Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 144 of 210
Found at i:43873300 original size:18 final size:20
Alignment explanation
Indices: 43873264--43873306 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
43873254 ATATATTATT
43873264 AAGAAAAAAAAGAATGAAAA
1 AAGAAAAAAAAGAATGAAAA
*
43873284 AAGAAAAGAAA-AA-GAAAA
1 AAGAAAAAAAAGAATGAAAA
43873302 AAGAA
1 AAGAA
43873307 GTAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 2 0.09
20 10 0.45
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (20 bp):
AAGAAAAAAAAGAATGAAAA
Found at i:43878993 original size:6 final size:6
Alignment explanation
Indices: 43878984--43879025 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
43878974 AATAAATAAT
43878984 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
43879026 AAAATTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:43887309 original size:27 final size:28
Alignment explanation
Indices: 43887268--43887321 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
43887258 AGGTTGAAGG
43887268 TTTAAGGTTCAGGGTTC-GAGTTCAAAA
1 TTTAAGGTTCAGGGTTCAGAGTTCAAAA
* *
43887295 TTTAAGGTTCTGGGTTCAGGGTTCAAA
1 TTTAAGGTTCAGGGTTCAGAGTTCAAA
43887322 GTAAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (28 bp):
TTTAAGGTTCAGGGTTCAGAGTTCAAAA
Found at i:43887978 original size:18 final size:19
Alignment explanation
Indices: 43887951--43887986 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
43887941 TTAGTAATAG
*
43887951 TAATATTTAAT-TTTTTTA
1 TAATACTTAATATTTTTTA
43887969 TAATACTTAATATTTTTT
1 TAATACTTAATATTTTTT
43887987 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATACTTAATATTTTTTA
Found at i:43887979 original size:25 final size:26
Alignment explanation
Indices: 43887934--43887983 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
43887924 TTTTCTTGTT
43887934 ATTTTTATTAGTAATAGTAATATTTA
1 ATTTTTATTAGTAATAGTAATATTTA
*
43887960 ATTTTT-TTA-TAATACTTAATATTT
1 ATTTTTATTAGTAATA-GTAATATTT
43887984 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 11 0.50
26 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTTTTATTAGTAATAGTAATATTTA
Found at i:43888234 original size:43 final size:43
Alignment explanation
Indices: 43888186--43888519 Score: 449
Period size: 43 Copynumber: 7.8 Consensus size: 43
43888176 TTTTAGAAAT
* * * **
43888186 AAACGCTGCTATAGACCATGACCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* *
43888229 AAACGCCACTATAGATCAGGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
43888272 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTT-CAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
*
43888314 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * *
43888357 AAACGCCACTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * *
43888400 AAATGCCGCTATAAATCAAGACCTTTAGCGGCGATTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* ** * *
43888443 AAACGCCACTATATCTCAAGACCTTTAGCAGCGTTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* *
43888486 AAACGCCGCTATAGAACAA-A-CTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
43888520 CTCGCAAAAA
Statistics
Matches: 258, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
41 11 0.04
42 42 0.16
43 205 0.79
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
Found at i:43888350 original size:128 final size:129
Alignment explanation
Indices: 43888186--43888533 Score: 477
Period size: 128 Copynumber: 2.7 Consensus size: 129
43888176 TTTTAGAAAT
* * * * *
43888186 AAACGCTGCTATAGACCATGACCTTTAGCGGCGCTTTACCCACAAACGCCACTATAGATCAGGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGATCAAGAC
* * * *
43888251 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTT-CAC
66 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAAATCAAGACCTTTAGCGGCGATTTTTCCAC
*
43888314 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGCTCAAGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGATCAAGAC
*
43888379 CTTTAGCGGCGCTTTTCCCAAAAATGCCGCTATAAATCAAGACCTTTAGCGGCGATTTTTCCAC
66 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAAATCAAGACCTTTAGCGGCGATTTTTCCAC
* ** * * * * *
43888443 AAACGCCACTATATCTCAAGACCTTTAGCAGCGTTTTTTCCACAAACGCCGCTATAGAACAA-A-
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGATCAAGAC
* * *
43888506 CTTTAGCGACGCTTCTCGCAAAAACGCC
66 CTTTAGCGGCGCTTTTCCCAAAAACGCC
43888534 ACTAAAAACA
Statistics
Matches: 195, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
127 24 0.12
128 115 0.59
129 56 0.29
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (129 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGATCAAGAC
CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAAATCAAGACCTTTAGCGGCGATTTTTCCAC
Found at i:43889738 original size:5 final size:5
Alignment explanation
Indices: 43889728--43889752 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
43889718 CTTTCTTGCC
43889728 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
43889753 CAAACAAGAA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:43892534 original size:7 final size:7
Alignment explanation
Indices: 43892524--43892561 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
43892514 CACTAACTCT
*
43892524 TAACCTC
1 TAACCCC
43892531 TAACCCC
1 TAACCCC
43892538 TAACCCC
1 TAACCCC
*
43892545 TAACCAC
1 TAACCCC
43892552 TAACCCC
1 TAACCCC
43892559 TAA
1 TAA
43892562 ACTTTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.18
Consensus pattern (7 bp):
TAACCCC
Found at i:43892696 original size:133 final size:132
Alignment explanation
Indices: 43892437--43892676 Score: 358
Period size: 133 Copynumber: 1.8 Consensus size: 132
43892427 AAGAACTTAA
* * *
43892437 TTAATATATAAATTAAAAAATACTAATTAATCTAAACCTTAAACCCTAACCCGACCCCGAATCTC
1 TTAATATATAAATAAAAAAATACTAATTAATCTAAACCCTAAACCCTAACCCGACACCGAATCTC
*
43892502 TAAATCCTAAATCACTAACTCTTAACCTCTAACCCCTAACCCCTAACCACTAACCCCTAAACTTT
66 TAAATCCTAAATCACTAACTCTTAACCTCTAACCACTAACCCCTAACCACTAACCCCTAAACTTT
43892567 AT
131 AT
** *
43892569 TTAATATATAAATCAAAAAAATACTAATTAATCTAAACCCTAAACCCTAACTTGACATCGAATC-
1 TTAATATATAAAT-AAAAAAATACTAATTAATCTAAACCCTAAACCCTAACCCGACACCGAATCT
* *
43892633 CATAAA-CCTTAAATCCCTAACTCTTAATCTCTAACCACTAACCC
65 C-TAAATCC-TAAATCACTAACTCTTAACCTCTAACCACTAACCC
43892677 TTAAATCACA
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
132 16 0.17
133 80 0.83
ACGTcount: A:0.42, C:0.29, G:0.02, T:0.28
Consensus pattern (132 bp):
TTAATATATAAATAAAAAAATACTAATTAATCTAAACCCTAAACCCTAACCCGACACCGAATCTC
TAAATCCTAAATCACTAACTCTTAACCTCTAACCACTAACCCCTAACCACTAACCCCTAAACTTT
AT
Found at i:43892712 original size:7 final size:7
Alignment explanation
Indices: 43892700--43892730 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
43892690 CTTAAACCAG
43892700 AATCCCT
1 AATCCCT
43892707 AATCCCT
1 AATCCCT
43892714 AATCCCT
1 AATCCCT
43892721 AATCCCT
1 AATCCCT
43892728 AAT
1 AAT
43892731 TCCATAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (7 bp):
AATCCCT
Found at i:43893198 original size:41 final size:41
Alignment explanation
Indices: 43893138--43893450 Score: 355
Period size: 41 Copynumber: 7.6 Consensus size: 41
43893128 AAATGTTTTT
* ** * *
43893138 GCGGCGCTTTATCAAAAACGCCGCTAAATTCCCGAGCACTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
*
43893179 GCTGCGCTTTTTCAAAAACGCCGCT-AAAGCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGC-CTGAGCATTA
* **
43893220 GCGGCGCTTTTTCAAAAATGATGCT-AAAGCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGC-CTGAGCATTA
* *
43893261 GCGGCGC-TCTTGAAAAAGCGCCGCTAAAAGCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAA-CGCCGCTAAAAGCCTGAGCATTA
* * *
43893302 GCGGTGCTTTTTCAAAATCGCCGCTAAAAGCTTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
** * * *
43893343 GCATCGCTTTTTTAAAAATGCCGTTAAAAGCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
* * * *
43893384 ACGGCGCTATTTT-AAAAACGCAGTTAAAAGCCTAAGCATTA
1 GCGGCGCT-TTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
43893425 GCGGCGCTTTTTCAAAAACGCCGCTA
1 GCGGCGCTTTTTCAAAAACGCCGCTA
43893451 CAGCCCCAAA
Statistics
Matches: 229, Mismatches: 37, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
40 15 0.07
41 198 0.86
42 16 0.07
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
Found at i:43896012 original size:6 final size:6
Alignment explanation
Indices: 43895991--43896024 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
43895981 AAATAAAGAC
43895991 AATTAA AATTGCAA AATTAA AATTAA AATTAA AA
1 AATTAA AATT--AA AATTAA AATTAA AATTAA AA
43896025 ACTTTTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.77
8 6 0.23
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (6 bp):
AATTAA
Found at i:43902847 original size:15 final size:16
Alignment explanation
Indices: 43902826--43902863 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
43902816 AGATTTGAAG
43902826 AATGAGGGAT-ATTGA
1 AATGAGGGATGATTGA
*
43902841 GATGAGGGATGATTGA
1 AATGAGGGATGATTGA
43902857 AATGAGG
1 AATGAGG
43902864 AGTGAGTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.39, T:0.24
Consensus pattern (16 bp):
AATGAGGGATGATTGA
Found at i:43904843 original size:63 final size:62
Alignment explanation
Indices: 43904770--43904890 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 62
43904760 CACACGTTCA
* * * * * *
43904770 TGTCTCTGGCCTGTATGACTCTAATTC-CAAAATAATGAGTTACATGGCCTGGACACACGACCG
1 TGTCCCTGGCCCGTAGGACACTAATTCAC-AAACAATGAGTTACACGGCCTGG-CACACGACCG
* *
43904833 TGTCCCTGGCCCGTGGGACACTAATTCACAAACAGTGAGTTACACGGCCTGGCACACG
1 TGTCCCTGGCCCGTAGGACACTAATTCACAAACAATGAGTTACACGGCCTGGCACACG
43904891 GCTATGTGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 6 0.12
63 42 0.86
64 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (62 bp):
TGTCCCTGGCCCGTAGGACACTAATTCACAAACAATGAGTTACACGGCCTGGCACACGACCG
Found at i:43905405 original size:14 final size:14
Alignment explanation
Indices: 43905386--43905432 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
43905376 TGTGAAAACC
43905386 AAAAAGAATAAGAG
1 AAAAAGAATAAGAG
43905400 AAAAAGAAT-A-A-
1 AAAAAGAATAAGAG
*
43905411 CAAAAGAATAAGAG
1 AAAAAGAATAAGAG
43905425 AAAAAGAA
1 AAAAAGAA
