Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold129
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: 3652842
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 48564 characters in sequence are not A, C, G, or T
File 20 of 23
Found at i:3108576 original size:19 final size:21
Alignment explanation
Indices: 3108528--3108583 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
3108518 AATTTCTACA
3108528 ATTTGTATCGATACAAACAGT
1 ATTTGTATCGATACAAACAGT
** *
3108549 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAACAGT
*
3108569 -TTTGTATCCATACAA
1 ATTTGTATCGATACAA
3108584 TGTATCGATA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 11 0.39
20 3 0.11
21 14 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (21 bp):
ATTTGTATCGATACAAACAGT
Found at i:3114384 original size:124 final size:124
Alignment explanation
Indices: 3114185--3114555 Score: 661
Period size: 124 Copynumber: 3.0 Consensus size: 124
3114175 TAAAGTTCCC
** *
3114185 TTCAAAAATGATGAAAAAGTCAAAGGTAATAAAAAGGGGGGAAAAGAAAAAAAAGAAAAAGTGCA
1 TTCAAAAATGATGAAAAAGTCAAAGGTAA-AAAAAATGGGGAGAAGAAAAAAAAGAAAAAGTGCA
*
3114250 AATAAAGAAAAGGAACAACAAAAATTGAAAAACAAGAACATGAATGCTCGTATGAATAGA
65 AATAAAGAAAAGGAACAACAAAAATCGAAAAACAAGAACATGAATGCTCGTATGAATAGA
3114310 TTCAAAAATGATGAAAAAGTCAAAGGTAAAAAAAATGGGGAGAAGAAAAAAAAGAAAAAGTGCAA
1 TTCAAAAATGATGAAAAAGTCAAAGGTAAAAAAAATGGGGAGAAGAAAAAAAAGAAAAAGTGCAA
3114375 ATAAAGAAAAGGAACAACAAAAATCGAAAAACAAGAACATGAATGCTCGTATGAATAGA
66 ATAAAGAAAAGGAACAACAAAAATCGAAAAACAAGAACATGAATGCTCGTATGAATAGA
3114434 TTCAAAAATGATGAAAAAGTCAAAGGTAAAAAAAATGGGGAGAAGAAAAAAAAGAAAAAGTGCAA
1 TTCAAAAATGATGAAAAAGTCAAAGGTAAAAAAAATGGGGAGAAGAAAAAAAAGAAAAAGTGCAA
* * * *
3114499 ATAAAGAAAATGAACAACAAAAATCGAAAAACACGAAGATGAATGCCCGTATGAATA
66 ATAAAGAAAAGGAACAACAAAAATCGAAAAACAAGAACATGAATGCTCGTATGAATA
3114556 TAAATGATCC
Statistics
Matches: 238, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
124 209 0.88
125 29 0.12
ACGTcount: A:0.59, C:0.08, G:0.19, T:0.13
Consensus pattern (124 bp):
TTCAAAAATGATGAAAAAGTCAAAGGTAAAAAAAATGGGGAGAAGAAAAAAAAGAAAAAGTGCAA
ATAAAGAAAAGGAACAACAAAAATCGAAAAACAAGAACATGAATGCTCGTATGAATAGA
Found at i:3115635 original size:13 final size:13
Alignment explanation
Indices: 3115612--3115655 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
3115602 ACATTAACAA
3115612 CATCA-TTATTTG
1 CATCATTTATTTG
3115624 CATCATTTATTTG
1 CATCATTTATTTG
*
3115637 CATCATGTATTTG
1 CATCATTTATTTG
3115650 CATCAT
1 CATCAT
3115656 CACCACATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 5 0.17
13 25 0.83
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (13 bp):
CATCATTTATTTG
Found at i:3115857 original size:64 final size:64
Alignment explanation
Indices: 3115756--3115911 Score: 217
Period size: 64 Copynumber: 2.4 Consensus size: 64
3115746 CTCTGTGGCA
*
3115756 CCCTTTTAAGTTCATAACTCCATGGCACTTTTTATTCAGA-GTCCATGACTTCGTGGCACCGC-T
1 CCCTTTTAAGTTTATAACTCCATGGCACTTTTTATTCA-ACGTCCATGACTTCGTGGCACC-CTT
3115819 T
64 T
* *
3115820 CCCTTTTAAGTTTATAACTCCTTGGCACTTTTTATTCAACGTCCATGGCTTCGTGGCACCCTTT
1 CCCTTTTAAGTTTATAACTCCATGGCACTTTTTATTCAACGTCCATGACTTCGTGGCACCCTTT
** * *
3115884 TTCTTTTAAGTCTACAACTCCATGGCAC
1 CCCTTTTAAGTTTATAACTCCATGGCAC
3115912 CCTTTTTCTT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
63 2 0.02
64 80 0.98
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (64 bp):
CCCTTTTAAGTTTATAACTCCATGGCACTTTTTATTCAACGTCCATGACTTCGTGGCACCCTTT
Found at i:3115944 original size:34 final size:33
Alignment explanation
Indices: 3115871--3115950 Score: 110
Period size: 33 Copynumber: 2.4 Consensus size: 33
3115861 TCCATGGCTT
3115871 CGTGGCACCCTTTTTCTTTTAAGTCTACAACTC
1 CGTGGCACCCTTTTTCTTTTAAGTCTACAACTC
* *
3115904 CATGGCACCCTTTTTCTTTTTCAGT-TCACAACTC
1 CGTGGCACCCTTTTTC-TTTTAAGTCT-ACAACTC
3115938 CGTGGCA-CCTTTT
1 CGTGGCACCCTTTT
3115951 AGTCCTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 22 0.52
34 20 0.48
ACGTcount: A:0.16, C:0.31, G:0.12, T:0.40
Consensus pattern (33 bp):
CGTGGCACCCTTTTTCTTTTAAGTCTACAACTC
Found at i:3116191 original size:37 final size:37
Alignment explanation
Indices: 3116111--3116194 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
3116101 TTTATTTGGA
3116111 TTTTTCCTTTTGTCTTTAAAGAGCAAGACACATTTCT
1 TTTTTCCTTTTGTCTTTAAAGAGCAAGACACATTTCT
** * * *
3116148 GCTTTCCTTTTGTCTTTAAGGAGCAGGACGCA-TTCTT
1 TTTTTCCTTTTGTCTTTAAAGAGCAAGACACATTTC-T
3116185 TTTTTCCTTT
1 TTTTTCCTTT
3116195 CCCCTTTGTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
36 3 0.08
37 36 0.92
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (37 bp):
TTTTTCCTTTTGTCTTTAAAGAGCAAGACACATTTCT
Found at i:3116565 original size:31 final size:30
Alignment explanation
Indices: 3116487--3116573 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 30
3116477 TTCCTTTTCT
* *
3116487 AAAGCCCACATGAATTGGTGGCACCCTAGTC
1 AAAGCCCACA-GAGTTGGTGGCACCCGAGTC
*
3116518 AAAGCCTGCACA-AGTTGG-GGACACTCGAGTC
1 AAAGCC--CACAGAGTTGGTGG-CACCCGAGTC
3116549 AAAGCCCACAGGAGTTGGTGGCACC
1 AAAGCCCACA-GAGTTGGTGGCACC
3116574 TAAGTTTGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
29 4 0.09
30 2 0.04
31 34 0.74
32 2 0.04
33 4 0.09
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (30 bp):
AAAGCCCACAGAGTTGGTGGCACCCGAGTC
Found at i:3116684 original size:31 final size:31
Alignment explanation
Indices: 3116646--3116718 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
3116636 AAGGCTGATG
* *
3116646 CAAGTTGGTGGTA-CCGTAGTTAAAGCCCACA
1 CAAGTTGGTAGTACCCG-AGTCAAAGCCCACA
*
3116677 CAAGTTGGCAGTACCCGAGTCAAAGCCCACA
1 CAAGTTGGTAGTACCCGAGTCAAAGCCCACA
**
3116708 TGAGTTGGTAG
1 CAAGTTGGTAG
3116719 CACCTAAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (31 bp):
CAAGTTGGTAGTACCCGAGTCAAAGCCCACA
Found at i:3116771 original size:149 final size:148
Alignment explanation
Indices: 3116487--3116926 Score: 501
Period size: 149 Copynumber: 3.0 Consensus size: 148
3116477 TTCCTTTTCT
* * * ** * * *
3116487 AAAGCCCACATGAATTGGTGGCACCCTAGTCAAAGCCTGCACAAGTTGGGGACACTCGAGTCAAA
1 AAAGCCCACA-GAGTTGGTGTCACCGTAGTCAAAGCCCACACAAGTTGGAGATACCCGAGTCAAA
* * * *
3116552 GCCCACAGGAGTTGGTGGCACCTAAGTTTGAGTCAAGTCCACATGTA-TTGCCACCTATCTAAGG
65 GCCCACACGAGTTGGTGGCACCTAAGTTCGAGTCAAGTCCACAT-TAGTTGGCACCTGTCTAAGG
3116616 AGGTTAAGCCTTAAAATGTC
129 AGGTTAAGCCTTAAAATGTC
* ** *
3116636 AAGGCTGATGCA-AGTTGGTGGT-ACCGTAGTTAAAGCCCACACAAGTTGGCAG-TACCCGAGTC
1 AAAGCCCA--CAGAGTTGGT-GTCACCGTAGTCAAAGCCCACACAAGTTGG-AGATACCCGAGTC
* * *
3116698 AAAGCCCACATGAGTTGGTAGCACCTAAGTTCAAGTCAAGTCCACATTAGTTGGCACCTGTCTAA
62 AAAGCCCACACGAGTTGGTGGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAA
* *
3116763 GGAGGTTAAGCCCTAGAATGTC
127 GGAGGTTAAGCCTTAAAATGTC
* * * * *
3116785 AAAGCCCACATGAGTTGGTGTCACCTTAGTCAAAGCTCATACAAGTTGGTGATACCCAAGTCAAA
1 AAAGCCCACA-GAGTTGGTGTCACCGTAGTCAAAGCCCACACAAGTTGGAGATACCCGAGTCAAA
** * * *
3116850 GCCCACACGAGTTATTGGCACCTAGGTTCGAGCCAAGTCCACGTTAGTTGGCACCTGTCTAAGGA
65 GCCCACACGAGTTGGTGGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAAGGA
*
3116915 GGTTAAACCTTA
130 GGTTAAGCCTTA
3116927 GAAAACCAAA
Statistics
Matches: 243, Mismatches: 39, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
147 2 0.01
148 5 0.02
149 232 0.95
150 2 0.01
151 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (148 bp):
AAAGCCCACAGAGTTGGTGTCACCGTAGTCAAAGCCCACACAAGTTGGAGATACCCGAGTCAAAG
CCCACACGAGTTGGTGGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAAGGAG
GTTAAGCCTTAAAATGTC
Found at i:3116820 original size:31 final size:31
Alignment explanation
Indices: 3116782--3116862 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
3116772 GCCCTAGAAT
* **
3116782 GTCAAAGCCCACATGAGTTGGTG-TCACCTTA
1 GTCAAAGCCCACACGAGTTGGTGAT-ACCCAA
* * *
3116813 GTCAAAGCTCATACAAGTTGGTGATACCCAA
1 GTCAAAGCCCACACGAGTTGGTGATACCCAA
3116844 GTCAAAGCCCACACGAGTT
1 GTCAAAGCCCACACGAGTT
3116863 ATTGGCACCT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 39 0.98
32 1 0.03
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (31 bp):
GTCAAAGCCCACACGAGTTGGTGATACCCAA
Found at i:3117442 original size:20 final size:20
Alignment explanation
Indices: 3117417--3117505 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
3117407 TTTTTCATTT
3117417 TGTATCGATACAATAGTAAA
1 TGTATCGATACAATAGTAAA
3117437 TGTATCGATAC---A-T-AA
1 TGTATCGATACAATAGTAAA
* *
3117452 TGTATCGATACATTAGTGAA
1 TGTATCGATACAATAGTAAA
* ***
3117472 TGTATCGAAACAAGCCTAAAA
1 TGTATCGATACAATAGT-AAA
3117493 TGTATCGATACAA
1 TGTATCGATACAA
3117506 AACTACCCTG
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
15 13 0.23
16 1 0.02
17 1 0.02
18 1 0.02
19 1 0.02
20 25 0.45
21 14 0.25
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAATAGTAAA
Found at i:3117455 original size:15 final size:15
Alignment explanation
Indices: 3117435--3117464 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3117425 TACAATAGTA
3117435 AATGTATCGATACAT
1 AATGTATCGATACAT
3117450 AATGTATCGATACAT
1 AATGTATCGATACAT
3117465 TAGTGAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
AATGTATCGATACAT
Found at i:3118619 original size:12 final size:12
Alignment explanation
Indices: 3118602--3118635 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3118592 CTTGTAGTTT
**
3118602 TGTCACAAGCCA
1 TGTCACAAAACA
3118614 TGTCACAAAACA
1 TGTCACAAAACA
3118626 TGTCACAAAA
1 TGTCACAAAA
3118636 TTTTTGGCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.18
Consensus pattern (12 bp):
TGTCACAAAACA
Found at i:3122700 original size:157 final size:160
Alignment explanation
Indices: 3122256--3122832 Score: 456
Period size: 157 Copynumber: 3.6 Consensus size: 160
3122246 CCTTAAAGGG
* * * * * *
3122256 TACCTTCAAC-TTAGAAGTATCT-GATACCCCTAAAGGACTTAAAAAAGAT-TA-TAGATGGGAC
1 TACCTTCAACGTGA-AAATATCTCGATAACCCTAAAGGACTTAAAAATGATATAGAAGATGGGAT
* * * * * * * *
3122317 GAACCTATCCTAAATACCCA-CATTCGGCATGAAAGCAGACCCGGTGACAACCTAAGACTTGATT
65 GAACCCATCCTAAATACCCACCTTTCGGCATAAAAGCACACTCGATGACAACCTAGGACTTGGTT
* *
3122381 CTAGAA-AATTATCAAAATAC-CCCTAGAAGA
130 CTA-AATAATTATCAAAATGCTCCCTAGAGGA
** * * * * * ** * * *
3122411 TACCTTTGACCTGAAAATATCCCAATACCCCTACAGGGTTTAAAAAGGTTGTAGCTAAGATGGGA
1 TACCTTCAACGTGAAAATATCTCGATAACCCTAAAGGACTTAAAAATGATATAG--AAGATGGGA
* * * * ** * * *
3122476 TGAATCCATCCTAAATACCTACC-TTCAGCATAGAAGCGGACTCGGT-AGTAACCTAAGG-CTCG
64 TGAACCCATCCTAAATACCCACCTTTCGGCATAAAAGCACACTCGATGA-CAACCT-AGGACTTG
3122538 GTTCTAAGA-AATTA-CAAAAATGCT-CCTATG-GGTA
127 GTTCTAA-ATAATTATC-AAAATGCTCCCTA-GAGG-A
* * * * *
3122572 TACCTTCGACGTGAAAGTGT-T-GCAGTAACCCTGAAGGACTTAAAAA-GAT-TAG-AGATGTGA
1 TACCTTCAACGTGAAAATATCTCG-A-TAACCCTAAAGGACTTAAAAATGATATAGAAGATGGGA
* *
3122632 TGAACCCCATCTTAAATACCCACC-TTCGGCATGAAAGCACACTCGATGACAACCTAGGACTTGG
64 TGAA-CCCATCCTAAATACCCACCTTTCGGCATAAAAGCACACTCGATGACAACCTAGGACTTGG
3122696 TTCTAAATAATTATCAAAATGCTCCCTAGAGGA
128 TTCTAAATAATTATCAAAATGCTCCCTAGAGGA
*
3122729 TACCTTCAACGTGAAAATATCTCGATACCCCTAAAGGACTTAAAAATGATATAGCTAAGATGGGA
1 TACCTTCAACGTGAAAATATCTCGATAACCCTAAAGGACTTAAAAATGATATAG--AAGATGGGA
* *
3122794 TGAACCGATCCTAAATACCCACCTTTTGGCATAAAAGCA
64 TGAACCCATCCTAAATACCCACCTTTCGGCATAAAAGCA
3122833 AACCTGGCAA
Statistics
Matches: 330, Mismatches: 61, Indels: 55
0.74 0.14 0.12
Matches are distributed among these distances:
155 14 0.04
156 38 0.12
157 101 0.31
158 13 0.04
159 10 0.03
160 76 0.23
161 54 0.16
162 24 0.07
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (160 bp):
TACCTTCAACGTGAAAATATCTCGATAACCCTAAAGGACTTAAAAATGATATAGAAGATGGGATG
