Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 120 of 167
Found at i:40087860 original size:34 final size:34
Alignment explanation
Indices: 40087817--40087892 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
40087807 TTGCATACTA
* *
40087817 TACTGAAATGGGCTAAGGCCCAGATTGCCTCTAT
1 TACTGAAATGGGCTAAGGCCCAGACTGACTCTAT
* *
40087851 TACTGAAATGGGCTCAGGCCCAGACTGATTCTAT
1 TACTGAAATGGGCTAAGGCCCAGACTGACTCTAT
40087885 TACTGAAA
1 TACTGAAA
40087893 AAGTGGTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (34 bp):
TACTGAAATGGGCTAAGGCCCAGACTGACTCTAT
Found at i:40099446 original size:46 final size:45
Alignment explanation
Indices: 40099345--40099502 Score: 163
Period size: 46 Copynumber: 3.4 Consensus size: 45
40099335 TGATATGTGT
* ** **
40099345 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCCCATTATAAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTAAGATAA-A
* * **
40099391 GCCAATGTAAGACATGTCTGGGACATGCATCGGTATTAAGATGAAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTAAGAT-AAA
* *
40099437 GCTAGTGTAAAACATGTCTGGGACATGCATCGGCCTTGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTT-A-AGATA-AA
*
40099485 GCTAGTGTAAGACCTGTC
1 GCTAGTGTAAGACATGTC
40099503 AGGTACAGGG
Statistics
Matches: 91, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 66 0.73
47 4 0.04
48 21 0.23
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTAAGATAAA
Found at i:40099603 original size:49 final size:49
Alignment explanation
Indices: 40099532--40099661 Score: 140
Period size: 49 Copynumber: 2.7 Consensus size: 49
40099522 GTTGTGTGTT
* * *
40099532 AGTGTCAA-ACCTATCTAGGACATGGCATCGACAC-CGATAGATGAGAG-C
1 AGTGT-AAGACCTATCTGGGACATGGCATCGAC-CTCAATAGATGAAAGTC
* * * *
40099580 TAGTGTAAGACTTATCTGGGACATGGTATCGGCCTCAATATATGAAAGTC
1 -AGTGTAAGACCTATCTGGGACATGGCATCGACCTCAATAGATGAAAGTC
*
40099630 AGTGTAAGACCTGTCTGGGACATGGCATCGAC
1 AGTGTAAGACCTATCTGGGACATGGCATCGAC
40099662 TTTAACGTGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
48 3 0.04
49 63 0.94
50 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCTATCTGGGACATGGCATCGACCTCAATAGATGAAAGTC
Found at i:40117834 original size:46 final size:45
Alignment explanation
Indices: 40117675--40117837 Score: 215
Period size: 46 Copynumber: 3.6 Consensus size: 45
40117665 TGATATGTGT
*
40117675 GCTAGTGTAAGACATGTCTGGAACATGCATCAGCCACATTATA-A-G-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAG---CATTA-AGACGAA
* * *
40117721 GCCAGTGTAAGACATGTCTGAGACATGCATCAGCATTGAGACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTAAGACGA-A
40117767 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTAAGACGAAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTAAGACG-AA
40117813 GCTAGTGTAAGACATGTCTGGGACA
1 GCTAGTGTAAGACATGTCTGGGACA
40117838 GGGCGTCAGC
Statistics
Matches: 105, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
42 1 0.01
43 5 0.05
44 1 0.01
46 97 0.92
47 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.22
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTAAGACGAA
Found at i:40117936 original size:49 final size:49
Alignment explanation
Indices: 40117877--40117987 Score: 127
Period size: 49 Copynumber: 2.3 Consensus size: 49
40117867 GACTTGTCTG
* *
40117877 GGACATGGCATCGACAC-CGATAGATGAGA-TCTAGTGTAAAACCTATCTA
1 GGACATGGCATCGAC-CTCGATAGATGAAAGTC-AGTGTAAAACCTACCTA
* * * * *
40117926 GGACACGGCATCGGCCTCGATATATGAAAGTCAGTGTAAGACCTACCTG
1 GGACATGGCATCGACCTCGATAGATGAAAGTCAGTGTAAAACCTACCTA
40117975 GGACATGGCATCG
1 GGACATGGCATCG
40117988 TCTTTAACAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
48 1 0.02
49 49 0.94
50 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.21
Consensus pattern (49 bp):
GGACATGGCATCGACCTCGATAGATGAAAGTCAGTGTAAAACCTACCTA
Found at i:40120311 original size:30 final size:30
Alignment explanation
Indices: 40120275--40120334 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40120265 TTAGACACAA
40120275 ACACAAGTCATATAGACACCACAATACCAT
1 ACACAAGTCATATAGACACCACAATACCAT
40120305 ACACAAGTCATATAGACACCACAATACCAT
1 ACACAAGTCATATAGACACCACAATACCAT
40120335 CAATCACCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.30, G:0.07, T:0.17
Consensus pattern (30 bp):
ACACAAGTCATATAGACACCACAATACCAT
Found at i:40120665 original size:25 final size:25
Alignment explanation
Indices: 40120631--40120681 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
40120621 TTCTAGCTAC
40120631 CCATCTAGAGCTTTCCCTTTTAACA
1 CCATCTAGAGCTTTCCCTTTTAACA
*
40120656 CCATTTAGAGCTTTCCCTTTTAACA
1 CCATCTAGAGCTTTCCCTTTTAACA
40120681 C
1 C
40120682 ACTCTTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.08, T:0.37
Consensus pattern (25 bp):
CCATCTAGAGCTTTCCCTTTTAACA
Found at i:40122540 original size:18 final size:19
Alignment explanation
Indices: 40122517--40122568 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
40122507 CAAGTTTATG
*
40122517 GTAAAAATAAT-TACATGT
1 GTAAAAATAATATACATAT
*
40122535 GTAAAAGTAATATACATAT
1 GTAAAAATAATATACATAT
*
40122554 GTATATAATAATATA
1 GTA-AAAATAATATA
40122569 TGCAATACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 10 0.36
19 9 0.32
20 9 0.32
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.35
Consensus pattern (19 bp):
GTAAAAATAATATACATAT
Found at i:40122601 original size:5 final size:5
Alignment explanation
Indices: 40122591--40123453 Score: 1710
Period size: 5 Copynumber: 172.8 Consensus size: 5
40122581 TATTTAAGTA
40122591 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40122641 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40122691 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40122741 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40122791 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40122841 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40122891 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40122941 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40122991 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40123041 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40123091 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40123141 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40123191 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40123241 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40123291 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40123341 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40123391 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
40123441 TATAA TA-AT TATA
1 TATAT TATAT TATA
40123454 AAAGAATAAA
Statistics
Matches: 855, Mismatches: 2, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
4 3 0.00
5 852 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:40123559 original size:13 final size:13
Alignment explanation
Indices: 40123518--40123560 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
40123508 GAAGTAAAAT
40123518 GAAAGAAAAAGAAA
1 GAAAGAAAAAG-AA
*
40123532 GAAGGAAAAA-AA
1 GAAAGAAAAAGAA
*
40123544 GAAAGAAAAAGGA
1 GAAAGAAAAAGAA
40123557 GAAA
1 GAAA
40123561 AAGTCAAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 11 0.44
13 5 0.20
14 9 0.36
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
GAAAGAAAAAGAA
Found at i:40123561 original size:19 final size:20
Alignment explanation
Indices: 40123525--40123563 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
40123515 AATGAAAGAA
40123525 AAAGAAAGAAGGAAAAAAAG
1 AAAGAAAGAAGGAAAAAAAG
*
40123545 AAAGAAA-AAGGAGAAAAAG
1 AAAGAAAGAAGGAAAAAAAG
40123564 TCAAGGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAGGAAAAAAAG
Found at i:40143952 original size:30 final size:30
Alignment explanation
Indices: 40143916--40143980 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
40143906 CTCCAGGCCC
*
40143916 TGTCCTTCATACGACTGAGACACACGGTCG
1 TGTCCTTCACACGACTGAGACACACGGTCG
*
40143946 TGTCCTTCACACGGCTGAGACACACGGTCG
1 TGTCCTTCACACGACTGAGACACACGGTCG
40143976 TGTCC
1 TGTCC
40143981 CTACCCATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.20, C:0.32, G:0.25, T:0.23
Consensus pattern (30 bp):
TGTCCTTCACACGACTGAGACACACGGTCG
Found at i:40145750 original size:43 final size:43
Alignment explanation
Indices: 40145703--40145789 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
40145693 CACATGATAC
*
40145703 AACATCACATTAATTATATATACTTACCATACATGCAATATCA
1 AACATCACATTAATTAGATATACTTACCATACATGCAATATCA
40145746 AACATCACATTAATTAGATATACTTACCATACATGCAATATCA
1 AACATCACATTAATTAGATATACTTACCATACATGCAATATCA
40145789 A
1 A
40145790 GCATTTAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (43 bp):
AACATCACATTAATTAGATATACTTACCATACATGCAATATCA
Found at i:40148088 original size:20 final size:19
Alignment explanation
Indices: 40148040--40148091 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
40148030 CAAGTGTGTG
*
40148040 GTAAAAATAAT-TACATGT
1 GTAAAAATAATATACATAT
40148058 GTAAAAATAATATACATAT
1 GTAAAAATAATATACATAT
*
40148077 GTATATAATAATATA
1 GTA-AAAATAATATA
40148092 TGTAATACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.37
19 9 0.30
20 10 0.33
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.35
Consensus pattern (19 bp):
GTAAAAATAATATACATAT
Found at i:40148185 original size:17 final size:17
Alignment explanation
Indices: 40148163--40148201 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
40148153 AAGAATAAAC
40148163 AAATAATAAAAGAAAT-G
1 AAATAA-AAAAGAAATAG
*
40148180 AAATAAAAAAGGAATAG
1 AAATAAAAAAGAAATAG
40148197 AAATA
1 AAATA
40148202 GAGAAGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
