Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 96 of 132
Found at i:29545745 original size:88 final size:89
Alignment explanation
Indices: 29545619--29545804 Score: 213
Period size: 88 Copynumber: 2.1 Consensus size: 89
29545609 CCTTATTTTA
* ** * *
29545619 TTTTAAAAATATGT-TT-T-GCCCCCAAACTTTCCAAAAATTTAAATTT-GGCCTTCAAACTTTG
1 TTTTAAAAAT-TGTATTATGGCCCACAAACTTTCCAAAAATTTAAATTTAACCCCT-AAACTTTC
*
29545680 TAGAAATTATATTTT-AGCCC-AAAC
64 TAAAAATTATATTTTAAGCCCTAAAC
* * *
29545704 TTTCTAAAAATTGTATTATGGCCCACAAACTTTCTAAAAATTTCATTTTAACCCCTAAACTTTCT
1 TTT-TAAAAATTGTATTATGGCCCACAAACTTTCCAAAAATTTAAATTTAACCCCTAAACTTTCT
*
29545769 AAAAATTATATTTTAATCCCTAAAC
65 AAAAATTATATTTTAAGCCCTAAAC
29545794 TTTTAAAAATT
1 TTTTAAAAATT
29545805 ACATTTTAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
85 6 0.07
86 9 0.11
87 1 0.01
88 46 0.55
89 15 0.18
90 7 0.08
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.39
Consensus pattern (89 bp):
TTTTAAAAATTGTATTATGGCCCACAAACTTTCCAAAAATTTAAATTTAACCCCTAAACTTTCTA
AAAATTATATTTTAAGCCCTAAAC
Found at i:29545810 original size:29 final size:29
Alignment explanation
Indices: 29545672--29545848 Score: 160
Period size: 30 Copynumber: 6.0 Consensus size: 29
29545662 TTTGGCCTTC
* * * *
29545672 AAACTTTGTAGAAATTATATTTTAGCCC-
1 AAACTTTCTAAAAATTACATTTTAACCCT
** * ** *
29545700 AAACTTTCTAAAAATTGTATTATGGCCCAC
1 AAACTTTCTAAAAATTACATTTTAACCC-T
*
29545730 AAACTTTCTAAAAATTTCATTTTAACCCCT
1 AAACTTTCTAAAAATTACATTTTAA-CCCT
*
29545760 AAACTTTCTAAAAATTATATTTTAATCCCT
1 AAACTTTCTAAAAATTACATTTTAA-CCCT
29545790 AAACTTT-TAAAAATTACATTTTAACACCT
1 AAACTTTCTAAAAATTACATTTTAAC-CCT
* * **
29545819 AAACTTTCCAAAATTTTGATTTTAACCCT
1 AAACTTTCTAAAAATTACATTTTAACCCT
29545848 A
1 A
29545849 TTTTTTCCTT
Statistics
Matches: 125, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.19
29 30 0.24
30 68 0.54
31 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (29 bp):
AAACTTTCTAAAAATTACATTTTAACCCT
Found at i:29545821 original size:59 final size:58
Alignment explanation
Indices: 29545672--29545848 Score: 180
Period size: 59 Copynumber: 3.0 Consensus size: 58
29545662 TTTGGCCTTC
* * * * * * ** *
29545672 AAACTTTGTAGAAATTATATTTTAGCCC-AAACTTTCTAAAAATTGTATTATGGCCCAC
1 AAACTTTCTAAAAATTACATTTTAACCCTAAACTTTCTAAAAATTATATTTTAACCC-T
*
29545730 AAACTTTCTAAAAATTTCATTTTAACCCCTAAACTTTCTAAAAATTATATTTTAATCCCT
1 AAACTTTCTAAAAATTACATTTTAA-CCCTAAACTTTCTAAAAATTATATTTTAA-CCCT
* *
29545790 AAACTTT-TAAAAATTACATTTTAACACCTAAACTTTC-CAAAATTTTGATTTTAACCCT
1 AAACTTTCTAAAAATTACATTTTAAC-CCTAAACTTTCTAAAAATTAT-ATTTTAACCCT
29545848 A
1 A
29545849 TTTTTTCCTT
Statistics
Matches: 101, Mismatches: 13, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
58 33 0.33
59 37 0.37
60 28 0.28
61 3 0.03
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (58 bp):
AAACTTTCTAAAAATTACATTTTAACCCTAAACTTTCTAAAAATTATATTTTAACCCT
Found at i:29554637 original size:29 final size:29
Alignment explanation
Indices: 29554579--29554639 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
29554569 GCAATAATTC
* **
29554579 AAACACAGTAGAGAAAGATTCATTAAAAA
1 AAACACAGTAGAGAAAGATGCAGGAAAAA
* *
29554608 AAACACAGTAGAGAAAGA-GGAGGAAGAA
1 AAACACAGTAGAGAAAGATGCAGGAAAAA
29554636 AAAC
1 AAAC
29554640 CTACCTTGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.59, C:0.10, G:0.21, T:0.10
Consensus pattern (29 bp):
AAACACAGTAGAGAAAGATGCAGGAAAAA
Found at i:29555747 original size:42 final size:42
Alignment explanation
Indices: 29555695--29555858 Score: 140
Period size: 42 Copynumber: 4.0 Consensus size: 42
29555685 TAGCTGCGTT
* * *
29555695 TTTCGCATAAACGTCACTAATGCTCTTTACCTTTTACGGCGG
1 TTTCCCATAAACGCCACTAATGCTCTTTACCTTTTACGGCAG
* *
29555737 TTTCCCATAAACGCCGCT-ATAGCTCTTTACCTTTTACGG-TG
1 TTTCCCATAAACGCCACTAAT-GCTCTTTACCTTTTACGGCAG
* * * * * *
29555778 TTTCTCCAAAAATGCCACTATTG--C-TTAGCTTTTGCGGCAT
1 TTTC-CCATAAACGCCACTAATGCTCTTTACCTTTTACGGCAG
* * * *
29555818 TTTCCCATAAATGCCGCTATTGCTCTTTACCTTTGACGGCA
1 TTTCCCATAAACGCCACTAATGCTCTTTACCTTTTACGGCA
29555859 TTTTTGAGAA
Statistics
Matches: 98, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
39 27 0.28
40 5 0.05
41 8 0.08
42 57 0.58
43 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (42 bp):
TTTCCCATAAACGCCACTAATGCTCTTTACCTTTTACGGCAG
Found at i:29555911 original size:41 final size:39
Alignment explanation
Indices: 29555842--29555953 Score: 109
Period size: 41 Copynumber: 2.8 Consensus size: 39
29555832 CGCTATTGCT
* * * *
29555842 CTTTACCTTTGACGGCATTTTTGAGAAAAACGTCGCCATTA
1 CTTTACCTTTTACGGCGTTTATGGGAAAAAC-T-GCCATTA
* * *
29555883 CTTTACCTTTTACTGCGTTTATGGGAAAACACTGCTATTG
1 CTTTACCTTTTACGGCGTTTATGGGAAAA-ACTGCCATTA
* *
29555923 CTTTACCTTTTGCGGTGTTTAT-GGAAAAACT
1 CTTTACCTTTTACGGCGTTTATGGGAAAAACT
29555954 CTGCTGTTGC
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
38 3 0.05
39 6 0.10
40 24 0.40
41 25 0.42
42 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (39 bp):
CTTTACCTTTTACGGCGTTTATGGGAAAAACTGCCATTA
Found at i:29555927 original size:40 final size:40
Alignment explanation
Indices: 29555833--29555973 Score: 131
Period size: 40 Copynumber: 3.5 Consensus size: 40
29555823 CATAAATGCC
* * * *
29555833 GCTATTGCTCTTTACCTTTGACGGCATTTTTGAGAAAAAC-GT
1 GCTATTG--CTTTACCTTTTACGGCGTTTATG-GAAAAACACT
* * * *
29555875 CGCCATTACTTTACCTTTTACTGCGTTTATGGGAAAACACT
1 -GCTATTGCTTTACCTTTTACGGCGTTTATGGAAAAACACT
* * *
29555916 GCTATTGCTTTACCTTTTGCGGTGTTTATGGAAAAACTCT
1 GCTATTGCTTTACCTTTTACGGCGTTTATGGAAAAACACT
*
29555956 GCTGTTGCTTTACCTTTT
1 GCTATTGCTTTACCTTTT
29555974 GCGAAGTTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
40 56 0.69
41 20 0.25
43 5 0.06
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (40 bp):
GCTATTGCTTTACCTTTTACGGCGTTTATGGAAAAACACT
Found at i:29555974 original size:40 final size:40
Alignment explanation
Indices: 29555883--29555976 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 40
29555873 GTCGCCATTA
* * *
29555883 CTTTACCTTTTACTGCGTTTATGGGAAAACACTGCTATTG
1 CTTTACCTTTTGCGGCGTTTATGGAAAAACACTGCTATTG
* * *
29555923 CTTTACCTTTTGCGGTGTTTATGGAAAAACTCTGCTGTTG
1 CTTTACCTTTTGCGGCGTTTATGGAAAAACACTGCTATTG
29555963 CTTTACCTTTTGCG
1 CTTTACCTTTTGCG
29555977 AAGTTTTCGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (40 bp):
CTTTACCTTTTGCGGCGTTTATGGAAAAACACTGCTATTG
Found at i:29556935 original size:16 final size:17
Alignment explanation
Indices: 29556896--29556939 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
29556886 TTAAATTAAG
*
29556896 ATTTATTTTTTAATTTA
1 ATTTATTATTTAATTTA
*
29556913 ATGTATTATTT-ATTTA
1 ATTTATTATTTAATTTA
*
29556929 TTTTATTATTT
1 ATTTATTATTT
29556940 TTCACATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
ATTTATTATTTAATTTA
Found at i:29566222 original size:29 final size:31
Alignment explanation
Indices: 29566184--29566548 Score: 163
Period size: 29 Copynumber: 12.5 Consensus size: 31
29566174 TACCCGGGGT
**
29566184 AAAATGGTAA-TTTTGGATGCTTCGAGGG-A
1 AAAATGGTAATTTTTGGACACTTCGAGGGCA
* * *
29566213 AAAATGGTAATTTTTAGACACTTCGGGGGTA
1 AAAATGGTAATTTTTGGACACTTCGAGGGCA
* * *
29566244 AAAATGGTAATTTTTGGATACTT-GGGGGCG
1 AAAATGGTAATTTTTGGACACTTCGAGGGCA
* * *
29566274 AAAAT-ATAACTTTTGGACA-TTC-AGGGAGA
1 AAAATGGTAATTTTTGGACACTTCGAGGG-CA
*
29566303 AAAATGGTGATTTTTGGACAC-TCGAGGGCA
1 AAAATGGTAATTTTTGGACACTTCGAGGGCA
* * *
29566333 AAAATGGTAA-TTTTGGAAAATTTG-GGGTC-
1 AAAATGGTAATTTTTGGACACTTCGAGGG-CA
* * *
29566362 AAAATGG-AAATTTTAGA-AGTTCG-GGGTCA
1 AAAATGGTAATTTTTGGACACTTCGAGGG-CA
* * * **
29566391 AAAAT-G-AATTTTTGGA-AGTTTGGGGGTT
1 AAAATGGTAATTTTTGGACACTTCGAGGGCA
* *
29566419 AAAATGGTAA-TTTTGGAGAAATT--AGGGTCA
1 AAAATGGTAATTTTTGGA-CACTTCGAGGG-CA
* * * * *
29566449 AAAAT-GAAACTTTTAGA-AGTTCGAGGTCA
1 AAAATGGTAATTTTTGGACACTTCGAGGGCA
* * *
29566478 AAAATGG-AATTTTTAGA-AGTTCGAGGTC-
1 AAAATGGTAATTTTTGGACACTTCGAGGGCA
* * *
29566506 AAAATGG-AATTTTTGGA-AGTTTGGGGGTC-
1 AAAATGGTAATTTTTGGACACTTCGAGGG-CA
29566535 AAAATGGTAATTTT
1 AAAATGGTAATTTT
29566549 GGAAAATTTA
Statistics
Matches: 270, Mismatches: 43, Indels: 45
0.75 0.12 0.13
Matches are distributed among these distances:
28 61 0.23
29 107 0.40
30 73 0.27
31 29 0.11
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGACACTTCGAGGGCA
Found at i:29566244 original size:59 final size:58
Alignment explanation
Indices: 29566157--29566551 Score: 205
Period size: 59 Copynumber: 6.8 Consensus size: 58
29566147 AACGGAGTTG
* * * * *
29566157 AAAATGCAATTTTTGGATA-CCCGGGGTAAAATGGTAATTTTGGATGCTTCGAGGG-A
1 AAAATGTAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGATACTTCGAGGGCA
* * *
29566213 AAAATGGTAATTTTTAGACACTTCGGGGGTAAAAATGGTAATTTTTGGATACTT-GGGGGCG
1 AAAAT-GTAATTTTTGGACA-TTCGGGGGT-AAAATGGTAA-TTTTGGATACTTCGAGGGCA
* * * * * *
29566274 AAAATATAACTTTTGGACATTCAGGGAGAAAAATGGTGATTTTTGGACAC-TCGAGGGCA
1 AAAATGTAATTTTTGGACATTC-GGGGGTAAAATGGT-AATTTTGGATACTTCGAGGGCA
* * * * *
29566333 AAAATGGTAA-TTTTGGAAAATT-TGGGGTCAAAATGGAAATTTTAGA-AGTTCG-GGGTCA
1 AAAAT-GTAATTTTTGG-ACATTCGGGGGT-AAAATGGTAATTTTGGATACTTCGAGGG-CA
* * *
29566391 AAAATG-AATTTTTGGA-AGTTTGGGGGTTAAAATGGTAATTTTGGAGAAATT--AGGGTCA
1 AAAATGTAATTTTTGGACA-TTCGGGGG-TAAAATGGTAATTTTGGA-TACTTCGAGGG-CA
* * * * * * *
29566449 AAAATGAAACTTTTAGA-AGTTC-GAGGTCAAAAATGG-AATTTTTAGA-AGTTCGAGGTC-
1 AAAATGTAATTTTTGGACA-TTCGGGGGT--AAAATGGTAA-TTTTGGATACTTCGAGGGCA
* *
29566506 AAAATGGAATTTTTGGA-AGTTTGGGGGTCAAAATGGTAATTTTGGA
1 AAAATGTAATTTTTGGACA-TTCGGGGGT-AAAATGGTAATTTTGGA
29566552 AAATTTAGGG
Statistics
Matches: 266, Mismatches: 44, Indels: 57
0.72 0.12 0.16
Matches are distributed among these distances:
55 1 0.00
56 10 0.04
57 76 0.29
58 46 0.17
59 80 0.30
60 37 0.14
61 16 0.06
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (58 bp):
AAAATGTAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGATACTTCGAGGGCA
Found at i:29566278 original size:30 final size:30
Alignment explanation
Indices: 29566184--29566346 Score: 145
Period size: 30 Copynumber: 5.5 Consensus size: 30
29566174 TACCCGGGGT
**
29566184 AAAATGGTAA-TTTTGGATGCTTCGAGGG-A
1 AAAATGGTAATTTTTGGACACTT-GAGGGCA
* * *
29566213 AAAATGGTAATTTTTAGACACTTCGGGGGTA
1 AAAATGGTAATTTTTGGACACTT-GAGGGCA
* * *
29566244 AAAATGGTAATTTTTGGATACTTGGGGGCG
1 AAAATGGTAATTTTTGGACACTTGAGGGCA
* * * *
29566274 AAAAT-ATAACTTTTGGACA-TTCAGGGAGA
1 AAAATGGTAATTTTTGGACACTTGAGGG-CA
* *
29566303 AAAATGGTGATTTTTGGACACTCGAGGGCA
1 AAAATGGTAATTTTTGGACACTTGAGGGCA
29566333 AAAATGGTAATTTT
1 AAAATGGTAATTTT
29566347 GGAAAATTTG
Statistics
Matches: 107, Mismatches: 22, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
28 5 0.05
29 26 0.24
30 49 0.46
31 27 0.25
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGACACTTGAGGGCA
Found at i:29566403 original size:28 final size:29
Alignment explanation
Indices: 29566356--29566548 Score: 182
Period size: 29 Copynumber: 6.7 Consensus size: 29
29566346 TGGAAAATTT
*
29566356 GGGGTC-AAAATGGAAATTTTAGAAGTTC
1 GGGGTCAAAAATGGAATTTTTAGAAGTTC
* *
29566384 GGGGTCAAAAAT-GAATTTTTGGAAGTTTG
1 GGGGTCAAAAATGGAATTTTTAGAAG-TTC
* * *
29566413 GGGGT-TAAAATGGTAATTTTGGAGAAATT-
1 GGGGTCAAAAATGG-AATTTT-TAGAAGTTC
* * *
29566442 AGGGTCAAAAATGAAACTTTTAGAAGTTC
1 GGGGTCAAAAATGGAATTTTTAGAAGTTC
*
29566471 GAGGTCAAAAATGGAATTTTTAGAAGTTC
1 GGGGTCAAAAATGGAATTTTTAGAAGTTC
* * *
29566500 GAGGTC-AAAATGGAATTTTTGGAAGTTTG
1 GGGGTCAAAAATGGAATTTTTAGAAG-TTC
29566529 GGGGTC-AAAATGGTAATTTT
1 GGGGTCAAAAATGG-AATTTT
29566549 GGAAAATTTA
Statistics
Matches: 136, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
28 46 0.34
29 67 0.49
30 20 0.15
31 3 0.02
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (29 bp):
GGGGTCAAAAATGGAATTTTTAGAAGTTC
Found at i:29566452 original size:58 final size:57
Alignment explanation
Indices: 29566327--29566595 Score: 223
Period size: 58 Copynumber: 4.7 Consensus size: 57
29566317 TGGACACTCG
* * *
29566327 AGGG-CAAAAATGGTAA-TTTTGGAAAATTT-GGGGTCAAAATGGAAATTTT-AGAAGTT
1 AGGGTCAAAAAT-G-AATTTTTGG-AAGTTTGGGGGTCAAAATGGTAATTTTGAGAAATT
* *
