Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 20 of 145
Found at i:6360192 original size:20 final size:20
Alignment explanation
Indices: 6360156--6360211 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
6360146 TAATAATGAG
6360156 AATAAAAA-AAAGTAAAAGTAAA
1 AATAAAAATAAA--AAAA-TAAA
*
6360178 AATAAAACTAAAAAAATAAA
1 AATAAAAATAAAAAAATAAA
6360198 AATAAAAATAAAAA
1 AATAAAAATAAAAA
6360212 TCTATGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.55
21 4 0.13
22 7 0.23
23 3 0.10
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (20 bp):
AATAAAAATAAAAAAATAAA
Found at i:6360198 original size:6 final size:6
Alignment explanation
Indices: 6360162--6360212 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
6360152 TGAGAATAAA
* *
6360162 AAAAAGT AAAAGT AAAAAT AAAACTAA AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAA-T AAAAAT AAAAAT AAAA--AT AAAAAT AAAAAT AAAAAT AAAAAT
6360213 CTATGTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 29 0.76
7 4 0.11
8 5 0.13
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:6367118 original size:45 final size:45
Alignment explanation
Indices: 6367067--6367158 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
6367057 AGTAAAAGAT
*
6367067 ACACAAATAACCAGCCAAAGGCACACCCAAATGTTCGACACAACA
1 ACACAAATAACCAACCAAAGGCACACCCAAATGTTCGACACAACA
6367112 ACACAAATAACCAACCAAAGGCACACCCAAATGTTCGACACAACA
1 ACACAAATAACCAACCAAAGGCACACCCAAATGTTCGACACAACA
6367157 AC
1 AC
6367159 CTATTTATAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.48, C:0.34, G:0.10, T:0.09
Consensus pattern (45 bp):
ACACAAATAACCAACCAAAGGCACACCCAAATGTTCGACACAACA
Found at i:6373187 original size:57 final size:59
Alignment explanation
Indices: 6373123--6373244 Score: 178
Period size: 61 Copynumber: 2.1 Consensus size: 59
6373113 GTTACACATA
6373123 AGTCACTAAATTATG-AGAATCAGA-TTCCGTTATGGTTAATT-AAAAAAATTACAATTT
1 AGTCACTAAATTATGAAGAATCA-ATTTCCGTTATGGTTAATTAAAAAAAATTACAATTT
*
6373180 AGTCACTAAATTATGAATAAGAATCAATTTTCGTTATGGTTAATTAAAAAAAATTACAATTT
1 AGTCACTAAATTATG---AAGAATCAATTTCCGTTATGGTTAATTAAAAAAAATTACAATTT
6373242 AGT
1 AGT
6373245 TATTTAATTG
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
57 15 0.26
60 1 0.02
61 23 0.40
62 19 0.33
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (59 bp):
AGTCACTAAATTATGAAGAATCAATTTCCGTTATGGTTAATTAAAAAAAATTACAATTT
Found at i:6373788 original size:31 final size:30
Alignment explanation
Indices: 6373748--6373816 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
6373738 CAACCCAATG
* *
6373748 ACTAGAATGAAAACATTT-GAATAGTTTAGTG
1 ACTA-AATGAAAAC-TTTCGAATAATTTAGTA
6373779 ACATAAATGAAAACTTTCGAATAATTTAGTA
1 AC-TAAATGAAAACTTTCGAATAATTTAGTA
6373810 ACTAAAT
1 ACTAAAT
6373817 TGTAACTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 8 0.24
31 24 0.71
32 2 0.06
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (30 bp):
ACTAAATGAAAACTTTCGAATAATTTAGTA
Found at i:6374986 original size:38 final size:38
Alignment explanation
Indices: 6374944--6375016 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
6374934 TACATAGAAA
6374944 ATCAAAATAAATTT-AGACACATGATATTTATATATATG
1 ATCAAAATAAATTTCA-ACACATGATATTTATATATATG
* * *
6374982 ATCAAAGTAAATTTCAACACGTGATATTTGTATAT
1 ATCAAAATAAATTTCAACACATGATATTTATATAT
6375017 GTAATTAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
38 30 0.97
39 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (38 bp):
ATCAAAATAAATTTCAACACATGATATTTATATATATG
Found at i:6377952 original size:15 final size:15
Alignment explanation
Indices: 6377929--6377964 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6377919 CTAACCCGAC
*
6377929 CCTTGAATCCCTAAA
1 CCTTAAATCCCTAAA
*
6377944 CCTTAAATCCCTAAC
1 CCTTAAATCCCTAAA
6377959 CCTTAA
1 CCTTAA
6377965 CCTATAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (15 bp):
CCTTAAATCCCTAAA
Found at i:6377961 original size:21 final size:21
Alignment explanation
Indices: 6377940--6378020 Score: 87
Period size: 21 Copynumber: 3.8 Consensus size: 21
6377930 CTTGAATCCC
6377940 TAAACCTTAAATCCCTAACCCT
1 TAAACC-TAAATCCCTAACCCT
**
6377962 T-AACCTATAATGTCTAACCCT
1 TAAACCTA-AATCCCTAACCCT
6377983 TAAACCCTAAATCCC-AACCCT
1 TAAA-CCTAAATCCCTAACCCT
6378004 TAAACC-ATAATCCCTAA
1 TAAACCTA-AATCCCTAA
6378021 TCCATAATCC
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.02
20 10 0.20
21 28 0.56
22 7 0.14
23 4 0.08
ACGTcount: A:0.38, C:0.35, G:0.01, T:0.26
Consensus pattern (21 bp):
TAAACCTAAATCCCTAACCCT
Found at i:6378037 original size:15 final size:15
Alignment explanation
Indices: 6377987--6378051 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 15
6377977 AACCCTTAAA
*
6377987 CCCTAAATCC-CAA-
1 CCCTAAATCCATAAT
6378000 CCCTTAAA-CCATAAT
1 CCC-TAAATCCATAAT
6378015 CCCT-AATCCATAAT
1 CCCTAAATCCATAAT
* *
6378029 CCCTAAATCTATACT
1 CCCTAAATCCATAAT
6378044 CCCCTAAA
1 -CCCTAAA
6378052 CCTTAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
13 7 0.16
14 18 0.42
15 11 0.26
16 7 0.16
ACGTcount: A:0.37, C:0.38, G:0.00, T:0.25
Consensus pattern (15 bp):
CCCTAAATCCATAAT
Found at i:6379009 original size:41 final size:40
Alignment explanation
Indices: 6378691--6379007 Score: 309
Period size: 41 Copynumber: 7.8 Consensus size: 40
6378681 AATGTTTTTT
*
6378691 GCGGCGCTTTTTCAAAAATGCCGCTAAAGA--CCGAGCATTA
1 GCGGCGC-TTTTCAAAAACGCCGCTAAA-ACCCCGAGCATTA
* *
6378731 GCGGCGCCTTTTCACAAATGCCGCTAAAACCCCGAGCATTA
1 GCGGCG-CTTTTCAAAAACGCCGCTAAAACCCCGAGCATTA
* * * * * **
6378772 GCAGCACTTTTCCAAAAACGCCGTTAAAGCTCTTAGCATTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAACCCCGAGCATTA
* * * *
6378813 GCGGCGCATTTGCAAAACCACCGCTAAAACCCCTAGCATTA
1 GCGGCGC-TTTTCAAAAACGCCGCTAAAACCCCGAGCATTA
* * * *
6378854 GCGGCGCATTTGCAAAACCGCTGCTAAAACCCCTAGCATTA
1 GCGGCGC-TTTTCAAAAACGCCGCTAAAACCCCGAGCATTA
* *
6378895 GCGGCGCTTTTCCAAAAATGCCGCTAAAACCTCGAG--TTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAACCCCGAGCATTA
* *
6378934 GCGGCGCTTTTTCAAAAACGTCGCTAAAACCCCAAGCATTA
1 GCGGCGC-TTTTCAAAAACGCCGCTAAAACCCCGAGCATTA
* *
6378975 GCGGCGCTTTCTCAAAAACGCCACTAAAGCCCC
1 GCGGCGCTTT-TCAAAAACGCCGCTAAAACCCC
6379008 AAAAGGTGAC
Statistics
Matches: 233, Mismatches: 34, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
39 31 0.13
40 40 0.17
41 159 0.68
42 3 0.01
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.21
Consensus pattern (40 bp):
GCGGCGCTTTTCAAAAACGCCGCTAAAACCCCGAGCATTA
Found at i:6379135 original size:40 final size:40
Alignment explanation
Indices: 6379064--6379142 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 40
6379054 TAATGCTCTT
* * * * *
6379064 TTTAGCGGCGTTTTTCAGAAATCGCCACTAATGTTCGATC
1 TTTAGCGGCATTTTCCAGAAAGCACCACTAATGCTCGATC
* *
6379104 TTTAGCGGCATTTTCCATAAAGCACCGCTAATGCTCGAT
1 TTTAGCGGCATTTTCCAGAAAGCACCACTAATGCTCGAT
6379143 TTTTCCCATC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (40 bp):
TTTAGCGGCATTTTCCAGAAAGCACCACTAATGCTCGATC
Found at i:6386384 original size:152 final size:152
Alignment explanation
Indices: 6386108--6386417 Score: 557
Period size: 152 Copynumber: 2.0 Consensus size: 152
6386098 AAAATAGCAT
*
6386108 CCAATCCCCCTTCCCATGACCGGCCATGTGTAACACCCTTATCCTGTACCCATTGTTGGAATAGG
1 CCAATCCCCCTTCCCATGACCGGCCATGTGTAACACCCTTATCCCGTACCCATTGTTGGAATAGG
* *
6386173 GTTACGGAGCATTATCGAAAGTTTACACCTCAAAACTATCAAATATTCAAAACATTTAAATCATA
66 GTTACGGAGCATTATCAAAAGTTTACAACTCAAAACTATCAAATATTCAAAACATTTAAATCATA
6386238 ACATCATTCATAGAAAAATCAA
131 ACATCATTCATAGAAAAATCAA
* * *
6386260 CCAATCCCCTTTCCCATGACCGGCCATGTGTAACACTCTTATCCCGTATCCATTGTTGGAATAGG
1 CCAATCCCCCTTCCCATGACCGGCCATGTGTAACACCCTTATCCCGTACCCATTGTTGGAATAGG
6386325 GTTACGGAGCATTATCAAAAGTTTACAACTCAAAACTATCAAATATTCAAAACATTTAAATCATA
66 GTTACGGAGCATTATCAAAAGTTTACAACTCAAAACTATCAAATATTCAAAACATTTAAATCATA
6386390 ACATCATTCATAGAAAAATCAA
131 ACATCATTCATAGAAAAATCAA
*
6386412 TCAATC
1 CCAATC
6386418 TCACACATAT
Statistics
Matches: 151, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 151 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (152 bp):
CCAATCCCCCTTCCCATGACCGGCCATGTGTAACACCCTTATCCCGTACCCATTGTTGGAATAGG
GTTACGGAGCATTATCAAAAGTTTACAACTCAAAACTATCAAATATTCAAAACATTTAAATCATA
ACATCATTCATAGAAAAATCAA
Found at i:6395249 original size:44 final size:44
Alignment explanation
Indices: 6395194--6395442 Score: 340
Period size: 44 Copynumber: 5.7 Consensus size: 44
6395184 ACAGTCTTTG
* *
6395194 CCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACATTCTTCCT
1 CCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCA
* ** * * *
6395238 CCTATTGCACTGCTATTCAGGGAGCTAGGACTTATAGTCTTCCA
1 CCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCA
* *
6395282 CCTATTCCACTGCTGGTCAGGAAGCTAGGATTTACAATCTTCCG
1 CCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCA
* *
6395326 CCTATTCCACTGCT-TTCAGGGAGCTAGGACTTT-CAGTCTTCCA
1 CCTATTCCACTGCTGGTCAGGGAGCTAGGA-TTTACAATCTTCCA
* *
6395369 CCTATTCCAATGCTGGTCAGGGAGCTAGGATTTATAATCTTCCA
1 CCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCA
*
6395413 CCTATTCCACTGCTGTTCAGGGAGCTAGGA
1 CCTATTCCACTGCTGGTCAGGGAGCTAGGA
6395443 CTTATAGTTT
Statistics
Matches: 177, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
43 37 0.21
44 140 0.79
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (44 bp):
CCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCA
Found at i:6395366 original size:131 final size:132
Alignment explanation
Indices: 6395193--6395442 Score: 378
Period size: 131 Copynumber: 1.9 Consensus size: 132
6395183 TACAGTCTTT
* * * * *
6395193 GCCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACATTCTTCCTCCTATTGCACTGCTATTCAG
1 GCCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAGTCTTCCACCTATTCCAATGCTAGTCAG
*
6395258 GGAGCTAGGACTTATAGTCTTCCACCTATTCCACTGCTGGTCAGGAAGCTAGGATTTACAATCTT
66 GGAGCTAGGACTTATAATCTTCCACCTATTCCACTGCTGGTCAGGAAGCTAGGATTTACAATCTT
6395323 CC
131 CC
* *
