Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, whole genome shotgun sequence
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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 12 of 91
Found at i:2108381 original size:31 final size:31
Alignment explanation
Indices: 2108345--2108425 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
2108335 ATTAGAAGGA
* *
2108345 TAAATTTTAAATTTTATGCAAGTATATGGAC
1 TAAATTTTAAATTTTATGCAAGTATAAGAAC
*
2108376 TAAATTTTAAATTTTATGCAAGTATAAGAAT
1 TAAATTTTAAATTTTATGCAAGTATAAGAAC
2108407 TAAATTTTAAATTTGTATG
1 TAAATTTTAAATTT-TATG
2108426 AGTATAGGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 42 0.91
32 4 0.09
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (31 bp):
TAAATTTTAAATTTTATGCAAGTATAAGAAC
Found at i:2111365 original size:8 final size:7
Alignment explanation
Indices: 2111331--2111458 Score: 67
Period size: 6 Copynumber: 18.6 Consensus size: 7
2111321 TTTATGTATT
2111331 TTAT-TA
1 TTATATA
*
2111337 TTATTTA
1 TTATATA
2111344 TTAT-TA
1 TTATATA
2111350 TTATATA
1 TTATATA
2111357 TTAATATA
1 TT-ATATA
*
2111365 TGTATATC
1 T-TATATA
2111373 TT-TAT-
1 TTATATA
*
2111378 TTATTTA
1 TTATATA
*
2111385 TTTATTTA
1 -TTATATA
* *
2111393 TTTTCTA
1 TTATATA
2111400 TTA-ATA
1 TTATATA
2111406 TT-TATA
1 TTATATA
2111412 TGTATTATA
1 T-TA-TATA
2111421 TTTATATA
1 -TTATATA
*
2111429 GT-TATA
1 TTATATA
2111435 -TATATA
1 TTATATA
2111441 TTATTATA
1 TTA-TATA
2111449 TTAT-TA
1 TTATATA
2111455 TTAT
1 TTAT
2111459 TTTTTTCTCT
Statistics
Matches: 100, Mismatches: 7, Indels: 30
0.73 0.05 0.22
Matches are distributed among these distances:
5 3 0.03
6 37 0.37
7 23 0.23
8 29 0.29
9 7 0.07
10 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (7 bp):
TTATATA
Found at i:2111402 original size:56 final size:56
Alignment explanation
Indices: 2111321--2111457 Score: 131
Period size: 56 Copynumber: 2.5 Consensus size: 56
2111311 TCTTTTGTAT
*
2111321 TTTATGTATTTTATTATTATTTATTATTATTATATAT-TAATATATGTATATCTTTA
1 TTTATGTATTTTATTATTATTTATTAATATT-TATATGTAATATATGTATATCTTTA
* * * **
2111377 TTTATTTA-TTTATTTATT-TTCTATTAATATTTATATGTATTATATTTATATAGTTA
1 TTTATGTATTTTA-TTATTATT-TATTAATATTTATATGTAATATATGTATATCTTTA
* *
2111433 TATATATATTATTA-TATTA-TTATTA
1 TTTATGTATT-TTATTATTATTTATTA
2111458 TTTTTTTCTC
Statistics
Matches: 67, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
55 16 0.24
56 47 0.70
57 1 0.01
58 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (56 bp):
TTTATGTATTTTATTATTATTTATTAATATTTATATGTAATATATGTATATCTTTA
Found at i:2111456 original size:66 final size:65
Alignment explanation
Indices: 2111332--2111461 Score: 144
Period size: 66 Copynumber: 2.0 Consensus size: 65
2111322 TTATGTATTT
* * *
2111332 TATTATTATTTATTATTATTATATATTAATATATGTATATCTTTATTTATTTATTTATTTATTTT
1 TATTAATATTTATTATTATTATATATTAATATATATATATCATTATTTATTTATTTA-TTATTTT
2111397 C
65 C
2111398 TATTAATATTTA-TATGTATTATAT-TTATATAGTTATATATAT-ATTA-TTATATTA-TTATTA
1 TATTAATATTTATTAT-TATTATATATTA-ATA--TATATATATCATTATTTAT-TTATTTATTA
2111458 TTTT
61 TTTT
2111462 TTTCTCTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
65 13 0.23
66 29 0.52
67 6 0.11
68 8 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (65 bp):
TATTAATATTTATTATTATTATATATTAATATATATATATCATTATTTATTTATTTATTATTTTC
Found at i:2111906 original size:26 final size:25
Alignment explanation
Indices: 2111862--2111916 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
2111852 CTGGGAGTGA
*
2111862 GAAAAATTTTTTTAGAAATTTTTGG
1 GAAAAATTTTTTTAGAAATTTCTGG
2111887 CGAAAAATTTTTTT-GAAAATTTCTGG
1 -GAAAAATTTTTTTAG-AAATTTCTGG
2111913 GAAA
1 GAAA
2111917 TTTCCAGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (25 bp):
GAAAAATTTTTTTAGAAATTTCTGG
Found at i:2112429 original size:6 final size:6
Alignment explanation
Indices: 2112409--2112451 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
2112399 TTTAATATTC
*
2112409 TTTTAT CTTTA- TTTTAT TTTTAT TTTGT-T TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT TTTTAT TTTTAT TT
2112452 ATTTTCACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.16
6 26 0.81
7 1 0.03
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:2112468 original size:29 final size:28
Alignment explanation
Indices: 2112409--2112480 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
2112399 TTTAATATTC
* * **
2112409 TTTTATCTTTATTTTATTTTTATTTTGTT
1 TTTTATTTTTA-TTTATTTTCATTTCATT
2112438 TTTTATTTTTATTTATTTTCACTTTCATT
1 TTTTATTTTTATTTATTTTCA-TTTCATT
*
2112467 TTTTTTATTTTATT
1 TTTTAT-TTTTATT
2112481 ATTCTATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 9 0.25
29 20 0.56
30 7 0.19
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (28 bp):
TTTTATTTTTATTTATTTTCATTTCATT
Found at i:2112489 original size:22 final size:21
Alignment explanation
Indices: 2112425--2112495 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
2112415 CTTTATTTTA
* *
2112425 TTTTTATTTTGTTTTTTATTT
1 TTTTTATTTTATTTTCTATTT
*
2112446 TTATTTATTTTCACTTTC-ATTT
1 TT-TTTATTTT-ATTTTCTATTT
2112468 TTTTTATTTTATTATTCTATTT
1 TTTTTATTTTATT-TTCTATTT
*
2112490 TCTTTA
1 TTTTTA
2112496 AATAAAAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
20 2 0.05
21 13 0.32
22 23 0.56
23 3 0.07
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.76
Consensus pattern (21 bp):
TTTTTATTTTATTTTCTATTT
Found at i:2112629 original size:118 final size:119
Alignment explanation
Indices: 2112500--2113026 Score: 659
Period size: 118 Copynumber: 4.5 Consensus size: 119
2112490 TCTTTAAATA
*
2112500 AAAATCAAAATTTTCAAAAAAAATAGTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAA
1 AAAATCAAAA-TTTC-AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAA
**** *
2112565 TAAA-TTTC-AAAAAGGGGTTTTTGAAG-AAAAGTTGAAAGTATCAATTTTCCTTG
64 TAAATTTTCAAAAAAAATATTTTTGAGGAAAAAGTTGAAAGTATCAATTTTCCTTG
* * * *
2112618 AAAATCAAAATTTCTAAAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTTAGAAATA
1 AAAATCAAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATA
*
2112683 AATTTTTC-AAAAAAATATTTTT-AGGAAAAAGTTAAAAGTATCAATTTTCCTTG
66 AA-TTTTCAAAAAAAATATTTTTGAGGAAAAAGTTGAAAGTATCAATTTTCCTTG
*** * * * *
2112736 AAAATCAAAATTTTTGAAAAGTATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTAGAAATA
1 AAAATCAAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATA
2112801 AATTTTCAAAAAAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTT-
66 AATTTTC----AAAAAAAATATTTTTGAGGAAAAAGTTGAAAGTATCAATTTTCCTTG
*
2112857 AAGAAT--AAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAT
1 AA-AATCAAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
* *
2112919 AAATTTCCAAAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCC-TA
65 AAATTTTC-AAAAAAAATATTTTTGAGGAAAAAGTTGAAAGTATCAA-TTTTCCTTG
*
2112974 AAAAT--AAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAATCAAAATTT-CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
2113027 TTCTACACAA
Statistics
Matches: 368, Mismatches: 27, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
115 2 0.01
116 93 0.25
117 58 0.16
118 112 0.30
119 11 0.03
120 45 0.12
121 2 0.01
122 42 0.11
123 3 0.01
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (119 bp):
AAAATCAAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATA
AATTTTCAAAAAAAATATTTTTGAGGAAAAAGTTGAAAGTATCAATTTTCCTTG
Found at i:2113029 original size:59 final size:58
Alignment explanation
Indices: 2112511--2113026 Score: 591
Period size: 59 Copynumber: 8.8 Consensus size: 58
2112501 AAATCAAAAT
* *
2112511 TTTCAAAAAAAATAGTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
1 TTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
**** * *
2112569 TTT-CAAAAAGGGGTTTTT-GAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAA
1 TTTCCAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAA
* * * *
2112628 TTT-CTAAAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTTAGAAATAAA
1 TTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
* * * *
2112685 TTTTTCAAAAAAATATTTTTAGGAAAAAGTTAAAAGTATCAATTTTCCTTGAAAATCAAAA
1 -TTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAA
*** * * * *
2112746 TTT-TTGAAAAGTATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTAGAAATAAA
1 TTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
* *
2112803 TTTTCAAAAAAAAAAAATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAA
1 -TTTC----CAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
2112866 TTTCC-AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAA
1 TTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
2112922 TTTCCAAAAAAAAATATTTTT-GGGAAAAAGTTGAAAGTATCAATTTTTCC-TAAAAATAAA
1 TTTCC--AAAAAAATATTTTTAGGG-AAAAGTTGAAAGTATCAA-TTTTCCTTAAAAATAAA
*
2112982 TTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 TTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
2113027 TTCTACACAA
Statistics
Matches: 394, Mismatches: 41, Indels: 47
0.82 0.09 0.10
Matches are distributed among these distances:
56 13 0.03
57 92 0.23
58 45 0.11
59 169 0.43
60 23 0.06
61 3 0.01
62 5 0.01
63 44 0.11
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (58 bp):
TTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
Found at i:2120165 original size:21 final size:21
Alignment explanation
Indices: 2120139--2120199 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
2120129 CAAAGAAACG
*
2120139 TTTTTTTTTTCTTTTTTGCTT
1 TTTTTTTTTTCTTTTTTCCTT
*
2120160 TTTTTTTTGTCTTTTTTTCCTT
1 TTTTTTTTTTC-TTTTTTCCTT
*
2120182 TTTGCTTTTTT-TTTTTTC
1 TTT-TTTTTTTCTTTTTTC
2120200 GGTTTCGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 17 0.50
22 12 0.35
23 5 0.15
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (21 bp):
TTTTTTTTTTCTTTTTTCCTT
Found at i:2121024 original size:20 final size:21
Alignment explanation
Indices: 2120986--2121029 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2120976 AAAATTTTTT
2120986 ATTAAAAATAATTAAATTAAA
1 ATTAAAAATAATTAAATTAAA
* *
2121007 ATTAAAATTAA-TATATTAAA
1 ATTAAAAATAATTAAATTAAA
2121027 ATT
1 ATT
2121030 TTTTGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAAAAATAATTAAATTAAA
Found at i:2121108 original size:13 final size:12
Alignment explanation
Indices: 2121056--2121132 Score: 54
Period size: 13 Copynumber: 6.4 Consensus size: 12
2121046 AAGTGTGTAA
2121056 ATTTTAA-AAA-
1 ATTTTAATAAAT
2121066 ATTTTAATAAAT
1 ATTTTAATAAAT
*
2121078 -TTTATATATATAT
1 ATTT-TA-ATAAAT
*
2121091 TTTTTAGATAAAT
1 ATTTTA-ATAAAT
*
2121104 ATTTTTAATAAAA
1 A-TTTTAATAAAT
*
2121117 ATATTAATAAA-
1 ATTTTAATAAAT
2121128 ATTTT
1 ATTTT
2121133 TATTATCAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
10 7 0.13
11 10 0.19
12 11 0.20
13 18 0.33
14 8 0.15
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (12 bp):
ATTTTAATAAAT
Found at i:2121294 original size:24 final size:24
Alignment explanation
Indices: 2121233--2121296 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
2121223 ATTTAAATTT
*
2121233 TTTATTAAATTATTTTTTAAAAAAA
1 TTTATTAAATT-TTATTTAAAAAAA
*
2121258 TTTCA-TAACTTTTATTT-AAAAAA
1 TTT-ATTAAATTTTATTTAAAAAAA
2121281 TTTATGTAAATTTTAT
1 TTTAT-TAAATTTTAT
2121297 CCGTAATAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 1 0.03
23 9 0.27
24 14 0.42
25 8 0.24
26 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTATTAAATTTTATTTAAAAAAA
Found at i:2123131 original size:21 final size:22
Alignment explanation
Indices: 2123101--2123152 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
2123091 GATATTTTAA
2123101 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
2123121 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
2123143 AATATTTTAT
1 AATATTTTAT
2123153 TAATTTCGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:2124013 original size:8 final size:8
Alignment explanation
Indices: 2124000--2124043 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
2123990 CATGGCACTC
2124000 TTTTTTTA
1 TTTTTTTA
2124008 TTTTTTTA
1 TTTTTTTA
*
2124016 TTTTCCTTA
1 TTTT-TTTA
2124025 TTTTTCCTTA
1 TTTTT--TTA
2124035 TTTTTTTA
1 TTTTTTTA
2124043 T
1 T
2124044 ATTTAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
8 16 0.52
9 7 0.23
10 8 0.26
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2125047 original size:20 final size:19
Alignment explanation
Indices: 2125012--2125051 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2125002 GTTCACCTCC
2125012 TTTTGTTTTTGTTTTTGTTT
1 TTTTGTTTTTGTTTTT-TTT
2125032 TTTTGTTTTT-TATTTTTTT
1 TTTTGTTTTTGT-TTTTTTT
2125051 T
1 T
2125052 AATTAGGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.88
Consensus pattern (19 bp):
TTTTGTTTTTGTTTTTTTT
Found at i:2127585 original size:26 final size:25
Alignment explanation
Indices: 2127555--2127621 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 25
2127545 TGAGTACATC
2127555 ATTTTATTTCATGTTTATGCTGAATA
1 ATTTTATTT-ATGTTTATGCTGAATA
*
2127581 ATTTTATTTGATGCTTATGCTGAATA
1 ATTTTATTT-ATGTTTATGCTGAATA
*
2127607 AGTTCTATTTATGTT
1 A-TTTTATTTATGTT
2127622 GCTTGCACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 29 0.81
27 7 0.19
ACGTcount: A:0.25, C:0.07, G:0.13, T:0.54
Consensus pattern (25 bp):
ATTTTATTTATGTTTATGCTGAATA
Found at i:2134555 original size:15 final size:15
Alignment explanation
Indices: 2134535--2134566 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2134525 TTTAGTTATA
*
2134535 AATTATATAAATTTT
1 AATTATACAAATTTT
2134550 AATTATACAAATTTT
1 AATTATACAAATTTT
2134565 AA
1 AA
2134567 AAAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTATACAAATTTT
Found at i:2134583 original size:10 final size:10
Alignment explanation
Indices: 2134560--2134603 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
2134550 AATTATACAA
* *
2134560 ATTTTAAAAA
1 ATTTTAATAT
*
2134570 ATTTTAATTT
1 ATTTTAATAT
2134580 ATTTTAATAT
1 ATTTTAATAT
2134590 ATTTTTAATAT
1 A-TTTTAATAT
2134601 ATT
1 ATT
2134604 AATTTAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 19 0.66
11 10 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:2134597 original size:11 final size:11
Alignment explanation
Indices: 2134571--2134613 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2134561 TTTTAAAAAA
*
2134571 TTTTAATTTA-
1 TTTTAATATAT
2134581 TTTTAATATAT
1 TTTTAATATAT
2134592 TTTTAATATAT
1 TTTTAATATAT
2134603 TAATTTAATAT
1 T--TTTAATAT
2134614 TATTAGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 9 0.31
11 12 0.41
13 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:2144204 original size:16 final size:17
Alignment explanation
Indices: 2144183--2144231 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
2144173 ATAATACTTG
2144183 AATTTAAATTT-T-ATTA
1 AATTT-AATTTATAATTA
2144199 AATTTAATTTATAATTA
1 AATTTAATTTATAATTA
2144216 AATAATT-ATTTATAAT
1 AAT--TTAATTTATAAT
2144232 AAAAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.17
16 6 0.21
17 7 0.24
18 9 0.31
19 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTAATTTATAATTA
Found at i:2144228 original size:18 final size:18
Alignment explanation
Indices: 2144203--2144250 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
2144193 TTATTAAATT
*
2144203 TAATTTATAATTAAATAA
1 TAATTTATAATTAAAAAA
* *
2144221 TTATTTATAATAAAAAAA
1 TAATTTATAATTAAAAAA
*
2144239 TAATTTAAAATT
1 TAATTTATAATT
2144251 TAATTATTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTTATAATTAAAAAA
Found at i:2144293 original size:37 final size:35
Alignment explanation
Indices: 2144251--2144336 Score: 84
Period size: 37 Copynumber: 2.3 Consensus size: 35
2144241 ATTTAAAATT
*
2144251 TAATTATTTAATCGAATTAAATCAA-TTTTAATCGATA
1 TAATTATTTAAT-GAATTAAA--AATTTTTAATCAATA
* * *
2144288 TAATTATAATTAATTATTTAAAAATTTTTAATCAATT
1 TAATTAT--TTAATGAATTAAAAATTTTTAATCAATA
2144325 TAATTATTTAAT
1 TAATTATTTAAT
2144337 TATTAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
35 5 0.12
36 2 0.05
37 24 0.57
38 6 0.14
39 5 0.12
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (35 bp):
TAATTATTTAATGAATTAAAAATTTTTAATCAATA
Found at i:2147935 original size:17 final size:17
Alignment explanation
Indices: 2147915--2147948 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2147905 TATCATATAT
*
2147915 TTAAAATAATTCATAAA
1 TTAAAATAATTAATAAA
*
