Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold193
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: 3104049
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 172765 characters in sequence are not A, C, G, or T
File 15 of 18
Found at i:2504600 original size:2 final size:2
Alignment explanation
Indices: 2504593--2504645 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2504583 ATCCAACTTT
2504593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2504635 TA TA TA TA TA T
1 TA TA TA TA TA T
2504646 GTGTGTGTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2506818 original size:13 final size:12
Alignment explanation
Indices: 2506763--2506822 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
2506753 ATTTATTTAA
*
2506763 AAATAAAATA-T
1 AAATTAAATATT
*
2506774 ATAATTAAATA-A
1 A-AATTAAATATT
2506786 AAATTAAATATGT
1 AAATTAAATAT-T
2506799 AAA-TAAATATT
1 AAATTAAATATT
2506810 AAATTTAAATATT
1 AAA-TTAAATATT
2506823 TAAAATAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
11 14 0.34
12 16 0.39
13 11 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
AAATTAAATATT
Found at i:2506819 original size:25 final size:25
Alignment explanation
Indices: 2506762--2506835 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 25
2506752 AATTTATTTA
* *
2506762 AAAATAAAATATATAATTAAATA--
1 AAAATTAAATATATAAATAAATATT
*
2506785 AAAATTAAATATGTAAATAAATATT
1 AAAATTAAATATATAAATAAATATT
* * *
2506810 AAATTTAAATATTTAAAATAATTATT
1 AAAATTAAATATAT-AAATAAATATT
2506836 TATGTACATA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 20 0.48
25 12 0.29
26 10 0.24
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (25 bp):
AAAATTAAATATATAAATAAATATT
Found at i:2507521 original size:2 final size:2
Alignment explanation
Indices: 2507514--2507550 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2507504 TCTAAGAAGG
2507514 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2507551 ACAGATGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2508562 original size:16 final size:17
Alignment explanation
Indices: 2508541--2508573 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2508531 CGTTCAATTA
2508541 CTCCTTTCTC-TTTCAT
1 CTCCTTTCTCATTTCAT
*
2508557 CTCCTTTTTCATTTCAT
1 CTCCTTTCTCATTTCAT
2508574 TTTTCAAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (17 bp):
CTCCTTTCTCATTTCAT
Found at i:2510382 original size:15 final size:14
Alignment explanation
Indices: 2510362--2510391 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2510352 TTTAATGAAT
2510362 AAGAAAATAAAGAAA
1 AAGAAAATAAA-AAA
2510377 AAGAAAATAAAAAA
1 AAGAAAATAAAAAA
2510391 A
1 A
2510392 TTTGTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (14 bp):
AAGAAAATAAAAAA
Found at i:2510890 original size:195 final size:196
Alignment explanation
Indices: 2510563--2510922 Score: 544
Period size: 195 Copynumber: 1.8 Consensus size: 196
2510553 GCATAGTGTA
*
2510563 ATATTTTAATTATTTTTCTCATGTTGTTGATGTTACGTTATAATTCATCTCATATTTTATATAAT
1 ATATTTTAATTA-TTTTCTCATGATGTTGATGTTACGTTATAATTCATCTCATATTTTATATAAT
* * * * * *
2510628 TTTTTATATTCAATTTTAATTTTAAGTTCATTGAATTAAAAATTGGATCATTATTTATGCTGTAC
65 TTATCATATTCAATTTTAACTTTAAGTTCATTGAATTAAAAATTAGATAATTATATATGCTGTAC
*
2510693 ATTAATATAAATATCAAGTTCAAAACTTTAATTTGTATTGTGTTTATGTTACTTTTGGTGTTATA
130 ATTAATATAAATATCAAGTTCAAAACTCTAATTTGTATTGTGTTTATGTTACTTTTGGTGTTATA
2510758 CG
195 CG
* * * *
2510760 ATATTTTAATTA-TTTCTCATGATGTTGATGTTATGTTTTAATTCATGTTATATTTTATATAATT
1 ATATTTTAATTATTTTCTCATGATGTTGATGTTACGTTATAATTCATCTCATATTTTATATAATT
* ** *
2510824 TATCATATTTAATTTTAACTTTAAGTTCATTGGTTTAAAAATTAGATAATTGTATATG-TCGTAC
66 TATCATATTCAATTTTAACTTTAAGTTCATTGAATTAAAAATTAGATAATTATATATGCT-GTAC
2510888 ATTAATATAAATATCAAGTTCAAAACTCTAATTTG
130 ATTAATATAAATATCAAGTTCAAAACTCTAATTTG
2510923 ATTTCCTACA
Statistics
Matches: 146, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
194 1 0.01
195 133 0.91
197 12 0.08
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (196 bp):
ATATTTTAATTATTTTCTCATGATGTTGATGTTACGTTATAATTCATCTCATATTTTATATAATT
TATCATATTCAATTTTAACTTTAAGTTCATTGAATTAAAAATTAGATAATTATATATGCTGTACA
TTAATATAAATATCAAGTTCAAAACTCTAATTTGTATTGTGTTTATGTTACTTTTGGTGTTATAC
G
Found at i:2516696 original size:24 final size:24
Alignment explanation
Indices: 2516663--2516748 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
2516653 AAGAGAAAGA
* *
2516663 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATAATAGGAGG
* *
2516687 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATAATAGGAGG
*
2516705 AGAGATAGGAGGGATAATAGGAGG
1 AGAGACAGGAGGGATAATAGGAGG
*
2516729 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATAATAG
2516749 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 5 0.10
22 2 0.04
24 29 0.59
ACGTcount: A:0.43, C:0.02, G:0.44, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATAATAGGAGG
Found at i:2516715 original size:42 final size:42
Alignment explanation
Indices: 2516654--2516772 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
2516644 TAGCCCTCAA
* *
2516654 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
2516696 AGAGATAGTAGAGATAGGAGGGATAATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
2516738 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
2516773 GAGAGAAGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.44, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:2516756 original size:18 final size:18
Alignment explanation
Indices: 2516687--2516757 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
2516677 TGATAGGAGG
* *
2516687 AGAGACAGGAGAGATAGT
1 AGAGAGAGGAGAGATAAT
* *
2516705 AGAGATAGGAGGGATAAT
1 AGAGAGAGGAGAGATAAT
2516723 AGGAGGAGAGACAGGAGAGATAAT
1 ---A-GAGAG--AGGAGAGATAAT
2516747 AGAGAGAGGAG
1 AGAGAGAGGAG
2516758 GGATGACAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
18 20 0.48
20 5 0.12
21 2 0.05
22 4 0.10
24 11 0.26
ACGTcount: A:0.45, C:0.03, G:0.42, T:0.10
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:2517107 original size:12 final size:12
Alignment explanation
Indices: 2517090--2517120 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2517080 TACAATAGGG
2517090 AGCTTCATACAA
1 AGCTTCATACAA
2517102 AGCTTCATACAA
1 AGCTTCATACAA
2517114 AGCTTCA
1 AGCTTCA
2517121 AGGTTTGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.26
Consensus pattern (12 bp):
AGCTTCATACAA
Found at i:2528160 original size:52 final size:52
Alignment explanation
Indices: 2528082--2528209 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
2528072 CGAAATATGA
*
2528082 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCAATACATCTGGGC
*
2528134 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCAATACATCTGGGC
2528186 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2528210 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCAATACATCTGGGC
Found at i:2528222 original size:51 final size:50
Alignment explanation
Indices: 2528082--2528229 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 50
2528072 CGAAATATGA
* *
2528082 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGC
2528134 AAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGC
2528186 AAA-TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
2528230 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.38
52 46 0.52
53 1 0.01
54 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGC
Found at i:2528236 original size:13 final size:13
Alignment explanation
Indices: 2528218--2528242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2528208 CAAAGATCAG
2528218 TGTATCGATACAA
1 TGTATCGATACAA
2528231 TGTATCGATACA
1 TGTATCGATACA
2528243 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2528320 original size:33 final size:33
Alignment explanation
Indices: 2528283--2528349 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2528273 AGTAGCTTAA
2528283 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2528316 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2528349 A
1 A
2528350 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2528323 original size:13 final size:13
Alignment explanation
Indices: 2528305--2528329 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2528295 CAAAAAAATA
2528305 TGTATCGATACAT
1 TGTATCGATACAT
2528318 TGTATCGATACA
1 TGTATCGATACA
2528330 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2528928 original size:84 final size:82
Alignment explanation
Indices: 2528805--2529432 Score: 344
Period size: 83 Copynumber: 7.5 Consensus size: 82
2528795 GGCTTTAGAG
* * * *
2528805 AAAGTTGCCACCAACTTGTGTGGGCTTTGAAAGGATGCCACTAACTTATTGGTTTTGAGAAGGCG
1 AAAGGTGCCACTAAC-T-TGTGGGCTTTGAAAGG-TGCCACTAACTTATGGGCTTTGAGAAGGCG
2528870 CCACTGA-TATGCGGGCTTTG-
63 CCACTGACT-TGCGGGC-TTGA
* * * * *
2528890 AGAGGATGCCACTGACTTGTGGGCTTTGAGAAGGTGCCACTAACTTCTGGGCTTTGAGAATGTGC
1 AAAGG-TGCCACTAACTTGTGGGCTTTGA-AAGGTGCCACTAACTTATGGGCTTTGAGAAGGCGC
*
2528955 CACTGACTTGTGGGCTTGA
64 CACTGACTTGCGGGCTTGA
* * * * **
2528974 AAAGGTGCCACTAACTTGTGGGCTTTGAAATGGTGCAATTGACTTGTGGGCTTTGTA-AAGATGC
1 AAAGGTGCCACTAACTTGTGGGCTTTGAAA-GGTGCCACTAACTTATGGGCTTTG-AGAAGGCGC
* *
2529038 CACTGACTTGTGGGCTTGG
64 CACTGACTTGCGGGCTTGA
* * * * * * * * * *
2529057 AAATGTGCCATTGACTTGTGGGCTTTGAAGGGGTGCCACTGACTTGTAGACTATGA-AAGGATGC
1 AAAGGTGCCACTAACTTGTGGGCTTTGAA-AGGTGCCACTAACTTATGGGCTTTGAGAAGG-CGC
* * * *
2529121 CACTAACTTGTGGACTTTA
64 CACTGACTTGCGGGCTTGA
* * * **
2529140 AAAGGATGCCATTGACTTGTGGGCTTT-AAAGAGATGCCACTAACTTGTGGGCTTTGA-AGAGAT
1 AAAGG-TGCCACTAACTTGTGGGCTTTGAAAG-G-TGCCACTAACTTATGGGCTTTGAGA-AGGC
* *
2529203 GCTACTAACTT-CTGGGCTTTG-
62 GCCACTGACTTGC-GGGC-TTGA
* * * * * **
2529224 AAAGGATGCCATTGACTTGTGAGCTTTGAAAGGATGCC-CTGACTTGTGGGCTTT-AGAATGATG
1 AAAGG-TGCCACTAACTTGTGGGCTTTGAAAGG-TGCCACTAACTTATGGGCTTTGAGAA-GGCG
* * *
2529287 CCACTAACTTGTGAGCTTTG-
63 CCACTGACTTGCGGGC-TTGA
* * * * * * * * * *
2529307 GAAGGATACCACTAACTTATGGGCTTTAGAAAGATTCCATTGACTTGTGGGCTTAGA-AAGGGTG
1 AAAGG-TGCCACTAACTTGTGGGCTTT-GAAAGGTGCCACTAACTTATGGGCTTTGAGAA-GGCG
* * *
2529371 CCACTAACTGGTGGGCTTTGA
63 CCACTGACTTGCGGGC-TTGA
** *
2529392 AAAAATGCCACTAACTCGTGGGCTTTGAAAGGGGTGCCACT
1 AAAGGTGCCACTAACTTGTGGGCTTTGAAA--GGTGCCACT
2529433 GATTGGTAGG
Statistics
Matches: 447, Mismatches: 72, Indels: 48
0.79 0.13 0.08
Matches are distributed among these distances:
82 9 0.02
83 202 0.45
84 202 0.45
85 26 0.06
86 8 0.02
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (82 bp):
AAAGGTGCCACTAACTTGTGGGCTTTGAAAGGTGCCACTAACTTATGGGCTTTGAGAAGGCGCCA
CTGACTTGCGGGCTTGA
Found at i:2529477 original size:28 final size:29
Alignment explanation
Indices: 2528823--2529479 Score: 553
Period size: 28 Copynumber: 23.5 Consensus size: 29
2528813 CACCAACTTG
*
2528823 TGTGGGCTTTG-AAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * * * *
2528851 TATTGGTTTTGAGAAGG-CGCCACTGA-T
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
2528878 ATGCGGGCTTTG-AGAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
2528907 TGTGGGCTTTGAGAAGG-TGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2528935 TCTGGGCTTTGAGAATG-TGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
2528963 TGTGGGC-TTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2528990 TGTGGGCTTTGAAATGG-TGCAATTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
2529018 TGTGGGCTTTGTAAA-GATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2529046 TGTGGGC-TTGGAAATG-TGCCATTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
2529073 TGTGGGCTTTG-AAGGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * * *
2529101 TGTAGACTATG-AAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
2529129 TGTGGACTTT-AAAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
2529157 TGTGGGCTTT--AAAGAGATGCCACTAACT
1 TGTGGGCTTTGAAAAG-GATGCCACTGACT
* * *
2529185 TGTGGGCTTTGAAGA-GATGCTACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
2529213 TCTGGGCTTTG-AAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
2529241 TGTGAGCTTTG-AAAGGATGCC-CTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2529268 TGTGGGCTTT-AGAATGATGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * * *
2529296 TGTGAGCTTTG-GAAGGATACCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2529324 TATGGGCTTT-AGAAA-GATTCCATTGACT
1 TGTGGGCTTTGA-AAAGGATGCCACTGACT
* * *
2529352 TGTGGGCTTAG-AAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2529380 GGTGGGCTTTGAAAA-AATGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2529408 CGTGGGCTTTGAAAGGGGTGCCACTGA-T
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
2529436 TGGTAGGCTTTGAAAAGGA-GCCACTGGCT
1 T-GTGGGCTTTGAAAAGGATGCCACTGACT
*
2529465 CGTGGGCTTTGAAAA
1 TGTGGGCTTTGAAAA
2529480 TAGATTATAT
Statistics
Matches: 508, Mismatches: 95, Indels: 52
0.78 0.15 0.08
Matches are distributed among these distances:
27 86 0.17
28 384 0.76
29 36 0.07
30 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACT
Found at i:2534997 original size:15 final size:15
Alignment explanation
Indices: 2534958--2535002 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2534948 AATGTTCGAC
*
2534958 GATTTTGTGGTGGGT
1 GATTTTGTGGTGGAT
* **
2534973 TATTAGGTGGTGGAT
1 GATTTTGTGGTGGAT
2534988 GATTTTGTGGTGGAT
1 GATTTTGTGGTGGAT
2535003 TTGACGGAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.42, T:0.44
Consensus pattern (15 bp):
GATTTTGTGGTGGAT
Found at i:2546103 original size:27 final size:27
Alignment explanation
Indices: 2546010--2546639 Score: 466
Period size: 28 Copynumber: 22.9 Consensus size: 27
2546000 GACCTCTCTA
*
2546010 AAGTCCACAACTCCGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * * * *
2546037 AGAGTCCACAACTTCATAGTATCCTTTT
1 A-AGTCCACAACTCCGTGGCACCCTTTT
* * **
2546065 GAAGTCCATAACTTCGTGGCATTCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
*
2546093 AAGTCCATAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
2546120 AAGTCCACAACTCCATGGCATCTCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
*
2546148 AAAGTCCACAACTCCGTAGCACCC--TT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
2546174 -A----A-AACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
2546195 GAAGTCCACAATTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
*
2546223 AAAGTCCACAACTCCGTGGCACCTTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
*
2546251 AAGTCCACAACTCCGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
2546278 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
2546305 AAGTCCACAACTCCATGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
2546332 AAGTCCATAACTCCGTGGCATCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
* * *
2546360 AAGTCCACAAGTCAGTGGCACCCTTTC
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * * * *
2546387 AAGCCCATAAGTCAGTGGCACTCCTTTCA
1 AAGTCCACAACTCCGTGGCAC-CCTTT-T
* * **
2546416 AAGCCCACAAGTAAGTGGCACTCCTTTT
1 AAGTCCACAACTCCGTGGCAC-CCTTTT
* * ** *
2546444 AAAGCCCACAAATCAATGGCACTCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* * **
2546472 CAAAGCCCACAAATGAGTGGCACCCTTTT
1 --AAGTCCACAACTCCGTGGCACCCTTTT
* * * * *
2546501 CAAAGCCCACAAGTCAGTGGCACTCTTTCA
1 --AAGTCCACAACTCCGTGGCACCCTTT-T
* * * *
2546531 AAGCCCACAAGTCAGTGGCACCCTTTCA
1 AAGTCCACAACTCCGTGGCACCCTTT-T
* * ** *
2546559 AAGCCCACAAGTTAGTGGCACCCTTTC
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * * *
2546586 AGAGCCCACAAGTCAGTGGCACCCTTTCG
1 A-AGTCCACAACTCCGTGGCACCCTTT-T
* * * *
2546615 AAGCCCACAAGTCAGTGGCAACCTT
1 AAGTCCACAACTCCGTGGCACCCTT
2546640 ACGAAGCCCA
Statistics
Matches: 522, Mismatches: 60, Indels: 41
0.84 0.10 0.07
Matches are distributed among these distances:
19 14 0.03
20 1 0.00
21 2 0.00
23 1 0.00
24 1 0.00
26 2 0.00
27 164 0.31
28 224 0.43
29 113 0.22
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:2546762 original size:32 final size:31
Alignment explanation
Indices: 2546365--2547144 Score: 584
Period size: 32 Copynumber: 25.8 Consensus size: 31
2546355 CTTTTAAGTC
* *
2546365 CACAAGTCAGTGGC-ACCCTTTC-AAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
* * *
2546392 CATAAGTCAGTGGC-ACTCCTTTCAAAG-CC-
1 CACAAGTCGGTGGCAAC-CTTTTCAAAGCCCA
** *
2546421 CACAAGTAAGTGGCACTCCTTTT-AAAGCCCA
1 CACAAGTCGGTGGCA-ACCTTTTCAAAGCCCA
**
2546452 CA-AA-TCAATGGC-ACTCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAAC-CTTTTCAAAGCCCA
*
2546481 CA-AA-T-GAGTGGCACCCTTTTCAAAG-CC-
1 CACAAGTCG-GTGGCAACCTTTTCAAAGCCCA
*
2546508 CACAAGTCAGTGGC-A-CTCTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCT-TTTCAAAGCCCA
* *
2546536 CACAAGTCAGTGGC-ACCCTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
** * *
2546564 CACAAGTTAGTGGC-ACCCTTTCAGAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
* * *
2546592 CACAAGTCAGTGGC-ACCCTTTCGAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
* * *
2546620 CACAAGTCAGTGGCAACC-TTACGAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
* * *
2546648 CACAAGTCAGTGGCAACC-TTACGAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
* **
2546676 CACAATTCAATGGC-A-CTCTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCT-TTTCAAAGCCCA
2546706 CACAAGTCGGTGGC-A-CTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCT-TTTCAAAGCCCA
* *
2546736 CAAAAGTCGGTGGCAACCTATTTCAAAGCCTA
1 CACAAGTCGGTGGCAACCT-TTTCAAAGCCCA
2546768 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
*
2546800 CACAAGTCGGTGGCAACCCTTTTTAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
* *
2546832 CACAAGTCGATGGC-A-CTATTTTAAAGCCCA
1 CACAAGTCGGTGGCAACCT-TTTCAAAGCCCA
* *
2546862 TACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
*
2546894 CACAAGTCGGTGGTAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
*
2546926 CACAAGTCGGTAGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
* *
2546958 CACAAGTCGGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
2546990 CACAAGTCGGTGGCAATCCATTTT-AAAGCCCA
1 CACAAGTCGGTGGCAA-CC-TTTTCAAAGCCCA
2547022 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
* * * *
2547054 CACAAGTTGATGGGAACCTCTTTCAAAAGTCCA
1 CACAAGTCGGTGGCAACCT-TTTC-AAAGCCCA
** * * *
2547087 CACTTGT-GGTGGAAACCCTTTTAAAAACCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
* * *
2547118 CGCAAGTCAGTGGTAACCCTTTTCAAA
1 CACAAGTCGGTGGCAA-CCTTTTCAAA
2547145 TCACCATTTT
Statistics
Matches: 653, Mismatches: 67, Indels: 61
0.84 0.09 0.08
Matches are distributed among these distances:
26 1 0.00
27 21 0.03
28 170 0.26
29 68 0.10
30 72 0.11
31 23 0.04
32 276 0.42
33 22 0.03
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (31 bp):
CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
Found at i:2547000 original size:96 final size:96
Alignment explanation
Indices: 2546365--2547144 Score: 644
Period size: 96 Copynumber: 8.6 Consensus size: 96
2546355 CTTTTAAGTC
* * *
2546365 CACAAGTCAGTGGC-ACCC-TTTC-AAG-CC-CATAAGTCAGTGGC-ACTCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAAC-CCTTTTCAAAGCCCA
** *
2546421 CACAAGTAAGTGGC-ACTCC-TTTTAAAGCCCA
65 CACAAGTCGGTGGCAAC-CCATTTCAAAGCCCA
** *
2546452 CA-AA-TCAATGGC-ACTCTTTTCAAAGCCCACA-AA-T-GAGTGGC-ACCCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG-GTGGCAACCCTTTTCAAAGCCCA
* *
2546508 CACAAGTCAGTGGC-ACTC-TTTCAAAG-CC-
65 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* ** *
2546536 CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACAAGTTAGTGGC-ACCC-TTTCAGAG-CC-C
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
* *
2546593 ACAAGTCAGTGGC-ACCC-TTTCGAAG-CC-
66 ACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * * * *
2546620 CACAAGTCAGTGGCAA-CC-TTACGAAG-CC-CACAAGTCAGTGGCAA-CC-TTACGAAG-CC-C
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
* ** *
2546677 ACAATTCAATGGC-ACTC-TTTCAAAGCCCA
66 ACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
2546706 CACAAGTCGGTGGC-A--CTATTTCAAAGCCCACAAAAGTCGGTGGCAA-CCTATTTCAAAGCCT
1 CACAAGTCGGTGGCAACCCT-TTTCAAAGCCCACACAAGTCGGTGGCAACCCT-TTTCAAAGCCC
*
2546767 ACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
64 ACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * ** *
2546800 CACAAGTCGGTGGCAACCCTTTTTAAAGCCCACACAAGTCGATGGC-ACTATTTT-AAAGCCCAT
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
2546863 ACAAGTCGGTGGCAACCCATTTCAAAGCCCA
66 ACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
2546894 CACAAGTCGGTGGTAACCCTTTTCAAAGCCCACACAAGTCGGTAGCAACCCTTTTCAAAGCCCAC
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
*
2546959 ACAAGTCGGTGGTAACCCATTTCAAAGCCCA
66 ACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
2546990 CACAAGTCGGTGGCAATCCATTTT-AAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* * * *
2547054 CACAAGTTGATGGGAACCTC-TTTCAAAAGTCCA
65 CACAAGTCGGTGGCAACC-CATTTC-AAAGCCCA
** * * * * * *
2547087 CACTTGT-GGTGGAAACCCTTTTAAAAACCCACGCAAGTCAGTGGTAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAA
2547145 TCACCATTTT
Statistics
Matches: 593, Mismatches: 65, Indels: 61
0.82 0.09 0.08
Matches are distributed among these distances:
83 2 0.00
84 110 0.19
85 37 0.06
86 45 0.08
87 40 0.07
88 20 0.03
89 2 0.00
90 6 0.01
91 1 0.00
92 11 0.02
93 3 0.01
94 105 0.18
95 17 0.03
96 173 0.29
97 21 0.04
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (96 bp):
CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
ACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:2552898 original size:280 final size:278
Alignment explanation
Indices: 2552370--2552907 Score: 699
Period size: 280 Copynumber: 1.9 Consensus size: 278
2552360 CTATCGCGAT
* *
2552370 GTGCGCTCCACCCCGGTGATAGGGCAAATGAGGCATGCCCGACTTAACATCCCTCATGATTGGGG
1 GTGCGCTCCACCCCGGTGATAGGGCAAATGAGGCACGCCCGACTTAACATCCCTCACGATTGGGG
* * ** * * *
