Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009464.1 Corchorus capsularis cultivar CVL-1 contig09485, 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: 109949
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2986 original size:33 final size:33
Alignment explanation
Indices: 2944--3035 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 33
2934 AGCTAAAGGA
2944 TCATGTGGCCGGTTATGGCCGGGCATGGCCAAG
1 TCATGTGGCCGGTTATGGCCGGGCATGGCCAAG
* * ** *
2977 TCATGTGGCCGGGTGTGGCCGCACATGGCCATG
1 TCATGTGGCCGGTTATGGCCGGGCATGGCCAAG
*** *
3010 TTGCGTGGCCGGTGATGGCCGGGCAT
1 TCATGTGGCCGGTTATGGCCGGGCAT
3036 CTCCATGTCG
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.12, C:0.25, G:0.41, T:0.22
Consensus pattern (33 bp):
TCATGTGGCCGGTTATGGCCGGGCATGGCCAAG
Found at i:3042 original size:33 final size:33
Alignment explanation
Indices: 3005--3088 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
2995 CCGCACATGG
* *
3005 CCATGTTGCGTGGCCGGTGATGGC-CGGGCATCT
1 CCATGTCGCATGGCCGGTG-TGGCACGGGCATCT
*
3038 CCATGTCGCATGGCCGGTGTTGCACGGGCATCT
1 CCATGTCGCATGGCCGGTGTGGCACGGGCATCT
*
3071 CCAAGTCGCATGGCCGGT
1 CCATGTCGCATGGCCGGT
3089 CACTTATGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 3 0.07
33 43 0.93
ACGTcount: A:0.12, C:0.30, G:0.36, T:0.23
Consensus pattern (33 bp):
CCATGTCGCATGGCCGGTGTGGCACGGGCATCT
Found at i:8172 original size:10 final size:10
Alignment explanation
Indices: 8157--8206 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
8147 CCGCATCGAG
8157 CAACCGGCCA
1 CAACCGGCCA
8167 CAACCGGCCA
1 CAACCGGCCA
* *
8177 TC-ACTTGGGC-
1 -CAAC-CGGCCA
8187 CAACCGGCCA
1 CAACCGGCCA
8197 CAACCGGCCA
1 CAACCGGCCA
8207 ATGTATCCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 4 0.12
10 24 0.75
11 4 0.12
ACGTcount: A:0.26, C:0.46, G:0.22, T:0.06
Consensus pattern (10 bp):
CAACCGGCCA
Found at i:12160 original size:36 final size:34
Alignment explanation
Indices: 12061--12205 Score: 157
Period size: 35 Copynumber: 4.1 Consensus size: 34
12051 ACTAAATTTC
* * * *
12061 ATTACTCTGAATTAAGTCGATCAATGACCTGCTTA
1 ATTACCCTGAATTAAGTCGAT-TATGACTTACTTA
*
12096 ATTACCCTGAATTAAGT-TATGTATTGACTTACTTA
1 ATTACCCTGAATTAAGTCGAT-TA-TGACTTACTTA
* *
12131 ATTACCCTGGATTTAAGTCGATTACTGACTCACTTA
1 ATTACCCT-GAATTAAGTCGATTA-TGACTTACTTA
* *
12167 ATTACCCTGAATTAAGTTGATTATTACTTACTTA
1 ATTACCCTGAATTAAGTCGATTATGACTTACTTA
12201 ATTAC
1 ATTAC
12206 TGACTCACTT
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
34 17 0.18
35 46 0.49
36 28 0.30
37 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (34 bp):
ATTACCCTGAATTAAGTCGATTATGACTTACTTA
Found at i:12210 original size:50 final size:51
Alignment explanation
Indices: 12151--12253 Score: 172
Period size: 50 Copynumber: 2.0 Consensus size: 51
12141 ATTTAAGTCG
**
12151 ATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTA-TTACTTACTTA
1 ATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACCGACTTACTTA
*
12201 ATTACTGACTCACTTAATTACCCTGAATTAAGTTTATTACCGACTTACTTA
1 ATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACCGACTTACTTA
12252 AT
1 AT
12254 CACCCTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 38 0.78
51 11 0.22
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (51 bp):
ATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACCGACTTACTTA
Found at i:12217 original size:16 final size:16
Alignment explanation
Indices: 12151--12221 Score: 54
Period size: 16 Copynumber: 4.3 Consensus size: 16
12141 ATTTAAGTCG
12151 ATTACTGACTCACTTA
1 ATTACTGACTCACTTA
* * * *
12167 ATTACCCTGAATTAAGTTG
1 ATTA--CTG-ACTCACTTA
* *
12186 ATTA-TTACTTACTTA
1 ATTACTGACTCACTTA
12201 ATTACTGACTCACTTA
1 ATTACTGACTCACTTA
12217 ATTAC
1 ATTAC
12222 CCTGAATTAA
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
15 9 0.22
16 19 0.47
18 3 0.08
19 9 0.22
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (16 bp):
ATTACTGACTCACTTA
Found at i:12251 original size:35 final size:35
Alignment explanation
Indices: 12201--12378 Score: 286
Period size: 35 Copynumber: 5.1 Consensus size: 35
12191 TACTTACTTA
* *
12201 ATTACTGACTCACTTAATTACCCTGAATTAAGTTT
1 ATTACTGACTTACTTAATTACCCTGAATTAAGTTG
* * *
12236 ATTACCGACTTACTTAATCACCCTGAATTAAATTG
1 ATTACTGACTTACTTAATTACCCTGAATTAAGTTG
12271 ATTACTGACTTACTTAATTACCCTGAATTAAGTTG
1 ATTACTGACTTACTTAATTACCCTGAATTAAGTTG
* *
12306 ATTA-TTACTTACTTAATTGCCCTGAATTAAGTTG
1 ATTACTGACTTACTTAATTACCCTGAATTAAGTTG
12340 ATTACTGACTTACTTAATTACCCTGAATTAAGTTG
1 ATTACTGACTTACTTAATTACCCTGAATTAAGTTG
12375 ATTA
1 ATTA
12379 TTACTGATTC
Statistics
Matches: 130, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
34 32 0.25
35 98 0.75
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (35 bp):
ATTACTGACTTACTTAATTACCCTGAATTAAGTTG
Found at i:12310 original size:120 final size:121
Alignment explanation
Indices: 12092--12323 Score: 378
Period size: 120 Copynumber: 1.9 Consensus size: 121
12082 CAATGACCTG
** * * *
12092 CTTAATTACCCTGAATTAAGTTATGTATTGACTTACTTAATTACCCTGGATTTAAGTCGATTACT
1 CTTAATTACCCTGAATTAAGTTATGTACCGACTTACTTAATCACCCTGGAATTAAATCGATTACT
12157 GACTCACTTAATTACCCTGAATTAAGTTGATTATTACTTACTTAATTACTGACTCA
66 GACTCACTTAATTACCCTGAATTAAGTTGATTATTACTTACTTAATTACTGACTCA
*
12213 CTTAATTACCCTGAATTAAGTTTAT-TACCGACTTACTTAATCACCCT-GAATTAAATTGATTAC
1 CTTAATTACCCTGAATTAAG-TTATGTACCGACTTACTTAATCACCCTGGAATTAAATCGATTAC
*
12276 TGACTTACTTAATTACCCTGAATTAAGTTGATTATTACTTACTTAATT
65 TGACTCACTTAATTACCCTGAATTAAGTTGATTATTACTTACTTAATT
12324 GCCCTGAATT
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
120 60 0.58
121 39 0.38
122 4 0.04
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.41
Consensus pattern (121 bp):
CTTAATTACCCTGAATTAAGTTATGTACCGACTTACTTAATCACCCTGGAATTAAATCGATTACT
GACTCACTTAATTACCCTGAATTAAGTTGATTATTACTTACTTAATTACTGACTCA
Found at i:12347 original size:69 final size:69
Alignment explanation
Indices: 12201--12383 Score: 294
Period size: 69 Copynumber: 2.6 Consensus size: 69
12191 TACTTACTTA
* * **
12201 ATTACTGACTCACTTAATTACCCTGAATTAAGTTTATTACCGACTTACTTAATCACCCTGAATTA
1 ATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTA-TTACTTACTTAATCACCCTGAATTA
12266 AATTG
65 AATTG
**
12271 ATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTATTACTTACTTAATTGCCCTGAATTAA
1 ATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTATTACTTACTTAATCACCCTGAATTAA
*
12336 GTTG
66 ATTG
12340 ATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTATTACT
1 ATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTATTACT
12384 GATTCACCTT