AAATAAAAAAGAAATAG
Found at i:40148249 original size:13 final size:13
Alignment explanation
Indices: 40148214--40148256 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
40148204 GAAGTAAAAT
40148214 GAAAGAAAAA-GA
1 GAAAGAAAAAGGA
* *
40148226 AAGAAGGAAAAGGA
1 GA-AAGAAAAAGGA
40148240 GAAAGAAAAAGGA
1 GAAAGAAAAAGGA
40148253 GAAA
1 GAAA
40148257 AAGCTAGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 1 0.04
13 21 0.84
14 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
GAAAGAAAAAGGA
Found at i:40148250 original size:22 final size:22
Alignment explanation
Indices: 40148217--40148259 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
40148207 GTAAAATGAA
*
40148217 AGAAAAAGAAAGAAGGAAAAGG
1 AGAAAAAGAAAGAAGAAAAAGG
*
40148239 AGAAAGAA-AAAGGAGAAAAAG
1 AGAAA-AAGAAAGAAGAAAAAG
40148260 CTAGGGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (22 bp):
AGAAAAAGAAAGAAGAAAAAGG
Found at i:40149241 original size:40 final size:40
Alignment explanation
Indices: 40149122--40149254 Score: 128
Period size: 40 Copynumber: 3.4 Consensus size: 40
40149112 CTTCGAGTCG
* ***
40149122 ATGAGACACTAGGTGTCAATTTATTACTTCGGATTAATTTG
1 ATGAGACACTGGGTGTCAATTTATTACTTCGGATT-ATCCA
* * * * * *
40149163 ATGAGGCACCGGGTGCCAA--T-TTACTTTGGTTTAGCCA
1 ATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCCA
*
40149200 ATGAGACACTGGGTGTCAATTTATTACTTCGAATTATCCA
1 ATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCCA
*
40149240 ATGAGGCACTGGGTG
1 ATGAGACACTGGGTG
40149255 CCAAACTGGT
Statistics
Matches: 71, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
37 17 0.24
38 10 0.14
39 2 0.03
40 27 0.38
41 15 0.21
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCCA
Found at i:40150412 original size:23 final size:23
Alignment explanation
Indices: 40150382--40150427 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
40150372 TTTAATTAGA
40150382 AAAAAAATCCAATTAACGTTCTT
1 AAAAAAATCCAATTAACGTTCTT
*
40150405 AAAAAAATCCAATTAATGTTCTT
1 AAAAAAATCCAATTAACGTTCTT
40150428 TATTCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAAAAATCCAATTAACGTTCTT
Found at i:40150469 original size:19 final size:20
Alignment explanation
Indices: 40150427--40150479 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40150417 TTAATGTTCT
* *
40150427 TTATTCTTTTTATTTTTATA
1 TTATTCTTTTTCTTATTATA
*
40150447 TTATTCTTTTTCTTATT-TC
1 TTATTCTTTTTCTTATTATA
*
40150466 TTATTCATTTTCTT
1 TTATTCTTTTTCTT
40150480 TGTTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTCTTTTTCTTATTATA
Found at i:40150654 original size:34 final size:34
Alignment explanation
Indices: 40150611--40150679 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
40150601 CTTAAGATTA
40150611 TCTATGCGTTTTTAGGAAATAAATGAGGTATTGG
1 TCTATGCGTTTTTAGGAAATAAATGAGGTATTGG
40150645 TCTATGCGTTTTTAGGAAATAAATGAGGTATTGG
1 TCTATGCGTTTTTAGGAAATAAATGAGGTATTGG
40150679 T
1 T
40150680 TTGTTGGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (34 bp):
TCTATGCGTTTTTAGGAAATAAATGAGGTATTGG
Found at i:40152517 original size:24 final size:23
Alignment explanation
Indices: 40152488--40152550 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
40152478 AACCGAATTT
* * *
40152488 GCACACATAGTGCTTATTACACTC
1 GCACACATAGTGCATAGTAAAC-C
40152512 GCACACATAGTGCCATAGTAAACC
1 GCACACATAGTG-CATAGTAAACC
40152536 GCACACATAGTGCAT
1 GCACACATAGTGCAT
40152551 TGGATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.09
24 25 0.71
25 7 0.20
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (23 bp):
GCACACATAGTGCATAGTAAACC
Found at i:40157874 original size:55 final size:55
Alignment explanation
Indices: 40157804--40157914 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
40157794 GCCATACTAT
40157804 TTTTAGGTTAATTCCCACCTTTATAAATTCCTAGAGTCGTCAAGCCTAGGGTTTA
1 TTTTAGGTTAATTCCCACCTTTATAAATTCCTAGAGTCGTCAAGCCTAGGGTTTA
*
40157859 TTTTAGGTTAATTCCCACCTTTATAACTTCCTAGAGTCGTCAAGCCTAGGGTTTA
1 TTTTAGGTTAATTCCCACCTTTATAAATTCCTAGAGTCGTCAAGCCTAGGGTTTA
40157914 T
1 T
40157915 GTTCTCTTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (55 bp):
TTTTAGGTTAATTCCCACCTTTATAAATTCCTAGAGTCGTCAAGCCTAGGGTTTA
Found at i:40159146 original size:3 final size:3
Alignment explanation
Indices: 40159108--40159193 Score: 74
Period size: 3 Copynumber: 29.7 Consensus size: 3
40159098 AAATTATATA
* * *
40159108 TAT TA- TAT TA- TAT TA- TAT AAT TGAT TAT TAT AAT TAT TAAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT T-AT TAT
**
40159152 TAT GGT T-T TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40159194 AATAAATTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
2 10 0.15
3 51 0.76
4 6 0.09
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:40159479 original size:33 final size:33
Alignment explanation
Indices: 40159442--40159511 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
40159432 TATTTATACA
* *
40159442 ATTATAATATT-TTATTTAAATT-AGTATATATTT
1 ATTAT-ATATTATTATTAAAATTAAG-AGATATTT
*
40159475 ATTATTTATTATTATTAAAATTAAGAGATATTT
1 ATTATATATTATTATTAAAATTAAGAGATATTT
40159508 ATTA
1 ATTA
40159512 ATTAAATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 4 0.12
33 26 0.81
34 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (33 bp):
ATTATATATTATTATTAAAATTAAGAGATATTT
Found at i:40159533 original size:33 final size:33
Alignment explanation
Indices: 40159469--40159533 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
40159459 AAATTAGTAT
* *
40159469 ATATTTATTATTTATTATTATTAAAATTAAGAG
1 ATATTTATTATTAAATATTATTAAAATTAAGAG
40159502 ATATTTATTAATTAAATAGTTA-TAAAA-TAAGA
1 ATATTTATT-ATTAAATA-TTATTAAAATTAAGA
40159534 CTTTTATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 14 0.50
34 11 0.39
35 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (33 bp):
ATATTTATTATTAAATATTATTAAAATTAAGAG
Found at i:40159701 original size:22 final size:20
Alignment explanation
Indices: 40159666--40159715 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
40159656 AATATAATAT
40159666 AAATAAAATAAAATAAAAAG
1 AAATAAAATAAAATAAAAAG
*
40159686 AAATAAAGCATAAAATAAATAG
1 AAATAAA--ATAAAATAAAAAG
*
40159708 AAACAAAA
1 AAATAAAA
40159716 CAAACAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 8 0.31
22 18 0.69
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (20 bp):
AAATAAAATAAAATAAAAAG
Found at i:40159769 original size:12 final size:12
Alignment explanation
Indices: 40159754--40159797 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
40159744 AAAACAGGGG
40159754 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
40159766 AGAAAAAGGGAA
1 AGAAAAAGAGAA
* *
40159778 AGAAATAGAAAA
1 AGAAAAAGAGAA
40159790 AGGAAAAA
1 A-GAAAAA
40159798 CTAGAGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:40160801 original size:12 final size:12
Alignment explanation
Indices: 40160784--40160808 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40160774 GCGGACTACT
40160784 GTTACTGTTACC
1 GTTACTGTTACC
40160796 GTTACTGTTACC
1 GTTACTGTTACC
40160808 G
1 G
40160809 ATTCGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:40160839 original size:45 final size:45
Alignment explanation
Indices: 40160786--40160892 Score: 160
Period size: 45 Copynumber: 2.4 Consensus size: 45
40160776 GGACTACTGT
* *
40160786 TACTGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTCGAA
* *
40160831 TATTGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTCGAA
**
40160876 TACTGTTATTGTTACTG
1 TACTGTTACCGTTACTG
40160893 CTACTGCTAC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTCGAA
Found at i:40163301 original size:20 final size:20
Alignment explanation
Indices: 40163276--40163315 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40163266 GAGCCTATTT
40163276 ATACTTTGATTGATCCTGGA
1 ATACTTTGATTGATCCTGGA
40163296 ATACTTTGATTGATCCTGGA
1 ATACTTTGATTGATCCTGGA
40163316 TCTTCACACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
ATACTTTGATTGATCCTGGA
Found at i:40166976 original size:5 final size:5
Alignment explanation
Indices: 40166966--40167136 Score: 328
Period size: 5 Copynumber: 34.6 Consensus size: 5
40166956 AATAATTAAG
40166966 TATAT TATA- T-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40167014 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40167064 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40167114 TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TAT
40167137 TATATATAAA
Statistics
Matches: 164, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
3 2 0.01
4 2 0.01
5 160 0.98
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:40168265 original size:45 final size:45
Alignment explanation
Indices: 40168212--40168317 Score: 142
Period size: 45 Copynumber: 2.4 Consensus size: 45
40168202 GACTACTGTT
* * *
40168212 ACTGTTACCGTTACTTTTACCGATTC-GACACTTTGTGTGTCGAAT
1 ACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAAA
* *
40168257 ATTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAAA
1 ACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAAA
*
40168302 ACTGTTACTGTTACTG
1 ACTGTTACCGTTACTG
40168318 CTACTGCTAC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
45 52 0.98
46 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (45 bp):
ACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAAA
Found at i:40170197 original size:3 final size:3
Alignment explanation
Indices: 40170189--40170248 Score: 111
Period size: 3 Copynumber: 19.7 Consensus size: 3
40170179 GTGGCTGTTA
40170189 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40170237 TAT TATT TAT TA
1 TAT TA-T TAT TA
