Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_19 ID=scaffold_19-JGI_221_v2.0
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: 140400
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 11929 characters in sequence are not A, C, G, or T
Found at i:2954 original size:236 final size:236
Alignment explanation
Indices: 2538--3011 Score: 921
Period size: 236 Copynumber: 2.0 Consensus size: 236
2528 CTGATTTGAA
2538 ATCCACATATGTTTGTGATGGTGATTATGGAATAAAGAATCAATAGAGACGTCTAGAAGTCTATC
1 ATCCACATATGTTTGTGATGGTGATTATGGAATAAAGAATCAATAGAGACGTCTAGAAGTCTATC
2603 CTACTAGATTTGTTGCATTCTCCGAAGTGAATGCAAATATAAAGAAAATAAAATATATAATCATG
66 CTACTAGATTTGTTGCATTCTCCGAAGTGAATGCAAATATAAAGAAAATAAAATATATAATCATG
*
2668 GACCACTAAAAGTGAGAACATAATAATAAAAAAGAGAATAATGGGAGTTCTTAATATAACTCTTC
131 GACCACTAAAAGTGAGAACATAATAATAAAAAAGAGAATAATGAGAGTTCTTAATATAACTCTTC
2733 AAAGAGTAAATATAACATATGTTACCAATGCGATATGAAAG
196 AAAGAGTAAATATAACATATGTTACCAATGCGATATGAAAG
2774 ATCCACATATGTTTGTGATGGTGATTATGGAATAAAGAATCAATAGAGACGTCTAGAAGTCTATC
1 ATCCACATATGTTTGTGATGGTGATTATGGAATAAAGAATCAATAGAGACGTCTAGAAGTCTATC
2839 CTACTAGATTTGTTGCATTCTCCGAAGTGAATGCAAATATAAAGAAAATAAAATATATAATCATG
66 CTACTAGATTTGTTGCATTCTCCGAAGTGAATGCAAATATAAAGAAAATAAAATATATAATCATG
*
2904 GACCACTAAAAGTGAGAACATAATAATAAATAAGAGAATAATGAGAGTTCTTAATATAACTCTTC
131 GACCACTAAAAGTGAGAACATAATAATAAAAAAGAGAATAATGAGAGTTCTTAATATAACTCTTC
*
2969 AAAGAGTAAATATAACTTATGTTACCAATGCGATATGAAAG
196 AAAGAGTAAATATAACATATGTTACCAATGCGATATGAAAG
3010 AT
1 AT
3012 TATTGGCCAC
Statistics
Matches: 235, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
236 235 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (236 bp):
ATCCACATATGTTTGTGATGGTGATTATGGAATAAAGAATCAATAGAGACGTCTAGAAGTCTATC
CTACTAGATTTGTTGCATTCTCCGAAGTGAATGCAAATATAAAGAAAATAAAATATATAATCATG
GACCACTAAAAGTGAGAACATAATAATAAAAAAGAGAATAATGAGAGTTCTTAATATAACTCTTC
AAAGAGTAAATATAACATATGTTACCAATGCGATATGAAAG
Found at i:5603 original size:3 final size:3
Alignment explanation
Indices: 5595--5644 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
5585 TGACCAGGGT
5595 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5643 AA
1 AA
5645 AAGTTACATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20112 original size:22 final size:22
Alignment explanation
Indices: 20087--20129 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20077 ATCGATATTA
*
20087 TAATATTTTAATTATTTATTTT
1 TAATATTTTAATAATTTATTTT
*
20109 TAATTTTTTAATAATTTATTT
1 TAATATTTTAATAATTTATTT
20130 ACTTTAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TAATATTTTAATAATTTATTTT
Found at i:20666 original size:14 final size:15
Alignment explanation
Indices: 20629--20682 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 15
20619 CAATATACCG
*
20629 TAAACCT-TAACCA-
1 TAAACCTATAAACAT
* *
20642 TAAATCT-TAAACTT
1 TAAACCTATAAACAT
20656 TAAA-CTATAAACAT
1 TAAACCTATAAACAT
20670 TAAACCTATAAAC
1 TAAACCTATAAAC
20683 CACAAACAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 12 0.35
14 14 0.41
15 8 0.24
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAACCTATAAACAT
Found at i:21448 original size:113 final size:112
Alignment explanation
Indices: 21213--21465 Score: 273
Period size: 113 Copynumber: 2.2 Consensus size: 112
21203 TTTTTTAGAA
* * *
21213 AAGCACCGCTAATGGCACTATAGCTCAAGATTAAACGATGCGTTTTGGTTAACATTTTGCTGCGT
1 AAGCACCGCTAATGCCACTATAGCTCAAGATCAAACGATGCGTTTTAGTTAACATTTTGCTGCGT
* *
21278 TTATAATTAAGCGTCGTTAATACCGATCTTTAGCGGCATTTTCAAGTT
66 TTATAATGAAGCGCCGTTAATACCGATCTTTAGCGGCATTTT-AAGTT
* * * * * *
21326 -AGCGCCGCTAACGCCAGTATAGCTCAAGATCGAACGCTGCGTTTTAGTTAACATTTT-TTCGAC
1 AAGCACCGCTAATGCCACTATAGCTCAAGATCAAACGATGCGTTTTAGTTAACATTTTGCT-G-C
** * *
21389 GTTT-TTCTAGAAGCGCCGTTAATACCGAT-TTATAGCGGCGTTTT-TGTTT
64 GTTTATAAT-GAAGCGCCGTTAATACCGATCTT-TAGCGGCATTTTAAG-TT
*
21438 AAGCACCGCTAATGCTACTATAGCTCAA
1 AAGCACCGCTAATGCCACTATAGCTCAA
21466 CAAGGAAAAG
Statistics
Matches: 115, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
111 2 0.02
112 56 0.49
113 57 0.50
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (112 bp):
AAGCACCGCTAATGCCACTATAGCTCAAGATCAAACGATGCGTTTTAGTTAACATTTTGCTGCGT
TTATAATGAAGCGCCGTTAATACCGATCTTTAGCGGCATTTTAAGTT
Found at i:24372 original size:2 final size:2
Alignment explanation
Indices: 24365--24403 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24355 TACAACTTTA
24365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24404 AACATGAATG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28663 original size:19 final size:19
Alignment explanation
Indices: 28635--28673 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28625 AAAAGTATGT
28635 ATATAAGTATATATATATA
1 ATATAAGTATATATATATA
*
28654 ATATACGTATATATATATA
1 ATATAAGTATATATATATA
28673 A
1 A
28674 AAGCAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
ATATAAGTATATATATATA
Found at i:30294 original size:132 final size:131
Alignment explanation
Indices: 30101--30488 Score: 555
Period size: 132 Copynumber: 2.9 Consensus size: 131
30091 GGTTTGTGGT
* * * *
30101 TTAAATTTACTTC-CCTACTACCTTAGGAAGATAAGATTCACCATCTTTGATCTGTTCCACTACT
1 TTAAATCTACTTCTCC-ACTATCTTAGGAAGATAAGATTCA-CATCTTCGATCTGCTCCACTACT
* * * * * *
30165 GCTTAGGGAGACAGAATTTGCAATCTTCAACCTACTCCATTGCTGCTCAGAGAGATAGGGCTAAT
64 GCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAAT
30230 GGC
129 GGC
*
30233 TTAAATCTACTTCTCCACTATCTTAGGAAGATAAGATTCACGACCTTCGATCTGCTCCACTACTG
1 TTAAATCTACTTCTCCACTATCTTAGGAAGATAAGATTCAC-ATCTTCGATCTGCTCCACTACTG
*
30298 CTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGAGATAGGACTAATG
65 CTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATG
30363 GC
130 GC
* * *
30365 TTAAATCTGCTTCTCCACTATCTT-GAGAAGATAAAATTCATCATCTTCGATCGGCTCCACTACT
1 TTAAATCTACTTCTCCACTATCTTAG-GAAGATAAGATTCA-CATCTTCGATCTGCTCCACTACT
* * *
30429 ACTTAGGGTGACAGAATCTGCAATCTTCAACCTATTCCACTACTGCTTAGGGAGATAGGA
64 GCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGA
30489 TCTGCAATCT
Statistics
Matches: 232, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
131 2 0.01
132 227 0.98
133 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (131 bp):
TTAAATCTACTTCTCCACTATCTTAGGAAGATAAGATTCACATCTTCGATCTGCTCCACTACTGC
TTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGG
C
Found at i:30494 original size:176 final size:176
Alignment explanation
Indices: 30287--30661 Score: 590
Period size: 176 Copynumber: 2.1 Consensus size: 176
30277 CTTCGATCTG
*
30287 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGAGA
* * * *
30352 TAGGACTAATGGCTTAAATCTGCTTCTCCACTATCTT-GAGAAGATAAAATTCATCATCTTCGAT
66 TAGGACTAACGACTTAAATCTGATTCTCCACTATCTTAG-GAAGATAAAATTCACCATCTTCGAT
* *
30416 CGGCTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCTA
130 CGGCTCCACTACTACTTAGGGAGACAGAATCTACAATCTTCAACCTA
* * * *
30463 TTCCACTACTGCTTAGGGAGATAGGATCTGCAATCTTTAACCTACTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGAGA
* *
30528 TAGGACTAACGACTTAAATCTGATTCTCCATTATCTTAGGAAGATAAGATTCACCATCTTCGATC
66 TAGGACTAACGACTTAAATCTGATTCTCCACTATCTTAGGAAGATAAAATTCACCATCTTCGATC
* * *
30593 TGTTCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTA
131 GGCTCCACTACTACTTAGGGAGACAGAATCTACAATCTTCAACCTA
30639 CTCCACTACTGCTTAGGGAGATA
1 CTCCACTACTGCTTAGGGAGATA
30662 AGACTAATGG
Statistics
Matches: 181, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
176 180 0.99
177 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (176 bp):
CTCCACTACTGCTTAGGGAGATAGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGAGA
TAGGACTAACGACTTAAATCTGATTCTCCACTATCTTAGGAAGATAAAATTCACCATCTTCGATC
GGCTCCACTACTACTTAGGGAGACAGAATCTACAATCTTCAACCTA
Found at i:30529 original size:132 final size:131
Alignment explanation
Indices: 30122--31447 Score: 512
Period size: 132 Copynumber: 10.0 Consensus size: 131
30112 TCCCTACTAC
* * * * *
30122 CTTAGGAAGATAAGATTCACCATCTTTGATCTGTTCCACTACTGCTTAGGGAGACAGAATTTGCA
1 CTTAGGAAGATAAGATTCATCATCTTAGATCTGCTCCACTACTACTTAGGGAGACAGAATCTGCA
* * * * * *
30187 ATCTTCAACCTACTCCATTGCTGCTCAGAGAGATAGG-GCT-AATGGCTTAAATCTACTTCTCCA
66 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATCTCAAT--CTTAAA-C--CTACTCCA
30250 CTA-T-
126 CTACTG
* * *
30254 CTTAGGAAGATAAGATTCA-CGACCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGC
1 CTTAGGAAGATAAGATTCATC-ATCTTAGATCTGCTCCACTACTACTTAGGGAGACAGAATCTGC
* *
30318 AATCTTCAACCTACTCCACCACTGCTTAGGGAGATAGGA-CT-AATGGCTTAAATCTGCTTCTCC
65 AATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATCTCAAT--CTTAAA-C--CTACTCC
30381 ACTA-T-
125 ACTACTG
* * * *
30386 CTT-GAGAAGATAAAATTCATCATCTTCGATCGGCTCCACTACTACTTAGGGTGACAGAATCTGC
1 CTTAG-GAAGATAAGATTCATCATCTTAGATCTGCTCCACTACTACTTAGGGAGACAGAATCTGC
* *
30450 AATCTTCAACCTATTCCACTACTGCTTAGGGAGATAGGATCTGCAATCTTTAACCTACTCCACTA
65 AATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATCT-CAATCTTAAACCTACTCCACTA
30515 CTG
129 CTG
* * * * * * * * *
30518 CTTAGGGAGATAGGACT-AACGA-CTTAAATCTGATTCTCCATTA-T-CTTAGGAAGATAAGATT
1 CTTAGGAAGATAAGATTCATC-ATCTTAGATCTG---CTCCACTACTACTTAGGGAGA-CAGAAT
* * * * ** * * *
30579 C-ACCATCTTCGATCTGTTCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCC
61 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATCT-CAATCTTAAACCTACTCC
30643 ACTACTG
125 ACTACTG
* * * ** * * * *
30650 CTTAGGGAGATAAGACTAAT-GGCTTAAATCTGCTTCC-CCACTATCTT-GGGAAGATAAGATTC
1 CTTAGGAAGATAAGATTCATCATCTTAGATCTGC-TCCACTACTA-CTTAGGG-AGA-CAGAATC
* * * * * * * *
