Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007746.1 Hibiscus syriacus cultivar Beakdansim tig00110009_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: 3674400
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 15
Found at i:3295 original size:20 final size:20
Alignment explanation
Indices: 3272--3310 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3262 AAATTTTGGC
*
3272 TTTTTTGGCTTTTTTTTTGT
1 TTTTTTGCCTTTTTTTTTGT
3292 TTTTTTGCCTTTTTTTTTG
1 TTTTTTGCCTTTTTTTTTG
3311 AAAAAAAAAT
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:0.00, C:0.08, G:0.13, T:0.79
Consensus pattern (20 bp):
TTTTTTGCCTTTTTTTTTGT
Found at i:3308 original size:19 final size:19
Alignment explanation
Indices: 3272--3308 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3262 AAATTTTGGC
*
3272 TTTTTTGGCTTTTTTTTTG
1 TTTTTTGGCCTTTTTTTTG
*
3291 TTTTTTTGCCTTTTTTTT
1 TTTTTTGGCCTTTTTTTT
3309 TGAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (19 bp):
TTTTTTGGCCTTTTTTTTG
Found at i:9531 original size:15 final size:15
Alignment explanation
Indices: 9495--9524 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9485 AGTGCTTCAA
9495 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
9509 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
9524 T
1 T
9525 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:9550 original size:24 final size:26
Alignment explanation
Indices: 9523--9576 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
9513 TTTGCTTTTC
9523 TTCTTTTT-GAGTGC-T-AGATTTGTT
1 TTCTTTTTGGAGTGCTTCA-ATTTGTT
9547 TTCTTTTTGGAGTGCTTCAATTTGTT
1 TTCTTTTTGGAGTGCTTCAATTTGTT
9573 TTCT
1 TTCT
9577 GATTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 8 0.30
25 6 0.22
26 12 0.44
27 1 0.04
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (26 bp):
TTCTTTTTGGAGTGCTTCAATTTGTT
Found at i:12101 original size:19 final size:20
Alignment explanation
Indices: 12073--12112 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
12063 GAATAATAAT
12073 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
*
12093 ATAAG-AATGAAATTAAATA
1 ATAAGTAATGAAAATAAATA
12112 A
1 A
12113 AGAAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:18595 original size:19 final size:20
Alignment explanation
Indices: 18571--18609 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
18561 ATCCTTTCTA
*
18571 TATTTCATTTCATT-CTTAT
1 TATTTCATTTAATTACTTAT
*
18590 TATTTCTTTTAATTACTTAT
1 TATTTCATTTAATTACTTAT
18610 ATTATTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTCATTTAATTACTTAT
Found at i:18612 original size:19 final size:18
Alignment explanation
Indices: 18569--18612 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
18559 CTATCCTTTC
*
18569 TATATTTCATTTCATTCT
1 TATATTTCATTTAATTCT
*
18587 TATTATTTCTTTTAATTACT
1 TA-TATTTCATTTAATT-CT
18607 TATATT
1 TATATT
18613 ATTATTCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 16 0.73
20 4 0.18
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATTTCATTTAATTCT
Found at i:18913 original size:19 final size:20
Alignment explanation
Indices: 18871--18918 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
18861 ATTGGAGTGC
18871 AAAAAGAA-AGAAAAAGATA
1 AAAAAGAAGAGAAAAAGATA
*
18890 AAAAAGAAGAGAAAAA-TTA
1 AAAAAGAAGAGAAAAAGATA
*
18909 GAAAAGAAGA
1 AAAAAGAAGA
18919 AAAGAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (20 bp):
AAAAAGAAGAGAAAAAGATA
Found at i:29685 original size:11 final size:13
Alignment explanation
Indices: 29653--29682 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29643 TGGCCAAAGA
29653 TGAAAAGGTATGT
1 TGAAAAGGTATGT
29666 TGAAAAGGTATG-
1 TGAAAAGGTATGT
29678 TGAAA
1 TGAAA
29683 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:44058 original size:19 final size:20
Alignment explanation
Indices: 44034--44073 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
44024 TATCCTTTCT
44034 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
44053 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
44073 T
1 T
44074 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:44360 original size:9 final size:10
Alignment explanation
Indices: 44338--44402 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
44328 ATTGGAGTGC
44338 AAAAAGAAAG
1 AAAAAGAAAG
*
44348 AAAAAGATA-
1 AAAAAGAAAG
44357 AAAAAGAAGAG
1 AAAAAGAA-AG
**
44368 AAAAA-TCAG
1 AAAAAGAAAG
44377 -AAAAG-AAG
1 AAAAAGAAAG
44385 -AAAAGAAAAG
1 AAAAAG-AAAG
44395 AAAAAGAA
1 AAAAAGAA
44403 TTCAAAAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
8 11 0.25
9 9 0.20
10 14 0.32
11 10 0.23
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:49820 original size:19 final size:20
Alignment explanation
Indices: 49796--49835 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
49786 TATCCTTTCT
49796 TTATTTAATTTCATT-CTTA
1 TTATTTAATTTCATTACTTA
**
49815 TTATTTCTTTTCATTACTTA
1 TTATTTAATTTCATTACTTA
49835 T
1 T
49836 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTAATTTCATTACTTA
Found at i:50131 original size:20 final size:19
Alignment explanation
Indices: 50100--50161 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
50090 ATTGGAGTGC
50100 AAAAAGAA-AGAAAAAGACA
1 AAAAAGAAGAGAAAAA-ACA
*
50119 AAAAAGAAGAGAAAAATCA
1 AAAAAGAAGAGAAAAAACA
* *
50138 AAAAAGAAGAAAAGAAAAGA
1 AAAAAGAAGAGAA-AAAACA
50158 AAAA
1 AAAA
50162 TAATTCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 22 0.59
20 15 0.41
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAAGAAGAGAAAAAACA
Found at i:50140 original size:18 final size:20
Alignment explanation
Indices: 50100--50147 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
50090 ATTGGAGTGC
50100 AAAAAGAA-AGAAAAAGACA
1 AAAAAGAAGAGAAAAAGACA
*
50119 AAAAAGAAGAGAAAAA-TCA
1 AAAAAGAAGAGAAAAAGACA
50138 AAAAAGAAGA
1 AAAAAGAAGA
50148 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAAGAAGAGAAAAAGACA
Found at i:50141 original size:27 final size:27
Alignment explanation
Indices: 50110--50162 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
50100 AAAAAGAAAG
*
50110 AAAAAGACAAAAAAGAAGAGAAAAATCA
1 AAAAAGA-AAAAAAGAAAAGAAAAATCA
*
50138 AAAAAGAAGAAAAGAAAAGAAAAAT
1 AAAAAGAAAAAAAGAAAAGAAAAAT
50163 AATTCAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (27 bp):
AAAAAGAAAAAAAGAAAAGAAAAATCA
Found at i:54874 original size:6 final size:6
Alignment explanation
Indices: 54863--54905 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
54853 GATGTGGGAG
* *
54863 TCTTTT TC-TTT TCTTTT TCCTTT TCTTCTT TTTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
54906 GTTGCTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:54914 original size:20 final size:20
Alignment explanation
Indices: 54868--54904 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54858 GGGAGTCTTT
54868 TTCTTTTCTTTTTCCTTTTC
1 TTCTTTTCTTTTTCCTTTTC
54888 TTCTTTT-TTTTT-CTTTT
1 TTCTTTTCTTTTTCCTTTT
54905 TGTTGCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (20 bp):
TTCTTTTCTTTTTCCTTTTC
Found at i:58603 original size:27 final size:27
Alignment explanation
Indices: 58554--58610 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
58544 TAAAATCAGA
*
58554 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAATTGAAGCACTCAAAAAG-AAG
*
58582 AAAGAAATT-CAGCACTCAAAAAGAAG
1 AAAGAAATTGAAGCACTCAAAAAGAAG
58608 AAA
1 AAA
58611 AACAAAGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 6 0.22
27 12 0.44
28 9 0.33
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.11
Consensus pattern (27 bp):
AAAGAAATTGAAGCACTCAAAAAGAAG
Found at i:62303 original size:14 final size:13
Alignment explanation
Indices: 62281--62341 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 13
62271 TTGGAGTACA
62281 AAAAGAAAGAAAAAG
1 AAAA-AAAG-AAAAG
*
62296 AAAAAAAGGAAGAG
1 AAAAAAA-GAAAAG
*
62310 AAAAATCAGAAAAG
1 AAAAA-AAGAAAAG
*
62324 AAGAAAAGAAAAG
1 AAAAAAAGAAAAG
62337 AAAAA
1 AAAAA
62342 GAATTCAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.29
14 21 0.55
15 6 0.16
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:62326 original size:19 final size:19
Alignment explanation
Indices: 62280--62341 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
62270 ATTGGAGTAC
62280 AAAAAGAA-AGAAAAAGAA
1 AAAAAGAAGAGAAAAAGAA
62298 AAAAAGGAAGAGAAAAATCAGAA
1 AAAAA-GAAGAG-AAAA--AGAA
* *
62321 AAGAAGAAAAG-AAAAGAA
1 AAAAAGAAGAGAAAAAGAA
