Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 110 of 135
Found at i:40598123 original size:19 final size:19
Alignment explanation
Indices: 40598101--40598137 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40598091 ATATATTTAT
*
40598101 TAATTAAATAATAATAAAG
1 TAATAAAATAATAATAAAG
40598120 TAATAAAATAATAATAAA
1 TAATAAAATAATAATAAA
40598138 ATACTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
TAATAAAATAATAATAAAG
Found at i:40615550 original size:29 final size:31
Alignment explanation
Indices: 40615490--40615554 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 31
40615480 GTGGTTCATT
* *
40615490 TGATACTTGTACTTTAGTAAAATGTCTAATG
1 TGATACTTATACTTTAGTAAAATATCTAATG
*
40615521 TGATACTTATACTTT-G-AAAATATTTAATG
1 TGATACTTATACTTTAGTAAAATATCTAATG
40615550 TGATA
1 TGATA
40615555 TCTGAAGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 16 0.52
30 1 0.03
31 14 0.45
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (31 bp):
TGATACTTATACTTTAGTAAAATATCTAATG
Found at i:40618191 original size:16 final size:15
Alignment explanation
Indices: 40618166--40618195 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40618156 ATATATGTGC
40618166 AATAAGTATATAAAT
1 AATAAGTATATAAAT
40618181 AATAGAGTATATAAA
1 AATA-AGTATATAAA
40618196 AATGTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (15 bp):
AATAAGTATATAAAT
Found at i:40628704 original size:126 final size:124
Alignment explanation
Indices: 40628356--40628857 Score: 639
Period size: 125 Copynumber: 4.0 Consensus size: 124
40628346 TAATTTTTTG
* *
40628356 GGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAGACGCTTCAAGCAG
1 GGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAA-ATGCTTCAAGCAG
* * * *
40628421 GATGCTATTTGAGAAGAATTTCTGAAATCGCGCCCT-TGTGGACGCGCTTTTACTACAGTT
65 GATGCTATATGAGAAGAATTTCTGAAATCGCG-CCTACGTGGACGCGCTTTTGCTACAGTA
* * * * * *
40628481 GGTCTTGGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTAT-AAAATCGCTTCTACCA
1 GGTCCT-GAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAT-GCTTCAAGCA
* * *
40628545 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCTAAGTGGACGCGCTTTTGCTACAGTA
64 GGATGCTATATGAGAAGAATTTCTGAAATCGCGCCTACGTGGACGCGCTTTTGCTACAGTA
* * *
40628606 GGTCTTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAATGCTTCAAGCA
1 GGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTAT--AAAAATGCTTCAAGCA
* * * * * *
40628671 GGATGCGATCTGAGAAGAATTTCTGAAATCGCGCCTTCGTAGACGCTCTTTTGCTACAGTT
64 GGATGCTATATGAGAAGAATTTCTGAAATCGCGCCTACGTGGACGCGCTTTTGCTACAGTA
* * *
40628732 GGTCCTGAAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAATTGCTTCTAGTAG
1 GGTCCTGAAA-AAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAATGCTTCAAGCAG
* * * * *
40628797 GATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTATAGTA
65 GATGCTATATGAGAAGAATTTCTGAAATCGCGCCTACGTGGACGCGCTTTTGCTACAGTA
40628857 G
1 G
40628858 CATGTTTGGG
Statistics
Matches: 325, Mismatches: 45, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
124 42 0.13
125 137 0.42
126 106 0.33
127 40 0.12
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (124 bp):
GGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAATGCTTCAAGCAGG
ATGCTATATGAGAAGAATTTCTGAAATCGCGCCTACGTGGACGCGCTTTTGCTACAGTA
Found at i:40628803 original size:251 final size:250
Alignment explanation
Indices: 40628356--40628857 Score: 799
Period size: 251 Copynumber: 2.0 Consensus size: 250
40628346 TAATTTTTTG
*
40628356 GGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAGACGCTTCAAGCAG
1 GGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAACGCTTCAAGCAG
* * * *
40628421 GATGCTATTTGAGAAGAATTTCTGAAATCGCGCCCTTGTGGACGCGCTTTTACTACAGTTGGTCT
66 GATGCGATCTGAGAAGAATTTCTGAAATCGCGCCCTTGTAGACGCGCTTTTACTACAGTTGGTCC
* * *
40628486 TGGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGC
131 TGAAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGC
* *
40628551 TTTATGAGAAGAATTTGTGAAATCGCGCCTAAGTGGACGCGCTTTTGCTACAGTA
196 TTTATGAGAAGAATTTGTGAAATCGCACCCAAGTGGACGCGCTTTTGCTACAGTA
* * *
40628606 GGTCTTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAATGCTTCAAGCA
1 GGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTAAGCAAATAGTAT-AAAAAACGCTTCAAGCA
* *
40628671 GGATGCGATCTGAGAAGAATTTCTGAAATCGCG-CCTTCGTAGACGCTCTTTTGCTACAGTTGGT
65 GGATGCGATCTGAGAAGAATTTCTGAAATCGCGCCCTT-GTAGACGCGCTTTTACTACAGTTGGT
* **
40628735 CCTGAAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAATTGCTTCTAGTAGGAT
129 CCTGAAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGAT
* *
40628800 GCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTATAGTA
194 GCTTTATGAGAAGAATTTGTGAAATCGCACCCAAGTGGACGCGCTTTTGCTACAGTA
40628857 G
1 G
40628858 CATGTTTGGG
Statistics
Matches: 230, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
250 49 0.21
251 181 0.79
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (250 bp):
GGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAACGCTTCAAGCAG
GATGCGATCTGAGAAGAATTTCTGAAATCGCGCCCTTGTAGACGCGCTTTTACTACAGTTGGTCC
TGAAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGC
TTTATGAGAAGAATTTGTGAAATCGCACCCAAGTGGACGCGCTTTTGCTACAGTA
Found at i:40632084 original size:22 final size:22
Alignment explanation
Indices: 40632048--40633146 Score: 483
Period size: 22 Copynumber: 50.7 Consensus size: 22
40632038 TGTTAGGGTT
* *
40632048 TTTAGGTTAAAGGTTCATGGAA
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632070 TTTAAGTTCAGGGTT--TACAA
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632090 TTTTTAAGTTAAGGG-TCAGGGTT
1 --TTTAAGTTAAGGGTTCATGGAA
* *
40632113 TTTAGGTTAAGGGTTTATGGAA
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632135 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* *
40632157 TTTAAGTTAAAGGTT-A-GGATT
1 TTTAAGTTAAGGGTTCATGGA-A
* * **
40632178 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * * **
40632200 TTTAAGTTAAGGTTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * **
40632222 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * * **
40632244 TTTAAGTTAAGGTTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * * **
40632266 TTTAAGTTAATGGTTTAAGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * **
40632288 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * **
40632310 TTTAAGTTAAGAGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * *
40632331 TTTAGGTTAAGAGTTTATGGAA
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632353 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* *
40632374 TTTAGGTTAAGGGTTTATGGAA
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632396 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* *
40632417 TTTAGGTTAAGGGTTTATGGAA
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632439 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * **
40632460 TTTAGGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * * * **
40632481 TTTAGGTTAATGGTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * **
40632503 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * **
40632525 TTTAAGTTAAAGGTTTATGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632547 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* *
40632568 TTTAGGTTAAGGGTTTATGGAA
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632590 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * *
40632611 TTTAGGTTAAGGGTTTATAGAA
1 TTTAAGTTAAGGGTTCATGGAA
* * * **
40632633 TTTAAGATAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632655 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* *
40632676 TTTAGGTTAAGGGTTTATGGAA
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632698 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * **
40632719 TTTAGGTTAAGGGTTTTATGGTT
1 TTTAAGTTAAGGG-TTCATGGAA
* **
40632742 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * *
40632763 TTTAGGTTAAGGGTTTATAGAA
1 TTTAAGTTAAGGGTTCATGGAA
* * * **
40632785 TTTAAGATAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632807 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * *
40632828 TTTAGGTTAAGGGTTTATAGAA
1 TTTAAGTTAAGGGTTCATGGAA
* * * **
40632850 TTTAAGATAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632872 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * *
40632893 TTTAGGTTAAGGGTTTATAGAA
1 TTTAAGTTAAGGGTTCATGGAA
* * * **
40632915 TTTAAGATAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* **
40632937 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* * *
40632958 TTTAGGTTAAGGGTTTATAGAA
1 TTTAAGTTAAGGGTTCATGGAA
* * * **
40632980 TTTAAGATAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* **
40633002 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* *
40633023 TTTAGGTTAAGGGTTTATGGAA
1 TTTAAGTTAAGGGTTCATGGAA
* * **
40633045 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* **
40633067 TTTAAGTTAAGGGTT-AGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
* *
40633088 TTTAGGTTAAGGGTTTATGGAA
1 TTTAAGTTAAGGGTTCATGGAA
* * * **
40633110 TTTAAGTTAAGAGTTTAGGGTT
1 TTTAAGTTAAGGGTTCATGGAA
40633132 TTTAAGTTAAGGGTT
1 TTTAAGTTAAGGGTT
40633147 TGGGGTTTTA
Statistics
Matches: 884, Mismatches: 170, Indels: 46
0.80 0.15 0.04
Matches are distributed among these distances:
20 5 0.01
21 309 0.35
22 551 0.62
23 19 0.02
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTCATGGAA
Found at i:40632115 original size:65 final size:65
Alignment explanation
Indices: 40632039--40633296 Score: 1535
Period size: 65 Copynumber: 19.4 Consensus size: 65
40632029 AAACCTTTAT
* * * ***
40632039 GTTAGGGTTTTTAGGTTAAAGGTTCATGGAATTTAAGTTCAGGGTTTACAATTTTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* * *
40632104 GTCAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTATGGTTTTTAAGTTAAAG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* ** * *
40632169 GTTAGGATTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAGGTTTTAGGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* * * * ** * *
40632234 GTTTATGGTTTTTAAGTTAAGGTTTTAGGGTTTTTAAGTTAATGGTTTAAGGTTTTTAAGTTAAG
1 G-TTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAG
40632299 G
65 G
* * * ** * * * **
40632300 GTTTAGGGTTTTTAAGTTAAGAG-TTAGGGTTTTTAGGTTAAGAGTTTATGGAATTTAAGTTAAG
1 G-TTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAG
40632364 G
65 G
*
40632365 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* ** * * ** * *
40632429 GTTTATGGAATTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGG-TTAGGGTTTTTAGGTTAAT
1 G-TTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAA-
40632492 GG
64 GG
* ** * *
40632494 TTTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAAGGTTTATGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
*
40632559 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
** ** * * * ** *
40632623 GTTTATAGAATTTAAGATAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAG
1 G-TTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAG
40632687 G
65 G
* ** * * ** * *
40632688 GTTTATGGAATTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGTTTTATGGTTTTTAAGTTAA
1 G-TTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGG-TTTAGGGTTTTTAAGTTAA
40632752 GG
64 GG
* *
40632754 GTTAGGGTTTTTAGGTTAAGGGTTTATAGAATTTAAGATAAGGGTTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* *
40632819 GTTAGGGTTTTTAGGTTAAGGGTTTATAGAATTTAAGATAAGGGTTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* *
40632884 GTTAGGGTTTTTAGGTTAAGGGTTTATAGAATTTAAGATAAGGGTTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* *
40632949 GTTAGGGTTTTTAGGTTAAGGGTTTATAGAATTTAAGATAAGGGTTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
40633014 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
*
40633079 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGAGTTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
* * * ** * * *
40633144 GTTTGGGGTTTTAAGGTT-AGGGTTTAGGGTTTTTAGGTTAAGGGTTTAAGGTTTTTAGGTTAAG
1 G-TTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAG
40633208 G
65 G
** * ** * * * *
40633209 GTTAAAGTTTTTAGCTTAAGGGTTTATGGTTTTTAGGTTTAGGATTTA-GCTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
*
40633273 GTTAGGGTTTTTAAGTTAAGGGTT
1 GTTAGGGTTTTTAGGTTAAGGGTT
40633297 AGGATTAGGG
Statistics
Matches: 1061, Mismatches: 120, Indels: 25
0.88 0.10 0.02
Matches are distributed among these distances:
64 172 0.16
65 750 0.71
66 139 0.13
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (65 bp):
GTTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGG
Found at i:40632139 original size:43 final size:44
Alignment explanation
Indices: 40632040--40633296 Score: 1363
Period size: 43 Copynumber: 29.0 Consensus size: 44
40632030 AACCTTTATG
* * * * ** *
40632040 TTAGGGTTTTTAGGTTAAAGGTTCATGGAATTTAAGTTCAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
*** * *
40632084 TTACAATTTTTAAGTTAAGGG-TCAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* ** * *
40632127 TTATGGAATTTAAGTTAAGGGTTTATGGTTTTTAAGTTAAAGG-
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* * * *
40632170 TTAGGATTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAGGTT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* * *
40632214 TTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAGGTT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* *
40632258 TTAGGGTTTTTAAGTTAATGGTTTAAGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* * *
40632302 TTAGGGTTTTTAAGTTAAGAG-TTAGGGTTTTTAGGTTAAGAGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* ** *
40632345 TTATGGAATTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* ** *
40632388 TTATGGAATTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* ** *
40632431 TTATGGAATTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* * *
40632473 TTAGGGTTTTTAGGTTAATGGTTTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* * *
40632517 TTATGGTTTTTAAGTTAAAGGTTTATGGTTTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* * **
40632560 TTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* ** ** *
40632603 TTAGGGTTTTTAGGTTAAGGGTTTATAGAATTTAAGATAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
*
40632647 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* ** *
40632690 TTATGGAATTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGTT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-T
* *
40632734 TTATGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
** ** *
40632777 TTATAGAATTTAAGATAAGGGTTTAGGGTTTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* ** ** *
40632820 TTAGGGTTTTTAGGTTAAGGGTTTATAGAATTTAAGATAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
*
40632864 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
** ** *
40632907 TTATAGAATTTAAGATAAGGGTTTAGGGTTTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* ** ** *
40632950 TTAGGGTTTTTAGGTTAAGGGTTTATAGAATTTAAGATAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
*
40632994 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* **
40633037 TTATGGAATTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
* * ** *
40633080 TTAGGGTTTTTAGGTTAAGGGTTTATGGAATTTAAGTTAAGAGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
*
40633124 TTAGGGTTTTTAAGTTAAGGGTTT-GGGGTTTTAAGGTT-AGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAA-GTTAAGGGT
* * *
40633167 TTAGGGTTTTTAGGTTAAGGGTTTAAGGTTTTTAGGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
** * * * *
40633210 TTAAAGTTTTT-AGCTTAAGGGTTTATGGTTTTTAGGTTTAGGAT
1 TTAGGGTTTTTAAG-TTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
*
40633254 TTA-GCTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
40633296 T
1 T
40633297 AGGATTAGGG
Statistics
Matches: 1045, Mismatches: 150, Indels: 38
0.85 0.12 0.03
Matches are distributed among these distances:
42 36 0.03
43 633 0.61
44 376 0.36
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (44 bp):
TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGT
Found at i:40633578 original size:16 final size:17
Alignment explanation
Indices: 40633546--40633579 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
40633536 CAGTTACGCG
40633546 CTGGATTCCTCCTTTGT
1 CTGGATTCCTCCTTTGT
40633563 CTGGATTCCT-CTTTGT
1 CTGGATTCCTCCTTTGT
40633579 C
1 C
40633580 CAGCTTCCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.06, C:0.29, G:0.18, T:0.47
Consensus pattern (17 bp):
CTGGATTCCTCCTTTGT
Found at i:40633910 original size:18 final size:18
Alignment explanation
Indices: 40633887--40633926 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40633877 GACTCGAAAA
* *
40633887 AGGATACATATAAGGGTT
1 AGGATACATAAAAGGGCT
40633905 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
40633923 AGGA
1 AGGA
40633927 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.30, T:0.20
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:40637398 original size:4 final size:4
Alignment explanation
Indices: 40637389--40637451 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
40637379 TCACCCCTAC
40637389 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
40637437 ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACA
40637452 AGATTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:40638160 original size:14 final size:16
Alignment explanation
Indices: 40638141--40638174 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
40638131 TTATAACTTT
40638141 TTAAAAT-TAAA-TTA
1 TTAAAATGTAAATTTA
40638155 TTAAAATGTAAATTTA
1 TTAAAATGTAAATTTA
40638171 TTAA
1 TTAA
40638175 TAGTTGAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 4 0.22
16 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TTAAAATGTAAATTTA
Found at i:40639267 original size:120 final size:119
Alignment explanation
Indices: 40639132--40639371 Score: 471
Period size: 120 Copynumber: 2.0 Consensus size: 119
40639122 TATTTTAAAG
40639132 TTTACATTAAAGTAGTATTATATATTTAGTATAGGTTTGTTTTTTTAATGTGTTTTAAATTACAT
1 TTTACATTAAAGTAGTATTATATATTTAGTATAGGTTTGTTTTTTTAATGTGTTTTAAATTACAT
40639197 AATATAAAGTATTATAAACTTAAAAATGGGTCGGGCTGGGTCAGGGCTTGGGCCT
66 AATATAAAGTATTATAAACTTAAAAATGGGTCGGGCTGGGTCA-GGCTTGGGCCT
40639252 TTTACATTAAAGTAGTATTATATATTTAGTATAGGTTTGTTTTTTTAATGTGTTTTAAATTACAT
1 TTTACATTAAAGTAGTATTATATATTTAGTATAGGTTTGTTTTTTTAATGTGTTTTAAATTACAT
40639317 AATATAAAGTATTATAAACTTAAAAATGGGTCGGGCTGGGTCAGGCTTGGGCCT
66 AATATAAAGTATTATAAACTTAAAAATGGGTCGGGCTGGGTCAGGCTTGGGCCT
40639371 T
1 T
40639372 AATTGATCAA
Statistics
Matches: 120, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 12 0.10
120 108 0.90
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (119 bp):
TTTACATTAAAGTAGTATTATATATTTAGTATAGGTTTGTTTTTTTAATGTGTTTTAAATTACAT
AATATAAAGTATTATAAACTTAAAAATGGGTCGGGCTGGGTCAGGCTTGGGCCT
Found at i:40641240 original size:131 final size:131
Alignment explanation
Indices: 40641093--40641364 Score: 418
Period size: 131 Copynumber: 2.1 Consensus size: 131
40641083 AATAAGCTCG
* * * *
40641093 CCTTTGTTTTTATTTAAAACACATTTATTTTAGTTTTAAAAGGATATTTAATTGTTTAGGTTCAA
1 CCTTTATTTTTATTTAAAACACAGTTATTTTAGTTTTAAAAGGATATTCAATTATTTAGGTTCAA
* * *
40641158 CGCGAGAAAAACTGAAACCCAATAAGTTAGGACACAACTTCTCGAATTTCCAAATACGGAATATT
66 CGCAAGAAAAACTGAAACCCAATAAATTAGGACACAACTTCTCGAATTTCCAAATACGGAATATA
40641223 A
131 A
**
40641224 CCTTTATTTTTATTTAAAACACAGTTATTTTAGTTTTAAAAGGATATTCGGTTATTTAGGTTCAA
1 CCTTTATTTTTATTTAAAACACAGTTATTTTAGTTTTAAAAGGATATTCAATTATTTAGGTTCAA
* * * *
40641289 CGCAAGAAAAATTGAAACCCAGTAAATTAGGGCACAACTTCTCGAATTTCTAAATACGGAATATA
66 CGCAAGAAAAACTGAAACCCAATAAATTAGGACACAACTTCTCGAATTTCCAAATACGGAATATA
40641354 A
131 A
*
40641355 TCTTTATTTT
1 CCTTTATTTT
40641365 CAAGATTTTC
Statistics
Matches: 127, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
131 127 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (131 bp):
CCTTTATTTTTATTTAAAACACAGTTATTTTAGTTTTAAAAGGATATTCAATTATTTAGGTTCAA
CGCAAGAAAAACTGAAACCCAATAAATTAGGACACAACTTCTCGAATTTCCAAATACGGAATATA
A
Found at i:40642569 original size:19 final size:19
Alignment explanation
Indices: 40642545--40642585 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40642535 TCCTTCTTTA
*
40642545 AAATAAAATAA-AATAAACG
1 AAATAAAAAAAGAATAAA-G
40642564 AAATAAAAAAAGAATAAAG
1 AAATAAAAAAAGAATAAAG
40642583 AAA
1 AAA
40642586 CTACCTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.12
Consensus pattern (19 bp):
AAATAAAAAAAGAATAAAG
Found at i:40643009 original size:44 final size:46
Alignment explanation
Indices: 40642941--40643066 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 46
40642931 ACTTATCATG
* * *
40642941 GTAGATTTAATCCGAC-CTACTGCAACTTCAGAGG-TATAGGATTCA
1 GTAGCTTTAATCCGACTCCACTGCAACTTCAGAGGAGATAGGATT-A
* *
40642986 -TCGTTTTAATCC-ACTCCACTGCAACTTCAG-GGAGATAGGATTA
1 GTAGCTTTAATCCGACTCCACTGCAACTTCAGAGGAGATAGGATTA
* *
40643029 GTAGCTTCAA-CCTACTCCACTGCAACTTCAGA-GAGATA
1 GTAGCTTTAATCCGACTCCACTGCAACTTCAGAGGAGATA
40643067 AGGTTTGTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
43 7 0.10
44 62 0.90
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (46 bp):
GTAGCTTTAATCCGACTCCACTGCAACTTCAGAGGAGATAGGATTA
Found at i:40643203 original size:93 final size:90
Alignment explanation
Indices: 40643077--40643248 Score: 229
Period size: 93 Copynumber: 1.9 Consensus size: 90
40643067 AGGTTTGTTA
* * * *
40643077 CTTCAACTTGCTCCACTGCAACTTCAGAGAGATAAAGTTCGTGGCTTTGATTTGCTCTATTGCAA
1 CTTCAACTTGCTCCACTGCAACTTCAGAGAGATAAAGTT--T-GATATGATCTGCTCTACTGCAA
*
40643142 CTTCAGGGAAATAAGATTTGTAACCGCT
63 CTTCAGAGAAATAAGATTTGTAACCGCT
* *
40643170 CTTCAA-TCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACT
1 CTTCAACT-TGCTCCACTGCAACTTCAGAGAGATAAAGTTTGATATGATCTGCTCTACTGCAACT
*
40643234 TCAGAGAGATAAGAT
65 TCAGAGAAATAAGAT
40643249 CCGTAACTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
90 33 0.47
91 1 0.01
92 1 0.01
93 35 0.50
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (90 bp):
CTTCAACTTGCTCCACTGCAACTTCAGAGAGATAAAGTTTGATATGATCTGCTCTACTGCAACTT
CAGAGAAATAAGATTTGTAACCGCT
Found at i:40643331 original size:136 final size:136
Alignment explanation
Indices: 40643169--40643522 Score: 507
Period size: 136 Copynumber: 2.6 Consensus size: 136
40643159 TTGTAACCGC
