Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 94 of 292
Found at i:28885233 original size:55 final size:56
Alignment explanation
Indices: 28885168--28885282 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
28885158 AGCATGGCTG
* * *
28885168 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
28885224 CCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
28885279 CCAG
1 CCAG
28885283 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (56 bp):
CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:28885279 original size:28 final size:27
Alignment explanation
Indices: 28885193--28885282 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
28885183 GTGACAGAGT
*
28885193 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
28885222 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
28885249 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
28885277 CACCAG
1 CACCAG
28885283 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:28885441 original size:28 final size:27
Alignment explanation
Indices: 28885388--28885451 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 27
28885378 AAATTAACCC
*
28885388 TAGGGGTATAAGGTCATTTTGCATACA
1 TAGGGGTATAAGGTAATTTTGCATACA
28885415 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAA-GGTAATTTTGCATACA
28885443 TAGGGGTAT
1 TAGGGGTAT
28885452 CTAGTACATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 11 0.31
28 24 0.69
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (27 bp):
TAGGGGTATAAGGTAATTTTGCATACA
Found at i:28889354 original size:34 final size:33
Alignment explanation
Indices: 28889281--28889363 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 33
28889271 CTGTATTAAA
* **
28889281 ATGGGCTAAGGCCTACACTGATACTATTACTGT
1 ATGGGCTAAGGCCCACACTGATACTACGACTGT
* *
28889314 ATTGGGCTAAGGCCCACACTGATATTGCGACTGAT
1 A-TGGGCTAAGGCCCACACTGATACTACGACTG-T
*
28889349 ATGGGCTTAGGCCCA
1 ATGGGCTAAGGCCCA
28889364 AACTATTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 1 0.02
34 39 0.93
35 2 0.05
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (33 bp):
ATGGGCTAAGGCCCACACTGATACTACGACTGT
Found at i:28897424 original size:47 final size:47
Alignment explanation
Indices: 28897371--28897501 Score: 176
Period size: 47 Copynumber: 2.8 Consensus size: 47
28897361 GTGCGAATAA
* *
28897371 TACCTTGATTTGGCTATGGGCCATGCTATAGGTA-TTC-AGAGTGGAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTTCGAGA-T-AAGT
* *
28897418 TACCTTGATTTGGTTACGGGCCATGGTATAGGTACTTCGAGATAAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTTCGAGATAAGT
* *
28897465 TGCCTTGATTTGGCTATGAGCCATGGTATAGGTACTT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTT
28897502 ATCGATTATA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
47 67 0.91
48 4 0.05
49 3 0.04
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.35
Consensus pattern (47 bp):
TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTTCGAGATAAGT
Found at i:28899082 original size:29 final size:29
Alignment explanation
Indices: 28899049--28899109 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
28899039 CATTTACATA
28899049 CATTTATGCATTTAATATCAAAATCCATT
1 CATTTATGCATTTAATATCAAAATCCATT
28899078 CATTTATGCATTTAATATCAAAATCCATT
1 CATTTATGCATTTAATATCAAAATCCATT
28899107 CAT
1 CAT
28899110 CTCAATCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (29 bp):
CATTTATGCATTTAATATCAAAATCCATT
Found at i:28899233 original size:21 final size:20
Alignment explanation
Indices: 28899185--28899225 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28899175 CTAAACCGAT
*
28899185 CACATATAAAAATTTCTGAA
1 CACATAGAAAAATTTCTGAA
*
28899205 CACTTAGAAAAATTTCATGAA
1 CACATAGAAAAATTTC-TGAA
28899226 ATCATAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (20 bp):
CACATAGAAAAATTTCTGAA
Found at i:28902189 original size:23 final size:23
Alignment explanation
Indices: 28902158--28902294 Score: 168
Period size: 23 Copynumber: 6.0 Consensus size: 23
28902148 GGAATCTATA
28902158 GGCTACAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* * * *
28902181 GGCTGCAATATAGTTGTAGCTTT
1 GGCTACAATACAGTGGTAGCTTC
*
28902204 GGCTAC-ATCTCAGTGGTAGCTTC
1 GGCTACAAT-ACAGTGGTAGCTTC
*
28902227 GGCTACAATACAGTGGTAGCTTT
1 GGCTACAATACAGTGGTAGCTTC
28902250 GGCTACAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* ** *
28902273 AGCTACGTTACAGTGATAGCTT
1 GGCTACAATACAGTGGTAGCTT
28902295 GGACTATATT
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
22 2 0.02
23 92 0.96
24 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCTACAATACAGTGGTAGCTTC
Found at i:28902225 original size:46 final size:46
Alignment explanation
Indices: 28902158--28902294 Score: 186
Period size: 46 Copynumber: 3.0 Consensus size: 46
28902148 GGAATCTATA
* * *
28902158 GGCTACAATACAGTGGTAGCTTCGGCTGCAATATAGTTGTAGCTTT
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTT
*
28902204 GGCTAC-ATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTT
1 GGCTACAAT-ACAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTT
* ** *
28902250 GGCTACAATACAGTGGTAGCTTCAGCTACGTTACAGTGATAGCTT
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTT
28902295 GGACTATATT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
45 2 0.03
46 76 0.95
47 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (46 bp):
GGCTACAATACAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTT
Found at i:28902310 original size:69 final size:69
Alignment explanation
Indices: 28902158--28902294 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 69
28902148 GGAATCTATA
* * * ** *
28902158 GGCTACAATACAGTGGTAGCTTCGGCTGCAATATAGTTGTAGCTTTGGCTACATCTCAGTGGTAG
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTCAGCTACATCTCAGTGATAG
28902223 CTTC
66 CTTC
* *
28902227 GGCTACAATACAGTGGTAGCTTTGGCTACAATACAGTGGTAGCTTCAGCTACGT-TACAGTGATA
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTCAGCTACATCT-CAGTGATA
28902291 GCTT
65 GCTT
28902295 GGACTATATT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
68 1 0.02
69 58 0.98
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (69 bp):
GGCTACAATACAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTCAGCTACATCTCAGTGATAG
CTTC
Found at i:28904604 original size:27 final size:28
Alignment explanation
Indices: 28904574--28904648 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
28904564 CATATCTGTA
*
28904574 GCTAGTATTACTGAAATACCCCTAT-AG
1 GCTAGAATTACTGAAATACCCCTATAAG
*
28904601 GCTAGAATTACTGAAATGCCCCTATAAG
1 GCTAGAATTACTGAAATACCCCTATAAG
*
28904629 G-TAGAATTACTAAAATACCC
1 GCTAGAATTACTGAAATACCC
28904649 TTGCTTTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 40 0.93
28 3 0.07
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (28 bp):
GCTAGAATTACTGAAATACCCCTATAAG
Found at i:28904663 original size:27 final size:27
Alignment explanation
Indices: 28904633--28904699 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
28904623 TATAAGGTAG
28904633 AATTACTAAAATACCCTTGCTTTACAA
1 AATTACTAAAATACCCTTGCTTTACAA
* * *
28904660 AATTACT-AAATAACTTTGGTTTACAA
1 AATTACTAAAATACCCTTGCTTTACAA
28904686 AATTACTAAAATAC
1 AATTACTAAAATAC
28904700 TGTAACAGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 23 0.66
27 12 0.34
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.34
Consensus pattern (27 bp):
AATTACTAAAATACCCTTGCTTTACAA
Found at i:28906240 original size:24 final size:24
Alignment explanation
Indices: 28906208--28906291 Score: 159
Period size: 24 Copynumber: 3.5 Consensus size: 24
28906198 AATCTCAAAT
28906208 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
28906232 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATG
28906256 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
28906280 GCACTATGTGTG
1 GCACTATGTGTG
28906292 TGAACATAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:28906307 original size:48 final size:48
Alignment explanation
Indices: 28906208--28906316 Score: 166
Period size: 48 Copynumber: 2.3 Consensus size: 48
28906198 AATCTCAAAT
** *
28906208 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGACATAATATA
*
28906256 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGTGAACATAATA-A
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCG-ACATAATATA
28906304 GCACTATGTGTGC
1 GCACTATGTGTGC
28906317 AACGTTTGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
48 51 0.91
49 5 0.09
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (48 bp):
GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGACATAATATA
Found at i:28907918 original size:27 final size:27
Alignment explanation
Indices: 28907615--28907920 Score: 234
Period size: 27 Copynumber: 11.4 Consensus size: 27
28907605 CGGGTGTTAC
* * *
28907615 AAATA-CCTTCGATTAGCAAAATTGCCA
1 AAATACCCTT-GATTTGTAAAATTACCA
28907642 AAATACCCCTT--TTTGTAAAATTACCA
1 AAATA-CCCTTGATTTGTAAAATTACCA
* *
28907668 AAATACCCCTGATTTGTAAAATTA-CT
1 AAATACCCTTGATTTGTAAAATTACCA
* * *
28907694 AAATACCCTTAACTTGTAAAATTACCG
1 AAATACCCTTGATTTGTAAAATTACCA
** *
28907721 AAATACCCTCAATTTTTAAAATTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
* * * *
28907748 AAATACCCCTAATTTGGAAAATTACCG
1 AAATACCCTTGATTTGTAAAATTACCA
*
28907775 AAATACCCTTGATTTAG-AAAATTA-TA
1 AAATACCCTTGATTT-GTAAAATTACCA
* **
28907801 GAAATACCCCTGATTTACAAAATTA-CA
1 -AAATACCCTTGATTTGTAAAATTACCA
**
28907828 GAAATA-CCTTGACTTTCAAAAATTA-CA
