Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 100 of 185
Found at i:31567017 original size:21 final size:21
Alignment explanation
Indices: 31566991--31567038 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31566981 GTTATCGATT
31566991 CAACTCCAAGAGG-AGCCAGTC
1 CAACTCCAAG-GGTAGCCAGTC
**
31567012 CAACTCCAAGGGTAGTTAGTC
1 CAACTCCAAGGGTAGCCAGTC
31567033 CAACTC
1 CAACTC
31567039 AGATGAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (21 bp):
CAACTCCAAGGGTAGCCAGTC
Found at i:31567099 original size:84 final size:84
Alignment explanation
Indices: 31567006--31567206 Score: 278
Period size: 84 Copynumber: 2.4 Consensus size: 84
31566996 CCAAGAGGAG
31567006 CCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCACCTCATCGAGTCAATCC
1 CCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCACCTCATCGAGTCAATCC
*
31567071 CATAGCTCAACTTCAATTA
66 CATAGCTCAACCTCAATTA
* ** * * *
31567090 CCAGTCCAACTCCAATGGTAGTTAGTCCAACTTGGATGAGGACGTCCACCTCATCTAGTCAATCT
1 CCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCACCTCATCGAGTCAATCC
*
31567155 CATAGCTCAACCTCAGTTA
66 CATAGCTCAACCTCAATTA
* * * *
31567174 TCAGTTCAACTCTAAGAGG-AGTCAGTCCAACTC
1 CCAGTCCAACTCCAAG-GGTAGTTAGTCCAACTC
31567207 CAAGGGTAGT
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 100 0.98
85 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (84 bp):
CCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCACCTCATCGAGTCAATCC
CATAGCTCAACCTCAATTA
Found at i:31567141 original size:189 final size:189
Alignment explanation
Indices: 31566902--31567246 Score: 593
Period size: 189 Copynumber: 1.8 Consensus size: 189
31566892 CAAGAGGATT
31566902 CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCC
1 CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCC
*
31566967 ATAGCTCAACTTCAGTTATC-GATTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAG
66 ATAGCTCAACCTCAGTTATCAG-TTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAG
31567031 TCCAACTCAGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTAC
130 TCCAACTCAGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTAC
* * * * *
31567091 CAGTCCAACTCCAATGGTAGTTAGTCCAACTTGGATGAGGACGTCCACCTCATCTAGTCAATCTC
1 CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCC
* *
31567156 ATAGCTCAACCTCAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAAGGGTAGTTAGT
66 ATAGCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGT
*
31567221 CCAACTCGGATGAGGACATCCACCTC
131 CCAACTCAGATGAGGACATCCACCTC
31567247 TAGCTCAACC
Statistics
Matches: 146, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
189 145 0.99
190 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.23
Consensus pattern (189 bp):
CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCC
ATAGCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGT
CCAACTCAGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTAC
Found at i:31567221 original size:21 final size:21
Alignment explanation
Indices: 31567174--31567227 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
31567164 ACCTCAGTTA
* *
31567174 TCAGTTCAACTCTAAGAGGAG
1 TCAGTCCAACTCCAAGAGGAG
31567195 TCAGTCCAACTCCAAG-GGTAG
1 TCAGTCCAACTCCAAGAGG-AG
*
31567216 TTAGTCCAACTC
1 TCAGTCCAACTC
31567228 GGATGAGGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGAGGAG
Found at i:31567256 original size:90 final size:90
Alignment explanation
Indices: 31567157--31567426 Score: 425
Period size: 90 Copynumber: 3.0 Consensus size: 90
31567147 GTCAATCTCA
* *
31567157 TAGCTCAACCTCAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAAGGGTAGTTAGTC
1 TAGCTCAACCTCAGTTATCAATTCAACTCTAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
31567222 CAACTCGGATGAGGACATCCACCTC
66 CAACTCGGATGAGGACATCCACCTC
*
31567247 TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
1 TAGCTCAACCTCAGTTATCAATTCAACTCTAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
* *
31567312 CAAATCGGATGAGGATATCCACCTC
66 CAACTCGGATGAGGACATCCACCTC
** * *
31567337 TAGCTCAACCTCAGTTATCAATTCAACT-TCAAGAGGAGTTAGTCCTTCTCCAAGGGTAGTCAAT
1 TAGCTCAACCTCAGTTATCAATTCAACTCT-AAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGT
**
31567401 CCAACTCAAATGAGGACATCCACCTC
65 CCAACTCGGATGAGGACATCCACCTC
31567427 ATCTAGTCAA
Statistics
Matches: 165, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
90 165 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (90 bp):
TAGCTCAACCTCAGTTATCAATTCAACTCTAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
CAACTCGGATGAGGACATCCACCTC
Found at i:31567295 original size:21 final size:21
Alignment explanation
Indices: 31567270--31567314 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
31567260 GTTATCAATT
31567270 CAACTCCAAGAGG-AGTTAGTC
1 CAACTCCAAG-GGTAGTTAGTC
31567291 CAACTCCAAGGGTAGTTAGTC
1 CAACTCCAAGGGTAGTTAGTC
31567312 CAA
1 CAA
31567315 ATCGGATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
CAACTCCAAGGGTAGTTAGTC
Found at i:31572770 original size:41 final size:41
Alignment explanation
Indices: 31572688--31572839 Score: 107
Period size: 41 Copynumber: 3.7 Consensus size: 41
31572678 GAATATTGTC
* * * * * **
31572688 GCTAATGTTTGGGGTTTTAGCGACGTTTTTAGTTTTGCGCC-
1 GCTAATGCTCGGGGTTTTAGCGGCGTTTATAG-ATAACGCCG
* *
31572729 GCTAATGCTCGTGGTTTTAGCGGCGTTTCT-GATTCAACGCCG
1 GCTAATGCTCGGGGTTTTAGCGGCGTTTATAGA-T-AACGCCG
* *
31572771 GC-AAAGACT-GGGGTTTTAGCGGCGTTTATAGATAA-GCACT
1 GCTAATG-CTCGGGGTTTTAGCGGCGTTTATAGATAACGC-CG
*
31572811 GCTAATGCTCGGGGTTTTTAGCGGAGTTT
1 GCTAATGCTCGGGG-TTTTAGCGGCGTTT
31572840 TTGACAAAGC
Statistics
Matches: 88, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
39 2 0.02
40 9 0.10
41 58 0.66
42 19 0.22
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.36
Consensus pattern (41 bp):
GCTAATGCTCGGGGTTTTAGCGGCGTTTATAGATAACGCCG
Found at i:31573473 original size:7 final size:7
Alignment explanation
Indices: 31573461--31573509 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
31573451 CTTGTATGGA
31573461 TTTAGGG
1 TTTAGGG
*
31573468 TTTAGGA
1 TTTAGGG
*
31573475 TTTAAGG
1 TTTAGGG
31573482 TTTAGGG
1 TTTAGGG
*
31573489 TTTAGGA
1 TTTAGGG
31573496 TTTAAGGG
1 TTT-AGGG
31573504 -TTAGGG
1 TTTAGGG
31573510 GTTAAAAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
6 4 0.11
7 28 0.80
8 3 0.09
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (7 bp):
TTTAGGG
Found at i:31573487 original size:21 final size:21
Alignment explanation
Indices: 31573461--31573509 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
31573451 CTTGTATGGA
31573461 TTTAGGGTTTAGGATTTAAGG
1 TTTAGGGTTTAGGATTTAAGG
31573482 TTTAGGGTTTAGGATTTAAGG
1 TTTAGGGTTTAGGATTTAAGG
*
31573503 GTTAGGG
1 TTTAGGG
31573510 GTTAAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (21 bp):
TTTAGGGTTTAGGATTTAAGG
Found at i:31573790 original size:13 final size:14
Alignment explanation
Indices: 31573772--31573802 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31573762 GTGGACACTT
31573772 GTTT-GGATTTAGG
1 GTTTGGGATTTAGG
31573785 GTTTGGGATTTAGG
1 GTTTGGGATTTAGG
31573799 GTTT
1 GTTT
31573803 AGGGGTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (14 bp):
GTTTGGGATTTAGG
Found at i:31575051 original size:336 final size:334
Alignment explanation
Indices: 31574213--31575320 Score: 1184
Period size: 336 Copynumber: 3.3 Consensus size: 334
31574203 CGTGTTTAAA
* * * * *
31574213 AAAATGCCAGAACTGTGCATTGAAGCTTAATAAAACGGCGCAGTTTCCGATTAGAACTTTAACA-
1 AAAACGCCAGAAATGTGCATTAAAGCTTAATAAAACGGCGCCGTTTCGGATTAGAACTTTAA-AT
* * * * * * *
31574277 ATTAGTGGCGTTTTTGTTA-AAAACACCGCTAATGCT-GAAGTAATAGCGGCGTTTGTACAAGAA
65 TTTAGTGGCG-CTTT-TTAGAAAACGCCGCAAATG-TACAAGCAATAGCGGCGTTTGT-CCAGAA
* * * *
31574340 AT-GCCGCAAAAGTGACTTAAAATTTTGGCTGAACGACGCCGTTTCTGTCCACGATTTTTA-ACT
126 ATCGCCGCAAAAGTGTCTTAAAATTTTGTCTAAACGACGCCGTTTCTGTACACG-TTTTTATACT
* * * * * *
31574403 TAGTATTTTCTCTATATTAATTAAACGGCGCCGTTTATGTTAAATTTTAGTGGCATTTGTTCAGG
190 TAGCATTTTCTCTATATTAATTCAACGGCTCCGTTTCTGTT-AATTTTAGTGGCGTTT-TTCACG
* * * * * * * *
31574468 AAACGCCGCAAAAGTGACTTGAAATATTGGCTAAAAGTCGACGTCTAACTTAAGCAAATTAATTT
253 AAACGCTGCAAAAGTGACTTAAAATATTGCCTAAACGACCACGTTTAGCTTAAGCAAATTAATTT
* *
31574533 TTAGTGGCATTTTAAAGG
318 TTACTGGCATTTTACA-G
* * * *
31574551 AAAACGCCAGAAATGTGCATTAAATCTTAACAAAACGGTGCCGTTTCGGATTAGAACCTT-AATT
1 AAAACGCCAGAAATGTGCATTAAAGCTTAATAAAACGGCGCCGTTTCGGATTAGAACTTTAAATT
* * * * *
31574615 CTTTGTGGCGCTTCTTTAG-AAACGCCGCAAATATACAAGCTATAGCGGCGTTTGTTCA-ATAAA
66 -TTAGTGGCGCTT-TTTAGAAAACGCCGCAAATGTACAAGCAATAGCGGCGTTTGTCCAGA-AAT
* * * *
31574678 CGCCGTATAAGTGTCTTAAAATTTT-TGGTAAACGACGCCGTCTCTGTACACGTTTTTATACTTA
128 CGCCGCAAAAGTGTCTTAAAATTTTGT-CTAAACGACGCCGTTTCTGTACACGTTTTTATACTTA
* **
31574742 GCATTTTCTCTATATTAATTCAACGGCTCCGTTTCTGTTAATTTCTTGTGGCGTTTTTACATAAA
192 GCATTTTCTCTATATTAATTCAACGGCTCCGTTTCTGTTAATTT-TAGTGGCGTTTTT-CACGAA
* * **
31574807 ACGCTGCAAAAGTGACATAAAATATTGCCTAAACGGCTTCGTTTAGCTTAAGCAAATTAATTTTT
255 ACGCTGCAAAAGTGACTTAAAATATTGCCTAAACGACCACGTTTAGCTTAAGCAAATTAATTTTT
*
31574872 ACTGGCGTTTTAGCAG
320 ACTGGCATTTTA-CAG
*
31574888 AAAACGCCAAAAATGTGC-TTAAAGCTTAATAAAACGGCGCCGTTTCGGATTAGAACTTTAAATT
1 AAAACGCCAGAAATGTGCATTAAAGCTTAATAAAACGGCGCCGTTTCGGATTAGAACTTTAAATT
* * * *
31574952 TTAGTGGCGCTTTTTAGAAAACGCCGCAAATGTACAAGCAATAGCGGCATTTGTCCAGGATTCAC
66 TTAGTGGCGCTTTTTAGAAAACGCCGCAAATGTACAAGCAATAGCGGCGTTTGTCCAGAAATCGC
* *
31575017 CGCAAAATTGTCTTAAAATTTTGTCTAAACGACGCCATTTCTGTACTA-GTTTTT-TAACTTAGC
131 CGCAAAAGTGTCTTAAAATTTTGTCTAAACGACGCCGTTTCTGTAC-ACGTTTTTAT-ACTTAGC
* * *
31575080 ATTTTCTCTAAATTAATCCAACGG-TGCCGTTTCTCTTAATTTATAGTGGCGTTTTTGCACGAAA