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 69 0.65
70 37 0.35
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (69 bp):
ATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTATTACTTACTTAATCACCCTGAATTAA
ATTG
Found at i:13057 original size:20 final size:21
Alignment explanation
Indices: 13019--13058 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
13009 TTCACAAATT
*
13019 ACTTAAAAGATTTAATCTTTC
1 ACTTAAAAGATTCAATCTTTC
13040 ACTTAAAA-ATTCAATCTTT
1 ACTTAAAAGATTCAATCTTT
13059 ATTTACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (21 bp):
ACTTAAAAGATTCAATCTTTC
Found at i:13167 original size:150 final size:154
Alignment explanation
Indices: 12868--13238 Score: 452
Period size: 150 Copynumber: 2.4 Consensus size: 154
12858 CACATTATTC
* *
12868 AAAGATTTCATCTTTTACTTAAAAGATTTAATCTTTATTTACAAAAATTACTTAAAAG-TTCAAT
1 AAAGATTTAATCTTTTACTTAAAA-ATTCAATCTTTATTTAC--AAATTACTTAAAAGCTT-AAT
* * * * *
12932 CTTTTAATCAAAGATTACATTTTTTATTTACAAACTTACTTAAAAGCTTAATCTTTCAATTAAAA
62 CTTTCAATCAAAAATTACATTCTCTATTTACAAACTTACTTAAAAGATTAATCTTTCAATTAAAA
* *
12997 ATTCAATCTTTATTCACAAATTAC-TTA
127 ATCCAATCTTTATTCACAAATCACTTTA
*
13024 AAAGATTTAATCTTTCACTTAAAAATTCAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
1 AAAGATTTAATCTTTTACTTAAAAATTCAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
* * *
13089 CAATTAAAAATT-CA-TCTCTATTTACAAA-TTACTTGAAAGATTCATC-TTCTAATTAAAAATC
66 CAATCAAAAATTACATTCTCTATTTACAAACTTACTTAAAAGATTAATCTTTC-AATTAAAAATC
* *
13150 CCA-CTTTCATTTACAAATCACTTTA
130 CAATCTTT-ATTCACAAATCACTTTA
* * * * *
13175 AAA-ATTCAATCTTTTACTTAAAAAATCAATCTTTATATATAAATTACTTAAAAGCTTAAACTTT
1 AAAGATTTAATCTTTTACTTAAAAATTCAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
13239 GTACCAGATT
Statistics
Matches: 190, Mismatches: 21, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
149 7 0.04
150 93 0.49
151 18 0.09
152 2 0.01
153 30 0.16
154 2 0.01
155 16 0.08
156 22 0.12
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.42
Consensus pattern (154 bp):
AAAGATTTAATCTTTTACTTAAAAATTCAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
CAATCAAAAATTACATTCTCTATTTACAAACTTACTTAAAAGATTAATCTTTCAATTAAAAATCC
AATCTTTATTCACAAATCACTTTA
Found at i:13226 original size:50 final size:51
Alignment explanation
Indices: 12851--13228 Score: 380
Period size: 51 Copynumber: 7.5 Consensus size: 51
12841 AGATTTCATT
* * * *
12851 TTTATTT-CACATTA-TTCAAAGATTTC-ATCTTTTACTTAAAAGATTTAATC
1 TTTATTTACAAATTACTTAAAAGA-TTCAATCTTTTAATTAAAA-ATTCAATC
* * * *
12901 TTTATTTACAAAAATTACTTAAAAG-TTCAATCTTTTAATCAAAGATTACATTT
1 TTTATTTAC--AAATTACTTAAAAGATTCAATCTTTTAATTAAAAATT-CAATC
* *
12954 TTTATTTACAAACTTACTTAAAAGCTT-AATCTTTCAATTAAAAATTCAATC
1 TTTATTTACAAA-TTACTTAAAAGATTCAATCTTTTAATTAAAAATTCAATC
* * * *
13005 TTTATTCACAAATTACTTAAAAGATTTAATCTTTCACTTAAAAATTCAATC
1 TTTATTTACAAATTACTTAAAAGATTCAATCTTTTAATTAAAAATTCAATC
* *
13056 TTTATTTACAAATTACTTAAAAGCTT-AATCTTTCAATTAAAAATTC-ATC
1 TTTATTTACAAATTACTTAAAAGATTCAATCTTTTAATTAAAAATTCAATC
* * * * *
13105 TCTATTTACAAATTACTTGAAAGATTC-ATCTTCTAATTAAAAATCCCA-C
1 TTTATTTACAAATTACTTAAAAGATTCAATCTTTTAATTAAAAATTCAATC
* * *
13154 TTTCATTTACAAATCACTTTAAAA-ATTCAATCTTTTACTTAAAAAATCAATC
1 TTT-ATTTACAAATTAC-TTAAAAGATTCAATCTTTTAATTAAAAATTCAATC
* *
13206 TTTATATATAAATTACTTAAAAG
1 TTTATTTACAAATTACTTAAAAG
13229 CTTAAACTTT
Statistics
Matches: 276, Mismatches: 36, Indels: 31
0.80 0.10 0.09
Matches are distributed among these distances:
49 45 0.16
50 62 0.22
51 96 0.35
52 37 0.13
53 30 0.11
54 6 0.02
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (51 bp):
TTTATTTACAAATTACTTAAAAGATTCAATCTTTTAATTAAAAATTCAATC
Found at i:17728 original size:56 final size:57
Alignment explanation
Indices: 17647--17762 Score: 145
Period size: 56 Copynumber: 2.1 Consensus size: 57
17637 ACAATTAAGT
*
17647 AAAGAGAAGGTAATCAGTAATTAGTTTAACTC-AGAGTAATT-AGACTAAAAAGAGTA
1 AAAGAGAAGGTAATCAGCAATTAGTTTAACTCAAGAGTAATTAAG-CTAAAAAGAGTA
*
17703 AAAG-GAAGAGTAATCAGCAGA-TAGTTTAATTCAAGAGTAATTAAGCT-AAAA-AGTA
1 AAAGAGAAG-GTAATCAGCA-ATTAGTTTAACTCAAGAGTAATTAAGCTAAAAAGAGTA
17758 AAAGA
1 AAAGA
17763 AATAAGCACT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
55 12 0.23
56 27 0.51
57 12 0.23
58 2 0.04
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (57 bp):
AAAGAGAAGGTAATCAGCAATTAGTTTAACTCAAGAGTAATTAAGCTAAAAAGAGTA
Found at i:17838 original size:22 final size:21
Alignment explanation
Indices: 17808--17881 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
17798 AGTAGAATGG
* *
17808 AGTAGAAGTAAAATAACTAATC
1 AGTAAAAGTAAAA-AAGTAATC
* **
17830 AGTAAAAGTAAAAGAGTAAAAG
1 AGTAAAAGTAAAAAAGT-AATC
17852 AGTAAAAGTAAAAAAAGTAATC
1 AGTAAAAGT-AAAAAAGTAATC
17874 AGTAAAAG
1 AGTAAAAG
17882 GAGTAAAAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 2 0.05
22 33 0.79
23 7 0.17
ACGTcount: A:0.61, C:0.04, G:0.18, T:0.18
Consensus pattern (21 bp):
AGTAAAAGTAAAAAAGTAATC
Found at i:17870 original size:31 final size:31
Alignment explanation
Indices: 17844--17943 Score: 157
Period size: 31 Copynumber: 3.3 Consensus size: 31
17834 AAAGTAAAAG
17844 AGTAAAA-GAGTAAAAGTAAAAAAAGTAATC
1 AGTAAAAGGAGTAAAAGTAAAAAAAGTAATC
* *
17874 AGTAAAAGGAGTAAAAGCAAAAGAAGTAATC
1 AGTAAAAGGAGTAAAAGTAAAAAAAGTAATC
* *
17905 AGTAAAAGGAGTAAACGTAAAAGAAGTAATC
1 AGTAAAAGGAGTAAAAGTAAAAAAAGTAATC
17936 AGTAAAAG
1 AGTAAAAG
17944 TAAAGAGCAA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 7 0.11
31 58 0.89
ACGTcount: A:0.59, C:0.05, G:0.21, T:0.15
Consensus pattern (31 bp):
AGTAAAAGGAGTAAAAGTAAAAAAAGTAATC
Found at i:17940 original size:53 final size:51
Alignment explanation
Indices: 17788--17943 Score: 118
Period size: 53 Copynumber: 2.9 Consensus size: 51
17778 GGTAATCAAG
* * *
17788 AGAAGTAATCAGTAGAATGGAGTAGAAGTAAAATAACTAATCAGTAAAAGTAAA
1 AGAAGTAATCAGTA-AAAGGAGTA-AAGTAAAAGAA-TAATCAGTAAAAGCAAA
** * ** * **
17842 AG-AGTAAAAGAGTAAAAGTAAAAAAAGTAATCAGTAA-AAGGAGTAAAAGCAAA
1 AGAAGT-AATCAGTAAAAG-GAGTAAAGTAA-AAG-AATAATCAGTAAAAGCAAA
17895 AGAAGTAATCAGTAAAAGGAGTAAACGTAAAAGAAGTAATCAGTAAAAG
1 AGAAGTAATCAGTAAAAGGAGTAAA-GTAAAAGAA-TAATCAGTAAAAG
17944 TAAAGAGCAA
Statistics
Matches: 75, Mismatches: 19, Indels: 17
0.68 0.17 0.15
Matches are distributed among these distances:
51 2 0.03
52 6 0.08
53 51 0.68
54 14 0.19
55 2 0.03
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.17
Consensus pattern (51 bp):
AGAAGTAATCAGTAAAAGGAGTAAAGTAAAAGAATAATCAGTAAAAGCAAA
Found at i:17942 original size:16 final size:16
Alignment explanation
Indices: 17788--18051 Score: 121
