Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009086.1 Hibiscus syriacus cultivar Beakdansim tig00112530_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: 1596699
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:791133 original size:23 final size:23
Alignment explanation
Indices: 791107--791151 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
791097 CACCACAGCT
*
791107 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
791130 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
791152 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:791294 original size:25 final size:25
Alignment explanation
Indices: 791266--791334 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
791256 TATATATATA
791266 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
791291 TCCCGAAGGACCGCATAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
791316 TCCCGAATGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
791335 CCCTCTACTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:793001 original size:64 final size:63
Alignment explanation
Indices: 792903--793063 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 63
792893 TAATGAAGGT
* * *
792903 ATGCATCGATGCACTACACCATGCATCGATGCATATATCATATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCACATTCGATGTTTTGTATTTAAAT--
792966 AG
62 AG
* * **
792968 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCCATTCGATGTTTTTTATTTAAATTT
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCACATTCGATGTTTTGTATTTAAATAG
* *
793032 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
793064 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 55 0.66
65 24 0.29
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCACATTCGATGTTTTGTATTTAAATAG
Found at i:802180 original size:32 final size:32
Alignment explanation
Indices: 802139--802211 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
802129 AAAATGGACG
*
802139 TTTTGTAACAGTTTGATAAAACTTAATGAGCA
1 TTTTGTAACAGTTTGATAAAACTTAACGAGCA
*
802171 TTTTGTAACAGTTTGATAAAATTTAACGAGCA
1 TTTTGTAACAGTTTGATAAAACTTAACGAGCA
802203 TTTTGTAAC
1 TTTTGTAAC
802212 TTTGAAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.40
Consensus pattern (32 bp):
TTTTGTAACAGTTTGATAAAACTTAACGAGCA
Found at i:804785 original size:338 final size:337
Alignment explanation
Indices: 804170--804846 Score: 1336
Period size: 338 Copynumber: 2.0 Consensus size: 337
804160 TTCCTGTCTC
804170 ACGGCTGCACCGGTTTTTGGTCCAACTTCTGTTTTTCTTCAGGCATAGTTAGATTGCCAGAAAAA
1 ACGGCTGCACCGGTTTTTGGTCCAACTTCTGTTTTTCTTCAGGCATAGTTAGATTGCCAGAAAAA
804235 AAAAACTCTATCATGTCACTTTGTTTAACATTGAGAACTGTTTAGGTACTATCAAAGTGTGCAAA
66 AAAAACTCTATCATGTCACTTTGTTTAACATTGAGAACTGTTTAGGTACTATCAAAGTGTGCAAA
804300 AGAAACATATATTGGATCCAAACATAAACTCACAGGTCCTATAGTGCTAACTTTTGGAGTCTGCA
131 AGAAACATATATTGGATCCAAACATAAACTCACAGGTCCTATAGTGCTAACTTTTGGAGTCTGCA
804365 ATATTAGTTCGGTTCATTTAGGAAGGGAAACGAAGTAAAAGGACAGGCAGCAACGACAAATCTAA
196 ATATTAGTTCGGTTCATTTAGGAAGGGAAACGAAGTAAAAGGACAGGCAGCAACGACAAATCTAA
804430 CAAATTACAGCCTCAAGAAAGATTCGATACAAGCAAAAGCCAAGGAACAATCAACTTATATCCAC
261 CAAATTACAGCCTCAAGAAAGATTCGATACAAGCAAAAGCCAAGGAACAATCAACTTATATCCAC
804495 ACGATTTCAACA
326 ACGATTTCAACA
*
804507 ACGGCTGCACTGGTTTTTGGTCCAACTTCTGTTTTTCTTCAGGCATAGTTAGATTGCCAGAAAAA
1 ACGGCTGCACCGGTTTTTGGTCCAACTTCTGTTTTTCTTCAGGCATAGTTAGATTGCCAG-AAAA
804572 AAAAAACTCTATCATGTCACTTTGTTTAACATTGAGAACTGTTTAGGTACTATCAAAGTGTGCAA
65 AAAAAACTCTATCATGTCACTTTGTTTAACATTGAGAACTGTTTAGGTACTATCAAAGTGTGCAA
804637 AAGAAACATATATTGGATCCAAACATAAACTCACAGGTCCTATAGTGCTAACTTTTGGAGTCTGC
130 AAGAAACATATATTGGATCCAAACATAAACTCACAGGTCCTATAGTGCTAACTTTTGGAGTCTGC
804702 AATATTAGTTCGGTTCATTTAGGAAGGGAAACGAAGTAAAAGGACAGGCAGCAACGACAAATCTA
195 AATATTAGTTCGGTTCATTTAGGAAGGGAAACGAAGTAAAAGGACAGGCAGCAACGACAAATCTA
804767 ACAAATTACAGCCTCAAGAAAGATTCGATACAAGCAAAAGCCAAGGAACAATCAACTTATATCCA
260 ACAAATTACAGCCTCAAGAAAGATTCGATACAAGCAAAAGCCAAGGAACAATCAACTTATATCCA
804832 CACGATTTCAACA
325 CACGATTTCAACA
804845 AC
1 AC
804847 AAACCGTATT
Statistics
Matches: 338, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
337 59 0.17
338 279 0.83
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (337 bp):
ACGGCTGCACCGGTTTTTGGTCCAACTTCTGTTTTTCTTCAGGCATAGTTAGATTGCCAGAAAAA
AAAAACTCTATCATGTCACTTTGTTTAACATTGAGAACTGTTTAGGTACTATCAAAGTGTGCAAA
AGAAACATATATTGGATCCAAACATAAACTCACAGGTCCTATAGTGCTAACTTTTGGAGTCTGCA
ATATTAGTTCGGTTCATTTAGGAAGGGAAACGAAGTAAAAGGACAGGCAGCAACGACAAATCTAA
CAAATTACAGCCTCAAGAAAGATTCGATACAAGCAAAAGCCAAGGAACAATCAACTTATATCCAC
ACGATTTCAACA
Found at i:815666 original size:27 final size:27
Alignment explanation
Indices: 815628--815709 Score: 137
Period size: 27 Copynumber: 3.0 Consensus size: 27
815618 CTTCAGTTTG
815628 AACAGCAGCGGCAGTTGGAACTTCAGC
1 AACAGCAGCGGCAGTTGGAACTTCAGC
* *
815655 AACAGAAGCGGCAGTTGAAACTTCAGC
1 AACAGCAGCGGCAGTTGGAACTTCAGC
*
815682 AACAGCAGCGGCTGTTGGAACTTCAGC
1 AACAGCAGCGGCAGTTGGAACTTCAGC
815709 A
1 A
815710 GCGGCGGCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (27 bp):
AACAGCAGCGGCAGTTGGAACTTCAGC
Found at i:815750 original size:30 final size:30
Alignment explanation
Indices: 815630--815750 Score: 110
Period size: 27 Copynumber: 4.2 Consensus size: 30
815620 TCAGTTTGAA
*
815630 CAGCAGCGGCAGTTGGAACTTCAGCA--A-
1 CAGCAGCAGCAGTTGGAACTTCAGCAGCAG
* * *
815657 CAGAAGCGGCAGTTGAAACTTCAGCA--A-
1 CAGCAGCAGCAGTTGGAACTTCAGCAGCAG
* * *
815684 CAGCAGCGGCTGTTGGAACTTCAGCAGCGG
1 CAGCAGCAGCAGTTGGAACTTCAGCAGCAG
* * *
815714 CGGCAGCAGCAGTTGGAGCTTCAGCGGCAG
1 CAGCAGCAGCAGTTGGAACTTCAGCAGCAG
815744 CAGCAGC
1 CAGCAGC
815751 TGGAACATAT
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
27 48 0.62
30 30 0.38
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.14
Consensus pattern (30 bp):
CAGCAGCAGCAGTTGGAACTTCAGCAGCAG
Found at i:815770 original size:27 final size:27
Alignment explanation
Indices: 815740--815847 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 27
815730 AGCTTCAGCG
815740 GCAGCAGCAGCTGGAACATATATGGGA
1 GCAGCAGCAGCTGGAACATATATGGGA
815767 GCAGCAGCAGCTGGAACAGCTGGAACGTATGCGGGA
1 GCAGCAGCAGCTGGAACA--T---A--TAT--GGGA
* ** *
815803 GCAGCAGCAGCTGGAACGTATGCGAGA
1 GCAGCAGCAGCTGGAACATATATGGGA
815830 GCAGCAGCAGCTGGAACA
1 GCAGCAGCAGCTGGAACA
815848 GCTGAAACGT
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
27 38 0.57
29 2 0.03
31 1 0.01
32 1 0.01
34 4 0.06
36 21 0.31
ACGTcount: A:0.31, C:0.22, G:0.36, T:0.11
Consensus pattern (27 bp):
GCAGCAGCAGCTGGAACATATATGGGA
Found at i:815787 original size:36 final size:36
Alignment explanation
Indices: 815747--815819 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
815737 GCGGCAGCAG
*
815747 CAGCTGGAACATATATGGGAGCAGCAGCAGCTGGAA
1 CAGCTGGAACATATACGGGAGCAGCAGCAGCTGGAA
* *
815783 CAGCTGGAACGTATGCGGGAGCAGCAGCAGCTGGAA
1 CAGCTGGAACATATACGGGAGCAGCAGCAGCTGGAA
815819 C
1 C
815820 GTATGCGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.30, C:0.22, G:0.36, T:0.12
Consensus pattern (36 bp):
CAGCTGGAACATATACGGGAGCAGCAGCAGCTGGAA
Found at i:815810 original size:63 final size:63
Alignment explanation
Indices: 815740--815874 Score: 216
Period size: 63 Copynumber: 2.1 Consensus size: 63
815730 AGCTTCAGCG
* * * *
815740 GCAGCAGCAGCTGGAACATATATGGGAGCAGCAGCAGCTGGAACAGCTGGAACGTATGCGGGA
1 GCAGCAGCAGCTGGAACATATACGAGAGCAGCAGCAGCTGGAACAGCTGAAACGTATGCGAGA
* *
815803 GCAGCAGCAGCTGGAACGTATGCGAGAGCAGCAGCAGCTGGAACAGCTGAAACGTATGCGAGA
1 GCAGCAGCAGCTGGAACATATACGAGAGCAGCAGCAGCTGGAACAGCTGAAACGTATGCGAGA
815866 GCAGCAGCA
1 GCAGCAGCA
815875 TCATAACCAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.31, C:0.22, G:0.36, T:0.11
Consensus pattern (63 bp):
GCAGCAGCAGCTGGAACATATACGAGAGCAGCAGCAGCTGGAACAGCTGAAACGTATGCGAGA
Found at i:815832 original size:24 final size:26
Alignment explanation
Indices: 815783--815846 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 26
815773 GCAGCTGGAA
815783 CAGCTGGAACGTATGCGGGAGCAGCAG
1 CAGCTGGAACGTATGC-GGAGCAGCAG
815810 CAGCTGGAACGTATGCGAGAGCAGCAG
1 CAGCTGGAACGTATGCG-GAGCAGCAG
815837 CAGCTGGAAC
1 CAGCTGGAAC
815847 AGCTGAAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.28, C:0.23, G:0.38, T:0.11
Consensus pattern (26 bp):
CAGCTGGAACGTATGCGGAGCAGCAG
Found at i:819151 original size:16 final size:16
Alignment explanation
Indices: 819130--819162 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
819120 CAAAAGTTAC
819130 AACTTACAAGATTCTA
1 AACTTACAAGATTCTA
819146 AACTTACAAGATTCTA
1 AACTTACAAGATTCTA
819162 A
1 A
819163 GTCATGCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.30
Consensus pattern (16 bp):
AACTTACAAGATTCTA
Found at i:824250 original size:14 final size:14
Alignment explanation
Indices: 824206--824250 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
824196 ATCGCTTGTC
824206 ATGCATGCATATCA
1 ATGCATGCATATCA
*
824220 ATACATGCATATCA
1 ATGCATGCATATCA
824234 ATGCATGCATATCA