1 -AAATACCCTTGA-TTTGTAAAATTACCA
** * * *
28907855 GAAATACTATTGGTTTGAAAAATTACCG
1 -AAATACCCTTGATTTGTAAAATTACCA
*
28907883 AAATACCCTTGATTTGTAAATTTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
*
28907910 AAACACCCTTG
1 AAATACCCTTG
28907921 TAGGGTGAAA
Statistics
Matches: 228, Mismatches: 40, Indels: 22
0.79 0.14 0.08
Matches are distributed among these distances:
25 4 0.02
26 44 0.19
27 171 0.75
28 5 0.02
29 4 0.02
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATACCCTTGATTTGTAAAATTACCA
Found at i:28908203 original size:41 final size:41
Alignment explanation
Indices: 28908158--28908280 Score: 183
Period size: 41 Copynumber: 3.0 Consensus size: 41
28908148 GGAGGAAGAA
28908158 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
**
28908199 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCATTG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
* * * * *
28908240 ATTAAGGATTGCATGGGTGCTTGATGATCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
28908281 GTGGCTTTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.28
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
Found at i:28910512 original size:16 final size:16
Alignment explanation
Indices: 28910493--28910536 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
28910483 CTAAAATGCT
28910493 GAAAAGCCAAAATACC
1 GAAAAGCCAAAATACC
*
28910509 GAAAAGCCAAAATGCC
1 GAAAAGCCAAAATACC
*
28910525 GAAAAGACAAAA
1 GAAAAGCCAAAA
28910537 GTTTGTCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.59, C:0.20, G:0.16, T:0.05
Consensus pattern (16 bp):
GAAAAGCCAAAATACC
Found at i:28910789 original size:29 final size:29
Alignment explanation
Indices: 28910747--28910871 Score: 180
Period size: 29 Copynumber: 4.3 Consensus size: 29
28910737 GAAAGCATGT
28910747 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
28910776 ATATGAAAGTGATTTGGGCCTAATGAGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
28910805 ATACGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * *
28910834 ATATGAATGAGA-TTAGGCCTAATGGGTC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
28910862 ATATGCATGT
1 ATATGAATGT
28910872 ATGTAGACTT
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 22 0.26
29 63 0.74
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:28912158 original size:27 final size:26
Alignment explanation
Indices: 28912128--28912219 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 26
28912118 ATTACCAAAG
* *
28912128 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTA-CGTTT
*
28912155 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTA-CGTTT
28912182 TACCCTC-AGTTTACAAAATTACTGTTT
1 TACCCTCGA-TTTACAAAATTAC-GTTT
*
28912209 TACCTTCGATT
1 TACCCTCGATT
28912220 GTGAAATTAC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.04
27 53 0.95
28 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (26 bp):
TACCCTCGATTTACAAAATTACGTTT
Found at i:28912161 original size:54 final size:53
Alignment explanation
Indices: 28912103--28912229 Score: 125
Period size: 54 Copynumber: 2.4 Consensus size: 53
28912093 TATGGAAATG
* *
28912103 CCCTCGACTTGTAAAATTACCAAAGTACCCTC-GATTTATAGAATTA-TCGTTTTA
1 CCCTCGA-TTGTAAAATTACCAAAGTACCCTCAG-TTTACAAAATTACT-GTTTTA
***
28912157 CCCTCGATT-TACAAAATTACCATTTTACCCTCAGTTTACAAAATTACTGTTTTA
1 CCCTCGATTGT--AAAATTACCAAAGTACCCTCAGTTTACAAAATTACTGTTTTA
* *
28912211 CCTTCGATTGTGAAATTAC
1 CCCTCGATTGTAAAATTAC
28912230 TGAAATACCC
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
52 1 0.02
53 9 0.15
54 48 0.79
55 3 0.05
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (53 bp):
CCCTCGATTGTAAAATTACCAAAGTACCCTCAGTTTACAAAATTACTGTTTTA
Found at i:28912262 original size:27 final size:27
Alignment explanation
Indices: 28912223--28912376 Score: 116
Period size: 27 Copynumber: 5.7 Consensus size: 27
28912213 TTCGATTGTG
**
28912223 AAATTACTGAAATACCCCTA-TAGGATA
1 AAATTACCAAAATACCCCTAGTAGG-TA
* **
28912250 GAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTAGGTA
**
28912277 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTAGGTA
* * * ** *
28912304 AAATTACCGAAATACCACTGGTTTGTG
1 AAATTACCAAAATACCCCTAGTAGGTA
* **
28912331 AAATTA-CATAAATA-CCCTCAATTTGTA
1 AAATTACCA-AAATACCCCT-AGTAGGTA
28912358 AAATTACCAAAATACCCCT
1 AAATTACCAAAATACCCCT
28912377 GATTTACAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.04
27 95 0.89
28 8 0.07
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTAGGTA
Found at i:28912290 original size:54 final size:52
Alignment explanation
Indices: 28912218--28912401 Score: 190
Period size: 54 Copynumber: 3.4 Consensus size: 52
28912208 TTACCTTCGA
* * ** *
28912218 TTGTGAAATTACTGAAATACCCCTATAGGATAGAATTACCAAAATACCCCTAGT
1 TTGTAAAATTACAGAAATACCCCTATTTG-TAAAATTACCAAAATACCCCT-GT
* *
28912272 TTGTAAAATTACCA-AAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGT
1 TTGTAAAATTA-CAGAAATACCCCTA-TTTGTAAAATTACCAAAATACCCCT-GT
* * *
28912326 TTGTGAAATTACATAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGAT
1 TTGTAAAATTACAGAAATACCC-CTATTTGTAAAATTACCAAAATACCCCTG-T
**
28912380 TTACAAAATTACAGAAATACCC
1 TTGTAAAATTACAGAAATACCC
28912402 TTGACTTTCT
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
53 3 0.03
54 101 0.93
55 5 0.05
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.29
Consensus pattern (52 bp):
TTGTAAAATTACAGAAATACCCCTATTTGTAAAATTACCAAAATACCCCTGT
Found at i:28912344 original size:81 final size:81
Alignment explanation
Indices: 28912251--28912400 Score: 216
Period size: 81 Copynumber: 1.9 Consensus size: 81
28912241 TATAGGATAG
* ** *
28912251 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCCCT-AGTTTGTAAAATTACCGA
1 AATTACCAAAATACCCTC-AATTTGTAAAATTACCAAAATACCCCTGA-TTTACAAAATTACAGA
28912314 AATACCACTGGTTTGTGA
64 AATACCACTGGTTTGTGA
28912332 AATTA-CATAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
1 AATTACCA-AAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
28912396 ATACC
65 ATACC
28912401 CTTGACTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
80 2 0.03
81 58 0.94
82 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAA
TACCACTGGTTTGTGA
Found at i:28912381 original size:27 final size:28
Alignment explanation
Indices: 28912251--28912484 Score: 173
Period size: 27 Copynumber: 8.6 Consensus size: 28
28912241 TATAGGATAG
28912251 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCCTGAGTTTGTAA
28912278 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCCTGAGTTTGTAA
* * *
28912305 AATTACCGAAATACCACTG-GTTTGTGA
1 AATTACCAAAATACCCCTGAGTTTGTAA
* *
28912332 AATTA-CATAAATA-CCCTCAATTTGTAA
1 AATTACCA-AAATACCCCTGAGTTTGTAA
**
28912359 AATTACCAAAATACCCCTGA-TTTACAA
1 AATTACCAAAATACCCCTGAGTTTGTAA
* * *
28912386 AATTA-CAGAAATACCCTTGACTTTCTAAA
1 AATTACCA-AAATACCCCTGAGTTTGT-AA
* ** **
28912415 AATTA-TAGAAATACCATTG-GTTTACAA
1 AATTACCA-AAATACCCCTGAGTTTGTAA
** * *
28912442 AATTACTGAAATACCCTTG-GTTTGTAG
1 AATTACCAAAATACCCCTGAGTTTGTAA
* *
28912469 ATTTACCAAAACACCC
1 AATTACCAAAATACCC
28912485 TTGTAGAATG
Statistics
Matches: 170, Mismatches: 28, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
26 6 0.04
27 131 0.77
28 14 0.08
29 19 0.11
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (28 bp):
AATTACCAAAATACCCCTGAGTTTGTAA
Found at i:28913429 original size:25 final size:24
Alignment explanation
Indices: 28913391--28913460 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
28913381 AGGAAGTGCT
*
28913391 AAAAGGGCTCTGCCCTAGTTTACC
1 AAAAGGGCTTTGCCCTAGTTTACC
*
28913415 GAAAAGGGCTTTGCCCTAGTTTATC
1 -AAAAGGGCTTTGCCCTAGTTTACC
*
28913440 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCTAGTT
28913461 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCTAGTTTACC
Found at i:28913473 original size:24 final size:24
Alignment explanation
Indices: 28913391--28913473 Score: 87
Period size: 25 Copynumber: 3.4 Consensus size: 24
28913381 AGGAAGTGCT
* * *
28913391 AAAAGGGCTCTGCCCTAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTATC
*
28913415 GAAAAGGGCTTTGCCCTAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTATC
*
28913440 AGAAAGGGCTTTGCCCCAG-TTATT
1 A-AAAGGGCTTTGCCCCAGTTTATC
28913464 AAAAGAGGCT
1 AAAAG-GGCT
28913474 AGGCCTCTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:28913667 original size:42 final size:42
Alignment explanation
Indices: 28913608--28913741 Score: 241
Period size: 42 Copynumber: 3.2 Consensus size: 42
28913598 TAGTCTCCCC
28913608 AAATGGGCTTGCATACATACATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATACATTGACATTACATGTGATATTG
*
28913650 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATACATTGACATTACATGTGATATTG
* *
28913692 AAATGGGCTTGCATACATCCATTGACATTAAATGTGATATTG
1 AAATGGGCTTGCATACATACATTGACATTACATGTGATATTG
28913734 AAATGGGC
1 AAATGGGC
28913742 CTAAGGGCCA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATACATTGACATTACATGTGATATTG
Found at i:28913800 original size:31 final size:31
Alignment explanation
Indices: 28913765--28913871 Score: 153
Period size: 31 Copynumber: 3.5 Consensus size: 31
28913755 CGTTTACAGT
* *
28913765 AAAGGCTTCGGCCCAGTGATACGATTTATAA
1 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
28913796 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
1 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
* *
28913827 AAAGGCTTCAGCCCAGTGATATA-ATTTATGG
1 AAAGGCTTCGGCCCAGTGATA-AGATTTATGA
*
28913858 AAAGGCTTTGGCCC