6395325 GCCTATTCCACTGCT-TTCAGGGAGCTAGGACTTT-CAGTCTTCCACCTATTCCAATGCTGGTCA
1 GCCTATTCCACTGCTGGTCAGGGAGCTAGGA-TTTACAGTCTTCCACCTATTCCAATGCTAGTCA
* * *
6395388 GGGAGCTAGGATTTATAATCTTCCACCTATTCCACTGCTGTTCAGGGAGCTAGGA
65 GGGAGCTAGGACTTATAATCTTCCACCTATTCCACTGCTGGTCAGGAAGCTAGGA
6395443 CTTATAGTTT
Statistics
Matches: 106, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
131 88 0.83
132 18 0.17
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (132 bp):
GCCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAGTCTTCCACCTATTCCAATGCTAGTCAG
GGAGCTAGGACTTATAATCTTCCACCTATTCCACTGCTGGTCAGGAAGCTAGGATTTACAATCTT
CC
Found at i:6395395 original size:87 final size:88
Alignment explanation
Indices: 6395171--6395445 Score: 412
Period size: 87 Copynumber: 3.1 Consensus size: 88
6395161 TACTGCTCAC
* * ** *
6395171 GGAGCTGGGACTTACAGTCTT-TGCCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACATTCTT
1 GGAGCTAGGACTTTCAGTCTTCCACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTT
* *
6395235 CCTCCTATTGCACTGCTATTCAG
66 CCACCTATTCCACTGCTATTCAG
*
6395258 GGAGCTAGGACTTAT-AGTCTTCCACCTATTCCACTGCTGGTCAGGAAGCTAGGATTTACAATCT
1 GGAGCTAGGACTT-TCAGTCTTCCACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCT
*
6395322 TCCGCCTATTCCACTGCT-TTCAG
65 TCCACCTATTCCACTGCTATTCAG
* *
6395345 GGAGCTAGGACTTTCAGTCTTCCACCTATTCCAATGCTGGTCAGGGAGCTAGGATTTATAATCTT
1 GGAGCTAGGACTTTCAGTCTTCCACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTT
*
6395410 CCACCTATTCCACTGCTGTTCAG
66 CCACCTATTCCACTGCTATTCAG
6395433 GGAGCTAGGACTT
1 GGAGCTAGGACTT
6395446 ATAGTTTCAC
Statistics
Matches: 172, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
86 1 0.01
87 99 0.58
88 72 0.42
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (88 bp):
GGAGCTAGGACTTTCAGTCTTCCACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTT
CCACCTATTCCACTGCTATTCAG
Found at i:6398437 original size:26 final size:26
Alignment explanation
Indices: 6398383--6398479 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 26
6398373 TGATAGTAAC
* *
6398383 TAAAAATTTACAATTTTGTCCCTATTTT
1 TAAAATTTTACAA-TTT-CCCCTATTTT
* *
6398411 TTACATTTTACAATTTCCCCTATTTT
1 TAAAATTTTACAATTTCCCCTATTTT
* ** * *
6398437 TCAGGTTTTATAATTTTCCCTTATTTT
1 TAAAATTTTACAA-TTTCCCCTATTTT
*
6398464 TAAAATTTTACTATTT
1 TAAAATTTTACAATTT
6398480 TGACCCAAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
26 21 0.39
27 23 0.43
28 10 0.19
ACGTcount: A:0.27, C:0.15, G:0.03, T:0.55
Consensus pattern (26 bp):
TAAAATTTTACAATTTCCCCTATTTT
Found at i:6398454 original size:27 final size:26
Alignment explanation
Indices: 6398402--6398479 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 26
6398392 ACAATTTTGT
*
6398402 CCCTATTTTTTACATTTTACAATTTC
1 CCCTATTTTTCACATTTTACAATTTC
** *
6398428 CCCTATTTTTCAGGTTTTATAATTTTC
1 CCCTATTTTTCACATTTTACAA-TTTC
* * * *
6398455 CCTTATTTTTAAAATTTTACTATTT
1 CCCTATTTTTCACATTTTACAATTT
6398480 TGACCCAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 21 0.51
27 20 0.49
ACGTcount: A:0.23, C:0.18, G:0.03, T:0.56
Consensus pattern (26 bp):
CCCTATTTTTCACATTTTACAATTTC
Found at i:6398480 original size:27 final size:26
Alignment explanation
Indices: 6398383--6398480 Score: 72
Period size: 26 Copynumber: 3.7 Consensus size: 26
6398373 TGATAGTAAC
* *
6398383 TAAAAATTTACAATTTTGTCCCTATTTT
1 TAAAATTTTACTA-TTT-TCCCTATTTT
* * * *
6398411 TTACATTTTACAATTTCCCCTATTTT
1 TAAAATTTTACTATTTTCCCTATTTT
* **
6398437 TCAGGTTTTA-TAATTTTCCCTTATTTT
1 TAAAATTTTACT-ATTTTCCC-TATTTT
6398464 TAAAATTTTACTATTTT
1 TAAAATTTTACTATTTT
6398481 GACCCAAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
26 23 0.42
27 21 0.38
28 11 0.20
ACGTcount: A:0.27, C:0.15, G:0.03, T:0.55
Consensus pattern (26 bp):
TAAAATTTTACTATTTTCCCTATTTT
Found at i:6407772 original size:50 final size:50
Alignment explanation
Indices: 6407646--6407884 Score: 196
Period size: 50 Copynumber: 4.7 Consensus size: 50
6407636 GATAATAACA
* * * ** * * *
6407646 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGAGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* ** * **
6407695 TGCCAATGACATACCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
6407745 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
6407795 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
6407851 TGCC-ATGTCTATGTCCCAGACATGGTCTTACATG
1 TGCCAATG-CCATGTCCCAGACATGGTCTTACATG
6407885 AGATCTCTTT
Statistics
Matches: 151, Mismatches: 30, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.23
50 81 0.54
53 2 0.01
55 2 0.01
56 30 0.20
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:6422629 original size:28 final size:28
Alignment explanation
Indices: 6422591--6422792 Score: 167
Period size: 28 Copynumber: 7.2 Consensus size: 28
6422581 TAACTCAGAA
* * *
6422591 TTTACAATTTTTCCCCTATTTTTTAGAT
1 TTTACAATTTTGCCCCTATTTTTCAAAT
*
6422619 TTTACAATTTTACCCCTATTTTTCAAAT
1 TTTACAATTTTGCCCCTATTTTTCAAAT
** * **
6422647 TTTACCCTTTTTCCATTATTTTTCAAAT
1 TTTACAATTTTGCCCCTATTTTTCAAAT
* ** *
6422675 TTTACTGA-TTTGAACCTA-TTTTCTAGAT
1 TTTAC-AATTTTGCCCCTATTTTTC-AAAT
*
6422703 TTTACAATTTTGCCCCTACTTTT-AAGAT
1 TTTACAATTTTGCCCCTATTTTTCAA-AT
* * * *
6422731 TATATAGTTTTGCCGCTATTTTTCAAAT
1 TTTACAATTTTGCCCCTATTTTTCAAAT
* *
6422759 TTTACAATTTTATCCCCTATTTTACAAAT
1 TTTACAATTTT-GCCCCTATTTTTCAAAT
6422788 TTTAC
1 TTTAC
6422793 TGTTTTGACC
Statistics
Matches: 136, Mismatches: 31, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
27 7 0.05
28 104 0.76
29 25 0.18
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.51
Consensus pattern (28 bp):
TTTACAATTTTGCCCCTATTTTTCAAAT
Found at i:6422751 original size:84 final size:84
Alignment explanation
Indices: 6422605--6422763 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
6422595 CAATTTTTCC
* * * * * *
6422605 CCTATTTTTTAGATTTTACAATTTTACCCCTATTTTTCAAATTTTACCCTTTTTCCATTATTTTT
1 CCTATTTTCTAGATTTTACAATTTTACCCCTACTTTTCAAATTATACACTTTTGCCACTATTTTT
6422670 CAAATTTTACTGATTTGAA
66 CAAATTTTACTGATTTGAA
* * * *
6422689 CCTATTTTCTAGATTTTACAATTTTGCCCCTACTTTT-AAGATTATATAGTTTTGCCGCTATTTT
1 CCTATTTTCTAGATTTTACAATTTTACCCCTACTTTTCAA-ATTATACACTTTTGCCACTATTTT
6422753 TCAAATTTTAC
65 TCAAATTTTAC
6422764 AATTTTATCC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
83 2 0.03
84 62 0.97
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.52
Consensus pattern (84 bp):
CCTATTTTCTAGATTTTACAATTTTACCCCTACTTTTCAAATTATACACTTTTGCCACTATTTTT
CAAATTTTACTGATTTGAA
Found at i:6427950 original size:26 final size:25
Alignment explanation
Indices: 6427915--6427975 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
6427905 TTGACAATTT
6427915 TTTTCAAAAAATAAAATATAAAAAA
1 TTTTCAAAAAATAAAATATAAAAAA
* ***
6427940 TTTTCAAAAAATAAAATTTAAATTT
1 TTTTCAAAAAATAAAATATAAAAAA
6427965 TTTTCAAAAAA
1 TTTTCAAAAAA
6427976 ATGAAATCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (25 bp):
TTTTCAAAAAATAAAATATAAAAAA
Found at i:6427988 original size:26 final size:24
Alignment explanation
Indices: 6427910--6427989 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 24
6427900 CTATTTTGAC
6427910 AATTTTTTTCAAAAAATAAAATATA
1 AATTTTTTTCAAAAAATAAAATA-A
*** *
6427935 AAAAATTTTCAAAAAATAAAATTTA
1 AATTTTTTTCAAAAAATAAAA-TAA
*
6427960 AATTTTTTTCAAAAAAATGAAATCAA
1 AATTTTTTTC-AAAAAATAAAAT-AA
6427986 AATT
1 AATT
6427990 AAATAAGATT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
25 27 0.63
26 16 0.37
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.36
Consensus pattern (24 bp):
AATTTTTTTCAAAAAATAAAATAA
Found at i:6429867 original size:28 final size:28
Alignment explanation
Indices: 6429835--6429982 Score: 108
Period size: 28 Copynumber: 5.4 Consensus size: 28
6429825 CCCTTGTAAC
6429835 TCAAAATTTATAGTTTTGCCCCTATTTT
1 TCAAAATTTATAGTTTTGCCCCTATTTT
*
6429863 TCAAAATTTATCA--TTTGCCCTTATTTT
1 TCAAAATTTAT-AGTTTTGCCCCTATTTT
* ** *
6429890 TCAAATTTTACCGTGTTT-ACCCTATTTT
1 TCAAAATTTATAGT-TTTGCCCCTATTTT
* * * * * * *
6429918 T-AGATTTTAAATTTTTTCTCTTATTTT
1 TCAAAATTTATAGTTTTGCCCCTATTTT
*
6429945 T-AAAATTTTATATTTTTGCCCCTATTTT
1 TCAAAA-TTTATAGTTTTGCCCCTATTTT
*
6429973 TCAAATTTTA
1 TCAAAATTTA
6429983 CAATGTTATC
Statistics
Matches: 93, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
26 3 0.03
27 40 0.43
28 43 0.46
29 7 0.08
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.55
Consensus pattern (28 bp):
TCAAAATTTATAGTTTTGCCCCTATTTT
Found at i:6429887 original size:27 final size:27
Alignment explanation
Indices: 6429835--6429899 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
6429825 CCCTTGTAAC
6429835 TCAAAATTTATAGTTTTGCCCCTATTTT
1 TCAAAATTTATAG-TTTGCCCCTATTTT
*
6429863 TCAAAATTTATCA-TTTGCCCTTATTTT
1 TCAAAATTTAT-AGTTTGCCCCTATTTT
*
6429890 TCAAATTTTA
1 TCAAAATTTA
6429900 CCGTGTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 22 0.65
28 11 0.32
29 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.51
Consensus pattern (27 bp):
TCAAAATTTATAGTTTGCCCCTATTTT
Found at i:6451485 original size:17 final size:18
Alignment explanation
Indices: 6451463--6451496 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6451453 GTCTTTACTT
6451463 TATTTTAA-TTCTTAGGA
1 TATTTTAAGTTCTTAGGA
6451480 TATTTTAAGTTCTTAGG
1 TATTTTAAGTTCTTAGG
6451497 CTTAGGTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (18 bp):
TATTTTAAGTTCTTAGGA
Found at i:6453945 original size:20 final size:19
Alignment explanation
Indices: 6453920--6453981 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
6453910 TCCACACCAG
6453920 AGGCACCAAAGTGCAGACAA
1 AGGCACCAAAGTGCA-ACAA
* *
6453940 AGGCA-CAAATGTGCAATTAG
1 AGGCACCAAA-GTGCAA-CAA
6453960 AGGCACCAAAGTGCAAACAA
1 AGGCACCAAAGTGC-AACAA
6453980 AG
1 AG
6453982 ACATTGAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 5 0.15
20 23 0.68
21 6 0.18
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (19 bp):
AGGCACCAAAGTGCAACAA
