Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008421.1 Hibiscus syriacus cultivar Beakdansim tig00111201_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: 1159951
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:459761 original size:31 final size:31
Alignment explanation
Indices: 459724--459784 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
459714 GTACAGAAAA
* *
459724 CATCATATATTTAA-TCAATCAGAACATATAT
1 CATCATACATTTAACT-AATAAGAACATATAT
459755 CATCATACATTTAACTAATAAGAACATATA
1 CATCATACATTTAACTAATAAGAACATATA
459785 ACAATATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (31 bp):
CATCATACATTTAACTAATAAGAACATATAT
Found at i:459968 original size:23 final size:23
Alignment explanation
Indices: 459934--460011 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
459924 AGAAATTGCA
*
459934 CCAAAGTG-CCACATAGAAATGTC
1 CCAAAG-GACCACATAGAAATATC
* *
459957 CCAAAGGACCACATAGTATTATC
1 CCAAAGGACCACATAGAAATATC
* **
459980 CCGAAGGACCACATAGATTTATC
1 CCAAAGGACCACATAGAAATATC
*
460003 CCGAAGGAC
1 CCAAAGGAC
460012 TGAGTAGAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 1 0.02
23 47 0.98
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (23 bp):
CCAAAGGACCACATAGAAATATC
Found at i:460019 original size:23 final size:23
Alignment explanation
Indices: 459955--460011 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
459945 CATAGAAATG
*
459955 TCCCAAAGGACCACATAG-TATTA
1 TCCCGAAGGACCACATAGAT-TTA
459978 TCCCGAAGGACCACATAGATTTA
1 TCCCGAAGGACCACATAGATTTA
460001 TCCCGAAGGAC
1 TCCCGAAGGAC
460012 TGAGTAGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGATTTA
Found at i:463032 original size:35 final size:34
Alignment explanation
Indices: 462986--463116 Score: 187
Period size: 35 Copynumber: 3.9 Consensus size: 34
462976 TTGGTTTAGC
*
462986 ACTAGAGTGTATACCCAAGATACTTAGTGCATAA
1 ACTAGAGTGTATACCCAAGACACTTAGTGCATAA
*
463020 TACTAGAGTGTATACCCAATACACTTAGTGCATAA
1 -ACTAGAGTGTATACCCAAGACACTTAGTGCATAA
*
463055 CACTAGAGTGTATACCCAAGGA-ACTTATTGCAT-A
1 -ACTAGAGTGTATACCCAA-GACACTTAGTGCATAA
463089 AC-AGAGTGTATACCCAAGACACTTAGTG
1 ACTAGAGTGTATACCCAAGACACTTAGTG
463117 TATTTGGTGG
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
31 2 0.02
32 22 0.25
33 2 0.02
34 1 0.01
35 60 0.68
36 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (34 bp):
ACTAGAGTGTATACCCAAGACACTTAGTGCATAA
Found at i:467191 original size:18 final size:19
Alignment explanation
Indices: 467145--467191 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
467135 GGACCCTTAG
*
467145 TGCATCGATGCACTAAGAG
1 TGCATCGATGCACTAAGAA
467164 TGCATCGATGCA-TAA-AA
1 TGCATCGATGCACTAAGAA
467181 TGCATTCGATG
1 TGCA-TCGATG
467192 TTTCAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
19 12 0.46
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCACTAAGAA
Found at i:467296 original size:65 final size:64
Alignment explanation
Indices: 467143--467322 Score: 242
Period size: 65 Copynumber: 2.8 Consensus size: 64
467133 TTGGACCCTT
467143 AGTGCATCGATGCACTAAG-AGTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCT
1 AGTGCATCGATGCA-T-AGTAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCT
467206 G
64 G
* * *
467207 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTC
1 AGTGCATCGATGCATAG-TAGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-C
467270 TG
63 TG
*
467272 AGTGCATCGATGCATAGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAGTA-GTGCATCGATGCATAAAATGCATTCGATGTT
467323 CAATTTATAT
Statistics
Matches: 104, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 44 0.42
65 55 0.53
66 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATAGTAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTG
Found at i:467370 original size:65 final size:64
Alignment explanation
Indices: 467163--467362 Score: 239
Period size: 65 Copynumber: 3.1 Consensus size: 64
467153 TGCACTAAGA
* *
467163 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA-AATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAATA-TCTGAGTGCATCGATGCATGGTTG
* * *
467227 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTCTGAGTGCATCGATGCATAGTA
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAATAATA-TCTGAGTGCATCGATGCATGGT-
467291 T-
63 TG
* *
467292 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATATCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA-TAATATC-TGAGTGCATCGATGCATGG-T
467355 TG
63 TG
467357 GTGCAT
1 GTGCAT
467363 TGGTGCATCA
Statistics
Matches: 118, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
63 3 0.03
64 48 0.41
65 66 0.56
66 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAATATCTGAGTGCATCGATGCATGGTTG
Found at i:467737 original size:24 final size:24
Alignment explanation
Indices: 467708--467767 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
467698 CCTTACTCTA
467708 ACACTTCTCCCCTTTAACACTTTT
1 ACACTTCTCCCCTTTAACACTTTT
467732 ACACTTCTCCCCTTTAACACTTTT
1 ACACTTCTCCCCTTTAACACTTTT
467756 ACACTTCTCCCC
1 ACACTTCTCCCC
467768 CTTTTTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.20, C:0.42, G:0.00, T:0.38
Consensus pattern (24 bp):
ACACTTCTCCCCTTTAACACTTTT
Found at i:467844 original size:2 final size:2
Alignment explanation
Indices: 467837--467885 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
467827 TTAATTAGTC
467837 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
467879 AT AT AT A
1 AT AT AT A
467886 GCTTAAGCTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:470142 original size:21 final size:21
Alignment explanation
Indices: 470080--470159 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 21
470070 GCATGACCTT
470080 GTGCATCGATGCACATTCAAG
1 GTGCATCGATGCACATTCAAG
* * * *
470101 ACGTGCATCGGTGTACCTTCATG
1 --GTGCATCGATGCACATTCAAG
*
470124 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTCAAG
470145 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
470160 TGTTAGGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 17 0.37
22 12 0.26
23 17 0.37
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (21 bp):
GTGCATCGATGCACATTCAAG
Found at i:470175 original size:20 final size:21
Alignment explanation
Indices: 470084--470178 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 21
470074 GACCTTGTGC
*
470084 ATCGATGCACATTCAAGACGTGC
1 ATCGATGCACATTCAAG--GTGT
* * * *
470107 ATCGGTGTACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
470128 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
470150 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
470170 ATCGATGCA
1 ATCGATGCA
470179 TTAAGCACAA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 11 0.19
21 21 0.36
22 13 0.22
23 13 0.22
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:476023 original size:65 final size:65
Alignment explanation
Indices: 475875--476034 Score: 184
Period size: 65 Copynumber: 2.5 Consensus size: 65
475865 TGCACTAAGA
* *
475875 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCAATGTTTTCAAAATAGCCTGAGTGCATCGATGCATAGCTG
* * *
475939 GTGTATCAATGCATCAAATGCATTCAATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAG-
1 GTGCATCGATGCATAAAATGCATTCAATGTTTTCA-AAATAGC-CTGAGTGCATCGATGCATAGC
*
476001 TAT
64 T-G
* * *
476004 GTGCATCGATGTATGAAATGCATTCCATGTT
1 GTGCATCGATGCATAAAATGCATTCAATGTT
476035 CAATTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
64 27 0.33
65 51 0.63
66 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCAATGTTTTCAAAATAGCCTGAGTGCATCGATGCATAGCTG
Found at i:479909 original size:71 final size:70
Alignment explanation
Indices: 479834--480412 Score: 327
Period size: 71 Copynumber: 8.2 Consensus size: 70
479824 TGGACCTCAA
* * * *
479834 TCATGAAGGACACCCTATTAGTAGACGAACCCTCAACCATAGAGGAATTCGAATGCAACCCTGAG
1 TCATGAAGGACACCCCATTAGTAGACAAACCCTCAACCATGGAGGAATTCAAATGCAACCC-GAG
479899 CCTTAG
65 CCTTAG
* * * * * * * * * * * *
479905 TCATGAAAGATAACCAACTAGTTGGA-AAACCCTCAACAATAGAGAAAATCAAACGTAATCCCGA
1 TCATGAAGGACACCCCATTAG-TAGACAAACCCTCAACCATGGAGGAATTCAAATGCAA-CCCGA
*
479969 GCATTAG
64 GCCTTAG
* * * ** ** * * * **
479976 TAATGAAGGGCATCCTGTTTTTAGGCAAACCCTCAGCCATGGAGGAATCCAAATGCAATCTAGAG
1 TCATGAAGGACACCCCATTAGTAGACAAACCCTCAACCATGGAGGAATTCAAATGCAA-CCCGAG
* *
480041 CCTCAT
65 CCTTAG
* * ** * **
480047 TCATGGAGGACACCCCATTAGTAGGCAAACCCTCAGTCATGGAGGAATCCAAATGCAATCTAGAG
1 TCATGAAGGACACCCCATTAGTAGACAAACCCTCAACCATGGAGGAATTCAAATGCAA-CCCGAG
* *
480112 CCTCAT
65 CCTTAG
* * * * * * * * *
480118 TCATGGAGGACACCCCATTAGTAGGCAAACCTTTAGCCATGAAGTAAGTCGAA--CAATCCCGAG
1 TCATGAAGGACACCCCATTAGTAGACAAACCCTCAACCATGGAGGAATTCAAATGCAA-CCCGAG
480181 CCTTAG
65 CCTTAG
* * *
480187 TCAT-AGAGGACA-CCCATTTAGTAGACGAACCCTCAGCCATGGATGAAGTT-AAATGCAACCAC
1 TCATGA-AGGACACCCCA-TTAGTAGACAAACCCTCAACCATGGAGGAA-TTCAAATGCAACC-C
