Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 62
Found at i:3726433 original size:105 final size:104
Alignment explanation
Indices: 3726251--3726570 Score: 480
Period size: 105 Copynumber: 3.2 Consensus size: 104
3726241 ACAAGCAGCG
*
3726251 GTCGTGGAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1 GTCGTGAAGTTGAACTTGC-TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
3726316 TGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTC
65 TGAGATTGGGAAGTTGTTGTTGACAAGCAACGGTCCCTTC
3726356 GTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1 GTCGTGAAGTTGAACTTGC-TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
3726421 TGAGATTGGGAAGTTGTTGTTGACAAGCAACGGCCCCTTC
65 TGAGATTGGGAAGTTGTTGTTGACAAGCAACGGTCCCTTC
3726461 GTCGTGAAGTTGAA----CTTG-C---A--CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 GTCGTGAAGTTGAACTTGCTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
* * *
3726516 GAAATTGAGAAGTTGTTGTTGACAAGCAATGGTCCCTTC
66 GAGATTGGGAAGTTGTTGTTGACAAGCAACGGTCCCTTC
* *
3726555 GTCATGGAGTTGAACT
1 GTCGTGAAGTTGAACT
3726571 CGCGGATGTT
Statistics
Matches: 203, Mismatches: 10, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
94 82 0.40
96 1 0.00
99 1 0.00
100 3 0.01
101 1 0.00
105 115 0.57
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (104 bp):
GTCGTGAAGTTGAACTTGCTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
GAGATTGGGAAGTTGTTGTTGACAAGCAACGGTCCCTTC
Found at i:3726552 original size:199 final size:194
Alignment explanation
Indices: 3726086--3726570 Score: 566
Period size: 199 Copynumber: 2.5 Consensus size: 194
3726076 TTTCGAGTCT
* * * ** * * *
3726086 AATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAACCAGCC
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAGCAGCG
* **
3726151 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAA
65 GTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAA
* *
3726216 ATTGACTCTGAATGAAATTTTGTTGACAAGCAGCGGTCGTGGAGTTGAACTTGCGTTGTCTGGAG
130 ATTGACTCTGAATGAAATTTTGTTGACAAGCAACGGCCGTGGAGTTGAACTTGCGTTGTC--GAG
3726281 TCC
193 -CC
*
3726284 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGCAGCGG
* *
3726349 TCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
66 TCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
* * * ** *
3726414 TTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAACGGCCCCT-TCGTCGTGAAGTTGAAC-T
131 TTGACTCTGA-A-T--GAAATT-TTGTTGACAAGCAACGG-CCGTGGAGT--TGAACTTG--CGT
3726477 TG-C-A-CC
186 TGTCGAGCC
* **
3726483 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAATGG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGCAGCGG
* *
3726548 TCCCTTCGTCATGGAGTTGAACT
66 TCCCTTCGTCGTGAAGTTGAACT
3726571 CGCGGATGTT
Statistics
Matches: 249, Mismatches: 28, Indels: 19
0.84 0.09 0.06
Matches are distributed among these distances:
197 84 0.34
198 42 0.17
199 85 0.34
201 6 0.02
202 18 0.07
203 2 0.01
204 8 0.03
205 3 0.01
206 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (194 bp):
AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
TTGACTCTGAATGAAATTTTGTTGACAAGCAACGGCCGTGGAGTTGAACTTGCGTTGTCGAGCC
Found at i:3726786 original size:36 final size:36
Alignment explanation
Indices: 3726739--3726814 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
3726729 TGTTTGGAGA
* * *
3726739 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
3726775 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
3726811 GAAA
1 GAAA
3726815 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:3726935 original size:106 final size:104
Alignment explanation
Indices: 3726714--3727033 Score: 477
Period size: 106 Copynumber: 3.1 Consensus size: 104
3726704 TTCGTTAAAT
* ** * *
3726714 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTCGTTTCAAGGGA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTGTTTCGAGGGA
* *
3726777 AACTATCTCA-AGCGAGATAAAATTCATTTCAAGGGAAA
66 AACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
*
3726815 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGATACAAAATTTTTTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTTTGTTTCGAGGG
*
3726880 AAACTATCTCAAGAGAGAGAAAAAAATCATTTCAAGGGAAA
65 AAACTATCTC-AGAGAGAGAAAAAATTCATTTCAAGGGAAA
* *
3726921 TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTTAAGGGAGACAAAAATTTTTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATTTTTGTTTCGAGGG
*
3726986 AAACTATCTCAG-GAGAGAAAAAATTAATTTCAAGGGAAA
65 AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
3727025 TGTTTTCAA
1 TGTTTTCAA
3727034 GAGAAACTGT
Statistics
Matches: 199, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
101 45 0.23
104 55 0.28
105 3 0.02
106 92 0.46
107 4 0.02
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTGTTTCGAGGGA
AACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:3726990 original size:39 final size:38
Alignment explanation
Indices: 3726936--3727010 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 38
3726926 TCAATGTTTA
3726936 TGTTTCAAGAGAAACTATCTTAAGG-GAGACAAAAATTTT
1 TGTTTCAAGAGAAACTATC-TAAGGAGAGA-AAAAATTTT
* * *
3726975 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTAAGGAGAGAAAAAATT
3727011 AATTTCAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 11 0.34
39 21 0.66
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (38 bp):
TGTTTCAAGAGAAACTATCTAAGGAGAGAAAAAATTTT
Found at i:3727252 original size:72 final size:74
Alignment explanation
Indices: 3727104--3727279 Score: 198
Period size: 72 Copynumber: 2.4 Consensus size: 74
3727094 TAAAATCTTC
* ** * * ** *
3727104 TTAAAAAAAACAGCCTTTAGTGAAATAAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAATCACAAGCGAGA
3727169 CAAATCTTGTT
64 CAAATCTTGTT
*
3727180 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAATCACAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAATCACAAGCGAGACA
3727243 AAT-TATGTT
66 AATCT-TGTT
*
3727252 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
3727280 TCATCTGCAT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
71 1 0.01
72 47 0.53
73 14 0.16
75 4 0.05
76 22 0.25
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAATCACAAGCGAGACA
AATCTTGTT
Found at i:3727274 original size:36 final size:36
Alignment explanation
Indices: 3727165--3727276 Score: 120
Period size: 36 Copynumber: 3.1 Consensus size: 36
3727155 GGTCTCAAGC
3727165 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
1 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* * * ** ***
3727201 GAAATAAATCTTCTTTCGAGAAAAACAATCACAAGT
1 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
3727237 GAGACAAAT-TATGTTTTAAGAAAAACAAAT-TTGAGT
1 GAGACAAATCT-TGTTTTAAGAAAAAC-AATCTTGAGT
3727273 GAGA
1 GAGA
3727277 TAATCATCTG
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
35 1 0.02
36 54 0.93
37 3 0.05
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.28
Consensus pattern (36 bp):
GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
Found at i:3728641 original size:183 final size:183
Alignment explanation
Indices: 3728331--3729050 Score: 1298
Period size: 183 Copynumber: 3.9 Consensus size: 183
3728321 ATCAGGTTTA
* *
3728331 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCAAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
3728396 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
3728460 TTCCTCTATAACCAATTGACTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
3728514 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
3728579 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGTTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
* *
3728644 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAAGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
3728697 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
3728762 GCCAAGTGTCCGAGCAGTGTCATAGTTTAAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
3728827 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
3728880 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
3728945 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
3729010 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
3729051 CGGATTTAAT
Statistics
Matches: 515, Mismatches: 21, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
183 514 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:3733372 original size:26 final size:25
Alignment explanation
Indices: 3733290--3733414 Score: 72
Period size: 27 Copynumber: 4.6 Consensus size: 25
3733280 AAAAGAAAAG
3733290 AAAACAAATTAAGTAAAATGATAAAATAAA
1 AAAACAAA-TAA-TAAAAT-AT--AATAAA
* *
3733320 GAAAGCAAA-GATAAAATAGTAAGTAAA
1 -AAAACAAATAATAAAATA-TAA-TAAA
3733347 AAAACAAATAATAAAATATATATAAA
1 AAAACAAATAATAAAATATA-ATAAA
* * * *
3733373 AAAGAAAAAGAAAATAAATAAAATAAA
1 AAA-ACAAATAATA-AAATATAATAAA
*
3733400 TAAACAAAATAATAA
1 AAAAC-AAATAATAA
3733415 TAACAAAGTA
Statistics
Matches: 75, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
26 20 0.27
27 34 0.45
28 13 0.17
29 1 0.01
31 7 0.09
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.18
Consensus pattern (25 bp):
AAAACAAATAATAAAATATAATAAA
Found at i:3733386 original size:24 final size:23
Alignment explanation
Indices: 3733345--3733395 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
3733335 ATAGTAAGTA
*
3733345 AAAAAACAAATAATAAAATATATAT
1 AAAAAACAAATAAGAAAATA-A-AT
*
3733370 AAAAAAGAAA-AAGAAAATAAAT
1 AAAAAACAAATAAGAAAATAAAT
3733392 AAAA
1 AAAA
3733396 TAAATAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.25
23 1 0.04
24 8 0.33
25 9 0.38
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAAAACAAATAAGAAAATAAAT
Found at i:3733601 original size:16 final size:16
Alignment explanation
Indices: 3733582--3733615 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3733572 AATATTAAAG
*
3733582 AAATATAATAATAATA
1 AAATATAATAAAAATA
*
3733598 AAATATAGTAAAAATA
1 AAATATAATAAAAATA
3733614 AA
1 AA
3733616 TGAAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATATAATAAAAATA
Found at i:3734088 original size:37 final size:37
Alignment explanation
Indices: 3734038--3734142 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
3734028 GTGCTTGTGG
* * * *
3734038 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
3734075 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
3734112 ATCCTATTTTTAAGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
3734143 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:3734383 original size:99 final size:98
Alignment explanation
Indices: 3734212--3734409 Score: 369
Period size: 99 Copynumber: 2.0 Consensus size: 98
3734202 GAAAGAAGAA
*
3734212 ATTAAAGATCTTCATATTGAACTGATTCTTTTGTGAAAGAAGATTGAAATGTTGATGAAGTGTAA
1 ATTAAAAATCTTCATATTGAACTGATTCTTTTGTGAAAGAAGATTGAAATGTTGATGAAGTGTAA
3734277 TATTGTATTTATAGTGTTAGTCGTTATATTTAT
66 TATTGTATTTATAGTGTTAGTCGTTATATTTAT
*
3734310 ATTAAAAATCTTCATATTGAACTGATTCTTTTGTGAAAAGATGATTGAAATGTTGATGAAGTGTA
1 ATTAAAAATCTTCATATTGAACTGATTCTTTTGTG-AAAGAAGATTGAAATGTTGATGAAGTGTA
3734375 ATATTGTATTTATAGTGTTAGTCGTTATATTTAT
65 ATATTGTATTTATAGTGTTAGTCGTTATATTTAT
3734409 A
1 A
3734410 AATCAAAGGT
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
98 34 0.35
99 63 0.65
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (98 bp):
ATTAAAAATCTTCATATTGAACTGATTCTTTTGTGAAAGAAGATTGAAATGTTGATGAAGTGTAA
TATTGTATTTATAGTGTTAGTCGTTATATTTAT
Found at i:3734474 original size:22 final size:22
Alignment explanation
Indices: 3734449--3734532 Score: 150
Period size: 22 Copynumber: 3.8 Consensus size: 22
3734439 GTCTTTAAAT
3734449 TACCCAGTATTAGGGTTTTCTA
1 TACCCAGTATTAGGGTTTTCTA
3734471 TACCCAGTATTAGGGTTTTCTA
1 TACCCAGTATTAGGGTTTTCTA
* *
3734493 TACCCAGTATTAGGGTTTTTTG
1 TACCCAGTATTAGGGTTTTCTA
3734515 TACCCAGTATTAGGGTTT
1 TACCCAGTATTAGGGTTT
3734533 GTTGGTCGTC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (22 bp):
TACCCAGTATTAGGGTTTTCTA
Found at i:3740828 original size:21 final size:21
Alignment explanation
Indices: 3740794--3740870 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 21
3740784 AAATAGTAAG
3740794 TAAA-AAAACCAAAT-AATAAAA
1 TAAATAAAA-CAAATAAAT-AAA
*
3740815 TATATATAAA-AAATAAATAAA
1 TAAATA-AAACAAATAAATAAA
*
3740836 TAAATAAAACAAATAAACAAA
1 TAAATAAAACAAATAAATAAA
3740857 -ATAATAATAACAAA
1 TA-AATAA-AACAAA
3740871 GTATGAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
20 4 0.09
21 30 0.64
22 10 0.21
23 3 0.06
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAATAAAACAAATAAATAAA
Found at i:3740884 original size:2 final size:2
Alignment explanation
Indices: 3740877--3740901 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3740867 CAAAGTATGA
3740877 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 A
3740902 ATAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3741137 original size:18 final size:17
Alignment explanation
Indices: 3741114--3741156 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3741104 ATATATACAT
3741114 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
3741132 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
3741149 ATAA-AATA
1 ATAATAATA
3741157 TCTATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:3741563 original size:37 final size:37
Alignment explanation
Indices: 3741513--3741616 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
3741503 GTGCTTGTGG
* * * * *
3741513 ATCCTATCTTTAGGAATTTAAATCTTAGTATAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* * *
3741550 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
3741587 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
3741617 GAGCGAAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:3742512 original size:105 final size:105
Alignment explanation
Indices: 3742330--3742781 Score: 742
Period size: 105 Copynumber: 4.3 Consensus size: 105
3742320 ACAAGCAGCG
* *
3742330 GTCGTGGAGTTGAACTTGCGTTGTCTGGAGTACAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * * *
3742395 TGAGATTGGGAAGTTGTTGTTGACAAGCAGCAGTCCATTC
66 TGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTC
3742435 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
3742500 TGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTC
66 TGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTC
*
3742540 GTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
3742605 TGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTC
66 TGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTC
**
3742645 GTCGTGAAGTTGAACTTGTATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
3742710 TGAAATTAAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTC
66 TGAAATTGAGAAGTTG-TTGTTGACAAGCAGCGGTCCCTTC
* * *
3742751 GTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
1 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
3742782 GTCACGATAT
Statistics
Matches: 330, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
105 280 0.85
106 50 0.15
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (105 bp):
GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
TGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTC
Found at i:3742699 original size:210 final size:206
Alignment explanation
Indices: 3742160--3742776 Score: 865
Period size: 210 Copynumber: 3.0 Consensus size: 206
3742150 CATTGTTCCG
* * * * * * *
3742160 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGGAACTGGGAAATTGTTCGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTT-GTTGACAAG
* * * *
3742225 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
65 CAGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* *
3742290 TTGAAATTGACTCTGAA-TGAAATT-TTGTTGACAAGCAGCGG-----TCGTG-G-AGTTGAACT
130 TTGAAATTGGCTCTGAATTGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTGTGAAGTTGAACT
*
3742346 TGCGTTGTCTGG
195 TGCGTTGTCTGA
* *
3742358 AGTACAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
* *
3742423 AGCAGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
3742488 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-ATT--GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGT-GTGAAGTTGA
3742553 ACTTGCGTTGTCTGA
192 ACTTGCGTTGTCTGA
*
3742568 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
* *
3742633 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
3742698 TGAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
131 TGAAATTGGCTCTG-AATT--GAAGTTG-TTGTTGACAAGCAGCGGTCCCTTCG-TGTGAAGTTG
*
3742763 AACTTGTGTTGTCT
191 AACTTGCGTTGTCT
3742777 CGAGTGTCAC
Statistics
Matches: 373, Mismatches: 30, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
197 82 0.22
198 48 0.13
199 1 0.00
201 5 0.01
202 17 0.05
207 4 0.01
208 1 0.00
209 1 0.00
210 167 0.45
211 46 0.12
212 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (206 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
AGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATTGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTGTGAAGTTGAACTT
GCGTTGTCTGA
Found at i:3743028 original size:36 final size:36
Alignment explanation
Indices: 3742981--3743056 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
3742971 TGTTTGGAGA
* * *
3742981 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
* *
3743017 GAAACTATCTCAAGCGAGATAAAATTCATTTCAGGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
3743053 GAAA
1 GAAA
3743057 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:3743166 original size:104 final size:104
Alignment explanation
Indices: 3742958--3743273 Score: 460
Period size: 104 Copynumber: 3.1 Consensus size: 104
3742948 CGTTAAATTA
* ** * *
3742958 TTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA---TTCGTTTCAAGGGAA
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAA
* * *
3743020 ACTATCTCAAGCGAGATAAAATTCATTTCAGGGGAAATG
66 ACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAATG
*
3743059 TTTTCAATGTTTATGTTTCAAGATAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAA
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAA
* *
3743124 ACTCTCTCAAGAGAGAAAAAAATCATTTCAAGGGAAATG
66 ACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAATG
*
3743163 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAA
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAA
* * *
3743228 ACTTTCTCAGGAGAGAAAAAATTAACTTT-AAGGGAAATG
66 ACTATCTCAAGAGAGAAAAAATTCA-TTTCAAGGGAAATG
3743267 TTTTCAA
1 TTTTCAA
3743274 GAGAAACTCT
Statistics
Matches: 194, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
101 43 0.22
104 148 0.76
105 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (104 bp):
TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAA
ACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAATG
Found at i:3743230 original size:39 final size:39
Alignment explanation
Indices: 3743176--3743250 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
3743166 TCAATGTTTA
*
3743176 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTGTCTC-AGGAGAGAAAAAATTTTC
* * *
3743215 TGTTTCGAGGGAAACTTTCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAGGAGAGAAAAAATT
3743251 AACTTTAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTGTCTCAGGAGAGAAAAAATTTTC
Found at i:3743430 original size:36 final size:36
Alignment explanation
Indices: 3743390--3743503 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
3743380 CTTTCGAGTG
* *
3743390 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* ** * * * **
3743426 AAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
*
3743462 AAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TCTTGTTTTAAGA
3743498 AAAACA
1 AAAACA
3743504 AGTTTGAGTG
Statistics
Matches: 58, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
36 57 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:3743482 original size:72 final size:74
Alignment explanation
Indices: 3743344--3743519 Score: 207
Period size: 72 Copynumber: 2.4 Consensus size: 74
3743334 TAAAATCTTC
* ** * *
3743344 TTAAAAAAAACAGCCTTGAGTGAAATGAAATGTATTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAA-GTATTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
3743409 CAAA-TCTTGTT
64 CAAAGT-ATGTT
* *
3743420 TTAAGAAAAACAATCTTGAGTGAAATAAA-TCTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAAGTATTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
3743483 AAGTATGTT
66 AAGTATGTT
*
3743492 TTAAGAAAAACAAGT-TTGAGTGAGATAA
1 TTAAGAAAAACAA-TCTTGAGTGAAATAA
3743520 TCATCTCCAT
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
72 50 0.56
73 13 0.15
75 3 0.03
76 23 0.26
