Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 99 of 214
Found at i:28808757 original size:32 final size:32
Alignment explanation
Indices: 28808721--28808782 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
28808711 GCATCCTAAG
28808721 GCCTTTGTGACTCGTATCAGTTGGTAATGCAT
1 GCCTTTGTGACTCGTATCAGTTGGTAATGCAT
28808753 GCCTTTGTGACTCGTATCAGTTGGTAATGC
1 GCCTTTGTGACTCGTATCAGTTGGTAATGC
28808783 CTTGATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (32 bp):
GCCTTTGTGACTCGTATCAGTTGGTAATGCAT
Found at i:28811025 original size:17 final size:17
Alignment explanation
Indices: 28811003--28811039 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28810993 AACTTAAGTT
* *
28811003 AAATAATAATAAAAAGA
1 AAATAAAAAGAAAAAGA
28811020 AAATAAAAAGAAAAAGA
1 AAATAAAAAGAAAAAGA
28811037 AAA
1 AAA
28811040 GGAATTAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (17 bp):
AAATAAAAAGAAAAAGA
Found at i:28818267 original size:359 final size:359
Alignment explanation
Indices: 28817601--28818321 Score: 1343
Period size: 359 Copynumber: 2.0 Consensus size: 359
28817591 CACTCAAGAA
* *
28817601 CTTGACTTACTAGGATTTTTTCTTAATGCTCCTTGCATTGAGCCAGACTTTGTTGCCACTCCAGA
1 CTTGACTTACTAGAATTTTTCCTTAATGCTCCTTGCATTGAGCCAGACTTTGTTGCCACTCCAGA
* *
28817666 TCTGGTCTCTTACTGAAACTTCTAGGGCCCATGAATAGACTGCTCTGTGCTTGCTTCTATCTTGG
66 TCTGGTCTCTTACTGAAACTTCTAAGGCCCATGAATAGACTGCTCTATGCTTGCTTCTATCTTGG
* *
28817731 AGGGACAATCCTTAATCAAATGATCCTTGGATCCATATCCGAAACATGCCTCAGAACGTCTCCAA
131 AGGGACAACCCTTAATCAAATGATCCTTGGATCCATATCCGAAACATGCCCCAGAACGTCTCCAA
28817796 CATTCTCCTCCATAGCTTCTACCGAAGTGTTCATAGTTAACATTTCTTATTACTCTAGACCCTCT
196 CATTCTCCTCCATAGCTTCTACCGAAGTGTTCATAGTTAACATTTCTTATTACTCTAGACCCTCT
*
28817861 AGAGCTTGCCATAAAAATAGTTGATCTACTAAATCCTTCATGCCTGAAACTCGTAGGCTATGAAT
261 AGAGCTTGCCATAAAAATAGTTGATCTACTAAATCCTTCACGCCTGAAACTCGTAGGCTATGAAT
*
28817926 CTCTTCTTGAAGTTTAAAATGTTTGATATTTGAG
326 CTCTTCTTGAAGTTGAAAATGTTTGATATTTGAG
*
28817960 CTTGACTTACTAGAATTTTTCCTTAGTGCTCCTTGCATTGAGCCAGACTTTGTTGCCACTCCAGA
1 CTTGACTTACTAGAATTTTTCCTTAATGCTCCTTGCATTGAGCCAGACTTTGTTGCCACTCCAGA
28818025 TCTGGTCTCTTACTGAAACTTCTAAGGCCCATGAATAGACTGCTCTATGCTTGCTTCTATCTTGG
66 TCTGGTCTCTTACTGAAACTTCTAAGGCCCATGAATAGACTGCTCTATGCTTGCTTCTATCTTGG
*
28818090 AGGGACAACCCTTAATCAACTGATCCTTGGATCCATATCCGAAACATGCCCCAGAACGTCTCCAA
131 AGGGACAACCCTTAATCAAATGATCCTTGGATCCATATCCGAAACATGCCCCAGAACGTCTCCAA
*
28818155 CATTCTCCTCCATGGCTTCTACCGAAGTGTTCATAGTTAACATTTCTTATTACTCTAGACCCTCT
196 CATTCTCCTCCATAGCTTCTACCGAAGTGTTCATAGTTAACATTTCTTATTACTCTAGACCCTCT
28818220 AGAGCTTGCCATAAAAATAGTTGATCTACTAAATCCTTCACGCCTGAAACTCGTAGGCTATGAAT
261 AGAGCTTGCCATAAAAATAGTTGATCTACTAAATCCTTCACGCCTGAAACTCGTAGGCTATGAAT
28818285 CTCTTCTTGAAGTTGAAAATGTTTGATATTTGAG
326 CTCTTCTTGAAGTTGAAAATGTTTGATATTTGAG
28818319 CTT
1 CTT
28818322 CTTAAAACTT
Statistics
Matches: 351, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
359 351 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (359 bp):
CTTGACTTACTAGAATTTTTCCTTAATGCTCCTTGCATTGAGCCAGACTTTGTTGCCACTCCAGA
TCTGGTCTCTTACTGAAACTTCTAAGGCCCATGAATAGACTGCTCTATGCTTGCTTCTATCTTGG
AGGGACAACCCTTAATCAAATGATCCTTGGATCCATATCCGAAACATGCCCCAGAACGTCTCCAA
CATTCTCCTCCATAGCTTCTACCGAAGTGTTCATAGTTAACATTTCTTATTACTCTAGACCCTCT
AGAGCTTGCCATAAAAATAGTTGATCTACTAAATCCTTCACGCCTGAAACTCGTAGGCTATGAAT
CTCTTCTTGAAGTTGAAAATGTTTGATATTTGAG
Found at i:28822815 original size:25 final size:25
Alignment explanation
Indices: 28822725--28822812 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 25
28822715 ATGTTCATAT
* *
28822725 GAGCTATGAATCGATATGCTCTCAT
1 GAGCTATGAATCGATAAGCTCTCAC
* *
28822750 GAGCTATGAATCGAAAAGCTCACAC
1 GAGCTATGAATCGATAAGCTCTCAC
* *
28822775 GAGCTGA-GAATTGGTAAGCTCTCAC
1 GAGCT-ATGAATCGATAAGCTCTCAC
*
28822800 GAGCTATAAATCG
1 GAGCTATGAATCG
28822813 GTATGCTTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
24 1 0.02
25 49 0.96
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (25 bp):
GAGCTATGAATCGATAAGCTCTCAC
Found at i:28826958 original size:30 final size:31
Alignment explanation
Indices: 28826883--28826974 Score: 141
Period size: 31 Copynumber: 3.0 Consensus size: 31
28826873 GGCTGTTACA
* *
28826883 CCTATACTTTTTAAATCGGTCAAGTTTAGTC
1 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
* *
28826914 CTTTTACTTTTTGAATTGGTCAAGTTTAGTC
1 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
28826945 CCTATAC-TTTTGAATTGGTCAAGTTTAGTC
1 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
28826975 TTGACCCAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
30 23 0.42
31 32 0.58
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (31 bp):
CCTATACTTTTTGAATTGGTCAAGTTTAGTC
Found at i:28833994 original size:31 final size:31
Alignment explanation
Indices: 28833959--28834027 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
28833949 CAACAAAACG
*
28833959 GTCATTGAACTATTCAAAAGATTTCACTTAA
1 GTCATTGAACTATTCAAAACATTTCACTTAA
*
28833990 GTCATTGAACTATTCAAAACATTTCATTTAA
1 GTCATTGAACTATTCAAAACATTTCACTTAA
28834021 GTCATTG
1 GTCATTG
28834028 GACAATTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (31 bp):
GTCATTGAACTATTCAAAACATTTCACTTAA
Found at i:28835945 original size:11 final size:11
Alignment explanation
Indices: 28835929--28835959 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28835919 GCTGTTTGCA
28835929 ATTTGATTTTT
1 ATTTGATTTTT
28835940 ATTTGATTTTT
1 ATTTGATTTTT
*
28835951 ATTTAATTT
1 ATTTGATTT
28835960 CTAACTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (11 bp):
ATTTGATTTTT
Found at i:28843735 original size:25 final size:25
Alignment explanation
Indices: 28843701--28843749 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
28843691 AACGGCAAGT
28843701 ACTCCTCCCAATTGCCTCGGAAATC
1 ACTCCTCCCAATTGCCTCGGAAATC
28843726 ACTCCTCCCAATTGCCTCGGAAAT
1 ACTCCTCCCAATTGCCTCGGAAAT
28843750 TAATAACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.39, G:0.12, T:0.24
Consensus pattern (25 bp):
ACTCCTCCCAATTGCCTCGGAAATC
Found at i:28849507 original size:37 final size:37
Alignment explanation
Indices: 28849444--28849531 Score: 133
Period size: 37 Copynumber: 2.4 Consensus size: 37
28849434 ACACAAGTAG
* *
28849444 TCCAACCAA-AACACGCCAAACGCTCATAAGAGCTAA
1 TCCAACCAATAACACGCCAAACACTCATAAGACCTAA
* *
28849480 TCCAACCAATAACATGCCAAACACTCATGAGACCTAA
1 TCCAACCAATAACACGCCAAACACTCATAAGACCTAA
28849517 TCCAACCAATAACAC
1 TCCAACCAATAACAC
28849532 ACCTTGACAC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 9 0.20
37 37 0.80
ACGTcount: A:0.44, C:0.34, G:0.08, T:0.14
Consensus pattern (37 bp):
TCCAACCAATAACACGCCAAACACTCATAAGACCTAA
Found at i:28857443 original size:25 final size:26
Alignment explanation
Indices: 28857391--28857474 Score: 107
Period size: 26 Copynumber: 3.3 Consensus size: 26
28857381 GTACATAATA
* *
28857391 CCTGCTAAATATTCACCAGCTCAAAG
1 CCTGCTAAATAATCACCGGCTCAAAG
* *
28857417 CCTGCTAAATAAAC-CCGGCTCATAG
1 CCTGCTAAATAATCACCGGCTCAAAG
* *
28857442 CCTGCTAAGTAATCATCGGCTCAAAG
1 CCTGCTAAATAATCACCGGCTCAAAG
28857468 CCTGCTA
1 CCTGCTA
28857475 TTCAAGTACA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
25 21 0.43
26 28 0.57
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (26 bp):
CCTGCTAAATAATCACCGGCTCAAAG
Found at i:28858487 original size:12 final size:13
Alignment explanation
Indices: 28858463--28858491 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28858453 AACTAATAGA
28858463 AACTAATTTTTCC
1 AACTAATTTTTCC
28858476 AACTAA-TTTTCC
1 AACTAATTTTTCC
28858488 AACT
1 AACT
28858492 TTTATGACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (13 bp):
AACTAATTTTTCC
Found at i:28860726 original size:96 final size:96
Alignment explanation
Indices: 28860605--28860793 Score: 256
Period size: 96 Copynumber: 2.0 Consensus size: 96
28860595 GCCATAAATA
* * *
28860605 CAATAATATGATTGGCACAAAGCCATCAATAGC-AGTGATATGATCGGCACATAA-CCATCAATA
1 CAATAATATGATCGGCACAAAGCCATCAATAACGA-TAATATGATCGGCACA-AAGCCATCAATA
* *
28860668 ACGGTAATATGATCGGCACAAAGCCATCAGTAG
64 ACGGTAATATGATCAGCACAAAACCATCAGTAG
* * * * *
28860701 CAATGATATGATCGGCACACAGCCATCAGTAACGATAATATGATCGGCACAAAGTCATCAGTAAC
1 CAATAATATGATCGGCACAAAGCCATCAATAACGATAATATGATCGGCACAAAGCCATCAATAAC
28860766 GGTAATATGATCAGCACAAAACCATCAG
66 GGTAATATGATCAGCACAAAACCATCAG
28860794 CAACATCCCA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
95 2 0.02
96 78 0.96
97 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (96 bp):
CAATAATATGATCGGCACAAAGCCATCAATAACGATAATATGATCGGCACAAAGCCATCAATAAC
GGTAATATGATCAGCACAAAACCATCAGTAG
Found at i:28860793 original size:32 final size:32
Alignment explanation
Indices: 28860608--28860793 Score: 221
Period size: 32 Copynumber: 5.8 Consensus size: 32
28860598 ATAAATACAA
* * * *
28860608 TAATATGATTGGCACAAAGCCATCAATAGCAG
1 TAATATGATCGGCACAAAGCCATCAGTAACGG
* *
28860640 TGATATGATCGGCACATAA-CCATCAATAACGG
1 TAATATGATCGGCACA-AAGCCATCAGTAACGG
* **
28860672 TAATATGATCGGCACAAAGCCATCAGTAGCAA
1 TAATATGATCGGCACAAAGCCATCAGTAACGG
* * *
28860704 TGATATGATCGGCACACAGCCATCAGTAACGA
1 TAATATGATCGGCACAAAGCCATCAGTAACGG
*
28860736 TAATATGATCGGCACAAAGTCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAACGG
* *
28860768 TAATATGATCAGCACAAAACCATCAG
1 TAATATGATCGGCACAAAGCCATCAG
28860794 CAACATCCCA
Statistics
Matches: 132, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
31 2 0.02
32 128 0.97
33 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAACGG
Found at i:28860793 original size:64 final size:64
Alignment explanation
Indices: 28860607--28860793 Score: 257
Period size: 64 Copynumber: 2.9 Consensus size: 64
28860597 CATAAATACA
* * * *
28860607 ATAATATGATTGGCACAAAGCCATCAATAGCAGTGATATGATCGGCACATAACCATCAATAACG
1 ATAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACAAAACCATCAGTAACG
* * * *
28860671 GTAATATGATCGGCACAAAGCCATCAGTAGCAATGATATGATCGGCACACAGCCATCAGTAACG
1 ATAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACAAAACCATCAGTAACG
* * * * *
28860735 ATAATATGATCGGCACAAAGTCATCAGTAACGGTAATATGATCAGCACAAAACCATCAG
1 ATAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACAAAACCATCAG
28860794 CAACATCCCA
Statistics