Found at i:6455245 original size:29 final size:29
Alignment explanation
Indices: 6455171--6455230 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
6455161 ACCACTTAAT
6455171 TTATGACATGATTTTCTACCTTATTGCAA
1 TTATGACATGATTTTCTACCTTATTGCAA
6455200 TTATGACATGATTTTCTACCTTATTGCAA
1 TTATGACATGATTTTCTACCTTATTGCAA
6455229 TT
1 TT
6455231 TAGTCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.47
Consensus pattern (29 bp):
TTATGACATGATTTTCTACCTTATTGCAA
Found at i:6455274 original size:50 final size:50
Alignment explanation
Indices: 6455197--6455291 Score: 172
Period size: 50 Copynumber: 1.9 Consensus size: 50
6455187 TACCTTATTG
*
6455197 CAATTATGACATGATTTTCTACCTTATTGCAATTTAGTCTTTTTTTTCTT
1 CAATTATGACATGATTTTCTACATTATTGCAATTTAGTCTTTTTTTTCTT
*
6455247 CAATTATGACATGATTTTCTACATTATTGCAGTTTAGTCTTTTTT
1 CAATTATGACATGATTTTCTACATTATTGCAATTTAGTCTTTTTT
6455292 CTTAAATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.23, C:0.15, G:0.09, T:0.53
Consensus pattern (50 bp):
CAATTATGACATGATTTTCTACATTATTGCAATTTAGTCTTTTTTTTCTT
Found at i:6457291 original size:19 final size:19
Alignment explanation
Indices: 6457267--6457311 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
6457257 TTACTTCAAT
*
6457267 ATGTTATGAA-TGATTACTA
1 ATGTTATCAATTG-TTACTA
6457286 ATGTTATCAATTTGTTACTA
1 ATGTTATCAA-TTGTTACTA
6457306 ATGTTA
1 ATGTTA
6457312 GCTTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 12 0.52
21 2 0.09
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (19 bp):
ATGTTATCAATTGTTACTA
Found at i:6458202 original size:38 final size:38
Alignment explanation
Indices: 6458160--6458244 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 38
6458150 TTACATAAAG
*
6458160 AATCAAAATAAACCT-AGACACGTGATATTTAT-ATACAC
1 AATCAAAATAAACCTCA-ACACGTGATATTT-TCAAACAC
* **
6458198 AATCACAATAATTCTCAACACGTGATATTTTCAAACAC
1 AATCAAAATAAACCTCAACACGTGATATTTTCAAACAC
*
6458236 AATGAAAAT
1 AATCAAAAT
6458245 CATTTTATGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 1 0.03
38 37 0.95
39 1 0.03
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.27
Consensus pattern (38 bp):
AATCAAAATAAACCTCAACACGTGATATTTTCAAACAC
Found at i:6458708 original size:20 final size:21
Alignment explanation
Indices: 6458680--6458729 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
6458670 CTTCAAAATC
* *
6458680 TTTATTTTTAAAAAATTAA-T
1 TTTAATTTTAAAAAAGTAACT
*
6458700 TTTAATTTTTAAAAAGTAACT
1 TTTAATTTTAAAAAAGTAACT
6458721 TTATAATTT
1 TT-TAATTT
6458730 ATAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.64
21 3 0.12
22 6 0.24
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTAATTTTAAAAAAGTAACT
Found at i:6459831 original size:51 final size:51
Alignment explanation
Indices: 6459755--6459869 Score: 212
Period size: 51 Copynumber: 2.3 Consensus size: 51
6459745 TCCTCTCTAA
6459755 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
6459806 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
6459857 TCCCCTCAATTTC
1 TCCTCTCAATTTC
6459870 ATTTTTTAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (51 bp):
TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
Found at i:6459905 original size:30 final size:32
Alignment explanation
Indices: 6459871--6459935 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
6459861 CTCAATTTCA
6459871 TTTTTT-AAAATAATTTTAAA-TTTTTTATAT
1 TTTTTTAAAAATAATTTTAAATTTTTTTATAT
6459901 TTTTTTAAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAAATAATTTTAAATTTTTTTATAT
6459933 TTT
1 TTT
6459936 CATCAATGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 6 0.18
31 14 0.42
32 13 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (32 bp):
TTTTTTAAAAATAATTTTAAATTTTTTTATAT
Found at i:6460976 original size:7 final size:7
Alignment explanation
Indices: 6460964--6460988 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6460954 AGTCGATTGA
6460964 TATTTAG
1 TATTTAG
6460971 TATTTAG
1 TATTTAG
6460978 TATTTAG
1 TATTTAG
6460985 TATT
1 TATT
6460989 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:6462143 original size:17 final size:18
Alignment explanation
Indices: 6462118--6462151 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6462108 CAATTTGATG
6462118 TAAT-AAAAACCCTAACT
1 TAATAAAAAACCCTAACT
*
6462135 TAATTAAAAACCCTAAC
1 TAATAAAAAACCCTAAC
6462152 CNNNNNNNNN
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (18 bp):
TAATAAAAAACCCTAACT
Found at i:6463472 original size:13 final size:13
Alignment explanation
Indices: 6463435--6463478 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
6463425 TAATTGAAAA
* *
6463435 TAAATTCAAGTAC
1 TAAATTCAAATAT
6463448 TAAATT-AAATAT
1 TAAATTCAAATAT
6463460 TAAATTCAAATAT
1 TAAATTCAAATAT
*
6463473 CAAATT
1 TAAATT
6463479 AGAATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (13 bp):
TAAATTCAAATAT
Found at i:6463477 original size:25 final size:26
Alignment explanation
Indices: 6463435--6463484 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
6463425 TAATTGAAAA
*
6463435 TAAATTCAAGTACTAAATTA-AATAT
1 TAAATTCAAATACTAAATTAGAATAT
6463460 TAAATTCAAATA-TCAAATTAGAATA
1 TAAATTCAAATACT-AAATTAGAATA
6463485 AAAAACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 17 0.77
26 4 0.18
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (26 bp):
TAAATTCAAATACTAAATTAGAATAT
Found at i:6466772 original size:21 final size:21
Alignment explanation
Indices: 6466734--6466773 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6466724 CCGAGCCCGT
**
6466734 ATTTTTAAAATACCTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
6466755 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
6466774 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:6467123 original size:55 final size:55
Alignment explanation
Indices: 6467039--6467157 Score: 184
Period size: 55 Copynumber: 2.2 Consensus size: 55
6467029 TAGCAGAAAC
6467039 ATTGAATGCTACATTGAATATAATATAAAACATATTCAAAATGCATGAATCAAAT
1 ATTGAATGCTACATTGAATATAATATAAAACATATTCAAAATGCATGAATCAAAT
* * * *
6467094 ATTGAATGTTACATTGAGTATGATATAAAACATATTCAAAATTCATGAATCAAAT
1 ATTGAATGCTACATTGAATATAATATAAAACATATTCAAAATGCATGAATCAAAT
* *
6467149 TTTAAATGC
1 ATTGAATGC
6467158 ATGCCCTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (55 bp):
ATTGAATGCTACATTGAATATAATATAAAACATATTCAAAATGCATGAATCAAAT
Found at i:6469930 original size:32 final size:31
Alignment explanation
Indices: 6469876--6469942 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
6469866 CTAGAAACCG
* *
6469876 TAATTAGATTAAATAATTAAATAATTAGGAAT
1 TAATTAAATAAAATAATTAAATAATTA-GAAT
6469908 TAATTAAATAAAAT-ATTAAAATAATTAGAAT
1 TAATTAAATAAAATAATT-AAATAATTAGAAT
6469939 TAAT
1 TAAT
6469943 AATTTTAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (31 bp):
TAATTAAATAAAATAATTAAATAATTAGAAT
Found at i:6471482 original size:27 final size:27
Alignment explanation
Indices: 6471423--6471476 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
6471413 TATTAAACCT
* *
6471423 ATATATGTGTGGGTTTTGTTATATATA
1 ATATATGCGTGGATTTTGTTATATATA
6471450 ATATATGCGTGGATTTTGTTATATATA
1 ATATATGCGTGGATTTTGTTATATATA
6471477 CAATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.50
Consensus pattern (27 bp):
ATATATGCGTGGATTTTGTTATATATA
Found at i:6471680 original size:33 final size:35
Alignment explanation
Indices: 6471635--6471720 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
6471625 AATAGATATG
* **
6471635 TATATAAAATATATATTTATGA-G-TCTTGTTATA
1 TATATAAAATATATATGTAAAAGGATCTTGTTATA
* *
6471668 TATATAATATATATGTGTAAAAGGATCTTGTTATA
1 TATATAAAATATATATGTAAAAGGATCTTGTTATA
*
6471703 TATATAACATATATATGT
1 TATATAAAATATATATGT
6471721 GTGGATGAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 17 0.39
34 1 0.02
35 26 0.59
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (35 bp):
TATATAAAATATATATGTAAAAGGATCTTGTTATA
Found at i:6472337 original size:17 final size:17
Alignment explanation
Indices: 6472234--6472340 Score: 79
Period size: 17 Copynumber: 6.2 Consensus size: 17
6472224 ATGGTATAGA
* * *
6472234 TGAACTATTATATTGTA
1 TGAACTGTTATTTTGTG
* * **
6472251 TGAACTATTATTATGCA
1 TGAACTGTTATTTTGTG
*
6472268 TGAACTGTTATTTTATG
1 TGAACTGTTATTTTGTG
* * * *
6472285 CGAATTGTCTATTCTATG
1 TGAACTGT-TATTTTGTG
*
6472303 TGAACTGTTTAATTTGTG
1 TGAACTG-TTATTTTGTG
6472321 TGAACTGTTATTTTGTG
1 TGAACTGTTATTTTGTG
6472338 TGA
1 TGA
6472341 GTTGTGATAA
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
17 44 0.62
18 26 0.37
19 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (17 bp):
TGAACTGTTATTTTGTG
Found at i:6475054 original size:27 final size:27
Alignment explanation
Indices: 6475024--6475357 Score: 400
Period size: 27 Copynumber: 12.4 Consensus size: 27
6475014 CCCCAAAATA
* *
6475024 GGTAAAATAACCAAAATACCCCCATAA
1 GGTAAAATGACCAAAATACCCCCATAG
*
6475051 GGTAAAATGACCAAAATAACCCCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* *
6475078 GGTAAAATAACTAAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* **
6475105 GATAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
6475132 GGTAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
**
6475159 GGTAAAATGACCAAAATACCCCGGTAG
1 GGTAAAATGACCAAAATACCCCCATAG
* * *
6475186 GGTAAAAT-AACGAAATACCCTCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* *
6475212 GGTAGAATGACCAAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* *** *
6475239 GGTAACATGATTGAAATATCCCCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* ** *
6475266 GGTAAAATAACTGAAATACCCCCATAA
1 GGTAAAATGACCAAAATACCCCCATAG
* *
6475293 GATAAAATGACCAAAATACCCTCATAG
1 GGTAAAATGACCAAAATACCCCCATAG
* * *
6475320 GGTAAAATGATCAAAATACCCTCATAA
1 GGTAAAATGACCAAAATACCCCCATAG
6475347 GGTAAAATGAC
1 GGTAAAATGAC
6475358 TGTTATACCC
Statistics
Matches: 260, Mismatches: 46, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
26 20 0.08
27 240 0.92
