Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008463.1 Hibiscus syriacus cultivar Beakdansim tig00111276_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: 1833679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:460 original size:24 final size:24
Alignment explanation
Indices: 433--486 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
423 GTATTCGAAA
433 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
457 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
481 TTTGAT
1 TTTGAT
487 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3060 original size:140 final size:140
Alignment explanation
Indices: 2807--3089 Score: 530
Period size: 140 Copynumber: 2.0 Consensus size: 140
2797 GCAAACGTTG
2807 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
2872 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTTTTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTCCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
2937 CGAATTTGAC
131 CGAATTTGAC
*
2947 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTACCTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
3012 TTGAACATTGCTATGATCTGTCCAGTTGTTATCACTTATTACATATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTCCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3077 CGAATTTGAC
131 CGAATTTGAC
3087 TAT
1 TAT
3090 CGCAACGCAA
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTCCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:3085 original size:20 final size:20
Alignment explanation
Indices: 3060--3264 Score: 135
Period size: 20 Copynumber: 11.2 Consensus size: 20
3050 TTACATATTC
3060 ATTTGAATATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
3080 ATTTGACTATCGCAACGC-A
1 ATTTGAATATCGCAACGCGA
3099 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
3114 ATTT-AACTATCGCAACGCGA
1 ATTTGAA-TATCGCAACGCGA
*
3134 ATTT-AACTATCGCAACACGA
1 ATTTGAA-TATCGCAACGCGA
* *
3154 ATTTGACTATCGCAACGAGA
1 ATTTGAATATCGCAACGCGA
* * *
3174 ATATGACTATCACAACGC-A
1 ATTTGAATATCGCAACGCGA
*
3193 A----AA-ATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
*
3208 ATTTGACTATCGCAA--CG-
1 ATTTGAATATCGCAACGCGA
* *
3225 A---GAAAATCGCAAAGCGA
1 ATTTGAATATCGCAACGCGA
* *
3242 ATTAGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
3262 ATT
1 ATT
3265 GACTTTGGGT
Statistics
Matches: 148, Mismatches: 18, Indels: 38
0.73 0.09 0.19
Matches are distributed among these distances:
14 27 0.18
15 6 0.04
16 2 0.01
17 2 0.01
18 4 0.03
19 5 0.03
20 101 0.68
21 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:3157 original size:40 final size:39
Alignment explanation
Indices: 3067--3268 Score: 152
Period size: 34 Copynumber: 5.5 Consensus size: 39
3057 TTCATTTGAA
3067 TATCGCAACGCGAATTTGACTATCGCAACGC-AA--AA-
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTAAC
*
3102 -ATCGCAACGCGAATTTAACTATCGCAACGCGAATTTAAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAA-TTAAC
* * *
3141 TATCGCAACACGAATTTGACTATCGCAACGAGAATATGAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAAT-TAAC
* * * *
3181 TATCACAACGC-AA----A-AATCGCAACACGAATTTGAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAA-TTAAC
* *
3215 TATCGCAACGAGAA----A--ATCGCAAAGCGAATTAGAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTA-AC
3249 TATCGCAACGCGAA-TTGACT
1 TATCGCAACGCGAATTTGACT
3269 TTGGGTTGTG
Statistics
Matches: 136, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.01
34 79 0.58
35 7 0.05
37 1 0.01
38 2 0.01
39 3 0.02
40 42 0.31
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (39 bp):
TATCGCAACGCGAATTTGACTATCGCAACGCGAATTAAC
Found at i:3254 original size:54 final size:53
Alignment explanation
Indices: 3122--3268 Score: 144
Period size: 54 Copynumber: 2.7 Consensus size: 53
3112 GAATTTAACT
* *
3122 ATCGCAACGCGAATTTAACTATCGCAACACGAATTTGACTATCGCAACGAGAAT
1 ATCGCAAAGCGAA-TTAACTATCGCAACACGAATTTGACTATCGCAACGAGAAA
*
3176 AT-GACTATCACAACGCAA--AA--ATCGCAACACGAATTTGACTATCGCAACGAGAAA
1 ATCG-C-A--A-AGCG-AATTAACTATCGCAACACGAATTTGACTATCGCAACGAGAAA
*
3230 ATCGCAAAGCGAATTAGACTATCGCAACGCGAA-TTGACT
1 ATCGCAAAGCGAATTA-ACTATCGCAACACGAATTTGACT
3269 TTGGGTTGTG
Statistics
Matches: 76, Mismatches: 5, Indels: 25
0.72 0.05 0.24
Matches are distributed among these distances:
49 2 0.03
50 3 0.04
51 2 0.03
52 1 0.01
53 8 0.11
54 51 0.67
55 2 0.03
56 2 0.03
57 1 0.01
58 2 0.03
59 2 0.03
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (53 bp):
ATCGCAAAGCGAATTAACTATCGCAACACGAATTTGACTATCGCAACGAGAAA
Found at i:3324 original size:20 final size:20
Alignment explanation
Indices: 3281--3339 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
3271 GGGTTGTGAT
3281 TTTTG-CTTTCGCATTGCGA
1 TTTTGACTTTCGCATTGCGA
3300 TTTTGACTTTCGCATTGCGA
1 TTTTGACTTTCGCATTGCGA
* * *
3320 TTTTGAGTTTAGCGTTGCGA
1 TTTTGACTTTCGCATTGCGA
3340 AAGTGTACCT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 5 0.14
20 31 0.86
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.46
Consensus pattern (20 bp):
TTTTGACTTTCGCATTGCGA
Found at i:3639 original size:71 final size:71
Alignment explanation
Indices: 3391--3631 Score: 340
Period size: 71 Copynumber: 3.5 Consensus size: 71
3381 GATTGAAATC
* *
3391 AACAAATCAACTTTTACATTTCAATCAATTAAACAAGC---ACA-AATAAGAA---TTA-TTTAC
1 AACAAATCAACTTTTACA----AATCAATTAAACAAGCAAAAAATAATAAGAATTCTTATTTTCC
3448 TCATCAATTA
62 TCATCAATTA
3458 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATAAGAATTCTTATTTTCCTCAT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATAAGAATTCTTATTTTCCTCAT
3523 CAATTA
66 CAATTA
3529 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATAAGAATTCTTATTTTCCTCAT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATAAGAATTCTTATTTTCCTCAT
3594 CAATTA
66 CAATTA
3600 AACAAATCAGACTTTTA-AGAA-CAATTAAACAA
1 AACAAATCA-ACTTTTACA-AATCAATTAAACAA
3632 TAAAAAAAGT
Statistics
Matches: 162, Mismatches: 2, Indels: 16
0.90 0.01 0.09
Matches are distributed among these distances:
63 16 0.10
66 2 0.01
67 26 0.16
70 3 0.02
71 106 0.65
72 9 0.06
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (71 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATAAGAATTCTTATTTTCCTCAT
CAATTA
Found at i:4980 original size:42 final size:42
Alignment explanation
Indices: 4921--5043 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 42
4911 GTGAATCGGG
** *
4921 CTCTTGAATAGTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
** *
4963 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTGAACGATGACAGGGGC
* * *
5005 CTCTTAAACGATAGGAGAGG-CCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACAGG
5044 TCAGTCGGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 61 0.92
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:4981 original size:21 final size:21
Alignment explanation
Indices: 4921--5035 Score: 79
Period size: 21 Copynumber: 5.5 Consensus size: 21
4911 GTGAATCGGG
** *
4921 CTCTTGAATAGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
4942 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
4963 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
* **
4984 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * * *
5005 CTCTTAAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
5026 CTCTTGAACG
1 CTCTTGAACG
5036 ATGACAGGTC
Statistics
Matches: 68, Mismatches: 24, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
20 3 0.04
21 63 0.93
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:5614 original size:20 final size:19
Alignment explanation
Indices: 5547--5614 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 19
5537 GAAACTTAAA
*
5547 ATCGCAAAGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
5567 ATCGCAACACGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
5587 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
5607 ATCGCAAC
1 ATCGCAAC
5615 AAGATAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:5647 original size:19 final size:20
Alignment explanation
Indices: 5620--5658 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5610 GCAACAAGAT
*
5620 AATCACAATGTGAAA-TAAA
1 AATCACAATGCGAAACTAAA
*
5639 AATCGCAATGCGAAACTAAA
1 AATCACAATGCGAAACTAAA
5659 TTCGCGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.15, G:0.13, T:0.18
Consensus pattern (20 bp):
AATCACAATGCGAAACTAAA
Found at i:5721 original size:33 final size:34
Alignment explanation
Indices: 5663--5738 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 34
5653 ACTAAATTCG
* * *
5663 CGTTACGATTTTCATTTTCGTATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* *
5697 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
5730 CGTTGCGAT
1 CGTTGCGAT
5739 AGTCAAATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 25 0.68
34 12 0.32
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:5755 original size:20 final size:20
Alignment explanation
Indices: 5730--5778 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
5720 GCGATTATCC
5730 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
5750 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
5770 CGTTGCGAT
1 CGTTGCGAT
5779 TTTAAGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:5788 original size:20 final size:20
Alignment explanation