2552435 ATTTCTATGGCATGGTAAGAGGTATGTGTTGAAAATAGGAAGATTGGTAGATGAATCACCCATCT
66 ATTTCCATGGCATGATAAGAAATATGTGTTGAAAAGAGGAAGATCGGTAGATGAATCACCCAACT
* * * * *
2552500 AACCGATCATTGACGGTCACCACAAAGTGATCAAAATTTTGGAGTCGTCATCGATCATTTTGGGC
131 AACCGATCATTGACGGTCACCACAAAGTGACCAAAATTTTGGAGTCATCATCAATCATTTCGGAC
2552565 TAGGCATGATCGTATGCCTATTGAAACCTATGTCTTGAGTTATGAAACTCGAGACATCGATCCTG
196 TAGGCATGATCGTATGCCTATTGAAACCTATGTCTTGAGTTATGAAACTCGAGACATCGATCCTG
2552630 TGATCTACGTGTCGCAAC
261 TGATCTACGTGTCGCAAC
* * * * * * *
2552648 GTGCGCTCGGACCCTGGTGATAGGGGCAGATGAGGCACGCCCGACTTAATATTCTTCGCGATTGG
1 GTGCGCTC-CACCCCGGTGATA-GGGCAAATGAGGCACGCCCGACTTAACATCCCTCACGATTGG
* * * * *
2552713 GGATTTCCATGGCATGATGAGAAATATATTGATT-AAAGGGGGAAGATCGGTAGATGAATCGCCC
64 GGATTTCCATGGCATGATAAGAAATAT-GTG-TTGAAAAGAGGAAGATCGGTAGATGAATCACCC
* * ** *
2552777 AACTAATCGATC-TTCGATGGTCACCATGAAGTGACCGAAA-TTTGGAGTCATCA-CTAATCATT
127 AACTAACCGATCATT-GACGGTCACCACAAAGTGACCAAAATTTTGGAGTCATCATC-AATCATT
2552839 TCGGACTAGGCATGATCAG-ATGCCTATTGAAACCTATGTCTTGAGTTATGAAACTCGAGACATC
190 TCGGACTAGGCATGATC-GTATGCCTATTGAAACCTATGTCTTGAGTTATGAAACTCGAGACATC
2552903 GATCC
254 GATCC
2552908 CGTAGTCTAC
Statistics
Matches: 222, Mismatches: 31, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
278 8 0.04
279 12 0.05
280 142 0.64
281 58 0.26
282 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (278 bp):
GTGCGCTCCACCCCGGTGATAGGGCAAATGAGGCACGCCCGACTTAACATCCCTCACGATTGGGG
ATTTCCATGGCATGATAAGAAATATGTGTTGAAAAGAGGAAGATCGGTAGATGAATCACCCAACT
AACCGATCATTGACGGTCACCACAAAGTGACCAAAATTTTGGAGTCATCATCAATCATTTCGGAC
TAGGCATGATCGTATGCCTATTGAAACCTATGTCTTGAGTTATGAAACTCGAGACATCGATCCTG
TGATCTACGTGTCGCAAC
Found at i:2555905 original size:20 final size:20
Alignment explanation
Indices: 2555880--2555917 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2555870 GTAAAAATAC
2555880 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
2555900 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
2555918 TGGGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:2562322 original size:38 final size:38
Alignment explanation
Indices: 2562266--2562376 Score: 109
Period size: 38 Copynumber: 2.9 Consensus size: 38
2562256 ACGGTTTTTG
* * * * *
2562266 TTTTGTTTTAAACTGTACCACTAGTTTAGAGTAGTGGT
1 TTTTGTTTCAAACTGTACCACCAGTTAAGAATAGTAGT
2562304 TTTTGTTTCAAA-TCGTACCACCAGTTAAGAATAGTAGT
1 TTTTGTTTCAAACT-GTACCACCAGTTAAGAATAGTAGT
* * * *
2562342 TTTTATTTCTAACTATACCACC-GATTGAGAATAGT
1 TTTTGTTTCAAACTGTACCACCAG-TTAAGAATAGT
2562377 GATTTTAGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
37 2 0.03
38 58 0.95
39 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (38 bp):
TTTTGTTTCAAACTGTACCACCAGTTAAGAATAGTAGT
Found at i:2563721 original size:21 final size:22
Alignment explanation
Indices: 2563697--2563745 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2563687 ATATAATTTG
*
2563697 AAATATTTATTTTTATAT-TAA
1 AAATATTTATTTTAATATATAA
*
2563718 AAATAATTATTTTAATATATAA
1 AAATATTTATTTTAATATATAA
*
2563740 ATATAT
1 AAATAT
2563746 ATTCAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATATTTATTTTAATATATAA
Found at i:2563748 original size:20 final size:19
Alignment explanation
Indices: 2563697--2563762 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
2563687 ATATAATTTG
* *
2563697 AAATATTTATTTTTATATT
1 AAATATATATTTTAATATT
*
2563716 AAAAATAATTATTTTAATATAT
1 AAATAT-A-TATTTTAATAT-T
**
2563738 AAATATATATTCAAATATT
1 AAATATATATTTTAATATT
2563757 CAAATA
1 -AAATA
2563763 AATAATTGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 6 0.16
20 14 0.38
21 11 0.30
22 6 0.16
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATATATATTTTAATATT
Found at i:2564619 original size:39 final size:39
Alignment explanation
Indices: 2564575--2564651 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
2564565 AGTTTTACAA
* *
2564575 CTAAGCACCTCAATTTTTATAAGATATAAGTTGCTATAT
1 CTAAGCACCTCAATTTCTATAAAATATAAGTTGCTATAT
* *
2564614 CTAAGCATCTTAATTTCTATAAAATATAAGTTGCTATA
1 CTAAGCACCTCAATTTCTATAAAATATAAGTTGCTATA
2564652 AATTTTAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (39 bp):
CTAAGCACCTCAATTTCTATAAAATATAAGTTGCTATAT
Found at i:2565686 original size:11 final size:11
Alignment explanation
Indices: 2565668--2565737 Score: 58
Period size: 10 Copynumber: 6.6 Consensus size: 11
2565658 CTAAATAACT
2565668 AAATAAATTAA
1 AAATAAATTAA
*
2565679 ACATAAA-TAA
1 AAATAAATTAA
*
2565689 AAATAAA-TAT
1 AAATAAATTAA
* *
2565699 AACTAATTTAA
1 AAATAAATTAA
*
2565710 AAAT-AACTAA
1 AAATAAATTAA
2565720 AAATAAA-TAA
1 AAATAAATTAA
2565730 AATATAAA
1 AA-ATAAA
2565738 CAAAACCTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
10 29 0.62
11 18 0.38
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATAAATTAA
Found at i:2565694 original size:21 final size:19
Alignment explanation
Indices: 2565655--2565737 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 19
2565645 ACATGAAAAA
2565655 AAACTAAATAACTAAATAAATT
1 AAACTAAATAA--AAATAAA-T
2565677 AAACATAAATAAAAATAAAT
1 AAAC-TAAATAAAAATAAAT
* *
2565697 ATAACTAATTTAAAAATAACT
1 A-AACTAA-ATAAAAATAAAT
*
2565718 AAAAATAAATAAAATATAAA
1 -AAACTAAATAAAA-ATAAA
2565738 CAAAACCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 10 0.20
21 29 0.57
22 5 0.10
23 7 0.14
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (19 bp):
AAACTAAATAAAAATAAAT
Found at i:2567994 original size:17 final size:17
Alignment explanation
Indices: 2567950--2568032 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 17
2567940 GCTTAAATAA
2567950 TTTT-ATTTTTTCATTT
1 TTTTAATTTTTTCATTT
** *
2567966 TTTTTCTCTTTTTCCTTT
1 TTTTAAT-TTTTTCATTT
*
2567984 TTTTAATTTTTTTC-TAAT
1 TTTTAA-TTTTTTCAT-TT
*
2568002 TTTAAATTTTTTCTAATTT
1 TTTTAATTTTTTC--ATTT
2568021 TTTTAATTTTTT
1 TTTTAATTTTTT
2568033 TTCAAAGAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
16 4 0.08
17 9 0.17
18 25 0.48
19 13 0.25
20 1 0.02
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTAATTTTTTCATTT
Found at i:2568022 original size:11 final size:10
Alignment explanation
Indices: 2567981--2568034 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
2567971 CTCTTTTTCC
2567981 TTTTTTTAAT
1 TTTTTTTAAT
2567991 TTTTTTCTAA-
1 TTTTTT-TAAT
*
2568001 --TTTTAAAT
1 TTTTTTTAAT
*
2568009 TTTTTCTAA-
1 TTTTTTTAAT
2568018 TTTTTTTAAT
1 TTTTTTTAAT
2568028 TTTTTTT
1 TTTTTTT
2568035 CAAAGAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
7 2 0.06
8 4 0.11
9 8 0.23
10 18 0.51
11 3 0.09
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:2579468 original size:92 final size:91
Alignment explanation
Indices: 2579320--2579645 Score: 243
Period size: 92 Copynumber: 3.5 Consensus size: 91
2579310 AATTTAACCA
* * * * *
2579320 AATTTATCGAACAAAATTATAAAATATTAACAAAA-CTGTAAATAATTTCATATATATCACTAAA
1 AATTTATCAAAC-TAATTTTAAAAAATTAACAAAATC-ATAAATAATTTCATATATATCACTAAA
2579384 TACAACATCTTTCAACAATAAATTAACTT
64 TACAA-ATCTTTCAACAATAAATTAACTT
* * * * * * *
2579413 AACTTATCAAACTAATTTTAAAAAATGAACAAAATCATAAATATTTTCATTTATATTAATTAATA
1 AATTTATCAAACTAATTTTAAAAAATTAACAAAATCATAAATAATTTCATATATATCACTAAATA
* * * *
2579478 CTTAATCATTAAACAAT-AATTAAACTA
66 C-AAATCTTTCAACAATAAATT-AACTT
* ** ** * *
2579505 AATTTATGAAAC-AAAATTACAAAATATTAACTCAATCATAAATAATGTCATATA-AACTACTAA
1 AATTTATCAAACTAATTTTA-AAAA-ATTAACAAAATCATAAATAATTTCATATATATC-ACTAA
*
2579568 ATACATAATCTTTC-A-AA-AAATAAACTT
63 ATACA-AATCTTTCAACAATAAATTAACTT
* ** * * *
2579595 AATTTATCAAACTAAATTATCTAATATTAACAATATCATAAATATTTTCAT
1 AATTTATCAAACT-AATTTTAAAAAATTAACAAAATCATAAATAATTTCAT
2579646 TTAAATTAAT
Statistics
Matches: 176, Mismatches: 47, Indels: 23
0.72 0.19 0.09
Matches are distributed among these distances:
90 36 0.20
91 16 0.09
92 76 0.43
93 48 0.27
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.35
Consensus pattern (91 bp):
AATTTATCAAACTAATTTTAAAAAATTAACAAAATCATAAATAATTTCATATATATCACTAAATA
CAAATCTTTCAACAATAAATTAACTT
Found at i:2579570 original size:185 final size:183
Alignment explanation
Indices: 2579258--2579670 Score: 505
Period size: 185 Copynumber: 2.2 Consensus size: 183
2579248 CAACAATGTT
* * * *
2579258 AAAATCATAAATAATTTCATTTAAATTTATTATTACTTAATATTTTAACAAAAATTTAACCAAAT
1 AAAATCATAAATATTTTCATTTAAATTAATTATTACTTAATATTTAAACAAAAATTAAACCAAAT
* * * *
2579323 TTATCGAACAAAATTATAAAATATTAACAAAACTGTAAATAATTTCATATATATCACTAAATACA
66 TTATCGAACAAAATTACAAAATATTAACAAAACTATAAATAATGTCATATAAATCACTAAATACA
* *
2579388 -ACATCTTTCAACAATAAATTAACTTAACTTATCAAACT-AATTTTAAAAAATGAAC
131 TA-ATCTTTC-A-AA-AAATAAACTTAACTTATCAAACTAAATTATAAAAAATGAAC
* * * *
2579443 AAAATCATAAATATTTTCATTTATATTAATTAATACTTAATCA-TTAAACAATAATTAAACTAAA
1 AAAATCATAAATATTTTCATTTAAATTAATTATTACTTAAT-ATTTAAACAAAAATTAAACCAAA
**
2579507 TTTAT-GAAACAAAATTACAAAATATTAACTCAA-TCATAAATAATGTCATATAAA-CTACTAAA
65 TTTATCG-AACAAAATTACAAAATATTAACAAAACT-ATAAATAATGTCATATAAATC-ACTAAA
* ** * *
2579569 TACATAATCTTTCAAAAAATAAACTTAATTTATCAAACTAAATTATCTAATATTAAC
127 TACATAATCTTTCAAAAAATAAACTTAACTTATCAAACTAAATTATAAAAAATGAAC
* *
2579626 AATATCATAAATATTTTCATTTAAATTAATCATTACTTAATATTT
1 AAAATCATAAATATTTTCATTTAAATTAATTATTACTTAATATTT
2579671 CAATAACAGT
Statistics
Matches: 196, Mismatches: 25, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
182 22 0.11
183 53 0.27
184 4 0.02
185 115 0.59
186 2 0.01
ACGTcount: A:0.50, C:0.12, G:0.01, T:0.37
Consensus pattern (183 bp):
AAAATCATAAATATTTTCATTTAAATTAATTATTACTTAATATTTAAACAAAAATTAAACCAAAT
TTATCGAACAAAATTACAAAATATTAACAAAACTATAAATAATGTCATATAAATCACTAAATACA
TAATCTTTCAAAAAATAAACTTAACTTATCAAACTAAATTATAAAAAATGAAC
Found at i:2580828 original size:3 final size:3
Alignment explanation
Indices: 2580820--2580867 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
2580810 TAAATAATCC
* * * * *
2580820 ATT ATT ATT ATT ATT ATT ATT ACT ACT AAT ATA ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2580868 TGGGATCAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:2582407 original size:3 final size:3
Alignment explanation
Indices: 2582399--2582425 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2582389 CCTTTGCTAA
2582399 TGC TGC TGC TGC TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC
2582426 CCCTTTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
TGC
Found at i:2584028 original size:20 final size:20
Alignment explanation
Indices: 2583988--2584028 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2583978 TTTTTTATTT
*
2583988 TGATATAAAATCATATCAAA
1 TGATATAAAATAATATCAAA
2584008 TGATATAAAACTAATAT-AAA
1 TGATATAAAA-TAATATCAAA
2584028 T
1 T
2584029 ATCATCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (20 bp):
TGATATAAAATAATATCAAA
Found at i:2584925 original size:17 final size:18
Alignment explanation
Indices: 2584903--2584967 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 18
2584893 TACACTGTTT
2584903 AAAATTA-ATTTTTATTA