43905433 CAAACGGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 8 0.29
12 2 0.07
13 2 0.07
14 16 0.57
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.06
Consensus pattern (14 bp):
AAAAAGAATAAGAG
Found at i:43905816 original size:4 final size:4
Alignment explanation
Indices: 43905807--43905853 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
43905797 TGGGCGTTAC
43905807 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
43905854 ATGCCTAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (4 bp):
AGAT
Found at i:43906469 original size:28 final size:28
Alignment explanation
Indices: 43906429--43906486 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
43906419 CAAATCAAAA
43906429 GTAGTTTAAATACTTGAGATTTGTATAG
1 GTAGTTTAAATACTTGAGATTTGTATAG
43906457 GTAGTTTAAATACTTGAGATTTGTATAG
1 GTAGTTTAAATACTTGAGATTTGTATAG
43906485 GT
1 GT
43906487 TTTATACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.43
Consensus pattern (28 bp):
GTAGTTTAAATACTTGAGATTTGTATAG
Found at i:43906493 original size:24 final size:26
Alignment explanation
Indices: 43906437--43906494 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
43906427 AAGTAGTTTA
43906437 AATACTTGAGATTTGTATAGGTAGTTT
1 AATACTTGAGATTTGTATAGGTA-TTT
43906464 AAATACTTGAGATTTGTATAGGT-TTT
1 -AATACTTGAGATTTGTATAGGTATTT
43906490 -ATACT
1 AATACT
43906495 AAGAGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.17
26 3 0.10
28 22 0.73
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (26 bp):
AATACTTGAGATTTGTATAGGTATTT
Found at i:43911247 original size:72 final size:71
Alignment explanation
Indices: 43911130--43911280 Score: 275
Period size: 72 Copynumber: 2.1 Consensus size: 71
43911120 AATCGACTTG
43911130 AATTATTTAATGAAAATTAGGTAATTACCAAACCTACCAAGACACCCTATTTGTTTCCTCCTTTA
1 AATTA-TTAATGAAAATTAGGTAATTACCAAACCTACCAAGACACCCTATTTGTTTCCTCCTTTA
*
43911195 GTCCCGA
65 GTCCCCA
43911202 AATTATTAATGAAAATTAGGTAAATTACCAAACCTACCAAGACACCCTATTTGTTTCCTCCTTTA
1 AATTATTAATGAAAATTAGGT-AATTACCAAACCTACCAAGACACCCTATTTGTTTCCTCCTTTA
43911267 GTCCCCA
65 GTCCCCA
43911274 AATTATT
1 AATTATT
43911281 TTTTTTTCTT
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
71 16 0.21
72 61 0.79
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (71 bp):
AATTATTAATGAAAATTAGGTAATTACCAAACCTACCAAGACACCCTATTTGTTTCCTCCTTTAG
TCCCCA
Found at i:43912335 original size:9 final size:10
Alignment explanation
Indices: 43912321--43912363 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
43912311 ATTAATATCC
43912321 AAAT-AAGTA
1 AAATAAAGTA
*
43912330 AAATAAAATA
1 AAATAAAGTA
43912340 AAATAAAGTAA
1 AAATAAAGT-A
43912351 TAAATAAAGTA
1 -AAATAAAGTA
43912362 AA
1 AA
43912364 GAAAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 14 0.48
11 2 0.07
12 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (10 bp):
AAATAAAGTA
Found at i:43918777 original size:44 final size:44
Alignment explanation
Indices: 43918714--43918799 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
43918704 CCTATCCGTG
*
43918714 AACACCTTACCCTGAACCGGTCTAGATTGTGAGGTCGAGAGATA
1 AACACCTTACCCTGAACCGGTCTAGACTGTGAGGTCGAGAGATA
*
43918758 AACACCTTACCCTGAACCGGTCTGGACTGTGAGGTCGAGAGA
1 AACACCTTACCCTGAACCGGTCTAGACTGTGAGGTCGAGAGA
43918800 AAAATAGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (44 bp):
AACACCTTACCCTGAACCGGTCTAGACTGTGAGGTCGAGAGATA
Found at i:43944156 original size:1 final size:1
Alignment explanation
Indices: 43944150--43944175 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
43944140 TTTTGGCTGC
43944150 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
43944176 GTGCGTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:43944344 original size:2 final size:2
Alignment explanation
Indices: 43944337--43944380 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
43944327 CTTTGTAACA
43944337 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
43944379 AT
1 AT
43944381 TGGGAATATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43956705 original size:18 final size:18
Alignment explanation
Indices: 43956682--43956743 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
43956672 GATGATATCA
43956682 ATATTGATGCTAGTGACG
1 ATATTGATGCTAGTGACG
*
43956700 ATATTGATGCTAGTAACG
1 ATATTGATGCTAGTGACG
* * *
43956718 CTATTGATGATAGTGGCG
1 ATATTGATGCTAGTGACG
*
43956736 CTATTGAT
1 ATATTGAT
43956744 AATGACCTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.35
Consensus pattern (18 bp):
ATATTGATGCTAGTGACG
Found at i:43956987 original size:18 final size:18
Alignment explanation
Indices: 43956947--43956989 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
43956937 GTTCAAGGTG
43956947 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
43956965 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
43956983 TAATTAA
1 TAATTAA
43956990 AAACTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:43962707 original size:13 final size:12
Alignment explanation
Indices: 43962689--43962731 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
43962679 ATATATACAT
43962689 ATATTAGTTAATA
1 ATATTA-TTAATA
*
43962702 ATATTAATAATA
1 ATATTATTAATA
*
43962714 ATATAATATAATA
1 ATATTAT-TAATA
43962727 ATATT
1 ATATT
43962732 TAATTCATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
ATATTATTAATA
Found at i:43963796 original size:40 final size:41
Alignment explanation
Indices: 43963741--43963836 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 41
43963731 ATCCACTAGC
* *
43963741 ACCTCCCAC-AGTACCACCCACACCATGATTCCTAATGGTA
1 ACCTCCCACGAGTACCACCCACACCATGATTCCTAACGATA
***
43963781 ACCTCCCACGA-TACCACCCATGGCATGATTCCTAACGATA
1 ACCTCCCACGAGTACCACCCACACCATGATTCCTAACGATA
*
43963821 ACCTTCCACGAGTACC
1 ACCTCCCACGAGTACC
43963837 CTCCCACGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 43 0.90
41 5 0.10
ACGTcount: A:0.29, C:0.40, G:0.11, T:0.20
Consensus pattern (41 bp):
ACCTCCCACGAGTACCACCCACACCATGATTCCTAACGATA
Found at i:43963894 original size:39 final size:39
Alignment explanation
Indices: 43963846--43963945 Score: 110
Period size: 39 Copynumber: 2.6 Consensus size: 39
43963836 CCTCCCACGG
* * **
43963846 TAACCATCCACAAGTACCTCTTGCGATACCCTCCCATAA
1 TAACCATCCACGAGTACCACCCGCGATACCCTCCCATAA
* * * **
43963885 TAACAATCCAGGAGTACCACCCGCGATACCTTCCCATGG
1 TAACCATCCACGAGTACCACCCGCGATACCCTCCCATAA
*
43963924 TAACCATCCACGAGTACTACCC
1 TAACCATCCACGAGTACCACCC
43963946 ACTGAACCAT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.30, C:0.38, G:0.12, T:0.20
Consensus pattern (39 bp):
TAACCATCCACGAGTACCACCCGCGATACCCTCCCATAA
Found at i:43973624 original size:30 final size:30
Alignment explanation
Indices: 43973572--43973634 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
43973562 TCCTTTTCCG
*
43973572 CTTTTTGATAAATGACCCAATAT-TTTTTA
1 CTTTTTGATAAATGACCCAATATGTTTATA
*
43973601 CTTTTTGCATAAAT-AGCCTAATATGTTTATA
1 CTTTTTG-ATAAATGA-CCCAATATGTTTATA
43973632 CTT
1 CTT
43973635 CTTCTCCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.28
30 13 0.45
31 8 0.28
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (30 bp):
CTTTTTGATAAATGACCCAATATGTTTATA
Found at i:43974358 original size:3 final size:3
Alignment explanation
Indices: 43974352--43974381 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
43974342 CTCCTCCTCC
43974352 TCT TCT TCT TCT TCT TC- TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
43974382 TTACCGCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:43974372 original size:14 final size:14
Alignment explanation
Indices: 43974355--43974381 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43974345 CTCCTCCTCT
43974355 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
43974369 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
43974382 TTACCGCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTCTTCTTCTTC
Found at i:43974378 original size:17 final size:17
Alignment explanation
Indices: 43974337--43974381 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
43974327 GCATCTCCAT
* *
43974337 TTCTTCTCCTCCTCCTC
1 TTCTTCTTCTTCTCCTC
*
43974354 TTCTTCTTCTTCTTCTC
1 TTCTTCTTCTTCTCCTC
43974371 TTCTTCTTCTT
1 TTCTTCTTCTT
43974382 TTACCGCCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (17 bp):
TTCTTCTTCTTCTCCTC
Found at i:43974699 original size:23 final size:21
Alignment explanation
Indices: 43974649--43974699 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
43974639 ATTTATAATG
43974649 ATAA-TAATTAAAAACAATTT
1 ATAATTAATTAAAAACAATTT
*
43974669 ATTAAATTAATTTAAAACTATATTT
1 A-T-AATTAATTAAAAAC-A-ATTT
43974694 ATAATT
1 ATAATT
43974700 TTAAAAGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.04
21 1 0.04
22 2 0.08
23 14 0.56
24 2 0.08
25 5 0.20
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATTAATTAAAAACAATTT
Found at i:43986699 original size:22 final size:22
Alignment explanation
Indices: 43986671--43986823 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
43986661 TGTTGATAGT
*
43986671 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
43986693 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
43986715 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
43986737 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
43986759 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
43986781 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
43986803 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
43986824 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:43989454 original size:12 final size:13
Alignment explanation
Indices: 43989439--43989467 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
43989429 TATATGAATC
43989439 AGCAACATTTA-A
1 AGCAACATTTAGA
43989451 AGCAACATTTAGA
1 AGCAACATTTAGA
43989464 AGCA
1 AGCA
43989468 GTCCAAGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (13 bp):
AGCAACATTTAGA
Found at i:43993075 original size:25 final size:25
Alignment explanation
Indices: 43993047--43993107 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
43993037 ATTTAGAAAA
* *
43993047 TAAATTTTCATTGCT-ATTTTACATT
1 TAAATTTTAATTGATAATTTTACA-T
