Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007851.1 Hibiscus syriacus cultivar Beakdansim tig00110210_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: 1608033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1352455 original size:32 final size:32
Alignment explanation
Indices: 1352419--1352597 Score: 137
Period size: 32 Copynumber: 5.6 Consensus size: 32
1352409 AGCAGTGTGA
* * *
1352419 TGCATCCAGATAATGCACAACT-TTGTTAGTGT
1 TGCATTCAGATAATGCA-AAATAGTGTTAGTGT
* * * *
1352451 TGCATTTAGATAATGCATAGTAGTGTCAGTGT
1 TGCATTCAGATAATGCAAAATAGTGTTAGTGT
**
1352483 CACATTCAGATAATGCAAAATAGTGTTAGTGT
1 TGCATTCAGATAATGCAAAATAGTGTTAGTGT
* *
1352515 TGCATTCAGATAATGC-ATATCAGTGTTATTGT
1 TGCATTCAGATAATGCAAAAT-AGTGTTAGTGT
*** *** * *
1352547 CATATTCAGATAATGTGCAGTAGTGTTAATGT
1 TGCATTCAGATAATGCAAAATAGTGTTAGTGT
* *
1352579 CGCATTTAGATAATGCAAA
1 TGCATTCAGATAATGCAAA
1352598 GCAGTTACAG
Statistics
Matches: 114, Mismatches: 30, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
31 5 0.04
32 108 0.95
33 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (32 bp):
TGCATTCAGATAATGCAAAATAGTGTTAGTGT
Found at i:1352510 original size:64 final size:64
Alignment explanation
Indices: 1352425--1352595 Score: 202
Period size: 64 Copynumber: 2.7 Consensus size: 64
1352415 GTGATGCATC
* *
1352425 CAGATAATGCACAACT-TTGTTAGTGTTGCATTTAGATAATGCATAGT-AGTGTCAGTGTCACAT
1 CAGATAATGCA-AAATAGTGTTAGTGTTGCATTTAGATAATGCATA-TCAGTGTCAGTGTCACAT
1352488 T
64 T
* * * *
1352489 CAGATAATGCAAAATAGTGTTAGTGTTGCATTCAGATAATGCATATCAGTGTTATTGTCATATT
1 CAGATAATGCAAAATAGTGTTAGTGTTGCATTTAGATAATGCATATCAGTGTCAGTGTCACATT
*** * * *
1352553 CAGATAATGTGCAGTAGTGTTAATGTCGCATTTAGATAATGCA
1 CAGATAATGCAAAATAGTGTTAGTGTTGCATTTAGATAATGCA
1352596 AAGCAGTTAC
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 4 0.04
64 88 0.96
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (64 bp):
CAGATAATGCAAAATAGTGTTAGTGTTGCATTTAGATAATGCATATCAGTGTCAGTGTCACATT
Found at i:1355318 original size:14 final size:14
Alignment explanation
Indices: 1355299--1355325 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1355289 GTATGCTTTG
1355299 ATAAAAATGAAATA
1 ATAAAAATGAAATA
1355313 ATAAAAATGAAAT
1 ATAAAAATGAAAT
1355326 CATCATTTTG
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:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (14 bp):
ATAAAAATGAAATA
Found at i:1356313 original size:23 final size:21
Alignment explanation
Indices: 1356270--1356314 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1356260 TAAATCCGAA
* *
1356270 TTTAAATATAAACTTTAATTT
1 TTTAAAAATAAAATTTAATTT
*
1356291 TTTAAAAATAAAATTTAATAT
1 TTTAAAAATAAAATTTAATTT
1356312 TTT
1 TTT
1356315 GTGACTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAAAAATAAAATTTAATTT
Found at i:1356463 original size:27 final size:26
Alignment explanation
Indices: 1356431--1356484 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
1356421 CATATATTGA
1356431 ATTTTAGAAGTTTTA-TTAGAAATATAT
1 ATTTTA-AA-TTTTACTTAGAAATATAT
1356458 ATTTTAAATTTTATCTTAGAAATATAT
1 ATTTTAAATTTTA-CTTAGAAATATAT
1356485 TATAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 5 0.20
26 2 0.08
27 18 0.72
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (26 bp):
ATTTTAAATTTTACTTAGAAATATAT
Found at i:1357170 original size:20 final size:19
Alignment explanation
Indices: 1357147--1357193 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1357137 CGATATAACA
*
1357147 GGTAAAAATATGATAAAATC
1 GGTAAAAA-ATGATAAAACC
*
1357167 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1357187 GGTAAAA
1 GGTAAAA
1357194 CGCTACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1357188 original size:180 final size:182
Alignment explanation
Indices: 1356754--1357226 Score: 700
Period size: 180 Copynumber: 2.6 Consensus size: 182
1356744 GATCCAAAAT
* * * **
1356754 AAAAATGTATCGATCCACAACGATATAATAGGTAAAACTATGACAAAATCGGTATTGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
* * * * * *
1356819 AAATCGGTAAAATGGTATCGGATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
1356884 GTTAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
131 GTGAATTTAAAAGAGAAACAGTTTTAGCCCCTATAAAGTGTCGATACTTT-AA
*
1356937 AAAAATGTATCGGTCCACAACGATATAACAGGTAAAAATATGATAAAA-CTGGTATCAAAATGAT
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAATC-GGTATCAAAATGAT
* * * *
1357001 GAAACCGGTAAAACACTACCAGATATATTGAAAATGTCGATACTTT-ATATAAGGATCGACACTT
65 AAAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * * *
1357065 TGTGAATTTAAAAGAGAAGCAGTTTTAGCCCCTATAATGTGTTGATACTTT-A
130 CGTGAATTTAAAAGAGAAACAGTTTTAGCCCCTATAAAGTGTCGATACTTTAA
1357117 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
*
1357182 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTTGATACTTT
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT
1357227 CGTAAGTACG
Statistics
Matches: 260, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
180 103 0.40
181 1 0.00
182 64 0.25
183 92 0.35
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAACAGTTTTAGCCCCTATAAAGTGTCGATACTTTAA
Found at i:1359472 original size:21 final size:21
Alignment explanation
Indices: 1359446--1359510 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
1359436 AAGATAATCA
* *
1359446 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAAAGAAACTTGAG
1359467 AGAGTCGAAAAGAAACTTGAG
1 AGAGTCGAAAAGAAACTTGAG
* * *
1359488 AGAGTCGAATATACACTTGAG
1 AGAGTCGAAAAGAAACTTGAG
1359509 AG
1 AG
1359511 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.11, G:0.28, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAAAGAAACTTGAG
Found at i:1359586 original size:33 final size:33
Alignment explanation
Indices: 1359544--1359609 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1359534 AAATAGATGG
*
1359544 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
1359577 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1359610 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1359820 original size:18 final size:18
Alignment explanation
Indices: 1359797--1359862 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
1359787 AAAATATGAA
1359797 GAAGAA-AAGAGGGAGGAG
1 GAAGAAGAAGAGGGA-GAG
*
1359815 GAAGAAGAAGA-AGAGATG
1 GAAGAAGAAGAGGGAGA-G
*
1359833 GAAGAA-AAGAGGGACGAC
1 GAAGAAGAAGAGGGA-GAG
1359851 GAAGAAGAAGAG
1 GAAGAAGAAGAG
1359863 ATGGAAGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 6 0.15
18 23 0.57
19 11 0.28
ACGTcount: A:0.53, C:0.03, G:0.42, T:0.02
Consensus pattern (18 bp):
GAAGAAGAAGAGGGAGAG
Found at i:1359844 original size:36 final size:35
Alignment explanation
Indices: 1359797--1359886 Score: 121
Period size: 33 Copynumber: 2.6 Consensus size: 35
1359787 AAAATATGAA
1359797 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAAGAGATG
1 GAAGAAAAGA-GGAGGAGGAAGAAGAAGAAGAGATG
* *
1359833 GAAGAAAAGA-G-GGACGACGAAGAAGAAGAGATG
1 GAAGAAAAGAGGAGGAGGAAGAAGAAGAAGAGATG
*
1359866 GAAGAAATGAGGAGGAAGGAA
1 GAAGAAAAGAGGAGG-AGGAA
1359887 ATCGATGTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
33 29 0.63
34 2 0.04
35 2 0.04
36 13 0.28
ACGTcount: A:0.52, C:0.02, G:0.42, T:0.03
Consensus pattern (35 bp):
GAAGAAAAGAGGAGGAGGAAGAAGAAGAAGAGATG
Found at i:1361461 original size:19 final size:19
Alignment explanation
Indices: 1361437--1361485 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1361427 AATGTAGGGT
1361437 TAATTTTGTATATGATTTA
1 TAATTTTGTATATGATTTA
1361456 TAATTTTGTATATGATTTA
1 TAATTTTGTATATGATTTA
1361475 TAATTTTGTAT
1 TAATTTTGTAT
1361486 GTGAATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (19 bp):
TAATTTTGTATATGATTTA
Found at i:1361762 original size:21 final size:21
Alignment explanation
Indices: 1361737--1361791 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
1361727 GTGCAACCAT
1361737 AAAGTGTCGATCCATATATAA
1 AAAGTGTCGATCCATATATAA
1361758 AAAGTGTCGATCCATATATAA
1 AAAGTGTCGATCCATATATAA
1361779 AAAGTGTCGATCC
1 AAAGTGTCGATCC
1361792 CTGAAACATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (21 bp):
AAAGTGTCGATCCATATATAA
Found at i:1362104 original size:200 final size:200
Alignment explanation
Indices: 1361758--1362720 Score: 1662
Period size: 200 Copynumber: 4.8 Consensus size: 200
1361748 CCATATATAA
* * *
1361758 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCTGAAACATTGAAACCCATATGTATAATGTA
1 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
* *
1361823 ATATGTAATTTTTCAATCTAACTGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
66 ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
*
1361888 TGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGCAAACAAGGTGCA
131 TGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGCAAACAGGGTGCA
1361953 ACCAT
196 ACCAT
* *
1361958 AAAGTGTCGATCCATACATAAATAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
1 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
* *
1362023 ATAGGTATTTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTAT-ATAAT
66 ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAAT-AT
*
1362087 ATGTATCGACGCTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGCAAACAGGGTGC
130 ATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGCAAACAGGGTGC
1362152 AACCAT
195 AACCAT
*
1362158 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCTATAAGTATAATGTA
1 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
1362223 ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
66 ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
* *
1362288 TGTATCGACACTTTTTAATTTTGTGTCAATACTATTGGTCCAGAATGAATGGAAAACAGGGTGCA
131 TGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGCAAACAGGGTGCA
1362353 ACCAT
196 ACCAT
* *
1362358 AAAGTATCGATCCATATATAAAAA-TATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
1 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
* * *
1362422 ATTGGTAATTTTTCAATCTAACCGGTATAAGTATATCGGTTTTATGAGAGATTAGGTAT-ATAAT
66 ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAAT-AT
* *
1362486 ATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAAAATGAATGGCAAACATGGTGC
130 ATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGCAAACAGGGTGC
1362551 AACCAT
195 AACCAT
1362557 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
1 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
* * * *
1362622 ATAGGTAATTTTTCAACCTAACCGGTATAAGTATACCTGTTTTATGAGATAATAGGTGTAATATA
66 ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
1362687 TGTATCGACACTTTTTAATTTTGTGTCGATACTA
131 TGTATCGACACTTTTTAATTTTGTGTCGATACTA
1362721 ATTTAAATAT
Statistics
Matches: 720, Mismatches: 38, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
198 2 0.00
199 188 0.26
200 526 0.73
201 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (200 bp):
AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
TGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGCAAACAGGGTGCA
ACCAT
Found at i:1362585 original size:399 final size:400
Alignment explanation
Indices: 1361758--1362720 Score: 1712
Period size: 399 Copynumber: 2.4 Consensus size: 400
1361748 CCATATATAA
* * *
1361758 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCTGAAACATTGAAACCCATATGTATAATGTA
1 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
* *
1361823 ATATGTAATTTTTCAATCTAACTGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