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.18
Consensus pattern (27 bp):
GGTAAAATGACCAAAATACCCCCATAG
Found at i:6475155 original size:81 final size:81
Alignment explanation
Indices: 6475024--6475368 Score: 442
Period size: 81 Copynumber: 4.3 Consensus size: 81
6475014 CCCCAAAATA
** * *
6475024 GGTAAAATAACCAAAATACCCCCATAAGGTAAAATGACCAAAATAACCCCATAGGGTAAAATAAC
1 GGTAAAATAACTGAAATACCCCCATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGAC
6475089 TAAAATACCCCCATAG
66 TAAAATACCCCCATAG
* * *
6475105 GATAAAATGACTGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGAC
1 GGTAAAATAACTGAAATACCCCCATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGAC
* **
6475170 CAAAATACCCCGGTAG
66 TAAAATACCCCCATAG
* * * * * *
6475186 GGTAAAATAAC-GAAATACCCTCATAGGGTAGAATGACCAAAATACCCCTATAGGGTAACATGAT
1 GGTAAAATAACTGAAATACCCCCATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGAC
* *
6475250 TGAAATATCCCCATAG
66 TAAAATACCCCCATAG
* *
6475266 GGTAAAATAACTGAAATACCCCCATAAGATAAAATGACCAAAATACCCTCATAGGGTAAAATGA-
1 GGTAAAATAACTGAAATACCCCCATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGAC
* *
6475330 TCAAAATACCCTCATAA
66 T-AAAATACCCCCATAG
* **
6475347 GGTAAAATGACTGTTATACCCC
1 GGTAAAATAACTGAAATACCCC
6475369 TAGAAGATGA
Statistics
Matches: 226, Mismatches: 36, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
80 71 0.31
81 155 0.69
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19
Consensus pattern (81 bp):
GGTAAAATAACTGAAATACCCCCATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGAC
TAAAATACCCCCATAG
Found at i:6477399 original size:12 final size:13
Alignment explanation
Indices: 6477377--6477405 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6477367 GATTAAGTTA
6477377 ATTTGATTTATTT
1 ATTTGATTTATTT
6477390 ATTT-ATTTATTT
1 ATTTGATTTATTT
6477402 ATTT
1 ATTT
6477406 TGGAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
ATTTGATTTATTT
Found at i:6479166 original size:19 final size:18
Alignment explanation
Indices: 6479117--6479172 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
6479107 ACTAAAGTTT
6479117 TTTAT-TATTTAAATATTA
1 TTTATATATTTAAAT-TTA
*
6479135 TTTATTTATTTTAAATTTA
1 TTTATATA-TTTAAATTTA
*
6479154 TTTATAATATTTATATTTA
1 TTTAT-ATATTTAAATTTA
6479173 GATGTTAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 5 0.15
19 19 0.58
20 9 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATATATTTAAATTTA
Found at i:6479398 original size:233 final size:234
Alignment explanation
Indices: 6479133--6479599 Score: 927
Period size: 233 Copynumber: 2.0 Consensus size: 234
6479123 ATTTAAATAT
6479133 TATTTATTTATTTTAAATTTATTTATAATATTTATATTTAGATGTTAGCTTAGTAATATGATTGA
1 TATTTATTTATTTTAAATTTATTTATAATATTTATATTTAGATGTTAGCTTAGTAATATGATTGA
6479198 AAAAGGTTAATGTTAAATAATTATTTTAAATTATATTATATTTATATTTAAATGCCAATTAAGTA
66 AAAAGGTTAATGTTAAATAATTATTTTAAATTATATTATATTTATATTTAAATGCCAATTAAGTA
6479263 ATATCACTCGTCTATTCAAAAAAGATTGAAACTCGTGTTTATATATATTAACAAATCTTATTAGC
131 ATATCACTCGTCTATTCAAAAAAGATTGAAACTCGTGTTTATATATATTAACAAATCTTATTAGC
6479328 CAAATATTAATTCATTTCTCCCTTAGTGAACTCTAGTAA
196 CAAATATTAATTCATTTCTCCCTTAGTGAACTCTAGTAA
6479367 TATTTATTTA-TTTAAATTTATTTATAATATTTATATTTAGATGTTAGCTTAGTAATATGATTGA
1 TATTTATTTATTTTAAATTTATTTATAATATTTATATTTAGATGTTAGCTTAGTAATATGATTGA
6479431 AAAAGGTTAATGTTAAATAATTATTTTAAATTATATTATATTTATATTTAAATGCCAATTAAGTA
66 AAAAGGTTAATGTTAAATAATTATTTTAAATTATATTATATTTATATTTAAATGCCAATTAAGTA
6479496 ATATCACTCGTCTATTCAAAAAAGATTGAAACTCGTGTTTATATATATTAACAAATCTTATTAGC
131 ATATCACTCGTCTATTCAAAAAAGATTGAAACTCGTGTTTATATATATTAACAAATCTTATTAGC
6479561 CAAATATTAATTCATTTCTCCCTTAGTGAACTCTAGTAA
196 CAAATATTAATTCATTTCTCCCTTAGTGAACTCTAGTAA
6479600 AACATGACAC
Statistics
Matches: 233, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
233 223 0.96
234 10 0.04
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (234 bp):
TATTTATTTATTTTAAATTTATTTATAATATTTATATTTAGATGTTAGCTTAGTAATATGATTGA
AAAAGGTTAATGTTAAATAATTATTTTAAATTATATTATATTTATATTTAAATGCCAATTAAGTA
ATATCACTCGTCTATTCAAAAAAGATTGAAACTCGTGTTTATATATATTAACAAATCTTATTAGC
CAAATATTAATTCATTTCTCCCTTAGTGAACTCTAGTAA
Found at i:6486158 original size:9 final size:9
Alignment explanation
Indices: 6486144--6486180 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
6486134 TATAGTTTGA
6486144 TATTCGAAT
1 TATTCGAAT
6486153 TATTCGAAT
1 TATTCGAAT
* *
6486162 GATTCGAGT
1 TATTCGAAT
6486171 TATTCGAAT
1 TATTCGAAT
6486180 T
1 T
6486181 CAAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6499080 original size:107 final size:107
Alignment explanation
Indices: 6498793--6499059 Score: 302
Period size: 107 Copynumber: 2.5 Consensus size: 107
6498783 GGTTCATGAA
* ** * * * * *** * *
6498793 GCTGCTCACAAAAGCTAACAAGAATCCGCAACGTATGCAGGATCTCAGTCATTATAATGATCGAT
1 GCTGCTCACACAAGCTGTCGAGAATCCGCAACATATGTAGGATCTCAGCCATCGGAACGATCTAT
* * ** *
6498858 TTCATCAGTACAGAGTATTCATTCATTTCACCAATTCACGAT
66 ATCATCAGAACAGAGTAGCCATTCAATTCACCAATTCACGAT
* * *
6498900 GCTGCTCACACAAGCTGTTGAGAATCTGCAACATGTGTAGGATCTCAGCCATCGGAACGATCTAT
1 GCTGCTCACACAAGCTGTCGAGAATCCGCAACATATGTAGGATCTCAGCCATCGGAACGATCTAT
* *
6498965 GTCATCAGAATAGAGTAGCCATTCAATTCACCAATTCACGAT
66 ATCATCAGAACAGAGTAGCCATTCAATTCACCAATTCACGAT
* *
6499007 GCTGCTCATACAAGCTGTCGAGAATCCG-AGACATATGTAGGATCTCGGCCATC
1 GCTGCTCACACAAGCTGTCGAGAATCCGCA-ACATATGTAGGATCTCAGCCATC
6499060 ATGATGGTGT
Statistics
Matches: 133, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
106 1 0.01
107 132 0.99
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (107 bp):
GCTGCTCACACAAGCTGTCGAGAATCCGCAACATATGTAGGATCTCAGCCATCGGAACGATCTAT
ATCATCAGAACAGAGTAGCCATTCAATTCACCAATTCACGAT
Found at i:6500400 original size:124 final size:125
Alignment explanation
Indices: 6500179--6500428 Score: 493
Period size: 124 Copynumber: 2.0 Consensus size: 125
6500169 AAATATATAT
6500179 TATTTTTAATCAAATATACTTTTTAACTTTCATGTTTCACTTTCGTTATCAGATCGTGCCCTCCC
1 TATTTTTAATCAAATATACTTTTTAACTTTCATGTTTCACTTTCGTTATCAGATCGTGCCCTCCC
6500244 TTTTTTTCCCAATTCTAAAATCAAGCTTCAAAATCCCTAAGCCCTAACTCACCACCTCCA
66 TTTTTTTCCCAATTCTAAAATCAAGCTTCAAAATCCCTAAGCCCTAACTCACCACCTCCA
6500304 TATTTTTAATC-AATATACTTTTTAACTTTCATGTTTCACTTTCGTTATCAGATCGTGCCCTCCC
1 TATTTTTAATCAAATATACTTTTTAACTTTCATGTTTCACTTTCGTTATCAGATCGTGCCCTCCC
6500368 TTTTTTTCCCAATTCTAAAATCAAGCTTCAAAATCCCTAAGCCCTAACTCACCACCTCCA
66 TTTTTTTCCCAATTCTAAAATCAAGCTTCAAAATCCCTAAGCCCTAACTCACCACCTCCA
6500428 T
1 T
6500429 CGATCCACCT
Statistics
Matches: 125, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
124 114 0.91
125 11 0.09
ACGTcount: A:0.27, C:0.29, G:0.06, T:0.39
Consensus pattern (125 bp):
TATTTTTAATCAAATATACTTTTTAACTTTCATGTTTCACTTTCGTTATCAGATCGTGCCCTCCC
TTTTTTTCCCAATTCTAAAATCAAGCTTCAAAATCCCTAAGCCCTAACTCACCACCTCCA
Found at i:6510776 original size:19 final size:19
Alignment explanation
Indices: 6510752--6510791 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
6510742 GTCCAAGGAA
6510752 CATCAAAGACGAATTAAAT
1 CATCAAAGACGAATTAAAT
6510771 CATCAAAGACGAATTAAAT
1 CATCAAAGACGAATTAAAT
6510790 CA
1 CA
6510792 ATCATTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (19 bp):
CATCAAAGACGAATTAAAT
Found at i:6512126 original size:66 final size:66
Alignment explanation
Indices: 6512044--6512175 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
6512034 GCATTGCAAG
6512044 GGGAAAGCATTCATATGTCATTTGAAATACTTCAAGGATCAGAAATTGCAAACTATCTTTAAGTT
1 GGGAAAGCATTCATATGTCATTTGAAATACTTCAAGGATCAGAAATTGCAAACTATCTTTAAGTT
6512109 A
66 A
6512110 GGGAAAGCATTCATATGTCATTTGAAATACTTCAAGGATCAGAAATTGCAAACTATCTTTAAGTT
1 GGGAAAGCATTCATATGTCATTTGAAATACTTCAAGGATCAGAAATTGCAAACTATCTTTAAGTT
6512175 A
66 A
6512176 TGCTTTAAGG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (66 bp):
GGGAAAGCATTCATATGTCATTTGAAATACTTCAAGGATCAGAAATTGCAAACTATCTTTAAGTT
A
Found at i:6524921 original size:29 final size:29
Alignment explanation
Indices: 6524879--6524937 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
6524869 CCTTTTTTGC
6524879 CATTGATTGCAGAGGAGACATAGATATTT
1 CATTGATTGCAGAGGAGACATAGATATTT
6524908 CATTGATTGCAGAGGAGACATAGATATTT
1 CATTGATTGCAGAGGAGACATAGATATTT
6524937 C
1 C
6524938 CGGTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (29 bp):
CATTGATTGCAGAGGAGACATAGATATTT
Found at i:6528959 original size:16 final size:16
Alignment explanation
Indices: 6528934--6528973 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
6528924 TTCGTTCGCT
*
6528934 GTAATAGAATAGATGC
1 GTAATAGAATAGAGGC
*
6528950 GTAATGGAATAGAGGC
1 GTAATAGAATAGAGGC
6528966 GTAATAGA
1 GTAATAGA
6528974 TAATTCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.30, T:0.23
Consensus pattern (16 bp):
GTAATAGAATAGAGGC
Found at i:6529046 original size:44 final size:47
Alignment explanation
Indices: 6528950--6529047 Score: 132
Period size: 44 Copynumber: 2.2 Consensus size: 47
6528940 GAATAGATGC
* * *
6528950 GTAATGGAATAGAGGCGTAATAGATAATTCTTTTGTTTGGTTGAATA
1 GTAATAGAATAGAGGCGTAATAGATAACTCTTATGTTTGGTTGAATA
*
6528997 G-AATAGAATAGAGGTGTAATAG-T-ACTCTTATGTTTGGTTGAAT-
1 GTAATAGAATAGAGGCGTAATAGATAACTCTTATGTTTGGTTGAATA
6529040 GTAATAGA
1 GTAATAGA
6529048 GCTGTAATAG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.02
44 24 0.52
45 1 0.02
46 19 0.41
47 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.37
Consensus pattern (47 bp):
GTAATAGAATAGAGGCGTAATAGATAACTCTTATGTTTGGTTGAATA
Found at i:6529292 original size:20 final size:21
Alignment explanation
Indices: 6529253--6529292 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
6529243 AATTTACTAA
*
6529253 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
6529274 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
6529293 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:6529326 original size:59 final size:59
Alignment explanation
Indices: 6529263--6529444 Score: 173
Period size: 64 Copynumber: 3.1 Consensus size: 59