* **
40643169 TCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACT
1 TCTTCAGTCTGCT-CACTGCAACTTCAGGGAGATAAGACTTGATATGATCTGCTCTACTGCAACT
* * *
40643234 TCAGAGAGATAAGATCCGTAACTTATAGCTTTAATC-GTTCTACTGCGACTTTAGGGAAATAAGA
65 TCAGAGAGATAAGATCCGTAACTTATAGCTTCAATCTGTTCCACTGCGACTTCAGGGAAATAAGA
40643298 TTCGCTA
130 TTCGCTA
*
40643305 TCTTCAGTCTGCTCAACTGCAACTTCAGGGAGATAAAACTTGATATGATCTGCTCTACTGCAACT
1 TCTTCAGTCTGCTC-ACTGCAACTTCAGGGAGATAAGACTTGATATGATCTGCTCTACTGCAACT
* * *
40643370 TCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGTGACTTCAGGGAAATAAGA
65 TCAGAGAGATAAGATCCGTAACTTATAGCTTCAATCTGTTCCACTGCGACTTCAGGGAAATAAGA
40643435 TTCGCTA
130 TTCGCTA
* * * *
40643442 TCTTCAGTCTGCTC-CTGCAACTTCAGGGAGATAAGACTTGTATCTTTAACCTGCTCTACTACAA
1 TCTTCAGTCTGCTCACTGCAACTTCAGGGAGATAAGACTTG-A--TATGATCTGCTCTACTGCAA
40643506 CTTCA-AGGAGATAAGAT
63 CTTCAGA-GAGATAAGAT
40643523 TTGCTATCTT
Statistics
Matches: 197, Mismatches: 15, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
135 26 0.13
136 93 0.47
137 47 0.24
138 31 0.16
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (136 bp):
TCTTCAGTCTGCTCACTGCAACTTCAGGGAGATAAGACTTGATATGATCTGCTCTACTGCAACTT
CAGAGAGATAAGATCCGTAACTTATAGCTTCAATCTGTTCCACTGCGACTTCAGGGAAATAAGAT
TCGCTA
Found at i:40643582 original size:89 final size:89
Alignment explanation
Indices: 40643418--40643654 Score: 293
Period size: 89 Copynumber: 2.7 Consensus size: 89
40643408 TTCCACTGTG
* *
40643418 ACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT-C-CTGCAACTTCAGGGAGATAAGACTT
1 ACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT
* * *
40643481 GTATCTTTAACCTGCTCTACTACA
66 GTATCTTCAACCTGCCCCACTACA
* * * *
40643505 ACTTCAAGGAGATAAGATTTGCTATCTTTAGTCTGTTCCACTGTAACTTCAGGGAGATAAGACTT
1 ACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT
40643570 GTAAT-TTCAACCTGCCCCACTACA
66 GT-ATCTTCAACCTGCCCCACTACA
* * ** ** *
40643594 ACTTCAGGGGGGTAAGA-TTAATGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 ACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
40643655 TTCGTCATGA
Statistics
Matches: 127, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
87 32 0.25
88 37 0.29
89 56 0.44
90 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (89 bp):
ACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT
GTATCTTCAACCTGCCCCACTACA
Found at i:40643655 original size:44 final size:44
Alignment explanation
Indices: 40642999--40643656 Score: 295
Period size: 44 Copynumber: 14.7 Consensus size: 44
40642989 TTTTAATCCA
* * * *
40642999 CTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAACCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAATCTG
* * **
40643043 CTCCACTGCAACTTCAGAGAGATAAGGTTTGTTA-CTTCAA-CTTG
1 CTCCACTGCAACTTCAGGGAGATAA-GATTAATAGCTTCAATC-TG
* ** * ** *
40643087 CTCCACTGCAACTTCAGAGAGATAA-AGTTCGTGGCTTTGATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TTAATAGCTTCAATCTG
* * * **
40643131 CTCTATTGCAACTTCAGGGAAATAAGATTTGTAACCGCTCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA--T-TAATAG--CTTCAATCTG
* * *
40643180 CTCCACTGCAACTTCAGGGAGATAAGGTT--T-GATAT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAATAGCT-TCAATCTG
* * *
40643221 CTCTACTGCAACTTCAGAGAGATAAGATCCGTAACTTATAGCTTTAATC-G
1 CTCCACTGCAACTTCAGGGAGATAAGAT---T-A---ATAGCTTCAATCTG
* * * * * ** * *
40643271 TTCTACTGCGACTTTAGGGAAATAAGATTCGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-AATAGCTTCAATCTG
* * * *
40643316 CTCAACTGCAACTTCAGGGAGATAAAACTTGATA---T-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TTAATAGCTTCAATCTG
* *
40643357 CTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA--T-T-A---ATAGCTTCAATCTG
* ** * ** * *
40643408 TTCCACTGTGACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-AATAGCTTCAATCTG
* * * *
40643453 CT-C-CTGCAACTTCAGGGAGATAAGACTT-GTATCTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TTAATAGCTTCAATCTG
* * * ** * * *
40643495 CTCTACTACAACTTCAAGGAGATAAGATTTGCTATCTTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TTAATAGCTTCAATCTG
* * * ** *
40643540 TTCCACTGTAACTTCAGGGAGATAAGACTT-GTAATTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TTAATAGCTTCAATCTG
* * * * *
40643584 CCCCACTACAACTTCAGGGGGGTAAGATTAATGGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAATCTG
40643628 CTCCACTGCAACTTCAGGGAGATAAGATT
1 CTCCACTGCAACTTCAGGGAGATAAGATT
40643657 CGTCATGATG
Statistics
Matches: 460, Mismatches: 115, Indels: 78
0.70 0.18 0.12
Matches are distributed among these distances:
41 59 0.13
42 16 0.03
43 27 0.06
44 179 0.39
45 78 0.17
46 4 0.01
47 7 0.02
48 1 0.00
49 31 0.07
50 27 0.06
51 31 0.07
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAATCTG
Found at i:40644569 original size:16 final size:18
Alignment explanation
Indices: 40644540--40644579 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
40644530 TTGGCCTCTC
*
40644540 TTTTTTCGTTTTC-TTAT
1 TTTTTTCGTGTTCTTTAT
40644557 TTTTTTC-TGTTCTTTAT
1 TTTTTTCGTGTTCTTTAT
40644574 TTTTTT
1 TTTTTT
40644580 ATGAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTTTCGTGTTCTTTAT
Found at i:40649399 original size:131 final size:131
Alignment explanation
Indices: 40649207--40649481 Score: 408
Period size: 131 Copynumber: 2.1 Consensus size: 131
40649197 GAGAATAAGC
* * * * *
40649207 TTGCTTTTGTTTTTATTTAAAACACAATTATTTTGGTTTTAAAAGGATATTCGGTTATTTAGATT
1 TTGCCTTTATTTTTATTTAAAACACAATTATTCTAGTTTTAAAAGGATATTCGATTATTTAGATT
* *
40649272 CAACGCAAGAAAAATCGAAACCCAGTAAGTTAGGGCACAACTTCTCGAATTTCCAAATAC-AGAA
66 CAACGCAAGAAAAATCGAAACCCAATAAATTAGGGCACAACTTCTCGAATTTCCAAATACGA-AA
40649336 TA
130 TA
* * *
40649338 TTGCCTTTATTTTTATTTAAAACACATTTATTCTAGTTTTAAAAGGATATTCGATTTTTTAGGTT
1 TTGCCTTTATTTTTATTTAAAACACAATTATTCTAGTTTTAAAAGGATATTCGATTATTTAGATT
* * *
40649403 CAACGCGAGAAAAATCGAAACCCAATAAATTAGGGCACAACTTCTTGAATTTCTAAATACGAAAT
66 CAACGCAAGAAAAATCGAAACCCAATAAATTAGGGCACAACTTCTCGAATTTCCAAATACGAAAT
40649468 A
131 A
*
40649469 TTACCTTTATTTT
1 TTGCCTTTATTTT
40649482 CAAGATTTTC
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
131 128 0.99
132 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (131 bp):
TTGCCTTTATTTTTATTTAAAACACAATTATTCTAGTTTTAAAAGGATATTCGATTATTTAGATT
CAACGCAAGAAAAATCGAAACCCAATAAATTAGGGCACAACTTCTCGAATTTCCAAATACGAAAT
A
Found at i:40649783 original size:3 final size:3
Alignment explanation
Indices: 40649775--40649823 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
40649765 AGTTAAACAC
40649775 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40649823 T
1 T
40649824 GAAATATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:40650725 original size:19 final size:19
Alignment explanation
Indices: 40650701--40650741 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40650691 CTTTAAAATA
*
40650701 AAATAAAATAA-AATAAACG
1 AAATAAAAAAAGAATAAA-G
40650720 AAATAAAAAAAGAATAAAG
1 AAATAAAAAAAGAATAAAG
40650739 AAA
1 AAA
40650742 CTACCTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.12
Consensus pattern (19 bp):
AAATAAAAAAAGAATAAAG
Found at i:40650742 original size:24 final size:24
Alignment explanation
Indices: 40650696--40650742 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40650686 TCCTTCTTTA
* *
40650696 AAATAAAATAAAATAAAATAAACG
1 AAATAAAAAAAAATAAAAGAAACG
40650720 AAATAAAAAAAGAAT-AAAGAAAC
1 AAATAAAAAAA-AATAAAAGAAAC
40650743 TACCTCTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (24 bp):
AAATAAAAAAAAATAAAAGAAACG
Found at i:40655500 original size:72 final size:72
Alignment explanation
Indices: 40655407--40655550 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
40655397 AGAGGGACTA
*
40655407 ATTTGCTCAATTTTGAAATTAAGAGGGATTAGAGAGGTCTTTTCACCTAATTGAATCAATTTGTA
1 ATTTGCTCAATTTTGAAATTAAGAGGGATTAGAGAGGTCTTTTCACCTAATTGAATCAAATTGTA
40655472 AACACAT
66 AACACAT
*
40655479 ATTTGCTCAATTTTGAAATTAAGAGGGATTGGAGAGGTCTTTTCACCTAATTGAATCAAATTGTA
1 ATTTGCTCAATTTTGAAATTAAGAGGGATTAGAGAGGTCTTTTCACCTAATTGAATCAAATTGTA
40655544 AACACAT
66 AACACAT
40655551 GTATGTTAAC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (72 bp):
ATTTGCTCAATTTTGAAATTAAGAGGGATTAGAGAGGTCTTTTCACCTAATTGAATCAAATTGTA
AACACAT
Found at i:40660954 original size:30 final size:28
Alignment explanation
Indices: 40660891--40660957 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
40660881 CGATTTCGCG
*
40660891 AAAAATGGCCCATTCCGGTAAATAATCA
1 AAAAATGGCCCATTCCGGTAAATAATAA
* **
40660919 AAAAATCGGCCCATTTCGGTAAATTTTGAA
1 AAAAAT-GGCCCATTCCGGTAAATAAT-AA
40660949 AAAAATGGC
1 AAAAATGGC
40660958 TTTTATTGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 6 0.18
29 20 0.61
30 7 0.21
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (28 bp):
AAAAATGGCCCATTCCGGTAAATAATAA
Found at i:40669520 original size:23 final size:23
Alignment explanation
Indices: 40669480--40669527 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
40669470 AATTGTCAAG
**
40669480 TTTAGACCCTGATATAGAAACAA
1 TTTAGACCCCAATATAGAAACAA
* *
40669503 TTTAGACCCCAATGTAGAAGCAA
1 TTTAGACCCCAATATAGAAACAA
40669526 TT
1 TT
40669528 ATTAAGTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (23 bp):
TTTAGACCCCAATATAGAAACAA
Found at i:40671452 original size:17 final size:18
Alignment explanation
Indices: 40671419--40671454 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40671409 TTTACCATTG
*
40671419 TTACAAATATTAATTTAT
1 TTACAAATATAAATTTAT
40671437 TTACAAAT-TAAATTTAT
1 TTACAAATATAAATTTAT
40671454 T
1 T
40671455 ATTGTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
TTACAAATATAAATTTAT
Found at i:40677558 original size:2 final size:2
Alignment explanation
Indices: 40677551--40677584 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
40677541 CTCTCCACCA
*
40677551 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40677585 TCATCTCTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40677632 original size:51 final size:52
Alignment explanation
Indices: 40677553--40677655 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 52
40677543 CTCCACCAAT
* *
40677553 ATATATATATATATATATATATGTATATATATTCATCTCTGGCTCTCTTAAA
1 ATATATATATAAAAATATATATGTATATATATTCATCTCTGGCTCTCTTAAA
40677605 ATATATATA-AAAAATATATATGTATATATATTCATCTCTGGCTCTCTTAAA
1 ATATATATATAAAAATATATATGTATATATATTCATCTCTGGCTCTCTTAAA
40677656 GTAATTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 40 0.82
52 9 0.18
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.44
Consensus pattern (52 bp):
ATATATATATAAAAATATATATGTATATATATTCATCTCTGGCTCTCTTAAA
Found at i:40683912 original size:59 final size:54
Alignment explanation
Indices: 40683839--40683975 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 54
40683829 TAGGGTCTGA
* * * *
40683839 ATTTAGCCTGGACTGGTAATTCAGATCCAGGCTC-ATTAGAGTAATTGTCATTGCAGGGG
1 ATTTAGCCTGGACTGGTAATTCAGA-CAAGACTCTA-T-GAGT--TTAT-ATTACAGGGG
* * *
40683898 ATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTACAGGGG
1 ATTTAGCCTGGACTGGTAATTCAGACAAGACTCTATGAGTTTATATTACAGGGG
40683952 ATTTAGCCTGGACTGGTAATTCAG
1 ATTTAGCCTGGACTGGTAATTCAG
40683976 CTGTAAGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