2147932 TTAATATAATTAATAAA
1 TTAAAATAATTAATAAA
2147949 AAATGATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAATAATTAATAAA
Found at i:2148854 original size:34 final size:33
Alignment explanation
Indices: 2148811--2148881 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
2148801 TCAAAATCTC
2148811 ATTTTAAAAAACTCACTTATA-AAGCTTAATTTTG
1 ATTTTAAAAAAC-CACTTATAGAA-CTTAATTTTG
* * *
2148845 ATTTTAAAAATCCATTTGTAGAACTTAATTTTG
1 ATTTTAAAAAACCACTTATAGAACTTAATTTTG
2148878 ATTT
1 ATTT
2148882 GGGATATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 20 0.61
34 13 0.39
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (33 bp):
ATTTTAAAAAACCACTTATAGAACTTAATTTTG
Found at i:2149209 original size:33 final size:33
Alignment explanation
Indices: 2149166--2149238 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
2149156 AAGATTGTCC
* * * *
2149166 ATTTTAATTTTAAAAA-CTCATTTGTAGAGCTTA
1 ATTTTGATTTTAAAAATC-CATTTGAACAACTTA
*
2149199 ATTTTGATTTTGAAAATCCATTTGAACAACTTA
1 ATTTTGATTTTAAAAATCCATTTGAACAACTTA
2149232 ATTTTGA
1 ATTTTGA
2149239 GATAAATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (33 bp):
ATTTTGATTTTAAAAATCCATTTGAACAACTTA
Found at i:2149624 original size:22 final size:21
Alignment explanation
Indices: 2149575--2149624 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2149565 ATAATTTAAA
** *
2149575 ATTTTAATAAAAATTATAAAT
1 ATTTTAATAAAAAAAAAAAAT
2149596 ATGTTTAATAAAATAAAAAAAAT
1 AT-TTTAATAAAA-AAAAAAAAT
2149619 ATTTTA
1 ATTTTA
2149625 TATTTTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 14 0.58
23 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTTAATAAAAAAAAAAAAT
Found at i:2159375 original size:23 final size:23
Alignment explanation
Indices: 2159349--2159392 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2159339 ATTAATAATG
*
2159349 TCTCTCTATAA-TCAAATCAATTT
1 TCTCTCTA-AACTCAAACCAATTT
2159372 TCTCTCTAAACTCAAACCAAT
1 TCTCTCTAAACTCAAACCAAT
2159393 CAACAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (23 bp):
TCTCTCTAAACTCAAACCAATTT
Found at i:2160717 original size:77 final size:79
Alignment explanation
Indices: 2160527--2160724 Score: 253
Period size: 78 Copynumber: 2.5 Consensus size: 79
2160517 TAATATTTTC
* * * * *
2160527 AATTTGATTTGGTTTTGATGAAATTAATTGTATTTATATTTAATAGCTTAAAATTTTCTCTTAAT
1 AATTTGATTTGATTTTGATTAAATTAATTATATTTATCTTTAATAGATTAAAATTTTCTCTTAAT
2160592 TAATTTTAATTCTT
66 TAATTTTAATTCTT
* * *
2160606 AA-TTGATTTGATTTTAACTAAATTAATTACATTTA-CTTTAATAGATT-AAA-TTTCT-TTCAA
1 AATTTGATTTGATTTTGATTAAATTAATTATATTTATCTTTAATAGATTAAAATTTTCTCTT-AA
2160666 TTAATTTTAATTCTT
65 TTAATTTTAATTCTT
* *
2160681 AATTTAATTTGATTTTGATTTAAATTAATAATATTTATCTTTAA
1 AATTTGATTTGATTTTGA-TTAAATTAATTATATTTATCTTTAA
2160725 CATTAGATAA
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
74 2 0.02
75 24 0.24
76 16 0.16
77 25 0.25
78 33 0.32
79 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (79 bp):
AATTTGATTTGATTTTGATTAAATTAATTATATTTATCTTTAATAGATTAAAATTTTCTCTTAAT
TAATTTTAATTCTT
Found at i:2160932 original size:17 final size:17
Alignment explanation
Indices: 2160910--2160947 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2160900 ATTAAGTATC
*
2160910 TTTTAATTAATTTTAAT
1 TTTTAATTAAATTTAAT
*
2160927 TTTTAATTAAATTTGAT
1 TTTTAATTAAATTTAAT
2160944 TTTT
1 TTTT
2160948 TCAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTAATTAAATTTAAT
Found at i:2161001 original size:78 final size:76
Alignment explanation
Indices: 2160838--2161002 Score: 181
Period size: 78 Copynumber: 2.1 Consensus size: 76
2160828 TTTCTCTCTC
* * *
2160838 AATTAATTTTAATTCTTAATTAATTTGATTATAACCAAATTAATTACATTTATTTTTAATAGATT
1 AATTAATTTTAATTCTTAATTAATTTGATTATAACAAAAATAATCACATTTATTTTTAATAGATT
2160903 AAGTATCTTTT
66 AAGTATCTTTT
* * ** * * *
2160914 AATTAATTTTAATTTTTAATTAAATTTGATTTTTTCAAAAAATAATCATATTTATTTTTGATAGC
1 AATTAATTTTAATTCTTAATT-AATTTGATTATAAC-AAAAATAATCACATTTATTTTTAATAGA
*
2160979 TT-A-TATTTTTGTT
64 TTAAGTA-TCTT-TT
2160992 AATTAATTTTA
1 AATTAATTTTA
2161003 TTTATTATTT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
76 22 0.30
77 15 0.20
78 37 0.50
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.54
Consensus pattern (76 bp):
AATTAATTTTAATTCTTAATTAATTTGATTATAACAAAAATAATCACATTTATTTTTAATAGATT
AAGTATCTTTT
Found at i:2161935 original size:101 final size:101
Alignment explanation
Indices: 2161794--2161996 Score: 345
Period size: 101 Copynumber: 2.0 Consensus size: 101
2161784 ATCGTCAATT
*
2161794 GTTAGTGGATTTTGGAGAATTGGGTTGGCTGCTTTACTTGATATAAAATGATTCTTACTTCTTTC
1 GTTAGTGGATTTTGGAGAATTGAGTTGGCTGCTTTACTTGATATAAAATGATTCTTACTTCTTTC
*
2161859 TTAGCATCAACATTGTCAATTGTTAGTGGATTTTGG
66 TTAGCATCAACATTGTCAATTGTCAGTGGATTTTGG
* * *
2161895 GTTAGTGGATTTTAGG-GCATTGAGTTGGCTGCTTTTCTTGATGTAAAATGATTCTTACTTCTTT
1 GTTAGTGGATTTT-GGAGAATTGAGTTGGCTGCTTTACTTGATATAAAATGATTCTTACTTCTTT
2161959 CTTAGCATCAACATTGTCAATTGTCAGTGGATTTTGG
65 CTTAGCATCAACATTGTCAATTGTCAGTGGATTTTGG
2161996 G
1 G
2161997 GAATTGGGTT
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
101 94 0.98
102 2 0.02
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (101 bp):
GTTAGTGGATTTTGGAGAATTGAGTTGGCTGCTTTACTTGATATAAAATGATTCTTACTTCTTTC
TTAGCATCAACATTGTCAATTGTCAGTGGATTTTGG
Found at i:2164794 original size:20 final size:20
Alignment explanation
Indices: 2164757--2164794 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2164747 ATTATTTTGT
*
2164757 AATTAAATTTTGATTGTTGA
1 AATTAAATTTTGAATGTTGA
2164777 AATTAAAATTTT-AATGTT
1 AATT-AAATTTTGAATGTT
2164795 TGAATTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
AATTAAATTTTGAATGTTGA
Found at i:2164797 original size:21 final size:19
Alignment explanation
Indices: 2164750--2164798 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
2164740 ATAACAAATT
* *
2164750 ATTTTGTAATTAAATTTTG
1 ATTTTGAAATTAAATTTTA
2164769 ATTGTTGAAATTAAAATTTTA
1 ATT-TTGAAATT-AAATTTTA
2164790 ATGTTTGAA
1 AT-TTTGAA
2164799 TTGTTGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.12
20 7 0.28
21 14 0.56
22 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (19 bp):
ATTTTGAAATTAAATTTTA
Found at i:2167371 original size:31 final size:31
Alignment explanation
Indices: 2167312--2167411 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 31
2167302 AATTATAAAT
*
2167312 AATTTTTGTATTAATATAA-ATCATAATATAT-
1 AATTTTTATATTAATATAATAT-A-AATATATG
*
2167343 AATTTTTATATAAAATATAATATAAATATATG
1 AATTTTTATAT-TAATATAATATAAATATATG
* *
2167375 AATATTTTATATTTTATATGATATAAATATATG
1 AAT-TTTTATA-TTAATATAATATAAATATATG
2167408 AATT
1 AATT
2167412 ATTAGATTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
31 17 0.29
32 12 0.20
33 29 0.49
34 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (31 bp):
AATTTTTATATTAATATAATATAAATATATG
Found at i:2168192 original size:14 final size:14
Alignment explanation
Indices: 2168173--2168201 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2168163 AAAAATAATA
2168173 TTTTTATTTTTATT
1 TTTTTATTTTTATT
2168187 TTTTTATTTTTATT
1 TTTTTATTTTTATT
2168201 T
1 T
2168202 CATTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:2169681 original size:14 final size:14
Alignment explanation
Indices: 2169675--2169704 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2169665 TTTCTTTATT
*
2169675 TTTATTTTTATTTC
1 TTTAATTTTATTTC
2169689 TTTAATTTTATTTC
1 TTTAATTTTATTTC
2169703 TT
1 TT
2169705 CATCTCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTAATTTTATTTC
Found at i:2169687 original size:20 final size:20
Alignment explanation
Indices: 2169662--2169701 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2169652 TTTCAAATTC
*
2169662 TTATTTCTTTATTTTTATTT
1 TTATTTCTTTAATTTTATTT
2169682 TTATTTCTTTAATTTTATTT
1 TTATTTCTTTAATTTTATTT
2169702 CTTCATCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (20 bp):
TTATTTCTTTAATTTTATTT
Found at i:2171897 original size:2 final size:2
Alignment explanation
Indices: 2171885--2171927 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2171875 ACATATTTGT
*
2171885 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2171927 T