AACCCATCCTAAATACCCACCTTTCGGCATAAAAGCACACTCGATGACAACCTAGGACTTGGTTC
TAAATAATTATCAAAATGCTCCCTAGAGGA
Found at i:3122895 original size:318 final size:317
Alignment explanation
Indices: 3122283--3122907 Score: 742
Period size: 318 Copynumber: 2.0 Consensus size: 317
3122273 TATCTGATAC
* *
3122283 CCCTAAAGGACTTAAAAAAGATTATAGATGGGACGAACCTATCCTAAATACCCACATTCGGCATG
1 CCCTAAAGGACTTAAAAAAGATTAGAGATGGGACGAACCCATCCTAAATACCCACATTCGGCATG
* *
3122348 AAAGCAGACCCGGTGACAACCTAAGACTTGATTCTAGAAAATTATCAAAATACCCCTAGAAGATA
66 AAAGCACACCCGATGACAACCTAAGACTTGATTCTAGAAAATTATCAAAATACCCCTAGAAGATA
** * ** * *
3122413 CCTTTGACCTGAAAATATCCCAATACCCCTACAGGGTTTAAAAAGGTTGTAGCTAAGATGGGATG
131 CCTTCAACCTGAAAATATCCCAATACCCCTAAAGGACTTAAAAAGGATATAGCTAAGATGGGATG
* * ** * ** *
3122478 AATCCATCCTAAATACCTACCTTCAGCATAGAAGCGGACTCGGTAGTAACCTAAGGCTCGGTTCT
196 AATCCATCCTAAATACCCACCTTCAGCATAAAAGCAAACTCGGCAACAACCTAAGGCTCGATTCT
* * * *
3122543 AAGAAATTACAAAAATGCTCCTATGGGTATACCTTCGACGTGAAAGTGTTGCAGTAA
261 AAGAAATTACAAAAATACCCCTATGGGGATACCTTCGACGTAAAAGTGTTGCAGTAA
* * * * *
3122600 CCCTGAAGGACTT-AAAAAGATTAGAGATGTGATGAACCCCATCTTAAATACCCACCTTCGGCAT
1 CCCTAAAGGACTTAAAAAAGATTAGAGATGGGACGAA-CCCATCCTAAATACCCACATTCGGCAT
* * * * *
3122664 GAAAGCACACTCGATGACAACCTAGGACTTGGTTCTA-AATAATTATCAAAATGCTCCCTAGAGG
65 GAAAGCACACCCGATGACAACCTAAGACTTGATTCTAGAA-AATTATCAAAATAC-CCCTAGAAG
* * * *
3122728 ATACCTTCAACGTGAAAATATCTCGATACCCCTAAAGGACTTAAAAATGATATAGCTAAGATGGG
128 ATACCTTCAACCTGAAAATATCCCAATACCCCTAAAGGACTTAAAAAGGATATAGCTAAGATGGG
** *
3122793 ATGAA-CCGATCCTAAATACCCACCTTTTGGCATAAAAGCAAAC-CTGGCAACAACTTAAGAG-T
193 ATGAATCC-ATCCTAAATACCCACC-TTCAGCATAAAAGCAAACTC-GGCAACAACCTAAG-GCT
* * *
3122855 TGATTCTATA-AAATTACTAAAATACCCCTA-GGGGATACCTTTGACGTAAAAGT
254 CGATTCTA-AGAAATTACAAAAATACCCCTATGGGGATACCTTCGACGTAAAAGT
3122908 ATCCGATATC
Statistics
Matches: 257, Mismatches: 43, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
316 22 0.09
317 83 0.32
318 103 0.40
319 47 0.18
320 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.24
Consensus pattern (317 bp):
CCCTAAAGGACTTAAAAAAGATTAGAGATGGGACGAACCCATCCTAAATACCCACATTCGGCATG
AAAGCACACCCGATGACAACCTAAGACTTGATTCTAGAAAATTATCAAAATACCCCTAGAAGATA
CCTTCAACCTGAAAATATCCCAATACCCCTAAAGGACTTAAAAAGGATATAGCTAAGATGGGATG
AATCCATCCTAAATACCCACCTTCAGCATAAAAGCAAACTCGGCAACAACCTAAGGCTCGATTCT
AAGAAATTACAAAAATACCCCTATGGGGATACCTTCGACGTAAAAGTGTTGCAGTAA
Found at i:3122937 original size:318 final size:315
Alignment explanation
Indices: 3122231--3122938 Score: 741
Period size: 318 Copynumber: 2.2 Consensus size: 315
3122221 AGCTCAAGAA
* ** * * * *
3122231 AAATTACAAAAATGA-CCTTAAAGGG-TACCTTCAACTTAGAAGTATCTGATACCCCTAAAGGAC
1 AAATTACAAAAAT-ACCCCTATGGGGATACCTTCGACGTAAAAGTATCTGATAACCCTAAAGGAC
* * *
3122294 TTAAAAAAGATTATAGATGGGACGAACCTATCCTAAATACCCACATTCGGCATGAAAGCAGACCC
65 -TAAAAAAGATTAGAGATGGGACGAACCCATCCTAAATACCCACATTCGGCATGAAAGCACACCC
* **
3122359 GGTGACAACCTAAGACTTGATTCTAGAAAATTATCAAAATACCCCTAGAAGATACCTTTGACCTG
129 GATGACAACCTAAGACTTGATTCTAGAAAATTATCAAAATACCCCTAGAAGATACCTTCAACCTG
* ** * *
3122424 AAAATATCCCAATACCCCTACAGGGTTTAAAAAGGTTGTAGCTAAGATGGGATGAATCCATCCTA
194 AAAATATCCCAATACCCCTAAAGGACTTAAAAAGGATATAGCTAAGATGGGATGAATCCATCCTA
* * ** * ** *
3122489 AATACCTACCTTCAGCATAGAAGCGGACTCGGTAGTAACCTAAGGCTCGGTTCTAAG
259 AATACCCACCTTCAGCATAAAAGCAAACTCGGCAACAACCTAAGGCTCGATTCTAAG
* * * * * *
3122546 AAATTACAAAAATGCTCCTATGGGTATACCTTCGACGTGAAAGTGT-TGCAGTAACCCTGAAGGA
1 AAATTACAAAAATACCCCTATGGGGATACCTTCGACGTAAAAGTATCTG-A-TAACCCTAAAGGA
* * * * * *
3122610 CTTAAAAAGATTAGAGATGTGATGAACCCCATCTTAAATACCCACCTTCGGCATGAAAGCACACT
64 CTAAAAAAGATTAGAGATGGGACGAA-CCCATCCTAAATACCCACATTCGGCATGAAAGCACACC
* * * *
3122675 CGATGACAACCTAGGACTTGGTTCTA-AATAATTATCAAAATGCTCCCTAGAGGATACCTTCAAC
128 CGATGACAACCTAAGACTTGATTCTAGAA-AATTATCAAAATAC-CCCTAGAAGATACCTTCAAC
* * * *
3122739 GTGAAAATATCTCGATACCCCTAAAGGACTTAAAAATGATATAGCTAAGATGGGATGAA-CCGAT
191 CTGAAAATATCCCAATACCCCTAAAGGACTTAAAAAGGATATAGCTAAGATGGGATGAATCC-AT
** * *
3122803 CCTAAATACCCACCTTTTGGCATAAAAGCAAAC-CTGGCAACAACTTAAGAG-TTGATTCTATA-
255 CCTAAATACCCACC-TTCAGCATAAAAGCAAACTC-GGCAACAACCTAAG-GCTCGATTCTA-AG
* * * * *
3122865 AAATTACTAAAATACCCCTA-GGGGATACCTTTGACGTAAAAGTATCCGATATCCCTAAAGAACT
1 AAATTACAAAAATACCCCTATGGGGATACCTTCGACGTAAAAGTATCTGATAACCCTAAAGGACT
3122929 CAAAAAAGAT
66 -AAAAAAGAT
3122939 ATGTGATAAT
Statistics
Matches: 317, Mismatches: 62, Indels: 25
0.78 0.15 0.06
Matches are distributed among these distances:
315 20 0.06
316 39 0.12
317 95 0.30
318 113 0.36
319 48 0.15
320 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (315 bp):
AAATTACAAAAATACCCCTATGGGGATACCTTCGACGTAAAAGTATCTGATAACCCTAAAGGACT
AAAAAAGATTAGAGATGGGACGAACCCATCCTAAATACCCACATTCGGCATGAAAGCACACCCGA
TGACAACCTAAGACTTGATTCTAGAAAATTATCAAAATACCCCTAGAAGATACCTTCAACCTGAA
AATATCCCAATACCCCTAAAGGACTTAAAAAGGATATAGCTAAGATGGGATGAATCCATCCTAAA
TACCCACCTTCAGCATAAAAGCAAACTCGGCAACAACCTAAGGCTCGATTCTAAG
Found at i:3124704 original size:14 final size:12
Alignment explanation
Indices: 3124685--3124763 Score: 52
Period size: 14 Copynumber: 6.1 Consensus size: 12
3124675 TATAATTCGT
3124685 AAAATTATATCATA
1 AAAATTA-AT-ATA
*
3124699 AAAATTAATAAA
1 AAAATTAATATA
3124711 AAAATTAAATTATAA
1 AAAATT-AA-TAT-A
* *
3124726 AAAATTAAAACTTG
1 AAAATTAATA--TA
3124740 AAAATTAATAT-
1 AAAATTAATATA
*
3124751 AAAATTTATATA
1 AAAATTAATATA
3124763 A
1 A
3124764 TTAATTTTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
11 10 0.19
12 10 0.19
13 5 0.09
14 20 0.38
15 8 0.15
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:3124729 original size:15 final size:15
Alignment explanation
Indices: 3124685--3124734 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
3124675 TATAATTCGT
* *
3124685 AAAATTATATCAT-A
1 AAAATTAAATTATAA
3124699 AAAATT-AA-TA-AA
1 AAAATTAAATTATAA
3124711 AAAATTAAATTATAA
1 AAAATTAAATTATAA
3124726 AAAATTAAA
1 AAAATTAAA
3124735 ACTTGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 8 0.27
13 3 0.10
14 8 0.27
15 11 0.37
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATTAAATTATAA
Found at i:3125088 original size:19 final size:19
Alignment explanation
Indices: 3125066--3125137 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 19
3125056 AAAACTCGTG
3125066 AAAATAAATTAAAATTTTA
1 AAAATAAATTAAAATTTTA
* *
3125085 AAAATAAATTAATATGAATTA
1 AAAATAAATTAAAAT--TTTA
3125106 AATAATAATATTTGACAAATTTTA
1 AA-AATAA-A-TT-A-AAATTTTA
3125130 AAAATAAA
1 AAAATAAA
3125138 AAACCCATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
19 14 0.33
21 5 0.12
22 6 0.14
23 6 0.14
24 7 0.17
25 1 0.02
26 3 0.07
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (19 bp):
AAAATAAATTAAAATTTTA
Found at i:3125690 original size:12 final size:12
Alignment explanation
Indices: 3125673--3125701 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3125663 TCAAGTTTTT
3125673 AAAAAAAATCTC
1 AAAAAAAATCTC
3125685 AAAAAAAATCTC
1 AAAAAAAATCTC
3125697 AAAAA
1 AAAAA
3125702 TAGGAAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAATCTC
Found at i:3127241 original size:13 final size:13
Alignment explanation
Indices: 3127223--3127250 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3127213 TACATGGCAT
3127223 ATTGTATCGATAC
1 ATTGTATCGATAC
3127236 ATTGTATCGATAC
1 ATTGTATCGATAC
3127249 AT
1 AT
3127251 GATGAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:3127268 original size:33 final size:33
Alignment explanation
Indices: 3127204--3127272 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
3127194 CTACCATTGT
*
3127204 TTGTATCGATACATGGCATATTGTATCGATACA
1 TTGTATCGATACATGGCATATTATATCGATACA
*
3127237 TTGTATCGATACAT-G-ATGAATTATATTGATACA
1 TTGTATCGATACATGGCAT--ATTATATCGATACA
3127270 TTG
1 TTG
3127273 CTTCTAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 2 0.06
32 1 0.03
33 29 0.91
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGGCATATTATATCGATACA
Found at i:3128725 original size:36 final size:36
Alignment explanation
Indices: 3128685--3128766 Score: 146
Period size: 36 Copynumber: 2.3 Consensus size: 36
3128675 TTCTCAATAG
3128685 TCGAAGAATCATCATAGGAAGCTAAAGTCACTACCC
1 TCGAAGAATCATCATAGGAAGCTAAAGTCACTACCC
*
3128721 TCGAAGAATCATTATAGGAAGCTAAAGTCACTACCC
1 TCGAAGAATCATCATAGGAAGCTAAAGTCACTACCC
*
3128757 TCGAAAAATC
1 TCGAAGAATC
3128767 CAAGGATCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (36 bp):
TCGAAGAATCATCATAGGAAGCTAAAGTCACTACCC
Found at i:3133582 original size:21 final size:22
Alignment explanation
Indices: 3133558--3133607 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
3133548 ATCAAATTTT
* *
3133558 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
3133579 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
3133601 --TCAAAAT
1 CTTCAAAAT
3133608 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:3136049 original size:13 final size:13
Alignment explanation
Indices: 3136031--3136055 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3136021 TACATGGCGC
3136031 ATTGTATCGATAT
1 ATTGTATCGATAT
3136044 ATTGTATCGATA
1 ATTGTATCGATA
3136056 CATGATGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:3136068 original size:33 final size:33
Alignment explanation
Indices: 3136012--3136080 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
3136002 TTACCACTAT
* * *
3136012 TTGTATCGATACATGGCGCATTGTATCGATATA
1 TTGTATCGATACATGACGAATTGTATCGATACA
* *
3136045 TTGTATCGATACATGATGAATTGTATTGATACA
1 TTGTATCGATACATGACGAATTGTATCGATACA
3136078 TTG
1 TTG
3136081 CTTCTAATGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGACGAATTGTATCGATACA
Found at i:3137199 original size:42 final size:42
Alignment explanation
Indices: 3136973--3137364 Score: 224
Period size: 41 Copynumber: 9.5 Consensus size: 42
3136963 AGGGGATAAA
* * * *
3136973 GGTTTACCAAGGACTAAGCCAATAGGTAAACAAAAGATGAA-
1 GGTTGACCAGGGACTAAGCCGATAGGTAAACAAAGGATGAAG
** * * *
3137014 GGTTGACCAGAAACTAAGCTGACAGGTTAACAAAGGATG-AG
1 GGTTGACCAGGGACTAAGCCGATAGGTAAACAAAGGATGAAG
* * * * * **
3137055 GGTTTACTAGGGACTGAGCCGACAAGTAAACATGGGATGAA-
1 GGTTGACCAGGGACTAAGCCGATAGGTAAACAAAGGATGAAG
* * * ** * *
3137096 GGTTGACTAGAGACTGAGTTGATAGGTCAATAAA-GATGAGAG
1 GGTTGACCAGGGACTAAGCCGATAGGTAAACAAAGGATGA-AG
* * ** * *
3137138 GTTTAATGA-GGACTGAGCCGATAGGTAAACAACGGATGAAG
1 GGTTGACCAGGGACTAAGCCGATAGGTAAACAAAGGATGAAG
* * * * *
3137179 GGTTGACCGGGGACTAAGCCGACAGGTCACCAAGGGGAT-AAG
1 GGTTGACCAGGGACTAAGCCGATAGGTAAACAA-AGGATGAAG
* * * *
3137221 GGTTTACCAAGGACTAAGTCGATAGGTAAATAAAGGATGAA-
1 GGTTGACCAGGGACTAAGCCGATAGGTAAACAAAGGATGAAG
* ** * * ** *
3137262 GGTTGA-CTGAAAACTGAGCTGATAGGTCGACAAAGGATGAGG
1 GGTTGACCAG-GGACTAAGCCGATAGGTAAACAAAGGATGAAG
* * * * * *
3137304 GGTTTACCAGGGACTGAGTCGACAGGTAAATAAGGGATGAAG
1 GGTTGACCAGGGACTAAGCCGATAGGTAAACAAAGGATGAAG
*
3137346 GGTTGATCAGGGACTAAGC
1 GGTTGACCAGGGACTAAGC
3137365 TGACAGGTCA
Statistics
Matches: 254, Mismatches: 86, Indels: 21
0.70 0.24 0.06
Matches are distributed among these distances:
40 7 0.03
41 139 0.55
42 102 0.40
43 6 0.02
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (42 bp):
GGTTGACCAGGGACTAAGCCGATAGGTAAACAAAGGATGAAG
Found at i:3137339 original size:125 final size:124
Alignment explanation
Indices: 3136961--3137363 Score: 379
Period size: 125 Copynumber: 3.2 Consensus size: 124
3136951 GATAGGTCAC
* * * * * *
3136961 TAAGGGGAT-AAAGGTTTACCAAGGACTAAGCCAATAGGTAAACAAAAGATGAAGGTTGAC-CAG
1 TAAGGGGATGAAGGGTTGACCAAGGACTAAGTCGATAGGTAAA-TAAAGATGAAGGTTGACTGA-
* * * * *