1 AAAGGCTTCGGCCC
28913872 GGTATATGTC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
31 68 0.99
32 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATAAGATTTATGA
Found at i:28917157 original size:20 final size:18
Alignment explanation
Indices: 28917118--28917168 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
28917108 GGCTATAGAG
*
28917118 GAAAAGAAGAAGA-A-GA
1 GAAAATAAGAAGAGAGGA
28917134 GAAAATAGATGAAGAGAGGA
1 GAAAATA-A-GAAGAGAGGA
28917154 GAAAATAAGAAGAGA
1 GAAAATAAGAAGAGA
28917169 AAAGAATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.20
17 1 0.03
18 12 0.40
19 2 0.07
20 9 0.30
ACGTcount: A:0.63, C:0.00, G:0.31, T:0.06
Consensus pattern (18 bp):
GAAAATAAGAAGAGAGGA
Found at i:28917174 original size:18 final size:18
Alignment explanation
Indices: 28917121--28917174 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
28917111 TATAGAGGAA
28917121 AAGAAGAAGAAGAGAAAAT
1 AAGAAG-AGAAGAGAAAAT
*
28917140 AGATGAAGAGAGGAGAAAAT
1 A-A-GAAGAGAAGAGAAAAT
*
28917160 AAGAAGAGAAAAGAA
1 AAGAAGAGAAGAGAA
28917175 TTGTCAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 11 0.37
19 2 0.07
20 13 0.43
21 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.06
Consensus pattern (18 bp):
AAGAAGAGAAGAGAAAAT
Found at i:28918311 original size:19 final size:18
Alignment explanation
Indices: 28918274--28918317 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
28918264 ATACATACAG
28918274 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
28918291 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
28918310 TACTAATT
1 TAATAATT
28918318 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:28919331 original size:17 final size:18
Alignment explanation
Indices: 28919298--28919331 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28919288 TATAAGGAAG
28919298 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
28919316 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
28919332 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:28922378 original size:16 final size:16
Alignment explanation
Indices: 28922356--28922407 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
28922346 GGTAAATCTT
28922356 GAAATGCCAAAAA-AC
1 GAAATGCCAAAAAGAC
*
28922371 GAAAATGCCAAAAAGTC
1 G-AAATGCCAAAAAGAC
*
28922388 GAAATGCCAAAAAGCC
1 GAAATGCCAAAAAGAC
28922404 GAAA
1 GAAA
28922408 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 1 0.03
16 30 0.91
17 2 0.06
ACGTcount: A:0.56, C:0.19, G:0.17, T:0.08
Consensus pattern (16 bp):
GAAATGCCAAAAAGAC
Found at i:28922672 original size:28 final size:29
Alignment explanation
Indices: 28922621--28922676 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
28922611 AGCATGTATA
*
28922621 TGAATGTGATTTGGGCCTAATGGGCCATG
1 TGAATGAGATTTGGGCCTAATGGGCCATG
*
28922650 TGAATGAGA-TTGGGCCTAGTGGGCCAT
1 TGAATGAGATTTGGGCCTAATGGGCCAT
28922677 ATACATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (29 bp):
TGAATGAGATTTGGGCCTAATGGGCCATG
Found at i:28931399 original size:45 final size:46
Alignment explanation
Indices: 28931335--28931509 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
28931325 TGTAACCCGC
28931335 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
*
28931380 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCAT
* * * *
28931430 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
*
28931473 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
28931510 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 38 0.34
46 29 0.26
47 28 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:28931501 original size:93 final size:92
Alignment explanation
Indices: 28931343--28931513 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 92
28931333 GCCCATAAGT
*
28931343 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
28931408 GAGCTCGGATGCCTAGTTACATCTCAC
66 GAGCTCGGATGCCTAGTTACATCTCAC
*
28931435 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28931500 CGAGTTCGGATGCC
65 CGAGCTCGGATGCC
28931514 CAAATATCCA
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 27 0.36
93 48 0.64
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCAC
Found at i:28933923 original size:29 final size:29
Alignment explanation
Indices: 28933886--28933969 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
28933876 GATAACAAGA
*
28933886 AAACC-GAATAAAGAAATCCAAGATAGAG
1 AAACCGGAATAAAGAAATCCAAGATAAAG
28933914 AAACCGGAATAAAGAAATCC-AGAATAAAG
1 AAACCGGAATAAAGAAATCCAAG-ATAAAG
* *
28933943 AGATCCAGG-ATAAAGAAACCCAAGATA
1 A-AACC-GGAATAAAGAAATCCAAGATA
28933970 CGATACTATG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
28 7 0.15
29 20 0.42
30 17 0.35
31 4 0.08
ACGTcount: A:0.56, C:0.15, G:0.18, T:0.11
Consensus pattern (29 bp):
AAACCGGAATAAAGAAATCCAAGATAAAG
Found at i:28933940 original size:15 final size:15
Alignment explanation
Indices: 28933882--28933960 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
28933872 CAAAGATAAC
*
28933882 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
28933896 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
28933911 GAGAAA-CCGGAATA
1 AAGAAATCCAGAATA
28933925 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
28933940 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
28933955 AAGAAA
1 AAGAAA
28933961 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.13, G:0.19, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:28933969 original size:15 final size:15
Alignment explanation
Indices: 28933893--28933969 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
28933883 AGAAAACCGA
28933893 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
28933908 ATAGAGAAA-CC-GG
1 ATAAAGAAATCCAAG
28933921 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
28933936 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
28933952 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
28933967 ATA
1 ATA
28933970 CGATACTATG
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 38 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.14, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:28940209 original size:20 final size:20
Alignment explanation
Indices: 28940184--28940228 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28940174 ATGGACTAAA
* *
28940184 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
28940204 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
28940224 ATGAA
1 ATGAA
28940229 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:28951462 original size:27 final size:27
Alignment explanation
Indices: 28951445--28951513 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
28951435 ATAGTGAGTC
28951445 CGCACACTTAGTGCCATATAATCAACT
1 CGCACACTTAGTGCCATATAATCAACT
* *
28951472 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCCATATAATC-AACT
28951500 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28951514 TATACAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCCATATAATCAACT
Found at i:28951508 original size:28 final size:27
Alignment explanation
Indices: 28951445--28951517 Score: 119
Period size: 28 Copynumber: 2.7 Consensus size: 27
28951435 ATAGTGAGTC
*
28951445 CGCACACTTAGTGCCATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
28951472 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
28951500 CGCACACTTAGTGCTATA
1 CGCACACTTAGTGCTATA
28951518 CAAATTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
27 21 0.49
28 22 0.51
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:28959259 original size:28 final size:27
Alignment explanation
Indices: 28959196--28959265 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
28959186 ATAGTGAGTC
28959196 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
28959223 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
28959251 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28959266 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:28962471 original size:25 final size:26
Alignment explanation
Indices: 28962419--28962514 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
28962409 GAGGAAGTGC
*
28962419 AAAAGGGC-TATGCCCCAG-TTACCG
1 AAAAGGGCTTTTGCCCCAGTTTACCG
*
28962443 AAAAGGGC-TTTGCCCTAGTTTACCG
1 AAAAGGGCTTTTGCCCCAGTTTACCG
* *
28962468 AAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTTGCCCCAGTTTACCG
28962494 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGCTTTTGCCCCAGTT
28962515 ATTAAAAGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 16 0.25
25 14 0.22
26 35 0.54
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCCAGTTTACCG
Found at i:28962527 original size:25 final size:26
Alignment explanation
Indices: 28962429--28962527 Score: 93
Period size: 25 Copynumber: 3.9 Consensus size: 26
28962419 AAAAGGGCTA
*
28962429 TGCCCCAG-TTACCGAAAAG-GGC-TT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
* *
28962453 TGCCCTAGTTTACCGAAAAG-GGCTTT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
28962479 TGCCCCAGTTTATCAAAA-AGGGCTTT
1 TGCCCCAGTTTATCAAAAGA-GGCTTT
*
28962505 TGCCCCAG-TTATTAAAAGAGGCT
1 TGCCCCAGTTTATCAAAAGAGGCT
28962528 AGGCCTCCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
24 7 0.11
25 30 0.45
26 29 0.44
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (26 bp):
TGCCCCAGTTTATCAAAAGAGGCTTT
Found at i:28964777 original size:12 final size:12
Alignment explanation