29566383 CGGGGTCAAAAATGAATTTTTGGAAGTTTGGGGGTTAAAATGGTAATTTTGGAGAAATT
1 -AGGGTCAAAAATGAATTTTTGGAAGTTTGGGGGTCAAAATGGTAATTTT-GAGAAATT
* * * * * *
29566442 AGGGTCAAAAATGAAACTTTTAGAAG-TTCGAGGTCAAAAATGG-AATTTTTAGAAGTT
1 AGGGTCAAAAATG-AATTTTTGGAAGTTTGGGGGTC-AAAATGGTAATTTTGAGAAATT
*
29566499 CGAGGTC-AAAATGGAATTTTTGGAAGTTTGGGGGTCAAAATGGTAATTTTG-GAAAATTT
1 AG-GGTCAAAAAT-GAATTTTTGGAAGTTTGGGGGTCAAAATGGTAATTTTGAG-AAA-TT
* * **
29566558 AGGGTTAAAATAT-AATTTTTAGAAGTTTAAGGGTCAAA
1 AGGGTCAAAA-ATGAATTTTTGGAAGTTTGGGGGTCAAA
29566596 GTATGATTTT
Statistics
Matches: 172, Mismatches: 25, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
56 7 0.04
57 58 0.34
58 76 0.44
59 29 0.17
60 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.32
Consensus pattern (57 bp):
AGGGTCAAAAATGAATTTTTGGAAGTTTGGGGGTCAAAATGGTAATTTTGAGAAATT
Found at i:29566483 original size:87 final size:87
Alignment explanation
Indices: 29566333--29566548 Score: 264
Period size: 87 Copynumber: 2.5 Consensus size: 87
29566323 CTCGAGGGCA
* *
29566333 AAAATGGTAATTTTGGAAAATTTGGGGTCAAAATGGAAATTTTAGAAGTTCGGGGTCAAAAAT-G
1 AAAATGGTAATTTTGGAAAATTTAGGGTCAAAATGGAAATTTTAGAAGTTCGAGGTCAAAAATGG
*
29566397 AATTTTTGGAAGTTTGGGGGTT
66 AATTTTTAGAAGTTTGGGGGTT
29566419 AAAATGGTAATTTTGGAGAAA-TTAGGGTCAAAAAT-GAAACTTTTAGAAGTTCGAGGTCAAAAA
1 AAAATGGTAATTTTGGA-AAATTTAGGGTC-AAAATGGAAA-TTTTAGAAGTTCGAGGTCAAAAA
* * *
29566482 TGGAATTTTTAGAAG-TTCGAGGTC
63 TGGAATTTTTAGAAGTTTGGGGGTT
* * *
29566506 AAAATGG-AATTTTTGG-AAGTTTGGGGGTCAAAATGGTAATTTT
1 AAAATGGTAA-TTTTGGAAAATTT-AGGGTCAAAATGGAAATTTT
29566549 GGAAAATTTA
Statistics
Matches: 113, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
85 2 0.02
86 41 0.36
87 58 0.51
88 12 0.11
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.33
Consensus pattern (87 bp):
AAAATGGTAATTTTGGAAAATTTAGGGTCAAAATGGAAATTTTAGAAGTTCGAGGTCAAAAATGG
AATTTTTAGAAGTTTGGGGGTT
Found at i:29566549 original size:29 final size:28
Alignment explanation
Indices: 29566333--29566552 Score: 178
Period size: 29 Copynumber: 7.6 Consensus size: 28
29566323 CTCGAGGGCA
* *
29566333 AAAATGGTAA-TTTTGGAAAATTTGGGGTC
1 AAAATGG-AATTTTTGG-AAGTTCGGGGTC
* *
29566362 AAAATGGAAATTTTAGAAGTTCGGGGTC
1 AAAATGGAATTTTTGGAAGTTCGGGGTC
* *
29566390 AAAAAT-GAATTTTTGGAAGTTTGGGGGTT
1 -AAAATGGAATTTTTGGAAG-TTCGGGGTC
* * *
29566419 AAAATGGTAATTTTGGAGAAATT-AGGGTC
1 AAAATGG-AATTTTTG-GAAGTTCGGGGTC
* * * *
29566448 AAAAATGAAACTTTTAGAAGTTCGAGGTC
1 -AAAATGGAATTTTTGGAAGTTCGGGGTC
* *
29566477 AAAAATGGAATTTTTAGAAGTTCGAGGTC
1 -AAAATGGAATTTTTGGAAGTTCGGGGTC
*
29566506 AAAATGGAATTTTTGGAAGTTTGGGGGTC
1 AAAATGGAATTTTTGGAAG-TTCGGGGTC
29566535 AAAATGGTAA-TTTTGGAA
1 AAAATGG-AATTTTTGGAA
29566553 AATTTAGGGT
Statistics
Matches: 158, Mismatches: 23, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
28 51 0.32
29 87 0.55
30 17 0.11
31 3 0.02
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTC
Found at i:29566577 original size:29 final size:29
Alignment explanation
Indices: 29566502--29566611 Score: 80
Period size: 29 Copynumber: 3.8 Consensus size: 29
29566492 AGAAGTTCGA
** * * **
29566502 GGTCAAAATGGAATTTTTGGAAGTTTGGG
1 GGTCAAAATATAATTTTTGAAAATTTAAG
* *
29566531 GGTCAAAATGGTAATTTTGGAAAATTT-AG
1 GGTCAAAAT-ATAATTTTTGAAAATTTAAG
* *
29566560 GGTTAAAATATAATTTTT-AGAAGTTTAAG
1 GGTCAAAATATAATTTTTGA-AAATTTAAG
* *
29566589 GGTCAAAGTATGATTTTTGAAAA
1 GGTCAAAATATAATTTTTGAAAA
29566612 GTTCAGGGAC
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
27 1 0.02
28 12 0.19
29 37 0.58
30 14 0.22
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
GGTCAAAATATAATTTTTGAAAATTTAAG
Found at i:29566593 original size:116 final size:116
Alignment explanation
Indices: 29566357--29566595 Score: 344
Period size: 116 Copynumber: 2.1 Consensus size: 116
29566347 GGAAAATTTG
* *
29566357 GGGTC-AAAATGGAAATTTTAGAAGTTCGGGGTCAAAAATGAATTTTTGGAAGTTTGGGGGTTAA
1 GGGTCAAAAATGGAAATTTTAGAAGTTCGAGGTCAAAAATGAATTTTTGGAAGTTTGGGGGTCAA
*
29566421 AATGGTAATTTTGGAGAAATTAGGGTCAAAAATGAAACTTTTAGAAGTTCGA
66 AATGGTAATTTTGGAGAAATTAGGGTCAAAAAT-AAACTTTTAGAAGTTCAA
*
29566473 -GGTCAAAAATGGAATTTTTAGAAGTTCGAGGTC-AAAATGGAATTTTTGGAAGTTTGGGGGTCA
1 GGGTCAAAAATGGAAATTTTAGAAGTTCGAGGTCAAAAAT-GAATTTTTGGAAGTTTGGGGGTCA
* * *
29566536 AAATGGTAATTTTGGA-AAATTTAGGGT-TAAAATATAATTTTTAGAAGTTTAA
65 AAATGGTAATTTTGGAGAAA-TTAGGGTCAAAAATA-AACTTTTAGAAGTTCAA
29566588 GGGTCAAA
1 GGGTCAAA
29566596 GTATGATTTT
Statistics
Matches: 111, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
114 1 0.01
115 31 0.28
116 79 0.71
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (116 bp):
GGGTCAAAAATGGAAATTTTAGAAGTTCGAGGTCAAAAATGAATTTTTGGAAGTTTGGGGGTCAA
AATGGTAATTTTGGAGAAATTAGGGTCAAAAATAAACTTTTAGAAGTTCAA
Found at i:29568543 original size:12 final size:12
Alignment explanation
Indices: 29568526--29568550 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29568516 ACATTTTGTA
29568526 ATTTGGACTTTT
1 ATTTGGACTTTT
29568538 ATTTGGACTTTT
1 ATTTGGACTTTT
29568550 A
1 A
29568551 ACGTTTAAAT
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:0.08, G:0.16, T:0.56
Consensus pattern (12 bp):
ATTTGGACTTTT
Found at i:29568593 original size:5 final size:6
Alignment explanation
Indices: 29568554--29568657 Score: 51
Period size: 6 Copynumber: 18.5 Consensus size: 6
29568544 ACTTTTAACG
* * **
29568554 TTTAAA TTTAAC TTGAAA --TAAA TTTAAA TTTAAA -TTAAA TCCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * * *
29568599 CTCAAA -ATAAG TTCAAA TTTAAA -GTAAA TTCAAA TTTAAA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
29568643 TTTAGA TTTAAA TTT
1 TTTAAA TTTAAA TTT
29568658 TAAAAATGGG
Statistics
Matches: 70, Mismatches: 21, Indels: 14
0.67 0.20 0.13
Matches are distributed among these distances:
4 7 0.10
5 11 0.16
6 52 0.74
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (6 bp):
TTTAAA
Found at i:29568608 original size:34 final size:33
Alignment explanation
Indices: 29568569--29568656 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 33
29568559 ATTTAACTTG
29568569 AAATAAATTTAAATTTAAATTAAATCCAAACTCA
1 AAATAAATTTAAATTTAAATTAAATCCAAA-TCA
* * * * **
29568603 AAATAAGTTCAAATTTAAAGTAAATTCAAATTT
1 AAATAAATTTAAATTTAAATTAAATCCAAATCA
*
29568636 AAATAAATTTAGATTTAAATT
1 AAATAAATTTAAATTTAAATT
29568657 TTAAAAATGG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 18 0.41
34 26 0.59
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.36
Consensus pattern (33 bp):
AAATAAATTTAAATTTAAATTAAATCCAAATCA
Found at i:29568630 original size:17 final size:16
Alignment explanation
Indices: 29568569--29568655 Score: 84
Period size: 17 Copynumber: 5.2 Consensus size: 16
29568559 ATTTAACTTG
*
29568569 AAATAAATTTAAATTT
1 AAATAAATTCAAATTT
* **
29568585 AAATTAAATCCAAACTCA
1 AAA-TAAATTCAAA-TTT
*
29568603 AAATAAGTTCAAATTT
1 AAATAAATTCAAATTT
29568619 AAAGTAAATTCAAATTT
1 AAA-TAAATTCAAATTT
* *
29568636 AAATAAATTTAGATTT
1 AAATAAATTCAAATTT
29568652 AAAT
1 AAAT
29568656 TTTAAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
16 22 0.39
17 31 0.54
18 4 0.07
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (16 bp):
AAATAAATTCAAATTT
Found at i:29582459 original size:20 final size:21
Alignment explanation
Indices: 29582436--29582474 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29582426 TTGTTATTTG
29582436 ATTGTT-AT-TTTCTATTTTTT
1 ATTGTTCATATTTC-ATTTTTT
29582456 ATTGTTCATATTTCATTTT
1 ATTGTTCATATTTCATTTT
29582475 GTAACAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.69
Consensus pattern (21 bp):
ATTGTTCATATTTCATTTTTT
Found at i:29584586 original size:52 final size:51
Alignment explanation
Indices: 29584527--29584751 Score: 290
Period size: 52 Copynumber: 4.3 Consensus size: 51
29584517 ATTATGAGCT
*
29584527 ATCGTGAGTATATGAATCCTTTACGGATTAAATGGTTCGATGACTAAGTGTC
1 ATCGTGAGTATATGAATCCTTTACGGATTAAA-GGTCCGATGACTAAGTGTC
* * *
29584579 ATCGTGAGTATATGAATCCTTTACGGATTAAACAGCCCGATGACTAAGTGCC
1 ATCGTGAGTATATGAATCCTTTACGGATTAAA-GGTCCGATGACTAAGTGTC
* **
29584631 ATCGTGAGTATATGTATCCTTTACGGATTAAGAGGTCCGATGACTCTGTGTC
1 ATCGTGAGTATATGAATCCTTTACGGATTAA-AGGTCCGATGACTAAGTGTC
* * * * *
29584683 ATCGTGAGTATACGAATCCCTTGCGGATTATAAGGTCC-AGTGGCTATGTGTC
1 ATCGTGAGTATATGAATCCTTTACGGATTA-AAGGTCCGA-TGACTAAGTGTC
29584735 ATCGTGAGTATATGAAT
1 ATCGTGAGTATATGAAT
29584752 GAAGTGAAAT
Statistics
Matches: 152, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
51 1 0.01
52 149 0.98
53 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (51 bp):
ATCGTGAGTATATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTGTC
Found at i:29592353 original size:24 final size:24
Alignment explanation
Indices: 29592326--29592407 Score: 137
Period size: 24 Copynumber: 3.4 Consensus size: 24
29592316 AGCCCACACG
*
29592326 AGCCCAAAATGGTTAGCTCTTACA
1 AGCCCAGAATGGTTAGCTCTTACA
*
29592350 AGCCCAGAATGGTTAGCTCTTACG
1 AGCCCAGAATGGTTAGCTCTTACA
*
29592374 AGCCTAGAATGGTTAGCTCTTACA
1 AGCCCAGAATGGTTAGCTCTTACA
29592398 AGCCCAGAAT
1 AGCCCAGAAT
29592408 CAGAATAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (24 bp):
AGCCCAGAATGGTTAGCTCTTACA
Found at i:29592441 original size:27 final size:27
Alignment explanation
Indices: 29592388--29592490 Score: 125
Period size: 27 Copynumber: 3.8 Consensus size: 27
29592378 TAGAATGGTT
* *
29592388 AGCTCTTACAAGCCCAGAATCAGAATAA
1 AGCTCTTTCAAG-CCAGAATCAAAATAA
*
29592416 TGCTCTTTCAAGCCAGAATCAAAATAA
1 AGCTCTTTCAAGCCAGAATCAAAATAA
* * *
29592443 AGCTCTTTCGAGCTAGAATCACAATAA
1 AGCTCTTTCAAGCCAGAATCAAAATAA
* *
29592470 CGCTCTTTCGAGCCAGAATCA
1 AGCTCTTTCAAGCCAGAATCA
29592491 GATTACTCCT
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 56 0.85
28 10 0.15
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (27 bp):
AGCTCTTTCAAGCCAGAATCAAAATAA
Found at i:29598843 original size:26 final size:26
Alignment explanation
Indices: 29598801--29598854 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
29598791 ATTCTGGGCG
29598801 CAATTCTAGACACGTTCATGCAGCGA
1 CAATTCTAGACACGTTCATGCAGCGA
*
29598827 CAATTCT-GTACATGTTCATGCAGCGA
1 CAATTCTAG-ACACGTTCATGCAGCGA
29598853 CA
1 CA
29598855 TTCCTGGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (26 bp):
CAATTCTAGACACGTTCATGCAGCGA
Found at i:29617497 original size:59 final size:59
Alignment explanation
Indices: 29617406--29617776 Score: 539
Period size: 59 Copynumber: 6.2 Consensus size: 59
29617396 ACCCGAGGGC
29617406 AAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
* * **
29617464 AAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAATCTTCGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
* * *
29617523 -AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGAGGGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
* **
29617581 AACATGGTAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGAGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTC--GGGGGT
* * * *
29617642 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAGTTTCAGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
* *
29617701 AACATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTC---GGGGGT
29617763 AAAATGGTAATTTT
1 AAAATGGTAATTTT
29617777 TGAAAGTTTT
Statistics
Matches: 278, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
58 68 0.24
59 140 0.50
61 52 0.19
62 18 0.06
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
Found at i:29617688 original size:120 final size:119
Alignment explanation
Indices: 29617406--29617776 Score: 570
Period size: 120 Copynumber: 3.1 Consensus size: 119
29617396 ACCCGAGGGC
* * * *
29617406 AAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATG
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGAGGGTAACATG
* * **
29617470 GTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAATCTTC-GGGGGT
66 GTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGGT
29617523 -AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGAGGGTAACATG
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGAGGGTAACATG
**
29617587 GTAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGAGGGGGT
66 GTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCG-GGGGGT
*
29617642 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAGTTTC-AGGGGTAACAT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGA-GGGTAACAT
*
29617706 GGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGGGGT
65 GGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTC--GGGGGGT
29617763 AAAATGGTAATTTT
1 AAAATGGTAATTTT
29617777 TGAAAGTTTT
Statistics
Matches: 233, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
116 13 0.06
117 87 0.37
119 7 0.03
120 105 0.45
121 20 0.09
122 1 0.00
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (119 bp):
AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGAGGGTAACATG
GTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGGT
Found at i:29617813 original size:30 final size:30
Alignment explanation
Indices: 29617763--29617869 Score: 137
Period size: 30 Copynumber: 3.5 Consensus size: 30
29617753 CGGGGGGGGT
*
29617763 AAAATGGTAATTTTTG-AAAGTTTTGAGGTC
1 AAAAT-GTAATTTTGGAAAAGTTTTGAGGTC
*
29617793 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGAGGTC
* *
29617823 AAAATATAATTTTGGAAAAATTTT-AGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGA-GGTC
29617853 AAAATGTAATTTCTGGA
1 AAAATGTAATTT-TGGA
29617870 CAATTTAGGG
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
29 9 0.13
30 55 0.81
31 4 0.06
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTGAGGTC
Found at i:29617836 original size:120 final size:117
Alignment explanation
Indices: 29617406--29617837 Score: 421
Period size: 120 Copynumber: 3.6 Consensus size: 117
29617396 ACCCGAGGGC
* * * * *
29617406 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGG
1 AAAATGGTAATTTT-GTGAAATCGAGGTTAAAAATGAAATTTTAAAAGTTTCAGGGGTAAAATGA
* ** * **
29617471 TAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAATCTTC--GGGGGT
65 TAATTTT-GGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGAGGGGGT
* * * *
29617523 -AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTC-GAGGGTAACAT
1 AAAATGGTAATTTT--GTGAAATCGAGGTTAAAAATGAAATTTTAAAAGTTTCAG-GGGTAAAAT
*
29617586 GGTAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGAGGGGGT
63 GATAATTTT-GGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGAGGGGGT
* * *
29617642 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAGTTTCAGGGGTAACATG
1 AAAATGGTAATTTT--GTGAAATCGAGGTTAAAAATGAAATTTTAAAAGTTTCAGGGGTAAAATG
* ** *
29617707 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGGGGT
64 ATAA-TTTTGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTC-GAGGGGGT
* * * *
29617763 AAAATGGTAATTTT-TGAAAGTTTTGAGG-TCAAAATGTAATTTTGGAAAAGTTT-TGGGGTCAA
1 AAAATGGTAATTTTGTGAAA---TCGAGGTTAAAAATGAAATTTT--AAAAGTTTCAGGGGT-AA
29617825 AAT-ATAATTTTGG
60 AATGATAATTTTGG
29617838 AAAAATTTTA
Statistics
Matches: 280, Mismatches: 21, Indels: 25
0.86 0.06 0.08
Matches are distributed among these distances:
116 14 0.05
117 86 0.31
118 5 0.02
119 6 0.02
120 120 0.43
121 38 0.14
122 11 0.04
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (117 bp):
AAAATGGTAATTTTGTGAAATCGAGGTTAAAAATGAAATTTTAAAAGTTTCAGGGGTAAAATGAT
AATTTTGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGAGGGGGT
Found at i:29617875 original size:30 final size:29
Alignment explanation
Indices: 29617759--29617879 Score: 131
Period size: 30 Copynumber: 4.1 Consensus size: 29
29617749 GATTCGGGGG
* *
29617759 GGGT-AAAATGGTAATTTTTGAAAGTTTT-
1 GGGTCAAAAT-GTAATTTTGGAAAATTTTA
*
29617787 GAGGTCAAAATGTAATTTTGGAAAAGTTTTG
1 G-GGTCAAAATGTAATTTTGGAAAA-TTTTA
*
29617818 GGGTCAAAATATAATTTTGGAAAAATTTTA
1 GGGTCAAAATGTAATTTTGG-AAAATTTTA
*
29617848 GGGTCAAAATGTAATTTCTGGACAA-TTTA
1 GGGTCAAAATGTAATTT-TGGAAAATTTTA
29617877 GGG
1 GGG
29617880 ACTTACAAAG
Statistics
Matches: 81, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.01
29 22 0.27
30 50 0.62
31 8 0.10
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGGAAAATTTTA
Found at i:29618209 original size:161 final size:162
Alignment explanation
Indices: 29617940--29618285 Score: 475
Period size: 161 Copynumber: 2.1 Consensus size: 162
29617930 GTATCTAGAG
* * *
29617940 GTCAAGGGACTAATTTGA-AAACCTTGAAAAATTTTTGGACCAATTTTGTAATTAAATAAAAGTT
1 GTCAAAGGACTAATTT-ATAAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTT
* * *
29618004 AATTCAAGGACTAAATGAAAATAAATTAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAAAA-
65 AATTCAAGGACTAAATGAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAC
*
29618068 ATTGACACGTGGCAACCTCTGGTGCAGTCAAACA
130 A-TGACACGTGGCAACCTCTGGTACAGTCAAACA
* *
29618102 GTCAAAGGACTAGTTTATAAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAA-ATAAAGTT
1 GTCAAAGGACTAATTTATAAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATA-AAAGTT
* ** * * * *
29618166 GATT-TGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAC
65 AATTCAAGGACTAAATGAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAC
*
29618230 ATGACACGTGGCAATCTCTGGTACAGTCAAACA
130 ATGACACGTGGCAACCTCTGGTACAGTCAAACA
*
29618263 GTCAAAGGACTAAATTATAAACC
1 GTCAAAGGACTAATTTATAAACC
29618286 AATTAAAATT
Statistics
Matches: 162, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
161 103 0.64
162 59 0.36
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (162 bp):
GTCAAAGGACTAATTTATAAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTTA
ATTCAAGGACTAAATGAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAACA
TGACACGTGGCAACCTCTGGTACAGTCAAACA
Found at i:29618358 original size:161 final size:160
Alignment explanation
Indices: 29618009--29618358 Score: 386
Period size: 161 Copynumber: 2.2 Consensus size: 160
29617999 AAGTTAATTC
* * * *
29618009 AAGGACTAAATGAAAATAAATTAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAAAAATTGAC
1 AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
* ** **
29618074 ACGTGGCAACCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTGAAAAATTATTG
66 ACGTGGCAACCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCTT-AAAAATTACAG
** * * * **
29618139 GGCCAATTTCGTAATTAAAATAAAGTTGATT
130 GGAAAATTTCGCAAATAAAATAAAGATGAAA
** * * *
29618170 TGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAACA-TGA
1 AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAA-ATTGA
*
29618234 CACGTGGCAATCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCAATT-AAAATTAC
65 CACGTGGCAACCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACC--TTAAAAATTAC
29618298 AGGGAAAATTT-GCAAATAATTAA-AAAGATGCAAA
128 AGGGAAAATTTCGCAAATAA--AATAAAGATG-AAA
* *
29618332 AAGGACTAAATTGAAGCAAA-TAAAAAT
1 AAGGACTAAATTAAAACAAATTAAAAAT
29618359 GCGGAAGGAT
Statistics
Matches: 156, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
160 6 0.04
161 129 0.83
162 19 0.12
163 2 0.01
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.23
Consensus pattern (160 bp):
AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
ACGTGGCAACCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCTTAAAAATTACAGG
GAAAATTTCGCAAATAAAATAAAGATGAAA
Found at i:29619735 original size:14 final size:14
Alignment explanation
Indices: 29619716--29619758 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
29619706 TTGGGCCTAT
29619716 TTGGGCCATTGTAA
1 TTGGGCCATTGTAA
29619730 TTGGGCC-TT-TAA
1 TTGGGCCATTGTAA
29619742 TTTGGGCCATTGTAA
1 -TTGGGCCATTGTAA
29619757 TT
1 TT
29619759 TGGACCGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 9 0.35
14 11 0.42
15 3 0.12
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.42
Consensus pattern (14 bp):
TTGGGCCATTGTAA
Found at i:29619759 original size:15 final size:15
Alignment explanation
Indices: 29619714--29619761 Score: 75
Period size: 13 Copynumber: 3.4 Consensus size: 15
29619704 CATTGGGCCT
29619714 ATTTGGGCCATTGTA
1 ATTTGGGCCATTGTA
29619729 A-TTGGGCC-TT-TA
1 ATTTGGGCCATTGTA
29619741 ATTTGGGCCATTGTA
1 ATTTGGGCCATTGTA
29619756 ATTTGG
1 ATTTGG
29619762 ACCGAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.10
13 9 0.30
14 9 0.30
15 9 0.30
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (15 bp):
ATTTGGGCCATTGTA
Found at i:29619854 original size:6 final size:6
Alignment explanation
Indices: 29619845--29619935 Score: 54
Period size: 6 Copynumber: 15.8 Consensus size: 6
29619835 ACTTTTCTTT
*
29619845 TTTAAA TTTATAA --TAATA TT-AAA TTTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA
* * *
29619892 TTTAAA -TTGAA TTTAAA -GTAAA TTTAAGA -TTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAA
29619936 TTTTCAAATG
Statistics
Matches: 66, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
4 1 0.02
5 23 0.35
6 36 0.55
7 6 0.09
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:29619889 original size:17 final size:16
Alignment explanation
Indices: 29619846--29619938 Score: 73
Period size: 17 Copynumber: 5.5 Consensus size: 16
29619836 CTTTTCTTTT
29619846 TTAAATTTATAA-TAATA
1 TTAAATTTA-AATTAA-A
29619863 TTAAATTTTAAATTAAA
1 TTAAA-TTTAAATTAAA
29619880 TTCAAATTTAAATTTAAA
1 TT-AAATTTAAA-TTAAA
* *
29619898 TTGAATTTAAAGTAAA
1 TTAAATTTAAATTAAA
*
29619914 TTTAAGA-TTAAAATAAA
1 -TTAA-ATTTAAATTAAA
*
29619931 TTTAATTT
1 TTAAATTT
29619939 TCAAATGGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.02
16 9 0.14
17 36 0.56
18 18 0.28
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:29619904 original size:11 final size:11
Alignment explanation
Indices: 29619862--29619938 Score: 75
Period size: 11 Copynumber: 6.8 Consensus size: 11
29619852 TTATAATAAT
29619862 ATTAAATTTTAA
1 ATTAAA-TTTAA
*
29619874 ATTAAATTCAA
1 ATTAAATTTAA
29619885 ATTTAAATTTAA
1 A-TTAAATTTAA
*
29619897 ATTGAATTTAA
1 ATTAAATTTAA
*
29619908 AGTAAATTTAA
1 ATTAAATTTAA
*
29619919 GATTAAA-ATAA
1 -ATTAAATTTAA
*
29619930 ATTTAATTT
1 ATTAAATTT
29619939 TCAAATGGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.09
11 27 0.51
12 21 0.40
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:29621440 original size:58 final size:58
Alignment explanation
Indices: 29621360--29621496 Score: 179
Period size: 58 Copynumber: 2.3 Consensus size: 58
29621350 AATTTTTACT
* * *
29621360 AATTCATATTTTAATAAAAATTATATTAAAAATATTATTAAATTACA-TATTATT-TTATTA
1 AATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTA-ATTAATATTATTATTA
* *
29621420 AATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAATTAATATTATTATTA
1 AATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAATATTATTATTA
29621478 AATTATATTTAATAATAAT
1 AATTATATTTAATAATAAT
29621497 CATTAAAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
56 1 0.01
57 22 0.32
58 40 0.58
59 2 0.03
60 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (58 bp):
AATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAATATTATTATTA
Found at i:29621460 original size:21 final size:22
Alignment explanation
Indices: 29621436--29621503 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 22
29621426 ATTTAATAAT
*
29621436 AATTATGTTAA-AATATAATTA
1 AATTATATTAATAATATAATTA
* *
29621457 AATTA-ATTAATATTATTATTA
1 AATTATATTAATAATATAATTA
*
29621478 AATTATATTTAATAATAATCATTA
1 AATTATA-TTAATAAT-ATAATTA
29621502 AA
1 AA
29621504 ATTTAATAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.11
21 18 0.47
22 1 0.03
23 7 0.18
24 8 0.21
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (22 bp):
AATTATATTAATAATATAATTA
Found at i:29621493 original size:26 final size:26
Alignment explanation
Indices: 29621410--29621494 Score: 66
Period size: 31 Copynumber: 3.1 Consensus size: 26
29621400 AATTACATAT
*
29621410 TATT-TTATTAAATTGTATTTAATAA
1 TATTATTATTAAATTATATTTAATAA
* *
29621435 TAATTATGT-TAAAATATAATTAAATTAATTAA
1 T-ATTAT-TATTAAAT-T-A-T-ATTTAA-TAA
29621467 TATTATTATTAAATTATATTTAATAA
1 TATTATTATTAAATTATATTTAATAA
29621493 TA
1 TA
29621495 ATCATTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 17
0.68 0.07 0.25
Matches are distributed among these distances:
25 1 0.02
26 8 0.17
27 11 0.24
28 3 0.07
29 1 0.02
30 3 0.07
31 15 0.33