Period size: 16 Copynumber: 16.9 Consensus size: 16
17778 GGTAATCAAG
17788 AGAAGTAATCAGTAGAA
1 AGAAGTAATCAGTA-AA
* *
17805 TGGAGTAGA--AGTAAA
1 AGAAGTA-ATCAGTAAA
* *
17820 ATAACTAATCAGTAAA
1 AGAAGTAATCAGTAAA
*
17836 AGTAA--AA-GAGTAAA
1 AG-AAGTAATCAGTAAA
*
17850 AG-AGTAA-AAGTAAA
1 AGAAGTAATCAGTAAA
*
17864 AAAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
* * *
17880 AGGAGTAA-AAGCAAA
1 AGAAGTAATCAGTAAA
17895 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
* *
17911 AGGAGTAAAC-GTAAA
1 AGAAGTAATCAGTAAA
17926 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
** *
17942 AGTAAAG-AGCAAAAGTAGA
1 AG--AAGTA--ATCAGTAAA
*
17961 AGAAATAATCAG-AAA
1 AGAAGTAATCAGTAAA
* *
17976 A-ATGGTAATC---AAG
1 AGA-AGTAATCAGTAAA
* *
17989 AGAAGTAATTAGCAAA
1 AGAAGTAATCAGTAAA
*
18005 AGAAGTAATTAGTAAA
1 AGAAGTAATCAGTAAA
*
18021 ATGGAGTGAA--AGTAAA
1 A-GAAGT-AATCAGTAAA
18037 AGAAGTAATCAGTAA
1 AGAAGTAATCAGTAA
18052 GTTGGTAATT
Statistics
Matches: 185, Mismatches: 38, Indels: 49
0.68 0.14 0.18
Matches are distributed among these distances:
12 1 0.01
13 8 0.04
14 22 0.12
15 49 0.26
16 76 0.41
17 14 0.08
18 7 0.04
19 8 0.04
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.17
Consensus pattern (16 bp):
AGAAGTAATCAGTAAA
Found at i:18059 original size:76 final size:72
Alignment explanation
Indices: 17913--18096 Score: 179
Period size: 76 Copynumber: 2.5 Consensus size: 72
17903 TCAGTAAAAG
* * * ** *
17913 GAGTAAACGTAAAAGAAGTAATCAGTAAAAGTAAAGAGCAAAAGTAGAAGAAATAATCAGAAAAA
1 GAGTAAAAGCAAAAGAAGTAATCAGTAAAA-T--GGAGTGAAAGTAAAAGAAATAATCAGAAAAA
17978 TGGTAATCAAGA
63 TGGTAAT-AA-A
* * * * **
17990 GAAGTAATTAGCAAAAGAAGTAATTAGTAAAATGGAGTGAAAGTAAAAGAAGTAATCAGTAAGTT
1 G-AGTAA-AAGCAAAAGAAGTAATCAGTAAAATGGAGTGAAAGTAAAAGAAATAATCAGAAAAAT
*
18055 GGTAATTAA
64 GGTAATAAA
*
18064 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGG
1 GAGTAAAAGCAAAAGAAGTAATCAGTAAAATGG
18097 TAATTAAGAG
Statistics
Matches: 89, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
72 24 0.27
73 5 0.06
74 2 0.02
75 1 0.01
76 30 0.34
77 1 0.01
78 6 0.07
79 20 0.22
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (72 bp):
GAGTAAAAGCAAAAGAAGTAATCAGTAAAATGGAGTGAAAGTAAAAGAAATAATCAGAAAAATGG
TAATAAA
Found at i:18074 original size:40 final size:40
Alignment explanation
Indices: 18024--18133 Score: 184
Period size: 40 Copynumber: 2.8 Consensus size: 40
18014 TAGTAAAATG
* **
18024 GAGTGAAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
18064 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
*
18104 GAGTAACAGTAAAAGAAGTAATCAGTAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAA
18134 GTAAAGAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.22
Consensus pattern (40 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
Found at i:18088 original size:116 final size:110
Alignment explanation
Indices: 17889--18134 Score: 304
Period size: 116 Copynumber: 2.2 Consensus size: 110
17879 AAGGAGTAAA
17889 AGCAAAAGAAGTAATCAGTAAAAGGAGTAAACGTAAAAGAAGTAATCAGTAAAAGTAAAGAGCAA
1 AGCAAAAGAAGTAATCAGTAAAAGGAGTAAACGTAAAAGAAGTAATCAGTAAAAGTAAAGAGCAA
*
17954 AAGTAGAAGAAATAATCAGAAAAATGGTAATCAAGAGAAGTAATT
66 AAGTAAAAGAAATAATCAGAAAAATGGTAATCAAGAGAAGTAATT
* **
17999 AGCAAAAGAAGTAATTAGTAAAATGGAGTGAAA-GTAAAAGAAGTAATCAGTAAGTTGGTAATTA
1 AGCAAAAGAAGTAATCAGTAAAA-GGAGT-AAACGTAAAAGAAGTAATCAGTAA--AAGT-A--A
* * * * *
18063 AGAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAAT-TA-AG-AGTAA-C
59 AGAGCAAAAGTAAAAGAAATAATCAGAAAAATGGTAATCAAGAGAAGTAATT
*
18111 AGTAAAAGAAGTAATCAGTAAAAG
1 AGCAAAAGAAGTAATCAGTAAAAG
18135 TAAAGAAAAG
Statistics
Matches: 118, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
110 22 0.19
111 26 0.22
112 24 0.20
113 7 0.06
114 3 0.03
115 1 0.01
116 35 0.30
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (110 bp):
AGCAAAAGAAGTAATCAGTAAAAGGAGTAAACGTAAAAGAAGTAATCAGTAAAAGTAAAGAGCAA
AAGTAAAAGAAATAATCAGAAAAATGGTAATCAAGAGAAGTAATT
Found at i:18090 original size:16 final size:15
Alignment explanation
Indices: 18062--18134 Score: 54
Period size: 16 Copynumber: 5.2 Consensus size: 15
18052 GTTGGTAATT
*
18062 AAGAGTAA-AAGTAA
1 AAGAGTAATCAGTAA
18076 AAGAAGTAATCAGTAA
1 AAG-AGTAATCAGTAA
18092 AATG-GTAAT---T--
1 AA-GAGTAATCAGTAA
18102 AAGAGTAA-CAGTAA
1 AAGAGTAATCAGTAA
18116 AAGAAGTAATCAGTAA
1 AAG-AGTAATCAGTAA
18132 AAG
1 AAG
18135 TAAAGAAAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 20
0.69 0.01 0.29
Matches are distributed among these distances:
9 1 0.02
10 6 0.13
12 2 0.04
14 6 0.13
15 15 0.32
16 16 0.34
17 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (15 bp):
AAGAGTAATCAGTAA
Found at i:18252 original size:14 final size:14
Alignment explanation
Indices: 18233--18259 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18223 TAATCAGTAC
18233 TAATCAGTAAAGAG
1 TAATCAGTAAAGAG
18247 TAATCAGTAAAGA
1 TAATCAGTAAAGA
18260 AAAATGGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAATCAGTAAAGAG
Found at i:18286 original size:59 final size:58
Alignment explanation
Indices: 18179--18290 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 58
18169 AATGGTAAAG
* * *
18179 AGTAAAGAGTAATTAGCAAAAAGTAAAATGGTAAAAGGAAATGATAATCAGTACTAATC
1 AGTAAAGAGTAATCAG-AAAAAGAAAAATGGTAAAAGAAAATGATAATCAGTACTAATC
*
18238 AGTAAAGAGTAATCAG-TAAAGAAAAATGGTAAAGAGTAAAAT-AGTAATCAGTA
1 AGTAAAGAGTAATCAGAAAAAGAAAAATGGTAAA-AG-AAAATGA-TAATCAGTA
18291 AAAGGTAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
57 15 0.33
58 3 0.07
59 28 0.61
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (58 bp):
AGTAAAGAGTAATCAGAAAAAGAAAAATGGTAAAAGAAAATGATAATCAGTACTAATC
Found at i:18338 original size:33 final size:33
Alignment explanation
Indices: 18272--18338 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
18262 AATGGTAAAG
* * *
18272 AGTAAAATAGTAATCAGTAAAAGGTAATCAGTA
1 AGTAAAATAGTAATCAGCAAAAAGTAAACAGTA
* *
18305 AGTAAAATAGTAATCGGCAAAAAGTAAAGAGTA
1 AGTAAAATAGTAATCAGCAAAAAGTAAACAGTA
18338 A
1 A
18339 TCAGTAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (33 bp):
AGTAAAATAGTAATCAGCAAAAAGTAAACAGTA
Found at i:18485 original size:18 final size:17
Alignment explanation
Indices: 18435--18479 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
18425 AGAGTAAAGA
18435 GTAATCAGTAAAAAAATG
1 GTAATCAGT-AAAAAATG
**
18453 GTAAAGAGTAAAAAATG
1 GTAATCAGTAAAAAATG
18470 GTAATCAGTA
1 GTAATCAGTA
18480 GGAAAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (17 bp):
GTAATCAGTAAAAAATG
Found at i:20840 original size:15 final size:15