Indices: 5730--5797 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
5720 GCGATTATCC
*
5730 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* *
5750 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
5770 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATAGTAAGTTTCG
*
5790 TGTTGCGA
1 CGTTGCGA
5798 CTATTCTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.03
20 39 0.98
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:7151 original size:20 final size:20
Alignment explanation
Indices: 7128--7168 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
7118 TCTGAAACTT
*
7128 AAAATCACAACACGAAAATG
1 AAAACCACAACACGAAAATG
*
7148 AAAACCGCAACACGAAAATG
1 AAAACCACAACACGAAAATG
7168 A
1 A
7169 CTATCGCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.22, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAACCACAACACGAAAATG
Found at i:7176 original size:20 final size:20
Alignment explanation
Indices: 7135--7198 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
7125 CTTAAAATCA
** *
7135 CAACACGAAAATGAAAACCG
1 CAACACGAAAATGACTATCG
7155 CAACACGAAAATGACTATCG
1 CAACACGAAAATGACTATCG
* *
7175 CAACGC-AAATTTGACTATCG
1 CAACACGAAA-ATGACTATCG
7195 CAAC
1 CAAC
7199 GAGATAATCG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 3 0.08
20 35 0.92
ACGTcount: A:0.45, C:0.27, G:0.14, T:0.14
Consensus pattern (20 bp):
CAACACGAAAATGACTATCG
Found at i:7228 original size:19 final size:19
Alignment explanation
Indices: 7204--7246 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
7194 GCAACGAGAT
7204 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
7223 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
7242 AATCG
1 AATCG
7247 TGTTGCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:7668 original size:22 final size:22
Alignment explanation
Indices: 7641--7716 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
7631 GAGATAGACA
* *
7641 GATTTCGCCGGAGATGAGGATG
1 GATTTCGTCGGAGATGGGGATG
7663 GATTTCGTCGGAGATGGGGATG
1 GATTTCGTCGGAGATGGGGATG
* *
7685 GATTTTGTCGGAGATGGGGACG
1 GATTTCGTCGGAGATGGGGATG
*
7707 GATGTCGTCG
1 GATTTCGTCG
7717 TAGAGAGTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.18, C:0.12, G:0.43, T:0.26
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGATG
Found at i:8039 original size:19 final size:19
Alignment explanation
Indices: 8015--8051 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8005 TGCGATACTG
*
8015 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
8034 GAGATCGTATTGCGATTT
1 GAGATCGCATTGCGATTT
8052 TGTTGGTCAT
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:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:8370 original size:2 final size:2
Alignment explanation
Indices: 8363--8394 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8353 TAAAATTAAT
8363 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
8395 AGAAAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9450 original size:20 final size:20
Alignment explanation
Indices: 9425--9502 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
9415 AACGCGAATA
* *
9425 TGTAAATCGTAACACAAATT
1 TGTAAATCGCAACACAAATC
*
9445 TGTAAATCGCAACGCAAATC
1 TGTAAATCGCAACACAAATC
* *
9465 TGTAAATCGCAACGCGAATC
1 TGTAAATCGCAACACAAATC
9485 TGTAAATCGCAACACAAA
1 TGTAAATCGCAACACAAA
9503 AGTCAAATTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (20 bp):
TGTAAATCGCAACACAAATC
Found at i:9459 original size:40 final size:40
Alignment explanation
Indices: 9414--9502 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
9404 TCCAAATTCA
* * *
9414 CAACGCGAATATGTAAATCGTAACACAAATTTGTAAATCG
1 CAACGCAAATATGTAAATCGCAACACAAATCTGTAAATCG
* * *
9454 CAACGCAAATCTGTAAATCGCAACGCGAATCTGTAAATCG
1 CAACGCAAATATGTAAATCGCAACACAAATCTGTAAATCG
*
9494 CAACACAAA
1 CAACGCAAA
9503 AGTCAAATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (40 bp):
CAACGCAAATATGTAAATCGCAACACAAATCTGTAAATCG
Found at i:9594 original size:20 final size:19
Alignment explanation
Indices: 9555--9619 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
9545 ACAAATTCAT
*
9555 AACACCGAATTTCAAATTCGC
1 AACA-CGAATTT-TAATTCGC
* *
9576 AACTCGATTTTTGAATTCGC
1 AACACGAATTTT-AATTCGC
9596 AACACGAATTTTAATTTCGC
1 AACACGAATTTTAA-TTCGC
9616 AACA
1 AACA
9620 GGTTTTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 32 0.86
21 3 0.08
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (19 bp):
AACACGAATTTTAATTCGC
Found at i:10500 original size:18 final size:18
Alignment explanation
Indices: 10477--10512 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10467 AAGCAAAAGG
*
10477 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
10495 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
10513 CAACCGGCTT
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:10709 original size:29 final size:29
Alignment explanation
Indices: 10671--10726 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
10661 CAGATTTTTT
*
10671 GTTGCGATTGTTGCGAAAGTCAAATTCAC
1 GTTGCAATTGTTGCGAAAGTCAAATTCAC
10700 GTTGCAATTGTTGCGAAAGTCAAATTC
1 GTTGCAATTGTTGCGAAAGTCAAATTC
10727 GAAACACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (29 bp):
GTTGCAATTGTTGCGAAAGTCAAATTCAC
Found at i:10783 original size:20 final size:20
Alignment explanation
Indices: 10758--10823 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
10748 AAAATCGCAA
*
10758 TGCGAATTTGACTTTCACGT
1 TGCGAATTTGACTTTCGCGT
* **
10778 TGCGAATTTGACTATCGCAA
1 TGCGAATTTGACTTTCGCGT
*
10798 CGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTTTCGCGT
10818 TGCGAA
1 TGCGAA
10824 AGTGTACATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (20 bp):
TGCGAATTTGACTTTCGCGT
Found at i:10983 original size:64 final size:64
Alignment explanation
Indices: 10882--11032 Score: 232
Period size: 64 Copynumber: 2.4 Consensus size: 64
10872 AATTTAAAAC
*
10882 AACAAATCAACTTTTACAAATAAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** **
10946 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACTTATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*
11010 AACAAAACAAC-TTTACAAATCAA
1 AACAAATCAACTTTTACAAATCAA
11033 CTTTTACAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 12 0.15
64 68 0.85
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:11033 original size:13 final size:14
Alignment explanation
Indices: 11011--11043 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
11001 TATCAATTAA
*
11011 ACAAAACAAC-TTT
1 ACAAATCAACTTTT
11024 ACAAATCAACTTTT
1 ACAAATCAACTTTT
11038 ACAAAT
1 ACAAAT
11044 ACATCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:11369 original size:22 final size:22
Alignment explanation
Indices: 11344--11387 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
11334 TAAAATGCCG
11344 AAACCACAAGCCTACTGCACCT
1 AAACCACAAGCCTACTGCACCT
11366 AAACCACAAGCCTACTGCACCT
1 AAACCACAAGCCTACTGCACCT
11388 CTATCTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.41, G:0.09, T:0.14
Consensus pattern (22 bp):
AAACCACAAGCCTACTGCACCT
Found at i:12443 original size:21 final size:21
Alignment explanation
Indices: 12414--12484 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
12404 GTGATTCGGG
* *
12414 CTCTCGAACGGTGGAAGGGAC
1 CTCTTGAACGGTGGAAGGGGC
**
12435 CTCTTGAACAAT-GACAGGGGC
1 CTCTTGAACGGTGGA-AGGGGC
* *
12456 CTCTTGAATGGTGGGAGGGGC
1 CTCTTGAACGGTGGAAGGGGC
12477 CTCTTGAA
1 CTCTTGAA
12485 GGATGATAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.93
22 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGGTGGAAGGGGC
Found at i:15210 original size:20 final size:20
Alignment explanation
Indices: 15182--15238 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
15172 GTGAATTTGA
*
15182 ATTCTGTGTTGCGAATTACAT
1 ATTC-GTGTTGCGAATTACAG
* *
15203 ATTCGTGTTGCGATTTATAG
1 ATTCGTGTTGCGAATTACAG
*
15223 ATTCGCGTTGCGAATT
1 ATTCGTGTTGCGAATT
15239 TGGAAAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTCGTGTTGCGAATTACAG
Found at i:15611 original size:3 final size:3
Alignment explanation
Indices: 15605--15640 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
15595 TAATAATAGT
15605 TTA TTA TTA TT- TTA TT- TTA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15641 ATAATGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.20
3 24 0.80
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:15620 original size:11 final size:11
Alignment explanation
Indices: 15605--15640 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
15595 TAATAATAGT
15605 TTATTATTATT-
1 TTATT-TTATTA
15616 TTATTTTATTA
1 TTATTTTATTA
15627 TTATTTTATTA
1 TTATTTTATTA
15638 TTA
1 TTA
15641 ATAATGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:15625 original size:16 final size:16
Alignment explanation
Indices: 15604--15636 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15594 ATAATAATAG
15604 TTTATTATTATTTTAT
1 TTTATTATTATTTTAT
15620 TTTATTATTATTTTAT
1 TTTATTATTATTTTAT
15636 T
1 T
15637 ATTAATAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTATTATTTTAT
Found at i:18355 original size:18 final size:18
Alignment explanation
Indices: 18332--18366 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18322 TCTCACTAAC
*
18332 TTTTTCCTTTCATTTTTT
