
1414851 TTCTTTTCA
1 TT-TTTTCA
1414860 TTTTTTC-
1 TTTTTTCA
* *
1414867 --CTTTCG
1 TTTTTTCA
1414873 TTTTTTCCA
1 TTTTTT-CA
*
1414882 TCATTTTTCTT
1 T--TTTTTC-A
1414893 TTTTTCTCA
1 TTTTT-TCA
1414902 TTTTTTCA
1 TTTTTTCA
1414910 TTTTTTC
1 TTTTTTC
1414917 TCTTTTATTT
Statistics
Matches: 81, Mismatches: 10, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
5 4 0.05
7 14 0.17
8 31 0.38
9 23 0.28
10 3 0.04
11 6 0.07
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.73
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1414832 original size:25 final size:23
Alignment explanation
Indices: 1414793--1414934 Score: 98
Period size: 25 Copynumber: 5.9 Consensus size: 23
1414783 TCTCCTTTTA
1414793 TTTCTC-TTTTTTTTTCTTCATT
1 TTTCTCTTTTTTTTTTCTTCATT
1414815 TTTCTCTTTTTTCATTTTC--CATT
1 TTTCTCTTTTTT--TTTTCTTCATT
1414838 TTT-TCTTTTTTTTTTCTTTTCATT
1 TTTCTCTTTTTTTTTTC--TTCATT
* *
1414862 TTT-TCCTTTCGTTTTTTCCATCATT
1 TTTCT-CTTT--TTTTTTTCTTCATT
*
1414887 TTTCT-TTTTTTCTCATTTTTTCATTT
1 TTTCTCTTTTTT-T--TTTCTTCA-TT
*
1414913 TTTCTCTTTTATTTCTTCTTCA
1 TTTCTCTTTT-TTTTTTCTTCA
1414935 AGCAAAATAT
Statistics
Matches: 96, Mismatches: 7, Indels: 31
0.72 0.05 0.23
Matches are distributed among these distances:
20 5 0.05
22 17 0.18
23 13 0.14
24 11 0.11
25 28 0.29
26 8 0.08
27 12 0.12
28 2 0.02
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.73
Consensus pattern (23 bp):
TTTCTCTTTTTTTTTTCTTCATT
Found at i:1414863 original size:13 final size:13
Alignment explanation
Indices: 1414821--1414879 Score: 68
Period size: 13 Copynumber: 4.5 Consensus size: 13
1414811 CATTTTTCTC
1414821 TTTTTTCATTTTCCA
1 TTTTTTC-TTTT-CA
1414836 TTTTTTCTTTT--
1 TTTTTTCTTTTCA
1414847 TTTTTTCTTTTCA
1 TTTTTTCTTTTCA
* *
1414860 TTTTTTCCTTTCG
1 TTTTTTCTTTTCA
1414873 TTTTTTC
1 TTTTTTC
1414880 CATCATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
11 11 0.28
13 18 0.45
14 4 0.10
15 7 0.17
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTTCTTTTCA
Found at i:1414880 original size:13 final size:13
Alignment explanation
Indices: 1414834--1414889 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1414824 TTTCATTTTC
1414834 CATTTTTT-CTTT
1 CATTTTTTCCTTT
* *
1414846 -TTTTTTTCTTTT
1 CATTTTTTCCTTT
1414858 CATTTTTTCCTTT
1 CATTTTTTCCTTT
* *
1414871 CGTTTTTTCC-AT
1 CATTTTTTCCTTT
1414883 CATTTTT
1 CATTTTT
1414890 CTTTTTTTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
11 6 0.17
12 10 0.29
13 19 0.54
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (13 bp):
CATTTTTTCCTTT
Found at i:1414890 original size:19 final size:18
Alignment explanation
Indices: 1414868--1414929 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
1414858 CATTTTTTCC
1414868 TTTCGTTTTTTCCATCA-TT
1 TTTC-TTTTTTCC-TCATTT
*
1414887 TTTCTTTTTTTCTCATTT
1 TTTCTTTTTTCCTCATTT
*
1414905 TTTCATTTTTT-CTCTTTT
1 TTTC-TTTTTTCCTCATTT
1414923 ATTTCTT
1 -TTTCTT
1414930 CTTCAAGCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.08
18 21 0.55
19 14 0.37
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTCTTTTTTCCTCATTT
Found at i:1414896 original size:18 final size:19
Alignment explanation
Indices: 1414868--1414916 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
1414858 CATTTTTTCC
*
1414868 TTTCGTTTTTTCCATCA-TT
1 TTTCATTTTTTCC-TCATTT
*
1414887 TTTC-TTTTTTTCTCATTT
1 TTTCATTTTTTCCTCATTT
1414905 TTTCATTTTTTC
1 TTTCATTTTTTC
1414917 TCTTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 3 0.12
18 13 0.50
19 10 0.38
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTCATTTTTTCCTCATTT
Found at i:1414929 original size:9 final size:8
Alignment explanation
Indices: 1414801--1414929 Score: 52
Period size: 8 Copynumber: 15.2 Consensus size: 8
1414791 TATTTCTCTT
1414801 TTTTTTTC
1 TTTTTTTC
1414809 TTCATTTTTC
1 TT--TTTTTC
1414819 TCTTTTTTC
1 T-TTTTTTC
* *
1414828 -ATTTTCC
1 TTTTTTTC
*
1414835 ATTTTTTC
1 TTTTTTTC
1414843 TTTTTTT-
1 TTTTTTTC
1414850 TTTCTTTTC
1 TTT-TTTTC
*
1414859 ATTTTTTC
1 TTTTTTTC
*
1414867 ---CTTTC
1 TTTTTTTC
*
1414872 GTTTTTTCC
1 -TTTTTTTC
*
1414881 ATCATTTTTC
1 -T-TTTTTTC
1414891 TTTTTTTC
1 TTTTTTTC
1414899 TCATTTTTTC
1 T--TTTTTTC
1414909 ATTTTTTCTC
1 -TTTTTT-TC
1414919 TTTTATTTC
1 TTTT-TTTC
1414928 TT
1 TT
1414930 CTTCAAGCAA
Statistics
Matches: 92, Mismatches: 13, Indels: 31
0.68 0.10 0.23
Matches are distributed among these distances:
5 4 0.04
7 8 0.09
8 29 0.32
9 26 0.28
10 23 0.25
11 2 0.02
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1424626 original size:45 final size:47
Alignment explanation
Indices: 1424558--1424646 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
1424548 TGCTTTGTTA
1424558 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTAG
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTAG
*
1424605 TTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
1424647 ATTTATTCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (47 bp):
TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTAG
Found at i:1432473 original size:15 final size:16
Alignment explanation
Indices: 1432453--1432490 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1432443 GTATTGCCCT
*
1432453 AATGCAACGATA-CTA
1 AATGCAAAGATACCTA
1432468 AATGCAAAGATATCCTA
1 AATGCAAAGATA-CCTA
1432485 AATGCA
1 AATGCA
1432491 CAAGCATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.21
Consensus pattern (16 bp):
AATGCAAAGATACCTA
Found at i:1437497 original size:22 final size:22
Alignment explanation
Indices: 1437471--1437519 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1437461 AATTTAAGAA
1437471 CACTTCAGACCTTTAATGAATG
1 CACTTCAGACCTTTAATGAATG
*
1437493 CACTTCAGACCTTTAATGGATG
1 CACTTCAGACCTTTAATGAATG
1437515 CACTT
1 CACTT
1437520 TCACCTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (22 bp):
CACTTCAGACCTTTAATGAATG
Found at i:1437527 original size:21 final size:21
Alignment explanation
Indices: 1437471--1437527 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
1437461 AATTTAAGAA
1437471 CACTTCAGACCTTTAATGAATG
1 CACTTCA-ACCTTTAATGAATG
*
1437493 CACTTCAGACCTTTAATGGATG
1 CACTTCA-ACCTTTAATGAATG
1437515 CACTTTC-ACCTTT
1 CAC-TTCAACCTTT
1437528 TTCTATCCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 6 0.18
22 24 0.73
23 3 0.09
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (21 bp):
CACTTCAACCTTTAATGAATG
Found at i:1437629 original size:20 final size:19
Alignment explanation
Indices: 1437568--1437630 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
1437558 TTCTTTCTTG
*
1437568 AAAGGGATCGATTCTTTTCA
1 AAAGGGATCGATTC-TTTGA
*** *
1437588 CGGGGGATCGATCCTCTTGA
1 AAAGGGATCGATTCT-TTGA
1437608 AAAGGGATCGATTCTTTGGA
1 AAAGGGATCGATTCTTT-GA
1437628 AAA
1 AAA
1437631 CAAAAACTTT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (19 bp):
AAAGGGATCGATTCTTTGA
Found at i:1439070 original size:2 final size:2
Alignment explanation
Indices: 1439063--1439104 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1439053 ACATATTCAA
