Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009331.1 Hibiscus syriacus cultivar Beakdansim tig00113098_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: 375911
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 2
Found at i:4960 original size:12 final size:12
Alignment explanation
Indices: 4937--5002 Score: 66
Period size: 12 Copynumber: 5.6 Consensus size: 12
4927 AGATATCAGA
4937 AATT-AGAACAG
1 AATTCAGAACAG
*
4948 AATTCAGATCAG
1 AATTCAGAACAG
4960 -ATATCAGAACAG
1 AAT-TCAGAACAG
*
4972 AATCCAGATA-AG
1 AATTCAGA-ACAG
*
4984 AAATCAGAACAG
1 AATTCAGAACAG
4996 AATTCAG
1 AATTCAG
5003 GTAATGGATC
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
11 7 0.16
12 34 0.77
13 3 0.07
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (12 bp):
AATTCAGAACAG
Found at i:4968 original size:24 final size:24
Alignment explanation
Indices: 4931--5039 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
4921 AAACGGAGAT
*
4931 ATCAGAAATTAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
4955 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
4979 ATAAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
5003 GTAATG-GATCATAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
5026 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
5040 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 1 0.01
24 67 0.97
25 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:9680 original size:24 final size:24
Alignment explanation
Indices: 9653--9724 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
9643 AAACGGAGAT
9653 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
9677 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
9701 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
9725 GTAATGTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:9682 original size:12 final size:12
Alignment explanation
Indices: 9655--9724 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
9645 ACGGAGATAT
* *
9655 CAGAAATCAAAA
1 CAGAATTCAGAA
*
9667 CAGAATTCAGAT
1 CAGAATTCAGAA
*
9679 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
9691 CAGAATCCAGAT
1 CAGAATTCAGAA
*
9703 CAGAAATCAGAA
1 CAGAATTCAGAA
9715 CAGAATTCAG
1 CAGAATTCAG
9725 GTAATGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:9756 original size:48 final size:48
Alignment explanation
Indices: 9656--9761 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 48
9646 CGGAGATATC
* * * *
9656 AGAAATCAAAACAGAATTCAGATCAGATATCATAACAGAATCCAGATC
1 AGAAATCAGAACAGAATTCAGATAAGATATCATAACAGAATCAAGATA
* *
9704 AGAAATCAGAACAGAATTCAGGTAATG-TATCATAACATAATTCAAG-TA
1 AGAAATCAGAACAGAATTCAGATAA-GATATCATAACAGAA-TCAAGATA
9752 AGAAATCAGA
1 AGAAATCAGA
9762 TAAAATATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 45 0.90
49 5 0.10
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (48 bp):
AGAAATCAGAACAGAATTCAGATAAGATATCATAACAGAATCAAGATA
Found at i:9759 original size:24 final size:25
Alignment explanation
Indices: 9656--9759 Score: 83
Period size: 24 Copynumber: 4.3 Consensus size: 25
9646 CGGAGATATC
* *
9656 AGAAATCAAAACAGAATTC-AGATC
1 AGAAATCATAACAGAATTCAAGATA
* * *
9680 AGATATCATAACAGAA-TCCAGATC
1 AGAAATCATAACAGAATTCAAGATA
* *
9704 AGAAATCAGAACAGAATTC-AGGTA
1 AGAAATCATAACAGAATTCAAGATA
* *
9728 ATG-TATCATAACATAATTCAAG-TA
1 A-GAAATCATAACAGAATTCAAGATA
9752 AGAAATCA
1 AGAAATCA
9760 GATAAAATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
23 3 0.05
24 57 0.88
25 5 0.08
ACGTcount: A:0.50, C:0.15, G:0.13, T:0.21
Consensus pattern (25 bp):
AGAAATCATAACAGAATTCAAGATA
Found at i:35674 original size:2 final size:2
Alignment explanation
Indices: 35667--35692 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35657 AAAACCAACA
35667 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
35693 CATGGATTTT
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:37411 original size:2 final size:2
Alignment explanation
Indices: 37404--37444 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
37394 TATTAGTTTA
* **
37404 AT AT AT AT GT AT AT AT GC 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 AT A
37445 CACACGTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:46279 original size:82 final size:83
Alignment explanation
Indices: 46140--46347 Score: 287
Period size: 82 Copynumber: 2.5 Consensus size: 83
46130 AGATGCTCCA
* * * *
46140 TTAGGTTGGCTTCCTTTGCTATGTGCTTAGGGTAAGGCCTA-CTGACTTACGAACTTAAGGATAC
1 TTAGGTTGGCTCCCTTTGCTGTGTGCTTAGGGTAAGCCCTATCTGACTTAAGAACTTAAGGATAC
46204 AGGCCCCAAAGCCTATCC
66 AGGCCCCAAAGCCTATCC
* *
46222 TTAGGTTAGCTCCCTTTGCTGTGTGCTTAGGGTAAGCCCTATC-GACTTATAG-GCTTAAGGATA
1 TTAGGTTGGCTCCCTTTGCTGTGTGCTTAGGGTAAGCCCTATCTGACTTA-AGAACTTAAGGATA
*
46285 CAGGTCCCAAAGCCTATCC
65 CAGGCCCCAAAGCCTATCC
* *
46304 TTAGGTTGGCTTCCTCTTTGTTGTGTGCTTAAGGTAAGCCCTAT
1 TTAGGTTGGC-TCC-CTTTGCTGTGTGCTTAGGGTAAGCCCTAT
46348 TGGACGCAGT
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
82 80 0.71
83 5 0.04
84 27 0.24
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.33
Consensus pattern (83 bp):
TTAGGTTGGCTCCCTTTGCTGTGTGCTTAGGGTAAGCCCTATCTGACTTAAGAACTTAAGGATAC
AGGCCCCAAAGCCTATCC
Found at i:48440 original size:48 final size:48
Alignment explanation
Indices: 48364--48455 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
48354 ATCTCAAGGT
** *
48364 GAGAAGGGTTATTTGTCAACCAAAACCTTCGAGTTTGATTACATAGGC
1 GAGAAGGGTTATCCGTCAACCAAAACCTTCGAGTTCGATTACATAGGC
48412 GAGAAGGGTTATCCGTCAA-CAAAGACCTTCGAGTTCGATTACAT
1 GAGAAGGGTTATCCGTCAACCAAA-ACCTTCGAGTTCGATTACAT
48456 TCAGCTGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 4 0.10
48 36 0.90
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (48 bp):
GAGAAGGGTTATCCGTCAACCAAAACCTTCGAGTTCGATTACATAGGC
Found at i:48589 original size:85 final size:85
Alignment explanation
Indices: 48408--49431 Score: 1371
Period size: 85 Copynumber: 12.1 Consensus size: 85
48398 TTGATTACAT
* *
48408 AGGCGAGAAGGGTTATCCGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTGAAAGGCATAT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
*
48473 C------ACAGCATATCTCA
66 CAAATTTACAGCATAGCTCA
* * *
48487 AGGCAAGAAGGGTTATCTGTCAACCAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGCATAT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
* *
48552 CAAATTTACAACATATCTCA
66 CAAATTTACAGCATAGCTCA
* *
48572 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCAAATTCGATTACATTCAGCTCAAAGGCATAT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
*
48637 CAAATTTACAGCATAACTCA
66 CAAATTTACAGCATAGCTCA
* * * * *
48657 AGGCTAGAAGGGTTATCTATCAACCAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGACATAT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
48722 CAAATTTACAGCATAGCTCA
66 CAAATTTACAGCATAGCTCA
* * *
48742 AGGCGAGAAGGGATATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATTT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
* *
48807 CAAATTTACATCATAACTCA
66 CAAATTTACAGCATAGCTCA
* * * * *
48827 AGGCTAGAAGGGTTATCTGTCAACCAAGACCTTCGATTTTGATTACATTTAGCTCAAAGGCATAT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
* *
48892 CAAATTTACAGTATAGCTAA
66 CAAATTTACAGCATAGCTCA
* * * *
48912 AGACAATAAGGGTTATCTGTCAACAAAGACCTTCTAGTTCGATTACATTCAGCTCAAAGGCATAT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
* * *
48977 CAAATTTATAACATAACTCA
66 CAAATTTACAGCATAGCTCA
* * *
48997 AGGCGAGAAGGGTTATCTGTCAACCAAGACCTTTGAATTCGATTACATTCAGCTCAAAGGCATAT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
49062 CAAATTTACAGCATAGCTCA
66 CAAATTTACAGCATAGCTCA
* * * ** * *
49082 AGGTGAGAAGGGCTATTTGTCATTAAAGACCTTCGAGTTCGATTACGTTCAGCTCAAACGCATAT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
* * *
49147 AAAATTTATAGCATAGATCA
66 CAAATTTACAGCATAGCTCA
* * * * *
49167 AGGCGAGAAGGGCTATTTGTCAACAAAGACCTTCAAGTTTGATTACATTCAACTCAAAGGCATAT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
*
49232 CAAATTTACAGTATAGCTCA
66 CAAATTTACAGCATAGCTCA
* * * * * *
49252 AGGCGAGAAGGGCTATCTGTCAACAAATACCTTTGAGTTCAATTACATTCAGCTCAAAGGTATAC
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
* * * *
49317 CAGATTTGCAGTATAACTCA
66 CAAATTTACAGCATAGCTCA
* * * *
49337 AGGTGAGAAGGGTTATCTGTCAAC-AA-ACCCTCGAGTTCGATTACATTCAGCTCAAGGGTATAT
1 AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
*
49400 CAAATTTACATCATAGCTCA
66 CAAATTTACAGCATAGCTCA
49420 AGGCGAGAAGGG
1 AGGCGAGAAGGG
49432 CTATTTGTAA
Statistics
Matches: 827, Mismatches: 112, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
79 61 0.07
83 58 0.07
84 2 0.00
85 706 0.85
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (85 bp):
AGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATAT
CAAATTTACAGCATAGCTCA
Found at i:51370 original size:12 final size:12
Alignment explanation
Indices: 51353--51377 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51343 ATCGAATCTC
51353 TAAATTTTAATT
1 TAAATTTTAATT
51365 TAAATTTTAATT
1 TAAATTTTAATT
51377 T
1 T
51378 TCACAATTAT
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:0.00, T:0.60
Consensus pattern (12 bp):
TAAATTTTAATT
Found at i:59424 original size:32 final size:32
Alignment explanation
Indices: 59388--59487 Score: 121
Period size: 32 Copynumber: 3.1 Consensus size: 32
59378 GTGCCAACCT
* *
59388 AAGGGAATATCTTGGGGCCCAAGAGCCTACCC
1 AAGGGAATACCTTGGGGCCTAAGAGCCTACCC
* *
59420 AAGGGAGTACCTTAGGGCCTAAGAGCCTA-CC
1 AAGGGAATACCTTGGGGCCTAAGAGCCTACCC
* * *
59451 AAAGGAAGTACCTTGGGTCCTTAGAGCCTACCC
1 AAGGGAA-TACCTTGGGGCCTAAGAGCCTACCC
59484 AAGG
1 AAGG
59488 AAATGCATTA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
