Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 79 of 226
Found at i:28843020 original size:29 final size:30
Alignment explanation
Indices: 28842977--28843050 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
28842967 CCGAATATAA
*
28842977 TAAATATATATTTTTATTTTTAAAA-ATATTT
1 TAAA-ATACATTTTTATTTTTAAAATAT-TTT
28843008 TAAAATAC-TTTTTATTTTTAAAATATTTT
1 TAAAATACATTTTTATTTTTAAAATATTTT
28843037 TAAAATACATTTTT
1 TAAAATACATTTTT
28843051 TAATTTTCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 26 0.65
30 10 0.25
31 4 0.10
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
TAAAATACATTTTTATTTTTAAAATATTTT
Found at i:28843026 original size:18 final size:17
Alignment explanation
Indices: 28843005--28843038 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
28842995 TTTAAAAATA
28843005 TTTTAAAATACTTTTTAT
1 TTTTAAAATA-TTTTTAT
28843023 TTTTAAAATATTTTTA
1 TTTTAAAATATTTTTA
28843039 AAATACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAATATTTTTAT
Found at i:28843050 original size:13 final size:11
Alignment explanation
Indices: 28842991--28843043 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
28842981 TATATATTTT
28842991 TATTTTTAAAA
1 TATTTTTAAAA
28843002 -ATATTTTAAAA
1 TAT-TTTTAAAA
*
28843013 TACTTTT----
1 TATTTTTAAAA
28843020 TATTTTTAAAA
1 TATTTTTAAAA
28843031 TATTTTTAAAA
1 TATTTTTAAAA
28843042 TA
1 TA
28843044 CATTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
7 6 0.18
10 2 0.06
11 25 0.74
12 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:28843066 original size:30 final size:28
Alignment explanation
Indices: 28842987--28843067 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
28842977 TAAATATATA
*
28842987 TTTTTATTTTTAAAAATATTTTAAAATAC
1 TTTTTAATTTTAAAAAT-TTTTAAAATAC
*
28843016 TTTTTATTTTTAAAATATTTTTAAAATAC
1 TTTTTAATTTTAAAA-ATTTTTAAAATAC
**
28843045 ATTTTTTAATTTTCTAAATTTTT
1 --TTTTTAATTTTAAAAATTTTT
28843068 TTTGTGTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 26 0.57
30 8 0.17
31 12 0.26
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTAATTTTAAAAATTTTTAAAATAC
Found at i:28844963 original size:98 final size:102
Alignment explanation
Indices: 28844842--28845035 Score: 236
Period size: 102 Copynumber: 1.9 Consensus size: 102
28844832 GCACCAAAAT
*
28844842 TTTTTTTATTGAATTTAGGGCCTCCACATGAAGA-GAG-CA-CTGAAAAA-TTCAAA-AAAAAAT
1 TTTTTTTATTGAATTTAGGGCCTCCACATGAAAATGAGACATC-GAAAAATTTCAAATAAAAAAT
*
28844902 GTTGGTGCCGCCACATTTGGAGTTGGCACTAGGGGGAA
65 GCTGGTGCCGCCACATTTGGAGTTGGCACTAGGGGGAA
** * * * * * * *
28844940 TTTTTTTATTGGTTTTCGTGCCTCTACATGAAAATGTGACATCGAAAAATTTTAAATTAAAATTG
1 TTTTTTTATTGAATTTAGGGCCTCCACATGAAAATGAGACATCGAAAAATTTCAAATAAAAAATG
*
28845005 CTGGTGTCGCCACATTTGGAGTTGGCACTAG
66 CTGGTGCCGCCACATTTGGAGTTGGCACTAG
28845036 AAAAATAAAG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
98 28 0.35
99 2 0.03
100 8 0.10
101 6 0.08
102 35 0.44
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (102 bp):
TTTTTTTATTGAATTTAGGGCCTCCACATGAAAATGAGACATCGAAAAATTTCAAATAAAAAATG
CTGGTGCCGCCACATTTGGAGTTGGCACTAGGGGGAA
Found at i:28846209 original size:16 final size:17
Alignment explanation
Indices: 28846188--28846233 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
28846178 GGCAATGTGT
28846188 TGATTGTTTAAAAG-TA
1 TGATTGTTTAAAAGTTA
* **
28846204 TGATTGTTCATTAGTTA
1 TGATTGTTTAAAAGTTA
28846221 T-ATTGTTTAAAAG
1 TGATTGTTTAAAAG
28846234 GGTGATTTAG
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (17 bp):
TGATTGTTTAAAAGTTA
Found at i:28854489 original size:34 final size:34
Alignment explanation
Indices: 28854444--28854533 Score: 135
Period size: 34 Copynumber: 2.6 Consensus size: 34
28854434 ACTTATACAA
28854444 ATATCATATCAGAATGTCATATTACCAAAAACAT
1 ATATCATATCAGAATGTCATATTACCAAAAACAT
* * **
28854478 ATATCAGATCAGAATGTCATATTTCCAAATGCAT
1 ATATCATATCAGAATGTCATATTACCAAAAACAT
*
28854512 ATATCATATCAGGATGTCATAT
1 ATATCATATCAGAATGTCATAT
28854534 CAAATCAGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (34 bp):
ATATCATATCAGAATGTCATATTACCAAAAACAT
Found at i:28858083 original size:882 final size:874
Alignment explanation
Indices: 28856182--28858131 Score: 2356
Period size: 876 Copynumber: 2.2 Consensus size: 874
28856172 GGCCGTGTAA
* * * * *
28856182 CTCTATTTTATTTTTAATATTATTTTAT-TCTATTTATTTTCCTTTTATTTTTCAAGTATAGCAG
1 CTCT-TTTTATTTTTAATAATATTTTATGGCCATTTATTTTCCTTTTATTTTGCAAGTATAGCAA
* * * * *
28856246 TTCCTCCTTCTACAGGTTTTACAAGTAAAGTAAGTAGGCAAACATCATATTAGAAACCTATAATG
65 TT--TTCTTCTACAGG-TTTACAAGCAAAGTAGGAAGGCAAACATCATA-TAGGAACCTATAATG
* *
28856311 GTTGGGTAGACATAGAAGAATGATGTGACATTAGAATTGATAACCCATCTTCACCACACAATATT
126 GTCGGGTAGACATAGAAGAATGATGTGACATTAGAATTGATAACCCATCTCCACCACACAATATT
* * *
28856376 CACCGCCGATGTTGGTCTATTCAATAGGCCTTACCTTCAAAAGTACTTGTTATTGGCACATCGGT
191 CACCGCCAATATTGGTATATTCAATAGGCCTTACCTTCAAAAGTACTTGTTATTGGCACATCGGT
* * * *
28856441 TCGCAATCCTTCTAGCGAAATCAATTTTATTTCTAATTTGAAGTTTCTTTACTATTTTGAAATTT
256 TCGCAATCATTCTAGCGAAATAAATTTTATTTCTAATTTGAAGATTCTTTACAATTTTGAAATTT
* * * *
28856506 AGTCCCTTTTAGTATTATATAGTTAAATAGTGTAATCACCCCTCGAATATTAATTGACGTACTGT
321 AGTCCCTTTTAGTACTAGATAGTTAAATAGTGTAATCACCCCTCGAATATAAATTGACGTACTAT
*
28856571 AATATGTAGTGAGTAGCTAGCTAGACTTATTGTTTACATGCATTTTCATTGTTAATCACCTTATC
386 AATATGTAGTGAGTAGCTAGCTAGACTTATTGTTTACATGCATCTTCATTGTTAATCACCTTATC
* * * *
28856636 ACCCGAACTCTTTTGGGTTAGATCATTGGAATACTCGAAGTGTTCTATTCTGACAATAAAAATTA
451 ACCCGAACTCTCTTGGGTTAGATCATTGGAATACTCGAAGTGTTCCATTCTAACAATAAAAAATA
* *
28856701 TTACTTTTCACACTAGCAGACACCACTACATTTATAATTGTGTTGATTCATAGTCTTGACGCAAG
516 TTACTTTTCACACTAGCAGACACAACTACATTTATAATTGTGTTGATTCATACTCTTGACGCAAG
** * *
28856766 CACGGTGGGGTGCGATCAATATCCTTTATTAATTAATTAAAATTTTAAATGTTATAATATGCTAG
581 CACGGCAGGGCGCAATCAATATCCTTTATTAA-TAATTAAAATTTTAAATGTTATAATATGCTAG
* * * ** * * *
28856831 AATAGCTCAGTTGGTTAGAGTGTGTGGCTGTTAACTATAAGTTTGAAGGTTCAAACCCTTCTTCT
645 AACAACTCAGTTAGTTAGAGCATGTGGCTGTTAACCAAAAGTTCGAAGGTTCAAACCCTTCTTCT
** * *
28856896 AGTGAAATTAATTTTATTTTTAAATTGGACACTCTTTAGTGTTTCAACTTTGCTCTTTTTTCTCA
710 AGCAAAATTAATTTTATTTTTAAATTGAACACTCTTTAGTGTTTCAACGTTGCTCTTTTTTCTCA
* * * * *
28856961 CTTTTATTATTAATAATGTTTTTATTTTTGGCCCTTTTACTAGAAAAATATTTTTTCTTTTATAA
775 ATTTTATTATTAATAATATCTTTATTTTTGGCCCTTTTACTAGAAAAATAATTTTTCATTTATAA
* *
28857026 TTTGAACCTTCTTTAATGTTTTGGTGTTGCTATTT
840 TTTGAACCTTCTTTAATGGTTTGGTGTTGCTAGTT
* * *
28857061 CTCTTTTTATTTTTAATAATATTTTATGGCCATTTATTTTCCCTTTGTTTTGCTAA-TATAACAA
1 CTCTTTTTATTTTTAATAATATTTTATGGCCATTTATTTTCCTTTTATTTTGC-AAGTATAGCAA
* * * * *
28857125 -TTTCTCCTCCAAGTTTACAAGCAATGTAGGAAGGCAAACATCATATTGGAAACCTATAATGGTC
65 TTTTCTTCTACAGGTTTACAAGCAAAGTAGGAAGGCAAACATCATATAGG-AACCTATAATGGTC
* * * *
28857189 GGGTACACATAGAAGAATGATGTGACATCAGTATTGATAACCCATCTCCACCACACAATATTTAC
129 GGGTAGACATAGAAGAATGATGTGACATTAGAATTGATAACCCATCTCCACCACACAATATTCAC
* ** * * **
28857254 TGCCAATATTGGTATATTCTGTAGGCCTTACCTTTACAAGTA-TTGGTTATTGGCATGTCGGTTC
194 CGCCAATATTGGTATATTCAATAGGCCTTACCTTCAAAAGTACTT-GTTATTGGCACATCGGTTC
* *
28857318 -CAATCATTCTAGTGAAATAAATTTTATTTCTAATTTTAAGATTCTTTACAATTTTGAAATTTAG
258 GCAATCATTCTAGCGAAATAAATTTTATTTCTAATTTGAAGATTCTTTACAATTTTGAAATTTAG
** * * * * **
28857382 TCTTTTTTTTTGTGCTAGATAGTTAAATAGTGTAATCATCCCTTGAATATAAATTTCCGTACTAT
323 TC--CCTTTTAGTACTAGATAGTTAAATAGTGTAATCACCCCTCGAATATAAATTGACGTACTAT
* * * * * *
28857447 AATATTTAGTGAGTAGCTAGCTAGGCTTCTTGTTTGCATGTATCTTCATTGTTAATCACTTTATC
386 AATATGTAGTGAGTAGCTAGCTAGACTTATTGTTTACATGCATCTTCATTGTTAATCACCTTATC
* * * * *
28857512 ACCCGAACTCTCTTGGGTTTGATCCTTGGAATATTGGAAGTGTTCCATTCTAACACTAAAAAAAT
451 ACCCGAACTCTCTTGGGTTAGATCATTGGAATACTCGAAGTGTTCCATTCTAACAAT-AAAAAAT
* * * * *
28857577 ATTACATCTAACCTGTCATACTTGCATA-ACAAGTTATATTTATAATTATATTTGTGTTGATTCA
515 ATTAC-T-T----T-TCACACTAGCAGACACAA-CTACA-TT-T-A-TA-A-TTGTGTTGATTCA
* * * * * *
28857641 TAC-CTCTGACGCACGCATGGCAGGGCGCAATCAATATGCTTTA-T-A-AATTTAATTTTTAAGT
566 TACTCT-TGACGCAAGCACGGCAGGGCGCAATCAATATCCTTTATTAATAATTAAAATTTTAAAT
* *
28857702 GTTATAATATGCTAGAACAACTCAGTTAGTTAGAGCATGTGGTTGTTAACCACAAAG-TCGAATG
630 GTTATAATATGCTAGAACAACTCAGTTAGTTAGAGCATGTGGCTGTTAACCA-AAAGTTCGAAGG
** * * *
28857766 TTTGAA-CC-TCTTTCTAGCAAAATTAATTTTATTTTTAATTTGAACCCTTTTTAGTGTTTCAAC
694 TTCAAACCCTTC-TTCTAGCAAAATTAATTTTATTTTTAAATTGAACACTCTTTAGTGTTTCAAC
* * *
28857829 GTTGCTC-TTTTTCTCAATTTTATTATTCATATTATCTTTGTTTTTGGCCCTCTTT-CTAGAAAA
758 GTTGCTCTTTTTTCTCAATTTTATTATTAATAATATCTTTATTTTTGGCCCT-TTTACTAGAAAA
* *
28857892 ATAAATTTTT-ATTTCTAATTTGAACTTTCTTTAATGGTTTGGTGTTGCT-GTT
822 AT-AATTTTTCATTTATAATTTGAACCTTCTTTAATGGTTTGGTGTTGCTAGTT
*
28857944 CTC-TTTTATTTTTAATAATATTTTCTGGCCATTTATTTTCCTTTTATTTTGCAAGTATAGCAAT
1 CTCTTTTTATTTTTAATAATATTTTATGGCCATTTATTTTCCTTTTATTTTGCAAGTATAGCAAT
* *
28858008 TGTTCTTCT-C-GGTTTACAAGCAAGGTAGGAAGGCAAACATCATAGTAGGAACCTATAATAGTC
66 T-TTCTTCTACAGGTTTACAAGCAAAGTAGGAAGGCAAACATCATA-TAGGAACCTATAATGGTC
* * * *
28858071 GGGTAGACATAGAAGAATGATGTGACATTAGCATTGATATCGCATATCCACCACACAATAT
129 GGGTAGACATAGAAGAATGATGTGACATTAGAATTGATAACCCATCTCCACCACACAATAT
28858132 GCATCATTGA
Statistics
Matches: 910, Mismatches: 131, Indels: 57
0.83 0.12 0.05
Matches are distributed among these distances:
874 64 0.07
875 152 0.17
876 164 0.18
877 11 0.01
878 24 0.03
879 31 0.03
880 2 0.00
881 2 0.00
882 153 0.17
883 14 0.02
884 104 0.11
885 65 0.07
886 68 0.07
887 4 0.00
888 3 0.00
889 4 0.00
890 45 0.05
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (874 bp):
CTCTTTTTATTTTTAATAATATTTTATGGCCATTTATTTTCCTTTTATTTTGCAAGTATAGCAAT
TTTCTTCTACAGGTTTACAAGCAAAGTAGGAAGGCAAACATCATATAGGAACCTATAATGGTCGG
GTAGACATAGAAGAATGATGTGACATTAGAATTGATAACCCATCTCCACCACACAATATTCACCG
CCAATATTGGTATATTCAATAGGCCTTACCTTCAAAAGTACTTGTTATTGGCACATCGGTTCGCA
ATCATTCTAGCGAAATAAATTTTATTTCTAATTTGAAGATTCTTTACAATTTTGAAATTTAGTCC
CTTTTAGTACTAGATAGTTAAATAGTGTAATCACCCCTCGAATATAAATTGACGTACTATAATAT
GTAGTGAGTAGCTAGCTAGACTTATTGTTTACATGCATCTTCATTGTTAATCACCTTATCACCCG
AACTCTCTTGGGTTAGATCATTGGAATACTCGAAGTGTTCCATTCTAACAATAAAAAATATTACT
TTTCACACTAGCAGACACAACTACATTTATAATTGTGTTGATTCATACTCTTGACGCAAGCACGG
CAGGGCGCAATCAATATCCTTTATTAATAATTAAAATTTTAAATGTTATAATATGCTAGAACAAC
TCAGTTAGTTAGAGCATGTGGCTGTTAACCAAAAGTTCGAAGGTTCAAACCCTTCTTCTAGCAAA
ATTAATTTTATTTTTAAATTGAACACTCTTTAGTGTTTCAACGTTGCTCTTTTTTCTCAATTTTA
TTATTAATAATATCTTTATTTTTGGCCCTTTTACTAGAAAAATAATTTTTCATTTATAATTTGAA
CCTTCTTTAATGGTTTGGTGTTGCTAGTT
Found at i:28861945 original size:27 final size:27
Alignment explanation
Indices: 28861897--28862099 Score: 183
Period size: 27 Copynumber: 7.5 Consensus size: 27
28861887 AGTACTGAGA
* **
28861897 CCCTCATAGGGTAAAATAACCGTAATGT
1 CCCT-ATAGGGTAAAATGACCGTAATAC
*
28861925 CCCTATAAGGTAAAATGACCGTAATAC
1 CCCTATAGGGTAAAATGACCGTAATAC
* *
28861952 CCCTATAGGGTAAAATGACAG-AAAAC