32 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TATTATTATTAAATTATATTTAATAA
Found at i:29621681 original size:46 final size:44
Alignment explanation
Indices: 29621591--29621684 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
29621581 ATTACAGCAT
* *
29621591 CATTCCATTTAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATTATTACAGCTCTATTC
*
29621635 CATTCCAATCAACCAAACA-ATTGAATTATTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TATT-ATTACAGCTCTATTC
29621681 CATT
1 CATT
29621685 ACAGTTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 20 0.45
45 4 0.09
46 19 0.43
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.33
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATTATTACAGCTCTATTC
Found at i:29621687 original size:16 final size:16
Alignment explanation
Indices: 29621666--29621721 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
29621656 TGAATTATTG
29621666 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
29621682 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
* *
29621698 ATTACACCTATATTCC
1 ATTACAGCTCTATTCC
29621714 ATTACAGC
1 ATTACAGC
29621722 GAACCAAACG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:29624279 original size:82 final size:82
Alignment explanation
Indices: 29624137--29624291 Score: 220
Period size: 82 Copynumber: 1.9 Consensus size: 82
29624127 ACGAATACTG
* * * * * * * *
29624137 AATTGTGGACCCTTTCGATGGCTGAGTCTTCGCGTATGTTATGAATTCTTATCAACTTGTGTGAG
1 AATTCTGGACCATATCGATCGCTGAGTCTTCGCGTATGTCACGAATTCTCATCAACTTGTGTAAG
29624202 CAACATCGAGAGTGAGA
66 CAACATCGAGAGTGAGA
*
29624219 AATTCTGGACCATATCGATCGCTGAGTCTTCGCGTATGTCGCGAATTCTCATCAACTTGTGTAAG
1 AATTCTGGACCATATCGATCGCTGAGTCTTCGCGTATGTCACGAATTCTCATCAACTTGTGTAAG
*
29624284 CAGCATCG
66 CAACATCG
29624292 TATACTAGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (82 bp):
AATTCTGGACCATATCGATCGCTGAGTCTTCGCGTATGTCACGAATTCTCATCAACTTGTGTAAG
CAACATCGAGAGTGAGA
Found at i:29624363 original size:24 final size:24
Alignment explanation
Indices: 29624301--29624400 Score: 94
Period size: 24 Copynumber: 4.1 Consensus size: 24
29624291 GTATACTAGT
*
29624301 TAACTATTCTAGGCTTGTAAGAGC
1 TAACTATTCTAGGCTCGTAAGAGC
* * * *
29624325 TAACCATTTTGGGCTCATAAGAGC
1 TAACTATTCTAGGCTCGTAAGAGC
* *
29624349 TAACTATCCTAGGCTCGTGAGAGC
1 TAACTATTCTAGGCTCGTAAGAGC
* *
29624373 TAA-TATTGTCTAAGCTCGTATGAGC
1 TAACTA-T-TCTAGGCTCGTAAGAGC
29624398 TAA
1 TAA
29624401 AATTTGGAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
23 2 0.03
24 41 0.69
25 16 0.27
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (24 bp):
TAACTATTCTAGGCTCGTAAGAGC
Found at i:29629959 original size:11 final size:11
Alignment explanation
Indices: 29629943--29629989 Score: 94
Period size: 11 Copynumber: 4.3 Consensus size: 11
29629933 AGCTTCTATC
29629943 TTTAATAAGTT
1 TTTAATAAGTT
29629954 TTTAATAAGTT
1 TTTAATAAGTT
29629965 TTTAATAAGTT
1 TTTAATAAGTT
29629976 TTTAATAAGTT
1 TTTAATAAGTT
29629987 TTT
1 TTT
29629990 TTTTTTTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (11 bp):
TTTAATAAGTT
Found at i:29634807 original size:149 final size:149
Alignment explanation
Indices: 29634530--29634819 Score: 499
Period size: 149 Copynumber: 1.9 Consensus size: 149
29634520 GTCCTCATGG
*
29634530 ACTTCTTCTAGGATTTTCTTGGCTTCGATAGTGTCCACACATCTTTGTAACACCTGATCCTTTCT
1 ACTTCTTCTAGGATTTTCTTGGCTTCGATAGTGTCCACACATCTTAGTAACACCTGATCCTTTCT
*
29634595 CTTTTTGTATAAGATCTCTCCATCTAGGACATACTCATTTGTCAACCTTCTTATCGTCCTTTTAT
66 CTTTTTATATAAGATCTCTCCATCTAGGACATACTCATTTGTCAACCTTCTTATCGTCCTTTTAT
29634660 CATTCAAGATTGTTTATGT
131 CATTCAAGATTGTTTATGT
* ** *
29634679 ACTTTTTCTAGGATTTTCTTGGCTTCGATAGTGTCCATGCATCTTAGTAACACTTGATCCTTTCT
1 ACTTCTTCTAGGATTTTCTTGGCTTCGATAGTGTCCACACATCTTAGTAACACCTGATCCTTTCT
* * *
29634744 CTTTTTATATAGGATCTCTCCGTCTAGGACATACTCATTTGTCAACCTTCTTATCGTCTTTTTAT
66 CTTTTTATATAAGATCTCTCCATCTAGGACATACTCATTTGTCAACCTTCTTATCGTCCTTTTAT
29634809 CATTCAAGATT
131 CATTCAAGATT
29634820 ATTTGCTTAG
Statistics
Matches: 132, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
149 132 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (149 bp):
ACTTCTTCTAGGATTTTCTTGGCTTCGATAGTGTCCACACATCTTAGTAACACCTGATCCTTTCT
CTTTTTATATAAGATCTCTCCATCTAGGACATACTCATTTGTCAACCTTCTTATCGTCCTTTTAT
CATTCAAGATTGTTTATGT
Found at i:29640634 original size:9 final size:9
Alignment explanation
Indices: 29640599--29640641 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
29640589 GATTGCAACA
*
29640599 ATGATGAGA
1 ATGATGAGG
*
29640608 ATGATGATG
1 ATGATGAGG
*
29640617 ACGATGAGG
1 ATGATGAGG
29640626 ATGATGAGG
1 ATGATGAGG
*
29640635 AAGATGA
1 ATGATGA
29640642 TTCTTTGATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.40, C:0.02, G:0.37, T:0.21
Consensus pattern (9 bp):
ATGATGAGG
Found at i:29642607 original size:24 final size:21
Alignment explanation
Indices: 29642580--29642646 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
29642570 AAGAAAAAAG
29642580 TTTATATATTATTAAAATTATTGT
1 TTTATATATT-TTAAAATT-TT-T
* *
29642604 TTTAAATATTTTTATAATTTTT
1 TTTATATA-TTTTAAAATTTTT
*
29642626 TTTATAAAGTTTTAAAATTTT
1 TTTATATA-TTTTAAAATTTT
29642647 ATCAAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 18 0.50
23 2 0.06
24 14 0.39
25 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (21 bp):
TTTATATATTTTAAAATTTTT
Found at i:29643755 original size:33 final size:33
Alignment explanation
Indices: 29643718--29643787 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
29643708 TTTCAATTTA
* * *
29643718 TCTCATTTCAGTGTTTTCAACTATCTTATTTTC
1 TCTCATTTAAGGGTTTTAAACTATCTTATTTTC
* *
29643751 TCTCATTTAAGGGTTTTAAATTATTTTATTTTC
1 TCTCATTTAAGGGTTTTAAACTATCTTATTTTC
29643784 TCTC
1 TCTC
29643788 CCTTCAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.56
Consensus pattern (33 bp):
TCTCATTTAAGGGTTTTAAACTATCTTATTTTC
Found at i:29644484 original size:14 final size:14
Alignment explanation
Indices: 29644462--29644495 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29644452 TATAACAACA
*
29644462 ACATCCATAATTAT
1 ACATTCATAATTAT
*
29644476 ACATTCATAGTTAT
1 ACATTCATAATTAT
29644490 ACATTC
1 ACATTC
29644496 TTTATTAAAT
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:0.21, G:0.03, T:0.38
Consensus pattern (14 bp):
ACATTCATAATTAT
Found at i:29645149 original size:29 final size:29
Alignment explanation
Indices: 29645111--29645186 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
29645101 TTTTAAAAAT
* *
29645111 AAAATATATTTAACATATTGATAAATATA
1 AAAATATATTTAACATAATGACAAATATA
29645140 AAAATATATTTTAACATAATGACAAATATA
1 AAAATATA-TTTAACATAATGACAAATATA
* * *
29645170 TATATATATTTATCATA
1 AAAATATATTTAACATA
29645187 CAATTACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATATATTTAACATAATGACAAATATA
Found at i:29651310 original size:21 final size:22
Alignment explanation
Indices: 29651286--29651334 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
29651276 ATAATAATAA
* *
29651286 ATAATTTATTCATATT-TTAAC
1 ATAATTTAATAATATTCTTAAC
*
29651307 ATAATTTAATAATATTCTTAAT
1 ATAATTTAATAATATTCTTAAC
29651329 ATAATT
1 ATAATT
29651335 ATTATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATTTAATAATATTCTTAAC
Found at i:29655295 original size:19 final size:19
Alignment explanation
Indices: 29655256--29655296 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
29655246 ACAAAAATTA
* *
29655256 CATAGAGAAAGGGTATTTG
1 CATAGAGAAAGGGCATCTG
29655275 CATAGAGAAAGGGCATCTG
1 CATAGAGAAAGGGCATCTG
29655294 CAT
1 CAT
29655297 GCAACAGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (19 bp):
CATAGAGAAAGGGCATCTG
Found at i:29661420 original size:18 final size:19
Alignment explanation
Indices: 29661392--29661496 Score: 103
Period size: 18 Copynumber: 5.8 Consensus size: 19
29661382 CGAAAGGATT
29661392 AGCATACTGGCTCGTTTTG
1 AGCATACTGGCTCGTTTTG
*
29661411 -GCATATTGGCTCG-TTTG
1 AGCATACTGGCTCGTTTTG
* *
29661428 AGCATACTGGCTC-ATTGG
1 AGCATACTGGCTCGTTTTG
* *
29661446 AGCATAGTGGCTCGTTCT-
1 AGCATACTGGCTCGTTTTG
* *
29661464 AGCATATTGGCTCG-TTAG
1 AGCATACTGGCTCGTTTTG
*
29661482 AGCATACTAGCTCGT
1 AGCATACTGGCTCGT
29661497 AAGAGCATTA
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
17 5 0.07
18 63 0.91
19 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (19 bp):
AGCATACTGGCTCGTTTTG
Found at i:29661474 original size:54 final size:54
Alignment explanation
Indices: 29661392--29661494 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
29661382 CGAAAGGATT
* * * *
29661392 AGCATACTGGCTCGTTTTGGCATATTGGCTCGTTTGAGCATACTGGCTCATTGG
1 AGCATACTGGCTCGTTCTAGCATATTGGCTCGTTAGAGCATACTAGCTCATTGG
*
29661446 AGCATAGTGGCTCGTTCTAGCATATTGGCTCGTTAGAGCATACTAGCTC
1 AGCATACTGGCTCGTTCTAGCATATTGGCTCGTTAGAGCATACTAGCTC
29661495 GTAAGAGCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.33
Consensus pattern (54 bp):
AGCATACTGGCTCGTTCTAGCATATTGGCTCGTTAGAGCATACTAGCTCATTGG
Found at i:29661503 original size:54 final size:54
Alignment explanation
Indices: 29661392--29661510 Score: 157
Period size: 54 Copynumber: 2.2 Consensus size: 54
29661382 CGAAAGGATT
* * * * **
29661392 AGCATACTGGCTCGTTTTGGCATATTGGCTCGTTTGAGCATACTGGCTCATTGG
1 AGCATACTGGCTCGTTCTAGCATATTGGCTCGTTAGAGCATACTAGCTCATAAG
* *
29661446 AGCATAGTGGCTCGTTCTAGCATATTGGCTCGTTAGAGCATACTAGCTCGTAAG
1 AGCATACTGGCTCGTTCTAGCATATTGGCTCGTTAGAGCATACTAGCTCATAAG
29661500 AGCATTACTGG
1 AGCA-TACTGG
29661511 ATCGCAAGAG
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
54 50 0.91
55 5 0.09
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (54 bp):
AGCATACTGGCTCGTTCTAGCATATTGGCTCGTTAGAGCATACTAGCTCATAAG
Found at i:29661504 original size:36 final size:36
Alignment explanation
Indices: 29661392--29661510 Score: 114
Period size: 36 Copynumber: 3.3 Consensus size: 36
29661382 CGAAAGGATT
* * *
29661392 AGCATACTGGCTCGTTTTG-GCATATTGGCTCGTTTG
1 AGCATACTGGCTCG-TTAGAGCATACTGGCTCGTTAG
* * * **
29661428 AGCATACTGGCTCATTGGAGCATAGTGGCTCGTTCT
1 AGCATACTGGCTCGTTAGAGCATACTGGCTCGTTAG
* * *
29661464 AGCATATTGGCTCGTTAGAGCATACTAGCTCGTAAG
1 AGCATACTGGCTCGTTAGAGCATACTGGCTCGTTAG
29661500 AGCATTACTGG
1 AGCA-TACTGG
29661511 ATCGCAAGAG
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
35 3 0.04
36 59 0.88
37 5 0.07
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (36 bp):
AGCATACTGGCTCGTTAGAGCATACTGGCTCGTTAG
Found at i:29674173 original size:3 final size:3
Alignment explanation
Indices: 29674167--29674192 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29674157 TTTGTTGTTG
29674167 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
29674193 TAGTTATTTG
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:29674435 original size:27 final size:28
Alignment explanation
Indices: 29674386--29674449 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
29674376 ACATGCTTGC
*
29674386 TTTTATTTAATTTTATTTATTTATG-TA
1 TTTTATTTAATTTTATATATTTATGCTA
*
29674413 TTTTATTTATTTGTTATAT-TTTATGCTA
1 TTTTATTTAATT-TTATATATTTATGCTA
29674441 TTTGTATTT
1 TTT-TATTT
29674450 TTGCTTTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 17 0.53
28 10 0.31
29 5 0.16
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (28 bp):
TTTTATTTAATTTTATATATTTATGCTA
Found at i:29674716 original size:22 final size:24
Alignment explanation
Indices: 29674678--29674730 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
29674668 TTTAATACTA
**
29674678 TAATTATATTTTTTTGT-GTTA-T
1 TAATTATATTTGATTGTCGTTATT
*
29674700 TAATTATATTTGATTGTCTTTATT
1 TAATTATATTTGATTGTCGTTATT
29674724 TAATTAT
1 TAATTAT
29674731 TTATATTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 15 0.58
23 3 0.12
24 8 0.31
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (24 bp):
TAATTATATTTGATTGTCGTTATT
Found at i:29678611 original size:30 final size:30
Alignment explanation
Indices: 29678577--29678708 Score: 101
Period size: 30 Copynumber: 4.4 Consensus size: 30
29678567 TTTTATTAAG
**
29678577 AAATTCAGTTTTGGCCCCT-AAATTATCCAA
1 AAATTCAGTTTTAACCCCTAAAATT-TCCAA