31 7 0.12
32 44 0.79
33 5 0.09
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.17
Consensus pattern (32 bp):
AAGGGAATACCTTGGGGCCTAAGAGCCTACCC
Found at i:59488 original size:32 final size:32
Alignment explanation
Indices: 59402--59489 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
59392 GAATATCTTG
* *
59402 GGGCCCAAGAGCCTACCCAAGGGAGTACCTTA
1 GGGCCTAAGAGCCTACCCAAGGAAGTACCTTA
*
59434 GGGCCTAAGAGCCTACCAAAGGAAGTACCTT-
1 GGGCCTAAGAGCCTACCCAAGGAAGTACCTTA
*
59465 GGGTCCTTAGAGCCTACCCAAGGAA
1 GGG-CCTAAGAGCCTACCCAAGGAA
59490 ATGCATTAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
31 3 0.06
32 47 0.94
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (32 bp):
GGGCCTAAGAGCCTACCCAAGGAAGTACCTTA
Found at i:61654 original size:24 final size:24
Alignment explanation
Indices: 61622--61667 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
61612 TACCATATTG
61622 AATTTTCTT-TTAAACTTTCTTTTT
1 AATTTTCTTCTTAAAC-TTCTTTTT
*
61646 AATTTTCTTCTTAATCTTCTTT
1 AATTTTCTTCTTAAACTTCTTT
61668 GAAATCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (24 bp):
AATTTTCTTCTTAAACTTCTTTTT
Found at i:62394 original size:29 final size:28
Alignment explanation
Indices: 62329--62395 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 28
62319 TTGAAATACA
62329 TTATTCGAACAGTGCAAAAAAAAATTGAT
1 TTATTCGAACAGTGCAAAAAAAAA-TGAT
*
62358 TTAGTTCGAACAGTGCAGAAAAAACA-GAT
1 TTA-TTCGAACAGTGCA-AAAAAAAATGAT
62387 TTGATTCGA
1 TT-ATTCGA
62396 TTTGTGCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
29 13 0.38
30 14 0.41
31 7 0.21
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (28 bp):
TTATTCGAACAGTGCAAAAAAAAATGAT
Found at i:62521 original size:31 final size:32
Alignment explanation
Indices: 62477--62546 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
62467 ATAGTGCACT
*
62477 ATTCTAACAGTAAAAA-AACAGTACAATTTTG
1 ATTCGAACAGTAAAAACAACAGTACAATTTTG
*
62508 ATTCGAACGGTAAAAACAACAGTACAATTTTG
1 ATTCGAACAGTAAAAACAACAGTACAATTTTG
*
62540 GTTCGAA
1 ATTCGAA
62547 GAGTGAGTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 14 0.40
32 21 0.60
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.27
Consensus pattern (32 bp):
ATTCGAACAGTAAAAACAACAGTACAATTTTG
Found at i:64636 original size:16 final size:16
Alignment explanation
Indices: 64615--64645 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64605 AAAAAATCCT
*
64615 TTTTCTTTTATTTTCG
1 TTTTCTTTAATTTTCG
64631 TTTTCTTTAATTTTC
1 TTTTCTTTAATTTTC
64646 TTTCAAGTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTCTTTAATTTTCG
Found at i:65198 original size:12 final size:12
Alignment explanation
Indices: 65163--65208 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
65153 TACCATATTG
*
65163 AATTTTCTTTTA
1 AATTTTCTTTTT
*
65175 AACTTTCTTTTT
1 AATTTTCTTTTT
65187 AATTTTCTTTTT
1 AATTTTCTTTTT
*
65199 AATCTTCTTT
1 AATTTTCTTT
65209 GAAATCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (12 bp):
AATTTTCTTTTT
Found at i:68648 original size:2 final size:2
Alignment explanation
Indices: 68641--68673 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
68631 TTCTCATTGG
68641 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 A
68674 ATACTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69857 original size:18 final size:19
Alignment explanation
Indices: 69831--69869 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
69821 AACAATAATA
*
69831 AAAAATAAATATC-AAATT
1 AAAAATAAACATCAAAATT
*
69849 AAAATTAAACATCAAAATT
1 AAAAATAAACATCAAAATT
69868 AA
1 AA
69870 TATATCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATAAACATCAAAATT
Found at i:70077 original size:19 final size:19
Alignment explanation
Indices: 70039--70085 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
70029 TATTATTGTT
70039 AATTAAAATTAAAAAACAA
1 AATTAAAATTAAAAAACAA
* ** *
70058 ATTTAAAATTAATTATCAA
1 AATTAAAATTAAAAAACAA
70077 AATTAAAAT
1 AATTAAAAT
70086 AAAGTCAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTAAAATTAAAAAACAA
Found at i:72178 original size:29 final size:29
Alignment explanation
Indices: 72146--72205 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
72136 GTTTAACAAT
*
72146 TTAGAGAGTTAGGTTAAAGTGATTTAGGG
1 TTAGAGAGTTAGGTTAAAATGATTTAGGG
* ** * *
72175 TTAGGGTTTTATGTTAAAATGGTTTAGGG
1 TTAGAGAGTTAGGTTAAAATGATTTAGGG
72204 TT
1 TT
72206 TTTTTAGAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.32, T:0.42
Consensus pattern (29 bp):
TTAGAGAGTTAGGTTAAAATGATTTAGGG
Found at i:72400 original size:31 final size:30
Alignment explanation
Indices: 72359--72445 Score: 120
Period size: 31 Copynumber: 2.9 Consensus size: 30
72349 ACATCTTGTA
* *
72359 AAATAAAAGAAAATAAAATCACATTAATTG
1 AAATACAAGAAAATAAAATCACATAAATTG
72389 AAAGTACAAGAAAATAAAATCACATAAATTG
1 AAA-TACAAGAAAATAAAATCACATAAATTG
** *
72420 AAATATTAGAAAATAAAATTACATAA
1 AAATACAAGAAAATAAAATCACATAA
72446 GTAATGGTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.45
31 28 0.55
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (30 bp):
AAATACAAGAAAATAAAATCACATAAATTG
Found at i:73289 original size:32 final size:32
Alignment explanation
Indices: 73248--73318 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
73238 ATATATATAT
73248 AATAT-TA-ATAA-ATTTA-AT-TTAAATTAA
1 AATATATATATAATATTTATATATTAAATTAA
*
73275 AATATATATATAATATTTATATATTTAATTAA
1 AATATATATATAATATTTATATATTAAATTAA
73307 AATATATATATA
1 AATATATATATA
73319 CCTGGCCCGA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 5 0.13
28 2 0.05
29 4 0.11
30 5 0.13
31 2 0.05
32 20 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
AATATATATATAATATTTATATATTAAATTAA
Found at i:73318 original size:38 final size:38
Alignment explanation
Indices: 73231--73318 Score: 117
Period size: 38 Copynumber: 2.3 Consensus size: 38
73221 TATTAAAAAT
*
73231 AAATAT-TATATATATATAATATTAATAAATTTAATTT
1 AAATATATATATATATATAATATTAATAAATTTAATTA
* * *
73268 AAAT-TAAAATATATATATAATATTTATATATTTAATTA
1 AAATAT-ATATATATATATAATATTAATAAATTTAATTA
73306 AAATATATATATA
1 AAATATATATATA
73319 CCTGGCCCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
36 1 0.02
37 4 0.09
38 37 0.86
39 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (38 bp):
AAATATATATATATATATAATATTAATAAATTTAATTA
Found at i:73337 original size:12 final size:12
Alignment explanation
Indices: 73316--73346 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
73306 AAATATATAT
*
73316 ATACCTGGCCCG
1 ATACCCGGCCCG
73328 ATACCCGGCCCG
1 ATACCCGGCCCG
73340 ATACCCG
1 ATACCCG
73347 TTTAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (12 bp):
ATACCCGGCCCG
Found at i:76415 original size:274 final size:274
Alignment explanation
Indices: 75926--76467 Score: 1057
Period size: 274 Copynumber: 2.0 Consensus size: 274
75916 ATTTAATATA
75926 AAAATATATTTCATCATATACTCAAAAAATTATTTATAAACGGACTCAATATTAAAATTACCTTA
1 AAAATATATTTCATCATATACTCAAAAAATTATTTATAAACGGACTCAATATTAAAATTACCTTA
75991 ATAATAATGAGAAGACAAATGGCTCATTCACGACCAGACATAAAAAGGACATGCGATACCAAGCT
66 ATAATAATGAGAAGACAAATGGCTCATTCACGACCAGACATAAAAAGGACATGCGATACCAAGCT
*
76056 CATGATCGGAGAAGAAGAAGCAACCGCCAATAACAATTTTACTATAATTCGTTGCCCAACACATT
131 CATGATCGGAGAAGAAGAAACAACCGCCAATAACAATTTTACTATAATTCGTTGCCCAACACATT
76121 TTTCTAAACAGAAATGCCAAAACTGCAAAGCCCCAACTCAATCTGCTGACTACTTCAAAATTAGT
196 TTTCTAAACAGAAATGCCAAAACTGCAAAGCCCCAACTCAATCTGCTGACTACTTCAAAATTAGT
76186 GAGGTGACTACTTC
261 GAGGTGACTACTTC
76200 AAAATATATTTCATCATATACTCAAAAAATTATTTATAAACGGACTCAATATTAAAATTACCTTA
1 AAAATATATTTCATCATATACTCAAAAAATTATTTATAAACGGACTCAATATTAAAATTACCTTA
*
76265 ATAATAATGAGAAGACAAATGGCTCATTCACGACCAGACATAAAAAGGACATGTGATACCAAGCT
66 ATAATAATGAGAAGACAAATGGCTCATTCACGACCAGACATAAAAAGGACATGCGATACCAAGCT
*
76330 CATGATTGGAGAAGAAGAAACAACCGCCAATAACAATTTTACTATAATTCGTTGCCCAACACATT
131 CATGATCGGAGAAGAAGAAACAACCGCCAATAACAATTTTACTATAATTCGTTGCCCAACACATT
76395 TTTCTAAACAGAAATGCCAAAACTGCAAAGCCCCAACTCAATCTGCTGACTACTTCAAAATTAGT
196 TTTCTAAACAGAAATGCCAAAACTGCAAAGCCCCAACTCAATCTGCTGACTACTTCAAAATTAGT
76460 GAGGTGAC
261 GAGGTGAC
76468 GCAACCACAT
Statistics
Matches: 265, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
274 265 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (274 bp):
AAAATATATTTCATCATATACTCAAAAAATTATTTATAAACGGACTCAATATTAAAATTACCTTA
ATAATAATGAGAAGACAAATGGCTCATTCACGACCAGACATAAAAAGGACATGCGATACCAAGCT
CATGATCGGAGAAGAAGAAACAACCGCCAATAACAATTTTACTATAATTCGTTGCCCAACACATT
TTTCTAAACAGAAATGCCAAAACTGCAAAGCCCCAACTCAATCTGCTGACTACTTCAAAATTAGT
GAGGTGACTACTTC
Found at i:77055 original size:22 final size:23
Alignment explanation
Indices: 77002--77056 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
76992 TTAAAATTTT
77002 AAATAATACTAAAAAATTAAATTA
1 AAATAATACTAAAAAA-TAAATTA
* *
77026 ATAA-AATATTCAAAAA-AAATTA
1 A-AATAATACTAAAAAATAAATTA
77048 AAATAATAC
1 AAATAATAC
77057 AATTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
21 2 0.08
22 11 0.42
24 11 0.42
25 2 0.08
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATAATACTAAAAAATAAATTA
Found at i:87184 original size:25 final size:26
Alignment explanation
Indices: 87156--87205 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
87146 TGAAAAACTG
* *
87156 ACAATTCAAGG-TTGAAGAAAATGGA
1 ACAATCCAAGGTTTAAAGAAAATGGA
*
87181 ACAATCCAGGGTTTAAAGAAAATGG
1 ACAATCCAAGGTTTAAAGAAAATGG
87206 GCAAATGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.20
Consensus pattern (26 bp):
ACAATCCAAGGTTTAAAGAAAATGGA
Found at i:89911 original size:2 final size:2
Alignment explanation
Indices: 89904--89937 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