1 AAAATTATATTTTTATTA
*
2584920 AAAATTATATTATTAAATTA
1 AAAATTATATT-TT-TATTA
*
2584940 AAAA-TAT-TTTTTAATA
1 AAAATTATATTTTTATTA
*
2584956 AATATTATATTT
1 AAAATTATATTT
2584968 AATATTTACT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 6 0.15
17 12 0.31
18 8 0.21
19 5 0.13
20 8 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATTATATTTTTATTA
Found at i:2584957 original size:21 final size:20
Alignment explanation
Indices: 2584916--2584958 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2584906 ATTAATTTTT
*
2584916 ATTAAAAATTATATTATTAA
1 ATTAAAAATTATATTAATAA
* *
2584936 ATTAAAAATATTTTTTAATAA
1 ATTAAAAAT-TATATTAATAA
2584957 AT
1 AT
2584959 ATTATATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAAAAATTATATTAATAA
Found at i:2585020 original size:20 final size:20
Alignment explanation
Indices: 2584962--2585021 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
2584952 AATAAATATT
* *
2584962 ATATTTAATAT-TTACTT-A
1 ATATTTAAAATATTATTTAA
*
2584980 ATA-TTAAAATTATT-TTAAA
1 ATATTTAAAA-TATTATTTAA
2584999 ATATTTAAAATATTATTTAA
1 ATATTTAAAATATTATTTAA
2585019 ATA
1 ATA
2585022 AAATTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 5 0.15
18 5 0.15
19 10 0.30
20 13 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTTAAAATATTATTTAA
Found at i:2585051 original size:21 final size:20
Alignment explanation
Indices: 2585023--2585062 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2585013 ATTTAAATAA
*
2585023 AATTATTAAATTAATAATTG
1 AATTATTAAATTAAAAATTG
2585043 AATTGATTAAATTAAAAATT
1 AATT-ATTAAATTAAAAATT
2585063 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
AATTATTAAATTAAAAATTG
Found at i:2585073 original size:6 final size:7
Alignment explanation
Indices: 2585051--2585076 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2585041 TGAATTGATT
2585051 AAATTAA
1 AAATTAA
2585058 AAATTAA
1 AAATTAA
2585065 AAATTAA
1 AAATTAA
2585072 AAATT
1 AAATT
2585077 TTTACTGATG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATTAA
Found at i:2587715 original size:69 final size:69
Alignment explanation
Indices: 2587630--2587765 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 69
2587620 TTTTTTTTTT
* * * * *
2587630 TTTGTTAAACAAACAAAATTAGCCTACGTAAAAAATGGCAAAAACAGCCAAAACAAATGAAGCTG
1 TTTGTTAAACAAACAAAATAAACCAAAGTAAAAAATGGAAAAAACAGCCAAAACAAATGAAGCTG
2587695 ATTG
66 ATTG
* *
2587699 TTTGTTAAACAAACAAAATAAACCAAAGTAAAAAATGGAAAAAATAGCCAAAATAAATGAAGCTG
1 TTTGTTAAACAAACAAAATAAACCAAAGTAAAAAATGGAAAAAACAGCCAAAACAAATGAAGCTG
2587764 AT
66 AT
2587766 CAGATAAAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (69 bp):
TTTGTTAAACAAACAAAATAAACCAAAGTAAAAAATGGAAAAAACAGCCAAAACAAATGAAGCTG
ATTG
Found at i:2588472 original size:2 final size:2
Alignment explanation
Indices: 2588465--2588500 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2588455 AGAATAAGAC
*
2588465 AT AT AT AT AG 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
2588501 GAAATTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2589779 original size:16 final size:16
Alignment explanation
Indices: 2589744--2589787 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2589734 AAAATAAAAT
* *
2589744 TAAAATCAATTATTTTA
1 TAAAAT-AAATATTTAA
2589761 TAAAATAAATATTTAA
1 TAAAATAAATATTTAA
*
2589777 TAAATTAAATA
1 TAAAATAAATA
2589788 ATCATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATAAATATTTAA
Found at i:2589782 original size:28 final size:28
Alignment explanation
Indices: 2589727--2589783 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
2589717 TTATTCTAAA
*
2589727 ATTTTATAAAATAAAATTAAAATCAATT
1 ATTTTATAAAATAAAATTAAAATAAATT
*
2589755 ATTTTATAAAATAAATATT-TAATAAATT
1 ATTTTATAAAATAAA-ATTAAAATAAATT
2589783 A
1 A
2589784 AATAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
ATTTTATAAAATAAAATTAAAATAAATT
Found at i:2592181 original size:14 final size:14
Alignment explanation
Indices: 2592164--2592192 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2592154 AATTTATAAG
2592164 TAAGAATTTTAATT
1 TAAGAATTTTAATT
2592178 TAAGAATTTTAATT
1 TAAGAATTTTAATT
2592192 T
1 T
2592193 TATAAAAAGT
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TAAGAATTTTAATT
Found at i:2593204 original size:12 final size:12
Alignment explanation
Indices: 2593187--2593219 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2593177 ACATATGGTA
2593187 TTTATTTTACTG
1 TTTATTTTACTG
2593199 TTTATTTTACTG
1 TTTATTTTACTG
2593211 TTTATTTTA
1 TTTATTTTA
2593220 GATTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (12 bp):
TTTATTTTACTG
Found at i:2593595 original size:22 final size:24
Alignment explanation
Indices: 2593548--2593595 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
2593538 TATATTTTTA
*
2593548 TTAAATATTTATTATATTTAATAT
1 TTAAATATTTATTATATTTAAAAT
2593572 TTAAATTATTT-TTA-A-TTAAAAT
1 TTAAA-TATTTATTATATTTAAAAT
2593594 TT
1 TT
2593596 TCGATTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 8 0.36
23 1 0.05
24 8 0.36
25 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTAAATATTTATTATATTTAAAAT
Found at i:2594693 original size:9 final size:9
Alignment explanation
Indices: 2594679--2594708 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2594669 CACGTTGTAG
2594679 ATAGTAATA
1 ATAGTAATA
2594688 ATAGTAATA
1 ATAGTAATA
*
2594697 ATAATAATA
1 ATAGTAATA
2594706 ATA
1 ATA
2594709 ATTTCTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (9 bp):
ATAGTAATA
Found at i:2595327 original size:20 final size:20
Alignment explanation
Indices: 2595293--2595330 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2595283 CACATGGTAG
**
2595293 GTTTTATTTTTATTTTTTTT
1 GTTTTATTTAAATTTTTTTT
2595313 GTTTTATTTAAATTTTTT
1 GTTTTATTTAAATTTTTT
2595331 ATATTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (20 bp):
GTTTTATTTAAATTTTTTTT
Found at i:2595337 original size:20 final size:20
Alignment explanation
Indices: 2595294--2595338 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2595284 ACATGGTAGG
** * *
2595294 TTTTATTTTTATTTTTTTTG
1 TTTTATTTAAATTTTTTATA
2595314 TTTTATTTAAATTTTTTATA
1 TTTTATTTAAATTTTTTATA
2595334 TTTTA
1 TTTTA
2595339 AAGGATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTATTTAAATTTTTTATA
Found at i:2595468 original size:42 final size:42
Alignment explanation
Indices: 2595383--2595468 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
2595373 TTTTATTTTA
* **
2595383 TTAATGATTTATATATTTTTTATTTATTTTTAAATTATGTAT
1 TTAATGATTTATAGATTTTTTATTTATTTTTAAAAAATGTAT
* *
2595425 TTAATGATTTTTGGATTTTTTATTTTATTTTTAAAAAAT-TAT
1 TTAATGATTTATAGATTTTTTA-TTTATTTTTAAAAAATGTAT
2595467 TT
1 TT
2595469 TATTTTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 24 0.63
43 14 0.37
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (42 bp):
TTAATGATTTATAGATTTTTTATTTATTTTTAAAAAATGTAT
Found at i:2595489 original size:19 final size:19
Alignment explanation
Indices: 2595444--2595488 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
2595434 TTTGGATTTT
2595444 TTATTTTATTTTTAAAAAA
1 TTATTTTATTTTTAAAAAA
*
2595463 TTATTTTATTTTTAAATAA
1 TTATTTTATTTTTAAAAAA
2595482 TGTATTT
1 T-TATTT
2595489 AAAAAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATTTTATTTTTAAAAAA
Found at i:2595728 original size:32 final size:32
Alignment explanation
Indices: 2595664--2595726 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 32
2595654 TGAATAAAAT
*
2595664 TTTTTTAAAATAATTTAAAATGATTGATTTTA
1 TTTTTAAAAATAATTTAAAATGATTGATTTTA
2595696 TTTTTAAATAATAATTTAAAATGATTGATTT
1 TTTTTAAA-AATAATTTAAAATGATTGATTT
2595727 ATACATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (32 bp):
TTTTTAAAAATAATTTAAAATGATTGATTTTA
Found at i:2600389 original size:3 final size:3
Alignment explanation
Indices: 2600381--2600437 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
2600371 TGTTGTAGAA
* * *
2600381 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAC AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2600429 AAT AAT AAT
1 AAT AAT AAT
2600438 TTCTTGACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2601174 original size:20 final size:20
Alignment explanation
Indices: 2601137--2601175 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2601127 TTTATTAATA
** *
2601137 ATTTTTAAATTTTTTATTTT
1 ATTTTTAAATAATATATTTT
2601157 ATTTTTAAATAATATATTT
1 ATTTTTAAATAATATATTT
2601176 AAAATAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTTAAATAATATATTTT
Found at i:2602571 original size:16 final size:17
Alignment explanation
Indices: 2602552--2602584 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2602542 ATATAACTCG
*
2602552 TTAATTATATA-TAAAT
1 TTAATGATATATTAAAT
2602568 TTAATGATATATTAAAT
1 TTAATGATATATTAAAT
2602585 ATAAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTAATGATATATTAAAT
Found at i:2603033 original size:24 final size:24
Alignment explanation
Indices: 2602988--2603033 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2602978 TAAAATAAAA
* *
2602988 TTTAAATATCAAATTAATAATTTT
1 TTTAAATATCAAACTAAAAATTTT
* *
2603012 TTTAAATATTAAGCTAAAAATT
1 TTTAAATATCAAACTAAAAATT
2603034 AAATTAATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTAAATATCAAACTAAAAATTTT
Found at i:2604152 original size:22 final size:21
Alignment explanation
Indices: 2604106--2604152 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
2604096 TTTATTATTT
*
2604106 TTAATATTAAAATATATTTAT
1 TTAATATTAAAATATATTTAA
*
2604127 TTAATATTTAAAT-TAATTTCAA
1 TTAATATTAAAATAT-ATTT-AA
2604149 TTAA
1 TTAA
2604153 ATCATTGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATATTAAAATATATTTAA
Found at i:2604467 original size:18 final size:18
Alignment explanation
Indices: 2604446--2604480 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2604436 GTGACACATA
* *
2604446 TTTTATTTATTTTTTATT
1 TTTTATATATATTTTATT
2604464 TTTTATATATATTTTAT
1 TTTTATATATATTTTAT
2604481 GAAATATGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATATATATTTTATT
Found at i:2605308 original size:9 final size:9
Alignment explanation
Indices: 2605296--2605343 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
2605286 TTTTATACAT
2605296 TATATAATA
1 TATATAATA
*
2605305 TATATGATA
1 TATATAATA
*
2605314 TATAATTTATA
1 TAT-A-TAATA
2605325 TATATAATA
1 TATATAATA
2605334 T-TATAATA
1 TATATAATA
2605342 TA
1 TA
2605344 AATATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 8 0.24
9 16 0.48
10 2 0.06
11 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (9 bp):
TATATAATA
Found at i:2606287 original size:24 final size:23
Alignment explanation
Indices: 2606241--2606293 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
2606231 TTTATTTTTA
**
2606241 TTTAATTTTTAATAAATTTATAT
1 TTTAATTTTTAATAAATAAATAT
2606264 TATTAATTTTTAA-AATATAAATAT
1 T-TTAATTTTTAATAA-ATAAATAT
2606288 TTTAAT
1 TTTAAT
