Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 12 of 16
Found at i:1827554 original size:19 final size:18
Alignment explanation
Indices: 1827492--1827586 Score: 71
Period size: 19 Copynumber: 5.6 Consensus size: 18
1827482 TTTTAAAGAA
*
1827492 TTTATTTATTTTT-A-TT
1 TTTAATTATTTTTAATTT
1827508 TTTAA--ATTTTTAGATTT
1 TTTAATTATTTTTA-ATTT
1827525 TTT--TTATTTTTTAATTT
1 TTTAATTA-TTTTTAATTT
**
1827542 TTTAATTACTTTTTGTTTT
1 TTTAATTA-TTTTTAATTT
*
1827561 TTTGATTATTTTT-A-TT
1 TTTAATTATTTTTAATTT
1827577 TTTAATTATT
1 TTTAATTATT
1827587 CAATATCAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
14 6 0.09
16 16 0.25
17 13 0.20
18 11 0.17
19 18 0.28
ACGTcount: A:0.21, C:0.01, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTAATTATTTTTAATTT
Found at i:1827554 original size:25 final size:24
Alignment explanation
Indices: 1827492--1827561 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 24
1827482 TTTTAAAGAA
*
1827492 TTTATTTATTTTTATTTTTAAATT
1 TTTAATTATTTTTATTTTTAAATT
* *
1827516 TTTAGATTTTTTTTATTTTTTAATTT
1 TTTA-ATTATTTTTA-TTTTTAAATT
*
1827542 TTTAATTACTTTTTGTTTTT
1 TTTAATTA-TTTTTATTTTT
1827562 TTGATTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
24 4 0.11
25 16 0.42
26 18 0.47
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (24 bp):
TTTAATTATTTTTATTTTTAAATT
Found at i:1828720 original size:27 final size:26
Alignment explanation
Indices: 1828685--1828756 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
1828675 AATCATCCAT
*
1828685 TGTTTGTCAAAAATTGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTT-TTTTG
* * *
1828712 TGTTTGTCATAAATGGTAGTTTTTTT
1 TGTTTGTCAAAAATGGTGGTTTTTTG
* *
1828738 TATTTGTAAAAAATGGTGG
1 TGTTTGTCAAAAATGGTGG
1828757 CATGTTGTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
26 19 0.51
27 18 0.49
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (26 bp):
TGTTTGTCAAAAATGGTGGTTTTTTG
Found at i:1833287 original size:27 final size:25
Alignment explanation
Indices: 1833251--1833340 Score: 92
Period size: 27 Copynumber: 3.5 Consensus size: 25
1833241 AAACCACCCA
*
1833251 TTGTTTGTCAAAAATTGTGGTTACTT
1 TTGTTTGTCAAAAATGGTGGTTA-TT
* *
1833277 TGTGTTTGTCATAAATGGTGGTTTTTT
1 T-TGTTTGTCAAAAATGGTGG-TTATT
* * *
1833304 TTATTTGTCAAAAATGGTGG-CATG
1 TTGTTTGTCAAAAATGGTGGTTATT
1833328 TTGTTTGTCAAAA
1 TTGTTTGTCAAAA
1833341 TTTGTGGCTA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
24 13 0.25
26 18 0.34
27 20 0.38
28 2 0.04
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.48
Consensus pattern (25 bp):
TTGTTTGTCAAAAATGGTGGTTATT
Found at i:1833318 original size:26 final size:27
Alignment explanation
Indices: 1833254--1833323 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
1833244 CCACCCATTG
* *
1833254 TTTGTCAAAAATTGTGGTTACTTTGTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
1833281 TTTGTCATAAATGGTGGTT-TTTTTTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
1833307 TTTGTCAAAAATGGTGG
1 TTTGTCAAAAATGGTGG
1833324 CATGTTGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 20 0.54
27 17 0.46
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.49
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:1833420 original size:13 final size:13
Alignment explanation
Indices: 1833402--1833446 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1833392 GGCTCCCTCC
1833402 TCCCTCTCAAGTA
1 TCCCTCTCAAGTA
*
1833415 TCCCTCTCAAGCA
1 TCCCTCTCAAGTA
**
1833428 T-CCTCTCTTGTA
1 TCCCTCTCAAGTA
1833440 TCCCTCT
1 TCCCTCT
1833447 TCAATTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.16, C:0.42, G:0.07, T:0.36
Consensus pattern (13 bp):
TCCCTCTCAAGTA
Found at i:1834096 original size:82 final size:82
Alignment explanation
Indices: 1833992--1834158 Score: 203
Period size: 82 Copynumber: 2.0 Consensus size: 82
1833982 TGATGTTCAT
* * *
1833992 TTAGACTGTCAAACATATAAACTAATACAAAAAGGATTGTAATGAATTATGTTC-A-AGTAAGAT
1 TTAGACTGTCAAACATATAAACTAATACAAAAAGGATTATAACGAATTATG--CGATACTAAGAT
*
1834055 TTATTTATGAGGACATACA
64 TTATTTATGAAGACATACA
* * * * * *
1834074 TTAGACTGTCAGACATGTAAACTAATATAGACATGATTATAACGAATTATGCGATACTAAGATTT
1 TTAGACTGTCAAACATATAAACTAATACAAAAAGGATTATAACGAATTATGCGATACTAAGATTT
*
1834139 ATTTATGAAGATATACA
66 ATTTATGAAGACATACA
1834156 TTA
1 TTA
1834159 ATATTGTCCA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
80 1 0.01
81 1 0.01
82 70 0.97
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (82 bp):
TTAGACTGTCAAACATATAAACTAATACAAAAAGGATTATAACGAATTATGCGATACTAAGATTT
ATTTATGAAGACATACA
Found at i:1834189 original size:40 final size:40
Alignment explanation
Indices: 1834133--1834219 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
1834123 TGCGATACTA
* * *
1834133 AGATTTATTTATGAAGATATACATTAATATTGTCCA-ACAT
1 AGATTTATTTACGAAGAGATACATTAACATTGT-CAGACAT
* *
1834173 AGATTTATTTGCGAAGAGATATATTAACATTGTCAGACAT
1 AGATTTATTTACGAAGAGATACATTAACATTGTCAGACAT
1834213 A-ATTTAT
1 AGATTTAT
1834220 CCTACCAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 8 0.20
40 33 0.80
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (40 bp):
AGATTTATTTACGAAGAGATACATTAACATTGTCAGACAT
Found at i:1837255 original size:20 final size:18
Alignment explanation
Indices: 1837208--1837258 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 18
1837198 TACATCAATT
*
1837208 TAAACAAAAAAAATATAA
1 TAAACAAAATAAATATAA
1837226 TAACATCAAAATAAATATAAA
1 TAA-A-CAAAATAAATAT-AA
1837247 CTAAACAAAATA
1 -TAAACAAAATA
1837259 CATTTTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.11
19 1 0.04
20 18 0.64
21 3 0.11
22 3 0.11
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (18 bp):
TAAACAAAATAAATATAA
Found at i:1837314 original size:24 final size:24
Alignment explanation
Indices: 1837283--1837334 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1837273 TAAATAATTT
1837283 TAAATTCAAA-TCACAAA-ACCTAA
1 TAAATTCAAAGT-ACAAAGACCTAA
*
1837306 TAAATTTCAAAGTACAAAGACTTAA
1 TAAA-TTCAAAGTACAAAGACCTAA
1837331 TAAA
1 TAAA
1837335 AAAACGTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 4 0.16
24 11 0.44
25 10 0.40
ACGTcount: A:0.56, C:0.15, G:0.04, T:0.25
Consensus pattern (24 bp):
TAAATTCAAAGTACAAAGACCTAA
Found at i:1837508 original size:18 final size:18
Alignment explanation
Indices: 1837483--1837519 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1837473 AGAGATGCAA
*
1837483 GAAAAAAAAAAGAATGGAG
1 GAAAAAAAATAGAA-GGAG
1837502 GAAAAAAAATAGAAGGAG
1 GAAAAAAAATAGAAGGAG
1837520 AAATATATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (18 bp):
GAAAAAAAATAGAAGGAG
Found at i:1838189 original size:34 final size:32
Alignment explanation
Indices: 1838116--1838190 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 32
1838106 ATTGTTTTAC
* * *
1838116 TTTAAATTATTATTTAATATTTATATTTAAAT
1 TTTAAAATATTATTTAATATTTATAATTAAAA
* *
1838148 TTATAAAATATTTTTTATTAATTTATAATTAATAA
1 TT-TAAAATATTATTTAAT-ATTTATAATTAA-AA
1838183 TTTAAAAT
1 TTTAAAAT
1838191 TTCAGATCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 2 0.06
33 13 0.37
34 17 0.49
35 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TTTAAAATATTATTTAATATTTATAATTAAAA
Found at i:1838467 original size:33 final size:33
Alignment explanation
Indices: 1838430--1838493 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1838420 TAGAAAAATT
* *
1838430 GAATTT-TTCATTTTTTGTTTTTAGATTTTTAAA
1 GAATTTATTCA-TTTTTATTTTTAAATTTTTAAA
*
1838463 GAATTTATTTATTTTTATTTTTAAATTTTTA
1 GAATTTATTCATTTTTATTTTTAAATTTTTA
1838494 GATTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.66
Consensus pattern (33 bp):
GAATTTATTCATTTTTATTTTTAAATTTTTAAA
Found at i:1838500 original size:9 final size:9
Alignment explanation
Indices: 1838488--1838566 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
1838478 TATTTTTAAA
*
1838488 TTTTTAGAT
1 TTTTTATAT
*
1838497 TTTTTTTAT
1 TTTTTATAT
*
1838506 TTTTTTTAT
1 TTTTTATAT
1838515 TTTTT-TAT
1 TTTTTATAT
*
1838523 TTTTTAAAAT
1 TTTTT-ATAT
* *
1838533 TTTTAATTAC
1 TTTTTA-TAT
*
1838543 TTTTTATTT
1 TTTTTATAT
1838552 TTTTTGATTAT
1 TTTTT-A-TAT
1838563 TTTT
