Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 28
Found at i:1474276 original size:16 final size:16
Alignment explanation
Indices: 1474251--1474283 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1474241 TTAAAAATAA
*
1474251 AATTTTAAATTTTTAT
1 AATTTCAAATTTTTAT
1474267 AATTTCAAATTTTTAT
1 AATTTCAAATTTTTAT
1474283 A
1 A
1474284 TTAAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTCAAATTTTTAT
Found at i:1474654 original size:20 final size:21
Alignment explanation
Indices: 1474629--1474721 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1474619 TTTTCCCAAT
*
1474629 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1474649 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1474670 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1474690 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1474711 TCGCAATGCGA
1 TCGCAATGCGA
1474722 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1474674 original size:41 final size:41
Alignment explanation
Indices: 1474629--1474721 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1474619 TTTTCCCAAT
1474629 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1474670 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1474711 TCGCAATGCGA
1 TCGCAATGCGA
1474722 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1474734 original size:41 final size:41
Alignment explanation
Indices: 1474648--1474782 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1474638 GAATAAGTAA
** *
1474648 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
1474689 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
1474730 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
1474771 TTCGCAACGCGA
1 ATCGCAACGCGA
1474783 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:1474735 original size:20 final size:20
Alignment explanation
Indices: 1474710--1474803 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1474700 AATTGGGAAA
*
1474710 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
1474730 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
1474751 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
1474771 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
1474791 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1474804 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:1475019 original size:22 final size:22
Alignment explanation
Indices: 1474991--1475034 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1474981 CACTCTCTCA
1474991 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1475013 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1475035 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1476590 original size:18 final size:18
Alignment explanation
Indices: 1476569--1476613 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1476559 TCCACTTCGG
* *
1476569 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
1476587 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
1476605 GAGCCATCA
1 GAGCCATCA
1476614 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:1477177 original size:19 final size:19
Alignment explanation
Indices: 1477085--1477186 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
1477075 TAGTTTACTT
* **
1477085 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
1477104 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1477124 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1477143 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1477157 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1477176 TCGCAATGCGA
1 TCGCAACGCGA
1477187 TTTGTGTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 35 0.51
20 17 0.25
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1477217 original size:14 final size:14
Alignment explanation
Indices: 1477198--1477255 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1477188 TTGTGTTTCG
1477198 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1477212 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1477228 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1477244 CGTTGCGATTTT
1 CGTTGCGATTTT
1477256 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1477232 original size:32 final size:33
Alignment explanation
Indices: 1477193--1477271 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1477183 GCGATTTGTG
1477193 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1477225 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1477258 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1477272 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1477270 original size:19 final size:19
Alignment explanation
Indices: 1477212--1477329 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
1477202 GCGATTTTGT
1477212 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1477230 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1477244 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1477263 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1477283 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1477302 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1477322 TGTTGCGA
1 CGTTGCGA
1477330 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1479243 original size:19 final size:19
Alignment explanation
Indices: 1479219--1479315 Score: 141
Period size: 19 Copynumber: 5.4 Consensus size: 19
1479209 AAAACAGACT
* *
1479219 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
1479238 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1479257 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1479276 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
1479290 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1479309 ATCGCAA
1 ATCGCAA
1479316 CGAGAAAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
14 11 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 54 0.76
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1479289 original size:14 final size:14
Alignment explanation
Indices: 1479272--1479329 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 14
1479262 AATGCGAAAT
1479272 GAAAATCGCAACGA
1 GAAAATCGCAACGA
1479286 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
1479304 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
1479319 GAAAATCGCAA
1 GAAAATCGCAA
1479330 TGCTATTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 22 0.56
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 11 0.28
ACGTcount: A:0.50, C:0.19, G:0.21, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1479347 original size:33 final size:33
Alignment explanation
Indices: 1479219--1479332 Score: 165
Period size: 33 Copynumber: 3.3 Consensus size: 33
1479209 AAAACAGACT
* *
1479219 ATCGCAACGCGAAATGGAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
1479257 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1479290 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1479323 ATCGCAATGC
1 ATCGCAATGC
1479333 TATTTTCATT
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
33 47 0.64
34 1 0.01
36 2 0.03
38 24 0.32
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:1479410 original size:20 final size:20
Alignment explanation
Indices: 1479361--1479410 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1479351 CGATTTTCTT
*
1479361 GTTGCGATAACCATTTTCAC
1 GTTGCGATAGCCATTTTCAC
*
1479381 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCAC
1479401 GTTGCGATAG
1 GTTGCGATAG
1479411 TCAAATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCAC
Found at i:1480474 original size:24 final size:24
Alignment explanation
Indices: 1480447--1480500 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1480437 GTATTCGAAA
* *
1480447 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1480471 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1480495 TTTGAT
1 TTTGAT
1480501 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1480692 original size:12 final size:12
Alignment explanation
Indices: 1480675--1480699 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1480665 ATATAATCCT
1480675 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1480687 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1480699 G
1 G
1480700 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1482996 original size:19 final size:19
Alignment explanation
Indices: 1482974--1483104 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
1482964 GGAAATTACT
1482974 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1482993 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1483007 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1483026 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1483040 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1483059 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1483073 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1483092 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1483105 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1483016 original size:33 final size:33
Alignment explanation
Indices: 1482974--1483100 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
1482964 GGAAATTACT