Matches: 107, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 107 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (64 bp):
ATAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACAAAACCATCAGTAACG
Found at i:28861076 original size:27 final size:25
Alignment explanation
Indices: 28861046--28861199 Score: 112
Period size: 27 Copynumber: 5.7 Consensus size: 25
28861036 CATTACGGTT
*
28861046 ATTTTACCTTACAGTGGTATTTTGGTC
1 ATTTTACCTT-CAG-GGTAATTTGGTC
** *
28861073 ATTTTACCCTAAGAGGGT-ATCTTAGTC
1 ATTTTA-CCT-TCAGGGTAAT-TTGGTC
* *
28861100 ATTTTACCCTTCAGGGATAATTCGATC
1 ATTTTA-CCTTCAGGG-TAATTTGGTC
*
28861127 ATGTTACCTTTCAAGGGTAATTTGGTC
1 ATTTTACC-TTC-AGGGTAATTTGGTC
*
28861154 ATTTTACTCTTCAGGGGTAATTTAGTC
1 ATTTTAC-CTTCA-GGGTAATTTGGTC
28861181 ATTTTATCCTTCGAGGGTA
1 ATTTTA-CCTTC-AGGGTA
28861200 TTTCGGTAAT
Statistics
Matches: 102, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
26 8 0.08
27 80 0.78
28 14 0.14
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (25 bp):
ATTTTACCTTCAGGGTAATTTGGTC
Found at i:28861198 original size:54 final size:53
Alignment explanation
Indices: 28861046--28861199 Score: 134
Period size: 54 Copynumber: 2.8 Consensus size: 53
28861036 CATTACGGTT
* * * **
28861046 ATTTTACCTTACAGTGGTATTTTGGTCATTTTACCCTAAGAGGGT-ATCTTAGTC
1 ATTTTACCTT-CAGGGGTAATTTAGTCATTTTA-CCTTCGAGGGTAATCTTAGTC
* * * * *
28861100 ATTTTACCCTTCAGGGATAA-TTCGATCATGTTACCTTTCAAGGGTAAT-TTGGTC
1 ATTTTA-CCTTCAGGGGTAATTTAG-TCATTTTACC-TTCGAGGGTAATCTTAGTC
28861154 ATTTTACTCTTCAGGGGTAATTTAGTCATTTTATCCTTCGAGGGTA
1 ATTTTAC-CTTCAGGGGTAATTTAGTCATTTTA-CCTTCGAGGGTA
28861200 TTTCGGTAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
53 6 0.08
54 63 0.79
55 11 0.14
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (53 bp):
ATTTTACCTTCAGGGGTAATTTAGTCATTTTACCTTCGAGGGTAATCTTAGTC
Found at i:28861218 original size:27 final size:27
Alignment explanation
Indices: 28861073--28861479 Score: 273
Period size: 27 Copynumber: 15.1 Consensus size: 27
28861063 TATTTTGGTC
** *
28861073 ATTTTACCCTAAGAGGGTATCTT-AGTC
1 ATTTTACCCTTCGAGGGTAT-TTCAGTA
* *
28861100 ATTTTACCCTTC-AGGGATAATTC-GATC
1 ATTTTACCCTTCGAGGG-TATTTCAG-TA
* * * * *
28861127 ATGTTACCTTTCAAGGGTAATTT-GGTC
1 ATTTTACCCTTCGAGGGT-ATTTCAGTA
* *
28861154 ATTTTACTCTTC-AGGGGTAATTT-AGTC
1 ATTTTACCCTTCGA-GGGT-ATTTCAGTA
* *
28861181 ATTTTATCCTTCGAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
* *
28861208 ATATTACCCTTCG-GGAGTATTTCAGAA
1 ATTTTACCCTTCGAGG-GTATTTCAGTA
* *
28861235 ATTTTATTCATT-GAGGGTATTTCAGTA
1 ATTTTA-CCCTTCGAGGGTATTTCAGTA
* * *
28861262 ACTTTACCCATCAAGGGTATTTC-GATA
1 ATTTTACCCTTCGAGGGTATTTCAG-TA
** *
28861289 ATTTTACCAATCGAGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
*
28861316 ATTTTACCCTTCGAGGGTATTTTAGTA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
*
28861343 GTTTTACCCTTCG-GGGCTATTTCAGTA
1 ATTTTACCCTTCGAGGG-TATTTCAGTA
* *
28861370 ATTTTACCCTTCGAGGGTATCTC-G-G
1 ATTTTACCCTTCGAGGGTATTTCAGTA
* * * * *
28861395 ACTTTACCCATCGATGTTATTT-TGATA
1 ATTTTACCCTTCGAGGGTATTTCAG-TA
* *
28861422 ATTTTACCCATCGACGGTATTTCAGTA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
* * * *
28861449 ATTTTACCCATCAAGGGCATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
28861476 ATTT
1 ATTT
28861480 GCCCATGAAT
Statistics
Matches: 305, Mismatches: 54, Indels: 42
0.76 0.13 0.10
Matches are distributed among these distances:
25 18 0.06
26 21 0.07
27 248 0.81
28 18 0.06
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCAGTA
Found at i:28863983 original size:29 final size:31
Alignment explanation
Indices: 28863930--28863989 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
28863920 GATATTAGTC
28863930 ATGCAGTGAACAGTATGTAATATCATTAATCG
1 ATGCAGTGAACAGTA-GTAATATCATTAATCG
28863962 ATGCAGT-AACAGTA-TAATATCATTAATC
1 ATGCAGTGAACAGTAGTAATATCATTAATC
28863990 AGTGCAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 14 0.50
31 7 0.25
32 7 0.25
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (31 bp):
ATGCAGTGAACAGTAGTAATATCATTAATCG
Found at i:28863995 original size:29 final size:31
Alignment explanation
Indices: 28863923--28863996 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
28863913 AGTAACAGAT
*
28863923 ATTAGTCA-TGCAGTGAACAGTATGTAATATC
1 ATTAATCAGTGCAGTGAACAGTA-GTAATATC
28863954 ATTAATC-GATGCAGT-AACAGTA-TAATATC
1 ATTAATCAG-TGCAGTGAACAGTAGTAATATC
28863983 ATTAATCAGTGCAG
1 ATTAATCAGTGCAG
28863997 ATATGCAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 19 0.49
30 1 0.03
31 13 0.33
32 6 0.15
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (31 bp):
ATTAATCAGTGCAGTGAACAGTAGTAATATC
Found at i:28864408 original size:27 final size:27
Alignment explanation
Indices: 28864378--28864438 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
28864368 TTATCTCCTA
*
28864378 GGGGTATAACAGTCATTTTATCCTATG
1 GGGGTATAACAGTCATTTTACCCTATG
****
28864405 GGGGTATTTTGGTCATTTTACCCTATG
1 GGGGTATAACAGTCATTTTACCCTATG
*
28864432 AGGGTAT
1 GGGGTAT
28864439 TTTGGTTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.39
Consensus pattern (27 bp):
GGGGTATAACAGTCATTTTACCCTATG
Found at i:28864439 original size:27 final size:27
Alignment explanation
Indices: 28864389--28864461 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
28864379 GGGTATAACA
* *
28864389 GTCATTTTATCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTTG
28864416 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTTG
* *
28864443 GTTATTCTACCCTAT-AGGG
1 GTCATTTTACCCTATGAGGG
28864462 GTGTTTCGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 4 0.10
27 38 0.90
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTTG
Found at i:28864463 original size:27 final size:26
Alignment explanation
Indices: 28864389--28864474 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
28864379 GGGTATAACA
* *
28864389 GTCATTTTATCCTATGGGGGTATTTTG
1 GTCATTCTACCCTAT-GGGGTATTTTG
*
28864416 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTCTACCCTATG-GGGTATTTTG
* * *
28864443 GTTATTCTACCCTATAGGGGTGTTTCG
1 GTCATTCTACCCTAT-GGGGTATTTTG
28864470 GTCAT
1 GTCAT
28864475 AACAGTATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
26 1 0.02
27 49 0.96
28 1 0.02
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.44
Consensus pattern (26 bp):
GTCATTCTACCCTATGGGGTATTTTG
Found at i:28884124 original size:3 final size:3
Alignment explanation
Indices: 28884102--28884162 Score: 59
Period size: 3 Copynumber: 20.3 Consensus size: 3
28884092 TTTGCTGAGA
* * * * * * *
28884102 TTG TTG CTG TTG TTG CTG TTG TTG CTG CTG CTG CTG CTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
28884150 TTG TTG TTG TTG T
1 TTG TTG TTG TTG T
28884163 CGGTGATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.00, C:0.11, G:0.33, T:0.56
Consensus pattern (3 bp):
TTG
Found at i:28884162 original size:9 final size:9
Alignment explanation
Indices: 28884102--28884161 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
28884092 TTTGCTGAGA
28884102 TTGTTGCTG
1 TTGTTGCTG
28884111 TTGTTGCTG
1 TTGTTGCTG
28884120 TTGTTGCTG
1 TTGTTGCTG
* *
28884129 CTGCTGCTG
1 TTGTTGCTG
* *
28884138 CTGTTGTTG
1 TTGTTGCTG
*
28884147 TTGTTGTTG
1 TTGTTGCTG
28884156 TTGTTG
1 TTGTTG
28884162 TCGGTGATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.00, C:0.12, G:0.33, T:0.55
Consensus pattern (9 bp):
TTGTTGCTG
Found at i:28894622 original size:28 final size:28
Alignment explanation
Indices: 28894557--28894624 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
28894547 AGTAACAACG
* *
28894557 TACAGTAGCAGTCTGGGCCTGAGCCCTA
1 TACAGTAACAGTCTGGGCCTGAGCCCAA
** * * *
28894585 TACAACAACAGTGTGGGTCTTAGCCCAA
1 TACAGTAACAGTCTGGGCCTGAGCCCAA
28894613 TACAGTAACAGT
1 TACAGTAACAGT
28894625 ACAATGCAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (28 bp):
TACAGTAACAGTCTGGGCCTGAGCCCAA
Found at i:28894764 original size:26 final size:26
Alignment explanation
Indices: 28894735--28894806 Score: 117
Period size: 26 Copynumber: 2.8 Consensus size: 26
28894725 AATATCGCAG
28894735 CAAAGCTGCCAGTAACAGTAATGCAA
1 CAAAGCTGCCAGTAACAGTAATGCAA
* *
28894761 CAAAGCTGCCAGTAACGGTAATGCAG
1 CAAAGCTGCCAGTAACAGTAATGCAA
*
28894787 CAAAGCTGCCAATAACAGTA
1 CAAAGCTGCCAGTAACAGTA
28894807 TATGTGGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (26 bp):
CAAAGCTGCCAGTAACAGTAATGCAA
Found at i:28895012 original size:27 final size:27
Alignment explanation
Indices: 28894982--28895209 Score: 282
Period size: 27 Copynumber: 8.5 Consensus size: 27
28894972 GGGTATAACA
*
28894982 GTCATTTTATCCTATCG-GGGTATTTCG
1 GTCATTTTA-CCCATCGAGGGTATTTCG
*
28895009 GTCATTTTACCCTTCG-GGGTTATTTCG
1 GTCATTTTACCCATCGAGGG-TATTTCG
* * *
28895036 ATCATTTTACCTATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* * * **
28895063 ATTATTTTGCCCATCGAGGGTATTTTA
1 GTCATTTTACCCATCGAGGGTATTTCG
*
28895090 GCCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
28895117 GTTATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
28895144 GTCATTTTACCCATCGAGAGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
28895171 GTCATTTTACCCATCGAGAGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
28895198 GTTA-TTTACCCA
1 GTCATTTTACCCA
28895210 CGAATCACAA
Statistics
Matches: 178, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
26 16 0.09
27 159 0.89
28 3 0.02
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTCG
Found at i:28896678 original size:22 final size:23
Alignment explanation
Indices: 28896636--28896678 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
28896626 AGATCTTAAA
28896636 AAAATTATTTATTGATATAAAAG
1 AAAATTATTTATTGATATAAAAG
28896659 AAAATATATTT-TT-ATATAAA
1 AAAAT-TATTTATTGATATAAA
28896679 GAATAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (23 bp):
AAAATTATTTATTGATATAAAAG
Found at i:28905320 original size:3 final size:3
Alignment explanation
Indices: 28905308--28905346 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
28905298 GTGTGTCCAT
*
28905308 TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TCC TT- TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