1 CCCTATAGGGTAAAATGACCGTAATAC
* * *
28861978 CCCCATAGGGTAAAATGATCGTAATGC
1 CCCTATAGGGTAAAATGACCGTAATAC
*
28862005 CCCTGTAGGGTAAAATGACCGTAATAC
1 CCCTATAGGGTAAAATGACCGTAATAC
* * * * **
28862032 CCCCACAGGGTTAAATAACCAAAATAC
1 CCCTATAGGGTAAAATGACCGTAATAC
* * * * *
28862059 CCCTGTAAGGTAAATTGATCGTAATGC
1 CCCTATAGGGTAAAATGACCGTAATAC
* *
28862086 TCCTAAAGGGTAAA
1 CCCTATAGGGTAAA
28862100 GGATTATTTT
Statistics
Matches: 136, Mismatches: 38, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
26 22 0.16
27 110 0.81
28 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (27 bp):
CCCTATAGGGTAAAATGACCGTAATAC
Found at i:28862034 original size:80 final size:81
Alignment explanation
Indices: 28861896--28862099 Score: 241
Period size: 80 Copynumber: 2.5 Consensus size: 81
28861886 AAGTACTGAG
* * * * * * *
28861896 ACCCTCATAGGGTAAAATAACCGTAATGTCCCTATAAGGTAAAATGACCGTAATACCCCTATAGG
1 ACCCCCATAGGGTAAAATGATCGTAATGCCCCTATAGGGTAAAATGACCGTAATACCCCCACAGG
*
28861961 GTAAAATGA-CAGAAA-
66 GTAAAATAACCA-AAAT
*
28861976 ACCCCCATAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCCACAGG
1 ACCCCCATAGGGTAAAATGATCGTAATGCCCCTATAGGGTAAAATGACCGTAATACCCCCACAGG
*
28862041 GTTAAATAACCAAAAT
66 GTAAAATAACCAAAAT
** * * * *
28862057 ACCCCTGTAAGGTAAATTGATCGTAATGCTCCTAAAGGGTAAA
1 ACCCCCATAGGGTAAAATGATCGTAATGCCCCTATAGGGTAAA
28862100 GGATTATTTT
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
80 67 0.64
81 38 0.36
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (81 bp):
ACCCCCATAGGGTAAAATGATCGTAATGCCCCTATAGGGTAAAATGACCGTAATACCCCCACAGG
GTAAAATAACCAAAAT
Found at i:28862150 original size:24 final size:24
Alignment explanation
Indices: 28862122--28862169 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
28862112 CCCAGGAGTG
*
28862122 TAAATGTCTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
28862146 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
28862170 GGTATAACTG
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:0.23, C:0.08, G:0.21, T:0.48
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:28862179 original size:24 final size:24
Alignment explanation
Indices: 28862129--28862185 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
28862119 GTGTAAATGT
* *
28862129 CTGATTTGTCTGTGATTTAAATGA
1 CTGATTTGTCTGTGATTGAAATAA
**
28862153 CTGATTTGTCTGTGATTGGTATAA
1 CTGATTTGTCTGTGATTGAAATAA
28862177 CTGATTTGT
1 CTGATTTGT
28862186 ATGACTGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.47
Consensus pattern (24 bp):
CTGATTTGTCTGTGATTGAAATAA
Found at i:28862340 original size:26 final size:26
Alignment explanation
Indices: 28862311--28862363 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
28862301 TTGGCCATAT
* *
28862311 TACTTTTACGGGCAGCTTTGCTGCGA
1 TACTGTTACCGGCAGCTTTGCTGCGA
* *
28862337 TACTGTTGCCGGTAGCTTTGCTGCGA
1 TACTGTTACCGGCAGCTTTGCTGCGA
28862363 T
1 T
28862364 GCTATTGATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.13, C:0.23, G:0.28, T:0.36
Consensus pattern (26 bp):
TACTGTTACCGGCAGCTTTGCTGCGA
Found at i:28862410 original size:32 final size:32
Alignment explanation
Indices: 28862369--28862536 Score: 203
Period size: 32 Copynumber: 5.3 Consensus size: 32
28862359 GCGATGCTAT
* *
28862369 TGATGGCTTTGTACCGGTCATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
** * *
28862401 TGATGGCTTTGTGTTGATCATATTATCATTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
28862433 TGATGGCTTTGTGCCGATCATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* * * *
28862465 TGATGGCTTTATGCCGATCATATCACTGCTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* * *
28862497 TGATGGCTTTGTGCCAATAATATTACTG-TAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
*
28862528 TTATGGCTT
1 TGATGGCTT
28862537 GTAGCCATTC
Statistics
Matches: 117, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
31 11 0.09
32 106 0.91
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATTACCGTTAC
Found at i:28867689 original size:324 final size:324
Alignment explanation
Indices: 28867078--28867712 Score: 836
Period size: 324 Copynumber: 2.0 Consensus size: 324
28867068 GGTGTTGCTA
* **
28867078 TTTCTCTTTTATTTTTAATAATAATTTTTGGCCATTTATTTTTCCTTTATTTTTGCAAGTATAGT
1 TTTCTCTTTTATTTTTAATAAT-ATTTTTGGCCATTTATTTTCCCTTTATTTTTGCAAGTATAAC
* * * *
28867143 AGTTCCTTCCCCAGGTTCACAAGAAAAGTAGGAAGGCAGACATCATAGTAGGAACCTATAATGGT
65 AATTCCTTCCCCAGGTTCACAAGAAAAGAAGGAAGGCAAACATCATAGTAGAAACCTATAATGGT
* * *
28867208 CGAGTAAACACAAAATAATGATGTGACATTAGTATTTATAACCCCTCTCAACCACACAATATTCA
130 CGAGTAAACACAAAATAATGATGTGACATTAGTATTGATAACCCATCTCAACCACACAATAGTCA
* * * *
28867273 TCGTCAATGTTGGTCTATTCTGTAGGCCTTATCTTCACAAGTACTTGTTATTAGTATGTCGGTTC
195 TCGTCAATGTTGGTCTATTCTGTAAGCCTTACCTTCACAAGTACTTGTTATTAGCATGTCGATTC
*
28867338 ACAATTTTTCTAGCAAAATCAATTTTATTTCTAATTTGAACTT-TATTTACTATTTCACATTGCC
260 ACAATCTTTCTAGCAAAATCAATTTTATTTCTAATTTGAACTTCT-TTTACTATTTCACATTGCC
28867402 T
324 T
* *
28867403 TTTCTCTTTTA-TTTTAAT-AT-TTTTTTGTCATTTATTTTCCCTTTCA-TTTTGCAAGTATAAC
1 TTTCTCTTTTATTTTTAATAATATTTTTGGCCATTTATTTTCCCTTT-ATTTTTGCAAGTATAAC
** * *
28867464 AATTCCTCATTCTTCAGGTTTACAAGTAAAA-AAGGAAGGTAAACATCATAGTAGAAACCTATAA
65 AATT-C-C-TTCCCCAGGTTCACAAG-AAAAGAAGGAAGGCAAACATCATAGTAGAAACCTATAA
* * *
28867528 TGGTCGGGTAAACACAGAAA-AATGATGTGACATTAGTATTGATAACCCATCTCCACCACACTAT
126 TGGTCGAGTAAACACA-AAATAATGATGTGACATTAGTATTGATAACCCATCTCAACCACACAAT
* * * * *
28867592 AGTCA-CTGTCGATGTTGGTTTATTTTGTAAGTCTTACCTTCACAAGTACTTGTTATTGGCATGT
190 AGTCATC-GTCAATGTTGGTCTATTCTGTAAGCCTTACCTTCACAAGTACTTGTTATTAGCATGT
* * **
28867656 TGATTCACAATCTTTCTAGCGAAATTTATTTTATTTCTAATTTGAACTTCTTTTACT
254 CGATTCACAATCTTTCTAGCAAAATCAATTTTATTTCTAATTTGAACTTCTTTTACT
28867713 GTTTTGAAAT
Statistics
Matches: 269, Mismatches: 33, Indels: 17
0.84 0.10 0.05
Matches are distributed among these distances:
321 37 0.14
322 2 0.01
323 4 0.01
324 207 0.77
325 19 0.07
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (324 bp):
TTTCTCTTTTATTTTTAATAATATTTTTGGCCATTTATTTTCCCTTTATTTTTGCAAGTATAACA
ATTCCTTCCCCAGGTTCACAAGAAAAGAAGGAAGGCAAACATCATAGTAGAAACCTATAATGGTC
GAGTAAACACAAAATAATGATGTGACATTAGTATTGATAACCCATCTCAACCACACAATAGTCAT
CGTCAATGTTGGTCTATTCTGTAAGCCTTACCTTCACAAGTACTTGTTATTAGCATGTCGATTCA
CAATCTTTCTAGCAAAATCAATTTTATTTCTAATTTGAACTTCTTTTACTATTTCACATTGCCT
Found at i:28877784 original size:29 final size:29
Alignment explanation
Indices: 28877742--28877797 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
28877732 ACAGCAGAAC
28877742 AGGGGTAAGTTTGAAGATTTTACTATAAT
1 AGGGGTAAGTTTGAAGATTTTACTATAAT
28877771 AGGGGTAAGTTTGAAGATTTTACTATA
1 AGGGGTAAGTTTGAAGATTTTACTATA
28877798 GTTATTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.38
Consensus pattern (29 bp):
AGGGGTAAGTTTGAAGATTTTACTATAAT
Found at i:28880213 original size:12 final size:12
Alignment explanation
Indices: 28880193--28880223 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28880183 TCAGTAGCTT
*
28880193 CACATGGCCTAG
1 CACACGGCCTAG
28880205 CACACGGCCTAG
1 CACACGGCCTAG
28880217 CACACGG
1 CACACGG
28880224 GCGTGTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.39, G:0.26, T:0.10
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:28884946 original size:22 final size:22
Alignment explanation
Indices: 28884897--28884939 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28884887 CCATGGATGT
* *
28884897 ATTATGCTAATATAATTGATTG
1 ATTATGCCAATATAATTGAATG
28884919 ATTATGCCAATATAATTGAAT
1 ATTATGCCAATATAATTGAAT
28884940 ATTTATGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (22 bp):
ATTATGCCAATATAATTGAATG
Found at i:28887756 original size:15 final size:17
Alignment explanation
Indices: 28887721--28887760 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
28887711 TGTGGCTGGC
28887721 GTGTGCACCACACGGGT
1 GTGTGCACCACACGGGT
28887738 GTGTGCACCACACGGGT
1 GTGTGCACCACACGGGT
28887755 GTGTGC
1 GTGTGC
28887761 GATTACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.20
Consensus pattern (17 bp):
GTGTGCACCACACGGGT
Found at i:28893536 original size:19 final size:18
Alignment explanation
Indices: 28893498--28893548 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
28893488 TTTTTTCTCA
* *
28893498 CTATTGTTATTATTTTAT
1 CTATTATTATTATATTAT
28893516 CTATTATTATTATCATTAT
1 CTATTATTATTAT-ATTAT
*
28893535 CTATTTTTATTATA
1 CTATTATTATTATA
28893549 AATTGCACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (18 bp):
CTATTATTATTATATTAT
Found at i:28893749 original size:12 final size:12
Alignment explanation
Indices: 28893734--28893758 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28893724 TTATCATTGC
28893734 TATTATTTATTT
1 TATTATTTATTT
28893746 TATTATTTATTT
1 TATTATTTATTT
28893758 T
1 T
28893759 TTCCTTTGAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTATTTATTT
Found at i:28895089 original size:21 final size:21
Alignment explanation
Indices: 28895065--28895115 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
28895055 AATAACACGC
28895065 CCGTGTGACAAAGGCAAACGA
1 CCGTGTGACAAAGGCAAACGA
*
28895086 CCGTGTGACAAAGGCACACGA
1 CCGTGTGACAAAGGCAAACGA
28895107 CCGTGTGAC
1 CCGTGTGAC
28895116 TGGAAGACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.27, G:0.29, T:0.12
Consensus pattern (21 bp):
CCGTGTGACAAAGGCAAACGA
Found at i:28898829 original size:31 final size:32
Alignment explanation
Indices: 28898784--28898846 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
28898774 AGATAATTTT
28898784 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
28898816 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
28898847 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
AAAGAGTTTTTATTAGGATTCAATTACTCTTG
Found at i:28900385 original size:10 final size:10
Alignment explanation
Indices: 28900370--28900399 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28900360 AGTACATATC
28900370 AATCACATTT
1 AATCACATTT
*
28900380 AATCACATTC
1 AATCACATTT
28900390 AATCACATTT
1 AATCACATTT
28900400 TATGATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (10 bp):
AATCACATTT
Found at i:28902873 original size:10 final size:10
Alignment explanation
Indices: 28902858--28902887 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28902848 AGTACATATC
28902858 AATCACATTT
1 AATCACATTT
*
28902868 AATCACATTC
1 AATCACATTT
28902878 AATCACATTT
1 AATCACATTT
28902888 TATGATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (10 bp):
AATCACATTT
Found at i:28905115 original size:221 final size:226
Alignment explanation
Indices: 28904706--28905118 Score: 599
Period size: 221 Copynumber: 1.8 Consensus size: 226
28904696 AAAACCTGAC
* ** *
28904706 CAAATCCTCATATTTCAAACCACTAGAACCACATATACCAACTGTCCTCAATGTTAGGACTCTAT
