Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_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: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 16
Found at i:3354627 original size:138 final size:133
Alignment explanation
Indices: 3354444--3354783 Score: 412
Period size: 133 Copynumber: 2.5 Consensus size: 133
3354434 TGAAACAGTA
* * * * * ** *
3354444 TCAAAGTTTATGTTTCAAGGGAAACTATTTCTAGTGGGACGAAATTTTTTTTAAGAAAAACAATC
1 TCAAAGTTTGTGTTTCAAGGGAAACTGTCTCAAGTGAGATAAAATTTATTTTAAGAAAAACAATC
* * *
3354509 TCAATTGAAACGGAATTTATTTTAAGAAAAAAAAATCTCAAGTGAGATAAGATTTCTTTTTAGTG
66 TCAAATGAAACGAAATTT-GTTTAA-AAAAAAAAATCTCAAGTGAGATAAGA--T-TTTTTAGTG
3354574 -AAATGATC
126 AAAAT-ATC
* * * *
3354582 TCAAAGTTTGTGTTTCAAGAGAAACTGTCTCGAGCGAGATAAAATTTGTTTTAAGAAAAACAATC
1 TCAAAGTTTGTGTTTCAAGGGAAACTGTCTCAAGTGAGATAAAATTTATTTTAAGAAAAACAATC
* **
3354647 TCAAATGAGACGAAATTTGTTTAAAAAAAACCATCTCAAGTGAGATAAGATTTTTTAGTGAAAAT
66 TCAAATGAAACGAAATTTGTTTAAAAAAAAAAATCTCAAGTGAGATAAGATTTTTTAGTGAAAAT
3354712 ATC
131 ATC
* * * * *
3354715 TTAAAGTTCGTATTTCGAGGGAAATTGTCTCAAGTGAGATAAAATTTATTTTAAGAAAAACAATC
1 TCAAAGTTTGTGTTTCAAGGGAAACTGTCTCAAGTGAGATAAAATTTATTTTAAGAAAAACAATC
3354780 TCAA
66 TCAA
3354784 GTGAGATAAG
Statistics
Matches: 176, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
133 72 0.41
134 5 0.03
136 24 0.14
137 5 0.03
138 70 0.40
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (133 bp):
TCAAAGTTTGTGTTTCAAGGGAAACTGTCTCAAGTGAGATAAAATTTATTTTAAGAAAAACAATC
TCAAATGAAACGAAATTTGTTTAAAAAAAAAAATCTCAAGTGAGATAAGATTTTTTAGTGAAAAT
ATC
Found at i:3354676 original size:35 final size:36
Alignment explanation
Indices: 3354623--3354691 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
3354613 GAGCGAGATA
*
3354623 AAATTTGTTTTAAGAAAAACAATCTCAAATGAGACG
1 AAATTTGTTTTAAAAAAAACAATCTCAAATGAGACG
* *
3354659 AAATTTG-TTTAAAAAAAACCATCTCAAGTGAGA
1 AAATTTGTTTTAAAAAAAACAATCTCAAATGAGA
3354692 TAAGATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 23 0.77
36 7 0.23
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.28
Consensus pattern (36 bp):
AAATTTGTTTTAAAAAAAACAATCTCAAATGAGACG
Found at i:3354875 original size:101 final size:97
Alignment explanation
Indices: 3354658--3354884 Score: 249
Period size: 101 Copynumber: 2.3 Consensus size: 97
3354648 CAAATGAGAC
* *
3354658 GAAATTTGTTTAAAAAAAACCATCTCAAGTGAGATAAGATTTTTTAGTGAAAATATCTTAAAGTT
1 GAAATTTGTTTAAAAAAAACAATCTCAAGTGAGATAAGATTTTTTAGTGAAAATATCTCAAAGTT
* * * * **
3354723 CGTATTTCGAGGGAAATTGTCTCAAGTGAGAT
66 CATATTTCAAGAGAAACTGTCTCAAGCAAGAT
* * *
3354755 AAAATTTATTTTAAGAAAAACAATCTCAAGTGAGATAAGATTTCTTTTGAGTG-AAATGATCTCA
1 GAAATTT-GTTTAAAAAAAACAATCTCAAGTGAGATAAGA-TT-TTTT-AGTGAAAAT-ATCTCA
* * **
3354819 AAGTTTATGTTTCAAGAGAAACTGTCTTGAGCAAGAT
61 AAGTTCATATTTCAAGAGAAACTGTCTCAAGCAAGAT
*
3354856 GAAATTTGTGTTAATAAAAACAATCTCAA
1 GAAATTTGT-TTAAAAAAAACAATCTCAA
3354885 TTGACATGAA
Statistics
Matches: 106, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
97 6 0.06
98 29 0.27
99 2 0.02
100 9 0.08
101 60 0.57
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (97 bp):
GAAATTTGTTTAAAAAAAACAATCTCAAGTGAGATAAGATTTTTTAGTGAAAATATCTCAAAGTT
CATATTTCAAGAGAAACTGTCTCAAGCAAGAT
Found at i:3354911 original size:36 final size:36
Alignment explanation
Indices: 3354854--3354924 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
3354844 CTTGAGCAAG
*
3354854 ATGAAATTTGTGTTAATAAAAACAATCTCAATTGAC
1 ATGAAATTTGTGTTAAGAAAAACAATCTCAATTGAC
*
3354890 ATGAAATTTGTTTTAAGAAAAACAATCTCAATTGA
1 ATGAAATTTGTGTTAAGAAAAACAATCTCAATTGA
3354925 AATAATATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (36 bp):
ATGAAATTTGTGTTAAGAAAAACAATCTCAATTGAC
Found at i:3355014 original size:137 final size:135
Alignment explanation
Indices: 3354742--3355203 Score: 432
Period size: 136 Copynumber: 3.4 Consensus size: 135
3354732 AGGGAAATTG
* * *
3354742 TCTCAAGTGAGATAAAATTTATTTTAAGAAAAACAATCTCAAGTGAGATAAGATTTCTTTTGAGT
1 TCTCAAGTGAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA-ATATATTTTGAGT
* * * * *
3354807 GAAATGATCTCAAAGTTTATGTTTCAAGAGAAACTGTCT--TGAGCAAGATGAAATTTGTGTTAA
65 GAAATGATCTTAAAGTTTATGTTT-AAGGGAAATTGTCTCATGAG--AGATGAAATTTATTTTAA
*
3354870 TAAAAACAA
127 GAAAAACAA
* * * * * * *
3354879 TCTCAATTGACATGAAATTTGTTTTAAGAAAAACAATCTCAATTGAAATAATATCTATTTTGAAT
1 TCTCAAGTGAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA-ATATATTTTGAGT
* * *
3354944 GAAA-GATCTTAAAGTTTATGTTTGGAGGGAAATTGTCTCATGTGAGACGAAATTT-TTTTCAAG
65 GAAATGATCTTAAAGTTTATGTTT-AAGGGAAATTGTCTCATGAGAGATGAAATTTATTTT-AA-
**
3355007 GGGAAACAA
127 GAAAAACAA
* * * * * *
3355016 CCTCAAGTAAGATAAAAATTTGTTCTAA-AAAGACAATCGCAAGTGAGATAAA-ATGTTTTGAGT
1 TCTCAAGTGAGAT-AAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATATATTTTGAGT
* * * * * * * *
3355079 GAAATTATATTAAAATTTGTGTTTCAGAGGATATTGTCTCATGCGAGATAAAATTTATTTTTAAG
65 GAAATGATCTTAAAGTTTATGTTTAAG-GGAAATTGTCTCATGAGAGATGAAATTTA-TTTTAAG
*
3355144 AAAAACAT
128 AAAAACAA
* * *
3355152 TCTCAAGTGAGATAAAATTTGTTTTAAGAAAAGCAATTTCAAGTAAGATAAA
1 TCTCAAGTGAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
3355204 ATTTCTTTTC
Statistics
Matches: 261, Mismatches: 54, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
135 30 0.11
136 117 0.45
137 95 0.36
138 19 0.07
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.34
Consensus pattern (135 bp):
TCTCAAGTGAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATATATTTTGAGTG
AAATGATCTTAAAGTTTATGTTTAAGGGAAATTGTCTCATGAGAGATGAAATTTATTTTAAGAAA
AACAA
Found at i:3355194 original size:36 final size:36
Alignment explanation
Indices: 3355123--3355212 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
3355113 TGTCTCATGC
*
3355123 GAGATAAAATTTATTTTTAAGAAAAACATTCTCAAGT
1 GAGATAAAATTT-CTTTTAAGAAAAACATTCTCAAGT
* *
3355160 GAGATAAAATTTGTTTTAAGAAAAGCAATT-TCAAGT
1 GAGATAAAATTTCTTTTAAGAAAAAC-ATTCTCAAGT
*
3355196 AAGATAAAATTTCTTTT
1 GAGATAAAATTTCTTTT
3355213 CATATTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
36 33 0.69
37 15 0.31
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (36 bp):
GAGATAAAATTTCTTTTAAGAAAAACATTCTCAAGT
Found at i:3376445 original size:55 final size:55
Alignment explanation
Indices: 3376372--3376937 Score: 722
Period size: 55 Copynumber: 10.2 Consensus size: 55
3376362 AATGCACAAG
* ** *
3376372 TAGTGTCTGTACAATTATTCATCAACTCATGATGAATTCCGTGGTTTTGCTCACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACT
* * * *
3376427 TAGTGCCTGTACGGTTATTCATCATCTCATGATGAATTTCCATAGTTTTTTCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAA-TTCCGT-GGTTTTGCACACT
* * *
3376484 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATGT-TGTGGTTTTGTACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAAT-TCCGTGGTTTTGCACACT
* * * *
3376539 TAGTTCCTGTACAGTTATTCATCAACTCATGATGAATTTTCATGGTTTTGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAA-TTCCGTGGTTTTGCACACT
* * **
3376595 TAGTGCCTATACAGTTATTCATCAACTCATGATGAATTCCGTATTTTTGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACT
* * *
3376650 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTTCGTAGTTTTTCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAA-TTCCGTGGTTTTGCACACT
* * * ** *
3376706 TAGTACCTGTACGAG-TATTCATAAACACATGGGGAATTCCGTAGTTTTGCACACT
1 TAGTGCCTGTACG-GTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACT
* *
3376761 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTTCATGGTTTTGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAA-TTCCGTGGTTTTGCACACT
* * *
3376817 TAGTACATGTACGGTTATTCATCAACACATGATGAATTCCGTGGTTTTGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACT
* * *
3376872 TAGTGCCTGTACGGTTACTCATCAACTCATGATGAATTCCGTAGTTTTGCACAGT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACT
*
3376927 TCGTGCCTGTA
1 TAGTGCCTGTA
3376938 GTACACGTAG
Statistics
Matches: 443, Mismatches: 59, Indels: 18
0.85 0.11 0.03
Matches are distributed among these distances:
54 1 0.00
55 247 0.56
56 149 0.34
57 46 0.10
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (55 bp):
TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACT
Found at i:3376649 original size:111 final size:111
Alignment explanation
Indices: 3376372--3376937 Score: 769
Period size: 111 Copynumber: 5.1 Consensus size: 111
3376362 AATGCACAAG
* * *
3376372 TAGTGTCTGTACAATTATTCATCAACTCATGATGAATTCCGTGGTTTTGCTCACTTAGTGCCTGT
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACTTAGTGCCTGT
* * * *
3376437 ACGGTTATTCATCATCTCATGATGAATTTCCATAGTTTTTTCACACT
66 ACGGTTATTCATCAACTCATGATGAATTTTCAT-GGTTTTGCACACT
* * * * *
3376484 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATGT-TGTGGTTTTGTACACTTAGTTCCTG
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAAT-TCCGTGGTTTTGCACACTTAGTGCCTG
*
3376548 TACAGTTATTCATCAACTCATGATGAATTTTCATGGTTTTGCACACT
65 TACGGTTATTCATCAACTCATGATGAATTTTCATGGTTTTGCACACT
* **
3376595 TAGTGCCTATACAGTTATTCATCAACTCATGATGAATTCCGTATTTTTGCACACTTAGTGCCTGT
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACTTAGTGCCTGT
* * *
3376660 ACGGTTATTCATCAACTCATGATGAATTTTCGTAGTTTTTCACACT
66 ACGGTTATTCATCAACTCATGATGAATTTTCATGGTTTTGCACACT
* * * ** *
3376706 TAGTACCTGTACGAG-TATTCATAAACACATGGGGAATTCCGTAGTTTTGCACACTTAGTGCCTG
1 TAGTGCCTGTAC-AGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACTTAGTGCCTG
3376770 TACGGTTATTCATCAACTCATGATGAATTTTCATGGTTTTGCACACT
65 TACGGTTATTCATCAACTCATGATGAATTTTCATGGTTTTGCACACT
* * * *
