Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 124 of 144
Found at i:29730443 original size:27 final size:27
Alignment explanation
Indices: 29730413--29730506 Score: 86
Period size: 27 Copynumber: 3.4 Consensus size: 27
29730403 AAAAATTTAC
29730413 TAACTTTTAAGGGCCCCAAAAAACTTT
1 TAACTTTTAAGGGCCCCAAAAAACTTT
* **
29730440 TAACTTTTAATGTG--CC-AAATTCTTTTTT
1 TAACTTTTAA-GGGCCCCAAAAAAC---TTT
29730468 ACTAACTTTTAAGGGCCCCAAAAAACTTT
1 --TAACTTTTAAGGGCCCCAAAAAACTTT
29730497 TAACTTTTAA
1 TAACTTTTAA
29730507 TGTGCCAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
25 4 0.08
26 2 0.04
27 20 0.38
28 5 0.10
29 5 0.10
30 10 0.19
31 2 0.04
32 4 0.08
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (27 bp):
TAACTTTTAAGGGCCCCAAAAAACTTT
Found at i:29730475 original size:57 final size:57
Alignment explanation
Indices: 29730408--29730538 Score: 253
Period size: 57 Copynumber: 2.3 Consensus size: 57
29730398 AAAAAAAAAA
29730408 TTTACTAACTTTTAAGGGCCCCAAAAAACTTTTAACTTTTAATGTGCCAAATTCTTT
1 TTTACTAACTTTTAAGGGCCCCAAAAAACTTTTAACTTTTAATGTGCCAAATTCTTT
29730465 TTTACTAACTTTTAAGGGCCCCAAAAAACTTTTAACTTTTAATGTGCCAAATTCTTT
1 TTTACTAACTTTTAAGGGCCCCAAAAAACTTTTAACTTTTAATGTGCCAAATTCTTT
*
29730522 TTTACCAACTTTTAAGG
1 TTTACTAACTTTTAAGG
29730539 AATTTAAAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 73 1.00
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.40
Consensus pattern (57 bp):
TTTACTAACTTTTAAGGGCCCCAAAAAACTTTTAACTTTTAATGTGCCAAATTCTTT
Found at i:29730476 original size:30 final size:30
Alignment explanation
Indices: 29730440--29730536 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 30
29730430 AAAAAACTTT
29730440 TAACTTTTAATGTGCCAAATTCTTTTTTAC
1 TAACTTTTAATGTGCCAAATTCTTTTTTAC
* **
29730470 TAACTTTTAA-GGGCCCCAAAAAAC---TTT--
1 TAACTTTTAATGTG--CC-AAATTCTTTTTTAC
29730497 TAACTTTTAATGTGCCAAATTCTTTTTTAC
1 TAACTTTTAATGTGCCAAATTCTTTTTTAC
*
29730527 CAACTTTTAA
1 TAACTTTTAA
29730537 GGAATTTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 18
0.67 0.09 0.24
Matches are distributed among these distances:
25 4 0.08
26 2 0.04
27 10 0.20
28 5 0.10
29 5 0.10
30 19 0.37
31 2 0.04
32 4 0.08
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (30 bp):
TAACTTTTAATGTGCCAAATTCTTTTTTAC
Found at i:29730524 original size:27 final size:27
Alignment explanation
Indices: 29730437--29730525 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 27
29730427 CCCAAAAAAC
29730437 TTTTAACTTTTAATGTGCCAAATTCTTT
1 TTTTAACTTTTAATGTGCCAAATTC-TT
* **
29730465 TTTACTAACTTTTAA-GGGCCCCAAAAAAC--
1 TTT--TAACTTTTAATGTG--CC-AAATTCTT
29730494 TTTTAACTTTTAATGTGCCAAATTCTT
1 TTTTAACTTTTAATGTGCCAAATTCTT
29730521 TTTTA
1 TTTTA
29730526 CCAACTTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 17
0.67 0.09 0.24
Matches are distributed among these distances:
25 4 0.09
26 2 0.04
27 15 0.32
28 5 0.11
29 5 0.11
30 10 0.21
31 2 0.04
32 4 0.09
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (27 bp):
TTTTAACTTTTAATGTGCCAAATTCTT
Found at i:29733248 original size:21 final size:21
Alignment explanation
Indices: 29733222--29733272 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
29733212 TAATAACATG
*
29733222 TTAAATAAATTTTTTCT-ATTT
1 TTAAAT-AATTTTTTATGATTT
*
29733243 TTAAATATTTTTTTATGATTT
1 TTAAATAATTTTTTATGATTT
29733264 TT-AATAATT
1 TTAAATAATT
29733273 CATTAAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTAAATAATTTTTTATGATTT
Found at i:29733925 original size:23 final size:23
Alignment explanation
Indices: 29733890--29733949 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
29733880 ATTTGTATTT
29733890 TAAAA-TTTAAAAAGTAAAAAAA
1 TAAAATTTTAAAAAGTAAAAAAA
29733912 TAAAATTTTAAAAA-TAAAAAAA
1 TAAAATTTTAAAAAGTAAAAAAA
**
29733934 TTTAATTTATAAAAAG
1 TAAAATTT-TAAAAAG
29733950 CATAGTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (23 bp):
TAAAATTTTAAAAAGTAAAAAAA
Found at i:29734159 original size:6 final size:6
Alignment explanation
Indices: 29734148--29734185 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
29734138 AGATTGATGG
29734148 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CC
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CC
29734186 TTGTACTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCTCT
Found at i:29742338 original size:6 final size:6
Alignment explanation
Indices: 29742296--29742330 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
29742286 TAGTTTGAAA
*
29742296 TATATG TATATG TATATG TATATG TATATG CATAT
1 TATATG TATATG TATATG TATATG TATATG TATAT
29742331 ATGCATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (6 bp):
TATATG
Found at i:29742342 original size:12 final size:12
Alignment explanation
Indices: 29742296--29742343 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
29742286 TAGTTTGAAA
*
29742296 TATATGTATATG
1 TATATATATATG
*
29742308 TATATGTATATG
1 TATATATATATG
29742320 TATATGCATATATG
1 TATAT--ATATATG
*
29742334 CATATATATA
1 TATATATATA
29742344 ATGACTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 22 0.69
14 10 0.31
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (12 bp):
TATATATATATG
Found at i:29746353 original size:17 final size:17
Alignment explanation
Indices: 29746331--29746368 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
29746321 TTATAAAATA
29746331 TTAATAT-TTAATATATT
1 TTAATATATTAATA-ATT
*
29746348 TTAATATATTATTAATT
1 TTAATATATTAATAATT
29746365 TTAA
1 TTAA
29746369 ATAGTGAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAATATATTAATAATT
Found at i:29746566 original size:25 final size:25
Alignment explanation
Indices: 29746526--29746577 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
29746516 AAAATTAAAC
29746526 ATATTTAAAATAATTATTAATTATT
1 ATATTTAAAATAATTATTAATTATT
**
29746551 ATATTTAATAAT-ATTATTGGTTATT
1 ATATTTAA-AATAATTATTAATTATT
29746576 AT
1 AT
29746578 GTTTTTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
ATATTTAAAATAATTATTAATTATT
Found at i:29755063 original size:18 final size:19
Alignment explanation
Indices: 29755026--29755063 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
29755016 ATTATATAAT
29755026 ATTTAAATATATATAGTTTA
1 ATTTAAATATATATA-TTTA
*
29755046 ATTTAAATGTATAT-TTTA
1 ATTTAAATATATATATTTA
29755064 TTTTTGGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTTAAATATATATATTTA
Found at i:29761602 original size:2 final size:2
Alignment explanation
Indices: 29761597--29761632 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29761587 AATTGAAAGA
29761597 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29761633 TGTAATTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29768505 original size:22 final size:21
Alignment explanation
Indices: 29768474--29768515 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
29768464 TCAATATTTT
*
29768474 TTAAAAATTATTTTTGAATTG
1 TTAAAAATTATTTTTAAATTG
29768495 TTAAATAATTATTTTTAAATT
1 TTAAA-AATTATTTTTAAATT
29768516 ATTTTTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TTAAAAATTATTTTTAAATTG
Found at i:29769771 original size:2 final size:2
Alignment explanation
Indices: 29769764--29769795 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29769754 CTAACCCTTG
29769764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29769796 GATTATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29773052 original size:13 final size:13
Alignment explanation
Indices: 29773036--29773089 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
29773026 TAAATCAAAA
29773036 TTTTTAAAATTAT
1 TTTTTAAAATTAT
*
29773049 TTTTAAAAATTAAT
1 TTTTTAAAATT-AT
*
29773063 TTTTT-AAAGTAT
1 TTTTTAAAATTAT
*
29773075 TTTTTAAAAATAT
1 TTTTTAAAATTAT
29773088 TT
1 TT
29773090 CTCAAAAGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 7 0.20
13 22 0.63
14 6 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
TTTTTAAAATTAT
Found at i:29773078 original size:27 final size:26
Alignment explanation
Indices: 29773034--29773085 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
29773024 CTTAAATCAA
*
29773034 AATTTTTAAAATTATTTTTAAAAATT
1 AATTTTTAAAAGTATTTTTAAAAATT
*
29773060 AATTTTTTAAAGTATTTTTTAAAAAT
1 AATTTTTAAAAGTA-TTTTTAAAAAT
29773086 ATTTCTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
AATTTTTAAAAGTATTTTTAAAAATT
Found at i:29775471 original size:22 final size:21
Alignment explanation
Indices: 29775446--29775497 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
29775436 ATTATATTAT
*
29775446 TGTTTTGGTGCTGTATTTTTAC
1 TGTTTTGGTGCTGT-TTTATAC
*
29775468 TGTTTTGGTGTTGTTTTATAC
1 TGTTTTGGTGCTGTTTTATAC
*
29775489 TATTTTGGT
1 TGTTTTGGT
29775498 TGTTATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.10, C:0.06, G:0.23, T:0.62
Consensus pattern (21 bp):
TGTTTTGGTGCTGTTTTATAC
Found at i:29775494 original size:21 final size:21
Alignment explanation
Indices: 29775448--29775506 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
29775438 TATATTATTG
* * *
29775448 TTTTGGTGCTGTATTTTTACTG
1 TTTTGGTGTTGT-TTTATACTA
29775470 TTTTGGTGTTGTTTTATACTA
1 TTTTGGTGTTGTTTTATACTA
*
29775491 TTTTGGTTGTTATTTT
1 TTTTGG-TGTTGTTTT
29775507 GGTGCTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.10, C:0.05, G:0.20, T:0.64
Consensus pattern (21 bp):
TTTTGGTGTTGTTTTATACTA
Found at i:29775506 original size:12 final size:12
Alignment explanation
Indices: 29775489--29775592 Score: 56
Period size: 12 Copynumber: 9.1 Consensus size: 12
29775479 TGTTTTATAC
29775489 TATTTTGGTTGT
1 TATTTTGGTTGT
*
29775501 TATTTTGG-TGC
1 TATTTTGGTTGT
**
29775512 TATTTT--TTAC
1 TATTTTGGTTGT
*
29775522 TATTTTGG-TAT
1 TATTTTGGTTGT
* * * *
29775533 TGTTTTTGCTAT
1 TATTTTGGTTGT
* *
29775545 TGTTTT-GCTGT
1 TATTTTGGTTGT
* *
29775556 TATTTTTGTTGC
1 TATTTTGGTTGT
29775568 TATTTTGGTTGT
1 TATTTTGGTTGT
*
29775580 TATTTTTGTTGT
1 TATTTTGGTTGT
29775592 T
1 T
29775593 TGAATGTTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
10 8 0.11
11 25 0.33
12 42 0.56
ACGTcount: A:0.10, C:0.05, G:0.19, T:0.66
Consensus pattern (12 bp):
TATTTTGGTTGT
Found at i:29775559 original size:55 final size:55
Alignment explanation
Indices: 29775448--29775573 Score: 148