3137024 AAACTAAGCTGACAGGTTAACAAAGGATGAGGGTTTACTAGGGACTGAGCCGACAAGTAAA
64 AAACTGAGCTGATAGGTAAACAAAGGATGAGGGTTTACCAGGGACTGAGCCGACAGGTAAA
* * * * * * * *
3137085 -CATGGGATGAA-GGTTGA-CTAGAGACTGAGTTGATAGGTCAATAAAGATGAGAGGTTTAATGA
1 TAAGGGGATGAAGGGTTGACCAAG-GACTAAGTCGATAGGTAAATAAAGATGA-AGGTTGACTGA
** * * * * * * *
3137147 GGACTGAGCCGATAGGTAAACAACGGATGAAGGGTTGACCGGGGACTAAGCCGACAGGTCAC
64 AAACTGAGCTGATAGGTAAACAAAGGATG-AGGGTTTACCAGGGACTGAGCCGACAGGTAAA
* *
3137209 CAAGGGGAT-AAGGGTTTACCAAGGACTAAGTCGATAGGTAAATAAAGGATGAAGGTTGACTGAA
1 TAAGGGGATGAAGGGTTGACCAAGGACTAAGTCGATAGGTAAATAAA-GATGAAGGTTGACTGAA
** *
3137273 AACTGAGCTGATAGGTCGACAAAGGATGAGGGGTTTACCAGGGACTGAGTCGACAGGTAAA
65 AACTGAGCTGATAGGTAAACAAAGGATGA-GGGTTTACCAGGGACTGAGCCGACAGGTAAA
* *
3137334 TAA-GGGATGAAGGGTTGATCAGGGACTAAG
1 TAAGGGGATGAAGGGTTGACCAAGGACTAAG
3137364 CTGACAGGTC
Statistics
Matches: 216, Mismatches: 52, Indels: 21
0.75 0.18 0.07
Matches are distributed among these distances:
122 11 0.05
123 53 0.25
124 36 0.17
125 108 0.50
126 8 0.04
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (124 bp):
TAAGGGGATGAAGGGTTGACCAAGGACTAAGTCGATAGGTAAATAAAGATGAAGGTTGACTGAAA
ACTGAGCTGATAGGTAAACAAAGGATGAGGGTTTACCAGGGACTGAGCCGACAGGTAAA
Found at i:3137728 original size:42 final size:42
Alignment explanation
Indices: 3137639--3137902 Score: 138
Period size: 42 Copynumber: 6.3 Consensus size: 42
3137629 AGATTGAAAA
* *
3137639 AAGAAATCTTTCAGGACTGAGCTGATGGGCAGACGAAAGATG
1 AAGAAGTCTTTCAGGACTGAGCTGATGGGCAGACAAAAGATG
*
3137681 AAGAAGTCTTTC-GAGACTGA-CTCGATGGGTAGACAAAAGATG
1 AAGAAGTCTTTCAG-GACTGAGCT-GATGGGCAGACAAAAGATG
** ** * * * * *
3137723 AAGAAGTCTCACAGCTCTAAGCCGATGGGCAAACAAAGGATA
1 AAGAAGTCTTTCAGGACTGAGCTGATGGGCAGACAAAAGATG
** *** * * * ** * * *
3137765 AAGAAGTCTCCCAACTCTAAGTTAACAGGCAAACAAAGGGTG
1 AAGAAGTCTTTCAGGACTGAGCTGATGGGCAGACAAAAGATG
* * * *
3137807 AAGAAGTCTCTCGGGTCTAAGCTGATGGGCAGACAAAGAGATG
1 AAGAAGTCTTTCAGGACTGAGCTGATGGGCAGACAAA-AGATG
** * * * * * * *
3137850 AAGAAGTCTCCCGGGTCTAAGCCGATGGGAAGACAAAGGATA
1 AAGAAGTCTTTCAGGACTGAGCTGATGGGCAGACAAAAGATG
3137892 AAGAAGT-TTTC
1 AAGAAGTCTTTC
3137903 GGAGTCTGAA
Statistics
Matches: 177, Mismatches: 40, Indels: 11
0.78 0.18 0.05
Matches are distributed among these distances:
41 5 0.03
42 133 0.75
43 39 0.22
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (42 bp):
AAGAAGTCTTTCAGGACTGAGCTGATGGGCAGACAAAAGATG
Found at i:3137886 original size:127 final size:127
Alignment explanation
Indices: 3137703--3138017 Score: 354
Period size: 127 Copynumber: 2.5 Consensus size: 127
3137693 GAGACTGACT
* *
3137703 CGATGGGTAGACAAA-AGATGAAGAAGTCTCACAGCTCTAAGCCGATGGGCAA-ACAAAGGATAA
1 CGATGGGCAGACAAAGAGATGAAGAAGTCTCACAGGTCTAAGCCGATGGG-AAGACAAAGGATAA
* * * *
3137766 AGAAGTCTCCCAACTCT-AAGTTAACAGGCAAACAAAGGGTGAAGA-AGTCTCTCGGGTCTAAGC
65 AGAAGTCTCCCAACTCTGAA-TCAACAGGCAAACAAAGGAT-AAAATAATCTCTCGGGTCTAAGC
* * *
3137829 TGATGGGCAGACAAAGAGATGAAGAAGTCTCCCGGGTCTAAGCCGATGGGAAGACAAAGGATAAA
1 CGATGGGCAGACAAAGAGATGAAGAAGTCTCACAGGTCTAAGCCGATGGGAAGACAAAGGATAAA
* * ** * * * *
3137894 GAAGTTTTCGGAGTCTGAATCGACGGGCAAACAAAGGATAAAATAATCTCTCGGGTCTATGC
66 GAAGTCTCCCAACTCTGAATCAACAGGCAAACAAAGGATAAAATAATCTCTCGGGTCTAAGC
* * * * *
3137956 CGATGGGCAGACAAAG-GAT-AAAATAGTCTCTCATGTCTAAACCGATGGGCAGACAAAGGATA
1 CGATGGGCAGACAAAGAGATGAAGA-AGTCTCACAGGTCTAAGCCGATGGGAAGACAAAGGATA
3138018 TAAGGTGTTT
Statistics
Matches: 160, Mismatches: 24, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
125 3 0.02
126 54 0.34
127 101 0.63
128 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (127 bp):
CGATGGGCAGACAAAGAGATGAAGAAGTCTCACAGGTCTAAGCCGATGGGAAGACAAAGGATAAA
GAAGTCTCCCAACTCTGAATCAACAGGCAAACAAAGGATAAAATAATCTCTCGGGTCTAAGC
Found at i:3137964 original size:42 final size:41
Alignment explanation
Indices: 3137703--3138017 Score: 238
Period size: 42 Copynumber: 7.5 Consensus size: 41
3137693 GAGACTGACT
* * * * * *
3137703 CGATGGGTAGACAAAAGATGAAGAAGTCTCACAGCTCTAAGC
1 CGATGGGCAGACAAAGGAT-AAAAAGTCTCTCGGGTCTAAGC
* * *** *
3137745 CGATGGGCAAACAAAGGATAAAGAAGTCTCCCAACTCTAAGT
1 CGATGGGCAGACAAAGGATAAA-AAGTCTCTCGGGTCTAAGC
** ** * * *
3137787 TAACAGGCAAACAAAGGGTGAAGAAGTCTCTCGGGTCTAAGC
1 CGATGGGCAGACAAAGGAT-AAAAAGTCTCTCGGGTCTAAGC
* * *
3137829 TGATGGGCAGACAAAGAGATGAAGAAGTCTCCCGGGTCTAAGC
1 CGATGGGCAGACAAAG-GAT-AAAAAGTCTCTCGGGTCTAAGC
* * *
3137872 CGATGGGAAGACAAAGGATAAAGAAGT-TTTCGGAGTCTGAA-T
1 CGATGGGCAGACAAAGGATAAA-AAGTCTCTCGG-GTCT-AAGC
* * * *
3137914 CGACGGGCAAACAAAGGATAAAATAATCTCTCGGGTCTATGC
1 CGATGGGCAGACAAAGGATAAAA-AGTCTCTCGGGTCTAAGC
** *
3137956 CGATGGGCAGACAAAGGATAAAATAGTCTCTCATGTCTAAAC
1 CGATGGGCAGACAAAGGATAAAA-AGTCTCTCGGGTCTAAGC
3137998 CGATGGGCAGACAAAGGATA
1 CGATGGGCAGACAAAGGATA
3138018 TAAGGTGTTT
Statistics
Matches: 220, Mismatches: 44, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
41 10 0.05
42 163 0.74
43 47 0.21
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (41 bp):
CGATGGGCAGACAAAGGATAAAAAGTCTCTCGGGTCTAAGC
Found at i:3138437 original size:89 final size:89
Alignment explanation
Indices: 3138285--3138451 Score: 212
Period size: 89 Copynumber: 1.9 Consensus size: 89
3138275 AGTTCTCCCT
* ** *
3138285 TTGCCCCAAGGAAAATCAGGCTTCGTGATGCATCAGTACCATTTAATGGTTGGATGAAAGGGATA
1 TTGCCCCAAGGAAAATCAGGCTTCGTGATGCATCAATACCACCTAATGGTTAGATGAAAGGGATA
*
3138350 CAATTGGGAATGTGTGAGCTACACC
66 -AATTAGGAATGTGTGAGCTACACC
* * * *
3138375 TTGCCCCATGG-AAATCAGGCTTTGTGATGCGTCAATACCACCTAGTGGTTA-AGTGAAAGGGAT
1 TTGCCCCAAGGAAAATCAGGCTTCGTGATGCATCAATACCACCTAATGGTTAGA-TGAAAGGGAT
*
3138438 ATATTAGGAATGTG
65 AAATTAGGAATGTG
3138452 GGGTTGAGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
88 12 0.18
89 44 0.67
90 10 0.15
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (89 bp):
TTGCCCCAAGGAAAATCAGGCTTCGTGATGCATCAATACCACCTAATGGTTAGATGAAAGGGATA
AATTAGGAATGTGTGAGCTACACC
Found at i:3139592 original size:112 final size:109
Alignment explanation
Indices: 3139387--3139711 Score: 296
Period size: 111 Copynumber: 2.9 Consensus size: 109
3139377 GTGGGCCTAG
* * * * ** *
3139387 AAATTTCAAAACTGATAGGGTGCATGCCTTATTTTCCTAGGCACGAATGGGCCGGAACGTATGAA
1 AAATTTCAAAACTGATAAGATACGTG-CTTATTTTCCTAGGCACGAATGGATCGAAACGTAT-AA
** *
3139452 ATATGGGTTTCTTTC-AAAATCTAACAAATTTGATGTTGCGGAGCTCA
64 ATATGAATTTC-TTCGAAAAT-TAACAAATTTGATGTTACGGAGCTCA
3139499 AAGATTTCAAAACTGATAAGATACGTGCTT-TATTTCCTAGGCACGAATGGATCGAAACGTATAA
1 AA-ATTTCAAAACTGATAAGATACGTGCTTAT-TTTCCTAGGCACGAATGGATCGAAACGTATAA
* * *
3139563 AGTATGAATTTCTTCGAAAATTAAGCAAATATGATGTTATGGGGCTCA
64 A-TATGAATTTCTTCGAAAATTAA-CAAATTTGATGTTACGGAGCTCA
** * * * ** * ** *
3139611 AAAAGTCGAAACTGACAAGATATGTGCCCATTTTCCTAAGCAAAAATGGATC-AAGATGTATAAA
1 AAATTTCAAAACTGATAAGATACGTGCTTATTTTCCTAGGCACGAATGGATCGAA-ACGTAT-AA
* *
3139675 ACATGAATTTCTTTGAAAATTAAACAAATTTGATGTT
64 ATATGAATTTCTTCGAAAATT-AACAAATTTGATGTT
3139712 CTTCCAAGTT
Statistics
Matches: 177, Mismatches: 27, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
110 2 0.01
111 83 0.47
112 72 0.41
113 20 0.11
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (109 bp):
AAATTTCAAAACTGATAAGATACGTGCTTATTTTCCTAGGCACGAATGGATCGAAACGTATAAAT
ATGAATTTCTTCGAAAATTAACAAATTTGATGTTACGGAGCTCA
Found at i:3140003 original size:9 final size:9
Alignment explanation
Indices: 3139991--3140023 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3139981 CCATTTCTCT
3139991 TTTTTCTTC
1 TTTTTCTTC
3140000 TTTTTCATT-
1 TTTTTC-TTC
3140009 TTTTTCTTC
1 TTTTTCTTC
3140018 TTTTTC
1 TTTTTC
3140024 ACAACTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:3140005 original size:18 final size:18
Alignment explanation
Indices: 3139990--3140024 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3139980 TCCATTTCTC
3139990 TTTTTTCTTCTTTTTCAT
1 TTTTTTCTTCTTTTTCAT
3140008 TTTTTTCTTCTTTTTCA
1 TTTTTTCTTCTTTTTCA
3140025 CAACTTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTCTTCTTTTTCAT
Found at i:3140273 original size:11 final size:10
Alignment explanation
Indices: 3140257--3140328 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 10
3140247 TTCCTCATAT
3140257 TTTTTCTTTC
1 TTTTTCTTTC
*
3140267 ATTTTTCTCTTT
1 -TTTTTCT-TTC
*
3140279 TTTTGTACCTTC
1 TTTT-T-CTTTC
*
3140291 TTTTTCATTTGA
1 TTTTTC-TTT-C
3140303 TTTTTCTTTC
1 TTTTTCTTTC
3140313 TTTTTCTTTTC
1 TTTTTC-TTTC
3140324 TTTTT
1 TTTTT
3140329 TTCTTTTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
10 7 0.14
11 26 0.53
12 15 0.31
13 1 0.02
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:3141172 original size:16 final size:16
Alignment explanation
Indices: 3141151--3141182 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3141141 TTTATCTAGG
3141151 GAATCACGGTTTGGGT
1 GAATCACGGTTTGGGT
*
3141167 GAATCATGGTTTGGGT
1 GAATCACGGTTTGGGT
3141183 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.09, G:0.38, T:0.34
Consensus pattern (16 bp):
GAATCACGGTTTGGGT
Found at i:3144578 original size:160 final size:158
Alignment explanation
Indices: 3143964--3144624 Score: 492
Period size: 160 Copynumber: 4.2 Consensus size: 158
3143954 GAATTACCCG
**
3143964 ATACCCCTAAAGGACTTAAAAAAGAT-TA-TAGATGGGACAAACCTATCCTAAATACCCACCTTT
1 ATACCCCTAAAGGACTTAAAAAAGATATAGTAGATGGGATGAACCTATCCTAAATACCCACCTTT
* * * * * * * * *
3144027 GGCATAAAAGCGGACCTGGTGACAACCTAGGACTTGGCTCTAAAAAATTACCAAAATACCCTTAG
66 GGAATAAAAGCAGACCCGGAGACAACCTAAGACTTGGTTTTAAAAAATTACCAAAATGCCCTAAG
* * * *
3144092 AAGACACATTC-AGCGTGAAAGTATCTCG
131 AGGACACTTTCGA-CGTGAAAGTATCCCA
* * ** * *
3144120 GTACCCCT-AAGTACTTAAAAGGGATATAGCTAAGGTGGGATGAACCTATCCTAAATACCTACCT
1 ATACCCCTAAAGGACTTAAAAAAGATATAG-T-AGATGGGATGAACCTATCCTAAATACCCACCT
* * * * * * * * **
3144184 TCT-GCATAGAAGCAAATCC-GATGGCAACCTAAGACTCGATTTTCAAGAAATTATGAAAATGCC
64 T-TGGAATAAAAGCAGACCCGGA-GACAACCTAAGACTTGGTTTT-AAAAAATTACCAAAATGCC
* * * * *
3144247 TTATG-GGTATACCTTCGACGTGAAAGTATCCCC
126 CTAAGAGG-ACACTTTCGACGTGAAAGTATCCCA
* * * * * * * * * *
3144280 GTAACCCTAGAGGACTT-AAAACGAT-TAG-ACATGGGATGAACCTATCGTAAAAACTCATCTTC
1 ATACCCCTAAAGGACTTAAAAAAGATATAGTAGATGGGATGAACCTATCCTAAATACCCACCTTT
* * * * *
3144342 GGAATGAAAA-CGGACCC-AATGACAGCCTAGGACTTGGTTTTAAAAAATTACCAAAATGCCCTT
66 GGAAT-AAAAGCAGACCCGGA-GACAACCTAAGACTTGGTTTTAAAAAATTACCAAAATGCCCTA
3144405 AGAGGACACTTTCGACGTGAAAGTATCCCA
129 AGAGGACACTTTCGACGTGAAAGTATCCCA
* * * *
3144435 ATACCCCTAGAGGACTTAAAAATGATATAGCTAAGATGGGATGAACCTATCCCAAATGCCCACCT
1 ATACCCCTAAAGGACTTAAAAAAGATATAG-T-AGATGGGATGAACCTATCCTAAATACCCACCT
* * * * *
3144500 TTGGAATAAAAGTAGACCCGGCAG-CAACCTAAGAGTTGGTTTTGAAAAATTACTAAAATACCCC
64 TTGGAATAAAAGCAGACCCGG-AGACAACCTAAGACTTGGTTTTAAAAAATTACCAAAAT-GCCC
* *
3144564 TAAG-GGATACTTTCGAAGT-AGAAGTA-CCCA
127 TAAGAGGACACTTTCGACGTGA-AAGTATCCCA
* * *
3144594 ATATCCCTAAAGGGCTCAAAAAAGATA-AGTA
1 ATACCCCTAAAGGACTTAAAAAAGATATAGTA
3144625 ATAATGACTT
Statistics
Matches: 389, Mismatches: 93, Indels: 46
0.74 0.18 0.09
Matches are distributed among these distances:
155 69 0.18
156 70 0.18
157 7 0.02
158 4 0.01
159 90 0.23
160 134 0.34
161 14 0.04
162 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.23
Consensus pattern (158 bp):
ATACCCCTAAAGGACTTAAAAAAGATATAGTAGATGGGATGAACCTATCCTAAATACCCACCTTT
GGAATAAAAGCAGACCCGGAGACAACCTAAGACTTGGTTTTAAAAAATTACCAAAATGCCCTAAG
AGGACACTTTCGACGTGAAAGTATCCCA
Found at i:3147891 original size:32 final size:33
Alignment explanation
Indices: 3147835--3147896 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
3147825 CACCTAGATA
* *
3147835 TATCGATACATGTTGCTTAGTATCGATACATTG