3376817 TAGTACATGTACGGTTATTCATCAACACATGATGAATTCCGTGGTTTTGCACACTTAGTGCCTGT
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACTTAGTGCCTGT
* * * * *
3376882 ACGGTTACTCATCAACTCATGATGAA-TTCCGTAGTTTTGCACAGT
66 ACGGTTATTCATCAACTCATGATGAATTTTCATGGTTTTGCACACT
*
3376927 TCGTGCCTGTA
1 TAGTGCCTGTA
3376938 GTACACGTAG
Statistics
Matches: 401, Mismatches: 49, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
110 25 0.06
111 288 0.72
112 87 0.22
113 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (111 bp):
TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACTTAGTGCCTGT
ACGGTTATTCATCAACTCATGATGAATTTTCATGGTTTTGCACACT
Found at i:3377386 original size:20 final size:20
Alignment explanation
Indices: 3377357--3377404 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3377347 GTTTCGAAAT
*
3377357 GGTATCGATACCTTTCC-TTC
1 GGTATCGATA-CTTCCCATTC
*
3377377 GGTATTGATACTTCCCATTC
1 GGTATCGATACTTCCCATTC
3377397 GGTATCGA
1 GGTATCGA
3377405 CACTGATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (20 bp):
GGTATCGATACTTCCCATTC
Found at i:3377543 original size:78 final size:78
Alignment explanation
Indices: 3377414--3377570 Score: 244
Period size: 78 Copynumber: 2.0 Consensus size: 78
3377404 ACACTGATTT
* *
3377414 AAGCAATATCGATACTACTTAACAGATTCATCATATTTTAGCCTATAGTATCGGTATTGTTATAT
1 AAGCAATATCGATACTACTTAACAGATTCATCATATTTTACCCTATAGTATCGGTACTGTTATAT
*
3377479 CAGTACCGATACC
66 CAGTACCGAAACC
* * *
3377492 AAGCAGTATCGATACTACTTAGA-AGATTCATTATATTTTACCCTATAGTATCGGTACTGTTCTA
1 AAGCAATATCGATACTACTTA-ACAGATTCATCATATTTTACCCTATAGTATCGGTACTGTTATA
3377556 TCAGTACCGAAACC
65 TCAGTACCGAAACC
3377570 A
1 A
3377571 GTACCCAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
78 71 0.99
79 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (78 bp):
AAGCAATATCGATACTACTTAACAGATTCATCATATTTTACCCTATAGTATCGGTACTGTTATAT
CAGTACCGAAACC
Found at i:3383033 original size:56 final size:56
Alignment explanation
Indices: 3382904--3383291 Score: 525
Period size: 56 Copynumber: 7.0 Consensus size: 56
3382894 AATGGACAAG
* *
3382904 TAGTGCATGTACGGTTATTCATCAACTCATGATGAA-TTCCGTGGTTTTGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCTGTGGTTTTGCACACT
* * * *
3382959 TAATACCTGTACGGTTATTCATCAACTCATGATGAATTTCCGTGGGTTTGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCTGTGGTTTTGCACACT
* * * *
3383015 TAGTTCCTATACGATTATTCATCAACTCATGATGAATTT-TGTTGTTTTGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCTGTGGTTTTGCACACT
* * *
3383070 TAGTGCATGTGCGGTTATTCATCAACTCATGATGAATTTATGTGGTTTTGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCTGTGGTTTTGCACACT
* * * *
3383126 TAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTT-TTTAGTTTTGAACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCTGTGGTTTTGCACACT
* * *
3383181 TAATGCCTGTACGGTTATTCATCAACTCATGATGAATATATGTGGTTTTGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCTGTGGTTTTGCACACT
** *
3383237 TAGTGTTTGTATGGTGT-TTCATCAACTCATGATGAA-TTCTGTGGTTTTGCACACT
1 TAGTGCCTGTACGGT-TATTCATCAACTCATGATGAATTTCTGTGGTTTTGCACACT
3383292 AAGTTCATGT
Statistics
Matches: 294, Mismatches: 35, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
55 146 0.50
56 147 0.50
57 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (56 bp):
TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCTGTGGTTTTGCACACT
Found at i:3383120 original size:111 final size:111
Alignment explanation
Indices: 3382911--3383291 Score: 532
Period size: 111 Copynumber: 3.4 Consensus size: 111
3382901 AAGTAGTGCA
* * *
3382911 TGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACTTAATACCTGTACGGTTA
1 TGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTTTGCACACTTAATGCATGTACGGTTA
** *
3382976 TTCATCAACTCATGATGAATTTCCGTGGGTTTGCACACTTAGTTCC
66 TTCATCAACTCATGATGAATTTATGTGGTTTTGCACACTTAGTTCC
* * * * * *
3383022 TATACGATTATTCATCAACTCATGATGAATTTTGTTGTTTTGCACACTTAGTGCATGTGCGGTTA
1 TGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTTTGCACACTTAATGCATGTACGGTTA
*
3383087 TTCATCAACTCATGATGAATTTATGTGGTTTTGCACACTTAGTGCC
66 TTCATCAACTCATGATGAATTTATGTGGTTTTGCACACTTAGTTCC
* * * * * *
3383133 TGTACGGTTGTTCATCAACTCATGATGAATTTTTTAGTTTTGAACACTTAATGCCTGTACGGTTA
1 TGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTTTGCACACTTAATGCATGTACGGTTA
* *
3383198 TTCATCAACTCATGATGAATATATGTGGTTTTGCACACTTAGTGT-T
66 TTCATCAACTCATGATGAATTTATGTGGTTTTGCACACTTAGT-TCC
*
3383244 TGTATGGTGT-TTCATCAACTCATGATGAATTCTGTGGTTTTGCACACT
1 TGTACGGT-TATTCATCAACTCATGATGAATTCTGTGGTTTTGCACACT
3383292 AAGTTCATGT
Statistics
Matches: 238, Mismatches: 30, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
111 237 1.00
112 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (111 bp):
TGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTTTGCACACTTAATGCATGTACGGTTA
TTCATCAACTCATGATGAATTTATGTGGTTTTGCACACTTAGTTCC
Found at i:3384468 original size:18 final size:17
Alignment explanation
Indices: 3384414--3384462 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3384404 TTGGACCCTT
* *
3384414 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
3384432 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
3384450 AGTGCATTCGATG
1 AGTGCA-TCGATG
3384463 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:3384531 original size:46 final size:45
Alignment explanation
Indices: 3384433--3384538 Score: 144
Period size: 45 Copynumber: 2.3 Consensus size: 45
3384423 GTGCACTAAG
* * *
3384433 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCTAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACCTAC
3384478 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCT-C
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATA-CCTAC
3384524 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
3384539 GGTATGTGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
45 29 0.53
46 21 0.38
47 5 0.09
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACCTAC
Found at i:3384618 original size:28 final size:28
Alignment explanation
Indices: 3384587--3384642 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3384577 ATTTAATTCA
*
3384587 TGGTGCATTGATGCATGGATTGGTGCAT
1 TGGTGCATCGATGCATGGATTGGTGCAT
3384615 TGGTGCATCGATGCATGGATTGGTGCAT
1 TGGTGCATCGATGCATGGATTGGTGCAT
3384643 CACTCTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.12, G:0.36, T:0.34
Consensus pattern (28 bp):
TGGTGCATCGATGCATGGATTGGTGCAT
Found at i:3387287 original size:23 final size:22
Alignment explanation
Indices: 3387253--3387331 Score: 97
Period size: 23 Copynumber: 3.6 Consensus size: 22
3387243 CATGGCCTTG
3387253 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
* * *
3387276 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
* *
3387297 TGTATTGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
3387319 TGCATCGATGCAC
1 TGCATCGATGCAC
3387332 TATTAGGTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 16 0.36
22 11 0.24
23 18 0.40
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:3387314 original size:21 final size:20
Alignment explanation
Indices: 3387256--3387350 Score: 75
Period size: 21 Copynumber: 4.5 Consensus size: 20
3387246 GGCCTTGTGC
*
3387256 ATCGATGCACATTCAAGGCATGC
1 ATCGATGCACATTC-AGG--TGT
* *
3387279 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCA-GGTGT
* *
3387300 ATTGATGCACATTCAAGGATGC
1 ATCGATGCACATTC-AGG-TGT
3387322 ATCGATGCACTATT-AGGTGT
1 ATCGATGCAC-ATTCAGGTGT
3387342 ATCGATGCA
1 ATCGATGCA
3387351 TTAAGCACAA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
20 11 0.19
21 18 0.31
22 13 0.22
23 17 0.29
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (20 bp):
ATCGATGCACATTCAGGTGT
Found at i:3393275 original size:64 final size:61
Alignment explanation
Indices: 3393115--3393276 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 61
3393105 ACCGTTGGAC
* * *
3393115 CCTTAGTGCATCGGTGCACT-AAGAGTGCATCGATGCATCAAGTGTATTCGATGTTTCAAAATA
1 CCTTAGTGCATCGATGCA-TGAA-A-TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATA
** ***
3393178 GCCAGAGTGCATCGATGCATGGCTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAT
1 -CCTTAGTGCATCGATGCAT-GAAATGCATCGATGCATCAAATGCATTCGATG-TTTCA--AAAT
3393243 -
61 A
3393243 CCTTAGTGCATCGATGCATGAAATGCATTCGATG
1 CCTTAGTGCATCGATGCATGAAATGCA-TCGATG
3393277 TTCAATTTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
63 32 0.41
64 43 0.54
66 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (61 bp):
CCTTAGTGCATCGATGCATGAAATGCATCGATGCATCAAATGCATTCGATGTTTCAAAATA
Found at i:3393598 original size:20 final size:21
Alignment explanation
Indices: 3393573--3393622 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
3393563 TCAACAAAAT
*
3393573 GGTATCGATAACTTCCC-TTC
1 GGTATCGATAACTCCCCTTTC
*
3393593 GGTATCGAT-AGTCCCCTTTC
1 GGTATCGATAACTCCCCTTTC
3393613 GGTATCGATA
1 GGTATCGATA
3393623 CTGATTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (21 bp):
GGTATCGATAACTCCCCTTTC
Found at i:3397306 original size:20 final size:20
Alignment explanation
Indices: 3397278--3397328 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
3397268 CACCCAAGAT
*
3397278 TCCATTGAGCCCAAAGGAAC
1 TCCACTGAGCCCAAAGGAAC
3397298 TCCACTGAGCCCAAAGGAAC
1 TCCACTGAGCCCAAAGGAAC
3397318 TCCACTGAGCC
1 TCCACTGAGCC
3397329 AAGCTCTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.35, G:0.20, T:0.14
Consensus pattern (20 bp):
TCCACTGAGCCCAAAGGAAC
Found at i:3401453 original size:3 final size:3
Alignment explanation