194 ATTTTCTCTATATTAATTCAACGGCT-CCGTTTCTGTTAATTT-TAGTGGCGTTTTT-CACGAAA
* * * *
31575144 CGCTGCAAAA-TGACTTAAAATATTGTCTAAACGACCCCGTTTTGCTTAAGAAAATTAATTTTTA
256 CGCTGCAAAAGTGACTTAAAATATTGCCTAAACGACCACGTTTAGCTTAAGCAAATTAATTTTTA
**
31575208 CTACCATTTTTACAG
321 CTGGCA-TTTTACAG
* * * * * * * *
31575223 AAAATGCCAGAACTGTGCAATAAAGCTTAATTAAACGGTGCCGTTTCAG-TTTGAACTTTAATTT
1 AAAACGCCAGAAATGTGCATTAAAGCTTAATAAAACGGCGCCGTTTCGGATTAGAACTTTAAATT
** *
31575287 TTAGTGGCATTTTTTTAAAAAACGCCGCAAATGT
66 TTAGTGGC-GCTTTTTAGAAAACGCCGCAAATGT
31575321 TTCTTAAACT
Statistics
Matches: 648, Mismatches: 100, Indels: 46
0.82 0.13 0.06
Matches are distributed among these distances:
335 97 0.15
336 272 0.42
337 218 0.34
338 61 0.09
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (334 bp):
AAAACGCCAGAAATGTGCATTAAAGCTTAATAAAACGGCGCCGTTTCGGATTAGAACTTTAAATT
TTAGTGGCGCTTTTTAGAAAACGCCGCAAATGTACAAGCAATAGCGGCGTTTGTCCAGAAATCGC
CGCAAAAGTGTCTTAAAATTTTGTCTAAACGACGCCGTTTCTGTACACGTTTTTATACTTAGCAT
TTTCTCTATATTAATTCAACGGCTCCGTTTCTGTTAATTTTAGTGGCGTTTTTCACGAAACGCTG
CAAAAGTGACTTAAAATATTGCCTAAACGACCACGTTTAGCTTAAGCAAATTAATTTTTACTGGC
ATTTTACAG
Found at i:31576115 original size:10 final size:10
Alignment explanation
Indices: 31576100--31576124 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31576090 GCTCTGTAGT
31576100 TGTTAAACAA
1 TGTTAAACAA
31576110 TGTTAAACAA
1 TGTTAAACAA
31576120 TGTTA
1 TGTTA
31576125 CACGATTTCT
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:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (10 bp):
TGTTAAACAA
Found at i:31576631 original size:13 final size:13
Alignment explanation
Indices: 31576615--31576678 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
31576605 TGAAATATAT
*
31576615 TACATAACTTAAA
1 TACATTACTTAAA
31576628 TACATTACTTACTAA
1 TACATTACTTA--AA
31576643 -A-ATTTACTTAAA
1 TACA-TTACTTAAA
*
31576655 TATATTACTTAAA
1 TACATTACTTAAA
*
31576668 TACATGACTTA
1 TACATTACTTA
31576679 CTAAAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
12 2 0.05
13 30 0.70
14 9 0.21
15 2 0.05
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (13 bp):
TACATTACTTAAA
Found at i:31576634 original size:18 final size:17
Alignment explanation
Indices: 31576593--31576636 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
31576583 TTACATTACT
*
31576593 TACATTACTTACTGAAA
1 TACATTACTAACTGAAA
* *
31576610 TATATTACATAACTTAAA
1 TACATTAC-TAACTGAAA
31576628 TACATTACT
1 TACATTACT
31576637 TACTAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (17 bp):
TACATTACTAACTGAAA
Found at i:31576636 original size:31 final size:31
Alignment explanation
Indices: 31576578--31576636 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
31576568 ATTTTCCGCT
* *
31576578 ATATATTACATTACTTACATTACTTACTGAA
1 ATATATTACATAACTTACAATACTTACTGAA
31576609 ATATATTACATAACTTA-AATACATTACT
1 ATATATTACATAACTTACAATAC-TTACT
31576637 TACTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.41
Consensus pattern (31 bp):
ATATATTACATAACTTACAATACTTACTGAA
Found at i:31576672 original size:40 final size:38
Alignment explanation
Indices: 31576577--31576724 Score: 140
Period size: 40 Copynumber: 3.9 Consensus size: 38
31576567 TATTTTCCGC
** * *
31576577 TATATATTACATTACTTACATTACTTACTGAAATAT-A-
1 TATATATTAC-TTAAATACATTACTTACTAAAATTTAAG
* * **
31576614 T-TACATAACTTAAATACATTACTTACTAAAATTTACT
1 TATATATTACTTAAATACATTACTTACTAAAATTTAAG
*
31576651 TAAATATATTACTTAAATACATGACTTACTAAAATTTAAG
1 T--ATATATTACTTAAATACATTACTTACTAAAATTTAAG
**
31576691 TATATATTACATTACTTACATTACTTACTAAAAT
1 TATATATTAC-TTAAATACATTACTTACTAAAAT
31576725 ATATTACATT
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
35 21 0.23
36 6 0.07
37 2 0.02
38 9 0.10
39 20 0.22
40 32 0.36
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (38 bp):
TATATATTACTTAAATACATTACTTACTAAAATTTAAG
Found at i:31576736 original size:18 final size:18
Alignment explanation
Indices: 31576710--31576761 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
31576700 CATTACTTAC
31576710 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
* *
31576727 ATTACATTACTTAAATGT
1 ATTACATTACTAAAATAT
*
31576745 ATTAAATTACTTAAAAT
1 ATTACATTAC-TAAAAT
31576762 TTATACAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 5 0.17
18 19 0.66
19 5 0.17
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:31576783 original size:114 final size:112
Alignment explanation
Indices: 31576577--31576783 Score: 292
Period size: 114 Copynumber: 1.8 Consensus size: 112
31576567 TATTTTCCGC
* *
31576577 TATATATTACATTACTTACATTACTTACTGAAATATATTACATAACTTAAATACATTACTTACTA
1 TATATATTACATTACTTACATTACTTACTAAAATATATTACATAACTTAAATACATTAATTACTA
*
31576642 AAATTTACTTAAATATATTACTTAAATACATGACTTACTAAAATTTAAG
66 AAATTTAC-TAAATATATTA-TAAAATACATGACTTACTAAAATTTAAG
* **
31576691 TATATATTACATTACTTACATTACTTACTAAAATATATTACATTACTTAAATGTATTAAATTACT
1 TATATATTACATTACTTACATTACTTACTAAAATATATTACATAACTTAAATACATT-AATTAC-
31576756 TAAAATTTA-TACAGATATATT-TAAAATA
64 TAAAATTTACTA-A-ATATATTATAAAATA
31576784 TTTATATATG
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
114 61 0.73
115 6 0.07
116 16 0.19
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (112 bp):
TATATATTACATTACTTACATTACTTACTAAAATATATTACATAACTTAAATACATTAATTACTA
AAATTTACTAAATATATTATAAAATACATGACTTACTAAAATTTAAG
Found at i:31577004 original size:44 final size:44
Alignment explanation
Indices: 31576941--31577746 Score: 415
Period size: 44 Copynumber: 18.5 Consensus size: 44
31576931 TAACATTTCT
*
31576941 TACATAACTTACATAATACATAATACACAACTTAATTAATATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
* *
31576985 TACATAACATACGTAATACATAATACACAACTTAATTAAGATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
*
31577029 TACATAACATACATAATACATAATACAC-A--TAACTTACATA--G
1 TACATAACATACATAATACATAATACACAACTTAA-TTA-ATATTA
* * *
31577070 TACAT---A-AC-T-A-ACATTATACACAACTTACA-TACTA-CA
1 TACATAACATACATAATACATAATACACAACTTA-ATTAATATTA
** * * *
31577106 TTTATTACATA-ACT--TACATTATACACAACTTAAATAATATTA
1 TACATAACATACA-TAATACATAATACACAACTTAATTAATATTA
*
31577148 TACATAACGTACATAATACATAATACACAACTTAATTAATATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
* *
31577192 TACATAACGTACATAATACATAATACACAACTTAATTAAGATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
*
31577236 TACATAACATACATAATACATAATACAC-A--TAACTTACATA--G
1 TACATAACATACATAATACATAATACACAACTTAA-TTA-ATATTA
* ** *
31577277 TACAT---A-AC-T-A-ACATTATACACAACTTACGTAA-CTTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
* ** * * * **
31577313 -A-ATAACGTACATAATACATAACTTTGATAACTAACATTATACACAA
1 TACATAACATACATAATACATAA--TACACAACTTA-ATTA-ATATTA
** * ** *
31577359 CTTACAT-AC-TACAATTCTTACATAACTTACATTATACACAATTTAAATAATATTA
1 --TACATAACATAC-A-TAATACATAA--TACA-CA-ACTTAA-TT-AATAT---TA
* *
31577414 TACATAACGTACATAATATATAATACACAACTTAATTAATATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
* * * *
31577458 TACATAACGTACATAATACACAATAAACAACTTAATTAAGATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
*
31577502 TACATAACATACATAATACATAATACAC-A--TAACTTACATA--G
1 TACATAACATACATAATACATAATACACAACTTAA-TTA-ATATTA
* * ** * *
31577543 TACATAAC-TAACATTATACACAACTTACGTAACTTAAATAATGTACATAA
1 TACATAACAT-ACATAATACATAA--TACACAACTTAATTAA--T--ATTA
* *** * *
31577593 TACATAACTTTGGTAACTGACATTATACACAACTT-A--CATA--A
1 TACATAACATACATAA-T-ACATAATACACAACTTAATTAATATTA
** * * * *
31577634 TACATTTCTTACATAACTTTCATTATACACAACTTAAATAATATTA
1 TACATAACATACATAA--TACATAATACACAACTTAATTAATATTA
*
31577680 TACATAACGTACATAATACATAATACACAACTTAATTAATATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
* *
31577724 TACATAACGTACCTAATACATAA
1 TACATAACATACATAATACATAA
31577747 ATATATATCA
Statistics
Matches: 592, Mismatches: 94, Indels: 152
0.71 0.11 0.18
Matches are distributed among these distances:
34 22 0.04
35 8 0.01
36 9 0.02
37 8 0.01
38 5 0.01
39 2 0.00
40 4 0.01
41 92 0.16
42 20 0.03
43 21 0.04
44 285 0.48
45 4 0.01
46 19 0.03
47 5 0.01
48 6 0.01
49 9 0.02
50 33 0.06
51 9 0.02
52 11 0.02
53 13 0.02
54 3 0.01
55 4 0.01
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.32
Consensus pattern (44 bp):
TACATAACATACATAATACATAATACACAACTTAATTAATATTA
Found at i:31577058 original size:25 final size:25
Alignment explanation
Indices: 31576942--31577283 Score: 160
Period size: 25 Copynumber: 14.9 Consensus size: 25
31576932 AACATTTCTT
31576942 ACATAACTTACATAATACATAATAC
1 ACATAACTTACATAATACATAATAC
* *
31576967 AC--AACTTA-AT--TA-ATATTAT
1 ACATAACTTACATAATACATAATAC
* *
31576986 ACATAACATACGTAATACATAATAC
1 ACATAACTTACATAATACATAATAC
* * *
31577011 AC--AACTTA-AT--TA-AGATTAT
1 ACATAACTTACATAATACATAATAC
*
31577030 ACATAACATACATAATACATAATAC
1 ACATAACTTACATAATACATAATAC
*
31577055 ACATAACTTACATAGTACATAACTA-
1 ACATAACTTACATAATACATAA-TAC
* * *
31577080 ACATTA--TACACAACTTACATACTAC
1 ACATAACTTACATAA--TACATAATAC
* * *
31577105 A-TTTA-TTACATAACTTACATTATAC
1 ACATAACTTACATAA--TACATAATAC
* *
31577130 AC--AACTT--A-AATA-ATATTAT
1 ACATAACTTACATAATACATAATAC
*
31577149 ACATAACGTACATAATACATAATAC
1 ACATAACTTACATAATACATAATAC
* *
31577174 AC--AACTTA-AT--TA-ATATTAT
1 ACATAACTTACATAATACATAATAC
*
31577193 ACATAACGTACATAATACATAATAC
1 ACATAACTTACATAATACATAATAC
* * *
31577218 AC--AACTTA-AT--TA-AGATTAT
1 ACATAACTTACATAATACATAATAC
*
31577237 ACATAACATACATAATACATAATAC
1 ACATAACTTACATAATACATAATAC
*
31577262 ACATAACTTACATAGTACATAA
1 ACATAACTTACATAATACATAA
31577284 CTAACATTAT
Statistics
Matches: 232, Mismatches: 48, Indels: 74
0.66 0.14 0.21
Matches are distributed among these distances:
19 32 0.14
20 10 0.04
21 24 0.10
22 16 0.07
23 28 0.12
24 18 0.08
25 102 0.44
26 2 0.01