1 ATGCATGCATATCA
824248 ATG
1 ATG
824251 ACTTTAGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (14 bp):
ATGCATGCATATCA
Found at i:826645 original size:21 final size:20
Alignment explanation
Indices: 826559--826716 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
826549 AAATGACCAA
**
826559 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
826578 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
826598 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
826618 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
826639 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
826660 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
826680 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
826701 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
826717 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:826747 original size:40 final size:40
Alignment explanation
Indices: 826683--826834 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
826673 CGATTTTCCA
* ** * *
826683 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAACACAT
* * *
826723 AAATCGCAACGTGTATCCGTAAATCGCAAC-ATATATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAGA-A-CACAT
* * *
826763 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAACACAT
826803 AAAATCGCAACGCGTATCCGTAAATCGCAACG
1 -AAATCGCAACGCGTATCCGTAAATCGCAACG
826835 CGATATTTAA
Statistics
Matches: 94, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.01
40 59 0.63
41 34 0.36
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGAGAACACAT
Found at i:826835 original size:20 final size:20
Alignment explanation
Indices: 826683--826836 Score: 141
Period size: 20 Copynumber: 7.7 Consensus size: 20
826673 CGATTTTCCA
* ** *
826683 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
826703 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
826723 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
***
826743 AAATCGCAACATATATCCGT
1 AAATCGCAACGCGTATCCGT
*
826763 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
826783 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
826803 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
826824 AAATCGCAACGCG
1 AAATCGCAACGCG
826837 ATATTTAAAG
Statistics
Matches: 108, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.02
20 88 0.81
21 17 0.16
22 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:827258 original size:33 final size:33
Alignment explanation
Indices: 827219--827289 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
827209 TTCACTTAGA
*
827219 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
827252 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
827285 TTTCA
1 TTTCA
827290 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:827413 original size:20 final size:20
Alignment explanation
Indices: 827369--827478 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
827359 TGCAGAAGAG
*
827369 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
827390 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
827410 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
827431 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
827445 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
827464 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
827479 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:827426 original size:41 final size:38
Alignment explanation
Indices: 827362--827478 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
827352 TTCAATTTGC
* *
827362 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
827400 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
827441 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
827474 AGAAT
1 AGAAT
827479 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:827448 original size:14 final size:14
Alignment explanation
Indices: 827429--827485 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
827419 GAGAAATGAA
827429 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
827443 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
827462 AATCGCAACGAGAG
1 AATCGCAACGAGAG
827476 AATCGCAACG
1 AATCGCAACG
827486 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:827461 original size:33 final size:33
Alignment explanation
Indices: 827421--827501 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
827411 CGCAACGAGA
827421 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
827454 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
827487 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
827502 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:827519 original size:19 final size:19
Alignment explanation
Indices: 827497--827580 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
827487 GAAACCAAAA
*
827497 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
827516 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
827535 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
827549 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
827568 TCGCGTTGCGATT
1 TCGCGTTGCGATT
827581 CTCTCGTTGC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 41 0.72
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:827557 original size:14 final size:14
Alignment explanation
Indices: 827538--827594 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
827528 TTTCATTTCG
827538 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
827552 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
827571 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
827585 CGTTGCGATT
1 CGTTGCGATT
827595 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:827561 original size:33 final size:33
Alignment explanation
Indices: 827519--827602 Score: 168
Period size: 33 Copynumber: 2.5 Consensus size: 33
827509 TTTCATTTCG
827519 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
827552 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
827585 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
827603 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:829606 original size:93 final size:93
Alignment explanation
Indices: 829301--829583 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
829291 TAGATTGCTT
*
829301 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
829366 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
829394 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
829459 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
829487 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
829552 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
829579 AGTAA
1 AGTAA
829584 TGCAATCCAT
Statistics
Matches: 189, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
92 6 0.03
93 183 0.97
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:829671 original size:19 final size:19
Alignment explanation
Indices: 829631--829759 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
829621 TAGTTTACTT
* *
829631 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
829651 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* **
829670 TCGCAACACGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
829689 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
829703 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
829722 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
829736 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
829755 TCGCA
1 TCGCA
829760 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:829715 original size:33 final size:32
Alignment explanation
Indices: 829667--829759 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
829657 CGCGAAACCA
* **
829667 AAATCGCAACACGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
829699 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
829732 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
829760 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:829757 original size:52 final size:52
Alignment explanation
Indices: 829631--829759 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
829621 TAGTTTACTT
**
829631 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACACGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACACGAAA
* * *
829683 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAAC-ACGAA-A
*
829736 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
829760 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.66
53 4 0.06
54 6 0.10
55 2 0.03
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACACGAAA
Found at i:829777 original size:19 final size:18
Alignment explanation
Indices: 829755--829873 Score: 110
Period size: 19 Copynumber: 6.8 Consensus size: 18
829745 GAAACCAAAA
*
829755 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
829774 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