1482974 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1483007 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1483039 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1483073 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1483101 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1483081 original size:66 final size:66
Alignment explanation
Indices: 1482975--1483107 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1482965 GAAATTACTA
*
1482975 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1483040 T
66 T
*
1483041 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1483106 T
66 T
1483107 T
1 T
1483108 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1483122 original size:19 final size:20
Alignment explanation
Indices: 1483100--1483142 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1483090 AAATCGCAAC
1483100 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1483119 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1483139 GCGA
1 GCGA
1483143 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1483127 original size:14 final size:14
Alignment explanation
Indices: 1483128--1483161 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1483118 TGCGATTTTC
1483128 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1483142 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1483156 ATTTTC
1 ATTTTC
1483162 ATTCGCATTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1483302 original size:14 final size:14
Alignment explanation
Indices: 1483283--1483319 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1483273 CATCAATTAA
1483283 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1483297 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1483311 ACAAATCAA
1 ACAAATCAA
1483320 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1484744 original size:42 final size:42
Alignment explanation
Indices: 1484698--1484781 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1484688 CGATGACAGT
* * *
1484698 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1484740 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
1484782 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1486759 original size:16 final size:16
Alignment explanation
Indices: 1486734--1486765 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1486724 TTTTGGTTGA
1486734 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
*
1486750 AATGAGAATCGCAACG
1 AATGAAAATCGCAACG
1486766 CGGAAATGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (16 bp):
AATGAAAATCGCAACG
Found at i:1486831 original size:32 final size:33
Alignment explanation
Indices: 1486732--1486849 Score: 139
Period size: 32 Copynumber: 3.5 Consensus size: 33
1486722 TCTTTTGGTT
** *
1486732 GAAATGAAAATCGCAACGAATGAGAATCGCAACGC
1 GAAATGACTATCGCAACG-A-GACAATCGCAACGC
*
1486767 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGACTATCGCAACGAGACAATCGCAACGC
*
1486801 GAAATGACTATCGCGAC-AGACAATCGCAACGC
1 GAAATGACTATCGCAACGAGACAATCGCAACGC
**
1486833 GAAATGAAAATCGCAAC
1 GAAATGACTATCGCAAC
1486850 CGCGAAATAA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 28 0.37
33 16 0.21
34 14 0.19
35 1 0.01
36 16 0.21
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGACTATCGCAACGAGACAATCGCAACGC
Found at i:1486846 original size:19 final size:19
Alignment explanation
Indices: 1486732--1486911 Score: 154
Period size: 19 Copynumber: 10.1 Consensus size: 19
1486722 TCTTTTGGTT
1486732 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1486749 G-AATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
1486767 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1486785 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
1486801 GAAATG---A-C-TATCGC
1 GAAATGAAAATCGCAACGC
* *
1486815 GACA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1486833 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1486853 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1486872 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1486891 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1486910 GA
1 GA
1486912 TTTTGGTTTC
Statistics
Matches: 132, Mismatches: 15, Indels: 30
0.75 0.08 0.17
Matches are distributed among these distances:
13 1 0.01
14 16 0.12
15 2 0.02
16 17 0.13
17 3 0.02
18 10 0.08
19 53 0.40
20 30 0.23
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1486865 original size:39 final size:38
Alignment explanation
Indices: 1486822--1486911 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
1486812 CGCGACAGAC
1486822 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
1486861 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
1486899 AATCGCAATGCGA
1 AATCGCAACGCGA
1486912 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:1486940 original size:19 final size:19
Alignment explanation
Indices: 1486907--1486951 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1486897 AAAATCGCAA
*
1486907 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1486926 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
1486945 TGCGATT
1 TGCGATT
1486952 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1487519 original size:20 final size:20
Alignment explanation
Indices: 1487494--1487545 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1487484 CGCTATGTAA
*
1487494 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
1487514 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
1487534 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1487546 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:1487602 original size:20 final size:20
Alignment explanation
Indices: 1487577--1487648 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
1487567 TAGTAAGTAT
1487577 CGTTGCGATTTTCCAATTCG
1 CGTTGCGATTTTCCAATTCG
**
1487597 CGTTGCGATTTTACTTATTCG
1 CGTTGCGATTTT-CCAATTCG
*
1487618 CATTGCGATTTTCCAATTCG
1 CGTTGCGATTTTCCAATTCG
1487638 CGTTGCGATTT
1 CGTTGCGATTT
1487649 ACTTATTCGC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCCAATTCG
Found at i:1487656 original size:20 final size:20
Alignment explanation
Indices: 1487577--1487665 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
1487567 TAGTAAGTAT
*
1487577 CGTTGCGATTTTCCAATTCG
1 CGTTGCGATTTACCAATTCG
**
1487597 CGTTGCGATTTTACTTATTCG
1 CGTTGCGA-TTTACCAATTCG
* *
1487618 CATTGCGATTTTCCAATTCG
1 CGTTGCGATTTACCAATTCG
**
1487638 CGTTGCGATTTACTTATTCG
1 CGTTGCGATTTACCAATTCG
*
1487658 CATTGCGA
1 CGTTGCGA
1487666 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 40 0.71
21 16 0.29
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTACCAATTCG
Found at i:1487661 original size:40 final size:41
Alignment explanation
Indices: 1487579--1487665 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
1487569 GTAAGTATCG
1487579 TTGCGATTTTCCAATTCGCGTTGCGATTTTACTTATTCGCA
1 TTGCGATTTTCCAATTCGCGTTGCGATTTTACTTATTCGCA
1487620 TTGCGATTTTCCAATTCGCGTTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCAATTCGCGTTGCGATTTTACTTATTCGCA
1487660 TTGCGA
1 TTGCGA
1487666 ATTGGGAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 20 0.43
41 26 0.57
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (41 bp):
TTGCGATTTTCCAATTCGCGTTGCGATTTTACTTATTCGCA
Found at i:1488284 original size:15 final size:14
Alignment explanation
Indices: 1488251--1488297 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
1488241 TTCATTTTCC
*
1488251 TTTCTCTCCCTCTCA
1 TTTCTCTCCCTCT-T
1488266 TTTCTCTCCCTCATT
1 TTTCTCTCCCTC-TT
*
1488281 TTTCTCCCCCTCTT
1 TTTCTCTCCCTCTT
1488295 TTT
1 TTT
1488298 AAAATCTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 5 0.17
15 23 0.79
16 1 0.03
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTCTCTCCCTCTT
Found at i:1489297 original size:32 final size:32
Alignment explanation
Indices: 1489261--1489362 Score: 93
Period size: 32 Copynumber: 3.1 Consensus size: 32
1489251 TAAATAAATT
*
1489261 TTATTTTAATTTGAGATATTAAAAAGATATAT
1 TTATTTTAATTTGAGATATTAAAAAGATATAA
* *
1489293 TTATTTTAATATTCA-A-AGTTAAATAGATAATAA
1 TTATTTTAAT-TTGAGATA-TTAAAAAGAT-ATAA
* *
1489326 ATACCTTTTAATTTGAGATATTCAAAAGA-ATAA
1 TTA--TTTTAATTTGAGATATTAAAAAGATATAA
1489359 TTAT
1 TTAT
1489363 CATACTAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
31 2 0.04
32 20 0.36
33 14 0.25
34 3 0.05
35 15 0.27
36 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (32 bp):
TTATTTTAATTTGAGATATTAAAAAGATATAA
Found at i:1489300 original size:61 final size:61
Alignment explanation
Indices: 1489203--1489317 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 61
1489193 TAATAATATC
* * * *
1489203 TTTTAATTTGAAATATTCAAAATATAGATACCTTTTACTATTCAAACTTAAATAAATTTTA
1 TTTTAATTTGAAATATTAAAAAGATAGATACATTTTAATATTCAAACTTAAATAAATTTTA
* * ** *
1489264 TTTTAATTTGAGATATTAAAAAGATATATTTATTTTAATATTCAAAGTTAAATA
1 TTTTAATTTGAAATATTAAAAAGATAGATACATTTTAATATTCAAACTTAAATA
1489318 GATAATAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 45 1.00
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (61 bp):
TTTTAATTTGAAATATTAAAAAGATAGATACATTTTAATATTCAAACTTAAATAAATTTTA
Found at i:1489382 original size:67 final size:67
Alignment explanation
Indices: 1489264--1489389 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 67
1489254 ATAAATTTTA
** *
1489264 TTTTAATTTGAGATATTAAAAAGATATATTTATTTTAATATTCAAAGTTAAATAGATAATAAATA
1 TTTTAATTTGAGATATTAAAAAGATATATTTATACTAATATTCAAAGTTAAAGAGATAATAAATA
1489329 CC
66 CC
*
1489331 TTTTAATTTGAGATATTCAAAAGA-ATAATTATCATACTAATATTC-AA-TTAAAGAGATAA