6529253 TAAAATCATA
6529263 ATATATAATACTAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT-AAAA-
1 ATATATAATACTAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
* * * * * *
6529320 ATATATAAT-TTAATAAT-T--CTTAATATTAAATATTCTT--ATATGAATTTACTAAAATCAT
1 ATATATAATACTAA-AATATAATTTAA-AATAATTATTATTAAATAT-AATTTAATAAAA--AT
*
6529378 AATATATAATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
1 -ATATATAATAC--TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
6529440 ATATA
1 ATATA
6529445 ATTTAATAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 28
0.70 0.09 0.20
Matches are distributed among these distances:
53 4 0.04
54 11 0.11
55 13 0.14
56 4 0.04
57 13 0.14
59 9 0.09
61 8 0.08
62 6 0.06
63 9 0.09
64 15 0.16
65 4 0.04
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (59 bp):
ATATATAATACTAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
Found at i:6529335 original size:118 final size:116
Alignment explanation
Indices: 6529204--6529464 Score: 420
Period size: 118 Copynumber: 2.2 Consensus size: 116
6529194 CTGTTATAAA
*
6529204 ATATAATTTAATAAAATTGTTAATAAATATTCTTATATGAATTTACTAATAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATAAATATTCTTATATGAATTTAC---TAAAATCATAATATAT
*
6529269 AATAC-TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
63 AATACATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
6529322 ATATAATTTAAT--AATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTT-A-A-TAAATATTCTTATATGAATTTACTAAAATCATAATATAT
6529385 AATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
63 AATAC-ATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
6529440 ATATAATTTAATAAAATTCTTAATA
1 ATATAATTTAATAAAATTCTTAATA
6529465 TAAAACTAGA
Statistics
Matches: 134, Mismatches: 2, Indels: 15
0.89 0.01 0.10
Matches are distributed among these distances:
116 27 0.20
117 3 0.02
118 73 0.54
119 24 0.18
120 7 0.05
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (116 bp):
ATATAATTTAATAAAATTCTTAATAAATATTCTTATATGAATTTACTAAAATCATAATATATAAT
ACATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
Found at i:6529416 original size:13 final size:12
Alignment explanation
Indices: 6529392--6529432 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
6529382 TATAATACTA
6529392 TAAAATATAATT
1 TAAAATATAATT
6529404 TAAAATAATAATT
1 TAAAAT-ATAATT
*
6529417 ATTAAATATAATT
1 -TAAAATATAATT
6529430 TAA
1 TAA
6529433 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:6529740 original size:24 final size:24
Alignment explanation
Indices: 6529705--6529754 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
6529695 GATAAAGTAT
*
6529705 TTATCACCTCAAATGTGATTTGGG
1 TTATCACATCAAATGTGATTTGGG
6529729 TTATCACATCAAATGTGATTTGGG
1 TTATCACATCAAATGTGATTTGGG
6529753 TT
1 TT
6529755 CAAATTATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
TTATCACATCAAATGTGATTTGGG
Found at i:6530797 original size:24 final size:24
Alignment explanation
Indices: 6530764--6530811 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
6530754 CTCACAAATT
*
6530764 GAAAACTACAGAAACCATTTTCAA
1 GAAAAATACAGAAACCATTTTCAA
6530788 GAAAAATACAGAAACCATTTTCAA
1 GAAAAATACAGAAACCATTTTCAA
6530812 TTGAAAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (24 bp):
GAAAAATACAGAAACCATTTTCAA
Found at i:6534121 original size:24 final size:23
Alignment explanation
Indices: 6534062--6534122 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
6534052 ATATTTTTTC
*
6534062 TATTA-ATTA-ATTTATTATTAT
1 TATTATATTATATTTATTATCAT
* *
6534083 TTTTATATTACTATTTATTATCCT
1 TATTATATTA-TATTTATTATCAT
6534107 TATTACTATTATATTT
1 TATTA-TATTATATTT
6534123 GATAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
24 19 0.59
25 5 0.16
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATATTATATTTATTATCAT
Found at i:6536579 original size:18 final size:16
Alignment explanation
Indices: 6536549--6536582 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
6536539 ACCTAAAATT
6536549 TTTTATTACTTTTAAA
1 TTTTATTACTTTTAAA
6536565 TTTTATCTACATTTTAAA
1 TTTTAT-TAC-TTTTAAA
6536583 AAATTTCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTATTACTTTTAAA
Found at i:6538997 original size:2 final size:2
Alignment explanation
Indices: 6538990--6539019 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6538980 CATCATGTAT
*
6538990 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6539020 AGTTTCATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6539293 original size:19 final size:20
Alignment explanation
Indices: 6539252--6539293 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
6539242 ATTGTTATGC
* *
6539252 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
6539272 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
6539291 CAT
1 CAT
6539294 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:6543040 original size:24 final size:24
Alignment explanation
Indices: 6543013--6543058 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6543003 AGAACAGTCC
* *
6543013 CAAAAGGAAATGTAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
6543037 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
6543059 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.26, T:0.13
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:6551201 original size:84 final size:85
Alignment explanation
Indices: 6551060--6551215 Score: 194
Period size: 84 Copynumber: 1.8 Consensus size: 85
6551050 CCGATAATCC
* * ** *
6551060 TATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAATGGAGCAGATTAAAAGCACAGATCTTATCTCTCTGAAGTTGCAGAG
6551125 A-GCAGATCGCATCTAGTCT
66 AGGCAGATCGCATCTAGTCT
*
6551144 TATCTCCCTGAAGTTGCAATGGAGCAGATTAAGCAAGCA-AG-TCTTAT-TGTCCTGAAGTTGCA
1 TATCTCCCTGAAGTTGCAATGGAGCAGATTAA--AAGCACAGATCTTATCTCT-CTGAAGTTGCA
*
6551206 GTGAGGCAGA
63 GAGAGGCAGA
6551216 CTGAAGATGG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
83 2 0.03
84 48 0.79
85 7 0.11
86 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (85 bp):
TATCTCCCTGAAGTTGCAATGGAGCAGATTAAAAGCACAGATCTTATCTCTCTGAAGTTGCAGAG
AGGCAGATCGCATCTAGTCT
Found at i:6551249 original size:45 final size:45
Alignment explanation
Indices: 6551141--6551613 Score: 194
Period size: 45 Copynumber: 10.8 Consensus size: 45
6551131 TCGCATCTAG
* * *
6551141 TCTTATCTCCCTGAAGTTGCAATG-GAGCAGATT-AAGCA-AGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGAG-GCAGATTAAAG-ATGGCAAA
* * * *
6551185 TCTTAT-TGTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAA
1 TCTTATCT-CCCTGAAGTTGCAGTGAGGCAGATTAAAGATGGCAAA
* **
6551230 TCTTATCTCCCTGAAGTTGCAGTG-GCGCAGGTTAAAG-CCG-ATAA
1 TCTTATCTCCCTGAAGTTGCAGTGAG-GCAGATTAAAGATGGCA-AA
* * * ** * *
6551274 TCCTATCTTCCTGAAGTTGCAGTGAAGTGGATTAAAAACCTTG--AA
1 TCTTATCTCCCTGAAGTTGCAGTGAGGCAGATTAAAGA--TGGCAAA
** * * *
6551319 TCTTATCTCTTTGAAGTTGCAGAGA-GCAGA-T--CGCAT--CAAG
1 TCTTATCTCCCTGAAGTTGCAGTGAGGCAGATTAAAG-ATGGCAAA
* *
6551359 TCTTAT-TCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGAGGCAGATTAAAGATGGCAAA
* * **
6551404 TCTTATCTCCCTGAAGTTGTAGTG-GAGCAGGTTAAAG-CCG-ATAA
1 TCTTATCTCCCTGAAGTTGCAGTGAG-GCAGATTAAAGATGGCA-AA
** * * * ** *
6551448 TCCGATCTTCCTGAAGTTGCAATGAAGTGGATTAAAAACCTTGG---A
1 TCTTATCTCCCTGAAGTTGCAGTGAGGCAGATTAAAGA---TGGCAAA
* * * * *
6551493 TCTTATCTCTCTGAAGTTGCAGAGA-GCAGA-T--CG-TAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGAGGCAGATTAAAGATGGCAAA
* * * *
6551533 TCTTAT-TCTCCTGAAGTTACAGTGAGGTAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGAGGCAGATTAAAGATGGCAAA
6551578 TCTTATCTCCCTGAAGTTGCAGTG-GAGCAGATTAAA
1 TCTTATCTCCCTGAAGTTGCAGTGAG-GCAGATTAAA
6551614 ACCAATAATC
Statistics
Matches: 312, Mismatches: 77, Indels: 79
0.67 0.16 0.17
Matches are distributed among these distances:
37 2 0.01
39 4 0.01
40 40 0.13
41 9 0.03
42 3 0.01
43 7 0.02
44 99 0.32
45 141 0.45
46 5 0.02
47 1 0.00
48 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGAGGCAGATTAAAGATGGCAAA
Found at i:6551286 original size:89 final size:88
Alignment explanation
Indices: 6551141--6551642 Score: 392
Period size: 89 Copynumber: 5.7 Consensus size: 88
6551131 TCGCATCTAG
* * * * *
6551141 TCTTATCTCCCTGAAGTTGCAATGGAGCAGATT-AAGCAAGCA-AGTCTTATTGTCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-CG-ATAATCCTATTCTCCTGAAGTTG
*
6551204 CAGTGAGGCAGACTGAAGATGGAAAA
64 CAGTGAGGTAGACTGAAGATGG-AAA
* *
6551230 TCTTATCTCCCTGAAGTTGCAGTGGCGCAGGTTAAAGCCGATAATCCTA-TCTTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATTC-TCCTGAAGTTGC
* * * * * *
6551294 AGTGAAGTGGATTAAAAACCTTG-AA
65 AGTGAGGTAGACTGAAGA--TGGAAA
** * * *
6551319 TCTTATCTCTTTGAAGTTGCAG-AGAGCAGA-T--CG-C-ATCAAGTCTTATTCTCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT-AA-TCCTATTCTCCTGAAGTTG
*
6551378 CAGTGAGGCAGACTGAAGATGGCAAA
64 CAGTGAGGTAGACTGAAGATGG-AAA
* * *
6551404 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTAAAGCCGATAATCCGA-TCTTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATTC-TCCTGAAGTTGC
* * * * * *
6551468 AATGAAGTGGATTAAAAACCTTGG--A
65 AGTGAGGTAGACTGAAGA---TGGAAA
* * *** * * *
6551493 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGTAG-C-A-AGTCTTATTCTCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATTCTCCTGAAGTTGCA
6551554 GTGAGGTAGACTGAAGATGGCAAA
66 GTGAGGTAGACTGAAGATGG-AAA
* *
6551578 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAATAATCCTA-TCTCCTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATTCTCC-TGAAGTTGC
6551642 A
65 A
6551643 ATGGACCGGA
Statistics
Matches: 315, Mismatches: 69, Indels: 58
0.71 0.16 0.13
Matches are distributed among these distances:
82 3 0.01
83 4 0.01
84 3 0.01
85 99 0.31
86 20 0.06
87 4 0.01
88 24 0.08
89 144 0.46
90 7 0.02
91 4 0.01
92 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATTCTCCTGAAGTTGCA
GTGAGGTAGACTGAAGATGGAAA
Found at i:6551383 original size:174 final size:174
Alignment explanation