480249 GAGCCTTAG
62 GAGCCTTAG
* ** * * * * * *
480258 TTACA-G-AGGAAAATCCATTAGTAGACCAACCTTGAACCATGGAGGAAGTCGAATACAACCACG
1 -T-CATGAAGGACACCCCATTAGTAGACAAACCCTCAACCATGGAGGAATTCAAATGCAACC-CG
480321 AGCCTTAG
63 AGCCTTAG
* * * *
480329 TCATG--GGACACCCCATTAGTATACAAACCCTCAACCATGGAAGAAGTT-GAACGCAACACCGA
1 TCATGAAGGACACCCCATTAGTAGACAAACCCTCAACCATGGAGGAA-TTCAAATGCAAC-CCGA
* *
480391 GCCTCAA
64 GCCTTAG
480398 TCAT-AGAGGACACCC
1 TCATGA-AGGACACCC
480413 TATTTAATTT
Statistics
Matches: 395, Mismatches: 93, Indels: 40
0.75 0.18 0.08
Matches are distributed among these distances:
68 4 0.01
69 100 0.25
70 10 0.03
71 269 0.68
72 10 0.03
73 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (70 bp):
TCATGAAGGACACCCCATTAGTAGACAAACCCTCAACCATGGAGGAATTCAAATGCAACCCGAGC
CTTAG
Found at i:480052 original size:35 final size:35
Alignment explanation
Indices: 480013--480127 Score: 124
Period size: 35 Copynumber: 3.3 Consensus size: 35
480003 AACCCTCAGC
480013 CATGGAGGAATCCAAATGCAATCTAGAGCCTCATT
1 CATGGAGGAATCCAAATGCAATCTAGAGCCTCATT
* * * * ** * * *
480048 CATGGAGGACACCCCATTAGTAGGC-AAACCCTCAGT
1 CATGGAGGA-ATCCAAAT-GCAATCTAGAGCCTCATT
480084 CATGGAGGAATCCAAATGCAATCTAGAGCCTCATT
1 CATGGAGGAATCCAAATGCAATCTAGAGCCTCATT
480119 CATGGAGGA
1 CATGGAGGA
480128 CACCCCATTA
Statistics
Matches: 59, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
34 3 0.05
35 31 0.53
36 22 0.37
37 3 0.05
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (35 bp):
CATGGAGGAATCCAAATGCAATCTAGAGCCTCATT
Found at i:480087 original size:36 final size:36
Alignment explanation
Indices: 480041--480148 Score: 112
Period size: 36 Copynumber: 3.0 Consensus size: 36
480031 CAATCTAGAG
480041 CCTCATTCATGGAGGACACCCCATTAGTAGGCAAAC
1 CCTCATTCATGGAGGACACCCCATTAGTAGGCAAAC
* * * * * ** * *
480077 CCTCAGTCATGGAGGA-ATCCAAAT-GCAATCTAGAG
1 CCTCATTCATGGAGGACACCCCATTAGTAGGC-AAAC
480112 CCTCATTCATGGAGGACACCCCATTAGTAGGCAAAC
1 CCTCATTCATGGAGGACACCCCATTAGTAGGCAAAC
480148 C
1 C
480149 TTTAGCCATG
Statistics
Matches: 51, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
34 3 0.06
35 22 0.43
36 23 0.45
37 3 0.06
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.19
Consensus pattern (36 bp):
CCTCATTCATGGAGGACACCCCATTAGTAGGCAAAC
Found at i:480209 original size:140 final size:141
Alignment explanation
Indices: 480038--480375 Score: 352
Period size: 140 Copynumber: 2.4 Consensus size: 141
480028 ATGCAATCTA
* * * *
480038 GAGCCTCATTCATGGAGGACACCCCATTAGTAGGCAAACCCTCAGTCATGGAGGAA-TCCAAATG
1 GAGCCTTAGTCAT-GAGGACACCCCATTAGTAGACAAACCCTCAGCCATGGAGGAAGT-CAAATG
* * * * * * *
480102 CAATCTA-GAGCCTCA-TT-CATGGAGGACACCCCATTAGTAGGCAAACCTTTAGCCATGAAGTA
64 CAA-CCACGAGCCTCAGTTACA--GAGGAAAACCCATTAGTAGACAAACCTTGAACCATGAAGGA
480164 AGTCG-A-ACAATCC-C
126 AGTCGAATACAA-CCAC
* * *
480178 GAGCCTTAGTCATAGAGGACA-CCCATTTAGTAGACGAACCCTCAGCCATGGATGAAGTTAAATG
1 GAGCCTTAGTCAT-GAGGACACCCCA-TTAGTAGACAAACCCTCAGCCATGGAGGAAGTCAAATG
* * * *
480242 CAACCACGAGCCTTAGTTACAGAGGAAAATCCATTAGTAGACCAACCTTGAACCATGGAGGAAGT
64 CAACCACGAGCCTCAGTTACAGAGGAAAACCCATTAGTAGACAAACCTTGAACCATGAAGGAAGT
480307 CGAATACAACCAC
129 CGAATACAACCAC
* * *
480320 GAGCCTTAGTCATG-GGACACCCCATTAGTATACAAACCCTCAACCATGGAAGAAGT
1 GAGCCTTAGTCATGAGGACACCCCATTAGTAGACAAACCCTCAGCCATGGAGGAAGT
480376 TGAACGCAAC
Statistics
Matches: 166, Mismatches: 23, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
139 6 0.04
140 129 0.78
141 11 0.07
142 20 0.12
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.20
Consensus pattern (141 bp):
GAGCCTTAGTCATGAGGACACCCCATTAGTAGACAAACCCTCAGCCATGGAGGAAGTCAAATGCA
ACCACGAGCCTCAGTTACAGAGGAAAACCCATTAGTAGACAAACCTTGAACCATGAAGGAAGTCG
AATACAACCAC
Found at i:480559 original size:3 final size:3
Alignment explanation
Indices: 480551--480675 Score: 85
Period size: 3 Copynumber: 40.3 Consensus size: 3
480541 TAGTTGTTAT
* *
480551 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA ATA TT- TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
480597 TTA CTA TTAA ATA TTAA TTA GTA TTA TTA TAA TTA GTTA TTA CTA TTTA
1 TTA TTA TT-A TTA TT-A TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA
* *
480646 TTTA TT- TTA GTTA CTA TTA CTAA TTA TTA T
1 -TTA TTA TTA -TTA TTA TTA -TTA TTA TTA T
480676 AATAATTAAA
Statistics
Matches: 96, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
2 6 0.06
3 71 0.74
4 19 0.20
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:480636 original size:13 final size:12
Alignment explanation
Indices: 480553--480683 Score: 66
Period size: 13 Copynumber: 10.3 Consensus size: 12
480543 GTTGTTATTT
*
480553 ATTATTATTATT
1 ATTATTATTATA
*
480565 ATTATTATTATT
1 ATTATTATTATA
*
480577 ATTAATATTAATA
1 ATTATTATT-ATA
* *
480590 TTTTTTATTACT-
1 ATTATTATTA-TA
* *
480602 ATTAAATATTAATT
1 ATT-ATTATT-ATA
*
480616 AGTATTATTATA
1 ATTATTATTATA
480628 ATTAGTTATTACTA
1 ATTA-TTATTA-TA
* *
480642 TTTATTTATTTTA
1 ATTA-TTATTATA
* *
480655 GTTACTATTACTA
1 ATTATTATTA-TA
*
480668 ATTATTATAATA
1 ATTATTATTATA
480680 ATTA
1 ATTA
480684 AATATAAAGA
Statistics
Matches: 90, Mismatches: 21, Indels: 16
0.71 0.17 0.13
Matches are distributed among these distances:
12 38 0.42
13 39 0.43
14 13 0.14
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (12 bp):
ATTATTATTATA
Found at i:484147 original size:27 final size:27
Alignment explanation
Indices: 484116--484179 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
484106 GTACATCCTA
484116 ACAAGTTTGACAAA-TTTAACCAATTTG
1 ACAAGTTTGA-AAATTTTAACCAATTTG
* *
484143 ACAAGTTAGAAAATTTTGACCAATTTG
1 ACAAGTTTGAAAATTTTAACCAATTTG
484170 ACAAGTTTGA
1 ACAAGTTTGA
484180 TATGTAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 3 0.09
27 30 0.91
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (27 bp):
ACAAGTTTGAAAATTTTAACCAATTTG
Found at i:484178 original size:9 final size:9
Alignment explanation
Indices: 484116--484179 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
484106 GTACATCCTA
484116 ACAAGTTTG
1 ACAAGTTTG
* *
484125 ACAAATTTA
1 ACAAGTTTG
484134 ACCAA-TTTG
1 A-CAAGTTTG
*
484143 ACAAGTTAG
1 ACAAGTTTG
* *
484152 AAAATTTTG
1 ACAAGTTTG
484161 ACCAA-TTTG
1 A-CAAGTTTG
484170 ACAAGTTTG
1 ACAAGTTTG
484179 A
1 A
484180 TATGTAAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
8 6 0.14
9 32 0.74
10 5 0.12
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (9 bp):
ACAAGTTTG
Found at i:487160 original size:22 final size:21
Alignment explanation
Indices: 487131--487173 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
487121 TTCGTACCGA
487131 TACTCAAAGAAGTATCGATAC
1 TACTCAAAGAAGTATCGATAC
*
487152 TACTACAAAGTAGTATCGATAC
1 TACT-CAAAGAAGTATCGATAC
487174 CGTAAACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (21 bp):
TACTCAAAGAAGTATCGATAC
Found at i:489675 original size:350 final size:349
Alignment explanation
Indices: 489030--489731 Score: 1145
Period size: 350 Copynumber: 2.0 Consensus size: 349
489020 TGCAAGAATT
* *
489030 AAAAGAATCACATAAGTTTGATAATAGTTTGATCGCTATAGCAGATAAGATAAGGCAGGAGAAGC
1 AAAAGAATCACAAAAGTTTGATAATAGTTTGATCACTATAGCAGATAAGATAAGGCAGGAGAAGC
* ** * *
489095 ACTAGGCTTTAAATTGTGAGATGGAAATGTATTGTATTTTAGAGGGTGACTCTGTGTTCCAATTT
66 ACTAGGATTTAAATTACGAGATGGAAATGTATTGTATTTTAGAGGGCGACTCTGTGTTCCAATTA
489160 GTAAGCTAAGAGATAGGATCATTCGTGAGGCACATAGTGATCCTTTTACTATGCATCCAGGAAGT
131 GTAAGCTAAGAGATAGGATCATTCGTGAGGCACATAGTGATCCTTTTACTATGCATCCAGGAAGT
*
489225 AAAAAGATGTATTAAGAGCTACATCATTTTATTGGTGGCCAAGGATGAAGAGGGATGTGTTAGAG
196 AAAAAGATGTATTAAGAGCTACATCATTTTATTGGTGGCCAAGAATGAAGAGGGATGTGTTAGAG
*
489290 TATGCGACTCGATGCTTAGCTTGTTAACAGGTTAAGGTAGAGCAACATGTTCCTTCAAGTATTCT
261 TATGCGACTCGATGCTTAGCTTGTTAACAGGTTAAGATAGAGCAACATGTTCCTT-AAGTATTCT
*
489355 TCAGCCTATCGAGATTCTGTAGTGG
325 TCAGCCTATCGAGATTCTGCAGTGG
* * * * *
489380 AAAA-AATCACAAAATTTTGATTATAGTTTGATCACTATAGCATATAAGGTAAGGTAGGAGAAGC
1 AAAAGAATCACAAAAGTTTGATAATAGTTTGATCACTATAGCAGATAAGATAAGGCAGGAGAAGC
*
489444 ACTAGGATTTAAATTACGAAGATGGAAATGTATTGTATTTTAGAGGGCGATTCTGTGTTCCAATT
66 ACTAGGATTTAAATTACG-AGATGGAAATGTATTGTATTTTAGAGGGCGACTCTGTGTTCCAATT
* * *
489509 AGTAAGCTAAGATATAGGATCATTCGTGAGGCACATAGTGGTCCTTTTGCTATGCATCCAGGAAG
130 AGTAAGCTAAGAGATAGGATCATTCGTGAGGCACATAGTGATCCTTTTACTATGCATCCAGGAAG
* * * *
489574 TAACAAGATGTATTAGGAGCTACGTCATTTTATTGGTGGCCAAGAATGAAGAGTGATGTGTTAGA
195 TAAAAAGATGTATTAAGAGCTACATCATTTTATTGGTGGCCAAGAATGAAGAGGGATGTGTTAGA
* * *
489639 GTATGCGACTCGATTCTTGGCTTGTTAACAGGTTAAGATAGAGCAACATGTTCCTTAAGTCTTCT
260 GTATGCGACTCGATGCTTAGCTTGTTAACAGGTTAAGATAGAGCAACATGTTCCTTAAGTATTCT
489704 TCAGCCTATCGAGATTCTGCAGTGG
325 TCAGCCTATCGAGATTCTGCAGTGG
489729 AAA
1 AAA
489732 TGGGATGGTC
Statistics
Matches: 325, Mismatches: 26, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