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.31
Consensus pattern (25 bp):
ACATAACTTACATAATACATAATAC
Found at i:31577074 original size:16 final size:15
Alignment explanation
Indices: 31577055--31577137 Score: 61
Period size: 16 Copynumber: 5.7 Consensus size: 15
31577045 TACATAATAC
31577055 ACATAACTTACATAGT
1 ACATAACTTACATA-T
*
31577071 ACATAACTAACATTAT
1 ACATAACTTACA-TAT
*
31577087 ACACAACTTACATACT
1 ACATAACTTACATA-T
31577103 ACAT---TT--AT-T
1 ACATAACTTACATAT
31577112 ACATAACTTACATTAT
1 ACATAACTTACA-TAT
*
31577128 ACACAACTTA
1 ACATAACTTA
31577138 AATAATATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
9 5 0.09
11 2 0.04
12 2 0.04
13 2 0.04
14 1 0.02
15 3 0.06
16 36 0.68
17 2 0.04
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.33
Consensus pattern (15 bp):
ACATAACTTACATAT
Found at i:31577075 original size:32 final size:32
Alignment explanation
Indices: 31577029--31577106 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
31577019 ATTAAGATTA
31577029 TACATAACATACATAA-T-ACATAATACACATAACT
1 TACAT-AC-TACATAACTAACATAATACAC--AACT
* *
31577063 TACATAGTACATAACTAACATTATACACAACT
1 TACATACTACATAACTAACATAATACACAACT
31577095 TACATACTACAT
1 TACATACTACAT
31577107 TTATTACATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 22 0.56
33 2 0.05
34 15 0.38
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.28
Consensus pattern (32 bp):
TACATACTACATAACTAACATAATACACAACT
Found at i:31577281 original size:16 final size:15
Alignment explanation
Indices: 31577262--31577336 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 15
31577252 TACATAATAC
31577262 ACATAACTTACATAGT
1 ACATAACTTACATA-T
*
31577278 ACATAACTAACATTAT
1 ACATAACTTACA-TAT
* *
31577294 ACACAACTTACGTAACTT
1 ACATAACTTACAT-A--T
* *
31577312 AAATAACGTACATAAT
1 ACATAACTTACAT-AT
31577328 ACATAACTT
1 ACATAACTT
31577337 TGATAACTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
15 1 0.02
16 30 0.67
17 2 0.04
18 12 0.27
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (15 bp):
ACATAACTTACATAT
Found at i:31577336 original size:25 final size:25
Alignment explanation
Indices: 31576941--31577226 Score: 71
Period size: 21 Copynumber: 12.5 Consensus size: 25
31576931 TAACATTTCT
31576941 TACATAACTT-ACATAA-TACATAA
1 TACATAACTTAACATAACTACATAA
* * *
31576964 TACACAACTTAA-TTAA-T--ATTA
1 TACATAACTTAACATAACTACATAA
* *
31576985 TACATAACAT-ACGTAA-TACATAA
1 TACATAACTTAACATAACTACATAA
* * * *
31577008 TACACAACTT-A-ATTA--AGATTA
1 TACATAACTTAACATAACTACATAA
*
31577029 TACATAACAT-ACATAA-TACATAA
1 TACATAACTTAACATAACTACATAA
*
31577052 TACACATAACTT-ACAT-AGTACAT-A
1 T--ACATAACTTAACATAACTACATAA
* *
31577076 -AC-TAACATTATACACAACTTACATAC
1 TACATAAC-TTA-ACATAAC-TACATAA
* *
31577102 TACATTTA-TT-ACATAACTTACATTA
1 TACA-TAACTTAACATAAC-TACATAA
* *
31577127 TACACAACTTAA-ATAA-T--ATTA
1 TACATAACTTAACATAACTACATAA
*
31577148 TACATAACGT-ACATAA-TACATAA
1 TACATAACTTAACATAACTACATAA
* * *
31577171 TACACAACTTAA-TTAA-T--ATTA
1 TACATAACTTAACATAACTACATAA
*
31577192 TACATAACGT-ACATAA-TACATAA
1 TACATAACTTAACATAACTACATAA
*
31577215 TACACAACTTAA
1 TACATAACTTAA
31577227 TTAAGATTAT
Statistics
Matches: 194, Mismatches: 41, Indels: 55
0.67 0.14 0.19
Matches are distributed among these distances:
20 7 0.04
21 64 0.33
22 5 0.03
23 60 0.31
24 7 0.04
25 44 0.23
26 1 0.01
27 4 0.02
29 2 0.01
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (25 bp):
TACATAACTTAACATAACTACATAA
Found at i:31577349 original size:266 final size:266
Alignment explanation
Indices: 31577073--31577746 Score: 1240
Period size: 266 Copynumber: 2.5 Consensus size: 266
31577063 TACATAGTAC
*
31577073 ATAACTAACATTATACACAACTTACATACTACATTTATTACATAACTTACATTATACACAACTTA
1 ATAACTAACATTATACACAACTTACATACTACATTTCTTACATAACTTACATTATACACAACTTA
31577138 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
66 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
*
31577203 CATAATACATAATACACAACTTAATTAAGATTATACATAACATACATAATACATAATACACATAA
131 CATAATACATAATAAACAACTTAATTAAGATTATACATAACATACATAATACATAATACACATAA
31577268 CTTACATAGTACATAACTAACATTATACACAACTTACGTAACTTAAATAACGTACATAATACATA
196 CTTACATAGTACATAACTAACATTATACACAACTTACGTAACTTAAATAACGTACATAATACATA
31577333 ACTTTG
261 ACTTTG
* *
31577339 ATAACTAACATTATACACAACTTACATACTACAATTCTTACATAACTTACATTATACACAATTTA
1 ATAACTAACATTATACACAACTTACATACTACATTTCTTACATAACTTACATTATACACAACTTA
*
31577404 AATAATATTATACATAACGTACATAATATATAATACACAACTTAATTAATATTATACATAACGTA
66 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
*
31577469 CATAATACACAATAAACAACTTAATTAAGATTATACATAACATACATAATACATAATACACATAA
131 CATAATACATAATAAACAACTTAATTAAGATTATACATAACATACATAATACATAATACACATAA
*
31577534 CTTACATAGTACATAACTAACATTATACACAACTTACGTAACTTAAATAATGTACATAATACATA
196 CTTACATAGTACATAACTAACATTATACACAACTTACGTAACTTAAATAACGTACATAATACATA
31577599 ACTTTG
261 ACTTTG
* * * *
31577605 GTAACTGACATTATACACAACTTACATAATACATTTCTTACATAACTTTCATTATACACAACTTA
1 ATAACTAACATTATACACAACTTACATACTACATTTCTTACATAACTTACATTATACACAACTTA
31577670 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
66 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
*
31577735 CCTAATACATAA
131 CATAATACATAA
31577747 ATATATATCA
Statistics
Matches: 392, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
266 392 1.00
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.32
Consensus pattern (266 bp):
ATAACTAACATTATACACAACTTACATACTACATTTCTTACATAACTTACATTATACACAACTTA
AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
CATAATACATAATAAACAACTTAATTAAGATTATACATAACATACATAATACATAATACACATAA
CTTACATAGTACATAACTAACATTATACACAACTTACGTAACTTAAATAACGTACATAATACATA
ACTTTG
Found at i:31577387 original size:9 final size:9
Alignment explanation
Indices: 31577236--31577390 Score: 59
Period size: 9 Copynumber: 18.6 Consensus size: 9
31577226 ATTAAGATTA
*
31577236 TACATAACA
1 TACATAACT
31577245 TACATAA--
1 TACATAACT
31577252 TACATAA-T
1 TACATAACT
*
31577260 ACACATAACT
1 -TACATAACT
*
31577270 TACAT-A-G
1 TACATAACT
31577277 TACATAACT
1 TACATAACT
* *
31577286 AACATTA--
1 TACATAACT
*
31577293 TACACAACT
1 TACATAACT
*
31577302 TACGTAACT
1 TACATAACT
* *
31577311 TAAATAACG
1 TACATAACT
31577320 TACATAA--
1 TACATAACT
31577327 TACATAACT
1 TACATAACT
**
31577336 TTGATAACT
1 TACATAACT
* *
31577345 AACATTA--
1 TACATAACT
*
31577352 TACACAACT
1 TACATAACT
31577361 TACAT-AC-
1 TACATAACT
*
31577368 TACA-ATTCT
1 TACATA-ACT
31577377 TACATAACT
1 TACATAACT
31577386 TACAT
1 TACAT
31577391 TATACACAAT
Statistics
Matches: 104, Mismatches: 27, Indels: 30
0.65 0.17 0.19
Matches are distributed among these distances:
7 31 0.30
8 5 0.05
9 66 0.63
10 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.30
Consensus pattern (9 bp):
TACATAACT
Found at i:31577415 original size:21 final size:21
Alignment explanation
Indices: 31577389--31577475 Score: 84
Period size: 21 Copynumber: 4.0 Consensus size: 21
31577379 CATAACTTAC
*
31577389 ATTATACACAATTTAAATAAT
1 ATTATACACAACTTAAATAAT
* * *
31577410 ATTATACATAACGTACATAAT
1 ATTATACACAACTTAAATAAT
*
31577431 ATATAATACACAACTTAATTAAT
1 AT-T-ATACACAACTTAAATAAT
* * *
31577454 ATTATACATAACGTACATAAT
1 ATTATACACAACTTAAATAAT
31577475 A
1 A
31577476 CACAATAAAC
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
21 34 0.65
22 2 0.04
23 16 0.31
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTATACACAACTTAAATAAT
Found at i:31577547 original size:16 final size:16
Alignment explanation
Indices: 31577528--31577570 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
31577518 TACATAATAC
31577528 ACATAACTTACA-TAGT
1 ACATAACTTACATTA-T
*
31577544 ACATAACTAACATTAT
1 ACATAACTTACATTAT
*
31577560 ACACAACTTAC
1 ACATAACTTAC
31577571 GTAACTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (16 bp):
ACATAACTTACATTAT
Found at i:31577634 original size:41 final size:41
Alignment explanation
Indices: 31577586--31577676 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
31577576 TTAAATAATG
***
31577586 TACATAATACATAACTTTGGTAACTGACATTATACACAACT
1 TACATAATACATAACTTACATAACTGACATTATACACAACT
** **
31577627 TACATAATACATTTCTTACATAACTTTCATTATACACAACT
1 TACATAATACATAACTTACATAACTGACATTATACACAACT
*
31577668 TAAATAATA
1 TACATAATA
31577677 TTATACATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (41 bp):
TACATAATACATAACTTACATAACTGACATTATACACAACT
Found at i:31577669 original size:25 final size:23
Alignment explanation
Indices: 31577641--31577713 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 23
31577631 TAATACATTT
31577641 CTTACATAACTTTCATTATACACAA
1 CTTACATAA--TTCATTATACACAA
* *
31577666 CTTAAATAA-T-ATTATACATAA
1 CTTACATAATTCATTATACACAA
* * *
31577687 CGTACATAATACATAATACACAA
1 CTTACATAATTCATTATACACAA
31577710 CTTA
1 CTTA
31577714 ATTAATATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 17 0.45
22 1 0.03
23 12 0.32
25 8 0.21
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (23 bp):
CTTACATAATTCATTATACACAA
Found at i:31577681 original size:21 final size:21
Alignment explanation
Indices: 31577655--31577727 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
31577645 CATAACTTTC
31577655 ATTATACACAACTTAAATAAT
1 ATTATACACAACTTAAATAAT
* * *
31577676 ATTATACATAACGTACATAAT
1 ATTATACACAACTTAAATAAT
* *
31577697 ACATAATACACAACTTAATTAAT
1 --ATTATACACAACTTAAATAAT
31577720 ATTATACA
1 ATTATACA
31577728 TAACGTACCT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 25 0.61
23 16 0.39
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.33
Consensus pattern (21 bp):
ATTATACACAACTTAAATAAT
Found at i:31580516 original size:21 final size:21
Alignment explanation