1439063 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
1439105 TTCGTAAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1441284 original size:79 final size:79
Alignment explanation
Indices: 1441106--1441425 Score: 428
Period size: 79 Copynumber: 4.1 Consensus size: 79
1441096 ACTAATGAAC
* * *
1441106 AAAAGAATAATGCATATGGGTGCGTTAATGGCATGAAAGGATGCCATAGTTGATATGTATAT-GG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGATATGTATATGGG
*
1441170 TACATTATCGGCAT
66 TACATTATCAGCAT
* * *
1441184 AAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATAGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGATATGTATATGGG
1441249 TACATTATCAGCAT
66 TACATTATCAGCAT
* **
1441263 AAAAGAATAATGCATATGGGTGCTTTATTGGCATGAAAATATG-CATTAGCTGATATGTATATGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-TAGCTGATATGTATATGG
*
1441327 GTACATTATCGGCAT
65 GTACATTATCAGCAT
** * * * * * *
1441342 ATCAGAATAATTCATATGGGTGCATTATTGGCATGAAAGGTTGCCAAAGTTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGATATGTATATGGG
* *
1441407 TGCATTATCAACAT
66 TACATTATCAGCAT
1441421 AAAAG
1 AAAAG
1441426 TATGCTATAA
Statistics
Matches: 211, Mismatches: 28, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
78 59 0.28
79 150 0.71
80 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGATATGTATATGGG
TACATTATCAGCAT
Found at i:1441954 original size:81 final size:81
Alignment explanation
Indices: 1441791--1441965 Score: 215
Period size: 81 Copynumber: 2.2 Consensus size: 81
1441781 ATTAAAAGTA
* * * *
1441791 AGTAAAATAATAATGGTTTAAATGGGTAATTGACAGAAAGATGTCGATTATGCTAGATAGATGAA
1 AGTAAAAGAATAATGGTTTAAATGGGCAATTGACAGAAAGATGTCAATTATGCCAGATAGATGAA
** *
1441856 CAGTTAAGTACCGTTG
66 CAGTTAAACACCATTG
* * * *
1441872 AGTAAAAGAATAATGGTTTAACTGGGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGAATAATGGTTTAAATGGGCAATTGACAGAAAGATGTCAATTATGCCAGATAGATGAA
** *
1441937 GGGTTAAACACTATTG
66 CAGTTAAACACCATTG
*
1441953 AGTAAGAGAATAA
1 AGTAAAAGAATAA
1441966 AGGAATTTTA
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.27
Consensus pattern (81 bp):
AGTAAAAGAATAATGGTTTAAATGGGCAATTGACAGAAAGATGTCAATTATGCCAGATAGATGAA
CAGTTAAACACCATTG
Found at i:1442026 original size:2 final size:2
Alignment explanation
Indices: 1442019--1442049 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1442009 TGAAGGGATG
1442019 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 A
1442050 ATGTACAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1442122 original size:45 final size:44
Alignment explanation
Indices: 1442086--1442193 Score: 112
Period size: 44 Copynumber: 2.4 Consensus size: 44
1442076 AATGAATGTT
**
1442086 ATAAAGGAAAATGTA-AATAGAACATAAAAGGCATGAAAGCTTGCC
1 ATAAAGG-AAATGTATAATAGAACATAAAA-GCATGAAAGAATGCC
* * *
1442131 ATAAAGGAAATGTATAATAGTATATAAAAGCATGAAAGGA-GACC
1 ATAAAGGAAATGTATAATAGAACATAAAAGCATGAAAGAATG-CC
*
1442175 ATAATGGAAATGGTATAAT
1 ATAAAGGAAAT-GTATAAT
1442194 GGTGTATTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
43 1 0.02
44 28 0.51
45 26 0.47
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.21
Consensus pattern (44 bp):
ATAAAGGAAATGTATAATAGAACATAAAAGCATGAAAGAATGCC
Found at i:1442177 original size:44 final size:44
Alignment explanation
Indices: 1442086--1442211 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 44
1442076 AATGAATGTT
* * **
1442086 ATAAAGGAAAATGTA-AATAGAACATAAAAGGCATGAAAGCTTGCC
1 ATAAAGG-AAATGTATAATAGTATATAAAA-GCATGAAAGCGAGCC
1442131 ATAAAGGAAATGTATAATAGTATATAAAAGCATGAAAG-GAGACC
1 ATAAAGGAAATGTATAATAGTATATAAAAGCATGAAAGCGAG-CC
* * * *
1442175 ATAATGGAAATGGTATAATGGTGTATTATAAGCATGA
1 ATAAAGGAAAT-GTATAATAGTATA-TAAAAGCATGA
1442212 TGGAATGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.01
44 28 0.41
45 30 0.43
46 10 0.14
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.23
Consensus pattern (44 bp):
ATAAAGGAAATGTATAATAGTATATAAAAGCATGAAAGCGAGCC
Found at i:1446544 original size:79 final size:79
Alignment explanation
Indices: 1446413--1446814 Score: 551
Period size: 79 Copynumber: 5.1 Consensus size: 79
1446403 AAACTAATGA
*
1446413 ATAAAAGAATAATGCATATGGGTGCATTAGTGGAATGAAAGGATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGTATGAAAGGATGCCTTAGCTGATATGTATATG
1446478 GGTACATTATCAGC
66 GGTACATTATCAGC
* * *
1446492 ATAAAATAATAATGCATATTGGTGCATTAGTGGTATGAAAGGATGCATTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGTATGAAAGGATGCCTTAGCTGATATGTATATG
1446557 GGTACATTATC-GAC
66 GGTACATTATCAG-C
* * * *
1446571 ATAAAAGAATAATACATATGGGTACATTATTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGTATGAAAGGATGCCTTAGCTGATATGTATATG
*
1446636 GGTACATTTTC-GAC
66 GGTACATTATCAG-C
*
1446650 ATAAAAGAATAATGCATATGGGTGCATTAGTGGGATGAAAGGATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGTATGAAAGGATGCCTTAGCTGATATGTATATG
*
1446715 GGTACATTAT-ATGT
66 GGTACATTATCA-GC
** * * * * * *
1446729 ATATTAGAATAATGCATATGGGTGCATTATTGGTATGAAAGGAT-TCTAAAGTTGAAATGCATAT
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGTATGAAAGGATGCCT-TAGCTGATATGTATAT
* *
1446793 GGGTGCATTATCAAC
65 GGGTACATTATCAGC
1446808 ATAAAAG
1 ATAAAAG
1446815 TATGCTATAA
Statistics
Matches: 286, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
78 3 0.01
79 281 0.98
80 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTAGTGGTATGAAAGGATGCCTTAGCTGATATGTATATG
GGTACATTATCAGC
Found at i:1447342 original size:81 final size:81
Alignment explanation
Indices: 1447179--1447353 Score: 224
Period size: 81 Copynumber: 2.2 Consensus size: 81
1447169 ATTAAAAGTA
*
1447179 AGTAAAAGAATAATGGTTTAACTGGGAAATTGACAGAAAGATGTCGATTATGCCAGATAGATGAA
1 AGTAAAAGAATAATGGTTTAACTGGGAAATTGACAGAAAGATGTCAATTATGCCAGATAGATGAA
** *
1447244 CGCTTAAGTACCGTTG
66 CGCTTAAACACCATTG
* * * * * *
1447260 AGTAAAAGAATAATGGTTTAACTGGGCAATTGGCAGAAAGGTGTCAATTATTCTAGTTAGATGAA
1 AGTAAAAGAATAATGGTTTAACTGGGAAATTGACAGAAAGATGTCAATTATGCCAGATAGATGAA
* * *
1447325 TGGTTAAACACTATTG
66 CGCTTAAACACCATTG
*
1447341 AGTAAGAGAATAA
1 AGTAAAAGAATAA
1447354 AGGAATTTTA
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.27
Consensus pattern (81 bp):
AGTAAAAGAATAATGGTTTAACTGGGAAATTGACAGAAAGATGTCAATTATGCCAGATAGATGAA
CGCTTAAACACCATTG
Found at i:1447559 original size:44 final size:45
Alignment explanation
Indices: 1447483--1447585 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 45
1447473 TAAACAGAAC
* *
1447483 ATAAAAGGCATTAAAGGATGCCATAAAGGAAAT-GTATAATAGTAT
1 ATAAAA-GCATGAAAGGAGGCCATAAAGGAAATGGTATAATAGTAT
* * * *
1447528 ATAAAAGCATGAAAGGAGGCTATAATGGAAATGGTATAATGGTGT
1 ATAAAAGCATGAAAGGAGGCCATAAAGGAAATGGTATAATAGTAT
*
1447573 ATTATAAGCATGA
1 A-TAAAAGCATGA
1447586 TGGAATGCTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 22 0.45
45 17 0.35
46 10 0.20
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (45 bp):
ATAAAAGCATGAAAGGAGGCCATAAAGGAAATGGTATAATAGTAT
Found at i:1474895 original size:97 final size:97
Alignment explanation
Indices: 1474700--1474907 Score: 235