30712 -ACCATCTTCGATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTACTTCA
62 TGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATCT-CAATCTTAAACCTACTCCA
30776 CTACTG
126 CTACTG
* * * * ** * * * * * *
30782 CTTAGGGAGATAGGACT-AACGGCTTAAATCTGCTTCTCCACTATCTT-GGGAAGATAAGATTC-
1 CTTAGGAAGATAAGATTCATCATCTTAGATCTGCTCCACTACTA-CTTAGGG-AGA-CAGAATCT
* * ** * * * * * * **
30844 ACCATCTTTGATCTGCTCCACTACTGCTTAGGG-GAACAGAATATACAATATTCGACCTACTCCA
63 GCAATCTTCAACCTACTCCACTACTGCTTAGGGAG-ATAGGATCT-CAATCTTAAACCTACTCCA
30908 CTACTG
126 CTACTG
* * * * ** * * * * * * * *
30914 CTTAGGGAGATAGGACTAAT-GGCTTAAATTTGCTTCACCACTATCTTAGGAAGATAAGATTC-A
1 CTTAGGAAGATAAGATTCATCATCTTAGATCTGCTCCACTACTA-CTTAGGGAGA-CAGAATCTG
* * * * * * * * ** *
30977 CCATCTTCGATCTGCTCCACTACTGCTTAGGGGGACAGAATATGCAATCTTCGACCTACTCTACT
64 CAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATCT-CAATCTTAAACCTACTCCACT
31042 ACTG
128 ACTG
* * * * ** * * * * * *
31046 CTTAGGGAGATAGGACTAAT-GGCTTAAATCTGCTTCTCCACTATCTT-GGGAAGATAAGATTC-
1 CTTAGGAAGATAAGATTCATCATCTTAGATCTGCTCCACTACTA-CTTAGGG-AGA-CAGAATCT
* * * * * * * * * *
31108 ACCACCTTCGATCTGCTCCACTACTGCTTAGGGGGACAGAATCTGCAATCTTTAACCTACTCCAC
63 GCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATCT-CAATCTTAAACCTACTCCAC
31173 TACTG
127 TACTG
* * * * * * * * *
31178 CTTAGGGAGATAGGACT-AACGA-CTTAAATCTGATTCTCCATTA-T-CTTAGGAAGATAAGATT
1 CTTAGGAAGATAAGATTCATC-ATCTTAGATCTG---CTCCACTACTACTTAGGGAGA-CAGAAT
* * * * ** * * *
31239 C-ACCATCTTCGATCTGTTCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCC
61 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATCT-CAATCTTAAACCTACTCC
31303 ACTACTG
125 ACTACTG
* * * ** * * * *
31310 CTTAGGGAGATAAGACTAAT-GGCTTAAATCTGCTTCC-CCACTATCTT-GGGAAGATAAGATTC
1 CTTAGGAAGATAAGATTCATCATCTTAGATCTGC-TCCACTACTA-CTTAGGG-AGA-CAGAATC
* * * * * * *
31372 -ACCATCTTCGATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTACTCCA
62 TGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATCT-CAATCTTAAACCTACTCCA
31436 CTACTG
126 CTACTG
31442 CTTAGG
1 CTTAGG
31448 GNNNNNNNNN
Statistics
Matches: 1049, Mismatches: 103, Indels: 84
0.85 0.08 0.07
Matches are distributed among these distances:
129 4 0.00
130 18 0.02
131 23 0.02
132 966 0.92
133 23 0.02
134 8 0.01
135 7 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (131 bp):
CTTAGGAAGATAAGATTCATCATCTTAGATCTGCTCCACTACTACTTAGGGAGACAGAATCTGCA
ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATCTCAATCTTAAACCTACTCCACTACT
G
Found at i:30720 original size:308 final size:309
Alignment explanation
Indices: 30155--30796 Score: 1020
Period size: 308 Copynumber: 2.1 Consensus size: 309
30145 CTTTGATCTG
* * * * *
30155 TTCCACTACTGCTTAGGGAGACAGAATTTGCAATCTTCAACCTACTCCATTGCTGCTCAGAGAGA
1 TTCCACTACTGCTTAGGGAGATAGGATCTGCAATCTTCAACCTACTCCACTACTGCTCAGAGAGA
* * * *
30220 TAGGGCTAATGGCTTAAATCTACTTCTCCACTATCTTAGGAAGATAAGATTCACGACCTTCGATC
66 TAGGACTAACGACTTAAATCTACTTCTCCACTATCTTAGGAAGATAAGATTCACCACCTTCGATC
*
30285 TGCTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGA
131 TGCTCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCCACCACTGCTTAGGGA
* * *
30350 GATAGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGAGAAGATAAAATTCATCATCTTCGA
196 GATAAGACTAATGGCTTAAATCTGCTTCCCCACTATCTTGAGAAGATAAAATTCACCATCTTCGA
*
30415 TCGGCTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCTA-
261 TCGACTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCTAC
* * *
30463 TTCCACTACTGCTTAGGGAGATAGGATCTGCAATCTTTAACCTACTCCACTACTGCTTAGGGAGA
1 TTCCACTACTGCTTAGGGAGATAGGATCTGCAATCTTCAACCTACTCCACTACTGCTCAGAGAGA
* *
30528 TAGGACTAACGACTTAAATCTGA-TTCTCCATTATCTTAGGAAGATAAGATTCACCATCTTCGAT
66 TAGGACTAACGACTTAAATCT-ACTTCTCCACTATCTTAGGAAGATAAGATTCACCACCTTCGAT
* *
30592 CTGTTCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCCACTACTGCTTAGGG
130 CTGCTCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCCACCACTGCTTAGGG
* *
30657 AGATAAGACTAATGGCTTAAATCTGCTTCCCCACTATCTTGGGAAGATAAGATTCACCATCTTCG
195 AGATAAGACTAATGGCTTAAATCTGCTTCCCCACTATCTTGAGAAGATAAAATTCACCATCTTCG
* * *
30722 ATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTAC
260 ATCGACTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCTAC
30772 TT-CACTACTGCTTAGGGAGATAGGA
1 TTCCACTACTGCTTAGGGAGATAGGA
30797 CTAACGGCTT
Statistics
Matches: 306, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
308 303 0.99
309 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (309 bp):
TTCCACTACTGCTTAGGGAGATAGGATCTGCAATCTTCAACCTACTCCACTACTGCTCAGAGAGA
TAGGACTAACGACTTAAATCTACTTCTCCACTATCTTAGGAAGATAAGATTCACCACCTTCGATC
TGCTCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCCACCACTGCTTAGGGA
GATAAGACTAATGGCTTAAATCTGCTTCCCCACTATCTTGAGAAGATAAAATTCACCATCTTCGA
TCGACTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCTAC
Found at i:30910 original size:308 final size:305
Alignment explanation
Indices: 30155--30923 Score: 892
Period size: 308 Copynumber: 2.5 Consensus size: 305
30145 CTTTGATCTG
* * * * * * * * *
30155 TTCCACTACTGCTTAGGGAGACAGAATTTGCAATCTTCAACCTACTCCATTGCTGCTCAGAGAGA
1 TTCCACTACTGCTTAGGGAGATAGGATCT-CAAGCTTAAACCTACTCCACTACTGCTTAGGGAGA
* * *** * * **
30220 TAGGGCTAATGGCTTAAATCTACTTCTCCACTATCTTAGGAAGATAAGATTCACGACCTTCGATC
65 TAAGACTAACCACTTAAATCT--GTCTCCACTATCTTAGGAAGATAAGATTCACAATATTCGATC
*
30285 TGCTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGA
128 TGCTCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCCACCACTGCTTAGGGA
* * *
30350 GATAGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGAGAAGATAAAATTCATCATCTTCGA
193 GATAAGACTAATGGCTTAAATCTGCTTCCCCACTATCTTGAGAAGATAAAATTCACCATCTTCGA
*
30415 TCGGCTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCTA
258 TCGACTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCTA
* *
30463 TTCCACTACTGCTTAGGGAGATAGGATCTGCAATCTTTAACCTACTCCACTACTGCTTAGGGAGA
1 TTCCACTACTGCTTAGGGAGATAGGATCT-CAAGCTTAAACCTACTCCACTACTGCTTAGGGAGA
* * * * *
30528 TAGGACTAACGACTTAAATCTGATTCTCCATTATCTTAGGAAGATAAGATTCACCATCTTCGATC
65 TAAGACTAACCACTTAAATCTG--TCTCCACTATCTTAGGAAGATAAGATTCACAATATTCGATC
* *
30593 TGTTCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGA
128 TGCTCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCCACCACTGCTTAGGGA
* *
30658 GATAAGACTAATGGCTTAAATCTGCTTCCCCACTATCTTGGGAAGATAAGATTCACCATCTTCGA
193 GATAAGACTAATGGCTTAAATCTGCTTCCCCACTATCTTGAGAAGATAAAATTCACCATCTTCGA
* * *
30723 TCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTA
258 TCGACTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCTA
*
30771 CTT-CACTACTGCTTAGGGAGATAGGA-CT-AACGGCTTAAATCTGCTTCTCCACTA-T-CTT-G
1 -TTCCACTACTGCTTAGGGAGATAGGATCTCAA--GCTTAAA-C--CTACTCCACTACTGCTTAG
* * ** *
30830 GGAAGATAAGATTCACCATCTTTGATCTG-CTCCACTACTGCTTAGG-GGA-ACAGAATAT-ACA
60 GG-AGATAAGACTAACCA-CTTAAATCTGTCTCCACTA-T-CTTAGGAAGATA-AG-AT-TCACA
* *
30891 ATATTCGACCTACTCCACTACTGCTTAGGGAGA
118 ATATTCGATCTGCTCCACTACTGCTTAGGGAGA
30924 TAGGACTAAT
Statistics
Matches: 403, Mismatches: 43, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
305 2 0.00
306 8 0.02
307 15 0.04
308 356 0.88
309 12 0.03
310 10 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (305 bp):
TTCCACTACTGCTTAGGGAGATAGGATCTCAAGCTTAAACCTACTCCACTACTGCTTAGGGAGAT
AAGACTAACCACTTAAATCTGTCTCCACTATCTTAGGAAGATAAGATTCACAATATTCGATCTGC
TCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCCACCACTGCTTAGGGAGAT
AAGACTAATGGCTTAAATCTGCTTCCCCACTATCTTGAGAAGATAAAATTCACCATCTTCGATCG
ACTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCTA
Found at i:31379 original size:88 final size:89
Alignment explanation
Indices: 30287--31448 Score: 430
Period size: 88 Copynumber: 13.2 Consensus size: 89
30277 CTTCGATCTG
* * * * * * *
30287 CTCCACTACTGCTTAGGGAGA-CAGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGAG
1 CTCCACTACTGCTTAGGGAGATAAGATTC-ACCATCTTCGATCTACTCCACTACTGCTTAGGGAG
*
30351 ATAGGACT-AATGGCTTAAATCTGCTT
65 ATAAGACTCAAT--CTTAAATCTGCTT
* * * ** * *
30377 CTCCACTA-T-CTT-GAGAAGATAAAATTCATCATCTTCGATCGGCTCCACTACTACTTAGGGTG
1 CTCCACTACTGCTTAG-GGAGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGAG
* *
30439 A-CAGAATCTGCAATCTTCAA-C--CTAT
65 ATAAG-A-CT-CAATCTTAAATCTGCT-T
* ** *
30464 -TCCACTACTGCTTAGGGAGATAGGATCTGCA--ATCTTTAACCTACTCCACTACTGCTTAGGGA
1 CTCCACTACTGCTTAGGGAGATAAGAT-T-CACCATCTTCGATCTACTCCACTACTGCTTAGGGA
* * *
30526 GATAGGACT-AACGACTTAAATCTGATT
64 GATAAGACTCAA--TCTTAAATCTGCTT
* * **
30553 CTCCATTA-T-CTTAGGAAGATAAGATTCACCATCTTCGATCTGTTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGAGA
* * *
30616 -CAGAATCTACAATCTTCAA-C--CTA
66 TAAG-A-CT-CAATCTTAAATCTGCTT
* ** *
30639 CTCCACTACTGCTTAGGGAGATAAGACT-A--ATGGCTTAAATCTGCTTCCCCACTA-T-CTT-G
1 CTCCACTACTGCTTAGGGAGATAAGATTCACCAT--CTTCGATCTAC-T--CCACTACTGCTTAG
* ** *
30698 GGAAGATAAGATTCACCATCTTCGA--T-CTA
61 GG-AGATAAGACTCA--ATCTTAAATCTGCTT
* * * * * * *
30727 CTCCACTACTGCTTAGGGTGAT-AGAATCTGCAATCTTCAACCTACTTCACTACTGCTTAGGGAG
1 CTCCACTACTGCTTAGGGAGATAAGATTC-ACCATCTTCGATCTACTCCACTACTGCTTAGGGAG
* *
30791 ATAGGACT-AACGGCTTAAATCTGCTT
65 ATAAGACTCAA--TCTTAAATCTGCTT
* *
30817 CTCCACTA-T-CTT-GGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGG-G
1 CTCCACTACTGCTTAGGG-AGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGAG
* * ** *
30878 A-ACAGAATATACAATATTCGA-C--CTA
65 ATA-AG-A-CT-CAATCTTAAATCTGCTT
* * ** * * * * * *
30903 CTCCACTACTGCTTAGGGAGATAGGACT-A--ATGGCTTAAATTTGCTTCACCACTATCTTAGGA
1 CTCCACTACTGCTTAGGGAGATAAGATTCACCAT--CTTCGATCTACTCCACTACT-GCTTAGGG