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAAGTATTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
AAGTATGTT
Found at i:3744966 original size:183 final size:183
Alignment explanation
Indices: 3744658--3745194 Score: 941
Period size: 183 Copynumber: 2.9 Consensus size: 183
3744648 ATCAGGTTTA
*
3744658 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
3744723 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
3744787 TTCCTCTATAAACAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
3744841 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACATCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
3744906 GCCAAGTGTCCGAGCAGTGTCATAGTTTAAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
3744971 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * * *
3745024 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCTTGACAAAAGTAATTGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
3745089 GCCAAATGTCCGAGCAGTGTCATAGTTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
3745154 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
3745195 CGGATTTAAT
Statistics
Matches: 336, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
183 335 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:3749227 original size:27 final size:26
Alignment explanation
Indices: 3749191--3749282 Score: 75
Period size: 27 Copynumber: 3.5 Consensus size: 26
3749181 AAATGATAAA
*
3749191 ATAAAGAAAACAAAGATAAAATAGTA-
1 ATAAAAAAAACAAAGATAAAATA-TAT
*
3749217 AGTAAAAAAAACAAATAATAAAATATAT
1 A-TAAAAAAAACAAA-GATAAAATATAT
* *
3749245 ATAAAAAAGAA-AAAGA-AAAAGA-AA
1 ATAAAAAA-AACAAAGATAAAATATAT
*
3749269 ATAAATAAAACAAA
1 ATAAAAAAAACAAA
3749283 TAAACAAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
23 2 0.04
24 11 0.20
25 5 0.09
26 2 0.04
27 24 0.44
28 11 0.20
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (26 bp):
ATAAAAAAAACAAAGATAAAATATAT
Found at i:3749237 original size:28 final size:27
Alignment explanation
Indices: 3749190--3749316 Score: 84
Period size: 28 Copynumber: 4.7 Consensus size: 27
3749180 AAAATGATAA
* *
3749190 AATAAAGAAAACAAA-GATAAAATAGT
1 AATAAAAAAAACAAATAATAAAATAGT
3749216 AAGTAAAAAAAACAAATAATAAAATA-T
1 AA-TAAAAAAAACAAATAATAAAATAGT
* * * *
3749243 -ATATAAAAAAGAAA-AAGAAAA-AGAA
1 AATAAAAAAAACAAATAATAAAATAG-T
* * *
3749268 AATAAATAAAACAAATAAACAAAATAAT
1 AATAAAAAAAACAAAT-AATAAAATAGT
* *
3749296 AATAACAAAATACGAATAATA
1 AATAA-AAAAAACAAATAATA
3749317 TATATATATA
Statistics
Matches: 76, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
23 1 0.01
24 6 0.08
25 11 0.14
26 14 0.18
27 13 0.17
28 22 0.29
29 9 0.12
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.16
Consensus pattern (27 bp):
AATAAAAAAAACAAATAATAAAATAGT
Found at i:3749270 original size:58 final size:59
Alignment explanation
Indices: 3749161--3749271 Score: 131
Period size: 58 Copynumber: 1.9 Consensus size: 59
3749151 AATTAAAATG
* * *
3749161 AAAAGAAAACAAATTAAGTAAAATGATAAAATAAAGAAAACAAAGATAAAATAGTAAGT
1 AAAAGAAAACAAATTAAGTAAAATGATAAAAAAAAGAAAACAAAAAGAAAATAGTAAGT
*
3749220 AAAA-AAAACAAA-TAA-TAAAAT-ATATATAAAAAAGAAAAAGAAAAAGAAAATA
1 AAAAGAAAACAAATTAAGTAAAATGATA-A-AAAAAAG-AAAACAAAAAGAAAATA
3749272 AATAAAACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
55 3 0.07
56 7 0.16
57 9 0.20
58 22 0.49
59 4 0.09
ACGTcount: A:0.73, C:0.03, G:0.09, T:0.15
Consensus pattern (59 bp):
AAAAGAAAACAAATTAAGTAAAATGATAAAAAAAAGAAAACAAAAAGAAAATAGTAAGT
Found at i:3749572 original size:18 final size:17
Alignment explanation
Indices: 3749549--3749591 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3749539 ATATATACAT
3749549 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
3749567 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
3749584 ATAA-AATA
1 ATAATAATA
3749592 TCTATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:3749592 original size:58 final size:56
Alignment explanation
Indices: 3749469--3749599 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 56
3749459 AATATTAAAG
* * *
3749469 AAATATATATATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATA
1 AAATATATATATATATACATATAATAATAAAACATAATAAAAAAATAAATG-AAATA
3749526 ATTTAATATATATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATA
1 A---AATATATATATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATA
*
3749587 AAATATCTATATA
1 AAATATATATATA
3749600 ATAAATAAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
57 1 0.02
58 11 0.17
60 28 0.44
61 9 0.14
62 4 0.06
63 11 0.17
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (56 bp):
AAATATATATATATATACATATAATAATAAAACATAATAAAAAAATAAATGAAATA
Found at i:3749990 original size:37 final size:37
Alignment explanation
Indices: 3749940--3750044 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
3749930 GTGCTTGTGG
* * * *
3749940 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
3749977 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
3750014 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
3750045 GACGAAAATA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:3751044 original size:19 final size:19
Alignment explanation
Indices: 3750990--3751044 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
3750980 AACCAATAAT
3750990 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
3751009 GATGAAA-AAAATGAAATTG
1 AATAAAATAAAAT-AAATTG
3751028 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
3751045 GAAGATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 5 0.17
18 1 0.03
19 18 0.62
20 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:3751242 original size:27 final size:27
Alignment explanation
Indices: 3751195--3751279 Score: 75
Period size: 30 Copynumber: 3.1 Consensus size: 27
3751185 TAATGTATGT
*
3751195 ATAAT-ATAATAAA-ATACAAAATAGTA
1 ATAATAATAATAAATA-AAAAAATAGTA
*
3751221 ATAATAATAATAAATAAAAAAATAAATA
1 ATAATAATAATAAATAAAAAAAT-AGTA
* * *
3751249 TACATATAATATTAACTAAAAAAATAGTA
1 -ATA-ATAATAATAAATAAAAAAATAGTA
3751278 AT
1 AT
3751280 CATAGAAGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 5 0.11
27 14 0.30
28 5 0.11
29 5 0.11
30 18 0.38
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (27 bp):
ATAATAATAATAAATAAAAAAATAGTA
Found at i:3751472 original size:23 final size:24
Alignment explanation
Indices: 3751437--3751484 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
3751427 ACGCAAAGAA
3751437 AAATGAAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAAA-TATAATTAAAT
*
3751461 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAAAAAAATATAATTAAAT
3751484 A
1 A
3751485 TATACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATGAAAAAAAATATAATTAAAT
Found at i:3751993 original size:37 final size:37
Alignment explanation
Indices: 3751900--3752001 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
3751890 ATGCTTGTGG
* * ** * *
3751900 ATCCTATATTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAACTCT
*
3751937 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAACTCT
3751974 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
3752002 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAACTCT
Found at i:3752938 original size:106 final size:106
Alignment explanation
Indices: 3752753--3753713 Score: 1359
Period size: 106 Copynumber: 9.0 Consensus size: 106
3752743 AGCATTGTTC
* * * *
3752753 CGAGTCCAATATCCTCCG-TCATGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* * *
3752817 AACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* * * **
3752859 CGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTAGCTCCAAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3752924 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* *
3752965 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
3753030 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* * * * *
3753071 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3753136 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* * *
3753177 GGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
3753242 ACCAGCGGTCCCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTT
66 ACCA---G---CGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* ** * ** * *
3753289 GGAGTCCAATATATTTCGCTGTGAAGTTGAAATTAGCTCCAAAATTGGGAAACTGTTTGATGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3753354 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* *
3753395 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTAACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** **
3753460 ACCAGCGGTCCCTTTTTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* * * * *
3753501 GGAGTCCAATTTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
3753566 ACTAGCGGTCCCTTCGTCGTGAAGTTAAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* * * *
3753607 GGAGTCCAATGTCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3753672 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
3753713 C
1 C
3753714 AAGTGGCACG
Statistics
Matches: 773, Mismatches: 74, Indels: 16
0.90 0.09 0.02
Matches are distributed among these distances:
106 672 0.87
107 2 0.00
109 2 0.00
112 97 0.13
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
Found at i:3753550 original size:430 final size:424
Alignment explanation
Indices: 3752754--3753713 Score: 1530
Period size: 430 Copynumber: 2.2 Consensus size: 424
3752744 GCATTGTTCC
* * * *
3752754 GAGTCCAATATCCTCCGTCATGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
3752819 CCA-ACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTTGTTGTGA
65 CCAGTCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTTGCTGTGA
* *
3752883 AGTTGAAATTAGCTCCAAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCATGAAG
130 AGTTGAAATTAGCTCCAAAATTGGGAAACTGTTTGATGACAACCAGCGGTCCCTTCGTCATGAAG
*
3752948 TTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
195 TTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
* * * **
3753013 GAAGTTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCC
260 GAAATTATTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCC
*
3753078 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAGTTGTTTGTTGACAACCAGCG
325 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCG
*
3753143 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