28905347 TTTATAACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:28913775 original size:25 final size:26
Alignment explanation
Indices: 28913747--28913800 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
28913737 TAATTAGTAT
* *
28913747 AAAATATT-AATAATTCAATA-ATTTG
1 AAAA-ATTAAATAATTAAATAGAATTG
28913772 AAAAATTAAATAATTAAATAGAATTG
1 AAAAATTAAATAATTAAATAGAATTG
28913798 AAA
1 AAA
28913801 TTTAGGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 15 0.60
26 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (26 bp):
AAAAATTAAATAATTAAATAGAATTG
Found at i:28914649 original size:22 final size:22
Alignment explanation
Indices: 28914622--28914699 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
28914612 TTGTTTTTGT
28914622 TGTTTTTGAATTATTTGAAAAA
1 TGTTTTTGAATTATTTGAAAAA
* ***
28914644 TGTTTTTGATTTA-TTG--GGT
1 TGTTTTTGAATTATTTGAAAAA
*
28914663 TATTTTTGAATTATTT-AACAAA
1 TGTTTTTGAATTATTTGAA-AAA
*
28914685 TGTTTTTGATTTATT
1 TGTTTTTGAATTATT
28914700 GAGATTGTGA
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
19 11 0.27
20 2 0.05
21 3 0.07
22 25 0.61
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (22 bp):
TGTTTTTGAATTATTTGAAAAA
Found at i:28915037 original size:27 final size:27
Alignment explanation
Indices: 28914999--28915060 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
28914989 TAAATAAGCT
*
28914999 TATTATA-TATTGT-TTAGTATTT-TTG
1 TATTATATTATTGTACTA-TATTTATTG
28915024 TATTGATATTATTGTACTATATTTATTG
1 TATT-ATATTATTGTACTATATTTATTG
28915052 TATTATATT
1 TATTATATT
28915061 TAGGTGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 4 0.12
26 3 0.09
27 16 0.50
28 9 0.28
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (27 bp):
TATTATATTATTGTACTATATTTATTG
Found at i:28915038 original size:14 final size:13
Alignment explanation
Indices: 28914999--28915060 Score: 65
Period size: 14 Copynumber: 4.7 Consensus size: 13
28914989 TAAATAAGCT
28914999 TATTATA-TATTG
1 TATTATATTATTG
*
28915011 T-TTAGTATTTTTG
1 TATTA-TATTATTG
28915024 TATTGATATTATTG
1 TATT-ATATTATTG
*
28915038 TACTATATTTATTG
1 TATTATA-TTATTG
28915052 TATTATATT
1 TATTATATT
28915061 TAGGTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
11 3 0.07
12 3 0.07
13 10 0.24
14 24 0.59
15 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (13 bp):
TATTATATTATTG
Found at i:28915061 original size:14 final size:14
Alignment explanation
Indices: 28915006--28915062 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
28914996 GCTTATTATA
28915006 TATTGT-TTAGTATT
1 TATTGTATTA-TATT
28915020 T-TTGTATTGATA-T
1 TATTGTATT-ATATT
*
28915033 TATTGTACTATATT
1 TATTGTATTATATT
28915047 TATTGTATTATATT
1 TATTGTATTATATT
28915061 TA
1 TA
28915063 GGTGTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.24
14 27 0.73
15 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (14 bp):
TATTGTATTATATT
Found at i:28915346 original size:43 final size:43
Alignment explanation
Indices: 28915298--28915441 Score: 195
Period size: 43 Copynumber: 3.3 Consensus size: 43
28915288 TTATCTGAAA
**
28915298 AAACGCCGCTAAAAATAATGACCTTTAGCTGCGCTTTTATCAC
1 AAACGCCGCTAAAAATCTTGACCTTTAGCTGCGCTTTTATCAC
* *
28915341 AAACGCCGCAAAAAATCTTGACCTTTAGC-GCCACTTTTATCAC
1 AAACGCCGCTAAAAATCTTGACCTTTAGCTG-CGCTTTTATCAC
*
28915384 AAGCGCCGC-AAAAGATCTTGACCTTTAG-TGGCGCTTTTATCAC
1 AAACGCCGCTAAAA-ATCTTGACCTTTAGCT-GCGCTTTTATCAC
28915427 AAACGCCGCTAAAAA
1 AAACGCCGCTAAAAA
28915442 CATAACCTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
42 5 0.06
43 79 0.89
44 5 0.06
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAAATCTTGACCTTTAGCTGCGCTTTTATCAC
Found at i:28919896 original size:23 final size:23
Alignment explanation
Indices: 28919853--28919897 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28919843 TATATCAATA
* *
28919853 CTATTTTAACTTATTTATTAATT
1 CTATTTAAACTAATTTATTAATT
28919876 CTATTTAAACTAATATT-TTAAT
1 CTATTTAAACTAAT-TTATTAAT
28919898 ATATCAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (23 bp):
CTATTTAAACTAATTTATTAATT
Found at i:28920352 original size:21 final size:21
Alignment explanation
Indices: 28920312--28920352 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28920302 AACCCTAAAT
* * *
28920312 CCTTAACTCTTAATCTCTAAC
1 CCTTAACCCTTAACCCCTAAC
28920333 CCTTAACCCTTAACCCCTAA
1 CCTTAACCCTTAACCCCTAA
28920353 ATCACAACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (21 bp):
CCTTAACCCTTAACCCCTAAC
Found at i:28920391 original size:14 final size:15
Alignment explanation
Indices: 28920372--28920404 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
28920362 CTTAAACTAG
28920372 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
28920386 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
28920401 AATC
1 AATC
28920405 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:28920917 original size:40 final size:40
Alignment explanation
Indices: 28920841--28920917 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
28920831 CGCTTTTTTT
* *
28920841 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGTGTTTTATG
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCAGCGTTTTATG
*
28920881 TAAAGCGCCGCTAATGCTCGATTTTTAGCAGCGTTTT
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCAGCGTTTT
28920918 TTGTCCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (40 bp):
TAAAGCGCCGCTAATGCTCGATCTTTAGCAGCGTTTTATG
Found at i:28924927 original size:27 final size:27
Alignment explanation
Indices: 28924886--28924949 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
28924876 CCAAAAGTGG
* *
28924886 AAGCCTCTGTGGCAATCTT-TAAAATGA
1 AAGCCTTTGTTGCAAT-TTATAAAATGA
* *
28924913 AAGTCTTTGTTGCAATTTATGAAATGA
1 AAGCCTTTGTTGCAATTTATAAAATGA
28924940 AAGCCTTTGT
1 AAGCCTTTGT
28924950 AGCATAGCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 2 0.06
27 29 0.94
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (27 bp):
AAGCCTTTGTTGCAATTTATAAAATGA
Found at i:28925609 original size:17 final size:18
Alignment explanation
Indices: 28925577--28925610 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28925567 TTCTTATCGA
28925577 AAAATATATAAAAATTTT
1 AAAATATATAAAAATTTT
*
28925595 AAAATA-ATTAAAATTT
1 AAAATATATAAAAATTT
28925611 ACTTATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATATAAAAATTTT
Found at i:28934275 original size:25 final size:25
Alignment explanation
Indices: 28934241--28934294 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
28934231 GATTAGCATG
*
28934241 TTTGGGTGTAAAATAAAATGGGTAA
1 TTTGGGTGTAAAAGAAAATGGGTAA
*
28934266 TTTGGGTGTAAAAGAAAATGGGTTA
1 TTTGGGTGTAAAAGAAAATGGGTAA
28934291 TTTG
1 TTTG
28934295 CATGTTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (25 bp):
TTTGGGTGTAAAAGAAAATGGGTAA
Found at i:28949323 original size:29 final size:29
Alignment explanation
Indices: 28949286--28949345 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
28949276 ACTAATTAAA
28949286 TTAATTAACCTAAAATAACCTAATGGAAT
1 TTAATTAACCTAAAATAACCTAATGGAAT
* *
28949315 TTAATTAACCTAAGATATCCTAATGGAAT
1 TTAATTAACCTAAAATAACCTAATGGAAT
28949344 TT
1 TT
28949346 CCTATTCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (29 bp):
TTAATTAACCTAAAATAACCTAATGGAAT
Found at i:28953082 original size:29 final size:29
Alignment explanation
Indices: 28953019--28953086 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
28953009 TAATCAACCG
28953019 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
28953048 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
28953077 CGCACACTTA
1 CGCACACTTA
28953087 CCTTTTTCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:28953206 original size:175 final size:174
Alignment explanation
Indices: 28952908--28953236 Score: 613
Period size: 175 Copynumber: 1.9 Consensus size: 174
28952898 AACTCAAGGT
* *
28952908 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
28952973 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
28953038 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
28953082 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
1 ACTTACC-TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
28953147 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
65 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
* *
28953212 TACTTTAAACTCGCACACTTAGTGC
130 CACTTTAAACTCACACACTTAGTGC
28953237 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
174 7 0.05
175 143 0.95
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:28953228 original size:29 final size:30
Alignment explanation
Indices: 28953189--28953267 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
28953179 CTTAATAATC
28953189 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
28953219 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
28953248 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28953268 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:28959796 original size:21 final size:21
Alignment explanation
Indices: 28959739--28959780 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28959729 TCATTTTCTA
28959739 AAACCACTTGACCTTAGGGTC
1 AAACCACTTGACCTTAGGGTC
28959760 AAACCACTTGACCTTAGGGTC
1 AAACCACTTGACCTTAGGGTC
28959781 TTACCACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
AAACCACTTGACCTTAGGGTC
Found at i:28973701 original size:5 final size:6
Alignment explanation
Indices: 28973687--28973711 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28973677 GAGTTAGCAA
28973687 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
28973712 AATTGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:28979572 original size:22 final size:22
Alignment explanation
Indices: 28979547--28979591 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
28979537 ACTATATGTA
28979547 TTAATTTATAAT-ATAATTAATT
1 TTAATTTAT-ATCATAATTAATT
*
28979569 TTAATTTATATCATATTTAATT
1 TTAATTTATATCATAATTAATT
28979591 T
1 T
28979592 GGGTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTTATATCATAATTAATT
Found at i:28980002 original size:18 final size:19
Alignment explanation
Indices: 28979974--28980010 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28979964 GCATTCACAT
