Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007769.1 Hibiscus syriacus cultivar Beakdansim tig00110045_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 634091
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 3
Found at i:1419 original size:15 final size:15
Alignment explanation
Indices: 1399--1429 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1389 ATCTAAAACT
*
1399 ATAAGAAATTTTAGA
1 ATAAGAAATTTCAGA
1414 ATAAGAAATTTCAGA
1 ATAAGAAATTTCAGA
1429 A
1 A
1430 CACAGCGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (15 bp):
ATAAGAAATTTCAGA
Found at i:1844 original size:31 final size:32
Alignment explanation
Indices: 1792--1909 Score: 130
Period size: 39 Copynumber: 3.4 Consensus size: 32
1782 TTTTTTTTAA
* *
1792 ATTCGGGTTTGGGTCGAGGTTTTTTAAGTTTGAT
1 ATTCGGG-TCGGGTCG-GGTTTTTTAAGTGTGAT
1826 ATTCGGGTC-GGTCGGGTTTTTTAAGTGTGAT
1 ATTCGGGTCGGGTCGGGTTTTTTAAGTGTGAT
1857 ATTCGGGTCGGGTTCGGGTTGGGTTTTTTTAAGTGTGAT
1 ATTCGGGTCGGG-TC-----GGG-TTTTTTAAGTGTGAT
1896 ATTCGGGTCGGGTC
1 ATTCGGGTCGGGTC
1910 TCGGTGGAGG
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
31 25 0.34
32 7 0.09
33 3 0.04
34 7 0.09
38 5 0.07
39 27 0.36
ACGTcount: A:0.12, C:0.09, G:0.36, T:0.42
Consensus pattern (32 bp):
ATTCGGGTCGGGTCGGGTTTTTTAAGTGTGAT
Found at i:8651 original size:11 final size:12
Alignment explanation
Indices: 8627--8652 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8617 AACTTTTAAA
8627 TTTTATGTATTT
1 TTTTATGTATTT
8639 TTTTATGTATTT
1 TTTTATGTATTT
8651 TT
1 TT
8653 AAAATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTATGTATTT
Found at i:9052 original size:36 final size:36
Alignment explanation
Indices: 9005--9074 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
8995 TAAAGTCTAG
9005 TTTTGTTTCATTCAGTATTCCATTCAAAATTTGATT
1 TTTTGTTTCATTCAGTATTCCATTCAAAATTTGATT
**
9041 TTTTGTTTCATTCAGTATTCTGTTCAAAATTTGA
1 TTTTGTTTCATTCAGTATTCCATTCAAAATTTGA
9075 CATTAACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (36 bp):
TTTTGTTTCATTCAGTATTCCATTCAAAATTTGATT
Found at i:15023 original size:64 final size:63
Alignment explanation
Indices: 14937--15096 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
14927 ATTGTTTAAG
* * ** *
14937 ATGCATCGATGCACATGCAGTGCATCGATGCAT-GATTTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCA-AAGCAGTGCATCGATGCATCCACATTAAATA-AAAACATCGAAT-GCATTT
15000 T
63 T
* *
15001 ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCA-AAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTT
* * *
15065 ATGCACCGATGCACAGTAGTGCATCGATGCAT
1 ATGCATCGATGCAAAGCAGTGCATCGATGCAT
15097 ACATTCATTG
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 19 0.23
64 57 0.69
65 7 0.08
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCAAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTT
Found at i:15807 original size:30 final size:30
Alignment explanation
Indices: 15773--15836 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
15763 AAGGAATATA
*
15773 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
15803 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
15833 TGGA
1 TGGA
15837 CAGGTCCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:19231 original size:64 final size:64
Alignment explanation
Indices: 19145--19305 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
19135 ATTGTTTAAG
* * ** *
19145 ATGCATCGATGCACATGCAGTGCATCGATGCAT-GATTTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATA-AAAACATCGAAT-GCATTT
19208 T
64 T
* * *
19209 ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTT
* *
19273 ATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT
19306 ACATTCATTG
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 2 0.02
64 75 0.89
65 7 0.08
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTT
Found at i:20018 original size:30 final size:30
Alignment explanation
Indices: 19982--20045 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
19972 AAGGAACATA
* *
19982 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
20012 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
20042 TGGA
1 TGGA
20046 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:23748 original size:12 final size:12
Alignment explanation
Indices: 23731--23755 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23721 ACAAAGCACC
23731 ATTTGGTGCCTA
1 ATTTGGTGCCTA
23743 ATTTGGTGCCTA
1 ATTTGGTGCCTA
23755 A
1 A
23756 ATTATTTGAC
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:26603 original size:22 final size:24
Alignment explanation
Indices: 26567--26611 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
26557 TTGAAAACAT
26567 TTTTCAAAGAAACATTTACCAAAC
1 TTTTCAAAGAAACATTTACCAAAC
*
26591 TTTT-AAA-AAACATTTTCCAAA
1 TTTTCAAAGAAACATTTACCAAA
26612 GTTGGTTGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 3 0.15
24 4 0.20
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (24 bp):
TTTTCAAAGAAACATTTACCAAAC
Found at i:31183 original size:22 final size:24
Alignment explanation
Indices: 31147--31191 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
31137 TTGAAAACAT
31147 TTTTCAAAGAAACATTTACCAAAC
1 TTTTCAAAGAAACATTTACCAAAC
*
31171 TTTT-AAA-AAACATTTTCCAAA
1 TTTTCAAAGAAACATTTACCAAA
31192 GTTGGTTGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 3 0.15
24 4 0.20
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (24 bp):
TTTTCAAAGAAACATTTACCAAAC
Found at i:31691 original size:15 final size:15
Alignment explanation
Indices: 31671--31721 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
31661 TGAGACATTA
31671 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
31686 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
* *
31701 CCCACCCCACATCCG
1 CCCGCCCCGCATCCG
31716 CCCGCC
1 CCCGCC
31722 TAGCTAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.10, C:0.69, G:0.16, T:0.06
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:37626 original size:8 final size:8
Alignment explanation
Indices: 37615--37640 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
37605 ATTATAAGTA
37615 TATATATT
1 TATATATT
37623 TATATATT
1 TATATATT
37631 TATATATT
1 TATATATT
37639 TA
1 TA
37641 ATTATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATATT
Found at i:39594 original size:9 final size:9
Alignment explanation
Indices: 39582--39621 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
39572 TGTTGATGTT
39582 GATGATGAG
1 GATGATGAG
39591 GATGATGAG
1 GATGATGAG
* *
39600 GATGGTGAT
1 GATGATGAG
*
39609 GATGATGGG
1 GATGATGAG
39618 GATG
1 GATG
39622 TTGGTTCGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.47, T:0.25
Consensus pattern (9 bp):
GATGATGAG
Found at i:46562 original size:38 final size:39
Alignment explanation
Indices: 46487--46564 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
46477 AAAGTAAGAG
46487 CAAATATGAGGTCAAAACAGACCAAAAGATTGAGATTAC
1 CAAATATGAGGTCAAAACAGACCAAAAGATTGAGATTAC
46526 CAAATATGAGGTCAAAACAGACC-AAAGATTGAGATTAC
1 CAAATATGAGGTCAAAACAGACCAAAAGATTGAGATTAC
46564 C
1 C
46565 TGTGCAGCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 16 0.41
39 23 0.59
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.18
Consensus pattern (39 bp):
CAAATATGAGGTCAAAACAGACCAAAAGATTGAGATTAC
Found at i:54053 original size:2 final size:2
Alignment explanation
Indices: 54046--54074 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54036 TTATAGTCCT
54046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54075 TTGCATGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:67830 original size:15 final size:15
Alignment explanation
Indices: 67810--67866 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
67800 AATCGGATAT
67810 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
67825 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
67842 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
67857 CGGGTACCCG
1 CGGGTACCCG
67867 TAACATCCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:67846 original size:17 final size:16
Alignment explanation
Indices: 67810--67878 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
67800 AATCGGATAT
**
67810 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
67825 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