Period size: 97 Copynumber: 2.1 Consensus size: 97
1474690 ACCATAGCTT
*
1474700 ATAAACCAGTAAATTCCATGATTCCATAAATCAAGATAAATTCATATTTTCCAGTGAAAACAGGA
1 ATAAACCAGTAAATTCCATGATTCCATAAATCAAGATAAATTCATATTTTCCAGTGAAAACACGA
* **
1474765 AACCCGATAACACATTGCAAGTATCATAATTC
66 AACCAGATAACACATACCAAGTATCATAATTC
* * * *
1474797 ATAAACCAGTAAATTCCATGGTTCTATAAATCATGA-ACAATTCATAGTTTTCGA-TGAAAAC-C
1 ATAAACCAGTAAATTCCATGATTCCATAAATCAAGATA-AATTCATA-TTTTCCAGTGAAAACAC
* * * **
1474859 GAAATCAGATATCACATACCATGT-TGCCATGGTTC
64 GAAACCAGATAACACATACCAAGTAT--CATAATTC
1474894 ATAAACCAGTAAAT
1 ATAAACCAGTAAAT
1474908 CAATACTTTC
Statistics
Matches: 94, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
95 1 0.01
96 19 0.20
97 68 0.72
98 6 0.06
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (97 bp):
ATAAACCAGTAAATTCCATGATTCCATAAATCAAGATAAATTCATATTTTCCAGTGAAAACACGA
AACCAGATAACACATACCAAGTATCATAATTC
Found at i:1486187 original size:17 final size:16
Alignment explanation
Indices: 1486156--1486189 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1486146 CACGTGAGGA
1486156 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1486172 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1486189 T
1 T
1486190 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1486750 original size:18 final size:19
Alignment explanation
Indices: 1486709--1486743 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1486699 CGAAAATCAT
1486709 AAAGTATGACATTTTTAGA
1 AAAGTATGACATTTTTAGA
1486728 AAAGT-TGAC-TTTTTAG
1 AAAGTATGACATTTTTAG
1486744 TCAAAGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (19 bp):
AAAGTATGACATTTTTAGA
Found at i:1486888 original size:31 final size:31
Alignment explanation
Indices: 1486831--1486891 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1486821 TTGACTCGGT
* * *
1486831 CAGGTCAAGTGGGTTGGGCTGGCGGGTCAGA
1 CAGGTCAAGTGGGTTAGGCAGACGGGTCAGA
1486862 CAGG-CAAGTCGGGTTAGGCAGACGGGTCAG
1 CAGGTCAAGT-GGGTTAGGCAGACGGGTCAG
1486892 TTCTGGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.20, C:0.18, G:0.46, T:0.16
Consensus pattern (31 bp):
CAGGTCAAGTGGGTTAGGCAGACGGGTCAGA
Found at i:1488671 original size:2 final size:2
Alignment explanation
Indices: 1488664--1488695 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1488654 ATATAAAACA
1488664 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
1488696 CAATTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1494976 original size:14 final size:14
Alignment explanation
Indices: 1494957--1495017 Score: 77
Period size: 14 Copynumber: 4.3 Consensus size: 14
1494947 AAAGTCAACA
1494957 GGTTGACTCGGACG
1 GGTTGACTCGGACG
*
1494971 GGTTGAGTCGGACG
1 GGTTGACTCGGACG
*
1494985 AGTTGACTCGGACG
1 GGTTGACTCGGACG
* *
1494999 AGTTGACTCAGACCG
1 GGTTGACTCGGA-CG
1495014 GGTT
1 GGTT
1495018 TGTAATACCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
14 36 0.88
15 5 0.12
ACGTcount: A:0.18, C:0.20, G:0.39, T:0.23
Consensus pattern (14 bp):
GGTTGACTCGGACG
Found at i:1495833 original size:22 final size:21
Alignment explanation
Indices: 1495808--1495864 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 21
1495798 ACCGGAAGGG
1495808 GTATCAGTACCATAGCATGGTA
1 GTATC-GTACCATAGCATGGTA
1495830 GTATCGGTACCATAGCATGGTA
1 GTATC-GTACCATAGCATGGTA
1495852 GTATCGATACCAT
1 GTATCG-TACCAT
1495865 GGTAAGGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (21 bp):
GTATCGTACCATAGCATGGTA
Found at i:1495949 original size:116 final size:116
Alignment explanation
Indices: 1495743--1495955 Score: 295
Period size: 116 Copynumber: 1.8 Consensus size: 116
1495733 AGGGTATTGG
* * **
1495743 TACCATGGTAAGGGTATCAATACTAGGAATCATCAAAACTAAAATTGGTATCGATACCGGAAGGG
1 TACCATGGTAAGGGTATCAATACCAGGAAACATCAAAACTAAAATTGGTATCGATACCAAAAGGG
* * *
1495808 GTATCAGTACCATAGCATGGTAGTATCGGTACCATAGCATGGTAGTATCGA
66 GTATCAGTACCATAACATAGAAGTATCGGTACCATAGCATGGTAGTATCGA
* * *
1495859 TACCATGGTAAGGGTATCGATACCA-GACAACATCGAACCTAAAATTGGTATCGATA-CAAAAGG
1 TACCATGGTAAGGGTATCAATACCAGGA-AACATCAAAACTAAAATTGGTATCGATACCAAAA-G
*
1495922 GGGTATCGGTACCATAACATAGAAGTATCGGTAC
64 GGGTATCAGTACCATAACATAGAAGTATCGGTAC
1495956 TAGGGTAGTA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
115 5 0.06
116 79 0.94
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (116 bp):
TACCATGGTAAGGGTATCAATACCAGGAAACATCAAAACTAAAATTGGTATCGATACCAAAAGGG
GTATCAGTACCATAACATAGAAGTATCGGTACCATAGCATGGTAGTATCGA
Found at i:1496918 original size:68 final size:69
Alignment explanation
Indices: 1496754--1496940 Score: 286
Period size: 68 Copynumber: 2.7 Consensus size: 69
1496744 ATTTAAGGTT
*
1496754 TAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTTAAGTTCCT
1 TAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC--A--TAAGTTCCT
1496819 TTGAGGCC
62 TTGAGGCC
* *
1496827 TAACTGTCCATTTGACATAAAGGTGTCAATTATGCTAGTTAGATGAAAGGC-TAAGTTCCTTTGA
1 TAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCATAAGTTCCTTTGA
*
1496891 GGGC
66 GGCC
*
1496895 TAACTGTGTATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGA
1 TAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGA
1496941 GCAGTTAAGT
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
68 59 0.55
73 48 0.45
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (69 bp):
TAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCATAAGTTCCTTTGA
GGCC
Found at i:1497493 original size:79 final size:79
Alignment explanation
Indices: 1496959--1497482 Score: 832
Period size: 79 Copynumber: 6.6 Consensus size: 79
1496949 GTATCGTTGA
* *
1496959 ATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATT
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
*
1497024 GGTACATTGTCAAC
66 GGTACATTGTCAGC
* * * *
1497038 ATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAGGATGTCACATCTGAAATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
* *
1497103 GGTACATTGCCAGT
66 GGTACATTGTCAGC
* * * *
1497117 ATAAAATAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAGCTGATATGTACATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
1497182 GGTACATTGTCAGC
66 GGTACATTGTCAGC
1497196 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
*
1497261 GGTACATTGTTAGC
66 GGTACATTGTCAGC
* * * * * *
1497275 ACAAACGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAACTTAATTGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
1497340 GGTACATTGTCAGC
66 GGTACATTGTCAGC
*
1497354 ATAAAAGAATAATGCATATCGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
1497419 GGTACATTGTCAGC
66 GGTACATTGTCAGC
* * *
1497433 ATAAGAGAATAATGCATATGGGTGCAATATTGGCATGAAAAGATGCCATA
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATA
1497483 AATAAAATGT
Statistics
Matches: 405, Mismatches: 40, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 405 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
GGTACATTGTCAGC
Found at i:1497551 original size:45 final size:46
Alignment explanation