62339 AAA
1 AAA
62342 GAATTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 11 0.31
19 3 0.08
20 5 0.14
21 4 0.11
22 5 0.14
23 8 0.22
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (19 bp):
AAAAAGAAGAGAAAAAGAA
Found at i:66565 original size:19 final size:20
Alignment explanation
Indices: 66537--66574 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
66527 TCTTTATTTC
66537 ATTTCATTTCATT-CTTATT
1 ATTTCATTTCATTACTTATT
*
66556 ATTTCTTTTCATTACTTAT
1 ATTTCATTTCATTACTTAT
66575 ATTATTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.21, C:0.16, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTCATTTCATTACTTATT
Found at i:67314 original size:22 final size:21
Alignment explanation
Indices: 67277--67317 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
67267 CCATCTCCAT
*
67277 TTCATCATCAACACCATCATC
1 TTCATCATCAAAACCATCATC
67298 TTCATCCATCAAAACCATCA
1 TTCAT-CATCAAAACCATCA
67318 ATTCCGAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (21 bp):
TTCATCATCAAAACCATCATC
Found at i:73213 original size:24 final size:24
Alignment explanation
Indices: 73186--73236 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
73176 TGTGGATCAC
* *
73186 CAAAAGTCACGTTTATTGATTCTT
1 CAAAAGACACGTTTATTGAATCTT
* *
73210 CAAAAGACATGTTTCTTGAATCTT
1 CAAAAGACACGTTTATTGAATCTT
73234 CAA
1 CAA
73237 CTTAAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (24 bp):
CAAAAGACACGTTTATTGAATCTT
Found at i:74738 original size:14 final size:14
Alignment explanation
Indices: 74719--74750 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
74709 TGGTTATGGC
*
74719 GATGAAACAAAGGG
1 GATGAAAAAAAGGG
74733 GATGAAAAAAAGGG
1 GATGAAAAAAAGGG
74747 GATG
1 GATG
74751 GAAGTGAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.38, T:0.09
Consensus pattern (14 bp):
GATGAAAAAAAGGG
Found at i:77382 original size:33 final size:34
Alignment explanation
Indices: 77315--77385 Score: 90
Period size: 36 Copynumber: 2.1 Consensus size: 34
77305 TAAGATACTA
** *
77315 CCTATAACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATAGTCCACCACC--TTTCACG
77351 CCTATAACATCACCATAGTCCACCACC-TTCACG
1 CCTATAACATCACCATAGTCCACCACCTTTCACG
77384 CC
1 CC
77386 AATTCCATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 8 0.25
36 24 0.75
ACGTcount: A:0.28, C:0.42, G:0.04, T:0.25
Consensus pattern (34 bp):
CCTATAACATCACCATAGTCCACCACCTTTCACG
Found at i:77808 original size:20 final size:20
Alignment explanation
Indices: 77785--77823 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
77775 CAAAAGCAAC
*
77785 AAAAAGAAAAAAAAAAGAAG
1 AAAAACAAAAAAAAAAGAAG
*
77805 AAAAACAAAAAGAAAAGAA
1 AAAAACAAAAAAAAAAGAA
77824 AAAGACTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAACAAAAAAAAAAGAAG
Found at i:77814 original size:17 final size:17
Alignment explanation
Indices: 77786--77826 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 17
77776 AAAAGCAACA
77786 AAAAGAAAAA-AAAAAG
1 AAAAGAAAAACAAAAAG
77802 --AAGAAAAACAAAAAG
1 AAAAGAAAAACAAAAAG
77817 AAAAGAAAAA
1 AAAAGAAAAA
77827 GACTCCTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.36
15 6 0.27
17 8 0.36
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAACAAAAAG
Found at i:87237 original size:46 final size:46
Alignment explanation
Indices: 87170--87260 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
87160 ATGTGCTGTA
87170 ATGAAGCTCATAAGGATTCGGCTAGGAAGCTTGTTCACAAAATAGT
1 ATGAAGCTCATAAGGATTCGGCTAGGAAGCTTGTTCACAAAATAGT
87216 ATGAAGCTCATAAGGATTCGGCTAGGAAGCTTGTTCACAAAATAG
1 ATGAAGCTCATAAGGATTCGGCTAGGAAGCTTGTTCACAAAATAG
87261 CCCAAGCTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (46 bp):
ATGAAGCTCATAAGGATTCGGCTAGGAAGCTTGTTCACAAAATAGT
Found at i:88286 original size:23 final size:24
Alignment explanation
Indices: 88258--88317 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
88248 AAATCCAACA
* *
88258 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCAAAAAC
*
88281 AAGAAATTAAAAGCACTCAAAAAC
1 AAGAAAATAAAAGCACTCAAAAAC
*
88305 AAGAAAAGAAAAG
1 AAGAAAATAAAAG
88318 AAAGAAGTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.65, C:0.13, G:0.13, T:0.08
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCAAAAAC
Found at i:91998 original size:19 final size:19
Alignment explanation
Indices: 91966--92004 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
91956 TTCGACCAAG
*
91966 ATTATTTATCTTCATTAAA
1 ATTATGTATCTTCATTAAA
*
91985 ATTATGTATTTTCATTAAA
1 ATTATGTATCTTCATTAAA
92004 A
1 A
92005 AATAATGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (19 bp):
ATTATGTATCTTCATTAAA
Found at i:92465 original size:35 final size:35
Alignment explanation
Indices: 92355--92464 Score: 141
Period size: 35 Copynumber: 3.1 Consensus size: 35
92345 AAGATACTAT
*
92355 CTATAACA-TACCATCTTCCATCACCATTTTCACGC
1 CTATAACATTACCATCTTCCATTACCA-TTTCACGC
* * *
92390 CTATAACATCACCATCTTCCATTACCATTGCATGC
1 CTATAACATTACCATCTTCCATTACCATTTCACGC
* * *
92425 CTATATCATTACCATATTCTATTACCATTTCACGC
1 CTATAACATTACCATCTTCCATTACCATTTCACGC
92460 CTATA
1 CTATA
92465 TAACCACCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 48 0.75
36 16 0.25
ACGTcount: A:0.29, C:0.33, G:0.04, T:0.35
Consensus pattern (35 bp):
CTATAACATTACCATCTTCCATTACCATTTCACGC
Found at i:93406 original size:15 final size:15
Alignment explanation
Indices: 93386--93425 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
93376 GGAATATGAA
93386 ATAAGAAATGAAATG
1 ATAAGAAATGAAATG
93401 ATAAGAAATGAAATG
1 ATAAGAAATGAAATG
*
93416 AAAAGAAATG
1 ATAAGAAATG
93426 TTACCAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.20, T:0.17
Consensus pattern (15 bp):
ATAAGAAATGAAATG
Found at i:98409 original size:498 final size:498
Alignment explanation
Indices: 97472--98441 Score: 1868
Period size: 498 Copynumber: 1.9 Consensus size: 498
97462 AACTCAAGTG
*
97472 ATGCAAGCACGTTTTCAACTATAAAGGGAGTACTCTTGAACATCTTTTAATGCATTTACTTTATA
1 ATGCAAGCACATTTTCAACTATAAAGGGAGTACTCTTGAACATCTTTTAATGCATTTACTTTATA
** * *
97537 ATAGCCTTATAATATATACTATTATATTGCATATCATTCTAAGGATATTAGTTATGAAGTTAAAG
66 ATAGCCTTATAATATATACTATTATATTAAATATCATGCTAAGAATATTAGTTATGAAGTTAAAG
97602 AATAACTTAGTATGAATACATCTTACACATTGTTATTTTAATATGTTAAGCATGTTAGGATAGCT
131 AATAACTTAGTATGAATACATCTTACACATTGTTATTTTAATATGTTAAGCATGTTAGGATAGCT
*
97667 ATATAATTATATTATGTATGATTATAACATATACATCAAGGCAGCATACTTATAATGTATTTCAT
196 ATATAATTATATTATGTATGATTATAACATATACATCAAGGCAACATACTTATAATGTATTTCAT
97732 TAATTCATTTGTATTCATATTAGCTCTTAGGCTTTATACCTTACCTTACACATATTAGGAGATGA
261 TAATTCATTTGTATTCATATTAGCTCTTAGGCTTTATACCTTACCTTACACATATTAGGAGATGA
97797 TATAATTAGCTCATGACATTCAAACTTAGCTCACATTACCATAATCAAACATGTCAGCAAGGTAA
326 TATAATTAGCTCATGACATTCAAACTTAGCTCACATTACCATAATCAAACATGTCAGCAAGGTAA
97862 TTAGCTCATATTAGCTCAATACCATGGAATTACCTTGTTTCCTTGCACATGTAGGTACATTGGAG
391 TTAGCTCATATTAGCTCAATACCATGGAATTACCTTGTTTCCTTGCACATGTAGGTACATTGGAG
97927 CATAATGAATGTTTAGGACCAATCGGCCTAAAGAAGGGGGATA
456 CATAATGAATGTTTAGGACCAATCGGCCTAAAGAAGGGGGATA
* *
97970 ATGCAAGCACATTTTCAGCTATAAAGGGAGTACTCTTGAACATCTTTTAATGCATTTGCTTTATA
1 ATGCAAGCACATTTTCAACTATAAAGGGAGTACTCTTGAACATCTTTTAATGCATTTACTTTATA
98035 ATAGCCTTATAATATATACTATTATATTAAATATCATGCTAAGAATATTAGTTATGAAGTTAAAG
66 ATAGCCTTATAATATATACTATTATATTAAATATCATGCTAAGAATATTAGTTATGAAGTTAAAG
98100 AATAACTTAGTATGAATACATCTTACACATTGTTATTTTAATATGTTAAGCATGTTAGGATAGCT
131 AATAACTTAGTATGAATACATCTTACACATTGTTATTTTAATATGTTAAGCATGTTAGGATAGCT
98165 ATATAATTATATTATGTATGATTATAACATATACATCAAGGCAACATACTTATAATGTATTTCAT
196 ATATAATTATATTATGTATGATTATAACATATACATCAAGGCAACATACTTATAATGTATTTCAT
98230 TAATTCATTTGTATTCATATTAGCTCTTAGGCTTTATACCTTACCTTACACATATTAGGAGATGA
261 TAATTCATTTGTATTCATATTAGCTCTTAGGCTTTATACCTTACCTTACACATATTAGGAGATGA
98295 TATAATTAGCTCATGACATTCAAACTTAGCTCACATTACCATAATCAAACATGTCAGCAAGGTAA
326 TATAATTAGCTCATGACATTCAAACTTAGCTCACATTACCATAATCAAACATGTCAGCAAGGTAA
98360 TTAGCTCATATTAGCTCAATACCATGGAATTACCTTGTTTCCTTGCACATGTAGGTACATTGGAG
391 TTAGCTCATATTAGCTCAATACCATGGAATTACCTTGTTTCCTTGCACATGTAGGTACATTGGAG
98425 CATAATGAATGTTTAGG
456 CATAATGAATGTTTAGG
98442 TAGATTGGTT
Statistics
Matches: 464, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
498 464 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (498 bp):
ATGCAAGCACATTTTCAACTATAAAGGGAGTACTCTTGAACATCTTTTAATGCATTTACTTTATA
ATAGCCTTATAATATATACTATTATATTAAATATCATGCTAAGAATATTAGTTATGAAGTTAAAG