66 ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
*
1361888 TGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGCAAACAAGGTGCA
131 TGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGAAAACAAGGTGCA
* * *
1361953 ACCATAAAGTGTCGATCCATACATAAATAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATA
196 ACCATAAAGTATCGATCCATACATAAATAATATCGATCCCAGAAACATCGAAACCCATAAGTATA
*
1362018 ATGTAATAGGTATTTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTATA
261 ATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTATA
* *
1362083 TAATATGTATCGACGCTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGCAAACAGG
326 TAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAAAATGAATGGCAAACAGG
1362148 GTGCAACCAT
391 GTGCAACCAT
*
1362158 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCTATAAGTATAATGTA
1 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
1362223 ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
66 ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
* *
1362288 TGTATCGACACTTTTTAATTTTGTGTCAATACTATTGGTCCAGAATGAATGGAAAACAGGGTGCA
131 TGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGAAAACAAGGTGCA
*
1362353 ACCATAAAGTATCGATCCATATATAAA-AATATCGATCCCAGAAACATCGAAACCCATAAGTATA
196 ACCATAAAGTATCGATCCATACATAAATAATATCGATCCCAGAAACATCGAAACCCATAAGTATA
* *
1362417 ATGTAATTGGTAATTTTTCAATCTAACCGGTATAAGTATATCGGTTTTATGAGAGATTAGGTATA
261 ATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTATA
*
1362482 TAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAAAATGAATGGCAAACATG
326 TAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAAAATGAATGGCAAACAGG
1362547 GTGCAACCAT
391 GTGCAACCAT
1362557 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
1 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
* * * *
1362622 ATAGGTAATTTTTCAACCTAACCGGTATAAGTATACCTGTTTTATGAGATAATAGGTGTAATATA
66 ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
1362687 TGTATCGACACTTTTTAATTTTGTGTCGATACTA
131 TGTATCGACACTTTTTAATTTTGTGTCGATACTA
1362721 ATTTAAATAT
Statistics
Matches: 538, Mismatches: 25, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
399 327 0.61
400 211 0.39
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (400 bp):
AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
ATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTGTAATATA
TGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAATGGAAAACAAGGTGCA
ACCATAAAGTATCGATCCATACATAAATAATATCGATCCCAGAAACATCGAAACCCATAAGTATA
ATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGATTAGGTATA
TAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAAAATGAATGGCAAACAGG
GTGCAACCAT
Found at i:1364221 original size:12 final size:12
Alignment explanation
Indices: 1364206--1364252 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
1364196 GGTCAATCAA
*
1364206 GATGAAGCTGAC
1 GATGAAGATGAC
1364218 GATGAAGATGAC
1 GATGAAGATGAC
1364230 GATGAAGATGAC
1 GATGAAGATGAC
*
1364242 GATGATGATGA
1 GATGAAGATGA
1364253 TGATCCAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.34, T:0.19
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1364256 original size:6 final size:6
Alignment explanation
Indices: 1364204--1364252 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
1364194 GCGGTCAATC
* * * * *
1364204 AAGATG AAGCTG ACGATG AAGATG ACGATG AAGATG ACGATG ATGATG
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG
1364252 A
1 A
1364253 TGATCCAAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.41, C:0.08, G:0.33, T:0.18
Consensus pattern (6 bp):
AAGATG
Found at i:1366156 original size:185 final size:184
Alignment explanation
Indices: 1365636--1366352 Score: 1303
Period size: 184 Copynumber: 3.9 Consensus size: 184
1365626 ATATCATCAT
*
1365636 AAAGTGTCGATACCATTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
*
1365701 ATAGGTAATTTTGTAATATAATCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
*
1365766 TATATCGACACTTTTTAATATTGCGTCGCTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
1365820 AAAGTGTCGATACCTTTTCAAAAAGTGTCAATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
*
1365885 ATAGGTAATTTTGTAATATAATCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
*
1365950 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGAATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
1366004 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAAATATCGGAACCCATAATTATAATGT
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTG-AAAAAACATCGGAACCCATAATTATAATGT
1366069 AATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAAC
65 AATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAAC
1366134 CTATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATG-AA
130 CTATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
* *
1366188 AAAGTGTCGATACCTTTTTAAAAAGTGTCGATTGAAAAAACATCAGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* *
1366253 ATAGGTAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
1366318 TATATCGACACTTTTTAATATTGTGTC-CATACTTT
131 TATATCGACACTTTTTAATATTGTGTCGC-TACTTT
1366353 TAAGTAACGC
Statistics
Matches: 518, Mismatches: 13, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
182 1 0.00
183 125 0.24
184 248 0.48
185 144 0.28
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (184 bp):
AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
Found at i:1369601 original size:23 final size:23
Alignment explanation
Indices: 1369520--1369592 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
1369510 ATAGATAAAA
*
1369520 ATATAATGTAATAGGTAGCGCTT
1 ATATAATATAATAGGTAGCGCTT
1369543 ATATAATATAATAGGTAGCGCTT
1 ATATAATATAATAGGTAGCGCTT
*
1369566 ATGTAATATAATAGGTAGCGCTT
1 ATATAATATAATAGGTAGCGCTT
1369589 ATAT
1 ATAT
1369593 TGTAAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (23 bp):
ATATAATATAATAGGTAGCGCTT
Found at i:1370099 original size:581 final size:579
Alignment explanation
Indices: 1368992--1370104 Score: 1824
Period size: 581 Copynumber: 1.9 Consensus size: 579
1368982 AAATATGATG
*
1368992 TAATAGGTAGCGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCAC
1 TAATAGGTAGCGCTTATATTGTAAAATATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCAC
1369057 TGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATATCAATTTAGTAATTA
66 TGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA-ATATCAATTTAGTAATTA
*
1369122 TACGCGTCTAATGATTTATTTTTATGTTACGGTATATATTATTATTAAATTAAAAACAAAAAACA
130 TACGCATCTAATGATTTATTTTTATGTTACGGTATATATTATTATTAAATTAAAAACAAAAAACA
*
1369187 TATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTT
195 TATATATTACATATGTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTT
1369252 TATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGG
260 TATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGG
*
1369317 TAGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAATATGG
325 TAGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAATATCG
* * ** *
1369382 ATCCTTTTTATAAAAAGTATGGACACTTTCAACATATCAGGTAAATTTTACCTTTTTTATCATAA
390 ATCATTTTTATAAAAAGTATGGACACTTTCAACATATCAGGTAAATGTTACCTTTTTTAAAAGAA
* * * * * * * *
1369447 TGTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAAGGATCGATACTGTACAATATAAT
455 AGTTACCTGACA-GATGAAAGTATCAATAC-TTTTATAAAAACGATCGATACTGAACAATATAAC
1369512 AGATAAAAATATAATGTAATAGGTAGCGCTTATATAATATAATAGGTAGCGCTTATGTAATA
518 AGATAAAAATATAATGTAATAGGTAGCGCTTATATAATATAATAGGTAGCGCTTATGTAATA
*
1369574 TAATAGGTAGCGCTTATATTGTAAAATATCTATCCTTTTTATAAAAGTGTTCATACTTATTTCAC
1 TAATAGGTAGCGCTTATATTGTAAAATATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCAC
1369639 TGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAG-ATATCAATTTAGTAATTAT
66 TGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGAATATCAATTTAGTAATTAT
* ** *
1369703 ACGTATCTAATGATTTATTTTTTATGTTATTGTATATATTATTATTAAATTAAAAACAATAAACA
131 ACGCATCTAATGATTTA-TTTTTATGTTACGGTATATATTATTATTAAATTAAAAACAAAAAACA
1369768 TATATATTACATATGTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTT
195 TATATATTACATATGTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTT
1369833 TATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGG
260 TATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGG
* *
1369898 TGGAAAACATGAAACACTATTAAAAAAGGATTGAAACATAAATTACATAACTTTAAAAAAAGTAT
325 TAGAAAACATGAAACACTATTAAAAAA--ATTGAAACATAAATTACATAACTTTAAAAAAAATAT
1369963 CGATCATTTTTATAAAAAGTATGGACACTTTCAACATATCAGGTAAATGTTACCTTTTTTAAAAG
388 CGATCATTTTTATAAAAAGTATGGACACTTTCAACATATCAGGTAAATGTTACCTTTTTTAAAAG
* * * * *
1370028 AGAAGTTATAGC-GCCA-AT-AAAGTGTCAATAC-TTTATAAAAATCTATCGATCCAT-AACAAT
453 A-AAG-T-TACCTGACAGATGAAAGTATCAATACTTTTATAAAAA-CGATCGATAC-TGAACAAT
1370088 ATAACAGATAAAAATAT
513 ATAACAGATAAAAATAT
1370105 GACAAAATCG
Statistics
Matches: 494, Mismatches: 29, Indels: 17
0.91 0.05 0.03
Matches are distributed among these distances:
580 44 0.09
581 227 0.46
582 119 0.24
583 96 0.19
584 2 0.00
585 3 0.01
586 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (579 bp):
TAATAGGTAGCGCTTATATTGTAAAATATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCAC
TGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGAATATCAATTTAGTAATTAT
ACGCATCTAATGATTTATTTTTATGTTACGGTATATATTATTATTAAATTAAAAACAAAAAACAT
ATATATTACATATGTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTT
ATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGT
AGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAATATCGA
TCATTTTTATAAAAAGTATGGACACTTTCAACATATCAGGTAAATGTTACCTTTTTTAAAAGAAA
GTTACCTGACAGATGAAAGTATCAATACTTTTATAAAAACGATCGATACTGAACAATATAACAGA
TAAAAATATAATGTAATAGGTAGCGCTTATATAATATAATAGGTAGCGCTTATGTAATA
Found at i:1370554 original size:87 final size:87
Alignment explanation
Indices: 1370449--1370611 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
1370439 AAATAGGTCA
*
1370449 ATATAAGCGCTACCTATTACATTATATAAGTGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1370514 CCGGTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
** *
1370536 ATATAAGCGCTATTTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1370601 CCGGTTAAATA
66 CCGGTTAAATA
1370612 ATATAACATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:1371226 original size:44 final size:43
Alignment explanation
Indices: 1371173--1371306 Score: 151
Period size: 44 Copynumber: 3.0 Consensus size: 43
1371163 CCAGTACCTT
* ***
1371173 TCATTTTGCTCTATTATGTCACATAAGAAGTTGAATCAGCATCA
1 TCATTTTGCTCGATTCCATCACATAAGAAGTTG-ATCAGCATCA
* *
1371217 TCATTTTGCTCGATTCCATCATATAAGAAATTTGATCAGCATCA
1 TCATTTTGCTCGATTCCATCACATAAG-AAGTTGATCAGCATCA
* * * *
1371261 TCATCTCGCTCGATTCCATCACATAAGGAGTTGGATCAGCGTCA
1 TCATTTTGCTCGATTCCATCACATAAGAAGTT-GATCAGCATCA
1371305 TC
1 TC
1371307 TCACTTAAGA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 3 0.04
44 68 0.89
45 5 0.07
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (43 bp):
TCATTTTGCTCGATTCCATCACATAAGAAGTTGATCAGCATCA
Found at i:1371395 original size:36 final size:36
Alignment explanation
Indices: 1371355--1371530 Score: 187
Period size: 36 Copynumber: 4.9 Consensus size: 36
1371345 CACTCAAGAT
1371355 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAGAA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAGAA
* * * * *