67842 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
67857 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
67874 CGGGT
1 CGGGT
67879 CGGGACACGG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.48
16 6 0.14
17 17 0.39
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:67851 original size:32 final size:32
Alignment explanation
Indices: 67810--67878 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
67800 AATCGGATAT
67810 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
67842 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
67874 CGGGT
1 CGGGT
67879 CGGGACACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:69190 original size:9 final size:9
Alignment explanation
Indices: 69176--69219 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
69166 GAAATCTGGA
69176 AACCGGTTT
1 AACCGGTTT
*
69185 AACCGGTTG
1 AACCGGTTT
69194 AACCGGTTTT
1 AACCGG-TTT
*
69204 GACCGGTTT
1 AACCGGTTT
*
69213 GACCGGT
1 AACCGGT
69220 CCTGACCCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 24 0.77
10 7 0.23
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:69219 original size:19 final size:19
Alignment explanation
Indices: 69176--69211 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
69166 GAAATCTGGA
69176 AACCGG-TTTAACCGGTTG
1 AACCGGTTTTAACCGGTTG
*
69194 AACCGGTTTTGACCGGTT
1 AACCGGTTTTAACCGGTT
69212 TGACCGGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (19 bp):
AACCGGTTTTAACCGGTTG
Found at i:69240 original size:13 final size:13
Alignment explanation
Indices: 69222--69259 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
69212 TGACCGGTCC
69222 TGACCCGACCCGT
1 TGACCCGACCCGT
*
69235 TGACCCTACCCGT
1 TGACCCGACCCGT
69248 TGACCCGACCCG
1 TGACCCGACCCG
69260 ACCGTTGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:69282 original size:31 final size:31
Alignment explanation
Indices: 69223--69283 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
69213 GACCGGTCCT
* *
69223 GACCCGACCCGTTGACCCTACCCGTTGACCC
1 GACCCGACCCGTTGACCCTAACCATTGACCC
*
69254 GACCCGA-CCGTTGACCGTTAACCATTGACC
1 GACCCGACCCGTTGACC-CTAACCATTGACC
69284 GTTGATCGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.18
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCTAACCATTGACCC
Found at i:69445 original size:29 final size:28
Alignment explanation
Indices: 69374--69475 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
69364 AATTTTTTTG
* * *
69374 GAAAAAGTGATATTCTGGGAATTAATTC
1 GAAAAGGTGCTATTTTGGGAATTAATTC
* *
69402 GAAATTGGTGATATTTTGGGAATTAATTC
1 GAAA-AGGTGCTATTTTGGGAATTAATTC
* * *
69431 GAAAAGGATGCTATTTTGGTAATTATTTT
1 GAAAAGG-TGCTATTTTGGGAATTAATTC
*
69460 AAAAAGGGTGCTATTT
1 GAAAA-GGTGCTATTT
69476 ATGTAAAATG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
28 6 0.10
29 54 0.87
30 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (28 bp):
GAAAAGGTGCTATTTTGGGAATTAATTC
Found at i:71477 original size:2 final size:2
Alignment explanation
Indices: 71470--71508 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
71460 GGATCATAAC
71470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71509 GGCATGATCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:77201 original size:3 final size:3
Alignment explanation
Indices: 77193--77226 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
77183 GAGATGTCAT
77193 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
77227 ATAATTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:85357 original size:31 final size:33
Alignment explanation
Indices: 85286--85364 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 33
85276 AGTTCTGTAA
* * * * *
85286 TAGTTCAATAAAT-TTTAATAATTATTTTATAT
1 TAGTTTAATAACTATTTCATAATAATTTAATAT
85318 TAGTTTAATAACTATTTCATAATAATTTAATA-
1 TAGTTTAATAACTATTTCATAATAATTTAATAT
*
85350 TA-TTTAATAATTATT
1 TAGTTTAATAACTATT
85365 AAAATTTCAG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 12 0.30
32 13 0.32
33 15 0.38
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.52
Consensus pattern (33 bp):
TAGTTTAATAACTATTTCATAATAATTTAATAT
Found at i:85364 original size:11 final size:11
Alignment explanation
Indices: 85299--85364 Score: 66
Period size: 11 Copynumber: 6.2 Consensus size: 11
85289 TTCAATAAAT
85299 TTTAATAATTA
1 TTTAATAATTA
*
85310 TTTTAT-ATTA
1 TTTAATAATTA
*
85320 GTTTAATAACTA
1 -TTTAATAATTA
* *
85332 TTTCATAATAA
1 TTTAATAATTA
85343 TTTAAT-A-TA
1 TTTAATAATTA
85352 TTTAATAATTA
1 TTTAATAATTA
85363 TT
1 TT
85365 AAAATTTCAG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
9 7 0.16
10 6 0.14
11 27 0.63
12 3 0.07
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAATAATTA
Found at i:86116 original size:7 final size:7
Alignment explanation
Indices: 86104--86148 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
86094 TCGGTTGATT
86104 GAAGGGA
1 GAAGGGA
86111 GAAGGGA
1 GAAGGGA
86118 GAAGGGA
1 GAAGGGA
86125 GAAGGGA
1 GAAGGGA
86132 GAAGGGA
1 GAAGGGA
86139 GAAGGGA
1 GAAGGGA
86146 GAA
1 GAA
86149 CTGTTTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (7 bp):
GAAGGGA
Found at i:86186 original size:3 final size:3
Alignment explanation
Indices: 86178--86203 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
86168 TAGGATCTTT
86178 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
86204 TTTGGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:90953 original size:31 final size:31
Alignment explanation
Indices: 90916--90992 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
90906 TTGTTAACAA
*
90916 TAGGTGTCTAATGTTTTCTCTATTACATTTT
1 TAGGTGTCTAATGTTTTCTCCATTACATTTT
* * *
90947 TAGGTGTCTAAAGTTTTCTCCGTTATATTTT
1 TAGGTGTCTAATGTTTTCTCCATTACATTTT
*
90978 TAGGTGTCTACTGTT
1 TAGGTGTCTAATGTT
90993 ATATTTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.52
Consensus pattern (31 bp):
TAGGTGTCTAATGTTTTCTCCATTACATTTT
Found at i:93244 original size:30 final size:29
Alignment explanation
Indices: 93210--93411 Score: 171
Period size: 30 Copynumber: 6.8 Consensus size: 29
93200 AAATGGGAGC
*
93210 AATAGAAACTTAAGGGATTAAAATAGCAAA
1 AATAGAAACTTAAGGGACTAAAATAG-AAA
93240 AATAGAAAGC-TAAGGGACTAAAATAGAAA
1 AATAGAAA-CTTAAGGGACTAAAATAGAAA
* * * *
93269 ATATATAAACTTAAAGGACTAACACAGTAAA
1 A-ATAGAAACTTAAGGGACTAAAATAG-AAA
* * *
93300 AACCA-AAACTTAAGGG-TTGAAATAGAAA
1 AA-TAGAAACTTAAGGGACTAAAATAGAAA
* * *
93328 ATATA-AACATTTAAAGGACTAAAATAAAAA
1 A-ATAGAA-ACTTAAGGGACTAAAATAGAAA
* *
93358 ATATAGACATTTAAGGG-CTAAAATAGAAAA
1 A-ATAGAAACTTAAGGGACTAAAATAG-AAA
93388 AATAGAAACTTAAGGGACTAAAAT
1 AATAGAAACTTAAGGGACTAAAAT
93412 GGTATTAACA
Statistics
Matches: 139, Mismatches: 22, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
28 7 0.05
29 39 0.28
30 86 0.62
31 7 0.05
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.20
Consensus pattern (29 bp):
AATAGAAACTTAAGGGACTAAAATAGAAA
Found at i:94714 original size:16 final size:16
Alignment explanation
Indices: 94693--94732 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
94683 ATGGGTAAGG
*
94693 TCTCGGGTCAGCCAGA
1 TCTCGGGTCACCCAGA
94709 TCTCGGGTCACCCAGA
1 TCTCGGGTCACCCAGA
94725 TCTCGGGT
1 TCTCGGGT
94733 TGCTGGGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.15, C:0.33, G:0.30, T:0.23
Consensus pattern (16 bp):
TCTCGGGTCACCCAGA
Found at i:97073 original size:37 final size:36
Alignment explanation
Indices: 96998--97073 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
96988 TTTTTATATT
*
96998 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
97034 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
97071 TTT
1 TTT
97074 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:100103 original size:228 final size:227
Alignment explanation
Indices: 99701--100148 Score: 790
Period size: 228 Copynumber: 2.0 Consensus size: 227
99691 GTAAATTATC
* * *
99701 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
* *
99766 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACTATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
99831 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
99896 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
99929 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
99994 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-ATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