AATAACTTAGTATGAATACATCTTACACATTGTTATTTTAATATGTTAAGCATGTTAGGATAGCT
ATATAATTATATTATGTATGATTATAACATATACATCAAGGCAACATACTTATAATGTATTTCAT
TAATTCATTTGTATTCATATTAGCTCTTAGGCTTTATACCTTACCTTACACATATTAGGAGATGA
TATAATTAGCTCATGACATTCAAACTTAGCTCACATTACCATAATCAAACATGTCAGCAAGGTAA
TTAGCTCATATTAGCTCAATACCATGGAATTACCTTGTTTCCTTGCACATGTAGGTACATTGGAG
CATAATGAATGTTTAGGACCAATCGGCCTAAAGAAGGGGGATA
Found at i:111099 original size:11 final size:11
Alignment explanation
Indices: 111085--111123 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
111075 TTTAAAAAAA
111085 CAAAAAAAAGG
1 CAAAAAAAAGG
111096 CAAAAAAAAGG
1 CAAAAAAAAGG
111107 CAAAAAAAAGG
1 CAAAAAAAAGG
111118 CAAAAA
1 CAAAAA
111124 TAAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.74, C:0.10, G:0.15, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGG
Found at i:111110 original size:22 final size:20
Alignment explanation
Indices: 111078--111142 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 20
111068 CTATTTTTTT
111078 AAAAAAACAAAAAAAAGGCA
1 AAAAAAACAAAAAAAAGGCA
111098 AAAAAAAGGCAAAAAAAAGGCA
1 AAAAAAA--CAAAAAAAAGGCA
* *
111120 AAAATAAA-ATAAAAAAGCCA
1 AAAA-AAACAAAAAAAAGGCA
111140 AAA
1 AAA
111143 TTGAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
20 20 0.50
22 17 0.43
23 3 0.08
ACGTcount: A:0.77, C:0.09, G:0.11, T:0.03
Consensus pattern (20 bp):
AAAAAAACAAAAAAAAGGCA
Found at i:111152 original size:19 final size:19
Alignment explanation
Indices: 111108--111152 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
111098 AAAAAAAGGC
*
111108 AAAAAAAAGGCAAAAATAA
1 AAAAAAAAGCCAAAAATAA
*
111127 AATAAAAAAGCCAAAATTGAA
1 AA-AAAAAAGCCAAAAAT-AA
111148 AAAAA
1 AAAAA
111153 TTGAAAACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 16 0.73
21 4 0.18
ACGTcount: A:0.76, C:0.07, G:0.09, T:0.09
Consensus pattern (19 bp):
AAAAAAAAGCCAAAAATAA
Found at i:131464 original size:11 final size:13
Alignment explanation
Indices: 131432--131461 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
131422 TGGCCAAAGA
131432 TGAAAAGGTATGT
1 TGAAAAGGTATGT
131445 TGAAAAGGTATG-
1 TGAAAAGGTATGT
131457 TGAAA
1 TGAAA
131462 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:143941 original size:12 final size:13
Alignment explanation
Indices: 143900--143942 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
143890 TGGCCAAAGA
143900 TGAAAAGGTATGT
1 TGAAAAGGTATGT
*
143913 TGAAAAAGTATGT
1 TGAAAAGGTATGT
143926 TGAAAAGGTATG-
1 TGAAAAGGTATGT
143938 TGAAA
1 TGAAA
143943 GGTGTTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 5 0.18
13 23 0.82
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:154948 original size:13 final size:13
Alignment explanation
Indices: 154926--154955 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
154916 ACTAAACACA
154926 TTTC-ACATACCT
1 TTTCAACATACCT
154938 TTTCAACATACCT
1 TTTCAACATACCT
154951 TTTCA
1 TTTCA
154956 TCTTTAGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:157724 original size:24 final size:23
Alignment explanation
Indices: 157697--157756 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
157687 ACTTTTCTTT
* *
157697 CTTTCTTTTTCTTATTTTTTAGTG
1 CTTTCTTTTTCTT-CTTTTGAGTG
**
157721 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTCTTTTGAGTG
157744 CTTT-TATTTTCTT
1 CTTTCT-TTTTCTT
157757 TGCTGATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.10, C:0.15, G:0.08, T:0.67
Consensus pattern (23 bp):
CTTTCTTTTTCTTCTTTTGAGTG
Found at i:157743 original size:23 final size:23
Alignment explanation
Indices: 157712--157756 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
157702 TTTTTCTTAT
*
157712 TTTTTAGTGCTTTCAATTTCTTC
1 TTTTGAGTGCTTTCAATTTCTTC
* *
157735 TTTTGAGTGCTTTTATTTTCTT
1 TTTTGAGTGCTTTCAATTTCTT
157757 TGCTGATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.64
Consensus pattern (23 bp):
TTTTGAGTGCTTTCAATTTCTTC
Found at i:159854 original size:19 final size:20
Alignment explanation
Indices: 159830--159869 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
159820 TATCCTTTCT
159830 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
159849 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
159869 T
1 T
159870 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:160128 original size:16 final size:16
Alignment explanation
Indices: 160109--160144 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
160099 AGAAAAGAAG
160109 AAAAGAAAAAGAATTC
1 AAAAGAAAAAGAATTC
160125 AAAAGAAAAAGAATTC
1 AAAAGAAAAAGAATTC
160141 AAAA
1 AAAA
160145 CAAGGCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.72, C:0.06, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAGAAAAAGAATTC
Found at i:164309 original size:19 final size:20
Alignment explanation
Indices: 164285--164324 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
164275 TATCCTTTCT
*
164285 TTATTTCATTTGATT-CTTA
1 TTATTTCATTTCATTACTTA
*
164304 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
164324 T
1 T
164325 CTTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:166317 original size:17 final size:17
Alignment explanation
Indices: 166295--166350 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
166285 AAATTTGAGT
166295 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
* *
166312 ACAAAAAGAAAAAAAAT
1 ACAAAAAGAAAGAAAAG
*
166329 TCAGAAAA-AAAGAAAAG
1 ACA-AAAAGAAAGAAAAG
166346 A-AAAA
1 ACAAAA
166351 GAATAGAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 3 0.09
16 1 0.03
17 24 0.75
18 4 0.12
ACGTcount: A:0.79, C:0.05, G:0.12, T:0.04
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:171071 original size:19 final size:20
Alignment explanation
Indices: 171035--171074 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
171025 GGATAATAAT
*
171035 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATCAAAAGAAATA
*
171055 ATAAG-AATCAAATGAAATA
1 ATAAGTAATCAAAAGAAATA
171074 A
1 A
171075 AGAAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (20 bp):
ATAAGTAATCAAAAGAAATA
Found at i:176898 original size:12 final size:11
Alignment explanation
Indices: 176868--176896 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
176858 GAAATTTTGG
176868 TTTTTTTGTTT
1 TTTTTTTGTTT
176879 TTTTTTTGTTT
1 TTTTTTTGTTT
176890 TTTTTTT
1 TTTTTTT
176897 TGAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:178687 original size:11 final size:11
Alignment explanation
Indices: 178634--178713 Score: 74
Period size: 11 Copynumber: 7.3 Consensus size: 11
178624 TCTTTTTGAA
178634 CTTCTTTTTCTT
1 CTTCTTTTT-TT
*
178646 -TTCTTTTCTT
1 CTTCTTTTTTT
*
178656 CTTAATTTTTTT
1 CTT-CTTTTTTT
***
178668 CTGAATTTTTT
1 CTTCTTTTTTT
178679 CTTCTTTTTTT
1 CTTCTTTTTTT
178690 CTTCTTTTTTT
1 CTTCTTTTTTT
*
178701 CTT-TTCTTTT
1 CTTCTTTTTTT
178711 CTT
1 CTT
178714 TTTGCACTCC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
10 11 0.19
11 38 0.67
12 8 0.14
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.76
Consensus pattern (11 bp):
CTTCTTTTTTT
Found at i:179011 original size:19 final size:20
Alignment explanation
Indices: 178984--179023 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
178974 GGATAATAAT
178984 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
179004 ATAA-TAATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
179023 A
1 A
179024 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:180425 original size:30 final size:31
Alignment explanation
Indices: 180384--180443 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
180374 ACATGCTGCC
180384 ATGATATCT-AAACGATATGCAAACATAATAA
1 ATGATATCTAAAAC-ATATGCAAACATAATAA
*
180415 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
180444 TAAAACTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:183247 original size:11 final size:13
Alignment explanation
Indices: 183215--183244 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
183205 TGGCCAAAGA
183215 TGAAAAGGTATGT
1 TGAAAAGGTATGT
183228 TGAAAAGGTATG-
1 TGAAAAGGTATGT
183240 TGAAA
1 TGAAA
183245 GGTTTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:186885 original size:11 final size:11
Alignment explanation
Indices: 186863--186909 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
186853 ATTGGAGTGC
186863 AAAAAGAA-AG
1 AAAAAGAAGAG
186873 AAAAAGAAGAG
1 AAAAAGAAGAG
186884 AAAAAGAAGA-
1 AAAAAGAAGAG
*
186894 AAAGAAGAAAAG
1 AAA-AAGAAGAG