349 103 0.32
350 222 0.68
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (349 bp):
AAAAGAATCACAAAAGTTTGATAATAGTTTGATCACTATAGCAGATAAGATAAGGCAGGAGAAGC
ACTAGGATTTAAATTACGAGATGGAAATGTATTGTATTTTAGAGGGCGACTCTGTGTTCCAATTA
GTAAGCTAAGAGATAGGATCATTCGTGAGGCACATAGTGATCCTTTTACTATGCATCCAGGAAGT
AAAAAGATGTATTAAGAGCTACATCATTTTATTGGTGGCCAAGAATGAAGAGGGATGTGTTAGAG
TATGCGACTCGATGCTTAGCTTGTTAACAGGTTAAGATAGAGCAACATGTTCCTTAAGTATTCTT
CAGCCTATCGAGATTCTGCAGTGG
Found at i:491939 original size:19 final size:19
Alignment explanation
Indices: 491893--491929 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
491883 TATGATTTGG
491893 AATTGTATATTATTAGTTT
1 AATTGTATATTATTAGTTT
491912 AATTGTATATTATTAGTT
1 AATTGTATATTATTAGTT
491930 ACATATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (19 bp):
AATTGTATATTATTAGTTT
Found at i:492739 original size:26 final size:26
Alignment explanation
Indices: 492698--492755 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
492688 GGAGCTCCAC
*
492698 ATATTTTTTTATATAACTATTTGA-G
1 ATATTTTTTAATATAACTATTTGATG
492723 ATATTATTTTAATATAACTATTTGATG
1 ATATT-TTTTAATATAACTATTTGATG
492750 ATATTT
1 ATATTT
492756 CTCTTATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 5 0.17
26 19 0.63
27 6 0.20
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (26 bp):
ATATTTTTTAATATAACTATTTGATG
Found at i:492764 original size:27 final size:24
Alignment explanation
Indices: 492702--492766 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 24
492692 CTCCACATAT
492702 TTTTTTATATAACTATTTGAGATA
1 TTTTTTATATAACTATTTGAGATA
492726 TTATTTTAATATAACTATTTGATGATA
1 TT-TTTT-ATATAACTATTTGA-GATA
492753 TTTCTCTTATATAA
1 TTT-T-TTATATAA
492767 AAATTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 2 0.06
25 4 0.11
26 15 0.42
27 13 0.36
28 2 0.06
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTTTTATATAACTATTTGAGATA
Found at i:492950 original size:30 final size:31
Alignment explanation
Indices: 492916--492988 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 31
492906 ATATATTTCA
* * * *
492916 AAAATTATTTTCCAA-TTATTCATTTTACCT
1 AAAATAATTTTCCAAGTAATTCAGTTTACAT
492946 AAAATAATTTT-CAAGTAATTCAGTTTACAT
1 AAAATAATTTTCCAAGTAATTCAGTTTACAT
*
492976 -AAATCATTTTCCA
1 AAAATAATTTTCCA
492989 TAAAATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 12 0.33
30 24 0.67
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (31 bp):
AAAATAATTTTCCAAGTAATTCAGTTTACAT
Found at i:493126 original size:30 final size:30
Alignment explanation
Indices: 493086--493193 Score: 83
Period size: 30 Copynumber: 3.6 Consensus size: 30
493076 CCAAAAAATA
* *
493086 TAATTCATTTTACATGAAACACTTATT-AGG
1 TAATTTATTTTACATAAAACACTT-TTCAGG
** * *
493116 TAATTTATTTTATGTAAAACAGTTTTCATG
1 TAATTTATTTTACATAAAACACTTTTCAGG
* * * **
493146 TAATTTATTTTACGTAAACCAGTTTTCATA
1 TAATTTATTTTACATAAAACACTTTTCAGG
**
493176 TAATTCCTTTTACATAAA
1 TAATTTATTTTACATAAA
493194 TTATTTTTCA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 2 0.03
30 63 0.97
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (30 bp):
TAATTTATTTTACATAAAACACTTTTCAGG
Found at i:493329 original size:23 final size:23
Alignment explanation
Indices: 493289--493336 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
493279 TATTATGATA
493289 TTTTAAAAATAATGTTA-TTATT
1 TTTTAAAAATAATGTTATTTATT
*
493311 TTTTAATAAATAATTTTATTTATT
1 TTTTAA-AAATAATGTTATTTATT
493335 TT
1 TT
493337 ATTTGATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.26
23 10 0.43
24 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTAAAAATAATGTTATTTATT
Found at i:493337 original size:22 final size:22
Alignment explanation
Indices: 493281--493337 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
493271 TTGTTTGTTA
*
493281 TTATGATATTTTAAAAATAATG
1 TTATTATATTTTAAAAATAATG
* *
493303 TTATTATTTTTTAATAAATAATT
1 TTATTATATTTTAA-AAATAATG
493326 TTATT-TATTTTA
1 TTATTATATTTTA
493338 TTTGATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
TTATTATATTTTAAAAATAATG
Found at i:493427 original size:13 final size:14
Alignment explanation
Indices: 493411--493440 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
493401 ACTAAAAAAC
493411 TTTT-AAAAAATAA
1 TTTTCAAAAAATAA
493424 TTTTCAAAAAATAA
1 TTTTCAAAAAATAA
493438 TTT
1 TTT
493441 ATTTTACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTTCAAAAAATAA
Found at i:496520 original size:15 final size:15
Alignment explanation
Indices: 496500--496529 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
496490 CTGTGAGGTT
496500 GTGCACTATGATGTC
1 GTGCACTATGATGTC
496515 GTGCACTATGATGTC
1 GTGCACTATGATGTC
496530 ACCACAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (15 bp):
GTGCACTATGATGTC
Found at i:496579 original size:23 final size:23
Alignment explanation
Indices: 496549--496607 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
496539 TATATAAATG
496549 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
* * *
496572 CACCGAAGTGTCGCGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTA
496595 CACC-ATAGTGCCA
1 CACCGA-AGTGCCA
496608 TATAAGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.19
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:497318 original size:63 final size:64
Alignment explanation
Indices: 497251--497391 Score: 155
Period size: 65 Copynumber: 2.2 Consensus size: 64
497241 GCACTATCTA
* * *
497251 TGCATCGATACA-TAAAT-CCTATTCGATGTTTGTA-TTTAAGGGGGTGCATCGATGCAC-TACT
1 TGCATCGATACACT-AATGCC-ATTCGATGTTTGTATTTTAAAGGAGTGCATCGATGCACGT-CA
497312 TG
63 TG
* * * *
497314 TGCATCGATACACTGATGGCATTCGATGTTTTTATTTTTAAAGTAGTGCATCGATGCACGTCATG
1 TGCATCGATACACTAATGCCATTCGATGTTTGTA-TTTTAAAGGAGTGCATCGATGCACGTCATG
497379 TGCATCGATACAC
1 TGCATCGATACAC
497392 CTTGAACAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
63 27 0.41
64 2 0.03
65 36 0.55
66 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (64 bp):
TGCATCGATACACTAATGCCATTCGATGTTTGTATTTTAAAGGAGTGCATCGATGCACGTCATG
Found at i:500050 original size:3 final size:3
Alignment explanation
Indices: 500042--500101 Score: 59
Period size: 3 Copynumber: 19.3 Consensus size: 3
500032 ATATAGTAGC
* *
500042 ATT ATT ATTT ATT ATA ATAT ATT ATT ATT ATT A-T ATA ATAT ATT ATT
1 ATT ATT A-TT ATT ATT AT-T ATT ATT ATT ATT ATT ATT AT-T ATT ATT
*
500089 ATT ATT ATA ATT A
1 ATT ATT ATT ATT A
500102 CAAGACCCGA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 2 0.04
3 38 0.81
4 7 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:500080 original size:21 final size:21
Alignment explanation
Indices: 500042--500097 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
500032 ATATAGTAGC
500042 ATTATTATTTATTATAATATATT
1 ATTATTA-TTA-TATAATATATT
500065 ATTATTATTATATAATATATT
1 ATTATTATTATATAATATATT
500086 ATTATTATTATA
1 ATTATTATTATA
500098 ATTACAAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 23 0.70
22 3 0.09
23 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTATTATATAATATATT
Found at i:508863 original size:20 final size:20
Alignment explanation
Indices: 508838--508896 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
508828 CTCACAAAGC
*
508838 TGTAAAACCTTTGGGTCATT
1 TGTAAAACCTTCGGGTCATT
*
508858 TGTAAAACCTCCGGGTCATT
1 TGTAAAACCTTCGGGTCATT
508878 TGTAAAACCTTCGGGTCAT
1 TGTAAAACCTTCGGGTCAT
508897 CTATTAGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (20 bp):
TGTAAAACCTTCGGGTCATT
Found at i:509152 original size:36 final size:36
Alignment explanation
Indices: 508988--509300 Score: 328
Period size: 36 Copynumber: 8.6 Consensus size: 36
508978 CTCAAATCTG
* * *
508988 ACCTTCACGGAAGAGTAGTGAAGTAAAGTAACGTAATTTCA
1 ACCTTCACGGAAGAGTAGTGAAGT--CG-ATC--ATTTTCA
* * **
509029 ACCTTCACGGAAGAGTAGTGAAGTAGAACA-AGTCA
1 ACCTTCACGGAAGAGTAGTGAAGTCGATCATTTTCA
** * **
509064 ACCTTCACGGAAGAGTAGTGAAGTAAAACA-AGTCA
1 ACCTTCACGGAAGAGTAGTGAAGTCGATCATTTTCA
*
509099 ACCTTCATGGAAGAGTAGTGAAGTCGATCATTTTCA
1 ACCTTCACGGAAGAGTAGTGAAGTCGATCATTTTCA
* *
509135 ACCTTCACGGAACAGTAGTGACGTCGATCATTTTCA
1 ACCTTCACGGAAGAGTAGTGAAGTCGATCATTTTCA
509171 ACCTTCACGGAAGAGTAGTGAAGTCGATCATTTTCA
1 ACCTTCACGGAAGAGTAGTGAAGTCGATCATTTTCA
**
509207 ACCTTCACGGAAGAGTAGTGAAGTTAATCATTTTCA
1 ACCTTCACGGAAGAGTAGTGAAGTCGATCATTTTCA
* * * * *
509243 TCCTTCATGGAAGAGTAGTGAAGT-AATTCAATCT-A
1 ACCTTCACGGAAGAGTAGTGAAGTCGA-TCATTTTCA
* *
509278 GCCTTCATGGAAGAGTAGTGAAG
1 ACCTTCACGGAAGAGTAGTGAAG
509301 CAAGATCAGA
Statistics
Matches: 249, Mismatches: 21, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
35 88 0.35
36 132 0.53
38 3 0.01
39 2 0.01
41 24 0.10
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26
Consensus pattern (36 bp):
ACCTTCACGGAAGAGTAGTGAAGTCGATCATTTTCA
Found at i:509441 original size:3 final size:3
Alignment explanation