* *
43993072 TAAATATTAATTGATAATTTTATAT
1 TAAATTTTAATTGATAATTTTACAT
*
43993097 TAAATTATAAT
1 TAAATTTTAAT
43993108 ATATTTACAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.52
Consensus pattern (25 bp):
TAAATTTTAATTGATAATTTTACAT
Found at i:43997574 original size:113 final size:112
Alignment explanation
Indices: 43997297--43997875 Score: 428
Period size: 114 Copynumber: 5.1 Consensus size: 112
43997287 CCTGAAGAAC
* * * *
43997297 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGAGTTT-ATTGTAAGCGCCGC
1 TAGTGGCGTTT-TTAAAAAACGCCGTAAAAGAACAT-ATTAGTGGCGTTTAACTGAAAGCGCCGC
* * *
43997361 AAA-ATACTTAACCAAAACGCAGCGTTGGTTCA-ATT---GTATATTAGA-AT
64 AAATAT-CTTAACCAAAACGCACCGTT--TT-ATCTTGAGGTAGATTAGATAT
* ** * * **
43997408 TCGTGGCGTTTTTTATAAAAAAACGCCGCGAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGC
1 TAGTGGCG--TTTT-T-AAAAAACGCCGTAAAAGAACA-TATTAGTGGCGTTTAACTGAAAGCGC
**
43997473 CGCAAATATCTTAAGGAAAACGCACCGTTTTATCTTGAGGTAGATTA-ATAT
61 CGCAAATATCTTAACCAAAACGCACCGTTTTATCTTGAGGTAGATTAGATAT
** * *
43997524 TAGTGGCGTTTTTAAAAAAGCGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGATGCGCCGC
1 TAGTGGCGTTTTTAAAAAA-CGCCGTAAAAGAACAT-ATTAGTGGCGTTTAACTGAAAGCGCCGC
* * ** ** * * *
43997589 AAAATACCTTAACCAAAACGCAGCGTTTGGT-TCAATTGTATATTAGACAT
64 -AAATATCTTAACCAAAACGCACCGTTTTATCTTGA-GGTAGATTAGATAT
* * * * * *
43997639 T-GTGGCGTTTTCTATAAAACGCCGCAAAAGAATAGTATTAGTGGCGTTT-TCGGTAAAGCGCCA
1 TAGTGGCGTTTT-TAAAAAACGCCGTAAAAGAACA-TATTAGTGGCGTTTAACTG-AAAGCGCCG
** **
43997702 CAAATATCTTAATGAAAACGCACCGTTTCGTCTTGAGGTAGATTAG-TAT
63 CAAATATCTTAACCAAAACGCACCGTTTTATCTTGAGGTAGATTAGATAT
** ** *
43997751 TAGTGGCGTTTTTAGAAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTTTTATGCGCCGC
1 TAGTGGCGTTTTTA-AAAAACGCCGTAAAAGAACAT-ATTAGTGGCGTTTAACTGAAAGCGCCGC
* * ** * *
43997816 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA-AT
64 -AAATATCTTAACCAAAACGCACCGTTTTATCTTGAGGTAGATTAGATAT
43997865 TAGTGGCGTTT
1 TAGTGGCGTTT
43997876 ACGATAAAAC
Statistics
Matches: 369, Mismatches: 72, Indels: 51
0.75 0.15 0.10
Matches are distributed among these distances:
111 7 0.02
112 15 0.04
113 125 0.34
114 161 0.44
115 43 0.12
116 18 0.05
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (112 bp):
TAGTGGCGTTTTTAAAAAACGCCGTAAAAGAACATATTAGTGGCGTTTAACTGAAAGCGCCGCAA
ATATCTTAACCAAAACGCACCGTTTTATCTTGAGGTAGATTAGATAT
Found at i:43997699 original size:227 final size:226
Alignment explanation
Indices: 43997297--43997893 Score: 864
Period size: 227 Copynumber: 2.6 Consensus size: 226
43997287 CCTGAAGAAC
* * *
43997297 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGAGTTTA-TTGTAAGCGCCGC
1 TAGTGGCGTTT-TTAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGC
* *
43997361 AAAATA-CTTAACCAAAACGCAGCG-TTGGTTCAATTGTATATTAGAATTCGTGGCGTTTTTTAT
65 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCTAT
* *
43997424 AAAAAAACGCCGCGAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGG
130 ---AAAACGCCGCAAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCACAAATATCTTAAGG
*
43997489 AAAACGCACCGTTTTATCTTGAGGTAGATTAATAT
192 AAAACGCACCGTTTCATCTTGAGGTAGATTAATAT
*
43997524 TAGTGGCGTTTTTAAAAAAGCGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGATGCGCCGC
1 TAGTGGCGTTTTTAAAAAA-CGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGC
43997589 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGACATT-GTGGCGTTTTCTA
65 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGA-ATTAGTGGCGTTTTCTA
* * ** *
43997653 TAAAACGCCGCAAAAGAATAGTATTAGTGGCGTTT-TCGGTAAAGCGCCACAAATATCTTAATGA
129 TAAAACGCCGCAAAAGAATAGTATTAGCGGCGTTTAAC-AAAAAGCGCCACAAATATCTTAAGGA
* *
43997717 AAACGCACCGTTTCGTCTTGAGGTAGATTAGTAT
193 AAACGCACCGTTTCATCTTGAGGTAGATTAATAT
* *
43997751 TAGTGGCGTTTTTAGAAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTTTTATGCGCCGC
1 TAGTGGCGTTTTTA-AAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGC
** * * *
43997816 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGA-GGTATATTAGAATTAGTGGCGTTTACGA
65 AAAATACCTTAACCAAAACGCAGCGTTTGG-TTCAATTGTATATTAGAATTAGTGGCGTTTTCTA
43997880 TAAAACGCCGCAAA
129 TAAAACGCCGCAAA
43997894 TATCTTAACG
Statistics
Matches: 338, Mismatches: 23, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
226 11 0.03
227 247 0.73
228 25 0.07
229 18 0.05
230 34 0.10
231 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (226 bp):
TAGTGGCGTTTTTAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGCA
AAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCTATA
AAACGCCGCAAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCACAAATATCTTAAGGAAAA
CGCACCGTTTCATCTTGAGGTAGATTAATAT
Found at i:43997917 original size:74 final size:75
Alignment explanation
Indices: 43997810--43997949 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 75
43997800 TATTTTTATG
* * *
43997810 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA-ATTAGTGGCGT
1 CGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTA-ATATTAGTGGCGT
43997874 TTACGATAAAA
65 TTACGATAAAA
* *
43997885 CGCCGC-AAATATCTTAACGAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
1 CGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
43997949 T
66 T
43997950 TTAAAAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
73 1 0.02
74 52 0.88
75 6 0.10
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
TACGATAAAA
Found at i:43997917 original size:188 final size:188
Alignment explanation
Indices: 43997675--43998075 Score: 649
Period size: 188 Copynumber: 2.1 Consensus size: 188
43997665 AAAGAATAGT
* * *
43997675 ATTAGTGGCGTTTTCGGTAAAGCGCCACAAATATCTTAATGAAAACGCACCGTTTCGTCTTGAGG
1 ATTAGTGGCGTTTACGGTAAAACGCCACAAATATCTTAACGAAAACGCACCGTTTCGTCTTGAGG
* * *
43997740 TAGATTAGTATTAGTGGCGTTTTTAGAAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTT
66 TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
** *
43997805 TTATGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA
131 GGAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA
* * *
43997863 ATTAGTGGCGTTTACGATAAAACGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTTGAGG
1 ATTAGTGGCGTTTACGGTAAAACGCCACAAATATCTTAACGAAAACGCACCGTTTCGTCTTGAGG
*
43997928 TAGATTAATATTAGTGGCGTTTTTAAAAAAATGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
66 TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
* * *
43997993 GGAAGCGCCGCAAAATGCCTTAACCAAAACGCAGTGTTTGGTTTTGATGTATATTAGA
131 GGAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA
*
43998051 ATTAGTGGCGTTTATGGTAAAACGC
1 ATTAGTGGCGTTTACGGTAAAACGC
43998076 TGCTAAAGAA
Statistics
Matches: 195, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
188 195 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (188 bp):
ATTAGTGGCGTTTACGGTAAAACGCCACAAATATCTTAACGAAAACGCACCGTTTCGTCTTGAGG
TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
GGAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA
Found at i:43998546 original size:7 final size:7
Alignment explanation
Indices: 43998536--43998579 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
43998526 GGTTTATGGA
43998536 TTAGGGG
1 TTAGGGG
43998543 TTAGGGG
1 TTAGGGG
*
43998550 TTATGGG
1 TTAGGGG
43998557 TTAGGGG
1 TTAGGGG
43998564 TTA--GG
1 TTAGGGG
43998569 TTAGGGG
1 TTAGGGG
43998576 TTAG
1 TTAG
43998580 ATGTTAAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
7 28 0.85
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (7 bp):
TTAGGGG
Found at i:43998555 original size:21 final size:21
Alignment explanation
Indices: 43998529--43998568 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43998519 GATTTAAGGT
43998529 TTATGGATTAGGGGTTAGGGG
1 TTATGGATTAGGGGTTAGGGG
*
43998550 TTATGGGTTAGGGGTTAGG
1 TTATGGATTAGGGGTTAGG
43998569 TTAGGGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.47, T:0.35
Consensus pattern (21 bp):
TTATGGATTAGGGGTTAGGGG
Found at i:43998559 original size:45 final size:45
Alignment explanation
Indices: 43998431--43998541 Score: 197
Period size: 45 Copynumber: 2.5 Consensus size: 45
43998421 AATTTTAAGT
43998431 TTTATAGATTATGGATTAGGGATTCTGGTTTAAGGGTTAATGTGA
1 TTTATAGATTATGGATTAGGGATTCTGGTTTAAGGGTTAATGTGA
43998476 TTTATAGATTATGGATTAGGGATTCTGGTTTAAGGGTTAATGTGA
1 TTTATAGATTATGGATTAGGGATTCTGGTTTAAGGGTTAATGTGA
*
43998521 TTTA-AGGTTTATGGATTAGGG
1 TTTATA-GATTATGGATTAGGG
43998542 GTTAGGGGTT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
44 1 0.02
45 63 0.98
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.42
Consensus pattern (45 bp):
TTTATAGATTATGGATTAGGGATTCTGGTTTAAGGGTTAATGTGA
Found at i:43998585 original size:14 final size:12
Alignment explanation
Indices: 43998541--43998579 Score: 60
Period size: 12 Copynumber: 3.1 Consensus size: 12
43998531 ATGGATTAGG
43998541 GGTTAGGGGTTA
1 GGTTAGGGGTTA
43998553 TGGGTTAGGGGTTA
1 --GGTTAGGGGTTA
43998567 GGTTAGGGGTTA
1 GGTTAGGGGTTA
43998579 G
1 G
43998580 ATGTTAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 13 0.52
14 12 0.48
ACGTcount: A:0.15, C:0.00, G:0.51, T:0.33
Consensus pattern (12 bp):
GGTTAGGGGTTA
Found at i:43998592 original size:26 final size:26
Alignment explanation
Indices: 43998541--43998593 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
43998531 ATGGATTAGG
* *
43998541 GGTTAGGGGTTATGGGTTAGGGGTTA
1 GGTTAGGGGTTATGGGTTAAGAGTTA
*
43998567 GGTTAGGGGTTA-GATGTTAAGAGTTA
1 GGTTAGGGGTTATG-GGTTAAGAGTTA
43998593 G
1 G
43998594 AGTTTAGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (26 bp):
GGTTAGGGGTTATGGGTTAAGAGTTA
Found at i:43998690 original size:7 final size:7
Alignment explanation
Indices: 43998678--43998760 Score: 87
Period size: 7 Copynumber: 11.9 Consensus size: 7
43998668 TAAATAAGTT
43998678 TTAGGGG
1 TTAGGGG
43998685 TTAGGGG
1 TTAGGGG
*
43998692 TTAGAGG
1 TTAGGGG
* *
43998699 TCATGGG
1 TTAGGGG
*
43998706 TTAAGGGT
1 TT-AGGGG
43998714 TTA-GGG
1 TTAGGGG
*
43998720 TTAAGGG
1 TTAGGGG
43998727 TTAGGGG
1 TTAGGGG
*
43998734 TTAAGGG
1 TTAGGGG
43998741 TTAGGGG
1 TTAGGGG
*
43998748 TTAGGGT
1 TTAGGGG
43998755 TTAGGG
1 TTAGGG
43998761 ATTGGGTTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
6 5 0.08