*
829790 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
*
829807 TCGCGTTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
829823 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
*
829840 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
829859 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
829874 AAGTTTCGTG
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 16 0.19
16 10 0.12
17 10 0.12
19 47 0.57
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:829796 original size:14 final size:14
Alignment explanation
Indices: 829777--829833 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
829767 TTTCATTTCG
829777 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
829791 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
829808 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
829824 CGTTGCGATT
1 CGTTGCGATT
829834 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:829802 original size:33 final size:33
Alignment explanation
Indices: 829760--829852 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
829750 CAAAATCGCA
*
829760 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
**
829793 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
829826 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
829853 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:829881 original size:20 final size:19
Alignment explanation
Indices: 829755--829889 Score: 105
Period size: 19 Copynumber: 7.6 Consensus size: 19
829745 GAAACCAAAA
*
829755 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
829774 TCGCGTTGCGA--TT-CTT
1 TCGCGTTGCGATTTTAGTT
*
829790 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
*
829807 TCGCGTTGCGATTCT-G--
1 TCGCGTTGCGATTTTAGTT
829823 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
829840 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
829859 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-AGTT
*
829879 TCGTGTTGCGA
1 TCGCGTTGCGA
829890 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 7, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
14 19 0.20
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAGTT
Found at i:831833 original size:14 final size:14
Alignment explanation
Indices: 831814--831849 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
831804 ATTGTTTAAT
831814 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
831828 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
831842 TGATTTGT
1 TGATTTGT
831850 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:831980 original size:19 final size:19
Alignment explanation
Indices: 831956--832053 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
831946 AAAATTGACT
831956 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
831975 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
831994 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
832008 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
832027 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
832047 ATCGCAA
1 ATCGCAA
832054 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:832085 original size:53 final size:53
Alignment explanation
Indices: 831956--832072 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
831946 AAAATTGACT
*
831956 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
832008 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
832061 ATCGCAATGCGA
1 ATCGCAATGCGA
832073 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:832090 original size:19 final size:19
Alignment explanation
Indices: 832062--832264 Score: 194
Period size: 19 Copynumber: 11.7 Consensus size: 19
832052 AACGGGAGAA
* *
832062 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
832081 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
832097 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
832114 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
832133 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
832149 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
832166 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
832185 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
* *
832199 TCCCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
832218 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
832236 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
832252 TCGCATTGCGATT
1 TCGCATTGCGATT
832265 CTCTCGTTGC
Statistics
Matches: 151, Mismatches: 12, Indels: 42
0.74 0.06 0.20
Matches are distributed among these distances:
14 32 0.21
16 19 0.13
17 17 0.11
18 1 0.01
19 68 0.45
20 14 0.09
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:832125 original size:52 final size:52
Alignment explanation
Indices: 832062--832236 Score: 314
Period size: 52 Copynumber: 3.3 Consensus size: 52
832052 AACGGGAGAA
* *
832062 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
832114 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
832166 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCCCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
832218 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
832237 GTTGGGATTT
Statistics
Matches: 119, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 102 0.86
53 17 0.14
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:832286 original size:33 final size:33
Alignment explanation
Indices: 832068--832278 Score: 214
Period size: 33 Copynumber: 6.2 Consensus size: 33
832058 AGAATCGCAA
*
832068 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
832101 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
832139 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
*
832172 TGCGATTTTCATTTCGCATTGCGATTCTCCCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
832205 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
832239 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
832272 TGCGATT
1 TGCGATT
832279 GTAATTTCCG
Statistics
Matches: 146, Mismatches: 18, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 71 0.49
34 29 0.20
35 5 0.03
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:834793 original size:24 final size:24
Alignment explanation
Indices: 834759--834805 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
834749 CTGAAACATC
834759 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
834783 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
834806 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:835516 original size:20 final size:20
Alignment explanation
Indices: 835488--835717 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
835478 AAATTTCAGT
* * *
835488 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
835508 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
835528 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
835548 GTTGCGATTTACGTATTATC
1 GTTGCGATTTACGGATTCGC
*
835568 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
835588 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
835608 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
835628 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
835648 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
835668 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
835688 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
835708 GTTGCGATTT
1 GTTGCGATTT
835718 TGGAAACTGA
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:836095 original size:2 final size:2
Alignment explanation
Indices: 836090--836125 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
836080 TAAAAAAAGA
836090 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
836126 TTAGAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:842139 original size:19 final size:19
Alignment explanation
Indices: 842115--842153 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
842105 TCGAATGCAT
842115 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
842134 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
842153 T
1 T
842154 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:842258 original size:64 final size:65
Alignment explanation
Indices: 842101--842261 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
842091 GAATTAATTG
* * *** *
842101 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
842166 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGTCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
842229 A
65 A
* *
842230 AACATCGAATGCGTTTCATGTATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
842262 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 35 0.42
65 48 0.58
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:848145 original size:22 final size:22
Alignment explanation
Indices: 848120--848162 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
848110 GAAAGTCAAC
