Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 64 of 214
Found at i:18354648 original size:27 final size:27
Alignment explanation
Indices: 18354610--18354665 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
18354600 GTGGTATCGA
18354610 AAATAATGGTTTCGGGACCACAATTCT
1 AAATAATGGTTTCGGGACCACAATTCT
18354637 AAATAATGGTTTCGGGACCACAATTCT
1 AAATAATGGTTTCGGGACCACAATTCT
18354664 AA
1 AA
18354666 CTTTTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (27 bp):
AAATAATGGTTTCGGGACCACAATTCT
Found at i:18356824 original size:33 final size:33
Alignment explanation
Indices: 18356782--18356848 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
18356772 TGGTTAAATG
18356782 TTTCAATTGTGGTGCCAATTAGGGCATAGTGGT
1 TTTCAATTGTGGTGCCAATTAGGGCATAGTGGT
*
18356815 TTTCAATTGTGGTGCCAATTAGGGCATATTGGT
1 TTTCAATTGTGGTGCCAATTAGGGCATAGTGGT
18356848 T
1 T
18356849 AGACACTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (33 bp):
TTTCAATTGTGGTGCCAATTAGGGCATAGTGGT
Found at i:18368412 original size:115 final size:114
Alignment explanation
Indices: 18368273--18368529 Score: 363
Period size: 115 Copynumber: 2.2 Consensus size: 114
18368263 TAAAATGACA
** * * **
18368273 AAATGTCAATTTGGTATCAATACCAATATACAGTATCGATACTTATCTTCAAAGATCGGTACTTT
1 AAATGTCAAAATGATATCAATACCAATATACAGTATCGATACTTATCTCCAAAGATCAATACTTT
18368338 ATAAAGGTATC-GATACAGGTTGACTTGTCTCCAAATTTTTGAAAAAGGCT
66 ATAAAGGTATCAG-TACAGGTTGACTTGTCTCCAAATTTTTG-AAAAGGCT
* *
18368388 AAATGTCAAAATGATATCAATACCAATATACAGTATTGATATTTATCTCCAAAGATCAATACTTT
1 AAATGTCAAAATGATATCAATACCAATATACAGTATCGATACTTATCTCCAAAGATCAATACTTT
* * *
18368453 ATAAAGGTATCAGTACAGGTTGGCTTGTGTCCAAATTTTTGAAATGGCT
66 ATAAAGGTATCAGTACAGGTTGACTTGTCTCCAAATTTTTGAAAAGGCT
* *
18368502 AAATGCCAAAACGATATCAATACGCAAT
1 AAATGTCAAAATGATATCAATAC-CAAT
18368530 TTGGTATCGA
Statistics
Matches: 127, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
114 28 0.22
115 98 0.77
116 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (114 bp):
AAATGTCAAAATGATATCAATACCAATATACAGTATCGATACTTATCTCCAAAGATCAATACTTT
ATAAAGGTATCAGTACAGGTTGACTTGTCTCCAAATTTTTGAAAAGGCT
Found at i:18368805 original size:20 final size:20
Alignment explanation
Indices: 18368780--18368853 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
18368770 CACGAAGTTG
18368780 TTAAATGAATTGATATTTGA
1 TTAAATGAATTGATATTTGA
* * *
18368800 TTAAATTAATTGAGAAGTTG-
1 TTAAATGAATTGA-TATTTGA
*
18368820 TTAAATGAATTGATTTTTGA
1 TTAAATGAATTGATATTTGA
*
18368840 TTAAATTAATTGAT
1 TTAAATGAATTGAT
18368854 GTGAATTGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.07
20 37 0.84
21 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (20 bp):
TTAAATGAATTGATATTTGA
Found at i:18368828 original size:40 final size:40
Alignment explanation
Indices: 18368773--18368852 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
18368763 TATCGTACAC
18368773 GAAGTTGTTAAATGAATTGATATTTGATTAAATTAATTGA
1 GAAGTTGTTAAATGAATTGATATTTGATTAAATTAATTGA
*
18368813 GAAGTTGTTAAATGAATTGATTTTTGATTAAATTAATTGA
1 GAAGTTGTTAAATGAATTGATATTTGATTAAATTAATTGA
18368853 TGTGAATTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (40 bp):
GAAGTTGTTAAATGAATTGATATTTGATTAAATTAATTGA
Found at i:18372182 original size:34 final size:35
Alignment explanation
Indices: 18372102--18372185 Score: 116
Period size: 35 Copynumber: 2.4 Consensus size: 35
18372092 AAATCGACTC
*
18372102 AAAAGAGGTTGGGATAGACCAGTCTATGCCAACCTT
1 AAAA-AGGTTGGGATAGACCAGTCTAAGCCAACCTT
* * *
18372138 AAAAAGGTTGGGTTAGACCCGTCTAAGGCAACCTT
1 AAAAAGGTTGGGATAGACCAGTCTAAGCCAACCTT
18372173 -AAAAGGTTGGGAT
1 AAAAAGGTTGGGAT
18372186 GGACTTTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 12 0.28
35 27 0.63
36 4 0.09
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (35 bp):
AAAAAGGTTGGGATAGACCAGTCTAAGCCAACCTT
Found at i:18378515 original size:13 final size:13
Alignment explanation
Indices: 18378499--18378541 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
18378489 AGTACTGTGA
18378499 AAAAATATTTTTG
1 AAAAATATTTTTG
* *
18378512 AAAAGTA-TTGTG
1 AAAAATATTTTTG
18378524 AAAAAGTATTTTTG
1 AAAAA-TATTTTTG
18378538 AAAA
1 AAAA
18378542 GTACTGTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (13 bp):
AAAAATATTTTTG
Found at i:18378554 original size:13 final size:13
Alignment explanation
Indices: 18378486--18378556 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
18378476 GTTGCTTTTG
*
18378486 AAAAGTACTGTGA
1 AAAAGTATTGTGA
* *
18378499 AAAAATATTTTTG-
1 AAAAGTA-TTGTGA
18378512 AAAAGTATTGTGA
1 AAAAGTATTGTGA
*
18378525 AAAAGTATTTTTG-
1 AAAAGTA-TTGTGA
*
18378538 AAAAGTACTGTGA
1 AAAAGTATTGTGA
18378551 AAAAGT
1 AAAAGT
18378557 GCTTTTAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
12 7 0.15
13 32 0.70
14 7 0.15
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.32
Consensus pattern (13 bp):
AAAAGTATTGTGA
Found at i:18378555 original size:26 final size:26
Alignment explanation
Indices: 18378481--18378556 Score: 134
Period size: 26 Copynumber: 2.9 Consensus size: 26
18378471 GGCCAGTTGC
*
18378481 TTTTGAAAAGTACTGTGAAAAAATAT
1 TTTTGAAAAGTACTGTGAAAAAGTAT
*
18378507 TTTTGAAAAGTATTGTGAAAAAGTAT
1 TTTTGAAAAGTACTGTGAAAAAGTAT
18378533 TTTTGAAAAGTACTGTGAAAAAGT
1 TTTTGAAAAGTACTGTGAAAAAGT
18378557 GCTTTTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.36
Consensus pattern (26 bp):
TTTTGAAAAGTACTGTGAAAAAGTAT
Found at i:18378562 original size:26 final size:26
Alignment explanation
Indices: 18378480--18378569 Score: 126
Period size: 26 Copynumber: 3.5 Consensus size: 26
18378470 GGGCCAGTTG
*
18378480 CTTTTGAAAAGTACTGTGAAAAAATA
1 CTTTTGAAAAGTACTGTGAAAAAGTA
* *
18378506 TTTTTGAAAAGTATTGTGAAAAAGTA
1 CTTTTGAAAAGTACTGTGAAAAAGTA
* *
18378532 TTTTTGAAAAGTACTGTGAAAAAGTG
1 CTTTTGAAAAGTACTGTGAAAAAGTA
*
18378558 CTTTTAAAAAGT
1 CTTTTGAAAAGT
18378570 TTGGTTTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (26 bp):
CTTTTGAAAAGTACTGTGAAAAAGTA
Found at i:18381433 original size:13 final size:13
Alignment explanation
Indices: 18381417--18381441 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18381407 TTAAGATATA
18381417 TTATTATTTTTAG
1 TTATTATTTTTAG
18381430 TTATTATTTTTA
1 TTATTATTTTTA
18381442 ATTTATCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTATTTTTAG
Found at i:18383197 original size:12 final size:12
Alignment explanation
Indices: 18383180--18383204 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18383170 ACTTAGAGTG
18383180 TGTGATATAGTA
1 TGTGATATAGTA
18383192 TGTGATATAGTA
1 TGTGATATAGTA
18383204 T
1 T
18383205 TAATGAAATA
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:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TGTGATATAGTA
Found at i:18383252 original size:27 final size:27
Alignment explanation
Indices: 18383200--18383253 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
18383190 TATGTGATAT
*
18383200 AGTATTAATGAAATAATACATTTTATA
1 AGTATTAATGAAATAATACATATTATA
18383227 AGTATTAAT-ATAATAACTAC-TATTATA
1 AGTATTAATGA-AATAA-TACATATTATA
18383254 TTATAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.04
27 20 0.83
28 3 0.12
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (27 bp):
AGTATTAATGAAATAATACATATTATA
Found at i:18386532 original size:22 final size:22
Alignment explanation
Indices: 18386483--18386526 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
18386473 ATATATATTT
18386483 AAACCCAAACCCAATACCAACC
1 AAACCCAAACCCAATACCAACC
* *
18386505 AAACCCAAATCCTATACCAACC
1 AAACCCAAACCCAATACCAACC
18386527 TCACCCCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.43, G:0.00, T:0.09
Consensus pattern (22 bp):
AAACCCAAACCCAATACCAACC
Found at i:18387199 original size:20 final size:20
Alignment explanation
Indices: 18387174--18387213 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18387164 ATTTTCTTTT
18387174 GTTTCTTCACCGAATATGGA
1 GTTTCTTCACCGAATATGGA
18387194 GTTTCTTCACCGAATATGGA
1 GTTTCTTCACCGAATATGGA
18387214 AGGAAAGAAC
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:0.20, G:0.20, T:0.35
Consensus pattern (20 bp):
GTTTCTTCACCGAATATGGA
Found at i:18388971 original size:12 final size:12
Alignment explanation
Indices: 18388954--18388980 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
18388944 TCAGTTGCAC
18388954 CATTATAAGTGG
1 CATTATAAGTGG
18388966 CATTATAAGTGG
1 CATTATAAGTGG
18388978 CAT
1 CAT
18388981 ACCACCACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (12 bp):
CATTATAAGTGG
Found at i:18389663 original size:21 final size:21
Alignment explanation
Indices: 18389625--18389665 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18389615 CCAAAATCAT
*
18389625 ATGATTTACCAAACTAAAACA
1 ATGATTTACAAAACTAAAACA
* *
18389646 ATGATTTTCAAAATTAAAAC
1 ATGATTTACAAAACTAAAAC
18389666 TCTAGAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (21 bp):
ATGATTTACAAAACTAAAACA
Found at i:18391747 original size:21 final size:21
Alignment explanation
Indices: 18391718--18391761 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
18391708 ACACCAAAAC
* *
18391718 AGGCTTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
18391739 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
18391760 AG
1 AG
18391762 CGCCGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.30, T:0.41
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGCTTTTT
Found at i:18391927 original size:86 final size:85
Alignment explanation
Indices: 18391831--18392018 Score: 225
Period size: 86 Copynumber: 2.2 Consensus size: 85
18391821 ACATCGCTAA
* * * * * *
18391831 CTTTTGCGGCGTTTATGAGAAAAAACGCCACTAAAGAACATGACCTTTAGCGGTGCTTT-GCCAC
1 CTTTAGCGGCGTTTA--ACAAAAAACGCCACTAAAGAACATGACCTTTAACAGCGCTTTACCCAC
*
18391895 AAATGCCGCTAAAGAACATGAC
64 AAACGCCGCTAAAGAACATGAC
* * * * *
18391917 CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGATCTTTAACAGCGCTTTACCCACA
1 CTTTAGCGGCG-TTTAACAAAAAACGCCACTAAAGAACATGACCTTTAACAGCGCTTTACCCACA
18391982 AACGCCGCTAAAGAACATGAC
65 AACGCCGCTAAAGAACATGAC
18392003 CTTTAGCGGCGGTTTA
1 CTTTAGCGGC-GTTTA
18392019 CCTACAAACG
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