1371391 TTTATCTCACTTGAGTTTTTTTTTCTTAATATA-TA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAGAA
* *
1371426 TTATATCTCACTTGAGATTGTTTTTCTTAAAACATAT
1 TT-TATCTCACTTGAGATTGTTTTTCTTAAAACAGAA
* * *
1371463 TTTATCTCACATGAGATTTTTTTTCTTAAAATAG-A
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAGAA
* * *
1371498 TTCTATCTTATTTGAAATTG-TTTTCTTTAAAAC
1 TT-TATCTCACTTGAGATTGTTTTTC-TTAAAAC
1371531 TAATTTTCTC
Statistics
Matches: 114, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
35 10 0.09
36 102 0.89
37 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.51
Consensus pattern (36 bp):
TTTATCTCACTTGAGATTGTTTTTCTTAAAACAGAA
Found at i:1371537 original size:72 final size:72
Alignment explanation
Indices: 1371351--1371543 Score: 246
Period size: 72 Copynumber: 2.7 Consensus size: 72
1371341 ATTTCACTCA
* * * *
1371351 AGATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGAATTTATCTCACTTGAGTTTTTTTTTC
1 AGATTATATCTCACTTGAGATTGTTTTTCTTAAAACAGATTTTATCTCACATGAGATTTTTTTTC
*
1371416 TTAATAT
66 TTAAAAT
* *
1371423 ATATTATATCTCACTTGAGATTGTTTTTCTTAAAACATATTTTATCTCACATGAGATTTTTTTTC
1 AGATTATATCTCACTTGAGATTGTTTTTCTTAAAACAGATTTTATCTCACATGAGATTTTTTTTC
1371488 TTAAAAT
66 TTAAAAT
* * * * *
1371495 AGATTCTATCTTATTTGAAATTG-TTTTCTTTAAAACTA-ATTTTCTCTCA
1 AGATTATATCTCACTTGAGATTGTTTTTC-TTAAAAC-AGATTTTATCTCA
1371544 TTTGAAAGTG
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
71 5 0.05
72 100 0.94
73 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (72 bp):
AGATTATATCTCACTTGAGATTGTTTTTCTTAAAACAGATTTTATCTCACATGAGATTTTTTTTC
TTAAAAT
Found at i:1371543 original size:108 final size:107
Alignment explanation
Indices: 1371353--1371578 Score: 237
Period size: 108 Copynumber: 2.1 Consensus size: 107
1371343 TTCACTCAAG
* * * *
1371353 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGAATTTATCTCACTTGAGTTTTTTTTTCTT
1 ATTTTATCTCACATGAGATTGTTTTTCTTAAAACAGAATTTATCTCACTTGAATTGTTTTCTCTT
* * *
1371418 AATATATATTATATCTCACTTGAGATTGTTT-TTCTTAAAACA
66 AAAATATATTATATCTCACTTGAAAGTGTTTCTT-TTAAAACA
* * * *
1371460 TATTTTATCTCACATGAGATTTTTTTTCTTAAAATAG-ATTCTATCTTATTTGAAATTGTTTTCT
1 -ATTTTATCTCACATGAGATTGTTTTTCTTAAAACAGAATT-TATCTCACTTG-AATTGTTTTCT
* * * *
1371524 -TTAAAACTA-ATTTTCTCTCATTTGAAAGTGTTTCTTTTGAAACA
63 CTTAAAA-TATATTATATCTCACTTGAAAGTGTTTCTTTTAAAACA
1371568 ATTTT-TCTCAC
1 ATTTTATCTCAC
1371579 TCAAGGCAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
106 6 0.06
107 8 0.08
108 73 0.74
109 12 0.12
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (107 bp):
ATTTTATCTCACATGAGATTGTTTTTCTTAAAACAGAATTTATCTCACTTGAATTGTTTTCTCTT
AAAATATATTATATCTCACTTGAAAGTGTTTCTTTTAAAACA
Found at i:1371558 original size:35 final size:35
Alignment explanation
Indices: 1371507--1371577 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
1371497 ATTCTATCTT
*
1371507 ATTTGAAATTGTTTTC-TTTAAAACTAATTTTCTCTC
1 ATTTGAAAGTGTTTTCTTTTAAAAC-AATTTT-TCTC
*
1371543 ATTTGAAAGTG-TTTCTTTTGAAACAATTTTTCTC
1 ATTTGAAAGTGTTTTCTTTTAAAACAATTTTTCTC
1371577 A
1 A
1371578 CTCAAGGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 5 0.16
35 10 0.31
36 17 0.53
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (35 bp):
ATTTGAAAGTGTTTTCTTTTAAAACAATTTTTCTC
Found at i:1372127 original size:26 final size:27
Alignment explanation
Indices: 1372094--1372150 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
1372084 TAAGCATTGG
**
1372094 TTTATTTGGGGTTGGTGA-CATTCATA
1 TTTATTTGGGCCTGGTGACCATTCATA
*
1372120 TTTATTTGGGCCTGGTGACCATTCATT
1 TTTATTTGGGCCTGGTGACCATTCATA
1372147 TTTA
1 TTTA
1372151 AAATCTTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.18, C:0.12, G:0.23, T:0.47
Consensus pattern (27 bp):
TTTATTTGGGCCTGGTGACCATTCATA
Found at i:1372761 original size:23 final size:23
Alignment explanation
Indices: 1372735--1372788 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1372725 CAGAGGCTGT
1372735 CATGGTGGCGAGACAGTGGTCGG
1 CATGGTGGCGAGACAGTGGTCGG
*
1372758 CATGGTGGCGAGATAGTGGTCGG
1 CATGGTGGCGAGACAGTGGTCGG
1372781 CATGGTGG
1 CATGGTGG
1372789 TAAGACGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.15, G:0.48, T:0.20
Consensus pattern (23 bp):
CATGGTGGCGAGACAGTGGTCGG
Found at i:1373375 original size:17 final size:16
Alignment explanation
Indices: 1373349--1373401 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 16
1373339 TTAATTATTT
*
1373349 ATTTATTTATTTTCTTA
1 ATTTAATTATTTT-TTA
*
1373366 ATTTAATTATTTTTTT
1 ATTTAATTATTTTTTA
1373382 ATTTCAAATTATTTTTTA
1 ATTT--AATTATTTTTTA
1373400 AT
1 AT
1373402 GTTTTAGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 6 0.19
17 12 0.39
18 13 0.42
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTAATTATTTTTTA
Found at i:1380127 original size:58 final size:57
Alignment explanation
Indices: 1380014--1380130 Score: 132
Period size: 58 Copynumber: 2.0 Consensus size: 57
1380004 CTTAAATATC
* * * *
1380014 TAATAAAAGTAATTTGATTTACATATATAATATATATTCAATAAAAATAATTTATTTT
1 TAATAAAAGTAAATTGATTAAAATATATAATATATATTCAATAAAAAT-AGTTATTTT
1380072 TAATAAAA-TAAATTGAATTAAAATATATATATATAATTATT-AATAAAAAT-GTTATTTT
1 TAATAAAAGTAAATTG-ATTAAAATATATA-ATAT-A-TATTCAATAAAAATAGTTATTTT
1380130 T
1 T
1380131 TTTGCATTCG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
57 6 0.12
58 27 0.53
59 4 0.08
60 10 0.20
61 4 0.08
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.44
Consensus pattern (57 bp):
TAATAAAAGTAAATTGATTAAAATATATAATATATATTCAATAAAAATAGTTATTTT
Found at i:1380225 original size:18 final size:19
Alignment explanation
Indices: 1380198--1380233 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1380188 TATATACACT
*
1380198 TAAAATTAAATTA-TTTAA
1 TAAAAATAAATTACTTTAA
1380216 TAAAAATAAATTACTTTA
1 TAAAAATAAATTACTTTA
1380234 TTAATTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAAATAAATTACTTTAA
Found at i:1380320 original size:25 final size:26
Alignment explanation
Indices: 1380288--1380342 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
1380278 TGTTAACTTT
*
1380288 ATTAAATA-ATTTAATTT-TAAAAATA
1 ATTAAATATATAT-ATTTATAAAAATA
1380313 ATTAAATATATATATTTAATAAAAATA
1 ATTAAATATATATATTT-ATAAAAATA
1380340 ATT
1 ATT
1380343 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 12 0.46
26 3 0.12
27 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTAAATATATATATTTATAAAAATA
Found at i:1380385 original size:39 final size:43
Alignment explanation
Indices: 1380291--1380388 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 43
1380281 TAACTTTATT
*
1380291 AAATAATTTAATTTTAAAAATAATTAAATATATATATTTAATAA
1 AAATAATTT-ATTTTTAAAATAATTAAATATATATATTTAATAA
1380335 AAATAA--T-TTTTTAAAAT-A-T-AATATATAT-TTATAAT-A
1 AAATAATTTATTTTTAAAATAATTAAATATATATATT-TAATAA
1380371 AAATAATTTATTTTTAAA
1 AAATAATTTATTTTTAAA
1380389 TAAAAATAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
36 9 0.18
37 13 0.27
38 2 0.04
39 9 0.18
40 9 0.18
42 1 0.02
44 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (43 bp):
AAATAATTTATTTTTAAAATAATTAAATATATATATTTAATAA
Found at i:1380394 original size:21 final size:22
Alignment explanation
Indices: 1380346--1380397 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1380336 AATAATTTTT
1380346 TAAAATATAATATATATTTATAA
1 TAAAA-ATAATATATATTTATAA
* *
1380369 T-AAAATAATTTATTTTTA-AA
1 TAAAAATAATATATATTTATAA
1380389 TAAAAATAA
1 TAAAAATAA
1380398 AATAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.73
22 3 0.12
23 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAATAATATATATTTATAA
Found at i:1381833 original size:3 final size:3
Alignment explanation
Indices: 1381825--1381891 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
1381815 TTAAATAGGC
1381825 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1381873 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
1381892 AGTCTCTAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1385757 original size:5 final size:5
Alignment explanation
Indices: 1385747--1385781 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
1385737 AAAATTTAAA
1385747 AATAT AATAT -ATAT -ATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
1385782 AATTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:1385837 original size:18 final size:19
Alignment explanation
Indices: 1385747--1385837 Score: 77
Period size: 18 Copynumber: 5.1 Consensus size: 19
1385737 AAAATTTAAA
* *
1385747 AATATAATATATA-TATAT
1 AATATATTATAAACTATAT
* *
1385765 AATATAATAT-AA-TATAA
1 AATATATTATAAACTATAT
1385782 AAT-TATATATAAACTATAT
1 AATATAT-TATAAACTATAT
*
1385801 -TTATATTATAAACTATAT
1 AATATATTATAAACTATAT
*
1385819 AAT-TATTATAAGCTATAT
1 AATATATTATAAACTATAT
1385837 A
1 A
1385838 TATCAATTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
16 2 0.03
17 11 0.18
18 40 0.66
19 8 0.13
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (19 bp):
AATATATTATAAACTATAT
Found at i:1385846 original size:20 final size:18
Alignment explanation
Indices: 1385789--1385847 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
1385779 TAAAATTATA
*
1385789 TATAAACTATAT-TTATAT
1 TATAAACTATATAATA-AT
*
1385807 TATAAACTATATAATTAT
1 TATAAACTATATAATAAT
*
1385825 TATAAGCTATATATATCAAT
1 TATAAACTATATA-AT-AAT
1385845 TAT
1 TAT
1385848 GTTTATGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 26 0.76
19 3 0.09
20 5 0.15
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (18 bp):
TATAAACTATATAATAAT
Found at i:1385883 original size:15 final size:14
Alignment explanation
Indices: 1385863--1385969 Score: 61
Period size: 15 Copynumber: 7.9 Consensus size: 14
1385853 TGTGTATGTA
1385863 TATAAACTATATAT
1 TATAAACTATATAT
1385877 GTATAAAC--TATA-
1 -TATAAACTATATAT
*
1385889 -A-AAAGTATATAGTT
1 TATAAACTATATA--T
*
1385903 TATAAAATAT-TAT
1 TATAAACTATATAT
* *
1385916 T-TATACTAATATAG
1 TATAAACT-ATATAT
*
1385930 TATATA-TATATA-
1 TATAAACTATATAT
1385942 TATAAACTATATAT
1 TATAAACTATATAT
1385956 GTATAAACTATATA
1 -TATAAACTATATA
1385970 AAAATATATA
Statistics
Matches: 73, Mismatches: 6, Indels: 26
0.70 0.06 0.25
Matches are distributed among these distances:
9 3 0.04
10 1 0.01
11 4 0.05
12 9 0.12
13 19 0.26
14 4 0.05
15 27 0.37
16 6 0.08
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (14 bp):
TATAAACTATATAT
Found at i:1386014 original size:80 final size:79
Alignment explanation
Indices: 1385861--1386018 Score: 244
Period size: 80 Copynumber: 2.0 Consensus size: 79
1385851 TATGTGTATG
* *
1385861 TATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAAATATTATTTATACTAAT
1 TATATAAACTATATATGTATAAACTATAAAAAATATATAGTTTATAAAATATAATTTATACTAAT
1385926 ATAGTATATATATA
66 ATAGTATATATATA
*** *
1385940 TATATAAACTATATATGTATAAACTATATAAAAATATATAGTTTATACGTTATAATTTATATTAA
1 TATATAAACTATATATGTATAAACTATA-AAAAATATATAGTTTATAAAATATAATTTATACTAA
*
1386005 TATATTATATATAT
65 TATAGTATATATAT
1386019 GTATGCATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 28 0.39
80 43 0.61
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (79 bp):
TATATAAACTATATATGTATAAACTATAAAAAATATATAGTTTATAAAATATAATTTATACTAAT
ATAGTATATATATA
Found at i:1386186 original size:29 final size:29
Alignment explanation
Indices: 1386123--1386188 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
1386113 AGTAATTTAC
* * *
1386123 TTTATATAGTTTATATATATAGGTATATA
1 TTTATATAGTTTATATATACAGATACATA
* *
1386152 TATATATAGTTTATATATACA-ATACATGG