848120 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
848142 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
848163 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:848183 original size:19 final size:19
Alignment explanation
Indices: 848161--848258 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
848151 TCGGGTCGGG
848161 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
848180 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
848199 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
848218 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
848238 TAAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
848258 T
1 T
848259 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 17 0.25
21 9 0.13
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:848189 original size:10 final size:9
Alignment explanation
Indices: 848159--848257 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
848149 GGTCGGGTCG
*
848159 GGTCAGACC
1 GGTCAAACC
848168 GGTCAAACC
1 GGTCAAACC
*
848177 GGTTCAGACC
1 GG-TCAAACC
848187 GGTCAAACC
1 GGTCAAACC
*
848196 GGTTCGAACC
1 GG-TCAAACC
*
848206 GGTTGAAACC
1 GG-TCAAACC
848216 GGTCAAACC
1 GGTCAAACC
848225 GGTCAGAACC
1 GGTCA-AACC
*
848235 GGTTAAAAACC
1 GG-T-CAAACC
*
848246 GGTTAAACC
1 GGTCAAACC
848255 GGT
1 GGT
848258 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:848216 original size:29 final size:26
Alignment explanation
Indices: 848165--848257 Score: 51
Period size: 29 Copynumber: 3.2 Consensus size: 26
848155 GTCGGGTCAG
* *
848165 ACCGGTCAAACCGGTTCAGACCGGTCAA
1 ACCGGTCAAACCGG-TCAAACCGGT-TA
* * *
848193 ACCGGTTCGAACCGGTTGAAACCGGTCAA
1 ACCGG-TCAAACCGG-TCAAACCGGT-TA
*
848222 ACCGGTCAGAACCGGTTAAAAACCGGTTAA
1 ACCGGTCA-AACCGG-T-CAAACCGGTT-A
848252 ACCGGT
1 ACCGGT
848258 TTCCAGCAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.13
29 33 0.60
30 15 0.27
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (26 bp):
ACCGGTCAAACCGGTCAAACCGGTTA
Found at i:852078 original size:21 final size:21
Alignment explanation
Indices: 852036--852079 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
852026 ACCCCGGGAG
*
852036 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
852057 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
852078 CT
1 CT
852080 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:853175 original size:65 final size:64
Alignment explanation
Indices: 853057--853266 Score: 214
Period size: 65 Copynumber: 3.2 Consensus size: 64
853047 TATTCAAAGG
* ** *
853057 CATGCACCGATGCATC-AGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCATCGATGCA-CAAG-CCATGCATCGATGCATC-A-GAATATTTTTCAAACATCGAATGCA
853119 -TT
62 TTT
* *** *
853121 CTATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCAT
1 C-ATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGAATATTTTTC-AAACATCGAATGCAT
853185 TT
63 TT
* **
853187 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
853251 CATGCATCGATGCACA
1 CATGCATCGATGCACA
853267 CTTGGTGCAC
Statistics
Matches: 123, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
63 6 0.05
64 54 0.44
65 61 0.50
66 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:853281 original size:64 final size:64
Alignment explanation
Indices: 853057--853286 Score: 218
Period size: 64 Copynumber: 3.6 Consensus size: 64
853047 TATTCAAAGG
* * * *
853057 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
853119 -TT
62 TTT
* * *
853121 CTATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATT
1 C-ATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATT
853186 T
64 T
* ** **
853187 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
853251 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
853287 AGTGTTCCAA
Statistics
Matches: 139, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
63 6 0.04
64 70 0.50
65 61 0.44
66 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:855916 original size:17 final size:17
Alignment explanation
Indices: 855861--855906 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
855851 GACCTTATTC
855861 AAATAAAATATTATTAT
1 AAATAAAATATTATTAT
855878 AAATAAAATATTATTAT
1 AAATAAAATATTATTAT
855895 AAATAAAATATT
1 AAATAAAATATT
855907 TTGTTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATAAAATATTATTAT
Found at i:859720 original size:23 final size:23
Alignment explanation
Indices: 859694--859760 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
859684 CACCACAGCT
*
859694 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
859717 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
859740 CGTAGAAATGCACCGAAGTGC
1 CGTAGAAATGCACCGAAGTGC
859761 TATATAAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:861004 original size:9 final size:10
Alignment explanation
Indices: 860979--861012 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
860969 ACAATTAATG
860979 TAAT-ACATA
1 TAATCACATA
860988 TAATCACATA
1 TAATCACATA
860998 TAA-CACATA
1 TAATCACATA
861007 TAATCA
1 TAATCA
861013 TAACAACCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.57
10 10 0.43
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (10 bp):
TAATCACATA
Found at i:861023 original size:19 final size:19
Alignment explanation
Indices: 860983--861029 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
860973 TTAATGTAAT
*
860983 ACATATAATCACATATAAC
1 ACATATAATCACATACAAC
*
861002 ACATATAATCATA-ACAAC
1 ACATATAATCACATACAAC
*
861020 -CACATAATCA
1 ACATATAATCA
861030 TGTTCATGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.36
18 4 0.16
19 12 0.48
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (19 bp):
ACATATAATCACATACAAC
Found at i:866391 original size:17 final size:16
Alignment explanation
Indices: 866362--866395 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
866352 TGATTTAAGG
866362 AAAAAACAAAATACAA
1 AAAAAACAAAATACAA
*
866378 AAAAAATAATAATACAA
1 AAAAAACAA-AATACAA
866395 A
1 A
866396 GGGTGTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAAACAAAATACAA
Found at i:867381 original size:29 final size:30
Alignment explanation
Indices: 867308--867374 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
867298 TGAGGTAACG
867308 GTAGTTGCTAAATTTGTGCCTAAAAAAAAA
1 GTAGTTGCTAAATTTGTGCCTAAAAAAAAA
867338 GTAGTTGCTAAATTTGTGCCT-AAAAAAAA
1 GTAGTTGCTAAATTTGTGCCTAAAAAAAAA
867367 GTAGTTGC
1 GTAGTTGC
867375 CTAATTTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 16 0.43
30 21 0.57
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.31
Consensus pattern (30 bp):
GTAGTTGCTAAATTTGTGCCTAAAAAAAAA
Found at i:868730 original size:2 final size:2
Alignment explanation
Indices: 868723--868750 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
868713 ATGTGTTGGG
868723 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
868751 GCTTATCCAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:871366 original size:34 final size:33
Alignment explanation
Indices: 871315--871391 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 33
871305 TAGGTTAAAA
*
871315 TTATTTCAAATTATAGTTACTTGATGTTTTGTG
1 TTATTTCAAATTATAGTTACTTGAGGTTTTGTG
* *
871348 TTATTTCAGAGTTATAGTTACTTTAGGTTTTGTG
1 TTATTTCA-AATTATAGTTACTTGAGGTTTTGTG
871382 TTATTTCAAA
1 TTATTTCAAA
871392 AGGGATAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 9 0.23
34 30 0.77
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (33 bp):
TTATTTCAAATTATAGTTACTTGAGGTTTTGTG
Found at i:871782 original size:51 final size:51
Alignment explanation
Indices: 871716--871815 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 51
871706 CTTAAGCAAG
* * *
871716 ATCAGGTGTTCGAAACCTGATGATTGCGAATGAAGCAAACTGTGTTAGGGT
1 ATCAGGTATTCGAAACCTGACGATTGCGAATGAAGCAAACTGGGTTAGGGT
* *
871767 ATCAGGTATTTGAAACCTGACGATTGCGAATGGAGCAAACTGGGTTAGG
1 ATCAGGTATTCGAAACCTGACGATTGCGAATGAAGCAAACTGGGTTAGG
871816 AGGGTCGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (51 bp):
ATCAGGTATTCGAAACCTGACGATTGCGAATGAAGCAAACTGGGTTAGGGT
Found at i:875619 original size:13 final size:13
Alignment explanation
Indices: 875600--875630 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
875590 ACATTCGATT
875600 ATTGCTTGGATGG
1 ATTGCTTGGATGG
*
875613 CTTGCTTGGATGG
1 ATTGCTTGGATGG
875626 ATTGC
1 ATTGC
875631 CTACTAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.35, T:0.39
Consensus pattern (13 bp):
ATTGCTTGGATGG
Found at i:886739 original size:16 final size:16
Alignment explanation
Indices: 886718--886753 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
886708 CCACCACCGG
* *
886718 TTTTTTAATATCCATT
1 TTTTTTAAAATCAATT
886734 TTTTTTAAAATCAATT
1 TTTTTTAAAATCAATT
886750 TTTT
1 TTTT
886754 CAAACCGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTTAAAATCAATT
Found at i:887844 original size:6 final size:6
Alignment explanation
Indices: 887833--887863 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