85 33 0.38
86 49 0.56
87 5 0.06
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (85 bp):
CTTTAGCGGCGTTTAACAAAAAACGCCACTAAAGAACATGACCTTTAACAGCGCTTTACCCACAA
ACGCCGCTAAAGAACATGAC
Found at i:18391952 original size:43 final size:43
Alignment explanation
Indices: 18391853--18392036 Score: 271
Period size: 43 Copynumber: 4.3 Consensus size: 43
18391843 TTATGAGAAA
* * *
18391853 AAACGCCACTAAAGAACATGACCTTTAGCGGTGCTTT-GCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
*
18391895 AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
* * *
18391938 AAACGCCGCTAAAGAACATGATCTTTAACAGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
* *
18391981 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGGTTTACCTAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
*
18392024 AAACGCTGCTAAA
1 AAACGCCGCTAAA
18392037 AGTACGGTTA
Statistics
Matches: 127, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 34 0.27
43 93 0.73
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
Found at i:18392633 original size:28 final size:28
Alignment explanation
Indices: 18392564--18392633 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
18392554 TAGAGATATG
* * * *
18392564 ATCAAATTAGTCCCTCTACTATTAAATGG
1 ATCAAA-TAGTCCCTATACTATAAAAAGA
* *
18392593 ATCAATTCAGTCCCTATCCTATAAAAAGA
1 ATCAAAT-AGTCCCTATACTATAAAAAGA
18392622 ATCAAATAGTCC
1 ATCAAATAGTCC
18392634 ATTTTCCAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (28 bp):
ATCAAATAGTCCCTATACTATAAAAAGA
Found at i:18396567 original size:45 final size:43
Alignment explanation
Indices: 18396432--18396587 Score: 163
Period size: 43 Copynumber: 3.6 Consensus size: 43
18396422 TGATTCATCC
**
18396432 GATGATGCACTGTGTGTGTTAGTATATTTT-TTTGGTATATCA
1 GATGATGCACTGTGTGTGCCAGTATATTTTCTTTGGTATATCA
* * * *
18396474 GATGATACACTGTGTGTGACAGTATATTTGCTTCGGTATATCCA
1 GATGATGCACTGTGTGTGCCAGTATATTTTCTTTGGTATAT-CA
* * * *
18396518 -ATGATGCACTCTGTGTGCCAGTATATTTTTCTTTGGTTTTGTCT
1 GATGATGCACTGTGTGTGCCAGTATA-TTTTCTTTGG-TATATCA
* *
18396562 GATGATGCATTGTGTGTGCTAGTATA
1 GATGATGCACTGTGTGTGCCAGTATA
18396588 GTAGCTTCGA
Statistics
Matches: 93, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 26 0.28
43 31 0.33
44 11 0.12
45 25 0.27
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.44
Consensus pattern (43 bp):
GATGATGCACTGTGTGTGCCAGTATATTTTCTTTGGTATATCA
Found at i:18405524 original size:16 final size:16
Alignment explanation
Indices: 18405485--18405517 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18405475 AGTGAAATTT
18405485 AACTTAAA-TAATAAA
1 AACTTAAATTAATAAA
18405500 AACTTAAATTAATAAA
1 AACTTAAATTAATAAA
18405516 AA
1 AA
18405518 TATAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
AACTTAAATTAATAAA
Found at i:18405769 original size:22 final size:23
Alignment explanation
Indices: 18405741--18405785 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
18405731 ATGTGCTCTT
18405741 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
18405763 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
18405786 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:18415826 original size:22 final size:22
Alignment explanation
Indices: 18415798--18415841 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
18415788 CACCACATGT
18415798 GAGAATGGCGAGAGCCGTGGGG
1 GAGAATGGCGAGAGCCGTGGGG
18415820 GAGAATGGCGAGAGCCGTGGGG
1 GAGAATGGCGAGAGCCGTGGGG
18415842 CAATCTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.55, T:0.09
Consensus pattern (22 bp):
GAGAATGGCGAGAGCCGTGGGG
Found at i:18417671 original size:4 final size:4
Alignment explanation
Indices: 18417650--18417683 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
18417640 TATAAAAATT
18417650 TAAA CTAAA TAAA CTAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA TAAA -TAAA TAAA TAAA TAAA TAAA
18417684 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:18417677 original size:8 final size:9
Alignment explanation
Indices: 18417650--18417683 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
18417640 TATAAAAATT
18417650 TAAACTAAA
1 TAAACTAAA
18417659 TAAACTAAA
1 TAAACTAAA
18417668 TAAA-TAAA
1 TAAACTAAA
18417676 TAAA-TAAA
1 TAAACTAAA
18417684 AATAAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 12 0.48
9 13 0.52
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (9 bp):
TAAACTAAA
Found at i:18419080 original size:23 final size:22
Alignment explanation
Indices: 18419028--18419080 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
18419018 TCCACGTCTT
*
18419028 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
18419050 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
18419073 TTTCTTTT
1 TTTCTTTT
18419081 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:18421453 original size:4 final size:4
Alignment explanation
Indices: 18421432--18421465 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
18421422 TATAAAAATT
18421432 TAAA CTAAA TAAA CTAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA TAAA -TAAA TAAA TAAA TAAA TAAA
18421466 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:18421459 original size:8 final size:9
Alignment explanation
Indices: 18421432--18421465 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
18421422 TATAAAAATT
18421432 TAAACTAAA
1 TAAACTAAA
18421441 TAAACTAAA
1 TAAACTAAA
18421450 TAAA-TAAA
1 TAAACTAAA
18421458 TAAA-TAAA
1 TAAACTAAA
18421466 AATAAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 12 0.48
9 13 0.52
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (9 bp):
TAAACTAAA
Found at i:18426670 original size:40 final size:40
Alignment explanation
Indices: 18426603--18426682 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
18426593 GAATAGTATG
*
18426603 AATTTCATGCAAGAAACAAGGGATTCATGCAAGAAAACAC
1 AATTTCATGCAAGAAACAAGAGATTCATGCAAGAAAACAC
** *
18426643 AATTTCCATGCAAGAAGTAAGAG-TTCATGCAGGAAAACAC
1 AATTT-CATGCAAGAAACAAGAGATTCATGCAAGAAAACAC
18426683 GTAAAATGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 21 0.60
41 14 0.40
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (40 bp):
AATTTCATGCAAGAAACAAGAGATTCATGCAAGAAAACAC
Found at i:18427378 original size:60 final size:60
Alignment explanation
Indices: 18427285--18427401 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
18427275 CTTTAAAAAT
18427285 ATTTTATGCATGCACTCAAGATAAAACATGATTCGACTTATATTCATAAAGTACCTAAAG
1 ATTTTATGCATGCACTCAAGATAAAACATGATTCGACTTATATTCATAAAGTACCTAAAG
*
18427345 ATTTTATGCATGCACTCAAGATAAAACATGATTCGACTTATATTCATAAATTACCTA
1 ATTTTATGCATGCACTCAAGATAAAACATGATTCGACTTATATTCATAAAGTACCTA
18427402 CCAATGTCAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (60 bp):
ATTTTATGCATGCACTCAAGATAAAACATGATTCGACTTATATTCATAAAGTACCTAAAG
Found at i:18427414 original size:60 final size:60
Alignment explanation
Indices: 18427290--18427415 Score: 200
Period size: 60 Copynumber: 2.1 Consensus size: 60
18427280 AAAATATTTT
* *
18427290 ATGCATGCACTCAAGATAAAACATGATTCGACTTATATTCATAAAGTACCTAAAGATTTT
1 ATGCATGCACTCAAGATAAAACATGATTCGACTTATATTCATAAAGTACCTAAAGATGTC
* *
18427350 ATGCATGCACTCAAGATAAAACATGATTCGACTTATATTCATAAATTACCTACCA-ATGTC
1 ATGCATGCACTCAAGATAAAACATGATTCGACTTATATTCATAAAGTACCTA-AAGATGTC
18427410 ATGCAT
1 ATGCAT
18427416 TTAAACAATG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 60 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (60 bp):
ATGCATGCACTCAAGATAAAACATGATTCGACTTATATTCATAAAGTACCTAAAGATGTC
Found at i:18430035 original size:49 final size:49
Alignment explanation
Indices: 18429923--18430109 Score: 169
Period size: 49 Copynumber: 3.6 Consensus size: 49
18429913 GAGATCCCAT
* * *
18429923 GTAAGACCATGTCTGGGACATGGCATCGGCATCCTTGAGATCATGAAAGGTCCCC
1 GTAAGACCATGTCTGGGACATGGC-TTGGCA-CC--GAGATGA-G-AACGTCCCC
*
18429978 TGTAAGACCATCTCTGGGACATGGCGTTGGCACCGAGATGAGAA-GTCCCC
1 -GTAAGACCATGTCTGGGACATGGC-TTGGCACCGAGATGAGAACGTCCCC
* * * * * *
18430028 GTAAGACCATGTCTGGGACATGGCATGAGCACCAACATGAAAACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCTTG-GCACCGAGATGAGAACGTCCC-C
*
18430079 GTAAGATCATGTCTGGGACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGC-TTGGCA
18430110 TGTTTTTACC
Statistics
Matches: 114, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
48 2 0.02
49 35 0.31
50 10 0.09
51 28 0.25
52 3 0.03
53 6 0.05
55 2 0.02
56 28 0.25
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCTTGGCACCGAGATGAGAACGTCCCC
Found at i:18430109 original size:100 final size:103
Alignment explanation
Indices: 18429923--18430109 Score: 249
Period size: 100 Copynumber: 1.8 Consensus size: 103
18429913 GAGATCCCAT
** *
18429923 GTAAGACCATGTCTGGGACATGGCATCGGCATCCTTGAGATCATGAAAGGTCCCCTGTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATCGGCATCC-T-AGATCATGAAACATCCCATGTAAGACCA
18429988 TCTCTGGGACATGGCGTTGGCACCGAGATGAGAAGTCCCC
64 TCTCTGGGACATGGCGTTGGCACCGAGATGAGAAGTCCCC
*
18430028 GTAAGACCATGTCTGGGACATGGCAT-GAGCA-CC-A-A-CATGAAAACATCCCATGTAAGATCA
1 GTAAGACCATGTCTGGGACATGGCATCG-GCATCCTAGATCATG-AAACATCCCATGTAAGACCA
* *
18430088 TGTCTGGGACATGGCTTTGGCA
64 TCTCTGGGACATGGCGTTGGCA
18430110 TGTTTTTACC
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
99 4 0.05
100 37 0.50
101 1 0.01
104 3 0.04
105 29 0.39
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (103 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCATCCTAGATCATGAAACATCCCATGTAAGACCATC
TCTGGGACATGGCGTTGGCACCGAGATGAGAAGTCCCC
Found at i:18442427 original size:15 final size:15
Alignment explanation
Indices: 18442409--18442441 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
18442399 AACACACATC
*
18442409 TTCTACTCTGTTCTG
1 TTCTACTCTGCTCTG
18442424 TTCTACTCTGCTCTG
1 TTCTACTCTGCTCTG
18442439 TTC
1 TTC
18442442 GATTCTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.30, G:0.12, T:0.52
Consensus pattern (15 bp):
TTCTACTCTGCTCTG
Found at i:18449348 original size:136 final size:129
Alignment explanation
Indices: 18449129--18449397 Score: 475
Period size: 136 Copynumber: 2.0 Consensus size: 129
18449119 GAAGTGAAAT
18449129 ATTTATTTTAGCAACCTCAATCAACTTCTTCTAAATCAATTTTAATCTTTGATTATCTCAAACAC