Period size: 54 Copynumber: 2.3 Consensus size: 55
29775438 TATATTATTG
* * * *
29775448 TTTTGGTGCTGTATTTTTACTGTTTTGGTGTTGTTTTATACTATTTTGGTTGTTA-
1 TTTTGGTGCTAT-TTTTTACTATTTTGGTATTGTTTTATACTATTTTGGCTGTTAT
* *
29775503 TTTTGGTGCTATTTTTTACTATTTTGGTATTGTTTT-TGCTATTGTTTTGCTGTTAT
1 TTTTGGTGCTATTTTTTACTATTTTGGTATTGTTTTATACTA-T-TTTGGCTGTTAT
*
29775559 TTTTGTTGCTATTTT
1 TTTTGGTGCTATTTT
29775574 GGTTGTTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
53 4 0.07
54 23 0.38
55 20 0.33
56 14 0.23
ACGTcount: A:0.10, C:0.06, G:0.19, T:0.64
Consensus pattern (55 bp):
TTTTGGTGCTATTTTTTACTATTTTGGTATTGTTTTATACTATTTTGGCTGTTAT
Found at i:29779591 original size:16 final size:15
Alignment explanation
Indices: 29779570--29779601 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29779560 ATGTGTGATT
29779570 AGATTAAGCTTAATTA
1 AGATTAAG-TTAATTA
29779586 AGATTAAGTTAATTA
1 AGATTAAGTTAATTA
29779601 A
1 A
29779602 ACTTAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (15 bp):
AGATTAAGTTAATTA
Found at i:29783887 original size:32 final size:32
Alignment explanation
Indices: 29783851--29783918 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
29783841 GCAGACTTAA
* *
29783851 GGTGGGTTTGAATGTATGGTGGGTCATGGTGC
1 GGTGGGTTTGAATGTACGGTGGATCATGGTGC
29783883 GGTGGGTTTGAATGTACGGTGGATCATGGTGC
1 GGTGGGTTTGAATGTACGGTGGATCATGGTGC
29783915 GGTG
1 GGTG
29783919 CGGTACGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.13, C:0.07, G:0.47, T:0.32
Consensus pattern (32 bp):
GGTGGGTTTGAATGTACGGTGGATCATGGTGC
Found at i:29783904 original size:17 final size:17
Alignment explanation
Indices: 29783851--29783904 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
29783841 GCAGACTTAA
*
29783851 GGTGGGTTTGAATGTAT
1 GGTGGGTTTGAATGTAC
* *
29783868 GGTGGG--T-CATGGTGC
1 GGTGGGTTTGAAT-GTAC
29783883 GGTGGGTTTGAATGTAC
1 GGTGGGTTTGAATGTAC
29783900 GGTGG
1 GGTGG
29783905 ATCATGGTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
14 2 0.07
15 9 0.32
17 15 0.54
18 2 0.07
ACGTcount: A:0.13, C:0.06, G:0.48, T:0.33
Consensus pattern (17 bp):
GGTGGGTTTGAATGTAC
Found at i:29798987 original size:27 final size:27
Alignment explanation
Indices: 29798951--29799148 Score: 209
Period size: 27 Copynumber: 7.3 Consensus size: 27
29798941 CCTTTAGGTG
* * *
29798951 CGCCAAAAAGGCTT-TTCTTTCTTACTT
1 CGCCACAAAGG-TTATTCTTTCATAGTT
* *
29798978 CACCACAAAGGCTATTCTTTCATAGTT
1 CGCCACAAAGGTTATTCTTTCATAGTT
*
29799005 CGTCACAAAGGTTATTCTTTCATAGTT
1 CGCCACAAAGGTTATTCTTTCATAGTT
*
29799032 CGTCACAAAGGTTATTCTTTCATAGTT
1 CGCCACAAAGGTTATTCTTTCATAGTT
* * *
29799059 CGCCACAAAAAGCTATTCTTTCATAATT
1 CGCCAC-AAAGGTTATTCTTTCATAGTT
** * *
29799087 CTTCACGAAGGCTATTCTTTCATAGTT
1 CGCCACAAAGGTTATTCTTTCATAGTT
* * * *
29799114 TGCCATAAAGGCTATTATTTCATAGTT
1 CGCCACAAAGGTTATTCTTTCATAGTT
29799141 CGCCACAA
1 CGCCACAA
29799149 TACGTGAGGT
Statistics
Matches: 144, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
26 1 0.01
27 121 0.84
28 22 0.15
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37
Consensus pattern (27 bp):
CGCCACAAAGGTTATTCTTTCATAGTT
Found at i:29799103 original size:82 final size:82
Alignment explanation
Indices: 29798951--29799148 Score: 247
Period size: 82 Copynumber: 2.4 Consensus size: 82
29798941 CCTTTAGGTG
* * * * * *
29798951 CGCCAAAAAGGCTT-TTCTTTCTTACTTCACCAC-AAAGGCTATTCTTTCATAGTTCGTCACAAA
1 CGCCACAAAGG-TTATTCTTTCATAGTTCGCCACAAAAAGCTATTCTTTCATAATTCGTCACAAA
*
29799014 GGTTATTCTTTCATAGTT
65 GGCTATTCTTTCATAGTT
* * *
29799032 CGTCACAAAGGTTATTCTTTCATAGTTCGCCACAAAAAGCTATTCTTTCATAATTCTTCACGAAG
1 CGCCACAAAGGTTATTCTTTCATAGTTCGCCACAAAAAGCTATTCTTTCATAATTCGTCACAAAG
29799097 GCTATTCTTTCATAGTT
66 GCTATTCTTTCATAGTT
* * * *
29799114 TGCCATAAAGGCTATTATTTCATAGTTCGCCACAA
1 CGCCACAAAGGTTATTCTTTCATAGTTCGCCACAA
29799149 TACGTGAGGT
Statistics
Matches: 100, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
80 2 0.02
81 25 0.25
82 73 0.73
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37
Consensus pattern (82 bp):
CGCCACAAAGGTTATTCTTTCATAGTTCGCCACAAAAAGCTATTCTTTCATAATTCGTCACAAAG
GCTATTCTTTCATAGTT
Found at i:29801103 original size:29 final size:30
Alignment explanation
Indices: 29801061--29801117 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
29801051 TATTTAGAAA
*
29801061 TTAGTTCTCATATTTTT-ACTTTTAAAATT
1 TTAGTTCTCATATTTTTAAATTTTAAAATT
29801090 TTAGTCTCTC-TATTTTTAAATTTTAAAA
1 TTAGT-TCTCATATTTTTAAATTTTAAAA
29801118 ATTCAAGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.56
Consensus pattern (30 bp):
TTAGTTCTCATATTTTTAAATTTTAAAATT
Found at i:29802192 original size:22 final size:22
Alignment explanation
Indices: 29802167--29802208 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29802157 TAATAAATAA
*
29802167 AAAATATAAAATTAT-TAAATTT
1 AAAATA-AAAATAATATAAATTT
29802189 AAAATAAAAATAATATAAAT
1 AAAATAAAAATAATATAAAT
29802209 GTTTATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAATAAAAATAATATAAATTT
Found at i:29814449 original size:24 final size:24
Alignment explanation
Indices: 29814421--29814481 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
29814411 AGAAATAATC
29814421 TTTCAGTTAAACTCTATTTATTTA
1 TTTCAGTTAAACTCTATTTATTTA
* *
29814445 TTTCAATTAAACTCTGTTTATTTA
1 TTTCAGTTAAACTCTATTTATTTA
* *
29814469 TTTGAGTCAAACT
1 TTTCAGTTAAACT
29814482 TTTATTAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTA
Found at i:29815045 original size:64 final size:63
Alignment explanation
Indices: 29814944--29815072 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 63
29814934 ATTACAAGCC
*
29814944 AACAACCTAACGCAAAACGTACGTTAGAACCATACCTATACATATTACAAAAAAAAAGTTTTAA
1 AACAACATAACGCAAAACGTACGTTAGAACCATACCTATACATATTAC-AAAAAAAAGTTTTAA
29815008 AACAACATAACGCAAAACGTACGTTAGAACCATACCTATACATATTACAAAAAAAAGTTTTAA
1 AACAACATAACGCAAAACGTACGTTAGAACCATACCTATACATATTACAAAAAAAAGTTTTAA
29815071 AA
1 AA
29815073 GTTAATAAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 17 0.27
64 47 0.73
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.22
Consensus pattern (63 bp):
AACAACATAACGCAAAACGTACGTTAGAACCATACCTATACATATTACAAAAAAAAGTTTTAA
Found at i:29815059 original size:35 final size:35
Alignment explanation
Indices: 29814956--29815059 Score: 85
Period size: 35 Copynumber: 3.1 Consensus size: 35
29814946 CAACCTAACG
29814956 CAAAACGTACGTTAGAACCATACCTATACATATTA
1 CAAAACGTACGTTAGAACCATACCTATACATATTA
*** * ** ***
29814991 CAAAAAAAAAGTTTTAA--A-A-C-A-ACATAACG
1 CAAAACGTACGTTAGAACCATACCTATACATATTA
29815020 CAAAACGTACGTTAGAACCATACCTATACATATTA
1 CAAAACGTACGTTAGAACCATACCTATACATATTA
29815055 CAAAA
1 CAAAA
29815060 AAAAGTTTTA
Statistics
Matches: 45, Mismatches: 18, Indels: 12
0.60 0.24 0.16
Matches are distributed among these distances:
29 16 0.36
30 1 0.02
31 2 0.04
32 2 0.04
33 2 0.04
34 1 0.02
35 21 0.47
ACGTcount: A:0.50, C:0.20, G:0.08, T:0.22
Consensus pattern (35 bp):
CAAAACGTACGTTAGAACCATACCTATACATATTA
Found at i:29815094 original size:22 final size:22
Alignment explanation
Indices: 29815069--29815127 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
29815059 AAAAAGTTTT
* **
29815069 AAAAGTTAATAAAAATATTTAA
1 AAAAATTAATAAAAATAAGTAA
*
29815091 AAAAAATAATAAAAATAAGTAA
1 AAAAATTAATAAAAATAAGTAA
29815113 AAAAATTAATAAAAA
1 AAAAATTAATAAAAA
29815128 AGGAAAACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (22 bp):
AAAAATTAATAAAAATAAGTAA
Found at i:29815618 original size:18 final size:18
Alignment explanation
Indices: 29815591--29815625 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29815581 TTTCATGTAT
29815591 AAAATTATATA-AAAATC
1 AAAATTATATATAAAATC
29815608 AAAATTTATATATAAAAT
1 AAAA-TTATATATAAAAT
29815626 TTCACATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTATATATAAAATC
Found at i:29815670 original size:3 final size:3
Alignment explanation
Indices: 29815662--29815686 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29815652 GATTTAAACA
29815662 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
29815687 TATGTGTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:29826093 original size:21 final size:21
Alignment explanation
Indices: 29826067--29826108 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29826057 CACACTCACC
29826067 AACAAA-ATCAAAACAAGAAAA
1 AACAAACATCAAAA-AAGAAAA
29826088 AACAAACATCAAAAAAGAAAA
1 AACAAACATCAAAAAAGAAAA
29826109 GATTCGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.76, C:0.14, G:0.05, T:0.05
Consensus pattern (21 bp):
AACAAACATCAAAAAAGAAAA
Found at i:29828650 original size:58 final size:57
Alignment explanation
Indices: 29828474--29828661 Score: 200
Period size: 58 Copynumber: 3.2 Consensus size: 57
29828464 TAATATAATT
* * * * ** *
29828474 TTTGGTACTTAAACTTTATATTTTTCTTAATTTTGTATTTAAACTTTTTTTATTCAA
1 TTTGGTACTTAAACTTGACATTTTTTTTAATTTGGTACCTAAAATTTTTTTATTCAA
* * *
29828531 ATTGGTACTTGAACTTGACATTTTTTTTCTAATTTGGTACCT-AAATTTTTTTGGATCCAA
1 TTTGGTACTTAAACTTGACA-TTTTTTT-TAATTTGGTACCTAAAATTTTTTT--ATTCAA
* *
29828591 TTTAGTACCTAAAC-TGACATTTTTTTTAATTTGGTACCTAAAATTTTTTTAAATTCAA
1 TTTGGTACTTAAACTTGACATTTTTTTTAATTTGGTACCTAAAATTTTTTT--ATTCAA
29828649 TTTGGTACTTAAA
1 TTTGGTACTTAAA
29828662 TTTATTAAAT
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
57 29 0.27
58 48 0.45
59 15 0.14
60 15 0.14
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.52
Consensus pattern (57 bp):
TTTGGTACTTAAACTTGACATTTTTTTTAATTTGGTACCTAAAATTTTTTTATTCAA
Found at i:29828873 original size:57 final size:56
Alignment explanation
Indices: 29828798--29828905 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 56
29828788 AATTAATATT
* * *
29828798 AAAAAAATTAGATATCAAATTA-GAAAAAAGTGTCAAGTTTGAGTACCAAATTGAAC
1 AAAAAAATTAGATATCAAATTAGGAAAAAA-TGACAAATTTAAGTACCAAATTGAAC
* *
29828854 AAAAAAATTTAGGTGTCAAATTAGGAAAAAATGACAAATTTAAGTACCAAAT
1 AAAAAAA-TTAGATATCAAATTAGGAAAAAATGACAAATTTAAGTACCAAAT
29828906 GTTATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 7 0.16
57 31 0.69
58 7 0.16
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (56 bp):
AAAAAAATTAGATATCAAATTAGGAAAAAATGACAAATTTAAGTACCAAATTGAAC
Found at i:29829005 original size:15 final size:14