887823 CACGGGGAAC
887833 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T
887864 CTGAGCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:889104 original size:31 final size:31
Alignment explanation
Indices: 889061--889128 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
889051 TAACCGTTAA
* *
889061 CACCTAACAGTGTAACAGATAAAACATTAGG
1 CACCTAAAAGTGTAACAGAGAAAACATTAGG
* *
889092 CACCTAAAAGTGTAATAGAGAAAATATTAGG
1 CACCTAAAAGTGTAACAGAGAAAACATTAGG
889123 CACCTA
1 CACCTA
889129 TTTTTAACGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.21
Consensus pattern (31 bp):
CACCTAAAAGTGTAACAGAGAAAACATTAGG
Found at i:892375 original size:29 final size:29
Alignment explanation
Indices: 892343--892401 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
892333 TTCACGAATA
* *
892343 GGTGCCTAAATTATTTTTTGATTGATCCC
1 GGTGCCTAAAATATTTTTTGAATGATCCC
*
892372 GGTGTCTAAAATATTTTTTGAATGATCCC
1 GGTGCCTAAAATATTTTTTGAATGATCCC
892401 G
1 G
892402 ATGCTAACGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (29 bp):
GGTGCCTAAAATATTTTTTGAATGATCCC
Found at i:895413 original size:23 final size:23
Alignment explanation
Indices: 895368--895418 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
895358 ATTAAAAGAG
* *
895368 AAAAGGATGCTATATTCCTACCA
1 AAAAGAATGCTAGATTCCTACCA
*
895391 TAAAGAATGCTAGAGTTCC-ACCA
1 AAAAGAATGCTAGA-TTCCTACCA
895414 AAAAG
1 AAAAG
895419 CATCAACAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (23 bp):
AAAAGAATGCTAGATTCCTACCA
Found at i:913010 original size:20 final size:20
Alignment explanation
Indices: 912985--913035 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
912975 CACGGAATGT
*
912985 AAGATTATCAGTGAAAATAA
1 AAGATTACCAGTGAAAATAA
*
913005 AAGATTACCAGTGAGAATAA
1 AAGATTACCAGTGAAAATAA
913025 AAGATTACCAG
1 AAGATTACCAG
913036 GGAATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTGAAAATAA
Found at i:913758 original size:224 final size:225
Alignment explanation
Indices: 913330--913778 Score: 819
Period size: 224 Copynumber: 2.0 Consensus size: 225
913320 AAGTATAGAT
913330 TTTTTTTGTAAATCTAAAATATTTGAAGGATAAATTTGTAATTTAACATTAGTAGAATTTTTATT
1 TTTTTTTGTAAATCTAAAATATTTGAAGGATAAATTTGTAATTTAACATTAGTAGAATTTTTATT
913395 ATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAATTTAAGGACATTTTAGTCCAAAACA
66 ATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAATTTAAGGACATTTTAGTCCAAAACA
913460 CCGATAATCCAACAATACCTAAGGAAAGGGAGGTAATGACATTCCCGATAATATACCCCAAAAAA
131 CCGATAATCCAACAATACCTAAGGAAAGGGAGGTAATGACATTCCCGATAATATACCCCAAAAAA
* *
913525 TCTACTATTGGTAATGTAAGATTACTAGGA
196 TCCACTATTGGTAATGTAAGATTACCAGGA
* * *
913555 TTTTTTTGTAAATCTAAAATATTTGAAGGATAAATTTGTAATTTAACCTTCGTAGATTTTTTATT
1 TTTTTTTGTAAATCTAAAATATTTGAAGGATAAATTTGTAATTTAACATTAGTAGAATTTTTATT
913620 ATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAA-TTAAGGACATTTTAGTCCAAAACA
66 ATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAATTTAAGGACATTTTAGTCCAAAACA
* * *
913684 CCGGTAATCCAACAATACCTAAGGAAATGGAGGTAATGACATTCCCGGTAATATACCCCAAAAAA
131 CCGATAATCCAACAATACCTAAGGAAAGGGAGGTAATGACATTCCCGATAATATACCCCAAAAAA
913749 TCCACTATTGGTAATGTAAGATTACCAGGA
196 TCCACTATTGGTAATGTAAGATTACCAGGA
913779 ATGACATTAT
Statistics
Matches: 216, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
224 114 0.53
225 102 0.47
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (225 bp):
TTTTTTTGTAAATCTAAAATATTTGAAGGATAAATTTGTAATTTAACATTAGTAGAATTTTTATT
ATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAATTTAAGGACATTTTAGTCCAAAACA
CCGATAATCCAACAATACCTAAGGAAAGGGAGGTAATGACATTCCCGATAATATACCCCAAAAAA
TCCACTATTGGTAATGTAAGATTACCAGGA
Found at i:914240 original size:19 final size:20
Alignment explanation
Indices: 914216--914259 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
914206 TGATTAATAC
* *
914216 AAATAAAATAATTATAA-AT
1 AAATAAAATAAATAGAACAT
914235 AAAT-AAATAAATAGAACAT
1 AAATAAAATAAATAGAACAT
914254 AAATAA
1 AAATAA
914260 TTATCATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 10 0.48
19 10 0.48
20 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
AAATAAAATAAATAGAACAT
Found at i:915335 original size:35 final size:34
Alignment explanation
Indices: 915262--915341 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 34
915252 AACATAGTCA
* *
915262 TCAATTATATTCTAAATCCCAAATTAAAAAATGTT
1 TCAATTACATTCTAAATCCCAAATTAAAAAA-GCT
915297 TCAATTACATTCTAAA-CCTCAAATTTCAAAAAA-CT
1 TCAATTACATTCTAAATCC-CAAA-TT-AAAAAAGCT
915332 TCAATTACAT
1 TCAATTACAT
915342 ACCCAACCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
34 2 0.05
35 30 0.75
36 2 0.05
37 6 0.15
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTACATTCTAAATCCCAAATTAAAAAAGCT
Found at i:916111 original size:148 final size:148
Alignment explanation
Indices: 915842--916111 Score: 423
Period size: 148 Copynumber: 1.8 Consensus size: 148
915832 AAAGACTATT
* * * * * * * * *
915842 TAAATTATAATCAAATAATTTTGTAGTATTATAAATATTTATAATTAAATTTAAATAGAAACTCG
1 TAAATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTGAAACAGAAACTCA
915907 AAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTTGAGTCAA
66 AAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTTGAGTCAA
915972 CTATTTTATAAATTGAAC
131 CTATTTTATAAATTGAAC
*
915990 TAAATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTGAAACATAAACTCA
1 TAAATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTGAAACAGAAACTCA
* * *
916055 AAAATTCAATTCAATTCGACTTTATTTAAATTTTATAAACTCAAATCGAAACAAATT
66 AAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATT
916112 CACTTATAGT
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
148 109 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (148 bp):
TAAATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTGAAACAGAAACTCA
AAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTTGAGTCAA
CTATTTTATAAATTGAAC
Found at i:916283 original size:35 final size:35
Alignment explanation
Indices: 916244--916320 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
916234 GTTGGGTATG
*
916244 TAATTGAAGTATTTTAGAATTTGAGGTTTAGAATA
1 TAATTGAAGCATTTTAGAATTTGAGGTTTAGAATA
* * * *
916279 TAATTGAAGCATTTTGGATTTTGGGGTTTAGAATG
1 TAATTGAAGCATTTTAGAATTTGAGGTTTAGAATA
916314 TAATTGA
1 TAATTGA
916321 TACATGTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.43
Consensus pattern (35 bp):
TAATTGAAGCATTTTAGAATTTGAGGTTTAGAATA
Found at i:919779 original size:22 final size:21
Alignment explanation
Indices: 919738--919779 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
919728 TCAACATCTC
* *
919738 CTGGTCCATTTGGTTTTGAAG
1 CTGGTCCATGTGCTTTTGAAG
919759 CTGGTCCAATGTGCTTTTGAA
1 CTGGTCC-ATGTGCTTTTGAA
919780 ATTCTCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (21 bp):
CTGGTCCATGTGCTTTTGAAG
Found at i:924149 original size:20 final size:20
Alignment explanation
Indices: 924124--924196 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
924114 GTCCGAGGGT
924124 ACAGATTCCCCCCAGGGGGA
1 ACAGATTCCCCCCAGGGGGA
924144 ACAGATTCCCCCCAGGGGGTA
1 ACAGATTCCCCCCAGGGGG-A
*
924165 TC-GATT--CCCC---GGGA
1 ACAGATTCCCCCCAGGGGGA
924179 ACAGATTCCCCCCAGGGG
1 ACAGATTCCCCCCAGGGG
924197 TATCGATTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
14 2 0.05
15 7 0.16
17 4 0.09
18 4 0.09
20 25 0.57
21 2 0.05
ACGTcount: A:0.22, C:0.36, G:0.29, T:0.14
Consensus pattern (20 bp):
ACAGATTCCCCCCAGGGGGA
Found at i:924197 original size:34 final size:35
Alignment explanation
Indices: 924140--924224 Score: 154
Period size: 34 Copynumber: 2.5 Consensus size: 35
924130 TCCCCCCAGG
924140 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
924175 GGGAACAGATTCCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
*
924209 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
924225 TGCATGGTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 31 0.63
35 18 0.37
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
Found at i:924219 original size:15 final size:15
Alignment explanation
Indices: 924167--924223 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
924157 AGGGGGTATC
*
924167 GATTCCCCGGGAACA
1 GATTCCCCGGGTACA
924182 GATTCCCCCCAGGGGTATC-
1 GATT--CCCC--GGGTA-CA
924201 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
924216 GATTCCCC
1 GATTCCCC
924224 CTGCATGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 17 0.49
17 8 0.23
19 8 0.23
20 1 0.03
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.19
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Found at i:924361 original size:21 final size:21
Alignment explanation
Indices: 924335--924376 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
924325 TATTTGAATA
*
924335 TTATGAAGGGGTATCGATTCC
1 TTATGAAGGGGTACCGATTCC
924356 TTATGAAGGGGTACCGATTCC
1 TTATGAAGGGGTACCGATTCC
924377 CCCCATTCTG
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:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (21 bp):