1 T
2171928 CATCTCTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2173321 original size:21 final size:20
Alignment explanation
Indices: 2173287--2173326 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2173277 GATCTTAGAG
*
2173287 AGAGAGAAAGAAAGAGAAAAT
1 AGAGAGAAAAAAAGA-AAAAT
*
2173308 AGAGATAAAAAAAGAAAAA
1 AGAGAGAAAAAAAGAAAAA
2173327 GTTTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (20 bp):
AGAGAGAAAAAAAGAAAAAT
Found at i:2173548 original size:121 final size:122
Alignment explanation
Indices: 2173413--2173654 Score: 425
Period size: 122 Copynumber: 2.0 Consensus size: 122
2173403 TACATGAAAT
*
2173413 TTTAACTTAGTTGATAAAAAATTTAAT-GTGTTAA-TTTTTCATCCAAATAAAGAGTTAATTATA
1 TTTAACTTAATTGATAAAAAA-TTAATGGTGTTAATTTTTTCATCCAAATAAAGAGTTAATTATA
*
2173476 TATAAATAAATATTGAAGAAATTAATTAATTATAATAAAAAATAAAATTTTGTATAAC
65 TATAAATAAATATTGAAGAAATTAATTAATTATAATAAAAAATAAAAATTTGTATAAC
2173534 TTTAACTTAATTGATAAAAAATTAATGGTGTTAATTTTTTCATCCAAATAAAGAGTTAATTATAT
1 TTTAACTTAATTGATAAAAAATTAATGGTGTTAATTTTTTCATCCAAATAAAGAGTTAATTATAT
* *
2173599 ATAAATAAATATTGAAGAATTTGATTAATTATAATAAAAAATAAAAATTTGTATAA
66 ATAAATAAATATTGAAGAAATTAATTAATTATAATAAAAAATAAAAATTTGTATAA
2173655 TTTTTTAATT
Statistics
Matches: 115, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
120 5 0.04
121 27 0.23
122 83 0.72
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.40
Consensus pattern (122 bp):
TTTAACTTAATTGATAAAAAATTAATGGTGTTAATTTTTTCATCCAAATAAAGAGTTAATTATAT
ATAAATAAATATTGAAGAAATTAATTAATTATAATAAAAAATAAAAATTTGTATAAC
Found at i:2174576 original size:27 final size:27
Alignment explanation
Indices: 2174538--2174598 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
2174528 TATTTTTATT
2174538 TAAAAATCAATAAAATT-GTATAAATAA
1 TAAAAATCAATAAAATTAGTAT-AATAA
*
2174565 TAAAACTCAATAAAATTACAGTATAATAA
1 TAAAAATCAATAAAATT--AGTATAATAA
2174594 TAAAA
1 TAAAA
2174599 TTTAATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 16 0.53
29 10 0.33
30 4 0.13
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (27 bp):
TAAAAATCAATAAAATTAGTATAATAA
Found at i:2174605 original size:29 final size:31
Alignment explanation
Indices: 2174555--2174628 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
2174545 CAATAAAATT
2174555 GTATAAATAATAAAACTCAATAA-AATTAC-A
1 GTAT-AATAATAAAACTCAATAATAATTACTA
* * *
2174585 GTATAATAATAAAATTTAATAATAATTCCTA
1 GTATAATAATAAAACTCAATAATAATTACTA
*
2174616 ATATAATAATAAA
1 GTATAATAATAAA
2174629 TTTGATCTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 16 0.42
30 9 0.24
31 13 0.34
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (31 bp):
GTATAATAATAAAACTCAATAATAATTACTA
Found at i:2182140 original size:7 final size:7
Alignment explanation
Indices: 2182128--2182157 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2182118 ATGTGGTCCG
2182128 AACTCCA
1 AACTCCA
2182135 AACTCCA
1 AACTCCA
2182142 AACTCCA
1 AACTCCA
2182149 AACTCCA
1 AACTCCA
2182156 AA
1 AA
2182158 ATTAGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (7 bp):
AACTCCA
Found at i:2182354 original size:15 final size:16
Alignment explanation
Indices: 2182328--2182366 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
2182318 ATAGGACCAC
2182328 TTTATT-TAATATAAT
1 TTTATTATAATATAAT
2182343 TTT-TTATAATATAAT
1 TTTATTATAATATAAT
2182358 TTTATTATA
1 TTTATTATA
2182367 TTTTATCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 15 0.68
16 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATTATAATATAAT
Found at i:2184519 original size:15 final size:13
Alignment explanation
Indices: 2184488--2184527 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
2184478 TTGACTAAAA
2184488 AAATAATTTTTTT
1 AAATAATTTTTTT
2184501 AAATAATTTTTTT
1 AAATAATTTTTTT
*
2184514 AGA-AATTATTTTT
1 AAATAATT-TTTTT
2184527 A
1 A
2184528 TCAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
AAATAATTTTTTT
Found at i:2205904 original size:34 final size:35
Alignment explanation
Indices: 2205857--2205923 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
2205847 AAGATGGTAT
*
2205857 ATGGCTTCCAATCACTGATTAGA-CCTCAAAAACC
1 ATGGCTTCAAATCACTGATTAGACCCTCAAAAACC
2205891 ATGGCTTCAAATCACTGATTAGACCCTCAAAAA
1 ATGGCTTCAAATCACTGATTAGACCCTCAAAAA
2205924 ATTTTCATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 22 0.71
35 9 0.29
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (35 bp):
ATGGCTTCAAATCACTGATTAGACCCTCAAAAACC
Found at i:2221768 original size:20 final size:20
Alignment explanation
Indices: 2221743--2221782 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2221733 GCAACCCTTT
2221743 GTTTCTAAGCAATTAAGCCC
1 GTTTCTAAGCAATTAAGCCC
*
2221763 GTTTCTAAGCAATTATGCCC
1 GTTTCTAAGCAATTAAGCCC
2221783 ACTCAGGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (20 bp):
GTTTCTAAGCAATTAAGCCC
Found at i:2228770 original size:13 final size:13
Alignment explanation
Indices: 2228752--2228779 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2228742 ATGTCAAAAA
2228752 AATTTTAAAATAT
1 AATTTTAAAATAT
2228765 AATTTTAAAATAT
1 AATTTTAAAATAT
2228778 AA
1 AA
2228780 AAAAATGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTTTAAAATAT
Found at i:2229162 original size:17 final size:18
Alignment explanation
Indices: 2229140--2229173 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2229130 CCTAATCGAA
2229140 TTTTTA-TATTTAAATTT
1 TTTTTATTATTTAAATTT
*
2229157 TTTTTATTATTTTAATT
1 TTTTTATTATTTAAATT
2229174 AATAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATTATTTAAATTT
Found at i:2229653 original size:22 final size:21
Alignment explanation
Indices: 2229619--2229661 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2229609 TATCTAAATG
*
2229619 ATTTCATTGTTAATATAATATT
1 ATTTCATTGTTAA-AAAATATT
2229641 ATTTCATAT-TTAAAAAATATT
1 ATTTCAT-TGTTAAAAAATATT
2229662 TAATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 11 0.58
23 1 0.05
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTCATTGTTAAAAAATATT
Found at i:2235238 original size:18 final size:19
Alignment explanation
Indices: 2235206--2235243 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2235196 AGAGGCCAAT
2235206 TCTTCACACTCTCTCTCTC
1 TCTTCACACTCTCTCTCTC
*
2235225 TCTT-ACACTTTCTCTCTC
1 TCTTCACACTCTCTCTCTC
2235243 T
1 T
2235244 AATCTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.42, G:0.00, T:0.47
Consensus pattern (19 bp):
TCTTCACACTCTCTCTCTC
Found at i:2238137 original size:32 final size:32
Alignment explanation
Indices: 2238101--2238177 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
2238091 TTTATTTATC
*
2238101 TTAAATTTAATTTAATTTTATATTTATAATAT
1 TTAAATTTAATTTAATTTAATATTTATAATAT
* * * * *
2238133 TTAAATTTTATTTAATTTAATTTTTTTATTTT
1 TTAAATTTAATTTAATTTAATATTTATAATAT
*
2238165 TTATATTTAATTT
1 TTAAATTTAATTT
2238178 TGATTCAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (32 bp):
TTAAATTTAATTTAATTTAATATTTATAATAT
Found at i:2238172 original size:38 final size:37
Alignment explanation
Indices: 2238105--2238187 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 37
2238095 TTTATCTTAA
2238105 ATTTAATTTAATTTTATATTTATAATATTTAAATTTT-
1 ATTTAATTTAATTTTATATTTATAATATTT-AATTTTG
* * *
2238142 ATTTAATTTAATTTTTTTATTTTTTATATTTAATTTTG
1 ATTTAATTTAA-TTTTATATTTATAATATTTAATTTTG
*
2238180 ATTCAATT
1 ATTTAATT
2238188 AATAATATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 17 0.43
38 23 0.57
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (37 bp):
ATTTAATTTAATTTTATATTTATAATATTTAATTTTG
Found at i:2238861 original size:20 final size:19
Alignment explanation
Indices: 2238836--2238883 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
2238826 AAATATTTAA
*
2238836 TATTTAATATGATATATGAT
1 TATTTAATATAATAT-TGAT
*
2238856 TATTTAATATAATATTTAT
1 TATTTAATATAATATTGAT
2238875 T-TTTAATAT
1 TATTTAATAT
2238884 TATTAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 8 0.31
19 4 0.15
20 14 0.54
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
TATTTAATATAATATTGAT
Found at i:2238887 original size:16 final size:17
Alignment explanation