1 TTTTTCATTTCATTTTTT
*
18350 TTTTTCATTTTATTTTT
1 TTTTTCATTTCATTTTT
18367 ATTATTTGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTCATTTCATTTTTT
Found at i:20359 original size:14 final size:13
Alignment explanation
Indices: 20334--20395 Score: 65
Period size: 14 Copynumber: 4.6 Consensus size: 13
20324 AATTAGAACA
20334 AAAAGAAAAAAGAG
1 AAAA-AAAAAAGAG
20348 AAAAAAATAAAG-G
1 AAAAAAA-AAAGAG
*
20361 -AAAAAGAAAGAG
1 AAAAAAAAAAGAG
20373 AAAATAAAAAAGAG
1 AAAA-AAAAAAGAG
20387 AAACAAAAA
1 AAA-AAAAA
20396 CAAAGGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
11 4 0.10
12 6 0.15
13 7 0.17
14 23 0.56
15 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:20417 original size:29 final size:31
Alignment explanation
Indices: 20361--20422 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
20351 AAAATAAAGG
*
20361 AAAAAGAAAGAGAAAATAAAAAAGAGAA-AC
1 AAAAACAAAGAGAAAATAAAAAAGAGAAGAC
*
20391 AAAAACAAAG-GAAAAGTGAAAAA-AGAAGAC
1 AAAAACAAAGAGAAAA-TAAAAAAGAGAAGAC
20421 AA
1 AA
20423 GACGCATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (31 bp):
AAAAACAAAGAGAAAATAAAAAAGAGAAGAC
Found at i:21513 original size:32 final size:32
Alignment explanation
Indices: 21443--21531 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
21433 AGGAACAATG
* *
21443 GGGGCATCTTTGAAGATTCAACATCAAATGTA
1 GGGGCATCTTTGGAGATTCAACATCAAATATA
* * *
21475 GAGGCAT-TTTCGGAGATTCAACATCGAATATT
1 GGGGCATCTTT-GGAGATTCAACATCAAATATA
* *
21507 GGGGCATCTTTGGGGATTCCACATC
1 GGGGCATCTTTGGAGATTCAACATC
21532 CTGATGCGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
31 3 0.06
32 41 0.87
33 3 0.06
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (32 bp):
GGGGCATCTTTGGAGATTCAACATCAAATATA
Found at i:22696 original size:39 final size:36
Alignment explanation
Indices: 22597--22785 Score: 234
Period size: 37 Copynumber: 5.1 Consensus size: 36
22587 GTTTTACATT
* * *
22597 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
22633 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTA
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
22670 AAATAAATTTCTTTGTCTCTCTTGAGACAATTTCTCTTG
1 AAACAAA--T-TTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
22709 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
22745 AAACAAAGTTTTGTCACTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
22782 AAAC
1 AAAC
22786 CTAATCTTTG
Statistics
Matches: 130, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
36 37 0.28
37 60 0.46
38 1 0.01
39 32 0.25
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:22768 original size:73 final size:73
Alignment explanation
Indices: 22597--22785 Score: 236
Period size: 73 Copynumber: 2.5 Consensus size: 73
22587 GTTTTACATT
* * * * * *
22597 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTAAATTTTATCTCTCTTGAGACAGT
*
22662 TTCTCTTA
66 TTCCCTTA
* *
22670 AAATAAATTTCTTTGTCTCTCTTGAGACAATTTCTCTTGAAAC-AAATTTTATCTCTCTTGAGAC
1 AAACAAA--T-TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTAAATTTTATCTCTCTTGAGAC
*
22734 AGTTTCCCTTG
63 AGTTTCCCTTA
*
22745 AAACAAAGTTTTGTCACTCTTGAGACAGTTTCTCTTGAAAC
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
22786 CTAATCTTTG
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
73 36 0.36
74 1 0.01
75 35 0.35
76 27 0.27
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTAAATTTTATCTCTCTTGAGACAGT
TTCCCTTA
Found at i:22897 original size:33 final size:34
Alignment explanation
Indices: 22838--22915 Score: 124
Period size: 33 Copynumber: 2.3 Consensus size: 34
22828 CCTAAAGACA
22838 GTTTCTCTT-AAACACAAAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACAC-AAAAAAACCTTTGAAATC
22872 GTTTCTCTTGAAACAC-AAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAATC
*
22905 ATTTCTCTTGA
1 GTTTCTCTTGA
22916 GAAACTCTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 27 0.64
34 9 0.21
35 6 0.14
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAACCTTTGAAATC
Found at i:23295 original size:3 final size:3
Alignment explanation
Indices: 23289--23325 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
23279 TAATAATAAT
23289 TTA TTA TTA TT- TTA TT- TTA TTA TTA -TA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
23326 AATGTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.19
3 25 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:23307 original size:16 final size:16
Alignment explanation
Indices: 23288--23341 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
23278 ATAATAATAA
23288 TTTATTATTATTTTAT
1 TTTATTATTATTTTAT
*
23304 TTTATTATTATATTAT
1 TTTATTATTATTTTAT
*
23320 TATTATAATGTAATTTTAT
1 T-TTATTAT-T-ATTTTAT
23339 TTT
1 TTT
23342 TACAAGCCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 16 0.50
17 6 0.19
18 3 0.09
19 7 0.22
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTATTATTATTTTAT
Found at i:23713 original size:20 final size:20
Alignment explanation
Indices: 23688--23938 Score: 168
Period size: 20 Copynumber: 12.5 Consensus size: 20
23678 GATTTTCCAT
* *
23688 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
23708 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
* * *
23728 AATCACAACACG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
23747 CTATCGCAACGAGTATCCGTA
1 -AATCGCAACGCGAATACGTA
23768 AATCGCAACGACG-ATACGTAA
1 AATCGCAACG-CGAATACGT-A
* * *
23789 AATCGCAACGCGTATCCATA
1 AATCGCAACGCGAATACGTA
*
23809 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
23829 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
** *
23849 AATCATAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * * * *
23869 AATCACAATGTGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
23889 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
23909 AATCGCAATGTGAATATGTA
1 AATCGCAACGCGAATACGTA
23929 AATCGCAACG
1 AATCGCAACG
23939 AGATTCTGAC
Statistics
Matches: 182, Mismatches: 40, Indels: 18
0.76 0.17 0.08
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 156 0.86
21 21 0.12
22 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:23843 original size:40 final size:40
Alignment explanation
Indices: 23749--23941 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
23739 GATTCTGACT
*
23749 ATCGCAACGAGTATCCGTAAATCGCAACGACG-ATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGA-GAATACGT-AA
*
23790 ATCGCAACGCGTATCCATAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* **
23830 ATCGCAACGCGTATCTGTAAATCATAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* * * * *
23870 ATCACAATGTGTATCCGTAAATCGCAATGCGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* * * **
23910 ATCGCAATGTGAATATGTAAATCGCAACGAGA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGA
23942 TTCTGACTAT
Statistics
Matches: 131, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
40 97 0.74
41 34 0.26
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
Found at i:24830 original size:24 final size:24
Alignment explanation
Indices: 24773--24832 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
24763 TAGTCAGTAT
24773 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
24797 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
24821 TCGAATTTTGAT
1 TCGAAATTTGAT
24833 GATGTTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:26115 original size:19 final size:19
Alignment explanation
Indices: 26091--26238 Score: 90
Period size: 19 Copynumber: 8.4 Consensus size: 19
26081 GCAACGAGAG
26091 AATCGCAATACGAAATGAA
1 AATCGCAATACGAAATGAA
26110 AATCGC-A-AC-AAATGAA
1 AATCGCAATACGAAATGAA
*
26126 AATCGC-A-AC-AACTG--
1 AATCGCAATACGAAATGAA
* *
26140 AATCACAATGCGAAAATGAA
1 AATCGCAATACG-AAATGAA
* *
26160 AATCGC-A-ACG---CGAG
1 AATCGCAATACGAAATGAA
* *
26174 AATCACAATGCGAAATGAA
1 AATCGCAATACGAAATGAA
**
26193 AATCGCAACGCGAAATGAA
1 AATCGCAATACGAAATGAA
*
26212 AATCG-ATATGCGAAATGAA
1 AATCGCA-ATACGAAATGAA
26231 AATCGCAA
1 AATCGCAA
26239 CGAGTGAAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
14 12 0.12
15 2 0.02
16 23 0.23
17 2 0.02
18 8 0.08
19 48 0.48
20 6 0.06
ACGTcount: A:0.49, C:0.19, G:0.18, T:0.14
Consensus pattern (19 bp):
AATCGCAATACGAAATGAA
Found at i:26122 original size:16 final size:16
Alignment explanation
Indices: 26103--26141 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
26093 TCGCAATACG
26103 AAATGAAAATCGCAAC
1 AAATGAAAATCGCAAC
26119 AAATGAAAATCGCAAC
1 AAATGAAAATCGCAAC
*
26135 AACTGAA
1 AAATGAA
26142 TCACAATGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.56, C:0.18, G:0.13, T:0.13
Consensus pattern (16 bp):
AAATGAAAATCGCAAC
Found at i:26160 original size:34 final size:33
Alignment explanation
Indices: 26119--26201 Score: 123
Period size: 34 Copynumber: 2.5 Consensus size: 33
26109 AAATCGCAAC
*
26119 AAATGAAAATCGCAACAAC-TGAATCACAATGCG
1 AAATGAAAATCGCAAC-ACGAGAATCACAATGCG
*
26152 AAAATGAAAATCGCAACGCGAGAATCACAATGCG
1 -AAATGAAAATCGCAACACGAGAATCACAATGCG
26186 AAATGAAAATCGCAAC
1 AAATGAAAATCGCAAC
26202 GCGAAATGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
33 17 0.37
34 29 0.63
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.13
Consensus pattern (33 bp):
AAATGAAAATCGCAACACGAGAATCACAATGCG
Found at i:26457 original size:14 final size:14
Alignment explanation