1 TTTT
1838567 ATTTTTATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
8 8 0.15
9 28 0.51
10 13 0.24
11 6 0.11
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.77
Consensus pattern (9 bp):
TTTTTATAT
Found at i:1838508 original size:7 final size:8
Alignment explanation
Indices: 1838474--1838572 Score: 63
Period size: 8 Copynumber: 11.4 Consensus size: 8
1838464 AATTTATTTA
1838474 TTTTTATT
1 TTTTTATT
**
1838482 TTTAAATT
1 TTTTTATT
**
1838490 TTTAGATTT
1 TTTTTA-TT
1838499 TTTTTATTT
1 TTTTTA-TT
1838508 TTTTTATT
1 TTTTTATT
1838516 TTTTTATT
1 TTTTTATT
* *
1838524 TTTTAAAAT
1 TTTT-TATT
*
1838533 TTTTAATT
1 TTTTTATT
1838541 ACTTTTTATTT
1 --TTTTTA-TT
1838552 TTTTTGATT
1 TTTTT-ATT
1838561 ATTTTTATT
1 -TTTTTATT
1838570 TTT
1 TTT
1838573 ATTTATTCAA
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
8 31 0.41
9 31 0.41
10 11 0.15
11 2 0.03
ACGTcount: A:0.20, C:0.01, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTTATT
Found at i:1838519 original size:35 final size:34
Alignment explanation
Indices: 1838466--1838554 Score: 90
Period size: 35 Copynumber: 2.6 Consensus size: 34
1838456 TTTTAAAGAA
**
1838466 TTTATTTATTTTTA-TTTTTAAATTTTTAGATTTTT
1 TTTATTT-TTTTTATTTTTTAAATTTTTA-AAATTT
* *
1838501 TTTATTTTTTTTATTTTTTTATTTTTTAAAATTT
1 TTTATTTTTTTTATTTTTTAAATTTTTAAAATTT
* *
1838535 TTAATTACTTTTTATTTTTT
1 TTTATT-TTTTTTATTTTTT
1838555 TTGATTATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 15 0.33
35 31 0.67
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (34 bp):
TTTATTTTTTTTATTTTTTAAATTTTTAAAATTT
Found at i:1838533 original size:44 final size:45
Alignment explanation
Indices: 1838471--1838572 Score: 149
Period size: 44 Copynumber: 2.3 Consensus size: 45
1838461 AAGAATTTAT
*
1838471 TTATTTTTA-TTTTTAAATTTTTAGATT-TTTTTTATTTTTTTT-A
1 TTATTTTTATTTTTTAAATTTTTA-ATTACTTTTTATTTTTTTTGA
1838514 TT-TTTTTATTTTTTAAAATTTTTAATTACTTTTTATTTTTTTTGA
1 TTATTTTTATTTTTT-AAATTTTTAATTACTTTTTATTTTTTTTGA
1838559 TTATTTTTATTTTT
1 TTATTTTTATTTTT
1838573 ATTTATTCAA
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
42 6 0.11
43 10 0.19
44 23 0.43
45 3 0.06
46 11 0.21
ACGTcount: A:0.21, C:0.01, G:0.02, T:0.76
Consensus pattern (45 bp):
TTATTTTTATTTTTTAAATTTTTAATTACTTTTTATTTTTTTTGA
Found at i:1839762 original size:18 final size:17
Alignment explanation
Indices: 1839741--1839807 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 17
1839731 AATAATTAAA
1839741 ATATAAAATGATAAAAAT
1 ATATAAAAT-ATAAAAAT
* *
1839759 ATATGAATATATTAAAAT
1 ATAT-AAAATATAAAAAT
* *
1839777 TTATATAATAT-AAAAT
1 ATATAAAATATAAAAAT
*
1839793 AT-TAATATATAAAAA
1 ATATAAAATATAAAAA
1839808 GTTATATGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 6 0.15
16 10 0.26
17 5 0.13
18 14 0.36
19 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
ATATAAAATATAAAAAT
Found at i:1839807 original size:16 final size:17
Alignment explanation
Indices: 1839732--1839807 Score: 54
Period size: 16 Copynumber: 4.6 Consensus size: 17
1839722 TATGAAAAAA
* *
1839732 ATAATTAAAATA-TAAA
1 ATAATAAAAATATTAAT
*
1839748 ATGATAAAAATATATGAAT
1 ATAATAAAAATAT-T-AAT
*
1839767 AT-ATTAAAAT-TT-AT
1 ATAATAAAAATATTAAT
1839781 ATAATATAAAATATTAAT
1 ATAATA-AAAATATTAAT
1839799 AT-ATAAAAA
1 ATAATAAAAA
1839808 GTTATATGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
14 4 0.08
15 2 0.04
16 20 0.42
17 6 0.12
18 12 0.25
19 4 0.08
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
ATAATAAAAATATTAAT
Found at i:1839813 original size:32 final size:35
Alignment explanation
Indices: 1839754--1839821 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 35
1839744 TAAAATGATA
* *
1839754 AAAATATATGAATATATTAAAATTTATAT-AATAT
1 AAAATATATGAATATATAAAAAGTTATATGAATAT
1839788 AAAATAT-T-AATATATAAAAAGTTATATGAATAT
1 AAAATATATGAATATATAAAAAGTTATATGAATAT
1839821 A
1 A
1839822 TCTCAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 17 0.55
33 7 0.23
34 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (35 bp):
AAAATATATGAATATATAAAAAGTTATATGAATAT
Found at i:1841048 original size:2 final size:2
Alignment explanation
Indices: 1841041--1841071 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1841031 ATTAATATTT
1841041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1841072 TCTTATTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1841893 original size:21 final size:22
Alignment explanation
Indices: 1841861--1841904 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
1841851 TAAAATAAAA
1841861 ATATATTTTTATAA-TAATATTT
1 ATATATTTTTATAATTAA-ATTT
1841883 ATATA-TTTTATAATTAAATTT
1 ATATATTTTTATAATTAAATTT
1841904 A
1 A
1841905 AATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATATTTTTATAATTAAATTT
Found at i:1841943 original size:20 final size:19
Alignment explanation
Indices: 1841892--1841945 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1841882 TATATATTTT
1841892 ATAATTAAATTTAAATAAAA
1 ATAATTAAA-TTAAATAAAA
* ** *
1841912 ATATTTTTATTAATTAAATA
1 ATAATTAAATTAAATAAA-A
1841932 ATAATTAAATTAAA
1 ATAATTAAATTAAA
1841946 CCAAATTAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATTAAATTAAATAAAA
Found at i:1842181 original size:5 final size:5
Alignment explanation
Indices: 1842171--1842201 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1842161 GAAAGCTAAC
*
1842171 AATAT AATAT AATAT AACAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT A
1842202 TTTTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:1843687 original size:17 final size:17
Alignment explanation
Indices: 1843635--1843688 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1843625 AAAATATTTT
1843635 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
**
1843651 T-AAA-TTAT-TACGTA
1 TAAAATTTATATAAATA
1843665 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
1843683 TAAAAT
1 TAAAAT
1843689 AATTTTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
13 1 0.03
14 7 0.24
15 3 0.10
16 4 0.14
17 9 0.31
18 5 0.17
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1849284 original size:137 final size:136
Alignment explanation
Indices: 1849044--1849303 Score: 371
Period size: 137 Copynumber: 1.9 Consensus size: 136
1849034 TTTATGCAAC
* *
1849044 GTTGTAATCATTGTTTGGTTTTATAATCTTTGGGTGTTTCATTAGTTGGAATATATATTGTTTTA
1 GTTGTAATCATTG-TT-GTTTTAAAATCTTTGGGTGTTTCATTAGTTGGAATATATACTGTTTTA
** ***
1849109 TTCATTTTGTTTTATAAATTCTTTTACGGTATTGTTTTTATATTATTTTCTATTACTGCAACCAT
64 TTCATTTTGTTTTATAAATTCTTTTACAATACCATTTTTATATTATTTTC-A-TACTGCAACCAT
1849174 CTTTGTATAT
127 CTTTGTATAT
*
1849184 GTTGTAATCATTG-T-TTTTAAAATCTTTGGGTGTTTTTATTAGTTGGAATATATACTGTTTTAT
1 GTTGTAATCATTGTTGTTTTAAAATCTTTGGGTG-TTTCATTAGTTGGAATATATACTGTTTTAT
* *
1849247 TCATTTTGTTTTATAAATTCTTTTACAATACCATTTTTGTATTGTTTTCATACTGCA
65 TCATTTTGTTTTATAAATTCTTTTACAATACCATTTTTATATTATTTTCATACTGCA
1849304 GTCATTGATT
Statistics
Matches: 109, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
135 7 0.06
136 18 0.17
137 70 0.64
138 1 0.01
140 13 0.12
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (136 bp):
GTTGTAATCATTGTTGTTTTAAAATCTTTGGGTGTTTCATTAGTTGGAATATATACTGTTTTATT
CATTTTGTTTTATAAATTCTTTTACAATACCATTTTTATATTATTTTCATACTGCAACCATCTTT
GTATAT
Found at i:1850377 original size:30 final size:30
Alignment explanation
Indices: 1850343--1850408 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1850333 TTGAGTAGTA
* *
1850343 AAATTCAATCAAAAATTAAATAT-TATTGAT
1 AAATTCAAT-AAAAAATAAATATGTAGTGAT
*
1850373 AAATTTCAATAAAAAATAACTATGTAGTGAT
1 AAA-TTCAATAAAAAATAAATATGTAGTGAT
1850404 AAATT
1 AAATT
1850409 TACCTAAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (30 bp):
AAATTCAATAAAAAATAAATATGTAGTGAT
Found at i:1850381 original size:31 final size:31
Alignment explanation
Indices: 1850341--1850409 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
1850331 AATTGAGTAG
* * *
1850341 TAAAATTCAATCAAAAATTAAATAT-TATTGA
1 TAAATTTCAAT-AAAAAATAAATATGTAGTGA
*
1850372 TAAATTTCAATAAAAAATAACTATGTAGTGA
1 TAAATTTCAATAAAAAATAAATATGTAGTGA
1850403 TAAATTT
1 TAAATTT
