Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 87 of 322
Found at i:28019957 original size:21 final size:21
Alignment explanation
Indices: 28019882--28019947 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
28019872 GTCTTGAATT
*
28019882 TGTTAGATATTGAATTTATTA
1 TGTTAGATATTGAATTTATTC
* *
28019903 TGTTTTAAGCTTGTTGAATTTATTC
1 TG--TT-AG-ATATTGAATTTATTC
28019928 TGTTAGATATTGAATTTATT
1 TGTTAGATATTGAATTTATT
28019948 TGGTTGGATA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 14 0.39
22 2 0.06
23 4 0.11
24 2 0.06
25 14 0.39
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (21 bp):
TGTTAGATATTGAATTTATTC
Found at i:28021301 original size:19 final size:19
Alignment explanation
Indices: 28021277--28021355 Score: 117
Period size: 19 Copynumber: 4.2 Consensus size: 19
28021267 AATATTTAAG
28021277 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
28021296 GATATGCAATCATAGATAT
1 GATATGCAATCTTAGATAT
28021315 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28021332 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
28021353 GAT
1 GAT
28021356 CTTGTAATCT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
17 16 0.30
19 29 0.54
21 9 0.17
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28024674 original size:51 final size:51
Alignment explanation
Indices: 28024605--28024709 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
28024595 GAAGCAATTT
* *
28024605 CATAAATCGATTTATTTTCGTTACAATAAAATGACTATACGACCTTTCACC
1 CATAAATCGATTTATTTTCATTACAATAAAACGACTATACGACCTTTCACC
*
28024656 CATAAATCGATTTATTTTCATTACAATCAAACGACTATACGACCTTTCACC
1 CATAAATCGATTTATTTTCATTACAATAAAACGACTATACGACCTTTCACC
28024707 CAT
1 CAT
28024710 CCTATGACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.34
Consensus pattern (51 bp):
CATAAATCGATTTATTTTCATTACAATAAAACGACTATACGACCTTTCACC
Found at i:28024997 original size:27 final size:27
Alignment explanation
Indices: 28024905--28025054 Score: 144
Period size: 27 Copynumber: 5.5 Consensus size: 27
28024895 ATATTGAGCC
*
28024905 CGCACACTCAGTGCTATACA-A-TCAACT
1 CGCACACTTAGTGC-A-ACATAGTCAACT
* *
28024932 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCAACATAGTCA-ACT
** * *
28024960 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAACATAGTCAACT
* * **
28024987 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGCAACATAGTCAACT
28025014 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCAACATAGTC-AACT
28025041 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28025055 TGTACAATTT
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
25 3 0.03
26 1 0.01
27 75 0.73
28 24 0.23
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCAACATAGTCAACT
Found at i:28031789 original size:41 final size:41
Alignment explanation
Indices: 28031731--28031812 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
28031721 TGGGATATCT
*
28031731 CCCTACACGGGGCTTCAATACTGGTGCCGTTTGTTTCTATG
1 CCCTACACGGGGATTCAATACTGGTGCCGTTTGTTTCTATG
*
28031772 CCCTACACGGGGATTCAATACTGTTGCCGTTTGTTTCTATG
1 CCCTACACGGGGATTCAATACTGGTGCCGTTTGTTTCTATG
28031813 AAAACTAGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.35
Consensus pattern (41 bp):
CCCTACACGGGGATTCAATACTGGTGCCGTTTGTTTCTATG
Found at i:28032842 original size:27 final size:27
Alignment explanation
Indices: 28032812--28032991 Score: 121
Period size: 27 Copynumber: 6.6 Consensus size: 27
28032802 GTATATTGAG
* *
28032812 CTCGCACACTCAGTGCTATACAATCAA
1 CTCGCACACTTAGTGCTACACAATCAA
* **
28032839 CTCGCACACTTAGTGCCACGTAATCAA
1 CTCGCACACTTAGTGCTACACAATCAA
* * * *
28032866 ATCGCACACTTAGTGCTACATAGTTAGA
1 CTCGCACACTTAGTGCTACACAATCA-A
** ***
28032894 CTCGCACACTTAGTGCCGCATGGTCAA
1 CTCGCACACTTAGTGCTACACAATCAA
* * * *
28032921 TTCGCACACTTAGTGC-ATCATATTCAT
1 CTCGCACACTTAGTGCTA-CACAATCAA
* * * *
28032948 TTCGCACACTTAGTGCAACATAGTCGAA
1 CTCGCACACTTAGTGCTACACAATC-AA
28032976 -TCGCACACTTAGTGCT
1 CTCGCACACTTAGTGCT
28032992 GTACAATTTA
Statistics
Matches: 126, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
27 102 0.81
28 24 0.19
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CTCGCACACTTAGTGCTACACAATCAA
Found at i:28032908 original size:55 final size:55
Alignment explanation
Indices: 28032813--28032991 Score: 206
Period size: 54 Copynumber: 3.3 Consensus size: 55
28032803 TATATTGAGC
* * *
28032813 TCGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAA
1 TCGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAA
* * *
28032867 TCGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAAT
1 TCGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAA
** * *
28032922 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAA
1 TCGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAA
28032976 TCGCACACTTAGTGCT
1 TCGCACACTTAGTGCT
28032992 GTACAATTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 57 0.54
55 45 0.43
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (55 bp):
TCGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAA
Found at i:28032953 original size:82 final size:81
Alignment explanation
Indices: 28032835--28032990 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
28032825 TGCTATACAA
* * *
28032835 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
28032900 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
28032917 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
28032981 CACTTAGTGC
65 CACTTAGTGC
28032991 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28054686 original size:11 final size:11
Alignment explanation
Indices: 28054672--28054698 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28054662 AAAAATCAAT
28054672 ACAAAAGTTTC
1 ACAAAAGTTTC
28054683 ACAAAAGTTTC
1 ACAAAAGTTTC
28054694 ACAAA
1 ACAAA
28054699 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:28086115 original size:79 final size:81
Alignment explanation
Indices: 28085979--28086163 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
28085969 TTGAATGATG
*
28085979 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28086043 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28086058 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
28086120 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
28086138 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28086164 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:28086177 original size:40 final size:40
Alignment explanation
Indices: 28085980--28086163 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
28085970 TGAATGATGT
* * * *
28085980 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28086020 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
28086060 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28086098 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28086139 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28086164 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28086185 original size:79 final size:79
Alignment explanation
Indices: 28086032--28086196 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
28086022 GGACTAAGAT
* **
28086032 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28086097 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28086111 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28086174 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28086190 CCGAAGG
1 CCGAAGG
28086197 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28088266 original size:27 final size:27
Alignment explanation
Indices: 28088228--28088394 Score: 248
Period size: 27 Copynumber: 6.2 Consensus size: 27
28088218 TTATAGGACC
28088228 GTAATGCCCCTGTAGAGTAAAATGACT
1 GTAATGCCCCTGTAGAGTAAAATGACT
*
28088255 GTAATGCCCCTGTAGAGTAGAATGA-T
1 GTAATGCCCCTGTAGAGTAAAATGACT
* *
28088281 CGTAATGCCCTTGTAGAGTAAAATGACC
1 -GTAATGCCCCTGTAGAGTAAAATGACT
*
28088309 GTAATGCCCCTGTAGAGTAAAATGACC
1 GTAATGCCCCTGTAGAGTAAAATGACT
*
28088336 GTAATGCCCCTGTAG-GACAAAATGACT
1 GTAATGCCCCTGTAGAG-TAAAATGACT
*
28088363 GTAATGCCCCTGTAGGGTAAAATGACT
1 GTAATGCCCCTGTAGAGTAAAATGACT
28088390 GTAAT
1 GTAAT
28088395 ACACCTATAT
Statistics
Matches: 128, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
26 2 0.02
27 125 0.98
28 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (27 bp):
GTAATGCCCCTGTAGAGTAAAATGACT
Found at i:28088410 original size:27 final size:27
Alignment explanation
Indices: 28088224--28088413 Score: 208
Period size: 27 Copynumber: 7.0 Consensus size: 27
28088214 GTCATTATAG
28088224 GACCGTAATGCCCCTGTA-GAGTAAAAT
1 GACCGTAATGCCCCTGTAGGA-TAAAAT
* *
28088251 GACTGTAATGCCCCTGTA-GAGTAGAAT
1 GACCGTAATGCCCCTGTAGGA-TAAAAT
* *
28088278 GATCGTAATGCCCTTGTA-GAGTAAAAT
1 GACCGTAATGCCCCTGTAGGA-TAAAAT
28088305 GACCGTAATGCCCCTGTA-GAGTAAAAT
1 GACCGTAATGCCCCTGTAGGA-TAAAAT
*
28088332 GACCGTAATGCCCCTGTAGGACAAAAT
1 GACCGTAATGCCCCTGTAGGATAAAAT
* *
28088359 GACTGTAATGCCCCTGTAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGATAAAAT
* * * * *
28088386 GACTGTAATACACCTATATGATAAAAT
1 GACCGTAATGCCCCTGTAGGATAAAAT
28088413 G
1 G
28088414 TCGATTATGC
Statistics
Matches: 145, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
27 143 0.99
28 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (27 bp):
GACCGTAATGCCCCTGTAGGATAAAAT
Found at i:28088608 original size:27 final size:27
Alignment explanation
Indices: 28088559--28088637 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
28088549 AGTTCTATAC
* *
28088559 TGGTGACTATGTCAC-ATTCACTGTTAA
1 TGGTGGCTATGCCACAATT-ACTGTTAA
* *
28088586 TGGTGGCTATGCCACAATTACTGATAC
1 TGGTGGCTATGCCACAATTACTGTTAA
** * *
28088613 TGGAAGCTTTGCCACATTTACTGTT
1 TGGTGGCTATGCCACAATTACTGTT
28088638 TCTGGCAGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 39 0.93
28 3 0.07
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
TGGTGGCTATGCCACAATTACTGTTAA
Found at i:28088887 original size:33 final size:33
Alignment explanation
Indices: 28088837--28088924 Score: 151
Period size: 33 Copynumber: 2.7 Consensus size: 33
28088827 CTGCTATTGT
28088837 ATAGGGC-TAGGGCCCAGACTGTACTGATACTGA
1 ATAGGGCTTA-GGCCCAGACTGTACTGATACTGA
*
28088870 ATAGGGCTTAGGTCCAGACTGTACTGATACTGA
1 ATAGGGCTTAGGCCCAGACTGTACTGATACTGA
28088903 ATAGGGCTTAGGCCCAGACTGT
1 ATAGGGCTTAGGCCCAGACTGT
28088925 GTTATTCACT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 50 0.96
34 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (33 bp):
ATAGGGCTTAGGCCCAGACTGTACTGATACTGA
Found at i:28093346 original size:14 final size:14
Alignment explanation
Indices: 28093327--28093356 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
28093317 CTAATGTTGG
28093327 CTTGGTTTTAATGT
1 CTTGGTTTTAATGT
28093341 CTTGGTTTTAATGT
1 CTTGGTTTTAATGT
28093355 CT
1 CT
28093357 CAACCGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.10, G:0.20, T:0.57