Indices: 3401447--3401524 Score: 138
Period size: 3 Copynumber: 26.0 Consensus size: 3
3401437 TAATGGGTAA
3401447 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
3401495 AAT AAT AAT AAT AAT AAT AGT CAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3401525 GGAATTTGAA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3404360 original size:21 final size:21
Alignment explanation
Indices: 3404334--3404389 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
3404324 AACTTTATGG
* *
3404334 AAGTTTCGAAACTATGACTCG
1 AAGTTTCGAAACTATGACCCA
* *
3404355 GAGTTTTGAAACTATGACCCA
1 AAGTTTCGAAACTATGACCCA
3404376 AAGTTTCGAAACTA
1 AAGTTTCGAAACTA
3404390 ATATCGATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (21 bp):
AAGTTTCGAAACTATGACCCA
Found at i:3418016 original size:29 final size:29
Alignment explanation
Indices: 3417983--3418038 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
3417973 ACTTTTTTTG
3417983 TTGACTTGAT-GAAGTAGTTGTTATGTTCA
1 TTGACTTGATGGAA-TAGTTGTTATGTTCA
3418012 TTGACTTGATGGAATAGTTGTTATGTT
1 TTGACTTGATGGAATAGTTGTTATGTT
3418039 GATATTATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.46
Consensus pattern (29 bp):
TTGACTTGATGGAATAGTTGTTATGTTCA
Found at i:3420004 original size:20 final size:20
Alignment explanation
Indices: 3419976--3420039 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
3419966 TGCAAACACA
*
3419976 CAAAAGCAAAGATGCGAATG
1 CAAATGCAAAGATGCGAATG
** *
3419996 CAAATGCAAAGATATGAATC
1 CAAATGCAAAGATGCGAATG
3420016 CAAATGC-AA-ATGCGTAATG
1 CAAATGCAAAGATGCG-AATG
3420035 CAAAT
1 CAAAT
3420040 ACAACAAATG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 3 0.08
19 10 0.28
20 23 0.64
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.17
Consensus pattern (20 bp):
CAAATGCAAAGATGCGAATG
Found at i:3423286 original size:27 final size:29
Alignment explanation
Indices: 3423248--3423306 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
3423238 TGAGTAATAG
*
3423248 TTAACAATGAGA-ATGCTATGGCAAA-TT
1 TTAACAATGAGATAGGCTATGGCAAAGTT
3423275 TTAAC-ATAGAGATAGGCTATGGCAAAGTT
1 TTAACAAT-GAGATAGGCTATGGCAAAGTT
3423304 TTA
1 TTA
3423307 TTCCTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 9 0.32
28 12 0.43
29 5 0.18
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (29 bp):
TTAACAATGAGATAGGCTATGGCAAAGTT
Found at i:3435465 original size:21 final size:21
Alignment explanation
Indices: 3435411--3435465 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
3435401 CGATACCCAC
3435411 ATCAGTATCGATACTAATTGT
1 ATCAGTATCGATACTAATTGT
*
3435432 ATCCGTATCGATACTAATTGT
1 ATCAGTATCGATACTAATTGT
* *
3435453 ATCAATATTGATA
1 ATCAGTATCGATA
3435466 TTGTTGATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
ATCAGTATCGATACTAATTGT
Found at i:3440846 original size:49 final size:49
Alignment explanation
Indices: 3440775--3441062 Score: 344
Period size: 49 Copynumber: 5.9 Consensus size: 49
3440765 CGATGTTGCC
* * * * *
3440775 AAAA-TAAAGGCATAACGGTGCATTTTGTCATAAAAAGTACCATTAATG
1 AAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCATTAATG
* * *
3440823 AAAATTAAATGCATAACAGTGCATTTCGGCATAAAAGGTGTCATTAATA
1 AAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCATTAATG
* * * * * *
3440872 AAAATTAAATACCTAACGGTGTATTTTGGAATAAAAGGTGCCACTAATG
1 AAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCATTAATG
* *
3440921 AAAATTAAATGCATAACGGTGCATTTCGGCATGAAAGGTGCCACTAATG
1 AAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCATTAATG
* *
3440970 AAAGTTAAAGGCATAACGGTGCATTTCGGCATAAAAGGTGCCATTAATG
1 AAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCATTAATG
* * * * **
3441019 ATAGTTAAATACATAACTGTGCATTATCAACATAAAAGGTGCCA
1 AAAATTAAATGCATAACGGTGCATT-TCGGCATAAAAGGTGCCA
3441063 CCCATGGTAT
Statistics
Matches: 205, Mismatches: 33, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
48 4 0.02
49 185 0.90
50 16 0.08
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (49 bp):
AAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCATTAATG
Found at i:3459956 original size:2 final size:2
Alignment explanation
Indices: 3459949--3460034 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
3459939 CTTTCTATGA
3459949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3459991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3460033 AT
1 AT
3460035 CATCTTAGGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3460601 original size:3 final size:3
Alignment explanation
Indices: 3460593--3460631 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3460583 AAATAAAAAT
3460593 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3460632 CAAAATATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3475147 original size:30 final size:30
Alignment explanation
Indices: 3475111--3475172 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
3475101 TGAGTATACT
3475111 CACTATCATTATTGAACTCAATAACATGAA
1 CACTATCATTATTGAACTCAATAACATGAA
*
3475141 CACTATCATTATTGAACTCGATAACATGAA
1 CACTATCATTATTGAACTCAATAACATGAA
3475171 CA
1 CA
3475173 TTTAATGAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (30 bp):
CACTATCATTATTGAACTCAATAACATGAA
Found at i:3475947 original size:13 final size:13
Alignment explanation
Indices: 3475929--3475955 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3475919 TCATCTCAAG
3475929 TGAAGCATAGATT
1 TGAAGCATAGATT
3475942 TGAAGCATAGATT
1 TGAAGCATAGATT
3475955 T
1 T
3475956 TCGATGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (13 bp):
TGAAGCATAGATT
Found at i:3478013 original size:2 final size:2
Alignment explanation
Indices: 3478006--3478035 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3477996 TTCAAACTAA
3478006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3478036 TCGTTACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3481184 original size:35 final size:36
Alignment explanation
Indices: 3481117--3481184 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
3481107 GTACAGTCAT
*
3481117 TTTTCCTGTACTATTTCATTTTCCTGTACTATTTCA
1 TTTTCCTATACTATTTCATTTTCCTGTACTATTTCA
3481153 TTTTCCTATACTA-TTCATTTTCCTGTACTATT
1 TTTTCCTATACTATTTCATTTTCCTGTACTATT
3481185 CCTTTTTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 19 0.61
36 12 0.39
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (36 bp):
TTTTCCTATACTATTTCATTTTCCTGTACTATTTCA
Found at i:3481190 original size:17 final size:18
Alignment explanation
Indices: 3481117--3481184 Score: 120
Period size: 18 Copynumber: 3.8 Consensus size: 18
3481107 GTACAGTCAT
3481117 TTTTCCTGTACTATTTCA
1 TTTTCCTGTACTATTTCA
3481135 TTTTCCTGTACTATTTCA
1 TTTTCCTGTACTATTTCA
*
3481153 TTTTCCTATACTA-TTCA
1 TTTTCCTGTACTATTTCA
3481170 TTTTCCTGTACTATT
1 TTTTCCTGTACTATT
3481185 CCTTTTTAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.34
18 31 0.66
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTTCCTGTACTATTTCA
Found at i:3494157 original size:2 final size:2
Alignment explanation
Indices: 3494150--3494191 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3494140 GTTATTTATG
3494150 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3494192 CTTTGATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3496693 original size:28 final size:27
Alignment explanation
Indices: 3496653--3496716 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 27
3496643 CTTAAGCCGT
* * * *
3496653 GTTGACTGAGCCGAGTCACGTTGATCGA
1 GTTGATTGAGCCGAGCCAAGTTAATC-A
3496681 GTTGATTGAGCCGAGCCAAGTTAATCA
1 GTTGATTGAGCCGAGCCAAGTTAATCA
3496708 -TTGATTGAG
1 GTTGATTGAG
3496717 TCAAGTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 9 0.28
27 1 0.03
28 22 0.69
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (27 bp):
GTTGATTGAGCCGAGCCAAGTTAATCA
Found at i:3496744 original size:21 final size:21
Alignment explanation
Indices: 3496697--3496738 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3496687 TGAGCCGAGC
*
3496697 CAAGTTAATCATTGATTGAGT
1 CAAGTTAATAATTGATTGAGT
3496718 CAAGTTAATAATTGATTGAGT
1 CAAGTTAATAATTGATTGAGT
3496739 TGAGTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (21 bp):
CAAGTTAATAATTGATTGAGT
Found at i:3498534 original size:39 final size:39
Alignment explanation
Indices: 3498491--3498617 Score: 148
Period size: 39 Copynumber: 3.3 Consensus size: 39
3498481 TCTATGACTT
* * **
3498491 GTAAGTCCTTATTGTAGGCTCATATGCTTTGTGCACTGG
1 GTAAGTCCTTACTGCAGGCTCATATGCTTTGTGCACAAG
* * * *
3498530 GTAAGTCCTTACCGCAGGCT-ACTCTACTTTGTGCTCAAG
1 GTAAGTCCTTACTGCAGGCTCA-TATGCTTTGTGCACAAG
* *
3498569 GTAAGTCCTTACTGCAGGCTCCTTTGCTTTGTGCACAAG
1 GTAAGTCCTTACTGCAGGCTCATATGCTTTGTGCACAAG
3498608 GTAAGTCCTT
1 GTAAGTCCTT
3498618 CCCGTAGACC
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 72 0.99
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (39 bp):
GTAAGTCCTTACTGCAGGCTCATATGCTTTGTGCACAAG
Found at i:3501149 original size:25 final size:23
Alignment explanation
Indices: 3501092--3501181 Score: 69
Period size: 25 Copynumber: 3.8 Consensus size: 23
3501082 ATATTATTTT
* *
3501092 TTTAT-AATAATCTTAATATAAA
1 TTTATAAATAATATTAATATTAA
* *
3501114 TTTGTATATAATTATTAATATTTAA
1 TTTATAAATAA-TATTAATA-TTAA
3501139 TTTATAAATAATTAAATTAA-ATTAA
1 TTTATAAATAA-T--ATTAATATTAA
*
3501164 TATATAAATAA-ATTAATA
1 TTTATAAATAATATTAATA
3501182 AAAAATTACA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
21 5 0.09
22 5 0.09
23 4 0.07
24 7 0.13
25 28 0.51
26 1 0.02
27 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (23 bp):