Indices: 26438--26472 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
26428 TCAATTAAAT
26438 AAATCAACATTTAC
1 AAATCAACATTTAC
* *
26452 AAATCATCTTTTAC
1 AAATCAACATTTAC
26466 AAATCAA
1 AAATCAA
26473 TTAAACAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACATTTAC
Found at i:29455 original size:20 final size:20
Alignment explanation
Indices: 29430--29492 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
29420 TTTTGGTTGA
29430 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
29450 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
29469 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
29490 AAT
1 AAT
29493 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:29472 original size:40 final size:39
Alignment explanation
Indices: 29428--29539 Score: 112
Period size: 40 Copynumber: 3.0 Consensus size: 39
29418 TCTTTTGGTT
29428 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGCG
1 GAAATGAAAATCGCAACG-GAGAATGAAAATCGCAACGCG
**
29468 GAAATGACTATCGCAAC-GAG-A-G--AATCGCAACGC-
1 GAAATGAAAATCGCAACGGAGAATGAAAATCGCAACGCG
* * *
29501 GAAATGAAAATTGCAAAGCGA-AATTAAAATCGCAACGCG
1 GAAATGAAAATCGCAACG-GAGAATGAAAATCGCAACGCG
29540 ATCGCAATGC
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
33 13 0.22
34 11 0.19
35 3 0.05
36 1 0.02
37 1 0.02
38 14 0.24
40 15 0.26
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (39 bp):
GAAATGAAAATCGCAACGGAGAATGAAAATCGCAACGCG
Found at i:29521 original size:19 final size:19
Alignment explanation
Indices: 29428--29540 Score: 110
Period size: 19 Copynumber: 6.1 Consensus size: 19
29418 TCTTTTGGTT
*
29428 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
29447 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
29467 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
29485 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
29501 GAAATGAAAATTGCAAAGC
1 GAAATGAAAATCGCAACGC
*
29520 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
29539 GA
1 GA
29541 TCGCAATGCG
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 31 0.41
20 28 0.37
21 2 0.03
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:29597 original size:21 final size:20
Alignment explanation
Indices: 29578--29649 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
29568 CGATTCTCTC
29578 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
29598 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
29619 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
29639 GTTGCGATTTT
1 GTTGCGATTTT
29650 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:30225 original size:20 final size:20
Alignment explanation
Indices: 30191--30385 Score: 123
Period size: 20 Copynumber: 9.6 Consensus size: 20
30181 TTAAAAATCG
30191 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGTATTGT
* * *
30212 CATTGCGATTTACGGATACG-
1 CGTTGCGATTTACGTAT-TGT
* * *
30232 CATTACGATTTACGTATTCT
1 CGTTGCGATTTACGTATTGT
* *
30252 CGTTGAGATTTACAG-ATACG-
1 CGTTGCGATTTAC-GTAT-TGT
*
30272 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTGT
* *
30292 CGTTGCGATTTACGGATACG-
1 CGTTGCGATTTACGTAT-TGT
*
30312 CGTTGCGATTTTATGTATTGT
1 CGTTGCGA-TTTACGTATTGT
* *
30333 CGTTGCGATTTACGGATACG-
1 CGTTGCGATTTACGTAT-TGT
* *
30353 CGTTGCGATTTTACGGATACG-
1 CGTTGCGA-TTTACGTAT-TGT
30374 CGTTGCGATTTA
1 CGTTGCGATTTA
30386 TATGTTCGCG
Statistics
Matches: 139, Mismatches: 24, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
19 1 0.01
20 93 0.67
21 45 0.32
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTGT
Found at i:30262 original size:40 final size:40
Alignment explanation
Indices: 30189--30443 Score: 269
Period size: 40 Copynumber: 6.3 Consensus size: 40
30179 CTTTAAAAAT
* *
30189 CGCGTTGCGATTTTACGTATTGTCATTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
* * * *
30230 CGCATTACGATTTACGTATTCTCGTTGAGATTTACAGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
30270 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* *
30310 CGCGTTGCGATTTTATGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
* * * ** *
30351 CGCGTTGCGATTTTACGGATACGCGTTGCGATTTATATG-TT
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTA-CGGATA
** * * * ** *
30392 CGCGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
30432 CGCGTTGCGATT
1 CGCGTTGCGATT
30444 ATGGAAAATC
Statistics
Matches: 182, Mismatches: 29, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
40 104 0.57
41 77 0.42
42 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (40 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:30343 original size:81 final size:82
Alignment explanation
Indices: 30189--30443 Score: 295
Period size: 81 Copynumber: 3.1 Consensus size: 82
30179 CTTTAAAAAT
* * * * * *
30189 CGCGTTGCGATTTTACGTATTGTCATTGCGATTTACGGATACGCATTACGA-TTTACGTATTCTC
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTGTC
*
30253 GTTGAGATTTACAGATA
66 GTTGCGATTTACAGATA
30270 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTGTC
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTGTC
*
30334 GTTGCGATTTACGGATA
66 GTTGCGATTTACAGATA
* * * ** * *
30351 CGCGTTGCGATTTTACGGATACGCGTTGCGATTTATATG-TTCGCGTTGCGATTTATATGT-TCG
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTA-CGGATACGCGTTGCGATTT-TATGTATTG
* * *
30414 -CGTTGCGATTTTCATATT
64 TCGTTGCGATTTACAGATA
30432 CGCGTTGCGATT
1 CGCGTTGCGATT
30444 ATGGAAAATC
Statistics
Matches: 151, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
80 36 0.24
81 72 0.48
82 37 0.25
83 6 0.04
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (82 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTGTC
GTTGCGATTTACAGATA
Found at i:30395 original size:20 final size:20
Alignment explanation
Indices: 30270--30443 Score: 124
Period size: 20 Copynumber: 8.6 Consensus size: 20
30260 TTTACAGATA
** *
30270 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTATATGTT
* ** *
30290 CTCGTTGCGATTTA-CGGATA
1 CGCGTTGCGATTTATATG-TT
30310 CGCGTTGCGATTT-TATGTAT
1 CGCGTTGCGATTTATATGT-T
* ** *
30330 TGTCGTTGCGATTTA-CGGATA
1 CG-CGTTGCGATTTATATG-TT
* *
30351 CGCGTTGCGATTT-TACGGATA
1 CGCGTTGCGATTTATA-TG-TT
30372 CGCGTTGCGATTTATATGTT
1 CGCGTTGCGATTTATATGTT
30392 CGCGTTGCGATTTATATGTT
1 CGCGTTGCGATTTATATGTT
*
30412 CGCGTTGCGATTT-TCATATT
1 CGCGTTGCGATTTAT-ATGTT
30432 CGCGTTGCGATT
1 CGCGTTGCGATT
30444 ATGGAAAATC
Statistics
Matches: 126, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
19 2 0.02
20 89 0.71
21 32 0.25
22 3 0.02
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40
Consensus pattern (20 bp):
CGCGTTGCGATTTATATGTT
Found at i:30416 original size:61 final size:60
Alignment explanation
Indices: 30270--30443 Score: 192
Period size: 61 Copynumber: 2.9 Consensus size: 60
30260 TTTACAGATA
* * *
30270 CGCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGGATACGCGTTGCGATTTTATGTAT
1 CGCGTTGCGATTTA-ATGTTCGCGTTGCGATTTTACGGATACGCGTTGCGATTTTATGTAT
* ** *
30330 TGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACGCGTTGCGATTTATATGT-T
1 CG-CGTTGCGATTTAATG-TTCGCGTTGCGATTTTACGGATACGCGTTGCGATTT-TATGTAT
** *
30392 CGCGTTGCGATTTATATGTTCGCGTTGCGATTTT-CATATTCGCGTTGCGATT
1 CGCGTTGCGATTTA-ATGTTCGCGTTGCGATTTTACGGATACGCGTTGCGATT
30444 ATGGAAAATC
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
60 16 0.17
61 49 0.51
62 26 0.27
63 5 0.05
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40
Consensus pattern (60 bp):
CGCGTTGCGATTTAATGTTCGCGTTGCGATTTTACGGATACGCGTTGCGATTTTATGTAT
Found at i:30496 original size:21 final size:21
Alignment explanation
Indices: 30478--30529 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
30468 TACTATCGCA
30478 TTGCGATTCTTCATAATCGTG
1 TTGCGATTCTTCATAATCGTG
*
30499 TTGCGATTCTTCATAATTGTG
1 TTGCGATTCTTCATAATCGTG
30520 TTGCGATTCT
1 TTGCGATTCT
30530 GGGAACTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.46
Consensus pattern (21 bp):
TTGCGATTCTTCATAATCGTG
Found at i:37501 original size:14 final size:15
Alignment explanation
Indices: 37482--37511 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37472 AAGATAAGAC
37482 AAATTT-TTGGGGCA
1 AAATTTGTTGGGGCA
37496 AAATTTGTTGGGGCA
1 AAATTTGTTGGGGCA
37511 A
1 A
37512 GTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (15 bp):
AAATTTGTTGGGGCA
Found at i:38158 original size:43 final size:43
Alignment explanation
Indices: 38111--38435 Score: 173
Period size: 43 Copynumber: 7.5 Consensus size: 43
38101 CCAGATCTCT
* * *
38111 TCATCATGTAGGAGCCGTGTCAACCTTAGATAACCAGCCATCC
1 TCATCACGTAGGAACCGTGTCAACCCTAGATAACCAGCCATCC
* * ** ** *
38154 TCATCACGTAAGAACCGTGTTATCATCTATAATGATGGCCTGCCATCC
1 TCATCACGTAGGAACCGTG---TCAACCCT-A-GATAACCAGCCATCC
* * * *
38202 TCATCACGTAGGAACCATGTCATCCCTCG---ACCAGATC-TCC
1 TCATCACGTAGGAACCGTGTCAACCCTAGATAACCAG-CCATCC
* * *
38242 TCATCACGTAGGAGCCGTGTCAACCCTAGATAACCAACCGTCC
1 TCATCACGTAGGAACCGTGTCAACCCTAGATAACCAGCCATCC
* * ** * *
38285 TCATCACGTAGGAATCGTGTTAACATCCATA-ATGATGGCATGTCGTCC
1 TCATCACGTAGGAACCGTGTCAAC--CC-TAGAT-A-ACCA-GCCATCC
* * *
38333 TCATCACGTAGGAACCGTGTCATCCCTCG---ACCAGATC-TCC
1 TCATCACGTAGGAACCGTGTCAACCCTAGATAACCAG-CCATCC
* * * * * * *
38373 TCTTCACGTAGGAGCTGTGTCAACCTTACATAACCAGCCGTCT
1 TCATCACGTAGGAACCGTGTCAACCCTAGATAACCAGCCATCC