Consensus pattern (14 bp):
CTTGGTTTTAATGT
Found at i:28106499 original size:39 final size:40
Alignment explanation
Indices: 28106404--28106665 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
28106394 TTGAATGATG
*
28106404 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28106442 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
28106483 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
28106522 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28106561 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
28106600 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
28106639 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28106666 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28110059 original size:60 final size:60
Alignment explanation
Indices: 28109966--28110088 Score: 210
Period size: 60 Copynumber: 2.0 Consensus size: 60
28109956 TTTAAGGGGG
* *
28109966 GAGAGTTGTAACAGCCTGTTTTCACTGAAATCGGAACAGTAGTTTCTGGAGCACAAATAC
1 GAGAGTTGTAACAGCCTGTTTTCACTGAAATCGGAACACTAGTTTCTGGACCACAAATAC
* *
28110026 GAGAGTTGTAACAGCCTGTTTTCACTGAAATCGGAATACTGGTTTCTGGACCACAAATAC
1 GAGAGTTGTAACAGCCTGTTTTCACTGAAATCGGAACACTAGTTTCTGGACCACAAATAC
28110086 GAG
1 GAG
28110089 TTAAAAAGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (60 bp):
GAGAGTTGTAACAGCCTGTTTTCACTGAAATCGGAACACTAGTTTCTGGACCACAAATAC
Found at i:28120294 original size:50 final size:49
Alignment explanation
Indices: 28120177--28120352 Score: 228
Period size: 50 Copynumber: 3.5 Consensus size: 49
28120167 CTAGTACGTA
* *
28120177 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCT-AGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGA-TACACG
* **
28120226 TTGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCTGATACACG
* * * *
28120276 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCTGATACACG
28120327 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
28120353 TGCGACCTCA
Statistics
Matches: 111, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
49 30 0.27
50 44 0.40
51 37 0.33
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGATACACG
Found at i:28120360 original size:101 final size:99
Alignment explanation
Indices: 28120177--28120360 Score: 269
Period size: 101 Copynumber: 1.8 Consensus size: 99
28120167 CTAGTACGTA
* * * *
28120177 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTAGTACACGTTGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCGAGTACACATAGTAGCCTGCACTTA
*
28120242 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACCTAACCATCTGATACACG
* * *
28120276 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACACATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCGAGTACACATAGTAGCCTGCACT
*
28120341 TAGTACTACACATGCGACCT
64 TAGTACTACACACGCGACCT
28120361 CACAATAGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 29 0.39
100 3 0.04
101 42 0.57
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCGAGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTAACCATCTGATACACG
Found at i:28124189 original size:28 final size:28
Alignment explanation
Indices: 28124178--28124303 Score: 155
Period size: 29 Copynumber: 4.4 Consensus size: 28
28124168 ATTTGGACTG
28124178 GATGGGCCATATAAATGAGATTGGGCCT
1 GATGGGCCATATAAATGAGATTGGGCCT
* * *
28124206 AATGGGCCATATGAATGTAAATTGGGCCT
1 GATGGGCCATATAAATG-AGATTGGGCCT
* * * *
28124235 GATTGGCCATATGAATGCGAATTGGGCCG
1 GATGGGCCATATAAATGAG-ATTGGGCCT
28124264 GATGGGCCATATAAATGAGATTGGGCCT
1 GATGGGCCATATAAATGAGATTGGGCCT
28124292 -AGTGGGCCATAT
1 GA-TGGGCCATAT
28124304 GCATGTATGT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.01
28 33 0.40
29 49 0.59
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (28 bp):
GATGGGCCATATAAATGAGATTGGGCCT
Found at i:28131108 original size:29 final size:29
Alignment explanation
Indices: 28131027--28131178 Score: 184
Period size: 29 Copynumber: 5.3 Consensus size: 29
28131017 GTGAGCATGA
* *
28131027 ATATG-ATGTGATTTGGGCCGGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* * *
28131055 ATATAAATGAG-ATTGGGCCTAATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
28131083 ATATGAATGTGAATTGGGCCTGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* *
28131112 ATATGAATGCGAATTGGGCCGGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* * *
28131141 ATATAAATGTG-ATTGGACCTTATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
*
28131169 ATATGCATGT
1 ATATGAATGT
28131179 ATGTAGGGGT
Statistics
Matches: 105, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
28 49 0.47
29 56 0.53
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTGATGGGCC
Found at i:28131114 original size:57 final size:58
Alignment explanation
Indices: 28131027--28131172 Score: 190
Period size: 57 Copynumber: 2.6 Consensus size: 58
28131017 GTGAGCATGA
* * *
28131027 ATATG-ATGTGATTTGGGCCGGATGGGCCATATAAATGAG-ATTGGGCCTAATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCCATATAAATGAGAATTGGGCCGAATGGGCC
* * *
28131083 ATATGAATGTGAATTGGGCCTGATGGGCCATATGAATGCGAATTGGGCCGGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCCATATAAATGAGAATTGGGCCGAATGGGCC
* * *
28131141 ATATAAATGTG-ATTGGACCTTATGGGCCATAT
1 ATATGAATGTGAATTGGGCCTGATGGGCCATAT
28131173 GCATGTATGT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
56 5 0.06
57 49 0.62
58 25 0.32
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.27
Consensus pattern (58 bp):
ATATGAATGTGAATTGGGCCTGATGGGCCATATAAATGAGAATTGGGCCGAATGGGCC
Found at i:28137635 original size:50 final size:50
Alignment explanation
Indices: 28137575--28137721 Score: 179
Period size: 50 Copynumber: 2.9 Consensus size: 50
28137565 ATCATTCATT
* * *
28137575 TGGCCTAATATACAAGATCAAATATAATATCACATATATGCATACCTATG
1 TGGCCAAATATACAAGATCAAATATAATATCACATATGTGCATACCTATA
* * *
28137625 TGGCCAAATATGCAAGATCAAATATAATATCACATATGTGCTTACTTATA
1 TGGCCAAATATACAAGATCAAATATAATATCACATATGTGCATACCTATA
*** * *
28137675 TGGTTGAATATACAA-ATTCAAATATAATGTCACATTTGTGCATACCT
1 TGGCCAAATATACAAGA-TCAAATATAATATCACATATGTGCATACCT
28137722 TTGATCCAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 1 0.01
50 81 0.99
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (50 bp):
TGGCCAAATATACAAGATCAAATATAATATCACATATGTGCATACCTATA
Found at i:28144360 original size:27 final size:27
Alignment explanation
Indices: 28144330--28144507 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28144320 ATATTGAGTC
* * * *
28144330 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28144357 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28144384 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28144412 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28144439 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28144466 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28144493 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28144508 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28144469 original size:82 final size:81
Alignment explanation
Indices: 28144351--28144506 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28144341 TGCTATATAA
* *
28144351 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28144416 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28144433 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28144497 CACTTAGTGC
65 CACTTAGTGC
28144507 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28152547 original size:27 final size:27
Alignment explanation
Indices: 28152517--28152694 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28152507 ATATTGAGTC
* * * *
28152517 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28152544 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28152571 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28152599 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28152626 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28152653 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28152680 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28152695 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28152656 original size:82 final size:81
Alignment explanation
Indices: 28152538--28152693 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28152528 TGCTATATAA
* *
28152538 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28152603 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28152620 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28152684 CACTTAGTGC
65 CACTTAGTGC
28152694 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28156956 original size:50 final size:50
Alignment explanation
Indices: 28156902--28157117 Score: 256
Period size: 50 Copynumber: 4.3 Consensus size: 50
28156892 ATCATTCATT
* *
28156902 TGGCCGAATATACAAGAT-AAATTATAATATCACATATATGCATACCTATG
1 TGGCCGAATATACAAGATCAAA-TATAATATCACATATGTGCATACCTATA
* * * *
28156952 TGGCCAAATATGCAAGATCAAATATAATATCACATATGTGCTTACTTATA
1 TGGCCGAATATACAAGATCAAATATAATATCACATATGTGCATACCTATA
* * *
28157002 TGGCTGAATATACAA-ATCCAAATATAATATCACATTTGTGCATACCTTTA
1 TGGCCGAATATACAAGAT-CAAATATAATATCACATATGTGCATACCTATA
** * * * *
28157052 TATCCGAATATACAAGATCCAATATAACATCACATATGTACATACCTATG
1 TGGCCGAATATACAAGATCAAATATAATATCACATATGTGCATACCTATA
*
28157102 TGGCCGAATATTCAAG
1 TGGCCGAATATACAAG
28157118 GTCATTTAGC
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
49 2 0.01
50 131 0.95
51 5 0.04
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (50 bp):
TGGCCGAATATACAAGATCAAATATAATATCACATATGTGCATACCTATA
Found at i:28162244 original size:43 final size:43
Alignment explanation
Indices: 28162089--28162245 Score: 185
Period size: 43 Copynumber: 3.7 Consensus size: 43
28162079 CAATGCTATA
* * * *
28162089 TCCCAGATAT-GTCTTACATGTTATCA-TATATCGATGCCACTG
1 TCCCAGACATGGTCTTACATGTAATCACAATAT-GATGCCAATG
* * * *
28162131 TCCCAGATA-GAGTCTTACATGAAATCATAATACGATGCCAATG
1 TCCCAGACATG-GTCTTACATGTAATCACAATATGATGCCAATG
* *
28162174 TCCCAGACATGGTCTTACACGTAATCACAATATAATGCCAATG
1 TCCCAGACATGGTCTTACATGTAATCACAATATGATGCCAATG
28162217 TCCCAGACATGGTCTTACATGTAATCACA
1 TCCCAGACATGGTCTTACATGTAATCACA
28162246 TCTTGATAAC
Statistics
Matches: 99, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
42 9 0.09
43 86 0.87
44 4 0.04
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACATGTAATCACAATATGATGCCAATG
Found at i:28167341 original size:200 final size:200
Alignment explanation
Indices: 28166998--28167397 Score: 773
Period size: 200 Copynumber: 2.0 Consensus size: 200
28166988 ACTCGTGTTA
28166998 AAGCGATATACCCTTTTCAAAAACCGGAATAAACTAAAATTTCTCGTTTTTTTCATATCACAACT
1 AAGCGATATACCCTTTTCAAAAACCGGAATAAACTAAAATTTCTCGTTTTTTTCATATCACAACT
28167063 AAACTTTACATTGAATTCGCATTTTTGAAAATTAAGACAACATGTGTTTATGAGATACCAATTTT