29678607 AAATT-ATGTTTTAACCCCTAAAATTTCCAA
1 AAATTCA-GTTTTAACCCCTAAAATTTCCAA
* * * *
29678637 AAATTCAGATTTAA-CCCTCGAACTTTCTAA
1 AAATTCAGTTTTAACCCCT-AAAATTTCCAA
** * *
29678667 AAATT-ATGTTTTAACCTTTGAACTTTCCAA
1 AAATTCA-GTTTTAACCCCTAAAATTTCCAA
*
29678697 AAATTAAGTTTT
1 AAATTCAGTTTT
29678709 GATCCTTGAA
Statistics
Matches: 85, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
29 6 0.07
30 70 0.82
31 9 0.11
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (30 bp):
AAATTCAGTTTTAACCCCTAAAATTTCCAA
Found at i:29678675 original size:60 final size:60
Alignment explanation
Indices: 29678605--29678817 Score: 189
Period size: 60 Copynumber: 3.6 Consensus size: 60
29678595 TAAATTATCC
* *
29678605 AAAAATTATGTTTTAACCCCTAAAATTTCCAAAAATTCAGATTTAACCCTCGAACTTTCT
1 AAAAATTATGTTTTAACCCCTAAACTTTCCAAAAATTAAGATTTAACCCTCGAACTTTCT
** * * * * * * *
29678665 AAAAATTATGTTTTAACCTTTGAACTTTCCAAAAATTAAGTTTTGATCCTTGAACTTCCC
1 AAAAATTATGTTTTAACCCCTAAACTTTCCAAAAATTAAGATTTAACCCTCGAACTTTCT
* * * * * * * *
29678725 AAAAATT-TGAATTTAACCCTTGAACTTTCTAAAATTTTAGATTTAGCCCTCAAACTTT-T
1 AAAAATTATG-TTTTAACCCCTAAACTTTCCAAAAATTAAGATTTAACCCTCGAACTTTCT
* **
29678784 CAAAAACTATGTTTTGGCCCC-AAACTTTCCAAAA
1 -AAAAATTATGTTTTAACCCCTAAACTTTCCAAAA
29678818 TTCTATTTTT
Statistics
Matches: 119, Mismatches: 31, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
59 13 0.11
60 104 0.87
61 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (60 bp):
AAAAATTATGTTTTAACCCCTAAACTTTCCAAAAATTAAGATTTAACCCTCGAACTTTCT
Found at i:29678718 original size:30 final size:30
Alignment explanation
Indices: 29678602--29678758 Score: 156
Period size: 30 Copynumber: 5.2 Consensus size: 30
29678592 CCCTAAATTA
* * * *
29678602 TCCAAAAATTATGTTTTAACCCCTAAAATT
1 TCCAAAAATTAAGTTTTAACCCTTGAACTT
* * *
29678632 TCCAAAAATTCAGATTTAACCCTCGAACTT
1 TCCAAAAATTAAGTTTTAACCCTTGAACTT
* * *
29678662 TCTAAAAATTATGTTTTAACCTTTGAACTT
1 TCCAAAAATTAAGTTTTAACCCTTGAACTT
* *
29678692 TCCAAAAATTAAGTTTTGATCCTTGAACTT
1 TCCAAAAATTAAGTTTTAACCCTTGAACTT
*
29678722 CCCAAAAATTTGAA--TTTAACCCTTGAACTT
1 TCCAAAAA-TT-AAGTTTTAACCCTTGAACTT
*
29678752 TCTAAAA
1 TCCAAAA
29678759 TTTTAGATTT
Statistics
Matches: 102, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
30 98 0.96
31 2 0.02
32 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (30 bp):
TCCAAAAATTAAGTTTTAACCCTTGAACTT
Found at i:29678769 original size:30 final size:30
Alignment explanation
Indices: 29678602--29678789 Score: 148
Period size: 30 Copynumber: 6.3 Consensus size: 30
29678592 CCCTAAATTA
* * * *
29678602 TCCAAAAA-TTATGTTTTAACCCCTAAAATT
1 TCCAAAAATTTA-GATTTAACCCTTGAACTT
* *
29678632 TCCAAAAATTCAGATTTAACCCTCGAACTT
1 TCCAAAAATTTAGATTTAACCCTTGAACTT
* * *
29678662 TCTAAAAA-TTATGTTTTAACCTTTGAACTT
1 TCCAAAAATTTA-GATTTAACCCTTGAACTT
* * * *
29678692 TCCAAAAATTAAGTTTTGATCCTTGAACTT
1 TCCAAAAATTTAGATTTAACCCTTGAACTT
*
29678722 CCCAAAAATTT-GAATTTAACCCTTGAACTT
1 TCCAAAAATTTAG-ATTTAACCCTTGAACTT
* * * **
29678752 TCTAAAATTTTAGATTTAGCCCTCAAACTT
1 TCCAAAAATTTAGATTTAACCCTTGAACTT
*
29678782 TTCAAAAA
1 TCCAAAAA
29678790 CTATGTTTTG
Statistics
Matches: 123, Mismatches: 30, Indels: 10
0.75 0.18 0.06
Matches are distributed among these distances:
29 3 0.02
30 115 0.93
31 5 0.04
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (30 bp):
TCCAAAAATTTAGATTTAACCCTTGAACTT
Found at i:29678809 original size:29 final size:29
Alignment explanation
Indices: 29678770--29678834 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
29678760 TTTAGATTTA
*
29678770 GCCCTCAAACTTTTCAAAA-ACTATGTTTTG
1 GCCC-CAAACTTTCCAAAATACTAT-TTTTG
*
29678800 GCCCCAAACTTTCCAAAATTCTATTTTTG
1 GCCCCAAACTTTCCAAAATACTATTTTTG
*
29678829 ACCCCA
1 GCCCCA
29678835 TTTTTCCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (29 bp):
GCCCCAAACTTTCCAAAATACTATTTTTG
Found at i:29689471 original size:30 final size:30
Alignment explanation
Indices: 29689309--29689663 Score: 235
Period size: 30 Copynumber: 11.9 Consensus size: 30
29689299 TTTTATCTAA
* * * * *
29689309 AAAATTATATTTTGACTCTCGAAC-TTTCT
1 AAAATTACATTTTAACCCTCAAACTTTTCC
* * **
29689338 AAAATTATATTTTGA-CCTCGCACTTTTCC
1 AAAATTACATTTTAACCCTCAAACTTTTCC
* *
29689367 AACAATCATATTTTAACCC-CTAAAC-TTTCC
1 AA-AATTACATTTTAACCCTC-AAACTTTTCC
* * * * *
29689397 TAAAATTATATTTTAACCCCCGAACTTCTCT
1 -AAAATTACATTTTAACCCTCAAACTTTTCC
* *
29689428 AAAATCACATTTTAACCCTCGAACTTTTCC
1 AAAATTACATTTTAACCCTCAAACTTTTCC
* *
29689458 AAAATCACATTTTAACCCCCAAAC-TTTCTC
1 AAAATTACATTTTAACCCTCAAACTTTTC-C
* * ** *
29689488 GAAATTACATTTTGACCAGCAAACATTTCC
1 AAAATTACATTTTAACCCTCAAACTTTTCC
* *
29689518 AAAATTAAATTTTAACCC-CTAAAC-TTCCC
1 AAAATTACATTTTAACCCTC-AAACTTTTCC
* * *
29689547 AAAATTACATTTTAGCCCCCAAAGTTTTCC
1 AAAATTACATTTTAACCCTCAAACTTTTCC
* * * *
29689577 AAAAGTT-CATTTTGACCTTTAAACTTTTCT
1 AAAA-TTACATTTTAACCCTCAAACTTTTCC
* * *
29689607 AAGATTACATTCTAACCC-CTAAACTTTCCC
1 AAAATTACATTTTAACCCTC-AAACTTTTCC
*
29689637 AAAATTACATTTTAACCC-CAAATTTTT
1 AAAATTACATTTTAACCCTCAAACTTTT
29689664 TCGAAACTTC
Statistics
Matches: 261, Mismatches: 50, Indels: 30
0.77 0.15 0.09
Matches are distributed among these distances:
28 6 0.02
29 57 0.22
30 182 0.70
31 16 0.06
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTCAAACTTTTCC
Found at i:29689493 original size:90 final size:89
Alignment explanation
Indices: 29689309--29689655 Score: 276
Period size: 90 Copynumber: 3.9 Consensus size: 89
29689299 TTTTATCTAA
* * * * *
29689309 AAAATTATATTTTGACTCTCGAACTTTCTAAAATTATATTTTGA-CCTCGCACTTTTCCAACAAT
1 AAAATTATATTTTGACCCCCGAACTTTCTAAAATTAAATTTTAACCCTCGAACTTTTCCAA-AAT
* *
29689373 CATATTTTAACCCCTAAACTTTCCT
65 CACATTTTAACCCCCAAACTTTCCT
* * *
29689398 AAAATTATATTTTAACCCCCGAACTTCTCTAAAATCACATTTTAACCCTCGAACTTTTCCAAAAT
1 AAAATTATATTTTGACCCCCGAACTT-TCTAAAATTAAATTTTAACCCTCGAACTTTTCCAAAAT
29689463 CACATTTTAACCCCCAAACTTT-CT
65 CACATTTTAACCCCCAAACTTTCCT
* * ** * * * *
29689487 CGAAATTACATTTTGACCAGCAAACATTTCCAAAATTAAATTTTAACCC-CTAAAC-TTCCCAAA
1 -AAAATTATATTTTGACCCCCGAAC-TTTCTAAAATTAAATTTTAACCCTC-GAACTTTTCCAAA
* * *
29689550 ATTACATTTTAGCCCCCAAAGTTTTCC-
63 ATCACATTTTAACCCCCAAA-CTTTCCT
* **** * * * * *
29689577 AAAAGTT-CATTTTGACCTTTAAACTTTTCTAAGATTACATTCTAACCC-CTAAACTTTCCCAAA
1 AAAA-TTATATTTTGACCCCCGAAC-TTTCTAAAATTAAATTTTAACCCTC-GAACTTTTCCAAA
*
29689640 ATTACATTTTAACCCC
63 ATCACATTTTAACCCC
29689656 AAATTTTTTC
Statistics
Matches: 216, Mismatches: 33, Indels: 17
0.81 0.12 0.06
Matches are distributed among these distances:
89 93 0.43
90 105 0.49
91 18 0.08
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.35
Consensus pattern (89 bp):
AAAATTATATTTTGACCCCCGAACTTTCTAAAATTAAATTTTAACCCTCGAACTTTTCCAAAATC
ACATTTTAACCCCCAAACTTTCCT
Found at i:29689588 original size:89 final size:87
Alignment explanation
Indices: 29689449--29689678 Score: 255
Period size: 89 Copynumber: 2.6 Consensus size: 87
29689439 TTAACCCTCG
* * *
29689449 AACTTTTCCAAAATCACATTTTAACCCCCAAACTTTCTCGAAATTACATTTTGACCAGCAAACAT
1 AACTTTCCCAAAATTACATTTT-ACCCCCAAATTTTC-CGAAATT-CATTTTGACCAGCAAACAT
*
29689514 TTCCAAAATTAAATTTTAACCCCTA
63 TTCCAAAATTAAATTCTAACCCCTA
* *** *
29689539 AAC-TTCCCAAAATTACATTTTAGCCCCCAAAGTTTTCCAAAAGTTCATTTTGACCTTTAAACTT
1 AACTTTCCCAAAATTACATTTTA-CCCCCAAA-TTTTCCGAAA-TTCATTTTGACCAGCAAACAT
* * *
29689603 TTCTAAGATTACATTCTAACCCCTA
63 TTCCAAAATTAAATTCTAACCCCTA
* *
29689628 AACTTTCCCAAAATTACATTTTAACCCCAAATTTTTTCGAAACTTCATTTT
1 AACTTTCCCAAAATTACATTTTACCCCCAAA-TTTTCCGAAA-TTCATTTT
29689679 TGAGCCTTTT
Statistics
Matches: 119, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
88 1 0.01
89 90 0.76
90 28 0.24
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (87 bp):
AACTTTCCCAAAATTACATTTTACCCCCAAATTTTCCGAAATTCATTTTGACCAGCAAACATTTC
CAAAATTAAATTCTAACCCCTA
Found at i:29695817 original size:49 final size:48
Alignment explanation
Indices: 29695745--29695940 Score: 146
Period size: 49 Copynumber: 4.0 Consensus size: 48
29695735 CCAAAAAAAA
** *
29695745 CATGAAGATGCGATGGGAAAGGTTAAGACTACAACGGCAAACTCTGTAC
1 CATGAAGATTTGAAGGGAAAGGTTAAGACTACAACGGCAAAC-CTGTAC
* * * * **
29695794 CATGAAGATTTTAAGGGAAAGGTTGAGGCTAAAACCTCAAACCTAGTACC
1 CATGAAGATTTGAAGGGAAAGGTTAAGACTACAACGGCAAACCT-GTA-C
* * * * *
29695844 CA-GAAGATGTGATGGGAAAGGTTGAGGAC-ACAACGGCCAACCCCGTAC
1 CATGAAGATTTGAAGGGAAAGGTT-AAGACTACAACGG-CAAACCTGTAC
* * * * *
29695892 CATGAAGATTTGAATGGAAA-GTTGAGGCTGCAACGACAAACCTAGTAC
1 CATGAAGATTTGAAGGGAAAGGTTAAGACTACAACGGCAAACCT-GTAC
29695940 C
1 C
29695941 TTAGAAATAT
Statistics
Matches: 110, Mismatches: 30, Indels: 15
0.71 0.19 0.10
Matches are distributed among these distances:
47 7 0.06
48 18 0.16
49 75 0.68
50 10 0.09
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.18
Consensus pattern (48 bp):
CATGAAGATTTGAAGGGAAAGGTTAAGACTACAACGGCAAACCTGTAC
Found at i:29696265 original size:41 final size:41
Alignment explanation
Indices: 29696220--29696475 Score: 235
Period size: 41 Copynumber: 6.0 Consensus size: 41
29696210 CAAATTAAAA
*
29696220 ATTCCAGTCTTTTACCCCTAATTAAGAGGGGCAGATTGAAG
1 ATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGATTGAAG
*
29696261 ATTCCAGTCTTTTACCCCTAATCAAGAAGGGCAGATTGAAG
1 ATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGATTGAAG
* * * *
29696302 ATTCCAATCTTTTACCCTTAATCAAGAGGGGCAAATTAAAG
1 ATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGATTGAAG
* * * * *
29696343 ATTCTAGTCTTTTACCCTTAATAAAGAAGGGCGGATTGAAG
1 ATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGATTGAAG
** * * * *
29696384 TTATCATCCCA-TCTCATACCCTTAAGTTAAGAGGGGCAAATTGCAG
1 --AT--T-CCAGTCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG
* *
29696430 TCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCATATTGAAG
1 --AT--TCCAGTCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG
29696476 CCACATTCTG
Statistics
Matches: 179, Mismatches: 29, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
41 109 0.61
43 2 0.01
45 16 0.09
46 52 0.29
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (41 bp):
ATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGATTGAAG
Found at i:29696357 original size:82 final size:83
Alignment explanation
Indices: 29696220--29696475 Score: 280
Period size: 82 Copynumber: 3.0 Consensus size: 83
29696210 CAAATTAAAA
* * *
29696220 ATTCCAGTCTTTTACCCCTAATTAAGAGGGGCAGATTGAAGATTCCAGTCTTTTACCCCTAATCA
1 ATTCCAATCTTTTACCCTTAATTAAGAGGGGCAAATTGAAGATTCCAGTCTTTTACCCCTAATCA
29696285 AGAAGGGCAGATTGAAG-
66 AGAAGGGCAGATTGAAGT
* * * * *
29696302 ATTCCAATCTTTTACCCTTAATCAAGAGGGGCAAATTAAAGATTCTAGTCTTTTACCCTTAATAA
1 ATTCCAATCTTTTACCCTTAATTAAGAGGGGCAAATTGAAGATTCCAGTCTTTTACCCCTAATCA
*
29696367 AGAAGGGCGGATTGAAGTT
66 AGAAGGGCAGATTGAAG-T
* ** * *
29696386 ATCATCCCATCTCATACCCTTAAGTTAAGAGGGGCAAATTGCAGTCATCATCCAATCTTTTACCC
1 AT--TCCAATCTTTTACCCTTAA-TTAAGAGGGGCAAATTGAAG--AT--TCCAGTCTTTTACCC
* *
29696451 CTAAGTCAAGAGGGGCATATTGAAG
59 CTAA-TCAAGAAGGGCAGATTGAAG
29696476 CCACATTCTG
Statistics
Matches: 142, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
82 73 0.51
84 2 0.01
86 16 0.11
87 17 0.12
89 2 0.01
91 16 0.11
92 16 0.11
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (83 bp):
ATTCCAATCTTTTACCCTTAATTAAGAGGGGCAAATTGAAGATTCCAGTCTTTTACCCCTAATCA
AGAAGGGCAGATTGAAGT
Found at i:29696688 original size:85 final size:85
Alignment explanation
Indices: 29696524--29696692 Score: 196
Period size: 85 Copynumber: 2.0 Consensus size: 85
29696514 ATAAAACCCT
* * *
29696524 ATCTTCCTGATGAGATACAAAAAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTGGCGAGATG
1 ATCTTCCTGATGAGATACAAAAAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTGACAAGATA
* *
29696589 CAGATAAGTGGACCAAATCC
66 CAGAGAAGTAGACCAAATCC
* * * * * * *
29696609 ATCTTCCTGATGAGATACAGAGAAGTGGATTGAAA-CAATGAAGCGGTCATCTTCCTGATAAGAT
1 ATCTTCCTGATGAGATACAAAAAAGTGG-GTCAAAGCAATAAAGCGATCATCTTCCTGACAAGAT
**
29696673 ATGGAGAAGTAGACCAAATC
65 ACAGAGAAGTAGACCAAATC
29696693 AATGAAGCGA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
85 65 0.94
86 4 0.06