1 TATCAATACATATTGCTTAGTATCGATACATTG
*
3147868 TATCAATACATATT-CTTTGTATCGATACA
1 TATCAATACATATTGCTTAGTATCGATACA
3147897 CCATAAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (33 bp):
TATCAATACATATTGCTTAGTATCGATACATTG
Found at i:3149474 original size:3 final size:3
Alignment explanation
Indices: 3149466--3149512 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
3149456 CAACCATCAT
*
3149466 TGA TGA TGA AGA T-A TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
3149513 GGTTGACTCG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:3152442 original size:28 final size:28
Alignment explanation
Indices: 3152402--3152890 Score: 611
Period size: 28 Copynumber: 17.2 Consensus size: 28
3152392 GATGTATATG
* *
3152402 TTGAAAGGGTGCCATTGACTTATGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
*
3152430 TTGAAAGGGTGCCACTGACTCGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
** *
3152458 TTGAAAGAATGCCACTTACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* *
3152486 TTGAAAAGAGTGCCACTGACTTATGGGCT
1 TTG-AAAGGGTGCCACTGACTTGTGGGCT
*
3152515 TTGAAAGGATGCCACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
*
3152543 TTGAAAAGAGTGCCACTGACTTGTGGGCT
1 TTG-AAAGGGTGCCACTGACTTGTGGGCT
** *
3152572 TTGAAAGGGTTTCACTGACTTATGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
3152600 TTGAAA-GGTGCCACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
*
3152627 TTGAAAGGATGCCACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* *
3152655 TTGAAAAGAGTTGCCACTGACTCGTGGGCT
1 TTG-AAAG-GGTGCCACTGACTTGTGGGCT
* *
3152685 TTGAAAAGAGTTGCCACTGACTCGTGGGCT
1 TTG-AAAG-GGTGCCACTGACTTGTGGGCT
* *
3152715 TTGAAAAGAGTTGCCACTGACTCGTGGGCT
1 TTG-AAAG-GGTGCCACTGACTTGTGGGCT
** * **
3152745 TTGAAAGGAAGCTACTGACTCATGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* *
3152773 TTGAAAGGATGCCACTGACTTGCGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
3152801 TTGAAAGGGTGCCACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* * *
3152829 TGGAAAGGATGCGACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* *
3152857 TTAAAAGGGTACCACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
3152885 TTGAAA
1 TTGAAA
3152891 AGATGAACGT
Statistics
Matches: 411, Mismatches: 45, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
27 24 0.06
28 246 0.60
29 59 0.14
30 82 0.20
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (28 bp):
TTGAAAGGGTGCCACTGACTTGTGGGCT
Found at i:3157141 original size:52 final size:52
Alignment explanation
Indices: 3157070--3157172 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
3157060 CGAAATATGA
* **
3157070 AAATTTGCCTACATTTATCGATACATTGCAT-AATGTATCGATACATCTGAGC
1 AAATTTGCCTACATGTATCGATACAAAG-ATCAATGTATCGATACATCTGAGC
* * *
3157122 AAATTTGCCTGCATGTATCGATACAAAGGTCAATGTATCGATACATTTGAG
1 AAATTTGCCTACATGTATCGATACAAAGATCAATGTATCGATACATCTGAG
3157173 TAATGTATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
51 1 0.02
52 43 0.98
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTACATGTATCGATACAAAGATCAATGTATCGATACATCTGAGC
Found at i:3157243 original size:19 final size:18
Alignment explanation
Indices: 3157219--3157281 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
3157209 AGCGATACAT
3157219 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
3157238 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
3157251 TGTATCCATACAACACTTA
1 TGTATCGATACAA-ACTTA
3157270 TGTATCGATACA
1 TGTATCGATACA
3157282 GTTACAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:3157252 original size:32 final size:32
Alignment explanation
Indices: 3157211--3157281 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
3157201 AGCTTCATAG
*
3157211 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCCATACAAAACTTATGTAT
*
3157243 CGATACATTGTATCCATACAACACTTATGTAT
1 CGATACATTGTATCCATACAAAACTTATGTAT
3157275 CGATACA
1 CGATACA
3157282 GTTACAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCCATACAAAACTTATGTAT
Found at i:3158178 original size:98 final size:101
Alignment explanation
Indices: 3158016--3158281 Score: 278
Period size: 98 Copynumber: 2.7 Consensus size: 101
3158006 TGCCAATGCA
* ** * *
3158016 CTGATTCAAGGCCAACGACATTGGGTTTTAAAGATAACGAAGGCACCAATATGCTGATTCAAGGC
1 CTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGACAAAGGCACCAATATGCTGATTCAAGGC
* *
3158081 CAGCGATACT-GATCTTTAAA-GATGAA-C-C-AATGTG
65 CAGCGATACTGGA-C-TTAAATGACGAAGCACTAATATG
* * * *
3158115 CTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGGCGCTAATATGCTGATTTAAGGCC
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCACCAATATGCTGATTCAAGGCC
*
3158180 AGCGATATTGGACTTAAAGTTGACGAAGGCACTAATATG
66 AGCGATACTGGACTTAAA--TGACGAA-GCACTAATATG
* ** *
3158219 CTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGCCAATGTGCTGATTCAAGGCC
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCACCAATATGCTGATTCAAGGCC
3158281 A
66 A
3158282 ACGACATTGG
Statistics
Matches: 141, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
97 5 0.04
98 45 0.32
99 22 0.16
100 5 0.04
101 24 0.17
102 1 0.01
103 1 0.01
104 38 0.27
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (101 bp):
CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCACCAATATGCTGATTCAAGGCC
AGCGATACTGGACTTAAATGACGAAGCACTAATATG
Found at i:3158191 original size:52 final size:51
Alignment explanation
Indices: 3158016--3158303 Score: 279
Period size: 52 Copynumber: 5.7 Consensus size: 51
3158006 TGCCAATGCA
* ** * * *
3158016 CTGATTCAAGGCCAACGACATTGGGTTTTAAAGATAACGAAGGCACCAATATG
1 CTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGAC-AAGGCGCTAATATG
* * *
3158069 CTGATTCAAGGCCAGCGATACT-GATCTTTAAAGATG--AA--C-C-AATGTG
1 CTGATTCAAGGCCAGCGACATTGGA-C-TTAAAGATGACAAGGCGCTAATATG
*
3158115 CTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGGCGCTAATATG
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC-AAGGCGCTAATATG
* * * *
3158167 CTGATTTAAGGCCAGCGATATTGGACTTAAAGTTGACGAAGGCACTAATATG
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC-AAGGCGCTAATATG
* * * *
3158219 CTGATTCAAGGCCAGCGATATTGGACTTAAAGATG--AAGGTGCCAATGTG
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAGGCGCTAATATG
* *
3158268 CTGATTCAAGGCCAACGACATTGGTCTTAAAGATGA
1 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
3158304 TGAGGATGAG
Statistics
Matches: 198, Mismatches: 26, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
45 9 0.05
46 25 0.13
47 3 0.02
48 3 0.02
49 42 0.21
50 3 0.02
51 2 0.01
52 84 0.42
53 27 0.14
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (51 bp):
CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAGGCGCTAATATG
Found at i:3158226 original size:150 final size:151
Alignment explanation
Indices: 3158016--3158303 Score: 402
Period size: 150 Copynumber: 1.9 Consensus size: 151
3158006 TGCCAATGCA
**
3158016 CTGATTCAAGGCCAACGACATTGGGTTTTAAAGATAACGAAGGCACCAATATGCTGATTCAAGGC
1 CTGATTCAAGGCCAACGACATTGGGACTTAAAGATAACGAAGGCACCAATATGCTGATTCAAGGC
**
3158081 CAGCGATACT-GATCTTTAAAGATGAA-CCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTA
66 CAGCGATACTGGA-C-TTAAAGATGAAGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTA
3158144 AAGATGACAAAGGCGCTAATATG
129 AAGATGACAAAGGCGCTAATATG
* * * * * *
3158167 CTGATTTAAGGCCAGCGATATT-GGACTTAAAGTTGACGAAGGCACTAATATGCTGATTCAAGGC
1 CTGATTCAAGGCCAACGACATTGGGACTTAAAGATAACGAAGGCACCAATATGCTGATTCAAGGC
* *
3158231 CAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTT
66 CAGCGATACTGGACTTAAAGATGAA---GCCAATGTGCTGATTCAAGGCCAACGACATTGGACTT
3158296 AAAGATGA
128 AAAGATGA
3158304 TGAGGATGAG
Statistics
Matches: 120, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
149 11 0.09
150 47 0.39
151 21 0.17
153 41 0.34
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (151 bp):
CTGATTCAAGGCCAACGACATTGGGACTTAAAGATAACGAAGGCACCAATATGCTGATTCAAGGC
CAGCGATACTGGACTTAAAGATGAAGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAA
GATGACAAAGGCGCTAATATG
Found at i:3158381 original size:49 final size:49
Alignment explanation
Indices: 3158324--3158521 Score: 227
Period size: 49 Copynumber: 4.0 Consensus size: 49
3158314 AAAAGTGATA
* * * * *
3158324 AAGGTGCCAATATGCTGATTCAGGGCTAGTGATATTGGGCTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATG
**
3158373 AAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATG
* *
3158422 AAGATGCCAATGTGCTGATTCAAGGCCAGTGACATTGGTCTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATG
** * *
3158471 AAGAAG-GCACCAACATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGA
1 AAG--GTG--CCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTA-AAGA
3158522 AGATGCCACC
Statistics
Matches: 127, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
49 90 0.71
50 1 0.01
52 32 0.25
53 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (49 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATG
Found at i:3158629 original size:28 final size:28
Alignment explanation
Indices: 3158538--3158633 Score: 131
Period size: 28 Copynumber: 3.4 Consensus size: 28
3158528 CACCAACTTG
*
3158538 TGTGGGCTTTTGAAGGTTGCCATTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
3158566 TGTGGGCTTTGGAAAAGAG-TGCCACTGACT
1 TGTGGGCTTTTG--AAG-GTTGCCACTGACT
*
3158596 TGTGGGCTTTTGAAGGTTGCGACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
3158624 TGTGGGCTTT
1 TGTGGGCTTT
3158634 GGAAAAGGTG
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.02
28 34 0.57
30 24 0.40
31 1 0.02
ACGTcount: A:0.16, C:0.15, G:0.34, T:0.35
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:3160080 original size:1 final size:1
Alignment explanation
Indices: 3160074--3160197 Score: 95
Period size: 1 Copynumber: 124.0 Consensus size: 1
3160064 CATCCAGACC
** * * * * * *
3160074 TTTTTTTTTTTTTTTTTGGTTTGTTTTTTTGTTTTTTTTCTTTGTTTTTTTTCTTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * *
3160139 TTTGTTTATTTGTTTTTTTTTGTTTTGTTTTTTTGTTTGTTTTTTTGTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3160198 GTGGAGGATG
Statistics
Matches: 91, Mismatches: 32, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 91 1.00
ACGTcount: A:0.01, C:0.02, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:3160100 original size:13 final size:12
Alignment explanation
Indices: 3160074--3160199 Score: 115
Period size: 12 Copynumber: 10.8 Consensus size: 12
3160064 CATCCAGACC
3160074 TTTTTTT-TTT-
1 TTTTTTTGTTTG
3160084 TTTTTTTGGTTTG
1 TTTTTTT-GTTTG
3160097 TTTTTTTG--T-
1 TTTTTTTGTTTG
*
3160106 TTTTTTTCTTTG
1 TTTTTTTGTTTG
*
3160118 TTTTTTT-TCTTT
1 TTTTTTTGT-TTG
3160130 TTTTTTTGTTTTG
1 TTTTTTTG-TTTG
*
3160143 TTTATTTG-TT-
1 TTTTTTTGTTTG
3160153 TTTTTTTGTTTTG
1 TTTTTTTG-TTTG
3160166 TTTTTTTGTTTG
1 TTTTTTTGTTTG
*
3160178 TTTTTTTGTTCTT
1 TTTTTTTGTT-TG
3160191 TTTTTTTGT
1 TTTTTTTGT
3160200 GGAGGATGCC
Statistics
Matches: 97, Mismatches: 6, Indels: 23
0.77 0.05 0.18
Matches are distributed among these distances:
9 7 0.07
10 15 0.15
11 4 0.04
12 36 0.37
13 34 0.35
14 1 0.01
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.86
Consensus pattern (12 bp):
TTTTTTTGTTTG
Found at i:3160100 original size:23 final size:23
Alignment explanation
Indices: 3160074--3160197 Score: 121
Period size: 23 Copynumber: 5.4 Consensus size: 23
3160064 CATCCAGACC
3160074 TTTTTTTTTTTTTTTTTGGTTTG
1 TTTTTTTTTTTTTTTTTGGTTTG
*
3160097 TTTTTTTGTTTTTTTTCTTTG-TT-
1 TTTTTTT-TTTTTTTT-TTGGTTTG
* *
3160120 TTTTTTCTTTTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTTTTGGTTTG
* * *