Indices: 1497463--1497562 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 46
1497453 GGTGCAATAT
* * *
1497463 TGGCATGAAAAGATGCCATAAATAAAATGTACGACGATGTATAAAA
1 TGGCATGAAAAGATGCCATAAATAAAATGTACAAAGATATATAAAA
** *
1497509 -GGCATGAAATTATGCCATAAATAAAATGTATAATAG-TATATAAAA
1 TGGCATGAAAAGATGCCATAAATAAAATGTACAA-AGATATATAAAA
1497554 TGGCATGAA
1 TGGCATGAA
1497563 CGGTTTCCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 37 0.80
46 9 0.20
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (46 bp):
TGGCATGAAAAGATGCCATAAATAAAATGTACAAAGATATATAAAA
Found at i:1500349 original size:94 final size:94
Alignment explanation
Indices: 1500176--1500361 Score: 241
Period size: 94 Copynumber: 2.0 Consensus size: 94
1500166 TACTGAAGAT
* * * *
1500176 GTAGTATAGATACCATGGTAATCGTATCGGTACCAGGAATCATCGAAATTAAAATTGTTATCGAT
1 GTAGTATAGATACCATGGTAAGCGTATCGATACCAGGAATCATCGAAACTAAAATTGGTATCGAT
** *
1500241 ACCGGAAGGTGTATCGATACCATAGCACG
66 ACCAAAAGGGGTATCGATACCATAGCACG
* * *
1500270 GTAGTATCGATACCATGGTAAGGGTATCGATACCAGGCAA-CATCGAACCTAAAATTGGTATCGA
1 GTAGTATAGATACCATGGTAAGCGTATCGATACCAGG-AATCATCGAAACTAAAATTGGTATCGA
*
1500334 TA-CAAAAGGGGGTATCGGTACCATAGCA
65 TACCAAAA-GGGGTATCGATACCATAGCA
1500362 TAGAAGTATG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
93 3 0.04
94 74 0.94
95 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (94 bp):
GTAGTATAGATACCATGGTAAGCGTATCGATACCAGGAATCATCGAAACTAAAATTGGTATCGAT
ACCAAAAGGGGTATCGATACCATAGCACG
Found at i:1500816 original size:59 final size:59
Alignment explanation
Indices: 1500731--1500928 Score: 222
Period size: 59 Copynumber: 3.4 Consensus size: 59
1500721 CTAAGTGTGC
*
1500731 AAAGTTAAGAAATTCATACTAAGTGTATGAA-TTTCTGTATTGGGCACTTTGTGTGCTAA
1 AAAGATAAGAAATTCATACTAAGTGTATGAATTTTC-GTATTGGGCACTTTGTGTGCTAA
* * * * * * *
1500790 AAACATAAGAAATTCATTCTATGTGTATAAATTTTCGTATTGAGCACTTTCTATGCTAA
1 AAAGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCTAA
* * * * * * *
1500849 AATGGTAAGAAATGCATACTAAGTGTATGAATTTTCGTA-TGGGAAATATGTGTG-TAT
1 AAAGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCTAA
*
1500906 AAAGATAAGAAATTCATAATAAG
1 AAAGATAAGAAATTCATACTAAG
1500929 GAAATGGATT
Statistics
Matches: 112, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
57 21 0.19
58 9 0.08
59 78 0.70
60 4 0.04
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.35
Consensus pattern (59 bp):
AAAGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCTAA
Found at i:1501376 original size:68 final size:67
Alignment explanation
Indices: 1501234--1501486 Score: 398
Period size: 68 Copynumber: 3.7 Consensus size: 67
1501224 AAAAGATTTA
* * * *
1501234 AGGCCTAACTATGCATTTGACAAAAAAGTGTCAATTATGCAATTAGATGAAAGGCTAAGTGCCTT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCAGTTAGATGAAAGGCTAAGTGCCTT
1501299 TG
66 TG
1501301 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAAAGGCTAAGTGCCT
1501366 TTG
65 TTG
* * * *
1501369 AGGCCTAACTGTGCTTTTGAAATAAAGATGTCAATTATGACAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAAAGGCTAAGTGCCT
1501434 TTG
65 TTG
* *
1501437 AGGCCTAACTGTGTATTTGATAGAAAGGTGTCAATTATGCAGTTAGATGA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCAGTTAGATGA
1501487 CCAGTTAAGT
Statistics
Matches: 171, Mismatches: 14, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
67 47 0.27
68 124 0.73
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.30
Consensus pattern (67 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCAGTTAGATGAAAGGCTAAGTGCCTT
TG
Found at i:1501636 original size:79 final size:79
Alignment explanation
Indices: 1501506--1501694 Score: 319
Period size: 79 Copynumber: 2.4 Consensus size: 79
1501496 TGCCGTTGAG
* *
1501506 TAAAAGAATAATGCATAT-GGTGCATTATTGTCATGAAAGGATGGCATAGCTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGAAATGTATATGG
*
1501570 GTGCATTGTCAGCA
66 GTACATTGTCAGCA
1501584 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGAT-ACAATAGCTGAAATGTATATG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGAC-ATAGCTGAAATGTATATG
1501648 GGTACATTGTCAGCA
65 GGTACATTGTCAGCA
*
1501663 TAAAAGAATAATGGATATGGGTGCATTATTGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGG
1501695 TGTTGAAAAC
Statistics
Matches: 105, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
78 19 0.18
79 86 0.82
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGAAATGTATATGG
GTACATTGTCAGCA
Found at i:1504187 original size:18 final size:18
Alignment explanation
Indices: 1504163--1504214 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
1504153 GACTGGTTAC
* *
1504163 AACCCGACCTGTTTACCCT
1 AACCCGACCCGTTGA-CCT
1504182 -ACCCGACCCGTTGACCT
1 AACCCGACCCGTTGACCT
1504199 AACCCGACCCGTTGAC
1 AACCCGACCCGTTGAC
1504215 AGTTGACCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 27 0.90
ACGTcount: A:0.21, C:0.44, G:0.15, T:0.19
Consensus pattern (18 bp):
AACCCGACCCGTTGACCT
Found at i:1506749 original size:24 final size:24
Alignment explanation
Indices: 1506715--1506787 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
1506705 ATACATTACC
*
1506715 TGAATTATGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * * *
1506739 TGGATTCTGTTCTTATATCTGATC
1 TGAATTCTGTTCTGATTTCTGATA
*
1506763 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
1506787 T
1 T
1506788 TTCTGTTTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:1510292 original size:23 final size:23
Alignment explanation
Indices: 1510221--1510303 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
1510211 GTTCTTAATA
* *
1510221 GTGCATCGATGCATCTCTTTGAAT
1 GTGCATCGATGCA-CACCTTGAAT
* *
1510245 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
1510266 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
1510289 GTGCATCGATGCACA
1 GTGCATCGATGCACA
1510304 AGGCCATGCA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
21 15 0.32
22 1 0.02
23 21 0.45
24 10 0.21
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:1512270 original size:29 final size:28
Alignment explanation
Indices: 1512238--1512295 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1512228 GGATGTTTAA
1512238 ATTTGATGGTTGT-TGGATGTTTTGAACTT
1 ATTTG-TGGTTGTATGGAT-TTTTGAACTT
* *
1512267 ATTTGTTGTTTTATGGATTTTTGAACTT
1 ATTTGTGGTTGTATGGATTTTTGAACTT
1512295 A
1 A
1512296 ATATCTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.55
Consensus pattern (28 bp):
ATTTGTGGTTGTATGGATTTTTGAACTT
Found at i:1512473 original size:2 final size:2
Alignment explanation
Indices: 1512466--1512494 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1512456 CAGCTTAAGC
1512466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1512495 CAATTGGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1513092 original size:65 final size:65
Alignment explanation
Indices: 1512978--1513121 Score: 179
Period size: 65 Copynumber: 2.2 Consensus size: 65
1512968 TGCACCAATC
* * *
1512978 CATGCATCGATGCA-CATACTATGCATCGATGCACTCAGAGTTTTATGAAAACATCGATTGCATT
1 CATGCATCGATGCACCATACCATGCATCGATACACTCAGAGTTTTATG-AAACATCGAATGCATT