1 ATTTATTTTAGCAACCTCAATCAACTTCTTCTAAATCAATTTTAATCTTTGATTATCTCAAACAC
18449194 AAAATAATAATAATGATAATAATAATATATATATCTATGTTTTTACATTTAAAGTTGAGAGAGGA
66 AAAATAATAATAATG---ATAAT-A-ATATATA--TATGTTTTTACATTTAAAGTTGAGAGAGGA
18449259 AATGGG
124 AATGGG
18449265 ATTTATTTTAGCAACCTCAATCAACTTCTTCTAAATCAATTTTAATCTTTGATTATCTCAAACAC
1 ATTTATTTTAGCAACCTCAATCAACTTCTTCTAAATCAATTTTAATCTTTGATTATCTCAAACAC
18449330 AAAATAATAATAATGATAATAATATATATATGTTTTTACATTTAAAGTTGAGAGAGGAAATGGG
66 AAAATAATAATAATGATAATAATATATATATGTTTTTACATTTAAAGTTGAGAGAGGAAATGGG
18449394 ATTT
1 ATTT
18449398 GAAGGTAAAA
Statistics
Matches: 133, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
129 40 0.30
131 7 0.05
132 1 0.01
133 5 0.04
136 80 0.60
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.39
Consensus pattern (129 bp):
ATTTATTTTAGCAACCTCAATCAACTTCTTCTAAATCAATTTTAATCTTTGATTATCTCAAACAC
AAAATAATAATAATGATAATAATATATATATGTTTTTACATTTAAAGTTGAGAGAGGAAATGGG
Found at i:18455699 original size:53 final size:54
Alignment explanation
Indices: 18455626--18455739 Score: 185
Period size: 53 Copynumber: 2.1 Consensus size: 54
18455616 TGTTAAAATA
* *
18455626 TTAAAAATAAAATAAAAATTTAAATAGTTAATTGAGATTCTTTAAATAATAG-T
1 TTAAAAATAAAATAAAAATTTAAATAGTTAATTGAAATTCTTTAAAGAATAGTT
* *
18455679 TTAAAAATAATATAATAATTTAAATAGTTAATTGAAATTCTTTAAAGAATAGTT
1 TTAAAAATAAAATAAAAATTTAAATAGTTAATTGAAATTCTTTAAAGAATAGTT
18455733 TTAAAAA
1 TTAAAAA
18455740 ATACTGTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
53 48 0.86
54 8 0.14
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (54 bp):
TTAAAAATAAAATAAAAATTTAAATAGTTAATTGAAATTCTTTAAAGAATAGTT
Found at i:18457244 original size:12 final size:12
Alignment explanation
Indices: 18457227--18457252 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18457217 CAACACAGGC
18457227 TTTTAGCGGCGT
1 TTTTAGCGGCGT
18457239 TTTTAGCGGCGT
1 TTTTAGCGGCGT
18457251 TT
1 TT
18457253 GTTTTCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:18457642 original size:109 final size:113
Alignment explanation
Indices: 18457428--18457630 Score: 288
Period size: 109 Copynumber: 1.8 Consensus size: 113
18457418 CCAAAAGATT
* * *
18457428 AGGGCTTTAGTGGCGTTTCTGAGAAAGCGCCGCAAACAAACTTAAGCCCAACGATGTCGTTTCCT
1 AGGGCTTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACTTAAGCCCAACGATGCCGTTTCCT
* *
18457493 GAGCTTTTGGGGATTTAGCGGTGTTTTTAGTAAAGCGCCGCTAATGCG
66 GAGCTTTTGGGGATATAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCG
* * *
18457541 AGGGCTTTAGCGGCGTTT-TGGGAAAGCGCCG-AAAAAAAC-TCAGCCCAACGATGCCGTTT-TT
1 AGGGCTTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACTTAAGCCCAACGATGCCGTTTCCT
* *
18457602 GAGCTTTTGTGGATATAGTGGCGTTTTTA
66 GAGCTTTTGGGGATATAGCGGCGTTTTTA
18457631 AGAAAGTGCC
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
109 26 0.32
110 18 0.22
111 7 0.09
112 12 0.15
113 17 0.21
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (113 bp):
AGGGCTTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACTTAAGCCCAACGATGCCGTTTCCT
GAGCTTTTGGGGATATAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCG
Found at i:18457702 original size:73 final size:73
Alignment explanation
Indices: 18457546--18457784 Score: 315
Period size: 73 Copynumber: 3.3 Consensus size: 73
18457536 ATGCGAGGGC
* * * *
18457546 TTTAGCGGCG-TTTTGGGAAAGCGCCG-AAAAAAA-CTCAGCCCAACGATGCCGTTTT-TGAGCT
1 TTTAGCGGCGTTTTTAGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGATCT
*
18457607 TTTGTGGA
66 TTTGGGGA
* * * * * *
18457615 TATAGTGGCGTTTTTAAGAAAGTGCCGCAAAAAAACCTAAACCCAACGACGTCGTTTTCTGATCT
1 TTTAGCGGCGTTTTTAGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGATCT
18457680 TTTGGGGA
66 TTTGGGGA
* *
18457688 TTTAGCGGCGTTTTTAGGAAAGCGCCGCAAAAAAACCTAAGCACAACGGCGCCGTTTTCTGATCT
1 TTTAGCGGCGTTTTTAGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGATCT
*
18457753 TTTGGGGC
66 TTTGGGGA
*
18457761 TTTAGCGGCGTTTTTGGGAAAGCG
1 TTTAGCGGCGTTTTTAGGAAAGCG
18457785 TCGCTAATGC
Statistics
Matches: 145, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
69 8 0.06
70 13 0.09
71 7 0.05
72 18 0.12
73 99 0.68
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTAGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGATCT
TTTGGGGA
Found at i:18457812 original size:10 final size:10
Alignment explanation
Indices: 18457797--18457821 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18457787 GCTAATGCTC
18457797 AAATAGTTTA
1 AAATAGTTTA
18457807 AAATAGTTTA
1 AAATAGTTTA
18457817 AAATA
1 AAATA
18457822 TTTGTTAAAA
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (10 bp):
AAATAGTTTA
Found at i:18457831 original size:12 final size:12
Alignment explanation
Indices: 18457814--18457844 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
18457804 TTAAAATAGT
18457814 TTAAAATATTTG
1 TTAAAATATTTG
18457826 TTAAAATATTTG
1 TTAAAATATTTG
18457838 TTAAAAT
1 TTAAAAT
18457845 GAAAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (12 bp):
TTAAAATATTTG
Found at i:18458040 original size:22 final size:22
Alignment explanation
Indices: 18458014--18458081 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
18458004 TAGTGTGTAA
*
18458014 GGGTTAGGAGCTTATGGTTTAG
1 GGGTTATGAGCTTATGGTTTAG
* * *
18458036 GGGTTATGAGCTTAGGGTCTAT
1 GGGTTATGAGCTTATGGTTTAG
*
18458058 AGGTTAATG-GCTTATGGTTTAG
1 GGGTT-ATGAGCTTATGGTTTAG
18458080 GG
1 GG
18458082 TTTAATCAAG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 33 0.92
23 3 0.08
ACGTcount: A:0.19, C:0.06, G:0.38, T:0.37
Consensus pattern (22 bp):
GGGTTATGAGCTTATGGTTTAG
Found at i:18458132 original size:15 final size:15
Alignment explanation
Indices: 18458123--18458169 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
18458113 GGGTTTATGC
18458123 TTTAGAGGTTTAAGG
1 TTTAGAGGTTTAAGG
18458138 TTTAGAGGGTTTAAGG
1 TTTAGA-GGTTTAAGG
*
18458154 TTTAGGGGTTT-AGG
1 TTTAGAGGTTTAAGG
18458168 TT
1 TT
18458170 ATCGTCTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 5 0.17
15 11 0.37
16 14 0.47
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (15 bp):
TTTAGAGGTTTAAGG
Found at i:18458150 original size:16 final size:16
Alignment explanation
Indices: 18458106--18458169 Score: 82
Period size: 15 Copynumber: 4.2 Consensus size: 16
18458096 TATATTTAGG
*
18458106 GGTTTA-AGGGTTTAT
1 GGTTTAGAGGGTTTAA
*
18458121 GCTTTAGA-GGTTTAA
1 GGTTTAGAGGGTTTAA
18458136 GGTTTAGAGGGTTTAA
1 GGTTTAGAGGGTTTAA
18458152 GGTTTAG-GGGTTT-A
1 GGTTTAGAGGGTTTAA
18458166 GGTT
1 GGTT
18458170 ATCGTCTTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
14 5 0.11
15 24 0.55
16 15 0.34
ACGTcount: A:0.20, C:0.02, G:0.36, T:0.42
Consensus pattern (16 bp):
GGTTTAGAGGGTTTAA
Found at i:18458166 original size:8 final size:8
Alignment explanation
Indices: 18458100--18458167 Score: 52
Period size: 8 Copynumber: 8.8 Consensus size: 8
18458090 AGAGTTTATA
18458100 TTTAGGGG
1 TTTAGGGG
*
18458108 TTTAAGGG
1 TTTAGGGG
* *
18458116 TTTA-TGC
1 TTTAGGGG
*
18458123 TTTAGAGG
1 TTTAGGGG
*
18458131 TTTA-AGG
1 TTTAGGGG
18458138 TTTAGAGGG
1 TTTAG-GGG
*
18458147 TTTA-AGG
1 TTTAGGGG
18458154 TTTAGGGG
1 TTTAGGGG
18458162 TTTAGG
1 TTTAGG
18458168 TTATCGTCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
7 18 0.38
8 24 0.50
9 6 0.12
ACGTcount: A:0.21, C:0.01, G:0.37, T:0.41
Consensus pattern (8 bp):
TTTAGGGG
Found at i:18458340 original size:14 final size:14
Alignment explanation
Indices: 18458204--18458340 Score: 68
Period size: 14 Copynumber: 9.9 Consensus size: 14
18458194 TGGTTTACGA
*
18458204 TTTAGTGTTTATAG
1 TTTAGTGTTTAGAG
* *
18458218 TTTAGGGTGTA-AG
1 TTTAGTGTTTAGAG
*
18458231 TTTATGGGTTTA-AG
1 TTTA-GTGTTTAGAG
*
18458245 TAT-GTAGTTTATGA-
1 TTTAGT-GTTTA-GAG
*
18458259 TTTAGTGTTAAGAG
1 TTTAGTGTTTAGAG
18458273 TTTAGTGTTTATG-G
1 TTTAGTGTTTA-GAG
* * *
18458287 TTTAGGGTGTAGGG
1 TTTAGTGTTTAGAG
* * **
18458301 TGTAGGGTTTATTG
1 TTTAGTGTTTAGAG
*
18458315 TTTATTGTTTAGAG
1 TTTAGTGTTTAGAG
*
18458329 TTTAGAGTTTAG
1 TTTAGTGTTTAG
18458341 CTAGTAGCTT
Statistics
Matches: 94, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
12 1 0.01
13 14 0.15
14 75 0.80
15 4 0.04
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (14 bp):
TTTAGTGTTTAGAG
Found at i:18458540 original size:103 final size:103
Alignment explanation
Indices: 18458322--18458540 Score: 375
Period size: 103 Copynumber: 2.1 Consensus size: 103
18458312 TTGTTTATTG
* * * * *
18458322 TTTAGAGTTTAGAGTTTAGCTAGTAGCTTAGAGTTTAGGGATTAATACGGGCATAGGGTATATGG
1 TTTAGGGTTTAGGGTTTAGCTAGTAGCTTAAAGTTTAAGGATTAATACGAGCATAGGGTATATGG
18458387 GTTAAGAAGGCATATGGTTTAGGGTTTAAATTTTATAT
66 GTTAAGAAGGCATATGGTTTAGGGTTTAAATTTTATAT
*
18458425 TTTAAGGTTTAGGGTTTAGCTAGTAGCTTAAAGTTTAAGGATTAATACGAGCATAGGGTATATGG
1 TTTAGGGTTTAGGGTTTAGCTAGTAGCTTAAAGTTTAAGGATTAATACGAGCATAGGGTATATGG
*
18458490 GTTAAGAGGGCATATGGTTTAGGGTTTAAATTTTATAT
66 GTTAAGAAGGCATATGGTTTAGGGTTTAAATTTTATAT
18458528 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
18458541 ATTATGGTAA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (103 bp):
TTTAGGGTTTAGGGTTTAGCTAGTAGCTTAAAGTTTAAGGATTAATACGAGCATAGGGTATATGG
GTTAAGAAGGCATATGGTTTAGGGTTTAAATTTTATAT
Found at i:18459074 original size:116 final size:114
Alignment explanation
Indices: 18458782--18459080 Score: 318
Period size: 116 Copynumber: 2.6 Consensus size: 114
18458772 TTAGTTTCCA
* * * *
18458782 TTTTAGTGGTGTTTCTTC-ATAAACGCCGCAATTATTTTTTAAGTCTTTGCTAAACACTGTCG-T
1 TTTTAGTGGCGTTT-TTCAATAAACGCCGCAATTATGTTTTAAGTATTTGCTAAACGCTGTCGTT
* ** * ** *
18458845 TTTAAATTGCGTTTTAGTGGCGTTTTCTCTTATGTGCCGTAAAATTTCGG
65 TTTATATTGCGTTTTAGTGGCGTTTTCTCTTAAATGCCGCAAAAGGTAGG
* * * *
18458895 TTTTTGTGGC-TTTTTTATGATAAACGCCGCAGTTATGTTTTAAGTATTTGCTAAACGCAGTCGT
1 TTTTAGTGGCGTTTTTCA--ATAAACGCCGCAATTATGTTTTAAGTATTTGCTAAACGCTGTCGT
* * *
18458959 TTTTATTTTGCGTTATTAGTGGCGTTTT-TCGTTAAATGCCGCAATAGGTATG
64 TTTTATATTGCGTT-TTAGTGGCGTTTTCTC-TTAAATGCCGCAAAAGGTAGG
* * * *
18459011 TTTTAGTGGCGTTTTGTCAATAAACGCCGCAAATATGTTTTAAGTGTTTGCTAAACGGTGTCGTA
1 TTTTAGTGGCGTTTT-TCAATAAACGCCGCAATTATGTTTTAAGTATTTGCTAAACGCTGTCGTT
18459076 TTTAT
65 TTTAT
18459081 CTGCCATTTT