* **
30965 AGATAAGATTCACCATCTTCGATCTG---
63 AGATAAGACTCA--ATCTTAAATCTGCTT
* * * *
30991 CTCCACTACTGCTTAGGGGGA-CAGAATATGCA--ATCTTCGACCTACTCTACTACTGCTTAGGG
1 CTCCACTACTGCTTAGGGAGATAAG-AT-T-CACCATCTTCGATCTACTCCACTACTGCTTAGGG
*
31053 AGATAGGACT-AATGGCTTAAATCTGCTT
63 AGATAAGACTCAAT--CTTAAATCTGCTT
* * *
31081 CTCCACTA-T-CTT-GGGAAGATAAGATTCACCACCTTCGATCTGCTCCACTACTGCTTAGGGGG
1 CTCCACTACTGCTTAGGG-AGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGAG
* * *
31143 A-CAGAATCTGCAATCTTTAA-C--CTA
65 ATAAG-A-CT-CAATCTTAAATCTGCTT
* * * * ** * *
31167 CTCCACTACTGCTTAGGGAGATAGGACTAACGA-CTTAAATCTGATTCTCCATTA-T-CTTAGGA
1 CTCCACTACTGCTTAGGGAGATAAGATTCACCATCTTCGATCT-A--CTCCACTACTGCTTAGGG
* **
31229 AGATAAGATTCACCATCTTCGATCTG--T
63 AGATAAGACTCA--ATCTTAAATCTGCTT
* * * * *
31256 -TCCACTACTGCTTAGGGAGA-CAGAATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAG
1 CTCCACTACTGCTTAGGGAGATAAGATTC-ACCATCTTCGATCTACTCCACTACTGCTTAGGGAG
31319 ATAAGACT-AATGGCTTAAATCTGCTT
65 ATAAGACTCAAT--CTTAAATCTGCTT
* *
31345 CCCCACTA-T-CTT-GGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTG
1 CTCCACTACTGCTTAGGG-AGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGAG
* *
31407 AT-AGAATCTGCAATCTTCAA-C--CTA
65 ATAAG-A-CT-CAATCTTAAATCTGCTT
31431 CTCCACTACTGCTTAGGG
1 CTCCACTACTGCTTAGGG
31449 NNNNNNNNNN
Statistics
Matches: 795, Mismatches: 161, Indels: 233
0.67 0.14 0.20
Matches are distributed among these distances:
85 11 0.01
86 69 0.09
87 104 0.13
88 427 0.54
89 111 0.14
90 55 0.07
91 18 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (89 bp):
CTCCACTACTGCTTAGGGAGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGAGA
TAAGACTCAATCTTAAATCTGCTT
Found at i:31448 original size:132 final size:132
Alignment explanation
Indices: 30464--31448 Score: 1558
Period size: 132 Copynumber: 7.5 Consensus size: 132
30454 TTCAACCTAT
* * *
30464 TCCACTACTGCTTAGGGAGATAGGATCTGCAATCTTTAACCTACTCCACTACTGCTTAGGGAGAT
1 TCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGAT
* * * * *
30529 AGGACTAACGACTTAAATCTGATTCTCCATTATCTTAGGAAGATAAGATTCACCATCTTCGATCT
66 AGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCT
*
30594 GT
131 GC
*
30596 TCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGAT
1 TCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGAT
* *
30661 AAGACTAATGGCTTAAATCTGCTTCCCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCT
66 AGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCT
*
30726 AC
131 GC
* * *
30728 TCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTACTTCACTACTGCTTAGGGAGAT
1 TCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGAT
* *
30793 AGGACTAACGGCTTAAATCTGCTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTTGATCT
66 AGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCT
30858 GC
131 GC
* * * *
30860 TCCACTACTGCTTAGGG-GAACAGAATATACAATATTCGACCTACTCCACTACTGCTTAGGGAGA
1 TCCACTACTGCTTAGGGAG-ACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGA
* * *
30924 TAGGACTAATGGCTTAAATTTGCTTCACCACTATCTTAGGAAGATAAGATTCACCATCTTCGATC
65 TAGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATC
30989 TGC
130 TGC
* * * *
30992 TCCACTACTGCTTAGGGGGACAGAATATGCAATCTTCGACCTACTCTACTACTGCTTAGGGAGAT
1 TCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGAT
*
31057 AGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGGGAAGATAAGATTCACCACCTTCGATCT
66 AGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCT
31122 GC
131 GC
* *
31124 TCCACTACTGCTTAGGGGGACAGAATCTGCAATCTTTAACCTACTCCACTACTGCTTAGGGAGAT
1 TCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGAT
* * * * *
31189 AGGACTAACGACTTAAATCTGATTCTCCATTATCTTAGGAAGATAAGATTCACCATCTTCGATCT
66 AGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCT
*
31254 GT
131 GC
*
31256 TCCACTACTGCTTAGGGAGACAGAATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGAT
1 TCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGAT
* *
31321 AAGACTAATGGCTTAAATCTGCTTCCCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCT
66 AGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCT
*
31386 AC
131 GC
* *
31388 TCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGG
1 TCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGG
31449 NNNNNNNNNN
Statistics
Matches: 785, Mismatches: 66, Indels: 4
0.92 0.08 0.00
Matches are distributed among these distances:
131 1 0.00
132 783 1.00
133 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (132 bp):
TCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGAT
AGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCT
GC
Found at i:31752 original size:44 final size:44
Alignment explanation
Indices: 31569--31753 Score: 123
Period size: 44 Copynumber: 4.2 Consensus size: 44
31559 GATTCACCAC
* *
31569 CTTCGATCTGCTCCACTACTGCTTAGGGGGACAGAATATGCAAT
1 CTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
* * * *
31613 CTTCGACCTACTCCACTACTGCTTAGGGAGATAGGA-CT--AAT
1 CTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
** * * * * * *
31654 GGCTTAAATCTCCTTCTCCACTA-T-CTT-GGGAAGATAAGATTC-ACCAC
1 --CTTCGA--T-CTGCTCCACTACTGCTTAGGG-AGA-CAGAATCTGCAAT
*
31701 CTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAAT
1 CTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
31745 CTTCGATCT
1 CTTCGATCT
31754 ACTTCGCTGC
Statistics
Matches: 103, Mismatches: 24, Indels: 28
0.66 0.15 0.18
Matches are distributed among these distances:
41 3 0.03
42 10 0.10
43 15 0.15
44 53 0.51
45 10 0.10
46 11 0.11
47 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (44 bp):
CTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
Found at i:31793 original size:46 final size:46
Alignment explanation
Indices: 31736--32029 Score: 480
Period size: 46 Copynumber: 6.4 Consensus size: 46
31726 GGGTGACAGA
* *
31736 ATCTGCAATCTTCGATCTACTTCGCTGCCAAATACAGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAG
31782 ATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAG
* * *
31828 ATCTGCTATCTTTGATCTACTCCGCTACCAAATATAGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAG
**
31874 ATCTGCTATCTTCGATCTACTCCGCTGTAAAATACAGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAG
*
31920 ATCTGCTATCTTCGATCTACTCCGCCGCCAAATACAGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAG
* * *
31966 ATCTGCTATCTTCGATCTACTCTGCTGTCAAATACAGGAAGATAAG
1 ATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAG
*
32012 ATTTGCTATCTTCGATCT
1 ATCTGCTATCTTCGATCT
32030 GTTCTCTGGG
Statistics
Matches: 230, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 230 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (46 bp):
ATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAG
Found at i:33243 original size:6 final size:6
Alignment explanation
Indices: 33234--33290 Score: 51
Period size: 6 Copynumber: 8.7 Consensus size: 6
33224 TTGACCTCTC
* *
33234 CTTTTT CTTTTTT CTTTTT CTTCTCT CTTCTT CTTTCTCT CTTTCTT CTTTTT
1 CTTTTT C-TTTTT CTTTTT CTT-TTT CTTTTT CTTT-T-T CTTT-TT CTTTTT
33287 CTTT
1 CTTT
33291 CTTTCCCCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
6 19 0.44
7 17 0.40
8 7 0.16
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (6 bp):
CTTTTT
Found at i:33258 original size:25 final size:28
Alignment explanation
Indices: 33229--33283 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
33219 TCACCTTGAC
* *
33229 CTCTCCTTTTTCTTT-TTTCTTT-TTCTT
1 CTCT-CTTCTTCTTTCTCTCTTTCTTCTT
33256 CTCTCTTCTTCTTTCTCTCTTTCTTCTT
1 CTCTCTTCTTCTTTCTCTCTTTCTTCTT
33284 TTTCTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 10 0.42
28 5 0.21
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (28 bp):
CTCTCTTCTTCTTTCTCTCTTTCTTCTT
Found at i:38807 original size:3 final size:3
Alignment explanation
Indices: 38799--38851 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
38789 TTTAGCAATT
* *
38799 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA GTA -TA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
38844 ATA TTA TT
1 TTA TTA TT
38852 GACATTATTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:39487 original size:18 final size:19
Alignment explanation
Indices: 39442--39490 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
39432 GCTTAGGTGC
* *
39442 TTTAATTTTTATTTGTTCA
1 TTTACTTTTTATTTATTCA
*
39461 TTTAC-TTTTATTTATTGA
1 TTTACTTTTTATTTATTCA
39479 TTT-CTTTTTATT
1 TTTACTTTTTATT
39491 ATATGTTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 21 0.81
19 4 0.15
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTACTTTTTATTTATTCA
Found at i:51443 original size:42 final size:43
Alignment explanation
Indices: 51395--51484 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
51385 GGTTGAAGCA
* *
51395 TGGAGTAGATCG-GCTATGAA-TCCTATTTCCCTGAAGTTGCAG
1 TGGAGTAGATCGAGATAT-AAGTCCTATTTCCCTGAAGATGCAG
* * *
51437 TGGAGTAGGTTGAAGATATAAGTCTTATTTCCCTGAAGATGCAG
1 TGGAGTAGATCG-AGATATAAGTCCTATTTCCCTGAAGATGCAG
51481 TGGA
1 TGGA
51485 ACAGACTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 10 0.25
43 2 0.05
44 28 0.70
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (43 bp):
TGGAGTAGATCGAGATATAAGTCCTATTTCCCTGAAGATGCAG
Found at i:51593 original size:208 final size:208
Alignment explanation
Indices: 51217--51593 Score: 549
Period size: 208 Copynumber: 1.8 Consensus size: 208
51207 CCTTGTCTCT
* * * **
51217 CTGAAGTTGTAGTAGAGCAGGTTGAAGTTACCAGTCTTATTTCCCTGAAGATGCAGTGGAGTAAA
1 CTGAAGTTGCAGTAGAGCAGGTTGAAGATACAAGTCTTATTTCCCTGAAGATGCAGTGGAACAAA