Alignment explanation
Indices: 29828987--29829078 Score: 62
Period size: 15 Copynumber: 6.2 Consensus size: 14
29828977 TCATATTAAT
29828987 TTTTTATATTATTTA
1 TTTTTA-ATTATTTA
*
29829002 TTTTTAATATAATTA
1 TTTTTAAT-TATTTA
29829017 -TTTTAATT-TTATA
1 TTTTTAATTATT-TA
**
29829030 TTTTTAAATTATAGA
1 TTTTT-AATTATTTA
* *
29829045 TTTTTAATAACTTAA
1 TTTTTAATTA-TTTA
29829060 TTTTTAAAATTATTTA
1 TTTTT--AATTATTTA
29829076 TTT
1 TTT
29829079 ATCATACAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
12 1 0.02
13 3 0.05
14 17 0.28
15 28 0.47
16 7 0.12
17 4 0.07
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (14 bp):
TTTTTAATTATTTA
Found at i:29853251 original size:30 final size:28
Alignment explanation
Indices: 29853210--29853281 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
29853200 CTCGGGGGCA
* *
29853210 AAAATGTAATTTTAGGAAAATTTAGGGTT
1 AAAATGGAATTTT-GGAAAATTTAGGGGT
* *
29853239 AGAAATGGAATTTTGGAAAGTTTGGGGGT
1 A-AAATGGAATTTTGGAAAATTTAGGGGT
29853268 AAAATGGTAATTTT
1 AAAATGG-AATTTT
29853282 TTGGTGAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.16
29 20 0.54
30 11 0.30
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAATTTAGGGGT
Found at i:29853278 original size:59 final size:59
Alignment explanation
Indices: 29853233--29853635 Score: 430
Period size: 59 Copynumber: 6.8 Consensus size: 59
29853223 AGGAAAATTT
*
29853233 AGGGTTAGAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTTGGTGAAATT
1 AGGGTTAGAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAA-TTTTTGGTGAAATC
* * * * * *
29853293 AGGGTCAAAAATAGAATTTTGGAAGGTTCGAGGGTAAAATGGTAA-TTTTGGTGAAATC
1 AGGGTTAGAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATC
* * * * * * *
29853351 GGGGTTAAAAATGGAACTTT-GAAAGATTCGAGGGTAAAATGATATTTTTTGGTGAAATC
1 AGGGTTAGAAATGGAATTTTGGAAAG-TTTGGGGGTAAAATGGTAATTTTTGGTGAAATC
**
29853410 AGGGTT-GAAAATAGG-ATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAATC
1 AGGGTTAG-AAAT-GGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATC
* *
29853469 -GAGGTT-GAAAAT-AAGATTTTGGAAAG-TTCGGGGTAAAATGGTAATTTTTGGTGAAATC
1 AG-GGTTAG-AAATGGA-ATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATC
* * *
29853527 GGGGTT-GAAAAT-GAGATTTTGGAAAGTTTGAGGGTGAAATGGTAATTTTTGGTGAAATC
1 AGGGTTAG-AAATGGA-ATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATC
* * * *
29853586 GGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTT
1 AGGGTTAGAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTT
29853636 AGAAAGTTTT
Statistics
Matches: 298, Mismatches: 33, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
57 4 0.01
58 99 0.33
59 147 0.49
60 48 0.16
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
AGGGTTAGAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATC
Found at i:29853429 original size:117 final size:117
Alignment explanation
Indices: 29853234--29853635 Score: 535
Period size: 117 Copynumber: 3.4 Consensus size: 117
29853224 GGAAAATTTA
* * * *
29853234 GGGTTAGAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTTGGTGAAATTAGGGTC
1 GGGTTAAAAATGGAATTTTGGAAAG-TTCGGGGTAAAATGGTAA-TTTTTGGTGAAATCAGGGTT
* * *
29853299 AAAAATAGAATTTTGGAAGGTTCGAGGGTAAAATGGTAA-TTTTGGTGAAATCG
64 GAAAATAGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCG
* * *
29853352 GGGTTAAAAATGGAACTTT-GAAAGATTCGAGGGTAAAATGATATTTTTTGGTGAAATCAGGGTT
1 GGGTTAAAAATGGAATTTTGGAAAG-TTCG-GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTT
29853416 GAAAATAGGATTTTGGAAAGTTC-AGGGGTAAAATGGTAATTTTTGGTGAAATCG
64 GAAAATAGGATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGGTGAAATCG
* * * *
29853470 AGGTTGAAAAT-AAGATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTG
1 GGGTTAAAAATGGA-ATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTG
* *
29853534 AAAAT-GAGATTTTGGAAAGTTTGAGGGTGAAATGGTAATTTTTGGTGAAATCG
65 AAAATAG-GATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCG
* *
29853587 GGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTT
1 GGGTTAAAAATGGAATTTTGGAAAG-TTCGGGGTAAAATGGTAATTTTT
29853636 AGAAAGTTTT
Statistics
Matches: 250, Mismatches: 25, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
116 2 0.01
117 159 0.64
118 84 0.34
119 5 0.02
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (117 bp):
GGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTGA
AAATAGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCG
Found at i:29853531 original size:176 final size:176
Alignment explanation
Indices: 29853233--29853635 Score: 557
Period size: 176 Copynumber: 2.3 Consensus size: 176
29853223 AGGAAAATTT
* * *
29853233 AGGGTTAGAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTTGGTGAAATTAGGGT
1 AGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAA-TTTTTGGTGAAATGAGGGT
*
29853298 CAAAAATAGAATTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAAT
65 CAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAAT
*
29853363 G-GAACTTT-GAAAGATTCGAGGGTAAAATGATATTTTTTGGTGAAATC
130 GAG-ACTTTGGAAAG-TTCGAGGGTAAAATGATAATTTTTGGTGAAATC
* *
29853410 AGGGTTGAAAATAGG-ATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAATCGA-GG
1 AGGGTTAAAAAT-GGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAAT-GAGGG
** *
29853473 TTGAAAATA-AGATTTTGGAAAGTTCG-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTGAA
64 TCAAAAATAGA-ATTTTGGAAAGTTCGAGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAA
* * * *
29853536 AATGAGATTTTGGAAAGTTTGAGGGTGAAATGGTAATTTTTGGTGAAATC
127 AATGAGACTTTGGAAAGTTCGAGGGTAAAATGATAATTTTTGGTGAAATC
* *
29853586 GGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTT
1 AGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT
29853636 AGAAAGTTTT
Statistics
Matches: 201, Mismatches: 18, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
175 17 0.08
176 137 0.68
177 45 0.22
178 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (176 bp):
AGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATGAGGGTC
AAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATG
AGACTTTGGAAAGTTCGAGGGTAAAATGATAATTTTTGGTGAAATC
Found at i:29853620 original size:30 final size:31
Alignment explanation
Indices: 29853586--29853650 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
29853576 TGGTGAAATC
29853586 GGGGTTAAAAATGG-AA-TTTTAGAAAGTTTA
1 GGGGTT-AAAATGGTAATTTTTAGAAAGTTTA
*
29853616 GGGG-TAAAATGGTAATTTTTAGAAAGTTTT
1 GGGGTTAAAATGGTAATTTTTAGAAAGTTTA
29853646 GGGGT
1 GGGGT
29853651 CAAAGTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 7 0.23
29 3 0.10
30 21 0.68
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.35
Consensus pattern (31 bp):
GGGGTTAAAATGGTAATTTTTAGAAAGTTTA
Found at i:29853662 original size:30 final size:30
Alignment explanation
Indices: 29853602--29853663 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
29853592 AAAAATGGAA
*
29853602 TTTTAGAAAGTTTAGGGGTAAAATGGTAAT
1 TTTTAGAAAGTTTAGGGGTAAAATGATAAT
* *
29853632 TTTTAGAAAGTTTTGGGGTCAAA-GTATAAT
1 TTTTAGAAAGTTTAGGGGTAAAATG-ATAAT
29853662 TT
1 TT
29853664 ATGAACAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.40
Consensus pattern (30 bp):
TTTTAGAAAGTTTAGGGGTAAAATGATAAT
Found at i:29855529 original size:12 final size:12
Alignment explanation
Indices: 29855512--29855549 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
29855502 TCTTTTGGGT
29855512 TTTTAATTTAAA
1 TTTTAATTTAAA
29855524 TTTTAA-TTAAA
1 TTTTAATTTAAA
*
29855535 TTTAAATTTAAA
1 TTTTAATTTAAA
29855547 TTT
1 TTT
29855550 ATTTCAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAATTTAAA
Found at i:29855531 original size:6 final size:6
Alignment explanation
Indices: 29855516--29855601 Score: 56
Period size: 6 Copynumber: 14.3 Consensus size: 6
29855506 TTGGGTTTTT
*
29855516 AATTTA AATTTT AA-TTA AATTTA AATTTA AATTT- -ATTTCAA ATATTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT--A A-A-TTTA
* * *
29855565 AATTTA AA-ATA AATTTA TATTT- AATAATA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AAT-TTA AATTTA AA
29855602 CCTAAAAAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
4 4 0.06
5 10 0.16
6 38 0.61
7 4 0.06
8 2 0.03
9 1 0.02
10 3 0.05
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (6 bp):
AATTTA
Found at i:29855538 original size:17 final size:17
Alignment explanation
Indices: 29855516--29855548 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29855506 TTGGGTTTTT
*
29855516 AATTTAAATTTTAATTA
1 AATTTAAATTTAAATTA
29855533 AATTTAAATTTAAATT
1 AATTTAAATTTAAATT
29855549 TATTTCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTAAATTA
Found at i:29855586 original size:17 final size:18
Alignment explanation
Indices: 29855561--29855601 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
29855551 TTTCAAATAT
29855561 TTTAAATTTAA-AATAAA
1 TTTAAATTTAATAATAAA
*
29855578 TTTATATTTAATAATAAA
1 TTTAAATTTAATAATAAA
29855596 TTTAAA
1 TTTAAA
29855602 CCTAAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAAATTTAATAATAAA
Found at i:29855593 original size:18 final size:17
Alignment explanation
Indices: 29855530--29855601 Score: 69
Period size: 16 Copynumber: 4.3 Consensus size: 17
29855520 TAAATTTTAA
*
29855530 TTAAATTTAAATTTAAAT
1 TTAAATTTAAA-ATAAAT
* *
29855548 TT--ATTTCAAAT-ATT
1 TTAAATTTAAAATAAAT
29855562 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
*
29855579 TTATATTTAATAATAAAT
1 TTAAATTTAA-AATAAAT
29855597 TTAAA
1 TTAAA
29855602 CCTAAAAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
14 4 0.09
15 1 0.02
16 14 0.33
17 11 0.26
18 13 0.30
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:29873249 original size:239 final size:242
Alignment explanation
Indices: 29872827--29873303 Score: 888
Period size: 239 Copynumber: 2.0 Consensus size: 242
29872817 AGAGCCATAT
*
29872827 CACTGGGAAATTAATTAACAGATGTGTCTTCTTCCTTATTATGTAAGGTGAGTTGCAATTTTCAG
1 CACTGGGAAATAAATTAACAGATGTGTCTTCTTCCTTATTATGTAAGGTGAGTTGCAATTTTCAG
*
29872892 ATTAAGATGAAAATTATTTTTCAGAACCACTGAATAGCATCCAGCATCTGTGGCAGGTGATGTTG
66 ATTAAGATGAAAATTATTTTTCAGAACCACTGAATAGCATCCAGCATCTGCGGCAGGTGATGTTG
29872957 TAATTCCTTGCCAGAAAGTAAATCAAAATCAGCACTAAAATCTCCATTAGAAAAATGATCTGATT