54 31 0.46
55 3 0.04
57 4 0.06
58 6 0.09
59 24 0.35
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (54 bp):
ATTTAGCCTGGACTGGTAATTCAGACAAGACTCTATGAGTTTATATTACAGGGG
Found at i:40687130 original size:26 final size:28
Alignment explanation
Indices: 40687101--40687162 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
40687091 TCTCATCCCT
40687101 ATTTTACTCCCAG-TAAA-ATTTTGACG
1 ATTTTACTCCCAGATAAATATTTTGACG
* *
40687127 ATTTTAC-CCCCGATAAATTTTTTGACG
1 ATTTTACTCCCAGATAAATATTTTGACG
*
40687154 GTTTTACTC
1 ATTTTACTC
40687163 TGCTAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 4 0.13
26 11 0.37
27 14 0.47
28 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (28 bp):
ATTTTACTCCCAGATAAATATTTTGACG
Found at i:40688489 original size:15 final size:16
Alignment explanation
Indices: 40688471--40688508 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
40688461 CAGAAGGGAA
40688471 AAAGAAAGAAAA-AAG
1 AAAGAAAGAAAAGAAG
*
40688486 AAAGAAAGAAAAGGAG
1 AAAGAAAGAAAAGAAG
40688502 AAAGAAA
1 AAAGAAA
40688509 AGCTAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAAAGAAG
Found at i:40691777 original size:85 final size:85
Alignment explanation
Indices: 40691616--40691777 Score: 198
Period size: 85 Copynumber: 1.9 Consensus size: 85
40691606 CGTACTTGTG
* * * * *
40691616 TTGTTGTAGGTATGTCACAGCATCATCCGAAACTGAATTCTAACTTAATCTCTGACATTGTTTTA
1 TTGTTGCAGGTATGTCACAGCATCATCCGAAACTGAATTCTAACATAATATCTGACATTATCTTA
*
40691681 CTTATAATGAAATACTTATA
66 CCTATAATGAAATACTTATA
* * * * * * *
40691701 TTGTTGCAGGTATGTCACAGGATCATCTGAAATTGGATTCTGACATGATATCTGACGTTATCTTA
1 TTGTTGCAGGTATGTCACAGCATCATCCGAAACTGAATTCTAACATAATATCTGACATTATCTTA
*
40691766 CCTATAGTGAAA
66 CCTATAATGAAA
40691778 GCGAGTGATA
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 63 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (85 bp):
TTGTTGCAGGTATGTCACAGCATCATCCGAAACTGAATTCTAACATAATATCTGACATTATCTTA
CCTATAATGAAATACTTATA
Found at i:40692161 original size:14 final size:14
Alignment explanation
Indices: 40692125--40692163 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
40692115 TCAGAGAACA
*
40692125 TTGAAGAAAACAAC
1 TTGAAGAACACAAC
40692139 TTGAAGAACACAAC
1 TTGAAGAACACAAC
40692153 TTGAAGAACAC
1 TTGAAGAACAC
40692164 CATTGGAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (14 bp):
TTGAAGAACACAAC
Found at i:40700453 original size:31 final size:32
Alignment explanation
Indices: 40700415--40700485 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 32
40700405 GGGGGATTAG
*
40700415 TTAAAATTTTTAAAGAGC-TAATTAAAATTTT
1 TTAAAATTTTTAAAGAGCATAATGAAAATTTT
*
40700446 TTAAAA-TTTTGAAGAGCATAATGAAAATTTT
1 TTAAAATTTTTAAAGAGCATAATGAAAATTTT
*
40700477 TCAAAATTT
1 TTAAAATTT
40700486 AGGCAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 10 0.29
31 23 0.66
32 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (32 bp):
TTAAAATTTTTAAAGAGCATAATGAAAATTTT
Found at i:40702266 original size:109 final size:109
Alignment explanation
Indices: 40702075--40702387 Score: 527
Period size: 109 Copynumber: 2.9 Consensus size: 109
40702065 ATGAATAATT
* * * * *
40702075 GGATAAAGTCCAACCATAGCAAATGCACACATGTTAGGATTGAAGACCCACACATCATAGATACA
1 GGATAAAATCCAACTATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
40702140 TACGATGAGACTCAAATTTAGGAACCAATAGAGAACACAACGCA
66 TACGATGAGACTCAAATTTAGGAACCAATAGAGAACACAACGCA
40702184 GGATAAAATCCAACTATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
1 GGATAAAATCCAACTATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
*
40702249 TACGATGAGACTCAAATTTAGGAACCAATAGAGAACACATCGCA
66 TACGATGAGACTCAAATTTAGGAACCAATAGAGAACACAACGCA
* *
40702293 GGATAAAATCCAACTATGGCAAATGCACACATATTAGGACTGGAGACCCACACATCATAAATACA
1 GGATAAAATCCAACTATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
* * *
40702358 TATGATGGGACTCAAATTTAGGAATCAATA
66 TACGATGAGACTCAAATTTAGGAACCAATA
40702388 CAAAATAAAT
Statistics
Matches: 193, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 193 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (109 bp):
GGATAAAATCCAACTATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
TACGATGAGACTCAAATTTAGGAACCAATAGAGAACACAACGCA
Found at i:40702406 original size:109 final size:109
Alignment explanation
Indices: 40702075--40702489 Score: 514
Period size: 109 Copynumber: 3.8 Consensus size: 109
40702065 ATGAATAATT
* * * *
40702075 GGATAAAGTCCAACCATAGCAAATGCACACATGTTAGGATTGAAGACCCACACATCATAGATACA
1 GGATAAAATCCAACCATAGCAAATGCACACATATTAGGACTGAAGACCCACACATCATAAATACA
40702140 TACGATGAGACTCAAATTTAGGAACCAATAGAGAACACAA-CGCA
66 TACGATGAGACTCAAATTTAGGAACCAATAGAGAACA-AATCGCA
* * *
40702184 GGATAAAATCCAACTATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
1 GGATAAAATCCAACCATAGCAAATGCACACATATTAGGACTGAAGACCCACACATCATAAATACA
*
40702249 TACGATGAGACTCAAATTTAGGAACCAATAGAGAACACATCGCA
66 TACGATGAGACTCAAATTTAGGAACCAATAGAGAACAAATCGCA
* * *
40702293 GGATAAAATCCAACTATGGCAAATGCACACATATTAGGACTGGAGACCCACACATCATAAATACA
1 GGATAAAATCCAACCATAGCAAATGCACACATATTAGGACTGAAGACCCACACATCATAAATACA
* * * * * * * *
40702358 TATGATGGGACTCAAATTTAGGAATCAATACAAAATAAATAGCT
66 TACGATGAGACTCAAATTTAGGAACCAATAGAGAACAAATCGCA
* * * * * * * * *
40702402 GGATAAAA-CCTATCCATAACAAATG--TACATATTAAGACTAAAGACTCGCACATTACAAATAC
1 GGATAAAATCC-AACCATAGCAAATGCACACATATTAGGACTGAAGACCCACACATCATAAATAC
* *
40702464 ATATGATAAGACTCAAATTTAGGAAC
65 ATACGATGAGACTCAAATTTAGGAAC
40702490 TGGATAAAAT
Statistics
Matches: 272, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
107 52 0.19
108 3 0.01
109 217 0.80
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.20
Consensus pattern (109 bp):
GGATAAAATCCAACCATAGCAAATGCACACATATTAGGACTGAAGACCCACACATCATAAATACA
TACGATGAGACTCAAATTTAGGAACCAATAGAGAACAAATCGCA
Found at i:40704589 original size:100 final size:100
Alignment explanation
Indices: 40704472--40704719 Score: 455
Period size: 99 Copynumber: 2.5 Consensus size: 100
40704462 AAAAAAATTC
* *
40704472 TTTTTTTTTCGTTTCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAATTTGGGTGTTGG
1 TTTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAATTTGGGTGTTGC
40704537 CCTGTCAATGGCCGACACCCAGTACAAATTTTAAA
66 CCTGTCAATGGCCGACACCCAGTACAAATTTTAAA
40704572 TTTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTT-AAAAAATTTGGGTGTTGC
1 TTTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAATTTGGGTGTTGC
40704636 CCTGTCAATGGCCGACACCCAGTACAAATTTTAAA
66 CCTGTCAATGGCCGACACCCAGTACAAATTTTAAA
*
40704671 TTTTTTTTTCGTGTCAGAGTCAGATATTAATATACGAAAAAAA-TTAAAA
1 TTTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTTAAAA
40704720 TTTTTTTAAA
Statistics
Matches: 144, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
98 2 0.01
99 97 0.67
100 45 0.31
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (100 bp):
TTTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAATTTGGGTGTTGC
CCTGTCAATGGCCGACACCCAGTACAAATTTTAAA
Found at i:40704624 original size:208 final size:201
Alignment explanation
Indices: 40704305--40704719 Score: 559
Period size: 208 Copynumber: 2.0 Consensus size: 201
40704295 AAAAAAGAAA
* ***
40704305 AAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAAAAAATTTTTTCTTTTTT
1 AAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGACACCC-ACAGT-AAAAAATTTTAAATTTTTT
*
40704370 TTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATAAAAAAAATTTTGGTGCTAG-CCTGTC
64 TTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTG-TAGCCCTGTC
* * *
40704434 AATGGCCGGCACCCAGTACAATTTTTAAAAAAAAATTCTTTTTTTTTCGTTTCAGAGTCAGATAT
128 AATGGCCGACACCCAGTACAAATTTT------AAA---TTTTTTTTTCGTGTCAGAGTCAGATAT
40704499 AAATATACGAAAAAAATTT
184 AAATATACGAAAAAAA-TT
* *
40704518 AAAAAAATTTGGGTGTTGGCCTGTCAATGGCCGACA-CC-CAGT-ACAAATTTTAAATTTTTTTT
1 AAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGACACCCACAGTAAAAAATTTTAAATTTTTTTT
** *
40704580 TCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAATTTGGGTGTTGCCCTGTCAAT
66 TCGTGTCAGAGTCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGTAGCCCTGTCAAT
*
40704645 GGCCGACACCCAGTACAAATTTTAAATTTTTTTTTCGTGTCAGAGTCAGATATTAATATACGAAA
131 GGCCGACACCCAGTACAAATTTTAAATTTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAA
40704710 AAAATT
196 AAAATT
40704716 AAAA
1 AAAA
40704720 TTTTTTTAAA
Statistics
Matches: 187, Mismatches: 14, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
198 6 0.03
199 41 0.22
202 3 0.02
207 2 0.01
208 95 0.51
210 4 0.02
212 2 0.01
213 34 0.18
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (201 bp):
AAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGACACCCACAGTAAAAAATTTTAAATTTTTTTT
TCGTGTCAGAGTCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGTAGCCCTGTCAAT
GGCCGACACCCAGTACAAATTTTAAATTTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAA
AAAATT
Found at i:40706248 original size:24 final size:26
Alignment explanation
Indices: 40706227--40706283 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
40706217 TTTATGTTTT
*
40706227 GTTTTGTTTTTTTT-TTAATGTTCAG
1 GTTTGGTTTTTTTTATTAATGTTCAG
40706252 GTTTGGTTTTTTTTATTAAT-TTCA-
1 GTTTGGTTTTTTTTATTAATGTTCAG
*
40706276 ATTTGGTT
1 GTTTGGTT
40706284 CTTATAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 7 0.24
25 17 0.59
26 5 0.17
ACGTcount: A:0.14, C:0.04, G:0.16, T:0.67
Consensus pattern (26 bp):
GTTTGGTTTTTTTTATTAATGTTCAG
Found at i:40706782 original size:31 final size:32
Alignment explanation
Indices: 40706666--40706783 Score: 84
Period size: 31 Copynumber: 3.8 Consensus size: 32
40706656 TTCAGGGATT
* * * *
40706666 TAATTAA-AATTTTTAAAATTTTTGAGAGCTT
1 TAATTAAGAATTTCTAAAATTTTTGAAAGGTC
**
40706697 TAA-GGAGAATTGTC-AAAATTTTTGAAAGGTC
1 TAATTAAGAATT-TCTAAAATTTTTGAAAGGTC
* * * *
40706728 TAATTAAAAATTT-TAGAACTTTTGGAAGG-C
1 TAATTAAGAATTTCTAAAATTTTTGAAAGGTC
* *
40706758 TTATTTAGAATTTCTAAAATTTTTGA
1 TAATTAAGAATTTCTAAAATTTTTGA
40706784 GGGGGAGTTT
Statistics
Matches: 64, Mismatches: 18, Indels: 10
0.70 0.20 0.11
Matches are distributed among these distances:
30 12 0.19
31 46 0.72
32 6 0.09
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.42
Consensus pattern (32 bp):
TAATTAAGAATTTCTAAAATTTTTGAAAGGTC
Found at i:40709546 original size:78 final size:79
Alignment explanation
Indices: 40709431--40709588 Score: 255
Period size: 79 Copynumber: 2.0 Consensus size: 79
40709421 ATTTTGGATT
* *
40709431 TTTTTTATGTTTTCATTTTTACGTTAGCCAGTCAGTGAT-AAAAAAATCATAATTAAGTGATCAT
1 TTTTTGATGTTTTCATTTTTACGTTAGCCAATCAGTGATAAAAAAAATCATAATTAAGTGATCAT
*
40709495 TTTGTAACTTTTCA
66 TTTGAAACTTTTCA
* * *
40709509 TTTTTGATGTTTTTATTTTTATGTTAGCCAATTAGTGATAAAAAAAATCATAATTAAGTGATCAT
1 TTTTTGATGTTTTCATTTTTACGTTAGCCAATCAGTGATAAAAAAAATCATAATTAAGTGATCAT
40709574 TTTGAAACTTTTCA
66 TTTGAAACTTTTCA
40709588 T
1 T
40709589 AGTTAAGTGA
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 34 0.47
79 39 0.53
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.47
Consensus pattern (79 bp):
TTTTTGATGTTTTCATTTTTACGTTAGCCAATCAGTGATAAAAAAAATCATAATTAAGTGATCAT
TTTGAAACTTTTCA
Found at i:40709604 original size:52 final size:54
Alignment explanation