1513042 T
65 T
* * *
1513043 GATGCATCGATGCACCA-GCCATGCATCGATACACTCTG-GCTATTT-TGAAACATCGAATGCAT
1 CATGCATCGATGCACCATACCATGCATCGATACACTCAGAG-T-TTTATGAAACATCGAATGCAT
1513105 TT
64 TT
1513107 CATGCATCGATGCAC
1 CATGCATCGATGCAC
1513122 TCTTAGTGCA
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
64 31 0.45
65 33 0.48
66 5 0.07
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (65 bp):
CATGCATCGATGCACCATACCATGCATCGATACACTCAGAGTTTTATGAAACATCGAATGCATTT
Found at i:1514098 original size:79 final size:79
Alignment explanation
Indices: 1513852--1514280 Score: 644
Period size: 79 Copynumber: 5.4 Consensus size: 79
1513842 TAACTCAACA
* * * * * *
1513852 ATTGGCATGAACGGATGCCATTGCTGAAAGGTATATGGGTATATTGTTAACATAAAAGAATAATG
1 ATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATG
*
1513917 CATATGGGTGAATT
66 CATATGGGTGCATT
* * *
1513931 ATTGGCATGAAAGGATGCCATATCTGAAATGTATATGGGTACATT-TCAGTATAAAAGAATAAGG
1 ATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATG
1513995 CATATGGGTGCATT
66 CATATGGGTGCATT
* ** *
1514009 ATTAGCATGAAATAATGCCATAGCTGAAATGTATATGAGTACATTGTCAGCATAAAAGAATAATG
1 ATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATG
*
1514074 CATATTGGTGCATT
66 CATATGGGTGCATT
*
1514088 ATTGGCATGAAAGGATGACATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATG
1 ATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATG
1514153 CATATGGGTGCATT
66 CATATGGGTGCATT
* * * *
1514167 ATTGACATGAAAGGATTCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATACTA
1 ATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATG
1514232 CATATGGGTGCATT
66 CATATGGGTGCATT
* **
1514246 ATTGGCATGAAAAGATGCCATAAATGAAATGTATA
1 ATTGGCATGAAAGGATGCCATAGCTGAAATGTATA
1514281 ACGGTGCATA
Statistics
Matches: 315, Mismatches: 34, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
78 68 0.22
79 247 0.78
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (79 bp):
ATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATG
CATATGGGTGCATT
Found at i:1542554 original size:21 final size:21
Alignment explanation
Indices: 1542534--1542613 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
1542524 TGTACCCCTG
*
1542534 ATGGAGTATCAATACTACCTG
1 ATGGAGTATCAATACTACCTA
1542555 ATGGAGTATCAATACTACCTA
1 ATGGAGTATCAATACTACCTA
* ** *
1542576 ATGGAGTACCTTTACTACTTA
1 ATGGAGTATCAATACTACCTA
1542597 ATGGAGTATCAATACTA
1 ATGGAGTATCAATACTA
1542614 AGCTACATCA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (21 bp):
ATGGAGTATCAATACTACCTA
Found at i:1545985 original size:20 final size:21
Alignment explanation
Indices: 1545962--1546002 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1545952 TATTATATGT
**
1545962 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
1545982 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
1546003 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:1546915 original size:18 final size:17
Alignment explanation
Indices: 1546892--1546927 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1546882 GTATATTTGT
*
1546892 TTTTTTTTCCTTTCTCTG
1 TTTTTTTT-CGTTCTCTG
1546910 TTTTTTTTCGTTCTCTG
1 TTTTTTTTCGTTCTCTG
1546927 T
1 T
1546928 CTCTGTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.00, C:0.19, G:0.08, T:0.72
Consensus pattern (17 bp):
TTTTTTTTCGTTCTCTG
Found at i:1547433 original size:3 final size:3
Alignment explanation
Indices: 1547425--1547513 Score: 160
Period size: 3 Copynumber: 29.7 Consensus size: 3
1547415 AATGTATATT
*
1547425 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1547473 TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1547514 TGGATAAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1548038 original size:40 final size:43
Alignment explanation
Indices: 1547994--1548100 Score: 159
Period size: 40 Copynumber: 2.5 Consensus size: 43
1547984 GTTGAACAAA
1547994 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTC-A-GATGAG
1 TTCTTCTCATTATGAACTTCTCTCTTCCTTCTTCAATGATGAG
*
1548034 TTCTTCTCATTATGAAC-TCTCTCTTCTTTCTTCAGATGATGAG
1 TTCTTCTCATTATGAACTTCTCTCTTCCTTCTTCA-ATGATGAG
1548077 TTCTTCTCATTATGAACCTTCTCT
1 TTCTTCTCATTATGAA-CTTCTCT
1548101 GGAAAAGCTA
Statistics
Matches: 60, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
39 3 0.05
40 28 0.47
42 1 0.02
43 22 0.37
44 1 0.02
45 5 0.08
ACGTcount: A:0.18, C:0.25, G:0.09, T:0.48
Consensus pattern (43 bp):
TTCTTCTCATTATGAACTTCTCTCTTCCTTCTTCAATGATGAG
Found at i:1548038 original size:113 final size:114
Alignment explanation
Indices: 1547767--1548057 Score: 471
Period size: 113 Copynumber: 2.6 Consensus size: 114
1547757 TTTTGATGAG
*
1547767 TTCTTCTCATTATGAAC-TCTCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* *
1547831 GAAAAAAATAACCCATCAAGTAATAGATTTGAGCAAAAAGGTTGAACAAA
65 GAAAAAAATAACCCATCAAGTAATAGAATTCAGCAAAAAGGTTGAACAAA
1547881 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
** * *
1547946 GCAAAAATAATCCATCAAGTGAT-GAATTCAG-ACAAAAGGTTGAACAAA
66 AAAAAAATAACCCATCAAGTAATAGAATTCAGCA-AAAAGGTTGAACAAA
*
1547994 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1548058 TCTTTCTTCA
Statistics
Matches: 167, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
112 1 0.01
113 84 0.50
114 79 0.47
115 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (114 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
AAAAAAATAACCCATCAAGTAATAGAATTCAGCAAAAAGGTTGAACAAA
Found at i:1548142 original size:270 final size:267
Alignment explanation
Indices: 1547761--1548323 Score: 918
Period size: 270 Copynumber: 2.1 Consensus size: 267
1547751 ATAAGCTTTT
*
1547761 GATGAGTTCTTCTCATTATGAACTCTCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 GATGAGTTCTTCTCATTATGAACTCTCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACCT
* * *
1547826 TCTCTGAAAAAAATAACCCATCAAGTAATAGATTTGAGCAAAAAGGTTGAACAAATTCTTCTCAT
66 TCTCTGAAAAAAATAACCCATCAAGTAATAGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCAT
1547891 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAA-ATA
131 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGG-AAAAGATA
*
1547955 ATCCATCAA-GTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
194 ATCCATCAATGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
1548019 CCTTCTTCA
259 CCTTCTTCA
1548028 GATGAGTTCTTCTCATTATGAACTCTCTCTTCTTTCTTCAGATGATGAGTTCTTCTCATTATGAA
1 GATGAGTTCTTCTCATTATGAACTCTCTCTTCTTTCTTC--A-GATGAGTTCTTCTCATTATGAA
* ** * * *
1548093 CCTTCTCTGGAAAAGCTAATCCATCAATTTGAT-GAATTCA-AATAAAAGGTTGAACAAATTCTT
63 CCTTCTCTGAAAAAAATAACCCATCAA-GTAATAGAATTCAGAA-AAAAGGTTGAACAAATTCTT
1548156 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAG
126 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAG
* *
1548221 ATAATCCATCAATTTGATGAATTCAAATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
191 ATAATCCATCAATGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
1548286 CTTCCTTCTTCA
256 CTTCCTTCTTCA
1548298 GATGAGTTCTTCTCATTATGAACTCT