Indices: 28964760--28964784 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28964750 TATGTATGTT
28964760 TGAAAATTTTTA
1 TGAAAATTTTTA
28964772 TGAAAATTTTTA
1 TGAAAATTTTTA
28964784 T
1 T
28964785 TATTTGCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGAAAATTTTTA
Found at i:28964846 original size:3 final size:3
Alignment explanation
Indices: 28964838--28964883 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
28964828 TGTTTATGAA
28964838 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
28964884 AATATGTAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:28967025 original size:25 final size:25
Alignment explanation
Indices: 28966996--28967043 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28966986 TTATAATATG
* *
28966996 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTTTACCCCTAGGTA
28967021 AAAATGACCATTTTACCCCTAGG
1 AAAATGACCATTTTACCCCTAGG
28967044 GTTTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (25 bp):
AAAATGACCATTTTACCCCTAGGTA
Found at i:28967148 original size:20 final size:20
Alignment explanation
Indices: 28967125--28967166 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
28967115 TATATGATTT
28967125 ATATATACGATATGCACATG
1 ATATATACGATATGCACATG
* *
28967145 ATATGTATGATATGCACATG
1 ATATATACGATATGCACATG
28967165 AT
1 AT
28967167 GTATTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (20 bp):
ATATATACGATATGCACATG
Found at i:28967265 original size:25 final size:26
Alignment explanation
Indices: 28967213--28967308 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
28967203 GAGGAAGTGC
*
28967213 AAAAGGGC-TATGCCCCAG-TTACCG
1 AAAAGGGCTTTTGCCCCAGTTTACCG
28967237 AAAAGGGC-TTTGCCCCAGTTTACCG
1 AAAAGGGCTTTTGCCCCAGTTTACCG
* *
28967262 AAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTTGCCCCAGTTTACCG
*
28967288 AAAAGGGCTTTTGCCCTAGTT
1 AAAAGGGCTTTTGCCCCAGTT
28967309 ATTAAAAGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
24 17 0.26
25 14 0.21
26 35 0.53
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCCAGTTTACCG
Found at i:28967321 original size:25 final size:26
Alignment explanation
Indices: 28967223--28967321 Score: 93
Period size: 25 Copynumber: 3.9 Consensus size: 26
28967213 AAAAGGGCTA
*
28967223 TGCCCCAG-TTACCGAAAAG-GGC-TT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
*
28967247 TGCCCCAGTTTACCGAAAAG-GGCTTT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
28967273 TGCCCCAGTTTATCAAAA-AGGGCTTT
1 TGCCCCAGTTTATCAAAAGA-GGCTTT
* *
28967299 TGCCCTAG-TTATTAAAAGAGGCT
1 TGCCCCAGTTTATCAAAAGAGGCT
28967322 ATGTAACACC
Statistics
Matches: 67, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.12
25 30 0.45
26 29 0.43
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (26 bp):
TGCCCCAGTTTATCAAAAGAGGCTTT
Found at i:28968191 original size:30 final size:31
Alignment explanation
Indices: 28968110--28968192 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
28968100 TCAGTCTCGA
28968110 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
28968140 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
28968171 CATATCACT-GGCCAAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
28968193 ACTGTAAGTG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 17 0.33
31 34 0.67
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:28968440 original size:25 final size:25
Alignment explanation
Indices: 28968412--28968481 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
28968402 ATCTTTTAAT
* *
28968412 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGACA
* *
28968437 AACTAGGGCAAAGCCCTTTTCGGCA
1 AACTGGGGCAAAGCCCTTTTCGACA
*
28968462 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
28968482 AGCACTTCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGACA
Found at i:28969460 original size:29 final size:27
Alignment explanation
Indices: 28969391--28969498 Score: 105
Period size: 27 Copynumber: 3.9 Consensus size: 27
28969381 GTAAATCTAC
28969391 AAACCAAGGGTATTTC-AGTAATTTTCT
1 AAACCAAGGGTATTTCTA-TAATTTTCT
*
28969418 AAACCAATGGTATTTCTATAATTTT-T
1 AAACCAAGGGTATTTCTATAATTTTCT
* *
28969444 AGAAAGCCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCTATAATTTTCT
* *
28969474 AAATCAGGGGTATTT-TGATAATTTT
1 AAACCAAGGGTATTTCT-ATAATTTT
28969499 ACAAATTGAG
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
26 2 0.03
27 39 0.57
28 7 0.10
29 20 0.29
30 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (27 bp):
AAACCAAGGGTATTTCTATAATTTTCT
Found at i:28969504 original size:27 final size:27
Alignment explanation
Indices: 28969454--28969577 Score: 94
Period size: 27 Copynumber: 4.6 Consensus size: 27
28969444 AGAAAGCCAA
**
28969454 GGGTATTTCTG-TAATTTTGTAAA-TCAG
1 GGGTATTT-TGATAATTTTACAAACT-AG
*
28969481 GGGTATTTTGATAATTTTACAAA-TTG
1 GGGTATTTTGATAATTTTACAAACTAG
* * *
28969507 AGGGTATTTCGGTAATTTCACAAACTAG
1 -GGGTATTTTGATAATTTTACAAACTAG
* * *
28969535 TGGTATTTT-AGTAATTTTACGAACTAA
1 GGGTATTTTGA-TAATTTTACAAACTAG
*
28969562 GGGTATTTTGGTAATT
1 GGGTATTTTGATAATT
28969578 CTACCCTATA
Statistics
Matches: 77, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
26 3 0.04
27 72 0.94
28 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGATAATTTTACAAACTAG
Found at i:28969596 original size:54 final size:54
Alignment explanation
Indices: 28969388--28969577 Score: 145
Period size: 54 Copynumber: 3.5 Consensus size: 54
28969378 TTGGTAAATC
* * * * **
28969388 TACAAACCAAGGGTATTTCAGTAATTTTC-TAAACCAATGGTATTTCTA-TAATTTT
1 TACAAACTAAGGGTATTTCGGTAA-TTTCACAAACTAGGGGTATTT-TAGTAA-TTT
* * * ***
28969443 TAGAAAGCCAAGGGTATTTCTGTAATTTTGTAAA-TCAGGGGTATTTT-GATAATTT
1 TACAAA-CTAAGGGTATTTCGGTAATTTCACAAACT-AGGGGTATTTTAG-TAATTT
* * *
28969498 TACAAATTGAGGGTATTTCGGTAATTTCACAAACTAGTGGTATTTTAGTAATTT
1 TACAAACTAAGGGTATTTCGGTAATTTCACAAACTAGGGGTATTTTAGTAATTT
* *
28969552 TACGAACTAAGGGTATTTTGGTAATT
1 TACAAACTAAGGGTATTTCGGTAATT
28969578 CTACCCTATA
Statistics
Matches: 109, Mismatches: 19, Indels: 15
0.76 0.13 0.10
Matches are distributed among these distances:
54 58 0.53
55 19 0.17
56 32 0.29
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (54 bp):
TACAAACTAAGGGTATTTCGGTAATTTCACAAACTAGGGGTATTTTAGTAATTT
Found at i:28969617 original size:27 final size:27
Alignment explanation
Indices: 28969475--28969643 Score: 73
Period size: 27 Copynumber: 6.3 Consensus size: 27
28969465 TAATTTTGTA
* *
28969475 AATC-AGGGGTATTT-TGATAATTTTAC
1 AATCGAGGGGTATTTCAG-TAATTTCAC
* *
28969501 AAATTGA-GGGTATTTCGGTAATTTCAC
1 -AATCGAGGGGTATTTCAGTAATTTCAC
* * * * *
28969528 AAACTAGTGGTATTTTAGTAATTTTAC
1 AATCGAGGGGTATTTCAGTAATTTCAC
* * ** *
28969555 GAA-CTAAGGGTATTTTGGTAATTCTACCC
1 -AATCGAGGGGTATTTCAGTAATT-T-CAC
*
28969584 TAT--AGGGGTATTTCAGTAATTTCAC
1 AATCGAGGGGTATTTCAGTAATTTCAC
*** *
28969609 AATCGA-GGGTAAAACTGTAATTTCAC
1 AATCGAGGGGTATTTCAGTAATTTCAC
28969635 AATCGAGGG
1 AATCGAGGG
28969644 TAAAATAGTA
Statistics
Matches: 107, Mismatches: 25, Indels: 20
0.70 0.16 0.13
Matches are distributed among these distances:
25 4 0.04
26 26 0.24
27 70 0.65
28 6 0.06
29 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (27 bp):
AATCGAGGGGTATTTCAGTAATTTCAC
Found at i:28969628 original size:26 final size:26
Alignment explanation
Indices: 28969599--28969683 Score: 102
Period size: 26 Copynumber: 3.2 Consensus size: 26
28969589 GGGTATTTCA
28969599 GTAATTTCACAATCGAGGGTAAAACT
1 GTAATTTCACAATCGAGGGTAAAACT
28969625 GTAATTTCACAATCGAGGGTAAAA-T
1 GTAATTTCACAATCGAGGGTAAAACT
* * *
28969650 AGTAA-TTCTATAAATCAAGGGTAAAACA
1 -GTAATTTC-A-CAATCGAGGGTAAAACT
28969678 GTAATT
1 GTAATT
28969684 CTATAAATCG
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
25 4 0.08
26 29 0.57
27 17 0.33
28 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (26 bp):
GTAATTTCACAATCGAGGGTAAAACT
Found at i:28969710 original size:27 final size:27
Alignment explanation
Indices: 28969609--28969699 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
28969599 GTAATTTCAC
* *
28969609 AATCGAGGGTAAAACTGTAATT-TCA-C
1 AATCGAGGGTAAAACAGTAATTCT-ATA
*
28969635 AATCGAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTATA
*
28969662 AATCAAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTATA
28969689 AATCGAGGGTA
1 AATCGAGGGTA
28969700 CTTTGGTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 21 0.37
27 36 0.63
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTATA
Found at i:28970977 original size:31 final size:31
Alignment explanation
Indices: 28970942--28971019 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
28970932 GTTTACAGTA
*
28970942 AAAGGCTTCGGCCCAGTGAGATGAATAATGC
1 AAAGGCTTCGGCCCAGTGACATGAATAATGC
*
28970973 AAAGGCTTCAGCCCAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGACATGAATAATGC
28971004 AAAGGCTTCGGCCCAG
1 AAAGGCTTCGGCCCAG
28971020 CATATGTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGACATGAATAATGC
Found at i:28972047 original size:30 final size:30
Alignment explanation
Indices: 28972013--28972073 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
28972003 TTCCCGAGCC
28972013 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
28972043 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
28972073 T
1 T
28972074 GAGTTAACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:28972688 original size:64 final size:65
Alignment explanation
Indices: 28972564--28972746 Score: 255
Period size: 64 Copynumber: 2.8 Consensus size: 65