Indices: 6551141--6551730 Score: 817
Period size: 174 Copynumber: 3.3 Consensus size: 174
6551131 TCGCATCTAG
* * * *
6551141 TCTTATCTCCCTGAAGTTGCA-ATGGAGCAGATTAAGCAAGCAAGTCTTATTGTCCTGAAGTTGC
1 TCTTATCTCTCTGAAGTTGCAGA--GAGCAGA-T-CGC-ATCAAGTCTTATTCTCCTGAAGTTGC
* *
6551205 AGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGCGCAGGTTAAAGCCG
61 AGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCG
* *
6551270 ATAATCCTATCTTCCTGAAGTTGCAGTGAAGTGGATTAAAAACCTTGAA
126 ATAATCCTATCTTCCTGAAGTTGCAATGAAGTGGATTAAAAACCTTGGA
*
6551319 TCTTATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCAAGTCTTATTCTCCTGAAGTTGCAGTGA
1 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCAAGTCTTATTCTCCTGAAGTTGCAGTGA
*
6551384 GGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTAAAGCCGATAAT
66 GGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCGATAAT
*
6551449 CCGATCTTCCTGAAGTTGCAATGAAGTGGATTAAAAACCTTGGA
131 CCTATCTTCCTGAAGTTGCAATGAAGTGGATTAAAAACCTTGGA
* * *
6551493 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGTAGCAAGTCTTATTCTCCTGAAGTTACAGTGA
1 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCAAGTCTTATTCTCCTGAAGTTGCAGTGA
* * * *
6551558 GGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAATAAT
66 GGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCGATAAT
* ** **
6551623 CCTATC-TCCTTGAAGTTGCAATGGACCGGATTGGAACCACAAATTTTGGA
131 CCTATCTTCC-TGAAGTTGCAATGAAGTGGATT---A--A-AAACCTTGGA
* *
6551673 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCTAGTCTTA-TCTCCCTGAAGTT
1 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCAAGTCTTATTCT-CCTGAAGTT
6551731 ACAGAGGAGT
Statistics
Matches: 373, Mismatches: 30, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
173 3 0.01
174 277 0.74
175 2 0.01
176 1 0.00
177 8 0.02
178 19 0.05
179 5 0.01
180 58 0.16
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (174 bp):
TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCAAGTCTTATTCTCCTGAAGTTGCAGTGA
GGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCGATAAT
CCTATCTTCCTGAAGTTGCAATGAAGTGGATTAAAAACCTTGGA
Found at i:6553109 original size:12 final size:11
Alignment explanation
Indices: 6553094--6553155 Score: 72
Period size: 12 Copynumber: 5.4 Consensus size: 11
6553084 TTTTTCTTTA
6553094 TTTTTTATTAAT
1 TTTTTTATT-AT
6553106 TTTTTTATTAT
1 TTTTTTATTAT
*
6553117 TCTTTTTATTCT
1 T-TTTTTATTAT
6553129 TTTTTTATATAT
1 TTTTTTAT-TAT
6553141 TTTTTGTATT-T
1 TTTTT-TATTAT
6553152 TTTT
1 TTTT
6553156 ATTTTTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
11 15 0.33
12 27 0.60
13 3 0.07
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:6553122 original size:24 final size:23
Alignment explanation
Indices: 6553094--6553155 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
6553084 TTTTTCTTTA
6553094 TTTTTTATTAATTTTTTTAT-TAT
1 TTTTTTATT-ATTTTTTTATATAT
*
6553117 TCTTTTTATTCTTTTTTTATATAT
1 T-TTTTTATTATTTTTTTATATAT
6553141 TTTTTGTATT-TTTTT
1 TTTTT-TATTATTTTT
6553156 ATTTTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (23 bp):
TTTTTTATTATTTTTTTATATAT
Found at i:6553150 original size:9 final size:8
Alignment explanation
Indices: 6553085--6553162 Score: 54
Period size: 8 Copynumber: 9.8 Consensus size: 8
6553075 ATGGGTCCCT
6553085 TTTTCTTTA
1 TTTT-TTTA
6553094 -TTTTTTA
1 TTTTTTTA
**
6553101 TTAATTT-
1 TTTTTTTA
*
6553108 TTTTATTA
1 TTTTTTTA
6553116 TTCTTTTTA
1 TT-TTTTTA
*
6553125 TTCTTTT-
1 TTTTTTTA
* *
6553132 TTTATATA
1 TTTTTTTA
6553140 TTTTTTGTA
1 TTTTTT-TA
6553149 TTTTTTTA
1 TTTTTTTA
6553157 TTTTTT
1 TTTTTT
6553163 AAATATATGT
Statistics
Matches: 52, Mismatches: 12, Indels: 11
0.69 0.16 0.15
Matches are distributed among these distances:
7 12 0.23
8 25 0.48
9 15 0.29
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (8 bp):
TTTTTTTA
Found at i:6556271 original size:16 final size:17
Alignment explanation
Indices: 6556250--6556281 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6556240 GATTGAGTTG
6556250 AGAAAATT-ATTTAATT
1 AGAAAATTAATTTAATT
6556266 AGAAAATTAATTTAAT
1 AGAAAATTAATTTAAT
6556282 AAATAATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
AGAAAATTAATTTAATT
Found at i:6558428 original size:13 final size:13
Alignment explanation
Indices: 6558410--6558435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6558400 TCTTTATCTT
6558410 TTTATAGTAAATA
1 TTTATAGTAAATA
6558423 TTTATAGTAAATA
1 TTTATAGTAAATA
6558436 AAAGTATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTATAGTAAATA
Found at i:6573868 original size:14 final size:14
Alignment explanation
Indices: 6573849--6573883 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6573839 TTCTGAAAAG
6573849 CACTTTTTTTATAA
1 CACTTTTTTTATAA
6573863 CACTTTTTTTATAA
1 CACTTTTTTTATAA
*
6573877 CAATTTT
1 CACTTTT
6573884 CAAAAGCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (14 bp):
CACTTTTTTTATAA
Found at i:6581651 original size:92 final size:91
Alignment explanation
Indices: 6581494--6581702 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 91
6581484 TTGATTTTAG
* * * *
6581494 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTGTTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
6581559 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
6581586 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
6581650 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
6581678 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
6581703 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 70 0.68
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:6581665 original size:24 final size:25
Alignment explanation
Indices: 6581630--6581677 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
6581620 TTATGAAATT
6581630 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
6581654 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
6581678 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:6581849 original size:18 final size:17
Alignment explanation
Indices: 6581821--6581855 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6581811 ATTATTAAGA
*
6581821 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
6581838 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
6581856 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:6582112 original size:16 final size:16
Alignment explanation
Indices: 6582091--6582142 Score: 104
Period size: 16 Copynumber: 3.2 Consensus size: 16
6582081 GATTTGCTAT
6582091 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
6582107 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
6582123 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
6582139 TACA
1 TACA
6582143 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.38, C:0.37, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:6583594 original size:19 final size:20
Alignment explanation
Indices: 6583549--6583594 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
6583539 TAACGTGTCT
6583549 AATTAAGTTTCAATTAGATGA
1 AATT-AGTTTCAATTAGATGA
*
6583570 ATTTAGTTT-AATTAAGA-GA
1 AATTAGTTTCAATT-AGATGA
6583589 AATTAG
1 AATTAG
6583595 GAAAAATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 11 0.50
20 8 0.36
21 3 0.14
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.39
Consensus pattern (20 bp):
AATTAGTTTCAATTAGATGA
Found at i:6583949 original size:15 final size:15
Alignment explanation
Indices: 6583929--6583961 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
6583919 TATTAAATAC
6583929 TATTATTGTTTA-TAT
1 TATTATT-TTTATTAT
6583944 TATTATTTTTATTAT
1 TATTATTTTTATTAT
6583959 TAT
1 TAT
6583962 ATTATGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TATTATTTTTATTAT
Found at i:6593975 original size:11 final size:11
Alignment explanation
Indices: 6593959--6594037 Score: 63
Period size: 11 Copynumber: 7.2 Consensus size: 11
6593949 TCCTCTCTCA
6593959 AATTTCCTCTT
1 AATTTCCTCTT
*
6593970 AATTTCCTCTC
1 AATTTCCTCTT
**
6593981 AATTTCCTTCAA
1 AATTTCC-TCTT
*
6593993 AAATT-CTCTT
1 AATTTCCTCTT
* *
6594003 AAGTTACTCTT
1 AATTTCCTCTT
*
6594014 AAGTTCCTCTT
1 AATTTCCTCTT
6594025 AAGTTT-CTCTT
1 AA-TTTCCTCTT
6594036 AA
1 AA
6594038 CTCCCTTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
10 6 0.11
11 42 0.75
12 8 0.14
ACGTcount: A:0.25, C:0.24, G:0.04, T:0.47
Consensus pattern (11 bp):
AATTTCCTCTT
Found at i:6595199 original size:7 final size:7
Alignment explanation
Indices: 6595187--6595211 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6595177 AGTCGATTGA
6595187 TATTTAG
1 TATTTAG
6595194 TATTTAG
1 TATTTAG
6595201 TATTTAG
1 TATTTAG
6595208 TATT
1 TATT
6595212 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:6595889 original size:18 final size:18
Alignment explanation
Indices: 6595862--6595897 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6595852 CAGGTGCGTT
*
6595862 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
6595880 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
6595898 CCATTTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:6615478 original size:26 final size:27
Alignment explanation
Indices: 6615413--6615476 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
6615403 ACCAAAAATT
6615413 TATTTTAAAAATAAAAAATAAAAAAAG
1 TATTTTAAAAATAAAAAATAAAAAAAG
6615440 TATTTTAAAAATAAAAAATAAAAAAAG
1 TATTTTAAAAATAAAAAATAAAAAAAG
6615467 TATTTTAAAA
1 TATTTTAAAA
6615477 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (27 bp):
TATTTTAAAAATAAAAAATAAAAAAAG
Found at i:6622317 original size:12 final size:12
Alignment explanation
Indices: 6622302--6622326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6622292 TGTCAACATG
6622302 TTTGGAATAAAC
1 TTTGGAATAAAC
6622314 TTTGGAATAAAC
1 TTTGGAATAAAC
6622326 T
1 T
6622327 AACCATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTGGAATAAAC
Found at i:6628398 original size:12 final size:11
Alignment explanation