89894 TATTTAAAAG
89904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89938 GACTGATATA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90970 original size:3 final size:3
Alignment explanation
Indices: 90953--91036 Score: 136
Period size: 3 Copynumber: 28.0 Consensus size: 3
90943 TTTGGGCTTG
90953 TAA TAA -AA TTAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
90999 TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
91037 ATAAAAAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.05
3 68 0.88
4 5 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:91384 original size:117 final size:118
Alignment explanation
Indices: 91231--91801 Score: 312
Period size: 113 Copynumber: 5.0 Consensus size: 118
91221 GATGACAATT
* *
91231 TATCTCCTTCTGTGATGTAATCTAGCAAAAAGTTGAACAAATTCTCCTCTTTATGAACTTCTTCT
1 TATCTCCTTCTGTGATGTAATCTAGCAAAAAGTTGAACAAACTCTCCTCATTATGAACTTCTTCT
* * *
91296 TCTTC-AGATGAGTTCTTCTCATTATGAACTCCT-TCTGGAAATGCTGATGATA
66 TCTTCTAGATAAGCTCTTCTCATTATGAAC-CCTCTCTGGAAAAGCTGATGATA
* * * *
91348 TATCTCCTTCTGTGATAG-AGT-TATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT
1 TATCTCCTTCTGTGAT-GTAATCTA-GCAAAAAGTTGAACAAACTCTCCTCATTATGAACTTCTT
* *
91411 CTTCTTCTTTAGATAAGCTCTTCTTATTATGAACCTTCTCTGGAAAAGC---TG---
64 CTTCTTC--TAGATAAGCTCTTCTCATTATGAACCCTCTCTGGAAAAGCTGATGATA
* * * * * * * *
91462 -A--TCCATCGAGTGATG-GATTTGAGCAAAAAGTTGAACAAATTCTTCTTATTATGAATTTCTT
1 TATCTCCTTC-TGTGATGTAATCT-AGCAAAAAGTTGAACAAACTCTCCTCATTATGAACTTCTT
** * * *
91523 CTTCCTTCTTCAGACGAGTTCTTCTCATTATAAACTCTAC-CTGGAAAAGC---TG---
64 CTT-CTTC-T-AGATAAGCTCTTCTCATTATGAACCCT-CTCTGGAAAAGCTGATGATA
* * * * ** *
91575 -A--TCCATCGAGTGATG-GATTTGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTT
1 TATCTCCTTC-TGTGATGTAATCT-AGCAAAAAGTTGAACAAACTCTCCTCATTATGAACTTCTT
* **
91636 CTTCTTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGC---TG---
64 CTTC-TTC-T-AGATAAGCTCTTCTCATTATGAACCCTCTCTGGAAAAGCTGATGATA
* * * * * * *
91688 -A--TCCATCGAGTGATG-GATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT
1 TATCTCCTTC-TGTGATGTAATCT-AGCAAAAAGTTGAACAAACTCTCCTCATTATGAACTTCTT
* ** *
91749 CTTCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTTTGGAAAAGCTGAT
64 CTTCTTC-T-AGATAAGCTCTTCTCATTATGAACCCTCTCTGGAAAAGCTGAT
91802 CCATCGAGTG
Statistics
Matches: 400, Mismatches: 37, Indels: 36
0.85 0.08 0.08
Matches are distributed among these distances:
111 7 0.02
112 91 0.23
113 203 0.51
114 1 0.00
115 1 0.00
116 2 0.00
117 61 0.15
118 1 0.00
119 2 0.00
120 31 0.08
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (118 bp):
TATCTCCTTCTGTGATGTAATCTAGCAAAAAGTTGAACAAACTCTCCTCATTATGAACTTCTTCT
TCTTCTAGATAAGCTCTTCTCATTATGAACCCTCTCTGGAAAAGCTGATGATA
Found at i:91583 original size:113 final size:114
Alignment explanation
Indices: 91372--91898 Score: 859
Period size: 113 Copynumber: 4.7 Consensus size: 114
91362 ATAGAGTTAT
* * *
91372 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTTAGATAAGCTCTTCTT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
91436 ATTATGAAC-CTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTCTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
* ** * * **
91484 GCAAAAAGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
* *
91549 ATTATAAACTCTAC-CTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTCTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
* * *
91597 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
91662 ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTCTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
91710 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
*
91774 ATTATGAACT-TTCTTTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTCTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
*
91822 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
91887 ATTATGAACTCT
66 ATTATGAACTCT
91899 ACCTGGTAAT
Statistics
Matches: 385, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
112 149 0.39
113 232 0.60
114 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (114 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
ATTATGAACTCTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
Found at i:91795 original size:225 final size:225
Alignment explanation
Indices: 91372--91896 Score: 856
Period size: 225 Copynumber: 2.3 Consensus size: 225
91362 ATAGAGTTAT
* * *
91372 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGATAAGCTCTTCTTA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCA
* *
91437 TTATGAACCTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAAGTTGAACAAAC
* * *
91502 TCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATAAACTCTACCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACAAGTTCTTCTCATTATAAACTCTACCTGG
91567 AAAAGCTGATCCATCGAGTGATGGATTTGA
196 AAAAGCTGATCCATCGAGTGATGGATTTGA
* *
91597 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATAAGTTCTTCTC
* *
91662 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAG
65 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAAGTTGAACAAA
* * * *
91727 CTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTTT
130 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACAAGTTCTTCTCATTATAAACTCTAC-CT
91790 GGAAAAGCTGATCCATCGAGTGATGGATTTGA
194 GGAAAAGCTGATCCATCGAGTGATGGATTTGA
*
91822 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTC
91887 ATTATGAACT
65 ATTATGAACT
91897 CTACCTGGTA
Statistics
Matches: 278, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
224 2 0.01
225 173 0.62
226 103 0.37
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (225 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAAGTTGAACAAAC
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACAAGTTCTTCTCATTATAAACTCTACCTGG
AAAAGCTGATCCATCGAGTGATGGATTTGA
Found at i:92038 original size:76 final size:76
Alignment explanation
Indices: 91912--92066 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 76
91902 TGGTAATGCT
* *
91912 GATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTG
1 GATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
91977 TAGGACTTACA
66 CAGGACTTACA
*
91988 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
92053 CAGGACTTACA
66 CAGGACTTACA
92064 GAT
1 GAT
92067 ATGGGAAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (76 bp):
GATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
CAGGACTTACA
Found at i:92302 original size:37 final size:37
Alignment explanation
Indices: 92261--92550 Score: 199
Period size: 37 Copynumber: 7.9 Consensus size: 37
92251 GACAAATCTT
* * *
92261 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTA
1 TGTTTCAAGAAAAACAATCTCAAGCGAGATAAAGTTC
* ** ** *
92298 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAAGTTC
1 TGTTTCAAGAAAAACAATCTCAAGCGAGATAAAGTTC
* * ** ** * *
92335 TATTTCGAGTGAAACTGTCTCGAGCGAGACAAAGTTC
1 TGTTTCAAGAAAAACAATCTCAAGCGAGATAAAGTTC
* * * *
92372 TGTTTTAAGAAAAACAATATCAAGTGAGATAAA-TTGT
1 TGTTTCAAGAAAAACAATCTCAAGCGAGATAAAGTT-C
* ** ** * *
92409 TGTTTCGAGGGAAACTTTCTCAAGCGAGA-AAAATTT
1 TGTTTCAAGAAAAACAATCTCAAGCGAGATAAAGTTC
* *
92445 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTC
1 TGTTTCAAGAAAAACAATCTCAAGCGAGATAAAGTTC
* ** ** * *
92482 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAA-TTT
1 TGTTTCAAGAAAAACAATCTCAAGCGAGATAAAGTTC
* *
92518 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 TGTTTCAAGAAAAACAATCTCAAGCGAGATAAA
92551 TTTGACTTCA
Statistics
Matches: 193, Mismatches: 57, Indels: 7
0.75 0.22 0.03
Matches are distributed among these distances:
36 55 0.28
37 138 0.72
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGAAAAACAATCTCAAGCGAGATAAAGTTC
Found at i:92469 original size:73 final size:72
Alignment explanation
Indices: 92315--92552 Score: 341
Period size: 73 Copynumber: 3.2 Consensus size: 72
92305 AGTGAAACTG
* * * * * *
92315 TCTCAAGCGAGACAAAGTTCTATTTCGAGTGAAACTGTCTCGAGCGAGACAAAGTTCTGTTTTAA
1 TCTCAAGTGAGATAAA-TTCTGTTTCGAGTGAAACTGTCTCAAGCGAGA-AAAATTTTGTTTTAA
92380 GAAAAACAA
64 GAAAAACAA
* * * *
92389 TATCAAGTGAGATAAATTGTTGTTTCGAGGGAAACTTTCTCAAGCGAGAAAAATTTTGTTTTAAG
1 TCTCAAGTGAGATAAATT-CTGTTTCGAGTGAAACTGTCTCAAGCGAGAAAAATTTTGTTTTAAG
92454 AAAAACAA
65 AAAAACAA
*
92462 TCTCAAGTGAGATAAAGTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAG
1 TCTCAAGTGAGATAAA-TTCTGTTTCGAGTGAAACTGTCTCAAGCGAGAAAAATTTTGTTTTAAG
92527 AAAAACAA
65 AAAAACAA
92535 TCTCAAGTGAGATAAATT
1 TCTCAAGTGAGATAAATT
92553 TGACTTCAAA
Statistics
Matches: 147, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
72 2 0.01
73 105 0.71
74 40 0.27
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (72 bp):
TCTCAAGTGAGATAAATTCTGTTTCGAGTGAAACTGTCTCAAGCGAGAAAAATTTTGTTTTAAGA
AAAACAA
Found at i:92859 original size:22 final size:22
Alignment explanation
Indices: 92834--92910 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
92824 AATAAAGCTT
92834 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
92856 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
92878 TCATCTTTGAAAAGAAAATCTA
1 TCATCTTTGAAAAGAGAATCTA
92900 TCATCTTTGAA
1 TCATCTTTGAA
92911 GAGTGTAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:94288 original size:75 final size:75
Alignment explanation
Indices: 94195--94369 Score: 188
Period size: 76 Copynumber: 2.3 Consensus size: 75
94185 AGGATGATAT
* * *
94195 GGGCCTTCAGCATGCCCCAACATTGGCTAATACAAGTGTTCAAAATACGTCAACAGTCCTGATTC
1 GGGCTTTCAGCATGCCCCAACATTGGCTAATACAAATATTCAAAATACGTCAACAGTCCTGATTC
*
94260 TGATTGAAAG
66 TGATTGAAAA