1 TTTTAATTTGAGATATTAAAAAGATAT-ATT-T-ATACTAATATTCAAAGTTAAAGAGATAA
1489390 ATTTAAATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
66 2 0.04
67 37 0.71
68 3 0.06
69 10 0.19
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (67 bp):
TTTTAATTTGAGATATTAAAAAGATATATTTATACTAATATTCAAAGTTAAAGAGATAATAAATA
CC
Found at i:1490766 original size:309 final size:303
Alignment explanation
Indices: 1490330--1490923 Score: 929
Period size: 309 Copynumber: 1.9 Consensus size: 303
1490320 CTATTTTTTT
*
1490330 TCATGAACACAAAATACCCATAATGCACTCTTGCACTCATACAAGCAAACAAACTACACTAATGA
1 TCATGAACACAAAATACCCATAATACACTCTTGCACTCATACAAGCAAACAAACTACACTAATGA
* *
1490395 TCTACAAGCGTTATAGACGAGTTAGGAGTGTGTTACCTTGGTCCTAGCTGATGGGAAAAACCTCC
66 TCTACAAGCGTTATAGACGAGTTAGGAATGTGTTACATTGGTCCTAGCTGATGGGAAAAACCTCC
* *
1490460 AAGTTACTAAAGCATTAGCTTCTATTAT-TTTTTTCCTTTGAAGCACTCTCTAACTTTTCTCACC
131 AAGTTACTAAAGCATTAGCTTCTATT-TGTTCTTGCCTTTGAAGCACTCTCTAACTTTTCTCACC
1490524 AATAACAAGAAAAGAAAATAAATTACTAACTCGTTTTAGGAATTAAAATGAGTGGGAATATGATT
195 AATAACAAGAAAAG-AAATAAATTACTAACTCGTTTTAGGAATTAAAATGAGTGGG-A-ATGATT
*
1490589 TCCATCCTTTAGAATTGGATTGGAAACAACATCAAAATATCATTTTCC
257 TCCATCATTTAGAATTGGA-TGGAAACAACATCAAAATATCATTTTCC
*
1490637 TCATGAACACAAATATACCCATAATACACTCTTGCACTCATACAAGCAAACAAGCTACACTTAAT
1 TCATGAACACAAA-ATACCCATAATACACTCTTGCACTCATACAAGCAAACAAACTACAC-TAAT
* * * * * *
1490702 GATCTTCAAGCGTTATATATGATTTAGGAATGTTTTACATTGGTCCTAGCTGCTGGGAAAAACCT
64 GATCTACAAGCGTTATAGACGAGTTAGGAATGTGTTACATTGGTCCTAGCTGATGGGAAAAACCT
* * * * *
1490767 CCAAGTTACTAAATCATTAGTTTCTCTTTGTTCTTGCCTTTGGAGCACTCTCTAACTTTTCTCGC
129 CCAAGTTACTAAAGCATTAGCTTCTATTTGTTCTTGCCTTTGAAGCACTCTCTAACTTTTCTCAC
* * *
1490832 CAATCACAAGCAAAGAAATGAATTACTAACTCGTTTTAGGAATTAAAATGAGTGGGAATGATTTC
194 CAATAACAAGAAAAGAAATAAATTACTAACTCGTTTTAGGAATTAAAATGAGTGGGAATGATTTC
1490897 CATCATTTAGAATTGGATGGAAACAAC
259 CATCATTTAGAATTGGATGGAAACAAC
1490924 CTAAAGCCCT
Statistics
Matches: 263, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
305 10 0.04
306 24 0.09
307 14 0.05
308 85 0.32
309 130 0.49
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (303 bp):
TCATGAACACAAAATACCCATAATACACTCTTGCACTCATACAAGCAAACAAACTACACTAATGA
TCTACAAGCGTTATAGACGAGTTAGGAATGTGTTACATTGGTCCTAGCTGATGGGAAAAACCTCC
AAGTTACTAAAGCATTAGCTTCTATTTGTTCTTGCCTTTGAAGCACTCTCTAACTTTTCTCACCA
ATAACAAGAAAAGAAATAAATTACTAACTCGTTTTAGGAATTAAAATGAGTGGGAATGATTTCCA
TCATTTAGAATTGGATGGAAACAACATCAAAATATCATTTTCC
Found at i:1494460 original size:40 final size:42
Alignment explanation
Indices: 1494387--1494472 Score: 131
Period size: 40 Copynumber: 2.1 Consensus size: 42
1494377 AACGTCATAA
* *
1494387 TAATGTTATTTAATCTATTTTAGGCATTATTTTCACCTAAT-C
1 TAATGTAATATAATCTA-TTTAGGCATTATTTTCACCTAATGC
1494429 TAATGTAATATAATCTA-TTAGGCATTATTTTCACCTAATGC
1 TAATGTAATATAATCTATTTAGGCATTATTTTCACCTAATGC
1494470 TAA
1 TAA
1494473 GATGTGATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 22 0.54
41 4 0.10
42 15 0.37
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (42 bp):
TAATGTAATATAATCTATTTAGGCATTATTTTCACCTAATGC
Found at i:1496805 original size:47 final size:48
Alignment explanation
Indices: 1496736--1496830 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
1496726 ATATGGATAT
1496736 AACATTAAAAGAATATTTAAAAG-TTTAAAGTGGGAGATTACTCTGAA
1 AACATTAAAAGAATATTTAAAAGTTTTAAAGTGGGAGATTACTCTGAA
1496783 AACATTAAAAGAATATTTAAAAGTTTTAAAGTGGGAGATTACTCTGAA
1 AACATTAAAAGAATATTTAAAAGTTTTAAAGTGGGAGATTACTCTGAA
1496831 TCACATGGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 23 0.49
48 24 0.51
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (48 bp):
AACATTAAAAGAATATTTAAAAGTTTTAAAGTGGGAGATTACTCTGAA
Found at i:1499684 original size:26 final size:26
Alignment explanation
Indices: 1499629--1499678 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1499619 ACCATAAGCA
1499629 GGGTATCGATACCTAAGGGCCAGAAG
1 GGGTATCGATACCTAAGGGCCAGAAG
1499655 GGGTATCGATACCTAAGGGCCAGA
1 GGGTATCGATACCTAAGGGCCAGA
1499679 TTGGGTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.34, T:0.16
Consensus pattern (26 bp):
GGGTATCGATACCTAAGGGCCAGAAG
Found at i:1500213 original size:45 final size:45
Alignment explanation
Indices: 1500158--1500303 Score: 152
Period size: 45 Copynumber: 3.3 Consensus size: 45
1500148 GTATAAAGAA
* *** * *
1500158 AAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTG
1 AAATGCATATGGGTACATTATCAACATGAAAGCATGCTATAGTTG
* * * *
1500203 AAATGTATATGAGTACATTATCAACA-GAAAAGCATACTTTAGTTG
1 AAATGCATATGGGTACATTATCAACATG-AAAGCATGCTATAGTTG
* * *
1500248 AAATGTATATGGGTACATTATCAACATGAAAGTATG-TAGAGTTG
1 AAATGCATATGGGTACATTATCAACATGAAAGCATGCTATAGTTG
1500292 AAATGCATATGG
1 AAATGCATATGG
1500304 TTTAAATGAA
Statistics
Matches: 83, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
44 18 0.22
45 64 0.77
46 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (45 bp):
AAATGCATATGGGTACATTATCAACATGAAAGCATGCTATAGTTG
Found at i:1500833 original size:2 final size:2
Alignment explanation
Indices: 1500820--1500859 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1500810 TGAAGGAATC
* *
1500820 TA TA TA TG TA TA TA TA TA TA TG 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
1500860 ATGTACAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1500837 original size:14 final size:14
Alignment explanation
Indices: 1500820--1500859 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
1500810 TGAAGGAATC
1500820 TATATATGTATATA
1 TATATATGTATATA
1500834 TATATATGTATATA
1 TATATATGTATATA
*
1500848 TATATATATATA
1 TATATATGTATA
1500860 ATGTACAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (14 bp):
TATATATGTATATA
Found at i:1504270 original size:2 final size:2
Alignment explanation
Indices: 1504265--1504294 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1504255 ATAAAAATGG
1504265 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
1504295 TCTTATATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1504798 original size:22 final size:21
Alignment explanation
Indices: 1504749--1504808 Score: 95
Period size: 22 Copynumber: 2.9 Consensus size: 21
1504739 AGGGTCTACG
*
1504749 TGGTCCTTC-GGACATATACA
1 TGGTCCTTCGGGACAAATACA
1504769 TGGTCCTTCGGGACAAATACA
1 TGGTCCTTCGGGACAAATACA
1504790 TAGGTCCTTCGGGACAAAT
1 T-GGTCCTTCGGGACAAAT
1504809 TTCATATGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
20 9 0.24
21 11 0.30
22 17 0.46
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
TGGTCCTTCGGGACAAATACA
Found at i:1505123 original size:15 final size:16
Alignment explanation
Indices: 1505081--1505125 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
1505071 GATAAAAAGA
*
1505081 ATTAGTGATAATATATG
1 ATTAATGATAA-ATATG
*
1505098 ATTATTGATAAATATG
1 ATTAATGATAAATATG
1505114 -TTAATGATAAAT
1 ATTAATGATAAAT
1505126 GTATAGGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 11 0.42
16 5 0.19
17 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (16 bp):
ATTAATGATAAATATG
Found at i:1505547 original size:18 final size:17
Alignment explanation
Indices: 1505521--1505573 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 17
1505511 ATGAACGTTT
1505521 TAAATTTTATGAATTTA
1 TAAATTTTATGAATTTA
* *
1505538 TACATATTTATAAAATTTTA
1 TAAAT-TTTAT-GAA-TTTA
1505558 TAAATTTTATGAATTT
1 TAAATTTTATGAATTT
1505574 TATGAATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 7 0.24
20 8 0.28
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
TAAATTTTATGAATTTA
Found at i:1505557 original size:10 final size:9
Alignment explanation
Indices: 1505521--1505582 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
1505511 ATGAACGTTT
1505521 TAAATTTTA
1 TAAATTTTA
*
1505530 TGAA-TTTA
1 TAAATTTTA
*
1505538 TACATATTTA
1 TAAAT-TTTA
1505548 TAAAATTTTA
1 T-AAATTTTA
1505558 TAAATTTTA
1 TAAATTTTA
*
1505567 TGAATTTTA
1 TAAATTTTA
*
1505576 TGAATTT
1 TAAATTT
1505583 CGGGTACTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.13
9 26 0.58
10 10 0.22
11 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (9 bp):
TAAATTTTA
Found at i:1505574 original size:18 final size:18
Alignment explanation
Indices: 1505521--1505582 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
1505511 ATGAACGTTT
1505521 TAAATTTTATGAA-TTTA
1 TAAATTTTATGAATTTTA
* *
1505538 TACATATTTATAAAATTTTA
1 TAAAT-TTTAT-GAATTTTA
1505558 TAAATTTTATGAATTTTA
1 TAAATTTTATGAATTTTA
*
1505576 TGAATTT
1 TAAATTT
1505583 CGGGTACTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.11
18 18 0.49
19 7 0.19
20 8 0.22
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (18 bp):
TAAATTTTATGAATTTTA
Found at i:1509513 original size:31 final size:31
Alignment explanation
Indices: 1509475--1509541 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1509465 AGTTACGTCG
* *
1509475 GGGACCATATTGGAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACAGACTAAATGTTGA
*
1509506 GGGACCATATTGCAAACAGACTAAATGTTGG
1 GGGACCATATTGCAAACAGACTAAATGTTGA
1509537 GGGAC
1 GGGAC
1509542 TGTATTACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACTAAATGTTGA
Found at i:1510257 original size:32 final size:32
Alignment explanation
Indices: 1510220--1510407 Score: 236
Period size: 32 Copynumber: 5.9 Consensus size: 32
1510210 ATTGACGCTC
*
1510220 CTGTGCATTATCTGAATGCAACACTAACTTTG
1 CTGTGCATTATCTGAATGCAACACTGACTTTG
* *
1510252 TTGTGCATTATCTGAATGCAACACTAACTTTG
1 CTGTGCATTATCTGAATGCAACACTGACTTTG