131 TAATTCCTTGCCAGAAAGTAAATCAAAATCAGCACTAAAATCTCCATTAGAAAAATGATCTGATT
29873022 CAACGCTAACAAAATTTATTTTTAAGATAAATGAAAAAAAGCTGAAC
196 CAACGCTAACAAAATTTATTTTTAAGATAAATGAAAAAAAGCTGAAC
*
29873069 CACTGGGAAATAAATTAACAGAT-T-T-TTCTTCTTTATTATGTAAGGTGAGTTGCAATTTTCAG
1 CACTGGGAAATAAATTAACAGATGTGTCTTCTTCCTTATTATGTAAGGTGAGTTGCAATTTTCAG
*
29873131 ATTAAGATGAAAATTATTTTTCAGAACCACTGAGTAGCATCCAGCATCTGCGGCAGGTGATGTTG
66 ATTAAGATGAAAATTATTTTTCAGAACCACTGAATAGCATCCAGCATCTGCGGCAGGTGATGTTG
29873196 TAATTCCTTGCCAGAAAGTAAATCAAAATCAGCACTAAAATCTCCATTAGAAAAATGATCTGATT
131 TAATTCCTTGCCAGAAAGTAAATCAAAATCAGCACTAAAATCTCCATTAGAAAAATGATCTGATT
*
29873261 CAACGCTAACAAAATTTGTTTTTAAGATAAATGAAAAAAAGCT
196 CAACGCTAACAAAATTTATTTTTAAGATAAATGAAAAAAAGCT
29873304 TTACTTCCAG
Statistics
Matches: 230, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
239 206 0.90
240 1 0.00
241 1 0.00
242 22 0.10
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (242 bp):
CACTGGGAAATAAATTAACAGATGTGTCTTCTTCCTTATTATGTAAGGTGAGTTGCAATTTTCAG
ATTAAGATGAAAATTATTTTTCAGAACCACTGAATAGCATCCAGCATCTGCGGCAGGTGATGTTG
TAATTCCTTGCCAGAAAGTAAATCAAAATCAGCACTAAAATCTCCATTAGAAAAATGATCTGATT
CAACGCTAACAAAATTTATTTTTAAGATAAATGAAAAAAAGCTGAAC
Found at i:29880269 original size:20 final size:21
Alignment explanation
Indices: 29880230--29880271 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
29880220 ATTTCTAAAA
* *
29880230 TATAAAATGAATATTGATATG
1 TATAAAATGAACAATGATATG
29880251 TATAAAA-GAACAATGATATG
1 TATAAAATGAACAATGATATG
29880271 T
1 T
29880272 TGACATGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.33
Consensus pattern (21 bp):
TATAAAATGAACAATGATATG
Found at i:29886219 original size:10 final size:10
Alignment explanation
Indices: 29886204--29886251 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
29886194 TTTAACATAA
29886204 TTTTAATTTT
1 TTTTAATTTT
*
29886214 TTTTAATATT
1 TTTTAATTTT
*
29886224 TTAT-ATTTT
1 TTTTAATTTT
* *
29886233 TTTAAAGTTT
1 TTTTAATTTT
29886243 TTTTAATTT
1 TTTTAATTT
29886252 GCTAGAATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
9 6 0.21
10 23 0.79
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:29887348 original size:60 final size:60
Alignment explanation
Indices: 29887243--29887357 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
29887233 GCACATAAGG
* * *
29887243 GTCAAATCTTTCAAAATGGTCATATAAAGGCTTAACATTTACGAAAGTGCTCAAATGAAA
1 GTCAAATCTTTCAAAATGATCATATAAAGGCTGAACATTTACGAAAGTACTCAAATGAAA
*
29887303 GTCAAATCTTTCAAAATGATCGA-A-AAAGAGCTGAACCTTCT-CGAAAGTACTCAAA
1 GTCAAATCTTTCAAAATGATC-ATATAAAG-GCTGAACATT-TACGAAAGTACTCAAA
29887358 CAAGGGCCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 4 0.08
60 42 0.88
61 2 0.04
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (60 bp):
GTCAAATCTTTCAAAATGATCATATAAAGGCTGAACATTTACGAAAGTACTCAAATGAAA
Found at i:29891710 original size:20 final size:20
Alignment explanation
Indices: 29891684--29891730 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
29891674 TTTTAAATCC
29891684 AATT-TTTT-TATTT-TAAT
1 AATTATTTTCTATTTATAAT
*
29891701 AATTGATTTTCTATTTATTAT
1 AATT-ATTTTCTATTTATAAT
29891722 AATTATTTT
1 AATTATTTT
29891731 AATACAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.16
19 4 0.16
20 10 0.40
21 7 0.28
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
AATTATTTTCTATTTATAAT
Found at i:29895144 original size:22 final size:21
Alignment explanation
Indices: 29895101--29895158 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
29895091 AAAAAAATGT
29895101 AAAAGCTTTTTAAAAATAAAAA
1 AAAAG-TTTTTAAAAATAAAAA
* *
29895123 AAAAGTTTTTAGAATTACAAAA
1 AAAAGTTTTTAAAAATA-AAAA
*
29895145 GAAA--TTTTAAAAAT
1 AAAAGTTTTTAAAAAT
29895159 TCAAAAGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.27
21 10 0.33
22 12 0.40
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (21 bp):
AAAAGTTTTTAAAAATAAAAA
Found at i:29895159 original size:21 final size:21
Alignment explanation
Indices: 29895108--29895169 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
29895098 TGTAAAAGCT
*
29895108 TTTTAAAAA-TA-AAAAAAAA
1 TTTTAAAAATTACAAAAGAAA
* *
29895127 GTTTTTAGAATTACAAAAGAAA
1 -TTTTAAAAATTACAAAAGAAA
29895149 TTTTAAAAATT-CAAAAGAAA
1 TTTTAAAAATTACAAAAGAAA
29895169 T
1 T
29895170 ATTTTTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 17 0.49
21 11 0.31
22 7 0.20
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (21 bp):
TTTTAAAAATTACAAAAGAAA
Found at i:29897874 original size:30 final size:30
Alignment explanation
Indices: 29897817--29897893 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
29897807 AAATTTTAAA
* * *
29897817 TTAATAATAATAAAATTATACTTTAATTCTC
1 TTAAAAATATTAAAATTATAATTTAATT-TC
*
29897848 TTAAAAATATTAAAATT-TAATTTAATTTT
1 TTAAAAATATTAAAATTATAATTTAATTTC
*
29897877 TTAAAAATTATAAAAAT
1 TTAAAAA-TATTAAAAT
29897894 ATAGATTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 8 0.20
30 17 0.43
31 15 0.38
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (30 bp):
TTAAAAATATTAAAATTATAATTTAATTTC
Found at i:29897938 original size:84 final size:82
Alignment explanation
Indices: 29897777--29897953 Score: 189
Period size: 82 Copynumber: 2.1 Consensus size: 82
29897767 AAAATGAAAA
* * * * *
29897777 AAAATTT-ATTTAAGTTTTTTATAATTTATAAAATTTTAAATTAATAATAATAAAATTATACTTT
1 AAAATTTAATTTAAGTTTTTTAAAAATTATAAAAATATAAATTAAAAATAATAAAATTATACTTT
* *
29897841 AATTCTCTTAAAAATATT
66 AATTATCTTAAAAACA-T
* * *
29897859 AAAATTTAATTTAA-TTTTTTAAAAATTATAAAAATATAGATTATCAAAATGATGAAATTATACT
1 AAAATTTAATTTAAGTTTTTTAAAAATTATAAAAATATAAATTA--AAAATAATAAAATTATACT
*
29897923 TTTATTAT-TATAAAAACAT
64 TTAATTATCT-TAAAAACAT
*
29897942 ACAATTTAATTT
1 AAAATTTAATTT
29897954 TGACAATAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
82 31 0.39
83 19 0.24
84 29 0.37
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (82 bp):
AAAATTTAATTTAAGTTTTTTAAAAATTATAAAAATATAAATTAAAAATAATAAAATTATACTTT
AATTATCTTAAAAACAT
Found at i:29903070 original size:21 final size:24
Alignment explanation
Indices: 29903041--29903092 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
29903031 AACATTAAAA
*
29903041 AAATATT-A-AGATAACTATATAT
1 AAATATTAATAGATAAATATATAT
29903063 AAAT-TTAATAGATAAATATATAT
1 AAATATTAATAGATAAATATATAT
29903086 AAA-ATTA
1 AAATATTA
29903093 TTAAATCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.08
22 5 0.19
23 19 0.73
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATTAATAGATAAATATATAT
Found at i:29905441 original size:24 final size:24
Alignment explanation
Indices: 29905406--29905464 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
29905396 TTAATAAGAG
* *
29905406 TTTAACTCAAACAAATAAACAGAA
1 TTTAACTGAAACAAATAAACAAAA
*
29905430 TTTAATTGAAACAAATAAACAAAA
1 TTTAACTGAAACAAATAAACAAAA
29905454 TTTAACTGAAA
1 TTTAACTGAAA
29905465 GATTATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (24 bp):
TTTAACTGAAACAAATAAACAAAA
Found at i:29924675 original size:20 final size:20
Alignment explanation
Indices: 29924647--29924685 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29924637 TCAAAAGGTT
29924647 AAATCAATAA-ATATAATAAA
1 AAATCAATAATAT-TAATAAA
*
29924667 AAATTAATAATATTAATAA
1 AAATCAATAATATTAATAA
29924686 TTATATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATCAATAATATTAATAAA
Found at i:29924739 original size:20 final size:21
Alignment explanation
Indices: 29924698--29924739 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29924688 ATATCTAATT
29924698 TTAAAATTTTAAAAATAGAAA
1 TTAAAATTTTAAAAATAGAAA
* *
29924719 TTAAATTTTTATAAATA-AAA
1 TTAAAATTTTAAAAATAGAAA
29924739 T
1 T
29924740 CCAAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAAAATTTTAAAAATAGAAA
Found at i:29928544 original size:21 final size:20
Alignment explanation
Indices: 29928509--29928554 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
29928499 ATCTCATATC
*
29928509 ATATA-ATAGATTAATGGTTT
1 ATATATATAAATTAAT-GTTT
29928529 ATATATATAAATTAATGTTT
1 ATATATATAAATTAATGTTT
*
29928549 AAATAT
1 ATATAT
29928555 TATGATAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (20 bp):
ATATATATAAATTAATGTTT
Found at i:29932693 original size:29 final size:29
Alignment explanation
Indices: 29932618--29932696 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
29932608 AAAATGGAGT
*
29932618 TTTAAGTTTATTAAAAATTAGAGAAAAAAT
1 TTTAAGTTT-TTAAAAATTAGAGAAAAAAA
* * *
29932648 TTATAAATCTTTTAAAAGTT-GATAAAAAAA
1 TT-TAAGT-TTTTAAAAATTAGAGAAAAAAA
29932678 TTTAAGTTTTTAAAAATTA
1 TTTAAGTTTTTAAAAATTA
29932697 AAAATAGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
28 10 0.25
29 4 0.10
30 12 0.30
31 12 0.30
32 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.41
Consensus pattern (29 bp):
TTTAAGTTTTTAAAAATTAGAGAAAAAAA
Found at i:29939764 original size:17 final size:17
Alignment explanation
Indices: 29939744--29939778 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29939734 AAGCACACAC
* *
29939744 ATAAAATTTAAATTAAA
1 ATAAAATATAAACTAAA
29939761 ATAAAATATAAACTAAA
1 ATAAAATATAAACTAAA
29939778 A
1 A
29939779 AATCACATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATAAACTAAA
Found at i:29959066 original size:23 final size:25
Alignment explanation
Indices: 29959040--29959096 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
29959030 TTTTTAAAAA
*
29959040 TTTTAAAAA-ATATTTTTTATA-CT
1 TTTTAAAAATATATTTTTAATAGCT
*
29959063 TTTTAATAAATTTTATTTTTAATAGCT
1 TTTTAA-AAA-TATATTTTTAATAGCT
29959090 TTTTAAA
1 TTTTAAA
29959097 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 6 0.21
24 3 0.11
26 11 0.39
27 8 0.29
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTAAAAATATATTTTTAATAGCT
Found at i:29959201 original size:14 final size:15
Alignment explanation
Indices: 29959182--29959210 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29959172 ATCCATTTTG
29959182 AAATAA-TTTAAAAA
1 AAATAAGTTTAAAAA
29959196 AAATAAGTTTAAAAA
1 AAATAAGTTTAAAAA
29959211 TTAAAAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAATAAGTTTAAAAA
Found at i:29962480 original size:15 final size:15
Alignment explanation