1 CAAATCCTCATATGTCAAACCACTAGAACCACATATACCAACCATCCTCAATGTTAGGAATCTAT
*
28904771 CCCCCATCAAACTCTTCTAATATTCAGTAACCACTATCCCCCCTCAACACACAATCCTTCTTTAC
66 CCCCCATCAAACTCTTCTAATATTCAG--ACCACTATCCCCCCTCAACACACAACCCTTCTTTAC
*
28904836 ACTCGAAACCAACTCAAGCTCGAAAATCATACAAGAAGTACATAAAAAGAAAAGAAAGAAACAAA
129 ACTCGAAACCAACTCAAGCTCGAAAATCATACAAGAAGGACATAAAAAGAAAAGAAAGAAACAAA
28904901 AAAAAAAACCTACTTGACTTTGAAATGAAAGAG
194 AAAAAAAACCTACTTGACTTTGAAATGAAAGAG
*
28904934 CAAATCCTCAT-TCGTCAAA-CACTAGAACCACATATATCAACCAT-CTCCAATGTT-GGAAATC
1 CAAATCCTCATAT-GTCAAACCACTAGAACCACATATACCAACCATCCT-CAATGTTAGG-AATC
* * * *
28904995 TA-GCCCCATCAAACTTTTCTACTATTCAG-CC-C-ATCCCCCCTCAACCCACAACCCTTCTTTA
63 TATCCCCCATCAAACTCTTCTAATATTCAGACCACTATCCCCCCTCAACACACAACCCTTCTTTA
* * *
28905056 CACTCGAAACCAACTCAAGCTCGACAATCATACAAGAAGGGCATACAAAGAAAAGAAAGAAAC
128 CACTCGAAACCAACTCAAGCTCGAAAATCATACAAGAAGGACATAAAAAGAAAAGAAAGAAAC
28905119 CAAATAATAA
Statistics
Matches: 168, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
221 86 0.51
222 1 0.01
223 2 0.01
226 28 0.17
227 35 0.21
228 16 0.10
ACGTcount: A:0.40, C:0.30, G:0.09, T:0.21
Consensus pattern (226 bp):
CAAATCCTCATATGTCAAACCACTAGAACCACATATACCAACCATCCTCAATGTTAGGAATCTAT
CCCCCATCAAACTCTTCTAATATTCAGACCACTATCCCCCCTCAACACACAACCCTTCTTTACAC
TCGAAACCAACTCAAGCTCGAAAATCATACAAGAAGGACATAAAAAGAAAAGAAAGAAACAAAAA
AAAAAACCTACTTGACTTTGAAATGAAAGAG
Found at i:28915343 original size:98 final size:98
Alignment explanation
Indices: 28915174--28915368 Score: 336
Period size: 98 Copynumber: 2.0 Consensus size: 98
28915164 ATACAATAAA
* *
28915174 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCTAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
28915239 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
* *
28915272 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
28915337 CCTTTAGAATCTCAAACTCAGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCAGAATATTTCCTT
28915369 CATGATTTTT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
Found at i:28916880 original size:19 final size:19
Alignment explanation
Indices: 28916856--28916966 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
28916846 AATCATATAT
28916856 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
28916875 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
*
28916894 TCTGAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
28916913 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
28916932 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
28916951 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
28916967 CTCAAAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:28916907 original size:38 final size:37
Alignment explanation
Indices: 28916833--28916965 Score: 158
Period size: 38 Copynumber: 3.4 Consensus size: 37
28916823 AAATTAAATC
*
28916833 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATAT--TATA-TCT-AGATTGCATATCATA
*
28916875 TCTAAGATTATATATTATATCTGAGATTGCATATCATA
1 TCTAAGATTACATATTATATCT-AGATTGCATATCATA
* *
28916913 TCTAAGATTGCATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTACATATTATATCTA-GATTGCATATCATA
*
28916951 TCTAAGATTGCATAT
1 TCTAAGATTACATAT
28916966 CCTCAAAAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
37 1 0.01
38 66 0.79
39 4 0.05
41 3 0.04
42 10 0.12
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (37 bp):
TCTAAGATTACATATTATATCTAGATTGCATATCATA
Found at i:28922376 original size:34 final size:34
Alignment explanation
Indices: 28922333--28922401 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
28922323 AATATTTTTG
28922333 AACTTCCCACCTAAGACCATTATAACATGACCAA
1 AACTTCCCACCTAAGACCATTATAACATGACCAA
28922367 AACTTCCCACCTAAGACCATTATAACATGACCAA
1 AACTTCCCACCTAAGACCATTATAACATGACCAA
28922401 A
1 A
28922402 TTAACTCGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.32, G:0.06, T:0.20
Consensus pattern (34 bp):
AACTTCCCACCTAAGACCATTATAACATGACCAA
Found at i:28923257 original size:30 final size:30
Alignment explanation
Indices: 28923221--28923286 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
28923211 CTTTAACTCC
* *
28923221 TTTTTTTTTCAAAAATAACTCTCAATTACT
1 TTTTTTTTTCAAAAACAACTCTCAATTAAT
*
28923251 TTTTTTTTTCAAAAACAACTTTCAATTAAT
1 TTTTTTTTTCAAAAACAACTCTCAATTAAT
28923281 TTTTTT
1 TTTTTT
28923287 CAAACTGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTTTTTTTCAAAAACAACTCTCAATTAAT
Found at i:28923612 original size:20 final size:20
Alignment explanation
Indices: 28923587--28923625 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28923577 CGTAAAATGA
*
28923587 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
28923607 TTTCTGTAAAATGATTTAC
1 TTTCTGGAAAATGATTTAC
28923626 AGAAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28923631 original size:34 final size:34
Alignment explanation
Indices: 28923572--28923637 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
28923562 CAGTAAAATA
* *
28923572 TTTTCCGTAAAATGATTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTCTAGAAAATATTTTAC
*
28923606 TTTTCTGTAAAATGATTTAC-AGAAAATATTTT
1 TTTTCCGTAAAATGATTT-CTAGAAAATATTTT
28923638 CTAGTGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (34 bp):
TTTTCCGTAAAATGATTTCTAGAAAATATTTTAC
Found at i:28929487 original size:2 final size:2
Alignment explanation
Indices: 28929480--28929525 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
28929470 GATGGTGGAC
28929480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28929522 AT AT
1 AT AT
28929526 TTCACATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28930623 original size:37 final size:37
Alignment explanation
Indices: 28930579--28930655 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
28930569 AAATGTTAGT
*
28930579 ATTGTCAAAATTCTTTTATTAAATTAATTATTGTTAC
1 ATTGTCAAAATTCTTTTATTAAATTAATTATTGTGAC
*
28930616 ATTGTCAAAATTCTTTTATTAAATTTATTATTGTGAC
1 ATTGTCAAAATTCTTTTATTAAATTAATTATTGTGAC
28930653 ATT
1 ATT
28930656 TTGACATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (37 bp):
ATTGTCAAAATTCTTTTATTAAATTAATTATTGTGAC
Found at i:28930776 original size:22 final size:23
Alignment explanation
Indices: 28930739--28930781 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
28930729 TTGAATTTAT
28930739 TAAAAATAAAAGAATTAAATTTC
1 TAAAAATAAAAGAATTAAATTTC
28930762 TAAAAATAAAA-AATTAAATT
1 TAAAAATAAAAGAATTAAATT
28930782 AAAAATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAAAATAAAAGAATTAAATTTC
Found at i:28937984 original size:100 final size:98
Alignment explanation
Indices: 28937818--28938009 Score: 253
Period size: 100 Copynumber: 1.9 Consensus size: 98
28937808 AGCATCAATG
* * ** *
28937818 ACTCGTTCTGTTAAGGTGTGGTGGTAACTATGACACAAAATTAAATTTTAAAAATTAAAAATAAT
1 ACTCGTTCTGTTAAGGTGTAGTGATAACTACAACACAAAATCAAA-TTTAAAAA-TAAAAATAAT
28937883 AAAAGCAACTAAAAACAATAAAAAAAAAATCAACA
64 AAAAGCAACTAAAAACAATAAAAAAAAAATCAACA
*
28937918 ACTCGTTCTGTTAAGGTGTAGTGATACCTACAACACAAAATCAAA-TTAAAAA-AAAAATTACAA
1 ACTCGTTCTGTTAAGGTGTAGTGATAACTACAACACAAAATCAAATTTAAAAATAAAAA-T---A
*
28937981 ATAAAAGCAACTAAACACAATAAAAAAAA
62 ATAAAAGCAACTAAAAACAATAAAAAAAA
28938010 TAATTGAGTG
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
96 5 0.06
97 1 0.01
98 7 0.09
100 68 0.84
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.23
Consensus pattern (98 bp):
ACTCGTTCTGTTAAGGTGTAGTGATAACTACAACACAAAATCAAATTTAAAAATAAAAATAATAA
AAGCAACTAAAAACAATAAAAAAAAAATCAACA
Found at i:28943923 original size:98 final size:98
Alignment explanation
Indices: 28943755--28943940 Score: 279
Period size: 98 Copynumber: 1.9 Consensus size: 98
28943745 GCACCTGCAT
* *
28943755 TTTTCGTGTAAAAATTTCGATTCCAGAAAAGAGAAAAAAGATACATTTTTACCCAAAAGAATAGG
1 TTTTCGTGTAAAAATTTCAATTCCAGAAAAGAGAAAAAAGACACATTTTTACCCAAAAGAATAGG
*
28943820 TTAGAGAAAGTAGTGTCAAATATATAGGTCATA
66 TTAGAGAAAGCAGTGTCAAATATATAGGTCATA
* *
28943853 TTTTC-TGTAAAAATTTCAATTCCAGAAAGAGGGGAAAAA-ACACATATTTGT-CCCAAAAGAAT
1 TTTTCGTGTAAAAATTTCAATTCCAGAAA-AGAGAAAAAAGACACAT-TTT-TACCCAAAAGAAT
28943915 AGGTTAGAGAAAGCAGTGTCAAATAT
63 AGGTTAGAGAAAGCAGTGTCAAATAT
28943941 TTAGAGGGAT
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
97 27 0.34
98 52 0.65
99 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (98 bp):
TTTTCGTGTAAAAATTTCAATTCCAGAAAAGAGAAAAAAGACACATTTTTACCCAAAAGAATAGG
TTAGAGAAAGCAGTGTCAAATATATAGGTCATA
Found at i:28946720 original size:6 final size:6
Alignment explanation
Indices: 28946709--28946743 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
28946699 CTTTTCTCGG
* *
28946709 TCCCTA TCCCTA TCCTTA TCTCTA TCCCTA TCCCT
1 TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TCCCT
28946744 GTGGCGATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.14, C:0.46, G:0.00, T:0.40
Consensus pattern (6 bp):
TCCCTA
Found at i:28946730 original size:24 final size:24
Alignment explanation
Indices: 28946696--28946743 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28946686 CACGATCACG
* *
28946696 ATCCTTTTCTCGGTCCCTATCCCT
1 ATCCTTATCTCGATCCCTATCCCT
*
28946720 ATCCTTATCTCTATCCCTATCCCT
1 ATCCTTATCTCGATCCCTATCCCT
28946744 GTGGCGATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.12, C:0.42, G:0.04, T:0.42
Consensus pattern (24 bp):
ATCCTTATCTCGATCCCTATCCCT
Found at i:28948607 original size:2 final size:2
Alignment explanation
Indices: 28948602--28948627 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28948592 ATTACAAAAA
28948602 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28948628 TTCCTCAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28949206 original size:20 final size:21
Alignment explanation
Indices: 28949181--28949220 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28949171 TAAAAACAAA
28949181 AAAATA-TA-TATCTAAAAATT
1 AAAATATTATTAT-TAAAAATT
28949201 AAAATATTATTATTAAAAAT
1 AAAATATTATTATTAAAAAT
28949221 AACTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 9 0.50
22 3 0.17
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATATTATTATTAAAAATT
Found at i:28950565 original size:18 final size:17
Alignment explanation
Indices: 28950489--28950567 Score: 106
Period size: 18 Copynumber: 4.5 Consensus size: 17
28950479 TTAAAAAATA
*
28950489 ACCGAATT-ACCTGAATA
1 ACCGAATTAACC-GAATT
28950506 ACCGAATTAACCGAATT
1 ACCGAATTAACCGAATT
28950523 AACCGAATTAACCGAATT
1 -ACCGAATTAACCGAATT
28950541 ACCCGAATTAACCGAATT
1 A-CCGAATTAACCGAATT
28950559 ACTCGAATT
1 AC-CGAATT
28950568 GAATTTCCTC
Statistics
Matches: 57, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
17 14 0.25
18 43 0.75
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (17 bp):
ACCGAATTAACCGAATT
Found at i:28950567 original size:9 final size:9
Alignment explanation
Indices: 28950487--28950559 Score: 114