Indices: 509420--509481 Score: 99
Period size: 3 Copynumber: 20.3 Consensus size: 3
509410 TATATAGTAG
509420 ATT ATTT ATT A-T ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
509466 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
509482 CAAGACCCGA
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 48 0.86
4 6 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:515493 original size:12 final size:12
Alignment explanation
Indices: 515478--515502 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
515468 CGTTGCTTCC
515478 GACGAGGATCGT
1 GACGAGGATCGT
515490 GACGAGGATCGT
1 GACGAGGATCGT
515502 G
1 G
515503 TCGTGCATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.44, T:0.16
Consensus pattern (12 bp):
GACGAGGATCGT
Found at i:515594 original size:29 final size:29
Alignment explanation
Indices: 515532--515666 Score: 126
Period size: 29 Copynumber: 4.5 Consensus size: 29
515522 AACCCAACCA
* * **
515532 TAGGTCGCCAAGCACTCCAAGCGACCTAC
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
*
515561 AAGGTCGCCATGCACTCCCAGCGACCTTG
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
* * * *
515590 TAGGTCGCCAAGCAATCCCGGCGACCAAGATGG
1 TAGGTCGCCATGCACTCCCAGCGACC----TTG
* * *
515623 TAGGTCGCCATGTACGCCCAGCGACCTTA
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
515652 TAGGTCGCCATGCAC
1 TAGGTCGCCATGCAC
515667 GCCGGCGTCC
Statistics
Matches: 84, Mismatches: 18, Indels: 8
0.76 0.16 0.07
Matches are distributed among these distances:
29 61 0.73
33 23 0.27
ACGTcount: A:0.24, C:0.35, G:0.25, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCTTG
Found at i:516334 original size:21 final size:21
Alignment explanation
Indices: 516309--516352 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
516299 AATTTAGTTA
516309 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
516330 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
516351 AT
1 AT
516353 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:516366 original size:28 final size:28
Alignment explanation
Indices: 516329--516382 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
516319 TAGTATAAAT
*
516329 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
516357 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
516383 ATAGATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:519527 original size:60 final size:59
Alignment explanation
Indices: 519455--520209 Score: 913
Period size: 60 Copynumber: 13.2 Consensus size: 59
519445 TTTATAAGAT
* *
519455 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATTTGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAA--TGA
* *
519516 -TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
519574 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* *
519634 TTTAGTAATGATTAGTAATAATGAAATCATTATTAATTTTTAATGATTTGATAATAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* *
519694 TTTAGTAATGATTAGTAAAAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* * *
519754 TTTAGTCATGATTAGTAATAATGAAATCATTATTAATTTTTAATGATTTGATAATAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
519814 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
*
519874 TTTAGTAATGATTAGTAATAATGAAATTATTATTAA-ATTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* * * * * * *
519933 TTAGTAAT-AAT-GAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TT-A-A-TAATGA
1 TTAGTAATGATTAGTAATAATGA--AATTATTATTAATTT--T--TAATGATTTGATAGTAATGA
519992 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAAT-A----AT--T--TGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
520042 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
520100 TTAG---T-A--A-TAAT-A--AAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* *
520149 TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
520197 TTTAGTAATGATT
1 -TTAGTAATGATT
520210 TGATAGTAAT
Statistics
Matches: 627, Mismatches: 36, Indels: 68
0.86 0.05 0.09
Matches are distributed among these distances:
48 32 0.05
49 94 0.15
50 5 0.01
51 1 0.00
52 7 0.01
53 2 0.00
54 3 0.00
55 5 0.01
56 9 0.01
57 3 0.00
58 23 0.04
59 52 0.08
60 374 0.60
61 9 0.01
62 2 0.00
63 6 0.01
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
Found at i:519936 original size:48 final size:49
Alignment explanation
Indices: 519876--519989 Score: 203
Period size: 48 Copynumber: 2.3 Consensus size: 49
519866 AGTAATGATT
519876 TAGTAATGATTAGTAATAATGAAATTATTATTAA-ATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
519924 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
519973 TAGTAATGATTAATAAT
1 TAGTAATGATTAGTAAT
519990 GATTAGTAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
48 34 0.54
49 29 0.46
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:519989 original size:10 final size:10
Alignment explanation
Indices: 519973--520009 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
519963 AATGATTTGA
519973 TAGTAATGAT
1 TAGTAATGAT
*
519983 TAATAATGAT
1 TAGTAATGAT
519993 TAGTAATGAT
1 TAGTAATGAT
520003 TAGTAAT
1 TAGTAAT
520010 AATGAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:520001 original size:69 final size:69
Alignment explanation
Indices: 519924--520058 Score: 252
Period size: 69 Copynumber: 2.0 Consensus size: 69
519914 AATGATTTGA
*
519924 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAATAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATAATTTGATAGTAATGATTAATAA
519989 TGAT
66 TGAT
*
519993 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATAATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATAATTTGATAGTAATGATTAATAA
520058 T
66 T
520059 AATGAAATTA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (69 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATAATTTGATAGTAATGATTAATAA
TGAT
Found at i:520049 original size:49 final size:49
Alignment explanation
Indices: 519993--520205 Score: 365
Period size: 49 Copynumber: 4.3 Consensus size: 49
519983 TAATAATGAT
*
519993 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATAATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
520042 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
520091 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* *
520140 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
520188 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
520206 GATTTGATAG
Statistics
Matches: 158, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
48 34 0.22
49 124 0.78
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:520193 original size:14 final size:14
Alignment explanation
Indices: 520177--520224 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
520167 TATTAATATT
*
520177 TAATGATTTGATAT
1 TAATGATTTGATAG
520191 TAATGA-TT--TAG
1 TAATGATTTGATAG
520202 TAATGATTTGATAG
1 TAATGATTTGATAG
520216 TAATGATTT
1 TAATGATTT
520225 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:520194 original size:167 final size:165
Alignment explanation
Indices: 519756--520223 Score: 584
Period size: 167 Copynumber: 2.8 Consensus size: 165
519746 AGTAATGATT
* * *
519756 TAGTCATGATTAGTAATAATGAAATCATTATTAATTTTTAATGATTTGATAATAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTA
* * * * * * *
519821 ATGATTAGTAATAATGAA-ATT-ATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATG
65 ATGATTAGTAATAATTAATATTAATGATT-ATTATTAATGTTTTAATAAT-TTGA--TAGTAATG
519884 ATTAGTAATAATGAAATTATTATTAAATTTAATGATTTGA
126 ATTAGTAATAATGAAATTATTATTAAATTTAATGATTTGA
*
519924 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAATAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
* * *
519989 TGATTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTTTAATAATTTGATAGTAATGATT
66 TGATTAGTAATAATTAATATTAATG--ATTATTATTAATGTTTTAATAATTTGATAGTAATGATT
*
520053 AGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
129 AGTAATAATGAAATTATTATTAA-ATTTAATGATTTGA
*
520091 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
* * * * * *
520156 TAATAATTTATTATTAATATTTAATGATT-TGATATTAATGATTTAGTAATGATTTGATAGTAAT
66 TGATTAGTAATAATTAATA-TTAATGATTAT--TATTAATG-TTT--TAATAATTTGATAGTAAT
520220 GATT
125 GATT
520224 TACGACTTGA
Statistics
Matches: 263, Mismatches: 25, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
165 1 0.00
166 37 0.14
167 116 0.44
168 65 0.25
169 12 0.05
170 8 0.03
171 24 0.09
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (165 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
TGATTAGTAATAATTAATATTAATGATTATTATTAATGTTTTAATAATTTGATAGTAATGATTAG
TAATAATGAAATTATTATTAAATTTAATGATTTGA
Found at i:522479 original size:16 final size:16
Alignment explanation
Indices: 522446--522492 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
522436 ACAAAAAATT
*