2606294 ATATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTAATTTTTAATAAATAAATAT
Found at i:2606330 original size:29 final size:29
Alignment explanation
Indices: 2606252--2606332 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 29
2606242 TTAATTTTTA
* *
2606252 ATAAAT-TTATATTATTA-ATTTTTAAAAT
1 ATAAATATTATAATATTATATTTTT-TAAT
*
2606280 ATAAATATTTTAATA-TAT-TTTTTTAAT
1 ATAAATATTATAATATTATATTTTTTAAT
**
2606307 ATTTATATTATAATATTATATTTTTT
1 ATAAATATTATAATATTATATTTTTT
2606333 TATAATATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 15 0.35
28 16 0.37
29 12 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
ATAAATATTATAATATTATATTTTTTAAT
Found at i:2606347 original size:30 final size:29
Alignment explanation
Indices: 2606270--2606353 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 29
2606260 ATATTATTAA
* **
2606270 TTTTTAAAATATAAA-TATTTTAATATAT
1 TTTTTTAAATATAAATTATAATAATATAT
* * *
2606298 TTTTTTAATATTTATATTATAATATTATAT
1 TTTTTTAA-ATATAAATTATAATAATATAT
2606328 TTTTTTATAATATAAATTAT-ATAATA
1 TTTTTTA-AATATAAATTATAATAATA
2606354 CATATTAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
28 7 0.16
29 10 0.23
30 26 0.59
31 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTTTTAAATATAAATTATAATAATATAT
Found at i:2606349 original size:27 final size:27
Alignment explanation
Indices: 2606252--2606349 Score: 63
Period size: 30 Copynumber: 3.4 Consensus size: 27
2606242 TTAATTTTTA
* *
2606252 ATAAATTTATATTAT-TAATTTTTAAAAT
1 ATAAA-TTATATTATAT-TTTTTTATAAT
* * *
2606280 ATAAATATTTTAATATATTTTTTTAATATTT
1 AT-AA-ATTATATTATATTTTTTT-ATA-AT
* *
2606311 ATATTATAATATTATATTTTTTTATAAT
1 ATA-AATTATATTATATTTTTTTATAAT
2606339 ATAAATTATAT
1 ATAAATTATAT
2606350 AATACATATT
Statistics
Matches: 52, Mismatches: 12, Indels: 13
0.68 0.16 0.17
Matches are distributed among these distances:
27 6 0.12
28 6 0.12
29 17 0.33
30 20 0.38
31 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATAAATTATATTATATTTTTTTATAAT
Found at i:2606358 original size:18 final size:17
Alignment explanation
Indices: 2606334--2606396 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
2606324 ATATTTTTTT
2606334 ATAATATAAATTATATA
1 ATAATATAAATTATATA
2606351 ATACATATTAATATTA-A-A
1 ATA-ATA-TAA-ATTATATA
*
2606369 ATAATATATATTATATA
1 ATAATATAAATTATATA
2606386 ATTAATA-AAAT
1 A-TAATATAAAT
2606397 AAATCAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 4 0.11
16 3 0.08
17 11 0.29
18 12 0.32
19 4 0.11
20 4 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATATAAATTATATA
Found at i:2606374 original size:21 final size:23
Alignment explanation
Indices: 2606348--2606390 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
2606338 TATAAATTAT
2606348 ATAATACATATTA-AT-ATTAAA
1 ATAATACATATTATATAATTAAA
*
2606369 ATAATATATATTATATAATTAA
1 ATAATACATATTATATAATTAA
2606391 TAAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAATACATATTATATAATTAAA
Found at i:2606606 original size:30 final size:30
Alignment explanation
Indices: 2606570--2606630 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2606560 GTGAAATGAT
*
2606570 ATTAAATTA-ATTAAAAAATATAAAATTAAA
1 ATTAAATTATAATAAAAAA-ATAAAATTAAA
**
2606600 ATTAAATTATAATATTAAAATAAAATTAAA
1 ATTAAATTATAATAAAAAAATAAAATTAAA
2606630 A
1 A
2606631 GTATTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (30 bp):
ATTAAATTATAATAAAAAAATAAAATTAAA
Found at i:2606610 original size:19 final size:19
Alignment explanation
Indices: 2606583--2606627 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2606573 AAATTAATTA
*
2606583 AAAAATATAAAATTAAAAT
1 AAAATTATAAAATTAAAAT
* *
2606602 TAAATTATAATATTAAAAT
1 AAAATTATAAAATTAAAAT
2606621 AAAATTA
1 AAAATTA
2606628 AAAGTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTATAAAATTAAAAT
Found at i:2606623 original size:5 final size:6
Alignment explanation
Indices: 2606584--2606630 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
2606574 AATTAATTAA
2606584 AAAATAT AAAATT AAAATT -AAATT ATAATATT AAAA-T AAAATT AAAA
1 AAAAT-T AAAATT AAAATT AAAATT A-AA-ATT AAAATT AAAATT AAAA
2606631 GTATTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 10 0.28
6 13 0.36
7 9 0.25
8 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:2607536 original size:17 final size:18
Alignment explanation
Indices: 2607489--2607536 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
2607479 TATATGATAT
*
2607489 TTTAAAAAGTTAAAAAATA
1 TTTAAAAA-TTATAAAATA
*
2607508 TTTTAAAA-TATAAAATA
1 TTTAAAAATTATAAAATA
2607525 -TTAAAAATTATA
1 TTTAAAAATTATA
2607537 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 6 0.24
17 12 0.48
19 7 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TTTAAAAATTATAAAATA
Found at i:2607757 original size:13 final size:13
Alignment explanation
Indices: 2607739--2607764 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2607729 TTATTTTAAT
2607739 TTTTAAAAAATTA
1 TTTTAAAAAATTA
2607752 TTTTAAAAAATTA
1 TTTTAAAAAATTA
2607765 AAAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTTAAAAAATTA
Found at i:2610907 original size:35 final size:35
Alignment explanation
Indices: 2610861--2610931 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2610851 TAATTAATTG
2610861 AGGATCTTTTAATTTTTCATAAAGTTTGAGGACTT
1 AGGATCTTTTAATTTTTCATAAAGTTTGAGGACTT
2610896 AGGATCTTTTAATTTTTCATAAAGTTTGAGGACTT
1 AGGATCTTTTAATTTTTCATAAAGTTTGAGGACTT
2610931 A
1 A
2610932 TTAGGCATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (35 bp):
AGGATCTTTTAATTTTTCATAAAGTTTGAGGACTT
Found at i:2617278 original size:40 final size:40
Alignment explanation
Indices: 2617219--2617301 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 40
2617209 TGATGTGTGT
* * * *
2617219 ATTCTCATTGCCCATTCATAGCATTTTAGTTATGATATTC
1 ATTCTCATTACCCAATCATAGCATTTTAGTTACGACATTC
*
2617259 ATTCTTATTACCCAATCATAGCATTTTAGTTACGACATTC
1 ATTCTCATTACCCAATCATAGCATTTTAGTTACGACATTC
2617299 ATT
1 ATT
2617302 GACTTTTTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.43
Consensus pattern (40 bp):
ATTCTCATTACCCAATCATAGCATTTTAGTTACGACATTC
Found at i:2618233 original size:14 final size:13
Alignment explanation
Indices: 2618206--2618252 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
2618196 ACATTTTTGC
*
2618206 TTAGATTTTTAAA
1 TTAGATTTTAAAA
2618219 TTAGAGTTTTAAAA
1 TTAGA-TTTTAAAA
2618233 TTCAGATTTTAAAA
1 TT-AGATTTTAAAA
2618247 TT-GATT
1 TTAGATT
2618253 ACACTGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 4 0.13
13 5 0.16
14 19 0.61
15 3 0.10
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (13 bp):
TTAGATTTTAAAA
Found at i:2620214 original size:30 final size:30
Alignment explanation
Indices: 2620178--2620238 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2620168 TAGTATACTT
*
2620178 TATCACACAAAGTTGTAGAGTCACTAGAGC
1 TATCACACAAAGTTGTAGAGTCACGAGAGC
2620208 TATCACACAAAGTTGTAGAGTCACGAGAGC
1 TATCACACAAAGTTGTAGAGTCACGAGAGC
2620238 T
1 T
2620239 TTAATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (30 bp):
TATCACACAAAGTTGTAGAGTCACGAGAGC
Found at i:2624674 original size:51 final size:51
Alignment explanation
Indices: 2624598--2624723 Score: 227
Period size: 51 Copynumber: 2.5 Consensus size: 51
2624588 TACCTAGTTG
*
2624598 ACTTTAAAG-AGCACTTTTAAATAGGTCGAAGGGAAAACTAAGTCATATTGC
1 ACTTT-AAGTAGCACTTTTAAATAGGTCAAAGGGAAAACTAAGTCATATTGC
2624649 ACTTTAAGTAGCACTTTTAAATAGGTCAAAGGGAAAACTAAGTCATATTGC
1 ACTTTAAGTAGCACTTTTAAATAGGTCAAAGGGAAAACTAAGTCATATTGC
2624700 ACTTTAAGTAGCACTTTTAAATAG
1 ACTTTAAGTAGCACTTTTAAATAG
2624724 TTATTTCCTG
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
50 3 0.04
51 70 0.96
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (51 bp):
ACTTTAAGTAGCACTTTTAAATAGGTCAAAGGGAAAACTAAGTCATATTGC
Found at i:2629308 original size:16 final size:16
Alignment explanation
Indices: 2629284--2629322 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2629274 AGTGTTATTG
*
2629284 TGAACTTTGACTATTTA
1 TGAA-TTTGACTATTCA
*
2629301 TGAATTTGAGTATTCA
1 TGAATTTGACTATTCA
2629317 TGAATT
1 TGAATT
2629323 ATGTATATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (16 bp):
TGAATTTGACTATTCA
Found at i:2630035 original size:14 final size:14
Alignment explanation
Indices: 2630013--2630086 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
2630003 TCGATTTTAA
2630013 ATATATTTTATTAT
1 ATATATTTTATTAT
*
2630027 ATGTATTTTA--A-
1 ATATATTTTATTAT
*
2630038 ATATATTTTATTAA
1 ATATATTTTATTAT
2630052 ATATATTTTATTAT
1 ATATATTTTATTAT
*
2630066 ATGTATTTTA--A-
1 ATATATTTTATTAT
2630077 ATATATTTTA
1 ATATATTTTA
2630087 AATATTTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
11 18 0.35
12 2 0.04
13 1 0.02
14 31 0.60
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
ATATATTTTATTAT
Found at i:2630040 original size:25 final size:25
Alignment explanation
Indices: 2630006--2630091 Score: 113
Period size: 25 Copynumber: 3.4 Consensus size: 25
2629996 ATTGTTTTCG
* *
2630006 ATTTTAAATATATTTTATTATATGT
1 ATTTTAAATATATTTTATTAAATAT
2630031 ATTTTAAATATATTTTATTAAATAT
1 ATTTTAAATATATTTTATTAAATAT
*
2630056 ATTTT-ATTATATGTATT-TTAAATAT
1 ATTTTAAATATAT-T-TTATTAAATAT
2630081 ATTTTAAATAT
1 ATTTTAAATAT
2630092 TTTAAATATT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
24 6 0.11
25 42 0.78
26 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTTAAATATATTTTATTAAATAT
Found at i:2630057 original size:39 final size:39
Alignment explanation
Indices: 2630009--2630086 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2629999 GTTTTCGATT
2630009 TTAAATATATTTTATTATATGTATTTTAAATATATTTTA
1 TTAAATATATTTTATTATATGTATTTTAAATATATTTTA
2630048 TTAAATATATTTTATTATATGTATTTTAAATATATTTTA
1 TTAAATATATTTTATTATATGTATTTTAAATATATTTTA
2630087 AATATTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (39 bp):
TTAAATATATTTTATTATATGTATTTTAAATATATTTTA
Found at i:2630974 original size:2 final size:2
Alignment explanation
Indices: 2630967--2630995 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2630957 ACCTTTTTAT
2630967 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 T
2630996 GAGGAAAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2634977 original size:20 final size:20
Alignment explanation
Indices: 2634940--2634977 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2634930 TGTGACATAT
*
2634940 TCTAGCCATCTCATCAATCA
1 TCTAGCCATCTCAACAATCA
2634960 TCTA-CCATCATCAACAAT
1 TCTAGCCATC-TCAACAAT
2634978 AAAAGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (20 bp):
TCTAGCCATCTCAACAATCA
Found at i:2638007 original size:20 final size:20
Alignment explanation
Indices: 2637982--2638026 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
2637972 TTAAAGTTTA
2637982 TATTTGATAAATGATGTATG
1 TATTTGATAAATGATGTATG
2638002 TATTTGATAAATGATGTATG
1 TATTTGATAAATGATGTATG
2638022 TATTT
1 TATTT
2638027 ATATATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (20 bp):