Indices: 29962460--29962489 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29962450 TTGAGCAATA
29962460 GAAAAGAAGAAAAAG
1 GAAAAGAAGAAAAAG
*
29962475 GAAAAGGAGAAAAAG
1 GAAAAGAAGAAAAAG
29962490 AGAAGCAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
GAAAAGAAGAAAAAG
Found at i:29962599 original size:13 final size:13
Alignment explanation
Indices: 29962581--29962614 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
29962571 ATCTTTATCC
29962581 CTTTTTTTCTTCT
1 CTTTTTTTCTTCT
*
29962594 CTTTTTCTCTTCT
1 CTTTTTTTCTTCT
29962607 CTTTTTTT
1 CTTTTTTT
29962615 TTTCCTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTTTTTCTTCT
Found at i:29963863 original size:26 final size:26
Alignment explanation
Indices: 29963815--29963864 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
29963805 ATTCTTTTAA
**
29963815 ATTTTTATGAATTTTTTTATATTTTG
1 ATTTTTATGAATTTTTGAATATTTTG
29963841 ATTTTTAT-AATTTTTGAATTATTT
1 ATTTTTATGAATTTTTGAA-TATTT
29963865 ATTGAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (26 bp):
ATTTTTATGAATTTTTGAATATTTTG
Found at i:29967732 original size:18 final size:18
Alignment explanation
Indices: 29967709--29967747 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
29967699 CATCGGTGTC
29967709 CCAAAAAATCTCCAAAGT
1 CCAAAAAATCTCCAAAGT
* *
29967727 CCAAAAAGTCTCCAAATT
1 CCAAAAAATCTCCAAAGT
29967745 CCA
1 CCA
29967748 TCTTTCGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.31, G:0.05, T:0.18
Consensus pattern (18 bp):
CCAAAAAATCTCCAAAGT
Found at i:29986039 original size:95 final size:96
Alignment explanation
Indices: 29985926--29986098 Score: 219
Period size: 96 Copynumber: 1.8 Consensus size: 96
29985916 TTTACATTAA
*
29985926 AAAAATAATTTTTTGGTGTCAACCAAATC-ATAGCCGACACCC-AAAAAATACGAAT-AAAAAAT
1 AAAAATAATTTTTTGGTGTCAACC-AACCAATAGCCGACACCCAAAAAAATACGAATAAAAAAAT
29985988 AATTTTTTGGATGTTAATCATGGCTCAAGTCCC
65 -ATTTTTTGGATGTTAATCATGGCTCAAGTCCC
*** * **
29986021 AAAAAT-ATTTTTTGGGTGTTTGCCAACCAATGGTTGACACCCAAAAAAATACGAATAAAAAAAT
1 AAAAATAATTTTTT-GGTGTCAACCAACCAATAGCCGACACCCAAAAAAATACGAATAAAAAAAT
*
29986085 ATTTTTTGGGTGTT
65 ATTTTTTGGATGTT
29986099 TGCCACCCAA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
94 10 0.15
95 23 0.35
96 26 0.39
97 7 0.11
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (96 bp):
AAAAATAATTTTTTGGTGTCAACCAACCAATAGCCGACACCCAAAAAAATACGAATAAAAAAATA
TTTTTTGGATGTTAATCATGGCTCAAGTCCC
Found at i:29986244 original size:115 final size:116
Alignment explanation
Indices: 29986123--29986426 Score: 422
Period size: 115 Copynumber: 2.6 Consensus size: 116
29986113 CTAACCACCC
* *
29986123 AAAAAATATTTTTAAATTTGAAAAAAGTGATGTAGGCCATTGGGTGGCAAACACTCCAAAAAAAT
1 AAAAAATATTTTTAAATTTGAAAAAAGTGGTGTAGGCCATTGAGTGGCAAACACTCCAAAAAAAT
* *
29986188 ATTTTTAAATCTGAGAAAGATAGTATA-AGTCATTAGGTGGCAAATACTC-A
66 ATTTTTAAATCTGAGAAAGATAGTATAGA-TCATTAGATGGCAAACACTCAA
*
29986238 AAAAAATATTTTTAAATTTGAAAAATGTGGTGTAGGCCATTGAGTGGCAAACAC-CCAAAAAAAT
1 AAAAAATATTTTTAAATTTGAAAAAAGTGGTGTAGGCCATTGAGTGGCAAACACTCCAAAAAAAT
* * * * *
29986302 ATTTTTAAATTTGAGAAAGTTGGTGTAGATCATTTGATGGCAAACACTCAA
66 ATTTTTAAATCTGAGAAAGATAGTATAGATCATTAGATGGCAAACACTCAA
* * *
29986353 AAAAAATATTTTTAAACTTGGAAAATA-TGGTGTAGGCCATTGAGTGAC-AACACT-CAAAATAA
1 AAAAAATATTTTTAAA-TTTGAAAAAAGTGGTGTAGGCCATTGAGTGGCAAACACTCCAAAA-AA
29986415 ATATTTTTAAAT
64 ATATTTTTAAAT
29986427 ATGGAAAAAG
Statistics
Matches: 170, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
114 60 0.35
115 103 0.61
116 7 0.04
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (116 bp):
AAAAAATATTTTTAAATTTGAAAAAAGTGGTGTAGGCCATTGAGTGGCAAACACTCCAAAAAAAT
ATTTTTAAATCTGAGAAAGATAGTATAGATCATTAGATGGCAAACACTCAA
Found at i:29986285 original size:57 final size:56
Alignment explanation
Indices: 29986123--29986479 Score: 384
Period size: 57 Copynumber: 6.2 Consensus size: 56
29986113 CTAACCACCC
* *
29986123 AAAAAATATTTTTAAATTTGAAAAAAGTGATGTAGGCCATTGGGTGGCAAACACTCCA
1 AAAAAATATTTTTAAATTTG-AAAAAGTGGTGTAGGCCATTGAGTGGCAAACACT-CA
* * * * * * *
29986181 AAAAAATATTTTTAAATCTGAGAAAGATAGTATAAGTCATT-AGGTGGCAAATACTCA
1 AAAAAATATTTTTAAATTTGAAAAAG-TGGTGTAGGCCATTGA-GTGGCAAACACTCA
*
29986238 AAAAAATATTTTTAAATTTGAAAAATGTGGTGTAGGCCATTGAGTGGCAAACACCCA
1 AAAAAATATTTTTAAATTTGAAAAA-GTGGTGTAGGCCATTGAGTGGCAAACACTCA
* **
29986295 AAAAAATATTTTTAAATTTGAGAAAGTTGGTGTAGATCATTTGA-TGGCAAACACTCAA
1 AAAAAATATTTTTAAATTTGAAAAAG-TGGTGTAGGCCA-TTGAGTGGCAAACACTC-A
* *
29986353 AAAAAATATTTTTAAACTTGGAAAATA-TGGTGTAGGCCATTGAGTGAC-AACACTCA
1 AAAAAATATTTTTAAA-TTTGAAAA-AGTGGTGTAGGCCATTGAGTGGCAAACACTCA
* * *
29986409 AAATAAATATTTTTAAATATGGAAAAAGTGGTGTAGGCAATT-AGGTGACAAACA-TCCA
1 AAA-AAATATTTTTAAAT-TTGAAAAAGTGGTGTAGGCCATTGA-GTGGCAAACACT-CA
29986467 AAAAAATATTTTT
1 AAAAAATATTTTT
29986480 TTTATTCGTA
Statistics
Matches: 256, Mismatches: 27, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
56 8 0.03
57 157 0.61
58 84 0.33
59 6 0.02
60 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (56 bp):
AAAAAATATTTTTAAATTTGAAAAAGTGGTGTAGGCCATTGAGTGGCAAACACTCA
Found at i:29986419 original size:172 final size:172
Alignment explanation
Indices: 29986118--29986479 Score: 445
Period size: 172 Copynumber: 2.1 Consensus size: 172
29986108 ATGGCCTAAC
* * *
29986118 CACCC-AAAAAATATTTTTAAATTTGAAAAAAGTGATGTAGGCCATTGGGTGGCAAACACTCCAA
1 CACCCAAAAAAATATTTTTAAATTTGAAAAAAGTGATGTAGACCATTGGATGGCAAACACTCAAA
* * *
29986182 AAAAATATTTTTAAATCTGAGAAAGATAGTATAAGTCATTAGGTGGCAAATACTCAAAAAAATAT
66 AAAAATATTTTTAAATCTGAGAAAGATAGTATAAGCCATTAGGTGACAAACACTCAAAAAAATAT
* * *
29986247 TTTTAAAT-TTGAAAAATGTGGTGTAGGCCATT-GAGTGGCAAA
131 TTTTAAATATGGAAAAA-GTGGTGTAGGCAATTAG-GTGACAAA
* * * *
29986289 CACCCAAAAAAATATTTTTAAATTTG-AGAAAGTTGGTGTAGATCATTTGATGGCAAACACTCAA
1 CACCCAAAAAAATATTTTTAAATTTGAAAAAAG-TGATGTAGACCATTGGATGGCAAACACTCAA
* *
29986353 AAAAAATATTTTTAAA-CTTG-GAAA-ATATGGTGTAGGCCATT-GAGTGAC-AACACTCAAAAT
65 AAAAAATATTTTTAAATC-TGAGAAAGATA--GTATAAGCCATTAG-GTGACAAACACTCAAAA-
29986413 AAATATTTTTAAATATGGAAAAAGTGGTGTAGGCAATTAGGTGACAAA
125 AAATATTTTTAAATATGGAAAAAGTGGTGTAGGCAATTAGGTGACAAA
*
29986461 CATCCAAAAAAATATTTTT
1 CACCCAAAAAAATATTTTT
29986480 TTTATTCGTA
Statistics
Matches: 166, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
170 3 0.02
171 26 0.16
172 129 0.78
173 8 0.05
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (172 bp):
CACCCAAAAAAATATTTTTAAATTTGAAAAAAGTGATGTAGACCATTGGATGGCAAACACTCAAA
AAAAATATTTTTAAATCTGAGAAAGATAGTATAAGCCATTAGGTGACAAACACTCAAAAAAATAT
TTTTAAATATGGAAAAAGTGGTGTAGGCAATTAGGTGACAAA
Found at i:29986441 original size:115 final size:112
Alignment explanation
Indices: 29986123--29986479 Score: 409
Period size: 115 Copynumber: 3.1 Consensus size: 112
29986113 CTAACCACCC
* * * *
29986123 AAAAAATATTTTTAAATTTGAAAAAAGTGATGTAGGCCATTGGGTGGCAAACACTCCAAAAAAAT
1 AAAAAATATTTTTAAATTGGAAAATA-TGGTGTAGGCCATTGAGTGGCAAACACT-CAAAAAAAT
* * *
29986188 ATTTTTAAATCTGAGAAAGATAGTATA-AGTCATTAGGTGGCAAATACTCA
64 ATTTTTAAAT-TGAGAAAGATGGTGTAGA-TCATTAGGTGGCAAACACTCA
* * *
29986238 AAAAAATATTTTTAAATTTGAAAAATGTGGTGTAGGCCATTGAGTGGCAAACACCCAAAAAAATA
1 AAAAAATATTTTTAAA-TTGGAAAATATGGTGTAGGCCATTGAGTGGCAAACACTCAAAAAAATA
* * *
29986303 TTTTTAAATTTGAGAAAGTTGGTGTAGATCATTTGATGGCAAACACTCAA
65 TTTTTAAA-TTGAGAAAGATGGTGTAGATCATTAGGTGGCAAACACTC-A
*
29986353 AAAAAATATTTTTAAACTTGGAAAATATGGTGTAGGCCATTGAGTGAC-AACACTCAAAATAAAT
1 AAAAAATATTTTTAAA-TTGGAAAATATGGTGTAGGCCATTGAGTGGCAAACACTCAAAA-AAAT
* * *
29986417 ATTTTTAAATATG-GAAAAAGTGGTGTAG-GCAATTAGGTGACAAACA-TCCA
64 ATTTTTAAAT-TGAGAAAGA-TGGTGTAGATC-ATTAGGTGGCAAACACT-CA
29986467 AAAAAATATTTTT
1 AAAAAATATTTTT
29986480 TTTATTCGTA
Statistics
Matches: 209, Mismatches: 24, Indels: 19
0.83 0.10 0.08
Matches are distributed among these distances:
114 79 0.38
115 124 0.59
116 6 0.03
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (112 bp):
AAAAAATATTTTTAAATTGGAAAATATGGTGTAGGCCATTGAGTGGCAAACACTCAAAAAAATAT
TTTTAAATTGAGAAAGATGGTGTAGATCATTAGGTGGCAAACACTCA
Found at i:29986653 original size:102 final size:105
Alignment explanation
Indices: 29986467--29986655 Score: 251
Period size: 102 Copynumber: 1.8 Consensus size: 105
29986457 CAAACATCCA
* **
29986467 AAAAAATATTTTTTTTATTCGTATTTTTTTGGATGTCGGTTATGGATTGACAAACACTCAAAAAA
1 AAAAAATATATTTTTTATTCGTATTTTTTTGGATGTCGGCCATGGATTGACAAACACTCAAAAAA
*
29986532 ATATTTTTTGGACCTAAAAAAGGGGCTTTGGCCGACACCC
66 ATATTTTTTGAACCTAAAAAAGGGGCTTTGGCCGACACCC
* ***
29986572 AAAAAAT-TATTTTTTATTCGTA-TTTTTTGG-TGTCGGCCATGGCTTGATTGACACTCAAAAAA
1 AAAAAATATATTTTTTATTCGTATTTTTTTGGATGTCGGCCATGGATTGACAAACACTCAAAAAA
* **
29986634 TTATTTTTT-AATGTAAAAAAGG
66 ATATTTTTTGAACCTAAAAAAGG
29986656 AGATGTCGGT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
101 10 0.14
102 34 0.47
103 8 0.11
104 14 0.19
105 7 0.10
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (105 bp):
AAAAAATATATTTTTTATTCGTATTTTTTTGGATGTCGGCCATGGATTGACAAACACTCAAAAAA
ATATTTTTTGAACCTAAAAAAGGGGCTTTGGCCGACACCC
Found at i:29992647 original size:14 final size:14
Alignment explanation
Indices: 29992606--29992649 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
29992596 TTTTACATGA
*
29992606 ATAATACAAAAAAA
1 ATAATACAAAAAAT
* *
29992620 ATTATACACCAAAAT
1 ATAATACA-AAAAAT
29992635 ATAATACAAAAAAT
1 ATAATACAAAAAAT
29992649 A
1 A
29992650 AAATTAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAATACAAAAAAT
Found at i:29992681 original size:2 final size:2
Alignment explanation
Indices: 29992668--29992697 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
29992658 AACTTAAATA
*
29992668 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29992698 TAATCCATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29996021 original size:26 final size:26
Alignment explanation
Indices: 29995972--29996021 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
29995962 TTTGTTTAAA
**
29995972 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
29995998 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
29996022 GCAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:29996051 original size:24 final size:24
Alignment explanation
Indices: 29996024--29996072 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29996014 GAGGTTTAGC