7 52 0.84
8 5 0.08
ACGTcount: A:0.19, C:0.01, G:0.48, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:43998767 original size:13 final size:14
Alignment explanation
Indices: 43998709--43998768 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
43998699 TCATGGGTTA
43998709 AGGGTTTAGGG-TT
1 AGGGTTTAGGGATT
*
43998722 AAGGG-TTAGGGGTT
1 -AGGGTTTAGGGATT
*
43998736 AAGGG-TTAGGGGTT
1 -AGGGTTTAGGGATT
43998750 AGGGTTTAGGGATT
1 AGGGTTTAGGGATT
43998764 -GGGTT
1 AGGGTT
43998769 ATGATTTAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
13 15 0.35
14 28 0.65
ACGTcount: A:0.18, C:0.00, G:0.48, T:0.33
Consensus pattern (14 bp):
AGGGTTTAGGGATT
Found at i:43998909 original size:96 final size:96
Alignment explanation
Indices: 43998727--43998915 Score: 217
Period size: 96 Copynumber: 2.0 Consensus size: 96
43998717 GGGTTAAGGG
* * *
43998727 TTAGGGGTTAAGGGTTAGGGGTTAGGGTTTAGGGATTGGGTTATGATTTAAGGTTTAGATTAATT
1 TTAGGGGTTAAGGGTTAGGGGTTAGGGTTTAGGGATCGGGTTAGGATTTAAGATTTAGATTAATT
* * * * *
43998792 AGTGTTTTTTATTTTATATATTAAATAAAGT
66 AGTCTTATTTAATTAACATATTAAATAAAGT
*
43998823 TTAGGGGTT-AGTGGTTA-GGGTTATGGGTTT--GGAGTCGGGTTAGGGA-TTAAGATTTGGATT
1 TTAGGGGTTAAG-GGTTAGGGGTTA-GGGTTTAGGGA-TCGGGTTA-GGATTTAAGATTTAGATT
43998883 AATTAGTACTTATTTAATTAACATATTAAATAA
62 AATTAGT-CTTATTTAATTAACATATTAAATAA
43998916 GTTCTTTATA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
94 3 0.04
95 34 0.43
96 42 0.53
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.42
Consensus pattern (96 bp):
TTAGGGGTTAAGGGTTAGGGGTTAGGGTTTAGGGATCGGGTTAGGATTTAAGATTTAGATTAATT
AGTCTTATTTAATTAACATATTAAATAAAGT
Found at i:43999005 original size:14 final size:14
Alignment explanation
Indices: 43998986--43999012 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43998976 GATATGCAAT
43998986 ATATAATAATTTGA
1 ATATAATAATTTGA
43999000 ATATAATAATTTG
1 ATATAATAATTTG
43999013 GAATTGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
ATATAATAATTTGA
Found at i:43999052 original size:20 final size:20
Alignment explanation
Indices: 43999014--43999054 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43999004 AATAATTTGG
**
43999014 AATTGTAAAAATTGTAAAAA
1 AATTGTAAAAATTACAAAAA
*
43999034 AATTGTCAAAATTACAAAAA
1 AATTGTAAAAATTACAAAAA
43999054 A
1 A
43999055 TAAAATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (20 bp):
AATTGTAAAAATTACAAAAA
Found at i:43999075 original size:8 final size:8
Alignment explanation
Indices: 43999062--43999094 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
43999052 AAATAAAATG
43999062 AAAATAAA
1 AAAATAAA
43999070 AAAAT-AA
1 AAAATAAA
43999077 AAAATAAA
1 AAAATAAA
43999085 AAAACTAAA
1 AAAA-TAAA
43999094 A
1 A
43999095 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
8 11 0.48
9 5 0.22
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:43999082 original size:15 final size:16
Alignment explanation
Indices: 43999062--43999094 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
43999052 AAATAAAATG
43999062 AAAATAAAAAAA-TAA
1 AAAATAAAAAAACTAA
43999077 AAAATAAAAAAACTAA
1 AAAATAAAAAAACTAA
43999093 AA
1 AA
43999095 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAATAAAAAAACTAA
Found at i:43999890 original size:198 final size:197
Alignment explanation
Indices: 43999562--43999972 Score: 635
Period size: 198 Copynumber: 2.1 Consensus size: 197
43999552 GGCGTTTATG
** *
43999562 TATAAACGCCGCAATTTTAAGAAATTGTTTACGAAAATGGCTCCGTTTTCTTATTTATCTTTAGT
1 TATAAACGCCGCAA-AGTAAGAAATTGTTTACGAAAACGGCTCCGTTTTCTTATTTATCTTTAGT
* * * *
43999627 GGCGCTTTTAGTACACGCCGCAAAATTATTTTAATTTTTATGGAGATGATGCCGTTTTGTCTAAA
65 GGCGCTTTTAGTAAACGCCGCAAAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAA
* * ** * *
43999692 ACGCCATGAGTTTTAGTTTACTAATCGGGGAACGACAGCGTTTGATCATATTACTAGTGGCGCTA
130 ACGCAATGACTTAGAGTTAACTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTA
43999757 GTA
195 GTA
* *
43999760 TATAAACGCCGCAAAGTACAGAAATTGTTTAGGAAAACGGCTTCGTTTTCTTATTTA-CTTTTAG
1 TATAAACGCCGCAAAGTA-AGAAATTGTTTACGAAAACGGCTCCGTTTTCTTATTTATC-TTTAG
*
43999824 TGGCGCTTTTAGTAAACGCCGCAAAAATGTTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAA
64 TGGCGCTTTTAGTAAACGCCGCAAAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAA
*
43999889 AACGCAATGACTTAGAGTTAACTGATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCT
129 AACGCAATGACTTAGAGTTAACTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCT
43999954 AGTA
194 AGTA
43999958 TATAAACGCCGCAAA
1 TATAAACGCCGCAAA
43999973 TGGGTTAATT
Statistics
Matches: 194, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
197 3 0.02
198 191 0.98
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (197 bp):
TATAAACGCCGCAAAGTAAGAAATTGTTTACGAAAACGGCTCCGTTTTCTTATTTATCTTTAGTG
GCGCTTTTAGTAAACGCCGCAAAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAA
CGCAATGACTTAGAGTTAACTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTAG
TA
Found at i:44000487 original size:10 final size:10
Alignment explanation
Indices: 44000472--44000496 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44000462 TCGAAAATTG
44000472 CAAAATTGTT
1 CAAAATTGTT
44000482 CAAAATTGTT
1 CAAAATTGTT
44000492 CAAAA
1 CAAAA
44000497 CCATGTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (10 bp):
CAAAATTGTT
Found at i:44002676 original size:13 final size:13
Alignment explanation
Indices: 44002658--44002709 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
44002648 TTTTACTCTT
*
44002658 AATATATTACTTG
1 AATATATTACTTA
44002671 AATATATTACTTA
1 AATATATTACTTA
*
44002684 AATAAATTACTTA
1 AATATATTACTTA
*
44002697 AATACATTACTTA
1 AATATATTACTTA
44002710 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (13 bp):
AATATATTACTTA
Found at i:44002734 original size:53 final size:53
Alignment explanation
Indices: 44002677--44002812 Score: 200
Period size: 53 Copynumber: 2.6 Consensus size: 53
44002667 CTTGAATATA
**
44002677 TTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
* ** * *
44002730 TTACTTAAATATGTTACTCAGTTACATTAATTACTAAAATTTGGTTAAATTTT
1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
*
44002783 TTACTTAAATATGTTACTTGAATACATTAC
1 TTACTTAAATATGTTACTTAAATACATTAC
44002813 CCGCTATAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 71 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (53 bp):
TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
Found at i:44002981 original size:9 final size:9
Alignment explanation
Indices: 44002957--44003197 Score: 130
Period size: 9 Copynumber: 27.8 Consensus size: 9
44002947 TATGTACAAG
44002957 AACTTACAT
1 AACTTACAT
* *
44002966 AATTTACAC
1 AACTTACAT
*
44002975 AACTTACTT
1 AACTTACAT
*
44002984 AACCTACAT
1 AACTTACAT
44002993 AACTTACAT
1 AACTTACAT
44003002 AA--TACA-
1 AACTTACAT
44003008 AAGCTTACAT
1 AA-CTTACAT
* *
44003018 AACTAAAAT
1 AACTTACAT
* *
44003027 AGCTTACAC
1 AACTTACAT
44003036 AACTTACAT
1 AACTTACAT
*
44003045 AACTTACAG
1 AACTTACAT
* *
44003054 AAGTTATAT
1 AACTTACAT
*
44003063 AATACATA-AT
1 -A-ACTTACAT
44003073 AACTTAC--
1 AACTTACAT
44003080 AACTTACAT
1 AACTTACAT
*
44003089 AACATACAT
1 AACTTACAT
* **
44003098 TACTTTGAT
1 AACTTACAT
44003107 AACTTACAT
1 AACTTACAT
*
44003116 AAGTTACAT
1 AACTTACAT
*
44003125 AA--TACAC
1 AACTTACAT
44003132 AAC-TACAT
1 AACTTACAT
** *
44003140 AGTTTACTT
1 AACTTACAT
*
44003149 AA--TACAA
1 AACTTACAT
44003156 AACTTACAT
1 AACTTACAT
44003165 AACTT--AT
1 AACTTACAT
*
44003172 ACACGTACAT
1 A-ACTTACAT
*
44003182 AACCTACAT
1 AACTTACAT
*
44003191 AATTTAC
1 AACTTAC
44003198 TTAATACATA
Statistics
Matches: 171, Mismatches: 45, Indels: 32
0.69 0.18 0.13
Matches are distributed among these distances:
6 2 0.01
7 25 0.15
8 12 0.07
9 121 0.71
10 8 0.05
11 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:44003146 original size:24 final size:24
Alignment explanation
Indices: 44003107--44003165 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
44003097 TTACTTTGAT
*
44003107 AACTTACATAAGTTACATAATACAC
1 AACTTACAT-AGTTACATAATACAA
*
44003132 AAC-TACATAGTTTACTTAATACAA
1 AACTTACATAG-TTACATAATACAA
44003156 AACTTACATA
1 AACTTACATA
44003166 ACTTATACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 2 0.07
24 19 0.63
25 9 0.30
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (24 bp):
AACTTACATAGTTACATAATACAA
Found at i:44009925 original size:27 final size:27
Alignment explanation
Indices: 44009895--44009970 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
44009885 GACTAACTCG
*
44009895 TGTTTATTGTCCCGACGGACTACCCTA
1 TGTTCATTGTCCCGACGGACTACCCTA
* ** * *
44009922 TGTTCATTATCTTGTCGGACTACCCTG
1 TGTTCATTGTCCCGACGGACTACCCTA
* *
44009949 TGTTCATTGTCCCAACAGACTA
1 TGTTCATTGTCCCGACGGACTA
44009971 TTCATTGTTT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.36
Consensus pattern (27 bp):
TGTTCATTGTCCCGACGGACTACCCTA
Found at i:44017275 original size:285 final size:286
Alignment explanation
Indices: 44016757--44017294 Score: 918
Period size: 285 Copynumber: 1.9 Consensus size: 286
44016747 TTTAACAGCG
*
44016757 AACTTGACGCAAGTTTTACATTAAAATTAGAAAAACAAAAAAACTGTTAAAACGTATTGCATCGT
1 AACTTGACGCAAGTTTTACATTAAAATAAGAAAAACAAAAAAACTGTTAAAACGTATTGCATCGT
* * *
44016822 CATTTTTATGTAGTATTTGTGTTTTCAAATGAATGTGTTTAGATATGTATTTTTCGATTTCGTGT
66 CATTTTTATGTAGTATTTATGTTTCCAAATGAATGTGTTTAGATATGTATTTTTCGATTCCGTGT
*
44016887 TTGAACGACACATTTCTCAAAGCTAAATTGAACATTTTGCAACATTGAATTTATTATAAATAACT
131 TTGAACGACACATTTCTCAAAGCTAAATTGAACATTTTGCAACATCGAATTTATTATAAATAACT
44016952 TGTCAAAATATATTACTCATATTATTTTATACAATTTTGGATATTATAAATAAAATGGACCCAAG
196 TGTCAAAATATATTACTCATATTATTTTATACAATTTTGGATATTATAAATAAAATGGACCCAAG
44017017 TATCCAAAATCAGAGTTTTCACATCA
261 TATCCAAAATCAGAGTTTTCACATCA
* * * *
44017043 AACTTGACGCAAGTTTTATATTAAAATAAGGAAAAC-AAAACACTGTTAAAACGTGTTGCATCGT
1 AACTTGACGCAAGTTTTACATTAAAATAAGAAAAACAAAAAAACTGTTAAAACGTATTGCATCGT
* *
44017107 CATTTTTATGTAGTATTTATGTTTCCAAA-GAAATGTGTTTAGATATGTATTTTTTGGTTCCGTG
66 CATTTTTATGTAGTATTTATGTTTCCAAATG-AATGTGTTTAGATATGTATTTTTCGATTCCGTG
*
44017171 TTTGAACGACACATTTCTCAAAGCTAAATTGAACATTTTGCAACATCGAATTTATTGTAAATAAC
130 TTTGAACGACACATTTCTCAAAGCTAAATTGAACATTTTGCAACATCGAATTTATTATAAATAAC