Statistics
Matches: 152, Mismatches: 26, Indels: 13
0.80 0.14 0.07
Matches are distributed among these distances:
111 2 0.01
112 3 0.02
113 8 0.05
114 39 0.26
115 14 0.09
116 80 0.53
117 4 0.03
118 2 0.01
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.44
Consensus pattern (114 bp):
TTTTAGTGGCGTTTTTCAATAAACGCCGCAATTATGTTTTAAGTATTTGCTAAACGCTGTCGTTT
TTATATTGCGTTTTAGTGGCGTTTTCTCTTAAATGCCGCAAAAGGTAGG
Found at i:18461433 original size:9 final size:9
Alignment explanation
Indices: 18461388--18461584 Score: 101
Period size: 9 Copynumber: 20.4 Consensus size: 9
18461378 CTTATATATA
*
18461388 AACTTGCAT
1 AACTTACAT
18461397 AACTTACTCAGT
1 AACTTA--CA-T
*
18461409 AACATA-AT
1 AACTTACAT
*
18461417 ATCTTACAT
1 AACTTACAT
18461426 AACTTACAT
1 AACTTACAT
* *
18461435 AAATTAAAT
1 AACTTACAT
18461444 AACTTACAT
1 AACTTACAT
18461453 AACTTACAT
1 AACTTACAT
* *
18461462 AAATTAAAT
1 AACTTACAT
18461471 AACTTACATATT
1 AACTTAC--A-T
*
18461483 AACTTATAT
1 AACTTACAT
* *
18461492 AAGTTATCTAC
1 AACTTA-C-AT
*
18461503 AAGCTTATATAT
1 AA-C-T-TACAT
*
18461515 AAACTTGCAT
1 -AACTTACAT
18461525 AACTTACAT
1 AACTTACAT
*
18461534 AA-TAACAT
1 AACTTACAT
18461542 AATATCTTACAT
1 -A-A-CTTACAT
18461554 AACTTACAT
1 AACTTACAT
*
18461563 AAATTACAT
1 AACTTACAT
* *
18461572 AAATTAAAT
1 AACTTACAT
18461581 AACT
1 AACT
18461585 GGCGTTTTAA
Statistics
Matches: 143, Mismatches: 28, Indels: 34
0.70 0.14 0.17
Matches are distributed among these distances:
8 10 0.07
9 94 0.66
10 6 0.04
11 8 0.06
12 20 0.14
13 3 0.02
14 2 0.01
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:18461451 original size:27 final size:27
Alignment explanation
Indices: 18461414--18461480 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
18461404 TCAGTAACAT
*
18461414 AATATCTTACATAACTTACATAAATTA
1 AATAACTTACATAACTTACATAAATTA
18461441 AATAACTTACATAACTTACATAAATTA
1 AATAACTTACATAACTTACATAAATTA
18461468 AATAACTTACATA
1 AATAACTTACATA
18461481 TTAACTTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (27 bp):
AATAACTTACATAACTTACATAAATTA
Found at i:18461583 original size:128 final size:128
Alignment explanation
Indices: 18461344--18461584 Score: 421
Period size: 128 Copynumber: 1.9 Consensus size: 128
18461334 GGTTTACATT
*
18461344 ACTTACATATTAACTTACATAAGTTATCTACAAGCTTATATATAAACTTGCATAACTTACTCAGT
1 ACTTACATATTAACTTACATAAGTTATCTACAAGCTTATATATAAACTTGCATAACTTACTCAAT
* *
18461409 AACATAATATCTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAAATTAAATA
66 AACATAATATCTTACATAACTTACATAAATTAAATAAATTAAATAACTTACATAAATTAAATA
*
18461472 ACTTACATATTAACTTATATAAGTTATCTACAAGCTTATATATAAACTTGCATAACTTACAT-AA
1 ACTTACATATTAACTTACATAAGTTATCTACAAGCTTATATATAAACTTGCATAACTTAC-TCAA
*
18461536 TAACATAATATCTTACATAACTTACATAAATTACATAAATTAAATAACT
65 TAACATAATATCTTACATAACTTACATAAATTAAATAAATTAAATAACT
18461585 GGCGTTTTAA
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
128 106 0.99
129 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.36
Consensus pattern (128 bp):
ACTTACATATTAACTTACATAAGTTATCTACAAGCTTATATATAAACTTGCATAACTTACTCAAT
AACATAATATCTTACATAACTTACATAAATTAAATAAATTAAATAACTTACATAAATTAAATA
Found at i:18463459 original size:21 final size:21
Alignment explanation
Indices: 18463433--18463482 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
18463423 CTACAACTTA
*
18463433 AAGCAGAGG-TGGCAGCGAGGG
1 AAGCAGAGGCT-GCAGCGAGAG
18463454 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
18463475 AAGCAGAG
1 AAGCAGAG
18463483 CAGAGCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.34, C:0.16, G:0.46, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:18463868 original size:42 final size:41
Alignment explanation
Indices: 18463820--18464017 Score: 199
Period size: 42 Copynumber: 4.8 Consensus size: 41
18463810 TAAAGAATAG
18463820 AAAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAA
1 AAAAAAACGCCGCTAAAGA-AATGTTCTTTAGCGGCGCTTAA
* * * *
18463862 AAAAAAACGCCGCAAAAGAACATGGTCTTTA-----GCATAG
1 AAAAAAACGCCGCTAAAGAA-ATGTTCTTTAGCGGCGCTTAA
* * * * *
18463899 AAAAAAACGCTGCTAAAGACCATGTTCTTTAGAGGCGCTCAG
1 AAAAAAACGCCGCTAAAGA-AATGTTCTTTAGCGGCGCTTAA
* *
18463941 AAAAAAACGTCGCTAAAGACCATGTTCTTTAGCGGCGCTTAA
1 AAAAAAACGCCGCTAAAGA-AATGTTCTTTAGCGGCGCTTAA
* *
18463983 GAAAAAACGCCGCTAAAGAACATGATCTTTAGCGG
1 AAAAAAACGCCGCTAAAGAA-ATGTTCTTTAGCGG
18464018 TGTTTTTCTC
Statistics
Matches: 129, Mismatches: 19, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
37 30 0.23
41 1 0.01
42 98 0.76
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (41 bp):
AAAAAAACGCCGCTAAAGAAATGTTCTTTAGCGGCGCTTAA
Found at i:18463947 original size:79 final size:79
Alignment explanation
Indices: 18463816--18463973 Score: 226
Period size: 79 Copynumber: 2.0 Consensus size: 79
18463806 CCGCTAAAGA
* * *
18463816 ATAGAAAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAAAAAAAAACGCCGCAAAAGA
1 ATAGAAAAAAACGCCGCTAAAGACAATGTTCTTTAGAGGCGCTCAAAAAAAAACGCCGCAAAAGA
18463881 ACATGGTCTTTAGC
66 ACATGGTCTTTAGC
* * * * *
18463895 ATAGAAAAAAACGCTGCTAAAGACCATGTTCTTTAGAGGCGCTCAGAAAAAAACGTCGCTAAAGA
1 ATAGAAAAAAACGCCGCTAAAGACAATGTTCTTTAGAGGCGCTCAAAAAAAAACGCCGCAAAAGA
* *
18463960 CCATGTTCTTTAGC
66 ACATGGTCTTTAGC
18463974 GGCGCTTAAG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.22
Consensus pattern (79 bp):
ATAGAAAAAAACGCCGCTAAAGACAATGTTCTTTAGAGGCGCTCAAAAAAAAACGCCGCAAAAGA
ACATGGTCTTTAGC
Found at i:18464041 original size:42 final size:42
Alignment explanation
Indices: 18463990--18464108 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
18463980 TAAGAAAAAA
* *
18463990 CGCCGCTAAAGAACATGATCTTTAGCGGTGTTTTTCTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCTCTAAG
* * * *
18464032 CGCCTCTAAAGAACATGGTTTTTAACGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCTCTAAG
18464074 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
18464109 GTTTGTGCGC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCTCTAAG
Found at i:18464041 original size:84 final size:84
Alignment explanation
Indices: 18463953--18464108 Score: 188
Period size: 84 Copynumber: 1.9 Consensus size: 84
18463943 AAAAACGTCG
* *
18463953 CTAAAGACCAT-GTTCTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAGAACATGATCTTTAGCG
1 CTAAAGAACATGGTT-TTTAACGGCGCTTAAGAAAAAACGCCGCTAAAGAACATGATCTTTAGCG
*
18464017 GTGTTTTTCTCTAAGCGCCT
65 GCGTTTTTCTCTAAGCGCCT
* ****** * *
18464037 CTAAAGAACATGGTTTTTAACGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGG
1 CTAAAGAACATGGTTTTTAACGGCGCTTAAGAAAAAACGCCGCTAAAGAACATGATCTTTAGCGG
18464102 CGTTTTT
66 CGTTTTT
18464109 GTTTGTGCGC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
84 56 0.95
85 3 0.05
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (84 bp):
CTAAAGAACATGGTTTTTAACGGCGCTTAAGAAAAAACGCCGCTAAAGAACATGATCTTTAGCGG
CGTTTTTCTCTAAGCGCCT
Found at i:18464542 original size:21 final size:19
Alignment explanation
Indices: 18464517--18464557 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
18464507 AAGGTTAATG
18464517 ACCAAATTTAACTAAAAAATA
1 ACCAAA-TTAAC-AAAAAATA
18464538 ACCAAATTAACAAAAAATA
1 ACCAAATTAACAAAAAATA
18464557 A
1 A
18464558 AATCTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 5 0.25
21 6 0.30
ACGTcount: A:0.66, C:0.15, G:0.00, T:0.20
Consensus pattern (19 bp):
ACCAAATTAACAAAAAATA
Found at i:18467269 original size:54 final size:54
Alignment explanation
Indices: 18467197--18467316 Score: 161
Period size: 54 Copynumber: 2.2 Consensus size: 54
18467187 CACATGGCCA
* *
18467197 TGTGACTCAAGTTAGAGAGTTACACGGGCT-GAAACATGACCTAACACATGCCTG
1 TGTGACTCAAGTTAGAGAGTTACACGGGCTAG-AACATGACCTAACACAAGCCCG
* * * *
18467251 TGTGACTCAAGTTAGAGAGTTACATGGTCTAGCACATGGCCTAACACAAGCCCG
1 TGTGACTCAAGTTAGAGAGTTACACGGGCTAGAACATGACCTAACACAAGCCCG
*
18467305 TGCGACTCAAGT
1 TGTGACTCAAGT
18467317 CAAAGAGCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 57 0.98
55 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (54 bp):
TGTGACTCAAGTTAGAGAGTTACACGGGCTAGAACATGACCTAACACAAGCCCG
Found at i:18467334 original size:54 final size:54
Alignment explanation
Indices: 18467200--18467340 Score: 140
Period size: 54 Copynumber: 2.6 Consensus size: 54
18467190 ATGGCCATGT
* * * * * * *
18467200 GACTCAAGTTAGAGAGTTACACGGGCTGAA-ACATGACCTAACACATGCCTGTGT
1 GACTCAAGTCAAAGAGCTACACGGTCT-AACACATGACCTAACACAAGCCCGTGC
* * * * * *
18467254 GACTCAAGTTAGAGAGTTACATGGTCTAGCACATGGCCTAACACAAGCCCGTGC
1 GACTCAAGTCAAAGAGCTACACGGTCTAACACATGACCTAACACAAGCCCGTGC
*
18467308 GACTCAAGTCAAAGAGCTGCACGGTCTAACACA
1 GACTCAAGTCAAAGAGCTACACGGTCTAACACA
18467341 CGCCCATGTG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
53 1 0.01
54 72 0.99
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (54 bp):
GACTCAAGTCAAAGAGCTACACGGTCTAACACATGACCTAACACAAGCCCGTGC
Found at i:18472294 original size:20 final size:21
Alignment explanation
Indices: 18472269--18472308 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
18472259 TTTTATTAGG
18472269 GGCAAAATAC-CAAAAAAAGA
1 GGCAAAATACACAAAAAAAGA
* *
18472289 GGCAAATTACACATAAAAAG
1 GGCAAAATACACAAAAAAAG
18472309 GGGGGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.60, C:0.15, G:0.15, T:0.10
Consensus pattern (21 bp):
GGCAAAATACACAAAAAAAGA
Found at i:18472769 original size:19 final size:19
Alignment explanation
Indices: 18472725--18472769 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
18472715 GGACGAGGTT
*
18472725 TTTAATTTTTTAATATTTTA
1 TTTAA-TTTTTAATAATTTA
*
18472745 -TAAATTTTTAATAATTTA
1 TTTAATTTTTAATAATTTA
18472763 TTTAATT
1 TTTAATT
18472770 AAATTAGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTAATTTTTAATAATTTA
Found at i:18473967 original size:19 final size:21
Alignment explanation
Indices: 18473939--18473988 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
18473929 GGTTTTTTAC
*
18473939 TAAAATAATAC-AAAAGAA-A
1 TAAAAAAATACTAAAAGAATA
*
18473958 TAAAAAAATACTAAAATAATA
1 TAAAAAAATACTAAAAGAATA
18473979 TATAAAAAAT
1 TA-AAAAAAT
18473989 TATTTATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 10 0.38
20 6 0.23
21 3 0.12
22 7 0.27
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAAAAAATACTAAAAGAATA
Found at i:18474077 original size:27 final size:27
Alignment explanation
Indices: 18474039--18474101 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
18474029 GGTAATGGAA
*
18474039 TGGCGGCACCGGTGGTGCC-TTTCTCAT
1 TGGCGGCACCGGTGGTGCCATTCCT-AT
18474066 TGGCGGCACCGGTGGTGCCATTCCTAT
1 TGGCGGCACCGGTGGTGCCATTCCTAT
18474093 TGGCGGCAC
1 TGGCGGCAC
18474102 AGGACTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 30 0.88
28 4 0.12
ACGTcount: A:0.10, C:0.30, G:0.35, T:0.25
Consensus pattern (27 bp):
TGGCGGCACCGGTGGTGCCATTCCTAT
Found at i:18474556 original size:88 final size:86
Alignment explanation
Indices: 18474284--18474556 Score: 190
Period size: 88 Copynumber: 3.1 Consensus size: 86
18474274 AAGTATAAAC
*
18474284 TAATTCGCATTTTATGTATTATTTTGGTAATTTGATAAGAATAGTTTATTAAATAAAAAAATTTA
1 TAATTCGCA-TTTATGTATTATTTTGGTAATTTGATGAGAATAGTTTATTAAATAAAAAAATTTA
* * *
18474349 CTAATTTTGGTGAGAATAGTTTA
65 CTAAATTT-ATAAGAATAGTTTA
*** * * * * * * * **
18474372 TAATTATAATTTATTTTTTCTATTTGAGTTACATTT-ATGGGTGATCAGTTTTATT-ATTACATT
1 TAATTCGCATTTATGTATTAT-TTTG-G-TA-ATTTGATGAG-AAT-AG-TTTATTAAATAAAAA
* **** * ** * *
18474435 TATGGGTTACATTTATAATTATAATTTCC
59 AATTTACTAAATTTATAAGAATAGTTT-A
18474464 TAATTCGCATATTATGTATTATTTTGGTAATTTGATGAGAATAGTTTATTAAATAAAAAAATTTA
1 TAATTCGCAT-TTATGTATTATTTTGGTAATTTGATGAGAATAGTTTATTAAATAAAAAAATTTA
18474529 CTAAATTTAATAAGAATAGTTTA
65 CTAAATTT-ATAAGAATAGTTTA
18474552 TAATT
1 TAATT
18474557 ATAATTTATT
Statistics
Matches: 125, Mismatches: 48, Indels: 24
0.63 0.24 0.12
Matches are distributed among these distances:
87 15 0.12
88 29 0.23
89 17 0.14
90 11 0.09
91 15 0.12
92 24 0.19
93 14 0.11
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (86 bp):
TAATTCGCATTTATGTATTATTTTGGTAATTTGATGAGAATAGTTTATTAAATAAAAAAATTTAC
TAAATTTATAAGAATAGTTTA
Found at i:18475174 original size:27 final size:27
Alignment explanation
Indices: 18475136--18475194 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
18475126 TTTTAGTCCT
* *
18475136 GTGCCACCAATGGGAATGGCACCACCG
1 GTGCCACCAATGAGAAAGGCACCACCG
* *
18475163 GTGCCGCCAATGAGAAAGGCACCACTG
1 GTGCCACCAATGAGAAAGGCACCACCG
18475190 GTGCC
1 GTGCC
18475195 CCCATTCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.32, G:0.31, T:0.12
Consensus pattern (27 bp):
GTGCCACCAATGAGAAAGGCACCACCG
Found at i:18475280 original size:11 final size:11
Alignment explanation
Indices: 18475250--18475301 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
18475240 TGGTAAATAA
18475250 ATTTTTTTGTAT
1 ATTTTTTTG-AT
*
18475262 ATTATTTTGAT
1 ATTTTTTTGAT
*
18475273 ATTTTTTTTAT
1 ATTTTTTTGAT
18475284 ATTTTTTTG-T
1 ATTTTTTTGAT
18475294 ATTATTTT
1 ATT-TTTT
18475302 AGTAAAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 4 0.11
11 23 0.66
12 8 0.23
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (11 bp):
ATTTTTTTGAT
Found at i:18479690 original size:5 final size:5
Alignment explanation
Indices: 18479682--18479730 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
18479672 ATAGAAAAAA
* *
18479682 AAAGC AAAGC AAAGC AAAGC -AAG- AGAAG- AAAAC AAAGC AGAGC AAAGC
1 AAAGC AAAGC AAAGC AAAGC AAAGC A-AAGC AAAGC AAAGC AAAGC AAAGC
18479730 A
1 A
18479731 GAATAGAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
4 5 0.14
5 32 0.86
ACGTcount: A:0.61, C:0.16, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAGC
Found at i:18483129 original size:48 final size:48
Alignment explanation
Indices: 18483075--18483171 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
18483065 AGAAGCAATT
* *
18483075 ATACATAACATATAACACATACAAAGTCATATTAATTTACTCTTTTCA
1 ATACATAACATACAACACATACAAAGTCATATTAACTTACTCTTTTCA
* *
18483123 ATACATAATATACATCACATACAAAGTCATATTAACTTACTCTTTTCA
1 ATACATAACATACAACACATACAAAGTCATATTAACTTACTCTTTTCA
18483171 A
1 A
18483172 ATCCTTCCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (48 bp):
ATACATAACATACAACACATACAAAGTCATATTAACTTACTCTTTTCA
Found at i:18483907 original size:2 final size:2
Alignment explanation
Indices: 18483900--18483943 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
18483890 TCACAACTCT
*
18483900 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
18483942 CA
1 CA
18483944 TAGAACTAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:18498010 original size:50 final size:50
Alignment explanation
Indices: 18497950--18498094 Score: 157
Period size: 50 Copynumber: 2.9 Consensus size: 50
18497940 CATTGAGACT
* ** *
18497950 ATGATAGGTCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCGAG
1 ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCGAG
** * *
18498000 ATGAAAGGTCCCCCGTAAGACCATGTCTAGGACATGACATGGGCACCGAT
1 ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCGAG
* * * * *
18498050 ATGAGAA-TTCCCATGTAAGATCATATCTGGGATATGACATTGGCA
1 ATGA-AAGGTCCCATGTAAGACCATGTCTGGGACATGACATGGGCA
18498095 ATACAAGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
50 76 0.97
51 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (50 bp):
ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCGAG
Found at i:18498958 original size:72 final size:72
Alignment explanation
Indices: 18498880--18499030 Score: 277
Period size: 72 Copynumber: 2.1 Consensus size: 72
18498870 ATCAAGTTAG
* *
18498880 ATTCAAGAAATAGAGGTTGAAGGAGAGGGGAAATCAAGTTAAAGATTGAAATCAATAGAGCAAGG
1 ATTCAAGAAATAGAGGCTGAAGGAGAGGGAAAATCAAGTTAAAGATTGAAATCAATAGAGCAAGG
18498945 TAAGAAC
66 TAAGAAC
18498952 ATTCAAGAAATAGAGGCTGAAGGAGAGGGAAAATCAAGTTAAAGATTGAAATCAATAGAGCAAGG
1 ATTCAAGAAATAGAGGCTGAAGGAGAGGGAAAATCAAGTTAAAGATTGAAATCAATAGAGCAAGG
18499017 TAAGAAC
66 TAAGAAC
18499024 A-TCAAGA
1 ATTCAAGA
18499031 TTTCAATATA
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 6 0.08
72 71 0.92
ACGTcount: A:0.48, C:0.08, G:0.26, T:0.17
Consensus pattern (72 bp):
ATTCAAGAAATAGAGGCTGAAGGAGAGGGAAAATCAAGTTAAAGATTGAAATCAATAGAGCAAGG
TAAGAAC
Found at i:18499243 original size:19 final size:19
Alignment explanation
Indices: 18499219--18499256 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18499209 TTAAATATTA
18499219 AAATACTATAGAGAAAGGG
1 AAATACTATAGAGAAAGGG
18499238 AAATACTATAGAGAAAGGG
1 AAATACTATAGAGAAAGGG
18499257 TTTTAGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.26, T:0.16
Consensus pattern (19 bp):
AAATACTATAGAGAAAGGG
Found at i:18500559 original size:57 final size:57
Alignment explanation
Indices: 18500453--18500561 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
18500443 GATCCTATCC
* **
18500453 TGATATAGCCCTCCCGAAGAATATGTGTGTAAAAGATCTAGTGCAGACGGGTGATCT
1 TGATATAGCCCTCCCGAAGAATATGTGAGTAAAAGATCTAGCCCAGACGGGTGATCT
* *
18500510 TGATATAGCCCTCCCGAAGAATATGT-AG-AAAATGGATTTAGCCCGGACGGGT
1 TGATATAGCCCTCCCGAAGAATATGTGAGTAAAA--GATCTAGCCCAGACGGGT
18500562 AATCCAAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
55 4 0.09
56 1 0.02
57 40 0.89
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (57 bp):
TGATATAGCCCTCCCGAAGAATATGTGAGTAAAAGATCTAGCCCAGACGGGTGATCT
Found at i:18505905 original size:26 final size:27
Alignment explanation
Indices: 18505871--18505922 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
18505861 TTTAGCAATC
18505871 AAATAATAA-AATAAACAAC-AATATAG
1 AAATAATAATAAT-AACAACGAATATAG
18505897 AAATAATAATAATAACAACGAATATA
1 AAATAATAATAATAACAACGAATATA
18505923 AAACAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (27 bp):
AAATAATAATAATAACAACGAATATAG
Found at i:18505936 original size:26 final size:26
Alignment explanation
Indices: 18505878--18505936 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
18505868 ATCAAATAAT
* *
18505878 AAAATAAACAACAATATAGAAATAATA
1 AAAAT-AACAACAATATAGAAACAACA
*
18505905 ATAATAACAACGAATATA-AAACAACA
1 AAAATAACAAC-AATATAGAAACAACA
18505931 AAAATA
1 AAAATA
18505937 TCAATTTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.17
Consensus pattern (26 bp):
AAAATAACAACAATATAGAAACAACA
Found at i:18506096 original size:18 final size:16
Alignment explanation
Indices: 18506050--18506118 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 16
18506040 GAAATGCAGG
* *
18506050 ATACAATAAAAAAATAA
1 ATACAATAATATAAT-A
*
18506067 ATACATTAATATAATA
1 ATACAATAATATAATA
18506083 ATACCTAATAATATACA-A
1 ATA-C-AATAATATA-ATA
18506101 ATACAAT-ATATAATA
1 ATACAATAATATAATA
18506116 ATA
1 ATA
18506119 TATAAATGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 1 0.02
15 9 0.20
16 7 0.16
17 14 0.32
18 12 0.27
19 1 0.02
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
ATACAATAATATAATA
Found at i:18506108 original size:23 final size:23
Alignment explanation
Indices: 18506082--18506125 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
18506072 TTAATATAAT
*
18506082 AATACCTAATAATATACAAATAC
1 AATACATAATAATATACAAATAC
* *
18506105 AATATATAATAATATATAAAT
1 AATACATAATAATATACAAAT
18506126 GAAATAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (23 bp):
AATACATAATAATATACAAATAC
Found at i:18507546 original size:45 final size:44
Alignment explanation
Indices: 18507489--18507639 Score: 137
Period size: 45 Copynumber: 3.4 Consensus size: 44
18507479 TTCAATCTAT
*
18507489 TCCACTGTAACTTCATGGAAATAAGATTTGCTATCTTCAGTCTGC
1 TCCACTGCAACTTCA-GGAAATAAGATTTGCTATCTTCAGTCTGC
* * *
18507534 TCCACTGCAACTTCAAGGAAATGAGATTCT-CTATCCTT-AGTTTAC
1 TCCACTGCAACTTC-AGGAAATAAGATT-TGCTAT-CTTCAGTCTGC
* * * * *
18507579 TCCACTGCAACTTCAGTGAGATATGACTTG-TAGCTTCAATCTGC
1 TCCACTGCAACTTCAG-GAAATAAGATTTGCTATCTTCAGTCTGC
* *
18507623 CCCACTACAACTTCAGG
1 TCCACTGCAACTTCAGG
18507640 GGGATAAGAT
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
43 4 0.05
44 23 0.27
45 54 0.63
46 5 0.06
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGAAATAAGATTTGCTATCTTCAGTCTGC
Found at i:18507949 original size:143 final size:143
Alignment explanation
Indices: 18507716--18508027 Score: 405
Period size: 143 Copynumber: 2.2 Consensus size: 143
18507706 GTTTTAATTC
* * * *
18507716 GCTCCACTACAACTTCAAGGAGAT-AGGATTGGTGGCTTCAATCTGCTTCATACAAATTCAGAAA
1 GCTCCACTGCAACTTCAGGGAGATAAGGATTGGTGGCTTCAATATGCTCCATACAAATTCAGAAA
* * **