Indices: 2238828--2238898 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
2238818 TTATTGGAAA
*
2238828 ATAT-TTAATATTTAAT
1 ATATATTAATTTTTAAT
*
2238844 ATGATATATGATTATTTAAT
1 AT-ATAT-TAATT-TTTAAT
*
2238864 ATAATATTTATTTTTAAT
1 AT-ATATTAATTTTTAAT
*
2238882 AT-TATTAATTTTAAAT
1 ATATATTAATTTTTAAT
2238898 A
1 A
2238899 ATGAGATATC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
16 15 0.33
17 2 0.04
18 9 0.20
19 7 0.16
20 12 0.27
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATATATTAATTTTTAAT
Found at i:2239706 original size:11 final size:11
Alignment explanation
Indices: 2239672--2239707 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2239662 AATATGATAC
2239672 AAAAATAATAT
1 AAAAATAATAT
*
2239683 AAATAAGAATAT
1 AAA-AATAATAT
2239695 AAAAATAATAT
1 AAAAATAATAT
2239706 AA
1 AA
2239708 TTTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:2239738 original size:18 final size:17
Alignment explanation
Indices: 2239717--2239750 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2239707 ATTTAAAATT
2239717 TTAATAAAAATAAAAAAA
1 TTAA-AAAAATAAAAAAA
*
2239735 TTAACAAAATAAAAAA
1 TTAAAAAAATAAAAAA
2239751 TATATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
TTAAAAAAATAAAAAAA
Found at i:2241571 original size:14 final size:14
Alignment explanation
Indices: 2241519--2241569 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
2241509 TAATTATTTA
2241519 TATTCATATAAATT
1 TATTCATATAAATT
2241533 TATTCATAATAAATT
1 TATTCAT-ATAAATT
* *
2241548 AATT-ATATTAATT
1 TATTCATATAAATT
*
2241561 TATTAATAT
1 TATTCATAT
2241570 TATAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 9 0.28
14 13 0.41
15 10 0.31
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTCATATAAATT
Found at i:2247174 original size:24 final size:24
Alignment explanation
Indices: 2247147--2247193 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2247137 TAAAAAATTC
2247147 AAAAAATCT-ATAAAAATAAAAATA
1 AAAAAAT-TAATAAAAATAAAAATA
*
2247171 AAAATATTAATAAAAATAAAAAT
1 AAAAAATTAATAAAAATAAAAAT
2247194 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (24 bp):
AAAAAATTAATAAAAATAAAAATA
Found at i:2247207 original size:6 final size:6
Alignment explanation
Indices: 2247156--2247193 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
2247146 CAAAAAATCT
**
2247156 ATAAAA ATAAAA ATAAAA ATATTA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT
2247194 TTTTAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
ATAAAA
Found at i:2247238 original size:18 final size:17
Alignment explanation
Indices: 2247164--2247238 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 17
2247154 CTATAAAAAT
*
2247164 AAAAATAAAAATATTAA
1 AAAAATAAAAATATTTA
*
2247181 TAAAAATAAAAATTTTTA
1 -AAAAATAAAAATATTTA
2247199 AAATAA-AAAAA-ATTTCACA
1 AAA-AATAAAAATATTT---A
2247218 AAAACATAAAAATATTTA
1 AAAA-ATAAAAATATTTA
2247236 AAA
1 AAA
2247239 TACAAAAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
16 3 0.06
17 8 0.17
18 22 0.47
19 5 0.11
20 5 0.11
21 4 0.09
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATAAAAATATTTA
Found at i:2247364 original size:26 final size:26
Alignment explanation
Indices: 2247335--2247385 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2247325 TCATATTTTG
*
2247335 AAATTTTCA-TTTTTTATATTTTATTA
1 AAATTTTAAGTTTTTTAT-TTTTATTA
2247361 AAATTTTAAGTTTTTTATTTTTATT
1 AAATTTTAAGTTTTTTATTTTTATT
2247386 TTTTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (26 bp):
AAATTTTAAGTTTTTTATTTTTATTA
Found at i:2247439 original size:18 final size:18
Alignment explanation
Indices: 2247418--2247494 Score: 57
Period size: 19 Copynumber: 4.2 Consensus size: 18
2247408 TTTAGAATGT
* *
2247418 TTTAGATTTTTGAAAATA
1 TTTAGATTTTTCAAAAAA
2247436 TTTAGATTATTTCAAAAAA
1 TTTAGATT-TTTCAAAAAA
* **
2247455 TTTATATTTATTTTAAAAA
1 TTTAGATTT-TTCAAAAAA
* *
2247474 TTATA-AATTTTAAAAAAA
1 TT-TAGATTTTTCAAAAAA
2247492 TTT
1 TTT
2247495 TAGGTTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
17 1 0.02
18 18 0.38
19 27 0.56
20 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (18 bp):
TTTAGATTTTTCAAAAAA
Found at i:2247457 original size:19 final size:19
Alignment explanation
Indices: 2247418--2247473 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2247408 TTTAGAATGT
* *
2247418 TTTAGATT-TTTGAAAATA
1 TTTAGATTATTTCAAAAAA
2247436 TTTAGATTATTTCAAAAAA
1 TTTAGATTATTTCAAAAAA
* *
2247455 TTTATATTTATTTTAAAAA
1 TTTAGA-TTATTTCAAAAA
2247474 TTATAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 8 0.25
19 13 0.41
20 11 0.34
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTAGATTATTTCAAAAAA
Found at i:2247548 original size:10 final size:10
Alignment explanation
Indices: 2247513--2247601 Score: 60
Period size: 10 Copynumber: 9.1 Consensus size: 10
2247503 TTTAATTATC
2247513 AATTTTT-AA
1 AATTTTTAAA
2247522 AA-TTTTAAA
1 AATTTTTAAA
2247531 GAATTTTTAAA
1 -AATTTTTAAA
**
2247542 AATTTTTTTA
1 AATTTTTAAA
* **
2247552 GATTATTT-TT
1 AATT-TTTAAA
*
2247562 AATTTTTAAG
1 AATTTTTAAA
*
2247572 AATTTTTGAA
1 AATTTTTAAA
*
2247582 AATTTTT-AT
1 AATTTTTAAA
2247591 AATTTTTAAA
1 AATTTTTAAA
2247601 A
1 A
2247602 CTAGTAAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
8 4 0.06
9 15 0.24
10 34 0.54
11 10 0.16
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:2247566 original size:30 final size:29
Alignment explanation
Indices: 2247513--2247601 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
2247503 TTTAATTATC
* *
2247513 AATTTTT-AAAATTTTAAAGAATTTTTAAA
1 AATTTTTGAAAATTTT-TATAATTTTTAAA
** * * *
2247542 AATTTTTTTAGATTATTTTTAATTTTTAAG
1 AATTTTTGAAAATT-TTTATAATTTTTAAA
2247572 AATTTTTGAAAATTTTTATAATTTTTAAA
1 AATTTTTGAAAATTTTTATAATTTTTAAA
2247601 A
1 A
2247602 CTAGTAAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 21 0.45
30 24 0.51
31 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (29 bp):
AATTTTTGAAAATTTTTATAATTTTTAAA
Found at i:2247585 original size:20 final size:19
Alignment explanation
Indices: 2247513--2247601 Score: 85
Period size: 19 Copynumber: 4.6 Consensus size: 19
2247503 TTTAATTATC
*
2247513 AATTTTTAAAATTTTAAAG
1 AATTTTTAAAATTTTTAAG
*
2247532 AATTTTTAAAAATTTTTTTAG
1 AATTTTT-AAAA-TTTTTAAG
2247553 ATTATTTTT--AATTTTTAAG
1 A--ATTTTTAAAATTTTTAAG
*
2247572 AATTTTTGAAAATTTTT-AT
1 AATTTTT-AAAATTTTTAAG
2247591 AATTTTTAAAA
1 AATTTTTAAAA
2247602 CTAGTAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
17 6 0.10
18 4 0.07
19 23 0.39
20 13 0.22
21 7 0.12
23 6 0.10
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
AATTTTTAAAATTTTTAAG
Found at i:2247638 original size:21 final size:21
Alignment explanation
Indices: 2247614--2247747 Score: 78
Period size: 20 Copynumber: 6.3 Consensus size: 21
2247604 AGTAAAAAAT
2247614 TTTTTAAAAAAATTTTTAGAA
1 TTTTTAAAAAAATTTTTAGAA
* **
2247635 -TTTTGAAATGA-TTTTAGAA
1 TTTTTAAAAAAATTTTTAGAA
**
2247654 TTTAAAAAAATTTAAGTTTTATAGAA
1 TTTTTAAAAA---AA-TTTT-TAGAA
* **
2247680 -TTTTAAAAAAAATTGAAGAA
1 TTTTTAAAAAAATTTTTAGAA
* *
2247700 TTTTAAAAAAAATTTTAAGAA
1 TTTTTAAAAAAATTTTTAGAA
* * *
2247721 TTTTT-TACAACTTTTTAGAA
1 TTTTTAAAAAAATTTTTAGAA
2247741 TTTTTAA
1 TTTTTAA
2247748 GTTTTTTTTA
Statistics
Matches: 82, Mismatches: 22, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
19 8 0.10
20 33 0.40
21 23 0.28
22 2 0.02
23 1 0.01
25 10 0.12
26 5 0.06
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (21 bp):
TTTTTAAAAAAATTTTTAGAA
Found at i:2247701 original size:20 final size:21
Alignment explanation
Indices: 2247676--2247724 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
2247666 TAAGTTTTAT
2247676 AGAATTTTAAAAAAAA-TTGA
1 AGAATTTTAAAAAAAATTTGA
*
2247696 AGAATTTTAAAAAAAATTTTA
1 AGAATTTTAAAAAAAATTTGA
2247717 AGAATTTT
1 AGAATTTT
2247725 TTACAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (21 bp):
AGAATTTTAAAAAAAATTTGA
Found at i:2252184 original size:31 final size:29
Alignment explanation
Indices: 2252112--2252187 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
2252102 AATTATAAAA
* *
2252112 TAAGAGTTTATTTAGATATAAATTAAAGT
1 TAAGAGTTTATTTGGATATAAAGTAAAGT
* * *
2252141 TCAAGGGCTTATTTGGAGTGTAAAGTAAAGAT