** * * * * * * *
94270 GGGCTTTCAGCATGCCCCAGTATTTTGCTGATATAAATATTCAGAATACTTCAATATTCCTGATT
1 GGGCTTTCAGCATGCCCCAACA-TTGGCTAATACAAATATTCAAAATACGTCAACAGTCCTGATT
94335 CTGATTGAAAA
65 CTGATTGAAAA
* * * *
94346 GGGTTTTCACCATACCACAACATT
1 GGGCTTTCAGCATGCCCCAACATT
94370 CGCTTCTTGT
Statistics
Matches: 80, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
75 21 0.26
76 59 0.74
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (75 bp):
GGGCTTTCAGCATGCCCCAACATTGGCTAATACAAATATTCAAAATACGTCAACAGTCCTGATTC
TGATTGAAAA
Found at i:97887 original size:16 final size:15
Alignment explanation
Indices: 97858--97886 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
97848 TTTTTTTGCC
97858 TTTTTGTTTTTTTTA
1 TTTTTGTTTTTTTTA
97873 TTTTTGTTTTTTTT
1 TTTTTGTTTTTTTT
97887 TCTTCTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (15 bp):
TTTTTGTTTTTTTTA
Found at i:97904 original size:20 final size:20
Alignment explanation
Indices: 97881--97919 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
97871 TATTTTTGTT
97881 TTTTTTTCTTCTTCTTTCTC
1 TTTTTTTCTTCTTCTTTCTC
97901 TTTTTTTCTTCTTCTTTCT
1 TTTTTTTCTTCTTCTTTCT
97920 TTGTTGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTTCTTCTTCTTTCTC
Found at i:98222 original size:2 final size:2
Alignment explanation
Indices: 98215--98242 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
98205 ACAACAAATG
98215 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98243 TAAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99848 original size:27 final size:27
Alignment explanation
Indices: 99818--99873 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
99808 GTAATTATGT
99818 AAAAATGAAAATGTAAATACAAAGGTA
1 AAAAATGAAAATGTAAATACAAAGGTA
* *
99845 AAAAATGAAAATGTAAATGCAAATGTA
1 AAAAATGAAAATGTAAATACAAAGGTA
99872 AA
1 AA
99874 TATATGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.62, C:0.04, G:0.14, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGTAAATACAAAGGTA
Found at i:99948 original size:20 final size:20
Alignment explanation
Indices: 99893--99948 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
99883 GTAACAATAA
* * *
99893 AAATGCAAATTGTATAGTAC
1 AAATGCAAAATGAAAAGTAC
* *
99913 AAAAGCAAATAT-AAAAGTAT
1 AAATGCAAA-ATGAAAAGTAC
99933 AAATGCAAAATGAAAA
1 AAATGCAAAATGAAAA
99949 ATGCAAGGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 2 0.07
20 25 0.89
21 1 0.04
ACGTcount: A:0.59, C:0.07, G:0.12, T:0.21
Consensus pattern (20 bp):
AAATGCAAAATGAAAAGTAC
Found at i:103702 original size:3 final size:3
Alignment explanation
Indices: 103694--103745 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
103684 GGAATAAAAT
* *
103694 TAA TAA TAAA TAA TAA TAT TAA TAA TAA TAA TAA AAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
103740 TAA TAA
1 TAA TAA
103746 AAAAAAACCA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:103703 original size:12 final size:12
Alignment explanation
Indices: 103686--103745 Score: 75
Period size: 12 Copynumber: 4.9 Consensus size: 12
103676 TTGGGCTTGG
*
103686 AATAAAATTAAT
1 AATAAAAATAAT
103698 AATAAATAATAAT
1 AATAAA-AATAAT
* *
103711 ATTAATAATAAT
1 AATAAAAATAAT
103723 AATAAAAATAAT
1 AATAAAAATAAT
*
103735 AATAATAATAA
1 AATAAAAATAA
103746 AAAAAAACCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
12 32 0.78
13 9 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:103990 original size:75 final size:75
Alignment explanation
Indices: 103909--104089 Score: 211
Period size: 75 Copynumber: 2.4 Consensus size: 75
103899 TTTTCTAGAC
* * *
103909 TTAATATTATGGTTCGAGTCTTAAAATTTGACACTTAAATATTATGATTT-TATTATAGATTTTA
1 TTAATATTGTGGTTTGAGTCTTAAAATTTGACACTTAAATATTATGGTTTAT-TTATAGATTTTA
* *
103973 TTATTCTAAAA
65 CTATCCTAAAA
* * * * * *
103984 TTAATATTGTGGTTTGAATCTTGAAATTTAACATTTTAATATTATGGTTTATTTATGGATTTTAC
1 TTAATATTGTGGTTTGAGTCTTAAAATTTGACACTTAAATATTATGGTTTATTTATAGATTTTAC
* *
104049 TGTCCTAAAC
66 TATCCTAAAA
* *
104059 TTAATATTGTGATTTGAGTCTTAATATTTGA
1 TTAATATTGTGGTTTGAGTCTTAAAATTTGA
104090 TTTTATTTAT
Statistics
Matches: 87, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
75 86 0.99
76 1 0.01
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (75 bp):
TTAATATTGTGGTTTGAGTCTTAAAATTTGACACTTAAATATTATGGTTTATTTATAGATTTTAC
TATCCTAAAA
Found at i:116758 original size:24 final size:24
Alignment explanation
Indices: 116717--116765 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
116707 ATAAACGAAC
***
116717 ATGAACATGTTTGCGAACACATAA
1 ATGAACATGTTCAAGAACACATAA
*
116741 ATGAACATGTTCAAGAACATATAA
1 ATGAACATGTTCAAGAACACATAA
116765 A
1 A
116766 CGAATATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (24 bp):
ATGAACATGTTCAAGAACACATAA
Found at i:120814 original size:41 final size:41
Alignment explanation
Indices: 120733--120917 Score: 147
Period size: 39 Copynumber: 4.7 Consensus size: 41
120723 TTTTTCGAAA
* * * * *
120733 ATATATATACTATATAGCTTTTAAAAACACAT-TGAAAATAT
1 ATATATATATTATATAGTTTTTGAAAACATATAT-ATAATAT
120774 ATATATATATTATATAGTTTTTGAAAACATATATATAATAT
1 ATATATATATTATATAGTTTTTGAAAACATATATATAATAT
* ***
120815 ATAGT-T-T-TTGA-AAACACTTTGAAAACATATATAT-ATAT
1 ATA-TATATATT-ATATAGTTTTTGAAAACATATATATAATAT
* * * *
120853 ATATATATAATATATAG-TTTTGAAAACAT-TTTAGAA-AC
1 ATATATATATTATATAGTTTTTGAAAACATATATATAATAT
120891 ATATAT-TATATATATAGTTTTTGAAAA
1 ATATATATAT-TATATAGTTTTTGAAAA
120918 ACATTTTGAA
Statistics
Matches: 117, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
37 3 0.03
38 25 0.21
39 44 0.38
40 5 0.04
41 38 0.32
42 2 0.02
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (41 bp):
ATATATATATTATATAGTTTTTGAAAACATATATATAATAT
Found at i:120815 original size:28 final size:30
Alignment explanation
Indices: 120764--120830 Score: 111
Period size: 28 Copynumber: 2.3 Consensus size: 30
120754 TAAAAACACA
*
120764 TTGAAAATATATATATATATTATATAGTTT
1 TTGAAAACATATATATATATTATATAGTTT
120794 TTGAAAACATATATATA-A-TATATAGTTT
1 TTGAAAACATATATATATATTATATAGTTT
120822 TTGAAAACA
1 TTGAAAACA
120831 CTTTGAAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 19 0.53
29 1 0.03
30 16 0.44
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (30 bp):
TTGAAAACATATATATATATTATATAGTTT
Found at i:120816 original size:69 final size:69
Alignment explanation
Indices: 120699--120860 Score: 202
Period size: 69 Copynumber: 2.3 Consensus size: 69
120689 TATATTTAAT
* * *
120699 ATATATATATAATAATATATAATTTTTTTCGAAAATATATATACTATATAGCTTTTAAAAACACA
1 ATATATATAT-ATATTATAT-ATGTTTTTCGAAAATATATATAATATATAGCTTTTAAAAACACA
120764 TTGAAA
64 TTGAAA
* * *
120770 ATATATATATATATTATATA-GTTTTT-GAAAACATATATATAATATATAGTTTTTGAAAACACT
1 ATATATATATATATTATATATGTTTTTCG-AAA-ATATATATAATATATAGCTTTTAAAAACACA
120833 TTGAAA
64 TTGAAA
*
120839 ACATATATATATATATATATAT
1 ATATATATATATAT-TATATAT
120861 AATATATAGT
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
67 1 0.01
68 8 0.10
69 47 0.59
70 14 0.17
71 10 0.12
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (69 bp):
ATATATATATATATTATATATGTTTTTCGAAAATATATATAATATATAGCTTTTAAAAACACATT
GAAA
Found at i:120901 original size:49 final size:51
Alignment explanation
Indices: 120802--120906 Score: 171
Period size: 50 Copynumber: 2.1 Consensus size: 51
120792 TTTTGAAAAC
120802 ATATATATAATATATAGTTTTTGAAAACACTTTGAAAACATATATATATAT
1 ATATATATAATATATAGTTTTTGAAAACACTTTGAAAACATATATATATAT
*
120853 ATATATATAATATATAG-TTTTGAAAACA-TTTTAGAAACATATAT-TATAT
1 ATATATATAATATATAGTTTTTGAAAACACTTTGA-AAACATATATATATAT
120902 ATATA
1 ATATA
120907 GTTTTTGAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
49 14 0.27
50 21 0.40
51 17 0.33
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (51 bp):
ATATATATAATATATAGTTTTTGAAAACACTTTGAAAACATATATATATAT
Found at i:120904 original size:38 final size:40
Alignment explanation
Indices: 120851--120944 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
120841 ATATATATAT
120851 ATATATATATAATATATAG-TTTTG-AAAACATTTTAGAAA-C
1 ATATAT-TAT-ATATATAGTTTTTGAAAAACATTTT-GAAAGC
120891 ATATATTATATATATAGTTTTTGAAAAACATTTTGAAAGC
1 ATATATTATATATATAGTTTTTGAAAAACATTTTGAAAGC
*
120931 ATATATAATATATA
1 ATATATTATATATA
120945 ATTTTAAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
38 8 0.16
39 12 0.24
40 30 0.60
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.41
Consensus pattern (40 bp):
ATATATTATATATATAGTTTTTGAAAAACATTTTGAAAGC
Found at i:121041 original size:31 final size:31
Alignment explanation
Indices: 121006--121064 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
120996 TTTCGAAATA
121006 TATTTTATAATATAATTT-TTATTTATTTTTT
1 TATTTT-TAATATAATTTATTATTTATTTTTT
** *
121037 TATTTTTTTTATTATTTATTATTTATTT
1 TATTTTTAATATAATTTATTATTTATTT
121065 ACTATTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (31 bp):
TATTTTTAATATAATTTATTATTTATTTTTT
Found at i:134374 original size:2 final size:2
Alignment explanation
Indices: 134321--134354 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
134311 GTTCAATTTA
*
134321 AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
134355 ATTTTTTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:134465 original size:2 final size:2
Alignment explanation
Indices: 134400--134445 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
134390 AACACTTTGA
*
134400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
134441 AT AT A
1 AT AT A
134446 GTTTTTGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134482 original size:26 final size:28
Alignment explanation
Indices: 134430--134483 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
134420 ATATATATAT
* *