* *
1510284 TTGTGCATTATCTGAATGTAACACTGACTCTT-
1 CTGTGCATTATCTGAATGCAACACTGACT-TTG
* * *
1510316 CTGTGTATTATCTGAATACAACACTGA-TTATA
1 CTGTGCATTATCTGAATGCAACACTGACTT-TG
* *
1510348 CTATGCATTATCTGAATGCAATACTGACTTTG
1 CTGTGCATTATCTGAATGCAACACTGACTTTG
* *
1510380 CTGTGCATTATATAAATGCAACACTGAC
1 CTGTGCATTATCTGAATGCAACACTGAC
1510408 ACTAATATAC
Statistics
Matches: 136, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.01
31 2 0.01
32 129 0.95
33 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (32 bp):
CTGTGCATTATCTGAATGCAACACTGACTTTG
Found at i:1510355 original size:96 final size:96
Alignment explanation
Indices: 1510192--1510407 Score: 254
Period size: 96 Copynumber: 2.2 Consensus size: 96
1510182 TATATGTTGA
* ** * * * * ** *
1510192 GCATTATCTAAATGCGGCATTGACGCTCCTGTGCATTATCTGAATGCAACACTAACTTTGTTGTG
1 GCATTATATAAATGCAACACTGACTCTTCTGTGCATTATCTGAATACAACACTAACTTTACTATG
*
1510257 CATTATCTGAATGCAACACTAACTTTGTTGT
66 CATTATCTGAATGCAACACTAACTTTGCTGT
* * * * *
1510288 GCATTATCTGAATGTAACACTGACTCTTCTGTGTATTATCTGAATACAACACTGA-TTATACTAT
1 GCATTATATAAATGCAACACTGACTCTTCTGTGCATTATCTGAATACAACACTAACTT-TACTAT
* *
1510352 GCATTATCTGAATGCAATACTGACTTTGCTGT
65 GCATTATCTGAATGCAACACTAACTTTGCTGT
1510384 GCATTATATAAATGCAACACTGAC
1 GCATTATATAAATGCAACACTGAC
1510408 ACTAATATAC
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
95 2 0.02
96 98 0.98
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (96 bp):
GCATTATATAAATGCAACACTGACTCTTCTGTGCATTATCTGAATACAACACTAACTTTACTATG
CATTATCTGAATGCAACACTAACTTTGCTGT
Found at i:1513372 original size:311 final size:310
Alignment explanation
Indices: 1512805--1513424 Score: 1008
Period size: 311 Copynumber: 2.0 Consensus size: 310
1512795 ATGCGAAACA
*
1512805 TCAAAATATCCTATTTTCCTCATGAACACAAATATATCCATAATGCACTCTTGCACTCATACAAG
1 TCAAAATATCCTATTTTCCTCATGAACACAAATATACCCATAATGCACTCTTGCACTCATACAAG
*
1512870 AAAACAAATACACTTAATGATCTACAAGCGTTATAGACGAGTTAGGAGTGTGTTACCTTGGACCT
66 AAAACAAATACACTTAATGATCTACAAGCGTTATAGACGAGTTAGAAGTGTGTTACCTTGGACCT
* * * * * *
1512935 AGTTGTTGGGGAAAATCTCCAAGTTACTAAAGCATTAGCTTCTCTTTGTTCTTTCCTTTGGAGCA
131 AGCTGCTGGGAAAAACCTCCAACTTACTAAAGCATTAGCTTCTCTTTGTTCTTGCCTTTGGAGCA
* *
1513000 CTCTCTAACTTTTCTCACCAATCACAAGCAAAGAAAATGAATTACTAACTCGTTTTAGGAATTAA
196 CTCTCTAACTTTTCTCACCAATCACAAGCAAAGAAAATGAATTAATAACTCGTTCTAGGAATTAA
* * *
1513065 AACGAGTGGGAATATGATTTATAACCTTTAGAATTGGATTGGAAGCAACG
261 AACGAGTGGGAATATGATTTACAACCTTTAGAATTAGATTGGAAACAACG
* * **
1513115 TCAAAATATCCTATTTTCCTCATGAACACACATATACCCATGATGCGTTCTTGCACTCATACAAG
1 TCAAAATATCCTATTTTCCTCATGAACACAAATATACCCATAATGCACTCTTGCACTCATACAAG
* * *
1513180 CAAACAAACTACGCTTAATGATCTACAAGCGTTATAGACGAGTTAGAAGTGTGTTACCTTGGTCC
66 AAAACAAA-TACACTTAATGATCTACAAGCGTTATAGACGAGTTAGAAGTGTGTTACCTTGGACC
*
1513245 TAGCTGCTGGGAAAAACCTTCAACTTACTAAAGCATTAGCTTCTCTTTGTTCTTGCCTTTGGAGC
130 TAGCTGCTGGGAAAAACCTCCAACTTACTAAAGCATTAGCTTCTCTTTGTTCTTGCCTTTGGAGC
1513310 ACTCT-TAAACTTTTCTCACCAATCACAAGCAAAGAAAATGAATTAATAACTCGTTCTAGGAATT
195 ACTCTCT-AACTTTTCTCACCAATCACAAGCAAAGAAAATGAATTAATAACTCGTTCTAGGAATT
* *
1513374 AAAATGAGTGGGAATATGATTTCCAACCTTTAGAATTAGATTGGAAACAAC
259 AAAACGAGTGGGAATATGATTTACAACCTTTAGAATTAGATTGGAAACAAC
1513425 CTAAAGCCCT
Statistics
Matches: 285, Mismatches: 23, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
310 68 0.24
311 217 0.76
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (310 bp):
TCAAAATATCCTATTTTCCTCATGAACACAAATATACCCATAATGCACTCTTGCACTCATACAAG
AAAACAAATACACTTAATGATCTACAAGCGTTATAGACGAGTTAGAAGTGTGTTACCTTGGACCT
AGCTGCTGGGAAAAACCTCCAACTTACTAAAGCATTAGCTTCTCTTTGTTCTTGCCTTTGGAGCA
CTCTCTAACTTTTCTCACCAATCACAAGCAAAGAAAATGAATTAATAACTCGTTCTAGGAATTAA
AACGAGTGGGAATATGATTTACAACCTTTAGAATTAGATTGGAAACAACG
Found at i:1518365 original size:18 final size:18
Alignment explanation
Indices: 1518342--1518395 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
1518332 ATATGTAACT
1518342 GATTTTAAAGATGATTGG
1 GATTTTAAAGATGATTGG
1518360 GA-TTT-----TGATTGG
1 GATTTTAAAGATGATTGG
*
1518372 GATTTTAAAGATGATTGC
1 GATTTTAAAGATGATTGG
1518390 GATTTT
1 GATTTT
1518396 GATTGCCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
12 9 0.31
13 3 0.10
17 3 0.10
18 14 0.48
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.44
Consensus pattern (18 bp):
GATTTTAAAGATGATTGG
Found at i:1518368 original size:12 final size:12
Alignment explanation
Indices: 1518353--1518377 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1518343 ATTTTAAAGA
1518353 TGATTGGGATTT
1 TGATTGGGATTT
1518365 TGATTGGGATTT
1 TGATTGGGATTT
1518377 T
1 T
1518378 AAAGATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (12 bp):
TGATTGGGATTT
Found at i:1518376 original size:30 final size:30
Alignment explanation
Indices: 1518342--1518400 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1518332 ATATGTAACT
*
1518342 GATTTTAAAGATGATTGGGATTTTGATTGG
1 GATTTTAAAGATGATTGCGATTTTGATTGG
1518372 GATTTTAAAGATGATTGCGATTTTGATTG
1 GATTTTAAAGATGATTGCGATTTTGATTG
1518401 CCTTTTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (30 bp):
GATTTTAAAGATGATTGCGATTTTGATTGG
Found at i:1520468 original size:12 final size:12
Alignment explanation
Indices: 1520451--1520475 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1520441 TCTTCGGGGA
1520451 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1520463 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1520475 C
1 C
1520476 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1521781 original size:20 final size:20
Alignment explanation
Indices: 1521756--1521813 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1521746 ATTCATTTGA
1521756 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1521776 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1521796 CTATTGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1521814 CGCAATGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1522000 original size:14 final size:14
Alignment explanation
Indices: 1521981--1522017 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1521971 CATCAATTAA
1521981 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1521995 ACAAATCATCTTTT
1 ACAAATCAACATTT
1522009 ACAAATCAA
1 ACAAATCAA
1522018 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1523915 original size:20 final size:19
Alignment explanation
Indices: 1523875--1523940 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1523865 GAAACTTAAA
*
1523875 ATCGCAACGCAAAATGACT
1 ATCGCAACGCGAAATGACT
*
1523894 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* *
1523914 ATCGCAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
1523932 ATCGCAACG
1 ATCGCAACG
1523941 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.20
19 16 0.40
20 16 0.40
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1523949 original size:14 final size:14
Alignment explanation
Indices: 1523930--1523987 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
1523920 ATGCGAAATG
1523930 AAATCGCAACGACA
1 AAATCGCAACGACA
*
1523944 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
1523963 AAATCGCAACGACA
1 AAATCGCAACGACA
1523977 AAATCGCAACG
1 AAATCGCAACG
1523988 CGAAACACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:1523950 original size:32 final size:33
Alignment explanation
Indices: 1523914--1523992 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1523904 GGAAATGGCT
1523914 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1523946 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1523979 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1523993 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 16 0.36
33 29 0.64
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1523965 original size:19 final size:19
Alignment explanation
Indices: 1523856--1523973 Score: 77
Period size: 19 Copynumber: 6.4 Consensus size: 19
1523846 TAGTTTACTT
* *
1523856 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
1523876 TCGCAACGCAAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
1523895 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1523915 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1523933 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
1523947 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1523966 TCGCAACG
1 TCGCAACG
1523974 ACAAAATCGC
Statistics
Matches: 78, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
14 10 0.13
16 4 0.05
18 8 0.10
19 29 0.37
20 27 0.35
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1524000 original size:33 final size:33
Alignment explanation
Indices: 1523914--1524003 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
1523904 GGAAATGGCT
* *
1523914 ATCGCAATGCGAAAT-GAAATCGCAACGACAAA
1 ATCGCAACGCGAAATCAAAATCGCAACGACAAA
* *
1523946 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATCAAAATCGCAACGACAAA
1523979 ATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAACGCGAAATCA-AAATCGCA
1524004 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 16 0.30
33 37 0.70
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATCAAAATCGCAACGACAAA
Found at i:1524038 original size:14 final size:14
Alignment explanation
Indices: 1524015--1524078 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
1524005 TGCGATTTTC
1524015 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