3160143 TTTATTTGTTTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTTTTGGTTTG
*
3160166 TTTTTTTGTTTGTTTTTTT-G-TTC
1 TTTTTTT-TTT-TTTTTTTGGTTTG
3160189 TTTTTTTTT
1 TTTTTTTTT
3160198 GTGGAGGATG
Statistics
Matches: 84, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
21 2 0.02
22 12 0.14
23 48 0.57
24 12 0.14
25 10 0.12
ACGTcount: A:0.01, C:0.02, G:0.10, T:0.86
Consensus pattern (23 bp):
TTTTTTTTTTTTTTTTTGGTTTG
Found at i:3165407 original size:13 final size:13
Alignment explanation
Indices: 3165389--3165415 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3165379 GGACAGCTTT
3165389 GTTGCTTTTGTAC
1 GTTGCTTTTGTAC
3165402 GTTGCTTTTGTAC
1 GTTGCTTTTGTAC
3165415 G
1 G
3165416 AGAATGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (13 bp):
GTTGCTTTTGTAC
Found at i:3174229 original size:19 final size:18
Alignment explanation
Indices: 3174205--3174261 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
3174195 ACATTATATT
3174205 GATACAAAACTTATGTATC
1 GATAC-AAACTTATGTATC
3174224 GATAC--A--T-TGTATC
1 GATACAAACTTATGTATC
3174237 GATACAACACTTATGTATC
1 GATACAA-ACTTATGTATC
3174256 GATACA
1 GATACA
3174262 GTTACAGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.34
14 1 0.03
16 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (18 bp):
GATACAAACTTATGTATC
Found at i:3174236 original size:13 final size:13
Alignment explanation
Indices: 3174218--3174242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3174208 ACAAAACTTA
3174218 TGTATCGATACAT
1 TGTATCGATACAT
3174231 TGTATCGATACA
1 TGTATCGATACA
3174243 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3174241 original size:32 final size:32
Alignment explanation
Indices: 3174191--3174261 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
3174181 AGCTTCGTAG
*
3174191 CGATACATTATATTGATACAAAACTTATGTAT
1 CGATACATTATATCGATACAAAACTTATGTAT
* *
3174223 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTATATCGATACAAAACTTATGTAT
3174255 CGATACA
1 CGATACA
3174262 GTTACAGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (32 bp):
CGATACATTATATCGATACAAAACTTATGTAT
Found at i:3174276 original size:21 final size:18
Alignment explanation
Indices: 3174230--3174283 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
3174220 TATCGATACA
3174230 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
*
3174248 TATGTATCGATACAGTTACAGT
1 T-TGTATCGATACA---ACACT
3174270 TTGTATCGATACAA
1 TTGTATCGATACAA
3174284 ATTGTTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.06
19 12 0.39
21 12 0.39
22 5 0.16
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (18 bp):
TTGTATCGATACAACACT
Found at i:3174727 original size:36 final size:35
Alignment explanation
Indices: 3174648--3174727 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 35
3174638 CCCCATTTTG
* * *
3174648 TTTTTTTGTTATTTTTTCCTTCGTTTTTTTGTTTC
1 TTTTTTTTTTATTTTTTCCTTCGTTTTTTTCTTTA
*
3174683 TTTATTTTTTTATTTTTTTCC-TGGTTTTTTTCTATTA
1 TTT-TTTTTTTA-TTTTTTCCTTCGTTTTTTTCT-TTA
3174720 TTTTTTTT
1 TTTTTTTT
3174728 ATGTTCTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
35 3 0.08
36 22 0.58
37 13 0.34
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (35 bp):
TTTTTTTTTTATTTTTTCCTTCGTTTTTTTCTTTA
Found at i:3181953 original size:2 final size:2
Alignment explanation
Indices: 3181946--3181982 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3181936 TGTGATTCTT
3181946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3181983 CAACTCGAGC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3188180 original size:20 final size:19
Alignment explanation
Indices: 3188155--3188229 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
3188145 AAAAAGACAT
3188155 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
*
3188174 GAATGTATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* * *
3188195 CATGCATCGATTCATTGAAA
1 AATGTATCGATACATTG-AA
3188215 AATGTATCGATACAT
1 AATGTATCGATACAT
3188230 CTAGATACTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:3188219 original size:40 final size:39
Alignment explanation
Indices: 3188152--3188229 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
3188142 GGTAAAAAGA
* *
3188152 CATAATGTATCGATACATTGAAGAATGTATCGATACATT
1 CATAATGCATCGATACATTGAAAAATGTATCGATACATT
*
3188191 CATACATGCATCGATTCATTGAAAAATGTATCGATACAT
1 CATA-ATGCATCGATACATTGAAAAATGTATCGATACAT
3188230 CTAGATACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (39 bp):
CATAATGCATCGATACATTGAAAAATGTATCGATACATT
Found at i:3188929 original size:17 final size:17
Alignment explanation
Indices: 3188907--3188941 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3188897 TTCAATTTAG
3188907 TCCCTATGTAATTAAAA
1 TCCCTATGTAATTAAAA
3188924 TCCCTATGTAATTAAAA
1 TCCCTATGTAATTAAAA
3188941 T
1 T
3188942 ACAAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (17 bp):
TCCCTATGTAATTAAAA
Found at i:3189485 original size:20 final size:21
Alignment explanation
Indices: 3189460--3189503 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
3189450 TGTTTATACG
3189460 AAAAATCAAAATCATATC-AC
1 AAAAATCAAAATCATATCAAC
*
3189480 AAAAATCAACATCATATCAAC
1 AAAAATCAAAATCATATCAAC
3189501 AAA
1 AAA
3189504 CAACATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAAATCAAAATCATATCAAC
Found at i:3193655 original size:184 final size:181
Alignment explanation
Indices: 3193406--3193855 Score: 607
Period size: 184 Copynumber: 2.5 Consensus size: 181
3193396 TTTTATTTAA
* ** * * *
3193406 TTTTTAATTTCTAAAAATTT-ATTTCGTACCTTAATACAGAACCGAAAAGATATGAAAAGTTTTA
1 TTTTTAATTTTTAAAAATTTCATTTCGTACCTTAATGGAAAACCAAAAAGATA-GAAAAATTTTA
* * *
3193470 AAGATTTCTATACCTCTATGGAAAACCATAAGAATATTAGAAATCTTGAAAAATTAAGATAATAA
65 AATATTTCTATACCT-TACGGAAAACCATAAGAATAATAGAAATCTTGAAAAATTAAGATAATAA
* *
3193535 TTTTTATTTAGCGATAAAATAATATTCATTTATTATTTTATTTATTTTATAATT
129 TTTTTATTTAGCGATAAAATAATATTCATTCATTACTTTATTTATTTTATAA-T
* *
3193589 TTTTTAATTTTTTAAAATTTCATTTCGTACCTTAATGGAAAACTAAAAAGATACGAAAAATTTTA
1 TTTTTAATTTTTAAAAATTTCATTTCGTACCTTAATGGAAAACCAAAAAGATA-GAAAAATTTTA
* * * * **
3193654 AATATTTCTATACACTTACGGACAACCATAAGAATAATATAAATTTTGAAAAATTAGGATAATGG
65 AATATTTCTATAC-CTTACGGAAAACCATAAGAATAATAGAAATCTTGAAAAATTAAGATAATAA
* *
3193719 TTTTTATTTAGTGATAAAATAATATTTATTCATTACTTTATTTATTTTATAAT
129 TTTTTATTTAGCGATAAAATAATATTCATTCATTACTTTATTTATTTTATAAT
* *
3193772 TTTTT-ATTTTTAAAAATTTCATTTCGTACCTTAAAGGAAAACCAAAAAGATAAAGAAAATTTTA
1 TTTTTAATTTTTAAAAATTTCATTTCGTACCTTAATGGAAAACCAAAAAGATAGA-AAAATTTTA
*
3193836 AATATTTTTATACCCTTACG
65 AATATTTCTATA-CCTTACG
3193856 TCTATAATAG
Statistics
Matches: 236, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
181 1 0.00
182 70 0.30
183 25 0.11
184 138 0.58
185 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (181 bp):
TTTTTAATTTTTAAAAATTTCATTTCGTACCTTAATGGAAAACCAAAAAGATAGAAAAATTTTAA
ATATTTCTATACCTTACGGAAAACCATAAGAATAATAGAAATCTTGAAAAATTAAGATAATAATT
TTTATTTAGCGATAAAATAATATTCATTCATTACTTTATTTATTTTATAAT
Found at i:3196128 original size:52 final size:52
Alignment explanation
Indices: 3196065--3196251 Score: 241
Period size: 52 Copynumber: 3.6 Consensus size: 52
3196055 ATTTGCCTGC
* *
3196065 ATGTATCGATACATTGA-AGAATGTATCAATACATTTGGGTCAAAAACCCAGA
1 ATGTATAGATACAATGAGA-AATGTATCAATACATTTGGGTCAAAAACCCAGA
* * * *
3196117 ATGTATAGATACAATGAGAAATGTATCGATATATTTAGGTCAAAAACCTAGA
1 ATGTATAGATACAATGAGAAATGTATCAATACATTTGGGTCAAAAACCCAGA
* * * *
3196169 ATGTATCGATATAATGAGAAATGTATCGATACATTTGGGACAAAAACCCAGA
1 ATGTATAGATACAATGAGAAATGTATCAATACATTTGGGTCAAAAACCCAGA
* * *
3196221 ATGTATCGAGATAATGAGAAATGTATCAATA
1 ATGTATAGATACAATGAGAAATGTATCAATA
3196252 TAATTGTAAA
Statistics
Matches: 120, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
52 119 0.99
53 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (52 bp):
ATGTATAGATACAATGAGAAATGTATCAATACATTTGGGTCAAAAACCCAGA
Found at i:3196245 original size:104 final size:104
Alignment explanation
Indices: 3196065--3196253 Score: 290
Period size: 104 Copynumber: 1.8 Consensus size: 104
3196055 ATTTGCCTGC
* * *
3196065 ATGTATCGATACATTGAAGAATGTATCAATACATTTGGGTCAAAAACCCAGAATGTATAGATACA
1 ATGTATCGATACAATGAAGAATGTATCAATACATTTGGGACAAAAACCCAGAATGTATAGAGACA
*
3196130 ATGAGAAATGTATCGATATATTTAGGTCAAAAACCTAGA
66 ATGAGAAATGTATCAATATATTTAGGTCAAAAACCTAGA
* * * *
3196169 ATGTATCGATATAATG-AGAAATGTATCGATACATTTGGGACAAAAACCCAGAATGTATCGAGAT
1 ATGTATCGATACAATGAAG-AATGTATCAATACATTTGGGACAAAAACCCAGAATGTATAGAGAC
3196233 AATGAGAAATGTATCAATATA
65 AATGAGAAATGTATCAATATA
3196254 ATTGTAAACA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
103 2 0.03
104 74 0.97
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.28
Consensus pattern (104 bp):
ATGTATCGATACAATGAAGAATGTATCAATACATTTGGGACAAAAACCCAGAATGTATAGAGACA
ATGAGAAATGTATCAATATATTTAGGTCAAAAACCTAGA
Found at i:3196338 original size:13 final size:13
Alignment explanation
Indices: 3196322--3196347 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3196312 CAGGGTGATT
3196322 TTGTATCGATATA
1 TTGTATCGATATA
3196335 TTGTATCGATATA
1 TTGTATCGATATA
3196348 AAACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TTGTATCGATATA
Found at i:3203729 original size:97 final size:97
Alignment explanation
Indices: 3203537--3203722 Score: 232
Period size: 97 Copynumber: 1.9 Consensus size: 97
3203527 TTTTGGTTGC
* * * * *
3203537 AAAATAGGGTTTAAGTATCTCCTCGAAAGGATGGGGTTGGAGTATCCCCAACGATGACAATTTGA
1 AAAACAGGGTTTAAGTATCCCCTCGAAAGAATGGGATTGGAGTATCCCCAACGATGAAAATTTGA
*
3203602 GCAAAAATAAGATTTAAACCTTGAGAAGTTTA
66 GCAAAAATAAAATTTAAACCTTGAGAAGTTTA
* * * *
3203634 AAAACAGGG-TTAGAGTATCCCCTCAGAAA-AATGGGATTGGAGTATTCTCGATGATGAAAATTT
1 AAAACAGGGTTTA-AGTATCCCCTC-GAAAGAATGGGATTGGAGTATCCCCAACGATGAAAATTT
* *
3203697 GAGTAAAAATAAAATTTAAATCTTGA
64 GAGCAAAAATAAAATTTAAACCTTGA
3203723 CGAGTTTGAA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
96 3 0.04
97 68 0.91
98 4 0.05
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (97 bp):
AAAACAGGGTTTAAGTATCCCCTCGAAAGAATGGGATTGGAGTATCCCCAACGATGAAAATTTGA
GCAAAAATAAAATTTAAACCTTGAGAAGTTTA
Found at i:3203770 original size:97 final size:97
Alignment explanation
Indices: 3203589--3203773 Score: 221
Period size: 97 Copynumber: 1.9 Consensus size: 97
3203579 TATCCCCAAC
* * *
3203589 GATGACAATTTGAGCAAAAATAAGATTTAAACCTTGAGAAGTTTAAAAACAGGGTTAGAGTATCC
1 GATGAAAATTTGAGCAAAAATAAAATTTAAACCTTGAGAAGTTTAAAAACAGAGTTAGAGTATCC
* *
3203654 CCTCAGAAAAATGGGATTGGAGTATTCTCGAT
66 CCTCAGAAAAACGGAATTGGAGTATTCTCGAT
* * * * *
3203686 GATGAAAATTTGAGTAAAAATAAAATTTAAATCTTGACG-AGTTTGAAAA-TGAAGTTGGAGTAT
1 GATGAAAATTTGAGCAAAAATAAAATTTAAACCTTGA-GAAGTTTAAAAACAG-AGTTAGAGTAT
** *
3203749 CCCCTTGGAAGAACGGAATTGGAGT
64 CCCCTCAGAAAAACGGAATTGGAGT
3203774 GCCTCTGAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
96 1 0.01
97 71 0.97
98 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (97 bp):
GATGAAAATTTGAGCAAAAATAAAATTTAAACCTTGAGAAGTTTAAAAACAGAGTTAGAGTATCC
CCTCAGAAAAACGGAATTGGAGTATTCTCGAT
Found at i:3204604 original size:13 final size:13
Alignment explanation
Indices: 3204586--3204611 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3204576 AATTTTTTTG
3204586 TGTATCGATACAT
1 TGTATCGATACAT
3204599 TGTATCGATACAT
1 TGTATCGATACAT
3204612 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3204622 original size:32 final size:34
Alignment explanation
Indices: 3204565--3204629 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
3204555 TACAAGCCAA
*