28972554 TAATACGGGA
* * * *
28972564 TGTATACCATGT-GTACAAGAGAGCTACGAGACATTATGAGGTAGCTAGGTCGCATGGGTGATAC
1 TGTACACCATGTAG-ACAAGAGAGCTAC-AGAGA-TAT-ATGTAGCTAGGTCGCATAGGTGATAC
28972628 TATG
62 TATG
28972632 TGTACACCATGTAGACAAGAGAGCTACAG-GATATATGTAGCTAGGTCGCATAGGTGATACTATG
1 TGTACACCATGTAGACAAGAGAGCTACAGAGATATATGTAGCTAGGTCGCATAGGTGATACTATG
* *
28972696 TGTACACCATGTAGACAAGAGAGCTAC-GAGATAAATGTAGCTAGGTTGCAT
1 TGTACACCATGTAGACAAGAGAGCTACAGAGATATATGTAGCTAGGTCGCAT
28972747 GTATGGTTCC
Statistics
Matches: 107, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
63 1 0.01
64 75 0.70
65 3 0.03
66 1 0.01
67 2 0.02
68 24 0.22
69 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.25
Consensus pattern (65 bp):
TGTACACCATGTAGACAAGAGAGCTACAGAGATATATGTAGCTAGGTCGCATAGGTGATACTATG
Found at i:28975931 original size:30 final size:31
Alignment explanation
Indices: 28975875--28975937 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
28975865 CCTTTTCATA
28975875 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
28975906 TTTCATATTTCATATTACT-GGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
28975936 TT
1 TT
28975938 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:28976181 original size:24 final size:24
Alignment explanation
Indices: 28976130--28976272 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
28976120 GCTTTATCAT
*
28976130 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
28976155 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
28976179 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
28976202 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
28976226 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
28976250 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
28976273 TACTTCCTCC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:28976209 original size:47 final size:48
Alignment explanation
Indices: 28976130--28976271 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
28976120 GCTTTATCAT
* *
28976130 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
28976179 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
28976226 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
28976272 TTACTTCCTC
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:28976230 original size:71 final size:72
Alignment explanation
Indices: 28976129--28976272 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
28976119 TGCTTTATCA
*
28976129 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
28976194 GCCCTTT
66 GCCCTTT
* * **
28976201 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
28976264 AGCCCTTT
65 AGCCCTTT
28976272 T
1 T
28976273 TACTTCCTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:28976347 original size:20 final size:20
Alignment explanation
Indices: 28976322--28976381 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
28976312 TATGATTACC
28976322 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
28976342 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
28976362 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
28976382 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:28976352 original size:11 final size:11
Alignment explanation
Indices: 28976322--28976376 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
28976312 TATGATTACC
28976322 TCATGTGCATA
1 TCATGTGCATA
*
28976333 TCA--TACATA
1 TCATGTGCATA
28976342 TCATGTGCATA
1 TCATGTGCATA
* *
28976353 TCA--TACATT
1 TCATGTGCATA
28976362 TCATGTGCATA
1 TCATGTGCATA
28976373 TCAT
1 TCAT
28976377 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:28976456 original size:25 final size:25
Alignment explanation
Indices: 28976424--28976471 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28976414 ATACATAAAC
* * *
28976424 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
28976449 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
28976472 ATATTATAAG
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:28985028 original size:93 final size:93
Alignment explanation
Indices: 28984916--28985087 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28984906 GCCCATAAGT
* *
28984916 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28984981 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
28985009 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28985074 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
28985088 CAAATATCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:28985083 original size:46 final size:46
Alignment explanation
Indices: 28984908--28985083 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
28984898 TGTAACCCGC
* * *
28984908 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28984954 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
28985004 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
28985047 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28985084 TGCCCAAATA
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 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28987504 original size:29 final size:29
Alignment explanation
Indices: 28987465--28987552 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
28987455 CAAAGATAAC
*
28987465 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
28987494 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
28987523 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
28987553 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:28987523 original size:15 final size:15
Alignment explanation
Indices: 28987465--28987543 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
28987455 CAAAGATAAC
*
28987465 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
28987479 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
28987494 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
28987508 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
28987523 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
28987538 AAGAAA
1 AAGAAA
28987544 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:28987552 original size:15 final size:15
Alignment explanation
Indices: 28987476--28987552 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
28987466 AGAAAACCGA
28987476 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
28987491 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
28987505 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
28987519 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
28987535 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
28987550 ATA
1 ATA
28987553 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:28990560 original size:46 final size:46
Alignment explanation
Indices: 28990493--28990666 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
28990483 TGTAACCCGC
*
28990493 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
28990539 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
28990589 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGAC-ATCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
28990631 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
28990667 ATGCCCAAAT
Statistics
Matches: 110, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 1 0.01
44 3 0.03
45 28 0.25
46 35 0.32
47 28 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:28990659 original size:92 final size:93
Alignment explanation
Indices: 28990501--28990671 Score: 308
Period size: 92 Copynumber: 1.8 Consensus size: 93
28990491 GCCCATAAGT
* *
28990501 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
28990566 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
28990594 GAACTCGGACTCAACTCAACGAGTTCGGAC-ATCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
28990658 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
28990672 CAAATATCCC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 47 0.63
93 28 0.37
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:28992369 original size:38 final size:38
Alignment explanation
Indices: 28992310--28992417 Score: 198
Period size: 38 Copynumber: 2.8 Consensus size: 38
28992300 TCAATCATGC
*
28992310 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTTCATAAT
28992349 ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
28992387 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATT
28992418 ACTGGGCCGA
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
38 57 0.84
39 11 0.16
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (38 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
Found at i:28992371 original size:31 final size:31
Alignment explanation
Indices: 28992333--28992434 Score: 132
Period size: 31 Copynumber: 3.1 Consensus size: 31
28992323 CCTTTTCATA
28992333 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCAT
1 TTTCATATTTCATAATACTGGGCCGAAG-C----C-T
28992370 ATTTCATATTTCATAATACTGGGCCGAAGCCT
1 -TTTCATATTTCATAATACTGGGCCGAAGCCT
*
28992402 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
28992433 TT
1 TT
28992435 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
31 32 0.51
32 1 0.02
33 1 0.02
37 1 0.02
38 28 0.44
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:28992677 original size:24 final size:24
Alignment explanation
Indices: 28992640--28992792 Score: 245
Period size: 24 Copynumber: 6.4 Consensus size: 24