* *
100058 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
100123 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
100149 GCAGTTTTTA
Statistics
Matches: 210, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
227 4 0.02
228 123 0.59
229 83 0.40
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:100249 original size:20 final size:21
Alignment explanation
Indices: 100210--100259 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
100200 AAAACGATAT
100210 ACCAGGTAAAAAATATGATAAA
1 ACCA-GTAAAAAATATGATAAA
*
100232 ACCAGTAACAAA-ATGATAAA
1 ACCAGTAAAAAATATGATAAA
100252 ACC-GTAAA
1 ACCAGTAAA
100260 TTTAAAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 11 0.42
21 7 0.27
22 4 0.15
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (21 bp):
ACCAGTAAAAAATATGATAAA
Found at i:100403 original size:20 final size:19
Alignment explanation
Indices: 100380--100425 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
100370 CGATATAACA
100380 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
100400 GGTAACAAATGATAAAACC
1 GGTAAAAAATGATAAAACC
100419 GGTAAAA
1 GGTAAAA
100426 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:102688 original size:21 final size:21
Alignment explanation
Indices: 102641--102705 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
102631 AAGACAATCA
* *
102641 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
102663 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
102683 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
102704 AG
1 AG
102706 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:102781 original size:33 final size:33
Alignment explanation
Indices: 102739--102804 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
102729 AAATAGATGG
*
102739 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
102772 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
102805 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:104625 original size:18 final size:19
Alignment explanation
Indices: 104581--104628 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
104571 AATGTCGAGT
104581 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
104600 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
104619 T-ATTTTGTAT
1 TAATTTTGTAT
104629 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:105168 original size:198 final size:199
Alignment explanation
Indices: 104747--105907 Score: 2069
Period size: 198 Copynumber: 5.9 Consensus size: 199
104737 CAATATGGCC
* * *
104747 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
104812 ACCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
104876 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
**
104941 ATGGAA
194 ATTAAA
*
104947 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAA
105012 CCAAAAG-ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
105076 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
105140 TTAAA
195 TTAAA
*
105145 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAC
105209 CAAAAGTATAATGTAATATGTAATTTTTC-ATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
105273 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTTGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
105338 TAAA
196 TAAA
*
105342 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAC
105407 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
105471 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
105536 TAAA
196 TAAA
* *
105540 AACAATGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAC
*
105605 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACAGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
105670 AATATGTCTAAATAA--TGT-GACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
**
105732 GGAA
196 TAAA
105736 AACAAGGTGCACCCAT-AAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCG-AAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAC
105798 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
105863 AATATGTCTAAATAATGTGTCGACACTAATATAG-TTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
105908 CTAATTTAAA
Statistics
Matches: 936, Mismatches: 16, Indels: 23
0.96 0.02 0.02
Matches are distributed among these distances:
193 81 0.09
194 25 0.03
195 32 0.03
196 162 0.17
197 107 0.11
198 323 0.35
199 171 0.18
200 35 0.04
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
TAAA
Found at i:105543 original size:395 final size:396
Alignment explanation
Indices: 104747--105907 Score: 2092
Period size: 395 Copynumber: 2.9 Consensus size: 396
104737 CAATATGGCC
* * *
104747 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
104812 ACCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
104876 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
*
104941 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
194 ATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
105006 CGAAAACCAAAAG-ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
259 CG--AACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
105070 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGA
322 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGA
105135 ATGAATTAAA
387 ATGAATTAAA
105145 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
105209 CAAAAGTATAATGTAATATGTAATTTTTC-ATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
105273 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTTGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
**
105338 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
105403 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATG
261 AA-CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
105467 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
325 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAAT
105532 GAATTAAA
389 GAATTAAA
*
105540 AACAATGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
105605 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACAGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
105670 AATATGTCTAAATAA--TGT-GACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
105732 GGAAAACAAGGTGCACCCAT-AAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
105795 AACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
261 AACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
105860 GAGAATATGTCTAAATAATGTGTCGACACTAATATAG-TTGTGTCGATA
326 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
105908 CTAATTTAAA
Statistics
Matches: 742, Mismatches: 14, Indels: 21
0.95 0.02 0.03
Matches are distributed among these distances:
391 62 0.08
392 75 0.10
393 20 0.03
394 127 0.17
395 289 0.39
396 86 0.12
397 49 0.07
398 34 0.05
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (396 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGA
ATTAAA
Found at i:107383 original size:18 final size:18
Alignment explanation
Indices: 107362--107429 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
107352 AGCGGTCGCA
107362 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
107380 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
107401 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
107422 GAAGATGA
1 GAAGATGA
107430 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:107386 original size:6 final size:6
Alignment explanation
Indices: 107362--107459 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
107352 AGCGGTCGCA
* * * * * *
107362 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
107410 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
107458 GA
1 GA
107460 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:107397 original size:3 final size:3
Alignment explanation
Indices: 107377--107463 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
107367 TGAAGCTGAC
* * * * * ** *
107377 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
107425 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
107464 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:107412 original size:42 final size:42
Alignment explanation
Indices: 107365--107455 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
107355 GGTCGCAGAA
*
107365 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