40170249 CAATAATAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40172995 original size:9 final size:9
Alignment explanation
Indices: 40172966--40173023 Score: 50
Period size: 8 Copynumber: 6.7 Consensus size: 9
40172956 AATCATTTTT
40172966 AAAATTA-A
1 AAAATTATA
*
40172974 AATATTAATA
1 AAAATT-ATA
40172984 AAAATTATA
1 AAAATTATA
40172993 AAAA-TATA
1 AAAATTATA
* *
40173001 AGAATT-TT
1 AAAATTATA
*
40173009 AAAATTTTA
1 AAAATTATA
40173018 AAAATT
1 AAAATT
40173024 TCTAAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
8 18 0.45
9 16 0.40
10 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAATTATA
Found at i:40173024 original size:17 final size:17
Alignment explanation
Indices: 40172981--40173031 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
40172971 TAAAATATTA
* *
40172981 ATAAAAATTATAAAAAT
1 ATAAAAATTTTAAAATT
*
40172998 ATAAGAATTTTAAAATT
1 ATAAAAATTTTAAAATT
*
40173015 TTAAAAATTTCTAAAAT
1 ATAAAAATTT-TAAAAT
40173032 AAAAATTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 22 0.79
18 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
ATAAAAATTTTAAAATT
Found at i:40177399 original size:204 final size:201
Alignment explanation
Indices: 40177007--40177414 Score: 507
Period size: 204 Copynumber: 2.0 Consensus size: 201
40176997 CATATGTTTT
* *
40177007 TTTTATTTTTTTAATTTGGTTATGCCAACTTTAACTGTTTTGTCACTCATCTGTTCTTCTCATTC
1 TTTTATTTTTTTAATTTGGTTATGCCAACTGTAACTGTTTTGTCACTCATCTGTTCTTCTCATGC
** * * * * * ** *
40177072 TGATTGGGATACAAAATTGTAATTTCTTTTCCGTAGTCTCCCTCCTTTTTCTTCCTCATGCTATC
66 TGAAAGGGATACAAAAATGAAATTTCTTTTCCCTAGTCTCCCTCCTTTCTCTTCCACACACTAAC
* * * *
40177137 AGTCAAGAACTAGAATTTCTAACTGAATTGGGGAGAACATAACCTGTTTTAACTTCCATTGCTGA
131 AGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACCTGTGTTAACTTCCATTGCTAA
40177202 TATTGA
196 TATTGA
* * * *
40177208 TTTTCTTTTTTT-ATTTGGTTATGCCATCTGTAACTGTTTTGTCATTCTTCTGTTCTTCCTCATG
1 TTTTATTTTTTTAATTTGGTTATGCCAACTGTAACTGTTTTGTCACTCATCTGTTCTT-CTCATG
*
40177272 CTGAAAGGGATACAAAAATGAAATTTCTTTTCCACT-GTCTCCTTCCTTTCTCTTCTTCACACAC
65 CTGAAAGGGATACAAAAATGAAATTTCTTTTCC-CTAGTCTCCCTCCTTTCTCTTC--CACACAC
* * * *
40177336 TCAACAGTCAAGAACTAGAGTTTTTAACTG-ATATAGGGAGAACACAACTTGTGTTAGCTTCCAT
127 T-AACAGTCAAGAACTAGAATTTCTAACTGAAT-TAGGGAGAACACAACCTGTGTTAACTTCCAT
*
40177400 TGCTAATATTTA
190 TGCTAATATTGA
40177412 TTT
1 TTT
40177415 ATTAACATAC
Statistics
Matches: 175, Mismatches: 26, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
200 41 0.23
201 62 0.35
202 1 0.01
203 7 0.04
204 64 0.37
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (201 bp):
TTTTATTTTTTTAATTTGGTTATGCCAACTGTAACTGTTTTGTCACTCATCTGTTCTTCTCATGC
TGAAAGGGATACAAAAATGAAATTTCTTTTCCCTAGTCTCCCTCCTTTCTCTTCCACACACTAAC
AGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACCTGTGTTAACTTCCATTGCTAA
TATTGA
Found at i:40181144 original size:16 final size:18
Alignment explanation
Indices: 40181118--40181150 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40181108 TTACTTTAGA
40181118 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
40181135 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
40181151 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:40191343 original size:18 final size:18
Alignment explanation
Indices: 40191320--40191370 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 18
40191310 GAGGAATGGA
40191320 TAGAATTCAACACTATTC
1 TAGAATTCAACACTATTC
40191338 TAGAATTCAACAACACTATTC
1 TAGAATT---CAACACTATTC
40191359 TAGAATTCAACA
1 TAGAATTCAACA
40191371 AGGTTCTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 12 0.40
21 18 0.60
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (18 bp):
TAGAATTCAACACTATTC
Found at i:40191353 original size:21 final size:21
Alignment explanation
Indices: 40191327--40191371 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
40191317 GGATAGAATT
40191327 CAACACTATTCTAGAATTCAA
1 CAACACTATTCTAGAATTCAA
40191348 CAACACTATTCTAGAATTCAA
1 CAACACTATTCTAGAATTCAA
40191369 CAA
1 CAA
40191372 GGTTCTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.27
Consensus pattern (21 bp):
CAACACTATTCTAGAATTCAA
Found at i:40194784 original size:38 final size:38
Alignment explanation
Indices: 40194733--40194809 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
40194723 CAAGAGCCTT
40194733 AGTCTTTGGGGGCCTTGTGAGTGTTTTTTATTATTGAA
1 AGTCTTTGGGGGCCTTGTGAGTGTTTTTTATTATTGAA
40194771 AGTCTTTGGGGGCCTTGTGAGTGTTTTTTATTATTGAA
1 AGTCTTTGGGGGCCTTGTGAGTGTTTTTTATTATTGAA
40194809 A
1 A
40194810 AAAGAGTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.17, C:0.08, G:0.29, T:0.47
Consensus pattern (38 bp):
AGTCTTTGGGGGCCTTGTGAGTGTTTTTTATTATTGAA
Found at i:40198885 original size:18 final size:19
Alignment explanation
Indices: 40198864--40198907 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
40198854 ACCAAAAGCA
* *
40198864 GCGAGCTTTATTAAAAG-T
1 GCGAGCTTCATAAAAAGAT
40198882 GCGAGC-TCATAAAAAGAT
1 GCGAGCTTCATAAAAAGAT
40198900 GCGAGCTT
1 GCGAGCTT
40198908 AACTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 13 0.59
19 1 0.05
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (19 bp):
GCGAGCTTCATAAAAAGAT
Found at i:40199833 original size:29 final size:29
Alignment explanation
Indices: 40199796--40199851 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
40199786 TCCTGAATTA
40199796 ACTAAAATTGTGATTTCGATAGAAATTCG
1 ACTAAAATTGTGATTTCGATAGAAATTCG
* * *
40199825 ACTACAATTGTGATTTTGGTAGAAATT
1 ACTAAAATTGTGATTTCGATAGAAATT
40199852 GCTTAGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (29 bp):
ACTAAAATTGTGATTTCGATAGAAATTCG
Found at i:40200982 original size:63 final size:64
Alignment explanation
Indices: 40200859--40200982 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 64
40200849 ACAATTTAGA
* *
40200859 CATTCAAACAAAACTTAGTTTCATCAATTGAAACATAAAAATCTTTGTCATTAGATGAACCGAG
1 CATTCAAACAAAACTTAGTTTCATCAATAGAAACATAAAAATCTTTGTCATCAGATGAACCGAG
* * * * *
40200923 CATTCGAACAAAACTTGGTTTCAT-TATAGAAATATACAAATCTTTGTCATCAGATGAACC
1 CATTCAAACAAAACTTAGTTTCATCAATAGAAACATAAAAATCTTTGTCATCAGATGAACC
40200983 ATACTAAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
63 31 0.58
64 22 0.42
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (64 bp):
CATTCAAACAAAACTTAGTTTCATCAATAGAAACATAAAAATCTTTGTCATCAGATGAACCGAG
Found at i:40202755 original size:5 final size:5
Alignment explanation
Indices: 40202745--40202769 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40202735 TAATTCGTGA
40202745 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
40202770 TTCATATATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:40213486 original size:21 final size:19
Alignment explanation
Indices: 40213460--40213501 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
40213450 AGCAAACTCA
40213460 ATGTCGCAACATAACCCTCCT
1 ATGTCGCAACAT-ACCC-CCT
*
40213481 ATGTCGCGACATACCCCCT
1 ATGTCGCAACATACCCCCT
40213500 AT
1 AT
40213502 TCTTGGTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.26, C:0.38, G:0.12, T:0.24
Consensus pattern (19 bp):
ATGTCGCAACATACCCCCT
Found at i:40213902 original size:14 final size:14
Alignment explanation
Indices: 40213863--40213903 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
40213853 ATCCATGAGC
40213863 ATCTCTTTTCTTT-T
1 ATCTC-TTTCTTTAT
40213877 AT-TCTATTCTTTAT
1 ATCTCT-TTCTTTAT
40213891 ATCTCTTTCTTTA
1 ATCTCTTTCTTTA
40213904 GCATTGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.04
13 8 0.33
14 12 0.50
15 3 0.12
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.66
Consensus pattern (14 bp):
ATCTCTTTCTTTAT
Found at i:40215746 original size:12 final size:12
Alignment explanation
Indices: 40215731--40215771 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
40215721 GTTTATTCCC
40215731 TGTTTTAAATTT
1 TGTTTTAAATTT
40215743 TGTTTTAAATTT
1 TGTTTTAAATTT
*
40215755 TGTTTT-ATTTT
1 TGTTTTAAATTT
40215766 TGTTTT
1 TGTTTT
40215772 TACTTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (12 bp):
TGTTTTAAATTT
Found at i:40215803 original size:19 final size:20
Alignment explanation
Indices: 40215757--40215810 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
40215747 TTAAATTTTG
*
40215757 TTTTATTTTTGTT--TTTAC
1 TTTTATTTTTATTAATTTAC
40215775 TTTTATTTTTTATTAATTTA-
1 TTTTA-TTTTTATTAATTTAC
40215795 TTTTATTTTTATTAAT
1 TTTTATTTTTATTAAT
40215811 ATTTGTTGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 5 0.16
19 18 0.56
20 5 0.16
21 4 0.12
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTATTTTTATTAATTTAC
Found at i:40215806 original size:6 final size:6
Alignment explanation
Indices: 40215757--40215807 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
40215747 TTAAATTTTG
* *
40215757 TTTTAT TTTTGT TTTTAC TTTTATT TTTTAT TAATTTA- TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT T--TTTAT TTTTAT TTTTAT
40215807 T
1 T
40215808 AATATTTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 4 0.11
6 23 0.62
7 6 0.16
8 4 0.11
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:40256832 original size:37 final size:37
Alignment explanation
Indices: 40256782--40256855 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
40256772 GATCGATGTC
40256782 GTTGTGATTAGCCA-AATGTAT-TGGCTTATAATGATTT
1 GTTGTGATTAGCCATAA-G-ATGTGGCTTATAATGATTT
40256819 GTTGT-ATGTAGCCATAAGATGTGGCTTATAATGATTT
1 GTTGTGAT-TAGCCATAAGATGTGGCTTATAATGATTT
40256856 TGGCTTGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
36 4 0.12
37 28 0.82
38 2 0.06
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (37 bp):
GTTGTGATTAGCCATAAGATGTGGCTTATAATGATTT