522446 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
*
522461 TAATATATTAAACTAA
1 TAATATAATAAACTAA
522477 TAA-ACTAATAAACTAA
1 TAATA-TAATAAACTAA
522493 ACTTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:522566 original size:29 final size:30
Alignment explanation
Indices: 522534--522602 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
522524 CCCCTTAAAC
*
522534 AACTAATAAACTATTC-TTAATATAACGTT-
1 AACTAATAAACTATTCTTTAATATAA-ATTA
522563 AACTAATAAACTATTCTTTAATATAAATTA
1 AACTAATAAACTATTCTTTAATATAAATTA
522593 AACTAATAAA
1 AACTAATAAA
522603 TGATTTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.36
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAAATTA
Found at i:522612 original size:29 final size:29
Alignment explanation
Indices: 522534--522613 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 29
522524 CCCCTTAAAC
* *
522534 AACTAATAAACTATTCTTAATATAACGTT
1 AACTAATAAACTATTTTTAATATAACATT
522563 AACTAATAAACTATTCTTTAATATAA-ATT
1 AACTAATAAACTATT-TTTAATATAACATT
522592 AAACTAATAAA-TGATTTTTAAT
1 -AACTAATAAACT-ATTTTTAAT
522614 TATTTTACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 24 0.52
30 22 0.48
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (29 bp):
AACTAATAAACTATTTTTAATATAACATT
Found at i:522835 original size:21 final size:20
Alignment explanation
Indices: 522811--522854 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
522801 TTTCTATATG
522811 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAA-A
522832 ATATAACTTAAACTAACAAA
1 ATATAACTTAAACTAACAAA
522852 ATA
1 ATA
522855 ATTAACTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (20 bp):
ATATAACTTAAACTAACAAA
Found at i:522931 original size:18 final size:18
Alignment explanation
Indices: 522878--522932 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
522868 TTGTTTTACC
*
522878 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
522896 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
522908 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
522925 CTAATTTA
1 CTAATTTA
522933 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:522994 original size:33 final size:35
Alignment explanation
Indices: 522952--523019 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
522942 TCTTTTATAT
*
522952 AACTT-AA-ACTAATAAACTATTTTTTTATATAAA
1 AACTTAAACACTAATAAACTAATTTTTTATATAAA
522985 AACTTAAACTACTAATAAACTAATTTTTTATATAA
1 AACTTAAAC-ACTAATAAACTAATTTTTTATATAA
523020 TATAAATTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 5 0.16
34 2 0.06
36 24 0.77
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (35 bp):
AACTTAAACACTAATAAACTAATTTTTTATATAAA
Found at i:523081 original size:27 final size:29
Alignment explanation
Indices: 523046--523110 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
523036 AAAATATAAC
*
523046 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
523073 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
523101 TTAATTATTT
1 TTAAATATTT
523111 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:523224 original size:9 final size:9
Alignment explanation
Indices: 523192--523229 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
523182 CTAACAAACT
523192 AATAATTTAA
1 AATAA-TTAA
523202 AATAA-TAA
1 AATAATTAA
*
523210 ACTAATTAA
1 AATAATTAA
523219 AATAATTAA
1 AATAATTAA
523228 AA
1 AA
523230 AAAACTTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:523559 original size:29 final size:28
Alignment explanation
Indices: 523512--523595 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 28
523502 AAAGGCATAG
523512 GTCGTTGGGATCCCTTGGCGACCTACAAT
1 GTCGTTGGGATCCC-TGGCGACCTACAAT
*
523541 GTCGTTGGGATGCTCTGGCGACCTACAAT
1 GTCGTTGGGAT-CCCTGGCGACCTACAAT
* *
523570 GTCGCTGGTATTCCCTGGCGACCTAC
1 GTCGTTGGGA-TCCCTGGCGACCTAC
523596 CCACGTTGCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 46 0.94
30 3 0.06
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (28 bp):
GTCGTTGGGATCCCTGGCGACCTACAAT
Found at i:523668 original size:42 final size:42
Alignment explanation
Indices: 523621--523710 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
523611 CCATGCACAA
*
523621 CCATGCAGAGACTCCAACCTCGCCCAGACCCATGCCACGTTG
1 CCATGCAGAGACTCCAACCTCGCCCAGACACATGCCACGTTG
523663 CCATGCAGAGACTCCAACCTCGCCCAGACACATGCCACGTTG
1 CCATGCAGAGACTCCAACCTCGCCCAGACACATGCCACGTTG
523705 CCATGC
1 CCATGC
523711 CGCCATGCAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.42, G:0.19, T:0.14
Consensus pattern (42 bp):
CCATGCAGAGACTCCAACCTCGCCCAGACACATGCCACGTTG
Found at i:528036 original size:11 final size:11
Alignment explanation
Indices: 528020--528053 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
528010 TTTTTATACA
528020 AATATAAGATT
1 AATATAAGATT
528031 AATATAAGA-T
1 AATATAAGATT
*
528041 AATATAAGTTT
1 AATATAAGATT
528052 AA
1 AA
528054 ATAGTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (11 bp):
AATATAAGATT
Found at i:528452 original size:57 final size:56
Alignment explanation
Indices: 528364--528471 Score: 171
Period size: 57 Copynumber: 1.9 Consensus size: 56
528354 GAGTGATTTT
* *
528364 AATGATTAAATGGAGTGTTAGTTTTTCTTAAGATCTAACTTCGAACAATTGTATCCC
1 AATGATTAAACGGAGTGCTAGTTTTTCTTAAGATCTAACTT-GAACAATTGTATCCC
* *
528421 AATGATTAAACGGAGTGCTAGTTTTTCTTAAGGTCTAACTTTAACAATTGT
1 AATGATTAAACGGAGTGCTAGTTTTTCTTAAGATCTAACTTGAACAATTGT
528472 GTCTACAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
56 9 0.19
57 38 0.81
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (56 bp):
AATGATTAAACGGAGTGCTAGTTTTTCTTAAGATCTAACTTGAACAATTGTATCCC
Found at i:529518 original size:60 final size:60
Alignment explanation
Indices: 529394--529521 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
529384 ATAGTTGAAT
* * * * * *
529394 GACCATTTTATAACTTTTAATAGTTAAGTGACTCAACAAAGTGTCATCTTATAATTGATA
1 GACCATTTTATAACCTTTAATAATTAAGTAACTCAACAAAGTATCATCTTATAATCGAGA
* * *
529454 GACCATTTTGTAACCTTTAATAATTGAAG-AACTCAACAAAGTATCAATC-TATAGTCGAGG
1 GACCATTTTATAACCTTTAATAATT-AAGTAACTCAACAAAGTATC-ATCTTATAATCGAGA
529514 GACCATTT
1 GACCATTT
529522 ACATACTTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 51 0.89
61 6 0.11
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (60 bp):
GACCATTTTATAACCTTTAATAATTAAGTAACTCAACAAAGTATCATCTTATAATCGAGA
Found at i:531941 original size:2 final size:2
Alignment explanation
Indices: 531934--532004 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
531924 CCAAACATAA
531934 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
531976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
532005 CACCATTTCC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:537736 original size:23 final size:23
Alignment explanation
Indices: 537702--537770 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
537692 CACCACATCT
*
537702 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
537725 CGTAGAATTGCACCTAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
537748 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
537771 TATAAGATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:538053 original size:30 final size:29
Alignment explanation
Indices: 538000--538058 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
537990 TGTAAACATA
* *
538000 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
538030 TCACATATACATTTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
538059 GTAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:547881 original size:21 final size:21
Alignment explanation
Indices: 547855--547925 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
547845 TAAGCATGAC
547855 ATCCATAACAACAAACTTGAA
1 ATCCATAACAACAAACTTGAA
547876 ATCCATAACAACAAACTTGAA
1 ATCCATAACAACAAACTTGAA
*
547897 ATCCATAACAACCAACTTGAA
1 ATCCATAACAACAAACTTGAA
547918 ATCCATAA
1 ATCCATAA
547926 TAATAAATCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.51, C:0.25, G:0.04, T:0.20
Consensus pattern (21 bp):
ATCCATAACAACAAACTTGAA
Found at i:554413 original size:42 final size:42
Alignment explanation
Indices: 554297--554425 Score: 159
Period size: 42 Copynumber: 3.0 Consensus size: 42
554287 GACAATCGCA
* * * *
554297 ACGTTTATAATAAAAACGTCACTAAGGTACATGACTATTGCG
1 ACGTTTATTACAAAAACGCCACTAAAGTACATGACTATTGCG
* * * * *
554339 GCGTTTATTACAAAAAATGCCACTAAATTACATGATTATTGTG
1 ACGTTTATTAC-AAAAACGCCACTAAAGTACATGACTATTGCG
*
554382 ATGTTTATTACAAAAACGCCACTAAAGTACATGACTATTGCG
1 ACGTTTATTACAAAAACGCCACTAAAGTACATGACTATTGCG
554424 AC
1 AC
554426 ATTTGAACAA
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 36 0.51
43 34 0.49
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (42 bp):
ACGTTTATTACAAAAACGCCACTAAAGTACATGACTATTGCG
Found at i:554530 original size:82 final size:82
Alignment explanation