38416 TCATCACGTAGGAACCGTGT
1 TCATCACGTAGGAACCGTGT
38436 TATCATCCAT
Statistics
Matches: 212, Mismatches: 48, Indels: 44
0.70 0.16 0.14
Matches are distributed among these distances:
40 57 0.27
41 5 0.02
42 2 0.01
43 69 0.33
45 11 0.05
46 10 0.05
47 3 0.01
48 55 0.26
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (43 bp):
TCATCACGTAGGAACCGTGTCAACCCTAGATAACCAGCCATCC
Found at i:38254 original size:40 final size:41
Alignment explanation
Indices: 38199--38576 Score: 160
Period size: 40 Copynumber: 8.7 Consensus size: 41
38189 TGGCCTGCCA
*
38199 TCCTCATCACGTAGGAACCATGTCATCCCTCGACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCG
* * * *
38239 TCCTCATCACGTAGGAGCCGTGTCAACCCTAGATAACCA-ACCG
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCG---ACCAGATCG
* * * *
38282 TCCTCATCACGTAGGAATCGTGTTAACATCCATAATGATGGCATG-TCG
1 TCCTCATCACGTAGGAACCGTG-T--CATCCCT--CGA--CCA-GATCG
38330 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCG
* * * * * * *
38370 TCCTCTTCACGTAGGAGCTGTGTCAACCTTACATAACCAG-CCG
1 TCCTCATCACGTAGGAACCGTGTCATCCCT-C--GACCAGATCG
* * ** *
38413 TCTTCATCACGTAGGAACCGTGTTATCATCCAT-GATAATGGTATGTTG
1 TCCTCATCACGTAGGAACCGTG---TCATCCCTCGACCA--G-A--TCG
* * * *
38461 TCCTCATCACGTAGGAACCGTGTTATCATCCCTAACAATGGCCTG-CCA
1 TCCTCATCACGTAGGAACCGTG---TCATCCCT--C---GACCAGATCG
* * *
38509 TCCTCATCATGTAGGAATCGTGTCATCCCTCGACTAGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCG
**
38549 TCCTCATCACGTAGGAGTCGTGTCATCC
1 TCCTCATCACGTAGGAACCGTGTCATCC
38577 TTTATATAAC
Statistics
Matches: 253, Mismatches: 51, Indels: 68
0.68 0.14 0.18
Matches are distributed among these distances:
40 83 0.33
41 6 0.02
42 5 0.02
43 50 0.20
44 2 0.01
45 15 0.06
46 11 0.04
47 3 0.01
48 76 0.30
52 1 0.00
54 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (41 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCG
Found at i:38352 original size:48 final size:47
Alignment explanation
Indices: 38280--38531 Score: 152
Period size: 48 Copynumber: 5.5 Consensus size: 47
38270 GATAACCAAC
* *
38280 CGTCCTCATCACGTAGGAATCGTGTTAACATCCATAATGATGGCATGT
1 CGTCCTCATCACGTAGGAACCGTGTT-ACATCCATAATAATGGCATGT
* ** *
38328 CGTCCTCATCACGTAGGAACCGTG-T-CATCCCT--CGA--CCA-GAT
1 CGTCCTCATCACGTAGGAACCGTGTTACATCCATAATAATGGCATG-T
* * * * * * *
38369 C-TCCTCTTCACGTAGGAGCTGTG-T-CAACCTTACATAA--CCA-GC
1 CGTCCTCATCACGTAGGAACCGTGTTACATCCATA-ATAATGGCATGT
* * *
38411 CGTCTTCATCACGTAGGAACCGTGTTATCATCCATGATAATGGTATGT
1 CGTCCTCATCACGTAGGAACCGTGTTA-CATCCATAATAATGGCATGT
* * * * *
38459 TGTCCTCATCACGTAGGAACCGTGTTATCATCCCTAACAATGGCCTGC
1 CGTCCTCATCACGTAGGAACCGTGTTA-CATCCATAATAATGGCATGT
* * *
38507 CATCCTCATCATGTAGGAATCGTGT
1 CGTCCTCATCACGTAGGAACCGTGT
38532 CATCCCTCGA
Statistics
Matches: 159, Mismatches: 34, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
40 26 0.16
41 4 0.03
42 1 0.01
43 25 0.16
44 1 0.01
45 10 0.06
46 5 0.03
47 2 0.01
48 85 0.53
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (47 bp):
CGTCCTCATCACGTAGGAACCGTGTTACATCCATAATAATGGCATGT
Found at i:38466 original size:179 final size:180
Alignment explanation
Indices: 38281--38623 Score: 474
Period size: 179 Copynumber: 1.9 Consensus size: 180
38271 ATAACCAACC
* ** * *
38281 GTCCTCATCACGTAGGAATCGTGTTAACATCCATAATGATGGCATGTCGTCCTCATCACGTAGGA
1 GTCCTCATCACGTAGGAACCGTGTTAACATCCATAACAATGGCATGCCATCCTCATCACGTAGGA
*
38346 ACCGTGTCATCCCTCGACCAGATCTCCTCTTCACGTAGGAG-CTGTGTCAACC-TTACATAACCA
66 ACCGTGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAGTC-GTGTCAACCTTTACATAACCA
* *
38409 GCCGTCTTCATCACGTAGGAACCGTGTTATCATCCATGATAATGGTATGTT
130 ACCGTCCTCATCACGTAGGAACCGTGTTATCATCCATGATAATGGTATGTT
* * * *
38460 GTCCTCATCACGTAGGAACCGTGTTATCATCCCTAACAATGGCCTGCCATCCTCATCATGTAGGA
1 GTCCTCATCACGTAGGAACCGTGTTAACATCCATAACAATGGCATGCCATCCTCATCACGTAGGA
* * * * *
38525 ATCGTGTCATCCCTCGACTAGATCTCCTCATCACGTAGGAGTCGTGTCATCCTTTATATAACTAA
66 ACCGTGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAGTCGTGTCAACCTTTACATAACCAA
* * * *
38590 TCGTCCTCGTCATGTAGGAATCGTGTTATCATCC
131 CCGTCCTCATCACGTAGGAACCGTGTTATCATCC
38624 TTAGACGATC
Statistics
Matches: 141, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
179 102 0.72
180 39 0.28
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (180 bp):
GTCCTCATCACGTAGGAACCGTGTTAACATCCATAACAATGGCATGCCATCCTCATCACGTAGGA
ACCGTGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAGTCGTGTCAACCTTTACATAACCAA
CCGTCCTCATCACGTAGGAACCGTGTTATCATCCATGATAATGGTATGTT
Found at i:38480 original size:131 final size:131
Alignment explanation
Indices: 38088--38483 Score: 587
Period size: 131 Copynumber: 3.0 Consensus size: 131
38078 CACAACAATT
* * *
38088 TGTCATCCAC-CGACCAGATCTCTTCATCATGTAGGAGCCGTGTCAACCTTAGATAACCAGCCAT
1 TGTCATCC-CTCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGT
* * * * *
38152 CCTCATCACGTAAGAACCGTGTTATCATCTATAATGATGGCCTGCCATCCTCATCACGTAGGAAC
65 CCTCATCACGTAGGAACCGTGTTATCATCCATAATGATGGCATGTCGTCCTCATCACGTAGGAAC
*
38217 CA
130 CG
* *
38219 TGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCTAGATAACCAACCGTC
1 TGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTC
* *
38284 CTCATCACGTAGGAATCGTGTTAACATCCATAATGATGGCATGTCGTCCTCATCACGTAGGAACC
66 CTCATCACGTAGGAACCGTGTTATCATCCATAATGATGGCATGTCGTCCTCATCACGTAGGAACC
38349 G
131 G
* * *
38350 TGTCATCCCTCGACCAGATCTCCTCTTCACGTAGGAGCTGTGTCAACCTTACATAACCAGCCGTC
1 TGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTC
* * * * *
38415 TTCATCACGTAGGAACCGTGTTATCATCCATGATAATGGTATGTTGTCCTCATCACGTAGGAACC
66 CTCATCACGTAGGAACCGTGTTATCATCCATAATGATGGCATGTCGTCCTCATCACGTAGGAACC
38480 G
131 G
38481 TGT
1 TGT
38484 TATCATCCCT
Statistics
Matches: 239, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
130 1 0.00
131 238 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (131 bp):
TGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTC
CTCATCACGTAGGAACCGTGTTATCATCCATAATGATGGCATGTCGTCCTCATCACGTAGGAACC
G
Found at i:38819 original size:3 final size:3
Alignment explanation
Indices: 38811--38848 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
38801 GTTTAAAAAA
38811 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
38849 CCTACCCTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40175 original size:13 final size:12
Alignment explanation
Indices: 40150--40174 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40140 TTAAAGAACG
40150 ATTGTTTTTAAA
1 ATTGTTTTTAAA
40162 ATTGTTTTTAAA
1 ATTGTTTTTAAA
40174 A
1 A
40175 AGACGTTTTT
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
ATTGTTTTTAAA
Found at i:41879 original size:21 final size:21
Alignment explanation
Indices: 41855--41900 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
41845 AACAGTTCGC
41855 GGAGGTGGAAAACAACCTGAG
1 GGAGGTGGAAAACAACCTGAG
41876 GGAGGTGGAAAACAACCTGAG
1 GGAGGTGGAAAACAACCTGAG
41897 GGAG
1 GGAG
41901 CTGCTGCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.41, T:0.09
Consensus pattern (21 bp):
GGAGGTGGAAAACAACCTGAG
Found at i:42855 original size:14 final size:14
Alignment explanation
Indices: 42836--42871 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
42826 CCTAATTAAT
42836 TTTATGTTAGTTCG
1 TTTATGTTAGTTCG
*
42850 TTTATGTTCGTTCG
1 TTTATGTTAGTTCG
*
42864 TTTGTGTT
1 TTTATGTT
42872 TGTTTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.08, C:0.08, G:0.22, T:0.61
Consensus pattern (14 bp):
TTTATGTTAGTTCG
Found at i:44085 original size:208 final size:208
Alignment explanation
Indices: 43722--44147 Score: 834
Period size: 208 Copynumber: 2.0 Consensus size: 208
43712 CACGAGCACA
43722 TGCGTTTTTGAAAATTTTTCTCTCCACCGTCATCCACCCATTGTCCACCGACGTCGTCCGCCACC
1 TGCG-TTTTGAAAATTTTTCTCTCCACCGTCATCCACCCATTGTCCACCGACGTCGTCCGCCACC
43787 CGCCGCCGCCGTCCGCCGCCACACTCTGACCACCGTTTGGACGTCGTTTTTTAGTGGGAAGATCG
65 CGCCGCCGCCGTCCGCCGCCACACTCTGACCACCGTTTGGACGTCGTTTTTTAGTGGGAAGATCG
43852 CCAGATCAAGGTGTTTCCTAATCTGGGATTGGTTTTGCGATTAAGACTCTGATTCGACGCAGATC
130 CCAGATCAAGGTGTTTCCTAATCTGGGATTGGTTTTGCGATTAAGACTCTGATTCGACGCAGATC
43917 TTCAAGCTGCTCAC
195 TTCAAGCTGCTCAC
43931 TGCGTTTTGAAAATTTTTCTCTCCACCGTCATCCACCCATTGTCCACCGACGTCGTCCGCCACCC
1 TGCGTTTTGAAAATTTTTCTCTCCACCGTCATCCACCCATTGTCCACCGACGTCGTCCGCCACCC
43996 GCCGCCGCCGTCCGCCGCCACACTCTGACCACCGTTTGGACGTCGTTTTTTAGTGGGAAGATCGC
66 GCCGCCGCCGTCCGCCGCCACACTCTGACCACCGTTTGGACGTCGTTTTTTAGTGGGAAGATCGC
44061 CAGATCAAGGTGTTTCCTAATCTGGGATTGGTTTTGCGATTAAGACTCTGATTCGACGCAGATCT
131 CAGATCAAGGTGTTTCCTAATCTGGGATTGGTTTTGCGATTAAGACTCTGATTCGACGCAGATCT
44126 TCAAGCTGCTCAC
196 TCAAGCTGCTCAC
44139 TGCCGTTTT
1 TG-CGTTTT
44148 TGCCTCCACC
Statistics
Matches: 216, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
208 206 0.95
209 10 0.05
ACGTcount: A:0.18, C:0.31, G:0.22, T:0.29
Consensus pattern (208 bp):
TGCGTTTTGAAAATTTTTCTCTCCACCGTCATCCACCCATTGTCCACCGACGTCGTCCGCCACCC
GCCGCCGCCGTCCGCCGCCACACTCTGACCACCGTTTGGACGTCGTTTTTTAGTGGGAAGATCGC
CAGATCAAGGTGTTTCCTAATCTGGGATTGGTTTTGCGATTAAGACTCTGATTCGACGCAGATCT
TCAAGCTGCTCAC
Found at i:50634 original size:69 final size:70
Alignment explanation
Indices: 50538--50713 Score: 169
Period size: 69 Copynumber: 2.5 Consensus size: 70
50528 AAACACTATG
* * * * * *
50538 TTCGGTTCAAACAGACAATAGTCGGACAAGGAAGCCGAAGA-CACCACAAACTGA-AAACAAAAC