29996024 AAATGACATTAAACGATCATAAGT
1 AAATGACATTAAACGATCATAAGT
29996048 AAATGACATTAAACGATCATAAGT
1 AAATGACATTAAACGATCATAAGT
29996072 A
1 A
29996073 GTTGTTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (24 bp):
AAATGACATTAAACGATCATAAGT
Found at i:29999083 original size:17 final size:17
Alignment explanation
Indices: 29999063--29999096 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29999053 TTTTACATGA
*
29999063 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
29999080 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
29999097 AATTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:29999491 original size:15 final size:15
Alignment explanation
Indices: 29999467--29999504 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
29999457 CGTATCAGTA
29999467 TTTT-TTTAAA-AAT
1 TTTTATTTAAATAAT
29999480 TTATTATTTAAATAAT
1 TT-TTATTTAAATAAT
29999496 TTTTATTTA
1 TTTTATTTA
29999505 TTTAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 2 0.09
15 13 0.59
16 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATTTAAATAAT
Found at i:29999510 original size:15 final size:16
Alignment explanation
Indices: 29999471--29999504 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
29999461 TCAGTATTTT
29999471 TTTAAA-AATTTATTA
1 TTTAAATAATTTATTA
29999486 TTTAAATAATTT-TTA
1 TTTAAATAATTTATTA
29999501 TTTA
1 TTTA
29999505 TTTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTAAATAATTTATTA
Found at i:30000307 original size:2 final size:2
Alignment explanation
Indices: 30000302--30000330 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30000292 TATGATTTTC
30000302 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30000331 CTGATGATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30001227 original size:81 final size:83
Alignment explanation
Indices: 30001133--30001429 Score: 245
Period size: 84 Copynumber: 3.6 Consensus size: 83
30001123 AAAATATAAG
* * *
30001133 TTTATTATGTATTAATTTATAATTT-TATTATTTTTGAA-AGGACT-AAAT-AAAAA-AATCATT
1 TTTACTATATATTAATTTATAATTTCT-TTATTTAT-AAGAGGACTGAAATGAAAAATAATCATT
30001193 TTAAGCG-GA-TCAAAGTGCAAT
64 TT-AG-GAGACT-AAAGTGCAAT
* * **
30001214 TTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGATTGAATTGAAAAATTTTCATTTT
1 TTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGACTGAAATGAAAAATAATCATTTT
30001279 AGGAGACTAAAGTGCAAT
66 AGGAGACTAAAGTGCAAT
* ** * * * ** *
30001297 TTTACTATAATATTAATTTATAATTTATCCATTTATAAGAGGATTG-AATTAAAATTTTTAATTT
1 TTTACTAT-ATATTAATTTATAATTTCTTTATTTATAAGAGGACTGAAATGAAAAATAATCA-TT
* *
30001361 TTGAGAGGGAC-AAAGTACAAT
64 TT-AG-GAGACTAAAGTGCAAT
** * *
30001382 TTTACTATATATTAATTTATAAACTATTTATTTATAGGAGGACT-AAAT
1 TTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGACTGAAAT
30001430 TAATATTTTT
Statistics
Matches: 182, Mismatches: 22, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
80 2 0.01
81 35 0.19
82 5 0.03
83 38 0.21
84 79 0.43
85 19 0.10
86 4 0.02
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.43
Consensus pattern (83 bp):
TTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGACTGAAATGAAAAATAATCATTTT
AGGAGACTAAAGTGCAAT
Found at i:30001319 original size:84 final size:84
Alignment explanation
Indices: 30001203--30001449 Score: 311
Period size: 84 Copynumber: 2.9 Consensus size: 84
30001193 TTAAGCGGAT
*
30001203 CAAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGATTGAATTGAAAA
1 CAAAGTGCAATTTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGATTGAATT-AAAA
*
30001268 ATTTTCA-TTTT-AG-GAGA
65 ATTTTAATTTTTGAGAGAGA
**
30001285 CTAAAGTGCAATTTTACTATAATATTAATTTATAATTTATCCATTTATAAGAGGATTGAATTAAA
1 C-AAAGTGCAATTTTACTAT-ATATTAATTTATAATTTATTTATTTATAAGAGGATTGAATTAAA
* *
30001350 ATTTTTAATTTTTGAGAGGGA
64 AATTTTAATTTTTGAGAGAGA
* ** * * * * *
30001371 CAAAGTACAATTTTACTATATATTAATTTATAAACTATTTATTTATAGGAGGACTAAATTAATAT
1 CAAAGTGCAATTTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGATTGAATTAAAAA
*
30001436 TTTTAGTTTTTGAG
66 TTTTAATTTTTGAG
30001450 GCCAAGGCCT
Statistics
Matches: 144, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
82 1 0.01
83 27 0.19
84 93 0.65
85 19 0.13
86 4 0.03
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (84 bp):
CAAAGTGCAATTTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGATTGAATTAAAAA
TTTTAATTTTTGAGAGAGA
Found at i:30024090 original size:90 final size:90
Alignment explanation
Indices: 30023931--30024258 Score: 473
Period size: 90 Copynumber: 3.7 Consensus size: 90
30023921 TGTAGGTCCC
* * * *
30023931 AAAACTTTTCTAAAATTATATTTTGAGCCCAAAACTTTTCCAAAATTACATTTTAACCTTAAAAC
1 AAAACTTTTCTAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAAC
*
30023996 TTTTCCGAAATTACATTTTAACCCT
66 TTTTCCAAAATTACATTTTAACCCT
* * * *
30024021 AAAACTTTTCCAAAATTACATTTTAACCCTAAAAC-TTTCAAAAATTACAATTTAACCCTAAAAC
1 AAAACTTTTCTAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAAC
30024085 TTTTTCCAAAATTACATTTTAACCC-
66 -TTTTCCAAAATTACATTTTAACCCT
* * *
30024110 AAAAGCTTTTCTAAAATTACATTTTGACCCCAAAAC-TTTCCAAAATTACATTTTGACCTTAAAA
1 AAAA-CTTTTCTAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAA
* *
30024174 CTTTTCCAAAATCACATTTTGACCCT
65 CTTTTCCAAAATTACATTTTAACCCT
* *
30024200 AAAACTTTTCTAATATTACATTTTAACCCCAAAACTTTTCCAATATTACATTTTAACCC
1 AAAACTTTTCTAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCC
30024259 CGATTTTGCC
Statistics
Matches: 211, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
89 81 0.38
90 130 0.62
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (90 bp):
AAAACTTTTCTAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAAC
TTTTCCAAAATTACATTTTAACCCT
Found at i:30024259 original size:30 final size:30
Alignment explanation
Indices: 30023928--30024259 Score: 418
Period size: 30 Copynumber: 11.1 Consensus size: 30
30023918 CTCTGTAGGT
* * * *
30023928 CCCAAAACTTTTCTAAAATTATATTTTGAG
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
30023958 CCCAAAACTTTTCCAAAATTACATTTTAAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
** *
30023988 CTTAAAACTTTTCCGAAATTACATTTTAAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
*
30024018 CCTAAAACTTTTCCAAAATTACATTTTAAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
* * *
30024048 CCTAAAAC-TTTCAAAAATTACAATTTAAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
*
30024077 CCTAAAACTTTTTCCAAAATTACATTTTAA-
1 CCCAAAAC-TTTTCCAAAATTACATTTTAAC
* *
30024107 CCCAAAAGCTTTTCTAAAATTACATTTTGAC
1 CCCAAAA-CTTTTCCAAAATTACATTTTAAC
*
30024138 CCCAAAAC-TTTCCAAAATTACATTTTGAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
** * *
30024167 CTTAAAACTTTTCCAAAATCACATTTTGAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
* * *
30024197 CCTAAAACTTTTCTAATATTACATTTTAAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
*
30024227 CCCAAAACTTTTCCAATATTACATTTTAAC
1 CCCAAAACTTTTCCAAAATTACATTTTAAC
30024257 CCC
1 CCC
30024260 GATTTTGCCA
Statistics
Matches: 270, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
29 53 0.20
30 191 0.71
31 26 0.10
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (30 bp):
CCCAAAACTTTTCCAAAATTACATTTTAAC
Found at i:30027027 original size:28 final size:29
Alignment explanation
Indices: 30026996--30027057 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
30026986 TGAAAATGAG
30026996 ATTTTTGGAT-AC-CGGGGGCAAAA-AGGTA
1 ATTTTTGG-TCACTCGGGGGCAAAATA-GTA
*
30027024 ATTTTTGGTCACTCGGGGGTAAAATAGTA
1 ATTTTTGGTCACTCGGGGGCAAAATAGTA
30027053 ATTTT
1 ATTTT
30027058 GGGGAAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 1 0.03
28 10 0.33
29 18 0.60
30 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (29 bp):
ATTTTTGGTCACTCGGGGGCAAAATAGTA
Found at i:30027240 original size:59 final size:59
Alignment explanation
Indices: 30027132--30027299 Score: 173
Period size: 59 Copynumber: 2.8 Consensus size: 59
30027122 AATCGGGATA
* * * * * *
30027132 AAAAATAGAATTTT-GAAAAGTTCGAGGGTAAAAAGGTAATTTTTGGAAAAAATAAGGTC
1 AAAAATGGAATTTTGGAAAGGTT-GCGGGTAAAAATGTAATTTTTAGAAAAAATAAGGCC
* * * * *
30027191 -AAAATGGATTTTTTTGG-AAGTTTAG-GGGTAAAAATGTAAATTTTAGAAAAATTAGGGCC
1 AAAAATGGA--ATTTTGGAAAGGTT-GCGGGTAAAAATGTAATTTTTAGAAAAAATAAGGCC
30027250 AAAAATGGAATTTTGGAAAGGTTGCGGGTAAAAATGTAATTTTTAGAAAA
1 AAAAATGGAATTTTGGAAAGGTTGCGGGTAAAAATGTAATTTTTAGAAAA
30027300 TTCGAGGTCG
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
58 14 0.16
59 57 0.64
60 17 0.19
61 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.30
Consensus pattern (59 bp):
AAAAATGGAATTTTGGAAAGGTTGCGGGTAAAAATGTAATTTTTAGAAAAAATAAGGCC
Found at i:30027246 original size:30 final size:30
Alignment explanation
Indices: 30027212--30027299 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
30027202 TTTTGGAAGT
30027212 TTAGGGGTAAAAATGTAAATTTTAGAAAAA
1 TTAGGGGTAAAAATGTAAATTTTAGAAAAA
** * * **
30027242 TTAGGGCCAAAAATG-GAATTTTGGAAAGG
1 TTAGGGGTAAAAATGTAAATTTTAGAAAAA
*
30027271 TT-GCGGGTAAAAATGTAATTTTTAGAAAA
1 TTAG-GGGTAAAAATGTAAATTTTAGAAAA
30027300 TTCGAGGTCG
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
28 1 0.02
29 21 0.48
30 22 0.50
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.30
Consensus pattern (30 bp):
TTAGGGGTAAAAATGTAAATTTTAGAAAAA
Found at i:30027318 original size:59 final size:59
Alignment explanation
Indices: 30027132--30027327 Score: 157
Period size: 59 Copynumber: 3.3 Consensus size: 59
30027122 AATCGGGATA
* * * * * * * * *
30027132 AAAAATAGAATTTT-GAAAAGTTCGAGGGTAAAAAGGTAATTTTTGGAAAAAATAAGGTC
1 AAAAATGGAATTTTAGAAAGGTT-GCGGGTAAAAATGTAAATTTTAGAAAAATTAGGGCC
* * * *
30027191 -AAAATGGATTTTTTTGGAAGTTTAG-GGGTAAAAATGTAAATTTTAGAAAAATTAGGGCC
1 AAAAATGGA-ATTTTAGAAAGGTT-GCGGGTAAAAATGTAAATTTTAGAAAAATTAGGGCC
* * * *
30027250 AAAAATGGAATTTTGGAAAGGTTGCGGGTAAAAATGTAATTTTTAG-AAAATTCGAGGTC
1 AAAAATGGAATTTTAGAAAGGTTGCGGGTAAAAATGTAAATTTTAGAAAAATTAG-GGCC
* *
30027309 GAAAGTGGAATTTTAGAAA
1 AAAAATGGAATTTTAGAAA
30027328 AGTTCAGGGA
Statistics
Matches: 110, Mismatches: 22, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
58 15 0.14
59 81 0.74
60 14 0.13
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.30
Consensus pattern (59 bp):