1524028 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
1524042 ATTTCATTTCGCATTGCG
1 ATTT--TGTCG--TTGCG
1524060 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
1524074 ATTTT
1 ATTTT
1524079 CATTTCGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.14
14 21 0.48
16 8 0.18
18 9 0.20
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:1524085 original size:33 final size:33
Alignment explanation
Indices: 1524004--1524094 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1523994 ACAAATCGCA
* *
1524004 TTGCGATTTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1524037 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1524069 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1524095 AGCCATTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1524130 original size:20 final size:20
Alignment explanation
Indices: 1524081--1524133 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1524071 GCGATTTTCA
*
1524081 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
1524101 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
1524121 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
1524134 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:1524659 original size:18 final size:18
Alignment explanation
Indices: 1524617--1524659 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1524607 CGATCAGATG
* *
1524617 ATGGCTCTGGGTGAGGTG
1 ATGGCTCTGGGCGAGGTA
*
1524635 ATAGCTCTGGGCGAGGTA
1 ATGGCTCTGGGCGAGGTA
1524653 ATGGCTC
1 ATGGCTC
1524660 CCGAAGTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.26
Consensus pattern (18 bp):
ATGGCTCTGGGCGAGGTA
Found at i:1526024 original size:20 final size:20
Alignment explanation
Indices: 1525976--1526034 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1525966 AATAGTTTCT
** *
1525976 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1525996 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1526016 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1526035 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1526296 original size:22 final size:22
Alignment explanation
Indices: 1526269--1526312 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1526259 GATGGAGATA
1526269 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1526291 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1526313 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1526582 original size:41 final size:42
Alignment explanation
Indices: 1526480--1526596 Score: 123
Period size: 41 Copynumber: 2.9 Consensus size: 42
1526470 CGCTTTGAAA
* * **
1526480 ATCGCATTGCGAAAGTCAGAATCGCGTTGCGA--AAGTCAGT
1 ATCGCATTGCGAAAGTCAGTATCACGTTGCGATTTTGTCAGT
* * * *
1526520 ATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGAAAGTCAGTATCACGTTGCGATTTTGTCAGT
* *
1526561 ATCGCATTGCGATAGTCAGTATCACATTGCGATTTT
1 ATCGCATTGCGAAAGTCAGTATCACGTTGCGATTTT
1526597 CCCAATTCGC
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 28 0.44
41 33 0.52
42 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
ATCGCATTGCGAAAGTCAGTATCACGTTGCGATTTTGTCAGT
Found at i:1526593 original size:20 final size:20
Alignment explanation
Indices: 1526480--1526592 Score: 102
Period size: 20 Copynumber: 5.6 Consensus size: 20
1526470 CGCTTTGAAA
*
1526480 ATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGAAAGTCAGT
*
1526500 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGAAAGTCAGT
* *
1526520 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGAAAGTCAGT
* * ** *
1526540 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--AAGTCAGT
*
1526561 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGAAAGTCAGT
*
1526581 ATCACATTGCGA
1 ATCGCATTGCGA
1526593 TTTTCCCAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (20 bp):
ATCGCATTGCGAAAGTCAGT
Found at i:1526612 original size:41 final size:41
Alignment explanation
Indices: 1526519--1526614 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
1526509 CGAAAGTCAG
* * * ** *
1526519 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCAA
* *
1526560 TATCGCATTGCGATAGTCAGTATCACATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCACATTGCGATTTT-CCAA
1526602 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
1526615 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCAA
Found at i:1529358 original size:2 final size:2
Alignment explanation
Indices: 1529353--1529380 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1529343 AAAAATACGA
1529353 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
1529381 GGTTAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1530537 original size:16 final size:17
Alignment explanation
Indices: 1530516--1530551 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1530506 TTTTTTGCCC
1530516 ATTTGTTTATTTATT-T
1 ATTTGTTTATTTATTAT
1530532 ATTTGTTTATTTATTAT
1 ATTTGTTTATTTATTAT
1530549 ATT
1 ATT
1530552 AATTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (17 bp):
ATTTGTTTATTTATTAT
Found at i:1530556 original size:9 final size:10
Alignment explanation
Indices: 1530538--1530585 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 10
1530528 ATTTATTTGT
*
1530538 TTATTTATTA
1 TTATTAATTA
1530548 -TATTAATTA
1 TTATTAATTA
1530557 TTATTAGTATTA
1 TTATTA--ATTA
1530569 TTATT-ATTA
1 TTATTAATTA
1530578 TTATTAAT
1 TTATTAAT
1530586 CTTTTACAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 17 0.52
10 7 0.21
12 9 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TTATTAATTA
Found at i:1530559 original size:3 final size:3
Alignment explanation
Indices: 1530542--1530583 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
1530532 ATTTGTTTAT
*
1530542 TTA TTA -TA TTAA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1530584 ATCTTTTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1532958 original size:27 final size:27
Alignment explanation
Indices: 1532918--1532971 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1532908 TAATTTATAC
*
1532918 GTATTTCATATTTAGGTCATTGATTTA
1 GTATTTCATATTTAGGTCACTGATTTA
* *
1532945 GTATTTTATGTTTAGGTCACTGATTTA
1 GTATTTCATATTTAGGTCACTGATTTA
1532972 TTTCTGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (27 bp):
GTATTTCATATTTAGGTCACTGATTTA
Found at i:1534671 original size:45 final size:46
Alignment explanation
Indices: 1534602--1534711 Score: 186
Period size: 45 Copynumber: 2.4 Consensus size: 46
1534592 TTAGTCATTT
1534602 ATTTCATTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGG
1 ATTT-ATTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGG
*
1534649 -TTTATTTTTTGAATAAGCATGCGAATTAGATATCATGCGGTTAGG
1 ATTTATTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGG
1534694 ATTTATTTTTGTGAATAA
1 ATTTATTTTT-TGAATAA
1534712 CAAAGCATGG
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
45 41 0.68
46 12 0.20
47 7 0.12
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (46 bp):
ATTTATTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGG
Found at i:1540775 original size:2 final size:2
Alignment explanation
Indices: 1540763--1540796 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1540753 AGATCATCCC
*
1540763 AT AT GT 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
1540797 CTTCTCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1544310 original size:29 final size:28
Alignment explanation
Indices: 1544270--1544345 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
1544260 TTGAAGAAGA
1544270 AATAAAAGAGAA-AAAAAAAATGAAAAAT
1 AATAAAAGAGAAGAAAAAAAA-GAAAAAT
* *
1544298 AATAAAATTAGAAGAAGAAAAAGAAAAA-
1 AATAAAA-GAGAAGAAAAAAAAGAAAAAT
*
1544326 AAGAAAA-AG-AGAAAAGAAAA
1 AATAAAAGAGAAGAAAA-AAAA
1544346 TGATGGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
25 5 0.12
26 6 0.15
28 13 0.32
29 10 0.24
30 7 0.17
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (28 bp):
AATAAAAGAGAAGAAAAAAAAGAAAAAT
Found at i:1544328 original size:8 final size:8
Alignment explanation
Indices: 1544309--1544430 Score: 68
Period size: 8 Copynumber: 14.2 Consensus size: 8
1544299 ATAAAATTAG
1544309 AAGAAGAAA
1 AAGAA-AAA
1544318 AAGAAAAA
1 AAGAAAAA
1544326 AAGAAAAA
1 AAGAAAAA
*
1544334 GAGAAAAGAA
1 AAG-AAA-AA
**
1544344 AATGATGGAA
1 AA-GA-AAAA
**
1544354 AA-ACGAA
1 AAGAAAAA
1544361 AAGAAAAA
1 AAGAAAAA
1544369 AAGAAAAA
1 AAGAAAAA
1544377 AATGGAAAATA
1 AA--GAAAA-A
1544388 GAAGAAAAA
1 -AAGAAAAA
*
1544397 ATGAAAAA
1 AAGAAAAA
*
1544405 AA-ATGAAA
1 AAGA-AAAA
1544413 AAGAAAAA
1 AAGAAAAA
*
1544421 ATGAAAAA
1 AAGAAAAA
1544429 AA
1 AA
1544431 AGAGAAAAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 23
0.71 0.10 0.18
Matches are distributed among these distances:
7 6 0.07
8 51 0.57
9 10 0.11
10 18 0.20
11 2 0.02
12 2 0.02
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (8 bp):
AAGAAAAA
Found at i:1544356 original size:29 final size:30
Alignment explanation
Indices: 1544323--1544440 Score: 95
Period size: 30 Copynumber: 3.9 Consensus size: 30
1544313 AGAAAAAGAA
* **
1544323 AAAAAGAAAAAG-AGAAAAGAAAATGATGG
1 AAAAAGAAAAAGAAAAAAAGAAAAAAATGG
1544352 AAAAACG-AAAAGAAAAAAAGAAAAAAATGG
1 AAAAA-GAAAAAGAAAAAAAGAAAAAAATGG
*
1544382 AAAATAG---AAGAAAAAATGAAAAAAAAT-G
1 AAAA-AGAAAAAGAAAAAAAG-AAAAAAATGG
*
1544410 AAAAAGAAAAAATGAAAAAAAAGAGAAAAAT
1 AAAAAG-AAAAA-G-AAAAAAAGAAAAAAAT
1544441 TAAGATGAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
27 2 0.03
28 15 0.21
29 18 0.25
30 20 0.27