390 GTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTG
*
3753178 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
3753243 CCAGCGGTCCCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT-ATTTCG
65 CCA---GT-CC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTT-G
3753307 CTGTGAAGTTGAAATTAGCTCCAAAATTGGGAAACTGTTTGATGACAACCAGCGGTCCCTTCGTC
124 CTGTGAAGTTGAAATTAGCTCCAAAATTGGGAAACTGTTTGATGACAACCAGCGGTCCCTTCGTC
*
3753372 GTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
189 ATGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
* **
3753437 AATTGGGAAATTGTTTATTAACAACCAGCGGTCCCTTTTTCGTGAAGTTGAACTTGCATTGTCTG
254 AATTGGGAAATTATTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
*
3753502 GAGTCCAATTTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
319 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
3753567 CTAGCGGTCCCTTCGTCGTGAAGTTAAACTTGTGTTGTCTG
384 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTG
* * *
3753608 GAGTCCAATGTCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
3753673 CCAGT-CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 CCAGTCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
3753714 AAGTGGCACG
Statistics
Matches: 490, Mismatches: 38, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
424 92 0.19
425 2 0.00
427 2 0.00
429 5 0.01
430 389 0.79
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (424 bp):
GAGTCCAATATCCTTCGTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGTCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTTGCTGTGAA
GTTGAAATTAGCTCCAAAATTGGGAAACTGTTTGATGACAACCAGCGGTCCCTTCGTCATGAAGT
TGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
AAATTATTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTG
Found at i:3754258 original size:18 final size:19
Alignment explanation
Indices: 3754229--3754265 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3754219 TGTTGAATCC
3754229 CCAAATAATGCCCCAATAT
1 CCAAATAATGCCCCAATAT
*
3754248 CCAAA-AATGCCCTAATAT
1 CCAAATAATGCCCCAATAT
3754266 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.22
Consensus pattern (19 bp):
CCAAATAATGCCCCAATAT
Found at i:3759688 original size:20 final size:19
Alignment explanation
Indices: 3759638--3759693 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
3759628 AACCAATAAT
3759638 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
3759657 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
3759677 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
3759694 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:3759830 original size:21 final size:21
Alignment explanation
Indices: 3759791--3759910 Score: 59
Period size: 21 Copynumber: 5.5 Consensus size: 21
3759781 AAATATGATG
* *
3759791 AAAATAAATAAATAGTATAAAT
1 AAAAT-AATAAAAAATATAAAT
*
3759813 AAAATAATAAAAAATATATAT
1 AAAATAATAAAAAATATAAAT
* **
3759834 ATAAA-AATATAAAAATGTATGT
1 A-AAATAATA-AAAAATATAAAT
*
3759856 ATAAT-ATAATAAAATACTAAAT
1 AAAATAATAA-AAAATA-TAAAT
*
3759878 AGTAATAATAATAATAA-ATAAAT
1 A-AAATAATAA-AA-AATATAAAT
*
3759901 GAAA-AATAAA
1 AAAATAATAAA
3759911 TATACATATA
Statistics
Matches: 79, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
20 2 0.03
21 33 0.42
22 25 0.32
23 9 0.11
24 8 0.10
25 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAATAATAAAAAATATAAAT
Found at i:3759858 original size:22 final size:21
Alignment explanation
Indices: 3759791--3759869 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 21
3759781 AAATATGATG
*
3759791 AAAATAAATAAATAGTATAAATAA
1 AAAATAAA-AAATA-TATATAT-A
3759815 AATAATAAAAAATATATATATA
1 AA-AATAAAAAATATATATATA
* *
3759837 AAAATATAAAAATGTATGTATA
1 AAAATA-AAAAATATATATATA
3759859 ATATAATAAAA
1 A-A-AATAAAA
3759870 TACTAAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 4 0.08
22 17 0.35
23 10 0.21
24 11 0.23
25 6 0.12
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAATAAAAAATATATATATA
Found at i:3760142 original size:23 final size:23
Alignment explanation
Indices: 3760108--3760154 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
3760098 ACGCAAAGAA
3760108 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
3760131 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
3760154 A
1 A
3760155 TATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:3760620 original size:37 final size:37
Alignment explanation
Indices: 3760579--3760663 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
3760569 GAATCATATC
* * *
3760579 TTTAGGAGTTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATACTATT
* ** *
3760616 TTTAGGAGTTTGAATCCTAGCAAAATTCTATACTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATACTATT
*
3760653 TTTAGCAGTTT
1 TTTAGGAGTTT
3760664 GAATCCTAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATACTATT
Found at i:3765987 original size:24 final size:25
Alignment explanation
Indices: 3765950--3766019 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
3765940 GGTACCGATA
* *
3765950 CCAACACCGGAAAAGGA-GCCATTTT
1 CCAACGCC-GAAAAGGATACCATTTT
*
3765975 CCAACGCCGAAAAAGATACCATTTT
1 CCAACGCCGAAAAGGATACCATTTT
3766000 CCAACGCCGAAAAGG-TACCA
1 CCAACGCCGAAAAGGATACCA
3766020 ATTTGTAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 12 0.30
25 28 0.70
ACGTcount: A:0.39, C:0.30, G:0.17, T:0.14
Consensus pattern (25 bp):
CCAACGCCGAAAAGGATACCATTTT
Found at i:3775016 original size:56 final size:53
Alignment explanation
Indices: 3774954--3775180 Score: 222
Period size: 56 Copynumber: 4.2 Consensus size: 53
3774944 TTGCAGCACT
* *
3774954 GAGGTGCTCAATCGTTTGTCAAAGCACTGAGGTGTCAGATTTTAGATTGAAACACA
1 GAGGTGCTCAATC-TTT-T-AAAGCACAGAGGTGTCAGATTCTAGATTGAAACACA
** * * *
3775010 GAGGTGCTCAATCATCCTAAAGCACAGAAGTGTCAGATCCTAGATTGAAGCACA
1 GAGGTGCTCAATC-TTTTAAAGCACAGAGGTGTCAGATTCTAGATTGAAACACA
* * * **
3775064 TAGGTGCTCAATCATTAAAAGCACAGAGGTGTCAGATTCTAGA-CCAAAGCACA
1 GAGGTGCTCAATCTTTTAAAGCACAGAGGTGTCAGATTCTAGATTGAAA-CACA
* * * * *
3775117 GAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTCAGATTGTCGATTGAAGCACA
1 GAGGTGCTCAATC--TTTTAA-AGCACAGAGGTGTCAGATTCTAGATTGAAACACA
3775173 GAGGTGCT
1 GAGGTGCT
3775181 GTGAATTCAG
Statistics
Matches: 138, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
52 2 0.01
53 39 0.28
54 43 0.31
55 5 0.04
56 47 0.34
57 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (53 bp):
GAGGTGCTCAATCTTTTAAAGCACAGAGGTGTCAGATTCTAGATTGAAACACA
Found at i:3775054 original size:54 final size:52
Alignment explanation
Indices: 3774974--3775180 Score: 218
Period size: 54 Copynumber: 3.8 Consensus size: 52
3774964 ATCGTTTGTC
* *
3774974 AAAGCACTGAGGTGTCAGATTTTAGATTGAAACACAGAGGTGCTCAATCATCCT
1 AAAGCACAGAGGTGTCAGATTCTAGATTGAAACACAGAGGTGCTCAATCAT--T
* * * *
3775028 AAAGCACAGAAGTGTCAGATCCTAGATTGAAGCACATAGGTGCTCAATCATT
1 AAAGCACAGAGGTGTCAGATTCTAGATTGAAACACAGAGGTGCTCAATCATT
** *
3775080 AAAAGCACAGAGGTGTCAGATTCTAGA-CCAAAGCACAGAGGTGCTCAGTCATTTTT
1 -AAAGCACAGAGGTGTCAGATTCTAGATTGAAA-CACAGAGGTGCTCAATCA---TT
* * * *
3775136 AACTGCACAGAGGTGTCAGATTGTCGATTGAAGCACAGAGGTGCT
1 AA-AGCACAGAGGTGTCAGATTCTAGATTGAAACACAGAGGTGCT
3775181 GTGAATTCAG
Statistics
Matches: 127, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
52 3 0.02
53 40 0.31
54 45 0.35
55 2 0.02
56 35 0.28
57 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (52 bp):
AAAGCACAGAGGTGTCAGATTCTAGATTGAAACACAGAGGTGCTCAATCATT
Found at i:3775119 original size:107 final size:109
Alignment explanation
Indices: 3774942--3775180 Score: 268
Period size: 107 Copynumber: 2.2 Consensus size: 109
3774932 CTTAGTTGTC
* * * * * * **
3774942 GATTGCAGCACTGAGGTGCTCAATCGTTTGTCAAAGCACTGAGGTGTCAGATTTTAGATTGAAAC
1 GATTGAAGCACAGAGGTGCTCAATC--AT-TAAAAGCACAGAGGTGTCAGATTCTAGATCCAAAC
3775007 ACAGAGGTGCTCAATCA-TCCTAA-AGCACAGAAGTGTCAGATCCTA
63 ACAGAGGTGCTCAATCATTCCTAACAGCACAGAAGTGTCAGATCCTA
*
3775052 GATTGAAGCACATAGGTGCTCAATCATTAAAAGCACAGAGGTGTCAGATTCTAGA-CCAAAGCAC
1 GATTGAAGCACAGAGGTGCTCAATCATTAAAAGCACAGAGGTGTCAGATTCTAGATCCAAA-CAC
* ** * * ** *
3775116 AGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTCAGATTGTC
65 AGAGGTGCTCAATCATTCCTAACAGCACAGAAGTGTCAGATCCTA
3775161 GATTGAAGCACAGAGGTGCT
1 GATTGAAGCACAGAGGTGCT
3775181 GTGAATTCAG
Statistics
Matches: 108, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
106 3 0.03
107 42 0.39
108 5 0.05
109 36 0.33
110 22 0.20
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (109 bp):
GATTGAAGCACAGAGGTGCTCAATCATTAAAAGCACAGAGGTGTCAGATTCTAGATCCAAACACA
GAGGTGCTCAATCATTCCTAACAGCACAGAAGTGTCAGATCCTA
Found at i:3787012 original size:32 final size:32
Alignment explanation
Indices: 3786971--3787040 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
3786961 ACCCAATCTG
3786971 TCCCCAACACTTGCGAGTACGATTTTGGGGAA
1 TCCCCAACACTTGCGAGTACGATTTTGGGGAA
3787003 TCCCCAACACTTGCGAGTACGATTTTGGGGAA
1 TCCCCAACACTTGCGAGTACGATTTTGGGGAA
3787035 TCCCCA
1 TCCCCA
3787041 TTATATGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (32 bp):
TCCCCAACACTTGCGAGTACGATTTTGGGGAA
Found at i:3787893 original size:36 final size:36
Alignment explanation
Indices: 3787853--3787967 Score: 212
Period size: 36 Copynumber: 3.2 Consensus size: 36
3787843 ATAGAAACAT
*
3787853 GAAACATGAAACATGGGCAGTCGAGCATCCATGATA
1 GAAACACGAAACATGGGCAGTCGAGCATCCATGATA
*
3787889 GAAACACGAAACATGGGCAATCGAGCATCCATGATA
1 GAAACACGAAACATGGGCAGTCGAGCATCCATGATA
3787925 GAAACACGAAACATGGGCAGTCGAGCATCCATGATA
1 GAAACACGAAACATGGGCAGTCGAGCATCCATGATA
3787961 GAAACAC
1 GAAACAC
3787968 TTGAAGTGGT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 76 1.00
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (36 bp):
GAAACACGAAACATGGGCAGTCGAGCATCCATGATA
Found at i:3795449 original size:124 final size:116
Alignment explanation
Indices: 3795308--3796136 Score: 1002
Period size: 116 Copynumber: 7.0 Consensus size: 116
3795298 CAATCTAAAG
* * * * * *
3795308 ATTG-ATGCTGCTTGTGGGCACGATATCCTTCGTCGTGAAGATGAAATCGTGGAGGGCCCCTTCG
1 ATTGAATGTTGCTGGTGAGCACGAT-TCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCG
3795372 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
65 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
* * ** * *
3795424 ATCTAAAGATGATTGTTGCTGGTGGGCACAATTCTCTTCGTTATGAAGTTGAAATCGTGAATGGC
1 AT-T---GA--A-TGTTGCTGGTGAGCACGATTC-CTTCGTCGTGAAGTTGAAACCGTGGATGGC