* * * * *
51282 CTGAAAACAACAAGTCATGTCTCCCTAAAGTTGTAGTGGAGCAGACAGTAGATAGTGGTTCTTAT
66 CTGAAAACAACAAGGCATGTCTCCCTAAAGTTGTAGCGGAGCAGACAGAAGATAGCGATTCTTAT
* * *
51347 CATGTTGAATCTTATTTCCCTGAAGTTGCAGCGGAATAGGTTGAAGCATGGAGTAGATCGGCTAT
131 CATGTTGAATCTCATTCCCCTAAAGTTGCAGCGGAATAGGTTGAAGCATGGAGTAGATCGGCTAT
51412 GAATCCTATTTCC
196 GAATCCTATTTCC
* * * *
51425 CTGAAGTTGCAGTGGAGTAGGTTGAAGATATAAGTCTTATTTCCCTGAAGATGCAGTGGAACAGA
1 CTGAAGTTGCAGTAGAGCAGGTTGAAGATACAAGTCTTATTTCCCTGAAGATGCAGTGGAACAAA
* *
51490 CTGAAAACAACAAGGCGTGTCTCCCTAAAGTTGTAGCGGAGCGGACAGAAGATAGCGATTCTTAT
66 CTGAAAACAACAAGGCATGTCTCCCTAAAGTTGTAGCGGAGCAGACAGAAGATAGCGATTCTTAT
* *
51555 CATGTCT-AATCTCATTCCCCTAAAGTTGTAGTGGAATAG
131 CATGT-TGAATCTCATTCCCCTAAAGTTGCAGCGGAATAG
51594 ATAGAAGCGA
Statistics
Matches: 147, Mismatches: 21, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
208 146 0.99
209 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (208 bp):
CTGAAGTTGCAGTAGAGCAGGTTGAAGATACAAGTCTTATTTCCCTGAAGATGCAGTGGAACAAA
CTGAAAACAACAAGGCATGTCTCCCTAAAGTTGTAGCGGAGCAGACAGAAGATAGCGATTCTTAT
CATGTTGAATCTCATTCCCCTAAAGTTGCAGCGGAATAGGTTGAAGCATGGAGTAGATCGGCTAT
GAATCCTATTTCC
Found at i:53313 original size:3 final size:3
Alignment explanation
Indices: 53305--53365 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
53295 TTTAGCAATT
* * *
53305 TTA TTA TTA TTA TTA TTA TTG TTA TTA GTA -TA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
53350 TTGA -TA TTA TTG TTA T
1 TT-A TTA TTA TTA TTA T
53366 GTTTTTTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
2 3 0.06
3 41 0.87
4 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:53428 original size:14 final size:14
Alignment explanation
Indices: 53411--53450 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
53401 GATATATATG
*
53411 TTTTATTATATTAT
1 TTTTATTATATAAT
53425 TTTTATTATATAAT
1 TTTTATTATATAAT
53439 TGTTTA-TATATA
1 T-TTTATTATATA
53451 TGCGTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TTTTATTATATAAT
Found at i:53994 original size:18 final size:19
Alignment explanation
Indices: 53949--53997 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
53939 GCTTAGGTGC
* *
53949 TTTAATTTTTATTTGTTCA
1 TTTACTTTTTATTTATTCA
*
53968 TTTAC-TTTTATTTATTGA
1 TTTACTTTTTATTTATTCA
53986 TTT-CTTTTTATT
1 TTTACTTTTTATT
53998 ATATGTTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 21 0.81
19 4 0.15
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTACTTTTTATTTATTCA
Found at i:59017 original size:2 final size:2
Alignment explanation
Indices: 59010--59044 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
59000 TACAACTTTA
59010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59045 AACATGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60878 original size:45 final size:44
Alignment explanation
Indices: 60812--61017 Score: 188
Period size: 45 Copynumber: 4.6 Consensus size: 44
60802 ACCTCAAAAT
60812 TAATGCCATAGTATCTTTCAACTATGGTCTTGATCGTTACCGATG
1 TAATGCCATAGTATCTTTCAACTATGGTCTT-ATCGTTACCGATG
* * * *
60857 TGATGCCATAGTATCTTTCAACTATGGTCTTAT-TTGTATCGAATT
1 TAATGCCATAGTATCTTTCAACTATGGTCTTATCGT-TACCG-ATG
* * * * *
60902 TAATGCCATAATATCTTTCAATTATGGTCTTA-CATAGTCCCGATT
1 TAATGCCATAGTATCTTTCAACTATGGTCTTATCGT--TACCGATG
* * * *
60947 TAGTTCCATACTATCTTTCAACTATGGTCTTATTCATT-CC-A-G
1 TAATGCCATAGTATCTTTCAACTATGGTCTTA-TCGTTACCGATG
60989 TAAAATGCCATAGTATCTTTCAACTATGG
1 T--AATGCCATAGTATCTTTCAACTATGG
61018 CCTTTCTCAT
Statistics
Matches: 135, Mismatches: 18, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 31 0.23
45 94 0.70
46 4 0.03
47 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (44 bp):
TAATGCCATAGTATCTTTCAACTATGGTCTTATCGTTACCGATG
Found at i:60964 original size:90 final size:90
Alignment explanation
Indices: 60811--61017 Score: 240
Period size: 90 Copynumber: 2.3 Consensus size: 90
60801 GACCTCAAAA
* * * *
60811 TTAATGCCATAGTATCTTTCAACTATGGTCTTGATCGTTACCGATGTGATGCCATAGTATCTTTC
1 TTAATGCCATAATATCTTTCAACTATGGTCTTCATAGTTACCGATGTGATGCCATACTATCTTTC
60876 AACTATGGTCTTATTTGTATCGAAT
66 AACTATGGTCTTATTTGTATCGAAT
* * * *
60901 TTAATGCCATAATATCTTTCAATTATGGTCTTACATAG-TCCCGAT-TTAGTTCCATACTATCTT
1 TTAATGCCATAATATCTTTCAACTATGGTCTT-CATAGTTACCGATGTGA-TGCCATACTATCTT
** * *
60964 TCAACTATGGTCTTATTCAT-TCCAGT
64 TCAACTATGGTCTTATTTGTATCGAAT
** *
60990 AAAATGCCATAGTATCTTTCAACTATGG
1 TTAATGCCATAATATCTTTCAACTATGG
61018 CCTTTCTCAT
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
89 30 0.30
90 66 0.67
91 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (90 bp):
TTAATGCCATAATATCTTTCAACTATGGTCTTCATAGTTACCGATGTGATGCCATACTATCTTTC
AACTATGGTCTTATTTGTATCGAAT
Found at i:64809 original size:49 final size:49
Alignment explanation
Indices: 64654--64816 Score: 173
Period size: 49 Copynumber: 3.3 Consensus size: 49
64644 TTGCTAGTAC
** ** *
64654 GTTATGGATGAACCACTGGTTGTTGCAGATAAACTATTGACTGAAATAT
1 GTTATGGATGAACCACTGGTCATTGCAGATAAACTGCTGACTAAAATAT
* * * * *
64703 GTTGTGAATGAACCACTGGTGATTTCAGATAAATTGCTGACTAAAATAT
1 GTTATGGATGAACCACTGGTCATTGCAGATAAACTGCTGACTAAAATAT
* * * * *
64752 GTTGTGGATGAACCACTAGTCATTGCAGACAAACTGCTAACTAAAATAC
1 GTTATGGATGAACCACTGGTCATTGCAGATAAACTGCTGACTAAAATAT
* *
64801 ATTATGGATAAACCAC
1 GTTATGGATGAACCAC
64817 CGTCGTCGCA
Statistics
Matches: 94, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 94 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (49 bp):
GTTATGGATGAACCACTGGTCATTGCAGATAAACTGCTGACTAAAATAT
Found at i:64979 original size:34 final size:33
Alignment explanation
Indices: 64884--65027 Score: 132
Period size: 34 Copynumber: 4.3 Consensus size: 33
64874 ATGCAACATG
* *
64884 ACATGCTTATAATAGATCAATACGATAGCAATA
1 ACATGCTTATAATAGATCAATAAGGTAGCAATA
* * *
64917 ACATTCTTATAGAAAG-TCGATACA-GTAGCATATA
1 ACATGCTTATA-ATAGATCAATA-AGGTAGCA-ATA
*
64951 TCATGCTTATAATAGATCAATAAGGTAGCAATTA
1 ACATGCTTATAATAGATCAATAAGGTAGCAA-TA
* *
64985 ACATGCTTATAACAGATCATTATA-GTAGCAATAA
1 ACATGCTTATAATAGATCAATA-AGGTAGCAAT-A
*
65019 ACTTGCTTA
1 ACATGCTTA
65028 ACATGTATTT
Statistics
Matches: 90, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
33 26 0.29
34 63 0.70
35 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (33 bp):
ACATGCTTATAATAGATCAATAAGGTAGCAATA
Found at i:66677 original size:22 final size:22
Alignment explanation
Indices: 66649--66694 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
66639 AAAAAAAGAT
* *
66649 ATTTTATATATAAATATT-AATA
1 ATTTTAT-TAAAAAAATTAAATA
66671 ATTTTATTAAAAAAATTAAATA
1 ATTTTATTAAAAAAATTAAATA
66693 AT
1 AT
66695 AATTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTTATTAAAAAAATTAAATA
Found at i:68759 original size:29 final size:29
Alignment explanation
Indices: 68727--68829 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 29
68717 TCCAAAAAAT
68727 TTAAAATTACAATTTGACTCTCAAATTTC
1 TTAAAATTACAATTTGACTCTCAAATTTC
* * *
68756 TTAAAATTAC-ATTTAACTTCTCTAACTT-
1 TTAAAATTACAATTTGAC-TCTCAAATTTC
*
68784 TTAAAATTACATTTTGAC-CAT-AAACTTTC
1 TTAAAATTACAATTTGACTC-TCAAA-TTTC
*
68813 TTAAAATTACATTTTGA
1 TTAAAATTACAATTTGA
68830 GCCCAAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
27 3 0.05
28 19 0.31
29 40 0.65
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.44
Consensus pattern (29 bp):
TTAAAATTACAATTTGACTCTCAAATTTC
Found at i:68788 original size:28 final size:27
Alignment explanation
Indices: 68726--68797 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
68716 ATCCAAAAAA
* *
68726 TTTAAAATTACAATTTGACTCTCAAATT
1 TTTAAAATTAC-ATTTAACTCTCAAACT
*
68754 TCTTAAAATTACATTTAACTTCTCTAACT
1 T-TTAAAATTACATTTAAC-TCTCAAACT
68783 TTTAAAATTACATTT
1 TTTAAAATTACATTT
68798 TGACCATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 21 0.54
29 18 0.46
ACGTcount: A:0.38, C:0.15, G:0.01, T:0.46
Consensus pattern (27 bp):
TTTAAAATTACATTTAACTCTCAAACT
Found at i:69899 original size:3 final size:3
Alignment explanation
Indices: 69877--69950 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
69867 CAAAATCCGG
* * * *
69877 ATT ATC ATT GTT ACT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
69925 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
69951 CACTTTCAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:73244 original size:13 final size:13
Alignment explanation
Indices: 73226--73251 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
73216 ATAATCTGAA
73226 ATCAAAAGCATTT
1 ATCAAAAGCATTT
73239 ATCAAAAGCATTT
1 ATCAAAAGCATTT
73252 TTCGAAAACA
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
ATCAAAAGCATTT
Found at i:73635 original size:20 final size:19
Alignment explanation
Indices: 73612--73671 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
73602 AGAGTTTAGG
73612 GTTTTTTTTATATTTTTTAA
1 GTTTTTTTTATATTTTTT-A
*
73632 GTTTTTTTTATATATCCTTTA
1 GTTTTTTTTATAT-T-TTTTA
*
73653 GTTTATTTTATAATTTTTT
1 GTTTTTTTTAT-ATTTTTT
73672 TGATGCAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 16 0.47
21 13 0.38
22 5 0.15
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (19 bp):
GTTTTTTTTATATTTTTTA
Found at i:74815 original size:73 final size:73
Alignment explanation
Indices: 74637--74840 Score: 311
Period size: 72 Copynumber: 2.8 Consensus size: 73
74627 TTTTTAGACT
* *
74637 CCAACGACGCCGTTTTCTGAGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAA
1 CCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAA
74702 AACTAAGC
66 AACTAAGC
* * * ** *
74710 CCAACG-CGCCATTTTCTAAGCTTTAGGGGATTTAGCGGCATTTTTGGGAAAGCGCTGCAAAAAA