1 TTTATATAGTTTATATATACAGATACAT-A
1386181 TTTATATA
1 TTTATATA
1386189 TATATATTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (29 bp):
TTTATATAGTTTATATATACAGATACATA
Found at i:1386202 original size:20 final size:19
Alignment explanation
Indices: 1386134--1386204 Score: 55
Period size: 20 Copynumber: 3.9 Consensus size: 19
1386124 TTATATAGTT
1386134 TATATATA-TAGG--TATA
1 TATATATATTAGGTTTATA
1386150 TATATATA-TA-GTTTATA
1 TATATATATTAGGTTTATA
* *
1386167 TATACA-ATACATGGTTTATA
1 TATATATAT-TA-GGTTTATA
1386187 TATATATATTAGGGTTTA
1 TATATATATTA-GGTTTA
1386205 GGGTTTAGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
15 1 0.02
16 11 0.26
17 9 0.21
18 1 0.02
20 19 0.44
21 2 0.05
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.46
Consensus pattern (19 bp):
TATATATATTAGGTTTATA
Found at i:1386511 original size:20 final size:20
Alignment explanation
Indices: 1386475--1386532 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
1386465 CGCCAACTTC
* * *
1386475 CTAAATTTTTCTA-TTCCTT
1 CTAAATTTCTCAATTTCCCT
1386494 CTAAATTTCTCAATTTCCCT
1 CTAAATTTCTCAATTTCCCT
1386514 CTAAA-TTCTCAATTTCCCT
1 CTAAATTTCTCAATTTCCCT
1386533 ATATTCTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 25 0.71
20 10 0.29
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (20 bp):
CTAAATTTCTCAATTTCCCT
Found at i:1386646 original size:2 final size:2
Alignment explanation
Indices: 1386639--1386715 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
1386629 ACTTTGAATA
1386639 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
* *
1386681 AT AT AT AT AT AT AT AT AT AC AT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1386716 ATTAAACATA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1387167 original size:2 final size:2
Alignment explanation
Indices: 1387160--1387196 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1387150 TATGTTTAAT
1387160 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1387197 TATTCAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1387357 original size:46 final size:46
Alignment explanation
Indices: 1387269--1387358 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
1387259 TTTTATTTTG
* *
1387269 GAATTTAGAGGGAAATTATGAAATTTTGAGAATATAGGAAAATTGA
1 GAATTTAGAGGGAAATTATGAAATTTAGAGAATATAGAAAAATTGA
*
1387315 GAATTTAGAGGGAAATT-TGGAAATTTAGAGGGA-ATAGAAAAATT
1 GAATTTAGAGGGAAATTAT-GAAATTTAGA-GAATATAGAAAAATT
1387359 TGGGAAGTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
45 1 0.03
46 36 0.92
47 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.29
Consensus pattern (46 bp):
GAATTTAGAGGGAAATTATGAAATTTAGAGAATATAGAAAAATTGA
Found at i:1388853 original size:13 final size:13
Alignment explanation
Indices: 1388835--1388861 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1388825 CGATGCACAG
1388835 GAAGTGCATCGAT
1 GAAGTGCATCGAT
1388848 GAAGTGCATCGAT
1 GAAGTGCATCGAT
1388861 G
1 G
1388862 CACCCCTTTA
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:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (13 bp):
GAAGTGCATCGAT
Found at i:1388971 original size:64 final size:65
Alignment explanation
Indices: 1388850--1388993 Score: 184
Period size: 64 Copynumber: 2.2 Consensus size: 65
1388840 GCATCGATGA
* *
1388850 AGTGCATCGATGCACCCCTTTAAAAATGGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG
1 AGTGCATCGATGCACCCCTTTAAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGG
1388915 -
65 T
* * * * * * *
1388915 AGTGTATCGATGCATCCCTTT-AATATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGT
1 AGTGCATCGATGCACCCCTTTAAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCATAGGT
1388979 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
1388994 ATGTTAAAGA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
63 2 0.03
64 46 0.69
65 19 0.28
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (65 bp):
AGTGCATCGATGCACCCCTTTAAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCATAGGT
Found at i:1389026 original size:20 final size:23
Alignment explanation
Indices: 1388981--1389034 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 23
1388971 GCATGGGTAG
1388981 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTT-AAGAA
1389005 TGCATCGATGCAC-TG-T-AGAA
1 TGCATCGATGCACATGTTAAGAA
1389025 TGCATCGATG
1 TGCATCGATG
1389035 TACTTCAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 14 0.47
22 1 0.03
23 2 0.07
24 13 0.43
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCACATGTTAAGAA
Found at i:1390682 original size:23 final size:23
Alignment explanation
Indices: 1390614--1390682 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1390604 ACATCTTATA
*
1390614 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
1390637 CGGTACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
1390660 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
1390683 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1391499 original size:16 final size:16
Alignment explanation
Indices: 1391480--1391510 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1391470 TCCTTTACAA
1391480 GTCAGGTTAAAAACAG
1 GTCAGGTTAAAAACAG
*
1391496 GTCAGGTTGAAAACA
1 GTCAGGTTAAAAACA
1391511 AGTCGAGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (16 bp):
GTCAGGTTAAAAACAG
Found at i:1394928 original size:347 final size:347
Alignment explanation
Indices: 1394293--1394973 Score: 1182
Period size: 347 Copynumber: 2.0 Consensus size: 347
1394283 AAGGATTATA
* *
1394293 AATGATTAATAACATGTTTGAAATTATGGTATGATTTTGAGATTCAAGTGTTATAATGAGATTTT
1 AATGATTAATAACATGTTTGAAATCATGGTATGATTTTGAGATTCAAGTGTTATAATGAGAATTT
*
1394358 GGATATTTAGGAGTATTAAATGGAGATAAGTTGGTTTTAATGAATGGAATTGAGTTTAAAGGCCT
66 GGATATTTAGGAGTATTAAATGGAGATAAGTTGGTTTTAATGAATGAAATTGAGTTTAAAGGCCT
* * *
1394423 AAAGGGAGATAAAAGTAGGAGATTTAGGTAAGTTTTGGTTAATTTTTGAAATGGAAATGATAATA
131 AAAGGGAGATAAAAGTAAGAGATTTAGGTAAATTTTGGTTAATTTTCGAAATGGAAATGATAATA
* * * *
1394488 TCTGGGCAAGGGTATCGATACTGGAATAACAGTATCGATACTTCAAGGCTAAACCAATTTGAATT
196 TATGGGCAAGGGTATCGATACTGGAAAAACAATACCGATACTTCAAGGCTAAACCAATTTGAATT
* * *
1394553 CGAGGATCAGTATCGGTATTGATTGAAGGAGATACCGATACTGAAAAGGGAGTATTGATACCAAG
261 CAAGGATCAATATCGGTACTGATTGAAGGAGATACCGATACTGAAAAGGGAGTATTGATACCAAG
1394618 AGTAAGGTACCATTATTGTTCT
326 AGTAAGGTACCATTATTGTTCT
*
1394640 AATGATTAATAACATGTTTGAAATCATGGTATGATTTTGAGATTCAAGTGTTCTAATGAGAATTT
1 AATGATTAATAACATGTTTGAAATCATGGTATGATTTTGAGATTCAAGTGTTATAATGAGAATTT
*
1394705 GGATATTTAGGAGTATTAAATGGAGATAAGTTGGTTTTGATGAATGAAATTGAGTTTAAAGGCCT
66 GGATATTTAGGAGTATTAAATGGAGATAAGTTGGTTTTAATGAATGAAATTGAGTTTAAAGGCCT
*
1394770 AAAGGGAGATAAAAGTAAGAGATTTAGGTAAATTTTGGTTAATTTTCGAAATGGAAATGATAATT
131 AAAGGGAGATAAAAGTAAGAGATTTAGGTAAATTTTGGTTAATTTTCGAAATGGAAATGATAATA
*
1394835 TATGGGCAAGGGTATCGATACTGGAAAAACAATACCGATACTTCAAGGGTAAACCAATTTGAATT
196 TATGGGCAAGGGTATCGATACTGGAAAAACAATACCGATACTTCAAGGCTAAACCAATTTGAATT
* * *
1394900 CAAGGATCAATATCGGTACTGATTGAAGGAGGTACCGATACTGAAAGGGGAGTATTGATACCGAG
261 CAAGGATCAATATCGGTACTGATTGAAGGAGATACCGATACTGAAAAGGGAGTATTGATACCAAG
1394965 AGTAAGGTA
326 AGTAAGGTA
1394974 TCGATACCAT
Statistics
Matches: 314, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
347 314 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (347 bp):
AATGATTAATAACATGTTTGAAATCATGGTATGATTTTGAGATTCAAGTGTTATAATGAGAATTT
GGATATTTAGGAGTATTAAATGGAGATAAGTTGGTTTTAATGAATGAAATTGAGTTTAAAGGCCT
AAAGGGAGATAAAAGTAAGAGATTTAGGTAAATTTTGGTTAATTTTCGAAATGGAAATGATAATA
TATGGGCAAGGGTATCGATACTGGAAAAACAATACCGATACTTCAAGGCTAAACCAATTTGAATT
CAAGGATCAATATCGGTACTGATTGAAGGAGATACCGATACTGAAAAGGGAGTATTGATACCAAG
AGTAAGGTACCATTATTGTTCT
Found at i:1395880 original size:22 final size:22
Alignment explanation
Indices: 1395852--1395901 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1395842 TAAGTCAAAG
1395852 ACTTAGCATGTCATTGTTTCAC
1 ACTTAGCATGTCATTGTTTCAC
*
1395874 ACTTAGCGTGTCATTGTTTCAC
1 ACTTAGCATGTCATTGTTTCAC
*
1395896 AATTAG
1 ACTTAG
1395902 GTTTGAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (22 bp):
ACTTAGCATGTCATTGTTTCAC
Found at i:1397284 original size:21 final size:20
Alignment explanation
Indices: 1397260--1397311 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1397250 TCAAAGTTTT
1397260 ATAAAATATAA-TTATATAAAA
1 ATAAAAT-TAACTTA-ATAAAA
1397281 ATAAAATTAACTTAATAAAA
1 ATAAAATTAACTTAATAAAA
*
1397301 CTAAAAGTTAA
1 ATAAAA-TTAA
1397312 AGAATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (20 bp):
ATAAAATTAACTTAATAAAA
Found at i:1408017 original size:36 final size:36
Alignment explanation
Indices: 1407965--1408067 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
1407955 AGTTGAGTAT
* *
1407965 TATCAGCTTTGATACATTCGTGTATTAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
1408001 TATCAGTTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
1408037 TATCAGCTTTGGTACAGTT-GTATATCAATGT
1 TATCAGCTTTGGTACA-TTCGTGTATCAATGT
1408068 CCAGCAACGT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 59 0.97
37 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.44
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:1425231 original size:15 final size:15
Alignment explanation
Indices: 1425211--1425239 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1425201 ACATTACTAG
1425211 GGAGCAAAGTGTATA
1 GGAGCAAAGTGTATA
1425226 GGAGCAAAGTGTAT
1 GGAGCAAAGTGTAT
1425240 TTCTTTACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.34, T:0.21
Consensus pattern (15 bp):
GGAGCAAAGTGTATA
Found at i:1427653 original size:149 final size:149
Alignment explanation
Indices: 1427383--1427686 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
1427373 CGAAGTGTCC
*
1427383 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1427448 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
1427513 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
1427532 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1427597 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
1427662 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
1427681 CGTAGA
1 CGTAGA
1427687 CCCTCTACCC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:1431903 original size:16 final size:18
Alignment explanation
Indices: 1431872--1431904 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1431862 AATAGCTTAG
1431872 TCTTTCTTTCTTTTCTTC
1 TCTTTCTTTCTTTTCTTC
1431890 TCTTT-TTT-TTTTCTT
1 TCTTTCTTTCTTTTCTT
1431905 ATGGGGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TCTTTCTTTCTTTTCTTC
Found at i:1440405 original size:30 final size:30
Alignment explanation
Indices: 1440371--1440466 Score: 111
Period size: 32 Copynumber: 3.0 Consensus size: 30
1440361 TTTTTCATAC
1440371 AAGTATTTAAAGTATTTTTTTGGTCAAAAT
1 AAGTATTTAAAGTATTTTTTTGGTCAAAAT
**
1440401 AAGTATTTAAAGTTATTTTTTATTTATCAAAAT
1 AAGTATTTAAAG-TA-TTTTT-TTGGTCAAAAT
* *
1440434 AGGTACTTAAAAGTATTTTTTTGGGTCAAAAT
1 AAGTA-TTTAAAGTATTTTTTT-GGTCAAAAT
1440466 A
1 A
1440467 GGTACCTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
30 12 0.22
31 4 0.07
32 18 0.33
33 15 0.27
34 6 0.11
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (30 bp):
AAGTATTTAAAGTATTTTTTTGGTCAAAAT
Found at i:1440444 original size:33 final size:32
Alignment explanation
Indices: 1440377--1440478 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