3204565 TGTATCGATACAATTTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTATTTTGTGTATCGATACAT
3204599 TGTATCGATAC-A-TATTTTGTGTATCGATACA
1 TGTATCGATACAATTATTTTGTGTATCGATACA
3204630 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 18 0.60
33 1 0.03
34 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (34 bp):
TGTATCGATACAATTATTTTGTGTATCGATACAT
Found at i:3204734 original size:20 final size:20
Alignment explanation
Indices: 3204681--3204736 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
3204671 AAATCTTTTT
*
3204681 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
3204701 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
3204720 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
3204737 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:3207166 original size:13 final size:13
Alignment explanation
Indices: 3207148--3207185 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3207138 ATAATCCCCC
3207148 TGTATCGATACAG
1 TGTATCGATACAG
*
3207161 TGTATCGATACAT
1 TGTATCGATACAG
3207174 TGTATCGATACA
1 TGTATCGATACA
3207186 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3207199 original size:20 final size:20
Alignment explanation
Indices: 3207174--3207304 Score: 88
Period size: 20 Copynumber: 7.6 Consensus size: 20
3207164 ATCGATACAT
3207174 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
*
3207194 TGTATCGATAC-------AT
1 TGTATCGATACAAAGAAAAA
3207207 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
*
3207227 TGTATCGATAC-------AT
1 TGTATCGATACAAAGAAAAA
3207240 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
*
3207260 TGTATCGATAC-------AT
1 TGTATCGATACAAAGAAAAA
3207273 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
3207293 TGTATCGATACA
1 TGTATCGATACA
3207305 TTGAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 42
0.64 0.05 0.32
Matches are distributed among these distances:
13 36 0.43
20 48 0.57
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:3207203 original size:33 final size:33
Alignment explanation
Indices: 3207161--3207307 Score: 294
Period size: 33 Copynumber: 4.5 Consensus size: 33
3207151 ATCGATACAG
3207161 TGTATCGATACATTGTATCGATACAAAGAAAAA
1 TGTATCGATACATTGTATCGATACAAAGAAAAA
3207194 TGTATCGATACATTGTATCGATACAAAGAAAAA
1 TGTATCGATACATTGTATCGATACAAAGAAAAA
3207227 TGTATCGATACATTGTATCGATACAAAGAAAAA
1 TGTATCGATACATTGTATCGATACAAAGAAAAA
3207260 TGTATCGATACATTGTATCGATACAAAGAAAAA
1 TGTATCGATACATTGTATCGATACAAAGAAAAA
3207293 TGTATCGATACATTG
1 TGTATCGATACATTG
3207308 AATTTCCAGA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 114 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (33 bp):
TGTATCGATACATTGTATCGATACAAAGAAAAA
Found at i:3207212 original size:13 final size:13
Alignment explanation
Indices: 3207194--3207218 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3207184 CAAAGAAAAA
3207194 TGTATCGATACAT
1 TGTATCGATACAT
3207207 TGTATCGATACA
1 TGTATCGATACA
3207219 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3207245 original size:13 final size:13
Alignment explanation
Indices: 3207227--3207251 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3207217 CAAAGAAAAA
3207227 TGTATCGATACAT
1 TGTATCGATACAT
3207240 TGTATCGATACA
1 TGTATCGATACA
3207252 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3207278 original size:13 final size:13
Alignment explanation
Indices: 3207260--3207284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3207250 CAAAGAAAAA
3207260 TGTATCGATACAT
1 TGTATCGATACAT
3207273 TGTATCGATACA
1 TGTATCGATACA
3207285 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3209386 original size:15 final size:15
Alignment explanation
Indices: 3209366--3209396 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3209356 ATTTCGTTTG
*
3209366 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3209381 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3209396 G
1 G
3209397 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3213484 original size:13 final size:13
Alignment explanation
Indices: 3213466--3213491 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3213456 AATTTTTTTG
3213466 TGTATCGATACAT
1 TGTATCGATACAT
3213479 TGTATCGATACAT
1 TGTATCGATACAT
3213492 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3213502 original size:32 final size:34
Alignment explanation
Indices: 3213445--3213509 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
3213435 TACAAGCCAA
*
3213445 TGTATCGATACAATTTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTATTTTGTGTATCGATACAT
3213479 TGTATCGATAC-A-TATTTTGTGTATCGATACA
1 TGTATCGATACAATTATTTTGTGTATCGATACA
3213510 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 18 0.60
33 1 0.03
34 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (34 bp):
TGTATCGATACAATTATTTTGTGTATCGATACAT
Found at i:3213614 original size:20 final size:20
Alignment explanation
Indices: 3213561--3213616 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
3213551 ACATCTTTTT
*
3213561 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
*
3213581 CATGTATAGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
3213600 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
3213617 TAAGGGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:3214361 original size:22 final size:21
Alignment explanation
Indices: 3214336--3214376 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
3214326 AGGGAATTTC
3214336 ATGAAAATTTTAGGAAAAATGT
1 ATGAAAATTTT-GGAAAAATGT
3214358 ATGAAAATTTTGGAAAAAT
1 ATGAAAATTTTGGAAAAAT
3214377 TTGGTATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (21 bp):
ATGAAAATTTTGGAAAAATGT
Found at i:3214728 original size:404 final size:404
Alignment explanation
Indices: 3213979--3214780 Score: 1381
Period size: 404 Copynumber: 2.0 Consensus size: 404
3213969 TTGGGGTAGT
3213979 TCGAAGACAATCGAATGTCTCGGAATGAAGCTCAGTGAAACAACTCAATCTTGACTATAAACAAA
1 TCGAAGACAATCGAATGTCTCGGAATGAAGCTCAGTGAAACAACTCAATCTTGACTATAAACAAA
3214044 AACAGGAGACAACATCGCGCTATTTCACTTTTCGAATTTATTTTGGGTTGATTCAAAGGTTGTAG
66 AACAGGAGACAACATCGCGCTATTTCACTTTTCGAATTTATTTTGGGTTGATTCAAAGGTTGTAG
**
3214109 AGAGTGCATGAGGTACTGTTAGAAAGGTAACTCAACGAGGGTTAATCTAAAAATATTCCAAAAAT
131 AGAGTGCATGAGGTACCATTAGAAAGGTAACTCAACGAGGGTTAATCTAAAAATATTCCAAAAAT
* *
3214174 CTGAAAAAATTACTGTCATGGAGGAATAAATTTTTAAAGTCAGGATAATTACATTGCTAGCAAAA
196 CTGAAAAAATTACTGTCATAGAGGAATAAATTTTGAAAGTCAGGATAATTACATTGCTAGCAAAA
3214239 CATACGAGAGAAAGAGTGTGTCAAATTTTGAAAAATCATCTCAGACTCATTTAGTATAAAAAAAT
261 CATACGAGAGAAAGAGTGTGTCAAATTTTGAAAAATCATCTCAGACTCATTTAGTATAAAAAAAT
* *
3214304 TACAAACAATACCTTTCCATAAAGGGAATTTCATGAAAATTTTAGGAAAAATGTATGAAAATTTT
326 TACAAACAATACCTTTCCATAAACGGAATTTCATGAAAATTTTAGGAAAAATGTATGAAAAATTT
3214369 GGAAAAATTTGGTA
391 GGAAAAATTTGGTA
3214383 TCGAAGACAATCGAATGTCTCGGAATGAAGCTCAGTGAAACAACTCAATCTTGACTATAAACAAA
1 TCGAAGACAATCGAATGTCTCGGAATGAAGCTCAGTGAAACAACTCAATCTTGACTATAAACAAA
* * * * *
3214448 AATAGGGGATAACATCGTGCTATTTCACTTTTTGAATTTATTTTGGGTTGATTCAAAGGTTGTAG
66 AACAGGAGACAACATCGCGCTATTTCACTTTTCGAATTTATTTTGGGTTGATTCAAAGGTTGTAG
* * *
3214513 AGAGTGGATGAGGTACCATTAGAAAGGTAACTCAATGAGGGTTAATCTAAACATATTCCAAAAAT
131 AGAGTGCATGAGGTACCATTAGAAAGGTAACTCAACGAGGGTTAATCTAAAAATATTCCAAAAAT
* * * *
3214578 CTGAAAAAATTACTTTCCTAGAGGAATAAAATTTTGAAA-TCAGGATAATTACATTGTTGGCAAA
196 CTGAAAAAATTACTGTCATAGAGGAAT-AAATTTTGAAAGTCAGGATAATTACATTGCTAGCAAA
* * *
3214642 ACATACGAGAGAAAGGGTGTGTCAAATTTTGAAAAATCATCTCAGACTCATTTGGTATCAAAAAA
260 ACATACGAGAGAAAGAGTGTGTCAAATTTTGAAAAATCATCTCAGACTCATTTAGTATAAAAAAA
* *
3214707 TTACAAATAATACCTTTCCATAAACGGAATTTCATGAAAATTTTATGAAAAATGTATGAAAAATT
325 TTACAAACAATACCTTTCCATAAACGGAATTTCATGAAAATTTTAGGAAAAATGTATGAAAAATT
3214772 TGGAAAAAT
390 TGGAAAAAT
3214781 CATCTACTGG
Statistics
Matches: 374, Mismatches: 23, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
404 364 0.97
405 10 0.03
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (404 bp):
TCGAAGACAATCGAATGTCTCGGAATGAAGCTCAGTGAAACAACTCAATCTTGACTATAAACAAA
AACAGGAGACAACATCGCGCTATTTCACTTTTCGAATTTATTTTGGGTTGATTCAAAGGTTGTAG
AGAGTGCATGAGGTACCATTAGAAAGGTAACTCAACGAGGGTTAATCTAAAAATATTCCAAAAAT
CTGAAAAAATTACTGTCATAGAGGAATAAATTTTGAAAGTCAGGATAATTACATTGCTAGCAAAA
CATACGAGAGAAAGAGTGTGTCAAATTTTGAAAAATCATCTCAGACTCATTTAGTATAAAAAAAT
TACAAACAATACCTTTCCATAAACGGAATTTCATGAAAATTTTAGGAAAAATGTATGAAAAATTT
GGAAAAATTTGGTA
Found at i:3216523 original size:20 final size:20
Alignment explanation
Indices: 3216498--3216544 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3216488 GAATGTATTG
3216498 ATACAATGAAAAATATATCA
1 ATACAATGAAAAATATATCA
*
3216518 ATACAATGAAAAATATATCG
1 ATACAATGAAAAATATATCA
3216538 ATACAAT
1 ATACAAT
3216545 TTCTTTCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (20 bp):
ATACAATGAAAAATATATCA
Found at i:3216626 original size:20 final size:20
Alignment explanation
Indices: 3216601--3216654 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
3216591 CATTCCAAGC
**
3216601 ATGTATCGATACATTTGCTT
1 ATGTATCGATACATTACCTT
* *
3216621 ATGTATTGATATATTACCTT
1 ATGTATCGATACATTACCTT
*
3216641 ATTATATCGATACA
1 A-TGTATCGATACA
3216655 AATTATAGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTACCTT
Found at i:3219418 original size:97 final size:97
Alignment explanation
Indices: 3219268--3219481 Score: 290
Period size: 97 Copynumber: 2.2 Consensus size: 97
3219258 TATTCATCAG
* * *
3219268 GGATACTCCAACCCCATTCTTCCGAGGGGATACACTAACCCTATTTTTAAACTTCTCAAGATTTA
1 GGATACTCAAACCCCATTCTTCCGAAGGGATACACTAACCCGATTTTTAAACTTCTCAAGATTTA
* * *
3219333 AATCTTATTTTTGCTTAAATTGTCATCATTG-
66 AATCTTATTTTTGCCTAAATTATCATCATCGA
* * * *
3219364 GAGATACTCTAACCCTATTCTTCCGAAGGGATAC-TTCAACCCCGA-TTTTAAACTTGTCAAGAT
1 G-GATACTCAAACCCCATTCTTCCGAAGGGATACACT-AA-CCCGATTTTTAAACTTCTCAAGAT
3219427 TTAAATCTTATTTTTGCCTAAATTATCATCATCGA
63 TTAAATCTTATTTTTGCCTAAATTATCATCATCGA
3219462 GGATACTCAAACCCCATTCT
1 GGATACTCAAACCCCATTCT
3219482 CCCAAAGGAA
Statistics
Matches: 103, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
96 2 0.02
97 96 0.93
98 5 0.05
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (97 bp):
GGATACTCAAACCCCATTCTTCCGAAGGGATACACTAACCCGATTTTTAAACTTCTCAAGATTTA
AATCTTATTTTTGCCTAAATTATCATCATCGA
Found at i:3221467 original size:40 final size:40
Alignment explanation
Indices: 3221423--3221584 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 40
3221413 TTACCCAGAT
* *
3221423 TATCGATACATTTTTCGATGTATCAATACATGTATGAATG
1 TATCGATACATTTTTCAATGTATCGATACATGTATGAATG
**
3221463 TATCGATACATTCTTT-AATGTATCGATACATTCTGTCTTTTTACCCAGATG
1 TATCGATACATT-TTTCAATGTATCGATACA---TG------TA-TGA-ATG
* *
3221514 TATCGATACATTTTTCAACGTATCGATTCATGTATGAATG
1 TATCGATACATTTTTCAATGTATCGATACATGTATGAATG
*
3221554 TATCGATACATTCTTCAATGTATCGATACAT
1 TATCGATACATTTTTCAATGTATCGATACAT
3221585 CTAGTTAAAA
Statistics
Matches: 98, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
40 55 0.56
41 4 0.04
42 2 0.02
43 2 0.02
48 2 0.02
49 2 0.02
50 4 0.04
51 27 0.28
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (40 bp):
TATCGATACATTTTTCAATGTATCGATACATGTATGAATG
Found at i:3221496 original size:20 final size:19
Alignment explanation
Indices: 3221423--3221494 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
3221413 TTACCCAGAT
*
3221423 TATCGATACATTTTTCGATG
1 TATCGATACATTTTT-AATG
* * *
3221443 TATCAATACATGTATGAATG
1 TATCGATACAT-TTTTAATG
3221463 TATCGATACATTCTTTAATG
1 TATCGATACATT-TTTAATG
3221483 TATCGATACATT
1 TATCGATACATT
3221495 CTGTCTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.93