*
3795489 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTAAAATCCA
58 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
* * * *
3795548 ATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCATCGTGAAGCTGAAACTGTGGATGGC
1 A--T-----TGAATGTTGCTGGTGAGCACGATT-CCTTCGTCGTGAAGTTGAAACCGTGGATGGC
* * * * * *
3795613 TCCTTCGTTGTGAAGTTGAGCCTTAAATTAGATATCATTCGTCATGAAGTTAAAATCCA
58 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
* * * * * *
3795672 ATT-AATTTTGCTGGTGAGCACGATTCACTTTGTCATGAAATTGAAACCATGGGTGGCCCCTTCG
1 ATTGAATGTTGCTGGTGAGCACGATTC-CTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCG
*
3795736 TTGTGAAGTTGAGCCTTGAATTGGATATCATTCGTCGTGAAGTTGAAATCCA
65 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
* * *
3795788 A-TGAATGTTGCTGGTGAGCACGATTCCATTCATCGTGAAGTTAAAACTGTGGATGGCCCCTTCG
1 ATTGAATGTTGCTGGTGAGCACGATTCC-TTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCG
3795852 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
65 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
* * * *
3795904 ATT-AATGTTGCTGGTGAGCACGATTCCCTTCGTCATGAAGTTGAAACCGTAGATGGTCTCTTCG
1 ATTGAATGTTGCTGGTGAGCACGATT-CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCG
* *
3795968 TTGTGAAGTTGATCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCA
65 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
* * *
3796020 A-TGAATGTTACTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCA
1 ATTGAATGTTGCTGGTGAGCACGATT-CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCG
* * * * * *
3796084 TTTTGAAGTTGAGCCGTGACTTGAATATCCTTCATCGTGAAGTTAAAATCCA
65 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
3796136 A
1 A
3796137 GCTTGTATTG
Statistics
Matches: 619, Mismatches: 72, Indels: 44
0.84 0.10 0.06
Matches are distributed among these distances:
115 4 0.01
116 404 0.65
117 5 0.01
120 1 0.00
122 1 0.00
123 3 0.00
124 195 0.32
125 2 0.00
126 1 0.00
127 2 0.00
130 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (116 bp):
ATTGAATGTTGCTGGTGAGCACGATTCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGT
TGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
Found at i:3798742 original size:64 final size:63
Alignment explanation
Indices: 3798674--3798903 Score: 212
Period size: 64 Copynumber: 3.6 Consensus size: 63
3798664 TTGGAACACT
* *** *
3798674 TGATGCATCGGTGCACCAAGTGTGCATCAATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
3798738 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * * *
3798802 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAAT-TC
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAGC
*
3798865 A
63 C
* *
3798866 TCGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
3798904 CCTTTGAATA
Statistics
Matches: 137, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
63 4 0.03
64 69 0.50
65 64 0.47
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:3798826 original size:19 final size:19
Alignment explanation
Indices: 3798802--3798852 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3798792 GAAAATATTC
3798802 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
3798821 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
3798840 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
3798853 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:3798828 original size:65 final size:65
Alignment explanation
Indices: 3798695--3798854 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
3798685 TGCACCAAGT
* * ***
3798695 GTGCATCAATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
3798759 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
3798823 A
65 A
* *
3798824 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
3798855 CAATTAATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 36 0.43
65 47 0.57
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:3798894 original size:65 final size:64
Alignment explanation
Indices: 3798704--3798903 Score: 205
Period size: 65 Copynumber: 3.1 Consensus size: 64
3798694 TGTGCATCAA
* ** *
3798704 TGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGG-CTTG-TGCATCG
1 TGCATGAAATGCATTCGATGTTT-CAAAATATTCAGATGCATCGATGCATGGAC-TGATGCATCG
*
3798767 A
64 G
* *
3798768 TGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--GAGTGCATC
1 TGCATGAAATGCATTCGATG-TTTCAAAATATTCAGA-TGCATCGATGCATGGACTGA-TGCATC
3798831 GG
63 GG
* *
3798833 TGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGATGCATCGATGCATGGACTGATGCATC
1 TGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GATGCATCGATGCATGGACTGATGCATC
3798896 GG
63 GG
3798898 TGCATG
1 TGCATG
3798904 CCTTTGAATA
Statistics
Matches: 116, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
62 3 0.03
63 8 0.07
64 44 0.38
65 59 0.51
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (64 bp):
TGCATGAAATGCATTCGATGTTTCAAAATATTCAGATGCATCGATGCATGGACTGATGCATCGG
Found at i:3805221 original size:22 final size:21
Alignment explanation
Indices: 3805179--3805218 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3805169 GAGTTTGTTT
*
3805179 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3805200 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3805219 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3807207 original size:64 final size:63
Alignment explanation
Indices: 3807139--3807319 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 63
3807129 TTGGAACACT
* ***
3807139 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
3807203 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
3807267 AGAGTGCATCGATGCATGGAGAGTGCATCGATGCATGGAATGTATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
3807320 CAATTAATTC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
64 54 0.55
65 45 0.45
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:3807291 original size:19 final size:19
Alignment explanation
Indices: 3807267--3807305 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3807257 GAAAATATTC
3807267 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
3807286 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
3807305 A
1 A
3807306 ATGTATTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:3807293 original size:65 final size:65
Alignment explanation
Indices: 3807160--3807319 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 65
3807150 TGCACCAAGT
* ***
3807160 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
3807224 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
3807288 A
65 A
* *
3807289 GTGCATCGATGCATGGAATGTATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
3807320 CAATTAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:3807938 original size:35 final size:34
Alignment explanation
Indices: 3807877--3807943 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
3807867 ATGTACTCAT
*
3807877 AAAAAGAAATATGTCAAAGTTCAAAAACAAGTTAC
1 AAAAAGAAATATG-CAAAGTTAAAAAACAAGTTAC
3807912 AAAAAGAAATATG-AGAAGTTAAAAAAACAAGT
1 AAAAAGAAATATGCA-AAGTT-AAAAAACAAGT
3807944 CCAAACAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 1 0.03
34 5 0.17
35 23 0.79
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.18
Consensus pattern (34 bp):
AAAAAGAAATATGCAAAGTTAAAAAACAAGTTAC
Found at i:3810035 original size:18 final size:19
Alignment explanation
Indices: 3810008--3810044 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3809998 AATAAATACT
*
3810008 AAATAGATTAA-AGAAAAA
1 AAATAAATTAAGAGAAAAA
3810026 AAATAAATTAAGAGAAAAA
1 AAATAAATTAAGAGAAAAA
3810045 TATTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (19 bp):
AAATAAATTAAGAGAAAAA
Found at i:3811259 original size:14 final size:15
Alignment explanation
Indices: 3811224--3811270 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
3811214 GGCTCTGCAA
*
3811224 AATAAAAAAATAAAT
1 AATAATAAAATAAAT
3811239 AATAATAAAATAATTAT
1 AATAATAAAATAA--AT
3811256 AATAAT-AAATAAAT
1 AATAATAAAATAAAT
3811270 A
1 A
3811271 TTTTTTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.10
15 12 0.41
16 6 0.21
17 8 0.28
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAATAAAATAAAT
Found at i:3811946 original size:7 final size:7
Alignment explanation
Indices: 3811930--3812021 Score: 103
Period size: 7 Copynumber: 13.1 Consensus size: 7
3811920 GCTCACAGCA
3811930 CTATTCC
1 CTATTCC
*
3811937 CTAATCC
1 CTATTCC
3811944 CTATTCC
1 CTATTCC
3811951 CTATTCC
1 CTATTCC
*
3811958 CCATTCC
1 CTATTCC
*
3811965 CCATTCC
1 CTATTCC
*
3811972 CCATTCC
1 CTATTCC
*
3811979 CCATTCC
1 CTATTCC
*
3811986 CCATTCC
1 CTATTCC
*
3811993 CCATTCC
1 CTATTCC
*
3812000 CCATTCC
1 CTATTCC
*
3812007 CCATTCC
1 CTATTCC
3812014 CTATTCC
1 CTATTCC
3812021 C
1 C
3812022 ATCCCCATCC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 81 1.00
ACGTcount: A:0.15, C:0.52, G:0.00, T:0.33
Consensus pattern (7 bp):
CTATTCC
Found at i:3812056 original size:6 final size:7
Alignment explanation
Indices: 3811941--3812053 Score: 157
Period size: 7 Copynumber: 17.0 Consensus size: 7
3811931 TATTCCCTAA
*
3811941 TCCCTAT
1 TCCCCAT
*
3811948 TCCCTAT
1 TCCCCAT
3811955 TCCCCAT
1 TCCCCAT
3811962 TCCCCAT
1 TCCCCAT
3811969 TCCCCAT
1 TCCCCAT
3811976 TCCCCAT
1 TCCCCAT
3811983 TCCCCAT
1 TCCCCAT
3811990 TCCCCAT
1 TCCCCAT
3811997 TCCCCAT
1 TCCCCAT
3812004 TCCCCAT
1 TCCCCAT
*
3812011 TCCCTAT
1 TCCCCAT
3812018 T-CCCA-
1 TCCCCAT
3812023 TCCCCA-
1 TCCCCAT
3812029 TCCCCA-
1 TCCCCAT
3812035 TCCCCA-
1 TCCCCAT
3812041 TCCCCA-
1 TCCCCAT
3812047 TCCCCAT
1 TCCCCAT
3812054 CCCTTGCCCC
Statistics
Matches: 101, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
5 1 0.01
6 31 0.31
7 69 0.68
ACGTcount: A:0.15, C:0.57, G:0.00, T:0.28
Consensus pattern (7 bp):
TCCCCAT
Found at i:3813740 original size:14 final size:12
Alignment explanation
Indices: 3813713--3813752 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3813703 TAATTCAAGC
3813713 ATTTTTTTTTAT
1 ATTTTTTTTTAT
3813725 ATTTTTTTATTAAT
1 ATTTTTTT-TT-AT
*
3813739 ATTTTATTTTAT
1 ATTTTTTTTTAT
3813751 AT
1 AT
3813753 CCTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 12 0.48
13 4 0.16
14 9 0.36
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
ATTTTTTTTTAT
Found at i:3817008 original size:185 final size:184