Alignment explanation
Indices: 20820--20848 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20810 ACAATAAAAC
20820 TAAATTAAACTAAAT
1 TAAATTAAACTAAAT
20835 TAAATTAAACTAAA
1 TAAATTAAACTAAA
20849 GCTATGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAATTAAACTAAAT
Found at i:35045 original size:15 final size:15
Alignment explanation
Indices: 35022--35054 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35012 GAACACAATA
35022 AAACAAAATTAAACT
1 AAACAAAATTAAACT
*
35037 AAACTAAATTAAACT
1 AAACAAAATTAAACT
35052 AAA
1 AAA
35055 GCTATGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (15 bp):
AAACAAAATTAAACT
Found at i:37498 original size:22 final size:22
Alignment explanation
Indices: 37470--37511 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
37460 GACAAACCCG
37470 TAACCCGAATGATCC-AAGAAGT
1 TAACCCGAATGA-CCGAAGAAGT
*
37492 TAACCCGGATGACCGAAGAA
1 TAACCCGAATGACCGAAGAA
37512 TATTATAAAC
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:0.24, G:0.21, T:0.14
Consensus pattern (22 bp):
TAACCCGAATGACCGAAGAAGT
Found at i:38341 original size:131 final size:131
Alignment explanation
Indices: 38076--38470 Score: 702
Period size: 131 Copynumber: 3.0 Consensus size: 131
38066 ATTTAAGAAA
* * * *
38076 TATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAATTAGTAAAATGAT-AAAAATAAA
1 TATATTTAAAAAATTCTGATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAAT-AA
* *
38140 ATAGGTATAAGGATATTATATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
65 ATAGTTATAAGGATATTAGATTTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
38205 AAG
129 AAG
*
38208 TATATTTAAAAAATTCTGATATATATAAGTTTTTAAATTAAAATAGTAAAATGGTAAAAAATAAA
1 TATATTTAAAAAATTCTGATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAA
38273 TAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
66 TAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
38338 G
131 G
38339 TATATTTAAAAAATTCTGATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAA
1 TATATTTAAAAAATTCTGATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAA
38404 TAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
66 TAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
38469 G
131 G
38470 T
1 T
38471 TGATGCGCCA
Statistics
Matches: 254, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
131 167 0.66
132 81 0.32
133 6 0.02
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (131 bp):
TATATTTAAAAAATTCTGATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAA
TAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
G
Found at i:38738 original size:21 final size:20
Alignment explanation
Indices: 38712--38753 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
38702 TCTTGAAGGT
*
38712 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGA-CAA
*
38733 TTGAAGAGCATTGAAGACAA
1 TTGAAGACCATTGAAGACAA
38753 T
1 T
38754 AAGCAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGAAGACCATTGAAGACAA
Found at i:45854 original size:1 final size:1
Alignment explanation
Indices: 45850--45880 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
45840 AGAAAAAAGC
45850 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
45881 CCCAGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:46606 original size:2 final size:2
Alignment explanation
Indices: 46599--46635 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
46589 TTTCCCTGGA
46599 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
46636 TTCACTAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:47623 original size:17 final size:18
Alignment explanation
Indices: 47589--47627 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
47579 GTCCTCCTCA
47589 TTTCTTCTATTCTTTCTT
1 TTTCTTCTATTCTTTCTT
*
47607 TTTCTTCT-TTTTTTCTT
1 TTTCTTCTATTCTTTCTT
47624 TTTC
1 TTTC
47628 AGTAAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCTTCTATTCTTTCTT
Found at i:48037 original size:2 final size:2
Alignment explanation
Indices: 48030--48065 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
48020 AATACTTTAT
48030 TA TA TA TA TA TA -A TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48066 ATTACAATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48050 original size:18 final size:17
Alignment explanation
Indices: 48027--48064 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
48017 GTAAATACTT
48027 TATTATATATATATAATA
1 TATTATATATATAT-ATA
48045 TATTATATATATATATA
1 TATTATATATATATATA
48062 TAT
1 TAT
48065 AATTACAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTATATATATATATA
Found at i:49026 original size:28 final size:28
Alignment explanation
Indices: 48947--49028 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
48937 TTCATCGTGT
* *
48947 TAGTTTATTCTCAATCACGGAGTCCATG
1 TAGTTTATACTCAATCACGGAGTTCATG
* *
48975 TAGTTTATACTCAATCGCAGAGTTCATG
1 TAGTTTATACTCAATCACGGAGTTCATG
49003 TAGTTTATACTCAATCACGGAGTTCA
1 TAGTTTATACTCAATCACGGAGTTCA
49029 AATGTGGCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (28 bp):
TAGTTTATACTCAATCACGGAGTTCATG
Found at i:49381 original size:9 final size:9
Alignment explanation
Indices: 49354--49390 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
49344 TCTTTGATGA
49354 GGGCACTTG
1 GGGCACTTG
*
49363 AGGCACTTG
1 GGGCACTTG
49372 GGGCACTTG
1 GGGCACTTG
49381 GGGC-CTTG
1 GGGCACTTG
49389 GG
1 GG
49391 CCTCTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 6 0.23
9 20 0.77
ACGTcount: A:0.11, C:0.22, G:0.46, T:0.22
Consensus pattern (9 bp):
GGGCACTTG
Found at i:49533 original size:18 final size:16
Alignment explanation
Indices: 49508--49551 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
49498 TCTTTGATGA
49508 GGGCACTTGGGGCACTT
1 GGGCACTTGGGGC-CTT
*
49525 GGAGCACTTGGAGCCTT
1 GG-GCACTTGGGGCCTT
49542 GGGCA-TTGGG
1 GGGCACTTGGG
49552 CCTCTTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 4 0.17
16 3 0.12
17 7 0.29
18 10 0.42
ACGTcount: A:0.14, C:0.20, G:0.43, T:0.23
Consensus pattern (16 bp):
GGGCACTTGGGGCCTT
Found at i:49599 original size:161 final size:154
Alignment explanation
Indices: 49337--49657 Score: 543
Period size: 161 Copynumber: 2.0 Consensus size: 154
49327 ATAAAATAAT
* *
49337 TTTAAAGTCTTTGATGAGGGCACTTGAGGCACTTGGGGCACTTGGGGCCTTGGGCCTCTTGATTA
1 TTTAAAGTCTTTGATGAGGGCACTTGAGGCACTTGGAGCACTTGGGGCATTGGGCCTCTTGATTA
*
49402 ATAAACATATTTTTTGATATGTAAATAGTTATAATTATTTTTGGATAATTATAATTATTCAGTTT
66 ATAAACATATTTTTTGATATGTAAATACTTATAATTATTTTTGGATAATTATAATTATTCAGTTT
49467 TTAATTGAACAAACGTGTTTATCC