1 GATGAGTTCTTCTCATTATGAACTCT
1548324 ACCTGGCAAT
Statistics
Matches: 276, Mismatches: 13, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
267 39 0.14
268 4 0.01
269 22 0.08
270 208 0.75
271 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (267 bp):
GATGAGTTCTTCTCATTATGAACTCTCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACCT
TCTCTGAAAAAAATAACCCATCAAGTAATAGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCAT
TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATAAT
CCATCAATGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
TTCTTCA
Found at i:1548173 original size:157 final size:152
Alignment explanation
Indices: 1547881--1548213 Score: 542
Period size: 157 Copynumber: 2.2 Consensus size: 152
1547871 GTTGAACAAA
*
1547881 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTC-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
*
1547946 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 GCAAAAATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
1548011 TTCTTCTTCCTTCTTCAGATGAG
130 TTCTTCTTCCTTCTTCAGATGAG
*
1548034 TTCTTCTCATTATGAACTCTCTCTTCTTTCTTCAGATGATGAGTTCTTCTCATTATGAACCTTCT
1 TTCTTCTCATTATGAACT-TCTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACCTTCT
* * *
1548099 CTGG-AAAAGCTAATCCATCAATTTGATGAATTCAAATAAAAGGTTGAACAAATTCTTCTCATTA
62 CTGGCAAAA-ATAATCCATCAA-GTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTA
1548163 TGAACTTCTTCTTCCTTCTTCAGATGAG
125 TGAACTTCTTCTTCCTTCTTCAGATGAG
1548191 TTCTTCTCATTATGAACTTCTCT
1 TTCTTCTCATTATGAACTTCTCT
1548214 GGAAAAGATA
Statistics
Matches: 168, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
153 29 0.17
154 2 0.01
155 5 0.03
156 47 0.28
157 85 0.51
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (152 bp):
TTCTTCTCATTATGAACTTCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG
CAAAAATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATGAG
Found at i:1548465 original size:113 final size:114
Alignment explanation
Indices: 1548034--1548459 Score: 662
Period size: 113 Copynumber: 3.7 Consensus size: 114
1548024 TTCAGATGAG
* *
1548034 TTCTTCTCATTATGAAC-TCTCTCTTCTTTCTTCAGATGATGAGTTCTTCTCATTATGAACCTTC
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACTTTC
1548098 TCTGGAAAAGCTAATCCATCAATTTGATGAATTCAAATAAAAGGTTGAACAAA
62 TCTGGAAAAGCTAATCCATCAATTTGATGAATTCAAATAAAAGGTTGAACAAA
1548151 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
1548215 GAAAAGATAATCCATCAATTTGATGAATTCAAATAAAAGGTTGAACAAA
66 GAAAAGCTAATCCATCAATTTGATGAATTCAAATAAAAGGTTGAACAAA
*
1548264 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT
* * * * * **
1548328 GGCAATGTTGATCCATCAA-ATGATGAATTCAGGTAAAAGGTTGAACAAA
65 GGAAAAGCTAATCCATCAATTTGATGAATTCAAATAAAAGGTTGAACAAA
1548377 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
**
1548442 GAAAAGCTGCTCCATCAA
66 GAAAAGCTAATCCATCAA
1548460 GTGATGGATT
Statistics
Matches: 290, Mismatches: 15, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
112 2 0.01
113 214 0.74
114 40 0.14
115 3 0.01
117 28 0.10
118 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (114 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTAATCCATCAATTTGATGAATTCAAATAAAAGGTTGAACAAA
Found at i:1549179 original size:92 final size:86
Alignment explanation
Indices: 1549021--1549516 Score: 661
Period size: 83 Copynumber: 5.7 Consensus size: 86
1549011 TGCACTTCTT
* * * *
1549021 CGAATCAGATCAGATAACTTAAAGAACACTTCCAGAAGATACTATGAACACATTCATGTTCCGAA
1 CGAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
1549086 TTCAATGATTGGTTCTGGGGTTCTTA
66 TTCAATGATTGGTTCT--GG-TC--A
* *
1549112 CTGAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATGTTCCGA
1 C-GAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1549177 ATTCAATGATTGGTTCTGGGGTTCCTA
65 ATTCAATGATTGGTTCT--GG-T-C-A
*
1549204 CTGAATCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
1 C-GAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
*
1549269 ATTCAATGATTGGTT-TTGTCA
65 ATTCAATGATTGGTTCTGGTCA
*
1549290 --AA-CTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
1 CGAATC-AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
*
1549352 ATTCAATGATTGGTT-TCGTCA
65 ATTCAATGATTGGTTCTGGTCA
* * *
1549373 --AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATGAGCACATTCATCTTCCAAA
1 CGAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
1549436 TTCAATGATTGGTTCT-G-C-
66 TTCAATGATTGGTTCTGGTCA
* * *
1549454 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
1 CGAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCA
1549517 TTTAATGTTT
Statistics
Matches: 387, Mismatches: 11, Indels: 22
0.92 0.03 0.05
Matches are distributed among these distances:
82 2 0.01
83 213 0.55
84 2 0.01
86 1 0.00
87 1 0.00
88 1 0.00
89 1 0.00
91 2 0.01
92 163 0.42
93 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (86 bp):
CGAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
TTCAATGATTGGTTCTGGTCA
Found at i:1550303 original size:19 final size:20
Alignment explanation
Indices: 1550279--1550320 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1550269 AATAGAAAAT
*
1550279 AATAAATTGAATTTCCAA-A
1 AATAAATTGAATCTCCAATA
1550298 AATAAATTGAATCTCCAATA
1 AATAAATTGAATCTCCAATA
1550318 AAT
1 AAT
1550321 TGAACTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (20 bp):
AATAAATTGAATCTCCAATA
Found at i:1550666 original size:11 final size:10
Alignment explanation
Indices: 1550649--1550700 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
1550639 TTGACCCTCC
1550649 TTTTTCTTTT
1 TTTTTCTTTT
1550659 TCTTTTCTCTTT
1 T-TTTTCT-TTT
**
1550671 TTTCCCTTTT
1 TTTTTCTTTT
1550681 TTTTTCTTTT
1 TTTTTCTTTT
*
1550691 TCTTTCTTTT
1 TTTTTCTTTT
1550701 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 21 0.60
11 10 0.29
12 4 0.11
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:1550669 original size:7 final size:6
Alignment explanation
Indices: 1550648--1550695 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
1550638 CTTGACCCTC
*
1550648 CTTTTT CTTTTT CTTTTCT CTTTTTT CCCTTTT -TTTTT CTTTTT CTTT
1 CTTTTT CTTTTT CTTTT-T C-TTTTT -CTTTTT CTTTTT CTTTTT CTTT
1550696 CTTTTCTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 4 0.11
6 20 0.56
7 7 0.19
8 5 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:1550691 original size:27 final size:27
Alignment explanation
Indices: 1550650--1550701 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
1550640 TGACCCTCCT
1550650 TTTTCTTTTTCTTTTCTCTT-TTTTCCC
1 TTTTCTTTTTCTTTTCT-TTCTTTTCCC
1550677 TTTT-TTTTTCTTTTTCTTTCTTTTC
1 TTTTCTTTTTC-TTTTCTTTCTTTTC
1550702 TTCAAGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTCTTTTTCTTTTCTTTCTTTTCCC
Found at i:1562869 original size:17 final size:17
Alignment explanation
Indices: 1562847--1562881 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1562837 GTATATTTGT
*
1562847 TTTTTTTTCTTTCTCTG
1 TTTTTTTTCATTCTCTG
1562864 TTTTTTTTCATTCTCTG
1 TTTTTTTTCATTCTCTG
1562881 T