31 3 0.04
32 8 0.11
33 7 0.10
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.07
Consensus pattern (30 bp):
AAAAAGAAAAAGAAAAAAAGAAAAAAATGG
Found at i:1544356 original size:30 final size:31
Alignment explanation
Indices: 1544309--1544440 Score: 91
Period size: 30 Copynumber: 4.4 Consensus size: 31
1544299 ATAAAATTAG
* *
1544309 AAGAAGAAAAA-GAAAAAAAGAAAAAG-AGAA
1 AAGAA-AAAAATGGAAAAAAGAAAAAGAAAAA
** *
1544339 AAGAAAATGATGGAAAAACG-AAAAGAAAAA
1 AAGAAAAAAATGGAAAAAAGAAAAAGAAAAA
*
1544369 AAGAAAAAAATGGAAAATAG---AAGAAAAA
1 AAGAAAAAAATGGAAAAAAGAAAAAGAAAAA
*
1544397 ATGAAAAAAAAT-G-AAAAAGAAAAAATGAAAAAA
1 AAG-AAAAAAATGGAAAAAAG-AAAAA-G-AAAAA
*
1544430 AAGAGAAAAAT
1 AAGAAAAAAAT
1544441 TAAGATGAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
27 5 0.06
28 11 0.14
29 16 0.20
30 31 0.39
31 2 0.03
32 8 0.10
33 7 0.09
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (31 bp):
AAGAAAAAAATGGAAAAAAGAAAAAGAAAAA
Found at i:1544374 original size:51 final size:52
Alignment explanation
Indices: 1544309--1544430 Score: 142
Period size: 52 Copynumber: 2.3 Consensus size: 52
1544299 ATAAAATTAG
**
1544309 AAGAAGAAAAAGAAAAAAA-GAAAAAGAGAA-AAGAAAATGATGGAAAAACG-AA
1 AAGAA-AAAAAGAAAAAAATGAAAAAGAGAAGAA-AAAATGA-AAAAAAACGAAA
* * *
1544361 AAGAAAAAAAGAAAAAAATGGAAAATAGAAGAAAAAATGAAAAAAAATGAAA
1 AAGAAAAAAAGAAAAAAATGAAAAAGAGAAGAAAAAATGAAAAAAAACGAAA
*
1544413 AAGAAAAAATGAAAAAAA
1 AAGAAAAAAAGAAAAAAA
1544431 AGAGAAAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
51 19 0.31
52 40 0.66
53 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (52 bp):
AAGAAAAAAAGAAAAAAATGAAAAAGAGAAGAAAAAATGAAAAAAAACGAAA
Found at i:1544384 original size:10 final size:9
Alignment explanation
Indices: 1544359--1544440 Score: 54
Period size: 9 Copynumber: 9.6 Consensus size: 9
1544349 TGGAAAAACG
1544359 AAAA-GAAA
1 AAAATGAAA
1544367 AAAA-GAAA
1 AAAATGAAA
1544375 AAAATGGAAA
1 AAAAT-GAAA
1544385 ATAGAA-G-AA
1 A-A-AATGAAA
1544394 AAAATGAAAA
1 AAAATG-AAA
1544404 AAAATG--A
1 AAAATGAAA
1544411 AAAA-G-AA
1 AAAATGAAA
1544418 AAAATGAAA
1 AAAATGAAA
* *
1544427 AAAAAGAGA
1 AAAATGAAA
1544436 AAAAT
1 AAAAT
1544441 TAAGATGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
6 1 0.02
7 12 0.20
8 15 0.25
9 16 0.26
10 14 0.23
11 1 0.02
12 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (9 bp):
AAAATGAAA
Found at i:1544393 original size:28 final size:27
Alignment explanation
Indices: 1544282--1544421 Score: 90
Period size: 28 Copynumber: 4.9 Consensus size: 27
1544272 TAAAAGAGAA
* *
1544282 AAAAAAAATGAAAAATAATAAAATTAGAAG
1 AAAAAAAATGAAAAAGAAGAAAA--A-AAG
* *
1544312 AAGAAAAA-GAAAAA-AAGAAAAAGAG
1 AAAAAAAATGAAAAAGAAGAAAAAAAG
1544337 AAAAGAAAATGATGGAAAAACGAAAAGAAAAAAAG
1 -AAA-AAAA--AT-GAAAAA-G--AAGAAAAAAAG
*
1544372 -AAAAAAATGGAAAATAGAAGAAAAAATG
1 AAAAAAAAT-GAAAA-AGAAGAAAAAAAG
1544400 AAAAAAAATGAAAAAGAA-AAAA
1 AAAAAAAATGAAAAAGAAGAAAA
1544422 TGAAAAAAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
25 2 0.02
26 7 0.08
27 8 0.09
28 21 0.23
29 15 0.16
30 16 0.17
31 7 0.08
32 4 0.04
33 2 0.02
35 10 0.11
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.08
Consensus pattern (27 bp):
AAAAAAAATGAAAAAGAAGAAAAAAAG
Found at i:1544438 original size:24 final size:24
Alignment explanation
Indices: 1544329--1544438 Score: 84
Period size: 24 Copynumber: 4.5 Consensus size: 24
1544319 AGAAAAAAAG
**
1544329 AAAAAGAGAAAAG--AAAATGATGG
1 AAAAAGAGAAAAGAAAAAATGA-AA
* *
1544352 AAAAA-CGAAAAGAAAAAAAGAAA
1 AAAAAGAGAAAAGAAAAAATGAAA
* *
1544375 AAAATGGAAAATAGAAGAAAAAATGAAA
1 AAAA-AG-AGA-A-AAGAAAAAATGAAA
1544403 AAAAATGA-AAAAGAAAAAATGAAA
1 AAAAA-GAGAAAAGAAAAAATGAAA
1544427 AAAAAGAGAAAA
1 AAAAAGAGAAAA
1544439 ATTAAGATGA
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
22 6 0.09
23 11 0.16
24 29 0.42
25 1 0.01
26 2 0.03
27 2 0.03
28 18 0.26
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.06
Consensus pattern (24 bp):
AAAAAGAGAAAAGAAAAAATGAAA
Found at i:1545855 original size:55 final size:55
Alignment explanation
Indices: 1545772--1546247 Score: 528
Period size: 55 Copynumber: 8.9 Consensus size: 55
1545762 GAAGCAAACT
* *
1545772 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * *
1545823 AGTTCGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
** *
1545878 CGTTTCATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
*
1545933 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * *
1545988 CGTTT-TATGAAGATTGCTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACA
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * *
1546043 CGTTTGTTAAAGA---TT-GAGTCCTATA--CTCTGAAAGAATAG-GAGCGGAC-
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* *
1546090 CTGTTTATTGAAGATT-TTCCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 C-GTTTGTTGAAGATTGTT-CGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * *
1546146 CGTTTTATTGAAGATTG-TCAAG-TCTTATACTCTCTGAA-GAATAGAGAGCAGACA
1 CG-TTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACA
* *
1546200 CATTT-TATGAAGATT-TT-GAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 CGTTTGT-TGAAGATTGTTCGAGTTC-TATACTCT-CTGAAGGAATAGAGAGC
1546248 AGACTCATCA
Statistics
Matches: 369, Mismatches: 34, Indels: 42
0.83 0.08 0.09
Matches are distributed among these distances:
47 1 0.00
48 17 0.05
49 13 0.04
50 2 0.01
51 21 0.06
52 27 0.07
53 22 0.06
54 33 0.09
55 217 0.59
56 16 0.04
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
Found at i:1545920 original size:110 final size:109
Alignment explanation
Indices: 1545787--1546247 Score: 581
Period size: 110 Copynumber: 4.3 Consensus size: 109
1545777 GTTGAAGATT
* * * *
1545787 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
*
1545852 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATT-TTC
*
1545897 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
*
1545962 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGCTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATT-TTC
* *
1546007 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTAAAGA---TT-GAGTCCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
* *
1546068 --CTCTGAAAGAATAG-GAGCGGACCTG-TTTATTGAAGATTTTCC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTTT-C
* * * * *
1546110 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTG-TCAAG-TCTTA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACG-TTTGTTGAAGATTGTTCGAGTTC-TA
* * *
1546173 TACTCTCTGAA-GAATAGAGAGCAGACACATTTTATGAAGATTTT-
64 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTTTC
1546217 GAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGGGAGC
1546248 AGACTCATCA
Statistics
Matches: 312, Mismatches: 25, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
102 5 0.02
103 54 0.17
104 22 0.07
106 14 0.04
107 33 0.11
108 6 0.02
109 24 0.08
110 154 0.49
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (109 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTTTC
Found at i:1548915 original size:45 final size:45
Alignment explanation
Indices: 1548807--1549093 Score: 442
Period size: 45 Copynumber: 6.4 Consensus size: 45
1548797 TCATTTATCC
1548807 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA-TT-ATT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATT
*
1548850 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTAATT
1 -CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATT
1548896 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATT
*
1548941 CATAAGCTCGTAAGCTTATTTTACC-ATATAATTACCATTTAATT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATT
*
1548985 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATAC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAAT-T
**
1549031 CATAAGCTCGTAAGCTTA-TTTACCAATATACTTGTCA-TT-ATT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATT
* *
1549073 CCATAAGCTTGTAAGTTTATT
1 -CATAAGCTCGTAAGCTTATT
1549094 GCATGGTTAC
Statistics
Matches: 227, Mismatches: 10, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
43 18 0.08
44 83 0.37
45 105 0.46
46 21 0.09
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (45 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATT
Found at i:1548916 original size:89 final size:91
Alignment explanation
Indices: 1548807--1549093 Score: 453
Period size: 89 Copynumber: 3.2 Consensus size: 91
1548797 TCATTTATCC
1548807 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA-TT-ATTCCATAAGCTCGTAAGCTTAT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTAT
*
1548870 TTTACCAACATACTTACCATTTAATT
66 TTTACCAATATACTTACCATTTAATT
1548896 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATT-CATAAGCTCGTAAGCTTAT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTAT
*
1548960 TTTACC-ATATAATTACCATTTAATT
66 TTTACCAATATACTTACCATTTAATT
*
1548985 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTA-
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTAT
**
1549049 TTTACCAATATACTTGTCA-TT-ATT
66 TTTACCAATATACTTACCATTTAATT
* *
1549073 CCATAAGCTTGTAAGTTTATT
1 -CATAAGCTCGTAAGCTTATT
1549094 GCATGGTTAC
Statistics
Matches: 185, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
88 3 0.02
89 125 0.68
90 54 0.29
91 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (91 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTAT
TTTACCAATATACTTACCATTTAATT
Found at i:1549002 original size:134 final size:133