107407 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
107449 GATGAAG
1 GATGAAG
107456 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:107463 original size:18 final size:18
Alignment explanation
Indices: 107362--107459 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
107352 AGCGGTCGCA
* *
107362 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
107380 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
107398 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
107416 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
107434 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
107452 GAAGATGA
1 GAAGATGA
107460 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:109229 original size:183 final size:184
Alignment explanation
Indices: 108920--109627 Score: 1253
Period size: 183 Copynumber: 3.9 Consensus size: 184
108910 CTTTCAACAT
** * * * *
108920 ATTATAATAAAATAGGTAAATTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
* * *
108985 GGTATACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
* *
109050 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACCATTGAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
109104 ATTATAATGTAATAGATAATTTTGTAATATAACC-GTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
*
109168 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
* *
109233 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTT--ACATCGGAACCCATA
131 AATGTGTCGATACCATTGAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
109285 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
109350 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
109415 AATGTGTCGATACCATTGAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACCATTGAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
109469 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
*
109533 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
109598 AATGTGTCGATACCATTGAAAAAAGTGTCG
131 AATGTGTCGATACCATTGAAAAAAGTGTCG
109628 GTAATTTGAA
Statistics
Matches: 509, Mismatches: 12, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
181 49 0.10
182 129 0.25
183 267 0.52
184 64 0.13
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
AATGTGTCGATACCATTGAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:109593 original size:365 final size:365
Alignment explanation
Indices: 108920--109627 Score: 1265
Period size: 365 Copynumber: 1.9 Consensus size: 365
108910 CTTTCAACAT
* *
108920 ATTATAATAAAATAGGTAAATTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
* *
108985 GGTATACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTATACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
* *
109050 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
131 AATGTGTCGATACCATTGAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
109115 ATAGATAATTTTGTAATATAACCGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
196 ATAGATAATTTTGTAATATAACCGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
*
109180 ATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA
261 ATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA
* *
109245 CGATTTAAAAAAGTGTCGACATTTTACATCGGAACCCATA
326 CCATTGAAAAAAGTGTCGACATTTTACATCGGAACCCATA
** * *
109285 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATAAAATAGATAAATTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
*
109350 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTATACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
109415 AATGTGTCGATACCATTGAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
131 AATGTGTCGATACCATTGAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
109480 ATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACC-GTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
*
109544 TATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAAAATGTGTCGAT
260 TATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGAT
109609 ACCATTGAAAAAAGTGTCG
325 ACCATTGAAAAAAGTGTCG
109628 GTAATTTGAA
Statistics
Matches: 327, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
364 14 0.04
365 313 0.96
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (365 bp):
ATTATAATAAAATAGATAAATTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTATACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
AATGTGTCGATACCATTGAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
ATAGATAATTTTGTAATATAACCGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
ATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA
CCATTGAAAAAAGTGTCGACATTTTACATCGGAACCCATA
Found at i:112105 original size:25 final size:25
Alignment explanation
Indices: 112077--112136 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
112067 TTATCATTAA
112077 ATTTAGGTATGTATAATAACTACAT
1 ATTTAGGTATGTATAATAACTACAT
* **
112102 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTATAATAACTACAT
112127 ATTTAGGTAT
1 ATTTAGGTAT
112137 ACATCTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTTAGGTATGTATAATAACTACAT
Found at i:112455 original size:23 final size:23
Alignment explanation
Indices: 112424--112487 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
112414 ATAGGTAAAC
*
112424 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
112447 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
112470 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
112488 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:112494 original size:23 final size:23
Alignment explanation
Indices: 112424--112496 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
112414 ATAGGTAAAC
* **
112424 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
112447 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
112470 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
112493 ATAT
1 ATAT
112497 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:113434 original size:21 final size:21
Alignment explanation
Indices: 113404--113444 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
113394 AAATTGTTAA
* *
113404 AAATATTAATGTTTTAGATAT
1 AAATAATAATATTTTAGATAT
113425 AAATAATAATATTTTAGATA
1 AAATAATAATATTTTAGATA
113445 AATTTTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
AAATAATAATATTTTAGATAT
Found at i:114161 original size:29 final size:28
Alignment explanation
Indices: 114124--114190 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 28
114114 ATCTAGTTTG
*
114124 ATAAGATTAGTTTGTGTATAATCAAATAA
1 ATAA-ATTAATTTGTGTATAATCAAATAA
114153 ATAACATTAATTTGTGTATAATCAAATAA
1 ATAA-ATTAATTTGTGTATAATCAAATAA
114182 ATAAATTAA
1 ATAAATTAA
114191 GCCAACGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.37
Consensus pattern (28 bp):
ATAAATTAATTTGTGTATAATCAAATAA
Found at i:114595 original size:13 final size:13
Alignment explanation
Indices: 114577--114603 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
114567 TGCAGAATTT
114577 TGATTTGATCAAG
1 TGATTTGATCAAG
114590 TGATTTGATCAAG
1 TGATTTGATCAAG
114603 T
1 T
114604 AGATGGCGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (13 bp):
TGATTTGATCAAG
Found at i:117106 original size:10 final size:10
Alignment explanation
Indices: 117083--117116 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
117073 TATTAAACTA
*
117083 AATTTTTTAAT
1 AATTTTTT-TT
117094 AATTTTTTTT
1 AATTTTTTTT
117104 AATTTTTTTT
1 AATTTTTTTT
117114 AAT
1 AAT
117117 ATTGTTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
AATTTTTTTT
Found at i:121188 original size:20 final size:20
Alignment explanation
Indices: 121160--121207 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
121150 AGTCGTTTCT
121160 AGCCGTTGGAGATATTTTGG
1 AGCCGTTGGAGATATTTTGG
* * *
121180 AGTCGTTGGGGATGTTTTGG
1 AGCCGTTGGAGATATTTTGG
121200 AGCCGTTG
1 AGCCGTTG
121208 AGACTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.10, G:0.40, T:0.35
Consensus pattern (20 bp):
AGCCGTTGGAGATATTTTGG
Found at i:126800 original size:72 final size:72
Alignment explanation
Indices: 126680--126828 Score: 199
Period size: 72 Copynumber: 2.1 Consensus size: 72
126670 CTTACTTTGG
* * * * *
126680 GGCTGTACACCTTTTCCGAGATGGTTCTCGTAAATTCCTTGGATGGAGTTGAGGTGGAGCTTGTT
1 GGCTGAACACCTTTTCCGAGATGGTTCTCCTAAATTCCTTGGAAGGAGTAGAGGTGGAGCTTGAT
126745 AACTTCA
66 AACTTCA
* * * *