Found at i:40258616 original size:14 final size:15
Alignment explanation
Indices: 40258597--40258626 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
40258587 ATATTTGACT
40258597 TGTTCTTAATT-TTG
1 TGTTCTTAATTCTTG
40258611 TGTTCTTAATTCTTG
1 TGTTCTTAATTCTTG
40258626 T
1 T
40258627 TTTAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.63
Consensus pattern (15 bp):
TGTTCTTAATTCTTG
Found at i:40277673 original size:21 final size:20
Alignment explanation
Indices: 40277628--40277673 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
40277618 CTTAAACCAG
* *
40277628 GAACACGGGCGTGGAGGACC
1 GAACACGGGCGTGGAGAAAC
*
40277648 TAACACGGGCGTGGGAGAAAC
1 GAACACGGGCGT-GGAGAAAC
40277669 GAACA
1 GAACA
40277674 ACATCACACA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.33, C:0.22, G:0.39, T:0.07
Consensus pattern (20 bp):
GAACACGGGCGTGGAGAAAC
Found at i:40277881 original size:254 final size:255
Alignment explanation
Indices: 40277475--40277937 Score: 802
Period size: 254 Copynumber: 1.8 Consensus size: 255
40277465 ATGGACACAG
*
40277475 GCGTGTTGGGGGGGACACAGGCGTGGGAGAAACGAAGGGATCACCATATGGCCATGCGATGTGGC
1 GCGTGTTGGGGGGGACACAGGCGTGGGAGAAACGAAGGGATCACCACATGGCCATGCGATGTGGC
****
40277540 CGTATGGGTCATACGGCCTAGGAACACGGGTGTGTCCTCAGGCCGTGTGCGACACTGACTTGAAC
66 CGTATGGGTCATACGGCCTAGGAACACAAACGTGTCCTCAGGCCGTGTGCGACACTGACTTGAAC
*
40277605 ATCAACCCACAAGCTTAAACCAGGAACACGGGCGTGGAGGACCTAACACGGGCGTGGGAGAAACG
131 ATCAACCCACAAGCTTAAACCAGGAACACGGGCGTGGAGGACCTAACACGGGCGTGGGAGAAACA
40277670 AACAACATCACACATGGTCGTGCGATATGACCGTGTGAACCACACGGCCGGGACACACTA
196 AACAACATCACACATGGTCGTGCGATATGACCGTGTGAACCACACGGCCGGGACACACTA
* * *
40277730 GCGTGTT-GGGGGGACACGGGCGTGGGAGAAATGAAGGGATCACCACATGGCCATGCGATGTGGT
1 GCGTGTTGGGGGGGACACAGGCGTGGGAGAAACGAAGGGATCACCACATGGCCATGCGATGTGGC
* *
40277794 CGTGTGGGTTATACGGCCTAGGAACACAAACGTGTCCTCAGGCCGTGTGCGACACTGACTTGAAC
66 CGTATGGGTCATACGGCCTAGGAACACAAACGTGTCCTCAGGCCGTGTGCGACACTGACTTGAAC
* *
40277859 ATCAACCCATAAGCTTAAACCAGGAACATGGGCGTGGAGGACCTAACACGGGCGTGGGAGAAACA
131 ATCAACCCACAAGCTTAAACCAGGAACACGGGCGTGGAGGACCTAACACGGGCGTGGGAGAAACA
40277924 AACAACATCACACA
196 AACAACATCACACA
40277938 CAGTCGAGCA
Statistics
Matches: 195, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
254 188 0.96
255 7 0.04
ACGTcount: A:0.28, C:0.24, G:0.32, T:0.16
Consensus pattern (255 bp):
GCGTGTTGGGGGGGACACAGGCGTGGGAGAAACGAAGGGATCACCACATGGCCATGCGATGTGGC
CGTATGGGTCATACGGCCTAGGAACACAAACGTGTCCTCAGGCCGTGTGCGACACTGACTTGAAC
ATCAACCCACAAGCTTAAACCAGGAACACGGGCGTGGAGGACCTAACACGGGCGTGGGAGAAACA
AACAACATCACACATGGTCGTGCGATATGACCGTGTGAACCACACGGCCGGGACACACTA
Found at i:40278505 original size:26 final size:24
Alignment explanation
Indices: 40278463--40278515 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
40278453 CCTCCGCTAC
* *
40278463 TTTTTTTATTTTCTTTTACTGTTA
1 TTTTTTTATTTTATTTTAATGTTA
*
40278487 TTTTTTTATTCTTTATTTTAATTTTA
1 TTTTTTTA-T-TTTATTTTAATGTTA
40278513 TTT
1 TTT
40278516 CATCTCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.33
25 1 0.04
26 15 0.62
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (24 bp):
TTTTTTTATTTTATTTTAATGTTA
Found at i:40285416 original size:45 final size:45
Alignment explanation
Indices: 40285388--40285594 Score: 249
Period size: 45 Copynumber: 4.6 Consensus size: 45
40285378 CGATATGATA
* *
40285388 CCATAATGTCTTTCAACTATGATCTTATTCATTTTC-GTCATATTG
1 CCATAATGTCTTTCAACTATGGTCTTATTCATTTTCGGT-ATAGTG
* *
40285433 TCATAAT-TCCTTTCAACTATGGTCTTATTCGATTCT-GGTATAGTG
1 CCATAATGT-CTTTCAACTATGGTCTTATTC-ATTTTCGGTATAGTG
* * *
40285478 CTATAGTGTCTTTCAACTATGGTCTTATTCATTTTTGGTATAGTG
1 CCATAATGTCTTTCAACTATGGTCTTATTCATTTTCGGTATAGTG
** * * *
40285523 CCATTGTGCCTTTCGACTATGGTCTTATTCATTTCCGGTATAGTG
1 CCATAATGTCTTTCAACTATGGTCTTATTCATTTTCGGTATAGTG
*
40285568 CCATAATGTCTTTCATCTATGGTCTTA
1 CCATAATGTCTTTCAACTATGGTCTTA
40285595 CTCGTTTGAT
Statistics
Matches: 138, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
44 5 0.04
45 126 0.91
46 7 0.05
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (45 bp):
CCATAATGTCTTTCAACTATGGTCTTATTCATTTTCGGTATAGTG
Found at i:40285494 original size:90 final size:90
Alignment explanation
Indices: 40285388--40285594 Score: 274
Period size: 90 Copynumber: 2.3 Consensus size: 90
40285378 CGATATGATA
* * * *
40285388 CCATAATGTCTTTCAACTATGATCTTATTCA-TTTTCGTCATATTGTCATAATTCCTTTCAACTA
1 CCATAATGTCTTTCAACTATGGTCTTATTCATTTTTCGT-ATAGTGCCATAATGCCTTTCAACTA
*
40285452 TGGTCTTATTCGA-TTCTGGTATAGTG
65 TGGTCTTATTC-ATTTCCGGTATAGTG
* * * ** *
40285478 CTATAGTGTCTTTCAACTATGGTCTTATTCATTTTTGGTATAGTGCCATTGTGCCTTTCGACTAT
1 CCATAATGTCTTTCAACTATGGTCTTATTCATTTTTCGTATAGTGCCATAATGCCTTTCAACTAT
40285543 GGTCTTATTCATTTCCGGTATAGTG
66 GGTCTTATTCATTTCCGGTATAGTG
*
40285568 CCATAATGTCTTTCATCTATGGTCTTA
1 CCATAATGTCTTTCAACTATGGTCTTA
40285595 CTCGTTTGAT
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
89 1 0.01
90 94 0.93
91 6 0.06
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (90 bp):
CCATAATGTCTTTCAACTATGGTCTTATTCATTTTTCGTATAGTGCCATAATGCCTTTCAACTAT
GGTCTTATTCATTTCCGGTATAGTG
Found at i:40285615 original size:45 final size:45
Alignment explanation
Indices: 40285566--40285689 Score: 203
Period size: 45 Copynumber: 2.8 Consensus size: 45
40285556 TCCGGTATAG
*
40285566 TGCCATAATGTCTTTCATCTATGGTCTTACTCGTTTGATTCGTGA
1 TGCCATAGTGTCTTTCATCTATGGTCTTACTCGTTTGATTCGTGA
*
40285611 TGCCATAGTGTCTTTCATATATGGTCTTACTCGTTTGATTCGTGA
1 TGCCATAGTGTCTTTCATCTATGGTCTTACTCGTTTGATTCGTGA
* * *
40285656 TGCCATAGCGTCTTTTAGCTATGGTCTTACTCGT
1 TGCCATAGTGTCTTTCATCTATGGTCTTACTCGT
40285690 ATTTCAACCA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCATCTATGGTCTTACTCGTTTGATTCGTGA
Found at i:40285615 original size:90 final size:89
Alignment explanation
Indices: 40285388--40285639 Score: 251
Period size: 90 Copynumber: 2.8 Consensus size: 89
40285378 CGATATGATA
* * * * * * *
40285388 CCATAATGTCTTTCAACTATGATCTTATTCA-TTTTCGTCATATTGTCATAATTCCTTTCAACTA
1 CCATAATGTCTTTCAACTATGGTCTTACTCATTTTTCGT-AGAGTGCCATAGTGCCTTTC-ACTA
*
40285452 TGGTCTTATTCGATTCTGGTATAGTG
64 TGGTCTTATTCGATTCCGGTATAGTG
* * * * * *
40285478 CTATAGTGTCTTTCAACTATGGTCTTATTCATTTTTGGTATAGTGCCATTGTGCCTTTCGACTAT
1 CCATAATGTCTTTCAACTATGGTCTTACTCATTTTTCGTAGAGTGCCATAGTGCCTTTC-ACTAT
40285543 GGTCTTATTC-ATTTCCGGTATAGTG
65 GGTCTTATTCGA-TTCCGGTATAGTG
* * * *
40285568 CCATAATGTCTTTCATCTATGGTCTTACTCGTTTGATTCGT-GA-TGCCATAGTGTCTTTCATAT
1 CCATAATGTCTTTCAACTATGGTCTTACTCATTT--TTCGTAGAGTGCCATAGTGCCTTTCA-CT
40285631 ATGGTCTTA
63 ATGGTCTTA
40285640 CTCGTTTGAT
Statistics
Matches: 136, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
89 2 0.01
90 123 0.90
91 7 0.05
92 4 0.03
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (89 bp):
CCATAATGTCTTTCAACTATGGTCTTACTCATTTTTCGTAGAGTGCCATAGTGCCTTTCACTATG
GTCTTATTCGATTCCGGTATAGTG
Found at i:40288808 original size:13 final size:13
Alignment explanation
Indices: 40288774--40288846 Score: 53
Period size: 13 Copynumber: 5.8 Consensus size: 13
40288764 TGTTGATTCT
40288774 ATTTTT-ATTTT-
1 ATTTTTAATTTTA
*
40288785 A-TTTTATTTTTA
1 ATTTTTAATTTTA
40288797 ATTTTTAATTTTTA
1 ATTTTTAA-TTTTA
* **
40288811 ATTTTGAAAGTTA
1 ATTTTTAATTTTA
* *
40288824 TTTTTTAATTTTT
1 ATTTTTAATTTTA
*
40288837 ATTTTAAATT
1 ATTTTTAATT
40288847 ATATCATATA
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
10 4 0.09
11 5 0.11
12 1 0.02
13 24 0.52
14 12 0.26
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
ATTTTTAATTTTA
Found at i:40288809 original size:14 final size:14
Alignment explanation
Indices: 40288786--40288846 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 14
40288776 TTTTATTTTA
40288786 TTTT-ATTTTTAAT
1 TTTTAATTTTTAAT
40288799 TTTTAATTTTTAAT
1 TTTTAATTTTTAAT
* ** *
40288813 TTTGAA-AGTTATT
1 TTTTAATTTTTAAT
40288826 TTTTAATTTTT-AT
1 TTTTAATTTTTAAT
*
40288839 TTTAAATT
1 TTTTAATT
40288847 ATATCATATA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
13 21 0.57
14 16 0.43
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTAATTTTTAAT
Found at i:40288836 original size:27 final size:24
Alignment explanation
Indices: 40288798--40288848 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 24
40288788 TTATTTTTAA
40288798 TTTTTAATTTTTAATTTTGAAAGTTAT
1 TTTTTAATTTTT-ATTTT-AAA-TTAT
40288825 TTTTTAATTTTTATTTTAAATTAT
1 TTTTTAATTTTTATTTTAAATTAT
40288849 ATCATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 4 0.17
25 3 0.12
26 5 0.21
27 12 0.50
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTTTAATTTTTATTTTAAATTAT
Found at i:40288840 original size:6 final size:7
Alignment explanation
Indices: 40288786--40288846 Score: 56
Period size: 7 Copynumber: 9.1 Consensus size: 7
40288776 TTTTATTTTA
40288786 TTTT-AT
1 TTTTAAT
40288792 TTTTAAT
1 TTTTAAT
40288799 TTTTAAT
1 TTTTAAT
40288806 TTTTAAT
1 TTTTAAT
*
40288813 TTTGAA-
1 TTTTAAT
** *
40288819 AGTTATT
1 TTTTAAT
40288826 TTTTAAT
1 TTTTAAT
40288833 TTTT-AT
1 TTTTAAT
*
40288839 TTTAAAT
1 TTTTAAT
40288846 T
1 T
40288847 ATATCATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
6 11 0.26
7 32 0.74
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (7 bp):
TTTTAAT
Found at i:40289249 original size:31 final size:32
Alignment explanation
Indices: 40289214--40289275 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
40289204 TTATTTAGTT
*
40289214 AAATTTAACTCTTAA-TCTTTT-AAAAAGAGTG
1 AAATTTAACTATTAACT-TTTTGAAAAAGAGTG
*
40289245 AAATTTGACTATTAACTTTTTGAAAAAGAGT
1 AAATTTAACTATTAACTTTTTGAAAAAGAGT
40289276 CTAATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (32 bp):
AAATTTAACTATTAACTTTTTGAAAAAGAGTG