18507780 GATAAGATCCTCCATAATTTGTAGCTTTAATCTATTCCACTGTAACGTTAGAGAAATAAGATTCG
66 GATAAGATCCTACATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGAGAAATAAGATTCG
* * *
18507845 TTGTCTTTAGTCT
131 CTATCTTCAGTCT
* * ** *
18507858 GCTCCGCTGCAACTTTAGGGAGATAAGG-TTGGTGGCTTCAATATGCTCCACTGTAACTTCAGAA
1 GCTCCACTGCAACTTCAGGGAGATAAGGATTGGTGGCTTCAATATGCTCCA-TACAAATTCAGAA
* * *
18507922 AGATAAGAT-CTGACATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAGTAAGATT
65 AGATAAGATCCT-ACATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGAGAAATAAGATT
18507986 CGCTATCTTCAGTCT
129 CGCTATCTTCAGTCT
*
18508001 GCTCCACTGGAACTTCAGGGAGATAAG
1 GCTCCACTGCAACTTCAGGGAGATAAG
18508028 ACTTGTAACT
Statistics
Matches: 145, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
142 42 0.29
143 103 0.71
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (143 bp):
GCTCCACTGCAACTTCAGGGAGATAAGGATTGGTGGCTTCAATATGCTCCATACAAATTCAGAAA
GATAAGATCCTACATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGAGAAATAAGATTCG
CTATCTTCAGTCT
Found at i:18508028 original size:45 final size:44
Alignment explanation
Indices: 18507951--18508080 Score: 129
Period size: 44 Copynumber: 2.9 Consensus size: 44
18507941 TTGTAGCTTT
* **
18507951 AATCTGTTCCACTGCAACGCCAGGGA-AGTAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGA-TAAGATT-GCTATCTTC
* * *
18507996 AGTCTGCTCCACTGGAACTTCAGGGAGATAAGACTTG-TAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCTATCTTC
* * *
18508040 AACCTGCTCCATTGCAACTTCAGGGAGATAAGGTTTGCTAT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAA-GATTGCTAT
18508081 GATCTATTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
44 36 0.52
45 30 0.43
46 3 0.04
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGCTATCTTC
Found at i:18508040 original size:143 final size:143
Alignment explanation
Indices: 18507716--18508071 Score: 378
Period size: 143 Copynumber: 2.5 Consensus size: 143
18507706 GTTTTAATTC
* * * * ** * * *
18507716 GCTCCACTACAACTTCAAGGAGATAGGATTGGTGGCTTCAATC-TGCTTCA-TACAAATTCAGAA
1 GCTCCACTGCAACTTCAGGGAGATAAGCTTGGTAACTTCAA-CATGCTCCACTGCAACTTCAGAA
* * **
18507779 AGATAAGATCCTCCATAATTTGTAGCTTTAATCTATTCCACTGTAACGTTAGAGAAATAAGATTC
65 AGATAAGATCCTACATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGAGAAATAAGATTC
* * *
18507844 GTTGTCTTTAGTCT
130 GCTATCTTCAGTCT
* * * ** * *
18507858 GCTCCGCTGCAACTTTAGGGAGATAAGGTTGGTGGCTTCAATATGCTCCACTGTAACTTCAGAAA
1 GCTCCACTGCAACTTCAGGGAGATAAGCTTGGTAACTTCAACATGCTCCACTGCAACTTCAGAAA
* * *
18507923 GATAAGAT-CTGACATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAGTAAGATTC
66 GATAAGATCCT-ACATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGAGAAATAAGATTC
18507987 GCTATCTTCAGTCT
130 GCTATCTTCAGTCT
* * * **
18508001 GCTCCACTGGAACTTCAGGGAGATAAGACTT-GTAACTTCAACCTGCTCCATTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGGGAGATAAG-CTTGGTAACTTCAACATGCTCCACTGCAACTTCAGAA
18508065 AGATAAG
65 AGATAAG
18508072 GTTTGCTATG
Statistics
Matches: 177, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
142 43 0.24
143 132 0.75
144 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (143 bp):
GCTCCACTGCAACTTCAGGGAGATAAGCTTGGTAACTTCAACATGCTCCACTGCAACTTCAGAAA
GATAAGATCCTACATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAGAGAAATAAGATTCG
CTATCTTCAGTCT
Found at i:18516828 original size:19 final size:20
Alignment explanation
Indices: 18516804--18516850 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
18516794 TGGTGGACTT
* *
18516804 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
18516823 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
18516843 -AATGCAAA
1 TAATGCAAA
18516851 AAGGCGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:18522235 original size:240 final size:240
Alignment explanation
Indices: 18521812--18522296 Score: 853
Period size: 240 Copynumber: 2.0 Consensus size: 240
18521802 TGTGATGGAA
*
18521812 AAAAGAGACAGGACAAATGAAAGACAATCAACTAAGTCTGGTACTGGTTCACTGATTAAAATTAA
1 AAAAGAGACAGAACAAATGAAAGACAATCAACTAAGTCTGGTACTGGTTCACTGATTAAAATTAA
* * *
18521877 TGAGAGATCAACGGCCGTTGGCCAGTAGGCCGACCGGGAACAATGAAAATTTTAAGTTCGAACAT
66 TGAGAGATCAACGGCCGCTGGCCAGTAGGCCGACCGGGAACAATAAAAATTTTAAATTCGAACAT
* *
18521942 TCATAAATCGGGGCATCCACGAGTGATTAATCGCCTCAGGAATAAGGTGAGGCATGTACAACCCT
131 TCATAAATCGGGGCATCCACGAGCGATTAATCGCCTCAGGAATAAAGTGAGGCATGTACAACCCT
* *
18522007 AGATTTTGTTTCTAATAGTAATAAAATTGAGTGAAAAGAGAATGG
196 AGATTTTGATTCTAATAGAAATAAAATTGAGTGAAAAGAGAATGG
18522052 AAAAGAGACAGAACAAATGAAAGACAATCAACTAAGTCTGGTACTGGTTCACTGATTAAAATTAA
1 AAAAGAGACAGAACAAATGAAAGACAATCAACTAAGTCTGGTACTGGTTCACTGATTAAAATTAA
* * *
18522117 TGAGAGATCAACGGCTGCTGGCGAGTAGGCTGACCGGGAACAATAAAAATTTTAAATTCGAACAT
66 TGAGAGATCAACGGCCGCTGGCCAGTAGGCCGACCGGGAACAATAAAAATTTTAAATTCGAACAT
*
18522182 TCATAAATTGGGGCATCCACGAGCGATTAATCGCCTCAGGAATAAAGTGAGGCATGTACAACCCT
131 TCATAAATCGGGGCATCCACGAGCGATTAATCGCCTCAGGAATAAAGTGAGGCATGTACAACCCT
*
18522247 TGATTTTGATTCTAATAGAAATAAAATTGAGTGAAAAGAGAATGG
196 AGATTTTGATTCTAATAGAAATAAAATTGAGTGAAAAGAGAATGG
18522292 AAAAG
1 AAAAG
18522297 GTTCAACTGA
Statistics
Matches: 232, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
240 232 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (240 bp):
AAAAGAGACAGAACAAATGAAAGACAATCAACTAAGTCTGGTACTGGTTCACTGATTAAAATTAA
TGAGAGATCAACGGCCGCTGGCCAGTAGGCCGACCGGGAACAATAAAAATTTTAAATTCGAACAT
TCATAAATCGGGGCATCCACGAGCGATTAATCGCCTCAGGAATAAAGTGAGGCATGTACAACCCT
AGATTTTGATTCTAATAGAAATAAAATTGAGTGAAAAGAGAATGG
Found at i:18525294 original size:9 final size:9
Alignment explanation
Indices: 18525276--18525328 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
18525266 TACAAAATTT
*
18525276 GAAATTAAA
1 GAAATAAAA
18525285 GAAATAAAA
1 GAAATAAAA
*
18525294 GAAAGGGTTCAAA
1 GAAA----TAAAA
18525307 GAAATAAAA
1 GAAATAAAA
18525316 GAAATAAAA
1 GAAATAAAA
18525325 GAAA
1 GAAA
18525329 GGGCTCAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 29 0.78
13 8 0.22
ACGTcount: A:0.68, C:0.02, G:0.17, T:0.13
Consensus pattern (9 bp):
GAAATAAAA
Found at i:18525311 original size:31 final size:31
Alignment explanation
Indices: 18525276--18525338 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
18525266 TACAAAATTT
* *
18525276 GAAATTAAAGAAATAAAAGAAAGGGTTCAAA
1 GAAATAAAAGAAATAAAAGAAAGGGCTCAAA
18525307 GAAATAAAAGAAATAAAAGAAAGGGCTCAAA
1 GAAATAAAAGAAATAAAAGAAAGGGCTCAAA
18525338 G
1 G
18525339 GTTTGAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.62, C:0.05, G:0.21, T:0.13
Consensus pattern (31 bp):
GAAATAAAAGAAATAAAAGAAAGGGCTCAAA
Found at i:18526116 original size:21 final size:20
Alignment explanation
Indices: 18526090--18526130 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18526080 AATTATTTCT
*
18526090 GAAAAATGACTTACTTTTTTA
1 GAAAAATGA-ATACTTTTTTA
*
18526111 GAAAAATTAATACTTTTTTA
1 GAAAAATGAATACTTTTTTA
18526131 TGTTTGGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (20 bp):
GAAAAATGAATACTTTTTTA
Found at i:18526930 original size:17 final size:15
Alignment explanation
Indices: 18526895--18526925 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18526885 TTTATACTAC
*
18526895 AATATATTTATTATT
1 AATATATTTATAATT
18526910 AATATATTTATAATT
1 AATATATTTATAATT
18526925 A
1 A
18526926 TAATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATATTTATAATT
Found at i:18528080 original size:5 final size:5
Alignment explanation
Indices: 18528041--18528068 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
18528031 TTTTTGTGGG
18528041 TAATT TAATT TAATT TAATT TAATT TAA
1 TAATT TAATT TAATT TAATT TAATT TAA
18528069 ATATATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TAATT
Found at i:18535534 original size:21 final size:20
Alignment explanation
Indices: 18535509--18535547 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18535499 AGATTTCATC
18535509 AATTTAACTTTTATTTTTAAG
1 AATTTAA-TTTTATTTTTAAG
*
18535530 AATTTAATTTTTTTTTTA
1 AATTTAATTTTATTTTTA
18535548 CTTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
AATTTAATTTTATTTTTAAG
Found at i:18537701 original size:125 final size:125
Alignment explanation
Indices: 18537395--18537836 Score: 672
Period size: 125 Copynumber: 3.5 Consensus size: 125
18537385 GATAAAATCA
*
18537395 AAGCAGGATGCTTTATCAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
18537460 AGGTACTGAAAAAATAATTTTGAGTTGACGTTTATGAGAAAATAGTATAAAAAAACACTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAAACGCTTC
* * ** * *
18537521 AAGCAGGATGCTTTATTAGAAGAATTTCTGAAATCGCGCCCATGTGGTTGTGCTTTTACTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
*
18537586 TGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
*
18537646 AAGCAGGATGCTTTATCAGAAGAATTTCT-AAAGTCGCGCCCACGTGGACGCGCTTTTGCTAGAG
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAA-TCGCGCCCACGTGGACGCGCTTTTGCTACAG
18537710 TAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTA-AAAAAACGCTTC
65 TAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * ** * *
18537770 AAGCAGAATGCTTTATCAGAATAATTTAGGAAATCGCGCCCTCGTGGACGCACTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
18537835 AG
66 AG
18537837 CATGTTTGGG
Statistics
Matches: 286, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
124 71 0.25
125 114 0.40
126 101 0.35
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:18542668 original size:15 final size:15
Alignment explanation
Indices: 18542648--18542676 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18542638 AGGTTTTGGT
18542648 GTTTTTAAGTTAAGA
1 GTTTTTAAGTTAAGA
18542663 GTTTTTAAGTTAAG
1 GTTTTTAAGTTAAG
18542677 GGTTACGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (15 bp):
GTTTTTAAGTTAAGA
Found at i:18542702 original size:27 final size:28
Alignment explanation
Indices: 18542656--18542708 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
18542646 GTGTTTTTAA
*
18542656 GTTAAGAGTTTTTAAGTTAAGGGTTACG
1 GTTAAGAGGTTTTAAGTTAAGGGTTACG
18542684 GTTAAG-GGTTTTAAGTTAAGGGTTA
1 GTTAAGAGGTTTTAAGTTAAGGGTTA
18542709 TGATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.28, C:0.02, G:0.30, T:0.40
Consensus pattern (28 bp):
GTTAAGAGGTTTTAAGTTAAGGGTTACG