Period size: 9 Copynumber: 8.2 Consensus size: 9
28950477 GGTTAAAAAA
28950487 TAACCGAAT
1 TAACCGAAT
28950496 T-ACCTGAA-
1 TAACC-GAAT
28950504 TAACCGAAT
1 TAACCGAAT
28950513 TAACCGAAT
1 TAACCGAAT
28950522 TAACCGAAT
1 TAACCGAAT
28950531 TAACCGAAT
1 TAACCGAAT
*
28950540 TACCCGAAT
1 TAACCGAAT
28950549 TAACCGAAT
1 TAACCGAAT
28950558 TA
1 TA
28950560 CTCGAATTGA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.12
9 52 0.88
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.23
Consensus pattern (9 bp):
TAACCGAAT
Found at i:28952718 original size:10 final size:9
Alignment explanation
Indices: 28952703--28952758 Score: 62
Period size: 9 Copynumber: 6.1 Consensus size: 9
28952693 CTTTTAAAAT
28952703 AATTTTATTA
1 AATTTT-TTA
28952713 AA-TTTTTA
1 AATTTTTTA
*
28952721 AA-TTTTAA
1 AATTTTTTA
28952729 AATTTTTTAA
1 AATTTTTT-A
28952739 AATATTTTTA
1 AAT-TTTTTA
28952749 AATTTTTTA
1 AATTTTTTA
28952758 A
1 A
28952759 TTTAAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
8 12 0.29
9 14 0.34
10 10 0.24
11 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
AATTTTTTA
Found at i:28952723 original size:8 final size:8
Alignment explanation
Indices: 28952710--28952775 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 8
28952700 AATAATTTTA
28952710 TTAAATTT
1 TTAAATTT
28952718 TTAAATTT
1 TTAAATTT
*
28952726 TAAAATTTT
1 TTAAA-TTT
28952735 TTAAAATATTT
1 TT--AA-ATTT
28952746 TTAAATTT
1 TTAAATTT
*
28952754 TTTAATTT
1 TTAAATTT
**
28952762 AAAATATTT
1 TTAA-ATTT
28952771 TTAAA
1 TTAAA
28952776 ATACTTTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
8 25 0.56
9 12 0.27
11 7 0.16
12 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TTAAATTT
Found at i:28952736 original size:28 final size:29
Alignment explanation
Indices: 28952694--28952775 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 29
28952684 TTTAAAATAC
*
28952694 TTTTAAAATAATTTTATTAA-ATTTTTAAA
1 TTTTAAAATAATTTTA-AAATATTTTTAAA
*
28952723 TTTTAAAAT-TTTTTAAAATATTTTTAAA
1 TTTTAAAATAATTTTAAAATATTTTTAAA
*
28952751 TTTT---TTAA-TTTAAAATATTTTTAAA
1 TTTTAAAATAATTTTAAAATATTTTTAAA
28952776 ATACTTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
25 18 0.38
27 2 0.04
28 18 0.38
29 9 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTTAAAATAATTTTAAAATATTTTTAAA
Found at i:28952761 original size:36 final size:37
Alignment explanation
Indices: 28952654--28952800 Score: 155
Period size: 36 Copynumber: 4.0 Consensus size: 37
28952644 CGAATATAAT
* *
28952654 AAATATTTTT--ATTATTTTT-TATTTTTTAATTTTA
1 AAATATTTTTAAAATATTTTTAAATTTTTTAATTTTA
* *
28952688 AAATACTTTTAAAATAATTTTATTAAATTTTTAAATTTTA
1 AAATATTTTTAAAAT-A-TTT-TTAAATTTTTTAATTTTA
28952728 AAAT-TTTTTAAAATATTTTTAAATTTTTTAA-TTTA
1 AAATATTTTTAAAATATTTTTAAATTTTTTAATTTTA
*
28952763 AAATATTTTTAAAATACTTTTTTTAA-TTTTT-ATTTTA
1 AAATATTTTTAAAATA--TTTTTAAATTTTTTAATTTTA
28952800 A
1 A
28952801 TTTTTAAAAT
Statistics
Matches: 96, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
34 9 0.09
35 8 0.08
36 26 0.27
37 14 0.15
38 11 0.11
39 11 0.11
40 17 0.18
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (37 bp):
AAATATTTTTAAAATATTTTTAAATTTTTTAATTTTA
Found at i:28952775 original size:11 final size:11
Alignment explanation
Indices: 28952683--28952784 Score: 72
Period size: 11 Copynumber: 9.4 Consensus size: 11
28952673 TATTTTTTAA
*
28952683 TTTTAAAATAC
1 TTTTAAAATAT
*
28952694 TTTTAAAATAA
1 TTTTAAAATAT
*
28952705 TTTTATTAA-AT
1 TTTTA-AAATAT
28952716 TTTT--AA-A-
1 TTTTAAAATAT
28952723 TTTTAAAAT-T
1 TTTTAAAATAT
28952733 TTTTAAAATAT
1 TTTTAAAATAT
* *
28952744 TTTTAAATTTTT
1 TTTTAAA-ATAT
28952756 TAATTTAAAATAT
1 T--TTTAAAATAT
28952769 TTTTAAAATACT
1 TTTTAAAATA-T
28952781 TTTT
1 TTTT
28952785 TTAATTTTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
7 4 0.05
8 3 0.04
9 2 0.03
10 9 0.12
11 37 0.50
12 10 0.14
13 3 0.04
14 6 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:28952787 original size:25 final size:23
Alignment explanation
Indices: 28952731--28952788 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
28952721 AATTTTAAAA
*
28952731 TTTTTTAAAATATTTTTAAATTT
1 TTTTTTAAAATATTTTTAAATCT
28952754 TTTAATTTAAAATATTTTTAAAATACT
1 TTT--TTTAAAATATTTTT-AAAT-CT
28952781 TTTTTTAA
1 TTTTTTAA
28952789 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.10
25 19 0.63
26 4 0.13
27 4 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTTTAAAATATTTTTAAATCT
Found at i:28953115 original size:18 final size:18
Alignment explanation
Indices: 28953089--28953132 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28953079 AATTTTTATG
* *
28953089 ATTGAGTTGAGTTGGGTA
1 ATTGGGTTGAGTTGGATA
*
28953107 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGAGTTGGATA
28953125 ATTGGGTT
1 ATTGGGTT
28953133 TAGGTAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGAGTTGGATA
Found at i:28956215 original size:27 final size:27
Alignment explanation
Indices: 28956185--28956274 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
28956175 TCCCTATTGC
*
28956185 GATTTTCCTAACAGACTTCCACATTCA
1 GATTGTCCTAACAGACTTCCACATTCA
* *
28956212 GATTGTCTTGACAGACTTCC-CAATTACA
1 GATTGTCCTAACAGACTTCCAC-ATT-CA
* ***
28956240 -ATCGTCCTAGTGGACTTCCACATTCA
1 GATTGTCCTAACAGACTTCCACATTCA
28956266 GATTGTCCT
1 GATTGTCCT
28956275 GATGGACCTC
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
26 3 0.06
27 43 0.88
28 3 0.06
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (27 bp):
GATTGTCCTAACAGACTTCCACATTCA
Found at i:28956228 original size:54 final size:54
Alignment explanation
Indices: 28956190--28956295 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 54
28956180 ATTGCGATTT
28956190 TCCTAACAGACTTCCACATTCAGATTGTCTTGACAGACTTCCCAATTACAATCG
1 TCCTAACAGACTTCCACATTCAGATTGTCTTGACAGACTTCCCAATTACAATCG
*** * ** *
28956244 TCCTAGTGGACTTCCACATTCAGATTGTCCTGATGGACCTCCCAATTACAAT
1 TCCTAACAGACTTCCACATTCAGATTGTCTTGACAGACTTCCCAATTACAAT
28956296 TATCCTTACG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.30
Consensus pattern (54 bp):
TCCTAACAGACTTCCACATTCAGATTGTCTTGACAGACTTCCCAATTACAATCG
Found at i:28956301 original size:27 final size:26
Alignment explanation
Indices: 28956229--28956301 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 26
28956219 TTGACAGACT
*
28956229 TCCCAATTACAATCGTCCTAGTGGAC
1 TCCCAATTACAATTGTCCTAGTGGAC
*
28956255 TTCCACATT-CAGATTGTCCT-GATGGACC
1 TCCCA-ATTACA-ATTGTCCTAG-TGGA-C
*
28956283 TCCCAATTACAATTATCCT
1 TCCCAATTACAATTGTCCT
28956302 TACGAACTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
26 7 0.18
27 24 0.63
28 7 0.18
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (26 bp):
TCCCAATTACAATTGTCCTAGTGGAC
Found at i:28956311 original size:54 final size:54
Alignment explanation
Indices: 28956199--28956312 Score: 140
Period size: 54 Copynumber: 2.1 Consensus size: 54
28956189 TTCCTAACAG
* * * * *
28956199 ACTTCCACATTCAGATTGTCTTGACAGACTTCCCAATTACAATCGTCCTAGTGG
1 ACTTCCACATTCAGATTGTCCTGACAGACCTCCCAATTACAATCATCCTAGCGA
** *
28956253 ACTTCCACATTCAGATTGTCCTGATGGACCTCCCAATTACAATTATCCTTA-CGA
1 ACTTCCACATTCAGATTGTCCTGACAGACCTCCCAATTACAATCATCC-TAGCGA
28956307 ACTTCC
1 ACTTCC
28956313 CTCAATAGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 49 0.96
55 2 0.04
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (54 bp):
ACTTCCACATTCAGATTGTCCTGACAGACCTCCCAATTACAATCATCCTAGCGA
Found at i:28968248 original size:27 final size:27
Alignment explanation
Indices: 28968218--28968283 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
28968208 AACTTTCCCT
*
28968218 CATTAGATAGTCATTACGGGT-TTCTCA
1 CATTAGATAGCCATTACGGGTCTT-TCA
28968245 CATTAGATAGCCATTACGGGTCTTTCA
1 CATTAGATAGCCATTACGGGTCTTTCA
28968272 CATTAGATAGCC
1 CATTAGATAGCC
28968284 CTTGCGAAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (27 bp):
CATTAGATAGCCATTACGGGTCTTTCA
Found at i:28968299 original size:27 final size:26
Alignment explanation
Indices: 28968218--28968302 Score: 89
Period size: 27 Copynumber: 3.2 Consensus size: 26
28968208 AACTTTCCCT
* *
28968218 CATTAGATAGTCATTACGGGTTTCTCA
1 CATTAGATAGCCATTACGAG-TTCTCA
* *
28968245 CATTAGATAGCCATTACGGGTCTTTCA
1 CATTAGATAGCCATTACGAGT-TCTCA
* *
28968272 CATTAGATAGCCCTTGCGAAGTTCTCA
1 CATTAGATAGCCATTACG-AGTTCTCA
28968299 CATT
1 CATT
28968303 TACGGTAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.02
27 47 0.94
28 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (26 bp):
CATTAGATAGCCATTACGAGTTCTCA
Found at i:28969831 original size:18 final size:17
Alignment explanation
Indices: 28969789--28969831 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
28969779 TGTTTAAGTT
*
28969789 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
28969806 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
28969824 TATAATTT
1 TATAATTT
28969832 ATAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:28972956 original size:27 final size:28
Alignment explanation
Indices: 28972912--28973092 Score: 234
Period size: 27 Copynumber: 6.7 Consensus size: 28
28972902 CCCCAAACTA
*
28972912 TTATAAAATGACTGTTATGCCCTC-ATG
1 TTATAAAATGACTATTATGCCCTCTATG
**
28972939 TGGTAAAATGACTATTATGCCCTC-ATG
1 TTATAAAATGACTATTATGCCCTCTATG
**
28972966 TGGTAAAATGACTATTATGCCC-CTATG
1 TTATAAAATGACTATTATGCCCTCTATG
28972993 TTATAAAATGACTATTATG-CCTCTATG
1 TTATAAAATGACTATTATGCCCTCTATG
* *
28973020 TTATAAAATGA-TGGTTATGCCCT-AATG
1 TTATAAAATGACT-ATTATGCCCTCTATG
28973047 TTATAAAATGACTATTATGCCC-CTATG
1 TTATAAAATGACTATTATGCCCTCTATG
28973074 TTATAAAATGACTA-TATGC
1 TTATAAAATGACTATTATGC
28973093 TTAATGTTAT
Statistics
Matches: 139, Mismatches: 9, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
26 9 0.06
27 126 0.91
28 4 0.03
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (28 bp):
TTATAAAATGACTATTATGCCCTCTATG
Found at i:28973011 original size:81 final size:82
Alignment explanation
Indices: 28972912--28973092 Score: 262
Period size: 81 Copynumber: 2.2 Consensus size: 82
28972902 CCCCAAACTA
* * * *
28972912 TTATAAAATGACTGTTATGCCCTC-ATGTGGTAAAATGACT-ATTATGCCCTCATGTGGTAAAAT
1 TTATAAAATGACTATTATGCCCTCTATGTGATAAAATGA-TGATTATGCCCTAATGTGATAAAAT
28972975 GACTATTATGCCCCTATG
65 GACTATTATGCCCCTATG
* * *
28972993 TTATAAAATGACTATTATG-CCTCTATGTTATAAAATGATGGTTATGCCCTAATGTTATAAAATG
1 TTATAAAATGACTATTATGCCCTCTATGTGATAAAATGATGATTATGCCCTAATGTGATAAAATG
28973057 ACTATTATGCCCCTATG
66 ACTATTATGCCCCTATG
28973074 TTATAAAATGACTA-TATGC
1 TTATAAAATGACTATTATGC
28973093 TTAATGTTAT
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
80 9 0.10
81 81 0.90
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (82 bp):
TTATAAAATGACTATTATGCCCTCTATGTGATAAAATGATGATTATGCCCTAATGTGATAAAATG
ACTATTATGCCCCTATG
Found at i:28974393 original size:12 final size:12