Indices: 40709542--40709685 Score: 145
Period size: 52 Copynumber: 2.6 Consensus size: 54
40709532 TTAGCCAATT
* *
40709542 AGTGATAAAAAAAATCATAATTAAGTGATCATTTTGA-AAC-TTTTCATAGTT-A
1 AGTGATAAAAAAAATCATAATTAAATGACCATTTT-ATAACTTTTTCATAGTTGA
*
40709594 AGTGATAAAAAAGAAAAAAACCATAATTAAATGACCATTTTATAACTTTTTCATAGTTGA
1 AGTGAT-----A-AAAAAAATCATAATTAAATGACCATTTTATAACTTTTTCATAGTTGA
* *
40709654 A-TGAT-AAAAAAATCATAATTAGATGACTATTT
1 AGTGATAAAAAAAATCATAATTAAATGACCATTT
40709686 CATATAATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
52 30 0.39
57 2 0.03
58 28 0.36
59 15 0.19
60 2 0.03
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.34
Consensus pattern (54 bp):
AGTGATAAAAAAAATCATAATTAAATGACCATTTTATAACTTTTTCATAGTTGA
Found at i:40709613 original size:59 final size:59
Alignment explanation
Indices: 40709549--40709664 Score: 166
Period size: 58 Copynumber: 2.0 Consensus size: 59
40709539 ATTAGTGATA
* * *
40709549 AAAAAAATCATAATTAAGTGATCATTTTGA-AAC-TTTTCATAGTT-AAGTGATAAAAAAG
1 AAAAAAACCATAATTAAATGACCATTTT-ATAACTTTTTCATAGTTGAA-TGATAAAAAAG
40709607 AAAAAAACCATAATTAAATGACCATTTTATAACTTTTTCATAGTTGAATGATAAAAAA
1 AAAAAAACCATAATTAAATGACCATTTTATAACTTTTTCATAGTTGAATGATAAAAAA
40709665 ATCATAATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
57 1 0.02
58 28 0.54
59 21 0.40
60 2 0.04
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (59 bp):
AAAAAAACCATAATTAAATGACCATTTTATAACTTTTTCATAGTTGAATGATAAAAAAG
Found at i:40710544 original size:21 final size:20
Alignment explanation
Indices: 40710511--40710550 Score: 55
Period size: 19 Copynumber: 1.9 Consensus size: 20
40710501 ATAAAGAGCT
40710511 AAAAATATATTTT-ATTTTA
1 AAAAATATATTTTAATTTTA
40710530 AAAAATAATTATTTTAATTTT
1 AAAAAT-A-TATTTTAATTTT
40710551 TAGAGTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAAATATATTTTAATTTTA
Found at i:40714970 original size:20 final size:20
Alignment explanation
Indices: 40714927--40714970 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
40714917 TTAAAATACT
* *
40714927 TTTAAAATAATTTTTTTATT
1 TTTAAAATAATTTTTTAATG
40714947 TTTAAAATAATTTTTTAATG
1 TTTAAAATAATTTTTTAATG
40714967 TTTA
1 TTTA
40714971 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTAAAATAATTTTTTAATG
Found at i:40714975 original size:31 final size:31
Alignment explanation
Indices: 40714885--40714976 Score: 80
Period size: 31 Copynumber: 2.9 Consensus size: 31
40714875 CCGAATATAA
*
40714885 TAAATATATATTTTTT-ATTTTTATTTTTAATTT
1 TAAA-ATA-ATTTTTTAATATTTA-TTTTAATTT
* ** *
40714918 TAAAATACTTTTAAAATAATTT-TTTTATTTT
1 TAAAATAATTTTTTAAT-ATTTATTTTAATTT
*
40714949 TAAAATAATTTTTTAATGTTTATTTTAA
1 TAAAATAATTTTTTAATATTTATTTTAA
40714977 AAATGGGTTG
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
30 3 0.07
31 31 0.67
32 5 0.11
33 7 0.15
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (31 bp):
TAAAATAATTTTTTAATATTTATTTTAATTT
Found at i:40716198 original size:15 final size:16
Alignment explanation
Indices: 40716167--40716200 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40716157 TGTCAAGTGT
*
40716167 TTTATTTTTTTCTATA
1 TTTATTTTTTTCAATA
40716183 TTTATTTTTTT-AATA
1 TTTATTTTTTTCAATA
40716198 TTT
1 TTT
40716201 TAATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTTTTTCAATA
Found at i:40716493 original size:14 final size:14
Alignment explanation
Indices: 40716474--40716505 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
40716464 ATTTTAGCAA
40716474 TAATACACTGTAAT
1 TAATACACTGTAAT
40716488 TAATACACTGTAAT
1 TAATACACTGTAAT
40716502 TAAT
1 TAAT
40716506 TAATCCCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (14 bp):
TAATACACTGTAAT
Found at i:40717673 original size:22 final size:22
Alignment explanation
Indices: 40717637--40717686 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
40717627 AATCGAACAA
*
40717637 TAAATGAGTTGTAAACA-AACTT
1 TAAATGAGTTATAAA-AGAACTT
*
40717659 TAAATGATTTATAAAATGAACTT
1 TAAATGAGTTATAAAA-GAACTT
40717682 TAAAT
1 TAAAT
40717687 AAACATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 13 0.54
23 10 0.42
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (22 bp):
TAAATGAGTTATAAAAGAACTT
Found at i:40718101 original size:113 final size:113
Alignment explanation
Indices: 40717966--40718213 Score: 496
Period size: 113 Copynumber: 2.2 Consensus size: 113
40717956 GATCGTTCGA
40717966 TCGAATCGAATTGAATCGAATAAAAAAATTTCGAGTTAATCGAGTTGACGAATCATATTTTATCA
1 TCGAATCGAATTGAATCGAATAAAAAAATTTCGAGTTAATCGAGTTGACGAATCATATTTTATCA
40718031 TCCTAATTTGATTTGAAATTTTCTCGATCGAGTGGAGTGAGATGGAAT
66 TCCTAATTTGATTTGAAATTTTCTCGATCGAGTGGAGTGAGATGGAAT
40718079 TCGAATCGAATTGAATCGAATAAAAAAATTTCGAGTTAATCGAGTTGACGAATCATATTTTATCA
1 TCGAATCGAATTGAATCGAATAAAAAAATTTCGAGTTAATCGAGTTGACGAATCATATTTTATCA
40718144 TCCTAATTTGATTTGAAATTTTCTCGATCGAGTGGAGTGAGATGGAAT
66 TCCTAATTTGATTTGAAATTTTCTCGATCGAGTGGAGTGAGATGGAAT
40718192 TCGAATCGAATTGAATCGAATA
1 TCGAATCGAATTGAATCGAATA
40718214 TATTTGTTCG
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 135 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (113 bp):
TCGAATCGAATTGAATCGAATAAAAAAATTTCGAGTTAATCGAGTTGACGAATCATATTTTATCA
TCCTAATTTGATTTGAAATTTTCTCGATCGAGTGGAGTGAGATGGAAT
Found at i:40719136 original size:9 final size:9
Alignment explanation
Indices: 40719122--40719149 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
40719112 TATAGTTTGA
40719122 TATTCGAAT
1 TATTCGAAT
40719131 TATTCGAAT
1 TATTCGAAT
40719140 TATTCGAAT
1 TATTCGAAT
40719149 T
1 T
40719150 CGAAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40719701 original size:11 final size:10
Alignment explanation
Indices: 40719685--40719723 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
40719675 AATTTTTACA
40719685 ATTTTTCTTAT
1 ATTTTT-TTAT
*
40719696 ATTTTTTTACA
1 ATTTTTTTA-T
40719707 ATTTTTTTAT
1 ATTTTTTTAT
40719717 ATTTTTT
1 ATTTTTT
40719724 CAAGTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTTTTAT
Found at i:40719711 original size:21 final size:22
Alignment explanation
Indices: 40719677--40719723 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
40719667 GTGATAGTAA
40719677 TTTTTACAATTTTTCTTATATT
1 TTTTTACAATTTTTCTTATATT
40719699 TTTTTACAATTTTT-TTATATT
1 TTTTTACAATTTTTCTTATATT
40719720 TTTT
1 TTTT
40719724 CAAGTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTACAATTTTTCTTATATT
Found at i:40724621 original size:29 final size:29
Alignment explanation
Indices: 40724584--40724650 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
40724574 ATCAGAAAGT
** *
40724584 CAAACCTTTCAAAGTGCTCCAATAAGGGC
1 CAAACCTTTCAAAGTGCTAAAATAAGAGC
* * *
40724613 CAAAACTTTGAGAGTGCTAAAATAAGAGC
1 CAAACCTTTCAAAGTGCTAAAATAAGAGC
40724642 CAAACCTTT
1 CAAACCTTT
40724651 TTGAAATTGC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (29 bp):
CAAACCTTTCAAAGTGCTAAAATAAGAGC
Found at i:40727223 original size:16 final size:16
Alignment explanation
Indices: 40727174--40727225 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
40727164 GAAAAGCTAT
40727174 ATTTTTCATCTTTCT-
1 ATTTTTCATCTTTCTA
* *
40727189 ATTTTTCTACCCTTC-A
1 ATTTTTC-ATCTTTCTA
40727205 ATTTTTCATCTTTCTA
1 ATTTTTCATCTTTCTA
40727221 ATTTT
1 ATTTT
40727226 CTTTTCACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTCATCTTTCTA
Found at i:40727320 original size:2 final size:2
Alignment explanation
Indices: 40727313--40727344 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
40727303 TGCATTTGTA
40727313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40727345 CTCAACTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40728903 original size:13 final size:13
Alignment explanation
Indices: 40728869--40728903 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
40728859 TGGTATGGGT
40728869 TTATAGGTTTTGG
1 TTATAGGTTTTGG
40728882 TTATAAGGTTTTGG
1 TTAT-AGGTTTTGG
40728896 TTATAGGT
1 TTATAGGT
40728904 AAATGATGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (13 bp):
TTATAGGTTTTGG
Found at i:40729057 original size:24 final size:25
Alignment explanation
Indices: 40729030--40729078 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
40729020 AAGAGGAAAG
40729030 TTTAAAAAACATAAAA-GAAAAAAT
1 TTTAAAAAACATAAAACGAAAAAAT
** *
40729054 TTTAAATTACTTAAAACGAAAAAAT
1 TTTAAAAAACATAAAACGAAAAAAT
40729079 ATGGGGATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
TTTAAAAAACATAAAACGAAAAAAT
Found at i:40729357 original size:25 final size:25
Alignment explanation
Indices: 40729317--40729365 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
40729307 GTTTTTAATG
40729317 TTTATATTTTTTGTT-AATTTGGTT
1 TTTATATTTTTTGTTAAATTTGGTT
*
40729341 TTTATTTTTTTTAGTTAAATTTGGT
1 TTTATATTTTTT-GTTAAATTTGGT
40729366 CTCAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 3 0.14
26 8 0.36
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.69
Consensus pattern (25 bp):
TTTATATTTTTTGTTAAATTTGGTT
Found at i:40729376 original size:26 final size:24
Alignment explanation
Indices: 40729320--40729376 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 24
40729310 TTTAATGTTT
* **
40729320 ATATTTTTTGTTAATTTGGTTTTT
1 ATATTTTTTGTTAATTTGGTCTCA
*
40729344 ATTTTTTTTAGTTAAATTTGGTCTCA
1 ATATTTTTT-GTT-AATTTGGTCTCA
40729370 ATATTTT
1 ATATTTT
40729377 AAAAAGAGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 8 0.31
25 3 0.12
26 15 0.58
ACGTcount: A:0.21, C:0.04, G:0.11, T:0.65
Consensus pattern (24 bp):
ATATTTTTTGTTAATTTGGTCTCA
Found at i:40731236 original size:29 final size:29
Alignment explanation
Indices: 40731160--40731242 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
40731150 CTTCAAAAAC
* * *
40731160 TTTTAAAATCTTAATTAACCCTCCAAATTC
1 TTTTAAAATTTTAATTAAACC-CCAAATTA
* * *
40731190 TTTTAAAAAATCTCATTAAACCCCAAA-TA
1 TTTT-AAAATTTTAATTAAACCCCAAATTA
40731219 TTTTGAAAATTTTAATTAAACCCC
1 TTTT-AAAATTTTAATTAAACCCC
40731243 TTCAAAACTT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
29 21 0.50
30 9 0.21
31 12 0.29
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.37
Consensus pattern (29 bp):
TTTTAAAATTTTAATTAAACCCCAAATTA
Found at i:40734820 original size:43 final size:43
Alignment explanation
Indices: 40734759--40734852 Score: 161
Period size: 43 Copynumber: 2.2 Consensus size: 43
40734749 GATGTGACAA
40734759 ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
1 ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
* * *
40734802 ACATATTATCATATATGTAATGTCGTGTCATCTTGTTATTTCC
1 ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
40734845 ACATATTA
1 ACATATTA
40734853 CTCACTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (43 bp):
ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
Found at i:40735985 original size:10 final size:11
Alignment explanation
Indices: 40735969--40735998 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
40735959 ATTTACACGT
40735969 GTTTTATTTTC
1 GTTTTATTTTC
40735980 -TTTTATTTTC
1 GTTTTATTTTC
40735990 GTTTTATTT
1 GTTTTATTT
40735999 AGTATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.77
Consensus pattern (11 bp):
GTTTTATTTTC
Found at i:40739714 original size:43 final size:43