TTTATAAATAATATTAATATTAA
Found at i:3501161 original size:21 final size:21
Alignment explanation
Indices: 3501137--3501179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3501127 ATTAATATTT
* *
3501137 AATTTATAAATAATTAAATTA
1 AATTAATAAATAAATAAATTA
*
3501158 AATTAATATATAAATAAATTA
1 AATTAATAAATAAATAAATTA
3501179 A
1 A
3501180 TAAAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTAATAAATAAATAAATTA
Found at i:3501948 original size:18 final size:19
Alignment explanation
Indices: 3501927--3501964 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3501917 ACCAGATGAA
*
3501927 GATGAAGATGAAGAC-GAC
1 GATGAAGATCAAGACTGAC
*
3501945 GATGACGATCAAGACTGAC
1 GATGAAGATCAAGACTGAC
3501964 G
1 G
3501965 GCCCCGACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.39, C:0.16, G:0.32, T:0.13
Consensus pattern (19 bp):
GATGAAGATCAAGACTGAC
Found at i:3502316 original size:21 final size:20
Alignment explanation
Indices: 3502282--3502324 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
3502272 TTTTTTTAAC
* *
3502282 TTTTAAAATTTTAAAAATAA
1 TTTTAAAATATTAAAAAAAA
3502302 TTTTATAAATATTAAAAAAAA
1 TTTTA-AAATATTAAAAAAAA
3502323 TT
1 TT
3502325 AATGAACTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTAAAATATTAAAAAAAA
Found at i:3505890 original size:31 final size:32
Alignment explanation
Indices: 3505825--3505890 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
3505815 CCAACCAAAT
*
3505825 TGATTTTTTTGTAAATCGGTCGGTTAACAGTTAA
1 TGATTTTTTTGTAAAT--GTCGATTAACAGTTAA
* *
3505859 TGATTTTTTTTTAAAT-TCGATTATCAGTTAA
1 TGATTTTTTTGTAAATGTCGATTAACAGTTAA
3505890 T
1 T
3505891 TTTGTTCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 14 0.48
34 15 0.52
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (32 bp):
TGATTTTTTTGTAAATGTCGATTAACAGTTAA
Found at i:3506973 original size:26 final size:25
Alignment explanation
Indices: 3506925--3506977 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
3506915 GTTGGTTTGG
*
3506925 TTCTAAAAAATATTTTCTGTTTTTAT
1 TTCTAAAAAATATTTTCT-ATTTTAT
*
3506951 TTCTAGAAAATAGTTTT-TATTTTAT
1 TTCTAAAAAATA-TTTTCTATTTTAT
3506976 TT
1 TT
3506978 TTTTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 12 0.50
27 4 0.17
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (25 bp):
TTCTAAAAAATATTTTCTATTTTAT
Found at i:3508824 original size:38 final size:39
Alignment explanation
Indices: 3508772--3508856 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 39
3508762 GAGTCTATTA
*
3508772 GTAGAACCCACTTGAAAGTACATTAGT-AGAACCCACAT
1 GTAGTACCCACTTGAAAGTACATTAGTAAGAACCCACAT
3508810 GTAGTACCCACTTGAAAGTACATTAGTAGAAGAACCCACAT
1 GTAGTACCCACTTGAAAGTACATTAGT--AAGAACCCACAT
3508851 GTAGTA
1 GTAGTA
3508857 GGGATGGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
38 26 0.60
41 17 0.40
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (39 bp):
GTAGTACCCACTTGAAAGTACATTAGTAAGAACCCACAT
Found at i:3510139 original size:20 final size:20
Alignment explanation
Indices: 3510108--3510145 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3510098 CCTAAGATCT
3510108 AATAAATTAAA-GAAAAATA
1 AATAAATTAAAGGAAAAATA
3510127 AATAAATTTAAAGGAAAAA
1 AATAAA-TTAAAGGAAAAA
3510146 AAAAAGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (20 bp):
AATAAATTAAAGGAAAAATA
Found at i:3510155 original size:21 final size:20
Alignment explanation
Indices: 3510114--3510155 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
3510104 ATCTAATAAA
*
3510114 TTAAAGAAAAATAAATAAAT
1 TTAAAGAAAAATAAAAAAAT
3510134 TTAAAGGAAAAA-AAAAAGAAT
1 TTAAA-GAAAAATAAAAA-AAT
3510155 T
1 T
3510156 AACAAGCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (20 bp):
TTAAAGAAAAATAAAAAAAT
Found at i:3510157 original size:20 final size:20
Alignment explanation
Indices: 3510111--3510157 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3510101 AAGATCTAAT
3510111 AAATTAAAGAAAAATAAATA
1 AAATTAAAGAAAAATAAATA
*
3510131 AATTTAAAGGAAAAA-AAA-A
1 AAATTAAA-GAAAAATAAATA
3510150 AGAATTAA
1 A-AATTAA
3510158 CAAGCATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.09
20 15 0.65
21 6 0.26
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (20 bp):
AAATTAAAGAAAAATAAATA
Found at i:3510729 original size:6 final size:6
Alignment explanation
Indices: 3510710--3510741 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3510700 TATTTTAAAA
3510710 TAAACC TAAA-C TAAACC TAAACC TAAA-C TAAA
1 TAAACC TAAACC TAAACC TAAACC TAAACC TAAA
3510742 ACACACGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAACC
Found at i:3511371 original size:19 final size:20
Alignment explanation
Indices: 3511334--3511371 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3511324 TGTCATAACC
*
3511334 ATTTTTTAAATAATTATTAA
1 ATTTTTTAAATAATAATTAA
3511354 ATTTTTTAAA-AATAATTA
1 ATTTTTTAAATAATAATTA
3511372 TGACTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTTTAAATAATAATTAA
Found at i:3513809 original size:14 final size:15
Alignment explanation
Indices: 3513773--3513819 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
3513763 AAAAATAATG
*
3513773 TAAAATATTTAAATAA
1 TAAAATAATT-AATAA
3513789 -AATAATAATT-ATAA
1 TAA-AATAATTAATAA
3513803 TAAAATAATTAATAA
1 TAAAATAATTAATAA
3513818 TA
1 TA
3513820 TATATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 11 0.41
15 10 0.37
16 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATAATTAATAA
Found at i:3514168 original size:43 final size:44
Alignment explanation
Indices: 3514114--3514310 Score: 126
Period size: 43 Copynumber: 4.5 Consensus size: 44
3514104 ATAACACGGT
3514114 TCCTACGTGATGAGGACGACTGGTTATCTAGGGG-TGACACGAC
1 TCCTACGTGATGAGGACGACTGGTTATCTAGGGGATGACACGAC
** *
3514157 TCCTACGTGATGA-GAATATCTGG---TC--GGGGATGACAC-AGT
1 TCCTACGTGATGAGGACGA-CTGGTTATCTAGGGGATGACACGA-C
* ** * * *
3514196 TCATACGTGATGAGGACGGTTGGCTATCTTTAGGGAAGATAACACGAT
1 TCCTACGTGATGAGGACGACTGGTTATC--TAGGG--GATGACACGAC
* * * * *
3514244 TCCTACGTGATGAGGACGGCTGGTTATCTA-AGGTTGACGCGGC
1 TCCTACGTGATGAGGACGACTGGTTATCTAGGGGATGACACGAC
*
3514287 TCCTACATGATGAGGA-GATCTGGT
1 TCCTACGTGATGAGGACGA-CTGGT
3514311 CGGGAGATGA
Statistics
Matches: 119, Mismatches: 20, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
38 5 0.04
39 21 0.18
40 4 0.03
42 6 0.05
43 43 0.36
45 1 0.01
46 5 0.04
48 33 0.28
49 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (44 bp):
TCCTACGTGATGAGGACGACTGGTTATCTAGGGGATGACACGAC
Found at i:3514267 original size:130 final size:133
Alignment explanation
Indices: 3513982--3514320 Score: 389
Period size: 130 Copynumber: 2.5 Consensus size: 133
3513972 ACACTGCTCA
* ** * * * *
3513982 TACGTGATGAAGA-GGTCTGGTCGTCTAAGGGTGACACGACTCCTAAGTTATTAGGAGATTTGGT
1 TACGTGATGAGGACGG-CTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGT
* ** * *
3514046 CGGTGGATGGCATTGTTCCTACATGATGAGGATGTCTTGCCCATCTTTAGGGATGATGATAACAC
65 CGG-GGATGACACAGTTCATACATGATGAGGACGTCTTGCCCATCTTTAGGGA-GATGATAACAC
*
3514111 GGTTCC
128 GATTCC
* * * *
3514117 TACGTGATGAGGACGACTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGAATATCTGGTC
1 TACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTC
* * * *
3514182 GGGGATGACACAGTTCATACGTGATGAGGACG-GTTGGCTATCTTTAGGGA-A-GATAACACGAT
66 GGGGATGACACAGTTCATACATGATGAGGACGTCTTGCCCATCTTTAGGGAGATGATAACACGAT
3514244 TCC
131 TCC
* * * *
3514247 TACGTGATGAGGACGGCTGGTTATCTAAGGTTGACGCGGCTCCTACATGATGAGGAGATCTGGTC
1 TACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTC
3514312 GGGAGATGA
66 GGG-GATGA
3514321 TATGGTTACT
Statistics
Matches: 173, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
130 73 0.42
131 6 0.03
133 15 0.09
134 24 0.14
135 54 0.31
136 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (133 bp):
TACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTC
GGGGATGACACAGTTCATACATGATGAGGACGTCTTGCCCATCTTTAGGGAGATGATAACACGAT
TCC
Found at i:3514358 original size:130 final size:130
Alignment explanation
Indices: 3514086--3514361 Score: 322
Period size: 130 Copynumber: 2.1 Consensus size: 130
3514076 GATGTCTTGC
* *
3514086 CCATCTTTAGGGATGATGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGA
1 CCATCTTTAGGGA--A-GATAACACGATTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGA
* * ** ***
3514151 CACGACTCCTACGTGATGAGAATATCTGGTCGGGGATGACACAGTTCATACGTGATGAGGACGGT
63 CACGACTCCTACATGATGAGAAGATCTGGTCGGGGATGACACAGTTCATACGCAATGAGGACAAC
*
3514216 TGG
128 TGA
* * * *
3514219 CTATCTTTAGGGAAGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACGC
1 CCATCTTTAGGGAAGATAACACGATTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGACAC
* * * **
3514284 GGCTCCTACATGATGAGGAGATCTGGTCGGGAGATGATATGGTT-ACTACGCAATGAGGACAACT
66 GACTCCTACATGATGAGAAGATCTGGTCGGG-GATGACACAGTTCA-TACGCAATGAGGACAACT
3514348 GA
129 GA
3514350 CCAT-TTTAGGGA
1 CCATCTTTAGGGA
3514362 TTTATTTCAA
Statistics
Matches: 121, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
130 82 0.68
131 27 0.22
133 12 0.10
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (130 bp):
CCATCTTTAGGGAAGATAACACGATTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGACAC
GACTCCTACATGATGAGAAGATCTGGTCGGGGATGACACAGTTCATACGCAATGAGGACAACTGA
Found at i:3514471 original size:65 final size:65
Alignment explanation
Indices: 3514364--3514591 Score: 257
Period size: 65 Copynumber: 3.5 Consensus size: 65
3514354 TTTAGGGATT
* * * * *
3514364 TATTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTCATTTCAAGGAAAACGATCTCAAAGATGA