1440367 ATACAAGTAT
* *
1440377 TTAAAG-TATTTTTTTGG-TCAAAATAAGTAT
1 TTAAAGTTATTTTTTTGGATCAAAATAGGTAC
**
1440407 TTAAAGTTATTTTTTATTTATCAAAATAGGTAC
1 TTAAAGTTATTTTTT-TGGATCAAAATAGGTAC
*
1440440 TTAAAAG-TATTTTTTTGGGTCAAAATAGGTAC
1 TT-AAAGTTATTTTTTTGGATCAAAATAGGTAC
*
1440472 CTAAAGT
1 TTAAAGT
1440479 ACTTATTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
30 6 0.10
31 12 0.20
32 16 0.27
33 21 0.36
34 4 0.07
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (32 bp):
TTAAAGTTATTTTTTTGGATCAAAATAGGTAC
Found at i:1440463 original size:32 final size:31
Alignment explanation
Indices: 1440379--1440476 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 31
1440369 ACAAGTATTT
* *
1440379 AAAGTATTTTTTTGGTCAAAATAAGTA-TTT
1 AAAGTATTTTTTTGGTCAAAATAGGTACTTA
**
1440409 AAAGTTATTTTTTATTTATCAAAATAGGTACTTA
1 AAAG-TA-TTTTT-TTGGTCAAAATAGGTACTTA
*
1440443 AAAGTATTTTTTTGGGTCAAAATAGGTACCTA
1 AAAGTATTTTTTT-GGTCAAAATAGGTACTTA
1440475 AA
1 AA
1440477 GTACTTATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
30 4 0.07
31 4 0.07
32 27 0.48
33 15 0.27
34 6 0.11
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (31 bp):
AAAGTATTTTTTTGGTCAAAATAGGTACTTA
Found at i:1448877 original size:196 final size:191
Alignment explanation
Indices: 1448409--1448989 Score: 616
Period size: 197 Copynumber: 3.0 Consensus size: 191
1448399 CCACAAGTTC
* * *
1448409 AAACATACACACCTCTTCTAACTAATTCCAGCACTAAATACAGAAATCATTC---AAGTT-ACTG
1 AAACATAC-C-CCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGTTCAAGAAGTTCA-TG
* * *
1448470 CTAATTGGAGTAATCAAATGCACACAGAACAAAAACAGGACTTAAATTGAATGATTGAATCAACT
63 ATAATTGGAGTAA-CCAATGCACA-ACAACAAAAACAGGAC-----TT-AA--ATTGAATCAACT
* * * * * * *
1448535 CAAATAAGACCCAAATAAGTAAAACAATTCAAGCAAGTAACCTAGGGGGCTATAAATGTTTATAT
118 CAAATAAGACCCAAATAAGTGAAACAATTCAAACATGTAAACT-TGAGGCTATAAATGTCTATAT
* * *
1448600 TCTGCATCAT
182 TCTACATAAA
* * * * *
1448610 AAACAT-CCCCTCTTCTGAATAGTTCGAGCACTAAATACTGAAATCGCTCAAGAAGTTCCTGATA
1 AAACATACCCCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGTTCAAGAAGTTCATGATA
* *
1448674 ATTGGAGTAACCAATGCATCAACAACAAAAACAGGACTTAAACTGAATCAACTCAAACAAGACCC
66 ATTGGAGTAACCAATGCA-CAACAACAAAAACAGGACTTAAATTGAATCAACTCAAATAAGACCC
* *
1448739 CAATAATTGAAACAATTCAAACATGTAAACTTGAGGCTTATAAATGTCTATATTCTACATAAAAA
130 AAATAAGTGAAACAATTCAAACATGTAAACTTGAGGC-TATAAATGTCTATATTCTACAT--AAA
*
1448804 AAACATACCCCGTCTTCTGACTAATTCCAGAACTAAATACTGAAATCGTTCAAGAAGTTCATGAT
1 AAACATACCCC-TCTTCTGACTAATTCCAGCACTAAATACTGAAATCGTTCAAGAAGTTCATGAT
* * * * *
1448869 AATTGGAGTAATCAATGCACCAACAACAAAAAAGAGGAGTTAAATTGAATCAACGCAAATAAGGC
65 AATTGGAGTAACCAATGCA-CAACAAC-AAAAACAGGACTTAAATTGAATCAACTCAAATAAGAC
* *
1448934 CCTAATAAGTGAAACAATTCAAGA-ATGTAAACTTGAGGGCTATAAATGCCTATATT
128 CCAAATAAGTGAAACAATTCAA-ACATGTAAACTTGA-GGCTATAAATGTCTATATT
1448990 TTGAATCATA
Statistics
Matches: 325, Mismatches: 42, Indels: 30
0.82 0.11 0.08
Matches are distributed among these distances:
191 4 0.01
192 67 0.21
194 9 0.03
195 6 0.02
196 72 0.22
197 78 0.24
198 38 0.12
199 1 0.00
200 23 0.07
201 27 0.08
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (191 bp):
AAACATACCCCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGTTCAAGAAGTTCATGATA
ATTGGAGTAACCAATGCACAACAACAAAAACAGGACTTAAATTGAATCAACTCAAATAAGACCCA
AATAAGTGAAACAATTCAAACATGTAAACTTGAGGCTATAAATGTCTATATTCTACATAAA
Found at i:1457556 original size:38 final size:40
Alignment explanation
Indices: 1457482--1457588 Score: 132
Period size: 38 Copynumber: 2.8 Consensus size: 40
1457472 TTGAAAAAAT
1457482 AATTTAGAATGTTA-ATGTGAAATAATTTAAAAAATTAAG
1 AATTTAGAATGTTAGATGTGAAATAATTTAAAAAATTAAG
* * * * *
1457521 AATTTAGAATGTTAGGTG-GTAA-AATTTTAGAAATTAGG
1 AATTTAGAATGTTAGATGTGAAATAATTTAAAAAATTAAG
*
1457559 AATTTTGAATGTTAGA-GTGAAATAATTTAA
1 AATTTAGAATGTTAGATGTGAAATAATTTAA
1457589 TGTGAAATTA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
37 1 0.02
38 30 0.54
39 23 0.41
40 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (40 bp):
AATTTAGAATGTTAGATGTGAAATAATTTAAAAAATTAAG
Found at i:1459773 original size:3 final size:3
Alignment explanation
Indices: 1459767--1459819 Score: 63
Period size: 3 Copynumber: 17.0 Consensus size: 3
1459757 TTCATTTGGT
*
1459767 TTA TTA TTA TTA TTC TTA TTA TT- TTAA TTA TTTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA -TTA TTA TTA TTA
1459814 TTA TTA
1 TTA TTA
1459820 AATAATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 34 0.76
4 9 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1464239 original size:15 final size:15
Alignment explanation
Indices: 1464219--1464252 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1464209 AGGATCAATA
*
1464219 CATTTTGCATACATT
1 CATTTTACATACATT
1464234 CATTTTACATACATT
1 CATTTTACATACATT
1464249 CATT
1 CATT
1464253 GGTCATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (15 bp):
CATTTTACATACATT
Found at i:1471608 original size:6 final size:5
Alignment explanation
Indices: 1471580--1471650 Score: 74
Period size: 5 Copynumber: 13.6 Consensus size: 5
1471570 TATTATGCTT
*
1471580 AAAGA AGAAAA AAAGA AAA-A AAAGGA AAAGAA AAAGA AAAGA AAA-A
1 AAAGA A-AAGA AAAGA AAAGA AAA-GA AAAG-A AAAGA AAAGA AAAGA
1471626 AAAGGA AAAGAA AAAGA AAAGA AAA
1 AAA-GA AAAG-A AAAGA AAAGA AAA
1471651 AGTAGAAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
4 8 0.14
5 27 0.47
6 22 0.39
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:1471611 original size:26 final size:26
Alignment explanation
Indices: 1471580--1471651 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
1471570 TATTATGCTT
1471580 AAAGAAGAAA-AAAAGAAAAAAAAGGA
1 AAAGAA-AAAGAAAAGAAAAAAAAGGA
1471606 AAAGAAAAAGAAAAGAAAAAAAAGGA
1 AAAGAAAAAGAAAAGAAAAAAAAGGA
1471632 AAAGAAAAAGAAAAGAAAAA
1 AAAGAAAAAGAAAAGAAAAA
1471652 GTAGAAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 3 0.07
26 42 0.93
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAGAAAAGAAAAAAAAGGA
Found at i:1471645 original size:37 final size:37
Alignment explanation
Indices: 1471580--1471652 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
1471570 TATTATGCTT
*
1471580 AAAGAAGAAAAAAAGAAAAAAAAGGAAAAGAAAAAGA
1 AAAGAAGAAAAAAAGAAAAAAAAAGAAAAGAAAAAGA
*
1471617 AAAGAA-AAAAAAGGAAAAGAAAAAGAAAAGAAAAAG
1 AAAGAAGAAAAAAAGAAAA-AAAAAGAAAAGAAAAAG
1471653 TAGAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 11 0.33
37 22 0.67
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (37 bp):
AAAGAAGAAAAAAAGAAAAAAAAAGAAAAGAAAAAGA
Found at i:1471651 original size:6 final size:6
Alignment explanation
Indices: 1471584--1471666 Score: 64
Period size: 6 Copynumber: 13.5 Consensus size: 6
1471574 ATGCTTAAAG
* * *
1471584 AAGAAA AA-AAGA AA-AAA AAGGAA AAGAAA AAGAAAA GAAAAAA AAGGAA
1 AAGAAA AAGAA-A AAGAAA AAGAAA AAGAAA AAG-AAA -AAGAAA AAGAAA
*
1471633 AAGAAA AAG-AA AAGAAA AAGTAGAA AATAAA AAG
1 AAGAAA AAGAAA AAGAAA AAG-A-AA AAGAAA AAG
1471667 GAGGTTCAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
5 10 0.16
6 38 0.61
7 8 0.13
8 6 0.10
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:1471652 original size:11 final size:11
Alignment explanation
Indices: 1471580--1471652 Score: 78
Period size: 11 Copynumber: 6.4 Consensus size: 11
1471570 TATTATGCTT
1471580 AAAGAAGAA-AA
1 AAAGAA-AAGAA
1471591 AAAGAAAA-AA
1 AAAGAAAAGAA
*
1471601 AAGGAAAAGAA
1 AAAGAAAAGAA
1471612 AAAGAAAAGAAAAA
1 AAAGAAAAG---AA
1471626 AAAGGAAAAGAA
1 AAA-GAAAAGAA
1471638 AAAGAAAAGAA
1 AAAGAAAAGAA
1471649 AAAG
1 AAAG
1471653 TAGAAAATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
10 11 0.20
11 28 0.51
12 5 0.09
14 5 0.09
15 6 0.11
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:1471665 original size:26 final size:24
Alignment explanation
Indices: 1471582--1471666 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 24
1471572 TTATGCTTAA
*
1471582 AGAAGAAAAAAAG-AAA-AAAAAG
1 AGAAAAAAAAAAGAAAAGAAAAAG
* *
1471604 -GAAAAGAAAAAGAAAAGAAAAAAA
1 AGAAAAAAAAAAGAAAAG-AAAAAG
*
1471628 AGGAAAAGAAAAAGAAAAGAAAAAG
1 A-GAAAAAAAAAAGAAAAGAAAAAG
*
1471653 TAGAAAATAAAAAG
1 -AGAAAAAAAAAAG
1471667 GAGGTTCAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
21 10 0.19
22 3 0.06
24 5 0.10
25 16 0.31
26 18 0.35
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (24 bp):
AGAAAAAAAAAAGAAAAGAAAAAG
Found at i:1472031 original size:18 final size:18
Alignment explanation
Indices: 1472008--1472045 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1471998 CAAGTTTATC
1472008 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
1472026 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
1472044 TT
1 TT
1472046 CTTTTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTTTGAAATTCAATTTA
Found at i:1473491 original size:123 final size:123
Alignment explanation
Indices: 1473156--1473843 Score: 977
Period size: 123 Copynumber: 5.7 Consensus size: 123
1473146 TGGATCAACA
*
1473156 TTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
* * * * *
1473220 GAGCTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGAAGATAGATCAGCAT-CAACAT
66 GAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATAC-AC-T
* * *
1473279 TTT-CAGA-AGGAGTTCATAATGAGAAGAACTCGTCT-----A-AAGAAGAAGTTCATAATGAAA
1 TTTCCAGAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGA
*
1473336 AGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACTTACACT
65 AGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATACACT
*
1473395 TTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
* *
1473460 GAACTTGTTCAGCCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATAGACT
66 GAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATACACT
* *
1473518 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGATGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
* *
1473583 GAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATATATCAACATACACC
66 GAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATACACT
* * * * *
1473641 TTTCTAAAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
* * * *
1473706 GAATTTGTTCAACCTTTTGCATGACGCTATCACAGAAGGAGATAGATCATCAT-CAACA
66 GAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATAC-ACT
* * *
1473764 TTTCCAGA-AGAGTCCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
* *
1473828 AAATTTGTTCAACCTT
66 GAACTTGTTCAACCTT
1473844 GCCTTAATTT
Statistics
Matches: 513, Mismatches: 41, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
116 4 0.01
117 97 0.19
118 3 0.01
122 72 0.14
123 337 0.66
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATACACT
Found at i:1474212 original size:3 final size:3
Alignment explanation
Indices: 1474206--1474247 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
1474196 TTTATATGGT
*
1474206 TTA TTA TTA TTA TTA TT- TTA TTTA GTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
1474248 AATAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1474221 original size:21 final size:21
Alignment explanation
Indices: 1474197--1474242 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1474187 CTAGTTTTTT
* *
1474197 TTATATGGTTTATTATTATTA
1 TTATATGATTTAGTATTATTA
* *
1474218 TTATTTTATTTAGTATTATTA
1 TTATATGATTTAGTATTATTA
1474239 TTAT
1 TTAT
1474243 TATTAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (21 bp):
TTATATGATTTAGTATTATTA