Indices: 31580492--31580532 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31580482 AGCAAAGGCT
*
31580492 GTAGCGAGGGAAGCAGAGGTA
1 GTAGCGAGAGAAGCAGAGGTA
* *
31580513 GTAGTGAGAGAAGCTGAGGT
1 GTAGCGAGAGAAGCAGAGGT
31580533 TCAAAGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.07, G:0.46, T:0.15
Consensus pattern (21 bp):
GTAGCGAGAGAAGCAGAGGTA
Found at i:31580994 original size:85 final size:83
Alignment explanation
Indices: 31580896--31581317 Score: 366
Period size: 85 Copynumber: 5.0 Consensus size: 83
31580886 GCGTTTATAA
* ** ** * ** * *
31580896 AAAAATGCCGCTAAAGGTCCTGAGATATAGTGGCATTTGTGGAAAAAGTGCCACTAAAAATCCTG
1 AAAAAGGCCGCTAAAGACCCTGATCTATAGCGGCATTTGTAAAAAAAGTGCCGCTAAAGATCCTG
31580961 ATCTATAGCGGCGTTTTT
66 ATCTATAGCGGCGTTTTT
* * * *
31580979 AAAAAGGCACAGCTAAA-AGTCCTGATCTATAGCAGCATTTTTAAAAAAAGTGCCGCTAAAGGTC
1 AAAAAGGC-C-GCTAAAGA-CCCTGATCTATAGCGGCATTTGTAAAAAAAGTGCCGCTAAAGATC
* *
31581043 TTGATCTATAGCGGCGTTTGTA
63 CTGATCTATAGCGGCGTTT-TT
* * * **
31581065 AAAGAAGCGTCGCTAAAGACCCTGATCTATAACGGCGTTTGT-AAAAAAGTGCCGCTAAAGGCCC
1 AAA-AAG-GCCGCTAAAGACCCTGATCTATAGCGGCATTTGTAAAAAAAGTGCCGCTAAAGATCC
*
31581129 TGATCTATAGCGGCGTTTGTA
64 TGATCTATAGCGGCGTTT-TT
* * * *
31581150 AAAAAGTGCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAAAAGCGACGCTAAAGA-CAC
1 AAAAAG-GCCGCTAAAGACCCTGATCTATAGCGGCATTTGTAAAAAAAGTGCCGCTAAAGATC-C
* *
31581214 TGCTCTATAGCGGCGTTTGTG
64 TGATCTATAGCGGCGTTT-TT
* * ** ** * ** * *
31581235 GAGAAGCGCCGCTAAAGACCCTGATCTATAGCGGTGTTTGT-GGAGAAGCACCACTAAAGACCCT
1 AAAAAG-GCCGCTAAAGACCCTGATCTATAGCGGCATTTGTAAAAAAAGTGCCGCTAAAGATCCT
31581299 GATCTATAGCGGCGTTTTT
65 GATCTATAGCGGCGTTTTT
31581318 TCTATAAATG
Statistics
Matches: 287, Mismatches: 42, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
83 8 0.03
84 69 0.24
85 176 0.61
86 28 0.10
87 5 0.02
88 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (83 bp):
AAAAAGGCCGCTAAAGACCCTGATCTATAGCGGCATTTGTAAAAAAAGTGCCGCTAAAGATCCTG
ATCTATAGCGGCGTTTTT
Found at i:31581209 original size:127 final size:126
Alignment explanation
Indices: 31580885--31581315 Score: 452
Period size: 127 Copynumber: 3.4 Consensus size: 126
31580875 TAAAATTAGT
* * ** ** * * * * * *
31580885 GGCGTTTATAAAAAAATGCCGCTAAAGGTCCTGAGATATAGTGGCATTTGTGGAAAAAGTGCCAC
1 GGCGTTTGTAAAAAAGTGCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAAAAGCGACGC
* * * * *
31580950 TAAAAATCCTGATCTATAGCGGCGTTT-TTAAAAAGGCACAGCTAAAAGTCCTGATCTATAGC
66 TAAAGACCCTGATCTATAGCGGCGTTTGTAAAAAAGGC-C-GCTAAAGGCCCTGATCTATAGC
* * * ** * *
31581012 AGCATTTTTAAAAAAAGTGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTA-AAAGAAGCGTC
1 GGCGTTTGT-AAAAAAGTGCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAA-AAGCGAC
*
31581076 GCTAAAGACCCTGATCTATAACGGCGTTTGTAAAAAAGTGCCGCTAAAGGCCCTGATCTATAGC
64 GCTAAAGACCCTGATCTATAGCGGCGTTTGTAAAAAAG-GCCGCTAAAGGCCCTGATCTATAGC
31581140 GGCGTTTGTAAAAAAGTGCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAAAAGCGACGC
1 GGCGTTTGTAAAAAAGTGCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAAAAGCGACGC
* * ** * *
31581205 TAAAGACACTGCTCTATAGCGGCGTTTGTGGAGAAGCGCCGCTAAAGACCCTGATCTATAGC
66 TAAAGACCCTGATCTATAGCGGCGTTTGTAAAAAAG-GCCGCTAAAGGCCCTGATCTATAGC
* ** * ** *
31581267 GGTGTTTGTGGAGAAGCACCACTAAAGACCCTGATCTATAGCGGCGTTT
1 GGCGTTTGTAAAAAAGTGCCGCTAAAGACCCTGATCTATAGCGGCGTTT
31581316 TTTCTATAAA
Statistics
Matches: 258, Mismatches: 41, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
127 153 0.59
128 95 0.37
129 8 0.03
130 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (126 bp):
GGCGTTTGTAAAAAAGTGCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAAAAGCGACGC
TAAAGACCCTGATCTATAGCGGCGTTTGTAAAAAAGGCCGCTAAAGGCCCTGATCTATAGC
Found at i:31581276 original size:42 final size:42
Alignment explanation
Indices: 31580885--31581315 Score: 423
Period size: 42 Copynumber: 10.2 Consensus size: 42
31580875 TAAAATTAGT
* ** ** ** *
31580885 GGCGTTTATAAAAAAATGCCGCTAAAGGTCCTGAGATATAGT
1 GGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
* * * * * *
31580927 GGCATTTGTGGAAAAAGTGCCACTAAAAATCCTGATCTATAGC
1 GGCGTTTGT-AAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
* * * * *
31580970 GGCGTTTTTAAAAAGGCACAGCTAAA-AGTCCTGATCTATAGC
1 GGCGTTTGTAAAAAAGCGCCGCTAAAGA-CCCTGATCTATAGC
* * * * ** *
31581012 AGCATTTTTAAAAAAAGTGCCGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGT-AAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
* *
31581055 GGCGTTTGTAAAAGAAGCGTCGCTAAAGACCCTGATCTATAAC
1 GGCGTTTGTAAAA-AAGCGCCGCTAAAGACCCTGATCTATAGC
* *
31581098 GGCGTTTGTAAAAAAGTGCCGCTAAAGGCCCTGATCTATAGC
1 GGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
*
31581140 GGCGTTTGTAAAAAAGTGCCGCTAAAGACCCTGATCTATAGC
1 GGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
* * *
31581182 GGCGTTTGTAGAAAAAGCGACGCTAAAGACACTGCTCTATAGC
1 GGCGTTTGTA-AAAAAGCGCCGCTAAAGACCCTGATCTATAGC
** *
31581225 GGCGTTTGTGGAGAAGCGCCGCTAAAGACCCTGATCTATAGC
1 GGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
* ** * * *
31581267 GGTGTTTGTGGAGAAGCACCACTAAAGACCCTGATCTATAGC
1 GGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
31581309 GGCGTTT
1 GGCGTTT
31581316 TTTCTATAAA
Statistics
Matches: 329, Mismatches: 54, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
41 1 0.00
42 191 0.58
43 137 0.42
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (42 bp):
GGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
Found at i:31585637 original size:15 final size:15
Alignment explanation
Indices: 31585590--31585629 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
31585580 TATAAGTAAT
31585590 AAAACATAGTAATTA
1 AAAACATAGTAATTA
* *
31585605 AAAAAATAATTAATTA
1 AAAACAT-AGTAATTA
31585621 AAAACATAG
1 AAAACATAG
31585630 CTATTAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (15 bp):
AAAACATAGTAATTA
Found at i:31586166 original size:20 final size:20
Alignment explanation
Indices: 31586143--31586182 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31586133 TAGCTCTAAC
*
31586143 CAGCTCATTTGAGCTCAATT
1 CAGCTCATTCGAGCTCAATT
31586163 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAATT
31586183 TAGTTTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.33
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAATT
Found at i:31593266 original size:11 final size:11
Alignment explanation
Indices: 31593237--31593279 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
31593227 TAGTTTCTTC
31593237 GAAAAAAATTT
1 GAAAAAAATTT
31593248 GAACAAAAATTT
1 GAA-AAAAATTT
*
31593260 GAAAAAAATTC
1 GAAAAAAATTT
*
31593271 AAAAAAAAT
1 GAAAAAAAT
31593280 ATTTCCATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (11 bp):
GAAAAAAATTT
Found at i:31593335 original size:15 final size:15
Alignment explanation
Indices: 31593315--31593343 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31593305 GGATATCAAG
31593315 TTGTGAAAAAAAAAT
1 TTGTGAAAAAAAAAT
31593330 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
31593344 GTTAGTTTTG
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:0.00, G:0.14, T:0.24
Consensus pattern (15 bp):
TTGTGAAAAAAAAAT
Found at i:31597316 original size:21 final size:21
Alignment explanation
Indices: 31597286--31597336 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
31597276 TTCTCTCTCG
*
31597286 CTTTCCTTTTCGCCTTTTTCA
1 CTTTCATTTTCGCCTTTTTCA
* **
31597307 TTTTCATTTTCTTCTTTTTCA
1 CTTTCATTTTCGCCTTTTTCA
31597328 CTTT-ATTTT
1 CTTTCATTTT
31597337 TCTCTTCTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.08, C:0.24, G:0.02, T:0.67
Consensus pattern (21 bp):
CTTTCATTTTCGCCTTTTTCA
Found at i:31599381 original size:29 final size:27
Alignment explanation
Indices: 31599348--31599402 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
31599338 GTTATTAAAT
31599348 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
31599377 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
31599403 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:31629055 original size:15 final size:15
Alignment explanation
Indices: 31629035--31629065 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31629025 TGGCTATACC
31629035 TAAGGAAACAATAGT
1 TAAGGAAACAATAGT
31629050 TAAGGAAACAATAGT
1 TAAGGAAACAATAGT
31629065 T
1 T
31629066 CGCGGAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (15 bp):
TAAGGAAACAATAGT
Found at i:31637491 original size:15 final size:15
Alignment explanation
Indices: 31637471--31637501 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31637461 CCTATAGTAG
31637471 TTCTCAAAAGCAGAA
1 TTCTCAAAAGCAGAA
*
31637486 TTCTCACAAGCAGAA
1 TTCTCAAAAGCAGAA
31637501 T
1 T
31637502 AAATTTCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
TTCTCAAAAGCAGAA
Found at i:31639111 original size:39 final size:40
Alignment explanation
Indices: 31639068--31639176 Score: 114
Period size: 45 Copynumber: 2.6 Consensus size: 40
31639058 TTTTTTTATA
* *
31639068 TTTTC-TTGTTTTTCTTTTCTCATTTT-CTTTTCGCTTTCT
1 TTTTCTTTTTTTTTCTTTT-TCATTTTGCTTTTCGCTTTCG
**
31639107 TTTTCTATTTTTGCTTTCTTTTTTTCATTTTGCTTTTCTTTTTCG
1 TTTTCT-TTTTT--TTTC--TTTTTCATTTTGCTTTTCGCTTTCG
31639152 TTTTCTTTTTTTTTCTTTTTCATTT
1 TTTTCTTTTTTTTTCTTTTTCATTT
31639177 GATTGAGATA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
39 5 0.08
40 10 0.17
41 4 0.07
42 4 0.07
43 4 0.07
44 12 0.20
45 20 0.34
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.75
Consensus pattern (40 bp):
TTTTCTTTTTTTTTCTTTTTCATTTTGCTTTTCGCTTTCG
Found at i:31639117 original size:7 final size:6
Alignment explanation
Indices: 31639076--31639172 Score: 60
Period size: 6 Copynumber: 16.0 Consensus size: 6
31639066 TATTTTCTTG