Found at i:18542708 original size:21 final size:21
Alignment explanation
Indices: 18542683--18542882 Score: 291
Period size: 21 Copynumber: 9.5 Consensus size: 21
18542673 TAAGGGTTAC
18542683 GGTTAAGGG-TTTTAAGTTAAG
1 GGTT-AGGGTTTTTAAGTTAAG
* *
18542704 GGTTATGATTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
*
18542725 GATTAAGGG-TTTTAAGTTAAG
1 GGTT-AGGGTTTTTAAGTTAAG
18542746 GGTTAGTGG-TTTTAAGTTAAG
1 GGTTAG-GGTTTTTAAGTTAAG
18542767 GGTTAGGGTTTTTTAA-TTAAG
1 GGTTAGGG-TTTTTAAGTTAAG
18542788 GGTTAGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
18542809 GGTTTAGGGTTTTTAAGTTAAG
1 GG-TTAGGGTTTTTAAGTTAAG
*
18542831 TGTTAGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
18542852 GGTTAGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
18542873 GGTTAGGGTT
1 GGTTAGGGTT
18542883 AGGGTTTTTG
Statistics
Matches: 164, Mismatches: 8, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.08
21 123 0.75
22 28 0.17
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (21 bp):
GGTTAGGGTTTTTAAGTTAAG
Found at i:18542781 original size:85 final size:86
Alignment explanation
Indices: 18542657--18542880 Score: 200
Period size: 85 Copynumber: 2.6 Consensus size: 86
18542647 TGTTTTTAAG
* * *
18542657 TTAAGAGTTTTTAAGTTAAGGGTTACGGTTAAGGGTTTTAAGTTAAGGGTTA-TGATTTTTAAGT
1 TTAAGGGTTTTTAAGTTAAGGGTTA--G-T---GGTTTTAAGTTAAGGGTTAGGGGTTTTTAAGT
* *
18542721 TAAGGATTAAGGGTTTTAAGTTAAGG-G
60 TAAGGGTT-AGGGTTTTAAGTTAAGGAT
18542748 TT-AGTGG-TTTTAAGTTAAGGGTTAG-GGTTTTTTAA-TTAAGGGTTA-GGGTTTTTAAGTTAA
1 TTAAG-GGTTTTTAAGTTAAGGGTTAGTGG--TTTTAAGTTAAGGGTTAGGGGTTTTTAAGTTAA
18542808 GGGTTTAGGGTTTTTAAGTTAA-G-T
63 GGG-TTAGGG-TTTTAAGTTAAGGAT
18542832 GTT-AGGGTTTTTAAGTTAAGGGTTAG-GGTTTTTAAGTTAAGGGTTAGGG
1 -TTAAGGGTTTTTAAGTTAAGGGTTAGTGG-TTTTAAGTTAAGGGTTAGGG
18542881 TTAGGGTTTT
Statistics
Matches: 119, Mismatches: 5, Indels: 23
0.81 0.03 0.16
Matches are distributed among these distances:
83 2 0.02
84 39 0.33
85 53 0.45
86 2 0.02
88 1 0.01
90 19 0.16
91 3 0.03
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (86 bp):
TTAAGGGTTTTTAAGTTAAGGGTTAGTGGTTTTAAGTTAAGGGTTAGGGGTTTTTAAGTTAAGGG
TTAGGGTTTTAAGTTAAGGAT
Found at i:18545342 original size:23 final size:22
Alignment explanation
Indices: 18545300--18545345 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
18545290 AATAATTAAA
*
18545300 AATAGGAATTTAAGAGAAATTT
1 AATAGGAAATTAAGAGAAATTT
* *
18545322 AATAGGAAATTGAGAGAAAATT
1 AATAGGAAATTAAGAGAAATTT
18545344 AA
1 AA
18545346 AATTAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (22 bp):
AATAGGAAATTAAGAGAAATTT
Found at i:18545370 original size:51 final size:53
Alignment explanation
Indices: 18545293--18545394 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 53
18545283 TTTTAAAAAT
18545293 AATTAAAAATAGGAATTTAAGAGAAATTT-AATAGGAAATTGAGAGAAAATTAA
1 AATTAAAAATAGGAATTTAAGAGAAATTTGAA-AGGAAATTGAGAGAAAATTAA
* * * *
18545346 AATTAAATAT-GG-ATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAAATT
1 AATTAAAAATAGGAATTTAAGAGAAATTTGAAAGGAAATTGAGAGAAAATT
18545395 GAGAGGAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
51 32 0.73
52 3 0.07
53 9 0.20
ACGTcount: A:0.51, C:0.01, G:0.21, T:0.27
Consensus pattern (53 bp):
AATTAAAAATAGGAATTTAAGAGAAATTTGAAAGGAAATTGAGAGAAAATTAA
Found at i:18546612 original size:10 final size:10
Alignment explanation
Indices: 18546597--18546621 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18546587 GAGTTCATCG
18546597 TTTTTTTTAT
1 TTTTTTTTAT
18546607 TTTTTTTTAT
1 TTTTTTTTAT
18546617 TTTTT
1 TTTTT
18546622 ATATTCTTAT
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:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:18547376 original size:25 final size:27
Alignment explanation
Indices: 18547345--18547396 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
18547335 TTTTTCGTGT
**
18547345 ATTATTTTTAATTATT-TATA-CATTA
1 ATTATTTAAAATTATTATATATCATTA
18547370 ATTATTTAAAATTATTATATATCATTA
1 ATTATTTAAAATTATTATATATCATTA
18547397 TCTTTATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 4 0.17
27 5 0.22
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTATTTAAAATTATTATATATCATTA
Found at i:18555627 original size:25 final size:24
Alignment explanation
Indices: 18555599--18555655 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
18555589 CTCACGCACA
*
18555599 TTTCTTTTTCCTCTTCTT-CTTGTC
1 TTTCTTTTACCTCTTCTTCCTT-TC
* *
18555623 TTTTCCTTTACCTCTTTTTCCTTTC
1 -TTTCTTTTACCTCTTCTTCCTTTC
18555648 TTTCTTTT
1 TTTCTTTT
18555656 CAGTTTGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 7 0.26
25 17 0.63
26 3 0.11
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTCTTTTACCTCTTCTTCCTTTC
Found at i:18564347 original size:51 final size:51
Alignment explanation
Indices: 18564286--18564392 Score: 142
Period size: 51 Copynumber: 2.1 Consensus size: 51
18564276 TTCTTTTTAT
* * **
18564286 ATATTGATATATTAGCTCTTCTGGAGCTTTCAACTAATTTTGTGTTACCAA
1 ATATTAATATATTAGCTCTTCTAGAGCTTTCAACTAATTTTGTACTACCAA
** * *
18564337 ATATTAATATATTATTTCTTTTAGAGCTTTCGACTAATTTTGTACTACCAA
1 ATATTAATATATTAGCTCTTCTAGAGCTTTCAACTAATTTTGTACTACCAA
18564388 ATATT
1 ATATT
18564393 GTTATAATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (51 bp):
ATATTAATATATTAGCTCTTCTAGAGCTTTCAACTAATTTTGTACTACCAA
Found at i:18574322 original size:17 final size:18
Alignment explanation
Indices: 18574300--18574337 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
18574290 TTAATGAACG
*
18574300 ACAAATAATCAATA-AAT
1 ACAAATAAGCAATATAAT
18574317 ACAAATAAGCAATATAAT
1 ACAAATAAGCAATATAAT
18574335 ACA
1 ACA
18574338 CGTGAGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.21
Consensus pattern (18 bp):
ACAAATAAGCAATATAAT
Found at i:18574930 original size:26 final size:26
Alignment explanation
Indices: 18574859--18574946 Score: 95
Period size: 26 Copynumber: 3.3 Consensus size: 26
18574849 TAGAATAATT
* * *
18574859 TTAAAATAATTAATATATAAAACAAC
1 TTAAAATAAATAATATACAAAACAAG
* ** *
18574885 TAAAAATAAAATAATATACAAAGTAAT
1 TTAAAAT-AAATAATATACAAAACAAG
*
18574912 TTAAAATAAATAATTTACAAAACAAG
1 TTAAAATAAATAATATACAAAACAAG
18574938 TTAAAATAA
1 TTAAAATAA
18574947 CACATAATGA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
26 30 0.60
27 20 0.40
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (26 bp):
TTAAAATAAATAATATACAAAACAAG
Found at i:18579955 original size:132 final size:132
Alignment explanation
Indices: 18579789--18580678 Score: 1317
Period size: 132 Copynumber: 6.8 Consensus size: 132
18579779 TCTTGTGGTT
* ** *
18579789 TTCAATCTACTCCACTGCTGTTCAGGG-AGATAGAATTATTGGCTTCAATGTACTCCACTGTAAC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAAC
* * * *
18579853 CACAGGGAGGTAAAAT-TCACCATCTTTGATCTGCTCCATTACTGTTTAGGGAGACAAGATATGA
65 CACAGGGAGGTAAAATCT-GCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
18579917 AATC
129 AATC
* *
18579921 TTCAATCTATTCCACTGCTGCCCAGGAAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
* * *
18579986 TCAGGGAGGTAAAATCTGCCATTTTTGATCTGCCCCACTACTGCTTAGGGAGAC--GATCTGAAA
66 ACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
18580049 TC
131 TC
* * *
18580051 TTCAATCTATTCCGCTGCTGCCGAGGGAAGTAGAATTACTGGCTTCAATGTACTCCGCTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
* * *
18580116 ATAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGTAA
66 ACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
18580181 TC
131 TC
18580183 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
* * * *
18580248 ACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAA
66 ACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
18580313 TC
131 TC
* *
18580315 TTCAATCTATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
* * * * * *
18580380 AC-GAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCGCTGTATATGC--AGGAAGGCAAGATCT
66 ACAG-GGAGGTAAAATCTGCCATCTTTGATCTGCTCCAC--TA-CTGCTTAGGGAGACAAGATCT
* *
18580442 AAAACC
127 GAAATC
18580448 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
* * *
18580513 ACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
66 ACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
18580578 TC
131 TC
* *
18580580 TTCAATCTATTCCACTGCTGTCCAAGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
* *
18580645 ACAAGGAGGTAAAATCTGCCATCTTCGATCTGCT
66 ACAGGGAGGTAAAATCTGCCATCTTTGATCTGCT
18580679 TCGCTATCTA
Statistics
Matches: 679, Mismatches: 68, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
130 122 0.18
131 3 0.00
132 436 0.64
133 112 0.16
134 3 0.00
135 3 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
ACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
TC
Found at i:18580114 original size:262 final size:263
Alignment explanation
Indices: 18579789--18580678 Score: 1369
Period size: 265 Copynumber: 3.4 Consensus size: 263
18579779 TCTTGTGGTT
* * *
18579789 TTCAATCTACTCCACTGCTGTTCAGGG-AGATAGAATTATTGGCTTCAATGTACTCCACTGTAAC
1 TTCAATCTATTCCACTGCTGTCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAAC
* * *
18579853 CACAGGGAGGTAAAAT-TCACCATCTTTGATCTGCTCCATTACTGTTTAGGGAGACAAGATATGA
65 CACAGGGAGGTAAAATCT-GCCATCTTCGATCTGCTCCATTACTGTTTAGGGAGACAAGATCTGA
* *
18579917 AATCTTCAATCTATTCCACTGCTGCCCAGGAAAGTAGAATTACTGGCTTCAATGTACTCCACTGC
129 AATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* * * *
18579982 AACCTCAGGGAGGTAAAATCTGCCATTTTTGATCTGCCCCACTACTGCTTAGGGAGAC-GATCTG
194 AACCACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAGACAGATCTG
18580046 AAATC
259 AAATC
* *
18580051 TTCAATCTATTCCGCTGCTG-CCGAGGGAAGTAGAATTACTGGCTTCAATGTACTCCGCTGTAAC
1 TTCAATCTATTCCACTGCTGTCC-AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAAC
* * * * * *
18580115 CATAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGTA
65 CACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCATTACTGTTTAGGGAGACAAGATCTGAA
18580180 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
130 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
*
18580245 ACCACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAGACAAGGTCTG
195 ACCACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAGAC-AGATCTG