TTATGAAGGGGTACCGATTCC
Found at i:927738 original size:19 final size:20
Alignment explanation
Indices: 927699--927738 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
927689 ATCAGATTGT
927699 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
927719 CCAGGGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
927739 TAGAACAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.17, C:0.35, G:0.30, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:927780 original size:33 final size:34
Alignment explanation
Indices: 927704--927786 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 34
927694 ATTGTCCAGG
927704 GGGTACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGTACAGATT-CCCCCAGGGGGTATCGATTCCCC
** * *
927739 TAGAACAGATTCCCCCA-GGGGTATCGATTCGCC
1 GGGTACAGATTCCCCCAGGGGGTATCGATTCCCC
927772 GGGTACAGA-TCCCCC
1 GGGTACAGATTCCCCC
927787 TACATGGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 6 0.15
33 21 0.51
34 6 0.15
35 8 0.20
ACGTcount: A:0.20, C:0.34, G:0.27, T:0.19
Consensus pattern (34 bp):
GGGTACAGATTCCCCCAGGGGGTATCGATTCCCC
Found at i:927924 original size:21 final size:21
Alignment explanation
Indices: 927898--927939 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
927888 ATTTGAATAT
*
927898 TATGAAGGGGCATCGATTCCC
1 TATGAAGGGGCACCGATTCCC
*
927919 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGCACCGATTCCC
927940 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (21 bp):
TATGAAGGGGCACCGATTCCC
Found at i:941613 original size:12 final size:12
Alignment explanation
Indices: 941593--941643 Score: 93
Period size: 12 Copynumber: 4.2 Consensus size: 12
941583 TTAGCATAAG
941593 CGGTTATTTAAA
1 CGGTTATTTAAA
*
941605 CGATTATTTAAA
1 CGGTTATTTAAA
941617 CGGTTATTTAAA
1 CGGTTATTTAAA
941629 CGGTTATTTAAA
1 CGGTTATTTAAA
941641 CGG
1 CGG
941644 GTATCCCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (12 bp):
CGGTTATTTAAA
Found at i:945386 original size:14 final size:14
Alignment explanation
Indices: 945367--945393 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
945357 GCTGAAGACG
945367 ACGATAAACAGTCA
1 ACGATAAACAGTCA
945381 ACGATAAACAGTC
1 ACGATAAACAGTC
945394 GAGAGATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (14 bp):
ACGATAAACAGTCA
Found at i:949161 original size:14 final size:14
Alignment explanation
Indices: 949142--949177 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
949132 TTCTTAAAAA
949142 GAGATCTAGACGAG
1 GAGATCTAGACGAG
949156 GAGATCTAGACGAG
1 GAGATCTAGACGAG
949170 GAGATCTA
1 GAGATCTA
949178 TATGGAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.33, T:0.17
Consensus pattern (14 bp):
GAGATCTAGACGAG
Found at i:951622 original size:22 final size:22
Alignment explanation
Indices: 951597--951660 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
951587 CTGGTACATG
*
951597 TTTAATACAAGAGTTACAAAGC
1 TTTAATGCAAGAGTTACAAAGC
* *
951619 TTTAATGCAAGAGTTACATAGT
1 TTTAATGCAAGAGTTACAAAGC
* *
951641 TTTATTGCATGAGTTACAAA
1 TTTAATGCAAGAGTTACAAA
951661 TTGCTAGATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (22 bp):
TTTAATGCAAGAGTTACAAAGC
Found at i:974094 original size:55 final size:54
Alignment explanation
Indices: 974025--974410 Score: 332
Period size: 55 Copynumber: 7.1 Consensus size: 54
974015 GGGATAAATG
* * * * *
974025 AGACTTGAAAAATCTTCAAATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGTATA
1 AGACTCGAAAAATCTTCAAA-AACGGGTCTGCTCTCTATTCCTTCAGAG-AGTATA
* * * * *
974080 AGACTCGAACAATCTTCATAAAATGTGTATGCTCTCTATTCATTCAGAGAGTATA
1 AGACTCGAAAAATCTTCA-AAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATA
* *
974135 AGACTC-AAATAATCTTCAACAAACGGGTCTGCTCCCTATTCCTTCAAAGAGTATA
1 AGACTCGAAA-AATCTTCAA-AAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATA
* *
974190 AGACTCG----ATCTTCAATAAACGTGTCTGCTCTCTATTCATTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAA-AAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATA
* * *
974241 AGACTTGAACAATCTTCCATAAAACGGGTCTGCTCTCTATTTCTTCAGAGAGTAT-
1 AGACTCGAAAAATCTT-CA-AAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATA
* *
974296 AGAACTCGAAAAATCTTCAATAAACAGGTAC-GCTC-CTTATTCTTTCAGAGAGTATA
1 AG-ACTCGAAAAATCTTCAA-AAACGGGT-CTGCTCTC-TATTCCTTCAGAGAGTATA
* * * *
974352 GGACTC----AATCTTTAACAAACGTGTCCGCTC-CTTATTCCTTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAA-AAACGGGTCTGCTCTC-TATTCCTTCAGAGAGTATA
*
974403 GGACTCGA
1 AGACTCGA
974411 TCTTCATAAA
Statistics
Matches: 276, Mismatches: 36, Indels: 40
0.78 0.10 0.11
Matches are distributed among these distances:
50 1 0.00
51 89 0.32
54 5 0.02
55 130 0.47
56 50 0.18
57 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (54 bp):
AGACTCGAAAAATCTTCAAAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATA
Found at i:974313 original size:162 final size:160
Alignment explanation
Indices: 974053--974410 Score: 456
Period size: 162 Copynumber: 2.2 Consensus size: 160
974043 AATGACGAGC
* *
974053 CTGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAATGTGTATGCTCTCT
1 CTGCT-CCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCATAAAACGGGTATGCTCTCT
*
974117 ATTCATTCAGAGAGTATAAGACTCAAATAATCTTCAACAAACGGGT-CTGCTCCCTATTCCTTCA
64 ATTCATTCAGAGAGTATAAGACTCAAATAATCTTCAACAAACAGGTAC-GCTCCCTATTCCTTCA
* *
974181 AAGAGTATAAGACTCGATCTTCAATAAACGTGT
128 AAGAGTATAAGACTCAATCTTCAACAAACGTGT
* * *
974214 CTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCCATAAAACGGGTCTGCTCTCT
1 CTGCTC-CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTT-CATAAAACGGGTATGCTCTCT
* * *
974279 ATTTC-TTCAGAGAGTAT-AGAACTCGAAA-AATCTTCAATAAACAGGTACGCTCCTTATTCTTT
64 A-TTCATTCAGAGAGTATAAG-ACTC-AAATAATCTTCAACAAACAGGTACGCTCCCTATTCCTT
* * *
974341 CAGAGAGTATAGGACTCAATCTTTAACAAACGTGT
126 CAAAGAGTATAAGACTCAATCTTCAACAAACGTGT
* *
974376 CCGCTCCTTATTCCTTCAGAGAGTATAGGACTCGA
1 CTGCTCC-TATTCCTTCAGAGAGTATAAGACTCGA
974411 TCTTCATAAA
Statistics
Matches: 171, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
160 1 0.01
161 40 0.23
162 123 0.72
163 7 0.04
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (160 bp):
CTGCTCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAACGGGTATGCTCTCTAT
TCATTCAGAGAGTATAAGACTCAAATAATCTTCAACAAACAGGTACGCTCCCTATTCCTTCAAAG
AGTATAAGACTCAATCTTCAACAAACGTGT
Found at i:974466 original size:37 final size:36
Alignment explanation
Indices: 974425--974496 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
974415 CATAAAATGA
*
974425 GTTTGCTTCACTAATCTTCCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTTCCATGAAGGCTTA-AGATG
* *
974462 GTTTGCTTCACTACTCTTTCATGAAGGCTTAAGAT
1 GTTTGCTTCACTAATCTTCCATGAAGGCTTAAGAT
974497 TGACTTATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTTCCATGAAGGCTTAAGATG
Found at i:975790 original size:7 final size:7
Alignment explanation
Indices: 975765--975845 Score: 65
Period size: 7 Copynumber: 11.1 Consensus size: 7
975755 TGAACCCTTC
975765 CTTTATTT
1 CTTT-TTT
975773 C-TTTTT
1 CTTTTTT
975779 CTTTTTCT
1 CTTTTT-T
*
975787 TTTTTCTT
1 CTTTT-TT
975795 CTTTTTT
1 CTTTTTT
*
975802 CATTTTT
1 CTTTTTT
*
975809 CATTTTT
1 CTTTTTT
975816 CATTTTTT
1 C-TTTTTT
*
975824 ATTTTTT
1 CTTTTTT
*
975831 CATTTTT
1 CTTTTTT
*
975838 CATTTTT
1 CTTTTTT
975845 C
1 C
975846 ATTCATTATT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
6 4 0.06
7 41 0.66
8 16 0.26
9 1 0.02
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (7 bp):
CTTTTTT
Found at i:975798 original size:22 final size:23
Alignment explanation
Indices: 975771--975841 Score: 85
Period size: 22 Copynumber: 3.1 Consensus size: 23
975761 CTTCCTTTAT
*
975771 TTCTTTTTCTTTTTCTTTTTTC-
1 TTCTTTTTCTTTTTCATTTTTCA
975793 TTCTTTTTTCATTTTTCATTTTTCA
1 TTC-TTTTTC-TTTTTCATTTTTCA
975818 TT-TTTTAT-TTTTTCATTTTTCA
1 TTCTTTT-TCTTTTTCATTTTTCA
975840 TT
1 TT
975842 TTTCATTCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
22 19 0.43
23 10 0.23
24 13 0.30
25 2 0.05
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.77
Consensus pattern (23 bp):
TTCTTTTTCTTTTTCATTTTTCA
Found at i:975802 original size:29 final size:29
Alignment explanation
Indices: 975765--975848 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
975755 TGAACCCTTC
*
975765 CTTTATTTC-TTTTTC-TTTTTCTTTTTTCTT
1 CTTT-TTTCATTTTTCATTTTTC-ATTTT-TT
975795 CTTTTTTCATTTTTCATTTTTCATTTTTT
1 CTTTTTTCATTTTTCATTTTTCATTTTTT
*
975824 ATTTTTTCATTTTTCATTTTTCATT
1 CTTTTTTCATTTTTCATTTTTCATT
975849 CATTATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
29 30 0.60
30 14 0.28
31 6 0.12
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (29 bp):
CTTTTTTCATTTTTCATTTTTCATTTTTT
Found at i:975846 original size:7 final size:7
Alignment explanation
Indices: 975797--975848 Score: 86
Period size: 7 Copynumber: 7.3 Consensus size: 7
975787 TTTTTCTTCT
975797 TTTTTCA
1 TTTTTCA
975804 TTTTTCA
1 TTTTTCA
975811 TTTTTCA
1 TTTTTCA
*
975818 TTTTTTA