AAAAATGGAATTTTAGAAAGGTTGCGGGTAAAAATGTAAATTTTAGAAAAATTAGGGCC
Found at i:30029276 original size:16 final size:16
Alignment explanation
Indices: 30029246--30029322 Score: 57
Period size: 17 Copynumber: 4.8 Consensus size: 16
30029236 CTTTTTAAAG
30029246 TTTAAATTT-AATTAA
1 TTTAAATTTAAATTAA
30029261 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATT-AA
** * * *
30029278 TCCAAACTCAAAATAA
1 TTTAAATTTAAATTAA
* *
30029294 GTTCAAATTTAAATAAA
1 -TTTAAATTTAAATTAA
*
30029311 TTTAAAATTAAA
1 TTTAAATTTAAA
30029323 AAATGGGGTC
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
15 9 0.19
16 16 0.34
17 22 0.47
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.39
Consensus pattern (16 bp):
TTTAAATTTAAATTAA
Found at i:30032144 original size:22 final size:22
Alignment explanation
Indices: 30032119--30032163 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
30032109 TATTGAACTG
*
30032119 TCGCTATATGGGTTGATAAAGA
1 TCGCTATATAGGTTGATAAAGA
30032141 TCGCTATATAGGTTGATAAAGA
1 TCGCTATATAGGTTGATAAAGA
30032163 T
1 T
30032164 AATTAATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (22 bp):
TCGCTATATAGGTTGATAAAGA
Found at i:30032794 original size:90 final size:92
Alignment explanation
Indices: 30032539--30032819 Score: 239
Period size: 90 Copynumber: 3.0 Consensus size: 92
30032529 ATGATAAATC
* * *
30032539 GAAATTATAAATCTTTACAATGAAAATAGAAAAAAAAATTAGTTCAAGAATATAAAATAAAGCAC
1 GAAATTATAAATCTTT-CATTG-AAATAG-AAAAAAAATTAATTCAAGAATATAAAATAGAGCAC
* *
30032604 GTGTAGGTCGATAAACTCATTGCAAAGTACGT
63 GTGTAAGTCGATAAACTCATTACAAAGTA--T
* * * * * * * * *
30032636 GACAATTAATATATAC-ATCATT-AAATACAAAAAAAATAAATCCAAAAACAATATAATAGAACA
1 GA-AATT-ATAAAT-CTTTCATTGAAATAGAAAAAAAATTAATTCAAGAA-TATAAAATAGAGCA
**
30032699 CGTGTAAGTCGATAAACTGGTTAC-AA-T-T
62 CGTGTAAGTCGATAAACTCATTACAAAGTAT
* *
30032727 GAAACTATAAATCTTTGCATTGAAATAGACAAAAAATTAATTCAAGAATATAAAATAGAGCACGT
1 GAAATTATAAATCTTT-CATTGAAATAGAAAAAAAATTAATTCAAGAATATAAAATAGAGCACGT
* * * *
30032792 GTAAGTTGACAAACTCGTTGCAAAGTAT
65 GTAAGTCGATAAACTCATTACAAAGTAT
30032820 ACGTTAAGGA
Statistics
Matches: 143, Mismatches: 31, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
88 1 0.01
89 6 0.04
90 38 0.27
91 26 0.18
92 1 0.01
93 1 0.01
94 1 0.01
95 18 0.13
96 35 0.24
97 2 0.01
98 7 0.05
99 6 0.04
100 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (92 bp):
GAAATTATAAATCTTTCATTGAAATAGAAAAAAAATTAATTCAAGAATATAAAATAGAGCACGTG
TAAGTCGATAAACTCATTACAAAGTAT
Found at i:30032969 original size:182 final size:183
Alignment explanation
Indices: 30032539--30032991 Score: 522
Period size: 182 Copynumber: 2.5 Consensus size: 183
30032529 ATGATAAATC
*
30032539 GAAATTATAAATCTTTACAATGAAAATAGAAAAAAAAATTAGTTCAAGAATATAAAATAAAGCAC
1 GAAATTATAAATCTTTACAATGAAAATAG--AAAAAAATTAGTTCAAGAATATAAAATAGAGCAC
* * * ** * * *
30032604 GTGTAGGTCGATAAACTCATTGCAAAGTACGTGACAATTAATATATACATCATTAAATACAAAAA
64 GTGTAAGTTGATAAACTCGTTGCAAAGTACGT-ACAAGGAATAGACACATCAATAAATACAAAAA
* * *
30032669 AAATAAATCCAAAAACAATATAATAGAACACGTGTAAGTCGATAAACTGGTTACAATT
128 AAAT--ATCCAAAAACAATATAATAGAACACGTGTAAGCCAATAAACTGGTTACAACT
* * * *
30032727 GAAACTATAAATCTTTGCATTG-AAATAGACAAAAAATTAATTCAAGAATATAAAATAGAGCACG
1 GAAATTATAAATCTTTACAATGAAAATAGA-AAAAAATTAGTTCAAGAATATAAAATAGAGCACG
* * *
30032791 TGTAAGTTGACAAACTCGTTGCAAAGTATACGT-TAAGGAATAGGCACATCAATAAATACATAAA
65 TGTAAGTTGATAAACTCGTTGCAAAG--TACGTACAAGGAATAGACACATCAATAAATACA-AAA
* * * *
30032855 AAAAT-T-CAAAAAC-ATATAATAGAACACTTGTATGCCAATAAATTGGTTATAACT
127 AAAATATCCAAAAACAATATAATAGAACACGTGTAAGCCAATAAACTGGTTACAACT
* * * *
30032909 GAAATTATATATCGTTACAACGAAAATAGAAAAAAATTAGTTCAA-AAGTATAAAATAGAGCACT
1 GAAATTATAAATCTTTACAATGAAAATAGAAAAAAATTAGTTCAAGAA-TATAAAATAGAGCACG
*
30032973 TGTAAATTGATAAACTCGT
65 TGTAAGTTGATAAACTCGT
30032992 GATAAAGTAT
Statistics
Matches: 226, Mismatches: 33, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
181 2 0.01
182 96 0.42
183 14 0.06
184 1 0.00
185 1 0.00
186 74 0.33
187 14 0.06
188 24 0.11
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (183 bp):
GAAATTATAAATCTTTACAATGAAAATAGAAAAAAATTAGTTCAAGAATATAAAATAGAGCACGT
GTAAGTTGATAAACTCGTTGCAAAGTACGTACAAGGAATAGACACATCAATAAATACAAAAAAAA
TATCCAAAAACAATATAATAGAACACGTGTAAGCCAATAAACTGGTTACAACT
Found at i:30034244 original size:2 final size:2
Alignment explanation
Indices: 30034237--30034271 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
30034227 TGAAATAAAT
30034237 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30034272 TTTTCTAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30039840 original size:49 final size:50
Alignment explanation
Indices: 30039779--30039902 Score: 166
Period size: 49 Copynumber: 2.5 Consensus size: 50
30039769 TTTTTTTTTC
* * *
30039779 TAGTCTTC-ATCTAATCTCTCA-TCATCTCACTCTCCGTATATATTAATCA
1 TAGTTTTCTATCTAATCTCTCAGTC-TCTCACTCTCCATATATATAAATCA
*
30039828 TAGTTTT-TATCTAATCTCTCAGTCTCTCACTCTCCATATTTATAAATCA
1 TAGTTTTCTATCTAATCTCTCAGTCTCTCACTCTCCATATATATAAATCA
*
30039877 TAGTTTTCT-TCTAATCTCTCACTCTC
1 TAGTTTTCTATCTAATCTCTCAGTCTC
30039903 CATATATATC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
49 64 0.96
50 3 0.04
ACGTcount: A:0.24, C:0.27, G:0.04, T:0.44
Consensus pattern (50 bp):
TAGTTTTCTATCTAATCTCTCAGTCTCTCACTCTCCATATATATAAATCA
Found at i:30041627 original size:29 final size:30
Alignment explanation
Indices: 30041595--30041652 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
30041585 AAAATTTTTT
30041595 ATTTTCCCCCAAAACTTTTAC-TCCCTCTC
1 ATTTTCCCCCAAAACTTTTACTTCCCTCTC
***
30041624 ATTTTCCTGTAAAACTTTTACTTCCCTCT
1 ATTTTCCCCCAAAACTTTTACTTCCCTCT
30041653 AATCCCACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.21, C:0.34, G:0.02, T:0.43
Consensus pattern (30 bp):
ATTTTCCCCCAAAACTTTTACTTCCCTCTC
Found at i:30052441 original size:75 final size:75
Alignment explanation
Indices: 30052356--30052500 Score: 263
Period size: 75 Copynumber: 1.9 Consensus size: 75
30052346 GCTGAAATTA
* * *
30052356 TATAGTCATAAACTATAGTTGGCTTCATTTGGATGTTGAAACATTATCATGCCAAAAGCTCAGCA
1 TATAGTCATAAACTATAGTTGGCCTCATTTGGATATTGAAACATTATCATGCCAAAAGCACAGCA
30052421 TGAATGAAAT
66 TGAATGAAAT
30052431 TATAGTCATAAACTATAGTTGGCCTCATTTGGATATTGAAACATTATCATGCCAAAAGCACAGCA
1 TATAGTCATAAACTATAGTTGGCCTCATTTGGATATTGAAACATTATCATGCCAAAAGCACAGCA
30052496 TGAAT
66 TGAAT
30052501 CTCCAATTAA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (75 bp):
TATAGTCATAAACTATAGTTGGCCTCATTTGGATATTGAAACATTATCATGCCAAAAGCACAGCA
TGAATGAAAT
Found at i:30056870 original size:6 final size:6
Alignment explanation
Indices: 30056859--30056888 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
30056849 TCCGTACATA
30056859 GAGTTT GAGTTT GAGTTT GAGTTT GAGTTT
1 GAGTTT GAGTTT GAGTTT GAGTTT GAGTTT
30056889 AATATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
GAGTTT
Found at i:30058771 original size:38 final size:38
Alignment explanation
Indices: 30058729--30058841 Score: 91
Period size: 38 Copynumber: 3.2 Consensus size: 38
30058719 TCAATTACCG
30058729 AAAATATTATTTTTATATAATCTTACATTCAATATTAA
1 AAAATATTATTTTTATATAATCTTACATTCAATATTAA
* ** *
30058767 AAAATACATATTATTT-TA-AAGGTTAAATT---TATT--
1 AAAATA-TTATT-TTTATATAATCTTACATTCAATATTAA
* *
30058800 --ATTTTTATTTTTATATAATCTTACATTCAATATTAA
1 AAAATATTATTTTTATATAATCTTACATTCAATATTAA
30058836 AAAATA
1 AAAATA
30058842 CATATTATTT
Statistics
Matches: 52, Mismatches: 12, Indels: 22
0.60 0.14 0.26
Matches are distributed among these distances:
29 3 0.06
30 6 0.12
31 10 0.19
34 4 0.08
35 4 0.08
38 16 0.31
39 6 0.12
40 3 0.06
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (38 bp):
AAAATATTATTTTTATATAATCTTACATTCAATATTAA
Found at i:30058838 original size:69 final size:69
Alignment explanation
Indices: 30058735--30058871 Score: 265
Period size: 69 Copynumber: 2.0 Consensus size: 69
30058725 ACCGAAAATA
*
30058735 TTATTTTTATATAATCTTACATTCAATATTAAAAAATACATATTATTTTAAAGGTTAAATTTATT
1 TTATTTTTATATAATCTTACATTCAATATTAAAAAATACATATTATTTTAAAGGCTAAATTTATT
30058800 ATTT
66 ATTT
30058804 TTATTTTTATATAATCTTACATTCAATATTAAAAAATACATATTATTTTAAAGGCTAAATTTATT
1 TTATTTTTATATAATCTTACATTCAATATTAAAAAATACATATTATTTTAAAGGCTAAATTTATT
30058869 ATT
66 ATT
30058872 ATATCAATTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.50
Consensus pattern (69 bp):
TTATTTTTATATAATCTTACATTCAATATTAAAAAATACATATTATTTTAAAGGCTAAATTTATT
ATTT
Found at i:30077447 original size:35 final size:35
Alignment explanation
Indices: 30077377--30077447 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
30077367 TGTTCATCTA
*
30077377 ATTTTACATATAAAAAAATTAATGATATTCGAAAT
1 ATTTTACATATAAAAAAATTAATGATATTCAAAAT
* *
30077412 ATTTTACATATAAAAATAA-TAATTATATTTAAAAT
1 ATTTTACATATAAAAA-AATTAATGATATTCAAAAT
30077447 A
1 A
30077448 ATTATTTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 30 0.94
36 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (35 bp):
ATTTTACATATAAAAAAATTAATGATATTCAAAAT
Found at i:30077674 original size:28 final size:27
Alignment explanation
Indices: 30077637--30077689 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
30077627 TATATTTTTA
* * *
30077637 TTATAATAAAATATTTATTATTTAATT
1 TTATAATAAAAGAATTATTAATTAATT
30077664 TTATGAATAAAAGAATTATTAATTAA
1 TTAT-AATAAAAGAATTATTAATTAA
30077690 AAAGATGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (27 bp):
TTATAATAAAAGAATTATTAATTAATT
Found at i:30077773 original size:37 final size:35
Alignment explanation
Indices: 30077697--30077778 Score: 85
Period size: 37 Copynumber: 2.3 Consensus size: 35
30077687 TAAAAAGATG
** **
30077697 AATTAAAAATAAAAATTGAAAATAATATATTTATT
1 AATTAAAAATAAAAATTGAAAATAATATAAATAAA
30077732 AATTAAAAATAAAAAACTTG-AAATAATATGAAATAAA
1 AATTAAAAAT-AAAAA-TTGAAAATAATAT-AAATAAA
*
30077769 AATTACAAAT
1 AATTAAAAAT
30077779 GTGTTTAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
35 10 0.26
36 14 0.36
37 15 0.38
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (35 bp):
AATTAAAAATAAAAATTGAAAATAATATAAATAAA
Found at i:30102463 original size:15 final size:15
Alignment explanation
Indices: 30102443--30102474 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
30102433 AAAAATTAAG