1 CCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAA
*
74774 ACCTAAGC
66 AACTAAGC
*
74782 CCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGAAAACGCCGC
1 CCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGC
74841 TAATGCTCAA
Statistics
Matches: 114, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
72 63 0.55
73 51 0.45
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (73 bp):
CCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAA
AACTAAGC
Found at i:75071 original size:113 final size:113
Alignment explanation
Indices: 74740--75082 Score: 526
Period size: 112 Copynumber: 3.0 Consensus size: 113
74730 CTTTAGGGGA
* * *
74740 TTTAGCGGCATTTTTGGGAAAGCGCTGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAA-CTAAGCCCAACGGCGCCGTTTTCTGAGCT
* * *
74805 TTCGGGGATTTAGCGGCATTTTTAAGAAAACGCCGCTAATGCTCAAGGC
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
74854 TTTAGCAGCGTTTTTGGGAAAGCGCCGCAAAAAAACTAAGCCCAACAGCGCC-TTTTTTGAGCCT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGCTT
*
74918 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTTAGGGC
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
74966 TTTAGCGGCGTTTCTGGGAAAGCGCCACAAAAGAACTAAGCCCAACGGTGCCGTTTTCTGAGCTT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGCTT
*
75031 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGA
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
75079 TTTA
1 TTTA
75083 AAATAATTTA
Statistics
Matches: 207, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
112 100 0.48
113 75 0.36
114 32 0.15
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (113 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:75311 original size:7 final size:7
Alignment explanation
Indices: 75301--75431 Score: 77
Period size: 7 Copynumber: 17.9 Consensus size: 7
75291 GATTTAAGGT
75301 TTAGGGG
1 TTAGGGG
*
75308 TTAGGTG
1 TTAGGGG
* **
75315 TTATGCT
1 TTAGGGG
75322 TTA-GGG
1 TTAGGGG
75328 TTAGGGGG
1 TTA-GGGG
75336 ATTTAGGGG
1 --TTAGGGG
75345 TTAGGGG
1 TTAGGGG
* **
75352 TTATGCT
1 TTAGGGG
75359 TTA-GGG
1 TTAGGGG
75365 TTAGGGGG
1 TTA-GGGG
75373 ATTTAGGGG
1 --TTAGGGG
75382 TTAGGGG
1 TTAGGGG
* **
75389 TTATGCT
1 TTAGGGG
75396 TTAGGGG
1 TTAGGGG
75403 TTAGGGG
1 TTAGGGG
75410 ATTTAGGGG
1 --TTAGGGG
*
75419 TTAGGGT
1 TTAGGGG
75426 TTAGGG
1 TTAGGG
75432 TTTCAACGGT
Statistics
Matches: 96, Mismatches: 18, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
6 8 0.08
7 61 0.64
8 6 0.06
9 15 0.16
10 6 0.06
ACGTcount: A:0.16, C:0.02, G:0.46, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:75355 original size:37 final size:37
Alignment explanation
Indices: 75300--75424 Score: 225
Period size: 37 Copynumber: 3.4 Consensus size: 37
75290 GGATTTAAGG
*
75300 TTTAGGGGTTAGGTGTTATGCTTTAGGGTTAGGGGGA
1 TTTAGGGGTTAGGGGTTATGCTTTAGGGTTAGGGGGA
75337 TTTAGGGGTTAGGGGTTATGCTTTAGGGTTAGGGGGA
1 TTTAGGGGTTAGGGGTTATGCTTTAGGGTTAGGGGGA
75374 TTTAGGGGTTAGGGGTTATGCTTTAGGGGTTA-GGGGA
1 TTTAGGGGTTAGGGGTTATGCTTTA-GGGTTAGGGGGA
75411 TTTAGGGGTTAGGG
1 TTTAGGGGTTAGGG
75425 TTTAGGGTTT
Statistics
Matches: 86, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
37 80 0.93
38 6 0.07
ACGTcount: A:0.16, C:0.02, G:0.46, T:0.36
Consensus pattern (37 bp):
TTTAGGGGTTAGGGGTTATGCTTTAGGGTTAGGGGGA
Found at i:75432 original size:7 final size:7
Alignment explanation
Indices: 75279--75434 Score: 68
Period size: 7 Copynumber: 21.4 Consensus size: 7
75269 AGGGTATGGA
75279 TTTAGGG
1 TTTAGGG
75286 TTT-GGG
1 TTTAGGG
*
75292 ATTTAAGG
1 -TTTAGGG
75300 TTTAGGG
1 TTTAGGG
*
75307 GTTA-GG
1 TTTAGGG
* *
75313 TGTTATGC
1 T-TTAGGG
75321 TTTAGGG
1 TTTAGGG
75328 -TTAGGGGG
1 TTTA--GGG
75336 ATTTAGGG
1 -TTTAGGG
*
75344 GTTAGGG
1 TTTAGGG
* * *
75351 GTTATGC
1 TTTAGGG
75358 TTTAGGG
1 TTTAGGG
75365 -TTAGGGGG
1 TTTA--GGG
75373 ATTTAGGG
1 -TTTAGGG
*
75381 GTTAGGG
1 TTTAGGG
* * *
75388 GTTATGC
1 TTTAGGG
75395 TTTAGGG
1 TTTAGGG
*
75402 GTTAGGGG
1 TTTA-GGG
75410 ATTTAGGG
1 -TTTAGGG
*
75418 GTTAGGG
1 TTTAGGG
75425 TTTAGGG
1 TTTAGGG
75432 TTT
1 TTT
75435 CAACGGTTAA
Statistics
Matches: 112, Mismatches: 23, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
6 11 0.10
7 70 0.62
8 22 0.20
9 3 0.03
10 6 0.05
ACGTcount: A:0.16, C:0.02, G:0.44, T:0.38
Consensus pattern (7 bp):
TTTAGGG
Found at i:77772 original size:21 final size:24
Alignment explanation
Indices: 77734--77782 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 24
77724 TGTGGTTCAA
*
77734 ATTTTTCTCTTTTCTTTCAATTT-
1 ATTTTTCTCTTCTCTTTCAATTTG
*
77757 ATTTTTCT-TTCT-TTTCCATTTG
1 ATTTTTCTCTTCTCTTTCAATTTG
77779 ATTT
1 ATTT
77783 GCTACACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 7 0.30
23 8 0.35
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.69
Consensus pattern (24 bp):
ATTTTTCTCTTCTCTTTCAATTTG
Found at i:81503 original size:22 final size:22
Alignment explanation
Indices: 81461--81504 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
81451 AAAAGGTAGA
*
81461 TTTTGATTTCTTTTTGGTTTTT
1 TTTTGATTTCTTTTTCGTTTTT
81483 TTTTG-TTTCGTTTTTC-TTTTT
1 TTTTGATTTC-TTTTTCGTTTTT
81504 T
1 T
81505 GCTTTCTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.02, C:0.07, G:0.11, T:0.80
Consensus pattern (22 bp):
TTTTGATTTCTTTTTCGTTTTT
Found at i:82123 original size:3 final size:3
Alignment explanation
Indices: 82117--82168 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
82107 ATTAATCAAT
82117 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
82165 TTA T
1 TTA T
82169 CGTCGATATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:84086 original size:20 final size:21
Alignment explanation
Indices: 84064--84113 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
84054 TTCCATGTGC
84064 TTTCCATTT-TTTCTTCTTTCT
1 TTTCCATTTCTTT-TTCTTTCT
84085 TTTCC-TTTCTTTTTCTTTCT
1 TTTCCATTTCTTTTTCTTTCT
84105 TTTCCATTT
1 TTTCCATTT
84114 GATTTGCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTCCATTTCTTTTTCTTTCT
Found at i:84094 original size:10 final size:10
Alignment explanation
Indices: 84079--84109 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
84069 ATTTTTTCTT
84079 CTTTCTTTTC
1 CTTTCTTTTC
*
84089 CTTTCTTTTT
1 CTTTCTTTTC
84099 CTTTCTTTTC
1 CTTTCTTTTC
84109 C
1 C
84110 ATTTGATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
CTTTCTTTTC
Found at i:87112 original size:19 final size:18
Alignment explanation
Indices: 87072--87136 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
87062 ATAAACTTAA
* *
87072 AAAAATTGTAAAATTCATT
1 AAAAATTCTAAAAAT-ATT
87091 AAAAATTCTAAAAATATCT
1 AAAAATTCTAAAAATAT-T
* *
87110 AAATATTATAAAAACT-TAT
1 AAAAATTCTAAAAA-TAT-T
87129 AAAAATTC
1 AAAAATTC
87137 AAATAAATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.05
19 34 0.92
20 1 0.03
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAAATTCTAAAAATATT
Found at i:87123 original size:29 final size:28
Alignment explanation
Indices: 87091--87152 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
87081 AAAATTCATT
*
87091 AAAAATTCTAAAAATATCTAAAT-ATTATA
1 AAAAATTATAAAAAT-TC-AAATAATTATA
*
87120 AAAACTTATAAAAATTCAAATAAATTATA
1 AAAAATTATAAAAATTCAAAT-AATTATA
87149 AAAA
1 AAAA
87153 TAGAATTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.14
28 2 0.07
29 23 0.79
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAAATTATAAAAATTCAAATAATTATA
Found at i:87152 original size:57 final size:55
Alignment explanation
Indices: 87025--87153 Score: 136
Period size: 57 Copynumber: 2.3 Consensus size: 55
87015 AAAAATCATA
* * *
87025 AAAAAATTAT-AAAATTATGAAAATATTAAAATCTTATATAAACTTAAAAAAATT
1 AAAAAATTATAAAAATTATAAAAATATTAAAATATTATAAAAACTTAAAAAAATT
** * *
87079 GTAAAATTCATTAAAAATTCTAAAAATATCT-AAATATTATAAAAACTTATAAAAATT
1 AAAAAATT-A-TAAAAATTATAAAAATAT-TAAAATATTATAAAAACTTAAAAAAATT
87136 CAAATAAATTATAAAAAT
1 -AAA-AAATTATAAAAAT
87154 AGAATTAGGG
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
54 6 0.10
55 1 0.02
56 1 0.02
57 44 0.73
58 3 0.05
59 5 0.08
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (55 bp):
AAAAAATTATAAAAATTATAAAAATATTAAAATATTATAAAAACTTAAAAAAATT
Found at i:89356 original size:23 final size:24
Alignment explanation
Indices: 89311--89357 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
89301 ATCAATGAGC
*
89311 AAATCTTTATCATTTTGACAATTT
1 AAATCTTTATCATTTTGAAAATTT
* *
89335 AAAT-TTTATTATTTTTAAAATTT
1 AAATCTTTATCATTTTGAAAATTT
89358 TATGGGGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (24 bp):
AAATCTTTATCATTTTGAAAATTT
Found at i:93035 original size:3 final size:3
Alignment explanation
Indices: 93027--93058 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
93017 AATTTAGTCA
93027 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
93059 AATAATTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:93340 original size:18 final size:18
Alignment explanation
Indices: 93234--93341 Score: 102
Period size: 18 Copynumber: 6.3 Consensus size: 18
93224 TAATATGTGT
* *
93234 TATTATTTTTATCATCATA
1 TATTATTATTATTATCA-A
** *
93253 TATTATTATTAAAACCAA
1 TATTATTATTATTATCAA
93271 TATTATTATTATTAT---
1 TATTATTATTATTATCAA
93286 TATTATTATTATTAT---
1 TATTATTATTATTATCAA
* *
93301 TATTATTATTATTATTAT
1 TATTATTATTATTATCAA
93319 TATTATTATTATTATCAA
1 TATTATTATTATTATCAA
93337 TATTA
1 TATTA
93342 CCGTTATTAT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
15 30 0.39
18 34 0.44
19 13 0.17
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATTATTATTATCAA
Found at i:93352 original size:3 final size:3
Alignment explanation
Indices: 93271--93333 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
93261 TTAAAACCAA
93271 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
93319 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
93334 CAATATTACC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:93633 original size:18 final size:18
Alignment explanation
Indices: 93585--93633 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
93575 CATATCTTTG
*
93585 ATTTATATATATATACTT
1 ATTTATATATATATACTA
* *
93603 ATTTTTATCTATATTA-TA
1 ATTTATATATATA-TACTA
93621 ATTTATATATATA
1 ATTTATATATATA
93634 CATGTATTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATATATATACTA
Found at i:93692 original size:18 final size:18
Alignment explanation
Indices: 93669--93704 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
93659 TTTCTAAATT
*
93669 TTTATAAGTATATACATA
1 TTTATAAGTACATACATA
*
93687 TTTATATGTACATACATA
1 TTTATAAGTACATACATA
93705 CTTACATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTATAAGTACATACATA
Found at i:96158 original size:2 final size:2
Alignment explanation
Indices: 96151--96179 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
96141 TACAACTTTA
96151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
96180 AACATGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:96340 original size:70 final size:70
Alignment explanation
Indices: 96227--96365 Score: 242
Period size: 70 Copynumber: 2.0 Consensus size: 70
96217 TTCCAGTCAT
* *
96227 TTATTTTATTCAAAATATCCTGATTCCTAAAGTACTTGCATGTCCATTTGCTCCCTAAACCATTC
1 TTATTTTATTCAAAATATCCAGATTCATAAAGTACTTGCATGTCCATTTGCTCCCTAAACCATTC
96292 AACAA
66 AACAA
* *
96297 TTATTTTATTCAAAATATCCAGGTTCATAAAGTACTTGTATGTCCATTTGCTCCCTAAACCATTC
1 TTATTTTATTCAAAATATCCAGATTCATAAAGTACTTGCATGTCCATTTGCTCCCTAAACCATTC
96362 AACA
66 AACA
96366 CTTCTTTATT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (70 bp):
TTATTTTATTCAAAATATCCAGATTCATAAAGTACTTGCATGTCCATTTGCTCCCTAAACCATTC
AACAA
Found at i:99146 original size:62 final size:62
Alignment explanation
Indices: 99029--99148 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 62
99019 CACACACCCA
* * * *
99029 TGTAGTTCGCCTATGTGTCTCAAATTTTAGCTCAGTCAGTTACACAGCTTGCCACACGCCTG
1 TGTAGTTCGCCTATGTGTCTCAAATTTCAACTCAGTCAGTTACACAGCCTACCACACGCCTG
* * * * *
99091 TGTAGTTCGTCTGTGTGTTTCAAATTTCAACTCATTCAGTTACACGGCCTACCACACG
1 TGTAGTTCGCCTATGTGTCTCAAATTTCAACTCAGTCAGTTACACAGCCTACCACACG
99149 GCCCACCACA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (62 bp):
TGTAGTTCGCCTATGTGTCTCAAATTTCAACTCAGTCAGTTACACAGCCTACCACACGCCTG
Found at i:100291 original size:34 final size:34
Alignment explanation
Indices: 100253--100326 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
100243 TCGGTTGGAT
100253 TAAAAATCTACCAAGGGATCGATCTAATGAGAGG
1 TAAAAATCTACCAAGGGATCGATCTAATGAGAGG
*
100287 TAAAAATCTACCAAGGTATCGATCTAATGAGAGG
1 TAAAAATCTACCAAGGGATCGATCTAATGAGAGG
100321 TAAAAA
1 TAAAAA
100327 GGACTATCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.22
Consensus pattern (34 bp):
TAAAAATCTACCAAGGGATCGATCTAATGAGAGG
Found at i:100757 original size:17 final size:17
Alignment explanation
Indices: 100735--100773 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
100725 CTAATCTATA
*
100735 TGCAATAGGGACTAAAT
1 TGCAATAAGGACTAAAT
100752 TGCAATAAGGACTAAAT
1 TGCAATAAGGACTAAAT
100769 TGCAA
1 TGCAA
100774 AAAGTGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.23
Consensus pattern (17 bp):
TGCAATAAGGACTAAAT
Found at i:102335 original size:36 final size:36
Alignment explanation
Indices: 102295--102392 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 36
102285 TATATATATA
102295 TATATATGTATGCATTTGGCATATGTGGATT-ATAAG
1 TATATATGTATGCATTTGGCATATGTGG-TTGATAAG
* *
102331 --TATATGTATGTACATTCGGCACATGTGGTTGATAAG
1 TATATATGTATG--CATTTGGCATATGTGGTTGATAAG
* ** *
102367 TATAAAAATATGCTTTTGGCATATGT
1 TATATATGTATGCATTTGGCATATGT
102393 ATTTGAATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
34 10 0.20
35 2 0.04
36 30 0.61
38 7 0.14
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (36 bp):
TATATATGTATGCATTTGGCATATGTGGTTGATAAG
Found at i:102340 original size:34 final size:35
Alignment explanation
Indices: 102297--102370 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
102287 TATATATATA
* *
102297 TATATGTATG-CATTTGGCATATGTGGATT-ATAAG
1 TATATGTATGACATTCGGCACATGTGG-TTGATAAG
102331 TATATGTATGTACATTCGGCACATGTGGTTGATAAG
1 TATATGTATG-ACATTCGGCACATGTGGTTGATAAG
102367 TATA
1 TATA
102371 AAAATATGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 10 0.29
35 2 0.06
36 23 0.66
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.39
Consensus pattern (35 bp):
TATATGTATGACATTCGGCACATGTGGTTGATAAG
Found at i:106991 original size:49 final size:49
Alignment explanation
Indices: 106905--107027 Score: 138
Period size: 49 Copynumber: 2.5 Consensus size: 49
106895 GTTATGGATA
* * *
106905 AACCACTGGTCGTTGTAGATAAACTATTGACTGAAATATGTTGTGAACG
1 AACCACTGGTCATTGTAGATAAACTATCGACTAAAATATGTTGTGAACG
* * * * * *
106954 AACCACTGGTCATTTTAGTTAAATTGTCGACTAAAATATGTTGTGGATG
1 AACCACTGGTCATTGTAGATAAACTATCGACTAAAATATGTTGTGAACG
* * *
107003 AACCACTAGTCATTGCAGAAAAACT
1 AACCACTGGTCATTGTAGATAAACT
107028 GCTAACTAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (49 bp):
AACCACTGGTCATTGTAGATAAACTATCGACTAAAATATGTTGTGAACG
Found at i:107256 original size:34 final size:34
Alignment explanation
Indices: 107125--107268 Score: 109
Period size: 34 Copynumber: 4.3 Consensus size: 34
107115 ATACAACATG
* *
107125 ACATGCTTATAATAGATCAATA-CGATATCAA-TA
1 ACATGCTTATAATAGATCAATATAG-TAGCAATTA
* * * *
107158 ACATCCCTATAGAAAG-TCGATATAGTAGC-ATATA
1 ACATGCTTATA-ATAGATCAATATAGTAGCAAT-TA
* *
107192 TCATGCTTATAATAGATCAATA-AGGGAGCAATTA
1 ACATGCTTATAATAGATCAATATA-GTAGCAATTA
* * *
107226 ACATGCTTATAATAGATTATTATAGTAGCAATAA
1 ACATGCTTATAATAGATCAATATAGTAGCAATTA
*
107260 ACTTGCTTA
1 ACATGCTTA
107269 ACATGTATTT
Statistics
Matches: 85, Mismatches: 18, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
32 1 0.01
33 21 0.25
34 60 0.71
35 3 0.04
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (34 bp):
ACATGCTTATAATAGATCAATATAGTAGCAATTA
Found at i:108883 original size:22 final size:24
Alignment explanation
Indices: 108855--108902 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
108845 AAAAAGGAAT
*
108855 ATTTTATATATAAAT-ATT-AATA
1 ATTTTATATAAAAATAATTAAATA
*
108877 ATTTTATTTAAAAATAATTAAATA
1 ATTTTATATAAAAATAATTAAATA
108901 AT
1 AT
108903 AATTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 3 0.14
24 6 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTTATATAAAAATAATTAAATA
Found at i:111221 original size:16 final size:16
Alignment explanation
Indices: 111200--111230 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
111190 AAAAAAATTG
*
111200 TATGTATATATAAATA
1 TATGTATACATAAATA
111216 TATGTATACATAAAT
1 TATGTATACATAAAT
111231 TATAGAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (16 bp):
TATGTATACATAAATA
Found at i:112203 original size:37 final size:37
Alignment explanation
Indices: 112153--112229 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
112143 AAGGGCTTCT
*
112153 ACGGTCTCGATGCACGGAAGGAGTCACTGACGGCGGC
1 ACGGTCTCGATGCACGGAAGGAGTCACCGACGGCGGC
112190 ACGGTCTCGATGCACGGAAGGAGTCACCGACGGCGGC
1 ACGGTCTCGATGCACGGAAGGAGTCACCGACGGCGGC
112227 ACG
1 ACG
112230 CCGCAATAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.22, C:0.29, G:0.38, T:0.12
Consensus pattern (37 bp):
ACGGTCTCGATGCACGGAAGGAGTCACCGACGGCGGC
Found at i:117677 original size:11 final size:11
Alignment explanation
Indices: 117650--117739 Score: 101
Period size: 11 Copynumber: 8.2 Consensus size: 11
117640 ACTTAAATCC
117650 TTTCTCTCAAA
1 TTTCTCTCAAA
*
117661 -TTCTCTCATA
1 TTTCTCTCAAA
*
117671 TTTCTCTCCAA
1 TTTCTCTCAAA
117682 TATTCTCTCAAA
1 T-TTCTCTCAAA
*
117694 TTCCTCTCAAA
1 TTTCTCTCAAA
*
117705 TTCCTCTCAAA
1 TTTCTCTCAAA
*
117716 TTCCTCTCAAA
1 TTTCTCTCAAA
* *
117727 TTCCTCTTAAA
1 TTTCTCTCAAA
117738 TT
1 TT
117740 ACTTTTAAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
10 9 0.13
11 52 0.73
12 10 0.14
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:119604 original size:18 final size:18
Alignment explanation
Indices: 119568--119610 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
119558 TGCCAGGTGC
* * *
119568 GTATCCTAGCCTTTTTAT
1 GTATCCTAACCCTTATAT
119586 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
119604 GTTTCCT
1 GTATCCT
119611 TTTTTAAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:119885 original size:21 final size:22
Alignment explanation
Indices: 119839--119900 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 22
119829 CCAACACCGA
* *
119839 CAACCAG-ATCCCCTACCAGAG
1 CAACCAGAATCCCCTGCCGGAG
*
119860 GAACCAGAATCCCC-GCCGGAG
1 CAACCAGAATCCCCTGCCGGAG
*
119881 CAACCACAA-CCCCTGCCGGA
1 CAACCAGAATCCCCTGCCGGA
119901 AGCTAGACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.12
21 24 0.71
22 6 0.18
ACGTcount: A:0.31, C:0.44, G:0.19, T:0.06
Consensus pattern (22 bp):
CAACCAGAATCCCCTGCCGGAG
Found at i:120059 original size:34 final size:34
Alignment explanation
Indices: 120018--120120 Score: 144
Period size: 34 Copynumber: 3.1 Consensus size: 34
120008 TTTTGAATAT
120018 TTTTATATTATTTCATGTAATAAAATAGAAATTA
1 TTTTATATTATTTCATGTAATAAAATAGAAATTA
120052 TTTTATATTATTTCATGTAATAAAATAGAAATTTA