Found at i:40289407 original size:15 final size:16
Alignment explanation
Indices: 40289387--40289423 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
40289377 ACATTTCATA
*
40289387 ATTTTTTGAAT-TTTT
1 ATTTTTTAAATATTTT
40289402 A-TTTTTAAATATTTT
1 ATTTTTTAAATATTTT
40289417 ATTTTTT
1 ATTTTTT
40289424 TATGTGACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 8 0.42
15 6 0.32
16 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
ATTTTTTAAATATTTT
Found at i:40303943 original size:20 final size:22
Alignment explanation
Indices: 40303904--40303946 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
40303894 ATAAGAGAGT
*
40303904 AAAAAGAGAGAGAAATGGGCCA
1 AAAAAGAGAGAGAAACGGGCCA
40303926 AAAAAG-GAGA-AAACGGGCCA
1 AAAAAGAGAGAGAAACGGGCCA
40303946 A
1 A
40303947 CATAGGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.56, C:0.12, G:0.30, T:0.02
Consensus pattern (22 bp):
AAAAAGAGAGAGAAACGGGCCA
Found at i:40305740 original size:30 final size:30
Alignment explanation
Indices: 40305704--40305769 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
40305694 GTGTGTTCAG
*
40305704 AGGTTGGTCCTCTGGGTCGGGCTCCGCCAT
1 AGGTTGGTCCTCTGGGTCGGGCTCCACCAT
* *
40305734 ATGTTGGTCCTTTGGGTCGGGCTCCACCAT
1 AGGTTGGTCCTCTGGGTCGGGCTCCACCAT
40305764 AGGTTG
1 AGGTTG
40305770 ATTTCTACGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.09, C:0.26, G:0.35, T:0.30
Consensus pattern (30 bp):
AGGTTGGTCCTCTGGGTCGGGCTCCACCAT
Found at i:40308451 original size:54 final size:53
Alignment explanation
Indices: 40308374--40308479 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 53
40308364 TCTCAATACT
* *
40308374 AAAAAATAATTAAACTATTTTGTTCAAGACTGATAAT-ATTTTGTCTTACAAAA
1 AAAAAATAATTAAACTATTTTGTTCAAGACCGA-AATCATTGTGTCTTACAAAA
40308427 AAAAACATAATTAAACTATTTTGTTCAAGACCGAAATCATTGTGTCTTACAAA
1 AAAAA-ATAATTAAACTATTTTGTTCAAGACCGAAATCATTGTGTCTTACAAA
40308480 TTGAAAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
53 8 0.16
54 41 0.84
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (53 bp):
AAAAAATAATTAAACTATTTTGTTCAAGACCGAAATCATTGTGTCTTACAAAA
Found at i:40313332 original size:18 final size:17
Alignment explanation
Indices: 40313305--40313341 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
40313295 ATATATCAAA
40313305 GTCTTGATGAGTTAAAT
1 GTCTTGATGAGTTAAAT
*
40313322 GTCTATGATGAGTTGAAT
1 GTCT-TGATGAGTTAAAT
40313340 GT
1 GT
40313342 TGGTTATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (17 bp):
GTCTTGATGAGTTAAAT
Found at i:40318732 original size:18 final size:18
Alignment explanation
Indices: 40318706--40318743 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40318696 CTTTAAAGTT
40318706 ATGGAGAAAAAACTAAAA
1 ATGGAGAAAAAACTAAAA
* *
40318724 ATGGTGAAAAAACTGAAA
1 ATGGAGAAAAAACTAAAA
40318742 AT
1 AT
40318744 AACTTAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.18, T:0.16
Consensus pattern (18 bp):
ATGGAGAAAAAACTAAAA
Found at i:40322563 original size:14 final size:15
Alignment explanation
Indices: 40322544--40322599 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
40322534 TCTTAGATAT
40322544 GATATG-CAATCTTA
1 GATATGACAATCTTA
40322558 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
40322575 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
40322593 GATATGA
1 GATATGA
40322600 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:40322594 original size:35 final size:37
Alignment explanation
Indices: 40322530--40322620 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 37
40322520 TCAATGATTT
40322530 GCAATCTTAGATATGATATGCAATCTTAGATATGATA
1 GCAATCTTAGATATGATATGCAATCTTAGATATGATA
40322567 -CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
1 GCAATCTTAGATATGATATGCAATCTTAGATATGATA
40322602 TGCAATCTTAGA-A-GATATG
1 -GCAATCTTAGATATGATATG
40322621 ATTTTGTAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.43
36 19 0.37
37 10 0.20
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (37 bp):
GCAATCTTAGATATGATATGCAATCTTAGATATGATA
Found at i:40322620 original size:17 final size:19
Alignment explanation
Indices: 40322523--40322613 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
40322513 ATGATCTTCA
*
40322523 ATGATTTGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
40322542 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
40322561 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
40322578 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
40322596 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
40322614 AGATATGATT
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 36 0.53
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:40322639 original size:22 final size:22
Alignment explanation
Indices: 40322592--40322636 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
40322582 TTGCAATCTT
*
40322592 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATATTAGA
* *
40322614 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
40322637 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Found at i:40331429 original size:78 final size:78
Alignment explanation
Indices: 40331289--40331501 Score: 313
Period size: 78 Copynumber: 2.7 Consensus size: 78
40331279 TCTTCACATC
* ** *** *
40331289 GAAGTAGATCCAAGATGATTTGGCATC-CTTGCGTT-GAAAAGGAGCAGATCGAAGACATAGCAG
1 GAAGCAGATCCAAGATGATTTGGCATCTC-TGTATTAGACGGGGAGCAGATCGAAGACACAGCAG
40331352 ATATGACCTTCATT
65 ATATGACCTTCATT
40331366 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGA
1 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGA
*
40331431 TCTGACCTTCATT
66 TATGACCTTCATT
* *
40331444 GAAGCAGATCCAAGACGATTTGGCATCTCTGTATTAGACGGGGAGCAGAACGAAGACA
1 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACA
40331502 TAACAGATTG
Statistics
Matches: 124, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
77 30 0.24
78 94 0.76
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (78 bp):
GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGA
TATGACCTTCATT
Found at i:40331491 original size:41 final size:41
Alignment explanation
Indices: 40331368--40331492 Score: 100
Period size: 41 Copynumber: 3.1 Consensus size: 41
40331358 CCTTCATTGA
*
40331368 AGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
1 AGCAGATCCAAGACGATTTGGCATCTCTGTATTAGACGGGG
* ** ** * ** *
40331409 AGCAGATCGAAGAC-A--CAGCAGATCTG-ACCTT-CA-TTGA
1 AGCAGATCCAAGACGATTTGGCATCTCTGTA--TTAGACGGGG
40331446 AGCAGATCCAAGACGATTTGGCATCTCTGTATTAGACGGGG
1 AGCAGATCCAAGACGATTTGGCATCTCTGTATTAGACGGGG
40331487 AGCAGA
1 AGCAGA
40331493 ACGAAGACAT
Statistics
Matches: 57, Mismatches: 19, Indels: 16
0.62 0.21 0.17
Matches are distributed among these distances:
37 15 0.26
38 9 0.16
39 4 0.07
40 9 0.16
41 20 0.35
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22
Consensus pattern (41 bp):
AGCAGATCCAAGACGATTTGGCATCTCTGTATTAGACGGGG
Found at i:40331509 original size:78 final size:78
Alignment explanation
Indices: 40331329--40331509 Score: 317
Period size: 78 Copynumber: 2.3 Consensus size: 78
40331319 GCGTTGAAAA
*
40331329 GGAGCAGATCGAAGACATAGCAGATATGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCT
1 GGAGCAGATCGAAGACATAGCAGATATGACCTTCATTGAAGCAGATCCAAGACGATTTGGCATCT
40331394 CTGTATTAGACGG
66 CTGTATTAGACGG
* *
40331407 GGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGACGATTTGGCATCT
1 GGAGCAGATCGAAGACATAGCAGATATGACCTTCATTGAAGCAGATCCAAGACGATTTGGCATCT
40331472 CTGTATTAGACGG
66 CTGTATTAGACGG
* *
40331485 GGAGCAGAACGAAGACATAACAGAT
1 GGAGCAGATCGAAGACATAGCAGAT
40331510 TGTATTACAC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 97 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (78 bp):
GGAGCAGATCGAAGACATAGCAGATATGACCTTCATTGAAGCAGATCCAAGACGATTTGGCATCT
CTGTATTAGACGG
Found at i:40331545 original size:16 final size:16
Alignment explanation
Indices: 40331524--40331562 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
40331514 TTACACGGGG
40331524 AGCAGATCGAAGACAC
1 AGCAGATCGAAGACAC
40331540 AGCAGATCGAAGACAC
1 AGCAGATCGAAGACAC
40331556 AGCAGAT
1 AGCAGAT
40331563 TTGACCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.23, G:0.26, T:0.08
Consensus pattern (16 bp):
AGCAGATCGAAGACAC
Found at i:40331546 original size:37 final size:37
Alignment explanation
Indices: 40331473--40331546 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
40331463 TTGGCATCTC
* *
40331473 TGTATTAGACGGGGAGCAGAACGAAGACATAACAGAT
1 TGTATTACACGGGGAGCAGAACGAAGACACAACAGAT
* *
40331510 TGTATTACACGGGGAGCAGATCGAAGACACAGCAGAT
1 TGTATTACACGGGGAGCAGAACGAAGACACAACAGAT
40331547 CGAAGACACA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.16, G:0.30, T:0.16
Consensus pattern (37 bp):
TGTATTACACGGGGAGCAGAACGAAGACACAACAGAT
Found at i:40331848 original size:16 final size:16
Alignment explanation
Indices: 40331827--40331865 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
40331817 TTACACGGGG
40331827 AGCAGATCGAAGACAC
1 AGCAGATCGAAGACAC
40331843 AGCAGATCGAAGACAC
1 AGCAGATCGAAGACAC
40331859 AGCAGAT
1 AGCAGAT
40331866 TTGACCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.23, G:0.26, T:0.08
Consensus pattern (16 bp):
AGCAGATCGAAGACAC
Found at i:40331911 original size:94 final size:94
Alignment explanation
Indices: 40331749--40331935 Score: 311
Period size: 94 Copynumber: 2.0 Consensus size: 94
40331739 TTCGACGGAG
* * *
40331749 AGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAGCAGATCTAAGATGATTTGGCATCTAT
1 AGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGACATCTAT
*
40331814 GTATTACACGGGGAGCAGATCGAAGACAC
66 GTATTACACGAGGAGCAGATCGAAGACAC