1 TTCGGTCCAAACAAACAACAGTCGGACAAGGAAACCAAAGACCACCACAAAATGATAAACAAAAC
50601 CGGTA
66 CGGTA
*
50606 TTCGGTCCAGAACAAACAACAGTTGGACAAGGAAACCAAAGACGCACCACAAAATGATAAACGAA
1 TTCGGTCCA-AACAAACAACAGTCGGACAAGGAAACCAAAGAC-CACCACAAAATGATAAAC-AA
* * *
50671 ACCCGATT
63 AACCGGTA
* * * * *
50679 TTCGGTTCAAACAGACGACGGTC-GACATGGAAACC
1 TTCGGTCCAAACAAACAACAGTCGGACAAGGAAACC
50714 GATGAGTTGC
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
68 8 0.09
69 27 0.31
71 23 0.26
72 14 0.16
73 15 0.17
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.13
Consensus pattern (70 bp):
TTCGGTCCAAACAAACAACAGTCGGACAAGGAAACCAAAGACCACCACAAAATGATAAACAAAAC
CGGTA
Found at i:60489 original size:22 final size:22
Alignment explanation
Indices: 60420--60505 Score: 91
Period size: 22 Copynumber: 3.9 Consensus size: 22
60410 TATTTTCTCT
*
60420 TATCGGTGCTAAGGCACTTTAG
1 TATCAGTGCTAAGGCACTTTAG
* * ** *
60442 TATCAGTACAAATCACACTTTCG
1 TATCAGTGCTAA-GGCACTTTAG
*
60465 TATCAGTGCTGAGGCACTTTAG
1 TATCAGTGCTAAGGCACTTTAG
*
60487 TATTAGTGCTAAGGCACTT
1 TATCAGTGCTAAGGCACTT
60506 CTGATATGCA
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
22 33 0.67
23 16 0.33
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (22 bp):
TATCAGTGCTAAGGCACTTTAG
Found at i:61047 original size:3 final size:3
Alignment explanation
Indices: 61034--61087 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
61024 TCTACAAAAA
*
61034 ATT ATTT ATT ATT ATT ACT -TT ATT ATT ATT A-T ATTT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
*
61079 -TT TTT ATT A
1 ATT ATT ATT A
61088 AATATTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
2 5 0.12
3 33 0.77
4 5 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:61086 original size:14 final size:14
Alignment explanation
Indices: 61035--61087 Score: 72
Period size: 14 Copynumber: 3.7 Consensus size: 14
61025 CTACAAAAAA
61035 TTATTTATTATTA-
1 TTATTTATTATTAT
61048 TTACTTTATTATTAT
1 TTA-TTTATTATTAT
61063 TATATTTATTATTAT
1 T-TATTTATTATTAT
*
61078 TTTTTTATTA
1 TTATTTATTA
61088 AATATTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
13 3 0.08
14 18 0.50
15 13 0.36
16 2 0.06
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTTATTATTAT
Found at i:61096 original size:26 final size:26
Alignment explanation
Indices: 61042--61099 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
61032 AAATTATTTA
*
61042 TTATTATTACTTTATTATTATTATAT
1 TTATTATTACTTTATTATTAATATAT
* *
61068 TTATTATTATTTTTTTATTAA-ATATT
1 TTATTATTACTTTATTATTAATATA-T
61094 TTATTA
1 TTATTA
61100 CAATTTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TTATTATTACTTTATTATTAATATAT
Found at i:61097 original size:23 final size:27
Alignment explanation
Indices: 61040--61100 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 27
61030 AAAAATTATT
*
61040 TATTATTATTACTTTATTATTATTATA
1 TATTATTATTACTTTATTATTATTAAA
61067 T-TTATTATTA-TTT-TT-TTATTAAA
1 TATTATTATTACTTTATTATTATTAAA
61090 TATT-TTATTAC
1 TATTATTATTAC
61101 AATTTTGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 14 0.45
24 4 0.13
25 3 0.10
26 9 0.29
27 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (27 bp):
TATTATTATTACTTTATTATTATTAAA
Found at i:62949 original size:32 final size:32
Alignment explanation
Indices: 62895--62986 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
62885 AGTCGAGGGT
*
62895 TTACATATGTTCTACGGAACATATGGACATAA
1 TTACATATGTCCTACGGAACATATGGACATAA
* * *
62927 TTACCTATGTCCTTCGGGACATATGGACAGT-A
1 TTACATATGTCCTACGGAACATATGGACA-TAA
* *
62959 -TATC-TATGTTCTAAGGAACATATGGACA
1 TTA-CATATGTCCTACGGAACATATGGACA
62987 GTTTACCTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
31 22 0.44
32 27 0.54
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (32 bp):
TTACATATGTCCTACGGAACATATGGACATAA
Found at i:62979 original size:63 final size:62
Alignment explanation
Indices: 62900--63019 Score: 170
Period size: 62 Copynumber: 1.9 Consensus size: 62
62890 AGGGTTTACA
* * *
62900 TATGTTCTACGGAACATATGGACA-TAATTACCTATGTCCTTCGGGACATATGGACAGTATATC
1 TATGTTCTAAGGAACATATGGACAGT--TTACCTAGGTCCTTCAGGACATATGGACAGTATATC
* *
62963 TATGTTCTAAGGAACATATGGACAGTTTACCTAGGTTCTTCAGGACCTATGGACAGT
1 TATGTTCTAAGGAACATATGGACAGTTTACCTAGGTCCTTCAGGACATATGGACAGT
63020 TGTCGAGGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
62 27 0.53
63 23 0.45
64 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (62 bp):
TATGTTCTAAGGAACATATGGACAGTTTACCTAGGTCCTTCAGGACATATGGACAGTATATC
Found at i:63020 original size:31 final size:31
Alignment explanation
Indices: 62893--63020 Score: 118
Period size: 31 Copynumber: 4.1 Consensus size: 31
62883 AGAGTCGAGG
* *
62893 GTTTACATATGTTCTAC-GGAACATATGGACA
1 GTTTACCTATGTTCTTCAGG-ACATATGGACA
* *
62924 -TAATTACCTATGTCCTTCGGGACATATGGACA
1 GT--TTACCTATGTTCTTCAGGACATATGGACA
* * *
62956 GTATATCTATGTTC-TAAGGAACATATGGACA
1 GTTTACCTATGTTCTTCAGG-ACATATGGACA
* *
62987 GTTTACCTAGGTTCTTCAGGACCTATGGACA
1 GTTTACCTATGTTCTTCAGGACATATGGACA
63018 GTT
1 GTT
63021 GTCGAGGTTC
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
30 4 0.05
31 44 0.56
32 27 0.35
33 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCAGGACATATGGACA
Found at i:65357 original size:29 final size:28
Alignment explanation
Indices: 65318--65533 Score: 125
Period size: 29 Copynumber: 7.4 Consensus size: 28
65308 TTAATACCAT
*
65318 TTTAGACCCTTAATTTTCTATTTTTACTA
1 TTTAG-CCCTTAAGTTTCTATTTTTACTA
* *
65347 TTGTAGCCCTTTAAGTTTCT-TTTTTGCCA
1 TT-TAGCCC-TTAAGTTTCTATTTTTACTA
* * *
65376 TTTTAGTCCTTTAAATTT-TAGTTTTTACTG
1 -TTTAG-CCCTTAAGTTTCTA-TTTTTACTA
*
65406 TTTAGCCCTTTAAGTTTCTATTTTT-GTAA
1 TTTAGCCC-TTAAGTTTCTATTTTTACT-A
* * * * *
65435 TTTTAGTCCTTTTACTTTCTACTTTTATTA
1 -TTTAG-CCCTTAAGTTTCTATTTTTACTA
* * *
65465 TTTAGTCCTTTAAGTTTCTATTTTTTCTG
1 TTTAG-CCCTTAAGTTTCTATTTTTACTA
* *
65494 TTTAGCCTTTTAAATTTCTA-TTTTAGCTA
1 TTTAGCC-CTTAAGTTTCTATTTTTA-CTA
65523 TTTTAGCCCTT
1 -TTTAGCCCTT
65534 CAAGCTGTAG
Statistics
Matches: 145, Mismatches: 27, Indels: 30
0.72 0.13 0.15
Matches are distributed among these distances:
28 10 0.07
29 82 0.57
30 50 0.34
31 3 0.02
ACGTcount: A:0.19, C:0.16, G:0.08, T:0.57
Consensus pattern (28 bp):
TTTAGCCCTTAAGTTTCTATTTTTACTA
Found at i:65377 original size:59 final size:59
Alignment explanation
Indices: 65314--65533 Score: 236
Period size: 59 Copynumber: 3.7 Consensus size: 59
65304 TCTGTTAATA
* * *
65314 CCATTTTAGACCCTTAATTTTCTATTTTTACTATTGTAGCCCTTTAAGTTTCT-TTTTTG
1 CCATTTTAGTCCTTTAAATTTCTATTTTTACTATT-TAGCCCTTTAAGTTTCTATTTTTG
*
65373 CCATTTTAGTCCTTTAAATTT-TAGTTTTTACTGTTTAGCCCTTTAAGTTTCTATTTTTG
1 CCATTTTAGTCCTTTAAATTTCTA-TTTTTACTATTTAGCCCTTTAAGTTTCTATTTTTG
** * * * * *
65432 TAATTTTAGTCCTTTTACTTTCTACTTTTATTATTTAGTCCTTTAAGTTTCTATTTTT-
1 CCATTTTAGTCCTTTAAATTTCTATTTTTACTATTTAGCCCTTTAAGTTTCTATTTTTG
*
65490 TC-TGTTTAG-CCTTTTAAATTTCTA-TTTTAGCTATTTTAGCCCTT
1 CCAT-TTTAGTCC-TTTAAATTTCTATTTTTA-CTA-TTTAGCCCTT
65534 CAAGCTGTAG
Statistics
Matches: 137, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
57 8 0.06
58 37 0.27
59 90 0.66
60 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.08, T:0.57
Consensus pattern (59 bp):
CCATTTTAGTCCTTTAAATTTCTATTTTTACTATTTAGCCCTTTAAGTTTCTATTTTTG
Found at i:67292 original size:51 final size:51
Alignment explanation
Indices: 67196--67292 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
67186 AATATTGCAT
* * * *
67196 TTAAACTCTAACGAACCTGATTTATTAGAGATTGATGAGCTAATAAAACGA
1 TTAAACTCTAACAAACCTAATTTATCAGAGATTGATGAGCAAATAAAACGA
* * *
67247 TTAAACTCTAATAAACCTAATTTATCATAGATTGATGAGGAAATAA
1 TTAAACTCTAACAAACCTAATTTATCAGAGATTGATGAGCAAATAA
67293 TGGATGGGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (51 bp):
TTAAACTCTAACAAACCTAATTTATCAGAGATTGATGAGCAAATAAAACGA
Found at i:70362 original size:22 final size:22
Alignment explanation
Indices: 70337--70427 Score: 107
Period size: 22 Copynumber: 4.3 Consensus size: 22
70327 CGCAAATTCG
70337 CGTTGCGATAGTCTACAATTGT
1 CGTTGCGATAGTCTACAATTGT
* * *
70359 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAATTGT
*
70378 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATTGT
* *
70400 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATTGT
70422 CGTTGC
1 CGTTGC
70428 AATTTTCCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 10 0.18
20 6 0.11
21 5 0.09
22 36 0.63
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAATTGT
Found at i:70556 original size:6 final size:6
Alignment explanation
Indices: 70545--70586 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
70535 CATGTATTAT
70545 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC C-CGAC C
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC C
70587 CGAGACGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:71229 original size:22 final size:22
Alignment explanation
Indices: 71203--71334 Score: 107
Period size: 22 Copynumber: 6.3 Consensus size: 22
71193 TTGGAAAATT
*
71203 GCAACGACAACTGTAAACTTTC
1 GCAACGACAACTGTAAACTATC
* *
71225 GCAACAACAACTGTAGACTATC
1 GCAACGACAACTGTAAACTATC
* *
71247 GCAACG-CGAAATGGAAA--ATC
1 GCAACGAC-AACTGTAAACTATC
*
71267 GCAACGACAACTGTAGACTATC
1 GCAACGACAACTGTAAACTATC
** *
71289 GCAACGA-ATTTGGAAA--ATC
1 GCAACGACAACTGTAAACTATC
* *
71308 GCAACGAC-ATTGTAGACTATC