30102443 TGTGTTAAGGGGGCA
1 TGTGTTAAGGGGGCA
30102458 TGTGTTAAGGGGGCA
1 TGTGTTAAGGGGGCA
30102473 TG
1 TG
30102475 CTCTTGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.47, T:0.28
Consensus pattern (15 bp):
TGTGTTAAGGGGGCA
Found at i:30102757 original size:43 final size:43
Alignment explanation
Indices: 30102681--30102764 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
30102671 TTTAATTGTT
30102681 TTATTTTTTATTTTATTTTTGAAACAAATAAAATTACATTTTAA
1 TTATTTTTTATTTTATTTTTGAAACAAATAAAATTA-ATTTTAA
**
30102725 TTATTTTATT-TTTTA-TTTTGAAGTAAATAAAATTAATTTT
1 TTATTTT-TTATTTTATTTTTGAAACAAATAAAATTAATTTT
30102765 TAGTTTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 5 0.14
43 18 0.49
44 12 0.32
45 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (43 bp):
TTATTTTTTATTTTATTTTTGAAACAAATAAAATTAATTTTAA
Found at i:30102766 original size:43 final size:41
Alignment explanation
Indices: 30102663--30102766 Score: 111
Period size: 43 Copynumber: 2.5 Consensus size: 41
30102653 ATCTCAAGTT
* * *
30102663 TAAATTAATTTAATTGTTTTATTTTTTATTTTATTTTTGAAA
1 TAAATAAAATTAATT-TTTAATTTTTTATTTTATTTTTGAAA
* * *
30102705 CAAATAAAATTACA-TTTTAATTATTTTATTTTTTATTTTGAAG
1 TAAATAAAATTA-ATTTTTAATT-TTTTATTTTAT-TTTTGAAA
30102748 TAAATAAAATTAATTTTTA
1 TAAATAAAATTAATTTTTA
30102767 GTTTAAATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
41 6 0.12
42 21 0.41
43 24 0.47
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (41 bp):
TAAATAAAATTAATTTTTAATTTTTTATTTTATTTTTGAAA
Found at i:30107947 original size:19 final size:19
Alignment explanation
Indices: 30107905--30107948 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
30107895 GTTAGATTTT
* *
30107905 TTAAAAATGTTAACAGATA
1 TTAAAAATATTAAAAGATA
* *
30107924 ATAAAAATATTAAAATATA
1 TTAAAAATATTAAAAGATA
30107943 TTAAAA
1 TTAAAA
30107949 TTGCACAACA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (19 bp):
TTAAAAATATTAAAAGATA
Found at i:30121658 original size:33 final size:33
Alignment explanation
Indices: 30121572--30121658 Score: 131
Period size: 33 Copynumber: 2.7 Consensus size: 33
30121562 ATAAATGATT
*
30121572 TTTTAATAA-TTCACAATTGAAAACATAAATAA
1 TTTTAATAATTTCACAATTGAGAACATAAATAA
*
30121604 TTTTAATAATTTCACAATTGAGATCATAAATAA
1 TTTTAATAATTTCACAATTGAGAACATAAATAA
* *
30121637 TTTTAGTAATTTTACAATTGAG
1 TTTTAATAATTTCACAATTGAG
30121659 TTAAATTCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 9 0.18
33 41 0.82
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (33 bp):
TTTTAATAATTTCACAATTGAGAACATAAATAA
Found at i:30123905 original size:18 final size:17
Alignment explanation
Indices: 30123874--30123907 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30123864 CATCATAATT
*
30123874 ATTAAATAATAATCTAA
1 ATTAAATAAGAATCTAA
30123891 ATTAGAATAAGAATCTA
1 ATTA-AATAAGAATCTA
30123908 TACTATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (17 bp):
ATTAAATAAGAATCTAA
Found at i:30126338 original size:41 final size:41
Alignment explanation
Indices: 30126293--30126372 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
30126283 TGAAGAACCC
30126293 TAAATCCCAAATTCTCTCATTCTCCATTCAAATTCTTTAGA
1 TAAATCCCAAATTCTCTCATTCTCCATTCAAATTCTTTAGA
*
30126334 TAAATCCCAAATTCTCTCATTCTCCATTTAAATTCTTTA
1 TAAATCCCAAATTCTCTCATTCTCCATTCAAATTCTTTA
30126373 AAAATTGAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.31, C:0.26, G:0.01, T:0.41
Consensus pattern (41 bp):
TAAATCCCAAATTCTCTCATTCTCCATTCAAATTCTTTAGA
Found at i:30126370 original size:114 final size:114
Alignment explanation
Indices: 30126221--30126448 Score: 370
Period size: 115 Copynumber: 2.0 Consensus size: 114
30126211 TTTGAAGAAC
* * *
30126221 TAAATCTCAAATTCTTCCCTTTCCATTCAAATTCTTTAAAAATTGAAGCTTGAAACTC-CCTTTG
1 TAAATCCCAAATTCTTCCATTTCCATTCAAATTCTTTAAAAATTGAAGCTTGAAACTCTCCTTTA
30126285 AAGAACCCTAAATCCCAAATTCTCTCATTCTCCATTCAAATTCTTTAGA
66 AAGAACCCTAAATCCCAAATTCTCTCATTCTCCATTCAAATTCTTTAGA
*
30126334 TAAATCCCAAATTC-TCTCATTCTCCATTTAAATTCTTTAAAAATTGAAGCTTGAAACTCTCCTT
1 TAAATCCCAAATTCTTC-CATT-TCCATTCAAATTCTTTAAAAATTGAAGCTTGAAACTCTCCTT
* *
30126398 TAAAGAACCCTAAATCTCAAATTCTCTCATTTTCCATTCAAATTCTTTAGA
64 TAAAGAACCCTAAATCCCAAATTCTCTCATTCTCCATTCAAATTCTTTAGA
30126449 AATTAAAGCT
Statistics
Matches: 106, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
112 2 0.02
113 16 0.15
114 36 0.34
115 52 0.49
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (114 bp):
TAAATCCCAAATTCTTCCATTTCCATTCAAATTCTTTAAAAATTGAAGCTTGAAACTCTCCTTTA
AAGAACCCTAAATCCCAAATTCTCTCATTCTCCATTCAAATTCTTTAGA
Found at i:30128111 original size:16 final size:18
Alignment explanation
Indices: 30128083--30128120 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
30128073 AATTGGCTTA
30128083 TTATTTCTTGTTCTA-TT
1 TTATTTCTTGTTCTACTT
30128100 TTATTT-TTGTTCTACTT
1 TTATTTCTTGTTCTACTT
30128117 TTAT
1 TTAT
30128121 AATTCATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.13, C:0.11, G:0.05, T:0.71
Consensus pattern (18 bp):
TTATTTCTTGTTCTACTT
Found at i:30128338 original size:7 final size:7
Alignment explanation
Indices: 30128328--30128511 Score: 175
Period size: 7 Copynumber: 26.3 Consensus size: 7
30128318 TTCCTGTTTC
*
30128328 CCGTCAT
1 CCGTTAT
30128335 CCGTT-T
1 CCGTTAT
30128341 CCCGTTAT
1 -CCGTTAT
30128349 CCGTTAT
1 CCGTTAT
*
30128356 CCTTTAT
1 CCGTTAT
30128363 CCGTTAT
1 CCGTTAT
30128370 CCGTTAT
1 CCGTTAT
30128377 CCGTT-T
1 CCGTTAT
30128383 CCCGTTAT
1 -CCGTTAT
30128391 CCGTTAT
1 CCGTTAT
30128398 CCGTTAT
1 CCGTTAT
*
30128405 CTGTTAT
1 CCGTTAT
30128412 CCGTTAT
1 CCGTTAT
30128419 CCGTT-T
1 CCGTTAT
30128425 CCCGTT-T
1 -CCGTTAT
30128432 CCCGTTAT
1 -CCGTTAT
*
30128440 CCATT-T
1 CCGTTAT
30128446 CCCGTTAT
1 -CCGTTAT
30128454 CCGTTAT
1 CCGTTAT
30128461 CCGTTAT
1 CCGTTAT
*
30128468 TCGTT-T
1 CCGTTAT
30128474 CCCGTT-T
1 -CCGTTAT
*
30128481 CCCGTCAT
1 -CCGTTAT
*
30128489 CCGTCAT
1 CCGTTAT
*
30128496 CCGTCAT
1 CCGTTAT
*
30128503 CCGTCAT
1 CCGTTAT
30128510 CC
1 CC
30128512 TAAACCCTAA
Statistics
Matches: 157, Mismatches: 10, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
6 5 0.03
7 147 0.94
8 5 0.03
ACGTcount: A:0.11, C:0.35, G:0.13, T:0.41
Consensus pattern (7 bp):
CCGTTAT
Found at i:30128339 original size:21 final size:21
Alignment explanation
Indices: 30128313--30128465 Score: 197
Period size: 21 Copynumber: 7.3 Consensus size: 21
30128303 ATTCGCATTG
* *
30128313 TCCGTTTCCTGTT-TCCCGTCA
1 TCCGTTTCCCGTTAT-CCGTTA
30128334 TCCGTTTCCCGTTATCCGTTA
1 TCCGTTTCCCGTTATCCGTTA
*
30128355 TCC-TTTATCCGTTATCCGTTA
1 TCCGTTT-CCCGTTATCCGTTA
30128376 TCCGTTTCCCGTTATCCGTTA
1 TCCGTTTCCCGTTATCCGTTA
*
30128397 TCCGTTAT-CTGTTATCCGTTA
1 TCCGTT-TCCCGTTATCCGTTA
30128418 TCCGTTTCCCGTT-TCCCGTTA
1 TCCGTTTCCCGTTAT-CCGTTA
*
30128439 TCCATTTCCCGTTATCCGTTA
1 TCCGTTTCCCGTTATCCGTTA
30128460 TCCGTT
1 TCCGTT
30128466 ATTCGTTTCC
Statistics
Matches: 117, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.04
21 106 0.91
22 6 0.05
ACGTcount: A:0.10, C:0.33, G:0.13, T:0.44
Consensus pattern (21 bp):
TCCGTTTCCCGTTATCCGTTA
Found at i:30128520 original size:7 final size:7
Alignment explanation
Indices: 30128510--30129074 Score: 975
Period size: 7 Copynumber: 80.9 Consensus size: 7
30128500 CATCCGTCAT
30128510 CCTAAAC
1 CCTAAAC
30128517 CCTAAAC
1 CCTAAAC
30128524 CCTAAAC
1 CCTAAAC
30128531 CCTAAAC
1 CCTAAAC
30128538 CCTAAAC
1 CCTAAAC
30128545 CCTAAAC
1 CCTAAAC
30128552 CCTAAAC
1 CCTAAAC
30128559 CCTAAAC
1 CCTAAAC
30128566 CCTAAAC
1 CCTAAAC
30128573 CCTAAAC
1 CCTAAAC
30128580 CCT-AAC
1 CCTAAAC
30128586 CCTAAAC
1 CCTAAAC
30128593 CCTAAAC
1 CCTAAAC
30128600 CCTAAAC
1 CCTAAAC
30128607 CCTAAAC
1 CCTAAAC
30128614 CCTAAAC
1 CCTAAAC
30128621 CCTAAAAC
1 CCT-AAAC
30128629 CCTAAAC
1 CCTAAAC
30128636 CCTAAAC
1 CCTAAAC
30128643 CCTAAAC
1 CCTAAAC
30128650 CCTAAAC
1 CCTAAAC
30128657 CCT-AAC
1 CCTAAAC
30128663 CCTAAAC
1 CCTAAAC
30128670 CCTAAAC
1 CCTAAAC
30128677 CCTAAA-
1 CCTAAAC
30128683 CCTAAAC
1 CCTAAAC
30128690 CCTAAAC
1 CCTAAAC
30128697 CCTAAAC
1 CCTAAAC
30128704 CCTAAAC
1 CCTAAAC
30128711 CCTAAAC
1 CCTAAAC
30128718 CCTAAAC
1 CCTAAAC
30128725 CCTAAAC
1 CCTAAAC
30128732 CCTAAAC
1 CCTAAAC
30128739 CCTAAAC
1 CCTAAAC
30128746 CCTAAAC
1 CCTAAAC
30128753 CCTAAAC
1 CCTAAAC
30128760 CCTAAAC
1 CCTAAAC
*
30128767 CCGT-CAC
1 CC-TAAAC
30128774 CCTAAAC
1 CCTAAAC
*
30128781 CCGT-CAC
1 CC-TAAAC
30128788 CCTAAAC
1 CCTAAAC
*
30128795 CCGT-CAC
1 CC-TAAAC
*
30128802 CCGT-CAC
1 CC-TAAAC
30128809 CCTAAAC
1 CCTAAAC
30128816 CCTAAAC
1 CCTAAAC
30128823 CCTAAAC
1 CCTAAAC
30128830 CCTAAAC
1 CCTAAAC
30128837 CCTAAAC
1 CCTAAAC
30128844 CCTAAAC
1 CCTAAAC
30128851 CCTAAAC
1 CCTAAAC
30128858 CCTAAAC
1 CCTAAAC
30128865 CCTAAAC
1 CCTAAAC
30128872 CCTAAAC
1 CCTAAAC
30128879 CCTAAAC
1 CCTAAAC
30128886 CCTAAAAAC
1 CCT--AAAC
30128895 CCTAAAC
1 CCTAAAC
30128902 CCTAAAC
1 CCTAAAC
30128909 CCTAAAC
1 CCTAAAC
30128916 CCTAAAC
1 CCTAAAC
30128923 CCTAAAC
1 CCTAAAC
30128930 CCTAAAC
1 CCTAAAC
30128937 CCTAAAC
1 CCTAAAC
30128944 CCTAAAC
1 CCTAAAC
30128951 CCTAAAC
1 CCTAAAC
30128958 CCTAAAC
1 CCTAAAC
30128965 CCTAAAC
1 CCTAAAC
30128972 CCTAAAC
1 CCTAAAC
30128979 CCTAAAC
1 CCTAAAC
30128986 CCTAAAC
1 CCTAAAC
30128993 CCTAAAC
1 CCTAAAC
30129000 CCTAAAC
1 CCTAAAC
30129007 CCTAAAC
1 CCTAAAC
30129014 CCTAAAC
1 CCTAAAC
30129021 CCTAAAC
1 CCTAAAC
30129028 CCT-AAC
1 CCTAAAC
30129034 CCTAAAC
1 CCTAAAC
30129041 CCTAAAC
1 CCTAAAC
30129048 CCTAAAC
1 CCTAAAC
30129055 CCTAAAC
1 CCTAAAC
30129062 CCTAAAC
1 CCTAAAC
30129069 CCTAAA
1 CCTAAA
30129075 AATATAAGAT
Statistics
Matches: 539, Mismatches: 6, Indels: 26
0.94 0.01 0.05
Matches are distributed among these distances:
6 27 0.05
7 495 0.92
8 10 0.02
9 7 0.01
ACGTcount: A:0.42, C:0.43, G:0.01, T:0.14
Consensus pattern (7 bp):
CCTAAAC
Found at i:30134685 original size:13 final size:13
Alignment explanation
Indices: 30134664--30134701 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
30134654 TCGAGTTTGA
*
30134664 TTATGTGTATTTT
1 TTATTTGTATTTT
30134677 TTATTTGTATTTT
1 TTATTTGTATTTT
30134690 TTAATTT-TATTT
1 TT-ATTTGTATTT
30134702 ATTTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (13 bp):
TTATTTGTATTTT
Done.