** *
44017236 TTGTCAAAATATATTACTCATATTATTTTATGTAATTTTGGATATTATTAATAAAATGG
195 TTGTCAAAATATATTACTCATATTATTTTATACAATTTTGGATATTATAAATAAAATGG
44017295 TTGATGGAAA
Statistics
Matches: 236, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
284 1 0.00
285 202 0.86
286 33 0.14
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (286 bp):
AACTTGACGCAAGTTTTACATTAAAATAAGAAAAACAAAAAAACTGTTAAAACGTATTGCATCGT
CATTTTTATGTAGTATTTATGTTTCCAAATGAATGTGTTTAGATATGTATTTTTCGATTCCGTGT
TTGAACGACACATTTCTCAAAGCTAAATTGAACATTTTGCAACATCGAATTTATTATAAATAACT
TGTCAAAATATATTACTCATATTATTTTATACAATTTTGGATATTATAAATAAAATGGACCCAAG
TATCCAAAATCAGAGTTTTCACATCA
Found at i:44021168 original size:21 final size:21
Alignment explanation
Indices: 44021144--44021187 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
44021134 ATGTCCCCTC
* *
44021144 CACACAAGCGTGTGTGTCCTT
1 CACACAAGCATGTGTGGCCTT
**
44021165 CACACGGGCATGTGTGGCCTT
1 CACACAAGCATGTGTGGCCTT
44021186 CA
1 CA
44021188 TATGAGCGTG
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:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (21 bp):
CACACAAGCATGTGTGGCCTT
Found at i:44029114 original size:3 final size:3
Alignment explanation
Indices: 44029071--44029159 Score: 92
Period size: 3 Copynumber: 29.0 Consensus size: 3
44029061 TTTAGCAATC
* *
44029071 TTA TTA TT- TTG TTAA TTA TT- TTAA TGTA TTA TCA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TT-A T-TA TTA TTA -TTA TTA TTA TTA
* *
44029118 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44029160 CTACTATTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
2 4 0.05
3 61 0.84
4 7 0.10
5 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:44034755 original size:37 final size:37
Alignment explanation
Indices: 44034714--44034831 Score: 89
Period size: 37 Copynumber: 3.1 Consensus size: 37
44034704 ATATATTTCA
44034714 ATTTCACCGAATAATTATTACATTTTTATTCTATTTT
1 ATTTCACCGAATAATTATTACATTTTTATTCTATTTT
* * * *
44034751 ATTTCAACGAACTGAA-CA-TAC-TCTATTATTTTATATTCT
1 ATTTCACCGAA-T-AATTATTACAT-TTTTATTCTAT-TT-T
** * *
44034790 ATTTCTACTTAATAATTATTACATTTTTACTCTATTCT
1 ATTTC-ACCGAATAATTATTACATTTTTATTCTATTTT
44034828 ATTT
1 ATTT
44034832 TGTAAATACG
Statistics
Matches: 60, Mismatches: 12, Indels: 17
0.67 0.13 0.19
Matches are distributed among these distances:
36 1 0.02
37 22 0.37
38 11 0.18
39 11 0.18
40 14 0.23
41 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.52
Consensus pattern (37 bp):
ATTTCACCGAATAATTATTACATTTTTATTCTATTTT
Found at i:44041908 original size:21 final size:20
Alignment explanation
Indices: 44041884--44041932 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
44041874 TTTTCTACTG
44041884 TATTAAATTGACATTTAAAAA
1 TATTAAATTGA-ATTTAAAAA
* *
44041905 TATTTATAATTTAATTTAAAAT
1 TA-TTA-AATTGAATTTAAAAA
44041927 TATTAA
1 TATTAA
44041933 TTATAATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 1 0.04
21 5 0.21
22 13 0.54
23 5 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TATTAAATTGAATTTAAAAA
Found at i:44041922 original size:22 final size:22
Alignment explanation
Indices: 44041896--44041954 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 22
44041886 TTAAATTGAC
*
44041896 ATTTAAAAATATTTATAATT-T
1 ATTTAAAAATAATTATAATTCT
44041917 AATTTAAAATTATTAATTATAATTCT
1 -ATTTAAAA--A-TAATTATAATTCT
44041943 ATTTAAAAATAA
1 ATTTAAAAATAA
44041955 ATTGTGATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
22 11 0.34
23 1 0.03
24 1 0.03
25 18 0.56
26 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAAAAATAATTATAATTCT
Found at i:44042478 original size:18 final size:18
Alignment explanation
Indices: 44042455--44042490 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
44042445 TTACCACCAC
44042455 TATCAT-CATCATTTTCTT
1 TATCATGCAT-ATTTTCTT
44042473 TATCATGCATATTTTCTT
1 TATCATGCATATTTTCTT
44042491 GGTCAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.22, C:0.19, G:0.03, T:0.56
Consensus pattern (18 bp):
TATCATGCATATTTTCTT
Found at i:44043071 original size:26 final size:26
Alignment explanation
Indices: 44043042--44043091 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
44043032 CTTTTTAAAC
*
44043042 AAAAGTGATTTTA-AAAAGTGTGATGG
1 AAAAGTGA-TGTAGAAAAGTGTGATGG
44043068 AAAAGTGATGTAGAAAAGTGTGAT
1 AAAAGTGATGTAGAAAAGTGTGAT
44043092 TTATTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (26 bp):
AAAAGTGATGTAGAAAAGTGTGATGG
Found at i:44043240 original size:31 final size:31
Alignment explanation
Indices: 44043202--44043301 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
44043192 ATGATATTTA
44043202 AAAATAATAATCTAGTGGTATATAAGATAAG
1 AAAATAATAATCTAGTGGTATATAAGATAAG
** * * *
44043233 AAAATAAT--TCCT--TTTTAAATAA-TTAATTTA
1 AAAATAATAAT-CTAGTGGTATATAAGATAA---G
44043263 AAAATAATAATCTAGTGGTATATAAGATAAG
1 AAAATAATAATCTAGTGGTATATAAGATAAG
44043294 AAAATAAT
1 AAAATAAT
44043302 TCCTTTTTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 18
0.64 0.13 0.23
Matches are distributed among these distances:
27 3 0.06
28 7 0.14
29 1 0.02
30 10 0.20
31 18 0.36
32 1 0.02
33 7 0.14
34 3 0.06
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (31 bp):
AAAATAATAATCTAGTGGTATATAAGATAAG
Found at i:44043265 original size:61 final size:61
Alignment explanation
Indices: 44043197--44043325 Score: 249
Period size: 61 Copynumber: 2.1 Consensus size: 61
44043187 TTTAAATGAT
44043197 ATTTAAAAATAATAATCTAGTGGTATATAAGATAAGAAAATAATTCCTTTTTAAATAATTA
1 ATTTAAAAATAATAATCTAGTGGTATATAAGATAAGAAAATAATTCCTTTTTAAATAATTA
44043258 ATTTAAAAATAATAATCTAGTGGTATATAAGATAAGAAAATAATTCCTTTTTAAATAATTA
1 ATTTAAAAATAATAATCTAGTGGTATATAAGATAAGAAAATAATTCCTTTTTAAATAATTA
*
44043319 ATATAAA
1 ATTTAAA
44043326 TTACTTTTTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (61 bp):
ATTTAAAAATAATAATCTAGTGGTATATAAGATAAGAAAATAATTCCTTTTTAAATAATTA
Found at i:44044386 original size:16 final size:16
Alignment explanation
Indices: 44044365--44044400 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
44044355 TTTGGTTCGC
44044365 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
44044381 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
44044397 TGTA
1 TGTA
44044401 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:44044734 original size:125 final size:125
Alignment explanation
Indices: 44044582--44044807 Score: 389
Period size: 125 Copynumber: 1.8 Consensus size: 125
44044572 TTTAATAAGG
* * * *
44044582 TTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACCCATTTTAA
1 TTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACACATTATAA
*
44044647 TTAAAATATATAATTTCATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAATTAA
66 TTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAATTAA
* *
44044707 TTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAA
1 TTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACACATTATAA
44044772 TTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 TTAAAATATATAATTTAATAAAATTCTTAATAATTA
44044808 ATATTCTTAT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 94 1.00
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (125 bp):
TTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACACATTATAA
TTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAATTAA
Found at i:44044778 original size:16 final size:16
Alignment explanation
Indices: 44044741--44044782 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
44044731 TTAATCATAT
*
44044741 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
44044757 TT-AAATATATTATAA
1 TTAAAATATATTATAA
44044772 TTAAAATATAT
1 TTAAAATATAT
44044783 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:44044789 original size:14 final size:15
Alignment explanation
Indices: 44044750--44044791 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
44044740 TTTAAACATA
*
44044750 ATTATTATTAAATAT
1 ATTATAATTAAATAT
44044765 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
44044779 A-TATAATTTAATA
1 ATTATAATTAAATA
44044792 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:44044840 original size:125 final size:122
Alignment explanation
Indices: 44044594--44045036 Score: 449
Period size: 120 Copynumber: 3.6 Consensus size: 122
44044584 ATTATTATCA
* *** *
44044594 ATAATA-AATATTTTAATCATATTTAAACATAATTATTATTAAACCCATTTTAATTAAAATATAT
1 ATAATACAATAATTTAAT-ATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
* ** *** * ** * * *
44044658 AATTTCATAAAATTCTTAATAATTAGCA--GAAATTTGTTTTGGTAATTAATTATTAATAT
65 AATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATT--TACTAAATCA-TAATAT
44044717 CAATAATA-AATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATAT
1 --ATAATACAATAATTTAAT-ATATTTAAACATAATTATTATTAAATATATTATAATTAAAATAT
44044781 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATAT
63 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACT-AAATCATAATAT
* ** *
44044842 ATGATACTGTAA---AATATAAATT-AACATAATTATTATTAAATATATTATAATTAAAATATAT
1 ATAATACAATAATTTAATAT-ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
44044903 AATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATCATAATAT
65 AATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACT-AAATCATAATAT
* * * * * * * * *
44044962 ATGATACTATAAATGAA-A-ATTTGAA-ATAATTAATATTAAATATATTTTATTTAAAATATATG
1 ATAATACAATAATTTAATATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATA
44045024 ATTTAATAAAATT
66 ATTTAATAAAATT
44045037 TAAAATAATT
Statistics
Matches: 281, Mismatches: 28, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
120 159 0.57
121 8 0.03
122 1 0.00
123 7 0.02
124 3 0.01
125 93 0.33
126 4 0.01
127 6 0.02
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (122 bp):
ATAATACAATAATTTAATATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATA
ATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAATCATAATAT
Found at i:44044841 original size:61 final size:61
Alignment explanation
Indices: 44044776--44044963 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
44044766 TTATAATTAA
*
44044776 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATCAT
* * * * * * * * * * *
44044837 AATATATGATACT-GTAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATATTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTACTAAAATCAT
44044896 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATCAT
44044957 AATATAT
1 AATATAT
44044964 GATACTATAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
57 4 0.04
58 3 0.03
59 28 0.30
60 16 0.17
61 36 0.38
62 3 0.03
63 4 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATCAT
Found at i:44044907 original size:120 final size:121
Alignment explanation
Indices: 44044739--44045036 Score: 487
Period size: 120 Copynumber: 2.5 Consensus size: 121
44044729 ATTTAATCAT
*
44044739 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
44044804 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTAT-AAATGA-AA
44044861 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
44044924 ATTAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAATGAAA
* * * *
44044980 ATTTGAA-ATAATTAATATTAAATATATTTTATTTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
44045037 TAAAATAATT
Statistics
Matches: 167, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
119 7 0.04
120 155 0.93
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAATGAAA
Found at i:44044909 original size:14 final size:15
Alignment explanation
Indices: 44044860--44044911 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
44044850 GTAAAATATA
44044860 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
44044875 TATTAAATATATTAT
1 AATTAAATATATTAT
44044890 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
44044903 AATTTAATA
1 AATTAAATA
44044912 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:44044962 original size:59 final size:59
Alignment explanation
Indices: 44044779--44044962 Score: 164
Period size: 59 Copynumber: 3.1 Consensus size: 59
44044769 TAATTAAAAT
*
44044779 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATCATA
* * * * * * * * *
44044838 ATAT-ATGATACTGTAAAA-TATAAATTAACATAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATAAT-TTA--ATAAAATTCTTAA-TAA-TTAA-TATTCTTATATGA-ATT-TACTAAAATCA
44044898 T-
58 TA
44044899 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATCATA
44044958 ATATA
1 ATATA
44044963 TGATACTATA
Statistics
Matches: 93, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
56 6 0.06
57 12 0.13
58 8 0.09
59 19 0.20
60 8 0.09
61 14 0.15
62 8 0.09
63 12 0.13
64 6 0.06
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATCATA
Found at i:44045118 original size:18 final size:18
Alignment explanation
Indices: 44045092--44045133 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
44045082 TTTAAAATAA
*
44045092 TAATTATTACATA-TAATT
1 TAATAATTA-ATATTAATT
44045110 TAATAATTAATATTAATT
1 TAATAATTAATATTAATT
*
44045128 TCATAA
1 TAATAA
44045134 AAAATCNNNN
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATAATTAATATTAATT
Found at i:44045123 original size:24 final size:25
Alignment explanation
Indices: 44045077--44045124 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
44045067 TATGAATTTG
44045077 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
44045103 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
44045125 ATTTCATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:44049680 original size:17 final size:17
Alignment explanation
Indices: 44049654--44049696 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
44049644 TAAGCCATCC
*
44049654 ATACAAAGCTAACAATG
1 ATACATAGCTAACAATG
44049671 ATACATAGCTAACAATG
1 ATACATAGCTAACAATG
44049688 ATACATAGC
1 ATACATAGC
44049697 AAATCATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.21
Consensus pattern (17 bp):
ATACATAGCTAACAATG
Found at i:44050198 original size:20 final size:20
Alignment explanation
Indices: 44050160--44050198 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44050150 GCAAATTTCA
* *
44050160 GAGTTTTAATTTTGAAAATC
1 GAGTTCTAATTTGGAAAATC
*
44050180 GAGTTCTAATTTGGTAAAT
1 GAGTTCTAATTTGGAAAAT
44050199 TGTATAATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (20 bp):
GAGTTCTAATTTGGAAAATC
Found at i:44060099 original size:2 final size:2
Alignment explanation
Indices: 44060092--44060139 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
44060082 AGCTCAAAAG
44060092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44060134 TA TA TA
1 TA TA TA
44060140 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44069155 original size:41 final size:41
Alignment explanation
Indices: 44069110--44069231 Score: 105
Period size: 41 Copynumber: 3.1 Consensus size: 41
44069100 CCACACATCT
44069110 ATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGC
1 ATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGC
** * * * ** * *
44069151 ATGTGTTAGG-CCTGTGTGG--TT-TGA--GCCACACAT-C
1 ATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGC
44069185 TATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGC
1 -ATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGC
44069227 ATGTG
1 ATGTG
44069232 TTAGGCCGTG
Statistics
Matches: 55, Mismatches: 18, Indels: 16
0.62 0.20 0.18
Matches are distributed among these distances:
34 1 0.02
35 13 0.24
36 7 0.13
37 2 0.04
38 4 0.07
39 2 0.04
40 7 0.13
41 18 0.33
42 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.30
Consensus pattern (41 bp):
ATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGC
Found at i:44069220 original size:76 final size:75
Alignment explanation
Indices: 44069094--44069244 Score: 293
Period size: 76 Copynumber: 2.0 Consensus size: 75
44069084 AACTCATTAC
44069094 TTTGAGCCACACATCTATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGCATGTGTTA
1 TTTGAGCCACACATCTATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGCATGTGTTA
44069159 GGCCTGTGTGG
66 GGCC-GTGTGG
44069170 TTTGAGCCACACATCTATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGCATGTGTTA
1 TTTGAGCCACACATCTATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGCATGTGTTA
44069235 GGCCGTGTGG
66 GGCCGTGTGG
44069245 GCCACACAGG
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 6 0.08
76 69 0.92
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (75 bp):
TTTGAGCCACACATCTATGTGCCAGGTCGTGTATGGCATTAAGAGGGATATACGTGCATGTGTTA
GGCCGTGTGG
Found at i:44076045 original size:6 final size:6
Alignment explanation
Indices: 44076003--44076041 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
44075993 GTTTCCAAAT
* *
44076003 ATGGAA TTGGAA ATGGAA ATGGAA ATGGAA ATGAAA ATG
1 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATG
44076042 AAAACTTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.21
Consensus pattern (6 bp):
ATGGAA
Found at i:44077492 original size:42 final size:42
Alignment explanation
Indices: 44077446--44077548 Score: 161
Period size: 42 Copynumber: 2.5 Consensus size: 42
44077436 ACAATCATGT
*
44077446 TGGCACATAAGTGCATCATCGAATGTATCGAAGCAAATATAC
1 TGGCACATAAGTGCATCATCGAATATATCGAAGCAAATATAC
* * * *
44077488 TGGCACGTAAGTACATCATCGGATATATCGAAGCAATTATAC
1 TGGCACATAAGTGCATCATCGAATATATCGAAGCAAATATAC
44077530 TGGCACATAAGTGCATCAT
1 TGGCACATAAGTGCATCAT
44077549 TGGCTAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (42 bp):
TGGCACATAAGTGCATCATCGAATATATCGAAGCAAATATAC
Found at i:44081567 original size:22 final size:22
Alignment explanation
Indices: 44081542--44081584 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
44081532 ATTACTATAC
* *
44081542 TTATGGCTTGTAGCTATTCTGG
1 TTATAGCTTATAGCTATTCTGG
44081564 TTATAGCTTATAGCTATTCTG
1 TTATAGCTTATAGCTATTCTG
44081585 TTTACGACTT
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:0.19, C:0.14, G:0.21, T:0.47
Consensus pattern (22 bp):
TTATAGCTTATAGCTATTCTGG
Found at i:44081658 original size:26 final size:26
Alignment explanation
Indices: 44081607--44081658 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
44081597 AGCCATTCTG
** * *
44081607 ACTACTGGCAGCTCTGCTGTATTATT
1 ACTACTGGCAGCAATGCTGCAATATT
44081633 ACTACTGGCAGCAATGCTGCAATATT
1 ACTACTGGCAGCAATGCTGCAATATT
44081659 GGTGTGAGGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (26 bp):
ACTACTGGCAGCAATGCTGCAATATT
Found at i:44082297 original size:11 final size:11
Alignment explanation
Indices: 44082281--44082306 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44082271 AATAACACGA
44082281 AAGTATTGGAG
1 AAGTATTGGAG
44082292 AAGTATTGGAG
1 AAGTATTGGAG
44082303 AAGT
1 AAGT
44082307 CCTGGGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.27
Consensus pattern (11 bp):
AAGTATTGGAG
Found at i:44084485 original size:32 final size:32
Alignment explanation
Indices: 44084444--44084646 Score: 219
Period size: 32 Copynumber: 6.4 Consensus size: 32
44084434 GCTACGATGC
*
44084444 TACTGATGGCTTTGTGCCGATCATGTTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
44084476 TACTGATGGCTATGTGCCGTTCATGTTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * *
44084508 TACTGATGACTTTGTGTCAAACATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
44084540 TACTGATGGCTTTGTGCCGGTGATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * * *
44084572 TACTAATGGCTGTGTACCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
44084604 TACTGATGGCTTTGTGTCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
44084635 TACTTATGGCTT
1 TACTGATGGCTT
44084647 GTAGCCATTC
Statistics
Matches: 141, Mismatches: 30, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
31 11 0.08
32 130 0.92
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:44084608 original size:96 final size:95
Alignment explanation
Indices: 44084444--44084646 Score: 262
Period size: 96 Copynumber: 2.1 Consensus size: 95
44084434 GCTACGATGC
* * * * * * *
44084444 TACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTATGTGCCGTTCATGTTACCGTT
1 TACTGATGGCTTTGTGCCGATCATATTACCGTTACTAATGGCTATGTACCGATCATATCACCGCT
44084509 ACTGATGACTTTGTGTCAAACATATTACCG
66 ACTGATGACTTTGTGTCAAACATATTACCG
* * * *
44084539 TTACTGATGGCTTTGTGCCGGTGATATTACCGTTACTAATGGCTGTGTACCGATCATATCACTGC
1 -TACTGATGGCTTTGTGCCGATCATATTACCGTTACTAATGGCTATGTACCGATCATATCACCGC
* * *