1 T
1562882 CTCTGTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTTTTTCATTCTCTG
Found at i:1563369 original size:3 final size:3
Alignment explanation
Indices: 1563361--1563427 Score: 93
Period size: 3 Copynumber: 22.7 Consensus size: 3
1563351 AGTTTAATGT
*
1563361 ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1563409 TTA TATA ATA A-A AT- ATA AT
1 ATA -ATA ATA ATA ATA ATA AT
1563428 GGATAAAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 51 0.89
4 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1564076 original size:16 final size:15
Alignment explanation
Indices: 1564055--1564084 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1564045 CTGTTAAATT
1564055 TAATTATAAATATTTA
1 TAATTAT-AATATTTA
1564071 TAATTATAATATTT
1 TAATTATAATATTT
1564085 GATTCCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTATAATATTTA
Found at i:1565771 original size:188 final size:188
Alignment explanation
Indices: 1565524--1565902 Score: 717
Period size: 188 Copynumber: 2.0 Consensus size: 188
1565514 GCATCAATTT
1565524 AACCCTCAAATTGTTTAATTGCATCATTGTATACCCTATCCCTAACATAAAACCCTAAATTATAA
1 AACCCTCAAATTGTTTAATTGCATCATTG-ATACCCTATCCCTAACATAAAACCCTAAATTATAA
1565589 ACTATAAATAAGGGTTTAGGATTTATGCTTTAGAGGTTATGGGGTTATAGTTTAGGGTTATAATT
65 ACTATAAATAAGGGTTTAGGATTTATGCTTTAGAGGTTATGGGGTTATAGTTTAGGGTTATAATT
1565654 TAGGGATTTAAG-TACGGGTAAGGTATAAAATGATGCAATTGAGTAACTTCAATGGCTA
130 TAGGGATTTAAGTTACGGGTAAGGTATAAAATGATGCAATTGAGTAACTTCAATGGCTA
1565712 AACCCTCAAACTTGTTTAATTGCATCATTG-TACCCTATCCCTAACATTAAAACCCTAAATTATA
1 AACCCTCAAA-TTGTTTAATTGCATCATTGATACCCTATCCCTAACA-TAAAACCCTAAATTATA
1565776 AACTATAAATAAGGGTTTAGGATTTATGCTTTAGAGGTTATGGGGTTATAGTTTAGGGTTATAAT
64 AACTATAAATAAGGGTTTAGGATTTATGCTTTAGAGGTTATGGGGTTATAGTTTAGGGTTATAAT
1565841 TTAGGGATTTAAGTTACGGGTAAGGTATAAAATGATGCAATTGAGTAACTTCAATGGCTA
129 TTAGGGATTTAAGTTACGGGTAAGGTATAAAATGATGCAATTGAGTAACTTCAATGGCTA
1565901 AA
1 AA
1565903 TTGATGCGAA
Statistics
Matches: 188, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
187 16 0.09
188 105 0.56
189 67 0.36
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (188 bp):
AACCCTCAAATTGTTTAATTGCATCATTGATACCCTATCCCTAACATAAAACCCTAAATTATAAA
CTATAAATAAGGGTTTAGGATTTATGCTTTAGAGGTTATGGGGTTATAGTTTAGGGTTATAATTT
AGGGATTTAAGTTACGGGTAAGGTATAAAATGATGCAATTGAGTAACTTCAATGGCTA
Found at i:1567205 original size:104 final size:102
Alignment explanation
Indices: 1567025--1567224 Score: 348
Period size: 104 Copynumber: 1.9 Consensus size: 102
1567015 AGGCTATAAC
1567025 GATGTTTTTGGTGTTCGTGGTCATTGATTTATAGTGGTCAAAGGAAGGGTTGGTTCATCCCACGA
1 GATGTTTTTGGTGTTCGTGGTCATTGATTTATA--GGTCAAAGGAAGGGTTGGTTCATCCCACGA
1567090 AAAAGAGGAAAGGATTGAGAGAAACCCTAAATATAACGA
64 AAAAGAGGAAAGGATTGAGAGAAACCCTAAATATAACGA
1567129 GATGTTTTTGGGTGTTCGTGGTCATTGATTTATA-GTCAAAGGAAGGGTTGGTTCATCTCCCACG
1 GATGTTTTT-GGTGTTCGTGGTCATTGATTTATAGGTCAAAGGAAGGGTTGGTTCA--TCCCACG
1567193 AAAAAGAGGAAAGGATTGAGAGAAACCCTAAA
63 AAAAAGAGGAAAGGATTGAGAGAAACCCTAAA
1567225 ATTTTCCCTT
Statistics
Matches: 93, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
102 21 0.23
104 48 0.52
105 24 0.26
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (102 bp):
GATGTTTTTGGTGTTCGTGGTCATTGATTTATAGGTCAAAGGAAGGGTTGGTTCATCCCACGAAA
AAGAGGAAAGGATTGAGAGAAACCCTAAATATAACGA
Found at i:1567575 original size:21 final size:21
Alignment explanation
Indices: 1567555--1567634 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
1567545 ATGTCCCCTG
*
1567555 ATGGAGTATCAATACTACCTG
1 ATGGAGTATCAATACTACCTA
1567576 ATGGAGTATCAATACTACCTA
1 ATGGAGTATCAATACTACCTA
* ** *
1567597 ATGGAGTACCTTTACTACTTA
1 ATGGAGTATCAATACTACCTA
1567618 ATGGAGTATCAATACTA
1 ATGGAGTATCAATACTA
1567635 AGCTACATCA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (21 bp):
ATGGAGTATCAATACTACCTA
Found at i:1570976 original size:20 final size:21
Alignment explanation
Indices: 1570953--1570993 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1570943 TATTATATGT
**
1570953 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
1570973 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
1570994 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:1571903 original size:18 final size:17
Alignment explanation
Indices: 1571880--1571915 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1571870 GTATATTTGT
*
1571880 TTTTTTTTCCTTTCTCTG
1 TTTTTTTT-CATTCTCTG
1571898 TTTTTTTTCATTCTCTG
1 TTTTTTTTCATTCTCTG
1571915 T
1 T
1571916 CTCTGTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.03, C:0.19, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTTTTTTCATTCTCTG
Found at i:1572421 original size:3 final size:3
Alignment explanation
Indices: 1572413--1572494 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
1572403 AATGTATATT
*
1572413 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1572461 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1572495 TGGATAAAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 74 0.97
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1576636 original size:21 final size:21
Alignment explanation
Indices: 1576612--1576695 Score: 123
Period size: 21 Copynumber: 4.0 Consensus size: 21
1576602 TACATGTACC
1576612 CCTGATGGAGTATCAATACTA
1 CCTGATGGAGTATCAATACTA
1576633 CCTGATGGAGTATCAATACTA
1 CCTGATGGAGTATCAATACTA
* **
1576654 CCTGATGGAGTACCTTTACTA
1 CCTGATGGAGTATCAATACTA
* *
1576675 CTTAATGGAGTATCAATACTA
1 CCTGATGGAGTATCAATACTA
1576696 AGCTACATCA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (21 bp):
CCTGATGGAGTATCAATACTA
Found at i:1582129 original size:44 final size:45
Alignment explanation
Indices: 1582007--1582130 Score: 180
Period size: 45 Copynumber: 2.8 Consensus size: 45
1581997 TATAAAATTT
*
1582007 CTTATCATTTA-TCCTATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
* *
1582052 CTTACCATTTATTCCATAAGCTCGTAAGGTTATTTTACCCATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
1582097 CTTGCCA-TTATTCCATAAGCTCGTAACCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1582131 GCATGCTTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 25 0.35
45 44 0.61
46 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:1582313 original size:40 final size:40
Alignment explanation
Indices: 1582255--1582453 Score: 317
Period size: 40 Copynumber: 5.0 Consensus size: 40
1582245 ACCGTAGTGC
1582255 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
* *
1582295 TACATATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
* *
1582335 TACACATAAGGTCATGCCCAGCATATACACCAAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
** *
1582375 TACACATAAGGTCATGCCCAGTATATACACCAAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
**
1582415 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTA
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTA
1582454 CTATAAACTT
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 147 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