186906 AAAA
1 AAAA
186910 GAAAAAGACA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
10 11 0.33
11 19 0.58
12 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAGAAGAG
Found at i:188849 original size:533 final size:533
Alignment explanation
Indices: 187843--188900 Score: 1803
Period size: 533 Copynumber: 2.0 Consensus size: 533
187833 GGAGTTTGTC
* * * *
187843 GATTATGCTTTGATATGGTGGGATTAACTTACTGTTACTCGGAAGAGGAATGGAGAGAGACTAAT
1 GATTATGCTTTGATATGGTGGGATCAACTTACTATTACTCAGAAGAGGAATGGAGAGAGACCAAT
*
187908 TTCAACATGGCTCAAAATGAAAGGTATCATGCGTAAACGTTTCATTCCTACTCATTATCACCGGG
66 TTCAACATGGCTCAAAATGAAAGGTATCATGCGTAAACGTTTCATTCATACTCATTATCACCGGG
*
187973 ACATGTTTCAGAAATTGCAGAACCTAAAGCAAGGCCAAAGGAGTGTAGAGGATTACTATAAGGAA
131 ACATGTTTCAGAAATTGCAGAACCTAAAGCAAGGACAAAGGAGTGTAGAGGATTACTATAAGGAA
* * * *
188038 ATGGAAGTGGTAATTATCTGAGTCAATATTGAGGAGGATCGTGAAGCAACCATGGCTCGATTTCT
196 ATGGAAGTGGAAATGATCCGAGTCAATATTGAGGAGGATCGTAAAGCAACCATGGCTCGATTTCT
* *
188103 TACCGGACTTAATCCCGAGATTGCCAACACACTATAGTTGTACCATTACATAGAACTTGATGAAA
261 TACCGGACTTAATCCCGAGATTGCCAACACACTAGAGTTGTACCATTAAATAGAACTTGATGAAA
*
188168 TGGTGCAAATGGCTATGAAGATAGAGAGGCAACTACGGAGAAGATCTATATCTCACACTACCATA
326 TGGTGCAAATGGCTATGAAGATAGAGAGGCAACTACAGAGAAGATCTATATCTCACACTACCATA
* *
188233 CCTTCGAAATGGAGTCCTAACAATTTAAAGAAGTCTACTCATACTCCTATCAATGAAAAGGCCGA
391 CCTTCGAAATAGAGTCCTAACAATTTAAAGAAGTCTACTCATACTCCTATCAAGGAAAAGGCCGA
* * *
188298 ATCTTCAAATGCTTCCCAACTCAGCAAGGATAATCGAGGAAAAGAGATCCCTAAACGATCAAGAG
456 ATCCTCAAATACTTCCCAACTCAGCAAGGATAATCGAGGAAAAGAGATCCCTAAACAATCAAGAG
188363 ACATCCGTTTATT
521 ACATCCGTTTATT
*
188376 GATTATGCTTTGATATGGTGGGATCAACTTACTATTACTCAGAGGAGGAATGGAGAGAGACCAAT
1 GATTATGCTTTGATATGGTGGGATCAACTTACTATTACTCAGAAGAGGAATGGAGAGAGACCAAT
*
188441 TTCAACATGGCTCGAAATGAAAGGTATCATGCGTAAACGTTTCATTCATACTCATTATCACCGGG
66 TTCAACATGGCTCAAAATGAAAGGTATCATGCGTAAACGTTTCATTCATACTCATTATCACCGGG
* *
188506 ACATGTTTCAGAAATTGTAGAACCTAAAGCAAGGACAAATGAGTGTAGAGGATTACTATAAGGAA
131 ACATGTTTCAGAAATTGCAGAACCTAAAGCAAGGACAAAGGAGTGTAGAGGATTACTATAAGGAA
* **
188571 ATTGAAGTGGAAATGATCCGAGTCAATATTGAGGAGGATCGTAAAGCAACCATGGCTTTATTTCT
196 ATGGAAGTGGAAATGATCCGAGTCAATATTGAGGAGGATCGTAAAGCAACCATGGCTCGATTTCT
*
188636 TGCCGGACTTAATCCCGAGATTGCCAACACACTAGAGTTGTACCATTAAATAGAACTTGATGAAA
261 TACCGGACTTAATCCCGAGATTGCCAACACACTAGAGTTGTACCATTAAATAGAACTTGATGAAA
* * *
188701 TGGTGCAAATGGCTATGAAGATAGAGAGGCAACTACAGAGAAGATCTATATCTCGCACTACTATG
326 TGGTGCAAATGGCTATGAAGATAGAGAGGCAACTACAGAGAAGATCTATATCTCACACTACCATA
* * *
188766 CCTTC-AAGATAGAGTCCTAACAATTTGAAGAAGTCTACTCCTACTCCTATCAAGGAAAAGGTCG
391 CCTTCGAA-ATAGAGTCCTAACAATTTAAAGAAGTCTACTCATACTCCTATCAAGGAAAAGGCCG
*
188830 AATCCTCAAATACTTCCCAACTCAGCAAGGATAATCGAGGAAAAGAGATCCCTGAACAATCAAGA
455 AATCCTCAAATACTTCCCAACTCAGCAAGGATAATCGAGGAAAAGAGATCCCTAAACAATCAAGA
188895 GACATC
520 GACATC
188901 TGTTGTTTTA
Statistics
Matches: 491, Mismatches: 33, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
532 2 0.00
533 489 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (533 bp):
GATTATGCTTTGATATGGTGGGATCAACTTACTATTACTCAGAAGAGGAATGGAGAGAGACCAAT
TTCAACATGGCTCAAAATGAAAGGTATCATGCGTAAACGTTTCATTCATACTCATTATCACCGGG
ACATGTTTCAGAAATTGCAGAACCTAAAGCAAGGACAAAGGAGTGTAGAGGATTACTATAAGGAA
ATGGAAGTGGAAATGATCCGAGTCAATATTGAGGAGGATCGTAAAGCAACCATGGCTCGATTTCT
TACCGGACTTAATCCCGAGATTGCCAACACACTAGAGTTGTACCATTAAATAGAACTTGATGAAA
TGGTGCAAATGGCTATGAAGATAGAGAGGCAACTACAGAGAAGATCTATATCTCACACTACCATA
CCTTCGAAATAGAGTCCTAACAATTTAAAGAAGTCTACTCATACTCCTATCAAGGAAAAGGCCGA
ATCCTCAAATACTTCCCAACTCAGCAAGGATAATCGAGGAAAAGAGATCCCTAAACAATCAAGAG
ACATCCGTTTATT
Found at i:189560 original size:30 final size:31
Alignment explanation
Indices: 189524--189583 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
189514 CTTAGATTTA
**
189524 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
189554 TATTATGTTTTCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
189584 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:190500 original size:19 final size:20
Alignment explanation
Indices: 190476--190526 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
190466 CGTCCAAGAG
* *
190476 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
190495 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
190515 CATGTATTTTCA
1 CATGTATTTTCA
190527 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:190965 original size:19 final size:20
Alignment explanation
Indices: 190941--190980 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
190931 TCCCTTTTCT
190941 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
190960 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
190980 T
1 T
190981 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:193697 original size:407 final size:407
Alignment explanation
Indices: 192998--193733 Score: 1127
Period size: 407 Copynumber: 1.8 Consensus size: 407
192988 GTATTTGACT
* * *
192998 CCAAGATGAACAAGCATCACCATTCAGCCAAGGGAGATGCCTTCCCATCCTTAGCCAAATTATCA
1 CCAAGATGAAAAAGCATCACCATTCAGCCAAGGGAGATGCCTTCCCATACTTAGCCAAATCATCA
* * * * ** * *
193063 AGTCCCTTTATGAAGGGTTAGCTAAACCAACAACAAGCCTATAGACATGTTCTTTTATTTTGAAG
66 AGCCCCTTTATGAAGGGTTAGCCAAACCAACAACAAGCCCAAAGACATAATCTTTCATTTTAAAG
** * * * *
193128 CGTTATGTACCTTCCTAGAGACATGTATCTAGCTGAAACATCATGTAACCATTCGGCCATGCCTC
131 AATTATGTACCTTCATAAAGACATGTATCTAGCCGAAACATCATGTAACCATTCGGCCAAGCCTC
* *
193193 TCATTTCCTATAAATAGAGGGACTTGCCATCATTTGTACTCATCTCATCTCTTATATAAAAATAT
196 TCATTTCCTATAAATAGAGGGACTTGCCATCATTTGTAATCATCTCATCTCATATATAAAAATAT
*
193258 ACTCTTATGAGTTAATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAACACGTATAGTTC
261 ACTCTTATGAGTTAATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAACAAGTATAGTTC
193323 CTATTTGGCCACACACATGAGAACCTTTTGGCGCCAAAAATGAGAAGGCACATCACCATTTGGCC
326 CTATTTGGCCACACACATGAGAACCTTTTGGCGCCAAAAATGAGAAGGCACATCACCATTTGGCC
193388 ATGGGGAGAAAATGGTG
391 ATGGGGAGAAAATGGTG
* *
193405 CCAAGATGAAAAAGCATGC-CCATTCGGCCAAGGGAGATGCCTTCCCATACTTAGCCGAATCATC
1 CCAAGATGAAAAAGCAT-CACCATTCAGCCAAGGGAGATGCCTTCCCATACTTAGCCAAATCATC
* * *
193469 AAGCCCCTTTATGAAGGGTTAGCCGAACCATC-ACAAGCCCAAATGACTTAATCTTTCATTTTAA
65 AAGCCCCTTTATGAAGGGTTAGCCAAACCAACAACAAGCCCAAA-GACATAATCTTTCATTTTAA
* * * *
193533 AGAATTATGTATCTTTATAAAGTCATGTATCTAGCCGAAGCATCATGTAACCATTCGGCCAAGCC
129 AGAATTATGTACCTTCATAAAGACATGTATCTAGCCGAAACATCATGTAACCATTCGGCCAAG-C
* * *
193598 CTCTCATTTCTTATAAATAGAGTGACTTGCCATCATTTGTAATCATCTCATCTCATATATTAAAA
193 CTCTCATTTCCTATAAATAGAGGGACTTGCCATCATTTGTAATCATCTCATCTCATATATAAAAA
*
193663 T-TACTCTTGTGAGTTAATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAACAAGTATAG
258 TATACTCTTATGAGTTAATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAACAAGTATAG
193727 TTCCTAT
323 TTCCTAT
193734 ACTTGTGGCG
Statistics
Matches: 293, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
406 9 0.03
407 221 0.75
408 63 0.22
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (407 bp):
CCAAGATGAAAAAGCATCACCATTCAGCCAAGGGAGATGCCTTCCCATACTTAGCCAAATCATCA
AGCCCCTTTATGAAGGGTTAGCCAAACCAACAACAAGCCCAAAGACATAATCTTTCATTTTAAAG
AATTATGTACCTTCATAAAGACATGTATCTAGCCGAAACATCATGTAACCATTCGGCCAAGCCTC
TCATTTCCTATAAATAGAGGGACTTGCCATCATTTGTAATCATCTCATCTCATATATAAAAATAT
ACTCTTATGAGTTAATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAACAAGTATAGTTC
CTATTTGGCCACACACATGAGAACCTTTTGGCGCCAAAAATGAGAAGGCACATCACCATTTGGCC
ATGGGGAGAAAATGGTG
Found at i:195843 original size:22 final size:22
Alignment explanation
Indices: 195803--195844 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
195793 AAATATGTGG
*
195803 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
195825 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
195845 ACTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:197824 original size:13 final size:12
Alignment explanation
Indices: 197806--197839 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
197796 ACAAAACGAA
197806 AAAAAGAAAGAAG
1 AAAAAGAAA-AAG
197819 AAAAAGAAAAAG
1 AAAAAGAAAAAG
197831 AAAAA-AAAA
1 AAAAAGAAAA
197840 CTCCTACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 8 0.38
13 9 0.43
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:197825 original size:6 final size:6
Alignment explanation
Indices: 197806--197839 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
197796 ACAAAACGAA
197806 AAAAAG AAAGAAG AAAAAG AAAAAG AAAAA- AAAA