Alignment explanation
Indices: 28974372--28974402 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
28974362 GTATATGTAT
28974372 ATATATATATAAA
1 ATATA-ATATAAA
28974385 ATATAATATAAA
1 ATATAATATAAA
28974397 ATATAA
1 ATATAA
28974403 AAACATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:28975103 original size:21 final size:21
Alignment explanation
Indices: 28975077--28975116 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28975067 AATAAATACC
28975077 AAAAAAGTATTTTAAAAATTA
1 AAAAAAGTATTTTAAAAATTA
28975098 AAAAAAGTATTTTAAAAAT
1 AAAAAAGTATTTTAAAAAT
28975117 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAAAAGTATTTTAAAAATTA
Found at i:28975129 original size:31 final size:31
Alignment explanation
Indices: 28975078--28975247 Score: 141
Period size: 31 Copynumber: 5.8 Consensus size: 31
28975068 ATAAATACCA
28975078 AAAAAGTATTTTAAAAATTAAAAAAAGTATTTT
1 AAAAA-TATTTT-AAAATTAAAAAAAGTATTTT
**
28975111 AAAAATATTTTAAAATTAAAAAAA-T-TTAA
1 AAAAATATTTTAAAATTAAAAAAAGTATTTT
* ***
28975140 AAAAAGTATTTTAAAAATATTTTAAA--A--TT
1 AAAAA-TATTTTAAAATTA-AAAAAAGTATTTT
* *
28975169 AAAAA-AATTTAAAA-A-----AAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAGTATTTT
28975193 AAAAATATTTTAAAATTAAAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAGTATTTT
28975224 AAAAATATTTTAAAATTAAAAAAA
1 AAAAATATTTTAAAATTAAAAAAA
28975248 TAAATATATT
Statistics
Matches: 111, Mismatches: 12, Indels: 30
0.73 0.08 0.20
Matches are distributed among these distances:
20 2 0.02
22 1 0.01
24 7 0.06
25 8 0.07
27 8 0.07
29 12 0.11
30 13 0.12
31 49 0.44
32 6 0.05
33 5 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAATATTTTAAAATTAAAAAAAGTATTTT
Found at i:28975172 original size:72 final size:72
Alignment explanation
Indices: 28975078--28975248 Score: 231
Period size: 72 Copynumber: 2.3 Consensus size: 72
28975068 ATAAATACCA
**
28975078 AAAAAGTATTTTAAAAATTAAAAAAAGTATTTTAAAAA-TATTTT-AAAAT-TAAAAAAATTTAA
1 AAAAA-TATTTT-AAAATTAAAAAAA-T-TTAAAAAAAGTATTTTAAAAATATAAAAAAA-TTAA
28975140 AAAAAGTATTTT
61 AAAAAGTATTTT
***
28975152 AAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA
1 AAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATAAAAAAATTAAAAAAA
28975217 GTATTTT
66 GTATTTT
28975224 AAAAATATTTTAAAATTAAAAAAAT
1 AAAAATATTTTAAAATTAAAAAAAT
28975249 AAATATATTT
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
70 7 0.08
71 7 0.08
72 59 0.66
73 11 0.12
74 5 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (72 bp):
AAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATAAAAAAATTAAAAAAA
GTATTTT
Found at i:28975239 original size:41 final size:41
Alignment explanation
Indices: 28975090--28975238 Score: 248
Period size: 41 Copynumber: 3.6 Consensus size: 41
28975080 AAAGTATTTT
28975090 AAAAA-TTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
28975130 AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
28975171 AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
**
28975212 AAAAAGTATTTTAAAAA-TATTTTAAAA
1 AAAAA-T-TTAAAAAAAGTATTTTAAAA
28975239 TTAAAAAAAT
Statistics
Matches: 104, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
40 5 0.05
41 81 0.78
42 11 0.11
43 7 0.07
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (41 bp):
AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:28976780 original size:34 final size:33
Alignment explanation
Indices: 28976733--28976803 Score: 108
Period size: 34 Copynumber: 2.2 Consensus size: 33
28976723 TTTGAACTAT
*
28976733 TACTGTCATTGTAATAGGCTAAGGCCCACACTGA
1 TACTGTCACTGTAATAGGCTAAGGCCCA-ACTGA
*
28976767 TACTGTCACTGTAATGGGCTAAGGCCCAACTGA
1 TACTGTCACTGTAATAGGCTAAGGCCCAACTGA
28976800 -ACTG
1 TACTG
28976804 AACTGTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 4 0.11
33 5 0.14
34 26 0.74
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (33 bp):
TACTGTCACTGTAATAGGCTAAGGCCCAACTGA
Found at i:28981040 original size:114 final size:112
Alignment explanation
Indices: 28980836--28981269 Score: 371
Period size: 114 Copynumber: 3.8 Consensus size: 112
28980826 CCGTAGTTTT
* * **
28980836 TTGGGATTTAGCGGCGTTTTC-GGAGAAGCGCCGCTAAAAAACCAAAAAT-CCCAACGGCGTCGT
1 TTGGGATTTAGCGGCGTTTTCGGGA-AAGCGCCGC-AAAAAA--ATATATGCCCAACGGCACCGT
* * * **
28980899 TTTCTCAGCTTTCGTGTATTTAGCGGCGCTTCCACGAAAGCGCCGCTAATGC
62 TTTCTGAGCTTTCGGGGATTTAGCGGCG-TTTTACGAAAGCGCCGCTAATGC
*
28980951 TTAGGGATTTAGCGGCGTTTTCGGGAAAGCGCCGCAAAAAAATATATGTCCAACGGCACCGTTTT
1 TT-GGGATTTAGCGGCGTTTTCGGGAAAGCGCCGCAAAAAAATATATGCCCAACGGCACCGTTTT
* *
28981016 CTGAGCTTTCGGGGACTTAGCGGCGTTTTTACCAAAGCGCCGCTAATGC
65 CTGAGCTTTCGGGGATTTAGCGGCG-TTTTACGAAAGCGCCGCTAATGC
* * * ** * * * *
28981065 TGGGGGGTTTAGCGGCATTTT-GAAAAAAGCGCGGC-AATAAATCCTAAGCCCAACGGCACCGTT
1 T-TGGGATTTAGCGGCGTTTTCG-GGAAAGCGCCGCAAAAAAAT-ATATGCCCAACGGCACCGTT
* * * * *
28981128 TTCTTAACTTTCAGGGGATTTAACGGCGTTTTAAGAAAGCGCCACTAATGC
63 TTCTGAGCTTTC-GGGGATTTAGCGGCGTTTTACGAAAGCGCCGCTAATGC
** * * * * **
28981179 TT--CCTTTAGCGGCGTTTTCGTGAAAGCACCGCAAAGAAAACTA-A-GCCGAACGACGTCGTTT
1 TTGGGATTTAGCGGCGTTTTCGGGAAAGCGCCGCAAA-AAAA-TATATGCCCAACGGCACCGTTT
* *
28981240 TCGGAGCTTTTGGGGATTTAGCGGCGTTTT
64 TCTGAGCTTTCGGGGATTTAGCGGCGTTTT
28981270 TTGGGAAGCG
Statistics
Matches: 259, Mismatches: 49, Indels: 27
0.77 0.15 0.08
Matches are distributed among these distances:
110 18 0.07
111 41 0.16
112 4 0.02
113 14 0.05
114 130 0.50
115 21 0.08
116 28 0.11
117 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (112 bp):
TTGGGATTTAGCGGCGTTTTCGGGAAAGCGCCGCAAAAAAATATATGCCCAACGGCACCGTTTTC
TGAGCTTTCGGGGATTTAGCGGCGTTTTACGAAAGCGCCGCTAATGC
Found at i:28981568 original size:14 final size:14
Alignment explanation
Indices: 28981543--28981580 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
28981533 AGTTTAGGGG
*
28981543 TTAGGTGTTATGTCT
1 TTAGGGGTTATG-CT
28981558 TT-GGGGTTATGCT
1 TTAGGGGTTATGCT
28981571 TTAGGGGTTA
1 TTAGGGGTTA
28981581 GGGGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.19
14 15 0.71
15 2 0.10
ACGTcount: A:0.13, C:0.05, G:0.34, T:0.47
Consensus pattern (14 bp):
TTAGGGGTTATGCT
Found at i:28981953 original size:28 final size:27
Alignment explanation
Indices: 28981910--28981962 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
28981900 AAAAAATATG
28981910 GTTTAGGTTTATGGTTTGGGGTTTACA
1 GTTTAGGTTTATGGTTTGGGGTTTACA
28981937 GTTTAGAGTTTCA-GGTTTGGGGTTTA
1 GTTTAG-GTTT-ATGGTTTGGGGTTTA
28981963 GGATTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 6 0.25
28 17 0.71
29 1 0.04
ACGTcount: A:0.15, C:0.04, G:0.34, T:0.47
Consensus pattern (27 bp):
GTTTAGGTTTATGGTTTGGGGTTTACA
Found at i:28981980 original size:28 final size:28
Alignment explanation
Indices: 28981917--28981982 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
28981907 ATGGTTTAGG
* *
28981917 TTTATGGTTTGGGGTTTACAGTTTAGAG
1 TTTAAGGTTTGGGGTTTACAGTTTAGAA
* * *
28981945 TTTCAGGTTTGGGGTTTA-GGATTTATAA
1 TTTAAGGTTTGGGGTTTACAG-TTTAGAA
28981973 TTTAAGGTTT
1 TTTAAGGTTT
28981983 ATGGTATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.20, C:0.03, G:0.29, T:0.48
Consensus pattern (28 bp):
TTTAAGGTTTGGGGTTTACAGTTTAGAA
Found at i:28982624 original size:115 final size:114
Alignment explanation
Indices: 28982433--28982666 Score: 387
Period size: 115 Copynumber: 2.0 Consensus size: 114
28982423 GCGCTTCAGA
**
28982433 AAAAACGCCGCTAAAGGTGATATATTACCGGCGTTTTGTGAAGAACGCCGCAAATTTCCTTTAAC
1 AAAAACGCCGCTAAAGGTGATATATTACCGGCGTTTTACGAAGAACGCCGCAAATTTCCTTTAAC
*
28982498 TGTAACAAAGACGGTGCCGTTTTGTTGTTTGCTTTTAGTGGCGCATTTG
66 TGTAACAAAGACGGTGCCGTTTTGCTGTTTGCTTTTAGTGGCGCATTTG
* *
28982547 AAAAACGCCGCTAAAGGTGATATCTTACCGGCGTTTTACGAAGAAACGCCGTAAATTTCCTTTAA
1 AAAAACGCCGCTAAAGGTGATATATTACCGGCGTTTTACGAAG-AACGCCGCAAATTTCCTTTAA
* * *
28982612 CTGTAACAAAGACGGTGTCGTTTTGCTGTTTTCTTTTAGTGGCGCATTTT
65 CTGTAACAAAGACGGTGCCGTTTTGCTGTTTGCTTTTAGTGGCGCATTTG
28982662 AAAAA
1 AAAAA
28982667 TGCCACAAAT
Statistics
Matches: 111, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
114 40 0.36
115 71 0.64
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32
Consensus pattern (114 bp):
AAAAACGCCGCTAAAGGTGATATATTACCGGCGTTTTACGAAGAACGCCGCAAATTTCCTTTAAC
TGTAACAAAGACGGTGCCGTTTTGCTGTTTGCTTTTAGTGGCGCATTTG
Found at i:28982795 original size:73 final size:73
Alignment explanation
Indices: 28982718--28982948 Score: 249
Period size: 73 Copynumber: 3.2 Consensus size: 73
28982708 TTGTCCGTGT
*
28982718 TATTAGTGGCGTTTTTACTTTAAGCGCCACAAGTTTTACTCTAATGTGTGTTAAACGGCTGAGTT
1 TATTAGTGGCGTTTTTACTTTAAGCGCCACAAGTTTTACTCTAATGTGTGTTAAACGGCTGCGTT
28982783 TGTACTGA
66 TGTACTGA
* * ** * * *
28982791 TATTAGTGGCGCTTATTA--TTAAGCGCCGCAAAAATGT--T-TAATGTTATCTTATAACGG-TG
1 TATTAGTGGCG-TTTTTACTTTAAGCGCCAC-AAGTTTTACTCTAATG-TGTGTTA-AACGGCTG
* *
28982850 TCGTTTTGTCCGTGT
62 -CG-TTTGTAC-TGA
* *
28982865 TATTAGTGGCGTTTTTACTCTAAGCACCACAAGTTTTACTCTAATGTGTGTTAAACGGCTGCGTT
1 TATTAGTGGCGTTTTTACTTTAAGCGCCACAAGTTTTACTCTAATGTGTGTTAAACGGCTGCGTT
28982930 TGTACTGA
66 TGTACTGA
28982938 TATTAGTGGCG
1 TATTAGTGGCG
28982949 CTTATTGTTA
Statistics
Matches: 124, Mismatches: 21, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
70 5 0.04
71 8 0.06
72 16 0.13
73 39 0.31
74 28 0.23
75 15 0.12
76 8 0.06
77 5 0.04
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (73 bp):
TATTAGTGGCGTTTTTACTTTAAGCGCCACAAGTTTTACTCTAATGTGTGTTAAACGGCTGCGTT
TGTACTGA
Found at i:28982968 original size:147 final size:147
Alignment explanation
Indices: 28982696--28982969 Score: 494
Period size: 147 Copynumber: 1.9 Consensus size: 147
28982686 GAGTTGAGGA
* *
28982696 AACGGTGCCGTTTTGTCCGTGTTATTAGTGGCGTTTTTACTTTAAGCGCCACAAGTTTTACTCTA
1 AACGGTGCCGTTTTGTCCGTGTTATTAGTGGCGTTTTTACTCTAAGCACCACAAGTTTTACTCTA
28982761 ATGTGTGTTAAACGGCTGAGTTTGTACTGATATTAGTGGCGCTTATTATTAAGCGCCGCAAAAAT
66 ATGTGTGTTAAACGGCTGAGTTTGTACTGATATTAGTGGCGCTTATTATTAAGCGCCGCAAAAAT
28982826 GTTTAATGTTATCTTAT
131 GTTTAATGTTATCTTAT
*
28982843 AACGGTGTCGTTTTGTCCGTGTTATTAGTGGCGTTTTTACTCTAAGCACCACAAGTTTTACTCTA
1 AACGGTGCCGTTTTGTCCGTGTTATTAGTGGCGTTTTTACTCTAAGCACCACAAGTTTTACTCTA
* * *
28982908 ATGTGTGTTAAACGGCTGCGTTTGTACTGATATTAGTGGCGCTTATTGTTAAGCGTCGCAAA
66 ATGTGTGTTAAACGGCTGAGTTTGTACTGATATTAGTGGCGCTTATTATTAAGCGCCGCAAA
28982970 TTATTTCATT
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 121 1.00
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (147 bp):
AACGGTGCCGTTTTGTCCGTGTTATTAGTGGCGTTTTTACTCTAAGCACCACAAGTTTTACTCTA
ATGTGTGTTAAACGGCTGAGTTTGTACTGATATTAGTGGCGCTTATTATTAAGCGCCGCAAAAAT
GTTTAATGTTATCTTAT
Found at i:28983297 original size:173 final size:169
Alignment explanation
Indices: 28983007--28983346 Score: 511
Period size: 173 Copynumber: 2.0 Consensus size: 169
28982997 TCGCTTTTTT
*