* **
31639076 TTTTTC TTTTCTC ATTTTC -TTTTC GCTTTC TTTTTC TATTTTTGC TTTCTT-
1 TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC --TTTTT-C TTT-TTC
* *
31639127 TTTTTC ATTTTGC -TTTTC TTTTTC GTTTTC -TTTT- TTTTTC TTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
31639173 ATTTGATTGA
Statistics
Matches: 73, Mismatches: 7, Indels: 22
0.72 0.07 0.22
Matches are distributed among these distances:
5 19 0.26
6 33 0.45
7 13 0.18
8 7 0.10
9 1 0.01
ACGTcount: A:0.03, C:0.18, G:0.04, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:31639118 original size:20 final size:19
Alignment explanation
Indices: 31639095--31639150 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
31639085 TCTCATTTTC
31639095 TTTTCGCTTTCTTTTTCT-A
1 TTTT-GCTTTCTTTTTCTCA
*
31639114 TTTTTGCTTTCTTTTTTTCA
1 -TTTTGCTTTCTTTTTCTCA
31639134 TTTTGCTTTTCTTTTTC
1 TTTTGC-TTTCTTTTTC
31639151 GTTTTCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTTGCTTTCTTTTTCTCA
Found at i:31641629 original size:17 final size:16
Alignment explanation
Indices: 31641590--31641628 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
31641580 CACTTCACTC
*
31641590 TTTTTTTACTTCGTAT
1 TTTTTTTACTTCGAAT
31641606 TTTTTTTACTTCGAAT
1 TTTTTTTACTTCGAAT
31641622 TTTTTTT
1 TTTTTTT
31641629 TCAATTACAA
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:0.13, C:0.10, G:0.05, T:0.72
Consensus pattern (16 bp):
TTTTTTTACTTCGAAT
Found at i:31643718 original size:25 final size:25
Alignment explanation
Indices: 31643690--31643751 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
31643680 TGCATTGACC
*
31643690 GAAGCATGCATGAACGGCATTAAAA
1 GAAGCATGCATGAACGACATTAAAA
* *
31643715 GAAGCATGCATGAACGACATTCAAG
1 GAAGCATGCATGAACGACATTAAAA
*
31643740 GAAACATGCATG
1 GAAGCATGCATG
31643752 CTAATTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (25 bp):
GAAGCATGCATGAACGACATTAAAA
Found at i:31652233 original size:46 final size:46
Alignment explanation
Indices: 31652183--31652358 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
31652173 TGGTTGAGCA
31652183 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
31652229 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
31652274 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
31652322 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31652359 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 7 0.07
46 58 0.54
47 29 0.27
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:31652339 original size:93 final size:93
Alignment explanation
Indices: 31652180--31652351 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
31652170 GGATGGTTGA
* * *
31652180 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCGTTGAGT
31652245 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
31652273 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG-CCCAAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAA-CTCGTTGAG
31652337 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
31652352 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 4 0.05
93 71 0.95
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:31655308 original size:15 final size:15
Alignment explanation
Indices: 31655270--31655313 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
31655260 CATAGTATCG
* *
31655270 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTC
31655285 TAT-TCTGGATTTCTC
1 TATCT-TGGATTTCTC
31655300 TATCTTGGATTTCT
1 TATCTTGGATTTCT
31655314 TTATTCGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:31657299 original size:46 final size:46
Alignment explanation
Indices: 31657249--31657424 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
31657239 TGGTTGAGCA
31657249 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
31657295 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
31657340 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
31657388 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31657425 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 7 0.07
46 57 0.54
47 28 0.27
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:31657405 original size:93 final size:93
Alignment explanation
Indices: 31657246--31657417 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
31657236 GGATGGTTGA
* * *
31657246 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCGTTGAGT
*
31657311 TGAGTCTGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
31657339 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG-CCCAAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAA-CTCGTTGAG
31657403 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
31657418 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 4 0.05
93 70 0.95
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:31660848 original size:50 final size:52
Alignment explanation
Indices: 31660721--31660853 Score: 130
Period size: 50 Copynumber: 2.6 Consensus size: 52
31660711 AATGAACAAA
* *
31660721 TGAGTTACTTAATGCA-AGACTTAATTTAATGATGCAAACTTAAACTAACATG
1 TGAGTTACATAATGCATA-ACTTTATTTAATGATGCAAACTTAAACTAACATG
* * ** * * *
31660773 TGAGTTATATCATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATG
1 TGAGTTACATAATGCATAACTTTATTTAATGATGCAAACTTAAACTAACATG
*
31660823 -GAAGTTACATAATGCATAACTTTATTAAATG
1 TG-AGTTACATAATGCATAACTTTATTTAATG
31660854 CAGAACACAC
Statistics
Matches: 63, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
49 1 0.02
50 28 0.44
51 15 0.24
52 19 0.30
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (52 bp):
TGAGTTACATAATGCATAACTTTATTTAATGATGCAAACTTAAACTAACATG
Found at i:31665730 original size:27 final size:27
Alignment explanation
Indices: 31665691--31665743 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
31665681 AATGTGTTTT
*
31665691 ATTTTAATGCATGTTATTAATG-TGTCA
1 ATTTTAATACATGTT-TTAATGCTGTCA
*
31665718 ATTTTATTACATGTTTTAATGCTGTC
1 ATTTTAATACATGTTTTAATGCTGTC
31665744 CAAAGTCCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.51
Consensus pattern (27 bp):
ATTTTAATACATGTTTTAATGCTGTCA
Found at i:31672733 original size:17 final size:18
Alignment explanation
Indices: 31672711--31672747 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31672701 TGGAATAAAC
31672711 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
31672728 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
31672746 TT
1 TT
31672748 CAGCTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:31675110 original size:22 final size:21
Alignment explanation
Indices: 31675079--31675120 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
31675069 CACATTTAAC
*
31675079 ACTTAACTAAATTAATTAAAT
1 ACTTAACTAAATTAACTAAAT
31675100 ACTTAAACTAAATTAACTAAA
1 ACTT-AACTAAATTAACTAAA
31675121 ATTTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (21 bp):
ACTTAACTAAATTAACTAAAT
Found at i:31676978 original size:20 final size:20
Alignment explanation
Indices: 31676933--31676979 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31676923 TAAAGCTAAG
*
31676933 TTGAGCTCAAACGAGCTTAA
1 TTGAGCTCAAACGAACTTAA
*
31676953 TTGAGCTCAAATGAAC-TAA
1 TTGAGCTCAAACGAACTTAA
31676972 TTCGAGCT
1 TT-GAGCT
31676980 AGATAGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
TTGAGCTCAAACGAACTTAA
Found at i:31678843 original size:6 final size:6
Alignment explanation
Indices: 31678831--31678909 Score: 108
Period size: 6 Copynumber: 13.3 Consensus size: 6
31678821 TTTCTCACTC
*
31678831 TCATTT TCTTTT TCGA-TT TCATTT TCATTT TCATTT TCATTT TCATTT
1 TCATTT TCATTT TC-ATTT TCATTT TCATTT TCATTT TCATTT TCATTT
* *
31678879 TCATTT TCATTT TCTTTT TCAATT TC-TTT TC
1 TCATTT TCATTT TCATTT TCATTT TCATTT TC
31678910 TCGTTTTTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
5 5 0.08
6 60 0.92
ACGTcount: A:0.14, C:0.18, G:0.01, T:0.67
Consensus pattern (6 bp):
TCATTT
Found at i:31679774 original size:16 final size:16
Alignment explanation
Indices: 31679753--31679790 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31679743 TTCACTTCAT
31679753 TTTTTTATAC-TCGAA
1 TTTTTTATACTTCGAA
*
31679768 CTTTTTTTTACTTCGAA
1 -TTTTTTATACTTCGAA
31679785 TTTTTT
1 TTTTTT
31679791 CTATTACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.63
Consensus pattern (16 bp):
TTTTTTATACTTCGAA
Found at i:31679774 original size:17 final size:16
Alignment explanation
Indices: 31679751--31679790 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
31679741 ACTTCACTTC
31679751 ATTTTTTTATAC-TCGA
1 ATTTTTTT-TACTTCGA
31679767 ACTTTTTTTTACTTCGA
1 A-TTTTTTTTACTTCGA
31679784 ATTTTTT
1 ATTTTTT
31679791 CTATTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTTTTTTTACTTCGA
Found at i:31685950 original size:17 final size:14
Alignment explanation
Indices: 31685928--31685968 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 14
31685918 TTTTCTTCTC
31685928 TTTTTTTCACGAAAAT
1 TTTTTTTCACG--AAT
31685944 ATTTTTTTCACGAAT
1 -TTTTTTTCACGAAT
31685959 TTTTTTTCAC
1 TTTTTTTCAC
31685969 AACTTGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
17 11 0.46
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (14 bp):
TTTTTTTCACGAAT
Found at i:31687028 original size:21 final size:23
Alignment explanation
Indices: 31686983--31687029 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
31686973 TCACCTGCAA
* *
31686983 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
31687006 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
31687027 TAA
1 TAA
31687030 TCATAACACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:31692333 original size:14 final size:15
Alignment explanation
Indices: 31692294--31692330 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