Alignment explanation
Indices: 3816690--3817060 Score: 620
Period size: 185 Copynumber: 2.0 Consensus size: 184
3816680 ATTAAATTTT
* *
3816690 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCTAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCTAATTAATAA
3816755 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
* *
3816820 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
*
3816875 AAATATTAAATATATTATATATAACATTTGGGCTAAGCCCAAACAATTTAAAA-CTCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCT-AATTAATA
* * * *
3816939 ATTTAAGATCCAATAATTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-T
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATT
3817003 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
3817059 AA
1 AA
3817061 CATTTAATTT
Statistics
Matches: 175, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
184 17 0.10
185 155 0.89
186 3 0.02
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCTAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:3817188 original size:30 final size:30
Alignment explanation
Indices: 3817132--3817189 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3817122 CGAAATTAAA
* **
3817132 TCGGTTCGGTTAATATGTTTGAAAAAAAGT
1 TCGGTTCGGTTAACATGTTAAAAAAAAAGT
3817162 TCGGTTCGGTTAACA-GTTAAAGAAAAAA
1 TCGGTTCGGTTAACATGTTAAA-AAAAAA
3817190 AAAGTTCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (30 bp):
TCGGTTCGGTTAACATGTTAAAAAAAAAGT
Found at i:3825481 original size:22 final size:21
Alignment explanation
Indices: 3825429--3825488 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
3825419 GATTTCTGGG
3825429 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
3825450 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
3825470 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
3825489 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:3827067 original size:101 final size:102
Alignment explanation
Indices: 3826844--3827059 Score: 371
Period size: 103 Copynumber: 2.1 Consensus size: 102
3826834 GTCGAGGGTC
*
3826844 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACA-AC
* *
3826909 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
3826947 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACAC-ACT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAACT
* *
3827011 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TGATCCCTAGCATATGTATATGATTATTAAGGAATGA
3827048 TATGTGGTCCTT
1 TATGTGGTCCTT
3827060 ATGGACATTA
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
101 48 0.44
103 60 0.56
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAACT
TGATCCCTAGCATATGTATATGATTATTAAGGAATGA
Found at i:3827102 original size:23 final size:23
Alignment explanation
Indices: 3827075--3827143 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3827065 CATTATTATA
* * *
3827075 TGGCACTATGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTATACG
*
3827098 TGGCACTCCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
* *
3827121 TGGCACTTCGGTGTAATTATACG
1 TGGCACTACGGTGCAATTATACG
3827144 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:3830958 original size:16 final size:16
Alignment explanation
Indices: 3830934--3830972 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3830924 TGTTTATTAT
*
3830934 TATGCCTCACTAAGTC
1 TATGACTCACTAAGTC
3830950 TATGACTCACTAAGTC
1 TATGACTCACTAAGTC
3830966 TATGACT
1 TATGACT
3830973 TAGCGTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (16 bp):
TATGACTCACTAAGTC
Found at i:3831927 original size:14 final size:15
Alignment explanation
Indices: 3831908--3831937 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3831898 CTAGAACTAC
3831908 TTTAGTTTA-TTTTA
1 TTTAGTTTAGTTTTA
3831922 TTTAGTTTAGTTTTA
1 TTTAGTTTAGTTTTA
3831937 T
1 T
3831938 CAGTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (15 bp):
TTTAGTTTAGTTTTA
Found at i:3834416 original size:24 final size:23
Alignment explanation
Indices: 3834386--3834470 Score: 107
Period size: 24 Copynumber: 3.6 Consensus size: 23
3834376 TGTTCGATAA
*
3834386 TATGTTCGTTTATGTTTTATCATT
1 TATGTTCGTTTATGTTGT-TCATT
*
3834410 TATGTTCGTTTATGATCGTTCATT
1 TATGTTCGTTTATG-TTGTTCATT
* *
3834434 TATGTTCTTTTATGTTCGTTCGTT
1 TATGTTCGTTTATGTT-GTTCATT
3834458 TATGTTCGTTTAT
1 TATGTTCGTTTAT
3834471 TAGCCTAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.02
24 50 0.94
25 2 0.04
ACGTcount: A:0.14, C:0.11, G:0.15, T:0.60
Consensus pattern (23 bp):
TATGTTCGTTTATGTTGTTCATT
Found at i:3836629 original size:18 final size:18
Alignment explanation
Indices: 3836606--3836642 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3836596 CAACCCACTG
3836606 CCCATTTAAATTTTAAAA
1 CCCATTTAAATTTTAAAA
3836624 CCCATTTAAATTTTAAAA
1 CCCATTTAAATTTTAAAA
3836642 C
1 C
3836643 TAATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (18 bp):
CCCATTTAAATTTTAAAA
Found at i:3840154 original size:23 final size:23
Alignment explanation
Indices: 3840128--3840172 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
3840118 ATTGTAAACT
3840128 GTTTGTATACTGAATTATGCTTG
1 GTTTGTATACTGAATTATGCTTG
3840151 GTTTGTATACTGAATTATGCTT
1 GTTTGTATACTGAATTATGCTT
3840173 CCAGTTCTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (23 bp):
GTTTGTATACTGAATTATGCTTG
Found at i:3841206 original size:59 final size:60
Alignment explanation
Indices: 3841123--3841256 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 60
3841113 AAACATATGA
*
3841123 ATAATCGAGTAATCATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAATAACACCAT
1 ATAATCGAGGAATCATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAATAACACCAT
* * * * * * *
3841183 ATAATCG-GGAATTATTTTGTAACTTTTAATTGTTAGGAGACTCGACAAAATAAC-TC-T
1 ATAATCGAGGAATCATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAATAACACCAT
*
3841240 ATAATC-AGGGATCATTT
1 ATAATCGAGGAATCATTT
3841257 GTGTACTTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
57 15 0.24
58 1 0.02
59 40 0.63
60 7 0.11
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (60 bp):
ATAATCGAGGAATCATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAATAACACCAT
Found at i:3845482 original size:21 final size:21
Alignment explanation
Indices: 3845456--3845495 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3845446 CAGAACCCCA
*
3845456 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3845477 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3845496 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3845530 original size:20 final size:21
Alignment explanation
Indices: 3845476--3845538 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
3845466 GATTCCCCTG
3845476 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
3845500 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
3845520 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
3845539 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:3853826 original size:21 final size:22
Alignment explanation
Indices: 3853796--3853846 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
3853786 GATGTTTCCG
*
3853796 GGTATTGATACCCTCC-ACATA-
1 GGTATCGATA-CCTCCTACATAT
*
3853817 GGTATCGATACCTCCTCCATAT
1 GGTATCGATACCTCCTACATAT
3853839 GGTATCGA
1 GGTATCGA
3853847 CACTGTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 13 0.50
22 8 0.31
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (22 bp):
GGTATCGATACCTCCTACATAT
Found at i:3856117 original size:79 final size:79
Alignment explanation
Indices: 3855986--3856144 Score: 318
Period size: 79 Copynumber: 2.0 Consensus size: 79
3855976 TTATTTTTAT
3855986 TTTCATTTTTCTGGCCTTCATTATCGAATAAAGTAAATGTTGAATGTTGTAATCACAATACCAAA
1 TTTCATTTTTCTGGCCTTCATTATCGAATAAAGTAAATGTTGAATGTTGTAATCACAATACCAAA
3856051 TTTTAGAGTTGTTG
66 TTTTAGAGTTGTTG
3856065 TTTCATTTTTCTGGCCTTCATTATCGAATAAAGTAAATGTTGAATGTTGTAATCACAATACCAAA
1 TTTCATTTTTCTGGCCTTCATTATCGAATAAAGTAAATGTTGAATGTTGTAATCACAATACCAAA
3856130 TTTTAGAGTTGTTG
66 TTTTAGAGTTGTTG
3856144 T
1 T
3856145 AGTGGTTGAG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (79 bp):
TTTCATTTTTCTGGCCTTCATTATCGAATAAAGTAAATGTTGAATGTTGTAATCACAATACCAAA
TTTTAGAGTTGTTG
Found at i:3857918 original size:72 final size:72
Alignment explanation
Indices: 3857801--3857945 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
3857791 AAATGATCCG
3857801 ACATATTATTGAACTTATCTAATATTTACATGACTTAATTTTTACATGTAAGTTATCATTGATGA
1 ACATATTATTGAACTTATCTAATATTTACATGACTTAATTTTTACATGTAAGTTATCATTGATGA
3857866 AGTTAGA
66 AGTTAGA
3857873 ACATATTATTGAACTTATCTAATATTTACATGACTTAATTTTTACATGTAAGTTATCATTGATGA
1 ACATATTATTGAACTTATCTAATATTTACATGACTTAATTTTTACATGTAAGTTATCATTGATGA
3857938 AGTTAGA
66 AGTTAGA
3857945 A
1 A
3857946 ATTATGGATT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (72 bp):
ACATATTATTGAACTTATCTAATATTTACATGACTTAATTTTTACATGTAAGTTATCATTGATGA
AGTTAGA
Found at i:3858447 original size:20 final size:21
Alignment explanation
Indices: 3858422--3858473 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3858412 TTTTCCCAAT
*
3858422 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3858442 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3858463 TCGCAATGCGA
1 TCGCAATGCGA
3858474 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3858487 original size:20 final size:19
Alignment explanation
Indices: 3858462--3858595 Score: 106
Period size: 20 Copynumber: 6.7 Consensus size: 19
3858452 AATTGGGAAA
3858462 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
3858482 ATCGCAATGCGATACTACT
1 ATCGCAATGCGATACTACT
* *
3858501 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTAC--T
* *
3858522 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACT-ACT
* * *
3858542 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACT-ACT
* * * *
3858562 TTCGCAACGTGATAATACAT
1 ATCGCAATGCGATACTAC-T
3858582 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
3858596 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 22 0.23
20 47 0.50
21 23 0.24
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (19 bp):
ATCGCAATGCGATACTACT
Found at i:3858523 original size:60 final size:61
Alignment explanation
Indices: 3858459--3858595 Score: 186
Period size: 60 Copynumber: 2.3 Consensus size: 61
3858449 GCGAATTGGG
* *