1 TATTTCAAGAGAAACTGTCTAAAAAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
*
3514429 TATTTTAAGAGAAACTGTCTAAAAAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
1 TATTTCAAGAGAAACTGTCTAAAAAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
* * * * * * *
3514494 TGTTTCAAGAGAAACTATCTCAAGAGAGATAAAATTTTGTTTCAAGGGAAGC-ATACTCAAAGAT
1 TATTTCAAGAGAAACTGTCTAAAAAGAGACAAAA-TTCGTTTCAAGGGAAACGAT-CTCAAAGAT
3514558 --
64 GA
* * *
3514558 TTTTTTAAGAGAAACTGTCTCAAGAA-AGACAAAA
1 TATTTCAAGAGAAACTGTCT-AAAAAGAGACAAAA
3514592 ATTGTTTTGA
Statistics
Matches: 139, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
64 24 0.17
65 91 0.65
66 24 0.17
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (65 bp):
TATTTCAAGAGAAACTGTCTAAAAAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
Found at i:3536658 original size:18 final size:18
Alignment explanation
Indices: 3536611--3536662 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
3536601 CAAATATGTA
*
3536611 AATAATAATAATAATAAT
1 AATAATCATAATAATAAT
*
3536629 AATAATGATAATAATAAT
1 AATAATCATAATAATAAT
*
3536647 AA-AATCCTTAATAATA
1 AATAAT-CATAATAATA
3536663 TATATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 3 0.10
18 27 0.90
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (18 bp):
AATAATCATAATAATAAT
Found at i:3536662 original size:3 final size:3
Alignment explanation
Indices: 3536611--3536648 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3536601 CAAATATGTA
*
3536611 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3536649 AATCCTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3536667 original size:2 final size:2
Alignment explanation
Indices: 3536660--3536692 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3536650 ATCCTTAATA
3536660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3536693 ACACGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3537288 original size:13 final size:14
Alignment explanation
Indices: 3537267--3537306 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 14
3537257 GTCCAAATGT
3537267 AATTGGGTTTTGTG
1 AATTGGGTTTTGTG
3537281 AA-TGGG-TTTGT-
1 AATTGGGTTTTGTG
*
3537292 AATTGGGTTATGTG
1 AATTGGGTTTTGTG
3537306 A
1 A
3537307 TTTGTAATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
11 2 0.09
12 9 0.41
13 8 0.36
14 3 0.14
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (14 bp):
AATTGGGTTTTGTG
Found at i:3540699 original size:18 final size:18
Alignment explanation
Indices: 3540678--3540728 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
3540668 TCGGTCGGAC
3540678 CGGTTCGACCGATTGGAT
1 CGGTTCGACCGATTGGAT
*
3540696 CGGTTCGACCGATTAGAT
1 CGGTTCGACCGATTGGAT
*
3540714 CGATTCGACCGATTG
1 CGGTTCGACCGATTG
3540729 AACCAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (18 bp):
CGGTTCGACCGATTGGAT
Found at i:3540726 original size:9 final size:9
Alignment explanation
Indices: 3540675--3540727 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
3540665 CGATCGGTCG
*
3540675 GACCGGTTC
1 GACCGATTC
*
3540684 GACCGATTG
1 GACCGATTC
* *
3540693 GATCGGTTC
1 GACCGATTC
*
3540702 GACCGATTA
1 GACCGATTC
*
3540711 GATCGATTC
1 GACCGATTC
3540720 GACCGATT
1 GACCGATT
3540728 GAACCAATAA
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (9 bp):
GACCGATTC
Found at i:3543692 original size:28 final size:28
Alignment explanation
Indices: 3543660--3543743 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
3543650 GCACGTAGGA
3543660 GTAGGTCGCCATGCACGCCCAGCGACCT
1 GTAGGTCGCCATGCACGCCCAGCGACCT
* * *
3543688 GTAGGTCGCCATGCACTCCCCGCGACAT
1 GTAGGTCGCCATGCACGCCCAGCGACCT
* *
3543716 GCTAGGTCACCATGCACGCCCGGCGACC
1 G-TAGGTCGCCATGCACGCCCAGCGACC
3543744 AATGCTCCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 26 0.54
29 22 0.46
ACGTcount: A:0.18, C:0.40, G:0.27, T:0.14
Consensus pattern (28 bp):
GTAGGTCGCCATGCACGCCCAGCGACCT
Found at i:3543843 original size:28 final size:28
Alignment explanation
Indices: 3543811--3543872 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
3543801 ACGCCGACCT
3543811 ACATGGAGA-CTTGCACGACGCATGGAGG
1 ACATGGAGATC-TGCACGACGCATGGAGG
3543839 ACATGGAGATCTGCACGACGCATGGAGG
1 ACATGGAGATCTGCACGACGCATGGAGG
*
3543867 ATATGG
1 ACATGG
3543873 CGGCATGCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.35, T:0.16
Consensus pattern (28 bp):
ACATGGAGATCTGCACGACGCATGGAGG
Found at i:3544025 original size:3 final size:3
Alignment explanation
Indices: 3544019--3544082 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
3544009 GATGATGATG
3544019 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3544067 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
3544083 CGGTAAATTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3545749 original size:57 final size:55
Alignment explanation
Indices: 3545587--3545749 Score: 150
Period size: 62 Copynumber: 2.8 Consensus size: 55
3545577 TATAATTTTG
* *
3545587 TTTTGTAAAAGGAATTAAATCGTTGAATTTATTTCTTAAGAATCAAGTATGATTCTA
1 TTTTGTAAAA-GAAATAAATCGTTGAATTTATTT-TTAGGAATCAAGTATGATTCTA
* * *
3545644 TTTAAAAAGAAAGAAAGAAA-ATAATCATTGAATTTATTCTTT-GAGAATCAAGTATGATTCTA
1 TTT----TG-TA-AAAGAAATA-AATCGTTGAATTTATT-TTTAG-GAATCAAGTATGATTCTA
3545706 TTTTGTAATAAGAAATAAATCGTTGAATTTATTTATTAGGAATC
1 TTTTGTAA-AAGAAATAAATCGTTGAATTTATTT-TTAGGAATC
3545750 TTAATATGTT
Statistics
Matches: 85, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
56 2 0.02
57 32 0.38
58 3 0.04
61 2 0.02
62 42 0.49
63 4 0.05
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.39
Consensus pattern (55 bp):
TTTTGTAAAAGAAATAAATCGTTGAATTTATTTTTAGGAATCAAGTATGATTCTA
Found at i:3546999 original size:12 final size:12
Alignment explanation
Indices: 3546982--3547014 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3546972 AGTTTAATAT
3546982 TTTTTAAAATTA
1 TTTTTAAAATTA
3546994 TTTTTAAAATTA
1 TTTTTAAAATTA
3547006 -TTTTAAAAT
1 TTTTTAAAAT
3547015 AATAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTTAAAATTA
Found at i:3547009 original size:11 final size:11
Alignment explanation
Indices: 3546974--3547014 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 11
3546964 TAAAAATGAG
*
3546974 TTTAATATT-T
1 TTTAAAATTAT
3546984 TTTAAAATTATT
1 TTTAAAATTA-T
3546996 TTTAAAATTAT
1 TTTAAAATTAT
3547007 TTTAAAAT
1 TTTAAAAT
3547015 AATAATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 8 0.29
11 9 0.32
12 11 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAAAATTAT
Found at i:3547608 original size:26 final size:28
Alignment explanation
Indices: 3547560--3547623 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
3547550 ATTTTTTTAC
*
3547560 AATTAT-TTTAAAATAAAAATATA-T-A
1 AATTATATTAAAAATAAAAATATATTAA
*
3547585 AATTATATTAAAAATAAAATTATATTAA
1 AATTATATTAAAAATAAAAATATATTAA
3547613 AATTA-ATTAAA
1 AATTATATTAAA
3547624 TAATCCAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 6 0.18
26 15 0.44
27 7 0.21
28 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
AATTATATTAAAAATAAAAATATATTAA
Found at i:3553073 original size:20 final size:20
Alignment explanation
Indices: 3553047--3553101 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
3553037 TACCAGCCCA
3553047 CCAATATCGATACTAAGCAT
1 CCAATATCGATACTAAGCAT
** *
3553067 CTGATATCGATACTAAGCTT
1 CCAATATCGATACTAAGCAT
3553087 CCAATATCGATACTA
1 CCAATATCGATACTA
3553102 CAACCTTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (20 bp):
CCAATATCGATACTAAGCAT
Found at i:3553132 original size:41 final size:40
Alignment explanation
Indices: 3553046--3553139 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 40
3553036 ATACCAGCCC
* *
3553046 ACCAATATCGATACTAAGCATCTGATATCGATACTAAGCT
1 ACCAATATCGATACTAAACATCTGATATCGATACTAAGCG
* * * *
3553086 TCCAATATCGATACTACAACCT-TGTCTATCGATACTAAGGG
1 ACCAATATCGATACTA-AACATCTG-ATATCGATACTAAGCG
3553127 ACCAATATCGATA
1 ACCAATATCGATA
3553140 TCAGTTAATC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 17 0.38
41 28 0.62
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (40 bp):
ACCAATATCGATACTAAACATCTGATATCGATACTAAGCG
Found at i:3555310 original size:19 final size:18
Alignment explanation
Indices: 3555286--3555321 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
3555276 ACTTTAAAAC
3555286 AAAAATTATTAAATATATT
1 AAAAATTATTAAA-ATATT
3555305 AAAAATTATTAAAATAT
1 AAAAATTATTAAAATAT
3555322 GATATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTATTAAAATATT
Found at i:3555316 original size:10 final size:10
Alignment explanation
Indices: 3555286--3555318 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3555276 ACTTTAAAAC
3555286 AAAAATTATT
1 AAAAATTATT
*
3555296 AAATA-TATT
1 AAAAATTATT
3555305 AAAAATTATT
1 AAAAATTATT
3555315 AAAA
1 AAAA
3555319 TATGATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAAATTATT
Found at i:3555330 original size:19 final size:19
Alignment explanation
Indices: 3555289--3555348 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 19
3555279 TTAAAACAAA
3555289 AATTATTAAATATATTAA-A-
1 AATTATTAAA-ATA-TAATAT
*
3555308 AATTATTAAAATATGATAT
1 AATTATTAAAATATAATAT
* *
3555327 AATT-TTAGAATAAAATAT
1 AATTATTAAAATATAATAT
3555345 AATT
1 AATT
3555349 TCGAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.06
18 19 0.54
19 14 0.40
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AATTATTAAAATATAATAT
Found at i:3567063 original size:23 final size:23
Alignment explanation
Indices: 3566981--3567055 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