21 2 0.05
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (19 bp):
TATCGATACATTTTTAATG
Found at i:3221538 original size:20 final size:20
Alignment explanation
Indices: 3221511--3221584 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
3221501 TTTTACCCAG
3221511 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
3221531 ACGTATCGATTCATGTATGA
1 ATGTATCGATACATTTTTCA
*
3221551 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
3221571 ATGTATCGATACAT
1 ATGTATCGATACAT
3221585 CTAGTTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3221564 original size:91 final size:90
Alignment explanation
Indices: 3221410--3221584 Score: 296
Period size: 91 Copynumber: 1.9 Consensus size: 90
3221400 AAAAGTCACA
* *
3221410 TTTTTACCCAGATTATCGATACATTTTTCGATGTATCAATACATGTATGAATGTATCGATACATT
1 TTTTTACCCAGATTATCGATACATTTTTCAACGTATCAATACATGTATGAATGTATCGATACATT
*
3221475 CTTTAATGTATCGATACATTCTGTC
66 CTTCAATGTATCGATACATTCTGTC
* *
3221500 TTTTTACCCAGATGTATCGATACATTTTTCAACGTATCGATTCATGTATGAATGTATCGATACAT
1 TTTTTACCCAGAT-TATCGATACATTTTTCAACGTATCAATACATGTATGAATGTATCGATACAT
3221565 TCTTCAATGTATCGATACAT
65 TCTTCAATGTATCGATACAT
3221585 CTAGTTAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 13 0.16
91 66 0.84
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (90 bp):
TTTTTACCCAGATTATCGATACATTTTTCAACGTATCAATACATGTATGAATGTATCGATACATT
CTTCAATGTATCGATACATTCTGTC
Found at i:3226991 original size:14 final size:14
Alignment explanation
Indices: 3226972--3227012 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
3226962 TTATCCCTCA
3226972 TTTATGTTATTTTG
1 TTTATGTTATTTTG
*
3226986 TTTATGATT-GTTTG
1 TTTATG-TTATTTTG
3227000 TTTATGTTATTTT
1 TTTATGTTATTTT
3227013 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.71
Consensus pattern (14 bp):
TTTATGTTATTTTG
Found at i:3231990 original size:24 final size:23
Alignment explanation
Indices: 3231948--3231992 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
3231938 ACAAACATAA
* *
3231948 ATAATCAAAATAAACATAAAATC
1 ATAATAAAAATAAAAATAAAATC
3231971 ATAATAAAAACTAAAAATAAAA
1 ATAATAAAAA-TAAAAATAAAA
3231993 AACGTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (23 bp):
ATAATAAAAATAAAAATAAAATC
Found at i:3233577 original size:2 final size:2
Alignment explanation
Indices: 3233566--3233614 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
3233556 GGAAATATCC
3233566 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3233607 AT AT AT AT
1 AT AT AT AT
3233615 CTCAACCATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3234668 original size:2 final size:2
Alignment explanation
Indices: 3234663--3234701 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3234653 ACAGATGTAC
3234663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3234702 GTTAAAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3235244 original size:17 final size:17
Alignment explanation
Indices: 3235211--3235262 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
3235201 CAAGAATACA
*
3235211 CAACCTCTTTTTAAAATT
1 CAACCTC-TTTTGAAATT
3235229 CAACCTCTTTTGAAATT
1 CAACCTCTTTTGAAATT
*
3235246 CAACCTCCTTTGAAATT
1 CAACCTCTTTTGAAATT
3235263 TTCAATCCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 25 0.78
18 7 0.22
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (17 bp):
CAACCTCTTTTGAAATT
Found at i:3236877 original size:11 final size:11
Alignment explanation
Indices: 3236861--3236916 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
3236851 TATTAATTTT
3236861 TTTATATTATA
1 TTTATATTATA
* *
3236872 TTTATATCATG
1 TTTATATTATA
3236883 TTT-TAATTATA
1 TTTAT-ATTATA
* *
3236894 TTTGTATTATG
1 TTTATATTATA
*
3236905 TTTAAATTATA
1 TTTATATTATA
3236916 T
1 T
3236917 AATTTTATCA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
10 1 0.03
11 33 0.94
12 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (11 bp):
TTTATATTATA
Found at i:3236894 original size:22 final size:22
Alignment explanation
Indices: 3236860--3236916 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
3236850 ATATTAATTT
3236860 TTTTATATTATATTTATATCATG
1 TTTTA-ATTATATTTATATCATG
* *
3236883 TTTTAATTATATTTGTATTATG
1 TTTTAATTATATTTATATCATG
*
3236905 TTTAAATTATAT
1 TTTTAATTATAT
3236917 AATTTTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (22 bp):
TTTTAATTATATTTATATCATG
Found at i:3240225 original size:52 final size:52
Alignment explanation
Indices: 3240147--3240275 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
3240137 CGAAATATGA
*
3240147 AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* * *
3240199 AAATTTGCCTGCATGTACCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
3240251 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3240276 AAGATCAATG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:3240288 original size:52 final size:51
Alignment explanation
Indices: 3240147--3240295 Score: 176
Period size: 52 Copynumber: 2.9 Consensus size: 51
3240137 CGAAATATGA
* *
3240147 AAATTTACCTGCATGTATCGATAC-ATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACAATATCA-A-TGTATCGATACATCTAGGC
* * * *
3240199 AAATTTGCCTGCATGTACCGATACATTTTAT-AGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--ATATCAATGTATCGATACATCTAGGC
*
3240251 AAATTTGCCTGCATGTATCGATACAAAGATCAATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATAC-AATATCAATGTATCGATACA
3240296 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
51 2 0.02
52 76 0.93
53 1 0.01
54 1 0.01
55 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACAATATCAATGTATCGATACATCTAGGC
Found at i:3240299 original size:13 final size:13
Alignment explanation
Indices: 3240281--3240308 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3240271 ATACAAAGAT
3240281 CAATGTATCGATA
1 CAATGTATCGATA
3240294 CAATGTATCGATA
1 CAATGTATCGATA
3240307 CA
1 CA
3240309 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3240388 original size:32 final size:33
Alignment explanation
Indices: 3240349--3240412 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
3240339 AGTAGCTTAC
3240349 ATTGTATCGATACAAAAC-TTATGTATCGATAT
1 ATTGTATCGATACAAAACTTTATGTATCGATAT
*
3240381 ATTGTATCGATACAACACTTTATGTATCGATA
1 ATTGTATCGATACAAAACTTTATGTATCGATA
3240413 CAAATCGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAT
Found at i:3241311 original size:49 final size:49
Alignment explanation
Indices: 3241167--3241472 Score: 259
Period size: 49 Copynumber: 6.2 Consensus size: 49
3241157 AGCGTCATTA
* * * * *
3241167 GACTTAAAGAATAGAAGAATGCCAATGTGTTAATTCAAAGCCAGCGATATTT
1 GACTTAAAG-AT-GAAG-GTGCCAATGTGCTGATTCAAGGCCAGCGATATTG
* ** * *
3241219 GACTTAAAAGGTGACAAAGGCACCAATATGCTGATTTAAGGCCAGCGATATTG
1 GACTT-AAAGATG---AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTG
*
3241272 GACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTG
1 GACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTG
* * * *
3241321 GACTTAAAGAAGAA--TGCCAATGTGTTGATTCAAGGCCAACGACATTTGG
1 GACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATA-TT-G
** * * * * *
3241370 GTTTTAAAGATAAAGGTGCCAATATGCTAATTCAAGACTAGCGATATTG
1 GACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTG
*
3241419 GACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATACTG
1 GACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTG
3241462 GACTTAGAAGA
1 GACTTA-AAGA
3241473 AGATGCCACC
Statistics
Matches: 204, Mismatches: 37, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
43 37 0.18
45 1 0.00
47 28 0.14
48 3 0.01
49 60 0.29
50 2 0.01
51 24 0.12
52 12 0.06
53 34 0.17
54 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
GACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTG
Found at i:3241326 original size:102 final size:105
Alignment explanation
Indices: 3241137--3241328 Score: 266
Period size: 102 Copynumber: 1.9 Consensus size: 105
3241127 AAAAGGATGT
* * *
3241137 CAATATGCTGATTTACGGTCAGCGTCATTAGACTTAAAGAATAGAAGAATGCCAATGTGTTAATT
1 CAATATGCTGATTTAAGGCCAGCGTCATTAGACTTAAAGAATAGAAGAATGCCAATGTGCTAATT
* *
3241202 CAAAGCCAGCGATATTTGACTTAAAAGGTGACAAAGGCAC
66 CAAAGCCAGCGACATTGGACTTAAAAGGTGACAAAGGCAC
* * *
3241242 CAATATGCTGATTTAAGGCCAGCGAT-ATTGGACTTAAAG-AT-GAAG-GTGCCAATGTGCTGAT
1 CAATATGCTGATTTAAGGCCAGCG-TCATTAGACTTAAAGAATAGAAGAATGCCAATGTGCTAAT
*
3241303 TCAAGGCCAGCGACATTGGACTTAAA
65 TCAAAGCCAGCGACATTGGACTTAAA
3241329 GAAGAATGCC
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
102 36 0.47
103 4 0.05
104 2 0.03
105 34 0.44
106 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26
Consensus pattern (105 bp):
CAATATGCTGATTTAAGGCCAGCGTCATTAGACTTAAAGAATAGAAGAATGCCAATGTGCTAATT
CAAAGCCAGCGACATTGGACTTAAAAGGTGACAAAGGCAC
Found at i:3241446 original size:43 final size:43
Alignment explanation
Indices: 3241380--3241467 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
3241370 GTTTTAAAGA
* *
3241380 TAAAGGTGCCAATATGCTAATTCAAGACTAGCGATATTGGACT
1 TAAAGGTGCCAATATGCTAATTCAAGACCAGCGATACTGGACT
* * *
3241423 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATACTGGACT
1 TAAAGGTGCCAATATGCTAATTCAAGACCAGCGATACTGGACT
3241466 TA
1 TA
3241468 GAAGAAGATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTAATTCAAGACCAGCGATACTGGACT
Found at i:3241583 original size:29 final size:29
Alignment explanation
Indices: 3241535--3241826 Score: 381
Period size: 29 Copynumber: 10.0 Consensus size: 29
3241525 TTTTGAAGGT
* * *
3241535 TGCCATTGACTTGTGGGCTTTTGAAGAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* * * *
3241564 TACCACTGACTTATGCGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
3241594 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
*
3241623 TGCCA-TGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
* * *
3241652 TGCCATTGACTTGTGGGTTTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* ** *
3241681 TACCACTGACTTGTGGGCTTTAAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
3241711 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
*
3241740 TGCCACTGACTTGTGGGCTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
*
3241769 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
3241799 TGCCACTGACTTGTGGGCTTT-GAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
3241827 AAAAGGTGCC
Statistics
Matches: 229, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
28 22 0.10
29 116 0.51
30 91 0.40
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGGAAAAGA
Found at i:3241606 original size:59 final size:58
Alignment explanation
Indices: 3241530--3241825 Score: 414
Period size: 59 Copynumber: 5.1 Consensus size: 58
3241520 TGTGCTTTTG
* * * * * * *
3241530 AAGGTTGCCATTGACTTGTGGGCTTTTGAAGAGATACCACTGACTTATGCGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTT-GAA
3241589 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCA-TGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTT-GAA
* * * * *
3241647 AAGGGTGCCATTGACTTGTGGGTTTTTGAAAAGATACCACTGACTTGTGGGCTTTAAAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTT-GAA
3241706 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGAA
* * *
3241764 AAAGATGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAA-GATGCCACTGACTTGTGGGCTTTGAA
3241823 AAG
1 AAG
3241826 AAAAAGGTGC
Statistics
Matches: 213, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
58 84 0.39
59 129 0.61
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (58 bp):
AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGAA
Found at i:3241683 original size:117 final size:116
Alignment explanation
Indices: 3241530--3241825 Score: 441
Period size: 117 Copynumber: 2.5 Consensus size: 116
3241520 TGTGCTTTTG
* * * *
3241530 AAGGTTGCCATTGACTTGTGGGCTTTTGAAGAGATACCACTGACTTATGCGCTTTGGAAAAGGGT
1 AAGGATGCCATTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTT-GAAAAGGGT
3241595 GCCACTGACTTGTGGGCTTTGGAAAAGATGCCA-TGACTTGTGGGCTTTGGAA
65 GCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTT-GAA
* * *
3241647 AAGGGTGCCATTGACTTGTGGGTTTTTGAAAAGATACCACTGACTTGTGGGCTTTAAAAAAGGGT
1 AAGGATGCCATTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTT-GAAAAGGGT
3241712 GCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGAA
65 GCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGAA
* * * * *
3241764 AAAGATGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAG
1 AAGGATGCCATTGACTTGTGGGCTTTTGAAAA-GATACCACTGACTTGTGGGCTTTGAAAAG
3241826 AAAAAGGTGC
Statistics
Matches: 162, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
117 126 0.78
118 36 0.22
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (116 bp):
AAGGATGCCATTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTGAAAAGGGTG
CCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGAA
Found at i:3243363 original size:21 final size:19
Alignment explanation
Indices: 3243342--3243404 Score: 83
Period size: 20 Copynumber: 3.3 Consensus size: 19
3243332 TTTGTTGTTG
*
3243342 TTTTTTTTCCCTTCTTTTT
1 TTTTTTTTTCCTTCTTTTT
3243361 TGTTTTTTTTCCTTCTTTTT
1 T-TTTTTTTTCCTTCTTTTT
*
3243381 TTTCTTCTTT-CTTCTTTTT
1 TTT-TTTTTTCCTTCTTTTT
3243400 TTTTT
1 TTTTT
3243405 GTGGAGGACG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.05
19 15 0.38
20 23 0.57
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTTTTTTCCTTCTTTTT
Found at i:3243391 original size:20 final size:19
Alignment explanation
Indices: 3243342--3243404 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
3243332 TTTGTTGTTG
*
3243342 TTTTTT-TTCCCTTCTTTT
1 TTTTTTCTTTCCTTCTTTT
*
3243360 TTGTTTTTTTTCCTTCTTTT
1 TT-TTTTCTTTCCTTCTTTT
3243380 TTTTCTTCTTT-CTTCTTTT
1 TTTT-TTCTTTCCTTCTTTT
3243399 TTTTTT
1 TTTTTT
3243405 GTGGAGGACG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.10
19 18 0.45
20 18 0.45
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTTTCTTTCCTTCTTTT
Found at i:3248320 original size:52 final size:52
Alignment explanation
Indices: 3248250--3248370 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
3248240 GAAAATTTAT
*
3248250 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
3248302 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
3248354 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
3248371 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:3248383 original size:52 final size:51
Alignment explanation
Indices: 3248250--3248390 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
3248240 GAAAATTTAT
3248250 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
3248302 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
3248354 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
3248391 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:3248397 original size:13 final size:13
Alignment explanation
Indices: 3248379--3248403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3248369 CAAAGATCAG
3248379 TGTATCGATACAA
1 TGTATCGATACAA
3248392 TGTATCGATACA
1 TGTATCGATACA
3248404 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3248481 original size:33 final size:33
Alignment explanation
Indices: 3248444--3248510 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3248434 AGTAGCTTAA
3248444 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3248477 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3248510 A
1 A
3248511 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3248484 original size:13 final size:13
Alignment explanation
Indices: 3248466--3248490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3248456 CAAAAAAATA
3248466 TGTATCGATACAT
1 TGTATCGATACAT
3248479 TGTATCGATACA
1 TGTATCGATACA
3248491 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3249489 original size:49 final size:49
Alignment explanation
Indices: 3249417--3250381 Score: 1571
Period size: 49 Copynumber: 19.7 Consensus size: 49
3249407 AAAAGGATGT
* *
3249417 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3249466 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
3249514 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3249563 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3249611 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
3249660 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3249709 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3249758 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3249807 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3249855 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3249904 CAATATGCTGATTCAAGGCCAGCTACCTTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3249953 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3250002 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
3250051 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3250100 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3250149 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3250198 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3250246 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
3250295 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGGGA-AAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA-AA--GATGAAGGTGC
* * *
3250346 CAATATGCTGATTCAAGGCCAGTTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
3250382 GAAGGGTTGC
Statistics
Matches: 869, Mismatches: 40, Indels: 12
0.94 0.04 0.01
Matches are distributed among these distances:
48 185 0.21
49 638 0.73
50 2 0.00
51 42 0.05
52 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:3249818 original size:244 final size:243
Alignment explanation
Indices: 3249408--3250381 Score: 1606
Period size: 244 Copynumber: 4.0 Consensus size: 243
3249398 AAGATGAGAA
* * * * *
3249408 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATGTG
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATG
*
3249473 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAGGTGCCAATATGCTGATTCAAGGCCAGCT
65 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAGGTGCCAATATGCTGATTCAAGGCCAGCT
3249538 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
130 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
* *
3249603 TGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
195 TAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
3249652 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
3249717 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-AAGGTGCCAATATGCTGATTCAAGGCCAGCT
*
3249782 ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
130 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
*
3249847 TGAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
195 TAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
3249896 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACCTTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
* * *
3249961 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-AAGGTGCCAATATGCTGATTCAAGGCCAGCT
3250026 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
130 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
3250091 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
195 T-AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
3250141 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
* *
3250206 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAGGTGCCAATGTGCTGATTCAAGGCCAGCTA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
* * * *
3250271 CATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
131 CATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA-AA--
* * * *
3250336 GAAAAGGTGCCAATATGCTGATTCAAGGCCAGTTATATTGGGCTTA
193 GATAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
3250382 GAAGGGTTGC
Statistics
Matches: 691, Mismatches: 34, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
243 87 0.13
244 421 0.61
245 141 0.20
246 40 0.06
247 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (243 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
CATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
Found at i:3250408 original size:30 final size:31
Alignment explanation
Indices: 3250374--3250452 Score: 106
Period size: 33 Copynumber: 2.5 Consensus size: 31
3250364 CCAGTTATAT
3250374 TGGGC-TTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
* *
3250404 TGGGCTTTGGAAGAAAGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAG--GGTTGCCACCGACTTGTG
3250437 TGGGCTTTAGGAAGGG
1 TGGGCTTTA-GAAGGG
3250453 AGAAAGATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 5 0.12
31 6 0.15
32 1 0.02
33 25 0.61
34 4 0.10
ACGTcount: A:0.19, C:0.16, G:0.38, T:0.27
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:3250426 original size:33 final size:34
Alignment explanation
Indices: 3250387--3250450 Score: 121
Period size: 33 Copynumber: 1.9 Consensus size: 34
3250377 GCTTAGAAGG
3250387 GTTGCCACCGACTTGTGTGGGCTTT-GGAAGAAA
1 GTTGCCACCGACTTGTGTGGGCTTTAGGAAGAAA
3250420 GTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1 GTTGCCACCGACTTGTGTGGGCTTTAGGAAG
3250451 GGAGAAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (34 bp):
GTTGCCACCGACTTGTGTGGGCTTTAGGAAGAAA
Found at i:3250493 original size:34 final size:32
Alignment explanation
Indices: 3250455--3250864 Score: 266
Period size: 34 Copynumber: 12.6 Consensus size: 32
3250445 AGGAAGGGAG
*
3250455 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAA
1 AAAG-TGCCACGGAGTTGTGGGCTTAAAA-GG-AA
3250490 AAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAA
1 AA-AGTGCCACGGAGTTGTGGGC-TT-AAAA-GG-AA
**
3250527 GAAGAGTGCCACAAAGTTGTGGGCTTTAAAA-GAA
1 -AA-AGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
3250561 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 -AAAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
*
3250595 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 -AAAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* * *
3250629 GAAGGTGCCACGGAGTTGTGGACTTAAACGG--
1 -AAAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
3250660 ---GTGCCACGGAGTTGTGGACTTAAAGATGAAA
1 AAAGTGCCACGGAGTTGTGGGCTTAAA-A-GGAA
*
3250691 AAAGTGCCACGGAATTGTGGGCTTTAAAAGG--
1 AAAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
3250722 ---GTGCCACGGAGTTGTGGACTTAAAGATGAAA
1 AAAGTGCCACGGAGTTGTGGGCTTAAA-A-GGAA
*
3250753 AAAGTGCCACGGAATTGTGGGCTTTAAAAGG--
1 AAAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
3250784 ---GTGCCAC-GACGTTGTGGACTTAAAAGGAA
1 AAAGTGCCACGGA-GTTGTGGGCTTAAAAGGAA
* *
3250813 CAAAGTGCCATGGAGTTGTGGGCTTTAAA-GAA
1 -AAAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * *
3250845 AAAATGCCACTGAGTCGTGG
1 AAAGTGCCACGGAGTTGTGG
3250865 ACTTTGAGAC
Statistics
Matches: 317, Mismatches: 28, Indels: 64
0.78 0.07 0.16
Matches are distributed among these distances:
27 39 0.12
28 32 0.10
29 2 0.01
31 16 0.05
32 6 0.02
33 44 0.14
34 106 0.33
35 30 0.09
36 4 0.01
37 14 0.04
38 24 0.08
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.21
Consensus pattern (32 bp):
AAAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Done.