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
197840 CTCCTACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.15
6 17 0.63
7 6 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:202953 original size:20 final size:20
Alignment explanation
Indices: 202916--202966 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
202906 TTCTTTTCTT
** *
202916 TTCTTCTTTTCATATTTTTC
1 TTCTTCTTTTTGTATTTTTA
*
202936 TTCTTCTTTTTGTCTTTTTA
1 TTCTTCTTTTTGTATTTTTA
202956 TT-TTCTTTTTG
1 TTCTTCTTTTTG
202967 CACTTCAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.75
Consensus pattern (20 bp):
TTCTTCTTTTTGTATTTTTA
Found at i:207034 original size:19 final size:20
Alignment explanation
Indices: 207010--207048 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
207000 TCCCTTTTCT
207010 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
207029 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
207049 AATTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:207340 original size:25 final size:25
Alignment explanation
Indices: 207312--207359 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
207302 GCAAAAAGAA
207312 AGAAAAGACA-AAAAGAAAAAAAATT
1 AGAAAAGA-AGAAAAGAAAAAAAATT
*
207337 AGAATAGAAGAAAAGAAAAAAAA
1 AGAAAAGAAGAAAAGAAAAAAAA
207360 AGAATTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (25 bp):
AGAAAAGAAGAAAAGAAAAAAAATT
Found at i:211695 original size:19 final size:20
Alignment explanation
Indices: 211667--211706 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
211657 GAATAATAAT
211667 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
211687 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
211706 A
1 A
211707 AGAAAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:216879 original size:19 final size:20
Alignment explanation
Indices: 216851--216890 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
216841 GAATAATAAT
216851 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
216871 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
216890 A
1 A
216891 AGAAAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:228242 original size:161 final size:162
Alignment explanation
Indices: 227977--228300 Score: 625
Period size: 161 Copynumber: 2.0 Consensus size: 162
227967 GATACAAGTG
227977 TTATTCGGCCAAGGATCATTTCCCTCCATCAAGGGCCAAACCATCATCTCTTTTAGCATTTAAAT
1 TTATTCGGCCAAGGATCATTTCCCTCCATCAAGGGCCAAACCATCATCTCTTTTAGCATTTAAAT
228042 TATGTCTTTATAGGGAGATACATGGGCTGGCTGAACCATTATGTCTCTATTCGGCCTTGCCCCTC
66 TATGTCTTTATAGGGAGATACATGGGCTGGCTGAACCATTATGTCTCTATTCGGCCTTGCCCCTC
228107 CATTTA-TAT-AATAGAAAAAACCTATCTCAAT
131 CATTTACTATAAATAG-AAAAACCTATCTCAAT
228138 TTATTCGGCCAAGGATCATTTCCCTCCATCAAGGGCCAAACCATCATCTCTTTTAGCATTTAAAT
1 TTATTCGGCCAAGGATCATTTCCCTCCATCAAGGGCCAAACCATCATCTCTTTTAGCATTTAAAT
228203 TATGTCTTTATAGGGAGATACATGGGCTGGCTGAACCATTATGTCTCTATTCGGCCTTGCCCCTC
66 TATGTCTTTATAGGGAGATACATGGGCTGGCTGAACCATTATGTCTCTATTCGGCCTTGCCCCTC
228268 CATTTACTATAAATAGAAAAACCTATCTCAAT
131 CATTTACTATAAATAGAAAAACCTATCTCAAT
228300 T
1 T
228301 GTACTCAGAC
Statistics
Matches: 161, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
161 136 0.84
162 20 0.12
163 5 0.03
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (162 bp):
TTATTCGGCCAAGGATCATTTCCCTCCATCAAGGGCCAAACCATCATCTCTTTTAGCATTTAAAT
TATGTCTTTATAGGGAGATACATGGGCTGGCTGAACCATTATGTCTCTATTCGGCCTTGCCCCTC
CATTTACTATAAATAGAAAAACCTATCTCAAT
Found at i:236844 original size:23 final size:23
Alignment explanation
Indices: 236812--236873 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 23
236802 CCTTGGCTTG
236812 CTTTTCTCTTTT-TGAAATCTTT-TT
1 CTTTT-TCTTTTCTG-AAT-TTTCTT
236836 CTTTTTCTTTTCTGAATTTTCTT
1 CTTTTTCTTTTCTGAATTTTCTT
236859 CTTTTTGTCTTTTCT
1 C-TTTT-TCTTTTCT
236874 TTCTTTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.09
23 12 0.35
24 11 0.32
25 8 0.24
ACGTcount: A:0.08, C:0.18, G:0.05, T:0.69
Consensus pattern (23 bp):
CTTTTTCTTTTCTGAATTTTCTT
Found at i:236873 original size:16 final size:17
Alignment explanation
Indices: 236852--236883 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
236842 CTTTTCTGAA
236852 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
236868 TTTTCTTTCTTTTTGT
1 TTTTCTTTCTTTTTGT
236884 ACTCCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:241479 original size:19 final size:20
Alignment explanation
Indices: 241455--241505 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
241445 CGGCCAAGAG
* *
241455 CATGTATCTTCATTAA-AAT
1 CATGTATTTTCATCAAGAAT
*
241474 CATGTATTTTAATCAAGAAT
1 CATGTATTTTCATCAAGAAT
241494 CATGTATTTTCA
1 CATGTATTTTCA
241506 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAGAAT
Found at i:241949 original size:18 final size:18
Alignment explanation
Indices: 241926--241962 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
241916 CTTTATTTCA
241926 TTTCATT-CTTATTATTAT
1 TTTCATTACTTA-TATTAT
241944 TTTCATTACTTATATTAT
1 TTTCATTACTTATATTAT
241962 T
1 T
241963 GTCCCCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCATTACTTATATTAT
Found at i:242251 original size:8 final size:8
Alignment explanation
Indices: 242240--242267 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
242230 AAAGAAGAGA
242240 AAAAGAAG
1 AAAAGAAG
242248 AAAAGAAG
1 AAAAGAAG
242256 AAAAGAAG
1 AAAAGAAG
242264 AAAA
1 AAAA
242268 AAAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:242253 original size:19 final size:18
Alignment explanation
Indices: 242228--242280 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
242218 ATTGGAGTGC
242228 AAAAAGAAGAGAAAAAGA
1 AAAAAGAAGAGAAAAAGA
242246 AGAAAAGAAGA-AAAGAAGA
1 A-AAAAGAAGAGAAA-AAGA
242265 AAAAA-AA-AGAAAAAGA
1 AAAAAGAAGAGAAAAAGA
242281 GAAGTTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.16
17 5 0.16
18 8 0.25
19 14 0.44
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAAGAAGAGAAAAAGA
Found at i:242280 original size:16 final size:17
Alignment explanation
Indices: 242237--242280 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
242227 CAAAAAGAAG
*
242237 AGAAAAAGAAGAAAAGA
1 AGAAAAAGAAGAAAAAA
242254 AG-AAAAGAAGAAAAAAAA
1 AGAAAAAGAAG--AAAAAA
242272 AGAAAAAGA
1 AGAAAAAGA
242281 GAAGTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 7 0.30
19 6 0.26
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AGAAAAAGAAGAAAAAA
Found at i:243567 original size:24 final size:24
Alignment explanation
Indices: 243540--243607 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
243530 GACATGTCCT
* *
243540 TTGACGTTCCAATAGTTATGCCAC
1 TTGAAGTTCCAAAAGTTATGCCAC
* * *
243564 TTGAAGTTCAAAAAGATATGTCAC
1 TTGAAGTTCCAAAAGTTATGCCAC
*
243588 TTGAAGTGCCAAAAGTTATG
1 TTGAAGTTCCAAAAGTTATG
243608 ATAATTGAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (24 bp):
TTGAAGTTCCAAAAGTTATGCCAC
Found at i:244668 original size:30 final size:31
Alignment explanation
Indices: 244632--244691 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
244622 CTTAGCTTTA
**
244632 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
244662 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
244692 GGCAGTATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:245604 original size:19 final size:20
Alignment explanation
Indices: 245580--245631 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
245570 CGGCCAAGAG
* *
245580 CATGTATATTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
245599 CATGTATTTTCATAAAAAAAT
1 CATGTATTTTCAT-AAAAAAT
245620 CATGTATTTTCA
1 CATGTATTTTCA
245632 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
21 17 0.59
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:250482 original size:27 final size:28
Alignment explanation
Indices: 250430--250494 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
250420 AAAGAAAATC
*
250430 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
250458 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
250485 AGAAAAGAAA
1 AGAAAAGAAA
250495 AGAAAAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:250494 original size:5 final size:5
Alignment explanation
Indices: 250484--250508 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
250474 ATTCAAAAAG
250484 AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA
250509 TGAAAGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:263955 original size:6 final size:7