28979974 CTTTCCTCTCTTCTCTCCA
1 CTTTCCTCTCTTCTCTCCA
*
28979993 CTTT-CTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTCTCCA
28980011 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTCTCCA
Found at i:28980295 original size:21 final size:20
Alignment explanation
Indices: 28980250--28980295 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
28980240 TTGTTGGAAT
28980250 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
28980269 GCTTGAATTTAATTCGAA-TTA
1 GGTTGAATTTAA-TC-AATTTA
28980290 GGTTGA
1 GGTTGA
28980296 TTGCATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 7 0.32
21 10 0.45
22 2 0.09
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:28988145 original size:24 final size:24
Alignment explanation
Indices: 28988056--28988150 Score: 136
Period size: 24 Copynumber: 4.0 Consensus size: 24
28988046 CCCGAAATAG
* * *
28988056 TGAAAAGTTTGAAAAGGTTACTAA
1 TGAAAAGGTTGAAAAGGATACCAA
* *
28988080 TGAAAAGGTTGAAAAGGTTATCAA
1 TGAAAAGGTTGAAAAGGATACCAA
*
28988104 TGAAAAGGTCGAAAAGGATACCAA
1 TGAAAAGGTTGAAAAGGATACCAA
28988128 TGAAAAGGTTGAAAAGGATACCA
1 TGAAAAGGTTGAAAAGGATACCA
28988151 TTATATTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.47, C:0.07, G:0.24, T:0.21
Consensus pattern (24 bp):
TGAAAAGGTTGAAAAGGATACCAA
Found at i:28992760 original size:20 final size:20
Alignment explanation
Indices: 28992714--28992779 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
28992704 TATTTATAAT
* *
28992714 GATTTA-CAAAATTTCTAAG
1 GATTTACCAAAATATCCAAG
*
28992733 G-TTATACCAAAATATCCATG
1 GATT-TACCAAAATATCCAAG
* *
28992753 GATTTACCAACATATCTAAG
1 GATTTACCAAAATATCCAAG
28992773 GATTTAC
1 GATTTAC
28992780 TAAAGTTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.05
19 3 0.08
20 31 0.82
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (20 bp):
GATTTACCAAAATATCCAAG
Found at i:28992840 original size:20 final size:20
Alignment explanation
Indices: 28992801--28992860 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
28992791 AGGCTACTTG
*
28992801 GAAATTTTTGTAAATCCTTA
1 GAAATTTTGGTAAATCCTTA
*
28992821 GATATTTTGGTATAAT-CTTA
1 GAAATTTTGGTA-AATCCTTA
*
28992841 GAAATTTTGGTAAATTCTTA
1 GAAATTTTGGTAAATCCTTA
28992861 AGGTTTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.09
20 29 0.83
21 3 0.09
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (20 bp):
GAAATTTTGGTAAATCCTTA
Found at i:28992982 original size:20 final size:19
Alignment explanation
Indices: 28992939--28993052 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 19
28992929 AGTTAAAAAC
* *
28992939 CCTTAGAAATATTGGTAACT
1 CCTTA-AAATTTTGGTAAAT
*
28992959 CCTTGGAAATTTTGGTATAA-
1 CCTT-AAAATTTTGGTA-AAT
28992979 CCTTAAGAATTTTGGTAAAT
1 CCTTAA-AATTTTGGTAAAT
28992999 CCTTAAATATTTTGGTATAA-
1 CCTTAAA-ATTTTGGTA-AAT
28993019 CC-TACTAAATTTTGGTAAAT
1 CCTTA--AAATTTTGGTAAAT
28993039 CCTTAGAAATTTTG
1 CCTTA-AAATTTTG
28993053 ATATGCCAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
19 8 0.10
20 64 0.81
21 7 0.09
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (19 bp):
CCTTAAAATTTTGGTAAAT
Found at i:28992994 original size:40 final size:38
Alignment explanation
Indices: 28992945--28993052 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
28992935 AAACCCTTAG
* *
28992945 AAATATTGGTAACTCCTTGGAAATTTTGGTATAACCTTA-
1 AAATTTTGGTAAATCCTT-GAAATTTTGGTATAACC-TAC
*
28992984 AGAATTTTGGTAAATCCTTAAATATTTTGGTATAACCTAC
1 A-AATTTTGGTAAATCCTTGAA-ATTTTGGTATAACCTAC
28993024 TAAATTTTGGTAAATCCTTAGAAATTTTG
1 -AAATTTTGGTAAATCCTT-GAAATTTTG
28993053 ATATGCCAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
39 5 0.08
40 52 0.87
41 3 0.05
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (38 bp):
AAATTTTGGTAAATCCTTGAAATTTTGGTATAACCTAC
Found at i:28993120 original size:20 final size:20
Alignment explanation
Indices: 28993095--28993159 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
28993085 GGCACTAAGG
28993095 AAATCTCTAGAAATATTGGT
1 AAATCTCTAGAAATATTGGT
* * **
28993115 AAATCTTTCGAAGCATTGGT
1 AAATCTCTAGAAATATTGGT
* *
28993135 AAAT-TCTTAGCAATTTTGGT
1 AAATCTC-TAGAAATATTGGT
28993155 AAATC
1 AAATC
28993160 CTTAGATATT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (20 bp):
AAATCTCTAGAAATATTGGT
Found at i:28995593 original size:43 final size:43
Alignment explanation
Indices: 28995525--28995636 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 43
28995515 AACTAGTACA
** * * * *
28995525 ATGCCAACGTCCCAGACGTGATCTTACATGTAATCACATA-TCG
1 ATGCCAACGTCCCAGACAAGGTCTTACACGCAAACACA-AGTCG
28995568 ATGCC-ACTGTCCCAGACAAGGTCTTACACGCAAACACAAGTCG
1 ATGCCAAC-GTCCCAGACAAGGTCTTACACGCAAACACAAGTCG
**
28995611 ATGCCAACGTCCCAGACGTGGTCTTA
1 ATGCCAACGTCCCAGACAAGGTCTTA
28995637 AACGATAACG
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
42 3 0.05
43 53 0.91
44 2 0.03
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAAGGTCTTACACGCAAACACAAGTCG
Found at i:29001847 original size:43 final size:42
Alignment explanation
Indices: 29001780--29001950 Score: 172
Period size: 43 Copynumber: 4.0 Consensus size: 42
29001770 ACATAAGATT
* *
29001780 TCGATATGTGTTTTCGTGTAAGACCACATCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
* *
29001823 TCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TTGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
29001866 TCGTATT-TGATTT--GTGTAAGACC-CTGTCTGGGACAG-TGGCA
1 TCG-ATTGTG-TTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
* * * *
29001907 TCGATATTTGATTACATGTAAGACCACGTTTGGGACGTTGGCA
1 TCGAT-TGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
29001950 T
1 T
29001951 TGTACAAGTC
Statistics
Matches: 108, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
40 2 0.02
41 30 0.28
42 5 0.05
43 68 0.63
44 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (42 bp):
TCGATTGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:29001941 original size:84 final size:84
Alignment explanation
Indices: 29001795--29001950 Score: 201
Period size: 84 Copynumber: 1.9 Consensus size: 84
29001785 ATGTGTTTTC
* * *
29001795 GTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACA
1 GTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGACA
29001860 TTGGCATCGTATTTGATTT
66 TTGGCATCGTATTTGATTT
* * *
29001879 GTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATTTGATTACATGTAAGACCACGTTTGGG
1 GTGTAAGACCAC-ATCTGGGAC-GTTGGCATCGACT-TGTGATTACATGTAAGACCACGTCTGGG
*
29001941 ACGTTGGCAT
63 ACATTGGCAT
29001951 TGTACAAGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
83 2 0.03
84 59 0.95
85 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (84 bp):
GTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:29005359 original size:43 final size:43
Alignment explanation
Indices: 29005293--29005408 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 43
29005283 AACTAGTACA
* * * * *
29005293 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCACATA-TCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGCAAACACA-AGTCG
29005336 ATGCC-ACTATCCCAGACAG-GGTCTTACACGCAAACACAAGTCG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACACGCAAACACAAGTCG
*
29005379 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACATCCCAGACGTGGTCTTACACG
29005409 ATAACGCATG
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
42 4 0.06
43 55 0.89
44 3 0.05
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (43 bp):
ATGCCAACATCCCAGACGTGGTCTTACACGCAAACACAAGTCG
Found at i:29008096 original size:43 final size:43
Alignment explanation
Indices: 29008043--29008352 Score: 326
Period size: 43 Copynumber: 7.3 Consensus size: 43
29008033 TTTTAGAAAT
**
29008043 AAACGCCGCTATAGATCATGACCTTTAGTAGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
* * * * *
29008086 AAACACCGCTATAGATCAGGACTTTTAGCGGTGCTTTTTCCAT
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
*
29008129 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTAT--AC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTT-TCCAC
* * * * *
29008171 AAACGCCGCTATAGCTCAAGATCTTTAGCGGTGCTTATTCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
* * * * *
29008214 AAACACCAG-TATAGATCATGACTTTTAACGGTGCTTTTCCCAC
1 AAACGCC-GCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
* *
29008257 AAACGCCGCTATAGGTCATGA-CTTGTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATGACCTT-TAGCGGCGCTTTTTCCAC
* **
29008300 AAACGCCGCTATAGAACA-GACCTTTAGCGGC-AATTTTCACAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTC-CAC
*
29008342 AAACACCGCTA
1 AAACGCCGCTA
29008353 AAAACATATC
Statistics
Matches: 224, Mismatches: 35, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
41 5 0.02
42 59 0.26
43 158 0.71
44 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
Found at i:29008313 original size:86 final size:83
Alignment explanation
Indices: 29008043--29008352 Score: 336
Period size: 85 Copynumber: 3.6 Consensus size: 83
29008033 TTTTAGAAAT
** * *
29008043 AAACGCCGCTATAGATCATGACCTTTAGTAGCGCTTTTTCCACAAACACCGCTATAGATCAGGAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGC-TTTTCCACAAACGCCGCTATAGATCAAGAC
*
29008108 TTTTAGCGGTGCTTTTTCCAT
65 -TTTAGCGGTGC-TTTTCCAC
* ** *
29008129 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTATACAAACGCCGCTATAGCTCAAGATC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTATAGATCAAGA-C
29008194 TTTAGCGGTGCTTATTCCAC
65 TTTAGCGGTGCTT-TTCCAC
* * * * * *
29008214 AAACACCAG-TATAGATCATGACTTTTAACGGTGCTTTTCCCACAAACGCCGCTATAGGTCATGA
1 AAACGCC-GCTATAGATCATGACCTTTAGCGGCGCTTTT-CCACAAACGCCGCTATAGATCAAGA
*
29008278 CTTGTAGCGGCGCTTTTCCCAC
64 CTT-TAGCGGTGCTTTT-CCAC
* ** *
29008300 AAACGCCGCTATAGAACA-GACCTTTAGCGGCAATTTTCACACAAACACCGCTA
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTC-CACAAACGCCGCTA
29008353 AAAACATATC
Statistics
Matches: 189, Mismatches: 27, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
84 3 0.02
85 104 0.55
86 82 0.43
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (83 bp):
AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTATAGATCAAGACT
TTAGCGGTGCTTTTCCAC
Found at i:29008328 original size:128 final size:127