Alignment explanation
Indices: 40739653--40739746 Score: 161
Period size: 43 Copynumber: 2.2 Consensus size: 43
40739643 GATGTGACAA
40739653 ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
1 ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
* * *
40739696 ACATATTATCATATATGTAATGTCGTGTCATCTTGTTATTTCC
1 ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
40739739 ACATATTA
1 ACATATTA
40739747 CTCACTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (43 bp):
ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
Found at i:40740879 original size:10 final size:11
Alignment explanation
Indices: 40740863--40740892 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
40740853 ATTTACACGT
40740863 GTTTTATTTTC
1 GTTTTATTTTC
40740874 -TTTTATTTTC
1 GTTTTATTTTC
40740884 GTTTTATTT
1 GTTTTATTT
40740893 AGTATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.77
Consensus pattern (11 bp):
GTTTTATTTTC
Found at i:40741444 original size:9 final size:9
Alignment explanation
Indices: 40741430--40741460 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
40741420 TTTGGGGCTA
40741430 TTTTTATTT
1 TTTTTATTT
40741439 TTTTTATTT
1 TTTTTATTT
40741448 TTATTTATTT
1 TT-TTTATTT
40741458 TTT
1 TTT
40741461 AAAACACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTATTT
Found at i:40741446 original size:15 final size:16
Alignment explanation
Indices: 40741428--40741459 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40741418 TTTTTGGGGC
40741428 TATTTTTATTT-TTTT
1 TATTTTTATTTATTTT
40741443 TATTTTTATTTATTTT
1 TATTTTTATTTATTTT
40741459 T
1 T
40741460 TAAAACACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TATTTTTATTTATTTT
Found at i:40741619 original size:15 final size:16
Alignment explanation
Indices: 40741594--40741623 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40741584 CATATATTTT
40741594 TTATAATATATATACA
1 TTATAATATATATACA
40741610 TTAT-ATATATATAC
1 TTATAATATATATAC
40741624 TTTTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATAATATATATACA
Found at i:40742093 original size:12 final size:12
Alignment explanation
Indices: 40742065--40742111 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
40742055 GCAAGTTTAC
*
40742065 TTGTATACTATAC
1 TTGTATA-TATAT
40742078 TTGTATATATAT
1 TTGTATATATAT
*
40742090 TTGTAAATAT-T
1 TTGTATATATAT
40742101 TATGTATATAT
1 T-TGTATATAT
40742112 GCTTTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 2 0.07
12 21 0.70
13 7 0.23
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (12 bp):
TTGTATATATAT
Found at i:40743887 original size:19 final size:18
Alignment explanation
Indices: 40743863--40743908 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
40743853 AACGTCTCTT
*
40743863 TTTGCATTCATTTCATGCA
1 TTTGCATTCATTGCAT-CA
40743882 TTTGCATTTCATTGCATCA
1 TTTGCA-TTCATTGCATCA
*
40743901 TATGCATT
1 TTTGCATT
40743909 AAACACCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 9 0.38
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (18 bp):
TTTGCATTCATTGCATCA
Found at i:40744482 original size:34 final size:34
Alignment explanation
Indices: 40744443--40744511 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
40744433 AGTGAATGAA
40744443 GAGTTACCGAAGCAGTTGGAAGAAAGATACAGGT
1 GAGTTACCGAAGCAGTTGGAAGAAAGATACAGGT
40744477 GAGTTACCGAAGCAGTTGGAAGAAAGATACAGGT
1 GAGTTACCGAAGCAGTTGGAAGAAAGATACAGGT
40744511 G
1 G
40744512 GCTCGAAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.33, T:0.17
Consensus pattern (34 bp):
GAGTTACCGAAGCAGTTGGAAGAAAGATACAGGT
Found at i:40750390 original size:44 final size:43
Alignment explanation
Indices: 40750161--40750465 Score: 184
Period size: 45 Copynumber: 6.9 Consensus size: 43
40750151 NNNNNNNNAG
*
40750161 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAA
1 ATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAG-TAACAA
* * *** * * ** * * *
40750205 ATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAATACAG
1 ATCTTGTCTTCATGTACTGG-CGTGAAATAGATC-AAAGTA-ACAA
* * *
40750251 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAA-TATACAG
1 ATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAGTA-ACAA
* * * * * ** * *
40750294 ATCTCGCCTTC-TCATACTGGTGGCGAAGCAGATCGAAAGAAAGCAG
1 ATCTTGTCTTCAT-GTACTGG-CGTGAAATAGATC-AAAGTAA-CAA
40750340 ATCTTGTCTTCATGTA-TCGGCGTGAAATAGATCAAAGTCAACAA
1 ATCTTGTCTTCATGTACT-GGCGTGAAATAGATCAAAGT-AACAA
*** * * * *
40750384 ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAAATAGCAA
1 ATCTTGTCTTCATGTACTGG-CGTGAAATAGATC-AAAGTAACAA
40750429 ATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAG
1 ATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAG
40750466 ATAGTAGGTC
Statistics
Matches: 195, Mismatches: 52, Indels: 29
0.71 0.19 0.11
Matches are distributed among these distances:
42 1 0.01
43 24 0.12
44 58 0.30
45 69 0.35
46 42 0.22
47 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (43 bp):
ATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAGTAACAA
Found at i:40750465 original size:89 final size:88
Alignment explanation
Indices: 40750159--40750465 Score: 431
Period size: 89 Copynumber: 3.4 Consensus size: 88
40750149 NNNNNNNNNN
*
40750159 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAAATCTCGCCTTCCCATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAG-TAACAAATCTCGCCTTCCCATACTG
40750224 GTGGCGAAGCAGATCGAAGGAATA-C
65 GTGGCGAAGCAGATCGAA--AATAGC
* * * *
40750249 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAA-TATACAGATCTCGCCTTCTCATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAGTA-ACAAATCTCGCCTTCCCATACTG
*
40750313 GTGGCGAAGCAGATCGAAAGAAAGC
65 GTGGCGAAGCAGATCGAAA-ATAGC
* *
40750338 AGATCTTGTCTTCATGTA-TCGGCGTGAAATAGATCAAAGTCAACAAATCTTGTCTTCCCATACT
1 AGATCTTGTCTTCATGTACT-GGCGTGAAATAGATCAAAGT-AACAAATCTCGCCTTCCCATACT
* *
40750402 GGTGGTGAAGTAGATCGAAAATAGC
64 GGTGGCGAAGCAGATCGAAAATAGC
*
40750427 AAATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAG
1 AGATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAG
40750466 ATAGTAGGTC
Statistics
Matches: 196, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
87 1 0.01
88 5 0.03
89 114 0.58
90 75 0.38
91 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (88 bp):
AGATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAGTAACAAATCTCGCCTTCCCATACTGG
TGGCGAAGCAGATCGAAAATAGC
Found at i:40750556 original size:89 final size:89
Alignment explanation
Indices: 40750161--40750549 Score: 259
Period size: 89 Copynumber: 4.4 Consensus size: 89
40750151 NNNNNNNNAG
* * * * ** ** *
40750161 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAAAT-CTCGCCTTCCCATACTGG
1 ATCTTATCTTCATATACCGGCGTGAAATAGATCAAAGATAGTAGGTCCT-GTCTTCCCATACTGG
* * *
40750225 TGGCGAAGCAGATCGAAGGAATA-CAG
65 TAGCGAAGTAGATCGAA--AATAGCAA
* * * * * * * * * *
40750251 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAATATA-CAGAT-CTCGCCTTCTCATACTGG
1 ATCTTATCTTCATATACCGGCGTGAAATAGATCAAAGATAGTAGGTCCT-GTCTTCCCATACTGG
* * * *
40750314 TGGCGAAGCAGATCGAAAGAAAGCAG
65 TAGCGAAGTAGATCGAAA-ATAGCAA
* * * ** ** *
40750340 ATCTTGTCTTCATGTATCGGCGTGAAATAGATCAAAG-TCAACAAATCTTGTCTTCCCATACTGG
1 ATCTTATCTTCATATACCGGCGTGAAATAGATCAAAGAT-AGTAGGTCCTGTCTTCCCATACTGG
* *
40750404 TGGTGAAGTAGATCGAAAATAGCAA
65 TAGCGAAGTAGATCGAAAATAGCAA
* * * * *
40750429 ATCTTGTCTTCATGTACTGGCGTGAAATAGATCAAAGATAGTAGGTCCTGTCTTCCTATATTGGT
1 ATCTTATCTTCATATACCGGCGTGAAATAGATCAAAGATAGTAGGTCCTGTCTTCCCATACTGGT
* * *
40750494 AGCGAAGTGGATCGAATATA-CAT
66 AGCGAAGTAGATCGAAAATAGCAA
* *
40750517 ATTTTATCTTCCTATACCGGCGGTGAAATAGAT
1 ATCTTATCTTCATATACCGGC-GTGAAATAGAT
40750550 TGAAGATTAC
Statistics
Matches: 255, Mismatches: 37, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
87 1 0.00
88 21 0.08
89 160 0.63
90 72 0.28
91 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (89 bp):
ATCTTATCTTCATATACCGGCGTGAAATAGATCAAAGATAGTAGGTCCTGTCTTCCCATACTGGT
AGCGAAGTAGATCGAAAATAGCAA
Found at i:40751658 original size:10 final size:11
Alignment explanation
Indices: 40751642--40751671 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
40751632 ATTTACACGT
40751642 GTTTTATTTTC
1 GTTTTATTTTC
40751653 -TTTTATTTTC
1 GTTTTATTTTC
40751663 GTTTTATTT
1 GTTTTATTT
40751672 AGTATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.77
Consensus pattern (11 bp):
GTTTTATTTTC
Found at i:40752278 original size:12 final size:12
Alignment explanation
Indices: 40752242--40752280 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
40752232 TTTTTTAAAA
40752242 CATTATTATTAT
1 CATTATTATTAT
40752254 -ATTATATATTAT
1 CATTAT-TATTAT
*
40752266 CATTATTACTAT
1 CATTATTATTAT
40752278 CAT
1 CAT
40752281 CATCTCTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 5 0.21
12 14 0.58
13 5 0.21
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (12 bp):
CATTATTATTAT
Found at i:40752755 original size:12 final size:12
Alignment explanation
Indices: 40752727--40752773 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
40752717 GCAAGTTTAC
*
40752727 TTGTATACTATAC
1 TTGTATA-TATAT
40752740 TTGTATATATAT
1 TTGTATATATAT
*
40752752 TTGTAAATAT-T
1 TTGTATATATAT
40752763 TATGTATATAT
1 T-TGTATATAT
40752774 GCTTTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 2 0.07
12 21 0.70
13 7 0.23
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (12 bp):
TTGTATATATAT
Found at i:40756961 original size:29 final size:30
Alignment explanation
Indices: 40756902--40756961 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
40756892 CTATATATAT
* * **
40756902 TTAGTTTAAGATTTAATTAAGTTAATTTAA
1 TTAGTTTAAGACTTAATTAAATTAAACTAA
40756932 TTAGTTTAAG-CTTAATTAAATTAAACTAA
1 TTAGTTTAAGACTTAATTAAATTAAACTAA
40756961 T
1 T
40756962 CATACATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (30 bp):
TTAGTTTAAGACTTAATTAAATTAAACTAA
Found at i:40760398 original size:16 final size:16
Alignment explanation
Indices: 40760377--40760410 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40760367 TCAATGTTAC
40760377 TTGAAATGAAAACCAA
1 TTGAAATGAAAACCAA
* *
40760393 TTGAAATGCAAATCAA
1 TTGAAATGAAAACCAA
40760409 TT
1 TT
40760411 CAAAATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (16 bp):
TTGAAATGAAAACCAA
Found at i:40762125 original size:20 final size:21
Alignment explanation
Indices: 40762097--40762139 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
40762087 TTTAAAATAA
*
40762097 AATTTAAAAAATA-TATAAAG
1 AATTCAAAAAATAGTATAAAG
*
40762117 AATTCAAAAAATAGTATGAAG
1 AATTCAAAAAATAGTATAAAG
40762138 AA
1 AA
40762140 CACGTGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (21 bp):
AATTCAAAAAATAGTATAAAG
Found at i:40768697 original size:441 final size:440
Alignment explanation
Indices: 40767849--40768661 Score: 1563
Period size: 441 Copynumber: 1.8 Consensus size: 440
40767839 TTGGTTCATG
40767849 GTTAAACGGCGACATTTTCATTACTTGAATTTGAATTCTTGAATTTTTGCGTTTAGTTGTTGTAT
1 GTTAAACGGCGACATTTTCATTACTTGAATTTGAATTCTTGAATTTTTGCGTTTAGTTGTTGTAT
40767914 TAGTCCTTATGCTTTCGACTGATTGCAAATTTAGTCTTCTAAATGCTGTAATTTTTTTAATTTTA
66 TAGTCCTTATGCTTTCGACTGATTGCAAATTTAGTCTTCTAAATGCTGTAATTTTTTTAATTTTA