134430 ATATATGTAATATATAGTTTTTGAAAAC
1 ATATATATAATATATAGATTTTGAAAAC
134458 ATATATATAATATATA-ATTTT-AAAAC
1 ATATATATAATATATAGATTTTGAAAAC
134484 GCTTTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
27 4 0.17
28 15 0.62
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (28 bp):
ATATATATAATATATAGATTTTGAAAAC
Found at i:134483 original size:91 final size:93
Alignment explanation
Indices: 134321--134509 Score: 251
Period size: 91 Copynumber: 2.1 Consensus size: 93
134311 GTTCAATTTA
* *
134321 ATATATATATATATATATATATATAAAATATATAATTTTTTCAAAAATATATATAATATAGTCTT
1 ATATATATATATATATATATATATAAAATATATAAGTTTTTCAAAAATATATATAATATAGTATT
*
134386 TGAAAACAC-TTTGAATATATAT-ATAT
66 TGAAAACACTTTTGAAAATATATCATAT
** *
134412 ATATATATATATATATATATATATGTAATATAT-AGTTTTTGAAAACATATATATAATATA-TAA
1 ATATATATATATATATATATATATAAAATATATAAGTTTTTCAAAA-ATATATATAATATAGT-A
* *
134475 TTTTAAAACGCTTTTGAAAATATATCATAT
64 TTTGAAAACACTTTTGAAAATATATCATAT
*
134505 GTATA
1 ATATA
134510 GGCTTCGAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
90 11 0.13
91 54 0.64
92 12 0.14
93 8 0.09
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (93 bp):
ATATATATATATATATATATATATAAAATATATAAGTTTTTCAAAAATATATATAATATAGTATT
TGAAAACACTTTTGAAAATATATCATAT
Found at i:134575 original size:20 final size:18
Alignment explanation
Indices: 134550--134607 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 18
134540 TATAATATAC
134550 TTTTTATTATTATTTTTAT
1 TTTTTATT-TTATTTTTAT
*
134569 TTATTTATTTATATTTACTAT
1 TT-TTTATTT-TATTT-TTAT
134590 TTTTTAATTTTATTTTTA
1 TTTTT-ATTTTATTTTTA
134608 GGTCCAAGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 5 0.15
20 19 0.58
21 9 0.27
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATTTTATTTTTAT
Found at i:134578 original size:14 final size:13
Alignment explanation
Indices: 134550--134607 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 13
134540 TATAATATAC
134550 TTTTTA-TTATTA
1 TTTTTATTTATTA
134562 TTTTTATTTATTTA
1 TTTTTATTTA-TTA
* *
134576 TTTATATTTACTA
1 TTTTTATTTATTA
*
134589 TTTTTTAATT-TTA
1 -TTTTTATTTATTA
134602 TTTTTA
1 TTTTTA
134608 GGTCCAAGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 12 0.32
13 7 0.18
14 19 0.50
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTATTTATTA
Found at i:134590 original size:21 final size:20
Alignment explanation
Indices: 134566--134604 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
134556 TTATTATTTT
134566 TATTTATTT-ATTTATATTTAC
1 TATTT-TTTAATTT-TATTTAC
134587 TATTTTTTAATTTTATTT
1 TATTTTTTAATTTTATTT
134605 TTAGGTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTTTAATTTTATTTAC
Found at i:140047 original size:3 final size:3
Alignment explanation
Indices: 140039--140113 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
140029 GATTATAACC
140039 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
140087 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
140114 TACATACAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:140168 original size:30 final size:30
Alignment explanation
Indices: 140129--140204 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
140119 ACAAAAAATA
140129 GGACCCAAACCATTTACAAGA-CCCAAACCT
1 GGACCCAAACCATTTACAA-ATCCCAAACCT
* *
140159 GGGCCCAAACCATTTACAAATCCCAAACTT
1 GGACCCAAACCATTTACAAATCCCAAACCT
*
140189 GGACCCAAAACATTTA
1 GGACCCAAACCATTTA
140205 TAAACCCTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 1 0.02
30 40 0.98
ACGTcount: A:0.39, C:0.33, G:0.11, T:0.17
Consensus pattern (30 bp):
GGACCCAAACCATTTACAAATCCCAAACCT
Found at i:145661 original size:20 final size:21
Alignment explanation
Indices: 145614--145668 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
145604 TATGAGAAGG
*
145614 AAAAAC-TCTATCTTTACACTAT
1 AAAAACAT-TATCTTTACAC-AC
145636 AAAAACATTATCTTTACAC-C
1 AAAAACATTATCTTTACACAC
*
145656 AAAAACATCATCT
1 AAAAACATTATCT
145669 AATGCAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.40
22 17 0.57
23 1 0.03
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAACATTATCTTTACACAC
Found at i:147532 original size:81 final size:79
Alignment explanation
Indices: 147399--147560 Score: 297
Period size: 81 Copynumber: 2.0 Consensus size: 79
147389 TGAAAGAATC
*
147399 ATACCTATAAGAATGAGTTACAAAAGTAGGCACTAAATAGGACTTTCGAGAGTGATTTATGATTA
1 ATACCTATAAGAATAAGTTACAAAAGTAGGCACTAAATAGGACTTTCGAGAGTGATTTATGATTA
147464 TTAATGACATTATT
66 TTAATGACATTATT
147478 ATACCTATAAGAATATAAGTTACAAAAGTAGGCACTAAATAGGACTTTCGAGAGTGATTTATGAT
1 ATACCTATAAG-A-ATAAGTTACAAAAGTAGGCACTAAATAGGACTTTCGAGAGTGATTTATGAT
147543 TATTAATGACATTATT
64 TATTAATGACATTATT
147559 AT
1 AT
147561 TTTTAGCTAG
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
79 11 0.14
80 1 0.01
81 68 0.85
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (79 bp):
ATACCTATAAGAATAAGTTACAAAAGTAGGCACTAAATAGGACTTTCGAGAGTGATTTATGATTA
TTAATGACATTATT
Found at i:151617 original size:33 final size:33
Alignment explanation
Indices: 151574--151640 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
151564 ATTAGTATCC
* *
151574 TGGTGGCCAACATCAATGTTCAAGCCAGTTTCT
1 TGGTGCCCAACATCAATGTTCAAACCAGTTTCT
151607 TGGTGCCCAACATCAATGTTCAAACCAGTTTCT
1 TGGTGCCCAACATCAATGTTCAAACCAGTTTCT
151640 T
1 T
151641 TACCCTTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (33 bp):
TGGTGCCCAACATCAATGTTCAAACCAGTTTCT
Found at i:151696 original size:111 final size:111
Alignment explanation
Indices: 151502--151718 Score: 371
Period size: 111 Copynumber: 2.0 Consensus size: 111
151492 ATCCTGGTTT
* * *
151502 CCAACATCAATGTTCAAACCATTTTCTTTACCCTTTTGATCTTCTATGTTGGGTGTAGGCTTATT
1 CCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTCCTATGTTGGGTGTAGGCTTATT
* *
151567 AGTATCCTGGTGGCCAACATCAATGTTCAAGCCAGTTTCTTGGTGC
66 AATATCCTGGTGGCCAACATCAATGTTCAAACCAGTTTCTTGGTGC
*
151613 CCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTCCTATGTTGGTTGTAGGCTTATT
1 CCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTCCTATGTTGGGTGTAGGCTTATT
*
151678 AATATCCTGGTGGCCAACATCGATGTTCAAACCAGTTTCTT
66 AATATCCTGGTGGCCAACATCAATGTTCAAACCAGTTTCTT
151719 TACTCTTATG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 99 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (111 bp):
CCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTCCTATGTTGGGTGTAGGCTTATT
AATATCCTGGTGGCCAACATCAATGTTCAAACCAGTTTCTTGGTGC
Found at i:151738 original size:78 final size:78
Alignment explanation
Indices: 151607--152123 Score: 651
Period size: 78 Copynumber: 6.6 Consensus size: 78
151597 GCCAGTTTCT
* * *
151607 TGGTGCCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTCCTATGTTGGTTGTAGG
1 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTTCTATGTTGGGTGTAGG
*
151672 CTTATTAATATCC
66 CTTATTAGTATCC
* * *
151685 TGGTGGCCAACATCGATGTTCAAACCAGTTTCTTTACTCTTATGATATTCTATGTTGGGTGTAGG
1 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTTCTATGTTGGGTGTAGG
* * *
151750 CTTTTTAGGATTC
66 CTTATTAGTATCC
* ** * *
151763 TGGGGGCCAACATCAATGTTTGAACCAGTTTCTTTACCCTTATGATCTTTTATATTGGGTGTAGG
1 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTTCTATGTTGGGTGTAGG
151828 CTTATTAGTATCC
66 CTTATTAGTATCC
* * * * *
151841 TGGTGGCCAACATCGATGTTCGAACCAGTTTCTTTACCCTTTTGATCTTCTATATTTGGTGTAGG
1 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTTCTATGTTGGGTGTAGG
** * *
151906 GATATTTGCAT-C
66 CTTATTAGTATCC
** * * * * * * * *
151918 TCCATGGCTAACAACAAAGTCCAAATCAGCTCCTTTACCCTTGTGATCTTCTATGTTGGGTGTAG
1 T-GGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTTCTATGTTGGGTGTAG
151983 GCTTATTAGTATCC
65 GCTTATTAGTATCC
* * * * *
151997 TGGTGGCCAACATCAATGTTCAAACTAGTTTCTTTACCCTTTTGATCTTCTATCTTGGGAGCAGG
1 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTTCTATGTTGGGTGTAGG
152062 CTTATTAGTATCC
66 CTTATTAGTATCC
152075 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTCT-TGATCTT
1 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCT-TATGATCTT
152124 TGGAATCAAT
Statistics
Matches: 372, Mismatches: 64, Indels: 6
0.84 0.14 0.01
Matches are distributed among these distances:
77 2 0.01
78 367 0.99
79 3 0.01
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (78 bp):
TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATCTTCTATGTTGGGTGTAGG
CTTATTAGTATCC
Found at i:153511 original size:2 final size:2
Alignment explanation
Indices: 153504--153551 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
153494 TACTCGATAA
153504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
153546 AT AT AT
1 AT AT AT
153552 TCATTCTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:162790 original size:21 final size:21
Alignment explanation
Indices: 162766--162806 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
162756 GCTTTGGAAT
*
162766 TTTTCCTGGGTTGCAACCATC
1 TTTTCCTGGGATGCAACCATC
*
162787 TTTTCCTGGGATGTAACCAT
1 TTTTCCTGGGATGCAACCAT
162807 TGCTAACTTT
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:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (21 bp):
TTTTCCTGGGATGCAACCATC
Found at i:165194 original size:24 final size:24
Alignment explanation
Indices: 165140--165194 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
165130 TCAGAGTAGG
** *
165140 TTTCAATCCCTTTTTTACAATCGA
1 TTTCAATCCCCCTTTTACAATAGA
* *
165164 -TTGAATCCCCCTTTTACATTAGA
1 TTTCAATCCCCCTTTTACAATAGA
165187 TTTCAATC
1 TTTCAATC
165195 AGGTTTTATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.44
Consensus pattern (24 bp):
TTTCAATCCCCCTTTTACAATAGA
Found at i:165426 original size:23 final size:23
Alignment explanation