1850410 ACCTAAACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (31 bp):
TAAATTTCAATAAAAAATAAATATGTAGTGA
Found at i:1851021 original size:20 final size:20
Alignment explanation
Indices: 1850984--1851021 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1850974 TATTTTATCG
*
1850984 TATTTTAATTAATTTAAAAA
1 TATTTTAATTAATATAAAAA
1851004 TATTTTATATT-ATATAAA
1 TATTTTA-ATTAATATAAA
1851022 TTTTGATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTTAATTAATATAAAAA
Found at i:1851219 original size:18 final size:18
Alignment explanation
Indices: 1851196--1851244 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1851186 TTTAAATTCA
1851196 AATTTATTAATTTGATCT
1 AATTTATTAATTTGATCT
** *
1851214 AATTTATTCTTTTGATGT
1 AATTTATTAATTTGATCT
*
1851232 AATTAATTAATTT
1 AATTTATTAATTT
1851245 TTATTCGTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (18 bp):
AATTTATTAATTTGATCT
Found at i:1856649 original size:19 final size:19
Alignment explanation
Indices: 1856625--1856663 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1856615 TAATAATTTA
1856625 TTATATATT-TTTAAATATT
1 TTATAT-TTATTTAAATATT
*
1856644 TTATATTTATTTATATATT
1 TTATATTTATTTAAATATT
1856663 T
1 T
1856664 AATTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATATTTATTTAAATATT
Found at i:1856684 original size:23 final size:24
Alignment explanation
Indices: 1856635--1856701 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
1856625 TTATATATTT
** *
1856635 TTAAATATTTTATATTTATTTATATA
1 TTAAATA-TTTATAAAT-TTTAGATA
* *
1856661 TTTAATTTTTA-AAATTTTAGATA
1 TTAAATATTTATAAATTTTAGATA
1856684 TTAAATATTTATAAATTT
1 TTAAATATTTATAAATTT
1856702 AAAATTTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
23 16 0.48
24 8 0.24
25 4 0.12
26 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (24 bp):
TTAAATATTTATAAATTTTAGATA
Found at i:1856687 original size:15 final size:15
Alignment explanation
Indices: 1856668--1856714 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
1856658 ATATTTAATT
*
1856668 TTTAAAATTT-TAGA
1 TTTAAAATTTATAAA
1856682 TATTAAATATTTATAAA
1 T-TTAAA-ATTTATAAA
1856699 TTTAAAATTTAATAAA
1 TTTAAAATTT-ATAAA
1856715 GGTATATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 9 0.32
16 14 0.50
17 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TTTAAAATTTATAAA
Found at i:1857476 original size:17 final size:16
Alignment explanation
Indices: 1857433--1857476 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1857423 AAAAAAATTC
1857433 TTTAAAAAAATATAAT
1 TTTAAAAAAATATAAT
* *
1857449 TTTCTAAAAAATATCAT
1 TTT-AAAAAAATATAAT
1857466 TTTAAAGAAAA
1 TTTAAA-AAAA
1857477 AACTATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (16 bp):
TTTAAAAAAATATAAT
Found at i:1872438 original size:15 final size:17
Alignment explanation
Indices: 1872407--1872439 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1872397 TTGATAAACA
1872407 TTTTATAAAATATATTT
1 TTTTATAAAATATATTT
1872424 TTTTA-AAAATA-ATTT
1 TTTTATAAAATATATTT
1872439 T
1 T
1872440 ATAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATAAAATATATTT
Found at i:1872448 original size:15 final size:14
Alignment explanation
Indices: 1872406--1872451 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
1872396 TTTGATAAAC
1872406 ATTTTATAAAATATA
1 ATTTTATAAAA-ATA
* *
1872421 TTTTTTTAAAAATA
1 ATTTTATAAAAATA
1872435 ATTTTATAATAAATA
1 ATTTTATAA-AAATA
1872450 AT
1 AT
1872452 ATTAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTTATAAAAATA
Found at i:1873355 original size:2 final size:2
Alignment explanation
Indices: 1873348--1873376 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1873338 TAACAAAATG
1873348 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1873377 ACTAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1879968 original size:14 final size:14
Alignment explanation
Indices: 1879923--1879975 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
1879913 ATATATTTTA
1879923 TAATTTTAAATAAAAT
1 TAATTTT-AA-AAAAT
*
1879939 TAATTATT-AAATAT
1 TAATT-TTAAAAAAT
1879953 TAATTTTAAAAAAT
1 TAATTTTAAAAAAT
1879967 T-ATTTTAAA
1 TAATTTTAAA
1879976 TTAGTAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 10 0.30
14 15 0.45
15 1 0.03
16 5 0.15
17 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTTTAAAAAAT
Found at i:1879971 original size:59 final size:60
Alignment explanation
Indices: 1879878--1879998 Score: 133
Period size: 59 Copynumber: 2.0 Consensus size: 60
1879868 ATTTATTATT
* * * *
1879878 ATTATTTATTAAAAATTATTTTAATATTAATATTTATATATT-TTATAATTT-TAAATAAA
1 ATTAATTATTAAAAATTATTTTAATATAAATATTT-TAAATTATAATAATTTATAAATAAA
*
1879937 ATTAATTATTAAATATTAATTTTAA-A-AAATTATTTTAAATTAGTAATAATTTATAAATAAA
1 ATTAATTATTAAAAATT-ATTTTAATATAAA-TATTTTAAATTA-TAATAATTTATAAATAAA
1879998 A
1 A
1879999 AGCAATCAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
58 7 0.13
59 21 0.40
60 15 0.29
61 9 0.17
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (60 bp):
ATTAATTATTAAAAATTATTTTAATATAAATATTTTAAATTATAATAATTTATAAATAAA
Found at i:1879978 original size:24 final size:30
Alignment explanation
Indices: 1879923--1879976 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1879913 ATATATTTTA
1879923 TAATTTTAAATAAAATTAATTATTAAATAT
1 TAATTTTAAATAAAATTAATTATTAAATAT
1879953 TAATTTT-AA-AAAATT-ATT-TTAAAT
1 TAATTTTAAATAAAATTAATTATTAAAT
1879977 TAGTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 6 0.25
27 3 0.12
28 6 0.25
29 2 0.08
30 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TAATTTTAAATAAAATTAATTATTAAATAT
Found at i:1881132 original size:30 final size:29
Alignment explanation
Indices: 1881098--1881165 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
1881088 CTGTTACTAC
*
1881098 ATTTAAAAAAATATTTAATTTTTAAATTAT
1 ATTTAAAAAAAT-TTTAATATTTAAATTAT
* *
1881128 ATTTAAATAAAATTTTGATATTTAATTTAT
1 ATTTAAA-AAAATTTTAATATTTAAATTAT
1881158 ATTTAAAA
1 ATTTAAAA
1881166 TAAAAACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 28 0.82
31 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
ATTTAAAAAAATTTTAATATTTAAATTAT
Found at i:1881178 original size:13 final size:13
Alignment explanation
Indices: 1881160--1881184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1881150 TAATTTATAT
1881160 TTAAAATAAAAAC
1 TTAAAATAAAAAC
1881173 TTAAAATAAAAA
1 TTAAAATAAAAA
1881185 TTTACTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TTAAAATAAAAAC
Found at i:1881332 original size:19 final size:18
Alignment explanation
Indices: 1881290--1881332 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1881280 GGATATATTT
*
1881290 AAAATAAAAAAAAATCTA
1 AAAATAAAAAAAAATATA
*
1881308 AAAATAAATAAAATATATA
1 AAAATAAA-AAAAAATATA
*
1881327 ATAATA
1 AAAATA
1881333 TTTCAATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATAAAAAAAAATATA
Found at i:1881732 original size:3 final size:3
Alignment explanation
Indices: 1881724--1881757 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1881714 AAATTTGACC
1881724 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1881758 GCCTAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1882393 original size:2 final size:2
Alignment explanation
Indices: 1882388--1882427 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1882378 TCCTAAATCT
1882388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1882428 AGATTCTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1897316 original size:2 final size:2
Alignment explanation
Indices: 1897309--1897339 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1897299 AGCAATTGTT
1897309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1897340 TCCTTCAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1899275 original size:13 final size:13
Alignment explanation
Indices: 1899257--1899308 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
1899247 ATTTAATCGT
*
1899257 ATTATATATCATA
1 ATTATATATAATA
1899270 ATTATATATAATA
1 ATTATATATAATA
* *
1899283 AATAT-TATTATA
1 ATTATATATAATA
1899295 ATTA-ATTATAATA
1 ATTATA-TATAATA
1899308 A
1 A