1 TTTTATATTATTTCATGTAATAAAATAGAAA-TTA
* *
120087 CTTT-TA-TATTT--T-TAATAAAATAGAAATTC
1 TTTTATATTATTTCATGTAATAAAATAGAAATTA
120116 TTTTA
1 TTTTA
120121 AATAAGGCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
29 5 0.08
30 14 0.22
31 1 0.02
33 5 0.08
34 33 0.52
35 6 0.09
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.50
Consensus pattern (34 bp):
TTTTATATTATTTCATGTAATAAAATAGAAATTA
Found at i:120197 original size:58 final size:58
Alignment explanation
Indices: 120099--120406 Score: 239
Period size: 58 Copynumber: 5.3 Consensus size: 58
120089 TTTATATTTT
* *
120099 TAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTGAATATTTCTATATTATTTCATG
1 TAATAAAATAGAAATTCTTTTAAATAA---AGTATATTGAATATTTCTATATTATTTCATG
* * *
120160 TAATAAAATA-AAAGGTTGTTTTGAATAAAGTA-ATTGAA-ATTTACT-T-TTATATT--TT
1 TAATAAAATAGAAA--TTCTTTTAAATAAAGTATATTGAATATTT-CTATATTAT-TTCATG
* *
120215 TAATAAAATAGAAATTCTTTTAAATAAGGTAATATTTTAAATATTTCTATATTATTTCATG
1 TAATAAAATAGAAATTCTTTTAAATAAAGT-ATA--TTGAATATTTCTATATTATTTCATG
* *
120276 TAATAAAATA-AAAGGTTGTTTTGAATAAAGTA-ATTGAA-ATTTACTAT-TATATTT--T-
1 TAATAAAATAGAAA--TTCTTTTAAATAAAGTATATTGAATATTT-CTATAT-TATTTCATG
* * * *
120331 TAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTAAATATTTCTATATTATTTCATT
1 TAATAAAATAGAAATTCTTTTAAATAA---AGTATATTGAATATTTCTATATTATTTCATG
*
120392 TAATAAAATATAAAT
1 TAATAAAATAGAAAT
120407 AATACAACAT
Statistics
Matches: 199, Mismatches: 20, Indels: 56
0.72 0.07 0.20
Matches are distributed among these distances:
54 24 0.12
55 22 0.11
56 12 0.06
57 15 0.08
58 39 0.20
59 15 0.08
60 12 0.06
61 36 0.18
62 24 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (58 bp):
TAATAAAATAGAAATTCTTTTAAATAAAGTATATTGAATATTTCTATATTATTTCATG
Found at i:120200 original size:116 final size:116
Alignment explanation
Indices: 120079--120401 Score: 610
Period size: 116 Copynumber: 2.8 Consensus size: 116
120069 TAATAAAATA
*
120079 GAAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTGAATATT
1 GAAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTAAATATT
120144 TCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGTAATT
66 TCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGTAATT
*
120195 GAAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGTAATATTTTAAATATT
1 GAAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTAAATATT
120260 TCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGTAATT
66 TCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGTAATT
*
120311 GAAATTTACTATTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTAAATATT
1 GAAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTAAATATT
*
120376 TCTATATTATTTCATTTAATAAAATA
66 TCTATATTATTTCATGTAATAAAATA
120402 TAAATAATAC
Statistics
Matches: 202, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 202 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (116 bp):
GAAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTAAATATT
TCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGTAATT
Found at i:120224 original size:55 final size:55
Alignment explanation
Indices: 120160--120340 Score: 197
Period size: 55 Copynumber: 3.2 Consensus size: 55
120150 TTATTTCATG
120160 TAATAAAATAAAAGGTTGTTTTGAATAAAGTAATTGAAATTTACTTTTATATTTT
1 TAATAAAATAAAAGGTTGTTTTGAATAAAGTAATTGAAATTTACTTTTATATTTT
* * * * * *
120215 TAATAAAATAGAAA--TTCTTTTAAATAAGGTAATATTTTAAATATTTCTATATTAT-TTCATG
1 TAATAAAATA-AAAGGTTGTTTTGAATAAAGT-A-A-TTGAAAT-TTACT-T-TTATATT--TT
*
120276 TAATAAAATAAAAGGTTGTTTTGAATAAAGTAATTGAAATTTACTATTATATTTT
1 TAATAAAATAAAAGGTTGTTTTGAATAAAGTAATTGAAATTTACTTTTATATTTT
120331 TAATAAAATA
1 TAATAAAATA
120341 GAAATTCTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
54 13 0.13
55 22 0.22
56 8 0.08
57 8 0.08
58 8 0.08
59 9 0.09
60 8 0.08
61 12 0.12
62 13 0.13
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (55 bp):
TAATAAAATAAAAGGTTGTTTTGAATAAAGTAATTGAAATTTACTTTTATATTTT
Found at i:123664 original size:127 final size:127
Alignment explanation
Indices: 123359--123781 Score: 597
Period size: 126 Copynumber: 3.4 Consensus size: 127
123349 TAGGCCAAAT
* * * * *
123359 AAGAACTACTGTAGTAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGGA
1 AAGAACTACTGTAGCAAAAAAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACAATGCA
* * * *
123424 TCCTGCTTAAAGCATTTTTCATATTATTTGCTCAGAAACGTTTTCTCAAAATTA-TTTTTTC
66 TCCTGCTTAAAGCGTTTTTCACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTTC
* *
123485 AGGAACTACTGTAGCAAAAGAA-CGTCCACATGGGAGCTTCTTTTAGTACTTTTGCTGACAATGC
1 AAGAACTACTGTAGCAAAA-AAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACAATGC
* * *
123549 ATCCTGCTTAAAGCGTTTTTTACACTATTTTCTTAGAAACGTCTTCTCAAAATTATTTTTTTC
65 ATCCTGCTTAAAGCGTTTTTCACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTTC
* *
123612 AAGAACTACTGTAGCAAAAAAGCATCCACGTGGGAGTTTCTTTTAGTACTTTTGCTGACAATGCA
1 AAGAACTACTGTAGCAAAAAAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACAATGCA
* *
123677 TTCTGCTTAAAGCGTTTTTGC-CACTATTTGCTCAAAAACGTCTTCTCAAAATTATTTTTTT-
66 TCCTGCTTAAAGCGTTTTT-CACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTTC
* *
123738 AGGAACTACTGTAG-AAAAATATCGTCCACGTGGGAGCTT-TTTTA
1 AAGAACTACTGTAGCAAAAA-AGCGTCCACGTGGGAGCTTCTTTTA
123782 AATTAACAAA
Statistics
Matches: 265, Mismatches: 27, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
125 10 0.04
126 134 0.51
127 121 0.46
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (127 bp):
AAGAACTACTGTAGCAAAAAAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACAATGCA
TCCTGCTTAAAGCGTTTTTCACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTTC
Found at i:123908 original size:102 final size:99
Alignment explanation
Indices: 123775--124152 Score: 301
Period size: 102 Copynumber: 3.9 Consensus size: 99
123765 ACGTGGGAGC
* * * *
123775 TTTTTT-AAATTAACAAATAATTTAATTAAGTAACCCTAAACCCCAAACCTTAATTTATTTGAGT
1 TTTTTTAAAATTTATAATTAATTTAATCAAGTAACCCTAAA-CCCAAACCTTAATTTATTTGA-T
* *
123839 TTTTCCTTAAATACCT-TACACTAAAGCCTAATCTAAT
64 TTTTCCTTAAAAACCTAAACACTAAA-CCT-ATCTAAT
* *
123876 TTTTTTTAAATTTATAATTGATTTAATCAAGTAACCCTAAA--C---CC-TAATTTATTTGATTT
1 TTTTTTAAAATTTATAATTAATTTAATCAAGTAACCCTAAACCCAAACCTTAATTTATTTGATTT
* * *
123935 TTTCGTAAAAACCCTCAACACTAAA-C--TCTAAT
66 TTCCTTAAAAA-CCTAAACACTAAACCTATCTAAT
* * * *
123967 TTTTTAAAAATTTATAATTAATTTAATC-AG---CCCTAAACCTAAACCCTAATTTATTTTATTT
1 TTTTTTAAAATTTATAATTAATTTAATCAAGTAACCCTAAACCCAAACCTTAATTTATTTGA-TT
*
124028 TTTCCTTAAAAACCATAAACACGAAACCCTAGTCTAA-
65 TTTCCTTAAAAACC-TAAACACTAAA-CCTA-TCTAAT
* * * * *
124065 -TTTTGAAAATTCTATAATTAATTTAATTAAGAAACCCTAAACCCCAATCCCTT-ATTTATTTAA
1 TTTTTTAAAATT-TATAATTAATTTAATCAAGTAACCCTAAA-CCCAA-ACCTTAATTTATTTGA
* *
124128 TTTTT--TTAAAACCCTAAACCCTAAA
63 TTTTTCCTTAAAAACCTAAACACTAAA
124153 TCCAAAAACC
Statistics
Matches: 227, Mismatches: 27, Indels: 48
0.75 0.09 0.16
Matches are distributed among these distances:
87 7 0.03
90 2 0.01
91 31 0.14
92 2 0.01
93 13 0.06
94 33 0.15
95 15 0.07
96 11 0.05
97 10 0.04
98 15 0.07
99 17 0.07
100 8 0.04
101 6 0.03
102 41 0.18
103 13 0.06
104 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (99 bp):
TTTTTTAAAATTTATAATTAATTTAATCAAGTAACCCTAAACCCAAACCTTAATTTATTTGATTT
TTCCTTAAAAACCTAAACACTAAACCTATCTAAT
Found at i:124086 original size:93 final size:93
Alignment explanation
Indices: 123871--124091 Score: 259
Period size: 91 Copynumber: 2.3 Consensus size: 93
123861 AAAGCCTAAT
** * *
123871 CTAATTTTTTTTAAATTTATAATTGATTTAATCAAG---TAACCCTAAACCCTAATTTATTTGAT
1 CTAATTTTTTAAAAATTTATAATTAATTTAATC-AGCCCTAAACCTAAACCCTAATTTATTTGAT
* * * *
123933 TTTTTCGTAAAAACCCTCAACACTAAACT
65 TTTTTCGTAAAAACCATAAACACGAAACC
*
123962 CTAATTTTTTAAAAATTTATAATTAATTTAATCAGCCCTAAACCTAAACCCTAATTTATTTTATT
1 CTAATTTTTTAAAAATTTATAATTAATTTAATCAGCCCTAAACCTAAACCCTAATTTATTTGATT
*
124027 TTTTCCTTAAAAACCATAAACACGAAACC
66 TTTT-CGTAAAAACCATAAACACGAAACC
* *
124056 CTAGTCTAATTTTGAAAATTCTATAATTAATTTAAT
1 CTAAT-T--TTTTAAAAATT-TATAATTAATTTAAT
124092 TAAGAAACCC
Statistics
Matches: 110, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
90 2 0.02
91 30 0.27
93 29 0.26
94 23 0.21
95 1 0.01
97 10 0.09
98 15 0.14
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41
Consensus pattern (93 bp):
CTAATTTTTTAAAAATTTATAATTAATTTAATCAGCCCTAAACCTAAACCCTAATTTATTTGATT
TTTTCGTAAAAACCATAAACACGAAACC
Found at i:124148 original size:7 final size:7
Alignment explanation
Indices: 124136--124201 Score: 71
Period size: 7 Copynumber: 9.3 Consensus size: 7
124126 AATTTTTTTA
124136 AAACCCT
1 AAACCCT
124143 AAACCCT
1 AAACCCT
**
124150 AAATCCAA
1 AAA-CCCT
*
124158 AAACCCCC
1 AAA-CCCT
124166 AAACCCT
1 AAACCCT
*
124173 -AACCTT
1 AAACCCT
124179 AAACCCT
1 AAACCCT
124186 AAACCCT
1 AAACCCT
124193 AAACCCT
1 AAACCCT
124200 AA
1 AA
124202 CCCGCAGAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
6 5 0.10
7 34 0.69
8 10 0.20
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:124184 original size:13 final size:13
Alignment explanation
Indices: 124166--124204 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
124156 AAAAACCCCC
*
124166 AAACCCTAACCTT
1 AAACCCTAACCCT
124179 AAACCCTAAACCCT
1 AAACCCT-AACCCT
124193 AAACCCTAACCC
1 AAACCCTAACCC
124205 GCAGAGACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (13 bp):
AAACCCTAACCCT
Found at i:127630 original size:17 final size:17
Alignment explanation
Indices: 127604--127651 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
127594 AAATAAACAC