1 GCAACGACAACTGTAAACTATC
71329 GCAACG
1 GCAACG
71335 CGAAATGGAA
Statistics
Matches: 86, Mismatches: 17, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
19 15 0.17
20 15 0.17
21 16 0.19
22 40 0.47
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (22 bp):
GCAACGACAACTGTAAACTATC
Found at i:71269 original size:20 final size:20
Alignment explanation
Indices: 71244--71398 Score: 95
Period size: 20 Copynumber: 7.6 Consensus size: 20
71234 ACTGTAGACT
71244 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
71264 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAAATG--GAAA
*
71286 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-ATGGAAA
* **
71305 ATCGCAA--CGACATTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
71326 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
71346 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
71367 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
71387 ATCGCAACGCGA
1 ATCGCAACGCGA
71399 TTTTCAACTA
Statistics
Matches: 103, Mismatches: 21, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
19 16 0.16
20 45 0.44
21 27 0.26
22 12 0.12
23 3 0.03
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:71396 original size:41 final size:42
Alignment explanation
Indices: 71236--71423 Score: 255
Period size: 41 Copynumber: 4.6 Consensus size: 42
71226 CAACAACAAC
* *
71236 TGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACAAC
1 TGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACGAT
*
71278 TGTAGACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-AT
1 TGTAGACTATCGCAACGCGAA-ATGGAAAATCGCAACGACGAT
71318 TGTAGACTATCGCAACGCGAAATGGAAAATCGCAACG-CGAT
1 TGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACGAT
*
71359 TTTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACG-CGAT
1 TGT-AGACTATCGCAACGCGAAATGGAAAATCGCAACGACGAT
*
71400 TTTCA-ACTATCGCAACGCGAAATG
1 TGT-AGACTATCGCAACGCGAAATG
71424 CAACACGAAT
Statistics
Matches: 137, Mismatches: 4, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
40 21 0.15
41 96 0.70
42 20 0.15
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (42 bp):
TGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACGAT
Found at i:71427 original size:21 final size:21
Alignment explanation
Indices: 71323--71427 Score: 106
Period size: 21 Copynumber: 5.1 Consensus size: 21
71313 GACATTGTAG
*
71323 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
71344 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
71364 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
71385 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
71405 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
71426 AC
1 AC
71428 ACGAATTTGC
Statistics
Matches: 63, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 30 0.48
21 33 0.52
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:71976 original size:22 final size:22
Alignment explanation
Indices: 71936--71981 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
71926 TGCATAACTT
*
71936 ATTATAAAATATAATAATTATA
1 ATTATAAAATAAAATAATTATA
*
71958 ATTATAAAA-AAAATCAATTTTA
1 ATTATAAAATAAAAT-AATTATA
71980 AT
1 AT
71982 GATTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTATAAAATAAAATAATTATA
Found at i:73764 original size:20 final size:20
Alignment explanation
Indices: 73739--73786 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
73729 AAAAATAGAT
73739 TTTCAAATTATGTAATTAAG
1 TTTCAAATTATGTAATTAAG
73759 TTTCAAATTATGTAATTAAG
1 TTTCAAATTATGTAATTAAG
*
73779 TTACAAAT
1 TTTCAAAT
73787 AATAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (20 bp):
TTTCAAATTATGTAATTAAG
Found at i:76864 original size:26 final size:26
Alignment explanation
Indices: 76815--76867 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
76805 TTTGTTTGTC
*
76815 TCTTAATAGAATCATTTAACGTTGAA
1 TCTTAATAGAATCATTCAACGTTGAA
**
76841 TCTTAATAGAATCATTCAGTGTTGAA
1 TCTTAATAGAATCATTCAACGTTGAA
76867 T
1 T
76868 GTTGAACCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (26 bp):
TCTTAATAGAATCATTCAACGTTGAA
Found at i:78173 original size:16 final size:16
Alignment explanation
Indices: 78152--78190 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
78142 ATTATTTTAT
78152 TATGTTTCTTAATAGA
1 TATGTTTCTTAATAGA
*
78168 TATGTTTCTTAATGGA
1 TATGTTTCTTAATAGA
*
78184 AATGTTT
1 TATGTTT
78191 TTTTTATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.51
Consensus pattern (16 bp):
TATGTTTCTTAATAGA
Found at i:82963 original size:14 final size:16
Alignment explanation
Indices: 82932--82963 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
82922 TAGAACATAG
82932 TAATAAACAATGATAT
1 TAATAAACAATGATAT
82948 TAATAAA-AAT-ATAT
1 TAATAAACAATGATAT
82962 TA
1 TA
82964 TTTTGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
TAATAAACAATGATAT
Found at i:87262 original size:36 final size:36
Alignment explanation
Indices: 87193--87265 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
87183 ATCATGTTAC
* * * *
87193 AACCAAACAGAAGTAGCAAATAGTTGCAATGGCCTT
1 AACCAAACAAAAATAGCAAAGAGTTACAATGGCCTT
* *
87229 AACCAAACAAAAATAGCAAAGAGTTATAGTGGCCTT
1 AACCAAACAAAAATAGCAAAGAGTTACAATGGCCTT
87265 A
1 A
87266 CATTAGGGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (36 bp):
AACCAAACAAAAATAGCAAAGAGTTACAATGGCCTT
Found at i:88746 original size:30 final size:30
Alignment explanation
Indices: 88697--88757 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
88687 CTAAATTCAG
*
88697 AAAACAAATAAACGTGACAAT-ACCCTAGCT
1 AAAACAAATAAACGAGACAATAACCC-AGCT
88727 AAAACAAAT-AACTGAGACAATAACCCAGCT
1 AAAACAAATAAAC-GAGACAATAACCCAGCT
88757 A
1 A
88758 TAACTCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 3 0.11
30 21 0.75
31 4 0.14
ACGTcount: A:0.52, C:0.23, G:0.10, T:0.15
Consensus pattern (30 bp):
AAAACAAATAAACGAGACAATAACCCAGCT
Found at i:92918 original size:21 final size:21
Alignment explanation
Indices: 92894--92950 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
92884 GTCTCCCATG
92894 CTTTTCATGCCGCTTCTCATC
1 CTTTTCATGCCGCTTCTCATC
* * *
92915 CTTTTCATGTCGCTTCTCGTG
1 CTTTTCATGCCGCTTCTCATC
* *
92936 CTTTTCGTGCTGCTT
1 CTTTTCATGCCGCTT
92951 GTGCTTTTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.05, C:0.32, G:0.16, T:0.47
Consensus pattern (21 bp):
CTTTTCATGCCGCTTCTCATC
Found at i:92938 original size:9 final size:9
Alignment explanation
Indices: 92926--93001 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
92916 TTTTCATGTC
92926 GCTTCTCGT
1 GCTTCTCGT
*
92935 GCTTTTCGT
1 GCTTCTCGT
* *
92944 GCTGCTTGT
1 GCTTCTCGT
*
92953 GCTT-TTGCT
1 GCTTCTCG-T
92962 GC-TCTCGT
1 GCTTCTCGT
92970 GCTT-TCGTGCT
1 GCTTCTC--G-T
92981 GCTTCTCGT
1 GCTTCTCGT
92990 GCTT-TCGT
1 GCTTCTCGT
92998 GCTT
1 GCTT
93002 TTCCCTTGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
8 17 0.31
9 28 0.52
10 2 0.04
11 5 0.09
12 2 0.04
ACGTcount: A:0.00, C:0.28, G:0.25, T:0.47
Consensus pattern (9 bp):
GCTTCTCGT
Found at i:92956 original size:18 final size:18
Alignment explanation
Indices: 92933--92984 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
92923 GTCGCTTCTC
92933 GTGCTTTTCGTGCTGCTT
1 GTGCTTTTCGTGCTGCTT
*
92951 GTGCTTTT-GCTGCT-CTC
1 GTGCTTTTCG-TGCTGCTT
92968 GTGC-TTTCGTGCTGCTT
1 GTGCTTTTCGTGCTGCTT
92985 CTCGTGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 7 0.24
17 10 0.34
18 12 0.41
ACGTcount: A:0.00, C:0.25, G:0.27, T:0.48
Consensus pattern (18 bp):
GTGCTTTTCGTGCTGCTT
Found at i:92989 original size:20 final size:19
Alignment explanation
Indices: 92929--93000 Score: 98
Period size: 20 Copynumber: 3.9 Consensus size: 19
92919 TCATGTCGCT
92929 TCTCGTGCTTTTCGTGCTGC
1 TCTCGTGC-TTTCGTGCTGC
92949 T-T-GTGCTTT--TGCTGC
1 TCTCGTGCTTTCGTGCTGC
92964 TCTCGTGCTTTCGTGCTGC
1 TCTCGTGCTTTCGTGCTGC
92983 TTCTCGTGCTTTCGTGCT
1 -TCTCGTGCTTTCGTGCT
93001 TTTCCCTTGC
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.15
16 1 0.02
17 10 0.21
18 4 0.09
19 7 0.15
20 18 0.38
ACGTcount: A:0.00, C:0.28, G:0.25, T:0.47
Consensus pattern (19 bp):
TCTCGTGCTTTCGTGCTGC
Found at i:96709 original size:22 final size:21
Alignment explanation
Indices: 96678--96731 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
96668 AAAATTTTAT
*
96678 AAAATTTTAA-TAAAGTAAAA
1 AAAATTTTAATTAAAATAAAA
96698 ATAAATTATTAATTAAAATAAAA
1 A-AAATT-TTAATTAAAATAAAA
96721 AAAATATTTAA
1 AAAAT-TTTAA
96732 AATACATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 5 0.17
22 12 0.41
23 11 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATTTTAATTAAAATAAAA
Found at i:98939 original size:24 final size:24
Alignment explanation
Indices: 98910--98961 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
98900 CTTTGGTAAG
*
98910 TTCTCCCTTAGATCCTTCAGTCAC
1 TTCTCCCTTAGATCCTTAAGTCAC
98934 TTCTCCCTTAGATCCTTAAGTCAC
1 TTCTCCCTTAGATCCTTAAGTCAC
98958 TTCT
1 TTCT
98962 TCAATTCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.35, G:0.08, T:0.40
Consensus pattern (24 bp):
TTCTCCCTTAGATCCTTAAGTCAC
Found at i:99590 original size:22 final size:22
Alignment explanation
Indices: 99564--99606 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
99554 CCTAGTTTTT
99564 CCGGGCTAAACTAGAACCTTTA
1 CCGGGCTAAACTAGAACCTTTA