28983007 CCCATACATTTTACCGAAACTTAAACCCCTATCGTGACTTATCCCCCAAAATCCCATTCTCCCCC
1 CCCATACATTTAACCGAAACTTAAACCCCTATCGTGACTTATCCCCCAAAATCCCATTCTCCCCC
* * *
28983072 AAATCCCTAAATTTCCCCTAATCCAGATTTCCCCAAAGCCGACCTTTTGCAACGTTGCCATTTCC
66 AAATCCCTAAATTTCCCCTAATCCACATTTCCCCAAACCCGACCTCTTGCAACGTTGCCATTTCC
*
28983137 TCTGGCGCATCACCGTCTCCCTCCGTCGGTCCCCTCTAC
131 TCTAGCGCATCACCGTCTCCCTCCGTCGGTCCCCTCTAC
*
28983176 CCCATACATTTAACCGAAACTTAAACCCCAACTATTGTGACTTATCCCCCAAAAT-CCATTTCTC
1 CCCATACATTTAACCGAAACTTAAA-CCC--CTATCGTGACTTATCCCCCAAAATCCCA-TTCTC
* * * * **
28983240 TCCGAAATTCTTAAAATTTCCCCTAATCCACATTTCCCCAAACCCGACCTCTTGCAACGTTGCTG
62 CCCCAAATCCCT-AAATTTCCCCTAATCCACATTTCCCCAAACCCGACCTCTTGCAACGTTGCCA
*
28983305 TTTCCTCTAGCGCATCACCGTCTCCCTCCGTCGGTCTCCTCT
126 TTTCCTCTAGCGCATCACCGTCTCCCTCCGTCGGTCCCCTCT
28983347 GCCGCAACAA
Statistics
Matches: 153, Mismatches: 13, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
169 24 0.16
170 3 0.02
171 3 0.02
172 36 0.24
173 87 0.57
ACGTcount: A:0.23, C:0.39, G:0.09, T:0.29
Consensus pattern (169 bp):
CCCATACATTTAACCGAAACTTAAACCCCTATCGTGACTTATCCCCCAAAATCCCATTCTCCCCC
AAATCCCTAAATTTCCCCTAATCCACATTTCCCCAAACCCGACCTCTTGCAACGTTGCCATTTCC
TCTAGCGCATCACCGTCTCCCTCCGTCGGTCCCCTCTAC
Found at i:28985015 original size:9 final size:9
Alignment explanation
Indices: 28985001--28985514 Score: 203
Period size: 9 Copynumber: 58.8 Consensus size: 9
28984991 TTTAATTTAA
*
28985001 TACATAATT
1 TACATAACT
28985010 TACATAACT
1 TACATAACT
*
28985019 CACATAACT
1 TACATAACT
* *
28985028 TACAAAAGT
1 TACATAACT
* *
28985037 CACAT-ACA
1 TACATAACT
28985045 TACATAACT
1 TACATAACT
*
28985054 TA-ATAAAT
1 TACATAACT
*
28985062 GGTACATAGCT
1 --TACATAACT
*
28985073 TATATAACT
1 TACATAACT
28985082 TACATAA--
1 TACATAACT
28985089 TACATAACT
1 TACATAACT
* *
28985098 TAAATAA-A
1 TACATAACT
28985106 TACATAACT
1 TACATAACT
*
28985115 TATATAA--
1 TACATAACT
28985122 TACATAA--
1 TACATAACT
28985129 TACATAACT
1 TACATAACT
28985138 TACATAATAACT
1 TAC---ATAACT
*
28985150 TGCATAATATCT
1 TACAT-A-A-CT
28985162 TACATAATAACT
1 TAC---ATAACT
28985174 TACATAA-T
1 TACATAACT
* *
28985182 AATACATACCC
1 --TACATAACT
*
28985193 TACATAAAT
1 TACATAACT
* *
28985202 TAAATAAGT
1 TACATAACT
28985211 TACATAA--
1 TACATAACT
* *
28985218 TACACAA-A
1 TACATAACT
* *
28985226 AACAAAAACT
1 TAC-ATAACT
*
28985236 TACATAACC
1 TACATAACT
*
28985245 TACATTA--
1 TACATAACT
28985252 TACATAACT
1 TACATAACT
28985261 TACATAAGC-
1 TACATAA-CT
*
28985270 TACTTAA--
1 TACATAACT
*
28985277 TGCATAACT
1 TACATAACT
*
28985286 TGCATAACT
1 TACATAACT
*
28985295 TACTTAA--
1 TACATAACT
28985302 TACATAACT
1 TACATAACT
*
28985311 TGCATAACT
1 TACATAACT
28985320 TACATAA--
1 TACATAACT
*
28985327 TACACAACT
1 TACATAACT
*
28985336 TACAT--GT
1 TACATAACT
*
28985343 GTAAATAA--
1 -TACATAACT
*
28985351 TACACAACT
1 TACATAACT
28985360 TACATAACT
1 TACATAACT
28985369 TACATAA--
1 TACATAACT
28985376 TACATAACT
1 TACATAACT
*
28985385 TACATAACC
1 TACATAACT
*
28985394 TACTTAA--
1 TACATAACT
28985401 TACATAACT
1 TACATAACT
*
28985410 TGCATAACT
1 TACATAACT
28985419 TACATAA--
1 TACATAACT
*
28985426 TACACAACT
1 TACATAACT
28985435 TACATAACT
1 TACATAACT
* * *
28985444 TATATACCC
1 TACATAACT
*
28985453 TACATAAAT
1 TACATAACT
* *
28985462 TAAATAAGT
1 TACATAACT
28985471 TACATAA-T
1 TACATAACT
* *
28985479 AATACATACCC
1 --TACATAACT
*
28985490 TACATAAAT
1 TACATAACT
* *
28985499 TAAATAAGT
1 TACATAACT
28985508 TACATAA
1 TACATAA
28985515 TACACAAAAA
Statistics
Matches: 376, Mismatches: 82, Indels: 94
0.68 0.15 0.17
Matches are distributed among these distances:
7 74 0.20
8 24 0.06
9 234 0.62
10 18 0.05
11 5 0.01
12 17 0.05
13 1 0.00
14 1 0.00
15 2 0.01
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.31
Consensus pattern (9 bp):
TACATAACT
Found at i:28985050 original size:44 final size:40
Alignment explanation
Indices: 28984998--28985144 Score: 152
Period size: 44 Copynumber: 3.5 Consensus size: 40
28984988 TATTTTAATT
* * * *
28984998 TAATACATAATTTACATAACTCACATAACTTACAAAAGTCACA
1 TAATACATAACTTACATAAAT-ACATAACTTATATAA-T-ACA
*
28985041 TACATACATAACTTA-ATAAATGGTACATAGCTTATATAACTTACA
1 TA-ATACATAACTTACATAAA---TACATAACTTATATAA--TACA
*
28985086 TAATACATAACTTAAATAAATACATAACTTATATAATACA
1 TAATACATAACTTACATAAATACATAACTTATATAATACA
28985126 TAATACATAACTTACATAA
1 TAATACATAACTTACATAA
28985145 TAACTTGCAT
Statistics
Matches: 90, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
40 22 0.24
42 15 0.17
43 6 0.07
44 23 0.26
45 22 0.24
46 2 0.02
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (40 bp):
TAATACATAACTTACATAAATACATAACTTATATAATACA
Found at i:28985097 original size:16 final size:16
Alignment explanation
Indices: 28985076--28985441 Score: 124
Period size: 16 Copynumber: 22.8 Consensus size: 16
28985066 CATAGCTTAT
28985076 ATAACTTACATAATAC
1 ATAACTTACATAATAC
*
28985092 ATAACTTAAATAAATAC
1 ATAACTTACAT-AATAC
*
28985109 ATAACTTATATAATAC
1 ATAACTTACATAATAC
28985125 ATAA--TACATAACTTAC
1 ATAACTTACATAA--TAC
* * *
28985141 ATAA-TAACTTGCATA-
1 ATAACTTACAT-AATAC
*
28985156 ATATCTTACATAATA-
1 ATAACTTACATAATAC
* *
28985171 ACTTACATA-ATAATAC
1 A-TAACTTACATAATAC
* * *
28985187 ATACCCTACATAAATTAA
1 ATAACTTACAT-AA-TAC
*
28985205 ATAAGTTACATAATAC
1 ATAACTTACATAATAC
* ** *
28985221 ACAA-AAACAAAAACTTAC
1 ATAACTTAC-ATAA--TAC
* *
28985239 ATAACCTACATTATAC
1 ATAACTTACATAATAC
*
28985255 ATAACTTACATAA-GC
1 ATAACTTACATAATAC
*
28985270 -T-AC-T---TAATGC
1 ATAACTTACATAATAC
*
28985280 ATAACTTGCATAACTTAC
1 ATAACTTACATAA--TAC
* *
28985298 TTAA--TACATAACTTGC
1 ATAACTTACATAA--TAC
28985314 ATAACTTACATAATAC
1 ATAACTTACATAATAC
* ** *
28985330 ACAACTTACATGTGTAA
1 ATAACTTACAT-AATAC
*
28985347 ATAA--TACACAACTTAC
1 ATAACTTACATAA--TAC
28985363 ATAACTTACATAATAC
1 ATAACTTACATAATAC
28985379 ATAACTTACATAACCTAC
1 ATAACTTACATAA--TAC
* *
28985397 TTAA--TACATAACTTGC
1 ATAACTTACATAA--TAC
28985413 ATAACTTACATAATAC
1 ATAACTTACATAATAC
*
28985429 ACAACTTACATAA
1 ATAACTTACATAA
28985442 CTTATATACC
Statistics
Matches: 260, Mismatches: 55, Indels: 70
0.68 0.14 0.18
Matches are distributed among these distances:
9 3 0.01
10 2 0.01
11 1 0.00
12 3 0.01
13 3 0.01
14 7 0.03
15 24 0.09
16 138 0.53
17 27 0.10
18 50 0.19
19 2 0.01
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (16 bp):
ATAACTTACATAATAC
Found at i:28985099 original size:25 final size:24
Alignment explanation
Indices: 28985064--28985112 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
28985054 TAATAAATGG
* * *
28985064 TACATAGCTTATATAACTTACATAA
1 TACATAACTTAAATAA-ATACATAA
28985089 TACATAACTTAAATAAATACATAA
1 TACATAACTTAAATAAATACATAA
28985113 CTTATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (24 bp):
TACATAACTTAAATAAATACATAA
Found at i:28985149 original size:12 final size:12
Alignment explanation
Indices: 28985109--28985183 Score: 91
Period size: 12 Copynumber: 6.3 Consensus size: 12
28985099 AAATAAATAC
*
28985109 ATAACTTATATA
1 ATAACTTACATA
*
28985121 AT-ACATA-ATA
1 ATAACTTACATA
28985131 CATAACTTACATA
1 -ATAACTTACATA
*
28985144 ATAACTTGCATA
1 ATAACTTACATA
*
28985156 ATATCTTACATA
1 ATAACTTACATA
28985168 ATAACTTACATA
1 ATAACTTACATA
28985180 ATAA
1 ATAA
28985184 TACATACCCT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
10 3 0.06
11 6 0.11
12 42 0.78
13 3 0.06
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:28985260 original size:25 final size:25
Alignment explanation
Indices: 28985232--28985479 Score: 259
Period size: 25 Copynumber: 9.9 Consensus size: 25
28985222 CAAAAACAAA
* *
28985232 AACTTACATAACCTACATTATACAT
1 AACTTACATAACTTACATAATACAT
* *
28985257 AACTTACATAAGC-TACTTAATGCAT
1 AACTTACATAA-CTTACATAATACAT
* *
28985282 AACTTGCATAACTTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
* *
28985307 AACTTGCATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAT
* * *
28985332 AACTTACAT--GTGTAAATAATACAC
1 AACTTACATAACT-TACATAATACAT
28985356 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
28985381 AACTTACATAACCTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
* *
28985406 AACTTGCATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAT
* *
28985431 AACTTACATAACTTATATACCCTACAT
1 AACTTACATAACTTACATA--ATACAT
* * *
28985458 AAATTAAATAAGTTACATAATA
1 AACTTACATAACTTACATAATA
28985480 ATACATACCC
Statistics
Matches: 188, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.01
24 21 0.11
25 145 0.77
26 2 0.01
27 19 0.10
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:28985360 original size:99 final size:99
Alignment explanation
Indices: 28985251--28985439 Score: 317
Period size: 99 Copynumber: 1.9 Consensus size: 99
28985241 AACCTACATT
* * * * *
28985251 ATACATAACTTACATAAGC-TACTTAATGCATAACTTGCATAACTTACTTAATACATAACTTGCA
1 ATACACAACTTACATAA-CTTACATAATACATAACTTACATAACCTACTTAATACATAACTTGCA
28985315 TAACTTACATAATACACAACTTACATGTGTAAATA
65 TAACTTACATAATACACAACTTACATGTGTAAATA
28985350 ATACACAACTTACATAACTTACATAATACATAACTTACATAACCTACTTAATACATAACTTGCAT
1 ATACACAACTTACATAACTTACATAATACATAACTTACATAACCTACTTAATACATAACTTGCAT
28985415 AACTTACATAATACACAACTTACAT
66 AACTTACATAATACACAACTTACAT
28985440 AACTTATATA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
98 1 0.01
99 83 0.99
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (99 bp):
ATACACAACTTACATAACTTACATAATACATAACTTACATAACCTACTTAATACATAACTTGCAT
AACTTACATAATACACAACTTACATGTGTAAATA
Found at i:28985535 original size:25 final size:25
Alignment explanation
Indices: 28985507--28985554 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
28985497 ATTAAATAAG
28985507 TTACATAA-TACACAAAAACAAAAAC
1 TTACATAACT-CACAAAAACAAAAAC
*
28985532 TTACATAACTTACAAAAACAAAA
1 TTACATAACTCACAAAAACAAAA
28985555 TTTCAGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (25 bp):
TTACATAACTCACAAAAACAAAAAC
Found at i:28989531 original size:21 final size:21
Alignment explanation
Indices: 28989506--28989571 Score: 98
Period size: 21 Copynumber: 3.1 Consensus size: 21
28989496 CAACTTAAAA
*
28989506 CAGAGGCAGCAGCGAGGGAAG
1 CAGAGGCAGCAGCGAGAGAAG
28989527 CAGAGGCTA-CAGCGAGAGAAG
1 CAGAGGC-AGCAGCGAGAGAAG
*
28989548 CAGAGGCCGCAGCGAGAGAAG
1 CAGAGGCAGCAGCGAGAGAAG
28989569 CAG
1 CAG
28989572 CGAGAGAAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.42, T:0.02
Consensus pattern (21 bp):
CAGAGGCAGCAGCGAGAGAAG
Found at i:28989573 original size:12 final size:12
Alignment explanation
Indices: 28989536--28989583 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
28989526 GCAGAGGCTA
28989536 CAGCGAGAGAAG
1 CAGCGAGAGAAG
**
28989548 CA--GAG-GCCG
1 CAGCGAGAGAAG
28989557 CAGCGAGAGAAG
1 CAGCGAGAGAAG
28989569 CAGCGAGAGAAG
1 CAGCGAGAGAAG
28989581 CAG
1 CAG
28989584 AGGTTCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 4 0.14
10 3 0.10