28992630 TTGGAGGCCT
* *
28992640 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTGATAACTGGGGCATA
**
28992665 AGCCCTTTCAATAACTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
28992689 AGCCCTTTT-ATAACTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
28992712 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
28992736 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
*
28992760 AGCCCCTTTGATAACTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
28992784 AGCCCTTTT
1 AGCCCTTTT
28992793 TCACTTCCTC
Statistics
Matches: 122, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
23 23 0.19
24 95 0.78
25 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTGATAACTGGGGCATA
Found at i:28992868 original size:20 final size:20
Alignment explanation
Indices: 28992843--28992902 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
28992833 TATGATTACC
28992843 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
28992863 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
28992883 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
28992903 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:28992873 original size:11 final size:11
Alignment explanation
Indices: 28992843--28992897 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
28992833 TATGATTACC
28992843 TCATGTGCATA
1 TCATGTGCATA
*
28992854 TCA--TACATA
1 TCATGTGCATA
28992863 TCATGTGCATA
1 TCATGTGCATA
* *
28992874 TCA--TACATT
1 TCATGTGCATA
28992883 TCATGTGCATA
1 TCATGTGCATA
28992894 TCAT
1 TCAT
28992898 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:28992977 original size:25 final size:25
Alignment explanation
Indices: 28992945--28992992 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28992935 ATACATAAAC
* * *
28992945 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
28992970 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
28992993 AATATTATAA
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:28996090 original size:30 final size:30
Alignment explanation
Indices: 28996056--28996117 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
28996046 TTCCCGAGCC
*
28996056 TAGGGGAAAAAGTGTAAATATGCAATAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * *
28996086 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
28996116 TA
1 TA
28996118 ACTTAAGGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Found at i:28999815 original size:33 final size:33
Alignment explanation
Indices: 28999778--28999867 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
28999768 GTTTCAATTA
*
28999778 GGATTTAGCCTGGACTGGTAATCCTAATTGACT
1 GGATTTAGCCTGGACTGGTAATCCTAATCGACT
* * *
28999811 GGATTTAGCCTGGACTGGAAATTCTAATCGATT
1 GGATTTAGCCTGGACTGGTAATCCTAATCGACT
* * *
28999844 GAATTTAACCTGGACTAGTAATCC
1 GGATTTAGCCTGGACTGGTAATCC
28999868 AGATTTGACT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (33 bp):
GGATTTAGCCTGGACTGGTAATCCTAATCGACT
Found at i:29000091 original size:2 final size:2
Alignment explanation
Indices: 29000084--29000114 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29000074 AATGGATGAA
29000084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29000115 AGACTTCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29002783 original size:40 final size:39
Alignment explanation
Indices: 29002633--29002785 Score: 234
Period size: 39 Copynumber: 3.9 Consensus size: 39
29002623 GAATGTGCGA
* *
29002633 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
29002672 GTGATATCTGGGCTAAGCCCGAAGGCAATCGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
29002711 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
29002750 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
29002786 GGTTACCATA
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 86 0.83
40 17 0.17
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:29002801 original size:40 final size:39
Alignment explanation
Indices: 29002634--29002816 Score: 231
Period size: 39 Copynumber: 4.6 Consensus size: 39
29002624 AATGTGCGAG
* * *
29002634 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* *
29002673 TGATATCTGGGCTAAGCCCGAAGGCAATCGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
29002712 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
29002751 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
29002791 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
29002817 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 85 0.67
40 41 0.33
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:29009790 original size:40 final size:39
Alignment explanation
Indices: 29009638--29009789 Score: 223
Period size: 39 Copynumber: 3.9 Consensus size: 39
29009628 GAATGTGCGA
* *
29009638 GTGATATCCCGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAGTT
* *
29009677 GTGATATCCGGGCTAGGCCCGAAGGCAATCGTGCAAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAGTT
* *
29009716 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAGTT
* *
29009755 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGC
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGC
29009790 GGGTTACCAT
Statistics
Matches: 101, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 85 0.84
40 16 0.16
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAGTT
Found at i:29009806 original size:40 final size:40
Alignment explanation
Indices: 29009648--29009826 Score: 130
Period size: 39 Copynumber: 4.5 Consensus size: 40
29009638 GTGATATCCC
* * * *** *
29009648 GGCTAAG-CCCGAAGGCAATTGTGCAAATTGTGATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAACCG
* * * * ** *
29009687 GGCT-AGGCCCGAAGGCAATCGTGCAAGTTATGATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAACCG
* *** *
29009726 GGCTAAG-CCCGAAGGCAATTGTGCGAGTTGTGATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAACCG
* *
29009765 GGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAACCG
* *
29009805 GGCTATGTCCCGAAGGCGTTTG
1 GGCTAAGTCCCGAAGGCATTTG
29009827 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
38 2 0.02
39 72 0.60
40 47 0.39
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.23
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAACCG
Found at i:29012316 original size:21 final size:20
Alignment explanation
Indices: 29012288--29012327 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
29012278 CAAAACTTGT
29012288 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
29012308 ATAATCTATCATCAATCATT
1 ATAA-CTATCATCAAACATT
29012328 AAAGCTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:29020984 original size:40 final size:40
Alignment explanation
Indices: 29020906--29021128 Score: 283
Period size: 40 Copynumber: 5.5 Consensus size: 40
29020896 ACCCAAGTAT
* *
29020906 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * **
29020945 CTTCGGGTCTTAGCCCCGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
29020985 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
29021025 CTTC-GGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* * *
29021067 CTTCGGGACTTAGCCCGGATAAAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
29021107 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
29021129 CATCCGAATA
Statistics
Matches: 160, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.01
39 33 0.21
40 91 0.57
41 1 0.01
42 14 0.09
43 20 0.12
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:29021087 original size:82 final size:80
Alignment explanation
Indices: 29020906--29021128 Score: 283
Period size: 82 Copynumber: 2.8 Consensus size: 80
29020896 ACCCAAGTAT
* * * *
29020906 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCCGATATAG
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
**
29020969 TCACTAGCATGAATGC
65 TCACTAGCACAAATGC
*
29020985 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC-GGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
29021048 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
* * *
29021067 CTTCGGGACTTAGCCCGGATAAAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
29021129 CATCCGAATA
Statistics
Matches: 126, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 32 0.25
80 27 0.21
81 1 0.01
82 49 0.39
83 16 0.13
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:29021721 original size:2 final size:2
Alignment explanation
Indices: 29021716--29021747 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
29021706 ATATTCACAC
*
29021716 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29021748 TATGCCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29023128 original size:50 final size:49
Alignment explanation
Indices: 29023026--29023147 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 49
29023016 CATAGTAACT
* * ** *
29023026 TGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 TGCACTTAGTACTACACACGTGACCAACCATCCGATACACGTAGTAGCC
*
29023075 TGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCC
1 TGCACTTAGTACTACACACGTGACC-AACCATCCGATACACGTAGTAGCC
29023125 TGCACTTAGTACTACACACGTGA
1 TGCACTTAGTACTACACACGTGA
29023148 TCGAAGTTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
49 23 0.35
50 43 0.65
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (49 bp):
TGCACTTAGTACTACACACGTGACCAACCATCCGATACACGTAGTAGCC
Found at i:29024187 original size:27 final size:27
Alignment explanation
Indices: 29024157--29024300 Score: 189