Indices: 554444--554641 Score: 220
Period size: 82 Copynumber: 2.4 Consensus size: 82
554434 AAAAATATCG
* * * **
554444 CTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTATGAGTCTATAGAGGCG
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACACCACGAAAGTATAAGTCTATAGAGGAA
*
554509 TTTGTATACAAACGCCA
66 TTTCTATACAAACGCCA
* * * * * * * *
554526 CTAAAGAACGAGTTTATAGCGACGTTTATATACAAACACCACGAAAGTCTAAGTCTTTAGCGGAA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACACCACGAAAGTATAAGTCTATAGAGGAA
*
554591 TTTCTATACAAACGCCG
66 TTTCTATACAAACGCCA
* * *
554608 CTAAAGT-GGAGTCTTTTGCGGCGTTTG-ATAAAAA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAA
554642 ACGCCGCTAT
Statistics
Matches: 93, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
80 6 0.06
81 14 0.15
82 73 0.78
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (82 bp):
CTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACACCACGAAAGTATAAGTCTATAGAGGAA
TTTCTATACAAACGCCA
Found at i:554587 original size:41 final size:41
Alignment explanation
Indices: 554444--554614 Score: 157
Period size: 41 Copynumber: 4.2 Consensus size: 41
554434 AAAAATATCG
*
554444 CTAAAGTAC-AAGTCTATAGCGGCGTTTGTATAAAAACACCA
1 CTAAAGT-CTAAGTCTATAGCGGCGTTTGTATACAAACACCA
* * * *
554485 CTAAAGTATGAGTCTATAGAGGCGTTTGTATACAAACGCCA
1 CTAAAGTCTAAGTCTATAGCGGCGTTTGTATACAAACACCA
* * * * *
554526 CTAAAGAAC-GAGTTTATAGCGACGTTTATATACAAACACCA
1 CTAAAG-TCTAAGTCTATAGCGGCGTTTGTATACAAACACCA
* * ** * * *
554567 CGAAAGTCTAAGTCTTTAGCGGAATTTCTATACAAACGCCG
1 CTAAAGTCTAAGTCTATAGCGGCGTTTGTATACAAACACCA
554608 CTAAAGT
1 CTAAAGT
554615 GGAGTCTTTT
Statistics
Matches: 103, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
40 1 0.01
41 102 0.99
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (41 bp):
CTAAAGTCTAAGTCTATAGCGGCGTTTGTATACAAACACCA
Found at i:557300 original size:17 final size:19
Alignment explanation
Indices: 557262--557308 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
557252 ATATTCAGAG
557262 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
557281 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
557298 TGCATTCGATG
1 TGCA-TCGATG
557309 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:557331 original size:65 final size:62
Alignment explanation
Indices: 557152--557360 Score: 215
Period size: 65 Copynumber: 3.2 Consensus size: 62
557142 GCACCAAGTG
* * * *
557152 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGG--AGA
*
557216 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGAG-
557280 A
62 A
* * * *
557281 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCATCGATGCATCGATGCATGGACTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGA--G
557346 A
62 A
*
557347 TGCATCGGTGCATG
1 TGCATCGATGCATG
557361 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
63 1 0.01
64 38 0.30
65 66 0.53
66 19 0.15
67 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGAGA
Found at i:558349 original size:21 final size:21
Alignment explanation
Indices: 558315--558358 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
558305 CTGGAGGAGG
*
558315 AGGAGGAGCACGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
*
558336 AGGAGCAGCTCGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
558357 AG
1 AG
558359 CTCCCGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.36, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:559214 original size:21 final size:21
Alignment explanation
Indices: 559158--559221 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
559148 TCAATAAGCC
* *
559158 ATTAGGA-GCTTGAGGATCAGG
1 ATTAGGATG-TTGAGGAACGGG
* **
559179 ATTAGGTTGAGGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
559200 ATTAGGATGTTGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
559221 A
1 A
559222 GGACGGTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.42, T:0.22
Consensus pattern (21 bp):
ATTAGGATGTTGAGGAACGGG
Found at i:563845 original size:22 final size:21
Alignment explanation
Indices: 563803--563842 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
563793 GAGTTTGTTT
*
563803 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
563824 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
563843 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:565935 original size:17 final size:19
Alignment explanation
Indices: 565897--565943 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
565887 ATATTCAGAG
565897 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
565916 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
565933 TGCATTCGATG
1 TGCA-TCGATG
565944 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:565966 original size:65 final size:62
Alignment explanation
Indices: 565787--565995 Score: 215
Period size: 65 Copynumber: 3.2 Consensus size: 62
565777 GCACCAAGTG
* * * *
565787 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGG--AGA
*
565851 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGAG-
565915 A
62 A
* * * *
565916 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCATCGATGCATCGATGCATGGACTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGA--G
565981 A
62 A
*
565982 TGCATCGGTGCATG
1 TGCATCGATGCATG
565996 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
63 1 0.01
64 38 0.30
65 66 0.53
66 19 0.15
67 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGAGA
Found at i:566895 original size:21 final size:21
Alignment explanation
Indices: 566871--566910 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
566861 AAGACTTTAT
566871 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
566892 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
566911 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:570742 original size:23 final size:22
Alignment explanation
Indices: 570716--570767 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
570706 CTAGGTATCG
570716 TACCCCCTTTGAATGGGTACCGA
1 TACCCCC-TTGAATGGGTACCGA
*
570739 TACCATCCTTGAATGGGTACCGA
1 TACC-CCCTTGAATGGGTACCGA
570762 TACCCC
1 TACCCC
570768 TATAAGGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 1 0.04
23 23 0.88
24 2 0.08
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (22 bp):
TACCCCCTTGAATGGGTACCGA
Found at i:571265 original size:13 final size:13
Alignment explanation
Indices: 571240--571280 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
571230 TGAAAACTAC
571240 ACATTGATTTTCAA
1 ACATTG-TTTTCAA
571254 ACATTGTTTTCAA
1 ACATTGTTTTCAA
*
571267 ACATAGTTTTCAA
1 ACATTGTTTTCAA
571280 A
1 A
571281 ATTTGCCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
ACATTGTTTTCAA
Found at i:573477 original size:21 final size:21
Alignment explanation
Indices: 573453--573505 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
573443 ATGTTCAGAT
573453 GTACCGATACCTCCCTGGATG
1 GTACCGATACCTCCCTGGATG
*
573474 GTACCAATACCTCCCTGGATG
1 GTACCGATACCTCCCTGGATG
573495 GTACCGATACC
1 GTACCGATACC
573506 CCTAGTCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.23
Consensus pattern (21 bp):
GTACCGATACCTCCCTGGATG
Found at i:574311 original size:82 final size:82
Alignment explanation
Indices: 574224--574379 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 82
574214 AAAAACGTCG
** *
574224 CTAAAGTACTACT-TATTGCGGCGTTTGTTGAAAAAATGCCACTATATATGAACCCTATTACGAC
1 CTAAAGTACTACTCTATTGCGGCGTTTGTT-AAAAAACACCACTATAGATGAACCCTATTACGAC
*
574288 TTTTGTATAATAATACTA
65 ATTTGTATAATAATACTA
* *
574306 CTAAAGTACTACTCTGTTGCGGCGTTTGTTAAAAAACACCACTATAGATGAACCCTATTACGGCA
1 CTAAAGTACTACTCTATTGCGGCGTTTGTTAAAAAACACCACTATAGATGAACCCTATTACGACA
574371 TTTGTATAA
66 TTTGTATAA
574380 AAACACCATT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
82 52 0.78
83 15 0.22
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (82 bp):
CTAAAGTACTACTCTATTGCGGCGTTTGTTAAAAAACACCACTATAGATGAACCCTATTACGACA
TTTGTATAATAATACTA
Found at i:574387 original size:41 final size:41
Alignment explanation
Indices: 574262--574387 Score: 105
Period size: 41 Copynumber: 3.1 Consensus size: 41
574252 TGAAAAAATG
* * * * *
574262 CCACTATATATGAACCCTATTACGACTTTTGTATAATAATA
1 CCACTATAGATGAACCCTATTACGGCATTTGTATAAAAACA
* * * * * *
574303 CTACTAAAG-T-ACTACTCTGTTGCGGCGTTTGT-TAAAAAACA
1 CCACTATAGATGA--ACCCTATTACGGCATTTGTAT-AAAAACA
574344 CCACTATAGATGAACCCTATTACGGCATTTGTATAAAAACA
1 CCACTATAGATGAACCCTATTACGGCATTTGTATAAAAACA
574385 CCA
1 CCA
574388 TTAAATTTAC
Statistics
Matches: 63, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
39 1 0.02
40 2 0.03
41 57 0.90
42 2 0.03
43 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (41 bp):
CCACTATAGATGAACCCTATTACGGCATTTGTATAAAAACA
Found at i:575990 original size:2 final size:2
Alignment explanation
Indices: 575983--576010 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