1 TTTTTCA
975825 TTTTTTCA
1 -TTTTTCA
975833 TTTTTCA
1 TTTTTCA
975840 TTTTTCA
1 TTTTTCA
975847 TT
1 TT
975849 CATTATTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
7 36 0.86
8 6 0.14
ACGTcount: A:0.13, C:0.12, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:975854 original size:29 final size:29
Alignment explanation
Indices: 975796--975855 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
975786 TTTTTTCTTC
**
975796 TTTTTTCATTTTTCATTTTTCATTTTTTA
1 TTTTTTCATTTTTCATTTTTCATTCATTA
975825 TTTTTTCATTTTTCATTTTTCATTCATTA
1 TTTTTTCATTTTTCATTTTTCATTCATTA
975854 TT
1 TT
975856 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTTTTCATTTTTCATTTTTCATTCATTA
Found at i:975865 original size:29 final size:28
Alignment explanation
Indices: 975796--975870 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
975786 TTTTTTCTTC
**
975796 TTTTTTCATTTTTCATTTTTCATTTTTTA
1 TTTTTT-ATTTTTCATTTTTCATTCATTA
975825 TTTTTTCATTTTTCATTTTTCATTCATTA
1 TTTTTT-ATTTTTCATTTTTCATTCATTA
975854 TTATTATT-TTTTTCATT
1 TT-TT-TTATTTTTCATT
975871 ATTATTTTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 38 0.90
30 2 0.05
31 2 0.05
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTTTTATTTTTCATTTTTCATTCATTA
Found at i:985606 original size:45 final size:46
Alignment explanation
Indices: 985539--985642 Score: 156
Period size: 45 Copynumber: 2.3 Consensus size: 46
985529 CCATGCTTTG
*
985539 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAATCCTAACCGCATAATATCTAATTCGCATGC
* * *
985586 TTATTTAAAAAATAAA-CCTAACCGCATAATATCTAGTTTGCATGC
1 TTATTCAAAAAATAAATCCTAACCGCATAATATCTAATTCGCATGC
985631 TTATTCAAAAAA
1 TTATTCAAAAAA
985643 CGAAAATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
45 37 0.71
46 9 0.17
47 6 0.12
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAACCGCATAATATCTAATTCGCATGC
Found at i:990363 original size:31 final size:30
Alignment explanation
Indices: 990328--990404 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 30
990318 ATAACAGACA
990328 AGTGACCGATTTGTTATAAAATGATAACATT
1 AGTGACC-ATTTGTTATAAAATGATAACATT
* * *
990359 AGTGACCAATTCGTTATGAAATGATAATATT
1 AGTGACC-ATTTGTTATAAAATGATAACATT
990390 AGTGACCATTTGTTA
1 AGTGACCATTTGTTA
990405 CTTTTGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 7 0.17
31 34 0.83
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (30 bp):
AGTGACCATTTGTTATAAAATGATAACATT
Found at i:993377 original size:20 final size:20
Alignment explanation
Indices: 993317--993382 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
993307 AAAAATTTAA
*
993317 AGTTTAAGG-ACTAAAACTAC
1 AGTTT-AGGTACTAAAACTAT
*
993337 GGTTTAGGTACTAAAACTAT
1 AGTTTAGGTACTAAAACTAT
*
993357 AGTTTATGTACTAAATA-TAT
1 AGTTTAGGTACTAAA-ACTAT
993377 AGTTTA
1 AGTTTA
993383 CGCTATATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.08
20 36 0.90
21 1 0.03
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (20 bp):
AGTTTAGGTACTAAAACTAT
Found at i:999847 original size:10 final size:9
Alignment explanation
Indices: 999824--999853 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
999814 TGATTGAAGG
999824 ATTAAATTT
1 ATTAAATTT
999833 ATTAAATTAT
1 ATTAAATT-T
999843 ATTAAATTT
1 ATTAAATTT
999852 AT
1 AT
999854 GATCAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATTAAATTT
Found at i:1000412 original size:17 final size:17
Alignment explanation
Indices: 1000366--1000405 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1000356 ATATTGTTTT
*
1000366 ATATT-ATATTATTATA
1 ATATTAATACTATTATA
1000382 ATATTAATACTATTATA
1 ATATTAATACTATTATA
*
1000399 TTATTAA
1 ATATTAA
1000406 ATATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTAATACTATTATA
Found at i:1001149 original size:23 final size:23
Alignment explanation
Indices: 1001134--1001179 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1001124 AAATTTAATA
1001134 TTAAATTTTAAAAAAATTAAAAG
1 TTAAATTTTAAAAAAATTAAAAG
* *
1001157 TTTAATTTTAAAATAGATTAAAA
1 TTAAATTTTAAAA-AAATTAAAA
1001180 CTAATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
TTAAATTTTAAAAAAATTAAAAG
Found at i:1003047 original size:5 final size:5
Alignment explanation
Indices: 1003037--1003066 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1003027 TAATTGTTGG
1003037 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
1003067 CGATTTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:1003415 original size:31 final size:31
Alignment explanation
Indices: 1003377--1003436 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1003367 GGTTGAGCTT
*
1003377 CAGTTTTGGTCTATTTTAATACATAAACTAC
1 CAGTTTTGATCTATTTTAATACATAAACTAC
* *
1003408 CAGTTTTGATCTATTTTATTACCTAAACT
1 CAGTTTTGATCTATTTTAATACATAAACT
1003437 TTTGTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (31 bp):
CAGTTTTGATCTATTTTAATACATAAACTAC
Found at i:1005683 original size:135 final size:135
Alignment explanation
Indices: 1005349--1005762 Score: 394
Period size: 135 Copynumber: 3.0 Consensus size: 135
1005339 GAAATCACCG
* * * * *
1005349 GCGAGAAGGACCGCGTTGATGACGATGAAGCAATACTCCGAAATGGACG-ATTCCGAGCAGTGTA
1 GCGAGGAGGACCGCATTGTTAACGATGAAGCAGTAC-CCGAAATGGA-GAATTCCGAGCAG-GTA
* * * *
1005413 AGGAACAT-ATCGATCATGATAAAGGAA-GCGAACAACCTACACTAAGACCAAGAAGATCGCCAT
63 AGGAACATAAT-GATCATGATAAA-GAAGGCGAACAACCAACACT-A-ACCAAAAAGACCACCAT
1005476 CACCGTTACCGGT
124 CACCGTTA-CGGT
* * * * *
1005489 GCTGAGGAGGACTGCATTGTTAAC-AGTGAGGCAGTGCTCGGAAATGGATAATTCCGAGCACGGT
1 GC-GAGGAGGACCGCATTGTTAACGA-TGAAGCAGTAC-CCGAAATGGAGAATTCCGAGCA-GGT
* * *
1005553 AAGGAACATAATGATCATGATCACGAAGGCGAACATCCAACACT-ACCAAAAAGACCACCATCAC
62 AAGGAACATAATGATCATGATAAAGAAGGCGAACAACCAACACTAACCAAAAAGACCACCATCAC
1005617 CG-T-CGGTT
127 CGTTACGG-T
* *
1005625 GCGAGGAGGACCGCATTGTTAACGATTAAGCAGTACCCTGAAATGGAGAATTTCGAGCAGGGTAA
1 GCGAGGAGGACCGCATTGTTAACGATGAAGCAGTACCC-GAAATGGAGAATTCCGAGCA-GGTAA
* * * *
1005690 GGAACATAACGATCATGATAAAG-AGGTCGAGCAGCCCACACTAGGACCAAAAAGACCACCATCA
64 GGAACATAATGATCATGATAAAGAAGG-CGAACAACCAACACTA--ACCAAAAAGACCACCATCA
*
1005754 CCGATACGG
126 CCGTTACGG
1005763 ACGATGAGAA
Statistics
Matches: 228, Mismatches: 31, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
134 4 0.02
135 86 0.38
136 4 0.02
137 1 0.00
138 41 0.18
139 1 0.00
140 9 0.04
141 79 0.35
142 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (135 bp):
GCGAGGAGGACCGCATTGTTAACGATGAAGCAGTACCCGAAATGGAGAATTCCGAGCAGGTAAGG
AACATAATGATCATGATAAAGAAGGCGAACAACCAACACTAACCAAAAAGACCACCATCACCGTT
ACGGT
Found at i:1006499 original size:162 final size:162
Alignment explanation
Indices: 1006230--1006529 Score: 474
Period size: 162 Copynumber: 1.9 Consensus size: 162
1006220 CCCGGATCAC
**
1006230 CACCGTTACCAGCAACAAAGACAACAATGAAATGTTCAGAAATGGAGGATTCTGACCAAGGTGAG
1 CACCGTTACCAGCAACAAAGACAACAATGAAATGTTCAGAAATGGAGGATTCCAACCAAGGTGAG
* * * *
1006295 GAAAAGGAACCAACGGATTCAACACATGATTACAACGAACATAAAGATGATGATAAAGAAAGTGA
66 AAAAAGGAACCAACGGATTCAACACATGATGAAAACGAACATAAAGATGATCATAAAGAAAGTGA
1006360 AAAACCCGAGCCAAGGCCATCAGGATCACCAT
131 AAAACCCGAGCCAAGGCCATCAGGATCACCAT
* * * *
1006392 CACCGTTACCAGCGACAACGACAACAATGGAATGTTCAGAAATGGAGGATTCCAATCAAGGTGAG
1 CACCGTTACCAGCAACAAAGACAACAATGAAATGTTCAGAAATGGAGGATTCCAACCAAGGTGAG
* * *
1006457 AAAAAGGAACCAACGGATTCAACACATTATGAAAAGGAACATAAAGATGATCATGAAGAAAGTGA
66 AAAAAGGAACCAACGGATTCAACACATGATGAAAACGAACATAAAGATGATCATAAAGAAAGTGA
*
1006522 ACAACCCG
131 AAAACCCG
1006530 CACCAGGATC
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
162 124 1.00
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (162 bp):
CACCGTTACCAGCAACAAAGACAACAATGAAATGTTCAGAAATGGAGGATTCCAACCAAGGTGAG
AAAAAGGAACCAACGGATTCAACACATGATGAAAACGAACATAAAGATGATCATAAAGAAAGTGA
AAAACCCGAGCCAAGGCCATCAGGATCACCAT
Found at i:1006741 original size:129 final size:129
Alignment explanation
Indices: 1006564--1006881 Score: 483
Period size: 129 Copynumber: 2.5 Consensus size: 129
1006554 CAGCAACAAC
* * **
1006564 GAGCTCGGAAATGGAGGATAATGAGCAAGGTAAGAAACAGGAACCAACGGATTCAACACATGATA
1 GAGCTTGGAAAAGGAGGACCATGAGCAAGGTAAGAAACAGGAACCAACGGATTCAACACATGATA
* ** *
1006629 AAGAAAGTGAACAACCGGCGCCAGGATCACCATCTCCGTTACCGGAAACAACGAAGATAGAGGA
66 AAGAAAGTGAACAACCGGCGCCAAGATCACCATCAACGTTACCGGAAACAACGAAGATAGACGA
* *
1006693 GAGCTTGGAAAAGGAGGACCATGAGCAAGGTAAGAAACAGGAAGCAACGGATTCAGCACATGATA
1 GAGCTTGGAAAAGGAGGACCATGAGCAAGGTAAGAAACAGGAACCAACGGATTCAACACATGATA
* * * *
1006758 AAGAAAGTGAACAACCGGCGCCAAGATCACCATCAACGTTACGGGCAACAACGACGATATACGA
66 AAGAAAGTGAACAACCGGCGCCAAGATCACCATCAACGTTACCGGAAACAACGAAGATAGACGA
* * *
1006822 GTGCTTGGAAACGGAGGACCATGAGCAAGGTAAGAAACAGGAACCGACGGATTCAACACA
1 GAGCTTGGAAAAGGAGGACCATGAGCAAGGTAAGAAACAGGAACCAACGGATTCAACACA
1006882 ACATTACAAG
Statistics
Matches: 170, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 170 1.00
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (129 bp):
GAGCTTGGAAAAGGAGGACCATGAGCAAGGTAAGAAACAGGAACCAACGGATTCAACACATGATA