99586 CCGGGCTAAACTAGAACCTTT
1 CCGGGCTAAACTAGAACCTTT
99607 CCCTAGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (22 bp):
CCGGGCTAAACTAGAACCTTTA
Found at i:100751 original size:21 final size:21
Alignment explanation
Indices: 100722--100777 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
100712 ATTCTGACTA
*
100722 TCGCATTGCCATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
100743 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
100764 TCGCATTGCGATTT
1 TCGCATTGCGATTT
100778 ACGTATTCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:100827 original size:41 final size:41
Alignment explanation
Indices: 100725--100842 Score: 114
Period size: 41 Copynumber: 2.9 Consensus size: 41
100715 CTGACTATCG
* * * * * *
100725 CATTGCCATTTCCCAAATTCGCGTTGCGATTTTCCTAATTCG
1 CATTGCGATTTACCTAATTCGCGTTGCGATTTACGT-ATTCA
*
100767 CATTGCGATTTACGT-ATTCGCGTTGCGATTTACGTATTCA
1 CATTGCGATTTACCTAATTCGCGTTGCGATTTACGTATTCA
* * **
100807 CGTTGCGATTTTCCTAATTCGCAATGCGA-TTACGTA
1 CATTGCGATTTACCTAATTCGCGTTGCGATTTACGTA
100843 AATCGCAATG
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
40 23 0.37
41 29 0.46
42 11 0.17
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (41 bp):
CATTGCGATTTACCTAATTCGCGTTGCGATTTACGTATTCA
Found at i:100834 original size:21 final size:21
Alignment explanation
Indices: 100722--100855 Score: 112
Period size: 20 Copynumber: 6.5 Consensus size: 21
100712 ATTCTGACTA
* * *
100722 TCGCATTGCCATTTCCCAAAT
1 TCGCATTGCGATTTACCTAAT
* *
100743 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
*
100764 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTACCTAAT
* *
100784 TCGCGTTGCGATTTACGT-AT
1 TCGCATTGCGATTTACCTAAT
* * *
100804 TCACGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
* * *
100825 TCGCAATGCGA-TTACGTAAA
1 TCGCATTGCGATTTACCTAAT
*
100845 TCGCAATGCGA
1 TCGCATTGCGA
100856 ATTAGGAAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
20 53 0.56
21 42 0.44
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTACCTAAT
Found at i:100855 original size:61 final size:61
Alignment explanation
Indices: 100741--100855 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 61
100731 CATTTCCCAA
* * * **
100741 ATTCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTACGT
1 ATTCACGTTGCGATTTTCCTAATTCGCAATGCGATTTACGTAATCGCAATGCGATTTACGT
100802 ATTCACGTTGCGATTTTCCTAATTCGCAATGCGA-TTACGTAAATCGCAATGCGA
1 ATTCACGTTGCGATTTTCCTAATTCGCAATGCGATTTACGT-AATCGCAATGCGA
100856 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 6 0.12
61 42 0.88
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (61 bp):
ATTCACGTTGCGATTTTCCTAATTCGCAATGCGATTTACGTAATCGCAATGCGATTTACGT
Found at i:100866 original size:21 final size:21
Alignment explanation
Indices: 100825--100898 Score: 107
Period size: 20 Copynumber: 3.6 Consensus size: 21
100815 TTTTCCTAAT
100825 TCGCAATGCG-ATTACGTAAA
1 TCGCAATGCGAATTACGTAAA
* *
100845 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGTAAA
*
100866 TCGTAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGTAAA
100886 TCGCAATGCGAAT
1 TCGCAATGCGAAT
100899 CTGACTATTG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 27 0.59
21 19 0.41
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGTAAA
Found at i:101488 original size:21 final size:20
Alignment explanation
Indices: 101427--101502 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
101417 TTCTAAACTT
101427 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
101447 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAAAATG
**
101467 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
101488 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
101503 TAATCGCAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 30 0.61
21 19 0.39
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:101552 original size:19 final size:19
Alignment explanation
Indices: 101530--101618 Score: 64
Period size: 20 Copynumber: 4.9 Consensus size: 19
101520 CAAAATCGTA
101530 TTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTCACG
*
101549 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCACG
** *
101563 TT-CGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CACG
* *
101582 TTGCGATTTTCACTCTCTCG
1 TTGCGATTTTCA-TTTCACG
101602 TTGCGATTTTCATTTCA
1 TTGCGATTTTCATTTCA
101619 ACCAAAAGAC
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
13 3 0.06
14 6 0.11
15 2 0.04
17 3 0.06
18 1 0.02
19 14 0.26
20 22 0.42
21 2 0.04
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACG
Found at i:102182 original size:14 final size:14
Alignment explanation
Indices: 102160--102198 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
102150 TTTATTGTTT
102160 AATTGATTTGTAAA
1 AATTGATTTGTAAA
102174 AGA-TGATTTGTAAA
1 A-ATTGATTTGTAAA
102188 AATTGATTTGT
1 AATTGATTTGT
102199 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:102350 original size:33 final size:33
Alignment explanation
Indices: 102305--102384 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
102295 AAAAATGACT
* ** * *
102305 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
102338 ATCGCAACGCGAAATGAAAATCACAACGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
102371 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
102385 CTAAATTCGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGACAAA
Found at i:102453 original size:19 final size:18
Alignment explanation
Indices: 102396--102474 Score: 58
Period size: 19 Copynumber: 4.4 Consensus size: 18
102386 TAAATTCGTG
102396 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
**
102414 TTTGCGA--TTC-CCTCG-
1 -TTGCGATTTTCATTTCGC
102429 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
**
102447 ATTGCGATAGTCATTTCCGC
1 -TTGCGATTTTCATTT-CGC
102467 GTTGCGAT
1 -TTGCGAT
102475 AGACATTAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
14 6 0.13
16 6 0.13
17 6 0.13
19 19 0.40
20 10 0.21
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:102473 original size:20 final size:19
Alignment explanation
Indices: 102427--102481 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
102417 GCGATTCCCT
**
102427 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
102446 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
102466 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
102482 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:104950 original size:24 final size:24
Alignment explanation
Indices: 104923--104981 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
104913 CTGTTTCATC
104923 ATCAAAATTCGGGTATTGACCAAG
1 ATCAAAATTCGGGTATTGACCAAG
* *
104947 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGGGTATTGACCAAG
*
104971 ATCAAATTTCG
1 ATCAAAATTCG
104982 AATACTGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGGGTATTGACCAAG
Found at i:104990 original size:24 final size:24
Alignment explanation
Indices: 104939--104990 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
104929 ATTCGGGTAT
** *
104939 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
104963 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
104987 TGAC
1 TGAC
104991 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:105862 original size:20 final size:20
Alignment explanation
Indices: 105839--105926 Score: 79
Period size: 21 Copynumber: 4.3 Consensus size: 20
105829 AGAATCTCGT
105839 TGCGATTTAC-TAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
105859 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* * *
105879 TGCAAATTAGGAAAATCGCAA
1 TGC-GATTACGTAAATCGCAA
* ** *
105900 AGCGAATTTGGGAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
105921 TGCGAT
1 TGCGAT
105927 AGTCAGAATC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
19 4 0.07
20 20 0.35
21 33 0.58
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:105925 original size:21 final size:21
Alignment explanation
Indices: 105850--105925 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
105840 GCGATTTACT
* *
105850 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
*
105870 AAATCGCAATGCAAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
105891 AAATCGCAAAGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
105912 AAATCGCAATGCGA
1 AAATCGCAATGCGA
105926 TAGTCAGAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 12 0.26
21 35 0.74
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:106980 original size:22 final size:22
Alignment explanation
Indices: 106932--106980 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
106922 TTTTAAATCA
*
106932 AAATTTTGTTTTTCAAAACTAT
1 AAATTTTATTTTTCAAAACTAT
* * *
106954 CAATTTTATTTTTGAAAACTCT
1 AAATTTTATTTTTCAAAACTAT
106976 AAATT
1 AAATT
106981 CTTTTTCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (22 bp):
AAATTTTATTTTTCAAAACTAT
Found at i:107943 original size:34 final size:32
Alignment explanation
Indices: 107890--107959 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
107880 CCTTACAAAC
*
107890 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
107922 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
107956 TCCC
1 TCCC
107960 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Done.