575973 TTAATTATTA
575983 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
576011 TACATAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:577147 original size:27 final size:27
Alignment explanation
Indices: 577124--577184 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
577114 GATTTTGTGC
*
577124 ATTATCTTTTCTTTTGTTTATTTGACT
1 ATTATCTTGTCTTTTGTTTATTTGACT
577151 ATTATCTTGTCTTTTGTTTATTTGACT
1 ATTATCTTGTCTTTTGTTTATTTGACT
*
577178 ATGATCT
1 ATTATCT
577185 GAGAACCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.16, C:0.11, G:0.10, T:0.62
Consensus pattern (27 bp):
ATTATCTTGTCTTTTGTTTATTTGACT
Found at i:577458 original size:9 final size:9
Alignment explanation
Indices: 577446--577558 Score: 68
Period size: 9 Copynumber: 12.4 Consensus size: 9
577436 ATATATAATA
577446 TTTTT-TAT
1 TTTTTATAT
577454 TTTTTATAT
1 TTTTTATAT
**
577463 TAATTATAT
1 TTTTTATAT
* * *
577472 ATATAATAT
1 TTTTTATAT
*
577481 TTTATATAT
1 TTTTTATAT
*
577490 TTTATATTAAT
1 TTTTTA-T-AT
* *
577501 TATATATAAT
1 TTTTTAT-AT
* *
577511 ATTATATAT
1 TTTTTATAT
577520 TTTTTATA-
1 TTTTTATAT
577528 TTTTTATAT
1 TTTTTATAT
*
577537 TTTTTCTAT
1 TTTTTATAT
*
577546 TTTTTCTAT
1 TTTTTATAT
577555 TTTT
1 TTTT
577559 AATGAAAAAT
Statistics
Matches: 86, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
8 13 0.15
9 56 0.65
10 10 0.12
11 7 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTATAT
Found at i:577476 original size:34 final size:33
Alignment explanation
Indices: 577432--577529 Score: 153
Period size: 34 Copynumber: 3.0 Consensus size: 33
577422 CGCCCCGATT
*
577432 ATATATATATAATATTTTTTATTTTTTATATTA
1 ATATATATATAATATTTTATATTTTTTATATTA
*
577465 ATTATATATATAATATTTTATATATTTTATATTA
1 A-TATATATATAATATTTTATATTTTTTATATTA
*
577499 AT-TATATATAATATTATATATTTTTTATATT
1 ATATATATATAATATTTTATATTTTTTATATT
577530 TTTATATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 27 0.45
33 2 0.03
34 31 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
ATATATATATAATATTTTATATTTTTTATATTA
Found at i:577484 original size:32 final size:31
Alignment explanation
Indices: 577432--577529 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 31
577422 CGCCCCGATT
577432 ATATATATATAATATTTTTTATTTTTTATATTA
1 ATATATATATAATA--TTTTATTTTTTATATTA
577465 ATTATATATATAATATTTTATATATTTTATATTA
1 A-TATATATATAATATTTTAT-T-TTTTATATTA
577499 AT-TATATATAATATTATATATTTTTTATATT
1 ATATATATATAATATT-T-TATTTTTTATATT
577530 TTTATATTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
32 28 0.47
33 5 0.08
34 27 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
ATATATATATAATATTTTATTTTTTATATTA
Found at i:578866 original size:21 final size:21
Alignment explanation
Indices: 578842--578897 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
578832 TCCCATGCAA
* *
578842 TTTCGACGATCAATTGATTGC
1 TTTCGACGATCAATTGACTAC
578863 TTTCGACGATCAATTGACTAC
1 TTTCGACGATCAATTGACTAC
578884 TTTCGACGATCAAT
1 TTTCGACGATCAAT
578898 CGATGGCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (21 bp):
TTTCGACGATCAATTGACTAC
Found at i:579186 original size:16 final size:16
Alignment explanation
Indices: 579165--579196 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
579155 CACATGATGA
579165 GTCAAAAATATTTTAG
1 GTCAAAAATATTTTAG
579181 GTCAAAAATATTTTAG
1 GTCAAAAATATTTTAG
579197 ATACATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
GTCAAAAATATTTTAG
Found at i:582497 original size:21 final size:22
Alignment explanation
Indices: 582471--582511 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
582461 ATTAAATATA
* *
582471 AAATTATTAAA-AATGAAAATT
1 AAATTACTAAATAATAAAAATT
582492 AAATTACTAAATAATAAAAA
1 AAATTACTAAATAATAAAAA
582512 ATATTTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAATTACTAAATAATAAAAATT
Found at i:583105 original size:21 final size:21
Alignment explanation
Indices: 583081--583154 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 21
583071 TAATATATAT
583081 ATTTAATATTTTATTAATTTA
1 ATTTAATATTTTATTAATTTA
* * *
583102 ATTT-TTAGTTTTAGTATTTTA
1 ATTTAATA-TTTTATTAATTTA
*
583123 TATTTAAT-TTTT-TT-ATAT-
1 -ATTTAATATTTTATTAATTTA
583141 ATTTATATATTTTA
1 ATTTA-ATATTTTA
583155 AATTTTAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 13
0.67 0.12 0.22
Matches are distributed among these distances:
17 5 0.12
18 2 0.05
19 6 0.15
20 3 0.08
21 19 0.47
22 4 0.10
23 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (21 bp):
ATTTAATATTTTATTAATTTA
Found at i:587552 original size:34 final size:34
Alignment explanation
Indices: 587473--587541 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
587463 ATCATGAAAG
* *
587473 ATCTCTCAAACGACGTAATACAATGTGAAAATTA
1 ATCTCTCAAATGACGTAATACAATGTAAAAATTA
* *
587507 ATCTCTCAAATGACGTAGTCCAATGTAAAAATTA
1 ATCTCTCAAATGACGTAATACAATGTAAAAATTA
587541 A
1 A
587542 CTTTTCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (34 bp):
ATCTCTCAAATGACGTAATACAATGTAAAAATTA
Found at i:590144 original size:20 final size:22
Alignment explanation
Indices: 590119--590158 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
590109 TGTTGTATAT
590119 AGCCA-TTGGGGATG-TTTTGG
1 AGCCATTTGGGGATGATTTTGG
590139 AGCCATTTGGGGATGATTTT
1 AGCCATTTGGGGATGATTTT
590159 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (22 bp):
AGCCATTTGGGGATGATTTTGG
Found at i:590301 original size:20 final size:20
Alignment explanation
Indices: 590276--590338 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
590266 TTGATACATG
590276 GATGCATGGTAGGATGCATC
1 GATGCATGGTAGGATGCATC
590296 GATGCATGGTAGGATGCATC
1 GATGCATGGTAGGATGCATC
*
590316 GATGCATGGCAGGATGCATC
1 GATGCATGGTAGGATGCATC
590336 GAT
1 GAT
590339 ACACTAAGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (20 bp):
GATGCATGGTAGGATGCATC
Found at i:590437 original size:21 final size:21
Alignment explanation
Indices: 590411--590461 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
590401 GCAGGTGCAT
590411 GGATGCACTGCAGGGATACAG
1 GGATGCACTGCAGGGATACAG
* *
590432 GGATGCACTGCAGGGATGCAT
1 GGATGCACTGCAGGGATACAG
590453 GGATGCACT
1 GGATGCACT
590462 TTGACACCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.37, T:0.18
Consensus pattern (21 bp):
GGATGCACTGCAGGGATACAG
Found at i:590590 original size:30 final size:29
Alignment explanation
Indices: 590541--590598 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
590531 AAACTTTGAA
590541 TAAATTCAATTAAGTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
* *
590570 TAAATTCAATTTATGTCCAAAAATATTTT
1 TAAATTCAA-TTAAGTCCAAAAACATTTT
590599 TCCTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:593767 original size:20 final size:20
Alignment explanation
Indices: 593742--593827 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
593732 TTCCAGCCTT
593742 GATGCATCGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
593762 GATGCATC---G-AT-GC--
1 GATGCATCGATGCATGGCAG
*
593775 -ATGCATCGATTCATGGCAG
1 GATGCATCGATGCATGGCAG
* *
593794 GATGCATCGATTCATGGTAG
1 GATGCATCGATGCATGGCAG
593814 GATGCATCGATGCA
1 GATGCATCGATGCA
593828 CTAAGTGAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
12 7 0.13
15 2 0.04
16 4 0.07
17 3 0.05
20 39 0.71
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:593781 original size:32 final size:32
Alignment explanation
Indices: 593743--593809 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
593733 TCCAGCCTTG
593743 ATGCATCGATGCATGGCAGGATGCATCGATGC
1 ATGCATCGATGCATGGCAGGATGCATCGATGC
* *
593775 ATGCATCGATTCATGGCAGGATGCATCGATTC
1 ATGCATCGATGCATGGCAGGATGCATCGATGC
593807 ATG
1 ATG
593810 GTAGGATGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (32 bp):
ATGCATCGATGCATGGCAGGATGCATCGATGC
Found at i:594027 original size:29 final size:29
Alignment explanation
Indices: 594006--594062 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
593996 AAACTTTGAA
594006 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
*
594035 TAAATTCAATTCAAGTCCAAAAATATTT
1 TAAATTCAATTCAAGTCCAAAAACATTT
594063 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:594053 original size:30 final size:29
Alignment explanation
Indices: 594006--594064 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
593996 AAACTTTGAA
594006 TAAATTCAATTAAGTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
*
594035 TAAATTCAATTCAAGTCCAAAAATATTTTG
1 TAAATTCAATT-AAGTCCAAAAACATTTTG
594065 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:596773 original size:21 final size:21
Alignment explanation
Indices: 596731--596773 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
596721 TTTCTGAGCT
* *
596731 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
596752 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
596773 A