126752 GGCTGAACACTTTTTCTGAGATGGTTCTCCTAAATTCTTTGGAAGGAGTAGCGGTGGAGCTTGAT
1 GGCTGAACACCTTTTCCGAGATGGTTCTCCTAAATTCCTTGGAAGGAGTAGAGGTGGAGCTTGAT
* *
126817 ACCTTCG
66 AACTTCA
126824 GGCTG
1 GGCTG
126829 CAAATGCGTC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (72 bp):
GGCTGAACACCTTTTCCGAGATGGTTCTCCTAAATTCCTTGGAAGGAGTAGAGGTGGAGCTTGAT
AACTTCA
Found at i:127070 original size:2 final size:2
Alignment explanation
Indices: 127065--127090 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
127055 TTTTTCGCGC
127065 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
127091 TATTTACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133971 original size:20 final size:20
Alignment explanation
Indices: 133921--133978 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
133911 GATTCTGACT
*
133921 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACCAA
* **
133941 ATTCGCGTTGCGATTTACGTA
1 A-TCGCATTGCGATTTACCAA
133962 ATCGCATTGCGATTTAC
1 ATCGCATTGCGATTTAC
133979 ATAGCGTCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATTTACCAA
Found at i:134533 original size:20 final size:20
Alignment explanation
Indices: 134508--134558 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
134498 TTCTAAACTT
*
134508 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
134528 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
134548 ACTATCGCAAC
1 AAAATCGCAAC
134559 GAGAGAATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:134612 original size:33 final size:33
Alignment explanation
Indices: 134530--134612 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
134520 TGAAAATGAA
**
134530 AATCGCAACACGAAAATGACTATCGCAACGAGAG
1 AATCGCAACACG-AAATGAAAATCGCAACGAGAG
* * *
134564 AATCGCAATACGAAATGAAAATCGCAACGATAT
1 AATCGCAACACGAAATGAAAATCGCAACGAGAG
*
134597 AATCGCAACGCGAAAT
1 AATCGCAACACGAAAT
134613 ACGATTTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 31 0.74
34 11 0.26
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (33 bp):
AATCGCAACACGAAATGAAAATCGCAACGAGAG
Found at i:134695 original size:20 final size:20
Alignment explanation
Indices: 134642--134718 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
134632 GCGATTCTCT
* *
134642 CGTTGCGATTTTAATTT-CG
1 CGTTGCAATTTTCATTTCCG
* **
134661 CGTTACAATAGTCATTTCCG
1 CGTTGCAATTTTCATTTCCG
*
134681 CGTTGCAATTTTCA-TTCTCT
1 CGTTGCAATTTTCATTTC-CG
*
134701 CGTTGCGATTTTCATTTC
1 CGTTGCAATTTTCATTTC
134719 AACCAAAAGA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 15 0.33
20 27 0.60
21 3 0.07
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (20 bp):
CGTTGCAATTTTCATTTCCG
Found at i:136626 original size:94 final size:94
Alignment explanation
Indices: 136411--136972 Score: 949
Period size: 94 Copynumber: 6.1 Consensus size: 94
136401 TAGATTGCTT
* * *
136411 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
136472 ATTTGTCTTT-TGTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
136499 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
136564 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
136593 AGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
136658 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
136687 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
136752 ATTTATCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
136781 AGTAAATTTGTTCGGTTGCTGCAAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
136846 ATTTGTCTTTGTTTTGTCCTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
136875 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
136940 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
136968 AGTAA
1 AGTAA
136973 TGCAATCCAT
Statistics
Matches: 449, Mismatches: 19, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
88 35 0.08
90 3 0.01
91 2 0.00
92 29 0.06
93 21 0.05
94 359 0.80
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:137100 original size:20 final size:19
Alignment explanation
Indices: 137063--137164 Score: 78
Period size: 20 Copynumber: 5.2 Consensus size: 19
137053 TCTTTTGGTC
*
137063 GAAATGAAAATGGCAACGA
1 GAAATGAAAATCGCAACGA
* *
137082 GAGAATGAAAATCGTAACGC
1 GA-AATGAAAATCGCAACGA
* *
137102 GAAACGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
137121 GAAACCAAAAATCGCAACGC
1 GAAA-TGAAAATCGCAACGA
** *
137141 GAAACCAAAAATCGCAACGC
1 GAAA-TGAAAATCGCAACGA
137161 GAAA
1 GAAA
137165 CTATAATCGC
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 21 0.28
20 54 0.72
ACGTcount: A:0.50, C:0.22, G:0.21, T:0.08
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:137174 original size:19 final size:20
Alignment explanation
Indices: 137089--137165 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
137079 CGAGAGAATG
* *
137089 AAAATCGTAACGCGAAA-CG
1 AAAATCGCAACGCGAAACCA
137108 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
137128 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
137148 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
137166 TATAATCGCG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
19 16 0.29
20 39 0.71
ACGTcount: A:0.49, C:0.27, G:0.17, T:0.06
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:137198 original size:19 final size:19
Alignment explanation
Indices: 137171--137330 Score: 124
Period size: 19 Copynumber: 8.8 Consensus size: 19
137161 GAAACTATAA
137171 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
137190 CCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
137204 TCTCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
137223 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
137237 TCTCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
137256 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
137275 CTATCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
**
137295 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
137316 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
137331 AAGTTCCAGA
Statistics
Matches: 108, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
14 17 0.16
16 6 0.06
17 6 0.06
19 48 0.44
20 17 0.16
21 14 0.13
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:137217 original size:33 final size:33
Alignment explanation
Indices: 137174--137306 Score: 176
Period size: 33 Copynumber: 3.8 Consensus size: 33
137164 ACTATAATCG
* *
137174 CGTTGCGATTTTCATTCCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
137207 CGTTGTGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
137240 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTCATTCTAT
1 CGTTGCGATTTTCATTTCGCGTTGCGA--TTC--TC--T
137279 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
137307 AGTCATTTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
33 55 0.62
35 3 0.03
37 3 0.03
39 27 0.31
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:137287 original size:39 final size:37
Alignment explanation
Indices: 137174--137330 Score: 159
Period size: 33 Copynumber: 4.3 Consensus size: 37
137164 ACTATAATCG
* *
137174 CGTTGCGATTTTCATTCCGCATTGCGA-TTC--TC-T
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTCATTCTT
*
137207 CGTTGTGATTTTCATTTCGCGTTGCGA-TTC--TC-T
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTCATTCTT
*
137240 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTCATTCTAT
1 CGTTGCGATTTTCATTTCGCGTTGCGA-TTTCATTCT-T
* *
137279 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTTT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT-TTCATTCTT
137317 CACGTTGCGATTTT
1 --CGTTGCGATTTT
137331 AAGTTCCAGA
Statistics
Matches: 107, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
33 55 0.51
35 3 0.03
37 2 0.02
38 2 0.02
39 33 0.31
40 12 0.11
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (37 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTTCATTCTT
Found at i:137807 original size:42 final size:42
Alignment explanation
Indices: 137731--137819 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
137721 GACTCGCCTG
* *
137731 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTGAAGAGGCCCCTA
* * * * * *
137773 TCATTCCTCGAGAGTCCCCTCCCACCGTTTAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTGAAGAGGCCCCTA
137815 TCATC
1 TCATC
137820 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTGAAGAGGCCCCTA
Found at i:139159 original size:14 final size:14