66 AAACTTTACATTGAATTCGCATTTTTGAAAATTAAGACAACATGTGTTTATGAGATACCAATTTT
* *
28167128 TGGGCGTCGCGAGGGTGCTAATACCTGGCTCGCGCGTAACCGACTCCCGAACCCTAATTTTCCTC
131 TGGGCGTCGCGAGGCTGCTAATACCTGCCTCGCGCGTAACCGACTCCCGAACCCTAATTTTCCTC
28167193 TGGCT
196 TGGCT
28167198 AAGCGATATACCCTTTTCAAAAACCGGAATAAACTAAAATTTCTCGTTTTTTTCATATCACAACT
1 AAGCGATATACCCTTTTCAAAAACCGGAATAAACTAAAATTTCTCGTTTTTTTCATATCACAACT
28167263 AAACTTTACATTGAATTCGCATTTTTGAAAATTAAGACAACATGTGTTTATGAGATACCAATTTT
66 AAACTTTACATTGAATTCGCATTTTTGAAAATTAAGACAACATGTGTTTATGAGATACCAATTTT
*
28167328 TGGGCGTCGCGAGGCTGCTAATACCTTCCTCGCGCGTAACCGACTCCCGAACCCTAATTTTCCTC
131 TGGGCGTCGCGAGGCTGCTAATACCTGCCTCGCGCGTAACCGACTCCCGAACCCTAATTTTCCTC
28167393 TGGCT
196 TGGCT
28167398 TTTAACGTAG
Statistics
Matches: 197, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 197 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (200 bp):
AAGCGATATACCCTTTTCAAAAACCGGAATAAACTAAAATTTCTCGTTTTTTTCATATCACAACT
AAACTTTACATTGAATTCGCATTTTTGAAAATTAAGACAACATGTGTTTATGAGATACCAATTTT
TGGGCGTCGCGAGGCTGCTAATACCTGCCTCGCGCGTAACCGACTCCCGAACCCTAATTTTCCTC
TGGCT
Found at i:28170616 original size:16 final size:17
Alignment explanation
Indices: 28170588--28170627 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
28170578 ATTCATTTGA
*
28170588 CATT-CATGCATTCATT
1 CATTGCATGAATTCATT
28170604 CA-TGCATGAATTCATT
1 CATTGCATGAATTCATT
28170620 CATTGCAT
1 CATTGCAT
28170628 ATCCCATACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 15 0.71
17 5 0.24
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.40
Consensus pattern (17 bp):
CATTGCATGAATTCATT
Found at i:28179227 original size:76 final size:75
Alignment explanation
Indices: 28179101--28179515 Score: 579
Period size: 76 Copynumber: 5.5 Consensus size: 75
28179091 TTTGTTTTTC
*
28179101 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
28179166 GTTGTTAAAAA
66 GTT-TTAAAAA
*
28179177 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
28179242 GTTGTTAAAAA
66 GTT-TTAAAAA
** *
28179253 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
*
28179318 GTTTT---CA
66 GTTTTAAAAA
* * ** * * *
28179325 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
28179390 GTTTTCAAAAA
66 GTTTT-AAAAA
* * *
28179401 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAATT
*
28179465 TCTGTTTT-TAAA
63 TCTGTTTTAAAAA
*
28179477 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
28179516 ATTACACACT
Statistics
Matches: 310, Mismatches: 21, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
72 65 0.21
75 3 0.01
76 213 0.69
77 1 0.00
78 28 0.09
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (75 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTTTAAAAA
Found at i:28179402 original size:148 final size:149
Alignment explanation
Indices: 28179101--28180729 Score: 929
Period size: 145 Copynumber: 10.5 Consensus size: 149
28179091 TTTGTTTTTC
* *
28179101 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
* *
28179166 GTTGTTAAAAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA
66 GTT-TT--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAA
28179231 TTTCAATTTCTGTTGTTAAAAA
128 TTTCAATTTCTGTTGTTAAAAA
**
28179253 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
* * * ** * *
28179318 GTTTT-CAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
66 GTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTT
28179382 CAATTTCTGTT-TTCAAAAA
131 CAATTTCTGTTGTT-AAAAA
* * *
28179401 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACA--CTGAGGTAATTTCAATT
* * * *
28179465 TCTGTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGG
63 TCTG-TTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-A-GACACGCTGAGG
* * ** **
28179530 TATTTTTTTTCAA-TTCATATTGCGAGAAGT
125 TA----ATTTCAATTTC-TGTTGTTA-AAAA
* ** * * * ** * * * *** * * * * * **
28179560 GAGTTGAGCCTCAGGA-CACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAATCAACTCATATT
1 AAAATCA-ACTCA-TATTGCGA-GAGGTGAGTTGAGCCTCAG---GAC-ACACTGAGGT-A-ATT
* * * *
28179624 CCGAGAGGTGGGTTGAAC-CTTTTAATTTCTACTTTTTCAAAATCAGCTCATATTGCAAGAGGTG
57 TC-A-A--T---TT---CTGTTTTAA-----A-------AAAATCAACTCATATTGCGAGAGGTG
** * * * **
28179688 AGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTG-TGTT---TT
100 AGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTGTTAAAAA
** * *
28179734 AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCGAGGTATTTTCAATTA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACA--CTGAGGTAATTTC-----
*
28179799 AGCCTTTTGATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
59 A--------ATTTCTG-TTTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
* * * *
28179864 TCACACTGAGGTATTTTCCATTTCTGTT-TTCATTATTATGTTTTTGAA
114 ACACGCTGAGGTAATTTCAATTTCTGTTGTT-A--A--A--------AA
* ** * * *
28179912 AGAATCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACATTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
* * ** * *
28179977 GTTTT-CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
66 GTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTT
*
28180041 CAATTTCTGCTT-TT---CA
131 CAATTTCTG-TTGTTAAAAA
* * ** *
28180057 AAATTCAACTCATAGTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
* * * * *
28180122 GTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTAT
66 G-TTTT--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAA
*
28180187 TTTCCATTTCTGTT-TTCATTATTATGTTTTTGAA
128 TTTCAATTTCTGTTGTT-A--A--A--------AA
* ** * ** * *
28180221 AGAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
* * * * ** *
28180286 GCTTTT-CAAAATTCAAATCATATTGTGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATT
66 G-TTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATT
*
28180350 TCAATTTCTGTT-TT---CA
130 TCAATTTCTGTTGTTAAAAA
* * ** * ** *
28180366 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
* * * ** *
28180431 GCTTTT-CAAAATTCAACTCATAGTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATT
66 G-TTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATT
*
28180495 TCAATTTCTGTT-TT---CA
130 TCAATTTCTGTTGTTAAAAA
* * ** * ** *
28180511 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
* * * ** *
28180576 GCTTTT-CAAAATTCAACTCATAGTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATT
66 G-TTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATT
*
28180640 TCAATTTCTGTTTTTAAAAA
130 TCAATTTCTGTTGTTAAAAA
* * *
28180660 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACTGAGGTATTTTCCATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
28180725 GTTTT
66 GTTTT
28180730 CATTATTATG
Statistics
Matches: 1191, Mismatches: 179, Indels: 218
0.75 0.11 0.14
Matches are distributed among these distances:
145 340 0.29
146 6 0.01
147 4 0.00
148 112 0.09
149 116 0.10
150 20 0.02
151 6 0.01
152 98 0.08
153 1 0.00
154 10 0.01
157 3 0.00
158 11 0.01
159 5 0.00
160 65 0.05
161 77 0.06
162 66 0.06
163 11 0.01
164 67 0.06
165 6 0.01
166 1 0.00
167 1 0.00
168 5 0.00
169 5 0.00
170 2 0.00
171 2 0.00
172 16 0.01
173 17 0.01
174 9 0.01
175 1 0.00
176 10 0.01
177 1 0.00
178 41 0.03
179 10 0.01
180 2 0.00
183 10 0.01
185 34 0.03
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (149 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
GTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTT
CAATTTCTGTTGTTAAAAA
Found at i:28179940 original size:88 final size:87
Alignment explanation
Indices: 28179738--28179983 Score: 289
Period size: 88 Copynumber: 2.8 Consensus size: 87
28179728 TGTTTTAATT
* *
28179738 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCGAGGTATTTTCAATTAAGC-
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACA--CTGAGGTATTTTCAATT--TCT
* * *
28179802 CTTTTGATTTCTGTTTTTCAAAAAAA
62 GTTTTCATTTATGTTTTTCAAAAAAA
* *
28179828 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACTGAGGTATTTTCCATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTCTGTTT
* *
28179893 TCATTATTATGTTTTT-GAAAGAA
66 TCA-T-TTATGTTTTTCAAAAAAA
** * * * *
28179916 TCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTCTGTTT
28179981 TCA
66 TCA
28179984 AAATTCAACT
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.01
87 5 0.04
88 81 0.60
89 9 0.07
90 40 0.29
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (87 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTCTGTTT
TCATTTATGTTTTTCAAAAAAA
Found at i:28180087 original size:73 final size:72
Alignment explanation
Indices: 28179916--28180204 Score: 380
Period size: 73 Copynumber: 3.9 Consensus size: 72
28179906 TTTGAAAGAA
* *
28179916 TCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCTGTTT
28179981 TCAAAAT
66 TCAAAAT
** *
28179988 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCTG-TT
28180053 TTCAAAAT
65 TTCAAAAT
* * *
28180061 TCAACTCATAGTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCTG-TT
* *
28180126 TTAAAAAAAAA
65 TT---CAAAAT
** * * * * *
28180137 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCCATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCTGTTT
28180202 TCA
66 TCA
28180205 TTATTATGTT
Statistics
Matches: 194, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
72 60 0.31
73 72 0.37
75 4 0.02
76 58 0.30
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCTGTTT
TCAAAAT
Found at i:28180320 original size:73 final size:72
Alignment explanation
Indices: 28180225--28180731 Score: 744
Period size: 73 Copynumber: 6.9 Consensus size: 72
28180215 TTTGAAAGAA
* * *
28180225 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTTTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTG-TT
28180290 TTCAAAAT
65 TTCAAAAT
* * *
28180298 TCAAATCATATTGTGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTT
28180363 TCAAAAT
66 TCAAAAT
* * *
28180370 TCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTG-TT
28180435 TTCAAAAT
65 TTCAAAAT
* *
28180443 TCAACTCATAGTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTT
28180508 TCAAAAT
66 TCAAAAT
* * *
28180515 TCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTG-TT
28180580 TTCAAAAT
65 TTCAAAAT
* *
28180588 TCAACTCATAGTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTG-TT
* *
28180653 TTAAAAAAAAA
65 TT---CAAAAT
** * * *
28180664 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACTGAGGTATTTTCCATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTT
28180729 TCA
66 TCA
28180732 TTATTATGTT
Statistics
Matches: 391, Mismatches: 38, Indels: 11
0.89 0.09 0.03
Matches are distributed among these distances:
72 134 0.34
73 194 0.50
75 4 0.01
76 59 0.15
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTT
TCAAAAT
Found at i:28181129 original size:64 final size:63
Alignment explanation
Indices: 28181042--28181170 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 63