Alignment explanation
Indices: 29008043--29008352 Score: 392
Period size: 128 Copynumber: 2.4 Consensus size: 127
29008033 TTTTAGAAAT
** *
29008043 AAACGCCGCTATAGATCATGACCTTTAGTAGCGCTTTTTCCACAAACACCGCTATAGATCAGGAC
1 AAACGCCGCTATAGATCA-GACCTTTAGCGGCGCTTATTCCACAAACACCGCTATAGATCAGGAC
* * * *
29008108 TTTTAGCGGTGCTTTTTCCATAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTATAC
65 TTTTAACGGTGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTACAC
* * * *
29008171 AAACGCCGCTATAGCTCAAGATCTTTAGCGGTGCTTATTCCACAAACACCAG-TATAGATCATGA
1 AAACGCCGCTATAGATC-AGACCTTTAGCGGCGCTTATTCCACAAACACC-GCTATAGATCAGGA
* * *
29008235 CTTTTAACGGTGCTTTTCCCACAAACGCCGCTATAGGTCATGA-CTTGTAGCGGCGCTTTTCCCA
64 CTTTTAACGGTGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTT-TAGCGGCGCTTTT-ACA
29008299 C
127 C
* **
29008300 AAACGCCGCTATAGAACAGACCTTTAGCGGCAATT-TTCACACAAACACCGCTA
1 AAACGCCGCTATAGATCAGACCTTTAGCGGCGCTTATTC-CACAAACACCGCTA
29008353 AAAACATATC
Statistics
Matches: 156, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
127 7 0.04
128 130 0.83
129 19 0.12
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (127 bp):
AAACGCCGCTATAGATCAGACCTTTAGCGGCGCTTATTCCACAAACACCGCTATAGATCAGGACT
TTTAACGGTGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTACAC
Found at i:29009948 original size:70 final size:71
Alignment explanation
Indices: 29009805--29009948 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
29009795 TGACCTCTAC
29009805 AAAAAAAATTCAACCACATTTAATAGTTCTTTAAAAATCTTGAACCAAAAAAACCTAAAAAAAAG
1 AAAAAAAATTCAACCACATTTAATAGTTCTTTAAAAATCTTGAACCAAAAAAACCTAAAAAAAAG
29009870 TTTAAA
66 TTTAAA
29009876 AAAAAAAATTCAACCACATTTAATAGTTCTTTAAAAATCTTGAACCAAAAAAACCTAAAAAAAAG
1 AAAAAAAATTCAACCACATTTAATAGTTCTTTAAAAATCTTGAACCAAAAAAACCTAAAAAAAAG
29009941 TTTAAA
66 TTTAAA
29009947 AA
1 AA
29009949 CTCAAGCAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.57, C:0.14, G:0.04, T:0.25
Consensus pattern (71 bp):
AAAAAAAATTCAACCACATTTAATAGTTCTTTAAAAATCTTGAACCAAAAAAACCTAAAAAAAAG
TTTAAA
Found at i:29011555 original size:22 final size:22
Alignment explanation
Indices: 29011527--29011613 Score: 67
Period size: 22 Copynumber: 4.0 Consensus size: 22
29011517 CCCTAACCCG
*
29011527 ACCCCTAAATCCCTAACTCTTA
1 ACCCCTAAATCCCTAACCCTTA
*
29011549 ACCCCTAATAT--CTAACCCCTAA
1 ACCCCTAA-ATCCCTAA-CCCTTA
*
29011571 ACCCCT-AACCCCTAACTCC-TA
1 ACCCCTAAATCCCTAAC-CCTTA
* *
29011592 AACCTTAAATCCC-AACCCTTA
1 ACCCCTAAATCCCTAACCCTTA
29011613 A
1 A
29011614 ACCATAATCT
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
20 3 0.06
21 17 0.33
22 29 0.57
23 2 0.04
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.23
Consensus pattern (22 bp):
ACCCCTAAATCCCTAACCCTTA
Found at i:29011575 original size:8 final size:7
Alignment explanation
Indices: 29011527--29011592 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
29011517 CCCTAACCCG
29011527 ACCCCTAA
1 ACCCCT-A
*
29011535 ATCCCTA
1 ACCCCTA
* *
29011542 ACTCTTA
1 ACCCCTA
29011549 ACCCCTA
1 ACCCCTA
***
29011556 ATATCTA
1 ACCCCTA
29011563 ACCCCTAA
1 ACCCCT-A
29011571 ACCCCTA
1 ACCCCTA
29011578 ACCCCTA
1 ACCCCTA
*
29011585 ACTCCTA
1 ACCCCTA
29011592 A
1 A
29011593 ACCTTAAATC
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
7 32 0.73
8 12 0.27
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (7 bp):
ACCCCTA
Found at i:29011580 original size:15 final size:15
Alignment explanation
Indices: 29011560--29011616 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
29011550 CCCCTAATAT
29011560 CTAACCCCTAAACCC
1 CTAACCCCTAAACCC
*
29011575 CTAACCCCT-AACTC
1 CTAACCCCTAAACCC
* * *
29011589 CTAAACCTTAAATCC
1 CTAACCCCTAAACCC
*
29011604 C-AACCCTTAAACC
1 CTAACCCCTAAACC
29011617 ATAATCTCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
14 21 0.62
15 13 0.38
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (15 bp):
CTAACCCCTAAACCC
Found at i:29011870 original size:15 final size:14
Alignment explanation
Indices: 29011845--29011885 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
29011835 TGTCTAACCC
29011845 CTAAA-CCCTAAAT
1 CTAAATCCCTAAAT
29011858 CTTAAATCCCT-AAT
1 C-TAAATCCCTAAAT
29011872 CTATAATCCCTAAA
1 CTA-AATCCCTAAA
29011886 CCCATACTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.12
14 15 0.62
15 6 0.25
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.29
Consensus pattern (14 bp):
CTAAATCCCTAAAT
Found at i:29012308 original size:41 final size:41
Alignment explanation
Indices: 29012251--29012398 Score: 183
Period size: 41 Copynumber: 3.6 Consensus size: 41
29012241 AAGCCCCCAA
* * * *
29012251 CATTAACGGCGCTTTTTCAAAAATGCTGCTAAAACCCCGAG
1 CATTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAG
* *
29012292 CATTAGCGGTACTTTTT-AGAAAACGCCGCTAAAGCCCCGAG
1 CATTAGCGGCACTTTTTCA-AAAACGCCGCTAAAACCCCGAG
*
29012333 CATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAG
1 CATTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAG
* *
29012374 CATTACCGACACTTTTT-AGAAAACG
1 CATTAGCGGCACTTTTTCA-AAAACG
29012399 ACGTCGTTGG
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.02
41 89 0.97
42 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (41 bp):
CATTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAG
Found at i:29012349 original size:82 final size:82
Alignment explanation
Indices: 29012239--29012398 Score: 248
Period size: 82 Copynumber: 2.0 Consensus size: 82
29012229 CCAATTAAGA
* * * **
29012239 TAAAGCCCCCAACATTAACGGCGCTTTTTCAAAAATGCTGCTAAAACCCCGAGCATTAGCGGTAC
1 TAAAGCCCCCAACATTAACGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCATTACCGACAC
29012304 TTTTTAGAAAACGCCGC
66 TTTTTAGAAAACGCCGC
* * *
29012321 TAAAGCCCCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCATTACCGACAC
1 TAAAGCCCCCAACATTAACGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCATTACCGACAC
29012386 TTTTTAGAAAACG
66 TTTTTAGAAAACG
29012399 ACGTCGTTGG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (82 bp):
TAAAGCCCCCAACATTAACGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCATTACCGACAC
TTTTTAGAAAACGCCGC
Found at i:29018289 original size:50 final size:51
Alignment explanation
Indices: 29018228--29018367 Score: 210
Period size: 51 Copynumber: 2.8 Consensus size: 51
29018218 TATCATTCGA
* * * * *
29018228 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAA-CTTTCTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAGCCTTCCGG
*
29018278 TTCACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAGCCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAGCCTTCCGG
*
29018329 TACACATAGTAGCCTGCACATAGTACTACACATGTGACC
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACC
29018368 GTTATCTATC
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 38 0.47
51 43 0.53
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAGCCTTCCGG
Found at i:29018350 original size:51 final size:50
Alignment explanation
Indices: 29018228--29018411 Score: 208
Period size: 51 Copynumber: 3.6 Consensus size: 50
29018218 TATCATTCGA
* * * * *
29018228 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTCTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAACCTTCCGG
*
29018278 TTCACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAGCCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAA-CCTTCCGG
* ** * *
29018329 TACACATAGTAGCCTGCACATAGTACTACACATGTGACCGTTATCTAT-CGA
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACC-AAACCT-TCCGG
** *
29018380 TACACGTAGTAGCCTGCATTTAGTACTTCACA
1 TACACGTAGTAGCCTGCACATAGTACTACACA
29018412 CGTGTTTACA
Statistics
Matches: 115, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
50 38 0.33
51 75 0.65
52 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAACCTTCCGG
Found at i:29020541 original size:56 final size:56
Alignment explanation
Indices: 29020481--29020596 Score: 232
Period size: 56 Copynumber: 2.1 Consensus size: 56
29020471 CTCGAGTATC
29020481 GATACTCGAGGGATAAATATCGATACTTTATCCTGTTGTACCGATATTTTTCGATA
1 GATACTCGAGGGATAAATATCGATACTTTATCCTGTTGTACCGATATTTTTCGATA
29020537 GATACTCGAGGGATAAATATCGATACTTTATCCTGTTGTACCGATATTTTTCGATA
1 GATACTCGAGGGATAAATATCGATACTTTATCCTGTTGTACCGATATTTTTCGATA
29020593 GATA
1 GATA
29020597 GGTTTTTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (56 bp):
GATACTCGAGGGATAAATATCGATACTTTATCCTGTTGTACCGATATTTTTCGATA
Found at i:29022344 original size:19 final size:20
Alignment explanation
Indices: 29022303--29022344 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29022293 AGTGTTACAA
*
29022303 GTAAATCTTTAAAAATGTTG
1 GTAAATCATTAAAAATGTTG
*
29022323 GTAAATCATTAGAAAT-TTG
1 GTAAATCATTAAAAATGTTG
29022342 GTA
1 GTA
29022345 TGACGGAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (20 bp):
GTAAATCATTAAAAATGTTG
Found at i:29022452 original size:40 final size:40
Alignment explanation
Indices: 29022384--29022503 Score: 129
Period size: 40 Copynumber: 3.0 Consensus size: 40
29022374 GATACTCAGA
* *
29022384 AAATTTTTAGAAATTTTGAG-AAATCCTTAAAAATTTTGGT
1 AAATTCTTAGATATTTT-AGTAAATCCTTAAAAATTTTGGT
* **
29022424 -AATTCCTTAGATATTTTAGTATAA-CCTTAGAAATTTTAAT
1 AAATT-CTTAGATATTTTAGTA-AATCCTTAAAAATTTTGGT
* *
29022464 AAATTCTTAGATATTTTGGTAAATCCTTAAAAATATTGGT
1 AAATTCTTAGATATTTTAGTAAATCCTTAAAAATTTTGGT
29022504 TTCATTTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
39 8 0.12
40 51 0.78
41 6 0.09
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.43
Consensus pattern (40 bp):
AAATTCTTAGATATTTTAGTAAATCCTTAAAAATTTTGGT
Found at i:29022502 original size:20 final size:20
Alignment explanation
Indices: 29022390--29022503 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
29022380 CAGAAAATTT
29022390 TTAGAAATTTTGAG-AAATCC
1 TTAGAAATTTTG-GTAAATCC
* *
29022410 TTAAAAATTTTGGTAATTCC
1 TTAGAAATTTTGGTAAATCC
* *
29022430 TTAGATATTTTAGTATAA-CC
1 TTAGAAATTTTGGTA-AATCC
** *
29022450 TTAGAAATTTTAATAAATTC
1 TTAGAAATTTTGGTAAATCC
*
29022470 TTAGATATTTTGGTAAATCC
1 TTAGAAATTTTGGTAAATCC
* *
29022490 TTAAAAATATTGGT
1 TTAGAAATTTTGGT
29022504 TTCATTTTTT
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
19 3 0.04
20 71 0.95