40767979 TTTTTATTTCTCATTAGTCATAATGTTTTGTTAAATTTCATAAATATTATTGGCTCTTATAGTGA
131 TTTTTATTTCTCATTAGTCATAATGTTTTGTTAAATTTCATAAATATTATTGGCTCTTATAGTGA
40768044 ATATATTAAAGAAAATTTCATTCAAATTTAGTTTTTTATATATAACATAACGTAAAATTAGCTTA
196 ATATATTAAAGAAAATTTCATTCAAATTTAGTTTTTTATATATAACATAACGTAAAATTAGCTTA
*
40768109 GTATTTTTAATATGTTTATTTTTAATAAATTTTAAATATTAGGATTAACATTGTTTTCAAATTTT
261 GTATTTTTAATATGTTTATTTTTAATAAATTTTAAATATTAGGATTAACATTGTTTTCAAATATT
*
40768174 TTTTATTATAATTTTAAGGTACAGCATATCGTTATTTAAAATTATTAACATTGTTTTTAAAATTT
326 TTTTATTATAATTTTAAGGTACAACATATCGTTATTTAAAATTATTAACATTG-TTTTAAAATTT
* * *
40768239 ATCCTTTTCATTTTTAAACTTTATATCATTATATGTTTCATTATCTATATA
390 ATACTATTCATTTTTAAAATTTATATCATTATATGTTTCATTATCTATATA
40768290 GTTAAACGGCGACATTTTCATTACTTGAATTTGAATTCTTGAATTTTTGCGTTTAGTTGTTGTAT
1 GTTAAACGGCGACATTTTCATTACTTGAATTTGAATTCTTGAATTTTTGCGTTTAGTTGTTGTAT
40768355 TAGTCCTTATGCTTTCGACTGATTGCAAATTTAGTCTTCTAAATGCTGTAATTTTTTTAATTTTA
66 TAGTCCTTATGCTTTCGACTGATTGCAAATTTAGTCTTCTAAATGCTGTAATTTTTTTAATTTTA
40768420 TTTTTATTTCTCATTAGTCATAATGTTTTGTTAAATTTCATAAATATTATTGGCTCTTATAGTGA
131 TTTTTATTTCTCATTAGTCATAATGTTTTGTTAAATTTCATAAATATTATTGGCTCTTATAGTGA
40768485 ATATATTAAAGAAAATTTCATTCAAATTTAGTTTTTTATATATAACATAACGTAAAATTAGCTTA
196 ATATATTAAAGAAAATTTCATTCAAATTTAGTTTTTTATATATAACATAACGTAAAATTAGCTTA
*
40768550 GTATTTTTAATATGTTTATTTTTAATAAATTTTAAATATTAGTATTAACATTGTTTTCAAATATT
261 GTATTTTTAATATGTTTATTTTTAATAAATTTTAAATATTAGGATTAACATTGTTTTCAAATATT
40768615 TTTTATTATAATTTTAAGGTACAACATATCGTTATTTAAAATTATTA
326 TTTTATTATAATTTTAAGGTACAACATATCGTTATTTAAAATTATTA
40768662 TTAACATGTT
Statistics
Matches: 369, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
441 369 1.00
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.50
Consensus pattern (440 bp):
GTTAAACGGCGACATTTTCATTACTTGAATTTGAATTCTTGAATTTTTGCGTTTAGTTGTTGTAT
TAGTCCTTATGCTTTCGACTGATTGCAAATTTAGTCTTCTAAATGCTGTAATTTTTTTAATTTTA
TTTTTATTTCTCATTAGTCATAATGTTTTGTTAAATTTCATAAATATTATTGGCTCTTATAGTGA
ATATATTAAAGAAAATTTCATTCAAATTTAGTTTTTTATATATAACATAACGTAAAATTAGCTTA
GTATTTTTAATATGTTTATTTTTAATAAATTTTAAATATTAGGATTAACATTGTTTTCAAATATT
TTTTATTATAATTTTAAGGTACAACATATCGTTATTTAAAATTATTAACATTGTTTTAAAATTTA
TACTATTCATTTTTAAAATTTATATCATTATATGTTTCATTATCTATATA
Found at i:40773690 original size:29 final size:29
Alignment explanation
Indices: 40773620--40773699 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 29
40773610 TTTACAATTG
* *
40773620 TTGAAAATTGTAATTAGATCTTCTAAAGGAT
1 TTGAAAATTTTAATTAGA-CCTCTAAA-GAT
40773651 TTGAAAATTTTAATTAGACCTCTAAA-AT
1 TTGAAAATTTTAATTAGACCTCTAAAGAT
*
40773679 TATGAAAATTTTCATTA-ACCT
1 T-TGAAAATTTTAATTAGACCT
40773700 TCTCCCCACA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.16
29 14 0.31
30 7 0.16
31 17 0.38
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (29 bp):
TTGAAAATTTTAATTAGACCTCTAAAGAT
Found at i:40778232 original size:2 final size:2
Alignment explanation
Indices: 40778225--40778250 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40778215 TAAAACCCAT
40778225 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
40778251 AACAAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40789163 original size:20 final size:20
Alignment explanation
Indices: 40789130--40789170 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40789120 TAGACATTTG
** *
40789130 TTTTATTACCATTTTATATA
1 TTTTATTAAAATTTTAAATA
40789150 TTTTATTAAAATTTTAAATA
1 TTTTATTAAAATTTTAAATA
40789170 T
1 T
40789171 AAAAAGCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATTAAAATTTTAAATA
Found at i:40789297 original size:20 final size:21
Alignment explanation
Indices: 40789272--40789313 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
40789262 ATTCATCTCA
40789272 TATTTTAATTG-ATTT-ATTAT
1 TATTTT-ATTGAATTTCATTAT
40789292 TATTTTATTGAATTTCATTAT
1 TATTTTATTGAATTTCATTAT
40789313 T
1 T
40789314 CAAGTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (21 bp):
TATTTTATTGAATTTCATTAT
Found at i:40790373 original size:43 final size:42
Alignment explanation
Indices: 40790326--40790572 Score: 262
Period size: 43 Copynumber: 5.8 Consensus size: 42
40790316 GTGGAGAAAT
*
40790326 GCTGCTATAGAACATGACCTTTAGCGGCGCTTATCCCAGAAAC
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTT-TCCCACAAAC
* * *
40790369 GCTGCTATAGATCATGACATTTAGCGGCACTTTTCCCACAAAC
1 GCTGCTATAGAACATGACCTTTAGCGGCGC-TTTCCCACAAAC
* *
40790412 -CTTGCTATAGAACATGACCTTTAGCGGCGCCTTCCCCACAATC
1 GC-TGCTATAGAACATGACCTTTAGCGGCG-CTTTCCCACAAAC
* * * *
40790455 GCTGCTATAGAATATAACCTTTTGCGGCACTTTCCCACAAAC
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTTTCCCACAAAC
* * * * *
40790497 GCCGCTATAGAGCATGACCTTTAGTGACGCTTTCCCTACAAAT
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTTTCCC-ACAAAC
* * * * *
40790540 GCCGCTAAAGAATATGACTTTTAGTGGCGCTTT
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTTT
40790573 TTACCATAAA
Statistics
Matches: 170, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
42 40 0.24
43 126 0.74
44 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (42 bp):
GCTGCTATAGAACATGACCTTTAGCGGCGCTTTCCCACAAAC
Found at i:40790532 original size:85 final size:86
Alignment explanation
Indices: 40790329--40790605 Score: 278
Period size: 86 Copynumber: 3.2 Consensus size: 86
40790319 GAGAAATGCT
* * *
40790329 GCTATAGAACATGACCTTTAGCGGCGCTTAT-CCCAGAAACGCTGCTATAG-ATCATGACATTTA
1 GCTATAGAACATGACCTTTAGCGGCGCTT-TCCCCACAATCGCTGCTATAGAAT-ATAACATTTA
*
40790392 GCGGCACTTTTCCCACAAACCTT
64 GCGGCACTTTTCCCACAAACCTC
* * *
40790415 GCTATAGAACATGACCTTTAGCGGCGCCTTCCCCACAATCGCTGCTATAGAATATAACCTTTTGC
1 GCTATAGAACATGACCTTTAGCGGCGCTTTCCCCACAATCGCTGCTATAGAATATAACATTTAGC
40790480 GGCAC-TTTCCCACAAACGC-C
66 GGCACTTTTCCCACAAAC-CTC
* * * * * * * *
40790500 GCTATAGAGCATGACCTTTAGTGACGCTTTCCCTACAAAT-GCCGCTAAAGAATATGACTTTTAG
1 GCTATAGAACATGACCTTTAGCGGCGCTTTCCCCAC-AATCGCTGCTATAGAATATAACATTTAG
* * * * *
40790564 TGGCGCTTTTTACCATAAAAC-C
65 CGGCAC-TTTTCCCACAAACCTC
*
40790586 GCTAAAGAACATGACCTTTA
1 GCTATAGAACATGACCTTTA
40790606 ATGGTGCTTT
Statistics
Matches: 161, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
85 67 0.42
86 83 0.52
87 11 0.07
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (86 bp):
GCTATAGAACATGACCTTTAGCGGCGCTTTCCCCACAATCGCTGCTATAGAATATAACATTTAGC
GGCACTTTTCCCACAAACCTC
Found at i:40790904 original size:16 final size:16
Alignment explanation
Indices: 40790879--40790914 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40790869 AATGAAATAA
*
40790879 CAAAATTTATTATATT
1 CAAAAGTTATTATATT
40790895 CAAAAGTTATTATATT
1 CAAAAGTTATTATATT
40790911 -AAAA
1 CAAAA
40790915 TATTCTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
CAAAAGTTATTATATT
Found at i:40795328 original size:9 final size:9
Alignment explanation
Indices: 40795314--40795383 Score: 74
Period size: 9 Copynumber: 8.0 Consensus size: 9
40795304 TAAGTATAAT
40795314 TAAGTTATG
1 TAAGTTATG
40795323 TAAGTTATG
1 TAAGTTATG
* * *
40795332 ATATGATATA
1 -TAAGTTATG
*
40795342 T-ATTTATG
1 TAAGTTATG
40795350 T-A-TTATG
1 TAAGTTATG
40795357 TAAGTTATG
1 TAAGTTATG
40795366 TAAGTTATG
1 TAAGTTATG
40795375 TAAGTTATG
1 TAAGTTATG
40795384 ATCCAAAGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
7 6 0.12
8 6 0.12
9 33 0.65
10 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:40795383 original size:34 final size:34
Alignment explanation
Indices: 40795318--40795383 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
40795308 TATAATTAAG
* *
40795318 TTATGTAAGTTATGATATGATATATATTTATGTA
1 TTATGTAAGTTATGATAAGATATATAGTTATGTA
* *
40795352 TTATGTAAGTTATG-TAAGTTATGTAAGTTATG
1 TTATGTAAGTTATGATAAGATATAT-AGTTATG
40795384 ATCCAAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (34 bp):
TTATGTAAGTTATGATAAGATATATAGTTATGTA
Found at i:40795453 original size:13 final size:13
Alignment explanation
Indices: 40795435--40795460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40795425 TGATTATCAT
40795435 CTTTAAATTTTAA
1 CTTTAAATTTTAA
40795448 CTTTAAATTTTAA
1 CTTTAAATTTTAA
40795461 TAATTATATG
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:40797723 original size:15 final size:15
Alignment explanation
Indices: 40797703--40797734 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40797693 TGGCAGATAA
40797703 CAGAAAACTGGATGG
1 CAGAAAACTGGATGG
*
40797718 CAGAAAATTGGATGG
1 CAGAAAACTGGATGG
40797733 CA
1 CA
40797735 AATCTAAAGT
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:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (15 bp):
CAGAAAACTGGATGG
Found at i:40799010 original size:20 final size:20
Alignment explanation
Indices: 40798987--40799025 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40798977 TTTATGTAAT
40798987 ATTTAAAATAATTATATAAA
1 ATTTAAAATAATTATATAAA
* **
40799007 ATTTGAAATTTTTATATAA
1 ATTTAAAATAATTATATAA
40799026 TTTTTTATGT
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
ATTTAAAATAATTATATAAA
Found at i:40799505 original size:41 final size:41
Alignment explanation
Indices: 40799448--40799540 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
40799438 CGACGTTTAA
* * *
40799448 AAACGTCGCTAATGCTTGA-CTTTTTGTGGCATTTTTCTCAT
1 AAACGCCGCTAATGCTTGATC-GTTTGCGGCATTTTTCTCAT
* *
40799489 AAACGCCGCTATTGCTTGATCGTTTGCGGCGTTTTTCTCAT
1 AAACGCCGCTAATGCTTGATCGTTTGCGGCATTTTTCTCAT
* *
40799530 AAGCCCCGCTA
1 AAACGCCGCTA
40799541 CTGTTTTACC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 43 0.98
42 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (41 bp):
AAACGCCGCTAATGCTTGATCGTTTGCGGCATTTTTCTCAT
Found at i:40801128 original size:24 final size:24
Alignment explanation
Indices: 40801109--40801158 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
40801099 AGATTTAGTA
*
40801109 TTTATGAGTATAATATATTTAACT
1 TTTATGAGCATAATATATTTAACT
* *
40801133 TTTATTAGCATAATATATTTGACT
1 TTTATGAGCATAATATATTTAACT
40801157 TT
1 TT
40801159 GATTAGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTATGAGCATAATATATTTAACT
Found at i:40801163 original size:24 final size:24
Alignment explanation
Indices: 40801118--40801164 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
40801108 ATTTATGAGT
*
40801118 ATAATATATTTAACTTTTATTAGC
1 ATAATATATTTAACTTTGATTAGC
*
40801142 ATAATATATTTGACTTTGATTAG
1 ATAATATATTTAACTTTGATTAG
40801165 AATTAGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (24 bp):
ATAATATATTTAACTTTGATTAGC
Found at i:40802490 original size:28 final size:28
Alignment explanation
Indices: 40802458--40802513 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
40802448 TGTTTGACGG
*
40802458 AGTTGTCAGAACACTTAGTGATGTGCGA
1 AGTTGTCAGAACACTTAGTGACGTGCGA
40802486 AGTTGTCAGAACACTTAGTGACGTGCGA
1 AGTTGTCAGAACACTTAGTGACGTGCGA
40802514 CATGTTCCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (28 bp):
AGTTGTCAGAACACTTAGTGACGTGCGA
Found at i:40810028 original size:126 final size:125
Alignment explanation
Indices: 40809803--40810072 Score: 454
Period size: 126 Copynumber: 2.2 Consensus size: 125
40809793 GATAAAATCA
* * *
40809803 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