* *
40331843 AGCAGATCGAAGACACAGCAGATTTGACCTTCATTGAAGCAGATCCAAGATGATTTGACATCTCT
1 AGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGACATCTAT
*
40331908 GTATTAGACGAGGAGCAGATCGAAGACA
66 GTATTACACGAGGAGCAGATCGAAGACA
40331936 TAACAGATTG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (94 bp):
AGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGACATCTAT
GTATTACACGAGGAGCAGATCGAAGACAC
Found at i:40331972 original size:78 final size:77
Alignment explanation
Indices: 40331843--40332032 Score: 281
Period size: 78 Copynumber: 2.4 Consensus size: 77
40331833 TCGAAGACAC
* *
40331843 AGCAGATCGAAGACACAGCAGATTTGACCTTCATTGAAGCAGATCCAAGATGATTTGACATCTCT
1 AGCAGATCGAAGACATAGCAGA-TTGACCTTCATTAAAGCAGATCCAAGATGATTTGACATCTCT
*
40331908 GTATTAGACGAGG
65 ATATTAGACGAGG
* *
40331921 AGCAGATCGAAGACATAACAGATTGGACCTTCATTAAAGCAGATCCAAGATGATTTGGCATCTCT
1 AGCAGATCGAAGACATAGCAGATT-GACCTTCATTAAAGCAGATCCAAGATGATTTGACATCTCT
*
40331986 ATATTAGACGGGG
65 ATATTAGACGAGG
* *
40331999 AGTAGATCGAAGACATAGTAGATCTGACCTTCAT
1 AGCAGATCGAAGACATAGCAGAT-TGACCTTCAT
40332033 GTGTTTGCAT
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
77 2 0.02
78 98 0.97
79 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (77 bp):
AGCAGATCGAAGACATAGCAGATTGACCTTCATTAAAGCAGATCCAAGATGATTTGACATCTCTA
TATTAGACGAGG
Found at i:40332169 original size:89 final size:89
Alignment explanation
Indices: 40332062--40332231 Score: 268
Period size: 89 Copynumber: 1.9 Consensus size: 89
40332052 TCCAAGATGA
* * * *
40332062 CAGATTTGGCATCTCTGTATTAGACGGGGAGCACATTGGAGATAACAGATTTGGCATCTCTGTAT
1 CAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTAT
40332127 TAGACGGGGAGCAGATTGAAGAAG
66 TAGACGGGGAGCAGATTGAAGAAG
* * *
40332151 CAGATTTGGCGTCTCTGTATTAGACGAGGAGCAAATCGAAGATAACATATTTGGCGTCTCTGTAT
1 CAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTAT
*
40332216 TAGACGGGGAGTAGAT
66 TAGACGGGGAGCAGAT
40332232 CAAAGATAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (89 bp):
CAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTAT
TAGACGGGGAGCAGATTGAAGAAG
Found at i:40332238 original size:45 final size:45
Alignment explanation
Indices: 40332048--40332239 Score: 251
Period size: 45 Copynumber: 4.3 Consensus size: 45
40332038 TGCATCGAAT
* *
40332048 CAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAG
1 CAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
* * *
40332093 CACATTGGAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
1 CAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
* * * *
40332138 CAGATTGAAGA-AGCAGATTTGGCGTCTCTGTATTAGACGAGGAG
1 CAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
* * *
40332182 CAAATCGAAGATAACATATTTGGCGTCTCTGTATTAGACGGGGAG
1 CAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
* *
40332227 TAGATCAAAGATA
1 CAGATCGAAGATA
40332240 GTAGATATCA
Statistics
Matches: 128, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
44 39 0.30
45 89 0.70
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (45 bp):
CAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
Found at i:40332658 original size:22 final size:21
Alignment explanation
Indices: 40332596--40332658 Score: 76
Period size: 19 Copynumber: 3.0 Consensus size: 21
40332586 ATAATCTTCA
40332596 ATGATTTGCAATCTT--AGAT
1 ATGATTTGCAATCTTAGAGAT
*
40332615 ATGATATGCAATCTTAGAAGAT
1 ATGATTTGCAATCTTAG-AGAT
*
40332637 ATGATTTTGTAATCTTAGAGAT
1 ATGA-TTTGCAATCTTAGAGAT
40332659 TTAATTTGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 14 0.38
22 12 0.32
23 11 0.30
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (21 bp):
ATGATTTGCAATCTTAGAGAT
Found at i:40337284 original size:84 final size:84
Alignment explanation
Indices: 40337143--40337308 Score: 287
Period size: 84 Copynumber: 2.0 Consensus size: 84
40337133 CTATTTCATA
* * *
40337143 GTTTCCATGATTCAACTAGCCCTTTTAGCATAAATAGCACAAATTATGATAGTGATTAACCATTC
1 GTTTCCAAGATTCAACTAGCCCTTTTAGCATAAATAGCACAAATTATGAAAGTGATTAACCATCC
40337208 CCATGGCCAATCCTTGTTG
66 CCATGGCCAATCCTTGTTG
* *
40337227 GTTTCCAAGATTCAACTAGCCCTTTTTGCATAAATAGCACAATTTATGAAAGTGATTAACCATCC
1 GTTTCCAAGATTCAACTAGCCCTTTTAGCATAAATAGCACAAATTATGAAAGTGATTAACCATCC
40337292 CCATGGCCAATCCTTGT
66 CCATGGCCAATCCTTGT
40337309 CAAGCATATC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (84 bp):
GTTTCCAAGATTCAACTAGCCCTTTTAGCATAAATAGCACAAATTATGAAAGTGATTAACCATCC
CCATGGCCAATCCTTGTTG
Found at i:40338154 original size:39 final size:39
Alignment explanation
Indices: 40337914--40338439 Score: 713
Period size: 39 Copynumber: 13.5 Consensus size: 39
40337904 GCTCCTCGTT
* *
40337914 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
40337954 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
* * *
40337994 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
* * * * *
40338034 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGG-GCTTAGCCCGGAATTAGTATCTCGCA
* * *
40338074 CAAATGCCTTCGGATCTTAGTCCGG-A-T--CATCTCGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGAATTAGTATCTCGCA
40338110 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
40338149 CAAATGCCTTCGGGCTTAGCCCGGAATTAGCATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
**
40338188 CAAATGCCTTCGGGCTTAGCCCATAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
40338227 CAAATGCCTTCGGGCTTAGCCCGGAATTAGCATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
**
40338266 CAAATGCCTTCGGGCTTAGCCCATAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
40338305 CAAATGCCTTCGGGCTTAGCCCGGAATTAGCATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
**
40338344 CAAATGCCTTCGGGCTTAGCCCATAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
40338383 CAAATGCCTTCGGGCTTAGCCCGGAATTAGCATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40338422 CAAATGCCTTCGGGCTTA
1 CAAATGCCTTCGGGCTTA
40338440 TTCTTGCAAA
Statistics
Matches: 446, Mismatches: 33, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
35 9 0.02
36 20 0.04
37 1 0.00
38 1 0.00
39 281 0.63
40 132 0.30
41 2 0.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:40339071 original size:102 final size:102
Alignment explanation
Indices: 40338893--40339094 Score: 368
Period size: 102 Copynumber: 2.0 Consensus size: 102
40338883 TTGGCTAATA
40338893 CACACATATACACACTAGTAAAGCATCCTCTCCCTTTCCATCAATTTAACACATGCATTACTCAT
1 CACACATATACACACTAGTAAAGCATCCTCTCCCTTTCCATCAATTTAACACATGCATTACTCAT
*
40338958 TAATATACAAAAATTATATTCGGCCTTAGCACACACC
66 TAACATACAAAAATTATATTCGGCCTTAGCACACACC
*
40338995 CACACATATACACACTAGTAAAGCATCCTCTCCCTTTCCATCAATTTAACACATGCATTGCTCAT
1 CACACATATACACACTAGTAAAGCATCCTCTCCCTTTCCATCAATTTAACACATGCATTACTCAT
* *
40339060 TAACATGCAAAAGTTATATTCGGCCTTAGCACACA
66 TAACATACAAAAATTATATTCGGCCTTAGCACACA
40339095 ACTTGCTAGC
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.35, C:0.29, G:0.07, T:0.28
Consensus pattern (102 bp):
CACACATATACACACTAGTAAAGCATCCTCTCCCTTTCCATCAATTTAACACATGCATTACTCAT
TAACATACAAAAATTATATTCGGCCTTAGCACACACC
Found at i:40343841 original size:11 final size:11
Alignment explanation
Indices: 40343825--40343867 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
40343815 AAGTAATTTT
40343825 TCAATTCAATC
1 TCAATTCAATC
*
40343836 TCAATTCTAATTTT
1 TCAATTC-AA--TC
40343850 TCAATTCAATC
1 TCAATTCAATC
40343861 TCAATTC
1 TCAATTC
40343868 TAACCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 15 0.56
12 2 0.07
13 2 0.07
14 8 0.30
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (11 bp):
TCAATTCAATC
Found at i:40343882 original size:30 final size:25
Alignment explanation
Indices: 40343818--40343870 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
40343808 TCTAGTTAAG
40343818 TAATTTTTCAATTCAATCTCAATTC
1 TAATTTTTCAATTCAATCTCAATTC
40343843 TAATTTTTCAATTCAATCTCAATTC
1 TAATTTTTCAATTCAATCTCAATTC
40343868 TAA
1 TAA
40343871 CCTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (25 bp):
TAATTTTTCAATTCAATCTCAATTC
Found at i:40356667 original size:46 final size:46
Alignment explanation
Indices: 40356605--40356925 Score: 439
Period size: 46 Copynumber: 7.0 Consensus size: 46
40356595 AGTGTGCTCT
40356605 CTGATA-GAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
40356651 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
40356697 CTGATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCGAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
40356743 CTGATATGAAACGTGTAAGACCATGATTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
40356789 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** ** *
40356835 GTGACGGGGAAATGAATAAGACCATGGTTGAATGATACCATGGCAAC
1 CTGA-TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
40356882 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
40356926 TCATGTCGAA
Statistics
Matches: 247, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.00
46 206 0.83
47 40 0.16
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:40361210 original size:46 final size:46
Alignment explanation
Indices: 40361143--40361234 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
40361133 GATATACACA
*
40361143 TTACCAAACGTATTCACAAACTTCTAGCCTATACATGCCATACTTC
1 TTACCAAACATATTCACAAACTTCTAGCCTATACATGCCATACTTC
40361189 TTACCAAACATATTCACAAACTTCTAGCCTATACATGCCATACTTC
1 TTACCAAACATATTCACAAACTTCTAGCCTATACATGCCATACTTC
40361235 AATATATACA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.30
Consensus pattern (46 bp):
TTACCAAACATATTCACAAACTTCTAGCCTATACATGCCATACTTC
Found at i:40362826 original size:100 final size:102
Alignment explanation
Indices: 40362694--40362883 Score: 285