21 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (20 bp):
TTAGAAATTTTGGTAAATCC
Found at i:29041924 original size:13 final size:13
Alignment explanation
Indices: 29041888--29041917 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
29041878 AGGTGATTTA
29041888 TATATATCTA-TC
1 TATATATCTATTC
29041900 TATATATCTATTC
1 TATATATCTATTC
29041913 TATAT
1 TATAT
29041918 TATTATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATCTATTC
Found at i:29044286 original size:20 final size:20
Alignment explanation
Indices: 29044261--29044300 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29044251 TTTTCCGGAA
*
29044261 ATTTCTGAAAAATGATTTAC
1 ATTTCTGAAAAATAATTTAC
*
29044281 ATTTCTGGAAAATAATTTAC
1 ATTTCTGAAAAATAATTTAC
29044301 TGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
ATTTCTGAAAAATAATTTAC
Found at i:29044423 original size:20 final size:20
Alignment explanation
Indices: 29044398--29044436 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29044388 GTTATTACAT
29044398 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
29044418 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
29044437 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:29045589 original size:32 final size:32
Alignment explanation
Indices: 29045545--29045605 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
29045535 TGTCAATCAT
29045545 TTCAATAACTAACAAGCTTAAAACATAATAAA
1 TTCAATAACTAACAAGCTTAAAACATAATAAA
*
29045577 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATAACTAACAAGCTTAAAACATAAT
29045606 CAATATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATAACTAACAAGCTTAAAACATAATAAA
Found at i:29045612 original size:27 final size:27
Alignment explanation
Indices: 29045546--29045632 Score: 93
Period size: 27 Copynumber: 3.0 Consensus size: 27
29045536 GTCAATCATT
*
29045546 TCAATAACTAACAAGCTTAAAACATAATAAA
1 TCAATATCTAACAAGCTTAAAAC---AT-AA
29045577 TTCAATATCTAACAAGCTTAAAACATAA
1 -TCAATATCTAACAAGCTTAAAACATAA
** *
29045605 TCAATATCTAACAAATTTAAGACATAA
1 TCAATATCTAACAAGCTTAAAACATAA
29045632 T
1 T
29045633 AATTTCAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
27 25 0.49
28 2 0.04
29 2 0.04
32 22 0.43
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.28
Consensus pattern (27 bp):
TCAATATCTAACAAGCTTAAAACATAA
Found at i:29058591 original size:5 final size:5
Alignment explanation
Indices: 29058583--29058607 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29058573 TTTCATCCGA
29058583 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
29058608 AGCCGATTTG
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:29061798 original size:37 final size:37
Alignment explanation
Indices: 29061757--29061838 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
29061747 AAATATTTAT
* *
29061757 TAATCAATGTTCAAACTTTGAACATGCTTTATTAAAC
1 TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
*
29061794 TAATCAATGTTAAAACTTTGAACATGCTTTAATGAAC
1 TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
29061831 TAATCAAT
1 TAATCAAT
29061839 ATATTTATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.37
Consensus pattern (37 bp):
TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
Found at i:29061919 original size:33 final size:33
Alignment explanation
Indices: 29061881--29061956 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
29061871 TTAAAACTTG
*
29061881 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
29061914 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
29061947 AATTATACAT
1 AATTATACAT
29061957 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:29064430 original size:92 final size:91
Alignment explanation
Indices: 29064266--29064474 Score: 260
Period size: 92 Copynumber: 2.3 Consensus size: 91
29064256 TTGATTTTAG
* * * * *
29064266 TAAATCCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTTT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
29064331 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
29064358 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
29064422 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
29064450 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
29064475 GTTATAATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 69 0.68
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:29064437 original size:24 final size:25
Alignment explanation
Indices: 29064402--29064449 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
29064392 TTATGAAATT
29064402 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
29064426 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
29064450 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:29064603 original size:66 final size:64
Alignment explanation
Indices: 29064528--29064738 Score: 187
Period size: 66 Copynumber: 3.4 Consensus size: 64
29064518 AAATATATTT
29064528 AATATTAATTATTTCAAATTTTCATTTATAATATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTATAATATCATATATTATGATTTGAGTAAATTCATATAA
*
29064593 G
64 A
* * * **
29064594 AATATTAATTATTAAGAATTTTA-TTA-AAT-T-ATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTATAATATCATATATTATGATTTGAGTAAATTCATATAAA
*
29064648 AATAATAATTATGTT-AATTTATATTT-TACAGTATCATATATTATGATTTGAGTAAATTCATAT
1 AATATTAATTAT-TTAAATTT-TATTTATA-A-TATCATATATTATGATTTGAGTAAATTCATAT
29064711 AAA
62 AAA
*
29064714 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
29064739 AAATTATATA
Statistics
Matches: 114, Mismatches: 13, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
53 5 0.04
54 13 0.11
55 8 0.07
56 2 0.02
57 3 0.03
58 2 0.02
59 8 0.07
60 8 0.07
61 8 0.07
62 2 0.02
63 5 0.04
64 4 0.04
65 7 0.06
66 34 0.30
67 5 0.04
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTTTATTTATAATATCATATATTATGATTTGAGTAAATTCATATAAA
Found at i:29064627 original size:59 final size:59
Alignment explanation
Indices: 29064564--29064747 Score: 164
Period size: 59 Copynumber: 3.1 Consensus size: 59
29064554 TATAATATCA
*
29064564 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAAAT
* * * * * * * * *
29064623 TATA-TAT--TTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-CAGTAT
1 TATATTATGATTTGAGTA-AAT-TCATATAAAAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
29064682 CATATATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAAAT
29064743 TATAT
1 TATAT
29064748 ATTTTAATTA
Statistics
Matches: 93, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
56 6 0.06
57 11 0.12
58 9 0.10
59 19 0.20
60 8 0.09
61 14 0.15
62 9 0.10
63 11 0.12
64 6 0.06
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (59 bp):
TATATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAAAT
Found at i:29064628 original size:120 final size:120
Alignment explanation
Indices: 29064490--29064782 Score: 486
Period size: 120 Copynumber: 2.4 Consensus size: 120
29064480 AATTATTTTA
* * *
29064490 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
*
29064553 TTATA-A-TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TT-TACAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAG
29064610 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
29064675 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAG
29064730 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
29064783 TAAATATGAT
Statistics
Matches: 165, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
118 2 0.01
119 10 0.06
120 151 0.92
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAG
Found at i:29064650 original size:15 final size:15
Alignment explanation
Indices: 29064615--29064666 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29064605 TTAAGAATTT
*
29064615 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29064629 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29064643 TATTTAATAATAAT-
1 TATTTAATTATAATA
29064657 TATGTTAATT
1 TAT-TTAATT
29064667 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29064765 original size:16 final size:16
Alignment explanation
Indices: 29064744--29064785 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29064734 TTATTAAATT
*
29064744 ATATATTTTAATTATA
1 ATATATTTTAATAATA
29064760 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
29064775 AT-TATGTTTAA
1 ATATAT-TTTAA
29064786 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:29064770 original size:15 final size:15
Alignment explanation
Indices: 29064735--29064776 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29064725 TTAAGAATTT
*
29064735 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29064749 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29064763 TATTTAATAATAAT
1 TATTTAATTATAAT
29064777 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29064897 original size:157 final size:157
Alignment explanation
Indices: 29064719--29065035 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
29064709 ATAAAAATAT
*
29064719 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
29064784 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
29064849 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
29064876 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
29064941 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
29065006 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
29065033 TAA
1 TAA
29065036 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:29064916 original size:18 final size:17
Alignment explanation
Indices: 29064888--29064922 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29064878 ATTATTAAGA
*
29064888 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29064905 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29064923 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29065179 original size:16 final size:16
Alignment explanation
Indices: 29065158--29065209 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
29065148 GATTTGCTAT
29065158 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
29065174 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
* *
29065190 TACACATCTAATTCAA
1 TACACCTCTAATCCAA
29065206 TACA
1 TACA