Alignment explanation
Indices: 1548801--1549093 Score: 441
Period size: 134 Copynumber: 2.2 Consensus size: 133
1548791 ATTTTATCAT
* *
1548801 TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAATTACCATTATTCCATAAGCTCGTAAGC
*
1548866 TTATTTTACCAACATACTTACCATTTAAT-TCATAAGCTCGTAAGCTTATTTTACCAATATACTT
66 TTATTTTACCAACATACTTACCATTTAATACCATAAGCTCGTAAGCTTA-TTTACCAATATACTT
1548930 ACCA
130 ACCA
1548934 TTTAATT-CATAAGCTCGTAAGCTTATTTTACC-ATATAATTACCATTTAATT-CATAAGCTCGT
1 -TT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATAATTACCA-TT-ATTCCATAAGCTCGT
*
1548996 AAGCTTATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTACCAATATA
62 AAGCTTATTTTACCAACATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTACCAATATA
**
1549061 CTTGTCA
127 CTTACCA
* *
1549068 TTATTCCATAAGCTTGTAAGTTTATT
1 TTATTCCATAAGCTCGTAAGCTTATT
1549094 GCATGGTTAC
Statistics
Matches: 146, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
132 3 0.02
133 31 0.21
134 89 0.61
135 23 0.16
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (133 bp):
TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAATTACCATTATTCCATAAGCTCGTAAGC
TTATTTTACCAACATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTACCAATATACTTA
CCA
Found at i:1554601 original size:43 final size:43
Alignment explanation
Indices: 1554540--1554667 Score: 188
Period size: 43 Copynumber: 3.0 Consensus size: 43
1554530 TGGCTTTAGA
1554540 GAAGTTAGGAGTGAAAGTTATCCCTTATATGTAAAGTTTTGTT
1 GAAGTTAGGAGTGAAAGTTATCCCTTATATGTAAAGTTTTGTT
1554583 GAAGTTAGGAGTGAAAGTTATCTCC-TATATGTAAAGTTTTGTT
1 GAAGTTAGGAGTGAAAGTTATC-CCTTATATGTAAAGTTTTGTT
* * * * *
1554626 GAAGTTAGAAGTGAAAGCTA-CCTTTATATATAAAATTTTGTT
1 GAAGTTAGGAGTGAAAGTTATCCCTTATATGTAAAGTTTTGTT
1554668 TGATGTACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
41 1 0.01
42 17 0.22
43 58 0.74
44 2 0.03
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (43 bp):
GAAGTTAGGAGTGAAAGTTATCCCTTATATGTAAAGTTTTGTT
Found at i:1561575 original size:54 final size:52
Alignment explanation
Indices: 1561481--1561587 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 52
1561471 GATGATTGAG
*
1561481 AAATCTGGGCAGAAACCAGCCAAAGATGAATGTGTTGTCAAATGTTTTACGA
1 AAATCTGGGCAAAAACCAGCCAAAGATGAATGTGTTGTCAAATGTTTTACGA
*
1561533 AAATCTGGGCAAAAACCA-CAGGAAATGATGAATGTGTTGTCAAATGTTTTACGA
1 AAATCTGGGCAAAAACCAGC--CAAA-GATGAATGTGTTGTCAAATGTTTTACGA
1561587 A
1 A
1561588 CCAGTAATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
51 1 0.02
52 17 0.34
53 3 0.06
54 29 0.58
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (52 bp):
AAATCTGGGCAAAAACCAGCCAAAGATGAATGTGTTGTCAAATGTTTTACGA
Found at i:1561984 original size:22 final size:22
Alignment explanation
Indices: 1561956--1562018 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
1561946 ACATCTACAT
1561956 TCTTCAAAGATGATAGATTC-A
1 TCTTCAAAGATGATAGATTCTA
1561977 CTCTTCAAAGATGATAGATTCTA
1 -TCTTCAAAGATGATAGATTCTA
* *
1562000 TTTTCAAAGATGAAAGATT
1 TCTTCAAAGATGATAGATT
1562019 TATTGGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 37 0.97
23 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTA
Found at i:1562547 original size:122 final size:123
Alignment explanation
Indices: 1562393--1562848 Score: 736
Period size: 123 Copynumber: 3.7 Consensus size: 123
1562383 CACTCAATGG
*
1562393 ATCAACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* *
1562457 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGT
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAAATCAGC
*
1562516 ATCAACATTTCCAGAG-GAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
1562580 ATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCATAGAAAGAGATAAATCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAAATCAGC
* * **
1562638 ATCAATATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTTGTA
1 ATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
1562703 ATGAGAAGAACTTGTTTAACCTTTTGCTTGACTCTATCACAGAAGGAGATATATCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAAATCAGC
* *
1562761 ATCAATATTTCCATAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
1562826 ATGAGAAGAACTTGTTCGACCTT
66 ATGAGAAGAACTTGTTCAACCTT
1562849 AGCTTGATTC
Statistics
Matches: 307, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
122 114 0.37
123 192 0.63
124 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (123 bp):
ATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAAATCAGC
Found at i:1563099 original size:137 final size:138
Alignment explanation
Indices: 1562761--1563124 Score: 468
Period size: 139 Copynumber: 2.6 Consensus size: 138
1562751 ATATATCAGC
* *
1562761 ATCAATATTTCCATAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAG-GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * *
1562826 ATGAGAAGAACTTGTTCGACCTTAGCTTGATTCATCATCTATGGAGTTGAATGAAAGAAGAACTT
65 ATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCATCTATGAAGTTGAATCAAAGAAGAACCT
1562891 CACTTGAGG
130 CACTTGAGG
* * *
1562900 ATCAACATTTTCAGAGGAAGTTCATAATGAGAAGAAATCATCT-AAAATGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGG-AGTTCATAATGAGAAGAACTCATCTGAAGA-GGAAGAAGAAGTTCAT
* * * *
1562964 AATAAGAAGAACTTGTTCAACCTT-GACTTAATTCATTA-CATATGAAGTTGAATCAACG-A-CA
64 AATGAGAAGAACTTGTTCAACCTTAG-CTTAATTCATCATC-TATGAAGTTGAATCAAAGAAGAA
**
1563025 CCTCTTTTGAGG
127 CCTCACTTGAGG
* *
1563037 ATTAGCATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAG-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
1563102 ATGAGAATAACTTGTTCAACCTT
65 ATGAGAAGAACTTGTTCAACCTT
1563125 TTGTTAGATT
Statistics
Matches: 196, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
137 83 0.42
138 13 0.07
139 100 0.51
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (138 bp):
ATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCATCTATGAAGTTGAATCAAAGAAGAACCTC
ACTTGAGG
Found at i:1564867 original size:2 final size:2
Alignment explanation
Indices: 1564860--1564926 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1564850 ATATCATGCT
1564860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1564902 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 T
1564927 TTACTTTAGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1564987 original size:24 final size:23
Alignment explanation
Indices: 1564947--1565000 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1564937 TTTATTTACA
1564947 TTATTTTTTAAGGAAAAATTATC
1 TTATTTTTTAAGGAAAAATTATC
*
1564970 TTATTTTTTTAGGAAAAATTATC
1 TTATTTTTTAAGGAAAAATTATC
1564993 TTATTTTT
1 TTATTTTT
1565001 ATCAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (23 bp):
TTATTTTTTAAGGAAAAATTATC
Found at i:1565012 original size:21 final size:18
Alignment explanation
Indices: 1564988--1565027 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1564978 TTAGGAAAAA
1564988 TTATCTTATTTTTATCAATAT
1 TTAT-TTATTTTT-T-AATAT
1565009 TTATTTATTTTTTAATAT
1 TTATTTATTTTTTAATAT
1565027 T
1 T
1565028 AAGAATGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 1 0.05
20 8 0.42
21 4 0.21
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTATTTTTTAATAT
Found at i:1565204 original size:133 final size:136
Alignment explanation
Indices: 1564970--1565220 Score: 375
Period size: 133 Copynumber: 1.9 Consensus size: 136
1564960 AAAAATTATC
* ** **
1564970 TTATTTTTTTAGGAAAAATTATCTTATTTTTATCAATATTTATTTATTTTTTAATATTAAGAATG
1 TTATTTTCTTAGGAAAAATTATAATATTTTTATCAATATTTATTTATTTTTTAATATTAAGAAAA
* *
1565035 AGGCTGTCTTAAAACAACTAGATGTCATTTTCTGATATTTTGAAATAAATAAAATACTATATTTA
66 AAGATGTCTTAAAACAACTAGATGTCATTTTCTGATATTTTGAAATAAATAAAATACTATATTTA
1565100 TTTAAA
131 TTTAAA
*
1565106 TTATTTTCTTAGG-AAAATTATAATATTTTTAT-ATTTATTTATTTA-TTTTTAATATTAA-AAA
1 TTATTTTCTTAGGAAAAATTATAATATTTTTATCA-ATATTTATTTATTTTTTAATATTAAGAAA
* *
1565167 AAAGATGTCTTAAAGCAACTAGATGTCATTTTCTGATATTTTTAAATAAATAAA
65 AAAGATGTCTTAAAACAACTAGATGTCATTTTCTGATATTTTGAAATAAATAAA
1565221 TAAATACCCT
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
133 51 0.49
134 14 0.13
135 27 0.26
136 12 0.12
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.48
Consensus pattern (136 bp):
TTATTTTCTTAGGAAAAATTATAATATTTTTATCAATATTTATTTATTTTTTAATATTAAGAAAA
AAGATGTCTTAAAACAACTAGATGTCATTTTCTGATATTTTGAAATAAATAAAATACTATATTTA
TTTAAA
Found at i:1568650 original size:20 final size:20
Alignment explanation
Indices: 1568624--1568691 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
1568614 AATAGTTAAA
1568624 TCGCAACACGAATTTTGATT
1 TCGCAACACGAATTTTGATT
* *
1568644 TCACAACTCG-ATTTTCGGA-T
1 TCGCAACACGAATTTT--GATT
*
1568664 TCGCAACACGAATTTTAATT
1 TCGCAACACGAATTTTGATT
1568684 TCGCAACA
1 TCGCAACA
1568692 GCTTTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 6 0.15
20 26 0.67
21 7 0.18
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (20 bp):
TCGCAACACGAATTTTGATT
Found at i:1568857 original size:16 final size:16
Alignment explanation
Indices: 1568836--1568874 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1568826 TCCCCATCTC
* *
1568836 TAATTTTGTTTTTACA
1 TAATTTTATTTCTACA
*
1568852 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
1568868 TAATTTT
1 TAATTTT
1568875 TCAATGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:1571962 original size:18 final size:18
Alignment explanation
Indices: 1571939--1571974 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1571929 AAGAAAAAGG
*