Found at i:1585178 original size:2 final size:2
Alignment explanation
Indices: 1585171--1585241 Score: 112
Period size: 2 Copynumber: 37.0 Consensus size: 2
1585161 TTAGATACTG
*
1585171 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA T- 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
1585212 TA TA T- TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1585242 AAAAAATAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
1 3 0.05
2 61 0.95
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1585184 original size:17 final size:16
Alignment explanation
Indices: 1585171--1585241 Score: 112
Period size: 15 Copynumber: 4.6 Consensus size: 16
1585161 TTAGATACTG
*
1585171 TATATATATAGATATA
1 TATATATATATATATA
1585187 TATATATATATATATA
1 TATATATATATATATA
1585203 T-TATATATATATAT-
1 TATATATATATATATA
1585217 TATATATATATATATA
1 TATATATATATATATA
1585233 T-TATATATA
1 TATATATATA
1585242 AAAAAATAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
14 1 0.02
15 34 0.65
16 17 0.33
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (16 bp):
TATATATATATATATA
Found at i:1590373 original size:2 final size:2
Alignment explanation
Indices: 1590366--1590395 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1590356 ATTTAAACAA
*
1590366 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1590396 GATTAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1590413 original size:5 final size:5
Alignment explanation
Indices: 1590403--1590428 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1590393 TATGATTAAT
1590403 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
1590429 AATAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:1592475 original size:45 final size:45
Alignment explanation
Indices: 1592370--1593157 Score: 1064
Period size: 45 Copynumber: 17.5 Consensus size: 45
1592360 GAGGTCTTAT
* * * * * *
1592370 CATCTTGCACTGGAGGTCTTACAGATGACACAAAGGATTT-TAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* * *
1592414 CATCGTGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* * * * *
1592459 CATCATGCACTAAAGGTCTTACAAATGACCCCAAAGGTTTTAAAAA
1 CATCATGCACTGAAGGTCTTACAGATGA-CCCGAAGGCTTTGAAAA
* * * *
1592505 TATCATGCACTGAAGGGCTTACAGATAACCTGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* * * * * *
1592550 CATCATGCATTGAAGGGCTTACAGAT-ACCCCAAAAGATTTAAAAA
1 CATCATGCACTGAAGGTCTTACAGATGA-CCCGAAGGCTTTGAAAA
*
1592595 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* *
1592640 CATCAT-CTACTGAAGGTCTTACAGATGACCTGAAGGTTTTGAAAA
1 CATCATGC-ACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* *
1592685 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* * *
1592730 CATCAAGCACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* *
1592775 CATCCTGCACTGAAGGTCTTACAAATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
*
1592820 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* * * *
1592865 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGATAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* *
1592910 CATCCTGTACTGAAGGGT-TTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAA-GGTCTTACAGATGACCCGAAGGCTTTGAAAA
* *
1592955 CATCATGCACTGAAGGGCTTACAGATGACTCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
*
1593000 CATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
*
1593045 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* *
1593090 CATCCTGCACTGAAGGGT-TTACAGATGACCCAAAGGCTTTGAAAA
1 CATCATGCACTGAA-GGTCTTACAGATGACCCGAAGGCTTTGAAAA
*
1593135 CATCATGCACTTAAGGTCTTACA
1 CATCATGCACTGAAGGTCTTACA
1593158 AATGTGGGAA
Statistics
Matches: 666, Mismatches: 68, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
44 43 0.06
45 577 0.87
46 46 0.07
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (45 bp):
CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
Found at i:1593858 original size:22 final size:22
Alignment explanation
Indices: 1593833--1593911 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
1593823 AATAAAGCTT
* *
1593833 TCATCTTTGAAAAAAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
1593855 TCATCTTTGTAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1593877 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1593899 TCATCTTTGAAGA
1 TCATCTTTGAAGA
1593912 ATGTAGATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1594385 original size:54 final size:53
Alignment explanation
Indices: 1594298--1594624 Score: 336
Period size: 54 Copynumber: 6.1 Consensus size: 53
1594288 ATAATCAATG
* * * *
1594298 GTTCATAAAACATTTGGCAACACATTCATCATTTCTTGTTACTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTT-CTTCTGCACAGAT
*
1594352 GTTTGTAAAACATTTGACAACACATTCATCATTTCATGTGGT-TTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGT--TCTTCTGCACAGAT
* * * * * *
1594406 GTTCATCAAACATTTGACAACACATTCATTATTTCCTGTGTCTTCTGTATAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGT-TCTTCTGCACAGAT
* ** *
1594460 GTTCGTAATACATTTGACAACATGTTCATTC-TTTCATATGGT-TTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCA-TCATTTC--ATGTTCTTCTGCACAGAT
* * * *
1594514 GTTTGTAAAACATTTGACAACACATTCATCCTTTCCTGTGTCTTCTGTACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGT-TCTTCTGCACAGAT
* * * * *
1594568 GTTCGTAATACATTTGACAGCACATTCATCCTTTCATGTGGCTTCTGCACATAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGT-TCTTCTGCACAGAT
1594622 GTT
1 GTT
1594625 TTCTATTGAA
Statistics
Matches: 228, Mismatches: 36, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
52 2 0.01
53 5 0.02
54 216 0.95
55 2 0.01
56 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTTCTTCTGCACAGAT
Found at i:1594625 original size:108 final size:108
Alignment explanation
Indices: 1594302--1594625 Score: 454
Period size: 108 Copynumber: 3.0 Consensus size: 108
1594292 TCAATGGTTC
* * * *
1594302 ATAAAACATTTGGCAACACATTCATCATTTCTTGT-TACTTCTGCT-CAGATGTTTGTAAAACAT
1 ATAAAACATTTGACAACACATTCATCATTTCCTGTGT-CTTCTG-TACAGATGTTCGTAATACAT
* *
1594365 TTGACAACACATTCATCATTTCATGTGGTTTCTGCACAGATGTTC
64 TTGACAACACATTCATCCTTTCATGTGGTTTCTGCACAGATGTTT
* * *
1594410 ATCAAACATTTGACAACACATTCATTATTTCCTGTGTCTTCTGTATAGATGTTCGTAATACATTT
1 ATAAAACATTTGACAACACATTCATCATTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTT
** * *
1594475 GACAACATGTTCATTCTTTCATATGGTTTCTGCACAGATGTTT
66 GACAACACATTCATCCTTTCATGTGGTTTCTGCACAGATGTTT
* *
1594518 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTT
1 ATAAAACATTTGACAACACATTCATCATTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTT
* * *
1594583 GACAGCACATTCATCCTTTCATGTGGCTTCTGCACATATGTTT
66 GACAACACATTCATCCTTTCATGTGGTTTCTGCACAGATGTTT
1594626 TCTATTGAAG
Statistics
Matches: 189, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
107 1 0.01
108 187 0.99
109 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (108 bp):
ATAAAACATTTGACAACACATTCATCATTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTT
GACAACACATTCATCCTTTCATGTGGTTTCTGCACAGATGTTT
Done.