Alignment explanation
Indices: 139139--139175 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
139129 GATTGTTTAA
139139 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
139152 TATGATTTGTAAAAG
1 T-TGATTTGTAAAAG
139167 TTGATTTGT
1 TTGATTTGT
139176 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:139219 original size:36 final size:36
Alignment explanation
Indices: 139172--139260 Score: 171
Period size: 36 Copynumber: 2.5 Consensus size: 36
139162 AAAAGTTGAT
139172 TTGTTTAATTGATGTGAACATAATTCTTATTTGTGC
1 TTGTTTAATTGATGTGAACATAATTCTTATTTGTGC
139208 TTGTTTAATTGATGTGAACATAATTCTTATTTGTGC
1 TTGTTTAATTGATGTGAACATAATTCTTATTTGTGC
139244 TTGTTTAATTGAT-TGAA
1 TTGTTTAATTGATGTGAA
139261 ATGTAATGGT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 4 0.08
36 49 0.92
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.51
Consensus pattern (36 bp):
TTGTTTAATTGATGTGAACATAATTCTTATTTGTGC
Found at i:139340 original size:19 final size:19
Alignment explanation
Indices: 139318--139405 Score: 79
Period size: 19 Copynumber: 5.2 Consensus size: 19
139308 AAAAATGACT
139318 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
139337 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
139351 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
139370 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
139384 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
139403 ATC
1 ATC
139406 ACAACGACAA
Statistics
Matches: 53, Mismatches: 6, Indels: 20
0.67 0.08 0.25
Matches are distributed among these distances:
14 19 0.36
15 2 0.04
16 4 0.08
17 4 0.08
18 2 0.04
19 22 0.42
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:139360 original size:33 final size:33
Alignment explanation
Indices: 139318--139430 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
139308 AAAAATGACT
139318 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
139351 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
139384 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
139417 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
139431 CTAAATTCGC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:139458 original size:19 final size:19
Alignment explanation
Indices: 139436--139553 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
139426 CGAAACTAAA
139436 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
139455 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
139470 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
139488 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
139503 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
139521 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
139540 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
139554 AGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:139482 original size:33 final size:33
Alignment explanation
Indices: 139440--139533 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
139430 ACTAAATTCG
*
139440 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
139473 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
139506 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
139534 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:139599 original size:20 final size:20
Alignment explanation
Indices: 139527--139599 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
139517 TCATTTCGCA
* *
139527 TTGCGATAGTAATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* **
139547 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
139567 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
139588 TTGCGATAGTCA
1 TTGCGATAGTCA
139600 AATGAATGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:142211 original size:30 final size:30
Alignment explanation
Indices: 142177--142237 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
142167 AAATCGTTTG
142177 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
142207 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
142237 G
1 G
142238 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:144274 original size:22 final size:23
Alignment explanation
Indices: 144228--144274 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
144218 GAAAAATAAC
** *
144228 AATTTTTTTTTTTATAATTTCGA
1 AATTTTTTTTTAAAAAATTTCGA
144251 AATTTTTTTTTAAAAAATTT-GA
1 AATTTTTTTTTAAAAAATTTCGA
144273 AA
1 AA
144275 AATTCTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTTTTTTTTAAAAAATTTCGA
Found at i:144721 original size:21 final size:21
Alignment explanation
Indices: 144639--144722 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
144629 CAGAACCCCA
*
144639 GGGGGGTATCGATTCCC-C-T
1 GGGGGGGATCGATTCCCTCAT
* *
144658 GTGGGGGGAATCGGTTCCCCTTCAA
1 G-GGGGGG-ATCGATT-CCC-TCAT
* * *
144683 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGGATCGATTCCCTCAT
144704 GGGGGGGATCGATTCCCTC
1 GGGGGGGATCGATTCCCTC
144723 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 5 0.10
21 25 0.50
22 6 0.12
23 7 0.14
24 6 0.12
ACGTcount: A:0.14, C:0.25, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCTCAT
Found at i:148564 original size:22 final size:21
Alignment explanation
Indices: 148522--148561 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
148512 GAGTTTGTTT
*
148522 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
148543 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
148562 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:150808 original size:30 final size:30
Alignment explanation
Indices: 150774--150834 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
150764 AAATCGTTTG
150774 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
150804 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
150834 G
1 G
150835 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:151554 original size:14 final size:14
Alignment explanation
Indices: 151535--151561 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
151525 TCCCGTGGCA
151535 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
151549 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
151562 TTTCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:151828 original size:24 final size:24
Alignment explanation
Indices: 151777--151828 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
151767 ATCTGAGTAT
** *
151777 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
151801 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
151825 TGAC
1 TGAC
151829 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:152683 original size:20 final size:20
Alignment explanation
Indices: 152667--152716 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
152657 CAGAATCTCG
*
152667 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACATAATCGCA
*
152687 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATAATCGCA
152707 TTGCGATTTA
1 TTGCGATTTA
152717 GGAAAATCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACATAATCGCA
Found at i:153532 original size:59 final size:60
Alignment explanation
Indices: 153420--153533 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 60
153410 TCAGATTATA
* *
153420 ATTTTGTAACTTTTAATAGTTAGGAGACTCAACAAAATAATATCCTATAATTGGATGATC
1 ATTTTGTAACTTTTAAGAGTTAGGAGACTCAACAAAACAATATCCTATAATTGGATGATC
* * *
153480 ATTTTGTAACTTTTGAGAGTTAGG-GACTCAACAAAACAATATTCTATCATTGGA
1 ATTTTGTAACTTTTAAGAGTTAGGAGACTCAACAAAACAATATCCTATAATTGGA
153534 GGGCTATTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 27 0.55
60 22 0.45
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (60 bp):
ATTTTGTAACTTTTAAGAGTTAGGAGACTCAACAAAACAATATCCTATAATTGGATGATC
Found at i:167575 original size:74 final size:74
Alignment explanation
Indices: 167454--167605 Score: 304
Period size: 74 Copynumber: 2.1 Consensus size: 74
167444 ACGGTGTGGC
167454 ATATCAAAACAGAAATCACATGCCGAAAAAGCTCGGAAAAAAATGAAGAAAGCATGTTGCACACA
1 ATATCAAAACAGAAATCACATGCCGAAAAAGCTCGGAAAAAAATGAAGAAAGCATGTTGCACACA
167519 CACACATAT
66 CACACATAT
167528 ATATCAAAACAGAAATCACATGCCGAAAAAGCTCGGAAAAAAATGAAGAAAGCATGTTGCACACA
1 ATATCAAAACAGAAATCACATGCCGAAAAAGCTCGGAAAAAAATGAAGAAAGCATGTTGCACACA
167593 CACACATAT
66 CACACATAT
167602 ATAT
1 ATAT
167606 TTGACTAGCA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (74 bp):