28181032 ACAAAAAAAT
*
28181042 TTGGCTTATATAAGGGTCCAAAACGCACCGTTTTGGACCCCCCTTAAAGCAAAAAACGAGGCCG
1 TTGGCTTATATAAGGGTCCAAAACGCACCGTTTTGGA-CCCCCTTAAAGCAAAAAACGACGCCG
*
28181106 TTGGCTTATATAAGGGTCCAAAACGCACCGTTTTGGACCCCCTTAAAGCAGAAAACGACGCCG
1 TTGGCTTATATAAGGGTCCAAAACGCACCGTTTTGGACCCCCTTAAAGCAAAAAACGACGCCG
28181169 TT
1 TT
28181171 TTGATGCGGG
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
63 26 0.41
64 37 0.59
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (63 bp):
TTGGCTTATATAAGGGTCCAAAACGCACCGTTTTGGACCCCCTTAAAGCAAAAAACGACGCCG
Found at i:28181555 original size:21 final size:21
Alignment explanation
Indices: 28181510--28181574 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
28181500 TTTTATTAAA
* *
28181510 TATCATCATTATTTTTGAATTAT
1 TATCATCATTAATATT--ATTAT
*
28181533 TAAT-ATCATTAATATTGTTAT
1 T-ATCATCATTAATATTATTAT
*
28181554 TATCATCATTATTATTATTAT
1 TATCATCATTAATATTATTAT
28181575 GTGTTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 2 0.06
21 20 0.57
23 11 0.31
24 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (21 bp):
TATCATCATTAATATTATTAT
Found at i:28181559 original size:18 final size:18
Alignment explanation
Indices: 28181528--28181574 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
28181518 TTATTTTTGA
* *
28181528 ATTATTAATATCATTAAT
1 ATTATTATTATCATCAAT
* *
28181546 ATTGTTATTATCATCATT
1 ATTATTATTATCATCAAT
28181564 ATTATTATTAT
1 ATTATTATTAT
28181575 GTGTTAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTATTATTATCATCAAT
Found at i:28184353 original size:60 final size:60
Alignment explanation
Indices: 28184259--28184381 Score: 221
Period size: 60 Copynumber: 2.0 Consensus size: 60
28184249 ATGGGCCTTA
28184259 GTAGGGAAGGGTGACTTATGTTGGATACAAGTCACCCATTATGTCTTTTTTAATGATAAAG
1 GTAGGGAAGGGT-ACTTATGTTGGATACAAGTCACCCATTATGTCTTTTTTAATGATAAAG
28184320 GTAGGGAAAGGGT-CTTATGTTGGATACAAGTCACCCATTATGTCTTTTTTAATGATAAAG
1 GTAGGG-AAGGGTACTTATGTTGGATACAAGTCACCCATTATGTCTTTTTTAATGATAAAG
28184380 GT
1 GT
28184382 TAATGTAGAT
Statistics
Matches: 61, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
60 49 0.80
61 6 0.10
62 6 0.10
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.35
Consensus pattern (60 bp):
GTAGGGAAGGGTACTTATGTTGGATACAAGTCACCCATTATGTCTTTTTTAATGATAAAG
Found at i:28184898 original size:28 final size:29
Alignment explanation
Indices: 28184854--28184908 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
28184844 CATGACTATG
28184854 AATGTGATTTGGGCCTAATGGGCCATACA
1 AATGTGATTTGGGCCTAATGGGCCATACA
*
28184883 AATGTGA-TTGGGCCTAGTGGGCCATA
1 AATGTGATTTGGGCCTAATGGGCCATA
28184909 TGCATGTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.27
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAATGGGCCATACA
Found at i:28184915 original size:28 final size:29
Alignment explanation
Indices: 28184850--28184915 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
28184840 AAAGCATGAC
28184850 TATGAATGTGATTTGGGCCTAATGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
** *
28184879 TACAAATGTGA-TTGGGCCTAGTGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
*
28184907 TATGCATGT
1 TATGAATGT
28184916 ATGTTAACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (29 bp):
TATGAATGTGATTTGGGCCTAATGGGCCA
Found at i:28187212 original size:37 final size:37
Alignment explanation
Indices: 28187162--28187240 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
28187152 TTATTACGAA
* * *
28187162 GTCTTACCCGGACATAATCTTCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCTCACACGAAGTCATCGG
*
28187199 GTCTTACCCGGACAAAATCCTCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCTCACACGAAGTCATCGG
28187236 GTCTT
1 GTCTT
28187241 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCTCACACGAAGTCATCGG
Found at i:28187482 original size:47 final size:47
Alignment explanation
Indices: 28187359--28187648 Score: 382
Period size: 47 Copynumber: 6.1 Consensus size: 47
28187349 CCCTTCGGGA
* * * * * *
28187359 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28187406 CCTGTCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28187455 CTTATCATATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28187502 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
28187551 CCTATCACGTATATACACTTTCACATTCATCACATCGGTCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28187598 CCTATCACGTATATACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28187645 CTTA
1 CTTA
28187649 CTATCATTTC
Statistics
Matches: 215, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
47 133 0.62
49 82 0.38
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28187523 original size:96 final size:96
Alignment explanation
Indices: 28187359--28187648 Score: 422
Period size: 96 Copynumber: 3.0 Consensus size: 96
28187349 CCCTTCGGGA
* * * * * *
28187359 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCCTATCACATATATATAC
*
28187424 ACTTCCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
28187455 CTTATCATATATATACACTTTCACATTCATCACATCGACCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCCTATCACATATATATAC
28187520 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
28187551 CCTATCACGTATATACACTTTCACATTCATCACATCGGTCATTCGGCCCTATCAC--GTATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCCTATCACATATATATAC
*
28187614 ACTTTCTCATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
28187645 CTTA
1 CTTA
28187649 CTATCATTTC
Statistics
Matches: 173, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
94 40 0.23
96 133 0.77
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCCTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28187617 original size:143 final size:142
Alignment explanation
Indices: 28187359--28187648 Score: 411
Period size: 143 Copynumber: 2.0 Consensus size: 142
28187349 CCCTTCGGGA
* * * *
28187359 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATATAC
1 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACA-ATATATAC
* *
28187424 ACTTCCACATTCATCACATCGGCCATTAGGCCTTATCATATATATACACTTTCACATTCATCACA
65 ACTTCCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACA
28187489 TCGACCATTAGGC
130 TCGACCATTAGGC
* * *
28187502 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC-GTATATA
1 CTTATCACAT-T-TATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACAATATATA
* * * * *
28187566 CACTTTCACATTCATCACATCGGTCATTCGGCCCTATCACGTATATACACTTTCTCATTCATCAC
64 CACTTCCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCAC
*
28187631 ATCGGCCATTAGGC
129 ATCGACCATTAGGC
28187645 CTTA
1 CTTA
28187649 CTATCATTTC
Statistics
Matches: 130, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
143 91 0.70
144 1 0.01
145 38 0.29
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (142 bp):
CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACAATATATACA
CTTCCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACAT
CGACCATTAGGC
Found at i:28197009 original size:28 final size:29
Alignment explanation
Indices: 28196944--28197009 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
28196934 AAAGTATGAC
28196944 TATGAATGTGATTTGGGCCTAATGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
* *
28196973 TACGAATGTGA-TTGGGCCTAGTGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
*
28197001 TATGCATGT
1 TATGAATGT
28197010 TTGTTGACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 23 0.70
29 10 0.30
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (29 bp):
TATGAATGTGATTTGGGCCTAATGGGCCA
Found at i:28204798 original size:30 final size:30
Alignment explanation
Indices: 28204764--28204826 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
28204754 AACATGACTG
*
28204764 TGTGTCACACACGGTTAAGACACTCGCCCA
1 TGTGTCACACACGGTTAAGACACACGCCCA
28204794 TGTGTCACACACGGTTAAGACACACGCCCA
1 TGTGTCACACACGGTTAAGACACACGCCCA
28204824 TGT
1 TGT
28204827 CCCTGTCCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.21
Consensus pattern (30 bp):
TGTGTCACACACGGTTAAGACACACGCCCA
Found at i:28205759 original size:24 final size:25
Alignment explanation
Indices: 28205704--28205768 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
28205694 GAGTCATGGT
*
28205704 CGGTAAGCTCTTACTGAGCTGATAAA
1 CGGTAAGCTC-TATTGAGCTGATAAA
*
28205730 CAGTAAGCTCTATTGAGCTGA-AAA
1 CGGTAAGCTCTATTGAGCTGATAAA
*
28205754 CGGTAAGCTTTATTG
1 CGGTAAGCTCTATTG
28205769 TAGTGAACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 16 0.46
25 10 0.29
26 9 0.26
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (25 bp):
CGGTAAGCTCTATTGAGCTGATAAA
Found at i:28207564 original size:27 final size:27
Alignment explanation
Indices: 28207516--28207567 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
28207506 GCGAGGCTGC
*
28207516 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGATA
* * *
28207543 CAGATATTGTGGCTAGGCCACCAGA
1 CAGATATTGTGACGAAGCCACCAGA
28207568 ACAAATACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (27 bp):
CAGATATTGTGACGAAGCCACCAGATA
Found at i:28214582 original size:93 final size:93
Alignment explanation
Indices: 28214469--28214640 Score: 326
Period size: 93 Copynumber: 1.8 Consensus size: 93
28214459 CGCCCATAAG
*
28214469 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28214534 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
28214562 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28214627 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28214641 TCAACCATCC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28214637 original size:46 final size:46
Alignment explanation
Indices: 28214462--28214637 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
28214452 TGTAACCCGC
* *
28214462 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
28214508 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
28214558 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28214601 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28214638 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28220374 original size:31 final size:31
Alignment explanation
Indices: 28220333--28220396 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
28220323 CCTTTTCATA
*
28220333 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
** *
28220364 TTTCAAATTTCATATTACTGGGTCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
28220395 TT
1 TT
28220397 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:28220670 original size:23 final size:23
Alignment explanation
Indices: 28220590--28220683 Score: 109
Period size: 23 Copynumber: 4.0 Consensus size: 23
28220580 GCTTTATCAT
*
28220590 ATAACTGGAGGCCT-AGCCTCTTTA
1 ATAACTGG-GGCATAAGCC-CTTTA
* *
28220614 AGTAACTGGGGCAAAAGCCCTTTTT
1 A-TAACTGGGGCATAAGCCC-TTTA
*
28220639 ATAAGTGGGGCATAAGCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTA
28220662 ATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTT
28220684 TTCACTTCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
23 24 0.40
24 21 0.35
25 15 0.25
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (23 bp):
ATAACTGGGGCATAAGCCCTTTA
Found at i:28220759 original size:20 final size:20
Alignment explanation
Indices: 28220734--28220800 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
28220724 TTATGAGTAC
*
28220734 ATCATGTGCATATCATACTT
1 ATCATGTGCATATCATACAT
28220754 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28220774 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28220794 ACCATGT
1 ATCATGT
28220801 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:28220865 original size:25 final size:25
Alignment explanation
Indices: 28220837--28220884 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28220827 ATACATAAAC
* * *
28220837 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
28220862 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
28220885 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:28227227 original size:31 final size:31
Alignment explanation
Indices: 28227183--28227246 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
28227173 CCTTTTCATA
*
28227183 TTTCATATGTCATAACACTGGGCCGAAGCCT
1 TTTCAAATGTCATAACACTGGGCCGAAGCCT
* **
28227214 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATGTCATAACACTGGGCCGAAGCCT
28227245 TT
1 TT
28227247 ACTGTAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (31 bp):
TTTCAAATGTCATAACACTGGGCCGAAGCCT
Found at i:28227492 original size:24 final size:24
Alignment explanation
Indices: 28227440--28227557 Score: 152
Period size: 23 Copynumber: 5.0 Consensus size: 24
28227430 GCTTCATCAT
*
28227440 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
28227465 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
28227489 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
28227512 ATAACTGGGGCATAAGCCC-TTTC
1 ATAACTGGGGCATAAGCCCTTTTA
*
28227535 ATAACTAGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
28227558 TCACTTCCTC
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
23 43 0.51
24 29 0.35
25 12 0.14
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:28227632 original size:20 final size:20
Alignment explanation
Indices: 28227607--28227673 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
28227597 TTATGAGTAC
28227607 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
28227627 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28227647 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28227667 ACCATGT
1 ATCATGT
28227674 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:28227638 original size:11 final size:11
Alignment explanation
Indices: 28227607--28227662 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
28227597 TTATGAGTAC
28227607 ATCATGTGCAT
1 ATCATGTGCAT
*
28227618 ATCA--TACAT
1 ATCATGTGCAT
28227627 ATCATGTGCAT
1 ATCATGTGCAT
*
28227638 ATCA--TACAT
1 ATCATGTGCAT
*
28227647 GTCATGTGCAT
1 ATCATGTGCAT
28227658 ATCAT
1 ATCAT
28227663 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:28233405 original size:25 final size:24
Alignment explanation
Indices: 28233368--28233431 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
28233358 ATTAATGGCC
*
28233368 TTAATATATGTTATTTTGTAA-TGGA
1 TTAATA-A-GTTATTTGGTAATTGGA
28233393 TTAAATAAGGTTAATTTGGTAATTGGA
1 TT-AATAA-GTT-ATTTGGTAATTGGA
28233420 TTAATAAGTTAT
1 TTAATAAGTTAT
28233432 AATTAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 2 0.06
25 9 0.26
26 17 0.50
27 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (24 bp):
TTAATAAGTTATTTGGTAATTGGA
Found at i:28234668 original size:21 final size:21
Alignment explanation
Indices: 28234642--28234682 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28234632 TAAATATGCT
28234642 ATATGTACAAATGAAT-TGAGG
1 ATATGT-CAAATGAATATGAGG
*
28234663 ATATGTGAAATGAATATGAG
1 ATATGTCAAATGAATATGAG
28234683 CTATATGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.44, C:0.02, G:0.24, T:0.29
Consensus pattern (21 bp):
ATATGTCAAATGAATATGAGG
Found at i:28239171 original size:27 final size:27
Alignment explanation
Indices: 28239140--28239317 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
28239130 TAAATTGTAC
28239140 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28239167 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28239193 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28239221 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
28239249 AGCACTAAGCGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28239276 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28239303 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28239318 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 105 0.83
28 22 0.17
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28239254 original size:82 final size:81
Alignment explanation
Indices: 28239141--28239296 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
28239131 AAATTGTACA
* * *
28239141 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGCGTGCGAAATGAATACGTA-GCACTAAGTG
28239205 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28239222 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGCGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGCGTGCGAAATGAATACGTAGCACTAAGTG
*
28239287 TGCGAGTTGA
65 TGCGAATTGA
28239297 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGCGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28239308 original size:82 final size:81
Alignment explanation
Indices: 28239137--28239317 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
28239127 GATTAAATTG
* * *
28239137 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGCGTGCGAAATGAATACGATGCACTAA
28239202 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28239218 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGCGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGCGTGCGAAATGAATACGAT-GCACT
* **
28239282 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28239300 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28239318 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGCGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28248338 original size:11 final size:11
Alignment explanation
Indices: 28248302--28248357 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
28248292 CATGGTATAT
28248302 ATGATATGCAC
1 ATGATATGCAC
* *
28248313 ATGACATG--T
1 ATGATATGCAC
28248322 ATGATATGCAC
1 ATGATATGCAC
*
28248333 ATGATATG--T
1 ATGATATGCAC
28248342 ATGATATGCAC
1 ATGATATGCAC
28248353 ATGAT
1 ATGAT
28248358 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:28248357 original size:20 final size:20
Alignment explanation
Indices: 28248291--28248357 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
28248281 ATTTTGATAA
* *
28248291 ACATGGTATATATGATATGC
1 ACATGATATGTATGATATGC
*
28248311 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
28248331 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
28248351 ACATGAT
1 ACATGAT
28248358 GTATTCATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28248434 original size:24 final size:24
Alignment explanation
Indices: 28248407--28248561 Score: 265
Period size: 24 Copynumber: 6.4 Consensus size: 24
28248397 GAGGAAGTGC
28248407 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28248431 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28248455 AAAAAGGGCTTATGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTATT
* *
28248480 AAAAGGGCTTATTCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
28248504 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
28248528 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28248552 AAAAGAGGCT
1 AAAAG-GGCT
28248562 AGACATCCAG
Statistics
Matches: 124, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
24 96 0.77
25 28 0.23
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:28248479 original size:49 final size:49
Alignment explanation
Indices: 28248407--28248555 Score: 264
Period size: 49 Copynumber: 3.1 Consensus size: 49
28248397 GAGGAAGTGC
28248407 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTA
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTA
* *
28248456 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTA-TC
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTA
*
28248504 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATTA
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTA
28248553 AAA
1 AAA
28248556 GAGGCTAGAC
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
48 45 0.48
49 49 0.52
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (49 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTA
Found at i:28248526 original size:73 final size:72
Alignment explanation
Indices: 28248407--28248561 Score: 265
Period size: 73 Copynumber: 2.1 Consensus size: 72
28248397 GAGGAAGTGC
*
28248407 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTTATGCCC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT-AAAAGGGCTTATGCCC
28248472 CAGTTATT
65 CAGTTATT
* *
28248480 AAAAGGGCTTATTCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCC
28248545 AGTTATT
66 AGTTATT
28248552 AAAAGAGGCT
1 AAAAG-GGCT
28248562 AGACATCCAG
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
72 28 0.36
73 50 0.64
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCC
AGTTATT
Found at i:28248527 original size:48 final size:48
Alignment explanation
Indices: 28248406--28248775 Score: 253
Period size: 48 Copynumber: 7.5 Consensus size: 48
28248396 GGAGGAAGTG
*
28248406 CAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTA-T
*
28248455 AAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTAT
28248503 CAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTT-TTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATT-CCCCAGTTAT
* * * * * *
28248551 TAAAAGAGGC-TA-GACATCCAGTTATATGATAAAGCAG-TTATGCTGCCAGTGGA-
1 CAAAAG-GGCTTATG-C-CCCAGTTAT-T-A-AAAG-GGCTTATTC-CCCAGT-TAT
* ** **** * * * *
28248604 -AAGTTATGGG-TGGGTGGGTTGAGTTATTCCCCACATGG-TGTGTT---CAGTTAT
1 CAA---AAGGGCT-TAT-GCCCCAGTTATT---AAAAGGGCT-TATTCCCCAGTTAT
28248655 CAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTAT
28248703 CAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTT-TTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATT-CCCCAGTTAT
* *
28248751 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
28248776 ATGATGAAGC
Statistics
Matches: 254, Mismatches: 36, Indels: 62
0.72 0.10 0.18
Matches are distributed among these distances:
45 7 0.03
46 1 0.00
47 5 0.02
48 123 0.48