AAGAAAGTGAACAACCGGCGCCAAGATCACCATCAACGTTACCGGAAACAACGAAGATAGACGA
Found at i:1007993 original size:21 final size:21
Alignment explanation
Indices: 1007947--1008019 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
1007937 TTTTCCTAAT
** *
1007947 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
1007967 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
1007988 TTGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
1008009 TCGCAACGCGA
1 TCGCAATGCGA
1008020 TACTGACTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 12 0.26
21 34 0.74
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:1008033 original size:20 final size:20
Alignment explanation
Indices: 1008008--1008122 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
1007998 AATTTGGAAA
1008008 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1008028 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1008049 ATCGCAACTCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
1008069 TTCGCAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* * *
1008089 TTCGCAACTCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1008109 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1008123 ATACATAATC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 60 0.77
21 14 0.18
22 2 0.03
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1008105 original size:40 final size:41
Alignment explanation
Indices: 1008005--1008136 Score: 167
Period size: 41 Copynumber: 3.2 Consensus size: 41
1007995 GCGAATTTGG
* *
1008005 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACTCGATACTGACTTTCGCAACGCGATAATAC
* * *
1008046 AAAATCGCAACTCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACTCGATACTGACTTTCGCAACGCGATAATAC
** * *
1008086 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACTCGATACTGACTTTCGCAACGCGATAATAC
*
1008127 ATAATCGCAA
1 AAAATCGCAA
1008137 TGCGATTTTC
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 33 0.44
41 42 0.56
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACTCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1008323 original size:22 final size:22
Alignment explanation
Indices: 1008295--1008338 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1008285 ACTCTCTCAC
1008295 CCATCTCCGACGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
*
1008317 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
1008339 ATCTCCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCT
Found at i:1008610 original size:20 final size:19
Alignment explanation
Indices: 1008585--1008629 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1008575 TATCTCCTCG
1008585 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCG-GT
* **
1008605 TGCGATTGTCATTTTCGGT
1 TGCGATAGTCAAATTCGGT
1008624 TGCGAT
1 TGCGAT
1008630 TTCATTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (19 bp):
TGCGATAGTCAAATTCGGT
Found at i:1008636 original size:18 final size:20
Alignment explanation
Indices: 1008598--1008638 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1008588 GATAGTCAAA
1008598 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTGCGATTGTCATT
1008618 TTCG-GTTGCGATT-TCATT
1 TTCGCGTTGCGATTGTCATT
1008636 TTC
1 TTC
1008639 AGAAACTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.49
Consensus pattern (20 bp):
TTCGCGTTGCGATTGTCATT
Found at i:1010452 original size:17 final size:17
Alignment explanation
Indices: 1010418--1010462 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1010408 ACTGCTAAAC
1010418 TGTTTTT-GTTAGTATT
1 TGTTTTTGGTTAGTATT
* *
1010434 TGTTTTTGGTTTGTTTT
1 TGTTTTTGGTTAGTATT
1010451 TGTCTTTTGGTT
1 TGT-TTTTGGTT
1010463 GAAGTAATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 7 0.28
17 10 0.40
18 8 0.32
ACGTcount: A:0.04, C:0.02, G:0.22, T:0.71
Consensus pattern (17 bp):
TGTTTTTGGTTAGTATT
Found at i:1010569 original size:19 final size:20
Alignment explanation
Indices: 1010515--1010560 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1010505 TAGTTTACTT
* *
1010515 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1010535 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
1010555 TCGCAA
1 TCGCAA
1010561 TGTGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1010608 original size:19 final size:19
Alignment explanation
Indices: 1010515--1010617 Score: 63
Period size: 19 Copynumber: 5.6 Consensus size: 19
1010505 TAGTTTACTT
* **
1010515 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1010535 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
* *
1010555 TCGCAATGTGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1010574 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1010588 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1010607 TCGCAATGCGA
1 TCGCAACGCGA
1010618 TTTGTGTTTC
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 1 0.02
18 1 0.02
19 27 0.41
20 23 0.35
21 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1010689 original size:20 final size:20
Alignment explanation
Indices: 1010655--1010709 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1010645 TTGCGATTTT
*
1010655 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
1010674 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
1010694 CATTTCCGCGTTGCGA
1 CATTTCCGCGTTGCGA
1010710 AAGTAAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:1011109 original size:21 final size:20
Alignment explanation
Indices: 1011057--1011117 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
1011047 GACTAACCTG
1011057 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
1011077 CCAATCATTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
1011098 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
1011118 CCCACCGTTC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.43, G:0.11, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:1011144 original size:41 final size:42
Alignment explanation
Indices: 1011054--1011144 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
1011044 CCCGACTAAC
* *
1011054 CTGTCATCCCTCAAGAGTCCCCTCCAATCATTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
* * *
1011096 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
1011137 CTGTCATC
1 CTGTCATC
1011145 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.51
42 21 0.49
ACGTcount: A:0.23, C:0.42, G:0.14, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
Found at i:1012591 original size:14 final size:14
Alignment explanation
Indices: 1012557--1012595 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1012547 TCGATTGTTT
1012557 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1012571 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1012585 TGTTGATTTGT
1 AATTGATTTGT
1012596 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:1012741 original size:14 final size:14
Alignment explanation
Indices: 1012722--1012775 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1012712 GAAACTGACT
1012722 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1012736 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1012755 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
1012769 ACCGCAA
1 ATCGCAA
1012776 TGCAATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 17 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1012768 original size:19 final size:19
Alignment explanation
Indices: 1012732--1012768 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1012722 ATCGCAACGA
* *
1012732 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
1012751 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
1012769 ACCGCAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:1012832 original size:20 final size:20
Alignment explanation
Indices: 1012807--1012894 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
1012797 CGATATTCTA
1012807 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
***
1012827 GTTGCGATTTTTCA-TTTCGC
1 GTTGCGA-TAGCCATTTTCGC
* *
1012847 ATTGCGATAGCCATTTTAGC
1 GTTGCGATAGCCATTTTCGC
*
1012867 GTTGCGATAGCCATTTTTGC
1 GTTGCGATAGCCATTTTCGC
1012887 GTTGCGAT
1 GTTGCGAT
1012895 TTCCCCGTTA
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:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:1013133 original size:20 final size:20
Alignment explanation
Indices: 1013108--1013198 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
1013098 TTGAAGATGA
1013108 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1013128 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
1013148 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
1013169 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
1013189 TTGCGATTTT
1 TTGCGATTTT
1013199 TCAAATTCGC
Statistics
Matches: 53, Mismatches: 17, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
20 38 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Done.