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (85 bp):
ATCTTCCTGATGAGATACAAAAAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTGACAAGATA
CAGAGAAGTAGACCAAATCC
Found at i:29696696 original size:48 final size:48
Alignment explanation
Indices: 29696608--29696701 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
29696598 GGACCAAATC
* * **
29696608 CATCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAATGAAGCGGT
1 CATCTTCCTGATAAGATACAGAGAAGTAGATCCAAACAATGAAGCGGT
**
29696656 CATCTTCCTGATAAGATATGGAGAAGTAGA-CCAAATCAATGAAGCG
1 CATCTTCCTGATAAGATACAGAGAAGTAGATCCAAA-CAATGAAGCG
29696702 AAGTTCAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 3 0.08
48 36 0.92
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (48 bp):
CATCTTCCTGATAAGATACAGAGAAGTAGATCCAAACAATGAAGCGGT
Found at i:29698690 original size:30 final size:29
Alignment explanation
Indices: 29698629--29698880 Score: 215
Period size: 30 Copynumber: 8.4 Consensus size: 29
29698619 ACATTTGACC
* *
29698629 AACTTTT-TAAAAATTATATTTTGACCCTA
1 AACTTTTCT-AAAATTACATTTTAACCCTA
* *
29698658 AACTTTTCTAAAATCATATTTTAACCCTTA
1 AACTTTTCTAAAATTACATTTTAACCC-TA
* *
29698688 AACTTTCCTAAAATTACATTTTAACCCCCA
1 AACTTTTCTAAAATTACATTTTAA-CCCTA
* * *
29698718 AACTTCTCCAAAATCACATTTTAACCCCTA
1 AACTTTTCTAAAATTACATTTTAA-CCCTA
* * * *
29698748 AACTTTTCCAAAATCACATTTTGATCCTA
1 AACTTTTCTAAAATTACATTTTAACCCTA
* *
29698777 AAC-TTTCTCGAAATTACTTTTTTAACTGCC-A
1 AACTTTTCT-AAAATTAC-ATTTTAAC--CCTA
29698808 AAC-TTTCTCAAAATTACATTTTAACCCCTA
1 AACTTTTCT-AAAATTACATTTTAA-CCCTA
* *
29698838 AACTTTCCTAAAATTACATTTTGACACCTA
1 AACTTTTCTAAAATTACATTTTAAC-CCTA
*
29698868 AATTTTTCTAAAA
1 AACTTTTCTAAAA
29698881 CTTTATTTTT
Statistics
Matches: 186, Mismatches: 26, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.02
29 39 0.21
30 116 0.62
31 25 0.13
32 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
AACTTTTCTAAAATTACATTTTAACCCTA
Found at i:29698761 original size:90 final size:90
Alignment explanation
Indices: 29698653--29698869 Score: 262
Period size: 90 Copynumber: 2.4 Consensus size: 90
29698643 TATATTTTGA
* *
29698653 CCCTAAACTTTTCTAAAATCATATTTTAACCCTTAAACTTTC-CTAAAATTAC-ATTTTAACCCC
1 CCCTAAACTTTTCCAAAATCACATTTTAACCC-TAAACTTTCTC-AAAATTACTATTTTAACCCC
29698716 CAAAC-TTCTCCAAAATCACATTTTAAC
64 CAAACTTTCT-CAAAATCACATTTTAAC
* * * * **
29698743 CCCTAAACTTTTCCAAAATCACATTTTGATCCTAAACTTTCTCGAAATTACTTTTTTAACTGCCA
1 CCCTAAACTTTTCCAAAATCACATTTTAACCCTAAACTTTCTCAAAATTACTATTTTAACCCCCA
*
29698808 AACTTTCTCAAAATTACATTTTAAC
66 AACTTTCTCAAAATCACATTTTAAC
* *
29698833 CCCTAAAC-TTTCCTAAAATTACATTTTGACACCTAAA
1 CCCTAAACTTTTCC-AAAATCACATTTTAAC-CCTAAA
29698870 TTTTTCTAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
89 21 0.19
90 80 0.72
91 10 0.09
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (90 bp):
CCCTAAACTTTTCCAAAATCACATTTTAACCCTAAACTTTCTCAAAATTACTATTTTAACCCCCA
AACTTTCTCAAAATCACATTTTAAC
Found at i:29702759 original size:124 final size:124
Alignment explanation
Indices: 29702444--29703140 Score: 809
Period size: 124 Copynumber: 5.6 Consensus size: 124
29702434 AACACGCTTT
* * *
29702444 ACAA-GAAGCGAAGCTCAATGTGAGTGAAACTTCAAA-CCCTATCTTCCTGATGAGATACAAAGA
1 ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATATTCTTGATGAGATACAGAGA
* * * * **
29702507 AGTGGATTAAAATGATAAAGCGATCATCTTCCTGATAAGATACAAAATGAAGCAGAGCTCAACA
66 AGTGGATCAAAATGATGAAGCGGTCATCTTCCTGATGAGATAC-AAA-GAAGTGGA-C-CAA-A
* * * ** ** * * *
29702571 TCACTGAGGTTATAG-TGGA-GTAGAGTAAAAATTCAAACCCCTATATTCTTGATGAGATATAGA
1 ACAATGAAGCGA-AGCTCAATGT-GAGTGAAACTTCAAACCCCTATATTCTTGATGAGATACAGA
* * * *
29702634 GAAGTAGATCAAAACGATGAAGCAGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAA
64 GAAGTGGATCAAAATGATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTGGACCAAA
* * **
29702695 ACAGTGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATCTTCCCGATGAGATACAGAGA
1 ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATATTCTTGATGAGATACAGAGA
*
29702760 AGTGGATCAAAATGATGAAGCGGTCATCTTCTTGATGAGATACATAA-AAGTGGACCAAA
66 AGTGGATCAAAATGATGAAGCGGTCATCTTCCTGATGAGATACA-AAGAAGTGGACCAAA
* *
29702819 ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCCATATTCTTGATGAGATATAGAGA
1 ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATATTCTTGATGAGATACAGAGA
* * * *
29702884 AGTGGATCAAAATGATGAAACGGTCATCTTCTTGATGAGATATAGAGAAGTGGACCAAA
66 AGTGGATCAAAATGATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTGGACCAAA
** * *
29702943 ACAATGAAGTAAAGTTCAATGTGAGTGAAACTTCAAACCCC-ATATTCTTGATGACATACAGAGA
1 ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATATTCTTGATGAGATACAGAGA
* * * *
29703007 AGTAGATCAAACA--ATGAAGTGATCATCTTCCTGATGAGATACAAAGAAATGGACCAAA
66 AGTGGATCAAA-ATGATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTGGACCAAA
* * * * * *
29703065 ACAATGAAGTGAAGCTCAATGTGAGTGAAACTTCAAACCTC-ATCTTCTTGATGAGACATAGAGT
1 ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATATTCTTGATGAGATACAGAGA
*
29703129 AGTGGACCAAAA
66 AGTGGATCAAAA
29703141 GATAAAGTTA
Statistics
Matches: 488, Mismatches: 73, Indels: 24
0.83 0.12 0.04
Matches are distributed among these distances:
121 1 0.00
122 103 0.21
123 34 0.07
124 251 0.51
125 6 0.01
126 1 0.00
127 10 0.02
128 21 0.04
129 61 0.12
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (124 bp):
ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATATTCTTGATGAGATACAGAGA
AGTGGATCAAAATGATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTGGACCAAA
Found at i:29702922 original size:248 final size:248
Alignment explanation
Indices: 29702444--29703140 Score: 890
Period size: 248 Copynumber: 2.8 Consensus size: 248
29702434 AACACGCTTT
*
29702444 ACAA-GAAGCGAAGCTCAATGTGAGTGAAACTTCAAA-CCCTATCTTCCTGATGAGATACAAAGA
1 ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAGAGA
* * * ** *
29702507 AGTGGATTAAAATGATAAAGCGATCATCTTCCTGATAAGATACAAAATGAAGCAGAGCTCAACAT
66 AGTGGATCAAAATGATGAAGCGATCATCTTCCTGATGAGATAC-AAA-GAAGTGGA-C-CAA-AA
* * * ** * * *
29702572 CACTGAGGTTATAG-TGGA-GTAGAGTAAAAATTCAAACCCCTATATTCTTGATGAGATATAGAG
126 CAATGAAGTGA-AGCTCAATGT-GAGTGAAACTTCAAACCCCCATATTCTTGATGAGATATAGAG
* *
29702635 AAGTAGATCAAAACGATGAAGCAGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAA
189 AAGTGGATCAAAACGATGAAACAGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAA
* *
29702695 ACAGTGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATCTTCCCGATGAGATACAGAGA
1 ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAGAGA
* *
29702760 AGTGGATCAAAATGATGAAGCGGTCATCTTCTTGATGAGATACATAA-AAGTGGACCAAAACAAT
66 AGTGGATCAAAATGATGAAGCGATCATCTTCCTGATGAGATACA-AAGAAGTGGACCAAAACAAT
*
29702824 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCCATATTCTTGATGAGATATAGAGAAGTGG
130 GAAGTGAAGCTCAATGTGAGTGAAACTTCAAACCCCCATATTCTTGATGAGATATAGAGAAGTGG
* * * *
29702889 ATCAAAATGATGAAACGGTCATCTTCTTGATGAGATATAGAGAAGTGGACCAAA
195 ATCAAAACGATGAAACAGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAA
** * * * *
29702943 ACAATGAAGTAAAGTTCAATGTGAGTGAAACTTCAAACCCC-ATATTCTTGATGACATACAGAGA
1 ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAGAGA
* * *
29703007 AGTAGATCAAACA--ATGAAGTGATCATCTTCCTGATGAGATACAAAGAAATGGACCAAAACAAT
66 AGTGGATCAAA-ATGATGAAGCGATCATCTTCCTGATGAGATACAAAGAAGTGGACCAAAACAAT
* * * *
29703070 GAAGTGAAGCTCAATGTGAGTGAAACTTCAAA-CCTCATCTTCTTGATGAGACATAGAGTAGTGG
130 GAAGTGAAGCTCAATGTGAGTGAAACTTCAAACCCCCATATTCTTGATGAGATATAGAGAAGTGG
*
29703134 ACCAAAA
195 ATCAAAA
29703141 GATAAAGTTA
Statistics
Matches: 394, Mismatches: 45, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
245 36 0.09
246 74 0.19
247 31 0.08
248 141 0.36
249 5 0.01
250 1 0.00
251 8 0.02
252 33 0.08
253 65 0.16
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (248 bp):
ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAGAGA
AGTGGATCAAAATGATGAAGCGATCATCTTCCTGATGAGATACAAAGAAGTGGACCAAAACAATG
AAGTGAAGCTCAATGTGAGTGAAACTTCAAACCCCCATATTCTTGATGAGATATAGAGAAGTGGA
TCAAAACGATGAAACAGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAA
Found at i:29704914 original size:30 final size:30
Alignment explanation
Indices: 29704875--29705155 Score: 183
Period size: 30 Copynumber: 9.4 Consensus size: 30
29704865 TTGGCCCCCA
* * *
29704875 AACTATCCAAAAATTATGTTTTGACCCTTG
1 AACTTTCCAAAAATTATGATTTGACCCTCG
* * *
29704905 AACTTTCCAAAAATT-TAGATTTAACCCCCA
1 AACTTTCCAAAAATTAT-GATTTGACCCTCG
* *
29704935 AACTTTCTAAAAATTATG-TTTTATCCC-CTG
1 AACTTTCCAAAAATTATGATTTGA-CCCTC-G
* *
29704965 AACTTT-CAAAAATTTAAGTTTTGACTCC-CG
1 AACTTTCCAAAAA-TTATGATTTGAC-CCTCG
* * *
29704995 AACTTTCTAAAAGTTCA-GATCTGACCCTCG
1 AACTTTCCAAAAATT-ATGATTTGACCCTCG
29705025 AAC-TTCACAAAAATT-TGGATTTGACCCTCG
1 AACTTTC-CAAAAATTAT-GATTTGACCCTCG
* * *
29705055 AAATTTCCAAAAATT-TAGATTTGGCCC-CAA
1 AACTTTCCAAAAATTAT-GATTTGACCCTC-G
29705085 AACTTTCCAAAAATT-TAGATTT-AGCCCTCG
1 AACTTTCCAAAAATTAT-GATTTGA-CCCTCG
* * * *
29705115 AACTTTCCAAAATTTATGTTTTGGCCCT-A
1 AACTTTCCAAAAATTATGATTTGACCCTCG
29705144 AACTTTCCAAAA
1 AACTTTCCAAAA
29705156 TTCCATTTTA
Statistics
Matches: 202, Mismatches: 30, Indels: 39
0.75 0.11 0.14
Matches are distributed among these distances:
29 29 0.14
30 155 0.77
31 18 0.09
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (30 bp):
AACTTTCCAAAAATTATGATTTGACCCTCG
Found at i:29704948 original size:60 final size:60
Alignment explanation
Indices: 29704869--29705155 Score: 239
Period size: 60 Copynumber: 4.8 Consensus size: 60
29704859 TCAAATTTGG
* *
29704869 CCCCCAAACTATCCAAAAATTATGTTTTGACCCTTGAACTTTCCAAAAATTTAGATTTAA
1 CCCCCAAACTTTCCAAAAATTATGTTTTGACCCCTGAACTTTCCAAAAATTTAGATTTAA
* * *
29704929 CCCCCAAACTTTCTAAAAATTATGTTTT-ATCCCCTGAACTTT-CAAAAATTTAAGTTTTGA
1 CCCCCAAACTTTCCAAAAATTATGTTTTGA-CCCCTGAACTTTCCAAAAATTT-AGATTTAA
* * * * * * * *
29704989 CTCCCGAACTTTCTAAAAGTTCA-GATCTGA-CCCTCGAAC-TTCACAAAAATTTGGATTTGA
1 CCCCCAAACTTTCCAAAAATT-ATGTTTTGACCCCT-GAACTTTC-CAAAAATTTAGATTTAA
* * * ** *
29705049 CCCTCGAAA-TTTCCAAAAATT-TAGATTTGGCCCCAAAACTTTCCAAAAATTTAGATTTAG
1 CCC-CCAAACTTTCCAAAAATTAT-GTTTTGACCCCTGAACTTTCCAAAAATTTAGATTTAA
* * * * *
29705109 CCCTCGAACTTTCCAAAATTTATGTTTTG-GCCCTAAACTTTCCAAAA
1 CCCCCAAACTTTCCAAAAATTATGTTTTGACCCCTGAACTTTCCAAAA
29705156 TTCCATTTTA
Statistics
Matches: 182, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
59 34 0.19
60 127 0.70
61 21 0.12
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33
Consensus pattern (60 bp):
CCCCCAAACTTTCCAAAAATTATGTTTTGACCCCTGAACTTTCCAAAAATTTAGATTTAA
Found at i:29705126 original size:90 final size:90
Alignment explanation
Indices: 29704905--29705135 Score: 224
Period size: 90 Copynumber: 2.6 Consensus size: 90
29704895 TTGACCCTTG
* * * * * *
29704905 AACTTTCCAAAAATTTAGATTTAACCCCCAAACTTTCTAAAAATTATGTTTTATCCCCTGAACTT
1 AACTTTCCAAAAATTTAGATTTAGCCCTCGAACTTTCCAAAAATTATGTTTGATCCCCTGAAATT
* *
29704970 TCAAAAATTTAAGTTTTGACTCCCG
66 TCAAAAATTTAAGATTTGACTCCCA
* * * *
29704995 AACTTTCTAAAAGTTCAGATCT-GACCCTCGAAC-TTCACAAAAATT-TGGATTTGA--CCCTCG
1 AACTTTCCAAAAATTTAGATTTAG-CCCTCGAACTTTC-CAAAAATTAT-G-TTTGATCCCCT-G
*
29705055 AAATTTCCAAAAATTT-AGATTTGGC-CCCAA
61 AAATTT-CAAAAATTTAAGATTTGACTCCC-A
*
29705085 AACTTTCCAAAAATTTAGATTTAGCCCTCGAACTTTCCAAAATTTATGTTT
1 AACTTTCCAAAAATTTAGATTTAGCCCTCGAACTTTCCAAAAATTATGTTT
29705136 TGGCCCTAAA
Statistics
Matches: 113, Mismatches: 18, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
89 14 0.12
90 81 0.72
91 18 0.16
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (90 bp):
AACTTTCCAAAAATTTAGATTTAGCCCTCGAACTTTCCAAAAATTATGTTTGATCCCCTGAAATT
TCAAAAATTTAAGATTTGACTCCCA
Found at i:29711901 original size:18 final size:18
Alignment explanation
Indices: 29711878--29711935 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
29711868 ACCAGATAAT
* *
29711878 ATGCGATCACATAACCAG
1 ATGCGATAAAATAACCAG
* *
29711896 ATGCGATAAAAAAATCAG
1 ATGCGATAAAATAACCAG
* * *
29711914 ATGCAATTATATAACCAG
1 ATGCGATAAAATAACCAG
29711932 ATGC
1 ATGC
29711936 AACCACAAGC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.21