Found at i:1475748 original size:15 final size:15
Alignment explanation
Indices: 1475720--1475752 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1475710 ACTGAAATTA
1475720 AATTTAGATCTTTAT
1 AATTTAGATCTTTAT
1475735 AATTT-GATCTTT-T
1 AATTTAGATCTTTAT
1475748 AATTT
1 AATTT
1475753 TATTTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 7 0.39
15 5 0.28
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (15 bp):
AATTTAGATCTTTAT
Found at i:1476122 original size:38 final size:41
Alignment explanation
Indices: 1476074--1476155 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 41
1476064 ATTTTAATAC
1476074 TATAGTTTTAATTTT-T-T-TTTATTTT-AATCACTATTTAAT
1 TATAGTTTTAATTTTATATGTTTATTTTCAAT-A-TATTTAAT
1476113 TATA-TTTTAATTTTATATGTTTATTTTCAATATATTTAAT
1 TATAGTTTTAATTTTATATGTTTATTTTCAATATATTTAAT
1476153 TAT
1 TAT
1476156 TATTATTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
38 10 0.26
39 5 0.13
40 12 0.31
41 9 0.23
42 3 0.08
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (41 bp):
TATAGTTTTAATTTTATATGTTTATTTTCAATATATTTAAT
Found at i:1476556 original size:27 final size:27
Alignment explanation
Indices: 1476513--1476565 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1476503 TATTTCTATG
*
1476513 TAAATAAATATCTTATTTACAAAAATA
1 TAAATAAATATATTATTTACAAAAATA
*
1476540 TAAA-AAATATATATATTTATAAAAAT
1 TAAATAAATATAT-TATTTACAAAAAT
1476566 TAATATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (27 bp):
TAAATAAATATATTATTTACAAAAATA
Found at i:1476562 original size:19 final size:18
Alignment explanation
Indices: 1476538--1476575 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1476528 TTTACAAAAA
1476538 TATAAAAAATATATATATT
1 TATAAAAAATA-ATATATT
*
1476557 TATAAAAATTAATATATT
1 TATAAAAAATAATATATT
1476575 T
1 T
1476576 TTCTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAAAAAATAATATATT
Found at i:1476571 original size:20 final size:20
Alignment explanation
Indices: 1476538--1476587 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1476528 TTTACAAAAA
*
1476538 TATAAAAAAT-ATATATATT
1 TATAAAAATTAATATATATT
*
1476557 TATAAAAATTAATATATTTT
1 TATAAAAATTAATATATATT
* *
1476577 TCTTAAAATTA
1 TATAAAAATTA
1476588 TTGTAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAAAAATTAATATATATT
Found at i:1479009 original size:19 final size:20
Alignment explanation
Indices: 1478985--1479025 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1478975 TATTTATGTT
*
1478985 ATTTGTTT-TTTCTTTTTCG
1 ATTTGTTTATTTATTTTTCG
1479004 ATTTGTTTATTTATTTTTCG
1 ATTTGTTTATTTATTTTTCG
1479024 AT
1 AT
1479026 AATCGTTCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.12, C:0.07, G:0.10, T:0.71
Consensus pattern (20 bp):
ATTTGTTTATTTATTTTTCG
Found at i:1485068 original size:16 final size:16
Alignment explanation
Indices: 1485047--1485086 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1485037 ATGTTACAGG
1485047 CCAAATCACTACAAGC
1 CCAAATCACTACAAGC
1485063 CCAAATCACTACAAGC
1 CCAAATCACTACAAGC
1485079 CCAAATCA
1 CCAAATCA
1485087 GGCTATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.45, C:0.38, G:0.05, T:0.12
Consensus pattern (16 bp):
CCAAATCACTACAAGC
Found at i:1493223 original size:125 final size:125
Alignment explanation
Indices: 1493001--1493378 Score: 506
Period size: 125 Copynumber: 3.0 Consensus size: 125
1492991 AATACCAACA
* * *
1493001 TTGGGGCATGACTGAACCCCCATCATTTTGAAATGACAAGATCCAGACGAAGAAGGCATTGAGAA
1 TTGGGGCACGACTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
* * **
1493066 TGAGCCTTACAATTTGAGGTGTTGGGGTATTTTAAAGACCCGTACCTTTATAAGATAATG
66 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTAAAGACCCGTACCAGTATAAGATAATG
* **
1493126 TTGGGGCACGATTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
1 TTGGGGCACGACTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
* * *
1493191 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATGAGATAATG
66 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTAAAGACCCGTACCAGTATAAGATAATG
* * ** *
1493251 TTGGGGCGCGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAA
1 TTGGGGCACGACTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
* * * * * * * *
1493316 TGAGCCTTATAATTTGAGAT-ATTGAGGCATTTTGAAGGCCCATACCAGAATAAAATAATG
66 TGAGCCTTACAATTTGAGGTGA-TGGGGCATTTTAAAGACCCGTACCAGTATAAGATAATG
1493376 TTG
1 TTG
1493379 CGATATTAGT
Statistics
Matches: 224, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
124 1 0.00
125 223 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (125 bp):
TTGGGGCACGACTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
TGAGCCTTACAATTTGAGGTGATGGGGCATTTTAAAGACCCGTACCAGTATAAGATAATG
Found at i:1493876 original size:21 final size:21
Alignment explanation
Indices: 1493852--1493897 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1493842 GGTTAAAATG
1493852 AGAAATGACGTGGTGACATGA
1 AGAAATGACGTGGTGACATGA
1493873 AGAAATGACGTGGTGACATGA
1 AGAAATGACGTGGTGACATGA
1493894 AGAA
1 AGAA
1493898 TTGGGGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.09, G:0.33, T:0.17
Consensus pattern (21 bp):
AGAAATGACGTGGTGACATGA
Found at i:1494639 original size:36 final size:36
Alignment explanation
Indices: 1494599--1494833 Score: 223
Period size: 36 Copynumber: 6.5 Consensus size: 36
1494589 AAGTCAATCT
1494599 TAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCC
1 TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCAT-C
*
1494635 TAAGCCTTCACCGGAGA-ATAGTGAAGCAAACCATC
1 TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCATC
* * *
1494670 TGAAGCCTTCACCGGAGA-ATAGTGAAGCAATCAATC
1 T-AAGCCTTCACCGAAGAGATAGTGAAGCAAACCATC
*
1494706 TGAAGCCTTCACCGGAGA-ATAGTGAAGCAAACCATC
1 T-AAGCCTTCACCGAAGAGATAGTGAAGCAAACCATC
* *
1494742 ATAAGTCTTCACC--AGAGAGTAGTGAAGCAAACCATAT
1 -TAAGCCTTCACCGAAGAGA-TAGTGAAGCAAACCAT-C
* * * * *
1494779 TAAGTCTTCACCAAAAAG-TAGTGAAGCAGATCCATTT
1 TAAGCCTTCACCGAAGAGATAGTGAAGCA-AACCA-TC
* *
1494816 TAAGCCTTCTCAGAAGAG
1 TAAGCCTTCACCGAAGAG
1494834 TGTTGGAACA
Statistics
Matches: 175, Mismatches: 14, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
34 3 0.02
35 4 0.02
36 145 0.83
37 19 0.11
38 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (36 bp):
TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCATC
Found at i:1494801 original size:108 final size:108
Alignment explanation
Indices: 1494586--1494833 Score: 311
Period size: 108 Copynumber: 2.3 Consensus size: 108
1494576 ATGAGATTGG
* *
1494586 AGCAAGTCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAG
1 AGCAA-TCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCATAAGCCTTCACCAGAG
* * *
1494651 AATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGA
65 AATAGTGAAGCAAACCATATGAAGCCTTCACCGAAAAATAGTGA
* * *
1494695 AGCAATCAATCTGAAGCCTTCACCGGAGA-ATAGTGAAGCAAACCATCATAAGTCTTCACCAGAG
1 AGCAATCAATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCATAAGCCTTCACCAGAG
* * *
1494759 AGTAGTGAAGCAAACCATATTAAGTCTTCACC-AAAAAGTAGTGA
65 AATAGTGAAGCAAACCATATGAAGCCTTCACCGAAAAA-TAGTGA
* * * *
1494803 AGCAGATCCATTTTAAGCCTTCTCAGAAGAG
1 AGCA-ATCAATCTTAAGCCTTCACCGAAGAG
1494834 TGTTGGAACA
Statistics
Matches: 118, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
107 4 0.03
108 90 0.76
109 24 0.20
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (108 bp):
AGCAATCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCATAAGCCTTCACCAGAGA
ATAGTGAAGCAAACCATATGAAGCCTTCACCGAAAAATAGTGA
Found at i:1494806 original size:72 final size:70
Alignment explanation
Indices: 1494599--1494790 Score: 258
Period size: 72 Copynumber: 2.7 Consensus size: 70
1494589 AAGTCAATCT
* *
1494599 TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCAA
1 TAAGCCTTCACCG-AGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCAA
1494664 ACCATC
65 ACCATC
* * * *
1494670 TGAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGCA
1 T-AAGCCTTCACC-GAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCA
1494735 AACCATC
64 AACCATC
* * *
1494742 ATAAGTCTTCACCAGAGAGTAGTGAAGCAAACCATATTAAGTCTTCACC
1 -TAAGCCTTCACC-GAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACC
1494791 AAAAAGTAGT
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
71 1 0.01
72 101 0.97
73 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (70 bp):
TAAGCCTTCACCGAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAA
CCATC
Found at i:1495280 original size:51 final size:51
Alignment explanation
Indices: 1495204--1495643 Score: 566
Period size: 51 Copynumber: 8.5 Consensus size: 51
1495194 TGAAAATATG
*
1495204 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* *
1495255 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGA-GATGT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATG-T-T
* * * *
1495307 CTAAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAG-TTGAAGATGTT
1 C-GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCC-GTTTGAAGATGTT
* *
1495359 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTT
*
1495410 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
*
1495461 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
*
1495512 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTT
* * * *
1495565 CGAGTTCTATACTCCCTAGAGAAATAGGGAGCGAACCCATTTGTTGAAGATTGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCC--GT-TTGAAGA-TGTT
* *
1495620 CGAG-TCTTATACTCTCTGAAGAAA
1 CGAGTTC-TATACTCCCTAAAGAAA
1495644 TAGGGGCAGA
Statistics
Matches: 355, Mismatches: 18, Indels: 28
0.89 0.04 0.07
Matches are distributed among these distances:
49 2 0.01
50 3 0.01
51 226 0.64
52 6 0.02
53 84 0.24
54 7 0.02
55 24 0.07
56 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24
Consensus pattern (51 bp):
CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
Found at i:1495564 original size:206 final size:206
Alignment explanation
Indices: 1495204--1495602 Score: 653
Period size: 206 Copynumber: 1.9 Consensus size: 206
1495194 TGAAAATATG
*
1495204 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTC
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTC
*
1495269 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTAAGTTCCATACTCCCTAGAGAAAGA
66 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTAAGTTCCATACTCCCTAAAGAAAGA
*
1495334 GGGAGCGAACCCAGTTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
131 AGGAGCGAACCCAGTTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
1495399 GAAGAGATGTT
196 GAAGAGATGTT
* *
1495410 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTC
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTC
* * *
1495475 CTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGT-TCGAGTTCTATACTCCTTAAAGAAAG
66 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT-AAGTTCCATACTCCCTAAAGAAAG
*
1495537 AAGGAGCGAACCC-GTTTGAAGAGATGTTCGAGTTCTATACTCCCTAGAGAAATAGGGAGCGAAC
130 AAGGAGCGAACCCAG-TTG-A-AGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAAC
1495601 CC
192 CC
1495603 ATTTGTTGAA
Statistics
Matches: 180, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
203 2 0.01
204 41 0.23
205 2 0.01
206 135 0.75
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (206 bp):
CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTC
CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTAAGTTCCATACTCCCTAAAGAAAGA
AGGAGCGAACCCAGTTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
GAAGAGATGTT
Found at i:1495643 original size:55 final size:54
Alignment explanation
Indices: 1495204--1496096 Score: 486
Period size: 51 Copynumber: 16.8 Consensus size: 54
1495194 TGAAAATATG
* * * *
1495204 CGAGTTCTATACTC-CTTAAAGAAAGAAGGAGCGAACCC-GT-TTGAAGA-TGTT
1 CGAGTTCTATACTCTC-TGAAGAAATAGGGAGCGAACCCATTGTTGAAGATTGTT
* * * * * *
1495255 CGAGTTCCATACTC-CTTAAAGAAAGAAGGAGCGAACCC-GT-TTGAAGAGATG-T
1 CGAGTTCTATACTCTC-TGAAGAAATAGGGAGCGAACCCATTGTTGAAGA-TTGTT
* * * *
1495307 CTAAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCA--GTTGAAGA-TGTT
1 C-GAGTTCTATACTCTCTGA-AGAAATAGGGAGCGAACCCATTGTTGAAGATTGTT
* * *
1495359 CGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCC---G-TGAAGAGATGTT
1 CGAGTTCTATACTCTCTGA-AGAAATAGGGAGCGAACCCATTGTTGAAGA-TTGTT
* * * *
1495410 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCC-GT-TTGAAGA-TGTT
1 CGAGTTCTATACTCTCTGAAGAAATAGGGAGCGAACCCATTGTTGAAGATTGTT
* * * *
1495461 CGAGTTCTATACTC-CTTAAAGAAAGAAGGAGCGAACCC-GT-TTGAAGA-TGTT
1 CGAGTTCTATACTCTC-TGAAGAAATAGGGAGCGAACCCATTGTTGAAGATTGTT
* * * * *
1495512 CGAGTTCTATACTC-CTTAAAGAAAGAAGGAGCGAACCC-GT-TTGAAGAGATGTT
1 CGAGTTCTATACTCTC-TGAAGAAATAGGGAGCGAACCCATTGTTGAAGA-TTGTT
*
1495565 CGAGTTCTATACTCCCT-AGAGAAATAGGGAGCGAACCCATTTGTTGAAGATTGTT
1 CGAGTTCTATACTCTCTGA-AGAAATAGGGAGCGAACCCA-TTGTTGAAGATTGTT
* *
1495620 CGAG-TCTTATACTCTCTGAAGAAATAGGG-GC-AGACGCAATCGTTGAAGATTGTT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGA-AC-CCATTGTTGAAGATTGTT
* * * * *
1495674 CG-GGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG-T
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGAAC-CCATTGTTGAAGATTGTT
* * *
1495728 -G-GGTCTTATACTCTCTGAAGAAATAGGG-GAC-AGACACAATCGTTGAAGATTGTT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAG-CGA-AC-CCATTGTTGAAGATTGTT
* ** * * *
1495782 CGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGATGAAGATT-AT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGC-GAACCCATTGTTGAAGATTGTT
* * * *
1495836 -G-GGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGTTGAAGATTGTT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGA-AC-CCATTGTTGAAGATTGTT
* *
1495890 CGAG-TCTTATACTCTCTGAAGAAATAGGGGGC-AGA-CAAGTTTGTTGAAGA-TGATT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGA-ACCCA--TTGTTGAAGATTG-TT
* *
1495945 CAAG-TCTTATACTCTCTGAAGAAATAGGGAGCGAACCCATTTTTCTGAAGATT-TAT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGAACCCA-TTGT-TGAAGATTGT-T
* * * * * *
1496001 TGAATTCTATACTCCCTGAA-AAGGACTAGAGAGCTG-ACGCGATTTTTGAAGA-TGTT
1 CGAGTTCTATACTCTCTGAAGAA--A-TAGGGAGC-GAAC-CCATTGTTGAAGATTGTT
* * *
1496057 CGAGTTCTATTCTC-CTGGAGAAAGAGGGAGCGAACCCATT
1 CGAGTTCTATACTCTCTGAAGAAATAGGGAGCGAACCCATT
1496097 TTCAGAAGAT
Statistics
Matches: 732, Mismatches: 50, Indels: 119
0.81 0.06 0.13
Matches are distributed among these distances:
49 6 0.01
50 2 0.00
51 223 0.30
52 15 0.02
53 180 0.25
54 56 0.08
55 172 0.23
56 50 0.07
57 12 0.02
58 13 0.02
59 3 0.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (54 bp):
CGAGTTCTATACTCTCTGAAGAAATAGGGAGCGAACCCATTGTTGAAGATTGTT
Found at i:1495754 original size:53 final size:55
Alignment explanation
Indices: 1495607--1495973 Score: 507
Period size: 55 Copynumber: 6.8 Consensus size: 55
1495597 GAACCCATTT
1495607 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGCAGACGCAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * * *
1495661 GTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * * *
1495716 GATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGACAGACACAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * *
1495769 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * *
1495824 GATGAAGATT-AT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
*
1495877 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGA--CAAGTTT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA--TC
*
1495932 GTTGAAGA-TGATTCAAGTCTTATACTCTCTGAAGAAATAGGG
1 GTTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
1495974 AGCGAACCCA
Statistics
Matches: 277, Mismatches: 28, Indels: 15
0.87 0.09 0.05
Matches are distributed among these distances:
53 95 0.34
54 44 0.16
55 138 0.50
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (55 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
Found at i:1495789 original size:108 final size:109
Alignment explanation
Indices: 1495552--1495973 Score: 554
Period size: 108 Copynumber: 3.9 Consensus size: 109
1495542 GCGAACCCGT
* * * * * *
1495552 TTGAAGAGATGTTCGAGT-TCTATACTCCCT-AGAGAAATAGGGAGCGAAC-CCATTTGTTGAAG
1 TTGAAGA-TTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGGGCAAACGCGA-TTGATGAAG
1495614 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCAATCG
62 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCAATCG
*
1495662 TTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
* *
1495727 -T-GGGTCTTATACTCTCTGAAGAAATAGGGGACAGACACAATCG
66 TTCGAGTCTTATACTCTCTGAAGAAATAGGGG-CAGACGCAATCG
* *
1495770 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGATGAAGATT-
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
* *
1495834 AT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
66 TTCGAGTCTTATACTCTCTGAAGAAATA-GGGGCAGACGCAATCG
* ** * *
1495878 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGTTTGTTGAAGA-TG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
*
1495942 ATTCAAGTCTTATACTCTCTGAAGAAATAGGG
66 -TTCGAGTCTTATACTCTCTGAAGAAATAGGG
1495974 AGCGAACCCA
Statistics
Matches: 282, Mismatches: 21, Indels: 19
0.88 0.07 0.06
Matches are distributed among these distances:
107 29 0.10
108 167 0.59
109 52 0.18
110 34 0.12
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (109 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
TTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCAATCG
Found at i:1496445 original size:16 final size:16
Alignment explanation
Indices: 1496424--1496463 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1496414 ATGTTACAGG
1496424 CCAAATCACTACAAGC
1 CCAAATCACTACAAGC
1496440 CCAAATCACTACAAGC
1 CCAAATCACTACAAGC
1496456 CCAAATCA
1 CCAAATCA
1496464 GGCTATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.45, C:0.38, G:0.05, T:0.12
Consensus pattern (16 bp):
CCAAATCACTACAAGC
Found at i:1500266 original size:36 final size:35
Alignment explanation
Indices: 1500213--1500338 Score: 137
Period size: 36 Copynumber: 3.5 Consensus size: 35
1500203 TAATACAGAT
*
1500213 GATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 GATTTGTCTCACTTGAGATTGTTTTTCTTAAAACA
* *
1500248 GACTTTGTCTCACTTGAGATTGTTTTACTCGTAAGA-A
1 GA-TTTGTCTCACTTGAGATTGTTTT--TCTTAAAACA
* * **
1500285 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAA
1 GATTTGTCTCACTTGAGATTGTTTTTCTTAAAAC-A
*
1500321 GATTTGTCTCGCTTGAGA
1 GATTTGTCTCACTTGAGA
1500339 CCGTTTTCAC
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
34 6 0.08
35 2 0.03
36 55 0.76
37 3 0.04
38 6 0.08
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (35 bp):
GATTTGTCTCACTTGAGATTGTTTTTCTTAAAACA
Found at i:1500304 original size:72 final size:74
Alignment explanation
Indices: 1500213--1500386 Score: 219
Period size: 72 Copynumber: 2.4 Consensus size: 74
1500203 TAATACAGAT
* ** **
1500213 GATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AGACTTTGTCTCACTTGAGATTGTTTT-AC
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGA-TTTGTCTCACTTGAGACCGTTTTCAC
*
1500276 TCGTAAGAA-
65 TCGAAAGAAG
*
1500285 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACT
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACT
1500350 CGAAAGAAG
66 CGAAAGAAG
* *
1500359 GCATTTCATTTCACTCATGACTGTTTTT
1 G-ATTT-ATTTCACTCAAGATTGTTTTT
1500387 AAAGAAGATT
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
72 51 0.58
73 13 0.15
74 1 0.01
75 4 0.05
76 19 0.22
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (74 bp):
GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACT
CGAAAGAAG
Found at i:1500395 original size:72 final size:72
Alignment explanation
Indices: 1500235--1500411 Score: 184
Period size: 72 Copynumber: 2.5 Consensus size: 72
1500225 TTGAGATTGT
* * ** *
1500235 TTTTCTTAAAAC-AGACTTTGTCTCACTTGAGATTGTTTTACTCGTAAGAAGATTTATTTCACTC
1 TTTTCTTAAAACAAGATTTTGTCTCGCTTGAGACCGTTTTACTCGAAAGAAGATTTATTTCACTC
*
1500299 AAGATTG
66 AAGACTG
1500306 TTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATTT
1 -TTTTCTTAAAACAAGATTTTGTCTCGCTTGAGACCGTTTT-ACTCGAAAGAA-G-ATTT-ATTT
*
1500370 CACTCATGACTG
61 CACTCAAGACTG
* * *
1500382 -TTT-TT-AAAGAAGATTTTATCACGCTTGAGA
1 TTTTCTTAAAACAAGATTTTGTCTCGCTTGAGA
1500412 TAGTTTCCCT
Statistics
Matches: 90, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
72 39 0.43
73 29 0.32
74 4 0.04
75 4 0.04
76 14 0.16
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (72 bp):
TTTTCTTAAAACAAGATTTTGTCTCGCTTGAGACCGTTTTACTCGAAAGAAGATTTATTTCACTC
AAGACTG
Found at i:1500446 original size:39 final size:39
Alignment explanation
Indices: 1500391--1500585 Score: 311
Period size: 39 Copynumber: 5.0 Consensus size: 39
1500381 GTTTTTAAAG
* * *
1500391 AAGATTTTATCACGCTTGAGATAGTTTCCCTCAAAATAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
1500430 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC-A
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* *
1500468 AATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* *
1500507 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAGACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
*
1500546 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
1500585 A
1 A
1500586 TTTTGTCTCC
Statistics
Matches: 143, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
38 37 0.26
39 106 0.74
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
Found at i:1500493 original size:77 final size:78
Alignment explanation
Indices: 1500391--1500585 Score: 302
Period size: 77 Copynumber: 2.5 Consensus size: 78
1500381 GTTTTTAAAG
* *
1500391 AAGATTTTATCACGCTTGAGATAGTTTCCCTCAAAATAAAAGATTTTATCTCGCTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAAAAGATTTTATCTCGCTTGAGATAGTT
1500456 TCCCTCGAAAC-A
66 TCCCTCGAAACAA
* * * *
1500468 AATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAAAAGATTTTATCTCGCTTGAGATAGTT
*
1500533 TCCCTCGAGACAA
66 TCCCTCGAAACAA
**
1500546 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAAA
1500586 TTTTGTCTCC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 69 0.64
78 38 0.36
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (78 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAAAAGATTTTATCTCGCTTGAGATAGTT
TCCCTCGAAACAA
Found at i:1500500 original size:19 final size:19
Alignment explanation
Indices: 1500440--1500500 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
1500430 AAGATTTTAT
1500440 CTCGCTTGAGATAGTTTCC
1 CTCGCTTGAGATAGTTTCC
**** * * **
1500459 CTCGAAACAAATATTTTAT
1 CTCGCTTGAGATAGTTTCC
1500478 CTCGCTTGAGATAGTTTCC
1 CTCGCTTGAGATAGTTTCC
1500497 CTCG
1 CTCG
1500501 AAACAGAAGA
Statistics
Matches: 26, Mismatches: 16, Indels: 0
0.62 0.38 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (19 bp):
CTCGCTTGAGATAGTTTCC
Found at i:1500524 original size:116 final size:114
Alignment explanation
Indices: 1500389--1500608 Score: 341