29065210 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:29067315 original size:33 final size:33
Alignment explanation
Indices: 29067278--29067362 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
29067268 TACTCTATAT
*
29067278 TTGGTGTGTTGGTTGGATTAGCTCTTA-TGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTC-GAGTGAGCA
* * *
29067311 TTGGTGTGATGGATGGATTGGCTCGAGTGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCGAGTGAGCA
*
29067344 TCTGGTATGTTTGGTTGGA
1 T-TGGTGTG-TTGGTTGGA
29067363 CTAATGATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
32 1 0.02
33 28 0.67
34 6 0.14
35 7 0.17
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.39
Consensus pattern (33 bp):
TTGGTGTGTTGGTTGGATTAGCTCGAGTGAGCA
Found at i:29070391 original size:11 final size:11
Alignment explanation
Indices: 29070373--29070407 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
29070363 TTGCTCATAC
29070373 TAATTTTTATA
1 TAATTTTTATA
*
29070384 TTATTTTTATA
1 TAATTTTTATA
*
29070395 TAATTTTAATA
1 TAATTTTTATA
29070406 TA
1 TA
29070408 TATAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:29070640 original size:11 final size:11
Alignment explanation
Indices: 29070623--29070661 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
29070613 TAATAACAAT
29070623 AAAATAATAGC
1 AAAATAATAGC
* *
29070634 AACATAATAGT
1 AAAATAATAGC
*
29070645 AAAATGATAGC
1 AAAATAATAGC
29070656 AAAATA
1 AAAATA
29070662 GGGAGAAAGC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.21
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:29070640 original size:22 final size:22
Alignment explanation
Indices: 29070615--29070657 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29070605 TATCTAAATA
29070615 ATAACAATAAAATAATAGCAAC
1 ATAACAATAAAATAATAGCAAC
* * *
29070637 ATAATAGTAAAATGATAGCAA
1 ATAACAATAAAATAATAGCAA
29070658 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAATAGCAAC
Found at i:29075207 original size:18 final size:16
Alignment explanation
Indices: 29075174--29075206 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29075164 AATCAAAGTA
29075174 AATAAAATCTATATAT
1 AATAAAATCTATATAT
*
29075190 AATAAAATCTAAATAT
1 AATAAAATCTATATAT
29075206 A
1 A
29075207 TCTCTACTAA
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:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATCTATATAT
Found at i:29075917 original size:36 final size:36
Alignment explanation
Indices: 29075877--29075952 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
29075867 AGCATTGATA
29075877 GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
1 GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
* *
29075913 GCTATCTTGAGTATCATTTGTTAAATCTGATGTAAT
1 GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
29075949 GCTA
1 GCTA
29075953 AACGATGTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (36 bp):
GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
Found at i:29075967 original size:36 final size:35
Alignment explanation
Indices: 29075884--29075967 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
29075874 ATAGCTATCT
* *
29075884 TGAGTATCATTTATTAAACCTGATGTAATGCTATC
1 TGAGTACCATTTATTAAACCTGATGTAATGCTAAC
* * *
29075919 TTGAGTATCATTTGTTAAATCTGATGTAATGCTAAAC
1 -TGAGTACCATTTATTAAACCTGATGTAATGCT-AAC
29075956 -GATGTACCATTT
1 TGA-GTACCATTT
29075968 CACATGTGCG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 2 0.05
36 38 0.90
37 2 0.05
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (35 bp):
TGAGTACCATTTATTAAACCTGATGTAATGCTAAC
Found at i:29081905 original size:22 final size:22
Alignment explanation
Indices: 29081873--29081924 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
29081863 CCTTTTTAGG
* *
29081873 TATTTTCTTAATAGTTAAAAAA
1 TATTTTTTTAACAGTTAAAAAA
29081895 TATTTTTTTAACAGTTAAAAAA
1 TATTTTTTTAACAGTTAAAAAA
29081917 TATTTTTT
1 TATTTTTT
29081925 AACTGGTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTTTTTTAACAGTTAAAAAA
Found at i:29087785 original size:62 final size:59
Alignment explanation
Indices: 29087677--29087793 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
29087667 ATCACTTTAA
* * * *
29087677 TATTAAATTAATATAATATTTATTAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
*
29087736 TATTAAAATAATAGAATGTTTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATTTAT-T--AAGATAAACATTAAATTAAATTTAATATTAA
29087794 GAAAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
60 1 0.02
62 29 0.58
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:29089473 original size:15 final size:15
Alignment explanation
Indices: 29089449--29089480 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29089439 TATGCATGAA
*
29089449 AAATATAAAAGACAT
1 AAATACAAAAGACAT
29089464 AAATACAAAAGACAT
1 AAATACAAAAGACAT
29089479 AA
1 AA
29089481 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:29092830 original size:24 final size:24
Alignment explanation
Indices: 29092798--29092845 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29092788 CGTATGACAC
29092798 TTGTTAAATTCCACTAAGTAAGAT
1 TTGTTAAATTCCACTAAGTAAGAT
29092822 TTGTTAAATTCCACTAAGTAAGAT
1 TTGTTAAATTCCACTAAGTAAGAT
29092846 GAATCATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (24 bp):
TTGTTAAATTCCACTAAGTAAGAT
Found at i:29093776 original size:27 final size:27
Alignment explanation
Indices: 29093736--29093979 Score: 181
Period size: 27 Copynumber: 9.1 Consensus size: 27
29093726 ACACAACATC
29093736 AAAGAATAGCCTTTGTGGCAAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* *
29093763 AAAGAATAGTCTTTGTGG-AAAATCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * *
29093789 AAAGAATAGTCTTTGTAGCGAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * *
29093816 GAAGGATAGCCTTTGTGGCAAACTCTC
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * * * *
29093843 AAAGGATAACCTTTCTAGCAAACTTTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * ** *
29093870 AAAGAATAACCTTAGTGAAAAACTTTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
** * * *
29093897 AAAGGAAT-GCCTCAGTGGCGAACTTTAA
1 AAA-GAATAGCCTTTGTGGCAAACTCT-G
**
29093925 AAAGAAT-GCCTCAGTGGCAAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * *
29093951 AAAGGGAT-GCCTTTGTGGCAGATTCTG
1 AAA-GAATAGCCTTTGTGGCAAACTCTG
29093978 AA
1 AA
29093980 TGGAACGATT
Statistics
Matches: 176, Mismatches: 37, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
26 27 0.15
27 142 0.81
28 7 0.04
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (27 bp):
AAAGAATAGCCTTTGTGGCAAACTCTG
Found at i:29101552 original size:22 final size:21
Alignment explanation
Indices: 29101501--29101552 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
29101491 ATCGCTTAAT
*
29101501 GTCTTGAGACTTATCAAGCTA
1 GTCTTGAGACTAATCAAGCTA
* *
29101522 GTCTCGAGAC-AACTCAATCTA
1 GTCTTGAGACTAA-TCAAGCTA
29101543 GGTCTTGAGA
1 -GTCTTGAGA
29101553 AAAAATGATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 16 0.64
22 8 0.32
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (21 bp):
GTCTTGAGACTAATCAAGCTA
Found at i:29102233 original size:23 final size:21
Alignment explanation
Indices: 29102207--29102257 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
29102197 AAAGGTGACT
* *
29102207 TTTTTTCGATTTTTTTTATTTTC
1 TTTTTTC-ATTTCTGTTA-TTTC
29102230 TTTTATTCATTTCTGTTATTTC
1 TTTT-TTCATTTCTGTTATTTC
29102252 TTTTTT
1 TTTTTT
29102258 TCTTTCCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 8 0.32
23 12 0.48
24 3 0.12
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTTTCATTTCTGTTATTTC
Found at i:29105440 original size:109 final size:109
Alignment explanation
Indices: 29105234--29105766 Score: 739
Period size: 109 Copynumber: 4.9 Consensus size: 109
29105224 TTTTTTTTAA
* * *
29105234 AAAATGAGGCGATATTTTGCGTTTGGAAAGTCGAGAAAACGTTCCCTAATGTGTGCTGGGTTTCG
1 AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAA--TGTGCTGGGTTTCG
* * *
29105299 ATTTTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAAAATTTC
64 ATTTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTC
* * *
29105345 AAAATAAGGCAATGTTTTGCGTCTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
1 AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
*
29105410 TTTTCTCGCTCGACCAAATAGCCAAATATCCTTTTAAAAATTTC
66 TTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTC
* * * * *
29105454 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAATGCGCTGGGTTTCAAT
1 AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
*
29105519 TTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTA
66 TTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTC
* * * * *
29105563 AAAACGAGGCAATATTTTGCATGTAGAAATTCGAGAAAATGTGCCCTAATGTGCTGGG-TTCTGA
1 AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC-GA
* *
29105627 TTTTTCTTGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTT
65 TTTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTC
* * * * * *
29105672 AAAACGAGGTAATATTTTGTGTTTGGAAACTCGAGAAAACGTGCCCTAATGCGTTGGGTTTCGA-
1 AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
* *
29105736 TTTT-TCGTTGGACCAAATAGCCAAATATCCT
66 TTTTCTCGCTCGACCAAATAGCCAAATATCCT
29105767 CTTATATCTT
Statistics
Matches: 384, Mismatches: 36, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
107 24 0.06
108 7 0.02
109 307 0.80
110 3 0.01
111 43 0.11
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (109 bp):
AAAATGAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
TTTTCTCGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTC
Found at i:29108115 original size:227 final size:226
Alignment explanation
Indices: 29107775--29108505 Score: 864
Period size: 227 Copynumber: 3.2 Consensus size: 226
29107765 AATATAGCGT
* * * * * *
29107775 TTTGGTCTAGATGTATACTAGAATTAGTGGCGA-TTATAGGCAAACGCCGCTAAAGAAAGTATTA
1 TTTGGTCTTGAGGTATACTAGAATTAGTGGC-ACTTATGGGAAAACGCCGCTAAGGATAGTATTA
* * * * * * *
29107839 GCGGCGATCGCCAAACGCGCCGCAACATATCTTAACCAAAATGCAGAGTTTGGTTTTTATGTATA
65 GCGGCGGTCGTCAAAAGCGCCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATA
* * *
29107904 TTAGAATTAGTGGCGCATATGAAAAAACGCTGCTAAAGTA-AGTATTAGCGGCGATTTGTGAAAA