49 72 0.28
50 3 0.01
51 5 0.02
52 11 0.04
53 7 0.03
54 6 0.02
55 13 0.05
57 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (48 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTAT
Found at i:28248675 original size:24 final size:24
Alignment explanation
Indices: 28248648--28248775 Score: 186
Period size: 24 Copynumber: 5.3 Consensus size: 24
28248638 ATGGTGTGTT
*
28248648 CAGTTATCAAAAGGGCTTATGCCC
1 CAGTTATTAAAAGGGCTTATGCCC
*
28248672 CAGTTATTAAAAGGGCTTATTCCC
1 CAGTTATTAAAAGGGCTTATGCCC
*
28248696 CAGTTATCAAAAGGGCTTATGCCC
1 CAGTTATTAAAAGGGCTTATGCCC
*
28248720 CAGTTATTAAAAGGGCTTTTGCCC
1 CAGTTATTAAAAGGGCTTATGCCC
*
28248744 CAGTTATTAAAAGAGGC-TAGGCCTC
1 CAGTTATTAAAAG-GGCTTATGCC-C
28248769 CAGTTAT
1 CAGTTAT
28248776 ATGATGAAGC
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
24 83 0.88
25 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (24 bp):
CAGTTATTAAAAGGGCTTATGCCC
Found at i:28248799 original size:200 final size:201
Alignment explanation
Indices: 28248447--28248846 Score: 714
Period size: 200 Copynumber: 2.0 Consensus size: 201
28248437 GCTTATGCCC
28248447 CAGTTATTAAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTATCAAAAGGGC
1 CAGTTATTAAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTATCAAAAGGGC
28248512 TTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGACATCCAGTTATA
66 TTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGACATCCAGTTATA
* *
28248577 TGATAAAGCAGTTATGCTGCCAGTGGAAAGTTATGG-GTGGGTGGGTTGAGTTATTCCCCACATG
131 TGATAAAGCAGCTATGCTGCCAGTGGAAAGTTATGGCG-GGGTGGGTTGAGTTAATCCCCACATG
28248641 GTGTGTT
195 GTGTGTT
*
28248648 CAGTTA-TCAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTATCAAAAGGGC
1 CAGTTATTAAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTATCAAAAGGGC
* *
28248712 TTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTATA
66 TTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGACATCCAGTTATA
* *
28248777 TGATGAAGCAGCTATGCTGCCAGTGGAGAGTTATGGCGGGGTGGGTTGAGTTAATCCCCACATGG
131 TGATAAAGCAGCTATGCTGCCAGTGGAAAGTTATGGCGGGGTGGGTTGAGTTAATCCCCACATGG
28248842 TGTGT
196 TGTGT
28248847 AGGTTGGTAC
Statistics
Matches: 191, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
200 184 0.96
201 7 0.04
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (201 bp):
CAGTTATTAAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATTCCCCAGTTATCAAAAGGGC
TTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGACATCCAGTTATA
TGATAAAGCAGCTATGCTGCCAGTGGAAAGTTATGGCGGGGTGGGTTGAGTTAATCCCCACATGG
TGTGTT
Found at i:28252763 original size:27 final size:27
Alignment explanation
Indices: 28252733--28252906 Score: 161
Period size: 27 Copynumber: 6.4 Consensus size: 27
28252723 ATATTGAGTC
* *
28252733 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
28252760 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
28252787 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* ** ** *
28252815 CGCACACTGAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* ***
28252842 CGCACACTTAGTGC-ATCATATTCGTTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
28252869 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
28252896 CGCACACTTAG
1 CGCACACTTAG
28252907 GGCTGTACAA
Statistics
Matches: 122, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 99 0.81
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28260873 original size:27 final size:27
Alignment explanation
Indices: 28260843--28260993 Score: 151
Period size: 27 Copynumber: 5.6 Consensus size: 27
28260833 ATATTGAGTC
* *
28260843 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
28260870 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
28260897 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
28260925 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* ***
28260952 CGCACACTTAGTGC-ATCATATTCGTTT
1 CGCACACTTAGTGCTA-CATAATCAACT
28260979 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28260994 GTACAATTTA
Statistics
Matches: 105, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
27 82 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28260935 original size:55 final size:54
Alignment explanation
Indices: 28260843--28260992 Score: 158
Period size: 55 Copynumber: 2.8 Consensus size: 54
28260833 ATATTGAGTC
* * * *
28260843 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
* * ** *
28260897 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCCACATAATCAAAT
* ***
28260952 CGCACACTTAGTGC-ATCATATTCGTTTCGCACACTTAGTGC
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGC
28260993 TGTACAATTT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 36 0.44
55 45 0.56
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
Found at i:28276820 original size:24 final size:24
Alignment explanation
Indices: 28276789--28276848 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
28276779 TTATAACATG
*
28276789 AAAATGACCATTTTGCCCTAGGTA
1 AAAATGACCATTTTGCCCTAAGTA
28276813 AAAATGACCATTTTGCCCTAAGTA
1 AAAATGACCATTTTGCCCTAAGTA
28276837 AAAATGACCATT
1 AAAATGACCATT
28276849 ATACCCCTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.28
Consensus pattern (24 bp):
AAAATGACCATTTTGCCCTAAGTA
Found at i:28276943 original size:11 final size:11
Alignment explanation
Indices: 28276906--28276962 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
28276896 ACATGGTATG
28276906 CATGATATGCA
1 CATGATATGCA
*
28276917 CATGACATG--
1 CATGATATGCA
*
28276926 TATGATATGCA
1 CATGATATGCA
28276937 CATGATATG--
1 CATGATATGCA
*
28276946 TATGATATGCA
1 CATGATATGCA
28276957 CATGAT
1 CATGAT
28276963 GTATTCATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
9 15 0.42
11 21 0.58
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (11 bp):
CATGATATGCA
Found at i:28276962 original size:20 final size:20
Alignment explanation
Indices: 28276896--28276962 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
28276886 ATTTTGATAA
* *
28276896 ACATGGTATGCATGATATGC
1 ACATGATATGTATGATATGC
*
28276916 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
28276936 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
28276956 ACATGAT
1 ACATGAT
28276963 GTATTCATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28277039 original size:24 final size:24
Alignment explanation
Indices: 28277012--28277112 Score: 166
Period size: 24 Copynumber: 4.2 Consensus size: 24
28277002 GAGGAAGTGC
*
28277012 AAAAGGGCTTATGCCCCAGTCATT
1 AAAAGGGCTTATGCCCCAGTTATT
28277036 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28277060 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
28277084 AAAAGGGCTTTTACCCAAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28277108 AAAAG
1 AAAAG
28277113 AGGTAAGGCC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:28280802 original size:19 final size:19
Alignment explanation
Indices: 28280780--28280831 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
28280770 AGAGTGTGAA
28280780 AGAAAGAAAAAACAAAGTG
1 AGAAAGAAAAAACAAAGTG
** *
28280799 AGAAAAAGAAAAATGAAATTG
1 AG--AAAGAAAAAACAAAGTG
*
28280820 AAAAAGAAAAAA
1 AGAAAGAAAAAA
28280832 AATTGATCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 11 0.42
21 15 0.58
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.08
Consensus pattern (19 bp):
AGAAAGAAAAAACAAAGTG
Found at i:28280829 original size:18 final size:18
Alignment explanation
Indices: 28280800--28280924 Score: 67
Period size: 18 Copynumber: 6.9 Consensus size: 18
28280790 AACAAAGTGA
28280800 GAAAAAGAAAAATGAAATT
1 GAAAAAG-AAAATGAAATT
*
28280819 GAAAAAGAAAA-AAAATT
1 GAAAAAGAAAATGAAATT
** *
28280836 GATCAAGAAGA-GAAAATT
1 GAAAAAGAAAATG-AAATT
* **
28280854 GAAAAAGAAATTGAAAAA
1 GAAAAAGAAAATGAAATT
* * **
28280872 GAAAAAGAGAAGGAAAAA
1 GAAAAAGAAAATGAAATT
* * *
28280890 GAAAAAG-AGATCGAGAGT
1 GAAAAAGAAAAT-GAAATT
28280908 GAAAAAGAAAATTGAAA
1 GAAAAAGAAAA-TGAAA
28280925 AATAAATTGA
Statistics
Matches: 79, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
17 14 0.18
18 51 0.65
19 13 0.16
20 1 0.01
ACGTcount: A:0.66, C:0.02, G:0.21, T:0.11
Consensus pattern (18 bp):
GAAAAAGAAAATGAAATT
Found at i:28280917 original size:6 final size:6
Alignment explanation
Indices: 28280799--28280897 Score: 58
Period size: 6 Copynumber: 16.5 Consensus size: 6
28280789 AAACAAAGTG
* * * * ** *
28280799 AGAAAA AGAAAA ATGAAAT TGAAAA AGAAAA A-AAAT TGATCA AG-AAG
1 AGAAAA AGAAAA A-GAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
* * * * *
28280846 AGAAAA TTGAAAA AGAAAT TGAAAA AGAAAA AGAGAA GGAAAA AGAAAA
1 AGAAAA -AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
28280895 AGA
1 AGA
28280898 GATCGAGAGT
Statistics
Matches: 65, Mismatches: 24, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
5 5 0.08
6 51 0.78
7 9 0.14
ACGTcount: A:0.70, C:0.01, G:0.19, T:0.10
Consensus pattern (6 bp):
AGAAAA
Found at i:28289904 original size:42 final size:42
Alignment explanation
Indices: 28289753--28289904 Score: 182
Period size: 42 Copynumber: 3.6 Consensus size: 42
28289743 GTACCAATGG
** * **
28289753 CATATCCCAGATATGGTAATACATGTAA-TCTTGTATCGATGC
1 CATATCCCAGATATGGTCTTACACG-AAGTCTCATATCGATGC
* * *
28289795 CA-ATGGCCCAGCTATGGTCTTACACAAAGTCTCATATCGATGT
1 CATAT--CCCAGATATGGTCTTACACGAAGTCTCATATCGATGC
28289838 CATATCCCAGATATGGTCTTACACGAAGTCTCATATCGATGC
1 CATATCCCAGATATGGTCTTACACGAAGTCTCATATCGATGC
*
28289880 CATATCCCAGATGTGGTCTTACACG
1 CATATCCCAGATATGGTCTTACACG
28289905 TAATCTTAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.02
42 62 0.66
43 28 0.30
44 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (42 bp):
CATATCCCAGATATGGTCTTACACGAAGTCTCATATCGATGC
Found at i:28305011 original size:50 final size:50
Alignment explanation
Indices: 28304935--28305228 Score: 310
Period size: 50 Copynumber: 5.9 Consensus size: 50
28304925 TGATGCTAGG
* *
28304935 GAGATATGAGAGCTAGTGTAATACCATGTATAGGACATGGCATCGGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTC
* * * *
28304985 GAGATATGAGTGCTAATGTAAGACCATGTCTGGGACATGGCATTGGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTC
* *
28305035 GAGATATGAGAGCTACTGTAAGACCATGTCTAAGACATGGCATCGGCAC-C
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGC-CTC
* * * *
28305085 GATAGATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTC
* * * * *
28305135 GATATACGACAG-TCAGTGTAAGACCATGTCT-GGAACATGGCAT-AGACT-
1 GAGATATGAGAGCT-AGTGTAAGACCATGTCTAGG-ACATGGCATCGGCCTC
** * * * * *
28305183 TTGATGTGTGAGCCAGTGTAAGACTATGTCCAGGACATGGCATCGG
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGG
28305229 TACCTTACCC
Statistics
Matches: 203, Mismatches: 34, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
48 29 0.14
49 9 0.04
50 164 0.81
51 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (50 bp):
GAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTC
Found at i:28310297 original size:56 final size:56
Alignment explanation
Indices: 28310210--28310317 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
28310200 GTCCTAGGTG
*
28310210 TAACATCCCGAATTAGGGTCTAGTCGAAACAGTGGTTTTGAGACCACAAATTTGAA
1 TAACATCCCGAATTAGGGTCTAGTCGAAACAGTGGTTTTAAGACCACAAATTTGAA
*
28310266 TAACATCTCGAATTAGGGTCTAGTC-AGAACAGTGGTTTTAAGACCACAAATT
1 TAACATCCCGAATTAGGGTCTAGTCGA-AACAGTGGTTTTAAGACCACAAATT
28310318 CGAAGTAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
55 1 0.02
56 48 0.98
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (56 bp):
TAACATCCCGAATTAGGGTCTAGTCGAAACAGTGGTTTTAAGACCACAAATTTGAA
Found at i:28314253 original size:43 final size:42
Alignment explanation
Indices: 28314205--28314369 Score: 137
Period size: 42 Copynumber: 3.9 Consensus size: 42
28314195 TTCAAGATGT
*
28314205 GATTACATGTAAGACCATGTCTTGGACATTGGCATTGTATTG
1 GATTACATGTAAGACCATATCTTGGACATTGGCATTGTATTG
* * * *
28314247 AGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTATT-
1 -GATTACATGTAAGACCATATCTTGGACATTGGCATTG-TATTG
* * * *
28314290 GATTTCGTGTAAGACCCTAT-TTGGGACAATGG-ATTG-ATATG
1 GATTACATGTAAGACCATATCTT-GGACATTGGCATTGTAT-TG
28314331 TGA-TACTATGTAAGACCATATC-TGGA-ATATGGCATTGTA
1 -GATTAC-ATGTAAGACCATATCTTGGACAT-TGGCATTGTA
28314370 CGAGCTTATA
Statistics
Matches: 99, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 12 0.12
42 44 0.44
43 35 0.35
44 4 0.04
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (42 bp):
GATTACATGTAAGACCATATCTTGGACATTGGCATTGTATTG
Found at i:28316052 original size:24 final size:24
Alignment explanation
Indices: 28316023--28316071 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
28316013 TGAATCAAGC
28316023 TTGAGAATAGCTGAACCTAAGCTT
1 TTGAGAATAGCTGAACCTAAGCTT
*
28316047 TTGAGAATAGTTGAACCTAAGCTT
1 TTGAGAATAGCTGAACCTAAGCTT
28316071 T
1 T
28316072 CTTAATTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (24 bp):
TTGAGAATAGCTGAACCTAAGCTT
Found at i:28317088 original size:24 final size:24
Alignment explanation
Indices: 28317061--28317117 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
28317051 TTATGTAAGT
* *
28317061 TTGATTGTTTTGGTA-TGATTATGG
1 TTGATTATTTTGGTATTGA-AATGG
**
28317085 TTGAGAATTTTGGTATTGAAATGG
1 TTGATTATTTTGGTATTGAAATGG
28317109 TTGATTATT
1 TTGATTATT
28317118 AAATGACATG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (24 bp):
TTGATTATTTTGGTATTGAAATGG
Found at i:28321017 original size:24 final size:22
Alignment explanation
Indices: 28320989--28321071 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
28320979 CTAGCTCGTA
*
28320989 AGAGCTTATTGTTCTTAGCTCATGT
1 AGAGCTTACTGTTC--AGCTCAT-T
28321014 -GAGCTTACTGTTCAGCTCATT
1 AGAGCTTACTGTTCAGCTCATT
** *
28321035 AGAGCTTACTGCCCAGCTCAAT
1 AGAGCTTACTGTTCAGCTCATT
28321057 AGAGCTTACTGTTCA
1 AGAGCTTACTGTTCA
28321072 TCAGCTCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.02
22 38 0.75
24 12 0.24
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (22 bp):
AGAGCTTACTGTTCAGCTCATT
Found at i:28323619 original size:40 final size:39
Alignment explanation
Indices: 28323535--28323719 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 39
28323525 TTGAATGATG
* *
28323535 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
28323575 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28323615 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28323654 TCCGGGTTAAGTCCCGAAGGCTTTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
28323695 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
28323720 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 34 0.28
40 77 0.63
41 12 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28323671 original size:79 final size:81
Alignment explanation
Indices: 28323535--28323719 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
28323525 TTGAATGATG
28323535 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
28323599 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28323614 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTATTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGA-CAATATCCGGACTAAGAT-CCGAAGGC
* *
28323675 TTTTGTGCGAGTTACTATA
63 ATTTGTGCGAGATACTATA
* *
28323694 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28323720 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 1 0.01
79 55 0.60
80 35 0.38
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:28323741 original size:79 final size:79
Alignment explanation
Indices: 28323536--28323752 Score: 185
Period size: 79 Copynumber: 2.7 Consensus size: 79
28323526 TGAATGATGT
** * **
28323536 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCAT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAA-ATCCGGGTTAA-ATCCCGAAGGCAT
*
28323598 TTGTGCGAGATACTAATT
62 TTGTGCGAGATACTAATA
** * * * *
28323616 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCTTTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
28323681 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
28323695 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
28323753 TACGTGATTT
Statistics
Matches: 114, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
78 3 0.03
79 68 0.60
80 43 0.38
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:28330103 original size:42 final size:42
Alignment explanation
Indices: 28330025--28330105 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
28330015 GTACAGGTTT
*
28330025 CACACGGCCAAGACACACGCCCGTGTTCTAGGCCATGTGGTA
1 CACACGGCCAAGACACACGCCCGTGTTCTAGCCCATGTGGTA
* * *
28330067 CACATGGCTAAGACACATGCCCGTGTCTCT-GCCCATGTG
1 CACACGGCCAAGACACACGCCCGTGT-TCTAGCCCATGTG
28330106 CTCAATTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.20
Consensus pattern (42 bp):
CACACGGCCAAGACACACGCCCGTGTTCTAGCCCATGTGGTA
Found at i:28331160 original size:16 final size:17
Alignment explanation
Indices: 28331131--28331162 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28331121 GTTTTCATAT
28331131 ATCATTTGTCATGTATC
1 ATCATTTGTCATGTATC
28331148 ATCATTT-TCATGTAT
1 ATCATTTGTCATGTAT
28331163 TTCAGACGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50
Consensus pattern (17 bp):
ATCATTTGTCATGTATC
Found at i:28335119 original size:40 final size:40
Alignment explanation
Indices: 28335066--28335254 Score: 254
Period size: 40 Copynumber: 4.7 Consensus size: 40
28335056 GGATATAGCT
* * * * *
28335066 ACTCGCTCGAATGCCTTTGGGGCATAGCCCGG-TTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* * *
28335106 ATTCGCACCAATGCCTTCGGGACTTAGCCCGGATTTTGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
28335146 ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
28335186 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
28335226 GCTCGCACAAATGCCTTCAGGACTTAGCC
1 ACTCGCACAAATGCCTTCGGGACTTAGCC
28335255 TGGTTATCAT
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 131 0.98
41 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:28337625 original size:27 final size:27
Alignment explanation
Indices: 28337439--28337623 Score: 210
Period size: 27 Copynumber: 6.9 Consensus size: 27
28337429 ATAAATACCT
* *
28337439 CACAT-AGGGCAAAACAGTGAATTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
** * ***
28337465 CATGTAAAGGCATTTCAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
28337492 CACATAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
28337519 CAAATTAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
28337546 CACATAGGGGCAAAATAATCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
28337573 CACATAGGGGCAAAACAGTCATTTCAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
28337600 CATATAAGGGCAAAATAGTCATTT
1 CACATAAGGGCAAAACAGTCATTT
28337624 CATCAAATTG
Statistics
Matches: 131, Mismatches: 27, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
26 3 0.02
27 128 0.98
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:28341314 original size:34 final size:34
Alignment explanation
Indices: 28341271--28341356 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 34
28341261 TTTGTTTGCA
*
28341271 TACTGTTACTGTAATGGGCTCAAGCCCAAATTAC
1 TACTGTTACTGTAATGGGCTCAAGCCCAAACTAC
* *
28341305 TACTGTTACTGTAATGGGCTCAGGCCCAGACTAC
1 TACTGTTACTGTAATGGGCTCAAGCCCAAACTAC
* * *
28341339 TACTATTATTGAAATGGG
1 TACTGTTACTGTAATGGG
28341357 TTAAGGCCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (34 bp):
TACTGTTACTGTAATGGGCTCAAGCCCAAACTAC
Found at i:28344922 original size:32 final size:32
Alignment explanation
Indices: 28344881--28344944 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
28344871 TTATACATGT
28344881 AATCAACACAGTTACGATAGCATGCTAAAATA
1 AATCAACACAGTTACGATAGCATGCTAAAATA
28344913 AATCAACACAGTTACGATAGCATGCTAAAATA
1 AATCAACACAGTTACGATAGCATGCTAAAATA
28344945 TAAACATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (32 bp):
AATCAACACAGTTACGATAGCATGCTAAAATA
Found at i:28344990 original size:27 final size:27
Alignment explanation
Indices: 28344959--28345062 Score: 100
Period size: 27 Copynumber: 3.9 Consensus size: 27
28344949 CATATATCAC
*
28344959 ATAGGGGCAAAACAGTCAATTTACCAT
1 ATAGGGGCAAAACAGTCATTTTACCAT
* ***
28344986 GTAGGGGCATTTCAGTCATTTTACCAT
1 ATAGGGGCAAAACAGTCATTTTACCAT
* * *
28345013 ATAAGGGCAAAATAGTCATTTTACCAC
1 ATAGGGGCAAAACAGTCATTTTACCAT
** * *
28345040 ATAAAGGAAAAACATTCATTTTA
1 ATAGGGGCAAAACAGTCATTTTA
28345063 TCAATTAGGG
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (27 bp):
ATAGGGGCAAAACAGTCATTTTACCAT
Found at i:28346879 original size:46 final size:46
Alignment explanation
Indices: 28346756--28346881 Score: 198
Period size: 46 Copynumber: 2.7 Consensus size: 46
28346746 TGTAACCCGC
* * *
28346756 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCATTCGCAT
**
28346802 CCATAAGTGAACTCGGACTCAACTCAACGAGTTTGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCATTCGCAT
*
28346848 CCATAAGTGAACTCGAACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
28346882 GGATGCCTAG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCATTCGCAT
Found at i:28356906 original size:27 final size:27
Alignment explanation
Indices: 28356843--28356894 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
28356833 GTCATAAATA
* *
28356843 TCATAGGGGTATATCAGTCATTTTACG
1 TCATAGGGGTATAACAGTCATTTCACG
28356870 TCATAGGGGTATAACAGTCATTTCA
1 TCATAGGGGTATAACAGTCATTTCA
28356895 TCAGTATGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (27 bp):
TCATAGGGGTATAACAGTCATTTCACG
Found at i:28360133 original size:30 final size:30
Alignment explanation
Indices: 28360031--28360135 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
28360021 ATTGGGTTTA
*
28360031 AGCT-AAAATGAGCTAAGCTTTAGC-CCTTG
1 AGCTGAAAATGAGCTAAGGTTTAGCTCC-TG
* * * *
28360060 AGCT-AAAATTGAGCTGAGGTTAAACTCCTA