Indices: 165403--165447 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
165393 GAATCCGGGT
165403 TTGGGT-CGGGTTGCTTATTGGG
1 TTGGGTACGGGTTGCTTATTGGG
*
165425 TTGGGTATGGGTTGCTTATTGGG
1 TTGGGTACGGGTTGCTTATTGGG
165448 CATGTTCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.07, C:0.07, G:0.44, T:0.42
Consensus pattern (23 bp):
TTGGGTACGGGTTGCTTATTGGG
Found at i:165427 original size:12 final size:12
Alignment explanation
Indices: 165410--165447 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
165400 GGTTTGGGTC
165410 GGGTTGCTTATT
1 GGGTTGCTTATT
**
165422 GGGTTGGGTA-T
1 GGGTTGCTTATT
165433 GGGTTGCTTATT
1 GGGTTGCTTATT
165445 GGG
1 GGG
165448 CATGTTCCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.08, C:0.05, G:0.45, T:0.42
Consensus pattern (12 bp):
GGGTTGCTTATT
Found at i:166413 original size:255 final size:258
Alignment explanation
Indices: 165704--166659 Score: 1282
Period size: 257 Copynumber: 3.7 Consensus size: 258
165694 AGTGAGATCG
* * ** ** * ** *
165704 ACAGATAACCCGAAGGATTTAATCATCACACTCGAAAGACTTACAAAATGACATGAATGACTTAC
1 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATTGACCCGAAGGACTTAC
* * * *
165769 AAATTTTGGAAATAATTTATTGGGTAAAAAACTTTGAAAATCGCTTTCTTACTTTTAAAAAATTT
66 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
**
165834 CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATTTCTTTCTCATTTTTCAAATTTCATGTG
131 CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAA-TTCATGTG
* *
165899 AAAACATCCTACCCGAAGGTCTTATGGATAGCTC-AAATGACTTATCATCTTGCTCG-AAGACTT
195 AAAACATCCTACCCGAATGTCTTATGGATAGCCCGAAA-GACTTATCATCTTGCTCGAAAGACTT
* *
165962 ACAGATGACCCGAAGGATTTAAGCATCATGATCGAAAGACTTACTGA-TGGCCCGAAGGACTTAC
1 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATTGACCCGAAGGACTTAC
* * * ** *
166026 AAATTTTGGAAATAATTTAATAGGTAAGAAACATTGGAAATTACTTTTTTACTTTTCAAAAATTT
66 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
* * *
166091 CGTTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTGAAGTTCATGTGA
131 CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGA
* *
166156 AAACATCCTACCCGAATGTCTTACGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACTT
196 AAACATCCTACCCGAATGTCTTATGGATAGCCCGAAAGACTTATCATCTTGCTCGAAAGACTT
* *
166219 ACAAATGACCCGAAGAATTTAAGCATCATGCTCGAAAGACTTACTGATTG-CCCGAAGGACTTAC
1 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATTGACCCGAAGGACTTAC
**
166283 AAATTTTGGAAATAATTTACT-GGTAA-AAACTTTGGAAATTTCTTTCTTACTTTTCAAAAATTT
66 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
* *
166346 CATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGA
131 CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGA
* * * * * *
166411 AAACATCCTACCCGAAAT-TCTTATAGATTA-CCCGAAGGACTTATCATATTCCTTGAAAGACTG
196 AAACATCCTACCCG-AATGTCTTATGGA-TAGCCCGAAAGACTTATCATCTTGCTCGAAAGACTT
* * * * * * *
166474 ACAGTTGACCCAAAGGATTTAAGTATCATGCTCGAAAGACTTACTGA-TGACCAGATGTACTTAA
1 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATTGACCCGAAGGACTTAC
*
166538 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAACCGCTTTCTTACTTTTCAAAAATTT
66 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
* * * * ** *
166603 TATTTTCTAAAAAGATTTAAATGAGGAACTTTGGAAATCATTTTCTTATTTTTCAAA
131 CATTTTCTGAAAACA-TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAA
166660 AAAAAAAACT
Statistics
Matches: 620, Mismatches: 69, Indels: 18
0.88 0.10 0.03
Matches are distributed among these distances:
254 2 0.00
255 216 0.35
256 70 0.11
257 254 0.41
258 78 0.13
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (258 bp):
ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATTGACCCGAAGGACTTAC
AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGA
AAACATCCTACCCGAATGTCTTATGGATAGCCCGAAAGACTTATCATCTTGCTCGAAAGACTT
Found at i:175876 original size:25 final size:24
Alignment explanation
Indices: 175848--175918 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
175838 ATTCTTGGGT
*
175848 TTTTTTCACAGTAGGTTTCAATCCC
1 TTTTTT-ACAATAGGTTTCAATCCC
* *
175873 TTTTTTTACAATCGG-TTAAATCCC
1 -TTTTTTACAATAGGTTTCAATCCC
**
175897 CCTTTTACAATAGGTTTCAATC
1 TTTTTTACAATAGGTTTCAATC
175919 GAGTTTTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 11 0.30
24 14 0.38
25 6 0.16
26 6 0.16
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.44
Consensus pattern (24 bp):
TTTTTTACAATAGGTTTCAATCCC
Found at i:176266 original size:3 final size:3
Alignment explanation
Indices: 176258--176321 Score: 103
Period size: 3 Copynumber: 21.0 Consensus size: 3
176248 GAAACTTAAT
176258 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
176305 TAA TATA TATA TAA TAA
1 TAA TA-A TA-A TAA TAA
176322 CCCGGACAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 50 0.85
4 7 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:177414 original size:2 final size:2
Alignment explanation
Indices: 177407--177431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
177397 GATAAAAATA
177407 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 A
177432 ATAAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:178299 original size:17 final size:17
Alignment explanation
Indices: 178279--178316 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
178269 ATATAATATC
178279 ATATAATATTTAAATTA
1 ATATAATATTTAAATTA
**
178296 ATATCCTATTTAAATTA
1 ATATAATATTTAAATTA
178313 ATAT
1 ATAT
178317 CCTAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATATTTAAATTA
Found at i:178317 original size:17 final size:17
Alignment explanation
Indices: 178285--178320 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
178275 TATCATATAA
178285 TATTTAAATTAATATCC
1 TATTTAAATTAATATCC
178302 TATTTAAATTAATATCC
1 TATTTAAATTAATATCC
178319 TA
1 TA
178321 AAACAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTAAATTAATATCC
Found at i:180553 original size:193 final size:191
Alignment explanation
Indices: 180354--180771 Score: 527
Period size: 191 Copynumber: 2.2 Consensus size: 191
180344 CTATTAGCGG
*
180354 TATAAATGACAATTATGCATAACGTCACTTTATAA-TTGATACTCAATGACAACTAGTTACGTCA
1 TATAAATGACAATTATGCATAACGTCACTTTATAACTT-ATACTCAATGACAACTAGTTACATCA
180418 CTAAATAATAGAAAATTTTGTTATTAATAATTCACATCGTCACGAATAATAC-ATTAAAATCAAG
65 CTAAATAATAGAAAA-TTT-TTATTAATAATTCACATCGTCACGAATAATACGA-TAAAATCAA-
* * *
180482 C-TATATGTGACGAAAGATATATTGTTACATTTTTAGTGACGTAATATAACGTTACCTAATAGTA
126 CTTATATGTGACGAAAGAGATATTGTCAAATTTTTAGTGACGTAATATAACGTTACCTAATAGTA
180546 T
191 T
* * * * **
180547 TATAAATGACACTTATGCATAACGTCATTTTATAACTTATATTCCATGACAGTTAGTTACATCAC
1 TATAAATGACAATTATGCATAACGTCACTTTATAACTTATACTCAATGACAACTAGTTACATCAC
* * * * * * *
180612 TAAATTATATAATATTTTTATTAATAATTTATATCTTCATGAATAATACGATAAAATCAACTTAT
66 TAAATAATAGAAAATTTTTATTAATAATTCACATCGTCACGAATAATACGATAAAATCAACTTAT
* * **
180677 ATGTTACGAAATAGATATTGTCAAATTTTTAGTGACGTAATATAACGTTATGTAATAGTAT
131 ATGTGACGAAAGAGATATTGTCAAATTTTTAGTGACGTAATATAACGTTACCTAATAGTAT
* * ** * *
180738 TTTGAATGATGATTATGCATAACGCCACCTTATA
1 TATAAATGACAATTATGCATAACGTCACTTTATA
180772 CAATTTTCTC
Statistics
Matches: 193, Mismatches: 29, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
190 1 0.01
191 120 0.62
192 4 0.02
193 66 0.34
194 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (191 bp):
TATAAATGACAATTATGCATAACGTCACTTTATAACTTATACTCAATGACAACTAGTTACATCAC
TAAATAATAGAAAATTTTTATTAATAATTCACATCGTCACGAATAATACGATAAAATCAACTTAT
ATGTGACGAAAGAGATATTGTCAAATTTTTAGTGACGTAATATAACGTTACCTAATAGTAT
Found at i:188440 original size:10 final size:11
Alignment explanation
Indices: 188420--188444 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
188410 ATTTCATACG
188420 AAAGAAAAAAA
1 AAAGAAAAAAA
188431 AAAGAAAAAAA
1 AAAGAAAAAAA
188442 AAA
1 AAA
188445 CCTAGCTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:196068 original size:2 final size:2
Alignment explanation
Indices: 196061--196106 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
196051 ATTATCCAAA
*
196061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
196102 AT AT A
1 AT AT A
196107 GCAAACTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:199159 original size:132 final size:134
Alignment explanation
Indices: 198878--199174 Score: 329
Period size: 132 Copynumber: 2.2 Consensus size: 134
198868 AGGATCAATT
* * ** * *
198878 AAAAGATTGTTACTGATCCAACTCCTACTATGAAGAATCAAACAAAATGTCGATGTTGATCTACC
1 AAAAGATTGGTACTGATCCAATTCCTTTTGTGAAGAATCAAACAAAATGTCGATGATGATCTACC
* * * *
198943 TCATTCTGTGATATAATCGAGCAAAATAAAGTTATGCTAATTCAACTCCTTCTGTGAAGAATCAA
66 TCATTCTGTGATAGAATCAAGCAAAATAAAGTTATGCTAATCCAACTCCTTCTGCGAAGAATCAA
*
199008 ATGG
131 ATGC
* * *
199012 AATGACATT-GT--TGATCCAATTCCTTTTGTGAAGAATCAAACAAAATGTTGATGATGATCTAC
1 AA-AAGATTGGTACTGATCCAATTCCTTTTGTGAAGAATCAAACAAAATGTCGATGATGATCTAC
* * ** *
199074 CTCCTTCTGTGATAGAATCAAGCAAAATAATGTTATGCTGGTCCAACTCCTTTTGCGAATG-ATC
65 CTCATTCTGTGATAGAATCAAGCAAAATAAAGTTATGCTAATCCAACTCCTTCTGCGAA-GAATC
*
199138 -GA-GC
129 AAATGC
*
199142 AAAAGATTGGTACTGATCC-ATCTCCGTTTGTGA
1 AAAAGATTGGTACTGATCCAAT-TCCTTTTGTGA
199175 TTAAATCAAG
Statistics
Matches: 134, Mismatches: 23, Indels: 14
0.78 0.13 0.08
Matches are distributed among these distances:
129 4 0.03
130 5 0.04
131 3 0.02
132 114 0.85
133 1 0.01
134 3 0.02
135 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (134 bp):
AAAAGATTGGTACTGATCCAATTCCTTTTGTGAAGAATCAAACAAAATGTCGATGATGATCTACC
TCATTCTGTGATAGAATCAAGCAAAATAAAGTTATGCTAATCCAACTCCTTCTGCGAAGAATCAA
ATGC
Found at i:199535 original size:13 final size:13
Alignment explanation
Indices: 199517--199542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