18580310 AAATC
259 AAATC
*
18580315 TTCAATCTATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTGTAACC
1 TTCAATCTATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
* * * ** * * *
18580380 AC-GAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCGCTGTA-TATGCAGGAAGGCAAGATCTA
66 ACAG-GGAGGTAAAATCTGCCATCTTCGATCTGCTCC-AT-TACTGTTTAGGGAGACAAGATCTG
*
18580443 AAACCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTG
128 AAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTG
18580508 TAACCACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAGACAAGATC
193 TAACCACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAGAC-AGATC
18580573 TGAAATC
257 TGAAATC
*
18580580 TTCAATCTATTCCACTGCTGTCCAAGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
1 TTCAATCTATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
*
18580645 ACAAGGAGGTAAAATCTGCCATCTTCGATCTGCT
66 ACAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
18580679 TCGCTATCTA
Statistics
Matches: 576, Mismatches: 42, Indels: 17
0.91 0.07 0.03
Matches are distributed among these distances:
261 1 0.00
262 226 0.39
263 4 0.01
264 99 0.17
265 244 0.42
266 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (263 bp):
TTCAATCTATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
ACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCATTACTGTTTAGGGAGACAAGATCTGAAA
TCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
CCACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAGACAGATCTGAA
ATC
Found at i:18581962 original size:7 final size:7
Alignment explanation
Indices: 18581946--18581986 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
18581936 AGCCTCTCCA
*
18581946 TTTTCTT
1 TTTTCAT
18581953 TTTTCAT
1 TTTTCAT
18581960 TTTTCA-
1 TTTTCAT
18581966 TTTTCAT
1 TTTTCAT
18581973 CTTTTCAT
1 -TTTTCAT
18581981 TTTTCA
1 TTTTCA
18581987 CATCACTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
8 7 0.23
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:18581979 original size:21 final size:20
Alignment explanation
Indices: 18581944--18581986 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
18581934 TTAGCCTCTC
*
18581944 CATTTTCTTTTTTCATTTTT
1 CATTTTCTCTTTTCATTTTT
18581964 CATTTTCATCTTTTCATTTTT
1 CATTTTC-TCTTTTCATTTTT
18581985 CA
1 CA
18581987 CATCACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (20 bp):
CATTTTCTCTTTTCATTTTT
Found at i:18581998 original size:21 final size:22
Alignment explanation
Indices: 18581950--18581998 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
18581940 TCTCCATTTT
**
18581950 CTTTTTTCATTTTTCATTTTCA
1 CTTTTTTCATTTTTCATCATCA
*
18581972 -TCTTTTCATTTTTCA-CATCA
1 CTTTTTTCATTTTTCATCATCA
18581992 CTTTTTT
1 CTTTTTT
18581999 TTTTACTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.65
Consensus pattern (22 bp):
CTTTTTTCATTTTTCATCATCA
Found at i:18589561 original size:4 final size:4
Alignment explanation
Indices: 18589554--18589587 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
18589544 CCACTGGGAG
18589554 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
18589588 GTGTGTGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:18592630 original size:40 final size:40
Alignment explanation
Indices: 18592543--18592632 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 40
18592533 GGGATGTGTC
* * *
18592543 AGCAAATCGCGTCCACGTCAGTGCGATTACTTACGTGGCA
1 AGCAAATCGCGTCCACGTAAGCGCGATTACTGACGTGGCA
* *
18592583 A-CAAATCGCGTCCATGTAAGCGCGATTTGCTGACGTGG-A
1 AGCAAATCGCGTCCACGTAAGCGCGA-TTACTGACGTGGCA
18592622 AGCAAATCGCG
1 AGCAAATCGCG
18592633 CTTACGTGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
39 23 0.53
40 20 0.47
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.21
Consensus pattern (40 bp):
AGCAAATCGCGTCCACGTAAGCGCGATTACTGACGTGGCA
Found at i:18593908 original size:322 final size:311
Alignment explanation
Indices: 18593320--18593949 Score: 826
Period size: 322 Copynumber: 2.0 Consensus size: 311
18593310 AATACATATT
*
18593320 GGGGCAAAATACCAAAAAAAGCCCTATTTTTTAAAAATTTATCGAAATGGGCCCGGTATTTTATT
1 GGGGCAAAATACCAAAAAAAGCCCTATTTTTTAAAAATTTACCGAAATGGGCCCGGTATTTTATT
* * *
18593385 ATTTACCGGAATGAGCCATTTTCCCTGAAATCACGTCCACTTCAGCGCGATGTGTCAGCAAATCG
66 ATTTACCGAAATGAGCCATTTTCCCTGAAATCACGACCACGTCAGCGCGATGTGTCAGCAAATCG
* *
18593450 CGTCATCGTAGGCGCGATTTGTGTCCACGTAAGCAAAGCGTTCTGACGTGGACACGATTTGCTGA
131 CGTCATCGTAGGCGCGATTTGTGT-CACGTAAGCAAAGCGTCCTGACGAGGACACGATTTGCTGA
*
18593515 CACGTCCCCTGACATCGCGCTGACGTGGACACAATTTCGGGGAAAATGGTCCATTCCGGTAAATA
195 CACGTCCCCTGACATCGCGCTGACGTGGACACAATTTCGGGGAAAATGGCCCATTCCGGTAAATA
*
18593580 ATAAAATACCGGGCCCATTTCGGTAAATTTTAAAAAAATAGGACTTTTTTTG
260 ATAAAATACCGAGCCCATTTCGGTAAATTTTAAAAAAATAGGACTTTTTTTG
18593632 GGGGCAAAATACC-AAAAAAGCCCTATTTTTTTAAAAATTTACCGAAATGGGCCCGGTATTTTAT
1 GGGGCAAAATACCAAAAAAAGCCCTA-TTTTTTAAAAATTTACCGAAATGGGCCCGGTATTTTAT
* * *
18593696 TATTTACCGAAATGGGTCATTTTCCCTGAAATCGCGACCACGTCAGCGCGATGTCAGGGAACGTG
65 TATTTACCGAAATGAGCCATTTTCCCTGAAATCACGACCACGTCAGCGCGA--T--------GTG
18593761 TCAGCAAATCGCGTCCA-CGTCA-GCGCGATTTGCT-T-ACGTGGACA-CAAATCGCG-CCT-AC
120 TCAGCAAATCGCGT-CATCGT-AGGCGCGATTTG-TGTCACGT--A-AGCAAA--GCGTCCTGAC
** *** *
18593819 GAGGACACGATTTGCTGACACGTCCCCTGACATCGCGCTGGTGTGGACGTGATTTTGGGGAAAAT
177 GAGGACACGATTTGCTGACACGTCCCCTGACATCGCGCTGACGTGGACACAATTTCGGGGAAAAT
* ** * *
18593884 GGCCCATTTCGGTAAATAATAAAATATTGAGCCTATTTCGGTAAATTTTAAAAAAATAGGGCTTT
242 GGCCCATTCCGGTAAATAATAAAATACCGAGCCCATTTCGGTAAATTTTAAAAAAATAGGACTTT
18593949 T
307 T
18593950 ATGTGTAATT
Statistics
Matches: 277, Mismatches: 22, Indels: 28
0.85 0.07 0.09
Matches are distributed among these distances:
311 12 0.04
312 95 0.34
314 1 0.00
320 4 0.01
322 155 0.56
323 7 0.03
324 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (311 bp):
GGGGCAAAATACCAAAAAAAGCCCTATTTTTTAAAAATTTACCGAAATGGGCCCGGTATTTTATT
ATTTACCGAAATGAGCCATTTTCCCTGAAATCACGACCACGTCAGCGCGATGTGTCAGCAAATCG
CGTCATCGTAGGCGCGATTTGTGTCACGTAAGCAAAGCGTCCTGACGAGGACACGATTTGCTGAC
ACGTCCCCTGACATCGCGCTGACGTGGACACAATTTCGGGGAAAATGGCCCATTCCGGTAAATAA
TAAAATACCGAGCCCATTTCGGTAAATTTTAAAAAAATAGGACTTTTTTTG
Found at i:18594928 original size:34 final size:35
Alignment explanation
Indices: 18594879--18594970 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 35
18594869 TAATAATTAA
18594879 TAAATTATTTATAAATATAATGATACATAA-AATATTT
1 TAAA-TATTT-TAAATATAATGATACATAATAATA-TT
*
18594916 TAAA-ATTTTAAATATAAT-A-A-TTAATAATATT
1 TAAATATTTTAAATATAATGATACATAATAATATT
*
18594947 TAAATAATTT-AATATAATGATACA
1 TAAATATTTTAAATATAATGATACA
18594971 CAAAGTAGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
31 17 0.36
32 10 0.21
33 2 0.04
34 10 0.21
35 4 0.09
37 4 0.09
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (35 bp):
TAAATATTTTAAATATAATGATACATAATAATATT
Found at i:18596246 original size:20 final size:20
Alignment explanation
Indices: 18596223--18596261 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
18596213 ATTTTTTTAT
18596223 TTATTCAAATAGGTTGTTAC
1 TTATTCAAATAGGTTGTTAC
*
18596243 TTATTTAAATAGGTTGTTA
1 TTATTCAAATAGGTTGTTA
18596262 AGCTTTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (20 bp):
TTATTCAAATAGGTTGTTAC
Found at i:18600823 original size:20 final size:20
Alignment explanation
Indices: 18600798--18600843 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18600788 TGTTAATATT
* *
18600798 TTGTTATTTATTCAACTAGG
1 TTGTTACTTATTCAAATAGG
*
18600818 TTGTTACTTATTTAAATAGG
1 TTGTTACTTATTCAAATAGG
18600838 TTGTTA
1 TTGTTA
18600844 AGCTTTACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (20 bp):
TTGTTACTTATTCAAATAGG
Found at i:18603282 original size:114 final size:114
Alignment explanation
Indices: 18603081--18603287 Score: 288
Period size: 114 Copynumber: 1.8 Consensus size: 114
18603071 TTATTAAGTA
* * **
18603081 TTTTACTAAGTTGGTGCCACCCATCGACCGAGTCCCAACTCAATTAGGGAATTACCAAAATGTTA
1 TTTTACTAAGTTGGAGCCACCCATCAACCGAGTCCCAACTCAATTAGGGAATTACCAAAAAATTA
*
18603146 ATTTATATACCAAGTAAATTATATGATTAAGTAGGTGTTTTGTTAAGAT
66 ATTTATATACCAAGCAAATTATATGATTAAGTAGGTGTTTTGTTAAGAT
* ** * *
18603195 TTTTTCTAAGTTGGAGCCACCCATCAATTGAGTCCTAAGTCAATTAGGGAATTACCAAAAAATTA
1 TTTTACTAAGTTGGAGCCACCCATCAACCGAGTCCCAACTCAATTAGGGAATTACCAAAAAATTA
* * * *
18603260 TTTTATATGCTAAGCAAGTTATATGATT
66 ATTTATATACCAAGCAAATTATATGATT
18603288 GAGTGTGTAA
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
114 79 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (114 bp):
TTTTACTAAGTTGGAGCCACCCATCAACCGAGTCCCAACTCAATTAGGGAATTACCAAAAAATTA
ATTTATATACCAAGCAAATTATATGATTAAGTAGGTGTTTTGTTAAGAT
Found at i:18613338 original size:12 final size:12
Alignment explanation
Indices: 18613321--18613346 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18613311 GGTGGGTGCT
18613321 TTACCAAAAGTC
1 TTACCAAAAGTC
18613333 TTACCAAAAGTC
1 TTACCAAAAGTC
18613345 TT
1 TT
18613347 TTAACAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (12 bp):
TTACCAAAAGTC
Found at i:18616324 original size:17 final size:17
Alignment explanation
Indices: 18616294--18616331 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
18616284 CTGTGAAATT
18616294 TAATCATTTTATTGAAA
1 TAATCATTTTATTGAAA
*
18616311 TAAT-ATTTTAATTGAGA
1 TAATCATTTT-ATTGAAA
18616328 TAAT
1 TAAT
18616332 TTTCATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (17 bp):
TAATCATTTTATTGAAA
Found at i:18620990 original size:13 final size:13
Alignment explanation
Indices: 18620972--18620996 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18620962 TTGATTTGTT
18620972 TTGATTATGTAAA
1 TTGATTATGTAAA
18620985 TTGATTATGTAA
1 TTGATTATGTAA
18620997 TCTTGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:18626830 original size:21 final size:20
Alignment explanation
Indices: 18626796--18626834 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
18626786 ATCAATTTAA
*
18626796 TATTAAATAATAATATTTCC
1 TATTAAAGAATAATATTTCC
18626816 TATTAAAAGAATAATATTT
1 TATT-AAAGAATAATATTT
18626835 AAATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
TATTAAAGAATAATATTTCC
Done.