1899309 ATATTTACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 9 0.28
13 23 0.72
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTATATATAATA
Found at i:1899313 original size:22 final size:24
Alignment explanation
Indices: 1899260--1899312 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
1899250 TAATCGTATT
*
1899260 ATATATCATAATTATATATAATAA
1 ATATATTATAATTATATATAATAA
1899284 ATATTATTATAATTA-ATTATAATAA
1 ATA-TATTATAATTATA-TATAATAA
1899309 ATAT
1 ATAT
1899313 TTACCATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATATTATAATTATATATAATAA
Found at i:1899327 original size:25 final size:24
Alignment explanation
Indices: 1899266--1899327 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
1899256 TATTATATAT
*
1899266 CATAATTATATATAATAAATATTAT
1 CATAATTAT-TATAATAAATATTAC
*
1899291 TATAATTAATTATAATAAATATTTAC
1 CATAATT-ATTATAATAAATA-TTAC
*
1899317 CATAAATATTA
1 CATAATTATTA
1899328 GCGATGGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (24 bp):
CATAATTATTATAATAAATATTAC
Found at i:1903937 original size:3 final size:3
Alignment explanation
Indices: 1903929--1903954 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1903919 TACTTATCCA
1903929 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1903955 CTTGTCAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1904266 original size:2 final size:2
Alignment explanation
Indices: 1904259--1904290 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1904249 ACAAATTAAA
1904259 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1904291 CTATTTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1904485 original size:15 final size:15
Alignment explanation
Indices: 1904467--1904525 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
1904457 ATTTTTATGT
1904467 TATAATAATTAAAAA
1 TATAATAATTAAAAA
*
1904482 TATAAAAATTTAAATAA
1 TATAATAA-TTAAA-AA
*
1904499 TAATAATAATAAATAAA
1 T-ATAATAATTAA-AAA
1904516 TA-AAT-ATTAA
1 TATAATAATTAA
1904526 CATTTAACAG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 4 0.11
15 10 0.28
16 6 0.17
17 9 0.25
18 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TATAATAATTAAAAA
Found at i:1906669 original size:2 final size:2
Alignment explanation
Indices: 1906662--1906696 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1906652 GGGTAGTAAA
* *
1906662 AT AT AT AT AT AT AT AT AT AT AT AG AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1906697 ATAGAGACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1911397 original size:21 final size:22
Alignment explanation
Indices: 1911356--1911400 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1911346 CTAACCTTGC
1911356 ATCCCAAATTATTTGATATTAT
1 ATCCCAAATTATTTGATATTAT
1911378 ATCCCAAATTATTT-ATATTAT
1 ATCCCAAATTATTTGATATTAT
1911399 AT
1 AT
1911401 AATCTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (22 bp):
ATCCCAAATTATTTGATATTAT
Found at i:1914096 original size:16 final size:17
Alignment explanation
Indices: 1914075--1914118 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1914065 ATATATATCA
1914075 AAAATATAAAAAAAT-T
1 AAAATATAAAAAAATAT
* *
1914091 AAAATATAATATAATAT
1 AAAATATAAAAAAATAT
1914108 AAAA-ATAAAAA
1 AAAATATAAAAA
1914119 TTTATAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATATAAAAAAATAT
Found at i:1914186 original size:21 final size:20
Alignment explanation
Indices: 1914152--1914216 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 20
1914142 AATGTGTATG
1914152 ATATAATTATTAATATATTAAA
1 ATATAATTA-TAATAT-TTAAA
* *
1914174 AT-TTATATATAATATTTTAA
1 ATATAAT-TATAATATTTAAA
1914194 ATATAATTATAATATTTAAA
1 ATATAATTATAATATTTAAA
1914214 ATA
1 ATA
1914217 ATATAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 21 0.57
21 12 0.32
22 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATAATTATAATATTTAAA
Found at i:1914204 original size:20 final size:20
Alignment explanation
Indices: 1914152--1914216 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
1914142 AATGTGTATG
*
1914152 ATATAATTATTAATATATTAA
1 ATATAATTA-TAATATTTTAA
*
1914173 A-ATTTATATATAATATTTTAA
1 ATA-TAAT-TATAATATTTTAA
*
1914194 ATATAATTATAATATTTAAA
1 ATATAATTATAATATTTTAA
1914214 ATA
1 ATA
1914217 ATATAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 16 0.43
21 18 0.49
22 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATAATTATAATATTTTAA
Found at i:1914228 original size:40 final size:42
Alignment explanation
Indices: 1914152--1914237 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 42
1914142 AATGTGTATG
* * **
1914152 ATATAATTATTAATATATTAAAATTTATATATAATATTTTAA
1 ATATAATTATTAATATATTAAAATATATATAAAATATCATAA
1914194 ATATAATTA-TAATAT-TTAAAATA-ATATAAAAATATCATAA
1 ATATAATTATTAATATATTAAAATATATAT-AAAATATCATAA
1914234 ATAT
1 ATAT
1914238 TTGTGAAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 4 0.10
40 20 0.51
41 6 0.15
42 9 0.23
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (42 bp):
ATATAATTATTAATATATTAAAATATATATAAAATATCATAA
Found at i:1919775 original size:6 final size:6
Alignment explanation
Indices: 1919726--1919785 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
1919716 AAATTTATCA
** * * **
1919726 ATTAA- ATTAAT ACAAAT TTTAAT ATAAAT ATTAAT GCTAA- ATTAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
1919772 ATTAAT ATTAAT AT
1 ATTAAT ATTAAT AT
1919786 AAATGACTTA
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
5 8 0.20
6 33 0.80
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (6 bp):
ATTAAT
Found at i:1923629 original size:16 final size:16
Alignment explanation
Indices: 1923609--1923660 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1923599 ACCACCGTAA
1923609 ATTTAGATTATTTT-G
1 ATTTAGATTATTTTAG
*
1923624 AGTTTAAATTATTTTAG
1 A-TTTAGATTATTTTAG
* *
1923641 ATTTAGTTTATTTTAA
1 ATTTAGATTATTTTAG
1923657 ATTT
1 ATTT
1923661 GAATAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 1 0.03
16 28 0.90
17 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (16 bp):
ATTTAGATTATTTTAG
Found at i:1925712 original size:6 final size:6
Alignment explanation
Indices: 1925675--1925705 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1925665 AATTTCGTTG
*
1925675 TATTTT TCTTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT T
1925706 TTGTTTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:1929788 original size:64 final size:64
Alignment explanation
Indices: 1929687--1929817 Score: 262
Period size: 64 Copynumber: 2.0 Consensus size: 64
1929677 GCCAAGCAAG
1929687 ATAAAGAGCGCAAACAAAGAACATAGTTGTTTTGCTAAACGCTATCTGAAACTGTACTTTGAAT
1 ATAAAGAGCGCAAACAAAGAACATAGTTGTTTTGCTAAACGCTATCTGAAACTGTACTTTGAAT
1929751 ATAAAGAGCGCAAACAAAGAACATAGTTGTTTTGCTAAACGCTATCTGAAACTGTACTTTGAAT
1 ATAAAGAGCGCAAACAAAGAACATAGTTGTTTTGCTAAACGCTATCTGAAACTGTACTTTGAAT
1929815 ATA
1 ATA
1929818 GATACTGTGT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (64 bp):
ATAAAGAGCGCAAACAAAGAACATAGTTGTTTTGCTAAACGCTATCTGAAACTGTACTTTGAAT
Found at i:1929902 original size:2 final size:2
Alignment explanation
Indices: 1929890--1929928 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1929880 TGTGGTGTTG
*
1929890 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1929929 ACAATATCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:1938187 original size:2 final size:2
Alignment explanation
Indices: 1938180--1938230 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1938170 TCGATGTATG
1938180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1938222 TA TA TA TA T
1 TA TA TA TA T
1938231 CCACTATTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1939956 original size:2 final size:2
Alignment explanation
Indices: 1939949--1939979 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1939939 TGCACCCTAC
1939949 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1939980 TAAACCCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1946677 original size:18 final size:18
Alignment explanation
Indices: 1946654--1946688 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1946644 TAATGTCAAA
* *