131 TTAATTGAACAAACGTGTTTATCC
*
49491 TTTAAAGTCTTTGATGAGGGCACTTGGGGCACTTGGAGCACTTGGAGCCTTGGGCATTGGGCCTC
1 TTTAAAGTCTTTGATGAGGGCACTTGAGGCACTTGGAGCACTT---G----GGGCATTGGGCCTC
49556 TTGATTAATAAACATATTTTTTGATATGTAAATACTTATAATTATTTTTGGATAATTATAATTAT
59 TTGATTAATAAACATATTTTTTGATATGTAAATACTTATAATTATTTTTGGATAATTATAATTAT
49621 TCAGTTTTTAATTGAACAAACGTGTTTATCC
124 TCAGTTTTTAATTGAACAAACGTGTTTATCC
49652 TTTAAA
1 TTTAAA
49658 CAGTTACTTA
Statistics
Matches: 156, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
154 41 0.26
157 1 0.01
161 114 0.73
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (154 bp):
TTTAAAGTCTTTGATGAGGGCACTTGAGGCACTTGGAGCACTTGGGGCATTGGGCCTCTTGATTA
ATAAACATATTTTTTGATATGTAAATACTTATAATTATTTTTGGATAATTATAATTATTCAGTTT
TTAATTGAACAAACGTGTTTATCC
Found at i:54966 original size:28 final size:28
Alignment explanation
Indices: 54934--55006 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
54924 CATAAATGTA
54934 AGAAGATGAACCATTCCATAACATCCAT
1 AGAAGATGAACCATTCCATAACATCCAT
* *
54962 AGAAGAT-ACACCATGCCATAACATCTAT
1 AGAAGATGA-ACCATTCCATAACATCCAT
54990 AGGAAGATGAACCATTC
1 A-GAAGATGAACCATTC
55007 TCATTAATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.03
28 25 0.64
29 12 0.31
30 1 0.03
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (28 bp):
AGAAGATGAACCATTCCATAACATCCAT
Found at i:55090 original size:10 final size:10
Alignment explanation
Indices: 55075--55105 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
55065 GGATGTCCAT
55075 TGTTGGAGTA
1 TGTTGGAGTA
55085 TGTTGGAGTA
1 TGTTGGAGTA
*
55095 TTTTGGAGTA
1 TGTTGGAGTA
55105 T
1 T
55106 ATGCCTCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (10 bp):
TGTTGGAGTA
Found at i:63999 original size:16 final size:16
Alignment explanation
Indices: 63972--64105 Score: 114
Period size: 16 Copynumber: 8.5 Consensus size: 16
63962 CGAGGTCATA
63972 ACCCGA-ACCCG-ATAG
1 ACCCGAGACCCGAAT-G
*
63987 ACTCGAGACCCGAATG
1 ACCCGAGACCCGAATG
*
64003 ACCCGAGACCCAAATG
1 ACCCGAGACCCGAATG
* * *
64019 ACCCGAAACCTGTATG
1 ACCCGAGACCCGAATG
*
64035 ACCCGAGACTCGAATG
1 ACCCGAGACCCGAATG
* * *
64051 ACCGGAAACCCGAATA
1 ACCCGAGACCCGAATG
*
64067 ACTCGA-ACCC-AGATG
1 ACCCGAGACCCGA-ATG
* *
64082 ACCTGAAACCCGAATG
1 ACCCGAGACCCGAATG
64098 ACCCGAGA
1 ACCCGAGA
64106 AAACTGCCTA
Statistics
Matches: 92, Mismatches: 22, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
14 1 0.01
15 15 0.16
16 73 0.79
17 3 0.03
ACGTcount: A:0.35, C:0.34, G:0.21, T:0.10
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:64037 original size:32 final size:32
Alignment explanation
Indices: 63994--64105 Score: 136
Period size: 32 Copynumber: 3.5 Consensus size: 32
63984 TAGACTCGAG
63994 ACCCGAATGACCCGAGACCCAAATGACCCGAA
1 ACCCGAATGACCCGAGACCCAAATGACCCGAA
* * * * *
64026 ACCTGTATGACCCGAGACTCGAATGACCGGAA
1 ACCCGAATGACCCGAGACCCAAATGACCCGAA
* * * *
64058 ACCCGAATAACTCGA-ACCCAGATGACCTGAA
1 ACCCGAATGACCCGAGACCCAAATGACCCGAA
64089 ACCCGAATGACCCGAGA
1 ACCCGAATGACCCGAGA
64106 AAACTGCCTA
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
31 25 0.39
32 39 0.61
ACGTcount: A:0.36, C:0.33, G:0.21, T:0.11
Consensus pattern (32 bp):
ACCCGAATGACCCGAGACCCAAATGACCCGAA
Found at i:65012 original size:16 final size:16
Alignment explanation
Indices: 64993--65032 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
64983 CGAACCCGTG
*
64993 ACCCGAATGACCTGTA
1 ACCCGAATGACCTGAA
65009 ACCC-AGATGACCTGAA
1 ACCCGA-ATGACCTGAA
65025 ACCCGAAT
1 ACCCGAAT
65033 AACCCGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.35, C:0.33, G:0.17, T:0.15
Consensus pattern (16 bp):
ACCCGAATGACCTGAA
Found at i:65176 original size:3 final size:3
Alignment explanation
Indices: 65168--65192 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
65158 TAATTTTACC
65168 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
65193 TTACCTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:65183 original size:30 final size:30
Alignment explanation
Indices: 65147--65203 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
65137 ATACAATTTA
65147 TATTATTACTATAATTTTACCTATTATTAT
1 TATTATTACTATAATTTTACCTATTATTAT
* *
65177 TATTATTATTATTATTTTACCTATTAT
1 TATTATTACTATAATTTTACCTATTAT
65204 AAATTATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.60
Consensus pattern (30 bp):
TATTATTACTATAATTTTACCTATTATTAT
Found at i:65956 original size:16 final size:15
Alignment explanation
Indices: 65937--65985 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
65927 TGCGGTAGAC
65937 CCGAGACCCGAATGA
1 CCGAGACCCGAATGA
65952 TCCGA-ACCCCGAATGA
1 -CCGAGA-CCCGAATGA
*
65968 CATGAGACCCGAATGA
1 C-CGAGACCCGAATGA
65984 CC
1 CC
65986 TGAAGCCCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 2 0.07
16 25 0.89
17 1 0.04
ACGTcount: A:0.33, C:0.35, G:0.22, T:0.10
Consensus pattern (15 bp):
CCGAGACCCGAATGA
Found at i:65994 original size:16 final size:16
Alignment explanation
Indices: 65943--65999 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
65933 AGACCCGAGA
*
65943 CCCGAATGATCC-GAAC
1 CCCGAATGA-CCTGAAG
*
65959 CCCGAATGACATG-AG
1 CCCGAATGACCTGAAG
65974 ACCCGAATGACCTGAAG
1 -CCCGAATGACCTGAAG
*
65991 CCCGTATGA
1 CCCGAATGA
66000 TCCGCACCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 2 0.06
16 30 0.88
17 2 0.06
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.14
Consensus pattern (16 bp):
CCCGAATGACCTGAAG
Found at i:67253 original size:65 final size:64
Alignment explanation
Indices: 67155--67291 Score: 166
Period size: 65 Copynumber: 2.1 Consensus size: 64
67145 CGCCCCCACC
* * * ***
67155 GGGGCGGCCTGCCCTGCTAAGCCGCCCCGGTGGGGCGGCCTTTTCATGGGGAAGCCGCCCTCAT
1 GGGGCGGCCTGCCCTGCGAAGCCACCCCAGTGGGGCGGCCTGCCCATGGGGAAGCCGCCCTCAT
* * * *
67219 GGGGCGGCTTGCCGTGGCGAAGCCACCCCAGTGGGGCGGCCTGCCCATGGTGAAGCCGCCCTCTT
1 GGGGCGGCCTGCCCT-GCGAAGCCACCCCAGTGGGGCGGCCTGCCCATGGGGAAGCCGCCCTCAT
*
67284 GGGACGGC
1 GGGGCGGC
67292 ACAGGTCATC
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 13 0.21
65 48 0.79
ACGTcount: A:0.10, C:0.35, G:0.39, T:0.15
Consensus pattern (64 bp):
GGGGCGGCCTGCCCTGCGAAGCCACCCCAGTGGGGCGGCCTGCCCATGGGGAAGCCGCCCTCAT
Found at i:67254 original size:32 final size:32
Alignment explanation
Indices: 67155--67279 Score: 119
Period size: 33 Copynumber: 3.9 Consensus size: 32
67145 CGCCCCCACC
* * *
67155 GGGGCGGCCTGCCCT-GCTAAGCCGCCCCGGT
1 GGGGCGGCCTGCCATGGCGAAGCCGCCCCAGT
** *
67186 GGGGCGGCCTTTTCATGGGGAAGCCGCCCTCA-T
1 GGGGCGGCC-TGCCATGGCGAAGCCGCCC-CAGT
* * *
67219 GGGGCGGCTTGCCGTGGCGAAGCCACCCCAGT