44084604 TACTGATGGCTTTGTGTCAATCATATTACTG
65 TACTGATGACTTTGTGTCAAACATATTACCG
*
44084635 TACTTATGGCTT
1 TACTGATGGCTT
44084647 GTAGCCATTC
Statistics
Matches: 92, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
95 11 0.12
96 81 0.88
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (95 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGTTACTAATGGCTATGTACCGATCATATCACCGCT
ACTGATGACTTTGTGTCAAACATATTACCG
Found at i:44084663 original size:22 final size:22
Alignment explanation
Indices: 44084638--44084702 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
44084628 ATTACTGTAC
*
44084638 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTTATAGCCATTCTGT
* * *
44084660 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTTATAGCCATTCTGT
* * *
44084682 TTACGGGTTTTAGCCATTCTG
1 TTATGGCTTATAGCCATTCTG
44084703 ACTACTGGCA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (22 bp):
TTATGGCTTATAGCCATTCTGT
Found at i:44084875 original size:28 final size:28
Alignment explanation
Indices: 44084842--44084895 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
44084832 CATACTGATA
*
44084842 CTGTATCGGGCTTAGGCCCACACTGTTT
1 CTGTATCGGGCTAAGGCCCACACTGTTT
*
44084870 CTGTATTGGGCTAAGGCCCACACTGT
1 CTGTATCGGGCTAAGGCCCACACTGT
44084896 ACTGTTACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.30
Consensus pattern (28 bp):
CTGTATCGGGCTAAGGCCCACACTGTTT
Found at i:44087070 original size:23 final size:23
Alignment explanation
Indices: 44087044--44087188 Score: 272
Period size: 23 Copynumber: 6.3 Consensus size: 23
44087034 AGTGTTATTG
44087044 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGT
44087067 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGT
44087090 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGT
*
44087113 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGT
44087136 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGT
*
44087159 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGT
44087182 ATCAGTG
1 ATCAGTG
44087189 TGGCACTTAT
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 119 1.00
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACGT
Found at i:44090857 original size:21 final size:21
Alignment explanation
Indices: 44090831--44090883 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
44090821 CGACACATAA
44090831 GTGCCTGAAATGACACACGAG
1 GTGCCTGAAATGACACACGAG
* *
44090852 GTGCCTGATACGACACACGAG
1 GTGCCTGAAATGACACACGAG
*
44090873 GTGCTTGAAAT
1 GTGCCTGAAAT
44090884 ATGACACATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (21 bp):
GTGCCTGAAATGACACACGAG
Found at i:44090889 original size:23 final size:21
Alignment explanation
Indices: 44090831--44090891 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
44090821 CGACACATAA
*
44090831 GTGCCTGAAATGACACACGAG
1 GTGCCTGATATGACACACGAG
*
44090852 GTGCCTGATACGACACACGAG
1 GTGCCTGATATGACACACGAG
*
44090873 GTGCTTGAAATATGACACA
1 GTGCCTG--ATATGACACA
44090892 TAAAGTGCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 25 0.74
23 9 0.26
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
GTGCCTGATATGACACACGAG
Found at i:44091555 original size:19 final size:19
Alignment explanation
Indices: 44091484--44091556 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 19
44091474 TAATTATTTA
*
44091484 TATTTAATCATATAATAAAT
1 TATTTAAT-ATTTAATAAAT
44091504 TA-TTAATATAATTAATATAAT
1 TATTTAATAT--TTAATA-AAT
*
44091525 T-TATT-ATTTTTAATAAAT
1 TAT-TTAATATTTAATAAAT
44091543 TATTTAATATTTAA
1 TATTTAATATTTAA
44091557 ATTTTATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
18 8 0.19
19 19 0.44
20 7 0.16
21 7 0.16
22 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTTAATATTTAATAAAT
Found at i:44091654 original size:15 final size:15
Alignment explanation
Indices: 44091634--44091690 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
44091624 TATCAATATC
44091634 AATATTTTAATAATA
1 AATATTTTAATAATA
*
44091649 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
44091668 AATATATTAATAATA
1 AATATTTTAATAATA
*
44091683 AATGTTTT
1 AATATTTT
44091691 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:44093351 original size:33 final size:33
Alignment explanation
Indices: 44093311--44093375 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
44093301 ATATAGTACA
44093311 TACATATATTAATTAAAAATGTATACATATATG
1 TACATATATTAATTAAAAATGTATACATATATG
*
44093344 TACATATATTAATTACAAATGTATACATATAT
1 TACATATATTAATTAAAAATGTATACATATAT
44093376 TTATTACACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.40
Consensus pattern (33 bp):
TACATATATTAATTAAAAATGTATACATATATG
Found at i:44093360 original size:23 final size:23
Alignment explanation
Indices: 44093334--44093383 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
44093324 TAAAAATGTA
* *
44093334 TACATATATGTACATATATTAAT
1 TACAAATATATACATATATTAAT
* *
44093357 TACAAATGTATACATATATTTAT
1 TACAAATATATACATATATTAAT
44093380 TACA
1 TACA
44093384 CATGTATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (23 bp):
TACAAATATATACATATATTAAT
Found at i:44093388 original size:23 final size:23
Alignment explanation
Indices: 44093344--44093390 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
44093334 TACATATATG
44093344 TACATATATTAATTACAAATGTA
1 TACATATATTAATTACAAATGTA
* *
44093367 TACATATATTTATTACACATGTA
1 TACATATATTAATTACAAATGTA
44093390 T
1 T
44093391 TTATAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (23 bp):
TACATATATTAATTACAAATGTA
Found at i:44094141 original size:108 final size:108
Alignment explanation
Indices: 44093952--44094166 Score: 367
Period size: 108 Copynumber: 2.0 Consensus size: 108
44093942 TCACATTTGC
* *
44093952 AATTCACTATAATTTTGTAATTATGATGAGTATTATTTTTATGCGCGCTCAACGTTTATTTCATT
1 AATTCACTATAATTTTGTAATTATGACGAGTATTATTTGTATGCGCGCTCAACGTTTATTTCATT
**
44094017 AAATTTTACATTTTACCTTATTGGGTCAAGTGGGAGAATGTGT
66 AAATTTTACATTTTACCACATTGGGTCAAGTGGGAGAATGTGT
* * *
44094060 AATTCACTATAATTTTGTAATTGTGACGAGTGTTATTTGTATGCGCGCTCAATGTTTATTTCATT
1 AATTCACTATAATTTTGTAATTATGACGAGTATTATTTGTATGCGCGCTCAACGTTTATTTCATT
44094125 AAATTTTACATTTTACCACATTGGGTCAAGTGGGAGAATGTG
66 AAATTTTACATTTTACCACATTGGGTCAAGTGGGAGAATGTG
44094167 AGATTTTAGC
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 100 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (108 bp):
AATTCACTATAATTTTGTAATTATGACGAGTATTATTTGTATGCGCGCTCAACGTTTATTTCATT
AAATTTTACATTTTACCACATTGGGTCAAGTGGGAGAATGTGT
Found at i:44096759 original size:24 final size:23
Alignment explanation
Indices: 44096730--44096777 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
44096720 TATGTTAGCG
44096730 AACAAAAATATATAAATATAAATA
1 AACAAAAATATATAAATA-AAATA
* * *
44096754 AACAAATATTTATATATAAAATA
1 AACAAAAATATATAAATAAAATA
44096777 A
1 A
44096778 GATAAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (23 bp):
AACAAAAATATATAAATAAAATA
Found at i:44097168 original size:23 final size:20
Alignment explanation
Indices: 44097137--44097180 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 20
44097127 AAATTTTTGG
44097137 AAATATTCATGTATAAGGAGACA
1 AAATATTCAT-TA-AAGG-GACA
*
44097160 AAATTTTCATTAAAGGGACA
1 AAATATTCATTAAAGGGACA
44097180 A
1 A
44097181 TTAAATCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 4 0.20
22 2 0.10
23 9 0.45
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (20 bp):
AAATATTCATTAAAGGGACA
Found at i:44097217 original size:20 final size:21
Alignment explanation
Indices: 44097188--44097231 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
44097178 CAATTAAATC
*
44097188 AATTTGATTAAAATCAAATTA
1 AATTTGATTAAAATCAAATAA
*
44097209 AATTT-ATTAGAATCAAATAA
1 AATTTGATTAAAATCAAATAA
44097229 AAT
1 AAT
44097232 CAGGATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (21 bp):
AATTTGATTAAAATCAAATAA
Found at i:44099410 original size:20 final size:20
Alignment explanation
Indices: 44099387--44099426 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44099377 TTTTAAAATG
44099387 TATAATTAACACAACTTCTA
1 TATAATTAACACAACTTCTA
* *
44099407 TATAATTATCTCAACTTCTA
1 TATAATTAACACAACTTCTA
44099427 CAATCATTTA
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:0.20, G:0.00, T:0.40
Consensus pattern (20 bp):
TATAATTAACACAACTTCTA
Found at i:44106770 original size:14 final size:15
Alignment explanation
Indices: 44106751--44106781 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44106741 AAATGAAAAT
44106751 AAGTAAT-ATATATA
1 AAGTAATAATATATA
44106765 AAGTAATAATATATA
1 AAGTAATAATATATA
44106780 AA
1 AA
44106782 TGAGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
AAGTAATAATATATA
Found at i:44107704 original size:132 final size:132
Alignment explanation
Indices: 44107545--44107932 Score: 557
Period size: 131 Copynumber: 2.9 Consensus size: 132
44107535 CTGCAACTTT
* * * * * *
44107545 AGGGAGATAAGACTGATAGCTTAAATCTACTTCCCTACTACTTCAGGAAGATAAGACTCGTCGTC
1 AGGGAGATAGGACTGGTGGCTTAAATCTACTTCCCTACTACTTCGGGAAGATAAGATTTGTCGTC
* ** *
44107610 TTTGATTTGCTCCACTACTATTTAGGGAGACAGGATATACAATCTTCAACCTACTCCACTACTGC
66 TTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACTGC
44107675 TC
131 TC
*
44107677 AGGGAGATAGGACTGGTGGCTTAAATCTACTT-CCTATTA-TCTCGGGAAGATAAGATTTGTCGT
1 AGGGAGATAGGACTGGTGGCTTAAATCTACTTCCCTACTACT-TCGGGAAGATAAGATTTGTCGT
* * *
44107740 CTTTGATCTGCTCCGCTACTGCTTAGGGAGACAGGATCTACAATTTTCAACCTACTCCACTGCTG
65 CTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACTG
*
44107805 CTT
130 CTC
* * * * *
44107808 AAGGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTATCTT-GGGAAGATAAGATTTGCCAT
1 AGGGAGATAGGACTGGTGGCTTAAATCTACTTCCCTACTA-CTTCGGGAAGATAAGATTTGTCGT
44107872 CTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACT
65 CTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACT
44107933 GCAAACTCAG
Statistics
Matches: 229, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
130 1 0.00
131 114 0.50
132 112 0.49
133 1 0.00
134 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (132 bp):
AGGGAGATAGGACTGGTGGCTTAAATCTACTTCCCTACTACTTCGGGAAGATAAGATTTGTCGTC
TTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACTGC
TC