1 AGCTGAAAA-TGAGCTAAGGTTTAGCTCCTG
** *
28360090 AGCTGAAGTTGAGCTAAGGTTTAGCTCGTG
1 AGCTGAAAATGAGCTAAGGTTTAGCTCCTG
*
28360120 AGTTGAAAATGAGCTA
1 AGCTGAAAATGAGCTA
28360136 GGAGTAAGCT
Statistics
Matches: 58, Mismatches: 15, Indels: 5
0.74 0.19 0.06
Matches are distributed among these distances:
29 8 0.14
30 46 0.79
31 4 0.07
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (30 bp):
AGCTGAAAATGAGCTAAGGTTTAGCTCCTG
Found at i:28373583 original size:42 final size:42
Alignment explanation
Indices: 28373524--28373620 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
28373514 CACGTCCTGG
* *
28373524 CACACGGGCGTGTATGACCATTTTTAGGGCATACAGGCTAGC
1 CACACGGGCGTGTATGACCATTTTTAGGGCACACAAGCTAGC
28373566 CACACGGGCGTGTATGACCATTTTTAGGGCACACAAGCTAGC
1 CACACGGGCGTGTATGACCATTTTTAGGGCACACAAGCTAGC
* *
28373608 TACATGGGCGTGT
1 CACACGGGCGTGT
28373621 GTGTTTGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (42 bp):
CACACGGGCGTGTATGACCATTTTTAGGGCACACAAGCTAGC
Found at i:28374935 original size:43 final size:43
Alignment explanation
Indices: 28374886--28375042 Score: 228
Period size: 43 Copynumber: 3.7 Consensus size: 43
28374876 TGGGTTCTCG
*
28374886 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACA
* * *
28374929 TATAAGACCACATCTGGGACGTTGGCATCGGTATGTGATTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACA
*
28374972 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATATGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTACA
*
28375015 TGTAAGACCAGGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
28375043 TGTACAATAT
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
42 2 0.02
43 98 0.97
44 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACA
Found at i:28388857 original size:40 final size:39
Alignment explanation
Indices: 28388809--28389054 Score: 359
Period size: 40 Copynumber: 6.2 Consensus size: 39
28388799 GGACTAAGAT
28388809 CCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCC-GGCTAAGTC
*
28388849 CCGAAGGCATTTGTGCTAGTTACTATATCCGGACTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGG-CTAAGTC
*
28388889 CCGAAGGCATTTGTGCTAGTGACTATATCTGGACTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGG-CTAAGTC
28388929 CCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCC-GGCTAAGTC
* * * *
28388969 CCAAAGGCATCTGTGCTAGTTACTATATCTGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATC-CGGCTAAGTC
* *
28389009 CCGAAGGCATTTGTGCGAGTTG-CTATATCCGGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGCTAAGTC
28389048 CCGAAGG
1 CCGAAGG
28389055 TACTTGGGTT
Statistics
Matches: 188, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
39 17 0.09
40 168 0.89
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGCTAAGTC
Found at i:28389012 original size:120 final size:120
Alignment explanation
Indices: 28388797--28389054 Score: 414
Period size: 120 Copynumber: 2.2 Consensus size: 120
28388787 CGGATGATAA
* *
28388797 CCGGACTAAGAT-CCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTCCCGAAGGCATTT
1 CCGGACTAAG-TCCCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTCCCAAAGGCATCT
*
28388861 GTGCTAGTTACTATATCCGGACTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATAT
65 GTGCTAGTTACTATATCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTATAT
*
28388917 CTGGACTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTCCCAAAGGCATCTG
1 CCGGACTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTCCCAAAGGCATCTG
* *
28388982 TGCTAGTTACTATATCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATAT
66 TGCTAGTTACTATATCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATAT
*
28389037 CCGG-CTAAATCCCGAAGG
1 CCGGACTAAGTCCCGAAGG
28389055 TACTTGGGTT
Statistics
Matches: 128, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
119 14 0.11
120 112 0.88
121 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (120 bp):
CCGGACTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTCCCAAAGGCATCTG
TGCTAGTTACTATATCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:28392930 original size:33 final size:33
Alignment explanation
Indices: 28392886--28392950 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
28392876 GTGCTCTTTT
* *
28392886 TGGACCGATTGCTTTTTACTCTTTCCCTCTCTC
1 TGGACCAATTGCTTCTTACTCTTTCCCTCTCTC
*
28392919 TGGACCAATTGCTTCTTGCTCTTTCCCTCTCT
1 TGGACCAATTGCTTCTTACTCTTTCCCTCTCT
28392951 TCATCTTAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.09, C:0.34, G:0.12, T:0.45
Consensus pattern (33 bp):
TGGACCAATTGCTTCTTACTCTTTCCCTCTCTC
Found at i:28395898 original size:15 final size:15
Alignment explanation
Indices: 28395866--28395894 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28395856 ATTTTTTGTG
28395866 TTTATTATCTGTGAA
1 TTTATTATCTGTGAA
28395881 TTTA-TATCTGTGAA
1 TTTATTATCTGTGAA
28395895 ATTTTCGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (15 bp):
TTTATTATCTGTGAA
Found at i:28397068 original size:43 final size:43
Alignment explanation
Indices: 28397021--28397175 Score: 159
Period size: 43 Copynumber: 3.6 Consensus size: 43
28397011 TGTTCTCATG
* *
28397021 TAAGACCATGTATGGGATGTTGGCATTGATATATGATTATGTA
1 TAAGACCATGTCTGGGATGTTGGCATCGATATATGATTATGTA
* * * * * * *
28397064 TAAGACTAGGTCTGAGACGTTGGCATCGATATGTGGTTATGTG
1 TAAGACCATGTCTGGGATGTTGGCATCGATATATGATTATGTA
* * **
28397107 TAAGACCATGTCTGGGACAG-TGGCATCGATATGTGATTACATA
1 TAAGACCATGTCTGGGA-TGTTGGCATCGATATATGATTATGTA
* *
28397150 TAAGACCACGTCTGGGATGTTAGCAT
1 TAAGACCATGTCTGGGATGTTGGCAT
28397176 TGTATGATAT
Statistics
Matches: 90, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
42 1 0.01
43 88 0.98
44 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (43 bp):
TAAGACCATGTCTGGGATGTTGGCATCGATATATGATTATGTA
Found at i:28404102 original size:20 final size:21
Alignment explanation
Indices: 28404068--28404106 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28404058 TTATAATATC
*
28404068 ATAAATAATATGAATAAAAAA
1 ATAAATAATAGGAATAAAAAA
28404089 ATAAA-AATAGGAATAAAA
1 ATAAATAATAGGAATAAAA
28404107 GAAGAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (21 bp):
ATAAATAATAGGAATAAAAAA
Found at i:28409810 original size:46 final size:44
Alignment explanation
Indices: 28409657--28409865 Score: 154
Period size: 46 Copynumber: 4.5 Consensus size: 44
28409647 ATTGTGAGCT
* * * * *
28409657 AGTGTAAGACATGTCTGCGATATGCATCAGCCAC-ACTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAC-AT-A-AGTC
* * * * **
28409703 AGTGTAAGACCATGTCTGGGACATGGTATTGGC-ATTAAGACGAGTAC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CAACATAAGT-C
*
28409750 TAGTGTAAGACATGTTTGGGACATGCATCGGCCT-CGAGACATAAGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCGG-CTAC-A-ACATAAGTC
* **
28409797 AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACAACATAAGTC
28409841 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
28409866 GCATGGCACA
Statistics
Matches: 130, Mismatches: 21, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
44 15 0.12
45 18 0.14
46 46 0.35
47 30 0.23
48 20 0.15
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACAACATAAGTC
Found at i:28409913 original size:140 final size:140
Alignment explanation
Indices: 28409657--28409920 Score: 306
Period size: 140 Copynumber: 1.9 Consensus size: 140
28409647 ATTGTGAGCT
*
28409657 AGTGTAAGACATGTCTGCGATATGCATCAGCCACACTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGCGACATGCATCAGCCACAC-ATGAGAGCCAGTGTAAGACCATGTCTGG
* * * *
28409722 GACATGGTATTGGCATTAAGACGAGTACTAGTGTAAGACATGTTTGGGACAT-GCATCGGCCTCG
65 GACATGGCATTGGCAATAAGACGAGTACTAGTGTAAGACATGTCTGAGACATGGCATCGGCCTCG
28409786 AGACATAAGTC
130 AGACATAAGTC
* * * * *
28409797 AGTGTAAGACATGTCTGGGACATGCATCGGCTACA-A-GATGTGTCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGCGACATGCATCAGCCACACATGA-GAGCCAGTGTAAGACCATGTCTGG
* * *
28409860 GACATGGCA-TGGCACAGATATG-CTAG-AGCTTGTGTAAGACCATGTCTGAGACATGGCATCG
65 GACATGGCATTGG--CA-ATAAGACGAGTA-CTAGTGTAAGA-CATGTCTGAGACATGGCATCG
28409921 ACACTGTACC
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
137 5 0.05
138 32 0.31
139 15 0.14
140 46 0.44
141 6 0.06
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGCGACATGCATCAGCCACACATGAGAGCCAGTGTAAGACCATGTCTGGG
ACATGGCATTGGCAATAAGACGAGTACTAGTGTAAGACATGTCTGAGACATGGCATCGGCCTCGA
GACATAAGTC
Found at i:28414987 original size:28 final size:28
Alignment explanation
Indices: 28414922--28415002 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
28414912 AGCATAACTG
* * **
28414922 TAAATGTTATTGGGCTTAAT-GGCCGTA
1 TAAATGTGATTGGGCCTAATGGGCCACA
* *
28414949 TGAATTTGATTGGGCCTAATGGGCCACA
1 TAAATGTGATTGGGCCTAATGGGCCACA
28414977 TAAATGTGATTGGGCCTAATGGGCCA
1 TAAATGTGATTGGGCCTAATGGGCCA
28415003 TATATAGGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 16 0.36
28 29 0.64
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (28 bp):
TAAATGTGATTGGGCCTAATGGGCCACA
Found at i:28421007 original size:16 final size:16
Alignment explanation
Indices: 28420986--28421017 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28420976 GTTGTAACAC
28420986 CCCAAAAATCTCGAAA
1 CCCAAAAATCTCGAAA
*
28421002 CCCAAAAATCTTGAAA
1 CCCAAAAATCTCGAAA
28421018 TCTCGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (16 bp):
CCCAAAAATCTCGAAA
Found at i:28422204 original size:8 final size:8
Alignment explanation
Indices: 28422175--28422225 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
28422165 TTAGATTGGC
*
28422175 AAAAGCTG
1 AAAAGCCG
* *
28422183 AAATGCCA
1 AAAAGCCG
28422191 AAAAGCCG
1 AAAAGCCG
28422199 AAAAGCCG
1 AAAAGCCG
* *
28422207 AAATGCTG
1 AAAAGCCG
28422215 AAAAGCCG
1 AAAAGCCG
28422223 AAA
1 AAA
28422226 GTTTGGCTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.51, C:0.20, G:0.22, T:0.08
Consensus pattern (8 bp):
AAAAGCCG
Found at i:28422209 original size:24 final size:24
Alignment explanation
Indices: 28422175--28422225 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
28422165 TTAGATTGGC
*
28422175 AAAAGCTGAAATGCCAAAAAGCCG
1 AAAAGCCGAAATGCCAAAAAGCCG
**
28422199 AAAAGCCGAAATGCTGAAAAGCCG
1 AAAAGCCGAAATGCCAAAAAGCCG
28422223 AAA
1 AAA
28422226 GTTTGGCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.20, G:0.22, T:0.08
Consensus pattern (24 bp):
AAAAGCCGAAATGCCAAAAAGCCG
Found at i:28422222 original size:16 final size:16
Alignment explanation
Indices: 28422175--28422225 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
28422165 TTAGATTGGC
* *
28422175 AAAAGCTGAAATGCCA
1 AAAAGCTGAAAAGCCG
*
28422191 AAAAGCCGAAAAGCCG
1 AAAAGCTGAAAAGCCG
*
28422207 AAATGCTGAAAAGCCG
1 AAAAGCTGAAAAGCCG
28422223 AAA
1 AAA
28422226 GTTTGGCTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.51, C:0.20, G:0.22, T:0.08
Consensus pattern (16 bp):
AAAAGCTGAAAAGCCG
Done.