Consensus pattern (18 bp):
ATGCGATAAAATAACCAG
Found at i:29711936 original size:18 final size:18
Alignment explanation
Indices: 29711888--29711937 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
29711878 ATGCGATCAC
*
29711888 ATAACCAGATGCGATAAA
1 ATAACCAGATGCAATAAA
* * * *
29711906 AAAATCAGATGCAATTAT
1 ATAACCAGATGCAATAAA
29711924 ATAACCAGATGCAA
1 ATAACCAGATGCAA
29711938 CCACAAGCTC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (18 bp):
ATAACCAGATGCAATAAA
Found at i:29722863 original size:17 final size:18
Alignment explanation
Indices: 29722836--29722887 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
29722826 TCAAACTAGC
29722836 AAAAAAGGAAAAAGAAAAG
1 AAAAAA-GAAAAAGAAAAG
*
29722855 -AAAAAGAAAAAG-AGAG
1 AAAAAAGAAAAAGAAAAG
29722871 AAAAAAGAAAAAGAAAA
1 AAAAAAGAAAAAGAAAA
29722888 AAAGAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 3 0.10
17 19 0.66
18 7 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAGAAAAG
Found at i:29722864 original size:23 final size:23
Alignment explanation
Indices: 29722837--29722898 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
29722827 CAAACTAGCA
29722837 AAAAAG-GAAAAAGAAAAGAAAAAG
1 AAAAAGAG-AAAA-AAAAGAAAAAG
*
29722861 AAAAAGAGAGAAAAAAGAAAAAG
1 AAAAAGAGAAAAAAAAGAAAAAG
*
29722884 AAAAAAAGAAAAAAA
1 AAAAAGAGAAAAAAA
29722899 TGGAGGGGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 24 0.71
24 9 0.26
25 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAAAGAGAAAAAAAAGAAAAAG
Found at i:29722896 original size:6 final size:6
Alignment explanation
Indices: 29722837--29722888 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
29722827 CAAACTAGCA
* *
29722837 AAAAAGG AAAAAG -AAAAG AAAAAG AAAAAG AGAGA- AAAAAG AAAAAG
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
29722884 AAAAA
1 AAAAA
29722889 AAGAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
5 8 0.21
6 26 0.67
7 5 0.13
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:29722898 original size:17 final size:17
Alignment explanation
Indices: 29722836--29722898 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
29722826 TCAAACTAGC
*
29722836 AAAAAAGGAAAAAGAA-A
1 AAAAAAAGAAAAA-AAGA
* *
29722853 AGAAAAAGAAAAAGAGA
1 AAAAAAAGAAAAAAAGA
*
29722870 GAAAAAAG--AAAAAG-
1 AAAAAAAGAAAAAAAGA
29722884 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
29722899 TGGAGGGGCC
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 6 0.17
17 18 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAGA
Found at i:29724043 original size:99 final size:101
Alignment explanation
Indices: 29723893--29724119 Score: 250
Period size: 99 Copynumber: 2.3 Consensus size: 101
29723883 AATAGCAAAT
** *
29723893 CTCAACCTCCACTGAAGTTGCAGTGGAATAGAGTGAAGTCATAACCTCAAATCCTATATCCCTAA
1 CTCAACCTCC-CTGAAGTTGCAGTGGAATAGAGCAAAGTCACAACCTCAAATCCTATATCCCTAA
29723958 AGTTGTAAT--AGATCAGATTAAAA-TA-AGTAACGGAC
65 AGTTGTAATGAAG-T-AGATTAAAACTACAGTAACGGAC
* * * *
29723993 CTCAACCTCCCTGAAGTTGCAGTGGAAT-GAAGCAAAGTTACCACAC-CAAATCCTATCTTCCTA
1 CTCAACCTCCCTGAAGTTGCAGTGGAATAG-AGCAAAGTCACAAC-CTCAAATCCTATATCCCTA
* * * *
29724056 AAGTTGTAGTGAAGTGGATTAAAACTACAGTAGCGGAT
64 AAGTTGTAATGAAGTAGATTAAAACTACAGTAACGGAC
* *
29724094 CTCAATCTCCCTAAAGTTGCAGTGGA
1 CTCAACCTCCCTGAAGTTGCAGTGGA
29724120 GCAAGATGAA
Statistics
Matches: 108, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
98 1 0.01
99 59 0.55
100 14 0.13
101 34 0.31
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (101 bp):
CTCAACCTCCCTGAAGTTGCAGTGGAATAGAGCAAAGTCACAACCTCAAATCCTATATCCCTAAA
GTTGTAATGAAGTAGATTAAAACTACAGTAACGGAC
Found at i:29724231 original size:101 final size:100
Alignment explanation
Indices: 29723891--29724231 Score: 338
Period size: 101 Copynumber: 3.4 Consensus size: 100
29723881 AAAATAGCAA
* * * *
29723891 ATCTCAACCTCCACTGAAGTTGCAGTGGAAT-AGAGTGAAGTCAT-AAC-CTCAAATCCTATATC
1 ATCTCAATCTCC-CTGAAGTTGCAGTGGAATGA-AGTGAAG-CTTCAACAC-CAAATCCTATCTT
* * *
29723953 CCTAAAGTTGTAAT-AGATCAGATTAAAA-TAAGTAACGG
62 CCTAAAGTTGTAGTGA-AGCAGATTAAAACTAAGTAGCGG
* * ** *
29723991 ACCTCAACCTCCCTGAAGTTGCAGTGGAATGAAGCAAAG-TTACCACACCAAATCCTATCTTCCT
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGAAGTGAAGCTT-CAACACCAAATCCTATCTTCCT
**
29724055 AAAGTTGTAGTGAAGTGGATTAAAACTACAGTAGCGG
65 AAAGTTGTAGTGAAGCAGATTAAAACTA-AGTAGCGG
* *
29724092 ATCTCAATCTCCCTAAAGTTGCAGTGG-A-GCAAGATGAAGCTTCAACACCAAATCCGATCTTCC
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATG-AAG-TGAAGCTTCAACACCAAATCCTATCTTCC
* * *
29724155 TAAAGTTGCAGTGAAGCAAATTAAAACTATAGTAGCAG
64 TAAAGTTGTAGTGAAGCAGATTAAAACTA-AGTAGCGG
* * *
29724193 ATATCAATCTCTCTGAAGTTGCAGTGGAATGGAGTGAAG
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGAAGTGAAG
29724232 TTACATCATC
Statistics
Matches: 200, Mismatches: 29, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
97 1 0.00
99 59 0.29
100 20 0.10
101 114 0.57
102 5 0.03
103 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (100 bp):
ATCTCAATCTCCCTGAAGTTGCAGTGGAATGAAGTGAAGCTTCAACACCAAATCCTATCTTCCTA
AAGTTGTAGTGAAGCAGATTAAAACTAAGTAGCGG
Found at i:29724507 original size:81 final size:81
Alignment explanation
Indices: 29724242--29725017 Score: 964
Period size: 81 Copynumber: 9.5 Consensus size: 81
29724232 TTACATCATC
* * * * * * *
29724242 CCATCCAATCTTTTACCCCGACCATGGGGAAGATTGAAGAACATCCAATCTTTTACCCTATCTAG
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAG-CCATCCAATCTTTTACCCCAACAAG
29724307 AGGGCAGATTGAAGACA
65 AGGGCAGATTGAAGACA
* * * * * *
29724324 CCTTCAAATCTCTTACCCCAACCATGAGGCAGATTGAAGTCATCCAATTTTTTACCCTAA-AAGA
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCCAACAAGA
*
29724388 GGACAGATTGAAGACA
66 GGGCAGATTGAAGACA
* * *
29724404 CCATCCAATCTCTTACCTCAACCATGAGGCAGATTGAAGCCATCCAATCTTTTACCCCAATAAGA
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCCAACAAGA
*
29724469 GGGAAGATTGAAGACA
66 GGGCAGATTGAAGACA
* *
29724485 CCTTCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCGAACAAGA
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCCAACAAGA
* *
29724550 GGGTAGATTAAAGACA
66 GGGCAGATTGAAGACA
* * * ** *
29724566 CCATCCAATCTCTTACCCCGACCATGGGGTAGATTAAAGCCATTAAATCTTTTACCCTAACAAGA
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCCAACAAGA
29724631 GGGCAGATTGAAGACA
66 GGGCAGATTGAAGACA
* * * * *
29724647 CCATCCAATATTTTACCACAACCATGGGGCAGATCGAAGCCATCCAATCTTTGACCCCAACAAGA
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCCAACAAGA
*
29724712 GGGTAGATTGAAGACA
66 GGGCAGATTGAAGACA
* * * *
29724728 CCGTCCAATCTCTTACCCTAACCATGGGGTAGATCGAA-CCAATCCAATCTTTTACCCCAACAAG
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCC-ATCCAATCTTTTACCCCAACAAG
*
29724792 AGGGCAGATTGAAGGCA
65 AGGGCAGATTGAAGACA
* ** * *
29724809 TCATCCAATCTCTTACCCCAACCATTAGGCAGATAGAAGCCATCCAATCTTTTACCCTAACAAGA
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCCAACAAGA
29724874 GGGCA-AGTTGAAGACA
66 GGGCAGA-TTGAAGACA
* ** * * * * **
29724890 GCATCTGATCTCTTACCCTAACCATGGGGCAAAGTGAAGTCATCCAATCTTTTACCTTAACAAGA
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCCAACAAGA
*
29724955 GGGCAGATTGAAGCCA
66 GGGCAGATTGAAGACA
* * *
29724971 TCATCCAATCTCTTACCCCTAATCCAGAGGGGCAAATTGAAGCCATC
1 CCATCCAATCTCTTACCCC-AA-CCA-TGGGGCAGATTGAAGCCATC
29725018 ATCCAATCTC
Statistics
Matches: 602, Mismatches: 84, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
80 75 0.12
81 469 0.78
82 38 0.06
83 3 0.00
84 17 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (81 bp):
CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCCAACAAGA
GGGCAGATTGAAGACA
Found at i:29725947 original size:17 final size:17
Alignment explanation
Indices: 29725910--29725964 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
29725900 TTTTATTTAA
29725910 TTTTATTTATTTACG-TA-
1 TTTTATTTATTT--GTTAT
29725927 TTTTATTTATTTGTTAT
1 TTTTATTTATTTGTTAT
*
29725944 TTTTATGCTATTT-TTAT
1 TTTTAT-TTATTTGTTAT
29725961 TTTT
1 TTTT
29725965 GCCTTCATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 1 0.03
16 2 0.06
17 26 0.76
18 5 0.15
ACGTcount: A:0.18, C:0.04, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTATTTATTTGTTAT
Found at i:29725955 original size:27 final size:28
Alignment explanation
Indices: 29725899--29725962 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
29725889 TATATGCTTG
29725899 TTTTTATTTAATTTTATTTATTTACGTA
1 TTTTTATTTAATTTTATTTATTTACGTA
* *
29725927 -TTTTATTTATTTGTTA-TT-TTTATGCTA
1 TTTTTATTTAATT-TTATTTATTTACG-TA
29725954 TTTTTATTT
1 TTTTTATTT
29725963 TTGCCTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 5 0.16
27 15 0.48
28 11 0.35
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (28 bp):
TTTTTATTTAATTTTATTTATTTACGTA
Found at i:29729374 original size:21 final size:21
Alignment explanation
Indices: 29729348--29729395 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
29729338 AGATTACTAT
29729348 CGATACAAGTGATAGTTCTAC
1 CGATACAAGTGATAGTTCTAC
29729369 CGATACAAGTGATAGTTCTAC
1 CGATACAAGTGATAGTTCTAC
29729390 CGATAC
1 CGATAC
29729396 TAAAAACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (21 bp):
CGATACAAGTGATAGTTCTAC
Found at i:29730113 original size:40 final size:43
Alignment explanation
Indices: 29730065--29730215 Score: 137
Period size: 44 Copynumber: 3.5 Consensus size: 43
29730055 AGGTTCATGT
* *
29730065 GTCTTCCTTTTTAACA-A-TCTTATGCTC-TACCGAGTCATAA
1 GTCTTCCTTTTTAACATATTCTCACGCTCGTACCGAGTCATAA
* **
29730105 GTCTTCCTTCTTAAACATATTCTCACGCTCGTTTCGAGTCATAA
1 GTCTTCCTT-TTTAACATATTCTCACGCTCGTACCGAGTCATAA
* * ** * *
29730149 GTCTTCCTTTTTAAGCATATTCTCATGCTCATTTCAAGTCATGA
1 GTCTTCCTTTTTAA-CATATTCTCACGCTCGTACCGAGTCATAA
* *
29730193 GTCTTTCCTTCTAAACATATTCT
1 GTC-TTCCTTTTTAACATATTCT
29730216 GTAACAGCCC
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
40 9 0.10
41 6 0.06
42 1 0.01
43 12 0.13
44 56 0.60
45 9 0.10
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (43 bp):
GTCTTCCTTTTTAACATATTCTCACGCTCGTACCGAGTCATAA
Found at i:29730147 original size:44 final size:44
Alignment explanation
Indices: 29730095--29730215 Score: 172
Period size: 44 Copynumber: 2.8 Consensus size: 44
29730085 TATGCTCTAC
*
29730095 CGAGTCATAAGTCTTCCTTCTTAAACATATTCTCACGCTCGTTT
1 CGAGTCATAAGTCTTCCTTCTTAAACATATTCTCACGCTCATTT
* * *
29730139 CGAGTCATAAGTCTTCCTTTTTAAGCATATTCTCATGCTCATTT
1 CGAGTCATAAGTCTTCCTTCTTAAACATATTCTCACGCTCATTT
* *
29730183 CAAGTCATGAGTCTTTCCTTC-TAAACATATTCT
1 CGAGTCATAAGTC-TTCCTTCTTAAACATATTCT
29730216 GTAACAGCCC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 62 0.91
45 6 0.09
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (44 bp):
CGAGTCATAAGTCTTCCTTCTTAAACATATTCTCACGCTCATTT
Found at i:29731965 original size:52 final size:52
Alignment explanation
Indices: 29731873--29732064 Score: 321
Period size: 52 Copynumber: 3.7 Consensus size: 52
29731863 AATGAAAAAG
* *
29731873 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
29731925 GGTCTGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
29731977 GGTCCGATGGCTATGTGTCATCATGAGTATATGAATCCTTTATGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
29732029 GGTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAAT
29732065 GAAATGAAAT
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 130 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (52 bp):
GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:29738512 original size:18 final size:17
Alignment explanation
Indices: 29738482--29738529 Score: 78
Period size: 18 Copynumber: 2.8 Consensus size: 17
29738472 TGCATGCATA
*
29738482 GCATTTTAGTTGTCATT
1 GCATTTTATTTGTCATT
29738499 GCATTTTTATTTGTCATT
1 GCA-TTTTATTTGTCATT
29738517 GCATTTTATTTGT
1 GCATTTTATTTGT
29738530 TAGTACATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.58
Consensus pattern (17 bp):
GCATTTTATTTGTCATT
Found at i:29738538 original size:17 final size:17
Alignment explanation
Indices: 29738483--29738539 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