127604 AAAAA-AAAAAGTATTTT
1 AAAAATAAAAA-TATTTT
127621 AAAAATAAAAAATATTTT
1 AAAAAT-AAAAATATTTT
127639 AAAAATAAAAATA
1 AAAAATAAAAATA
127652 AATATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.41
18 12 0.41
19 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAAATAAAAATATTTT
Found at i:127630 original size:18 final size:18
Alignment explanation
Indices: 127604--127649 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
127594 AAATAAACAC
*
127604 AAAAA-AAAAAGTATTTT
1 AAAAATAAAAAATATTTT
127621 AAAAATAAAAAATATTTT
1 AAAAATAAAAAATATTTT
127639 AAAAATAAAAA
1 AAAAATAAAAA
127650 TAAATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAATAAAAAATATTTT
Found at i:127892 original size:18 final size:20
Alignment explanation
Indices: 127863--127909 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
127853 CCTATAATAA
* *
127863 AATATATTTTTAT-TATTTT
1 AATATTTTTTTATAAATTTT
127882 AAT-TTTTTTTATAAATTTT
1 AATATTTTTTTATAAATTTT
127901 AATATTTTT
1 AATATTTTT
127910 ATTTTTCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.33
19 11 0.46
20 5 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
AATATTTTTTTATAAATTTT
Found at i:131011 original size:13 final size:13
Alignment explanation
Indices: 130993--131027 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
130983 TCGACTAAAC
* *
130993 TTTTCATAAGTAT
1 TTTTCAAAAGCAT
131006 TTTTCAAAAGCAT
1 TTTTCAAAAGCAT
131019 TTTTCAAAA
1 TTTTCAAAA
131028 ACAATGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:131630 original size:21 final size:20
Alignment explanation
Indices: 131606--131667 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
131596 GAGTTTAGGG
131606 GTTTTTTTTTATATTTTTTAA
1 GTTTTTTTTTATATTTTTT-A
* **
131627 GTTTTTTTATATATCCTTTA
1 GTTTTTTTTTATATTTTTTA
131647 GTTTTTTTTTTATAATTTTTT
1 G-TTTTTTTTTAT-ATTTTTT
131668 TTAGATGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.06
21 26 0.79
22 5 0.15
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (20 bp):
GTTTTTTTTTATATTTTTTA
Found at i:132217 original size:16 final size:17
Alignment explanation
Indices: 132196--132262 Score: 70
Period size: 16 Copynumber: 4.1 Consensus size: 17
132186 AAGCAAGAAT
132196 AAAAAAG-AAAGAAAGA
1 AAAAAAGAAAAGAAAGA
* *
132212 AAAAAA-ACAAGCAAG-
1 AAAAAAGAAAAGAAAGA
*
132227 AAAAAAGCAAAG-AAGA
1 AAAAAAGAAAAGAAAGA
132243 AAAAAAGAAAAGAAGAGA
1 AAAAAAGAAAAGAA-AGA
132261 AA
1 AA
132263 GGGAGGAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 9 0.22
16 26 0.63
17 1 0.02
18 5 0.12
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAGAAAGA
Found at i:132399 original size:28 final size:27
Alignment explanation
Indices: 132368--132455 Score: 96
Period size: 24 Copynumber: 3.4 Consensus size: 27
132358 AGAAGAGAAA
* *
132368 AAAGAAAAAAGAAGAAGAAGAAAGAAAG
1 AAAGAAAAAAAAAGAAGAAGAAA-ACAG
* *
132396 AAAGAAGAAGAAAGAAG-AGAAAA-A-
1 AAAGAAAAAAAAAGAAGAAGAAAACAG
132420 AAAGAAAAAAAAAG-AGAA-AAAACAG
1 AAAGAAAAAAAAAGAAGAAGAAAACAG
132445 AAAGAAAAAAA
1 AAAGAAAAAAA
132456 TTTTTAAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
23 6 0.12
24 14 0.27
25 12 0.23
26 1 0.02
27 5 0.10
28 14 0.27
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.00
Consensus pattern (27 bp):
AAAGAAAAAAAAAGAAGAAGAAAACAG
Found at i:132428 original size:10 final size:10
Alignment explanation
Indices: 132365--132454 Score: 81
Period size: 10 Copynumber: 8.6 Consensus size: 10
132355 AGGAGAAGAG
132365 AAAAAAGAAA
1 AAAAAAGAAA
* *
132375 AAAGAAGAAG
1 AAAAAAGAAA
*
132385 AAGAAAGAAA
1 AAAAAAGAAA
* *
132395 GAAAGAAGAAG
1 -AAAAAAGAAA
*
132406 AAAGAAGAGAA
1 AAAAAAGA-AA
132417 AAAAAAGAAA
1 AAAAAAGAAA
132427 AAAAAAGAGAA
1 AAAAAAGA-AA
*
132438 AAAACAGAAA
1 AAAAAAGAAA
132448 GAAAAAA
1 -AAAAAA
132455 ATTTTTAAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
10 35 0.55
11 29 0.45
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:132435 original size:21 final size:20
Alignment explanation
Indices: 132365--132454 Score: 81
Period size: 21 Copynumber: 4.3 Consensus size: 20
132355 AGGAGAAGAG
* *
132365 AAAAAAGAAAAAAGAAGAAG
1 AAAAAAGAAAAAAAAAGAAA
* * *
132385 AAGAAAGAAAGAAAGAAGAAG
1 AAAAAAGAAA-AAAAAAGAAA
*
132406 AAAGAAGAGAAAAAAAAGAAA
1 AAAAAAGA-AAAAAAAAGAAA
*
132427 AAAAAAGAGAAAAAACAGAAA
1 AAAAAAGA-AAAAAAAAGAAA
132448 GAAAAAA
1 -AAAAAA
132455 ATTTTTAAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
20 9 0.15
21 43 0.72
22 8 0.13
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAAGAAA
Found at i:132794 original size:15 final size:15
Alignment explanation
Indices: 132769--132807 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
132759 CAGCCCAACC
132769 AGAAA-AAAAAAAGA
1 AGAAAGAAAAAAAGA
132783 AGAAAGAAAAAAAGA
1 AGAAAGAAAAAAAGA
*
132798 A-AAGGAAAAA
1 AGAAAGAAAAA
132808 GAAAAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AGAAAGAAAAAAAGA
Found at i:132797 original size:12 final size:11
Alignment explanation
Indices: 132773--132816 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
132763 CCAACCAGAA
132773 AAAAAAAAGAAG
1 AAAAAAAA-AAG
132785 AAAGAAAAAAAG
1 AAA-AAAAAAAG
*
132797 AAAAGGAAAAAG
1 AAAA-AAAAAAG
132809 AAAAAAAA
1 AAAAAAAA
132817 GAGGAGCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 4 0.14
12 19 0.68
13 5 0.18
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:132818 original size:21 final size:20
Alignment explanation
Indices: 132771--132815 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
132761 GCCCAACCAG
132771 AAAAAA-AAAAGAAGAAAGA
1 AAAAAAGAAAAGAAGAAAGA
132790 AAAAAAGAAAAGGAA-AAAGA
1 AAAAAAGAAAA-GAAGAAAGA
132810 AAAAAA
1 AAAAAA
132816 AGAGGAGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.25
20 15 0.62
21 3 0.12
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAGAAGAAAGA
Found at i:133368 original size:37 final size:36
Alignment explanation
Indices: 133300--133375 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
133290 CGACCTTAAG
* *
133300 AAAAAATTTTGTGTTTTCAACAATTCGTG-TTTCAA
1 AAAAAAATTTGTGTTTTCAACAATTCATGTTTTCAA
133335 AAAAAAATTTGTGTTTTC-ACAAATTTTCATGTTTTCAA
1 AAAAAAATTTGTGTTTTCAAC-AA--TTCATGTTTTCAA
133373 AAA
1 AAA
133376 TTTTTCATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 2 0.06
35 19 0.54
37 5 0.14
38 9 0.26
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (36 bp):
AAAAAAATTTGTGTTTTCAACAATTCATGTTTTCAA
Found at i:133382 original size:19 final size:18
Alignment explanation
Indices: 133346--133411 Score: 89
Period size: 18 Copynumber: 3.7 Consensus size: 18
133336 AAAAAATTTG
*
133346 TGTTTTCACAAATTTTCA
1 TGTTTTCAAAAATTTTCA
133364 TGTTTTCAAAAATTTTTCA
1 TGTTTTCAAAAA-TTTTCA
* *
133383 TG-TTTCAAAAATCTTCG
1 TGTTTTCAAAAATTTTCA
133400 TGTTTTCAAAAA
1 TGTTTTCAAAAA
133412 AAAAATTATG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 6 0.14
18 29 0.67
19 8 0.19
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.47
Consensus pattern (18 bp):
TGTTTTCAAAAATTTTCA
Found at i:133452 original size:21 final size:21
Alignment explanation
Indices: 133389--133465 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
133379 TTCATGTTTC
* **
133389 AAAAATCTTCGTGTTTTCAAA
1 AAAAATATTCGTGTTTTTTAA
* * * *
133410 AAAAAAATT-ATG-TGTTTCA
1 AAAAATATTCGTGTTTTTTAA
133429 AAAAATATTCGTGTTTTTTAA
1 AAAAATATTCGTGTTTTTTAA
133450 AAAAAT-TCTCGTGTTT
1 AAAAATAT-TCGTGTTT
133466 CGTAATTTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 11 0.26
20 5 0.12
21 26 0.62
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (21 bp):
AAAAATATTCGTGTTTTTTAA
Found at i:133466 original size:39 final size:38
Alignment explanation
Indices: 133300--133454 Score: 99
Period size: 36 Copynumber: 4.1 Consensus size: 38
133290 CGACCTTAAG
* * *
133300 AAAAAATTTTGTGTTTTC-AACA-ATTCGTG-TTTCAAA
1 AAAAAATTATGTG-TTTCAAAAATATTCGTGTTTTAAAA
* * * *
133336 AAAAAATT-TGTGTTTTCACAAATTTTCATGTTTT---C
1 AAAAAATTATGTG-TTTCAAAAATATTCGTGTTTTAAAA
* * * *
133371 AAAAATTTTTCATGTTTCAAAAATCTTCGTGTTTTCAAAA
1 AAAAAATTAT-GTGTTTCAAAAATATTCGTGTTTT-AAAA
**
133411 AAAAAATTATGTGTTTCAAAAAATATTCGTGTTTTTTAA
1 AAAAAATTATGTGTTTC-AAAAATATTCGTGTTTTAAAA
133450 AAAAA
1 AAAAA
133455 TTCTCGTGTT
Statistics
Matches: 92, Mismatches: 17, Indels: 17
0.73 0.13 0.13
Matches are distributed among these distances:
35 16 0.17
36 29 0.32
37 7 0.08
38 3 0.03
39 13 0.14
40 24 0.26
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.43
Consensus pattern (38 bp):
AAAAAATTATGTGTTTCAAAAATATTCGTGTTTTAAAA
Found at i:136622 original size:20 final size:18
Alignment explanation
Indices: 136594--136647 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
136584 GTTTAGGGGG
136594 TTTTTTATATTTTTTAAGT
1 TTTTTTATATTTTTT-AGT
**
136613 TTTTTATATATCCTTTAGT
1 TTTTT-TATATTTTTTAGT
136632 TTTTTTATAATTTTTT
1 TTTTTTAT-ATTTTTT
136648 TAGATGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.10
19 18 0.62
20 8 0.28
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (18 bp):
TTTTTTATATTTTTTAGT
Found at i:136649 original size:20 final size:18
Alignment explanation
Indices: 136593--136650 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
136583 AGTTTAGGGG
*
136593 GTTTTTTATATTTTTTAA
1 GTTTTTTATATTTTTTTA
**
136611 GTTTTTTATATATCCTTTA
1 GTTTTTTATAT-TTTTTTA
136630 GTTTTTTTATAATTTTTTTA
1 G-TTTTTTAT-ATTTTTTTA
136650 G
1 G
136651 ATGTAAAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 11 0.34
19 5 0.16
20 14 0.44
21 2 0.06
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (18 bp):
GTTTTTTATATTTTTTTA
Done.