Period size: 116 Copynumber: 1.9 Consensus size: 114
1500379 CTGTTTTTAA
*
1500389 AGAAGATTTTATCACGCTTGAGATAGTTTCCCTCAAAATAAAAGATTTTATCTCGCTTGAGATAG
1 AGAAGATTTTATCACGCTTGAGATAGTTTCCCTCAAAACAAAAGATTTTATCTCGCTTGAGATAG
* *
1500454 TTTCCCTCGAAACAAATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
66 TTTCCCTCGAAAC-AA-ATTTTATCTCCCTTGAGACAGTTTCCCTCGAAAC
* * * *
1500505 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAGACAAAAGATTTTATCTCGCTTGAGATAG
1 AGAAGATTTTATCACGCTTGAGATAGTTTCCCTCAAAACAAAAGATTTTATCTCGCTTGAGATAG
* *
1500570 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTT
66 TTTCCCTCGAAACAAATTTTATCTCCCTTGAGACAGTTT
1500609 GTCTTGAAAC
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 21 0.22
115 2 0.02
116 72 0.76
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (114 bp):
AGAAGATTTTATCACGCTTGAGATAGTTTCCCTCAAAACAAAAGATTTTATCTCGCTTGAGATAG
TTTCCCTCGAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTCGAAAC
Found at i:1500645 original size:65 final size:65
Alignment explanation
Indices: 1500570--1500713 Score: 207
Period size: 65 Copynumber: 2.2 Consensus size: 65
1500560 CTTGAGATAG
**
1500570 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTGTCTTGAAACATAAACATTGAAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAACA
** * * * *
1500635 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACATAAACTTTGAAAACG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAACA
*
1500700 TTTCCCTCGAAACA
1 TTTCCCTTGAAACA
1500714 CAAAATATTT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (65 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAACA
Found at i:1503228 original size:41 final size:41
Alignment explanation
Indices: 1503183--1503278 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
1503173 CGATTTTCCC
*
1503183 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGA
*
1503224 AATTCGTAATGCGAATAAGTAAATCGCAACACGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGA
*
1503265 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1503279 TACTGACTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGA
Found at i:1503247 original size:21 final size:21
Alignment explanation
Indices: 1503183--1503252 Score: 81
Period size: 20 Copynumber: 3.4 Consensus size: 21
1503173 CGATTTTCCC
1503183 AATTCGCAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGTA
* ** *
1503204 AA-TCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTA
*
1503224 AATTCGTAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGTA
1503245 AA-TCGCAA
1 AATTCGCAA
1503253 CACGAATTGG
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (21 bp):
AATTCGCAATGCGAATAAGTA
Found at i:1503269 original size:21 final size:21
Alignment explanation
Indices: 1503203--1503278 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 21
1503193 GCGAATAAGT
1503203 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* * * ** *
1503224 AATTCGTAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
*
1503244 AAATCGCAACACGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
1503265 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1503279 TACTGACTAT
Statistics
Matches: 39, Mismatches: 15, Indels: 2
0.70 0.27 0.04
Matches are distributed among these distances:
20 13 0.33
21 26 0.67
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1503309 original size:41 final size:41
Alignment explanation
Indices: 1503264--1503361 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
1503254 ACGAATTGGG
*
1503264 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAA
* * * * *
1503305 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAA
*
1503346 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
1503362 TTTCAAAGCG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAA
Found at i:1503313 original size:21 final size:20
Alignment explanation
Indices: 1503264--1503361 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
1503254 ACGAATTGGG
* *
1503264 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
1503284 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
* * * *
1503305 AAAATCGCAACGAGATACTT
1 AAAATCGCAATGCGATAATA
*** *
1503325 ACTTTCGCAACGCGATAATA
1 AAAATCGCAATGCGATAATA
*
1503345 CATAATCGCAATGCGAT
1 -AAAATCGCAATGCGAT
1503362 TTTCAAAGCG
Statistics
Matches: 56, Mismatches: 20, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
20 30 0.54
21 26 0.46
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.22
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:1503558 original size:22 final size:22
Alignment explanation
Indices: 1503530--1503573 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1503520 CACTCTCTCA
1503530 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1503552 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1503574 TATCTAAATC
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:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1503863 original size:20 final size:20
Alignment explanation
Indices: 1503838--1503875 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1503828 CGATTCTCTC
1503838 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1503858 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1503876 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1505214 original size:18 final size:18
Alignment explanation
Indices: 1505193--1505237 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1505183 TCCACTTCGG
*
1505193 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
1505211 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1505229 GAGCCATCA
1 GAGCCATCA
1505238 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1505764 original size:19 final size:20
Alignment explanation
Indices: 1505710--1505776 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1505700 TAGTTTACTT
* *
1505710 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1505730 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1505750 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1505769 TCGCAACG
1 TCGCAACG
1505777 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1505784 original size:14 final size:14
Alignment explanation
Indices: 1505765--1505822 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1505755 ATGCGAAATG
1505765 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1505779 AAAATCGCAACGCAAA
1 AAAATCGCAACG--AC
1505795 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1505811 AAAATCGCAACG
1 AAAATCGCAACG
1505823 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1505807 original size:32 final size:33
Alignment explanation
Indices: 1505749--1505839 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1505739 GGAAATGGCT
*
1505749 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
1505782 ATCGCAACGCAAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1505814 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
1505840 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1505833 original size:19 final size:19
Alignment explanation
Indices: 1505710--1505844 Score: 76
Period size: 19 Copynumber: 7.6 Consensus size: 19
1505700 TAGTTTACTT
* **
1505710 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1505730 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1505750 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1505769 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
1505783 TCGCAACGCAAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1505801 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1505815 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1505834 TCGCAATGCGA
1 TCGCAACGCGA
1505845 TTTGTGTTTC
Statistics
Matches: 90, Mismatches: 13, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 4 0.04
17 2 0.02
18 11 0.12
19 27 0.30
20 24 0.27
21 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1505875 original size:14 final size:14
Alignment explanation
Indices: 1505856--1505913 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1505846 TTGTGTTTCG
1505856 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1505870 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1505886 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1505902 CGTTGCGATTTT
1 CGTTGCGATTTT
1505914 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1505890 original size:32 final size:33
Alignment explanation
Indices: 1505851--1505929 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1505841 GCGATTTGTG
1505851 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1505883 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1505916 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1505930 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1505928 original size:19 final size:19
Alignment explanation
Indices: 1505872--1505971 Score: 77
Period size: 19 Copynumber: 5.5 Consensus size: 19
1505862 GATTTTGTCG
*
1505872 TTGCGA-TTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*
1505890 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
1505904 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*** *
1505923 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
**
1505943 TTGCGATAGTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1505962 TTGCGATTTT
1 TTGCGATTTT
1505972 AAGTTTCGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
14 6 0.09
15 3 0.05
16 4 0.06
17 4 0.06
18 9 0.14
19 23 0.35
20 17 0.26
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1505948 original size:20 final size:19
Alignment explanation
Indices: 1505914--1505968 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1505904 TTGCGATTTT
1505914 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
1505933 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
1505953 CATTTCGCATTGCGAT
1 CATTTCGCATTGCGAT
1505969 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:1507855 original size:14 final size:14
Alignment explanation
Indices: 1507836--1507871 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1507826 ATTGTTTAAT
1507836 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1507850 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1507864 TGATTTGT
1 TGATTTGT
1507872 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1507997 original size:14 final size:15
Alignment explanation
Indices: 1507978--1508054 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
1507968 CGAAATGGCT
1507978 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
1507992 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
1508010 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
1508029 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
1508043 ATCGCAATGCGA
1 ATCGCAA-GCGA
1508055 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:1508010 original size:19 final size:19
Alignment explanation
Indices: 1507988--1508054 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
1507978 ATCGCAACGA
1507988 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1508007 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1508025 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1508039 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1508055 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Done.