1 A
596774 ACGAATATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:596826 original size:20 final size:20
Alignment explanation
Indices: 596801--596838 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
596791 GAATGCTAGA
*
596801 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
596821 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
596839 TAATGAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:597542 original size:103 final size:103
Alignment explanation
Indices: 597317--597534 Score: 427
Period size: 103 Copynumber: 2.1 Consensus size: 103
597307 GTAGAGGGTC
*
597317 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
597382 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
597420 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
597485 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
597523 TATGTGGTCCTT
1 TATGTGGTCCTT
597535 ATGGACATTA
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:597585 original size:23 final size:23
Alignment explanation
Indices: 597551--597602 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
597541 ATTATTATAT
597551 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
597574 GGCACT-CTGGTGCAATTCTACGT
1 GGCACTAC-GGTGCAATTCTACGC
597597 GGCACT
1 GGCACT
597603 TAGGTACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:597612 original size:23 final size:23
Alignment explanation
Indices: 597550--597613 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
597540 CATTATTATA
597550 TGGCAC-TACGGTGCAATTCTACG
1 TGGCACTTA-GGTGCAATTCTACG
*
597573 CGGCACTCT-GGTGCAATTCTACG
1 TGGCACT-TAGGTGCAATTCTACG
*
597596 TGGCACTTAGGTACAATT
1 TGGCACTTAGGTGCAATT
597614 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 1 0.03
23 33 0.94
25 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:603745 original size:20 final size:20
Alignment explanation
Indices: 603720--603757 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
603710 GAATGCTAGA
*
603720 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
603740 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
603758 TAATGAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:604409 original size:103 final size:103
Alignment explanation
Indices: 604230--604447 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
604220 GTAGAGGGTC
* *
604230 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGAACATATATGTAATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
604295 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
604333 TATGTGGTCCTTCGGAACATATATGTAATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGAACATATATGTAATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
604398 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
604436 TATATGGTCCTT
1 TATGTGGTCCTT
604448 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGAACATATATGTAATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:604512 original size:22 final size:23
Alignment explanation
Indices: 604463--604525 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
604453 CATTATTATA
604463 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
604486 CGGCACTCCGGTGCAATT-TACG
1 TGGCACTACGGTGCAATTCTACG
604508 TGGCACTTA-GGTGCAATT
1 TGGCAC-TACGGTGCAATT
604526 ATATGAGCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:610981 original size:20 final size:20
Alignment explanation
Indices: 610956--611001 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
610946 TCAATCCTAG
* *
610956 AATTTAAAGTTAGAATGTTA
1 AATTTAAAGTTAGAAAGTGA
**
610976 AATTTATGGTTAGAAAGTGA
1 AATTTAAAGTTAGAAAGTGA
610996 AATTTA
1 AATTTA
611002 GACCATTTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.39
Consensus pattern (20 bp):
AATTTAAAGTTAGAAAGTGA
Found at i:612522 original size:2 final size:2
Alignment explanation
Indices: 612511--612539 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
612501 TATGAATTAG
612511 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
612540 ATTTATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:612849 original size:43 final size:44
Alignment explanation
Indices: 612788--612875 Score: 151
Period size: 43 Copynumber: 2.0 Consensus size: 44
612778 TATGAGATTG
*
612788 TTATAGATGTGAACTATAAAAACAACAAACCA-TAAACATTACA
1 TTATAGATGTGAACTATAAAAACAACAAACCATTAAACATGACA
*
612831 TTATAGATGTGAACTATAAAAACAACAAACTATTAAACATGACA
1 TTATAGATGTGAACTATAAAAACAACAAACCATTAAACATGACA
612875 T
1 T
612876 GAAGCATACC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 31 0.74
44 11 0.26
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (44 bp):
TTATAGATGTGAACTATAAAAACAACAAACCATTAAACATGACA
Found at i:613378 original size:3 final size:3
Alignment explanation
Indices: 613370--613435 Score: 60
Period size: 3 Copynumber: 22.0 Consensus size: 3
613360 CCCCATCATT
* * * * * * *
613370 CTC CTC CTC TTC ATC ATC ATC CTC ATC CTC ATC CTC CTC CTC ATC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
*
613418 CTC CTC ATC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC
613436 GTCATCATCA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.11, C:0.55, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:613383 original size:30 final size:30
Alignment explanation
Indices: 613347--613445 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
613337 CTTGTCGTCA
* *
613347 TCTTCATCGTCATCCCCATCATTC-TCCTCC
1 TCTTCATCATCATCCCCATC-CTCATCCTCC
*
613377 TCTTCATCATCATCCTCATCCTCATCCTCC
1 TCTTCATCATCATCCCCATCCTCATCCTCC
* * * * * *
613407 TCCTCATCCTCCTCCTCATCCTCCTCCTCG
1 TCTTCATCATCATCCCCATCCTCATCCTCC
*
613437 TCATCATCA
1 TCTTCATCA
613446 CTATCAACAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 56 0.97
ACGTcount: A:0.14, C:0.48, G:0.02, T:0.35
Consensus pattern (30 bp):
TCTTCATCATCATCCCCATCCTCATCCTCC
Found at i:613395 original size:6 final size:6
Alignment explanation
Indices: 613344--613435 Score: 78
Period size: 6 Copynumber: 15.3 Consensus size: 6
613334 ATCCTTGTCG
* * * * * * *
613344 TCATCT TCATCG TCATCC CCATCAT TC-TCC TCCTCT TCATCA TCATCC
1 TCATCC TCATCC TCATCC TCATC-C TCATCC TCATCC TCATCC TCATCC
* * *
613392 TCATCC TCATCC TCCTCC TCATCC TCCTCC TCATCC TCCTCC TC
1 TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TC
613436 GTCATCATCA
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
5 2 0.03
6 66 0.96
7 1 0.01
ACGTcount: A:0.13, C:0.50, G:0.01, T:0.36
Consensus pattern (6 bp):
TCATCC
Found at i:614592 original size:2 final size:2
Alignment explanation
Indices: 614546--614582 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
614536 TTTCCTATTA
614546 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
614583 AAACATATAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:615392 original size:14 final size:14
Alignment explanation
Indices: 615373--615403 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
615363 CAAAATTATT
615373 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
615387 TAAATAAATTCTAA
1 TAAATAAATTCAAA
615401 TAA
1 TAA
615404 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:615628 original size:15 final size:14
Alignment explanation
Indices: 615581--615624 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
615571 TTACAATTAA
*
615581 AATAATCAAATAAT
1 AATAATAAAATAAT
*
615595 AGATACTAAAATAAAT
1 A-ATAATAAAAT-AAT
615611 AATAATAAAATAAT
1 AATAATAAAATAAT
615625 TAATTACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:615651 original size:16 final size:15
Alignment explanation
Indices: 615632--615676 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
615622 AATTAATTAC
615632 TTAAATAATAAAAAA
1 TTAAATAATAAAAAA
*
615647 TTTAATGAATAAAAAA
1 TTAAAT-AATAAAAAA
* *
615663 ATAAATTATAAAAA
1 TTAAATAATAAAAA
615677 TAATTATACC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
TTAAATAATAAAAAA
Found at i:617741 original size:16 final size:16
Alignment explanation
Indices: 617729--617774 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
617719 AATAAACGTG
617729 CACGAACATAAACGAA
1 CACGAACATAAACGAA
*
617745 CACGAACATAAATGAA
1 CACGAACATAAACGAA
617761 CACGAACATAAACG
1 CACGAACATAAACG
617775 TTGGAGACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.54, C:0.24, G:0.13, T:0.09
Consensus pattern (16 bp):
CACGAACATAAACGAA
Found at i:618007 original size:24 final size:24
Alignment explanation
Indices: 617978--618035 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
617968 AAAAAATTAA
617978 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAACTCGAGACTC
618002 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAACTCGAGACTC
618026 GAGCTCGATT
1 GAGCTCGATT
618036 CAGAGCTCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (24 bp):
GAGCTCGATTAAAACTCGAGACTC
Done.