199507 AAAGTTCTAA
199517 CTCATGGTTTCAT
1 CTCATGGTTTCAT
199530 CTCATGGTTTCAT
1 CTCATGGTTTCAT
199543 GATTTCATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
CTCATGGTTTCAT
Found at i:199671 original size:41 final size:39
Alignment explanation
Indices: 199608--199691 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 39
199598 TCCTCATCCG
*
199608 TTCTAAAGTGTCATTTCAGGTTTTCACTTT-AGATTCACTT
1 TTCTAAAGTGCCATTTCAGGTTTTCACTTTGA-ATTCA-TT
* *
199648 TTCTCAAAGTGCCCTTTCGGGTTTTCACTTTGAATTCATT
1 TTCT-AAAGTGCCATTTCAGGTTTTCACTTTGAATTCATT
199688 TTCT
1 TTCT
199692 TTTATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 10 0.26
41 28 0.72
42 1 0.03
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.48
Consensus pattern (39 bp):
TTCTAAAGTGCCATTTCAGGTTTTCACTTTGAATTCATT
Found at i:199723 original size:6 final size:6
Alignment explanation
Indices: 199686--199771 Score: 61
Period size: 6 Copynumber: 13.7 Consensus size: 6
199676 TTTGAATTCA
* * *
199686 TTTTC- TTTTAT TTTTAT TTTTCT TCATT-T TTTTCT TTTTCT TTTTCTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT TTTTC-T
199734 CGTTTTCT TTTTCTT TTATTCT TTCTTC- TTTTCT TTTT
1 --TTTTCT TTTTC-T TT-TTCT TT-TTCT TTTTCT TTTT
199772 TCATTAGCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
5 9 0.13
6 37 0.55
7 12 0.18
8 4 0.06
9 5 0.07
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:199730 original size:15 final size:15
Alignment explanation
Indices: 199686--199770 Score: 57
Period size: 15 Copynumber: 5.5 Consensus size: 15
199676 TTTGAATTCA
* *
199686 TTTTCTTTTATTTTTA
1 TTTT-TTTTCTTTTTC
*
199702 TTTTTCTTCATTTTT-
1 TTTTTTTTC-TTTTTC
*
199717 TTCTTTTTCTTTTTC
1 TTTTTTTTCTTTTTC
**
199732 TTCGTTTTCTTTTTC
1 TTTTTTTTCTTTTTC
*
199747 -TTTTATTCTTTCTTC
1 TTTTTTTTCTTT-TTC
199762 TTTTCTTTT
1 TTTT-TTTT
199771 TTCATTAGCA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
14 13 0.24
15 27 0.49
16 12 0.22
17 3 0.05
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:199741 original size:21 final size:21
Alignment explanation
Indices: 199715--199771 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
199705 TTCTTCATTT
*
199715 TTTTCTTTTTCTTTTTCTTCG
1 TTTTCTTTTTCTTTTTATTCG
*
199736 TTTTCTTTTTC-TTTTATTCT
1 TTTTCTTTTTCTTTTTATTCG
199756 TTCTTC-TTTTCTTTTT
1 TT-TTCTTTTTCTTTTT
199772 TCATTAGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTCTTTTTCTTTTTATTCG
Found at i:200464 original size:8 final size:7
Alignment explanation
Indices: 200448--200541 Score: 57
Period size: 7 Copynumber: 12.6 Consensus size: 7
200438 TATTATTTTA
*
200448 TTTTATT
1 TTTTCTT
200455 TTGTTC-T
1 TT-TTCTT
200462 TTTTCTTT
1 TTTTC-TT
200470 TTTTCTTT
1 TTTTC-TT
200478 CTTTTCATAT
1 -TTTTC-T-T
*
200488 TTTCCTT
1 TTTTCTT
200495 TTTTCCTT
1 TTTT-CTT
* *
200503 TCTTATT
1 TTTTCTT
200510 TTTTC-T
1 TTTTCTT
*
200516 TTTTCTC
1 TTTTCTT
200523 TTTTCTCT
1 TTTTCT-T
200531 TTTTCTT
1 TTTTCTT
200538 TTTT
1 TTTT
200542 TTCAAGCAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
6 9 0.13
7 25 0.36
8 24 0.35
9 10 0.14
10 1 0.01
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTTCTT
Found at i:200533 original size:21 final size:21
Alignment explanation
Indices: 200478--200541 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
200468 TTTTTTCTTT
* *
200478 CTTTTCATATTTTCCTTTTTT
1 CTTTTCATCTTTTTCTTTTTT
*
200499 CCTTTCTTAT-TTTTTCTTTTTCT
1 -CTTT-TCATCTTTTTCTTTTT-T
200522 CTTTTC-TCTTTTTCTTTTTT
1 CTTTTCATCTTTTTCTTTTTT
200542 TTCAAGCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 2 0.06
21 12 0.33
22 18 0.50
23 4 0.11
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (21 bp):
CTTTTCATCTTTTTCTTTTTT
Found at i:200542 original size:8 final size:8
Alignment explanation
Indices: 200461--200544 Score: 57
Period size: 8 Copynumber: 10.8 Consensus size: 8
200451 TATTTTGTTC
200461 TTTTTCTT
1 TTTTTCTT
200469 TTTTTCTT
1 TTTTTCTT
*
200477 TCTTTTCAT
1 T-TTTTCTT
* *
200486 ATTTTCCT
1 TTTTTCTT
*
200494 TTTTTCCT
1 TTTTTCTT
* *
200502 TTCTT-AT
1 TTTTTCTT
200509 TTTTTCTT
1 TTTTTCTT
*
200517 TTTCTC-T
1 TTTTTCTT
*
200524 TTTCTCTT
1 TTTTTCTT
*
200532 TTTCT-TT
1 TTTTTCTT
200539 TTTTTC
1 TTTTTC
200545 AAGCAAAATA
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
7 18 0.29
8 38 0.61
9 6 0.10
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCTT
Found at i:208776 original size:16 final size:16
Alignment explanation
Indices: 208755--208790 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
208745 TCTTTCCACG
208755 ACCTGATATTGGTACA
1 ACCTGATATTGGTACA
*
208771 ACCTGATATTGGTACG
1 ACCTGATATTGGTACA
208787 ACCT
1 ACCT
208791 AGTTGTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (16 bp):
ACCTGATATTGGTACA
Found at i:208880 original size:19 final size:19
Alignment explanation
Indices: 208856--208902 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
208846 AAGCAATTTC
*
208856 TCATCTTGCAAAAATTTGA
1 TCATCTTGCAAAAATTCGA
208875 TCATCTTGCAAAAATTCGA
1 TCATCTTGCAAAAATTCGA
208894 TCATCTTGC
1 TCATCTTGC
208903 GACAGTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (19 bp):
TCATCTTGCAAAAATTCGA
Found at i:211249 original size:11 final size:11
Alignment explanation
Indices: 211220--211256 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
211210 TTTGGGACTA
211220 AAATAAAA-A-
1 AAATAAAAGAC
211229 AAAGTAAAAGAC
1 AAA-TAAAAGAC
211241 AAATAAAAGAC
1 AAATAAAAGAC
211252 AAATA
1 AAATA
211257 CAAAAGCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 3 0.12
10 5 0.20
11 14 0.56
12 3 0.12
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (11 bp):
AAATAAAAGAC
Found at i:214967 original size:15 final size:16
Alignment explanation
Indices: 214937--214978 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
214927 AGGGGTGTGT
214937 AAATTCGGGTACCCGA
1 AAATTCGGGTACCCGA
*
214953 AAATT-GGGTATCCGA
1 AAATTCGGGTACCCGA
214968 AATATTCGGGT
1 AA-ATTCGGGT
214979 TATTGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 11 0.48
16 8 0.35
17 4 0.17
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (16 bp):
AAATTCGGGTACCCGA
Found at i:217574 original size:45 final size:46
Alignment explanation
Indices: 217506--217608 Score: 115
Period size: 50 Copynumber: 2.2 Consensus size: 46
217496 CTAATGAATA
*
217506 AAAATAATAATAAACTAAAAATG-TT-T-CAATTCTAATTCCTAAT
1 AAAATAATAATAAACAAAAAATGTTTATACAATTCTAATTCCTAAT
*
217549 -AAATAATAATAAACCAAGAATAATGTTTTAATACAATTTTAATTCCTAAT
1 AAAATAATAATAAA-CAA-AA-AATG-TTT-ATACAATTCTAATTCCTAAT
217599 AAAATAATAA
1 AAAATAATAA
217609 ATCTAATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
42 13 0.27
43 2 0.04
44 2 0.04
45 4 0.08
47 2 0.04
49 1 0.02
50 16 0.33
51 9 0.18
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (46 bp):
AAAATAATAATAAACAAAAAATGTTTATACAATTCTAATTCCTAAT
Found at i:228959 original size:17 final size:16
Alignment explanation
Indices: 228922--228980 Score: 70
Period size: 17 Copynumber: 3.8 Consensus size: 16
228912 TATTTCGCCT
*
228922 AAAAAATGAAAAAGACT
1 AAAAAATGAAAAAGA-A
228939 AAAAAATGAAAAATGAA
1 AAAAAATGAAAAA-GAA
228956 AAAAAA-G-AAAAGAA
1 AAAAAATGAAAAAGAA
228970 AAAAAAT-AAAA
1 AAAAAATGAAAA
228981 GGATGGTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 9 0.24
15 7 0.18
16 1 0.03
17 19 0.50
18 2 0.05
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (16 bp):
AAAAAATGAAAAAGAA
Found at i:228970 original size:14 final size:14
Alignment explanation
Indices: 228948--228981 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
228938 TAAAAAATGA
228948 AAAATGAAAAAAAAG
1 AAAA-GAAAAAAAAG
*
228963 AAAAGAAAAAAAAT
1 AAAAGAAAAAAAAG
228977 AAAAG
1 AAAAG
228982 GATGGTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:230278 original size:48 final size:48
Alignment explanation
Indices: 230215--230346 Score: 205
Period size: 46 Copynumber: 2.8 Consensus size: 48
230205 TCAACTTCTC
* * **
230215 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTTTA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
*
230263 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG--TCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
230309 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
230347 GCTGATTCAA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 43 0.57
48 33 0.43
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
Found at i:230280 original size:112 final size:112
Alignment explanation
Indices: 230082--230304 Score: 349
Period size: 112 Copynumber: 2.0 Consensus size: 112
230072 TTTGATCCCA
* *
230082 ATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAATTGGAACATGTATCTCTTC
1 ATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGTGGAACAGGTATCTCTTC
*
230147 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTCG
66 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCT-CTTCG
* * * *
230195 ATTCAATGGATCAACT-TCTCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
1 ATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGTGGAACAGGTATCTCTTC
**
230259 TTTAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTC
66 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTC
230305 TCCAAGATTT
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
111 4 0.04
112 81 0.80
113 16 0.16
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (112 bp):
ATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGTGGAACAGGTATCTCTTC
TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCG
Found at i:230507 original size:113 final size:113
Alignment explanation
Indices: 230263--230670 Score: 648