Indices: 6628383--6628412 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
6628373 AAAAAAATAA
6628383 AAAAAGTATTTT
1 AAAAA-TATTTT
6628395 AAAAATATTTT
1 AAAAATATTTT
6628406 AAAAATA
1 AAAAATA
6628413 ACTGCCCGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:6631234 original size:26 final size:26
Alignment explanation
Indices: 6631205--6631270 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
6631195 TTTACATCGT
* *
6631205 TGCTCACACGAGCTGTGTAATGGGCC
1 TGCTCACACGAGCTGTGAAATAGGCC
6631231 TGCTCACACGAGCTGTGAAATAGGCC
1 TGCTCACACGAGCTGTGAAATAGGCC
* *
6631257 TACTCACATGAGCT
1 TGCTCACACGAGCT
6631271 ATGGGTTGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.24, C:0.27, G:0.26, T:0.23
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATAGGCC
Found at i:6640846 original size:33 final size:33
Alignment explanation
Indices: 6640808--6640874 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
6640798 ATCTTTATGC
*
6640808 CTTAAATTCAAAATGATTTTTA-TATAGGGGGAG
1 CTTAAATTCAAAATGACTTTTATTA-AGGGGGAG
**
6640841 CTTAAATTGGAAATGACTTTTATTAAGGGGGAG
1 CTTAAATTCAAAATGACTTTTATTAAGGGGGAG
6640874 C
1 C
6640875 AATCTATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (33 bp):
CTTAAATTCAAAATGACTTTTATTAAGGGGGAG
Found at i:6646094 original size:70 final size:70
Alignment explanation
Indices: 6646012--6646144 Score: 257
Period size: 70 Copynumber: 1.9 Consensus size: 70
6646002 AATCTTTGAT
*
6646012 AAGTCTAGATGTAATCAACCTGCTGGCAAATTACATACACAACTTTGAGTTTGCTATTTTTTTTT
1 AAGTCTAGATGTAATCAACCCGCTGGCAAATTACATACACAACTTTGAGTTTGCTATTTTTTTTT
6646077 TATCC
66 TATCC
6646082 AAGTCTAGATGTAATCAACCCGCTGGCAAATTACATACACAACTTTGAGTTTGCTATTTTTTT
1 AAGTCTAGATGTAATCAACCCGCTGGCAAATTACATACACAACTTTGAGTTTGCTATTTTTTT
6646145 GGCATGAGGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (70 bp):
AAGTCTAGATGTAATCAACCCGCTGGCAAATTACATACACAACTTTGAGTTTGCTATTTTTTTTT
TATCC
Found at i:6646370 original size:27 final size:28
Alignment explanation
Indices: 6646321--6646375 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
6646311 TTTAAAATAT
6646321 ATATAAAATTATTTTTAAAAAATTATAA
1 ATATAAAATTATTTTTAAAAAATTATAA
6646349 ATATAAAATT-TTTTTAAAAAATTATAA
1 ATATAAAATTATTTTTAAAAAATTATAA
6646376 TTTTTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATATAAAATTATTTTTAAAAAATTATAA
Found at i:6648731 original size:6 final size:6
Alignment explanation
Indices: 6648720--6649012 Score: 275
Period size: 6 Copynumber: 49.0 Consensus size: 6
6648710 TAGGGGAGAG
6648720 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
6648768 AGAAGA AGGAGA AGGAGA AGGAGA AGGAGA CGAAGG AGAAGA AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * *
6648816 AGGAGA AGAAGA AG-AGG AGAAGA AGGAGA AGGAGA AGGAGA AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * *
6648863 CGAAGG AGAAGA AGGAGA AGGAGA AGAAGA AGAAGG AGAAGG AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * *
6648911 AGCAGA AGGAGA AGGAGG AGAAGGA A-AAGG AGGAGA AGGAGA AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAA-GA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * *
6648959 AGAAGC AGGAGA AGGAGA AGGAGA AGAAGA AGAAGG AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
6649007 AGAAGA
1 AGAAGA
6649013 GTCAAAAGAT
Statistics
Matches: 248, Mismatches: 36, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
5 6 0.02
6 240 0.97
7 2 0.01
ACGTcount: A:0.56, C:0.01, G:0.43, T:0.00
Consensus pattern (6 bp):
AGAAGA
Found at i:6648734 original size:9 final size:9
Alignment explanation
Indices: 6648720--6649012 Score: 275
Period size: 9 Copynumber: 32.7 Consensus size: 9
6648710 TAGGGGAGAG
6648720 AGAAGAAGA
1 AGAAGAAGA
6648729 AGAAGAAGA
1 AGAAGAAGA
6648738 AGAAGAAGA
1 AGAAGAAGA
6648747 AGAAGAAGA
1 AGAAGAAGA
6648756 AGAAGAAGA
1 AGAAGAAGA
6648765 AGAAGAAGA
1 AGAAGAAGA
* *
6648774 AGGAGAAGG
1 AGAAGAAGA
*
6648783 AGAAGGAGA
1 AGAAGAAGA
* *
6648792 AGGAGACGA
1 AGAAGAAGA
*
6648801 AGGAGAAGA
1 AGAAGAAGA
* *
6648810 AGGAGAAGG
1 AGAAGAAGA
6648819 AGAAGAAGA
1 AGAAGAAGA
*
6648828 AG-AGGAGA
1 AGAAGAAGA
*
6648836 AGAAGGAGA
1 AGAAGAAGA
* *
6648845 AGGAGAAGG
1 AGAAGAAGA
*
6648854 AGAAGGAGA
1 AGAAGAAGA
* *
6648863 CGAAGGAGA
1 AGAAGAAGA
*
6648872 AGAAGGAGA
1 AGAAGAAGA
*
6648881 AGGAGAAGA
1 AGAAGAAGA
*
6648890 AGAAGAAGG
1 AGAAGAAGA
*
6648899 AGAAGGAGA
1 AGAAGAAGA
*
6648908 AGAAGCAGA
1 AGAAGAAGA
* *
6648917 AGGAGAAGG
1 AGAAGAAGA
*
6648926 AGGAGAAGGA
1 AGAAGAA-GA
* *
6648936 A-AAGGAGG
1 AGAAGAAGA
*
6648944 AGAAGGAGA
1 AGAAGAAGA
*
6648953 AGAAGGAGA
1 AGAAGAAGA
* *
6648962 AGCAGGAGA
1 AGAAGAAGA
* *
6648971 AGGAGAAGG
1 AGAAGAAGA
6648980 AGAAGAAGA
1 AGAAGAAGA
*
6648989 AGAAGGAGA
1 AGAAGAAGA
6648998 AGAAGAAGA
1 AGAAGAAGA
6649007 AGAAGA
1 AGAAGA
6649013 GTCAAAAGAT
Statistics
Matches: 237, Mismatches: 44, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
8 9 0.04
9 226 0.95
10 2 0.01
ACGTcount: A:0.56, C:0.01, G:0.43, T:0.00
Consensus pattern (9 bp):
AGAAGAAGA
Found at i:6648740 original size:15 final size:15
Alignment explanation
Indices: 6648720--6649012 Score: 275
Period size: 15 Copynumber: 19.6 Consensus size: 15
6648710 TAGGGGAGAG
6648720 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
6648735 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
6648750 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
*
6648765 AGAAGAAGAAGGAGA
1 AGAAGAAGAAGAAGA
* * *
6648780 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* *
6648795 AGACGAAGGAGAAGA
1 AGAAGAAGAAGAAGA
* *
6648810 AGGAGAAGGAGAAGA
1 AGAAGAAGAAGAAGA
*
6648825 AGAAG-AGGAGAAGA
1 AGAAGAAGAAGAAGA
* * *
6648839 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* * *
6648854 AGAAGGAGACGAAGG
1 AGAAGAAGAAGAAGA
* *
6648869 AGAAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
*
6648884 AGAAGAAGAAGAAGG
1 AGAAGAAGAAGAAGA
* *
6648899 AGAAGGAGAAGAAGC
1 AGAAGAAGAAGAAGA
* * *
6648914 AGAAGGAGAAGGAGG
1 AGAAGAAGAAGAAGA
* *
6648929 AGAAGGAA-AAGGAGG
1 AGAA-GAAGAAGAAGA
* *
6648944 AGAAGGAGAAGAAGG
1 AGAAGAAGAAGAAGA
* * *
6648959 AGAAGCAGGAGAAGG
1 AGAAGAAGAAGAAGA
*
6648974 AGAAGGAGAAGAAGA
1 AGAAGAAGAAGAAGA
*
6648989 AGAAGGAGAAGAAGA
1 AGAAGAAGAAGAAGA
6649004 AGAAGAAGA
1 AGAAGAAGA
6649013 GTCAAAAGAT
Statistics
Matches: 241, Mismatches: 34, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
14 15 0.06
15 224 0.93
16 2 0.01
ACGTcount: A:0.56, C:0.01, G:0.43, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAGAAGA
Found at i:6654626 original size:21 final size:20
Alignment explanation
Indices: 6654590--6654650 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
6654580 TAATCCGGTA
*
6654590 AAAATACTACAAAAGTTATAT
1 AAAATA-TAAAAAAGTTATAT
6654611 GAAAATATAAAAAAG-TAT-T
1 -AAAATATAAAAAAGTTATAT
*
6654630 AAGGAATATAAAAAAATTATA
1 AA--AATATAAAAAAGTTATA
6654651 AATGGGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 14 0.42
21 10 0.30
22 6 0.18
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
AAAATATAAAAAAGTTATAT
Found at i:6658583 original size:20 final size:19
Alignment explanation
Indices: 6658545--6658585 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
6658535 AAAGTAGTGA
*
6658545 AAATTTATTTTCTTAGAAT
1 AAATTTATTTTCTGAGAAT
*
6658564 AAATTCTATTTTCTGGGAAT
1 AAATT-TATTTTCTGAGAAT
6658584 AA
1 AA
6658586 TAATTTCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (19 bp):
AAATTTATTTTCTGAGAAT
Found at i:6661164 original size:19 final size:18
Alignment explanation
Indices: 6661136--6661183 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
6661126 AAATTACAAA
* *
6661136 AAAATCAAAATAGTTTTC
1 AAAATTAAAATAATTTTC
*
6661154 AGAAATTAAAAATAATTTTT
1 A-AAATT-AAAATAATTTTC
6661174 AAAATTAAAA
1 AAAATTAAAA
6661184 ATACTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 5 0.20
19 9 0.36
20 11 0.44
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAATTAAAATAATTTTC
Found at i:6661184 original size:19 final size:20
Alignment explanation
Indices: 6661142--6661186 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
6661132 CAAAAAAATC
*
6661142 AAAATAGTTTTCAGAAATTA
1 AAAATAATTTTCAGAAATTA
*
6661162 AAAATAATTTTTA-AAATTA
1 AAAATAATTTTCAGAAATTA
6661181 AAAATA
1 AAAATA
6661187 CTTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (20 bp):
AAAATAATTTTCAGAAATTA
Found at i:6661196 original size:19 final size:19
Alignment explanation
Indices: 6661156--6661198 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
6661146 TAGTTTTCAG
* *
6661156 AAATTAAAAATAATTTTTA
1 AAATTAAAAATAATTATAA
*
6661175 AAATTAAAAATACTTATAA
1 AAATTAAAAATAATTATAA
6661194 AAATT
1 AAATT
6661199 CCAAAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTAAAAATAATTATAA
Found at i:6661240 original size:18 final size:18
Alignment explanation
Indices: 6661188--6661241 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
6661178 TTAAAAATAC
* *
6661188 TTATAAAAATTCCAAAAT
1 TTATAAAAATTTCAAAAA
* ** *
6661206 TTATATATTTTTTAAAAA
1 TTATAAAAATTTCAAAAA
6661224 TTATAAAAATTTCAAAAA
1 TTATAAAAATTTCAAAAA
6661242 AAATCTAAAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (18 bp):
TTATAAAAATTTCAAAAA
Found at i:6666384 original size:34 final size:34
Alignment explanation
Indices: 6666326--6666404 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
6666316 GGTGGCATTT
* * *
6666326 AATATGCTTTTAACAGAACTATATGGTAGCAACC
1 AATATGCTTATAACAGAACGATATGGTAGCAAAC
** * * *
6666360 AATATGCTTATAACAGTTCGATATGGTGGTAAAT
1 AATATGCTTATAACAGAACGATATGGTAGCAAAC
6666394 AATATGCTTAT
1 AATATGCTTAT
6666405 CATGTGTTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (34 bp):
AATATGCTTATAACAGAACGATATGGTAGCAAAC
Found at i:6667215 original size:20 final size:22
Alignment explanation
Indices: 6667167--6667215 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
6667157 TTTGATTCGG
*
6667167 GAAGCAAAAATAATTTTAGCAAT
1 GAAG-AAAAATAATTTTAGCAAA
*
6667190 GGAGAAAAAT-ATTTT-GCAAA