31692284 GCTTGTTTTC
31692294 TTTTTTTTT-ACGAA
1 TTTTTTTTTCACGAA
31692308 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
31692323 TTTTTTTT
1 TTTTTTTT
31692331 CACAACTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.70
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:31692389 original size:11 final size:11
Alignment explanation
Indices: 31692373--31692400 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
31692363 TGGAAACTAA
31692373 TTTTTTTCGAT
1 TTTTTTTCGAT
31692384 TTTTTTTCGAT
1 TTTTTTTCGAT
31692395 TTTTTT
1 TTTTTT
31692401 AATTTTTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTCGAT
Found at i:31694708 original size:20 final size:20
Alignment explanation
Indices: 31694663--31694709 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31694653 TAAAGCTAAG
*
31694663 TTGAGCTCAAACGAGCTTAA
1 TTGAGCTCAAACGAACTTAA
*
31694683 TTGAGCTCAAATGAAC-TAA
1 TTGAGCTCAAACGAACTTAA
31694702 TTCGAGCT
1 TT-GAGCT
31694710 AGATAGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
TTGAGCTCAAACGAACTTAA
Found at i:31703227 original size:30 final size:30
Alignment explanation
Indices: 31703191--31703263 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
31703181 ACAAAGGAAA
31703191 AAGAAAATCAAGATTCACTTTCTTGTTTTC
1 AAGAAAATCAAGATTCACTTTCTTGTTTTC
*
31703221 AAGAAAATCAAGATTCACTTTCTTGTTTTT
1 AAGAAAATCAAGATTCACTTTCTTGTTTTC
31703251 AAGAAAATCAAGA
1 AAGAAAATCAAGA
31703264 AACCGAATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (30 bp):
AAGAAAATCAAGATTCACTTTCTTGTTTTC
Found at i:31707528 original size:29 final size:28
Alignment explanation
Indices: 31707492--31707569 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
31707482 TCATGAGATT
31707492 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
31707522 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
31707549 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
31707570 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:31707787 original size:174 final size:174
Alignment explanation
Indices: 31707522--31707849 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
31707512 AAATTGTACA
*
31707522 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATCGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
31707587 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
31707652 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
31707696 GCACTAAGTGTGTGAGTTTAAAGTACATCGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATCGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
31707761 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACGTGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
31707826 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
31707850 ACCTTGAGTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATCGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:31717048 original size:27 final size:26
Alignment explanation
Indices: 31717031--31717100 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
31717021 ATATTAAGTC
31717031 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
31717058 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
31717086 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
31717101 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:31717094 original size:28 final size:28
Alignment explanation
Indices: 31717031--31717128 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
31717021 ATATTAAGTC
*
31717031 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
31717058 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
31717086 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
31717115 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31717129 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:31717590 original size:12 final size:12
Alignment explanation
Indices: 31717573--31717598 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31717563 TGGGCATACT
31717573 TATGTATATATA
1 TATGTATATATA
31717585 TATGTATATATA
1 TATGTATATATA
31717597 TA
1 TA
31717599 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:31720355 original size:14 final size:14
Alignment explanation
Indices: 31720336--31720370 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
31720326 TTCAAAACTT
31720336 TTTTTTTGAATTCC
1 TTTTTTTGAATTCC
*
31720350 TTTTTTTGAATTTC
1 TTTTTTTGAATTCC
31720364 TTTTTTT
1 TTTTTTT
31720371 AAATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.11, C:0.09, G:0.06, T:0.74
Consensus pattern (14 bp):
TTTTTTTGAATTCC
Found at i:31721874 original size:10 final size:11
Alignment explanation
Indices: 31721848--31721876 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
31721838 AGACGAGCTC
31721848 ATTGAGCTAAG
1 ATTGAGCTAAG
31721859 ATTGAGCTAA-
1 ATTGAGCTAAG
31721869 ATTGAGCT
1 ATTGAGCT
31721877 CAACCAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (11 bp):
ATTGAGCTAAG
Found at i:31722414 original size:24 final size:23
Alignment explanation
Indices: 31722387--31722452 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 23
31722377 AATTTGAAGG
31722387 ATGTATAATGCTTTCCTTTAAATA
1 ATGTATAATGC-TTCCTTTAAATA
* * *
31722411 ATGTA-ACA-AC-TCCTTTGAATT
1 ATGTATA-ATGCTTCCTTTAAATA
31722432 ATGTATAATGCTCTCCTTTAA
1 ATGTATAATGCT-TCCTTTAA
31722453 TTGATGTAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
21 15 0.47
22 2 0.06
23 2 0.06
24 13 0.41
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (23 bp):
ATGTATAATGCTTCCTTTAAATA
Found at i:31722470 original size:21 final size:20
Alignment explanation
Indices: 31722400--31722470 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 20
31722390 TATAATGCTT
* *
31722400 TCCTTTAAATAATGTAACAAC
1 TCCTTT-AATTATGTAACAGC
31722421 TCCTTTGAATTATGTATA-ATGCTC
1 TCCTTT-AATTATGTA-ACA-G--C
31722445 TCCTTTAATTGATGTAACAGC
1 TCCTTTAATT-ATGTAACAGC
31722466 TCCTT
1 TCCTT
31722471 GTATGTAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
21 21 0.51
22 1 0.02
23 6 0.15
24 13 0.32
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.41
Consensus pattern (20 bp):
TCCTTTAATTATGTAACAGC
Found at i:31722821 original size:19 final size:19
Alignment explanation
Indices: 31722797--31722835 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
31722787 TTATTCCAGC
31722797 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
31722816 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
31722835 A
1 A
31722836 GTAATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:31724249 original size:20 final size:20
Alignment explanation
Indices: 31724209--31724249 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31724199 GTCTTAGCCG
*
31724209 AATTAAATGTGTCCTAGTTT
1 AATTAAATGTGTCCTAATTT
* *
31724229 AATTAAATTTGTCTTAATTT
1 AATTAAATGTGTCCTAATTT
31724249 A
1 A
31724250 TTACATGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (20 bp):
AATTAAATGTGTCCTAATTT
Found at i:31725960 original size:10 final size:10
Alignment explanation
Indices: 31725945--31725985 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
31725935 CGGTGTAAGT
31725945 ATTTGAAAAA
1 ATTTGAAAAA
31725955 ATTTGAAAAA
1 ATTTGAAAAA
* *
31725965 AATTAAAAAA
1 ATTTGAAAAA
*
31725975 ATTTCAAAAA
1 ATTTGAAAAA
31725985 A
1 A
31725986 ATTGTGAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (10 bp):
ATTTGAAAAA
Found at i:31725966 original size:11 final size:11
Alignment explanation
Indices: 31725945--31725993 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
31725935 CGGTGTAAGT
31725945 ATTTG-AAAAA
1 ATTTGAAAAAA
31725955 ATTTGAAAAAA
1 ATTTGAAAAAA
31725966 A-TT-AAAAAA
1 ATTTGAAAAAA
*
31725975 ATTTCAAAAAA
1 ATTTGAAAAAA
31725986 ATTGTGAA
1 ATT-TGAA
31725994 CGTGATTGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
9 7 0.21
10 9 0.26
11 15 0.44
12 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (11 bp):
ATTTGAAAAAA
Found at i:31725975 original size:20 final size:20
Alignment explanation
Indices: 31725950--31725988 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31725940 TAAGTATTTG
*
31725950 AAAAAATTTGAAAAAAATTA
1 AAAAAATTTCAAAAAAATTA
31725970 AAAAAATTTCAAAAAAATT
1 AAAAAATTTCAAAAAAATT
31725989 GTGAACGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAAAATTTCAAAAAAATTA
Found at i:31727205 original size:16 final size:17
Alignment explanation
Indices: 31727163--31727205 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
31727153 ATGAAAAAAC
31727163 AAAAGAAAAAGAAAGTA
1 AAAAGAAAAAGAAAGTA
31727180 AAAAGAAAAAGAAAGT-
1 AAAAGAAAAAGAAAGTA
31727196 AAAAGAAAAA
1 AAAAGAAAAA
31727206 AAAAAAGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAGAAAAAGAAAGTA
Found at i:31727263 original size:18 final size:20
Alignment explanation
Indices: 31727240--31727286 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
31727230 GCATGCGAGC
31727240 AAGAAAAGAAAG-TTGAA-A
1 AAGAAAAGAAAGATTGAAGA
*
31727258 AAGAAAA-AGAGATTGAAGA
1 AAGAAAAGAAAGATTGAAGA
31727277 AAGAAAAGAA
1 AAGAAAAGAA
31727287 CGTGTCCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.12
18 12 0.50
19 8 0.33
20 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (20 bp):
AAGAAAAGAAAGATTGAAGA
Found at i:31727267 original size:19 final size:19
Alignment explanation
Indices: 31727243--31727283 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
31727233 TGCGAGCAAG
31727243 AAAAGAAAGTTGAA-AAAGA
1 AAAAGAAA-TTGAAGAAAGA
*
31727262 AAAAGAGATTGAAGAAAGA
1 AAAAGAAATTGAAGAAAGA
31727281 AAA
1 AAA
31727284 GAACGTGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.68, C:0.00, G:0.22, T:0.10