Period size: 102 Copynumber: 1.9 Consensus size: 102
40362684 AAAGCTATCT
* *
40362694 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGGTACACGTAGTAG
1 GGTATGCATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGTTATCCGGTACACATAGTAG
40362757 CCTGCACTTAGTACTACACACGTGATCGAAGTTATTA
66 CCTGCACTTAGTACTACACACGTGATCGAAGTTATTA
* * * * * *
40362794 GGTATGCATAGTAGCCTGCATTTAGTAGTACACACGTGATCGAAGTTATCGGGTACGCATAGTAG
1 GGTATGCATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGTTATCCGGTACACATAGTAG
*
40362859 CCTGCACTTAGTGCTACACACGTGA
66 CCTGCACTTAGTACTACACACGTGA
40362884 CCTCACAATA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 35 0.44
101 3 0.04
102 41 0.52
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (102 bp):
GGTATGCATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGTTATCCGGTACACATAGTAG
CCTGCACTTAGTACTACACACGTGATCGAAGTTATTA
Found at i:40362827 original size:51 final size:51
Alignment explanation
Indices: 40362689--40362883 Score: 250
Period size: 51 Copynumber: 3.9 Consensus size: 51
40362679 TAGCCAAAGC
* * * * *
40362689 TATCTGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-T
1 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
* * *
40362738 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
* * * *
40362789 TATTAGGTATGCATAGTAGCCTGCATTTAGTAGTACACACGTGATCGAAGT
1 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
* *
40362840 TATCGGGTACGCATAGTAGCCTGCACTTAGTGCTACACACGTGA
1 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
40362884 CCTCACAATA
Statistics
Matches: 124, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
49 38 0.31
50 3 0.02
51 83 0.67
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (51 bp):
TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
Found at i:40364392 original size:43 final size:43
Alignment explanation
Indices: 40364326--40364481 Score: 131
Period size: 43 Copynumber: 3.6 Consensus size: 43
40364316 AGCTCGTACA
*
40364326 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACAGGGTCTTACATGTAATCAAATATCG
*** *
40364369 ATGCC-ACTGTCCCAGACAGGGTCTTACACAAAATCATATAT-G
1 ATGCCAAC-GTCCCAGACAGGGTCTTACATGTAATCAAATATCG
* * * * * * *
40364411 ATGTCGATGTCCCAAATATGGTCTTACATGTAAATCATAA-GTCG
1 ATGCCAACGTCCCAGACAGGGTCTTACATGT-AATCA-AATATCG
*
40364455 ATGCCAACGTCCTAGAC-GTGGTCTTAC
1 ATGCCAACGTCCCAGACAG-GGTCTTAC
40364482 GCGAAAACAC
Statistics
Matches: 85, Mismatches: 22, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
42 24 0.28
43 40 0.47
44 21 0.25
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACATGTAATCAAATATCG
Found at i:40367967 original size:24 final size:24
Alignment explanation
Indices: 40367939--40367985 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40367929 ACACATATTC
*
40367939 AATTCAATC-AATACAAATTCAATA
1 AATTC-ATCAAATACAAAATCAATA
40367963 AATTCATCAAATACAAAATCAAT
1 AATTCATCAAATACAAAATCAAT
40367986 CCATTTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (24 bp):
AATTCATCAAATACAAAATCAATA
Found at i:40374200 original size:28 final size:28
Alignment explanation
Indices: 40374168--40374233 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
40374158 ACAGTGCATG
*
40374168 CAGTAACAGTCTGGGCCTTAGCCCT-ATA
1 CAGTAACAGTCTGGGCCTAAG-CCTAATA
* *
40374196 CAGTAATAGTGTGGGCCTAAGCCTAATA
1 CAGTAACAGTCTGGGCCTAAGCCTAATA
*
40374224 CAGTATCAGT
1 CAGTAACAGT
40374234 ACAATGTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (28 bp):
CAGTAACAGTCTGGGCCTAAGCCTAATA
Found at i:40374419 original size:27 final size:27
Alignment explanation
Indices: 40374389--40374448 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
40374379 AGTTGCCAGA
*
40374389 AACAGTAAATGTGGCAAAGCCACCAAT
1 AACAGTAAATGTGACAAAGCCACCAAT
** * *
40374416 AACAGTGGATGTGACATAGTCACCAAT
1 AACAGTAAATGTGACAAAGCCACCAAT
40374443 -ACAGTA
1 AACAGTA
40374449 CTTCCTCCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (27 bp):
AACAGTAAATGTGACAAAGCCACCAAT
Found at i:40379705 original size:20 final size:19
Alignment explanation
Indices: 40379682--40379725 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
40379672 TTGGCTCGTT
40379682 ATGGGCCACGT-TGGGCCACA
1 ATGGGCC-CGTGTGGGCC-CA
40379702 ATGGG-CCGTGTGGGCCCA
1 ATGGGCCCGTGTGGGCCCA
40379720 ATGGGC
1 ATGGGC
40379726 TCGCTGGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 10 0.45
19 7 0.32
20 5 0.23
ACGTcount: A:0.16, C:0.27, G:0.41, T:0.16
Consensus pattern (19 bp):
ATGGGCCCGTGTGGGCCCA
Found at i:40380039 original size:27 final size:27
Alignment explanation
Indices: 40379965--40380039 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
40379955 CCCCAAAATA
* * *
40379965 GGTAAAATGACCATAATACCACTGTAG
1 GGTAAAATGACGATAATACCCCTATAG
* *
40379992 GGTAAAATGATTG-TAATACCCCTATAT
1 GGTAAAATGA-CGATAATACCCCTATAG
*
40380019 GGTAAAATGACGATTATACCC
1 GGTAAAATGACGATAATACCC
40380040 TTATGTTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (27 bp):
GGTAAAATGACGATAATACCCCTATAG
Found at i:40380215 original size:27 final size:26
Alignment explanation
Indices: 40380166--40380217 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40380156 TGGAGGAAGT
*
40380166 ACTATACTGGTGACTATGTCACATTC
1 ACTATACTGGTGACTATGCCACATTC
* *
40380192 ACTATTACTGGTGGCTTTGCCACATT
1 ACTA-TACTGGTGACTATGCCACATT
40380218 TACTGTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (26 bp):
ACTATACTGGTGACTATGCCACATTC
Found at i:40380425 original size:28 final size:28
Alignment explanation
Indices: 40380380--40380477 Score: 79
Period size: 28 Copynumber: 3.3 Consensus size: 28
40380370 ATTACACTGT
* * * * *
40380380 ACTGATACTGTATTGGGCTTAGGCCCAC
1 ACTGTTACTATATAGGGCTAAGGCCCAA
40380408 ACTGTTACTATATAGGGCTAAGGCCCAA
1 ACTGTTACTATATAGGGCTAAGGCCCAA
* * *
40380436 ACTGTACTAATACTGAATAGGGCTCAGGCCCAG
1 ACTGT--TACTA-T--ATAGGGCTAAGGCCCAA
40380469 ACTGTTACT
1 ACTGTTACT
40380478 GCATGTACTG
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 28 0.50
30 4 0.07
31 4 0.07
33 20 0.36
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (28 bp):
ACTGTTACTATATAGGGCTAAGGCCCAA
Found at i:40383286 original size:40 final size:40
Alignment explanation
Indices: 40383168--40383304 Score: 154
Period size: 40 Copynumber: 3.5 Consensus size: 40
40383158 CGGATGATAA
* * * *
40383168 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * * *
40383208 TCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
40383248 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
40383288 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
40383305 ATACTTGGGT
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
38 1 0.01
39 15 0.19
40 62 0.77
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:40383572 original size:22 final size:22
Alignment explanation
Indices: 40383532--40383573 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40383522 GAATGTGCAT
*
40383532 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
40383554 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
40383574 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:40396610 original size:45 final size:45
Alignment explanation
Indices: 40396546--40396675 Score: 192
Period size: 45 Copynumber: 2.9 Consensus size: 45
40396536 GTTGTACAGT
* *
40396546 ATTATTCGGGCCTTGGAGCCTAGCAGGCTATAATGCTGGTGAGAC
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGAC
* *
40396591 ATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGAC
* *
40396636 ATTTTTCGGGCC-TCGAGCCTAGCAGGC-AAAATGCCGGTGA
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
40396676 ATAAATTCAG
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 12 0.15
44 14 0.18
45 53 0.67
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (45 bp):
ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGAC
Found at i:40399363 original size:60 final size:59
Alignment explanation
Indices: 40399245--40399379 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 59
40399235 GTGTTAACTT
*
40399245 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCATTTACAGTATCAGAGTATATTA
1 GGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCATTTACAG-ATCAGAGTATATTA
* * * * *
40399306 GGCCTAGCCCATATCAGTATCAATCTGGGTCGTAGCCCTATTACA-AGTC-GAGATATATTG
1 GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCAT-TTACAGA-TCAGAG-TATATTA
*
40399366 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
40399380 TAACATAGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 4 0.06
60 51 0.80
61 9 0.14
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (59 bp):
GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCATTTACAGATCAGAGTATATTA
Found at i:40417561 original size:5 final size:5
Alignment explanation
Indices: 40417538--40417588 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
40417528 CATCAGCTTC
* * *
40417538 TGATA TG-TT TGAAA TGATA TGATA TGATA TGATA TGTTA TGATA TGATA
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
40417587 TG
1 TG
40417589 TGATGAAGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
4 3 0.08
5 36 0.92
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (5 bp):
TGATA
Found at i:40417571 original size:15 final size:14
Alignment explanation
Indices: 40417538--40417594 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 14
40417528 CATCAGCTTC
* *
40417538 TGATATGTTTGAAA
1 TGATATGTATGATA
40417552 TGATATGATATGATA
1 TGATATG-TATGATA
40417567 TGATATGTTATGATA
1 TGATATG-TATGATA
40417582 TGATATGTGATGA
1 TGATATGT-ATGA
40417595 AGGAGAAGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.21
15 30 0.79
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (14 bp):