29738473 GCATGCATAG
* * *
29738483 CATTTTAGTTGTCATTG
1 CATTTTATTTGTCAGTA
* *
29738500 CATTTTTATTTGTCATTG
1 CA-TTTTATTTGTCAGTA
*
29738518 CATTTTATTTGTTAGTA
1 CATTTTATTTGTCAGTA
29738535 CATTT
1 CATTT
29738540 GCATTGTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 19 0.54
18 16 0.46
ACGTcount: A:0.19, C:0.11, G:0.12, T:0.58
Consensus pattern (17 bp):
CATTTTATTTGTCAGTA
Found at i:29743231 original size:37 final size:37
Alignment explanation
Indices: 29743169--29743261 Score: 132
Period size: 37 Copynumber: 2.5 Consensus size: 37
29743159 GAATCCAAAT
* * * *
29743169 TTGCACCCAAAATTGTCGTCGCATGAGCACTTCTAGA
1 TTGCACCCAAAACTGTCGCCACATGAGCACTTCCAGA
* *
29743206 TTGCGCCCCAAACTGTCGCCACATGAGCACTTCCAGA
1 TTGCACCCAAAACTGTCGCCACATGAGCACTTCCAGA
29743243 TTGCACCCAAAACTGTCGC
1 TTGCACCCAAAACTGTCGC
29743262 TGCAAGAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (37 bp):
TTGCACCCAAAACTGTCGCCACATGAGCACTTCCAGA
Found at i:29753645 original size:24 final size:26
Alignment explanation
Indices: 29753587--29753647 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 26
29753577 GGGTGTTGAG
* *
29753587 AAGAGGAAG-AGAAAAGAGAATAAGA
1 AAGAAGAAGAAGAAAAGAGAAAAAGA
29753612 AAGAAG-AGAAGAAAAG-GAAAAAGA
1 AAGAAGAAGAAGAAAAGAGAAAAAGA
*
29753636 AA-ATGAAGAAGA
1 AAGAAGAAGAAGA
29753648 TTTTATGCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 2 0.06
24 17 0.55
25 12 0.39
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (26 bp):
AAGAAGAAGAAGAAAAGAGAAAAAGA
Found at i:29760507 original size:40 final size:40
Alignment explanation
Indices: 29760457--29760550 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
29760447 AGGTTCATGT
*
29760457 GTCTTCCTTTTTAACAATCTTATGCTCTACTAAGTCATAA
1 GTCTTCCTTTTTAACAATCTTATGCTCTACCAAGTCATAA
* * *
29760497 GTCTTTCTTTTTAACAATCTTATGCTGTACCGAGTCATAA
1 GTCTTCCTTTTTAACAATCTTATGCTCTACCAAGTCATAA
29760537 GTCTTCCTTTTTAA
1 GTCTTCCTTTTTAA
29760551 ACATATTCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (40 bp):
GTCTTCCTTTTTAACAATCTTATGCTCTACCAAGTCATAA
Found at i:29760586 original size:44 final size:44
Alignment explanation
Indices: 29760527--29760770 Score: 345
Period size: 44 Copynumber: 5.6 Consensus size: 44
29760517 TATGCTGTAC
*
29760527 CGAGTCATAAGTCTTCCTTTTTAAACATATTCTCATGCTCATTT
1 CGAGTCATGAGTCTTCCTTTTTAAACATATTCTCATGCTCATTT
* * *
29760571 CGAGTCATGATTCTTCCTTTTAAAACATATTCTCACGCTCATTT
1 CGAGTCATGAGTCTTCCTTTTTAAACATATTCTCATGCTCATTT
*
29760615 CGAGTCATGAGTCTTCCTTTTTAAACATATTCTCACGCTCATTT
1 CGAGTCATGAGTCTTCCTTTTTAAACATATTCTCATGCTCATTT
*
29760659 CAAGTCATGAGTCTTCCTTTTTAAACATATTCTCACT-CTCATTT
1 CGAGTCATGAGTCTTCCTTTTTAAACATATTCTCA-TGCTCATTT
* * *
29760703 CGAGTCATGAGTCTTCC--TTT-AACACATTCTCATTCTCATCT
1 CGAGTCATGAGTCTTCCTTTTTAAACATATTCTCATGCTCATTT
* *
29760744 CGAGACATGATTCTTCC-TTTTAAACAT
1 CGAGTCATGAGTCTTCCTTTTTAAACAT
29760771 CAAGAAATTC
Statistics
Matches: 182, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
40 1 0.01
41 32 0.18
42 6 0.03
43 4 0.02
44 139 0.76
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.41
Consensus pattern (44 bp):
CGAGTCATGAGTCTTCCTTTTTAAACATATTCTCATGCTCATTT
Found at i:29765434 original size:3 final size:3
Alignment explanation
Indices: 29765426--29765484 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
29765416 CATGTTTGTA
* * *
29765426 ATT ATT ATT GTT GTT GTT 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
29765474 ATT ATT ATT AT
1 ATT ATT ATT AT
29765485 AGTTGTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:29765571 original size:19 final size:19
Alignment explanation
Indices: 29765529--29765571 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
29765519 TATTATTACT
29765529 TTATTATTTTTTTATTGTA
1 TTATTATTTTTTTATTGTA
* *
29765548 GTATT-TTTTATTTATTTTA
1 TTATTATTTT-TTTATTGTA
29765567 TTATT
1 TTATT
29765572 CATGTAGCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (19 bp):
TTATTATTTTTTTATTGTA
Found at i:29771966 original size:20 final size:20
Alignment explanation
Indices: 29771930--29771969 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29771920 AATAAATTAA
*
29771930 GAAATTGTATTTTAAAAAAT
1 GAAATTGTATTTGAAAAAAT
29771950 GAAATTGT-TTTGGAAAAAAT
1 GAAATTGTATTT-GAAAAAAT
29771970 AATTTTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (20 bp):
GAAATTGTATTTGAAAAAAT
Found at i:29775699 original size:10 final size:10
Alignment explanation
Indices: 29775636--29775715 Score: 53
Period size: 10 Copynumber: 8.3 Consensus size: 10
29775626 CGACACAGAT
29775636 TAATTAAATA
1 TAATTAAATA
*
29775646 TTATTAAA-A
1 TAATTAAATA
29775655 -AATTAAA-A
1 TAATTAAATA
*
29775663 T-ATACAAATA
1 TAAT-TAAATA
* *
29775673 AAAATAAA-A
1 TAATTAAATA
29775682 TAATTAAATA
1 TAATTAAATA
* *
29775692 TTATTAAAAA
1 TAATTAAATA
29775702 TAATTAAATTA
1 TAATTAAA-TA
29775713 TAA
1 TAA
29775716 AAATAACATA
Statistics
Matches: 52, Mismatches: 12, Indels: 11
0.69 0.16 0.15
Matches are distributed among these distances:
8 9 0.17
9 11 0.21
10 27 0.52
11 5 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (10 bp):
TAATTAAATA
Found at i:29775718 original size:17 final size:20
Alignment explanation
Indices: 29775678--29775721 Score: 67
Period size: 17 Copynumber: 2.4 Consensus size: 20
29775668 AAATAAAAAT
29775678 AAAATAATTAAATATTATTA
1 AAAATAATTAAATATTATTA
29775698 AAAATAATT-AA-ATTA-TA
1 AAAATAATTAAATATTATTA
29775715 AAAATAA
1 AAAATAA
29775722 CATAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.38
18 4 0.17
19 2 0.08
20 9 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATAATTAAATATTATTA
Found at i:29775718 original size:18 final size:20
Alignment explanation
Indices: 29775678--29775718 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
29775668 AAATAAAAAT
*
29775678 AAAATAATTAAATATTATTA
1 AAAATAATTAAATATTATAA
29775698 AAAATAATT-AA-ATTATAA
1 AAAATAATTAAATATTATAA
29775716 AAA
1 AAA
29775719 TAACATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATAATTAAATATTATAA
Found at i:29775729 original size:42 final size:43
Alignment explanation
Indices: 29775636--29775732 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 43
29775626 CGACACAGAT
29775636 TAATTAAATATTATTAAAAAATTAAAATATACAAATAAAAATAAAA
1 TAATTAAATATTATTAAAAAATTAAAATAT---AATAAAAATAAAA
*
29775682 TAATTAAATATTATTAAAAATAATT-AAAT-T-ATAAAAATAACA
1 TAATTAAATATTATT-AAAA-AATTAAAATATAATAAAAATAAAA
29775724 TAATTAAAT
1 TAATTAAAT
29775733 TAAACGAATT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
42 20 0.42
46 16 0.33
47 8 0.17
48 4 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (43 bp):
TAATTAAATATTATTAAAAAATTAAAATATAATAAAAATAAAA
Found at i:29777144 original size:27 final size:27
Alignment explanation
Indices: 29777059--29777146 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
29777049 AAATTTCGGG
*
29777059 TGGTGCCTA-TGAGGTAGGTGACACTAA
1 TGGTGCCTATTG-GGTAGGTGGCACTAA
* * *
29777086 TGGTACCTATTGGGTAGGCGGCACCAA
1 TGGTGCCTATTGGGTAGGTGGCACTAA
*
29777113 TGGTGCCTATTGGGTAGGTGGCACTAG
1 TGGTGCCTATTGGGTAGGTGGCACTAA
29777140 TGGTGCC
1 TGGTGCC
29777147 ATTCAGATAG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
27 50 0.96
28 2 0.04
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.26
Consensus pattern (27 bp):
TGGTGCCTATTGGGTAGGTGGCACTAA
Found at i:29777158 original size:54 final size:54
Alignment explanation
Indices: 29777059--29777163 Score: 124
Period size: 54 Copynumber: 1.9 Consensus size: 54
29777049 AAATTTCGGG
* * *
29777059 TGGTGCCTATGAGGTAGGTGACACTAATGGTACCTATTGGGTAGGCGGCACCAA
1 TGGTGCCTATGAGGTAGGTGACACTAATGGTACCTATTAGATAGGCAGCACCAA
* * *
29777113 TGGTGCCTATTG-GGTAGGTGGCACTAGTGGTGCC-ATTCAGATAGGCAGCAC
1 TGGTGCCTA-TGAGGTAGGTGACACTAATGGTACCTATT-AGATAGGCAGCAC
29777164 TAGTGCCTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
53 3 0.07
54 38 0.88
55 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (54 bp):
TGGTGCCTATGAGGTAGGTGACACTAATGGTACCTATTAGATAGGCAGCACCAA
Found at i:29777247 original size:20 final size:20
Alignment explanation
Indices: 29777205--29777251 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29777195 GTTTAAACAT
* *
29777205 AAATTTTTGAAGAAGGAGAC
1 AAATTTTTGAAAAAGAAGAC
29777225 AAATTTTTGAACAAAGAAG-C
1 AAATTTTTGAA-AAAGAAGAC
29777245 AAATTTT
1 AAATTTT
29777252 GTTCAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (20 bp):
AAATTTTTGAAAAAGAAGAC
Found at i:29780281 original size:23 final size:24
Alignment explanation
Indices: 29780255--29780319 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 24
29780245 TATATTTTGG
29780255 TTTAAGGTTTATGCTTTTCAGGA-
1 TTTAAGGTTTATGCTTTTCAGGAT
*
29780278 TTTAAGGTTTATGATTTTCAGGAT
1 TTTAAGGTTTATGCTTTTCAGGAT
* *
29780302 TTTAAGGTTAAGGCTTTT
1 TTTAAGGTTTATGCTTTT
29780320 ACATAAATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 22 0.59
24 15 0.41
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.49
Consensus pattern (24 bp):
TTTAAGGTTTATGCTTTTCAGGAT
Found at i:29780588 original size:6 final size:6
Alignment explanation
Indices: 29780579--29780643 Score: 60
Period size: 6 Copynumber: 10.5 Consensus size: 6
29780569 ACTTAAACCC
* * *
29780579 TAAACA TAAACA TAAACA TAAACA TAATTA-A TTAAATA CAAACA TAAATA
1 TAAACA TAAACA TAAACA TAAACA TAA--ACA -TAAACA TAAACA TAAACA
*
29780629 TAAACG TAAACA TAA
1 TAAACA TAAACA TAA
29780644 TTAATTAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
6 42 0.88
7 2 0.04
8 4 0.08
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.23
Consensus pattern (6 bp):
TAAACA
Found at i:29780621 original size:20 final size:20
Alignment explanation
Indices: 29780598--29780663 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
29780588 ACATAAACAT
29780598 AAACATAATTAATTAAATAC
1 AAACATAATTAATTAAATAC
* ***
29780618 AAACATAAAT-A-TAAACGT
1 AAACATAATTAATTAAATAC
29780636 AAACATAATTAATTAAATAC
1 AAACATAATTAATTAAATAC
29780656 AAACATAA
1 AAACATAA
29780664 ACATAATTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 13 0.36
19 2 0.06
20 21 0.58
ACGTcount: A:0.62, C:0.11, G:0.02, T:0.26
Consensus pattern (20 bp):
AAACATAATTAATTAAATAC
Found at i:29780622 original size:38 final size:38
Alignment explanation
Indices: 29780580--29780669 Score: 162
Period size: 38 Copynumber: 2.4 Consensus size: 38
29780570 CTTAAACCCT
29780580 AAACATAAACATAAACATAAACATAATTAATTAAATAC
1 AAACATAAACATAAACATAAACATAATTAATTAAATAC
* *
29780618 AAACATAAATATAAACGTAAACATAATTAATTAAATAC
1 AAACATAAACATAAACATAAACATAATTAATTAAATAC
29780656 AAACATAAACATAA
1 AAACATAAACATAA
29780670 TTAATTCCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.63, C:0.12, G:0.01, T:0.23
Consensus pattern (38 bp):
AAACATAAACATAAACATAAACATAATTAATTAAATAC
Found at i:29780652 original size:26 final size:26
Alignment explanation
Indices: 29780623--29780675 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
29780613 AATACAAACA
* *
29780623 TAAATATAAACGTAAACATAATTAAT
1 TAAATACAAACATAAACATAATTAAT
29780649 TAAATACAAACATAAACATAATTAAT
1 TAAATACAAACATAAACATAATTAAT
29780675 T
1 T
29780676 CCAAATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (26 bp):
TAAATACAAACATAAACATAATTAAT
Found at i:29781191 original size:24 final size:24
Alignment explanation
Indices: 29781164--29781225 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
29781154 AGCTCTAGAA
29781164 CATGCTCGGGCTCGAGATCGAGCT
1 CATGCTCGGGCTCGAGATCGAGCT
** * * *
29781188 CATGCTTAGGCTCAAGCTCGGGCT
1 CATGCTCGGGCTCGAGATCGAGCT
**
29781212 CGGGCTCGGGCTCG
1 CATGCTCGGGCTCG
29781226 GGCGTTAGCA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.31, G:0.35, T:0.21
Consensus pattern (24 bp):
CATGCTCGGGCTCGAGATCGAGCT
Found at i:29781212 original size:6 final size:6
Alignment explanation
Indices: 29781203--29781228 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29781193 TTAGGCTCAA
29781203 GCTCGG GCTCGG GCTCGG GCTCGG GC
1 GCTCGG GCTCGG GCTCGG GCTCGG GC
29781229 GTTAGCAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.50, T:0.15
Consensus pattern (6 bp):
GCTCGG
Done.