3858459 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACT-ACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * * *
3858519 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGTGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
3858580 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
3858596 TTTCAAAGCG
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
60 34 0.52
61 31 0.48
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3859111 original size:19 final size:20
Alignment explanation
Indices: 3859068--3859115 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
3859058 GCGATTCTCT
3859068 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3859088 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
3859107 TGTTGCGAT
1 CGTTGCGAT
3859116 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3860918 original size:19 final size:19
Alignment explanation
Indices: 3860896--3860992 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
3860886 GGAAATGGCT
*
3860896 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3860915 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
3860929 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3860948 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3860962 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3860981 ATCGCAATGCGA
1 ATCGCAATGCGA
3860993 TTTGTGTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 3 0.05
18 2 0.03
19 31 0.50
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3860931 original size:14 final size:14
Alignment explanation
Indices: 3860912--3860970 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3860902 ATGTGAAATG
3860912 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3860926 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
3860945 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3860959 AAAATCGCAACG
1 AAAATCGCAACG
3860971 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3860943 original size:33 final size:33
Alignment explanation
Indices: 3860896--3860987 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
3860886 GGAAATGGCT
*
3860896 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3860929 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3860962 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3860988 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3861041 original size:18 final size:18
Alignment explanation
Indices: 3860999--3861156 Score: 116
Period size: 18 Copynumber: 8.9 Consensus size: 18
3860989 GCGATTTGTG
3860999 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
3861015 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
3861031 TTTCGCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
3861049 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
*
3861068 TTTCGCATTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
3861084 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
* * **
3861101 TTTCGCATTGTGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
* *
3861120 TTTCCGCATTGCGATAGTCA
1 TTT-CGCGTTGCGAT-TTCA
*
3861140 TTTTCGCGTTGCAATTT
1 -TTTCGCGTTGCGATTT
3861157 TAAGTTTCGT
Statistics
Matches: 114, Mismatches: 15, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
14 18 0.16
15 3 0.03
16 6 0.05
17 2 0.02
18 30 0.26
19 29 0.25
20 23 0.20
21 3 0.03
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:3861122 original size:52 final size:52
Alignment explanation
Indices: 3861036--3861134 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
3861026 TTTCATTTCG
* ***
3861036 CGTTGCGATTTCATTTCGCGTTGCGATTTTCATTT-CGCATTGCGATTTTGT
1 CGTTGCGATTTCATTTCGCATTGCGATAGCCATTTCCGCATTGCGATTTTGT
*
3861087 CGTTGCGATTTTCATTTCGCATTGTGATAGCCATTTCCGCATTGCGAT
1 CGTTGCGA-TTTCATTTCGCATTGCGATAGCCATTTCCGCATTGCGAT
3861135 AGTCATTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 8 0.20
52 22 0.54
53 11 0.27
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (52 bp):
CGTTGCGATTTCATTTCGCATTGCGATAGCCATTTCCGCATTGCGATTTTGT
Found at i:3861129 original size:20 final size:19
Alignment explanation
Indices: 3861099--3861142 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
3861089 TTGCGATTTT
*
3861099 CATTTCGCATTGTGATAGC
1 CATTTCGCATTGCGATAGC
*
3861118 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
3861138 CATTT
1 CATTT
3861143 TCGCGTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:3861616 original size:41 final size:42
Alignment explanation
Indices: 3861520--3861607 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
3861510 GACTCACCTG
* * *
3861520 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCACTCGTTCAAGAGGCCACTA
* *
3861562 TCCTCCCTCAAGAGTCCCCCCCACT-GTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACTCGTTCAAGAGGCCACTA
3861603 TCATC
1 TCATC
3861608 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 18 0.45
42 22 0.55
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.22
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCACTCGTTCAAGAGGCCACTA
Found at i:3863057 original size:14 final size:14
Alignment explanation
Indices: 3863023--3863061 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3863013 TTGATTGTTT
3863023 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
3863037 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
3863051 TGTTGATTTGT
1 AATTGATTTGT
3863062 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3863187 original size:14 final size:14
Alignment explanation
Indices: 3863168--3863221 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
3863158 AAAACAGACT
3863168 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
3863182 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
3863201 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
3863215 ATCGCAA
1 ATCGCAA
3863222 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:3863244 original size:19 final size:20
Alignment explanation
Indices: 3863216--3863255 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3863206 AACGAGAAAA
3863216 TCGCAATGCGATTTTC-AGT
1 TCGCAATGCGATTTTCTAGT
*
3863235 TCGCATTGCGATTTTCTAGT
1 TCGCAATGCGATTTTCTAGT
3863255 T
1 T
3863256 GCGATAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (20 bp):
TCGCAATGCGATTTTCTAGT
Found at i:3863268 original size:20 final size:20
Alignment explanation
Indices: 3863253--3863340 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
3863243 CGATTTTCTA
3863253 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
3863273 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
3863293 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
3863313 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
3863333 GTTGCGAT
1 GTTGCGAT
3863341 TTCCCCATTG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:3863278 original size:34 final size:36
Alignment explanation
Indices: 3863234--3863320 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 36
3863224 CGATTTTCAG
* *
3863234 TTCGCATTGCGATTTTC-T-AGTTGCGATAGCCATT
1 TTCGCGTTGCGATTTTCTTCAATTGCGATAGCCATT
3863268 TTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCATT
1 TTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCATT
3863308 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
3863321 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 11 0.24
35 5 0.11
38 1 0.02
39 1 0.02
40 27 0.60
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (36 bp):
TTCGCGTTGCGATTTTCTTCAATTGCGATAGCCATT
Found at i:3863429 original size:19 final size:20
Alignment explanation
Indices: 3863401--3863440 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3863391 CAAGAGAAAA
3863401 TCGCAATGCGATTTTC-AGT
1 TCGCAATGCGATTTTCTAGT
*
3863420 TCGCATTGCGATTTTCTAGT
1 TCGCAATGCGATTTTCTAGT
3863440 T
1 T
3863441 GCGATAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (20 bp):
TCGCAATGCGATTTTCTAGT
Found at i:3863453 original size:20 final size:20
Alignment explanation
Indices: 3863438--3863525 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
3863428 CGATTTTCTA
3863438 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
3863458 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
3863478 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
3863498 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
3863518 GTTGCGAT
1 GTTGCGAT
3863526 TTCCCCATTG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:3863463 original size:34 final size:36
Alignment explanation
Indices: 3863419--3863505 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 36
3863409 CGATTTTCAG
* *
3863419 TTCGCATTGCGATTTTC-T-AGTTGCGATAGCCATT
1 TTCGCGTTGCGATTTTCTTCAATTGCGATAGCCATT
3863453 TTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCATT
1 TTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCATT
3863493 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
3863506 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 11 0.24
35 5 0.11
38 1 0.02
39 1 0.02
40 27 0.60
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (36 bp):
TTCGCGTTGCGATTTTCTTCAATTGCGATAGCCATT
Found at i:3863521 original size:185 final size:186
Alignment explanation
Indices: 3863204--3863578 Score: 743
Period size: 185 Copynumber: 2.0 Consensus size: 186
3863194 AATGAAAATC
3863204 GCAACGAGAAAATCGCAATGCGATTTTCAGTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
1 GCAACGAGAAAATCGCAATGCGATTTTCAGTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
3863269 TCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCG
66 TCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCG
3863334 TTGCGATTTCCCCATTGCGATAGTCAAATGAATTGATAACAACTGAACAGATCATA
131 TTGCGATTTCCCCATTGCGATAGTCAAATGAATTGATAACAACTGAACAGATCATA
3863390 GCAA-GAGAAAATCGCAATGCGATTTTCAGTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
1 GCAACGAGAAAATCGCAATGCGATTTTCAGTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
3863454 TCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCG
66 TCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCG
3863519 TTGCGATTTCCCCATTGCGATAGTCAAATGAATTGATAACAACTGAACAGATCATA
131 TTGCGATTTCCCCATTGCGATAGTCAAATGAATTGATAACAACTGAACAGATCATA
3863575 GCAA
1 GCAA
3863579 TGTTCAAACT
Statistics