1 T-AAGAGTTTATTTGGA-TATAAAGTAAAG-T
2252173 TAAGAGTTTATTTGG
1 TAAGAGTTTATTTGG
2252188 GTACAACATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 1 0.03
30 12 0.32
31 22 0.59
32 2 0.05
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
TAAGAGTTTATTTGGATATAAAGTAAAGT
Found at i:2252613 original size:21 final size:21
Alignment explanation
Indices: 2252584--2252632 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2252574 TTTATTCTAA
*
2252584 AAATGTATTGATAA-ATTATTT
1 AAATATATTGA-AATATTATTT
*
2252605 AAATATATTTAAATATTATTT
1 AAATATATTGAAATATTATTT
2252626 ATAATAT
1 A-AATAT
2252633 TTAAAATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
AAATATATTGAAATATTATTT
Found at i:2252615 original size:10 final size:10
Alignment explanation
Indices: 2252595--2252637 Score: 54
Period size: 9 Copynumber: 4.4 Consensus size: 10
2252585 AATGTATTGA
2252595 TAAAT-TATT
1 TAAATATATT
2252604 TAAATATATT
1 TAAATATATT
2252614 TAAATATTATT
1 TAAATA-TATT
*
2252625 TATA-ATATT
1 TAAATATATT
2252634 TAAA
1 TAAA
2252638 ATCTTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 12 0.40
10 11 0.37
11 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TAAATATATT
Found at i:2252626 original size:11 final size:11
Alignment explanation
Indices: 2252598--2252633 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
2252588 GTATTGATAA
2252598 ATTATTTAAAT
1 ATTATTTAAAT
2252609 A-TATTTAAAT
1 ATTATTTAAAT
2252619 ATTATTTATAAT
1 ATTATTTA-AAT
2252631 ATT
1 ATT
2252634 TAAAATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.43
11 7 0.30
12 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTTAAAT
Found at i:2252639 original size:21 final size:21
Alignment explanation
Indices: 2252598--2252639 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2252588 GTATTGATAA
*
2252598 ATTATTTAAATATATTTAAAT
1 ATTATTTAAATATATTAAAAT
2252619 ATTATTTATAATAT-TTAAAAT
1 ATTATTTA-AATATATTAAAAT
2252640 CTTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATTTAAATATATTAAAAT
Found at i:2254534 original size:39 final size:38
Alignment explanation
Indices: 2254408--2254536 Score: 152
Period size: 39 Copynumber: 3.3 Consensus size: 38
2254398 CTTTGTACGC
*
2254408 TCTGTTACTTAGTCCTGAAGTTTGGGGTTTTTT-GGACT
1 TCTGTTACTTTGTCCTGAAGTTT-GGGTTTTTTGGGACT
* * *
2254446 TGTGTTACTTGGTCCTGAAGTTTGGAGTATTTTGGGACT
1 TCTGTTACTTTGTCCTGAAGTTTGG-GTTTTTTGGGACT
* * *
2254485 TGTTTTACTTTGTTCTGAAGTTTGAGGTTTTTTGGGACT
1 TCTGTTACTTTGTCCTGAAGTTTG-GGTTTTTTGGGACT
*
2254524 TCTGATACTTTGT
1 TCTGTTACTTTGT
2254537 ATTGGTGATC
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.03
38 27 0.35
39 48 0.62
40 1 0.01
ACGTcount: A:0.14, C:0.11, G:0.26, T:0.49
Consensus pattern (38 bp):
TCTGTTACTTTGTCCTGAAGTTTGGGTTTTTTGGGACT
Found at i:2254789 original size:26 final size:23
Alignment explanation
Indices: 2254732--2254785 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
2254722 CTTCTGTTCC
2254732 TTGCAGCACTAGTGGCCACCACA
1 TTGCAGCACTAGTGGCCACCACA
2254755 TTGCAGCACTAGTGGCCACCACA
1 TTGCAGCACTAGTGGCCACCACA
2254778 TTGCAGCA
1 TTGCAGCA
2254786 GCACCTCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.19
Consensus pattern (23 bp):
TTGCAGCACTAGTGGCCACCACA
Found at i:2259179 original size:13 final size:13
Alignment explanation
Indices: 2259161--2259185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2259151 CTTATATCTA
2259161 TAAATTTAATATG
1 TAAATTTAATATG
2259174 TAAATTTAATAT
1 TAAATTTAATAT
2259186 TTTTATTTAT
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TAAATTTAATATG
Found at i:2259914 original size:18 final size:20
Alignment explanation
Indices: 2259877--2259916 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2259867 GGAGATACGA
2259877 TTTATATGTGAGTAAAAAAT
1 TTTATATGTGAGTAAAAAAT
*
2259897 TTTATAT-T-AGTAAGAAAT
1 TTTATATGTGAGTAAAAAAT
2259915 TT
1 TT
2259917 GAATGAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (20 bp):
TTTATATGTGAGTAAAAAAT
Found at i:2260623 original size:2 final size:2
Alignment explanation
Indices: 2260616--2260651 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2260606 GAGGAAGACA
2260616 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
2260652 GAAAATTAGA
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:2265215 original size:6 final size:7
Alignment explanation
Indices: 2265189--2265214 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2265179 TTATAATTTC
2265189 CAAAAAT
1 CAAAAAT
2265196 CAAAAAT
1 CAAAAAT
2265203 CAAAAAT
1 CAAAAAT
2265210 CAAAA
1 CAAAA
2265215 TGCCTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (7 bp):
CAAAAAT
Found at i:2265986 original size:22 final size:21
Alignment explanation
Indices: 2265936--2266013 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 21
2265926 TTTTCATCTT
*
2265936 TATATTTTAATTTTAAAATAA
1 TATATTTTAATTTTAAGATAA
2265957 TATATTTTAATTTATAAGATAA
1 TATATTTTAATTT-TAAGATAA
* * * *
2265979 TGTTTTTTATTTTTAAGTAAAA
1 TATATTTTAATTTTAAG-ATAA
2266001 TTAATATTTTAAT
1 -T-ATATTTTAAT
2266014 ATAATATGCT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
21 17 0.38
22 20 0.44
23 1 0.02
24 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATTTTAATTTTAAGATAA
Found at i:2265995 original size:21 final size:22
Alignment explanation
Indices: 2265936--2265995 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
2265926 TTTTCATCTT
* *
2265936 TATA-TTTTAATTTTAAAATAA
1 TATATTTTTATTTTTAAGATAA
* *
2265957 TATATTTTAATTTATAAGATAA
1 TATATTTTTATTTTTAAGATAA
*
2265979 TGT-TTTTTATTTTTAAG
1 TATATTTTTATTTTTAAG
2265996 TAAAATTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TATATTTTTATTTTTAAGATAA
Found at i:2269068 original size:37 final size:38
Alignment explanation
Indices: 2269005--2269083 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 38
2268995 ATGAGTTTAA
* * *
2269005 TTTAATTAATTTATATAATTATTTTTAAGA-TATAATT
1 TTTAATAAATTTATAAAATTAATTTTAAGATTATAATT
*
2269042 TTTAATAAATTTA-AAAATTAAATTTTAATATTTATAATT
1 TTTAATAAATTTATAAAATT-AATTTTAAGA-TTATAATT
2269081 TTT
1 TTT
2269084 TTATTTAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
36 5 0.14
37 20 0.57
39 10 0.29
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (38 bp):
TTTAATAAATTTATAAAATTAATTTTAAGATTATAATT
Found at i:2269554 original size:15 final size:16
Alignment explanation
Indices: 2269525--2269554 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2269515 ACCAATAATA
2269525 TTATAAAAGAATTAAC
1 TTATAAAAGAATTAAC
2269541 TTATAAAA-AATTAA
1 TTATAAAAGAATTAA
2269555 TTTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
TTATAAAAGAATTAAC
Found at i:2276115 original size:22 final size:22
Alignment explanation
Indices: 2276055--2276115 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
2276045 ATTTAAATAT
2276055 ATTTATATATTTATATAATATGTAA
1 ATTT-TATATTT-T-TAATATGTAA
* * *
2276080 CTTATATATATTTAATATGTAA
1 ATTTTATATTTTTAATATGTAA
2276102 ATTTTATATTTTTA
1 ATTTTATATTTTTA
2276116 TTTATTTAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 21 0.70
23 1 0.03
24 6 0.20
25 2 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (22 bp):
ATTTTATATTTTTAATATGTAA
Found at i:2276117 original size:26 final size:23
Alignment explanation
Indices: 2276042--2276119 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 23
2276032 TTGCAAGTAA
*
2276042 TTTATTTAA-ATAT-ATTTATAT
1 TTTATTTAATATGTAATTTATAT
* *
2276063 ATTTATATAATATGTAACTTATA-
1 -TTTATTTAATATGTAATTTATAT
*
2276086 TATATTTAATATGTAAATTTTATATT
1 TTTATTTAATATGT-AA-TTTATA-T
2276112 TTTATTTA
1 TTTATTTA
2276120 TTTAACATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
22 20 0.47
23 5 0.12
24 11 0.26
26 7 0.16
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (23 bp):
TTTATTTAATATGTAATTTATAT
Found at i:2276573 original size:21 final size:21
Alignment explanation
Indices: 2276548--2276588 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2276538 TTATTTTTTA
*
2276548 ATAATTAATTTATTAAAATTG
1 ATAATTAATTAATTAAAATTG
2276569 ATAATTAATTAATTAAAATT
1 ATAATTAATTAATTAAAATT
2276589 TAATCCATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATAATTAATTAATTAAAATTG
Found at i:2279101 original size:25 final size:25
Alignment explanation
Indices: 2279063--2279115 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
2279053 CTCTAACCTT
2279063 TTTAAAGAAATATCCTATTATCATC
1 TTTAAAGAAATATCCTATTATCATC
**
2279088 TTTAAAGATGTATCCTATTATCATC
1 TTTAAAGAAATATCCTATTATCATC
2279113 TTT
1 TTT
2279116 TACTTGATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTAAAGAAATATCCTATTATCATC
Found at i:2282558 original size:21 final size:21
Alignment explanation
Indices: 2282534--2282575 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2282524 TTAAAACTAA
*
2282534 AATTATTTTTTTTATTTTTTC
1 AATTATTTTGTTTATTTTTTC
2282555 AATTATTTTGTTTATTTTTTC
1 AATTATTTTGTTTATTTTTTC
2282576 TAACAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (21 bp):
AATTATTTTGTTTATTTTTTC
Found at i:2283339 original size:18 final size:17
Alignment explanation
Indices: 2283313--2283360 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
2283303 TATTTTTTAA
*
2283313 TTATTTATTTATATATAT
1 TTATATATTTATATA-AT
* *
2283331 TTATGTATTTATTTAAT
1 TTATATATTTATATAAT
2283348 TT-TATATTTATAT
1 TTATATATTTATAT
2283361 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 9 0.35
17 4 0.15
18 13 0.50
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTATATATTTATATAAT
Found at i:2284878 original size:165 final size:169
Alignment explanation
Indices: 2284622--2284955 Score: 493
Period size: 166 Copynumber: 2.0 Consensus size: 169
2284612 TTAATCATAT
* *
2284622 TTGATGTGTCATTGATTTAGATGACAATTCTTTTTTTATAAAAATGAAAGAGTGTGATTTAATAC
1 TTGATGTGTCATTGATTTAGATGACAATTCGTTTTATATAAAAATGAAAGAGTGTGATTTAATAC
*
2284687 ATGATTTTTCATAAAGAATAT-AAAAAAAAAA-AAAAAAA-CCCATCTTATAATGAAGATCCTCT
66 ATGATTTTTCATAAAGAATATAAAAAAAAAAAGAAAAAAAGCCCACCTTATAATGAAGAT-CTCT
* *
2284749 TGTTGGAAGAAGATTGAAGA-TCCAAAATTC-TAAGAGAAA
130 TGTTAGAAGAAGATTGAAAATTCCAAAATTCATAA-AGAAA
* * * *
2284788 TTGATGTGTCATTGATTTGGATGACAATTCGTTTTATA-AAAAATTAAAGATTGTGATTTAATTC
1 TTGATGTGTCATTGATTTAGATGACAATTCGTTTTATATAAAAATGAAAGAGTGTGATTTAATAC
* *
2284852 ATGATTTTTC-TTAAGAATATTAAAAAAAAAAAGAAAAAAAGCCCACCTTATAATGAAGATTTCT
66 ATGATTTTTCATAAAGAATA-TAAAAAAAAAAAGAAAAAAAGCCCACCTTATAATGAAGATCTCT
2284916 TGTTAGAAGAAGATTGAAAATTCCAAAATTCATAAAGAAA
130 TGTTAGAAGAAGATTGAAAATTCCAAAATTCATAAAGAAA
2284956 ATACCCCATA
Statistics
Matches: 151, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
164 8 0.05
165 34 0.23
166 45 0.30
167 28 0.19
168 33 0.22
169 3 0.02
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (169 bp):
TTGATGTGTCATTGATTTAGATGACAATTCGTTTTATATAAAAATGAAAGAGTGTGATTTAATAC
ATGATTTTTCATAAAGAATATAAAAAAAAAAAGAAAAAAAGCCCACCTTATAATGAAGATCTCTT
GTTAGAAGAAGATTGAAAATTCCAAAATTCATAAAGAAA
Found at i:2291896 original size:30 final size:30
Alignment explanation
Indices: 2291841--2291934 Score: 109
Period size: 30 Copynumber: 3.0 Consensus size: 30
2291831 GCAAGTGATC
* *
2291841 AAATTATATCTAAACAATAAAAAATAAATAATT
1 AAATTATAT-T-AA-AATAATAAATAAATAATA
*
2291874 AAATTATATTAAAATAATAAATAAAAAATA
1 AAATTATATTAAAATAATAAATAAATAATA
*
2291904 AAATTATATTCAAATAATGAAA-AAATAATA
1 AAATTATATTAAAATAAT-AAATAAATAATA
2291934 A
1 A
2291935 GTAATAGTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
30 40 0.73
31 5 0.09
32 1 0.02
33 9 0.16
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (30 bp):
AAATTATATTAAAATAATAAATAAATAATA
Found at i:2294236 original size:16 final size:16
Alignment explanation
Indices: 2294215--2294253 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2294205 ATATATATAT
2294215 TATTTATTTAATTTTA
1 TATTTATTTAATTTTA
2294231 TATTTATTTAATTTTA
1 TATTTATTTAATTTTA
*
2294247 CATTTAT
1 TATTTAT
2294254 ATTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTATTTAATTTTA
Found at i:2294274 original size:22 final size:22
Alignment explanation
Indices: 2294249--2294297 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
2294239 TAATTTTACA
2294249 TTTATATTTAAAAAA-TAATTAT
1 TTTATATTTAAAAAATTAA-TAT
2294271 TTTATATTTAAAAAATTAATAT
1 TTTATATTTAAAAAATTAATAT
2294293 TTTAT
1 TTTAT
2294298 TAATTTCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTATATTTAAAAAATTAATAT
Found at i:2296792 original size:82 final size:82
Alignment explanation
Indices: 2296646--2296796 Score: 205
Period size: 82 Copynumber: 1.8 Consensus size: 82
2296636 CTAGTAAAGA
** * *
2296646 AAACAGTGACTACATATTTCCATTGAAAGTGTTTAAGACGATTGGGGGAAATTTGAACACATGCT
1 AAACAGTGACTACATATTTCCATTGAAAGTCCTAAAGACGATTGGGGGAAATTTGAACAAATGCT
2296711 AGAATTCACAAGAAACT
66 AGAATTCACAAGAAACT
* * * * *
2296728 AAACGGTGACTAGATATTTCCATTGAAAGTCCTAAAGA-TATTTGGGGGATATTTGAATAAATGC
1 AAACAGTGACTACATATTTCCATTGAAAGTCCTAAAGACGA-TTGGGGGAAATTTGAACAAATGC
2296792 TAGAA
65 TAGAA
2296797 CTTAACATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
81 1 0.02
82 58 0.98
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (82 bp):
AAACAGTGACTACATATTTCCATTGAAAGTCCTAAAGACGATTGGGGGAAATTTGAACAAATGCT
AGAATTCACAAGAAACT
Found at i:2306907 original size:25 final size:23
Alignment explanation
Indices: 2306863--2306909 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2306853 TTGTACATTG
*
2306863 TATTTTTCATTTTTTTTGAAATT
1 TATTTTTCATTTTTTATGAAATT
2306886 TATTATTTCATTTTTTAATGAAAT
1 TATT-TTTCATTTTTT-ATGAAAT
2306910 AAGCCACGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (23 bp):
TATTTTTCATTTTTTATGAAATT
Found at i:2311842 original size:30 final size:28
Alignment explanation
Indices: 2311777--2311852 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 28
2311767 ATTTTTTTAA
*
2311777 AAATAAATTTATATATTTTTATTATATTC
1 AAATAAATTTTTAT-TTTTTATTATATTC
* *
2311806 AAATAAATTTTTATTTTTTAATTTGTATTT
1 AAATAAATTTTTATTTTTT-A-TTATATTC
*
2311836 AAATAAATCTTTATTTT
1 AAATAAATTTTTATTTT
2311853 AAATAAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 5 0.12
29 14 0.34
30 22 0.54
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (28 bp):
AAATAAATTTTTATTTTTTATTATATTC
Found at i:2312721 original size:29 final size:30
Alignment explanation
Indices: 2312667--2312755 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
2312657 ATACTCAGAG
** **
2312667 TTTATTTAAATATAAATTAATGATTAATGA
1 TTTATTTAAATATAAATTAAAAATTAAAAA
*
2312697 TTTATTT-ATTATAAATTAAAAATTAAAAA
1 TTTATTTAAATATAAATTAAAAATTAAAAA
* *
2312726 TTTATTTGAATGT-AA-TAAAAATATAAAAA
1 TTTATTTAAATATAAATTAAAAAT-TAAAAA
2312755 T
1 T
2312756 GACAAAATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
28 7 0.14
29 33 0.66
30 10 0.20
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (30 bp):
TTTATTTAAATATAAATTAAAAATTAAAAA
Found at i:2315147 original size:16 final size:14
Alignment explanation
Indices: 2315096--2315136 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
2315086 CTGTAGAAAG
*
2315096 AAATTTTAATAAA-
1 AAATTTTATTAAAT
2315109 AAATTTATATTAAAT
1 AAATTT-TATTAAAT
2315124 AAATTTTATTAAA
1 AAATTTTATTAAA
2315137 ATTAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 6 0.24
14 13 0.52
15 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTTATTAAAT
Found at i:2315284 original size:2 final size:2
Alignment explanation
Indices: 2315279--2315303 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2315269 ATATAAAATT
2315279 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 T
2315304 TTGTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2316139 original size:2 final size:2
Alignment explanation
Indices: 2316121--2316157 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2316111 TACTTACTTA
* *
2316121 AT AT GT AT AT AT GT 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 AT AT AT AT A
2316158 CAAATTAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2316223 original size:2 final size:2
Alignment explanation
Indices: 2316218--2316243 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2316208 ATATAAAATT
2316218 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2316244 CTTGTCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2328133 original size:114 final size:111
Alignment explanation
Indices: 2327918--2328133 Score: 290