Alignment explanation
Indices: 263939--263963 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
263929 TTTACTTTTA
263939 TTTTTGT
1 TTTTTGT
263946 TTTTTGT
1 TTTTTGT
263953 TTTTTGT
1 TTTTTGT
263960 TTTT
1 TTTT
263964 CTCTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTGT
Found at i:267859 original size:24 final size:22
Alignment explanation
Indices: 267815--267857 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
267805 TCCACAAGAT
267815 ATGTCCTTTGAAATTTCAAAGG
1 ATGTCCTTTGAAATTTCAAAGG
267837 ATGTACCTCTTGAAA-TTCAAA
1 ATGT-CCT-TTGAAATTTCAAA
267858 AGAATGAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (22 bp):
ATGTCCTTTGAAATTTCAAAGG
Found at i:281580 original size:22 final size:21
Alignment explanation
Indices: 281543--281583 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
281533 ACCTCTCCAT
*
281543 TTCATCATCAACACCATCATC
1 TTCATCATCAAAACCATCATC
281564 TTCATCCATCAAAACCATCA
1 TTCAT-CATCAAAACCATCA
281584 ATTCCGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (21 bp):
TTCATCATCAAAACCATCATC
Found at i:281641 original size:21 final size:21
Alignment explanation
Indices: 281602--281645 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
281592 ACCATCTCTA
281602 TCCTTTCTTTATTTCATTTCAT
1 TCCTTTCTTTA-TTCATTTCAT
281624 TCCTTATCTTTA-TCATTTCAT
1 TCCTT-TCTTTATTCATTTCAT
281645 T
1 T
281646 AATCTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (21 bp):
TCCTTTCTTTATTCATTTCAT
Found at i:281920 original size:26 final size:26
Alignment explanation
Indices: 281891--281949 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
281881 CAAAAGGAAA
*
281891 AGAAAAGACAAAAAGAAGAA-AAATTC
1 AGAAAAGAAAAAAAGAA-AAGAAATTC
281917 AGAAAAGAAAAAAAGAAAAGAAATTC
1 AGAAAAGAAAAAAAGAAAAGAAATTC
281943 A-AAAAGA
1 AGAAAAGA
281950 GAAACCAAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 8 0.26
26 23 0.74
ACGTcount: A:0.73, C:0.05, G:0.15, T:0.07
Consensus pattern (26 bp):
AGAAAAGAAAAAAAGAAAAGAAATTC
Found at i:287516 original size:22 final size:23
Alignment explanation
Indices: 287491--287542 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
287481 ATTCCACAAC
287491 CATTTC-TATCCTT-TCTTTATTT
1 CATTTCAT-TCCTTATCTTTATTT
287513 CATTTCATTCCTTATCTTTA--T
1 CATTTCATTCCTTATCTTTATTT
287534 CATTTCATT
1 CATTTCATT
287543 AATCTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 10 0.36
22 11 0.39
23 7 0.25
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (23 bp):
CATTTCATTCCTTATCTTTATTT
Found at i:288839 original size:36 final size:35
Alignment explanation
Indices: 288742--288846 Score: 147
Period size: 35 Copynumber: 3.0 Consensus size: 35
288732 GGTGGTTATT
* * *
288742 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
* * *
288777 TAGGCGTGCAACGGTAATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
288812 TAGGCGTGAAAATGGTGATGGAAGATGGTGATGTT
1 TAGGCGTG-AAATGGTGATGGAAGATGGTGATGTT
288847 GATACGATCC
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 37 0.62
36 23 0.38
ACGTcount: A:0.31, C:0.05, G:0.37, T:0.27
Consensus pattern (35 bp):
TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
Found at i:294841 original size:19 final size:20
Alignment explanation
Indices: 294803--294845 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
294793 GAAACCCCTT
*
294803 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
294823 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
294842 TGAA
1 TGAA
294846 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:297607 original size:16 final size:16
Alignment explanation
Indices: 297558--297601 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
297548 ATATTTATAG
297558 TTATG-ATG-ATGATA
1 TTATGAATGTATGATA
297572 TTATGAATGTATGATA
1 TTATGAATGTATGATA
297588 TTATGAATGTATGA
1 TTATGAATGTATGA
297602 AGTTATTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.18
15 3 0.11
16 20 0.71
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
TTATGAATGTATGATA
Found at i:298031 original size:35 final size:35
Alignment explanation
Indices: 297992--298090 Score: 110
Period size: 35 Copynumber: 2.8 Consensus size: 35
297982 AGTGGTTAGT
*
297992 TAGGCATGAAATGGTGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
* * * * *
298027 TAGGCGTGCAATGGTAATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
*
298062 TAGGCGTGAAAATCGTGATA-AGAGATGGT
1 TAGGCGTG-AAATGGTGATAGA-AGATGGT
298091 GATGTTTAGG
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
35 38 0.73
36 14 0.27
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.26
Consensus pattern (35 bp):
TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
Found at i:305031 original size:19 final size:20
Alignment explanation
Indices: 304995--305037 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
304985 GAAACCCCTT
*
304995 TGAAAAAACATGATTTTTAA
1 TGAAAAAACATGAATTTTAA
*
305015 TGAAAATACAT-AATTTTAA
1 TGAAAAAACATGAATTTTAA
305034 TGAA
1 TGAA
305038 GTTAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAAAACATGAATTTTAA
Found at i:310214 original size:804 final size:804
Alignment explanation
Indices: 308665--310214 Score: 2589
Period size: 804 Copynumber: 1.9 Consensus size: 804
308655 TACAACCTTC
* * * *
308665 TGATGTGACCCTGAGTAGCACCAGTTTTATCCATTATCTTATCACATCATGGATGTTCTACCTTA
1 TGATGTGACCCTGACTAGCACCAGTTTTATCCATTATATTATCACATCATGGACGTTATACCTTA
* *
308730 TTGATTATAAGGGAGTTATTCCTTATTTTATAATATATTTACTCATTTATGCATACATTTTCATG
66 TTGATTATAAGGGAGTTATTCCTTATTTTATAATATATTTAATCATTTATGCATACATTTGCATG
* *
308795 TTAAATGTAAAGGATATGGCAGTGCACCTATTTTATCCAGTGGGCAGATCACGTCACCCATATTG
131 TTAAATGTAAAGGATATGGCAGTGCACATATTTTATCCAGTGGACAGATCACGTCACCCATATTG
* * *
308860 ATTGCCATATCTGAACATGTTCCAAGCATATTTGGGTGATAAAGTCTTCTTAACATTTGTTTCAC
196 ATCGCCATATATGAACATGTTCCAAGCATATTTGGGTGATAAAGTCTTCTTAACATTTGTTTCAA
* * * * *
308925 TATCTCTTATATTTCCAACGCAGTTTTAATCAAATTAATATGATATTTGGAGCTCGAGATATTGC
261 TATCTCTTATATTTCCAACGCACTTTGAATAAAATTAATATGATATTTGGAGATCGAGATATGGC
*
308990 CAAATTCCTGAAGACAGTGCAGGCTAGAAATAAGTACGGGATTTATAGCTATTCATCTACTTCAA
326 CAAATTACTGAAGACAGTGCAGGCTAGAAATAAGTACGGGATTTATAGCTATTCATCTACTTCAA
*
309055 TGGACTTATGCTTGAGAGGCCTTAACGGAGAACATGCCACATGTTAGGACAATCTAGTGGAGCAC
391 TAGACTTATGCTTGAGAGGCCTTAACGGAGAACATGCCACATGTTAGGACAATCTAGTGGAGCAC
* * * *
309120 CTATAAGACACATCCAGCTCACAAACATGGCAGCAAGGTTTATTGGAGCATTACACACAATTGGC
456 CTAGAAGACACATCCAGCTCAAAAACATGGCAGAAAGGTTTATTGGAGCATTACACAAAATTGGC
*
309185 AGCTTGCTGGAGCATTAAGGAAACATGACAACTCACCAACAATTCATGACAGATTGTGGGGCAGC
521 AGCTTGCTGGAGCATTAAGGAAACATGACAACTCACCAACAACTCATGACAGATTGTGGGGCAGC
*
309250 TTGTGGAGGGAATTTCATCTGGAAGTGCACAAATGACAAATCAACACCACCAGCCCTTTTTTTTT
586 TTGTGGAGGGAATTTCATCTGGAAGTGCACAAATCACAAATCAACACCACCAGCCCTTTTTTTTT
* *
309315 AGTTATCAACTCAAATTAAGCTTAAAATGAAGACAATACACCCTCAAATTGCTGCTGCACATCCT
651 AATTATCAACTCAAATTAAGCTTAAAATGAAGACAATACACCCTCAAATTGATGCTGCACATCCT
*
309380 ACACGAAATTGCACTACAAAACAGCCCATGTACACTAAAGAGAAGTTACCCTTCGATTTGAGGAC
716 ACACGAAATTGCACTACAAAACAACCCATGTACACTAAAGAGAAGTTACCCTTCGATTTGAGGAC
309445 AAATCGCCCAAAAGAAGGGGAGAA
781 AAATCGCCCAAAAGAAGGGGAGAA
* * *
309469 TGATGTGATCCTGACTAGCACCAGTTTTATCCATTATATTATCACATCGTGGACGTTATACCTTG
1 TGATGTGACCCTGACTAGCACCAGTTTTATCCATTATATTATCACATCATGGACGTTATACCTTA
* * *
309534 TTGATTATAAGTGATTTCTTCCTTATTTTATAATATATTTAATCATTTATGCATACATTTGCATG
66 TTGATTATAAGGGAGTTATTCCTTATTTTATAATATATTTAATCATTTATGCATACATTTGCATG
* *
309599 TTAAATGTAAAGGATATGGCAGTGCACATGTTTTATCCAGTGGACAGATCACGTCACCCATATTT
131 TTAAATGTAAAGGATATGGCAGTGCACATATTTTATCCAGTGGACAGATCACGTCACCCATATTG
* *
309664 ATCGCCATTTATGCACATGTTCCAAGCATATTTGGGTGATAAAGTCTTCTTAACATTTGTTTCAA
196 ATCGCCATATATGAACATGTTCCAAGCATATTTGGGTGATAAAGTCTTCTTAACATTTGTTTCAA
*
309729 TATCTCTTATCTTTCCAACGCACTTTGAATAAAATTAATATGATATTTGGAGATCGAGATATGGC
261 TATCTCTTATATTTCCAACGCACTTTGAATAAAATTAATATGATATTTGGAGATCGAGATATGGC
* * *
309794 CAAATTACTGAAGACAGTGCAGGTTGGAAATAAGTACGGGATTTATAGCTATTCATCTCCTTCAA
326 CAAATTACTGAAGACAGTGCAGGCTAGAAATAAGTACGGGATTTATAGCTATTCATCTACTTCAA
* *
309859 TAGACTTATGCTTGAGAGGCCTTAACGGAGAACATGCCACATGTTAGGATAGTCTAGTGGAGCAC
391 TAGACTTATGCTTGAGAGGCCTTAACGGAGAACATGCCACATGTTAGGACAATCTAGTGGAGCAC
* * *
309924 TTAGAAGACACATCCATCTCAAAAACATGGCATAAAGGTTTATTGGAGCATTACACAAAATTGGC
456 CTAGAAGACACATCCAGCTCAAAAACATGGCAGAAAGGTTTATTGGAGCATTACACAAAATTGGC
*
309989 AGCTTGTTGGAGCATTAAGGAAACATGACAACTCACCAACAACTCATGACAGATTGTGGGGCAGC