Matches: 189, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 185 0.98
186 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (186 bp):
GCAACGAGAAAATCGCAATGCGATTTTCAGTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
TCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCG
TTGCGATTTCCCCATTGCGATAGTCAAATGAATTGATAACAACTGAACAGATCATA
Found at i:3863715 original size:20 final size:21
Alignment explanation
Indices: 3863671--3863722 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3863661 ATAGTCAGTA
*
3863671 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
3863692 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
3863712 TCGCATTGCGA
1 TCGCATTGCGA
3863723 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:3863938 original size:12 final size:12
Alignment explanation
Indices: 3863919--3863952 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3863909 CTCTCCGGCG
3863919 ACATCCGTTCCT
1 ACATCCGTTCCT
*
3863931 ATATCCGTTCCT
1 ACATCCGTTCCT
3863943 ACATCC-TTCC
1 ACATCCGTTCC
3863953 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:3864550 original size:24 final size:23
Alignment explanation
Indices: 3864500--3864552 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
3864490 AGATTCAAAA
* *
3864500 TTTGATCTTGGTCATACCCGGAC
1 TTTGATATTGGTCATACCCAGAC
* *
3864523 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTC-ATACCCAGAC
3864547 TTTGAT
1 TTTGAT
3864553 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (23 bp):
TTTGATATTGGTCATACCCAGAC
Found at i:3867051 original size:19 final size:19
Alignment explanation
Indices: 3867027--3867125 Score: 83
Period size: 19 Copynumber: 5.7 Consensus size: 19
3867017 GCAACGAGAG
*
3867027 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
3867046 AATCGCAACGCG-AAT---
1 AATCGCAACGCGAAATGAA
* *
3867061 -TTCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
3867079 AATCGCAACGCG-AAT---
1 AATCGCAACGCGAAATGAA
* *
3867094 -TTCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
3867112 AATCGCAACGCGAA
1 AATCGCAACGCGAA
3867126 TTTAATTTCG
Statistics
Matches: 61, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 6 0.10
18 6 0.10
19 31 0.51
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3867051 original size:33 final size:33
Alignment explanation
Indices: 3867029--3867128 Score: 200
Period size: 33 Copynumber: 3.0 Consensus size: 33
3867019 AACGAGAGAA
3867029 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
3867062 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
3867095 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
3867128 T
1 T
3867129 AATTTCGCGT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:3867136 original size:19 final size:19
Alignment explanation
Indices: 3867057--3867136 Score: 53
Period size: 19 Copynumber: 4.5 Consensus size: 19
3867047 ATCGCAACGC
*
3867057 GAATTTCGCAATGCGAAAT
1 GAATTTCGCAACGCGAAAT
**
3867076 GAAAATCGCAACGC-----
1 GAATTTCGCAACGCGAAAT
*
3867090 GAATTTCGCAATGCGAAAT
1 GAATTTCGCAACGCGAAAT
** *
3867109 GAAAATCGCAACGCGAATT
1 GAATTTCGCAACGCGAAAT
*
3867128 TAATTTCGC
1 GAATTTCGC
3867137 GTTGCGATTC
Statistics
Matches: 43, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
14 11 0.26
19 32 0.74
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (19 bp):
GAATTTCGCAACGCGAAAT
Found at i:3867303 original size:14 final size:14
Alignment explanation
Indices: 3867284--3867320 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3867274 CATCAATTAA
3867284 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3867298 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3867312 ACAAATCAA
1 ACAAATCAA
3867321 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3868704 original size:21 final size:21
Alignment explanation
Indices: 3868638--3868704 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3868628 GTGAATCGGG
*
3868638 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3868658 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3868680 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3868701 CTCT
1 CTCT
3868705 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3868746 original size:42 final size:42
Alignment explanation
Indices: 3868677--3868756 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
3868667 CGATGACAGT
* * *
3868677 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * *
3868719 GGCCTCTTCAACGATAGGAGTGTACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
3868757 CAGGCGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:3870875 original size:20 final size:19
Alignment explanation
Indices: 3870830--3870948 Score: 78
Period size: 20 Copynumber: 6.7 Consensus size: 19
3870820 TCTTTTGGTT
*
3870830 GAAATGAAAATCGCTACGA
1 GAAATGAAAATCGCAACGA
* *
3870849 GATAATGAGAATCGCAACGTG
1 GA-AATGAAAATCGCAACG-A
**
3870870 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3870889 G--A-G--AATCACAACGA
1 GAAATGAAAATCGCAACGA
*
3870903 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
3870917 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
3870936 GAAATGAAAATCG
1 GAAATGAAAATCG
3870949 TAATGCGATT
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
14 22 0.27
16 2 0.02
17 2 0.02
19 27 0.33
20 28 0.34
21 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:3870902 original size:14 final size:14
Alignment explanation
Indices: 3870883--3870915 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3870873 ATGACTATCG
3870883 CAACGAGAGAATCA
1 CAACGAGAGAATCA
*
3870897 CAACGAGAGAATCG
1 CAACGAGAGAATCA
3870911 CAACG
1 CAACG
3870916 CGAAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.24, G:0.24, T:0.06
Consensus pattern (14 bp):
CAACGAGAGAATCA
Found at i:3870956 original size:19 final size:19
Alignment explanation
Indices: 3870906--3870948 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
3870896 ACAACGAGAG
3870906 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
3870925 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
3870944 AATCG
1 AATCG
3870949 TAATGCGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3870974 original size:19 final size:19
Alignment explanation
Indices: 3870952--3870996 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3870942 AAAATCGTAA
*
3870952 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
3870971 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
3870990 TGCGATT
1 TGCGATT
3870997 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:3871583 original size:20 final size:20
Alignment explanation
Indices: 3871558--3871669 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
3871548 GCTATGTAAA
3871558 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
3871578 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
3871598 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* *
3871619 TCGCATTGCGAT-TTACTAAT
1 TCGCATTGCGATGTAAGT-AT
* * *
3871639 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
*
3871659 TCGCAATGCGA
1 TCGCATTGCGA
3871670 ATTTGGAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 59 0.76
21 16 0.21
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:3871628 original size:41 final size:40
Alignment explanation
Indices: 3871576--3871669 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 40
3871566 CGATAGTAAG
*
3871576 ATTCGCATTGCGATTTACGT-ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTAC-TAATTCGCATTGCGATTTACCT
* *
3871616 AATTCGCATTGCGATTTACTAATTCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACTAATTCGCATTGCGATTTACCT
*
3871657 ATTCGCAATGCGA
1 ATTCGCATTGCGA
3871670 ATTTGGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACTAATTCGCATTGCGATTTACCT
Found at i:3871683 original size:21 final size:21
Alignment explanation
Indices: 3871659--3871731 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
3871649 ATTTACGTAT
*
3871659 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
3871680 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTAGGAAAA
*
3871700 TCGCAATGTGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
3871721 TCGCATTGCGA
1 TCGCAATGCGA
3871732 TAGTCAGTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:3871684 original size:61 final size:61
Alignment explanation
Indices: 3871555--3871684 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 61
3871545 GGCGCTATGT
* * * *
3871555 AAATCGCATTGCGATAGTAAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 AAATCGCATTGCGATACTAAGATTCGCATTGCGATTTACGTATTCGCAATGCGAATTTCCA
* * **
3871616 AATTCGCATTGCGATTTACT-A-ATTCGCGTTGCGATTTACGTATTCGCAATGCGAATTTGGA
1 AAATCGCATTGCGA--TACTAAGATTCGCATTGCGATTTACGTATTCGCAATGCGAATTTCCA
3871677 AAATCGCA
1 AAATCGCA
3871685 ACGCGAATAC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
61 54 0.93
62 1 0.02
63 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (61 bp):
AAATCGCATTGCGATACTAAGATTCGCATTGCGATTTACGTATTCGCAATGCGAATTTCCA
Found at i:3871807 original size:41 final size:40
Alignment explanation
Indices: 3871639--3871807 Score: 115
Period size: 41 Copynumber: 4.1 Consensus size: 40
3871629 ATTTACTAAT
* *
3871639 TCGCGTTGCGATTTACGTATTCGCAATGCGAATTTGGAAAA
1 TCGCATTGCGA-TTACTTATTCGCAATGCGAATTTGGAAAA
** * * * * *
3871680 TCGCAACGCGAATACGTAAATCGCAATGTGAATTAGGAAAA
1 TCGCATTGCGATTAC-TTATTCGCAATGCGAATTTGGAAAA
* * * * ** *
3871721 TCGCATTGCGA-TAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTACTTA-T-TCGCAATGCGAATTTGGAAAA
* * *
3871762 TCGCATTGCGATTTACTTATTCCCATTGCGAATTGGGAAAA
1 TCGCATTGCGA-TTACTTATTCGCAATGCGAATTTGGAAAA
3871803 TCGCA
1 TCGCA
3871808 ACGCGAAATT
Statistics
Matches: 94, Mismatches: 29, Indels: 10
0.71 0.22 0.08
Matches are distributed among these distances:
39 2 0.02
40 5 0.05
41 82 0.87
42 1 0.01
43 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (40 bp):
TCGCATTGCGATTACTTATTCGCAATGCGAATTTGGAAAA
Found at i:3871834 original size:21 final size:22
Alignment explanation
Indices: 3871785--3871834 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3871775 TACTTATTCC
*
3871785 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGGGAAAATAG
**
3871806 CAACGCGAAATT-GGAAAATAG
1 CATTGCGAAATTGGGAAAATAG
3871827 CATTGCGA
1 CATTGCGA
3871835 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGGGAAAATAG
Done.