TATTTGATAAATGATGTATG
Found at i:2638600 original size:20 final size:20
Alignment explanation
Indices: 2638577--2638615 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2638567 TAAAATATTA
2638577 ATTTAT-ATTAATATTTAAAC
1 ATTTATAATTAA-ATTTAAAC
2638597 ATTTATAATTAAATTTAAA
1 ATTTATAATTAAATTTAAA
2638616 TAAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTATAATTAAATTTAAAC
Found at i:2640460 original size:50 final size:50
Alignment explanation
Indices: 2640385--2640617 Score: 358
Period size: 50 Copynumber: 4.6 Consensus size: 50
2640375 AGTTGTTGCC
* * * *
2640385 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
2640435 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2640485 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * *
2640535 ATTGTTGACGATTCTTCACCAACCTTTAACAAATGGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATA
*
2640586 ATTGTTGACGATTCTTTACCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
2640618 ATGTGGCCAT
Statistics
Matches: 167, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
50 122 0.73
51 45 0.27
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:2646690 original size:32 final size:31
Alignment explanation
Indices: 2646616--2646684 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
2646606 ATTATTGAAC
* * *
2646616 AAATAATTTGATTTAAATTATTATTTTTATTAT
1 AAATAATTT-TTTTAAATTATCATTTTTA-TAA
2646649 AAATAATTTTTTTAAATTATCATTTTTA-AA
1 AAATAATTTTTTTAAATTATCATTTTTATAA
2646679 AAATAA
1 AAATAA
2646685 AATTTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 7 0.21
32 17 0.52
33 9 0.27
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (31 bp):
AAATAATTTTTTTAAATTATCATTTTTATAA
Found at i:2646697 original size:22 final size:22
Alignment explanation
Indices: 2646672--2646713 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2646662 AAATTATCAT
2646672 TTTTAAAAAATAAAATTTTAAA
1 TTTTAAAAAATAAAATTTTAAA
**
2646694 TTTTAAAATTTAAAATTTTA
1 TTTTAAAAAATAAAATTTTA
2646714 TTATATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTAAAAAATAAAATTTTAAA
Found at i:2646700 original size:15 final size:15
Alignment explanation
Indices: 2646682--2646713 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2646672 TTTTAAAAAA
*
2646682 TAAAATTTTAAATTT
1 TAAAATTTAAAATTT
2646697 TAAAATTTAAAATTT
1 TAAAATTTAAAATTT
2646712 TA
1 TA
2646714 TTATATTAAA
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:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAAATTTAAAATTT
Found at i:2646702 original size:8 final size:8
Alignment explanation
Indices: 2646682--2646713 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
2646672 TTTTAAAAAA
2646682 TAAAATTT
1 TAAAATTT
2646690 T-AAATTT
1 TAAAATTT
2646697 TAAAA-TT
1 TAAAATTT
2646704 TAAAATTT
1 TAAAATTT
2646712 TA
1 TA
2646714 TTATATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.64
8 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TAAAATTT
Found at i:2647833 original size:51 final size:50
Alignment explanation
Indices: 2647703--2647854 Score: 216
Period size: 49 Copynumber: 3.0 Consensus size: 50
2647693 GAAATGTTTT
* * *
2647703 AAGACTCGGACTCCGGAAGTAGGGAGGAATCAACCGCAAAGTAAAGCGTG
1 AAGACTCGGACTCCGGAAGTAAGGAGGAACCAACCGCAAATTAAAGCGTG
**
2647753 -AGACTCGGACTCCGGAAGCGAGGAGGAACCAACCGCAAATTAAAGCGTG
1 AAGACTCGGACTCCGGAAGTAAGGAGGAACCAACCGCAAATTAAAGCGTG
* * *
2647802 AAGACTCAAGACTCAGGAAGTAAGGAGGAACCAACCGCAAATTAAAGCATG
1 AAGACTC-GGACTCCGGAAGTAAGGAGGAACCAACCGCAAATTAAAGCGTG
2647853 AA
1 AA
2647855 CAGGAAAGCA
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
49 44 0.49
50 6 0.07
51 40 0.44
ACGTcount: A:0.39, C:0.21, G:0.28, T:0.11
Consensus pattern (50 bp):
AAGACTCGGACTCCGGAAGTAAGGAGGAACCAACCGCAAATTAAAGCGTG
Found at i:2648710 original size:16 final size:16
Alignment explanation
Indices: 2648689--2648744 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
2648679 TAAATACTTA
*
2648689 TTTTTTAATTTATTAT
1 TTTTTTAATATATTAT
2648705 TTTTTTAAAATATATTAT
1 TTTTTT--AATATATTAT
* * *
2648723 ATTTTTAAAATATAAT
1 TTTTTTAATATATTAT
2648739 TTTTTT
1 TTTTTT
2648745 CGATTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 19 0.58
18 14 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTAATATATTAT
Found at i:2648720 original size:18 final size:18
Alignment explanation
Indices: 2648668--2648744 Score: 70
Period size: 18 Copynumber: 4.3 Consensus size: 18
2648658 GATCTTTAAA
*
2648668 TTTTTAAAATATAAATACTT
1 TTTTTAAAATAT-ATTA-TT
* *
2648688 ATTTTT-TAATTTATTATT
1 -TTTTTAAAATATATTATT
*
2648706 TTTTTAAAATATATTATA
1 TTTTTAAAATATATTATT
2648724 TTTTTAAAATATA--ATT
1 TTTTTAAAATATATTATT
2648740 TTTTT
1 TTTTT
2648745 CGATTATAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
16 7 0.15
17 5 0.10
18 24 0.50
19 3 0.06
20 4 0.08
21 5 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTAAAATATATTATT
Found at i:2649816 original size:2 final size:2
Alignment explanation
Indices: 2649809--2649846 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2649799 TGACAGTTTA
2649809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2649847 GTGTGTGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2650174 original size:10 final size:10
Alignment explanation
Indices: 2650151--2650180 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2650141 AATATTAATA
2650151 ATATAAAAAT
1 ATATAAAAAT
2650161 -TATAAAAAT
1 ATATAAAAAT
2650170 ATATAAAAAT
1 ATATAAAAAT
2650180 A
1 A
2650181 ATTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:2650877 original size:22 final size:21
Alignment explanation
Indices: 2650846--2650889 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2650836 GGTTAAATCG
*
2650846 AGTTTAAGTCATTTTAGGTTTA
1 AGTTTAAGTCA-ATTAGGTTTA
*
2650868 AGTTTGAGTCAATTAGGTTTA
1 AGTTTAAGTCAATTAGGTTTA
2650889 A
1 A
2650890 TAGTTGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (21 bp):
AGTTTAAGTCAATTAGGTTTA
Found at i:2652022 original size:15 final size:17
Alignment explanation
Indices: 2652003--2652046 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
2651993 TATTATTTAT
*
2652003 TTTTTTATT-TAAAATA
1 TTTTTAATTATAAAATA
2652019 TTTTTAATTATAAAATTA
1 TTTTTAATTATAAAA-TA
*
2652037 TCTTTAATTA
1 TTTTTAATTA
2652047 CTATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 8 0.33
17 5 0.21
18 11 0.46
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAATTATAAAATA
Found at i:2652230 original size:16 final size:16
Alignment explanation
Indices: 2652205--2652237 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2652195 TATTTTAAAT
2652205 TTATTTTTAA-TTCAA
1 TTATTTTTAATTTCAA
2652220 TTATTTATTAATTTCAA
1 TTATTT-TTAATTTCAA
2652237 T
1 T
2652238 GTTAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 4 0.25
17 6 0.38
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTTTTAATTTCAA
Found at i:2652596 original size:16 final size:16
Alignment explanation
Indices: 2652567--2652604 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2652557 CATTTGAATT
*
2652567 ATAATATAACTTAATA
1 ATAATTTAACTTAATA
*
2652583 ATAATTTAATTTAATA
1 ATAATTTAACTTAATA
2652599 ATAATT
1 ATAATT
2652605 AAAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATTTAACTTAATA
Found at i:2652597 original size:26 final size:28
Alignment explanation
Indices: 2652558--2652615 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 28
2652548 ATGTACATGC
*
2652558 ATTTGAATTATAAT-ATAACTTAATAATA
1 ATTTGAATTATAATAATAA-TTAAAAATA
2652586 ATTT-AATT-TAATAATAATTAAAAATA
1 ATTTGAATTATAATAATAATTAAAAATA
2652612 ATTT
1 ATTT
2652616 TAAGATTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 16 0.57
27 8 0.29
28 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
ATTTGAATTATAATAATAATTAAAAATA
Found at i:2653088 original size:66 final size:69
Alignment explanation
Indices: 2653017--2653145 Score: 167
Period size: 69 Copynumber: 1.9 Consensus size: 69
2653007 TTTGTATAAA
** *
2653017 TTAATTAAATTTAAAAAAATTA-ATAAAT-AA-TAATGTATTAATTATTATTTT-TAATAAAAAT
1 TTAATTAAATTTAAAAAAATTACATAAATAAATTAAAATATTAATTATT-TTTTAAAATAAAAAT
2653078 AATAT
65 AATAT
* * *
2653083 TTAATTAACTTTAAAAAATTTACATTAATAAATTAAAATATTAATTATTTTTTAAAATAAAAA
1 TTAATTAAATTTAAAAAAATTACATAAATAAATTAAAATATTAATTATTTTTTAAAATAAAAA
2653146 ATTAAATTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
66 20 0.38
67 5 0.09
68 6 0.11
69 22 0.42
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (69 bp):
TTAATTAAATTTAAAAAAATTACATAAATAAATTAAAATATTAATTATTTTTTAAAATAAAAATA
ATAT
Found at i:2653207 original size:113 final size:111
Alignment explanation
Indices: 2653072--2653456 Score: 467
Period size: 113 Copynumber: 3.4 Consensus size: 111
2653062 TATTTTTAAT
*
2653072 AAAAATAATATTTAATTAACTTTAAAAAATTTACATTAATAAATTAAAATATTAATTATTTTTTA
1 AAAAATAATATTTAATTAACTTTAAAAAAATTACATTAATAAATTAAAATATTAATTATTTTTTA
**
2653137 AAATAAAAAATTAAATTAAAAAGCATTATTATTATTTTTTAATAAATA
66 AAAT-AAAAATTAAA-TAAAAAGTTTTATTATTATTTTTTAATAAATA
* * * *
2653185 AAAAATAAAATCTAATTAACTTTAAAAAAATTTATATT-ATAAACTAAAATATTAATTATTTTCT
1 AAAAATAATATTTAATTAACTTTAAAAAAA-TTACATTAATAAATTAAAATATTAATTATTTT-T
*
2653249 TAAAAT-AAAATTAAATAAAAAGTTTTATTATTATTATTTTCAATAAATT
64 TAAAATAAAAATTAAATAAAAAGTTTTATTATTATT-TTTT-AATAAATA
* *
2653298 AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATT-AAATATTAATTATTATATT
1 AAAAATAATATTTAATTAACTTTAAAAAAATTACATTAATAAATTAAAATATTAATTATT-T-TT
** ** **
2653362 T-TTATAAAAA-TAAA-AGTATTTTTTATTATTATTTTTTAATAAAATA
64 TAAAATAAAAATTAAATAAAAAGTTTTATTATTATTTTTTAAT-AAATA
* * * *
2653408 AAAAATGATATTTAATTAAATTTAAAAAAATTACATTAAAAAATGAAAA
1 AAAAATAATATTTAATTAACTTTAAAAAAATTACATTAATAAATTAAAA
2653457 AAAACATTTA
Statistics
Matches: 237, Mismatches: 25, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
109 3 0.01
110 49 0.21
111 36 0.15
112 39 0.16
113 96 0.41
114 14 0.06
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (111 bp):
AAAAATAATATTTAATTAACTTTAAAAAAATTACATTAATAAATTAAAATATTAATTATTTTTTA
AAATAAAAATTAAATAAAAAGTTTTATTATTATTTTTTAATAAATA
Found at i:2653481 original size:110 final size:111
Alignment explanation
Indices: 2653162--2653482 Score: 255
Period size: 110 Copynumber: 2.9 Consensus size: 111
2653152 TTAAAAAGCA
* * * * *
2653162 TTATTATTATT-TTTT-AATAAATAAAAAATAAAATCTAATTAACTTTAAAAAAATTTATATTAT
1 TTATTATTATTATTTTCAATAAATAAAAAATAATATTTAATTAAATTTAAAAAAA-TTACATTAA
* ** ** * ** **
2653225 AAACT-AAAATATTAATTAT--TTTCTTAAAATAAAATTAAATAAAAAGTT
65 AAAATGAAAA-AAAAATTATAAGATATTAAAA-AAAA-TAAA-AGTATTTT
* * *
2653273 TTATTATTATTATTTTCAATAAATTAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAAC
1 TTATTATTATTATTTTCAATAAATAAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAAA
* * ** * * * * *
2653338 AAATTAAATATTAATTATTATATTTTTATAAAAATAAAAGTATTTT
66 AAATGAAAAAAAAATTATAAGATATTAAAAAAAATAAAAGTATTTT
*