Found at i:44107930 original size:44 final size:44
Alignment explanation
Indices: 44107750--44107932 Score: 120
Period size: 44 Copynumber: 4.2 Consensus size: 44
44107740 CTTTGATCTG
* *
44107750 CTCCGCTACTGCTTAGGGAGACAGGATCTACAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTA
* * * **** * * *
44107794 CTCCACTGCTGCTTAAGGAGATAGGA-CTAGTGGCTTAAATCTG
1 CTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTA
* * * * * * ** * *
44107837 CTTCC-CTACTATCTT-GGGAAGATAAGATTTGCCATCTTTGATCTG
1 C-TCCACTACT-GCTTAGGG-AGACAGGATCTACAATCTTCAACCTA
44107882 CTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTA
44107926 CTCCACT
1 CTCCACT
44107933 GCAAACTCAG
Statistics
Matches: 99, Mismatches: 34, Indels: 12
0.68 0.23 0.08
Matches are distributed among these distances:
43 16 0.16
44 65 0.66
45 18 0.18
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTA
Found at i:44107933 original size:132 final size:131
Alignment explanation
Indices: 44107521--44107934 Score: 571
Period size: 132 Copynumber: 3.1 Consensus size: 131
44107511 AATTGGTAAT
* ** * *
44107521 TTCAACCTGCTCCACTGCAACTTTAGGGAGATAAGACTGATAGCTTAAATCTACTTCCCTACTA-
1 TTCAACCTACTCCACTGCTGC-TTAGGGAGATAGGACTG-TGGCTTAAATCTACTTCCCTACTAT
* * * * ** *
44107585 CTTCAGGAAGATAAGACTCGTCGTCTTTGATTTGCTCCACTACTATTTAGGGAGACAGGATATAC
64 CTT-GGGAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAC
44107650 AATC
128 AATC
* * *
44107654 TTCAACCTACTCCACTACTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTACTT-CCTATTATC
1 TTCAACCTACTCCACTGCTGCTTAGGGAGATAGGACT-GTGGCTTAAATCTACTTCCCTACTATC
* *
44107718 TCGGGAAGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTGCTTAGGGAGACAGGATCTACAA
65 TTGGGAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
*
44107783 TT
130 TC
* *
44107785 TTCAACCTACTCCACTGCTGCTTAAGGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTATC
1 TTCAACCTACTCCACTGCTGCTTAGGGAGATAGGACT-GTGGCTTAAATCTACTTCCCTACTATC
* *
44107850 TTGGGAAGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
65 TTGGGAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
44107915 TC
130 TC
44107917 TTCAACCTACTCCACTGC
1 TTCAACCTACTCCACTGC
44107935 AAACTCAGAG
Statistics
Matches: 249, Mismatches: 29, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
131 112 0.45
132 119 0.48
133 18 0.07
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (131 bp):
TTCAACCTACTCCACTGCTGCTTAGGGAGATAGGACTGTGGCTTAAATCTACTTCCCTACTATCT
TGGGAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAAT
C
Found at i:44108087 original size:88 final size:89
Alignment explanation
Indices: 44107926--44108220 Score: 387
Period size: 89 Copynumber: 3.3 Consensus size: 89
44107916 CTTCAACCTA
* * * * *
44107926 CTCCACTGCAAACTC-AGAGAGGCAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAA
1 CTCCGCTGCAAACTCAAG-GAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAA
* * * *
44107990 GATAAGATCTGCTGTTTTTAGTTTG
65 GACAAGATCTGCTATCTTCAGTTTG
* * *
44108015 CTCCGCTGCAAACTCAAGGAGGCAAGGCT-GTGTCTTCGATCTACTTCGCTGCCAACATAGGAAG
1 CTCCGCTGCAAACTCAAGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
*
44108079 ACAAGATCTGCTATCTTCAGTCTG
66 ACAAGATCTGCTATCTTCAGTTTG
* *
44108103 CTTCGCTGCAAACTCAAGGAGGCAAGGCTAGTGTCTTCGATCTGCTTTGCTGCCAATACAGGAAG
1 CTCCGCTGCAAACTCAAGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
* *
44108168 ACAAGATTTGCTATCGTCAGTTTG
66 ACAAGATCTGCTATCTTCAGTTTG
* * *
44108192 CTTCGCTGTAAACTCAGGGAGGCAAGGCT
1 CTCCGCTGCAAACTCAAGGAGGCAAGGCT
44108221 TCACTTCAAT
Statistics
Matches: 182, Mismatches: 22, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
88 76 0.42
89 104 0.57
90 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (89 bp):
CTCCGCTGCAAACTCAAGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
ACAAGATCTGCTATCTTCAGTTTG
Found at i:44108107 original size:45 final size:45
Alignment explanation
Indices: 44108058--44108199 Score: 123
Period size: 45 Copynumber: 3.2 Consensus size: 45
44108048 CTTCGATCTA
44108058 CTTCGCTGCCAACATAGGAAGACAAGATCTGCTATCTTCAGTCTG
1 CTTCGCTGCCAACATAGGAAGACAAGATCTGCTATCTTCAGTCTG
* * * *
44108103 CTTCGCTGCAAAC-TCAAGG-AGGCAAG-GCTAG-TGTCTTC-GATCTG
1 CTTCGCTGCCAACAT--AGGAAGACAAGATCT-GCTATCTTCAG-TCTG
* * * * * *
44108147 CTTTGCTGCCAATACAGGAAGACAAGATTTGCTATCGTCAGTTTG
1 CTTCGCTGCCAACATAGGAAGACAAGATCTGCTATCTTCAGTCTG
44108192 CTTCGCTG
1 CTTCGCTG
44108200 TAAACTCAGG
Statistics
Matches: 73, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
43 4 0.05
44 30 0.41
45 35 0.48
46 4 0.05
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (45 bp):
CTTCGCTGCCAACATAGGAAGACAAGATCTGCTATCTTCAGTCTG
Found at i:44108957 original size:45 final size:45
Alignment explanation
Indices: 44108753--44109111 Score: 232
Period size: 45 Copynumber: 8.0 Consensus size: 45
44108743 CAAGATCTGT
* * * * ** *
44108753 TATCTTCAGTCTACTCCGCTGCAAAC-TCAAGGAGGCAAGACTTGT
1 TATCTTCAGTCTGCTCCACTGC-AACTTTAGGGAGATAAGACTTGC
* * * *
44108798 TTTCTTCAGTCTGCTCCACTGCAACTTCAAGGATATAAGACTTG-
1 TATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGC
* * * *
44108842 TAACTTTAATCTGCTCCACTGCAACCTCT-GGGAGATAAGA-TTCGC
1 TATCTTCAGTCTGCTCCACTGCAA-CTTTAGGGAGATAAGACTT-GC
*
44108887 CATCTTCAGTCTGC-CTCACTGCAACTTTAGAGG-GATAAGACTTGC
1 TATCTTCAGTCTGCTC-CACTGCAACTTTAG-GGAGATAAGACTTGC
* * * *
44108932 TTTCTTCAGTCTGCTCCATTACAACTTAAGGGAGATAAGACTTG-
1 TATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGC
* * * * * * * ** **
44108976 TAACTTTAATCCGCTCCTACTGTAACTTCAAGGAGAT-AGGTTTAT
1 TATCTTCAGTCTGCTCC-ACTGCAACTTTAGGGAGATAAGACTTGC
** * * * * *
44109021 TGGCTTTAATCTGCCCCACTACAACTTCAGGGAGATAAGA-TTCGC
1 TATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTT-GC
* *
44109066 CATCTTCAGTCTGCTCCACTGCAACTTTAGGGGGATAAGACTTGC
1 TATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGC
44109111 T
1 T
44109112 TTATCACCGA
Statistics
Matches: 242, Mismatches: 57, Indels: 30
0.74 0.17 0.09
Matches are distributed among these distances:
43 2 0.01
44 73 0.30
45 160 0.66
46 7 0.03
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (45 bp):
TATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGC
Found at i:44109034 original size:134 final size:134
Alignment explanation
Indices: 44108789--44109109 Score: 359
Period size: 134 Copynumber: 2.4 Consensus size: 134
44108779 TCAAGGAGGC
* *
44108789 AAGACTTGTTTTCTTCAGTCTGCTCCACTGCAACTTCAA-GGATATAAGACTTGTAACTTTAATC
1 AAGACTTGCTTTCTTCAGTCTGCTCCACTGCAACTT-AAGGGAGATAAGACTTGTAACTTTAATC
* ** * * * *
44108853 TGCTCCACTGCAACCTCTGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTGCAACTTTAGA
65 CGCTCCACTGCAACCTCAAGGAGATAAGATTCGCCATCTTCAATCTGCCCCACTACAACTTCAG-
44108918 GG-GAT
129 GGAGAT
* *
44108923 AAGACTTGCTTTCTTCAGTCTGCTCCATTACAACTTAAGGGAGATAAGACTTGTAACTTTAATCC
1 AAGACTTGCTTTCTTCAGTCTGCTCCACTGCAACTTAAGGGAGATAAGACTTGTAACTTTAATCC
* * * *
44108988 GCTCCTACTGTAACTTCAAGGAGATAGGTTTATT-GGC-T-TT-AATCTGCCCCACTACAACTTC
66 GCTCC-ACTGCAACCTCAAGGAGATAAG---ATTCGCCATCTTCAATCTGCCCCACTACAACTTC
44109049 AGGGAGAT
127 AGGGAGAT
** * *
44109057 AAGA-TTCGCCATCTTCAGTCTGCTCCACTGCAACTTTAGGGGGATAAGACTTG
1 AAGACTT-GCTTTCTTCAGTCTGCTCCACTGCAACTTAAGGGAGATAAGACTTG
44109110 CTTTATCACC
Statistics
Matches: 159, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
133 6 0.04
134 128 0.81
135 19 0.12
136 1 0.01
137 2 0.01
138 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (134 bp):
AAGACTTGCTTTCTTCAGTCTGCTCCACTGCAACTTAAGGGAGATAAGACTTGTAACTTTAATCC
GCTCCACTGCAACCTCAAGGAGATAAGATTCGCCATCTTCAATCTGCCCCACTACAACTTCAGGG
AGAT
Found at i:44111562 original size:22 final size:22
Alignment explanation
Indices: 44111500--44111571 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
44111490 ATTGTTCAAA
* **
44111500 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
44111522 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
44111544 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
44111566 CATGAG
1 CATGAG
44111572 GGTTTATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:44113930 original size:22 final size:23
Alignment explanation
Indices: 44113902--44113966 Score: 100
Period size: 22 Copynumber: 3.0 Consensus size: 23
44113892 TATGCACTAT
44113902 TAAACAGAGAGCACTAAA-GTGC
1 TAAACAGAGAGCACTAAATGTGC
*
44113924 TATACAGAGAGCAC-AAATGTGC
1 TAAACAGAGAGCACTAAATGTGC
44113946 TAAACAGAGAGCACT-AATGTG
1 TAAACAGAGAGCACTAAATGTG
44113967 ATAATAATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.08
22 36 0.92
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (23 bp):
TAAACAGAGAGCACTAAATGTGC
Found at i:44113981 original size:25 final size:25
Alignment explanation
Indices: 44113906--44114128 Score: 213
Period size: 25 Copynumber: 9.4 Consensus size: 25
44113896 CACTATTAAA
*
44113906 CAGAGAGCACTAAAGTGCT-AT-A-
1 CAGAGAGCACTAATGTGCTAATAAT
*
44113928 CAGAGAGCACAAATGTGCT-A-AA-
1 CAGAGAGCACTAATGTGCTAATAAT
*
44113950 CAGAGAGCACTAATGTGATAATAAT
1 CAGAGAGCACTAATGTGCTAATAAT
* *
44113975 CAGAGAGC-GT-AT-TG---GTAAT
1 CAGAGAGCACTAATGTGCTAATAAT
* * *
44113994 CGGAGAGCACTGACGTGCTAATAAT
1 CAGAGAGCACTAATGTGCTAATAAT
44114019 CAGAGAGCAC-AGATGTGCTAATAAT
1 CAGAGAGCACTA-ATGTGCTAATAAT
*
44114044 CAGAGAGCACTGGA-GTGCTAATAAT
1 CAGAGAGCACT-AATGTGCTAATAAT
**
44114069 CAGAGAGCACTGTTGTGCTAATAAT
1 CAGAGAGCACTAATGTGCTAATAAT
* *
44114094 CAGATAGCACTGATGTGCTAATAAT
1 CAGAGAGCACTAATGTGCTAATAAT
44114119 CAGAGAGCAC
1 CAGAGAGCAC
44114129 GCTAAACTCT
Statistics
Matches: 169, Mismatches: 18, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
19 11 0.07
20 1 0.01
21 1 0.01
22 40 0.24
23 3 0.02
24 4 0.02
25 108 0.64
26 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (25 bp):
CAGAGAGCACTAATGTGCTAATAAT
Found at i:44120603 original size:25 final size:25
Alignment explanation
Indices: 44120570--44120618 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
44120560 AAATGAAAGA
44120570 AAAAAATGCCACCGAAGAGCATACG
1 AAAAAATGCCACCGAAGAGCATACG
*
44120595 AAAAAATGCTACCGAAGAGCATAC
1 AAAAAATGCCACCGAAGAGCATAC
44120619 TCATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.10
Consensus pattern (25 bp):
AAAAAATGCCACCGAAGAGCATACG
Done.