521 AGCTTGCTGGAGCATTAAGGAAACATGACAACTCACCAACAACTCATGACAGATTGTGGGGCAGC
* * * * *
310054 TTGTGGAGTGAATTTCGTCTGGAAGTGCACAAATCACAACTTAACACCACCAGCCTTTTTTTTTT
586 TTGTGGAGGGAATTTCATCTGGAAGTGCACAAATCACAAATCAACACCACCAGCCCTTTTTTTTT
* * *
310119 AATTATCTACTCAAATTAAGCTTGAAATGAAGACAATACACGCC-CAAATTGATGTTGCACATCC
651 AATTATCAACTCAAATTAAGCTTAAAATGAAGACAATACAC-CCTCAAATTGATGCTGCACATCC
310183 TACACGAAATTGCACTACAAAACAACCCATGT
715 TACACGAAATTGCACTACAAAACAACCCATGT
310215 GCATGCCAAC
Statistics
Matches: 690, Mismatches: 55, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
804 688 1.00
805 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (804 bp):
TGATGTGACCCTGACTAGCACCAGTTTTATCCATTATATTATCACATCATGGACGTTATACCTTA
TTGATTATAAGGGAGTTATTCCTTATTTTATAATATATTTAATCATTTATGCATACATTTGCATG
TTAAATGTAAAGGATATGGCAGTGCACATATTTTATCCAGTGGACAGATCACGTCACCCATATTG
ATCGCCATATATGAACATGTTCCAAGCATATTTGGGTGATAAAGTCTTCTTAACATTTGTTTCAA
TATCTCTTATATTTCCAACGCACTTTGAATAAAATTAATATGATATTTGGAGATCGAGATATGGC
CAAATTACTGAAGACAGTGCAGGCTAGAAATAAGTACGGGATTTATAGCTATTCATCTACTTCAA
TAGACTTATGCTTGAGAGGCCTTAACGGAGAACATGCCACATGTTAGGACAATCTAGTGGAGCAC
CTAGAAGACACATCCAGCTCAAAAACATGGCAGAAAGGTTTATTGGAGCATTACACAAAATTGGC
AGCTTGCTGGAGCATTAAGGAAACATGACAACTCACCAACAACTCATGACAGATTGTGGGGCAGC
TTGTGGAGGGAATTTCATCTGGAAGTGCACAAATCACAAATCAACACCACCAGCCCTTTTTTTTT
AATTATCAACTCAAATTAAGCTTAAAATGAAGACAATACACCCTCAAATTGATGCTGCACATCCT
ACACGAAATTGCACTACAAAACAACCCATGTACACTAAAGAGAAGTTACCCTTCGATTTGAGGAC
AAATCGCCCAAAAGAAGGGGAGAA
Found at i:313957 original size:22 final size:22
Alignment explanation
Indices: 313908--313958 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
313898 TTTATTTTCT
*
313908 TTTCTTCTTTTTGAGTGTTGGAA
1 TTTCTTCTTTTGGAGTGTT-GAA
*
313931 ATTCTTCTTTTGGAGTGCTT-AA
1 TTTCTTCTTTTGGAGTG-TTGAA
313953 TTTCTT
1 TTTCTT
313959 TTCTGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 7 0.29
23 15 0.62
24 2 0.08
ACGTcount: A:0.14, C:0.12, G:0.18, T:0.57
Consensus pattern (22 bp):
TTTCTTCTTTTGGAGTGTTGAA
Found at i:316306 original size:19 final size:20
Alignment explanation
Indices: 316268--316310 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
316258 GAAACCCCTT
*
316268 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
316288 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
316307 TGAA
1 TGAA
316311 GATAAATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:322861 original size:28 final size:26
Alignment explanation
Indices: 322830--322887 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
322820 TTTGAATGTA
322830 CTTTGCAA-CTTTCTTCACTTTTCTTTTT
1 CTTTG-AATCTTTCTTC-CTTTTC-TTTT
* *
322858 CTTTGAATTTTTCTTCTTTTTCTTTT
1 CTTTGAATCTTTCTTCCTTTTCTTTT
322884 CTTT
1 CTTT
322888 CTTTGGCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.30
27 7 0.26
28 12 0.44
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.67
Consensus pattern (26 bp):
CTTTGAATCTTTCTTCCTTTTCTTTT
Found at i:323168 original size:11 final size:11
Alignment explanation
Indices: 323152--323193 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
323142 TGGATAATTA
323152 AGAAATGAAAT
1 AGAAATGAAAT
323163 AGAAATGAAA-
1 AGAAATGAAAT
* *
323173 ATAATTGAAAT
1 AGAAATGAAAT
323184 AGAAA-GAAAT
1 AGAAATGAAAT
323194 GTTATCAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 13 0.50
11 13 0.50
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (11 bp):
AGAAATGAAAT
Found at i:323433 original size:36 final size:35
Alignment explanation
Indices: 323342--323450 Score: 130
Period size: 35 Copynumber: 3.1 Consensus size: 35
323332 GGTTGTTATT
* * * *
323342 TAGGCGAGAAATGGTGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
* * *
323377 TAGACGTGCAATGGTAATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
*
323412 TAGGCGTGAAAATGGTGATGGAAGATGGTGGTGTT-
1 TAGGCGTG-AAATGGTGATGGAAGATGGTGATGTTA
323447 TAGG
1 TAGG
323451 TAGTATCTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
35 39 0.63
36 23 0.37
ACGTcount: A:0.32, C:0.04, G:0.38, T:0.27
Consensus pattern (35 bp):
TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
Found at i:327401 original size:21 final size:21
Alignment explanation
Indices: 327362--327405 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
327352 ACCATCTCTA
327362 TCCTTTCTTTATTTCATTTCAT
1 TCCTTTCTTTA-TTCATTTCAT
327384 TCCTTATCTTTA-TCATTTCAT
1 TCCTT-TCTTTATTCATTTCAT
327405 T
1 T
327406 AATCTTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (21 bp):
TCCTTTCTTTATTCATTTCAT
Found at i:333674 original size:20 final size:19
Alignment explanation
Indices: 333638--333676 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
333628 AGATAATGCG
333638 TGAAGCATAAGAGCTAATA
1 TGAAGCATAAGAGCTAATA
* *
333657 TGAATGCATATGATCTAATA
1 TGAA-GCATAAGAGCTAATA
333677 AAACAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (19 bp):
TGAAGCATAAGAGCTAATA
Found at i:334952 original size:13 final size:13
Alignment explanation
Indices: 334930--334959 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
334920 ACTAAACACC
334930 TTTC-ACATACCT
1 TTTCAACATACCT
334942 TTTCAACATACCT
1 TTTCAACATACCT
334955 TTTCA
1 TTTCA
334960 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:348516 original size:50 final size:52
Alignment explanation
Indices: 348457--348553 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 52
348447 TGAATCAACA
* * *
348457 TCCCTTTGGTCGAATGGGGGTGTGCTTGTTCATCTTGGCA-CCAAAGACATC
1 TCCCTTTGGTCGAATGAGGATGTGCTGGTTCATCTTGGCACCCAAAGACATC
* *
348508 TCCC-TTGGTCGAATGATGATGTGCTGGTTCATTTTGGCACCCAAAG
1 TCCCTTTGGTCGAATGAGGATGTGCTGGTTCATCTTGGCACCCAAAG
348554 CTCTCATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 30 0.75
51 10 0.25
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.32
Consensus pattern (52 bp):
TCCCTTTGGTCGAATGAGGATGTGCTGGTTCATCTTGGCACCCAAAGACATC
Found at i:349930 original size:13 final size:13
Alignment explanation
Indices: 349876--349934 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 13
349866 CTACCTATAA
*
349876 CATCACCATCTTC
1 CATCACCATTTTC
349889 CATCACCATTTT-
1 CATCACCATTTTC
* * **
349901 CAT--GCATATAA
1 CATCACCATTTTC
349912 CATCACCATTTTC
1 CATCACCATTTTC
349925 CATCACCATT
1 CATCACCATT
349935 GCACGCCTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
10 4 0.11
11 3 0.09
12 3 0.09
13 25 0.71
ACGTcount: A:0.29, C:0.36, G:0.02, T:0.34
Consensus pattern (13 bp):
CATCACCATTTTC
Found at i:349981 original size:35 final size:35
Alignment explanation
Indices: 349869--349980 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
349859 TAAGATACTA
* *
349869 CCTATAACATCACCATCTTCCATCACCATTTTCATG
1 CCTATAACATCACCAACTTCCATCACCA-TTTCACG
* ** *
349905 CATATAACATCACCATTTTCCATCACCATTGCACG
1 CCTATAACATCACCAACTTCCATCACCATTTCACG
* *
349940 CCTATATCATCACCAACTTCTATCACCATTTCACG
1 CCTATAACATCACCAACTTCCATCACCATTTCACG
349975 CCTATA
1 CCTATA
349981 TAACCACCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 40 0.61
36 26 0.39
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.31
Consensus pattern (35 bp):
CCTATAACATCACCAACTTCCATCACCATTTCACG
Found at i:350358 original size:13 final size:13
Alignment explanation
Indices: 350340--350364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
350330 AAGCAACAAA
350340 AAGAAAAAGAAAT
1 AAGAAAAAGAAAT
350353 AAGAAAAAGAAA
1 AAGAAAAAGAAA
350365 AGACTCTTAT
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:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
AAGAAAAAGAAAT
Found at i:359842 original size:195 final size:198
Alignment explanation
Indices: 359496--359891 Score: 771
Period size: 195 Copynumber: 2.0 Consensus size: 198
359486 ATTTGAAGGA
359496 TTACCTTGGTAAGAGGATGAAGTACCTTGGTAATGTTCACTGAATCGAGATCTCCTTTGGATTTG
1 TTACCTTGGTAAGAGGATGAAGTACCTTGGTAATGTTCACTGAATCGAGATCTCCTTTGGATTTG
359561 TGCTTCGATTGTCATTGCTTTCTTTAGTGTATCTTCAAGGTTTTTGTAACCTTGTAGGTCAAGAA
66 TGCTTCGATTGTCATTGCTTTCTTTAGTGTATCTTCAAGGTTTTTGTAACCTTGTAGGTCAAGAA
359626 GATAAGTGATGTTTGAGTTTAAGCCAACGACGAATCTTGACACGGTGACCTC-TC-TTTTTGGTT
131 GATAAGTGATGTTTGAGTTTAAGCCAACGACGAATCTTGACACGGTGACCTCTTCTTTTTTGGTT
359689 ATG
196 ATG
359692 TTACCTTGGTAAG-GGATGAAGTACCTTGGTAATGTTCACTGAATCGAGATCTCCTTTGGATTTG
1 TTACCTTGGTAAGAGGATGAAGTACCTTGGTAATGTTCACTGAATCGAGATCTCCTTTGGATTTG
359756 TGCTTCGATTGTCATTGCTTTCTTTAGTGTATCTTCAAGGTTTTTGTAACCTTGTAGGTCAAGAA