1 GAAGAAAAATAATTTTAGCAAA
6667210 GAAGAA
1 GAAGAA
6667216 GATGAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 9 0.39
21 5 0.22
22 6 0.26
23 3 0.13
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.22
Consensus pattern (22 bp):
GAAGAAAAATAATTTTAGCAAA
Found at i:6669252 original size:39 final size:39
Alignment explanation
Indices: 6669197--6669369 Score: 256
Period size: 39 Copynumber: 4.4 Consensus size: 39
6669187 TATATAATTA
* * *
6669197 TACCCCTGATCGCACTTACGTGCCCTTGTTGTATTTTGG
1 TACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGG
* *
6669236 CACCCCTGATCGCACTTACGTGCCCCTATTGTACTTCGG
1 TACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGG
* *
6669275 TACCCTTGATCGCACTTACGTGCCGCTGTTGTACTTCGG
1 TACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGG
*
6669314 TACCCCTGATCGAACTTACGTGCCCCTGTTGTACTTCGG
1 TACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGG
* *
6669353 TACTCCTGATAGCACTT
1 TACCCCTGATCGCACTT
6669370 TCATGTTGAG
Statistics
Matches: 119, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 119 1.00
ACGTcount: A:0.15, C:0.32, G:0.20, T:0.33
Consensus pattern (39 bp):
TACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGG
Found at i:6669261 original size:20 final size:20
Alignment explanation
Indices: 6669238--6669341 Score: 81
Period size: 20 Copynumber: 5.3 Consensus size: 20
6669228 TATTTTGGCA
6669238 CCCCTGATCGCACTTACGTG
1 CCCCTGATCGCACTTACGTG
* * *
6669258 CCCCT-ATTGTACTT-CGGTA
1 CCCCTGATCGCACTTAC-GTG
*
6669277 CCCTTGATCGCACTTACGTG
1 CCCCTGATCGCACTTACGTG
* * * *
6669297 CCGCTG-TTGTACTT-CGGTA
1 CCCCTGATCGCACTTAC-GTG
*
6669316 CCCCTGATCGAACTTACGTG
1 CCCCTGATCGCACTTACGTG
6669336 CCCCTG
1 CCCCTG
6669342 TTGTACTTCG
Statistics
Matches: 62, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
18 2 0.03
19 26 0.42
20 32 0.52
21 2 0.03
ACGTcount: A:0.14, C:0.36, G:0.20, T:0.30
Consensus pattern (20 bp):
CCCCTGATCGCACTTACGTG
Found at i:6669360 original size:19 final size:19
Alignment explanation
Indices: 6669258--6669360 Score: 66
Period size: 19 Copynumber: 5.3 Consensus size: 19
6669248 CACTTACGTG
*
6669258 CCCCTATTGTACTTCGGTA
1 CCCCTGTTGTACTTCGGTA
* * * *
6669277 CCCTTGATCGCACTTAC-GTG
1 CCCCTG-TTGTACTT-CGGTA
*
6669297 CCGCTGTTGTACTTCGGTA
1 CCCCTGTTGTACTTCGGTA
* * *
6669316 CCCCTGATCGAACTTAC-GTG
1 CCCCTG-TTGTACTT-CGGTA
6669336 CCCCTGTTGTACTTCGGTA
1 CCCCTGTTGTACTTCGGTA
*
6669355 CTCCTG
1 CCCCTG
6669361 ATAGCACTTT
Statistics
Matches: 60, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
18 2 0.03
19 30 0.50
20 26 0.43
21 2 0.03
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.33
Consensus pattern (19 bp):
CCCCTGTTGTACTTCGGTA
Found at i:6680838 original size:11 final size:11
Alignment explanation
Indices: 6680818--6680853 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
6680808 CAAATTTTTG
*
6680818 AAAACAAAATA
1 AAAATAAAATA
*
6680829 AAAATCAAATA
1 AAAATAAAATA
6680840 AAAATAAAATA
1 AAAATAAAATA
6680851 AAA
1 AAA
6680854 TCCCATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:6693542 original size:44 final size:46
Alignment explanation
Indices: 6693470--6693564 Score: 115
Period size: 44 Copynumber: 2.1 Consensus size: 46
6693460 GCATTGACCT
* *
6693470 AAAATCAATAGTTCAATAACTTATATGCAA-AGAATTAA-CAAA-AA
1 AAAATCAATAGTTCAACAACTTACATGCAACA-AATTAACCAAATAA
** *
6693514 AAAATCAATAGTTTGACAATTTACATGCAACAAATTAACCAAATAA
1 AAAATCAATAGTTCAACAACTTACATGCAACAAATTAACCAAATAA
6693560 AAAAT
1 AAAAT
6693565 AAAAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
44 31 0.72
45 5 0.12
46 7 0.16
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.25
Consensus pattern (46 bp):
AAAATCAATAGTTCAACAACTTACATGCAACAAATTAACCAAATAA
Found at i:6695026 original size:18 final size:18
Alignment explanation
Indices: 6695003--6695045 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
6694993 ATCCAATCCA
**
6695003 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
6695021 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
6695039 AACCCAA
1 AACCCAA
6695046 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:6695169 original size:9 final size:9
Alignment explanation
Indices: 6695155--6695239 Score: 91
Period size: 9 Copynumber: 9.4 Consensus size: 9
6695145 GTAGTGATTC
*
6695155 AATTCGGGT
1 AATTCGGTT
6695164 AATTCGGTT
1 AATTCGGTT
*
6695173 AATTTTGG-T
1 AA-TTCGGTT
6695182 AATTCGGTT
1 AATTCGGTT
*
6695191 AATTCGGGT
1 AATTCGGTT
* *
6695200 AGTTTGGTT
1 AATTCGGTT
*
6695209 AATTCGATT
1 AATTCGGTT
*
6695218 AATTCGATT
1 AATTCGGTT
6695227 AATTCGGTT
1 AATTCGGTT
6695236 AATT
1 AATT
6695240 TTTAACCAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
8 4 0.06
9 55 0.87
10 4 0.06
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:6696830 original size:22 final size:21
Alignment explanation
Indices: 6696805--6696847 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
6696795 AAGCTATTGT
*
6696805 AGGTAAGTGGTTTAATTGCCTC
1 AGGTAAGTGGTTCAATT-CCTC
**
6696827 AGGTTGGTGGTTCAATTCCTC
1 AGGTAAGTGGTTCAATTCCTC
6696848 GCATGCTCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.37
Consensus pattern (21 bp):
AGGTAAGTGGTTCAATTCCTC
Found at i:6702951 original size:4 final size:4
Alignment explanation
Indices: 6702942--6702972 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
6702932 ATTAATATGT
6702942 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
6702973 TATATACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:6703032 original size:33 final size:34
Alignment explanation
Indices: 6702962--6703054 Score: 122
Period size: 33 Copynumber: 2.8 Consensus size: 34
6702952 ACATACATAC
*
6702962 ATACATACATATA-TATACAAGAATAAATATATAT
1 ATACATACATAGATTATACAAGAAT-AATATATAT
*
6702996 ATACATATATAGATTATACAAGAATAA-ATATAT
1 ATACATACATAGATTATACAAGAATAATATATAT
*
6703029 ATACATAGATAGATTATA-AA-AATAAT
1 ATACATACATAGATTATACAAGAATAAT
6703055 TACATAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
31 5 0.09
32 2 0.04
33 23 0.43
34 13 0.24
35 11 0.20
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.32
Consensus pattern (34 bp):
ATACATACATAGATTATACAAGAATAATATATAT
Found at i:6703071 original size:20 final size:21
Alignment explanation
Indices: 6703046--6703094 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
6703036 GATAGATTAT
6703046 AAAAATAATTACA-TAAAATA
1 AAAAATAATTACATTAAAATA
* *
6703066 AAAAATAATTACATTACATTA
1 AAAAATAATTACATTAAAATA
6703087 AAAAATAA
1 AAAAATAA
6703095 ATATGCGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATAATTACATTAAAATA
Found at i:6703088 original size:21 final size:20
Alignment explanation
Indices: 6703041--6703094 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
6703031 ACATAGATAG
6703041 ATTATAAAAATAATTACATAA
1 ATTA-AAAAATAATTACATAA
* *
6703062 AATAAAAAATAATTACATTAC
1 ATTAAAAAATAATTACA-TAA
6703083 ATTAAAAAATAA
1 ATTAAAAAATAA
6703095 ATATGCGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (20 bp):
ATTAAAAAATAATTACATAA
Found at i:6703228 original size:20 final size:21
Alignment explanation
Indices: 6703185--6703228 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
6703175 AAAAATACAA
* * *
6703185 AATACAAAATGAAAATTAATT
1 AATACAAAATAAAAATAAACT
6703206 AATA-AAAATAAAAATAAACT
1 AATACAAAATAAAAATAAACT
6703226 AAT
1 AAT
6703229 TTGAACTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (21 bp):
AATACAAAATAAAAATAAACT
Found at i:6703993 original size:28 final size:28
Alignment explanation
Indices: 6703949--6704003 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
6703939 CCGTTGCATA
* *
6703949 TAGATAACAACATATAATGAAATAACTG
1 TAGATAACAACAGATAAAGAAATAACTG
6703977 TAGATTAACAA-AGATAAAGAAATAACT
1 TAGA-TAACAACAGATAAAGAAATAACT
6704004 ATCAACCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (28 bp):
TAGATAACAACAGATAAAGAAATAACTG
Found at i:6704826 original size:44 final size:43
Alignment explanation
Indices: 6704597--6705137 Score: 240
Period size: 44 Copynumber: 12.5 Consensus size: 43
6704587 TGCAGTCCAT
* * * *
6704597 TCCACTGCAA-TGTCAGGGAGATAAGACTAGATAC--GATCTTC
1 TCCACTGCAACT-TCAGGGAGATAAGACTTGCTACTTAATCTGC
* * * * * *
6704638 T-CTCTGTAACTTCAGAGAGATAAGATCTGTGAT-TTTAATCCGC
1 TCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTACTTAATCTGC
* * *
6704681 TCCACTGCAACTTCAGGGAGATAGGATTATTGGC--CTTAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGA--CTT-GCTACTTAATCTGC
* * *
6704725 TCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTA-CTT-AATCTGC
* *
6704770 -CTTACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTGC
1 TC-CACTGCAACTTCAGGGA-GATAAGACTTGC-TACTTAATCTGC
* * *
6704814 TCCACTGCAACTTCAGGGAGATAAGACTAGATGC--AATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTACTTAATCTGC
* * * ** * * **
6704855 T-CTCTGCAACTTCAGAGAGAAAAGAGCCAAGAT-TTTAATCCAC
1 TCCACTGCAACTTCAGGGAGATAAGA--CTTGCTACTTAATCTGC
* * * *
6704898 TCCACTGCAACTTCAGGGAGATAGGATTATCGGCT--TTAACCTAC
1 TCCACTGCAACTTCAGGGAGATAAGACT-T--GCTACTTAATCTGC
* * * ** * *
6704942 TCCACCGCCACTTTAGGGAGATAAGGTTTGCCATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTA-CTT-AATCTGC
* * *
6704987 CCCACTGCAACTTCA-GGAGGATAAGATTTGCTTACTTAGTCTGC
1 TCCACTGCAACTTCAGGGA-GATAAGACTTGC-TACTTAATCTGC
* * * * *
6705031 TCTACTGCAACTTCAGGGAGATAAGACTAGATGC--GATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTACTTAATCTGC
* * ** * * *
6705072 T-CTCTGCAACTTCAGAGAGATAAGATCCAAGAT-TTTAATCCGC
1 TCCACTGCAACTTCAGGGAGATAAGA--CTTGCTACTTAATCTGC
6705115 TCCACTGCAACTTCAGGGAGATA
1 TCCACTGCAACTTCAGGGAGATA
6705138 GGATTATTGG
Statistics
Matches: 385, Mismatches: 78, Indels: 71
0.72 0.15 0.13
Matches are distributed among these distances:
40 61 0.16
41 21 0.05
42 15 0.04
43 22 0.06
44 192 0.50
45 72 0.19
46 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (43 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGCTACTTAATCTGC
Done.