1571939 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1571957 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1571975 CAGCCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1572435 original size:20 final size:20
Alignment explanation
Indices: 1572278--1572429 Score: 178
Period size: 20 Copynumber: 7.6 Consensus size: 20
1572268 AGGTACACTT
*
1572278 TCGCAACGCGAAAGTCAACA
1 TCGCAACGCGAAAGTCAAAA
* * *
1572298 TCGTAACGCGAAAGTTAAAT
1 TCGCAACGCGAAAGTCAAAA
*
1572318 TTGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
* *
1572338 CCGCAACGTGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
**
1572358 TCGCAATACGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
* * *
1572378 CCGCAACGCAAAAATCAAAA
1 TCGCAACGCGAAAGTCAAAA
* *
1572398 TCGCAGCGCGAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAA
1572418 TCGCAACGCGAA
1 TCGCAACGCGAA
1572430 CTTCAATTTG
Statistics
Matches: 106, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 106 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:1572459 original size:20 final size:20
Alignment explanation
Indices: 1572434--1572472 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1572424 CGCGAACTTC
1572434 AATTTGGAACATGCGTTGCG
1 AATTTGGAACATGCGTTGCG
*
1572454 AATTTGGAACATGTGTTGC
1 AATTTGGAACATGCGTTGC
1572473 AAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (20 bp):
AATTTGGAACATGCGTTGCG
Found at i:1572506 original size:20 final size:20
Alignment explanation
Indices: 1572483--1572567 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
1572473 AAAATTAAAG
*
1572483 TTCGCGTTGCGAATTTGACT
1 TTCGCGTTGCGATTTTGACT
* *
1572503 TTCGCGCTGCGATTTTGATT
1 TTCGCGTTGCGATTTTGACT
* *
1572523 TTCACGTTGCGGTTTTGACT
1 TTCGCGTTGCGATTTTGACT
****
1572543 TTTATTTTGCGATTTTGACT
1 TTCGCGTTGCGATTTTGACT
1572563 TTCGC
1 TTCGC
1572568 ATTGTGAAAA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTGACT
Found at i:1572640 original size:16 final size:16
Alignment explanation
Indices: 1572621--1572656 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1572611 TGCAGAGTCA
* *
1572621 AATTAAACAACAAATC
1 AATTAAACAAAAAAAC
1572637 AATTAAACAAAAAAAC
1 AATTAAACAAAAAAAC
1572653 AATT
1 AATT
1572657 CTTATTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (16 bp):
AATTAAACAAAAAAAC
Found at i:1572737 original size:20 final size:20
Alignment explanation
Indices: 1572715--1572843 Score: 150
Period size: 20 Copynumber: 6.5 Consensus size: 20
1572705 TTCCTTGAAT
* *
1572715 TCGCAACGCGAAAATCAAAT
1 TCGCAACGCGAAAGTCAAAA
*** * *
1572735 TCGCGTTGCGAAAGACAAAT
1 TCGCAACGCGAAAGTCAAAA
*
1572755 TCGCAACGTGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
1572775 TCGCAACGAGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
1572795 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
* **
1572815 TCACAACATGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
1572835 TCGCAACGC
1 TCGCAACGC
1572844 AAATTTGACT
Statistics
Matches: 90, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:1572808 original size:60 final size:60
Alignment explanation
Indices: 1572715--1572842 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
1572705 TTCCTTGAAT
* * *** * * *
1572715 TCGCAACGCGAAAATCAAATTCGCGTTGCGAAAGACAAATTCGCAACGTGAAAGTCAAAA
1 TCGCAACGAGAAAATCAAAATCGCAACGCGAAAGACAAAATCACAACATGAAAGTCAAAA
* *
1572775 TCGCAACGAGAAAGTCAAAATCGCAACGCGAAAGTCAAAATCACAACATGAAAGTCAAAA
1 TCGCAACGAGAAAATCAAAATCGCAACGCGAAAGACAAAATCACAACATGAAAGTCAAAA
1572835 TCGCAACG
1 TCGCAACG
1572843 CAAATTTGAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.14
Consensus pattern (60 bp):
TCGCAACGAGAAAATCAAAATCGCAACGCGAAAGACAAAATCACAACATGAAAGTCAAAA
Found at i:1572872 original size:20 final size:20
Alignment explanation
Indices: 1572847--1572963 Score: 139
Period size: 20 Copynumber: 5.8 Consensus size: 20
1572837 GCAACGCAAA
*
1572847 TTTGACTTTTGCGTTGGGAT
1 TTTGACTTTTGCGTTGCGAT
* *
1572867 TTTGACTTTCT-CGTTCCGAA
1 TTTGACTTT-TGCGTTGCGAT
*
1572887 TTTGACTTTGGCGTTGCGAT
1 TTTGACTTTTGCGTTGCGAT
1572907 TTTGACTTTCT-CGTTGCGAT
1 TTTGACTTT-TGCGTTGCGAT
* *
1572927 TTTGACTTTCGTGTTGCGAT
1 TTTGACTTTTGCGTTGCGAT
*
1572947 TTTGACTTTCGCGTTGC
1 TTTGACTTTTGCGTTGC
1572964 AAAAGTGTAC
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
20 82 0.99
21 1 0.01
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (20 bp):
TTTGACTTTTGCGTTGCGAT
Found at i:1572951 original size:60 final size:60
Alignment explanation
Indices: 1572847--1572963 Score: 166
Period size: 60 Copynumber: 1.9 Consensus size: 60
1572837 GCAACGCAAA
* *
1572847 TTTGACTTTTGCGTTGGGATTTTGACTTTCTCGTTCCGAATTTGACTTTGGCGTTGCGAT
1 TTTGACTTTTGCGTTGCGATTTTGACTTTCTCGTTCCGAATTTGACTTTCGCGTTGCGAT
* *
1572907 TTTGACTTTCT-CGTTGCGATTTTGACTTTCGT-GTTGCGATTTTGACTTTCGCGTTGC
1 TTTGACTTT-TGCGTTGCGATTTTGACTTTC-TCGTTCCGAATTTGACTTTCGCGTTGC
1572964 AAAAGTGTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (60 bp):
TTTGACTTTTGCGTTGCGATTTTGACTTTCTCGTTCCGAATTTGACTTTCGCGTTGCGAT
Found at i:1572962 original size:40 final size:40
Alignment explanation
Indices: 1572845--1572963 Score: 175
Period size: 40 Copynumber: 3.0 Consensus size: 40
1572835 TCGCAACGCA
* * *
1572845 AATTTGACTTTTGCGTTGGGATTTTGACTTTCTCGTTCCG
1 AATTTGACTTTCGCGTTGCGATTTTGACTTTCTCGTTGCG
*
1572885 AATTTGACTTTGGCGTTGCGATTTTGACTTTCTCGTTGCG
1 AATTTGACTTTCGCGTTGCGATTTTGACTTTCTCGTTGCG
* * *
1572925 ATTTTGACTTTCGTGTTGCGATTTTGACTTTCGCGTTGC
1 AATTTGACTTTCGCGTTGCGATTTTGACTTTCTCGTTGC
1572964 AAAAGTGTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (40 bp):
AATTTGACTTTCGCGTTGCGATTTTGACTTTCTCGTTGCG
Found at i:1573053 original size:14 final size:13
Alignment explanation
Indices: 1573019--1573128 Score: 68
Period size: 13 Copynumber: 8.5 Consensus size: 13
1573009 TGAAATTAAA
1573019 AAACAAATCAATT
1 AAACAAATCAATT
1573032 AAACAAATCAACTT
1 AAACAAATCAA-TT
**
1573046 TTACAAATCAATT
1 AAACAAATCAATT
*
1573059 AAAC-AAGCAA--
1 AAACAAATCAATT
*
1573069 AAA-ATAA-GAATT
1 AAACA-AATCAATT
* *
1573081 ATTTACACATCAATT
1 A--AACAAATCAATT
1573096 AAACAAATCAACTT
1 AAACAAATCAA-TT
**
1573110 TTACAAATCAATT
1 AAACAAATCAATT
1573123 AAACAA
1 AAACAA
1573129 GCAAAAATAA
Statistics
Matches: 72, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
10 5 0.07
11 2 0.03
12 6 0.08
13 29 0.40
14 24 0.33
15 6 0.08
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.25
Consensus pattern (13 bp):
AAACAAATCAATT
Found at i:1573099 original size:64 final size:64
Alignment explanation
Indices: 1573025--1573199 Score: 298
Period size: 63 Copynumber: 2.8 Consensus size: 64
1573015 TAAAAAACAA
1573025 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACAC
1 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACAC
*** * *
1573089 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAATAATTCTTATTTCCTC
1 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACAC
1573152 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAA
1 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAA
1573200 AGTGTACCCA
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
63 58 0.55
64 47 0.45
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.27
Consensus pattern (64 bp):
ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACAC
Found at i:1573120 original size:27 final size:27
Alignment explanation
Indices: 1573082--1573191 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 27
1573072 ATAAGAATTA
*
1573082 TTTACACATCAATTAAACAAATCAACT
1 TTTACAAATCAATTAAACAAATCAACT
1573109 TTTACAAATCAATTAAACAAGCAAAAAT-AATTCTT
1 TTTACAAATCAATT--A-AA-C--AAATCAA--C-T
* **
1573144 ATTTCCTCATCAATTAAACAAATCAACT
1 -TTTACAAATCAATTAAACAAATCAACT
1573172 TTTACAAATCAATTAAACAA
1 TTTACAAATCAATTAAACAA
1573192 GCAAAAAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
27 30 0.46
28 1 0.02
29 2 0.03
30 6 0.09
31 3 0.05
32 3 0.05
33 6 0.09
34 2 0.03
35 1 0.02
36 11 0.17
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.31
Consensus pattern (27 bp):
TTTACAAATCAATTAAACAAATCAACT
Found at i:1574564 original size:21 final size:21
Alignment explanation
Indices: 1574538--1574651 Score: 87
Period size: 21 Copynumber: 5.4 Consensus size: 21
1574528 GTGAATCTGG
* *
1574538 CTCTTGAACAGTGGGAGGGAC
1 CTCTTGAACAGTGGAAGGGGC
1574559 CTCTTGAAC-GAT-GATAGGGGC
1 CTCTTGAACAG-TGGA-AGGGGC
*
1574580 CTCTTGAATAGTGGAAGGGGC
1 CTCTTGAACAGTGGAAGGGGC
*
1574601 CTCTTGAA-GGAT-GATAGGGGC
1 CTCTTGAACAG-TGGA-AGGGGC
*
1574622 CTCTTGAAC-GATAGG-AGAGGC
1 CTCTTGAACAG-T-GGAAGGGGC
1574643 CTCTTGAAC
1 CTCTTGAAC
1574652 GATGACAGGT
Statistics
Matches: 79, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
20 5 0.06
21 70 0.89
22 3 0.04
23 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (21 bp):
CTCTTGAACAGTGGAAGGGGC
Found at i:1574604 original size:42 final size:40
Alignment explanation
Indices: 1574538--1574656 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 40
1574528 GTGAATCTGG
*
1574538 CTCTTGAACAGTGGGAGGGACCTCTTGAACGATGATAGGGGC
1 CTCTTGAA-AGT-GGAGGGGCCTCTTGAACGATGATAGGGGC
*
1574580 CTCTTGAATAGTGGAAGGGGCCTCTTGAAGGATGATAGGGGC
1 CTCTTGAA-AGTGG-AGGGGCCTCTTGAACGATGATAGGGGC
* *
1574622 CTCTTGAACGATAGGAGAGGCCTCTTGAACGATGA
1 CTCTTGAAAG-T-GGAGGGGCCTCTTGAACGATGA
1574657 CAGGTGAATC
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
41 3 0.04
42 63 0.93
43 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (40 bp):
CTCTTGAAAGTGGAGGGGCCTCTTGAACGATGATAGGGGC
Done.