1946654 TTTAATTATATATAAAAT
1 TTTAATAATAGATAAAAT
1946672 TTTAATAATAGATAAAA
1 TTTAATAATAGATAAAA
1946689 AATGTAGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
TTTAATAATAGATAAAAT
Found at i:1949586 original size:21 final size:20
Alignment explanation
Indices: 1949560--1949602 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1949550 TTACTTTTTT
* *
1949560 AAAATATTTTATTTATATTTA
1 AAAATATATAATTTA-ATTTA
1949581 AAAATATATAATTTAATTTA
1 AAAATATATAATTTAATTTA
1949601 AA
1 AA
1949603 TTAATCTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATATATAATTTAATTTA
Found at i:1954957 original size:15 final size:15
Alignment explanation
Indices: 1954933--1954962 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1954923 ATAAAAAAAG
*
1954933 TTTTATTTATTTATT
1 TTTTAATTATTTATT
1954948 TTTTAATTATTTATT
1 TTTTAATTATTTATT
1954963 AAGATTATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTAATTATTTATT
Found at i:1955909 original size:16 final size:18
Alignment explanation
Indices: 1955878--1955912 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1955868 GTAATTATTG
1955878 TTTTTTTTACTATTTTAA
1 TTTTTTTTACTATTTTAA
1955896 TTTTTTTTA-T-TTTTAA
1 TTTTTTTTACTATTTTAA
1955912 T
1 T
1955913 AAGTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTTTACTATTTTAA
Found at i:1958116 original size:245 final size:244
Alignment explanation
Indices: 1957560--1958282 Score: 812
Period size: 245 Copynumber: 3.0 Consensus size: 244
1957550 AAATATTTTT
* * ** * * ***
1957560 TTGTAGGTTTTGAGAAGCTGA-CGTCAAAACTAGACAAGCTAAAAATCCTTGACTTAAGTGAAAA
1 TTGTAGGTTTTGAGAAGCT-ATCATCAAAAGTAGACAAATTAGAATTCCTTGACTTAAGTTCTAA
* * ** * *
1957624 TCATTTTAATGATAGCATTTTAGTATATTTAAGTGAACTTTCATCACTTAAATCTTTAAATCTTG
65 TAATTTTGATGATAGCATTTTAGTATCGTTAAGTGAACTTTCATCACTCAAATCTTTAAATCTAG
*** * * ** * * ***
1957689 CTTACAACCAATTCACCGGATCAAATCTTAGCGATGGTAAAGTTAATATATGAA-TCTGCTACAC
130 CAGGCAACCAATTCACAGGATCAAATTTTAGTAATGGTAAAGTTAATTTATGAACT-TGATTTTC
* * * *
1957753 ATTGAAA-TAAATAAATTTTGCAACTCATATGA-ATTATGTATAACTTTTTTC
194 GTT-AAAGTTAATAAATTTTGCAACTAATAT-ATATTATGTATAACTTTTTCC
* * * * *
1957804 TTGTAGGTTTTGAGAAGTTGTTATCAAAAGTGGACAAATTAGAATTCCTTGACTTAAGTTTTAAT
1 TTGTAGGTTTTGAGAAGCTATCATCAAAAGTAGACAAATTAGAATTCCTTGACTTAAGTTCTAAT
* * *
1957869 AATTTTGATGATAACATTTTAGTATCGTTAAGTGAACTTTCATCACTCAAGTCCTTAAATCTAGC
66 AATTTTGATGATAGCATTTTAGTATCGTTAAGTGAACTTTCATCACTCAAATCTTTAAATCTAGC
* * *
1957934 AGGCAACCAATTCACAGGATCAAATTTTCGTAACGGTAAAGTTACATTTATGAACTTGATTTTGG
131 AGGCAACCAATTCACAGGATCAAATTTTAGTAATGGTAAAGTTA-ATTTATGAACTTGATTTTCG
* *
1957999 TTAAAGTTAATAAATTTTGCAACTTATATATATTTTGTATAACTTTTTCC
195 TTAAAGTTAATAAATTTTGCAACTAATATATATTATGTATAACTTTTTCC
* * * *
1958049 TTGTAGGTTTTGAGAAGCTATCATCGAAATTAGACAAATTAGAATTCTTTGATTTAAGTTCTAAT
1 TTGTAGGTTTTGAGAAGCTATCATCAAAAGTAGACAAATTAGAATTCCTTGACTTAAGTTCTAAT
* * *
1958114 AATTTCGATGATAGCATTTTAGCATCGTTAAGTGAACTTTCATCACTCAAATTTTTAAATCTAAG
66 AATTTTGATGATAGCATTTTAGTATCGTTAAGTGAACTTTCATCACTCAAATCTTTAAATCT-AG
* * * * *
1958179 -AGGCAATCAATTCACAGGATCAAATTCTAGTAATGGTAAAGTTAATCTT-TGAACCTAATTTTT
130 CAGGCAACCAATTCACAGGATCAAATTTTAGTAATGGTAAAGTTAAT-TTATGAACTTGATTTTC
* *
1958242 GTTAAAGTTAATAAATTTGGCAACTAATATAT-TTATTTATA
194 GTTAAAGTTAATAAATTTTGCAACTAATATATATTATGTATA
1958283 CTGATAATAA
Statistics
Matches: 404, Mismatches: 68, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
243 7 0.02
244 189 0.47
245 205 0.51
246 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (244 bp):
TTGTAGGTTTTGAGAAGCTATCATCAAAAGTAGACAAATTAGAATTCCTTGACTTAAGTTCTAAT
AATTTTGATGATAGCATTTTAGTATCGTTAAGTGAACTTTCATCACTCAAATCTTTAAATCTAGC
AGGCAACCAATTCACAGGATCAAATTTTAGTAATGGTAAAGTTAATTTATGAACTTGATTTTCGT
TAAAGTTAATAAATTTTGCAACTAATATATATTATGTATAACTTTTTCC
Found at i:1960528 original size:6 final size:7
Alignment explanation
Indices: 1960501--1960525 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1960491 CGCATGCATT
1960501 AAATTAA
1 AAATTAA
1960508 AAATTAA
1 AAATTAA
1960515 AAATTAA
1 AAATTAA
1960522 AAAT
1 AAAT
1960526 AAAGTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTAA
Found at i:1961733 original size:13 final size:15
Alignment explanation
Indices: 1961715--1961747 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1961705 AATAAGGAAA
1961715 TAAAATTAAA-A-AT
1 TAAAATTAAACATAT
1961728 TAAAATTAAACATAT
1 TAAAATTAAACATAT
1961743 TAAAA
1 TAAAA
1961748 GTGATTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 1 0.06
15 7 0.39
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAATTAAACATAT
Found at i:1963785 original size:7 final size:7
Alignment explanation
Indices: 1963773--1963797 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1963763 TAATGTTTTT
1963773 AATGTAA
1 AATGTAA
1963780 AATGTAA
1 AATGTAA
1963787 AATGTAA
1 AATGTAA
1963794 AATG
1 AATG
1963798 CTCTAACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (7 bp):
AATGTAA
Found at i:1965437 original size:69 final size:69
Alignment explanation
Indices: 1965326--1965471 Score: 256
Period size: 69 Copynumber: 2.1 Consensus size: 69
1965316 CTCCAACCTC
**
1965326 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTTGAGAG
1 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTCAAGAG
1965391 TCTA
66 TCTA
**
1965395 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATATCTGCCCTCAAGAG
1 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTCAAGAG
1965460 TCTA
66 TCTA
1965464 ACATCCCT
1 ACATCCCT
1965472 CCAAGTGTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (69 bp):
ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTCAAGAG
TCTA
Found at i:1969412 original size:6 final size:6
Alignment explanation
Indices: 1969393--1969434 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
1969383 GGTTGATTTT
* * *
1969393 TTAAAA TAAAAA TTAGAA TTAGAA TTAAAA TTAAAA TTAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
1969435 CAAAAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (6 bp):
TTAAAA
Found at i:1969440 original size:18 final size:18
Alignment explanation
Indices: 1969393--1969440 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1969383 GGTTGATTTT
*
1969393 TTAAAATAAAAATTAGAA
1 TTAAAATAAAAATTAAAA
* *
1969411 TTAGAATTAAAATTAAAA
1 TTAAAATAAAAATTAAAA
*
1969429 TTAAAACAAAAA
1 TTAAAATAAAAA
1969441 AAGAAAGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
TTAAAATAAAAATTAAAA
Found at i:1969487 original size:35 final size:35
Alignment explanation
Indices: 1969448--1969515 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
1969438 AAAAAGAAAG
*
1969448 AAAAATTACCAAACAGACTTTTTTATTTTCTAAAC
1 AAAAATTACCAAACAAACTTTTTTATTTTCTAAAC
*
1969483 AAAAATTACCAAACAAACTTTTTTGTTTTCTAA
1 AAAAATTACCAAACAAACTTTTTTATTTTCTAA
1969516 TTAACATCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (35 bp):
AAAAATTACCAAACAAACTTTTTTATTTTCTAAAC
Found at i:1970803 original size:21 final size:20
Alignment explanation
Indices: 1970766--1970804 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1970756 ATTAAAATAT
1970766 TATTTTTATTAATATTTATA
1 TATTTTTATTAATATTTATA
1970786 TATTTTATAATTAA-ATTTA
1 TATTTT-T-ATTAATATTTA
1970805 AATAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTATTAATATTTATA
Found at i:1977792 original size:22 final size:22
Alignment explanation
Indices: 1977756--1977818 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
1977746 CCATTTTAAT
1977756 ATACATAC--ATATATATATAC
1 ATACATACATATATATATATAC
1977776 ATACATACATATATATATATAC
1 ATACATACATATATATATATAC
*
1977798 ATACATATATATATATATATA
1 ATACATACATATATATATATA
1977819 ACGAGCCTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 8 0.20
22 32 0.80
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
ATACATACATATATATATATAC
Found at i:1977809 original size:4 final size:4
Alignment explanation
Indices: 1977754--1977818 Score: 67
Period size: 4 Copynumber: 16.2 Consensus size: 4
1977744 GGCCATTTTA
* * * * * * *
1977754 ATAT ACAT ACAT ATAT ATAT ACAT ACAT ACAT ATAT ATAT ATAC ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1977802 ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT A