TGATATGTATGATA
Found at i:40419286 original size:16 final size:17
Alignment explanation
Indices: 40419265--40419298 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40419255 CATTTTGATG
40419265 TAAATGAATCAAA-ATA
1 TAAATGAATCAAAGATA
*
40419281 TAAATGTATCAAAGATA
1 TAAATGAATCAAAGATA
40419298 T
1 T
40419299 GATGAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (17 bp):
TAAATGAATCAAAGATA
Found at i:40419555 original size:68 final size:68
Alignment explanation
Indices: 40419443--40419595 Score: 252
Period size: 68 Copynumber: 2.2 Consensus size: 68
40419433 GCGAATTCTC
* *
40419443 CACAGCTCGTTTGAGCAGCATCGTGTAGCTTACATTCTGACCCACTACTCGTGTGAGCAGGCCCA
1 CACAGCTCGTGTGAGCAGCATCGTGTAGCTTACATTCTGACCCACTACTCGTGTGAGCAAGCCCA
40419508 TTT
66 TTT
* *
40419511 CACAGCTCGTGTGAGTAGCATCGTGTAGCTTACATTCTGGCCCACTACTCGTGTGAGCAAGCCCA
1 CACAGCTCGTGTGAGCAGCATCGTGTAGCTTACATTCTGACCCACTACTCGTGTGAGCAAGCCCA
40419576 TTT
66 TTT
* *
40419579 CACAGTTTGTGTGAGCA
1 CACAGCTCGTGTGAGCA
40419596 TGGATGTAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 78 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (68 bp):
CACAGCTCGTGTGAGCAGCATCGTGTAGCTTACATTCTGACCCACTACTCGTGTGAGCAAGCCCA
TTT
Found at i:40425668 original size:70 final size:71
Alignment explanation
Indices: 40425580--40425735 Score: 280
Period size: 70 Copynumber: 2.2 Consensus size: 71
40425570 TGTATTAGTA
40425580 AAATA-ATAACTTAATGGATATTATATGCATTCCATATTAGTATTATAATATTTAAT-AATTTTA
1 AAATATATAA-TTAATGGATATTATATGCATTCCATATTAGTATTATAATATTTAATGAATTTTA
40425643 TAAGAGG
65 TAAGAGG
*
40425650 AAATATATAATTAATGGATATTATATGCATTCCATATTAGTATTATAATATTTAATGATTTTTAT
1 AAATATATAATTAATGGATATTATATGCATTCCATATTAGTATTATAATATTTAATGAATTTTAT
40425715 AAGAGG
66 AAGAGG
40425721 AAATATATAATTAAT
1 AAATATATAATTAAT
40425736 AAAAGTAAAT
Statistics
Matches: 83, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
70 51 0.61
71 32 0.39
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (71 bp):
AAATATATAATTAATGGATATTATATGCATTCCATATTAGTATTATAATATTTAATGAATTTTAT
AAGAGG
Found at i:40427475 original size:45 final size:45
Alignment explanation
Indices: 40427308--40427522 Score: 271
Period size: 45 Copynumber: 4.8 Consensus size: 45
40427298 TATCGTACGG
*
40427308 TACTATTTGGGCCTTTGAGCCTAGCAGGCTATGAAAT--CGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTAT--AATGCCGGTGAGA
*
40427353 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
40427398 TACTATTCAGGCCTTTGAGCCTAGCAGGCTATAATTCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
** *
40427443 TACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * *
40427488 TGA-TA-TCGAG-CTTCGAGCCTAGCAGGCGA-AATGCC
1 T-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCC
40427523 AGTGGATGAA
Statistics
Matches: 154, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
42 6 0.04
43 19 0.12
44 4 0.03
45 124 0.81
46 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:40436497 original size:23 final size:23
Alignment explanation
Indices: 40436450--40436497 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40436440 TATTTGTATG
*
40436450 ATTTATTAATGCATGAAGATTTC
1 ATTTATTAATGCATGAAGATATC
*
40436473 ATTTATTATTGGCATGAA-ATATC
1 ATTTATTAAT-GCATGAAGATATC
40436496 AT
1 AT
40436498 AGAAATGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.44
Consensus pattern (23 bp):
ATTTATTAATGCATGAAGATATC
Found at i:40446637 original size:26 final size:26
Alignment explanation
Indices: 40446601--40446656 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
40446591 TGATAAAAAT
40446601 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40446627 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40446653 TGAT
1 TGAT
40446657 GGGCATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40451640 original size:34 final size:34
Alignment explanation
Indices: 40451591--40451687 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
40451581 TTTAAATTTT
* *
40451591 TTTAAA-AAAAATAATTAAATTAGGTTTTAGGGG
1 TTTAAAGAAAATTAATTAAATTAGGGTTTAGGGG
* * *
40451624 TTTAAAGTAAATTAATTAAATTAGGGTTTATGGT
1 TTTAAAGAAAATTAATTAAATTAGGGTTTAGGGG
40451658 TTTAAAGAAAATTAATTAAATTAGGGTTTA
1 TTTAAAGAAAATTAATTAAATTAGGGTTTA
40451688 CGTTTTTTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 6 0.11
34 51 0.89
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.40
Consensus pattern (34 bp):
TTTAAAGAAAATTAATTAAATTAGGGTTTAGGGG
Found at i:40452071 original size:126 final size:125
Alignment explanation
Indices: 40451790--40452288 Score: 563
Period size: 125 Copynumber: 4.0 Consensus size: 125
40451780 TTTGTTTCTA
* * *
40451790 AAAAATTAATTTTGAGAAGATGATTCTGAAAAAATAATGTCAAAAATGCTTTAAGCATGATGCAC
1 AAAAA-TAATTTTGAGAAGACGATTCTGAAAAAATAATGTCAAAAATGCTTCAAGCAGGATGCAC
* * * * * * * *
40451855 TGTTAGAAAAAGTACTG-AAAAAGCTCTCATGTGGATGCTCTTTTTCTATAATAGTTCCTG
65 TGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGATGCTCTTTTTCTACAGTAGTTCCTG
* * *
40451915 AAAAAATAATTTTGAGAAGAC-AGTTCTGAAAAAATAATGTAAAAAACGCTTCAAGCATGATGCA
1 -AAAAATAATTTTGAGAAGACGA-TTCTGAAAAAATAATGTCAAAAATGCTTCAAGCAGGATGCA
* * * *
40451979 CTATCAGCAAAGTTATTGAAAAAAACTCCCACGTGGATGCTCTTTTTCTACAGTAGTTCTTG
64 CTGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGATGCTCTTTTTCTACAGTAGTTCCTG
* * * * * * *
40452041 AAATAATATTTTTAAGAAAATGGTTCTGAAAAAATAGTGTCAAAAATGCTTCAAGTAGGATGCAC
1 AAA-AATAATTTTGAGAAGACGATTCTGAAAAAATAATGTCAAAAATGCTTCAAGCAGGATGCAC
* * * * * * *
40452106 TGTCAGCAAAATTACTGAAAAAAGCTCTCACATGAACGTTCTTTTTCTACAGTAATTCCTG
65 TGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGATGCTCTTTTTCTACAGTAGTTCCTG
* * * * * *
40452167 AAAAATAATTTTGAGAAGACGATTATGAAAAAGTAGTTTTAGAAATGCTTCAAGCAGGATGCACT
1 AAAAATAATTTTGAGAAGACGATTCTGAAAAAATAATGTCAAAAATGCTTCAAGCAGGATGCACT
* * *
40452232 GTCAGCAAAATTACT-AAAAAAAGGTTCCATGTGGATGCTCTTTTTCTACAGTAGTTC
66 GTCAGCAAAATTACTGAAAAAAA-CTCCCACGTGGATGCTCTTTTTCTACAGTAGTTC
40452289 TTGCTTGGTA
Statistics
Matches: 310, Mismatches: 58, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
124 7 0.02
125 158 0.51
126 145 0.47
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (125 bp):
AAAAATAATTTTGAGAAGACGATTCTGAAAAAATAATGTCAAAAATGCTTCAAGCAGGATGCACT
GTCAGCAAAATTACTGAAAAAAACTCCCACGTGGATGCTCTTTTTCTACAGTAGTTCCTG
Found at i:40452268 original size:251 final size:251
Alignment explanation
Indices: 40451799--40452291 Score: 650
Period size: 251 Copynumber: 2.0 Consensus size: 251
40451789 AAAAAATTAA
* * * * *
40451799 TTTTGAGAAGATGATTCTGAAAAAATAATGTCAAAAATGCTTTAAGCATGATGCACTGTTAGAAA
1 TTTTAAGAAAATGATTCTGAAAAAATAATGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGAAA
** * * * *
40451864 AAGTACTGAAAAAGCTCTCATGTGGATGCTCTTTTTCTATAATAGTTCCTGAAAAAATAATTTTG
66 AAGTACTGAAAAAGCTCTCACATGAACGCTCTTTTTCTACAATAATTCCTGAAAAAATAATTTTG
* * *
40451929 AGAAGACAGTTCTGAAAAAATAATGTAAAAAACGCTTCAAGCATGATGCACTATCAGCAAAGTTA
131 AGAAGACAGTTATGAAAAAATAATGTAAAAAACGCTTCAAGCAGGATGCACTATCAGCAAAATTA
*
40451994 TTGAAAAAAACTCCCACGTGGATGCTCTTTTTCTACAGTAGTTCTTGAAATAATAT
196 CTGAAAAAAACTCCCACGTGGATGCTCTTTTTCTACAGTAGTTCTTGAAATAATAT
* * * *
40452050 TTTTAAGAAAATGGTTCTGAAAAAATAGTGTCAAAAATGCTTCAAGTAGGATGCACTGTCAGCAA
1 TTTTAAGAAAATGATTCTGAAAAAATAATGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGAAA
* * *
40452115 AATTACTGAAAAAAGCTCTCACATGAACGTTCTTTTTCTACAGTAATTCCTG-AAAAATAATTTT
66 AAGTACTG-AAAAAGCTCTCACATGAACGCTCTTTTTCTACAATAATTCCTGAAAAAATAATTTT
* * * * * * *
40452179 GAGAAGAC-GATTATGAAAAAGTAGTTTTAGAAATGCTTCAAGCAGGATGCACTGTCAGCAAAAT
130 GAGAAGACAG-TTATGAAAAAATAATGTAAAAAACGCTTCAAGCAGGATGCACTATCAGCAAAAT
* * *
40452243 TACT-AAAAAAAGGTTCCATGTGGATGCTCTTTTTCTACAGTAGTTCTTG
194 TACTGAAAAAAA-CTCCCACGTGGATGCTCTTTTTCTACAGTAGTTCTTG
40452292 CTTGGTATTA
Statistics
Matches: 207, Mismatches: 32, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
250 8 0.04
251 164 0.79
252 35 0.17
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (251 bp):
TTTTAAGAAAATGATTCTGAAAAAATAATGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGAAA
AAGTACTGAAAAAGCTCTCACATGAACGCTCTTTTTCTACAATAATTCCTGAAAAAATAATTTTG
AGAAGACAGTTATGAAAAAATAATGTAAAAAACGCTTCAAGCAGGATGCACTATCAGCAAAATTA
CTGAAAAAAACTCCCACGTGGATGCTCTTTTTCTACAGTAGTTCTTGAAATAATAT
Found at i:40455822 original size:18 final size:18
Alignment explanation
Indices: 40455785--40455822 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40455775 GGAAAAGGAA
* *
40455785 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAGAAT
40455803 ACATATAAGGGCTAGAAT
1 ACATATAAGGGCTAGAAT
40455821 AC
1 AC
40455823 GCACCTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGCTAGAAT
Found at i:40467020 original size:26 final size:25
Alignment explanation
Indices: 40466979--40467029 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
40466969 AACTTTTGAC
40466979 AATTTAAAAATAAAAAG-TGAAAATT
1 AATTTAAAAATAAAAAGAT-AAAATT
*
40467004 AATTTAAAAAATTAAAAGATAAAATT
1 AATTT-AAAAATAAAAAGATAAAATT
40467030 TATTCTGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 17 0.74
27 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (25 bp):
AATTTAAAAATAAAAAGATAAAATT
Found at i:40471849 original size:21 final size:20
Alignment explanation
Indices: 40471823--40471873 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
40471813 AGCGGTGGCA
40471823 GTGAGATTAATTACTGTAGCG
1 GTGAGATTAA-TACTGTAGCG
*
40471844 GTGAGATTGGATACTGTAGCG
1 GTGAGATT-AATACTGTAGCG
40471865 GTGAGATTA
1 GTGAGATTA
40471874 GAAACAATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.27, C:0.08, G:0.33, T:0.31
Consensus pattern (20 bp):
GTGAGATTAATACTGTAGCG
Done.