3566971 ATTATTATAT
*
3566981 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
3567004 GGCATTACGGTGCAATTCTACAC
1 GGCACTACGGTGCAATTCTACGC
* *
3567027 GGCACTATGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
3567050 GGCACT
1 GGCACT
3567056 TTGGTGCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3569409 original size:16 final size:16
Alignment explanation
Indices: 3569388--3569430 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3569378 GGTATTTAAA
3569388 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
3569404 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
3569421 GAGTGATAAG
1 GATTGATAAG
3569431 AACTGATGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:3572093 original size:23 final size:23
Alignment explanation
Indices: 3572042--3572103 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
3572032 ACATTATTAT
*
3572042 ATGGCACTACGGTGCAATTCTAT
1 ATGGCACTACGGTGCAATTCTAC
**
3572065 GCGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
*
3572088 ATGGCACTTCGGTGCA
1 ATGGCACTACGGTGCA
3572104 TTTATATGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:3574348 original size:126 final size:126
Alignment explanation
Indices: 3574210--3574599 Score: 735
Period size: 126 Copynumber: 3.1 Consensus size: 126
3574200 GATCCACTAA
* *
3574210 CAACACCCAAAAGCCAACAAAACTAGTTTTACTAGGATGAAACTTAACCATTTCCCTTGAATCCC
1 CAACACCCAAAAGCCAACAAAACTAGTTTTTCTAGGATGAAACTTAACCTTTTCCCTTGAATCCC
3574275 AAGAACACCCAAATACCCCAAAGCCAAACTTTTCTTAAATCTTAAGCCTAAAATCACCATC
66 AAGAACACCCAAATACCCCAAAGCCAAACTTTTCTTAAATCTTAAGCCTAAAATCACCATC
*
3574336 CAACACTCAAAAGCCAACAAAACTAGTTTTTCTAGGATGAAACTTAACCTTTTCCCTTGAATCCC
1 CAACACCCAAAAGCCAACAAAACTAGTTTTTCTAGGATGAAACTTAACCTTTTCCCTTGAATCCC
3574401 AAGAACACCCAAATACCCCAAAGCCAAACTTTTCTTAAATCTTAAGCCTAAAATCACCATC
66 AAGAACACCCAAATACCCCAAAGCCAAACTTTTCTTAAATCTTAAGCCTAAAATCACCATC
*
3574462 CAACACCCAAAAGCCAACAAAACTAGTTTTTCTAGGATGAAACTTAACCTTTTCCCTTGAATCTC
1 CAACACCCAAAAGCCAACAAAACTAGTTTTTCTAGGATGAAACTTAACCTTTTCCCTTGAATCCC
*
3574527 AAGAACACCCAAATACCCCAAAACCAAACTTTTCTTAAATCTTAAGCCTAAAATCACCATC
66 AAGAACACCCAAATACCCCAAAGCCAAACTTTTCTTAAATCTTAAGCCTAAAATCACCATC
3574588 CAACACCCAAAA
1 CAACACCCAAAA
3574600 CACCAAAACC
Statistics
Matches: 258, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 258 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (126 bp):
CAACACCCAAAAGCCAACAAAACTAGTTTTTCTAGGATGAAACTTAACCTTTTCCCTTGAATCCC
AAGAACACCCAAATACCCCAAAGCCAAACTTTTCTTAAATCTTAAGCCTAAAATCACCATC
Found at i:3575682 original size:15 final size:15
Alignment explanation
Indices: 3575662--3575691 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3575652 ATGTCACACA
3575662 CTAATTATTTAATAT
1 CTAATTATTTAATAT
3575677 CTAATTATTTAATAT
1 CTAATTATTTAATAT
3575692 ATGCAACGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
CTAATTATTTAATAT
Found at i:3576284 original size:15 final size:16
Alignment explanation
Indices: 3576250--3576284 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3576240 AAAGTGAAAC
3576250 AAAAGAACGAAATGCA
1 AAAAGAACGAAATGCA
* *
3576266 AAAAGAATGAAATGTA
1 AAAAGAACGAAATGCA
3576282 AAA
1 AAA
3576285 TGCAAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.17, T:0.11
Consensus pattern (16 bp):
AAAAGAACGAAATGCA
Found at i:3577674 original size:55 final size:55
Alignment explanation
Indices: 3577609--3577832 Score: 294
Period size: 55 Copynumber: 4.1 Consensus size: 55
3577599 ACATAGTGCG
* * *
3577609 TGTACGGTGATTCATCAACTCATGATGAACTCCATGGATTTGTACAC-AAGGTACC
1 TGTACGGTGATTCATCAACTCATGATGAATTCCATGAATATGTACACGAAGGT-CC
3577664 TGTACGGTGATTCATCAACTCATGATGAATTCCATGAATATGTACACGAA-GTGCC
1 TGTACGGTGATTCATCAACTCATGATGAATTCCATGAATATGTACACGAAGGT-CC
* * **
3577719 TATACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCGCACGAAGTGT-C
1 TGTACGGTGATTCATCAACTCATGATGAATTCCATGAATATGTACACGAAG-GTCC
* * *
3577774 TGTACGGTGATTCATCAACTTATGATGAATTCCGTGAATATGAACACGAA-GTGCC
1 TGTACGGTGATTCATCAACTCATGATGAATTCCATGAATATGTACACGAAGGT-CC
3577829 TGTA
1 TGTA
3577833 GTACACATAT
Statistics
Matches: 152, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
53 2 0.01
55 146 0.96
56 2 0.01
57 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (55 bp):
TGTACGGTGATTCATCAACTCATGATGAATTCCATGAATATGTACACGAAGGTCC
Found at i:3580410 original size:25 final size:25
Alignment explanation
Indices: 3580371--3580430 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
3580361 AATAAGAGTA
*
3580371 GCATGTTGTTAATTCATGTGGCATT
1 GCATGTTATTAATTCATGTGGCATT
* *
3580396 GCATGTTATTTATTCATGTTGCATT
1 GCATGTTATTAATTCATGTGGCATT
*
3580421 GCATTTTATT
1 GCATGTTATT
3580431 CATGTTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.50
Consensus pattern (25 bp):
GCATGTTATTAATTCATGTGGCATT
Found at i:3580506 original size:31 final size:31
Alignment explanation
Indices: 3580466--3580527 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
3580456 TAGTATGATA
3580466 CATTACATATTATATGGTTCATAAATAGTAG
1 CATTACATATTATATGGTTCATAAATAGTAG
* *
3580497 CATTGCATATTATATGGTTTATAAATAGTAG
1 CATTACATATTATATGGTTCATAAATAGTAG
3580528 TCCATGTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (31 bp):
CATTACATATTATATGGTTCATAAATAGTAG
Found at i:3584528 original size:26 final size:26
Alignment explanation
Indices: 3584492--3584551 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
3584482 TGAGTTATTA
3584492 AAGATGATGATGGGTTATATGGATAT
1 AAGATGATGATGGGTTATATGGATAT
3584518 AAGATGATGATGGGTTATATGGATAT
1 AAGATGATGATGGGTTATATGGATAT
3584544 AAGATGAT
1 AAGATGAT
3584552 TTGGATAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (26 bp):
AAGATGATGATGGGTTATATGGATAT
Found at i:3586493 original size:22 final size:22
Alignment explanation
Indices: 3586451--3586504 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3586441 GGTACCTATT
*
3586451 TCCTTCGGGATATATAGATAGG
1 TCCTTCGGGATACATAGATAGG
3586473 TCCTTCGGGATACAT-GTATAGG
1 TCCTTCGGGATACATAG-ATAGG
**
3586495 TTATTCGGGA
1 TCCTTCGGGA
3586505 CATATTTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (22 bp):
TCCTTCGGGATACATAGATAGG
Found at i:3586699 original size:12 final size:11
Alignment explanation
Indices: 3586674--3586762 Score: 73
Period size: 10 Copynumber: 8.5 Consensus size: 11
3586664 ATGTGAAGTG
3586674 ATATATGTGAT
1 ATATATGTGAT
3586685 ATATATGTGGAT
1 ATATATGT-GAT
*
3586697 ATATATAT-AT
1 ATATATGTGAT
*
3586707 ATATATAT-AT
1 ATATATGTGAT
*
3586717 ATATATAT-AT
1 ATATATGTGAT
*
3586727 ATATATAT-AT
1 ATATATGTGAT
*
3586737 ATATATAT-AT
1 ATATATGTGAT
*
3586747 ATATATAT-AT
1 ATATATGTGAT
3586757 ATATAT
1 ATATAT
3586763 ATAGTTGTCA
Statistics
Matches: 76, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
10 58 0.76
11 8 0.11
12 10 0.13
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (11 bp):
ATATATGTGAT
Found at i:3586700 original size:2 final size:2
Alignment explanation
Indices: 3586695--3586765 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
3586685 ATATATGTGG
3586695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3586737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3586766 GTTGTCATAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3590373 original size:18 final size:17
Alignment explanation
Indices: 3590338--3590377 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
3590328 ATATGTATTA
*
3590338 CATGATTTGTGTGAATG
1 CATGATTTGTATGAATG
*
3590355 CCATGATTTGTATGTATG
1 -CATGATTTGTATGAATG
3590373 CATGA
1 CATGA
3590378 CTATATTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (17 bp):
CATGATTTGTATGAATG
Found at i:3591486 original size:22 final size:22
Alignment explanation
Indices: 3591454--3591512 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
3591444 GTTACCTATA
3591454 TCCTTCAGGACATATAG-ATAGG
1 TCCTTCAGGACATAT-GCATAGG
* * *
3591476 TCCTTCGGGACACATGCATATG
1 TCCTTCAGGACATATGCATAGG
3591498 TCCTTCAGGACATAT
1 TCCTTCAGGACATAT
3591513 TTCACATGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (22 bp):
TCCTTCAGGACATATGCATAGG
Found at i:3597348 original size:15 final size:15
Alignment explanation
Indices: 3597328--3597357 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3597318 ATGTCATGCA
*
3597328 CTAATTATTTAATAT
1 CTAATTATCTAATAT
3597343 CTAATTATCTAATAT
1 CTAATTATCTAATAT
3597358 ATGCAACGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
CTAATTATCTAATAT
Found at i:3598563 original size:24 final size:24
Alignment explanation
Indices: 3598534--3598589 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
3598524 TAGAAGTTCG
3598534 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
3598558 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
3598582 ATTGAAGC
1 ATTGAAGC
3598590 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:3600800 original size:54 final size:54
Alignment explanation
Indices: 3600718--3600826 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
3600708 GCTAATGGTG
3600718 AATGGTTAAAAAGTACAGCACGATGTAATTAATTGAAGAAGAGTATGAAAGGTC
1 AATGGTTAAAAAGTACAGCACGATGTAATTAATTGAAGAAGAGTATGAAAGGTC
*
3600772 AATGGTTACAAAGTACAGCACGATGTAATTAATTGAAGAAGAGTATGAAAGGTC
1 AATGGTTAAAAAGTACAGCACGATGTAATTAATTGAAGAAGAGTATGAAAGGTC
3600826 A
1 A
3600827 TATGTTCGAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (54 bp):
AATGGTTAAAAAGTACAGCACGATGTAATTAATTGAAGAAGAGTATGAAAGGTC
Found at i:3602190 original size:30 final size:30
Alignment explanation