2653384 TTATTATTATT-TTTT-AATAAAATAAAAAATGATATTTAATTAAATTTAAAAAAATTACATTAA
1 TTATTATTATTATTTTCAAT-AAATAAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAA
2653447 AAAATGAAAAAAAACATT-TAAGGA-ATTAAAAAAAAT
65 AAAATGAAAAAAAA-ATTATAA-GATATTAAAAAAAAT
2653483 TTATCATTAT
Statistics
Matches: 172, Mismatches: 30, Indels: 17
0.79 0.14 0.08
Matches are distributed among these distances:
109 3 0.02
110 65 0.38
111 30 0.17
112 27 0.16
113 41 0.24
114 6 0.03
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (111 bp):
TTATTATTATTATTTTCAATAAATAAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAAA
AAATGAAAAAAAAATTATAAGATATTAAAAAAAATAAAAGTATTTT
Found at i:2653811 original size:15 final size:15
Alignment explanation
Indices: 2653791--2653820 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2653781 TAAAAAAAGT
2653791 TTTTTTAATTTAAAA
1 TTTTTTAATTTAAAA
*
2653806 TTTTTTATTTTAAAA
1 TTTTTTAATTTAAAA
2653821 AACATAATAA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTAATTTAAAA
Found at i:2653926 original size:123 final size:123
Alignment explanation
Indices: 2653791--2654131 Score: 475
Period size: 123 Copynumber: 2.8 Consensus size: 123
2653781 TAAAAAAAGT
*
2653791 TTTTTTAATTTAAAATTTTTTATTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGTAA
1 TTTTTTATTTTAAAATTTTTTATTTT-AAAAACATAATAATTAATATTTTAATTTGTTAATGTAA
* *
2653856 ATTTTTTAAATTTAATTAAATATTATTTTTATTTTATT-AAAAATTATAATAAAAAACC
65 ATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAATAATAATAAAAAACC
*
2653914 TTTTTTATTTTAAAATTTTTTATTTTTATAAAACATAATAATTAATATTTTAATTTATTAATGT-
1 TTTTTTATTTTAAAATTTTTTA-TTTTA-AAAACATAATAATTAATATTTTAATTTGTTAATGTA
*
2653978 AATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAATAAACC
64 AATTTTTTAAACTTAATTAAATATTATTTTT-ATTTTATTAAAAAATAATAATAAAAAACC
2654039 TTTTTTATTTTTATTTAAATTTTTTTATTTT---AA-A-AA-AATTAATATTTTAATTTGTTAAT
1 TTTTTTA-TTTTA---AAA-TTTTTTATTTTAAAAACATAATAATTAATATTTTAATTTGTTAAT
* *
2654098 ATAAA-TTTTTAAAGTTAATTAAATATTATTTTTA
61 GTAAATTTTTTAAACTTAATTAAATATTATTTTTA
2654132 ATTAAAAATA
Statistics
Matches: 200, Mismatches: 8, Indels: 22
0.87 0.03 0.10
Matches are distributed among these distances:
121 1 0.00
122 50 0.25
123 56 0.28
124 47 0.23
125 27 0.14
126 5 0.03
129 7 0.04
130 7 0.04
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (123 bp):
TTTTTTATTTTAAAATTTTTTATTTTAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAA
TTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAATAATAATAAAAAACC
Found at i:2654014 original size:124 final size:125
Alignment explanation
Indices: 2653791--2654134 Score: 483
Period size: 122 Copynumber: 2.8 Consensus size: 125
2653781 TAAAAAAAGT
* *
2653791 TTTTTTAATTTAAAATTTTTTA-TTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGTA
1 TTTTTTATTTTAAAATTTTTTATTTTTATAAAACATAATAATTAATATTTTAATTTGTTAATGT-
* *
2653855 AATTTTTTAAATTTAATTAAATATTATTTTT-ATTTTATT-AAAAATTATAATAAAAAACC
65 AATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAAAAAACC
*
2653914 TTTTTTATTTTAAAATTTTTTATTTTTATAAAACATAATAATTAATATTTTAATTTATTAATGTA
1 TTTTTTATTTTAAAATTTTTTATTTTTATAAAACATAATAATTAATATTTTAATTTGTTAATGTA
*
2653979 ATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAATAAACC
66 ATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAAAAAACC
*
2654039 TTTTTTATTTTTATTTAAATTTTTT-TATTT-T--AA-A-AA-AATTAATATTTTAATTTGTTAA
1 TTTTTTA-TTTTA---AAATTTTTTATTTTTATAAAACATAATAATTAATATTTTAATTTGTTAA
* * *
2654097 TATAAATTTTTAAAGTTAATTAAATATTATTTTTAATT
62 TGTAATTTTTTAAACTTAATTAAATATTATTTTTAATT
2654135 AAAAATAATA
Statistics
Matches: 203, Mismatches: 11, Indels: 15
0.89 0.05 0.07
Matches are distributed among these distances:
122 56 0.28
123 53 0.26
124 48 0.24
125 27 0.13
126 5 0.02
127 1 0.00
128 4 0.02
129 9 0.04
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (125 bp):
TTTTTTATTTTAAAATTTTTTATTTTTATAAAACATAATAATTAATATTTTAATTTGTTAATGTA
ATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAAAAAACC
Found at i:2654195 original size:122 final size:118
Alignment explanation
Indices: 2653829--2654198 Score: 292
Period size: 122 Copynumber: 3.0 Consensus size: 118
2653819 AAAACATAAT
* * * *
2653829 AATTAATATTTTAATTTGTTAATGTAAATTTTTTAAATTTAATTAAATATTATTTTTATTTTATT
1 AATTAATATTTTAATTTATTAATATAAA-TTTTTAAACTTAATTAAATATTATTTTTA--ATATT
* * * *
2653894 AAAAATTATAATAA-A-AAACC-TT-TT-TTATT-TTAAAATTTTTTATTTTTATAAAACATAA
63 AAAAA--ATAATAATATAAACCATTATTATTTTTATTTAAATTTATTA-ATTT-T--AA-A-AA
* *
2653952 TAATTAATATTTTAATTTATTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTAT
1 -AATTAATATTTTAATTTATTAATATAAATTTTTAAACTTAATTAAATATTATTTTTAA---TAT
* * * *
2654017 TAAAAAATAATAATAATAAACCTTTTTTATTTTTATTTAAATTTTTTTATTTTAAAAA
62 TAAAAAATAATAAT-ATAAACCATTATTATTTTTATTTAAATTTATTAATTTTAAAAA
* *
2654075 AATTAATATTTTAATTTGTTAATATAAATTTTTAAAGTTAATTAAATATTATTTTT-A-ATT-AA
1 AATTAATATTTTAATTTATTAATATAAATTTTTAAACTTAATTAAATATTATTTTTAATATTAAA
**
2654137 AAATAATAAT-TAATGCATTATTATTTATTAAAAATTTTAAATTTAATTAATTTATAAAAA
66 AAATAATAATATAAACCATTATTATTT-TT----A-TTTAAATTT-ATTAATTT-TAAAAA
2654197 AA
1 AA
2654199 CTGAAATGGC
Statistics
Matches: 210, Mismatches: 18, Indels: 38
0.79 0.07 0.14
Matches are distributed among these distances:
114 12 0.06
115 2 0.01
116 12 0.06
117 3 0.01
119 1 0.00
120 9 0.04
121 7 0.03
122 67 0.32
123 30 0.14
124 37 0.18
125 7 0.03
126 2 0.01
127 3 0.01
128 7 0.03
129 11 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (118 bp):
AATTAATATTTTAATTTATTAATATAAATTTTTAAACTTAATTAAATATTATTTTTAATATTAAA
AAATAATAATATAAACCATTATTATTTTTATTTAAATTTATTAATTTTAAAAA
Found at i:2654793 original size:91 final size:89
Alignment explanation
Indices: 2654607--2655732 Score: 1216
Period size: 91 Copynumber: 12.6 Consensus size: 89
2654597 TTGTAAGAAA
*
2654607 TAGACTAATGCATTG-ATTATATCTGAGAATCGGATT-TTTTTTAT-G--AAAAAAAAGTTGATT
1 TAGACTAATGCA-TGAATTATATCTGAGAATC-AATTCTTTTTTATAGAAAAAAAAAAGTTGATT
*
2654667 AATTGTAAATGTCAGACTGCAAGGAT
64 GATTGTAAATGTCAGACTGCAAGGAT
*
2654693 TAGACTAATGCATGAATTATATCTGAAAATCAATTCTTTTTTATAGAAAAAAAGAAAAGTTGATT
1 TAGACTAATGCATGAATTATATCTGAGAATCAATTCTTTTTTATAG-AAAAAA-AAAAGTTGATT
* *
2654758 GATTGTAAATGTTAGACTGCAAAGAT
64 GATTGTAAATGTCAGACTGCAAGGAT
* *
2654784 TAGATTAATGCATGAATTATATCTGAGAATCAGGTTCTTTTTTATAG--AAAAAAAAGTTGATTG
1 TAGACTAATGCATGAATTATATCTGAGAATCA-ATTCTTTTTTATAGAAAAAAAAAAGTTGATTG
* *
2654847 ATTGTAAATGTCAAACTGCAATGAT
65 ATTGTAAATGTCAGACTGCAAGGAT
*
2654872 TAGACTAACGCATGAATTATATCTGAGAATCAATTCTTTTTTATAG--AAAAAAAAGTTGATTGA
1 TAGACTAATGCATGAATTATATCTGAGAATCAATTCTTTTTTATAGAAAAAAAAAAGTTGATTGA
*
2654935 TTGTAAATGTCAGATTGCAAGGAT
66 TTGTAAATGTCAGACTGCAAGGAT
* * * ** *
2654959 TGGACTAATGCATTAATTATATATGAGAATCGGTTTCTTTTTTATGAAAAAAAAAAGGAAAAGTT
1 TAGACTAATGCATGAATTATATCTGAGAATC-AATTCTTTTTTAT---AGAAAAAA--AAAAGTT
* * * * *
2655024 GACTGCTTGTAAATGTCAAACTACAAGAAT
60 GATTGATTGTAAATGTCAGACTGCAAGGAT
* * * * *
2655054 TAGATTAATGCATAAATTATATTTGAAAATCAGATTCTTTTTTAT------AAAAAAGTTGACTG
1 TAGACTAATGCATGAATTATATCTGAGAATCA-ATTCTTTTTTATAGAAAAAAAAAAGTTGATTG
* * *
2655113 ATTATAAATGTCA-AATAGTAAGGAT
65 ATTGTAAATGTCAGACT-GCAAGGAT
* * * ** *
2655138 TAGACTAATGTATAAATTATATCTGAAAATTGGATTCTTTTTTAT---AAAAAAAAA--TGACTG
1 TAGACTAATGCATGAATTATATCTGAGAA-TCAATTCTTTTTTATAGAAAAAAAAAAGTTGATTG
*
2655198 ATTGTAAATGTCAGACTGAAAGGAT
65 ATTGTAAATGTCAGACTGCAAGGAT
* * *
2655223 TAGACTAATACATGAATTATATCTGAGAAT---TTCTTTTTTATATAAAAAAAAAGAAAGACTGA
1 TAGACTAATGCATGAATTATATCTGAGAATCAATTC-TTTTT-TATAGAAAAAAA-AAAG-TTGA
* *
2655285 TTGATTGTAAATTTTAGACTGCAAGGAT
62 TTGATTGTAAATGTCAGACTGCAAGGAT
* *
2655313 TAGACTAATGCATGAATTATATCTGAGAAT---TTCTTTTTTATATAAAAAAAAAAGAAAGACTG
1 TAGACTAATGCATGAATTATATCTGAGAATCAATTC-TTTTT-TAT-AGAAAAAAA-AAAG-TTG
* *
2655375 ATTGATTGTAAATTTTAGACTGCAAGGAT
61 ATTGATTGTAAATGTCAGACTGCAAGGAT
*
2655404 TAGACTAATGCATGAATTATATCTGAGAA-CTAATTCTTTTTTATAGAAAAAAGAAAAGTTAATT
1 TAGACTAATGCATGAATTATATCTGAGAATC-AATTCTTTTTTATAGAAAAAA-AAAAGTTGATT
* * * **
2655468 GATTATAAATGTTAGAATGCAAAAAT
64 GATTGTAAATGTCAGACTGCAAGGAT
2655494 TAGACTAATGCATGAATTATATCTGAGAATCAGATT-TTTTTTAT-GAAAAAAAAAAGTTGATTG
1 TAGACTAATGCATGAATTATATCTGAGAATCA-ATTCTTTTTTATAGAAAAAAAAAAGTTGATTG
2655557 ATTGTAAATGTCAGACTGCAAGGAT
65 ATTGTAAATGTCAGACTGCAAGGAT
* * *
2655582 TAGACTAACGCATGAATTATATCTGAGAATCAAATTCTTTTTTATAAAAAAAAAAGAAAGACTGA
1 TAGACTAATGCATGAATTATATCTGAGAATC-AATTCTTTTTTAT-AGAAAAAAA-AAAG-TTGA
2655647 TTGATT-TAAATGTCAGACTGCAAGGAT
62 TTGATTGTAAATGTCAGACTGCAAGGAT
* * *
2655674 TAGACTAATGTACGAATTATATCTGATAATCAGATTCTTTTTTATAGGAAAAAAGAAAA
1 TAGACTAATGCATGAATTATATCTGAGAATCA-ATTCTTTTTTATA-GAAAAAA-AAAA
2655733 ACTACAAGGA
Statistics
Matches: 909, Mismatches: 82, Indels: 92
0.84 0.08 0.08
Matches are distributed among these distances:
81 3 0.00
82 5 0.01
83 5 0.01
84 67 0.07
85 56 0.06
86 45 0.05
87 88 0.10
88 139 0.15
89 20 0.02
90 136 0.15
91 165 0.18
92 90 0.10
93 19 0.02
94 3 0.00
95 68 0.07
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.35
Consensus pattern (89 bp):
TAGACTAATGCATGAATTATATCTGAGAATCAATTCTTTTTTATAGAAAAAAAAAAGTTGATTGA
TTGTAAATGTCAGACTGCAAGGAT
Found at i:2654887 original size:179 final size:176
Alignment explanation
Indices: 2654607--2655719 Score: 1239
Period size: 179 Copynumber: 6.3 Consensus size: 176
2654597 TTGTAAGAAA
* *
2654607 TAGACTAATGCATTG-ATTATATCTGAGAATCGGATT-TTTTTTAT-GAAAAAAAAGTTGATTAA
1 TAGACTAATGCA-TGAATTATATCTGAGAATCGG-TTCTTTTTTATAAAAAAAAAAGTTGATTGA
*
2654669 TTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAAAATCAATTCTTTTT
64 TTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAATTCTTTTT
* *
2654734 TATAGAAAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAAGAT
129 TATAG-AAAAAA-AAAAGTTGATTGATTGTAAATGTCAGACTGCAAGGAT
* *
2654784 TAGATTAATGCATGAATTATATCTGAGAATCAGGTTCTTTTTTATAGAAAAAAAAGTTGATTGAT
1 TAGACTAATGCATGAATTATATCTGAGAATC-GGTTCTTTTTTATAAAAAAAAAAGTTGATTGAT
* * *
2654849 TGTAAATGTCAAACTGCAATGATTAGACTAACGCATGAATTATATCTGAGAATCAATTCTTTTTT
65 TGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAATTCTTTTTT
*
2654914 ATAG--AAAAAAAAGTTGATTGATTGTAAATGTCAGATTGCAAGGAT
130 ATAGAAAAAAAAAAGTTGATTGATTGTAAATGTCAGACTGCAAGGAT
* * *
2654959 TGGACTAATGCATTAATTATATATGAGAATCGGTTTCTTTTTTATGAAAAAAAAAAGGAAAAGTT
1 TAGACTAATGCATGAATTATATCTGAGAATCGG-TTCTTTTTTAT-----AAAAAA--AAAAGTT
* * * * * * * * *
2655024 GACTGCTTGTAAATGTCAAACTACAAGAATTAGATTAATGCATAAATTATATTTGAAAATCAGAT
58 GATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCA-AT
* * * *
2655089 TCTTTTTTAT------AAAAAAGTTGACTGATTATAAATGTCA-AATAGTAAGGAT
122 TCTTTTTTATAGAAAAAAAAAAGTTGATTGATTGTAAATGTCAGACT-GCAAGGAT
* * * * *
2655138 TAGACTAATGTATAAATTATATCTGAAAATTGGATTCTTTTTTAT-AAAAAAAAA--TGACTGAT
1 TAGACTAATGCATGAATTATATCTGAGAATCGG-TTCTTTTTTATAAAAAAAAAAGTTGATTGAT
* *
2655200 TGTAAATGTCAGACTGAAAGGATTAGACTAATACATGAATTATATCTGAGAAT---TTCTTTTTT