1977819 ACGAGCCTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (4 bp):
ATAT
Found at i:1977811 original size:18 final size:18
Alignment explanation
Indices: 1977754--1977814 Score: 104
Period size: 18 Copynumber: 3.3 Consensus size: 18
1977744 GGCCATTTTA
1977754 ATATACATACATATATAT
1 ATATACATACATATATAT
1977772 ATACATACATACATATATAT
1 AT--ATACATACATATATAT
1977792 ATATACATACATATATAT
1 ATATACATACATATATAT
1977810 ATATA
1 ATATA
1977815 TATAACGAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
18 23 0.56
20 18 0.44
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATACATACATATATAT
Found at i:1978350 original size:34 final size:33
Alignment explanation
Indices: 1978295--1978513 Score: 276
Period size: 34 Copynumber: 6.5 Consensus size: 33
1978285 GTAGATAATC
*
1978295 TGTTGATTAAATGGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCAT
* * *
1978328 TGTTGATTAAATAGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
* *
1978362 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
**
1978396 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATG-GTGATTTGGTAGCTTACCAT
* *
1978430 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
* * *
1978464 TGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGT-GATTTGGTAGCTTACCAT
1978498 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
1978514 GTTTTTACCA
Statistics
Matches: 162, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
33 17 0.10
34 144 0.89
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (33 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCAT
Found at i:1978487 original size:102 final size:101
Alignment explanation
Indices: 1978295--1978511 Score: 335
Period size: 102 Copynumber: 2.1 Consensus size: 101
1978285 GTAGATAATC
** * * * *
1978295 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATAGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTACC
1978360 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
*
1978396 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTAC
* * *
1978461 CATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1978498 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1978512 TGGTTTTTAC
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
101 14 0.13
102 91 0.87
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1982980 original size:34 final size:33
Alignment explanation
Indices: 1982923--1983143 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 33
1982913 AAGTGGGAGA
*
1982923 ATTGTTGATTAAATGGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACC
* * *
1982956 ATTGTTGATTAAATAGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
* *
1982990 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
**
1983024 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATG-GTGATTTGGTAGCTTACC
* *
1983058 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
* * *
1983092 ATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGT-GATTTGGTAGCTTACC
1983126 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1983144 GTTTTTACCA
Statistics
Matches: 164, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
33 19 0.12
34 144 0.88
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (33 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACC
Found at i:1983066 original size:102 final size:101
Alignment explanation
Indices: 1982923--1983141 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
1982913 AAGTGGGAGA
** * * * *
1982923 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATAGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTA
1982988 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
1983024 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTT
* * *
1983089 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1983126 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1983142 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1984091 original size:50 final size:50
Alignment explanation
Indices: 1984016--1984173 Score: 271
Period size: 50 Copynumber: 3.2 Consensus size: 50
1984006 GGTAGAAAGT
**
1984016 ACCTTTGACAATAGAGAGAGGTGGTCGCAATTGTTGACGATTCTTCATCA
1 ACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCATCA
1984066 ACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCATCA
1 ACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCATCA
* * *
1984116 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCATCA
1984166 ACCTTTGA
1 ACCTTTGA
1984174 TGATAAAGAA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 103 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (50 bp):
ACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCATCA
Found at i:1984190 original size:50 final size:50
Alignment explanation
Indices: 1984016--1984203 Score: 268
Period size: 50 Copynumber: 3.8 Consensus size: 50
1984006 GGTAGAAAGT
* **
1984016 ACCTTTGACAATAGAGAGAGGTGGTCGCAATTGTTGACGATTCTTCATCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCATCA
*
1984066 ACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCATCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCATCA
* *
1984116 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCATCA
** * * * *
1984166 ACCTTTGATGATAAAGAAAAGTGGCCGTAATTGTTGAC
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
1984204 TCTAAGTATA
Statistics
Matches: 127, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 127 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (50 bp):
ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCATCA
Found at i:1986374 original size:50 final size:50
Alignment explanation
Indices: 1986317--1986552 Score: 375
Period size: 50 Copynumber: 4.7 Consensus size: 50
1986307 AGTAGAAAGT
1986317 ACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGATGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGATGATTCTTCACCA
* *
1986367 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGATGATTCTTCACCA
* **
1986417 ACCTTTAACAATAGAGAGAGGTGATCGTAATTGTTGATGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGATGATTCTTCACCA
*
1986467 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTG-TGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGATGATTCTTCACCA
* * * *
1986516 ACCTTTGACAATAGAGAAATGTGGCTGCAATTGTTGA
1 ACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGA
1986553 CTCTAAGTAT
Statistics
Matches: 169, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
49 44 0.26
50 125 0.74
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (50 bp):
ACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGATGATTCTTCACCA
Found at i:1987109 original size:20 final size:21
Alignment explanation
Indices: 1987070--1987109 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1987060 TTAATAATTA
*
1987070 TTTATTATATTTTATATTTAT
1 TTTATTATATTTGATATTTAT
*
1987091 TTTATT-TATTTGATGTTTA
1 TTTATTATATTTGATATTTA
1987110 AAAATTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTATTATATTTGATATTTAT
Found at i:1988171 original size:30 final size:30
Alignment explanation
Indices: 1988115--1988171 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1988105 TTTTATTTGT
*
1988115 TAAATATATATTAAAAAATAATTTTTTCGA
1 TAAATATATATTAAAAAATAAATTTTTCGA
1988145 TAAATATA-A-TAAAAATATCAAATTTTT
1 TAAATATATATTAAAAA-AT-AAATTTTT
1988172 TAAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.25
29 3 0.12
30 15 0.62
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (30 bp):
TAAATATATATTAAAAAATAAATTTTTCGA
Found at i:1989296 original size:15 final size:14
Alignment explanation
Indices: 1989272--1989320 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
1989262 TCTATAAAAA
*
1989272 ATATTTAATATTTT
1 ATATTTAATATATT
1989286 ATATCTTAATATATT
1 ATAT-TTAATATATT
*
1989301 ATAATATAAGTATATT
1 AT-ATTTAA-TATATT
1989317 ATAT
1 ATAT
1989321 AATGTTAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 4 0.13
15 16 0.53
16 10 0.33
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (14 bp):
ATATTTAATATATT