40809868 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTAT-AAAAAACGCTTC
40809929 AAGCAGGATGCTTTATCAGAAGAAATTTC-AAAATCACGCCCACGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATCAGAAG-AATTTCTAAAATCACGCCCACGTGGACGCGCTTTTGCTACAG
* *
40809993 TAGGT-CTTACAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
65 TAGGTCCTGA-AAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
40810054 AAGCAGGATGCTTTATCAG
1 AAGCAGGATGCTTTATCAG
40810073 GATGCTTCAA
Statistics
Matches: 137, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
125 34 0.25
126 97 0.71
127 6 0.04
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
Found at i:40810075 original size:13 final size:13
Alignment explanation
Indices: 40810055--40810095 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
40810045 AAACGCTTCA
40810055 AGCAGGATGCTTT
1 AGCAGGATGCTTT
* *
40810068 ATCAGGATGCTTCA
1 AGCAGGATGCTT-T
40810082 AGCAGGATGCTTT
1 AGCAGGATGCTTT
40810095 A
1 A
40810096 AGTTAAGGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (13 bp):
AGCAGGATGCTTT
Found at i:40810089 original size:14 final size:14
Alignment explanation
Indices: 40810049--40810093 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
40810039 TATAAAAAAC
40810049 GCTTCAAGCAGGAT
1 GCTTCAAGCAGGAT
* *
40810063 GCTT-TATCAGGAT
1 GCTTCAAGCAGGAT
40810076 GCTTCAAGCAGGAT
1 GCTTCAAGCAGGAT
40810090 GCTT
1 GCTT
40810094 TAAGTTAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (14 bp):
GCTTCAAGCAGGAT
Found at i:40810118 original size:21 final size:21
Alignment explanation
Indices: 40810092--40810133 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40810082 AGCAGGATGC
40810092 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
40810113 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
40810134 AGGGTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:40810171 original size:12 final size:12
Alignment explanation
Indices: 40810156--40810198 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
40810146 AGGGTTTGTC
40810156 AATTAAATTATA
1 AATTAAATTATA
40810168 AATTAAATTATA
1 AATTAAATTATA
40810180 AATTATAAATTTATA
1 AA-T-TAAA-TTATA
40810195 AATT
1 AATT
40810199 TTTAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 14 0.50
13 2 0.07
14 5 0.18
15 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAAATTATA
Found at i:40810199 original size:8 final size:7
Alignment explanation
Indices: 40810159--40810198 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
40810149 GTTTGTCAAT
40810159 TAAATTA
1 TAAATTA
40810166 TAAA-T-
1 TAAATTA
40810171 TAAATTA
1 TAAATTA
40810178 TAAATTA
1 TAAATTA
40810185 TAAATTTA
1 TAAA-TTA
40810193 TAAATT
1 TAAATT
40810199 TTTAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.13
6 2 0.07
7 17 0.57
8 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAAATTA
Found at i:40810323 original size:21 final size:22
Alignment explanation
Indices: 40810299--40810357 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
40810289 GTCCGGCTTT
* *
40810299 CGGCAGGGG-TTGTGGTTGCTC
1 CGGCAGGGGATTCTGGTTCCTC
40810320 CGGC-GGGGATTCTGGTTCCTC
1 CGGCAGGGGATTCTGGTTCCTC
* *
40810341 CGGTAGGGCA-TCTGGTT
1 CGGCAGGGGATTCTGGTT
40810358 GTCGGTGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.07, C:0.22, G:0.42, T:0.29
Consensus pattern (22 bp):
CGGCAGGGGATTCTGGTTCCTC
Found at i:40810624 original size:18 final size:18
Alignment explanation
Indices: 40810598--40810640 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40810588 AACTCGAAAA
* * *
40810598 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
40810616 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
40810634 AGGATAC
1 AGGATAC
40810641 GCACCTGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:40811296 original size:7 final size:7
Alignment explanation
Indices: 40811286--40811311 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40811276 TTATATACAT
40811286 AATACTA
1 AATACTA
40811293 AATACTA
1 AATACTA
40811300 AATACTA
1 AATACTA
40811307 AATAC
1 AATAC
40811312 CAATCGACTA
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:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:40812384 original size:22 final size:22
Alignment explanation
Indices: 40812359--40812431 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
40812349 ATATGGATTG
*
40812359 GAGAGAAATTTG-GAAGGAAATT
1 GAGAGAAATTTGAG-AGCAAATT
40812381 GAGAGCAAA-TTGAGAGCAAATT
1 GAGAG-AAATTTGAGAGCAAATT
**
40812403 GAGAGGAAA-TTGAGAAAATAATT
1 GAGA-GAAATTTGAGAGCA-AATT
40812426 GAGAGA
1 GAGAGA
40812432 GGATTAGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
22 31 0.70
23 13 0.30
ACGTcount: A:0.48, C:0.03, G:0.30, T:0.19
Consensus pattern (22 bp):
GAGAGAAATTTGAGAGCAAATT
Found at i:40812392 original size:11 final size:11
Alignment explanation
Indices: 40812376--40812417 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
40812366 ATTTGGAAGG
40812376 AAATTGAGAGC
1 AAATTGAGAGC
40812387 AAATTGAGAGC
1 AAATTGAGAGC
*
40812398 AAATTGAGAGG
1 AAATTGAGAGC
40812409 AAATTGAGA
1 AAATTGAGA
40812418 AAATAATTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.48, C:0.05, G:0.29, T:0.19
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:40813345 original size:30 final size:29
Alignment explanation
Indices: 40813281--40813348 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
40813271 TTTGAAATTT
* *
40813281 GAAATTTAATTTTTATATTTTTATTTTCA
1 GAAATTTAATTTTTATATTTTTAATGTCA
40813310 GAAATTTAATTTCTT-TAATTTTTAAATGTCA
1 GAAATTTAATTT-TTAT-ATTTTT-AATGTCA
40813341 -AAATTTAA
1 GAAATTTAA
40813349 ATTTAACTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 13 0.38
30 16 0.47
31 5 0.15
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
GAAATTTAATTTTTATATTTTTAATGTCA
Found at i:40813993 original size:14 final size:14
Alignment explanation
Indices: 40813952--40814001 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
40813942 TACTGTTTTT
*
40813952 TACTATTTTCTTGT
1 TACTATTTTCTTGC
* *
40813966 TACTTTTTTTTTGC
1 TACTATTTTCTTGC
*
40813980 TACTATTTTGTTGC
1 TACTATTTTCTTGC
*
40813994 TATTATTT
1 TACTATTT
40814002 GGATATTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.14, C:0.12, G:0.08, T:0.66
Consensus pattern (14 bp):
TACTATTTTCTTGC
Found at i:40817730 original size:17 final size:17
Alignment explanation
Indices: 40817710--40817768 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
40817700 TTAATAGATA
40817710 ATTGAAGTGAATATGAT
1 ATTGAAGTGAATATGAT
*
40817727 ATTG-AGTTGATTAATAGAT
1 ATTGAAG-TGAAT-AT-GAT
*
40817746 AATTGAAGTGAATGTGAT
1 -ATTGAAGTGAATATGAT
40817764 ATTGA
1 ATTGA
40817769 GATTATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 4 0.12
20 8 0.24
21 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (17 bp):
ATTGAAGTGAATATGAT
Found at i:40817738 original size:37 final size:37
Alignment explanation
Indices: 40817697--40817769 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
40817687 AATTAATGAA
40817697 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
*
40817734 TGATTAATAGATAATTGAAGTGAATGTGATATTGAG
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAG
40817770 ATTATGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (37 bp):
TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
Found at i:40817750 original size:20 final size:19
Alignment explanation
Indices: 40817697--40817756 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
40817687 AATTAATGAA
40817697 TGATTAATAGATAATTGAAG
1 TGATTAATAGATAATTG-AG
*
40817717 TGAAT-AT-GAT-ATTGAG
1 TGATTAATAGATAATTGAG
40817733 TTGATTAATAGATAATTGAAG
1 -TGATTAATAGATAATTG-AG
40817754 TGA
1 TGA
40817757 ATGTGATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 2 0.06
17 8 0.24
18 5 0.15
19 5 0.15
20 11 0.33
21 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TGATTAATAGATAATTGAG
Found at i:40817908 original size:40 final size:39
Alignment explanation
Indices: 40817854--40817977 Score: 121
Period size: 40 Copynumber: 3.2 Consensus size: 39
40817844 AATCATTGTT
*
40817854 GGTTCATCCAACTAGAGCTGGGCTCACTATTTTTATCATC
1 GGTTTATCCAACTAGAGCTGGGCTCACTATTTTTATC-TC
* * * * * *
40817894 GGTTTATCCGACTAGCGCTGGGCGCA--AATATT-GCT-
1 GGTTTATCCAACTAGAGCTGGGCTCACTATTTTTATCTC
* *
40817929 AGTTTATCCAACTAGAGCTGGGCTCACTATTTATATCGTC
1 GGTTTATCCAACTAGAGCTGGGCTCACTATTTTTATC-TC
40817969 GGTTTATCC
1 GGTTTATCC
40817978 GACAAGTACT
Statistics
Matches: 63, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
35 22 0.35
36 1 0.02
37 4 0.06
38 5 0.08
39 1 0.02
40 30 0.48
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (39 bp):
GGTTTATCCAACTAGAGCTGGGCTCACTATTTTTATCTC
Found at i:40817940 original size:75 final size:75
Alignment explanation
Indices: 40817811--40818069 Score: 351
Period size: 75 Copynumber: 3.5 Consensus size: 75
40817801 TGAGTAATTG
* * *
40817811 ATATTGTCGGTTCATCCGACTAGCGCTGGGCGC-AATCATTGTTGGTTCATCCAACTAGAGCTGG
1 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAAT-ATTGTTGGTTTATCCAACTAGAGCTGG
40817875 GCTCACTATTT
65 GCTCACTATTT
* * * *
40817886 TTATCATCGGTTTATCCGACTAGCGCTGGGCGCAAATATTGCTAGTTTATCCAACTAGAGCTGGG
1 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATTGTTGGTTTATCCAACTAGAGCTGGG
40817951 CTCACTATTT
66 CTCACTATTT
* ** * * *
40817961 ATATCGTCGGTTTATCCGACAAGTACTGGGTGCAAATATCGTTGGTTTATCCAACCAGAGCTGGG
1 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATTGTTGGTTTATCCAACTAGAGCTGGG
*
40818026 CTCACTAATT
66 CTCACTATTT
* *
40818036 AT-TCGTCGGTATATCCGACTAGCGCTAGGCGCAA
1 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAA
40818070 CTTCCGTCAG
Statistics
Matches: 159, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
74 26 0.16
75 130 0.82
76 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (75 bp):
ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATTGTTGGTTTATCCAACTAGAGCTGGG
CTCACTATTT
Found at i:40818025 original size:35 final size:35
Alignment explanation
Indices: 40817894--40818025 Score: 97
Period size: 35 Copynumber: 3.6 Consensus size: 35
40817884 TTTTATCATC
* * * * *
40817894 GGTTTATCCGACTAGCGCTGGGCGCAAATATTGCT
1 GGTTTATCCAACTAGAGCTGGGTGCAAATATCGTT
* *
40817929 AGTTTATCCAACTAGAGCTGGGCT-CACTATTTATATCGTC
1 GGTTTATCCAACTAGAGCTGGG-TGCA--A---ATATCGTT
* *
40817969 GGTTTATCCGACAAGTA-CTGGGTGCAAATATCGTT
1 GGTTTATCCAACTAG-AGCTGGGTGCAAATATCGTT
*
40818004 GGTTTATCCAACCAGAGCTGGG
1 GGTTTATCCAACTAGAGCTGGG
40818026 CTCACTAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
34 1 0.01
35 46 0.61
37 1 0.01
38 1 0.01
39 1 0.01
40 24 0.32
41 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (35 bp):
GGTTTATCCAACTAGAGCTGGGTGCAAATATCGTT
Found at i:40822182 original size:19 final size:19
Alignment explanation
Indices: 40822158--40822195 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40822148 TTACTTATGA
*
40822158 ATTGGTTGTTAATACTTTG
1 ATTGGTTGGTAATACTTTG
*
40822177 ATTGGTTGGTAATATTTTG
1 ATTGGTTGGTAATACTTTG
40822196 TAACCCTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.03, G:0.24, T:0.53
Consensus pattern (19 bp):
ATTGGTTGGTAATACTTTG
Done.