Period size: 113 Copynumber: 3.7 Consensus size: 113
230253 CTCTTCTTTA
* * *
230263 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG--TCTCTTCTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* * *
230326 CAGAGTAAGTGGAACAAGTCT--GCTGATTCAATGGATAAACTTCCCC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
*
230372 AGATCTGATATTCCCTTCAGAGTAAGCAGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
*
230437 TAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
* *
230485 AGATCTGATATTCCCTTTAGAGTAAGCGGAACAGGTTTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
*
230550 CAGAGTAAGTGGAACAAGTCTACCCTGATTCAATGGATCAAC-TCCCTC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCC-C
*
230598 AGATCTGATATTCCCTTCAGAGTAAGCGAAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
*
230663 TAGA-AAAG
66 CAGAGAAAG
230671 AAGCGGAACA
Statistics
Matches: 276, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
109 32 0.12
111 46 0.17
112 7 0.03
113 191 0.69
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (113 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
Found at i:234709 original size:14 final size:14
Alignment explanation
Indices: 234674--234716 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
234664 AAAAAATATA
234674 TTATTTCAT-TATTT
1 TTATTT-ATATATTT
234688 TATATTTATATATTT
1 T-TATTTATATATTT
*
234703 TTATTTATAAATTT
1 TTATTTATATATTT
234717 AAATTCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTATATATTT
Found at i:235516 original size:6 final size:6
Alignment explanation
Indices: 235505--235603 Score: 198
Period size: 6 Copynumber: 16.5 Consensus size: 6
235495 GTTCTTTAAT
235505 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
235553 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
235601 AAA
1 AAA
235604 GATTTCTTTT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:236180 original size:27 final size:26
Alignment explanation
Indices: 236150--236200 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
236140 AAAATGTTAC
236150 ATTAAAAATTAAAAGATATATAAATAA
1 ATTAAAAATTAAAA-ATATATAAATAA
** *
236177 ATTATCAATTAAAAATATCTAAAT
1 ATTAAAAATTAAAAATATATAAAT
236201 TATATAAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (26 bp):
ATTAAAAATTAAAAATATATAAATAA
Found at i:238999 original size:7 final size:7
Alignment explanation
Indices: 238987--239017 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
238977 GTCAAAGAAA
238987 GTCAACG
1 GTCAACG
238994 GTCAACG
1 GTCAACG
239001 GTCAACG
1 GTCAACG
239008 GTCAACG
1 GTCAACG
239015 GTC
1 GTC
239018 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:239024 original size:5 final size:5
Alignment explanation
Indices: 239014--239066 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
239004 AACGGTCAAC
* *
239014 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG GGTCG
239063 GGTC
1 GGTC
239067 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:239039 original size:17 final size:17
Alignment explanation
Indices: 239019--239067 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
239009 TCAACGGTCG
239019 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
239036 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
239053 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
239068 GACCGGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:239062 original size:22 final size:22
Alignment explanation
Indices: 239007--239049 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
238997 AACGGTCAAC
239007 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
239029 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
239050 AACGGTCGGG
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:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:239087 original size:19 final size:19
Alignment explanation
Indices: 239065--239104 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
239055 TCGGGTCGGG
* *
239065 TCAGACCGGTCAACCCGGT
1 TCAGACCAGTCAAACCGGT
239084 TCAGACCAGTCAAACCGGT
1 TCAGACCAGTCAAACCGGT
239103 TC
1 TC
239105 GAACCGGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.35, G:0.23, T:0.17
Consensus pattern (19 bp):
TCAGACCAGTCAAACCGGT
Found at i:239124 original size:29 final size:31
Alignment explanation
Indices: 239092--239162 Score: 112
Period size: 29 Copynumber: 2.4 Consensus size: 31
239082 GTTCAGACCA
239092 GTCAAACCGGTTC-GAACCGGTTG-AAACCG
1 GTCAAACCGGTTCAGAACCGGTTGAAAACCG
239121 GTCAAACCGG-TCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTTCAGAACCGGTTGAAAACCG
*
239151 GTTAAACCGGTT
1 GTCAAACCGGTT
239163 TCCAGCAGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 20 0.53
30 15 0.39
31 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (31 bp):
GTCAAACCGGTTCAGAACCGGTTGAAAACCG
Found at i:239129 original size:9 final size:9
Alignment explanation
Indices: 239063--239161 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
239053 GGTCGGGTCG
*
239063 GGTCAGACC
1 GGTCAAACC
*
239072 GGTCAACCC
1 GGTCAAACC
*
239081 GGTTCAGACC
1 GG-TCAAACC
*
239091 AGTCAAACC
1 GGTCAAACC
*
239100 GGTTCGAACC
1 GG-TCAAACC
*
239110 GGTTGAAACC
1 GG-TCAAACC
239120 GGTCAAACC
1 GGTCAAACC
239129 GGTCAGAACC
1 GGTCA-AACC
*
239139 GGTTGAAAACC
1 GG-T-CAAACC
*
239150 GGTTAAACC
1 GGTCAAACC
239159 GGT
1 GGT
239162 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
9 35 0.49
10 29 0.40
11 7 0.10
12 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:246377 original size:22 final size:22
Alignment explanation
Indices: 246349--246391 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
246339 AACGGTCAAC
246349 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
246371 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
246392 AGACCGGTCA
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:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:246412 original size:19 final size:19
Alignment explanation
Indices: 246390--246467 Score: 120
Period size: 19 Copynumber: 4.1 Consensus size: 19
246380 TCGGGTCGGG
* *
246390 TCAGACCGGTCAACCCGGT
1 TCAGACCAGTCAAACCGGT
* *
246409 TCAGACCGGTTAAACCGGT
1 TCAGACCAGTCAAACCGGT
246428 TCAGACCAGTCAAACCGGT
1 TCAGACCAGTCAAACCGGT
246447 TCAGACCAGTCAAACCGGT
1 TCAGACCAGTCAAACCGGT
246466 TC
1 TC
246468 GAACCGGTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 55 1.00
ACGTcount: A:0.27, C:0.32, G:0.23, T:0.18
Consensus pattern (19 bp):
TCAGACCAGTCAAACCGGT
Found at i:246419 original size:10 final size:10
Alignment explanation
Indices: 246390--246496 Score: 75
Period size: 10 Copynumber: 11.1 Consensus size: 10
246380 TCGGGTCGGG
246390 TCAGACCGG-
1 TCAGACCGGT
246399 TCA-ACCCGGT
1 TCAGA-CCGGT
246409 TCAGACCGGT
1 TCAGACCGGT
*
246419 T-AAACCGGT
1 TCAGACCGGT
*
246428 TCAGACCAG-
1 TCAGACCGGT
*
246437 TCAAACCGGT
1 TCAGACCGGT
*
246447 TCAGACCAG-
1 TCAGACCGGT
*
246456 TCAAACCGGT
1 TCAGACCGGT
246466 TC-GAACCGGT
1 TCAG-ACCGGT
* *
246476 TGAAACCGG-
1 TCAGACCGGT
246485 TCAGAACCGGT
1 TCAG-ACCGGT
246496 T
1 T
246497 GAAAACCGGT
Statistics
Matches: 74, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
8 1 0.01
9 31 0.42
10 40 0.54
11 2 0.03
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:246432 original size:38 final size:38
Alignment explanation
Indices: 246390--246515 Score: 132
Period size: 38 Copynumber: 3.3 Consensus size: 38
246380 TCGGGTCGGG
*
246390 TCAGACCGGTCAACCCGGTTCAGACCGGTTAAACCGGT
1 TCAGACCGGTCAAACCGGTTCAGACCGGTTAAACCGGT
* * *
246428 TCAGACCAGTCAAACCGGTTCAGACCAGTCAAACCGGT
1 TCAGACCGGTCAAACCGGTTCAGACCGGTTAAACCGGT
*
246466 TC-GAACCGGTTGAAACCGG-TCAGAACCGGTTGAAAACCGGT
1 TCAG-ACCGG-TCAAACCGGTTCAG-ACCGGTT--AAACCGGT
*
246507 T-AAACCGGT
1 TCAGACCGGT
246516 TTCCATCAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
37 1 0.01
38 44 0.60
39 14 0.19
40 5 0.07
41 9 0.12
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (38 bp):
TCAGACCGGTCAAACCGGTTCAGACCGGTTAAACCGGT
Found at i:250314 original size:2 final size:2
Alignment explanation
Indices: 250307--250336 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
250297 TAACTGACAC
250307 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
250337 TTCAGATGAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:251769 original size:43 final size:43
Alignment explanation
Indices: 251718--251809 Score: 184
Period size: 43 Copynumber: 2.1 Consensus size: 43
251708 GAATTAACTT
251718 TCATTATGTGTAACTCGTATCTAAATATACTCTAATTTAAGTC
1 TCATTATGTGTAACTCGTATCTAAATATACTCTAATTTAAGTC
251761 TCATTATGTGTAACTCGTATCTAAATATACTCTAATTTAAGTC
1 TCATTATGTGTAACTCGTATCTAAATATACTCTAATTTAAGTC
251804 TCATTA
1 TCATTA
251810 ATCTGAATGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (43 bp):
TCATTATGTGTAACTCGTATCTAAATATACTCTAATTTAAGTC
Found at i:254863 original size:21 final size:22
Alignment explanation
Indices: 254824--254865 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
254814 TTAAAAATAG
254824 TAAAAAATTTATAAAATTATTT
1 TAAAAAATTTATAAAATTATTT
* *
254846 TAAAATATTTA-AATATTATT
1 TAAAAAATTTATAAAATTATT
254866 ATCTGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAAAATTTATAAAATTATTT
Found at i:257284 original size:21 final size:21
Alignment explanation
Indices: 257260--257306 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
257250 CACCGTCCAG
257260 CCACCGTTTGACAAACCGAAA
1 CCACCGTTTGACAAACCGAAA
* *
257281 CCACCGTTTGACGAACTGAAA
1 CCACCGTTTGACAAACCGAAA
257302 CCACC
1 CCACC
257307 ATCGTGTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.36, G:0.15, T:0.15
Consensus pattern (21 bp):
CCACCGTTTGACAAACCGAAA
Done.