Consensus pattern (19 bp):
AAAAGAAATTGAAGAAAGA
Found at i:31729667 original size:27 final size:27
Alignment explanation
Indices: 31729637--31729688 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
31729627 AATTGGTAGG
* *
31729637 TACATGCATGGACGACATTGAAGATAA
1 TACATGCATGGACAACAATGAAGATAA
31729664 TACATGCATGGACAACAATGAAGAT
1 TACATGCATGGACAACAATGAAGAT
31729689 GCTTCAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (27 bp):
TACATGCATGGACAACAATGAAGATAA
Found at i:31730993 original size:46 final size:46
Alignment explanation
Indices: 31730942--31731034 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
31730932 TAGTGTGGCA
31730942 TTCATCATATACCAAGGTTCCTATCATAATTGATAGTGGGTCGAGG
1 TTCATCATATACCAAGGTTCCTATCATAATTGATAGTGGGTCGAGG
**
31730988 TTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAGG
1 TTCATCATATACCAAGGTTCCTATCATAATTGATAGTGGGTCGAGG
31731034 T
1 T
31731035 CTTTTCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (46 bp):
TTCATCATATACCAAGGTTCCTATCATAATTGATAGTGGGTCGAGG
Found at i:31735377 original size:40 final size:40
Alignment explanation
Indices: 31735326--31735950 Score: 1090
Period size: 40 Copynumber: 15.6 Consensus size: 40
31735316 CATTTGAATG
31735326 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
31735366 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
31735406 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
31735446 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
31735486 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
31735526 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
31735566 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
31735606 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
31735646 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
31735686 ATATCCGGGATAAGACCCGAAGGCATTTGTGAGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
31735726 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* * *
31735766 ATATCCGGGATAAGACCCGAAGGCATTTGTGTGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
31735806 ATATCCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
31735846 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
31735886 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
31735926 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
31735951 ATTGAGCTTG
Statistics
Matches: 558, Mismatches: 25, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
39 2 0.00
40 555 0.99
41 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:31741103 original size:33 final size:34
Alignment explanation
Indices: 31741032--31741105 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
31741022 TTTTACTTTA
* * * *
31741032 TTTCTTTCTTCACTCGTTTCTTTTGTAGACTCTT
1 TTTCTTTCTTCACTCGTTTCTTTTGCAAACCCTC
31741066 TTTCTTTC-TCACTCGATTTCTTTT-CAAACCCTC
1 TTTCTTTCTTCACTCG-TTTCTTTTGCAAACCCTC
31741099 TTTCTTT
1 TTTCTTT
31741106 TTCTTTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 19 0.54
34 16 0.46
ACGTcount: A:0.11, C:0.27, G:0.05, T:0.57
Consensus pattern (34 bp):
TTTCTTTCTTCACTCGTTTCTTTTGCAAACCCTC
Found at i:31741152 original size:6 final size:6
Alignment explanation
Indices: 31741099--31741159 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
31741089 TCAAACCCTC
* * * *
31741099 TTTCTT TTTCTT TTTCAT TTTCAT TTTC-T TTT-A- TTTCAA TTTCTT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
31741144 TTTCAT TTTCAT TTTC
1 TTTCAT TTTCAT TTTC
31741160 TCGCTTGCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
4 3 0.06
5 5 0.10
6 40 0.83
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTCAT
Found at i:31744006 original size:10 final size:11
Alignment explanation
Indices: 31743991--31744038 Score: 59
Period size: 10 Copynumber: 4.7 Consensus size: 11
31743981 TTCGGTTAAG
31743991 ATTGAGCT-GA
1 ATTGAGCTCGA
31744001 ATTGAGCTCGA
1 ATTGAGCTCGA
31744012 A-TGAGCT-GA
1 ATTGAGCTCGA
*
31744021 CTTGAGCTCG-
1 ATTGAGCTCGA
31744031 ATTGAGCT
1 ATTGAGCT
31744039 TAACTAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 27 0.82
11 4 0.12
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (11 bp):
ATTGAGCTCGA
Found at i:31744016 original size:20 final size:20
Alignment explanation
Indices: 31743993--31744038 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
31743983 CGGTTAAGAT
31743993 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* *
31744013 TGAGCTGACTTGAGCTCGAT
1 TGAGCTGAATTGAGCTCGAA
31744033 TGAGCT
1 TGAGCT
31744039 TAACTAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:31751889 original size:15 final size:15
Alignment explanation
Indices: 31751869--31751899 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31751859 GTAGGTATAA
*
31751869 AAAAAGAAGAAAAAG
1 AAAAAGAAAAAAAAG
31751884 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
31751899 A
1 A
31751900 TGCATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:31757525 original size:14 final size:14
Alignment explanation
Indices: 31757506--31757532 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31757496 TTTTTGTTTT
31757506 GTTTCATATCTACG
1 GTTTCATATCTACG
31757520 GTTTCATATCTAC
1 GTTTCATATCTAC
31757533 TCGATCTTGG
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:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (14 bp):
GTTTCATATCTACG
Found at i:31762444 original size:20 final size:21
Alignment explanation
Indices: 31762419--31762458 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
31762409 TAGAAAGATG
31762419 GAAATGAGCTC-ATTGAGCTA
1 GAAATGAGCTCAATTGAGCTA
31762439 GAAATGAGCTCAATTGAGCT
1 GAAATGAGCTCAATTGAGCT
31762459 CAACAAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (21 bp):
GAAATGAGCTCAATTGAGCTA
Found at i:31764684 original size:12 final size:12
Alignment explanation
Indices: 31764667--31764721 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
31764657 CTTTTCTCGA
31764667 TCTTTCTTTTCT
1 TCTTTCTTTTCT
31764679 TCTTTCTTTCTCAT
1 TCTTTCTTT-TC-T
*
31764693 T-TTTATTTTCT
1 TCTTTCTTTTCT
31764704 T-TTTCGTTTTCT
1 TCTTTC-TTTTCT
31764716 CTCTTT
1 -TCTTT
31764722 TGTTCCATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 9 0.25
14 5 0.14
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.73
Consensus pattern (12 bp):
TCTTTCTTTTCT
Found at i:31764714 original size:26 final size:26
Alignment explanation
Indices: 31764652--31764716 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
31764642 CAGTACGTAA
*
31764652 TTTTTCTTTTCTCGATCTTTCTTTTC
1 TTTTTCTTTTCTCGATCTTTATTTTC
*
31764678 TTCTTTC-TTTCTC-ATTTTTATTTTC
1 TT-TTTCTTTTCTCGATCTTTATTTTC
31764703 TTTTTCGTTTTCTC
1 TTTTTC-TTTTCTC
31764717 TCTTTTGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.12
25 12 0.35
26 14 0.41
27 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.71
Consensus pattern (26 bp):
TTTTTCTTTTCTCGATCTTTATTTTC
Found at i:31767021 original size:40 final size:40
Alignment explanation
Indices: 31766966--31767159 Score: 325
Period size: 40 Copynumber: 4.8 Consensus size: 40
31766956 GAGCATTTGA
31766966 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
31767006 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
31767046 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* *
31767086 ATATATCCGGGCTAAGGCCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* ** * *
31767126 CTATGCCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
31767160 TTGTGGTAAT
Statistics
Matches: 145, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 145 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
Found at i:31774046 original size:40 final size:40
Alignment explanation
Indices: 31773991--31774264 Score: 449
Period size: 40 Copynumber: 6.8 Consensus size: 40
31773981 GAGCATTTGA
*
31773991 ATATATCCTGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
31774031 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
31774071 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
*
31774111 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
*
31774151 ATATATCCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* *
31774191 ATATATCCGGGCTAAGGCCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* ** * * *
31774231 CTATGCCCGAGTTAAGACCCGAAGGCAATTGTGC
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
31774265 TTGTGGTAAT
Statistics
Matches: 219, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 219 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
Found at i:31777770 original size:52 final size:52
Alignment explanation
Indices: 31777708--31777808 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
31777698 CATGCACATA
* *
31777708 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGTTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTATTG
*
31777760 TTTGAGCTTCAACCGCGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTA
31777809 CTTTTCCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTATTG
Found at i:31782001 original size:16 final size:18
Alignment explanation
Indices: 31781980--31782012 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31781970 AACTCAACAT
31781980 AATG-TTGC-ATTTCAAC
1 AATGTTTGCTATTTCAAC
31781996 AATGTTTGCTATTTCAA
1 AATGTTTGCTATTTCAA
31782013 AATTTAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (18 bp):
AATGTTTGCTATTTCAAC
Found at i:31784420 original size:52 final size:52
Alignment explanation
Indices: 31784342--31784442 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
31784332 CATGCACATA
*
31784342 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTACTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTACTGTCCATTATTG
*
31784394 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTACTGTCCATTA
31784443 CTTTTCCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTACTGTCCATTATTG
Found at i:31788954 original size:20 final size:20
Alignment explanation
Indices: 31788925--31789009 Score: 127
Period size: 20 Copynumber: 4.3 Consensus size: 20
31788915 AGCTAAAAAC
31788925 GAGCTC-AATGAGCTGAATT
1 GAGCTCGAATGAGCTGAATT
*
31788944 GAGCTTGAATGAGCTGAATT
1 GAGCTCGAATGAGCTGAATT
* *
31788964 GAGCTCAAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
*
31788984 GAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
31789004 GAGCTC
1 GAGCTC
31789010 AAGTGAGTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
19 5 0.08
20 55 0.92
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGAATT
Found at i:31788978 original size:40 final size:40
Alignment explanation
Indices: 31788925--31789021 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 40
31788915 AGCTAAAAAC
*
31788925 GAGCTC-AATGAGCTGAATTGAGCTTGAATGAGCTGAATT
1 GAGCTCAAATGAGCTGAATTGAGCTCGAATGAGCTGAATT
* *
31788964 GAGCTCAAATGAGCTGACTTGAGCTCGAATGAGCTGACTT
1 GAGCTCAAATGAGCTGAATTGAGCTCGAATGAGCTGAATT
* *
31789004 GAGCTCAAGTGAGTTGAA
1 GAGCTCAAATGAGCTGAA
31789022 CCACATGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 6 0.12
40 45 0.88
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (40 bp):
GAGCTCAAATGAGCTGAATTGAGCTCGAATGAGCTGAATT
Found at i:31789016 original size:10 final size:10
Alignment explanation
Indices: 31788933--31789008 Score: 84
Period size: 10 Copynumber: 7.6 Consensus size: 10
31788923 ACGAGCTCAA
31788933 TGAGCTGAAT
1 TGAGCTGAAT
31788943 TGAGCTTGAA-
1 TGAGC-TGAAT
31788953 TGAGCTGAAT
1 TGAGCTGAAT
* *
31788963 TGAGCTCAAA
1 TGAGCTGAAT
*
31788973 TGAGCTGACT
1 TGAGCTGAAT
31788983 TGAGCTCGAA-
1 TGAGCT-GAAT
*
31788993 TGAGCTGACT
1 TGAGCTGAAT
31789003 TGAGCT
1 TGAGCT
31789009 CAAGTGAGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
9 6 0.11
10 43 0.78
11 6 0.11
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (10 bp):
TGAGCTGAAT
Found at i:31789016 original size:20 final size:19
Alignment explanation
Indices: 31788925--31789021 Score: 122
Period size: 20 Copynumber: 4.9 Consensus size: 19
31788915 AGCTAAAAAC
31788925 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
*
31788944 GAGCTTGAATGAGCTGAATT
1 GAGC-TCAATGAGCTGAATT
*
31788964 GAGCTCAAATGAGCTGACTT
1 GAGCTC-AATGAGCTGAATT
*
31788984 GAGCTCGAATGAGCTGACTT
1 GAGCTC-AATGAGCTGAATT
*
31789004 GAGCTCAAGTGAGTTGAA
1 GAGCTCAA-TGAGCTGAA
31789022 CCACATGAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
19 7 0.10
20 62 0.90
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:31792546 original size:17 final size:18
Alignment explanation
Indices: 31792524--31792565 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
31792514 TATCATATCA
*
31792524 CTCATTTCTTT-TGCACT
1 CTCATTTCTTTCTGCAAT
*
31792541 CTCATTTCTTTCTTCAAT
1 CTCATTTCTTTCTGCAAT
31792559 CTCATTT
1 CTCATTT
31792566 TCAATTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.14, C:0.29, G:0.02, T:0.55
Consensus pattern (18 bp):
CTCATTTCTTTCTGCAAT
Found at i:31794509 original size:22 final size:23
Alignment explanation
Indices: 31794465--31794509 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
31794455 GTACCTATTT
*
31794465 CCAAATCTAATTCGTACCAAAAC
1 CCAAATCTAATTCGTAACAAAAC
* *
31794488 CCAAATCT-TTTCGTAACTAAAC
1 CCAAATCTAATTCGTAACAAAAC
31794510 ATAAATCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.40, C:0.29, G:0.04, T:0.27
Consensus pattern (23 bp):
CCAAATCTAATTCGTAACAAAAC
Found at i:31798486 original size:14 final size:13
Alignment explanation
Indices: 31798458--31798504 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
31798448 AATAAGTGAG
**
31798458 GAAAAAGAAGGAT
1 GAAAAAGAAAAAT
*
31798471 GAGAAGAGAAAAAT
1 GA-AAAAGAAAAAT
31798485 GAAAAAGAAAAA-
1 GAAAAAGAAAAAT
31798497 GAAAAAGA
1 GAAAAAGA
31798505 TGAAATGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 8 0.28
13 11 0.38
14 10 0.34
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (13 bp):
GAAAAAGAAAAAT
Found at i:31798546 original size:18 final size:18
Alignment explanation
Indices: 31798525--31798561 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31798515 TTTCAAAAAC
31798525 AAAAGAGAGTGAAAAGGA
1 AAAAGAGAGTGAAAAGGA
*
31798543 AAAAGAGATTGAAAAGGA
1 AAAAGAGAGTGAAAAGGA
31798561 A
1 A
31798562 GTAAGTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.08
Consensus pattern (18 bp):
AAAAGAGAGTGAAAAGGA
Found at i:31804195 original size:22 final size:22
Alignment explanation
Indices: 31804167--31804210 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31804157 TTTTGAACCA
31804167 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
31804189 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
31804211 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:31805005 original size:14 final size:14
Alignment explanation
Indices: 31804986--31805028 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
31804976 GGATATCAAG
31804986 TTGTGAAAAAAAAT
1 TTGTGAAAAAAAAT
31805000 TTGTGAAAAAAAAAAT
1 TTGTG--AAAAAAAAT
*
31805016 TCGTGAAAAAAAA
1 TTGTGAAAAAAAA
31805029 AAAGAAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.60, C:0.02, G:0.14, T:0.23
Consensus pattern (14 bp):
TTGTGAAAAAAAAT
Found at i:31805012 original size:16 final size:16
Alignment explanation
Indices: 31804991--31805030 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
31804981 TCAAGTTGTG
*
31804991 AAAAAAAATTTGTGAA
1 AAAAAAAATTCGTGAA
31805007 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTGAA
31805023 AAAAAAAA
1 AAAAAAAA
31805031 AGAAAACAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (16 bp):
AAAAAAAATTCGTGAA
Found at i:31821120 original size:15 final size:14
Alignment explanation
Indices: 31821058--31821124 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 14
31821048 AGATTGAGAG
31821058 ATGAA-AAAAAGAA
1 ATGAAGAAAAAGAA
31821071 ATGAAAGAAAAAGAA
1 ATG-AAGAAAAAGAA
* *
31821086 AT-CA-AAAAAGTA
1 ATGAAGAAAAAGAA
31821098 A-G-AGAAAAAGAAA
1 ATGAAGAAAAAG-AA
31821111 ATGAAG-AAAAGAA
1 ATGAAGAAAAAGAA
31821124 A
1 A
31821125 ATTGAAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
11 1 0.02
12 14 0.32
13 9 0.20
14 8 0.18
15 12 0.27
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.07
Consensus pattern (14 bp):
ATGAAGAAAAAGAA
Found at i:31821137 original size:18 final size:18
Alignment explanation
Indices: 31821114--31821162 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
31821104 AAAGAAAATG
31821114 AAGAAAAGAAAATTGAAA
1 AAGAAAAGAAAATTGAAA
** * *
31821132 AAGAAATTAAGATTGAGA
1 AAGAAAAGAAAATTGAAA
31821150 AAGAAAAGAAAAT
1 AAGAAAAGAAAAT
31821163 GAGTTAGAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.14
Consensus pattern (18 bp):
AAGAAAAGAAAATTGAAA
Found at i:31821138 original size:26 final size:25
Alignment explanation
Indices: 31821074--31821143 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
31821064 AAAAGAAATG
31821074 AAAGAAAAAGAAATCAA-AAAAGTA
1 AAAGAAAAAGAAATCAAGAAAAGTA
* *
31821098 AGAGAAAAAGAAAATGAAGAAAAG-A
1 AAAGAAAAAG-AAATCAAGAAAAGTA
*
31821123 AAATTGAAAAAGAAATTAAGA
1 AAA--GAAAAAGAAATCAAGA
31821144 TTGAGAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
24 9 0.24
25 9 0.24
26 13 0.34
27 7 0.18
ACGTcount: A:0.71, C:0.01, G:0.17, T:0.10
Consensus pattern (25 bp):
AAAGAAAAAGAAATCAAGAAAAGTA
Found at i:31821199 original size:27 final size:27
Alignment explanation
Indices: 31821147--31821201 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
31821137 ATTAAGATTG
* * *
31821147 AGAAAGAAAAGAAAATGAGTTAGAAAA
1 AGAAACAAAAGAAAAAGAGTGAGAAAA
*
31821174 AGAAACAAAAGAAAAAGA-TGAGGAAA
1 AGAAACAAAAGAAAAAGAGTGAGAAAA
31821200 AG
1 AG
31821202 GTAGTGAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (27 bp):
AGAAACAAAAGAAAAAGAGTGAGAAAA
Found at i:31829891 original size:18 final size:20
Alignment explanation
Indices: 31829870--31829919 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
31829860 AAAGGAAGAC
31829870 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
31829888 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
31829908 AGGAAAAAGAGA
1 A-GAAAAAGAGA
31829920 TTGAGAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 1 0.04
21 10 0.36
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:31841400 original size:16 final size:16
Alignment explanation
Indices: 31841379--31841411 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31841369 ATTGTAATTG
31841379 AAAAAAAATATATTCA
1 AAAAAAAATATATTCA
*
31841395 AAAAAAAATGTATTCA
1 AAAAAAAATATATTCA
31841411 A
1 A
31841412 TTTCTCCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAAAAATATATTCA
Found at i:31854244 original size:18 final size:18
Alignment explanation
Indices: 31854223--31854266 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
31854213 AAAGGAAGAC
31854223 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
31854241 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
31854259 AGAGAAAA
1 AGA-AAAA
31854267 AAGAGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:31857492 original size:29 final size:29
Alignment explanation
Indices: 31857429--31857496 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
31857419 TAATCAACCA
*
31857429 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
31857458 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
31857487 CGCACACTTA
1 CGCACACTTA
31857497 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Done.