130 TTAGAATTAGTGGCGCTTATGAGAAAACGCTGCTAAAGCATAGTATTAGCGGCGATTTGTGAAAA
29107968 GCGCCACAAAATATATTAACCAAAACGCAGAG
195 GCGCCACAAAATATATTAACCAAAACGCAGAG
* * *
29108000 TTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGGGAAAACGCTGCTAACGGATAGTATTA
1 TTTGGTCTTGAGGTATACTAGAATTAGTGGCACTTATGGGAAAACGCCGCTAA-GGATAGTATTA
* *
29108065 GTGGCGTGTCGTCAAAAGCGCCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTAT
65 GCGGCG-GTCGTCAAAAGCGCCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTAT
* * * * * * * *
29108130 ACTAGAATTAGTGGCGCTTATGGGAAAATGCCGCTAACGCATAGTATTAGTGGCG-TGTCGTCAA
129 ATTAGAATTAGTGGCGCTTATGAGAAAACGCTGCTAAAGCATAGTATTAGCGGCGAT-TTGTGAA
* * *
29108194 AA-CGCCGCAACATATCTTAACCAAAACGCAGAG
193 AAGCGCCACAAAATATATTAACCAAAACGCAGAG
* ** * *
29108227 TTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATTCGAAAACGCCGTTAATGCATAGTATTA
1 TTTGGTCTTGAGGTATACTAGAATTAGTGGCACTTATGGGAAAACGCCGCTAA-GGATAGTATTA
* * *
29108292 GCGGCGCGTCGTCAGAAGCGCCACAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTAT
65 GCGGCG-GTCGTCAAAAGCGCCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTAT
* *
29108357 ATTAGAATTAGTGGCGCTTATGAGAAAACGCTGCTAATGCATAGTATTAGCGGC-ACTTG-GTAG
129 ATTAGAATTAGTGGCGCTTATGAGAAAACGCTGCTAAAGCATAGTATTAGCGGCGATTTGTG-A-
* * * *
29108420 AAAGCGCCTCAAAATATTTTAACAAAAACGCA-ATCC
192 AAAGCGCCACAAAATATATTAACCAAAACGCAGA--G
* * * * *
29108456 TTTGGTCTTAATGTATACTAGCAGTAGTGGCACTTACGGGAAAACGCCGC
1 TTTGGTCTTGAGGTATACTAGAATTAGTGGCACTTATGGGAAAACGCCGC
29108506 GAAAACATAT
Statistics
Matches: 428, Mismatches: 67, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
225 45 0.11
226 17 0.04
227 282 0.66
228 43 0.10
229 41 0.10
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (226 bp):
TTTGGTCTTGAGGTATACTAGAATTAGTGGCACTTATGGGAAAACGCCGCTAAGGATAGTATTAG
CGGCGGTCGTCAAAAGCGCCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATAT
TAGAATTAGTGGCGCTTATGAGAAAACGCTGCTAAAGCATAGTATTAGCGGCGATTTGTGAAAAG
CGCCACAAAATATATTAACCAAAACGCAGAG
Found at i:29108118 original size:114 final size:114
Alignment explanation
Indices: 29107743--29108526 Score: 846
Period size: 114 Copynumber: 6.9 Consensus size: 114
29107733 TACTATCAAA
* *** * * * * *
29107743 CGCCGCAAAATCTCTTAACCAAAATATAGCGTTTTGGTCTAGATGTATACTAGAATTAGTGGCGA
1 CGCCGCAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAGAATTAGTGGCGC
* * * * * * *
29107808 TTATAGGCAAACGCCGCTAAAG-AAAGTATTAGCGGCG-ATCGCCAAACG
65 TTATGGGAAAACGCCGCTAACGCATAGTATTAGCGGCGTGTCGTCAAAAG
* * * * * *
29107856 CGCCGCAACATATCTTAACCAAAATGCAGAGTTTGGTTTTTATGTATATTAGAATTAGTGGCGCA
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
** * * * * *
29107921 TATGAAAAAACGCTGCTAAAGTA-AGTATTAGCGGCGAT-TTGTGAAAAG
66 TATGGGAAAACGCCGCTAACGCATAGTATTAGCGGCG-TGTCGTCAAAAG
* *
29107969 CGCCACAAAATATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * *
29108034 TATGGGAAAACGCTGCTAACGGATAGTATTAGTGGCGTGTCGTCAAAAG
66 TATGGGAAAACGCCGCTAACGCATAGTATTAGCGGCGTGTCGTCAAAAG
* *
29108083 CGCCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
29108148 TATGGGAAAATGCCGCTAACGCATAGTATTAGTGGCGTGTCGTCAAAA-
66 TATGGGAAAACGCCGCTAACGCATAGTATTAGCGGCGTGTCGTCAAAAG
* *
29108196 CGCCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCACT
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
** * * * *
29108261 TATTCGAAAACGCCGTTAATGCATAGTATTAGCGGCGCGTCGTCAGAAG
66 TATGGGAAAACGCCGCTAACGCATAGTATTAGCGGCGTGTCGTCAAAAG
* *
29108310 CGCCACAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * * * *
29108375 TATGAGAAAACGCTGCTAATGCATAGTATTAGCGGCACT-TGGT-AGAAAG
66 TATGGGAAAACGCCGCTAACGCATAGTATTAGCGGC-GTGTCGTCA-AAAG
* * * * * * * * * *
29108424 CGCCTCAAAATATTTTAACAAAAACGCA-ATCCTTTGGTCTTAATGTATACTAGCAGTAGTGGCA
1 CGCCGCAAAATATCTTAACCAAAACGCAGA--GTTTGGTCTTGAGGTATATTAGAATTAGTGGCG
* * ** *
29108488 CTTACGGGAAAACGCCGCGAAAACATATTATTAGCGGCG
64 CTTATGGGAAAACGCCGCTAACGCATAGTATTAGCGGCG
29108527 CGTTTTGGGA
Statistics
Matches: 580, Mismatches: 81, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
112 57 0.10
113 215 0.37
114 250 0.43
115 58 0.10
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (114 bp):
CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
TATGGGAAAACGCCGCTAACGCATAGTATTAGCGGCGTGTCGTCAAAAG
Found at i:29114398 original size:21 final size:21
Alignment explanation
Indices: 29114374--29114425 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
29114364 GGTGGTAGCA
29114374 AGGGAAGCAGAGGCTGCAGCG
1 AGGGAAGCAGAGGCTGCAGCG
*
29114395 AGGGAAGCAGAGGCTGCAGTG
1 AGGGAAGCAGAGGCTGCAGCG
*
29114416 AGAGAAGCAG
1 AGGGAAGCAG
29114426 CGAGAGAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.46, T:0.06
Consensus pattern (21 bp):
AGGGAAGCAGAGGCTGCAGCG
Found at i:29114882 original size:42 final size:43
Alignment explanation
Indices: 29114834--29114982 Score: 160
Period size: 42 Copynumber: 3.4 Consensus size: 43
29114824 GAACATTACT
*
29114834 TTTAGCGGCGTTTTTGTT-TAAGCGCCGCTAAAGAACATGATC
1 TTTAGCGGCGTTTTTTTTATAAGCGCCGCTAAAGAACATGATC
* *
29114876 ATTAGCGGCGTCTTTTTTTAAGCGATAAGCGCCGCTAAAGGACATGATC
1 TTTAGCGGCGT-TTTTTTT-----ATAAGCGCCGCTAAAGAACATGATC
* * *
29114925 TTTAGCGGCGTTTTTTTTGTAGAGC-CAG-TAAAGAACATGACC
1 TTTAGCGGCGTTTTTTTTATA-AGCGCCGCTAAAGAACATGATC
29114967 TTTAGCGGCGTTTTTT
1 TTTAGCGGCGTTTTTT
29114983 CTGTAAACGC
Statistics
Matches: 91, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
42 38 0.42
43 10 0.11
44 3 0.03
48 7 0.08
49 33 0.36
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTTTTATAAGCGCCGCTAAAGAACATGATC
Found at i:29114998 original size:42 final size:43
Alignment explanation
Indices: 29114823--29114992 Score: 157
Period size: 42 Copynumber: 3.9 Consensus size: 43
29114813 GAGCCGGTAT
* * * *
29114823 AGAACATTACTTTTAGCGGCGTTTTTGTT-TAAGCGCCGCTAA
1 AGAACATGACCTTTAGCGGCGTTTTTTTTGTAAACGCCGCTAA
* * *
29114865 AGAACATGATCATTAGCGGCGTCTTTTTTTAAGCGATAAGCGCCGCTAA
1 AGAACATGACCTTTAGCGGCGT-TTTTTTT----G-TAAACGCCGCTAA
* * *
29114914 AGGACATGATCTTTAGCGGCGTTTTTTTTGTAGA-GCCAG-TAA
1 AGAACATGACCTTTAGCGGCGTTTTTTTTGTAAACGCC-GCTAA
*
29114956 AGAACATGACCTTTAGCGGCGTTTTTTCTGTAAACGC
1 AGAACATGACCTTTAGCGGCGTTTTTTTTGTAAACGC
29114993 TGTAAAAGTT
Statistics
Matches: 106, Mismatches: 13, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
42 54 0.51
43 11 0.10
44 1 0.01
48 7 0.07
49 33 0.31
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (43 bp):
AGAACATGACCTTTAGCGGCGTTTTTTTTGTAAACGCCGCTAA
Found at i:29117133 original size:26 final size:26
Alignment explanation
Indices: 29117097--29117319 Score: 225
Period size: 26 Copynumber: 8.6 Consensus size: 26
29117087 CCTGAATAGA
*
29117097 AGGCCTTGAGCCGGTGTTTATTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * *
29117123 AGGCCTTGAGCCGATGTTTGTTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * * *
29117149 AGGCTTTGAGCCAGTGATTACTTAGT
1 AGGCTTTGAGCCGGTGTTTATTTAGC
** * *
29117175 AGGCTTTGAGCTAGTGATTACTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * *
29117201 AGGCTATGAGTCTGTGTTTATTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * * *
29117227 AGGCTTTGAGCTGATGATTATTTAAC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
*
29117253 AGGCTTTGAGCCGATGTTTA-TTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* *
29117278 AGACTTTGAGTCGGTGTTTATCTT-GC
1 AGGCTTTGAGCCGGTGTTTAT-TTAGC
29117304 AGGCTTTGAGCCGGTG
1 AGGCTTTGAGCCGGTG
29117320 AATGTTTATC
Statistics
Matches: 163, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
25 21 0.13
26 140 0.86
27 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.36
Consensus pattern (26 bp):
AGGCTTTGAGCCGGTGTTTATTTAGC
Found at i:29122254 original size:66 final size:63
Alignment explanation
Indices: 29122131--29122329 Score: 229
Period size: 70 Copynumber: 3.0 Consensus size: 63
29122121 AAATGATAAA
* * * *
29122131 TTCTTCATTATTTTCATT-AAAAAGTTAATTTTAATTCACATTGATTAGAGAACACTTTCATAT
1 TTCTTCATTATTTTCATTAAAAAAATTAATTTTAA-CCACATTGACTAGAGAATACTTTCATAT
29122194 TTCTTCATTATTTTCATTAAAAAAAATTAATTTTAACGCTACATTGACTAGAGAATACTTTCGTA
1 TTCTTCATTATTTTCATT-AAAAAAATTAATTTTAAC-C-ACATTGACTAGAGAATACTTTC---
29122259 ACTTAT
60 A--TAT
* * *
29122265 TTCTTCACTATTTTCATTAAACACATTAATTTTAACCACCCATTGACTAGAGAATACTTTCATAT
1 TTCTTCATTATTTTCATTAAAAAAATTAATTTTAACCA--CATTGACTAGAGAATACTTTCATAT
29122330 CTCACTTTTG
Statistics
Matches: 118, Mismatches: 7, Indels: 20
0.81 0.05 0.14
Matches are distributed among these distances:
63 18 0.15
65 19 0.16
66 20 0.17
67 1 0.01
68 1 0.01
69 2 0.02
70 37 0.31
71 20 0.17
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (63 bp):
TTCTTCATTATTTTCATTAAAAAAATTAATTTTAACCACATTGACTAGAGAATACTTTCATAT
Found at i:29122285 original size:71 final size:67
Alignment explanation
Indices: 29122131--29122359 Score: 220
Period size: 70 Copynumber: 3.4 Consensus size: 67
29122121 AAATGATAAA
* * * * *
29122131 TTCTTCATTATTTTCATT-AAAAAGTTAATTTTAATTCACATTGATTAGAGAACACTTTC--A--
1 TTCTTCACTATTTTCATTAAAAAAATTAATTTTAA-CCACATTGACTAGAGAATACTTTCTAACT
29122191 TAT
65 TAT
*
29122194 TTCTTCATTATTTTCATTAAAAAAAATTAATTTTAACGCTACATTGACTAGAGAATACTTTCGTA
1 TTCTTCACTATTTTCATT-AAAAAAATTAATTTTAAC-C-ACATTGACTAGAGAATACTTTC-TA
29122259 ACTTAT
62 ACTTAT
* * *
29122265 TTCTTCACTATTTTCATTAAACACATTAATTTTAACCACCCATTGACTAGAGAATACTTTCATAT
1 TTCTTCACTATTTTCATTAAAAAAATTAATTTTAACCA--CATTGACTAGAGAATACTTTC-TAA
*
29122330 CTCACT
63 CTTA-T
*
29122336 TT-TGT-ACTATTTTTATTAAAAAAA
1 TTCT-TCACTATTTTCATTAAAAAAA
29122360 AGTTAAATTT
Statistics
Matches: 140, Mismatches: 13, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
63 18 0.13
65 16 0.11
66 20 0.14
68 1 0.01
69 2 0.01
70 59 0.42
71 24 0.17
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (67 bp):
TTCTTCACTATTTTCATTAAAAAAATTAATTTTAACCACATTGACTAGAGAATACTTTCTAACTT
AT
Found at i:29126898 original size:18 final size:18
Alignment explanation
Indices: 29126875--29126911 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29126865 TAATGCTTAT
29126875 TGAGCCATCACATATCCG
1 TGAGCCATCACATATCCG
29126893 TGAGCCATCACATATCCG
1 TGAGCCATCACATATCCG
29126911 T
1 T
29126912 CCACATATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (18 bp):
TGAGCCATCACATATCCG
Done.