65 TGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAATTC-TTTTT
* * * *
2655262 ATATAAAAAAAAAGAAAGACTGATTGATTGTAAATTTTAGACTGCAAGGAT
129 -TATAGAAAAAAA-AAAG-TTGATTGATTGTAAATGTCAGACTGCAAGGAT
*
2655313 TAGACTAATGCATGAATTATATCTGAGAAT---TTCTTTTTTATATAAAAAAAAAAGAAAGACTG
1 TAGACTAATGCATGAATTATATCTGAGAATCGGTTC-TTTTT-TAT---AAAAAAA-AAAG-TTG
* *
2655375 ATTGATTGTAAATTTTAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAA-CTAATT
59 ATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATC-AATT
* * * * **
2655439 CTTTTTTATAGAAAAAAGAAAAGTTAATTGATTATAAATGTTAGAATGCAAAAAT
123 CTTTTTTATAGAAAAAA-AAAAGTTGATTGATTGTAAATGTCAGACTGCAAGGAT
*
2655494 TAGACTAATGCATGAATTATATCTGAGAATCAGATT-TTTTTTATGAAAAAAAAAAGTTGATTGA
1 TAGACTAATGCATGAATTATATCTGAGAATC-GGTTCTTTTTTAT-AAAAAAAAAAGTTGATTGA
*
2655558 TTGTAAATGTCAGACTGCAAGGATTAGACTAACGCATGAATTATATCTGAGAATCAAATTCTTTT
64 TTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATC-AATTCTTTT
* *
2655623 TTATAAAAAAAAAAGAAAGACTGATTGATT-TAAATGTCAGACTGCAAGGAT
128 TTAT-AGAAAAAAA-AAAG-TTGATTGATTGTAAATGTCAGACTGCAAGGAT
* * * *
2655674 TAGACTAATGTACGAATTATATCTGATAATCAGATTCTTTTTTATA
1 TAGACTAATGCATGAATTATATCTGAGAATC-GGTTCTTTTTTATA
2655720 GGAAAAAAGA
Statistics
Matches: 803, Mismatches: 84, Indels: 95
0.82 0.09 0.10
Matches are distributed among these distances:
165 3 0.00
166 5 0.01
167 3 0.00
169 51 0.06
171 7 0.01
172 5 0.01
173 11 0.01
174 6 0.01
175 121 0.15
176 8 0.01
177 35 0.04
178 72 0.09
179 172 0.21
180 74 0.09
181 126 0.16
182 76 0.09
183 23 0.03
184 3 0.00
185 2 0.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (176 bp):
TAGACTAATGCATGAATTATATCTGAGAATCGGTTCTTTTTTATAAAAAAAAAAGTTGATTGATT
GTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAATTCTTTTTTA
TAGAAAAAAAAAAGTTGATTGATTGTAAATGTCAGACTGCAAGGAT
Found at i:2655121 original size:84 final size:84
Alignment explanation
Indices: 2655017--2655728 Score: 401
Period size: 90 Copynumber: 8.1 Consensus size: 84
2655007 AAAAAAAAGG
* * * *
2655017 AAAAGTTGACTGCTTGTAAATGTCAAACTACAAGAATTAGATTAATGCATAAATTATATTTGAAA
1 AAAAGTTGACTGATTGTAAATGTCAAACTA-AAGGATTAGACTAATGCATAAATTATATCTGAAA
2655082 ATCAGATTCTTTTTTAT-AA
65 ATCAGATTCTTTTTTATAAA
* *
2655101 AAAAGTTGACTGATTATAAATGTCAAA-TAGTAAGGATTAGACTAATGTATAAATTATATCTGAA
1 AAAAGTTGACTGATTGTAAATGTCAAACTA--AAGGATTAGACTAATGCATAAATTATATCTGAA
**
2655165 AATTGGATTCTTTTTTATAAA
64 AATCAGATTCTTTTTTATAAA
** * * * *
2655186 AAAAAATGACTGATTGTAAATGTCAGACTGAAAGGATTAGACTAATACATGAATTATATCTGAGA
1 AAAAGTTGACTGATTGTAAATGTCAAACT-AAAGGATTAGACTAATGCATAAATTATATCTGAAA
2655251 AT----TTCTTTTTTATATAAAAAAAA
65 ATCAGATTC-TTTTT-TAT-----AAA
* * * * * * *
2655274 AGAAAGACTGATTGATTGTAAATTTTAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGA
1 A-AAAG-TTGACTGATTGTAAATGTCAAACT-AAAGGATTAGACTAATGCATAAATTATATCTGA
*
2655339 GAAT----TTCTTTTTTATATAAAAAAAAA
63 AAATCAGATTC-TTTTT-TAT------AAA
* * * * * * *
2655365 AGAAAGACTGATTGATTGTAAATTTTAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGA
1 A-AAAG-TTGACTGATTGTAAATGTCAAACT-AAAGGATTAGACTAATGCATAAATTATATCTGA
*
2655430 GAA-CTA-ATTCTTTTTTATAGAAAAAA
63 AAATC-AGATTCTTTTTTAT-----AAA
* * * * * *
2655456 GAAAAGTTAATTGATTATAAATGTTAGAA-TGCAAA-AATTAGACTAATGCATGAATTATATCTG
1 -AAAAGTTGACTGATTGTAAATGTCA-AACT--AAAGGATTAGACTAATGCATAAATTATATCTG
*
2655519 AGAATCAGATT-TTTTTTATGAAAAAA
62 AAAATCAGATTCTTTTTTAT----AAA
* * * * * *
2655545 AAAAGTTGATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAACGCATGAATTATATCTGAGA
1 AAAAGTTGACTGATTGTAAATGTCAAACT-AAAGGATTAGACTAATGCATAAATTATATCTGAAA
*
2655610 ATCAAATTCTTTTTTATAAAAAA
65 ATCAGATTCTTTTTTAT---AAA
** * * * **
2655633 AAAAGAAAGACTGATTGATTTAAATGTCAGACTGCAAGGATTAGACTAATGTACGAATTATATCT
1 AAAAG-TTGACTGATTG---TAAATGTCAAACT-AAAGGATTAGACTAATGCATAAATTATATCT
*
2655698 GATAATCAGATTCTTTTTTATAGGAA
61 GAAAATCAGATTCTTTTTTATA--AA
2655724 AAAAG
1 AAAAG
2655729 AAAAACTACA
Statistics
Matches: 546, Mismatches: 50, Indels: 57
0.84 0.08 0.09
Matches are distributed among these distances:
81 3 0.01
82 5 0.01
83 5 0.01
84 70 0.13
85 57 0.10
86 1 0.00
87 4 0.01
88 74 0.14
89 27 0.05
90 126 0.23
91 101 0.18
92 65 0.12
93 5 0.01
94 3 0.01
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (84 bp):
AAAAGTTGACTGATTGTAAATGTCAAACTAAAGGATTAGACTAATGCATAAATTATATCTGAAAA
TCAGATTCTTTTTTATAAA
Found at i:2662396 original size:34 final size:33
Alignment explanation
Indices: 2662358--2662472 Score: 92
Period size: 34 Copynumber: 3.4 Consensus size: 33
2662348 AAAATGGTGA
2662358 TGGCAATAAAGGCCAAGAAACTTCACCAAATATC
1 TGGCAATAAAGGCCAAGAAACTTCA-CAAATATC
** * * *
2662392 TGGCAATTAAA-GCC-AGAAAAAT-AGAATATGGTGA
1 TGGCAA-TAAAGGCCAAGAAACTTCACAA-AT-AT-C
2662426 TGGCAATAAAGGCCAAGAAACTTCATCAAATATC
1 TGGCAATAAAGGCCAAGAAACTTCA-CAAATATC
* *
2662460 TAGCAATTAAGGC
1 TGGCAATAAAGGC
2662473 AAACAAAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
31 2 0.03
32 3 0.05
33 11 0.18
34 29 0.48
35 11 0.18
36 3 0.05
37 2 0.03
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.20
Consensus pattern (33 bp):
TGGCAATAAAGGCCAAGAAACTTCACAAATATC
Found at i:2662748 original size:36 final size:36
Alignment explanation
Indices: 2662661--2662755 Score: 109
Period size: 36 Copynumber: 2.6 Consensus size: 36
2662651 ACAACTTAGT
* * * * *
2662661 TATACACATAACTATACACAACTTACAGCACTTAGT
1 TATACACATAACTGTACACAACTAACACCACCTAGC
* * *
2662697 TTTACATATAACTGTACACAACTAACACCCCCTAGC
1 TATACACATAACTGTACACAACTAACACCACCTAGC
*
2662733 TATACACATAGCTGTACACAACT
1 TATACACATAACTGTACACAACT
2662756 CCTTACAGCA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.39, C:0.28, G:0.06, T:0.26
Consensus pattern (36 bp):
TATACACATAACTGTACACAACTAACACCACCTAGC
Found at i:2662922 original size:37 final size:37
Alignment explanation
Indices: 2662872--2662942 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
2662862 AGTCTTGCAC
2662872 CTATGGGAGTCATATCTTTTAATTTTCTAGAATAGCT
1 CTATGGGAGTCATATCTTTTAATTTTCTAGAATAGCT
*
2662909 CTATGGGAGTCATATTTTTTAATTTTCTAGAATA
1 CTATGGGAGTCATATCTTTTAATTTTCTAGAATA
2662943 ACACCTAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (37 bp):
CTATGGGAGTCATATCTTTTAATTTTCTAGAATAGCT
Found at i:2662965 original size:15 final size:15
Alignment explanation
Indices: 2662945--2662974 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2662935 CTAGAATAAC
2662945 ACCTAGCTGTACACA
1 ACCTAGCTGTACACA
*
2662960 ACCTAGTTGTACACA
1 ACCTAGCTGTACACA
2662975 TAACTATACA
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:0.33, C:0.30, G:0.13, T:0.23
Consensus pattern (15 bp):
ACCTAGCTGTACACA
Found at i:2663003 original size:36 final size:35
Alignment explanation
Indices: 2662962--2663081 Score: 109
Period size: 36 Copynumber: 3.3 Consensus size: 35
2662952 TGTACACAAC
* *
2662962 CTAGTTGTACACATAACTATACACAACTTACAGCA
1 CTAGTTGTACACATAGCTGTACACAACTTACAGCA
* * *
2662997 CTTAGTTTTACATATAGCTGTACACAACTAATACCGC-
1 C-TAGTTGTACACATAGCTGTACACAACT--TACAGCA
2663034 CTAGCTT-TACACATAGCTGTACACAACTCTTTACAGCA
1 CTAG-TTGTACACATAGCTGTACACAA--C-TTACAGCA
2663072 CATAGTTGTA
1 C-TAGTTGTA
2663082 TACAACTCAC
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
35 1 0.01
36 44 0.65
37 8 0.12
38 9 0.13
39 6 0.09
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (35 bp):
CTAGTTGTACACATAGCTGTACACAACTTACAGCA
Found at i:2663076 original size:27 final size:24
Alignment explanation
Indices: 2663043--2663109 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 24
2663033 CCTAGCTTTA
2663043 CACATAGCTGTACACAACTCTTTACAG
1 CACATAGCTGTACACAACTC---ACAG
* *
2663070 CACATAGTTGTATACAACTCACAG
1 CACATAGCTGTACACAACTCACAG
* *
2663094 CACCTAGCTGCACACA
1 CACATAGCTGTACACA
2663110 TAGCTGTGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 16 0.47
27 18 0.53
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.22
Consensus pattern (24 bp):
CACATAGCTGTACACAACTCACAG
Found at i:2663150 original size:306 final size:306
Alignment explanation
Indices: 2662597--2663166 Score: 969
Period size: 306 Copynumber: 1.9 Consensus size: 306
2662587 TATTATAGCC
* *
2662597 ATAGCTCTATGGGAGTCATATCTTTTAATTTTCAAGAATAGCACCTAGCTGAACACAACTTAGTT
1 ATAGCTCTATGGGAGTCATATCTTTTAATTTTCAAGAATAACACCTAGCTGAACACAACCTAGTT
2662662 ATACACATAACTATACACAACTTACAGCACTTAGTTTTACATATAACTGTACACAACTAACACCC
66 ATACACATAACTATACACAACTTACAGCACTTAGTTTTACATATAACTGTACACAACTAACACCC
2662727 CCTAGCTATACACATAGCTGTACACAACTCCTTACAGCACATAGTTGTACACAACTCACAGCACC
131 CCTAGCTATACACATAGCTGTACACAACTCCTTACAGCACATAGTTGTACACAACTCACAGCACC
* * *
2662792 TGGCTACATACATAGTTGTACACAATTCTTTACAATAAGTGTTTTTTTCATTGACTGTTCTGAAC
196 TAGCTACACACATAGCTGTACACAATTCTTTACAATAAGTGTTTTTTTCATTGACTGTTCTGAAC
2662857 ATTCAAGTCTTGCACCTATGGGAGTCATATCTTTTAATTTTCTAGA
261 ATTCAAGTCTTGCACCTATGGGAGTCATATCTTTTAATTTTCTAGA
* * *
2662903 ATAGCTCTATGGGAGTCATATTTTTTAATTTTCTAGAATAACACCTAGCTGTACACAACCTAGTT
1 ATAGCTCTATGGGAGTCATATCTTTTAATTTTCAAGAATAACACCTAGCTGAACACAACCTAGTT
* * * *
2662968 GTACACATAACTATACACAACTTACAGCACTTAGTTTTACATATAGCTGTACACAACTAATACCG
66 ATACACATAACTATACACAACTTACAGCACTTAGTTTTACATATAACTGTACACAACTAACACCC
* * *
2663033 CCTAGCTTTACACATAGCTGTACACAACTCTTTACAGCACATAGTTGTATACAACTCACAGCACC
131 CCTAGCTATACACATAGCTGTACACAACTCCTTACAGCACATAGTTGTACACAACTCACAGCACC
* * * *
2663098 TAGCTGCACACATAGCTGTGCACAATTCTTTACAGTAAGTGTTTTTTTCATTGACTGTTTTGAAC
196 TAGCTACACACATAGCTGTACACAATTCTTTACAATAAGTGTTTTTTTCATTGACTGTTCTGAAC
2663163 ATTC
261 ATTC
2663167 GAGAATTGCA
Statistics
Matches: 245, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
306 245 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (306 bp):
ATAGCTCTATGGGAGTCATATCTTTTAATTTTCAAGAATAACACCTAGCTGAACACAACCTAGTT
ATACACATAACTATACACAACTTACAGCACTTAGTTTTACATATAACTGTACACAACTAACACCC
CCTAGCTATACACATAGCTGTACACAACTCCTTACAGCACATAGTTGTACACAACTCACAGCACC
TAGCTACACACATAGCTGTACACAATTCTTTACAATAAGTGTTTTTTTCATTGACTGTTCTGAAC
ATTCAAGTCTTGCACCTATGGGAGTCATATCTTTTAATTTTCTAGA
Found at i:2665012 original size:11 final size:11
Alignment explanation
Indices: 2664996--2665021 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2664986 AAAAAATTGT
2664996 ATAATTTATAA
1 ATAATTTATAA
2665007 ATAATTTATAA
1 ATAATTTATAA
2665018 ATAA
1 ATAA
2665022 AAAGTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAATTTATAA
Found at i:2665620 original size:34 final size:36
Alignment explanation
Indices: 2665579--2665663 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 36
2665569 AAATCATAAC
2665579 TTAATTTTTTTAAAAAAT-TAATTAA-ATATTATTT-
1 TTAA-TTTTTTAAAAAATATAATTAATATATTATTTA
*
2665613 TTAATTTTATAAAAAATAATAATTAATATATTATTTA
1 TTAATTTTTTAAAAAAT-ATAATTAATATATTATTTA
*
2665650 TTAAAATTTTTAAA
1 TT-AATTTTTTAAA
2665664 TTTAATTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
33 12 0.28
34 4 0.09
35 7 0.16
36 9 0.21
37 2 0.05
38 9 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TTAATTTTTTAAAAAATATAATTAATATATTATTTA
Done.