11 3 0.10
12 19 0.66
ACGTcount: A:0.38, C:0.21, G:0.42, T:0.00
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:28990122 original size:42 final size:42
Alignment explanation
Indices: 28990020--28990313 Score: 322
Period size: 42 Copynumber: 6.9 Consensus size: 42
28990010 TTTGTGAAAT
* * * ** **
28990020 AAGCGCCACTAAAGAACACTACTTTTAGCGGCATTTGTAGATG
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTT-TTTACC
* * *
28990063 AAGCGCTGCTAAAGAACATTACTTTTATCGGCGTTTTCTACC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
* *
28990105 AAGCGCTGCTATAGAACATTACTTTTAGCGGCGTTTTTTACC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
* *
28990147 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
* * *
28990189 TAAGCGCCGCTAAAGAACATGA-TCTTTAGCAGCGTTTTTTCCC
1 -AAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTTTACC
* * *
28990232 AAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTTTACC
* * *
28990274 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTT
1 -AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTT
28990314 TTTTGTAAGC
Statistics
Matches: 223, Mismatches: 24, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
42 121 0.54
43 102 0.46
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
Found at i:28990217 original size:85 final size:84
Alignment explanation
Indices: 28990019--28990313 Score: 335
Period size: 85 Copynumber: 3.5 Consensus size: 84
28990009 GTTTGTGAAA
* * ** ** *
28990019 TAAGCGCCACTAAAGAACACT-ACTTTTAGCGGCATTTGTAGATGAAGCGCTGCTAAAGAACATT
1 TAAGCGCCGCTAAAGAACA-TGAC-TTTAGCGGCGTTT-TTTACCAAGCGCCGCTAAAGAACATT
* * *
28990083 ACTTTTATCGGCGTTTTCTACC
63 ACTTTTAGCGGCGTTTTTTTCC
* * * *
28990105 -AAGCGCTGCTATAGAACATTACTTTTAGCGGCGTTTTTTACCAAGCGCCGCTATAGAACATTAC
1 TAAGCGCCGCTAAAGAACATGAC-TTTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACATTAC
28990169 TTTTAGCGGCGTTTTTTTCC
65 TTTTAGCGGCGTTTTTTTCC
* * *
28990189 TAAGCGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTTTCCCAAGCGCCGCTAAAGAACATGA-
1 TAAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACATTAC
*
28990253 TCATTAGCGGCGTTTTTTTCC
65 T-TTTAGCGGCGTTTTTTTCC
*
28990274 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTT
1 TAAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTTTTT
28990314 TTTTGTAAGC
Statistics
Matches: 181, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
84 41 0.23
85 139 0.77
86 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (84 bp):
TAAGCGCCGCTAAAGAACATGACTTTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACATTACT
TTTAGCGGCGTTTTTTTCC
Found at i:28993372 original size:19 final size:20
Alignment explanation
Indices: 28993350--28993403 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
28993340 TTAAAATTAG
28993350 AAAAAATA-TAAAAATCGTA
1 AAAAAATATTAAAAATCGTA
*
28993369 AAAAAATATTAAAAATTGTA
1 AAAAAATATTAAAAATCGTA
*
28993389 AAAAAA-ATTATAAAT
1 AAAAAATATTAAAAAT
28993404 TATATAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (20 bp):
AAAAAATATTAAAAATCGTA
Found at i:28993404 original size:19 final size:19
Alignment explanation
Indices: 28993350--28993404 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
28993340 TTAAAATTAG
*
28993350 AAAAAATATAAAAATCGTAA
1 AAAAAAT-TAAAAATTGTAA
28993370 AAAAATATTAAAAATTGTAA
1 AAAAA-ATTAAAAATTGTAA
*
28993390 AAAAAATTATAAATT
1 AAAAAATTAAAAATT
28993405 ATATAGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 9 0.28
20 21 0.66
21 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAAAATTAAAAATTGTAA
Found at i:29001688 original size:19 final size:19
Alignment explanation
Indices: 29001657--29001694 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
29001647 TCAATTACAC
*
29001657 CCAATTCAGTG-TTACCCA
1 CCAATTCAATGTTTACCCA
29001675 CCAATTACAATGTTTACCCA
1 CCAATT-CAATGTTTACCCA
29001695 AACATGTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.29
Consensus pattern (19 bp):
CCAATTCAATGTTTACCCA
Found at i:29003683 original size:44 final size:43
Alignment explanation
Indices: 29003609--29003742 Score: 137
Period size: 42 Copynumber: 3.1 Consensus size: 43
29003599 ATAGGATTCT
* * * * *
29003609 GATATGTGATCTCGTGTAAGATCACGTCTGGGACGTTGGCATC
1 GATATATGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC
* * * *
29003652 GATTTGAT-ATTTACGTGTAAGACCATATCTGGGACATTGGTATT
1 GATAT-ATGATTT-CGTGTAAGACCATGTCTGGGACATTGGCATC
* *
29003696 G-TATATGATTTCGTGTAAGACCCTGTCTGGGACAATGGCATC
1 GATATATGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC
29003738 GATAT
1 GATAT
29003743 TTAATTACAT
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
42 29 0.40
43 16 0.22
44 27 0.38
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (43 bp):
GATATATGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC
Found at i:29004382 original size:2 final size:2
Alignment explanation
Indices: 29004330--29004366 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
29004320 GATTTCATGG
*
29004330 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29004367 GGTGTTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:29015318 original size:131 final size:131
Alignment explanation
Indices: 29015084--29015440 Score: 624
Period size: 131 Copynumber: 2.7 Consensus size: 131
29015074 CCTTAATTTA
* * * ** * * *
29015084 ACTTAAAATTTTGTTTTTTTATTCAATCAAATAGCTGGACTTTACCTCCAGGTTGAGTTTGGAAC
1 ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
* *
29015149 TCAACTTTTCTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCGTTGT
66 TTAATTTTTCTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCGTTGT
29015214 T
131 T
29015215 ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
1 ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
29015280 TTAATTTTTCTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCGTTGT
66 TTAATTTTTCTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCGTTGT
29015345 T
131 T
29015346 ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
1 ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
29015411 TTAATTTTTCTAAAAACCTTAAATGGCTTA
66 TTAATTTTTCTAAAAACCTTAAATGGCTTA
29015441 GCACCTCTCT
Statistics
Matches: 216, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
131 216 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (131 bp):
ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
TTAATTTTTCTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCGTTGT
T
Found at i:29026027 original size:16 final size:16
Alignment explanation
Indices: 29026003--29026040 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
29025993 TTTGGTTCGC
* *
29026003 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
29026019 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
29026035 TGTAAT
1 TGTAAT
29026041 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:29026124 original size:39 final size:43
Alignment explanation
Indices: 29026019--29026128 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
29026009 GGATTAGAGG
29026019 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
29026064 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
29026104 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
29026129 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:29041402 original size:16 final size:16
Alignment explanation
Indices: 29041383--29041415 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29041373 TTATTTAAAA
*
29041383 AATGAGTTAAGTTTCG
1 AATGAGTCAAGTTTCG
29041399 AATGAGTCAAGTTTCG
1 AATGAGTCAAGTTTCG
29041415 A
1 A
29041416 GTAATACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (16 bp):
AATGAGTCAAGTTTCG
Found at i:29041501 original size:17 final size:18
Alignment explanation
Indices: 29041473--29041506 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29041463 AAAACTGTTG
*
29041473 CTTTTCTTTGCTGTTTTT
1 CTTTTCTTTGCTATTTTT
29041491 CTTTT-TTTGCTATTTT
1 CTTTTCTTTGCTATTTT
29041507 CTTATTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.03, C:0.15, G:0.09, T:0.74
Consensus pattern (18 bp):
CTTTTCTTTGCTATTTTT
Found at i:29041506 original size:16 final size:18
Alignment explanation
Indices: 29041473--29041509 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
29041463 AAAACTGTTG
*
29041473 CTTTTCTTTGCTGTTTTT
1 CTTTTCTTTGCTGATTTT
29041491 CTTTT-TTTGCT-ATTTT
1 CTTTTCTTTGCTGATTTT
29041507 CTT
1 CTT
29041510 ATTACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.03, C:0.16, G:0.08, T:0.73
Consensus pattern (18 bp):
CTTTTCTTTGCTGATTTT
Found at i:29041564 original size:12 final size:11
Alignment explanation
Indices: 29041545--29041575 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
29041535 TGTATAACTT
29041545 TTATTTTATTA
1 TTATTTTATTA
29041556 TTAATTTTATTA
1 TT-ATTTTATTA
29041568 TTATTTTA
1 TTATTTTA
29041576 GAGGCATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:29041766 original size:14 final size:15
Alignment explanation
Indices: 29041740--29041772 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
29041730 ATGCCTCTAA
29041740 AATAATAAAAAAATT
1 AATAATAAAAAAATT
29041755 AATAAT-AAAAAATT
1 AATAATAAAAAAATT
29041769 AATA
1 AATA
29041773 TGAACGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATAAAAAAATT
Found at i:29041947 original size:21 final size:23
Alignment explanation
Indices: 29041922--29041974 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
29041912 TGGGTTTAAA
29041922 AATTTTAATTTTAACTGA-A-TT
1 AATTTTAATTTTAACTGAGATTT
* *
29041943 AATTTTAAATTTAATTGAGATTT
1 AATTTTAATTTTAACTGAGATTT
*
29041966 AATTATAAT
1 AATTTTAAT
29041975 CTAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 16 0.62
22 1 0.04
23 9 0.35
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (23 bp):
AATTTTAATTTTAACTGAGATTT
Found at i:29042370 original size:7 final size:8
Alignment explanation
Indices: 29042345--29042369 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29042335 TATTGTTTAA
29042345 TTATTTTT
1 TTATTTTT
29042353 TTATTTTT
1 TTATTTTT
29042361 TTATTTTT
1 TTATTTTT
29042369 T
1 T
29042370 ACTGATAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:29049568 original size:139 final size:139
Alignment explanation
Indices: 29049314--29049593 Score: 515
Period size: 139 Copynumber: 2.0 Consensus size: 139
29049304 TTGGGGTGGG
29049314 AGATGATGTGATGGAGGAAGTGTTGGCAGTTTAATTATATGTCTTATCTAGTGGTTTGAAACCAC
1 AGATGATGTGATGGAGGAAGTGTTGGCAGTTTAATTATATGTCTTATCTAGTGGTTTGAAACCAC
*
29049379 ATATATTTGTTCTGATGGCTCAACCACATACATTAGTTTCTGGCGATTTACCGCATATTATTATC
66 ATATATTTGTTCTGATGGCTCAACCACATAAATTAGTTTCTGGCGATTTACCGCATATTATTATC
29049444 TTGAAGCTT
131 TTGAAGCTT
*
29049453 AGATGATGTGATGGAGGAAGTGTTGGCAGTTTAATTATATGTCTTATCTAGTGGTTTGAAACCAT
1 AGATGATGTGATGGAGGAAGTGTTGGCAGTTTAATTATATGTCTTATCTAGTGGTTTGAAACCAC