Period size: 114 Copynumber: 1.9 Consensus size: 111
2327908 ATTTCATTGG
* * * *
2327918 AACTGGTAATATGGGGATAGGAAGTAGCATTCGTTCATAGTTGTTGCTGCTCATGCAAGCAGCTG
1 AACTGGTAACATGGGAATAGGAAGTAGCATTCGTTCATAGTTGTTGCTGCTCATACAAGCAGCTA
* * *
2327983 CCACTGCTTTATTCAGCGGCTCTACAACTCTTATTTATTTGATCAA
66 CCACAGCTTTATTCAGCGACTCTACAACACTTATTTATTTGATCAA
*
2328029 AACTGGTAACATGGGCAAT-GGAAGTAGCATTCGTTCATAGTTGTTTCCGCTGCTCATACCAGCA
1 AACTGGTAACATGGG-AATAGGAAGTAGCATTCGTTCATAGTTG-TT--GCTGCTCATACAAGCA
* * *
2328093 GCTATCGCAGCTTTATTCAGCGACTCTACATCACTTATTTA
62 GCTACCACAGCTTTATTCAGCGACTCTACAACACTTATTTA
2328134 ATCAGAAGTG
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
111 38 0.42
112 4 0.04
114 48 0.53
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.32
Consensus pattern (111 bp):
AACTGGTAACATGGGAATAGGAAGTAGCATTCGTTCATAGTTGTTGCTGCTCATACAAGCAGCTA
CCACAGCTTTATTCAGCGACTCTACAACACTTATTTATTTGATCAA
Found at i:2328216 original size:110 final size:113
Alignment explanation
Indices: 2327918--2328229 Score: 325
Period size: 110 Copynumber: 2.8 Consensus size: 113
2327908 ATTTCATTGG
* * *
2327918 AACTGGTAATATGGGGATAGGAAGTAGCATTCGTTCATAGTTGTTGCTGCT-CATG--CAAGCAG
1 AACTGGTAATCTGGGGATAGGAAGTAGCATTCGTTCATAGTTGTTGCTGCTGCTTGTACCAGCAG
* * *
2327980 CTGCCACTGCTTTATTCAGCGGCTCTACAACTCTTATTTATTTGATCAA
66 CTACCACTGCTTTATTCAGCGGCTCTACAACTC-TACTTATTTAATCAA
* * * **
2328029 AACTGGTAA-CATGGGCA-ATGGAAGTAGCATTCGTTCATAGTTGTTTCCGCTGCTCATACCAGC
1 AACTGGTAATC-TGGGGATA-GGAAGTAGCATTCGTTCATAGTTGTTGCTGCTGCTTGTACCAGC
* * * * *
2328092 AGCTATCGCAGCTTTATTCAGCGACTCTAC-A-TC-ACTTATTTAATCAG
64 AGCTACCACTGCTTTATTCAGCGGCTCTACAACTCTACTTATTTAATCAA
* * * * * *
2328139 AAGTGGTAATCTGGGGATAGGAAGCAGCATTTGCTGATAGTTGCTGCTGCTGCTTGTACCAGCAG
1 AACTGGTAATCTGGGGATAGGAAGTAGCATTCGTTCATAGTTGTTGCTGCTGCTTGTACCAGCAG
* *
2328204 CCACCACTGCTTTATTTAGCGGCTCT
66 CTACCACTGCTTTATTCAGCGGCTCT
2328230 TTCTGTCACC
Statistics
Matches: 161, Mismatches: 33, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
110 82 0.51
111 46 0.29
112 3 0.02
113 1 0.01
114 29 0.18
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (113 bp):
AACTGGTAATCTGGGGATAGGAAGTAGCATTCGTTCATAGTTGTTGCTGCTGCTTGTACCAGCAG
CTACCACTGCTTTATTCAGCGGCTCTACAACTCTACTTATTTAATCAA
Found at i:2331483 original size:19 final size:20
Alignment explanation
Indices: 2331459--2331502 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
2331449 AATATTATTT
2331459 AATATT-ATTTTT-AATATGA
1 AATATTAATTTTTAAATAT-A
2331478 AATATTAATTTTTAAATATA
1 AATATTAATTTTTAAATATA
2331498 AATAT
1 AATAT
2331503 AAAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 12 0.52
21 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AATATTAATTTTTAAATATA
Found at i:2336360 original size:25 final size:24
Alignment explanation
Indices: 2336332--2336393 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
2336322 ACCCGAAATT
**
2336332 AATAAAATATTATTTTTTAAATATA
1 AATAAAATATTA-TAATTAAATATA
* *
2336357 AATATAAATAATATAATTATATATA
1 AATA-AAATATTATAATTAAATATA
*
2336382 AATAAAAAATTA
1 AATAAAATATTA
2336394 AAAAATAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 6 0.20
25 17 0.57
26 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AATAAAATATTATAATTAAATATA
Found at i:2338929 original size:12 final size:12
Alignment explanation
Indices: 2338912--2338938 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2338902 AATTTAAAAT
2338912 TTAAATATTATA
1 TTAAATATTATA
2338924 TTAAATATTATA
1 TTAAATATTATA
2338936 TTA
1 TTA
2338939 TAATTAAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATATTATA
Found at i:2338938 original size:17 final size:17
Alignment explanation
Indices: 2338916--2338951 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2338906 TAAAATTTAA
2338916 ATATTAT-ATTAAATATT
1 ATATTATAATTAAAT-TT
2338933 ATATTATAATTAAATTT
1 ATATTATAATTAAATTT
2338950 AT
1 AT
2338952 TCATGACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTATAATTAAATTT
Found at i:2339795 original size:16 final size:17
Alignment explanation
Indices: 2339774--2339806 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2339764 TTTTTTTAGA
2339774 TAAAA-TGTATTATTTT
1 TAAAATTGTATTATTTT
*
2339790 TAAAATTTTATTATTTT
1 TAAAATTGTATTATTTT
2339807 ATACATATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TAAAATTGTATTATTTT
Found at i:2339954 original size:42 final size:42
Alignment explanation
Indices: 2339879--2339958 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
2339869 TGACCATTAT
* *
2339879 AATTTTGATTTTATTATTTTATAACGAATTTTCTTTGTAAAA
1 AATTTTGATTTTATTATTTTATAAAGAAGTTTCTTTGTAAAA
* *
2339921 AATTTT-ATTTTATTTTTTTATAAAGACCGTTTCTTTGT
1 AATTTTGATTTTATTATTTTATAAAGA-AGTTTCTTTGT
2339959 TTTGTATTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 18 0.55
42 15 0.45
ACGTcount: A:0.29, C:0.06, G:0.07, T:0.57
Consensus pattern (42 bp):
AATTTTGATTTTATTATTTTATAAAGAAGTTTCTTTGTAAAA
Found at i:2348360 original size:14 final size:15
Alignment explanation
Indices: 2348335--2348363 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2348325 GAATGGAATA
2348335 TTTATCTATAATTTT
1 TTTATCTATAATTTT
2348350 TTTAT-TATAATTTT
1 TTTATCTATAATTTT
2348364 ACAATTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATCTATAATTTT
Found at i:2348483 original size:19 final size:20
Alignment explanation
Indices: 2348459--2348499 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2348449 ACAATTCTGA
2348459 ATTATAATTAA-TTAAT-TAT
1 ATTATAA-TAATTTAATGTAT
2348478 ATTATAATAATTTAATGTAT
1 ATTATAATAATTTAATGTAT
2348498 AT
1 AT
2348500 AGTAATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 12 0.60
20 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTATAATAATTTAATGTAT
Found at i:2349018 original size:15 final size:17
Alignment explanation
Indices: 2348985--2349019 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
2348975 AAAATTAAAG
2348985 TTATAAATTTTATTTTA
1 TTATAAATTTTATTTTA
2349002 TTAT-AATTTTA-TTTA
1 TTATAAATTTTATTTTA
2349017 TTA
1 TTA
2349020 AATATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 7 0.39
17 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATAAATTTTATTTTA
Found at i:2349192 original size:17 final size:19
Alignment explanation
Indices: 2349147--2349206 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
2349137 GATTTTAACA
**
2349147 AAATATAAAATATTTTTTG
1 AAATATAAAATATTTCATG
2349166 AAATATAAAATATTTCAT-
1 AAATATAAAATATTTCATG
*
2349184 AAA-ATAAAAT-TTTAACTG
1 AAATATAAAATATTTCA-TG
2349202 AAATA
1 AAATA
2349207 AATAAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 4 0.11
17 8 0.23
18 6 0.17
19 17 0.49
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATATAAAATATTTCATG
Found at i:2353796 original size:2 final size:2
Alignment explanation
Indices: 2353789--2353821 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2353779 AAAACAAAGC
2353789 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 T
2353822 TTGAAGTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2356096 original size:24 final size:24
Alignment explanation
Indices: 2356069--2356115 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2356059 TCATGAATAT
*
2356069 AAATATGAAAAT-AAATATAAAAAA
1 AAATATAAAAATGAAA-ATAAAAAA
*
2356093 AAATTTAAAAATGAAAATAAAAA
1 AAATATAAAAATGAAAATAAAAA
2356116 TACTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (24 bp):
AAATATAAAAATGAAAATAAAAAA
Found at i:2365817 original size:2 final size:2
Alignment explanation
Indices: 2365810--2365840 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2365800 AGCAACCATA
2365810 AT 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 AT A
2365841 GGAAGTATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2369756 original size:20 final size:20
Alignment explanation
Indices: 2369723--2369763 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2369713 GAAAATAAAT
* *
2369723 TGAAAAAAATGTTTTTTTAA
1 TGAAAAAAAGGTTTTTATAA
*
2369743 TGAAAAAAGGGTTTTTATAA
1 TGAAAAAAAGGTTTTTATAA
2369763 T
1 T
2369764 TCTTAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (20 bp):
TGAAAAAAAGGTTTTTATAA
Done.