Found at i:1989400 original size:50 final size:50
Alignment explanation
Indices: 1989345--1989679 Score: 402
Period size: 50 Copynumber: 6.7 Consensus size: 50
1989335 GGTGGAAAGT
** * * *
1989345 ACCTTTGACAATAGAGAGAGGTGATTATAATTGTTAATGGTTTTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTTTTCACCA
* * * * * * *
1989395 ACCTTTGATAATATAGAGAGATAATCGTAATTATTGATC-ATTTTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGA-CGATTTTTCACCA
* * *
1989445 AACTTTGACAATAGAGTGAGGTGACCATAATTGTTGACGATTTTTCATCA
1 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTTTTCACCA
* *
1989495 ACCTTTGACAATAGAGAGAGGTGACTATAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTTTTCACCA
*** **
1989545 ACCTTTGACAATAGAGAGAAACGGTCATAATTGTTGACGATTTTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTTTTCACCA
* *
1989595 ACCTTTGACAATAGAAAAAGGTGACCATAATTGTTGACGATTTTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTTTTCACCA
* * * *
1989645 ACATTTGACAATAGAAAAAGGTGGCCATAATTGTT
1 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTT
1989680 TACTCTAAGT
Statistics
Matches: 242, Mismatches: 41, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
49 1 0.00
50 241 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (50 bp):
ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTTTTCACCA
Found at i:1989617 original size:150 final size:150
Alignment explanation
Indices: 1989345--1989679 Score: 447
Period size: 150 Copynumber: 2.2 Consensus size: 150
1989335 GGTGGAAAGT
* * * * * *
1989345 ACCTTTGACAATAGAGAGAGGTGATTATAATTGTTAATGGTTTTTCACCAACCTTTGATAATATA
1 ACCTTTGACAATAGAGAGAGGTGACTATAATTGTTAACGATTCTTCACCAACCTTTGACAATAGA
* * * ***
1989410 GAGAGATAATCGTAATTATTGATCATTTTTCACCAAACTTTGACAATAGAGTGAGGTGACCATAA
66 GAGAAACAATCATAATTATTGATCATTTTTCACCAAACTTTGACAATAGAAAAAGGTGACCATAA
*
1989475 TTGTTGACGATTTTTCATCA
131 TTGTTGACGATTTTTCACCA
*
1989495 ACCTTTGACAATAGAGAGAGGTGACTATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGA
1 ACCTTTGACAATAGAGAGAGGTGACTATAATTGTTAACGATTCTTCACCAACCTTTGACAATAGA
** * *
1989560 GAGAAACGGTCATAATTGTTGA-CGATTTTTCACCAACCTTTGACAATAGAAAAAGGTGACCATA
66 GAGAAACAATCATAATTATTGATC-ATTTTTCACCAAACTTTGACAATAGAAAAAGGTGACCATA
1989624 ATTGTTGACGATTTTTCACCA
130 ATTGTTGACGATTTTTCACCA
* * * * *
1989645 ACATTTGACAATAGAAAAAGGTGGCCATAATTGTT
1 ACCTTTGACAATAGAGAGAGGTGACTATAATTGTT
1989680 TACTCTAAGT
Statistics
Matches: 161, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
149 1 0.01
150 160 0.99
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (150 bp):
ACCTTTGACAATAGAGAGAGGTGACTATAATTGTTAACGATTCTTCACCAACCTTTGACAATAGA
GAGAAACAATCATAATTATTGATCATTTTTCACCAAACTTTGACAATAGAAAAAGGTGACCATAA
TTGTTGACGATTTTTCACCA
Found at i:1990338 original size:21 final size:23
Alignment explanation
Indices: 1990295--1990338 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1990285 GATAATTTTG
1990295 AACACAATATTAATAAATGATAAA
1 AACACAATATTAATAAA-GATAAA
1990319 AACACAATATTAA-AAA-ATAA
1 AACACAATATTAATAAAGATAA
1990339 TTTAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
23 3 0.15
24 13 0.65
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (23 bp):
AACACAATATTAATAAAGATAAA
Found at i:1991054 original size:2 final size:2
Alignment explanation
Indices: 1991049--1991087 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1991039 TGTGTGTGTG
1991049 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1991088 TTGTCCATGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1991204 original size:27 final size:27
Alignment explanation
Indices: 1991174--1991250 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 27
1991164 TGAAATTATT
1991174 ATTTAATAAAAAAATATTTTTATTTAA
1 ATTTAATAAAAAAATATTTTTATTTAA
* ** *
1991201 ATTTAATTATAAAATATATTAATATTTAT
1 ATTTAA-TA-AAAAAATATTTTTATTTAA
*
1991230 A-TTAATATAAAAATATTTTTA
1 ATTTAATAAAAAAATATTTTTA
1991251 ATTTTTTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
26 10 0.25
27 8 0.20
28 6 0.15
29 16 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTAATAAAAAAATATTTTTATTTAA
Found at i:1991254 original size:27 final size:27
Alignment explanation
Indices: 1991172--1991263 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 27
1991162 TTTGAAATTA
*
1991172 TTAT-TTAATAAAAAAATATTTTT-AT
1 TTATATTAATATAAAAATATTTTTAAT
* * *
1991197 TTAAATTTAAT-TATAAAATATATTAATAT
1 TTATA-TTAATATA-AAAATATTTTTA-AT
1991226 TTATATTAATATAAAAATATTTTTAATT
1 TTATATTAATATAAAAATATTTTTAA-T
*
1991254 TTTTATTAAT
1 TTATATTAAT
1991264 TTTTAAATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 15 0.29
28 25 0.48
29 8 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATATTAATATAAAAATATTTTTAAT
Found at i:1991405 original size:2 final size:2
Alignment explanation
Indices: 1991398--1991425 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1991388 GAAACTAGAC
1991398 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1991426 AACAAACTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1991842 original size:2 final size:2
Alignment explanation
Indices: 1991837--1991895 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1991827 CATGTGTGTG
1991837 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1991879 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1991896 CTACAAATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1998871 original size:3 final size:3
Alignment explanation
Indices: 1998865--1998891 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1998855 TGTATTATTT
1998865 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1998892 TTGTATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1998926 original size:13 final size:13
Alignment explanation
Indices: 1998908--1998934 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1998898 TAATGATAAA
1998908 ATTTATTATTTTT
1 ATTTATTATTTTT
1998921 ATTTATTATTTTT
1 ATTTATTATTTTT
1998934 A
1 A
1998935 ATACATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTATTATTTTT
Found at i:1999121 original size:22 final size:21
Alignment explanation
Indices: 1999096--1999147 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
1999086 GTTCAATATT
1999096 ATAAATAAAAAAGTACATAATA
1 ATAAATAAAAAA-TACATAATA
* *
1999118 ATAAAT--TAAATATATAATA
1 ATAAATAAAAAATACATAATA
1999137 ATAAAATAAAA
1 AT-AAATAAAA
1999148 TATTTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
19 10 0.42
20 7 0.29
22 7 0.29
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAAATAAAAAATACATAATA
Found at i:1999134 original size:19 final size:18
Alignment explanation
Indices: 1999112--1999150 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1999102 AAAAAAGTAC
*
1999112 ATAATAATAAATTAAATAT
1 ATAATAATAAAATAAA-AT
1999131 ATAATAATAAAATAAAAT
1 ATAATAATAAAATAAAAT
1999149 AT
1 AT
1999151 TTATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATAATAAAATAAAAT
Found at i:1999274 original size:17 final size:17
Alignment explanation
Indices: 1999238--1999270 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1999228 ATTAATTAAA
1999238 AAATCATTCACTTTTTT
1 AAATCATTCACTTTTTT
1999255 AAATCATT-A-TTTTTT
1 AAATCATTCACTTTTTT
1999270 A
1 A
1999271 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATCATTCACTTTTTT
Found at i:2003937 original size:23 final size:26
Alignment explanation
Indices: 2003910--2003957 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 26
2003900 TTTTAAACTA
2003910 TTATTTAACA-GTAAT-GA-AATTAT
1 TTATTTAACAGGTAATAGAGAATTAT
*
2003933 TTATTTTACAGGTAATAGAGAATTA
1 TTATTTAACAGGTAATAGAGAATTA
2003958 AGGTTGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 2 0.10
26 5 0.24
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (26 bp):
TTATTTAACAGGTAATAGAGAATTAT
Found at i:2007924 original size:34 final size:34
Alignment explanation
Indices: 2007878--2008095 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
2007868 GTAAAAACCA
*
2007878 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2007912 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
2007946 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