1 GGGGCGGCCTGCCATGGCGAAGCCGCCCCAGT
*
67251 GGGGCGGCCTGCCCATGGTGAAGCCGCCC
1 GGGGCGGCCTG-CCATGGCGAAGCCGCCC
67280 TCTTGGGACG
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
31 11 0.15
32 28 0.38
33 33 0.45
34 1 0.01
ACGTcount: A:0.10, C:0.36, G:0.39, T:0.14
Consensus pattern (32 bp):
GGGGCGGCCTGCCATGGCGAAGCCGCCCCAGT
Found at i:68159 original size:14 final size:14
Alignment explanation
Indices: 68132--68173 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
68122 TAGATCTATC
68132 TATCTATAT-T-TA
1 TATCTATATATCTA
*
68144 TATTTATATATCTA
1 TATCTATATATCTA
*
68158 TATCTATTTATCTA
1 TATCTATATATCTA
68172 TA
1 TA
68174 GAGTATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 8 0.32
13 1 0.04
14 16 0.64
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (14 bp):
TATCTATATATCTA
Found at i:73313 original size:24 final size:22
Alignment explanation
Indices: 73286--73357 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 22
73276 CACTAATGTC
73286 CTTTTCCTTTTCCTGTTGCTCATT
1 CTTTT-CTTTT-CTGTTGCTCATT
* *
73310 CTTTT-TCTTCTGCTACTGCTCACT
1 CTTTTCTTTTCTG-T--TGCTCATT
73334 CTCTTTCTTCTTCTGTTGCTCATT
1 CT-TTTCTT-TTCTGTTGCTCATT
73358 TGCTTTCTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
21 3 0.08
22 4 0.11
24 21 0.55
25 3 0.08
26 2 0.05
27 5 0.13
ACGTcount: A:0.06, C:0.31, G:0.08, T:0.56
Consensus pattern (22 bp):
CTTTTCTTTTCTGTTGCTCATT
Found at i:73363 original size:24 final size:23
Alignment explanation
Indices: 73298--73365 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 23
73288 TTTCCTTTTC
73298 CTGTTGCTCA-TTCTTT-TTCTT
1 CTGTTGCTCATTTCTTTCTTCTT
*
73319 CTGCTACTGCTCACTCTCTTTCTTCTT
1 CTG-T--TGCTCA-TTTCTTTCTTCTT
73346 CTGTTGCTCATTTGCTTTCT
1 CTGTTGCTCATTT-CTTTCT
73366 GTTGTTGCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
21 3 0.08
22 1 0.03
23 2 0.05
24 18 0.47
26 6 0.16
27 8 0.21
ACGTcount: A:0.06, C:0.29, G:0.10, T:0.54
Consensus pattern (23 bp):
CTGTTGCTCATTTCTTTCTTCTT
Found at i:74956 original size:21 final size:21
Alignment explanation
Indices: 74930--74989 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
74920 GCATAACTTG
*
74930 GAATCGATTGGAATATTCCTA
1 GAATCGATTGGAATATTCATA
* * **
74951 GAATCGATTGTAGTAGACATA
1 GAATCGATTGGAATATTCATA
*
74972 GAATCAATTGGAATATTC
1 GAATCGATTGGAATATTC
74990 TTGCTCCAAA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (21 bp):
GAATCGATTGGAATATTCATA
Found at i:76941 original size:26 final size:27
Alignment explanation
Indices: 76880--76933 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
76870 TATTTCTTAA
*
76880 TTGC-CATT-AGGGGCATTTTTGTCAT
1 TTGCACATTCAGGGGCATTTTGGTCAT
76905 TTGCACATTCAGGGGCATTTTGGTCAT
1 TTGCACATTCAGGGGCATTTTGGTCAT
76932 TT
1 TT
76934 TAAGTTCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 4 0.15
26 4 0.15
27 18 0.69
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.43
Consensus pattern (27 bp):
TTGCACATTCAGGGGCATTTTGGTCAT
Found at i:78005 original size:17 final size:20
Alignment explanation
Indices: 77978--78016 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
77968 ATAATTTCAT
77978 CACTGCAATTT-A-TTCACA
1 CACTGCAATTTCACTTCACA
77996 CACTGC-ATTTCACTTCACA
1 CACTGCAATTTCACTTCACA
78015 CA
1 CA
78017 AGAACACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (20 bp):
CACTGCAATTTCACTTCACA
Found at i:81862 original size:24 final size:25
Alignment explanation
Indices: 81835--81885 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
81825 TATTGTGTTT
81835 ATGTAGCA-TATG-AATTCCATTTGG
1 ATGTAGCATTATGTAA-TCCATTTGG
* *
81859 ATGTATCATTGTGTAATCCATTTGG
1 ATGTAGCATTATGTAATCCATTTGG
81884 AT
1 AT
81886 TGGTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.30
25 14 0.61
26 2 0.09
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (25 bp):
ATGTAGCATTATGTAATCCATTTGG
Found at i:82109 original size:33 final size:32
Alignment explanation
Indices: 82072--82175 Score: 100
Period size: 33 Copynumber: 3.2 Consensus size: 32
82062 AAATGCTGCA
82072 AAATAGCGGCATTTACCTGAAGAAAACGCCACT
1 AAATAGCGGCATTTA-CTGAAGAAAACGCCACT
* * * *
82105 AAATAGTGGCGTTTTACTAAAGAAAACGCCCCT
1 AAATAGCGGC-ATTTACTGAAGAAAACGCCACT
* ** * * *
82138 AAGTAGCGGTGTCTACTGAAGAAAATGCCGCT
1 AAATAGCGGCATTTACTGAAGAAAACGCCACT
82170 AAATAG
1 AAATAG
82176 TGGTGTTTAC
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
32 22 0.39
33 31 0.54
34 4 0.07
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (32 bp):
AAATAGCGGCATTTACTGAAGAAAACGCCACT
Found at i:82181 original size:32 final size:32
Alignment explanation
Indices: 82088--82181 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
82078 CGGCATTTAC
* *
82088 CTGAAGAAAACGCCACTAAATAGTGGCGTTTTA
1 CTGAAGAAAACGCCACTAAATAGTGGTG-TCTA
* * * *
82121 CTAAAGAAAACGCCCCTAAGTAGCGGTGTCTA
1 CTGAAGAAAACGCCACTAAATAGTGGTGTCTA
* *
82153 CTGAAGAAAATGCCGCTAAATAGTGGTGT
1 CTGAAGAAAACGCCACTAAATAGTGGTGT
82182 TTACAAAATA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
32 27 0.54
33 23 0.46
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (32 bp):
CTGAAGAAAACGCCACTAAATAGTGGTGTCTA
Found at i:82246 original size:14 final size:14
Alignment explanation
Indices: 82227--82274 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
82217 ACATATATAA
82227 TTTCTAAATATTAT
1 TTTCTAAATATTAT
* *
82241 TTTCTAAAT-GTAA
1 TTTCTAAATATTAT
*
82254 TTTCTATATATTAT
1 TTTCTAAATATTAT
82268 TTTCTAA
1 TTTCTAA
82275 TTCTAATTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.56
Consensus pattern (14 bp):
TTTCTAAATATTAT
Found at i:82264 original size:27 final size:27
Alignment explanation
Indices: 82224--82284 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
82214 ATTACATATA
*
82224 TAATTTCTAAATATTATTTTCTAAATG
1 TAATTTCTAAATATTATTTTCTAAATC
* *
82251 TAATTTCTATATATTATTTTCTAATTC
1 TAATTTCTAAATATTATTTTCTAAATC
82278 TAATTTC
1 TAATTTC
82285 ATTACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.56
Consensus pattern (27 bp):
TAATTTCTAAATATTATTTTCTAAATC
Found at i:82311 original size:37 final size:37
Alignment explanation
Indices: 82263--82334 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
82253 ATTTCTATAT
* *
82263 ATTATTTTCTAATTCTAATTTCATTACATATATAAAC
1 ATTATTTTCTAAATATAATTTCATTACATATATAAAC
82300 ATTATTTTCTAAATATAATTTCATTACATATATAA
1 ATTATTTTCTAAATATAATTTCATTACATATATAA
82335 TTACTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTATTTTCTAAATATAATTTCATTACATATATAAAC
Found at i:82320 original size:14 final size:13
Alignment explanation
Indices: 82305--82413 Score: 58