Period size: 27 Copynumber: 5.3 Consensus size: 27
29024147 TACTGAAATG
** * *
29024157 CCCTCGATTTGTAGAATTTCTATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
*
29024184 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
*
29024211 CCCTCGATTTACAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
*
29024238 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* * * *
29024265 CCCTCAATTTACAAAATTGCCGTTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
29024292 CCCTCGATT
1 CCCTCGATT
29024301 GTGAAATTAC
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 106 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACCATTTTA
Found at i:29024319 original size:26 final size:25
Alignment explanation
Indices: 29024290--29024501 Score: 155
Period size: 26 Copynumber: 8.2 Consensus size: 25
29024280 ATTGCCGTTT
* **
29024290 TACCCTCGATTGTGAAATTACTGAAA
1 TACCCT-GATTGTAAAATTACCAAAA
* *
29024316 TACCCTG-TAGGATAAATTACCAAAA
1 TACCCTGATTGTA-AAATTACCAAAA
* *
29024341 TACCCTTAGTTTTAAAATTACCAAAA
1 TACCCTGA-TTGTAAAATTACCAAAA
*
29024367 TACCCTAGTTTGT-AAATTACCAAAA
1 TACCCT-GATTGTAAAATTACCAAAA
*
29024392 TACCCCTAGTTTGTAAAATTACCAAAA
1 TA-CCCT-GATTGTAAAATTACCAAAA
* * *
29024419 TACCACTGGTTTGTGAAATTA-CGAAA
1 TACC-CT-GATTGTAAAATTACCAAAA
*
29024445 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCT-GA-TTGTAAAATTACCAAAA
29024472 TACCCCTGATT-TACAAAATTA-CAAAA
1 TA-CCCTGATTGT--AAAATTACCAAAA
29024498 TACC
1 TACC
29024502 TTGACTTTCT
Statistics
Matches: 153, Mismatches: 21, Indels: 25
0.77 0.11 0.13
Matches are distributed among these distances:
24 2 0.01
25 36 0.24
26 67 0.44
27 44 0.29
28 4 0.03
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.30
Consensus pattern (25 bp):
TACCCTGATTGTAAAATTACCAAAA
Found at i:29024359 original size:51 final size:52
Alignment explanation
Indices: 29024299--29024476 Score: 193
Period size: 51 Copynumber: 3.4 Consensus size: 52
29024289 TTACCCTCGA
* ** *
29024299 TTGTGAAATTACTGAAATACCCT-GTAGGATAAATTACCAAAATACCCTTAGT
1 TTGTAAAATTACCAAAATACCCTAGTAGG-TAAATTACCAAAATACCCCTAGT
**
29024351 TT-TAAAATTACCAAAATACCCTAGTTTGTAAATTACCAAAATACCCCTAGT
1 TTGTAAAATTACCAAAATACCCTAGTAGGTAAATTACCAAAATACCCCTAGT
* ** * *
29024402 TTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTA-CGAAATA-CCCTCAAT
1 TTGTAAAATTACCAAAATACC-CTAGTAGGT-AAATTACCAAAATACCCCT-AGT
29024455 TTGTAAAATTACCAAAATACCC
1 TTGTAAAATTACCAAAATACCC
29024477 CTGATTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
51 41 0.37
52 28 0.25
53 37 0.33
54 6 0.05
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (52 bp):
TTGTAAAATTACCAAAATACCCTAGTAGGTAAATTACCAAAATACCCCTAGT
Found at i:29024418 original size:27 final size:27
Alignment explanation
Indices: 29024329--29024501 Score: 207
Period size: 26 Copynumber: 6.6 Consensus size: 27
29024319 CCTGTAGGAT
*
29024329 AAATTACCAAAATACCCTTAGTTT-TA
1 AAATTACCAAAATACCCCTAGTTTGTA
29024355 AAATTACCAAAATA-CCCTAGTTTGT-
1 AAATTACCAAAATACCCCTAGTTTGTA
29024380 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * *
29024407 AAATTACCAAAATACCACTGGTTTGTG
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
29024434 AAATTA-CGAAATA-CCCTCAATTTGTA
1 AAATTACCAAAATACCCCT-AGTTTGTA
**
29024460 AAATTACCAAAATACCCCT-GATTTACA
1 AAATTACCAAAATACCCCTAG-TTTGTA
29024487 AAATTA-CAAAATACC
1 AAATTACCAAAATACC
29024502 TTGACTTTCT
Statistics
Matches: 127, Mismatches: 13, Indels: 14
0.82 0.08 0.09
Matches are distributed among these distances:
25 25 0.20
26 52 0.41
27 46 0.36
28 4 0.03
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTTTGTA
Found at i:29024458 original size:53 final size:52
Alignment explanation
Indices: 29024328--29024476 Score: 214
Period size: 53 Copynumber: 2.9 Consensus size: 52
29024318 CCCTGTAGGA
*
29024328 TAAATTACCAAAATACCCTTAGTTT-TAAAATTACCAAAATACCCTAGTTTG
1 TAAATTACCAAAATACCCTCAGTTTGTAAAATTACCAAAATACCCTAGTTTG
*
29024379 TAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCACTGGTTTG
1 TAAATTACCAAAATACCCTC-AGTTTGTAAAATTACCAAAATACC-CTAGTTTG
* *
29024432 TGAAATTA-CGAAATACCCTCAATTTGTAAAATTACCAAAATACCC
1 T-AAATTACCAAAATACCCTCAGTTTGTAAAATTACCAAAATACCC
29024477 CTGATTTACA
Statistics
Matches: 89, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
51 23 0.26
52 19 0.21
53 40 0.45
54 7 0.08
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (52 bp):
TAAATTACCAAAATACCCTCAGTTTGTAAAATTACCAAAATACCCTAGTTTG
Found at i:29024491 original size:53 final size:53
Alignment explanation
Indices: 29024329--29024579 Score: 199
Period size: 53 Copynumber: 4.7 Consensus size: 53
29024319 CCTGTAGGAT
* **
29024329 AAATTACCAAAATACCCTTAGTTT-TAAAATTACCAAAATACC-CT-AGTTT-GT
1 AAATTA-CAAAATACCCTCAGTTTGTAAAATTACCAAAATACCACTGA-TTTACA
* ***
29024380 AAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTG
1 AAATTA-CAAAATACCCTC-AGTTTGTAAAATTACCAAAATACCACTGATTTACA
* * *
29024434 AAATTACGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACA
1 AAATTACAAAATACCCTCAGTTTGTAAAATTACCAAAATACCACTGATTTACA
* * * * * * *
29024487 AAATTACAAAATACCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACA
1 AAATTACAAAATACCCTCAGTTTGT-AAAATTACCA-AAATACCACTGATTTACA
* ** * *
29024541 AAATTACTGAAATACCCTTGGTTTGTAGATTTACCAAAA
1 AAATTAC-AAAATACCCTCAGTTTGTAAAATTACCAAAA
29024580 CACCCTTGTA
Statistics
Matches: 161, Mismatches: 29, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
51 22 0.14
52 18 0.11
53 64 0.40
54 44 0.27
55 13 0.08
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (53 bp):
AAATTACAAAATACCCTCAGTTTGTAAAATTACCAAAATACCACTGATTTACA
Found at i:29024543 original size:27 final size:27
Alignment explanation
Indices: 29024513--29024564 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
29024503 TGACTTTCTA
29024513 AAAATTA-TAGAAATACCATTGGTTTAC
1 AAAATTACT-GAAATACCATTGGTTTAC
*
29024540 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCATTGGTTT
29024565 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTACTGAAATACCATTGGTTTAC
Found at i:29024648 original size:27 final size:27
Alignment explanation
Indices: 29024605--29024678 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
29024595 AAATGACTAA
*
29024605 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
29024632 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
29024659 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
29024679 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:29024682 original size:27 final size:27
Alignment explanation
Indices: 29024618--29024682 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
29024608 ACCCCTAATA
*
29024618 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
29024645 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
29024672 GGTAAAATGAC
1 GGTAAAATGAC
29024683 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:29025530 original size:25 final size:25
Alignment explanation
Indices: 29025492--29025561 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
29025482 AGGAAGTGCT
* * *
29025492 AAAAGGGCTATGCCCTAGTTTA-CTG
1 AAAAGGGCTTTGCCCCAGTTTATC-A
*
29025517 AAAAGGGCTTTGCCCCAATTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
29025542 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
29025562 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 38 0.97
26 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:29025574 original size:24 final size:23
Alignment explanation
Indices: 29025491--29025588 Score: 79
Period size: 25 Copynumber: 4.0 Consensus size: 23
29025481 GAGGAAGTGC
*
29025491 TAAAAGGGCTATGCCCTAGTTTACT
1 TAAAAGGGCTATGCCCCAG-TTA-T
* * *
29025516 GAAAAGGGCTTTGCCCCAATTTAT
1 TAAAAGGGCTATGCCCC-AGTTAT
* *
29025540 CAAAAAGGGCTTTGCCCCAGTTAT
1 -TAAAAGGGCTATGCCCCAGTTAT
*
29025564 TAAAAGAGGCTAGGCCTCCAGTTAT
1 TAAAAG-GGCTATGCC-CCAGTTAT
29025589 ATGAAAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
23 5 0.08
24 13 0.22
25 41 0.68
26 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (23 bp):
TAAAAGGGCTATGCCCCAGTTAT
Found at i:29026852 original size:81 final size:79
Alignment explanation
Indices: 29026709--29026890 Score: 267
Period size: 81 Copynumber: 2.3 Consensus size: 79
29026699 ATTACCAAAG
*
29026709 TACCC-CGATTTACAGAATTATCGTTTTACCCCGATTTACATAATTACCATTTTACCCCTGATTT
1 TACCCTCGATTTACAGAATTA-CGTTTTACCCCGATTTACAGAATTACCATTTTACCCCTGATTT
*
29026773 ACATAATTACCGTTT
65 ACAGAATTACCGTTT
* * *
29026788 TACCCTCGATTTACAGAATTACAGTTTTACCCTCGATTTATAGAATTACTATTTTACCCTTGATT
1 TACCCTCGATTTACAGAATTAC-GTTTTACCC-CGATTTACAGAATTACCATTTTACCCCTGATT
*
29026853 TACAGAATTACTGTTT
64 TACAGAATTACCGTTT
*
29026869 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
29026891 TAAAATACCC
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
79 6 0.06
80 24 0.26
81 63 0.68
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (79 bp):
TACCCTCGATTTACAGAATTACGTTTTACCCCGATTTACAGAATTACCATTTTACCCCTGATTTA
CAGAATTACCGTTT
Found at i:29026891 original size:27 final size:27
Alignment explanation
Indices: 29026709--29026891 Score: 230
Period size: 27 Copynumber: 6.9 Consensus size: 27
29026699 ATTACCAAAG
29026709 TACCC-CGATTTACAGAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
* **
29026735 TACCC-CGATTTACATAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
29026761 TACCC-CTGATTTACATAATTACCGTTT
1 TACCCTC-GATTTACAGAATTACTGTTT
*
29026788 TACCCTCGATTTACAGAATTACAGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