* *
29049518 ATATATTTGTTCTGATGGCTCAGCCACATAAATTAGTTTCTGGCGGTTTACCGCATATTATTATC
66 ATATATTTGTTCTGATGGCTCAACCACATAAATTAGTTTCTGGCGATTTACCGCATATTATTATC
*
29049583 TTGCAGCTT
131 TTGAAGCTT
29049592 AG
1 AG
29049594 CTCACTACTT
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (139 bp):
AGATGATGTGATGGAGGAAGTGTTGGCAGTTTAATTATATGTCTTATCTAGTGGTTTGAAACCAC
ATATATTTGTTCTGATGGCTCAACCACATAAATTAGTTTCTGGCGATTTACCGCATATTATTATC
TTGAAGCTT
Found at i:29052989 original size:13 final size:13
Alignment explanation
Indices: 29052971--29052996 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29052961 TAAAACATGT
29052971 ATAACTAAGTTTA
1 ATAACTAAGTTTA
29052984 ATAACTAAGTTTA
1 ATAACTAAGTTTA
29052997 TGCCAAATCA
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:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATAACTAAGTTTA
Found at i:29053686 original size:38 final size:38
Alignment explanation
Indices: 29053582--29053779 Score: 254
Period size: 38 Copynumber: 5.2 Consensus size: 38
29053572 ATAAATTTTC
* *
29053582 AATA-CACCAGCACAAAGCCTGCTAGGCACATAGCTCG
1 AATATCACCGGCACAAAGCCTGCTAGGCACATAGCCCG
* * *
29053619 AATAACACCGGCACACAAAGCCTGTTAGGCACGTAGCCCG
1 AATATCACCGG--CACAAAGCCTGCTAGGCACATAGCCCG
* **
29053659 AATATCACTGGCACAAAGCCTGCTAGGCACATAGCCTT
1 AATATCACCGGCACAAAGCCTGCTAGGCACATAGCCCG
* *
29053697 AATATCACCGGCAAAAAGCCTGCTAGGCACATAGCTCG
1 AATATCACCGGCACAAAGCCTGCTAGGCACATAGCCCG
* * *
29053735 AATAACATCGGCACAAAGCCTGCTAGGCACATAGCCCA
1 AATATCACCGGCACAAAGCCTGCTAGGCACATAGCCCG
29053773 AATATCA
1 AATATCA
29053780 TTACGTTTCT
Statistics
Matches: 137, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
37 4 0.03
38 100 0.73
40 33 0.24
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (38 bp):
AATATCACCGGCACAAAGCCTGCTAGGCACATAGCCCG
Found at i:29054566 original size:11 final size:11
Alignment explanation
Indices: 29054550--29054577 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
29054540 TTTGTTTTAC
29054550 TTAATTTTATT
1 TTAATTTTATT
29054561 TTAATTTTATT
1 TTAATTTTATT
29054572 TTAATT
1 TTAATT
29054578 ACAATTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTAATTTTATT
Found at i:29055692 original size:29 final size:29
Alignment explanation
Indices: 29055660--29055753 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
29055650 GTGTGGTAAG
*
29055660 CCATGTGACAAACCGTGTGGGTCACACGG
1 CCATGTGACAAACCGTGTGGGTCACACGA
** * *
29055689 CCATGT-AGTTAGCCGTGTGGGTAACACGA
1 CCATGTGA-CAAACCGTGTGGGTCACACGA
* * **
29055718 TCGTGTGACAGCCCGTGTGGGTCACACGA
1 CCATGTGACAAACCGTGTGGGTCACACGA
29055747 CCATGTG
1 CCATGTG
29055754 GTTAGCCTTG
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
28 1 0.02
29 47 0.96
30 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (29 bp):
CCATGTGACAAACCGTGTGGGTCACACGA
Found at i:29055734 original size:58 final size:58
Alignment explanation
Indices: 29055663--29055774 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
29055653 TGGTAAGCCA
*
29055663 TGTGACAAACCGTGTGGGTCACACGGCCATGTAGTTAGCCGTGTGGGTAACACGATCG
1 TGTGACAAACCGTGTGGGTCACACGACCATGTAGTTAGCCGTGTGGGTAACACGATCG
** * * *
29055721 TGTGACAGCCCGTGTGGGTCACACGACCATGTGGTTAGCCTTGTGGGTTACACG
1 TGTGACAAACCGTGTGGGTCACACGACCATGTAGTTAGCCGTGTGGGTAACACG
29055775 TCTATGTGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (58 bp):
TGTGACAAACCGTGTGGGTCACACGACCATGTAGTTAGCCGTGTGGGTAACACGATCG
Found at i:29055795 original size:29 final size:29
Alignment explanation
Indices: 29055672--29055784 Score: 111
Period size: 29 Copynumber: 3.9 Consensus size: 29
29055662 ATGTGACAAA
* *
29055672 CCGTGTGGGTCACACGGCCATGTAGTTAG
1 CCGTGTGGGTCACACGACCATGTGGTTAG
* * * **
29055701 CCGTGTGGGTAACACGATCGTGT-GACAG
1 CCGTGTGGGTCACACGACCATGTGGTTAG
29055729 CCCGTGTGGGTCACACGACCATGTGGTTAG
1 -CCGTGTGGGTCACACGACCATGTGGTTAG
* * * *
29055759 CCTTGTGGGTTACACGTCTATGTGGT
1 CCGTGTGGGTCACACGACCATGTGGT
29055785 AGGTCGTGTG
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
28 3 0.04
29 61 0.91
30 3 0.04
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.27
Consensus pattern (29 bp):
CCGTGTGGGTCACACGACCATGTGGTTAG
Found at i:29058199 original size:22 final size:22
Alignment explanation
Indices: 29058171--29058214 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29058161 ATAGACTATG
* * *
29058171 ATTTAAGGATAAGAATCAAATT
1 ATTTAAGAATAAAAATAAAATT
29058193 ATTTAAGAATAAAAATAAAATT
1 ATTTAAGAATAAAAATAAAATT
29058215 CAAGGAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (22 bp):
ATTTAAGAATAAAAATAAAATT
Found at i:29060417 original size:22 final size:23
Alignment explanation
Indices: 29060392--29060444 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
29060382 ATATACATAT
29060392 AAATAT-GAAAATATTCATTAAA
1 AAATATAGAAAATATTCATTAAA
*
29060414 AAATATAGGAAAATATTCGTTAAA
1 AAATATA-GAAAATATTCATTAAA
*
29060438 ATATATA
1 AAATATA
29060445 TATATATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 6 0.22
24 21 0.78
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.32
Consensus pattern (23 bp):
AAATATAGAAAATATTCATTAAA
Found at i:29060427 original size:24 final size:24
Alignment explanation
Indices: 29060398--29060444 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
29060388 ATATAAATAT
29060398 GAAAATATTCATTAAAAAATATAG
1 GAAAATATTCATTAAAAAATATAG
* *
29060422 GAAAATATTCGTTAAAATATATA
1 GAAAATATTCATTAAAAAATATA
29060445 TATATATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (24 bp):
GAAAATATTCATTAAAAAATATAG
Found at i:29062083 original size:132 final size:132
Alignment explanation
Indices: 29061893--29062312 Score: 635
Period size: 132 Copynumber: 3.2 Consensus size: 132
29061883 AGACTTGTAG
** * * * * * *
29061893 CTTCAACCTTCTCTGCTACTGCCCAGGGAGACAAGGCTTGGTGGCTTTAATCTACTTCCCATTGT
1 CTTCAACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
*
29061958 CTTGGAAAGATAAGATTTGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
66 CTTGGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
29062023 AT
131 AT
* *
29062025 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATATGCTTCCCACTAT
1 CTTCAACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* * *
29062090 CTTGGAAAAATAAGATTCGCCGTCTTCGATCTGCTCCACTACTTCTTAGGGAGATAAGATCTACA
66 CTTGGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
*
29062155 CT
131 AT
*
29062157 CTTCAACCTTCTCCACTGCTGCTCAGGGAGACAATGCTTGGTGGCTTAAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* * *
29062222 CTTGGAAAGATAAGATTCG-TCGTCTTCGATCTGCTCTACTACTGCTTTAGAGAGATAAGATCTG
66 CTTGGAAAGATAAGATTCGCT-GTCTTCGATCTGCTCCACTACTGC-TTAGGGAGATAAGATCTA
*
29062286 CCAT
129 CAAT
29062290 CTTCAACCTTCTCCACTGCTGCT
1 CTTCAACCTTCTCCACTGCTGCT
29062313 TCCCACTTTT
Statistics
Matches: 262, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
132 221 0.84
133 41 0.16
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.31
Consensus pattern (132 bp):
CTTCAACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
CTTGGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
AT
Found at i:29074201 original size:21 final size:22
Alignment explanation
Indices: 29074175--29074221 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
29074165 ATATACATAT
29074175 AAATAT-GAAAATATTCATTAA
1 AAATATAGAAAATATTCATTAA
**
29074196 AAATATAGGAAAATATTTGTTAA
1 AAATATA-GAAAATATTCATTAA
29074219 AAA
1 AAA
29074222 AATATATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
23 16 0.73
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (22 bp):
AAATATAGAAAATATTCATTAA
Found at i:29076398 original size:3 final size:3
Alignment explanation
Indices: 29076328--29076379 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
29076318 TTTTTCACCC
29076328 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29076376 TTA T
1 TTA T
29076380 ATGATTATCG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29078628 original size:15 final size:16
Alignment explanation
Indices: 29078602--29078637 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
29078592 TCACTTTTTT
29078602 GGCCTGGGCCCGACCC
1 GGCCTGGGCCCGACCC
29078618 GGCCT-GGCCCGACCC
1 GGCCTGGGCCCGACCC
29078633 GGCCT
1 GGCCT
29078638 AAATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.06, C:0.50, G:0.36, T:0.08
Consensus pattern (16 bp):
GGCCTGGGCCCGACCC
Found at i:29078683 original size:24 final size:25
Alignment explanation
Indices: 29078656--29078714 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
29078646 AATAAATATA
*
29078656 TATTTTATT-TTAAAATACTTTTTT
1 TATTTTATTATTAAAATAATTTTTT
* *
29078680 TATTTT-TTATTTAATTAATTTTTT
1 TATTTTATTATTAAAATAATTTTTT
29078704 TATATTTATTA
1 TAT-TTTATTA
29078715 AAAATGGGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 2 0.07
24 21 0.72
25 3 0.10
26 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TATTTTATTATTAAAATAATTTTTT
Found at i:29081688 original size:60 final size:60
Alignment explanation
Indices: 29081623--29081738 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
29081613 TTTTTTTTTT
* * * * *
29081623 AATTTTT-AGAATTGGAACTAAATTGATAAATTTTGTAAATGTTGAGGGCTAAATTTATTG
1 AATTTTTAAG-ATTGGAACTAAAATAACAAATTTTGTAAATATTGAGGACTAAATTTATTG
* * *
29081683 AATTTTTAAGATTTGAATTAAAATAACAAATTTTGTAAATATTGAGGATTAAATTT
1 AATTTTTAAGATTGGAACTAAAATAACAAATTTTGTAAATATTGAGGACTAAATTT
29081739 GTTTAGTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 45 0.96
61 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.42
Consensus pattern (60 bp):
AATTTTTAAGATTGGAACTAAAATAACAAATTTTGTAAATATTGAGGACTAAATTTATTG
Found at i:29083199 original size:21 final size:21
Alignment explanation
Indices: 29083161--29083204 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
29083151 ATATGTAGTG
* *
29083161 ATACAATATGTATTATCTGTT
1 ATACAATATGTATGATCTATT
* *
29083182 ATACAATTTGTCTGATCTATT
1 ATACAATATGTATGATCTATT
29083203 AT
1 AT
29083205 TCATCAAGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (21 bp):
ATACAATATGTATGATCTATT
Found at i:29085735 original size:5 final size:5
Alignment explanation
Indices: 29085725--29085749 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29085715 GTTAATGTGG
29085725 GAGTT GAGTT GAGTT GAGTT GAGTT
1 GAGTT GAGTT GAGTT GAGTT GAGTT
29085750 TTTATATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
GAGTT
Found at i:29091613 original size:28 final size:27
Alignment explanation
Indices: 29091574--29091628 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
29091564 TTTAATTTTT
* * *
29091574 AAAATAATAAAATTTTAAATTTTAAAA
1 AAAATAATAAAATATAAAATATTAAAA
*
29091601 AAAATTATAAAAATATAAAATATTAAAA
1 AAAATAAT-AAAATATAAAATATTAAAA
29091629 TATTAAATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAATAATAAAATATAAAATATTAAAA
Done.