2007980 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2008013 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
2008047 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2008080 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2008096 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2007992 original size:68 final size:67
Alignment explanation
Indices: 2007876--2008095 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
2007866 TGGTAAAAAC
* * *
2007876 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
2007941 AT
66 AT
* * *
2007943 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
2008008 AAT
65 AAT
* * * * * *
2008011 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
2008076 AT
66 AT
2008078 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2008096 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:2012552 original size:34 final size:34
Alignment explanation
Indices: 2012506--2012722 Score: 280
Period size: 34 Copynumber: 6.4 Consensus size: 34
2012496 GTAAAAACCA
*
2012506 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2012540 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
2012574 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
2012608 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2012641 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
2012675 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2012708 CCATTTAATCAACAA
1 CCATTTAATCAACAA
2012723 ATTCTTCCCA
Statistics
Matches: 161, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 44 0.27
34 115 0.71
35 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2012620 original size:68 final size:67
Alignment explanation
Indices: 2012504--2012722 Score: 321
Period size: 67 Copynumber: 3.3 Consensus size: 67
2012494 TGGTAAAAAC
* * *
2012504 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
2012569 AT
66 AT
* * *
2012571 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
2012636 AAT
65 AAT
* * * * * *
2012639 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
2012704 AT
66 AT
2012706 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
2012723 ATTCTTCCCA
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:2013889 original size:69 final size:69
Alignment explanation
Indices: 2013778--2013923 Score: 256
Period size: 69 Copynumber: 2.1 Consensus size: 69
2013768 CTCCAACCTC
*
2013778 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTTGAGAG
1 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTTAAGAG
2013843 TCTA
66 TCTA
** *
2013847 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATATCTGCTCTTAAGAG
1 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTTAAGAG
2013912 TCTA
66 TCTA
2013916 ACATCCCT
1 ACATCCCT
2013924 CCAAGTTTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (69 bp):
ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTTAAGAG
TCTA
Found at i:2021114 original size:22 final size:23
Alignment explanation
Indices: 2021067--2021117 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
2021057 ATGTAACCAT
* * *
2021067 TATTT-TTATTTATAAATTAAAT
1 TATTTATTATTAATAAATAAAAA
2021089 TATTTATTATTAAT-AATAAAAA
1 TATTTATTATTAATAAATAAAAA
2021111 TATTTAT
1 TATTTAT
2021118 AATAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTTATTATTAATAAATAAAAA
Found at i:2024753 original size:17 final size:16
Alignment explanation
Indices: 2024724--2024761 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2024714 ATTTTTGAAA
2024724 TTAA-TTTTTATTTTT
1 TTAATTTTTTATTTTT
2024739 TTAATTTTTTGATTTTT
1 TTAATTTTTT-ATTTTT
*
2024756 ATAATT
1 TTAATT
2024762 ATGTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTAATTTTTTATTTTT
Found at i:2025173 original size:34 final size:34
Alignment explanation
Indices: 2025109--2025291 Score: 253
Period size: 34 Copynumber: 5.4 Consensus size: 34
2025099 TGTTTCATGC
*
2025109 TGTTGATTAAAT--GATGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGA-GATTTGGTAGCTTACCAT
* *
2025142 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
2025176 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
2025210 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
2025244 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
2025278 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2025292 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 11 0.08
34 119 0.90
35 2 0.02
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:2025652 original size:19 final size:19
Alignment explanation
Indices: 2025596--2025658 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2025586 TGGTTGTCGA
**
2025596 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
2025615 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
2025634 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
2025653 GTTACT
1 GGTACT
2025659 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:2029790 original size:34 final size:34
Alignment explanation
Indices: 2029724--2029908 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
2029714 AAGTGGGAGA
*
2029724 ATTGTTGATTAAAT--GATGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGA-GATTTGGTAGCTTACC
* *
2029757 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2029791 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
2029825 ATTATTGATTAAATGGGTGATTTGGTGGTTTACT
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2029859 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2029893 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2029909 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
33 13 0.10
34 117 0.89
35 2 0.02
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2031829 original size:2 final size:2
Alignment explanation
Indices: 2031824--2031853 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2031814 GGATCGTGTG
2031824 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2031854 CAAATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2034447 original size:32 final size:32
Alignment explanation
Indices: 2034410--2034473 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
2034400 AGAACATGAT
2034410 ATAAA-TAGATAAAATATTAAAATTTATATAAA
1 ATAAATTA-ATAAAATATTAAAATTTATATAAA
* * * *
2034442 ATAAATTATTCATATGTTAAAATTTATATAAA
1 ATAAATTAATAAAATATTAAAATTTATATAAA
2034474 TATATAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 25 0.93
33 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (32 bp):
ATAAATTAATAAAATATTAAAATTTATATAAA
Found at i:2034488 original size:27 final size:27
Alignment explanation
Indices: 2034408--2034489 Score: 65
Period size: 32 Copynumber: 2.9 Consensus size: 27
2034398 TCAGAACATG
* * *
2034408 ATATAAATAGATAAAATATTAAAATTT
1 ATATAAATAAATAATATTTTAAAATTT
*
2034435 ATATAAAATAAATTATTCATATGTTAAAATTT
1 ATAT-AAATAAA-TA---ATATTTTAAAATTT
* *
2034467 ATATAAATATATAGTATTTTAAA
1 ATATAAATAAATAATATTTTAAA
2034490 TATGATTATG
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
27 12 0.27
28 6 0.14
29 2 0.05
30 2 0.05
31 6 0.14
32 16 0.36
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (27 bp):
ATATAAATAAATAATATTTTAAAATTT
Found at i:2034778 original size:11 final size:11
Alignment explanation
Indices: 2034758--2034797 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2034748 TTTAATTATG
2034758 ATAAAAATAAC
1 ATAAAAATAAC
*
2034769 ATAAATATAAC
1 ATAAAAATAAC
* *
2034780 ATAAAAATTAT
1 ATAAAAATAAC
2034791 ATAAAAA
1 ATAAAAA
2034798 ATTACAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (11 bp):
ATAAAAATAAC
Found at i:2034828 original size:12 final size:11
Alignment explanation
Indices: 2034782--2034829 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
2034772 AATATAACAT
*
2034782 AAAAATTATATA
1 AAAAATTA-AAA
2034794 AAAAATTACAAA
1 AAAAATTA-AAA
2034806 AAAAATT-AAA
1 AAAAATTAAAA
*
2034816 AAATATTAAAA
1 AAAAATTAAAA
2034827 AAA
1 AAA
2034830 TGGATTACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.28
11 6 0.19
12 17 0.53
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATTAAAA
Done.