66 TGCTTCGATTGTCATTGCTTTCTTTAGTGTATCTTCAAGGTTTTTGTAACCTTGTAGGTCAAGAA
359821 GATAAGTGATGTTTGAGTTTAAGCCAACGACGAATCTTGACACGGTGACCTCTTCTTTTTTGGTT
131 GATAAGTGATGTTTGAGTTTAAGCCAACGACGAATCTTGACACGGTGACCTCTTCTTTTTTGGTT
359886 ATG
196 ATG
359889 TTA
1 TTA
359892 GCCCTATTGA
Statistics
Matches: 198, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
195 168 0.85
196 15 0.08
197 15 0.08
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (198 bp):
TTACCTTGGTAAGAGGATGAAGTACCTTGGTAATGTTCACTGAATCGAGATCTCCTTTGGATTTG
TGCTTCGATTGTCATTGCTTTCTTTAGTGTATCTTCAAGGTTTTTGTAACCTTGTAGGTCAAGAA
GATAAGTGATGTTTGAGTTTAAGCCAACGACGAATCTTGACACGGTGACCTCTTCTTTTTTGGTT
ATG
Found at i:368253 original size:15 final size:15
Alignment explanation
Indices: 368233--368263 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
368223 TGCCAAATGA
368233 CCAGCCCCCATGTGC
1 CCAGCCCCCATGTGC
368248 CCAGCCCCCATGTGC
1 CCAGCCCCCATGTGC
368263 C
1 C
368264 TTGCATGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.55, G:0.19, T:0.13
Consensus pattern (15 bp):
CCAGCCCCCATGTGC
Found at i:378674 original size:22 final size:22
Alignment explanation
Indices: 378648--378693 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
378638 AAATGGAGGG
378648 TGATAAGAGCTAAATACCTTGC
1 TGATAAGAGCTAAATACCTTGC
*
378670 TGATATGAGCTAAATACCTTGC
1 TGATAAGAGCTAAATACCTTGC
378692 TG
1 TG
378694 CCATGCATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (22 bp):
TGATAAGAGCTAAATACCTTGC
Found at i:379776 original size:35 final size:35
Alignment explanation
Indices: 379729--379806 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
379719 ATAAGATACT
* *
379729 ACCTATAACATCACCATCTTCCATCACCATTGCAC
1 ACCTATATCATCACCAACTTCCATCACCATTGCAC
* *
379764 ACCTATATCATCACCAACTTCTATCACCATTTCAC
1 ACCTATATCATCACCAACTTCCATCACCATTGCAC
379799 ACCTATAT
1 ACCTATAT
379807 AACTACCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.32, C:0.37, G:0.01, T:0.29
Consensus pattern (35 bp):
ACCTATATCATCACCAACTTCCATCACCATTGCAC
Found at i:384799 original size:17 final size:17
Alignment explanation
Indices: 384773--384807 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
384763 CGTCGACTTA
*
384773 AAAAATGGTTAGGGTAT
1 AAAAAGGGTTAGGGTAT
*
384790 AAAAAGGGTTATGGTAT
1 AAAAAGGGTTAGGGTAT
384807 A
1 A
384808 GGGGTAGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (17 bp):
AAAAAGGGTTAGGGTAT
Found at i:385337 original size:18 final size:18
Alignment explanation
Indices: 385295--385347 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 18
385285 TGCAAAAATT
385295 AAAGAAAT-AAATGAATAA
1 AAAGAAATGAAA-GAATAA
385313 AATAGAATATGAAAGAAT-A
1 AA-AGAA-ATGAAAGAATAA
385332 AAAGAAATGATAAGAA
1 AAAGAAATGA-AAGAA
385348 AAAGAAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.13
18 11 0.35
19 7 0.23
20 6 0.19
21 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (18 bp):
AAAGAAATGAAAGAATAA
Found at i:385360 original size:17 final size:15
Alignment explanation
Indices: 385331--385364 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
385321 ATGAAAGAAT
385331 AAAAGAAATGATAAGA
1 AAAAGAAATGAT-AGA
385347 AAAAGAAATGGATAGA
1 AAAAGAAAT-GATAGA
385363 AA
1 AA
385365 TGTAATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.12
Consensus pattern (15 bp):
AAAAGAAATGATAGA
Found at i:388220 original size:22 final size:23
Alignment explanation
Indices: 388158--388234 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 23
388148 ATGTGCCTAT
388158 ATGTATAACATAAAGAA-ATAACTA
1 ATGTATAA-AT-AAGAATATAACTA
388182 A-GTATAAATAA-ACATAT-A-TA
1 ATGTATAAATAAGA-ATATAACTA
*
388202 ATGTATAATATAAGAATATGAATTA
1 ATGTATAA-ATAAGAATAT-AACTA
388227 ATAGTATA
1 AT-GTATA
388235 TTATGATAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
20 4 0.09
21 10 0.23
22 12 0.27
23 7 0.16
24 2 0.05
25 4 0.09
26 5 0.11
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (23 bp):
ATGTATAAATAAGAATATAACTA
Found at i:388896 original size:24 final size:24
Alignment explanation
Indices: 388864--388909 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
388854 GAGTTACCAT
* *
388864 TCTTTGCTCTTCAATAGTCATAAC
1 TCTTAGCTCTTCAAAAGTCATAAC
*
388888 TCTTAGCTCTTGAAAAGTCATA
1 TCTTAGCTCTTCAAAAGTCATA
388910 TCCTTTAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (24 bp):
TCTTAGCTCTTCAAAAGTCATAAC
Found at i:393516 original size:15 final size:15
Alignment explanation
Indices: 393481--393509 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
393471 GTGCTTCAAA
393481 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
393495 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
393510 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:404932 original size:15 final size:15
Alignment explanation
Indices: 404921--404949 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
404911 ACTCAAAAAG
404921 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
404936 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
404950 GTTGAAGCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:412966 original size:21 final size:21
Alignment explanation
Indices: 412942--412991 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
412932 GTCCAAAGAA
412942 GCATGTATTATGGACTATGGT
1 GCATGTATTATGGACTATGGT
412963 GCATGTATTATGGACTATGGT
1 GCATGTATTATGGACTATGGT
412984 GCATGTAT
1 GCATGTAT
412992 CATTTCCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.10, G:0.28, T:0.38
Consensus pattern (21 bp):
GCATGTATTATGGACTATGGT
Found at i:425407 original size:19 final size:21
Alignment explanation
Indices: 425363--425415 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
425353 GAAACCCCTT
*
425363 TGAAAATACAAGACTTTTTAAA
1 TGAAAATACATGAC-TTTTAAA
425385 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
425404 TGAAGATACATG
1 TGAAAATACATG
425416 CTATTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
22 12 0.41
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:427484 original size:17 final size:17
Alignment explanation
Indices: 427459--427503 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
427449 GTATGCTCTC
*
427459 TTTGTATTCCAGTTCTT
1 TTTGAATTCCAGTTCTT
427476 TTTGAATTCCAGTTCTT
1 TTTGAATTCCAGTTCTT
*
427493 TTTGAACTCCA
1 TTTGAATTCCA
427504 CTCTCACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (17 bp):
TTTGAATTCCAGTTCTT
Found at i:429515 original size:72 final size:71
Alignment explanation
Indices: 429420--429558 Score: 183
Period size: 72 Copynumber: 1.9 Consensus size: 71
429410 AATACATCCT
* * * * *
429420 TTGGCTGAATTCATCCCACCTTGTGTGAACTTG-TTGATTTGTCTTCTATGGATGAATATTCATG
1 TTGGCTGAATTCATCCCACCTTGTGTGAACATGACT-ATTTGGCTTCT-TGCATGAATATGCATG
429484 AATGTATC
64 AATGTATC
*
429492 TTGGCTGAAATTCTTCCC-CCTTGTGTGAACATGACTATTTGGCTTCTTGCATGAATATGCATGA
1 TTGGCTG-AATTCATCCCACCTTGTGTGAACATGACTATTTGGCTTCTTGCATGAATATGCATGA
429556 ATG
65 ATG
429559 GATGAATTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
71 18 0.31
72 31 0.53
73 10 0.17
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (71 bp):
TTGGCTGAATTCATCCCACCTTGTGTGAACATGACTATTTGGCTTCTTGCATGAATATGCATGAA
TGTATC
Found at i:432389 original size:2 final size:2
Alignment explanation
Indices: 432382--432409 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
432372 TGGAAGCAGA
432382 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
432410 TGGTGATATG
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:433543 original size:19 final size:20
Alignment explanation
Indices: 433519--433561 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
433509 AGCATTTATC
*
433519 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
433538 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
433558 TTCA
1 TTCA
433562 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:433923 original size:13 final size:13
Alignment explanation
Indices: 433905--433962 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
433895 ACTACCTAAA
433905 CATCACCATCTTT
1 CATCACCATCTTT
433918 CATCACCAT-TTT
1 CATCACCATCTTT
* **
433930 CA-CACC-TATAA
1 CATCACCATCTTT
*
433941 CATCACCATCTTC
1 CATCACCATCTTT
*
433954 CATTACCAT
1 CATCACCAT
433963 TGCACACCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
10 1 0.03
11 7 0.19
12 9 0.25
13 19 0.53
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.33
Consensus pattern (13 bp):
CATCACCATCTTT
Done.