Indices: 3602123--3602226 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
3602113 CATATCTGAT
* * * *
3602123 TTAAAGGGCAAAAATAGCAAAATCAAAAAAA
1 TTAAAGGACTAAAATAGCAAAAAC-AAAAAC
*
3602154 TTAAAGGACTAAAATAGCAAAAACATAAAC
1 TTAAAGGACTAAAATAGCAAAAACAAAAAC
* * * * *
3602184 TTAAAGGGCTAAAACAACATAAACAGAAAC
1 TTAAAGGACTAAAATAGCAAAAACAAAAAC
*
3602214 TTAAAGGATTAAA
1 TTAAAGGACTAAA
3602227 TAATAAATAT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
30 40 0.66
31 21 0.34
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCAAAAACAAAAAC
Found at i:3602758 original size:2 final size:2
Alignment explanation
Indices: 3602751--3602778 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3602741 CTAGAAGTGA
3602751 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3602779 TTGAGAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3603683 original size:3 final size:3
Alignment explanation
Indices: 3603675--3603717 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3603665 TGTAAGATAT
3603675 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3603718 ATATAATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3604190 original size:131 final size:134
Alignment explanation
Indices: 3603986--3604291 Score: 399
Period size: 131 Copynumber: 2.3 Consensus size: 134
3603976 AGTTCTGGTT
* * ** * *
3603986 ATCTTTAGGAAGG-TGAT-ACATGGTTCCTGCACGATTAGGACGACTGGTTATCTAGGGGTGACA
1 ATCTTTAGG-AGGATGATAACACGGTTCCTACGTGATGAGGACAACTGGTTATCTAGGGGTGACA
* * *
3604049 CGGCTCCTACGTG-ATGAGGAGATCTGGT-AGGTGGATGACACGGTTCCTATGTGATGAGGATGA
65 CGGCACCTACGTGAAT-AGGAGATCTGGTCAGGGGGATGACACGGTTCCTACGTGATGAGGATGA
**
3604112 CATGCC
129 CAAACC
*
3604118 ATCTTTA-G-GGATGATAACACGGTTCCTATGTGATGAGGACAACTGGTTATCTAGGGGTGACAC
1 ATCTTTAGGAGGATGATAACACGGTTCCTACGTGATGAGGACAACTGGTTATCTAGGGGTGACAC
* * *
3604181 GGCACCTACGTGAATAGGAGGTCTGGTCGGGGGGATGATACGGTTCCTACGTGATGAGGATGACA
66 GGCACCTACGTGAATAGGAGATCTGGTCAGGGGGATGACACGGTTCCTACGTGATGAGGATGACA
3604246 AACC
131 AACC
*
3604250 ATCTTTAGGAAGGGTGATAACACGGTTCCTACGTGATGAGGA
1 ATCTTTAGG-AGGATGATAACACGGTTCCTACGTGATGAGGA
3604292 TGGTAGGCCA
Statistics
Matches: 150, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
129 2 0.01
130 4 0.03
131 63 0.42
132 51 0.34
133 1 0.01
135 29 0.19
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (134 bp):
ATCTTTAGGAGGATGATAACACGGTTCCTACGTGATGAGGACAACTGGTTATCTAGGGGTGACAC
GGCACCTACGTGAATAGGAGATCTGGTCAGGGGGATGACACGGTTCCTACGTGATGAGGATGACA
AACC
Found at i:3604333 original size:15 final size:15
Alignment explanation
Indices: 3604315--3604344 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3604305 TTAGGGATAA
*
3604315 TGTCTCAAGGGAGAC
1 TGTCTCAAGAGAGAC
3604330 TGTCTCAAGAGAGAC
1 TGTCTCAAGAGAGAC
3604345 AAAATTCGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (15 bp):
TGTCTCAAGAGAGAC
Found at i:3606107 original size:21 final size:19
Alignment explanation
Indices: 3606083--3606140 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
3606073 ATGTTTAATG
3606083 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
*
3606102 ACAAAAGGATATCAATTGTT-
1 A-AAAA-GATACCAATTGTTA
3606122 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
3606141 CCAATTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 5 0.15
21 12 0.35
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:3606154 original size:28 final size:28
Alignment explanation
Indices: 3606114--3606167 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
3606104 AAAAGGATAT
3606114 CAATTGTTAAAAAGATACCAATTGTTAC
1 CAATTGTTAAAAAGATACCAATTGTTAC
3606142 CAATTGTTAAAAAGATACCAATTGTT
1 CAATTGTTAAAAAGATACCAATTGTT
3606168 GGAAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (28 bp):
CAATTGTTAAAAAGATACCAATTGTTAC
Found at i:3607285 original size:20 final size:20
Alignment explanation
Indices: 3607262--3607310 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
3607252 TCAAATCATG
3607262 TTTCAAAATTTCATTTTGAT
1 TTTCAAAATTTCATTTTGAT
3607282 TTTCAAAATTTCATTTTGAT
1 TTTCAAAATTTCATTTTGAT
3607302 TTTCAAAAT
1 TTTCAAAAT
3607311 CAACTCTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTCAAAATTTCATTTTGAT
Found at i:3609358 original size:21 final size:21
Alignment explanation
Indices: 3609332--3609371 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3609322 GAGCAATCAT
*
3609332 AGGGGTATGGATACCCTTTGA
1 AGGGGTATCGATACCCTTTGA
3609353 AGGGGTATCGATACCCTTT
1 AGGGGTATCGATACCCTTT
3609372 TTCATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
AGGGGTATCGATACCCTTTGA
Found at i:3610184 original size:27 final size:29
Alignment explanation
Indices: 3610154--3610207 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
3610144 CTTGTCTTCT
3610154 TTTTTC-TTTTCTTTT-TCTTTGTTTTAA
1 TTTTTCTTTTTCTTTTCTCTTTGTTTTAA
*
3610181 TTTTTCTTTTTTTTTTCTCTTTGTTTT
1 TTTTTCTTTTTCTTTTCTCTTTGTTTT
3610208 TTCTCTCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.25
28 8 0.33
29 10 0.42
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.81
Consensus pattern (29 bp):
TTTTTCTTTTTCTTTTCTCTTTGTTTTAA
Found at i:3610186 original size:16 final size:14
Alignment explanation
Indices: 3610160--3610209 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 14
3610150 TTCTTTTTTC
3610160 TTTTCTTTTTCTTTG
1 TTTT-TTTTTCTTTG
3610175 TTTTAATTTTTCTTT-
1 TTTT--TTTTTCTTTG
*
3610190 TTTTTTTCTCTTTG
1 TTTTTTTTTCTTTG
3610204 TTTTTT
1 TTTTTT
3610210 CTCTCTGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 8 0.26
14 6 0.19
15 8 0.26
16 9 0.29
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTCTTTG
Found at i:3610197 original size:11 final size:11
Alignment explanation
Indices: 3610150--3610211 Score: 54
Period size: 12 Copynumber: 5.4 Consensus size: 11
3610140 GCTTCTTGTC
3610150 TTCTTTTTTCTT
1 TTCTTTTTT-TT
3610162 TTCTTTTTCTTT
1 TTCTTTTT-TTT
* **
3610174 GT-TTTAATTT
1 TTCTTTTTTTT
3610184 TTCTTTTTTTT
1 TTCTTTTTTTT
3610195 TTCTCTTTGTTTT
1 TTCT-TTT-TTTT
3610208 TTCT
1 TTCT
3610212 CTCTGCTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
10 4 0.10
11 13 0.32
12 14 0.35
13 9 0.22
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.81
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:3610201 original size:13 final size:13
Alignment explanation
Indices: 3610153--3610213 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
3610143 TCTTGTCTTC
*
3610153 TTTTT-TCTTTTC
1 TTTTTCTCTTTTT
3610165 TTTTTCT-TTGTTT
1 TTTTTCTCTT-TTT
3610178 TAATTTT-TCTTTTT
1 T--TTTTCTCTTTTT
*
3610192 TTTTTCTCTTTGT
1 TTTTTCTCTTTTT
3610205 TTTTTCTCT
1 TTTTTCTCT
3610214 CTGCTTTGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 11 0.27
13 19 0.46
14 5 0.12
15 6 0.15
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTTTCTCTTTTT
Found at i:3613931 original size:30 final size:30
Alignment explanation
Indices: 3613895--3613987 Score: 141
Period size: 30 Copynumber: 3.1 Consensus size: 30
3613885 ATTTAAAGGG
* *
3613895 AAAATAGCAAAAACAGAAAATTAAAGGACT
1 AAAATAGCAAAAACATAAACTTAAAGGACT
*
3613925 AAAATAGCAAAAACATAAACTTAAAGGGCT
1 AAAATAGCAAAAACATAAACTTAAAGGACT
* *
3613955 AAAACAGCATAAACATAAACTTAAAGGACT
1 AAAATAGCAAAAACATAAACTTAAAGGACT
3613985 AAA
1 AAA
3613988 CAACAAAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.60, C:0.13, G:0.12, T:0.15
Consensus pattern (30 bp):
AAAATAGCAAAAACATAAACTTAAAGGACT
Found at i:3614003 original size:29 final size:28
Alignment explanation
Indices: 3613904--3614011 Score: 101
Period size: 30 Copynumber: 3.7 Consensus size: 28
3613894 GAAAATAGCA
*
3613904 AAAACAGAAAATTAAAGGACTAAA-ATAGC
1 AAAACAGAAACTTAAAGGACTAAACA-A-C
* * *
3613933 AAAAACATAAACTTAAAGGGCTAAAACAGC
1 -AAAACAGAAACTTAAAGGACT-AAACAAC
*
3613963 ATAAACATAAACTTAAAGGACTAAACAAC
1 A-AAACAGAAACTTAAAGGACTAAACAAC
*
3613992 AAAATTAGAAACTTAAAGGA
1 AAAA-CAGAAACTTAAAGGA
3614012 TTGAATCATA
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
28 3 0.05
29 21 0.32
30 38 0.58
31 3 0.05
32 1 0.02
ACGTcount: A:0.59, C:0.13, G:0.12, T:0.16
Consensus pattern (28 bp):
AAAACAGAAACTTAAAGGACTAAACAAC
Found at i:3615487 original size:3 final size:3
Alignment explanation
Indices: 3615479--3615523 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3615469 GTAAGATATG
3615479 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3615524 ATATAGTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3619193 original size:20 final size:23
Alignment explanation
Indices: 3619168--3619208 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
3619158 GGTGCATTTG
3619168 TTAAAC-CAAA-TGG-CATGACC
1 TTAAACTCAAAGTGGCCATGACC
3619188 TTAAACTCAAAGTGGCCATGA
1 TTAAACTCAAAGTGGCCATGA
3619209 TGAGTTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 3 0.17
23 5 0.28
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (23 bp):
TTAAACTCAAAGTGGCCATGACC
Found at i:3625597 original size:17 final size:17
Alignment explanation
Indices: 3625577--3625609 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3625567 ATATTTATTT
3625577 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
3625594 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
3625610 TGTGATCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:3633044 original size:24 final size:24
Alignment explanation
Indices: 3633016--3633070 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
3633006 TTGGTTCATT
*
3633016 TATGTTCATGAACAAACTCGTTTA
1 TATGTTCACGAACAAACTCGTTTA
* *
3633040 TATGTTCACGAATAAATTCGTTTA
1 TATGTTCACGAACAAACTCGTTTA
*