ATATCAAAACAGAAATCACATGCCGAAAAAGCTCGGAAAAAAATGAAGAAAGCATGTTGCACACA
CACACATAT
Found at i:168598 original size:2 final size:2
Alignment explanation
Indices: 168591--168620 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
168581 TACAATGAAC
168591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
168621 CGAGTGTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:169248 original size:22 final size:23
Alignment explanation
Indices: 169202--169246 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
169192 ATTTTGTATT
*
169202 TTAAATTTTAAATTTTAATAAAA
1 TTAAATTTTAAAATTTAATAAAA
* *
169225 TTAATTTTTAAAATTTATTAAA
1 TTAAATTTTAAAATTTAATAAA
169247 TTTTATAACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAATTTTAAAATTTAATAAAA
Found at i:171690 original size:12 final size:12
Alignment explanation
Indices: 171673--171705 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
171663 TATAATTAAA
171673 ATAATATATTTT
1 ATAATATATTTT
171685 ATAATATA-TTT
1 ATAATATATTTT
171696 ATAAT-TATTT
1 ATAATATATTT
171706 ATTATATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.10
11 10 0.50
12 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATAATATATTTT
Found at i:171704 original size:10 final size:11
Alignment explanation
Indices: 171673--171712 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
171663 TATAATTAAA
171673 ATAATATATTTT
1 ATAATATA-TTT
171685 ATAATATATTT
1 ATAATATATTT
171696 ATAAT-TATTT
1 ATAATATATTT
*
171706 ATTATAT
1 ATAATAT
171713 GTAAATGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.35
11 9 0.35
12 8 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATAATATATTT
Found at i:171708 original size:26 final size:25
Alignment explanation
Indices: 171649--171708 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
171639 AGTCTGAATA
171649 TATTTATATTTTAATATAATTAAAAT
1 TATTTAT-TTTTAATATAATTAAAAT
* * * *
171675 AATATATTTTATAATATATTTATAAT
1 TATTTATTTT-TAATATAATTAAAAT
171701 TATTTATT
1 TATTTATT
171709 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTTATTTTTAATATAATTAAAAT
Found at i:172252 original size:20 final size:21
Alignment explanation
Indices: 172207--172276 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
172197 AGAGCGCTGT
**
172207 CTAAAATGTT-ATTTTTCTAC
1 CTAAAATGTTAATTTAACTAC
*
172227 CGAAAATGTTAATTTAACTA-
1 CTAAAATGTTAATTTAACTAC
*
172247 CTAAAAATGTTAATTTAGCTAC
1 CT-AAAATGTTAATTTAACTAC
172269 CTAAAATG
1 CTAAAATG
172277 AATATTTCCG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.24
21 30 0.71
22 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (21 bp):
CTAAAATGTTAATTTAACTAC
Found at i:174301 original size:147 final size:147
Alignment explanation
Indices: 174056--174393 Score: 547
Period size: 147 Copynumber: 2.3 Consensus size: 147
174046 TTTTATATCA
* * *
174056 TTTTAGGATCGTTTGATTGAAATGAATCAAAAGTTGAGATTAACTCTTTGTTTTTTTCTCAGTGA
1 TTTTAGGATC-TTTGATTGAAAAGAATCAAAAGCTGAGATTAACTCATTGTTTTTTTCTCAGTGA
* *
174121 ATATCTTCTTATTTTCCGCTGTTAATCTTAGCATTTGATTTCTCTTAATCCAACGATTCTAAAAA
65 AGATCTTCTCATTTTCCGCTGTTAATCTTAGCATTTGATTTCTCTTAATCCAACGATTCTAAAAA
174186 GATGTAAGTTTTACATTC
130 GATGTAAGTTTTACATTC
174204 TTTTAGGATCTTTTGATTGAAAAGAATCAAAAGCTGAGATTAACTCATTG-TTTTTTCTCAGTGA
1 TTTTAGGATC-TTTGATTGAAAAGAATCAAAAGCTGAGATTAACTCATTGTTTTTTTCTCAGTGA
174268 AGATCTTCTCATTTTCCGCTGTTAATCTTAGCATTTGATTTCTCTTAATCCAACGATTCTAAAAA
65 AGATCTTCTCATTTTCCGCTGTTAATCTTAGCATTTGATTTCTCTTAATCCAACGATTCTAAAAA
174333 GATGTAAGTTTTACATTC
130 GATGTAAGTTTTACATTC
* *
174351 TTTTAGGATCGTTGAATTGAAGAA-AAT-AAAATGCTAAGATTAA
1 TTTTAGGATCTTTG-ATTGAA-AAGAATCAAAA-GCTGAGATTAA
174394 GATCCACATT
Statistics
Matches: 179, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
146 7 0.04
147 124 0.69
148 48 0.27
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (147 bp):
TTTTAGGATCTTTGATTGAAAAGAATCAAAAGCTGAGATTAACTCATTGTTTTTTTCTCAGTGAA
GATCTTCTCATTTTCCGCTGTTAATCTTAGCATTTGATTTCTCTTAATCCAACGATTCTAAAAAG
ATGTAAGTTTTACATTC
Found at i:175441 original size:14 final size:14
Alignment explanation
Indices: 175422--175454 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
175412 GTTATTTTAG
175422 ATTTAAATCTTAAT
1 ATTTAAATCTTAAT
175436 ATTTAAATCTTAAT
1 ATTTAAATCTTAAT
175450 ATTTA
1 ATTTA
175455 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAAATCTTAAT
Found at i:176219 original size:16 final size:16
Alignment explanation
Indices: 176198--176232 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
176188 CACTCGGAGA
176198 AACCATGGTTGGGGTT
1 AACCATGGTTGGGGTT
176214 AACCATGGTTGGGGTT
1 AACCATGGTTGGGGTT
176230 AAC
1 AAC
176233 GATGAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.34, T:0.29
Consensus pattern (16 bp):
AACCATGGTTGGGGTT
Found at i:178174 original size:2 final size:2
Alignment explanation
Indices: 178167--178200 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
178157 TCCTATAAGG
178167 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
178201 TCCCTCCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:188390 original size:2 final size:2
Alignment explanation
Indices: 188383--188425 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
188373 TTAGTTTATT
188383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
188425 T
1 T
188426 TGTAAATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:193500 original size:18 final size:18
Alignment explanation
Indices: 193477--193512 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
193467 TAACATAAAC
193477 TAAATCTAGGTACAATAG
1 TAAATCTAGGTACAATAG
193495 TAAATCTAGGTACAATAG
1 TAAATCTAGGTACAATAG
193513 ATGAACTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
TAAATCTAGGTACAATAG
Found at i:194495 original size:4 final size:4
Alignment explanation
Indices: 194486--194512 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
194476 ATTGTGACTC
194486 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
194513 TAAGGCATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:195539 original size:21 final size:21
Alignment explanation
Indices: 195513--195552 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
195503 ATTATGACGG
195513 TGTACTATAGAAAAACTAAGA
1 TGTACTATAGAAAAACTAAGA
195534 TGTACTATAGAAAAACTAA
1 TGTACTATAGAAAAACTAA
195553 CTCATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (21 bp):
TGTACTATAGAAAAACTAAGA
Found at i:195809 original size:27 final size:27
Alignment explanation
Indices: 195771--195845 Score: 141
Period size: 27 Copynumber: 2.8 Consensus size: 27
195761 AGCTCCAGCT
195771 GGTGGAGGTGGAGGGCCAGGAGCTCCA
1 GGTGGAGGTGGAGGGCCAGGAGCTCCA
195798 GGTGGAGGTGGAGGGCCAGGAGCTCCA
1 GGTGGAGGTGGAGGGCCAGGAGCTCCA
*
195825 GGTGGAGGTGGAGGACCAGGA
1 GGTGGAGGTGGAGGGCCAGGA
195846 AATCGACCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.20, C:0.16, G:0.53, T:0.11
Consensus pattern (27 bp):
GGTGGAGGTGGAGGGCCAGGAGCTCCA
Found at i:195871 original size:15 final size:15
Alignment explanation
Indices: 195853--195915 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 15
195843 GGAAATCGAC
195853 CTCCAGGAGGTGGTG
1 CTCCAGGAGGTGGTG
* ** *
195868 CTCCAGGAGCTCCTC
1 CTCCAGGAGGTGGTG
*
195883 CACCAGGAGGTGGTG
1 CTCCAGGAGGTGGTG
*
195898 GT---GGAGGTGGTG
1 CTCCAGGAGGTGGTG
195910 CTCCAG
1 CTCCAG
195916 ATGAGGGAGG
Statistics
Matches: 33, Mismatches: 12, Indels: 6
0.65 0.24 0.12
Matches are distributed among these distances:
12 11 0.33
15 22 0.67
ACGTcount: A:0.14, C:0.25, G:0.41, T:0.19
Consensus pattern (15 bp):
CTCCAGGAGGTGGTG
Found at i:195952 original size:24 final size:21
Alignment explanation
Indices: 195900--195951 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
195890 AGGTGGTGGT
195900 GGAGGTGGTGCTCCAGATGAG
1 GGAGGTGGTGCTCCAGATGAG
*
195921 GGAGGTGGTGCTCCAGGTGAG
1 GGAGGTGGTGCTCCAGATGAG
*
195942 GGAGGCGGTG
1 GGAGGTGGTG
195952 GAGATGGCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.13, G:0.54, T:0.17
Consensus pattern (21 bp):
GGAGGTGGTGCTCCAGATGAG
Found at i:196120 original size:36 final size:36
Alignment explanation
Indices: 195975--196108 Score: 232
Period size: 36 Copynumber: 3.7 Consensus size: 36
195965 ATGCAGTGGA
195975 GGAGGAGCATTGGACGTTGGAGGTGGAGGAGGGGGT
1 GGAGGAGCATTGGACGTTGGAGGTGGAGGAGGGGGT
*
196011 GTAGGAGCATTGGACGTTGGAGGTGGAGGAGGGGGT