Period size: 15 Copynumber: 7.7 Consensus size: 13
82295 TAAACATTAT
82305 TTTCTAAATATAA
1 TTTCTAAATATAA
82318 TTTCATTACATATATAA
1 TTTC--TA-A-ATATAA
* * *
82335 TTACTAAATTTTA
1 TTTCTAAATATAA
*
82348 TTTCCTAATTATAA
1 TTT-CTAAATATAA
*
82362 TTTCTAAATAATTAT
1 TTTCTAAAT-A-TAA
82377 TTTCTAAATA-ATA
1 TTTCTAAATATA-A
*
82390 TTTCATTACATATAA
1 TTTC--TAAATATAA
*
82405 TTTATAAAT
1 TTTCTAAAT
82414 GTATAATTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
12 1 0.01
13 23 0.32
14 13 0.18
15 24 0.33
16 2 0.03
17 9 0.12
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTCTAAATATAA
Found at i:83740 original size:32 final size:32
Alignment explanation
Indices: 83635--83818 Score: 196
Period size: 32 Copynumber: 5.8 Consensus size: 32
83625 TTCTTATAAA
* *
83635 AAAAAGCCCCTAATTT-GGGGCGTCAATAGAAG
1 AAAACGCCCCT-ATTTAGGGGCGTCTATAGAAG
* ** *
83667 AAAAC-CCCTTAAAATAGGGGTGTCTATAGAAG
1 AAAACGCCCCT-ATTTAGGGGCGTCTATAGAAG
*
83699 -AAACGCCCCTATTTAGCGGCGTCTATAGAAG
1 AAAACGCCCCTATTTAGGGGCGTCTATAGAAG
* * *
83730 AAAACGCCCCTATTTAGGAGCGTCTGTTGAAG
1 AAAACGCCCCTATTTAGGGGCGTCTATAGAAG
* * *
83762 AAAACACCCCTATTTAGGGGCGTCTA-CGAGG
1 AAAACGCCCCTATTTAGGGGCGTCTATAGAAG
*
83793 AAAACGCCCCTATCTAGGGGCGTCTA
1 AAAACGCCCCTATTTAGGGGCGTCTA
83819 CGAGGAAAAT
Statistics
Matches: 127, Mismatches: 22, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
31 55 0.43
32 72 0.57
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (32 bp):
AAAACGCCCCTATTTAGGGGCGTCTATAGAAG
Found at i:83762 original size:63 final size:63
Alignment explanation
Indices: 83695--83817 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 63
83685 GGTGTCTATA
* *
83695 GAAG-AAACGCCCCTATTTAGCGGCGTCTATAGAAGAAAACGCCCCTATTTAGGAGCGTCTGTT
1 GAAGAAAACACCCCTATTTAGCGGCGTCTA-AGAAGAAAACGCCCCTATCTAGGAGCGTCTGTT
* * * *
83758 GAAGAAAACACCCCTATTTAGGGGCGTCTACGAGGAAAACGCCCCTATCTAGGGGCGTCT
1 GAAGAAAACACCCCTATTTAGCGGCGTCTAAGAAGAAAACGCCCCTATCTAGGAGCGTCT
83818 ACGAGGAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 30 0.57
64 23 0.43
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.21
Consensus pattern (63 bp):
GAAGAAAACACCCCTATTTAGCGGCGTCTAAGAAGAAAACGCCCCTATCTAGGAGCGTCTGTT
Found at i:83819 original size:31 final size:31
Alignment explanation
Indices: 83681--83827 Score: 161
Period size: 31 Copynumber: 4.7 Consensus size: 31
83671 CCCCTTAAAA
* *
83681 TAGGGGTGTCTATAGAAG-AAACGCCCCTATT
1 TAGGGGCGTCTA-CGAAGAAAACGCCCCTATT
* *
83712 TAGCGGCGTCTATAGAAGAAAACGCCCCTATT
1 TAGGGGCGTCTA-CGAAGAAAACGCCCCTATT
* ** *
83744 TAGGAGCGTCTGTTGAAGAAAACACCCCTATT
1 TAGGGGCGTCT-ACGAAGAAAACGCCCCTATT
* *
83776 TAGGGGCGTCTACGAGGAAAACGCCCCTATC
1 TAGGGGCGTCTACGAAGAAAACGCCCCTATT
*
83807 TAGGGGCGTCTACGAGGAAAA
1 TAGGGGCGTCTACGAAGAAAA
83828 TGCCTTAACA
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
31 52 0.51
32 49 0.49
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (31 bp):
TAGGGGCGTCTACGAAGAAAACGCCCCTATT
Found at i:89396 original size:28 final size:29
Alignment explanation
Indices: 89346--89406 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
89336 AAAGATATAA
* * *
89346 AAAATAAAAAAATATATATTTTA-TATTT
1 AAAATAAAAAAACATAAAATTTACTATTT
* *
89374 AAAATGAAAAAACATAAAATTTACTGTTT
1 AAAATAAAAAAACATAAAATTTACTATTT
89403 AAAA
1 AAAA
89407 CTTTCATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATAAAAAAACATAAAATTTACTATTT
Found at i:89820 original size:3 final size:3
Alignment explanation
Indices: 89812--89845 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
89802 ACATAACAAT
89812 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
89846 CGATATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:91237 original size:402 final size:405
Alignment explanation
Indices: 90225--91239 Score: 1174
Period size: 416 Copynumber: 2.5 Consensus size: 405
90215 TCTACAACTT
* * * * *
90225 TCATGAAGGACTGAAAAACCGATTTTCATGTTTCGATTCTAAAAAATGCTTCTTAAATTTTGTGG
1 TCATGAAGAACTCAAAAACCAATTTTAATGTTTCGATTCTTAAAAATGCTTCTTAAATTTTGTGG
* * * * * *
90290 TCTCGATTGTCGGTCTATCTAATATTGTATAATTTTTGATCCACTTGTCCGATTG-AGCTTGTTC
66 TTTTGATTGCCGGTCTATTTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAAG-TTGTTC
*
90354 AAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACTATCGTCAAGGACCTGAAAGCTGAATTTG
130 AAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACT-TC-ACAAGGACCTGAAAGCTGAATTTG
* *
90419 ATTAATGAGTTTCATGGAGGGTTCGAGAGAGAATTTTTATGTTTGGTCTCCATAAACAAATATAT
193 ATTAATGAGTTTCATGGAGGATTCGAGAGAGAATTTTTATGTTTCGTCTCCATAAACAAATATAT
* *
90484 TTTTTGCTGGATTATTTAACAAATGATCCTTATACTTTTATGCTTTATGCTATTTAATCATTTAC
258 TTTTTGCTGGATTATTTAACAAATGATCCTCATACTTTTATGCTTTATGCTATTGAATCATTTAC
* * * * *
90549 AATCATGGGTTGGACGATCTAACGCGTCAGCTTTTATTTTTGTATTTTCTGTTCTATTTGTCCGA
323 AATCATAGGTTGGACGATCTAA--C--CAGCTTTGACTTTTGTATTTTCTATTCTATTTGTCCCA
* *
90614 TCAGGGTAATCTCATGATCTACAA
384 TCAAGGTAATCTAATGATCT--AA
* * * * *
90638 CTTTCATGAAAAACTCAGAAATCAATTTTAATGTTTTGATTC-TAAAAAGTGTTTCTTAAATTTT
1 ---TCATGAAGAACTCAAAAACCAATTTTAATGTTTCGATTCTTAAAAA-TGCTTCTTAAATTTT
*
90702 GTGGTTTTGATTGCCGGTCTATTTAATATCGTATAATTTTCGGTCCACTTGTCCGATTGAAGTTG
62 GTGGTTTTGATTGCCGGTCTATTTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAAGTTG
* * * * *
90767 TTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCATTAAGGGCATGAAAGTTGAAT
127 TTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGAC-TTCA-CAAGGACCTGAAAGCTGAAT
* * * *
90832 TTGATTAATGAGTTTCGTGGAGGATT-GAAGAGGGAATTTTTATGTTTCGTCTTCATAAACTAAT
190 TTGATTAATGAGTTTCATGGAGGATTCG-AGAGAGAATTTTTATGTTTCGTCTCCATAAACAAAT
* * * * *
90896 ATTTTTTTTGCTGTATTATTTATCTAATGA-CCTCATAC-TTTATG-TTTCATGCTATTGAATCC
254 ATATTTTTTGCTGGATTATTTAACAAATGATCCTCATACTTTTATGCTTT-ATGCTATTGAATCA
* * * * * *
90958 TTTAGAGTTATAGGTTGGAGGATTTAA-C-GCTTTGACTTTTGT-TTTTGTATTCTATTTGTCCC
318 TTTACAATCATAGGTTGGACGATCTAACCAGCTTTGACTTTTGTATTTTCTATTCTATTTGTCCC
* * *
91020 ATTAAGGTGATTTAAGTG-TCT-A
383 ATCAAGGTAATCTAA-TGATCTAA
*
91042 -CATGAAGAACTCAAAAACCAATTTTAATGTTTC-AGTTCTTAAAAATGCTTCTGAAATTTTGTG
1 TCATGAAGAACTCAAAAACCAATTTTAATGTTTCGA-TTCTTAAAAATGCTTCTTAAATTTTGTG
* * *
91105 CTTTTGATTGCCGGTCTATTTAATATATTGTATAATTTTCGGTCCACTTGTCCAATTGAAGTTCT
65 GTTTTGATTGCCGGTCTATTT-A-ATATTGTATAATTTTCGGTCCACTTGTCCGATTGAAGTTGT
* * * * * *
91170 TCGAGTGTCAGTTAAAATGTAATTGTGTGATCTATGACATTCACGAAGGACCCGAAAGCTAAATT
128 TCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGAC-TTCAC-AAGGACCTGAAAGCTGAATT
91235 TGATT
191 TGATT
91240 CTCCAGTTAA
Statistics
Matches: 513, Mismatches: 74, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