29026815 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
29026842 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
29026869 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
29026892 AAAATACCCT
Statistics
Matches: 140, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
26 28 0.20
27 111 0.79
28 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:29026921 original size:26 final size:26
Alignment explanation
Indices: 29026883--29026980 Score: 126
Period size: 26 Copynumber: 3.7 Consensus size: 26
29026873 CTCGATTTAC
*
29026883 AAAATTACTAAAATACCCTAGTTTGT
1 AAAATTACCAAAATACCCTAGTTTGT
*
29026909 AAAATTATCAAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCC-TAGTTTGT
* * *
29026936 GAAATTACCGAAATACCCTCAATTT-T
1 AAAATTACCAAAATACCCT-AGTTTGT
29026962 AAAATTACCAAAATACCCT
1 AAAATTACCAAAATACCCT
29026981 GATTTACAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 35 0.56
27 27 0.44
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (26 bp):
AAAATTACCAAAATACCCTAGTTTGT
Found at i:29026995 original size:26 final size:25
Alignment explanation
Indices: 29026869--29027006 Score: 100
Period size: 26 Copynumber: 5.2 Consensus size: 25
29026859 ATTACTGTTT
*
29026869 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTT--AAAATTACCAAAA
* * *
29026896 TACCCTAGTTTGTAAAATTATCAAAA
1 TACCCTCGATT-TAAAATTACCAAAA
* * * *
29026922 TACCCTTAGTTTGTGAAATTACCGAAA
1 TACCC-TCGATT-TAAAATTACCAAAA
*
29026949 TACCCTCAATTTTAAAATTACCAAAA
1 TACCCTCGA-TTTAAAATTACCAAAA
29026975 TACCCT-GATTTACAAAGTTA-CAGAAA
1 TACCCTCGATTTA-AAA-TTACCA-AAA
29027001 TACCCT
1 TACCCT
29027007 TGACTTTCTA
Statistics
Matches: 92, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
24 4 0.04
25 6 0.07
26 47 0.51
27 34 0.37
28 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (25 bp):
TACCCTCGATTTAAAATTACCAAAA
Found at i:29027068 original size:27 final size:27
Alignment explanation
Indices: 29026609--29027064 Score: 143
Period size: 27 Copynumber: 17.0 Consensus size: 27
29026599 AATACTTTAG
* *
29026609 TTTACTAAAATTACCGAAATACCCTTAGT
1 TTTAC-AAAATTACTGAAATACCCTT-GA
*
29026638 TTGTA-AAAA-TACTGAAATACCCTCGA
1 TT-TACAAAATTACTGAAATACCCTTGA
**
29026664 TTTGTAAAATTACTGAAATA-CCTTCGA
1 TTTACAAAATTACTGAAATACCCTT-GA
* ** * *
29026691 CTTGTAAAATTAC-CAAAGTACCC-CGA
1 TTTACAAAATTACTGAAA-TACCCTTGA
* *** *
29026717 TTTACAGAATTA-TCGTTTTACCC-CGA
1 TTTACAAAATTACT-GAAATACCCTTGA
* * ** *
29026743 TTTACATAATTAC-CATTTTACCCCTGA
1 TTTACAAAATTACTGA-AATACCCTTGA
* * *** *
29026770 TTTACATAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACTGAAATACCCTTGA
* * *** *
29026797 TTTACAGAATTACAGTTTTACCCTCGA
1 TTTACAAAATTACTGAAATACCCTTGA
* * **
29026824 TTTATAGAATTACT-ATTTTACCCTTGA
1 TTTACAAAATTACTGA-AATACCCTTGA
* *** *
29026851 TTTACAGAATTACTGTTTTACCCTCGA
1 TTTACAAAATTACTGAAATACCCTTGA
* *
29026878 TTTACAAAATTACTAAAATACCCTAG-
1 TTTACAAAATTACTGAAATACCCTTGA
** *
29026904 TTTGTAAAATTA-TCAAAATACCCTT-A
1 TTTACAAAATTACT-GAAATACCCTTGA
*** * **
29026930 GTTTGTGAAATTACCGAAATACCCTCAA
1 -TTTACAAAATTACTGAAATACCCTTGA
* **
29026958 TTT-TAAAATTACCAAAATACCC-TGA
1 TTTACAAAATTACTGAAATACCCTTGA
* *
29026983 TTTACAAAGTTACAGAAATACCCTTGA
1 TTTACAAAATTACTGAAATACCCTTGA
* *
29027010 CTTT-CTAAAAATTA-TAGAAATACCATTGG
1 -TTTAC--AAAATTACT-GAAATACCCTTGA
29027039 TTTACAAAATTACTGAAATACCCTTG
1 TTTACAAAATTACTGAAATACCCTTG
29027065 GTTTGTAGAT
Statistics
Matches: 341, Mismatches: 59, Indels: 56
0.75 0.13 0.12
Matches are distributed among these distances:
25 6 0.02
26 101 0.30
27 198 0.58
28 14 0.04
29 20 0.06
30 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (27 bp):
TTTACAAAATTACTGAAATACCCTTGA
Found at i:29027152 original size:27 final size:27
Alignment explanation
Indices: 29027122--29027213 Score: 132
Period size: 27 Copynumber: 3.4 Consensus size: 27
29027112 ACCCCTATTA
* *
29027122 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAT
*
29027149 GGTAAAGTGACCGTAAAGCCCCTGTAT
1 GGTAAAATGACCGTAAAGCCCCTGTAT
*
29027176 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAT
29027203 GGTAAAATGAC
1 GGTAAAATGAC
29027214 GAATATGCCC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 59 0.98
28 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAT
Found at i:29028394 original size:25 final size:25
Alignment explanation
Indices: 29028365--29028412 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29028355 CTATAACATG
* * *
29028365 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
29028390 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
29028413 GTTTATGTAT
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:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:29028495 original size:11 final size:11
Alignment explanation
Indices: 29028459--29028514 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
29028449 CATGGTATGT
29028459 ATGATATGCAC
1 ATGATATGCAC
* *
29028470 ATGACATG--T
1 ATGATATGCAC
29028479 ATGATATGCAC
1 ATGATATGCAC
*
29028490 ATGATATG--T
1 ATGATATGCAC
29028499 ATGATATGCAC
1 ATGATATGCAC
29028510 ATGAT
1 ATGAT
29028515 GTAATCATAA
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:29028514 original size:20 final size:20
Alignment explanation
Indices: 29028448--29028514 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
29028438 GATTTGATAA
*
29028448 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
29028468 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
29028488 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
29028508 ACATGAT
1 ACATGAT
29028515 GTAATCATAA
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:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:29028623 original size:24 final size:23
Alignment explanation
Indices: 29028563--29028700 Score: 206
Period size: 24 Copynumber: 5.9 Consensus size: 23
29028553 GAGGAAGTGA
29028563 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
* *
29028586 TAAATGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
29028609 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
29028633 CAAAAGGGCTTATGCCCCAGTTGT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
29028657 TAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
29028681 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
29028701 GTTAAAAGAG
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
23 51 0.49
24 54 0.51
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:29028632 original size:47 final size:46
Alignment explanation
Indices: 29028563--29028700 Score: 206
Period size: 47 Copynumber: 3.0 Consensus size: 46
29028553 GAGGAAGTGA
*
29028563 AAAAGGGCTTATGCCCCAGTTATTAAATGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
29028609 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTGT
1 -AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
*
29028657 TAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTT
29028701 GTTAAAAGAG
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
46 10 0.12
47 54 0.64
48 20 0.24
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:29028713 original size:24 final size:24
Alignment explanation
Indices: 29028563--29028713 Score: 227
Period size: 23 Copynumber: 6.4 Consensus size: 24
29028553 GAGGAAGTGA
29028563 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
29028587 -AAATGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
29028610 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
29028634 AAAAGGGCTTATGCCCCAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTATT
29028658 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
29028681 AAAAGGGCTT-TGCCCCAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTATT
29028704 AAAAGAGGCT
1 AAAAG-GGCT
29028714 AGGCCTCCAA
Statistics
Matches: 117, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
23 60 0.51
24 57 0.49
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:29028954 original size:31 final size:31
Alignment explanation
Indices: 29028919--29028982 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
29028909 CGTTTACAGT
*
29028919 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
29028950 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29028981 AA
1 AA
29028983 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:29029779 original size:31 final size:31
Alignment explanation
Indices: 29029744--29029822 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
29029734 CGTTTACAAT
29029744 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
1 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
*
29029775 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
29029806 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
29029823 ATATGTCGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATAAGATTTATGA
Found at i:29029899 original size:34 final size:33
Alignment explanation
Indices: 29029855--29029926 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
29029845 CTTAGGCCCA
**
29029855 TACTGCTACTGTTTAAGGGCTAAGGCCCAGACTG
1 TACTGCTACTGAAT-AGGGCTAAGGCCCAGACTG
* ** *
29029889 TACTGTTACTGAATAGGGCTTTGGCCCAGATTG
1 TACTGCTACTGAATAGGGCTAAGGCCCAGACTG
29029922 TACTG
1 TACTG
29029927 ACACTGTGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 21 0.66
34 11 0.34
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (33 bp):
TACTGCTACTGAATAGGGCTAAGGCCCAGACTG
Done.