3633064 TAAGTTC
1 TATGTTC
3633071 GATTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (24 bp):
TATGTTCACGAACAAACTCGTTTA
Found at i:3635253 original size:31 final size:31
Alignment explanation
Indices: 3634649--3635247 Score: 858
Period size: 31 Copynumber: 19.3 Consensus size: 31
3634639 TACATTACAA
* *
3634649 CAATAAACTAGTACATCATTTACATCAATAG
1 CAATAAACCAGTACATCATTTACATCAACAG
* * *
3634680 TAATAAACCAATACATCATTTACATCAACAT
1 CAATAAACCAGTACATCATTTACATCAACAG
*
3634711 CAATAAACCAGTATATCATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
*
3634742 CAATAAACCATTACATCATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
* * * *
3634773 TAATAAACCAATACATTATTTACATCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
*
3634804 CAATAAACCAGTACATCATTTACATCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
* *
3634835 CAATAAACCAGTACATTATTTACATCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
* *
3634866 CAATAAACCAATACATCATTTACATCAACAT
1 CAATAAACCAGTACATCATTTACATCAACAG
* * *
3634897 AAATAAACTAGTACATCATTTACATCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
*
3634928 CAATAAACCAGTACATCATTTACATCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
* *
3634959 TAATAAACCAGTACATCATTTACATTAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
*
3634990 GAATAAACCAGTACATCATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
*
3635021 AAATAAACCAGTACATCATTTACATCAAC-G
1 CAATAAACCAGTACATCATTTACATCAACAG
3635051 ACAATAAACCAGTACATCATTTACATCAACAG
1 -CAATAAACCAGTACATCATTTACATCAACAG
* *
3635083 CAATAACCCAATACATCATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
*
3635114 CAATAAACCAGTACATCATTTACATCAACAT
1 CAATAAACCAGTACATCATTTACATCAACAG
* *
3635145 CAATACACCAGTACATCATTTACATCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
* * * *
3635176 TAATAAATCAATATATCATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
* *
3635207 CAATAAACCAATATATCATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
*
3635238 CAATGAACCA
1 CAATAAACCA
3635248 ATATATATAT
Statistics
Matches: 515, Mismatches: 51, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
30 1 0.00
31 513 1.00
32 1 0.00
ACGTcount: A:0.47, C:0.23, G:0.04, T:0.25
Consensus pattern (31 bp):
CAATAAACCAGTACATCATTTACATCAACAG
Found at i:3635522 original size:6 final size:6
Alignment explanation
Indices: 3635484--3635691 Score: 106
Period size: 6 Copynumber: 35.7 Consensus size: 6
3635474 GTTTTGAATA
* * ** ** * * *
3635484 GTTTGG GTTCGG GTTAGG GTTCAG GTTCAG GTTTGG GTTT-T GTCTCG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * * *
3635531 GTTTGG GTTTGG ATTTGG GTTTAGG GTTTGG G-TTCG ATTTAG ATTTAG
1 GTTTGG GTTTGG GTTTGG GTTT-GG GTTTGG GTTTGG GTTTGG GTTTGG
* * ** * *
3635579 GTTTGT GTTTGT G-TTCA GTTTGG GTTTGG GATTGG GTTTGG GATTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * **
3635626 GTTT-- GTTTGG GATTGG GTTT-- ATTTGG GTTTAT GTTTGG GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * *
3635670 GTTAGG GTCTGG GTTAGG GTTT
1 GTTTGG GTTTGG GTTTGG GTTT
3635692 AAGTTAGGGG
Statistics
Matches: 153, Mismatches: 41, Indels: 16
0.73 0.20 0.08
Matches are distributed among these distances:
4 7 0.05
5 9 0.06
6 131 0.86
7 6 0.04
ACGTcount: A:0.08, C:0.04, G:0.40, T:0.48
Consensus pattern (6 bp):
GTTTGG
Found at i:3635549 original size:12 final size:13
Alignment explanation
Indices: 3635532--3635564 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3635522 TTTGTCTCGG
3635532 TTTGGGTTT-GGA
1 TTTGGGTTTAGGA
*
3635544 TTTGGGTTTAGGG
1 TTTGGGTTTAGGA
3635557 TTTGGGTT
1 TTTGGGTT
3635565 CGATTTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.06, C:0.00, G:0.42, T:0.52
Consensus pattern (13 bp):
TTTGGGTTTAGGA
Found at i:3635635 original size:16 final size:16
Alignment explanation
Indices: 3635614--3635652 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3635604 TTGGGATTGG
3635614 GTTTGGGATTGGGTTT
1 GTTTGGGATTGGGTTT
3635630 GTTTGGGATTGGGTTT
1 GTTTGGGATTGGGTTT
*
3635646 ATTTGGG
1 GTTTGGG
3635653 TTTATGTTTG
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:0.08, C:0.00, G:0.44, T:0.49
Consensus pattern (16 bp):
GTTTGGGATTGGGTTT
Found at i:3635660 original size:28 final size:26
Alignment explanation
Indices: 3635602--3635672 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 26
3635592 TTCAGTTTGG
3635602 GTTTGGGATTGGGTTTGGGATTGGGTTT
1 GTTTGGGATTGGGTTT--GATTGGGTTT
3635630 GTTTGGGATTGGGTTT-ATTTGGGTTTAT
1 GTTTGGGATTGGGTTTGA-TTGGG-TT-T
*
3635658 GTTTGGGTTTGGGTT
1 GTTTGGGATTGGGTT
3635673 AGGGTCTGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 1 0.03
26 5 0.13
27 2 0.05
28 31 0.79
ACGTcount: A:0.07, C:0.00, G:0.42, T:0.51
Consensus pattern (26 bp):
GTTTGGGATTGGGTTTGATTGGGTTT
Found at i:3635697 original size:12 final size:12
Alignment explanation
Indices: 3635650--3635706 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
3635640 GGGTTTATTT
* *
3635650 GGGTTTATGTTT
1 GGGTTTAGGTTA
*
3635662 GGGTTTGGGTTA
1 GGGTTTAGGTTA
* *
3635674 GGGTCTGGGTTA
1 GGGTTTAGGTTA
*
3635686 GGGTTTAAGTTA
1 GGGTTTAGGTTA
*
3635698 GGGGTTAGG
1 GGGTTTAGG
3635707 GAAGATGAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.12, C:0.02, G:0.46, T:0.40
Consensus pattern (12 bp):
GGGTTTAGGTTA
Found at i:3635975 original size:113 final size:108
Alignment explanation
Indices: 3635803--3636123 Score: 439
Period size: 111 Copynumber: 2.9 Consensus size: 108
3635793 ATTTGTGGGG
3635803 TGTTTGATCGAAAAAAACACGAAATGGTTTGGGTTTA-GT-TTTTTGAAGATCAAATGAGGGTTT
1 TGTTTGATC-AAAAAAACACGAAATGGTTT-GGTTTAGGTGTTTTTGAAGATCAAATGAGGGTTT
*
3635866 TGGGGAAGAACTGTGATAAACAAATGAAGAACACAGATGAAAATTTGGA
64 TGGGGAAGAA-T-TGATGAACAAATGAAGAACACA-A-GAAAATTTGGA
3635915 TGTTTGATCAAAAAAACACGAAATGGTTTGTGTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTT
1 TGTTTGATCAAAAAAACACGAAATGGTTTG-GTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTT
* * *
3635980 GGGGGAAGAATTGAATGAACAAATGAAAAACACAAGAATATTTGGG
65 -GGGGAAGAATTG-ATGAACAAATGAAGAACACAAGAAAATTTGGA
* * *
3636026 TGTTTGATAAAAAAAAACACGAAAATGTTTTGGTTTTGGTGTTTTTGAAGATCAAATGAGGGTTT
1 TGTTTGAT-CAAAAAAACACG-AAATGGTTTGGTTTAGGTGTTTTTGAAGATCAAATGAGGGTTT
* *
3636091 TGGAGAAAAATTAGATGAACAAATGAAGAACAC
64 TGGGGAAGAATT-GATGAACAAATGAAGAACAC
3636124 GGTTGATTTT
Statistics
Matches: 191, Mismatches: 10, Indels: 17
0.88 0.05 0.08
Matches are distributed among these distances:
110 1 0.01
111 69 0.36
112 59 0.31
113 53 0.28
114 9 0.05
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (108 bp):
TGTTTGATCAAAAAAACACGAAATGGTTTGGTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTTG
GGGAAGAATTGATGAACAAATGAAGAACACAAGAAAATTTGGA
Found at i:3636221 original size:27 final size:28
Alignment explanation
Indices: 3636177--3636232 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
3636167 AGAGTAAGAG
*
3636177 AGAGAGCAAAATAATG-AAATGAGAAAA
1 AGAGAGCAAAATAATGAAAATGAAAAAA
* **
3636204 AGAGAGGAAAATGCTGAAAATGAAAAAA
1 AGAGAGCAAAATAATGAAAATGAAAAAA
3636232 A
1 A
3636233 TACCTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.62, C:0.04, G:0.23, T:0.11
Consensus pattern (28 bp):
AGAGAGCAAAATAATGAAAATGAAAAAA
Found at i:3636402 original size:61 final size:61
Alignment explanation
Indices: 3636326--3636462 Score: 195
Period size: 61 Copynumber: 2.2 Consensus size: 61
3636316 TCCTAGTTTT
* * * *
3636326 AAATTTGTTCAATTTAGTCCAAATTTAATGA-TACAATATATTAATTTAAGCTTTATATTTC
1 AAATTTGTTCAATTTAGTCAAAATTTAAT-ATTACAATATATTAATCTAAGCTTCATATTTA
* * *
3636387 AAATTTTTTCAATTTAGTCAAAATTTAATATTACAGTTTATTAATCTAAGCTTCATATTTA
1 AAATTTGTTCAATTTAGTCAAAATTTAATATTACAATATATTAATCTAAGCTTCATATTTA
3636448 AAATTTGTTCAATTT
1 AAATTTGTTCAATTT
3636463 GATCCATATA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 1 0.01
61 66 0.99
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.47
Consensus pattern (61 bp):
AAATTTGTTCAATTTAGTCAAAATTTAATATTACAATATATTAATCTAAGCTTCATATTTA
Found at i:3636575 original size:16 final size:16
Alignment explanation
Indices: 3636554--3636889 Score: 140
Period size: 16 Copynumber: 20.5 Consensus size: 16
3636544 TGAAATTTTC
3636554 AATATAGTTTATATAT
1 AATATAGTTTATATAT
3636570 AATATAGTTTATATAGT
1 AATATAGTTTATATA-T
* *
3636587 AATGA-ACTATATA-AT
1 AAT-ATAGTTTATATAT
* *
3636602 -ATATAGTTTGTATAC
1 AATATAGTTTATATAT
* * *
3636617 CATATACTATATAGGTAT
1 AATATAGTTTATA--TAT
* **
3636635 ATATACTAATGCACTATAT
1 A-ATA-TAGTTTA-TATAT
3636654 AATATAGTTGTATATACT
1 AATATAGTT-TATATA-T
3636672 -A-ATAGTTTATATAT
1 AATATAGTTTATATAT
* ** *
3636686 ACTA-A-TGAACTACAT
1 AATATAGTTTA-TATAT
3636701 AATATAGTTTATATAT
1 AATATAGTTTATATAT
* **
3636717 ACTA-ATGAAATATATAT
1 AATATA-G-TTTATATAT
*
3636734 AATGTAG-TTATATAT
1 AATATAGTTTATATAT
3636749 ACCATATAGTTTATATAT
1 A--ATATAGTTTATATAT
*
3636767 TATATAGTTTATATAT
1 AATATAGTTTATATAT
* * *
3636783 AATAAACTATATA-AT
1 AATATAGTTTATATAT
* *
3636798 -GTATAGTTTTTATAT
1 AATATAGTTTATATAT
3636813 ACCATATAGTTTATATACT
1 A--ATATAGTTTATATA-T
**
3636832 AATGA-ACGACTATATAT
1 AAT-ATA-GTTTATATAT
3636849 -ATATAGTTTATATAT
1 AATATAGTTTATATAT
*
3636864 ATTATACAGTTTATATAT
1 A--ATATAGTTTATATAT
*
3636882 ACTATAGT
1 AATATAGT
3636890 ATAATTATTT
Statistics
Matches: 235, Mismatches: 51, Indels: 68
0.66 0.14 0.19
Matches are distributed among these distances:
13 1 0.00
14 17 0.07
15 38 0.16
16 73 0.31
17 39 0.17
18 52 0.22
19 9 0.04
20 4 0.02
21 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (16 bp):
AATATAGTTTATATAT
Done.