399 1 0.00
400 68 0.13
401 7 0.01
402 95 0.19
404 1 0.00
407 30 0.06
408 14 0.03
409 1 0.00
413 3 0.01
414 39 0.08
415 13 0.03
416 238 0.46
417 3 0.01
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.41
Consensus pattern (405 bp):
TCATGAAGAACTCAAAAACCAATTTTAATGTTTCGATTCTTAAAAATGCTTCTTAAATTTTGTGG
TTTTGATTGCCGGTCTATTTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAAGTTGTTCA
AGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACTTCACAAGGACCTGAAAGCTGAATTTGATT
AATGAGTTTCATGGAGGATTCGAGAGAGAATTTTTATGTTTCGTCTCCATAAACAAATATATTTT
TTGCTGGATTATTTAACAAATGATCCTCATACTTTTATGCTTTATGCTATTGAATCATTTACAAT
CATAGGTTGGACGATCTAACCAGCTTTGACTTTTGTATTTTCTATTCTATTTGTCCCATCAAGGT
AATCTAATGATCTAA
Found at i:92580 original size:443 final size:443
Alignment explanation
Indices: 91738--92954 Score: 1657
Period size: 442 Copynumber: 2.8 Consensus size: 443
91728 TGGGTCCCAT
* * * * * *
91738 TCTCAATAAACAAATA-TTTTTTTGTTGAATTATTTATCAAATGATCCCT-ATACTCTTACGCTT
1 TCTCCATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGA-CCCTCAGACTTTTATGCTT
* * * * * *
91801 TTTACTATTTAGTCCCTCACAAGTTCTGGGTTGGACGA-TTGAACGTTTC-GTCTTTAATTCTTA
65 TATGCTATTTAGTTCCTCACAATTTCTGGGTTGGACGACTT-AACGTTTCAGACTTTAATTCTTT
* * * * * *
91864 TAGTTTTTGTTTTGCTTGTCCGATTAAGCTGA--TTCAAGTGTCTATTAAAAGGTAATTCCATAA
129 TATTTTTTGTTTTGCTTGTCCGATCAAGGTGATTTTCGAGTGTCTATTAAAAGGTAATTTCATGA
* * * * ** * *
91927 TCTACAACTTTCATGAAGGACTTAGAAGCCCATTTTAATGTTTTGATTCTAAAAAATGCTTCTGA
194 TCTACAACTTCCATGAAGGACTCAAAAACTAATTTTAATGTTTTGATTTTAAAAAATGCTTTTGA
** * * * * * *
91992 AATTTTGTGGGGTCGATTGCCGGTCTCTCTAATATTGTATAATTTTCGGTCCACTTGTCCGATTG
259 AATTTTGTGGTCTTGATTGCCGGTCTATTTGATATCGTATAATTTTTGGTCCACTTGTCCGATTG
* ** * * *
92057 AGATTGCTCAATTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGTTAAGGGCCTGAAAA
324 AGGTTATTCAAGTGTCGGTTAAAAGATTATTGTGTGATCTACGACTTTCGTTAAGGGCCTCAAAA
* * * * *
92122 CTGAATTTGATTAATGAGTTTCGTGGAGGGTTTCGAGAGGGAAATTTTGTGTTTGG
389 CTGAATTTAATTAATGAGTATCGTGGAGGG-TTCAAGAGGGAAAGTTTATGTTTGG
92178 -CTCCATAAACAAATATTTTTTTTTTGCTGGATTATTTATCAAATGACCCTCAGACTTTTATGCT
1 TCTCCATAAACAAATA--TTTTTTTTGCTGGATTATTTATCAAATGACCCTCAGACTTTTATGCT
92242 TTATGCTATTTAGTTCCTCACAATTTCTGGGTTGGACGACTTAACGTTTCAG-CTTTAATTCTTT
64 TTATGCTATTTAGTTCCTCACAATTTCTGGGTTGGACGACTTAACGTTTCAGACTTTAATTCTTT
* **
92306 TATTTTTTGTTTTGCTTGT-TGATCAAGGTGATTTTCGAGTGTCTATTAAAACATAATTTCATGA
129 TATTTTTTGTTTTGCTTGTCCGATCAAGGTGATTTTCGAGTGTCTATTAAAAGGTAATTTCATGA
92370 TCTACAACTTCCATGAAGGACTCAAAAACTAATTTTAATGTTTTGATTTTAAAAAATGCTTTTGA
194 TCTACAACTTCCATGAAGGACTCAAAAACTAATTTTAATGTTTTGATTTTAAAAAATGCTTTTGA
* * * * *
92435 AAGTTTGTGATCTTGGTTGCCGGTCTATTTGATATCGTATAATTTTTGATCCACTTGTCTGATTG
259 AATTTTGTGGTCTTGATTGCCGGTCTATTTGATATCGTATAATTTTTGGTCCACTTGTCCGATTG
* * * *
92500 AGGTTATTCAAGTGTCGGTTACAAGATTATTGTGTGATTTACGGCTTTCGTTAAGGGCCTCAAAG
324 AGGTTATTCAAGTGTCGGTTAAAAGATTATTGTGTGATCTACGACTTTCGTTAAGGGCCTCAAAA
* *
92565 CTGAATTTAATTAATGAGTATCGTGGATGGTTCAATAGGGAAAGTTTATGTTTGG
389 CTGAATTTAATTAATGAGTATCGTGGAGGGTTCAAGAGGGAAAGTTTATGTTTGG
* * * *
92620 TCTCCATAAACAAATATTGTTTTTGCCGGATTATTTATCAAATGATCCTCAGACTTTTATGTTTT
1 TCTCCATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGACCCTCAGACTTTTATGCTTT
*
92685 ATGCTATTTAGTTCCTCACAATTTCTAGGTTGGACGACTT-ACTGTTT-AGACTTTAATTCTTTT
66 ATGCTATTTAGTTCCTCACAATTTCTGGGTTGGACGACTTAAC-GTTTCAGACTTTAATTCTTTT
* *
92748 ATTTTTTGTTTTGCTTATCCAATCAAGGTGATTTTCGAGTGTCTATTAAAAGGTAATTTCATGAT
130 ATTTTTTGTTTTGCTTGTCCGATCAAGGTGATTTTCGAGTGTCTATTAAAAGGTAATTTCATGAT
* *
92813 CTACAACTTCCATGAAGGATTC-AAAAGTCAATTTTAATGTTTTGATTTTAAAAAATGCTTTTGA
195 CTACAACTTCCATGAAGGACTCAAAAACT-AATTTTAATGTTTTGATTTTAAAAAATGCTTTTGA
* *
92877 AATTTTGTGGTCTTGATTGCTGGTCTATTTGATATCGTATACTTTTTGGTCCACTTGTCCGATTG
259 AATTTTGTGGTCTTGATTGCCGGTCTATTTGATATCGTATAATTTTTGGTCCACTTGTCCGATTG
92942 AGGTTATTCAAGT
324 AGGTTATTCAAGT
92955 ACTACCTCCG
Statistics
Matches: 687, Mismatches: 77, Indels: 24
0.87 0.10 0.03
Matches are distributed among these distances:
439 14 0.02
440 4 0.01
441 136 0.20
442 298 0.43
443 235 0.34
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (443 bp):
TCTCCATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGACCCTCAGACTTTTATGCTTT
ATGCTATTTAGTTCCTCACAATTTCTGGGTTGGACGACTTAACGTTTCAGACTTTAATTCTTTTA
TTTTTTGTTTTGCTTGTCCGATCAAGGTGATTTTCGAGTGTCTATTAAAAGGTAATTTCATGATC
TACAACTTCCATGAAGGACTCAAAAACTAATTTTAATGTTTTGATTTTAAAAAATGCTTTTGAAA
TTTTGTGGTCTTGATTGCCGGTCTATTTGATATCGTATAATTTTTGGTCCACTTGTCCGATTGAG
GTTATTCAAGTGTCGGTTAAAAGATTATTGTGTGATCTACGACTTTCGTTAAGGGCCTCAAAACT
GAATTTAATTAATGAGTATCGTGGAGGGTTCAAGAGGGAAAGTTTATGTTTGG
Found at i:93313 original size:30 final size:31
Alignment explanation
Indices: 93278--93354 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
93268 GGTGTCAATT
*
93278 CAACACATGGCAAAACAAAGTTTCAATT-GA
1 CAACACATAGCAAAACAAAGTTTCAATTCGA
* * *
93308 CAACACGTAGCAGAACACAGTTTCAATTCGA
1 CAACACATAGCAAAACAAAGTTTCAATTCGA
*
93339 CAACACGTAGCCAAAA
1 CAACACATAG-CAAAA
93355 AAATTCAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 24 0.60
31 12 0.30
32 4 0.10
ACGTcount: A:0.44, C:0.25, G:0.14, T:0.17
Consensus pattern (31 bp):
CAACACATAGCAAAACAAAGTTTCAATTCGA
Found at i:93344 original size:31 final size:30
Alignment explanation
Indices: 93291--93349 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
93281 CACATGGCAA
93291 AACAAAGTTTCAATTGACAACACGTAGCAG
1 AACAAAGTTTCAATTGACAACACGTAGCAG
*
93321 AACACAGTTTCAATTCGACAACACGTAGC
1 AACAAAGTTTCAATT-GACAACACGTAGC
93350 CAAAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (30 bp):
AACAAAGTTTCAATTGACAACACGTAGCAG
Found at i:99376 original size:10 final size:10
Alignment explanation
Indices: 99361--99385 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
99351 TACGCCTTTT
99361 TTCTTTCTTC
1 TTCTTTCTTC
99371 TTCTTTCTTC
1 TTCTTTCTTC
99381 TTCTT
1 TTCTT
99386 CCCCAAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTCTTTCTTC
Found at i:102506 original size:25 final size:24
Alignment explanation
Indices: 102439--102506 Score: 59
Period size: 25 Copynumber: 2.7 Consensus size: 24
102429 AATTGGTTAT
*
102439 AATATTTAAATTAAA-TTTGAAGTA
1 AATATTT-AATTAAATTTTGAAGGA
*
102463 AATAATTAATTAAATATTTTG-AGGA
1 AATATTTAATT-AA-ATTTTGAAGGA
102488 AATATTTCAATTACAATTT
1 AATATTT-AATTA-AATTT
102507 CACTGAATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
23 4 0.11
24 8 0.22
25 15 0.42
26 9 0.25
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (24 bp):
AATATTTAATTAAATTTTGAAGGA
Done.