1 GGAGGAGCATTGGACGTTGGAGGTGGAGGAGGGGGT
* *
196047 GGAGCAGCATCGGACGTTGGAGGTGGAGGAGGGGGT
1 GGAGGAGCATTGGACGTTGGAGGTGGAGGAGGGGGT
*
196083 GGAGGAGCATTGGACGTTAGAGGTGG
1 GGAGGAGCATTGGACGTTGGAGGTGG
196109 TGCTGGAGGT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 91 1.00
ACGTcount: A:0.20, C:0.07, G:0.55, T:0.17
Consensus pattern (36 bp):
GGAGGAGCATTGGACGTTGGAGGTGGAGGAGGGGGT
Found at i:196880 original size:6 final size:6
Alignment explanation
Indices: 196870--196912 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
196860 AATTTGGGTA
* * * *
196870 GAGGTG TAGGTG GAGGTC GAGGTG GAGGCG GAGGCG GAGGTG G
1 GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG G
196913 CGGCGAGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.07, G:0.63, T:0.14
Consensus pattern (6 bp):
GAGGTG
Found at i:196909 original size:18 final size:18
Alignment explanation
Indices: 196870--196917 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
196860 AATTTGGGTA
* *
196870 GAGGTGTAGGTGGAGGTC
1 GAGGTGGAGGCGGAGGTC
196888 GAGGTGGAGGCGGAGG-C
1 GAGGTGGAGGCGGAGGTC
*
196905 GGAGGTGGCGGCG
1 -GAGGTGGAGGCG
196918 AGGGTGAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.15, C:0.10, G:0.62, T:0.12
Consensus pattern (18 bp):
GAGGTGGAGGCGGAGGTC
Found at i:197004 original size:42 final size:42
Alignment explanation
Indices: 196890--197105 Score: 314
Period size: 42 Copynumber: 5.2 Consensus size: 42
196880 TGGAGGTCGA
* *
196890 GGTGGAGGCGGAGGCGGAGGTGGCGGCGAGGGTGAGGATGAT
1 GGTGGAGGTGGAGGAGGAGGTGGCGGCGAGGGTGAGGATGAT
196932 GGTGGAGGTGGA--A-GAGGTGGCGGCGAGGGTGAGGATGAT
1 GGTGGAGGTGGAGGAGGAGGTGGCGGCGAGGGTGAGGATGAT
196971 GGTGGAGGTGGAGGAGGAGGTGGCGGCGAGGGTGAGGATGAT
1 GGTGGAGGTGGAGGAGGAGGTGGCGGCGAGGGTGAGGATGAT
* * *
197013 GGTGGAGGTGCAGGAGGAGGTGGCGGCGAGGAG-GAGGCTGTT
1 GGTGGAGGTGGAGGAGGAGGTGGCGGCGAGG-GTGAGGATGAT
* * *
197055 GGTGAAGGTGGAGGAGGAGGTGGCAGCAAGGGTGAGGATGAT
1 GGTGGAGGTGGAGGAGGAGGTGGCGGCGAGGGTGAGGATGAT
*
197097 GGTGAAGGT
1 GGTGGAGGT
197106 AGTGTTCTTG
Statistics
Matches: 158, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
39 38 0.24
41 2 0.01
42 117 0.74
43 1 0.01
ACGTcount: A:0.20, C:0.06, G:0.59, T:0.14
Consensus pattern (42 bp):
GGTGGAGGTGGAGGAGGAGGTGGCGGCGAGGGTGAGGATGAT
Found at i:202299 original size:31 final size:31
Alignment explanation
Indices: 202258--202319 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
202248 AAGTGTTCTA
*
202258 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGACCTGTGGCGAGAGGATGAAGCTTTGC
*
202289 TACGACCTGTGGTGAGAGGATGAAGCTTTGC
1 TACGACCTGTGGCGAGAGGATGAAGCTTTGC
202320 ATGCGCCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.24
Consensus pattern (31 bp):
TACGACCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:202354 original size:22 final size:22
Alignment explanation
Indices: 202326--202368 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
202316 TTGCATGCGC
202326 CATGCACGTCGGAAGAGGTCGT
1 CATGCACGTCGGAAGAGGTCGT
202348 CATGCACGTCGGAAGAGGTCG
1 CATGCACGTCGGAAGAGGTCG
202369 CCTGCATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.37, T:0.16
Consensus pattern (22 bp):
CATGCACGTCGGAAGAGGTCGT
Found at i:202464 original size:29 final size:29
Alignment explanation
Indices: 202413--202500 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
202403 AGGGTACAGG
**
202413 ACAAGGTCGCCAAGCGTGCATGGCGACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
* * * *
202442 ACCATGTCGCCTGGCGTGTATGGCGACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
* *
202471 ACAAGGTCGCCCGGAGGGCATGGCGACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
202500 A
1 A
202501 TGCTGGGAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.20, C:0.31, G:0.33, T:0.16
Consensus pattern (29 bp):
ACAAGGTCGCCCGGCGTGCATGGCGACCT
Found at i:203491 original size:42 final size:42
Alignment explanation
Indices: 203444--203563 Score: 204
Period size: 42 Copynumber: 2.9 Consensus size: 42
203434 TTTTCCGGAA
203444 TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
* *
203486 TTCTCGTGCTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
1 TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
* *
203528 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGGAA
1 TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
203564 TGTAATTCAT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.46
Consensus pattern (42 bp):
TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
Found at i:203851 original size:25 final size:25
Alignment explanation
Indices: 203817--203885 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
203807 TAATCAATTA
* *
203817 TATTATAATAAATA-AGATATTTTTT
1 TATTTTAATAAATATA-ATAATTTTT
203842 TATTTTAAT-AATATAATAATTTTT
1 TATTTTAATAAATATAATAATTTTT
203866 TATATTTAAT-AAT-TAATAAT
1 TAT-TTTAATAAATATAATAAT
203886 ATTATTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 22 0.55
25 18 0.45
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
TATTTTAATAAATATAATAATTTTT
Found at i:203864 original size:24 final size:25
Alignment explanation
Indices: 203814--203908 Score: 97
Period size: 25 Copynumber: 3.6 Consensus size: 25
203804 AAATAATCAA
*
203814 TTATATTATAATAA-ATAAGATATTTT
1 TTATATT-TAATAATATAATA-ATTTT
203840 TT-TATTTTAATAATATAATAATTTT
1 TTATA-TTTAATAATATAATAATTTT
203865 TTATATTTAATAAT-TAATAATATTAT
1 TTATATTTAATAATATAATAAT-TT-T
203891 TATATATTTAAATAATAT
1 T-TATATTT-AATAATAT
203909 TTTAATAAAG
Statistics
Matches: 60, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
24 7 0.12
25 26 0.43
26 13 0.22
27 7 0.12
28 6 0.10
29 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
TTATATTTAATAATATAATAATTTT
Found at i:203937 original size:23 final size:23
Alignment explanation
Indices: 203911--203955 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
203901 AATAATATTT
203911 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
203934 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
203956 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:204278 original size:14 final size:14
Alignment explanation
Indices: 204259--204292 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
204249 AAATGTAATT
204259 CATTTTACGAAAAA
1 CATTTTACGAAAAA
* *
204273 CATTTTCCGGAAAA
1 CATTTTACGAAAAA
204287 CATTTT
1 CATTTT
204293 TCAGAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (14 bp):
CATTTTACGAAAAA
Found at i:204343 original size:15 final size:15
Alignment explanation
Indices: 204301--204343 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
204291 TTTCAGAAAT
*
204301 GTAATTCATTTTCCA
1 GTAATTCATTTTTCA
**
204316 G-AATTCAAATTTCA
1 GTAATTCATTTTTCA
204330 GTAATTCATTTTTC
1 GTAATTCATTTTTC
204344 GAAAAACCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (15 bp):
GTAATTCATTTTTCA
Found at i:206908 original size:2 final size:2
Alignment explanation
Indices: 206901--206953 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
206891 TTAATAAGAT
206901 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
206943 TA TA TA TA TA T
1 TA TA TA TA TA T
206954 TACCCATAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:207250 original size:59 final size:60
Alignment explanation
Indices: 207147--207299 Score: 200
Period size: 59 Copynumber: 2.6 Consensus size: 60
207137 TATTAAGCCA
* * ** *
207147 CTCGACTATTAAAAGTTACAAAATGATCATCTAAATATAGAGTGTTGCCTTCTTGAGTCC
1 CTCGACTATTAAAAGTTACAAAATGGTCACCCGAATATAAAGTGTTGCCTTCTTGAGTCC
* * * *
207207 CTCGACTATT-AAAGTTACACAATGGTCACCCGACTATAAAGTGTTGCTTTGTTGAGTCC
1 CTCGACTATTAAAAGTTACAAAATGGTCACCCGAATATAAAGTGTTGCCTTCTTGAGTCC
* *
207266 CTCAACCATTAAAAGTTACAAAATGGTCACCCGA
1 CTCGACTATTAAAAGTTACAAAATGGTCACCCGA
207300 TTATTCTCTA
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 48 0.60
60 32 0.40
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (60 bp):
CTCGACTATTAAAAGTTACAAAATGGTCACCCGAATATAAAGTGTTGCCTTCTTGAGTCC
Found at i:207825 original size:17 final size:18
Alignment explanation
Indices: 207784--207825 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
207774 TCTCAACAAT
*
207784 ATAATAATTTTTTACATG
1 ATAATAATTCTTTACATG
207802 ATAATAATTCTTTA-ATG
1 ATAATAATTCTTTACATG
*
207819 ATGATAA
1 ATAATAA
207826 ATGTAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (18 bp):
ATAATAATTCTTTACATG
Done.